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Altun Z, Yuan H, Baran B, Aktaş S, Sönmez EE, Küçük C, Olgun N. Whole-exome sequencing reveals genetic variants in low-risk and high-risk neuroblastoma. Gene 2023; 860:147233. [PMID: 36736507 DOI: 10.1016/j.gene.2023.147233] [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: 09/06/2022] [Revised: 01/11/2023] [Accepted: 01/25/2023] [Indexed: 02/05/2023]
Abstract
This study aimed to investigate the genetic aberrations in neuroblastoma (NB) by comparing high and low-risk NB patients by whole-exome sequencing (WES) and to reveal the heterogeneity and association between somatic variants and clinical features. Seven NB patients with available clinical data were included in the study (4 in the low-risk group and 3 in the high-risk group). WES was performed and somatic variants associated with NB genes in the COSMIC database were selected through bioinformatics pipeline analysis. Variants were determined using the Integrative Genomics Viewer (IGV). Some gene variations were found in both groups, including variations in oncogene and tumor suppressor genes. In general, candidate gene variations were associated with chromatin remodeling complexes, the RAS pathway, cell proliferation, and DNA repair mechanism. Some variations in CSF1R, MSH6, PTPN11, SOX9, RET, TSC1, and DNMT1 genes were detected only in high-risk patients, while EP300, TET2, MYCN, PRDM1, and ARID2 gene variations were detected only in low-risk patients. When high-risk gene variants were compared with the cBioportal cancer genomic database, two common gene variants (ARID1A and NCOR2) were identified. However, when low-risk gene variants were compared with the cBioportal cancer genomic database, no common genes were found. GO/KEGG enrichment analysis was performed to find relevant biological processes and molecular pathways related to gene variants, which will help to decipher the molecular mechanisms of NB tumorigenesis and the phenotypic differences between high-risk and low-risk patients.
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Affiliation(s)
- Zekiye Altun
- Department of Basic Oncology, Institute of Oncology, Dokuz Eylül University, İzmir, Turkey.
| | - Hongling Yuan
- Department of Basic Oncology, Institute of Oncology, Dokuz Eylül University, İzmir, Turkey
| | - Burçin Baran
- Department of Basic Oncology, Institute of Oncology, Dokuz Eylül University, İzmir, Turkey
| | - Safiye Aktaş
- Department of Basic Oncology, Institute of Oncology, Dokuz Eylül University, İzmir, Turkey
| | - Esra Esmeray Sönmez
- İzmir Biomedicine and Genome Center, İzmir, Turkey; İzmir Biomedicine and Genome Institute, Dokuz Eylül University, İzmir, Turkey
| | - Can Küçük
- İzmir Biomedicine and Genome Center, İzmir, Turkey; İzmir Biomedicine and Genome Institute, Dokuz Eylül University, İzmir, Turkey; Department of Medical Biology, Faculty of Medicine, Dokuz Eylül University, İzmir, Turkey
| | - Nur Olgun
- Department of Pediatric Oncology, Institute of Oncology, Dokuz Eylül University, İzmir, Turkey
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Inchakalody VP, Hydrose SP, Krishnankutty R, Merhi M, Therachiyil L, Sasidharan Nair V, Elashi AA, Khan AQ, Taleb S, Raza A, Yoosuf ZSKM, Fernandes Q, Al-Zaidan L, Mestiri S, Taib N, Bedhiafi T, Moustafa D, Assami L, Maalej KM, Elkord E, Uddin S, Al Homsi U, Dermime S. The molecular mechanisms of apoptosis accompanied with the epigenetic regulation of the NY-ESO-1 antigen in non-small lung cancer cells treated with decitabine (5-aza-CdR). Eur J Pharmacol 2023; 945:175612. [PMID: 36822455 DOI: 10.1016/j.ejphar.2023.175612] [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: 11/29/2022] [Revised: 02/16/2023] [Accepted: 02/17/2023] [Indexed: 02/23/2023]
Abstract
Dysregulated epigenetic modifications are common in lung cancer but have been reversed using demethylating agent like 5-Aza-CdR. 5-Aza-CdR induces/upregulates the NY-ESO-1 antigen in lung cancer. Therefore, we investigated the molecular mechanisms accompanied with the epigenetic regulation of NY-ESO-1 in 5-Aza-CdR-treated NCI-H1975 cell line. We showed significant induction of the NY-ESO-1 protein (**p < 0.0097) using Cellular ELISA. Bisulfite-sequencing demonstrated 45.6% demethylation efficiency at the NY-ESO-1 gene promoter region and RT-qPCR analysis confirmed the significant induction of NY-ESO-1 at mRNA level (128-fold increase, *p < 0.050). We then investigated the mechanism by which 5-Aza-CdR inhibits cell proliferation in the NCI-H1975 cell line. Upregulation of the death receptors TRAIL (2.04-fold *p < 0.011) and FAS (2.1-fold *p < 0.011) indicate activation of the extrinsic apoptotic pathway. The upregulation of Voltage-dependent anion-selective channel protein 1 (1.9-fold), Major vault protein (1.8-fold), Bax (1.16-fold), and Cytochrome C (1.39-fold) indicate the activation of the intrinsic pathway. We also observed the differential expression of protein Complement C3 (3.3-fold), Destrin (-5.1-fold), Vimentin (-1.7-fold), Peroxiredoxin 4 (-1.6-fold), Fascin (-1.8-fold), Heme oxygenase-2 (-0.67-fold**p < 0.0055), Hsp27 (-0.57-fold**p < 0.004), and Hsp70 (-0.39-fold **p < 0.001), indicating reduced cell growth, cell migration, and metastasis. The upregulation of 40S ribosomal protein S9 (3-fold), 40S ribosomal protein S15 (4.2-fold), 40S ribosomal protein S18 (2.5-fold), and 60S ribosomal protein L22 (4.4-fold) implied the induction of translation machinery. These results reiterate the decisive role of 5-Aza-CdR in lung cancer treatment since it induces the epigenetic regulation of NY-ESO-1 antigen, inhibits cell proliferation, increases apoptosis, and decreases invasiveness.
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Affiliation(s)
- Varghese P Inchakalody
- National Center for Cancer Care and Research, Hamad Medical Corporation, Doha, Qatar; Translational Cancer Research Facility, Interim Translational Research Institute, Hamad Medical Corporation, Doha, Qatar
| | - Shereena P Hydrose
- National Center for Cancer Care and Research, Hamad Medical Corporation, Doha, Qatar; Translational Cancer Research Facility, Interim Translational Research Institute, Hamad Medical Corporation, Doha, Qatar
| | - Roopesh Krishnankutty
- Translational Research Institute, Academic Health System, Hamad Medical Corporation, Doha, Qatar
| | - Maysaloun Merhi
- National Center for Cancer Care and Research, Hamad Medical Corporation, Doha, Qatar; Translational Cancer Research Facility, Interim Translational Research Institute, Hamad Medical Corporation, Doha, Qatar
| | - Lubna Therachiyil
- Translational Research Institute, Academic Health System, Hamad Medical Corporation, Doha, Qatar; College of Pharmacy, Qatar University, Doha, Qatar
| | - Varun Sasidharan Nair
- Department of Experimental Immunology, Helmholtz Centre for Infection Research, Germany
| | - Asma A Elashi
- College of Health and Life Sciences, Hamad Bin Khalifa University, Doha, Qatar
| | - Abdul Q Khan
- Translational Research Institute, Academic Health System, Hamad Medical Corporation, Doha, Qatar
| | - Sara Taleb
- Genomics and Precision Medicine, Hamad Bin Khalifa University, Doha, Qatar
| | - Afsheen Raza
- National Center for Cancer Care and Research, Hamad Medical Corporation, Doha, Qatar; Translational Cancer Research Facility, Interim Translational Research Institute, Hamad Medical Corporation, Doha, Qatar
| | - Zeenath Safira K M Yoosuf
- Translational Cancer Research Facility, Interim Translational Research Institute, Hamad Medical Corporation, Doha, Qatar; College of Health and Life Sciences, Hamad Bin Khalifa University, Doha, Qatar
| | - Queenie Fernandes
- Translational Cancer Research Facility, Interim Translational Research Institute, Hamad Medical Corporation, Doha, Qatar; College of Medicine, Qatar University, Doha, Qatar
| | - Lobna Al-Zaidan
- National Center for Cancer Care and Research, Hamad Medical Corporation, Doha, Qatar; Translational Cancer Research Facility, Interim Translational Research Institute, Hamad Medical Corporation, Doha, Qatar
| | - Sarra Mestiri
- National Center for Cancer Care and Research, Hamad Medical Corporation, Doha, Qatar; Translational Cancer Research Facility, Interim Translational Research Institute, Hamad Medical Corporation, Doha, Qatar
| | - Nassiba Taib
- National Center for Cancer Care and Research, Hamad Medical Corporation, Doha, Qatar; Translational Cancer Research Facility, Interim Translational Research Institute, Hamad Medical Corporation, Doha, Qatar
| | - Takwa Bedhiafi
- National Center for Cancer Care and Research, Hamad Medical Corporation, Doha, Qatar; Translational Cancer Research Facility, Interim Translational Research Institute, Hamad Medical Corporation, Doha, Qatar
| | - Dina Moustafa
- National Center for Cancer Care and Research, Hamad Medical Corporation, Doha, Qatar; Translational Cancer Research Facility, Interim Translational Research Institute, Hamad Medical Corporation, Doha, Qatar
| | - Laila Assami
- National Center for Cancer Care and Research, Hamad Medical Corporation, Doha, Qatar; Translational Cancer Research Facility, Interim Translational Research Institute, Hamad Medical Corporation, Doha, Qatar
| | - Karama Makni Maalej
- National Center for Cancer Care and Research, Hamad Medical Corporation, Doha, Qatar; Translational Cancer Research Facility, Interim Translational Research Institute, Hamad Medical Corporation, Doha, Qatar
| | - Eyad Elkord
- Natural and Medical Sciences Research Center, University of Nizwa, Oman; Biomedical Research Center, School of Science, Engineering and Environment, University of Salford, Manchester, UK
| | - Shahab Uddin
- Translational Research Institute, Academic Health System, Hamad Medical Corporation, Doha, Qatar; Translational Research Institute and Dermatology Institute, Academic Health System, Doha, Qatar
| | - Ussama Al Homsi
- National Center for Cancer Care and Research, Hamad Medical Corporation, Doha, Qatar; Translational Cancer Research Facility, Interim Translational Research Institute, Hamad Medical Corporation, Doha, Qatar
| | - Said Dermime
- National Center for Cancer Care and Research, Hamad Medical Corporation, Doha, Qatar; Translational Cancer Research Facility, Interim Translational Research Institute, Hamad Medical Corporation, Doha, Qatar.
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Wei Y, Li G, Feng J, Wu F, Zhao Z, Bao Z, Zhang W, Su X, Li J, Qi X, Duan Z, Zhang Y, Vega SF, Jakola AS, Sun Y, Carén H, Jiang T, Fan X. Stalled oligodendrocyte differentiation in IDH-mutant gliomas. Genome Med 2023; 15:24. [PMID: 37055795 PMCID: PMC10103394 DOI: 10.1186/s13073-023-01175-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2022] [Accepted: 03/28/2023] [Indexed: 04/15/2023] Open
Abstract
BACKGROUND Roughly 50% of adult gliomas harbor isocitrate dehydrogenase (IDH) mutations. According to the 2021 WHO classification guideline, these gliomas are diagnosed as astrocytomas, harboring no 1p19q co-deletion, or oligodendrogliomas, harboring 1p19q co-deletion. Recent studies report that IDH-mutant gliomas share a common developmental hierarchy. However, the neural lineages and differentiation stages in IDH-mutant gliomas remain inadequately characterized. METHODS Using bulk transcriptomes and single-cell transcriptomes, we identified genes enriched in IDH-mutant gliomas with or without 1p19q co-deletion, we also assessed the expression pattern of stage-specific signatures and key regulators of oligodendrocyte lineage differentiation. We compared the expression of oligodendrocyte lineage stage-specific markers between quiescent and proliferating malignant single cells. The gene expression profiles were validated using RNAscope analysis and myelin staining and were further substantiated using data of DNA methylation and single-cell ATAC-seq. As a control, we assessed the expression pattern of astrocyte lineage markers. RESULTS Genes concordantly enriched in both subtypes of IDH-mutant gliomas are upregulated in oligodendrocyte progenitor cells (OPC). Signatures of early stages of oligodendrocyte lineage and key regulators of OPC specification and maintenance are enriched in all IDH-mutant gliomas. In contrast, signature of myelin-forming oligodendrocytes, myelination regulators, and myelin components are significantly down-regulated or absent in IDH-mutant gliomas. Further, single-cell transcriptomes of IDH-mutant gliomas are similar to OPC and differentiation-committed oligodendrocyte progenitors, but not to myelinating oligodendrocyte. Most IDH-mutant glioma cells are quiescent; quiescent cells and proliferating cells resemble the same differentiation stage of oligodendrocyte lineage. Mirroring the gene expression profiles along the oligodendrocyte lineage, analyses of DNA methylation and single-cell ATAC-seq data demonstrate that genes of myelination regulators and myelin components are hypermethylated and show inaccessible chromatin status, whereas regulators of OPC specification and maintenance are hypomethylated and show open chromatin status. Markers of astrocyte precursors are not enriched in IDH-mutant gliomas. CONCLUSIONS Our studies show that despite differences in clinical manifestation and genomic alterations, all IDH-mutant gliomas resemble early stages of oligodendrocyte lineage and are stalled in oligodendrocyte differentiation due to blocked myelination program. These findings provide a framework to accommodate biological features and therapy development for IDH-mutant gliomas.
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Affiliation(s)
- Yanfei Wei
- Department of Biology, Beijing Key Laboratory of Gene Resource and Molecular Development, School of Life Sciences, and Key Laboratory of Cell Proliferation and Regulation Biology, Ministry of Education, School of Life Sciences, Beijing Normal University, Beijing, China
| | - Guanzhang Li
- Beijing Neurosurgical Institute, Beijing, 100070, China
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, 100070, China
| | - Jing Feng
- Department of Biology, Beijing Key Laboratory of Gene Resource and Molecular Development, School of Life Sciences, and Key Laboratory of Cell Proliferation and Regulation Biology, Ministry of Education, School of Life Sciences, Beijing Normal University, Beijing, China
| | - Fan Wu
- Beijing Neurosurgical Institute, Beijing, 100070, China
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, 100070, China
| | - Zheng Zhao
- Beijing Neurosurgical Institute, Beijing, 100070, China
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, 100070, China
| | - Zhaoshi Bao
- Beijing Neurosurgical Institute, Beijing, 100070, China
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, 100070, China
| | - Wei Zhang
- Beijing Neurosurgical Institute, Beijing, 100070, China
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, 100070, China
| | - Xiaodong Su
- Biodynamic Optical Imaging Center (BIOPIC), School of Life Sciences, Peking University, Beijing, 100871, China
| | - Jiuyi Li
- College of Life Sciences, Sichuan Normal University, Chengdu, 610101, China
| | - Xueling Qi
- Department of Pathology, San Bo Brain Hospital, Capital Medical University, Beijing, 100093, China
| | - Zejun Duan
- Department of Pathology, San Bo Brain Hospital, Capital Medical University, Beijing, 100093, China
| | - Yunqiu Zhang
- Center of Growth Metabolism & Aging, Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, China
| | - Sandra Ferreyra Vega
- Department of Clinical Neuroscience, Institute of Neuroscience and Physiology, Sahlgrenska Academy, University of Gothenburg, Gothenburg, 41390, Sweden
- Sahlgrenska Center for Cancer Research, Department of Laboratory Medicine, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, 41390, Gothenburg, Sweden
| | - Asgeir Store Jakola
- Department of Clinical Neuroscience, Institute of Neuroscience and Physiology, Sahlgrenska Academy, University of Gothenburg, Gothenburg, 41390, Sweden
- Department of Neurosurgery, Sahlgrenska University Hospital, Gothenburg, 41390, Sweden
| | - Yingyu Sun
- Department of Biology, Beijing Key Laboratory of Gene Resource and Molecular Development, School of Life Sciences, and Key Laboratory of Cell Proliferation and Regulation Biology, Ministry of Education, School of Life Sciences, Beijing Normal University, Beijing, China
| | - Helena Carén
- Sahlgrenska Center for Cancer Research, Department of Laboratory Medicine, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, 41390, Gothenburg, Sweden.
| | - Tao Jiang
- Beijing Neurosurgical Institute, Beijing, 100070, China.
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, 100070, China.
- Chinese Glioma Genome Atlas Network (CGGA), Beijing, 100070, China.
| | - Xiaolong Fan
- Department of Biology, Beijing Key Laboratory of Gene Resource and Molecular Development, School of Life Sciences, and Key Laboratory of Cell Proliferation and Regulation Biology, Ministry of Education, School of Life Sciences, Beijing Normal University, Beijing, China.
- Chinese Glioma Genome Atlas Network (CGGA), Beijing, 100070, China.
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Turaga SM, Sardiu ME, Vishwakarma V, Mitra A, Bantis LE, Madan R, Merchant ML, Klein JB, Samuel G, Godwin AK. Identification of small extracellular vesicle protein biomarkers for pediatric Ewing Sarcoma. Front Mol Biosci 2023; 10:1138594. [PMID: 37122563 PMCID: PMC10140755 DOI: 10.3389/fmolb.2023.1138594] [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: 01/06/2023] [Accepted: 04/03/2023] [Indexed: 05/02/2023] Open
Abstract
Ewing Sarcoma (EWS) is the second most common osseous malignancy in children and young adults after osteosarcoma, while it is the fifth common osseous malignancy within adult age population. The clinical presentation of EWS is quite often non-specific, with the most common symptoms at presentation consisting of pain, swelling or general discomfort. The dearth of clinically relevant diagnostic or predictive biomarkers continues to remain a pressing clinical challenge. Identification of tumor specific biomarkers can lend towards an early diagnosis, expedited initiation of therapy, monitoring of therapeutic response, and early detection of recurrence of disease. We carried-out a complex analysis of cell lines and cell line derived small extracellular vesicles (sEVs) using label-free-based Quantitative Proteomic Profiling with an intent to determine shared and distinct features of these tumor cells and their respective sEVs. We analyzed EWS cells with different EWS-ETS fusions (EWS-FLI1 type I, II, and III and EWS-ERG) and their corresponding sEVs. Non-EWS controls included osteosarcoma, rhabdomyosarcoma, and benign cells, i.e., osteoid osteoma and mesenchymal stem cells. Proteomic profiling identified new shared markers between cells and their corresponding cell-derived sEVs and markers which were exclusively enriched in EWS-derived sEVs. These exo-biomarkers identified were validated by in silico approaches of publicly available protein databases and by capillary electrophoresis based western analysis (Wes). Here, we identified a protein biomarker named UGT3A2 and found its expression highly specific to EWS cells and their sEVs compared to control samples. Clinical validation of UGT3A2 expression in patient tumor tissues and plasma derived sEV samples demonstrated its specificity to EWS, indicating its potential as a EWS biomarker.
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Affiliation(s)
- Soumya M. Turaga
- Department of Pathology and Laboratory Medicine, The University of Kansas Medical Center, Kansas City, KS, United States
| | - Mihaela E. Sardiu
- Department of Biostatistics and Data Science, The University of Kansas Medical Center, Kansas City, KS, United States
- Kansas Institute for Precision Medicine, The University of Kansas Medical Center, Kansas City, KS, United States
- University of Kansas Cancer Center, Kansas City, KS, United States
| | - Vikalp Vishwakarma
- Department of Pathology and Laboratory Medicine, The University of Kansas Medical Center, Kansas City, KS, United States
| | - Amrita Mitra
- Department of Pathology and Laboratory Medicine, The University of Kansas Medical Center, Kansas City, KS, United States
| | - Leonidas E. Bantis
- Department of Biostatistics and Data Science, The University of Kansas Medical Center, Kansas City, KS, United States
| | - Rashna Madan
- Department of Pathology and Laboratory Medicine, The University of Kansas Medical Center, Kansas City, KS, United States
| | - Michael L. Merchant
- Clinical Proteomics Laboratory, Department of Medicine, University of Louisville, Louisville, KY, United States
| | - Jon B. Klein
- Robley Rex Veterans Administration Medical Center, Louisville, KY, United States
| | - Glenson Samuel
- University of Kansas Cancer Center, Kansas City, KS, United States
- Division of Pediatric Hematology Oncology and Bone Marrow Transplantation, Children’s Mercy-Kansas City, Kansas City, MO, United States
| | - Andrew K. Godwin
- Department of Pathology and Laboratory Medicine, The University of Kansas Medical Center, Kansas City, KS, United States
- Kansas Institute for Precision Medicine, The University of Kansas Medical Center, Kansas City, KS, United States
- University of Kansas Cancer Center, Kansas City, KS, United States
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105
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Dey H, Vasudevan K, Doss C. GP, Kumar SU, El Allali A, Alsamman AM, Zayed H. Integrated gene network analysis sheds light on understanding the progression of Osteosarcoma. Front Med (Lausanne) 2023; 10:1154417. [PMID: 37081847 PMCID: PMC10110863 DOI: 10.3389/fmed.2023.1154417] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Accepted: 03/20/2023] [Indexed: 04/07/2023] Open
Abstract
Introduction Osteosarcoma is a rare disorder among cancer, but the most frequently occurring among sarcomas in children and adolescents. It has been reported to possess the relapsing capability as well as accompanying collateral adverse effects which hinder the development process of an effective treatment plan. Using networks of omics data to identify cancer biomarkers could revolutionize the field in understanding the cancer. Cancer biomarkers and the molecular mechanisms behind it can both be understood by studying the biological networks underpinning the etiology of the disease. Methods In our study, we aimed to highlight the hub genes involved in gene-gene interaction network to understand their interaction and how they affect the various biological processes and signaling pathways involved in Osteosarcoma. Gene interaction network provides a comprehensive overview of functional gene analysis by providing insight into how genes cooperatively interact to elicit a response. Because gene interaction networks serve as a nexus to many biological problems, their employment of it to identify the hub genes that can serve as potential biomarkers remain widely unexplored. A dynamic framework provides a clear understanding of biological complexity and a pathway from the gene level to interaction networks. Results Our study revealed various hub genes viz. TP53, CCND1, CDK4, STAT3, and VEGFA by analyzing various topological parameters of the network, such as highest number of interactions, average shortest path length, high cluster density, etc. Their involvement in key signaling pathways, such as the FOXM1 transcription factor network, FAK-mediated signaling events, and the ATM pathway, makes them significant candidates for studying the disease. The study also highlighted significant enrichment in GO terms (Biological Processes, Molecular Function, and Cellular Processes), such as cell cycle signal transduction, cell communication, kinase binding, transcription factor activity, nucleoplasm, PML body, nuclear body, etc. Conclusion To develop better therapeutics, a specific approach toward the disease targeting the hub genes involved in various signaling pathways must have opted to unravel the complexity of the disease. Our study has highlighted the candidate hub genes viz. TP53, CCND1 CDK4, STAT3, VEGFA. Their involvement in the major signaling pathways of Osteosarcoma makes them potential candidates to be targeted for drug development. The highly enriched signaling pathways include FOXM1 transcription pathway, ATM signal-ling pathway, FAK mediated signaling events, Arf6 signaling events, mTOR signaling pathway, and Integrin family cell surface interactions. Targeting the hub genes and their associated functional partners which we have reported in our studies may be efficacious in developing novel therapeutic targets.
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Affiliation(s)
- Hrituraj Dey
- Department of Biotechnology, School of Applied Sciences, REVA University, Bangalore, India
| | - Karthick Vasudevan
- Department of Biotechnology, School of Applied Sciences, REVA University, Bangalore, India
| | - George Priya Doss C.
- Department of Integrative Biology, School of BioSciences and Technology, Vellore Institute of Technology (VIT), Vellore, India
| | - S. Udhaya Kumar
- Department of Integrative Biology, School of BioSciences and Technology, Vellore Institute of Technology (VIT), Vellore, India
| | - Achraf El Allali
- African Genome Center, Mohammed VI Polytechnic University, Ben Guerir, Morocco
| | - Alsamman M. Alsamman
- Agriculture Genetic Engineering Research Institute (AGERI), Agriculture Research Center (ARC), Giza, Egypt
- International Center for Agricultural Research in the Dry Areas (ICARDA), Giza, Egypt
| | - Hatem Zayed
- Department of Biomedical Sciences College of Health Sciences, QU Health, Qatar University, Doha, Qatar
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Whitehead CA, Fang H, Su H, Morokoff AP, Kaye AH, Hanssen E, Nowell CJ, Drummond KJ, Greening DW, Vella LJ, Mantamadiotis T, Stylli SS. Small extracellular vesicles promote invadopodia activity in glioblastoma cells in a therapy-dependent manner. Cell Oncol (Dordr) 2023:10.1007/s13402-023-00786-w. [PMID: 37014551 DOI: 10.1007/s13402-023-00786-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/16/2023] [Indexed: 04/05/2023] Open
Abstract
PURPOSE The therapeutic efficacy of radiotherapy/temozolomide treatment for glioblastoma (GBM) is limited by the augmented invasiveness mediated by invadopodia activity of surviving GBM cells. As yet, however the underlying mechanisms remain poorly understood. Due to their ability to transport oncogenic material between cells, small extracellular vesicles (sEVs) have emerged as key mediators of tumour progression. We hypothesize that the sustained growth and invasion of cancer cells depends on bidirectional sEV-mediated cell-cell communication. METHODS Invadopodia assays and zymography gels were used to examine the invadopodia activity capacity of GBM cells. Differential ultracentrifugation was utilized to isolate sEVs from conditioned medium and proteomic analyses were conducted on both GBM cell lines and their sEVs to determine the cargo present within the sEVs. In addition, the impact of radiotherapy and temozolomide treatment of GBM cells was studied. RESULTS We found that GBM cells form active invadopodia and secrete sEVs containing the matrix metalloproteinase MMP-2. Subsequent proteomic studies revealed the presence of an invadopodia-related protein sEV cargo and that sEVs from highly invadopodia active GBM cells (LN229) increase invadopodia activity in sEV recipient GBM cells. We also found that GBM cells displayed increases in invadopodia activity and sEV secretion post radiation/temozolomide treatment. Together, these data reveal a relationship between invadopodia and sEV composition/secretion/uptake in promoting the invasiveness of GBM cells. CONCLUSIONS Our data indicate that sEVs secreted by GBM cells can facilitate tumour invasion by promoting invadopodia activity in recipient cells, which may be enhanced by treatment with radio-chemotherapy. The transfer of pro-invasive cargos may yield important insights into the functional capacity of sEVs in invadopodia.
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Affiliation(s)
- Clarissa A Whitehead
- Department of Surgery, Royal Melbourne Hospital, The University of Melbourne, Parkville, VIC, Australia
| | - Haoyun Fang
- Molecular Proteomics, Baker Heart and Diabetes Institute, Melbourne, VIC, Australia
| | - Huaqi Su
- Centre for Stem Cell Systems, The University of Melbourne, Parkville, VIC, Australia
- Department of Biochemistry and Pharmacology, The University of Melbourne, Parkville, VIC, 3010, Australia
| | - Andrew P Morokoff
- Department of Surgery, Royal Melbourne Hospital, The University of Melbourne, Parkville, VIC, Australia
- Department of Surgery, The Royal Melbourne Hospital, The University of Melbourne, Level 5, Clinical Sciences Building, Parkville, VIC, 3050, Australia
| | - Andrew H Kaye
- Department of Surgery, Royal Melbourne Hospital, The University of Melbourne, Parkville, VIC, Australia
- Department of Neurosurgery, Hadassah Hebrew University Medical Centre, Jerusalem, Israel
| | - Eric Hanssen
- Department of Biochemistry and Pharmacology, The University of Melbourne, Parkville, VIC, 3010, Australia
- Advanced Microscopy Facility, The Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, VIC, 3010, Australia
| | - Cameron J Nowell
- Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences, Monash University, Melbourne, VIC, 3052, Australia
| | - Katharine J Drummond
- Department of Surgery, Royal Melbourne Hospital, The University of Melbourne, Parkville, VIC, Australia
- Department of Surgery, The Royal Melbourne Hospital, The University of Melbourne, Level 5, Clinical Sciences Building, Parkville, VIC, 3050, Australia
| | - David W Greening
- Molecular Proteomics, Baker Heart and Diabetes Institute, Melbourne, VIC, Australia
- Baker Department of Cardiovascular Research, Translation and Implementation, La Trobe University, Melbourne, VIC, Australia
- Central Clinical School, Monash University, Melbourne, VIC, Australia
- Baker Department of Cardiometabolic Health, University of Melbourne, Melbourne, VIC, Australia
| | - Laura J Vella
- Department of Surgery, Royal Melbourne Hospital, The University of Melbourne, Parkville, VIC, Australia
- Centre for Stem Cell Systems, The University of Melbourne, Parkville, VIC, Australia
| | - Theo Mantamadiotis
- Department of Surgery, Royal Melbourne Hospital, The University of Melbourne, Parkville, VIC, Australia
- Centre for Stem Cell Systems, The University of Melbourne, Parkville, VIC, Australia
- Department of Microbiology and Immunology, The University of Melbourne, Melbourne, VIC, Australia
| | - Stanley S Stylli
- Department of Surgery, Royal Melbourne Hospital, The University of Melbourne, Parkville, VIC, Australia.
- Department of Surgery, The Royal Melbourne Hospital, The University of Melbourne, Level 5, Clinical Sciences Building, Parkville, VIC, 3050, Australia.
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Kumari B, Sakode C, Lakshminarayanan R, Purohit P, Bhattacharjee A, Roy PK. A mechanistic analysis of spontaneous cancer remission phenomenon: identification of genomic basis and effector biomolecules for therapeutic applicability. 3 Biotech 2023; 13:113. [PMID: 36890970 PMCID: PMC9986194 DOI: 10.1007/s13205-023-03515-0] [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: 08/29/2022] [Accepted: 02/09/2023] [Indexed: 03/07/2023] Open
Abstract
Based on the well-documented studies, numerous tumors episodically regress permanently without treatment. Knowing the host tissue-initiated causative factors would offer considerable translational applicability, as a permanent regression process may be therapeutically replicated on patients. For this, we developed a systems biological formulation of the regression process with experimental verification and identified the relevant candidate biomolecules for therapeutic utility. We devised a cellular kinetics-based quantitative model of tumor extinction in terms of the temporal behavior of three main tumor-lysis entities: DNA blockade factor, cytotoxic T-lymphocyte and interleukin-2. As a case study, we analyzed the time-wise biopsy and microarrays of spontaneously regressing melanoma and fibrosarcoma tumors in mammalian/human hosts. We analyzed the differentially expressed genes (DEGs), signaling pathways, and bioinformatics framework of regression. Additionally, prospective biomolecules that could cause complete tumor regression were investigated. The tumor regression process follows a first-order cellular dynamics with a small negative bias, as verified by experimental fibrosarcoma regression; the bias is necessary to eliminate the residual tumor. We identified 176 upregulated and 116 downregulated DEGs, and enrichment analysis showed that the most significant were downregulated cell-division genes: TOP2A-KIF20A-KIF23-CDK1-CCNB1. Moreover, Topoisomerase-IIA inhibition might actuate spontaneous regression, with collateral confirmation provided from survival and genomic analysis of melanoma patients. Candidate molecules such as Dexrazoxane/Mitoxantrone, with interleukin-2 and antitumor lymphocytes, may potentially replicate permanent tumor regression process of melanoma. To conclude, episodic permanent tumor regression is a unique biological reversal process of malignant progression, and signaling pathway understanding, with candidate biomolecules, may plausibly therapeutically replicate the regression process on tumors clinically. Supplementary Information The online version contains supplementary material available at 10.1007/s13205-023-03515-0.
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Affiliation(s)
- Bindu Kumari
- School of Bio-Medical Engineering, Indian Institute of Technology (B.H.U.), Varanasi, 221005 India
| | - Chandrashekhar Sakode
- Department of Applied Sciences, Indian Institute of Information Technology, Nagpur, 44005 India
| | | | - Pratik Purohit
- School of Bio-Medical Engineering, Indian Institute of Technology (B.H.U.), Varanasi, 221005 India
| | - Anindita Bhattacharjee
- School of Bio-Medical Engineering, Indian Institute of Technology (B.H.U.), Varanasi, 221005 India
| | - Prasun K. Roy
- School of Bio-Medical Engineering, Indian Institute of Technology (B.H.U.), Varanasi, 221005 India
- Department of Life Sciences, Shiv Nadar University (S.N.U.), Delhi NCR, Dadri, UP 201314 India
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Li S, Zhai G, He R, Chen G, Wang S, Liu J, Cheng J, Yan H, Huang Z. Down-regulation and clinical significance of Sorbin and SH3 domain-containing protein 1 in bladder cancer tissues. IET Syst Biol 2023; 17:70-82. [PMID: 36854874 PMCID: PMC10116029 DOI: 10.1049/syb2.12060] [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: 02/27/2022] [Revised: 01/05/2023] [Accepted: 01/19/2023] [Indexed: 03/02/2023] Open
Abstract
Bladder cancer (BC) is a common cancer worldwide with a high prevalence. This study was conducted to elucidate the expression and clinical significance of Sorbin and SH3 domain-containing protein 1 (SORBS1) in BC as well as to explore its molecular mechanism in BC tumourigenesis. RNA-sequencing data, microarray, and Immunohistochemistry (IHC) were applied to elucidated the SORBS1 expression at multiple levels. After that, the relationship between tumour-immune infiltration and SORBS1 was also explored. Finally, SORBS1-related genes in BC were identified to perform functional enrichment analyses. The expression integration revealed that the comprehensive expression of SORBS1 at the mRNA level was -1.02 and that at the protein level was -3.73, based on 12 platforms, including 1221 BC and 187 non-BC samples. SORBS1 was negatively correlated with tumour purity (correlation = -0.342, p < 0.001) and positively correlated with macrophage (correlation = 0.358, p < 0.001). The results of enrichment analyses revealed that the most significant biological pathways of SORBS1-related genes were epithelial-mesenchymal transition. SORBS1 was significantly down-regulated in BC and may play a role as tumour suppressor. This study provides new directions and biomarkers for future BC diagnosis.
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Affiliation(s)
- Sheng‐Hua Li
- Department of UrologyThe First Affiliated Hospital of Guangxi Medical UniversityNanningGuangxi Zhuang Autonomous RegionChina
| | - Gao‐Qiang Zhai
- Department of UrologyThe First Affiliated Hospital of Guangxi Medical UniversityNanningGuangxi Zhuang Autonomous RegionChina
| | - Rong‐Quan He
- Department of Medical OncologyThe First Affiliated Hospital of Guangxi Medical UniversityNanningGuangxi Zhuang Autonomous RegionChina
| | - Gang Chen
- Department of Medical PathologyThe First Affiliated Hospital of Guangxi Medical UniversityNanningGuangxi Zhuang Autonomous RegionChina
| | - Shi‐Shuo Wang
- Department of Medical PathologyThe First Affiliated Hospital of Guangxi Medical UniversityNanningGuangxi Zhuang Autonomous RegionChina
| | - Jia‐Lin Liu
- Department of UrologyThe First Affiliated Hospital of Guangxi Medical UniversityNanningGuangxi Zhuang Autonomous RegionChina
| | - Ji‐Wen Cheng
- Department of UrologyThe First Affiliated Hospital of Guangxi Medical UniversityNanningGuangxi Zhuang Autonomous RegionChina
| | - Hai‐Biao Yan
- Department of UrologyThe First Affiliated Hospital of Guangxi Medical UniversityNanningGuangxi Zhuang Autonomous RegionChina
| | - Zhi‐Guang Huang
- Department of Medical PathologyThe First Affiliated Hospital of Guangxi Medical UniversityNanningGuangxi Zhuang Autonomous RegionChina
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109
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Kumar S, Das A. Peripheral Blood Mononuclear Cell derived Biomarker detection using eXplainable Artificial Intelligence (XAI) provides better diagnosis of Breast Cancer. Comput Biol Chem 2023; 104:107867. [PMID: 37030103 DOI: 10.1016/j.compbiolchem.2023.107867] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Revised: 03/22/2023] [Accepted: 04/01/2023] [Indexed: 04/05/2023]
Abstract
The incidence and mortality rate of breast cancer increases yearly by an average of 1.44 % and 0.23 %, respectively. Till 2021, there were 7.8 million women who had been diagnosed with breast cancer within 5 years. Biopsies of tumors are often expensive and invasive and raise the risk of serious complications like infection, excessive bleeding, and puncture damage to nearby tissues and organs. Early detection biomarkers are often variably expressed in different patients and may even be below the detection level at an early stage. Hence PBMC that shows alteration in gene profile as a result of interaction with tumor antigens may serve as a better early detection biomarker. Also, such alterations in immune gene profile in PBMCs are more prone to detection despite variability in different breast cancer mutants.This study aimed to identify potential diagnostic biomarkers for breast cancer using eXplainable Artificial Intelligence (XAI) on XGBoost machine learning (ML) models trained on a binary classification dataset containing the expression data of PBMCs from 252 breast cancer patients and 194 healthy women.After effectively adding SHAP values further into the XGBoost model, ten important genes related to breast cancer development were discovered to be effective potential biomarkers. Our studies showed that SVIP, BEND3, MDGA2, LEF1-AS1, PRM1, TEX14, MZB1, TMIGD2, KIT, and FKBP7 are key genes that impact model prediction. These genes may serve as early, non-invasive diagnostic and prognostic biomarkers for breast cancer patients.
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110
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Dadashkhan S, Mirmotalebisohi SA, Poursheykhi H, Sameni M, Ghani S, Abbasi M, Kalantari S, Zali H. Deciphering crucial genes in multiple sclerosis pathogenesis and drug repurposing: A systems biology approach. J Proteomics 2023; 280:104890. [PMID: 36966969 DOI: 10.1016/j.jprot.2023.104890] [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: 09/03/2022] [Revised: 02/14/2023] [Accepted: 03/09/2023] [Indexed: 04/10/2023]
Abstract
This study employed systems biology and high-throughput technologies to analyze complex molecular components of MS pathophysiology, combining data from multiple omics sources to identify potential biomarkers and propose therapeutic targets and repurposed drugs for MS treatment. This study analyzed GEO microarray datasets and MS proteomics data using geWorkbench, CTD, and COREMINE to identify differentially expressed genes associated with MS disease. Protein-protein interaction networks were constructed using Cytoscape and its plugins, and functional enrichment analysis was performed to identify crucial molecules. A drug-gene interaction network was also created using DGIdb to propose medications. This study identified 592 differentially expressed genes (DEGs) associated with MS disease using GEO, proteomics, and text-mining datasets. 37 DEGs were found to be important by topographical network studies, and 6 were identified as the most significant for MS pathophysiology. Additionally, we proposed six drugs that target these key genes. Crucial molecules identified in this study were dysregulated in MS and likely play a key role in the disease mechanism, warranting further research. Additionally, we proposed repurposing certain FDA-approved drugs for MS treatment. Our in silico results were supported by previous experimental research on some of the target genes and drugs. SIGNIFICANCE: As the long-lasting investigations continue to discover new pathological territories in neurodegeneration, here we apply a systems biology approach to determine multiple sclerosis's molecular and pathophysiological origin and identify multiple sclerosis crucial genes that contribute to candidating new biomarkers and proposing new medications.
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Affiliation(s)
- Sadaf Dadashkhan
- Molecular Medicine Research Centre, Universitätsklinikum Jena, Jena, Germany; Department of Biology, Science and Research Branch, Islamic Azad University, Tehran, Iran
| | - Seyed Amir Mirmotalebisohi
- Student Research Committee, Department of Biotechnology, School of Advanced Technologies in Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran; Cellular and Molecular Biology Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Hossein Poursheykhi
- Department of New Scientist, Faculty of Medical Sciences, Tehran Branch, Islamic Azad University, Tehran, Iran
| | - Marzieh Sameni
- Student Research Committee, Department of Biotechnology, School of Advanced Technologies in Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran; Cellular and Molecular Biology Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Sepideh Ghani
- Cellular and Molecular Biology Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran; Department of Biotechnology, School of Advanced Technologies in Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | | | - Sima Kalantari
- Cellular and Molecular Biology Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran; Department of Biotechnology, School of Advanced Technologies in Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran; Regenerative Medicine Group (REMED), Universal Scientific Education & Research Network (USERN), Tehran, Iran
| | - Hakimeh Zali
- Department of Tissue Engineering and Applied Cell Sciences, School of Advanced Technologies in Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
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Lin XH, Li DP, Liu ZY, Zhang S, Tang WQ, Chen RX, Weng SQ, Tseng YJ, Xue RY, Dong L. Six immune-related promising biomarkers may promote hepatocellular carcinoma prognosis: a bioinformatics analysis and experimental validation. Cancer Cell Int 2023; 23:52. [PMID: 36959615 PMCID: PMC10035283 DOI: 10.1186/s12935-023-02888-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Accepted: 02/23/2023] [Indexed: 03/25/2023] Open
Abstract
Background Abnormal miRNA and mRNA expression and dysregulated immune microenvironment have been found to frequently induce the progression of hepatocellular carcinoma (HCC) in recent reports. In particular, the immune-related competing endogenous RNAs (ceRNA) mechanism plays a crucial role in HCC progression. However, the underlying mechanisms remain unclear. Methods Differentially expressed immune-related genes were obtained from the Immport, GEO, and TCGA databases. The mRNA and protein expression levels in HCC tissues and adjacent normal tissues were confirmed, and we further investigated the methylation levels of these biomarkers to explore their function. Then, the TIMER and TISCH databases were used to assess the relationship between immune infiltration and hub genes. Survival analysis and univariate and multivariate Cox models were used to evaluate the association between hub genes and HCC diagnosis. Hub gene expression was experimentally validated in six HCC cell lines and 15 HCC samples using qRT-PCR and immunohistochemistry. The hub genes were uploaded to DSigDB for drug prediction enrichment analysis. Results We identified that patients with abnormal miRNAs (hsa-miR-125b-5p and hsa-miR-21-5p) and their targeted genes (NTF3, PSMD14, CD320, and SORT1) had a worse prognosis. Methylation analysis of miRNA-targeted genes suggested that alteration of methylation levels is also a factor in the induction of tumorigenesis. We also found that the development of HCC progression caused by miRNA-mRNA interactions may be closely correlated with the infiltration of immunocytes. Moreover, the GSEA, GO, and KEGG analysis suggested that several common immune-related biological processes and pathways were related to miRNA-targeted genes. The results of qRT-PCR, immunohistochemistry, and western blotting were consistent with our bioinformatics results, suggesting that abnormal miRNAs and their targeted genes may affect HCC progression. Conclusions Briefly, our study systematically describes the mechanisms of miRNA-mRNA interactions in HCC and predicts promising biomarkers that are associated with immune filtration for HCC progression. Supplementary Information The online version contains supplementary material available at 10.1186/s12935-023-02888-9.
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Affiliation(s)
- Xia-Hui Lin
- grid.8547.e0000 0001 0125 2443Department of Gastroenterology and Hepatology, Zhongshan Hospital, Fudan University, Shanghai, 200032 China
- grid.413087.90000 0004 1755 3939Shanghai Institute of Liver Disease, Shanghai, 200032 China
| | - Dong-ping Li
- grid.8547.e0000 0001 0125 2443Department of Gastroenterology and Hepatology, Zhongshan Hospital, Fudan University, Shanghai, 200032 China
- grid.413087.90000 0004 1755 3939Shanghai Institute of Liver Disease, Shanghai, 200032 China
| | - Zhi-Yong Liu
- grid.8547.e0000 0001 0125 2443Department of Gastroenterology and Hepatology, Zhongshan Hospital, Fudan University, Shanghai, 200032 China
- grid.413087.90000 0004 1755 3939Shanghai Institute of Liver Disease, Shanghai, 200032 China
| | - Si Zhang
- grid.8547.e0000 0001 0125 2443Key Laboratory of Glycoconjugate Research Ministry of Public Health, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Fudan University, Shanghai, 200032 China
| | - Wen-qing Tang
- grid.8547.e0000 0001 0125 2443Department of Gastroenterology and Hepatology, Zhongshan Hospital, Fudan University, Shanghai, 200032 China
- grid.413087.90000 0004 1755 3939Shanghai Institute of Liver Disease, Shanghai, 200032 China
| | - Rong-xin Chen
- grid.8547.e0000 0001 0125 2443Key Laboratory of Carcinogenesis and Cancer Invasion, Liver Cancer Institute, Zhongshan Hospital, Fudan University, Shanghai, 200032 China
| | - Shu-qiang Weng
- grid.8547.e0000 0001 0125 2443Department of Gastroenterology and Hepatology, Zhongshan Hospital, Fudan University, Shanghai, 200032 China
- grid.413087.90000 0004 1755 3939Shanghai Institute of Liver Disease, Shanghai, 200032 China
| | - Yu-jen Tseng
- grid.8547.e0000 0001 0125 2443Department of Digestive Diseases, Huashan Hospital, Fudan University, 12 Wulumuqi Middle Road, Shanghai, 200040 China
| | - Ru-yi Xue
- grid.8547.e0000 0001 0125 2443Department of Gastroenterology and Hepatology, Zhongshan Hospital, Fudan University, Shanghai, 200032 China
- grid.413087.90000 0004 1755 3939Shanghai Institute of Liver Disease, Shanghai, 200032 China
| | - Ling Dong
- grid.8547.e0000 0001 0125 2443Department of Gastroenterology and Hepatology, Zhongshan Hospital, Fudan University, Shanghai, 200032 China
- grid.413087.90000 0004 1755 3939Shanghai Institute of Liver Disease, Shanghai, 200032 China
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Kumari S, Kumar P. Design and Computational Analysis of an MMP9 Inhibitor in Hypoxia-Induced Glioblastoma Multiforme. ACS OMEGA 2023; 8:10565-10590. [PMID: 36969457 PMCID: PMC10035023 DOI: 10.1021/acsomega.3c00441] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/21/2023] [Accepted: 02/28/2023] [Indexed: 06/18/2023]
Abstract
The main therapeutic difficulties in treating hypoxia-induced glioblastoma multiforme (GBM) are toxicity of current treatments and the resistance brought on by the microenvironment. More effective therapeutic alternatives are urgently needed to reduce tumor lethality. Hence, we screened plant-based natural product panels intending to identify novel drugs without elevating drug resistance. We explored GEO for the hypoxia GBM model and compared hypoxic genes to non-neoplastic brain cells. A total of 2429 differentially expressed genes expressed exclusively in hypoxia were identified. The functional enrichment analysis demonstrated genes associated with GBM, further PPI network was constructed, and biological pathways associated with them were explored. Seven webtools, including GEPIA2.0, TIMER2.0, TCGA-GBM, and GlioVis, were used to validate 32 hub genes discovered using Cytoscape tool in GBM patient samples. Four GBM-specific hypoxic hub genes, LYN, MMP9, PSMB9, and TIMP1, were connected to the tumor microenvironment using TIMER analysis. 11 promising hits demonstrated positive drug-likeness with nontoxic characteristics and successfully crossed blood-brain barrier and ADMET analyses. Top-ranking hits have stable intermolecular interactions with the MMP9 protein according to molecular docking, MD simulation, MM-PBSA, PCA, and DCCM analyses. Herein, we have reported flavonoids, 7,4'-dihydroxyflavan, (3R)-3-(4-hydroxybenzyl)-6-hydroxy-8-methoxy-3,4-dihydro-2H-1-benzopyran, and 4'-hydroxy-7-methoxyflavan, to inhibit MMP9, a novel hypoxia gene signature that could serve as a promising predictor in various clinical applications, including GBM diagnosis, prognosis, and targeted therapy.
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113
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Xiao B, Liu Y, Chandrasiri I, Overby C, Benoit DSW. Impact of Nanoparticle Physicochemical Properties on Protein Corona and Macrophage Polarization. ACS APPLIED MATERIALS & INTERFACES 2023. [PMID: 36916683 DOI: 10.1021/acsami.2c22471] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Macrophages, the major component of the mononuclear phagocyte system, uptake and clear systemically administered nanoparticles (NPs). Therefore, leveraging macrophages as a druggable target may be advantageous to enhance NP-mediated drug delivery. Despite many studies focused on NP-cell interactions, NP-mediated macrophage polarization mechanisms are still poorly understood. This work aimed to explore the effect of NP physicochemical parameters (size and charge) on macrophage polarization. Upon exposure to biological fluids, proteins rapidly adsorb to NPs and form protein coronas. To this end, we hypothesized that NP protein coronas govern NP-macrophage interactions, uptake, and subsequent macrophage polarization. To test this hypothesis, model polystyrene NPs with various charges and sizes, as well as NPs relevant to drug delivery, were utilized. Data suggest that cationic NPs potentiate both M1 and M2 macrophage markers, while anionic NPs promote M1-to-M2 polarization. Additionally, anionic polystyrene nanoparticles (APNs) of 50 nm exhibit the greatest influence on M2 polarization. Proteomics was pursued to further understand the effect of NPs physicochemical parameters on protein corona, which revealed unique protein patterns based on NP charge and size. Several proteins impacting M1 and M2 macrophage polarization were identified within cationic polystyrene nanoparticles (CPNs) corona, while APNs corona included fewer M1 but more M2-promoting proteins. Nevertheless, size impacts protein corona abundance but not identities. Altogether, protein corona identities varied based on NP surface charge and correlated to dramatic differences in macrophage polarization. In contrast, NP size differentially impacts macrophage polarization, which is dominated by NP uptake level rather than protein corona. In this work, specific corona proteins were identified as a function of NP physicochemical properties. These proteins are correlated to specific macrophage polarization programs and may provide design principles for developing macrophage-mediated NP drug delivery systems.
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Affiliation(s)
- Baixue Xiao
- Department of Biomedical Engineering, University of Rochester, Rochester, New York 14623, United States
- Center for Musculoskeletal Research, University of Rochester Medical Center, Rochester, New York 14623, United States
| | - Yuxuan Liu
- Materials Science Program, University of Rochester, Rochester, New York 14623, United States
| | - Indika Chandrasiri
- Department of Biomedical Engineering, University of Rochester, Rochester, New York 14623, United States
- Center for Musculoskeletal Research, University of Rochester Medical Center, Rochester, New York 14623, United States
| | - Clyde Overby
- Department of Biomedical Engineering, University of Rochester, Rochester, New York 14623, United States
- Center for Musculoskeletal Research, University of Rochester Medical Center, Rochester, New York 14623, United States
| | - Danielle S W Benoit
- Department of Biomedical Engineering, University of Rochester, Rochester, New York 14623, United States
- Center for Musculoskeletal Research, University of Rochester Medical Center, Rochester, New York 14623, United States
- Department of Chemical Engineering, University of Rochester, Rochester, New York 14623, United States
- Materials Science Program, University of Rochester, Rochester, New York 14623, United States
- Phil and Penny Knight Campus for Accelerating Scientific Impact, Department of Bioengineering, University of Oregon, Eugene, Oregon 97403, United States
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S SH, G K, Dey H, Sangoji RV, Thirumal Kumar D, Zayed H, Vasudevan K, George Priya Doss C. Identification of potential circadian genes and associated pathways in colorectal cancer progression and prognosis using microarray gene expression analysis. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2023; 137:181-203. [PMID: 37709376 DOI: 10.1016/bs.apcsb.2023.02.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/16/2023]
Abstract
Colorectal cancer (CRC) is third cancer causing death in the world. CRC is associated with disrupting the circadian rhythm (CR), closely associating the CRC progression and the dysregulation of genes involved in the biological clock. In this study, we aimed to understand the circadian rhythm changes in patients diagnosed with CRC. We used the GEO database with the ID GSE46549 for our analysis, which consists of 32 patients with CRC and one as normal control. Our study has identified five essential genes involved in CRC, HAPLN1, CDH12, IGFBP5, DCHS2, and DOK5, and had different enriched pathways, such as the Wnt-signaling pathway, at different time points of study. As a part of our study, we also identified various related circadian genes, such as CXCL12, C1QTNF2, MRC2, and GLUL, from the Circadian Gene Expression database, that played a role in circadian rhythm and CRC development. As circadian timing can influence the host tissue's ability to tolerate anticancer medications, the genes reported can serve as a potential drug target for treating CRC and become beneficial to translational settings.
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Affiliation(s)
- Sri Hari S
- Department of Biotechnology, School of Applied Sciences, REVA University, Bengaluru, Karnataka, India
| | - Keerthana G
- Department of Biotechnology, School of Applied Sciences, REVA University, Bengaluru, Karnataka, India
| | - Hrituraj Dey
- Department of Biotechnology, School of Applied Sciences, REVA University, Bengaluru, Karnataka, India
| | - Rahul V Sangoji
- Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal, Karnataka, India
| | - D Thirumal Kumar
- Faculty of Allied Health Sciences, Meenakshi Academy of Higher Education and Research (MAHER), Chennai, Tamil Nadu, India
| | - Hatem Zayed
- Department of Biomedical Sciences, College of Health and Sciences, Qatar University, QU Health, Doha, Qatar
| | - Karthick Vasudevan
- Department of Biotechnology, School of Applied Sciences, REVA University, Bengaluru, Karnataka, India.
| | - C George Priya Doss
- Laboratory of Integrative Genomics, Department of Integrative Biology, School of Biosciences and Technology, Vellore Institute of Technology, Vellore, Tamil Nadu, India.
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Yang H, Zhang H, Gu H, Wang J, Zhang J, Zen K, Li D. Comparative Analyses of Human Exosome Proteomes. Protein J 2023:10.1007/s10930-023-10100-0. [PMID: 36892742 DOI: 10.1007/s10930-023-10100-0] [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: 02/27/2023] [Indexed: 03/10/2023]
Abstract
Exosomes are responsible for cell-to-cell communication and serves as a valuable drug delivery vehicle. However, exosome heterogeneity, non-standardized isolation methods and proteomics/bioinformatics approaches limit its clinical applications. To better understand exosome heterogeneity, biological function and molecular mechanism of its biogenesis, secretion and uptake, techniques in proteomics or bioinformatics were applied to investigate human embryonic kidney cell (293T cell line)-derived exosome proteome and enable an integrative comparison of exosomal proteins and protein-protein interaction (PPI) networks of eleven exosome proteomes extracted from diverse human samples, including 293T (two datasets), dermal fibroblast, mesenchymal stem cell, thymic epithelial primary cell, breast cancer cell line (MDA-MB-231), patient neuroblastoma cell, plasma, saliva, serum and urine. Mapping of exosome biogenesis/secretion/uptake-related proteins onto exosome proteomes highlights exosomal origin-specific routes of exosome biogenesis/secretion/uptake and exosome-dependent intercellular communication. The finding provides insight into comparative exosome proteomes and its biogenesis, secretion and uptake, and potentially contributes to clinical applications.
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Affiliation(s)
- Hao Yang
- State Key Laboratory of Pharmaceutical Biotechnology, Jiangsu Engineering Research Center for MicroRNA Biology and Biotechnology, School of Life Sciences, Nanjing University, 210023, Jiangsu, P.R. China
| | - Haiyang Zhang
- State Key Laboratory of Pharmaceutical Biotechnology, Jiangsu Engineering Research Center for MicroRNA Biology and Biotechnology, School of Life Sciences, Nanjing University, 210023, Jiangsu, P.R. China
| | - Hongwei Gu
- State Key Laboratory of Pharmaceutical Biotechnology, Jiangsu Engineering Research Center for MicroRNA Biology and Biotechnology, School of Life Sciences, Nanjing University, 210023, Jiangsu, P.R. China
| | - Jin Wang
- State Key Laboratory of Pharmaceutical Biotechnology, Jiangsu Engineering Research Center for MicroRNA Biology and Biotechnology, School of Life Sciences, Nanjing University, 210023, Jiangsu, P.R. China
| | - Junfeng Zhang
- State Key Laboratory of Pharmaceutical Biotechnology, Jiangsu Engineering Research Center for MicroRNA Biology and Biotechnology, School of Life Sciences, Nanjing University, 210023, Jiangsu, P.R. China
| | - Ke Zen
- State Key Laboratory of Pharmaceutical Biotechnology, Jiangsu Engineering Research Center for MicroRNA Biology and Biotechnology, School of Life Sciences, Nanjing University, 210023, Jiangsu, P.R. China
| | - Donghai Li
- State Key Laboratory of Pharmaceutical Biotechnology, Jiangsu Engineering Research Center for MicroRNA Biology and Biotechnology, School of Life Sciences, Nanjing University, 210023, Jiangsu, P.R. China.
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MYTHO is a novel regulator of skeletal muscle autophagy and integrity. Nat Commun 2023; 14:1199. [PMID: 36864049 PMCID: PMC9981687 DOI: 10.1038/s41467-023-36817-1] [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: 06/13/2022] [Accepted: 02/17/2023] [Indexed: 03/04/2023] Open
Abstract
Autophagy is a critical process in the regulation of muscle mass, function and integrity. The molecular mechanisms regulating autophagy are complex and still partly understood. Here, we identify and characterize a novel FoxO-dependent gene, d230025d16rik which we named Mytho (Macroautophagy and YouTH Optimizer), as a regulator of autophagy and skeletal muscle integrity in vivo. Mytho is significantly up-regulated in various mouse models of skeletal muscle atrophy. Short term depletion of MYTHO in mice attenuates muscle atrophy caused by fasting, denervation, cancer cachexia and sepsis. While MYTHO overexpression is sufficient to trigger muscle atrophy, MYTHO knockdown results in a progressive increase in muscle mass associated with a sustained activation of the mTORC1 signaling pathway. Prolonged MYTHO knockdown is associated with severe myopathic features, including impaired autophagy, muscle weakness, myofiber degeneration, and extensive ultrastructural defects, such as accumulation of autophagic vacuoles and tubular aggregates. Inhibition of the mTORC1 signaling pathway in mice using rapamycin treatment attenuates the myopathic phenotype triggered by MYTHO knockdown. Skeletal muscles from human patients diagnosed with myotonic dystrophy type 1 (DM1) display reduced Mytho expression, activation of the mTORC1 signaling pathway and impaired autophagy, raising the possibility that low Mytho expression might contribute to the progression of the disease. We conclude that MYTHO is a key regulator of muscle autophagy and integrity.
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Rivera RG, Regidor PJS, Ruamero Jr EC, Allanigue EJV, Salinas MV. A network pharmacology and molecular docking approach in the exploratory investigation of the biological mechanisms of lagundi (Vitex negundo L.) compounds against COVID-19. Genomics Inform 2023; 21:e4. [PMID: 37037462 PMCID: PMC10085743 DOI: 10.5808/gi.22060] [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: 09/22/2022] [Revised: 12/27/2022] [Accepted: 02/08/2023] [Indexed: 04/03/2023] Open
Abstract
Coronavirus disease 2019 (COVID-19) is an inflammatory and infectious disease caused by severe acute respiratory syndrome coronavirus 2 virus with a complex pathophysiology. While COVID-19 vaccines and boosters are available, treatment of the disease is primarily supportive and symptomatic. Several research have suggested the potential of herbal medicines as an adjunctive treatment for the disease. A popular herbal medicine approved in the Philippines for the treatment of acute respiratory disease is Vitex negundo L. In fact, the Department of Science and Technology of the Philippines has funded a clinical trial to establish its potential as an adjunctive treatment for COVID-19. Here, we utilized network pharmacology and molecular docking in determining pivotal targets of Vitex negundo compounds against COVID-19. The results showed that significant targets of Vitex negundo compounds in COVID-19 are CSB, SERPINE1, and PLG which code for cathepsin B, plasminogen activator inhibitor-1, and plasminogen, respectively. Molecular docking revealed that α-terpinyl acetate and geranyl acetate have good binding affinity in cathepsin B; 6,7,4-trimethoxyflavanone, 5,6,7,8,3',4',5'-heptamethoxyflavone, artemetin, demethylnobiletin, gardenin A, geranyl acetate in plasminogen; and 7,8,4-trimethoxyflavanone in plasminogen activator inhibitor-1. While the results are promising, these are bound to the limitations of computational methods and further experimentation are needed to completely establish the molecular mechanisms of Vitex negundo against COVID-19.
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Affiliation(s)
- Robertson G. Rivera
- Pharmaceutical Chemistry Department, College of Pharmacy, University of the Philippines Manila, Manila, Philippines
| | - Patrick Junard S. Regidor
- Pharmaceutical Chemistry Department, College of Pharmacy, University of the Philippines Manila, Manila, Philippines
| | - Edwin C. Ruamero Jr
- Pharmaceutical Chemistry Department, College of Pharmacy, University of the Philippines Manila, Manila, Philippines
| | - Eric John V. Allanigue
- Department of Pharmacology and Toxicology, College of Medicine, University of the Philippines Manila, Manila, Philippines
| | - Melanie V. Salinas
- Safety and Medical Affairs Department, Clinchoice Inc., Fort Washington, PA 19034, USA
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Zhang Z, Fan W, Gao Q, Han Y, Ma J, Gao W, Hu Y, Zhu H, Yang R, Wang H, Du B, Zhang Z, Zhong J. Hsa_Circ_0000826 inhibits the proliferation of colorectal cancer by targeting AUF1. J Genet Genomics 2023; 50:192-203. [PMID: 35940521 DOI: 10.1016/j.jgg.2022.07.006] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Revised: 07/25/2022] [Accepted: 07/28/2022] [Indexed: 11/17/2022]
Abstract
Many circular RNAs (circRNAs) are reported to be abnormally expressed during the progression of various tumors, and these circRNAs can be used as anti-tumor targets. Therefore, it is important to identify circRNAs that can be used effectively for the clinical diagnosis and treatment of colorectal cancer (CRC). Here, we report that hsa_Circ_0000826 (Circ_0000826), a circRNA with significantly reduced expression level in CRC tissues, is associated with a poor prognosis in patients. The silencing of Circ_0000826 promotes the proliferation of CRC cells. Conversely, the overexpression of Circ_0000826 restricted CRC cell proliferation both in vitro and in vivo. Furthermore, Circ_0000826 could target AU-rich element RNA-binding protein 1 (AUF1). AUF1, known as heterogeneous nuclear ribonucleoprotein D (hnRNP D), could bind to the c-MYC 3'-UTR and promote c-MYC expression. When Circ_0000826 binds to AUF1, it competitively inhibits the binding of AUF1 to the c-MYC 3'-UTR, which inhibits the c-MYC expression and cell proliferation. These results provide novel insights into the functional mechanism of Circ_0000826 action in CRC progression and indicate its potential use as a therapeutic target in CRC.
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Affiliation(s)
- Zheying Zhang
- Department of Pathology, School of Basic Medical Sciences, Xinxiang Medical University, Xinxiang, Henan 453003, China
| | - Wenyan Fan
- Department of Microscopic Morphology Laboratory, School of Basic Medical Sciences, Xinxiang Medical University, Xinxiang, Henan 453003, China
| | - Qingzu Gao
- Department of Pathology, The First Affiliated Hospital of Xinxiang Medical University, Xinxiang, Henan 453003, China
| | - Yifei Han
- Department of Pathology, School of Basic Medical Sciences, Xinxiang Medical University, Xinxiang, Henan 453003, China
| | - Jingyu Ma
- Department of Pathology, School of Basic Medical Sciences, Xinxiang Medical University, Xinxiang, Henan 453003, China
| | - Wuji Gao
- Department of Pathology, School of Basic Medical Sciences, Xinxiang Medical University, Xinxiang, Henan 453003, China
| | - Yuhan Hu
- Department of Microscopic Morphology Laboratory, School of Basic Medical Sciences, Xinxiang Medical University, Xinxiang, Henan 453003, China
| | - Huifang Zhu
- Department of Pathology, School of Basic Medical Sciences, Xinxiang Medical University, Xinxiang, Henan 453003, China
| | - Rui Yang
- School of Life Science and Technology, Xinxiang Medical University, Xinxiang, Henan 453003, China
| | - Haijun Wang
- Department of Pathology, School of Basic Medical Sciences, Xinxiang Medical University, Xinxiang, Henan 453003, China
| | - Baoshun Du
- Second Department of Neurosurgery, Xinxiang Central Hospital, Xinxiang, Henan 453003, China
| | - Zuoyang Zhang
- Department of Pathology, Anhui Medical University, Hefei, Anhui 230032, China.
| | - Jiateng Zhong
- Department of Pathology, School of Basic Medical Sciences, Xinxiang Medical University, Xinxiang, Henan 453003, China.
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Singh P, Szigyártó IC, Ricci M, Gaál A, Quemé‐Peña MM, Kitka D, Fülöp L, Turiák L, Drahos L, Varga Z, Beke‐Somfai T. Removal and identification of external protein corona members from RBC-derived extracellular vesicles by surface manipulating antimicrobial peptides. JOURNAL OF EXTRACELLULAR BIOLOGY 2023; 2:e78. [PMID: 38938416 PMCID: PMC11080927 DOI: 10.1002/jex2.78] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Revised: 01/27/2023] [Accepted: 02/20/2023] [Indexed: 06/29/2024]
Abstract
In the last years, extracellular vesicles (EVs), secreted by various cells and body fluids have shown extreme potential in biomedical applications. Increasing number of studies suggest that a protein corona could adhere to the surface of EVs which can have a fundamental effect on their function, targeting and therapeutical efficacy. However, removing and identifying these corona members is currently a challenging task to achieve. In this study we have employed red blood cell-derived extracellular vesicles (REVs) as a model system and three membrane active antimicrobial peptides (AMPs), LL-37, FK-16 and CM15, to test whether they can be used to remove protein corona members from the surface of vesicles. These AMPs were reported to preferentially exert their membrane-related activity via one of the common helical surface-covering models and do not significantly affect the interior of lipid bilayer bodies. The interaction between the peptides and the REVs was followed by biophysical techniques, such as flow-linear dichroism spectroscopy which provided the effective applicable peptide concentration for protein removal. REV samples were then subjected to subsequent size exclusion chromatography and to proteomics analysis. Based on the comparison of control REVs with the peptide treated samples, seventeen proteins were identified as external protein corona members. From the three investigated AMPs, FK-16 can be considered as the best candidate to further optimize EV-related applicability of AMPs. Our results on the REV model system envisage that membrane active peptides may become a useful set of tools in engineering and modifying surfaces of EVs and other lipid-based natural particles.
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Affiliation(s)
- Priyanka Singh
- Institute of Materials and Environmental ChemistryBiomolecular Self‐assembly Research GroupResearch Centre for Natural SciencesBudapestHungary
- Hevesy György PhD School of ChemistryELTE Eötvös Loránd UniversityBudapestHungary
| | - Imola Cs. Szigyártó
- Institute of Materials and Environmental ChemistryBiomolecular Self‐assembly Research GroupResearch Centre for Natural SciencesBudapestHungary
| | - Maria Ricci
- Institute of Materials and Environmental ChemistryBiomolecular Self‐assembly Research GroupResearch Centre for Natural SciencesBudapestHungary
| | - Anikó Gaál
- Institute of Materials and Environmental ChemistryBiological Nanochemistry Research Group, Research Centre for Natural SciencesBudapestHungary
| | - Mayra Maritza Quemé‐Peña
- Institute of Materials and Environmental ChemistryBiomolecular Self‐assembly Research GroupResearch Centre for Natural SciencesBudapestHungary
- Hevesy György PhD School of ChemistryELTE Eötvös Loránd UniversityBudapestHungary
| | - Diána Kitka
- Hevesy György PhD School of ChemistryELTE Eötvös Loránd UniversityBudapestHungary
- Institute of Materials and Environmental ChemistryBiological Nanochemistry Research Group, Research Centre for Natural SciencesBudapestHungary
| | - Lívia Fülöp
- Department of Medical ChemistryUniversity of SzegedSzegedHungary
| | - Lilla Turiák
- Institute of Organic ChemistryMS Proteomics Research Group, Research Centre for Natural SciencesBudapestHungary
| | - László Drahos
- Institute of Organic ChemistryMS Proteomics Research Group, Research Centre for Natural SciencesBudapestHungary
| | - Zoltán Varga
- Institute of Materials and Environmental ChemistryBiological Nanochemistry Research Group, Research Centre for Natural SciencesBudapestHungary
| | - Tamás Beke‐Somfai
- Institute of Materials and Environmental ChemistryBiomolecular Self‐assembly Research GroupResearch Centre for Natural SciencesBudapestHungary
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Lino JB, Robert AW, Stimamiglio MA, de Aguiar AM. Comparative analysis of the potential of the secretomes of cardiac resident stromal cells and fibroblasts. IUBMB Life 2023; 75:196-206. [PMID: 34590780 DOI: 10.1002/iub.2557] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Accepted: 09/13/2021] [Indexed: 11/10/2022]
Abstract
The secretome of different cell types has been applied on in vitro and in vivo assays, indicating considerable therapeutic potential. However, the choice of the ideal cell type and culture conditions for obtaining the best set of soluble factors, as well as the assays to assess specific effects, remain subjects of vigorous debate. In this study, we used mass spectrometry to characterize the secretomes of ventricle derived-cardiac resident stromal cells (vCRSC) and human dermal fibroblasts (HDFs) and evaluate them in an effort to understand the niche specificity of biological responses toward different cellular behaviors, such as cell proliferation, adhesion, migration, and differentiation. It was interesting to note that the HDF and vCRSC secretomes were both able to induce proliferation and cardiac differentiation of H9c2 cells, as well as to increase the adhesion activity of H9c2 cells and human umbilical vein endothelial cells. Analysis of the secretome composition showed that the vCRSCs derived from different donors secreted a similar set of proteins. Despite the differences, almost half of the proteins identified in conditioned medium were common to both HDF and vCRSC. Consequently, a high number of common biological processes were identified in the secretomes of the two cell types, which could help to explain the similar results observed in the in vitro assays. We show that soluble factors secreted by both HDF and vCRSC are able to promote proliferation and differentiation of cardiomyoblasts in vitro. Our study indicates the possible use of vCRSC or HDF secretomes in acellular therapies for regenerative medicine.
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Affiliation(s)
- Jhonatan Basso Lino
- Stem Cells Basic Biology Laboratory, Carlos Chagas Institute - FIOCRUZ/PR, Curitiba, Paraná, Brazil
| | - Anny Waloski Robert
- Stem Cells Basic Biology Laboratory, Carlos Chagas Institute - FIOCRUZ/PR, Curitiba, Paraná, Brazil
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Duan H, Chen B, Wang W, Luo H. Identification of GNG7 as a novel biomarker and potential therapeutic target for gastric cancer via bioinformatic analysis and in vitro experiments. Aging (Albany NY) 2023; 15:1445-1474. [PMID: 36863706 PMCID: PMC10042700 DOI: 10.18632/aging.204545] [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: 10/31/2022] [Accepted: 02/16/2023] [Indexed: 03/04/2023]
Abstract
Gastric cancer (GC) is one of the most common malignancies with unfavorable prognoses. The present study aimed to identify novel biomarkers or potential therapeutic targets in GC via bioinformatic analysis and in vitro experiments. The Gene Expression Omnibus and The Cancer Genome Atlas databases were used to screen the differentially expressed genes (DEGs). After protein-protein interaction network construction, both module and prognostic analyses were performed to identify prognosis-related genes in GC. The expression patterns and functions of G protein γ subunit 7 (GNG7) in GC were then visualized in multiple databases and further verified using in vitro experiments. A total of 897 overlapping DEGs were detected and 20 hub genes were identified via systematic analysis. After accessing the prognostic value of the hub genes using the online server Kaplan-Meier plotter, a six-gene prognostic signature was identified, which was also significantly correlated with the process of immune infiltration in GC. The results of open-access database analyses suggested that GNG7 is downregulated in GC; this downregulation was associated with tumor progression. Furthermore, the functional enrichment analysis unveiled that the GNG7-coexpressed genes or gene sets were closely correlated with the proliferation and cell cycle processes of GC cells. Finally, in vitro experiments further confirmed that GNG7 overexpression inhibited GC cell proliferation, colony formation, and cell cycle progression and induced apoptosis. As a tumor suppressor gene, GNG7 suppressed the growth of GC cells via cell cycle blockade and apoptosis induction and thus may be used as a potential biomarker and therapeutic target for GC.
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Affiliation(s)
- Houyu Duan
- Department of Gastroenterology, Renmin Hospital of Wuhan University, Wuhan 430060, Hubei, P.R. China
| | - Biao Chen
- Department of Oncology, Renmin Hospital of Wuhan University, Wuhan 430060, Hubei, P.R. China
| | - Wei Wang
- Department of Hepatobiliary Surgery, Renmin Hospital of Wuhan University, Wuhan 430060, Hubei, P.R. China
| | - Hesheng Luo
- Department of Gastroenterology, Renmin Hospital of Wuhan University, Wuhan 430060, Hubei, P.R. China
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Khokhar M, Purohit P, Gadwal A, Tomo S, Bajpai NK, Shukla R. The Differentially Expressed Genes Responsible for the Development of T Helper 9 Cells From T Helper 2 Cells in Various Disease States: Immuno-Interactomics Study. JMIR BIOINFORMATICS AND BIOTECHNOLOGY 2023; 4:e42421. [PMID: 38935935 PMCID: PMC11135241 DOI: 10.2196/42421] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/03/2022] [Revised: 01/18/2023] [Accepted: 01/25/2023] [Indexed: 06/29/2024]
Abstract
BACKGROUND T helper (Th) 9 cells are a novel subset of Th cells that develop independently from Th2 cells and are characterized by the secretion of interleukin (IL)-9. Studies have suggested the involvement of Th9 cells in variable diseases such as allergic and pulmonary diseases (eg, asthma, chronic obstructive airway disease, chronic rhinosinusitis, nasal polyps, and pulmonary hypoplasia), metabolic diseases (eg, acute leukemia, myelocytic leukemia, breast cancer, lung cancer, melanoma, pancreatic cancer), neuropsychiatric disorders (eg, Alzheimer disease), autoimmune diseases (eg, Graves disease, Crohn disease, colitis, psoriasis, systemic lupus erythematosus, systemic scleroderma, rheumatoid arthritis, multiple sclerosis, inflammatory bowel disease, atopic dermatitis, eczema), and infectious diseases (eg, tuberculosis, hepatitis). However, there is a dearth of information on its involvement in other metabolic, neuropsychiatric, and infectious diseases. OBJECTIVE This study aims to identify significant differentially altered genes in the conversion of Th2 to Th9 cells, and their regulating microRNAs (miRs) from publicly available Gene Expression Omnibus data sets of the mouse model using in silico analysis to unravel various pathogenic pathways involved in disease processes. METHODS Using differentially expressed genes (DEGs) identified from 2 publicly available data sets (GSE99166 and GSE123501) we performed functional enrichment and network analyses to identify pathways, protein-protein interactions, miR-messenger RNA associations, and disease-gene associations related to significant differentially altered genes implicated in the conversion of Th2 to Th9 cells. RESULTS We extracted 260 common downregulated, 236 common upregulated, and 634 common DEGs from the expression profiles of data sets GSE99166 and GSE123501. Codifferentially expressed ILs, cytokines, receptors, and transcription factors (TFs) were enriched in 7 crucial Kyoto Encyclopedia of Genes and Genomes pathways and Gene Ontology. We constructed the protein-protein interaction network and predicted the top regulatory miRs involved in the Th2 to Th9 differentiation pathways. We also identified various metabolic, allergic and pulmonary, neuropsychiatric, autoimmune, and infectious diseases as well as carcinomas where the differentiation of Th2 to Th9 may play a crucial role. CONCLUSIONS This study identified hitherto unexplored possible associations between Th9 and disease states. Some important ILs, including CCL1 (chemokine [C-C motif] ligand 1), CCL20 (chemokine [C-C motif] ligand 20), IL-13, IL-4, IL-12A, and IL-9; receptors, including IL-12RB1, IL-4RA (interleukin 9 receptor alpha), CD53 (cluster of differentiation 53), CD6 (cluster of differentiation 6), CD5 (cluster of differentiation 5), CD83 (cluster of differentiation 83), CD197 (cluster of differentiation 197), IL-1RL1 (interleukin 1 receptor-like 1), CD101 (cluster of differentiation 101), CD96 (cluster of differentiation 96), CD72 (cluster of differentiation 72), CD7 (cluster of differentiation 7), CD152 (cytotoxic T lymphocyte-associated protein 4), CD38 (cluster of differentiation 38), CX3CR1 (chemokine [C-X3-C motif] receptor 1), CTLA2A (cytotoxic T lymphocyte-associated protein 2 alpha), CTLA28, and CD196 (cluster of differentiation 196); and TFs, including FOXP3 (forkhead box P3), IRF8 (interferon regulatory factor 8), FOXP2 (forkhead box P2), RORA (RAR-related orphan receptor alpha), AHR (aryl-hydrocarbon receptor), MAF (avian musculoaponeurotic fibrosarcoma oncogene homolog), SMAD6 (SMAD family member 6), JUN (Jun proto-oncogene), JAK2 (Janus kinase 2), EP300 (E1A binding protein p300), ATF6 (activating transcription factor 6), BTAF1 (B-TFIID TATA-box binding protein associated factor 1), BAFT (basic leucine zipper transcription factor), NOTCH1 (neurogenic locus notch homolog protein 1), GATA3 (GATA binding protein 3), SATB1 (special AT-rich sequence binding protein 1), BMP7 (bone morphogenetic protein 7), and PPARG (peroxisome proliferator-activated receptor gamma, were able to identify significant differentially altered genes in the conversion of Th2 to Th9 cells. We identified some common miRs that could target the DEGs. The scarcity of studies on the role of Th9 in metabolic diseases highlights the lacunae in this field. Our study provides the rationale for exploring the role of Th9 in various metabolic disorders such as diabetes mellitus, diabetic nephropathy, hypertensive disease, ischemic stroke, steatohepatitis, liver fibrosis, obesity, adenocarcinoma, glioblastoma and glioma, malignant neoplasm of stomach, melanoma, neuroblastoma, osteosarcoma, pancreatic carcinoma, prostate carcinoma, and stomach carcinoma.
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Affiliation(s)
- Manoj Khokhar
- Department of Biochemistry, All India Institute of Medical Sciences Jodhpur, Jodhpur, India
| | - Purvi Purohit
- Department of Biochemistry, All India Institute of Medical Sciences Jodhpur, Jodhpur, India
| | - Ashita Gadwal
- Department of Biochemistry, All India Institute of Medical Sciences Jodhpur, Jodhpur, India
| | - Sojit Tomo
- Department of Biochemistry, All India Institute of Medical Sciences Jodhpur, Jodhpur, India
| | - Nitin Kumar Bajpai
- Department of Nephrology, All India Institute of Medical Sciences Jodhpur, Jodhpur, India
| | - Ravindra Shukla
- Department of Endocrinology and Metabolism, All India Institute of Medical Sciences Jodhpur, Jodhpur, India
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Li XG, Niu C, Lu P, Wan HW, Jin WD, Wang CX, Mao WY, Zhang ZP, Zhang WF, Li B. Screening and identification of hub-gene associated with brain metastasis in breast cancer. Medicine (Baltimore) 2023; 102:e32771. [PMID: 36800575 PMCID: PMC9935999 DOI: 10.1097/md.0000000000032771] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/19/2023] Open
Abstract
BACKGROUND The presence of breast cancer in the brain, also known as brain metastasis (BMS), is the primary reason for a bad prognosis in cases of breast cancer. Breast cancer is the most prevalent malignant tumor seen in women in developing nations. At present, there is no effective method to inhibit brain metastasis of breast cancer. Therefore, it is necessary to conduct a systematic study on BMS of breast cancer, which will not provide ideas and sites for follow-up studies on the treatment and inhibition of BMS. METHODS In this study, data set GSE43837 was screened from gene expression omnibus database, and then R language tool was used for differential analysis of its expression spectrum, The gene ontology functional enrichment and Kyoto encyclopedia of genes and genomes signal pathway enrichment analyses, as well as the interactive gene retrieval tool for hub-gene analysis, were performed. RESULTS According to the findings, the primary genes linked to breast cancer brain metastases are those that involve interactions between cytokines and their respective receptors and between neuroactive ligands and their respective receptors. The majority of the gene ontology enrichment took place in the extracellular structural tissues, the extracellular matrix tissues, and the second message-mediated signaling. We were able to identify 8 genes that are linked to breast cancer spreading to the brain. The gene score for matrix metallopeptidase1 (MMP-1) was the highest among them, and the genes MMP10, tumor necrosis factor alpha-inducible protein 8, collagen type I alpha 2 chain, vascular cell adhesion molecule 1, and TNF superfamily member 11 were all connected to 1 another in an interaction way. CONCLUSIONS There is a possibility that the 8 key genes that were identified in this research are connected to the progression of BMS in breast cancer. Among them, MMP1 is 1 that has the potential to have a role in the diagnosis and treatment of BMS in breast cancer.
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Affiliation(s)
- Xiao-Gang Li
- Department of General Surgery, Affiliated Hospital of Yunnan University, Kunming, China
| | - Chao Niu
- Department of General Surgery, Affiliated Hospital of Yunnan University, Kunming, China
| | - Ping Lu
- Department of General Surgery, Affiliated Hospital of Yunnan University, Kunming, China
| | - Hong-Wei Wan
- Department of General Surgery, Affiliated Hospital of Yunnan University, Kunming, China
| | - Wen-Di Jin
- Department of General Surgery, Affiliated Hospital of Yunnan University, Kunming, China
| | - Chun-Xiao Wang
- Department of General Surgery, Affiliated Hospital of Yunnan University, Kunming, China
| | - Wen-Yuan Mao
- Department of General Surgery, Affiliated Hospital of Yunnan University, Kunming, China
| | - Zhi-Ping Zhang
- Department of General Surgery, Affiliated Hospital of Yunnan University, Kunming, China
| | - Wan-Fu Zhang
- Department of General Surgery, Affiliated Hospital of Yunnan University, Kunming, China
| | - Bo Li
- Department of General Surgery, Affiliated Hospital of Yunnan University, Kunming, China
- * Correspondence: Bo Li, Department of General Surgery, Affiliated Hospital of Yunnan University, Kunming 650021, China (e-mail: )
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Hermida-Nogueira L, Blanco J, García Á. Secretome Profile of Leukocyte-Platelet-Rich Fibrin (L-PRF) Membranes. Methods Mol Biol 2023; 2628:207-219. [PMID: 36781788 DOI: 10.1007/978-1-0716-2978-9_14] [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] [Indexed: 02/15/2023]
Abstract
In the last years, platelet concentrates such as leukocyte-platelet-rich fibrin (L-PRF) have been used in different clinical scenarios as a huge source of growth factors to enhance wound healing. However, platelet concentrates release many other proteins that also participate in tissue regeneration processes. In this context, the analysis of the L-PRF secretome would provide relevant information on the different proteins and growth factors released by these platelet concentrates, how such secretion varies with the time, and how relevant this could be for the regenerative properties of these products. In the present chapter, we will provide a protocol for isolation, culture, and secretome analysis of L-PRF membranes. Qualitative and quantitative proteomic approaches will be presented, including gel-based and quantitative Sequential Window Acquisition of All Theoretical Mass Spectra (SWATH-MS)-based approaches. This protocol has been recently applied with success to define the L-PRF secretome composition, setting the stage for further research that can provide relevant information on the clinical properties of these platelet concentrates' subtype.
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Affiliation(s)
- Lidia Hermida-Nogueira
- Platelet Proteomics Group, Center for Research in Molecular Medicine and Chronic Diseases (CIMUS), Universidade de Santiago de Compostela, and Instituto de Investigación Sanitaria de Santiago de Compostela (IDIS), Santiago de Compostela, Spain
| | - Juan Blanco
- Periodontology Unit, Medical-Surgical Dentistry Research Group (OMEQUI), Faculty of Medicine and Odontology, Instituto de Investigación Sanitaria de Santiago de Compostela (IDIS), Universidade de Santiago de Compostela, Santiago de Compostela, Spain
| | - Ángel García
- Platelet Proteomics Group, Center for Research in Molecular Medicine and Chronic Diseases (CIMUS), Universidade de Santiago de Compostela, and Instituto de Investigación Sanitaria de Santiago de Compostela (IDIS), Santiago de Compostela, Spain.
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Heidarzadehpilehrood R, Pirhoushiaran M, Binti Osman M, Abdul Hamid H, Ling KH. Weighted Gene Co-Expression Network Analysis (WGCNA) Discovered Novel Long Non-Coding RNAs for Polycystic Ovary Syndrome. Biomedicines 2023; 11:biomedicines11020518. [PMID: 36831054 PMCID: PMC9953234 DOI: 10.3390/biomedicines11020518] [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: 12/27/2022] [Revised: 02/03/2023] [Accepted: 02/06/2023] [Indexed: 02/15/2023] Open
Abstract
Polycystic ovary syndrome (PCOS) affects reproductive-age women. This condition causes infertility, insulin resistance, obesity, and heart difficulties. The molecular basis and mechanism of PCOS might potentially generate effective treatments. Long non-coding RNAs (lncRNAs) show control over multifactorial disorders' growth and incidence. Numerous studies have emphasized its significance and alterations in PCOS. We used bioinformatic methods to find novel dysregulated lncRNAs in PCOS. To achieve this objective, the gene expression profile of GSE48301, comprising PCOS patients and normal control tissue samples, was evaluated using the R limma package with the following cut-off criterion: p-value < 0.05. Firstly, weighted gene co-expression network analysis (WGCNA) was used to determine the co-expression genes of lncRNAs; subsequently, hub gene identification and pathway enrichment analysis were used. With the defined criteria, nine novel dysregulated lncRNAs were identified. In WGCNA, different colors represent different modules. In the current study, WGCNA resulted in turquoise, gray, blue, and black co-expression modules with dysregulated lncRNAs. The pathway enrichment analysis of these co-expressed modules revealed enrichment in PCOS-associated pathways, including gene expression, signal transduction, metabolism, and apoptosis. In addition, CCT7, EFTUD2, ESR1, JUN, NDUFAB1, CTTNB1, GRB2, and CTNNB1 were identified as hub genes, and some of them have been investigated in PCOS. This study uncovered nine novel PCOS-related lncRNAs. To confirm how these lncRNAs control translational modification in PCOS, functional studies are required.
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Affiliation(s)
- Roozbeh Heidarzadehpilehrood
- Department of Obstetrics & Gynaecology, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, Serdang 43400, Malaysia
| | - Maryam Pirhoushiaran
- Department of Medical Genetics, School of Medicine, Tehran University of Medical Sciences, Tehran 1417613151, Iran
| | - Malina Binti Osman
- Department of Medical Microbiology, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, Serdang 43400, Malaysia
| | - Habibah Abdul Hamid
- Department of Obstetrics & Gynaecology, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, Serdang 43400, Malaysia
- Correspondence: (H.A.H.); (K.-H.L.)
| | - King-Hwa Ling
- Department of Biomedical Science, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, Serdang 43400, Malaysia
- Correspondence: (H.A.H.); (K.-H.L.)
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Raffo-Romero A, Aboulouard S, Bouchaert E, Rybicka A, Tierny D, Hajjaji N, Fournier I, Salzet M, Duhamel M. Establishment and characterization of canine mammary tumoroids for translational research. BMC Biol 2023; 21:23. [PMID: 36737789 PMCID: PMC9898911 DOI: 10.1186/s12915-023-01516-2] [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: 02/22/2022] [Accepted: 01/17/2023] [Indexed: 02/05/2023] Open
Abstract
BACKGROUND Cancer heterogeneity is a main obstacle for the development of effective therapies, as its replication in in vitro preclinical models is challenging. Around 96% of developed drugs are estimated to fail from discovery to the clinical trial phase probably because of the unsuitability and unreliability of current preclinical models (Front Pharmacol 9:6, 2018; Nat Rev Cancer 8: 147-56, 2008) in replicating the overall biology of tumors, for instance the tumor microenvironment. Breast cancer is the most frequent cancer among women causing the greatest number of cancer-related deaths. Breast cancer can typically be modeled in vitro through the use of tumoroids; however, current approaches using mouse tumoroids fail to reproduce crucial aspect of human breast cancer, while access to human cells is limited and the focus of ethical concerns. New models of breast cancer, such as companion dogs, have emerged given the resemblance of developed spontaneous mammary tumors to human breast cancer in many clinical and molecular aspects; however, they have so far failed to replicate the tumor microenvironment. The present work aimed at developing a robust canine mammary tumor model in the form of tumoroids which recapitulate the tumor diversity and heterogeneity. RESULTS We conducted a complete characterization of canine mammary tumoroids through histologic, molecular, and proteomic analysis, demonstrating their strong similarity to the primary tumor. We demonstrated that these tumoroids can be used as a drug screening model. In fact, we showed that paclitaxel, a human chemotherapeutic, could kill canine tumoroids with the same efficacy as human tumoroids with 0.1 to 1 μM of drug needed to kill 50% of the cells. Due to easy tissue availability, canine tumoroids can be produced at larger scale and cryopreserved to constitute a biobank. We have demonstrated that cryopreserved tumoroids keep the same histologic and molecular features (ER, PR, and HER2 expression) as fresh tumoroids. Furthermore, two cryopreservation techniques were compared from a proteomic point of view which showed that tumoroids made from frozen material allowed to maintain the same molecular diversity as from freshly dissociated tumor. CONCLUSIONS These findings revealed that canine mammary tumoroids can be easily generated and may provide an adequate and more reliable preclinical model to investigate tumorigenesis mechanisms and develop new treatments for both veterinary and human medicine.
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Affiliation(s)
- Antonella Raffo-Romero
- grid.410463.40000 0004 0471 8845Université Lille, Inserm, CHU Lille, U1192, Laboratoire Protéomique, Réponse Inflammatoire Et Spectrométrie de Masse (PRISM), Lille, France
| | - Soulaimane Aboulouard
- grid.410463.40000 0004 0471 8845Université Lille, Inserm, CHU Lille, U1192, Laboratoire Protéomique, Réponse Inflammatoire Et Spectrométrie de Masse (PRISM), Lille, France
| | - Emmanuel Bouchaert
- grid.410463.40000 0004 0471 8845Université Lille, Inserm, CHU Lille, U1192, Laboratoire Protéomique, Réponse Inflammatoire Et Spectrométrie de Masse (PRISM), Lille, France ,grid.487385.50000 0004 1789 0046OCR (Oncovet Clinical Research), Parc Eurasanté Lille Métropole, 80 Rue du Dr Yersin, 59120 Loos, France
| | - Agata Rybicka
- grid.410463.40000 0004 0471 8845Université Lille, Inserm, CHU Lille, U1192, Laboratoire Protéomique, Réponse Inflammatoire Et Spectrométrie de Masse (PRISM), Lille, France ,grid.487385.50000 0004 1789 0046OCR (Oncovet Clinical Research), Parc Eurasanté Lille Métropole, 80 Rue du Dr Yersin, 59120 Loos, France
| | - Dominique Tierny
- grid.410463.40000 0004 0471 8845Université Lille, Inserm, CHU Lille, U1192, Laboratoire Protéomique, Réponse Inflammatoire Et Spectrométrie de Masse (PRISM), Lille, France ,grid.487385.50000 0004 1789 0046OCR (Oncovet Clinical Research), Parc Eurasanté Lille Métropole, 80 Rue du Dr Yersin, 59120 Loos, France
| | - Nawale Hajjaji
- grid.410463.40000 0004 0471 8845Université Lille, Inserm, CHU Lille, U1192, Laboratoire Protéomique, Réponse Inflammatoire Et Spectrométrie de Masse (PRISM), Lille, France ,grid.452351.40000 0001 0131 6312Breast Cancer Unit, Oscar Lambret Center, Lille, France
| | - Isabelle Fournier
- grid.410463.40000 0004 0471 8845Université Lille, Inserm, CHU Lille, U1192, Laboratoire Protéomique, Réponse Inflammatoire Et Spectrométrie de Masse (PRISM), Lille, France ,grid.440891.00000 0001 1931 4817Institut Universitaire de France, Paris, France
| | - Michel Salzet
- Université Lille, Inserm, CHU Lille, U1192, Laboratoire Protéomique, Réponse Inflammatoire Et Spectrométrie de Masse (PRISM), Lille, France. .,Institut Universitaire de France, Paris, France.
| | - Marie Duhamel
- Université Lille, Inserm, CHU Lille, U1192, Laboratoire Protéomique, Réponse Inflammatoire Et Spectrométrie de Masse (PRISM), Lille, France.
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Nithya C, Kiran M, Nagarajaram HA. Dissection of hubs and bottlenecks in a protein-protein interaction network. Comput Biol Chem 2023; 102:107802. [PMID: 36603332 DOI: 10.1016/j.compbiolchem.2022.107802] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Revised: 11/20/2022] [Accepted: 12/08/2022] [Indexed: 12/23/2022]
Abstract
Analysis of degree centrality in conjunction with betweenness centrality of proteins in a human protein-protein interaction network revealed three categories of centrally important proteins: a) proteins with high degree and betweenness (hub-bottlenecks denoted as MX), b) proteins with high betweenness and low degree (non-hub-bottlenecks/pure bottlenecks denoted as PB) and c) proteins with high degree and low betweenness (hub-non-bottlenecks/pure hubs denoted as PH). When subjected to a detailed statistical analysis of their molecular-level properties, the proteins belonging to each of these categories were found to be associated with distinct canonical molecular properties, i.e., "molecular markers". The MX proteins are a) conformationally versatile, mainly comprising of essential proteins, b) the targets for interactions by the proteins of viral and bacterial pathogens, c) evolutionally constrained, involved in multiple pathways, enriched with disease genes and d) involved in the functions such as protein stabilization, phosphorylation, and mRNA slicing processes. PB proteins are a) enriched with extracellular and cancer-related proteins, b) enriched with the approved drug targets and c) involved in cell-cell signaling processes. Finally, PH are a) structurally versatile, b) enriched with essential proteins primarily involved in housekeeping processes (transcription and replication). The fact that the proteins belonging to these three categories form three distinct sets in terms of their molecular properties reveals the existence of trichotomy among hubs and bottlenecks, and this knowledge is of paramount importance while prioritizing protein targets for further studies such as drug design and disease association studies based on their network centrality values.
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Affiliation(s)
- Chandramohan Nithya
- Department of Biotechnology and Bioinformatics, School of Life Sciences, University of Hyderabad, Hyderabad, Telangana 500046, India
| | - Manjari Kiran
- Department of Systems and Computational Biology, School of Life Sciences, University of Hyderabad, Hyderabad, Telangana 500046, India
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Qiu L, Sheng P, Wang X. Identification of Metabolic Syndrome-Related miRNA-mRNA Regulatory Networks and Key Genes Based on Bioinformatics Analysis. Biochem Genet 2023; 61:428-447. [PMID: 35877019 DOI: 10.1007/s10528-022-10257-w] [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: 11/18/2021] [Accepted: 05/18/2022] [Indexed: 01/24/2023]
Abstract
Metabolic syndrome, which affects approximately one-quarter of the world's population, is a combination of multiple traits and is associated with high all-cause mortality, increased cancer risk, and other hazards. It has been shown that the epigenetic functions of miRNAs are closely related to metabolic syndrome, but epigenetic studies have not yet fully elucidated the regulatory network and key genes associated with metabolic syndrome. To perform data analysis and screening of potential differentially expressed target miRNAs, mRNAs and genes based on a bioinformatics approach using a metabolic syndrome mRNA and miRNA gene microarray, leading to further analysis and identification of metabolic syndrome-related miRNA-mRNA regulatory networks and key genes. The miRNA gene set (GSE98896) and mRNA gene set (GSE98895) of peripheral blood samples from patients with metabolic syndrome from the GEO database were screened, and set|logFC|> 1 and adjusted P < 0.05 were used to identify the differentially expressed miRNAs and mRNAs. Differentially expressed miRNA transcription factors were predicted using FunRich software and subjected to GO and KEGG enrichment analysis. Next, biological process enrichment analysis of differentially expressed mRNAs was performed with Metascape. Differentially expressed miRNAs and mRNAs were identified and visualized as miRNA-mRNA regulatory networks based on the complementary pairing principle. Data analysis of genome-wide metabolic syndrome-related mRNAs was performed using the gene set enrichment analysis (GSEA) database. Finally, further WGCNA of the set of genes most closely associated with metabolic syndrome was performed to validate the findings. A total of 217 differentially expressed mRNAs and 158 differentially expressed miRNAs were identified by screening the metabolic syndrome miRNA and mRNA gene sets, and these molecules mainly included transcription factors, such as SP1, SP4, and EGR1, that function in the IL-17 signalling pathway; cytokine-cytokine receptor interaction; proteoglycan syndecan-mediated signalling events; and the glypican pathway, which is involved in the inflammatory response and glucose and lipid metabolism. miR-34C-5P, which was identified by constructing a miRNA-mRNA regulatory network, could regulate DPYSL4 expression to influence insulin β-cells, the inflammatory response and glucose oxidative catabolism. Based on GSEA, metabolic syndrome is known to be closely related to oxidative phosphorylation, DNA repair, neuronal damage, and glycolysis. Finally, RStudio and DAVID were used to perform WGCNA of the gene sets most closely associated with metabolic syndrome, and the results further validated the conclusions. Metabolic syndrome is a common metabolic disease worldwide, and its mechanism of action is closely related to the inflammatory response, glycolipid metabolism, and impaired mitochondrial function. miR-34C-5P can regulate DPYSL4 expression and can be a potential research target. In addition, UQCRQ and NDUFA8 are core genes of oxidative phosphorylation and have also been identified as potential targets for the future treatment of metabolic syndrome.
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Affiliation(s)
- Lingyan Qiu
- The First Clinical Medical College, Nanjing University of Chinese Medicine, Nanjing, 210029, China.,The Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing, 210029, China
| | - Pei Sheng
- The First Clinical Medical College, Nanjing University of Chinese Medicine, Nanjing, 210029, China.,The Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing, 210029, China
| | - Xu Wang
- The First Clinical Medical College, Nanjing University of Chinese Medicine, Nanjing, 210029, China. .,The Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing, 210029, China.
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129
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Sookoian S, Pirola CJ. Genetics in non-alcoholic fatty liver disease: The role of risk alleles through the lens of immune response. Clin Mol Hepatol 2023; 29:S184-S195. [PMID: 36472053 PMCID: PMC10029961 DOI: 10.3350/cmh.2022.0318] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Accepted: 11/30/2022] [Indexed: 12/12/2022] Open
Abstract
The knowledge on the genetic component of non-alcoholic fatty liver disease (NAFLD) has grown exponentially over the last 10 to 15 years. This review summarizes the current evidence and the latest developments in the genetics of NAFLD and non-alcoholic steatohepatitis (NASH) from the immune system's perspective. Activation of innate and or adaptive immune response is an essential driver of NAFLD disease severity and progression. Lipid and immune pathways are crucial in the pathophysiology of NAFLD and NASH. Here, we highlight novel applications of genomic techniques, including single-cell sequencing and the genetics of gene expression, to elucidate the potential involvement of NAFLD/NASH-risk alleles in modulating immune system cells. Together, our focus is to provide an overview of the potential involvement of the NAFLD/NASH-related risk variants in mediating the immune-driven liver disease severity and diverse systemic pleiotropic effects.
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Affiliation(s)
- Silvia Sookoian
- Clinical and Molecular Hepatology. Centro de Altos Estudios en Ciencias Humanas y de la Salud (CAECIHS), Universidad Abierta Interamericana, Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - Carlos J Pirola
- Systems Biology of Complex Diseases, Centro de Altos Estudios en Ciencias Humanas y de la Salud (CAECIHS), Universidad Abierta Interamericana, Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
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130
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Guttapadu R, Katte T, Sayeeram D, Bhatia S, Abraham AR, Rajeev K, Amara ARR, Siri S, Bommana K, Rasalkar AA, Malempati R, Mustak MS, Narayanan P, Reddy SDN. Identification of novel biomarkers for lung squamous cell carcinoma. 3 Biotech 2023; 13:72. [PMID: 36742449 PMCID: PMC9895444 DOI: 10.1007/s13205-023-03489-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2022] [Accepted: 01/19/2023] [Indexed: 02/05/2023] Open
Abstract
Lung squamous cell carcinoma (LUSC) is the second most common subtype of lung cancer, accounting for a majority of lung cancer-related deaths. Detection or diagnosis of cancer at an early stage is an unmet clinical need that is being actively explored. In this study, we aimed to identify potential biomarkers for LUSC, by screening expression status of all human genes against LUSC patient samples available with The Cancer Genome Atlas (TCGA). This led to the identification of several genes that are upregulated in LUSC. Further analysis revealed that many of these genes also show higher expression at the protein level not only in lung cancer but also in other cancers. Additionally, some of these genes show stage-dependent higher expression and are associated with statistically significant poor survival of LUSC patients. As per our results, more than 60 genes are overexpressed in LUSC at the level of mRNA and some at the protein level. Thus, we identified genes such as MCC1, MRPL47, CRYGS, HSP40, DNAJC19, GMPS and PARL as novel potential biomarkers for LUSC in this study. We believe that these genes hold great potential as LUSC biomarkers for early detection as the data are derived from patient samples. Supplementary Information The online version contains supplementary material available at 10.1007/s13205-023-03489-z.
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Affiliation(s)
- Ranjitha Guttapadu
- Department of Biotechnology, BMS College of Engineering, Bull Temple Road, Basavanagudi, Bengaluru, 560019 India
| | - Teesta Katte
- Department of Biotechnology, BMS College of Engineering, Bull Temple Road, Basavanagudi, Bengaluru, 560019 India
| | - Deepak Sayeeram
- Department of Biotechnology, BMS College of Engineering, Bull Temple Road, Basavanagudi, Bengaluru, 560019 India
| | - Saloni Bhatia
- Department of Biotechnology, BMS College of Engineering, Bull Temple Road, Basavanagudi, Bengaluru, 560019 India
| | - Anika Rachel Abraham
- Department of Biotechnology, BMS College of Engineering, Bull Temple Road, Basavanagudi, Bengaluru, 560019 India
| | - Kiran Rajeev
- Department of Biotechnology, BMS College of Engineering, Bull Temple Road, Basavanagudi, Bengaluru, 560019 India
| | - Anish Raju R. Amara
- Department of Biotechnology, BMS College of Engineering, Bull Temple Road, Basavanagudi, Bengaluru, 560019 India
| | - Sharadhi Siri
- Department of Biotechnology, BMS College of Engineering, Bull Temple Road, Basavanagudi, Bengaluru, 560019 India
| | - Kavitha Bommana
- Department of Botany, Rayalaseema University, Kurnool, India
| | - Avinash Arvind Rasalkar
- in-DNA Life Science Pvt LtD, Plot, No. 368, Infocity Ave, Infocity, Sishu Vihar, Patia, Bhubaneswar, Odisha 751024 India
| | - Rajyalakshmi Malempati
- Department of Biotechnology, BMS College of Engineering, Bull Temple Road, Basavanagudi, Bengaluru, 560019 India
| | - Mohammed S. Mustak
- Department of Applied Zoology, Mangalore University, Mangalagangothri, Mangalore, 574199 India
| | - Prathibha Narayanan
- Department of Biotechnology, BMS College of Engineering, Bull Temple Road, Basavanagudi, Bengaluru, 560019 India
| | - S. Divijendra Natha Reddy
- Department of Biotechnology, BMS College of Engineering, Bull Temple Road, Basavanagudi, Bengaluru, 560019 India
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131
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Xu J, Wang Y, Jiang J, Yin C, Shi B. ADAM12 promotes clear cell renal cell carcinoma progression and triggers EMT via EGFR/ERK signaling pathway. J Transl Med 2023; 21:56. [PMID: 36717944 PMCID: PMC9885678 DOI: 10.1186/s12967-023-03913-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Accepted: 01/22/2023] [Indexed: 01/31/2023] Open
Abstract
BACKGROUND Clear cell renal cell carcinoma (ccRCC) is a major worldwide health problem due to its high prevalence and mortality rate. A disintegrin and metalloproteinase 12 (ADAM12) is aberrantly expressed in various cancers and plays an important role in tumor progression. However, its explicit effect and molecular mechanism in ccRCC remain unclear. METHODS We investigated the dysregulation of ADAM12 in ccRCC through public databases and bioinformatics analyses. The expression of ADAM12 was further verified in ccRCC tissues by RT-qPCR and immunohistochemistry (IHC). The relationship between ADAM12 expression and clinicopathological characteristics was analyzed statistically. The effects of ADAM12 on the proliferation, migration and invasion of ccRCC cells were examined by in vitro and in vivo experiments. RESULTS ADAM12 was significantly upregulated in ccRCC tissues and associated with poor prognosis in ccRCC patients. ADAM12 promoted ccRCC cell proliferation, migration and invasion in vitro and the growth of subcutaneous tumors in vivo. Knockdown of ADAM12 successfully suppressed its oncogenic function. Mechanistically, its overexpression induced epithelial-mesenchymal transition (EMT) by downregulating E-cadherin and upregulating N-cadherin and Snail. Moreover, ADAM12 participated in the epidermal growth factor receptor (EGFR) pathway and activated the downstream signal ERK1/2 by shedding the EGFR ligand, thereby upregulating target genes including c-Myc, enhancing cell survival and invasion ability, and promoting tumor progression, metastasis and the induction of EMT. CONCLUSIONS High expression of ADAM12 induced EMT and promoted cell proliferation, migration, and invasion by activating the EGFR/ERK signaling pathway in ccRCC.
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Affiliation(s)
- Jinming Xu
- Department of Urology, Shenzhen Second People's Hospital/First Affiliated Hospital of Shenzhen University, Shenzhen, 518035, Guangdong, China
- Shantou University Medical College, Shantou, 515041, Guangdong, China
| | - Yan Wang
- Department of Urology, Peking University Shenzhen Hospital, Shenzhen, 518036, Guangdong, China
| | - Jiahao Jiang
- Department of Urology, Shenzhen Second People's Hospital/First Affiliated Hospital of Shenzhen University, Shenzhen, 518035, Guangdong, China
| | - Cong Yin
- Department of Urology, Shenzhen Second People's Hospital/First Affiliated Hospital of Shenzhen University, Shenzhen, 518035, Guangdong, China
| | - Bentao Shi
- Department of Urology, Shenzhen Second People's Hospital/First Affiliated Hospital of Shenzhen University, Shenzhen, 518035, Guangdong, China.
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132
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Identification of Adipogenesis Subgroups and Immune Infiltration Characteristics in Diabetic Peripheral Neuropathy. J Immunol Res 2023; 2023:3673094. [PMID: 36741233 PMCID: PMC9893521 DOI: 10.1155/2023/3673094] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2022] [Revised: 12/19/2022] [Accepted: 12/26/2022] [Indexed: 01/20/2023] Open
Abstract
Dysregulation of adipogenesis is related to diabetic peripheral neuropathy (DPN) pathogenesis, which may be mediated by immune infiltration. Nevertheless, the expression patterns of multiple adipogenesis-related genes and the differences of immune infiltration in different lipid metabolism levels remain unknown. GSE95849, a gene expression matrix containing DPN patients and healthy participants, was downloaded from Gene Expression Omnibus (GEO) database. Differentially expressed adipogenesis-related genes (DEARGs) were screened by overlapping the adipogenesis-related genes with differentially expressed genes (DEGs). DPN patients from GSE24290 and GSE148059 were divided into two adipogenesis subgroups according to the expression of DEARGs. The single-sample gene set enrichment analysis (ssGSEA) was used to estimate the abundance of the immune cells between two subgroups. The analysis of immune infiltration suggested that a variety of immune cells and immune processes were elevated in the high expression group of DEARGs. The differentially expressed genes of the two subgroups were mainly enriched in biological processes and signaling pathways related to lipid metabolism. PPARG, FABP4, LIPE, FASN, SCD, DGAT2, PNPLA2, ADIPOQ, LEP, and CEBPA were identified as the hub genes of the two subgroups, whose related transcription factors (TFs) and miRNAs were predicted. An immunohistochemical assay was used to verify the expression of hub genes in DPN nerve tissues. Our comprehensive analysis of adipogenesis subgroups in DPN illustrated that different expression patterns of DEARGs may lead to different immune and inflammatory states. The identification of DEARGs may help to further distinguish the different characteristics of DPN patients and lay the foundation for targeted treatment. Our findings may bring a novel perspective to the diagnosis and treatment of DPN patients.
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133
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Li H, Hu X, Li J, Jiang W, Wang L, Tan X. Identification of key regulatory genes and their working mechanisms in type 1 diabetes. BMC Med Genomics 2023; 16:8. [PMID: 36650594 PMCID: PMC9843847 DOI: 10.1186/s12920-023-01432-y] [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: 07/04/2022] [Accepted: 01/04/2023] [Indexed: 01/18/2023] Open
Abstract
BACKGROUND Type 1 diabetes (T1D) is an autoimmune disease characterized by the destruction of beta cells in pancreatic islets. Identification of the key genes involved in T1D progression and their mechanisms of action may contribute to a better understanding of T1D. METHODS The microarray profile of T1D-related gene expression was searched using the Gene Expression Omnibus (GEO) database. Then, the expression data of two messenger RNAs (mRNAs) were integrated for Weighted Gene Co-Expression Network Analysis (WGCNA) to generate candidate genes related to T1D. In parallel, T1D microRNA (miRNA) data were analyzed to screen for possible regulatory miRNAs and their target genes. An miRNA-mRNA regulatory network was then established to predict the key regulatory genes and their mechanisms. RESULTS A total of 24 modules (i.e., clusters/communities) were selected using WGCNA analysis, in which three modules were significantly associated with T1D. Further correlation analysis of the gene module revealed 926 differentially expressed genes (DEGs), of which 327 genes were correlated with T1D. Analysis of the miRNA microarray showed that 13 miRNAs had significant expression differences in T1D. An miRNA-mRNA network was established based on the prediction of miRNA target genes and the combined analysis of mRNA, in which the target genes of two miRNAs were found in T1D correlated genes. CONCLUSION An miRNA-mRNA network for T1D was established, based on which 2 miRNAs and 12 mRNAs were screened, suggesting that they may play key regulatory roles in the initiation and development of T1D.
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Affiliation(s)
- Hui Li
- grid.508008.50000 0004 4910 8370Pediatric Department, The First Hospital of Changsha, No. 311, Yingpan Road, Kaifu District, Changsha, 410000 Hunan People’s Republic of China
| | - Xiao Hu
- grid.508008.50000 0004 4910 8370Pediatric Department, The First Hospital of Changsha, No. 311, Yingpan Road, Kaifu District, Changsha, 410000 Hunan People’s Republic of China
| | - Jieqiong Li
- grid.508008.50000 0004 4910 8370Pediatric Department, The First Hospital of Changsha, No. 311, Yingpan Road, Kaifu District, Changsha, 410000 Hunan People’s Republic of China
| | - Wen Jiang
- grid.508008.50000 0004 4910 8370Pediatric Department, The First Hospital of Changsha, No. 311, Yingpan Road, Kaifu District, Changsha, 410000 Hunan People’s Republic of China
| | - Li Wang
- grid.508008.50000 0004 4910 8370Pediatric Department, The First Hospital of Changsha, No. 311, Yingpan Road, Kaifu District, Changsha, 410000 Hunan People’s Republic of China
| | - Xin Tan
- grid.508008.50000 0004 4910 8370Pediatric Department, The First Hospital of Changsha, No. 311, Yingpan Road, Kaifu District, Changsha, 410000 Hunan People’s Republic of China
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Multiomics Study of a Novel Naturally Derived Small Molecule, NSC772864, as a Potential Inhibitor of Proto-Oncogenes Regulating Cell Cycle Progression in Colorectal Cancer. Cells 2023; 12:cells12020340. [PMID: 36672275 PMCID: PMC9856482 DOI: 10.3390/cells12020340] [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: 11/17/2022] [Revised: 12/24/2022] [Accepted: 01/04/2023] [Indexed: 01/18/2023] Open
Abstract
Colorectal cancer (CRC) is one of the most prevalent malignant tumors, and it contributes to high numbers of deaths globally. Although advances in understanding CRC molecular mechanisms have shed significant light on its pathogenicity, current treatment options, including combined chemotherapy and molecular-targeted agents, are still limited due to resistance, with almost 25% of patients developing distant metastasis. Therefore, identifying novel biomarkers for early diagnosis is crucial, as they will also influence strategies for new targeted therapies. The proto-oncogene, c-Met, a tyrosine kinase that promotes cell proliferation, motility, and invasion; c-MYC, a transcription factor associated with the modulation of the cell cycle, proliferation, apoptosis; and cyclin D1 (CCND1), an essential regulatory protein in the cell cycle, all play crucial roles in cancer progression. In the present study, we explored computational simulations through bioinformatics analysis and identified the overexpression of c-Met/GSK3β/MYC/CCND1 oncogenic signatures that were associated with cancer progression, drug resistance, metastasis, and poor clinical outcomes in CRC. We further demonstrated the anticancer activities of our newly synthesized quinoline-derived compound, NSC772864, against panels of the National Cancer Institute's human CRC cell lines. The compound exhibited cytotoxic activities against various CRC cell lines. Using target prediction tools, we found that c-Met/GSK3β/MYC/CCND1 were target genes for the NSC772864 compound. Subsequently, we performed in silico molecular docking to investigate protein-ligand interactions and discovered that NSC772864 exhibited higher binding affinities with these oncogenes compared to FDA-approved drugs. These findings strongly suggest that NSC772864 is a novel and potential antiCRC agent.
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Lazewski D, Kucinska M, Potapskiy E, Kuzminska J, Popenda L, Tezyk A, Goslinski T, Wierzchowski M, Murias M. Enhanced Cytotoxic Activity of PEGylated Curcumin Derivatives: Synthesis, Structure-Activity Evaluation, and Biological Activity. Int J Mol Sci 2023; 24:ijms24021467. [PMID: 36674983 PMCID: PMC9867315 DOI: 10.3390/ijms24021467] [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: 11/09/2022] [Revised: 12/25/2022] [Accepted: 01/06/2023] [Indexed: 01/14/2023] Open
Abstract
Curcumin has been modified in various ways to broaden its application in medicine and address its limitations. In this study, we present a series of curcumin-based derivatives obtained by replacing the hydroxy groups in the feruloyl moiety with polyethylene glycol (PEG) chains and the addition of the BF2 moiety to the carbonyl groups. Tested compounds were screened for their cytotoxic activity toward two bladder cancer cell lines, 5637 and SCaBER, and a noncancerous cell line derived from lung fibroblasts (MRC-5). Cell viability was analyzed under normoxic and hypoxic conditions (1% oxygen). Structure-activity relationships (SARs) are discussed, and curcumin derivatives equipped within feruloyl moieties with 3-methoxy and 4-{2-[2-(2-methoxyethoxy)ethoxy]ethoxy} substituents (5) were selected for further analysis. Compound 5 did not affect the viability of MRC-5 cells and exerted a stronger cytotoxic effect under hypoxic conditions. However, the flow cytometry studies showed that PEGylation did not improve cellular uptake. Another observation was that the lack of serum proteins limits the intracellular uptake of curcumin derivative 5. The preliminary mechanism of action studies indicated that compound 5 under hypoxic conditions induced G2/M arrest in a dose-dependent manner and increased the expression of stress-related proteins such as p21/CIP1, phosphorylated HSP27, ADAMTS-1, and phosphorylated JNK. In summary, the results of the studies indicated that PEGylated curcumin is a more potent compound against bladder cancer cell lines than the parent compound, and derivative 5 is worthy of further investigation to clarify its mechanism of anticancer action under hypoxic conditions.
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Affiliation(s)
- Dawid Lazewski
- Department of Chemical Technology of Drugs, Poznan University of Medical Sciences, Grunwaldzka 6 Street, 60-780 Poznan, Poland
| | - Malgorzata Kucinska
- Department of Toxicology, Poznan University of Medical Sciences, Dojazd 30 Street, 60-631 Poznan, Poland
| | - Edward Potapskiy
- Department of Chemical Technology of Drugs, Poznan University of Medical Sciences, Grunwaldzka 6 Street, 60-780 Poznan, Poland
| | - Joanna Kuzminska
- Department of Pharmaceutical Chemistry, Poznan University of Medical Sciences, Grunwaldzka 6 Street, 60-780 Poznan, Poland
| | - Lukasz Popenda
- NanoBioMedical Centre, Adam Mickiewicz University, Wszechnicy Piastowskiej 3 Street, 61-614 Poznan, Poland
| | - Artur Tezyk
- Department of Forensic Medicine, Poznan University of Medical Sciences, Rokietnicka 10 Street, 60-806 Poznan, Poland
| | - Tomasz Goslinski
- Department of Chemical Technology of Drugs, Poznan University of Medical Sciences, Grunwaldzka 6 Street, 60-780 Poznan, Poland
| | - Marcin Wierzchowski
- Department of Chemical Technology of Drugs, Poznan University of Medical Sciences, Grunwaldzka 6 Street, 60-780 Poznan, Poland
| | - Marek Murias
- Department of Toxicology, Poznan University of Medical Sciences, Dojazd 30 Street, 60-631 Poznan, Poland
- Center for Advanced Technology, Adam Mickiewicz University, Uniwersytetu Poznanskiego 10 Street, 61-614 Poznan, Poland
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Mokgautsi N, Kuo YC, Huang YJ, Chen CH, Mukhopadhyay D, Wu ATH, Huang HS. Preclinical Evaluation of a Novel Small Molecule LCC-21 to Suppress Colorectal Cancer Malignancy by Inhibiting Angiogenic and Metastatic Signatures. Cells 2023; 12:cells12020266. [PMID: 36672201 PMCID: PMC9856425 DOI: 10.3390/cells12020266] [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: 11/04/2022] [Revised: 12/06/2022] [Accepted: 01/04/2023] [Indexed: 01/12/2023] Open
Abstract
Colorectal cancer (CRC) is one of the most common cancers, and it frequently metastasizes to the liver and lymph nodes. Despite major advances in treatment modalities, CRC remains a poorly characterized biological malignancy, with high reported cases of deaths globally. Moreover, cancer stem cells (CSCs) and their microenvironment have been widely shown to promote colon cancer development, progression, and metastasis. Therefore, an understanding of the underlying mechanisms that contribute to the maintenance of CSCs and their markers in CRC is crucial in efforts to treat cancer metastasis and develop specific therapeutic targets for augmenting current standard treatments. Herein, we applied computational simulations using bioinformatics to identify potential theranostic markers for CRC. We identified the overexpression of vascular endothelial growth factor-α (VEGFA)/β-catenin/matrix metalloproteinase (MMP)-7/Cluster of Differentiation 44 (CD44) in CRC to be associated with cancer progression, stemness, resistance to therapy, metastasis, and poor clinical outcomes. To further investigate, we explored in silico molecular docking, which revealed potential inhibitory activities of LCC-21 as a potential multitarget small molecule for VEGF-A/CTNNB1/MMP7/CD44 oncogenic signatures, with the highest binding affinities displayed. We validated these finding in vitro and demonstrated that LCC-21 inhibited colony and sphere formation, migration, and invasion, and these results were further confirmed by a Western blot analysis in HCT116 and DLD-1 cells. Thus, the inhibitory effects of LCC-21 on these angiogenic and onco-immunogenic signatures could be of translational relevance as potential CRC biomarkers for early diagnosis.
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Affiliation(s)
- Ntlotlang Mokgautsi
- Ph.D. Program for Cancer Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical University and Academia Sinica, Taipei 11031, Taiwan
- Graduate Institute for Cancer Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical University, Taipei 11031, Taiwan
| | - Yu-Cheng Kuo
- Department of Pharmacology, School of Medicine, College of Medicine, Taipei Medical University, Taipei 11031, Taiwan
- School of Post-Baccalaureate Chinese Medicine, College of Chinese Medicine, China Medical University, Taichung 40402, Taiwan
| | - Yan-Jiun Huang
- Division of Colorectal Surgery, Department of Surgery, Taipei Medical University Hospital, Taipei Medical University, Taipei 11031, Taiwan
- Department of Surgery, College of Medicine, Taipei Medical University, Taipei 11031, Taiwan
- School of Medicine, College of Medicine, Taipei Medical University, Taipei 11031, Taiwan
| | - Chien-Hsin Chen
- Division of Colorectal Surgery, Department of Surgery, WanFang Hospital, Taipei Medical University, No. 111 Sec. 3 Xinglong Rd., Wenshan Dist., Taipei 11031, Taiwan
| | | | - Alexander T. H. Wu
- TMU Research Center of Cancer Translational Medicine, Taipei Medical University, Taipei 11031, Taiwan
- The Ph.D. Program of Translational Medicine, College of Medical Science and Technology, Taipei Medical University, Taipei 11031, Taiwan
- Clinical Research Center, Taipei Medical University Hospital, Taipei Medical University, Taipei 11031, Taiwan
- Graduate Institute of Medical Sciences, National Defense Medical Center, Taipei 11031, Taiwan
- Correspondence: (A.T.H.W.); (H.-S.H.); Tel.: +886-2-2697-2035 (ext. 112) (A.T.H.W.); +886-2-6638-2736 (ext. 1377) (H.-S.H.)
| | - Hsu-Shan Huang
- Ph.D. Program for Cancer Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical University and Academia Sinica, Taipei 11031, Taiwan
- Graduate Institute for Cancer Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical University, Taipei 11031, Taiwan
- School of Pharmacy, National Defense Medical Center, Taipei 11031, Taiwan
- Ph.D. Program in Biotechnology Research and Development, College of Pharmacy, Taipei Medical University, Taipei 11031, Taiwan
- Correspondence: (A.T.H.W.); (H.-S.H.); Tel.: +886-2-2697-2035 (ext. 112) (A.T.H.W.); +886-2-6638-2736 (ext. 1377) (H.-S.H.)
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137
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Heil BJ, Greene CS. The Field-Dependent Nature of PageRank Values in Citation Networks. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.05.522943. [PMID: 36711900 PMCID: PMC9881996 DOI: 10.1101/2023.01.05.522943] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 10/21/2023]
Abstract
The value of scientific research can be easier to assess at the collective level than at the level of individual contributions. Several journal-level and article-level metrics aim to measure the importance of journals or individual manuscripts. However, many are citation-based and citation practices vary between fields. To account for these differences, scientists have devised normalization schemes to make metrics more comparable across fields. We use PageRank as an example metric and examine the extent to which field-specific citation norms drive estimated importance differences. In doing so, we recapitulate differences in journal and article PageRanks between fields. We also find that manuscripts shared between fields have different PageRanks depending on which field's citation network the metric is calculated in. We implement a degree-preserving graph shuffling algorithm to generate a null distribution of similar networks and find differences more likely attributed to field-specific preferences than citation norms. Our results suggest that while differences exist between fields' metric distributions, applying metrics in a field-aware manner rather than using normalized global metrics avoids losing important information about article preferences. They also imply that assigning a single importance value to a manuscript may not be a useful construct, as the importance of each manuscript varies by the reader's field.
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Affiliation(s)
- Benjamin J. Heil
- Genomics and Computational Biology Graduate Group, Perelman School of Medicine, University of Pennsylvania
| | - Casey S. Greene
- Department of Pharmacology, University of Colorado School of Medicine; Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine
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Yang F, Zhou YL. Identification of a four-miRNA signature predicts the prognosis of papillary thyroid cancer. World J Clin Cases 2023; 11:92-103. [PMID: 36687184 PMCID: PMC9846980 DOI: 10.12998/wjcc.v11.i1.92] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Revised: 11/10/2022] [Accepted: 12/21/2022] [Indexed: 01/04/2023] Open
Abstract
BACKGROUND In recently diagnosed patients with thyroid cancer, papillary thyroid cancer (PTC), as the most common histological subtype, accounts for 90% of all cases. Although PTC is known as a relatively adolescent malignant disease, there still is a high possibility of recurrence in PTC patients with a poor prognosis. Therefore, new biomarkers are necessary to guide more effective stratification of PTC patients and personalize therapy to avoid overtreatment or inadequate treatment. Accumulating evidence demonstrates that microRNAs (miRNAs) have broad application prospects as diagnostic biomarkers in cancer.
AIM To explore novel markers consisting of miRNA-associated signatures for PTC prognostication.
METHODS We obtained and analyzed the data of 497 PTC patients from The Cancer Genome Atlas. The patients were randomly assigned to either a training or testing cohort.
RESULTS We discovered 237 differentially expressed miRNAs in tumorous thyroid tissues compared with normal tissues, which contained 172 up-regulated and 65 down-regulated miRNAs. The evaluation of differently expressed miRNAs was conducted using our risk score model. We then successfully generated a four-miRNA potential prognostic signature [risk score = (-0.001 × hsa-miR-181a-2-3p) + (0.003 × hsa-miR-138-5p) + (-0.018 × hsa-miR-424-3p) + (0.284 × hsa-miR-612)], which reliably distinguished patients from high and low risk with a significant difference in the overall survival (P < 0.01) and was effective in predicting the five-year disease survival rate with the area under the receiver operating characteristic curve of 0.937 and 0.812 in the training and testing cohorts, respectively. Additionally, there was a trend indicated that high-risk patients had shorter relapse-free survival, although statistical significance was not reached (P = 0.082) in our sequencing cohort.
CONCLUSION Our results indicated a four-miRNA signature that has a robust predictive effect on the prognosis of PTC. Accordingly, we would recommend more radical therapy and closer follow-ups for high-risk groups.
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Affiliation(s)
- Fan Yang
- Department of Thyroid Surgery, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou 325000, Zhejiang Province, China
| | - Yi-Li Zhou
- Department of Thyroid Surgery, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou 325000, Zhejiang Province, China
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Rahmoon MA, Elghaish RA, Ibrahim AA, Alaswad Z, Gad MZ, El-Khamisy SF, Elserafy M. High Glucose Increases DNA Damage and Elevates the Expression of Multiple DDR Genes. Genes (Basel) 2023; 14:144. [PMID: 36672885 PMCID: PMC9858638 DOI: 10.3390/genes14010144] [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: 10/22/2022] [Revised: 12/19/2022] [Accepted: 12/31/2022] [Indexed: 01/06/2023] Open
Abstract
The DNA Damage Response (DDR) pathways sense DNA damage and coordinate robust DNA repair and bypass mechanisms. A series of repair proteins are recruited depending on the type of breaks and lesions to ensure overall survival. An increase in glucose levels was shown to induce genome instability, yet the links between DDR and glucose are still not well investigated. In this study, we aimed to identify dysregulation in the transcriptome of normal and cancerous breast cell lines upon changing glucose levels. We first performed bioinformatics analysis using a microarray dataset containing the triple-negative breast cancer (TNBC) MDA-MB-231 and the normal human mammary epithelium MCF10A cell lines grown in high glucose (HG) or in the presence of the glycolysis inhibitor 2-deoxyglucose (2DG). Interestingly, multiple DDR genes were significantly upregulated in both cell lines grown in HG. In the wet lab, we remarkably found that HG results in severe DNA damage to TNBC cells as observed using the comet assay. In addition, several DDR genes were confirmed to be upregulated using qPCR analysis in the same cell line. Our results propose a strong need for DDR pathways in the presence of HG to oppose the severe DNA damage induced in cells.
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Affiliation(s)
- Mai A. Rahmoon
- Center for Genomics, Helmy Institute for Medical Sciences, Zewail City of Science and Technology, Giza 12578, Egypt
- Department of Pharmaceutical Biology, Faculty of Pharmacy and Biotechnology, German University in Cairo, Cairo 11835, Egypt
| | - Reem A. Elghaish
- Center for Genomics, Helmy Institute for Medical Sciences, Zewail City of Science and Technology, Giza 12578, Egypt
- University of Science and Technology, Zewail City of Science and Technology, Giza 12578, Egypt
| | - Aya A. Ibrahim
- Center for Genomics, Helmy Institute for Medical Sciences, Zewail City of Science and Technology, Giza 12578, Egypt
- University of Science and Technology, Zewail City of Science and Technology, Giza 12578, Egypt
| | - Zina Alaswad
- Center for Genomics, Helmy Institute for Medical Sciences, Zewail City of Science and Technology, Giza 12578, Egypt
- University of Science and Technology, Zewail City of Science and Technology, Giza 12578, Egypt
| | - Mohamed Z. Gad
- Department of Biochemistry, Faculty of Pharmacy and Biotechnology, German University in Cairo, Cairo 11835, Egypt
| | - Sherif F. El-Khamisy
- Center for Genomics, Helmy Institute for Medical Sciences, Zewail City of Science and Technology, Giza 12578, Egypt
- The Healthy Lifespan Institute and Institute of Neuroscience, School of Bioscience, University of Sheffield, Sheffield S10 2TN, UK
- The Institute of Cancer Therapeutics, University of Bradford, Bradford BD7 1 DP, UK
| | - Menattallah Elserafy
- Center for Genomics, Helmy Institute for Medical Sciences, Zewail City of Science and Technology, Giza 12578, Egypt
- University of Science and Technology, Zewail City of Science and Technology, Giza 12578, Egypt
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140
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Guo R, Gong X, Li K, Qiu Z, Yang L, Wan Y, Yao X, Long C, Xu J, Li K, Liu J, Liu J. Xanthine oxidase, a therapeutic target of realgar for non-small cell lung cancer. Heliyon 2023; 9:e12666. [PMID: 36685422 PMCID: PMC9849977 DOI: 10.1016/j.heliyon.2022.e12666] [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: 07/10/2022] [Revised: 11/18/2022] [Accepted: 12/20/2022] [Indexed: 01/05/2023] Open
Abstract
Background The effects of realgar against non-small cell lung cancer (NSCLC) have been massively studied, but the direct therapeutic targets of realgar remain unclear. This study aimed to identify the molecular targets of realgar against NSCLC and explore their therapeutic mechanisms based on a network pharmacology approach and experimental validations. Methods The BATMAN-TCM and Digsee databases were used to predict realgar targets and NSCLC-related genes, respectively. A protein-protein interaction network was constructed for each gene set, and the overlapping genes were identified as potential targets of realgar against NSCLC. The correlation between potential targets and NSCLC was analyzed using The Cancer Genome Atlas and International Cancer Genome Consortium databases, and the key target was validated by in-silico and in-vitro experiments. Results Twenty-three overlapping genes, including xanthine oxidase (XO), were identified as potential targets of realgar against NSCLC. XO was selected as the key target for validation, as it was found to be upregulated in NSCLC tumor tissue, which correlated with poor overall survival. A possible interaction between realgar and XO was revealed by molecular docking which was further validated experimentally. Realgar treatment suppressed the activity of XO in NSCLC cells, as demonstrated by the unchanged XO protein levels. Finally, the mechanism of action of XO as a target against NSCLC through the cell-cell junction organization pathway was investigated. Conclusions Overall, this study proposes a potential molecular mechanism illustrating that XO is a target of realgar against NSCLC and highlights the usefulness of XO as a therapeutic target for NSCLC.
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Affiliation(s)
- Rui Guo
- Central Laboratory, The Second Affiliated Hospital, School of Medicine, The Chinese University of Hong Kong, Longgang District People's Hospital of Shenzhen, Shenzhen, Guangdong, 518172, PR China
| | - Xiaoyu Gong
- Pharmacy Department, The Second Affiliated Hospital, School of Medicine, The Chinese University of Hong Kong, Longgang District People's Hospital of Shenzhen, Shenzhen, Guangdong, 518172, PR China
| | - Kongzhao Li
- Central Laboratory, The Second Affiliated Hospital, School of Medicine, The Chinese University of Hong Kong, Longgang District People's Hospital of Shenzhen, Shenzhen, Guangdong, 518172, PR China
| | - Zhengqi Qiu
- Central Laboratory, The Second Affiliated Hospital, School of Medicine, The Chinese University of Hong Kong, Longgang District People's Hospital of Shenzhen, Shenzhen, Guangdong, 518172, PR China
| | - Lina Yang
- Department of Cardiothoracic Surgery, The Second Affiliated Hospital, School of Medicine, The Chinese University of Hong Kong, Longgang District People's Hospital of Shenzhen, Shenzhen, Guangdong, 518172, PR China
| | - Yanbin Wan
- Central Laboratory, The Second Affiliated Hospital, School of Medicine, The Chinese University of Hong Kong, Longgang District People's Hospital of Shenzhen, Shenzhen, Guangdong, 518172, PR China
| | - Xinhuang Yao
- Central Laboratory, The Second Affiliated Hospital, School of Medicine, The Chinese University of Hong Kong, Longgang District People's Hospital of Shenzhen, Shenzhen, Guangdong, 518172, PR China
| | - Canling Long
- Central Laboratory, The Second Affiliated Hospital, School of Medicine, The Chinese University of Hong Kong, Longgang District People's Hospital of Shenzhen, Shenzhen, Guangdong, 518172, PR China
| | - Jiqing Xu
- Department of Cardiothoracic Surgery, The Second Affiliated Hospital, School of Medicine, The Chinese University of Hong Kong, Longgang District People's Hospital of Shenzhen, Shenzhen, Guangdong, 518172, PR China
| | - Kang Li
- Central Laboratory, The Second Affiliated Hospital, School of Medicine, The Chinese University of Hong Kong, Longgang District People's Hospital of Shenzhen, Shenzhen, Guangdong, 518172, PR China
| | - Jingyan Liu
- Emergency Department, The Second Affiliated Hospital, School of Medicine, The Chinese University of Hong Kong, Longgang District People's Hospital of Shenzhen, Shenzhen, Guangdong, 518172, PR China,Corresponding author. Emergency Department, The Second Affiliated Hospital, School of Medicine, The Chinese University of Hong Kong, Longgang District People's Hospital of Shenzhen, Shenzhen, Guangdong, 518172, PR China.
| | - Jia Liu
- Central Laboratory, The Second Affiliated Hospital, School of Medicine, The Chinese University of Hong Kong, Longgang District People's Hospital of Shenzhen, Shenzhen, Guangdong, 518172, PR China,Corresponding author. Central Laboratory, The Second Affiliated Hospital, School of Medicine, The Chinese University of Hong Kong, Longgang District People's Hospital of Shenzhen, Shenzhen, Guangdong, 518172, PR China.
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141
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Otávio KS, Passos JRS, Silva RF, Lima LF, Cadenas J, Paes VM, Correia HHV, Ferreira ACA, Canafístula FG, Bezerra MJB, Oliveira LLB, Carvalho GGC, Paier CRK, Pessoa C, Guerreiro DG, Moraes MEA, Figueiredo JR, Moura AA. Comprehensive proteomic profiling of early antral follicles from sheep. Anim Reprod Sci 2023; 248:107153. [PMID: 36502761 DOI: 10.1016/j.anireprosci.2022.107153] [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: 04/11/2022] [Revised: 11/12/2022] [Accepted: 11/14/2022] [Indexed: 11/23/2022]
Abstract
The present study evaluates the proteome of early antral follicles from Ovis aries. Fifty follicles were collected from ovaries of adult ewes and extracted proteins were trypsin-digested, desalted and analyzed by LC-MS/MS. Genes were screened for potential modulation by miRNAs and protein data, subjected to functional enrichment analysis. Label-free mass spectrometry allowed the identification of 2503 follicle proteins, confirming vimentin, actin, lamin, heat shock proteins and histones as the most abundant ones. In silico analyses indicated that miRNAs modulate the expression of genes coding proteins of the sheep follicles involved in cell cycle, cell differentiation, aging, apoptosis, cell death, adipocyte differentiation, cell division. The most important biological processes associated with the follicle proteins were innate immune response, translation, adaptive immune response and protein folding, while molecular functions linked to the proteome of sheep antral follicles related to metal ion binding, ATP binding, oxygen binding, RNA binding and GTP binding, among others. Upload of 2503 Uniport accession codes through DAVID platform matched 1274 genes, associated with translation, metabolic process, proteolysis involved in cellular protein catabolic process, zona pellucida receptor complex and others. KEEG pathways analysis indicated genes correlated with ovine follicular development, with major pathways listed as carbon metabolism, biosynthesis of amino acids, glutathione metabolism, oxidative phosphorylation, fatty acid degradation and oocyte meiosis. This represents a comprehensive atlas of proteins expressed in sheep early antral follicles and will contribute to future identification of biomarkers for follicular development and oocyte maturation.
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Affiliation(s)
- Kamila S Otávio
- Department of Animal Science, Federal University of Ceará, Fortaleza, Brazil
| | - José R S Passos
- Department of Animal Science, Federal University of Ceará, Fortaleza, Brazil
| | - Renato F Silva
- School of Veterinary Medicine, State University of Ceará, Fortaleza, Brazil
| | - Laritza F Lima
- School of Veterinary Medicine, State University of Ceará, Fortaleza, Brazil
| | - Jesús Cadenas
- School of Veterinary Medicine, State University of Ceará, Fortaleza, Brazil
| | - Victor M Paes
- School of Veterinary Medicine, State University of Ceará, Fortaleza, Brazil
| | - Hudson H V Correia
- School of Veterinary Medicine, State University of Ceará, Fortaleza, Brazil
| | | | | | | | - Laís L B Oliveira
- Drug Research and Development Center, School of Medicine, Federal University of Ceará, Fortaleza, Brazil
| | - Guilherme G C Carvalho
- Drug Research and Development Center, School of Medicine, Federal University of Ceará, Fortaleza, Brazil
| | - Carlos R K Paier
- Drug Research and Development Center, School of Medicine, Federal University of Ceará, Fortaleza, Brazil
| | - Claudia Pessoa
- Drug Research and Development Center, School of Medicine, Federal University of Ceará, Fortaleza, Brazil
| | - Denise G Guerreiro
- Department of Animal Science, Federal University of Ceará, Fortaleza, Brazil
| | - Maria Elisabete A Moraes
- Drug Research and Development Center, School of Medicine, Federal University of Ceará, Fortaleza, Brazil
| | | | - Arlindo A Moura
- Department of Animal Science, Federal University of Ceará, Fortaleza, Brazil; Drug Research and Development Center, School of Medicine, Federal University of Ceará, Fortaleza, Brazil.
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142
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cIAP1/TRAF2 interplay promotes tumor growth through the activation of STAT3. Oncogene 2023; 42:198-208. [PMID: 36400972 DOI: 10.1038/s41388-022-02544-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Revised: 10/26/2022] [Accepted: 11/04/2022] [Indexed: 11/19/2022]
Abstract
Cellular inhibitor of apoptosis-1 (cIAP1) is a signaling regulator with oncogenic properties. It is involved in the regulation of signaling pathways controlling inflammation, cell survival, proliferation, differentiation and motility. It is recruited into membrane-receptor-associated signaling complexes thanks to the molecular adaptor TRAF2. However, the cIAP1/TRAF2 complex exists, independently of receptor engagement, in several subcellular compartments. The present work strengthens the importance of TRAF2 in the oncogenic properties of cIAP1. cIAPs-deficient mouse embryonic fibroblasts (MEFs) were transformed using the HRas-V12 oncogene. Re-expression of cIAP1 enhanced tumor growth in a nude mice xenograft model, and promoted lung tumor nodes formation. Deletion or mutation of the TRAF2-binding site completely abolished the oncogenic properties of cIAP1. Further, cIAP1 mediated the clustering of TRAF2, which was sufficient to stimulate tumor growth. Our TRAF2 interactome analysis showed that cIAP1 was critical for TRAF2 to bind to its protein partners. Thus, cIAP1 and TRAF2 would be two essential subunits of a signaling complex promoting a pro-tumoral signal. cIAP1/TRAF2 promoted the activation of the canonical NF-κB and ERK1/2 signaling pathways. NF-κB-dependent production of IL-6 triggered the activation of the JAK/STAT3 axis in an autocrine manner. Inhibition or downregulation of STAT3 specifically compromised the growth of cIAP1-restored MEFs but not that of MEFs expressing a cIAP1-mutant and treating mice with the STAT3 inhibitor niclosamide completely abrogated cIAP1/TRAF2-mediated tumor growth. Altogether, we demonstrate that cIAP1/TRAF2 binding is essential to promote tumor growth via the activation of the JAK/STAT3 signaling pathway.
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143
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Rai B, Pande A, Tiwari S. TRAIL and EGFR Pathways Targeting microRNAs are Predominantly Regulated in Human Diabetic Nephropathy. Microrna 2023; 12:143-155. [PMID: 37098997 DOI: 10.2174/2211536612666230407093841] [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: 10/11/2022] [Revised: 01/02/2023] [Accepted: 02/01/2023] [Indexed: 04/27/2023]
Abstract
BACKGROUND Unbiased microRNA profiling of renal tissue and urinary extracellular vesicles (uEVs) from diabetic nephropathy (DN) subjects may unravel novel targets with diagnostic and therapeutic potential. Here we used the miRNA profile of uEVs and renal biopsies from DN subjects available on the GEO database. METHODS The miR expression profiles of kidney tissue (GSE51674) and urinary exosomes (GSE48318) from DN and control subjects were obtained by GEO2R tools from Gene Expression Omnibus (GEO) databases. Differentially expressed miRNAs in DN samples, relative to controls, were identified using a bioinformatic pipeline. Targets of miRs commonly regulated in both sample types were predicted by miRWalk, followed by functional gene enrichment analysis. Gene targets were identified by MiRTarBase, TargetScan and MiRDB. RESULTS Eight miRs, including let-7c, miR-10a, miR-10b and miR-181c, were significantly regulated in kidney tissue and uEVs in DN subjects versus controls. The top 10 significant pathways targeted by these miRs included TRAIL, EGFR, Proteoglycan syndecan, VEGF and Integrin Pathway. Gene target analysis by miRwalk upon validation using ShinyGO 70 targets with significant miRNA-mRNA interaction. CONCLUSION In silico analysis showed that miRs targeting TRAIL and EGFR signaling are predominately regulated in uEVs and renal tissue of DN subjects. After wet-lab validation, the identified miRstarget pairs may be explored for their diagnostic and/or therapeutic potential in diabetic nephropathy.
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Affiliation(s)
- Bhuvnesh Rai
- Department of Molecular Medicine & Biotechnology, Sanjay Gandhi Postgraduate Institute of Medical Sciences, Lucknow, India
| | - Akshara Pande
- Department of Molecular Medicine & Biotechnology, Sanjay Gandhi Postgraduate Institute of Medical Sciences, Lucknow, India
| | - Swasti Tiwari
- Department of Molecular Medicine & Biotechnology, Sanjay Gandhi Postgraduate Institute of Medical Sciences, Lucknow, India
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Eirin A, Chade AR. Cardiac epigenetic changes in VEGF signaling genes associate with myocardial microvascular rarefaction in experimental chronic kidney disease. Am J Physiol Heart Circ Physiol 2023; 324:H14-H25. [PMID: 36367693 PMCID: PMC9762979 DOI: 10.1152/ajpheart.00522.2022] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Revised: 11/07/2022] [Accepted: 11/08/2022] [Indexed: 11/13/2022]
Abstract
Chronic kidney disease (CKD) is common in patients with heart failure and often results in left ventricular diastolic dysfunction (LVDD). However, the mechanisms responsible for cardiac damage in CKD-LVDD remain to be elucidated. Epigenetic alterations may impose long-lasting effects on cellular transcription and function, but their exact role in CKD-LVDD is unknown. We investigate whether changes in cardiac site-specific DNA methylation profiles might be implicated in cardiac abnormalities in CKD-LVDD. CKD-LVDD and normal control pigs (n = 6 each) were studied for 14 wk. Renal and cardiac hemodynamics were quantified by multidetector CT and echocardiography. In randomly selected pigs (n = 3/group), cardiac site-specific 5-methylcytosine (5mC) immunoprecipitation (MeDIP)- and mRNA-sequencing (seq) were performed, followed by integrated (MeDiP-seq/mRNA-seq analysis), and confirmatory ex vivo studies. MeDIP-seq analysis revealed 261 genes with higher (fold change > 1.4; P < 0.05) and 162 genes with lower (fold change < 0.7; P < 0.05) 5mC levels in CKD-LVDD versus normal pigs, which were primarily implicated in vascular endothelial growth factor (VEGF)-related signaling and angiogenesis. Integrated MeDiP-seq/mRNA-seq analysis identified a select group of VEGF-related genes in which 5mC levels were higher, but mRNA expression was lower in CKD-LVDD versus normal pigs. Cardiac VEGF signaling gene and VEGF protein expression were blunted in CKD-LVDD compared with controls and were associated with decreased subendocardial microvascular density. Cardiac epigenetic changes in VEGF-related genes are associated with impaired angiogenesis and cardiac microvascular rarefaction in swine CKD-LVDD. These observations may assist in developing novel therapies to ameliorate cardiac damage in CKD-LVDD.NEW & NOTEWORTHY Chronic kidney disease (CKD) often leads to left ventricular diastolic dysfunction (LVDD) and heart failure. Using a novel translational swine model of CKD-LVDD, we characterize the cardiac epigenetic landscape, identifying site-specific 5-methylcytosine changes in vascular endothelial growth factor (VEGF)-related genes associated with impaired angiogenesis and cardiac microvascular rarefaction. These observations shed light on the mechanisms of cardiac microvascular damage in CKD-LVDD and may assist in developing novel therapies for these patients.
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Affiliation(s)
- Alfonso Eirin
- Division of Nephrology and Hypertension, Mayo Clinic, Rochester, Minnesota
| | - Alejandro R Chade
- Department of Medical Pharmacology and Physiology, University of Missouri-Columbia, Columbia, Missouri
- Department of Medicine, University of Missouri-Columbia, Columbia, Missouri
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145
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Vishal K, Bhuiyan P, Qi J, Chen Y, Zhang J, Yang F, Li J. Unraveling the Mechanism of Immunity and Inflammation Related to Molecular Signatures Crosstalk Among Obesity, T2D, and AD: Insights From Bioinformatics Approaches. Bioinform Biol Insights 2023; 17:11779322231167977. [PMID: 37124128 PMCID: PMC10134115 DOI: 10.1177/11779322231167977] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2022] [Accepted: 03/17/2023] [Indexed: 05/02/2023] Open
Abstract
Individuals with type 2 diabetes (T2D) and obesity have a higher risk of developing Alzheimer disease (AD), and increasing evidence indicates a link between impaired immune signaling pathways and the development of AD. However, the shared cellular mechanisms and molecular signatures among these 3 diseases remain unknown. The purpose of this study was to uncover similar molecular markers and pathways involved in obesity, T2D, and AD using bioinformatics and a network biology approach. First, we investigated the 3 RNA sequencing (RNA-seq) gene expression data sets and determined 224 commonly shared differentially expressed genes (DEGs) from obesity, T2D, and AD diseases. Gene ontology and pathway enrichment analyses revealed that mutual DEGs were mainly enriched with immune and inflammatory signaling pathways. In addition, we constructed a protein-protein interactions network for finding hub genes, which have not previously been identified as playing a critical role in these 3 diseases. Furthermore, the transcriptional factors and protein kinases regulating commonly shared DEGs among obesity, T2D, and AD were also identified. Finally, we suggested potential drug candidates as possible therapeutic interventions for 3 diseases. The results of this bioinformatics analysis provided a new understanding of the potential links between obesity, T2D, and AD pathologies.
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Affiliation(s)
- Kumar Vishal
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, China
- Key Laboratory of Human Functional Genomics of Jiangsu Province, Nanjing Medical University, Nanjing, China
- Department of Biochemistry & Molecular Biology, School of Basic Medical Sciences, Nanjing Medical University, Nanjing, China
| | - Piplu Bhuiyan
- Department of Anesthesiology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Junxia Qi
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, China
- Key Laboratory of Human Functional Genomics of Jiangsu Province, Nanjing Medical University, Nanjing, China
- Department of Biochemistry & Molecular Biology, School of Basic Medical Sciences, Nanjing Medical University, Nanjing, China
| | - Yang Chen
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, China
- Key Laboratory of Human Functional Genomics of Jiangsu Province, Nanjing Medical University, Nanjing, China
- Department of Biochemistry & Molecular Biology, School of Basic Medical Sciences, Nanjing Medical University, Nanjing, China
| | - Jubiao Zhang
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, China
- Key Laboratory of Human Functional Genomics of Jiangsu Province, Nanjing Medical University, Nanjing, China
- Department of Biochemistry & Molecular Biology, School of Basic Medical Sciences, Nanjing Medical University, Nanjing, China
| | - Fen Yang
- Department of Biochemistry & Molecular Biology, School of Basic Medical Sciences, Nanjing Medical University, Nanjing, China
| | - Juxue Li
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, China
- Key Laboratory of Human Functional Genomics of Jiangsu Province, Nanjing Medical University, Nanjing, China
- Department of Biochemistry & Molecular Biology, School of Basic Medical Sciences, Nanjing Medical University, Nanjing, China
- The Affiliated Eye Hospital, Nanjing Medical University, Nanjing, China
- The Second Affiliated Hospital of Nanjing Medical University, Nanjing, China
- Fen Yang, Department of Biochemistry & Molecular Biology, School of Basic Medical Sciences, Nanjing Medical University, 101 Longmian Avenue, Jiangning District, Nanjing 211166, Jiangsu, China.
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146
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Caglar HO, Duzgun Z. Identification of upregulated genes in glioblastoma and glioblastoma cancer stem cells using bioinformatics analysis. Gene X 2023; 848:146895. [DOI: 10.1016/j.gene.2022.146895] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Revised: 08/10/2022] [Accepted: 09/12/2022] [Indexed: 11/30/2022] Open
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147
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Murugaiyaa Pandiyan S, Shanmugaraj P, Manoharan JP, Vidyalakshmi S. A network pharmacological approach to reveal the multidrug resistance reversal and associated mechanisms of acetogenins against colorectal cancer. J Biomol Struct Dyn 2022; 40:13527-13546. [PMID: 34669561 DOI: 10.1080/07391102.2021.1990130] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Multidrug Resistance (MDR) in tumors is caused by the over-expression of ATP Binding Cassette transporter proteins such as Multidrug Resistance Protein 1 and Breast Cancer Resistance Protein 1. This in silico study focuses on identifying a MDR inhibitor among acetogenins (AGEs) of Annona muricata and also aims at predicting colorectal cancer (CRC) core targets of AGEs through a network pharmacological approach. Twenty-four AGEs were initially screened for their ADME properties. Molecular interaction studies were performed with the two proteins MRP1 and BCRP1. As the structure of MRP1 was not available, an inward-facing conformation of MRP1 was modeled. A Protein-protein interaction network was constructed for the correlating targets of CRC. KEGG pathway and Gene Ontology analysis were performed for the predicted CRC targets. We identified four lead AGEs: Muricatocin B, Annonacinone, Annonacin A and Annomuricin E having a higher binding affinity towards MDR proteins. MD simulation studies performed with the three lead AGEs and the MDR proteins showed that MRP1(DBD): Annomuricin E complex was stable throughout the simulation. Our analysis revealed ABCG2, ERBB2, STAT3, AR, SRC and ABCC1 as CRC targets of the lead molecules. The top 10 signaling pathways and functions of correlative CRC targets were also predicted. We conclude that the identified lead molecules might act as competitive inhibitors for reversing MDR in CRC. Additionally, network pharmacological studies established the correlative CRC targets and their mechanisms of action. Further experimental studies are needed to validate our findings. Communicated by Ramaswamy H. Sarma.
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148
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Ramasubramanian L, Jyothi H, Goldbloom-Helzner L, Light BM, Kumar P, Carney RP, Farmer DL, Wang A. Development and Characterization of Bioinspired Lipid Raft Nanovesicles for Therapeutic Applications. ACS APPLIED MATERIALS & INTERFACES 2022; 14:54458-54477. [PMID: 36448709 PMCID: PMC9756296 DOI: 10.1021/acsami.2c13868] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Accepted: 11/14/2022] [Indexed: 06/17/2023]
Abstract
Lipid rafts are highly ordered regions of the plasma membrane enriched in signaling proteins and lipids. Their biological potential is realized in exosomes, a subclass of extracellular vesicles (EVs) that originate from the lipid raft domains. Previous studies have shown that EVs derived from human placental mesenchymal stromal cells (PMSCs) possess strong neuroprotective and angiogenic properties. However, clinical translation of EVs is challenged by very low, impure, and heterogeneous yields. Therefore, in this study, lipid rafts are validated as a functional biomaterial that can recapitulate the exosomal membrane and then be synthesized into biomimetic nanovesicles. Lipidomic and proteomic analyses show that lipid raft isolates retain functional lipids and proteins comparable to PMSC-EV membranes. PMSC-derived lipid raft nanovesicles (LRNVs) are then synthesized at high yields using a facile, extrusion-based methodology. Evaluation of biological properties reveals that LRNVs can promote neurogenesis and angiogenesis through modulation of lipid raft-dependent signaling pathways. A proof-of-concept methodology further shows that LRNVs could be loaded with proteins or other bioactive cargo for greater disease-specific functionalities, thus presenting a novel type of biomimetic nanovesicles that can be leveraged as targeted therapeutics for regenerative medicine.
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Affiliation(s)
- Lalithasri Ramasubramanian
- Department
of Surgery, School of Medicine, University of California-Davis, Sacramento, California 95817, United States
- Institute
for Pediatric Regenerative Medicine, Shriners
Hospitals for Children, Sacramento, California 95817, United States
- Department
of Biomedical Engineering, University of
California-Davis, Davis, California 95616, United States
| | - Harsha Jyothi
- Department
of Surgery, School of Medicine, University of California-Davis, Sacramento, California 95817, United States
| | - Leora Goldbloom-Helzner
- Department
of Surgery, School of Medicine, University of California-Davis, Sacramento, California 95817, United States
- Institute
for Pediatric Regenerative Medicine, Shriners
Hospitals for Children, Sacramento, California 95817, United States
- Department
of Biomedical Engineering, University of
California-Davis, Davis, California 95616, United States
| | - Brandon M. Light
- Department
of Surgery, School of Medicine, University of California-Davis, Sacramento, California 95817, United States
| | - Priyadarsini Kumar
- Department
of Surgery, School of Medicine, University of California-Davis, Sacramento, California 95817, United States
- Institute
for Pediatric Regenerative Medicine, Shriners
Hospitals for Children, Sacramento, California 95817, United States
| | - Randy P. Carney
- Department
of Biomedical Engineering, University of
California-Davis, Davis, California 95616, United States
| | - Diana L. Farmer
- Department
of Surgery, School of Medicine, University of California-Davis, Sacramento, California 95817, United States
- Institute
for Pediatric Regenerative Medicine, Shriners
Hospitals for Children, Sacramento, California 95817, United States
| | - Aijun Wang
- Department
of Surgery, School of Medicine, University of California-Davis, Sacramento, California 95817, United States
- Institute
for Pediatric Regenerative Medicine, Shriners
Hospitals for Children, Sacramento, California 95817, United States
- Department
of Biomedical Engineering, University of
California-Davis, Davis, California 95616, United States
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Ganesan H, Nandy SK, Banerjee A, Pathak S, Zhang H, Sun XF. RNA-Interference-Mediated miR-122-Based Gene Regulation in Colon Cancer, a Structural In Silico Analysis. Int J Mol Sci 2022; 23:ijms232315257. [PMID: 36499586 PMCID: PMC9739210 DOI: 10.3390/ijms232315257] [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: 09/29/2022] [Revised: 11/18/2022] [Accepted: 12/02/2022] [Indexed: 12/12/2022] Open
Abstract
The role of microRNA 122 (miR-122) in colorectal cancer (CRC) has not been widely investigated. In the current study, we aimed to identify the prominent gene and protein interactors of miR122 in CRC. Based on their binding affinity, these targets were chosen as candidate genes for the creation of miR122-mRNA duplexes. Following this, we examined the miRNA-mediated silencing mechanism using the gene-silencing complex protein Argonaute (AGO). Public databases, STRING, and GeneMANIA were utilized to identify major proteins and genes interacting with miR-122. DAVID, PANTHER, UniProt, FunRich, miRwalk, and KEGG were used for functional annotation, pathway enrichment, binding affinity analysis, and expression of genes in different stages of cancer. Three-dimensional duplexes of hub genes and miR-122 were created using the RNA composer, followed by molecular interaction analysis using molecular docking with the AGO protein. We analyzed, classified, and scrutinized 93 miR-122 interactors using various bioinformatic approaches. A total of 14 hub genes were categorized as major interactors of miR-122. The study confirmed the role of various experimentally documented miR-122 interactors such as MTDH (Q86UE4), AKT1 (P31749), PTPN1 (P18031), MYC (P01106), GSK3B (P49841), RHOA (P61586), and PIK3CG (P48736) and put forth several novel interactors, with AKT3 (Q9Y243), NCOR2 (Q9Y618), PIK3R2 (O00459), SMAD4 (P61586), and TGFBR1 (P36897). Double-stranded RNA duplexes of the strongest interactors were found to exhibit higher binding affinity with AGO. In conclusions, the study has explored the role of miR-122 in CRC and has identified a closely related group of genes influencing the prognosis of CRC in multiple ways. Further, these genes prove to be targets of gene silencing through RNA interference and might serve as effective therapeutic targets in understanding and treating CRC.
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Affiliation(s)
- Harsha Ganesan
- Department of Medical Biotechnology, Faculty of Allied Health Sciences, Chettinad Academy of Research and Education, Chettinad Hospital and Research Institute, Kelambakkam, Chennai 603103, Tamil Nadu, India
| | - Suman K. Nandy
- BioNEST Bioincubator Facility, North-Eastern Hill University, Tura Campus, Chasingre, Tura 793022, Meghalaya, India
| | - Antara Banerjee
- Department of Medical Biotechnology, Faculty of Allied Health Sciences, Chettinad Academy of Research and Education, Chettinad Hospital and Research Institute, Kelambakkam, Chennai 603103, Tamil Nadu, India
| | - Surajit Pathak
- Department of Medical Biotechnology, Faculty of Allied Health Sciences, Chettinad Academy of Research and Education, Chettinad Hospital and Research Institute, Kelambakkam, Chennai 603103, Tamil Nadu, India
- Department of Oncology and Department of Biomedical and Clinical Sciences, Linköping University, 581 83 Linköping, Sweden
- Correspondence: (S.P.); (X.-F.S.)
| | - Hong Zhang
- School of Medical Sciences, Faculty of Medicine and Health, Orebro University, 702 81 Örebro, Sweden
| | - Xiao-Feng Sun
- Department of Oncology and Department of Biomedical and Clinical Sciences, Linköping University, 581 83 Linköping, Sweden
- Correspondence: (S.P.); (X.-F.S.)
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150
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Yu Y, Li M, Zhao Y, Fan F, Wu W, Gao Y, Bai C. Immune cell-derived extracellular vesicular microRNAs induce pancreatic beta cell apoptosis. Heliyon 2022; 8:e11995. [PMID: 36561684 PMCID: PMC9763775 DOI: 10.1016/j.heliyon.2022.e11995] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Revised: 10/01/2022] [Accepted: 11/23/2022] [Indexed: 12/03/2022] Open
Abstract
Background Type 1 diabetes mellitus (T1DM) is an autoimmune disease caused by an autoimmune response against pancreatic islet β cells. Increasing evidence indicates that specific microRNAs (miRNAs) from immune cells extracellular vesicles are involved in islet β cells apoptosis. Methods In this study, the microarray datasets GSE27997 and GSE137637 were downloaded from the Gene Expression Omnibus (GEO) database. miRNAs that promote islet β cells apoptosis in T1DM were searched in PubMed. We used the FunRich tool to determine the miRNA expression in extracellular vesicles derived from immune cells associated with islet β cell apoptosis, of which we selected candidate miRNAs based on fold change expression. Potential upstream transcription factors and downstream target genes of candidate miRNAs were predicted using TransmiR V2.0 and starBase database, respectively. Results Candidate miRNAs expressed in extracellular vesicles derived from T cells, pro-inflammatory macrophages, B cells, and dendritic cells were analyzed to identify the miRNAs involved in β cells apoptosis. Based on these candidate miRNAs, 25 downstream candidate genes, which positively regulate β cell functions, were predicted and screened; 17 transcription factors that positively regulate the candidate miRNAs were also identified. Conclusions Our study demonstrated that immune cell-derived extracellular vesicular miRNAs could promote islet β cell dysfunction and apoptosis. Based on these findings, we have constructed a transcription factor-miRNA-gene regulatory network, which provides a theoretical basis for clinical management of T1DM. This study provides novel insights into the mechanism underlying immune cell-derived extracellular vesicle-mediated islet β cell apoptosis.
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Affiliation(s)
- Yueyang Yu
- Institute of Precision Medicine, Jining Medical University, Jining, Shandong 272067, PR China
| | - Mengyin Li
- Department of Otorhinolaryngology Head and Neck Surgery, Affiliated Hospital of Jining Medical University, Jining, Shandong Province, 272067, PR China
| | - Yuxuan Zhao
- Institute of Precision Medicine, Jining Medical University, Jining, Shandong 272067, PR China
| | - Fangzhou Fan
- Institute of Precision Medicine, Jining Medical University, Jining, Shandong 272067, PR China
| | - Wenxiang Wu
- Institute of Precision Medicine, Jining Medical University, Jining, Shandong 272067, PR China
| | - Yuhua Gao
- Institute of Precision Medicine, Jining Medical University, Jining, Shandong 272067, PR China
- Corresponding author.
| | - Chunyu Bai
- Institute of Precision Medicine, Jining Medical University, Jining, Shandong 272067, PR China
- Corresponding author.
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