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Zhang X, Zhou S, Zhan Y, Mei Z, Qian A, Yuan Y, Zhang X, Fu T, Ma S, Li J. Molecular insights into the proteomic composition of porcine treated dentin matrix. Mater Today Bio 2024; 25:100990. [PMID: 38371466 PMCID: PMC10873736 DOI: 10.1016/j.mtbio.2024.100990] [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: 11/07/2023] [Revised: 01/23/2024] [Accepted: 02/03/2024] [Indexed: 02/20/2024] Open
Abstract
Background Human-treated dentin matrix (hTDM) has recently been studied as a natural extracellular matrix-based biomaterial for dentin pulp regeneration. However, porcine-treated dentin matrix (pTDM) is a potential alternative scaffold due to limited availability. However, there is a dearth of information regarding the protein composition and underlying molecular mechanisms of pTDM.Methods: hTDM and pTDM were fabricated using human and porcine teeth, respectively, and their morphological characteristics were examined using scanning electron microscopy. Stem cells derived from human exfoliated deciduous teeth (SHEDs) were isolated and characterized using flow cytometry and multilineage differentiation assays. SHEDs were cultured in three-dimensional environments with hTDM, pTDM, or biphasic hydroxyapatite/tricalcium phosphate. The expression of odontogenesis markers in SHEDs were assessed using real-time polymerase chain reaction and immunochemical staining. Subsequently, SHEDs/TDM and SHEDs/HA/TCP complexes were transplanted subcutaneously into nude mice. The protein composition of pTDM was analyzed using proteomics and compared to previously published data on hTDM.Results: pTDM and hTDM elicited comparable upregulation of odontogenesis-related genes and proteins in SHEDs. Furthermore, both demonstrated the capacity to stimulate root-related tissue regeneration in vivo. Proteomic analysis revealed the presence of 278 protein groups in pTDM, with collagens being the most abundant. Additionally, pTDM and hTDM shared 58 identical proteins, which may contribute to their similar abilities to induce odontogenesis. Conclusions Both hTDM and pTDM exhibit comparable capabilities in inducing odontogenesis, potentially owing to their distinctive bioactive molecular networks.
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Affiliation(s)
- Xiya Zhang
- College of Stomatology, Chongqing Medical University, Chongqing, China
- Chongqing Key Laboratory of Oral Diseases and Biomedical Sciences, Chongqing Medical University, Chongqing, China
- Chongqing Municipal Key Laboratory of Oral Biomedical Engineering of Higher Education, Chongqing Medical University, Chongqing, China
| | - Sha Zhou
- College of Stomatology, Chongqing Medical University, Chongqing, China
- Chongqing Key Laboratory of Oral Diseases and Biomedical Sciences, Chongqing Medical University, Chongqing, China
- Chongqing Municipal Key Laboratory of Oral Biomedical Engineering of Higher Education, Chongqing Medical University, Chongqing, China
| | - Yuzhen Zhan
- College of Stomatology, Chongqing Medical University, Chongqing, China
- Chongqing Key Laboratory of Oral Diseases and Biomedical Sciences, Chongqing Medical University, Chongqing, China
- Chongqing Municipal Key Laboratory of Oral Biomedical Engineering of Higher Education, Chongqing Medical University, Chongqing, China
| | - Ziyi Mei
- College of Stomatology, Chongqing Medical University, Chongqing, China
- Chongqing Key Laboratory of Oral Diseases and Biomedical Sciences, Chongqing Medical University, Chongqing, China
- Chongqing Municipal Key Laboratory of Oral Biomedical Engineering of Higher Education, Chongqing Medical University, Chongqing, China
| | - Aizhuo Qian
- College of Stomatology, Chongqing Medical University, Chongqing, China
- Chongqing Key Laboratory of Oral Diseases and Biomedical Sciences, Chongqing Medical University, Chongqing, China
- Chongqing Municipal Key Laboratory of Oral Biomedical Engineering of Higher Education, Chongqing Medical University, Chongqing, China
| | - Yu Yuan
- College of Stomatology, Chongqing Medical University, Chongqing, China
- Chongqing Key Laboratory of Oral Diseases and Biomedical Sciences, Chongqing Medical University, Chongqing, China
- Chongqing Municipal Key Laboratory of Oral Biomedical Engineering of Higher Education, Chongqing Medical University, Chongqing, China
| | - Xiaonan Zhang
- College of Stomatology, Chongqing Medical University, Chongqing, China
- Chongqing Key Laboratory of Oral Diseases and Biomedical Sciences, Chongqing Medical University, Chongqing, China
- Chongqing Municipal Key Laboratory of Oral Biomedical Engineering of Higher Education, Chongqing Medical University, Chongqing, China
| | - Tiwei Fu
- College of Stomatology, Chongqing Medical University, Chongqing, China
- Chongqing Key Laboratory of Oral Diseases and Biomedical Sciences, Chongqing Medical University, Chongqing, China
- Chongqing Municipal Key Laboratory of Oral Biomedical Engineering of Higher Education, Chongqing Medical University, Chongqing, China
| | - Shiyong Ma
- Basic Medicine Research and Innovation Center for Novel Target and Therapeutic Intervention, The Ministry of Education, Institute of Life Sciences, Chongqing Medical University, Chongqing, China
| | - Jie Li
- College of Stomatology, Chongqing Medical University, Chongqing, China
- Chongqing Key Laboratory of Oral Diseases and Biomedical Sciences, Chongqing Medical University, Chongqing, China
- Chongqing Municipal Key Laboratory of Oral Biomedical Engineering of Higher Education, Chongqing Medical University, Chongqing, China
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2
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Arroyo E, Pérez Sayáns M, Bravo SB, de Oliveira Barbeiro C, Paravani Palaçon M, Chamorro Petronacci CM, García Vence M, Chantada Vázquez MDP, Blanco Carrión A, Suárez Peñaranda JM, García García A, Gándara Vila P, Días Almeida J, Veríssimo da Costa GC, Sousa Nogueira FC, Medeiros Evaristo JA, de Abreu Pereira D, Rintala M, Salo T, Rautava J, Padín Iruegas E, Oliveira Alves MG, Morandin Ferrisse T, Albergoni da Silveira H, Esquiche León J, Vilela Silva E, Flores IL, Bufalino A. Identification of Proteomic Biomarkers in Proliferative Verrucous Leukoplakia through Liquid Chromatography With Tandem Mass Spectrometry. J Transl Med 2023; 103:100222. [PMID: 37507024 DOI: 10.1016/j.labinv.2023.100222] [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: 03/08/2023] [Revised: 07/13/2023] [Accepted: 07/19/2023] [Indexed: 07/30/2023] Open
Abstract
Proliferative verrucous leukoplakia (PVL) is an oral potentially malignant disorder associated with high risk of malignant transformation. Currently, there is no treatment available, and restrictive follow-up of patients is crucial for a better prognosis. Oral leukoplakia (OL) shares some clinical and microscopic features with PVL but exhibits different clinical manifestations and a lower rate of malignant transformation. This study aimed to investigate the proteomic profile of PVL in tissue and saliva samples to identify potential diagnostic biomarkers with therapeutic implications. Tissue and saliva samples obtained from patients with PVL were compared with those from patients with oral OL and controls. Label-free liquid chromatography with tandem mass spectrometry was employed, followed by qualitative and quantitative analyses, to identify differentially expressed proteins. Potential biomarkers were identified and further validated using immunohistochemistry. Staining intensity scan analyses were performed on tissue samples from patients with PVL, patients with OL, and controls from Brazil, Spain, and Finland. The study revealed differences in the immune system, cell cycle, DNA regulation, apoptosis pathways, and the whole proteome of PVL samples. In addition, liquid chromatography with tandem mass spectrometry analyses showed that calreticulin (CALR), receptor of activated protein C kinase 1 (RACK1), and 14-3-3 Tau-protein (YWHAQ) were highly expressed in PVL samples. Immunohistochemistry validation confirmed increased CARL expression in PVL compared with OL. Conversely, RACK1 and YWHA were highly expressed in oral potentially malignant disorder compared to the control group. Furthermore, significant differences in CALR and RACK1 expression were observed in the OL group when comparing samples with and without oral epithelial dysplasia, unlike the PVL. This research provides insights into the molecular mechanisms underlying these conditions and highlights potential targets for future diagnostic and therapeutic approaches.
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Affiliation(s)
- Esteban Arroyo
- Department of Diagnosis and Surgery, Araraquara, School of Dentistry, São Paulo State University (UNESP), Araraquara, São Paulo, Brazil
| | - Mario Pérez Sayáns
- Oral Medicine, Oral Surgery and Implantology Unit (MedOralRes), Faculty of Medicine and Dentistry, University of Santiago de Compostela, Instituto de los materiales de Santiago de Compostela (iMATUS), Santiago, Spain; Instituto de Investigación Sanitaria de Santiago (IDIS) (ORALRES Group), Santiago de Compostela, Spain.
| | - Susana Belen Bravo
- Proteomic Unit, Instituto de Investigación Sanitaria de Santiago (IDIS), Santiago de Compostela, Spain
| | - Camila de Oliveira Barbeiro
- Department of Diagnosis and Surgery, Araraquara, School of Dentistry, São Paulo State University (UNESP), Araraquara, São Paulo, Brazil
| | - Mariana Paravani Palaçon
- Department of Diagnosis and Surgery, Araraquara, School of Dentistry, São Paulo State University (UNESP), Araraquara, São Paulo, Brazil
| | | | - María García Vence
- Proteomic Unit, Instituto de Investigación Sanitaria de Santiago (IDIS), Santiago de Compostela, Spain
| | | | - Andrés Blanco Carrión
- Oral Medicine, Oral Surgery and Implantology Unit (MedOralRes), Faculty of Medicine and Dentistry, University of Santiago de Compostela, Instituto de los materiales de Santiago de Compostela (iMATUS), Santiago, Spain
| | - José M Suárez Peñaranda
- Servicio de Anatomia Patológica, Hospital Clinico Universitario de Santiago, Choupana s/n Santiago de Compostela, Spain
| | - Abel García García
- Oral Medicine, Oral Surgery and Implantology Unit (MedOralRes), Faculty of Medicine and Dentistry, University of Santiago de Compostela, Instituto de los materiales de Santiago de Compostela (iMATUS), Santiago, Spain
| | - Pilar Gándara Vila
- Oral Medicine, Oral Surgery and Implantology Unit (MedOralRes), Faculty of Medicine and Dentistry, University of Santiago de Compostela, Instituto de los materiales de Santiago de Compostela (iMATUS), Santiago, Spain; Instituto de Investigación Sanitaria de Santiago (IDIS) (ORALRES Group), Santiago de Compostela, Spain
| | - Janete Días Almeida
- Department of Bioscience and Buccal Diagnosis, São José dos Campos, Science and Technologies Institute, São Paulo State University (Unesp), São José dos Campos, São Paulo, Brazil
| | - Giovani Carlo Veríssimo da Costa
- Department of Basic Sciences, Nova Friburgo Health Institute, Univ. Federal Fluminense, Nova Friburgo, Rio de Janeiro, Brazil; Laboratory of Proteomics, Technological Development Support Laboratory (LADETEC), Institute of Chemistry, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Fábio César Sousa Nogueira
- Laboratory of Proteomics, Technological Development Support Laboratory (LADETEC), Institute of Chemistry, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Joseph Albert Medeiros Evaristo
- Laboratory of Proteomics, Technological Development Support Laboratory (LADETEC), Institute of Chemistry, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Denise de Abreu Pereira
- Program on Cellular and Molecular Oncobiology, Research Coordination, National Institute of Cancer (INCA), Rio de Janeiro, Brazil
| | - Mirjami Rintala
- Department of Oral Pathology, University of Turku, Turku, Finland
| | - Tuula Salo
- Department of Oral and Maxillofacial Diseases, Clinicum, University of Helsinki, Helsinki, Finland; Department of Pathology, HUSLAB, Helsinki, Finland; Department of Cancer and Translational Research Unit, University of Oulu, Oulu, Finland; Medical Research Center Oulu, Oulu, Finland
| | - Jaana Rautava
- Department of Oral Pathology, University of Turku, Turku, Finland; Department of Oral and Maxillofacial Diseases, Clinicum, University of Helsinki, Helsinki, Finland; Department of Pathology, HUSLAB, Helsinki, Finland
| | - Elena Padín Iruegas
- Human Anatomy and Embryology Area, Faculty of Physiotherapy, Department of Functional Biology and Health Sciences, Pontevedra, Spain
| | | | - Túlio Morandin Ferrisse
- Department of Dental Materials and Prosthodontics, São Paulo State University (UNESP), School of Dentistry, Araraquara, Brazil
| | - Heitor Albergoni da Silveira
- Department of Diagnosis and Surgery, Araraquara, School of Dentistry, São Paulo State University (UNESP), Araraquara, São Paulo, Brazil
| | - Jorge Esquiche León
- Oral Pathology, Department of Stomatology, Public Oral Health, and Forensic Dentistry, Ribeirão Preto Dental School (FORP/USP), University of São Paulo, Ribeirão Preto, São Paulo, Brazil
| | - Evânio Vilela Silva
- Department of Diagnosis and Surgery, Araraquara, School of Dentistry, São Paulo State University (UNESP), Araraquara, São Paulo, Brazil
| | - Isadora Luana Flores
- Oral Pathology Area, Conservative Dentistry Department, Dental School, Federal University of Rio Grande do Sul (UFRGS), Porto Alegre/RS, Brazil
| | - Andreia Bufalino
- Department of Diagnosis and Surgery, Araraquara, School of Dentistry, São Paulo State University (UNESP), Araraquara, São Paulo, Brazil
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3
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Liu J, Dong N, Li N, Zhao H, Li Y, Mao H, Ren H, Feng Y, Liu J, Du L, Mao H. IL-35 enhances angiogenic effects of small extracellular vesicles in breast cancer. FEBS J 2022; 289:3489-3504. [PMID: 35037402 DOI: 10.1111/febs.16359] [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] [Received: 10/06/2021] [Revised: 12/15/2021] [Accepted: 01/14/2022] [Indexed: 12/24/2022]
Abstract
As an indispensable process for breast cancer metastasis, tumour angiogenesis requires a tight interaction between cancer cells and endothelial cells in tumour microenvironment. Here, we explored the participation of small extracellular vesicles (sEVs) derived from breast cancer cells in modulating angiogenesis and investigated the effect of IL-35 in facilitating this process. Firstly, we characterized breast cancer cells-derived sEVs untreated or treated with IL-35 and visualized the internalization of these sEVs by human umbilical vein endothelial cells (HUVECs). Breast cancer cells-derived sEVs promoted endothelial cell proliferation through facilitating cell cycle progression and enhanced capillary-like structures formation and microvessel formation. Subsequent results proved that IL-35 further reinforced the angiogenic effect induced by breast cancer cells-derived sEVs. Moreover, sEVs from breast cancer cells significantly enhanced tumour growth and microvessel density in breast tumour-bearing mice model. Microarray analysis showed that IL-35 might alter the mRNA profiles of sEVs and activate the Ras/Raf/MEK/ERK signalling pathway. These findings demonstrated that IL-35 indirectly promoted angiogenesis in breast cancer through regulating the content of breast cancer cells-derived sEVs, which could be internalized by HUVECs.
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Affiliation(s)
- Jia Liu
- Department of Clinical Laboratory, The Second Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Nana Dong
- Department of Clinical Laboratory, The Second Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Ning Li
- Department of Clinical Laboratory, The Second Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Hui Zhao
- Department of Clinical Laboratory, The Second Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Yali Li
- Department of Clinical Laboratory, The Second Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Huihui Mao
- Department of Clinical Laboratory, The Second Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Hanxiao Ren
- Department of Clinical Laboratory, The Second Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Yimin Feng
- Department of Clinical Laboratory, The Second Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Jie Liu
- Department of Clinical Laboratory, The Second Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Lutao Du
- Department of Clinical Laboratory, The Second Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Haiting Mao
- Department of Clinical Laboratory, The Second Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China
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4
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Zhu Z, Wang W, Lin F, Jordan T, Li G, Silverman S, Qiu S, Joy AA, Chen C, Hockley DL, Zhang X, Zhou Q, Postovit LM, Zhang X, Hou Y, Mackey JR, Li B, Wong GKS. Genome profiles of pathologist-defined cell clusters by multiregional LCM and G&T-seq in one triple-negative breast cancer patient. CELL REPORTS MEDICINE 2021; 2:100404. [PMID: 34755126 PMCID: PMC8561166 DOI: 10.1016/j.xcrm.2021.100404] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Revised: 03/30/2021] [Accepted: 08/25/2021] [Indexed: 02/06/2023]
Abstract
Pathological examination is the gold standard for cancer diagnosis, and breast tumor cells are often found in clusters. We report a case study on one triple-negative breast cancer (TNBC) patient, analyzing tumor development, metastasis, and prognosis with simultaneous DNA and RNA sequencing of pathologist-defined cell clusters from multiregional frozen sections. The cell clusters are isolated by laser capture microdissection (LCM) from primary tumor tissue, lymphatic vessels, and axillary lymph nodes. Data are reported for a total of 97 cell clusters. A combination of tumor cell-cluster clonality and phylogeny reveals 3 evolutionarily distinct pathways for this patient, each associated with a unique mRNA signature, and each correlated with disparate survival outcomes. Hub gene analysis indicates that extensive downregulation of ribosomal protein mRNA is a potential marker of poor prognosis in breast cancer. Pathologically diverse cell clusters share genomic and transcriptomic profiles Transcriptome-defined clones are more complex than genome-defined clones Three distinct pathways were inferred, each with disparate survival outcomes Lower expression of ribosomal proteins may be an indicator of poor prognosis
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Affiliation(s)
- Zhongyi Zhu
- BGI-Shenzhen, Beishan Industrial Zone, Yantian District, Shenzhen 518083, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Weiwei Wang
- Department of Medicine, University of Alberta, Edmonton, AB T6G 2E1, Canada.,Geneis, Bldg A, 5 Guangshun North Street, Beijing 100102, China
| | - Feng Lin
- BGI-Shenzhen, Beishan Industrial Zone, Yantian District, Shenzhen 518083, China
| | - Tracy Jordan
- Department of Medicine, University of Alberta, Edmonton, AB T6G 2E1, Canada
| | - Guibo Li
- BGI-Shenzhen, Beishan Industrial Zone, Yantian District, Shenzhen 518083, China
| | - Sveta Silverman
- Department of Pathology and Laboratory Medicine, University of Alberta, Edmonton, AB T6G 2H7, Canada
| | - Si Qiu
- BGI-Shenzhen, Beishan Industrial Zone, Yantian District, Shenzhen 518083, China
| | - Anil Abraham Joy
- Division of Medical Oncology, Department of Oncology, University of Alberta, Cross Cancer Institute, Edmonton, AB T6G 1Z2, Canada
| | - Chao Chen
- BGI-Shenzhen, Beishan Industrial Zone, Yantian District, Shenzhen 518083, China
| | - Deanna L Hockley
- Division of Medical Oncology, Department of Oncology, University of Alberta, Cross Cancer Institute, Edmonton, AB T6G 1Z2, Canada
| | - Xi Zhang
- BGI-Shenzhen, Beishan Industrial Zone, Yantian District, Shenzhen 518083, China
| | - Qing Zhou
- BGI-Shenzhen, Beishan Industrial Zone, Yantian District, Shenzhen 518083, China
| | - Lynne M Postovit
- Department of Oncology, University of Alberta, Edmonton, AB T6G 2H7, Canada
| | - Xiuqing Zhang
- BGI-Shenzhen, Beishan Industrial Zone, Yantian District, Shenzhen 518083, China
| | - Yong Hou
- BGI-Shenzhen, Beishan Industrial Zone, Yantian District, Shenzhen 518083, China
| | - John R Mackey
- Division of Medical Oncology, Department of Oncology, University of Alberta, Cross Cancer Institute, Edmonton, AB T6G 1Z2, Canada
| | - Bo Li
- BGI-Shenzhen, Beishan Industrial Zone, Yantian District, Shenzhen 518083, China
| | - Gane Ka-Shu Wong
- BGI-Shenzhen, Beishan Industrial Zone, Yantian District, Shenzhen 518083, China.,Department of Medicine, University of Alberta, Edmonton, AB T6G 2E1, Canada.,Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E9, Canada
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5
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Arroyo EA, Donís SP, Petronacci CMC, Alves MGO, Mendía XM, Fernandes D, Pouso AIL, Bufalino A, Bravo López S, Sayáns MP. Usefulness of protein-based salivary markers in the diagnosis of oral potentially malignant disorders: A systematic review and meta-analysis. Cancer Biomark 2021; 32:411-424. [PMID: 34334380 DOI: 10.3233/cbm-203043] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
By using a meta-analytical approach, this study aimed to analyse the diagnostic capacity of protein-based biomarkers in saliva for the differential diagnosis of oral potentially malignant disorders (OPMDs) and oral squamous cell carcinoma (OSCC) from healthy individuals as control group (HCG).Articles on protein-based biomarkers in saliva, which provided quantitative expression in individuals with clinical and histopathological diagnosis of OPMD or oral leukoplakia (OL) were considered eligible. Searches were conducted in eight electronic databases. The methodological quality was assessed using the Quality Assessment of Diagnostic Studies tool (QUADAS-2). Functional analysis was also performed. Meta-analyses were performed using the OpenMeta tool (Analyst).Meta-analysis was possible for 4 of the 11 biomarkers studied. Only the carcinoembryonic antigen (CEA) and the soluble fragment of cytokeratin 19 (CYFRA21) were significant for the OSCC/OPMD subgroup, both with a very low heterogeneity. CEA had an OE = 25.854 (CI95%: 13.215-38.492, p< 0.001, I2 = 0) and CYFRA21 had an OE = 9.317 (CI95%: 9.014-9.619, p< 0.001, I2 = 0). For the OPMD/HCG subgroup, only CYFRA21 was significant, with an OE = 3.679 (CI95%: 0.663-6.696, p= 0.017) although with high heterogeneity (I2 = 91.24).The CEA and CYFRA21 markers proved very useful when differentiating OSCC from OPMD. The CYFRA21 was the only protein that was capable of distinguishing between OPMD and healthy controls.
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Affiliation(s)
- Esteban Alexis Arroyo
- Department of Diagnosis and Surgery, Araraquara, School of Dentistry, São Paulo State University, Araraquara, SP, Brazil
| | - Sergio Piñeiro Donís
- Oral Medicine, Oral Surgery and Implantology Unit, Faculty of Medicine and Dentistry, Universidade de Santiago de Compostela, Spain
| | - Cintia M Chamorro Petronacci
- Oral Medicine, Oral Surgery and Implantology Unit, Faculty of Medicine and Dentistry, Universidade de Santiago de Compostela, Spain.,Health Research Institute of Santiago de Compostela, Santiago de Compostela, Spain
| | - Monica G Oliveira Alves
- Anhembi Morumbi University, School of Medicine, São José dos Campos, São Paulo, Brazil.,Universidade Mogi das Cruzes, School of Dentistry, Mogi das Cruzes, São Paulo, Brazil
| | | | - Darcy Fernandes
- Department of Diagnosis and Surgery, Araraquara, School of Dentistry, São Paulo State University, Araraquara, SP, Brazil
| | - Alejandro I Lorenzo Pouso
- Oral Medicine, Oral Surgery and Implantology Unit, Faculty of Medicine and Dentistry, Universidade de Santiago de Compostela, Spain
| | - Andreia Bufalino
- Department of Diagnosis and Surgery, Araraquara, School of Dentistry, São Paulo State University, Araraquara, SP, Brazil
| | - Susana Bravo López
- Proteomic Unit, Health Research Institute of Santiago de Compostela, Santiago de Compostela, Spain
| | - Mario Pérez Sayáns
- Department of Diagnosis and Surgery, Araraquara, School of Dentistry, São Paulo State University, Araraquara, SP, Brazil.,Oral Medicine, Oral Surgery and Implantology Unit, Faculty of Medicine and Dentistry, Universidade de Santiago de Compostela, Spain
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6
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Ryan FJ, Carr JM, Furtado JM, Ma Y, Ashander LM, Simões M, Oliver GF, Granado GB, Dawson AC, Michael MZ, Appukuttan B, Lynn DJ, Smith JR. Zika Virus Infection of Human Iris Pigment Epithelial Cells. Front Immunol 2021; 12:644153. [PMID: 33968035 PMCID: PMC8100333 DOI: 10.3389/fimmu.2021.644153] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2020] [Accepted: 03/02/2021] [Indexed: 12/13/2022] Open
Abstract
During recent Zika epidemics, adults infected with Zika virus (ZIKV) have developed organ-specific inflammatory complications. The most serious Zika-associated inflammatory eye disease is uveitis, which is commonly anterior in type, affecting both eyes and responding to corticosteroid eye drops. Mechanisms of Zika-associated anterior uveitis are unknown, but ZIKV has been identified in the aqueous humor of affected individuals. The iris pigment epithelium is a target cell population in viral anterior uveitis, and it acts to maintain immune privilege within the anterior eye. Interactions between ZIKV and human iris pigment epithelial cells were investigated with infectivity assays and RNA-sequencing. Primary cell isolates were prepared from eyes of 20 cadaveric donors, and infected for 24 hours with PRVABC59 strain ZIKV or incubated uninfected as control. Cytoimmunofluorescence, RT-qPCR on total cellular RNA, and focus-forming assays of culture supernatant showed cell isolates were permissive to infection, and supported replication and release of infectious ZIKV. To explore molecular responses of cell isolates to ZIKV infection at the whole transcriptome level, RNA was sequenced on the Illumina NextSeq 500 platform, and results were aligned to the human GRCh38 genome. Multidimensional scaling showed clear separation between transcriptomes of infected and uninfected cell isolates. Differential expression analysis indicated a vigorous molecular response of the cell to ZIKV: 7,935 genes were differentially expressed between ZIKV-infected and uninfected cells (FDR < 0.05), and 99% of 613 genes that changed at least two-fold were up-regulated. Reactome and KEGG pathway and Gene Ontology enrichment analyses indicated strong activation of viral recognition and defense, in addition to biosynthesis processes. A CHAT network included 6275 molecular nodes and 24 contextual hubs in the cell response to ZIKV infection. Receptor-interacting serine/threonine kinase 1 (RIPK1) was the most significantly connected contextual hub. Correlation of gene expression with read counts assigned to the ZIKV genome identified a negative correlation between interferon signaling and viral load across isolates. This work represents the first investigation of mechanisms of Zika-associated anterior uveitis using an in vitro human cell model. The results suggest the iris pigment epithelium mounts a molecular response that limits intraocular pathology in most individuals.
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Affiliation(s)
- Feargal J Ryan
- Precision Medicine Theme, South Australian Health & Medical Research Institute, Adelaide, SA, Australia
| | - Jillian M Carr
- Flinders University College of Medicine and Public Health, Bedford Park, SA, Australia
| | - João M Furtado
- Ophthalmology Division, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, Brazil
| | - Yuefang Ma
- Flinders University College of Medicine and Public Health, Bedford Park, SA, Australia
| | - Liam M Ashander
- Flinders University College of Medicine and Public Health, Bedford Park, SA, Australia
| | - Milena Simões
- Ophthalmology Division, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, Brazil
| | - Genevieve F Oliver
- Flinders University College of Medicine and Public Health, Bedford Park, SA, Australia
| | - G Bracho Granado
- Flinders University College of Medicine and Public Health, Bedford Park, SA, Australia
| | - Abby C Dawson
- Flinders University College of Medicine and Public Health, Bedford Park, SA, Australia
| | - Michael Z Michael
- Flinders University College of Medicine and Public Health, Bedford Park, SA, Australia
| | - Binoy Appukuttan
- Flinders University College of Medicine and Public Health, Bedford Park, SA, Australia
| | - David J Lynn
- Precision Medicine Theme, South Australian Health & Medical Research Institute, Adelaide, SA, Australia.,Flinders University College of Medicine and Public Health, Bedford Park, SA, Australia
| | - Justine R Smith
- Precision Medicine Theme, South Australian Health & Medical Research Institute, Adelaide, SA, Australia.,Flinders University College of Medicine and Public Health, Bedford Park, SA, Australia
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7
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Neves LX, Granato DC, Busso-Lopes AF, Carnielli CM, Patroni FMDS, De Rossi T, Oliveira AK, Ribeiro ACP, Brandão TB, Rodrigues AN, Lacerda PA, Uno M, Cervigne NK, Santos-Silva AR, Kowalski LP, Lopes MA, Paes Leme AF. Peptidomics-Driven Strategy Reveals Peptides and Predicted Proteases Associated With Oral Cancer Prognosis. Mol Cell Proteomics 2020; 20:100004. [PMID: 33578082 PMCID: PMC7950089 DOI: 10.1074/mcp.ra120.002227] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Revised: 10/26/2020] [Accepted: 11/11/2020] [Indexed: 12/11/2022] Open
Abstract
Protease activity has been associated with pathological processes that can lead to cancer development and progression. However, understanding the pathological unbalance in proteolysis is challenging because changes can occur simultaneously at protease, their inhibitor, and substrate levels. Here, we present a pipeline that combines peptidomics, proteomics, and peptidase predictions for studying proteolytic events in the saliva of 79 patients and their association with oral squamous cell carcinoma (OSCC) prognosis. Our findings revealed differences in the saliva peptidome of patients with (pN+) or without (pN0) lymph-node metastasis and delivered a panel of ten endogenous peptides correlated with poor prognostic factors plus five molecules able to classify pN0 and pN+ patients (area under the receiver operating characteristic curve > 0.85). In addition, endopeptidases and exopeptidases putatively implicated in the processing of differential peptides were investigated using cancer tissue gene expression data from public repositories, reinforcing their association with poorer survival rates and prognosis in oral cancer. The dynamics of the OSCC-related proteolysis were further explored via the proteomic profiling of saliva. This revealed that peptidase/endopeptidase inhibitors exhibited reduced levels in the saliva of pN+ patients, as confirmed by selected reaction monitoring-mass spectrometry, while minor changes were detected in the level of saliva proteases. Taken together, our results indicated that proteolytic activity is accentuated in the saliva of patients with OSCC and lymph-node metastasis and, at least in part, is modulated by reduced levels of salivary peptidase inhibitors. Therefore, this integrated pipeline provided better comprehension and discovery of molecular features with implications in the oral cancer metastasis prognosis.
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Affiliation(s)
- Leandro Xavier Neves
- Brazilian Biosciences National Laboratory, National Center for Research in Energy and Materials, Campinas, Brazil
| | - Daniela C Granato
- Brazilian Biosciences National Laboratory, National Center for Research in Energy and Materials, Campinas, Brazil
| | - Ariane Fidelis Busso-Lopes
- Brazilian Biosciences National Laboratory, National Center for Research in Energy and Materials, Campinas, Brazil
| | - Carolina M Carnielli
- Brazilian Biosciences National Laboratory, National Center for Research in Energy and Materials, Campinas, Brazil
| | - Fábio M de Sá Patroni
- Molecular Biology and Genetic Engineering Center, University of Campinas, Campinas, Brazil
| | - Tatiane De Rossi
- Brazilian Biosciences National Laboratory, National Center for Research in Energy and Materials, Campinas, Brazil
| | - Ana Karina Oliveira
- Brazilian Biosciences National Laboratory, National Center for Research in Energy and Materials, Campinas, Brazil
| | | | | | - André Nimtz Rodrigues
- Department of Head and Neck Surgery, Faculty of Medicine of Jundiaí, Jundiaí, Brazil
| | - Pammela Araujo Lacerda
- Department of Internal Medicine, Molecular Biology and Cell Culture Laboratory, Faculty of Medicine of Jundiaí, Jundiaí, Brazil
| | - Miyuki Uno
- Center for Translational Research in Oncology, São Paulo Cancer Institute, São Paulo, Brazil
| | - Nilva K Cervigne
- Department of Internal Medicine, Molecular Biology and Cell Culture Laboratory, Faculty of Medicine of Jundiaí, Jundiaí, Brazil
| | - Alan Roger Santos-Silva
- Oral Diagnosis Department, Piracicaba Dental School, University of Campinas, Piracicaba, São Paulo, Brazil
| | - Luiz Paulo Kowalski
- Head and Neck Surgery, Faculty of Medicine, University of São Paulo, São Paulo, Brazil
| | - Marcio Ajudarte Lopes
- Oral Diagnosis Department, Piracicaba Dental School, University of Campinas, Piracicaba, São Paulo, Brazil
| | - Adriana F Paes Leme
- Brazilian Biosciences National Laboratory, National Center for Research in Energy and Materials, Campinas, Brazil.
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8
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Malik G, Agarwal T, Raj U, Sundararajan VS, Bandapalli OR, Suravajhala P. Hypothetical Proteins as Predecessors of Long Non-coding RNAs. Curr Genomics 2020; 21:531-535. [PMID: 33214769 PMCID: PMC7604745 DOI: 10.2174/1389202921999200611155418] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2020] [Revised: 04/28/2020] [Accepted: 05/16/2020] [Indexed: 02/07/2023] Open
Abstract
Hypothetical Proteins [HP] are the transcripts predicted to be expressed in an organism, but no evidence of it exists in gene banks. On the other hand, long non-coding RNAs [lncRNAs] are the transcripts that might be present in the 5’ UTR or intergenic regions of the genes whose lengths are above 200 bases. With the known unknown [KU] regions in the genomes rapidly existing in gene banks, there is a need to understand the role of open reading frames in the context of annotation. In this commentary, we emphasize that HPs could indeed be the predecessors of lncRNAs.
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Affiliation(s)
- Girik Malik
- 1Khoury College of Computer Sciences, Northeastern University, 360 Huntington Ave., Boston, MA02115, USA; 2Bioclues.org, Kukatpally, Hyderabad, 500072, India; 3Labrynthe Pvt. Ltd., New Delhi, India; 4NIIT University, NH8, Delhi- Jaipur Highway, District Alwar, Neemrana, Rajasthan 301705, India; 5Hopp Children's Cancer Center [KiTZ], Heidelberg, Germany; 6Division of Pediatric Neuro Oncology, German Cancer Research Center [DKFZ], German Cancer Consortium [DKTK], Heidelberg, Germany; 7Heidelberg University, Medical Faculty, Heidelberg, Germany; 8Department of Biotechnology and Bioinformatics, Birla Institute of Scientific Research, Statue Circle, Jaipur302021, RJ, India
| | - Tanu Agarwal
- 1Khoury College of Computer Sciences, Northeastern University, 360 Huntington Ave., Boston, MA02115, USA; 2Bioclues.org, Kukatpally, Hyderabad, 500072, India; 3Labrynthe Pvt. Ltd., New Delhi, India; 4NIIT University, NH8, Delhi- Jaipur Highway, District Alwar, Neemrana, Rajasthan 301705, India; 5Hopp Children's Cancer Center [KiTZ], Heidelberg, Germany; 6Division of Pediatric Neuro Oncology, German Cancer Research Center [DKFZ], German Cancer Consortium [DKTK], Heidelberg, Germany; 7Heidelberg University, Medical Faculty, Heidelberg, Germany; 8Department of Biotechnology and Bioinformatics, Birla Institute of Scientific Research, Statue Circle, Jaipur302021, RJ, India
| | - Utkarsh Raj
- 1Khoury College of Computer Sciences, Northeastern University, 360 Huntington Ave., Boston, MA02115, USA; 2Bioclues.org, Kukatpally, Hyderabad, 500072, India; 3Labrynthe Pvt. Ltd., New Delhi, India; 4NIIT University, NH8, Delhi- Jaipur Highway, District Alwar, Neemrana, Rajasthan 301705, India; 5Hopp Children's Cancer Center [KiTZ], Heidelberg, Germany; 6Division of Pediatric Neuro Oncology, German Cancer Research Center [DKFZ], German Cancer Consortium [DKTK], Heidelberg, Germany; 7Heidelberg University, Medical Faculty, Heidelberg, Germany; 8Department of Biotechnology and Bioinformatics, Birla Institute of Scientific Research, Statue Circle, Jaipur302021, RJ, India
| | - Vijayaraghava Seshadri Sundararajan
- 1Khoury College of Computer Sciences, Northeastern University, 360 Huntington Ave., Boston, MA02115, USA; 2Bioclues.org, Kukatpally, Hyderabad, 500072, India; 3Labrynthe Pvt. Ltd., New Delhi, India; 4NIIT University, NH8, Delhi- Jaipur Highway, District Alwar, Neemrana, Rajasthan 301705, India; 5Hopp Children's Cancer Center [KiTZ], Heidelberg, Germany; 6Division of Pediatric Neuro Oncology, German Cancer Research Center [DKFZ], German Cancer Consortium [DKTK], Heidelberg, Germany; 7Heidelberg University, Medical Faculty, Heidelberg, Germany; 8Department of Biotechnology and Bioinformatics, Birla Institute of Scientific Research, Statue Circle, Jaipur302021, RJ, India
| | - Obul Reddy Bandapalli
- 1Khoury College of Computer Sciences, Northeastern University, 360 Huntington Ave., Boston, MA02115, USA; 2Bioclues.org, Kukatpally, Hyderabad, 500072, India; 3Labrynthe Pvt. Ltd., New Delhi, India; 4NIIT University, NH8, Delhi- Jaipur Highway, District Alwar, Neemrana, Rajasthan 301705, India; 5Hopp Children's Cancer Center [KiTZ], Heidelberg, Germany; 6Division of Pediatric Neuro Oncology, German Cancer Research Center [DKFZ], German Cancer Consortium [DKTK], Heidelberg, Germany; 7Heidelberg University, Medical Faculty, Heidelberg, Germany; 8Department of Biotechnology and Bioinformatics, Birla Institute of Scientific Research, Statue Circle, Jaipur302021, RJ, India
| | - Prashanth Suravajhala
- 1Khoury College of Computer Sciences, Northeastern University, 360 Huntington Ave., Boston, MA02115, USA; 2Bioclues.org, Kukatpally, Hyderabad, 500072, India; 3Labrynthe Pvt. Ltd., New Delhi, India; 4NIIT University, NH8, Delhi- Jaipur Highway, District Alwar, Neemrana, Rajasthan 301705, India; 5Hopp Children's Cancer Center [KiTZ], Heidelberg, Germany; 6Division of Pediatric Neuro Oncology, German Cancer Research Center [DKFZ], German Cancer Consortium [DKTK], Heidelberg, Germany; 7Heidelberg University, Medical Faculty, Heidelberg, Germany; 8Department of Biotechnology and Bioinformatics, Birla Institute of Scientific Research, Statue Circle, Jaipur302021, RJ, India
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9
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Zhu N, Zhang P, Du L, Hou J, Xu B. Identification of key genes and expression profiles in osteoarthritis by co-expressed network analysis. Comput Biol Chem 2020; 85:107225. [PMID: 32135469 DOI: 10.1016/j.compbiolchem.2020.107225] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2019] [Revised: 01/11/2020] [Accepted: 01/25/2020] [Indexed: 12/15/2022]
Abstract
BACKGROUND The underlying molecular characteristics of osteoarthritis (OA), a common age-related joint disease, remains elusive. Here, we aimed to identify potential early diagnostic biomarkers and elucidate underlying mechanisms of OA using weighted gene co-expression network analysis (WGCNA). MATERIAL AND METHODS We obtained the gene expression profile dataset GSE55235, GSE55457, and GSE55584, from the Gene Expression Omnibus. WGCNA was used to investigate the changes in co-expressed genes between normal and OA synovial membrane samples. Modules that were highly correlated to OA were subjected to functional enrichment analysis using the R clusterProfiler package. Differentially expressed genes (DEGs) between the two samples were screened using the "limma" package in R. A Venn diagram was constructed to intersect the genes in significant modules and DEGs. RT -PCR was used to further verify the hub gene expression levels between normal and OA samples. RESULTS The preserved significant module was found to be highly associated with OA development and progression (P < 1e-200, correlation = 0.92). Functional enrichment analysis suggested that the antiquewhite4 module was highly correlated to FoxO signaling pathway, and the metabolism of fatty acids and 2-oxocarboxylic acid. A total of 13 hub genes were identified based on significant module network topology and DEG analysis, and RT-PCR confirmed that these genes were significantly increased in OA samples compared with that in normal samples. CONCLUSIONS We identified 13 hub genes correlated to the development and progression of OA, which may provide new biomarkers and drug targets for OA.
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Affiliation(s)
- Naiqiang Zhu
- Graduate School of Tianjin Medical University, Tianjin 300070, China; Second Department of Spinal Surgery, The Affiliated Hospital of Chengde Medical College, Chengde 067000, China
| | - Peng Zhang
- Graduate School of Tianjin Medical University, Tianjin 300070, China
| | - Lilong Du
- Department of Minimally Invasive Spine Surgery, Tianjin Hospital, Tianjin 300070, China
| | - Jingyi Hou
- Hebei Key Laboratory of Study and Exploitation of Chinese Medicine, Chengde Medical College, Chengde 067000, China
| | - Baoshan Xu
- Department of Minimally Invasive Spine Surgery, Tianjin Hospital, Tianjin 300070, China.
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10
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Mao Y, Wang Y, Dong L, Zhang Y, Zhang Y, Wang C, Zhang Q, Yang S, Cao L, Zhang X, Li X, Fu Z. Hypoxic exosomes facilitate angiogenesis and metastasis in esophageal squamous cell carcinoma through altering the phenotype and transcriptome of endothelial cells. JOURNAL OF EXPERIMENTAL & CLINICAL CANCER RESEARCH : CR 2019; 38:389. [PMID: 31488217 PMCID: PMC6727585 DOI: 10.1186/s13046-019-1384-8] [Citation(s) in RCA: 83] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/22/2019] [Accepted: 08/15/2019] [Indexed: 02/06/2023]
Abstract
Background In cancer progression, hypoxia, or low oxygen tension, is a major regulator of tumor aggressiveness and metastasis. However, how cancer cells adapt to the hypoxia and communicate with other mesenchymal cells in microenvironment during tumor development remains to be elucidated. Here, we investigated the involvement of exosomes in modulating angiogenesis and enhancing metastasis in esophageal squamous cell carcinoma (ESCC). Methods Differential centrifugation, transmission electron microscopy and nanoparticle tracking analysis were used to isolate and characterize exosomes. Colony formation and transwell assay were performed to assess the proliferation, migration and invasion of human umbilical vein endothelial cells (HUVECs). The tube formation assay and matrigel plug assay were used to evaluate the vascular formation ability of HUVECs in vitro and in vivo respectively. An in vivo nude mice model was established to detect the regulatory role of exosomes in ESCC progression. Microarray analysis was performed to analyze the transcriptome profiles in HUVECs. Results Exosomes derived from ESCC cells cultured under hypoxia played a better role in promoting proliferation, migration, invasion and tube formation of HUVECs in vitro and in vivo than exosomes from ESCC cells cultured under normoxia. Moreover, hypoxic exosomes significantly enhanced the tumor growth and lung metastasis compared with normoxic exosomes in nude mice models. Interestingly, endothelial cells were programmed by hypoxic and normoxic exosomes from ESCC cells which altered the transcriptome profile of HUVECs. Conclusions Taken together, our data identified an angiogenic role of exosomes from ESCC cells which shed light on the further application of exosomes as valuable therapeutic target for ESCC. Electronic supplementary material The online version of this article (10.1186/s13046-019-1384-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Yu Mao
- Department of Oncology, First Hospital of Qinhuangdao, Wenhua Road No. 258, Haigang District, Qinhuangdao, 066000, Hebei, China.
| | - Yimin Wang
- Department of General Surgery, First Hospital of Qinhuangdao, Hebei Medical University, Qinhuangdao, China
| | - Lixin Dong
- Department of Oncology, First Hospital of Qinhuangdao, Wenhua Road No. 258, Haigang District, Qinhuangdao, 066000, Hebei, China
| | - Yunjie Zhang
- Department of Oncology, First Hospital of Qinhuangdao, Wenhua Road No. 258, Haigang District, Qinhuangdao, 066000, Hebei, China
| | - Yanqiu Zhang
- Department of Oncology, First Hospital of Qinhuangdao, Wenhua Road No. 258, Haigang District, Qinhuangdao, 066000, Hebei, China
| | - Chao Wang
- Department of Thoracic Surgery, First Hospital of Qinhuangdao, Qinhuangdao, China
| | - Qiang Zhang
- Department of Oncology, First Hospital of Qinhuangdao, Wenhua Road No. 258, Haigang District, Qinhuangdao, 066000, Hebei, China
| | - Sen Yang
- Department of Oncology, First Hospital of Qinhuangdao, Wenhua Road No. 258, Haigang District, Qinhuangdao, 066000, Hebei, China
| | - Liyan Cao
- Department of Oncology, First Hospital of Qinhuangdao, Wenhua Road No. 258, Haigang District, Qinhuangdao, 066000, Hebei, China
| | - Xinyuan Zhang
- Department of Oncology, First Hospital of Qinhuangdao, Wenhua Road No. 258, Haigang District, Qinhuangdao, 066000, Hebei, China
| | - Xin Li
- Department of Oncology, First Hospital of Qinhuangdao, Wenhua Road No. 258, Haigang District, Qinhuangdao, 066000, Hebei, China
| | - Zhanzhao Fu
- Department of Oncology, First Hospital of Qinhuangdao, Wenhua Road No. 258, Haigang District, Qinhuangdao, 066000, Hebei, China.
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11
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Cardona C, Benincore E, Pimentel N, Reyes LH, Patarroyo C, Rodríguez-López A, Martin-Rufian M, Barrera LA, Alméciga-Díaz CJ. Identification of the iduronate-2-sulfatase proteome in wild-type mouse brain. Heliyon 2019; 5:e01667. [PMID: 31193135 PMCID: PMC6517578 DOI: 10.1016/j.heliyon.2019.e01667] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2019] [Revised: 03/30/2019] [Accepted: 05/02/2019] [Indexed: 01/11/2023] Open
Abstract
Iduronate-2-sulfatase (IDS) is a lysosomal enzyme involved in the metabolism of the glycosaminoglycans heparan (HS) and dermatan (DS) sulfate. Mutations on IDS gene produce mucopolysaccharidosis II (MPS II), characterized by the lysosomal accumulation of HS and DS, leading to severe damage of the central nervous system (CNS) and other tissues. In this study, we used a neurochemistry and proteomic approaches to identify the brain distribution of IDS and its interacting proteins on wild-type mouse brain. IDS immunoreactivity showed a robust staining throughout the entire brain, suggesting an intracellular reactivity in nerve cells and astrocytes. By using affinity purification and mass spectrometry we identified 187 putative IDS partners-proteins, mainly hydrolases, cytoskeletal proteins, transporters, transferases, oxidoreductases, nucleic acid binding proteins, membrane traffic proteins, chaperons and enzyme modulators, among others. The interactions with some of these proteins were predicted by using bioinformatics tools and confirmed by co-immunoprecipitation analysis and Blue Native PAGE. In addition, we identified cytosolic IDS-complexes containing proteins from predicted highly connected nodes (hubs), with molecular functions including catalytic activity, redox balance, binding, transport, receptor activity and structural molecule activity. The proteins identified in this study would provide new insights about IDS physiological role into the CNS and its potential role in the brain-specific protein networks.
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Affiliation(s)
- Carolina Cardona
- Institute for the Study of Inborn Errors of Metabolism, School of Sciences, Pontificia Universidad Javeriana, Bogotá, Colombia
| | - Eliana Benincore
- Institute for the Study of Inborn Errors of Metabolism, School of Sciences, Pontificia Universidad Javeriana, Bogotá, Colombia
| | - Natalia Pimentel
- Institute for the Study of Inborn Errors of Metabolism, School of Sciences, Pontificia Universidad Javeriana, Bogotá, Colombia
| | - Luis H Reyes
- Institute for the Study of Inborn Errors of Metabolism, School of Sciences, Pontificia Universidad Javeriana, Bogotá, Colombia.,Process and Product Design Group (GDPP), Department of Chemical Engineering, Universidad de los Andes, Bogotá, Colombia
| | - Camilo Patarroyo
- Institute for the Study of Inborn Errors of Metabolism, School of Sciences, Pontificia Universidad Javeriana, Bogotá, Colombia
| | - Alexander Rodríguez-López
- Institute for the Study of Inborn Errors of Metabolism, School of Sciences, Pontificia Universidad Javeriana, Bogotá, Colombia.,Chemistry Department, School of Sciences, Pontificia Universidad Javeriana, Bogotá, Colombia
| | - M Martin-Rufian
- Central Services Research Support, Proteomics Unit, Universidad de Malaga, Spain
| | - Luis Alejandro Barrera
- Institute for the Study of Inborn Errors of Metabolism, School of Sciences, Pontificia Universidad Javeriana, Bogotá, Colombia.,Clínica de Errores Innatos del Metabolismo, Hospital Universitario San Ignacio, Bogotá, Colombia
| | - Carlos J Alméciga-Díaz
- Institute for the Study of Inborn Errors of Metabolism, School of Sciences, Pontificia Universidad Javeriana, Bogotá, Colombia
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12
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Lie S, Rochet E, Segerdell E, Ma Y, Ashander LM, Shadforth AMA, Blenkinsop TA, Michael MZ, Appukuttan B, Wilmot B, Smith JR. Immunological Molecular Responses of Human Retinal Pigment Epithelial Cells to Infection With Toxoplasma gondii. Front Immunol 2019; 10:708. [PMID: 31118929 PMCID: PMC6506780 DOI: 10.3389/fimmu.2019.00708] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2018] [Accepted: 03/15/2019] [Indexed: 11/13/2022] Open
Abstract
Ocular toxoplasmosis is the commonest clinical manifestation of infection with obligate intracellular parasite, Toxoplasma gondii. Active ocular toxoplasmosis is characterized by replication of T. gondii tachyzoites in the retina, with reactive inflammation. The multifunctional retinal pigment epithelium is a key target cell population for T. gondii. Since the global gene expression profile is germane to understanding molecular involvements of retinal pigment epithelial cells in ocular toxoplasmosis, we performed RNA-Sequencing (RNA-Seq) of human cells following infection with T. gondii tachyzoites. Primary cell isolates from eyes of cadaveric donors (n = 3), and the ARPE-19 human retinal pigment epithelial cell line, were infected for 24 h with GT-1 strain T. gondii tachyzoites (multiplicity of infection = 5) or incubated uninfected as control. Total and small RNA were extracted from cells and sequenced on the Illumina NextSeq 500 platform; results were aligned to the human hg19 reference sequence. Multidimensional scaling showed good separation between transcriptomes of infected and uninfected primary cell isolates, which were compared in edgeR software. This differential expression analysis revealed a sizeable response in the total RNA transcriptome-with significantly differentially expressed genes totaling 7,234 (28.9% of assigned transcripts)-but very limited changes in the small RNA transcriptome-totaling 30 (0.35% of assigned transcripts) and including 8 microRNA. Gene ontology and pathway enrichment analyses of differentially expressed total RNA in CAMERA software, identified a strong immunologic transcriptomic signature. We conducted RT-qPCR for 26 immune response-related protein-coding and long non-coding transcripts in epithelial cell isolates from different cadaveric donors (n = 3), extracted by a different isolation protocol but similarly infected with T. gondii, to confirm immunological activity of infected cells. For microRNA, increases in miR-146b and miR-212 were detected by RT-qPCR in 2 and 3 of these independent cell isolates. Biological network analysis in the InnateDB platform, including 735 annotated differentially expressed genes plus 2,046 first-order interactors, identified 10 contextural hubs and 5 subnetworks in the transcriptomic immune response of cells to T. gondii. Our observations provide a solid base for future studies of molecular and cellular interactions between T. gondii and the human retinal pigment epithelium to illuminate mechanisms of ocular toxoplasmosis.
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Affiliation(s)
- Shervi Lie
- Eye and Vision Health, Flinders University College of Medicine and Public Health, Adelaide, SA, Australia
| | - Elise Rochet
- Eye and Vision Health, Flinders University College of Medicine and Public Health, Adelaide, SA, Australia
| | - Erik Segerdell
- Department of Biostatistics, Oregon Health and Sciences University, Portland, OR, United States
| | - Yuefang Ma
- Eye and Vision Health, Flinders University College of Medicine and Public Health, Adelaide, SA, Australia
| | - Liam M. Ashander
- Eye and Vision Health, Flinders University College of Medicine and Public Health, Adelaide, SA, Australia
| | - Audra M. A. Shadforth
- Queensland Eye Institute, Brisbane, QLD, Australia
- School of Biomedical Science, Queensland University of Technology, Brisbane, QLD, Australia
| | - Timothy A. Blenkinsop
- Departments of Cell, Developmental and Regenerative Biology, and Ophthalmology, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Michael Z. Michael
- Flinders Centre for Innovation in Cancer, Flinders University College of Medicine and Public Health, Adelaide, SA, Australia
| | - Binoy Appukuttan
- Eye and Vision Health, Flinders University College of Medicine and Public Health, Adelaide, SA, Australia
- Flinders Centre for Innovation in Cancer, Flinders University College of Medicine and Public Health, Adelaide, SA, Australia
| | - Beth Wilmot
- Department of Biostatistics, Oregon Health and Sciences University, Portland, OR, United States
| | - Justine R. Smith
- Eye and Vision Health, Flinders University College of Medicine and Public Health, Adelaide, SA, Australia
- Flinders Centre for Innovation in Cancer, Flinders University College of Medicine and Public Health, Adelaide, SA, Australia
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13
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Chaudhary R, Balhara M, Jangir DK, Dangi M, Dangi M, Chhillar AK. In Silico Protein Interaction Network Analysis of Virulence Proteins Associated with Invasive Aspergillosis for Drug Discovery. Curr Top Med Chem 2019; 19:146-155. [PMID: 30465504 DOI: 10.2174/1568026619666181120150633] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2018] [Revised: 10/05/2018] [Accepted: 11/04/2018] [Indexed: 01/08/2023]
Abstract
BACKGROUND Protein-Protein interaction (PPI) network analysis of virulence proteins of Aspergillus fumigatus is a prevailing strategy to understand the mechanism behind the virulence of A. fumigatus. The identification of major hub proteins and targeting the hub protein as a new antifungal drug target will help in treating the invasive aspergillosis. MATERIALS & METHOD In the present study, the PPI network of 96 virulence (drug target) proteins of A. fumigatus were investigated which resulted in 103 nodes and 430 edges. Topological enrichment analysis of the PPI network was also carried out by using STRING database and Network analyzer a cytoscape plugin app. The key enriched KEGG pathway and protein domains were analyzed by STRING. CONCLUSION Manual curation of PPI data identified three proteins (PyrABCN-43, AroM-34, and Glt1- 34) of A. fumigatus possessing the highest interacting partners. Top 10% hub proteins were also identified from the network using cytohubba on the basis of seven algorithms, i.e. betweenness, radiality, closeness, degree, bottleneck, MCC and EPC. Homology model and the active pocket of top three hub proteins were also predicted.
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Affiliation(s)
- Renu Chaudhary
- Centre for Biotechnology, Maharshi Dayanand University, Rohtak-124001, Haryana, India
| | - Meenakshi Balhara
- Centre for Biotechnology, Maharshi Dayanand University, Rohtak-124001, Haryana, India
| | - Deepak Kumar Jangir
- Centre for Biotechnology, Maharshi Dayanand University, Rohtak-124001, Haryana, India
| | - Mehak Dangi
- Centre for Bioinformatics, Maharshi Dayanand University, Rohtak-124001, Haryana, India
| | - Mrridula Dangi
- Centre for Biotechnology, Maharshi Dayanand University, Rohtak-124001, Haryana, India
| | - Anil K Chhillar
- Centre for Biotechnology, Maharshi Dayanand University, Rohtak-124001, Haryana, India
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14
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Lu Y, Wang X, Dong H, Wang X, Yang P, Han L, Wang Y, Zheng Z, Zhang W, Zhang L. Bioinformatics analysis of microRNA expression between patients with and without latent tuberculosis infections. Exp Ther Med 2019; 17:3977-3988. [PMID: 30988779 PMCID: PMC6447890 DOI: 10.3892/etm.2019.7424] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2018] [Accepted: 03/06/2019] [Indexed: 12/14/2022] Open
Abstract
Tuberculosis (TB) is a globally prevalent infectious disease. The mechanisms of latent TB infection (LTBI) remain to be fully elucidated and may provide novel approaches for diagnosis. As therapeutic targets and molecular diagnostic markers, microRNAs (miRs) have been studied and utilized in various diseases. In the present study, the differentially expressed miRs (DEMs) in LTBI were screened and analyzed to determine the underlying mechanisms and identify potential biomarkers, thereby contributing to the diagnosis of LTBI. The GSE25435 and GSE29190 datasets from Gene Expression Omnibus were selected for analysis. The 2 datasets were analyzed individually using the Bioconductor package to screen the DEMs with specific cut-off criteria [P<0.01 and |log (fold change)|≥1]. Target gene prediction and interaction network construction were performed using Targetscan, the Search Tool for the Retrieval of Interacting Genes and Proteins and Cytoscape individually, and were merged using the latter tool. The hub genes were finally selected based on their degree of connectivity (DC). Gene Ontology and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses were performed using the KEGG and GENCLIP. A total of 144 DEMs were identified from the 2 datasets. By exploring the overlapping miRs in the two datasets, Homo sapiens (hsa)-miR-29a and hsa-miR-15b were identified to be decreased, while hsa-miR-576-5p, hsa-miR-500 and hsa-miR-155 were identified to be upregulated. hsa-miR-500a-3p and hsa-miR-29a-3p, as well as 4 genes, namely cell division cycle (CDC)42, actin α1, skeletal muscle (ACTA1), phosphatase and tensin homolog (PTEN) and fos proto-oncogene (FOS), were selected as the key factors in this regulatory network. A total of 9 signaling pathways, including phosphoinositide-3 kinase (PI3K)/AKT and 11 biological processes, were identified to be associated with LTBI. In conclusion, the present analysis identified hsa-miR-500a-3p and hsa-miR-29a-3p, as well as CDC42, ACTA1, PTEN and FOS, as the most promising biomarkers and therapeutic candidates for LTBI. The PI3K/AKT signaling pathway is the key signaling pathway implicated in LTBI, and an in-depth investigation of the efficiency of PI3K/AKT signaling inhibitors may be used to prevent a chronic state of infection in LTBI.
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Affiliation(s)
- Yang Lu
- Department of Pathophysiology, The Key Laboratory for Xinjiang Endemic and Ethnic Diseases, Medical College of Shihezi University, Shihezi, Xinjiang 832000, P.R. China
| | - Xinmin Wang
- Department of Urinary Surgery, The First Affiliated Hospital, Medical College of Shihezi University, Shihezi, Xinjiang 832000, P.R. China
| | - Hongchang Dong
- Department of Biochemistry, The Key Laboratory for Xinjiang Endemic and Ethnic Diseases, Medical College of Shihezi University, Shihezi, Xinjiang 832000, P.R. China
| | - Xiaofang Wang
- Department of Pathophysiology, The Key Laboratory for Xinjiang Endemic and Ethnic Diseases, Medical College of Shihezi University, Shihezi, Xinjiang 832000, P.R. China
| | - Pu Yang
- Department of Pathophysiology, The Key Laboratory for Xinjiang Endemic and Ethnic Diseases, Medical College of Shihezi University, Shihezi, Xinjiang 832000, P.R. China
| | - Ling Han
- Department of Pathophysiology, The Key Laboratory for Xinjiang Endemic and Ethnic Diseases, Medical College of Shihezi University, Shihezi, Xinjiang 832000, P.R. China
| | - Yingzi Wang
- Department of Pathophysiology, The Key Laboratory for Xinjiang Endemic and Ethnic Diseases, Medical College of Shihezi University, Shihezi, Xinjiang 832000, P.R. China
| | - Zhihong Zheng
- Department of Pathophysiology, The Key Laboratory for Xinjiang Endemic and Ethnic Diseases, Medical College of Shihezi University, Shihezi, Xinjiang 832000, P.R. China
| | - Wanjiang Zhang
- Department of Pathophysiology, The Key Laboratory for Xinjiang Endemic and Ethnic Diseases, Medical College of Shihezi University, Shihezi, Xinjiang 832000, P.R. China
| | - Le Zhang
- Department of Pathophysiology, The Key Laboratory for Xinjiang Endemic and Ethnic Diseases, Medical College of Shihezi University, Shihezi, Xinjiang 832000, P.R. China
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Tiwari P, Saxena A, Gupta N, Medicherla KM, Suravajhala P, Mathur SK. Systems Genomics of Thigh Adipose Tissue From Asian Indian Type-2 Diabetics Revealed Distinct Protein Interaction Hubs. Front Genet 2019; 9:679. [PMID: 30671081 PMCID: PMC6331691 DOI: 10.3389/fgene.2018.00679] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2018] [Accepted: 12/07/2018] [Indexed: 12/13/2022] Open
Abstract
We performed a systematic analysis of genes implicated in thigh subcutaneous adipose tissue of Asian Indian Type 2 Diabetes Mellitus (AIT2DM) and created a phenome-interactome network. This analysis was performed on 60 subjects specific to limb thigh fat by integrating phenotypic traits and similarity scores associated with AIT2DM. Using a phenotypic attribute, a contextual neighbor was identified across all the traits, viz. body mass index (BMI) statistics, adipocyte size, lipid parameters, homeostatic model assessment- insulin resistance (HOMA-IR), HOMA-ß. In this work, we have attempted to characterize transcription signatures using the phenome-interactome maps where each of the traits under study including the intermediary phenotypes has a distinct set of genes forming the hubs. Furthermore, we have identified various clinical, biochemical, and radiological parameters which show significant correlation with distinct hubs. We observed a number of novel pathways and genes including those that are non-coding RNAs implicated in AIT2DM.We showed that they appear to be associated with pathways, viz. tyrosine kinase JAK2, NOTCH thereby recruiting signaling molecules such as STAT5 and Src family kinases on the cell surface regulated them and our analyses comprising significant hubs suggest that thigh subcutaneous adipose tissue plays a role in pathophysiology of AIT2DM.
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Affiliation(s)
- Pradeep Tiwari
- Department of Biotechnology and Bioinformatics, Birla Institute of Scientific Research, Jaipur, India.,Department of Endocrinology, Sawai Man Singh Medical College and Hospital, Jaipur, India.,Department of Chemistry, School of Basic Sciences, Manipal University Jaipur, Jaipur, India
| | - Aditya Saxena
- Department of Biotechnology, Institute of Applied Sciences and Humanities, GLA University, Mathura, India
| | - Nidhi Gupta
- Department of Biotechnology, The IIS University, Jaipur, India
| | - Krishna Mohan Medicherla
- Department of Biotechnology and Bioinformatics, Birla Institute of Scientific Research, Jaipur, India
| | - Prashanth Suravajhala
- Department of Biotechnology and Bioinformatics, Birla Institute of Scientific Research, Jaipur, India
| | - Sandeep Kumar Mathur
- Department of Chemistry, School of Basic Sciences, Manipal University Jaipur, Jaipur, India
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Agrin has a pathological role in the progression of oral cancer. Br J Cancer 2018; 118:1628-1638. [PMID: 29872149 PMCID: PMC6008410 DOI: 10.1038/s41416-018-0135-5] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2018] [Revised: 04/26/2018] [Accepted: 05/09/2018] [Indexed: 12/27/2022] Open
Abstract
Background The extracellular matrix modulates the hallmarks of cancer. Here we examined the role of agrin—a member of this matrix—in progression of oral squamous cell carcinoma (OSCC). Methods We evaluated the immunohistochemical expression of agrin in OSCC and dysplasias. Benign lesions were used as control. In subsequent experiments, we investigated whether the silencing of agrin interferes with tumour expansion both in vitro as well as in vivo. To gain insights into the role of agrin, we identified its protein network (interactome) using mass spectrometry-based proteomics and bioinformatics. Finally, we evaluated the clinical relevance of agrin interactome. Results Agrin was elevated in malignant and premalignant lesions. Further, we show that agrin silencing interferes with cancer cell motility, proliferation, invasion, colony and tumour spheroid formation, and it also reduces the phosphorylation of FAK, ERK and cyclin D1 proteins in OSCC cells. In orthotopic model, agrin silencing reduces tumour aggressiveness, like vascular and neural invasion. From a clinical perspective, agrin contextual hubs predict a poor clinical prognosis related with overall survival. Conclusions Altogether, our results demonstrate that agrin is a histological marker for the progression of oral cancer and is a strong therapeutic target candidate for both premalignant and OSCC lesions.
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Muetze T, Lynn DJ. Using the Contextual Hub Analysis Tool (CHAT) in Cytoscape to Identify Contextually Relevant Network Hubs. ACTA ACUST UNITED AC 2018; 59:8.24.1-8.24.13. [DOI: 10.1002/cpbi.35] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Tanja Muetze
- EMBL Australia Biomedical Informatics Group, Infection & Immunity Theme, South Australian Health and Medical Research Institute North Terrace Adelaide Australia
| | - David J. Lynn
- EMBL Australia Biomedical Informatics Group, Infection & Immunity Theme, South Australian Health and Medical Research Institute North Terrace Adelaide Australia
- School of Medicine, Flinders University Bedford Park Australia
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