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Nirgude S, Desai S, Choudhary B. Curcumin alters distinct molecular pathways in breast cancer subtypes revealed by integrated miRNA/mRNA expression analysis. Cancer Rep (Hoboken) 2022; 5:e1596. [PMID: 34981672 PMCID: PMC9575497 DOI: 10.1002/cnr2.1596] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2021] [Revised: 10/15/2021] [Accepted: 11/22/2021] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Curcumin is well known for its anticancer properties. Its cytotoxic activity has been documented in several cancer cell lines, including breast cancer. The pleiotropic activity of curcumin as an antioxidant, an antiangiogenic, antiproliferative, and pro-apoptotic, is due to its diverse targets, such as signaling pathways, protein/enzyme, or noncoding gene. AIM This study aimed to identify key miRNAs and mRNAs induced by curcumin in breast cancer cells MCF7, T47D (hormone positive), versus MDA-MB231 (hormone negative) using comparative analysis of global gene expression profiles. METHODS RNA was isolated and subjected to mRNA and miRNA library sequencing to study the global gene expression profile of curcumin-treated breast cancer cells. The differential expression of gene and miRNA was performed using the DESeq R package. The enriched pathways were studied using cluster profileR, and integrated miRNA-mRNA analysis was carried out using miRtarvis and miRmapper tools. RESULTS Curcumin treatment led to upregulation of 59% TSGs in MCF7, 21% in MDA-MB-231 cells, and 36% TSGs in T47D, and downregulation of 57% oncogenes in MCF7, 76% in MDA-MB-231, and 91% in T47D. Similarly, curcumin treatment led to upregulation of 32% TSmiRs in MCF7, 37.5% in MDA-MB231, and 62.5% in T47D, and downregulation of 77% oncomiRs in MCF7, 50% in MDA-MB231 and 28.6% in T47D. Integrated analysis of miRNA-mRNA led to the identification of a common NFKB pathway altered by curcumin in all three cell lines. Analysis of uniquely enriched pathway revealed non-integrin membrane-ECM interactions and laminin interactions in MCF7; extracellular matrix organization and degradation in MDA-MB-231 and cell cycle arrest and G2/M transition in T47D. CONCLUSION Curcumin regulates miRNA and mRNA in a cell type-specific manner. The integrative analysis led to the detection of miRNAs and mRNAs pairs, which can be used as biomarkers associated with carcinogenesis, diagnostic, and treatment response in breast cancer.
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Affiliation(s)
- Snehal Nirgude
- Institute of Bioinformatics and Applied BiotechnologyBangaloreIndia
- Division of Human GeneticsChildren's Hospital of PhiladelphiaPhiladelphiaUSA
| | - Sagar Desai
- Institute of Bioinformatics and Applied BiotechnologyBangaloreIndia
- Manipal Academy of Higher EducationManipalIndia
| | - Bibha Choudhary
- Institute of Bioinformatics and Applied BiotechnologyBangaloreIndia
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Lilley CM, Alarcon A, Ngo MH, Araujo JS, Marrero L, Mix KS. Orphan Nuclear Receptor NR4A2 Is Constitutively Expressed in Cartilage and Upregulated in Inflamed Synovium From hTNF-Alpha Transgenic Mice. Front Pharmacol 2022; 13:835697. [PMID: 35529439 PMCID: PMC9067626 DOI: 10.3389/fphar.2022.835697] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Accepted: 04/04/2022] [Indexed: 11/16/2022] Open
Abstract
Orphan nuclear receptor 4A2 (NR4A2/Nurr1) is a constitutively active transcription factor with potential roles in the onset and progression of inflammatory arthropathies. NR4A2 is overexpressed in synovium and cartilage from individuals with rheumatoid arthritis (RA), psoriatic arthritis, and osteoarthritis. This study documents the expression and tissue localization of NR4A2 and upstream regulator nuclear factor kappa B (NF-κB) in the human tumor necrosis factor-alpha (hTNF-α) transgenic mouse model of RA. Since TNF-α is a potent inducer of NR4A2 in vitro, we hypothesized that NR4A2 would also be upregulated and active during disease progression in this model. Expression levels of NR4A2, related receptors NR4A1 (Nur77) and 3 (NOR1), and NF-κB1 transcripts were quantified by RT-qPCR in hTNF-α and wild-type joints at three stages of disease. The protein distribution of NR4A2 and NF-κB subunit RelA (p65) was analyzed by quantitative immunohistochemistry. Global gene expression of 88 RA-related genes was also screened and compared between groups. Consistent with previous reports on the hTNF-α model, transgenic mice exhibited significant weight loss and severely swollen paws by 19 weeks of age compared to age-matched wild-type controls. NR4A1-3 and NF-κB1 were constitutively expressed at disease onset and in healthy joints. NF-κB1 transcript levels increased 2-fold in hTNF-α paws with established disease (12 weeks), followed by a 2-fold increase in NR4A2 at the late disease stage (19 weeks). NR4A2 and RelA proteins were overexpressed in inflamed synovium prior to symptoms of arthritis, suggesting that gene expression changes documented in whole paws were largely driven by elevated expression in diseased synovium. Broader screening of RA-related genes by RT-qPCR identified several differentially expressed genes in hTNF-α joints including those encoding inflammatory cytokines and chemokines, matrix-degrading enzymes and inhibitors, cell surface receptors, intracellular signaling proteins and transcription factors. Consensus binding sites for NR4A receptors and NF-κB1 were enriched in the promoters of differentially expressed genes suggesting central roles for these transcription factors in this model. This study is the first comprehensive analysis of NR4A2 in an animal model of RA and validates the hTNF-α model for testing of small molecules and genetic strategies targeting this transcription factor.
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Affiliation(s)
- Cullen M Lilley
- Department of Biological Sciences, Loyola University New Orleans, New Orleans, LA, United States
| | - Andrea Alarcon
- Department of Biological Sciences, Loyola University New Orleans, New Orleans, LA, United States
| | - My-Huyen Ngo
- Department of Biological Sciences, Loyola University New Orleans, New Orleans, LA, United States
| | - Jackeline S Araujo
- Department of Biological Sciences, Loyola University New Orleans, New Orleans, LA, United States
| | - Luis Marrero
- Department of Orthopaedic Surgery, Louisiana State University Health Sciences Center, New Orleans, LA, United States
| | - Kimberlee S Mix
- Department of Biological Sciences, Loyola University New Orleans, New Orleans, LA, United States
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Papadopoulou D, Drakopoulos A, Lagarias P, Melagraki G, Kollias G, Afantitis A. In Silico Identification and Evaluation of Natural Products as Potential Tumor Necrosis Factor Function Inhibitors Using Advanced Enalos Asclepios KNIME Nodes. Int J Mol Sci 2021; 22:10220. [PMID: 34638561 PMCID: PMC8508374 DOI: 10.3390/ijms221910220] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Revised: 09/10/2021] [Accepted: 09/17/2021] [Indexed: 12/26/2022] Open
Abstract
Tumor necrosis factor (TNF) is a regulator of several chronic inflammatory diseases, such as rheumatoid arthritis. Although anti-TNF biologics have been used in clinic, they render several drawbacks, such as patients' progressive immunodeficiency and loss of response, high cost, and intravenous administration. In order to find new potential anti-TNF small molecule inhibitors, we employed an in silico approach, aiming to find natural products, analogs of Ampelopsin H, a compound that blocks the formation of TNF active trimer. Two out of nine commercially available compounds tested, Nepalensinol B and Miyabenol A, efficiently reduced TNF-induced cytotoxicity in L929 cells and production of chemokines in mice joints' synovial fibroblasts, while Nepalensinol B also abolished TNF-TNFR1 binding in non-toxic concentrations. The binding mode of the compounds was further investigated by molecular dynamics and free energy calculation studies, using and advancing the Enalos Asclepios pipeline. Conclusively, we propose that Nepalensinol B, characterized by the lowest free energy of binding and by a higher number of hydrogen bonds with TNF, qualifies as a potential lead compound for TNF inhibitors' drug development. Finally, the upgraded Enalos Asclepios pipeline can be used for improved identification of new therapeutics against TNF-mediated chronic inflammatory diseases, providing state-of-the-art insight on their binding mode.
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Affiliation(s)
- Dimitra Papadopoulou
- Biomedical Sciences Research Center "Alexander Fleming", Institute for Bioinnovation, 16672 Vari, Greece
- Department of Physiology, Medical School, National and Kapodistrian University of Athens, 11527 Athens, Greece
| | | | | | - Georgia Melagraki
- Division of Physical Sciences and Applications, Hellenic Military Academy, 16673 Vari, Greece
| | - George Kollias
- Biomedical Sciences Research Center "Alexander Fleming", Institute for Bioinnovation, 16672 Vari, Greece
- Department of Physiology, Medical School, National and Kapodistrian University of Athens, 11527 Athens, Greece
- Center of New Biotechnologies & Precision Medicine, National and Kapodistrian University of Athens Medical School, 11527 Athens, Greece
- Joint Rheumatology Program, National and Kapodistrian University of Athens Medical School, 11527 Athens, Greece
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Zhao Y, Hasse S, Bourgoin SG. Phosphatidylserine-specific phospholipase A1: A friend or the devil in disguise. Prog Lipid Res 2021; 83:101112. [PMID: 34166709 DOI: 10.1016/j.plipres.2021.101112] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Revised: 04/30/2021] [Accepted: 06/18/2021] [Indexed: 02/06/2023]
Abstract
Various human tissues and cells express phospholipase A1 member A (PLA1A), including the liver, lung, prostate gland, and immune cells. The enzyme belongs to the pancreatic lipase family. PLA1A specifically hydrolyzes sn-1 fatty acid of phosphatidylserine (PS) or 1-acyl-lysophosphatidylserine (1-acyl-lysoPS). PS externalized by activated cells or apoptotic cells or extracellular vesicles is a potential source of substrate for the production of unsaturated lysoPS species by PLA1A. Maturation and functions of many immune cells, such as T cells, dendritic cells, macrophages, and mast cells, can be regulated by PLA1A and lysoPS. Several lysoPS receptors, including GPR34, GPR174 and P2Y10, have been identified. High serum levels and high PLA1A expression are associated with autoimmune disorders such as Graves' disease and systemic lupus erythematosus. Increased expression of PLA1A is associated with metastatic melanomas. PLA1A may contribute to cardiometabolic disorders through mediating cholesterol transportation and producing lysoPS. Furthermore, PLA1A is necessary for hepatitis C virus assembly and can play a role in the antivirus innate immune response. This review summarizes recent findings on PLA1A expression, lysoPS and lysoPS receptors in autoimmune disorders, cancers, cardiometabolic disorders, antivirus immune responses, as well as regulations of immune cells.
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Affiliation(s)
- Yang Zhao
- Centre de recherche du CHU de Québec-Université Laval, Centre ARThrite de l'Université Laval, Département de microbiologie-infectiologie et d'immunologie, Université Laval, Québec, G1V 4G2, Canada
| | - Stephan Hasse
- Centre de recherche du CHU de Québec-Université Laval, Centre ARThrite de l'Université Laval, Département de microbiologie-infectiologie et d'immunologie, Université Laval, Québec, G1V 4G2, Canada
| | - Sylvain G Bourgoin
- Centre de recherche du CHU de Québec-Université Laval, Centre ARThrite de l'Université Laval, Département de microbiologie-infectiologie et d'immunologie, Université Laval, Québec, G1V 4G2, Canada.
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Ntari L, Nikolaou C, Kranidioti K, Papadopoulou D, Christodoulou-Vafeiadou E, Chouvardas P, Meier F, Geka C, Denis MC, Karagianni N, Kollias G. Combination of subtherapeutic anti-TNF dose with dasatinib restores clinical and molecular arthritogenic profiles better than standard anti-TNF treatment. J Transl Med 2021; 19:165. [PMID: 33892739 PMCID: PMC8063445 DOI: 10.1186/s12967-021-02764-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Accepted: 02/22/2021] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND New medications for Rheumatoid Arthritis (RA) have emerged in the last decades, including Disease Modifying Antirheumatic Drugs (DMARDs) and biologics. However, there is no known cure, since a significant proportion of patients remain or become non-responders to current therapies. The development of new mode-of-action treatment schemes involving combination therapies could prove successful for the treatment of a greater number of RA patients. METHODS We investigated the effect of the Tyrosine Kinase inhibitors (TKIs) dasatinib and bosutinib, on the human TNF-dependent Tg197 arthritis mouse model. The inhibitors were administered either as a monotherapy or in combination with a subtherapeutic dose of anti-hTNF biologics and their therapeutic effect was assessed clinically, histopathologically as well as via gene expression analysis and was compared to that of an efficient TNF monotherapy. RESULTS Dasatinib and, to a lesser extent, bosutinib inhibited the production of TNF and proinflammatory chemokines from arthritogenic synovial fibroblasts. Dasatinib, but not bosutinib, also ameliorated significantly and in a dose-dependent manner both the clinical and histopathological signs of Tg197 arthritis. Combination of dasatinib with a subtherapeutic dose of anti-hTNF biologic agents, resulted in a synergistic inhibitory effect abolishing all arthritis symptoms. Gene expression analysis of whole joint tissue of Tg197 mice revealed that the combination of dasatinib with a low subtherapeutic dose of Infliximab most efficiently restores the pathogenic gene expression profile to that of the healthy state compared to either treatment administered as a monotherapy. CONCLUSION Our findings show that dasatinib exhibits a therapeutic effect in TNF-driven arthritis and can act in synergy with a subtherapeutic anti-hTNF dose to effectively treat the clinical and histopathological signs of the pathology. The combination of dasatinib and anti-hTNF exhibits a distinct mode of action in restoring the arthritogenic gene signature to that of a healthy profile. Potential clinical applications of combination therapies with kinase inhibitors and anti-TNF agents may provide an interesting alternative to high-dose anti-hTNF monotherapy and increase the number of patients responding to treatment.
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Affiliation(s)
| | - Christoforos Nikolaou
- Institute for Bioinnovation, Biomedical Sciences Research Center (BSRC), Alexander Fleming, 34 Alexander Fleming Street, 16672, Vari, Greece
| | | | - Dimitra Papadopoulou
- Institute for Bioinnovation, Biomedical Sciences Research Center (BSRC), Alexander Fleming, 34 Alexander Fleming Street, 16672, Vari, Greece
| | | | - Panagiotis Chouvardas
- Department of Medical Oncology, Inselspital, University Hospital and University of Bern, Bern, Switzerland
- Department for BioMedical Research (DBMR), University of Bern, Bern, Switzerland
| | - Florian Meier
- Division of Rheumatology, University Hospital Frankfurt, Goethe University, Frankfurt am Main, Germany
- Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Project Group Translational Medicine and Pharmacology TMP, Frankfurt am Main, Germany
| | | | | | | | - George Kollias
- Institute for Bioinnovation, Biomedical Sciences Research Center (BSRC), Alexander Fleming, 34 Alexander Fleming Street, 16672, Vari, Greece.
- Department of Physiology and Joint Rheumatology Program, School of Medicine, National and Kapodistrian University of Athens, Athens, Greece.
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Alolga RN, Opoku-Damoah Y, Alagpulinsa DA, Huang FQ, Ma G, Chavez Leon MASC, Kudzai C, Yin X, Ding Y. Metabolomic and transcriptomic analyses of the anti-rheumatoid arthritis potential of xylopic acid in a bioinspired lipoprotein nanoformulation. Biomaterials 2020; 268:120482. [PMID: 33307367 DOI: 10.1016/j.biomaterials.2020.120482] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Revised: 09/18/2020] [Accepted: 10/18/2020] [Indexed: 02/06/2023]
Abstract
Xylopic acid (XA), a diterpene kaurene and the major active ingredient of the African spice Xylopia aethiopica (Annonaceae), is reported to possess anti-inflammatory and analgesic properties. Here, we investigated the therapeutic potential of XA for rheumatoid arthritis (RA), a debilitating autoimmune inflammatory disease characterized by joint damage, in the complete Freund's adjuvant (CFA)-induced arthritis model in rats. We synthesized bioinspired reconstituted high-density lipoprotein (rHDL) nanoparticles loaded with purified XA crystals (rHDL/XA) that passively accumulate in inflamed joints of CFA-induced arthritic rats. Treatment with rHDL/XA minimized mononuclear cell infiltration of CFA-induced arthritic sites and ameliorated disease burden. Metabolomic and transcriptomic analyses revealed that the major molecular pathways perturbed following CFA-induced arthritis correlated with amino acid and lipid metabolism, which were restored to normal states by rHDL/XA treatment. This work demonstrates the anti-RA potential of XA in a nanoformulation and uncovers its underlying therapeutic mechanisms at the transcript and metabolite levels.
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Affiliation(s)
- Raphael N Alolga
- State Key Laboratory of Natural Medicines, Clinical Metabolomics Center, School of Traditional Chinese Pharmacy, China Pharmaceutical University, No. 639 Longmian Avenue, Nanjing, 211198, China
| | - Yaw Opoku-Damoah
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane, Qld, 4072, Australia
| | - David A Alagpulinsa
- Massachusetts General Hospital Vaccine & Immunotherapy Center, Harvard Medical School, Boston, MA, 02129, USA
| | - Feng-Qing Huang
- State Key Laboratory of Natural Medicines, Clinical Metabolomics Center, School of Traditional Chinese Pharmacy, China Pharmaceutical University, No. 639 Longmian Avenue, Nanjing, 211198, China
| | - Gaoxiang Ma
- State Key Laboratory of Natural Medicines, Clinical Metabolomics Center, School of Traditional Chinese Pharmacy, China Pharmaceutical University, No. 639 Longmian Avenue, Nanjing, 211198, China
| | - Maria A S C Chavez Leon
- State Key Laboratory of Natural Medicines, Clinical Metabolomics Center, School of Traditional Chinese Pharmacy, China Pharmaceutical University, No. 639 Longmian Avenue, Nanjing, 211198, China
| | - Chifodya Kudzai
- State Key Laboratory of Natural Medicines, Clinical Metabolomics Center, School of Traditional Chinese Pharmacy, China Pharmaceutical University, No. 639 Longmian Avenue, Nanjing, 211198, China
| | - Xiaojian Yin
- State Key Laboratory of Natural Medicines, Clinical Metabolomics Center, School of Traditional Chinese Pharmacy, China Pharmaceutical University, No. 639 Longmian Avenue, Nanjing, 211198, China.
| | - Yang Ding
- State Key Laboratory of Natural Medicines, Department of Pharmaceutics, China Pharmaceutical University, 24 Tongjiaxiang, Nanjing, 210009, China.
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A Systematic Review Comparing Experimental Design of Animal and Human Methotrexate Efficacy Studies for Rheumatoid Arthritis: Lessons for the Translational Value of Animal Studies. Animals (Basel) 2020; 10:ani10061047. [PMID: 32560528 PMCID: PMC7341304 DOI: 10.3390/ani10061047] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Revised: 06/11/2020] [Accepted: 06/12/2020] [Indexed: 12/15/2022] Open
Abstract
Simple Summary If we want to use animal studies to predict what will happen if we give a drug to humans, it makes sense to perform the animal studies as similarly to human studies as possible. For example, if animal tests of a drug only look at the effect of injecting the drug in young healthy animals, we cannot expect the results to be similar in human tests giving tablets to older patients who may have other diseases besides the one for which they receive the drug. We did an in-depth analysis of how 147 animal and 512 human studies of the drug methotrexate for rheumatoid arthritis were performed. Important differences were present, for example, animal studies used more males, while rheumatoid arthritis occurs more in females. We calculated the human-equivalent age of the animals, and they were on average younger than humans. Many studies did not fully report the way the experiments were performed. In spite of these differences, the drug methotrexate works well against rheumatoid arthritis in animal models and humans. Further (literature) research is still needed; we do not yet understand when we can reliably predict human effects from animal studies. Abstract Increased awareness and understanding of current practices in translational research is required for informed decision making in drug development. This paper describes a systematic review of methotrexate for rheumatoid arthritis, comparing trial design between 147 animal and 512 human studies. Animal studies generally included fewer subjects than human studies, and less frequently reported randomisation and blinding. In relation to life span, study duration was comparable for animals and humans, but included animals were younger than included humans. Animal studies often comprised males only (61%), human studies always included females (98% included both sexes). Power calculations were poorly reported in both samples. Analyses of human studies more frequently comprised Chi-square tests, those of animal studies more frequently reported analyses of variance. Administration route was more variable, and more frequently reported in animal than human studies. Erythrocyte sedimentation rate and c-reactive protein were analysed more frequently in human than in animal studies. To conclude, experimental designs for animal and human studies are not optimally aligned. However, methotrexate is effective in treating rheumatoid arthritis in animal models and humans. Further evaluation of the available evidence in other research fields is needed to increase the understanding of translational success before we can optimise translational strategies.
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Avila-Portillo LM, Aristizabal F, Perdomo S, Riveros A, Ospino B, Avila JP, Butti M, Abba MC. Comparative Analysis of the Biosimilar and Innovative G-CSF Modulated Pathways on Umbilical Cord Blood-Derived Mononuclear Cells. Bioinform Biol Insights 2020; 14:1177932220913307. [PMID: 32231428 PMCID: PMC7088127 DOI: 10.1177/1177932220913307] [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: 02/16/2020] [Accepted: 02/25/2020] [Indexed: 01/07/2023] Open
Abstract
Biosimilars of granulocyte colony-stimulating factor (G-CSF) have been routinely introduced into clinical practice. However, not functional genomics characterization has been performed yet in comparison with the innovator G-CSF. This study aimed to evaluate the transcriptomic changes in an in vitro model of umbilical cord blood cells (UBC) exposed to G-CSF for the identification of their modulated pathways. Umbilical cord blood cells-derived mononuclear cells (MNCs) were treated with biosimilar and innovator G-CSF for further gene expression profiling analysis using a microarray-based platform. Comparative analysis of biosimilar and innovator G-CSF gene expression signatures allowed us to identify the most commonly modulated pathways by both drugs. In brief, we observed predominantly upmodulation of transcripts related to PI3K-Akt, NF-kappaB, and tumor necrosis factor (TNF) signaling pathways as well as transcripts related to negative regulation of apoptotic process among others. In addition, hematopoietic colony-forming cell assays corroborate the G-CSF phenotypic effects over UBC-derived MNCs. In conclusion, our study suggests that G-CSF impacts UBC-derived cells through the modulation of several signaling pathways associated with cell survival, migration, and proliferation. The concordance observed between biosimilar and innovator G-CSF emphasizes their similarity in regards to their specificity and biological responses.
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Affiliation(s)
- L M Avila-Portillo
- Departamento de Farmacia, Universidad Nacional de Colombia, Bogotá, Colombia.,Stem Medicina Regenerativa/CryoHoldco, Bogotá, Colombia.,Unidad de Investigación, Hospital Militar Central, Bogotá, Colombia
| | - F Aristizabal
- Departamento de Farmacia, Universidad Nacional de Colombia, Bogotá, Colombia
| | - S Perdomo
- Facultad de Odontología, Universidad El Bosque, Bogotá, Colombia
| | - A Riveros
- Stem Medicina Regenerativa/CryoHoldco, Bogotá, Colombia
| | - B Ospino
- Stem Medicina Regenerativa/CryoHoldco, Bogotá, Colombia
| | - J P Avila
- Stem Medicina Regenerativa/CryoHoldco, Bogotá, Colombia
| | - M Butti
- CINIBA-CIC-PBA, Facultad de Ciencias Médicas, Universidad Nacional de La Plata, La Plata, Argentina
| | - M C Abba
- CINIBA-CIC-PBA, Facultad de Ciencias Médicas, Universidad Nacional de La Plata, La Plata, Argentina
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Monitoring the prolonged Tnf stimulation in space and time with topological-functional networks. Comput Struct Biotechnol J 2020; 18:220-229. [PMID: 32021663 PMCID: PMC6994266 DOI: 10.1016/j.csbj.2020.01.001] [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: 10/15/2019] [Revised: 12/18/2019] [Accepted: 01/03/2020] [Indexed: 11/21/2022] Open
Abstract
Genes in linear proximity often share regulatory inputs, expression and evolutionary patterns, even in complex eukaryote genomes with extensive intergenic sequences. Gene regulation, on the other hand, is effected through the co-ordinated activation (or suppression) of genes participating in common biological pathways, which are often transcribed from distant loci. Existing approaches for the study of gene expression focus on the functional aspect, taking positional constraints into account only marginally. In this work we propose a novel concept for the study of gene expression, through the combination of topological and functional information into bipartite networks. Starting from genome-wide expression profiles, we define extended chromosomal regions with consistent patterns of differential gene expression and then associate these domains with enriched functional pathways. By analyzing the resulting networks in terms of size, connectivity and modularity we can draw conclusions on the way genome organization may underlie the gene regulation program. Implementation of this approach in a detailed RNASeq profiling of sustained Tnf stimulation of mouse synovial fibroblasts, allowed us to identify unexpected regulatory changes taking place in the cells after 24 h of stimulation. Bipartite network analysis suggests that the cytokine response set by Tnf, progresses through two distinct transitions. An early generalization of the inflammatory response, that is followed by a late shutdown of immune-related functions and the redistribution of expression to developmental and cell adhesion pathways and distinct chromosomal regions. We show that the incorporation of topological information may provide additional insights in the complex propagation of Tnf activation.
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Machaj F, Rosik J, Szostak B, Pawlik A. The evolution in our understanding of the genetics of rheumatoid arthritis and the impact on novel drug discovery. Expert Opin Drug Discov 2019; 15:85-99. [PMID: 31661990 DOI: 10.1080/17460441.2020.1682992] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Introduction: Rheumatoid arthritis (RA) is an autoimmune disease that is characterized by chronic inflammation of the joints and affects 1% of the population. Polymorphisms of genes that encode proteins that primarily participate in inflammation may influence RA occurrence or become useful biomarkers for certain types of anti-rheumatic treatment.Areas covered: The authors summarize the recent progress in our understanding of the genetics of RA. In the last few years, multiple variants of genes that are associated with RA risk have been identified. The development of new technologies and the detection of new potential therapeutic targets that contribute to novel drug discovery are also described.Expert opinion: There is still the need to search for new genes which may be a potential target for RA therapy. The challenge is to develop appropriate strategies for achieving insight into the molecular pathways involved in RA pathogenesis. Understanding the genetics, immunogenetics, epigenetics and immunology of RA could help to identify new targets for RA therapy. The development of new technologies has enabled the detection of a number of new genes, particularly genes associated with proinflammatory cytokines and chemokines, B- and T-cell activation pathways, signal transducers and transcriptional activators, which might be potential therapeutic targets in RA.
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Affiliation(s)
- Filip Machaj
- Department of Physiology, Pomeranian Medical University, Szczecin, Poland
| | - Jakub Rosik
- Department of Physiology, Pomeranian Medical University, Szczecin, Poland
| | - Bartosz Szostak
- Department of Physiology, Pomeranian Medical University, Szczecin, Poland
| | - Andrzej Pawlik
- Department of Physiology, Pomeranian Medical University, Szczecin, Poland
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Gabay O, Vicenty J, Zack-Taylor A, Tiffany L, Wunderlin G, Smith D, Reyes-Munoz L, Edwards V, Wu WW, Phue JN, Santana-Quintero L, Lam PV, Clouse KA. Exposure to TNF antagonist therapies induces variations of the gut microbiota in an in vivo model using healthy mice. Joint Bone Spine 2019; 87:175-178. [PMID: 31513888 DOI: 10.1016/j.jbspin.2019.08.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2019] [Accepted: 08/29/2019] [Indexed: 12/26/2022]
Affiliation(s)
- Odile Gabay
- U.S. Food and Drug Administration, Center for Drug Evaluation and Research, Division of Biotechnology Review and Research 1, Silver Spring, MD, USA.
| | - Jonathan Vicenty
- U.S. Food and Drug Administration, Center for Drug Evaluation and Research, Division of Biotechnology Review and Research 1, Silver Spring, MD, USA
| | - Autumn Zack-Taylor
- U.S. Food and Drug Administration, Center for Drug Evaluation and Research, Division of Biotechnology Review and Research 1, Silver Spring, MD, USA
| | - Linda Tiffany
- U.S. Food and Drug Administration, Center for Drug Evaluation and Research, Division of Biotechnology Review and Research 1, Silver Spring, MD, USA
| | - Grant Wunderlin
- U.S. Food and Drug Administration, Center for Drug Evaluation and Research, Division of Biotechnology Review and Research 1, Silver Spring, MD, USA
| | - Dylan Smith
- U.S. Food and Drug Administration, Center for Drug Evaluation and Research, Division of Biotechnology Review and Research 1, Silver Spring, MD, USA
| | - Lismari Reyes-Munoz
- U.S. Food and Drug Administration, Center for Drug Evaluation and Research, Division of Biotechnology Review and Research 1, Silver Spring, MD, USA
| | - Vivienne Edwards
- U.S. Food and Drug Administration, Center for Drug Evaluation and Research, Division of Biotechnology Review and Research 1, Silver Spring, MD, USA
| | - Wells W Wu
- U.S. Food and Drug Administration, Center for Biologicals Evaluation and Research, Facility for Biotechnology Resources, Silver Spring, MD, USA
| | - Je-Nie Phue
- U.S. Food and Drug Administration, Center for Biologicals Evaluation and Research, Facility for Biotechnology Resources, Silver Spring, MD, USA
| | - Luis Santana-Quintero
- U.S. Food and Drug Administration, Center for Drug Evaluation and Research, Office of New Drugs, Office of Hematology and Oncology Products, Silver Spring, MD, USA
| | - Phuc VinhNguyen Lam
- U.S. Food and Drug Administration, Center for Biologics Evaluation and Research, Office of Biostatistics and Epidemiology, HIVE, Silver Spring, MD, USA
| | - Kathleen A Clouse
- U.S. Food and Drug Administration, Center for Drug Evaluation and Research, Division of Biotechnology Review and Research 1, Silver Spring, MD, USA
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