1
|
Debad S, Allen D, Bandele O, Bishop C, Blaylock M, Brown P, Bunger MK, Co JY, Crosby L, Daniel AB, Ferguson SS, Ford K, Gamboa da Costa G, Gilchrist KH, Grogg MW, Gwinn M, Hartung T, Hogan SP, Jeong YE, Kass GE, Kenyon E, Kleinstreuer NC, Kujala V, Lundquist P, Matheson J, McCullough SD, Melton-Celsa A, Musser S, Oh I, Oyetade OB, Patil SU, Petersen EJ, Sadrieh N, Sayes CM, Scruggs BS, Tan YM, Thelin B, Nelson MT, Tarazona JV, Wambaugh JF, Yang JY, Yu C, Fitzpatrick S. Trust your gut: Establishing confidence in gastrointestinal models - An overview of the state of the science and contexts of use. ALTEX 2024; 41:402-424. [PMID: 38898799 PMCID: PMC11413798 DOI: 10.14573/altex.2403261] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2024] [Indexed: 06/21/2024]
Abstract
The webinar series and workshop titled “Trust Your Gut: Establishing Confidence in Gastrointestinal Models – An Overview of the State of the Science and Contexts of Use” was co-organized by NICEATM, NIEHS, FDA, EPA, CPSC, DoD, and the Johns Hopkins Center for Alternatives to Animal Testing (CAAT) and hosted at the National Institutes of Health in Bethesda, MD, USA on October 11-12, 2023. New approach methods (NAMs) for assessing issues of gastrointestinal tract (GIT)- related toxicity offer promise in addressing some of the limitations associated with animal-based assessments. GIT NAMs vary in complexity, from two-dimensional monolayer cell line-based systems to sophisticated 3-dimensional organoid systems derived from human primary cells. Despite advances in GIT NAMs, challenges remain in fully replicating the complex interactions and processes occurring within the human GIT. Presentations and discussions addressed regulatory needs, challenges, and innovations in incorporating NAMs into risk assessment frameworks; explored the state of the science in using NAMs for evaluating systemic toxicity, understanding absorption and pharmacokinetics, evaluating GIT toxicity, and assessing potential allergenicity; and discussed strengths, limitations, and data gaps of GIT NAMs as well as steps needed to establish confidence in these models for use in the regulatory setting.
Collapse
Affiliation(s)
| | | | - Omari Bandele
- Center for Food Safety and Applied Nutrition, College Park, MD, USA
| | - Colin Bishop
- Wake Forest Institute for Regenerative Medicine, Winston Salem, NC, USA
| | | | - Paul Brown
- Center for Drug Evaluation and Research, US Food and Drug Administration, Silver Spring, MD, USA
| | | | - Julia Y Co
- Complex in vitro Systems, Genentech Inc, South San Francisco, CA, USA
| | - Lynn Crosby
- Center for Food Safety and Applied Nutrition, College Park, MD, USA
| | | | - Steve S Ferguson
- Mechanistic Toxicology Branch, Division of Translational Toxicology, NIEHS, National Institutes of Health, Bethesda, MD, USA
| | - Kevin Ford
- Office of Clinical Pharmacology, US Food and Drug Administration, Silver Spring, MD, USA
| | - Gonçalo Gamboa da Costa
- FDA National Center for Toxicological Research, US Food and Drug Administration, Jefferson, AR, USA
| | - Kristin H Gilchrist
- 4D Bio³ Center for Biotechnology, Uniformed Services University, Bethesda, MD, USA
| | - Matthew W Grogg
- 711th Human Performance Wing, Air Force Research Laboratory, Wright-Patterson AFB, OH, USA
| | - Maureen Gwinn
- U.S. Environmental Protection Agency, Office of Research and Development, RTP, NC, USA
| | - Thomas Hartung
- Johns Hopkins University, Bloomberg School of Public Health and Whiting School of Engineering, Doerenkamp-Zbinden-Chair for Evidence-based Toxicology, Center for Alternatives to Animal Testing (CAAT), Baltimore, MD, USA
- University of Konstanz, CAAT-Europe, Konstanz, Germany
| | - Simon P Hogan
- Mary H. Weiser Food Allergy Center, Department of Pathology, Michigan Medicine, University of Michigan, Ann Arbor, MI, USA
| | - Ye Eun Jeong
- Division of Applied Regulatory Science, Office of Clinical Pharmacology, Center for Drug Evaluation and Research, U.S. Food and Drug Administration, Silver Spring, MD, USA
| | | | - Elaina Kenyon
- U.S. Environmental Protection Agency, Office of Research and Development, RTP, NC, USA
| | | | | | | | | | | | - Angela Melton-Celsa
- Department of Microbiology and Immunology, Uniformed Services University, Bethesda, MD, USA
| | - Steven Musser
- Center for Food Safety and Applied Nutrition, College Park, MD, USA
| | - Ilung Oh
- Toxicology Research Division, Ministry of Food and Drug Safety, National Institute of Food and Drug Safety Evaluation, Republic of Korea
| | | | - Sarita U Patil
- Divisions of Allergy and Clinical Immunology, Departments of Medicine and Pediatrics, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Elijah J Petersen
- Biosystems and Biomaterials Division, National Institute of Standards and Technology, Gaithersburg, MD, USA
| | - Nakissa Sadrieh
- Center for Food Safety and Applied Nutrition, College Park, MD, USA
| | - Christie M Sayes
- Department of Environmental Science, Baylor University, Waco, TX, USA
| | | | - Yu-Mei Tan
- U.S. Environmental Protection Agency, Office of Pesticide Programs, Research Triangle Park, NC, USA
| | - Bill Thelin
- Altis Biosystems, Inc. Research Triangle Park, NC, USA
| | - M Tyler Nelson
- 711th Human Performance Wing, Air Force Research Laboratory, Wright-Patterson AFB, OH, USA
| | - José V Tarazona
- Spanish National Environmental Health Centre, Instituto de Salud Carlos III. Madrid, Spain
| | - John F Wambaugh
- U.S. Environmental Protection Agency, Office of Research and Development, RTP, NC, USA
| | - Jun-Young Yang
- Toxicology Research Division, Ministry of Food and Drug Safety, National Institute of Food and Drug Safety Evaluation, Cheongju, Republic of Korea
| | - Changwoo Yu
- Toxicology Research Division, Ministry of Food and Drug Safety, National Institute of Food and Drug Safety Evaluation, Cheongju, Republic of Korea
| | | |
Collapse
|
2
|
Ludwik KA, Greathouse FR, Han S, Stauffer K, Brenin DR, Stricker TP, Lannigan DA. Identifying the effectiveness of 3D culture systems to recapitulate breast tumor tissue in situ. Cell Oncol (Dordr) 2024; 47:481-496. [PMID: 37776423 PMCID: PMC11090829 DOI: 10.1007/s13402-023-00877-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/16/2023] [Indexed: 10/02/2023] Open
Abstract
PURPOSE Breast cancer heterogeneity contributes to chemotherapy resistance and decreased patient survival. To improve patient outcomes it is essential to develop a technology that is able to rapidly select the most efficacious therapy that targets the diverse phenotypes present within the tumor. Breast cancer organoid technologies are proposed as an attractive approach for evaluating drug responses prior to patient therapy. However, there remain challenges in evaluating the effectiveness of organoid cultures to recapitulate the heterogeneity present in the patient tumor in situ. METHOD Organoids were generated from seven normal breast and nineteen breast cancer tissues diagnosed as estrogen receptor positive or triple negative. The Jensen-Shannon divergence index, a measure of the similarity between distributions, was used to compare and evaluate heterogeneity in starting tissue and their resultant organoids. Heterogeneity was analyzed using cytokeratin 8 and cytokeratin 14, which provided an easily scored readout. RESULTS In the in vitro culture system HER1 and FGFR were able to drive intra-tumor heterogeneity to generate divergent phenotypes that have different sensitivities to chemotherapies. CONCLUSION Our methodology, which focuses on quantifiable cellular phenotypes, provides a tractable system that complements omics approaches to provide an unprecedented view of heterogeneity and will enhance the identification of novel therapies and facilitate personalized medicine.
Collapse
Affiliation(s)
- Katarzyna A Ludwik
- Department Pathology, Microbiology & Immunology, Vanderbilt University Medical Center, Nashville, TN, 37232, USA
| | - Frances R Greathouse
- Department Pathology, Microbiology & Immunology, Vanderbilt University Medical Center, Nashville, TN, 37232, USA
| | | | - Kimberly Stauffer
- Department Pathology, Microbiology & Immunology, Vanderbilt University Medical Center, Nashville, TN, 37232, USA
| | - David R Brenin
- Department Surgery, University of Virginia, Charlottesville, VA, 22908, USA
| | - Thomas P Stricker
- Department Pathology, Microbiology & Immunology, Vanderbilt University Medical Center, Nashville, TN, 37232, USA
| | - Deborah A Lannigan
- Department Pathology, Microbiology & Immunology, Vanderbilt University Medical Center, Nashville, TN, 37232, USA.
- Department Biomedical Engineering, Vanderbilt University, Nashville, TN, 37235, USA.
| |
Collapse
|
3
|
Cable J, Lutolf MP, Fu J, Park SE, Apostolou A, Chen S, Song CJ, Spence JR, Liberali P, Lancaster M, Meier AB, Pek NMQ, Wells JM, Capeling MM, Uzquiano A, Musah S, Huch M, Gouti M, Hombrink P, Quadrato G, Urenda JP. Organoids as tools for fundamental discovery and translation-a Keystone Symposia report. Ann N Y Acad Sci 2022; 1518:196-208. [PMID: 36177906 PMCID: PMC11293861 DOI: 10.1111/nyas.14874] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Complex three-dimensional in vitro organ-like models, or organoids, offer a unique biological tool with distinct advantages over two-dimensional cell culture systems, which can be too simplistic, and animal models, which can be too complex and may fail to recapitulate human physiology and pathology. Significant progress has been made in driving stem cells to differentiate into different organoid types, though several challenges remain. For example, many organoid models suffer from high heterogeneity, and it can be difficult to fully incorporate the complexity of in vivo tissue and organ development to faithfully reproduce human biology. Successfully addressing such limitations would increase the viability of organoids as models for drug development and preclinical testing. On April 3-6, 2022, experts in organoid development and biology convened at the Keystone Symposium "Organoids as Tools for Fundamental Discovery and Translation" to discuss recent advances and insights from this relatively new model system into human development and disease.
Collapse
Affiliation(s)
| | - Matthias P Lutolf
- Laboratory of Stem Cell Bioengineering, Institute of Bioengineering, School of Life Sciences (SV) and School of Engineering (STI), Lausanne, Switzerland
- Institute of Chemical Sciences and Engineering, School of Basic Science (SB), Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
- Roche Institute for Translational Bioengineering (ITB), Pharma Research and Early Development (pRED), F. Hoffmann-La Roche Ltd, Basel, Switzerland
| | - Jianping Fu
- Department of Mechanical Engineering, University of Michigan, Ann Arbor, Michigan, USA
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, Michigan, USA
- Department of Cell & Developmental Biology, University of Michigan, Ann Arbor, Michigan, USA
| | - Sunghee Estelle Park
- Department of Bioengineering and NSF Science and Technology Center for Engineering Mechanobiology, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Athanasia Apostolou
- Emulate Inc, Boston, Massachusetts, USA
- Department of Medicine, National and Kapodistrian University of Athens, Athens, Greece
| | - Shuibing Chen
- Department of Surgery, Weill Cornell Medical College, New York City, New York, USA
| | - Cheng Jack Song
- Keck Medicine of University of Southern California, Los Angeles, California, USA
| | - Jason R Spence
- Department of Cell & Developmental Biology, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Prisca Liberali
- Friedrich Miescher Institute for Biomedical Research (FMI) and University of Basel, Basel, Switzerland
| | | | - Anna B Meier
- First Department of Medicine, Cardiology, Klinikum rechts der Isar, Technical University of Munich, School of Medicine and Health, Munich, Germany
| | - Nicole Min Qian Pek
- Center for Stem Cell and Organoid Medicine (CuSTOM), Cincinnati, Ohio, USA
- Division of Pulmonary Biology, Perinatal Institute, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA
- College of Medicine, University of Cincinnati, Cincinnati, Ohio, USA
| | - James M Wells
- Center for Stem Cell and Organoid Medicine (CuSTOM), Cincinnati, Ohio, USA
- Division of Developmental Biology and Division of Endocrinology, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA
| | - Meghan M Capeling
- Department of Biomedical Engineering, University of Michigan College of Engineering, Ann Arbor, Michigan, USA
| | - Ana Uzquiano
- Department of Stem Cell and Regenerative Biology, Harvard University
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Samira Musah
- Developmental and Stem Cell Biology Program and Division of Nephrology, Department of Medicine and Department of Cell Biology, Duke University School of Medicine, Durham, North Carolina, USA
- Center for Biomolecular and Tissue Engineering, Durham, North Carolina, USA
- Department of Biomedical Engineering, Pratt School of Engineering, Durham, North Carolina, USA
- Duke Regeneration Center, Duke University, Durham, North Carolina, USA
| | - Meritxell Huch
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Mina Gouti
- Stem Cell Modelling of Development & Disease Group, Max Delbrück Center for Molecular Medicine, Berlin, Germany
| | - Pleun Hombrink
- University Medical Center Utrecht and HUB Organoids, Utrecht, Netherlands
| | - Giorgia Quadrato
- Department of Stem Cell Biology and Regenerative Medicine, Keck School of Medicine and Eli and Edythe Broad CIRM Center for Regenerative Medicine and Stem Cell Research, University of Southern California, Los Angeles, California, USA
| | - Jean-Paul Urenda
- Department of Stem Cell Biology and Regenerative Medicine, Keck School of Medicine and Eli and Edythe Broad CIRM Center for Regenerative Medicine and Stem Cell Research, University of Southern California, Los Angeles, California, USA
| |
Collapse
|
4
|
Pediaditakis I, Kodella KR, Manatakis DV, Le CY, Barthakur S, Sorets A, Gravanis A, Ewart L, Rubin LL, Manolakos ES, Hinojosa CD, Karalis K. A microengineered Brain-Chip to model neuroinflammation in humans. iScience 2022; 25:104813. [PMID: 35982785 PMCID: PMC9379671 DOI: 10.1016/j.isci.2022.104813] [Citation(s) in RCA: 29] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Revised: 06/10/2022] [Accepted: 07/18/2022] [Indexed: 11/30/2022] Open
Abstract
Species differences in brain and blood-brain barrier (BBB) biology hamper the translation of findings from animal models to humans, impeding the development of therapeutics for brain diseases. Here, we present a human organotypic microphysiological system (MPS) that includes endothelial-like cells, pericytes, glia, and cortical neurons and maintains BBB permeability at in vivo relevant levels. This human Brain-Chip engineered to recapitulate critical aspects of the complex interactions that mediate neuroinflammation and demonstrates significant improvements in clinical mimicry compared to previously reported similar MPS. In comparison to Transwell culture, the transcriptomic profiling of the Brain-Chip displayed significantly advanced similarity to the human adult cortex and enrichment in key neurobiological pathways. Exposure to TNF-α recreated the anticipated inflammatory environment shown by glia activation, increased release of proinflammatory cytokines, and compromised barrier permeability. We report the development of a robust brain MPS for mechanistic understanding of cell-cell interactions and BBB function during neuroinflammation.
Collapse
Affiliation(s)
| | - Konstantia R. Kodella
- Emulate Inc., 27 Drydock Avenue, Boston, MA 02210, USA
- University of Crete Medical School, Department of Pharmacology, Heraklion, 71110 Greece
| | | | | | | | | | - Achille Gravanis
- University of Crete Medical School, Department of Pharmacology, Heraklion, 71110 Greece
| | - Lorna Ewart
- Emulate Inc., 27 Drydock Avenue, Boston, MA 02210, USA
| | - Lee L. Rubin
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA
- Harvard Stem Cell Institute, Cambridge, MA, USA
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, USA
| | - Elias S. Manolakos
- Department of Informatics and Telecommunications, National and Kapodistrian University of Athens, Greece
- Northeastern University, Bouvé College of Health Sciences, Boston, MA, USA
| | | | - Katia Karalis
- Emulate Inc., 27 Drydock Avenue, Boston, MA 02210, USA
- Endocrine Division, Children’s Hospital, Harvard Medical School, Boston, MA, USA
| |
Collapse
|
5
|
Fan Y, Han Q, Li J, Ye G, Zhang X, Xu T, Li H. Revealing potential diagnostic gene biomarkers of septic shock based on machine learning analysis. BMC Infect Dis 2022; 22:65. [PMID: 35045818 PMCID: PMC8772133 DOI: 10.1186/s12879-022-07056-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Accepted: 01/07/2022] [Indexed: 12/26/2022] Open
Abstract
Background Sepsis is an inflammatory response caused by infection with pathogenic microorganisms. The body shock caused by it is called septic shock. In view of this, we aimed to identify potential diagnostic gene biomarkers of the disease. Material and methods Firstly, mRNAs expression data sets of septic shock were retrieved and downloaded from the GEO (Gene Expression Omnibus) database for differential expression analysis. Functional enrichment analysis was then used to identify the biological function of DEmRNAs (differentially expressed mRNAs). Machine learning analysis was used to determine the diagnostic gene biomarkers for septic shock. Thirdly, RT-PCR (real-time polymerase chain reaction) verification was performed. Lastly, GSE65682 data set was utilized to further perform diagnostic and prognostic analysis of identified superlative diagnostic gene biomarkers. Results A total of 843 DEmRNAs, including 458 up-regulated and 385 down-regulated DEmRNAs were obtained in septic shock. 15 superlative diagnostic gene biomarkers (such as RAB13, KIF1B, CLEC5A, FCER1A, CACNA2D3, DUSP3, HMGN3, MGST1 and ARHGEF18) for septic shock were identified by machine learning analysis. RF (random forests), SVM (support vector machine) and DT (decision tree) models were used to construct classification models. The accuracy of the DT, SVM and RF models were very high. Interestingly, the RF model had the highest accuracy. It is worth mentioning that ARHGEF18 and FCER1A were related to survival. CACNA2D3 and DUSP3 participated in MAPK signaling pathway to regulate septic shock. Conclusion Identified diagnostic gene biomarkers may be helpful in the diagnosis and therapy of patients with septic shock. Supplementary Information The online version contains supplementary material available at 10.1186/s12879-022-07056-4.
Collapse
|
6
|
Pediaditakis I, Kodella KR, Manatakis DV, Le CY, Hinojosa CD, Tien-Street W, Manolakos ES, Vekrellis K, Hamilton GA, Ewart L, Rubin LL, Karalis K. Modeling alpha-synuclein pathology in a human brain-chip to assess blood-brain barrier disruption. Nat Commun 2021; 12:5907. [PMID: 34625559 PMCID: PMC8501050 DOI: 10.1038/s41467-021-26066-5] [Citation(s) in RCA: 94] [Impact Index Per Article: 31.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2020] [Accepted: 09/15/2021] [Indexed: 01/08/2023] Open
Abstract
Parkinson's disease and related synucleinopathies are characterized by the abnormal accumulation of alpha-synuclein aggregates, loss of dopaminergic neurons, and gliosis of the substantia nigra. Although clinical evidence and in vitro studies indicate disruption of the Blood-Brain Barrier in Parkinson's disease, the mechanisms mediating the endothelial dysfunction is not well understood. Here we leveraged the Organs-on-Chips technology to develop a human Brain-Chip representative of the substantia nigra area of the brain containing dopaminergic neurons, astrocytes, microglia, pericytes, and microvascular brain endothelial cells, cultured under fluid flow. Our αSyn fibril-induced model was capable of reproducing several key aspects of Parkinson's disease, including accumulation of phosphorylated αSyn (pSer129-αSyn), mitochondrial impairment, neuroinflammation, and compromised barrier function. This model may enable research into the dynamics of cell-cell interactions in human synucleinopathies and serve as a testing platform for target identification and validation of novel therapeutics.
Collapse
Affiliation(s)
- Iosif Pediaditakis
- Emulate Inc., 27 Drydock Avenue, Boston, MA, USA.
- Serqet Therapeutics, Inc. 55 Cambridge Parkway, Suite 800E, Boston, MA, 02142, USA.
| | | | | | | | | | | | - Elias S Manolakos
- Department of Informatics and Telecommunications, National and Kapodistrian University of Athens, Athens, Greece
- Northeastern University, Bouvé College of Health Sciences, Boston, MA, USA
| | - Kostas Vekrellis
- Biomedical Research Foundation of Academy of Athens, Athens, Greece
| | | | - Lorna Ewart
- Emulate Inc., 27 Drydock Avenue, Boston, MA, USA
| | - Lee L Rubin
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA
- Harvard Stem Cell Institute, Cambridge, MA, USA
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, USA
| | - Katia Karalis
- Emulate Inc., 27 Drydock Avenue, Boston, MA, USA.
- Endocrine Division, Children's Hospital, Harvard Medical School, Boston, MA, USA.
- Regeneron Pharmaceuticals, 777 Old Saw Mill River Rd, Tarrytown, NY, 10591, USA.
| |
Collapse
|
7
|
Zhang X, Cui Y, Ding X, Liu S, Han B, Duan X, Zhang H, Sun T. Analysis of mRNA‑lncRNA and mRNA‑lncRNA-pathway co‑expression networks based on WGCNA in developing pediatric sepsis. Bioengineered 2021; 12:1457-1470. [PMID: 33949285 PMCID: PMC8806204 DOI: 10.1080/21655979.2021.1908029] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
Pediatric sepsis is a great threat to death worldwide. However, the pathogenesis has not been clearly understood until now in sepsis. This study identified differentially expressed mRNAs and lncRNAs based on Gene Expression Omnibus (GEO) database. And the weighted gene co-expression network analysis (WGCNA) was performed to explore co-expression modules associated with pediatric sepsis. Then, Gene Ontology (GO), KEGG (Kyoto Encyclopedia of Genes and Genomes) pathway, mRNA‑lncRNA and mRNA‑lncRNA-pathway co-expression network analysis was conducted in selected significant module. A total of 1941 mRNAs and 225 lncRNAs were used to conduct WGCNA. And turquoise module was selected as a significant module that was associated with particular traits. The mRNAs functions associated with many vital processes were also shown by GO and KEGG pathway analysis in the turquoise module. Finally, 15 mRNAs (MAPK14, ITGAM, HK3, ALOX5, CR1, HCK, NCF4, PYGL, FLOT1, CARD6, NLRC4, SH3GLB1, PGS1, RAB31, LTB4R) and 4 lncRNAs (GSEC, NONHSAT160878.1, XR_926068.1 and RARA-AS1) were selected as hub genes in mRNA‑lncRNA-Pathway co-expression network. We identified 15 mRNAs and 4 lncRNAs as diagnostic markers, which have potential functions in pediatric sepsis. Our study provides more directions to study the molecular mechanism of pediatric sepsis.Abbreviations: mRNA: messenger RNA; lncRNA: long noncoding RNAs; GEO: Gene Expression Omnibus; WGCNA: weighted gene co-expression network analysis; GO: Gene Ontology; KEGG: Kyoto Encyclopedia of Genes and Genomes; SIRS: systemic inflammatory response syndrome; TOM: topological overlap measure; BP: biological process; MF: molecular function; CC: cellular component; ROC: receiver operating characteristic curve; AUC: area under curve; MAPK14: Mitogen-activated protein kinase 14; ALI: acute lung injury; ITGAM: Integrin subunit alpha M; HK3: Hexokinase 3; LPS: lipopolysaccharide; 5-LO: 5-lipoxygenase; LTs: leukotrienes; LTB4R: leukotriene B4 receptor.
Collapse
Affiliation(s)
- Xiaojuan Zhang
- General ICU, Zhengzhou Key Laboratory of Sepsis, Henan Engineering Research Center for Critical Care Medicine, the First Affiliated Hospital of Zhengzhou University, Henan Key Laboratory of Critical Care Medicine, Zhengzhou, China
| | - Yuqing Cui
- General ICU, Zhengzhou Key Laboratory of Sepsis, Henan Engineering Research Center for Critical Care Medicine, the First Affiliated Hospital of Zhengzhou University, Henan Key Laboratory of Critical Care Medicine, Zhengzhou, China
| | - Xianfei Ding
- General ICU, Zhengzhou Key Laboratory of Sepsis, Henan Engineering Research Center for Critical Care Medicine, the First Affiliated Hospital of Zhengzhou University, Henan Key Laboratory of Critical Care Medicine, Zhengzhou, China
| | - Shaohua Liu
- General ICU, Zhengzhou Key Laboratory of Sepsis, Henan Engineering Research Center for Critical Care Medicine, the First Affiliated Hospital of Zhengzhou University, Henan Key Laboratory of Critical Care Medicine, Zhengzhou, China
| | - Bing Han
- General ICU, Zhengzhou Key Laboratory of Sepsis, Henan Engineering Research Center for Critical Care Medicine, the First Affiliated Hospital of Zhengzhou University, Henan Key Laboratory of Critical Care Medicine, Zhengzhou, China
| | - Xiaoguang Duan
- General ICU, Zhengzhou Key Laboratory of Sepsis, Henan Engineering Research Center for Critical Care Medicine, the First Affiliated Hospital of Zhengzhou University, Henan Key Laboratory of Critical Care Medicine, Zhengzhou, China
| | - Haibo Zhang
- Interdepartmental Division of Critical Care Medicine, Departments of Anesthesia and Physiology, University of Toronto, Toronto, Canada
| | - Tongwen Sun
- General ICU, Zhengzhou Key Laboratory of Sepsis, Henan Engineering Research Center for Critical Care Medicine, the First Affiliated Hospital of Zhengzhou University, Henan Key Laboratory of Critical Care Medicine, Zhengzhou, China
| |
Collapse
|
8
|
Zeng X, Feng J, Yang Y, Zhao R, Yu Q, Qin H, Wei L, Ji P, Li H, Wu Z, Zhang J. Screening of Key Genes of Sepsis and Septic Shock Using Bioinformatics Analysis. J Inflamm Res 2021; 14:829-841. [PMID: 33737824 PMCID: PMC7962593 DOI: 10.2147/jir.s301663] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Accepted: 02/26/2021] [Indexed: 12/20/2022] Open
Abstract
Objective Sepsis is a disease associated with high mortality. We performed bioinformatic analysis to identify key biomarkers associated with sepsis and septic shock. Methods The top 20% of genes showing the greatest variance between sepsis and controls in the GSE13904 dataset (children) were screened by co-expression network analysis. The differentially expressed genes (DEGs) were identified through analyzing differential gene expression between sepsis patients and control in the GSE13904 (children) and GSE154918 (adult) data sets. Intersection analysis of module genes and DEGs was performed to identify common DEGs for enrichment analysis, protein-protein interaction network (PPI network) analysis, and Short Time-series Expression Miner (STEM) analysis. The PPI network genes were ranked by degree of connectivity, and the top 100 sepsis-associated genes were identified based on the area under the receiver operating characteristic curve (AUC). In addition, we evaluated differences in immune cell infiltration between sepsis patients and controls in children (GSE13904, GSE25504) and adults (GSE9960, GSE154918). Finally, we analyzed differences in DNA methylation levels between sepsis patients and controls in GSE138074 (adults). Results The common genes were associated mainly with up-regulated inflammatory and metabolic responses, as well as down-regulated immune responses. Sepsis patients showed lower infiltration by most types of immune cells. Genes in the PPI network with AUC values greater than 0.9 in both GSE13904 (children) and GSE154918 (adults) were screened as key genes for diagnosis. These key genes (MAPK14, FGR, RHOG, LAT, PRKACB, UBE2Q2, ITK, IL2RB, and CD247) were also identified in STEM analysis to be progressively dysregulated across controls, sepsis patients and patients with septic shock. In addition, the expression of MAPK14, FGR, and CD247 was modified by methylation. Conclusion This study identified several potential diagnostic genes and inflammatory and metabolic responses mechanisms associated with the development of sepsis.
Collapse
Affiliation(s)
- Xiaoliang Zeng
- Department of Emergency Medicine, The Second Affiliated Hospital of Guangxi Medical University, Nanning, 530007, People's Republic of China
| | - Jihua Feng
- Department of Emergency Medicine, The Second Affiliated Hospital of Guangxi Medical University, Nanning, 530007, People's Republic of China
| | - Yanli Yang
- Department of Emergency Medicine, The Second Affiliated Hospital of Guangxi Medical University, Nanning, 530007, People's Republic of China
| | - Ruzhi Zhao
- Department of Emergency Medicine, The Second Affiliated Hospital of Guangxi Medical University, Nanning, 530007, People's Republic of China
| | - Qiao Yu
- Department of Emergency Medicine, The Second Affiliated Hospital of Guangxi Medical University, Nanning, 530007, People's Republic of China
| | - Han Qin
- Department of Emergency Medicine, The Second Affiliated Hospital of Guangxi Medical University, Nanning, 530007, People's Republic of China
| | - Lile Wei
- Department of Emergency Medicine, The Second Affiliated Hospital of Guangxi Medical University, Nanning, 530007, People's Republic of China
| | - Pan Ji
- Department of Emergency Medicine, The Second Affiliated Hospital of Guangxi Medical University, Nanning, 530007, People's Republic of China
| | - Hongyuan Li
- Department of Emergency Medicine, The Second Affiliated Hospital of Guangxi Medical University, Nanning, 530007, People's Republic of China
| | - Zimeng Wu
- Department of Emergency Medicine, The Second Affiliated Hospital of Guangxi Medical University, Nanning, 530007, People's Republic of China
| | - Jianfeng Zhang
- Department of Emergency Medicine, The Second Affiliated Hospital of Guangxi Medical University, Nanning, 530007, People's Republic of China
| |
Collapse
|