Human physiomimetic model integrating microphysiological systems of the gut, liver, and brain for studies of neurodegenerative diseases

Engineered model of the human gut-liver-brain axis can be used to study the link between the microbiome and Parkinson’s disease. Slow progress in the fight against neurodegenerative diseases (NDs) motivates an urgent need for highly controlled in vitro systems to investigate organ-organ– and organ-immune–specific interactions relevant for disease pathophysiology. Of particular interest is the gut/microbiome-liver-brain axis for parsing out how genetic and environmental factors contribute to NDs. We have developed a mesofluidic platform technology to study gut-liver-cerebral interactions in the context of Parkinson’s disease (PD). It connects microphysiological systems (MPSs) of the primary human gut and liver with a human induced pluripotent stem cell–derived cerebral MPS in a systemically circulated common culture medium containing CD4+ regulatory T and T helper 17 cells. We demonstrate this approach using a patient-derived cerebral MPS carrying the PD-causing A53T mutation, gaining two important findings: (i) that systemic interaction enhances features of in vivo–like behavior of cerebral MPSs, and (ii) that microbiome-associated short-chain fatty acids increase expression of pathology-associated pathways in PD.

[1]  L. Griffith,et al.  Fully synthetic matrices for in vitro culture of primary human intestinal enteroids and endometrial organoids. , 2020, Biomaterials.

[2]  Kevin S. Smith,et al.  C9orf72 suppresses systemic and neural inflammation induced by gut bacteria , 2020, Nature.

[3]  Linda G. Griffith,et al.  Gut-Liver physiomimetics reveal paradoxical modulation of IBD-related inflammation by short-chain fatty acids , 2019, bioRxiv.

[4]  Michael L. Shuler,et al.  Multi-organ system for the evaluation of efficacy and off-target toxicity of anticancer therapeutics , 2019, Science Translational Medicine.

[5]  B. Vervliet,et al.  The role of short-chain fatty acids in microbiota–gut–brain communication , 2019, Nature Reviews Gastroenterology & Hepatology.

[6]  David G. Brohawn,et al.  RNA Sequencing Reveals Small and Variable Contributions of Infectious Agents to Transcriptomes of Postmortem Nervous Tissues From Amyotrophic Lateral Sclerosis, Alzheimer’s Disease and Parkinson’s Disease Subjects, and Increased Expression of Genes From Disease-Activated Microglia , 2019, Front. Neurosci..

[7]  S. Meuth,et al.  Glial Activation Markers in CSF and Serum From Patients With Primary Progressive Multiple Sclerosis: Potential of Serum GFAP as Disease Severity Marker? , 2019, Front. Neurol..

[8]  K. Arai,et al.  Comparison of organ-specific endothelial cells in terms of microvascular formation and endothelial barrier functions. , 2019, Microvascular research.

[9]  Jason A. Papin,et al.  Medusa: Software to build and analyze ensembles of genome-scale metabolic network reconstructions , 2019, bioRxiv.

[10]  R. Keep,et al.  The year in review: progress in brain barriers and brain fluid research in 2018 , 2019, Fluids and Barriers of the CNS.

[11]  Robert V Farese,et al.  Lipidomic Analysis of α-Synuclein Neurotoxicity Identifies Stearoyl CoA Desaturase as a Target for Parkinson Treatment. , 2018, Molecular cell.

[12]  P. Searson,et al.  Benchmarking in vitro tissue-engineered blood–brain barrier models , 2018, Fluids and Barriers of the CNS.

[13]  O. Isacson,et al.  The glycoprotein GPNMB is selectively elevated in the substantia nigra of Parkinson's disease patients and increases after lysosomal stress , 2018, Neurobiology of Disease.

[14]  A. Visekruna,et al.  Regulation of the effector function of CD8+ T cells by gut microbiota-derived metabolite butyrate , 2018, Scientific Reports.

[15]  C. Soto,et al.  Protein misfolding, aggregation, and conformational strains in neurodegenerative diseases , 2018, Nature Neuroscience.

[16]  H. Wiley,et al.  A systems perspective of heterocellular signaling. , 2018, Essays in biochemistry.

[17]  D. L. Taylor,et al.  A glass-based, continuously zonated and vascularized human liver acinus microphysiological system (vLAMPS) designed for experimental modeling of diseases and ADME/TOX. , 2018, Lab on a chip.

[18]  Sean P Sheehy,et al.  A linked organ-on-chip model of the human neurovascular unit reveals the metabolic coupling of endothelial and neuronal cells , 2018, Nature Biotechnology.

[19]  J. Bajramovic,et al.  An Overview of in vitro Methods to Study Microglia , 2018, Front. Cell. Neurosci..

[20]  Panos Roussos,et al.  Brain Cell Type Specific Gene Expression and Co-expression Network Architectures , 2018, Scientific Reports.

[21]  D. Wilkinson,et al.  Cell Identity Switching Regulated by Retinoic Acid Signaling Maintains Homogeneous Segments in the Hindbrain , 2018, Developmental cell.

[22]  Gang Liu,et al.  Clinical analysis of 215 consecutive cases with fever of unknown origin , 2018, Medicine.

[23]  D. Adams,et al.  Liver sinusoidal endothelial cells — gatekeepers of hepatic immunity , 2018, Nature Reviews Gastroenterology & Hepatology.

[24]  E. Janda,et al.  Microglial Phagocytosis and Its Regulation: A Therapeutic Target in Parkinson’s Disease? , 2018, Front. Mol. Neurosci..

[25]  Emeran A. Mayer,et al.  The Brain-Gut-Microbiome Axis , 2018, Cellular and molecular gastroenterology and hepatology.

[26]  Murat Cirit,et al.  Interconnected Microphysiological Systems for Quantitative Biology and Pharmacology Studies , 2018, Scientific Reports.

[27]  Gordana Vunjak-Novakovic,et al.  Organs-on-a-Chip: A Fast Track for Engineered Human Tissues in Drug Development. , 2018, Cell stem cell.

[28]  Melissa R. Andrews,et al.  Integrin Activation: Implications for Axon Regeneration , 2018, Cells.

[29]  S. Chandran,et al.  Correction: Author Correction: Neurons and neuronal activity control gene expression in astrocytes to regulate their development and metabolism , 2018, Nature Communications.

[30]  R. Keep,et al.  Progress in brain barriers and brain fluid research in 2017 , 2018, Fluids and Barriers of the CNS.

[31]  M. Nedergaard,et al.  The Glymphatic System in Central Nervous System Health and Disease: Past, Present, and Future. , 2018, Annual review of pathology.

[32]  Zhisong He,et al.  Identification and characterization of functional modules reflecting transcriptome transition during human neuron maturation , 2017, bioRxiv.

[33]  Francisco J. Sánchez-Rivera,et al.  Corrigendum: In vivo genome editing and organoid transplantation models of colorectal cancer and metastasis , 2017, Nature Biotechnology.

[34]  Raehyun Kim,et al.  Formation of Human Colonic Crypt Array by Application of Chemical Gradients Across a Shaped Epithelial Monolayer , 2017, Cellular and molecular gastroenterology and hepatology.

[35]  T. Andersson,et al.  Functional coupling of human pancreatic islets and liver spheroids on-a-chip: Towards a novel human ex vivo type 2 diabetes model , 2017, Scientific Reports.

[36]  B. Stockwell,et al.  Ferroptosis: A Regulated Cell Death Nexus Linking Metabolism, Redox Biology, and Disease , 2017, Cell.

[37]  Y. Huang,et al.  Th17 Cells Induce Dopaminergic Neuronal Death via LFA-1/ICAM-1 Interaction in a Mouse Model of Parkinson’s Disease , 2016, Molecular Neurobiology.

[38]  Murat Cirit,et al.  Integrated Gut and Liver Microphysiological Systems for Quantitative In Vitro Pharmacokinetic Studies , 2017, The AAPS Journal.

[39]  I. Amit,et al.  A Unique Microglia Type Associated with Restricting Development of Alzheimer’s Disease , 2017, Cell.

[40]  Katayoun Khoshbin,et al.  Current insights into pathogenesis of Parkinson's disease: Approach to mevalonate pathway and protective role of statins. , 2017, Biomedicine & pharmacotherapy = Biomedecine & pharmacotherapie.

[41]  A. Rizvanov,et al.  Elevated Levels of Proinflammatory Cytokines in Cerebrospinal Fluid of Multiple Sclerosis Patients , 2017, Front. Immunol..

[42]  Bin Zhang,et al.  Directed Differentiation of Human Pluripotent Stem Cells to Microglia , 2017, Stem cell reports.

[43]  M. Donowitz,et al.  A primary human macrophage-enteroid co-culture model to investigate mucosal gut physiology and host-pathogen interactions , 2017, Scientific Reports.

[44]  A. Bush,et al.  Ferroptosis and cell death mechanisms in Parkinson's disease , 2017, Neurochemistry International.

[45]  E. Fraenkel,et al.  Hyper- and hypo- nutrition studies of the hepatic transcriptome and epigenome suggest that PPARα regulates anaerobic glycolysis , 2017, Scientific Reports.

[46]  Albert Gough,et al.  Functional Coupling of Human Microphysiology Systems: Intestine, Liver, Kidney Proximal Tubule, Blood-Brain Barrier and Skeletal Muscle , 2017, Scientific Reports.

[47]  L. Griffith,et al.  A liver microphysiological system of tumor cell dormancy and inflammatory responsiveness is affected by scaffold properties. , 2016, Lab on a chip.

[48]  Rob Knight,et al.  Gut Microbiota Regulate Motor Deficits and Neuroinflammation in a Model of Parkinson’s Disease , 2016, Cell.

[49]  K. Fassbender,et al.  Short chain fatty acids and gut microbiota differ between patients with Parkinson's disease and age-matched controls. , 2016, Parkinsonism & related disorders.

[50]  Li-Huei Tsai,et al.  Efficient derivation of microglia-like cells from human pluripotent stem cells , 2016, Nature Medicine.

[51]  L. Griffith,et al.  Modeling Therapeutic Antibody–Small Molecule Drug-Drug Interactions Using a Three-Dimensional Perfusable Human Liver Coculture Platform , 2016, Drug Metabolism and Disposition.

[52]  F. Bäckhed,et al.  From Dietary Fiber to Host Physiology: Short-Chain Fatty Acids as Key Bacterial Metabolites , 2016, Cell.

[53]  Yonatan Stelzer,et al.  Parkinson-associated risk variant in enhancer element produces subtle effect on target gene expression , 2016, Nature.

[54]  T. Preston,et al.  Formation of short chain fatty acids by the gut microbiota and their impact on human metabolism , 2016, Gut microbes.

[55]  A. Peet,et al.  Increased Blood Levels of Growth Factors, Proinflammatory Cytokines, and Th17 Cytokines in Patients with Newly Diagnosed Type 1 Diabetes , 2015, PloS one.

[56]  I. Ferrer,et al.  Altered machinery of protein synthesis is region- and stage-dependent and is associated with α-synuclein oligomers in Parkinson’s disease , 2015, Acta Neuropathologica Communications.

[57]  L. Griffith,et al.  Metabolite Profiling and Pharmacokinetic Evaluation of Hydrocortisone in a Perfused Three-Dimensional Human Liver Bioreactor , 2015, Drug Metabolism and Disposition.

[58]  L. Monasta,et al.  Pediatric patients with inflammatory bowel disease exhibit increased serum levels of proinflammatory cytokines and chemokines, but decreased circulating levels of macrophage inhibitory protein-1β, interleukin-2 and interleukin-17. , 2015, Experimental and therapeutic medicine.

[59]  Corey D. DeHaven,et al.  High Resolution Mass Spectrometry Improves Data Quantity and Quality as Compared to Unit Mass Resolution Mass Spectrometry in High- Throughput Profiling Metabolomics , 2014 .

[60]  S. Kang,et al.  Short chain fatty acids induce both effector and regulatory T cells by suppression of histone deacetylases and regulation of the mTOR-S6K pathway , 2014, Mucosal Immunology.

[61]  M. Tomita,et al.  Commensal microbe-derived butyrate induces the differentiation of colonic regulatory T cells , 2013, Nature.

[62]  A. MacLullich,et al.  Preoperative cerebrospinal fluid cytokine levels and the risk of postoperative delirium in elderly hip fracture patients , 2013, Journal of Neuroinflammation.

[63]  D. Surmeier,et al.  Neuronal vulnerability, pathogenesis, and Parkinson's disease , 2013, Movement disorders : official journal of the Movement Disorder Society.

[64]  L. Monasta,et al.  Cytokine Levels in the Serum of Healthy Subjects , 2013, Mediators of inflammation.

[65]  J. Vance Dysregulation of cholesterol balance in the brain: contribution to neurodegenerative diseases , 2012, Disease Models & Mechanisms.

[66]  Yuichiro J Suzuki,et al.  Faculty Opinions recommendation of Ferroptosis: an iron-dependent form of nonapoptotic cell death. , 2012 .

[67]  M. R. Lamprecht,et al.  Ferroptosis: An Iron-Dependent Form of Nonapoptotic Cell Death , 2012, Cell.

[68]  Sungha Park,et al.  Serum cytokine profiles in healthy young and elderly population assessed using multiplexed bead-based immunoassays , 2011, Journal of Translational Medicine.

[69]  Susan Lindquist,et al.  Generation of Isogenic Pluripotent Stem Cells Differing Exclusively at Two Early Onset Parkinson Point Mutations , 2011, Cell.

[70]  D. Nie,et al.  Short-chain fatty acids induced autophagy serves as an adaptive strategy for retarding mitochondria-mediated apoptotic cell death , 2011, Cell Death and Differentiation.

[71]  Yu Wang,et al.  Cerebrospinal fluid biomarkers for Parkinson disease diagnosis and progression , 2011, Annals of neurology.

[72]  Brit Mollenhauer,et al.  α-Synuclein and tau concentrations in cerebrospinal fluid of patients presenting with parkinsonism: a cohort study , 2011, The Lancet Neurology.

[73]  Gregory M. Miller,et al.  The emerging role of trace amine‐associated receptor 1 in the functional regulation of monoamine transporters and dopaminergic activity , 2011, Journal of neurochemistry.

[74]  Dan R. Littman,et al.  Induction of Intestinal Th17 Cells by Segmented Filamentous Bacteria , 2009, Cell.

[75]  T. Yamashima A putative link of PUFA, GPR40 and adult-born hippocampal neurons for memory , 2008, Progress in Neurobiology.

[76]  Y. Xing,et al.  A Transcriptome Database for Astrocytes, Neurons, and Oligodendrocytes: A New Resource for Understanding Brain Development and Function , 2008, The Journal of Neuroscience.

[77]  Pablo Tamayo,et al.  Gene set enrichment analysis: A knowledge-based approach for interpreting genome-wide expression profiles , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[78]  S. Hyman,et al.  Metabotropic Glutamate Receptors and Dopamine Receptors Cooperate to Enhance Extracellular Signal-Regulated Kinase Phosphorylation in Striatal Neurons , 2005, The Journal of Neuroscience.

[79]  N. Hattori,et al.  Ubiquitin, proteasome and parkin. , 2004, Biochimica et biophysica acta.

[80]  P. Bauer,et al.  Ceruloplasmin gene variations and substantia nigra hyperechogenicity in Parkinson disease , 2004, Neurology.

[81]  Kaori Nishikawa,et al.  Ubiquitin carboxy-terminal hydrolase L1 binds to and stabilizes monoubiquitin in neuron. , 2003, Human molecular genetics.

[82]  Soo-Youl Kim,et al.  Tissue transglutaminase-induced aggregation of α-synuclein: Implications for Lewy body formation in Parkinson's disease and dementia with Lewy bodies , 2003, Proceedings of the National Academy of Sciences of the United States of America.

[83]  M. Frasier,et al.  Magnesium Inhibits Spontaneous and Iron-induced Aggregation of α-Synuclein* , 2002, The Journal of Biological Chemistry.

[84]  John Hardy,et al.  The A53T α-Synuclein Mutation Increases Iron-Dependent Aggregation and Toxicity , 2000, The Journal of Neuroscience.

[85]  M. Vawter,et al.  TGFβ1 and TGFβ2 Concentrations Are Elevated in Parkinson's Disease in Ventricular Cerebrospinal Fluid , 1996, Experimental Neurology.

[86]  L. Golbe,et al.  Clinical genetic analysis of Parkinson's disease in the contursi kindred , 1996, Annals of neurology.

[87]  A. Thomson,et al.  Circulating proinflammatory cytokines (IL‐1β, TNF‐α, and IL‐6) and IL‐1 receptor antagonist (IL‐1Ra) in fulminant hepatic failure and acute hepatitis , 1994 .

[88]  J. Goldstein,et al.  Regulation of the mevalonate pathway , 1990, Nature.

[89]  G. Macfarlane,et al.  Short chain fatty acids in human large intestine, portal, hepatic and venous blood. , 1987, Gut.

[90]  Kanefusa Kato,et al.  Neuron-specific enolase and S-100 protein levels in cerebrospinal fluid of patients with various neurological diseases , 1983, Journal of the Neurological Sciences.

[91]  Hongwei Zhang,et al.  The clinical significance of the imbalance of Th 17 and Treg cells and their related cytokines in peripheral blood of Parkinson ’ s disease patients , 2016 .

[92]  R. Hampl,et al.  Selected pro- and anti-inflammatory cytokines in cerebrospinal fluid in normal pressure hydrocephalus. , 2014, Neuro endocrinology letters.

[93]  K. Anastos,et al.  Detectability and reproducibility of plasma levels of chemokines and soluble receptors. , 2013, Results in immunology.

[94]  T. Niki,et al.  Proper SUMO-1 conjugation is essential to DJ-1 to exert its full activities , 2006, Cell Death and Differentiation.

[95]  D. Holdstock Past, present--and future? , 2005, Medicine, conflict, and survival.

[96]  C. Evans,et al.  Markers of central nervous system glia and neurons in vivo during normal and pathological conditions. , 2002, Current topics in microbiology and immunology.

[97]  K. Cowan,et al.  Transforming growth factor-beta1 circulates in normal human plasma and is unchanged in advanced metastatic breast cancer. , 1995, Clinical cancer research : an official journal of the American Association for Cancer Research.