Organ Repair (liver, kidney, pancreas, etc.)
Research directed to the repair of organs encompasses the development of scaffold-less approach to engineer 3-D tissues, use of stem cell lines to create organs for repair and for research/ screening, and exploring genetically altered mice to understand mechanisms of tissue formation and organogenesis.
Researchers
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Benjamin AllenMedicine -
Laura ButtittaLSA -
Sriram ChandrasekaranMedicine -
Eugene ChenMedicine -
Mark CohenMedicine -
Gregory DresslerMedicine -
Cunming DuanLSA -
Jianping FuEngineering -
Dan GoldmanMedicine -
Gary HammerMedicine -
Sue HammoudMedicine
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Jennifer HarderMedicine -
Idse HeemskerkMedicine -
Todd HerronMedicine -
Matthias KretzlerMedicine
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Paul LeeMedicine
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Geeta MehtaEngineering -
Deepak NagrathEngineering -
Jack ParentMedicine -
Charles ParkosMedicine -
Indika RajapakseMedicine -
Liangyou RuiMedicine -
Linda SamuelsonMedicine -
Scott SoleimanpourMedicine -
Jason SpenceMedicine -
Rachel ZemansMedicine
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David ZopfMedicine
Select Publications
Allen BL et al. Dosage-dependent regulation of pancreatic cancer growth and angiogenesis by hedgehog signaling. Cell Rep. 2014.
Allen BL et al. Secreted HHIP1 interacts with heparan sulfate and regulates Hedgehog ligand localization and function. J Biol Chem. 2015.
Allen BL et al. Neuropilin-1 promotes Hedgehog signaling through a novel cytoplasmic motif. J Biol Chem. 2017.
Allen BL et al. Recovery of taste organs and sensory function after severe loss from Hedgehog/Smoothened inhibition with cancer drug sonidegib. Proc Natl Acad Sci U S A. 2017.
Allen BL et al. The Hedgehog co-receptor BOC differentially regulates SHH signaling during craniofacial development. Development. 2020.
Allen et al.Pancreatic Fibroblast Heterogeneity: From Development to Cancer. Cells. 2020
Arvan et al. GWAS of thyroid stimulating hormone highlights pleiotropic effects and inverse association with thyroid cancer. Nat Commun. 2020.
Besirli et al. Small molecule activation of metabolic enzyme pyruvate kinase muscle isozyme 2, PKM2, circumvents photoreceptor apoptosis. Sci Rep. 2020.
Besirli et al. Cryotherapy for the management of refractory hypotony secondary to post-goniotomy cyclodialysis cleft. Am J Ophthalmol Case Rep. 2020.
Besirli et al. Novel TMEM98, MFRP, PRSS56 variants in a large United States high hyperopia and nanophthalmos cohort. Sci Rep. 2020.
Buttitta LA et al. Protein Phosphatase 2A promotes the transition to G0 during terminal differentiation in Drosophila. Development. 2015.
Buttitta LA et al. Ecdysone signaling induces two phases of cell cycle exit in Drosophila cells. Biol Open. 2016.
Buttitta LA et al. Chromatin organization changes during the establishment and maintenance of the postmitotic state. Epigenetics Chromatin. 2017.
Buttitta LA et al. Changes in chromatin accessibility ensure robust cell cycle exit in terminally differentiated cells. PLoS Biol. 2019.
Buttitta LA et al. Polyploidy in the adult Drosophila brain. Elife. 2020.
Chandrasekaran et al. Purine metabolism regulates DNA repair and therapy resistance in glioblastoma. Nat Commun. 2020.
Chandrasekaran S et al. LIN28 Regulates Stem Cell Metabolism and Conversion to Primed Pluripotency. Cell Stem Cell. 2016.
Chandrasekaran S et al. Comprehensive mapping of pluripotent stem cell metabolism using dynamic genome-scale network modeling. Cell Rep. 2017.
Chandrasekaran S et al. Genome-scale network model of metabolism and histone acetylation reveals metabolic dependencies of histone deacetylase inhibitors. Genome Biol. 2019.
Chandrasekaran S et al. Dynamic Network Modeling of Stem Cell Metabolism, Methods in Molecular Biology: Computational Stem Cell Biology. Methods Mol Biol. 2019.
Chandrasekaran S et al. Nutrient Sensing by Histone Marks: Reading the Metabolic Histone Code Using Tracing, Omics, and Modeling. Bioessays. 2020.
Chen et al. MiCas9 increases large size gene knock-in rates and reduces undesirable on-target and off-target indel edits. Nat Commun. 2020.
Chen YE et al. Patient-specific cardiovascular progenitor cells derived from integration-free induced pluripotent stem cells for vascular tissue regeneration. Biomaterials. 2015.
Chen YE et al. Cell-free 3D scaffold with two-stage delivery of miRNA-26a to regenerate critical-sized bone defects. Nat Commun. 2016.
Chen YE et al. RS-1 enhances CRISPR/Cas9- and TALEN-mediated knock-in efficiency. Nat Commun. 2016.
Chen YE et al. Direct Reprogramming of Fibroblasts Into Smooth Muscle-Like Cells With Defined Transcription Factors. Arterioscler Thromb Vasc Biol. 2018.
Chen YE et al. In Vitro Lineage-Specific Differentiation of Vascular Smooth Muscle Cells in Response to SMAD3 Deficiency: Implications for SMAD3-Related Thoracic Aortic Aneurysm. Arterioscler Thromb Vasc Biol. 2020.
Duan C et al. Hypoxia converts the myogenic action of insulin-like growth factors into mitogenic action by differentially regulating multiple signaling pathways. Proc Natl Acad Sci U S A. 2010.
Duan C et al. Hypoxia-inducible factor 3 is an oxygen-dependent transcription activator and regulates a distinct transcriptional response to hypoxia. Cell Rep. 2014.
Duan C et al. Ca2+ concentration-dependent premature death of igfbp5a mutant zebrafish reveals a critical role of IGF signaling in adaptive epithelial growth. Sci Signal. 2018.
Duan C et al. Cell-autonomous regulation of epithelial cell quiescence by calcium channel Trpv6. Elife. 2019.
Duan C et al. The metalloproteinase Papp-aa controls epithelial cell quiescence to proliferation transition. Elife. 2020.
Fu J et al. Self-organized amniogenesis by human pluripotent stem cells in a biomimetic implantation-like niche. Nat Mater. 2017.
Fu J et al. A pluripotent stem cell-based model for post-implantation human amniotic sac development. Nat Commun. 2017.
Fu J et al. Mechanics-guided embryonic patterning of neuroectoderm tissue from human pluripotent stem cells. Nat Mater. 2018.
Fu J et al. Controlled modeling of human epiblast and amnion development using stem cells. Nature. 2019.
Fu J et al. Dorsal-ventral patterned neural cyst from human pluripotent stem cells in a biomimetic neurogenic niche. Sci Adv. 2019.
Fu J et al. Visualization and quantification of dynamic intercellular coupling in human embryonic stem cells using single cell sonoporation. Sci Rep. 2020.
Goldman D et al. A role for alpha1 tubulin-expressing Müller glia in regeneration of the injured zebrafish retina. J Neurosci. 2006.
Goldman D et al. Ascl1a regulates Müller glia dedifferentiation and retina regeneration via a Lin-28-dependent, let-7 miRNA signaling pathway. Nat Cell Biol. 2010.
Goldman D et al. HB-EGF is necessary and sufficient for Müller glia dedifferentiation and retina regeneration. Dev Cell. 2012.
Goldman D et al. Analysis of DNA methylation reveals a partial reprogramming of the Müller glia genome during retina regeneration. Proc Natl Acad Sci U S A. 2013.
Goldman D et al. Tgfb3 collaborates with PP2A and Notch signaling pathways to inhibit retina regeneration. Elife. 2020.
Hammer GD et al. Mouse models of adrenocortical tumors. Mol Cell Endocrinol. 2016.
Hammer GD et al. 5th International ACC Symposium: Introduction. Horm Cancer. 2016.
Hammer GD et al. Diagnosis and Treatment of Primary Adrenal Insufficiency: An Endocrine Society Clinical Practice Guideline. J Clin Endocrinol Metab. 2016.
Hammer GD et al. Molecular Heterogeneity in Aldosterone-Producing Adenomas. J Clin Endocrinol Metab. 2016.
Hammer GD et al. ATR-101, a Selective and Potent Inhibitor of Acyl-CoA Acyltransferase 1, Induces Apoptosis in H295R Adrenocortical Cells and in the Adrenal Cortex of Dogs. Endocrinology. 2016.
Hammoud et al. Regulation of meiotic progression by Sertoli-cell androgen signaling. Mol Biol Cell. 2020.
Harder JL et al. High-Throughput Screening Enhances Kidney Organoid Differentiation from Human Pluripotent Stem Cells and Enables Automated Multidimensional Phenotyping. Cell Stem Cell. 2018.
Harder JL et al. Organoid single cell profiling identifies a transcriptional signature of glomerular disease. JCI Insight. 2020.
Harder JL et al. Single cell transcriptomics identifies focal segmental glomerulosclerosis remission endothelial biomarker. JCI Insight. 2020.
Harder JL et al. SARS-CoV-2 receptor networks in diabetic and COVID-19 associated kidney disease. Kidney Int. 2020.
Heemskerk I Full of potential: Pluripotent stem cells for the systems biology of embryonic patterning. Dev Biol. 2020.
Heemskerk I et al. Tissue cartography: compressing bio-image data by dimensional reduction. Nat Methods. 2015.
Heemskerk I et al. Differential growth triggers mechanical feedback that elevates Hippo signaling. Proc Natl Acad Sci U S A. 2016.
Heemskerk I et al. Rapid changes in morphogen concentration control self-organized patterning in human embryonic stem cells. Elife. 2019.
Herron et al. Human perinatal stem cell derived extracellular matrix enables rapid maturation of hiPSC-CM structural and functional phenotypes. Sci Rep. 2020.
Herron et al.Repolarization studies using human stem cell-derived cardiomyocytes: Validation studies and best practice recommendations. Regul Toxicol Pharmacol. 2020
Herron TJ Stiffness triggers non-coding RNA pathology. Nat Biomed Eng. 2019.
Herron TJ et al. Deficient cMyBP-C protein expression during cardiomyocyte differentiation underlies human hypertrophic cardiomyopathy cellular phenotypes in disease specific human ES cell derived cardiomyocytes. J Mol Cell Cardiol. 2016.
Herron TJ et al. hiPSC-CM Monolayer Maturation State Determines Drug Responsiveness in High Throughput Pro-Arrhythmia Screen. Sci Rep. 2017.
Herron TJ et al. Functional cardiac fibroblasts derived from human pluripotent stem cells via second heart field progenitors. Nat Commun. 2019.
Herron TJ et al. Detection of Drug-Induced Torsades de Pointes Arrhythmia Mechanisms Using hiPSC-CM Syncytial Monolayers in a High-Throughput Screening Voltage Sensitive Dye Assay. Toxicol Sci. 2020.
Kretzler et al. The genetic architecture of membranous nephropathy and its potential to improve non-invasive diagnosis. Nat Commun. 2020.
Kretzler et al.Transcriptome analysis of primary podocytes reveals novel calcium regulated regulatory networks. FASEB J. 2020
Mehta G et al. Personalized Medicine–Based Approach to Model Patterns of Chemoresistance and Tumor Recurrence Using Ovarian Cancer Stem Cell Spheroids. Clin Cancer Res. 2017.
Mehta G et al. Integrated cancer tissue engineering models for precision medicine. PLoS One. 2019.
Mehta G et al. Engineered 3D Model of Cancer Stem Cell Enrichment and Chemoresistance. Neoplasia. 2019.
Mehta G et al. Ovarian cancer stem cells and macrophages reciprocally interact through the WNT pathway to promote pro-tumoral and malignant phenotypes in 3D engineered microenvironments. J Immunother Cancer. 2019.
Mehta G et al. Compressive Stimulation Enhances Ovarian Cancer Proliferation, Invasion, Chemoresistance, and Mechanotransduction via CDC42 in a 3D Bioreactor. Cancers (Basel). 2020.
Nagrath D et al. Genomic deletion of malic enzyme 2 confers collateral lethality in pancreatic cancer. Nature. 2017.
Nagrath D et al. Generation of Human Fatty Livers Using Custom-Engineered Induced Pluripotent Stem Cells with Modifiable SIRT1 Metabolism. Cell Metab. 2019.
Nagrath D et al. Tumour-reprogrammed stromal BCAT1 fuels branched-chain ketoacid dependency in stromal-rich PDAC tumours. Nat Metab. 2020.
Nagrath et al. Electron transport chain activity is a predictor and target for venetoclax sensitivity in multiple myeloma. Nat Commun. 2020.
Nagrath et al. ITLN1 modulates invasive potential and metabolic reprogramming of ovarian cancer cells in omental microenvironment. Nat Commun. 2020.
Parent et al.Seizure-Induced Neurogenesis: 1 Out of 3 Ain’t Bad. Epilepsy Curr. 2020
Parent JM et al. Critical roles of ɑII spectrin in brain development and epileptic encephalopathy. J Clin Invest. 2018.
Parent JM et al. Modeling genetic epilepsies in a dish. Dev Dyn. 2020.
Parent JM et al. Altered synaptic drive onto birthdated dentate granule cells in experimental temporal lobe epilepsy. J Neurosci. 2019.
Parent JM et al. Multimodal analysis of STRADA function in brain Development. Front Cell Neurosci. 2020.
Parent JM et al. Variant-Specific Changes in Persistent or Resurgent Sodium Current in SCN8A-Related Epilepsy Patient-Derived Neurons. Brain. 2020.
Parkos CA et al. JAM-A regulates permeability and inflammation in the intestine in vivo. J Exp Med. 2007.
Parkos CA et al. Compromised intestinal epithelial barrier induces adaptive immune compensation that protects from colitis. Immunity. 2012.
Parkos CA et al. Neutrophil-derived JAML inhibits repair of intestinal epithelial injury during acute inflammation. Mucosal Immunol. 2014.
Parkos CA et al. Epithelial CD47 is critical for mucosal repair in the murine intestine in vivo. Nat Commun. 2019.
Parkos CA et al. Neutrophil expressed CD47 regulates CD11b/CD18-dependent neutrophil transepithelial migration in the intestine in vivo. Mucosal Immunol. 2020.
Rajapakse I et al. On Emerging Nuclear order. J Cell Biol. 2011.
Rajapakse I et al. Dynamics and control of state-dependent networks for probing genomic organization. Proc Natl Acad Sci U S A. 2011.
Rajapakse I et al. Functional organization of the human 4D Nucleome. Proc Natl Acad Sci U S A. 2015.
Rajapakse I et al. Emergence of function from coordinated cells in a tissue. Proc Natl Acad Sci U S A. 2017.
Rajapakse I et al. An Algorithm for Cellular Reprogramming. Proc Natl Acad Sci U S A. 2017.
Rui et al. Leptin receptor-expressing neuron Sh2b1 supports sympathetic nervous system and protects against obesity and metabolic disease. Nat Commun. 2020.
Rui L et al. Insulin/Snail1 axis ameliorates fatty liver disease by epigenetically suppressing lipogenesis. Nat Commun. 2018.
Rui L et al. Brown fat activation mitigates alcohol-induced liver steatosis and injury in mice. J Clin Invest. 2019.
Rui L et al. Medullary thymic epithelial NF-kB-inducing kinase (NIK)/IKKα pathway shapes autoimmunity and liver and lung homeostasis in mice. Proc Natl Acad Sci U S A. 2019.
Rui L et al. Leptin receptor-expressing neuron Sh2b1 supports sympathetic nervous system and protects against obesity and metabolic disease. Nat Commun. 2020.
Rui L et al. Hepatic Slug epigenetically promotes liver lipogenesis, fatty liver disease, and type 2 diabetes. J Clin Invest. 2020.
Samuelson et al.A year of challenge and change. Physiology (Bethesda). 2020
Samuelson LC et al. Notch Signaling Modulates Proliferation and Differentiation of Intestinal Crypt Base Columnar Stem Cells. Development. 2012.
Samuelson LC et al. Notch Signaling Regulates Gastric Antral LGR5 Stem Cell Function. EMBO J. 2015.
Samuelson LC et al. Genome toxicity and impaired stem cell function after conditional activation of CreERT2 in the intestine. Stem Cell Reports. 2018.
Samuelson LC et al. Insulin-like Growth Factor-1 and mTORC1 Signaling Promote the Intestinal Regenerative Response after Irradiation Injury. Cell Mol Gastroenterol Hepatol. 2020.
Samuelson LC et al. Rapid Crypt Cell Remodeling Regenerates the Intestinal Stem Cell Niche after Notch Inhibition. Stem Cell Reports. 2020.
Soleimanpour SA et al. The pancreatic β cell and type 1 diabetes: innocent bystander or active participant?. Trends Endocrinol Metab. 2013.
Soleimanpour SA et al. The diabetes susceptibility gene Clec16a regulates mitophagy. Cell. 2014.
Soleimanpour SA et al. Diabetes susceptibility genes Pdx1 and Clec16a function in a pathway regulating mitophagy in beta cells. Diabetes. 2015.
Soleimanpour SA et al. Clec16a, Nrdp1, and USP8 form a ubiquitin-dependent tripartite complex that regulates beta cell mitophagy. Diabetes. 2018.
Soleimanpour SA et al. The E3 ubiquitin ligase parkin is dispensable for metabolic homeostasis in murine pancreatic beta cells and adipocytes. J Biol Chem. 2019.
Spence et al.The Lumen of Human Intestinal Organoids Poses Greater Stress to Bacteria Compared to the Germ-Free Mouse Intestine: Escherichia coli Deficient in RpoS as a Colonization Probe. mSphere. 2020
Spence et al.Low-Level Mouse DNA in Conditioned Medium Generates False Positive Cross-Species Contamination Results in Human Organoid Cultures. Front Cell Dev Biol. 2020
Zopf DA et al. Bioresorbable airway splint created with a three-dimensional printer. N Engl J Med. 2013.
Zopf DA et al. Computer aided-designed, 3-dimensionally printed porous tissue bioscaffolds for craniofacial soft tissue reconstruction. Otolaryngol Head Neck Surg. 2014.
Zopf DA et al. A multidisciplinary international collaborative implementing low cost, high fidelity 3D printed airway models to enhance Ethiopian anesthesia resident emergency cricothyroidotomy skills. Int J Pediatr Otorhinolaryngol. 2018.
Zopf DA et al. Anatomic-Based Design, Manufacturing, and Preclinical Assessment of a Novel 3D-Printed Bioscaffold for Total Nasal Reconstruction. Facial Plast Surg Aesthet Med. 2020.
Zopf DA et al. Hybrid Three-Dimensional-Printed Ear Tissue Scaffold With Autologous Cartilage Mitigates Soft Tissue Complications. Laryngoscope. 2020.