Browsing by Subject "Induced pluripotent stem cells"

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    5. Collaborative Study on the Genetics of Alcoholism: Functional genomics
    (Wiley, 2023) Gameiro-Ros, Isabel; Popova, Dina; Prytkova, Iya; Pang, Zhiping P.; Liu, Yunlong; Dick, Danielle; Bucholz, Kathleen K.; Agrawal, Arpana; Porjesz, Bernice; Goate, Alison M.; Xuei, Xiaoling; Kamarajan, Chella; COGA Collaborators; Tischfield, Jay A.; Edenberg, Howard J.; Slesinger, Paul A.; Hart, Ronald P.; Medical and Molecular Genetics, School of Medicine
    Alcohol Use Disorder is a complex genetic disorder, involving genetic, neural, and environmental factors, and their interactions. The Collaborative Study on the Genetics of Alcoholism (COGA) has been investigating these factors and identified putative alcohol use disorder risk genes through genome-wide association studies. In this review, we describe advances made by COGA in elucidating the functional changes induced by alcohol use disorder risk genes using multimodal approaches with human cell lines and brain tissue. These studies involve investigating gene regulation in lymphoblastoid cells from COGA participants and in post-mortem brain tissues. High throughput reporter assays are being used to identify single nucleotide polymorphisms in which alternate alleles differ in driving gene expression. Specific single nucleotide polymorphisms (both coding or noncoding) have been modeled using induced pluripotent stem cells derived from COGA participants to evaluate the effects of genetic variants on transcriptomics, neuronal excitability, synaptic physiology, and the response to ethanol in human neurons from individuals with and without alcohol use disorder. We provide a perspective on future studies, such as using polygenic risk scores and populations of induced pluripotent stem cell-derived neurons to identify signaling pathways related with responses to alcohol. Starting with genes or loci associated with alcohol use disorder, COGA has demonstrated that integration of multimodal data within COGA participants and functional studies can reveal mechanisms linking genomic variants with alcohol use disorder, and potential targets for future treatments.
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    A single-cell level comparison of human inner ear organoids with the human cochlea and vestibular organs
    (Cell Press, 2023) van der Valk, Wouter H.; van Beelen, Edward S. A.; Steinhart, Matthew R.; Nist-Lund, Carl; Osorio, Daniel; de Groot, John C. M. J.; Sun, Liang; van Benthem, Peter Paul G.; Koehler, Karl R.; Locher, Heiko; Otolaryngology -- Head and Neck Surgery, School of Medicine
    Inner ear disorders are among the most common congenital abnormalities; however, current tissue culture models lack the cell type diversity to study these disorders and normal otic development. Here, we demonstrate the robustness of human pluripotent stem cell-derived inner ear organoids (IEOs) and evaluate cell type heterogeneity by single-cell transcriptomics. To validate our findings, we construct a single-cell atlas of human fetal and adult inner ear tissue. Our study identifies various cell types in the IEOs including periotic mesenchyme, type I and type II vestibular hair cells, and developing vestibular and cochlear epithelium. Many genes linked to congenital inner ear dysfunction are confirmed to be expressed in these cell types. Additional cell-cell communication analysis within IEOs and fetal tissue highlights the role of endothelial cells on the developing sensory epithelium. These findings provide insights into this organoid model and its potential applications in studying inner ear development and disorders.
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    Development of a three-dimensional organoid model to explore early retinal phenotypes associated with Alzheimer’s disease
    (Springer Nature, 2023-08-24) Lavekar, Sailee S.; Harkin, Jade; Hernandez, Melody; Gomes, Cátia; Patil, Shruti; Huang, Kang‑Chieh; Puntambekar, Shweta S.; Lamb, Bruce T.; Meyer, Jason S.; Biology, School of Science
    Alzheimer's disease (AD) is a progressive neurodegenerative disorder characterized by the accumulation of Aβ plaques and neurofibrillary tangles, resulting in synaptic loss and neurodegeneration. The retina is an extension of the central nervous system within the eye, sharing many structural similarities with the brain, and previous studies have observed AD-related phenotypes within the retina. Three-dimensional retinal organoids differentiated from human pluripotent stem cells (hPSCs) can effectively model some of the earliest manifestations of disease states, yet early AD-associated phenotypes have not yet been examined. Thus, the current study focused upon the differentiation of hPSCs into retinal organoids for the analysis of early AD-associated alterations. Results demonstrated the robust differentiation of retinal organoids from both familial AD and unaffected control cell lines, with familial AD retinal organoids exhibiting a significant increase in the Aβ42:Aβ40 ratio as well as phosphorylated Tau protein, characteristic of AD pathology. Further, transcriptional analyses demonstrated the differential expression of many genes and cellular pathways, including those associated with synaptic dysfunction. Taken together, the current study demonstrates the ability of retinal organoids to serve as a powerful model for the identification of some of the earliest retinal alterations associated with AD.
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    Differentiation of pluripotent stem cells into endothelial cells
    (Wolters Kluwer, 2015-05) Yoder, Mervin C.; Department of Pediatrics, IU School of Medicine
    PURPOSE OF REVIEW: Methods to isolate endothelial cells from murine and human pluripotent stem cells continue to evolve and increasingly diverse endothelial cell populations have been generated. This review provides an update of key articles published within the past year that report on some of those advances. RECENT FINDINGS: Cooperative interactions among microRNA (miRNA), transcription factors and some downstream interacting proteins have been reported to enhance endothelial specification from embryonic stem cells (ESCs) and induced pluripotent stem cells (iPSCs). Endothelial cell differentiation can also be modulated by various growth factor additions, Notch pathway activation or inhibition, and modulation of the microenvironment of the differentiating ESC and iPSC. Functionality of the derived endothelium has been demonstrated by a variety of in-vitro and in-vivo assays. Finally, two recent reports have identified endothelial progenitor populations with robust proliferative potential. SUMMARY: Progress in differentiating endothelial cells from ESC and iPSC has been made. The recent report of formation of endothelial colony forming cells from human ESC and iPSC provides a protocol that can generate clinically relevant numbers of cells for human cell therapy.
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    Focal adhesion is associated with lithium response in bipolar disorder: evidence from a network-based multi-omics analysis
    (Springer Nature, 2024) Niemsiri, Vipavee; Rosenthal, Sara Brin; Nievergelt, Caroline M.; Maihofer, Adam X.; Marchetto, Maria C.; Santos, Renata; Shekhtman, Tatyana; Alliey-Rodriguez, Ney; Anand, Amit; Balaraman, Yokesh; Berrettini, Wade H.; Bertram, Holli; Burdick, Katherine E.; Calabrese, Joseph R.; Calkin, Cynthia V.; Conroy, Carla; Coryell, William H.; DeModena, Anna; Eyler, Lisa T.; Feeder, Scott; Fisher, Carrie; Frazier, Nicole; Frye, Mark A.; Gao, Keming; Garnham, Julie; Gershon, Elliot S.; Goes, Fernando S.; Goto, Toyomi; Harrington, Gloria J.; Jakobsen, Petter; Kamali, Masoud; Kelly, Marisa; Leckband, Susan G.; Lohoff, Falk W.; McCarthy, Michael J.; McInnis, Melvin G.; Craig, David; Millett, Caitlin E.; Mondimore, Francis; Morken, Gunnar; Nurnberger, John I.; O'Donovan, Claire; Øedegaard, Ketil J.; Ryan, Kelly; Schinagle, Martha; Shilling, Paul D.; Slaney, Claire; Stapp, Emma K.; Stautland, Andrea; Tarwater, Bruce; Zandi, Peter P.; Alda, Martin; Fisch, Kathleen M.; Gage, Fred H.; Kelsoe, John R.; Psychiatry, School of Medicine
    Lithium (Li) is one of the most effective drugs for treating bipolar disorder (BD), however, there is presently no way to predict response to guide treatment. The aim of this study is to identify functional genes and pathways that distinguish BD Li responders (LR) from BD Li non-responders (NR). An initial Pharmacogenomics of Bipolar Disorder study (PGBD) GWAS of lithium response did not provide any significant results. As a result, we then employed network-based integrative analysis of transcriptomic and genomic data. In transcriptomic study of iPSC-derived neurons, 41 significantly differentially expressed (DE) genes were identified in LR vs NR regardless of lithium exposure. In the PGBD, post-GWAS gene prioritization using the GWA-boosting (GWAB) approach identified 1119 candidate genes. Following DE-derived network propagation, there was a highly significant overlap of genes between the top 500- and top 2000-proximal gene networks and the GWAB gene list (Phypergeometric = 1.28E-09 and 4.10E-18, respectively). Functional enrichment analyses of the top 500 proximal network genes identified focal adhesion and the extracellular matrix (ECM) as the most significant functions. Our findings suggest that the difference between LR and NR was a much greater effect than that of lithium. The direct impact of dysregulation of focal adhesion on axon guidance and neuronal circuits could underpin mechanisms of response to lithium, as well as underlying BD. It also highlights the power of integrative multi-omics analysis of transcriptomic and genomic profiling to gain molecular insights into lithium response in BD.
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    Genetics of paediatric cardiomyopathies
    (Wolters Kluwer, 2017-10) Ware, Stephanie M.; Pediatrics, School of Medicine
    PURPOSE OF REVIEW: Paediatric cardiomyopathy is a rare disease with a genetic basis. The purpose of this review is to discuss the current status of genetic findings in the paediatric cardiomyopathy population and present recent progress in utilizing this information for management and therapy. RECENT FINDINGS: With increased clinical genetic testing, an understanding of the genetic causes of cardiomyopathy is improving and novel causes are identified at a rapid rate. Recent progress in identifying the scope of genetic variation in large population datasets has led to reassessment and refinement of our understanding of the significance of rare genetic variation. As a result, the stringency of variant interpretation has increased, at times leading to revision of previous mutation results. Transcriptome and epigenome studies are elucidating important pathways for disease progression and highlight similarities and differences in pathogenesis from adult cardiomyopathy. Therapy targeted towards the underlying cause of cardiomyopathy is emerging for a number of rare syndromes such as Pompe and Noonan syndromes, and genome editing and induced pluripotent stem cells provide promise for additional precision medicine approaches. SUMMARY: Genetics is moving at a rapid pace in paediatric cardiomyopathy. Genetic testing is increasingly being incorporated into clinical care. Although interpretation of rare genetic variation remains challenging, the opportunity to provide management and therapy targeted towards the underlying genetic cause is beginning to be realized.
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    Genome Editing and Induced Pluripotent Stem Cell Technologies for Personalized Study of Cardiovascular Diseases
    (Springer Nature, 2018-04-17) Chun, Young Wook; Durbin, Matthew D.; Hong, Charles C.; Pediatrics, School of Medicine
    PURPOSE OF REVIEW: The goal of this review is to highlight the potential of induced pluripotent stem cell (iPSC)-based modeling as a tool for studying human cardiovascular diseases. We present some of the current cardiovascular disease models utilizing genome editing and patient-derived iPSCs. RECENT FINDINGS: The incorporation of genome-editing and iPSC technologies provides an innovative research platform, providing novel insight into human cardiovascular disease at molecular, cellular, and functional level. In addition, genome editing in diseased iPSC lines holds potential for personalized regenerative therapies. The study of human cardiovascular disease has been revolutionized by cellular reprogramming and genome editing discoveries. These exceptional technologies provide an opportunity to generate human cell cardiovascular disease models and enable therapeutic strategy development in a dish. We anticipate these technologies to improve our understanding of cardiovascular disease pathophysiology leading to optimal treatment for heart diseases in the future.
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    Heparinized Gelatin-Based Hydrogels for Differentiation of Induced Pluripotent Stem Cells
    (American Chemical Society, 2022) Arkenberg, Matthew R.; Koehler, Karl; Lin, Chien-Chi; Biomedical Engineering, School of Engineering and Technology
    Chemically defined hydrogels are increasingly utilized to define the effects of extracellular matrix (ECM) components on cellular fate determination of human embryonic and induced pluripotent stem cell (hESC and hiPSCs). In particular, hydrogels cross-linked by orthogonal click chemistry, including thiol-norbornene photopolymerization and inverse electron demand Diels-Alder (iEDDA) reactions, are explored for 3D culture of hESC/hiPSCs owing to the specificity, efficiency, cytocompatibility, and modularity of the cross-linking reactions. In this work, we exploited the modularity of thiol-norbornene photopolymerization to create a biomimetic hydrogel platform for 3D culture and differentiation of hiPSCs. A cell-adhesive, protease-labile, and cross-linkable gelatin derivative, gelatin-norbornene (GelNB), was used as the backbone polymer for constructing hiPSC-laden biomimetic hydrogels. GelNB was further heparinized via the iEDDA click reaction using tetrazine-modified heparin (HepTz), creating GelNB-Hep. GelNB or GelNB-Hep was modularly cross-linked with either inert macromer poly(ethylene glycol)-tetra-thiol (PEG4SH) or another bioactive macromer-thiolated hyaluronic acid (THA). The formulations of these hydrogels were modularly tuned to afford biomimetic matrices with similar elastic moduli but varying bioactive components, enabling the understanding of each bioactive component on supporting hiPSC growth and ectodermal, mesodermal, and endodermal fate commitment under identical soluble differentiation cues.
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    HNRNPC haploinsufficiency affects alternative splicing of intellectual disability-associated genes and causes a neurodevelopmental disorder
    (Elsevier, 2023) Niggl, Eva; Bouman, Arjan; Briere, Lauren C.; Hoogenboezem, Remco M.; Wallaard, Ilse; Park, Joohyun; Admard, Jakob; Wilke, Martina; Harris-Mostert, Emilio D. R. O.; Elgersma, Minetta; Bain, Jennifer; Balasubramanian, Meena; Banka, Siddharth; Benke, Paul J.; Bertrand, Miriam; Blesson, Alyssa E.; Clayton-Smith, Jill; Ellingford, Jamie M.; Gillentine, Madelyn A.; Goodloe, Dana H.; Haack, Tobias B.; Jain, Mahim; Krantz, Ian; Luu, Sharon M.; McPheron, Molly; Muss, Candace L.; Raible, Sarah E.; Robin, Nathaniel H.; Spiller, Michael; Starling, Susan; Sweetser, David A.; Thiffault, Isabelle; Vetrini, Francesco; Witt, Dennis; Woods, Emily; Zhou, Dihong; Genomics England Research Consortium; Undiagnosed Diseases Network; Elgersma, Ype; van Esbroeck, Annelot C. M.; Medical and Molecular Genetics, School of Medicine
    Heterogeneous nuclear ribonucleoprotein C (HNRNPC) is an essential, ubiquitously abundant protein involved in mRNA processing. Genetic variants in other members of the HNRNP family have been associated with neurodevelopmental disorders. Here, we describe 13 individuals with global developmental delay, intellectual disability, behavioral abnormalities, and subtle facial dysmorphology with heterozygous HNRNPC germline variants. Five of them bear an identical in-frame deletion of nine amino acids in the extreme C terminus. To study the effect of this recurrent variant as well as HNRNPC haploinsufficiency, we used induced pluripotent stem cells (iPSCs) and fibroblasts obtained from affected individuals. While protein localization and oligomerization were unaffected by the recurrent C-terminal deletion variant, total HNRNPC levels were decreased. Previously, reduced HNRNPC levels have been associated with changes in alternative splicing. Therefore, we performed a meta-analysis on published RNA-seq datasets of three different cell lines to identify a ubiquitous HNRNPC-dependent signature of alternative spliced exons. The identified signature was not only confirmed in fibroblasts obtained from an affected individual but also showed a significant enrichment for genes associated with intellectual disability. Hence, we assessed the effect of decreased and increased levels of HNRNPC on neuronal arborization and neuronal migration and found that either condition affects neuronal function. Taken together, our data indicate that HNRNPC haploinsufficiency affects alternative splicing of multiple intellectual disability-associated genes and that the developing brain is sensitive to aberrant levels of HNRNPC. Hence, our data strongly support the inclusion of HNRNPC to the family of HNRNP-related neurodevelopmental disorders.
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    Human fibroblast and stem cell resource from the Dominantly Inherited Alzheimer Network
    (BMC, 2018-07-25) Karch, Celeste M.; Hernández, Damián Hernández; Wang, Jen-Chyong; Marsh, Jacob; Hewit, Alex W.; Hsu, Simon; Norton, Joanne; Levitch, Denise; Donahue, Tamara; Sigurdson, Wendy; Ghetti, Bernardino; Farlow, Martin; Chhatwal, Jasmeer; Berman, Sarah; Cruchaga, Carlos; Morris, John C.; Bateman, Randall J.; Dominantly Inherited Alzheimer Network (DIAN); Pébay, Alice; Goate, Alison M.; Pathology and Laboratory Medicine, School of Medicine
    BACKGROUND: Mutations in amyloid precursor protein (APP), presenilin 1 (PSEN1) and presenilin 2 (PSEN2) cause autosomal dominant forms of Alzheimer disease (ADAD). More than 280 pathogenic mutations have been reported in APP, PSEN1, and PSEN2. However, understanding of the basic biological mechanisms that drive the disease are limited. The Dominantly Inherited Alzheimer Network (DIAN) is an international observational study of APP, PSEN1, and PSEN2 mutation carriers with the goal of determining the sequence of changes in presymptomatic mutation carriers who are destined to develop Alzheimer disease. RESULTS: We generated a library of 98 dermal fibroblast lines from 42 ADAD families enrolled in DIAN. We have reprogrammed a subset of the DIAN fibroblast lines into patient-specific induced pluripotent stem cell (iPSC) lines. These cells were thoroughly characterized for pluripotency markers. CONCLUSIONS: This library represents a comprehensive resource that can be used for disease modeling and the development of novel therapeutics.