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Abbas G, Vyas R, Noble JC, Lin B, Lane RP. Transformation of an olfactory placode-derived cell into one with stem cell characteristics by disrupting epigenetic barriers. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.03.592460. [PMID: 38746208 PMCID: PMC11092772 DOI: 10.1101/2024.05.03.592460] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2024]
Abstract
The mammalian olfactory neuronal lineage is regenerative, and accordingly, maintains a population of pluripotent cells that replenish olfactory sensory neurons and other olfactory cell types during the life of the animal. Moreover, in response to acute injury, the early transit amplifying cells along the olfactory sensory neuronal lineage are able to de-differentiate to shift resources in support of tissue restoration. In order to further explore plasticity of various cellular stages along the olfactory sensory neuronal lineage, we challenged the epigenetic stability of two olfactory placode-derived cell lines that model immature olfactory sensory neuronal stages. We found that perturbation of the Ehmt2 chromatin modifier transformed the growth properties, morphology, and gene expression profiles towards states with several stem cell characteristics. This transformation was dependent on continued expression of the large T-antigen, and was enhanced by Sox2 over-expression. These findings may provide momentum for exploring inherent cellular plasticity within early cell types of the olfactory lineage, as well as potentially add to our knowledge of cellular reprogramming. SUMMARY STATEMENT Discovering how epigenetic modifications influence olfactory neuronal lineage plasticity offers insights into regenerative potential and cellular reprogramming.
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Sokolova K, Theesfeld CL, Wong AK, Zhang Z, Dolinski K, Troyanskaya OG. Atlas of primary cell-type-specific sequence models of gene expression and variant effects. CELL REPORTS METHODS 2023; 3:100580. [PMID: 37703883 PMCID: PMC10545936 DOI: 10.1016/j.crmeth.2023.100580] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Revised: 05/05/2023] [Accepted: 08/18/2023] [Indexed: 09/15/2023]
Abstract
Human biology is rooted in highly specialized cell types programmed by a common genome, 98% of which is outside of genes. Genetic variation in the enormous noncoding space is linked to the majority of disease risk. To address the problem of linking these variants to expression changes in primary human cells, we introduce ExPectoSC, an atlas of modular deep-learning-based models for predicting cell-type-specific gene expression directly from sequence. We provide models for 105 primary human cell types covering 7 organ systems, demonstrate their accuracy, and then apply them to prioritize relevant cell types for complex human diseases. The resulting atlas of sequence-based gene expression and variant effects is publicly available in a user-friendly interface and readily extensible to any primary cell types. We demonstrate the accuracy of our approach through systematic evaluations and apply the models to prioritize ClinVar clinical variants of uncertain significance, verifying our top predictions experimentally.
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Affiliation(s)
- Ksenia Sokolova
- Department of Computer Science, Princeton University, Princeton, NJ 08544, USA; Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA
| | - Chandra L Theesfeld
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA.
| | - Aaron K Wong
- Flatiron Institute, Simons Foundation, New York City, NY 10001, USA
| | - Zijun Zhang
- Flatiron Institute, Simons Foundation, New York City, NY 10001, USA; Division of Artificial Intelligence in Medicine, Cedars-Sinai Medical Center, 116 N. Robertson Boulevard, Los Angeles, CA 90048, USA
| | - Kara Dolinski
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA
| | - Olga G Troyanskaya
- Department of Computer Science, Princeton University, Princeton, NJ 08544, USA; Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA; Flatiron Institute, Simons Foundation, New York City, NY 10001, USA.
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3
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Sekulic M, Abdollahi N, Graf L, Deigendesch N, Puche R, Bodmer D, Petkovic V. Human blood-labyrinth barrier on a chip: a unique in vitro tool for investigation of BLB properties. RSC Adv 2023; 13:25508-25517. [PMID: 37636514 PMCID: PMC10450574 DOI: 10.1039/d3ra04704k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Accepted: 08/14/2023] [Indexed: 08/29/2023] Open
Abstract
Hearing loss is one of the leading causes of disability worldwide, usually as a result of hair cell damage in the inner ear due to aging, acoustic trauma, or exposure to antibiotics or chemotherapy. No drug therapies can protect or restore hearing and current in vitro and animal models used in drug discovery have a very low success rate, mostly due to major differences in anatomy and accessibility of the inner ear environment between species. The blood-labyrinth barrier (BLB) in the stria vascularis is a highly specialized capillary network that controls exchanges between the blood and interstitial space in the cochlea. The BLB is critical for normal hearing, functioning as a physical, transport, and metabolic barrier. To address its complexity and accessibility, we created the first micro-engineered human model of BLB on a chip using autogenous progenitor cells from adult temporal bones. We successfully isolated the BLB from post-mortem human tissue and established an endothelial cell and pericyte culture system on a BLB chip. Using biocompatible materials, we fabricated sustainable two chamber chips. We validated the size-dependent permeability limits of our BLB model by measuring the permeability to daptomycin (molecular weight 1.6 kDa) and midazolam (molecular weight 325.78 Da). Daptomycin did not pass through the BLB layer, whereas midazolam readily passed through the BLB in our system. Thus, our BLB-chip mimicked the integrity and permeability of human stria vascularis capillaries. This represents a major step towards establishing a reliable model for the development of hearing loss treatments.
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Affiliation(s)
- Marijana Sekulic
- Department of Biomedicine, University Hospital Basel, University of Basel Basel Switzerland
| | - Narjes Abdollahi
- Department of Biomedicine, University Hospital Basel, University of Basel Basel Switzerland
| | - Lukas Graf
- Clinic for Otolaryngology, Head and Neck Surgery, University Hospital Basel Basel Switzerland
| | | | - Raoul Puche
- Department of Biomedicine, University Hospital Basel, University of Basel Basel Switzerland
| | - Daniel Bodmer
- Department of Biomedicine, University Hospital Basel, University of Basel Basel Switzerland
- Clinic for Otolaryngology, Head and Neck Surgery, University Hospital Basel Basel Switzerland
| | - Vesna Petkovic
- Department of Biomedicine, University Hospital Basel, University of Basel Basel Switzerland
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Luxen M, van Meurs M, Molema G. Unlocking the Untapped Potential of Endothelial Kinase and Phosphatase Involvement in Sepsis for Drug Treatment Design. Front Immunol 2022; 13:867625. [PMID: 35634305 PMCID: PMC9136877 DOI: 10.3389/fimmu.2022.867625] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Accepted: 03/28/2022] [Indexed: 11/29/2022] Open
Abstract
Sepsis is a devastating clinical condition that can lead to multiple organ failure and death. Despite advancements in our understanding of molecular mechanisms underlying sepsis and sepsis-associated multiple organ failure, no effective therapeutic treatment to directly counteract it has yet been established. The endothelium is considered to play an important role in sepsis. This review highlights a number of signal transduction pathways involved in endothelial inflammatory activation and dysregulated endothelial barrier function in response to sepsis conditions. Within these pathways – NF-κB, Rac1/RhoA GTPases, AP-1, APC/S1P, Angpt/Tie2, and VEGF/VEGFR2 – we focus on the role of kinases and phosphatases as potential druggable targets for therapeutic intervention. Animal studies and clinical trials that have been conducted for this purpose are discussed, highlighting reasons why they might not have resulted in the expected outcomes, and which lessons can be learned from this. Lastly, opportunities and challenges that sepsis and sepsis-associated multiple organ failure research are currently facing are presented, including recommendations on improved experimental design to increase the translational power of preclinical research to the clinic.
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Affiliation(s)
- Matthijs Luxen
- Department of Pathology and Medical Biology, Medical Biology Section, University Medical Center Groningen, University of Groningen, Groningen, Netherlands
- Department of Critical Care, University Medical Center Groningen, University of Groningen, Groningen, Netherlands
- *Correspondence: Matthijs Luxen,
| | - Matijs van Meurs
- Department of Pathology and Medical Biology, Medical Biology Section, University Medical Center Groningen, University of Groningen, Groningen, Netherlands
- Department of Critical Care, University Medical Center Groningen, University of Groningen, Groningen, Netherlands
| | - Grietje Molema
- Department of Pathology and Medical Biology, Medical Biology Section, University Medical Center Groningen, University of Groningen, Groningen, Netherlands
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Sidorova OA, Sayed S, Paszkowski-Rogacz M, Seifert M, Camgöz A, Roeder I, Bornhäuser M, Thiede C, Buchholz F. RNAi-Mediated Screen of Primary AML Cells Nominates MDM4 as a Therapeutic Target in NK-AML with DNMT3A Mutations. Cells 2022; 11:cells11050854. [PMID: 35269477 PMCID: PMC8909053 DOI: 10.3390/cells11050854] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Revised: 02/15/2022] [Accepted: 02/23/2022] [Indexed: 12/22/2022] Open
Abstract
DNA-methyltransferase 3A (DNMT3A) mutations belong to the most frequent genetic aberrations found in adult acute myeloid leukemia (AML). Recent evidence suggests that these mutations arise early in leukemogenesis, marking leukemic progenitors and stem cells, and persist through consolidation chemotherapy, providing a pool for AML relapse. Currently, there are no therapeutic approaches directed specifically against this cell population. To unravel therapeutically actionable targets in mutant DNMT3A-driven AML cells, we have performed a focused RNAi screen in a panel of 30 primary AML samples, all carrying a DNMT3A R882 mutation. As one of the strongest hits, we identified MDM4 as a gene essential for proliferation of primary DNMT3AWT/R882X AML cells. We analyzed a publicly available RNA-Seq dataset of primary normal karyotype (NK) AML samples and found a trend towards MDM4 transcript overexpression particularly in DNMT3A-mutant samples. Moreover, we found that the MDM2/4 inhibitor ALRN-6924 impairs growth of DNMT3AWT/R882X primary cells in vitro by inducing cell cycle arrest through upregulation of p53 target genes. Our results suggest that MDM4 inhibition is a potential target in NK-AML patients bearing DNMT3A R882X mutations.
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Affiliation(s)
- Olga Alexandra Sidorova
- Medical Systems Biology, Faculty of Medicine, Technische Universität Dresden, 01307 Dresden, Germany; (O.A.S.); (S.S.); (M.P.-R.)
| | - Shady Sayed
- Medical Systems Biology, Faculty of Medicine, Technische Universität Dresden, 01307 Dresden, Germany; (O.A.S.); (S.S.); (M.P.-R.)
| | - Maciej Paszkowski-Rogacz
- Medical Systems Biology, Faculty of Medicine, Technische Universität Dresden, 01307 Dresden, Germany; (O.A.S.); (S.S.); (M.P.-R.)
| | - Michael Seifert
- Institute for Medical Informatics and Biometry (IMB), Technische Universität Dresden, 01307 Dresden, Germany; (M.S.); (I.R.)
| | - Aylin Camgöz
- Hopp Children’s Cancer Center Heidelberg, 69120 Heidelberg, Germany;
- German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany; (M.B.); (C.T.)
| | - Ingo Roeder
- Institute for Medical Informatics and Biometry (IMB), Technische Universität Dresden, 01307 Dresden, Germany; (M.S.); (I.R.)
| | - Martin Bornhäuser
- German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany; (M.B.); (C.T.)
- National Center for Tumor Diseases (NCT/UCC), 01307 Dresden, Germany
- Faculty of Medicine, University Hospital Carl Gustav Carus, Technische Universität Dresden, 01307 Dresden, Germany
- Helmholtz-Zentrum Dresden—Rossendorf (HZDR), 01328 Dresden, Germany
- Medical Clinic and Polyclinic I, University Hospital Carl Gustav Carus, Technische Universität Dresden, 01307 Dresden, Germany
- German Cancer Consortium (DKTK), Partner Site Dresden, 01307 Dresden, Germany
| | - Christian Thiede
- German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany; (M.B.); (C.T.)
- National Center for Tumor Diseases (NCT/UCC), 01307 Dresden, Germany
- Faculty of Medicine, University Hospital Carl Gustav Carus, Technische Universität Dresden, 01307 Dresden, Germany
- Helmholtz-Zentrum Dresden—Rossendorf (HZDR), 01328 Dresden, Germany
- Medical Clinic and Polyclinic I, University Hospital Carl Gustav Carus, Technische Universität Dresden, 01307 Dresden, Germany
- German Cancer Consortium (DKTK), Partner Site Dresden, 01307 Dresden, Germany
| | - Frank Buchholz
- Medical Systems Biology, Faculty of Medicine, Technische Universität Dresden, 01307 Dresden, Germany; (O.A.S.); (S.S.); (M.P.-R.)
- German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany; (M.B.); (C.T.)
- National Center for Tumor Diseases (NCT/UCC), 01307 Dresden, Germany
- Faculty of Medicine, University Hospital Carl Gustav Carus, Technische Universität Dresden, 01307 Dresden, Germany
- Helmholtz-Zentrum Dresden—Rossendorf (HZDR), 01328 Dresden, Germany
- German Cancer Consortium (DKTK), Partner Site Dresden, 01307 Dresden, Germany
- Correspondence:
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Seymour AJ, Westerfield AD, Cornelius VC, Skylar-Scott MA, Heilshorn SC. Bioprinted microvasculature: progressing from structure to function. Biofabrication 2022; 14:10.1088/1758-5090/ac4fb5. [PMID: 35086069 PMCID: PMC8988885 DOI: 10.1088/1758-5090/ac4fb5] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Accepted: 01/27/2022] [Indexed: 11/12/2022]
Abstract
Three-dimensional (3D) bioprinting seeks to unlock the rapid generation of complex tissue constructs, but long-standing challenges with efficientin vitromicrovascularization must be solved before this can become a reality. Microvasculature is particularly challenging to biofabricate due to the presence of a hollow lumen, a hierarchically branched network topology, and a complex signaling milieu. All of these characteristics are required for proper microvascular-and, thus, tissue-function. While several techniques have been developed to address distinct portions of this microvascularization challenge, no single approach is capable of simultaneously recreating all three microvascular characteristics. In this review, we present a three-part framework that proposes integration of existing techniques to generate mature microvascular constructs. First, extrusion-based 3D bioprinting creates a mesoscale foundation of hollow, endothelialized channels. Second, biochemical and biophysical cues induce endothelial sprouting to create a capillary-mimetic network. Third, the construct is conditioned to enhance network maturity. Across all three of these stages, we highlight the potential for extrusion-based bioprinting to become a central technique for engineering hierarchical microvasculature. We envision that the successful biofabrication of functionally engineered microvasculature will address a critical need in tissue engineering, and propel further advances in regenerative medicine andex vivohuman tissue modeling.
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Affiliation(s)
- Alexis J. Seymour
- Department of Bioengineering, Stanford University, 443 Via Ortega, Shriram Center Room 119, Stanford, CA 94305, USA
| | - Ashley D. Westerfield
- Department of Bioengineering, Stanford University, 443 Via Ortega, Shriram Center Room 119, Stanford, CA 94305, USA
| | - Vincent C. Cornelius
- Department of Bioengineering, Stanford University, 443 Via Ortega, Shriram Center Room 119, Stanford, CA 94305, USA
| | - Mark A. Skylar-Scott
- Department of Bioengineering, Stanford University, 443 Via Ortega, Shriram Center Room 119, Stanford, CA 94305, USA
| | - Sarah C. Heilshorn
- Department of Materials Science & Engineering, Stanford University, 476 Lomita Mall, McCullough Room 246, Stanford, CA 94305, USA,Author to whom any correspondence should be addressed.
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Olde Hanhof CJA, Yousef Yengej FA, Rookmaaker MB, Verhaar MC, van der Wijst J, Hoenderop JG. Modeling Distal Convoluted Tubule (Patho)Physiology: An Overview of Past Developments and an Outlook Toward the Future. Tissue Eng Part C Methods 2021; 27:200-212. [PMID: 33544049 DOI: 10.1089/ten.tec.2020.0345] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
The kidneys are essential for maintaining electrolyte homeostasis. Blood electrolyte composition is controlled by active reabsorption and secretion processes in dedicated segments of the kidney tubule. Specifically, the distal convoluted tubule (DCT) and connecting tubule are important for regulating the final excretion of sodium, magnesium, and calcium. Studies unravelling the specific function of these segments have greatly improved our understanding of DCT (patho)physiology. Over the years, experimental models used to study the DCT have changed and the field has advanced from early dissection studies with rats and rabbits to the use of various transgenic mouse models. Developments in dissection techniques and cell culture methods have resulted in immortalized mouse DCT cell lines and made it possible to specifically obtain DCT fragments for ex vivo studies. However, we still do not fully understand the complex (patho)physiology of this segment and there is need for advanced human DCT models. Recently, kidney organoids and tubuloids have emerged as new complex cell models that provide excellent opportunities for physiological studies, disease modeling, drug discovery, and even personalized medicine in the future. This review presents an overview of cell models used to study the DCT and provides an outlook on kidney organoids and tubuloids as model for DCT (patho)physiology. Impact statement This study provides a detailed overview of past and future developments on cell models used to study kidney (patho)physiology and specifically the distal convoluted tubule (DCT) segment. Hereby, we highlight the need for an advanced human cell model of this segment and summarize recent advances in the field of kidney organoids and tubuloids with a focus on DCT properties. The findings reported in this review are significant for future developments toward an advanced human model of the DCT that will help to increase our understanding of DCT (patho)physiology.
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Affiliation(s)
- Charlotte J A Olde Hanhof
- Department of Physiology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Fjodor A Yousef Yengej
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences, Utrecht, The Netherlands.,Department of Nephrology and Hypertension, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Maarten B Rookmaaker
- Department of Nephrology and Hypertension, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Marianne C Verhaar
- Department of Nephrology and Hypertension, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Jenny van der Wijst
- Department of Physiology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Joost G Hoenderop
- Department of Physiology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
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Current and future applications of induced pluripotent stem cell-based models to study pathological proteins in neurodegenerative disorders. Mol Psychiatry 2021; 26:2685-2706. [PMID: 33495544 PMCID: PMC8505258 DOI: 10.1038/s41380-020-00999-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Revised: 12/02/2020] [Accepted: 12/09/2020] [Indexed: 12/13/2022]
Abstract
Neurodegenerative disorders emerge from the failure of intricate cellular mechanisms, which ultimately lead to the loss of vulnerable neuronal populations. Research conducted across several laboratories has now provided compelling evidence that pathogenic proteins can also contribute to non-cell autonomous toxicity in several neurodegenerative contexts, including Alzheimer's, Parkinson's, and Huntington's diseases as well as Amyotrophic Lateral Sclerosis. Given the nearly ubiquitous nature of abnormal protein accumulation in such disorders, elucidating the mechanisms and routes underlying these processes is essential to the development of effective treatments. To this end, physiologically relevant human in vitro models are critical to understand the processes surrounding uptake, release and nucleation under physiological or pathological conditions. This review explores the use of human-induced pluripotent stem cells (iPSCs) to study prion-like protein propagation in neurodegenerative diseases, discusses advantages and limitations of this model, and presents emerging technologies that, combined with the use of iPSC-based models, will provide powerful model systems to propel fundamental research forward.
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