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Masters H, Wang S, Tu C, Nguyen Q, Sha Y, Karikomi MK, Fung PSR, Tran B, Martel C, Kwang N, Neel M, Jaime OG, Espericueta V, Johnson BA, Kessenbrock K, Nie Q, Monuki ES. Sequential emergence and contraction of epithelial subtypes in the prenatal human choroid plexus revealed by a stem cell model. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.12.598747. [PMID: 38948782 PMCID: PMC11212933 DOI: 10.1101/2024.06.12.598747] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/02/2024]
Abstract
Despite the major roles of choroid plexus epithelial cells (CPECs) in brain homeostasis and repair, their developmental lineage and diversity remain undefined. In simplified differentiations from human pluripotent stem cells, derived CPECs (dCPECs) displayed canonical properties and dynamic multiciliated phenotypes that interacted with Aβ uptake. Single dCPEC transcriptomes over time correlated well with human organoid and fetal CPECs, while pseudotemporal and cell cycle analyses highlighted the direct CPEC origin from neuroepithelial cells. In addition, time series analyses defined metabolic (type 1) and ciliogenic dCPECs (type 2) at early timepoints, followed by type 1 diversification into anabolic-secretory (type 1a) and catabolic-absorptive subtypes (type 1b) as type 2 cells contracted. These temporal patterns were then confirmed in independent derivations and mapped to prenatal stages using human tissues. In addition to defining the prenatal lineage of human CPECs, these findings suggest new dynamic models of ChP support for the developing human brain.
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2
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O’Connor SA, Garcia L, Patel AP, Hugnot JP, Paddison PJ, Plaisier CL. Breaking out of the cycle: Including quiescence in cell cycle classification. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.16.589816. [PMID: 38659838 PMCID: PMC11042294 DOI: 10.1101/2024.04.16.589816] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/26/2024]
Abstract
Single-cell transcriptomics has unveiled a vast landscape of cellular heterogeneity in which the cell cycle is a significant component. We trained a high-resolution cell cycle classifier (ccAFv2) using single cell RNA-seq (scRNA-seq) characterized human neural stem cells. The ccAFv2 classifies six cell cycle states (G1, Late G1, S, S/G2, G2/M, and M/Early G1) and a quiescent-like G0 state, and it incorporates a tunable parameter to filter out less certain classifications. The ccAFv2 classifier performed better than or equivalent to other state-of-the-art methods even while classifying more cell cycle states, including G0. We showcased the versatility of ccAFv2 by successfully applying it to classify cells, nuclei, and spatial transcriptomics data in humans and mice, using various normalization methods and gene identifiers. We provide methods to regress the cell cycle expression patterns out of single cell or nuclei data to uncover underlying biological signals. The classifier can be used either as an R package integrated with Seurat (https://github.com/plaisier-lab/ccafv2_R) or a PyPI package integrated with scanpy (https://pypi.org/project/ccAFv2/). We proved that ccAFv2 has enhanced accuracy, flexibility, and adaptability across various experimental conditions, establishing ccAFv2 as a powerful tool for dissecting complex biological systems, unraveling cellular heterogeneity, and deciphering the molecular mechanisms by which proliferation and quiescence affect cellular processes.
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Affiliation(s)
- Samantha A. O’Connor
- School of Biological and Health Systems Engineering, Arizona State University, Tempe AZ, USA
| | - Leonor Garcia
- Institut de Génomique Fonctionnelle, Université de Montpellier, CNRS, INSERM, 141 rue de la Cardonille, 34091, Montpellier, France
| | - Anoop P. Patel
- Brotman-Baty Institute for Precision Medicine, University of Washington, Seattle, WA, USA
- Department of Neurosurgery, Preston Robert Tisch Brain Tumor Center, Duke University, Durham, NC, USA
| | - Jean-Philippe Hugnot
- Institut de Génomique Fonctionnelle, Université de Montpellier, CNRS, INSERM, 141 rue de la Cardonille, 34091, Montpellier, France
| | - Patrick J. Paddison
- Human Biology Division, Fred Hutchinson Cancer Research Center, Seattle WA, USA
| | - Christopher L. Plaisier
- School of Biological and Health Systems Engineering, Arizona State University, Tempe AZ, USA
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3
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van der Weijden VA, Stötzel M, Iyer DP, Fauler B, Gralinska E, Shahraz M, Meierhofer D, Vingron M, Rulands S, Alexandrov T, Mielke T, Bulut-Karslioglu A. FOXO1-mediated lipid metabolism maintains mammalian embryos in dormancy. Nat Cell Biol 2024; 26:181-193. [PMID: 38177284 PMCID: PMC10866708 DOI: 10.1038/s41556-023-01325-3] [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] [Received: 06/23/2022] [Accepted: 11/29/2023] [Indexed: 01/06/2024]
Abstract
Mammalian developmental timing is adjustable in vivo by preserving pre-implantation embryos in a dormant state called diapause. Inhibition of the growth regulator mTOR (mTORi) pauses mouse development in vitro, yet how embryonic dormancy is maintained is not known. Here we show that mouse embryos in diapause are sustained by using lipids as primary energy source. In vitro, supplementation of embryos with the metabolite L-carnitine balances lipid consumption, puts the embryos in deeper dormancy and boosts embryo longevity. We identify FOXO1 as an essential regulator of the energy balance in dormant embryos and propose, through meta-analyses of dormant cell signatures, that it may be a common regulator of dormancy across adult tissues. Our results lift a constraint on in vitro embryo survival and suggest that lipid metabolism may be a critical metabolic transition relevant for longevity and stem cell function across tissues.
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Affiliation(s)
- Vera A van der Weijden
- Stem Cell Chromatin Group, Department of Genome Regulation, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Maximilian Stötzel
- Stem Cell Chromatin Group, Department of Genome Regulation, Max Planck Institute for Molecular Genetics, Berlin, Germany
- Institute of Chemistry and Biochemistry, Department of Biology, Chemistry and Pharmacy, Freie Universität Berlin, Berlin, Germany
| | - Dhanur P Iyer
- Stem Cell Chromatin Group, Department of Genome Regulation, Max Planck Institute for Molecular Genetics, Berlin, Germany
- Institute of Chemistry and Biochemistry, Department of Biology, Chemistry and Pharmacy, Freie Universität Berlin, Berlin, Germany
| | - Beatrix Fauler
- Microscopy and Cryo-Electron Microscopy Facility, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Elzbieta Gralinska
- Department of Computational Molecular Biology, Max Planck Institute for Molecular Genetics, Berlin, Germany
- Roche Innovation Center Zurich, Schlieren, Switzerland
| | - Mohammed Shahraz
- Structural and Computational Biology, European Molecular Biology Laboratory, Heidelberg, Germany
| | - David Meierhofer
- Mass Spectrometry Facility, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Martin Vingron
- Department of Computational Molecular Biology, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Steffen Rulands
- Max Planck Institute for the Physics of Complex Systems, Dresden, Germany
- Arnold Sommerfeld Center for Theoretical Physics, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Theodore Alexandrov
- Structural and Computational Biology, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Thorsten Mielke
- Microscopy and Cryo-Electron Microscopy Facility, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Aydan Bulut-Karslioglu
- Stem Cell Chromatin Group, Department of Genome Regulation, Max Planck Institute for Molecular Genetics, Berlin, Germany.
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4
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Beirute-Herrera J, López-Amo Calvo B, Edenhofer F, Esk C. The promise of genetic screens in human in vitro brain models. Biol Chem 2024; 405:13-24. [PMID: 37697643 DOI: 10.1515/hsz-2023-0174] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Accepted: 08/21/2023] [Indexed: 09/13/2023]
Abstract
Advances of in vitro culture models have allowed unprecedented insights into human neurobiology. At the same time genetic screening has matured into a robust and accessible experimental strategy allowing for the simultaneous study of many genes in parallel. The combination of both technologies is a newly emerging tool for neuroscientists, opening the door to identifying causal cell- and tissue-specific developmental and disease mechanisms. However, with complex experimental genetic screening set-ups new challenges in data interpretation and experimental scope arise that require a deep understanding of the benefits and challenges of individual approaches. In this review, we summarize the literature that applies genetic screening to in vitro brain models, compare experimental strengths and weaknesses and point towards future directions of these promising approaches.
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Affiliation(s)
- Julianne Beirute-Herrera
- Institute of Molecular Biology, University Innsbruck, Technikerstr. 25, A-6020 Innsbruck, Austria
- Center for Molecular Biosciences, University Innsbruck, Technikerstr. 25, A-6020 Innsbruck, Austria
| | - Beatriz López-Amo Calvo
- Institute of Molecular Biology, University Innsbruck, Technikerstr. 25, A-6020 Innsbruck, Austria
- Center for Molecular Biosciences, University Innsbruck, Technikerstr. 25, A-6020 Innsbruck, Austria
| | - Frank Edenhofer
- Institute of Molecular Biology, University Innsbruck, Technikerstr. 25, A-6020 Innsbruck, Austria
- Center for Molecular Biosciences, University Innsbruck, Technikerstr. 25, A-6020 Innsbruck, Austria
| | - Christopher Esk
- Institute of Molecular Biology, University Innsbruck, Technikerstr. 25, A-6020 Innsbruck, Austria
- Center for Molecular Biosciences, University Innsbruck, Technikerstr. 25, A-6020 Innsbruck, Austria
- Institute of Molecular Biotechnology of the Austrian Academy of Science (IMBA), Vienna BioCenter (VBC), Dr. Bohr Gasse 3, 1030 Vienna, Austria
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5
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Fu RZ, Cottrell O, Cutillo L, Rowntree A, Zador Z, Wurdak H, Papalopulu N, Marinopoulou E. Identification of genes with oscillatory expression in glioblastoma: the paradigm of SOX2. Sci Rep 2024; 14:2123. [PMID: 38267500 PMCID: PMC10808450 DOI: 10.1038/s41598-024-51340-z] [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] [Received: 11/10/2023] [Accepted: 01/03/2024] [Indexed: 01/26/2024] Open
Abstract
Quiescence, a reversible state of cell-cycle arrest, is an important state during both normal development and cancer progression. For example, in glioblastoma (GBM) quiescent glioblastoma stem cells (GSCs) play an important role in re-establishing the tumour, leading to relapse. While most studies have focused on identifying differentially expressed genes between proliferative and quiescent cells as potential drivers of this transition, recent studies have shown the importance of protein oscillations in controlling the exit from quiescence of neural stem cells. Here, we have undertaken a genome-wide bioinformatic inference approach to identify genes whose expression oscillates and which may be good candidates for controlling the transition to and from the quiescent cell state in GBM. Our analysis identified, among others, a list of important transcription regulators as potential oscillators, including the stemness gene SOX2, which we verified to oscillate in quiescent GSCs. These findings expand on the way we think about gene regulation and introduce new candidate genes as key regulators of quiescence.
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Affiliation(s)
- Richard Zhiming Fu
- Division of Developmental Biology and Medicine, School of Medical Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Oxford Road, Manchester, M13 9PT, UK
- Geoffrey Jefferson Brain Research Centre, University of Manchester, Manchester, M13 9PL, UK
- Department of Neurosurgery, Manchester Centre for Clinical Neurosciences, Salford Care Organisation, Northern Care Alliance NHS Foundation Trust, Salford Royal, Stott Lane, Salford, M6 8HD, UK
| | - Oliver Cottrell
- Division of Developmental Biology and Medicine, School of Medical Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Oxford Road, Manchester, M13 9PT, UK
| | - Luisa Cutillo
- School of Mathematics, University of Leeds, Woodhouse, Leeds, LS2 9JT, UK
| | - Andrew Rowntree
- Division of Developmental Biology and Medicine, School of Medical Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Oxford Road, Manchester, M13 9PT, UK
| | - Zsolt Zador
- Division of Neurosurgery, Department of Surgery, St. Michael's Hospital, 36 Queen St E, Toronto, ON, M5B 1W8, Canada
- Department of Surgery, McMaster University, 1280 Mains St W, Hamilton, ON, L8S 4L8, Canada
- Center for Discovery in Cancer Research (CDCR), McMaster University, 1280 Main St W, Hamilton, ON, L8S 4L8, Canada
| | - Heiko Wurdak
- Stem Cell and Brain Tumour Group, Leeds Institute of Medical Research at St James's, School of Medicine, University of Leeds, Leeds, LS9 7TF, UK
| | - Nancy Papalopulu
- Division of Developmental Biology and Medicine, School of Medical Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Oxford Road, Manchester, M13 9PT, UK.
| | - Elli Marinopoulou
- Division of Developmental Biology and Medicine, School of Medical Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Oxford Road, Manchester, M13 9PT, UK.
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6
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Schoof M, Epplen GD, Walter C, Ballast A, Holdhof D, Göbel C, Neyazi S, Varghese J, Albert TK, Kerl K, Schüller U. The tumor suppressor CREBBP and the oncogene MYCN cooperate to induce malignant brain tumors in mice. Oncogenesis 2023; 12:36. [PMID: 37407554 DOI: 10.1038/s41389-023-00481-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Revised: 05/26/2023] [Accepted: 06/20/2023] [Indexed: 07/07/2023] Open
Abstract
The tumor suppressor and chromatin modifier cAMP response element-binding protein binding protein (CREBBP) and v-myc avian myelocytomatosis viral oncogene neuroblastoma derived homolog (MYCN), a member of the MYC oncogene family, are critically involved in brain development. Both genes are frequently mutated in the same tumor entities, including high-grade glioma and medulloblastoma. Therefore, we hypothesized that alterations in both genes cooperate to induce brain tumor formation. For further investigation, hGFAP-cre::CrebbpFl/Fl::lsl-MYCN mice were generated, which combine Crebbp deletion with overexpression of MYCN in neural stem cells (NSCs). Within eight months, these animals developed aggressive forebrain tumors. The first tumors were detectable in the olfactory bulbs of seven-day-old mice. This location raises the possibility that presumptive founder cells are derived from the ventricular-subventricular zone (V-SVZ). To examine the cellular biology of these tumors, single-cell RNA sequencing was performed, which revealed high intratumoral heterogeneity. Data comparison with reference CNS cell types indicated the highest similarity of tumor cells with transit-amplifying NSCs or activated NSCs of the V-SVZ. Consequently, we analyzed V-SVZ NSCs of our mouse model aiming to confirm that the tumors originate from this stem cell niche. Mutant V-SVZ NSCs showed significantly increased cell viability and proliferation as well as reduced glial and neural differentiation in vitro compared to control cells. In summary, we demonstrate the oncogenic potential of a combined loss of function of CREBBP and overexpression of MYCN in this cell population. hGFAP-cre::CrebbpFl/Fl::lsl-MYCN mice thus provide a valuable tool to study tumor-driving mechanisms in a key neural stem/ progenitor cell niche.
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Affiliation(s)
- Melanie Schoof
- Research Institute Children`s Cancer Center, Hamburg, Germany
- Department of Pediatric Hematology and Oncology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | | | - Carolin Walter
- Institute of Medical Informatics, University of Münster, Münster, Germany
| | - Annika Ballast
- Department of Pediatric Hematology and Oncology, University Children's Hospital Münster, Münster, Germany
| | - Dörthe Holdhof
- Research Institute Children`s Cancer Center, Hamburg, Germany
- Department of Pediatric Hematology and Oncology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Carolin Göbel
- Research Institute Children`s Cancer Center, Hamburg, Germany
- Department of Pediatric Hematology and Oncology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Sina Neyazi
- Research Institute Children`s Cancer Center, Hamburg, Germany
- Department of Pediatric Hematology and Oncology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Julian Varghese
- Institute of Medical Informatics, University of Münster, Münster, Germany
| | - Thomas Karl Albert
- Department of Pediatric Hematology and Oncology, University Children's Hospital Münster, Münster, Germany
| | - Kornelius Kerl
- Department of Pediatric Hematology and Oncology, University Children's Hospital Münster, Münster, Germany
| | - Ulrich Schüller
- Research Institute Children`s Cancer Center, Hamburg, Germany.
- Department of Pediatric Hematology and Oncology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany.
- Institute of Neuropathology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany.
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7
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Paul EN, Carpenter TJ, Fitch S, Sheridan R, Lau KH, Arora R, Teixeira JM. Cysteine-rich intestinal protein 1 is a novel surface marker for human myometrial stem/progenitor cells. Commun Biol 2023; 6:686. [PMID: 37400623 DOI: 10.1038/s42003-023-05061-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Accepted: 06/21/2023] [Indexed: 07/05/2023] Open
Abstract
Myometrial stem/progenitor cells (MyoSPCs) have been proposed as the cells of origin for uterine fibroids, but the identity of the MyoSPC has not been well established. We previously identified SUSD2 as a possible MyoSPC marker, but the relatively poor enrichment in stem cell characteristics of SUSD2+ over SUSD2- cells compelled us to find better markers. We combined bulk RNA-seq of SUSD2+/- cells with single cell RNA-seq to identify markers for MyoSPCs. We observed seven distinct cell clusters within the myometrium, with the vascular myocyte cluster most highly enriched for MyoSPC characteristics and markers. CRIP1 expression was found highly upregulated by both techniques and was used as a marker to sort CRIP1+/PECAM1- cells that were both enriched for colony forming potential and able to differentiate into mesenchymal lineages, suggesting that CRIP1+/PECAM1- cells could be used to better study the etiology of uterine fibroids.
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Affiliation(s)
- Emmanuel N Paul
- Department of Obstetrics, Gynecology and Reproductive Biology, College of Human Medicine, Michigan State University, Grand Rapids, MI, 49503, USA
| | - Tyler J Carpenter
- Department of Obstetrics, Gynecology and Reproductive Biology, College of Human Medicine, Michigan State University, Grand Rapids, MI, 49503, USA
| | - Sarah Fitch
- Department of Obstetrics, Gynecology and Reproductive Biology, College of Human Medicine, Michigan State University, Grand Rapids, MI, 49503, USA
- Institute for Quantitative Health Science and Engineering, East Lansing, MI, 48824, USA
| | - Rachael Sheridan
- Flow Cytometry Core, Van Andel Institute, Grand Rapids, MI, 49503, USA
| | - Kin H Lau
- Bioinformatics and Biostatistics Core, Van Andel Institute, Grand Rapids, MI, 49503, USA
| | - Ripla Arora
- Department of Obstetrics, Gynecology and Reproductive Biology, College of Human Medicine, Michigan State University, Grand Rapids, MI, 49503, USA
- Institute for Quantitative Health Science and Engineering, East Lansing, MI, 48824, USA
| | - Jose M Teixeira
- Department of Obstetrics, Gynecology and Reproductive Biology, College of Human Medicine, Michigan State University, Grand Rapids, MI, 49503, USA.
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8
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Castillo SP, Galvez-Cancino F, Liu J, Pollard SM, Quezada SA, Yuan Y. The tumour ecology of quiescence: Niches across scales of complexity. Semin Cancer Biol 2023; 92:139-149. [PMID: 37037400 DOI: 10.1016/j.semcancer.2023.04.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Revised: 03/06/2023] [Accepted: 04/08/2023] [Indexed: 04/12/2023]
Abstract
Quiescence is a state of cell cycle arrest, allowing cancer cells to evade anti-proliferative cancer therapies. Quiescent cancer stem cells are thought to be responsible for treatment resistance in glioblastoma, an aggressive brain cancer with poor patient outcomes. However, the regulation of quiescence in glioblastoma cells involves a myriad of intrinsic and extrinsic mechanisms that are not fully understood. In this review, we synthesise the literature on quiescence regulatory mechanisms in the context of glioblastoma and propose an ecological perspective to stemness-like phenotypes anchored to the contemporary concepts of niche theory. From this perspective, the cell cycle regulation is multiscale and multidimensional, where the niche dimensions extend to extrinsic variables in the tumour microenvironment that shape cell fate. Within this conceptual framework and powered by ecological niche modelling, the discovery of microenvironmental variables related to hypoxia and mechanosignalling that modulate proliferative plasticity and intratumor immune activity may open new avenues for therapeutic targeting of emerging biological vulnerabilities in glioblastoma.
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Affiliation(s)
- Simon P Castillo
- Centre for Evolution and Cancer & Division of Molecular Pathology, The Institute of Cancer Research, London SM2 5NG, UK
| | - Felipe Galvez-Cancino
- Immune Regulation and Tumor Immunotherapy Group, Cancer Immunology Unit, Research Department of Haematology, UCL Cancer Institute, London WC1E 6DD, UK
| | - Jiali Liu
- Immune Regulation and Tumor Immunotherapy Group, Cancer Immunology Unit, Research Department of Haematology, UCL Cancer Institute, London WC1E 6DD, UK
| | - Steven M Pollard
- Centre for Regenerative Medicine and Cancer Research UK Scotland Centre, Institute for Regeneration and Repair, University of Edinburgh, Edinburgh EH16 4UU, UK
| | - Sergio A Quezada
- Immune Regulation and Tumor Immunotherapy Group, Cancer Immunology Unit, Research Department of Haematology, UCL Cancer Institute, London WC1E 6DD, UK
| | - Yinyin Yuan
- Centre for Evolution and Cancer & Division of Molecular Pathology, The Institute of Cancer Research, London SM2 5NG, UK.
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9
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Paul EN, Carpenter TJ, Fitch S, Sheridan R, Lau KH, Arora R, Teixeira JM. Cysteine-Rich Intestinal Protein 1 is a Novel Surface Marker for Myometrial Stem/Progenitor Cells. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.20.529273. [PMID: 36993447 PMCID: PMC10054937 DOI: 10.1101/2023.02.20.529273] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/19/2023]
Abstract
Myometrial stem/progenitor cells (MyoSPCs) have been proposed as the cells of origin for uterine fibroids, which are benign tumors that develop in the myometrium of most reproductive age women, but the identity of the MyoSPC has not been well established. We previously identified SUSD2 as a possible MyoSPC marker, but the relatively poor enrichment in stem cell characteristics of SUSD2+ over SUSD2- cells compelled us to find better discerning markers for more rigorous downstream analyses. We combined bulk RNA-seq of SUSD2+/- cells with single cell RNA-seq to identify markers capable of further enriching for MyoSPCs. We observed seven distinct cell clusters within the myometrium, with the vascular myocyte cluster most highly enriched for MyoSPC characteristics and markers, including SUSD2. CRIP1 expression was found highly upregulated in both techniques and was used as a marker to sort CRIP1+/PECAM1- cells that were both enriched for colony forming potential and able to differentiate into mesenchymal lineages, suggesting that CRIP1+/PECAM1- cells could be used to better study the etiology of uterine fibroids.
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Affiliation(s)
- Emmanuel N. Paul
- Department of Obstetrics, Gynecology and Reproductive Biology, College of Human Medicine, Michigan State University, Grand Rapids, MI 48824, USA
| | - Tyler J. Carpenter
- Department of Obstetrics, Gynecology and Reproductive Biology, College of Human Medicine, Michigan State University, Grand Rapids, MI 48824, USA
| | - Sarah Fitch
- Department of Obstetrics, Gynecology and Reproductive Biology, College of Human Medicine, Michigan State University, Grand Rapids, MI 48824, USA
- Institute for Quantitative Health Science and Engineering, East Lansing, MI 48824, USA
| | - Rachael Sheridan
- Flow Cytometry Core, Van Andel Institute, Grand Rapids, MI 49503, USA
| | - Kin H. Lau
- Bioinformatics and Biostatistics Core, Van Andel Institute, Grand Rapids, MI 49503, USA
| | - Ripla Arora
- Department of Obstetrics, Gynecology and Reproductive Biology, College of Human Medicine, Michigan State University, Grand Rapids, MI 48824, USA
- Institute for Quantitative Health Science and Engineering, East Lansing, MI 48824, USA
| | - Jose M. Teixeira
- Department of Obstetrics, Gynecology and Reproductive Biology, College of Human Medicine, Michigan State University, Grand Rapids, MI 48824, USA
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10
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Molecular subtypes of ALS are associated with differences in patient prognosis. Nat Commun 2023; 14:95. [PMID: 36609402 PMCID: PMC9822908 DOI: 10.1038/s41467-022-35494-w] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Accepted: 12/06/2022] [Indexed: 01/09/2023] Open
Abstract
Amyotrophic Lateral Sclerosis (ALS) is a neurodegenerative disease with poorly understood clinical heterogeneity, underscored by significant differences in patient age at onset, symptom progression, therapeutic response, disease duration, and comorbidity presentation. We perform a patient stratification analysis to better understand the variability in ALS pathology, utilizing postmortem frontal and motor cortex transcriptomes derived from 208 patients. Building on the emerging role of transposable element (TE) expression in ALS, we consider locus-specific TEs as distinct molecular features during stratification. Here, we identify three unique molecular subtypes in this ALS cohort, with significant differences in patient survival. These results suggest independent disease mechanisms drive some of the clinical heterogeneity in ALS.
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11
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Gulaia V, Shmelev M, Romanishin A, Shved N, Farniev V, Goncharov N, Biktimirov A, Vargas IL, Khodosevich K, Kagansky A, Kumeiko V. Single-nucleus transcriptomics of IDH1- and TP53-mutant glioma stem cells displays diversified commitment on invasive cancer progenitors. Sci Rep 2022; 12:18975. [PMID: 36348001 PMCID: PMC9643511 DOI: 10.1038/s41598-022-23646-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Accepted: 11/03/2022] [Indexed: 11/09/2022] Open
Abstract
Glioma is a devastating brain tumor with a high mortality rate attributed to the glioma stem cells (GSCs) possessing high plasticity. Marker mutations in isocitrate dehydrogenase type 1 (IDH1) and tumor protein 53 (TP53) are frequent in gliomas and impact the cell fate decisions. Understanding the GSC heterogeneity within IDH1- and TP53- mutant tumors may elucidate possible treatment targets. Here, we performed single-nucleus transcriptomics of mutant and wild-type glioma samples sorted for Sox2 stem cell marker. For the first time the rare subpopulations of Sox2 + IDH1- and TP53-mutant GSCs were characterized. In general, GSCs contained the heterogeneity root subpopulation resembling active neural stem cells capable of asymmetric division to quiescent and transit amplifying cell branches. Specifically, double-mutant GSCs revealed the commitment on highly invasive oligodendrocyte- and astroglia-like progenitors. Additionally, double-mutant GSCs displayed upregulated markers of collagen synthesis, altered lipogenesis and high migration, while wild-type GSCs expressed genes related to ATP production. Wild-type GSC root population was highly heterogeneous and lacked the signature marker expression, thus glioblastoma treatment should emphasize on establishing differentiation protocol directed against residual GSCs. For the more differentiated IDH1- and TP53-mutant gliomas we suggest therapeutic targeting of migration molecules, such as CD44.
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Affiliation(s)
- Valeriia Gulaia
- grid.440624.00000 0004 0637 7917Institute of Life Sciences and Biomedicine, Medical Center, Far Eastern Federal University, Vladivostok, 690922 Russia
| | - Mikhail Shmelev
- grid.440624.00000 0004 0637 7917Institute of Life Sciences and Biomedicine, Medical Center, Far Eastern Federal University, Vladivostok, 690922 Russia
| | - Aleksander Romanishin
- grid.440624.00000 0004 0637 7917Institute of Life Sciences and Biomedicine, Medical Center, Far Eastern Federal University, Vladivostok, 690922 Russia ,grid.410686.d0000 0001 1018 9204School of Life Sciences, Immanuel Kant Baltic Federal University, Kaliningrad, 236041 Russia
| | - Nikita Shved
- grid.440624.00000 0004 0637 7917Institute of Life Sciences and Biomedicine, Medical Center, Far Eastern Federal University, Vladivostok, 690922 Russia ,grid.417808.20000 0001 1393 1398A.V. Zhirmunsky National Scientific Center of Marine Biology, FEB RAS, Vladivostok, 690041 Russia
| | - Vladislav Farniev
- grid.440624.00000 0004 0637 7917Institute of Life Sciences and Biomedicine, Medical Center, Far Eastern Federal University, Vladivostok, 690922 Russia
| | - Nikolay Goncharov
- grid.440624.00000 0004 0637 7917Institute of Life Sciences and Biomedicine, Medical Center, Far Eastern Federal University, Vladivostok, 690922 Russia
| | - Arthur Biktimirov
- grid.440624.00000 0004 0637 7917Institute of Life Sciences and Biomedicine, Medical Center, Far Eastern Federal University, Vladivostok, 690922 Russia
| | - Irene Lisa Vargas
- grid.5254.60000 0001 0674 042XBiotech Research & Innovation Centre (BRIC), The Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Konstantin Khodosevich
- grid.5254.60000 0001 0674 042XBiotech Research & Innovation Centre (BRIC), The Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Alexander Kagansky
- grid.440624.00000 0004 0637 7917Institute of Life Sciences and Biomedicine, Medical Center, Far Eastern Federal University, Vladivostok, 690922 Russia
| | - Vadim Kumeiko
- grid.440624.00000 0004 0637 7917Institute of Life Sciences and Biomedicine, Medical Center, Far Eastern Federal University, Vladivostok, 690922 Russia ,grid.417808.20000 0001 1393 1398A.V. Zhirmunsky National Scientific Center of Marine Biology, FEB RAS, Vladivostok, 690041 Russia
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12
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Xue T, Wang X, Ru J, Zhang L, Yin H. The inhibitory effect of human umbilical cord mesenchymal stem cells expressing anti-HAAH scFv-sTRAIL fusion protein on glioma. Front Bioeng Biotechnol 2022; 10:997799. [DOI: 10.3389/fbioe.2022.997799] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Accepted: 10/26/2022] [Indexed: 11/10/2022] Open
Abstract
Glioma is the most common malignant intracranial tumor with low 5-year survival rate. In this study, we constructed a plasmid expressing anti-HAAH single-chain antibody and sTRAIL fusion protein (scFv-sTRAIL), and explored the effects of the double gene modified human umbilical cord mesenchyreal stem cells (hucMSCs) on the growth of glioma in vitro and in vivo. The isolated hucMSCs were identified by detecting the adipogenic differentiation ability and the osteogenic differentiation ability. The phenotypes of hucMSCs were determined by the flow cytometry. The hucMSCs were infected with lentivirus expression scFv-sTRAIL fusion protein. The expression of sTRAIL in hucMSCs were detected by immunofluorescence staining, western blot and ELISA. The tropism of hucMSCs toward U87G cells was assessed by transwell assay. The inhibitory effect of hucMSCs on U87G cells were explored by CCK8 and apoptosis assay. The xenograft tumor was established by subcutaneously injection of U87G cells into the back of mice. The hucMSCs were injected via tail veins. The inhibitory effect of hucMSCs on glioma in vivo was assessed by TUNEL assay. The hucMSCs migrated into the xenograft tumor were revealed by detecting the green fluorescent. The results showed that the scFv-sTRAIL expression did not affect the phenotypes of hucMSCs. The scFv-sTRAIL expression promoted the tropism of hucMSCs toward U87G cells, enhanced the inhibitory effect and tumor killing effect of hucMSCs on U87G cells. The in vivo study showed that hucMSCs expressing scFv-sTRAIL demonstrated significantly higher inhibitory effect and tumor killing effect than hucMSCs expressing sTRAIL. The green fluorescence intensity in the mice injected with hucMSCs expressing scFv-sTRAIL was significantly higher than that injected with hucMSCs expressing sTRAIL. These data suggested that the scFv conferred the targeting effect of hucMSCs tropism towards the xenograft tumor. In conclusion, the hucMSCs expressing scFv-sTRAIL fusion protein gained the capability to target and kill gliomas cells in vitro and in vivo. These findings shed light on a potential therapy for glioma treatment.
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13
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Lin JP, Kelly HM, Song Y, Kawaguchi R, Geschwind DH, Jacobson S, Reich DS. Transcriptomic architecture of nuclei in the marmoset CNS. Nat Commun 2022; 13:5531. [PMID: 36130924 PMCID: PMC9492672 DOI: 10.1038/s41467-022-33140-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Accepted: 09/02/2022] [Indexed: 11/11/2022] Open
Abstract
To understand the cellular composition and region-specific specialization of white matter - a disease-relevant, glia-rich tissue highly expanded in primates relative to rodents - we profiled transcriptomes of ~500,000 nuclei from 19 tissue types of the central nervous system of healthy common marmoset and mapped 87 subclusters spatially onto a 3D MRI atlas. We performed cross-species comparison, explored regulatory pathways, modeled regional intercellular communication, and surveyed cellular determinants of neurological disorders. Here, we analyze this resource and find strong spatial segregation of microglia, oligodendrocyte progenitor cells, and astrocytes. White matter glia are diverse, enriched with genes involved in stimulus-response and biomolecule modification, and predicted to interact with other resident cells more extensively than their gray matter counterparts. Conversely, gray matter glia preserve the expression of neural tube patterning genes into adulthood and share six transcription factors that restrict transcriptome complexity. A companion Callithrix jacchus Primate Cell Atlas (CjPCA) is available through https://cjpca.ninds.nih.gov .
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Affiliation(s)
- Jing-Ping Lin
- Translational Neuroradiology Section, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | - Hannah M Kelly
- Translational Neuroradiology Section, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | - Yeajin Song
- Translational Neuroradiology Section, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | - Riki Kawaguchi
- Psychiatry, Semel Institute for Neuroscience and Human Behavior, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Daniel H Geschwind
- Psychiatry, Semel Institute for Neuroscience and Human Behavior, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
- Departments of Neurology and Human Genetics, University of California, Los Angeles, Los Angeles, CA, USA
| | - Steven Jacobson
- Viral Immunology Section, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | - Daniel S Reich
- Translational Neuroradiology Section, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA.
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Szulzewsky F, Arora S, Arakaki AKS, Sievers P, Almiron Bonnin DA, Paddison PJ, Sahm F, Cimino PJ, Gujral TS, Holland EC. Both YAP1-MAML2 and constitutively active YAP1 drive the formation of tumors that resemble NF2 mutant meningiomas in mice. Genes Dev 2022; 36:gad.349876.122. [PMID: 36008139 PMCID: PMC9480855 DOI: 10.1101/gad.349876.122] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Accepted: 08/11/2022] [Indexed: 11/24/2022]
Abstract
YAP1 is a transcriptional coactivator regulated by the Hippo signaling pathway, including NF2. Meningiomas are the most common primary brain tumors; a large percentage exhibit heterozygous loss of chromosome 22 (harboring the NF2 gene) and functional inactivation of the remaining NF2 copy, implicating oncogenic YAP activity in these tumors. Recently, fusions between YAP1 and MAML2 have been identified in a subset of pediatric NF2 wild-type meningiomas. Here, we show that human YAP1-MAML2-positive meningiomas resemble NF2 mutant meningiomas by global and YAP-related gene expression signatures. We then show that expression of YAP1-MAML2 in mice induces tumors that resemble human YAP1 fusion-positive and NF2 mutant meningiomas by gene expression. We demonstrate that YAP1-MAML2 primarily functions by exerting TEAD-dependent YAP activity that is resistant to Hippo signaling. Treatment with YAP-TEAD inhibitors is sufficient to inhibit the viability of YAP1-MAML2-driven mouse tumors ex vivo. Finally, we show that expression of constitutively active YAP1 (S127/397A-YAP1) is sufficient to induce similar tumors, suggesting that the YAP component of the gene fusion is the critical driver of these tumors. In summary, our results implicate YAP1-MAML2 as a causal oncogenic driver and highlight TEAD-dependent YAP activity as an oncogenic driver in YAP1-MAML2 fusion meningioma as well as NF2 mutant meningioma in general.
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Affiliation(s)
- Frank Szulzewsky
- Human Biology Division, Fred Hutchinson Cancer Center, Seattle, Washington 98109, USA
| | - Sonali Arora
- Human Biology Division, Fred Hutchinson Cancer Center, Seattle, Washington 98109, USA
| | - Aleena K S Arakaki
- Human Biology Division, Fred Hutchinson Cancer Center, Seattle, Washington 98109, USA
| | - Philipp Sievers
- Department of Neuropathology, Institute of Pathology, University Hospital Heidelberg, 69120 Heidelberg, Germany
- Clinical Cooperation Unit Neuropathology, German Consortium for Translational Cancer Research (DKTK), German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | | | - Patrick J Paddison
- Human Biology Division, Fred Hutchinson Cancer Center, Seattle, Washington 98109, USA
- Department of Pharmacology, University of Washington, Seattle, Washington 98195, USA
| | - Felix Sahm
- Department of Neuropathology, Institute of Pathology, University Hospital Heidelberg, 69120 Heidelberg, Germany
- Clinical Cooperation Unit Neuropathology, German Consortium for Translational Cancer Research (DKTK), German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
- Hopp Children's Cancer Center Heidelberg (KiTZ), 69120 Heidelberg, Germany
| | - Patrick J Cimino
- Human Biology Division, Fred Hutchinson Cancer Center, Seattle, Washington 98109, USA
- Surgical Neurology Branch, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Taranjit S Gujral
- Human Biology Division, Fred Hutchinson Cancer Center, Seattle, Washington 98109, USA
- Department of Pharmacology, University of Washington, Seattle, Washington 98195, USA
| | - Eric C Holland
- Human Biology Division, Fred Hutchinson Cancer Center, Seattle, Washington 98109, USA
- Seattle Translational Tumor Research Center, Fred Hutchinson Cancer Center, Seattle, Washington 98109, USA
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15
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Adjei‐Sowah EA, O'Connor SA, Veldhuizen J, Lo Cascio C, Plaisier C, Mehta S, Nikkhah M. Investigating the Interactions of Glioma Stem Cells in the Perivascular Niche at Single-Cell Resolution using a Microfluidic Tumor Microenvironment Model. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2022; 9:e2201436. [PMID: 35619544 PMCID: PMC9313491 DOI: 10.1002/advs.202201436] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Revised: 04/25/2022] [Indexed: 05/03/2023]
Abstract
The perivascular niche (PVN) is a glioblastoma tumor microenvironment (TME) that serves as a safe haven for glioma stem cells (GSCs), and acts as a reservoir that inevitably leads to tumor recurrence. Understanding cellular interactions in the PVN that drive GSC treatment resistance and stemness is crucial to develop lasting therapies for glioblastoma. The limitations of in vivo models and in vitro assays have led to critical knowledge gaps regarding the influence of various cell types in the PVN on GSCs behavior. This study developed an organotypic triculture microfluidic model as a means to recapitulate the PVN and study its impact on GSCs. This triculture platform, comprised of endothelial cells (ECs), astrocytes, and GSCs, is used to investigate GSC invasion, proliferation and stemness. Both ECs and astrocytes significantly increased invasiveness of GSCs. This study futher identified 15 ligand-receptor pairs using single-cell RNAseq with putative chemotactic mechanisms of GSCs, where the receptor is up-regulated in GSCs and the diffusible ligand is expressed in either astrocytes or ECs. Notably, the ligand-receptor pair SAA1-FPR1 is demonstrated to be involved in chemotactic invasion of GSCs toward PVN. The novel triculture platform presented herein can be used for therapeutic development and discovery of molecular mechanisms driving GSC biology.
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Affiliation(s)
| | - Samantha A. O'Connor
- School of Biological and Health Systems EngineeringArizona State UniversityTempeAZ85287‐9709USA
| | - Jaimeson Veldhuizen
- School of Biological and Health Systems EngineeringArizona State UniversityTempeAZ85287‐9709USA
| | - Costanza Lo Cascio
- Ivy Brain Tumor Center, Barrow Neurological InstituteSt. Joseph's Hospital and Medical Center350 W Thomas RdPhoenixAZ85013USA
| | - Christopher Plaisier
- School of Biological and Health Systems EngineeringArizona State UniversityTempeAZ85287‐9709USA
| | - Shwetal Mehta
- Ivy Brain Tumor Center, Barrow Neurological InstituteSt. Joseph's Hospital and Medical Center350 W Thomas RdPhoenixAZ85013USA
| | - Mehdi Nikkhah
- School of Biological and Health Systems EngineeringArizona State UniversityTempeAZ85287‐9709USA
- Virginia G. Piper Biodesign Center for Personalized DiagnosticsArizona State UniversityTempeAZ85287‐9709USA
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The Intricate Epigenetic and Transcriptional Alterations in Pediatric High-Grade Gliomas: Targeting the Crosstalk as the Oncogenic Achilles’ Heel. Biomedicines 2022; 10:biomedicines10061311. [PMID: 35740334 PMCID: PMC9219798 DOI: 10.3390/biomedicines10061311] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Revised: 05/27/2022] [Accepted: 05/28/2022] [Indexed: 02/01/2023] Open
Abstract
Pediatric high-grade gliomas (pHGGs) are a deadly and heterogenous subgroup of gliomas for which the development of innovative treatments is urgent. Advances in high-throughput molecular techniques have shed light on key epigenetic components of these diseases, such as K27M and G34R/V mutations on histone 3. However, modification of DNA compaction is not sufficient by itself to drive those tumors. Here, we review molecular specificities of pHGGs subcategories in the context of epigenomic rewiring caused by H3 mutations and the subsequent oncogenic interplay with transcriptional signaling pathways co-opted from developmental programs that ultimately leads to gliomagenesis. Understanding how transcriptional and epigenetic alterations synergize in each cellular context in these tumors could allow the identification of new Achilles’ heels, thereby highlighting new levers to improve their therapeutic management.
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Herman JA, Arora S, Carter L, Zhu J, Biggins S, Paddison PJ. Functional dissection of human mitotic genes using CRISPR-Cas9 tiling screens. Genes Dev 2022; 36:495-510. [PMID: 35483740 PMCID: PMC9067404 DOI: 10.1101/gad.349319.121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Accepted: 04/12/2022] [Indexed: 12/03/2022]
Abstract
In this Resource/Methodology, Herman et al. developed a method that leverages CRISPR–Cas9-induced mutations across protein-coding genes for the a priori identification of functional regions at the sequence level. As a test case, they applied this method to 48 human mitotic genes, revealing hundreds of regions required for cell proliferation, including domains that were experimentally characterized, ones that were predicted based on homology, and novel ones. The identity of human protein-coding genes is well known, yet our in-depth knowledge of their molecular functions and domain architecture remains limited by shortcomings in homology-based predictions and experimental approaches focused on whole-gene depletion. To bridge this knowledge gap, we developed a method that leverages CRISPR–Cas9-induced mutations across protein-coding genes for the a priori identification of functional regions at the sequence level. As a test case, we applied this method to 48 human mitotic genes, revealing hundreds of regions required for cell proliferation, including domains that were experimentally characterized, ones that were predicted based on homology, and novel ones. We validated screen outcomes for 15 regions, including amino acids 387–402 of Mad1, which were previously uncharacterized but contribute to Mad1 kinetochore localization and chromosome segregation fidelity. Altogether, we demonstrate that CRISPR–Cas9-based tiling mutagenesis identifies key functional domains in protein-coding genes de novo, which elucidates separation of function mutants and allows functional annotation across the human proteome.
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Affiliation(s)
- Jacob A Herman
- Howard Hughes Medical Institute, Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA.,Human Biology Division, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA
| | - Sonali Arora
- Human Biology Division, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA
| | - Lucas Carter
- Human Biology Division, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA
| | - Jun Zhu
- Department of Genetics and Genomic Sciences, Icahn Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA
| | - Sue Biggins
- Howard Hughes Medical Institute, Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA
| | - Patrick J Paddison
- Human Biology Division, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA
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18
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Nussinov R, Tsai CJ, Jang H. How can same-gene mutations promote both cancer and developmental disorders? SCIENCE ADVANCES 2022; 8:eabm2059. [PMID: 35030014 PMCID: PMC8759737 DOI: 10.1126/sciadv.abm2059] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Accepted: 11/22/2021] [Indexed: 05/05/2023]
Abstract
The question of how same-gene mutations can drive both cancer and neurodevelopmental disorders has been puzzling. It has also been puzzling why those with neurodevelopmental disorders have a high risk of cancer. Ras, MEK, PI3K, PTEN, and SHP2 are among the oncogenic proteins that can harbor mutations that encode diseases other than cancer. Understanding why some of their mutations can promote cancer, whereas others promote neurodevelopmental diseases, and why even the same mutations may promote both phenotypes, has important clinical ramifications. Here, we review the literature and address these tantalizing questions. We propose that cell type–specific expression of the mutant protein, and of other proteins in the respective pathway, timing of activation (during embryonic development or sporadic emergence), and the absolute number of molecules that the mutations activate, alone or in combination, are pivotal in determining the pathological phenotypes—cancer and (or) developmental disorders.
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Affiliation(s)
- Ruth Nussinov
- Computational Structural Biology Section, Frederick National Laboratory for Cancer Research in the Laboratory of Cancer Immunometabolism, National Cancer Institute, Frederick, MD 21702, USA
- Department of Human Molecular Genetics and Biochemistry, Sackler School of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
| | - Chung-Jung Tsai
- Computational Structural Biology Section, Frederick National Laboratory for Cancer Research in the Laboratory of Cancer Immunometabolism, National Cancer Institute, Frederick, MD 21702, USA
| | - Hyunbum Jang
- Computational Structural Biology Section, Frederick National Laboratory for Cancer Research in the Laboratory of Cancer Immunometabolism, National Cancer Institute, Frederick, MD 21702, USA
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