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Saritas Erdogan S, Yilmaz AE, Kumbasar A. PIN1 is a novel interaction partner and a negative upstream regulator of the transcription factor NFIB. FEBS Lett 2024. [PMID: 39245791 DOI: 10.1002/1873-3468.15010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2024] [Accepted: 08/01/2024] [Indexed: 09/10/2024]
Abstract
NFIB is a transcription factor of the Nuclear Factor One (NFI) family that is essential for embryonic development. Post-translational control of NFIB or its upstream regulators have not been well characterized. Here, we show that PIN1 binds NFIB in a phosphorylation-dependent manner, via its WW domain. PIN1 interacts with the well-conserved N-terminal domains of all NFIs. Moreover, PIN1 attenuates the transcriptional activity of NFIB; this attenuation requires substrate binding by PIN1 but not its isomerase activity. Paradoxically, we found stabilization of NFIB by PIN1. We propose that PIN1 represses NFIB function not by regulating its abundance but by inducing a conformational change. These results identify NFIB as a novel PIN1 target and posit a role for PIN1 in post-translational regulation of NFIB and other NFIs.
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Affiliation(s)
| | - Ahmet Erdal Yilmaz
- Department of Molecular Biology and Genetics, Istanbul Technical University, Turkey
| | - Asli Kumbasar
- Department of Molecular Biology and Genetics, Istanbul Technical University, Turkey
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2
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Hartmann GG, Sage J. Small Cell Lung Cancer Neuronal Features and Their Implications for Tumor Progression, Metastasis, and Therapy. Mol Cancer Res 2024; 22:787-795. [PMID: 38912893 PMCID: PMC11374474 DOI: 10.1158/1541-7786.mcr-24-0265] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2024] [Revised: 05/30/2024] [Accepted: 06/20/2024] [Indexed: 06/25/2024]
Abstract
Small cell lung cancer (SCLC) is an epithelial neuroendocrine form of lung cancer for which survival rates remain dismal and new therapeutic approaches are greatly needed. Key biological features of SCLC tumors include fast growth and widespread metastasis, as well as rapid resistance to treatment. Similar to pulmonary neuroendocrine cells, SCLC cells have traits of both hormone-producing cells and neurons. In this study, we specifically discuss the neuronal features of SCLC. We consider how neuronal G protein-coupled receptors and other neuronal molecules on the surface of SCLC cells can contribute to the growth of SCLC tumors and serve as therapeutic targets in SCLC. We also review recent evidence for the role of neuronal programs expressed by SCLC cells in the fast proliferation, migration, and metastasis of these cells. We further highlight how these neuronal programs may be particularly relevant for the development of brain metastases and how they can assist SCLC cells to functionally interact with neurons and astrocytes. A greater understanding of the molecular and cellular neuronal features of SCLC is likely to uncover new vulnerabilities in SCLC cells, which may help develop novel therapeutic approaches. More generally, the epithelial-to-neuronal transition observed during tumor progression in SCLC and other cancer types can contribute significantly to tumor development and response to therapy.
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Affiliation(s)
- Griffin G Hartmann
- Department of Pediatrics, Stanford University, Stanford, California
- Department of Genetics, Stanford University, Stanford, California
| | - Julien Sage
- Department of Pediatrics, Stanford University, Stanford, California
- Department of Genetics, Stanford University, Stanford, California
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3
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MacArthur IC, Ma L, Huang CY, Bhavsar H, Suzuki M, Dawlaty MM. Developmental DNA demethylation is a determinant of neural stem cell identity and gliogenic competence. SCIENCE ADVANCES 2024; 10:eado5424. [PMID: 39196941 PMCID: PMC11352921 DOI: 10.1126/sciadv.ado5424] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2024] [Accepted: 07/24/2024] [Indexed: 08/30/2024]
Abstract
DNA methylation is extensively reconfigured during development, but the functional significance and cell type-specific dependencies of DNA demethylation in lineage specification remain poorly understood. Here, we demonstrate that developmental DNA demethylation, driven by ten-eleven translocation 1/2/3 (TET1/2/3) enzymes, is essential for establishment of neural stem cell (NSC) identity and gliogenic potential. We find that loss of all three TETs during NSC specification is dispensable for neural induction and neuronal differentiation but critical for astrocyte and oligodendrocyte formation, demonstrating a selective loss of glial competence. Mechanistically, TET-mediated demethylation was essential for commissioning neural-specific enhancers in proximity to master neurodevelopmental and glial transcription factor genes and for induction of these genes. Consistently, loss of all three TETs in embryonic NSCs in mice compromised glial gene expression and corticogenesis. Thus, TET-dependent developmental demethylation is an essential regulatory mechanism for neural enhancer commissioning during NSC specification and is a cell-intrinsic determinant of NSC identity and gliogenic potential.
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Affiliation(s)
- Ian C. MacArthur
- Ruth L. and David S. Gottesman Institute for Stem Cell and Regenerative Medicine Research, Albert Einstein College of Medicine, 1301 Morris Park Ave, Bronx, NY 1046142, USA
- Department of Genetics, Albert Einstein College of Medicine, 1301 Morris Park Ave, Bronx, NY 10461, USA
- Department of Developmental & Molecular Biology, Albert Einstein College of Medicine, 1300 Morris Park Ave, Bronx, NY 10461, USA
| | - Liyang Ma
- Ruth L. and David S. Gottesman Institute for Stem Cell and Regenerative Medicine Research, Albert Einstein College of Medicine, 1301 Morris Park Ave, Bronx, NY 1046142, USA
- Department of Genetics, Albert Einstein College of Medicine, 1301 Morris Park Ave, Bronx, NY 10461, USA
- Department of Developmental & Molecular Biology, Albert Einstein College of Medicine, 1300 Morris Park Ave, Bronx, NY 10461, USA
| | - Cheng-Yen Huang
- Ruth L. and David S. Gottesman Institute for Stem Cell and Regenerative Medicine Research, Albert Einstein College of Medicine, 1301 Morris Park Ave, Bronx, NY 1046142, USA
- Department of Genetics, Albert Einstein College of Medicine, 1301 Morris Park Ave, Bronx, NY 10461, USA
- Department of Developmental & Molecular Biology, Albert Einstein College of Medicine, 1300 Morris Park Ave, Bronx, NY 10461, USA
| | - Hrutvik Bhavsar
- Ruth L. and David S. Gottesman Institute for Stem Cell and Regenerative Medicine Research, Albert Einstein College of Medicine, 1301 Morris Park Ave, Bronx, NY 1046142, USA
- Department of Genetics, Albert Einstein College of Medicine, 1301 Morris Park Ave, Bronx, NY 10461, USA
- Department of Developmental & Molecular Biology, Albert Einstein College of Medicine, 1300 Morris Park Ave, Bronx, NY 10461, USA
| | - Masako Suzuki
- Department of Nutrition, Texas A&M University, 2253 TAMU, Carter Mattil 214A, College Station, TX 77840, USA
| | - Meelad M. Dawlaty
- Ruth L. and David S. Gottesman Institute for Stem Cell and Regenerative Medicine Research, Albert Einstein College of Medicine, 1301 Morris Park Ave, Bronx, NY 1046142, USA
- Department of Genetics, Albert Einstein College of Medicine, 1301 Morris Park Ave, Bronx, NY 10461, USA
- Department of Developmental & Molecular Biology, Albert Einstein College of Medicine, 1300 Morris Park Ave, Bronx, NY 10461, USA
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4
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Zou D, Huang S, Tian S, Kilunda FK, Murphy RW, Dahn HA, Zhou Y, Lee PS, Chen JM. Comparative genomics sheds new light on the convergent evolution of infrared vision in snakes. Proc Biol Sci 2024; 291:20240818. [PMID: 39043244 PMCID: PMC11265913 DOI: 10.1098/rspb.2024.0818] [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: 04/08/2024] [Revised: 05/30/2024] [Accepted: 06/19/2024] [Indexed: 07/25/2024] Open
Abstract
Infrared vision is a highly specialized sensory system that evolved independently in three clades of snakes. Apparently, convergent evolution occurred in the transient receptor potential ankyrin 1 (TRPA1) proteins of infrared-sensing snakes. However, this gene can only explain how infrared signals are received, and not the transduction and processing of those signals. We sequenced the genome of Xenopeltis unicolor, a key outgroup species of pythons, and performed a genome-wide analysis of convergence between two clades of infrared-sensing snakes. Our results revealed pervasive molecular adaptation in pathways associated with neural development and other functions, with parallel selection on loci associated with trigeminal nerve structural organization. In addition, we found evidence of convergent amino acid substitutions in a set of genes, including TRPA1 and TRPM2. The analysis also identified convergent accelerated evolution in non-coding elements near 12 genes involved in facial nerve structural organization and optic nerve development. Thus, convergent evolution occurred across multiple dimensions of infrared vision in vipers and pythons, as well as amino acid substitutions, non-coding elements, genes and functions. These changes enabled independent groups of snakes to develop and use infrared vision.
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Affiliation(s)
- Dahu Zou
- Engineering Research Center of Eco-Environment in Three Gorges Reservoir Region of Ministry of Education, China Three Gorges University, Yichang, Hubei443002, People’s Republic of China
| | - Song Huang
- The Anhui Provincial Key Laboratory of Biodiversity Conservation and Ecological Security in the Yangtze River Basin, College of Life Sciences, Anhui Normal University, Wuhu, Anhui241000, People’s Republic of China
| | - Shilin Tian
- Novogene Bioinformatics Institute, Beijing100000, People’s Republic of China
| | - Felista Kasyoka Kilunda
- Key Laboratory of Genetic Evolution and Animal Models and Yunnan Key Laboratory of Biodiversity and Ecological Conservation of Gaoligong Mountain, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan650223, People’s Republic of China
| | - Robert W. Murphy
- Reptilia Zoo and Education Centre, 2501 Rutherford Road, Vaughan, ONL4K 2N6, Canada
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, ONM5S 2C6, Canada
| | - Hollis A. Dahn
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, ONM5S 2C6, Canada
| | - Youbing Zhou
- Engineering Research Center of Eco-Environment in Three Gorges Reservoir Region of Ministry of Education, China Three Gorges University, Yichang, Hubei443002, People’s Republic of China
| | - Ping-Shin Lee
- The Anhui Provincial Key Laboratory of Biodiversity Conservation and Ecological Security in the Yangtze River Basin, College of Life Sciences, Anhui Normal University, Wuhu, Anhui241000, People’s Republic of China
| | - Jin-Min Chen
- The Anhui Provincial Key Laboratory of Biodiversity Conservation and Ecological Security in the Yangtze River Basin, College of Life Sciences, Anhui Normal University, Wuhu, Anhui241000, People’s Republic of China
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5
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Martins-Costa C, Wiegers A, Pham VA, Sidhaye J, Doleschall B, Novatchkova M, Lendl T, Piber M, Peer A, Möseneder P, Stuempflen M, Chow SYA, Seidl R, Prayer D, Höftberger R, Kasprian G, Ikeuchi Y, Corsini NS, Knoblich JA. ARID1B controls transcriptional programs of axon projection in an organoid model of the human corpus callosum. Cell Stem Cell 2024; 31:866-885.e14. [PMID: 38718796 DOI: 10.1016/j.stem.2024.04.014] [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: 05/17/2023] [Revised: 02/13/2024] [Accepted: 04/17/2024] [Indexed: 06/09/2024]
Abstract
Mutations in ARID1B, a member of the mSWI/SNF complex, cause severe neurodevelopmental phenotypes with elusive mechanisms in humans. The most common structural abnormality in the brain of ARID1B patients is agenesis of the corpus callosum (ACC), characterized by the absence of an interhemispheric white matter tract that connects distant cortical regions. Here, we find that neurons expressing SATB2, a determinant of callosal projection neuron (CPN) identity, show impaired maturation in ARID1B+/- neural organoids. Molecularly, a reduction in chromatin accessibility of genomic regions targeted by TCF-like, NFI-like, and ARID-like transcription factors drives the differential expression of genes required for corpus callosum (CC) development. Through an in vitro model of the CC tract, we demonstrate that this transcriptional dysregulation impairs the formation of long-range axonal projections, causing structural underconnectivity. Our study uncovers new functions of the mSWI/SNF during human corticogenesis, identifying cell-autonomous axonogenesis defects in SATB2+ neurons as a cause of ACC in ARID1B patients.
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Affiliation(s)
- Catarina Martins-Costa
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), 1030 Vienna, Austria; Vienna BioCenter PhD Program, Doctoral School of the University of Vienna and Medical University of Vienna, 1030 Vienna, Austria
| | - Andrea Wiegers
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), 1030 Vienna, Austria
| | - Vincent A Pham
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), 1030 Vienna, Austria
| | - Jaydeep Sidhaye
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), 1030 Vienna, Austria
| | - Balint Doleschall
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), 1030 Vienna, Austria; Vienna BioCenter PhD Program, Doctoral School of the University of Vienna and Medical University of Vienna, 1030 Vienna, Austria
| | - Maria Novatchkova
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), 1030 Vienna, Austria
| | - Thomas Lendl
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), 1030 Vienna, Austria
| | - Marielle Piber
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), 1030 Vienna, Austria
| | - Angela Peer
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), 1030 Vienna, Austria
| | - Paul Möseneder
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), 1030 Vienna, Austria
| | - Marlene Stuempflen
- Department of Biomedical Imaging and Image-Guided Therapy, Medical University of Vienna, 1090 Vienna, Austria
| | - Siu Yu A Chow
- Institute of Industrial Science, The University of Tokyo, 153-8505 Tokyo, Japan; Institute for AI and Beyond, The University of Tokyo, 113-0032 Tokyo, Japan
| | - Rainer Seidl
- Department of Pediatrics and Adolescent Medicine, Medical University of Vienna, 1090 Vienna, Austria
| | - Daniela Prayer
- Department of Biomedical Imaging and Image-Guided Therapy, Medical University of Vienna, 1090 Vienna, Austria
| | - Romana Höftberger
- Division of Neuropathology and Neurochemistry, Department of Neurology, Medical University of Vienna, 1090 Vienna, Austria
| | - Gregor Kasprian
- Department of Biomedical Imaging and Image-Guided Therapy, Medical University of Vienna, 1090 Vienna, Austria
| | - Yoshiho Ikeuchi
- Institute of Industrial Science, The University of Tokyo, 153-8505 Tokyo, Japan; Institute for AI and Beyond, The University of Tokyo, 113-0032 Tokyo, Japan
| | - Nina S Corsini
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), 1030 Vienna, Austria.
| | - Jürgen A Knoblich
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), 1030 Vienna, Austria; Department of Neurology, Medical University of Vienna, 1090 Vienna, Austria.
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6
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Wang J, Guo J, Yu S, Yu H, Kuraz AB, Jilo DD, Cheng G, Li A, Jia C, Zan L. Knockdown of NFIC Promotes Bovine Myoblast Proliferation through the CENPF/CDK1 Axis. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:12641-12654. [PMID: 38780097 DOI: 10.1021/acs.jafc.4c01811] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2024]
Abstract
As cellular transcription factors and DNA replicators, nuclear factor I (NFI) family members play an important role in mammalian development. However, there is still a lack of research on the muscle regeneration of NFI family members in cattle. In this study, the analysis of NFI family factors was conducted on their characterization, phylogenetics, and functional domains. We found that NFI family members were relatively conserved among different species, but there was heterogeneity in amino acid sequences, DNA coding sequences, and functional domain among members. Furthermore, among NFI family factors, we observed that NFIC exhibited highly expression in bovine muscle tissues, particularly influencing the expression of proliferation marker genes in myoblasts. To investigate the influence of NFIC on myoblast proliferation, we knocked down NFIC (si-NFIC) and found that the proliferation of myoblasts was significantly promoted. In terms of regulation mechanism, we identified that si-NFIC could counteract the inhibitory effect of the cell cycle inhibitor RO-3306. Interestingly, CENPF, as the downstream target gene of NFIC, could affect the expression of CDK1, CCNB1, and actively regulate the cell cycle pathway and cell proliferation. In addition, when CENPF was knocked down, the phosphorylation of p53 and the expression of Bax were increased, but the expression of Bcl2 was inhibited. Our findings mainly highlight the mechanism by which NFIC acts on the CENPF/CDK1 axis to regulate the proliferation of bovine myoblasts.
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Affiliation(s)
- Jianfang Wang
- College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China
| | - Juntao Guo
- College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China
| | - Shengchen Yu
- College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China
| | - Hengwei Yu
- College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China
| | - Abebe Belete Kuraz
- College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China
| | - Diba Dedacha Jilo
- College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China
| | - Gong Cheng
- College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China
| | - Anning Li
- College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China
| | - Cunling Jia
- College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China
| | - Linsen Zan
- College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China
- National Beef Cattle Improvement Center, Yangling 712100, China
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Ko JH, Lambert KE, Bhattacharya D, Lee MC, Colón CI, Hauser H, Sage J. Small Cell Lung Cancer Plasticity Enables NFIB-Independent Metastasis. Cancer Res 2024; 84:226-240. [PMID: 37963187 PMCID: PMC10842891 DOI: 10.1158/0008-5472.can-23-1079] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Revised: 09/29/2023] [Accepted: 11/08/2023] [Indexed: 11/16/2023]
Abstract
Metastasis is a major cause of morbidity and mortality in patients with cancer, highlighting the need to identify improved treatment and prevention strategies. Previous observations in preclinical models and tumors from patients with small cell lung cancer (SCLC), a fatal form of lung cancer with high metastatic potential, identified the transcription factor NFIB as a driver of tumor growth and metastasis. However, investigation into the requirement for NFIB activity for tumor growth and metastasis in relevant in vivo models is needed to establish NFIB as a therapeutic target. Here, using conditional gene knockout strategies in genetically engineered mouse models of SCLC, we found that upregulation of NFIB contributes to tumor progression, but NFIB is not required for metastasis. Molecular studies in NFIB wild-type and knockout tumors identified the pioneer transcription factors FOXA1/2 as candidate drivers of metastatic progression. Thus, while NFIB upregulation is a frequent event in SCLC during tumor progression, SCLC tumors can employ NFIB-independent mechanisms for metastasis, further highlighting the plasticity of these tumors. SIGNIFICANCE Small cell lung cancer cells overcome deficiency of the prometastatic oncogene NFIB to gain metastatic potential through various molecular mechanisms, which may represent targets to block progression of this fatal cancer type.
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Affiliation(s)
- Julie H. Ko
- Department of Pediatrics, Stanford University, Stanford, CA 94305, USA
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Kyle E. Lambert
- Department of Pediatrics, Stanford University, Stanford, CA 94305, USA
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Debadrita Bhattacharya
- Department of Pediatrics, Stanford University, Stanford, CA 94305, USA
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Myung Chang Lee
- Department of Pediatrics, Stanford University, Stanford, CA 94305, USA
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Caterina I. Colón
- Department of Pediatrics, Stanford University, Stanford, CA 94305, USA
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Haley Hauser
- Department of Pediatrics, Stanford University, Stanford, CA 94305, USA
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Julien Sage
- Department of Pediatrics, Stanford University, Stanford, CA 94305, USA
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
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8
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Ducreux B, Patrat C, Trasler J, Fauque P. Transcriptomic integrity of human oocytes used in ARTs: technical and intrinsic factor effects. Hum Reprod Update 2024; 30:26-47. [PMID: 37697674 DOI: 10.1093/humupd/dmad025] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Revised: 07/04/2023] [Indexed: 09/13/2023] Open
Abstract
BACKGROUND Millions of children have been born throughout the world thanks to ARTs, the harmlessness of which has not yet been fully demonstrated. For years, efforts to evaluate the specific effects of ART have focused on the embryo; however, it is the oocyte quality that mainly dictates first and foremost the developmental potential of the future embryo. Ovarian stimulation, cryopreservation, and IVM are sometimes necessary steps to obtain a mature oocyte, but they could alter the appropriate expression of the oocyte genome. Additionally, it is likely that female infertility, environmental factors, and lifestyle have a significant influence on oocyte transcriptomic quality, which may interfere with the outcome of an ART attempt. OBJECTIVE AND RATIONALE The objective of this review is to identify transcriptomic changes in the human oocyte caused by interventions specific to ART but also intrinsic factors such as age, reproductive health issues, and lifestyle. We also provide recommendations for future good practices to be conducted when attempting ART. SEARCH METHODS An in-depth literature search was performed on PubMed to identify studies assessing the human oocyte transcriptome following ART interventions, or in the context of maternal aging, suboptimal lifestyle, or reproductive health issues. OUTCOMES ART success is susceptible to external factors, maternal aging, lifestyle factors (smoking, BMI), and infertility due to endometriosis or polycystic ovary syndrome. Indeed, all of these are likely to increase oxidative stress and alter mitochondrial processes in the foreground. Concerning ART techniques themselves, there is evidence that different ovarian stimulation regimens shape the oocyte transcriptome. The perturbation of processes related to the mitochondrion, oxidative phosphorylation, and metabolism is observed with IVM. Cryopreservation might dysregulate genes belonging to transcriptional regulation, ubiquitination, cell cycle, and oocyte growth pathways. For other ART laboratory factors such as temperature, oxygen tension, air pollution, and light, the evidence remains scarce. Focusing on genes involved in chromatin-based processes such as DNA methylation, heterochromatin modulation, histone modification, and chromatin remodeling complexes, but also genomic imprinting, we observed systematic dysregulation of such genes either after ART intervention or lifestyle exposure, as well as due to internal factors such as maternal aging and reproductive diseases. Alteration in the expression of such epigenetic regulators may be a common mechanism linked to adverse oocyte environments, explaining global transcriptomic modifications. WIDER IMPLICATIONS Many IVF factors and additional external factors have the potential to impair oocyte transcriptomic integrity, which might not be innocuous for the developing embryo. Fortunately, it is likely that such dysregulations can be minimized by adapting ART protocols or reducing adverse exposure.
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Affiliation(s)
- Bastien Ducreux
- Université Bourgogne Franche-Comtés-Equipe Génétique des Anomalies du Développement (GAD) INSERM UMR1231, Dijon, France
| | - Catherine Patrat
- Université de Paris Cité, Faculty of Medicine, Inserm 1016, Paris, France
- Department of Reproductive Biology-CECOS, aphp.centre-Université Paris Cité, Paris, France
| | - Jacquetta Trasler
- Department of Pediatrics, McGill University and Research Institute of the McGill University Health Centre, Montreal, QC, Canada
- Department of Human Genetics, McGill University and Research Institute of the McGill University Health Centre, Montreal, QC, Canada
- Department of Pharmacology & Therapeutics, McGill University and Research Institute of the McGill University Health Centre, Montreal, QC, Canada
| | - Patricia Fauque
- Université Bourgogne Franche-Comtés-Equipe Génétique des Anomalies du Développement (GAD) INSERM UMR1231, Dijon, France
- CHU Dijon Bourgogne, Laboratoire de Biologie de la Reproduction-CECOS, Dijon, France
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9
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Pattnaik B, Negi V, Chaudhuri R, Desiraju K, Faizan MI, Akhtar A, Ansari MS, Shakir M, Gheware A, Prakash YS, Guleria R, Ghosh B, Agrawal A, Ahmad T. MiR-326-mediated overexpression of NFIB offsets TGF-β induced epithelial to mesenchymal transition and reverses lung fibrosis. Cell Mol Life Sci 2023; 80:357. [PMID: 37950757 PMCID: PMC11072886 DOI: 10.1007/s00018-023-05005-1] [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: 05/02/2023] [Revised: 09/08/2023] [Accepted: 09/11/2023] [Indexed: 11/13/2023]
Abstract
Idiopathic Pulmonary Fibrosis (IPF) is a progressively fatal and incurable disease characterized by the loss of alveolar structures, increased epithelial-mesenchymal transition (EMT), and aberrant tissue repair. In this study, we investigated the role of Nuclear Factor I-B (NFIB), a transcription factor critical for lung development and maturation, in IPF. Using both human lung tissue samples from patients with IPF, and a mouse model of lung fibrosis induced by bleomycin, we showed that there was a significant reduction of NFIB both in the lungs of patients and mice with IPF. Furthermore, our in vitro experiments using cultured human lung cells demonstrated that the loss of NFIB was associated with the induction of EMT by transforming growth factor beta (TGF-β). Knockdown of NFIB promoted EMT, while overexpression of NFIB suppressed EMT and attenuated the severity of bleomycin-induced lung fibrosis in mice. Mechanistically, we identified post-translational regulation of NFIB by miR-326, a miRNA with anti-fibrotic effects that is diminished in IPF. Specifically, we showed that miR-326 stabilized and increased the expression of NFIB through its 3'UTR target sites for Human antigen R (HuR). Moreover, treatment of mice with either NFIB plasmid or miR-326 reversed airway collagen deposition and fibrosis. In conclusion, our study emphasizes the critical role of NFIB in lung development and maturation, and its reduction in IPF leading to EMT and loss of alveolar structures. Our study highlights the potential of miR-326 as a therapeutic intervention for IPF. The schema shows the role of NFIB in maintaining the normal epithelial cell characteristics in the lungs and how its reduction leads to a shift towards mesenchymal cell-like features and pulmonary fibrosis. A In normal lungs, NFIB is expressed abundantly in the epithelial cells, which helps in maintaining their shape, cell polarity and adhesion molecules. However, when the lungs are exposed to factors that induce pulmonary fibrosis, such as bleomycin, or TGF-β, the epithelial cells undergo epithelial to mesenchymal transition (EMT), which leads to a decrease in NFIB. B The mesenchymal cells that arise from EMT appear as spindle-shaped with loss of cell junctions, increased cell migration, loss of polarity and expression of markers associated with mesenchymal cells/fibroblasts. C We designed a therapeutic approach that involves exogenous administration of NFIB in the form of overexpression plasmid or microRNA-326. This therapeutic approach decreases the mesenchymal cell phenotype and restores the epithelial cell phenotype, thus preventing the development or progression of pulmonary fibrosis.
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Affiliation(s)
- Bijay Pattnaik
- Molecular Immunogenetics Laboratory and Centre of Excellence for Translational Research in Asthma & Lung Disease, CSIR-Institute of Genomics and Integrative Biology, Mall Road, Delhi, 110007, India
- Department of Pulmonary, Critical Care & Sleep Medicine, All India Institute of Medical Sciences, Ansari Nagar, New Delhi, 110029, India
| | - Vinny Negi
- Molecular Immunogenetics Laboratory and Centre of Excellence for Translational Research in Asthma & Lung Disease, CSIR-Institute of Genomics and Integrative Biology, Mall Road, Delhi, 110007, India
| | - Rituparna Chaudhuri
- Molecular Immunogenetics Laboratory and Centre of Excellence for Translational Research in Asthma & Lung Disease, CSIR-Institute of Genomics and Integrative Biology, Mall Road, Delhi, 110007, India
| | - Koundinya Desiraju
- Molecular Immunogenetics Laboratory and Centre of Excellence for Translational Research in Asthma & Lung Disease, CSIR-Institute of Genomics and Integrative Biology, Mall Road, Delhi, 110007, India
| | - Md Imam Faizan
- Multidisciplinary Centre for Advanced Research & Studies, Jamia Millia Islamia, New Delhi, 110025, India
| | - Areej Akhtar
- Multidisciplinary Centre for Advanced Research & Studies, Jamia Millia Islamia, New Delhi, 110025, India
| | - Md Sufyan Ansari
- Multidisciplinary Centre for Advanced Research & Studies, Jamia Millia Islamia, New Delhi, 110025, India
| | - Md Shakir
- Multidisciplinary Centre for Advanced Research & Studies, Jamia Millia Islamia, New Delhi, 110025, India
| | - Atish Gheware
- Molecular Immunogenetics Laboratory and Centre of Excellence for Translational Research in Asthma & Lung Disease, CSIR-Institute of Genomics and Integrative Biology, Mall Road, Delhi, 110007, India
| | - Y S Prakash
- Departments of Anesthesiology, Physiology and Biomedical Engineering, Mayo Clinic, Rochester, MN, USA
| | - Randeep Guleria
- Department of Pulmonary, Critical Care & Sleep Medicine, All India Institute of Medical Sciences, Ansari Nagar, New Delhi, 110029, India
| | - Balaram Ghosh
- Molecular Immunogenetics Laboratory and Centre of Excellence for Translational Research in Asthma & Lung Disease, CSIR-Institute of Genomics and Integrative Biology, Mall Road, Delhi, 110007, India
| | - Anurag Agrawal
- Molecular Immunogenetics Laboratory and Centre of Excellence for Translational Research in Asthma & Lung Disease, CSIR-Institute of Genomics and Integrative Biology, Mall Road, Delhi, 110007, India.
- Trivedi School of Biosciences, Ashoka University, NH 44, Rajiv Gandhi Education City, Sonipat, Haryana, 131029, India.
| | - Tanveer Ahmad
- Molecular Immunogenetics Laboratory and Centre of Excellence for Translational Research in Asthma & Lung Disease, CSIR-Institute of Genomics and Integrative Biology, Mall Road, Delhi, 110007, India.
- Multidisciplinary Centre for Advanced Research & Studies, Jamia Millia Islamia, New Delhi, 110025, India.
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10
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Xu X, Xu S, Wan J, Wang D, Pang X, Gao Y, Ni N, Chen D, Sun X. Disturbing cytoskeleton by engineered nanomaterials for enhanced cancer therapeutics. Bioact Mater 2023; 29:50-71. [PMID: 37621771 PMCID: PMC10444958 DOI: 10.1016/j.bioactmat.2023.06.016] [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: 05/12/2023] [Revised: 06/14/2023] [Accepted: 06/20/2023] [Indexed: 08/26/2023] Open
Abstract
Cytoskeleton plays a significant role in the shape change, migration, movement, adhesion, cytokinesis, and phagocytosis of tumor cells. In clinical practice, some anti-cancer drugs achieve cytoskeletal therapeutic effects by acting on different cytoskeletal protein components. However, in the absence of cell-specific targeting, unnecessary cytoskeletal recombination in organisms would be disastrous, which would also bring about severe side effects during anticancer process. Nanomedicine have been proven to be superior to some small molecule drugs in cancer treatment due to better stability and targeting, and lower side effects. Therefore, this review summarized the recent developments of various nanomaterials disturbing cytoskeleton for enhanced cancer therapeutics, including carbon, noble metals, metal oxides, black phosphorus, calcium, silicon, polymers, peptides, and metal-organic frameworks, etc. A comprehensive analysis of the characteristics of cytoskeleton therapy as well as the future prospects and challenges towards clinical application were also discussed. We aim to drive on this emerging topic through refreshing perspectives based on our own work and what we have also learnt from others. This review will help researchers quickly understand relevant cytoskeletal therapeutic information to further advance the development of cancer nanomedicine.
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Affiliation(s)
- Xueli Xu
- School of Science, Shandong Jianzhu University, Jinan, 250101, China
| | - Shanbin Xu
- Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, 250117, China
| | - Jipeng Wan
- Department of Gynecology, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, 250021, China
| | - Diqing Wang
- Department of Gynecology, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, 250021, China
| | - Xinlong Pang
- School of Chemistry and Pharmaceutical Engineering, Medical Science and Technology Innovation Center, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, 250000, China
| | - Yuan Gao
- School of Chemistry and Pharmaceutical Engineering, Medical Science and Technology Innovation Center, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, 250000, China
| | - Nengyi Ni
- Department of Chemical and Biomolecular Engineering, National University of Singapore, 117585, Singapore
| | - Dawei Chen
- Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, 250117, China
| | - Xiao Sun
- Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, 250117, China
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11
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Abatti LE, Lado-Fernández P, Huynh L, Collado M, Hoffman M, Mitchell J. Epigenetic reprogramming of a distal developmental enhancer cluster drives SOX2 overexpression in breast and lung adenocarcinoma. Nucleic Acids Res 2023; 51:10109-10131. [PMID: 37738673 PMCID: PMC10602899 DOI: 10.1093/nar/gkad734] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Revised: 08/18/2023] [Accepted: 08/24/2023] [Indexed: 09/24/2023] Open
Abstract
Enhancer reprogramming has been proposed as a key source of transcriptional dysregulation during tumorigenesis, but the molecular mechanisms underlying this process remain unclear. Here, we identify an enhancer cluster required for normal development that is aberrantly activated in breast and lung adenocarcinoma. Deletion of the SRR124-134 cluster disrupts expression of the SOX2 oncogene, dysregulates genome-wide transcription and chromatin accessibility and reduces the ability of cancer cells to form colonies in vitro. Analysis of primary tumors reveals a correlation between chromatin accessibility at this cluster and SOX2 overexpression in breast and lung cancer patients. We demonstrate that FOXA1 is an activator and NFIB is a repressor of SRR124-134 activity and SOX2 transcription in cancer cells, revealing a co-opting of the regulatory mechanisms involved in early development. Notably, we show that the conserved SRR124 and SRR134 regions are essential during mouse development, where homozygous deletion results in the lethal failure of esophageal-tracheal separation. These findings provide insights into how developmental enhancers can be reprogrammed during tumorigenesis and underscore the importance of understanding enhancer dynamics during development and disease.
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Affiliation(s)
- Luis E Abatti
- Department of Cell and Systems Biology, University of Toronto, Toronto, Ontario, Canada
| | - Patricia Lado-Fernández
- Laboratory of Cell Senescence, Cancer and Aging, Health Research Institute of Santiago de Compostela (IDIS), Xerencia de Xestión Integrada de Santiago (XXIS/SERGAS), Santiago de Compostela, Spain
- Department of Physiology and Center for Research in Molecular Medicine and Chronic Diseases (CiMUS), Universidade de Santiago de Compostela, Santiago de Compostela, Spain
| | - Linh Huynh
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Manuel Collado
- Laboratory of Cell Senescence, Cancer and Aging, Health Research Institute of Santiago de Compostela (IDIS), Xerencia de Xestión Integrada de Santiago (XXIS/SERGAS), Santiago de Compostela, Spain
| | - Michael M Hoffman
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
- Department of Computer Science, University of Toronto, Toronto, Ontario, Canada
- Vector Institute for Artificial Intelligence, Toronto, Ontario, Canada
| | - Jennifer A Mitchell
- Department of Cell and Systems Biology, University of Toronto, Toronto, Ontario, Canada
- Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
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12
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Dini G, Verrotti A, Gorello P, Soliani L, Cordelli DM, Antona V, Mencarelli A, Colavito D, Prontera P. NFIA haploinsufficiency: case series and literature review. Front Pediatr 2023; 11:1292654. [PMID: 37915986 PMCID: PMC10616848 DOI: 10.3389/fped.2023.1292654] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Accepted: 09/27/2023] [Indexed: 11/03/2023] Open
Abstract
Background NFIA-related disorder (OMIM #613735) is an autosomal dominant neurodevelopmental disorder characterized by a variable degree of cognitive impairment and non-specific dysmorphic features. To date, fewer than thirty patients affected by this disorder have been described. Methods Our study included three children with NFIA haploinsufficiency recruited from three medical genetics centers. Clinical presentations were recorded on a standardized case report form. Results All patients presented a variable degree of intellectual disability. None of the individuals in our cohort had urinary tract malformations. Three novel mutations, c.344G>A, c.261T>G, and c.887_888del are reported here. Conclusion NFIA haploinsufficiency can be suspected through careful observation of specific dysmorphisms, including macrocephaly and craniofacial abnormalities. Instrumental tests such as MRI and renal ultrasound provide further diagnostic clues, while genetic testing can confirm the diagnosis.
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Affiliation(s)
- Gianluca Dini
- Department of Pediatrics, University of Perugia, Perugia, Italy
| | | | - Paolo Gorello
- Department of Chemistry, Biology and Biotechnology, University of Perugia, Perugia, Italy
| | - Luca Soliani
- IRCCS Istituto Delle Scienze Neurologiche di Bologna, UOC di Neuropsichiatria Dell'Età Pediatrica, Bologna, Italy
- Dipartimento di Scienze Mediche e Chirurgiche (DIMEC), Università di Bologna, Bologna, Italy
| | - Duccio Maria Cordelli
- IRCCS Istituto Delle Scienze Neurologiche di Bologna, UOC di Neuropsichiatria Dell'Età Pediatrica, Bologna, Italy
- Dipartimento di Scienze Mediche e Chirurgiche (DIMEC), Università di Bologna, Bologna, Italy
| | - Vincenzo Antona
- Department of Health Promotion, Mother and Child Care, Internal Medicine and Medical Specialties “G. D'Alessandro,” University of Palermo, Palermo, Italy
| | - Amedea Mencarelli
- Medical Genetics Unit, S. Maria della Misericordia Hospital, Perugia, Italy
| | | | - Paolo Prontera
- Medical Genetics Unit, S. Maria della Misericordia Hospital, Perugia, Italy
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13
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Popova G, Retallack H, Kim CN, Wang A, Shin D, DeRisi JL, Nowakowski T. Rubella virus tropism and single-cell responses in human primary tissue and microglia-containing organoids. eLife 2023; 12:RP87696. [PMID: 37470786 PMCID: PMC10370260 DOI: 10.7554/elife.87696] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/21/2023] Open
Abstract
Rubella virus is an important human pathogen that can cause neurological deficits in a developing fetus when contracted during pregnancy. Despite successful vaccination programs in the Americas and many developed countries, rubella remains endemic in many regions worldwide and outbreaks occur wherever population immunity is insufficient. Intense interest since rubella virus was first isolated in 1962 has advanced our understanding of clinical outcomes after infection disrupts key processes of fetal neurodevelopment. Yet it is still largely unknown which cell types in the developing brain are targeted. We show that in human brain slices, rubella virus predominantly infects microglia. This infection occurs in a heterogeneous population but not in a highly microglia-enriched monoculture in the absence of other cell types. By using an organoid-microglia model, we further demonstrate that rubella virus infection leads to a profound interferon response in non-microglial cells, including neurons and neural progenitor cells, and this response is attenuated by the presence of microglia.
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Affiliation(s)
- Galina Popova
- Department of Neurological Surgery, University of California, San FranciscoSan FranciscoUnited States
- Eli and Edythe Broad Center for Regeneration Medicine and Stem Cell Research, University of California, San FranciscoSan FranciscoUnited States
- Department of Anatomy, University of California, San FranciscoSan FranciscoUnited States
- Department of Psychiatry and Behavioral Sciences, University of California, San FranciscoSan FranciscoUnited States
- Weill Institute for Neurosciences, University of California, San FranciscoSan FranciscoUnited States
- Department of Biochemistry and Biophysics, University of California, San FranciscoSan FranciscoUnited States
| | - Hanna Retallack
- Department of Biochemistry and Biophysics, University of California, San FranciscoSan FranciscoUnited States
| | - Chang N Kim
- Department of Neurological Surgery, University of California, San FranciscoSan FranciscoUnited States
- Eli and Edythe Broad Center for Regeneration Medicine and Stem Cell Research, University of California, San FranciscoSan FranciscoUnited States
- Department of Anatomy, University of California, San FranciscoSan FranciscoUnited States
- Department of Psychiatry and Behavioral Sciences, University of California, San FranciscoSan FranciscoUnited States
- Weill Institute for Neurosciences, University of California, San FranciscoSan FranciscoUnited States
- Department of Biochemistry and Biophysics, University of California, San FranciscoSan FranciscoUnited States
| | - Albert Wang
- Department of Neurological Surgery, University of California, San FranciscoSan FranciscoUnited States
- Eli and Edythe Broad Center for Regeneration Medicine and Stem Cell Research, University of California, San FranciscoSan FranciscoUnited States
- Department of Anatomy, University of California, San FranciscoSan FranciscoUnited States
- Department of Psychiatry and Behavioral Sciences, University of California, San FranciscoSan FranciscoUnited States
- Weill Institute for Neurosciences, University of California, San FranciscoSan FranciscoUnited States
- Department of Biochemistry and Biophysics, University of California, San FranciscoSan FranciscoUnited States
| | - David Shin
- Department of Neurological Surgery, University of California, San FranciscoSan FranciscoUnited States
- Eli and Edythe Broad Center for Regeneration Medicine and Stem Cell Research, University of California, San FranciscoSan FranciscoUnited States
- Department of Anatomy, University of California, San FranciscoSan FranciscoUnited States
- Department of Psychiatry and Behavioral Sciences, University of California, San FranciscoSan FranciscoUnited States
- Weill Institute for Neurosciences, University of California, San FranciscoSan FranciscoUnited States
- Department of Biochemistry and Biophysics, University of California, San FranciscoSan FranciscoUnited States
| | - Joseph L DeRisi
- Department of Biochemistry and Biophysics, University of California, San FranciscoSan FranciscoUnited States
- Chan Zuckerberg BiohubSan FranciscoUnited States
| | - Tomasz Nowakowski
- Department of Neurological Surgery, University of California, San FranciscoSan FranciscoUnited States
- Eli and Edythe Broad Center for Regeneration Medicine and Stem Cell Research, University of California, San FranciscoSan FranciscoUnited States
- Department of Anatomy, University of California, San FranciscoSan FranciscoUnited States
- Department of Psychiatry and Behavioral Sciences, University of California, San FranciscoSan FranciscoUnited States
- Weill Institute for Neurosciences, University of California, San FranciscoSan FranciscoUnited States
- Department of Biochemistry and Biophysics, University of California, San FranciscoSan FranciscoUnited States
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14
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Kooblall KG, Stevenson M, Stewart M, Harris L, Zalucki O, Dewhurst H, Butterfield N, Leng H, Hough TA, Ma D, Siow B, Potter P, Cox RD, Brown SD, Horwood N, Wright B, Lockstone H, Buck D, Vincent TL, Hannan FM, Bassett JD, Williams GR, Lines KE, Piper M, Wells S, Teboul L, Hennekam RC, Thakker RV. A Mouse Model with a Frameshift Mutation in the Nuclear Factor I/X ( NFIX) Gene Has Phenotypic Features of Marshall-Smith Syndrome. JBMR Plus 2023; 7:e10739. [PMID: 37283649 PMCID: PMC10241085 DOI: 10.1002/jbm4.10739] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Revised: 03/05/2023] [Accepted: 03/09/2023] [Indexed: 03/15/2023] Open
Abstract
The nuclear factor I/X (NFIX) gene encodes a ubiquitously expressed transcription factor whose mutations lead to two allelic disorders characterized by developmental, skeletal, and neural abnormalities, namely, Malan syndrome (MAL) and Marshall-Smith syndrome (MSS). NFIX mutations associated with MAL mainly cluster in exon 2 and are cleared by nonsense-mediated decay (NMD) leading to NFIX haploinsufficiency, whereas NFIX mutations associated with MSS are clustered in exons 6-10 and escape NMD and result in the production of dominant-negative mutant NFIX proteins. Thus, different NFIX mutations have distinct consequences on NFIX expression. To elucidate the in vivo effects of MSS-associated NFIX exon 7 mutations, we used CRISPR-Cas9 to generate mouse models with exon 7 deletions that comprised: a frameshift deletion of two nucleotides (Nfix Del2); in-frame deletion of 24 nucleotides (Nfix Del24); and deletion of 140 nucleotides (Nfix Del140). Nfix +/Del2, Nfix +/Del24, Nfix +/Del140, Nfix Del24/Del24, and Nfix Del140/Del140 mice were viable, normal, and fertile, with no skeletal abnormalities, but Nfix Del2/Del2 mice had significantly reduced viability (p < 0.002) and died at 2-3 weeks of age. Nfix Del2 was not cleared by NMD, and NfixDel2/Del2 mice, when compared to Nfix +/+ and Nfix +/Del2 mice, had: growth retardation; short stature with kyphosis; reduced skull length; marked porosity of the vertebrae with decreased vertebral and femoral bone mineral content; and reduced caudal vertebrae height and femur length. Plasma biochemistry analysis revealed Nfix Del2/Del2 mice to have increased total alkaline phosphatase activity but decreased C-terminal telopeptide and procollagen-type-1-N-terminal propeptide concentrations compared to Nfix +/+ and Nfix +/Del2 mice. Nfix Del2/Del2 mice were also found to have enlarged cerebral cortices and ventricular areas but smaller dentate gyrus compared to Nfix +/+ mice. Thus, Nfix Del2/Del2 mice provide a model for studying the in vivo effects of NFIX mutants that escape NMD and result in developmental abnormalities of the skeletal and neural tissues that are associated with MSS. © 2023 The Authors. JBMR Plus published by Wiley Periodicals LLC on behalf of American Society for Bone and Mineral Research.
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Affiliation(s)
- Kreepa G. Kooblall
- Academic Endocrine Unit, Radcliffe Department of Medicine, Oxford Centre for Diabetes, Endocrinology and Metabolism (OCDEM)University of OxfordOxfordUK
| | - Mark Stevenson
- Academic Endocrine Unit, Radcliffe Department of Medicine, Oxford Centre for Diabetes, Endocrinology and Metabolism (OCDEM)University of OxfordOxfordUK
| | - Michelle Stewart
- MRC Harwell, Mary Lyon CentreHarwell Science and Innovation CampusOxfordshireUK
| | | | - Oressia Zalucki
- The School of Biomedical Sciences and The Queensland Brain InstituteThe University of QueenslandBrisbaneAustralia
| | - Hannah Dewhurst
- Molecular Endocrinology Laboratory, Department of Metabolism, Digestion and Reproduction, Imperial College LondonHammersmith HospitalLondonUK
| | - Natalie Butterfield
- Molecular Endocrinology Laboratory, Department of Metabolism, Digestion and Reproduction, Imperial College LondonHammersmith HospitalLondonUK
| | - Houfu Leng
- Centre for OA Pathogenesis Versus Arthritis, The Kennedy Institute of Rheumatology, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences (NDORMS)Medical Sciences Division University of OxfordOxfordUK
| | - Tertius A. Hough
- MRC Harwell, Mary Lyon CentreHarwell Science and Innovation CampusOxfordshireUK
| | - Da Ma
- Department of Internal MedicineWake Forest University School of MedicineWinston‐SalemNCUSA
| | | | - Paul Potter
- MRC Harwell, Mary Lyon CentreHarwell Science and Innovation CampusOxfordshireUK
| | - Roger D. Cox
- MRC Harwell, Mary Lyon CentreHarwell Science and Innovation CampusOxfordshireUK
| | - Stephen D.M. Brown
- MRC Harwell, Mary Lyon CentreHarwell Science and Innovation CampusOxfordshireUK
| | - Nicole Horwood
- Centre for OA Pathogenesis Versus Arthritis, The Kennedy Institute of Rheumatology, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences (NDORMS)Medical Sciences Division University of OxfordOxfordUK
| | - Benjamin Wright
- Oxford Genomics Centre, The Wellcome Centre for Human GeneticsUniversity of OxfordOxfordUK
| | - Helen Lockstone
- Oxford Genomics Centre, The Wellcome Centre for Human GeneticsUniversity of OxfordOxfordUK
| | - David Buck
- Oxford Genomics Centre, The Wellcome Centre for Human GeneticsUniversity of OxfordOxfordUK
| | - Tonia L. Vincent
- Centre for OA Pathogenesis Versus Arthritis, The Kennedy Institute of Rheumatology, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences (NDORMS)Medical Sciences Division University of OxfordOxfordUK
| | - Fadil M. Hannan
- Academic Endocrine Unit, Radcliffe Department of Medicine, Oxford Centre for Diabetes, Endocrinology and Metabolism (OCDEM)University of OxfordOxfordUK
- Nuffield Department of Women's and Reproductive HealthUniversity of OxfordOxfordUK
| | - J.H. Duncan Bassett
- Molecular Endocrinology Laboratory, Department of Metabolism, Digestion and Reproduction, Imperial College LondonHammersmith HospitalLondonUK
| | - Graham R. Williams
- Molecular Endocrinology Laboratory, Department of Metabolism, Digestion and Reproduction, Imperial College LondonHammersmith HospitalLondonUK
| | - Kate E. Lines
- Academic Endocrine Unit, Radcliffe Department of Medicine, Oxford Centre for Diabetes, Endocrinology and Metabolism (OCDEM)University of OxfordOxfordUK
| | - Michael Piper
- The School of Biomedical Sciences and The Queensland Brain InstituteThe University of QueenslandBrisbaneAustralia
| | - Sara Wells
- MRC Harwell, Mary Lyon CentreHarwell Science and Innovation CampusOxfordshireUK
| | - Lydia Teboul
- MRC Harwell, Mary Lyon CentreHarwell Science and Innovation CampusOxfordshireUK
| | - Raoul C. Hennekam
- Department of Pediatrics, Amsterdam UMCUniversity of AmsterdamAmsterdamThe Netherlands
| | - Rajesh V. Thakker
- Academic Endocrine Unit, Radcliffe Department of Medicine, Oxford Centre for Diabetes, Endocrinology and Metabolism (OCDEM)University of OxfordOxfordUK
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15
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Raviram R, Raman A, Preissl S, Ning J, Wu S, Koga T, Zhang K, Brennan CW, Zhu C, Luebeck J, Van Deynze K, Han JY, Hou X, Ye Z, Mischel AK, Li YE, Fang R, Baback T, Mugford J, Han CZ, Glass CK, Barr CL, Mischel PS, Bafna V, Escoubet L, Ren B, Chen CC. Integrated analysis of single-cell chromatin state and transcriptome identified common vulnerability despite glioblastoma heterogeneity. Proc Natl Acad Sci U S A 2023; 120:e2210991120. [PMID: 37155843 PMCID: PMC10194019 DOI: 10.1073/pnas.2210991120] [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: 06/27/2022] [Accepted: 03/09/2023] [Indexed: 05/10/2023] Open
Abstract
In 2021, the World Health Organization reclassified glioblastoma, the most common form of adult brain cancer, into isocitrate dehydrogenase (IDH)-wild-type glioblastomas and grade IV IDH mutant (G4 IDHm) astrocytomas. For both tumor types, intratumoral heterogeneity is a key contributor to therapeutic failure. To better define this heterogeneity, genome-wide chromatin accessibility and transcription profiles of clinical samples of glioblastomas and G4 IDHm astrocytomas were analyzed at single-cell resolution. These profiles afforded resolution of intratumoral genetic heterogeneity, including delineation of cell-to-cell variations in distinct cell states, focal gene amplifications, as well as extrachromosomal circular DNAs. Despite differences in IDH mutation status and significant intratumoral heterogeneity, the profiled tumor cells shared a common chromatin structure defined by open regions enriched for nuclear factor 1 transcription factors (NFIA and NFIB). Silencing of NFIA or NFIB suppressed in vitro and in vivo growths of patient-derived glioblastomas and G4 IDHm astrocytoma models. These findings suggest that despite distinct genotypes and cell states, glioblastoma/G4 astrocytoma cells share dependency on core transcriptional programs, yielding an attractive platform for addressing therapeutic challenges associated with intratumoral heterogeneity.
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Affiliation(s)
- Ramya Raviram
- Ludwig Institute for Cancer Research, University of California San Diego, La Jolla, CA92093
| | - Anugraha Raman
- Ludwig Institute for Cancer Research, University of California San Diego, La Jolla, CA92093
| | - Sebastian Preissl
- Center for Epigenomics, University of California San Diego, La Jolla, CA92093
- Institute of Experimental and Clinical Pharmacology and Toxicology, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Jiangfang Ning
- Department of Neurosurgery, University of Minnesota, Minneapolis, MN55455
| | - Shaoping Wu
- Department of Neurosurgery, University of Minnesota, Minneapolis, MN55455
| | - Tomoyuki Koga
- Department of Neurosurgery, University of Minnesota, Minneapolis, MN55455
| | - Kai Zhang
- Ludwig Institute for Cancer Research, University of California San Diego, La Jolla, CA92093
| | - Cameron W. Brennan
- Department of Neurosurgery, Memorial Sloan Kettering Cancer Center, New York, NY10065
| | - Chenxu Zhu
- Ludwig Institute for Cancer Research, University of California San Diego, La Jolla, CA92093
| | - Jens Luebeck
- Department of Computer Science and Engineering, Halicioglu Data Science Institute, University of California San Diego, La Jolla, CA92093
| | - Kinsey Van Deynze
- Ludwig Institute for Cancer Research, University of California San Diego, La Jolla, CA92093
| | - Jee Yun Han
- Center for Epigenomics, University of California San Diego, La Jolla, CA92093
| | - Xiaomeng Hou
- Center for Epigenomics, University of California San Diego, La Jolla, CA92093
| | - Zhen Ye
- Ludwig Institute for Cancer Research, University of California San Diego, La Jolla, CA92093
| | - Anna K. Mischel
- Ludwig Institute for Cancer Research, University of California San Diego, La Jolla, CA92093
| | - Yang Eric Li
- Ludwig Institute for Cancer Research, University of California San Diego, La Jolla, CA92093
| | - Rongxin Fang
- Ludwig Institute for Cancer Research, University of California San Diego, La Jolla, CA92093
| | - Tomas Baback
- Department of Computer Science and Engineering, Biomedical Sciences Graduate Program, San Diego, CA92121
| | - Joshua Mugford
- Department of Computer Science and Engineering, Biomedical Sciences Graduate Program, San Diego, CA92121
| | - Claudia Z. Han
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA92093
| | - Christopher K. Glass
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA92093
- Department of Medicine, University of California San Diego, La Jolla, CA92093
| | - Cathy L. Barr
- Program in Neurosciences and Mental Health, Hospital for Sick Children, Division of Experimental & Translational Neuroscience, Krembil Research Institute, University Health Network, Toronto, ONM5T 0S8, Canada
- Department of Psychiatry, University of Toronto, Toronto, ONM5T 0S8, Canada
- Department of Physiology, University of Toronto, Toronto, ONM5T 0S8, Canada
| | - Paul S. Mischel
- Department of Pathology, Stanford University, Stanford, CA94305
| | - Vineet Bafna
- Department of Computer Science and Engineering, Halicioglu Data Science Institute, University of California San Diego, La Jolla, CA92093
| | - Laure Escoubet
- Department of Computer Science and Engineering, Biomedical Sciences Graduate Program, San Diego, CA92121
| | - Bing Ren
- Ludwig Institute for Cancer Research, University of California San Diego, La Jolla, CA92093
- Center for Epigenomics, University of California San Diego, La Jolla, CA92093
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA92093
| | - Clark C. Chen
- Department of Neurosurgery, University of Minnesota, Minneapolis, MN55455
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16
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Cao S, Feng H, Yi H, Pan M, Lin L, Zhang YS, Feng Z, Liang W, Cai B, Li Q, Xiong Z, Shen Q, Ke M, Zhao X, Chen H, He Q, Min M, Cai Q, Liu H, Wang J, Pei D, Chen J, Ma Y. Single-cell RNA sequencing reveals the developmental program underlying proximal-distal patterning of the human lung at the embryonic stage. Cell Res 2023:10.1038/s41422-023-00802-6. [PMID: 37085732 PMCID: PMC10119843 DOI: 10.1038/s41422-023-00802-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2022] [Accepted: 03/21/2023] [Indexed: 04/23/2023] Open
Abstract
The lung is the primary respiratory organ in human, in which the proximal airway and the distal alveoli are responsible for air conduction and gas exchange, respectively. However, the regulation of proximal-distal patterning at the embryonic stage of human lung development is largely unknown. Here we investigated the early lung development of human embryos at weeks 4-8 post fertilization (Carnegie stages 12-21) using single-cell RNA sequencing, and obtained a transcriptomic atlas of 169,686 cells. We observed discernible gene expression patterns of proximal and distal epithelia at week 4, upon the initiation of lung organogenesis. Moreover, we identified novel transcriptional regulators of the patterning of proximal (e.g., THRB and EGR3) and distal (e.g., ETV1 and SOX6) epithelia. Further dissection revealed various stromal cell populations, including an early-embryonic BDNF+ population, providing a proximal-distal patterning niche with spatial specificity. In addition, we elucidated the cell fate bifurcation and maturation of airway and vascular smooth muscle progenitor cells at the early stage of lung development. Together, our study expands the scope of human lung developmental biology at early embryonic stages. The discovery of intrinsic transcriptional regulators and novel niche providers deepens the understanding of epithelial proximal-distal patterning in human lung development, opening up new avenues for regenerative medicine.
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Affiliation(s)
- Shangtao Cao
- Guangzhou Laboratory, Guangzhou, Guangdong, China.
- Hainan Provincial Key Laboratory for Human Reproductive Medicine and Genetic Research, Hainan Provincial Clinical Research Center for Thalassemia, Reproductive Medical Center, International Technology Cooperation Base "China-Myanmar Joint Research Center for Prevention and Treatment of Regional Major Disease" By the Ministry of Science and Technology of China, The First Affiliated Hospital of Hainan Medical University, Hainan Medical University, Haikou, Hainan, China.
- Center for Cell Lineage and Atlas (CCLA), Bioland Laboratory (Guangzhou Regenerative Medicine and Health Guangdong Laboratory), Guangzhou, Guangdong, China.
- The Fifth Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, China.
| | - Huijian Feng
- Center for Cell Lineage and Atlas (CCLA), Bioland Laboratory (Guangzhou Regenerative Medicine and Health Guangdong Laboratory), Guangzhou, Guangdong, China
- CAS Key Laboratory of Regenerative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, Guangdong, China
- University of the Chinese Academy of Sciences, Beijing, China
| | - Hongyan Yi
- Hainan Provincial Key Laboratory for Human Reproductive Medicine and Genetic Research, Hainan Provincial Clinical Research Center for Thalassemia, Reproductive Medical Center, International Technology Cooperation Base "China-Myanmar Joint Research Center for Prevention and Treatment of Regional Major Disease" By the Ministry of Science and Technology of China, The First Affiliated Hospital of Hainan Medical University, Hainan Medical University, Haikou, Hainan, China
- Laboratory of Cell Fate Control, School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China
| | - Mengjie Pan
- Guangzhou Laboratory, Guangzhou, Guangdong, China
| | - Lihui Lin
- CAS Key Laboratory of Regenerative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, Guangdong, China
- Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, Guangdong, China
| | - Yao Santo Zhang
- Center for Cell Lineage and Atlas (CCLA), Bioland Laboratory (Guangzhou Regenerative Medicine and Health Guangdong Laboratory), Guangzhou, Guangdong, China
| | - Ziyu Feng
- Guangzhou Laboratory, Guangzhou, Guangdong, China
- The Fifth Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Weifang Liang
- Center for Cell Lineage and Atlas (CCLA), Bioland Laboratory (Guangzhou Regenerative Medicine and Health Guangdong Laboratory), Guangzhou, Guangdong, China
| | - Baomei Cai
- Guangzhou Laboratory, Guangzhou, Guangdong, China
| | - Qi Li
- Hainan Provincial Key Laboratory for Human Reproductive Medicine and Genetic Research, Hainan Provincial Clinical Research Center for Thalassemia, Reproductive Medical Center, International Technology Cooperation Base "China-Myanmar Joint Research Center for Prevention and Treatment of Regional Major Disease" By the Ministry of Science and Technology of China, The First Affiliated Hospital of Hainan Medical University, Hainan Medical University, Haikou, Hainan, China
- Key Laboratory of the Ministry of Education for Reproductive Health Diseases Research and Translation, Hainan Medical University, Haikou, Hainan, China
| | - Zhi Xiong
- Center for Cell Lineage and Atlas (CCLA), Bioland Laboratory (Guangzhou Regenerative Medicine and Health Guangdong Laboratory), Guangzhou, Guangdong, China
- CAS Key Laboratory of Regenerative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, Guangdong, China
- Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, Guangdong, China
| | - Qingmei Shen
- Guangzhou Laboratory, Guangzhou, Guangdong, China
| | - Minjing Ke
- Center for Cell Lineage and Atlas (CCLA), Bioland Laboratory (Guangzhou Regenerative Medicine and Health Guangdong Laboratory), Guangzhou, Guangdong, China
- CAS Key Laboratory of Regenerative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, Guangdong, China
- University of the Chinese Academy of Sciences, Beijing, China
| | - Xing Zhao
- Hainan Provincial Key Laboratory for Human Reproductive Medicine and Genetic Research, Hainan Provincial Clinical Research Center for Thalassemia, Reproductive Medical Center, International Technology Cooperation Base "China-Myanmar Joint Research Center for Prevention and Treatment of Regional Major Disease" By the Ministry of Science and Technology of China, The First Affiliated Hospital of Hainan Medical University, Hainan Medical University, Haikou, Hainan, China
- Key Laboratory of the Ministry of Education for Reproductive Health Diseases Research and Translation, Hainan Medical University, Haikou, Hainan, China
| | - Huilin Chen
- Center for Cell Lineage and Atlas (CCLA), Bioland Laboratory (Guangzhou Regenerative Medicine and Health Guangdong Laboratory), Guangzhou, Guangdong, China
- CAS Key Laboratory of Regenerative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, Guangdong, China
- University of the Chinese Academy of Sciences, Beijing, China
| | - Qina He
- Hainan Provincial Key Laboratory for Human Reproductive Medicine and Genetic Research, Hainan Provincial Clinical Research Center for Thalassemia, Reproductive Medical Center, International Technology Cooperation Base "China-Myanmar Joint Research Center for Prevention and Treatment of Regional Major Disease" By the Ministry of Science and Technology of China, The First Affiliated Hospital of Hainan Medical University, Hainan Medical University, Haikou, Hainan, China
- Key Laboratory of the Ministry of Education for Reproductive Health Diseases Research and Translation, Hainan Medical University, Haikou, Hainan, China
| | - Mingwei Min
- Guangzhou Laboratory, Guangzhou, Guangdong, China
| | - Quanyou Cai
- Center for Cell Lineage and Atlas (CCLA), Bioland Laboratory (Guangzhou Regenerative Medicine and Health Guangdong Laboratory), Guangzhou, Guangdong, China
- CAS Key Laboratory of Regenerative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, Guangdong, China
- University of the Chinese Academy of Sciences, Beijing, China
| | - He Liu
- Center for Cell Lineage and Atlas (CCLA), Bioland Laboratory (Guangzhou Regenerative Medicine and Health Guangdong Laboratory), Guangzhou, Guangdong, China
- The Fifth Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Jie Wang
- CAS Key Laboratory of Regenerative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, Guangdong, China
- Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, Guangdong, China
| | - Duanqing Pei
- Laboratory of Cell Fate Control, School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China.
- Centre for Regenerative Medicine and Health, Hong Kong Institute of Science & Innovation, Chinese Academy of Sciences, Hong Kong, China.
| | - Jiekai Chen
- Center for Cell Lineage and Atlas (CCLA), Bioland Laboratory (Guangzhou Regenerative Medicine and Health Guangdong Laboratory), Guangzhou, Guangdong, China.
- CAS Key Laboratory of Regenerative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, Guangdong, China.
- University of the Chinese Academy of Sciences, Beijing, China.
- Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, Guangdong, China.
- Centre for Regenerative Medicine and Health, Hong Kong Institute of Science & Innovation, Chinese Academy of Sciences, Hong Kong, China.
| | - Yanlin Ma
- Hainan Provincial Key Laboratory for Human Reproductive Medicine and Genetic Research, Hainan Provincial Clinical Research Center for Thalassemia, Reproductive Medical Center, International Technology Cooperation Base "China-Myanmar Joint Research Center for Prevention and Treatment of Regional Major Disease" By the Ministry of Science and Technology of China, The First Affiliated Hospital of Hainan Medical University, Hainan Medical University, Haikou, Hainan, China.
- Key Laboratory of the Ministry of Education for Reproductive Health Diseases Research and Translation, Hainan Medical University, Haikou, Hainan, China.
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17
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Treatment-Resistant Schizophrenia, Clozapine Resistance, Genetic Associations, and Implications for Precision Psychiatry: A Scoping Review. Genes (Basel) 2023; 14:genes14030689. [PMID: 36980961 PMCID: PMC10048540 DOI: 10.3390/genes14030689] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Revised: 03/03/2023] [Accepted: 03/08/2023] [Indexed: 03/14/2023] Open
Abstract
Treatment-resistant schizophrenia (TRS) is often associated with severe burden of disease, poor quality of life and functional impairment. Clozapine is the gold standard for the treatment of TRS, although it is also known to cause significant side effects in some patients. In view of the burgeoning interest in the role of genetic factors in precision psychiatry, we conducted a scoping review to narratively summarize the current genetic factors associated with TRS, clozapine resistance and side effects to clozapine treatment. We searched PubMed from inception to December 2022 and included 104 relevant studies in this review. Extant evidence comprised associations between TRS and clozapine resistance with genetic factors related to mainly dopaminergic and serotoninergic neurotransmitter systems, specifically, TRS and rs4680, rs4818 within COMT, and rs1799978 within DRD2; clozapine resistance and DRD3 polymorphisms, CYP1A2 polymorphisms; weight gain with LEP and SNAP-25 genes; and agranulocytosis risk with HLA-related polymorphisms. Future studies, including replication in larger multi-site samples, are still needed to elucidate putative risk genes and the interactions between different genes and their correlations with relevant clinical factors such as psychopathology, psychosocial functioning, cognition and progressive changes with treatment over time in TRS and clozapine resistance.
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18
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Gao G, Hausmann S, Flores NM, Benitez AM, Shen J, Yang X, Person MD, Gayatri S, Cheng D, Lu Y, Liu B, Mazur PK, Bedford MT. The NFIB/CARM1 partnership is a driver in preclinical models of small cell lung cancer. Nat Commun 2023; 14:363. [PMID: 36690626 PMCID: PMC9870865 DOI: 10.1038/s41467-023-35864-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Accepted: 01/04/2023] [Indexed: 01/24/2023] Open
Abstract
The coactivator associated arginine methyltransferase (CARM1) promotes transcription, as its name implies. It does so by modifying histones and chromatin bound proteins. We identified nuclear factor I B (NFIB) as a CARM1 substrate and show that this transcription factor utilizes CARM1 as a coactivator. Biochemical studies reveal that tripartite motif 29 (TRIM29) is an effector molecule for methylated NFIB. Importantly, NFIB harbors both oncogenic and metastatic activities, and is often overexpressed in small cell lung cancer (SCLC). Here, we explore the possibility that CARM1 methylation of NFIB is important for its transforming activity. Using a SCLC mouse model, we show that both CARM1 and the CARM1 methylation site on NFIB are critical for the rapid onset of SCLC. Furthermore, CARM1 and methylated NFIB are responsible for maintaining similar open chromatin states in tumors. Together, these findings suggest that CARM1 might be a therapeutic target for SCLC.
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Affiliation(s)
- Guozhen Gao
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Simone Hausmann
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Natasha M Flores
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Ana Morales Benitez
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Jianjun Shen
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Xiaojie Yang
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Maria D Person
- Center for Biomedical Research Support, The University of Texas at Austin, Austin, TX, 78712, USA
| | - Sitaram Gayatri
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
- Evozyne Inc., Chicago, IL, 60614, USA
| | - Donghang Cheng
- Department of Pediatrics, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Yue Lu
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Bin Liu
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Pawel K Mazur
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA.
| | - Mark T Bedford
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA.
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19
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Ding W, Kaur D, Horvath S, Zhou W. Comparative epigenome analysis using Infinium DNA methylation BeadChips. Brief Bioinform 2023; 24:6974838. [PMID: 36617464 PMCID: PMC10147478 DOI: 10.1093/bib/bbac617] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Revised: 12/05/2022] [Accepted: 12/15/2022] [Indexed: 01/10/2023] Open
Abstract
The arrival of the Infinium DNA methylation BeadChips for mice and other nonhuman mammalian species has outpaced the development of the informatics that supports their use for epigenetics study in model organisms. Here, we present informatics infrastructure and methods to allow easy DNA methylation analysis on multiple species, including domesticated animals and inbred laboratory mice (in SeSAMe version 1.16.0+). First, we developed a data-driven analysis pipeline covering species inference, genome-specific data preprocessing and regression modeling. We targeted genomes of 310 species and 37 inbred mouse strains and showed that genome-specific preprocessing prevents artifacts and yields more accurate measurements than generic pipelines. Second, we uncovered the dynamics of the epigenome evolution in different genomic territories and tissue types through comparative analysis. We identified a catalog of inbred mouse strain-specific methylation differences, some of which are linked to the strains' immune, metabolic and neurological phenotypes. By streamlining DNA methylation array analysis for undesigned genomes, our methods extend epigenome research to broad species contexts.
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Affiliation(s)
- Wubin Ding
- Center for Computational and Genomic Medicine, The Children's Hospital of Philadelphia, PA, 19104, USA
| | - Diljeet Kaur
- Center for Computational and Genomic Medicine, The Children's Hospital of Philadelphia, PA, 19104, USA
| | - Steve Horvath
- Dept. of Human Genetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, 90095, USA.,Altos Labs, San Diego, CA, USA
| | - Wanding Zhou
- Center for Computational and Genomic Medicine, The Children's Hospital of Philadelphia, PA, 19104, USA.,Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
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20
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Joung J, Ma S, Tay T, Geiger-Schuller KR, Kirchgatterer PC, Verdine VK, Guo B, Arias-Garcia MA, Allen WE, Singh A, Kuksenko O, Abudayyeh OO, Gootenberg JS, Fu Z, Macrae RK, Buenrostro JD, Regev A, Zhang F. A transcription factor atlas of directed differentiation. Cell 2023; 186:209-229.e26. [PMID: 36608654 PMCID: PMC10344468 DOI: 10.1016/j.cell.2022.11.026] [Citation(s) in RCA: 54] [Impact Index Per Article: 54.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Revised: 08/04/2022] [Accepted: 11/23/2022] [Indexed: 01/07/2023]
Abstract
Transcription factors (TFs) regulate gene programs, thereby controlling diverse cellular processes and cell states. To comprehensively understand TFs and the programs they control, we created a barcoded library of all annotated human TF splice isoforms (>3,500) and applied it to build a TF Atlas charting expression profiles of human embryonic stem cells (hESCs) overexpressing each TF at single-cell resolution. We mapped TF-induced expression profiles to reference cell types and validated candidate TFs for generation of diverse cell types, spanning all three germ layers and trophoblasts. Targeted screens with subsets of the library allowed us to create a tailored cellular disease model and integrate mRNA expression and chromatin accessibility data to identify downstream regulators. Finally, we characterized the effects of combinatorial TF overexpression by developing and validating a strategy for predicting combinations of TFs that produce target expression profiles matching reference cell types to accelerate cellular engineering efforts.
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Affiliation(s)
- Julia Joung
- Department of Biological Engineering, MIT, Cambridge, MA 02139, USA; Department of Brain and Cognitive Science, MIT, Cambridge, MA 02139, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; McGovern Institute for Brain Research at MIT, Cambridge, MA 02139, USA; Howard Hughes Medical Institute, MIT, Cambridge, MA 02139, USA
| | - Sai Ma
- Department of Biology, MIT, Cambridge, MA 02139, USA; Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA; Gene Regulation Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Tristan Tay
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA; Gene Regulation Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Kathryn R Geiger-Schuller
- Department of Biology, MIT, Cambridge, MA 02139, USA; Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Paul C Kirchgatterer
- Department of Biological Engineering, MIT, Cambridge, MA 02139, USA; Department of Brain and Cognitive Science, MIT, Cambridge, MA 02139, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; McGovern Institute for Brain Research at MIT, Cambridge, MA 02139, USA; Howard Hughes Medical Institute, MIT, Cambridge, MA 02139, USA
| | - Vanessa K Verdine
- Department of Biological Engineering, MIT, Cambridge, MA 02139, USA; Department of Brain and Cognitive Science, MIT, Cambridge, MA 02139, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; McGovern Institute for Brain Research at MIT, Cambridge, MA 02139, USA; Howard Hughes Medical Institute, MIT, Cambridge, MA 02139, USA
| | - Baolin Guo
- McGovern Institute for Brain Research at MIT, Cambridge, MA 02139, USA; Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Mario A Arias-Garcia
- McGovern Institute for Brain Research at MIT, Cambridge, MA 02139, USA; Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - William E Allen
- Department of Biological Engineering, MIT, Cambridge, MA 02139, USA; Department of Brain and Cognitive Science, MIT, Cambridge, MA 02139, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; McGovern Institute for Brain Research at MIT, Cambridge, MA 02139, USA; Howard Hughes Medical Institute, MIT, Cambridge, MA 02139, USA; Society of Fellows, Harvard University, Cambridge, MA, USA
| | - Ankita Singh
- Department of Biological Engineering, MIT, Cambridge, MA 02139, USA; Department of Brain and Cognitive Science, MIT, Cambridge, MA 02139, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; McGovern Institute for Brain Research at MIT, Cambridge, MA 02139, USA; Howard Hughes Medical Institute, MIT, Cambridge, MA 02139, USA
| | - Olena Kuksenko
- Department of Biology, MIT, Cambridge, MA 02139, USA; Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Omar O Abudayyeh
- Department of Biological Engineering, MIT, Cambridge, MA 02139, USA; Department of Brain and Cognitive Science, MIT, Cambridge, MA 02139, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; McGovern Institute for Brain Research at MIT, Cambridge, MA 02139, USA; Howard Hughes Medical Institute, MIT, Cambridge, MA 02139, USA
| | - Jonathan S Gootenberg
- Department of Biological Engineering, MIT, Cambridge, MA 02139, USA; Department of Brain and Cognitive Science, MIT, Cambridge, MA 02139, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; McGovern Institute for Brain Research at MIT, Cambridge, MA 02139, USA; Howard Hughes Medical Institute, MIT, Cambridge, MA 02139, USA
| | - Zhanyan Fu
- McGovern Institute for Brain Research at MIT, Cambridge, MA 02139, USA; Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Rhiannon K Macrae
- Department of Biological Engineering, MIT, Cambridge, MA 02139, USA; Department of Brain and Cognitive Science, MIT, Cambridge, MA 02139, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; McGovern Institute for Brain Research at MIT, Cambridge, MA 02139, USA; Howard Hughes Medical Institute, MIT, Cambridge, MA 02139, USA
| | - Jason D Buenrostro
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA; Gene Regulation Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Aviv Regev
- Department of Biology, MIT, Cambridge, MA 02139, USA; Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Feng Zhang
- Department of Biological Engineering, MIT, Cambridge, MA 02139, USA; Department of Brain and Cognitive Science, MIT, Cambridge, MA 02139, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; McGovern Institute for Brain Research at MIT, Cambridge, MA 02139, USA; Howard Hughes Medical Institute, MIT, Cambridge, MA 02139, USA.
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21
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Shi K, Wang B, Dou L, Wang S, Fu X, Yu H. Integrated bioinformatics analysis of the transcription factor-mediated gene regulatory networks in the formation of spermatogonial stem cells. Front Physiol 2022; 13:949486. [PMID: 36569748 PMCID: PMC9773208 DOI: 10.3389/fphys.2022.949486] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2022] [Accepted: 11/28/2022] [Indexed: 12/14/2022] Open
Abstract
Background: In vitro induction of spermatogonial stem cells (SSCs) from embryonic stem cells (ESCs) provides a promising tool for the treatment of male infertility. A variety of molecules are involved in this complex process, which needs to be further clarified. Undoubtedly, the increased knowledge of SSC formation will be beneficial to facilitate the currently complex induction process. Methods: Based on ATAC-seq, DNase-seq, RNA-seq, and microarray data from GEO datasets, chromatin property data (ATAC-seq, DNase-seq) and gene expression data (RNA-seq, microarray data) were combined to search for SSC-specific transcription factors (TFs) and hub SSC-specific genes by using the WGCNA method. Then, we applied RNA-seq and microarray data screening for key SSC-specific TFs and constructed key SSC-specific TF-mediated gene regulatory networks (GRNs) using ChIP-seq data. Results: First, after analysis of the ATAC-seq and DNase-seq data of mouse ESCs, primordial germ cells (PGCs), and SSCs, 33 SSC-specific TFs and 958 targeting genes were obtained. RNA-seq and WGCNA revealed that the key modules (turquoise and red) were the most significantly related to 958 SSC-specific genes, and a total of 10 hub SSC-specific genes were identified. Next, when compared with the cell-specific TFs in human ESCs, PGCs, and SSCs, we obtained five overlapping SSC-specific TF motifs, including the NF1 family TF motifs (NFIA, NFIB, NFIC, and NFIX), GRE, Fox:Ebox, PGR, and ARE. Among these, Nfib and Nfix exhibited abnormally high expression levels relative to mouse ESCs and PGCs. Moreover, Nfib and Nfix were upregulated in the testis sample with impaired spermatogenesis when compared with the normal group. Finally, the ChIP-seq data results showed that NFIB most likely targeted the hub SSC-specific genes of the turquoise module (Rpl36al, Rps27, Rps21, Nedd8, and Sec61b) and the red module (Vcam1 and Ccl2). Conclusion: Our findings preliminarily revealed cell-specific TFs and cell-specific TF-mediated GRNs in the process of SSC formation. The hub SSC-specific genes and the key SSC-specific TFs were identified and suggested complex network regulation, which may play key roles in optimizing the induction efficiency of the differentiation of ESCs into SSCs in vitro.
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22
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Yan H, Wang R, Ma S, Huang D, Wang S, Ren J, Lu C, Chen X, Lu X, Zheng Z, Zhang W, Qu J, Zhou Y, Liu GH. Lineage Landscape: a comprehensive database that records lineage commitment across species. Nucleic Acids Res 2022; 51:D1061-D1066. [PMID: 36305824 PMCID: PMC9825468 DOI: 10.1093/nar/gkac951] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Revised: 09/23/2022] [Accepted: 10/11/2022] [Indexed: 01/30/2023] Open
Abstract
Commitment to specific cell lineages is critical for mammalian embryonic development. Lineage determination, differentiation, maintenance, and organogenesis result in diverse life forms composed of multiple cell types. To understand the formation and maintenance of living individuals, including human beings, a comprehensive database that integrates multi-omic information underlying lineage differentiation across multiple species is urgently needed. Here, we construct Lineage Landscape, a database that compiles, analyzes and visualizes transcriptomic and epigenomic information related to lineage development in a collection of species. This landscape draws together datasets that capture the ongoing changes in cell lineages from classic model organisms to human beings throughout embryonic, fetal, adult, and aged stages, providing comprehensive, open-access information that is useful to researchers of a broad spectrum of life science disciplines. Lineage Landscape contains single-cell gene expression and bulk transcriptomic, DNA methylation, histone modifications, and chromatin accessibility profiles. Using this database, users can explore genes of interest that exhibit dynamic expression patterns at the transcriptional or epigenetic levels at different stages of lineage development. Lineage Landscape currently includes over 6.6 million cells, 15 million differentially expressed genes and 36 million data entries across 10 species and 34 organs. Lineage Landscape is free to access, browse, search, and download at http://data.iscr.ac.cn/lineage/#/home.
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Affiliation(s)
| | | | | | | | | | | | - Changfa Lu
- Computer Network Information Center, Chinese Academy of Sciences, Beijing 100190, China
| | - Xin Chen
- Computer Network Information Center, Chinese Academy of Sciences, Beijing 100190, China
| | - Xiaoyong Lu
- University of Chinese Academy of Sciences, Beijing 100049, China,China National Center for Bioinformation, Beijing 100101, China,CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
| | - Zikai Zheng
- University of Chinese Academy of Sciences, Beijing 100049, China,China National Center for Bioinformation, Beijing 100101, China,CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
| | - Weiqi Zhang
- Correspondence may also be addressed to Weiqi Zhang. Tel: +86 10 8409 7838;
| | - Jing Qu
- Correspondence may also be addressed to Jing Qu. Tel: +86 10 6480 7768;
| | - Yuanchun Zhou
- Correspondence may also be addressed to Yuanchun Zhou. Tel: +86 10 5881 2561;
| | - Guang-Hui Liu
- To whom correspondence should be addressed. Tel: +86 10 6480 7583;
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23
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Lenk HÇ, Løvsletten Smith R, O'Connell KS, Jukić MM, Kringen MK, Andreassen OA, Ingelman‐Sundberg M, Molden E. Impact of NFIB and CYP1A variants on clozapine serum concentration-A retrospective naturalistic cohort study on 526 patients with known smoking habits. Clin Transl Sci 2022; 16:62-72. [PMID: 36152308 PMCID: PMC9841299 DOI: 10.1111/cts.13422] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Revised: 08/11/2022] [Accepted: 09/08/2022] [Indexed: 02/06/2023] Open
Abstract
Clinical response of clozapine is closely associated with serum concentration. Although tobacco smoking is the key environmental factor underlying interindividual variability in clozapine metabolism, recent genome-wide studies suggest that CYP1A and NFIB genetic variants may also be of significant importance, but their quantitative impact is unclear. We investigated the effects of the rs2472297 C>T (CYP1A) and rs28379954 T>C (NFIB) polymorphisms on serum concentrations in smokers and nonsmokers. The study retrospectively included 526 patients with known smoking habits (63.7% smokers) from a therapeutic drug monitoring service in Norway. Clozapine dose-adjusted concentrations (C/D) and patient proportions with subtherapeutic levels (<1070 nmol/L) were compared between CYP1A/NFIB variant allele carriers and homozygous wild-type carriers (noncarriers), in both smokers and nonsmokers. Clozapine C/D was reduced in patients carrying CYP1A-T and NFIB-C variants versus noncarriers, both among smokers (-48%; p < 0.0001) and nonsmokers (-35%; p = 0.028). Patients who smoke carrying CYP1A-T and NFIB-C variants had a 66% reduction in clozapine C/D versus nonsmoking noncarriers (p < 0.0001). The patient proportion with subtherapeutic levels was 2.9-fold higher in patients who smoke carrying NFIB-C and CYP1A-T variants versus nonsmoking noncarriers (p < 0.0001). In conclusion, CYP1A and NFIB variants have significant and additive impact on clozapine dose requirements for reaching target serum concentrations. Patients who smoke carrying the studied CYP1A and NFIB variants, comprising 2.5% of the study population, may need threefold higher doses to prevent risk of clozapine undertreatment. The results suggest that pre-emptive genotyping of NFIB and CYP1A may be utilized to guide clozapine dosing and improve clinical outcomes in patients with treatment-resistant schizophrenia.
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Affiliation(s)
- Hasan Çağın Lenk
- Center for PsychopharmacologyDiakonhjemmet HospitalOsloNorway,Section for Pharmacology and Pharmaceutical Biosciences, Department of PharmacyUniversity of OsloOsloNorway
| | - Robert Løvsletten Smith
- Center for PsychopharmacologyDiakonhjemmet HospitalOsloNorway,Division of Mental Health and Addiction, NORMENT CentreOslo University HospitalOsloNorway,Institute of Clinical MedicineUniversity of OsloOsloNorway
| | - Kevin S. O'Connell
- Division of Mental Health and Addiction, NORMENT CentreOslo University HospitalOsloNorway,Institute of Clinical MedicineUniversity of OsloOsloNorway
| | - Marin M. Jukić
- Section of Pharmacogenetics, Department of Physiology and PharmacologyKarolinska InstitutetStockholmSweden,Department of Physiology, Faculty of PharmacyUniversity of BelgradeBelgradeSerbia
| | - Marianne Kristiansen Kringen
- Center for PsychopharmacologyDiakonhjemmet HospitalOsloNorway,Department of Life Sciences and HealthOslo Metropolitan UniversityOsloNorway
| | - Ole A. Andreassen
- Division of Mental Health and Addiction, NORMENT CentreOslo University HospitalOsloNorway,Institute of Clinical MedicineUniversity of OsloOsloNorway
| | - Magnus Ingelman‐Sundberg
- Section of Pharmacogenetics, Department of Physiology and PharmacologyKarolinska InstitutetStockholmSweden
| | - Espen Molden
- Center for PsychopharmacologyDiakonhjemmet HospitalOsloNorway,Section for Pharmacology and Pharmaceutical Biosciences, Department of PharmacyUniversity of OsloOsloNorway
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Ingelman-Sundberg M. Cytochrome P450 polymorphism: From evolution to clinical use. ADVANCES IN PHARMACOLOGY (SAN DIEGO, CALIF.) 2022; 95:393-416. [PMID: 35953162 DOI: 10.1016/bs.apha.2022.04.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
The cytochromes P450s can be divided in two groups, those of high importance for endogenous functions being evolutionary quite stable and those participating in detoxification of drugs and other xenobiotics having less important endogenous functions. In the latter group extensive genetic diversity has been allowed and in addition this is of high importance for survival in different environments. The genetic polymorphisms in these genes have evolved to some extent based on dietary restrictions and environmental factors and have not been subject of conservation due to less importance for survival. In cases of high dietary selection events, gene multiplication and amplification events have been seen. The different variants in genes encoding drug metabolizing enzymes can be used as genetic biomarkers (pharmacogenomic labels) for adjustment of drug treatment leading to less adverse drug reactions and better response. Indeed, this has improved the use of personalized medicine, although the missing heredity seen based on twin studies indicates that there are indeed many more genetic variants to be discovered before one can achieve a satisfactory relationship between genotype and phenotype with respect to drug metabolism and toxicity.
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Affiliation(s)
- Magnus Ingelman-Sundberg
- Department of Physiology and Pharmacology, Section of Pharmacogenetics, Karolinska Institute, Stockholm, Sweden.
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25
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Liu W, Liao X, Yang Y, Lin H, Yeong J, Zhou X, Shi X, Liu J. Joint dimension reduction and clustering analysis of single-cell RNA-seq and spatial transcriptomics data. Nucleic Acids Res 2022; 50:e72. [PMID: 35349708 PMCID: PMC9262606 DOI: 10.1093/nar/gkac219] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2022] [Revised: 02/22/2022] [Accepted: 03/22/2022] [Indexed: 11/13/2022] Open
Abstract
Dimension reduction and (spatial) clustering is usually performed sequentially; however, the low-dimensional embeddings estimated in the dimension-reduction step may not be relevant to the class labels inferred in the clustering step. We therefore developed a computation method, Dimension-Reduction Spatial-Clustering (DR-SC), that can simultaneously perform dimension reduction and (spatial) clustering within a unified framework. Joint analysis by DR-SC produces accurate (spatial) clustering results and ensures the effective extraction of biologically informative low-dimensional features. DR-SC is applicable to spatial clustering in spatial transcriptomics that characterizes the spatial organization of the tissue by segregating it into multiple tissue structures. Here, DR-SC relies on a latent hidden Markov random field model to encourage the spatial smoothness of the detected spatial cluster boundaries. Underlying DR-SC is an efficient expectation-maximization algorithm based on an iterative conditional mode. As such, DR-SC is scalable to large sample sizes and can optimize the spatial smoothness parameter in a data-driven manner. With comprehensive simulations and real data applications, we show that DR-SC outperforms existing clustering and spatial clustering methods: it extracts more biologically relevant features than conventional dimension reduction methods, improves clustering performance, and offers improved trajectory inference and visualization for downstream trajectory inference analyses.
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Affiliation(s)
- Wei Liu
- Academy of Statistics and Interdisciplinary Sciences, East China Normal University, Shanghai, 200062, China
- Centre for Quantitative Medicine, Health Services & Systems Research, Duke-NUS Medical School, 169857, Singapore
| | - Xu Liao
- Centre for Quantitative Medicine, Health Services & Systems Research, Duke-NUS Medical School, 169857, Singapore
| | - Yi Yang
- Centre for Quantitative Medicine, Health Services & Systems Research, Duke-NUS Medical School, 169857, Singapore
| | - Huazhen Lin
- Center of Statistical Research and School of Statistics, Southwestern University of Finance and Economics, Chengdu, 611130, China
| | - Joe Yeong
- Institute of Molecular and Cell Biology(IMCB), Agency of Science, Technology and Research(A*STAR), 138673, Singapore
- Department of Anatomical Pathology, Singapore General Hospital, 169856, Singapore
| | - Xiang Zhou
- Department of Biostatistics, University of Michigan, Ann Arbor, 48109, USA
| | - Xingjie Shi
- Academy of Statistics and Interdisciplinary Sciences, East China Normal University, Shanghai, 200062, China
- Key Laboratory of Advanced Theory and Application in Statistics and Data Science-MOE, School of Statistics, East China Normal University, Shanghai, 200062, China
| | - Jin Liu
- Centre for Quantitative Medicine, Health Services & Systems Research, Duke-NUS Medical School, 169857, Singapore
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26
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Bioinformatics and Experimental Analyses Reveal NFIC as an Upstream Transcriptional Regulator for Ischemic Cardiomyopathy. Genes (Basel) 2022; 13:genes13061051. [PMID: 35741813 PMCID: PMC9222441 DOI: 10.3390/genes13061051] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Revised: 05/29/2022] [Accepted: 05/30/2022] [Indexed: 02/06/2023] Open
Abstract
Ischemic cardiomyopathy (ICM) caused by coronary artery disease always leads to myocardial infarction and heart failure. Identification of novel transcriptional regulators in ICM is an effective method to establish new diagnostic and therapeutic strategies. In this study, we used two RNA-seq datasets and one microarray dataset from different studies, including 25 ICM and 21 non-failing control (NF) samples of human left ventricle tissues for further analysis. In total, 208 differentially expressed genes (DEGs) were found by combining two RNA-seq datasets with batch effects removed. GO and KEGG analyses of DEGs indicated that the response to wounding, positive regulation of smooth muscle contraction, chromatin, PI3K-Akt signaling pathway, and transporters pathways are involved in ICM. Simple Enrichment Analysis found that NFIC-binding motifs are enriched in promoter regions of downregulated genes. The Gene Importance Calculator further proved that NFIC is vital. NFIC and its downstream genes were verified in the validating microarray dataset. Meanwhile, in rat cardiomyocyte cell line H9C2 cells, two genes (Tspan1 and Hopx) were confirmed, which decreased significantly along with knocking down Nfic expression. In conclusion, NFIC participates in the ICM process by regulating TSPAN1 and HOPX. NFIC and its downstream genes may be marker genes and potential diagnostic and therapeutic targets for ICM.
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27
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Ingelman-Sundberg M. The missing heritability in pharmacogenomics: role of NFIB and other factors. Pharmacogenomics 2022; 23:453-455. [PMID: 35546341 DOI: 10.2217/pgs-2022-0054] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Affiliation(s)
- Magnus Ingelman-Sundberg
- Department of Physiology & Pharmacology, Section of Pharmacogenetics, Biomedicum 5B, Karolinska Institutet, SE-171 77 Stockholm, Sweden
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28
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Lenk HÇ, Klöditz K, Johansson I, Smith RL, Jukić MM, Molden E, Ingelman-Sundberg M. The Polymorphic Nuclear Factor NFIB Regulates Hepatic CYP2D6 Expression and Influences Risperidone Metabolism in Psychiatric Patients. Clin Pharmacol Ther 2022; 111:1165-1174. [PMID: 35253216 PMCID: PMC9314634 DOI: 10.1002/cpt.2571] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Accepted: 02/21/2022] [Indexed: 12/02/2022]
Abstract
The genetic background for interindividual variability of the polymorphic CYP2D6 enzyme activity remains incompletely understood and the role of NFIB genetic polymorphism for this variability was evaluated in this translational study. We investigated the effect of NFIB expression in vitro using 3D liver spheroids, Huh7 cells, and the influence of the NFIB polymorphism on metabolism of risperidone in patients in vivo. We found that NFIB regulates several important pharmacogenes, including CYP2D6. NFIB inhibited CYP2D6 gene expression in Huh7 cells and NFIB expression in livers was predominantly nuclear and reduced at the mRNA and protein level in carriers of the NFIB rs28379954 T>C allele. Based on 604 risperidone treated patients genotyped for CYP2D6 and NFIB, we found that the rate of risperidone hydroxylation was elevated in NFIB rs28379954 T>C carriers among CYP2D6 normal metabolizers, resulting in a similar rate of drug metabolism to what is observed in CYP2D6 ultrarapid metabolizers, with no such effect observed in CYP2D6 poor metabolizers lacking functional enzyme. The results indicate that NFIB constitutes a novel nuclear factor in the regulation of cytochrome P450 genes, and that its polymorphism is a predictor for the rate of CYP2D6 dependent drug metabolism in vivo.
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Affiliation(s)
- Hasan Çağın Lenk
- Center for Psychopharmacology, Diakonhjemmet Hospital, Vinderen, Oslo, Norway.,Section for Pharmacology and Pharmaceutical Biosciences, Department of Pharmacy, University of Oslo, Oslo, Norway
| | - Katharina Klöditz
- Department of Physiology and Pharmacology, Section of Pharmacogenetics, Karolinska Institutet, Stockholm, Sweden
| | - Inger Johansson
- Department of Physiology and Pharmacology, Section of Pharmacogenetics, Karolinska Institutet, Stockholm, Sweden
| | - Robert Løvsletten Smith
- Center for Psychopharmacology, Diakonhjemmet Hospital, Vinderen, Oslo, Norway.,NORMENT, Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Marin M Jukić
- Department of Physiology and Pharmacology, Section of Pharmacogenetics, Karolinska Institutet, Stockholm, Sweden.,Department of Physiology, Faculty of Pharmacy, University of Belgrade, Belgrade, Serbia
| | - Espen Molden
- Center for Psychopharmacology, Diakonhjemmet Hospital, Vinderen, Oslo, Norway.,Section for Pharmacology and Pharmaceutical Biosciences, Department of Pharmacy, University of Oslo, Oslo, Norway
| | - Magnus Ingelman-Sundberg
- Department of Physiology and Pharmacology, Section of Pharmacogenetics, Karolinska Institutet, Stockholm, Sweden
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29
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Okhuijsen-Pfeifer C, van der Horst MZ, Bousman CA, Lin B, van Eijk KR, Ripke S, Ayhan Y, Babaoglu MO, Bak M, Alink W, van Beek H, Beld E, Bouhuis A, Edlinger M, Erdogan IM, Ertuğrul A, Yoca G, Everall IP, Görlitz T, Grootens KP, Gutwinski S, Hallikainen T, Jeger-Land E, de Koning M, Lähteenvuo M, Legge SE, Leucht S, Morgenroth C, Müderrisoğlu A, Narang A, Pantelis C, Pardiñas AF, Oviedo-Salcedo T, Schneider-Thoma J, Schreiter S, Repo-Tiihonen E, Tuppurainen H, Veereschild M, Veerman S, de Vos M, Wagner E, Cohen D, Bogers JPAM, Walters JTR, Yağcıoğlu AEA, Tiihonen J, Hasan A, Luykx JJ. Genome-wide association analyses of symptom severity among clozapine-treated patients with schizophrenia spectrum disorders. Transl Psychiatry 2022; 12:145. [PMID: 35393395 PMCID: PMC8989876 DOI: 10.1038/s41398-022-01884-3] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Revised: 02/24/2022] [Accepted: 03/07/2022] [Indexed: 12/26/2022] Open
Abstract
Clozapine is the most effective antipsychotic for patients with treatment-resistant schizophrenia. However, response is highly variable and possible genetic underpinnings of this variability remain unknown. Here, we performed polygenic risk score (PRS) analyses to estimate the amount of variance in symptom severity among clozapine-treated patients explained by PRSs (R2) and examined the association between symptom severity and genotype-predicted CYP1A2, CYP2D6, and CYP2C19 enzyme activity. Genome-wide association (GWA) analyses were performed to explore loci associated with symptom severity. A multicenter cohort of 804 patients (after quality control N = 684) with schizophrenia spectrum disorder treated with clozapine were cross-sectionally assessed using the Positive and Negative Syndrome Scale and/or the Clinical Global Impression-Severity (CGI-S) scale. GWA and PRS regression analyses were conducted. Genotype-predicted CYP1A2, CYP2D6, and CYP2C19 enzyme activities were calculated. Schizophrenia-PRS was most significantly and positively associated with low symptom severity (p = 1.03 × 10-3; R2 = 1.85). Cross-disorder-PRS was also positively associated with lower CGI-S score (p = 0.01; R2 = 0.81). Compared to the lowest tertile, patients in the highest schizophrenia-PRS tertile had 1.94 times (p = 6.84×10-4) increased probability of low symptom severity. Higher genotype-predicted CYP2C19 enzyme activity was independently associated with lower symptom severity (p = 8.44×10-3). While no locus surpassed the genome-wide significance threshold, rs1923778 within NFIB showed a suggestive association (p = 3.78×10-7) with symptom severity. We show that high schizophrenia-PRS and genotype-predicted CYP2C19 enzyme activity are independently associated with lower symptom severity among individuals treated with clozapine. Our findings open avenues for future pharmacogenomic projects investigating the potential of PRS and genotype-predicted CYP-activity in schizophrenia.
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Affiliation(s)
- C Okhuijsen-Pfeifer
- Department of Psychiatry, University Medical Center Utrecht, Utrecht University, Brain Center, Utrecht, The Netherlands
- Department of Translational Neuroscience, University Medical Center Utrecht, Utrecht University, Brain Center, Utrecht, The Netherlands
| | - M Z van der Horst
- Department of Psychiatry, University Medical Center Utrecht, Utrecht University, Brain Center, Utrecht, The Netherlands
- Department of Translational Neuroscience, University Medical Center Utrecht, Utrecht University, Brain Center, Utrecht, The Netherlands
- GGNet Mental Health, Warnsveld, The Netherlands
| | - C A Bousman
- Department of Medical Genetics, University of Calgary, Calgary, Canada
- Department of Psychiatry, University of Calgary, Calgary, Canada
- Department of Physiology & Pharmacology, University of Calgary, Calgary, Canada
- Department of Psychiatry, University of Melbourne, Melbourne Neuropsychiatry Centre, Melbourne, Australia
| | - B Lin
- Department of Psychiatry, University Medical Center Utrecht, Utrecht University, Brain Center, Utrecht, The Netherlands
- Department of Translational Neuroscience, University Medical Center Utrecht, Utrecht University, Brain Center, Utrecht, The Netherlands
| | - K R van Eijk
- Department of Translational Neuroscience, University Medical Center Utrecht, Utrecht University, Brain Center, Utrecht, The Netherlands
| | - S Ripke
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Department of Psychiatry and Psychotherapy, Berlin, Germany
| | - Y Ayhan
- Department of Psychiatry, Faculty of Medicine, Hacettepe University, Ankara, Turkey
| | - M O Babaoglu
- Department of Pharmacology, Faculty of Medicine, Hacettepe University, Ankara, Turkey
| | - M Bak
- Department of Psychiatry and Neuropsychology, Maastricht University, Maastricht, The Netherlands
- Mondriaan, Mental Health Institute, Maastricht, The Netherlands
| | - W Alink
- Multicomplexe Zorg, Pro Persona, Wolfheze, The Netherlands
| | - H van Beek
- Clinical Recovery Clinic, Mental Health Services Rivierduinen, Leiden, The Netherlands
| | - E Beld
- Mental Health Organization North-Holland North location Den Helder, Den Helder, The Netherlands
| | - A Bouhuis
- Program for early psychosis & severe mental illness, Pro Persona Mental Healthcare, Wolfheze, The Netherlands
| | - M Edlinger
- Department of Psychiatry, Psychotherapy and Psychosomatics, Division for Psychiatry I, Medical University Innsbruck, Innsbruck, Austria
| | - I M Erdogan
- Department of Psychiatry, Faculty of Medicine, Hacettepe University, Ankara, Turkey
| | - A Ertuğrul
- Department of Psychiatry, Faculty of Medicine, Hacettepe University, Ankara, Turkey
| | - G Yoca
- Department of Psychiatry, Faculty of Medicine, Hacettepe University, Ankara, Turkey
- Şarkışla State Hospital, Ministry of Health, Sivas, Turkey
| | - I P Everall
- Department of Psychiatry, University of Melbourne, Melbourne Neuropsychiatry Centre, Melbourne, Australia
- Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, United Kingdom
| | - T Görlitz
- Department of Psychiatry and Psychotherapy, University Hospital, LMU Munich, Munich, Germany
- Department of Psychiatry, Psychotherapy and Psychosomatics, Medical Faculty University Augsburg, Bezirkskrankenhaus Augsburg, Augsburg, Germany
| | - K P Grootens
- Reinier van Arkel, s-Hertogenbosch, The Netherlands
- Unit for Clinical Psychopharmacology and Neuropsychiatry, Radboud University Medical Centre, Nijmegen, The Netherlands
| | - S Gutwinski
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Department of Psychiatry and Psychotherapy, Berlin, Germany
| | - T Hallikainen
- Department of Forensic Psychiatry, University of Kuopio, Niuvanniemi Hospital, Kuopio, Finland
| | - E Jeger-Land
- Arkin, Institute for Mental Health, Amsterdam, The Netherlands
| | - M de Koning
- Arkin, Institute for Mental Health, Amsterdam, The Netherlands
- Amsterdam UMC, University of Amsterdam, Department of Psychiatry, Amsterdam, The Netherlands
| | - M Lähteenvuo
- Department of Forensic Psychiatry, University of Kuopio, Niuvanniemi Hospital, Kuopio, Finland
| | - S E Legge
- Division of Psychological Medicine and Clinical Neurosciences, MRC Centre for Neuropsychiatric Genetics and Genomics, School of Medicine, Cardiff University, Cardiff, United Kingdom
| | - S Leucht
- Department of Psychiatry and Psychotherapy, School of Medicine, Klinikum rechts der Isar, Technical University of Munich, Munich, Germany
| | - C Morgenroth
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Department of Psychiatry and Psychotherapy, Berlin, Germany
| | - A Müderrisoğlu
- Department of Pharmacology, Faculty of Medicine, Kırıkkale University, Kırıkkale, Turkey
| | - A Narang
- Department of Medical Genetics, University of Calgary, Calgary, Canada
| | - C Pantelis
- Department of Psychiatry, University of Melbourne, Melbourne Neuropsychiatry Centre, Melbourne, Australia
| | - A F Pardiñas
- Division of Psychological Medicine and Clinical Neurosciences, MRC Centre for Neuropsychiatric Genetics and Genomics, School of Medicine, Cardiff University, Cardiff, United Kingdom
| | - T Oviedo-Salcedo
- Department of Psychiatry and Psychotherapy, University Hospital, LMU Munich, Munich, Germany
| | - J Schneider-Thoma
- Department of Psychiatry and Psychotherapy, School of Medicine, Klinikum rechts der Isar, Technical University of Munich, Munich, Germany
| | - S Schreiter
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Department of Psychiatry and Psychotherapy, Berlin, Germany
- Berlin Institute of Health (BIH), BIH Biomedical Innovation Academy, Berlin, Germany
| | - E Repo-Tiihonen
- Department of Forensic Psychiatry, University of Kuopio, Niuvanniemi Hospital, Kuopio, Finland
| | - H Tuppurainen
- Department of Forensic Psychiatry, University of Kuopio, Niuvanniemi Hospital, Kuopio, Finland
| | | | - S Veerman
- Mental Health Organization North-Holland North location Alkmaar, Alkmaar, The Netherlands
| | - M de Vos
- GGNet Mental Health, Warnsveld, The Netherlands
| | - E Wagner
- Department of Psychiatry and Psychotherapy, University Hospital, LMU Munich, Munich, Germany
| | - D Cohen
- Mental Health Organization North-Holland North location Heerhugowaard, Heerhugowaard, The Netherlands
| | - J P A M Bogers
- High Care Clinics, Mental Health Services Rivierduinen, Leiden, The Netherlands
| | - J T R Walters
- Division of Psychological Medicine and Clinical Neurosciences, MRC Centre for Neuropsychiatric Genetics and Genomics, School of Medicine, Cardiff University, Cardiff, United Kingdom
| | - A E Anil Yağcıoğlu
- Department of Psychiatry, Faculty of Medicine, Hacettepe University, Ankara, Turkey
| | - J Tiihonen
- Department of Forensic Psychiatry, University of Kuopio, Niuvanniemi Hospital, Kuopio, Finland
- Department of Clinical Neuroscience, Karolinska Institutet, Solna, Sweden
- Center for Psychiatric Research, Stockholm City Council, Stockholm, Sweden
| | - A Hasan
- Department of Psychiatry and Psychotherapy, University Hospital, LMU Munich, Munich, Germany
- Department of Psychiatry, Psychotherapy and Psychosomatics, Medical Faculty University Augsburg, Bezirkskrankenhaus Augsburg, Augsburg, Germany
| | - J J Luykx
- Department of Psychiatry, University Medical Center Utrecht, Utrecht University, Brain Center, Utrecht, The Netherlands.
- Department of Translational Neuroscience, University Medical Center Utrecht, Utrecht University, Brain Center, Utrecht, The Netherlands.
- GGNet Mental Health, Warnsveld, The Netherlands.
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30
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Transcriptional Regulation of RIP2 Gene by NFIB Is Associated with Cellular Immune and Inflammatory Response to APEC Infection. Int J Mol Sci 2022; 23:ijms23073814. [PMID: 35409172 PMCID: PMC8998712 DOI: 10.3390/ijms23073814] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2022] [Revised: 03/23/2022] [Accepted: 03/29/2022] [Indexed: 02/04/2023] Open
Abstract
Avian pathogenic E. coli (APEC) can cause localized or systemic infection, resulting in large economic losses per year, and impact health of humans. Previous studies showed that RIP2 (receptor interacting serine/threonine kinase 2) and its signaling pathway played an important role in immune response against APEC infection. In this study, chicken HD11 cells were used as an in vitro model to investigate the function of chicken RIP2 and the transcription factor binding to the RIP2 core promoter region via gene overexpression, RNA interference, RT-qPCR, Western blotting, dual luciferase reporter assay, CHIP-PCR, CCK-8, and flow cytometry assay following APEC stimulation. Results showed that APEC stimulation promoted RIP2 expression and cells apoptosis, and inhibited cells viability. Knockdown of RIP2 significantly improved cell viability and suppressed the apoptosis of APEC-stimulated cells. Transcription factor NFIB (Nuclear factor I B) and GATA1 (globin transcription factor 1) binding site was identified in the core promoter region of RIP2 from −2300 bp to −1839 bp. However, only NFIB was confirmed to be bound to the core promoter of RIP2. Overexpression of NFIB exacerbated cell injuries with significant reduction in cell viability and increased cell apoptosis and inflammatory cytokines levels, whereas opposite results were observed in NFIB inhibition treatment group. Moreover, RIP2 was up-regulated by NFIB overexpression, and RIP2 silence mitigated the effect of NFIB overexpression in cell apoptosis, inflammation, and activation of NFκB signaling pathways. This study demonstrated that NFIB overexpression accelerated APEC-induced apoptosis and inflammation via up-regulation of RIP2 mediated downstream pathways in chicken HD11 cells.
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Abstract
Transcription factors (TFs) interact with several other proteins in the process of transcriptional regulation. Here, we identify 6703 and 1536 protein–protein interactions for 109 different human TFs through proximity-dependent biotinylation (BioID) and affinity purification mass spectrometry (AP-MS), respectively. The BioID analysis identifies more high-confidence interactions, highlighting the transient and dynamic nature of many of the TF interactions. By performing clustering and correlation analyses, we identify subgroups of TFs associated with specific biological functions, such as RNA splicing or chromatin remodeling. We also observe 202 TF-TF interactions, of which 118 are interactions with nuclear factor 1 (NFI) family members, indicating uncharacterized cross-talk between NFI signaling and other TF signaling pathways. Moreover, TF interactions with basal transcription machinery are mainly observed through TFIID and SAGA complexes. This study provides a rich resource of human TF interactions and also act as a starting point for future studies aimed at understanding TF-mediated transcription. Transcription factors (TFs) interact with several other proteins in the process of transcriptional regulation. Here the authors identify 6703 and 1536 protein–protein interactions for 109 different human TFs through BioID and AP-MS analyses, respectively.
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Uluca B, Lektemur Esen C, Saritas Erdogan S, Kumbasar A. NFI transcriptionally represses CDON and is required for SH-SY5Y cell survival. BIOCHIMICA ET BIOPHYSICA ACTA. GENE REGULATORY MECHANISMS 2022; 1865:194798. [PMID: 35151899 DOI: 10.1016/j.bbagrm.2022.194798] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Revised: 01/14/2022] [Accepted: 01/30/2022] [Indexed: 06/14/2023]
Abstract
Nuclear Factor One (NFI) family of transcription factors regulate proliferation and multiple aspects of differentiation, playing analogous roles in embryonic development and various types of cancer. While all NFI family members are expressed in the developing brain and are involved in progression of brain cancers, their role in neuroblastoma has not been studied. Here we show that NFIB is required for the survival and proliferation of SH-SY5Y neuroblastoma cells, assessed by viability and colony formation assays. Cdon, an Ig superfamily member, is a SHH dependence receptor that acts as a tumor suppressor in neuroblastoma. In the absence of NFI, Cdon is upregulated in the developing mouse brain, however the mechanisms by which its transcription is regulated remains unknown. We report CDON as a downstream target of NFIs in SH-SY5Y cells. There are three putative NFI binding sites within the one kb CDON promoter, two of which are occupied by NFIs in SH-SY5Y cells and human neural stem cells. In dual-luciferase assays, Nfib directly represses CDON proximal promoter activity. Moreover, silencing NFIB leads to upregulation of CDON in SH-SY5Y cells, however, decreased cell proliferation in NFIB silenced cells could not be rescued by concomitantly silencing CDON, suggesting other molecular players are involved. For instance, p21, an NFI target in glioblastoma and breast cancer cells, is also upregulated upon NFIB knock-down. We propose that NFIB is indispensable for SH-SY5Y cells which may involve regulation of apoptosis inducer proteins CDON and p21.
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Affiliation(s)
- Betül Uluca
- Department of Molecular Biology and Genetics, Istanbul Technical University, Maslak, Istanbul 34469, Turkey; Department of Molecular Biotechnology, Turkish-German University, Beykoz, Istanbul 34820, Turkey
| | - Cemre Lektemur Esen
- Department of Molecular Biology and Genetics, Istanbul Technical University, Maslak, Istanbul 34469, Turkey
| | - Sinem Saritas Erdogan
- Department of Molecular Biology and Genetics, Istanbul Technical University, Maslak, Istanbul 34469, Turkey
| | - Asli Kumbasar
- Department of Molecular Biology and Genetics, Istanbul Technical University, Maslak, Istanbul 34469, Turkey.
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33
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Huang H, Jin J, Wu L, Wu H, Pi H, Dong Y, Xiang R. A de novo Non-sense Nuclear Factor I B Mutation (p.Tyr290*) Is Responsible for Brain Malformation and Lung Lobulation Defects. Front Pediatr 2022; 10:865181. [PMID: 35433561 PMCID: PMC9005976 DOI: 10.3389/fped.2022.865181] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/29/2022] [Accepted: 03/07/2022] [Indexed: 12/02/2022] Open
Abstract
BACKGROUND Nuclear factor I B (NFIB) plays an important role in regulating the transcription of multiple biological processes. Mutations in NFIB cause intellectual disability and macrocephaly. However, studies on abnormal brain and lung development caused by NFIB mutations are lacking. METHODS In the present study, we enrolled a fetus with brain malformation and lung lobulation defects from China. Whole-exome sequencing (WES) was performed to detect the candidate genes and Sanger sequencing was performed for mutational analysis. RESULTS After data filtering and bioinformatics prediction, a novel non-sense mutation of NFIB (NM_001190737:c.870C > A;p.Tyr290*) was identified in the fetus. This variant was predicted to produce a truncated NFIB protein because of a premature stop codon and was absent in 200 healthy controls. CONCLUSION To the best of our knowledge, this is the first case of brain malformation and lung lobulation defects caused by a NFIB variant in Asia. These findings contribute to genetic diagnosis and family counseling and expand our understanding of NFIB mutations as well as brain and lung maturation.
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Affiliation(s)
- Hao Huang
- Department of Nephrology, Xiangya Hospital, Central South University, Changsha, China.,National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China.,Department of Cell Biology, School of Life Sciences, Central South University, Changsha, China
| | - Jieyuan Jin
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China.,Department of Cell Biology, School of Life Sciences, Central South University, Changsha, China
| | - Liping Wu
- Department of Medical Genetics and Prenatal Diagnosis, Shenzhen Longgang District Maternity and Child Healthcare Hospital, Shenzhen, China
| | - Huifen Wu
- Obstetric Inpatient Department, Shenzhen Longgang District Maternity and Child Healthcare Hospital, Shenzhen, China
| | - Huichun Pi
- Department of Medical Genetics and Prenatal Diagnosis, Shenzhen Longgang District Maternity and Child Healthcare Hospital, Shenzhen, China
| | - Yi Dong
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China.,Department of Cell Biology, School of Life Sciences, Central South University, Changsha, China
| | - Rong Xiang
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China.,Department of Cell Biology, School of Life Sciences, Central South University, Changsha, China
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34
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Perumal N, Kanchan RK, Doss D, Bastola N, Atri P, Chirravuri-Venkata R, Thapa I, Vengoji R, Maurya SK, Klinkebiel D, Talmon GA, Nasser MW, Batra SK, Mahapatra S. MiR-212-3p functions as a tumor suppressor gene in group 3 medulloblastoma via targeting nuclear factor I/B (NFIB). Acta Neuropathol Commun 2021; 9:195. [PMID: 34922631 PMCID: PMC8684142 DOI: 10.1186/s40478-021-01299-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Accepted: 12/01/2021] [Indexed: 12/30/2022] Open
Abstract
Haploinsufficiency of chromosome 17p and c-Myc amplification distinguish group 3 medulloblastomas which are associated with early metastasis, rapid recurrence, and swift mortality. Tumor suppressor genes on this locus have not been adequately characterized. We elucidated the role of miR-212-3p in the pathophysiology of group 3 tumors. First, we learned that miR-212-3p undergoes epigenetic silencing by histone modifications in group 3 tumors. Restoring its expression reduced cancer cell proliferation, migration, colony formation, and wound healing in vitro and attenuated tumor burden and improved survival in vivo. MiR-212-3p also triggered c-Myc destabilization and degradation, leading to elevated apoptosis. We then isolated an oncogenic target of miR-212-3p, i.e. NFIB, a nuclear transcription factor implicated in metastasis and recurrence in various cancers. Increased expression of NFIB was confirmed in group 3 tumors and associated with poor survival. NFIB silencing reduced cancer cell proliferation, migration, and invasion. Concurrently, reduced medullosphere formation and stem cell markers (Nanog, Oct4, Sox2, CD133) were noted. These results substantiate the tumor-suppressive role of miR-212-3p in group 3 MB and identify a novel oncogenic target implicated in metastasis and tumor recurrence.
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Affiliation(s)
- Naveenkumar Perumal
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, NE, 68198, USA
| | - Ranjana K Kanchan
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, NE, 68198, USA
| | - David Doss
- Department of Biomedical Sciences, Creighton University School of Medicine, Omaha, NE, 68124, USA
| | - Noah Bastola
- Department of Ophthalmology and Visual Sciences, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Pranita Atri
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, NE, 68198, USA
| | | | - Ishwor Thapa
- School of Interdisciplinary Informatics, University of Nebraska at Omaha, Omaha, NE, 68182, USA
| | - Raghupathy Vengoji
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, NE, 68198, USA
| | - Shailendra K Maurya
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, NE, 68198, USA
| | - David Klinkebiel
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, NE, 68198, USA
| | - Geoffrey A Talmon
- Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, NE, 68198, USA
| | - Mohd W Nasser
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, NE, 68198, USA
| | - Surinder K Batra
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, NE, 68198, USA
| | - Sidharth Mahapatra
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, NE, 68198, USA.
- Department of Pediatrics, University of Nebraska Medical Center, Omaha, NE, 68198, USA.
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35
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Pan D, Qian B, Zhao D, Yao B. Nfib promotes chondrocyte proliferation and inhibits differentiation by mildly regulating Sox9 and its downstream genes. Mol Biol Rep 2021; 48:7487-7497. [PMID: 34651294 DOI: 10.1007/s11033-021-06767-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Accepted: 09/15/2021] [Indexed: 01/18/2023]
Abstract
BACKGROUND Chondrocyte proliferation and differentiation play pivotal roles in regulating cartilage formation, endochondral bone formation, and repair. Cartilage damage and underdevelopment may cause severe joint diseases. Various transcription factors regulate cartilage development. Nuclear factor 1 B (Nfib) is a transcription factor that plays a regulatory role in various organs. However, the effect and mechanism of Nfib on the proliferation and differentiation of chondrocytes in cartilage are still largely unknown. METHODS AND RESULTS In the present study, we investigated the gene expression patterns in primary chondrocytes with Nfib overexpression or silencing by RNA sequencing (RNA-seq) technology. The results showed that Nfib overexpression significantly up-regulated genes that are related to chondrocyte proliferation and extracellular matrix (ECM) synthesis and significantly down-regulated genes related to chondrocyte differentiation and ECM degradation. However, with Nfib silencing, the genes involved in promoting chondrocyte differentiation were significantly up-regulated, whereas those involved in promoting chondrocyte proliferation were significantly down-regulated. Furthermore, quantitative real-time PCR (qRT-PCR), western blot, alcian blue staining and immunofluorescence staining assays further confirmed that Nfib potentially promotes chondrocyte proliferation and extracellular synthesis but inhibits differentiation. CONCLUSIONS The molecular mechanism of Nfib in promoting chondrocyte proliferation and inhibiting differentiation was probably achieved by stimulating Sox9 and its downstream genes. Thus, this study adds new insights regarding the underlying molecular mechanism of transcriptional regulation in cartilage.
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Affiliation(s)
- Daian Pan
- Jilin Ginseng Academy, Changchun University of Chinese Medicine, Changchun, China
| | - Benxin Qian
- Department of Thoracic Surgery, The First Hospital of Jilin University, Changchun, China
| | - Daqing Zhao
- Jilin Ginseng Academy, Changchun University of Chinese Medicine, Changchun, China.
| | - Baojin Yao
- Jilin Ginseng Academy, Changchun University of Chinese Medicine, Changchun, China.
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36
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Xu C, Xie X, Zhao L, Wu Y, Wang J. The critical role of nuclear factor I-C in tooth development. Oral Dis 2021; 28:2093-2099. [PMID: 34637578 DOI: 10.1111/odi.14046] [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] [Received: 09/06/2021] [Revised: 09/29/2021] [Accepted: 10/07/2021] [Indexed: 02/05/2023]
Abstract
OBJECTIVES Nuclear factor I-C (NFIC) plays a critical role in regulating epithelial-mesenchymal crosstalk during tooth development. However, it remains largely unknown about how NFIC functions in dentin and enamel formation. In the present review, we aim to summarize the most recent discoveries in the field and gain a better understanding of the roles NFIC performs during tooth formation. SUBJECTS AND METHODS Nfic-/- mice exhibit human dentin dysplasia type I (DDI)-like phenotypes signified by enlarged pulp chambers, the presence of short-root anomaly, and failure of odontoblast differentiation. Although loss of NFIC has little effect on molar crown morphology, researchers have detected aberrant microstructures of enamel in the incisors. Recently, accumulating evidence has further uncovered the novel function of NFIC in the process of enamel and dentin formation. RESULTS During epithelial-mesenchyme crosstalk, the expression of NFIC is under the control of SHH-PTCH-SMO-GLI1 pathway. NFIC is closely involved in odontoblast lineage cells proliferation and differentiation, and the maintenance of NFIC protein level in cytoplasm is negatively regulated by TGF-β signaling pathway. In addition, NFIC has mild effect on ameloblast differentiation, enamel mineralization and cementum formation. CONCLUSIONS NFIC plays an important role in tooth development and is required for the formation of dentin, enamel as well as cementum.
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Affiliation(s)
- Chunmei Xu
- State Key Laboratory of Oral Diseases, Department of Periodontics, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Xudong Xie
- State Key Laboratory of Oral Diseases, Department of Periodontics, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Lei Zhao
- State Key Laboratory of Oral Diseases, Department of Periodontics, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Yafei Wu
- State Key Laboratory of Oral Diseases, Department of Periodontics, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Jun Wang
- State Key Laboratory of Oral Diseases, Department of Periodontics, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
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37
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Abstract
In the mammalian neocortex, projection neuron types are sequentially generated by the same pool of neural progenitors. How neuron type specification is related to developmental timing remains unclear. To determine whether temporal gene expression in neural progenitors correlates with neuron type specification, we performed single-cell RNA sequencing (scRNA-Seq) analysis of the developing mouse neocortex. We uncovered neuroepithelial cell enriched genes such as Hmga2 and Ccnd1 when compared to radial glial cells (RGCs). RGCs display dynamic gene expression over time; for instance, early RGCs express higher levels of Hes5, and late RGCs show higher expression of Pou3f2 Interestingly, intermediate progenitor cell marker gene Eomes coexpresses temporally with known neuronal identity genes at different developmental stages, though mostly in postmitotic cells. Our results delineate neural progenitor cell diversity in the developing mouse neocortex and support that neuronal identity genes are transcriptionally evident in Eomes-positive cells.
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38
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Yeon GB, Shin WH, Yoo SH, Kim D, Jeon BM, Park WU, Bae Y, Park JY, You S, Na D, Kim DS. NFIB induces functional astrocytes from human pluripotent stem cell-derived neural precursor cells mimicking in vivo astrogliogenesis. J Cell Physiol 2021; 236:7625-7641. [PMID: 33949692 DOI: 10.1002/jcp.30405] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Revised: 04/12/2021] [Accepted: 04/15/2021] [Indexed: 12/18/2022]
Abstract
The ability to generate astrocytes from human pluripotent stem cells (hPSCs) offers a promising cellular model to study the development and physiology of human astrocytes. The extant methods for generating functional astrocytes required long culture periods and there remained much ambiguity on whether such paradigms follow the innate developmental program. In this report, we provided an efficient and rapid method for generating physiologically functional astrocytes from hPSCs. Overexpressing the nuclear factor IB in hPSC-derived neural precursor cells induced a highly enriched astrocyte population in 2 weeks. RNA sequencing and functional analyses demonstrated progressive transcriptomic and physiological changes in the cells, resembling in vivo astrocyte development. Further analyses substantiated previous results and established the MAPK pathway necessary for astrocyte differentiation. Hence, this differentiation paradigm provides a prospective in vitro model for human astrogliogenesis studies and the pathophysiology of neurological diseases concerning astrocytes.
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Affiliation(s)
- Gyu-Bum Yeon
- Department of Biotechnology, Korea University, Seoul, Korea
| | - Won-Ho Shin
- Department of Predictive Toxicology, Korea Institute of Toxicology, Daejeon, Korea
| | - Seo Hyun Yoo
- Department of Biotechnology, Korea University, Seoul, Korea
| | - Dongyun Kim
- Department of Biotechnology, Korea University, Seoul, Korea
| | | | - Won-Ung Park
- Department of Biotechnology, Korea University, Seoul, Korea
| | - Yeonju Bae
- School of Biosystem and Biomedical Science, College of Health Science, Korea University, Seoul, Korea
| | - Jae-Yong Park
- School of Biosystem and Biomedical Science, College of Health Science, Korea University, Seoul, Korea
| | - Seungkwon You
- Department of Biotechnology, Korea University, Seoul, Korea
| | - Dokyun Na
- School of Integrative Engineering, Chung-Ang University, Seoul, Korea
| | - Dae-Sung Kim
- Department of Biotechnology, Korea University, Seoul, Korea.,Department of Pediatrics, Korea University College of Medicine, Seoul, Korea
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39
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Curry RN, Glasgow SM. The Role of Neurodevelopmental Pathways in Brain Tumors. Front Cell Dev Biol 2021; 9:659055. [PMID: 34012965 PMCID: PMC8127784 DOI: 10.3389/fcell.2021.659055] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Accepted: 03/19/2021] [Indexed: 12/12/2022] Open
Abstract
Disruptions to developmental cell signaling pathways and transcriptional cascades have been implicated in tumor initiation, maintenance and progression. Resurgence of aberrant neurodevelopmental programs in the context of brain tumors highlights the numerous parallels that exist between developmental and oncologic mechanisms. A deeper understanding of how dysregulated developmental factors contribute to brain tumor oncogenesis and disease progression will help to identify potential therapeutic targets for these malignancies. In this review, we summarize the current literature concerning developmental signaling cascades and neurodevelopmentally-regulated transcriptional programs. We also examine their respective contributions towards tumor initiation, maintenance, and progression in both pediatric and adult brain tumors and highlight relevant differentiation therapies and putative candidates for prospective treatments.
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Affiliation(s)
- Rachel N. Curry
- Department of Neuroscience, Baylor College of Medicine, Center for Cell and Gene Therapy, Houston, TX, United States
- Integrative Molecular and Biomedical Sciences, Graduate School of Biomedical Sciences, Baylor College of Medicine, Houston, TX, United States
| | - Stacey M. Glasgow
- Neurobiology Section, Division of Biological Sciences, University of California, San Diego, San Diego, CA, United States
- Neurosciences Graduate Program, University of California, San Diego, San Diego, CA, United States
- Biomedical Sciences Graduate Program, University of California, San Diego, San Diego, CA, United States
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40
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Ko J, Winslow MM, Sage J. Mechanisms of small cell lung cancer metastasis. EMBO Mol Med 2021; 13:e13122. [PMID: 33296145 PMCID: PMC7799359 DOI: 10.15252/emmm.202013122] [Citation(s) in RCA: 99] [Impact Index Per Article: 33.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Revised: 11/02/2020] [Accepted: 11/05/2020] [Indexed: 12/12/2022] Open
Abstract
Metastasis is a major cause of morbidity and mortality in cancer patients. However, the molecular and cellular mechanisms underlying the ability of cancer cells to metastasize remain relatively poorly understood. Among all solid tumors, small cell lung cancer (SCLC) has remarkable metastatic proclivity, with a majority of patients diagnosed with metastatic disease. Our understanding of SCLC metastasis has been hampered for many years by the paucity of material from primary tumors and metastases, as well as the lack of faithful pre-clinical models. Here, we review recent advances that are helping circumvent these limitations. These advances include methods that employ circulating tumor cells from the blood of SCLC patients and the development of diverse genetically engineered mouse models of metastatic SCLC. New insights into the cellular mechanisms of SCLC metastasis include observations of cell fate changes associated with increased metastatic ability. Ongoing studies on cell migration and organ tropism promise to expand our understanding of SCLC metastasis. Ultimately, a better molecular understanding of metastatic phenotypes may be translated into new therapeutic options to limit metastatic spread and treat metastatic SCLC.
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Affiliation(s)
- Julie Ko
- Department of PediatricsStanford UniversityStanfordCAUSA
- Department of GeneticsStanford UniversityStanfordCAUSA
| | - Monte M Winslow
- Department of GeneticsStanford UniversityStanfordCAUSA
- Department of PathologyStanford UniversityStanfordCAUSA
| | - Julien Sage
- Department of PediatricsStanford UniversityStanfordCAUSA
- Department of GeneticsStanford UniversityStanfordCAUSA
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41
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Brenner M, Messing A. Regulation of GFAP Expression. ASN Neuro 2021; 13:1759091420981206. [PMID: 33601918 PMCID: PMC7897836 DOI: 10.1177/1759091420981206] [Citation(s) in RCA: 46] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Revised: 11/18/2020] [Accepted: 11/19/2020] [Indexed: 12/12/2022] Open
Abstract
Expression of the GFAP gene has attracted considerable attention because its onset is a marker for astrocyte development, its upregulation is a marker for reactive gliosis, and its predominance in astrocytes provides a tool for their genetic manipulation. The literature on GFAP regulation is voluminous, as almost any perturbation of development or homeostasis in the CNS will lead to changes in its expression. In this review, we limit our discussion to mechanisms proposed to regulate GFAP synthesis through a direct interaction with its gene or mRNA. Strengths and weaknesses of the supportive experimental findings are described, and suggestions made for additional studies. This review covers 15 transcription factors, DNA and histone methylation, and microRNAs. The complexity involved in regulating the expression of this intermediate filament protein suggests that GFAP function may vary among both astrocyte subtypes and other GFAP-expressing cells, as well as during development and in response to perturbations.
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Affiliation(s)
- Michael Brenner
- Department of Neurobiology, University of Alabama-Birmingham, Birmingham, Alabama, United States
| | - Albee Messing
- Waisman Center, University of Wisconsin-Madison, Madison, Wisconsin, United States
- Department of Comparative Biosciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, Wisconsin, United States
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42
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Zhao X, Chen J, Xiao P, Feng J, Nie Q, Zhao XM. Identifying age-specific gene signatures of the human cerebral cortex with joint analysis of transcriptomes and functional connectomes. Brief Bioinform 2020; 22:6048938. [PMID: 33367491 DOI: 10.1093/bib/bbaa388] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Revised: 11/10/2020] [Accepted: 11/27/2020] [Indexed: 11/13/2022] Open
Abstract
The human cerebral cortex undergoes profound structural and functional dynamic variations across the lifespan, whereas the underlying molecular mechanisms remain unclear. Here, with a novel method transcriptome-connectome correlation analysis (TCA), which integrates the brain functional magnetic resonance images and region-specific transcriptomes, we identify age-specific cortex (ASC) gene signatures for adolescence, early adulthood and late adulthood. The ASC gene signatures are significantly correlated with the cortical thickness (P-value <2.00e-3) and myelination (P-value <1.00e-3), two key brain structural features that vary in accordance with brain development. In addition to the molecular underpinning of age-related brain functions, the ASC gene signatures allow delineation of the molecular mechanisms of neuropsychiatric disorders, such as the regulation between ARNT2 and its target gene ETF1 involved in Schizophrenia. We further validate the ASC gene signatures with published gene sets associated with the adult cortex, and confirm the robustness of TCA on other brain image datasets. Availability: All scripts are written in R. Scripts for the TCA method and related statistics result can be freely accessed at https://github.com/Soulnature/TCA. Additional data related to this paper may be requested from the authors.
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Affiliation(s)
- Xingzhong Zhao
- Institute of Science and Technology for Brain-Inspired Intelligence, Fudan University, China
| | - Jingqi Chen
- Institute of Science and Technology for Brain-Inspired Intelligence, Fudan University, China
| | - Peipei Xiao
- Department of Electronic and Information Engineering, Tongji University, China
| | - Jianfeng Feng
- Institute of Science and Technology for Brain-Inspired Intelligence, Fudan University, China
| | - Qing Nie
- Department of Biomedical Engineering, University of California, Irvine, USA
| | - Xing-Ming Zhao
- ISTBI, RIICS, Fudan University, and MOE Key Laboratory of Computational Neuroscience and Brain-Inspired Intelligence, and Frontiers Center for Brain Science, China
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43
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Sah RK, Ma J, Bah FB, Xing Z, Adlat S, Oo ZM, Wang Y, Bahadar N, Bohio AA, Nagi FH, Feng X, Zhang L, Zheng Y. Targeted Disruption of Mouse Dip2B Leads to Abnormal Lung Development and Prenatal Lethality. Int J Mol Sci 2020; 21:E8223. [PMID: 33153107 PMCID: PMC7663123 DOI: 10.3390/ijms21218223] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Revised: 10/29/2020] [Accepted: 10/30/2020] [Indexed: 12/21/2022] Open
Abstract
Molecular and anatomical functions of mammalian Dip2 family members (Dip2A, Dip2B and Dip2C) during organogenesis are largely unknown. Here, we explored the indispensable role of Dip2B in mouse lung development. Using a LacZ reporter, we explored Dip2B expression during embryogenesis. This study shows that Dip2B expression is widely distributed in various neuronal, myocardial, endothelial, and epithelial cell types during embryogenesis. Target disruption of Dip2b leads to intrauterine growth restriction, defective lung formation and perinatal mortality. Dip2B is crucial for late lung maturation rather than early-branching morphogenesis. The morphological analysis shows that Dip2b loss leads to disrupted air sac formation, interstitium septation and increased cellularity. In BrdU incorporation assay, it is shown that Dip2b loss results in increased cell proliferation at the saccular stage of lung development. RNA-seq analysis reveals that 1431 genes are affected in Dip2b deficient lungs at E18.5 gestation age. Gene ontology analysis indicates cell cycle-related genes are upregulated and immune system related genes are downregulated. KEGG analysis identifies oxidative phosphorylation as the most overrepresented pathways along with the G2/M phase transition pathway. Loss of Dip2b de-represses the expression of alveolar type I and type II molecular markers. Altogether, the study demonstrates an important role of Dip2B in lung maturation and survival.
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Affiliation(s)
- Rajiv Kumar Sah
- Key Laboratory of Molecular Epigenetics, Institute of Genetics and Cytology, Northeast Normal University, Changchun 130024, China; (R.K.S.); (F.B.B.); (Z.X.); (S.A.); (Z.M.O.); (Y.W.); (N.B.); (A.A.B.); (F.H.N.); (L.Z.)
| | - Jun Ma
- Wenzhou Institute, University of Chinese Academy of Sciences, Wenzhou 325001, China;
| | - Fatoumata Binta Bah
- Key Laboratory of Molecular Epigenetics, Institute of Genetics and Cytology, Northeast Normal University, Changchun 130024, China; (R.K.S.); (F.B.B.); (Z.X.); (S.A.); (Z.M.O.); (Y.W.); (N.B.); (A.A.B.); (F.H.N.); (L.Z.)
| | - Zhenkai Xing
- Key Laboratory of Molecular Epigenetics, Institute of Genetics and Cytology, Northeast Normal University, Changchun 130024, China; (R.K.S.); (F.B.B.); (Z.X.); (S.A.); (Z.M.O.); (Y.W.); (N.B.); (A.A.B.); (F.H.N.); (L.Z.)
| | - Salah Adlat
- Key Laboratory of Molecular Epigenetics, Institute of Genetics and Cytology, Northeast Normal University, Changchun 130024, China; (R.K.S.); (F.B.B.); (Z.X.); (S.A.); (Z.M.O.); (Y.W.); (N.B.); (A.A.B.); (F.H.N.); (L.Z.)
| | - Zin Ma Oo
- Key Laboratory of Molecular Epigenetics, Institute of Genetics and Cytology, Northeast Normal University, Changchun 130024, China; (R.K.S.); (F.B.B.); (Z.X.); (S.A.); (Z.M.O.); (Y.W.); (N.B.); (A.A.B.); (F.H.N.); (L.Z.)
| | - Yajun Wang
- Key Laboratory of Molecular Epigenetics, Institute of Genetics and Cytology, Northeast Normal University, Changchun 130024, China; (R.K.S.); (F.B.B.); (Z.X.); (S.A.); (Z.M.O.); (Y.W.); (N.B.); (A.A.B.); (F.H.N.); (L.Z.)
| | - Noor Bahadar
- Key Laboratory of Molecular Epigenetics, Institute of Genetics and Cytology, Northeast Normal University, Changchun 130024, China; (R.K.S.); (F.B.B.); (Z.X.); (S.A.); (Z.M.O.); (Y.W.); (N.B.); (A.A.B.); (F.H.N.); (L.Z.)
| | - Ameer Ali Bohio
- Key Laboratory of Molecular Epigenetics, Institute of Genetics and Cytology, Northeast Normal University, Changchun 130024, China; (R.K.S.); (F.B.B.); (Z.X.); (S.A.); (Z.M.O.); (Y.W.); (N.B.); (A.A.B.); (F.H.N.); (L.Z.)
| | - Farooq Hayel Nagi
- Key Laboratory of Molecular Epigenetics, Institute of Genetics and Cytology, Northeast Normal University, Changchun 130024, China; (R.K.S.); (F.B.B.); (Z.X.); (S.A.); (Z.M.O.); (Y.W.); (N.B.); (A.A.B.); (F.H.N.); (L.Z.)
| | - Xuechao Feng
- Key Laboratory of Molecular Epigenetics, Institute of Genetics and Cytology, Northeast Normal University, Changchun 130024, China; (R.K.S.); (F.B.B.); (Z.X.); (S.A.); (Z.M.O.); (Y.W.); (N.B.); (A.A.B.); (F.H.N.); (L.Z.)
| | - Luqing Zhang
- Key Laboratory of Molecular Epigenetics, Institute of Genetics and Cytology, Northeast Normal University, Changchun 130024, China; (R.K.S.); (F.B.B.); (Z.X.); (S.A.); (Z.M.O.); (Y.W.); (N.B.); (A.A.B.); (F.H.N.); (L.Z.)
- Cardiovascular Research Institute, University of California, San Francisco, CA 94158, USA
| | - Yaowu Zheng
- Key Laboratory of Molecular Epigenetics, Institute of Genetics and Cytology, Northeast Normal University, Changchun 130024, China; (R.K.S.); (F.B.B.); (Z.X.); (S.A.); (Z.M.O.); (Y.W.); (N.B.); (A.A.B.); (F.H.N.); (L.Z.)
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44
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Barrus K, Rego S, Yip T, Martin PM, Glen OA, Van Ziffle J, Slavotinek AM. The expanding spectrum of NFIB-associated phenotypes in a diverse patient population-A report of two new patients. Am J Med Genet A 2020; 182:2959-2963. [PMID: 32902921 DOI: 10.1002/ajmg.a.61852] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Revised: 07/25/2020] [Accepted: 08/04/2020] [Indexed: 11/07/2022]
Abstract
NFIB (Nuclear Factor I B) haploinsufficiency has recently been identified as a cause of intellectual disability and macrocephaly. Here we describe two patients with pathogenic variants in NFIB. The first is a 6-year-old Latino male with developmental delays, mild hypotonia, facial anomalies, and brain magnetic resonance imaging findings comprising mild thinning of the corpus callosum, with more marked thinning of the splenium and blunting of the rostrum and cavum septum pellucidum. Exome sequencing identified a previously described de novo variant in NFIB, c.265C>T, predicting p.Arg89Ter. The second is a 5-year-old Latino male with developmental delays, hypotonia, dysmorphic features, a preauricular tag and pit, a small ventricular septal defect, and brain magnetic resonance imaging findings including a dysmorphic corpus callosum and a small posterior fossa. A single nucleotide polymorphism microarray identified a 92 kb interstitial deletion at 9p23 including several exons of NFIB and no other known genes. Our two patients add to the knowledge of this rare condition through our addition of new brain MRI findings and dysmorphic features. Additionally, these are the first known Latino patients to be described with NFIB haploinsufficiency, expanding our understanding of the associated facial features in diverse populations. Further data are needed to determine genotype-phenotype relationships for NFIB.
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Affiliation(s)
- Kathleen Barrus
- Institute for Human Genetics, University of California, San Francisco, San Francisco, California, USA.,Department of Genetics, Stanford University School of Medicine, Stanford, California, USA
| | - Shannon Rego
- Institute for Human Genetics, University of California, San Francisco, San Francisco, California, USA
| | - Tiffany Yip
- Institute for Human Genetics, University of California, San Francisco, San Francisco, California, USA
| | - Pierre-Marie Martin
- Institute for Human Genetics, University of California, San Francisco, San Francisco, California, USA
| | - Orit A Glen
- Department of Radiology and Biomedical Imaging, University of California, San Francisco, San Francisco, California, USA
| | - Jessica Van Ziffle
- Institute for Human Genetics, University of California, San Francisco, San Francisco, California, USA
| | - Anne M Slavotinek
- Institute for Human Genetics, University of California, San Francisco, San Francisco, California, USA.,Division of Medical Genetics, Department of Pediatrics, University of California, San Francisco, San Francisco, California, USA
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45
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Smith RL, O'Connell K, Athanasiu L, Djurovic S, Kringen MK, Andreassen OA, Molden E. Identification of a novel polymorphism associated with reduced clozapine concentration in schizophrenia patients-a genome-wide association study adjusting for smoking habits. Transl Psychiatry 2020; 10:198. [PMID: 32555152 PMCID: PMC7303159 DOI: 10.1038/s41398-020-00888-1] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Revised: 06/09/2020] [Accepted: 06/09/2020] [Indexed: 11/28/2022] Open
Abstract
Clozapine (CLZ) is the superior antipsychotic drug for treatment of schizophrenia, but exhibits an extensive interpatient pharmacokinetic variability. Here, we conducted a genome-wide association study (GWAS) of CLZ serum concentration adjusting for known smoking habits, which is a major nongenetic factor reducing CLZ levels. The study included 484 patients with 10,283 steady-state serum concentrations of CLZ and N-desmethylclozapine, prescribed dosing, co-medications and known smoking habits (n = 422; 9284 serum samples) from a therapeutic drug monitoring (TDM) service. The GWAS analyses were performed with and without smoking habits as covariate, where possible hits were assessed in relation to the target CLZ concentration range applied in the TDM service (300-2500 nmol/L). The smoking-independent analysis of N-desmethylclozapine serum concentration and the CLZ-to-N-desmethylclozapine ratio replicated the previously identified locus on chromosome 4. After adjusting for smoking habits in patients confirmed as 'smokers' (61%) or 'nonsmokers' (39%), a novel variant (rs28379954; minor T>C allele frequency 4.1%; 7.6% CT carriers in the population) within the gene encoding the nuclear factor 1 B-type (NFIB) was significantly associated with reduced CLZ serum concentration (p = 1.68 × 10-8, beta = -0.376; explained variance 7.63%). There was no significant association between rs28379954 and N-desmethylclozapine concentration in the GWAS analysis (p = 5.63 × 10-5). The fraction of CLZ TDM samples below 300 nmol/L was significantly higher in carriers vs. noncarriers of the rs28379954 minor C allele [12.0% (95% CI: 9.4-14.7) vs. 6.2% (95% CI: 5.7-6.8), p < 0.001]. We identified a novel variant in the NFIB gene associated with reduced CLZ levels and increased risk of subtherapeutic serum concentrations. This warrants testing of clinical relevance of screening for this gene variant, and also experimental studies to investigate the biological mechanisms of NFIB involvement in CLZ pharmacokinetics.
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Affiliation(s)
| | - Kevin O'Connell
- CoE NORMENT, Division of Mental Health and Addiction, Oslo University Hospital, and Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Lavinia Athanasiu
- CoE NORMENT, Division of Mental Health and Addiction, Oslo University Hospital, and Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Srdjan Djurovic
- Department of Medical Genetics, Oslo University Hospital, Oslo, Norway
- NORMENT, Department of Clinical Science, University of Bergen, Bergen, Norway
| | - Marianne Kristiansen Kringen
- Center for Psychopharmacology, Diakonhjemmet Hospital, Oslo, Norway
- Department of Life Sciences and Health, Oslo Metropolitan University, Oslo, Norway
| | - Ole A Andreassen
- CoE NORMENT, Division of Mental Health and Addiction, Oslo University Hospital, and Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Espen Molden
- Center for Psychopharmacology, Diakonhjemmet Hospital, Oslo, Norway.
- Department of Pharmacy, Section for Pharmacology and Pharmaceutical Biosciences, University of Oslo, Oslo, Norway.
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46
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Adam RC, Yang H, Ge Y, Infarinato NR, Gur-Cohen S, Miao Y, Wang P, Zhao Y, Lu CP, Kim JE, Ko JY, Paik SS, Gronostajski RM, Kim J, Krueger JG, Zheng D, Fuchs E. NFI transcription factors provide chromatin access to maintain stem cell identity while preventing unintended lineage fate choices. Nat Cell Biol 2020; 22:640-650. [PMID: 32393888 PMCID: PMC7367149 DOI: 10.1038/s41556-020-0513-0] [Citation(s) in RCA: 49] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2019] [Accepted: 03/30/2020] [Indexed: 12/13/2022]
Abstract
Tissue homeostasis and regeneration rely on resident stem cells (SCs), whose behaviour is regulated through niche-dependent crosstalk. The mechanisms underlying SC identity are still unfolding. Here, using spatiotemporal gene ablation in murine hair follicles, we uncover a critical role for the transcription factors (TFs) nuclear factor IB (NFIB) and IX (NFIX) in maintaining SC identity. Without NFI TFs, SCs lose their hair-regenerating capability, and produce skin bearing striking resemblance to irreversible human alopecia, which also displays reduced NFIs. Through single-cell transcriptomics, ATAC-Seq and ChIP-Seq profiling, we expose a key role for NFIB and NFIX in governing super-enhancer maintenance of the key hair follicle SC-specific TF genes. When NFIB and NFIX are genetically removed, the stemness epigenetic landscape is lost. Super-enhancers driving SC identity are decommissioned, while unwanted lineages are de-repressed ectopically. Together, our findings expose NFIB and NFIX as crucial rheostats of tissue homeostasis, functioning to safeguard the SC epigenome from a breach in lineage confinement that otherwise triggers irreversible tissue degeneration.
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Affiliation(s)
- Rene C Adam
- Robin Chemers Neustein Laboratory of Mammalian Cell Biology and Development, Howard Hughes Medical Institute, The Rockefeller University, New York, NY, USA
- Regeneron Pharmaceuticals, New York, NY, USA
| | - Hanseul Yang
- Robin Chemers Neustein Laboratory of Mammalian Cell Biology and Development, Howard Hughes Medical Institute, The Rockefeller University, New York, NY, USA
| | - Yejing Ge
- Robin Chemers Neustein Laboratory of Mammalian Cell Biology and Development, Howard Hughes Medical Institute, The Rockefeller University, New York, NY, USA
- Department of Cancer Biology, University of Texas, MD Anderson Cancer Center, Houston, TX, USA
| | - Nicole R Infarinato
- Robin Chemers Neustein Laboratory of Mammalian Cell Biology and Development, Howard Hughes Medical Institute, The Rockefeller University, New York, NY, USA
| | - Shiri Gur-Cohen
- Robin Chemers Neustein Laboratory of Mammalian Cell Biology and Development, Howard Hughes Medical Institute, The Rockefeller University, New York, NY, USA
| | - Yuxuan Miao
- Robin Chemers Neustein Laboratory of Mammalian Cell Biology and Development, Howard Hughes Medical Institute, The Rockefeller University, New York, NY, USA
| | - Ping Wang
- Department of Genetics, Albert Einstein College of Medicine, New York, NY, USA
| | - Yilin Zhao
- Department of Genetics, Albert Einstein College of Medicine, New York, NY, USA
| | - Catherine P Lu
- Robin Chemers Neustein Laboratory of Mammalian Cell Biology and Development, Howard Hughes Medical Institute, The Rockefeller University, New York, NY, USA
- The Hansjörg Wyss Department of Plastic Surgery, New York University School of Medicine, New York, NY, USA
| | - Jeong E Kim
- Department of Dermatology, College of Medicine, Hanyang University, Seoul, South Korea
| | - Joo Y Ko
- Department of Dermatology, College of Medicine, Hanyang University, Seoul, South Korea
| | - Seung S Paik
- Department of Pathology, College of Medicine, Hanyang University, Seoul, South Korea
| | - Richard M Gronostajski
- Department of Biochemistry, Developmental Genomics Group, NYS Center of Excellence in Bioinformatics and Life Sciences, State University of New York at Buffalo, New York, NY, USA
| | - Jaehwan Kim
- Laboratory for Investigative Dermatology, The Rockefeller University, New York, NY, USA
- Division of Dermatology, Montefiore Medical Center, Albert Einstein College of Medicine, New York, NY, USA
| | - James G Krueger
- Laboratory for Investigative Dermatology, The Rockefeller University, New York, NY, USA
| | - Deyou Zheng
- Department of Genetics, Albert Einstein College of Medicine, New York, NY, USA
- Departments of Neurology and Neuroscience, Albert Einstein College of Medicine, New York, NY, USA
| | - Elaine Fuchs
- Robin Chemers Neustein Laboratory of Mammalian Cell Biology and Development, Howard Hughes Medical Institute, The Rockefeller University, New York, NY, USA.
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47
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Expression of NFIA and NFIB within the murine spinal cord. Gene Expr Patterns 2020; 35:119098. [PMID: 32068188 DOI: 10.1016/j.gep.2020.119098] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Revised: 02/06/2020] [Accepted: 02/11/2020] [Indexed: 12/17/2022]
Abstract
The Nuclear factor I proteins comprise a family of transcription factors that are expressed in many developing and mature cell populations, including within the central nervous system. Within the embryonic mouse spinal cord, NFIA and NFIB are expressed by neural progenitor cells lining the central canal, where they act to promote astrocytic and oligodendrocytic lineage specification. Cells lining the mature spinal cord central canal retain characteristics of neural progenitor cells, but the expression of NFIA and NFIB within the mature spinal cord at a cell-type-specific level remains undefined. Here, we investigated where these two transcription factors are expressed within the adult mouse spinal cord. We reveal that both factors are expressed in similar cohorts of mature cells, including ependymal cells, interneurons and motor neurons. We also show robust and widespread expression of NFIA and NFIB within nestin-expressing cells following injury to the spinal cord. Collectively, these data provide a basis to further define what functional role(s) NFIA and NFIB play within the adult spinal cord.
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48
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Fraser J, Essebier A, Brown AS, Davila RA, Harkins D, Zalucki O, Shapiro LP, Penzes P, Wainwright BJ, Scott MP, Gronostajski RM, Bodén M, Piper M, Harvey TJ. Common Regulatory Targets of NFIA, NFIX and NFIB during Postnatal Cerebellar Development. CEREBELLUM (LONDON, ENGLAND) 2020; 19:89-101. [PMID: 31838646 PMCID: PMC7815246 DOI: 10.1007/s12311-019-01089-3] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Transcriptional regulation plays a central role in controlling neural stem and progenitor cell proliferation and differentiation during neurogenesis. For instance, transcription factors from the nuclear factor I (NFI) family have been shown to co-ordinate neural stem and progenitor cell differentiation within multiple regions of the embryonic nervous system, including the neocortex, hippocampus, spinal cord and cerebellum. Knockout of individual Nfi genes culminates in similar phenotypes, suggestive of common target genes for these transcription factors. However, whether or not the NFI family regulates common suites of genes remains poorly defined. Here, we use granule neuron precursors (GNPs) of the postnatal murine cerebellum as a model system to analyse regulatory targets of three members of the NFI family: NFIA, NFIB and NFIX. By integrating transcriptomic profiling (RNA-seq) of Nfia- and Nfix-deficient GNPs with epigenomic profiling (ChIP-seq against NFIA, NFIB and NFIX, and DNase I hypersensitivity assays), we reveal that these transcription factors share a large set of potential transcriptional targets, suggestive of complementary roles for these NFI family members in promoting neural development.
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Affiliation(s)
- James Fraser
- The School of Biomedical Sciences, The University of Queensland, Brisbane, 4072, Australia
| | - Alexandra Essebier
- The School of Chemistry and Molecular Bioscience, The University of Queensland, Brisbane, 4072, Australia
| | - Alexander S Brown
- Department of Developmental Biology, School of Medicine, Stanford University, Stanford, CA, USA
| | - Raul Ayala Davila
- The School of Biomedical Sciences, The University of Queensland, Brisbane, 4072, Australia
| | - Danyon Harkins
- The School of Biomedical Sciences, The University of Queensland, Brisbane, 4072, Australia
| | - Oressia Zalucki
- The School of Biomedical Sciences, The University of Queensland, Brisbane, 4072, Australia
| | - Lauren P Shapiro
- Department of Physiology, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Peter Penzes
- Department of Physiology, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Brandon J Wainwright
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, 4072, Australia
| | - Matthew P Scott
- Department of Developmental Biology, School of Medicine, Stanford University, Stanford, CA, USA
| | - Richard M Gronostajski
- Department of Biochemistry, Program in Genetics, Genomics and Bioinformatics, Center of Excellence in Bioinformatics and Life Sciences, State University of New York at Buffalo, Buffalo, NY, USA
| | - Mikael Bodén
- The School of Chemistry and Molecular Bioscience, The University of Queensland, Brisbane, 4072, Australia
| | - Michael Piper
- The School of Biomedical Sciences, The University of Queensland, Brisbane, 4072, Australia.
- Queensland Brain Institute, The University of Queensland, Brisbane, 4072, Australia.
| | - Tracey J Harvey
- The School of Biomedical Sciences, The University of Queensland, Brisbane, 4072, Australia.
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49
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Danoy M, Poulain S, Koui Y, Tauran Y, Scheidecker B, Kido T, Miyajima A, Sakai Y, Plessy C, Leclerc E. Transcriptome profiling of hiPSC-derived LSECs with nanoCAGE. Mol Omics 2020; 16:138-146. [PMID: 31989141 DOI: 10.1039/c9mo00135b] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Liver Sinusoidal Endothelial Cells (LSECs) are an important component of the liver as they compose the microvasculature which allows the supply of oxygen, blood, and nutrients. However, maintenance of these cells in vitro remains challenging as they tend to rapidly lose some of their characteristics such as fenestration or as their immortalized counterparts present poor characteristics. In this work, human induced pluripotent stem cells (hiPSCs) have been differentiated toward an LSEC phenotype. After differentiation, the RNA quantification allowed demonstration of high expression of specific vascular markers (CD31, CD144, and STAB2). Immunostaining performed on the cells was found to be positive for both Stabilin-1 and Stabilin-2. Whole transcriptome analysis performed with the nanoCAGE method further confirmed the overall vascular commitment of the cells. The gene expression profile revealed the upregulation of the APLN, LYVE1, VWF, ESAM and ANGPT2 genes while VEGFA appeared to be downregulated. Analysis of promoter motif activities highlighted several transcription factors (TFs) of interest in LSECs (IRF2, ERG, MEIS2, SPI1, IRF7, WRNIP1, HIC2, NFIX_NFIB, BATF, and PATZ1). Based on this investigation, we compiled the regulatory network involving the relevant TFs, their target genes as well as their related signaling pathways. The proposed hiPSC-derived LSEC model and its regulatory network were then confirmed by comparing the experimental data to primary human LSEC reference datasets. Thus, the presented model appears as a promising tool to generate more complex in vitro liver multi-cellular tissues.
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Affiliation(s)
- Mathieu Danoy
- CNRS UMI 2820, Laboratory for Integrated Micro Mechatronic Systems, Institute of Industrial Science, University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo 153-8505, Japan.
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50
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de Majo M, Koontz M, Rowitch D, Ullian EM. An update on human astrocytes and their role in development and disease. Glia 2020; 68:685-704. [PMID: 31926040 DOI: 10.1002/glia.23771] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2019] [Revised: 11/25/2019] [Accepted: 11/29/2019] [Indexed: 12/12/2022]
Abstract
Human astrocytes provide trophic as well as structural support to the surrounding brain cells. Furthermore, they have been implicated in many physiological processes important for central nervous system function. Traditionally astrocytes have been considered to be a homogeneous class of cells, however, it has increasingly become more evident that astrocytes can have very different characteristics in different regions of the brain, or even within the same region. In this review we will discuss the features of human astrocytes, their heterogeneity, and their generation during neurodevelopment and the extraordinary progress that has been made to model these fascinating cells in vitro, mainly from induced pluripotent stem cells. Astrocytes' role in disease will also be discussed with a particular focus on their role in neurodegenerative disorders. As outlined here, astrocytes are important for the homeostasis of the central nervous system and understanding their regional specificity is a priority to elucidate the complexity of the human brain.
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Affiliation(s)
- Martina de Majo
- Department of Ophthalmology, University of California, San Francisco, San Francisco, California
| | - Mark Koontz
- Department of Ophthalmology, University of California, San Francisco, San Francisco, California
| | - David Rowitch
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, California.,Department of Pediatrics, University of California, San Francisco, San Francisco, California.,Department of Paediatrics, University of Cambridge, Cambridge, UK
| | - Erik M Ullian
- Department of Ophthalmology, University of California, San Francisco, San Francisco, California
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