1
|
Chang YT, Lee YJ, Haque M, Chang HC, Javed S, Lin YC, Cho Y, Abramovitz J, Chin G, Khamis A, Raja R, Murai KK, Huang WH. Comparative analyses of the Smith-Magenis syndrome protein RAI1 in mice and common marmoset monkeys. J Comp Neurol 2024; 532:e25589. [PMID: 38289192 DOI: 10.1002/cne.25589] [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: 04/13/2023] [Revised: 11/11/2023] [Accepted: 12/17/2023] [Indexed: 02/01/2024]
Abstract
Retinoic acid-induced 1 (RAI1) encodes a transcriptional regulator critical for brain development and function. RAI1 haploinsufficiency in humans causes a syndromic autism spectrum disorder known as Smith-Magenis syndrome (SMS). The neuroanatomical distribution of RAI1 has not been quantitatively analyzed during the development of the prefrontal cortex, a brain region critical for cognitive function and social behaviors and commonly implicated in autism spectrum disorders, including SMS. Here, we performed comparative analyses to uncover the evolutionarily convergent and divergent expression profiles of RAI1 in major cell types during prefrontal cortex maturation in common marmoset monkeys (Callithrix jacchus) and mice (Mus musculus). We found that while RAI1 in both species is enriched in neurons, the percentage of excitatory neurons that express RAI1 is higher in newborn mice than in newborn marmosets. By contrast, RAI1 shows similar neural distribution in adult marmosets and adult mice. In marmosets, RAI1 is expressed in several primate-specific cell types, including intralaminar astrocytes and MEIS2-expressing prefrontal GABAergic neurons. At the molecular level, we discovered that RAI1 forms a protein complex with transcription factor 20 (TCF20), PHD finger protein 14 (PHF14), and high mobility group 20A (HMG20A) in the marmoset brain. In vitro assays in human cells revealed that TCF20 regulates RAI1 protein abundance. This work demonstrates that RAI1 expression and protein interactions are largely conserved but with some unique expression in primate-specific cells. The results also suggest that altered RAI1 abundance could contribute to disease features in disorders caused by TCF20 dosage imbalance.
Collapse
Affiliation(s)
- Ya-Ting Chang
- Department of Neurology and Neurosurgery, Centre for Research in Neuroscience, McGill University, Montréal, Québec, Canada
- Brain Repair and Integrative Neuroscience Program, The Research Institute of the McGill University Health Centre, Montréal, Québec, Canada
| | - Yu-Ju Lee
- Department of Neurology and Neurosurgery, Centre for Research in Neuroscience, McGill University, Montréal, Québec, Canada
- Brain Repair and Integrative Neuroscience Program, The Research Institute of the McGill University Health Centre, Montréal, Québec, Canada
| | - Minza Haque
- Department of Neurology and Neurosurgery, Centre for Research in Neuroscience, McGill University, Montréal, Québec, Canada
- Brain Repair and Integrative Neuroscience Program, The Research Institute of the McGill University Health Centre, Montréal, Québec, Canada
| | - Hao-Cheng Chang
- Department of Neurology and Neurosurgery, Centre for Research in Neuroscience, McGill University, Montréal, Québec, Canada
- Brain Repair and Integrative Neuroscience Program, The Research Institute of the McGill University Health Centre, Montréal, Québec, Canada
| | - Sehrish Javed
- Department of Neurology and Neurosurgery, Centre for Research in Neuroscience, McGill University, Montréal, Québec, Canada
- Brain Repair and Integrative Neuroscience Program, The Research Institute of the McGill University Health Centre, Montréal, Québec, Canada
| | - Yu Cheng Lin
- Department of Neurology and Neurosurgery, Centre for Research in Neuroscience, McGill University, Montréal, Québec, Canada
- Brain Repair and Integrative Neuroscience Program, The Research Institute of the McGill University Health Centre, Montréal, Québec, Canada
| | - Yoobin Cho
- Department of Neurology and Neurosurgery, Centre for Research in Neuroscience, McGill University, Montréal, Québec, Canada
- Brain Repair and Integrative Neuroscience Program, The Research Institute of the McGill University Health Centre, Montréal, Québec, Canada
| | - Joseph Abramovitz
- Department of Neurology and Neurosurgery, Centre for Research in Neuroscience, McGill University, Montréal, Québec, Canada
- Brain Repair and Integrative Neuroscience Program, The Research Institute of the McGill University Health Centre, Montréal, Québec, Canada
| | - Gabriella Chin
- Department of Neurology and Neurosurgery, Centre for Research in Neuroscience, McGill University, Montréal, Québec, Canada
- Brain Repair and Integrative Neuroscience Program, The Research Institute of the McGill University Health Centre, Montréal, Québec, Canada
| | - Asma Khamis
- Department of Neurology and Neurosurgery, Centre for Research in Neuroscience, McGill University, Montréal, Québec, Canada
- Brain Repair and Integrative Neuroscience Program, The Research Institute of the McGill University Health Centre, Montréal, Québec, Canada
| | - Reesha Raja
- Department of Neurology and Neurosurgery, Centre for Research in Neuroscience, McGill University, Montréal, Québec, Canada
- Brain Repair and Integrative Neuroscience Program, The Research Institute of the McGill University Health Centre, Montréal, Québec, Canada
| | - Keith K Murai
- Department of Neurology and Neurosurgery, Centre for Research in Neuroscience, McGill University, Montréal, Québec, Canada
- Brain Repair and Integrative Neuroscience Program, The Research Institute of the McGill University Health Centre, Montréal, Québec, Canada
| | - Wei-Hsiang Huang
- Department of Neurology and Neurosurgery, Centre for Research in Neuroscience, McGill University, Montréal, Québec, Canada
- Brain Repair and Integrative Neuroscience Program, The Research Institute of the McGill University Health Centre, Montréal, Québec, Canada
| |
Collapse
|
2
|
Li W, Du J, Yang L, Liang Q, Yang M, Zhou X, Du W. Chromosome-level genome assembly and population genomics of Mongolian racerunner (Eremias argus) provide insights into high-altitude adaptation in lizards. BMC Biol 2023; 21:40. [PMID: 36803146 PMCID: PMC9942394 DOI: 10.1186/s12915-023-01535-z] [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: 01/22/2022] [Accepted: 02/03/2023] [Indexed: 02/22/2023] Open
Abstract
BACKGROUND Although the extreme environmental adaptation of organisms is a hot topic in evolutionary biology, genetic adaptation to high-altitude environment remains poorly characterized in ectothermic animals. Squamates are among the most diverse terrestrial vertebrates, with tremendous ecological plasticity and karyotype diversity, and are a unique model system to investigate the genetic footprints of adaptation. RESULTS We report the first chromosome-level assembly of the Mongolian racerunner (Eremias argus) and our comparative genomics analyses found that multiple chromosome fissions/fusions events are unique to lizards. We further sequenced the genomes of 61 Mongolian racerunner individuals that were collected from altitudes ranging from ~ 80 to ~ 2600 m above sea level (m.a.s.l.). Population genomic analyses revealed many novel genomic regions under strong selective sweeps in populations endemic to high altitudes. Genes embedded in those genomic regions are mainly associated with energy metabolism and DNA damage repair pathways. Moreover, we identified and validated two substitutions of PHF14 that may enhance the lizards' tolerance to hypoxia at high altitudes. CONCLUSIONS Our study reveals the molecular mechanism of high-altitude adaptation in ectothermic animal using lizard as a research subject and provides a high-quality lizard genomic resource for future research.
Collapse
Affiliation(s)
- Weiming Li
- grid.9227.e0000000119573309Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101 China ,grid.410726.60000 0004 1797 8419University of Chinese Academic of Sciences, Beijing, China
| | - Juan Du
- grid.9227.e0000000119573309Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101 China ,grid.410726.60000 0004 1797 8419University of Chinese Academic of Sciences, Beijing, China
| | - Lingyun Yang
- grid.410753.4Novogene Bioinformatics Institute, Beijing, 100083 China
| | - Qiqi Liang
- grid.410753.4Novogene Bioinformatics Institute, Beijing, 100083 China
| | - Mengyuan Yang
- grid.9227.e0000000119573309Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101 China ,grid.410726.60000 0004 1797 8419University of Chinese Academic of Sciences, Beijing, China
| | - Xuming Zhou
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China.
| | - Weiguo Du
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China. .,Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, 650223, China.
| |
Collapse
|
3
|
Zhang D, Yong WH, Movassaghi M, Rodriguez FJ, Yang I, McKeever P, Qian J, Li JY, Mao Q, Newell KL, Green RM, Welsh CT, Heaney AP. Whole Exome Sequencing Identifies PHF14 Mutations in Neurocytoma and Predicts Responsivity to the PDGFR Inhibitor Sunitinib. Biomedicines 2022; 10:2842. [PMID: 36359362 PMCID: PMC9687778 DOI: 10.3390/biomedicines10112842] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Revised: 10/13/2022] [Accepted: 10/24/2022] [Indexed: 07/22/2023] Open
Abstract
Neurocytomas are rare low-grade brain tumors predominantly affecting young adults, but their cellular origin and molecular pathogenesis is largely unknown. We previously reported a sellar neurocytoma that secreted excess arginine vasopressin causing syndrome of inappropriate anti-diuretic hormone (SIADH). Whole exome sequencing in 21 neurocytoma tumor tissues identified somatic mutations in the plant homeodomain finger protein 14 (PHF14) in 3/21 (14%) tumors. Of these mutations, two were missense mutations and 4 caused splicing site losses, resulting in PHF14 dysfunction. Employing shRNA-mediated knockdown and CRISPR/Cas9-based knockout approaches, we demonstrated that loss of PHF14 increased proliferation and colony formation in five different human, mouse and rat mesenchymal and differentiated cell lines. Additionally, we demonstrated that PHF14 depletion resulted in upregulation of platelet derived growth factor receptor-alpha (PDGFRα) mRNA and protein in neuroblastoma SHSY-5Y cells and led to increased sensitivity to treatment with the PDGFR inhibitor Sunitinib. Furthermore, in a neurocytoma primary culture harboring splicing loss PHF14 mutations, overexpression of wild-type PHF14 and sunitinib treatment inhibited cell proliferation. Nude mice, inoculated with PHF14 knockout SHSY-5Y cells developed earlier and larger tumors than control cell-inoculated mice and Sunitinib administration caused greater tumor suppression in mice harboring PHF-14 knockout than control SHSY-5Y cells. Altogether our studies identified mutations of PHF14 in 14% of neurocytomas, demonstrate it can serve as an alternative pathway for certain cancerous behavior, and suggest a potential role for Sunitinib treatment in some patients with residual/recurrent neurocytoma.
Collapse
Affiliation(s)
- Dongyun Zhang
- Department of Medicine, David Geffen School of Medicine, University of California, Los Angeles, CA 90095, USA
| | - William H. Yong
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California, Los Angeles, CA 90095, USA
| | - Masoud Movassaghi
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California, Los Angeles, CA 90095, USA
| | - Fausto J. Rodriguez
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California, Los Angeles, CA 90095, USA
| | - Issac Yang
- Department of Neurosurgery, David Geffen School of Medicine, University of California, Los Angeles, CA 90095, USA
| | - Paul McKeever
- Department of Pathology and Clinical Laboratories, University of Michigan, Ann Arbor, MI 48109, USA
| | - Jiang Qian
- Department of Pathology, Albany Medical Center, Albany, NY 12208, USA
| | - Jian Yi Li
- Department of Pathology and Laboratory Medicine, North Shore University Hospital and Long Island Jewish Medical Center, Manhasset, NY 11040, USA
- Donald and Barbara Zucker School of Medicine at Hofstra/Northwell, Northwell Health System, Lake Success, NY 11549, USA
| | - Qinwen Mao
- Department of Pathology, University of Utah, Salt Lake City, UT 84112, USA
| | - Kathy L. Newell
- Department of Pathology and Laboratory Medicine, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Richard M. Green
- Neuro-Oncology Program, Kaiser Los Angeles Medical Center, Los Angeles, CA 90027, USA
| | - Cynthia T. Welsh
- Department of Pathology and Laboratory Medicine, Medical University of South Carolina, Charleston, SC 29425, USA
| | - Anthony P. Heaney
- Department of Medicine, David Geffen School of Medicine, University of California, Los Angeles, CA 90095, USA
- Department of Neurosurgery, David Geffen School of Medicine, University of California, Los Angeles, CA 90095, USA
| |
Collapse
|
4
|
Gómez-Marín E, Posavec-Marjanović M, Zarzuela L, Basurto-Cayuela L, Guerrero-Martínez JA, Arribas G, Yerbes R, Ceballos-Chávez M, Rodríguez-Paredes M, Tomé M, Durán RV, Buschbeck M, Reyes JC. The high mobility group protein HMG20A cooperates with the histone reader PHF14 to modulate TGFβ and Hippo pathways. Nucleic Acids Res 2022; 50:9838-9857. [PMID: 36124662 PMCID: PMC9508832 DOI: 10.1093/nar/gkac766] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Revised: 08/01/2022] [Accepted: 09/15/2022] [Indexed: 11/20/2022] Open
Abstract
High mobility group (HMG) proteins are chromatin regulators with essential functions in development, cell differentiation and cell proliferation. The protein HMG20A is predicted by the AlphaFold2 software to contain three distinct structural elements, which we have functionally characterized: i) an amino-terminal, intrinsically disordered domain with transactivation activity; ii) an HMG box with higher binding affinity for double-stranded, four-way-junction DNA than for linear DNA; and iii) a long coiled-coil domain. Our proteomic study followed by a deletion analysis and structural modeling demonstrates that HMG20A forms a complex with the histone reader PHF14, via the establishment of a two-stranded alpha-helical coiled-coil structure. siRNA-mediated knockdown of either PHF14 or HMG20A in MDA-MB-231 cells causes similar defects in cell migration, invasion and homotypic cell–cell adhesion ability, but neither affects proliferation. Transcriptomic analyses demonstrate that PHF14 and HMG20A share a large subset of targets. We show that the PHF14-HMG20A complex modulates the Hippo pathway through a direct interaction with the TEAD1 transcription factor. PHF14 or HMG20A deficiency increases epithelial markers, including E-cadherin and the epithelial master regulator TP63 and impaired normal TGFβ-trigged epithelial-to-mesenchymal transition. Taken together, these data indicate that PHF14 and HMG20A cooperate in regulating several pathways involved in epithelial–mesenchymal plasticity.
Collapse
Affiliation(s)
- Elena Gómez-Marín
- Genome Biology Department. Centro Andaluz de Biología Molecular y Medicina Regenerativa-CABIMER, Consejo Superior de Investigaciones Científicas-Universidad de Sevilla-Universidad Pablo de Olavide (CSIC-USE-UPO), Av. Americo Vespucio, 41092 Seville, Spain
| | - Melanija Posavec-Marjanović
- Program for Predictive and Personalized Medicine of Cancer, Germans Trias i Pujol Research Institute (PMPPC-IGTP), Badalona, Spain
| | - Laura Zarzuela
- Cell Dynamics and Signaling Department. Centro Andaluz de Biología Molecular y Medicina Regenerativa-CABIMER, Consejo Superior de Investigaciones Científicas-Universidad de Sevilla-Universidad Pablo de Olavide (CSIC-USE-UPO), Av. Americo Vespucio, 41092 Seville, Spain
| | - Laura Basurto-Cayuela
- Genome Biology Department. Centro Andaluz de Biología Molecular y Medicina Regenerativa-CABIMER, Consejo Superior de Investigaciones Científicas-Universidad de Sevilla-Universidad Pablo de Olavide (CSIC-USE-UPO), Av. Americo Vespucio, 41092 Seville, Spain
| | - José A Guerrero-Martínez
- Genome Biology Department. Centro Andaluz de Biología Molecular y Medicina Regenerativa-CABIMER, Consejo Superior de Investigaciones Científicas-Universidad de Sevilla-Universidad Pablo de Olavide (CSIC-USE-UPO), Av. Americo Vespucio, 41092 Seville, Spain
| | - Gonzalo Arribas
- Genome Biology Department. Centro Andaluz de Biología Molecular y Medicina Regenerativa-CABIMER, Consejo Superior de Investigaciones Científicas-Universidad de Sevilla-Universidad Pablo de Olavide (CSIC-USE-UPO), Av. Americo Vespucio, 41092 Seville, Spain
| | - Rosario Yerbes
- Cell Dynamics and Signaling Department. Centro Andaluz de Biología Molecular y Medicina Regenerativa-CABIMER, Consejo Superior de Investigaciones Científicas-Universidad de Sevilla-Universidad Pablo de Olavide (CSIC-USE-UPO), Av. Americo Vespucio, 41092 Seville, Spain
| | - María Ceballos-Chávez
- Genome Biology Department. Centro Andaluz de Biología Molecular y Medicina Regenerativa-CABIMER, Consejo Superior de Investigaciones Científicas-Universidad de Sevilla-Universidad Pablo de Olavide (CSIC-USE-UPO), Av. Americo Vespucio, 41092 Seville, Spain
| | - Manuel Rodríguez-Paredes
- Institute of Toxicology, University Medical Center Mainz, Johannes Gutenberg University, 55131 Mainz, Germany
| | - Mercedes Tomé
- Cell Dynamics and Signaling Department. Centro Andaluz de Biología Molecular y Medicina Regenerativa-CABIMER, Consejo Superior de Investigaciones Científicas-Universidad de Sevilla-Universidad Pablo de Olavide (CSIC-USE-UPO), Av. Americo Vespucio, 41092 Seville, Spain
| | - Raúl V Durán
- Cell Dynamics and Signaling Department. Centro Andaluz de Biología Molecular y Medicina Regenerativa-CABIMER, Consejo Superior de Investigaciones Científicas-Universidad de Sevilla-Universidad Pablo de Olavide (CSIC-USE-UPO), Av. Americo Vespucio, 41092 Seville, Spain
| | - Marcus Buschbeck
- Program for Predictive and Personalized Medicine of Cancer, Germans Trias i Pujol Research Institute (PMPPC-IGTP), Badalona, Spain.,Cancer and Leukaemia Epigenetics and Biology Program, Josep Carreras Leukaemia Research Institute (IJC), 08916 Badalona, Spain
| | - José C Reyes
- Genome Biology Department. Centro Andaluz de Biología Molecular y Medicina Regenerativa-CABIMER, Consejo Superior de Investigaciones Científicas-Universidad de Sevilla-Universidad Pablo de Olavide (CSIC-USE-UPO), Av. Americo Vespucio, 41092 Seville, Spain
| |
Collapse
|
5
|
Pan G, Zhang K, Geng S, Lan C, Hu X, Li C, Ji H, Li C, Hu X, Wang Y, LV M, Cui H. PHF14 knockdown causes apoptosis by inducing DNA damage and impairing the activity of the damage response complex in colorectal cancer. Cancer Lett 2022; 531:109-123. [DOI: 10.1016/j.canlet.2022.01.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2021] [Revised: 12/22/2021] [Accepted: 01/03/2022] [Indexed: 12/14/2022]
|
6
|
Zheng S, Bi Y, Chen H, Gong B, Jia S, Li H. Molecular basis for bipartite recognition of histone H3 by the PZP domain of PHF14. Nucleic Acids Res 2021; 49:8961-8973. [PMID: 34365506 PMCID: PMC8421203 DOI: 10.1093/nar/gkab670] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2020] [Revised: 07/13/2021] [Accepted: 07/23/2021] [Indexed: 11/14/2022] Open
Abstract
Histone recognition constitutes a key epigenetic mechanism in gene regulation and cell fate decision. PHF14 is a conserved multi-PHD finger protein that has been implicated in organ development, tissue homeostasis, and tumorigenesis. Here we show that PHF14 reads unmodified histone H3(1–34) through an integrated PHD1-ZnK-PHD2 cassette (PHF14PZP). Our binding, structural and HDX-MS analyses revealed a feature of bipartite recognition, in which PHF14PZP utilizes two distinct surfaces for concurrent yet separable engagement of segments H3-Nter (e.g. 1–15) and H3-middle (e.g. 14–34) of H3(1–34). Structural studies revealed a novel histone H3 binding mode by PHD1 of PHF14PZP, in which a PHF14-unique insertion loop but not the core β-strands of a PHD finger dominates H3K4 readout. Binding studies showed that H3-PHF14PZP engagement is sensitive to modifications occurring to H3 R2, T3, K4, R8 and K23 but not K9 and K27, suggesting multiple layers of modification switch. Collectively, our work calls attention to PHF14 as a ‘ground’ state (unmodified) H3(1–34) reader that can be negatively regulated by active marks, thus providing molecular insights into a repressive function of PHF14 and its derepression.
Collapse
Affiliation(s)
- Shuangping Zheng
- MOE Key Laboratory of Protein Sciences, Beijing Frontier Research Center for Biological Structure, Beijing Advanced Innovation Center for Structural Biology, Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing 100084, China
| | - Yucong Bi
- MOE Key Laboratory of Protein Sciences, Beijing Frontier Research Center for Biological Structure, Beijing Advanced Innovation Center for Structural Biology, Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing 100084, China
| | - Haining Chen
- MOE Key Laboratory of Protein Sciences, Beijing Frontier Research Center for Biological Structure, Beijing Advanced Innovation Center for Structural Biology, Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing 100084, China
| | - Bo Gong
- Key Laboratory of Biomembrane and Membrane Engineering, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Shunji Jia
- Key Laboratory of Biomembrane and Membrane Engineering, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Haitao Li
- MOE Key Laboratory of Protein Sciences, Beijing Frontier Research Center for Biological Structure, Beijing Advanced Innovation Center for Structural Biology, Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing 100084, China.,Tsinghua-Peking Center for Life Sciences, Beijing 100084, China
| |
Collapse
|
7
|
Wan X, Zhou M, Huang F, Zhao N, Chen X, Wu Y, Zhu W, Ni Z, Jin F, Wang Y, Hu Z, Chen X, Ren M, Zhang H, Zha X. AKT1-CREB stimulation of PDGFRα expression is pivotal for PTEN deficient tumor development. Cell Death Dis 2021; 12:172. [PMID: 33568640 PMCID: PMC7876135 DOI: 10.1038/s41419-021-03433-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Revised: 01/11/2021] [Accepted: 01/13/2021] [Indexed: 12/12/2022]
Abstract
As evidenced by the behavior of loss-of-function mutants of PTEN in the context of a gain-of-function mutation of AKT1, the PTEN-AKT1 signaling pathway plays a critical role in human cancers. In this study, we demonstrated that a deficiency in PTEN or activation of AKT1 potentiated the expression of platelet-derived growth factor receptor α (PDGFRα) based on studies on Pten-/- mouse embryonic fibroblasts, human cancer cell lines, the hepatic tissues of Pten conditional knockout mice, and human cancer tissues. Loss of PTEN enhanced PDGFRα expression via activation of the AKT1-CREB signaling cascade. CREB transactivated PDGFRα expression by direct binding of the promoter of the PDGFRα gene. Depletion of PDGFRα attenuated the tumorigenicity of Pten-null cells in nude mice. Moreover, the PI3K-AKT signaling pathway has been shown to positively correlate with PDGFRα expression in multiple cancers. Augmented PDGFRα was associated with poor survival of cancer patients. Lastly, combination treatment with the AKT inhibitor MK-2206 and the PDGFR inhibitor CP-673451 displayed synergistic anti-tumor effects. Therefore, activation of the AKT1-CREB-PDGFRα signaling pathway contributes to the tumor growth induced by PTEN deficiency and should be targeted for cancer treatment.
Collapse
Affiliation(s)
- Xiaofeng Wan
- Department of Biochemistry & Molecular Biology, School of Basic Medicine, Anhui Medical University, Hefei, China
- Department of Laboratory, Cancer Hospital, Chinese Academy of Sciences, Hefei, China
| | - Meng Zhou
- Department of Biochemistry & Molecular Biology, School of Basic Medicine, Anhui Medical University, Hefei, China
| | - Fuqiang Huang
- State Key Laboratory of Medical Molecular Biology, Department of Physiology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Na Zhao
- State Key Laboratory of Medical Molecular Biology, Department of Physiology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Xu Chen
- Department of Biochemistry & Molecular Biology, School of Basic Medicine, Anhui Medical University, Hefei, China
| | - Yuncui Wu
- Department of Biochemistry & Molecular Biology, School of Basic Medicine, Anhui Medical University, Hefei, China
| | - Wanhui Zhu
- Department of Breast Surgery, The First Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Zhaofei Ni
- Department of Biochemistry & Molecular Biology, School of Basic Medicine, Anhui Medical University, Hefei, China
| | - Fuquan Jin
- Department of Biochemistry & Molecular Biology, School of Basic Medicine, Anhui Medical University, Hefei, China
| | - Yani Wang
- Department of Biochemistry & Molecular Biology, School of Basic Medicine, Anhui Medical University, Hefei, China
| | - Zhongdong Hu
- Modern Research Center for Traditional Chinese Medicine, School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing, China
| | - Xianguo Chen
- Department of Urology, The First Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Min Ren
- Department of Breast Surgery, The First Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Hongbing Zhang
- State Key Laboratory of Medical Molecular Biology, Department of Physiology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China.
| | - Xiaojun Zha
- Department of Biochemistry & Molecular Biology, School of Basic Medicine, Anhui Medical University, Hefei, China.
| |
Collapse
|
8
|
Zhang L, Lu Y, Wang Y, Wang F, Zhai S, Chen Z, Cai Z. PHF14 is required for germinal center B cell development. Cell Immunol 2020; 358:104221. [PMID: 33035772 DOI: 10.1016/j.cellimm.2020.104221] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2020] [Revised: 09/03/2020] [Accepted: 09/17/2020] [Indexed: 10/23/2022]
Abstract
Germinal centers (GCs), which are the site of antibody diversification and affinity maturation, are vitally important for humoral immunity. GC B cell proliferation is essentially for these processes by providing enough templates for somatic hypermutation (SHM) and serving as a critical mechanism of positive selection. In the current study, we found a significant reduction of GC response in the spleens of GC B cell specific PHF14 knockout (PHF14GCB KO) mice compared with the wild-type control (PHF14GCB WT) when the mice were challenged with SRBCs or lymphocytic choriomeningitis virus. We also demonstrated that PHF14 did not affect the cell survival of GC B cells, but regulated the proliferation of GC B cells. In addition, PHF14 suppressed the expression of Cdkn1a (p21) though regulating the level of H3K4me3 to control the proliferation of GC B cells. Collectively, our data suggest that PHF14 plays an important role in the process of germinal center formation by regulating GC B cell proliferation in spleen.
Collapse
Affiliation(s)
- Le Zhang
- Department of Immunology, Key Laboratory of Immune Microenvironment and Diseases, Nanjing Medical University, Nanjin 211166, China; Analysis Center, Nanjing Medical University, Nanjing 211166, China
| | - Yanlai Lu
- Department of Immunology, Key Laboratory of Immune Microenvironment and Diseases, Nanjing Medical University, Nanjin 211166, China
| | - Yuliang Wang
- Department of Immunology, Key Laboratory of Immune Microenvironment and Diseases, Nanjing Medical University, Nanjin 211166, China
| | - Feng Wang
- Analysis Center, Nanjing Medical University, Nanjing 211166, China
| | - Sulan Zhai
- Department of Immunology, Key Laboratory of Immune Microenvironment and Diseases, Nanjing Medical University, Nanjin 211166, China
| | - Zhengjun Chen
- State Key Laboratory of Cell Biology, Shanghai Institute of Biochemistry and Cell Biology, CAS Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, 320 Yueyang Road, 200031 Shanghai, China; School of Life Science and Technology, Shanghai Tech University, Shanghai 200031, China
| | - Zhenming Cai
- Department of Immunology, Key Laboratory of Immune Microenvironment and Diseases, Nanjing Medical University, Nanjin 211166, China.
| |
Collapse
|
9
|
PHF14 Promotes Cell Proliferation and Migration through the AKT and ERK1/2 Pathways in Gastric Cancer Cells. BIOMED RESEARCH INTERNATIONAL 2020; 2020:6507510. [PMID: 32596345 PMCID: PMC7305535 DOI: 10.1155/2020/6507510] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/28/2019] [Accepted: 02/06/2020] [Indexed: 12/11/2022]
Abstract
PHF14 is a new member belonging to PHD finger proteins. PHF14 is involved in multiple biologic processes including Dandy–Walker syndrome, mesenchyme growth, lung fibrosis, renal fibrosis, persistent pulmonary hypertension, and tumor development. This study aims to explore whether PHF14 plays an important role in gastric cancer. Here, PHF14 is indicated as a tumor promoter. The expression of PHF14 enhances no matter in clinical samples or in gastric cancer cells. High expression of PHF14 impairs survival of patients. Attenuation of PHF14 inhibits cell proliferation in gastric cancer cells. PHF14 downregulation inhibits the expression of cell cycle-related proteins, CDK6 and cyclin D1. Furthermore, silencing of PHF14 reduces the level of phosphorylated AKT as well as phosphorylated ERK1/2. Finally, downregulation of PHF14 in gastric cancer cells inhibits colony formation in vitro and tumorigenesis in vivo. These results indicate that PHF14 promotes tumor development in gastric cancer, so PHF14 thereby acts as a potential target for gastric cancer therapy.
Collapse
|
10
|
Wu H, Gu X, Li J, Wang M, Li Y, Yuan L, Wang J, Ma E. Identification of potential platelet-derived growth factor receptor α inhibitors by computational screening and binding simulations. J Mol Graph Model 2019; 96:107527. [PMID: 31918319 DOI: 10.1016/j.jmgm.2019.107527] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2019] [Revised: 12/23/2019] [Accepted: 12/28/2019] [Indexed: 11/15/2022]
Abstract
Platelet-derived growth factor receptor α (PDGFRα) is considered as a promising target for the treatment of fibrotic diseases. In this study, two types of pharmacophore model, which generated by ligand-based and receptor-based method, were put forward to identify novel chemical entities as PDGFRα inhibitors. It was found that some pharmacophore characteristics established by the two approaches overlap each other. In order to elucidate detailed interactions, representative molecules were selected to predict the conformations and binding modes of the molecules by molecular docking method. The calculation results of binding free energy illustrated that the van der Waals energy and nonpolar solvation were the most prominent contribution to the interactions between the inhibitors and PDGFRα. To further verify the accuracy of the docking results and the stability of the complexes system, the binding modes of two potent PDGFRα inhibitors were examined by 100 ns molecular dynamics simulations. Herein, we reported the basic structural requirements of PDGFRα inhibitors for the first time through molecular docking and molecular dynamics simulations. Subsequently, the two pharmacophore models were used for virtual screening to query potential active molecules from Food and Drug Administration approved database. The hit molecules here might provide additional scaffolds for further optimization of PDGFRα inhibitors.
Collapse
Affiliation(s)
- Hairui Wu
- School of Life Sciences and Biopharmaceutical Science, Shenyang Pharmaceutical University, 103 Wenhua Road, Shenhe District, Shenyang, 110016, PR China
| | - Xi Gu
- Key Laboratory of Structure-Based Drug Design & Discovery of Ministry of Education, School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, 103 Wenhua Road, Shenhe District, Shenyang, 110016, PR China
| | - Jinling Li
- School of Life Sciences and Biopharmaceutical Science, Shenyang Pharmaceutical University, 103 Wenhua Road, Shenhe District, Shenyang, 110016, PR China
| | - Mingxing Wang
- Key Laboratory of Structure-Based Drug Design & Discovery of Ministry of Education, School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, 103 Wenhua Road, Shenhe District, Shenyang, 110016, PR China
| | - Yanchun Li
- School of Life Sciences and Biopharmaceutical Science, Shenyang Pharmaceutical University, 103 Wenhua Road, Shenhe District, Shenyang, 110016, PR China
| | - Lei Yuan
- Key Laboratory of Structure-Based Drug Design & Discovery of Ministry of Education, School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, 103 Wenhua Road, Shenhe District, Shenyang, 110016, PR China
| | - Jian Wang
- Key Laboratory of Structure-Based Drug Design & Discovery of Ministry of Education, School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, 103 Wenhua Road, Shenhe District, Shenyang, 110016, PR China.
| | - Enlong Ma
- School of Life Sciences and Biopharmaceutical Science, Shenyang Pharmaceutical University, 103 Wenhua Road, Shenhe District, Shenyang, 110016, PR China.
| |
Collapse
|
11
|
Wu S, Luo C, Li F, Hameed NUF, Jin Q, Zhang J. Silencing expression of PHF14 in glioblastoma promotes apoptosis, mitigates proliferation and invasiveness via Wnt signal pathway. Cancer Cell Int 2019; 19:314. [PMID: 31798343 PMCID: PMC6882144 DOI: 10.1186/s12935-019-1040-6] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2019] [Accepted: 11/16/2019] [Indexed: 02/07/2023] Open
Abstract
Background The plant homeodomain (PHD) finger protein 14 (PHF14) is a vital member of PHD finger protein families. Abnormal expression of PHF14 has been identified in various cancers and is known to be implicated in the pathogenesis of tumors. This study investigates the role and the underlying mechanisms of PHF14 in GBM (glioblastoma multiforme). Methods Tissue microarrays and public databases interrogation were used to explore the relationship between the expression of PHF14 and GBM. Three stable PHF14-silenced cell lines (U251, U87MG and A172) were constructed to assess the biological functions changes of GBM cells in vitro. In addition, tumorigenicity in vivo was also performed using U87MG cell line. To understand the mechanism of action of PHF14, RNA-Seq, qRT-PCR, Western blot, IC50 assay and subsequent pathway analysis were performed. Results Our results showed that the expression of PHF14 was upregulated in glioma, especially in GBM. Overexpression of PHF14 translated to poor prognosis in glioma patients. In vitro assays revealed that silencing expression of PHF14 in glioma cells inhibited migration, invasiveness and proliferation and promoted cell apoptosis. Animal assay further confirmed that over-expression of PHF14 was a dismal prognostic factor. Analysis based on RNA-Seq suggested a PHF14-dependent regulation of Wnt signaling networks, which was further validated by qRT-PCR, Western blot and IC50 analysis. In addition, the mRNA expression of several key markers of EMT (epithelial–mesenchymal transition) and angiogenesis was found to change upon PHF14 silencing. Conclusions Our data provide a new insight into the biological significance of PHF14 in glioma and its potential application in therapy and diagnosis.
Collapse
Affiliation(s)
- Shuai Wu
- 1Glioma Surgery Division, Neurologic Surgery Department, Huashan Hospital, Fudan University, Shanghai, 200040 China
| | - Chen Luo
- 1Glioma Surgery Division, Neurologic Surgery Department, Huashan Hospital, Fudan University, Shanghai, 200040 China.,2Department of Human Anatomy and Histoembryology, Fudan University, Shanghai, 200433 China
| | - Fengjiao Li
- 2Department of Human Anatomy and Histoembryology, Fudan University, Shanghai, 200433 China
| | - N U Farrukh Hameed
- 1Glioma Surgery Division, Neurologic Surgery Department, Huashan Hospital, Fudan University, Shanghai, 200040 China
| | - Qiuyan Jin
- 2Department of Human Anatomy and Histoembryology, Fudan University, Shanghai, 200433 China
| | - Jie Zhang
- 1Glioma Surgery Division, Neurologic Surgery Department, Huashan Hospital, Fudan University, Shanghai, 200040 China
| |
Collapse
|
12
|
Park JE, Tse SW, Xue G, Assisi C, Maqueda AS, Ramon GPX, Low JK, Kon OL, Tay CY, Tam JP, Sze SK. Pulsed SILAC-based proteomic analysis unveils hypoxia- and serum starvation-induced de novo protein synthesis with PHD finger protein 14 (PHF14) as a hypoxia sensitive epigenetic regulator in cell cycle progression. Oncotarget 2019; 10:2136-2150. [PMID: 31040906 PMCID: PMC6481330 DOI: 10.18632/oncotarget.26669] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2018] [Accepted: 12/27/2018] [Indexed: 12/27/2022] Open
Abstract
Hypoxia is an environmental cue that is associated with multiple tumorigenic processes such as immunosuppression, angiogenesis, cancer invasion, metastasis, drug resistance, and poor clinical outcomes. When facing hypoxic stress, cells initiate several adaptive responses such as cell cycle arrest to reduce excessive oxygen consumption and co-activation of oncogenic factors. In order to identify the critical novel proteins for hypoxia responses, we used pulsed-SILAC method to trace the active cellular translation events in A431 cells. Proteomic discovery data and biochemical assays showed that cancer cells selectively activate key glycolytic enzymes and novel ER-stress markers, while protein synthesis is severely suppressed. Interestingly, deprivation of oxygen affected the expression of various epigenetic regulators such as histone demethylases and NuRD (nucleosome remodeling and deacetylase) complex in A431 cells. In addition, we identified PHF14 (the plant homeodomain finger-14) as a novel hypoxia-sensitive epigenetic regulator that plays a key role in cell cycle progress and protein synthesis. Hypoxia-mediated inhibition of PHF14 was associated with increase of key cell cycle inhibitors, p14ARF, p15INK4b, and p16INK4a, which are responsible for G1-S phase transition and decrease of AKT-mTOR-4E-BP1/pS6K signaling pathway, a master regulator of protein synthesis, in response to environmental cues. Analysis of TCGA colon cancer (n=461) and skin cancer (n=470) datasets revealed a positive correlation between PHF14 expression and protein translation initiation factors, eIF4E, eIF4B, and RPS6. Significance of PHF14 gene was further demonstrated by in vivo mouse xenograft model using PHF14 KD cell lines.
Collapse
Affiliation(s)
- Jung Eun Park
- Division of Structural Biology and Biochemistry School of Biological Sciences, Nanyang Technological University, Singapore 637551
| | - Shun Wilford Tse
- Division of Structural Biology and Biochemistry School of Biological Sciences, Nanyang Technological University, Singapore 637551
| | - Guo Xue
- Division of Structural Biology and Biochemistry School of Biological Sciences, Nanyang Technological University, Singapore 637551
| | - Christina Assisi
- Division of Structural Biology and Biochemistry School of Biological Sciences, Nanyang Technological University, Singapore 637551
| | - Aida Serra Maqueda
- Division of Structural Biology and Biochemistry School of Biological Sciences, Nanyang Technological University, Singapore 637551
| | - Gallart Palau Xavier Ramon
- Division of Structural Biology and Biochemistry School of Biological Sciences, Nanyang Technological University, Singapore 637551
| | - Jee Keem Low
- Department of Oncology, Tan Tock Seng Hospital, Singapore 308433
| | - Oi Lian Kon
- Laboratory of Applied Human Genetics, Division of Medical Sciences, National Cancer Centre Singapore, Singapore 169610
| | - Chor Yong Tay
- Division of Materials Technology School of Materials Science and Engineering, Nanyang Technological University, Singapore 639798
| | - James P Tam
- Division of Structural Biology and Biochemistry School of Biological Sciences, Nanyang Technological University, Singapore 637551
| | - Siu Kwan Sze
- Division of Structural Biology and Biochemistry School of Biological Sciences, Nanyang Technological University, Singapore 637551
| |
Collapse
|
13
|
Reference-based analysis of lung single-cell sequencing reveals a transitional profibrotic macrophage. Nat Immunol 2019; 20:163-172. [PMID: 30643263 PMCID: PMC6340744 DOI: 10.1038/s41590-018-0276-y] [Citation(s) in RCA: 1987] [Impact Index Per Article: 397.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2018] [Accepted: 11/09/2018] [Indexed: 02/07/2023]
Abstract
Tissue fibrosis is a major cause of mortality that results from the deposition of matrix proteins by an activated mesenchyme. Macrophages accumulate in fibrosis, but the role of specific subgroups in supporting fibrogenesis has not been investigated in vivo. Here we used single-cell RNA sequencing (scRNA-seq) to characterize the heterogeneity of macrophages in bleomycin-induced lung fibrosis in mice. A novel computational framework for the annotation of scRNA-seq by reference to bulk transcriptomes (SingleR) enabled the subclustering of macrophages and revealed a disease-associated subgroup with a transitional gene expression profile intermediate between monocyte-derived and alveolar macrophages. These CX3CR1+SiglecF+ transitional macrophages localized to the fibrotic niche and had a profibrotic effect in vivo. Human orthologues of genes expressed by the transitional macrophages were upregulated in samples from patients with idiopathic pulmonary fibrosis. Thus, we have identified a pathological subgroup of transitional macrophages that are required for the fibrotic response to injury.
Collapse
|
14
|
Hayden LP, Cho MH, Raby BA, Beaty TH, Silverman EK, Hersh CP. Childhood asthma is associated with COPD and known asthma variants in COPDGene: a genome-wide association study. Respir Res 2018; 19:209. [PMID: 30373671 PMCID: PMC6206739 DOI: 10.1186/s12931-018-0890-0] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2018] [Accepted: 09/12/2018] [Indexed: 01/11/2023] Open
Abstract
BACKGROUND Childhood asthma is strongly influenced by genetics and is a risk factor for reduced lung function and chronic obstructive pulmonary disease (COPD) in adults. This study investigates self-reported childhood asthma in adult smokers from the COPDGene Study. We hypothesize that childhood asthma is associated with decreased lung function, increased risk for COPD, and that a genome-wide association study (GWAS) will show association with established asthma variants. METHODS We evaluated current and former smokers ages 45-80 of non-Hispanic white (NHW) or African American (AA) race. Childhood asthma was defined by self-report of asthma, diagnosed by a medical professional, with onset at < 16 years or during childhood. Subjects with a history of childhood asthma were compared to those who never had asthma based on lung function, development of COPD, and genetic variation. GWAS was performed in NHW and AA populations, and combined in meta-analysis. Two sets of established asthma SNPs from published literature were examined for association with childhood asthma. RESULTS Among 10,199 adult smokers, 730 (7%) reported childhood asthma and 7493 (73%) reported no history of asthma. Childhood asthmatics had reduced lung function and increased risk for COPD (OR 3.42, 95% CI 2.81-4.18). Genotype data was assessed for 8031 subjects. Among NHWs, 391(7%) had childhood asthma, and GWAS identified one genome-wide significant association in KIAA1958 (rs59289606, p = 4.82 × 10- 8). Among AAs, 339 (12%) had childhood asthma. No SNPs reached genome-wide significance in the AAs or in the meta-analysis combining NHW and AA subjects; however, potential regions of interest were identified. Established asthma SNPs were examined, seven from the NHGRI-EBI database and five with genome-wide significance in the largest pediatric asthma GWAS. Associations were found in the current childhood asthma GWAS with known asthma loci in IL1RL1, IL13, LINC01149, near GSDMB, and in the C11orf30-LRRC32 region (Bonferroni adjusted p < 0.05 for all comparisons). CONCLUSIONS Childhood asthmatics are at increased risk for COPD. Defining asthma by self-report is valid in populations at risk for COPD, identifying subjects with clinical and genetic characteristics known to associate with childhood asthma. This has potential to improve clinical understanding of asthma-COPD overlap (ACO) and enhance future research into ACO-specific treatment regimens. TRIAL REGISTRATION ClinicalTrials.gov, NCT00608764 (Active since January 28, 2008).
Collapse
Affiliation(s)
- Lystra P. Hayden
- Division of Respiratory Diseases, Boston Children’s Hospital, Boston, MA USA
- Channing Division of Network Medicine, Brigham and Women’s Hospital, 181 Longwood Avenue, Boston, MA 02115 USA
| | - Michael H. Cho
- Channing Division of Network Medicine, Brigham and Women’s Hospital, 181 Longwood Avenue, Boston, MA 02115 USA
- Division of Pulmonary and Critical Care Medicine, Brigham and Women’s Hospital, Boston, MA USA
| | - Benjamin A. Raby
- Division of Respiratory Diseases, Boston Children’s Hospital, Boston, MA USA
- Channing Division of Network Medicine, Brigham and Women’s Hospital, 181 Longwood Avenue, Boston, MA 02115 USA
- Division of Pulmonary and Critical Care Medicine, Brigham and Women’s Hospital, Boston, MA USA
| | - Terri H. Beaty
- Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD USA
| | - Edwin K. Silverman
- Channing Division of Network Medicine, Brigham and Women’s Hospital, 181 Longwood Avenue, Boston, MA 02115 USA
- Division of Pulmonary and Critical Care Medicine, Brigham and Women’s Hospital, Boston, MA USA
| | - Craig P. Hersh
- Channing Division of Network Medicine, Brigham and Women’s Hospital, 181 Longwood Avenue, Boston, MA 02115 USA
- Division of Pulmonary and Critical Care Medicine, Brigham and Women’s Hospital, Boston, MA USA
| |
Collapse
|
15
|
Miwa H, Era T. Tracing the destiny of mesenchymal stem cells from embryo to adult bone marrow and white adipose tissue via Pdgfrα expression. Development 2018; 145:145/2/dev155879. [DOI: 10.1242/dev.155879] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2017] [Accepted: 12/21/2017] [Indexed: 12/13/2022]
Abstract
ABSTRACT
Mesenchymal stem cells (MSCs) are somatic stem cells that can be derived from adult bone marrow (BM) and white adipose tissue (WAT), and that display multipotency and self-renewal capacity. Although MSCs are essential for tissue formation and have already been used in clinical therapy, the origins and markers of these cells remain unknown. In this study, we first investigated the developmental process of MSCs in mouse embryos using the gene encoding platelet-derived growth factor receptor α (Pdgfra) as a marker. We then traced cells expressing Pdgfra and other genes (brachyury, Sox1 and Pmx1) in various mutant mouse embryos until the adult stage. This tracing of MSC origins and destinies indicates that embryonic MSCs emerge in waves and that almost all adult BM MSCs and WAT MSCs originate from mesoderm and embryonic Pdgfrα-positive cells. Furthermore, we demonstrate that adult Pdgfrα-positive cells are involved in some pathological conditions.
Collapse
Affiliation(s)
- Hiroyuki Miwa
- Department of Cell Modulation, Institute of Molecular Embryology and Genetics, Kumamoto University, 2-2-1 Honjo, Chuo-ku, Kumamoto 860-0811, Japan
| | - Takumi Era
- Department of Cell Modulation, Institute of Molecular Embryology and Genetics, Kumamoto University, 2-2-1 Honjo, Chuo-ku, Kumamoto 860-0811, Japan
| |
Collapse
|
16
|
Zhang L, Huang Q, Lou J, Zou L, Wang Y, Zhang P, Yang G, Zhang J, Yu L, Yan D, Zhang C, Qiao J, Wang S, Wang S, Xu Y, Ji H, Chen Z, Zhang Z. A novel PHD-finger protein 14/KIF4A complex overexpressed in lung cancer is involved in cell mitosis regulation and tumorigenesis. Oncotarget 2017; 8:19684-19698. [PMID: 28160558 PMCID: PMC5386714 DOI: 10.18632/oncotarget.14962] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2016] [Accepted: 01/03/2017] [Indexed: 12/26/2022] Open
Abstract
The plant homeodomain (PHD) finger-containing proteins have been implicated in many human diseases including cancer. In this study, we found that PHF14, a newly identified PHD finger protein, is highly expressed in lung cancer. The high expression level of PHF14 was associated with adenocarcinoma and poor survival in lung cancer patients. Knocking down PHF14 suppressed cancer cell growth and carcinogenesis, while over-expressing PHF14 promoted cell proliferation. During cell division, PHF14 directly bound to and co-localized with KIF4A (a nuclear motor protein involved in lung carcinogenesis) to form a functional complex. Similarly to the effect of KIF4A depletion, silencing PHF14 in several cell lines caused cell mitotic defects, prolonged M phase, and inhibited cell proliferation. What's more, these two proteins had a synergistic effect on cell proliferation and were significantly co-overexpressed in lung cancer tissues. Our data provide new insights into the biological significance of PHD finger proteins and imply that PHF14 may be a potential biomarker for lung cancer.
Collapse
Affiliation(s)
- Lin Zhang
- Key Laboratory of Systems Biology, Shanghai Institute of Biochemistry and Cell Biology (SIBCB), Shanghai Institutes for Biological Sciences (SIBS), Chinese Academy of Science (CAS), Shanghai, China
| | - Qin Huang
- Key Laboratory of Systems Biology, Shanghai Institute of Biochemistry and Cell Biology (SIBCB), Shanghai Institutes for Biological Sciences (SIBS), Chinese Academy of Science (CAS), Shanghai, China
| | - Jiatao Lou
- Shanghai Lung Tumor Clinical Medical Center, Chest Hospital Affiliated to Shanghai Jiao Tong University, Shanghai, China
| | - Liangjian Zou
- Institute of Cardiothoracic Surgery, Changhai Hospital Affiliated to The Second Military Medical University, Shanghai, China
| | - Yiguo Wang
- Tsinghua-Peking Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, China
| | - Peng Zhang
- Key Laboratory of Systems Biology, Shanghai Institute of Biochemistry and Cell Biology (SIBCB), Shanghai Institutes for Biological Sciences (SIBS), Chinese Academy of Science (CAS), Shanghai, China
| | - Guang Yang
- Key Laboratory of Systems Biology, Shanghai Institute of Biochemistry and Cell Biology (SIBCB), Shanghai Institutes for Biological Sciences (SIBS), Chinese Academy of Science (CAS), Shanghai, China
| | - Junyi Zhang
- Key Laboratory of Systems Biology, Shanghai Institute of Biochemistry and Cell Biology (SIBCB), Shanghai Institutes for Biological Sciences (SIBS), Chinese Academy of Science (CAS), Shanghai, China
| | - Lan Yu
- Key Laboratory of Systems Biology, Shanghai Institute of Biochemistry and Cell Biology (SIBCB), Shanghai Institutes for Biological Sciences (SIBS), Chinese Academy of Science (CAS), Shanghai, China
| | - Dai Yan
- Key Laboratory of Systems Biology, Shanghai Institute of Biochemistry and Cell Biology (SIBCB), Shanghai Institutes for Biological Sciences (SIBS), Chinese Academy of Science (CAS), Shanghai, China
| | - Chenyi Zhang
- Key Laboratory of Systems Biology, Shanghai Institute of Biochemistry and Cell Biology (SIBCB), Shanghai Institutes for Biological Sciences (SIBS), Chinese Academy of Science (CAS), Shanghai, China
| | - Jing Qiao
- Key Laboratory of Systems Biology, Shanghai Institute of Biochemistry and Cell Biology (SIBCB), Shanghai Institutes for Biological Sciences (SIBS), Chinese Academy of Science (CAS), Shanghai, China
| | - Shuting Wang
- Key Laboratory of Systems Biology, Shanghai Institute of Biochemistry and Cell Biology (SIBCB), Shanghai Institutes for Biological Sciences (SIBS), Chinese Academy of Science (CAS), Shanghai, China
| | - Sai Wang
- Key Laboratory of Systems Biology, Shanghai Institute of Biochemistry and Cell Biology (SIBCB), Shanghai Institutes for Biological Sciences (SIBS), Chinese Academy of Science (CAS), Shanghai, China
| | - Yongdong Xu
- Shanghai Pudong Hospital, Fudan University Pudong Medical Center, Shanghai, China
| | - Hongbin Ji
- Key Laboratory of Systems Biology, Shanghai Institute of Biochemistry and Cell Biology (SIBCB), Shanghai Institutes for Biological Sciences (SIBS), Chinese Academy of Science (CAS), Shanghai, China.,School of Life Science and Technology, Shanghai Tech University, Shanghai, China.,CAS Center for Excellence in Molecular Cell Science, SIBCB, SIBS, CAS, Shanghai, China
| | - Zhengjun Chen
- Key Laboratory of Systems Biology, Shanghai Institute of Biochemistry and Cell Biology (SIBCB), Shanghai Institutes for Biological Sciences (SIBS), Chinese Academy of Science (CAS), Shanghai, China.,Cancer Research Center, Shanghai Xu-Hui Central Hospital, Shanghai Clinical Center, CAS, Shanghai, China.,School of Life Science and Technology, Shanghai Tech University, Shanghai, China
| | - Zhe Zhang
- Key Laboratory of Systems Biology, Shanghai Institute of Biochemistry and Cell Biology (SIBCB), Shanghai Institutes for Biological Sciences (SIBS), Chinese Academy of Science (CAS), Shanghai, China.,Cancer Research Center, Shanghai Xu-Hui Central Hospital, Shanghai Clinical Center, CAS, Shanghai, China
| |
Collapse
|
17
|
Schinagl C, Melum GR, Rødningen OK, Bjørgo K, Andresen JH. Severe persistent pulmonary hypertension of the newborn and dysmorphic features in neonate with a deletion involving TWIST1 and PHF14: a case report. J Med Case Rep 2017; 11:226. [PMID: 28814329 PMCID: PMC5559830 DOI: 10.1186/s13256-017-1402-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2017] [Accepted: 07/23/2017] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Persistent pulmonary hypertension is a well-known disease of the newborn that in most cases responds well to treatment with nitric oxide and treatment of any underlying causes. Genetic causes of persistent pulmonary hypertension of the newborn are rare. The TWIST1 gene is involved in morphogenetics, and deletions are known to cause Saethre-Chotzen syndrome. Deletions of PHF14 have never been reported in neonates, but animal studies have shown a link between severe defects in lung development and deletions of this gene. There have not, to the best of our knowledge, been any publications of a link between the genes TWIST1 and PHF14 and persistent pulmonary hypertension of the newborn, making this a novel finding. CASE PRESENTATION We describe a white male neonate born at term to non-consanguineous white parents; he presented with dysmorphic features and a therapy-refractory persistent pulmonary hypertension. Array-based comparative genomic hybridization revealed the presence of a 14.7 Mb interstitial deletion on chromosome 7, encompassing the genes TWIST1 and PHF14. CONCLUSIONS The TWIST1 gene can explain our patient's dysmorphic features. His severe persistent pulmonary hypertension has, however, not been described before in conjunction with the TWIST1 gene, but could be explained by involvement of PHF14, consistent with findings in animal experiments showing lethal respiratory failure with depletion of PHF14. These findings are novel and of importance for the clinical management and diagnostic workup of neonates with severe persistent pulmonary hypertension of the newborn and dysmorphic features.
Collapse
Affiliation(s)
- Carina Schinagl
- Department of Pediatrics, Oslo University Hospital, Oslo, Norway
| | | | | | - Kathrine Bjørgo
- Department of Medical Genetics, Oslo University Hospital, Oslo, Norway
| | | |
Collapse
|
18
|
Yang B, Chen S, Wu M, Zhang L, Ruan M, Chen X, Chen Z, Mei C, Mao Z. PHF14: an innate inhibitor against the progression of renal fibrosis following folic acid-induced kidney injury. Sci Rep 2017; 7:39888. [PMID: 28045076 PMCID: PMC5206671 DOI: 10.1038/srep39888] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2016] [Accepted: 11/29/2016] [Indexed: 02/06/2023] Open
Abstract
PHF14 is a newly identified regulator of mesenchyme growth in embryonic tissues. Previous studies have shown that phf14-null mutants die just after birth due to interstitial tissue hyperplasia in major organs, including the kidneys. The aim of this study was to investigate PHF14 function in renal fibrosis. By studying the chronic kidney injury mouse model, we found that PHF14 was upregulated in fibrotic kidneys after renal insults induced by folic acid administration. Compared with wild-type mice, PHF14-null mice showed more severe renal fibrosis after pro-fibrotic stimuli. Moreover, PHF14 in rat renal fibroblasts was upregulated by transforming growth factor-β (TGF-β) stimulation; while this upregulation was inhibited when smad3 phosphorylation was blocked. A chromatin immunoprecipitation (ChIP) assay further indicated that phospho-smad3 (p-smad3) acted as a transcription factor to enhance PHF14 expression. A lack of PHF14 expression enhanced collagen I and α-smooth muscle actin (α-SMA) synthesis induced by TGF-β in vitro. PHF14 was involved in inhibition of platelet-derived growth factor (PDGF) signaling overactivation by selectively repressing PDGF receptor-α (PDGFR-α) transcription. In summary, PHF14 expression was upregulated in fibrotic models in vivo and in vitro, and the TGF-β/smad3/PHF14 pathway acted as a self-limiting mechanism in the TGF-β-dominated renal pro-fibrotic process by suppressing PDGFR-α expression.
Collapse
Affiliation(s)
- Bo Yang
- Kidney Institute of CPLA, Division of Nephrology, Changzheng Hospital, Second Military Medical University, Shanghai, 200003, People's Republic of China
| | - Sixiu Chen
- Kidney Institute of CPLA, Division of Nephrology, Changzheng Hospital, Second Military Medical University, Shanghai, 200003, People's Republic of China
| | - Ming Wu
- Kidney Institute of CPLA, Division of Nephrology, Changzheng Hospital, Second Military Medical University, Shanghai, 200003, People's Republic of China
| | - Lin Zhang
- School of Life Science and Technology, Shanghai Tech University, Shanghai 200031, People's Republic of China
| | - Mengna Ruan
- Kidney Institute of CPLA, Division of Nephrology, Changzheng Hospital, Second Military Medical University, Shanghai, 200003, People's Republic of China
| | - Xujiao Chen
- Kidney Institute of CPLA, Division of Nephrology, Changzheng Hospital, Second Military Medical University, Shanghai, 200003, People's Republic of China
| | - Zhengjun Chen
- School of Life Science and Technology, Shanghai Tech University, Shanghai 200031, People's Republic of China.,State Key Laboratory of Molecular Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, People's Republic of China
| | - Changlin Mei
- Kidney Institute of CPLA, Division of Nephrology, Changzheng Hospital, Second Military Medical University, Shanghai, 200003, People's Republic of China
| | - Zhiguo Mao
- Kidney Institute of CPLA, Division of Nephrology, Changzheng Hospital, Second Military Medical University, Shanghai, 200003, People's Republic of China
| |
Collapse
|
19
|
Garay PM, Wallner MA, Iwase S. Yin-yang actions of histone methylation regulatory complexes in the brain. Epigenomics 2016; 8:1689-1708. [PMID: 27855486 PMCID: PMC5289040 DOI: 10.2217/epi-2016-0090] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2016] [Accepted: 10/05/2016] [Indexed: 02/07/2023] Open
Abstract
Dysregulation of histone methylation has emerged as a major driver of neurodevelopmental disorders including intellectual disabilities and autism spectrum disorders. Histone methyl writer and eraser enzymes generally act within multisubunit complexes rather than in isolation. However, it remains largely elusive how such complexes cooperate to achieve the precise spatiotemporal gene expression in the developing brain. Histone H3K4 methylation (H3K4me) is a chromatin signature associated with active gene-regulatory elements. We review a body of literature that supports a model in which the RAI1-containing H3K4me writer complex counterbalances the LSD1-containing H3K4me eraser complex to ensure normal brain development. This model predicts H3K4me as the nexus of previously unrelated neurodevelopmental disorders.
Collapse
Affiliation(s)
- Patricia Marie Garay
- Neuroscience Graduate Program, The University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | | | - Shigeki Iwase
- Neuroscience Graduate Program, The University of Michigan Medical School, Ann Arbor, MI 48109, USA
- Department of Human Genetics, The University of Michigan, Ann Arbor, MI 48109, USA
| |
Collapse
|
20
|
Abstract
Human induced pluripotent stem (hiPS) cells are very attractive tools for modeling diseases and regenerative medicine. However, to achieve them, the efficient differentiation methods of hiPS cells into aimed cell type in vitro are necessary. Because mesoderm cells are useful in particular, we have developed the differentiation of mouse embryonic stem (mES) cells into mesoderm cells previously. In this time, these methods were improved for hiPS cells and now human mesoderm cells are able to be obtained efficiently. It is certain that the new methods are applicable to various studies and therapies.
Collapse
|
21
|
Polymorphism in a lincRNA Associates with a Doubled Risk of Pneumococcal Bacteremia in Kenyan Children. Am J Hum Genet 2016; 98:1092-1100. [PMID: 27236921 PMCID: PMC4908194 DOI: 10.1016/j.ajhg.2016.03.025] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2016] [Accepted: 03/28/2016] [Indexed: 12/31/2022] Open
Abstract
Bacteremia (bacterial bloodstream infection) is a major cause of illness and death in sub-Saharan Africa but little is known about the role of human genetics in susceptibility. We conducted a genome-wide association study of bacteremia susceptibility in more than 5,000 Kenyan children as part of the Wellcome Trust Case Control Consortium 2 (WTCCC2). Both the blood-culture-proven bacteremia case subjects and healthy infants as controls were recruited from Kilifi, on the east coast of Kenya. Streptococcus pneumoniae is the most common cause of bacteremia in Kilifi and was thus the focus of this study. We identified an association between polymorphisms in a long intergenic non-coding RNA (lincRNA) gene (AC011288.2) and pneumococcal bacteremia and replicated the results in the same population (p combined = 1.69 × 10(-9); OR = 2.47, 95% CI = 1.84-3.31). The susceptibility allele is African specific, derived rather than ancestral, and occurs at low frequency (2.7% in control subjects and 6.4% in case subjects). Our further studies showed AC011288.2 expression only in neutrophils, a cell type that is known to play a major role in pneumococcal clearance. Identification of this novel association will further focus research on the role of lincRNAs in human infectious disease.
Collapse
|
22
|
PHF6 Degrees of Separation: The Multifaceted Roles of a Chromatin Adaptor Protein. Genes (Basel) 2015; 6:325-52. [PMID: 26103525 PMCID: PMC4488667 DOI: 10.3390/genes6020325] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2015] [Revised: 06/12/2015] [Accepted: 06/16/2015] [Indexed: 12/13/2022] Open
Abstract
The importance of chromatin regulation to human disease is highlighted by the growing number of mutations identified in genes encoding chromatin remodeling proteins. While such mutations were first identified in severe developmental disorders, or in specific cancers, several genes have been implicated in both, including the plant homeodomain finger protein 6 (PHF6) gene. Indeed, germline mutations in PHF6 are the cause of the Börjeson–Forssman–Lehmann X-linked intellectual disability syndrome (BFLS), while somatic PHF6 mutations have been identified in T-cell acute lymphoblastic leukemia (T-ALL) and acute myeloid leukemia (AML). Studies from different groups over the last few years have made a significant impact towards a functional understanding of PHF6 protein function. In this review, we summarize the current knowledge of PHF6 with particular emphasis on how it interfaces with a distinct set of interacting partners and its functional roles in the nucleoplasm and nucleolus. Overall, PHF6 is emerging as a key chromatin adaptor protein critical to the regulation of neurogenesis and hematopoiesis.
Collapse
|
23
|
Miwa H, Era T. Generation and characterization of PDGFRα-GFPCreERT2 knock-In mouse line. Genesis 2015; 53:329-36. [PMID: 25884589 DOI: 10.1002/dvg.22853] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2015] [Revised: 04/12/2015] [Accepted: 04/13/2015] [Indexed: 12/18/2022]
Abstract
Platelet-derived growth factor (PDGF) and its receptor play an important role in embryogenesis. PDGF receptor α (PDGFRα) is expressed specifically in the embryonic day 7.5 (E7.5) mesoderm and in the E9.5 neural crest among other tissues. PDGFRα-expressing cells and their descendants are involved in the formation of various tissues. To trace PDGFRα-expressing cells in vivo, we generated a knock-in mouse line that expressed a fusion protein of green fluorescent protein (GFP), Cre recombinase (Cre), and mutated estrogen receptor ligand-binding domain (ERT2) under the control of the PDGFRα promoter. In these mice, Cre activity in PDGFRα-expressing cells could be induced by tamoxifen treatment. Taken together, our results suggest that the knock-in mouse line generated here could be useful for studying PDGFRα-expressing cells and their descendants in vivo at various stages of development.
Collapse
Affiliation(s)
- Hiroyuki Miwa
- Department of Cell Modulation, Institute of Molecular Embryology and Genetics, Kumamoto University, Kumamoto, Japan
| | - Takumi Era
- Department of Cell Modulation, Institute of Molecular Embryology and Genetics, Kumamoto University, Kumamoto, Japan
| |
Collapse
|
24
|
Noskovičová N, Petřek M, Eickelberg O, Heinzelmann K. Platelet-Derived Growth Factor Signaling in the Lung. From Lung Development and Disease to Clinical Studies. Am J Respir Cell Mol Biol 2015; 52:263-84. [DOI: 10.1165/rcmb.2014-0294tr] [Citation(s) in RCA: 64] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
|
25
|
Fujie Y, Fusaki N, Katayama T, Hamasaki M, Soejima Y, Soga M, Ban H, Hasegawa M, Yamashita S, Kimura S, Suzuki S, Matsuzawa T, Akari H, Era T. New type of Sendai virus vector provides transgene-free iPS cells derived from chimpanzee blood. PLoS One 2014; 9:e113052. [PMID: 25479600 PMCID: PMC4257541 DOI: 10.1371/journal.pone.0113052] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2014] [Accepted: 10/17/2014] [Indexed: 12/20/2022] Open
Abstract
Induced pluripotent stem cells (iPSCs) are potentially valuable cell sources for disease models and future therapeutic applications; however, inefficient generation and the presence of integrated transgenes remain as problems limiting their current use. Here, we developed a new Sendai virus vector, TS12KOS, which has improved efficiency, does not integrate into the cellular DNA, and can be easily eliminated. TS12KOS carries KLF4, OCT3/4, and SOX2 in a single vector and can easily generate iPSCs from human blood cells. Using TS12KOS, we established iPSC lines from chimpanzee blood, and used DNA array analysis to show that the global gene-expression pattern of chimpanzee iPSCs is similar to those of human embryonic stem cell and iPSC lines. These results demonstrated that our new vector is useful for generating iPSCs from the blood cells of both human and chimpanzee. In addition, the chimpanzee iPSCs are expected to facilitate unique studies into human physiology and disease.
Collapse
Affiliation(s)
- Yasumitsu Fujie
- Department of Cell Modulation, Institute of Molecular Embryology and Genetics, Kumamoto University, 2-2-1 Honjo, Chuo-ku, Kumamoto 860-0811, Japan
| | - Noemi Fusaki
- DNAVEC Corporation, 6 Ookubo, Tsukuba, Ibaragi 300-2611, Japan
- Precursory Research for Embryonic Science and Technology, Japan Science and Technology Agency, 4-1-8 Honcho Kawaguchi, Saitama, Japan
| | - Tomohiko Katayama
- Department of Cell Modulation, Institute of Molecular Embryology and Genetics, Kumamoto University, 2-2-1 Honjo, Chuo-ku, Kumamoto 860-0811, Japan
| | - Makoto Hamasaki
- Department of Cell Modulation, Institute of Molecular Embryology and Genetics, Kumamoto University, 2-2-1 Honjo, Chuo-ku, Kumamoto 860-0811, Japan
| | - Yumi Soejima
- Department of Cell Modulation, Institute of Molecular Embryology and Genetics, Kumamoto University, 2-2-1 Honjo, Chuo-ku, Kumamoto 860-0811, Japan
| | - Minami Soga
- Department of Cell Modulation, Institute of Molecular Embryology and Genetics, Kumamoto University, 2-2-1 Honjo, Chuo-ku, Kumamoto 860-0811, Japan
| | - Hiroshi Ban
- DNAVEC Corporation, 6 Ookubo, Tsukuba, Ibaragi 300-2611, Japan
| | - Mamoru Hasegawa
- DNAVEC Corporation, 6 Ookubo, Tsukuba, Ibaragi 300-2611, Japan
| | - Satoshi Yamashita
- Department of Neurology, Graduate School of Medical Sciences, Kumamoto University, 1-1-1 Honjo, Chuo-ku, Kumamoto 860-8556, Japan
| | - Shigemi Kimura
- Department of Child Development, Graduate School of Medical Sciences, Kumamoto University, 1-1-1 Honjo, Chuo-ku, Kumamoto 860-8556, Japan
| | - Saori Suzuki
- Section of Comparative Microbiology and Immunology, Center for Human Evolution Modeling Research, Primate Research Institute, Kyoto University, Inuyama, Aichi 484-8506, Japan
| | - Tetsuro Matsuzawa
- Section of Language and Intelligence, Primate Research Institute, Kyoto University, Inuyama, Aichi 484-8506, Japan
| | - Hirofumi Akari
- Section of Comparative Microbiology and Immunology, Center for Human Evolution Modeling Research, Primate Research Institute, Kyoto University, Inuyama, Aichi 484-8506, Japan
- Laboratory of Evolutional Virology, Experimental Research Center for Infectious Diseases, Institute for Virus Research, Kyoto University, Kyoto, 606-8507, Japan
| | - Takumi Era
- Department of Cell Modulation, Institute of Molecular Embryology and Genetics, Kumamoto University, 2-2-1 Honjo, Chuo-ku, Kumamoto 860-0811, Japan
- * E-mail:
| |
Collapse
|
26
|
Integrative genomic and transcriptomic analysis identified candidate genes implicated in the pathogenesis of hepatosplenic T-cell lymphoma. PLoS One 2014; 9:e102977. [PMID: 25057852 PMCID: PMC4109958 DOI: 10.1371/journal.pone.0102977] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2014] [Accepted: 06/23/2014] [Indexed: 12/20/2022] Open
Abstract
Hepatosplenic T-cell lymphoma (HSTL) is an aggressive lymphoma cytogenetically characterized by isochromosome 7q [i(7)(q10)], of which the molecular consequences remain unknown. We report here results of an integrative genomic and transcriptomic (expression microarray and RNA-sequencing) study of six i(7)(q10)-positive HSTL cases, including HSTL-derived cell line (DERL-2), and three cases with ring 7 [r(7)], the recently identified rare variant aberration. Using high resolution array CGH, we profiled all cases and mapped the common deleted region (CDR) at 7p22.1p14.1 (34.88 Mb; 3506316-38406226 bp) and the common gained region (CGR) at 7q22.11q31.1 (38.77 Mb; 86259620–124892276 bp). Interestingly, CDR spans a smaller region of 13 Mb (86259620–99271246 bp) constantly amplified in cases with r(7). In addition, we found that TCRG (7p14.1) and TCRB (7q32) are involved in formation of r(7), which seems to be a byproduct of illegitimate somatic rearrangement of both loci. Further transcriptomic analysis has not identified any CDR-related candidate tumor suppressor gene. Instead, loss of 7p22.1p14.1 correlated with an enhanced expression of CHN2 (7p14.1) and the encoded β2-chimerin. Gain and amplification of 7q22.11q31.1 are associated with an increased expression of several genes postulated to be implicated in cancer, including RUNDC3B, PPP1R9A and ABCB1, a known multidrug resistance gene. RNA-sequencing did not identify any disease-defining mutation or gene fusion. Thus, chromosome 7 imbalances remain the only driver events detected in this tumor. We hypothesize that the Δ7p22.1p14.1-associated enhanced expression of CHN2/β2-chimerin leads to downmodulation of the NFAT pathway and a proliferative response, while upregulation of the CGR-related genes provides growth advantage for neoplastic δγT-cells and underlies their intrinsic chemoresistance. Finally, our study confirms the previously described gene expression profile of HSTL and identifies a set of 24 genes, including three located on chromosome 7 (CHN2, ABCB1 and PPP1R9A), distinguishing HSTL from other malignancies.
Collapse
|
27
|
Huang Q, Zhang L, Wang Y, Zhang C, Zhou S, Yang G, Li Z, Gao X, Chen Z, Zhang Z. Depletion of PHF14, a novel histone-binding protein gene, causes neonatal lethality in mice due to respiratory failure. Acta Biochim Biophys Sin (Shanghai) 2013; 45:622-33. [PMID: 23688586 DOI: 10.1093/abbs/gmt055] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
The plant homeodomain (PHD) finger is identified in many chromatin-binding proteins, and functions as a 'reader' that recognizes specific epigenetic marks on histone tails, bridging transcription factors and their associated complexes to chromatin, and regulating gene expression. PHD finger-containing proteins perform many biological functions and are involved in many human diseases including cancer. PHF14 is predicted to code for a protein with multiple PHD fingers. However, its function is unidentified. The aim of this study is to characterize PHF14 and investigate its biological significance by employing multiple approaches including mouse gene-targeting knockout, and molecular cloning and characterization. Three transcripts of PHF14 in human cell lines were identified by reverse transcriptase polymerase chain reaction. Two isoforms of PHF14 (PHF14α and PHF14β) were cloned in this study. It was found that PHF14 was ubiquitously expressed in mouse tissues and human cell lines. PHF14α, the major isoform of PHF14, was localized in the nucleus and also bound to chromatin during cell division. Interestingly, co-immunoprecipitation results suggested that PHF14α bound to histones via its PHD fingers. Strikingly, gene-targeting knockout of PHF14 in mice resulted in a neonatal lethality due to respiratory failure. Pathological analysis revealed severe disorders of tissue and cell structures in multiple organs, particularly in the lungs. These results indicated that PHF14 might be an epigenetic regulator and play an important role in the development of multiple organs in mouse.
Collapse
Affiliation(s)
- Qin Huang
- State Key Laboratory of Molecular Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | | | | | | | | | | | | | | | | | | |
Collapse
|
28
|
Akazawa T, Yasui K, Gen Y, Yamada N, Tomie A, Dohi O, Mitsuyoshi H, Yagi N, Itoh Y, Naito Y, Yoshikawa T. Aberrant expression of the PHF14 gene in biliary tract cancer cells. Oncol Lett 2013; 5:1849-1853. [PMID: 23833654 PMCID: PMC3700892 DOI: 10.3892/ol.2013.1278] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2012] [Accepted: 03/05/2013] [Indexed: 02/03/2023] Open
Abstract
DNA copy number aberrations in human biliary tract cancer (BTC) cell lines were investigated using a high-density oligonucleotide microarray. A novel homozygous deletion was detected at chromosomal region 7p21.3 in the OZ cell line. Further validation experiments using genomic PCR revealed a homozygous deletion of a single gene, plant homeodomain (PHD) finger protein 14 (PHF14). No PHF14 mRNA or protein expression was detected, thus demonstrating the absence of PHF14 expression in the OZ cell line. Although the PHD finger protein is considered to be involved in chromatin-mediated transcriptional regulation, little is known about the function of PHF14 in cancer. The present study observed that the knock down of PHF14 using small interfering RNA (siRNA) enhanced the growth of the BTC cells. These observations suggest that aberrant PHF14 expression may have a role in the tumorigenesis of BTC.
Collapse
Affiliation(s)
- Takako Akazawa
- Department of Molecular Gastroenterology and Hepatology, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kyoto 602-8566, Japan
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|