1
|
Olan I, Ando-Kuri M, Parry AJ, Handa T, Schoenfelder S, Fraser P, Ohkawa Y, Kimura H, Narita M, Narita M. HMGA1 orchestrates chromatin compartmentalization and sequesters genes into 3D networks coordinating senescence heterogeneity. Nat Commun 2024; 15:6891. [PMID: 39134516 PMCID: PMC11319441 DOI: 10.1038/s41467-024-51153-8] [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: 02/06/2024] [Accepted: 07/26/2024] [Indexed: 08/15/2024] Open
Abstract
HMGA1 is an abundant non-histone chromatin protein that has been implicated in embryonic development, cancer, and cellular senescence, but its specific role remains elusive. Here, we combine functional genomics approaches with graph theory to investigate how HMGA1 genomic deposition controls high-order chromatin networks in an oncogene-induced senescence model. While the direct role of HMGA1 in gene activation has been described previously, we find little evidence to support this. Instead, we show that the heterogeneous linear distribution of HMGA1 drives a specific 3D chromatin organization. HMGA1-dense loci form highly interactive networks, similar to, but independent of, constitutive heterochromatic loci. This, coupled with the exclusion of HMGA1-poor chromatin regions, leads to coordinated gene regulation through the repositioning of genes. In the absence of HMGA1, the whole process is largely reversed, but many regulatory interactions also emerge, amplifying the inflammatory senescence-associated secretory phenotype. Such HMGA1-mediated fine-tuning of gene expression contributes to the heterogeneous nature of senescence at the single-cell level. A similar 'buffer' effect of HMGA1 on inflammatory signalling is also detected in lung cancer cells. Our study reveals a mechanism through which HMGA1 modulates chromatin compartmentalization and gene regulation in senescence and beyond.
Collapse
Affiliation(s)
- Ioana Olan
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, University of Cambridge, Cambridge, UK
| | - Masami Ando-Kuri
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, University of Cambridge, Cambridge, UK
- Division of Tumor Biology and Immunology, The Netherlands Cancer Institute-Oncode In stitute, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Aled J Parry
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, University of Cambridge, Cambridge, UK
- Altos Labs Cambridge Institute, Portway Building, Granta Park, Cambridge, UK
| | - Tetsuya Handa
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, University of Cambridge, Cambridge, UK
| | | | - Peter Fraser
- Nuclear Dynamics Programme, The Babraham Institute, Babraham Research Campus, Cambridge, UK
- Enhanc3D Genomics Ltd, Cambridge, UK
| | - Yasuyuki Ohkawa
- Division of Transcriptomics, Medical Institute of Bioregulation, Kyushu University, 3-1-1 Maidashi, Higashi, Fukuoka, 812-0054, Japan
| | - Hiroshi Kimura
- Cell Biology Center, Institute of Innovative Research, Tokyo Institute of Technology, Yokohama, Japan
| | - Masako Narita
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, University of Cambridge, Cambridge, UK
| | - Masashi Narita
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, University of Cambridge, Cambridge, UK.
- Tokyo Tech World Research Hub Initiative (WRHI), Institute of Innovative Research, Tokyo Institute of Technology, Yokohama, Japan.
| |
Collapse
|
2
|
Zhang F, Sun J, Zhang L, Li R, Wang Y, Geng H, Shen C, Li L, Chen L. PARP inhibition leads to synthetic lethality with key splicing-factor mutations in myelodysplastic syndromes. Br J Cancer 2024; 131:231-242. [PMID: 38806724 PMCID: PMC11263539 DOI: 10.1038/s41416-024-02729-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Revised: 05/14/2024] [Accepted: 05/17/2024] [Indexed: 05/30/2024] Open
Abstract
BACKGROUND Splicing factors are frequently mutated in patients with myelodysplastic syndromes and acute myeloid leukaemia. Recent studies have revealed convergent molecular defects caused by splicing factor mutations, among which R-loop dysregulation and resultant genome instability are suggested as contributing factors to disease progression. On the other hand, understanding how mutant cells survive upon aberrant R-loop formation and genome instability is essential for developing novel therapeutics. METHODS The immunoprecipitation was performed to identify R-loops in association with PARP1/poly-ADP-ribosylation. The western blot, immunofluorescence, and flow cytometry assays were used to test the cell viability, cell cycle arrest, apoptosis, and ATM activation in mutant cells following the treatment of the PARP inhibitor. The Srsf2(P95H) knock-in murine hematopoietic cells and MLL-AF9 transformed leukaemia model were generated to investigate the potential of the PARP inhibitor as a therapy for haematological malignancies. RESULTS The disease-causing mutations in SRSF2 activate PARP and elevate the overall poly-ADP-ribosylation levels of proteins in response to R-loop dysregulation. In accordance, mutant cells are more vulnerable to the PARP inhibitors in comparison to the wild-type counterpart. Notably, the synthetic lethality was further validated in the Srsf2(P95H) knock-in murine hematopoietic cell and MLL-AF9 leukaemia model. CONCLUSIONS Our findings suggest that mutant cells antagonise the genome threat caused by R-loop disruption by PARP activation, thus making PARP targeting a promising therapeutic strategy for myeloid cancers with mutations in SRSF2.
Collapse
Affiliation(s)
- Fangliang Zhang
- RNA Institute, Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan, China
| | - Jianai Sun
- Department of Hematological Malignancies Translational Science, Gehr Family Center for Leukemia Research, Hematologic Malignancies and Stem Cell Transplantation Institute, Beckman Research Institute, City of Hope Medical Center, Duarte, CA, USA
- Department of Hematology, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
| | - Lei Zhang
- Department of Hematological Malignancies Translational Science, Gehr Family Center for Leukemia Research, Hematologic Malignancies and Stem Cell Transplantation Institute, Beckman Research Institute, City of Hope Medical Center, Duarte, CA, USA
| | - Ruiqi Li
- RNA Institute, Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan, China
| | - Yanzhen Wang
- RNA Institute, Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan, China
| | - Huichao Geng
- RNA Institute, Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan, China
| | - Chao Shen
- RNA Institute, Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan, China
| | - Ling Li
- Department of Hematological Malignancies Translational Science, Gehr Family Center for Leukemia Research, Hematologic Malignancies and Stem Cell Transplantation Institute, Beckman Research Institute, City of Hope Medical Center, Duarte, CA, USA.
| | - Liang Chen
- RNA Institute, Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan, China.
| |
Collapse
|
3
|
Lopes-Paciencia S, Bourdeau V, Rowell MC, Amirimehr D, Guillon J, Kalegari P, Barua A, Quoc-Huy Trinh V, Azzi F, Turcotte S, Serohijos A, Ferbeyre G. A senescence restriction point acting on chromatin integrates oncogenic signals. Cell Rep 2024; 43:114044. [PMID: 38568812 DOI: 10.1016/j.celrep.2024.114044] [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: 12/14/2022] [Revised: 02/12/2024] [Accepted: 03/19/2024] [Indexed: 04/05/2024] Open
Abstract
We identify a senescence restriction point (SeRP) as a critical event for cells to commit to senescence. The SeRP integrates the intensity and duration of oncogenic stress, keeps a memory of previous stresses, and combines oncogenic signals acting on different pathways by modulating chromatin accessibility. Chromatin regions opened upon commitment to senescence are enriched in nucleolar-associated domains, which are gene-poor regions enriched in repeated sequences. Once committed to senescence, cells no longer depend on the initial stress signal and exhibit a characteristic transcriptome regulated by a transcription factor network that includes ETV4, RUNX1, OCT1, and MAFB. Consistent with a tumor suppressor role for this network, the levels of ETV4 and RUNX1 are very high in benign lesions of the pancreas but decrease dramatically in pancreatic ductal adenocarcinomas. The discovery of senescence commitment and its chromatin-linked regulation suggests potential strategies for reinstating tumor suppression in human cancers.
Collapse
Affiliation(s)
- Stéphane Lopes-Paciencia
- Centre de recherche du Centre Hospitalier de l'Université de Montréal (CRCHUM), Montréal, QC H2X 0A9, Canada
| | - Véronique Bourdeau
- Département de Biochimie et Médecine Moléculaire, Université de Montréal, Montréal, QC H3C 3J7, Canada
| | - Marie-Camille Rowell
- Centre de recherche du Centre Hospitalier de l'Université de Montréal (CRCHUM), Montréal, QC H2X 0A9, Canada
| | - Davoud Amirimehr
- Département de Biochimie et Médecine Moléculaire, Université de Montréal, Montréal, QC H3C 3J7, Canada
| | - Jordan Guillon
- Centre de recherche du Centre Hospitalier de l'Université de Montréal (CRCHUM), Montréal, QC H2X 0A9, Canada
| | - Paloma Kalegari
- Centre de recherche du Centre Hospitalier de l'Université de Montréal (CRCHUM), Montréal, QC H2X 0A9, Canada
| | - Arnab Barua
- Département de Biochimie et Médecine Moléculaire, Université de Montréal, Montréal, QC H3C 3J7, Canada
| | - Vincent Quoc-Huy Trinh
- Centre de recherche du Centre Hospitalier de l'Université de Montréal (CRCHUM), Montréal, QC H2X 0A9, Canada; Institut de recherche en immunologie et en cancérologie (IRIC), Université de Montréal, Montréal, QC H3C 3J7, Canada; Département de pathologie, Centre hospitalier de l'Université de Montréal, Montréal, QC, Canada
| | - Feryel Azzi
- Centre de recherche du Centre Hospitalier de l'Université de Montréal (CRCHUM), Montréal, QC H2X 0A9, Canada
| | - Simon Turcotte
- Centre de recherche du Centre Hospitalier de l'Université de Montréal (CRCHUM), Montréal, QC H2X 0A9, Canada; Département de chirurgie, Service de chirurgie hépatopancréatobiliaire, Centre hospitalier de l'Université de Montréal, Montréal, QC, Canada
| | - Adrian Serohijos
- Département de Biochimie et Médecine Moléculaire, Université de Montréal, Montréal, QC H3C 3J7, Canada
| | - Gerardo Ferbeyre
- Centre de recherche du Centre Hospitalier de l'Université de Montréal (CRCHUM), Montréal, QC H2X 0A9, Canada; Département de Biochimie et Médecine Moléculaire, Université de Montréal, Montréal, QC H3C 3J7, Canada.
| |
Collapse
|
4
|
Boileau C, Deforges S, Peret A, Scavarda D, Bartolomei F, Giles A, Partouche N, Gautron J, Viotti J, Janowitz H, Penchet G, Marchal C, Lagarde S, Trebuchon A, Villeneuve N, Rumi J, Marissal T, Khazipov R, Khalilov I, Martineau F, Maréchal M, Lepine A, Milh M, Figarella-Branger D, Dougy E, Tong S, Appay R, Baudouin S, Mercer A, Smith JB, Danos O, Porter R, Mulle C, Crépel V. GluK2 Is a Target for Gene Therapy in Drug-Resistant Temporal Lobe Epilepsy. Ann Neurol 2023; 94:745-761. [PMID: 37341588 DOI: 10.1002/ana.26723] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 06/09/2023] [Accepted: 06/12/2023] [Indexed: 06/22/2023]
Abstract
OBJECTIVE Temporal lobe epilepsy (TLE) is characterized by recurrent seizures generated in the limbic system, particularly in the hippocampus. In TLE, recurrent mossy fiber sprouting from dentate gyrus granule cells (DGCs) crea an aberrant epileptogenic network between DGCs which operates via ectopically expressed GluK2/GluK5-containing kainate receptors (KARs). TLE patients are often resistant to anti-seizure medications and suffer significant comorbidities; hence, there is an urgent need for novel therapies. Previously, we have shown that GluK2 knockout mice are protected from seizures. This study aims at providing evidence that downregulating KARs in the hippocampus using gene therapy reduces chronic epileptic discharges in TLE. METHODS We combined molecular biology and electrophysiology in rodent models of TLE and in hippocampal slices surgically resected from patients with drug-resistant TLE. RESULTS Here, we confirmed the translational potential of KAR suppression using a non-selective KAR antagonist that markedly attenuated interictal-like epileptiform discharges (IEDs) in TLE patient-derived hippocampal slices. An adeno-associated virus (AAV) serotype-9 vector expressing anti-grik2 miRNA was engineered to specifically downregulate GluK2 expression. Direct delivery of AAV9-anti grik2 miRNA into the hippocampus of TLE mice led to a marked reduction in seizure activity. Transduction of TLE patient hippocampal slices reduced levels of GluK2 protein and, most importantly, significantly reduced IEDs. INTERPRETATION Our gene silencing strategy to knock down aberrant GluK2 expression demonstrates inhibition of chronic seizure in a mouse TLE model and IEDs in cultured slices derived from TLE patients. These results provide proof-of-concept for a gene therapy approach targeting GluK2 KARs for drug-resistant TLE patients. ANN NEUROL 2023;94:745-761.
Collapse
Affiliation(s)
| | - Severine Deforges
- Univ. Bordeaux, CNRS, Interdisciplinary Institute for Neuroscience IINS, UMR 5297, Bordeaux, France
| | | | - Didier Scavarda
- APHM, INSERM, Aix Marseille Univ, INS, Timone Hospital, Pediatric Neurosurgery, Marseille, France
| | - Fabrice Bartolomei
- APHM, INSERM, Aix Marseille Univ, INS, Timone Hospital, Epileptology Department, Marseille, France
| | | | - Nicolas Partouche
- Aix-Marseille Univ. INSERM, Marseille, France
- Corlieve Therapeutics SAS, uniQure NV, Paris, France
| | - Justine Gautron
- Univ. Bordeaux, CNRS, Interdisciplinary Institute for Neuroscience IINS, UMR 5297, Bordeaux, France
- Corlieve Therapeutics SAS, uniQure NV, Paris, France
| | - Julio Viotti
- Univ. Bordeaux, CNRS, Interdisciplinary Institute for Neuroscience IINS, UMR 5297, Bordeaux, France
| | | | | | - Cécile Marchal
- Pellegrin Hospital, Neurosurgery Department, Bordeaux, France
| | - Stanislas Lagarde
- APHM, INSERM, Aix Marseille Univ, INS, Timone Hospital, Epileptology Department, Marseille, France
| | - Agnès Trebuchon
- APHM, INSERM, Aix Marseille Univ, INS, Timone Hospital, Epileptology Department, Marseille, France
| | - Nathalie Villeneuve
- APHM, INSERM, Aix Marseille Univ, INS, Timone Hospital, Epileptology Department, Marseille, France
| | - Julie Rumi
- Univ. Bordeaux, CNRS, Interdisciplinary Institute for Neuroscience IINS, UMR 5297, Bordeaux, France
| | | | | | | | | | - Marine Maréchal
- Univ. Bordeaux, CNRS, Interdisciplinary Institute for Neuroscience IINS, UMR 5297, Bordeaux, France
| | - Anne Lepine
- APHM, INSERM, Aix Marseille Univ, INS, Timone Hospital, Epileptology Department, Marseille, France
| | - Mathieu Milh
- APHM, INSERM, Aix Marseille Univ, INS, Timone Hospital, Epileptology Department, Marseille, France
| | - Dominique Figarella-Branger
- APHM, CNRS, INP, Inst Neurophysiopathol, CHU Timone, Service d'Anatomie Pathologique et de Neuropathologie, Aix-Marseille Univ, Marseille, France
| | - Etienne Dougy
- APHM, CNRS, INP, Inst Neurophysiopathol, CHU Timone, Service d'Anatomie Pathologique et de Neuropathologie, Aix-Marseille Univ, Marseille, France
| | - Soutsakhone Tong
- APHM, CNRS, INP, Inst Neurophysiopathol, CHU Timone, Service d'Anatomie Pathologique et de Neuropathologie, Aix-Marseille Univ, Marseille, France
| | - Romain Appay
- APHM, CNRS, INP, Inst Neurophysiopathol, CHU Timone, Service d'Anatomie Pathologique et de Neuropathologie, Aix-Marseille Univ, Marseille, France
| | | | | | | | | | | | - Christophe Mulle
- Univ. Bordeaux, CNRS, Interdisciplinary Institute for Neuroscience IINS, UMR 5297, Bordeaux, France
| | | |
Collapse
|
5
|
Ye R, Hu N, Cao C, Su R, Xu S, Yang C, Zhou X, Xue Y. Capture RIC-seq reveals positional rules of PTBP1-associated RNA loops in splicing regulation. Mol Cell 2023; 83:1311-1327.e7. [PMID: 36958328 DOI: 10.1016/j.molcel.2023.03.001] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Revised: 01/10/2023] [Accepted: 02/27/2023] [Indexed: 03/25/2023]
Abstract
RNA-binding proteins (RBPs) bind at different positions of the pre-mRNA molecules to promote or reduce the usage of a particular exon. Seeking to understand the working principle of these positional effects, we develop a capture RIC-seq (CRIC-seq) method to enrich specific RBP-associated in situ proximal RNA-RNA fragments for deep sequencing. We determine hnRNPA1-, SRSF1-, and PTBP1-associated proximal RNA-RNA contacts and regulatory mechanisms in HeLa cells. Unexpectedly, the 3D RNA map analysis shows that PTBP1-associated loops in individual introns preferentially promote cassette exon splicing by accelerating asymmetric intron removal, whereas the loops spanning across cassette exon primarily repress splicing. These "positional rules" can faithfully predict PTBP1-regulated splicing outcomes. We further demonstrate that cancer-related splicing quantitative trait loci can disrupt RNA loops by reducing PTBP1 binding on pre-mRNAs to cause aberrant splicing in tumors. Our study presents a powerful method for exploring the functions of RBP-associated RNA-RNA proximal contacts in gene regulation and disease.
Collapse
Affiliation(s)
- Rong Ye
- Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Naijing Hu
- Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Changchang Cao
- Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Ruibao Su
- Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Shihan Xu
- State Key Laboratory of Ophthalmology, Optometry and Vision Science, Wenzhou, Zhejiang 325003, China
| | - Chen Yang
- State Key Laboratory of Ophthalmology, Optometry and Vision Science, Wenzhou, Zhejiang 325003, China
| | - Xiangtian Zhou
- State Key Laboratory of Ophthalmology, Optometry and Vision Science, Wenzhou, Zhejiang 325003, China
| | - Yuanchao Xue
- Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China.
| |
Collapse
|
6
|
PGC-1β maintains mitochondrial metabolism and restrains inflammatory gene expression. Sci Rep 2022; 12:16028. [PMID: 36163487 PMCID: PMC9512823 DOI: 10.1038/s41598-022-20215-6] [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: 06/01/2022] [Accepted: 09/09/2022] [Indexed: 11/08/2022] Open
Abstract
Metabolic programming of the innate immune cells known as dendritic cells (DCs) changes in response to different stimuli, influencing their function. While the mechanisms behind increased glycolytic metabolism in response to inflammatory stimuli are well-studied, less is known about the programming of mitochondrial metabolism in DCs. We used lipopolysaccharide (LPS) and interferon-β (IFN-β), which differentially stimulate the use of glycolysis and oxidative phosphorylation (OXPHOS), respectively, to identify factors important for mitochondrial metabolism. We found that the expression of peroxisome proliferator-activated receptor gamma co-activator 1β (PGC-1β), a transcriptional co-activator and known regulator of mitochondrial metabolism, decreases when DCs are activated with LPS, when OXPHOS is diminished, but not with IFN-β, when OXPHOS is maintained. We examined the role of PGC-1β in bioenergetic metabolism of DCs and found that PGC-1β deficiency indeed impairs their mitochondrial respiration. PGC-1β-deficient DCs are more glycolytic compared to controls, likely to compensate for reduced OXPHOS. PGC-1β deficiency also causes decreased capacity for ATP production at steady state and in response to IFN-β treatment. Loss of PGC-1β in DCs leads to increased expression of genes in inflammatory pathways, and reduced expression of genes encoding proteins important for mitochondrial metabolism and function. Collectively, these results demonstrate that PGC-1β is a key regulator of mitochondrial metabolism and negative regulator of inflammatory gene expression in DCs.
Collapse
|
7
|
Dong SS, Zhu DL, Zhou XR, Rong Y, Zeng M, Chen JB, Jiang F, Tuo XM, Feng Z, Yang TL, Guo Y. An Intronic Risk SNP rs12454712 for Central Obesity Acts As an Allele-Specific Enhancer To Regulate BCL2 Expression. Diabetes 2021; 70:1679-1688. [PMID: 34035043 DOI: 10.2337/db20-1151] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Accepted: 05/10/2021] [Indexed: 11/13/2022]
Abstract
Genome-wide association studies (GWAS) have reproducibly associated the single nucleotide polymorphism (SNP) rs12454712 with waist-to-hip ratio adjusted for BMI (WHRadjBMI), but the functional role underlying this intronic variant is unknown. Integrative genomic and epigenomic analyses supported rs12454712 as a functional independent variant. We further demonstrated that rs12454712 acted as an allele-specific enhancer regulating expression of its located gene BCL2 by using dual-luciferase reporter assays and clustered regularly interspaced short palindromic repeats (CRISPR)-Cas9. Specifically, the rs12454712-C allele can bind transcription factor ZNF329, which efficiently elevates the enhancer activity and increases BCL2 expression. Knocking down Bcl2 in 3T3-L1 cells led to the downregulation of adipogenic differentiation marker genes and increased cell apoptosis. A significant negative correlation between BCL2 expression in subcutaneous adipose tissues and obesity was observed. Our findings illustrate the molecular mechanisms behind the intronic SNP rs12454712 for central obesity, which would be a potential and promising target for developing appropriate therapies.
Collapse
Affiliation(s)
- Shan-Shan Dong
- Biomedical Informatics & Genomics Center, Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi, China
- Research Institute of Xi'an Jiaotong University, Hangzhou, Zhejiang, China
| | - Dong-Li Zhu
- Biomedical Informatics & Genomics Center, Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi, China
| | - Xiao-Rong Zhou
- Biomedical Informatics & Genomics Center, Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi, China
| | - Yu Rong
- Biomedical Informatics & Genomics Center, Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi, China
| | - Mengqi Zeng
- Center for Mitochondrial Biology and Medicine, Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi, China
| | - Jia-Bin Chen
- Biomedical Informatics & Genomics Center, Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi, China
| | - Feng Jiang
- Biomedical Informatics & Genomics Center, Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi, China
| | - Xiao-Mei Tuo
- Biomedical Informatics & Genomics Center, Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi, China
| | - Zhihui Feng
- Center for Mitochondrial Biology and Medicine, Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi, China
| | - Tie-Lin Yang
- Biomedical Informatics & Genomics Center, Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi, China
| | - Yan Guo
- Biomedical Informatics & Genomics Center, Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi, China
| |
Collapse
|
8
|
Torres AG, Rodríguez-Escribà M, Marcet-Houben M, Santos Vieira H, Camacho N, Catena H, Murillo Recio M, Rafels-Ybern À, Reina O, Torres F, Pardo-Saganta A, Gabaldón T, Novoa E, Ribas de Pouplana L. Human tRNAs with inosine 34 are essential to efficiently translate eukarya-specific low-complexity proteins. Nucleic Acids Res 2021; 49:7011-7034. [PMID: 34125917 PMCID: PMC8266599 DOI: 10.1093/nar/gkab461] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Revised: 05/07/2021] [Accepted: 05/18/2021] [Indexed: 12/11/2022] Open
Abstract
The modification of adenosine to inosine at the wobble position (I34) of tRNA anticodons is an abundant and essential feature of eukaryotic tRNAs. The expansion of inosine-containing tRNAs in eukaryotes followed the transformation of the homodimeric bacterial enzyme TadA, which generates I34 in tRNAArg and tRNALeu, into the heterodimeric eukaryotic enzyme ADAT, which modifies up to eight different tRNAs. The emergence of ADAT and its larger set of substrates, strongly influenced the tRNA composition and codon usage of eukaryotic genomes. However, the selective advantages that drove the expansion of I34-tRNAs remain unknown. Here we investigate the functional relevance of I34-tRNAs in human cells and show that a full complement of these tRNAs is necessary for the translation of low-complexity protein domains enriched in amino acids cognate for I34-tRNAs. The coding sequences for these domains require codons translated by I34-tRNAs, in detriment of synonymous codons that use other tRNAs. I34-tRNA-dependent low-complexity proteins are enriched in functional categories related to cell adhesion, and depletion in I34-tRNAs leads to cellular phenotypes consistent with these roles. We show that the distribution of these low-complexity proteins mirrors the distribution of I34-tRNAs in the phylogenetic tree.
Collapse
Affiliation(s)
- Adrian Gabriel Torres
- Institute for Research in Biomedicine, The Barcelona Institute of Science and Technology, Barcelona, Catalonia 08028, Spain
| | - Marta Rodríguez-Escribà
- Institute for Research in Biomedicine, The Barcelona Institute of Science and Technology, Barcelona, Catalonia 08028, Spain
| | - Marina Marcet-Houben
- Institute for Research in Biomedicine, The Barcelona Institute of Science and Technology, Barcelona, Catalonia 08028, Spain
- Barcelona Supercomputing Centre (BSC-CNS), Barcelona, Catalonia 08034, Spain
| | | | - Noelia Camacho
- Institute for Research in Biomedicine, The Barcelona Institute of Science and Technology, Barcelona, Catalonia 08028, Spain
| | - Helena Catena
- Institute for Research in Biomedicine, The Barcelona Institute of Science and Technology, Barcelona, Catalonia 08028, Spain
| | - Marina Murillo Recio
- Institute for Research in Biomedicine, The Barcelona Institute of Science and Technology, Barcelona, Catalonia 08028, Spain
| | - Àlbert Rafels-Ybern
- Institute for Research in Biomedicine, The Barcelona Institute of Science and Technology, Barcelona, Catalonia 08028, Spain
| | - Oscar Reina
- Institute for Research in Biomedicine, The Barcelona Institute of Science and Technology, Barcelona, Catalonia 08028, Spain
| | - Francisco Miguel Torres
- Institute for Research in Biomedicine, The Barcelona Institute of Science and Technology, Barcelona, Catalonia 08028, Spain
| | - Ana Pardo-Saganta
- Centre for Applied Medical Research (CIMA Universidad de Navarra), Pamplona 31008, Spain
| | - Toni Gabaldón
- Institute for Research in Biomedicine, The Barcelona Institute of Science and Technology, Barcelona, Catalonia 08028, Spain
- Barcelona Supercomputing Centre (BSC-CNS), Barcelona, Catalonia 08034, Spain
- Catalan Institution for Research and Advanced Studies, Barcelona, Catalonia 08010, Spain
| | - Eva Maria Novoa
- Centre for Genomic Regulation, The Barcelona Institute of Science and Technology, Barcelona, Catalonia 08003, Spain
- University Pompeu Fabra, Barcelona, Catalonia 08003, Spain
| | - Lluís Ribas de Pouplana
- Institute for Research in Biomedicine, The Barcelona Institute of Science and Technology, Barcelona, Catalonia 08028, Spain
- Catalan Institution for Research and Advanced Studies, Barcelona, Catalonia 08010, Spain
| |
Collapse
|
9
|
Lu M, Fang XX, Shi DD, Liu R, Ding Y, Zhang QF, Wang HQ, Tang JM, He XJ. A Selective TRPC3 Inhibitor Pyr3 Attenuates Myocardial Ischemia/Reperfusion Injury in Mice. Curr Med Sci 2021; 40:1107-1113. [PMID: 33428139 DOI: 10.1007/s11596-020-2293-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Accepted: 08/21/2020] [Indexed: 11/29/2022]
Abstract
An emerging body of evidence indicates that transient receptor potential TRP channels act as important mediators for a wide variety of physiological functions and are potential targets for drug discovery. Our previous study has identified transient receptor potential channel 3 (TRPC3) and TRPC6 as cation channels through which most of the damaging calcium enters, aggravates pathological changes in vivo and increases ischemia/reperfusion (I/R) injury in mice. This study aimed to verify the effects of TRPC3 inhibitor Pyr3 on myocardial I/R injury in mice. C57BL/6J wild-type male mice (8 to 12 weeks old) were anesthetized with 3.3% chloral hydrate. A murine I (30 min)/R (24 h) injury model was established by temporary occlusion of the left anterior descending (LAD) coronary artery. Pyr3 was administered at concentrations of 0, 2.5, 5, or 10 mg/kg via the right jugular vein 5 min before reperfusion. We observed that the selective TRPC3 inhibitor, 10 mg/kg Pyr3, significantly decreased the infarct size of left ventricle, and reduced the myocardial cell apoptosis rate and inflammatory response in mice. In a conclusion, TRPC3 can function as a candidate target for I/R injury prevention, and Pyr3 may directly bind to TRPC3 channel protein, inhibit TRPC3 channel activity, and improve TRPC3-related myocardial I/R injury. Pyr3 may be used for clarification of TRPC3 functions and for treatments of TRPC3-mediated diseases.
Collapse
Affiliation(s)
- Min Lu
- Hubei Key Laboratory of Embryonic Stem Cell Research, Hubei University of Medicine, Shiyan, Hubei, 442000, China
| | - Xiao-Xia Fang
- Department of Neurology, Taihe Hospital, Hubei University of Medicine, Shiyan, Hubei, 442000, China
| | - Dan-Dan Shi
- Hubei Key Laboratory of Embryonic Stem Cell Research, Hubei University of Medicine, Shiyan, Hubei, 442000, China
| | - Rui Liu
- Hubei Key Laboratory of Embryonic Stem Cell Research, Hubei University of Medicine, Shiyan, Hubei, 442000, China
| | - Yan Ding
- Hubei Key Laboratory of Embryonic Stem Cell Research, Hubei University of Medicine, Shiyan, Hubei, 442000, China
| | - Qiu-Fang Zhang
- Hubei Key Laboratory of Embryonic Stem Cell Research, Hubei University of Medicine, Shiyan, Hubei, 442000, China
| | - Han-Qin Wang
- Hubei Key Laboratory of Embryonic Stem Cell Research, Hubei University of Medicine, Shiyan, Hubei, 442000, China
| | - Jun-Ming Tang
- Hubei Key Laboratory of Embryonic Stem Cell Research, Hubei University of Medicine, Shiyan, Hubei, 442000, China
| | - Xi-Ju He
- Hubei Key Laboratory of Embryonic Stem Cell Research, Hubei University of Medicine, Shiyan, Hubei, 442000, China. .,Department of Ultrasound, Taihe Hospital, Hubei University of Medicine, Shiyan, Hubei, 442000, China.
| |
Collapse
|
10
|
Brambilla F, Garcia-Manteiga JM, Monteleone E, Hoelzen L, Zocchi A, Agresti A, Bianchi ME. Nucleosomes effectively shield DNA from radiation damage in living cells. Nucleic Acids Res 2020; 48:8993-9006. [PMID: 32710624 PMCID: PMC7498322 DOI: 10.1093/nar/gkaa613] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2019] [Revised: 06/22/2020] [Accepted: 07/10/2020] [Indexed: 12/16/2022] Open
Abstract
Eukaryotic DNA is organized in nucleosomes, which package DNA and regulate its accessibility to transcription, replication, recombination and repair. Here, we show that in living cells nucleosomes protect DNA from high-energy radiation and reactive oxygen species. We combined sequence-based methods (ATAC-seq and BLISS) to determine the position of both nucleosomes and double strand breaks (DSBs) in the genome of nucleosome-rich malignant mesothelioma cells, and of the same cells partially depleted of nucleosomes. The results were replicated in the human MCF-7 breast carcinoma cell line. We found that, for each genomic sequence, the probability of DSB formation is directly proportional to the fraction of time it is nucleosome-free; DSBs accumulate distal from the nucleosome dyad axis. Nucleosome free regions and promoters of actively transcribed genes are more sensitive to DSB formation, and consequently to mutation. We argue that this may be true for a variety of chemical and physical DNA damaging agents.
Collapse
Affiliation(s)
| | - Jose Manuel Garcia-Manteiga
- IRCCS San Raffaele Scientific Institute, via Olgettina 58, 20132 Milan, Italy
- Center for Omics Sciences, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | | | - Lena Hoelzen
- Università Vita-Salute San Raffaele, via Olgettina 58, 20132 Milan, Italy
- Faculty of Biology, Albert-Ludwigs-University Freiburg, D79104 Freiburg, Germany
| | - Angelica Zocchi
- Università Vita-Salute San Raffaele, via Olgettina 58, 20132 Milan, Italy
| | - Alessandra Agresti
- IRCCS San Raffaele Scientific Institute, via Olgettina 58, 20132 Milan, Italy
| | - Marco E Bianchi
- Università Vita-Salute San Raffaele, via Olgettina 58, 20132 Milan, Italy
| |
Collapse
|
11
|
Ma M, Xiong W, Hu F, Deng MF, Huang X, Chen JG, Man HY, Lu Y, Liu D, Zhu LQ. A novel pathway regulates social hierarchy via lncRNA AtLAS and postsynaptic synapsin IIb. Cell Res 2020; 30:105-118. [PMID: 31959917 DOI: 10.1038/s41422-020-0273-1] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2019] [Accepted: 12/30/2019] [Indexed: 12/16/2022] Open
Abstract
Dominance hierarchy is a fundamental phenomenon in grouped animals and human beings, however, the underlying regulatory mechanisms remain elusive. Here, we report that an antisense long non-coding RNA (lncRNA) of synapsin II, named as AtLAS, plays a crucial role in the regulation of social hierarchy. AtLAS is decreased in the prefrontal cortical excitatory pyramidal neurons of dominant mice; consistently, silencing or overexpression of AtLAS increases or decreases the social rank, respectively. Mechanistically, we show that AtLAS regulates alternative polyadenylation of synapsin II gene and increases synapsin 2b (syn2b) expression. Syn2b reduces AMPA receptor (AMPAR)-mediated excitatory synaptic transmission through a direct binding with AMPAR at the postsynaptic site via its unique C-terminal sequence. Moreover, a peptide disrupting the binding of syn2b with AMPARs enhances the synaptic strength and social ranks. These findings reveal a novel role for lncRNA AtLAS and its target syn2b in the regulation of social behaviors by controlling postsynaptic AMPAR trafficking.
Collapse
Affiliation(s)
- Mei Ma
- Department of Pathophysiology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, 430030, China
| | - Wan Xiong
- Department of Pathophysiology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, 430030, China
| | - Fan Hu
- Department of Pathophysiology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, 430030, China
| | - Man-Fei Deng
- Department of Pathophysiology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, 430030, China
| | - Xian Huang
- Department of Pathophysiology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, 430030, China
| | - Jian-Guo Chen
- The Institute of Brain Research, Collaborative Innovation Center for Brain Science, Huazhong University of Science and Technology, Wuhan, Hubei, 430030, China
| | - Heng-Ye Man
- Department of Biology, Boston University, Boston, MA, 02215, USA
| | - Youming Lu
- The Institute of Brain Research, Collaborative Innovation Center for Brain Science, Huazhong University of Science and Technology, Wuhan, Hubei, 430030, China
| | - Dan Liu
- Department of Pathophysiology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, 430030, China. .,The Institute of Brain Research, Collaborative Innovation Center for Brain Science, Huazhong University of Science and Technology, Wuhan, Hubei, 430030, China.
| | - Ling-Qiang Zhu
- Department of Pathophysiology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, 430030, China. .,The Institute of Brain Research, Collaborative Innovation Center for Brain Science, Huazhong University of Science and Technology, Wuhan, Hubei, 430030, China.
| |
Collapse
|
12
|
Lee D, Liu J, Junn HJ, Lee EJ, Jeong KS, Seol DW. No more helper adenovirus: production of gutless adenovirus (GLAd) free of adenovirus and replication-competent adenovirus (RCA) contaminants. Exp Mol Med 2019; 51:1-18. [PMID: 31659156 PMCID: PMC6817846 DOI: 10.1038/s12276-019-0334-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2019] [Revised: 09/13/2019] [Accepted: 09/18/2019] [Indexed: 12/13/2022] Open
Abstract
Gene therapy is emerging as an effective treatment option for various inherited genetic diseases. Gutless adenovirus (GLAd), also known as helper-dependent adenovirus (HDAd), has many notable characteristics as a gene delivery vector for this particular type of gene therapy, including broad tropism, high infectivity, a large transgene cargo capacity, and an absence of integration into the host genome. Additionally, GLAd ensures long-term transgene expression in host organisms owing to its minimal immunogenicity, since it was constructed following the deletion of all the genes from an adenovirus. However, the clinical use of GLAd for the treatment of inherited genetic diseases has been hampered by unavoidable contamination of the highly immunogenic adenovirus used as a helper for GLAd production. Here, we report the production of GLAd in the absence of a helper adenovirus, which was achieved with a helper plasmid instead. Utilizing this helper plasmid, we successfully produced large quantities of recombinant GLAd. Importantly, our helper plasmid-based system exclusively produced recombinant GLAd with no generation of helper plasmid-originating adenovirus and replication-competent adenovirus (RCA). The recombinant GLAd that was produced efficiently delivered transgenes regardless of their size and exhibited therapeutic potential for Huntington’s disease (HD) and Duchenne muscular dystrophy (DMD). Our data indicate that our helper plasmid-based GLAd production system could become a new platform for GLAd-based gene therapy. A new protocol allows for the manufacturing of a next-generation gene therapy vector without contamination of helper adenovirus and replication-competent adenovirus (RCA). Adenoviruses are often used to deliver therapeutic DNA, but their proteins can trigger immune reactions. So-called ‘gutless’ adenoviruses that lack all viral genes don’t cause the same problem but their production has traditionally relied on a helper adenovirus that remains as an unavoidable contaminant. A team led by Dai-Wu Seol from Chung-Ang University in Seoul, South Korea, has now prepared large quantities of gutless adenoviruses using helper plasmid, a circular DNA that encodes all the proteins needed for production of gutless adenoviruses but do not leave behind any contaminant adenoviruses. Gutless adenoviruse vectors made this way successfully delivered corrected copies of the faulty genes responsible for human diseseas into human cells and mice.
Collapse
Affiliation(s)
- Dongwoo Lee
- Genenmed Inc., 84 Seongsuil-ro, Seongdong-gu, Seoul, Republic of Korea
| | - Jida Liu
- College of Pharmacy, Chung-Ang University, Seoul, Republic of Korea
| | - Hyun Jung Junn
- Genenmed Inc., 84 Seongsuil-ro, Seongdong-gu, Seoul, Republic of Korea
| | - Eun-Joo Lee
- Department of Veterinary Pathology, College of Veterinary Medicine, Kyungpook National University, Daegu City, Republic of Korea
| | - Kyu-Shik Jeong
- Department of Veterinary Pathology, College of Veterinary Medicine, Kyungpook National University, Daegu City, Republic of Korea
| | - Dai-Wu Seol
- College of Pharmacy, Chung-Ang University, Seoul, Republic of Korea.
| |
Collapse
|
13
|
Thynn HN, Chen XF, Hu WX, Duan YY, Zhu DL, Chen H, Wang NN, Chen HH, Rong Y, Lu BJ, Yang M, Jiang F, Dong SS, Guo Y, Yang TL. An Allele-Specific Functional SNP Associated with Two Systemic Autoimmune Diseases Modulates IRF5 Expression by Long-Range Chromatin Loop Formation. J Invest Dermatol 2019; 140:348-360.e11. [PMID: 31421124 DOI: 10.1016/j.jid.2019.06.147] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2019] [Revised: 06/02/2019] [Accepted: 06/18/2019] [Indexed: 02/07/2023]
Abstract
Both systemic lupus erythematosus (SLE) and systemic sclerosis (SSc) are autoimmune diseases sharing similar genetic backgrounds. Genome-wide association studies have constantly disclosed numerous genetic variants conferring to both disease risks at 7q32.1, but the functional mechanisms underlying them are still largely unknown. Through a series of bioinformatics and functional analyses, we prioritized a potential independent functional single-nucleotide polymorphism (rs13239597) within TNPO3 promoter region, residing in a putative enhancer element and validated that IRF5 is the distal target gene (∼118 kb) of rs13239597, which is a key regulator involved in pathogenic autoantibody dysregulation, increasing risk of both SLE and SSc. We experimentally validated the long-range chromatin interactions between rs13239597 and IRF5 using chromosome conformation capture assay. We further demonstrated that rs13239597-A acted as an allele-specific enhancer regulating IRF5 expression, independently of TNPO3 by using dual-luciferase reporter assays and CRISPR-Cas9. Particularly, the transcription factor EVI1 could preferentially bind to rs13239597-A allele and increase the enhancer activity to regulate IRF5 expression. Taken together, our results uncovered a mechanistic insight of a noncoding functional variant acting as an allele-specific distal enhancer to directly modulate IRF5 expression, which might obligate in understanding of complex genetic architectures of SLE and SSc pathogenesis.
Collapse
Affiliation(s)
- Hlaing Nwe Thynn
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi 710049, China
| | - Xiao-Feng Chen
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi 710049, China
| | - Wei-Xin Hu
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi 710049, China
| | - Yuan-Yuan Duan
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi 710049, China
| | - Dong-Li Zhu
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi 710049, China
| | - Hao Chen
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi 710049, China
| | - Nai-Ning Wang
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi 710049, China
| | - Huan-Huan Chen
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi 710049, China
| | - Yu Rong
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi 710049, China
| | - Bing-Jie Lu
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi 710049, China
| | - Man Yang
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi 710049, China
| | - Feng Jiang
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi 710049, China
| | - Shan-Shan Dong
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi 710049, China
| | - Yan Guo
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi 710049, China
| | - Tie-Lin Yang
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi 710049, China.
| |
Collapse
|
14
|
Zhu Q, Yu L, Qin Z, Chen L, Hu H, Zheng X, Zeng S. Regulation of OCT2 transcriptional repression by histone acetylation in renal cell carcinoma. Epigenetics 2019; 14:791-803. [PMID: 31088315 PMCID: PMC6615535 DOI: 10.1080/15592294.2019.1615354] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2018] [Revised: 04/16/2019] [Accepted: 04/26/2019] [Indexed: 12/15/2022] Open
Abstract
Renal cell carcinoma (RCC) is a common malignant tumour affecting the urinary system, and multidrug resistance is one of the major reasons why chemotherapy for this type of cancer often fails. Previous studies have shown that loss of the human organic cation transporter OCT2 is the main factor contributing to oxaliplatin resistance in RCC, and that DNA hypermethylation and histone methylation play important roles in the transcriptional repression of OCT2 in RCC. In this study, we found that histone acetylation also regulates OCT2 repression in RCC and elucidated the underlying mechanisms. In normal renal cells, HDAC7 combines with MYC at the OCT2 promoter, resulting in a decrease in free HDAC7, which in turn increases the levels of H3K18ac and H3K27ac at the OCT2 promotor and activates OCT2 expression. In RCC cells, however, the interaction between HDAC7 and MYC does not occur, which leads a high abundance of HDAC7 and low levels of H3K18ac and H3K27ac at the OCT2 promoter, thereby resulting in the inhibition of OCT2 transcription. We found that combined treatment using the DNA methylation inhibitor decitabine and the histone deacetylase inhibitor vorinostat significantly increased the expression of OCT2 in RCC cell lines, which sensitized these cells to oxaliplatin. We accordingly propose that the combination of anticancer agents and epigenetic drugs can provide a novel chemotherapeutic regimen.
Collapse
Affiliation(s)
- Qianying Zhu
- Institute of Drug Metabolism and Pharmaceutical Analysis, Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, China
| | - Lushan Yu
- Institute of Drug Metabolism and Pharmaceutical Analysis, Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, China
| | - Zhiyuan Qin
- Institute of Drug Metabolism and Pharmaceutical Analysis, Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, China
| | - Lu Chen
- Institute of Drug Metabolism and Pharmaceutical Analysis, Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, China
| | - Haihong Hu
- Institute of Drug Metabolism and Pharmaceutical Analysis, Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, China
| | - Xiaoli Zheng
- Hangzhou Cancer Institution, Hangzhou Cancer Hospital, Hangzhou, China
| | - Su Zeng
- Institute of Drug Metabolism and Pharmaceutical Analysis, Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, China
| |
Collapse
|
15
|
Park SK, Kee Y, Ryu T, Kim H, Hwang BJ. Enzymatic construction of shRNA library from oligonucleotide library. Genes Genomics 2019; 41:573-581. [PMID: 30830681 DOI: 10.1007/s13258-019-00800-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2018] [Accepted: 02/19/2019] [Indexed: 10/27/2022]
Abstract
BACKGROUND Short hairpin RNAs (shRNAs) expressed from vectors have been used as an effective means of exploiting the RNA interference (RNAi) pathway in mammalian cells. Genome-scale screening with shRNA libraries has been used to investigate the relationship between genotypes and phenotypes on a large scale. Although several methods have been developed to construct shRNA libraries, their broad application has been limited by the high cost of constructing these libraries. OBJECTIVE We develop a new method that efficiently constructs a shRNA library at low cost, using treatments with several enzymes and an oligonucleotide library. METHODS The library of shRNA expression cassettes, which were cloned into a lentiviral plasmid, was produced through several enzymatic reactions, starting from a library of 20,000 different short oligonucleotides produced by microarray-based oligonucleotide synthesis. RESULTS The NGS sequence analysis of the library shows that 99.8% of them (19,956 from 20,000 sequences) were contained in the library: 63.2% of them represent the correct sequences and the rest showed one or two base pair differences from the expected sequences. CONCLUSION Considering the ease of our method, shRNA libraries of new genomes and of specific populations of genes can be prepared in a short period of time for genome-scale RNAi library screening.
Collapse
Affiliation(s)
- Seong Kyun Park
- Department of Molecular Bioscience, College of Biomedical Science, Kangwon National University, Chuncheon, Kangwon-do, 24341, South Korea
| | - Yun Kee
- Division of Biomedical Convergence, College of Biomedical Science, Kangwon National University, Chuncheon, Kangwon-do, 24341, South Korea
| | - Taehoon Ryu
- Celemics, 19F, Bldg.A, BYC Highcity, 131, Gasandigital 1-ro,Geumcheon-gu, Seoul, 153-718, Republic of Korea
| | - Hyoki Kim
- Celemics, 19F, Bldg.A, BYC Highcity, 131, Gasandigital 1-ro,Geumcheon-gu, Seoul, 153-718, Republic of Korea
| | - Byung Joon Hwang
- Department of Molecular Bioscience, College of Biomedical Science, Kangwon National University, Chuncheon, Kangwon-do, 24341, South Korea.
| |
Collapse
|
16
|
Fu Z, Löfqvist CA, Liegl R, Wang Z, Sun Y, Gong Y, Liu CH, Meng SS, Burnim SB, Arellano I, Chouinard MT, Duran R, Poblete A, Cho SS, Akula JD, Kinter M, Ley D, Pupp IH, Talukdar S, Hellström A, Smith LE. Photoreceptor glucose metabolism determines normal retinal vascular growth. EMBO Mol Med 2019; 10:76-90. [PMID: 29180355 PMCID: PMC5760850 DOI: 10.15252/emmm.201707966] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
The neural cells and factors determining normal vascular growth are not well defined even though vision‐threatening neovessel growth, a major cause of blindness in retinopathy of prematurity (ROP) (and diabetic retinopathy), is driven by delayed normal vascular growth. We here examined whether hyperglycemia and low adiponectin (APN) levels delayed normal retinal vascularization, driven primarily by dysregulated photoreceptor metabolism. In premature infants, low APN levels correlated with hyperglycemia and delayed retinal vascular formation. Experimentally in a neonatal mouse model of postnatal hyperglycemia modeling early ROP, hyperglycemia caused photoreceptor dysfunction and delayed neurovascular maturation associated with changes in the APN pathway; recombinant mouse APN or APN receptor agonist AdipoRon treatment normalized vascular growth. APN deficiency decreased retinal mitochondrial metabolic enzyme levels particularly in photoreceptors, suppressed retinal vascular development, and decreased photoreceptor platelet‐derived growth factor (Pdgfb). APN pathway activation reversed these effects. Blockade of mitochondrial respiration abolished AdipoRon‐induced Pdgfb increase in photoreceptors. Photoreceptor knockdown of Pdgfb delayed retinal vascular formation. Stimulation of the APN pathway might prevent hyperglycemia‐associated retinal abnormalities and suppress phase I ROP in premature infants.
Collapse
Affiliation(s)
- Zhongjie Fu
- Department of Ophthalmology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - Chatarina A Löfqvist
- Section for Ophthalmology, Department of Clinical Neuroscience and Rehabilitation, Institute of Neuroscience and Physiology, Sahlgrenska Academy, University of Gothenburg, Göteborg, Sweden
| | - Raffael Liegl
- Department of Ophthalmology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - Zhongxiao Wang
- Department of Ophthalmology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - Ye Sun
- Department of Ophthalmology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - Yan Gong
- Department of Ophthalmology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - Chi-Hsiu Liu
- Department of Ophthalmology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - Steven S Meng
- Department of Ophthalmology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - Samuel B Burnim
- Department of Ophthalmology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - Ivana Arellano
- Department of Ophthalmology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | | | - Rubi Duran
- Department of Ophthalmology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - Alexander Poblete
- Department of Ophthalmology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - Steve S Cho
- Department of Ophthalmology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - James D Akula
- Department of Ophthalmology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - Michael Kinter
- Aging and Metabolism Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, USA
| | - David Ley
- Pediatrics, Department of Clinical Sciences, Skåne University Hospital and University of Lund, Lund, Sweden
| | - Ingrid Hansen Pupp
- Pediatrics, Department of Clinical Sciences, Skåne University Hospital and University of Lund, Lund, Sweden
| | | | - Ann Hellström
- Section for Ophthalmology, Department of Clinical Neuroscience and Rehabilitation, Institute of Neuroscience and Physiology, Sahlgrenska Academy, University of Gothenburg, Göteborg, Sweden
| | - Lois Eh Smith
- Department of Ophthalmology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| |
Collapse
|
17
|
Bernard S, Myers M, Fang WB, Zinda B, Smart C, Lambert D, Zou A, Fan F, Cheng N. CXCL1 Derived from Mammary Fibroblasts Promotes Progression of Mammary Lesions to Invasive Carcinoma through CXCR2 Dependent Mechanisms. J Mammary Gland Biol Neoplasia 2018; 23:249-267. [PMID: 30094610 PMCID: PMC6582941 DOI: 10.1007/s10911-018-9407-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/17/2017] [Accepted: 07/24/2018] [Indexed: 12/21/2022] Open
Abstract
With improved screening methods, the numbers of abnormal breast lesions diagnosed in women have been increasing over time. However, it remains unclear whether these breast lesions will develop into invasive cancers. To more effectively predict the outcome of breast lesions and determine a more appropriate course of treatment, it is important to understand the underlying mechanisms that regulate progression of non-invasive lesions to invasive breast cancers. A hallmark of invasive breast cancers is the accumulation of fibroblasts. Fibroblast proliferation and activation in the mammary gland is in part regulated by the Transforming Growth Factor beta1 pathway (TGF-β). In animal models, TGF-β suppression of CCL2 and CXCL1 chemokine expression is associated with metastatic progression of mammary carcinomas. Here, we show that transgenic overexpression of the Polyoma middle T viral antigen in the mouse mammary gland of C57BL/6 mice results in slow growing non-invasive lesions that progress to invasive carcinomas in a stage dependent manner. Invasive carcinomas are associated with accumulation of fibroblasts that show decreased TGF-β expression and high levels of CXCL1, but not CCL2. Using co-transplant models, we show that decreased TGF-β signaling in fibroblasts contribute to mammary carcinoma progression through enhancement of CXCL1/CXCR2 dependent mechanisms. Using cell culture models, we show that CXCL1 mediated mammary carcinoma cell invasion through NF-κB, AKT, Stat3 and p42/44MAPK dependent mechanisms. These studies provide novel mechanistic insight into the progression of pre-invasive lesions and identify new stromal biomarkers, with important prognostic implications.
Collapse
Affiliation(s)
- Shira Bernard
- Department of Pathology and Laboratory Medicine, University of Kansas Medical Center, Kansas City, KS, 66160, USA
| | - Megan Myers
- Department of Pathology and Laboratory Medicine, University of Kansas Medical Center, Kansas City, KS, 66160, USA
| | - Wei Bin Fang
- Department of Pathology and Laboratory Medicine, University of Kansas Medical Center, Kansas City, KS, 66160, USA
| | - Brandon Zinda
- Department of Pathology and Laboratory Medicine, University of Kansas Medical Center, Kansas City, KS, 66160, USA
| | - Curtis Smart
- Department of Pathology and Laboratory Medicine, University of Kansas Medical Center, Kansas City, KS, 66160, USA
| | - Diana Lambert
- Department of Pathology and Laboratory Medicine, University of Kansas Medical Center, Kansas City, KS, 66160, USA
| | - An Zou
- Department of Pathology and Laboratory Medicine, University of Kansas Medical Center, Kansas City, KS, 66160, USA
| | - Fang Fan
- Department of Pathology and Laboratory Medicine, University of Kansas Medical Center, Kansas City, KS, 66160, USA
| | - Nikki Cheng
- Department of Pathology and Laboratory Medicine, University of Kansas Medical Center, Kansas City, KS, 66160, USA.
| |
Collapse
|
18
|
Phosphorylation of ULK1 affects autophagosome fusion and links chaperone-mediated autophagy to macroautophagy. Nat Commun 2018; 9:3492. [PMID: 30154410 PMCID: PMC6113293 DOI: 10.1038/s41467-018-05449-1] [Citation(s) in RCA: 117] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2016] [Accepted: 04/12/2018] [Indexed: 11/09/2022] Open
Abstract
The Unc-51 like autophagy activating kinase 1 (ULK1) complex plays a central role in the initiation stage of autophagy. However, the function of ULK1 in the late stage of autophagy is unknown. Here, we report that ULK1, a central kinase of the ULK1 complex involved in autophagy initiation, promotes autophagosome–lysosome fusion. PKCα phosphorylates ULK1 and prevents autolysosome formation. PKCα phosphorylation of ULK1 does not change its kinase activity; however, it decreases autophagosome–lysosome fusion by reducing the affinity of ULK1 for syntaxin 17 (STX17). Unphosphorylated ULK1 recruited STX17 and increased STX17′s affinity towards synaptosomal-associated protein 29 (SNAP29). Additionally, phosphorylation of ULK1 enhances its interaction with heat shock cognate 70 kDa protein (HSC70) and increases its degradation through chaperone-mediated autophagy (CMA). Our study unearths a key mechanism underlying autolysosome formation, a process in which the kinase activity of PKCα plays an instrumental role, and reveals the significance of the mutual regulation of macroautophagy and CMA in maintaining the balance of autophagy. The ULK complex plays a well-known role in initiating autophagy, to recycle cellular components in response to nutritional stress. Here, the authors demonstrate a late role for ULK in auotophagosome–lysosome fusion and provide a direct link between macroautophagy and chaperone mediated autophagy.
Collapse
|
19
|
Chen L, Chen JY, Huang YJ, Gu Y, Qiu J, Qian H, Shao C, Zhang X, Hu J, Li H, He S, Zhou Y, Abdel-Wahab O, Zhang DE, Fu XD. The Augmented R-Loop Is a Unifying Mechanism for Myelodysplastic Syndromes Induced by High-Risk Splicing Factor Mutations. Mol Cell 2018; 69:412-425.e6. [PMID: 29395063 PMCID: PMC5957072 DOI: 10.1016/j.molcel.2017.12.029] [Citation(s) in RCA: 198] [Impact Index Per Article: 33.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2017] [Revised: 11/29/2017] [Accepted: 12/28/2017] [Indexed: 11/24/2022]
Abstract
Mutations in several general pre-mRNA splicing factors have been linked to myelodysplastic syndromes (MDSs) and solid tumors. These mutations have generally been assumed to cause disease by the resultant splicing defects, but different mutations appear to induce distinct splicing defects, raising the possibility that an alternative common mechanism is involved. Here we report a chain of events triggered by multiple splicing factor mutations, especially high-risk alleles in SRSF2 and U2AF1, including elevated R-loops, replication stress, and activation of the ataxia telangiectasia and Rad3-related protein (ATR)-Chk1 pathway. We further demonstrate that enhanced R-loops, opposite to the expectation from gained RNA binding with mutant SRSF2, result from impaired transcription pause release because the mutant protein loses its ability to extract the RNA polymerase II (Pol II) C-terminal domain (CTD) kinase-the positive transcription elongation factor complex (P-TEFb)-from the 7SK complex. Enhanced R-loops are linked to compromised proliferation of bone-marrow-derived blood progenitors, which can be partially rescued by RNase H overexpression, suggesting a direct contribution of augmented R-loops to the MDS phenotype.
Collapse
Affiliation(s)
- Liang Chen
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92093-0651, USA
| | - Jia-Yu Chen
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92093-0651, USA
| | - Yi-Jou Huang
- Department of Pathology, Moores Cancer Center, University of California, San Diego, La Jolla, CA 92093-0651, USA
| | - Ying Gu
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92093-0651, USA
| | - Jinsong Qiu
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92093-0651, USA
| | - Hao Qian
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92093-0651, USA
| | - Changwei Shao
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92093-0651, USA
| | - Xuan Zhang
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92093-0651, USA
| | - Jing Hu
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92093-0651, USA
| | - Hairi Li
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92093-0651, USA
| | - Shunmin He
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Yu Zhou
- College of Life Sciences and Institute for Advanced Studies, Wuhan University, Wuhan, Hubei 40072, China
| | - Omar Abdel-Wahab
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center and Weill Cornel Medical College, New York, NY 10065, USA
| | - Dong-Er Zhang
- Department of Pathology, Moores Cancer Center, University of California, San Diego, La Jolla, CA 92093-0651, USA.
| | - Xiang-Dong Fu
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92093-0651, USA; Institute of Genomic Medicine, University of California, San Diego, La Jolla, CA 92093-0651, USA.
| |
Collapse
|
20
|
Smith LK, Boukhaled GM, Condotta SA, Mazouz S, Guthmiller JJ, Vijay R, Butler NS, Bruneau J, Shoukry NH, Krawczyk CM, Richer MJ. Interleukin-10 Directly Inhibits CD8 + T Cell Function by Enhancing N-Glycan Branching to Decrease Antigen Sensitivity. Immunity 2018; 48:299-312.e5. [PMID: 29396160 DOI: 10.1016/j.immuni.2018.01.006] [Citation(s) in RCA: 163] [Impact Index Per Article: 27.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2017] [Revised: 09/01/2017] [Accepted: 01/02/2018] [Indexed: 01/29/2023]
Abstract
Chronic viral infections remain a global health concern. The early events that facilitate viral persistence have been linked to the activity of the immunoregulatory cytokine IL-10. However, the mechanisms by which IL-10 facilitates the establishment of chronic infection are not fully understood. Herein, we demonstrated that the antigen sensitivity of CD8+ T cells was decreased during chronic infection and that this was directly mediated by IL-10. Mechanistically, we showed that IL-10 induced the expression of Mgat5, a glycosyltransferase that enhances N-glycan branching on surface glycoproteins. Increased N-glycan branching on CD8+ T cells promoted the formation of a galectin 3-mediated membrane lattice, which restricted the interaction of key glycoproteins, ultimately increasing the antigenic threshold required for T cell activation. Our study identified a regulatory loop in which IL-10 directly restricts CD8+ T cell activation and function through modification of cell surface glycosylation allowing the establishment of chronic infection.
Collapse
Affiliation(s)
- Logan K Smith
- Department of Microbiology and Immunology, McGill University, Montreal, QC, Canada; Microbiome and Disease Tolerance Centre, McGill University, Montreal, QC, Canada
| | - Giselle M Boukhaled
- Department of Physiology, Rosalind and Morris Goodman Cancer Research Centre, McGill University, Montreal, QC, Canada
| | - Stephanie A Condotta
- Department of Microbiology and Immunology, McGill University, Montreal, QC, Canada; Microbiome and Disease Tolerance Centre, McGill University, Montreal, QC, Canada
| | - Sabrina Mazouz
- Centre de Recherche du Centre hospitalier de l'Université de Montréal (CRCHUM), Montreal, QC, Canada; Department of Microbiology, Immunology and Infectiology, Université de Montréal, Montreal, QC, Canada
| | - Jenna J Guthmiller
- Department of Microbiology and Immunology, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
| | - Rahul Vijay
- Department of Microbiology and Immunology, University of Iowa, Iowa City, IA, USA
| | - Noah S Butler
- Department of Microbiology and Immunology, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA; Department of Microbiology and Immunology, University of Iowa, Iowa City, IA, USA
| | - Julie Bruneau
- Centre de Recherche du Centre hospitalier de l'Université de Montréal (CRCHUM), Montreal, QC, Canada; Department of Family Medicine and Emergency Medicine, Université de Montréal, Montreal, QC, Canada
| | - Naglaa H Shoukry
- Centre de Recherche du Centre hospitalier de l'Université de Montréal (CRCHUM), Montreal, QC, Canada; Department of Medicine, Université de Montréal, Montreal, QC, Canada
| | - Connie M Krawczyk
- Department of Microbiology and Immunology, McGill University, Montreal, QC, Canada; Department of Physiology, Rosalind and Morris Goodman Cancer Research Centre, McGill University, Montreal, QC, Canada
| | - Martin J Richer
- Department of Microbiology and Immunology, McGill University, Montreal, QC, Canada; Microbiome and Disease Tolerance Centre, McGill University, Montreal, QC, Canada.
| |
Collapse
|
21
|
Zhao L, Wang B, Zhao X, Wu X, Zhang Q, Wei C, Shi M, Li Y, Tang W, Zhang J, Yang J, Singh SK, Jia S, Luo Y. Gain of function in the mouse model of a recurrent mutation p53 N236S promotes the formation of double minute chromosomes and the oncogenic potential of p19 ARF. Mol Carcinog 2017; 57:147-158. [PMID: 28949402 DOI: 10.1002/mc.22737] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2017] [Revised: 08/11/2017] [Accepted: 09/05/2017] [Indexed: 01/08/2023]
Abstract
The mutation p53N236S (p53S) has been identified as one of the recurrent mutations in human cancers by TCGA database. Our in vitro data revealed the oncogenic gain of function of p53S. To understand the function of p53S in vivo, we generated the p53S knock-in mouse. The p53S/S mice manifested highly invasive lymphomas and metastatic sarcomas with dramatically increased double minute chromosomes. The survival curve, the incidence of tumors and the tumor spectrum of p53S/S mice is very similar to the p53R172H mouse model. The p53S/+ mice showed delayed onset of tumorigenesis and a high metastasis rate (40%) and low loss of heterozygosity rate (2/16). The activation of CDKN2A pathway in p53S/S MEF and tumors, and the accumulation of p19ARF protein in tumor tissues suggested p19ARF might contribute to the accumulation of mutant p53S protein in the tumor and promote tumorigenesis. The high expression of p19ARF correlated with mutant p53 accumulation and tumor progression, suggesting a dual role of p19ARF in tumor promotion or suppression that might depend on the p53 mutation status in tumor cells. The oncogenic gain of function of this recurrent mutation p53S prompts the reconsideration of p53 mutations function that occurs at a low frequency.
Collapse
Affiliation(s)
- Lanjun Zhao
- Lab of Molecular Genetics of Aging and Tumor, Faculty of Medicine, Kunming University of Science and Technology, Kunming, Yunnan Province, China.,Faculty of Environmental Science and Engineering, Kunming University of Science and Technology, Kunming, Yunnan Province, China
| | - Boyuan Wang
- Lab of Molecular Genetics of Aging and Tumor, Faculty of Medicine, Kunming University of Science and Technology, Kunming, Yunnan Province, China.,Faculty of Environmental Science and Engineering, Kunming University of Science and Technology, Kunming, Yunnan Province, China
| | - Xilong Zhao
- Department of Pathology, Kunming General Hospital, Kunming, Yunnan Province, China
| | - Xiaoming Wu
- Lab of Molecular Genetics of Aging and Tumor, Faculty of Medicine, Kunming University of Science and Technology, Kunming, Yunnan Province, China
| | - Qiushi Zhang
- Lab of Molecular Genetics of Aging and Tumor, Faculty of Medicine, Kunming University of Science and Technology, Kunming, Yunnan Province, China
| | - Chuanyu Wei
- Lab of Molecular Genetics of Aging and Tumor, Faculty of Medicine, Kunming University of Science and Technology, Kunming, Yunnan Province, China.,Faculty of Environmental Science and Engineering, Kunming University of Science and Technology, Kunming, Yunnan Province, China
| | - Minling Shi
- Lab of Molecular Genetics of Aging and Tumor, Faculty of Medicine, Kunming University of Science and Technology, Kunming, Yunnan Province, China
| | - Yunlong Li
- Lab of Molecular Genetics of Aging and Tumor, Faculty of Medicine, Kunming University of Science and Technology, Kunming, Yunnan Province, China
| | - Wenru Tang
- Lab of Molecular Genetics of Aging and Tumor, Faculty of Medicine, Kunming University of Science and Technology, Kunming, Yunnan Province, China
| | - Jihong Zhang
- Lab of Molecular Genetics of Aging and Tumor, Faculty of Medicine, Kunming University of Science and Technology, Kunming, Yunnan Province, China
| | - Julun Yang
- Department of Pathology, Kunming General Hospital, Kunming, Yunnan Province, China
| | - Sanjay K Singh
- Department of Diagnostic Radiology, MD Anderson Cancer Center, Houston, Texas
| | - Shuting Jia
- Lab of Molecular Genetics of Aging and Tumor, Faculty of Medicine, Kunming University of Science and Technology, Kunming, Yunnan Province, China
| | - Ying Luo
- Lab of Molecular Genetics of Aging and Tumor, Faculty of Medicine, Kunming University of Science and Technology, Kunming, Yunnan Province, China.,Faculty of Environmental Science and Engineering, Kunming University of Science and Technology, Kunming, Yunnan Province, China.,Yunnan Provincial Institute of Digestive Disease, Yunnan Province, China
| |
Collapse
|
22
|
Avivi S, Mor A, Dotan I, Tzadok S, Kanter I, Kinor N, Canaani D, Shav-Tal Y. Visualizing nuclear RNAi activity in single living human cells. Proc Natl Acad Sci U S A 2017; 114:E8837-E8846. [PMID: 29073029 PMCID: PMC5651755 DOI: 10.1073/pnas.1707440114] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
Nuclear RNA interference (RNAi) is mediated by the canonical RNAi machinery and can lead to transcriptional silencing, transcriptional activation, or modulation of alternative splicing patterns. These effects transpire through changes in histone and DNA modifications via RNAi-mediated recruitment of chromatin-modifying enzymes. To prove that nuclear RNAi occurs and modulates transcription in human cells, we used live-cell imaging to detect and track nuclear RNAi transcriptional repression in single living human cells. While employing reporter genes constructed with inducible promoters and cognate-inducible short hairpin RNA (shRNA) targeted against the reporter coding region, we have characterized the dynamics of the nuclear RNAi process in living human cells. We show that the silencing effect is mediated through the nascent mRNA, followed by activity of histone methylating enzymes, but not through DNA methylation.
Collapse
Affiliation(s)
- Shira Avivi
- The Mina & Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan 5290002, Israel
- Institute of Nanotechnology, Bar-Ilan University, Ramat Gan 5290002, Israel
| | - Amir Mor
- The Mina & Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan 5290002, Israel
- Institute of Nanotechnology, Bar-Ilan University, Ramat Gan 5290002, Israel
| | - Iris Dotan
- Department of Biochemistry & Molecular Biology, Faculty of Life Sciences, Tel-Aviv University, Tel Aviv 6997801, Israel
| | - Sivan Tzadok
- Department of Biochemistry & Molecular Biology, Faculty of Life Sciences, Tel-Aviv University, Tel Aviv 6997801, Israel
| | - Itamar Kanter
- The Mina & Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan 5290002, Israel
- Institute of Nanotechnology, Bar-Ilan University, Ramat Gan 5290002, Israel
| | - Noa Kinor
- The Mina & Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan 5290002, Israel
- Institute of Nanotechnology, Bar-Ilan University, Ramat Gan 5290002, Israel
| | - Dan Canaani
- Department of Biochemistry & Molecular Biology, Faculty of Life Sciences, Tel-Aviv University, Tel Aviv 6997801, Israel
| | - Yaron Shav-Tal
- The Mina & Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan 5290002, Israel;
- Institute of Nanotechnology, Bar-Ilan University, Ramat Gan 5290002, Israel
| |
Collapse
|
23
|
Szlachcic WJ, Wiatr K, Trzeciak M, Figlerowicz M, Figiel M. The Generation of Mouse and Human Huntington Disease iPS Cells Suitable for In vitro Studies on Huntingtin Function. Front Mol Neurosci 2017; 10:253. [PMID: 28848389 PMCID: PMC5550714 DOI: 10.3389/fnmol.2017.00253] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2017] [Accepted: 07/26/2017] [Indexed: 01/24/2023] Open
Abstract
Huntington disease (HD) is an incurable neurodegenerative disorder caused by expansion of CAG repeats in huntingtin (HTT) gene, resulting in expanded polyglutamine tract in HTT protein. Although, HD has its common onset in adulthood, subtle symptoms in patients may occur decades before diagnosis, and molecular and cellular changes begin much earlier, even in cells that are not yet lineage committed such as stem cells. Studies in induced pluripotent stem cell (iPSC) HD models have demonstrated that multiple molecular processes are altered by the mutant HTT protein and suggested its silencing as a promising therapeutic strategy. Therefore, we aimed to generate HD iPS cells with stable silencing of HTT and further to investigate the effects of HTT knock-down on deregulations of signaling pathways e.g., p53 downregulation, present in cells already in pluripotent state. We designed a gene silencing strategy based on RNAi cassette in piggyBAC vector for constant shRNA expression. Using such system we delivered and tested several shRNA targeting huntingtin in mouse HD YAC128 iPSC and human HD109, HD71, and Control iPSC. The most effective shRNA (shHTT2) reagent stably silenced HTT in all HD iPS cells and remained active upon differentiation to neural stem cells (NSC). When investigating the effects of HTT silencing on signaling pathways, we found that in mouse HD iPSC lines expressing shRNA the level of mutant HTT inversely correlated with p53 levels, resulting in p53 level normalization upon silencing of mutant HTT. We also found that p53 deregulation continues into the NSC developmental stage and it was reversed upon HTT silencing. In addition, we observed subtle effects of silencing on proteins of Wnt/β-catenin and ERK1/2 signaling pathways. In summary, we successfully created the first mouse and human shRNA-expressing HD iPS cells with stable and continuous HTT silencing. Moreover, we demonstrated reversal of HD p53 phenotype in mouse HD iPSC, therefore, the stable knockdown of HTT is well-suited for investigation on HD cellular pathways, and is potentially useful as a stand-alone therapy or component of cell therapy. In addition, the total HTT knock-down in our human cells has further implications for mutant allele selective approach in iPSC.
Collapse
Affiliation(s)
- Wojciech J Szlachcic
- Department of Molecular Neurobiology, Institute of Bioorganic Chemistry, Polish Academy of SciencesPoznań, Poland
| | - Kalina Wiatr
- Department of Molecular Neurobiology, Institute of Bioorganic Chemistry, Polish Academy of SciencesPoznań, Poland
| | - Marta Trzeciak
- Department of Molecular Neurobiology, Institute of Bioorganic Chemistry, Polish Academy of SciencesPoznań, Poland
| | - Marek Figlerowicz
- Department of Molecular and Systems Biology, Institute of Bioorganic Chemistry, Polish Academy of SciencesPoznań, Poland
| | - Maciej Figiel
- Department of Molecular Neurobiology, Institute of Bioorganic Chemistry, Polish Academy of SciencesPoznań, Poland
| |
Collapse
|
24
|
Song H, Wang D, De Jesus Perez F, Xie R, Liu Z, Chen CC, Yu M, Yuan L, Fernald RD, Zhao S. Rhythmic expressed clock regulates the transcription of proliferating cellular nuclear antigen in teleost retina. Exp Eye Res 2017; 160:21-30. [PMID: 28434813 DOI: 10.1016/j.exer.2017.04.004] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2016] [Revised: 03/30/2017] [Accepted: 04/11/2017] [Indexed: 11/28/2022]
Abstract
Teleost fish continues to grow their eyes throughout life with the body size. In Astatotilapia burtoni, the fish retina increases by adding new retinal cells at the ciliary marginal zone (CMZ) and in the outer nuclear layer (ONL). Cell proliferation at both sites exhibits a daily rhythm in number of dividing cells. To understand how this diurnal rhythm of new cell production is controlled in retinal progenitor cells, we studied the transcription pattern of clock genes in retina, including clock1a, clock1b, bmal1a (brain and muscle ARNT-Like), and per1b (period1b). We found that these genes have a strong diurnal rhythmic transcription during light-dark cycles but not in constant darkness. An oscillation in pcna transcription was also observed during light-dark cycles, but again not in constant darkness. Our results also indicate an association between Clock proteins and the upstream region of pcna (proliferating cellular nuclear antigen) gene. A luciferase reporter assay conducted in an inducible clock knockdown cell line further demonstrated that the mutation on predicted E-Boxes in pcna promoter region significantly attenuated the transcriptional activation induced by Clock protein. These results suggested that the diurnal rhythmic expression of clock genes in A. burtoni retina could be light dependent and might contribute to the daily regulation of the proliferation of the retina progenitors through key components of cell cycle machinery, for instance, pcna.
Collapse
Affiliation(s)
- Hang Song
- The Key Laboratory of Developmental Genes and Human Disease, Institute of Life Sciences, Southeast University, #2 Sipailou Road, Nanjing, Jiangsu Province 210096, China; Department of Biochemistry and Molecular Biology, School of Medicine, Southeast University, #87, Dingjiaqiao Road, Nanjing, Jiangsu Province 210009, China
| | - Defeng Wang
- The Key Laboratory of Developmental Genes and Human Disease, Institute of Life Sciences, Southeast University, #2 Sipailou Road, Nanjing, Jiangsu Province 210096, China; Department of Biochemistry and Molecular Biology, School of Medicine, Southeast University, #87, Dingjiaqiao Road, Nanjing, Jiangsu Province 210009, China
| | - Felipe De Jesus Perez
- Department of Biology & Program in Neuroscience, Stanford University, Stanford, CA 94305-5020, USA
| | - Rongrong Xie
- Department of Biochemistry and Molecular Biology, School of Medicine, Southeast University, #87, Dingjiaqiao Road, Nanjing, Jiangsu Province 210009, China
| | - Zhipeng Liu
- Department of Biochemistry and Molecular Biology, School of Medicine, Southeast University, #87, Dingjiaqiao Road, Nanjing, Jiangsu Province 210009, China
| | - Chun-Chun Chen
- Department of Biology & Program in Neuroscience, Stanford University, Stanford, CA 94305-5020, USA
| | - Meijuan Yu
- The Key Laboratory of Developmental Genes and Human Disease, Institute of Life Sciences, Southeast University, #2 Sipailou Road, Nanjing, Jiangsu Province 210096, China; Department of Biochemistry and Molecular Biology, School of Medicine, Southeast University, #87, Dingjiaqiao Road, Nanjing, Jiangsu Province 210009, China
| | - Liudi Yuan
- The Key Laboratory of Developmental Genes and Human Disease, Institute of Life Sciences, Southeast University, #2 Sipailou Road, Nanjing, Jiangsu Province 210096, China; Department of Biochemistry and Molecular Biology, School of Medicine, Southeast University, #87, Dingjiaqiao Road, Nanjing, Jiangsu Province 210009, China
| | - Russell D Fernald
- Department of Biology & Program in Neuroscience, Stanford University, Stanford, CA 94305-5020, USA.
| | - Sheng Zhao
- The Key Laboratory of Developmental Genes and Human Disease, Institute of Life Sciences, Southeast University, #2 Sipailou Road, Nanjing, Jiangsu Province 210096, China; Department of Biochemistry and Molecular Biology, School of Medicine, Southeast University, #87, Dingjiaqiao Road, Nanjing, Jiangsu Province 210009, China.
| |
Collapse
|
25
|
Yu Q, Liu Y, Zheng X, Zhu Q, Shen Z, Wang H, He H, Lin N, Jiang H, Yu L, Zeng S. Histone H3 Lysine 4 Trimethylation, Lysine 27 Trimethylation, and Lysine 27 Acetylation Contribute to the Transcriptional Repression of Solute Carrier Family 47 Member 2 in Renal Cell Carcinoma. Drug Metab Dispos 2016; 45:109-117. [DOI: 10.1124/dmd.116.073734] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2016] [Accepted: 11/02/2016] [Indexed: 02/03/2023] Open
|
26
|
Putative Cell Adhesion Membrane Protein Vstm5 Regulates Neuronal Morphology and Migration in the Central Nervous System. J Neurosci 2016; 36:10181-97. [PMID: 27683913 DOI: 10.1523/jneurosci.0541-16.2016] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2016] [Accepted: 08/16/2016] [Indexed: 11/21/2022] Open
Abstract
UNLABELLED During brain development, dynamic changes in neuronal membranes perform critical roles in neuronal morphogenesis and migration to create functional neural circuits. Among the proteins that induce membrane dynamics, cell adhesion molecules are important in neuronal membrane plasticity. Here, we report that V-set and transmembrane domain-containing protein 5 (Vstm5), a cell-adhesion-like molecule belonging to the Ig superfamily, was found in mouse brain. Knock-down of Vstm5 in cultured hippocampal neurons markedly reduced the complexity of dendritic structures, as well as the number of dendritic filopodia. Vstm5 also regulates neuronal morphology by promoting dendritic protrusions that later develop into dendritic spines. Using electroporation in utero, we found that Vstm5 overexpression delayed neuronal migration and induced multiple branches in leading processes during corticogenesis. These results indicate that Vstm5 is a new cell-adhesion-like molecule and is critically involved in synaptogenesis and corticogenesis by promoting neuronal membrane dynamics. SIGNIFICANCE STATEMENT Neuronal migration and morphogenesis play critical roles in brain development and function. In this study, we demonstrate for the first time that V-set and transmembrane domain-containing protein 5 (Vstm5), a putative cell adhesion membrane protein, modulates both the position and complexity of central neurons by altering their membrane morphology and dynamics. Vstm5 is also one of the target genes responsible for variations in patient responses to treatments for major depressive disorder. Our results provide the first evidence that Vstm5 is a novel factor involved in the modulation of the neuronal membrane and a critical element in normal neural circuit formation during mammalian brain development.
Collapse
|
27
|
The Transcriptional Repressor Polycomb Group Factor 6, PCGF6, Negatively Regulates Dendritic Cell Activation and Promotes Quiescence. Cell Rep 2016; 16:1829-37. [PMID: 27498878 DOI: 10.1016/j.celrep.2016.07.026] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2015] [Revised: 05/25/2016] [Accepted: 07/13/2016] [Indexed: 11/20/2022] Open
Abstract
Pro-inflammatory signals provided by the microenvironment are critical to activate dendritic cells (DCs), components of the innate immune system that shape both innate and adaptive immunity. However, to prevent inappropriate immune activation, mechanisms must be in place to restrain DC activation to ensure DCs are activated only once sufficient stimuli have been received. Here, we report that DC activation and immunogenicity are regulated by the transcriptional repressor Polycomb group factor 6 (PCGF6). Pcgf6 is rapidly downregulated upon stimulation, and this downregulation is necessary to permit full DC activation. Silencing PCGF6 expression enhanced both spontaneous and stimulated DC activation. We show that PCGF6 associates with the H3K4me3 demethylase JARID1c, and together, they negatively regulate H3K4me3 levels in DCs. Our results identify two key regulators, PCGF6 and JARID1c that temper DC activation and implicate active transcriptional silencing via histone demethylation as a previously unappreciated mechanism for regulating DC activation and quiescence.
Collapse
|
28
|
Gerin I, Ury B, Breloy I, Bouchet-Seraphin C, Bolsée J, Halbout M, Graff J, Vertommen D, Muccioli GG, Seta N, Cuisset JM, Dabaj I, Quijano-Roy S, Grahn A, Van Schaftingen E, Bommer GT. ISPD produces CDP-ribitol used by FKTN and FKRP to transfer ribitol phosphate onto α-dystroglycan. Nat Commun 2016; 7:11534. [PMID: 27194101 PMCID: PMC4873967 DOI: 10.1038/ncomms11534] [Citation(s) in RCA: 98] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2015] [Accepted: 04/06/2016] [Indexed: 01/27/2023] Open
Abstract
Mutations in genes required for the glycosylation of α-dystroglycan lead to muscle and brain diseases known as dystroglycanopathies. However, the precise structure and biogenesis of the assembled glycan are not completely understood. Here we report that three enzymes mutated in dystroglycanopathies can collaborate to attach ribitol phosphate onto α-dystroglycan. Specifically, we demonstrate that isoprenoid synthase domain-containing protein (ISPD) synthesizes CDP-ribitol, present in muscle, and that both recombinant fukutin (FKTN) and fukutin-related protein (FKRP) can transfer a ribitol phosphate group from CDP-ribitol to α-dystroglycan. We also show that ISPD and FKTN are essential for the incorporation of ribitol into α-dystroglycan in HEK293 cells. Glycosylation of α-dystroglycan in fibroblasts from patients with hypomorphic ISPD mutations is reduced. We observe that in some cases glycosylation can be partially restored by addition of ribitol to the culture medium, suggesting that dietary supplementation with ribitol should be evaluated as a therapy for patients with ISPD mutations.
Collapse
Affiliation(s)
- Isabelle Gerin
- WELBIO and de Duve Institute, Biological Chemistry, Université Catholique de Louvain, B-1200 Brussels, Belgium
| | - Benoît Ury
- WELBIO and de Duve Institute, Biological Chemistry, Université Catholique de Louvain, B-1200 Brussels, Belgium
| | - Isabelle Breloy
- Institute for Biochemistry II, Medical Faculty, University of Cologne, D-50931 Cologne, Germany
| | - Céline Bouchet-Seraphin
- AP-HP, Hôpital Bichat-Claude Bernard, Laboratoire de Biochimie Métabolique et Cellulaire, F-75018 Paris, France
| | - Jennifer Bolsée
- WELBIO and de Duve Institute, Biological Chemistry, Université Catholique de Louvain, B-1200 Brussels, Belgium
| | - Mathias Halbout
- WELBIO and de Duve Institute, Biological Chemistry, Université Catholique de Louvain, B-1200 Brussels, Belgium
| | - Julie Graff
- WELBIO and de Duve Institute, Biological Chemistry, Université Catholique de Louvain, B-1200 Brussels, Belgium
| | - Didier Vertommen
- WELBIO and de Duve Institute, Biological Chemistry, Université Catholique de Louvain, B-1200 Brussels, Belgium
| | - Giulio G Muccioli
- Louvain Drug Research Institute, Université Catholique de Louvain, B-1200 Brussels, Belgium
| | - Nathalie Seta
- AP-HP, Hôpital Bichat-Claude Bernard, Laboratoire de Biochimie Métabolique et Cellulaire, F-75018 Paris, France
| | - Jean-Marie Cuisset
- Hôpital Roger-Salengro, Service de neuropédiatrie, Centre de Référence des Maladies Neuromusculaires, CHRU, F-59000 Lille, France
| | - Ivana Dabaj
- AP-HP, Hôpital R Poincaré, Service de pédiatrie, F-92380 Garches, France
| | - Susana Quijano-Roy
- AP-HP, Hôpital R Poincaré, Service de pédiatrie, F-92380 Garches, France.,Centre de Référence des Maladies Neuromusculaires, F-92380 Garches, France.,Université de Versailles-St Quentin, U1179 UVSQ - INSERM, F-78180 Montigny, France
| | - Ammi Grahn
- WELBIO and de Duve Institute, Biological Chemistry, Université Catholique de Louvain, B-1200 Brussels, Belgium
| | - Emile Van Schaftingen
- WELBIO and de Duve Institute, Biological Chemistry, Université Catholique de Louvain, B-1200 Brussels, Belgium
| | - Guido T Bommer
- WELBIO and de Duve Institute, Biological Chemistry, Université Catholique de Louvain, B-1200 Brussels, Belgium
| |
Collapse
|
29
|
Slebe F, Rojo F, Vinaixa M, García-Rocha M, Testoni G, Guiu M, Planet E, Samino S, Arenas EJ, Beltran A, Rovira A, Lluch A, Salvatella X, Yanes O, Albanell J, Guinovart JJ, Gomis RR. FoxA and LIPG endothelial lipase control the uptake of extracellular lipids for breast cancer growth. Nat Commun 2016; 7:11199. [PMID: 27045898 PMCID: PMC4822041 DOI: 10.1038/ncomms11199] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2015] [Accepted: 03/01/2016] [Indexed: 12/26/2022] Open
Abstract
The mechanisms that allow breast cancer (BCa) cells to metabolically sustain rapid growth are poorly understood. Here we report that BCa cells are dependent on a mechanism to supply precursors for intracellular lipid production derived from extracellular sources and that the endothelial lipase (LIPG) fulfils this function. LIPG expression allows the import of lipid precursors, thereby contributing to BCa proliferation. LIPG stands out as an essential component of the lipid metabolic adaptations that BCa cells, and not normal tissue, must undergo to support high proliferation rates. LIPG is ubiquitously and highly expressed under the control of FoxA1 or FoxA2 in all BCa subtypes. The downregulation of either LIPG or FoxA in transformed cells results in decreased proliferation and impaired synthesis of intracellular lipids. Deregulation of lipid metabolism in cancer cells is critical to the maintenance of certain malignant features. Here, the authors show that the proliferation of breast cancer cells depends upon the extracellular activity of the endothelial lipase enzyme LIPG whose expression is regulated by the FoxA family of transcription factors.
Collapse
Affiliation(s)
- Felipe Slebe
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona 08028, Spain
| | - Federico Rojo
- Cancer Research Programme, IMIM (Hospital del Mar Medical Research Institute), Barcelona 08003 Spain.,Pathology Department, IIS-Fundación Jimenez Diaz, Madrid 28040, Spain
| | - Maria Vinaixa
- Centre for Omic Sciences, Universitat Rovira i Virgili, Reus 43204, Spain.,Department of Electronic Engineering, Universitat Rovira i Virgili, Tarragona 43003, Spain.,Spanish Biomedical Research Center in Diabetes and Associated Metabolic Disorders (CIBERDEM), Madrid 28029, Spain
| | - Mar García-Rocha
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona 08028, Spain
| | - Giorgia Testoni
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona 08028, Spain
| | - Marc Guiu
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona 08028, Spain
| | - Evarist Planet
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona 08028, Spain
| | - Sara Samino
- Centre for Omic Sciences, Universitat Rovira i Virgili, Reus 43204, Spain.,Spanish Biomedical Research Center in Diabetes and Associated Metabolic Disorders (CIBERDEM), Madrid 28029, Spain
| | - Enrique J Arenas
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona 08028, Spain
| | - Antoni Beltran
- Centre for Omic Sciences, Universitat Rovira i Virgili, Reus 43204, Spain.,Spanish Biomedical Research Center in Diabetes and Associated Metabolic Disorders (CIBERDEM), Madrid 28029, Spain
| | - Ana Rovira
- Cancer Research Programme, IMIM (Hospital del Mar Medical Research Institute), Barcelona 08003 Spain.,Medical Oncology Service, Hospital del Mar, Barcelona 08003, Spain
| | - Ana Lluch
- Medical Oncology Service, Hospital Clinico, Valencia 46010, Spain
| | - Xavier Salvatella
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona 08028, Spain.,Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona 08010, Spain
| | - Oscar Yanes
- Centre for Omic Sciences, Universitat Rovira i Virgili, Reus 43204, Spain.,Department of Electronic Engineering, Universitat Rovira i Virgili, Tarragona 43003, Spain.,Spanish Biomedical Research Center in Diabetes and Associated Metabolic Disorders (CIBERDEM), Madrid 28029, Spain
| | - Joan Albanell
- Cancer Research Programme, IMIM (Hospital del Mar Medical Research Institute), Barcelona 08003 Spain.,Medical Oncology Service, Hospital del Mar, Barcelona 08003, Spain.,Universitat Pompeu Fabra, Barcelona 08003, Spain
| | - Joan J Guinovart
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona 08028, Spain.,Spanish Biomedical Research Center in Diabetes and Associated Metabolic Disorders (CIBERDEM), Madrid 28029, Spain.,Department of Biochemistry and Molecular Biology, Universitat de Barcelona, Barcelona 08028, Spain
| | - Roger R Gomis
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona 08028, Spain.,Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona 08010, Spain
| |
Collapse
|
30
|
Kabachinski G, Kielar-Grevstad DM, Zhang X, James DJ, Martin TFJ. Resident CAPS on dense-core vesicles docks and primes vesicles for fusion. Mol Biol Cell 2016; 27:654-68. [PMID: 26700319 PMCID: PMC4750925 DOI: 10.1091/mbc.e15-07-0509] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2015] [Revised: 12/12/2015] [Accepted: 12/18/2015] [Indexed: 11/11/2022] Open
Abstract
The Ca(2+)-dependent exocytosis of dense-core vesicles in neuroendocrine cells requires a priming step during which SNARE protein complexes assemble. CAPS (aka CADPS) is one of several factors required for vesicle priming; however, the localization and dynamics of CAPS at sites of exocytosis in live neuroendocrine cells has not been determined. We imaged CAPS before, during, and after single-vesicle fusion events in PC12 cells by TIRF micro-scopy. In addition to being a resident on cytoplasmic dense-core vesicles, CAPS was present in clusters of approximately nine molecules near the plasma membrane that corresponded to docked/tethered vesicles. CAPS accompanied vesicles to the plasma membrane and was present at all vesicle exocytic events. The knockdown of CAPS by shRNA eliminated the VAMP-2-dependent docking and evoked exocytosis of fusion-competent vesicles. A CAPS(ΔC135) protein that does not localize to vesicles failed to rescue vesicle docking and evoked exocytosis in CAPS-depleted cells, showing that CAPS residence on vesicles is essential. Our results indicate that dense-core vesicles carry CAPS to sites of exocytosis, where CAPS promotes vesicle docking and fusion competence, probably by initiating SNARE complex assembly.
Collapse
Affiliation(s)
- Greg Kabachinski
- Department of Biochemistry, University of Wisconsin, Madison, WI 53706
| | | | - Xingmin Zhang
- Department of Biochemistry, University of Wisconsin, Madison, WI 53706
| | - Declan J James
- Department of Biochemistry, University of Wisconsin, Madison, WI 53706
| | - Thomas F J Martin
- Department of Biochemistry, University of Wisconsin, Madison, WI 53706
| |
Collapse
|
31
|
M.S. Castro-Raucci L, S. Francischini M, N. Teixeira L, P. Ferraz E, B. Lopes H, T. de Oliveira P, Hassan MQ, Rosa AL, Beloti MM. Titanium With Nanotopography Induces Osteoblast Differentiation by Regulating Endogenous Bone Morphogenetic Protein Expression and Signaling Pathway. J Cell Biochem 2016; 117:1718-26. [DOI: 10.1002/jcb.25469] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2015] [Accepted: 12/14/2015] [Indexed: 12/25/2022]
Affiliation(s)
- Larissa M.S. Castro-Raucci
- Cell Culture Laboratory; School of Dentistry of Ribeirão Preto; University of São Paulo; Ribeirão Preto São Paulo Brazil
| | - Marcelo S. Francischini
- Cell Culture Laboratory; School of Dentistry of Ribeirão Preto; University of São Paulo; Ribeirão Preto São Paulo Brazil
| | - Lucas N. Teixeira
- Cell Culture Laboratory; School of Dentistry of Ribeirão Preto; University of São Paulo; Ribeirão Preto São Paulo Brazil
| | - Emanuela P. Ferraz
- Cell Culture Laboratory; School of Dentistry of Ribeirão Preto; University of São Paulo; Ribeirão Preto São Paulo Brazil
| | - Helena B. Lopes
- Cell Culture Laboratory; School of Dentistry of Ribeirão Preto; University of São Paulo; Ribeirão Preto São Paulo Brazil
| | - Paulo T. de Oliveira
- Cell Culture Laboratory; School of Dentistry of Ribeirão Preto; University of São Paulo; Ribeirão Preto São Paulo Brazil
| | - Mohammad Q. Hassan
- Institute of Oral Health Research; University of Alabama at Birmingham; Birmingham Alabama
| | - Adalberto L. Rosa
- Cell Culture Laboratory; School of Dentistry of Ribeirão Preto; University of São Paulo; Ribeirão Preto São Paulo Brazil
| | - Marcio M. Beloti
- Cell Culture Laboratory; School of Dentistry of Ribeirão Preto; University of São Paulo; Ribeirão Preto São Paulo Brazil
| |
Collapse
|
32
|
He J, Huang L, Qiu H, Li J, Luo L, Li Y, Tian S, Kang K, Luo J, Liu L, Gou D. A new design of a lentiviral shRNA vector with inducible co-expression of ARGONAUTE 2 for enhancing gene silencing efficiency. Cell Biosci 2015; 5:67. [PMID: 26649169 PMCID: PMC4672530 DOI: 10.1186/s13578-015-0058-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2015] [Accepted: 11/19/2015] [Indexed: 12/13/2022] Open
Abstract
Background RNA interference (RNAi) is a robust tool for inhibiting specific gene expression, but it is limited by the uncertain efficiency of siRNA or shRNA constructs. It has been shown that the overexpression of ARGONAUTE 2 (AGO2) protein increases silencing efficiency. However, the key elements required for AGO2-mediated enhancement of gene silencing in lentiviral vector has not been well studied. Results To explore the application of AGO2-based shRNA system in mammalian cells, we designed shRNA vectors targeting the EGFP reporter gene and evaluated the effects of various factors on silencing efficiency including stem length, loop sequence, antisense location as well as the ratio between AGO2 and shRNA. We found that 19 ~ 21-bp stem and 6- or 9-nt loop structure in the sense-loop-antisense (S-L-AS) orientation was an optimal design in the AGO2-shRNA system. Then, we constructed a single lentiviral vector co-expressing shRNA and AGO2 and demonstrated that the simultaneous expression of shRNA and AGO2 can achieve robust silencing of exogenous DsRed2 and endogenous ID1 and P65 genes. However, the titers of packaged lentivirus from constitutive expression of AGO2 vector were extremely low, severely limiting its broad application. For the first time, we demonstrated that the problem can be significantly improved by using the inducible expression of AGO2 lentiviral system. Conclusions We reported a novel lentiviral vector with an optimal design of shRNA and inducible AGO2 overexpression which provides a new tool for RNAi research.
Collapse
Affiliation(s)
- Jiening He
- Shenzhen Key Laboratory of Microbial Genetic Engineering, Shenzhen Key Laboratory of Marine Bioresource and Eco-environmental Science, College of Life Sciences, Shenzhen University, Nanhai Ave 3688, Shenzhen, 518060 Guangdong China
| | - Lian Huang
- Shenzhen Key Laboratory of Microbial Genetic Engineering, Shenzhen Key Laboratory of Marine Bioresource and Eco-environmental Science, College of Life Sciences, Shenzhen University, Nanhai Ave 3688, Shenzhen, 518060 Guangdong China
| | - Huiling Qiu
- Shenzhen Key Laboratory of Microbial Genetic Engineering, Shenzhen Key Laboratory of Marine Bioresource and Eco-environmental Science, College of Life Sciences, Shenzhen University, Nanhai Ave 3688, Shenzhen, 518060 Guangdong China
| | - Jiexuan Li
- Shenzhen Key Laboratory of Microbial Genetic Engineering, Shenzhen Key Laboratory of Marine Bioresource and Eco-environmental Science, College of Life Sciences, Shenzhen University, Nanhai Ave 3688, Shenzhen, 518060 Guangdong China
| | - Lan Luo
- Shenzhen Key Laboratory of Microbial Genetic Engineering, Shenzhen Key Laboratory of Marine Bioresource and Eco-environmental Science, College of Life Sciences, Shenzhen University, Nanhai Ave 3688, Shenzhen, 518060 Guangdong China
| | - Yanjiao Li
- Shenzhen Key Laboratory of Microbial Genetic Engineering, Shenzhen Key Laboratory of Marine Bioresource and Eco-environmental Science, College of Life Sciences, Shenzhen University, Nanhai Ave 3688, Shenzhen, 518060 Guangdong China
| | - Shengli Tian
- Shenzhen Key Laboratory of Microbial Genetic Engineering, Shenzhen Key Laboratory of Marine Bioresource and Eco-environmental Science, College of Life Sciences, Shenzhen University, Nanhai Ave 3688, Shenzhen, 518060 Guangdong China
| | - Kang Kang
- Department of Physiology, Shenzhen University Health Science Center, Shenzhen University, Shenzhen, 518060 Guangdong China
| | - Jun Luo
- College of Animal Science and Technology, Northwest A&F University, Yangling, 712100 Shaanxi China
| | - Lin Liu
- Department of Physiological Sciences, Oklahoma State University, Stillwater, OK 74078 USA
| | - Deming Gou
- Shenzhen Key Laboratory of Microbial Genetic Engineering, Shenzhen Key Laboratory of Marine Bioresource and Eco-environmental Science, College of Life Sciences, Shenzhen University, Nanhai Ave 3688, Shenzhen, 518060 Guangdong China
| |
Collapse
|
33
|
Wang SP, Iwata S, Nakayamada S, Niiro H, Jabbarzadeh-Tabrizi S, Kondo M, Kubo S, Yoshikawa M, Tanaka Y. Amplification of IL-21 signalling pathway through Bruton’s tyrosine kinase in human B cell activation. Rheumatology (Oxford) 2015; 54:1488-1497. [DOI: 10.1093/rheumatology/keu532] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/30/2023] Open
|
34
|
Artificial MiRNA Knockdown of Platelet Glycoprotein lbα: A Tool for Platelet Gene Silencing. PLoS One 2015; 10:e0132899. [PMID: 26176854 PMCID: PMC4503784 DOI: 10.1371/journal.pone.0132899] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2015] [Accepted: 05/28/2015] [Indexed: 11/19/2022] Open
Abstract
In recent years, candidate genes and proteins implicated in platelet function have been identified by various genomic approaches. To elucidate their exact role, we aimed to develop a method to apply miRNA interference in platelet progenitor cells by using GPIbα as a proof-of-concept target protein. After in silico and in vitro screening of siRNAs targeting GPIbα (siGPIBAs), we developed artificial miRNAs (miGPIBAs), which were tested in CHO cells stably expressing GPIb-IX complex and megakaryoblastic DAMI cells. Introduction of siGPIBAs in CHO GPIb-IX cells resulted in 44 to 75% and up to 80% knockdown of GPIbα expression using single or combined siRNAs, respectively. Conversion of siGPIBAs to miGPIBAs resulted in reduced silencing efficiency, which could however be circumvented by tandem integration of two hairpins targeting different regions of GPIBA mRNA where 72% GPIbα knockdown was achieved. CHO GPIb-IX cells transfected with the miGPIBA construct displayed a significant decrease in their ability to aggregate characterized by lower aggregate numbers and size compared to control CHO GPIb-IX cells. More importantly, we successfully silenced GPIbα in differentiating megakaryoblastic DAMI cells that exhibited morphological changes associated with actin organization. In conclusion, we here report the successful use of miRNA technology to silence a platelet protein in megakaryoblastic cells and demonstrate its usefulness in functional assays. Hence, we believe that artificial miRNAs are suitable tools to unravel the role of a protein of interest in stem cells, megakaryocytes and platelets, thereby expanding their application to novel fields of basic and translational research.
Collapse
|
35
|
Zhang C, Zhang Q, Wang F, Liu Q. Knockdown of poc1b causes abnormal photoreceptor sensory cilium and vision impairment in zebrafish. Biochem Biophys Res Commun 2015; 465:651-7. [PMID: 26188096 DOI: 10.1016/j.bbrc.2015.06.083] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2015] [Accepted: 06/12/2015] [Indexed: 01/26/2023]
Abstract
Proteomic analysis of the mouse photoreceptor sensory cilium identified a set of cilia proteins, including Poc1 centriolar protein b (Poc1b). Previous functional studies in human cells and zebrafish embryos implicated that Poc1b plays important roles in centriole duplication and length control, as well as ciliogenesis. To study the function of Poc1b in photoreceptor sensory cilia and other primary cilia, we expressed a tagged recombinant Poc1b protein in cultured renal epithelial cells and rat retina. Poc1b was localized to the centrioles and spindle bundles during cell cycle progression, and to the basal body of photoreceptor sensory cilia. A morpholino knockdown and complementation assay of poc1b in zebrafish showed that loss of poc1b led to a range of morphological anomalies of cilia commonly associated with human ciliopathies. In the retina, the development of retinal laminae was significantly delayed and the length of photoreceptor outer segments was shortened. Visual behavior studies revealed impaired visual function in the poc1b morphants. In addition, ciliopathy-associated developmental defects, such as small eyes, curved body axis, heart defects, and shortened cilia in Kupffer's vesicle, were observed as well. These data suggest that poc1b is required for normal development and ciliogenesis of retinal photoreceptor sensory cilia and other cilia. Furthermore, this conclusion is supported by recent findings that mutations in POC1B gene have been identified in patients with inherited retinal dystrophy and syndromic retinal ciliopathy.
Collapse
Affiliation(s)
- Conghui Zhang
- Department of Ophthalmology, Shanghai Tenth People's Hospital, Tongji University, Shanghai, China
| | - Qi Zhang
- Ocular Genomics Institute, Department of Ophthalmology, Massachusetts Eye and Ear Infirmary, Harvard Medical School, Boston, MA, USA
| | - Fang Wang
- Department of Ophthalmology, Shanghai Tenth People's Hospital, Tongji University, Shanghai, China.
| | - Qin Liu
- Ocular Genomics Institute, Department of Ophthalmology, Massachusetts Eye and Ear Infirmary, Harvard Medical School, Boston, MA, USA; Berman-Gund Laboratory for the Study of Retinal Degenerations, Department of Ophthalmology, Massachusetts Eye and Ear Infirmary, Harvard Medical School, Boston, MA, USA.
| |
Collapse
|
36
|
Next-generation libraries for robust RNA interference-based genome-wide screens. Proc Natl Acad Sci U S A 2015; 112:E3384-91. [PMID: 26080438 DOI: 10.1073/pnas.1508821112] [Citation(s) in RCA: 76] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Genetic screening based on loss-of-function phenotypes is a powerful discovery tool in biology. Although the recent development of clustered regularly interspaced short palindromic repeats (CRISPR)-based screening approaches in mammalian cell culture has enormous potential, RNA interference (RNAi)-based screening remains the method of choice in several biological contexts. We previously demonstrated that ultracomplex pooled short-hairpin RNA (shRNA) libraries can largely overcome the problem of RNAi off-target effects in genome-wide screens. Here, we systematically optimize several aspects of our shRNA library, including the promoter and microRNA context for shRNA expression, selection of guide strands, and features relevant for postscreen sample preparation for deep sequencing. We present next-generation high-complexity libraries targeting human and mouse protein-coding genes, which we grouped into 12 sublibraries based on biological function. A pilot screen suggests that our next-generation RNAi library performs comparably to current CRISPR interference (CRISPRi)-based approaches and can yield complementary results with high sensitivity and high specificity.
Collapse
|
37
|
Knocking down schistosomes - promise for lentiviral transduction in parasites. Trends Parasitol 2015; 31:324-32. [PMID: 25933926 DOI: 10.1016/j.pt.2015.03.009] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2014] [Revised: 03/18/2015] [Accepted: 03/20/2015] [Indexed: 12/21/2022]
Abstract
Underpinned by major advances in our understanding of the genomes of schistosomes, progress in the development of functional genomic tools is providing unique prospects to gain insights into the intricacies of the biology of these blood flukes, their host relationships, and the diseases that they cause. This article reviews some key applications of double-stranded RNA interference (RNAi) in Schistosoma mansoni, appraises delivery systems for transgenesis and stable gene silencing, considers ways of increasing efficiency and specificity of gene silencing, and discusses the prospects of using a lentivirus delivery system for future functional genomic-phenomic explorations of schistosomes and other parasites. The ability to achieve effective and stable gene perturbation in parasites has major biological implications and could facilitate the development of new interventions.
Collapse
|
38
|
Nandakumar SK, Johnson K, Throm SL, Pestina TI, Neale G, Persons DA. Low-level GATA2 overexpression promotes myeloid progenitor self-renewal and blocks lymphoid differentiation in mice. Exp Hematol 2015; 43:565-77.e1-10. [PMID: 25907033 DOI: 10.1016/j.exphem.2015.04.002] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2014] [Revised: 04/08/2015] [Accepted: 04/10/2015] [Indexed: 01/09/2023]
Abstract
The transcription factor GATA2 is highly expressed in hematopoietic stem cells and is downregulated during lineage maturation. Gain of function mutations, loss of function mutations, and overexpression of GATA2 have been reported in acute myeloid leukemia. In previous studies, we and others showed that GATA2 overexpression at high levels, similar to that seen in hematopoietic stem cells, blocked differentiation of hematopoietic stem cells and progenitors. To better understand the effects of GATA2, we designed a Tamoxifen-inducible GATA2-estrogen receptor (ERT) vector. In the absence of Tamoxifen, small amounts of GATA2-ERT were still able to enter the nucleus in mouse bone marrow (BM) cells, providing us with a tool to test the effects of low-level GATA2 overexpression. We observed that this low-level GATA2 overexpression enhanced self-renewal of myeloid progenitors in vitro and resulted in immortalization of BM cells to myeloid cell lines. Continuous GATA2-ERT expression was required for the proliferation of these immortalized lines. Myeloid expansion and a block in T and B lineage differentiation were observed in mice transplanted with GATA2-ERT-expressing BM cells. Myeloid expansion occurred after the granulocyte monocyte progenitor stage, and lymphoid block was distal to the common lymphoid progenitor in transgenic mice. GATA2 appeared to induce growth via downstream activation of Nmyc and Hoxa9. Our results demonstrate that GATA2 overexpression at low level confers self-renewal capacity to myeloid progenitors and is relevant to myeloid leukemia development.
Collapse
Affiliation(s)
- Satish K Nandakumar
- Department of Experimental Hematology, St. Jude Children's Research Hospital, Memphis, TN, USA.
| | - Kyle Johnson
- Department of Experimental Hematology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Stacy L Throm
- Department of Experimental Hematology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Tamara I Pestina
- Department of Experimental Hematology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Geoffrey Neale
- Hartwell Center for Bioinformatics and Biotechnology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Derek A Persons
- Department of Experimental Hematology, St. Jude Children's Research Hospital, Memphis, TN, USA
| |
Collapse
|
39
|
Sheridan JM, Ritchie ME, Best SA, Jiang K, Beck TJ, Vaillant F, Liu K, Dickins RA, Smyth GK, Lindeman GJ, Visvader JE. A pooled shRNA screen for regulators of primary mammary stem and progenitor cells identifies roles for Asap1 and Prox1. BMC Cancer 2015; 15:221. [PMID: 25879659 PMCID: PMC4399223 DOI: 10.1186/s12885-015-1187-z] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2015] [Accepted: 03/12/2015] [Indexed: 12/31/2022] Open
Abstract
Background The molecular regulators that orchestrate stem cell renewal, proliferation and differentiation along the mammary epithelial hierarchy remain poorly understood. Here we have performed a large-scale pooled RNAi screen in primary mouse mammary stem cell (MaSC)-enriched basal cells using 1295 shRNAs against genes principally involved in transcriptional regulation. Methods MaSC-enriched basal cells transduced with lentivirus pools carrying shRNAs were maintained as non-adherent mammospheres, a system known to support stem and progenitor cells. Integrated shRNAs that altered culture kinetics were identified by next generation sequencing as relative frequency changes over time. RNA-seq-based expression profiling coupled with in vitro progenitor and in vivo transplantation assays was used to confirm a role for candidate genes in mammary stem and/or progenitor cells. Results Utilizing a mammosphere-based assay, the screen identified several candidate regulators. Although some genes had been previously implicated in mammary gland development, the vast majority of genes uncovered have no known function within the mammary gland. RNA-seq analysis of freshly purified primary mammary epithelial populations and short-term cultured mammospheres was used to confirm the expression of candidate regulators. Two genes, Asap1 and Prox1, respectively implicated in breast cancer metastasis and progenitor cell function in other systems, were selected for further analysis as their roles in the normal mammary gland were unknown. Both Prox1 and Asap1 were shown to act as negative regulators of progenitor activity in vitro, and Asap1 knock-down led to a marked increase in repopulating activity in vivo, implying a role in stem cell activity. Conclusions This study has revealed a number of novel genes that influence the activity or survival of mammary stem and/or progenitor cells. Amongst these, we demonstrate that Prox1 and Asap1 behave as negative regulators of mammary stem/progenitor function. Both of these genes have also been implicated in oncogenesis. Our findings provide proof of principle for the use of short-term cultured primary MaSC/basal cells in functional RNAi screens. Electronic supplementary material The online version of this article (doi:10.1186/s12885-015-1187-z) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Julie M Sheridan
- ACRF Stem Cells and Cancer Division, The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, VIC, 3052, Australia. .,Molecular Genetics of Cancer Division, The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, VIC, 3052, Australia. .,Department of Medical Biology, The University of Melbourne, Parkville, VIC, 3010, Australia.
| | - Matthew E Ritchie
- Molecular Medicine Division, The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, VIC, 3052, Australia. .,School of Mathematics and Statistics, The University of Melbourne, Parkville, VIC, 3010, Australia.
| | - Sarah A Best
- ACRF Stem Cells and Cancer Division, The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, VIC, 3052, Australia. .,Department of Medical Biology, The University of Melbourne, Parkville, VIC, 3010, Australia.
| | - Kun Jiang
- ACRF Stem Cells and Cancer Division, The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, VIC, 3052, Australia.
| | - Tamara J Beck
- ACRF Stem Cells and Cancer Division, The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, VIC, 3052, Australia.
| | - François Vaillant
- ACRF Stem Cells and Cancer Division, The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, VIC, 3052, Australia. .,Department of Medical Biology, The University of Melbourne, Parkville, VIC, 3010, Australia.
| | - Kevin Liu
- ACRF Stem Cells and Cancer Division, The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, VIC, 3052, Australia.
| | - Ross A Dickins
- Molecular Medicine Division, The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, VIC, 3052, Australia. .,Department of Medical Biology, The University of Melbourne, Parkville, VIC, 3010, Australia.
| | - Gordon K Smyth
- Bioinformatics Division, The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, VIC, 3052, Australia. .,School of Mathematics and Statistics, The University of Melbourne, Parkville, VIC, 3010, Australia.
| | - Geoffrey J Lindeman
- ACRF Stem Cells and Cancer Division, The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, VIC, 3052, Australia. .,Department of Medicine, The University of Melbourne, Parkville, VIC, 3010, Australia. .,Department of Medical Oncology, The Royal Melbourne Hospital, Grattan Street, Parkville, VIC, 3050, Australia.
| | - Jane E Visvader
- ACRF Stem Cells and Cancer Division, The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, VIC, 3052, Australia. .,Department of Medical Biology, The University of Melbourne, Parkville, VIC, 3010, Australia.
| |
Collapse
|
40
|
Hagen J, Scheerlinck JPY, Young ND, Gasser RB, Kalinna BH. Prospects for Vector-Based Gene Silencing to Explore Immunobiological Features of Schistosoma mansoni. ADVANCES IN PARASITOLOGY 2015; 88:85-122. [PMID: 25911366 DOI: 10.1016/bs.apar.2015.02.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Schistosomiasis is a prevalent, socioeconomically important disease of humans caused by parasites of the genus Schistosoma (schistosomes or blood flukes). Currently, more than 200 million people worldwide are infected with schistosomes. Despite major research efforts, there is only one drug routinely used for effective treatment, and no vaccine is available to combat schistosomiasis. The purpose of the present article is to (1) provide a background on the parasites and different forms of disease; (2) describe key immunomolecular aspects of disease induced in the host; and (3) critically appraise functional genomic methods employed to explore parasite biology, parasite-host interactions and disease at the molecular level. Importantly, the article also describes the features and advantages of lentiviral delivery of artificial microRNAs to silence genes. It also discusses the first successful application of such an approach in schistosomes, in order to explore the immunobiological role of selected target proteins known to be involved in egg-induced disease. The lentiviral transduction system provides exciting prospects for future, fundamental investigations of schistosomes, and is likely to have broad applicability to other eukaryotic pathogens and infectious diseases. The ability to achieve effective and stable gene perturbation in parasites has major biotechnological implications, and might facilitate the development of radically new methods for the treatment and control of parasitic diseases.
Collapse
Affiliation(s)
- Jana Hagen
- Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, Victoria, Australia
| | - Jean-Pierre Y Scheerlinck
- Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, Victoria, Australia
| | - Neil D Young
- Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, Victoria, Australia
| | - Robin B Gasser
- Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, Victoria, Australia
| | - Bernd H Kalinna
- Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, Victoria, Australia
| |
Collapse
|
41
|
Albers J, Danzer C, Rechsteiner M, Lehmann H, Brandt LP, Hejhal T, Catalano A, Busenhart P, Gonçalves AF, Brandt S, Bode PK, Bode-Lesniewska B, Wild PJ, Frew IJ. A versatile modular vector system for rapid combinatorial mammalian genetics. J Clin Invest 2015; 125:1603-19. [PMID: 25751063 PMCID: PMC4396471 DOI: 10.1172/jci79743] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2014] [Accepted: 01/20/2015] [Indexed: 01/29/2023] Open
Abstract
Here, we describe the multiple lentiviral expression (MuLE) system that allows multiple genetic alterations to be introduced simultaneously into mammalian cells. We created a toolbox of MuLE vectors that constitute a flexible, modular system for the rapid engineering of complex polycistronic lentiviruses, allowing combinatorial gene overexpression, gene knockdown, Cre-mediated gene deletion, or CRISPR/Cas9-mediated (where CRISPR indicates clustered regularly interspaced short palindromic repeats) gene mutation, together with expression of fluorescent or enzymatic reporters for cellular assays and animal imaging. Examples of tumor engineering were used to illustrate the speed and versatility of performing combinatorial genetics using the MuLE system. By transducing cultured primary mouse cells with single MuLE lentiviruses, we engineered tumors containing up to 5 different genetic alterations, identified genetic dependencies of molecularly defined tumors, conducted genetic interaction screens, and induced the simultaneous CRISPR/Cas9-mediated knockout of 3 tumor-suppressor genes. Intramuscular injection of MuLE viruses expressing oncogenic H-RasG12V together with combinations of knockdowns of the tumor suppressors cyclin-dependent kinase inhibitor 2A (Cdkn2a), transformation-related protein 53 (Trp53), and phosphatase and tensin homolog (Pten) allowed the generation of 3 murine sarcoma models, demonstrating that genetically defined autochthonous tumors can be rapidly generated and quantitatively monitored via direct injection of polycistronic MuLE lentiviruses into mouse tissues. Together, our results demonstrate that the MuLE system provides genetic power for the systematic investigation of the molecular mechanisms that underlie human diseases.
Collapse
|
42
|
Gillespie MA, Gold ES, Ramsey SA, Podolsky I, Aderem A, Ranish JA. An LXR-NCOA5 gene regulatory complex directs inflammatory crosstalk-dependent repression of macrophage cholesterol efflux. EMBO J 2015; 34:1244-58. [PMID: 25755249 DOI: 10.15252/embj.201489819] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2014] [Accepted: 02/13/2015] [Indexed: 02/04/2023] Open
Abstract
LXR-cofactor complexes activate the gene expression program responsible for cholesterol efflux in macrophages. Inflammation antagonizes this program, resulting in foam cell formation and atherosclerosis; however, the molecular mechanisms underlying this antagonism remain to be fully elucidated. We use promoter enrichment-quantitative mass spectrometry (PE-QMS) to characterize the composition of gene regulatory complexes assembled at the promoter of the lipid transporter Abca1 following downregulation of its expression. We identify a subset of proteins that show LXR ligand- and binding-dependent association with the Abca1 promoter and demonstrate they differentially control Abca1 expression. We determine that NCOA5 is linked to inflammatory Toll-like receptor (TLR) signaling and establish that NCOA5 functions as an LXR corepressor to attenuate Abca1 expression. Importantly, TLR3-LXR signal crosstalk promotes recruitment of NCOA5 to the Abca1 promoter together with loss of RNA polymerase II and reduced cholesterol efflux. Together, these data significantly expand our knowledge of regulatory inputs impinging on the Abca1 promoter and indicate a central role for NCOA5 in mediating crosstalk between pro-inflammatory and anti-inflammatory pathways that results in repression of macrophage cholesterol efflux.
Collapse
Affiliation(s)
| | | | - Stephen A Ramsey
- Department of Biomedical Sciences, Oregon State University, Corvallis, OR, USA
| | | | - Alan Aderem
- Seattle Biomedical Research Institute, Seattle, WA, USA
| | | |
Collapse
|
43
|
Sato T, Muroyama Y, Saito T. Control of Gene Expression in Neurons by the Use of In Vivo Electroporation and the Tetracycline System. ELECTROPORATION METHODS IN NEUROSCIENCE 2015. [DOI: 10.1007/978-1-4939-2459-2_15] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
|
44
|
Omega-1 knockdown in Schistosoma mansoni eggs by lentivirus transduction reduces granuloma size in vivo. Nat Commun 2014; 5:5375. [PMID: 25400038 PMCID: PMC4243216 DOI: 10.1038/ncomms6375] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2014] [Accepted: 09/25/2014] [Indexed: 02/06/2023] Open
Abstract
Schistosomiasis, one of the most important neglected tropical diseases worldwide, is caused by flatworms (blood flukes or schistosomes) that live in the bloodstream of humans. The hepatointestinal form of this debilitating disease results from a chronic infection with Schistosoma mansoni or Schistosoma japonicum. No vaccine is available to prevent schistosomiasis, and treatment relies predominantly on the use of a single drug, praziquantel. In spite of considerable research effort over the years, very little is known about the complex in vivo events that lead to granuloma formation and other pathological changes during infection. Here we use, for the first time, a lentivirus-based transduction system to deliver microRNA-adapted short hairpin RNAs (shRNAmirs) into the parasite to silence and explore selected protein-encoding genes of S. mansoni implicated in the disease process. This gene-silencing system has potential to be used for functional genomic–phenomic studies of a range of socioeconomically important pathogens. Schistosomiasis, a neglected tropical disease, is caused by flatworms such as Schistosoma mansoni. Here, Hagen et al. describe a lentivirus-based transduction system to deliver microRNA-adapted small hairpin RNAs into S. mansoni to inhibit transcription of selected genes implicated in the disease process.
Collapse
|
45
|
Myburgh R, Cherpin O, Schlaepfer E, Rehrauer H, Speck RF, Krause KH, Salmon P. Optimization of Critical Hairpin Features Allows miRNA-based Gene Knockdown Upon Single-copy Transduction. MOLECULAR THERAPY. NUCLEIC ACIDS 2014; 3:e207. [PMID: 25350582 PMCID: PMC4217082 DOI: 10.1038/mtna.2014.58] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/27/2014] [Accepted: 09/20/2014] [Indexed: 01/13/2023]
Abstract
Gene knockdown using micro RNA (miRNA)-based vector constructs is likely to become a prominent gene therapy approach. It was the aim of this study to improve the efficiency of gene knockdown through optimizing the structure of miRNA mimics. Knockdown of two target genes was analyzed: CCR5 and green fluorescent protein. We describe here a novel and optimized miRNA mimic design called mirGE comprising a lower stem length of 13 base pairs (bp), positioning of the targeting strand on the 5' side of the miRNA, together with nucleotide mismatches in upper stem positions 1 and 12 placed on the passenger strand. Our mirGE proved superior to miR-30 in four aspects: yield of targeting strand incorporation into RNA-induced silencing complex (RISC); incorporation into RISC of correct targeting strand; precision of cleavage by Drosha; and ratio of targeting strand over passenger strand. A triple mirGE hairpin cassette targeting CCR5 was constructed. It allowed CCR5 knockdown with an efficiency of over 90% upon single-copy transduction. Importantly, single-copy expression of this construct rendered transduced target cells, including primary human macrophages, resistant to infection with a CCR5-tropic strain of HIV. Our results provide new insights for a better knockdown efficiency of constructs containing miRNA. Our results also provide the proof-of-principle that cells can be rendered HIV resistant through single-copy vector transduction, rendering this approach more compatible with clinical applications.
Collapse
Affiliation(s)
- Renier Myburgh
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital of Zurich, University of Zurich, Zurich, Switzerland
- Department of Pathology and Immunology, Faculty of Medicine, University of Geneva, Geneva, Switzerland
- Department of Immunology, Faculty of Health Sciences, University of Pretoria, Pretoria, South Africa
| | - Ophélie Cherpin
- Department of Pathology and Immunology, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Erika Schlaepfer
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital of Zurich, University of Zurich, Zurich, Switzerland
| | - Hubert Rehrauer
- Functional Genomics Center, University of Zurich, Zurich, Switzerland
| | - Roberto F Speck
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital of Zurich, University of Zurich, Zurich, Switzerland
| | - Karl-Heinz Krause
- Department of Pathology and Immunology, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Patrick Salmon
- Department of Neurosciences, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| |
Collapse
|
46
|
Lentiviral-based approach for the validation of cancer therapeutic targets in vivo. Biotechniques 2014; 57:179, 181-7. [PMID: 25312087 DOI: 10.2144/000114214] [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: 04/29/2014] [Accepted: 08/05/2014] [Indexed: 11/23/2022] Open
Abstract
Despite the pressing need for novel cancer treatments, our improved understanding of tumor biology is not being successfully translated into better therapies. Here we present a lentiviral vector that enables in vivo validation of cancer therapeutic targets when combined with existing cancer animal models that faithfully reproduce the natural history of human disease. Unlike the conventional genetic approaches with targeted alleles, the outlined experimental strategy could be used to assess the preclinical efficacy of a growing number of putative therapeutic hits in a rapid and cost-effective manner.
Collapse
|
47
|
Payne LJ, Eves RL, Jia L, Mak AS. p53 Down regulates PDGF-induced formation of circular dorsal ruffles in rat aortic smooth muscle cells. PLoS One 2014; 9:e108257. [PMID: 25247424 PMCID: PMC4172730 DOI: 10.1371/journal.pone.0108257] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2014] [Accepted: 08/27/2014] [Indexed: 01/15/2023] Open
Abstract
The tumor suppressor, p53, negatively regulates cell migration and invasion in addition to its role in apoptosis, cell cycle regulation and senescence. Here, we study the roles of p53 in PDGF-induced circular dorsal ruffle (CDR) formation in rat aortic smooth muscle (RASM) cells. In primary and immortalized RASM cells, up-regulation of p53 expression or increase in activity with doxorubicin inhibits CDR formation. In contrast, shRNA-knockdown of p53 or inhibition of its activity with pifithrin α promotes CDR formation. p53 acts by up-regulating PTEN expression, which antagonizes Rac and Cdc42 activation. Both lipid and protein phosphatase activities of PTEN are required for maximal suppression of CDR, but the lipid activity clearly plays the dominant role. N-WASP, the downstream effector of Cdc42, is the major positive contributor to CDR formation in RASM, and is an indirect target of p53. The Rac effector, WAVE2, appears to also play a minor role, while WAVE1 has no significant effect in CDR formation. In sum, we propose that p53 suppresses PDGF-induced CDR formation in RASM cells by upregulating PTEN leading mainly to the inhibition of the Cdc42-N-WASP pathway.
Collapse
Affiliation(s)
- Laura J. Payne
- Department of Biomedical and Molecular Sciences, Queen's University, Kingston, Ontario, Canada
| | - Robert L. Eves
- Department of Biomedical and Molecular Sciences, Queen's University, Kingston, Ontario, Canada
| | - Lilly Jia
- Department of Biomedical and Molecular Sciences, Queen's University, Kingston, Ontario, Canada
| | - Alan S. Mak
- Department of Biomedical and Molecular Sciences, Queen's University, Kingston, Ontario, Canada
- * E-mail:
| |
Collapse
|
48
|
De Luca G, Ferretti R, Bruschi M, Mezzaroma E, Caruso M. Cyclin D3 critically regulates the balance between self-renewal and differentiation in skeletal muscle stem cells. Stem Cells 2014; 31:2478-91. [PMID: 23897741 PMCID: PMC3963451 DOI: 10.1002/stem.1487] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2013] [Revised: 05/26/2013] [Accepted: 06/21/2013] [Indexed: 12/28/2022]
Abstract
Satellite cells are mitotically quiescent myogenic stem cells resident beneath the basal lamina surrounding adult muscle myofibers. In response to injury, multiple extrinsic signals drive the entry of satellite cells into the cell cycle and then to proliferation, differentiation, and self-renewal of their downstream progeny. Because satellite cells must endure for a lifetime, their cell cycle activity must be carefully controlled to coordinate proliferative expansion and self-renewal with the onset of the differentiation program. In this study, we find that cyclin D3, a member of the family of mitogen-activated D-type cyclins, is critically required for proper developmental progression of myogenic progenitors. Using a cyclin D3-knockout mouse we determined that cyclin D3 deficiency leads to reduced myofiber size and impaired establishment of the satellite cell population within the adult muscle. Cyclin D3-null myogenic progenitors, studied ex vivo on isolated myofibers and in vitro, displayed impaired cell cycle progression, increased differentiation potential, and reduced self-renewal capability. Similarly, silencing of cyclin D3 in C2 myoblasts caused anticipated exit from the cell cycle and precocious onset of terminal differentiation. After induced muscle damage, cyclin D3-null myogenic progenitors exhibited proliferation deficits, a precocious ability to form newly generated myofibers and a reduced capability to repopulate the satellite cell niche at later stages of the regeneration process. These results indicate that cyclin D3 plays a cell-autonomous and nonredundant function in regulating the dynamic balance between proliferation, differentiation, and self-renewal that normally establishes an appropriate pool size of adult satellite cells.
Collapse
Affiliation(s)
- Giulia De Luca
- National Research Council, Institute of Cell Biology and Neurobiology, Fondazione Santa Lucia, Roma, Italy
| | | | | | | | | |
Collapse
|
49
|
Payne AW, Pant DK, Pan TC, Chodosh LA. Ceramide kinase promotes tumor cell survival and mammary tumor recurrence. Cancer Res 2014; 74:6352-63. [PMID: 25164007 DOI: 10.1158/0008-5472.can-14-1292] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Recurrent breast cancer is typically an incurable disease and, as such, is disproportionately responsible for deaths from this disease. Recurrent breast cancers arise from the pool of disseminated tumor cells (DTC) that survive adjuvant or neoadjuvant therapy, and patients with detectable DTCs following therapy are at substantially increased risk for recurrence. Consequently, the identification of pathways that contribute to the survival of breast cancer cells following therapy could aid in the development of more effective therapies that decrease the burden of residual disease and thereby reduce the risk of breast cancer recurrence. We now report that ceramide kinase (Cerk) is required for mammary tumor recurrence following HER2/neu pathway inhibition and is spontaneously upregulated during tumor recurrence in multiple genetically engineered mouse models for breast cancer. We find that Cerk is rapidly upregulated in tumor cells following HER2/neu downregulation or treatment with Adriamycin and that Cerk is required for tumor cell survival following HER2/neu downregulation. Consistent with our observations in mouse models, analysis of gene expression profiles from more than 2,200 patients revealed that elevated CERK expression is associated with an increased risk of recurrence in women with breast cancer. In addition, although CERK expression is associated with aggressive subtypes of breast cancer, including those that are estrogen receptor-negative, HER2(+), basal-like, or high grade, its association with poor clinical outcome is independent of these clinicopathologic variables. Together, our findings identify a functional role for Cerk in breast cancer recurrence and suggest the clinical utility of agents targeted against this prosurvival pathway.
Collapse
Affiliation(s)
- Ania W Payne
- Department of Cancer Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania. Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Dhruv K Pant
- Department of Cancer Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania. Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Tien-Chi Pan
- Department of Cancer Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania. Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Lewis A Chodosh
- Department of Cancer Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania. Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania. Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania.
| |
Collapse
|
50
|
van de Weijer ML, Bassik MC, Luteijn RD, Voorburg CM, Lohuis MAM, Kremmer E, Hoeben RC, LeProust EM, Chen S, Hoelen H, Ressing ME, Patena W, Weissman JS, McManus MT, Wiertz EJHJ, Lebbink RJ. A high-coverage shRNA screen identifies TMEM129 as an E3 ligase involved in ER-associated protein degradation. Nat Commun 2014; 5:3832. [PMID: 24807418 PMCID: PMC4024746 DOI: 10.1038/ncomms4832] [Citation(s) in RCA: 97] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2013] [Accepted: 04/08/2014] [Indexed: 01/05/2023] Open
Abstract
Misfolded ER proteins are retrotranslocated into the cytosol for degradation via the ubiquitin-proteasome system. The human cytomegalovirus protein US11 exploits this ER-associated protein degradation (ERAD) pathway to downregulate HLA class I molecules in virus-infected cells, thereby evading elimination by cytotoxic T-lymphocytes. US11-mediated degradation of HLA class I has been instrumental in the identification of key components of mammalian ERAD, including Derlin-1, p97, VIMP and SEL1L. Despite this, the process governing retrotranslocation of the substrate is still poorly understood. Here using a high-coverage genome-wide shRNA library, we identify the uncharacterized protein TMEM129 and the ubiquitin-conjugating E2 enzyme UBE2J2 to be essential for US11-mediated HLA class I downregulation. TMEM129 is an unconventional C4C4-type RING finger E3 ubiquitin ligase that resides within a complex containing various other ERAD components, including Derlin-1, Derlin-2, VIMP and p97, indicating that TMEM129 is an integral part of the ER-resident dislocation complex mediating US11-induced HLA class I degradation.
Collapse
Affiliation(s)
| | - Michael C Bassik
- 1] Department of Cellular and Molecular Pharmacology, California Institute for Quantitative Biomedical Research, Howard Hughes Medical Institute, University of California, San Francisco, California 94158, USA [2]
| | - Rutger D Luteijn
- Medical Microbiology, University Medical Center Utrecht, 3584CX Utrecht, The Netherlands
| | - Cornelia M Voorburg
- Medical Microbiology, University Medical Center Utrecht, 3584CX Utrecht, The Netherlands
| | - Mirjam A M Lohuis
- Medical Microbiology, University Medical Center Utrecht, 3584CX Utrecht, The Netherlands
| | - Elisabeth Kremmer
- Helmholtz Zentrum München, German Research Center for Environmental Health, Institute of Molecular Immunology, 81377 Munich, Germany
| | - Rob C Hoeben
- Department of Molecular Cell Biology, Leiden University Medical Center, 2333ZC Leiden, The Netherlands
| | - Emily M LeProust
- 1] Genomics Solution Unit, Agilent Technologies Inc., Santa Clara, California 95051, USA [2]
| | - Siyuan Chen
- 1] Genomics Solution Unit, Agilent Technologies Inc., Santa Clara, California 95051, USA [2]
| | - Hanneke Hoelen
- Medical Microbiology, University Medical Center Utrecht, 3584CX Utrecht, The Netherlands
| | - Maaike E Ressing
- 1] Medical Microbiology, University Medical Center Utrecht, 3584CX Utrecht, The Netherlands [2] Department of Molecular Cell Biology, Leiden University Medical Center, 2333ZC Leiden, The Netherlands
| | - Weronika Patena
- 1] Department of Cellular and Molecular Pharmacology, California Institute for Quantitative Biomedical Research, Howard Hughes Medical Institute, University of California, San Francisco, California 94158, USA [2] Department of Microbiology and Immunology, University of California, San Francisco, California 94143, USA [3]
| | - Jonathan S Weissman
- Department of Cellular and Molecular Pharmacology, California Institute for Quantitative Biomedical Research, Howard Hughes Medical Institute, University of California, San Francisco, California 94158, USA
| | - Michael T McManus
- Department of Microbiology and Immunology, University of California, San Francisco, California 94143, USA
| | - Emmanuel J H J Wiertz
- 1] Medical Microbiology, University Medical Center Utrecht, 3584CX Utrecht, The Netherlands [2]
| | - Robert Jan Lebbink
- 1] Medical Microbiology, University Medical Center Utrecht, 3584CX Utrecht, The Netherlands [2]
| |
Collapse
|