1
|
Zhang L, Zheng J, Ding F. Podocyte involvement in the pathogenesis of preterm-related long-term chronic kidney disease. Histol Histopathol 2024; 39:557-564. [PMID: 37994826 DOI: 10.14670/hh-18-675] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2023]
Abstract
With the continuous advancement of neonatal intensive care technology, the survival rate of preterm infants is gradually increasing. However, this improvement in survival is accompanied by long-term prognostic implications in various systems. In the field of renal diseases, current epidemiological data indicate that preterm birth is a significant risk factor for the development of long-term chronic kidney disease (CKD). This not only imposes an economic burden on patients families but also severely impacts their quality of life. Understanding the underlying mechanisms involved in this process could offer potential strategies for early prevention and management of CKD. Although the nephron number hypothesis is currently widely accepted as a mechanism, there has been limited exploration regarding podocytes - one of the most important structures within nephrons - in relation to long-term CKD associated with preterm birth. Therefore, this review aims to summarize current knowledge on how prematurity influences CKD development overall, while specifically focusing on our current understanding of podocytes in relation to prematurity.
Collapse
Affiliation(s)
- Lulu Zhang
- Department of Neonatology, Tianjin Central Hospital of Obstetrics and Gynecology, Tianjin, China
- Tianjin Key Laboratory of Human Development and Reproductive Regulation, Tianjin, China
- Department of Neonatology, Nankai University Maternity Hospital, Tianjin, China
| | - Jun Zheng
- Tianjin Key Laboratory of Human Development and Reproductive Regulation, Tianjin, China
- Department of Neonatology, Nankai University Maternity Hospital, Tianjin, China
- Department of Neonatology, Tianjin Central Hospital of Obstetrics and Gynecology, Tianjin, China.
| | - Fangrui Ding
- Tianjin Key Laboratory of Human Development and Reproductive Regulation, Tianjin, China
- Department of Neonatology, Nankai University Maternity Hospital, Tianjin, China
- Department of Neonatology, Tianjin Central Hospital of Obstetrics and Gynecology, Tianjin, China.
| |
Collapse
|
2
|
Mulas C. Control of cell state transitions by post-transcriptional regulation. Philos Trans R Soc Lond B Biol Sci 2024; 379:20230050. [PMID: 38432322 PMCID: PMC10909504 DOI: 10.1098/rstb.2023.0050] [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: 07/17/2023] [Accepted: 12/19/2023] [Indexed: 03/05/2024] Open
Abstract
Cell state transitions are prevalent in biology, playing a fundamental role in development, homeostasis and repair. Dysregulation of cell state transitions can lead to or occur in a wide range of diseases. In this letter, I explore and highlight the role of post-transcriptional regulatory mechanisms in determining the dynamics of cell state transitions. I propose that regulation of protein levels after transcription provides an under-appreciated regulatory route to obtain fast and sharp transitions between distinct cell states. This article is part of a discussion meeting issue 'Causes and consequences of stochastic processes in development and disease'.
Collapse
Affiliation(s)
- Carla Mulas
- Altos Labs Cambridge Institute of Science, Granta Park, Cambridge, CB21 6GP, UK
| |
Collapse
|
3
|
Jin SW, Seong Y, Yoon D, Kwon YS, Song H. Dissolution of ribonucleoprotein condensates by the embryonic stem cell protein L1TD1. Nucleic Acids Res 2024; 52:3310-3326. [PMID: 38165001 PMCID: PMC11014241 DOI: 10.1093/nar/gkad1244] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Revised: 11/22/2023] [Accepted: 12/18/2023] [Indexed: 01/03/2024] Open
Abstract
L1TD1 is a cytoplasmic RNA-binding protein specifically expressed in pluripotent stem cells and, unlike its mouse ortholog, is essential for the maintenance of stemness in human cells. Although L1TD1 is the only known protein-coding gene domesticated from a LINE-1 (L1) retroelement, the functional legacy of its ancestral protein, ORF1p of L1, and how it is manifested in L1TD1 are still unknown. Here, we determined RNAs associated with L1TD1 and found that, like ORF1p, L1TD1 binds L1 RNAs and localizes to high-density ribonucleoprotein (RNP) condensates. Unexpectedly, L1TD1 enhanced the translation of a subset of mRNAs enriched in the condensates. L1TD1 depletion promoted the formation of stress granules in embryonic stem cells. In HeLa cells, ectopically expressed L1TD1 facilitated the dissolution of stress granules and granules formed by pathological mutations of TDP-43 and FUS. The glutamate-rich domain and the ORF1-homology domain of L1TD1 facilitated dispersal of the RNPs and induced autophagy, respectively. These results provide insights into how L1TD1 regulates gene expression in pluripotent stem cells. We propose that the ability of L1TD1 to dissolve stress granules may provide novel opportunities for treatment of neurodegenerative diseases caused by disturbed stress granule dynamics.
Collapse
Affiliation(s)
- Sang Woo Jin
- Department of Biomedical Sciences, College of Medicine, Korea University, Seoul 02841, Republic of Korea
| | - Youngmo Seong
- Department of Biomedical Sciences, College of Medicine, Korea University, Seoul 02841, Republic of Korea
| | - Dayoung Yoon
- Department of Biomedical Sciences, College of Medicine, Korea University, Seoul 02841, Republic of Korea
| | - Young-Soo Kwon
- Department of Integrative Bioscience & Biotechnology, Sejong University, Seoul 05006, Republic of Korea
| | - Hoseok Song
- Department of Biomedical Sciences, College of Medicine, Korea University, Seoul 02841, Republic of Korea
| |
Collapse
|
4
|
Popescu MC, Haddock NL, Burgener EB, Rojas-Hernandez LS, Kaber G, Hargil A, Bollyky PL, Milla CE. The Inovirus Pf4 Triggers Antiviral Responses and Disrupts the Proliferation of Airway Basal Epithelial Cells. Viruses 2024; 16:165. [PMID: 38275975 PMCID: PMC10818373 DOI: 10.3390/v16010165] [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: 01/01/2024] [Revised: 01/18/2024] [Accepted: 01/19/2024] [Indexed: 01/27/2024] Open
Abstract
BACKGROUND The inovirus Pf4 is a lysogenic bacteriophage of Pseudomonas aeruginosa (Pa). People with Cystic Fibrosis (pwCF) experience chronic airway infection with Pa and a significant proportion have high numbers of Pf4 in their airway secretions. Given the known severe damage in the airways of Pa-infected pwCF, we hypothesized a high Pf4 burden can affect airway healing and inflammatory responses. In the airway, basal epithelial cells (BCs) are a multipotent stem cell population critical to epithelium homeostasis and repair. We sought to investigate the transcriptional responses of BCs under conditions that emulate infection with Pa and exposure to high Pf4 burden. METHODS Primary BCs isolated from pwCF and wild-type (WT) donors were cultured in vitro and exposed to Pf4 or bacterial Lipopolysaccharide (LPS) followed by transcriptomic and functional assays. RESULTS We found that BCs internalized Pf4 and this elicits a strong antiviral response as well as neutrophil chemokine production. Further, we found that BCs that take up Pf4 demonstrate defective migration and proliferation. CONCLUSIONS Our findings are highly suggestive of Pf4 playing a role in the pathogenicity of Pa in the airways. These findings provide additional evidence for the ability of inoviruses to interact with mammalian cells and disrupt cell function.
Collapse
Affiliation(s)
- Medeea C. Popescu
- Department of Infectious Diseases, Stanford University, Stanford, CA 94305, USA (P.L.B.)
- Immunology Program, Stanford University, Stanford, CA 94305, USA
| | - Naomi L. Haddock
- Department of Infectious Diseases, Stanford University, Stanford, CA 94305, USA (P.L.B.)
- Immunology Program, Stanford University, Stanford, CA 94305, USA
| | - Elizabeth B. Burgener
- Center for Excellence in Pulmonary Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Laura S. Rojas-Hernandez
- Center for Excellence in Pulmonary Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Gernot Kaber
- Department of Infectious Diseases, Stanford University, Stanford, CA 94305, USA (P.L.B.)
| | - Aviv Hargil
- Department of Infectious Diseases, Stanford University, Stanford, CA 94305, USA (P.L.B.)
| | - Paul L. Bollyky
- Department of Infectious Diseases, Stanford University, Stanford, CA 94305, USA (P.L.B.)
| | - Carlos E. Milla
- Center for Excellence in Pulmonary Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| |
Collapse
|
5
|
Harris SM, Su AL, Dou JF, Loch-Caruso R, Elkin ER, Jaber S, Bakulski KM. Placental cell conditioned media modifies hematopoietic stem cell transcriptome invitro. Placenta 2024; 145:117-125. [PMID: 38128222 DOI: 10.1016/j.placenta.2023.12.016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Revised: 12/07/2023] [Accepted: 12/11/2023] [Indexed: 12/23/2023]
Abstract
INTRODUCTION Hematopoietic stem cells are cells that differentiate into blood cell types. Although the placenta secretes hormones, proteins and other factors important for maternal/fetal health, cross-talk between placental and hematopoietic stem cells is poorly understood. Moreover, toxicant impacts on placental-hematopoietic stem cell communication is understudied. The goals of this study were to determine if factors secreted from placental cells alter transcriptomic responses in hematopoietic stem cells and if monoethylhexyl phthalate (MEHP), the bioactive metabolite of the pollutant diethylhexyl phthalate, modifies these effects. METHODS We used K-562 and BeWo cells as in vitro models of hematopoietic stem cells and placental syncytiotrophoblasts, respectively. We treated K-562 cells with medium conditioned by incubation with BeWo cells, medium conditioned with BeWo cells treated with 10 μM MEHP for 24 h, or controls treated with unconditioned medium. We extracted K-562 cell RNA, performed RNA sequencing, then conducted differential gene expression and pathway analysis. RESULTS Relative to controls, K-562 cells treated with BeWo cell conditioned medium differentially expressed 173 genes (FDR<0.05 and fold-change>2.0), including 2.4-fold upregulatation of tropomyosin 4 (TPM4, a cytoskeletal regulator involved in processes such as cell morphology and migration) and 3.3-fold upregulatation of sphingosine-1-phosphate receptor 3 (S1PR3, a mediator of myeloid cell differentiation and inflammatory responses). Upregulated genes were enriched for pathways including stem cell maintenance, cell proliferation and immune processes. Downregulated genes were enriched for terms involved in protein translation and transcriptional regulation. MEHP treatment differentially expressed eight genes (FDR<0.05), including genes involved in lipid metabolism (e.g., Perilipin 2, fold-change: 1.4; Carnitine Palmitoyltransferase 1A, fold-change: 1.4). DISCUSSION K-562 cells, a model of hematopoietic stem cells, are responsive to media conditioned by placental cells, potentially impacting pathways like stem cell maintenance.
Collapse
Affiliation(s)
- Sean M Harris
- School of Public Health, Department of Environmental Health Sciences, University of Michigan, 1415 Washington Heights, Ann Arbor, MI, 48109, USA.
| | - Anthony L Su
- Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA, 19104
| | - John F Dou
- School of Public Health, Department of Epidemiology, University of Michigan, 1415 Washington Heights, Ann Arbor, MI, 48109, USA
| | - Rita Loch-Caruso
- School of Public Health, Department of Environmental Health Sciences, University of Michigan, 1415 Washington Heights, Ann Arbor, MI, 48109, USA
| | - Elana R Elkin
- School of Public Health, Division of Environmental Health, San Diego State University, San Diego, CA, 92182, USA
| | - Sammy Jaber
- School of Public Health, Department of Environmental Health Sciences, University of Michigan, 1415 Washington Heights, Ann Arbor, MI, 48109, USA
| | - Kelly M Bakulski
- School of Public Health, Department of Epidemiology, University of Michigan, 1415 Washington Heights, Ann Arbor, MI, 48109, USA
| |
Collapse
|
6
|
Diniz F, Ngo NYN, Colon-Leyva M, Edgington-Giordano F, Hilliard S, Zwezdaryk K, Liu J, El-Dahr SS, Tortelote GG. Acetyl-CoA is a key molecule for nephron progenitor cell pool maintenance. Nat Commun 2023; 14:7733. [PMID: 38007516 PMCID: PMC10676360 DOI: 10.1038/s41467-023-43513-7] [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: 10/18/2022] [Accepted: 11/10/2023] [Indexed: 11/27/2023] Open
Abstract
Nephron endowment at birth impacts long-term renal and cardiovascular health, and it is contingent on the nephron progenitor cell (NPC) pool. Glycolysis modulation is essential for determining NPC fate, but the underlying mechanism is unclear. Combining RNA sequencing and quantitative proteomics we identify 267 genes commonly targeted by Wnt activation or glycolysis inhibition in NPCs. Several of the impacted pathways converge at Acetyl-CoA, a co-product of glucose metabolism. Notably, glycolysis inhibition downregulates key genes of the Mevalonate/cholesterol pathway and stimulates NPC differentiation. Sodium acetate supplementation rescues glycolysis inhibition effects and favors NPC maintenance without hindering nephrogenesis. Six2Cre-mediated removal of ATP-citrate lyase (Acly), an enzyme that converts citrate to acetyl-CoA, leads to NPC pool depletion, glomeruli count reduction, and increases Wnt4 expression at birth. Sodium acetate supplementation counters the effects of Acly deletion on cap-mesenchyme. Our findings show a pivotal role of acetyl-CoA metabolism in kidney development and uncover new avenues for manipulating nephrogenesis and preventing adult kidney disease.
Collapse
Affiliation(s)
- Fabiola Diniz
- Section of Pediatric Nephrology, Department of Pediatrics, Tulane University School of Medicine, New Orleans, LA, 70112, USA
| | - Nguyen Yen Nhi Ngo
- Section of Pediatric Nephrology, Department of Pediatrics, Tulane University School of Medicine, New Orleans, LA, 70112, USA
| | - Mariel Colon-Leyva
- Section of Pediatric Nephrology, Department of Pediatrics, Tulane University School of Medicine, New Orleans, LA, 70112, USA
| | - Francesca Edgington-Giordano
- Section of Pediatric Nephrology, Department of Pediatrics, Tulane University School of Medicine, New Orleans, LA, 70112, USA
| | - Sylvia Hilliard
- Section of Pediatric Nephrology, Department of Pediatrics, Tulane University School of Medicine, New Orleans, LA, 70112, USA
| | - Kevin Zwezdaryk
- Department of Microbiology and Immunology, Tulane University School of Medicine, New Orleans, LA, 70112, USA
| | - Jiao Liu
- Department of Human Genetics, Tulane University School of Medicine, New Orleans, LA, 70112, USA
| | - Samir S El-Dahr
- Section of Pediatric Nephrology, Department of Pediatrics, Tulane University School of Medicine, New Orleans, LA, 70112, USA
| | - Giovane G Tortelote
- Section of Pediatric Nephrology, Department of Pediatrics, Tulane University School of Medicine, New Orleans, LA, 70112, USA.
| |
Collapse
|
7
|
Li B, Jin X, Chan HM. Effects of low doses of methylmercury (MeHg) exposure on definitive endoderm cell differentiation in human embryonic stem cells. Arch Toxicol 2023; 97:2625-2641. [PMID: 37612375 PMCID: PMC10475006 DOI: 10.1007/s00204-023-03580-7] [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: 07/13/2023] [Accepted: 08/03/2023] [Indexed: 08/25/2023]
Abstract
Fetal development is one of the most sensitive windows to methylmercury (MeHg) toxicity. Laboratory and epidemiological studies have shown a dose-response relationship between fetal MeHg exposure and neuro performance in different life stages from infants to adults. In addition, MeHg exposure has been reported to be associated with disorders in endoderm-derived organs, such as morphological changes in liver cells and pancreatic cell dysfunctions. However, the mechanisms of the effects of MeHg on non-neuronal organs or systems, especially during the early development of endoderm-derived organs, remain unclear. Here we determined the effects of low concentrations of MeHg exposure during the differentiation of definitive endoderm (DE) cells from human embryonic stem cells (hESCs). hESCs were exposed to MeHg (0, 10, 100, and 200 nM) that covers the range of Hg concentrations typically found in human maternal blood during DE cell induction. Transcriptomic analysis showed that sub-lethal doses of MeHg exposure could alter global gene expression patterns during hESC to DE cell differentiation, leading to increased expression of endodermal genes/proteins and the over-promotion of endodermal fate, mainly through disrupting calcium homeostasis and generating ROS. Bioinformatic analysis results suggested that MeHg exerts its developmental toxicity mainly by disrupting ribosome biogenesis during early cell lineage differentiation. This disruption could lead to aberrant growth or dysfunctions of the developing endoderm-derived organs, and it may be the underlying mechanism for the observed congenital diseases later in life. Based on the results, we proposed an adverse outcome pathway for the effects of MeHg exposure during human embryonic stem cells to definitive endoderm differentiation.
Collapse
Affiliation(s)
- Bai Li
- Department of Biology, University of Ottawa, 30 Marie Curie, Ottawa, ON, K1N 6N5, Canada
| | - Xiaolei Jin
- Regulatory Toxicology Research Division, Bureau of Chemical Safety, Food Directorate, HPFB, Health Canada, 251 Sir Frederick Banting Driveway, Ottawa, ON, K1A 0K9, Canada.
| | - Hing Man Chan
- Department of Biology, University of Ottawa, 30 Marie Curie, Ottawa, ON, K1N 6N5, Canada.
| |
Collapse
|
8
|
Wu R, Ma R, Duan X, Zhang J, Li K, Yu L, Zhang M, Liu P, Wang C. Identification of specific prognostic markers for lung squamous cell carcinoma based on tumor progression, immune infiltration, and stem index. Front Immunol 2023; 14:1236444. [PMID: 37841237 PMCID: PMC10570622 DOI: 10.3389/fimmu.2023.1236444] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Accepted: 09/12/2023] [Indexed: 10/17/2023] Open
Abstract
Introduction Lung squamous cell carcinoma (LUSC) is a unique subform of nonsmall cell lung cancer (NSCLC). The lack of specific driver genes as therapeutic targets leads to worse prognoses in patients with LUSC, even with chemotherapy, radiotherapy, or immune checkpoint inhibitors. Furthermore, research on the LUSC-specific prognosis genes is lacking. This study aimed to develop a comprehensive LUSC-specific differentially expressed genes (DEGs) signature for prognosis correlated with tumor progression, immune infiltration,and stem index. Methods RNA sequencing data for LUSC and lung adenocarcinoma (LUAD) were extracted from The Cancer Genome Atlas (TCGA) data portal, and DEGs analyses were conducted in TCGA-LUSC and TCGA-LUAD cohorts to identify specific DEGs associated with LUSC. Functional analysis and protein-protein interaction network were performed to annotate the roles of LUSC-specific DEGs and select the top 100 LUSC-specific DEGs. Univariate Cox regression and least absolute shrinkage and selection operator regression analyses were performed to select prognosis-related DEGs. Results Overall, 1,604 LUSC-specific DEGs were obtained, and a validated seven-gene signature was constructed comprising FGG, C3, FGA, JUN, CST3, CPSF4, and HIST1H2BH. FGG, C3, FGA, JUN, and CST3 were correlated with poor LUSC prognosis, whereas CPSF4 and HIST1H2BH were potential positive prognosis markers in patients with LUSC. Receiver operating characteristic analysis further confirmed that the genetic profile could accurately estimate the overall survival of LUSC patients. Analysis of immune infiltration demonstrated that the high risk (HR) LUSC patients exhibited accelerated tumor infiltration, relative to low risk (LR) LUSC patients. Molecular expressions of immune checkpoint genes differed significantly between the HR and LR cohorts. A ceRNA network containing 19 lncRNAs, 50 miRNAs, and 7 prognostic DEGs was constructed to demonstrate the prognostic value of novel biomarkers of LUSC-specific DEGs based on tumor progression, stemindex, and immune infiltration. In vitro experimental models confirmed that LUSC-specific DEG FGG expression was significantly higher in tumor cells and correlated with immune tumor progression, immune infiltration, and stem index. In vitro experimental models confirmed that LUSC-specific DEG FGG expression was significantly higher in tumor cells and correlated with immune tumor progression, immune infiltration, and stem index. Conclusion Our study demonstrated the potential clinical implication of the 7- DEGs signature for prognosis prediction of LUSC patients based on tumor progression, immune infiltration, and stem index. And the FGG could be an independent prognostic biomarker of LUSC promoting cell proliferation, migration, invasion, THP-1 cell infiltration, and stem cell maintenance.
Collapse
Affiliation(s)
- Rihan Wu
- School of Life Science, Inner Mongolia University, Hohhot, China
- The Department of Oncology, Affiliated Hospital of Inner Mongolia Medical University, Hohhot, China
| | - Ru Ma
- School of Life Science, Inner Mongolia University, Hohhot, China
| | - Xiaojun Duan
- School of Life Science, Inner Mongolia University, Hohhot, China
- School of Basic Medicine, Inner Mongolia Medical University, Hohhot, China
| | - Jiandong Zhang
- School of Life Science, Inner Mongolia University, Hohhot, China
| | - Kexin Li
- School of Life Science, Inner Mongolia University, Hohhot, China
| | - Lei Yu
- School of Life Science, Inner Mongolia University, Hohhot, China
| | - Mingyang Zhang
- School of Life Science, Inner Mongolia University, Hohhot, China
| | - Pengxia Liu
- School of Life Science, Inner Mongolia University, Hohhot, China
| | - Changshan Wang
- School of Life Science, Inner Mongolia University, Hohhot, China
| |
Collapse
|
9
|
Puppo M, Valluru MK, Croset M, Ceresa D, Iuliani M, Khan A, Wicinski J, Charafe-Jauffret E, Ginestier C, Pantano F, Ottewell PD, Clézardin P. MiR-662 is associated with metastatic relapse in early-stage breast cancer and promotes metastasis by stimulating cancer cell stemness. Br J Cancer 2023; 129:754-771. [PMID: 37443350 PMCID: PMC10449914 DOI: 10.1038/s41416-023-02340-9] [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: 09/28/2022] [Revised: 06/01/2023] [Accepted: 06/20/2023] [Indexed: 07/15/2023] Open
Abstract
BACKGROUND Breast cancer (BC) metastasis, which often occurs in bone, contributes substantially to mortality. MicroRNAs play a fundamental role in BC metastasis, although microRNA-regulated mechanisms driving metastasis progression remain poorly understood. METHODS MiRome analysis in serum from BC patients was performed by TaqMan™ low-density array. MiR-662 was overexpressed following MIMIC-transfection or lentivirus transduction. Animal models were used to investigate the role of miR-662 in BC (bone) metastasis. The effect of miR-662-overexpressing BC cell conditioned medium on osteoclastogenesis was investigated. ALDEFLUOR assays were performed to study BC stemness. RNA-sequencing transcriptomic analysis of miR-662-overexpressing BC cells was performed to evaluate gene expression changes. RESULTS High levels of hsa-miR-662 (miR-662) in serum from BC patients, at baseline (time of surgery), were associated with future recurrence in bone. At an early-stage of the metastatic disease, miR-662 could mask the presence of BC metastases in bone by inhibiting the differentiation of bone-resorbing osteoclasts. Nonetheless, metastatic miR-662-overexpressing BC cells then progressed as overt osteolytic metastases thanks to increased stem cell-like traits. CONCLUSIONS MiR-662 is involved in BC metastasis progression, suggesting it may be used as a prognostic marker to identify BC patients at high risk of metastasis.
Collapse
Affiliation(s)
- Margherita Puppo
- Department of Oncology and Metabolism, Medical School, University of Sheffield, Sheffield, UK.
- INSERM, Research Unit UMR_S1033, LyOS, Faculty of Medicine Lyon-Est, Lyon, France.
- Univ Lyon, Université Claude Bernard Lyon 1, F-69008, Lyon, France.
| | - Manoj Kumar Valluru
- Department of Oncology and Metabolism, Medical School, University of Sheffield, Sheffield, UK
- Department of Infection, Immunity and Cardiovascular, Medical School, University of Sheffield, Sheffield, UK
| | - Martine Croset
- INSERM, Research Unit UMR_S1033, LyOS, Faculty of Medicine Lyon-Est, Lyon, France
- Univ Lyon, Université Claude Bernard Lyon 1, F-69008, Lyon, France
- INSERM U1052, CNRS UMR_5286, Centre Léon Bérard, Centre de Recherche en Cancérologie de Lyon, Lyon, France
| | - Davide Ceresa
- IRCCS AOU San Martino, Università degli studi di Genova, Genova, Italy
| | - Michele Iuliani
- Medical Oncology, Fondazione Policlinico Universitario Campus Bio-Medico, Via Alvaro del Portillo 200, 00128, Roma, Italy
- Department of Medicine and Surgery, Università Campus Bio-Medico di Roma, Via Alvaro del Portillo 21, 00128, Roma, Italy
| | - Ashrin Khan
- Department of Oncology and Metabolism, Medical School, University of Sheffield, Sheffield, UK
| | - Julien Wicinski
- Aix-Marseille Univ, Inserm, CNRS, Institut Paoli-Calmettes, CRCM, Epithelial Stem Cells and Cancer Lab, "Equipe labellisée Ligue Contre le Cancer", Marseille, France
| | - Emmanuelle Charafe-Jauffret
- Aix-Marseille Univ, Inserm, CNRS, Institut Paoli-Calmettes, CRCM, Epithelial Stem Cells and Cancer Lab, "Equipe labellisée Ligue Contre le Cancer", Marseille, France
| | - Christophe Ginestier
- Aix-Marseille Univ, Inserm, CNRS, Institut Paoli-Calmettes, CRCM, Epithelial Stem Cells and Cancer Lab, "Equipe labellisée Ligue Contre le Cancer", Marseille, France
| | - Francesco Pantano
- Medical Oncology, Fondazione Policlinico Universitario Campus Bio-Medico, Via Alvaro del Portillo 200, 00128, Roma, Italy
- Department of Medicine and Surgery, Università Campus Bio-Medico di Roma, Via Alvaro del Portillo 21, 00128, Roma, Italy
| | - Penelope Dawn Ottewell
- Department of Oncology and Metabolism, Medical School, University of Sheffield, Sheffield, UK
| | - Philippe Clézardin
- Department of Oncology and Metabolism, Medical School, University of Sheffield, Sheffield, UK.
- INSERM, Research Unit UMR_S1033, LyOS, Faculty of Medicine Lyon-Est, Lyon, France.
- Univ Lyon, Université Claude Bernard Lyon 1, F-69008, Lyon, France.
| |
Collapse
|
10
|
Gonzalez-Menendez P, Phadke I, Olive ME, Joly A, Papoin J, Yan H, Galtier J, Platon J, Kang SWS, McGraw KL, Daumur M, Pouzolles M, Kondo T, Boireau S, Paul F, Young DJ, Lamure S, Mirmira RG, Narla A, Cartron G, Dunbar CE, Boyer-Clavel M, Porat-Shliom N, Dardalhon V, Zimmermann VS, Sitbon M, Dever TE, Mohandas N, Da Costa L, Udeshi ND, Blanc L, Kinet S, Taylor N. Arginine metabolism regulates human erythroid differentiation through hypusination of eIF5A. Blood 2023; 141:2520-2536. [PMID: 36735910 PMCID: PMC10273172 DOI: 10.1182/blood.2022017584] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Revised: 01/20/2023] [Accepted: 01/20/2023] [Indexed: 02/05/2023] Open
Abstract
Metabolic programs contribute to hematopoietic stem and progenitor cell (HSPC) fate, but it is not known whether the metabolic regulation of protein synthesis controls HSPC differentiation. Here, we show that SLC7A1/cationic amino acid transporter 1-dependent arginine uptake and its catabolism to the polyamine spermidine control human erythroid specification of HSPCs via the activation of the eukaryotic translation initiation factor 5A (eIF5A). eIF5A activity is dependent on its hypusination, a posttranslational modification resulting from the conjugation of the aminobutyl moiety of spermidine to lysine. Notably, attenuation of hypusine synthesis in erythroid progenitors, by the inhibition of deoxyhypusine synthase, abrogates erythropoiesis but not myeloid cell differentiation. Proteomic profiling reveals mitochondrial translation to be a critical target of hypusinated eIF5A, and accordingly, progenitors with decreased hypusine activity exhibit diminished oxidative phosphorylation. This affected pathway is critical for eIF5A-regulated erythropoiesis, as interventions augmenting mitochondrial function partially rescue human erythropoiesis under conditions of attenuated hypusination. Levels of mitochondrial ribosomal proteins (RPs) were especially sensitive to the loss of hypusine, and we find that the ineffective erythropoiesis linked to haploinsufficiency of RPS14 in chromosome 5q deletions in myelodysplastic syndrome is associated with a diminished pool of hypusinated eIF5A. Moreover, patients with RPL11-haploinsufficient Diamond-Blackfan anemia as well as CD34+ progenitors with downregulated RPL11 exhibit a markedly decreased hypusination in erythroid progenitors, concomitant with a loss of mitochondrial metabolism. Thus, eIF5A-dependent protein synthesis regulates human erythropoiesis, and our data reveal a novel role for RPs in controlling eIF5A hypusination in HSPCs, synchronizing mitochondrial metabolism with erythroid differentiation.
Collapse
Affiliation(s)
- Pedro Gonzalez-Menendez
- Institut de Génétique Moléculaire de Montpellier, Université de Montpellier, Centre National de la Recherche Scientifique (CNRS), Montpellier, France
- Laboratory of Excellence GR-Ex, Paris, France
| | - Ira Phadke
- Institut de Génétique Moléculaire de Montpellier, Université de Montpellier, Centre National de la Recherche Scientifique (CNRS), Montpellier, France
- Laboratory of Excellence GR-Ex, Paris, France
- Pediatric Oncology Branch, National Cancer Institute (NCI), Center for Cancer Research (CCR), National Institutes of Health (NIH), Bethesda, MD
| | - Meagan E. Olive
- Proteomics Platform, Broad Institute, Massachusetts Institute of Technology and Harvard University, Cambridge, MA
| | - Axel Joly
- Institut de Génétique Moléculaire de Montpellier, Université de Montpellier, Centre National de la Recherche Scientifique (CNRS), Montpellier, France
- Laboratory of Excellence GR-Ex, Paris, France
| | - Julien Papoin
- Feinstein Institute for Medical Research, Manhasset, NY
- EA4666 HEMATIM, Université Picardie Jules Verne, Amiens, France
| | | | - Jérémy Galtier
- Institut de Génétique Moléculaire de Montpellier, Université de Montpellier, Centre National de la Recherche Scientifique (CNRS), Montpellier, France
- Laboratory of Excellence GR-Ex, Paris, France
| | - Jessica Platon
- EA4666 HEMATIM, Université Picardie Jules Verne, Amiens, France
| | | | - Kathy L. McGraw
- Laboratory of Receptor Biology and Gene Expression, NCI, CCR, NIH, Bethesda, MD
| | - Marie Daumur
- Institut de Génétique Moléculaire de Montpellier, Université de Montpellier, Centre National de la Recherche Scientifique (CNRS), Montpellier, France
- Laboratory of Excellence GR-Ex, Paris, France
| | - Marie Pouzolles
- Pediatric Oncology Branch, National Cancer Institute (NCI), Center for Cancer Research (CCR), National Institutes of Health (NIH), Bethesda, MD
| | - Taisuke Kondo
- Pediatric Oncology Branch, National Cancer Institute (NCI), Center for Cancer Research (CCR), National Institutes of Health (NIH), Bethesda, MD
| | - Stéphanie Boireau
- Institut de Génétique Moléculaire de Montpellier, Université de Montpellier, Centre National de la Recherche Scientifique (CNRS), Montpellier, France
- Montpellier Ressources Imagerie, BioCampus, University of Montpellier, CNRS, INSERM, Montpellier, France
| | - Franciane Paul
- Department of Clinical Hematology, Centre Hospitalier Universitaire de Montpellier, Montpellier, France
| | - David J. Young
- Translational Stem Cell Biology Branch, National Heart, Lung, and Blood Institute, NIH, Bethesda, MD
| | - Sylvain Lamure
- Institut de Génétique Moléculaire de Montpellier, Université de Montpellier, Centre National de la Recherche Scientifique (CNRS), Montpellier, France
- Department of Clinical Hematology, Centre Hospitalier Universitaire de Montpellier, Montpellier, France
| | | | - Anupama Narla
- Division of Pediatric Hematology/Oncology, Stanford University, Stanford, CA
| | - Guillaume Cartron
- Institut de Génétique Moléculaire de Montpellier, Université de Montpellier, Centre National de la Recherche Scientifique (CNRS), Montpellier, France
- Department of Clinical Hematology, Centre Hospitalier Universitaire de Montpellier, Montpellier, France
| | - Cynthia E. Dunbar
- Translational Stem Cell Biology Branch, National Heart, Lung, and Blood Institute, NIH, Bethesda, MD
| | - Myriam Boyer-Clavel
- Institut de Génétique Moléculaire de Montpellier, Université de Montpellier, Centre National de la Recherche Scientifique (CNRS), Montpellier, France
| | | | - Valérie Dardalhon
- Institut de Génétique Moléculaire de Montpellier, Université de Montpellier, Centre National de la Recherche Scientifique (CNRS), Montpellier, France
| | - Valérie S. Zimmermann
- Institut de Génétique Moléculaire de Montpellier, Université de Montpellier, Centre National de la Recherche Scientifique (CNRS), Montpellier, France
| | - Marc Sitbon
- Institut de Génétique Moléculaire de Montpellier, Université de Montpellier, Centre National de la Recherche Scientifique (CNRS), Montpellier, France
- Laboratory of Excellence GR-Ex, Paris, France
| | - Thomas E. Dever
- Section on Protein Biosynthesis, Eunice Kennedy Shriver National Institute of Child Health and Human Development, NIH, Bethesda, MD
| | | | - Lydie Da Costa
- Laboratory of Excellence GR-Ex, Paris, France
- EA4666 HEMATIM, Université Picardie Jules Verne, Amiens, France
- Service d'Hématologie Biologique (Hematology Diagnostic Laboratory), Assistance Publique–Hôpitaux de Paris, Robert Debr Hôpital, Paris, France
- Paris Cité University, Paris, France
| | - Namrata D. Udeshi
- Proteomics Platform, Broad Institute, Massachusetts Institute of Technology and Harvard University, Cambridge, MA
| | - Lionel Blanc
- Feinstein Institute for Medical Research, Manhasset, NY
| | - Sandrina Kinet
- Institut de Génétique Moléculaire de Montpellier, Université de Montpellier, Centre National de la Recherche Scientifique (CNRS), Montpellier, France
- Laboratory of Excellence GR-Ex, Paris, France
| | - Naomi Taylor
- Institut de Génétique Moléculaire de Montpellier, Université de Montpellier, Centre National de la Recherche Scientifique (CNRS), Montpellier, France
- Laboratory of Excellence GR-Ex, Paris, France
- Pediatric Oncology Branch, National Cancer Institute (NCI), Center for Cancer Research (CCR), National Institutes of Health (NIH), Bethesda, MD
| |
Collapse
|
11
|
Rodrigues A, MacQuarrie KL, Freeman E, Lin A, Willis AB, Xu Z, Alvarez AA, Ma Y, White BEP, Foltz DR, Huang S. Nucleoli and the nucleoli-centromere association are dynamic during normal development and in cancer. Mol Biol Cell 2023; 34:br5. [PMID: 36753381 PMCID: PMC10092642 DOI: 10.1091/mbc.e22-06-0237] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Revised: 01/19/2023] [Accepted: 01/30/2023] [Indexed: 02/09/2023] Open
Abstract
Centromeres are known to cluster around nucleoli in Drosophila and mammalian cells, but the significance of the nucleoli-centromere interaction remains underexplored. To determine whether the interaction is dynamic under different physiological and pathological conditions, we examined nucleolar structure and centromeres at various differentiation stages using cell culture models and the results showed dynamic changes in nucleolar characteristics and nucleoli-centromere interactions through differentiation and in cancer cells. Embryonic stem cells usually have a single large nucleolus, which is clustered with a high percentage of centromeres. As cells differentiate into intermediate states, the nucleolar number increases and the centromere association decreases. In terminally differentiated cells, including myotubes, neurons, and keratinocytes, the number of nucleoli and their association with centromeres are at the lowest. Cancer cells demonstrate the pattern of nucleoli number and nucleoli-centromere association that is akin to proliferative cell types, suggesting that nucleolar reorganization and changes in nucleoli-centromere interactions may play a role in facilitating malignant transformation. This idea is supported in a case of pediatric rhabdomyosarcoma, in which induced differentiation reduces the nucleolar number and centromere association. These findings suggest active roles of nucleolar structure in centromere function and genome organization critical for cellular function in both normal development and cancer.
Collapse
Affiliation(s)
- Aaron Rodrigues
- Department of Cell and Developmental Biology, Northwestern University Feinberg School of Medicine, Chicago, IL 60611
| | - Kyle L. MacQuarrie
- Division of Hematology, Oncology, and Stem Cell Transplantation, Department of Pediatrics, Northwestern University Feinberg School of Medicine, Chicago, IL 60611
| | - Emma Freeman
- Department of Cell and Developmental Biology, Northwestern University Feinberg School of Medicine, Chicago, IL 60611
| | - Alicia Lin
- Department of Cell and Developmental Biology, Northwestern University Feinberg School of Medicine, Chicago, IL 60611
| | - Alexander B. Willis
- Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, IL 60611
| | - Zhaofa Xu
- Departments of Pediatrics, Neurology and Neuroscience, Northwestern University Feinberg School of Medicine, Chicago, IL 60611
- Ann & Robert H. Lurie Children’s Hospital of Chicago, Chicago, IL 60611
| | - Angel A. Alvarez
- Stem Cell Core and Ken & Ruth Davee Department of Neurology, Northwestern University Feinberg School of Medicine, Chicago, IL 60611
| | - Yongchao Ma
- Departments of Pediatrics, Neurology and Neuroscience, Northwestern University Feinberg School of Medicine, Chicago, IL 60611
- Ann & Robert H. Lurie Children’s Hospital of Chicago, Chicago, IL 60611
| | - Bethany E. Perez White
- Department of Dermatology and Skin Biology and Diseases Resource-based Center, Northwestern University Feinberg School of Medicine, Chicago, IL 60611
| | - Daniel R. Foltz
- Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, IL 60611
| | - Sui Huang
- Department of Cell and Developmental Biology, Northwestern University Feinberg School of Medicine, Chicago, IL 60611
| |
Collapse
|
12
|
Harris SM, Su AL, Dou JF, Loch-Caruso R, Elkin ER, Jaber S, Bakulski KM. Placental Cell Conditioned Media Modifies Hematopoietic Stem Cell Transcriptome In Vitro. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.27.534393. [PMID: 37034658 PMCID: PMC10081206 DOI: 10.1101/2023.03.27.534393] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/19/2023]
Abstract
Background Hematopoietic stem cells are cells that differentiate into all blood cell types. Although the placenta secretes hormones, proteins and other factors important for maternal and fetal health, cross-talk between placental cells and hematopoietic stem cells is poorly understood. Moreover, toxicant impacts on placental-hematopoietic stem cell communication is understudied. The goals of this study were to determine if factors secreted from placental cells alter transcriptomic responses in hematopoietic stem cells and if monoethylhexyl phthalate (MEHP), the bioactive metabolite of the pollutant diethylhexyl phthalate, modifies these effects. Methods We used K-562 and BeWo cells as in vitro models of hematopoietic stem cells and placental syncytiotrophoblasts, respectively. We treated K-562 cells with medium conditioned by incubation with BeWo cells, medium conditioned with BeWo cells treated with 10 μM MEHP for 24 hours, or controls treated with unconditioned medium. We extracted K-562 cell RNA, performed RNA sequencing, then conducted differential gene expression and pathway analysis by treatment group. Results Relative to controls, K-562 cells treated with BeWo cell conditioned medium differentially expressed 173 genes (FDR<0.05 and fold-change>2.0), including 2.4 fold upregulatation of TPM4 and 3.3 fold upregulatation of S1PR3. Upregulated genes were enriched for pathways including stem cell maintenance, cell proliferation and immune processes. Downregulated genes were enriched for terms involved in protein translation and transcriptional regulation. MEHP treatment differentially expressed eight genes (FDR<0.05), including genes involved in lipid metabolism (PLIN2, fold-change: 1.4; CPT1A, fold-change: 1.4). Conclusion K-562 cells, a model of hematopoietic stem cells, are responsive to media conditioned by placental cells, potentially impacting pathways like stem cell maintenance and proliferation.
Collapse
Affiliation(s)
- Sean M. Harris
- School of Public Health, Department of Environmental Health Sciences, University of Michigan, 1415 Washington Heights, Ann Arbor, MI, 48109, USA
| | - Anthony L. Su
- Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA 19104
| | - John F. Dou
- School of Public Health, Department of Epidemiology, University of Michigan, 1415 Washington Heights, Ann Arbor, MI, 48109, USA
| | - Rita Loch-Caruso
- School of Public Health, Department of Environmental Health Sciences, University of Michigan, 1415 Washington Heights, Ann Arbor, MI, 48109, USA
| | - Elana R. Elkin
- School of Public Health, Department of Environmental Health Sciences, University of Michigan, 1415 Washington Heights, Ann Arbor, MI, 48109, USA
| | - Sammy Jaber
- School of Public Health, Department of Environmental Health Sciences, University of Michigan, 1415 Washington Heights, Ann Arbor, MI, 48109, USA
| | - Kelly M. Bakulski
- School of Public Health, Department of Epidemiology, University of Michigan, 1415 Washington Heights, Ann Arbor, MI, 48109, USA
| |
Collapse
|
13
|
The P-body protein 4E-T represses translation to regulate the balance between cell genesis and establishment of the postnatal NSC pool. Cell Rep 2023; 42:112242. [PMID: 36924490 DOI: 10.1016/j.celrep.2023.112242] [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: 08/25/2022] [Revised: 01/19/2023] [Accepted: 02/23/2023] [Indexed: 03/17/2023] Open
Abstract
Here, we ask how developing precursors maintain the balance between cell genesis for tissue growth and establishment of adult stem cell pools, focusing on postnatal forebrain neural precursor cells (NPCs). We show that these NPCs are transcriptionally primed to differentiate and that the primed mRNAs are associated with the translational repressor 4E-T. 4E-T also broadly associates with other NPC mRNAs encoding transcriptional regulators, and these are preferentially depleted from ribosomes, consistent with repression. By contrast, a second translational regulator, Cpeb4, associates with diverse target mRNAs that are largely ribosome associated. The 4E-T-dependent mRNA association is functionally important because 4E-T knockdown or conditional knockout derepresses proneurogenic mRNA translation and perturbs maintenance versus differentiation of early postnatal NPCs in culture and in vivo. Thus, early postnatal NPCs are primed to differentiate, and 4E-T regulates the balance between cell genesis and stem cell expansion by sequestering and repressing mRNAs encoding transcriptional regulators.
Collapse
|
14
|
Cordero-Véliz C, Larraín J, Faunes F. Transcriptome analysis of the response to thyroid hormone in Xenopus neural stem and progenitor cells. Dev Dyn 2023; 252:294-304. [PMID: 36065982 DOI: 10.1002/dvdy.535] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2022] [Revised: 08/19/2022] [Accepted: 08/28/2022] [Indexed: 11/12/2022] Open
Abstract
BACKGROUND The thyroid hormones-thyroxine (T4) and 3,5,3'triiodothyronine (T3)-regulate the development of the central nervous system (CNS) in vertebrates by acting in different cell types. Although several T3 target genes have been identified in the brain, the changes in the transcriptome in response to T3 specifically in neural stem and progenitor cells (NSPCs) during the early steps of NSPCs activation and neurogenesis have not been studied in vivo. Here, we characterized the transcriptome of FACS-sorted NSPCs in response to T3 during Xenopus laevis metamorphosis. RESULTS We identified 1252 upregulated and 726 downregulated genes after 16 hours of T3 exposure. Gene ontology and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis revealed that T3-upregulated genes were significantly enriched in rRNA processing and maturation, protein folding, ribosome biogenesis, translation, mitochondrial function, and proteasome. These results suggest that NSPCs activation induced by T3 is characterized by an early proteome remodeling through the synthesis of the translation machinery and the degradation of proteins by the proteasome. CONCLUSION This work provides new insights into the dynamics of activation of NPSCs in vivo in response to T3 during a critical period of neurogenesis in the metamorphosis.
Collapse
Affiliation(s)
- Camila Cordero-Véliz
- Departamento de Ciencias Biológicas, Facultad de Ciencias de la Vida, Universidad Andres Bello, Viña del Mar, Chile
| | - Juan Larraín
- Center for Aging and Regeneration, Faculty of Biological Sciences, P. Universidad Católica de Chile, Santiago, Chile
| | - Fernando Faunes
- Departamento de Ciencias Biológicas, Facultad de Ciencias de la Vida, Universidad Andres Bello, Viña del Mar, Chile
| |
Collapse
|
15
|
Domingo-Muelas A, Duart-Abadia P, Morante-Redolat JM, Jordán-Pla A, Belenguer G, Fabra-Beser J, Paniagua-Herranz L, Pérez-Villalba A, Álvarez-Varela A, Barriga FM, Gil-Sanz C, Ortega F, Batlle E, Fariñas I. Post-transcriptional control of a stemness signature by RNA-binding protein MEX3A regulates murine adult neurogenesis. Nat Commun 2023; 14:373. [PMID: 36690670 PMCID: PMC9871011 DOI: 10.1038/s41467-023-36054-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Accepted: 01/12/2023] [Indexed: 01/25/2023] Open
Abstract
Neural stem cells (NSCs) in the adult murine subependymal zone balance their self-renewal capacity and glial identity with the potential to generate neurons during the lifetime. Adult NSCs exhibit lineage priming via pro-neurogenic fate determinants. However, the protein levels of the neural fate determinants are not sufficient to drive direct differentiation of adult NSCs, which raises the question of how cells along the neurogenic lineage avoid different conflicting fate choices, such as self-renewal and differentiation. Here, we identify RNA-binding protein MEX3A as a post-transcriptional regulator of a set of stemness associated transcripts at critical transitions in the subependymal neurogenic lineage. MEX3A regulates a quiescence-related RNA signature in activated NSCs that is needed for their return to quiescence, playing a role in the long-term maintenance of the NSC pool. Furthermore, it is required for the repression of the same program at the onset of neuronal differentiation. Our data indicate that MEX3A is a pivotal regulator of adult murine neurogenesis acting as a translational remodeller.
Collapse
Grants
- EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Excellent Science | H2020 European Research Council (H2020 Excellent Science - European Research Council)
- Ministerio de Ciencia e Innovación (MICINN, Spain) - PID2020-119917RB-I00.
- Regional Government of Valencia | Conselleria d'Educació, Investigació, Cultura i Esport (Conselleria d'Educació, Investigació, Cultura i Esport de la Generalitat Valenciana)
- Ministerio de Ciencia e Innovación (MICINN, Spain) - PID2020-117937GB-I00, PID2020-119917RB-I00, PID 2019-109155RB-I00, PID2020-114227RB-I00, RyC-2015-19058, PRE2018-084838. Centro de Investigación Biomédica en Red Enfermedades Neurodegenerativas (CIBERNED, Spain) - MICINN- CB06/05/0086.
Collapse
Affiliation(s)
- Ana Domingo-Muelas
- Departamento de Biología Celular, Biología Funcional y Antropología Física, Universidad de Valencia, Valencia, Spain
- Instituto de Biotecnología y Biomedicina (BIOTECMED), Universidad de Valencia, Valencia, Spain
- Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas (CIBERNED), Valencia, Spain
| | - Pere Duart-Abadia
- Departamento de Biología Celular, Biología Funcional y Antropología Física, Universidad de Valencia, Valencia, Spain
- Instituto de Biotecnología y Biomedicina (BIOTECMED), Universidad de Valencia, Valencia, Spain
- Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas (CIBERNED), Valencia, Spain
| | - Jose Manuel Morante-Redolat
- Departamento de Biología Celular, Biología Funcional y Antropología Física, Universidad de Valencia, Valencia, Spain
- Instituto de Biotecnología y Biomedicina (BIOTECMED), Universidad de Valencia, Valencia, Spain
- Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas (CIBERNED), Valencia, Spain
| | - Antonio Jordán-Pla
- Instituto de Biotecnología y Biomedicina (BIOTECMED), Universidad de Valencia, Valencia, Spain
| | - Germán Belenguer
- Departamento de Biología Celular, Biología Funcional y Antropología Física, Universidad de Valencia, Valencia, Spain
- Instituto de Biotecnología y Biomedicina (BIOTECMED), Universidad de Valencia, Valencia, Spain
- Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas (CIBERNED), Valencia, Spain
| | - Jaime Fabra-Beser
- Departamento de Biología Celular, Biología Funcional y Antropología Física, Universidad de Valencia, Valencia, Spain
- Instituto de Biotecnología y Biomedicina (BIOTECMED), Universidad de Valencia, Valencia, Spain
| | - Lucía Paniagua-Herranz
- Departamento de Bioquímica y Biología Molecular, Universidad Complutense de Madrid (UCM), Madrid, Spain
- Instituto Universitario de Investigación en Neuroquímica (IUIN), Madrid, Spain
- Instituto de Investigación Sanitaria San Carlos (IdISSC), Madrid, Spain
| | - Ana Pérez-Villalba
- Departamento de Biología Celular, Biología Funcional y Antropología Física, Universidad de Valencia, Valencia, Spain
- Instituto de Biotecnología y Biomedicina (BIOTECMED), Universidad de Valencia, Valencia, Spain
- Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas (CIBERNED), Valencia, Spain
| | - Adrián Álvarez-Varela
- Institute for Research in Biomedicine (IRB Barcelona), Barcelona, Spain
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Barcelona, Spain
| | - Francisco M Barriga
- Institute for Research in Biomedicine (IRB Barcelona), Barcelona, Spain
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Barcelona, Spain
| | - Cristina Gil-Sanz
- Departamento de Biología Celular, Biología Funcional y Antropología Física, Universidad de Valencia, Valencia, Spain
- Instituto de Biotecnología y Biomedicina (BIOTECMED), Universidad de Valencia, Valencia, Spain
- Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas (CIBERNED), Valencia, Spain
| | - Felipe Ortega
- Departamento de Bioquímica y Biología Molecular, Universidad Complutense de Madrid (UCM), Madrid, Spain
- Instituto Universitario de Investigación en Neuroquímica (IUIN), Madrid, Spain
- Instituto de Investigación Sanitaria San Carlos (IdISSC), Madrid, Spain
| | - Eduard Batlle
- Institute for Research in Biomedicine (IRB Barcelona), Barcelona, Spain.
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Barcelona, Spain.
- ICREA, Barcelona, Spain.
| | - Isabel Fariñas
- Departamento de Biología Celular, Biología Funcional y Antropología Física, Universidad de Valencia, Valencia, Spain.
- Instituto de Biotecnología y Biomedicina (BIOTECMED), Universidad de Valencia, Valencia, Spain.
- Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas (CIBERNED), Valencia, Spain.
| |
Collapse
|
16
|
Zhang L, Chen Z, Gao Q, Liu G, Zheng J, Ding F. Preterm birth leads to a decreased number of differentiated podocytes and accelerated podocyte differentiation. Front Cell Dev Biol 2023; 11:1142929. [PMID: 36936687 PMCID: PMC10018169 DOI: 10.3389/fcell.2023.1142929] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Accepted: 02/20/2023] [Indexed: 03/06/2023] Open
Abstract
Preterm birth was previously identified as a high-risk factor for the long-term development of chronic kidney disease. However, the detailed pattern of podocyte (PD) changes caused by preterm birth and the potential mechanism underlying this process have not been well clarified. In present study, a rat model of preterm birth was established by delivery of pups 2 days early and podometric methods were applied to identify the changes in PDs number caused by preterm birth. In addition, single-cell RNA sequencing (scRNA-seq) and subsequent bioinformatic analysis were performed in the preterm rat kidney to explore the possible mechanism caused by preterm birth. As results, when the kidney completely finished nephrogenesis at the age of 3 weeks, a reduction in the total number of differentiated PDs in kidney sections was detected. In addition, 20 distinct clusters and 12 different cell types were identified after scRNA-seq in preterm rats (postnatal day 2) and full-term rats (postnatal day 0). The numbers of PDs and most types of inherent kidney cells were decreased in the preterm birth model. In addition, 177 genes were upregulated while 82 genes were downregulated in the PDs of full-term rats compared with those of preterm rats. Further functional GO analysis revealed that ribosome-related genes were enriched in PDs from full-term rats, and kidney development-related genes were enriched in PDs from preterm rats. Moreover, known PD-specific and PD precursor genes were highly expressed in PDs from preterm rats, and pseudotemporal analysis showed that PDs were present earlier in preterm rats than in full-term rats. In conclusion, the present study showed that preterm birth could cause a reduction in the number of differentiated PDs and accelerate the differentiation of PDs.
Collapse
Affiliation(s)
- Lulu Zhang
- Department of Neonatology, Tianjin Central Hospital of Obstetrics and Gynecology, Tianjin, China
- Tianjin Key Laboratory of Human Development and Reproductive Regulation, Tianjin, China
- Department of Neonatology, Nankai University Maternity Hospital, Tianjin, China
| | - Zhihui Chen
- Department of Neonatology, Tianjin Central Hospital of Obstetrics and Gynecology, Tianjin, China
- Tianjin Key Laboratory of Human Development and Reproductive Regulation, Tianjin, China
- Department of Neonatology, Nankai University Maternity Hospital, Tianjin, China
| | - Qi Gao
- Department of Neonatology, Tianjin Central Hospital of Obstetrics and Gynecology, Tianjin, China
- Tianjin Key Laboratory of Human Development and Reproductive Regulation, Tianjin, China
- Department of Neonatology, Nankai University Maternity Hospital, Tianjin, China
| | - Ge Liu
- Department of Neonatology, Tianjin Central Hospital of Obstetrics and Gynecology, Tianjin, China
- Tianjin Key Laboratory of Human Development and Reproductive Regulation, Tianjin, China
- Department of Neonatology, Nankai University Maternity Hospital, Tianjin, China
| | - Jun Zheng
- Department of Neonatology, Tianjin Central Hospital of Obstetrics and Gynecology, Tianjin, China
- Tianjin Key Laboratory of Human Development and Reproductive Regulation, Tianjin, China
- Department of Neonatology, Nankai University Maternity Hospital, Tianjin, China
- *Correspondence: Jun Zheng, (JZ); Fangrui Ding, (FD)
| | - Fangrui Ding
- Department of Neonatology, Tianjin Central Hospital of Obstetrics and Gynecology, Tianjin, China
- Tianjin Key Laboratory of Human Development and Reproductive Regulation, Tianjin, China
- Department of Neonatology, Nankai University Maternity Hospital, Tianjin, China
- *Correspondence: Jun Zheng, (JZ); Fangrui Ding, (FD)
| |
Collapse
|
17
|
Abstract
The methyltransferase-like (METTL) family is a diverse group of methyltransferases that can methylate nucleotides, proteins, and small molecules. Despite this diverse array of substrates, they all share a characteristic seven-beta-strand catalytic domain, and recent evidence suggests many also share an important role in stem cell biology. The most well characterized family members METTL3 and METTL14 dimerize to form an N6-methyladenosine (m6A) RNA methyltransferase with established roles in cancer progression. However, new mouse models indicate that METTL3/METTL14 are also important for embryonic stem cell (ESC) development and postnatal hematopoietic and neural stem cell self-renewal and differentiation. METTL1, METTL5, METTL6, METTL8, and METTL17 also have recently identified roles in ESC pluripotency and differentiation, while METTL11A/11B, METTL4, METTL7A, and METTL22 have been shown to play roles in neural, mesenchymal, bone, and hematopoietic stem cell development, respectively. Additionally, a variety of other METTL family members are translational regulators, a role that could place them as important players in the transition from stem cell quiescence to differentiation. Here we will summarize what is known about the role of METTL proteins in stem cell differentiation and highlight the connection between their growing importance in development and their established roles in oncogenesis.
Collapse
Affiliation(s)
- John G Tooley
- Department of Biochemistry, Jacobs School of Medicine and Biomedical Sciences, State University of New York at Buffalo, 955 Main St., Buffalo, NY, 14203, USA
| | - James P Catlin
- Department of Biochemistry, Jacobs School of Medicine and Biomedical Sciences, State University of New York at Buffalo, 955 Main St., Buffalo, NY, 14203, USA
| | - Christine E Schaner Tooley
- Department of Biochemistry, Jacobs School of Medicine and Biomedical Sciences, State University of New York at Buffalo, 955 Main St., Buffalo, NY, 14203, USA.
| |
Collapse
|
18
|
Caruso M, Meurant S, Detraux D, Mathieu A, Gilson M, Dieu M, Fattaccioli A, Demazy C, Najimi M, Sokal E, Arnould T, Verfaillie C, Lafontaine DLJ, Renard P. The global downregulation of protein synthesis observed during hepatogenic maturation is associated with a decrease in TOP mRNA translation. Stem Cell Reports 2022; 18:254-268. [PMID: 36563686 PMCID: PMC9860114 DOI: 10.1016/j.stemcr.2022.11.020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Revised: 11/18/2022] [Accepted: 11/21/2022] [Indexed: 12/24/2022] Open
Abstract
Translational regulation is of paramount importance for proteome remodeling during stem cell differentiation at both the global and the transcript-specific levels. In this study, we characterized translational remodeling during hepatogenic differentiation of induced pluripotent stem cells (iPSCs) by polysome profiling. We demonstrate that protein synthesis increases during exit from pluripotency and is then globally repressed during later steps of hepatogenic maturation. This global downregulation of translation is accompanied by a decrease in the abundance of protein components of the translation machinery, which involves a global reduction in translational efficiency of terminal oligopyrimidine tract (TOP) mRNA encoding translation-related factors. Despite global translational repression during hepatogenic differentiation, key hepatogenic genes remain efficiently translated, and the translation of several transcripts involved in hepatospecific functions and metabolic maturation is even induced. We conclude that, during hepatogenic differentiation, a global decrease in protein synthesis is accompanied by a specific translational rewiring of hepatospecific transcripts.
Collapse
Affiliation(s)
- Marino Caruso
- Laboratory of Biochemistry and Cell Biology (URBC), Namur Research Institute for Life Sciences (NARILIS), University of Namur (UNamur), Namur, Belgium
| | - Sébastien Meurant
- Laboratory of Biochemistry and Cell Biology (URBC), Namur Research Institute for Life Sciences (NARILIS), University of Namur (UNamur), Namur, Belgium
| | - Damien Detraux
- Laboratory of Biochemistry and Cell Biology (URBC), Namur Research Institute for Life Sciences (NARILIS), University of Namur (UNamur), Namur, Belgium
| | - Amandine Mathieu
- Laboratory of Biochemistry and Cell Biology (URBC), Namur Research Institute for Life Sciences (NARILIS), University of Namur (UNamur), Namur, Belgium; Laboratory of Pediatric Hepatology and Cell Therapy, Institut de Recherche Clinique et Expérimentale (IREC), Catholic University of Louvain, Brussels, Belgium
| | - Manon Gilson
- Laboratory of Biochemistry and Cell Biology (URBC), Namur Research Institute for Life Sciences (NARILIS), University of Namur (UNamur), Namur, Belgium
| | - Marc Dieu
- Mass Spectrometry Facility (MaSUN), University of Namur, Namur, Belgium
| | - Antoine Fattaccioli
- Laboratory of Biochemistry and Cell Biology (URBC), Namur Research Institute for Life Sciences (NARILIS), University of Namur (UNamur), Namur, Belgium
| | - Catherine Demazy
- Laboratory of Biochemistry and Cell Biology (URBC), Namur Research Institute for Life Sciences (NARILIS), University of Namur (UNamur), Namur, Belgium; Mass Spectrometry Facility (MaSUN), University of Namur, Namur, Belgium
| | - Mustapha Najimi
- Laboratory of Pediatric Hepatology and Cell Therapy, Institut de Recherche Clinique et Expérimentale (IREC), Catholic University of Louvain, Brussels, Belgium
| | - Etienne Sokal
- Laboratory of Pediatric Hepatology and Cell Therapy, Institut de Recherche Clinique et Expérimentale (IREC), Catholic University of Louvain, Brussels, Belgium
| | - Thierry Arnould
- Laboratory of Biochemistry and Cell Biology (URBC), Namur Research Institute for Life Sciences (NARILIS), University of Namur (UNamur), Namur, Belgium
| | - Catherine Verfaillie
- Department of Development and Regeneration, Stem Cell Institute, KU Leuven, Leuven, Belgium
| | - Denis L J Lafontaine
- RNA Molecular Biology, Fonds de la Recherche Scientifique (FRS/FNRS), Université Libre de Bruxelles (ULB), Biopark Campus, Gosselies, Belgium
| | - Patricia Renard
- Laboratory of Biochemistry and Cell Biology (URBC), Namur Research Institute for Life Sciences (NARILIS), University of Namur (UNamur), Namur, Belgium; Laboratory of Pediatric Hepatology and Cell Therapy, Institut de Recherche Clinique et Expérimentale (IREC), Catholic University of Louvain, Brussels, Belgium.
| |
Collapse
|
19
|
Burramsetty AK, Nishimura K, Kishimoto T, Hamzah M, Kuno A, Fukuda A, Hisatake K. Locus-Specific Isolation of the Nanog Chromatin Identifies Regulators Relevant to Pluripotency of Mouse Embryonic Stem Cells and Reprogramming of Somatic Cells. Int J Mol Sci 2022; 23:ijms232315242. [PMID: 36499566 PMCID: PMC9740452 DOI: 10.3390/ijms232315242] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Revised: 11/28/2022] [Accepted: 11/30/2022] [Indexed: 12/11/2022] Open
Abstract
Pluripotency is a crucial feature of pluripotent stem cells, which are regulated by the core pluripotency network consisting of key transcription factors and signaling molecules. However, relatively less is known about the molecular mechanisms that modify the core pluripotency network. Here we used the CAPTURE (CRISPR Affinity Purification in situ of Regulatory Elements) to unbiasedly isolate proteins assembled on the Nanog promoter in mouse embryonic stem cells (mESCs), and then tested their functional relevance to the maintenance of mESCs and reprogramming of somatic cells. Gene ontology analysis revealed that the identified proteins, including many RNA-binding proteins (RBPs), are enriched in RNA-related functions and gene expression. ChIP-qPCR experiments confirmed that BCLAF1, FUBP1, MSH6, PARK7, PSIP1, and THRAP3 occupy the Nanog promoter region in mESCs. Knockdown experiments of these factors show that they play varying roles in self-renewal, pluripotency gene expression, and differentiation of mESCs as well as in the reprogramming of somatic cells. Our results show the utility of unbiased identification of chromatin-associated proteins on a pluripotency gene in mESCs and reveal the functional relevance of RBPs in ESC differentiation and somatic cell reprogramming.
Collapse
Affiliation(s)
- Arun Kumar Burramsetty
- Laboratory of Gene Regulation, Faculty of Medicine, University of Tsukuba, 1-1-1 Tennodai, Tsukuba 305-8575, Japan
| | - Ken Nishimura
- Laboratory of Gene Regulation, Faculty of Medicine, University of Tsukuba, 1-1-1 Tennodai, Tsukuba 305-8575, Japan
- Correspondence: (K.N.); (K.H.)
| | - Takumi Kishimoto
- Laboratory of Gene Regulation, Faculty of Medicine, University of Tsukuba, 1-1-1 Tennodai, Tsukuba 305-8575, Japan
| | - Muhammad Hamzah
- Laboratory of Gene Regulation, Faculty of Medicine, University of Tsukuba, 1-1-1 Tennodai, Tsukuba 305-8575, Japan
| | - Akihiro Kuno
- Laboratory of Animal Resource Center, Department of Anatomy and Embryology, Faculty of Medicine, University of Tsukuba, 1-1-1 Tennodai, Tsukuba 305-8575, Japan
- Ph.D. Program in Human Biology, School of Integrative and Global Majors, University of Tsukuba, Tsukuba 305-8575, Japan
| | - Aya Fukuda
- Laboratory of Gene Regulation, Faculty of Medicine, University of Tsukuba, 1-1-1 Tennodai, Tsukuba 305-8575, Japan
| | - Koji Hisatake
- Laboratory of Gene Regulation, Faculty of Medicine, University of Tsukuba, 1-1-1 Tennodai, Tsukuba 305-8575, Japan
- Correspondence: (K.N.); (K.H.)
| |
Collapse
|
20
|
Fluorescence Spectroscopy of Low-Level Endogenous β-adrenergic Receptor Expression at the Plasma Membrane of Differentiating Human iPSC-Derived Cardiomyocytes. Int J Mol Sci 2022; 23:ijms231810405. [PMID: 36142320 PMCID: PMC9499492 DOI: 10.3390/ijms231810405] [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: 07/24/2022] [Revised: 09/02/2022] [Accepted: 09/06/2022] [Indexed: 11/17/2022] Open
Abstract
The potential of human-induced pluripotent stem cells (hiPSCs) to be differentiated into cardiomyocytes (CMs) mimicking adult CMs functional morphology, marker genes and signaling characteristics has been investigated since over a decade. The evolution of the membrane localization of CM-specific G protein-coupled receptors throughout differentiation has received, however, only limited attention to date. We employ here advanced fluorescent spectroscopy, namely linescan Fluorescence Correlation Spectroscopy (FCS), to observe how the plasma membrane abundance of the β1- and β2-adrenergic receptors (β1/2-ARs), labelled using a bright and photostable fluorescent antagonist, evolves during the long-term monolayer culture of hiPSC-derived CMs. We compare it to the kinetics of observed mRNA levels in wildtype (WT) hiPSCs and in two CRISPR/Cas9 knock-in clones. We conduct these observations against the backdrop of our recent report of cell-to-cell expression variability, as well as of the subcellular localization heterogeneity of β-ARs in adult CMs.
Collapse
|
21
|
Lv K, Tong W. A protein synthesis brake for hematopoietic stem cell maintenance. Genes Dev 2022; 36:871-873. [PMID: 36207141 PMCID: PMC9575693 DOI: 10.1101/gad.350107.122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
Bmi1 is essential for normal and leukemic hematopoiesis, but its target genes in hematopoietic stem cells (HSCs) are incompletely understood. In this issue of Genes & Development, Burgess et al. (pp. 887-900) demonstrate a novel role of Bmi1 in regulating ribosome biogenesis and protein synthesis. Bmi1-deficient HSCs exhibited reduced transplantability, with the up-regulation of ARX and genes involved in ribosome biogenesis. However, depletion of ARX or its known targets, p16 Ink4a /p19 Arf , only partially rescues Bmi1 loss-induced hematopoietic defects. They further demonstrate an increased protein synthesis rate and resultant proteostatic stress in Bmi1 -/- HSCs, indicating a novel mechanism by which Bmi1 controls HSC maintenance.
Collapse
Affiliation(s)
- Kaosheng Lv
- Department of Biochemistry, School of Medicine, Southern University of Science and Technology, Shenzhen, Guangdong 518000, China
| | - Wei Tong
- Children's Hospital of Philadelphia; Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| |
Collapse
|
22
|
Guo YL, Gurung C, Fendereski M, Huang F. Dicer and PKR as Novel Regulators of Embryonic Stem Cell Fate and Antiviral Innate Immunity. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2022; 208:2259-2266. [PMID: 35577384 PMCID: PMC9179006 DOI: 10.4049/jimmunol.2200042] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Accepted: 03/21/2022] [Indexed: 05/17/2023]
Abstract
Embryonic stem cells (ESCs) represent a unique cell population in the blastocyst stage embryo. They have been intensively studied as a promising cell source for regenerative medicine. Recent studies have revealed that both human and mouse ESCs are deficient in expressing IFNs and have attenuated inflammatory responses. Apparently, the ability to express IFNs and respond to certain inflammatory cytokines is not "innate" to ESCs but rather is developmentally acquired by somatic cells during differentiation. Accumulating evidence supports a hypothesis that the attenuated innate immune response may serve as a protective mechanism allowing ESCs to avoid immunological cytotoxicity. This review describes our current understanding of the molecular basis that shapes the immune properties of ESCs. We highlight the recent findings on Dicer and dsRNA-activated protein kinase R as novel regulators of ESC fate and antiviral immunity and discuss how ESCs use alternative mechanisms to accommodate their stem cell properties.
Collapse
Affiliation(s)
- Yan-Lin Guo
- Cell and Molecular Biology Program, University of Southern Mississippi, Hattiesburg, MS; and
| | - Chandan Gurung
- Cell and Molecular Biology Program, University of Southern Mississippi, Hattiesburg, MS; and
| | - Mona Fendereski
- Cell and Molecular Biology Program, University of Southern Mississippi, Hattiesburg, MS; and
| | - Faqing Huang
- Chemistry and Biochemistry Program, University of Southern Mississippi, Hattiesburg, MS
| |
Collapse
|
23
|
Rehn M, Wenzel A, Frank AK, Schuster MB, Pundhir S, Jørgensen N, Vitting-Seerup K, Ge Y, Jendholm J, Michaut M, Schoof EM, Jensen TL, Rapin N, Sapio RT, Andersen KL, Lund AH, Solimena M, Holzenberger M, Pestov DG, Porse BT. PTBP1 promotes hematopoietic stem cell maintenance and red blood cell development by ensuring sufficient availability of ribosomal constituents. Cell Rep 2022; 39:110793. [PMID: 35545054 DOI: 10.1016/j.celrep.2022.110793] [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: 06/07/2021] [Revised: 03/14/2022] [Accepted: 04/15/2022] [Indexed: 11/18/2022] Open
Abstract
Ribosomopathies constitute a range of disorders associated with defective protein synthesis mainly affecting hematopoietic stem cells (HSCs) and erythroid development. Here, we demonstrate that deletion of poly-pyrimidine-tract-binding protein 1 (PTBP1) in the hematopoietic compartment leads to the development of a ribosomopathy-like condition. Specifically, loss of PTBP1 is associated with decreases in HSC self-renewal, erythroid differentiation, and protein synthesis. Consistent with its function as a splicing regulator, PTBP1 deficiency results in splicing defects in hundreds of genes, and we demonstrate that the up-regulation of a specific isoform of CDC42 partly mimics the protein-synthesis defect associated with loss of PTBP1. Furthermore, PTBP1 deficiency is associated with a marked defect in ribosome biogenesis and a selective reduction in the translation of mRNAs encoding ribosomal proteins. Collectively, this work identifies PTBP1 as a key integrator of ribosomal functions and highlights the broad functional repertoire of RNA-binding proteins.
Collapse
Affiliation(s)
- Matilda Rehn
- The Finsen Laboratory, Rigshospitalet, Faculty of Health Sciences, University of Copenhagen, 2200 Copenhagen, Denmark; Biotech Research and Innovation Center (BRIC), University of Copenhagen, 2200 Copenhagen, Denmark; Novo Nordisk Foundation Center for Stem Cell Biology, DanStem, Faculty of Health Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Anne Wenzel
- The Finsen Laboratory, Rigshospitalet, Faculty of Health Sciences, University of Copenhagen, 2200 Copenhagen, Denmark; Biotech Research and Innovation Center (BRIC), University of Copenhagen, 2200 Copenhagen, Denmark; Novo Nordisk Foundation Center for Stem Cell Biology, DanStem, Faculty of Health Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Anne-Katrine Frank
- The Finsen Laboratory, Rigshospitalet, Faculty of Health Sciences, University of Copenhagen, 2200 Copenhagen, Denmark; Biotech Research and Innovation Center (BRIC), University of Copenhagen, 2200 Copenhagen, Denmark; Novo Nordisk Foundation Center for Stem Cell Biology, DanStem, Faculty of Health Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Mikkel Bruhn Schuster
- The Finsen Laboratory, Rigshospitalet, Faculty of Health Sciences, University of Copenhagen, 2200 Copenhagen, Denmark; Biotech Research and Innovation Center (BRIC), University of Copenhagen, 2200 Copenhagen, Denmark; Novo Nordisk Foundation Center for Stem Cell Biology, DanStem, Faculty of Health Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Sachin Pundhir
- The Finsen Laboratory, Rigshospitalet, Faculty of Health Sciences, University of Copenhagen, 2200 Copenhagen, Denmark; Biotech Research and Innovation Center (BRIC), University of Copenhagen, 2200 Copenhagen, Denmark; Novo Nordisk Foundation Center for Stem Cell Biology, DanStem, Faculty of Health Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Nanna Jørgensen
- The Finsen Laboratory, Rigshospitalet, Faculty of Health Sciences, University of Copenhagen, 2200 Copenhagen, Denmark; Biotech Research and Innovation Center (BRIC), University of Copenhagen, 2200 Copenhagen, Denmark; Novo Nordisk Foundation Center for Stem Cell Biology, DanStem, Faculty of Health Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
| | | | - Ying Ge
- The Finsen Laboratory, Rigshospitalet, Faculty of Health Sciences, University of Copenhagen, 2200 Copenhagen, Denmark; Biotech Research and Innovation Center (BRIC), University of Copenhagen, 2200 Copenhagen, Denmark; Novo Nordisk Foundation Center for Stem Cell Biology, DanStem, Faculty of Health Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Johan Jendholm
- The Finsen Laboratory, Rigshospitalet, Faculty of Health Sciences, University of Copenhagen, 2200 Copenhagen, Denmark; Biotech Research and Innovation Center (BRIC), University of Copenhagen, 2200 Copenhagen, Denmark; Novo Nordisk Foundation Center for Stem Cell Biology, DanStem, Faculty of Health Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Magali Michaut
- The Finsen Laboratory, Rigshospitalet, Faculty of Health Sciences, University of Copenhagen, 2200 Copenhagen, Denmark; Biotech Research and Innovation Center (BRIC), University of Copenhagen, 2200 Copenhagen, Denmark; Novo Nordisk Foundation Center for Stem Cell Biology, DanStem, Faculty of Health Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Erwin M Schoof
- The Finsen Laboratory, Rigshospitalet, Faculty of Health Sciences, University of Copenhagen, 2200 Copenhagen, Denmark; Biotech Research and Innovation Center (BRIC), University of Copenhagen, 2200 Copenhagen, Denmark; Novo Nordisk Foundation Center for Stem Cell Biology, DanStem, Faculty of Health Sciences, University of Copenhagen, 2200 Copenhagen, Denmark; DTU Bioengineering, Danish Technical University, 2800 Kgs. Lyngby, Denmark
| | - Tanja Lyholm Jensen
- The Finsen Laboratory, Rigshospitalet, Faculty of Health Sciences, University of Copenhagen, 2200 Copenhagen, Denmark; Biotech Research and Innovation Center (BRIC), University of Copenhagen, 2200 Copenhagen, Denmark; Novo Nordisk Foundation Center for Stem Cell Biology, DanStem, Faculty of Health Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Nicolas Rapin
- The Finsen Laboratory, Rigshospitalet, Faculty of Health Sciences, University of Copenhagen, 2200 Copenhagen, Denmark; Biotech Research and Innovation Center (BRIC), University of Copenhagen, 2200 Copenhagen, Denmark; Novo Nordisk Foundation Center for Stem Cell Biology, DanStem, Faculty of Health Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Russell T Sapio
- Department of Cell Biology and Neuroscience, Rowan University School of Osteopathic Medicine, Stratford, NJ 08084, USA
| | | | - Anders H Lund
- Biotech Research and Innovation Center (BRIC), University of Copenhagen, 2200 Copenhagen, Denmark
| | - Michele Solimena
- Molecular Diabetology, University Hospital and Faculty of Medicine, Technische Universität Dresden, Dresden, Germany; Paul Langerhans Institute Dresden of the Helmholtz Center Munich at University Hospital and Faculty of Medicine, Technische Universität Dresden, Dresden, Germany; Max Planck Institute for Molecular Cell Biology and Genetics, Dresden, Germany; German Center for Diabetes Research (DZD e.V.), Neuherberg, Germany
| | - Martin Holzenberger
- Sorbonne University, INSERM, Research Center Saint-Antoine, CRSA, 75012 Paris, France
| | - Dimitri G Pestov
- Department of Cell Biology and Neuroscience, Rowan University School of Osteopathic Medicine, Stratford, NJ 08084, USA
| | - Bo Torben Porse
- The Finsen Laboratory, Rigshospitalet, Faculty of Health Sciences, University of Copenhagen, 2200 Copenhagen, Denmark; Biotech Research and Innovation Center (BRIC), University of Copenhagen, 2200 Copenhagen, Denmark; Novo Nordisk Foundation Center for Stem Cell Biology, DanStem, Faculty of Health Sciences, University of Copenhagen, 2200 Copenhagen, Denmark.
| |
Collapse
|
24
|
Chen C, Zhang X, Wang Y, Chen X, Chen W, Dan S, She S, Hu W, Dai J, Hu J, Cao Q, Liu Q, Huang Y, Qin B, Kang B, Wang YJ. Translational and post-translational control of human naïve versus primed pluripotency. iScience 2022; 25:103645. [PMID: 35005567 PMCID: PMC8718978 DOI: 10.1016/j.isci.2021.103645] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Revised: 10/22/2021] [Accepted: 12/10/2021] [Indexed: 01/05/2023] Open
Abstract
Deciphering the regulatory network for human naive and primed pluripotency is of fundamental theoretical and applicable significance. Here, by combining quantitative proteomics, phosphoproteomics, and acetylproteomics analyses, we revealed RNA processing and translation as the most differentially regulated processes between naive and primed human embryonic stem cells (hESCs). Although glycolytic primed hESCs rely predominantly on the eukaryotic initiation factor 4E (eIF4E)-mediated cap-dependent pathway for protein translation, naive hESCs with reduced mammalian target of rapamycin complex (mTORC1) activity are more tolerant to eIF4E inhibition, and their bivalent metabolism allows for translating selective mRNAs via both eIF4E-dependent and eIF4E-independent/eIF4A2-dependent pathways to form a more compact naive proteome. Globally up-regulated proteostasis and down-regulated post-translational modifications help to further refine the naive proteome that is compatible with the more rapid cycling of naive hESCs, where CDK1 plays an indispensable coordinative role. These findings may assist in better understanding the unrestricted lineage potential of naive hESCs and in further optimizing conditions for future clinical applications RNA processing and translation are most different between naive and primed hESCs Glycolytic primed hESCs mainly rely on eIF4E-dependent translation Bivalent metabolism in naive hESCs promotes eIF4E-independent translation CDK1 is required for naive pluripotency partially by activating E-cadherin signaling
Collapse
Affiliation(s)
- Cheng Chen
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang 310003, China.,Shaoxing People's Hospital, Shaoxing Hospital, Zhejiang University School of Medicine, Shaoxing, Zhejiang 312000, China
| | - Xiaobing Zhang
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang 310003, China
| | - Yisha Wang
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang 310003, China
| | - Xinyu Chen
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang 310003, China
| | - Wenjie Chen
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang 310003, China
| | - Songsong Dan
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang 310003, China
| | - Shiqi She
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang 310003, China.,Zhejiang Museum of Natural History, Hangzhou, Zhejiang 310014, China
| | - Weiwei Hu
- Shanghai Bioprofile Technology Co., Ltd., Shanghai 200241, China
| | - Jie Dai
- Shanghai Bioprofile Technology Co., Ltd., Shanghai 200241, China
| | - Jianwen Hu
- Shanghai Bioprofile Technology Co., Ltd., Shanghai 200241, China
| | - Qingyi Cao
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang 310003, China
| | - Qianyu Liu
- College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Yinghua Huang
- Laboratory of Metabolism and Cell Fate, Center for Cell Lineage and Development, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
| | - Baoming Qin
- Laboratory of Metabolism and Cell Fate, Center for Cell Lineage and Development, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
| | - Bo Kang
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang 310003, China
| | - Ying-Jie Wang
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang 310003, China.,Cancer Center, Zhejiang University, Hangzhou, Zhejiang 310058, China
| |
Collapse
|
25
|
Sepich-Poore C, Zheng Z, Schmitt E, Wen K, Zhang ZS, Cui XL, Dai Q, Zhu AC, Zhang L, Sanchez Castillo A, Tan H, Peng J, Zhuang X, He C, Nachtergaele S. The METTL5-TRMT112 N 6-methyladenosine methyltransferase complex regulates mRNA translation via 18S rRNA methylation. J Biol Chem 2022; 298:101590. [PMID: 35033535 PMCID: PMC8857481 DOI: 10.1016/j.jbc.2022.101590] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Revised: 01/03/2022] [Accepted: 01/05/2022] [Indexed: 12/13/2022] Open
Abstract
Ribosomal RNAs (rRNAs) have long been known to carry chemical modifications, including 2'O-methylation, pseudouridylation, N6-methyladenosine (m6A), and N6,6-dimethyladenosine. While the functions of many of these modifications are unclear, some are highly conserved and occur in regions of the ribosome critical for mRNA decoding. Both 28S rRNA and 18S rRNA carry single m6A sites, and while the methyltransferase ZCCHC4 has been identified as the enzyme responsible for the 28S rRNA m6A modification, the methyltransferase responsible for the 18S rRNA m6A modification has remained unclear. Here, we show that the METTL5-TRMT112 methyltransferase complex installs the m6A modification at position 1832 of human 18S rRNA. Our work supports findings that TRMT112 is required for METTL5 stability and reveals that human METTL5 mutations associated with microcephaly and intellectual disability disrupt this interaction. We show that loss of METTL5 in human cancer cell lines and in mice regulates gene expression at the translational level; additionally, Mettl5 knockout mice display reduced body size and evidence of metabolic defects. While recent work has focused heavily on m6A modifications in mRNA and their roles in mRNA processing and translation, we demonstrate here that deorphanizing putative methyltransferase enzymes can reveal previously unappreciated regulatory roles for m6A in noncoding RNAs.
Collapse
Affiliation(s)
- Caraline Sepich-Poore
- Department of Chemistry, University of Chicago, Chicago, Illinois, USA; Institute for Biophysical Dynamics, University of Chicago, Chicago, Illinois, USA; Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, Illinois, USA; University of Chicago Medical Scientist Training Program, Chicago, Illinois, USA
| | - Zhong Zheng
- Department of Chemistry, University of Chicago, Chicago, Illinois, USA; Institute for Biophysical Dynamics, University of Chicago, Chicago, Illinois, USA
| | - Emily Schmitt
- Department of Chemistry, University of Chicago, Chicago, Illinois, USA; Institute for Biophysical Dynamics, University of Chicago, Chicago, Illinois, USA
| | - Kailong Wen
- Department of Neurobiology, University of Chicago, Chicago, Illinois, USA
| | - Zijie Scott Zhang
- Department of Chemistry, University of Chicago, Chicago, Illinois, USA; Institute for Biophysical Dynamics, University of Chicago, Chicago, Illinois, USA
| | - Xiao-Long Cui
- Department of Chemistry, University of Chicago, Chicago, Illinois, USA; Institute for Biophysical Dynamics, University of Chicago, Chicago, Illinois, USA
| | - Qing Dai
- Department of Chemistry, University of Chicago, Chicago, Illinois, USA
| | - Allen C Zhu
- Department of Chemistry, University of Chicago, Chicago, Illinois, USA; Institute for Biophysical Dynamics, University of Chicago, Chicago, Illinois, USA; Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, Illinois, USA; University of Chicago Medical Scientist Training Program, Chicago, Illinois, USA
| | - Linda Zhang
- Department of Chemistry, University of Chicago, Chicago, Illinois, USA; Institute for Biophysical Dynamics, University of Chicago, Chicago, Illinois, USA
| | - Arantxa Sanchez Castillo
- Department of Chemistry, University of Chicago, Chicago, Illinois, USA; Institute for Biophysical Dynamics, University of Chicago, Chicago, Illinois, USA
| | - Haiyan Tan
- Center for Proteomics and Metabolomics, St Jude Children's Research Hospital, Memphis, Tennessee, USA; Departments of Structural Biology and Developmental Neurobiology, St Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Junmin Peng
- Center for Proteomics and Metabolomics, St Jude Children's Research Hospital, Memphis, Tennessee, USA; Departments of Structural Biology and Developmental Neurobiology, St Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Xiaoxi Zhuang
- Department of Neurobiology, University of Chicago, Chicago, Illinois, USA
| | - Chuan He
- Department of Chemistry, University of Chicago, Chicago, Illinois, USA; Institute for Biophysical Dynamics, University of Chicago, Chicago, Illinois, USA; Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, Illinois, USA; Howard Hughes Medical Institute, University of Chicago, Chicago, Illinois, USA.
| | - Sigrid Nachtergaele
- Department of Chemistry, University of Chicago, Chicago, Illinois, USA; Institute for Biophysical Dynamics, University of Chicago, Chicago, Illinois, USA.
| |
Collapse
|
26
|
Salamon I, Rasin MR. Evolution of the Neocortex Through RNA-Binding Proteins and Post-transcriptional Regulation. Front Neurosci 2022; 15:803107. [PMID: 35082597 PMCID: PMC8784817 DOI: 10.3389/fnins.2021.803107] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Accepted: 12/16/2021] [Indexed: 12/24/2022] Open
Abstract
The human neocortex is undoubtedly considered a supreme accomplishment in mammalian evolution. It features a prenatally established six-layered structure which remains plastic to the myriad of changes throughout an organism’s lifetime. A fundamental feature of neocortical evolution and development is the abundance and diversity of the progenitor cell population and their neuronal and glial progeny. These evolutionary upgrades are partially enabled due to the progenitors’ higher proliferative capacity, compartmentalization of proliferative regions, and specification of neuronal temporal identities. The driving force of these processes may be explained by temporal molecular patterning, by which progenitors have intrinsic capacity to change their competence as neocortical neurogenesis proceeds. Thus, neurogenesis can be conceptualized along two timescales of progenitors’ capacity to (1) self-renew or differentiate into basal progenitors (BPs) or neurons or (2) specify their fate into distinct neuronal and glial subtypes which participate in the formation of six-layers. Neocortical development then proceeds through sequential phases of proliferation, differentiation, neuronal migration, and maturation. Temporal molecular patterning, therefore, relies on the precise regulation of spatiotemporal gene expression. An extensive transcriptional regulatory network is accompanied by post-transcriptional regulation that is frequently mediated by the regulatory interplay between RNA-binding proteins (RBPs). RBPs exhibit important roles in every step of mRNA life cycle in any system, from splicing, polyadenylation, editing, transport, stability, localization, to translation (protein synthesis). Here, we underscore the importance of RBP functions at multiple time-restricted steps of early neurogenesis, starting from the cell fate transition of transcriptionally primed cortical progenitors. A particular emphasis will be placed on RBPs with mostly conserved but also divergent evolutionary functions in neural progenitors across different species. RBPs, when considered in the context of the fascinating process of neocortical development, deserve to be main protagonists in the story of the evolution and development of the neocortex.
Collapse
|
27
|
Chung WM, Molony RD, Lee YF. Non-stem bladder cancer cell-derived extracellular vesicles promote cancer stem cell survival in response to chemotherapy. Stem Cell Res Ther 2021; 12:533. [PMID: 34627375 PMCID: PMC8502272 DOI: 10.1186/s13287-021-02600-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Accepted: 09/23/2021] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Chemosenstive non-stem cancer cells (NSCCs) constitute the bulk of tumors and are considered as part of the cancer stem cell (CSC) niche in the tumor microenvironment (TME). Tumor-derived extracellular vesicles (EVs) mediate the communication between tumors and the TME. In this study, we sought to investigate the impacts of EVs released by NSCCs on the maintenance of CSC properties and chemoresistance. METHODS We employed murine MB49 bladder cancer (BC) sub-lines representing CSCs and NSCCs as a model system. Chemotherapy drugs were used to treat NSCCs in order to collect conditioned EVs. The impacts of NSCC-derived EVs on CSC progression were evaluated through sphere formation, cytotoxicity, migration, and invasion assays, and by analyzing surface marker expression on these BC cells. Differential proteomic analyses were conducted to identify cargo protein candidates involved in the EV-mediated communication between NSCCs and CSCs. RESULTS NSCC-derived EVs contained cargo proteins enriched in proteostasis-related functions, and significantly altered the development of CSCs such that they were more intrinsically chemoresistant, aggressive, and better able to undergo self-renewal. CONCLUSIONS We thus identified a novel communication mechanism whereby NSCC-EVs can alter the relative fitness of CSCs to promote disease progression and the acquisition of chemoresistance.
Collapse
Affiliation(s)
- Wei-Min Chung
- Department of Urology, University of Rochester Medical Center, 601 Elmwood Ave, Box 656, Rochester, NY, 14642, USA
| | - Ryan D Molony
- Department of Urology, University of Rochester Medical Center, 601 Elmwood Ave, Box 656, Rochester, NY, 14642, USA
| | - Yi-Fen Lee
- Department of Urology, University of Rochester Medical Center, 601 Elmwood Ave, Box 656, Rochester, NY, 14642, USA. .,Pathology and Laboratory Medicine, University of Rochester Medical Center, Rochester, NY, USA. .,Wilmot Cancer Institute, University of Rochester Medical Center, Rochester, NY, USA.
| |
Collapse
|
28
|
Gomes-Júnior R, Shigunov P, Dallagiovanna B, Pereira IT. Accessing the Human Pluripotent Stem Cell Translatome by Polysome Profiling. METHODS IN MOLECULAR BIOLOGY (CLIFTON, N.J.) 2021; 2520:309-319. [PMID: 34611819 DOI: 10.1007/7651_2021_437] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Polysome profiling is a technique that uses sucrose density gradient ultracentrifugation to separate complexes of mRNAs associated with one or more ribosomes. Here we describe polysome profiling analysis in human pluripotent stem cells (hPSCs) using a continuous ultraviolet spectrophotometer and a gradient fractionator. We provide protocols for processing sucrose gradient fractions for isolation of RNA for RT-qPCR or large-scale sequencing analysis, used to establish the translational status of specific mRNAs and identify the role of noncoding RNA in translation.
Collapse
|
29
|
Kling MJ, Griggs CN, McIntyre EM, Alexander G, Ray S, Challagundla KB, Joshi SS, Coulter DW, Chaturvedi NK. Synergistic efficacy of inhibiting MYCN and mTOR signaling against neuroblastoma. BMC Cancer 2021; 21:1061. [PMID: 34565342 PMCID: PMC8474810 DOI: 10.1186/s12885-021-08782-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Accepted: 09/14/2021] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Neuroblastoma (NB) patients with MYCN amplification or overexpression respond poorly to current therapies and exhibit extremely poor clinical outcomes. PI3K-mTOR signaling-driven deregulation of protein synthesis is very common in NB and various other cancers that promote MYCN stabilization. In addition, both the MYCN and mTOR signaling axes can directly regulate a common translation pathway that leads to increased protein synthesis and cell proliferation. However, a strategy of concurrently targeting MYCN and mTOR signaling in NB remains unexplored. This study aimed to investigate the therapeutic potential of targeting dysregulated protein synthesis pathways by inhibiting the MYCN and mTOR pathways together in NB. METHODS Using small molecule/pharmacologic approaches, we evaluated the effects of combined inhibition of MYCN transcription and mTOR signaling on NB cell growth/survival and associated molecular mechanism(s) in NB cell lines. We used two well-established BET (bromodomain extra-terminal) protein inhibitors (JQ1, OTX-015), and a clinically relevant mTOR inhibitor, temsirolimus, to target MYCN transcription and mTOR signaling, respectively. The single agent and combined efficacies of these inhibitors on NB cell growth, apoptosis, cell cycle and neurospheres were assessed using MTT, Annexin-V, propidium-iodide staining and sphere assays, respectively. Effects of inhibitors on global protein synthesis were quantified using a fluorescence-based (FamAzide)-based protein synthesis assay. Further, we investigated the specificities of these inhibitors in targeting the associated pathways/molecules using western blot analyses. RESULTS Co-treatment of JQ1 or OTX-015 with temsirolimus synergistically suppressed NB cell growth/survival by inducing G1 cell cycle arrest and apoptosis with greatest efficacy in MYCN-amplified NB cells. Mechanistically, the co-treatment of JQ1 or OTX-015 with temsirolimus significantly downregulated the expression levels of phosphorylated 4EBP1/p70-S6K/eIF4E (mTOR components) and BRD4 (BET protein)/MYCN proteins. Further, this combination significantly inhibited global protein synthesis, compared to single agents. Our findings also demonstrated that both JQ1 and temsirolimus chemosensitized NB cells when tested in combination with cisplatin chemotherapy. CONCLUSIONS Together, our findings demonstrate synergistic efficacy of JQ1 or OTX-015 and temsirolimus against MYCN-driven NB, by dual-inhibition of MYCN (targeting transcription) and mTOR (targeting translation). Additional preclinical evaluation is warranted to determine the clinical utility of targeted therapy for high-risk NB patients.
Collapse
Affiliation(s)
- Matthew J Kling
- Department of Pediatrics, Hematology/Oncology Division, University of Nebraska Medical Center, 986395, Nebraska Medical Center, Omaha, NE, USA
| | - Connor N Griggs
- Department of Pediatrics, Hematology/Oncology Division, University of Nebraska Medical Center, 986395, Nebraska Medical Center, Omaha, NE, USA
| | - Erin M McIntyre
- Department of Pediatrics, Hematology/Oncology Division, University of Nebraska Medical Center, 986395, Nebraska Medical Center, Omaha, NE, USA
| | - Gracey Alexander
- Department of Pediatrics, Hematology/Oncology Division, University of Nebraska Medical Center, 986395, Nebraska Medical Center, Omaha, NE, USA
| | - Sutapa Ray
- Department of Pediatrics, Hematology/Oncology Division, University of Nebraska Medical Center, 986395, Nebraska Medical Center, Omaha, NE, USA
| | - Kishore B Challagundla
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, NE, USA
| | - Shantaram S Joshi
- Department of Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, NE, USA
| | - Don W Coulter
- Department of Pediatrics, Hematology/Oncology Division, University of Nebraska Medical Center, 986395, Nebraska Medical Center, Omaha, NE, USA
| | - Nagendra K Chaturvedi
- Department of Pediatrics, Hematology/Oncology Division, University of Nebraska Medical Center, 986395, Nebraska Medical Center, Omaha, NE, USA.
| |
Collapse
|
30
|
Norris K, Hopes T, Aspden JL. Ribosome heterogeneity and specialization in development. WILEY INTERDISCIPLINARY REVIEWS. RNA 2021; 12:e1644. [PMID: 33565275 PMCID: PMC8647923 DOI: 10.1002/wrna.1644] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Revised: 01/08/2021] [Accepted: 01/11/2021] [Indexed: 12/13/2022]
Abstract
Regulation of protein synthesis is a vital step in controlling gene expression, especially during development. Over the last 10 years, it has become clear that rather than being homogeneous machines responsible for mRNA translation, ribosomes are highly heterogeneous and can play an active part in translational regulation. These "specialized ribosomes" comprise of specific protein and/or rRNA components, which are required for the translation of particular mRNAs. However, while there is extensive evidence for ribosome heterogeneity, support for specialized functions is limited. Recent work in a variety of developmental model organisms has shed some light on the biological relevance of ribosome heterogeneity. Tissue-specific expression of ribosomal components along with phenotypic analysis of ribosomal gene mutations indicate that ribosome heterogeneity and potentially specialization are common in key development processes like embryogenesis, spermatogenesis, oogenesis, body patterning, and neurogenesis. Several examples of ribosome specialization have now been proposed but strong links between ribosome heterogeneity, translation of specific mRNAs by defined mechanisms, and role of these translation events remain elusive. Furthermore, several studies have indicated that heterogeneous ribosome populations are a product of tissue-specific expression rather than specialized function and that ribosomal protein phenotypes are the result of extra-ribosomal function or overall reduced ribosome levels. Many important questions still need to be addressed in order to determine the functional importance of ribosome heterogeneity to development and disease, which is likely to vary across systems. It will be essential to dissect these issues to fully understand diseases caused by disruptions to ribosomal composition, such as ribosomopathies. This article is categorized under: Translation > Translation Regulation Translation > Ribosome Structure/Function RNA in Disease and Development > RNA in Development.
Collapse
Affiliation(s)
- Karl Norris
- Faculty of Biological Sciences, School of Molecular and Cellular BiologyUniversity of LeedsLeedsUK
- Leeds OmicsUniversity of LeedsLeedsUK
| | - Tayah Hopes
- Faculty of Biological Sciences, School of Molecular and Cellular BiologyUniversity of LeedsLeedsUK
- Leeds OmicsUniversity of LeedsLeedsUK
| | - Julie Louise Aspden
- Faculty of Biological Sciences, School of Molecular and Cellular BiologyUniversity of LeedsLeedsUK
- Leeds OmicsUniversity of LeedsLeedsUK
| |
Collapse
|
31
|
Kondo S, Ferdousi F, Yamauchi K, Suidasari S, Yokozawa M, Harrabi MM, Tominaga KI, Isoda H. Comprehensive transcriptome analysis of erythroid differentiation potential of olive leaf in haematopoietic stem cells. J Cell Mol Med 2021; 25:7229-7243. [PMID: 34180123 PMCID: PMC8335692 DOI: 10.1111/jcmm.16752] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Revised: 05/15/2021] [Accepted: 06/08/2021] [Indexed: 12/13/2022] Open
Abstract
Anaemia is one of the leading causes of disability in young adults and is associated with increased morbidity and mortality in elderly. With a global target to reduce the disease burden of anaemia, recent researches focus on novel compounds with the ability to induce erythropoiesis and regulate iron homeostasis. We aimed to explore the biological events and potential polypharmacological effects of water-extracted olive leaf (WOL) on human bone marrow-derived haematopoietic stem cells (hHSCs) using a comprehensive gene expression analysis. HPLC analysis identifies six bioactive polyphenols in the WOL. Treatment with WOL for 12 days regulated gene expressions related to erythroid differentiation, oxygen homeostasis, iron homeostasis, haem metabolism and Hb biosynthesis in hHSCs. Functional clustering analysis reveals several major functions of WOL such as ribosomal biogenesis and mitochondrial translation machinery, glycolytic process, ATP biosynthesis and immune response. Additionally, the colonies of both primitive and mature erythroid progenitors, CFU-E and BFU-E, were significantly increased in WOL-treated hHSCs. The expressions of erythroid markers, CD47, glycophorin A (GYPA), and transferrin receptor (TFRC) and adult Hb subunits-HBA and HBB were also confirmed in immunofluorescent staining and flow cytometer analysis in WOL-treated hHSCs. It is well known that induction of lineage-specific differentiation, as well as the maturation of early haematopoietic precursors into fully mature erythrocytes, involves multiple simultaneous biological events and complex signalling networks. In this regard, our genome-wide transcriptome profiling with microarray study on WOL-treated hHSCs provides general insights into the multitarget prophylactic and/or therapeutic potential of WOL in anaemia and other haematological disorders.
Collapse
Affiliation(s)
- Shinji Kondo
- R&D Center for Tailor-Made QOL, University of Tsukuba, Tsukuba, Japan
| | - Farhana Ferdousi
- Alliance for Research on the Mediterranean and North Africa (ARENA), University of Tsukuba, Tsukuba, Japan.,AIST-University of Tsukuba Open innovation laboratory for food and medicinal resource engineering (FoodMed-OIL), University of Tsukuba, Tsukuba, Japan.,Faculty of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Japan
| | | | | | | | - Mohamed Moncef Harrabi
- Alliance for Research on the Mediterranean and North Africa (ARENA), University of Tsukuba, Tsukuba, Japan
| | - Ken-Ichi Tominaga
- AIST-University of Tsukuba Open innovation laboratory for food and medicinal resource engineering (FoodMed-OIL), University of Tsukuba, Tsukuba, Japan
| | - Hiroko Isoda
- R&D Center for Tailor-Made QOL, University of Tsukuba, Tsukuba, Japan.,Alliance for Research on the Mediterranean and North Africa (ARENA), University of Tsukuba, Tsukuba, Japan.,AIST-University of Tsukuba Open innovation laboratory for food and medicinal resource engineering (FoodMed-OIL), University of Tsukuba, Tsukuba, Japan.,Faculty of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Japan
| |
Collapse
|
32
|
Terrey M, Adamson SI, Chuang JH, Ackerman SL. Defects in translation-dependent quality control pathways lead to convergent molecular and neurodevelopmental pathology. eLife 2021; 10:e66904. [PMID: 33899734 PMCID: PMC8075583 DOI: 10.7554/elife.66904] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Accepted: 04/05/2021] [Indexed: 12/27/2022] Open
Abstract
Translation-dependent quality control pathways such as no-go decay (NGD), non-stop decay (NSD), and nonsense-mediated decay (NMD) govern protein synthesis and proteostasis by resolving non-translating ribosomes and preventing the production of potentially toxic peptides derived from faulty and aberrant mRNAs. However, how translation is altered and the in vivo defects that arise in the absence of these pathways are poorly understood. Here, we show that the NGD/NSD factors Pelo and Hbs1l are critical in mice for cerebellar neurogenesis but expendable for survival of these neurons after development. Analysis of mutant mouse embryonic fibroblasts revealed translational pauses, alteration of signaling pathways, and translational reprogramming. Similar effects on signaling pathways, including mTOR activation, the translatome and mouse cerebellar development were observed upon deletion of the NMD factor Upf2. Our data reveal that these quality control pathways that function to mitigate errors at distinct steps in translation can evoke similar cellular responses.
Collapse
Affiliation(s)
- Markus Terrey
- Howard Hughes Medical Institute, Department of Cellular and Molecular Medicine, Section of Neurobiology, Division of Biological Sciences, University of California San DiegoLa JollaUnited States
- Graduate School of Biomedical Sciences and Engineering, University of MaineOronoUnited States
| | - Scott I Adamson
- The Jackson Laboratory for Genomic MedicineFarmingtonUnited States
- Department of Genetics and Genome Sciences, Institute for Systems Genomics, UConn HealthFarmingtonUnited States
| | - Jeffrey H Chuang
- The Jackson Laboratory for Genomic MedicineFarmingtonUnited States
- Department of Genetics and Genome Sciences, Institute for Systems Genomics, UConn HealthFarmingtonUnited States
| | - Susan L Ackerman
- Howard Hughes Medical Institute, Department of Cellular and Molecular Medicine, Section of Neurobiology, Division of Biological Sciences, University of California San DiegoLa JollaUnited States
| |
Collapse
|
33
|
Transcriptomic and proteomic analysis of Hemidactylus frenatus during initial stages of tail regeneration. Sci Rep 2021; 11:3675. [PMID: 33574494 PMCID: PMC7878758 DOI: 10.1038/s41598-021-83283-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Accepted: 01/28/2021] [Indexed: 11/08/2022] Open
Abstract
Epimorphic regeneration of appendages is a complex and complete phenomenon found in selected animals. Hemidactylus frenatus, house gecko has the remarkable ability to regenerate the tail tissue upon autotomy involving epimorphic regeneration mechanism. This study has identified and evaluated the molecular changes at gene and protein level during the initial stages, i.e., during the wound healing and repair mechanism initiation stage of tail regeneration. Based on next generation transcriptomics and De novo analysis the transcriptome library of the gecko tail tissue was generated. A total of 254 genes and 128 proteins were found to be associated with the regeneration of gecko tail tissue upon amputation at 1, 2 and 5-day post amputation (dpa) against control, 0-dpa through differential transcriptomic and proteomic analysis. To authenticate the expression analysis, 50 genes were further validated involving RTPCR. 327 genes/proteins identified and mapped from the study showed association for Protein kinase A signaling, Telomerase BAG2 signaling, paxillin signaling, VEGF signaling network pathways based on network pathway analysis. This study empanelled list of transcriptome, proteome and the list of genes/proteins associated with the tail regeneration.
Collapse
|
34
|
Buddika K, Xu J, Ariyapala IS, Sokol NS. I-KCKT allows dissection-free RNA profiling of adult Drosophila intestinal progenitor cells. Development 2021; 148:dev196568. [PMID: 33246929 PMCID: PMC7803463 DOI: 10.1242/dev.196568] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Accepted: 11/19/2021] [Indexed: 12/13/2022]
Abstract
The adult Drosophila intestinal epithelium is a model system for stem cell biology, but its utility is limited by current biochemical methods that lack cell type resolution. Here, we describe a new proximity-based profiling method that relies upon a GAL4 driver, termed intestinal-kickout-GAL4 (I-KCKT-GAL4), that is exclusively expressed in intestinal progenitor cells. This method uses UV crosslinked whole animal frozen powder as its starting material to immunoprecipitate the RNA cargoes of transgenic epitope-tagged RNA binding proteins driven by I-KCKT-GAL4 When applied to the general mRNA-binder, poly(A)-binding protein, the RNA profile obtained by this method identifies 98.8% of transcripts found after progenitor cell sorting, and has low background noise despite being derived from whole animal lysate. We also mapped the targets of the more selective RNA binder, Fragile X mental retardation protein (FMRP), using enhanced crosslinking and immunoprecipitation (eCLIP), and report for the first time its binding motif in Drosophila cells. This method will therefore enable the RNA profiling of wild-type and mutant intestinal progenitor cells from intact flies exposed to normal and altered environments, as well as the identification of RNA-protein interactions crucial for stem cell function.
Collapse
Affiliation(s)
- Kasun Buddika
- Department of Biology, Indiana University, Bloomington, IN 47405, USA
| | - Jingjing Xu
- Department of Biology, Indiana University, Bloomington, IN 47405, USA
| | | | - Nicholas S Sokol
- Department of Biology, Indiana University, Bloomington, IN 47405, USA
| |
Collapse
|
35
|
Gupta S, Santoro R. Regulation and Roles of the Nucleolus in Embryonic Stem Cells: From Ribosome Biogenesis to Genome Organization. Stem Cell Reports 2020; 15:1206-1219. [PMID: 32976768 PMCID: PMC7724472 DOI: 10.1016/j.stemcr.2020.08.012] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2020] [Revised: 08/25/2020] [Accepted: 08/25/2020] [Indexed: 12/13/2022] Open
Abstract
The nucleolus is the largest compartment of the eukaryotic cell's nucleus. It acts as a ribosome factory, thereby sustaining the translation machinery. The nucleolus is also the subnuclear compartment with the highest transcriptional activity in the cell, where hundreds of ribosomal RNA (rRNA) genes transcribe the overwhelming majority of RNAs. The structure and composition of the nucleolus change according to the developmental state. For instance, in embryonic stem cells (ESCs), rRNA genes display a hyperactive transcriptional state and open chromatin structure compared with differentiated cells. Increasing evidence indicates that the role of the nucleolus and rRNA genes might go beyond the control of ribosome biogenesis. One such role is linked to the genome architecture, since repressive domains are often located close to the nucleolus. This review highlights recent findings describing how the nucleolus is regulated in ESCs and its role in regulating ribosome biogenesis and genome organization for the maintenance of stem cell identity.
Collapse
Affiliation(s)
- Shivani Gupta
- Department of Molecular Mechanisms of Disease, DMMD, University of Zurich, 8057 Zurich, Switzerland
| | - Raffaella Santoro
- Department of Molecular Mechanisms of Disease, DMMD, University of Zurich, 8057 Zurich, Switzerland.
| |
Collapse
|
36
|
Ertay A, Liu H, Liu D, Peng P, Hill C, Xiong H, Hancock D, Yuan X, Przewloka MR, Coldwell M, Howell M, Skipp P, Ewing RM, Downward J, Wang Y. WDHD1 is essential for the survival of PTEN-inactive triple-negative breast cancer. Cell Death Dis 2020; 11:1001. [PMID: 33221821 PMCID: PMC7680459 DOI: 10.1038/s41419-020-03210-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2020] [Revised: 11/02/2020] [Accepted: 11/05/2020] [Indexed: 12/24/2022]
Abstract
Triple-negative breast cancer (TNBC) is the most aggressive type of breast cancer that lacks the oestrogen receptor, progesterone receptor and human epidermal growth factor receptor 2, making it difficult to target therapeutically. Targeting synthetic lethality is an alternative approach for cancer treatment. TNBC shows frequent loss of phosphatase and tensin homologue (PTEN) expression, which is associated with poor prognosis and treatment response. To identify PTEN synthetic lethal interactions, TCGA analysis coupled with a whole-genome siRNA screen in isogenic PTEN-negative and -positive cells were performed. Among the candidate genes essential for the survival of PTEN-inactive TNBC cells, WDHD1 (WD repeat and high-mobility group box DNA-binding protein 1) expression was increased in the low vs. high PTEN TNBC samples. It was also the top hit in the siRNA screen and its knockdown significantly inhibited cell viability in PTEN-negative cells, which was further validated in 2D and 3D cultures. Mechanistically, WDHD1 is important to mediate a high demand of protein translation in PTEN-inactive TNBC. Finally, the importance of WDHD1 in TNBC was confirmed in patient samples obtained from the TCGA and tissue microarrays with clinic-pathological information. Taken together, as an essential gene for the survival of PTEN-inactive TNBC cells, WDHD1 could be a potential biomarker or a therapeutic target for TNBC.
Collapse
Affiliation(s)
- Ayse Ertay
- Biological Sciences, Faculty of Environmental and Life Sciences, University of Southampton, Southampton, SO17 1BJ, UK
| | - Huiquan Liu
- Department of Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, 430030, Wuhan, China
| | - Dian Liu
- Department of Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, 430030, Wuhan, China
| | - Ping Peng
- Department of Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, 430030, Wuhan, China
| | - Charlotte Hill
- Biological Sciences, Faculty of Environmental and Life Sciences, University of Southampton, Southampton, SO17 1BJ, UK
| | - Hua Xiong
- Department of Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, 430030, Wuhan, China
| | - David Hancock
- Oncogene Biology, The Francis Crick Institute, London, NW1 1AT, UK
| | - Xianglin Yuan
- Department of Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, 430030, Wuhan, China
| | - Marcin R Przewloka
- Biological Sciences, Faculty of Environmental and Life Sciences, University of Southampton, Southampton, SO17 1BJ, UK
- Institute for Life Sciences, University of Southampton, Southampton, SO17 1BJ, UK
| | - Mark Coldwell
- Biological Sciences, Faculty of Environmental and Life Sciences, University of Southampton, Southampton, SO17 1BJ, UK
- Institute for Life Sciences, University of Southampton, Southampton, SO17 1BJ, UK
| | - Michael Howell
- High-Throughput Screening, The Francis Crick Institute, London, NW1 1AT, UK
| | - Paul Skipp
- Biological Sciences, Faculty of Environmental and Life Sciences, University of Southampton, Southampton, SO17 1BJ, UK
- Institute for Life Sciences, University of Southampton, Southampton, SO17 1BJ, UK
- Centre for Proteomic Research, Institute for Life Sciences, University of Southampton, Southampton, SO17 1BJ, UK
| | - Rob M Ewing
- Biological Sciences, Faculty of Environmental and Life Sciences, University of Southampton, Southampton, SO17 1BJ, UK
- Institute for Life Sciences, University of Southampton, Southampton, SO17 1BJ, UK
| | - Julian Downward
- Oncogene Biology, The Francis Crick Institute, London, NW1 1AT, UK.
| | - Yihua Wang
- Biological Sciences, Faculty of Environmental and Life Sciences, University of Southampton, Southampton, SO17 1BJ, UK.
- Institute for Life Sciences, University of Southampton, Southampton, SO17 1BJ, UK.
- NIHR Southampton Biomedical Research Centre, University Hospital Southampton, Southampton, SO16 6YD, UK.
| |
Collapse
|
37
|
How Do the Different Proteomic Strategies Cope with the Complexity of Biological Regulations in a Multi-Omic World? Critical Appraisal and Suggestions for Improvements. Proteomes 2020; 8:proteomes8030023. [PMID: 32899323 PMCID: PMC7564458 DOI: 10.3390/proteomes8030023] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Revised: 08/30/2020] [Accepted: 09/01/2020] [Indexed: 12/12/2022] Open
Abstract
In this second decade of the 21st century, we are lucky enough to have different types of proteomic analyses at our disposal. Furthermore, other functional omics such as transcriptomics have also undergone major developments, resulting in mature tools. However, choice equals questions, and the major question is how each proteomic strategy is fit for which purpose. The aim of this opinion paper is to reposition the various proteomic strategies in the frame of what is known in terms of biological regulations in order to shed light on the power, limitations, and paths for improvement for the different proteomic setups. This should help biologists to select the best-suited proteomic strategy for their purposes in order not to be driven by raw availability or fashion arguments but rather by the best fitness for purpose. In particular, knowing the limitations of the different proteomic strategies helps in interpreting the results correctly and in devising the validation experiments that should be made downstream of the proteomic analyses.
Collapse
|
38
|
Nakazawa K, Shichino Y, Iwasaki S, Shiina N. Implications of RNG140 (caprin2)-mediated translational regulation in eye lens differentiation. J Biol Chem 2020; 295:15029-15044. [PMID: 32839273 DOI: 10.1074/jbc.ra120.012715] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2020] [Revised: 08/07/2020] [Indexed: 01/02/2023] Open
Abstract
Regulation of gene expression at the translational level is key to determining cell fate and function. An RNA-binding protein, RNG140 (caprin2), plays a role in eye lens differentiation and has been reported to function in translational regulation. However, the mechanism and its role in eyes has remained unclear. Here, we show that RNG140 binds to the translation initiation factor eukaryotic initiation factor 3 (eIF3) and suppresses translation through mechanisms involving suppression of eIF3-dependent translation initiation. Comprehensive ribosome profiling revealed that overexpression of RNG140 in cultured Chinese hamster ovary cells reduces translation of long mRNAs, including those associated with cell proliferation. RNG140-mediated translational regulation also operates in the mouse eye, where RNG140 knockout increased the translation of long mRNAs. mRNAs involved in lens differentiation, such as crystallin mRNAs, are short and can escape translational inhibition by RNG140 and be translated in differentiating lenses. Thus, this study provides insights into the mechanistic basis of lens cell transition from proliferation to differentiation via RNG140-mediated translational regulation.
Collapse
Affiliation(s)
- Kaori Nakazawa
- Laboratory of Neuronal Cell Biology, National Institute for Basic Biology, Okazaki, Aichi, Japan; Department of Basic Biology, SOKENDAI (Graduate University for Advanced Studies), Okazaki, Aichi, Japan
| | - Yuichi Shichino
- RNA Systems Biochemistry Laboratory, RIKEN Cluster for Pioneering Research, Saitama, Japan
| | - Shintaro Iwasaki
- RNA Systems Biochemistry Laboratory, RIKEN Cluster for Pioneering Research, Saitama, Japan; Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, University of Tokyo, Chiba, Japan
| | - Nobuyuki Shiina
- Laboratory of Neuronal Cell Biology, National Institute for Basic Biology, Okazaki, Aichi, Japan; Department of Basic Biology, SOKENDAI (Graduate University for Advanced Studies), Okazaki, Aichi, Japan; Exploratory Research Center on Life and Living Systems (ExCELLS), Okazaki, Aichi, Japan.
| |
Collapse
|
39
|
Mikedis MM, Fan Y, Nicholls PK, Endo T, Jackson EK, Cobb SA, de Rooij DG, Page DC. DAZL mediates a broad translational program regulating expansion and differentiation of spermatogonial progenitors. eLife 2020; 9:56523. [PMID: 32686646 PMCID: PMC7445011 DOI: 10.7554/elife.56523] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Accepted: 07/20/2020] [Indexed: 01/28/2023] Open
Abstract
Fertility across metazoa requires the germline-specific DAZ family of RNA-binding proteins. Here we examine whether DAZL directly regulates progenitor spermatogonia using a conditional genetic mouse model and in vivo biochemical approaches combined with chemical synchronization of spermatogenesis. We find that the absence of Dazl impairs both expansion and differentiation of the spermatogonial progenitor population. In undifferentiated spermatogonia, DAZL binds the 3' UTRs of ~2,500 protein-coding genes. Some targets are known regulators of spermatogonial proliferation and differentiation while others are broadly expressed, dosage-sensitive factors that control transcription and RNA metabolism. DAZL binds 3' UTR sites conserved across vertebrates at a UGUU(U/A) motif. By assessing ribosome occupancy in undifferentiated spermatogonia, we find that DAZL increases translation of its targets. In total, DAZL orchestrates a broad translational program that amplifies protein levels of key spermatogonial and gene regulatory factors to promote the expansion and differentiation of progenitor spermatogonia.
Collapse
Affiliation(s)
| | - Yuting Fan
- Whitehead Institute, Cambridge, United States.,Reproductive Medicine Center, Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | | | | | - Emily K Jackson
- Whitehead Institute, Cambridge, United States.,Department of Biology, Massachusetts Institute of Technology, Cambridge, United States
| | | | | | - David C Page
- Whitehead Institute, Cambridge, United States.,Department of Biology, Massachusetts Institute of Technology, Cambridge, United States.,Howard Hughes Medical Institute, Whitehead Institute, Cambridge, United States
| |
Collapse
|
40
|
Global translation during early development depends on the essential transcription factor PRDM10. Nat Commun 2020; 11:3603. [PMID: 32681107 PMCID: PMC7368010 DOI: 10.1038/s41467-020-17304-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2019] [Accepted: 05/21/2020] [Indexed: 01/08/2023] Open
Abstract
Members of the PR/SET domain-containing (PRDM) family of zinc finger transcriptional regulators play diverse developmental roles. PRDM10 is a yet uncharacterized family member, and its function in vivo is unknown. Here, we report an essential requirement for PRDM10 in pre-implantation embryos and embryonic stem cells (mESCs), where loss of PRDM10 results in severe cell growth inhibition. Detailed genomic and biochemical analyses reveal that PRDM10 functions as a sequence-specific transcription factor. We identify Eif3b, which encodes a core component of the eukaryotic translation initiation factor 3 (eIF3) complex, as a key downstream target, and demonstrate that growth inhibition in PRDM10-deficient mESCs is in part mediated through EIF3B-dependent effects on global translation. Our work elucidates the molecular function of PRDM10 in maintaining global translation, establishes its essential role in early embryonic development and mESC homeostasis, and offers insights into the functional repertoire of PRDMs as well as the transcriptional mechanisms regulating translation.
Collapse
|
41
|
Tabatabaei N, Hou S, Kim KW, Tahmasebi S. Signaling pathways that control mRNA translation initiation in macrophages. Cell Signal 2020; 73:109700. [PMID: 32593651 DOI: 10.1016/j.cellsig.2020.109700] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Revised: 06/11/2020] [Accepted: 06/23/2020] [Indexed: 12/14/2022]
Abstract
Translational control in mammalian cells plays a critical role in regulating differentiation, cell growth, cell cycle and response to diverse stresses. Macrophages are one of the most versatile cell types in the body. They are professional phagocytic cells that can be found in almost all tissues and adapt tissue-specific functions. Recent studies highlight the importance of translational control in macrophages during invasion of pathogens, exposure to cytokines and in the context of tissue specific functions. In this review, we summarize the current knowledge regarding the role of mRNA translational control in regulation of macrophages.
Collapse
Affiliation(s)
- Negar Tabatabaei
- Department of Pharmacology and Regenerative Medicine, University of Illinois College of Medicine, Chicago, IL, USA
| | - Shikun Hou
- Department of Pharmacology and Regenerative Medicine, University of Illinois College of Medicine, Chicago, IL, USA
| | - Ki-Wook Kim
- Department of Pharmacology and Regenerative Medicine, University of Illinois College of Medicine, Chicago, IL, USA.
| | - Soroush Tahmasebi
- Department of Pharmacology and Regenerative Medicine, University of Illinois College of Medicine, Chicago, IL, USA.
| |
Collapse
|
42
|
Sharifi S, da Costa HFR, Bierhoff H. The circuitry between ribosome biogenesis and translation in stem cell function and ageing. Mech Ageing Dev 2020; 189:111282. [PMID: 32531294 DOI: 10.1016/j.mad.2020.111282] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2020] [Revised: 05/11/2020] [Accepted: 06/01/2020] [Indexed: 12/13/2022]
Abstract
Ribosome biogenesis takes place mainly in the nucleolus, a nuclear, non-membrane bound organelle forming around the gene arrays encoding ribosomal RNA (rRNA). Nucleolar activity comprises synthesis, processing and maturation of rRNAs, followed by their assembly with ribosomal proteins into pre-ribosomal particles. The final formation of translation-competent ribosomes in the cytoplasm is the prerequisite for protein synthesis, which is the most energy-consuming cellular process. In adult stem cells, ribosome biogenesis and protein synthesis determine the switch between the quiescent and the activated state, but also decide whether activated stem cells self-renew or differentiate. Given this major impact on cellular function, it seems likely that perturbations of the circuitry between nucleolar activity and translation lead to ageing-related stem cell deterioration. This review provides an overview of how ribosome biogenesis and translation govern stem cell function and discusses the resultant implication in stem cell ageing.
Collapse
Affiliation(s)
- Samim Sharifi
- Institute of Biochemistry and Biophysics, Center for Molecular Biomedicine (CMB), Friedrich Schiller University Jena, Hans-Knöll-Str. 2, 07745 Jena, Germany; Leibniz-Institute on Aging - Fritz Lipmann Institute (FLI), Beutenbergstrasse 11, 07745 Jena, Germany
| | - Hugo Filipe Rangel da Costa
- Institute of Biochemistry and Biophysics, Center for Molecular Biomedicine (CMB), Friedrich Schiller University Jena, Hans-Knöll-Str. 2, 07745 Jena, Germany
| | - Holger Bierhoff
- Institute of Biochemistry and Biophysics, Center for Molecular Biomedicine (CMB), Friedrich Schiller University Jena, Hans-Knöll-Str. 2, 07745 Jena, Germany; Leibniz-Institute on Aging - Fritz Lipmann Institute (FLI), Beutenbergstrasse 11, 07745 Jena, Germany.
| |
Collapse
|
43
|
Buddika K, Ariyapala IS, Hazuga MA, Riffert D, Sokol NS. Canonical nucleators are dispensable for stress granule assembly in Drosophila intestinal progenitors. J Cell Sci 2020; 133:jcs243451. [PMID: 32265270 PMCID: PMC7325430 DOI: 10.1242/jcs.243451] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2019] [Accepted: 03/26/2020] [Indexed: 12/18/2022] Open
Abstract
Stressed cells downregulate translation initiation and assemble membrane-less foci termed stress granules (SGs). Although SGs have been extensively characterized in cultured cells, the existence of such structures in stressed adult stem cell pools remains poorly characterized. Here, we report that the Drosophila orthologs of the mammalian SG components AGO1, ATX2, CAPRIN, eIF4E, FMRP, G3BP, LIN-28, PABP and TIAR are enriched in adult fly intestinal progenitor cells, where they accumulate in small cytoplasmic messenger ribonucleoprotein complexes (mRNPs). Treatment with sodium arsenite or rapamycin reorganized these mRNPs into large cytoplasmic granules. Formation of these intestinal progenitor stress granules (IPSGs) depended on polysome disassembly, led to translational downregulation and was reversible. Although the canonical SG nucleators ATX2 and G3BP were sufficient for IPSG formation in the absence of stress, neither of them, nor TIAR, either individually or collectively, were required for stress-induced IPSG formation. This work therefore finds that IPSGs do not assemble via a canonical mechanism, raising the possibility that other stem cell populations employ a similar stress-response mechanism.
Collapse
Affiliation(s)
- Kasun Buddika
- Department of Biology, Indiana University, Bloomington, IN 47405, USA
| | | | - Mary A Hazuga
- Department of Biology, Indiana University, Bloomington, IN 47405, USA
| | - Derek Riffert
- Department of Biology, Indiana University, Bloomington, IN 47405, USA
| | - Nicholas S Sokol
- Department of Biology, Indiana University, Bloomington, IN 47405, USA
| |
Collapse
|
44
|
Liao Y, Xiao H, Cheng M, Fan X. Bioinformatics Analysis Reveals Biomarkers With Cancer Stem Cell Characteristics in Lung Squamous Cell Carcinoma. Front Genet 2020; 11:427. [PMID: 32528520 PMCID: PMC7247832 DOI: 10.3389/fgene.2020.00427] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2020] [Accepted: 04/06/2020] [Indexed: 12/18/2022] Open
Abstract
Background Tumor stem cells play important roles in the survival, proliferation, metastasis and recurrence of tumors. We aimed to identify new prognostic biomarkers for lung squamous cell carcinoma (LUSC) based on the cancer stem cell theory. Methods RNA-seq data and relevant clinical information were downloaded from The Cancer Genome Atlas (TCGA) database. Weighted gene coexpression network analysis (WGCNA) was applied to identify significant modules and hub genes, and prognostic signatures were constructed with the prognostic hub genes. Results LUSC patients in the TCGA database have higher mRNA expression-based stemness index (mRNAsi) in tumor tissue than in adjacent normal tissue. In addition, some clinical features and outcomes were highly correlated with the mRNAsi. WGCNA revealed that the pink and yellow modules were the most significant modules related to the mRNAsi; the top 10 hub genes in the pink module were enriched mostly in epidermal development, the secretory granule membrane, receptor regulator activity and the cytokine-cytokine receptor interaction. The protein–protein interaction (PPI) network revealed that the top 10 hub genes were significantly correlated with each other at the transcriptional level. In addition, the top 10 hub genes were all highly expressed in LUSC, and some were differentially expressed in different TNM stages. Regarding the survival analysis, the nomogram of a prognostic signature with three hub genes showed high predictive value. Conclusion mRNAsi-related hub genes could be a potential biomarker of LUSC.
Collapse
Affiliation(s)
- Yi Liao
- Department of Respiratory and Critical Care Medicine II, The Affiliated Hospital of Southwest Medical University, Luzhou, China
| | - Hua Xiao
- Department of Respiratory and Critical Care Medicine II, The Affiliated Hospital of Southwest Medical University, Luzhou, China
| | - Mengqing Cheng
- Department of Respiratory and Critical Care Medicine II, The Affiliated Hospital of Southwest Medical University, Luzhou, China
| | - Xianming Fan
- Department of Respiratory and Critical Care Medicine II, The Affiliated Hospital of Southwest Medical University, Luzhou, China
| |
Collapse
|
45
|
Chaturvedi NK, Kling MJ, Griggs CN, Kesherwani V, Shukla M, McIntyre EM, Ray S, Liu Y, McGuire TR, Sharp JG, Band H, Joshi SS, Coulter DW. A Novel Combination Approach Targeting an Enhanced Protein Synthesis Pathway in MYC-driven (Group 3) Medulloblastoma. Mol Cancer Ther 2020; 19:1351-1362. [PMID: 32371591 DOI: 10.1158/1535-7163.mct-19-0996] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2019] [Revised: 01/15/2020] [Accepted: 03/31/2020] [Indexed: 11/16/2022]
Abstract
The MYC oncogene is frequently amplified in patients with medulloblastoma, particularly in group 3 patients, who have the worst prognosis. mTOR signaling-driven deregulated protein synthesis is very common in various cancers, including medulloblastoma, that can promote MYC stabilization. As a transcription factor, MYC itself is further known to regulate transcription of several components of protein synthesis machinery, leading to an enhanced protein synthesis rate and proliferation. Thus, inhibiting enhanced protein synthesis by targeting the MYC and mTOR pathways together may represent a highly relevant strategy for the treatment of MYC-driven medulloblastoma. Here, using siRNA and small-molecule inhibitor approaches, we evaluated the effects of combined inhibition of MYC transcription and mTOR signaling on medulloblastoma cell growth/survival and associated molecular mechanism(s) in MYC-amplified (group 3) medulloblastoma cell lines and xenografts. Combined inhibition of MYC and mTOR synergistically suppressed medulloblastoma cell growth and induced G1 cell-cycle arrest and apoptosis. Mechanistically, the combined inhibition significantly downregulated the expression levels of key target proteins of MYC and mTOR signaling. Our results with RNA-sequencing revealed that combined inhibition synergistically modulated global gene expression including MYC/mTOR components. In addition, the combination treatment significantly delayed tumor growth and prolonged survival of MYC-amplified medulloblastoma xenografted mice by downregulating expression of MYC and the key downstream components of mTOR signaling, compared with single-agent therapy. Together, our findings demonstrated that dual inhibition of MYC (transcription) and mTOR (translation) of the protein synthesis pathway can be a novel therapeutic approach against MYC-driven medulloblastoma.
Collapse
Affiliation(s)
| | - Matthew J Kling
- Department of Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, Nebraska
| | - Connor N Griggs
- Department of Pediatrics, University of Nebraska Medical Center, Omaha, Nebraska
| | - Varun Kesherwani
- Child Health Research Institute Cancer, University of Nebraska Medical Center, Omaha, Nebraska
| | - Mamta Shukla
- Department of Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, Nebraska
| | - Erin M McIntyre
- Department of Pharmacy Practice and Science, University of Nebraska Medical Center, Omaha, Nebraska
| | - Sutapa Ray
- Department of Pediatrics, University of Nebraska Medical Center, Omaha, Nebraska
| | - Yutong Liu
- Department of Radiology, University of Nebraska Medical Center, Omaha, Nebraska
| | - Timothy R McGuire
- Department of Pharmacy Practice and Science, University of Nebraska Medical Center, Omaha, Nebraska
| | - J Graham Sharp
- Department of Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, Nebraska
| | - Hamid Band
- Department of Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, Nebraska.,Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center, Omaha, Nebraska.,Fred & Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, Nebraska.,Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, Nebraska
| | - Shantaram S Joshi
- Department of Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, Nebraska
| | - Don W Coulter
- Department of Pediatrics, University of Nebraska Medical Center, Omaha, Nebraska
| |
Collapse
|
46
|
Han W, Zhang C, Shi CT, Gao XJ, Zhou MH, Shao QX, Shen XJ, Wu CJ, Cao F, Hu YW, Yuan JL, Ding HZ, Wang QH, Wang HN. Roles of eIF3m in the tumorigenesis of triple negative breast cancer. Cancer Cell Int 2020; 20:141. [PMID: 32368187 PMCID: PMC7191806 DOI: 10.1186/s12935-020-01220-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2020] [Accepted: 04/17/2020] [Indexed: 12/24/2022] Open
Abstract
Background Without targets, triple negative breast cancer (TNBC) has the worst prognosis in all subtypes of breast cancer (BC). Recently, eukaryotic translation initiation factor 3 m (eIF3m) has been declared to be involved in the malignant progression of various neoplasms. The aim of this study is to explore biological functions of eIF3m in TNBC. Methods Multiple databases, including Oncomine, KM-plotter and so on, were performed to analyze prognosis and function of eIF3m in TNBC. After transfection of eIF3m-shRNA lentivirus, CCK-8, colony formation assay, cell cycle analysis, wound healing assay, transwell assays, mitochondrial membrane potential assay and cell apoptosis analysis were performed to explore the roles of eIF3m in TNBC cell bio-behaviors. In addition, western blotting was conducted to analyze the potential molecular mechanisms of eIF3m. Results In multiple databases, up-regulated eIF3m had lower overall survival, relapse-free survival and post progression survival in BC. EIF3m expression in TNBC was obviously higher than in non-TNBC or normal breast tissues. Its expression in TNBC was positively related to differentiation, lymph node invasion and distant metastasis. After knockdown of eIF3m, cell proliferation, migration, invasion and levels of mitochondrial membrane potential of MDA-MB-231 and MDA-MB-436 were all significantly suppressed, while apoptosis rates of them were obviously increased. In addition, eIF3m could regulate cell-cycle, epithelial–mesenchymal transition and apoptosis-related proteins. Combined with public databases and RT-qPCR, 14 genes were identified to be modulated by eIF3m in the development of TNBC. Conclusions eIF3m is an unfavorable indicator of TNBC, and plays a vital role in the process of TNBC tumorigenesis.
Collapse
Affiliation(s)
- Wei Han
- 1Department of General Surgery, Kunshan First People's Hospital Affiliated to Jiangsu University, Kunshan Jiangsu, 215300 People's Republic of China
| | - Cong Zhang
- Department of Pharmacy, Kunshan Hospital of Traditional Chinese Medicine, Kunshan Jiangsu, 215300 People's Republic of China
| | - Chun-Tao Shi
- Department of General Surgery, Wuxi Xishan People's Hospital, Kunshan Wuxi Jiangsu, 214000 People's Republic of China
| | - Xiao-Jiao Gao
- 4Department of Pathology, Kunshan First People's Hospital Affiliated to Jiangsu University, Kunshan Jiangsu, 215300 People's Republic of China
| | - Ming-Hui Zhou
- 5Centralab, Kunshan First People's Hospital Affiliated to Jiangsu University, Jiangsu, 215300 Kunshan People's Republic of China
| | - Qi-Xiang Shao
- 6Department of Immunology, Key Laboratory of Medical Science and Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang Jiangsu, 212013 People's Republic of China
| | - Xiao-Jun Shen
- 1Department of General Surgery, Kunshan First People's Hospital Affiliated to Jiangsu University, Kunshan Jiangsu, 215300 People's Republic of China
| | - Cheng-Jiang Wu
- 7Department of Clinical Laboratory, The Second Affiliated Hospital of Soochow University, Suzhou Jiangsu, 215000 People's Republic of China
| | - Fang Cao
- 1Department of General Surgery, Kunshan First People's Hospital Affiliated to Jiangsu University, Kunshan Jiangsu, 215300 People's Republic of China
| | - Yong-Wei Hu
- 1Department of General Surgery, Kunshan First People's Hospital Affiliated to Jiangsu University, Kunshan Jiangsu, 215300 People's Republic of China
| | - Jian-Liang Yuan
- 1Department of General Surgery, Kunshan First People's Hospital Affiliated to Jiangsu University, Kunshan Jiangsu, 215300 People's Republic of China
| | - Hou-Zhong Ding
- 1Department of General Surgery, Kunshan First People's Hospital Affiliated to Jiangsu University, Kunshan Jiangsu, 215300 People's Republic of China
| | - Qing-Hua Wang
- 1Department of General Surgery, Kunshan First People's Hospital Affiliated to Jiangsu University, Kunshan Jiangsu, 215300 People's Republic of China
| | - Hao-Nan Wang
- Oncology Department, Wuxi Fifth People's Hospital, Wuxi Jiangsu, 214000 People's Republic of China
| |
Collapse
|
47
|
Lund-Ricard Y, Cormier P, Morales J, Boutet A. mTOR Signaling at the Crossroad between Metazoan Regeneration and Human Diseases. Int J Mol Sci 2020; 21:E2718. [PMID: 32295297 PMCID: PMC7216262 DOI: 10.3390/ijms21082718] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Revised: 04/09/2020] [Accepted: 04/10/2020] [Indexed: 02/06/2023] Open
Abstract
A major challenge in medical research resides in controlling the molecular processes of tissue regeneration, as organ and structure damage are central to several human diseases. A survey of the literature reveals that mTOR (mechanistic/mammalian target of rapamycin) is involved in a wide range of regeneration mechanisms in the animal kingdom. More particularly, cellular processes such as growth, proliferation, and differentiation are controlled by mTOR. In addition, autophagy, stem cell maintenance or the newly described intermediate quiescence state, Galert, imply upstream monitoring by the mTOR pathway. In this review, we report the role of mTOR signaling in reparative regenerations in different tissues and body parts (e.g., axon, skeletal muscle, liver, epithelia, appendages, kidney, and whole-body), and highlight how the mTOR kinase can be viewed as a therapeutic target to boost organ repair. Studies in this area have focused on modulating the mTOR pathway in various animal models to elucidate its contribution to regeneration. The diversity of metazoan species used to identify the implication of this pathway might then serve applied medicine (in better understanding what is required for efficient treatments in human diseases) but also evolutionary biology. Indeed, species-specific differences in mTOR modulation can contain the keys to appreciate why certain regeneration processes have been lost or conserved in the animal kingdom.
Collapse
Affiliation(s)
| | | | | | - Agnès Boutet
- Centre National de la Recherche Scientifique (CNRS), Sorbonne Université, Integrative Biology of Marine Models (LBI2M), UMR 8227, Station Biologique de Roscoff (SBR), 29680 Roscoff, France; (Y.L.-R.); (P.C.); (J.M.)
| |
Collapse
|
48
|
The translational landscape of ground state pluripotency. Nat Commun 2020; 11:1617. [PMID: 32238817 PMCID: PMC7113317 DOI: 10.1038/s41467-020-15449-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2019] [Accepted: 03/09/2020] [Indexed: 12/30/2022] Open
Abstract
Translational control plays a central role in regulation of gene expression and can lead to significant divergence between mRNA- and protein-abundance. Here, we used genome-wide approaches combined with time-course analysis to measure the mRNA-abundance, mRNA-translation rate and protein expression during the transition of naïve-to-primed mouse embryonic stem cells (ESCs). We find that the ground state ESCs cultured with GSK3-, MEK-inhibitors and LIF (2iL) display higher ribosome density on a selective set of mRNAs. This set of mRNAs undergo strong translational buffering to maintain stable protein expression levels in 2iL-ESCs. Importantly, we show that the global alteration of cellular proteome during the transition of naïve-to-primed pluripotency is largely accompanied by transcriptional rewiring. Thus, we provide a comprehensive and detailed overview of the global changes in gene expression in different states of ESCs and dissect the relative contributions of mRNA-transcription, translation and regulation of protein stability in controlling protein abundance. Translational control of gene expression can lead to significant divergence between mRNA and protein abundance. Here, the authors describe transcriptional rewiring and translational buffering during transition from naïve to primed pluripotency through quantitation of mRNA-abundance, translation rate and protein expression.
Collapse
|
49
|
The rRNA m 6A methyltransferase METTL5 is involved in pluripotency and developmental programs. Genes Dev 2020; 34:715-729. [PMID: 32217665 PMCID: PMC7197354 DOI: 10.1101/gad.333369.119] [Citation(s) in RCA: 80] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2019] [Accepted: 03/05/2020] [Indexed: 01/12/2023]
Abstract
Covalent chemical modifications of cellular RNAs directly impact all biological processes. However, our mechanistic understanding of the enzymes catalyzing these modifications, their substrates and biological functions, remains vague. Amongst RNA modifications N6-methyladenosine (m6A) is widespread and found in messenger (mRNA), ribosomal (rRNA), and noncoding RNAs. Here, we undertook a systematic screen to uncover new RNA methyltransferases. We demonstrate that the methyltransferase-like 5 (METTL5) protein catalyzes m6A in 18S rRNA at position A1832 We report that absence of Mettl5 in mouse embryonic stem cells (mESCs) results in a decrease in global translation rate, spontaneous loss of pluripotency, and compromised differentiation potential. METTL5-deficient mice are born at non-Mendelian rates and develop morphological and behavioral abnormalities. Importantly, mice lacking METTL5 recapitulate symptoms of patients with DNA variants in METTL5, thereby providing a new mouse disease model. Overall, our biochemical, molecular, and in vivo characterization highlights the importance of m6A in rRNA in stemness, differentiation, development, and diseases.
Collapse
|
50
|
Guzzi N, Bellodi C. Novel insights into the emerging roles of tRNA-derived fragments in mammalian development. RNA Biol 2020; 17:1214-1222. [PMID: 32116113 PMCID: PMC7549657 DOI: 10.1080/15476286.2020.1732694] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
tRNA-derived fragments or tRFs were long considered merely degradation intermediates of full-length tRNAs; however, emerging research is highlighting unanticipated new and highly distinct functions in epigenetic control, metabolism, immune activity and stem cell fate commitment. Importantly, recent studies suggest that RNA epitranscriptomic modifications may provide an additional regulatory layer that dynamically directs tRF activity in stem and cancer cells. In this review, we explore current work illustrating unanticipated roles of tRFs in mammalian stem cells with a focus on the impact of post-transcriptional RNA modifications for the biogenesis and function of this growing class of small noncoding RNAs.
Collapse
Affiliation(s)
- Nicola Guzzi
- Division of Molecular Hematology, Department of Laboratory Medicine, Lund Stem Cell Center, Faculty of Medicine, Lund University , Lund, Sweden
| | - Cristian Bellodi
- Division of Molecular Hematology, Department of Laboratory Medicine, Lund Stem Cell Center, Faculty of Medicine, Lund University , Lund, Sweden
| |
Collapse
|