1
|
Liu W, Kurkewich JL, Stoddart A, Khan S, Anandan D, Gaubil AN, Wolfgeher DJ, Jueng L, Kron SJ, McNerney ME. CUX1 regulates human hematopoietic stem cell chromatin accessibility via the BAF complex. Cell Rep 2024; 43:114227. [PMID: 38735044 PMCID: PMC11163479 DOI: 10.1016/j.celrep.2024.114227] [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: 07/27/2023] [Revised: 03/16/2024] [Accepted: 04/26/2024] [Indexed: 05/14/2024] Open
Abstract
CUX1 is a homeodomain-containing transcription factor that is essential for the development and differentiation of multiple tissues. CUX1 is recurrently mutated or deleted in cancer, particularly in myeloid malignancies. However, the mechanism by which CUX1 regulates gene expression and differentiation remains poorly understood, creating a barrier to understanding the tumor-suppressive functions of CUX1. Here, we demonstrate that CUX1 directs the BAF chromatin remodeling complex to DNA to increase chromatin accessibility in hematopoietic cells. CUX1 preferentially regulates lineage-specific enhancers, and CUX1 target genes are predictive of cell fate in vivo. These data indicate that CUX1 regulates hematopoietic lineage commitment and homeostasis via pioneer factor activity, and CUX1 deficiency disrupts these processes in stem and progenitor cells, facilitating transformation.
Collapse
Affiliation(s)
- Weihan Liu
- Department of Pathology, The University of Chicago, Chicago, IL 60637, USA; Committee on Cancer Biology, The University of Chicago, Chicago, IL 60637, USA
| | | | - Angela Stoddart
- Department of Pathology, The University of Chicago, Chicago, IL 60637, USA
| | - Saira Khan
- Department of Pathology, The University of Chicago, Chicago, IL 60637, USA
| | - Dhivyaa Anandan
- Department of Pathology, The University of Chicago, Chicago, IL 60637, USA
| | - Alexandre N Gaubil
- Department of Pathology, The University of Chicago, Chicago, IL 60637, USA
| | - Donald J Wolfgeher
- Department of Molecular Genetics and Cell Biology, The University of Chicago, Chicago, IL 60637, USA
| | - Lia Jueng
- Department of Pathology, The University of Chicago, Chicago, IL 60637, USA
| | - Stephen J Kron
- The University of Chicago Medicine Comprehensive Cancer Center, The University of Chicago, Chicago, IL 60637, USA; Committee on Cancer Biology, The University of Chicago, Chicago, IL 60637, USA; Department of Molecular Genetics and Cell Biology, The University of Chicago, Chicago, IL 60637, USA
| | - Megan E McNerney
- Department of Pathology, The University of Chicago, Chicago, IL 60637, USA; The University of Chicago Medicine Comprehensive Cancer Center, The University of Chicago, Chicago, IL 60637, USA; Committee on Cancer Biology, The University of Chicago, Chicago, IL 60637, USA; Department of Pediatrics, Section of Hematology/Oncology, The University of Chicago, Chicago, IL 60637, USA.
| |
Collapse
|
2
|
UM171 cooperates with PIM1 inhibitors to restrict HSC expansion markers and suppress leukemia progression. Cell Death Dis 2022; 8:448. [PMID: 36335089 PMCID: PMC9637110 DOI: 10.1038/s41420-022-01244-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Revised: 10/24/2022] [Accepted: 10/27/2022] [Indexed: 11/08/2022]
Abstract
The pyrimido-indole derivative UM171 promotes human Hematopoietic Stem Cells Expansion (HSCE), but its impact on leukemia is not known. Herein, we show in a mouse model of erythroleukemia that UM171 strongly suppresses leukemia progression. UM171 inhibits cell cycle progression and apoptosis of leukemic cells in culture. The effect of UM171 on leukemia differentiation was accompanied by increased expression of HSCE markers. RNAseq analysis combined with Q-RT-PCR and western blotting revealed that the PIM1 protein kinase is highly elevated in response to UM171 treatment. Moreover, docking analysis combined with immunoprecipitation assays revealed high binding affinity of UM171 to PIM1. Interestingly, pan-PIM kinase inhibitors counteracted the effect of UM171 on HSCE marker expression and PIM1 transcription, but not its suppression of leukemic cell growth. Moreover, combination treatment with UM171 and a pan-PIM inhibitor further suppressed leukemic cell proliferation compared to each drug alone. To uncover the mechanism of growth inhibition, we showed strong upregulation of the cyclin-dependent kinase inhibitor P21CIP1 and the transcription factor KLF2 by UM171. In accordance, KLF2 knockdown attenuated growth inhibition by UM171. KLF2 upregulation by UM171 is also responsible for the activation of P21CIP1 in leukemic cells leading to a G1/S arrest and suppression of leukemogenesis. Thus, suppression of leukemic growth by UM171 through KLF2 and P21CIP1 is thwarted by PIM-mediated expansion of leukemic stemness, uncovering a novel therapeutic modality involving combined UM171 plus PIM inhibitors.
Collapse
|
3
|
Gong Y, Yang J, Li X, Zhou C, Chen Y, Wang Z, Qiu X, Liu Y, Zhang H, Greenbaum J, Cheng L, Hu Y, Xie J, Yang X, Li Y, Bai Y, Wang YP, Chen Y, Tan LJ, Shen H, Xiao HM, Deng HW. A systematic dissection of human primary osteoblasts in vivo at single-cell resolution. Aging (Albany NY) 2021; 13:20629-20650. [PMID: 34428745 PMCID: PMC8436943 DOI: 10.18632/aging.203452] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Accepted: 06/19/2021] [Indexed: 12/12/2022]
Abstract
Human osteoblasts are multifunctional bone cells, which play essential roles in bone formation, angiogenesis regulation, as well as maintenance of hematopoiesis. However, the categorization of primary osteoblast subtypes in vivo in humans has not yet been achieved. Here, we used single-cell RNA sequencing (scRNA-seq) to perform a systematic cellular taxonomy dissection of freshly isolated human osteoblasts from one 31-year-old male with osteoarthritis and osteopenia after hip replacement. Based on the gene expression patterns and cell lineage reconstruction, we identified three distinct cell clusters including preosteoblasts, mature osteoblasts, and an undetermined rare osteoblast subpopulation. This novel subtype was found to be the major source of the nuclear receptor subfamily 4 group A member 1 and 2 (NR4A1 and NR4A2) in primary osteoblasts, and the expression of NR4A1 was confirmed by immunofluorescence staining on mouse osteoblasts in vivo. Trajectory inference analysis suggested that the undetermined cluster, together with the preosteoblasts, are involved in the regulation of osteoblastogenesis and also give rise to mature osteoblasts. Investigation of the biological processes and signaling pathways enriched in each subpopulation revealed that in addition to bone formation, preosteoblasts and undetermined osteoblasts may also regulate both angiogenesis and hemopoiesis. Finally, we demonstrated that there are systematic differences between the transcriptional profiles of human and mouse osteoblasts, highlighting the necessity for studying bone physiological processes in humans rather than solely relying on mouse models. Our findings provide novel insights into the cellular heterogeneity and potential biological functions of human primary osteoblasts at the single-cell level.
Collapse
Affiliation(s)
- Yun Gong
- Tulane Center for Biomedical Informatics and Genomics, Deming Department of Medicine, School of Medicine, Tulane University, New Orleans, LA 70112, USA
| | - Junxiao Yang
- Department of Orthopedics, Xiangya Hospital, Central South University, Changsha 410008, China
| | - Xiaohua Li
- Laboratory of Molecular and Statistical Genetics, College of Life Sciences, Hunan Normal University, Changsha 410081, China
| | - Cui Zhou
- Laboratory of Molecular and Statistical Genetics, College of Life Sciences, Hunan Normal University, Changsha 410081, China
| | - Yu Chen
- Laboratory of Molecular and Statistical Genetics, College of Life Sciences, Hunan Normal University, Changsha 410081, China
| | - Zun Wang
- Xiangya Nursing School, Central South University, Changsha 410013, China
| | - Xiang Qiu
- School of Basic Medical Science, Central South University, Changsha 410008, China
| | - Ying Liu
- Laboratory of Molecular and Statistical Genetics, College of Life Sciences, Hunan Normal University, Changsha 410081, China
| | - Huixi Zhang
- Laboratory of Molecular and Statistical Genetics, College of Life Sciences, Hunan Normal University, Changsha 410081, China
| | - Jonathan Greenbaum
- Tulane Center for Biomedical Informatics and Genomics, Deming Department of Medicine, School of Medicine, Tulane University, New Orleans, LA 70112, USA
| | - Liang Cheng
- Department of Orthopedics and National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha 410008, China
| | - Yihe Hu
- Department of Orthopedics, Xiangya Hospital, Central South University, Changsha 410008, China
| | - Jie Xie
- Department of Orthopedics, Xiangya Hospital, Central South University, Changsha 410008, China
| | - Xuecheng Yang
- Department of Orthopedics, Xiangya Hospital, Central South University, Changsha 410008, China
| | - Yusheng Li
- Department of Orthopedics, Xiangya Hospital, Central South University, Changsha 410008, China
| | - Yuntong Bai
- Tulane Center for Bioinformatics and Genomics, Department of Biomedical Engineering, Tulane University, New Orleans, LA 70112, USA
| | - Yu-Ping Wang
- Tulane Center for Bioinformatics and Genomics, Department of Biomedical Engineering, Tulane University, New Orleans, LA 70112, USA
| | - Yiping Chen
- Department of Cell and Molecular Biology, School of Science and Engineering, Tulane University, New Orleans, LA 70112, USA
| | - Li-Jun Tan
- Laboratory of Molecular and Statistical Genetics, College of Life Sciences, Hunan Normal University, Changsha 410081, China
| | - Hui Shen
- Tulane Center for Biomedical Informatics and Genomics, Deming Department of Medicine, School of Medicine, Tulane University, New Orleans, LA 70112, USA
| | - Hong-Mei Xiao
- Center of Reproductive Health, System Biology and Data Information, Institute of Reproductive and Stem Cell Engineering, School of Basic Medical Science, Central South University, Changsha 410081, China.,School of Basic Medical Science, Central South University, Changsha 410008, China
| | - Hong-Wen Deng
- Tulane Center for Biomedical Informatics and Genomics, Deming Department of Medicine, School of Medicine, Tulane University, New Orleans, LA 70112, USA.,School of Basic Medical Science, Central South University, Changsha 410008, China
| |
Collapse
|
4
|
Kaehler M, Dworschak M, Rodin JP, Ruemenapp J, Vater I, Penas EMM, Liu C, Cascorbi I, Nagel I. ZFP36L1 plays an ambiguous role in the regulation of cell expansion and negatively regulates CDKN1A in chronic myeloid leukemia cells. Exp Hematol 2021; 99:54-64.e7. [PMID: 34090970 DOI: 10.1016/j.exphem.2021.05.006] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Revised: 05/26/2021] [Accepted: 05/31/2021] [Indexed: 12/20/2022]
Abstract
The mRNA-destabilizing proteins ZFP36L1 and ZFP36L2 are described as mediators of quiescence and play a pivotal role in hematopoietic malignancies. Both genes are mainly classified as tumor suppressor genes as they posttranscriptionally downregulate the expression of oncogenes and contribute to cellular quiescence. Here, we analyzed the role of ZFP36L1 and ZFP36L2 in chronic myeloid leukemia (CML). We found ZFP36L1 and ZFP36L2 expression to be deregulated in patients with CML. By use of in vitro models of tyrosine kinase inhibitor resistance, an increase in ZFP36L1 and ZFP36L2 expression was detected during the development of imatinib resistance. CRISPR/Cas9-derived knockout of ZFP36L1, but not of ZFP36L2, in imatinib-sensitive cells led to decreased proliferation rates in response to tyrosine kinase inhibitor treatment. This effect was also observed in untreated ZFP36L1 knockout cells, albeit to a lower extent. Genomewide gene expression analyses of ZFP36L1 knockout cells revealed differential expression of cell cycle regulators, in particular upregulation of the cell cycle inhibitor CDKN1A. In addition, the 3' untranslated region of CDKN1A was proven to be a direct target of ZFP36L1. This indicates that tumor suppressor genes can also be targeted by ZFP36L1. Hence, ZFP36L1 cannot unambiguously be regarded as a tumor suppressor gene.
Collapse
Affiliation(s)
- Meike Kaehler
- Institute of Experimental and Clinical Pharmacology, University Hospital Schleswig-Holstein, Campus Kiel, Kiel, Germany
| | - Maike Dworschak
- Institute of Experimental and Clinical Pharmacology, University Hospital Schleswig-Holstein, Campus Kiel, Kiel, Germany
| | - Julian Phillip Rodin
- Institute of Experimental and Clinical Pharmacology, University Hospital Schleswig-Holstein, Campus Kiel, Kiel, Germany
| | - Johanna Ruemenapp
- Institute of Experimental and Clinical Pharmacology, University Hospital Schleswig-Holstein, Campus Kiel, Kiel, Germany
| | - Inga Vater
- Institute of Human Genetics, University Hospital Schleswig-Holstein, Campus Kiel, Kiel Germany
| | - Eva Maria Murga Penas
- Institute of Human Genetics, University Hospital Schleswig-Holstein, Campus Kiel, Kiel Germany
| | - Catherine Liu
- Institute of Experimental and Clinical Pharmacology, University Hospital Schleswig-Holstein, Campus Kiel, Kiel, Germany
| | - Ingolf Cascorbi
- Institute of Experimental and Clinical Pharmacology, University Hospital Schleswig-Holstein, Campus Kiel, Kiel, Germany.
| | - Inga Nagel
- Institute of Experimental and Clinical Pharmacology, University Hospital Schleswig-Holstein, Campus Kiel, Kiel, Germany; Institute of Human Genetics, University Hospital Schleswig-Holstein, Campus Kiel, Kiel Germany
| |
Collapse
|
5
|
Bertesi M, Fantini S, Alecci C, Lotti R, Martello A, Parenti S, Carretta C, Marconi A, Grande A, Pincelli C, Zanocco-Marani T. Promoter Methylation Leads to Decreased ZFP36 Expression and Deregulated NLRP3 Inflammasome Activation in Psoriatic Fibroblasts. Front Med (Lausanne) 2021; 7:579383. [PMID: 33585499 PMCID: PMC7874095 DOI: 10.3389/fmed.2020.579383] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Accepted: 12/17/2020] [Indexed: 12/24/2022] Open
Abstract
The mRNA-destabilizing protein tristetraprolin (TTP), encoded by the ZFP36 gene, is known to be able to end inflammatory responses by directly targeting and destabilizing mRNAs encoding pro-inflammatory cytokines. We analyzed its role in psoriasis, a disease characterized by chronic inflammation. We observed that TTP is downregulated in fibroblasts deriving from psoriasis patients compared to those deriving from healthy individuals and that psoriatic fibroblasts exhibit abnormal inflammasome activity compared to their physiological counterpart. This phenomenon depends on TTP downregulation. In fact, following restoration, TTP is capable of directly targeting for degradation NLRP3 mRNA, thereby drastically decreasing inflammasome activation. Moreover, we provide evidence that ZFP36 undergoes methylation in psoriasis, by virtue of the presence of long stretches of CpG dinucleotides both in the promoter and the coding region. Besides confirming that a perturbation of TTP expression might underlie the pathogenesis of psoriasis, we suggest that deregulated inflammasome activity might play a role in the disease alongside deregulated cytokine expression.
Collapse
Affiliation(s)
- Matteo Bertesi
- Laboratory of Applied Biology, Department of Life Sciences, University of Modena and Reggio Emilia, Modena, Italy
| | - Sebastian Fantini
- Department of Life Sciences, Centre for Regenerative Medicine "Stefano Ferrari", University of Modena and Reggio Emilia, Modena, Italy
| | - Claudia Alecci
- Laboratory of Applied Biology, Department of Life Sciences, University of Modena and Reggio Emilia, Modena, Italy
| | - Roberta Lotti
- Laboratory of Cutaneous Biology, Department of Surgical, Medical, Dental and Morphological Sciences, University of Modena and Reggio Emilia, Modena, Italy
| | - Andrea Martello
- University College London, Institute of Ophthalmology London, London, United Kingdom
| | - Sandra Parenti
- Department of Life Sciences, Centre for Regenerative Medicine "Stefano Ferrari", University of Modena and Reggio Emilia, Modena, Italy
| | - Chiara Carretta
- Department of Life Sciences, Centre for Regenerative Medicine "Stefano Ferrari", University of Modena and Reggio Emilia, Modena, Italy
| | - Alessandra Marconi
- Laboratory of Cutaneous Biology, Department of Surgical, Medical, Dental and Morphological Sciences, University of Modena and Reggio Emilia, Modena, Italy
| | - Alexis Grande
- Laboratory of Applied Biology, Department of Life Sciences, University of Modena and Reggio Emilia, Modena, Italy
| | - Carlo Pincelli
- Laboratory of Cutaneous Biology, Department of Surgical, Medical, Dental and Morphological Sciences, University of Modena and Reggio Emilia, Modena, Italy
| | - Tommaso Zanocco-Marani
- Laboratory of Applied Biology, Department of Life Sciences, University of Modena and Reggio Emilia, Modena, Italy
| |
Collapse
|
6
|
Characterization of New ATM Deletion Associated with Hereditary Breast Cancer. Genes (Basel) 2021; 12:genes12020136. [PMID: 33494414 PMCID: PMC7911716 DOI: 10.3390/genes12020136] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Revised: 01/11/2021] [Accepted: 01/18/2021] [Indexed: 12/12/2022] Open
Abstract
Next-generation sequencing (NGS)-based cancer risk screening with multigene panels has become the most successful method for programming cancer prevention strategies. ATM germ-line heterozygosity has been described to increase tumor susceptibility. In particular, families carrying heterozygous germ-line variants of ATM gene have a 5- to 9-fold risk of developing breast cancer. Recent studies identified ATM as the second most mutated gene after CHEK2 in BRCA-negative patients. Nowadays, more than 170 missense variants and several truncating mutations have been identified in ATM gene. Here, we present the molecular characterization of a new ATM deletion, identified thanks to the CNV algorithm implemented in the NGS analysis pipeline. An automated workflow implementing the SOPHiA Genetics’ Hereditary Cancer Solution (HCS) protocol was used to generate NGS libraries that were sequenced on Illumina MiSeq Platform. NGS data analysis allowed us to identify a new inactivating deletion of exons 19–27 of ATM gene. The deletion was characterized both at the DNA and RNA level.
Collapse
|
7
|
Mammoli F, Parenti S, Lomiento M, Gemelli C, Atene CG, Grande A, Corradini R, Manicardi A, Fantini S, Zanocco-Marani T, Ferrari S. Physiological expression of miR-130a during differentiation of CD34 + human hematopoietic stem cells results in the inhibition of monocyte differentiation. Exp Cell Res 2019; 382:111445. [PMID: 31152707 DOI: 10.1016/j.yexcr.2019.05.026] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2018] [Revised: 05/20/2019] [Accepted: 05/23/2019] [Indexed: 01/24/2023]
Abstract
MicroRNAs (miRNA) are small noncoding RNAs that regulate gene expression by targeting mRNAs in a sequence specific manner, thereby determining their degradation or inhibiting translation. They are involved in processes such as proliferation, differentiation and apoptosis by fine-tuning the expression of genes underlying such events. The expression of specific miRNAs is involved in hematopoietic differentiation and their deregulation contributes to the development of hematopoietic malignancies such as acute myeloid leukemia (AML). miR-130a is over-expressed in AML. Here we show that miR-130a is physiologically expressed in myeloblasts and down-regulated during monocyte differentiation. Gain- and loss-of-function experiments performed on CD34+ human hematopoietic stem cells confirmed that expression of miR-130a inhibits monocyte differentiation by interfering with the expression of key transcription factors HOXA10, IRF8, KLF4, MAFB and PU-1. The data obtained in this study highlight that the correct modulation of miR-130a is necessary for normal differentiation to occur and confirming that deregulation of this miRNA might underlie the differentiation block occurring in AML.
Collapse
Affiliation(s)
- Fabiana Mammoli
- Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori (IRST) Srl - IRCCS, Italy.
| | - Sandra Parenti
- Department of Life Sciences, University of Modena and Reggio Emilia, Via Campi 287, 41125, Modena, Italy.
| | - Mariana Lomiento
- Sant'Orsola Malpighi Hospital, University of Bologna, Bologna, Italy.
| | - Claudia Gemelli
- Department of Life Sciences, University of Modena and Reggio Emilia, Via Campi 287, 41125, Modena, Italy.
| | - Claudio Giacinto Atene
- Department of Life Sciences, University of Modena and Reggio Emilia, Via Campi 287, 41125, Modena, Italy.
| | - Alexis Grande
- Department of Life Sciences, University of Modena and Reggio Emilia, Via Campi 287, 41125, Modena, Italy.
| | - Roberto Corradini
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parco Area delle Scienze 17/A, I-43124 Parma, Italy.
| | - Alex Manicardi
- Department of Organic and Macromolecular Chemistry Organic and Biomimetic Chemistry Research Group (OBCR) Faculty of Sciences - Ghent University Campus Sterre, Krijgslaan, 281 S4 B-9000 Gent, Belgium.
| | - Sebastian Fantini
- Department of Life Sciences, University of Modena and Reggio Emilia, Via Campi 287, 41125, Modena, Italy.
| | - Tommaso Zanocco-Marani
- Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori (IRST) Srl - IRCCS, Italy.
| | - Sergio Ferrari
- Department of Life Sciences, University of Modena and Reggio Emilia, Via Campi 287, 41125, Modena, Italy.
| |
Collapse
|
8
|
Kelly MJ, So J, Rogers AJ, Gregory G, Li J, Zethoven M, Gearhart MD, Bardwell VJ, Johnstone RW, Vervoort SJ, Kats LM. Bcor loss perturbs myeloid differentiation and promotes leukaemogenesis. Nat Commun 2019; 10:1347. [PMID: 30902969 PMCID: PMC6430802 DOI: 10.1038/s41467-019-09250-6] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2018] [Accepted: 02/28/2019] [Indexed: 12/26/2022] Open
Abstract
The BCL6 Corepressor (BCOR) is a component of a variant Polycomb repressive complex 1 (PRC1) that is essential for normal development. Recurrent mutations in the BCOR gene have been identified in acute myeloid leukaemia and myelodysplastic syndrome among other cancers; however, its function remains poorly understood. Here we examine the role of BCOR in haematopoiesis in vivo using a conditional mouse model that mimics the mutations observed in haematological malignancies. Inactivation of Bcor in haematopoietic stem cells (HSCs) results in expansion of myeloid progenitors and co-operates with oncogenic KrasG12D in the initiation of an aggressive and fully transplantable acute leukaemia. Gene expression analysis and chromatin immunoprecipitation sequencing reveals differential regulation of a subset of PRC1-target genes including HSC-associated transcription factors such as Hoxa7/9. This study provides mechanistic understanding of how BCOR regulates cell fate decisions and how loss of function contributes to the development of leukaemia.
Collapse
Affiliation(s)
- Madison J Kelly
- The Peter MacCallum Cancer Centre, Melbourne, VIC, 3000, Australia.,The Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, VIC, 3052, Australia
| | - Joan So
- The Peter MacCallum Cancer Centre, Melbourne, VIC, 3000, Australia
| | - Amy J Rogers
- The Peter MacCallum Cancer Centre, Melbourne, VIC, 3000, Australia
| | - Gareth Gregory
- The Peter MacCallum Cancer Centre, Melbourne, VIC, 3000, Australia.,The Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, VIC, 3052, Australia.,Monash Haematology, Monash Health and School of Clinical Sciences at Monash Health, Monash University, Clayton, VIC, 3168, Australia
| | - Jason Li
- The Peter MacCallum Cancer Centre, Melbourne, VIC, 3000, Australia
| | - Magnus Zethoven
- The Peter MacCallum Cancer Centre, Melbourne, VIC, 3000, Australia
| | - Micah D Gearhart
- Department of Genetics, Cell Biology and Development and the Masonic Cancer Center, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Vivian J Bardwell
- Department of Genetics, Cell Biology and Development and the Masonic Cancer Center, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Ricky W Johnstone
- The Peter MacCallum Cancer Centre, Melbourne, VIC, 3000, Australia.,The Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, VIC, 3052, Australia
| | | | - Lev M Kats
- The Peter MacCallum Cancer Centre, Melbourne, VIC, 3000, Australia. .,The Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, VIC, 3052, Australia.
| |
Collapse
|
9
|
Martínez-Calle N, Pascual M, Ordoñez R, Enériz ESJ, Kulis M, Miranda E, Guruceaga E, Segura V, Larráyoz MJ, Bellosillo B, Calasanz MJ, Besses C, Rifón J, Martín-Subero JI, Agirre X, Prosper F. Epigenomic profiling of myelofibrosis reveals widespread DNA methylation changes in enhancer elements and ZFP36L1 as a potential tumor suppressor gene that is epigenetically regulated. Haematologica 2019; 104:1572-1579. [PMID: 30655376 PMCID: PMC6669145 DOI: 10.3324/haematol.2018.204917] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2018] [Accepted: 01/15/2019] [Indexed: 12/19/2022] Open
Abstract
In this study we interrogated the DNA methylome of myelofibrosis patients using high-density DNA methylation arrays. We detected 35,215 differentially methylated CpG, corresponding to 10,253 genes, between myelofibrosis patients and healthy controls. These changes were present both in primary and secondary myelofibrosis, which showed no differences between them. Remarkably, most differentially methylated CpG were located outside gene promoter regions and showed significant association with enhancer regions. This aberrant enhancer hypermethylation was negatively correlated with the expression of 27 genes in the myelofibrosis cohort. Of these, we focused on the ZFP36L1 gene and validated its decreased expression and enhancer DNA hypermethylation in an independent cohort of patients and myeloid cell-lines. In vitro reporter assay and 5’-azacitidine treatment confirmed the functional relevance of hyper-methylation of ZFP36L1 enhancer. Furthermore, in vitro rescue of ZFP36L1 expression had an impact on cell proliferation and induced apoptosis in SET-2 cell line indicating a possible role of ZFP36L1 as a tumor suppressor gene in myelofibrosis. Collectively, we describe the DNA methylation profile of myelofibrosis, identifying extensive changes in enhancer elements and revealing ZFP36L1 as a novel candidate tumor suppressor gene.
Collapse
Affiliation(s)
- Nicolás Martínez-Calle
- Área de Hemato-Oncología, Centro de Investigación Médica Aplicada, IDISNA, Universidad de Navarra, Pamplona.,Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid
| | - Marien Pascual
- Área de Hemato-Oncología, Centro de Investigación Médica Aplicada, IDISNA, Universidad de Navarra, Pamplona.,Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid
| | - Raquel Ordoñez
- Área de Hemato-Oncología, Centro de Investigación Médica Aplicada, IDISNA, Universidad de Navarra, Pamplona.,Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid
| | - Edurne San José Enériz
- Área de Hemato-Oncología, Centro de Investigación Médica Aplicada, IDISNA, Universidad de Navarra, Pamplona.,Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid
| | - Marta Kulis
- Fundació Clínic per a la Recerca Biomèdica, Barcelona
| | - Estíbaliz Miranda
- Área de Hemato-Oncología, Centro de Investigación Médica Aplicada, IDISNA, Universidad de Navarra, Pamplona.,Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid
| | - Elisabeth Guruceaga
- Unidad de Bioinformática, Centro de Investigación Médica Aplicada, Universidad de Navarra, Pamplona
| | - Víctor Segura
- Unidad de Bioinformática, Centro de Investigación Médica Aplicada, Universidad de Navarra, Pamplona
| | | | | | - María José Calasanz
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid.,CIMA Laboratory of Diagnostics, Universidad de Navarra, Pamplona
| | - Carles Besses
- Departmento de Hematología, Hospital del Mar, Barcelona
| | - José Rifón
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid.,Departamento de Hematología, Clínica Universidad de Navarra, Universidad de Navarra, Pamplona
| | - José I Martín-Subero
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid.,Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona.,Departament de Fonaments Clinics, Facultat de Medicina, Universitat de Barcelona, Barcelona, Spain
| | - Xabier Agirre
- Área de Hemato-Oncología, Centro de Investigación Médica Aplicada, IDISNA, Universidad de Navarra, Pamplona .,Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid
| | - Felipe Prosper
- Área de Hemato-Oncología, Centro de Investigación Médica Aplicada, IDISNA, Universidad de Navarra, Pamplona .,Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid.,Departamento de Hematología, Clínica Universidad de Navarra, Universidad de Navarra, Pamplona
| |
Collapse
|
10
|
Son YO, Kim HE, Choi WS, Chun CH, Chun JS. RNA-binding protein ZFP36L1 regulates osteoarthritis by modulating members of the heat shock protein 70 family. Nat Commun 2019; 10:77. [PMID: 30622281 PMCID: PMC6325149 DOI: 10.1038/s41467-018-08035-7] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2018] [Accepted: 12/12/2018] [Indexed: 12/22/2022] Open
Abstract
Osteoarthritis (OA) is a whole-joint disease characterized by cartilage destruction and other whole-joint pathological changes. There is currently no effective disease-modifying therapy. Here we investigate the post-transcriptional mRNA regulation of OA-modulating proteins in chondrocytes and show that the ZFP36 family member, ZFP36L1, is specifically upregulated in OA chondrocytes and OA cartilage of humans and mice. Adenovirus-mediated overexpression of ZFP36L1 alone in mouse knee-joint tissue does not modulate OA pathogenesis. However, genetic ablation or silencing of Zfp36l1 significantly abrogates experimental OA in mice. Knockdown of Zfp36l1 increases the mRNA expression of two heat shock protein 70 (HSP70) family members, which act as its direct targets. Furthermore, overexpression of HSPA1A in joint tissues protects mice against experimental OA by inhibiting chondrocyte apoptosis. Our results indicate that the RNA-binding protein, ZFP36L1, regulates HSP70 family members that appear to protect against OA pathogenesis by inhibiting chondrocyte apoptosis. Osteoarthritis is characterised by degeneration of joint cartilage. Here the authors show that the RNA-binding protein ZFP36L1 is upregulated in chondrocytes of humans and mice with osteoarthritis, and that its knockdown in mouse joints protects chondrocytes against apoptosis by modulating the function of heat shock proteins.
Collapse
Affiliation(s)
- Young-Ok Son
- National Creative Research Initiatives Center for Osteoarthritis Pathogenesis and School of Life Sciences, Gwangju Institute of Science and Technology, Gwangju, 61005, Republic of Korea
| | - Hyo-Eun Kim
- National Creative Research Initiatives Center for Osteoarthritis Pathogenesis and School of Life Sciences, Gwangju Institute of Science and Technology, Gwangju, 61005, Republic of Korea
| | - Wan-Su Choi
- National Creative Research Initiatives Center for Osteoarthritis Pathogenesis and School of Life Sciences, Gwangju Institute of Science and Technology, Gwangju, 61005, Republic of Korea
| | - Churl-Hong Chun
- Department of Orthopedic Surgery, Wonkwang University School of Medicine, Iksan, 54538, Republic of Korea
| | - Jang-Soo Chun
- National Creative Research Initiatives Center for Osteoarthritis Pathogenesis and School of Life Sciences, Gwangju Institute of Science and Technology, Gwangju, 61005, Republic of Korea.
| |
Collapse
|
11
|
Moore KS, Yagci N, van Alphen F, Meijer AB, ‘t Hoen PAC, von Lindern M. Strap associates with Csde1 and affects expression of select Csde1-bound transcripts. PLoS One 2018; 13:e0201690. [PMID: 30138317 PMCID: PMC6107111 DOI: 10.1371/journal.pone.0201690] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2017] [Accepted: 07/22/2018] [Indexed: 02/06/2023] Open
Abstract
Erythropoiesis is regulated at many levels, including control of mRNA translation. Changing environmental conditions, such as hypoxia or the availability of nutrients and growth factors, require a rapid response enacted by the enhanced or repressed translation of existing transcripts. Cold shock domain protein e1 (Csde1/Unr) is an RNA-binding protein required for erythropoiesis and strongly upregulated in erythroblasts relative to other hematopoietic progenitors. The aim of this study is to identify the Csde1-containing protein complexes and investigate their role in post-transcriptional expression control of Csde1-bound transcripts. We show that Serine/Threonine kinase receptor-associated protein (Strap/Unrip), was the protein most strongly associated with Csde1 in erythroblasts. Strap is a WD40 protein involved in signaling and RNA splicing, but its role when associated with Csde1 is unknown. Reduced expression of Strap did not alter the pool of transcripts bound by Csde1. Instead, it altered the mRNA and/or protein expression of several Csde1-bound transcripts that encode for proteins essential for translational regulation during hypoxia, such as Hmbs, eIF4g3 and Pabpc4. Also affected by Strap knockdown were Vim, a Gata-1 target crucial for erythrocyte enucleation, and Elavl1, which stabilizes Gata-1 mRNA. The major cellular processes affected by both Csde1 and Strap were ribosome function and cell cycle control.
Collapse
Affiliation(s)
- Kat S. Moore
- Sanquin Research, Department of Hematopoiesis, and Landsteiner Laboratory Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
| | - Nurcan Yagci
- Sanquin Research, Department of Hematopoiesis, and Landsteiner Laboratory Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
| | - Floris van Alphen
- Sanquin Research, Department of Research Facilities, Amsterdam, The Netherlands
| | - Alexander B. Meijer
- Sanquin Research, Department of Research Facilities, Amsterdam, The Netherlands
- Department of Biomolecular Mass Spectrometry and Proteomics, Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Utrecht, The Netherlands
| | - Peter A. C. ‘t Hoen
- Centre for Molecular and Biomolecular Informatics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Marieke von Lindern
- Sanquin Research, Department of Hematopoiesis, and Landsteiner Laboratory Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
- * E-mail:
| |
Collapse
|
12
|
Moore KS, von Lindern M. RNA Binding Proteins and Regulation of mRNA Translation in Erythropoiesis. Front Physiol 2018; 9:910. [PMID: 30087616 PMCID: PMC6066521 DOI: 10.3389/fphys.2018.00910] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2018] [Accepted: 06/21/2018] [Indexed: 12/12/2022] Open
Abstract
Control of gene expression in erythropoiesis has to respond to signals that may emerge from intracellular processes or environmental factors. Control of mRNA translation allows for relatively rapid modulation of protein synthesis from the existing transcriptome. For instance, the protein synthesis rate needs to be reduced when reactive oxygen species or unfolded proteins accumulate in the cells, but also when iron supply is low or when growth factors are lacking in the environment. In addition, regulation of mRNA translation can be important as an additional layer of control on top of gene transcription, in which RNA binding proteins (RBPs) can modify translation of a set of transcripts to the cell’s actual protein requirement. The 5′ and 3′ untranslated regions of mRNA (5′UTR, 3′UTR) contain binding sites for general and sequence specific translation factors. They also contain secondary structures that may hamper scanning of the 5′UTR by translation complexes or may help to recruit translation factors. In addition, the term 5′UTR is not fully correct because many transcripts contain small open reading frames in their 5′UTR that are translated and contribute to regulation of mRNA translation. It is becoming increasingly clear that the transcriptome only partly predicts the proteome. The aim of this review is (i) to summarize how the availability of general translation initiation factors can selectively regulate transcripts because the 5′UTR contains secondary structures or short translated sequences, (ii) to discuss mechanisms that control the length of the mRNA poly(A) tail in relation to mRNA translation, and (iii) to give examples of sequence specific RBPs and their targets. We focused on transcripts and RBPs required for erythropoiesis. Whereas differentiation of erythroblasts to erythrocytes is orchestrated by erythroid transcription factors, the production of erythrocytes needs to respond to the availability of growth factors and nutrients, particularly the availability of iron.
Collapse
Affiliation(s)
- Kat S Moore
- Department of Hematopoiesis, Sanquin Research, and Landsteiner Laboratory, Amsterdam UMC, Amsterdam, Netherlands
| | - Marieke von Lindern
- Department of Hematopoiesis, Sanquin Research, and Landsteiner Laboratory, Amsterdam UMC, Amsterdam, Netherlands
| |
Collapse
|
13
|
Liu LL, Liu L, Liu HH, Ren SS, Dou CY, Cheng PP, Wang CL, Wang LN, Chen XL, Zhang H, Chen MT. Levamisole suppresses adipogenesis of aplastic anaemia-derived bone marrow mesenchymal stem cells through ZFP36L1-PPARGC1B axis. J Cell Mol Med 2018; 22:4496-4506. [PMID: 29993187 PMCID: PMC6111807 DOI: 10.1111/jcmm.13761] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2018] [Accepted: 06/08/2018] [Indexed: 11/26/2022] Open
Abstract
Aplastic anaemia (AA) is a life‐threatening hematopoietic disorder characterized by hypoplasia and pancytopenia with increasing fat cells in the bone marrow (BM). The BM‐derived mesenchymal stem cells (MSCs) from AA are more susceptible to be induced into adipogenic differentiation compared with that from control, which may be causatively associated with the fatty BM and defective hematopoiesis of AA. Here in this study, we first demonstrated that levamisole displayed a significant suppressive effect on the in vitro adipogenic differentiation of AA BM‐MSCs. Mechanistic investigation revealed that levamisole could increase the expression of ZFP36L1 which was subsequently demonstrated to function as a negative regulator of adipogenic differentiation of AA BM‐MSCs through lentivirus‐mediated ZFP36L1 knock‐down and overexpression assay. Peroxisome proliferator‐activated receptor gamma coactivator 1 beta (PPARGC1B) whose 3′‐untranslated region bears adenine‐uridine‐rich elements was verified as a direct downstream target of ZFP36L1, and knock‐down of PPARGC1B impaired the adipogenesis of AA BM‐MSCs. Collectively, our work demonstrated that ZFP36L1‐mediated post‐transcriptional control of PPARGC1B expression underlies the suppressive effect of levamisole on the adipogenic differentiation of AA BM‐MSCs, which not only provides novel therapeutic targets for alleviating the BM fatty phenomenon of AA patients, but also lays the theoretical and experimental foundation for the clinical application of levamisole in AA therapy.
Collapse
Affiliation(s)
- Lu-Lu Liu
- Central Laboratory, Affiliated Hospital of Jining Medical University, Jining, China
| | - Lei Liu
- Department of Hematology, Affiliated Hospital of Jining Medical University, Jining, China
| | - Hai-Hui Liu
- Department of Hematology, Affiliated Hospital of Jining Medical University, Jining, China.,Department of Graduate School, Jining Medical University, Jining, China
| | - Sai-Sai Ren
- Department of Hematology, Affiliated Hospital of Jining Medical University, Jining, China
| | - Cui-Yun Dou
- Department of Hematology, Affiliated Hospital of Jining Medical University, Jining, China
| | - Pan-Pan Cheng
- Department of Hematology, Affiliated Hospital of Jining Medical University, Jining, China
| | - Cui-Ling Wang
- Department of Hematology, Affiliated Hospital of Jining Medical University, Jining, China
| | - Li-Na Wang
- Central Laboratory, Affiliated Hospital of Jining Medical University, Jining, China
| | - Xiao-Li Chen
- Department of Graduate School, Jining Medical University, Jining, China
| | - Hao Zhang
- Department of Hematology, Affiliated Hospital of Jining Medical University, Jining, China
| | - Ming-Tai Chen
- Central Laboratory, Affiliated Hospital of Jining Medical University, Jining, China
| |
Collapse
|
14
|
Zhao H, Wang X, Yi P, Si Y, Tan P, He J, Yu S, Ren Y, Ma Y, Zhang J, Wang D, Wang F, Yu J. KSRP specifies monocytic and granulocytic differentiation through regulating miR-129 biogenesis and RUNX1 expression. Nat Commun 2017; 8:1428. [PMID: 29127290 PMCID: PMC5681548 DOI: 10.1038/s41467-017-01425-3] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2016] [Accepted: 09/15/2017] [Indexed: 01/11/2023] Open
Abstract
RNA-binding proteins (RBPs) integrate the processing of RNAs into post-transcriptional gene regulation, but the direct contribution of them to myeloid cell specification is poorly understood. Here, we report the first global RBP transcriptomic analysis of myeloid differentiation by combining RNA-seq analysis with myeloid induction in CD34+ hematopoietic progenitor cells. The downregulated expression of the KH-Type Splicing Regulatory Protein (KSRP) during monocytopoiesis and up-regulated expression during granulopoiesis suggests that KSRP has divergent roles during monocytic and granulocytic differentiation. A further comparative analysis of miRNA transcripts reveals that KSRP promotes the biogenesis of miR-129, and the expression patterns and roles of miR-129 in myeloid differentiation are equivalent to those of KSRP. Finally, miR-129 directly blocks the expression of Runt Related Transcription Factor 1 (RUNX1), which evokes transcriptional modulation by RUNX1. Based on our findings, KSRP, miR-129, and RUNX1 participate in a regulatory axis to control the outcome of myeloid differentiation.
Collapse
Affiliation(s)
- Hongmei Zhao
- State Key Laboratory of Medical Molecular Biology, Department of Biochemistry & Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences (CAMS) & Peking Union Medical College (PUMC), Beijing, 100005, China.,State Key Laboratory of Medical Molecular Biology, Department of Physiology and Pathophysiology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences (CAMS) & Peking Union Medical College (PUMC), Beijing, 100005, China
| | - Xiaoshuang Wang
- State Key Laboratory of Medical Molecular Biology, Department of Biochemistry & Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences (CAMS) & Peking Union Medical College (PUMC), Beijing, 100005, China
| | - Ping Yi
- Department of Obstetrics and Gynecology, The Third Affiliated Hospital of Chongqing Medical University, Chongqing, 401120, China
| | - Yanmin Si
- State Key Laboratory of Medical Molecular Biology, Department of Biochemistry & Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences (CAMS) & Peking Union Medical College (PUMC), Beijing, 100005, China
| | - Puwen Tan
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, China
| | - Jinrong He
- State Key Laboratory of Medical Molecular Biology, Department of Biochemistry & Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences (CAMS) & Peking Union Medical College (PUMC), Beijing, 100005, China
| | - Shan Yu
- State Key Laboratory of Medical Molecular Biology, Department of Biochemistry & Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences (CAMS) & Peking Union Medical College (PUMC), Beijing, 100005, China
| | - Yue Ren
- State Key Laboratory of Medical Molecular Biology, Department of Biochemistry & Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences (CAMS) & Peking Union Medical College (PUMC), Beijing, 100005, China
| | - Yanni Ma
- State Key Laboratory of Medical Molecular Biology, Department of Biochemistry & Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences (CAMS) & Peking Union Medical College (PUMC), Beijing, 100005, China
| | - Junwu Zhang
- State Key Laboratory of Medical Molecular Biology, Department of Biochemistry & Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences (CAMS) & Peking Union Medical College (PUMC), Beijing, 100005, China
| | - Dong Wang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, China. .,Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu, 610054, China.
| | - Fang Wang
- State Key Laboratory of Medical Molecular Biology, Department of Biochemistry & Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences (CAMS) & Peking Union Medical College (PUMC), Beijing, 100005, China.
| | - Jia Yu
- State Key Laboratory of Medical Molecular Biology, Department of Biochemistry & Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences (CAMS) & Peking Union Medical College (PUMC), Beijing, 100005, China.
| |
Collapse
|
15
|
Schultz DJ, Muluhngwi P, Alizadeh-Rad N, Green MA, Rouchka EC, Waigel SJ, Klinge CM. Genome-wide miRNA response to anacardic acid in breast cancer cells. PLoS One 2017; 12:e0184471. [PMID: 28886127 PMCID: PMC5590942 DOI: 10.1371/journal.pone.0184471] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2017] [Accepted: 08/24/2017] [Indexed: 02/06/2023] Open
Abstract
MicroRNAs are biomarkers and potential therapeutic targets for breast cancer. Anacardic acid (AnAc) is a dietary phenolic lipid that inhibits both MCF-7 estrogen receptor α (ERα) positive and MDA-MB-231 triple negative breast cancer (TNBC) cell proliferation with IC50s of 13.5 and 35 μM, respectively. To identify potential mediators of AnAc action in breast cancer, we profiled the genome-wide microRNA transcriptome (microRNAome) in these two cell lines altered by the AnAc 24:1n5 congener. Whole genome expression profiling (RNA-seq) and subsequent network analysis in MetaCore Gene Ontology (GO) algorithm was used to characterize the biological pathways altered by AnAc. In MCF-7 cells, 69 AnAc-responsive miRNAs were identified, e.g., increased let-7a and reduced miR-584. Fewer, i.e., 37 AnAc-responsive miRNAs were identified in MDA-MB-231 cells, e.g., decreased miR-23b and increased miR-1257. Only two miRNAs were increased by AnAc in both cell lines: miR-612 and miR-20b; however, opposite miRNA arm preference was noted: miR-20b-3p and miR-20b-5p were upregulated in MCF-7 and MDA-MB-231, respectively. miR-20b-5p target EFNB2 transcript levels were reduced by AnAc in MDA-MB-231 cells. AnAc reduced miR-378g that targets VIM (vimentin) and VIM mRNA transcript expression was increased in AnAc-treated MCF-7 cells, suggesting a reciprocal relationship. The top three enriched GO terms for AnAc-treated MCF-7 cells were B cell receptor signaling pathway and ribosomal large subunit biogenesis and S-adenosylmethionine metabolic process for AnAc-treated MDA-MB-231 cells. The pathways modulated by these AnAc-regulated miRNAs suggest that key nodal molecules, e.g., Cyclin D1, MYC, c-FOS, PPARγ, and SIN3, are targets of AnAc activity.
Collapse
Affiliation(s)
- David J. Schultz
- Department of Biology, University of Louisville, Louisville, Kentucky, United States of America
| | - Penn Muluhngwi
- Department of Biochemistry & Molecular Genetics, University of Louisville School of Medicine, Louisville, Kentucky, United States of America
| | - Negin Alizadeh-Rad
- Department of Biochemistry & Molecular Genetics, University of Louisville School of Medicine, Louisville, Kentucky, United States of America
| | - Madelyn A. Green
- Department of Biochemistry & Molecular Genetics, University of Louisville School of Medicine, Louisville, Kentucky, United States of America
| | - Eric C. Rouchka
- Bioinformatics and Biomedical Computing Laboratory, Department of Computer Engineering and Computer Science, Louisville, Kentucky, United States of America
| | - Sabine J. Waigel
- Department of Medicine, University of Louisville School of Medicine, Louisville, Kentucky, United States of America
| | - Carolyn M. Klinge
- Department of Biochemistry & Molecular Genetics, University of Louisville School of Medicine, Louisville, Kentucky, United States of America
| |
Collapse
|
16
|
McClelland L, Jasper H, Biteau B. Tis11 mediated mRNA decay promotes the reacquisition of Drosophila intestinal stem cell quiescence. Dev Biol 2017; 426:8-16. [PMID: 28445691 DOI: 10.1016/j.ydbio.2017.04.013] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2017] [Revised: 04/05/2017] [Accepted: 04/20/2017] [Indexed: 10/19/2022]
Abstract
Adult stem cell proliferation rates are precisely regulated to maintain long-term tissue homeostasis. Defects in the mechanisms controlling stem cell proliferation result in impaired regeneration and hyperproliferative diseases. Many stem cell populations increase proliferation in response to tissue damage and reacquire basal proliferation rates after tissue repair is completed. Although proliferative signals have been extensively studied, much less is known about the molecular mechanisms that restore stem cell quiescence. Here we show that Tis11, an Adenine-uridine Rich Element (ARE) binding protein that promotes mRNA degradation, is required to re-establish basal proliferation rates of adult Drosophila intestinal stem cells (ISC) after a regenerative episode. We find that Tis11 limits ISC proliferation specifically after proliferation has been stimulated in response to heat stress or infection, and show that Tis11 expression and activity are increased in ISCs during tissue repair. Based on stem cell transcriptome analysis and RNA immunoprecipitation, we propose that Tis11 activation represents an integral part of a negative feedback mechanism that limits the expression of key components of several signaling pathways that control ISC function and proliferation. Our results identify Tis11 mediated mRNA decay as an evolutionarily conserved mechanism of re-establishing basal proliferation rates of stem cells in regenerating tissues.
Collapse
Affiliation(s)
- Lindy McClelland
- Department of Biomedical Genetics, University of Rochester Medical Center, 601 Elmwood Avenue, Rochester, NY 14642, USA; The Buck Institute for Research on Aging, 8001 Redwood Boulevard, Novato, CA 94945, USA
| | - Heinrich Jasper
- The Buck Institute for Research on Aging, 8001 Redwood Boulevard, Novato, CA 94945, USA
| | - Benoît Biteau
- Department of Biomedical Genetics, University of Rochester Medical Center, 601 Elmwood Avenue, Rochester, NY 14642, USA.
| |
Collapse
|
17
|
Shen XH, Sun NN, Yin YF, Liu SF, Liu XL, Peng HL, Dai CW, Xu YX, Deng MY, Luo YY, Zheng WL, Zhang GS. A TET2 rs3733609 C/T genotype is associated with predisposition to the myeloproliferative neoplasms harboring JAK2(V617F) and confers a proliferative potential on erythroid lineages. Oncotarget 2017; 7:9550-60. [PMID: 26843622 PMCID: PMC4891059 DOI: 10.18632/oncotarget.7072] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2015] [Accepted: 01/13/2016] [Indexed: 01/05/2023] Open
Abstract
Common germline single-nucleotide polymorphisms (SNPs) at JAK2 locus have been associated with Myeloproliferative neoplasms (MPN). And, the germline sequence variant rs2736100 C in TERT is related to risk of MPN, suggesting a complex association between SNPs and the pathogenesis of MPN. Our previous study (unpublished data) showed that there was a high frequency distribution in rs3733609 C/T genotype at Ten-Eleven Translocation 2 (TET2) locus in one Chinese familial primary myelofibrosis. In the present study, we evaluate the role and clinical significance of rs3733609 C/T genotype in JAK2V617F-positive sporadic MPN (n = 181). TET2 rs3733609 C/T genotype had a higher incidence (13.81%; 25/181) in JAK2V617F-positive sporadic MPN patients than that in normal controls (n = 236) (6.35%; 15/236), which was predisposing to MPN (odds ratio(OR) = 2.361; P = 0.01). MPN patients with rs3733609 C/T genotype had increased leukocyte and platelets counts, elevated hemoglobin concentration in comparison with T/T genotype. Thrombotic events were more common in MPN patients with rs3733609 C/T than those with T/T genotype (P < 0.01). We confirmed that rs3733609 C/T genotype downregulated TET2 mRNA transcription, and the mechanism may be involved in a disruption of the interaction between CCAAT/enhancer binding protein alpha (C/EBPA) and TET2 rs3733609 C/T locus.TET2 rs3733609 C/T genotype stimulated the erythroid hematopoiesis in MPN patients. Altogether, we found a novel hereditary susceptible factor-TET2 rs3733609 C/T variant for the development of MPN, suggesting the variant may be partially responsible for the pathogenesis and accumulation of MPN.
Collapse
Affiliation(s)
- Xiao-hui Shen
- Division of Hematology, Institute of Molecular Hematology, The Second Xiang-Ya Hospital, Central South University, Changsha, Hunan 410011, P.R. China
| | - Nan-nan Sun
- Division of Hematology, Institute of Molecular Hematology, The Second Xiang-Ya Hospital, Central South University, Changsha, Hunan 410011, P.R. China
| | - Ya-fei Yin
- Division of Hematology, Institute of Molecular Hematology, The Second Xiang-Ya Hospital, Central South University, Changsha, Hunan 410011, P.R. China
| | - Su-fang Liu
- Division of Hematology, Institute of Molecular Hematology, The Second Xiang-Ya Hospital, Central South University, Changsha, Hunan 410011, P.R. China
| | - Xiao-liu Liu
- Division of Hematology, Institute of Molecular Hematology, The Second Xiang-Ya Hospital, Central South University, Changsha, Hunan 410011, P.R. China
| | - Hong-ling Peng
- Division of Hematology, Institute of Molecular Hematology, The Second Xiang-Ya Hospital, Central South University, Changsha, Hunan 410011, P.R. China
| | - Chong-wen Dai
- Division of Hematology, Institute of Molecular Hematology, The Second Xiang-Ya Hospital, Central South University, Changsha, Hunan 410011, P.R. China
| | - Yun-xiao Xu
- Division of Hematology, Institute of Molecular Hematology, The Second Xiang-Ya Hospital, Central South University, Changsha, Hunan 410011, P.R. China
| | - Ming-yang Deng
- Division of Hematology, Institute of Molecular Hematology, The Second Xiang-Ya Hospital, Central South University, Changsha, Hunan 410011, P.R. China
| | - Yun-ya Luo
- Division of Hematology, Institute of Molecular Hematology, The Second Xiang-Ya Hospital, Central South University, Changsha, Hunan 410011, P.R. China
| | - Wen-li Zheng
- Division of Hematology, Institute of Molecular Hematology, The Second Xiang-Ya Hospital, Central South University, Changsha, Hunan 410011, P.R. China
| | - Guang-sen Zhang
- Division of Hematology, Institute of Molecular Hematology, The Second Xiang-Ya Hospital, Central South University, Changsha, Hunan 410011, P.R. China
| |
Collapse
|
18
|
Chen MT, Dong L, Zhang XH, Yin XL, Ning HM, Shen C, Su R, Li F, Song L, Ma YN, Wang F, Zhao HL, Yu J, Zhang JW. ZFP36L1 promotes monocyte/macrophage differentiation by repressing CDK6. Sci Rep 2015; 5:16229. [PMID: 26542173 PMCID: PMC4635361 DOI: 10.1038/srep16229] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2015] [Accepted: 10/12/2015] [Indexed: 12/15/2022] Open
Abstract
RNA binding proteins (RBPs)-mediated post-transcriptional control has been implicated in influencing various aspects of RNA metabolism and playing important roles in mammalian development and pathological diseases. However, the functions of specific RBPs and the molecular mechanisms through which they act in monocyte/macrophage differentiation remain to be determined. In this study, through bioinformatics analysis and experimental validation, we identify that ZFP36L1, a member of ZFP36 zinc finger protein family, exhibits significant decrease in acute myeloid leukemia (AML) patients compared with normal controls and remarkable time-course increase during monocyte/macrophage differentiation of PMA-induced THP-1 and HL-60 cells as well as induction culture of CD34+ hematopoietic stem/progenitor cells (HSPCs). Lentivirus-mediated gain and loss of function assays demonstrate that ZFP36L1 acts as a positive regulator to participate in monocyte/macrophage differentiation. Mechanistic investigation further reveals that ZFP36L1 binds to the CDK6 mRNA 3′untranslated region bearing adenine-uridine rich elements and negatively regulates the expression of CDK6 which is subsequently demonstrated to impede the in vitro monocyte/macrophage differentiation of CD34+ HSPCs. Collectively, our work unravels a ZFP36L1-mediated regulatory circuit through repressing CDK6 expression during monocyte/macrophage differentiation, which may also provide a therapeutic target for AML therapy.
Collapse
Affiliation(s)
- Ming-Tai Chen
- The State Key Laboratory of Medical Molecular Biology and the Department of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100005, China
| | - Lei Dong
- The State Key Laboratory of Medical Molecular Biology and the Department of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100005, China
| | - Xin-Hua Zhang
- Haematology Department, the 303 Hospital, Nanning, China
| | - Xiao-Lin Yin
- Haematology Department, the 303 Hospital, Nanning, China
| | - Hong-Mei Ning
- Department of Hematopoietic Stem Cell Transplantation, Affiliated Hospital to Academy of Military Medical Science, Beijing, China
| | - Chao Shen
- The State Key Laboratory of Medical Molecular Biology and the Department of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100005, China
| | - Rui Su
- The State Key Laboratory of Medical Molecular Biology and the Department of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100005, China
| | - Feng Li
- The State Key Laboratory of Medical Molecular Biology and the Department of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100005, China
| | - Li Song
- The State Key Laboratory of Medical Molecular Biology and the Department of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100005, China
| | - Yan-Ni Ma
- The State Key Laboratory of Medical Molecular Biology and the Department of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100005, China
| | - Fang Wang
- The State Key Laboratory of Medical Molecular Biology and the Department of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100005, China
| | - Hua-Lu Zhao
- The State Key Laboratory of Medical Molecular Biology and the Department of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100005, China
| | - Jia Yu
- The State Key Laboratory of Medical Molecular Biology and the Department of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100005, China
| | - Jun-Wu Zhang
- The State Key Laboratory of Medical Molecular Biology and the Department of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100005, China
| |
Collapse
|
19
|
Kallionpää H, Laajala E, Öling V, Härkönen T, Tillmann V, Dorshakova NV, Ilonen J, Lähdesmäki H, Knip M, Lahesmaa R. Standard of hygiene and immune adaptation in newborn infants. Clin Immunol 2014; 155:136-147. [PMID: 25245264 DOI: 10.1016/j.clim.2014.09.009] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2014] [Revised: 09/08/2014] [Accepted: 09/10/2014] [Indexed: 01/09/2023]
Abstract
The prevalence of immune-mediated diseases, such as allergies and type 1 diabetes, is on the rise in the developed world. In order to explore differences in the gene expression patterns induced in utero in infants born in contrasting standards of living and hygiene, we collected umbilical cord blood RNA samples from infants born in Finland (modern society), Estonia (rapidly developing society) and the Republic of Karelia, Russia (poor economic conditions). The whole blood transcriptome of Finnish and Estonian neonates differed from their Karelian counterparts, suggesting exposure to toll-like receptor (TLR) ligands and a more matured immune response in infants born in Karelia. These results further support the concept of a conspicuous plasticity in the developing immune system: the environmental factors that play a role in the susceptibility/protection towards immune-mediated diseases begin to shape the neonatal immunity already in utero and direct the maturation in accordance with the surrounding microbial milieu.
Collapse
Affiliation(s)
- Henna Kallionpää
- Turku Centre for Biotechnology, University of Turku and Åbo Akademi University, 20521 Turku, Finland; Turku Doctoral Programme of Biomedical Sciences, Kiinamyllynkatu 13, 20520 Turku, Finland; The Finnish Centre of Excellence in Molecular Systems Immunology and Physiology Research, Finland
| | - Essi Laajala
- Turku Centre for Biotechnology, University of Turku and Åbo Akademi University, 20521 Turku, Finland; The Finnish Centre of Excellence in Molecular Systems Immunology and Physiology Research, Finland; The National Graduate School in Informational and Structural Biology, 20520 Turku, Finland; Department of Information and Computer Science, Aalto University School of Science, 00076 Aalto, Finland
| | - Viveka Öling
- Turku Centre for Biotechnology, University of Turku and Åbo Akademi University, 20521 Turku, Finland; The Finnish Centre of Excellence in Molecular Systems Immunology and Physiology Research, Finland
| | - Taina Härkönen
- The Finnish Centre of Excellence in Molecular Systems Immunology and Physiology Research, Finland; Children's Hospital, University of Helsinki and Helsinki University Central Hospital, 00014 Helsinki, Finland; Diabetes and Obesity Research Program, University of Helsinki, 00014 Helsinki, Finland
| | - Vallo Tillmann
- Department of Pediatrics, University of Tartu and Tartu University Hospital, 51014 Tartu, Estonia
| | | | - Jorma Ilonen
- Immunogenetics Laboratory, University of Turku, 20520 Turku, Finland; Department of Clinical Microbiology, University of Eastern Finland, 70210 Kuopio, Finland
| | - Harri Lähdesmäki
- Turku Centre for Biotechnology, University of Turku and Åbo Akademi University, 20521 Turku, Finland; The Finnish Centre of Excellence in Molecular Systems Immunology and Physiology Research, Finland; Department of Information and Computer Science, Aalto University School of Science, 00076 Aalto, Finland
| | - Mikael Knip
- The Finnish Centre of Excellence in Molecular Systems Immunology and Physiology Research, Finland; Children's Hospital, University of Helsinki and Helsinki University Central Hospital, 00014 Helsinki, Finland; Diabetes and Obesity Research Program, University of Helsinki, 00014 Helsinki, Finland; Folkhälsan Research Center, 00290 Helsinki, Finland; Department of Pediatrics, Tampere University Hospital, 33521 Tampere, Finland
| | - Riitta Lahesmaa
- Turku Centre for Biotechnology, University of Turku and Åbo Akademi University, 20521 Turku, Finland; The Finnish Centre of Excellence in Molecular Systems Immunology and Physiology Research, Finland.
| | | |
Collapse
|
20
|
Zekavati A, Nasir A, Alcaraz A, Aldrovandi M, Marsh P, Norton JD, Murphy JJ. Post-transcriptional regulation of BCL2 mRNA by the RNA-binding protein ZFP36L1 in malignant B cells. PLoS One 2014; 9:e102625. [PMID: 25014217 PMCID: PMC4094554 DOI: 10.1371/journal.pone.0102625] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2013] [Accepted: 06/22/2014] [Indexed: 12/25/2022] Open
Abstract
The human ZFP36 zinc finger protein family consists of ZFP36, ZFP36L1, and ZFP36L2. These proteins regulate various cellular processes, including cell apoptosis, by binding to adenine uridine rich elements in the 3' untranslated regions of sets of target mRNAs to promote their degradation. The pro-apoptotic and other functions of ZFP36 family members have been implicated in the pathogenesis of lymphoid malignancies. To identify candidate mRNAs that are targeted in the pro-apoptotic response by ZFP36L1, we reverse-engineered a gene regulatory network for all three ZFP36 family members using the 'maximum information coefficient' (MIC) for target gene inference on a large microarray gene expression dataset representing cells of diverse histological origin. Of the three inferred ZFP36L1 mRNA targets that were identified, we focussed on experimental validation of mRNA for the pro-survival protein, BCL2, as a target for ZFP36L1. RNA electrophoretic mobility shift assay experiments revealed that ZFP36L1 interacted with the BCL2 adenine uridine rich element. In murine BCL1 leukemia cells stably transduced with a ZFP36L1 ShRNA lentiviral construct, BCL2 mRNA degradation was significantly delayed compared to control lentiviral expressing cells and ZFP36L1 knockdown in different cell types (BCL1, ACHN, Ramos), resulted in increased levels of BCL2 mRNA levels compared to control cells. 3' untranslated region luciferase reporter assays in HEK293T cells showed that wild type but not zinc finger mutant ZFP36L1 protein was able to downregulate a BCL2 construct containing the BCL2 adenine uridine rich element and removal of the adenine uridine rich core from the BCL2 3' untranslated region in the reporter construct significantly reduced the ability of ZFP36L1 to mediate this effect. Taken together, our data are consistent with ZFP36L1 interacting with and mediating degradation of BCL2 mRNA as an important target through which ZFP36L1 mediates its pro-apoptotic effects in malignant B-cells.
Collapse
Affiliation(s)
- Anna Zekavati
- Division of Immunology, Infection and Inflammatory Disease, King's College London, London, United Kingdom
| | - Asghar Nasir
- Division of Immunology, Infection and Inflammatory Disease, King's College London, London, United Kingdom
| | - Amor Alcaraz
- Department of Biomedical Sciences, University of Westminster, London, United Kingdom
| | - Maceler Aldrovandi
- Division of Immunology, Infection and Inflammatory Disease, King's College London, London, United Kingdom
| | - Phil Marsh
- Division of Endocrinology, King's College London, London, United Kingdom
| | - John D. Norton
- School of Biological Sciences, University of Essex, Colchester, Essex, United Kingdom
| | - John J. Murphy
- Division of Immunology, Infection and Inflammatory Disease, King's College London, London, United Kingdom
- Department of Biomedical Sciences, University of Westminster, London, United Kingdom
- * E-mail:
| |
Collapse
|
21
|
Yuan J, Muljo SA. Exploring the RNA world in hematopoietic cells through the lens of RNA-binding proteins. Immunol Rev 2013; 253:290-303. [PMID: 23550653 DOI: 10.1111/imr.12048] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The discovery of microRNAs has renewed interest in posttranscriptional modes of regulation, fueling an emerging view of a rich RNA world within our cells that deserves further exploration. Much work has gone into elucidating genetic regulatory networks that orchestrate gene expression programs and direct cell fate decisions in the hematopoietic system. However, the focus has been to elucidate signaling pathways and transcriptional programs. To bring us one step closer to reverse engineering the molecular logic of cellular differentiation, it will be necessary to map posttranscriptional circuits as well and integrate them in the context of existing network models. In this regard, RNA-binding proteins (RBPs) may rival transcription factors as important regulators of cell fates and represent a tractable opportunity to connect the RNA world to the proteome. ChIP-seq has greatly facilitated genome-wide localization of DNA-binding proteins, helping us to understand genomic regulation at a systems level. Similarly, technological advances such as CLIP-seq allow transcriptome-wide mapping of RBP binding sites, aiding us to unravel posttranscriptional networks. Here, we review RBP-mediated posttranscriptional regulation, paying special attention to findings relevant to the immune system. As a prime example, we highlight the RBP Lin28B, which acts as a heterochronic switch between fetal and adult lymphopoiesis.
Collapse
Affiliation(s)
- Joan Yuan
- Integrative Immunobiology Unit, Laboratory of Immunology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892-1892, USA
| | | |
Collapse
|
22
|
ZFP36L1 negatively regulates plasmacytoid differentiation of BCL1 cells by targeting BLIMP1 mRNA. PLoS One 2012; 7:e52187. [PMID: 23284928 PMCID: PMC3527407 DOI: 10.1371/journal.pone.0052187] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2012] [Accepted: 11/09/2012] [Indexed: 12/03/2022] Open
Abstract
The ZFP36/Tis11 family of zinc-finger proteins regulate cellular processes by binding to adenine uridine rich elements in the 3′ untranslated regions of various mRNAs and promoting their degradation. We show here that ZFP36L1 expression is largely extinguished during the transition from B cells to plasma cells, in a reciprocal pattern to that of ZFP36 and the plasma cell transcription factor, BLIMP1. Enforced expression of ZFP36L1 in the mouse BCL1 cell line blocked cytokine-induced differentiation while shRNA-mediated knock-down enhanced differentiation. Reconstruction of regulatory networks from microarray gene expression data using the ARACNe algorithm identified candidate mRNA targets for ZFP36L1 including BLIMP1. Genes that displayed down-regulation in plasma cells were significantly over-represented (P = <0.0001) in a set of previously validated ZFP36 targets suggesting that ZFP36L1 and ZFP36 target distinct sets of mRNAs during plasmacytoid differentiation. ShRNA-mediated knock-down of ZFP36L1 in BCL1 cells led to an increase in levels of BLIMP1 mRNA and protein, but not for mRNAs of other transcription factors that regulate plasmacytoid differentiation (xbp1, irf4, bcl6). Finally, ZFP36L1 significantly reduced the activity of a BLIMP1 3′ untranslated region-driven luciferase reporter. Taken together, these findings suggest that ZFP36L1 negatively regulates plasmacytoid differentiation, at least in part, by targeting the expression of BLIMP1.
Collapse
|
23
|
Selmi T, Martello A, Vignudelli T, Ferrari E, Grande A, Gemelli C, Salomoni P, Ferrari S, Zanocco-Marani T. ZFP36 expression impairs glioblastoma cell lines viability and invasiveness by targeting multiple signal transduction pathways. Cell Cycle 2012; 11:1977-87. [PMID: 22544323 DOI: 10.4161/cc.20309] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
RNA binding proteins belonging to the TIS11/TTP gene family regulate the stability of multiple targets. Their inactivation or deregulated expression has recently been related to cancer, and it has been suggested that they are capable of displaying tumor suppressor activities. Here we describe three new targets of ZFP36 (PIM-1, PIM-3 and XIAP) and show by different approaches that its ectopic expression is capable of impairing glioblastoma cell lines viability and invasiveness by interfering with different transduction pathways. Moreover, we provide evidence that compounds capable of inducing the expression of TIS11/TTP genes determine a comparable biological effect on the same cell contexts.
Collapse
Affiliation(s)
- Tommaso Selmi
- Dipartimento di Scienze Biomediche, Sezione di Chimica Biologica, Università di Modena e Reggio Emilia, Modena, Italy
| | | | | | | | | | | | | | | | | |
Collapse
|
24
|
Abstract
Posttranscriptional mechanisms are now widely acknowledged to play a central role in orchestrating gene-regulatory networks in hematopoietic cell growth, differentiation, and tumorigenesis. Although much attention has focused on microRNAs as regulators of mRNA stability/translation, recent data have highlighted the role of several diverse classes of AU-rich RNA-binding protein in the regulation of mRNA decay/stabilization. AU-rich elements are found in the 3'-untranslated region of many mRNAs that encode regulators of cell growth and survival, such as cytokines and onco/tumor-suppressor proteins. These are targeted by a burgeoning number of different RNA-binding proteins. Three distinct types of AU-rich RNA binding protein (ARE poly-U-binding degradation factor-1/AUF1, Hu antigen/HuR/HuA/ELAVL1, and the tristetraprolin/ZFP36 family of proteins) are essential for normal hematopoiesis. Together with 2 further AU-rich RNA-binding proteins, nucleolin and KHSRP/KSRP, the functions of these proteins are intimately associated with pathways that are dysregulated in various hematopoietic malignancies. Significantly, all of these AU-rich RNA-binding proteins function via an interconnected network that is integrated with microRNA functions. Studies of these diverse types of RNA binding protein are providing novel insight into gene-regulatory mechanisms in hematopoiesis in addition to offering new opportunities for developing mechanism-based targeted therapeutics in leukemia and lymphoma.
Collapse
|