1
|
Prusty AB, Hirmer A, Sierra-Delgado JA, Huber H, Guenther UP, Schlosser A, Dybkov O, Yildirim E, Urlaub H, Meyer KC, Jablonka S, Erhard F, Fischer U. RNA helicase IGHMBP2 regulates THO complex to ensure cellular mRNA homeostasis. Cell Rep 2024; 43:113802. [PMID: 38368610 DOI: 10.1016/j.celrep.2024.113802] [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: 08/03/2023] [Revised: 12/21/2023] [Accepted: 01/31/2024] [Indexed: 02/20/2024] Open
Abstract
RNA helicases constitute a large protein family implicated in cellular RNA homeostasis and disease development. Here, we show that the RNA helicase IGHMBP2, linked to the neuromuscular disorder spinal muscular atrophy with respiratory distress type 1 (SMARD1), associates with polysomes and impacts translation of mRNAs containing short, GC-rich, and structured 5' UTRs. The absence of IGHMBP2 causes ribosome stalling at the start codon of target mRNAs, leading to reduced translation efficiency. The main mRNA targets of IGHMBP2-mediated regulation encode for components of the THO complex (THOC), linking IGHMBP2 to mRNA production and nuclear export. Accordingly, failure of IGHMBP2 regulation of THOC causes perturbations of the transcriptome and its encoded proteome, and ablation of THOC subunits phenocopies these changes. Thus, IGHMBP2 is an upstream regulator of THOC. Of note, IGHMBP2-dependent regulation of THOC is also observed in astrocytes derived from patients with SMARD1 disease, suggesting that deregulated mRNA metabolism contributes to SMARD1 etiology and may enable alternative therapeutic avenues.
Collapse
Affiliation(s)
| | - Anja Hirmer
- Department of Biochemistry 1, Biocenter, University of Würzburg, 97074 Würzburg, Germany
| | | | - Hannes Huber
- Department of Biochemistry 1, Biocenter, University of Würzburg, 97074 Würzburg, Germany
| | | | - Andreas Schlosser
- Rudolf-Virchow-Center, Center for Integrative and Translational Bioimaging, University of Würzburg, 97080 Würzburg, Germany
| | - Olexandr Dybkov
- Bioanalytical Mass Spectrometry, Max Planck Institute for Multidisciplinary Sciences, 37077 Göttingen, Germany
| | - Ezgi Yildirim
- Institute of Clinical Neurobiology, University Hospital Würzburg, 97078 Würzburg, Germany
| | - Henning Urlaub
- Bioanalytical Mass Spectrometry, Max Planck Institute for Multidisciplinary Sciences, 37077 Göttingen, Germany; Department of Clinical Chemistry, University Medical Center Göttingen, 37075 Göttingen, Germany; Cluster of Excellence "Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells" (MBExC), University of Göttingen, Göttingen, Germany; Göttingen Center for Molecular Biosciences, University of Göttingen, Göttingen, Germany
| | - Kathrin C Meyer
- Nationwide Children's Hospital, Center for Gene Therapy, Columbus, OH 43205, USA; Department of Pediatrics, Ohio State University, Columbus, OH 43210, USA
| | - Sibylle Jablonka
- Institute of Clinical Neurobiology, University Hospital Würzburg, 97078 Würzburg, Germany
| | - Florian Erhard
- Institute for Virology and Immunobiology, University of Würzburg, 97078 Würzburg, Germany; Faculty for Informatics and Data Science, University of Regensburg, 93053 Regensburg, Germany.
| | - Utz Fischer
- Department of Biochemistry 1, Biocenter, University of Würzburg, 97074 Würzburg, Germany; Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), 97080 Würzburg, Germany.
| |
Collapse
|
2
|
Polenkowski M, Allister AB, Burbano de Lara S, Pierce A, Geary B, El Bounkari O, Wiehlmann L, Hoffmann A, Whetton AD, Tamura T, Tran DDH. THOC5 complexes with DDX5, DDX17, and CDK12 to regulate R loop structures and transcription elongation rate. iScience 2022; 26:105784. [PMID: 36590164 PMCID: PMC9800341 DOI: 10.1016/j.isci.2022.105784] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Revised: 11/10/2022] [Accepted: 12/07/2022] [Indexed: 12/14/2022] Open
Abstract
THOC5, a member of the THO complex, is essential for the 3'processing of some inducible genes, the export of a subset of mRNAs and stem cell survival. Here we show that THOC5 depletion results in altered 3'cleavage of >50% of mRNAs and changes in RNA polymerase II binding across genes. THOC5 is recruited close to high-density polymerase II sites, suggesting that THOC5 is involved in transcriptional elongation. Indeed, measurement of elongation rates in vivo demonstrated decreased rates in THOC5-depleted cells. Furthermore, THOC5 is preferentially recruited to its target genes in slow polymerase II cells compared with fast polymerase II cells. Importantly chromatin-associated THOC5 interacts with CDK12 (a modulator of transcription elongation) and RNA helicases DDX5, DDX17, and THOC6 only in slow polymerase II cells. The CDK12/THOC5 interaction promotes CDK12 recruitment to R-loops in a THOC6-dependent manner. These data demonstrate a novel function of THOC5 in transcription elongation.
Collapse
Affiliation(s)
- Mareike Polenkowski
- Department of Gastroenterology, Hepatology and Endocrinology, Hannover Medical School, Hannover D-30623, Germany,Institut für Zellbiochemie, Medizinische Hochschule Hannover, Hannover D-30623, Germany
| | - Aldrige Bernardus Allister
- Department of Gastroenterology, Hepatology and Endocrinology, Hannover Medical School, Hannover D-30623, Germany,Institut für Humangenetik, Medizinische Hochschule Hannover, Hannover D-30623, Germany
| | | | - Andrew Pierce
- Stem Cell and Leukemia Protoemics Laboratory, University of Manchester, Manchester M20 3LJ, UK
| | - Bethany Geary
- Stem Cell and Leukemia Protoemics Laboratory, University of Manchester, Manchester M20 3LJ, UK
| | - Omar El Bounkari
- Institute for Stroke and Dementia Research, Ludwig-Maximilians-Universität, 81377 Munich, Germany
| | - Lutz Wiehlmann
- Pädiatrische Pneumologie Hannover Medical School, Hannover D-30623, Germany
| | - Andrea Hoffmann
- Department of Orthopedic Surgery, Hannover Medical School, Hannover D-30623, Germany
| | - Anthony D. Whetton
- Stoller Biomarker Discovery Centre, University of Manchester, Manchester M13 9PL, UK
| | - Teruko Tamura
- Institut für Zellbiochemie, Medizinische Hochschule Hannover, Hannover D-30623, Germany
| | - Doan Duy Hai Tran
- Department of Gastroenterology, Hepatology and Endocrinology, Hannover Medical School, Hannover D-30623, Germany,Institut für Zellbiochemie, Medizinische Hochschule Hannover, Hannover D-30623, Germany,Corresponding author
| |
Collapse
|
3
|
Chou YJ, Lin CC, Hsu YC, Syu JL, Tseng LM, Chiu JH, Lo JF, Lin CH, Fu SL. Andrographolide suppresses the malignancy of triple-negative breast cancer by reducing THOC1-promoted cancer stem cell characteristics. Biochem Pharmacol 2022; 206:115327. [PMID: 36330949 DOI: 10.1016/j.bcp.2022.115327] [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: 08/02/2022] [Revised: 10/11/2022] [Accepted: 10/19/2022] [Indexed: 12/14/2022]
Abstract
Triple-negative breast cancers (TNBCs) are difficult to cure and currently lack of effective treatment strategies. Cancer stem cells (CSCs) are highly associated with the poor clinical outcome of TNBCs. Thoc1 is a core component of the THO complex (THOC) that regulates the elongation, processing and nuclear export of mRNA. The function of thoc1 in TNBC and whether Thoc1 serves as a drug target are poorly understood. In this study, we demonstrated that thoc1 expression is elevated in TNBC cell lines and human TNBC patient tissues. Knockdown of thoc1 decreased cancer stem cell populations, reduced mammosphere formation, impaired THOC function, and downregulated the expression of stemness-related proteins. Moreover, the thoc1-knockdown 4T1 cells showed less lung metastasis in an orthotopic breast cancer mouse model. Overexpression of Thoc1 promoted TNBC malignancy and the mRNA export of stemness-related genes. Furthermore, treatment of TNBC cells with the natural compound andrographolide reduced the expression of Thoc1 expression, impaired homeostasis of THOC, suppressed CSC properties, and delayed tumor growth in a 4T1-implanted orthotopic mouse model. Andrographolide also reduced the activity of NF-κB, an upstream transcriptional regulator of Thoc1. Notably, thoc1 overexpression attenuates andrographolide-suppressed cellular proliferation. Altogether, our results demonstrate that THOC1 promotes cancer stem cell characteristics of TNBC, and andrographolide is a potential natural compound for eliminating CSCs of TNBCs by downregulating the NF-κB-thoc1 axis.
Collapse
Affiliation(s)
- Yi-Ju Chou
- Program in Molecular Medicine, School of Life Sciences, National Yang Ming Chiao Tung University and Academia Sinica, Taipei 11221, Taiwan
| | - Ching-Cheng Lin
- Institute of Microbiology and Immunology, National Yang Ming Chiao Tung University, Taipei 11221, Taiwan
| | - Ya-Chi Hsu
- Institute of Traditional Medicine, National Yang Ming Chiao Tung University, Taipei 11221, Taiwan
| | - Jia-Ling Syu
- Institute of Traditional Medicine, National Yang Ming Chiao Tung University, Taipei 11221, Taiwan
| | - Ling-Ming Tseng
- Comprehensive Breast Health Center, Department of Surgery, Taipei Veterans General Hospital, Taipei, Taiwan
| | - Jen-Hwey Chiu
- Comprehensive Breast Health Center, Department of Surgery, Taipei Veterans General Hospital, Taipei, Taiwan
| | - Jeng-Fan Lo
- Institute of Oral Biology, National Yang Ming Chiao Tung University, Taipei 11221, Taiwan
| | - Chao-Hsiung Lin
- Department of Life Sciences and Institute of Genome Sciences, National Yang Ming Chiao Tung University, Taipei 11221, Taiwan
| | - Shu-Ling Fu
- Program in Molecular Medicine, School of Life Sciences, National Yang Ming Chiao Tung University and Academia Sinica, Taipei 11221, Taiwan; Institute of Traditional Medicine, National Yang Ming Chiao Tung University, Taipei 11221, Taiwan.
| |
Collapse
|
4
|
Kamp JA, Lemmens BBLG, Romeijn RJ, González-Prieto R, Olsen J, Vertegaal ACO, van Schendel R, Tijsterman M. THO complex deficiency impairs DNA double-strand break repair via the RNA surveillance kinase SMG-1. Nucleic Acids Res 2022; 50:6235-6250. [PMID: 35670662 PMCID: PMC9226523 DOI: 10.1093/nar/gkac472] [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: 02/13/2021] [Revised: 05/11/2022] [Accepted: 06/02/2022] [Indexed: 12/25/2022] Open
Abstract
The integrity and proper expression of genomes are safeguarded by DNA and RNA surveillance pathways. While many RNA surveillance factors have additional functions in the nucleus, little is known about the incidence and physiological impact of converging RNA and DNA signals. Here, using genetic screens and genome-wide analyses, we identified unforeseen SMG-1-dependent crosstalk between RNA surveillance and DNA repair in living animals. Defects in RNA processing, due to viable THO complex or PNN-1 mutations, induce a shift in DNA repair in dividing and non-dividing tissues. Loss of SMG-1, an ATM/ATR-like kinase central to RNA surveillance by nonsense-mediated decay (NMD), restores DNA repair and radio-resistance in THO-deficient animals. Mechanistically, we find SMG-1 and its downstream target SMG-2/UPF1, but not NMD per se, to suppress DNA repair by non-homologous end-joining in favour of single strand annealing. We postulate that moonlighting proteins create short-circuits in vivo, allowing aberrant RNA to redirect DNA repair.
Collapse
Affiliation(s)
| | | | - Ron J Romeijn
- Department of Human Genetics, Leiden University Medical Center, Einthovenweg 20, 2333 ZC Leiden, The Netherlands
| | - Román González-Prieto
- Department of Cell & Chemical Biology, Leiden University Medical Center, Einthovenweg 20, 2333 ZC, Leiden, The Netherlands
| | - Jesper V Olsen
- Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Blegdamsvej 3B, DK-2200 Copenhagen, Denmark
| | - Alfred C O Vertegaal
- Department of Cell & Chemical Biology, Leiden University Medical Center, Einthovenweg 20, 2333 ZC, Leiden, The Netherlands
| | - Robin van Schendel
- Department of Human Genetics, Leiden University Medical Center, Einthovenweg 20, 2333 ZC Leiden, The Netherlands
| | | |
Collapse
|
5
|
Mun SH, Oh B, Lee MJ, Bae S, Yang Y, Park-Min KH. THOC5 regulates human osteoclastogenesis. Eur J Cell Biol 2022; 101:151248. [PMID: 35688054 PMCID: PMC11058851 DOI: 10.1016/j.ejcb.2022.151248] [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: 12/30/2021] [Revised: 06/02/2022] [Accepted: 06/03/2022] [Indexed: 11/30/2022] Open
Abstract
Osteoclasts are bone resorbing cells that are responsible for physiological and pathological bone resorption. Macrophage colony stimulating factor (M-CSF) binds to the M-CSF receptor (c-FMS) and plays a key role in the differentiation and survival of macrophages and osteoclasts. THOC5, a member of the THO complex, has been shown to regulate hematopoiesis and M-CSF-induced macrophage differentiation. However, the role of THOC5 in osteoclasts remains unclear. Here, our study reveals a new role of THOC5 in osteoclast formation. We found that THOC5 shuttles between nucleus and cytoplasm in an M-CSF signaling dependent manner. THOC5 bound to FICD, a proteolytic cleavage product of c-FMS, and THOC5 facilitates the nuclear translocations of FICD. Decreased expression of THOC5 by siRNA-mediated knock down suppressed osteoclast differentiation, in part, by regulating RANK, a key receptor of osteoclasts. Mechanistically, knock down of THOC5 inhibited the expression of RANKL-induced FOS and NFATc1. Our findings highlight THOC5's function as a positive regulator of osteoclasts.
Collapse
Affiliation(s)
- Se Hwan Mun
- Arthritis and Tissue Degeneration Program, David Z. Rosensweig Genomics Research Center, Hospital for Special Surgery, New York, NY 10021, USA; Research Institute of Women's Health, Sookmyung Women's University, Seoul 04310, Republic of Korea
| | - Brian Oh
- Arthritis and Tissue Degeneration Program, David Z. Rosensweig Genomics Research Center, Hospital for Special Surgery, New York, NY 10021, USA
| | - Min Joon Lee
- Arthritis and Tissue Degeneration Program, David Z. Rosensweig Genomics Research Center, Hospital for Special Surgery, New York, NY 10021, USA
| | - Seyeon Bae
- Arthritis and Tissue Degeneration Program, David Z. Rosensweig Genomics Research Center, Hospital for Special Surgery, New York, NY 10021, USA; Department of Medicine, Weill Cornell Medical College, New York, NY 10065, USA
| | - Young Yang
- Research Institute of Women's Health, Sookmyung Women's University, Seoul 04310, Republic of Korea.
| | - Kyung-Hyun Park-Min
- Arthritis and Tissue Degeneration Program, David Z. Rosensweig Genomics Research Center, Hospital for Special Surgery, New York, NY 10021, USA; Department of Medicine, Weill Cornell Medical College, New York, NY 10065, USA; BCMB allied program, Weill Cornell Graduate School of Medical Sciences, New York, NY 10021, USA.
| |
Collapse
|
6
|
Polenkowski M, Burbano de Lara S, Allister AB, Nguyen TNQ, Tamura T, Tran DDH. Identification of Novel Micropeptides Derived from Hepatocellular Carcinoma-Specific Long Noncoding RNA. Int J Mol Sci 2021; 23:ijms23010058. [PMID: 35008483 PMCID: PMC8744898 DOI: 10.3390/ijms23010058] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Revised: 12/16/2021] [Accepted: 12/20/2021] [Indexed: 12/13/2022] Open
Abstract
Identification of cancer-specific target molecules and biomarkers may be useful in the development of novel treatment and immunotherapeutic strategies. We have recently demonstrated that the expression of long noncoding (lnc) RNAs can be cancer-type specific due to abnormal chromatin remodeling and alternative splicing. Furthermore, we identified and determined that the functional small protein C20orf204-189AA encoded by long intergenic noncoding RNA Linc00176 that is expressed predominantly in hepatocellular carcinoma (HCC), enhances transcription of ribosomal RNAs and supports growth of HCC. In this study we combined RNA-sequencing and polysome profiling to identify novel micropeptides that originate from HCC-specific lncRNAs. We identified nine lncRNAs that are expressed exclusively in HCC cells but not in the liver or other normal tissues. Here, DNase-sequencing data revealed that the altered chromatin structure plays a key role in the HCC-specific expression of lncRNAs. Three out of nine HCC-specific lncRNAs contain at least one open reading frame (ORF) longer than 50 amino acid (aa) and enriched in the polysome fraction, suggesting that they are translated. We generated a peptide specific antibody to characterize one candidate, NONHSAT013026.2/Linc013026. We show that Linc013026 encodes a 68 amino acid micropeptide that is mainly localized at the perinuclear region. Linc013026-68AA is expressed in a subset of HCC cells and plays a role in cell proliferation, suggesting that Linc013026-68AA may be used as a HCC-specific target molecule. Our finding also sheds light on the role of the previously ignored ’dark proteome’, that originates from noncoding regions in the maintenance of cancer.
Collapse
Affiliation(s)
- Mareike Polenkowski
- Institut fuer Zellbiochemie, OE4310, Medizinische Hochschule Hannover, Carl-Neuberg-Str. 1, 30623 Hannover, Germany; (M.P.); (S.B.d.L.); (A.B.A.); (T.N.Q.N.)
| | - Sebastian Burbano de Lara
- Institut fuer Zellbiochemie, OE4310, Medizinische Hochschule Hannover, Carl-Neuberg-Str. 1, 30623 Hannover, Germany; (M.P.); (S.B.d.L.); (A.B.A.); (T.N.Q.N.)
- Systems Biology of Signal Transduction B200, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120 Heidelberg, Germany
| | - Aldrige Bernardus Allister
- Institut fuer Zellbiochemie, OE4310, Medizinische Hochschule Hannover, Carl-Neuberg-Str. 1, 30623 Hannover, Germany; (M.P.); (S.B.d.L.); (A.B.A.); (T.N.Q.N.)
| | - Thi Nhu Quynh Nguyen
- Institut fuer Zellbiochemie, OE4310, Medizinische Hochschule Hannover, Carl-Neuberg-Str. 1, 30623 Hannover, Germany; (M.P.); (S.B.d.L.); (A.B.A.); (T.N.Q.N.)
| | - Teruko Tamura
- Institut fuer Zellbiochemie, OE4310, Medizinische Hochschule Hannover, Carl-Neuberg-Str. 1, 30623 Hannover, Germany; (M.P.); (S.B.d.L.); (A.B.A.); (T.N.Q.N.)
| | - Doan Duy Hai Tran
- Institut fuer Zellbiochemie, OE4310, Medizinische Hochschule Hannover, Carl-Neuberg-Str. 1, 30623 Hannover, Germany; (M.P.); (S.B.d.L.); (A.B.A.); (T.N.Q.N.)
- Correspondence: ; Tel.: +49-511-532-2857
| |
Collapse
|
7
|
Genetic risk model for in-stent restenosis of second-and third-generation drug-eluting stents. iScience 2021; 24:103082. [PMID: 34585120 PMCID: PMC8455661 DOI: 10.1016/j.isci.2021.103082] [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: 05/06/2021] [Revised: 07/20/2021] [Accepted: 08/31/2021] [Indexed: 12/02/2022] Open
Abstract
The new generation, i.e., second- and third-generation, drug-eluting stents (DESs) remain a risk of in-stent restenosis (ISR). We evaluated the power of a genetic risk score (GRS) model to identify high-risk populations for new generation DES ISR. We enrolled patients with coronary artery disease (CAD) treated with new generations DESs by a single-center cohort study in Taiwan and evaluated their genetic profile. After propensity score matching, there were 343 patients and 153 patients in the derivation and validation cohorts, respectively. Five selected single-nucleotide polymorphisms (SNPs), i.e., SNPs in CAMLG, GALNT2, C11orf84, THOC5, and SAMD11, were included to calculate the GRS for new generation DES ISR. In the derivation and the validation cohorts, patients with a GRS greater than or equal to 3 had significantly higher new generation DES ISR rates. We provide biological information for interventional cardiologists prior to percutaneous coronary intervention by specific five SNP-derived GRS. A validated GRS model identified high-risk population for new generation DES ISR This GRS includes 5 SNPs in exons: CAMLG, GALNT2, C11orf84, THOC5, and SAMD11 The patients with high GRSs (≥3) had higher rates of new generation DES ISR The GRS provides crucial information in shared decision-making process clinically
Collapse
|
8
|
Xie Y, Luo X, He H, Pan T, He Y. Identification of an individualized RNA binding protein-based prognostic signature for diffuse large B-cell lymphoma. Cancer Med 2021; 10:2703-2713. [PMID: 33749163 PMCID: PMC8026940 DOI: 10.1002/cam4.3859] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2021] [Revised: 02/19/2021] [Accepted: 03/08/2021] [Indexed: 12/19/2022] Open
Abstract
RNA binding proteins (RBPs) are increasingly appreciated as being essential for normal hematopoiesis and have a critical role in the progression of hematological malignancies. However, their functional consequences and clinical significance in diffuse large B‐cell lymphoma (DLBCL) remain unknown. Here, we conducted a systematic analysis to identify RBP‐related genes affecting DLBCL prognosis based on the Gene Expression Omnibus database. By univariate and multivariate Cox proportional hazards regression (CPHR) methods, six RBPs‐related genes (CMSS1, MAEL, THOC5, PSIP1, SNIP1, and ZCCHC7) were identified closely related to the overall survival (OS) of DLBCL patients. The RBPs signature could efficiently distinguished low‐risk from high‐risk patients and could serve as an independent and reliable factor for predicting OS. Moreover, Gene Set Enrichment Analysis revealed 17 significantly enriched pathways between high‐ versus low‐risk group, including the regulation of autophagy, chronic myeloid leukemia, NOTCH signaling pathway, and B cell receptor signaling pathway. Then we developed an RBP‐based nomogram combining other clinical risk factors. The receiver operating characteristic curve analysis demonstrated high prognostic predictive efficiency of this model with the area under the curve values were 0.820 and 0.780, respectively, in the primary set and entire set. In summary, our RBP‐based model could be a novel prognostic predictor and had the potential for developing treatment targets for DLBCL.
Collapse
Affiliation(s)
- Yongzhi Xie
- Department of Neurology, The Third Xiangya Hospital, Central South University, Changsha, China
| | - Ximei Luo
- School of Computer Science and Technology, Harbin Institute of Technology, Harbin, China
| | - Haiqing He
- Department of Urology, Second Xiangya Hospital, Central South University, Changsha, China
| | - Tao Pan
- Department of Lymphoma & Hematology, The Affiliated Tumor Hospital of Xiangya Medical School, Central South University, Changsha, China
| | - Yizi He
- Department of Lymphoma & Hematology, The Affiliated Tumor Hospital of Xiangya Medical School, Central South University, Changsha, China
| |
Collapse
|
9
|
Alqassim EY, Sharma S, Khan ANMNH, Emmons TR, Cortes Gomez E, Alahmari A, Singel KL, Mark J, Davidson BA, Robert McGray AJ, Liu Q, Lichty BD, Moysich KB, Wang J, Odunsi K, Segal BH, Baysal BE. RNA editing enzyme APOBEC3A promotes pro-inflammatory M1 macrophage polarization. Commun Biol 2021; 4:102. [PMID: 33483601 PMCID: PMC7822933 DOI: 10.1038/s42003-020-01620-x] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Accepted: 12/15/2020] [Indexed: 02/07/2023] Open
Abstract
Pro-inflammatory M1 macrophage polarization is associated with microbicidal and antitumor responses. We recently described APOBEC3A-mediated cytosine-to-uracil (C > U) RNA editing during M1 polarization. However, the functional significance of this editing is unknown. Here we find that APOBEC3A-mediated cellular RNA editing can also be induced by influenza or Maraba virus infections in normal human macrophages, and by interferons in tumor-associated macrophages. Gene knockdown and RNA_Seq analyses show that APOBEC3A mediates C>U RNA editing of 209 exonic/UTR sites in 203 genes during M1 polarization. The highest level of nonsynonymous RNA editing alters a highly-conserved amino acid in THOC5, which encodes a nuclear mRNA export protein implicated in M-CSF-driven macrophage differentiation. Knockdown of APOBEC3A reduces IL6, IL23A and IL12B gene expression, CD86 surface protein expression, and TNF-α, IL-1β and IL-6 cytokine secretion, and increases glycolysis. These results show a key role of APOBEC3A cytidine deaminase in transcriptomic and functional polarization of M1 macrophages.
Collapse
Affiliation(s)
- Emad Y Alqassim
- Department of Cancer Prevention and Control, Roswell Park Comprehensive Cancer Center, Buffalo, NY, 14203, USA
- Department of Pathology, Faculty of Medicine, Jazan University, Jazan, 45142, Saudi Arabia
| | - Shraddha Sharma
- Department of Pathology, Roswell Park Comprehensive Cancer Center, Buffalo, NY, 14203, USA
- Translate Bio, Lexington, MA, 02421, USA
| | - A N M Nazmul H Khan
- Department of Internal Medicine,, Roswell Park Comprehensive Cancer Center, Buffalo, NY, 14203, USA
| | - Tiffany R Emmons
- Department of Immunology,, Roswell Park Comprehensive Cancer Center, Buffalo, NY, 14203, USA
| | - Eduardo Cortes Gomez
- Department of Biostatistics/Bioinformatics, Roswell Park Comprehensive Cancer Center, Buffalo, NY, 14203, USA
| | - Abdulrahman Alahmari
- Department of Pharmacology and Therapeutics, Roswell Park Comprehensive Cancer Center, Buffalo, NY, 14203, USA
- Department of Medical Laboratory Sciences, Prince Sattam Bin Abdulaziz University, Al-Kharj, 16278, Saudi Arabia
| | - Kelly L Singel
- Department of Immunology,, Roswell Park Comprehensive Cancer Center, Buffalo, NY, 14203, USA
- Office of Evaluation, Performance, and Reporting, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Jaron Mark
- Department of Gynecologic Oncology,, Roswell Park Comprehensive Cancer Center, Buffalo, NY, 14203, USA
- The Start Center for Cancer Care, 4383 Medical Drive, San Antonio, TX, 78229, USA
| | - Bruce A Davidson
- Departments of Anesthesiology, Pathology and Anatomical Sciences, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, NY, 14203, USA
| | - A J Robert McGray
- Center for Immunotherapy, Roswell Park Comprehensive Cancer Center, Buffalo, NY, 14203, USA
| | - Qian Liu
- Department of Biostatistics/Bioinformatics, Roswell Park Comprehensive Cancer Center, Buffalo, NY, 14203, USA
| | - Brian D Lichty
- McMaster Immunology Research Centre, McMaster University, 1200 Main St W, Hamilton, ON, L8N 3Z5, Canada
| | - Kirsten B Moysich
- Department of Cancer Prevention and Control, Roswell Park Comprehensive Cancer Center, Buffalo, NY, 14203, USA
| | - Jianmin Wang
- Department of Biostatistics/Bioinformatics, Roswell Park Comprehensive Cancer Center, Buffalo, NY, 14203, USA
| | - Kunle Odunsi
- Department of Immunology,, Roswell Park Comprehensive Cancer Center, Buffalo, NY, 14203, USA
- Department of Gynecologic Oncology,, Roswell Park Comprehensive Cancer Center, Buffalo, NY, 14203, USA
- Center for Immunotherapy, Roswell Park Comprehensive Cancer Center, Buffalo, NY, 14203, USA
| | - Brahm H Segal
- Department of Internal Medicine,, Roswell Park Comprehensive Cancer Center, Buffalo, NY, 14203, USA.
- Department of Immunology,, Roswell Park Comprehensive Cancer Center, Buffalo, NY, 14203, USA.
- Departments of Medicine, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, NY, 14203, USA.
| | - Bora E Baysal
- Department of Pathology, Roswell Park Comprehensive Cancer Center, Buffalo, NY, 14203, USA.
| |
Collapse
|
10
|
Yu T, Fan K, Özata DM, Zhang G, Fu Y, Theurkauf WE, Zamore PD, Weng Z. Long first exons and epigenetic marks distinguish conserved pachytene piRNA clusters from other mammalian genes. Nat Commun 2021; 12:73. [PMID: 33397987 PMCID: PMC7782496 DOI: 10.1038/s41467-020-20345-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Accepted: 11/17/2020] [Indexed: 02/06/2023] Open
Abstract
In the male germ cells of placental mammals, 26-30-nt-long PIWI-interacting RNAs (piRNAs) emerge when spermatocytes enter the pachytene phase of meiosis. In mice, pachytene piRNAs derive from ~100 discrete autosomal loci that produce canonical RNA polymerase II transcripts. These piRNA clusters bear 5' caps and 3' poly(A) tails, and often contain introns that are removed before nuclear export and processing into piRNAs. What marks pachytene piRNA clusters to produce piRNAs, and what confines their expression to the germline? We report that an unusually long first exon (≥ 10 kb) or a long, unspliced transcript correlates with germline-specific transcription and piRNA production. Our integrative analysis of transcriptome, piRNA, and epigenome datasets across multiple species reveals that a long first exon is an evolutionarily conserved feature of pachytene piRNA clusters. Furthermore, a highly methylated promoter, often containing a low or intermediate level of CG dinucleotides, correlates with germline expression and somatic silencing of pachytene piRNA clusters. Pachytene piRNA precursor transcripts bind THOC1 and THOC2, THO complex subunits known to promote transcriptional elongation and mRNA nuclear export. Together, these features may explain why the major sources of pachytene piRNA clusters specifically generate these unique small RNAs in the male germline of placental mammals.
Collapse
Affiliation(s)
- Tianxiong Yu
- Department of Thoracic Surgery, Clinical Translational Research Center, Shanghai Pulmonary Hospital, The School of Life Sciences and Technology, Tongji University, 200092, Shanghai, China
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, MA, 01605, USA
| | - Kaili Fan
- Department of Thoracic Surgery, Clinical Translational Research Center, Shanghai Pulmonary Hospital, The School of Life Sciences and Technology, Tongji University, 200092, Shanghai, China
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, MA, 01605, USA
| | - Deniz M Özata
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, MA, 01605, USA
| | - Gen Zhang
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA, 01605, USA
| | - Yu Fu
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, MA, 01605, USA
- Bioinformatics Program, Boston University, 44 Cummington Mall, Boston, MA, 02215, USA
- Oncology Drug Discovery Unit, Takeda Pharmaceuticals, Cambridge, MA, 02139, USA
| | - William E Theurkauf
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA, 01605, USA.
| | - Phillip D Zamore
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, MA, 01605, USA.
| | - Zhiping Weng
- Department of Thoracic Surgery, Clinical Translational Research Center, Shanghai Pulmonary Hospital, The School of Life Sciences and Technology, Tongji University, 200092, Shanghai, China.
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, MA, 01605, USA.
| |
Collapse
|
11
|
Tang CC, Castro Andrade CD, O'Meara MJ, Yoon SH, Sato T, Brooks DJ, Bouxsein ML, Martins JDS, Wang J, Gray NS, Misof B, Roschger P, Blouin S, Klaushofer K, Velduis-Vlug A, Vegting Y, Rosen CJ, O'Connell D, Sundberg TB, Xavier RJ, Ung P, Schlessinger A, Kronenberg HM, Berdeaux R, Foretz M, Wein MN. Dual targeting of salt inducible kinases and CSF1R uncouples bone formation and bone resorption. eLife 2021; 10:67772. [PMID: 34160349 PMCID: PMC8238509 DOI: 10.7554/elife.67772] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Accepted: 06/16/2021] [Indexed: 12/17/2022] Open
Abstract
Bone formation and resorption are typically coupled, such that the efficacy of anabolic osteoporosis treatments may be limited by bone destruction. The multi-kinase inhibitor YKL-05-099 potently inhibits salt inducible kinases (SIKs) and may represent a promising new class of bone anabolic agents. Here, we report that YKL-05-099 increases bone formation in hypogonadal female mice without increasing bone resorption. Postnatal mice with inducible, global deletion of SIK2 and SIK3 show increased bone mass, increased bone formation, and, distinct from the effects of YKL-05-099, increased bone resorption. No cell-intrinsic role of SIKs in osteoclasts was noted. In addition to blocking SIKs, YKL-05-099 also binds and inhibits CSF1R, the receptor for the osteoclastogenic cytokine M-CSF. Modeling reveals that YKL-05-099 binds to SIK2 and CSF1R in a similar manner. Dual targeting of SIK2/3 and CSF1R induces bone formation without concomitantly increasing bone resorption and thereby may overcome limitations of most current anabolic osteoporosis therapies.
Collapse
Affiliation(s)
- Cheng-Chia Tang
- Endocrine Unit, Massachusetts General Hospital, Harvard Medical SchoolBostonUnited States
| | | | - Maureen J O'Meara
- Endocrine Unit, Massachusetts General Hospital, Harvard Medical SchoolBostonUnited States
| | - Sung-Hee Yoon
- Endocrine Unit, Massachusetts General Hospital, Harvard Medical SchoolBostonUnited States
| | - Tadatoshi Sato
- Endocrine Unit, Massachusetts General Hospital, Harvard Medical SchoolBostonUnited States
| | - Daniel J Brooks
- Endocrine Unit, Massachusetts General Hospital, Harvard Medical SchoolBostonUnited States,Center for Advanced Orthopaedic Studies, Department of Orthopedic Surgery, Beth Israel Deaconess Medical Center, Harvard Medical SchoolBostonUnited States
| | - Mary L Bouxsein
- Endocrine Unit, Massachusetts General Hospital, Harvard Medical SchoolBostonUnited States,Center for Advanced Orthopaedic Studies, Department of Orthopedic Surgery, Beth Israel Deaconess Medical Center, Harvard Medical SchoolBostonUnited States
| | | | - Jinhua Wang
- Dana Farber Cancer Institute, Harvard Medical SchoolBostonUnited States
| | - Nathanael S Gray
- Dana Farber Cancer Institute, Harvard Medical SchoolBostonUnited States
| | - Barbara Misof
- Ludwig Boltzmann Institute of Osteology at Hanusch Hospital of OEGK and AUVA Trauma Centre, Meidling, 1st Medical Department Hanusch HospitalViennaAustria
| | - Paul Roschger
- Ludwig Boltzmann Institute of Osteology at Hanusch Hospital of OEGK and AUVA Trauma Centre, Meidling, 1st Medical Department Hanusch HospitalViennaAustria
| | - Stephane Blouin
- Ludwig Boltzmann Institute of Osteology at Hanusch Hospital of OEGK and AUVA Trauma Centre, Meidling, 1st Medical Department Hanusch HospitalViennaAustria
| | - Klaus Klaushofer
- Ludwig Boltzmann Institute of Osteology at Hanusch Hospital of OEGK and AUVA Trauma Centre, Meidling, 1st Medical Department Hanusch HospitalViennaAustria
| | - Annegreet Velduis-Vlug
- Center for Bone Quality, Leiden University Medical CenterLeidenNetherlands,Center for Clinical and Translational Research, Maine Medical Center Research InstituteScarboroughCanada
| | - Yosta Vegting
- Department of Endocrinology and Metabolism, Academic Medical CenterAmsterdamNetherlands
| | - Clifford J Rosen
- Center for Clinical and Translational Research, Maine Medical Center Research InstituteScarboroughCanada
| | | | | | - Ramnik J Xavier
- Broad Institute of MIT and HarvardCambridgeUnited States,Center for Computational and Integrative Biology, Massachusetts General HospitalBostonUnited States
| | - Peter Ung
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount SinaiNew YorkUnited States
| | - Avner Schlessinger
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount SinaiNew YorkUnited States
| | - Henry M Kronenberg
- Endocrine Unit, Massachusetts General Hospital, Harvard Medical SchoolBostonUnited States
| | - Rebecca Berdeaux
- Department of Integrative Biology and Pharmacology, McGovern Medical School at The University of Texas Health Science Center at Houston (UTHealth)HoustonUnited States
| | - Marc Foretz
- Université de Paris, Institut Cochin, CNRSParisFrance
| | - Marc N Wein
- Endocrine Unit, Massachusetts General Hospital, Harvard Medical SchoolBostonUnited States,Broad Institute of MIT and HarvardCambridgeUnited States,Harvard Stem Cell InstituteCambridgeUnited States
| |
Collapse
|
12
|
Differential immune response modulation in early Leishmania amazonensis infection of BALB/c and C57BL/6 macrophages based on transcriptome profiles. Sci Rep 2019; 9:19841. [PMID: 31882833 PMCID: PMC6934472 DOI: 10.1038/s41598-019-56305-1] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2019] [Accepted: 12/10/2019] [Indexed: 12/26/2022] Open
Abstract
The fate of Leishmania infection can be strongly influenced by the host genetic background. In this work, we describe gene expression modulation of the immune system based on dual global transcriptome profiles of bone marrow-derived macrophages (BMDMs) from BALB/c and C57BL/6 mice infected with Leishmania amazonensis. A total of 12,641 host transcripts were identified according to the alignment to the Mus musculus genome. Differentially expressed genes (DEGs) profiling revealed a differential modulation of the basal genetic background between the two hosts independent of L. amazonensis infection. In addition, in response to early L. amazonensis infection, 10 genes were modulated in infected BALB/c vs. non-infected BALB/c macrophages; and 127 genes were modulated in infected C57BL/6 vs. non-infected C57BL/6 macrophages. These modulated genes appeared to be related to the main immune response processes, such as recognition, antigen presentation, costimulation and proliferation. The distinct gene expression was correlated with the susceptibility and resistance to infection of each host. Furthermore, upon comparing the DEGs in BMDMs vs. peritoneal macrophages, we observed no differences in the gene expression patterns of Jun, Fcgr1 and Il1b, suggesting a similar activation trends of transcription factor binding, recognition and phagocytosis, as well as the proinflammatory cytokine production in response to early L. amazonensis infection. Analysis of the DEG profile of the parasite revealed only one DEG among the 8,282 transcripts, indicating that parasite gene expression in early infection does not depend on the host genetic background.
Collapse
|
13
|
Myc/Max dependent intronic long antisense noncoding RNA, EVA1A-AS, suppresses the expression of Myc/Max dependent anti-proliferating gene EVA1A in a U2 dependent manner. Sci Rep 2019; 9:17319. [PMID: 31754186 PMCID: PMC6872820 DOI: 10.1038/s41598-019-53944-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2019] [Accepted: 10/22/2019] [Indexed: 01/26/2023] Open
Abstract
The Myc gene has been implicated in the pathogenesis of most types of human cancerous tumors. Myc/Max activates large numbers of pro-tumor genes; however it also induces anti-proliferation genes. When anti-proliferation genes are activated by Myc, cancer cells can only survive if they are downregulated. Hepatocellular carcinoma (HCC) specific intronic long noncoding antisense (lnc-AS) RNA, the EVA1A-AS gene, is located within the second intron (I2) of the EVA1A gene (EVA-1 homolog A) that encodes an anti-proliferation factor. Indeed, EVA1A, but not EVA1A-AS, is expressed in normal liver. Depletion of EVA1A-AS suppressed cell proliferation of HepG2 cells by upregulation of EVA1A. Overexpression of EVA1A caused cell death at the G2/M phase via microtubule catastrophe. Furthermore, suppressed EVA1A expression levels are negatively correlated with differentiation grade in 365 primary HCCs, while EVA1A-AS expression levels are positively correlated with patient survival. Notably, both EVA1A and EVA1A-AS were activated by the Myc/Max complex. Eva1A-AS is transcribed in the opposite direction near the 3′splice site of EVA1A I2. The second intron did not splice out in a U2 dependent manner and EVA1A mRNA is not exported. Thus, the Myc/Max dependent anti-proliferating gene, EVA1A, is controlled by Myc/Max dependent anti-sense noncoding RNA for HCC survival.
Collapse
|
14
|
Yuan X, Zhang T, Yao F, Liao Y, Liu F, Ren Z, Han L, Diao L, Li Y, Zhou B, He F, Wang L. THO Complex-Dependent Posttranscriptional Control Contributes to Vascular Smooth Muscle Cell Fate Decision. Circ Res 2019; 123:538-549. [PMID: 30026254 DOI: 10.1161/circresaha.118.313527] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
RATIONALE Modulation of vascular smooth muscle cell (VSMC) phenotype plays a fundamental role in vascular development and diseases. Although extensive studies uncovered the roles of transcriptional regulation in VSMC-specific gene expression, how posttranscriptional regulation contributes to VSMC fate decisions remains to be determined. OBJECTIVE To establish THO complex-dependent VSMC gene expression as a novel regulatory basis controlling VSMC phenotypes. METHODS AND RESULTS Immunohistochemical staining against THOC2 and THOC5, 2 components of the THO complex, revealed a dramatic reduction in their expression in human arteries undergoing carotid endarterectomy compared with normal internal mammary arteries. Silencing of THOC2 or THOC5 led to dedifferentiation of VSMCs in vitro, characterized by decreased VSMC marker gene expression and increased migration and proliferation. Furthermore, RNA high-throughput sequencing (Seq) revealed that THOC5 silencing closely resembled the gene expression changes induced on PDGF (platelet-derived growth factor)-BB/PDGF-DD treatments in cultured VSMCs. Mechanistically, THOC2 and THOC5 physically interacted with and functionally relied on each other to bind to specific motifs on VSMC marker gene mRNAs. Interestingly, mRNAs that lost THOC2 or THOC5 binding during VSMC dedifferentiation were enriched for genes important for the differentiated VSMC phenotype. Last, THOC5 overexpression in injured rat carotid arteries significantly repressed loss of VSMC marker gene expression and neointima formation. CONCLUSIONS Our data introduce dynamic binding of THO to VSMC marker gene mRNAs as a novel mechanism contributing to VSMC phenotypic switching and imply THOC5 as a potential intervention node for vascular diseases.
Collapse
Affiliation(s)
- Xinli Yuan
- From the State Key Laboratory of Cardiovascular Disease, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College (X.Y., F.Y., Y.L., F.L., Z.R., B.Z., L.W.).,Key Laboratory of Cardiac Regenerative Medicine, National Healthy Commission (X.Y., L.W.)
| | - Tao Zhang
- Fuwai Hospital, Beijing, China; Department of Vascular Surgery, Peking University People's Hospital, Beijing, China (T.Z.)
| | - Fang Yao
- From the State Key Laboratory of Cardiovascular Disease, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College (X.Y., F.Y., Y.L., F.L., Z.R., B.Z., L.W.)
| | - Yingnan Liao
- From the State Key Laboratory of Cardiovascular Disease, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College (X.Y., F.Y., Y.L., F.L., Z.R., B.Z., L.W.)
| | - Fei Liu
- From the State Key Laboratory of Cardiovascular Disease, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College (X.Y., F.Y., Y.L., F.L., Z.R., B.Z., L.W.)
| | - Zongna Ren
- From the State Key Laboratory of Cardiovascular Disease, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College (X.Y., F.Y., Y.L., F.L., Z.R., B.Z., L.W.)
| | - Leng Han
- Department of Biochemistry and Molecular Biology, University of Texas Health Science Center at Houston McGovern Medical School (L.H.)
| | - Lixia Diao
- Department of Bioinformatics and Computational Biology, University of Texas MD Anderson Cancer Center, Houston (L.D.)
| | - Yankui Li
- Department of Vascular Surgery, the Second Hospital of Tianjin Medical University, China (Y.L.)
| | - Bingying Zhou
- From the State Key Laboratory of Cardiovascular Disease, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College (X.Y., F.Y., Y.L., F.L., Z.R., B.Z., L.W.)
| | - Fan He
- Department of Nephrology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China (F.H.)
| | - Li Wang
- From the State Key Laboratory of Cardiovascular Disease, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College (X.Y., F.Y., Y.L., F.L., Z.R., B.Z., L.W.).,Key Laboratory of Cardiac Regenerative Medicine, National Healthy Commission (X.Y., L.W.)
| |
Collapse
|
15
|
Maeder CI, Kim JI, Liang X, Kaganovsky K, Shen A, Li Q, Li Z, Wang S, Xu XZS, Li JB, Xiang YK, Ding JB, Shen K. The THO Complex Coordinates Transcripts for Synapse Development and Dopamine Neuron Survival. Cell 2018; 174:1436-1449.e20. [PMID: 30146163 DOI: 10.1016/j.cell.2018.07.046] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2017] [Revised: 05/11/2018] [Accepted: 07/26/2018] [Indexed: 01/07/2023]
Abstract
Synaptic vesicle and active zone proteins are required for synaptogenesis. The molecular mechanisms for coordinated synthesis of these proteins are not understood. Using forward genetic screens, we identified the conserved THO nuclear export complex (THOC) as an important regulator of presynapse development in C. elegans dopaminergic neurons. In THOC mutants, synaptic messenger RNAs are retained in the nucleus, resulting in dramatic decrease of synaptic protein expression, near complete loss of synapses, and compromised dopamine function. CRE binding protein (CREB) interacts with THOC to mark synaptic transcripts for efficient nuclear export. Deletion of Thoc5, a THOC subunit, in mouse dopaminergic neurons causes severe defects in synapse maintenance and subsequent neuronal death in the substantia nigra compacta. These cellular defects lead to abrogated dopamine release, ataxia, and animal death. Together, our results argue that nuclear export mechanisms can select specific mRNAs and be a rate-limiting step for neuronal differentiation and survival.
Collapse
Affiliation(s)
- Celine I Maeder
- Department of Biology, Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305, USA
| | - Jae-Ick Kim
- Department of Neurosurgery, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Xing Liang
- Department of Biology, Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305, USA
| | - Konstantin Kaganovsky
- Department of Neurosurgery, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Ao Shen
- Department of Pharmacology, University of California, Davis, Davis, CA 95616, USA
| | - Qin Li
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Zhaoyu Li
- Life Sciences Institute and Department of Molecular and Integrative Physiology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Sui Wang
- Department of Opthalmology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - X Z Shawn Xu
- Life Sciences Institute and Department of Molecular and Integrative Physiology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Jin Billy Li
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Yang Kevin Xiang
- Department of Pharmacology, University of California, Davis, Davis, CA 95616, USA
| | - Jun B Ding
- Department of Neurosurgery, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA 94305, USA.
| | - Kang Shen
- Department of Biology, Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305, USA.
| |
Collapse
|
16
|
Niehus SE, Tran DDH, Mischak M, Koch A. Colony-stimulating factor-1 receptor provides a growth advantage in epithelial cancer cell line A431 in the presence of epidermal growth factor receptor inhibitor gefitinib. Cell Signal 2018; 51:191-198. [PMID: 30075184 DOI: 10.1016/j.cellsig.2018.07.014] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2018] [Revised: 07/25/2018] [Accepted: 07/30/2018] [Indexed: 11/25/2022]
Abstract
Although epidermal growth factor receptor (EGFR) has been identified as a potent "oncogenic driver" in various tumors of epithelial origin, EGFR-targeted therapies are often of limited success. One of the challenges of improving targeted therapies is to overcome bypassing signaling pathways. Analysis of RNA-seq data of 1006 cell lines from the Cancer Cell Line Encyclopedia (CCLE) revealed that more than 12% of carcinoma cell lines expressed markedly elevated mRNA levels of colony-stimulating factor (CSF)-1 receptor (CSF-1R). Since epithelial cells also express CSF-1, elevated levels of CSF-1R may participate in providing alternative growth and survival signals under targeted therapies. To address this question, we ectopically expressed CSF-1R in A431 cells that express EGFR at high levels, but no biologically relevant level of CSF-1R. In the presence of EGFR inhibitor gefitinib, CSF-1R provided a significant growth advantage in A431 cells. As expected, activation of both receptors, EGFR or CSF-1R, induced phosphorylation of extracellular signal-regulated kinase (Erk)1/2, Akt, protein kinase C (PKC) and signal transducer and activator of transcription (STAT)3. However, EGFR, but not CSF-1R, also induced STAT5 phosphorylation. Inhibitor of phosphatidylinositol 3-kinase (PI3K) (AZD8186), MAPK/ERK kinase (MEK)1/2 (U0126), PKCs (Bisindolylmaleimide I or Gö6976) or STAT3 (Stattic) partially reduced proliferation of CSF-1R expressing A431 cells in the presence of gefitinib. Moreover, multi-kinase inhibitor, cabozantinib, suppressed CSF-1R activation and drastically reduced cell growth when combined with gefitinib. These data suggest that CSF-1R has the potential to reduce sensitivity to gefitinib and may be involved in resistance development.
Collapse
Affiliation(s)
- Svenja Ellen Niehus
- Institut fuer Zellbiochemie, OE4310, Medizinische Hochschule Hannover, Carl-Neuberg-Str. 1, D-30625 Hannover, Germany.
| | - Doan Duy Hai Tran
- Institut fuer Zellbiochemie, OE4310, Medizinische Hochschule Hannover, Carl-Neuberg-Str. 1, D-30625 Hannover, Germany.
| | - Michaela Mischak
- Institut fuer Zellbiochemie, OE4310, Medizinische Hochschule Hannover, Carl-Neuberg-Str. 1, D-30625 Hannover, Germany
| | - Alexandra Koch
- Institut fuer Zellbiochemie, OE4310, Medizinische Hochschule Hannover, Carl-Neuberg-Str. 1, D-30625 Hannover, Germany.
| |
Collapse
|
17
|
Abstract
TRanscription and EXport (TREX) is a conserved multisubunit complex essential for embryogenesis, organogenesis and cellular differentiation throughout life. By linking transcription, mRNA processing and export together, it exerts a physiologically vital role in the gene expression pathway. In addition, this complex prevents DNA damage and regulates the cell cycle by ensuring optimal gene expression. As the extent of TREX activity in viral infections, amyotrophic lateral sclerosis and cancer emerges, the need for a greater understanding of TREX function becomes evident. A complete elucidation of the composition, function and interactions of the complex will provide the framework for understanding the molecular basis for a variety of diseases. This review details the known composition of TREX, how it is regulated and its cellular functions with an emphasis on mammalian systems.
Collapse
|
18
|
Tran DDH, Saran S, Koch A, Tamura T. mRNA export protein THOC5 as a tool for identification of target genes for cancer therapy. Cancer Lett 2016; 373:222-6. [DOI: 10.1016/j.canlet.2016.01.045] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2015] [Revised: 01/26/2016] [Accepted: 01/26/2016] [Indexed: 11/25/2022]
|
19
|
Tran DDH, Koch A, Saran S, Armbrecht M, Ewald F, Koch M, Wahlicht T, Wirth D, Braun A, Nashan B, Gaestel M, Tamura T. Extracellular-signal regulated kinase (Erk1/2), mitogen-activated protein kinase-activated protein kinase 2 (MK2) and tristetraprolin (TTP) comprehensively regulate injury-induced immediate early gene (IEG) response in in vitro liver organ culture. Cell Signal 2016; 28:438-447. [PMID: 26876787 DOI: 10.1016/j.cellsig.2016.02.007] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2015] [Revised: 02/04/2016] [Accepted: 02/09/2016] [Indexed: 12/18/2022]
Abstract
Differentiated hepatocytes are long-lived and normally do not undergo cell division, however they have the unique capacity to autonomously decide their replication fate after liver injury. In this context, the key players of liver regeneration immediately after injury have not been adequately studied. Using an in vitro liver culture system, we show that after liver injury, p38 mitogen-activated protein kinase (p38MAPK), mitogen-activated protein kinase-activated protein kinase 2 (MK2) and extracellular-signal regulated kinase (Erk)1/2 were activated within 15 min and continued to be phosphorylated for more than 2h. Both p38MAPK and Erk1/2 were activated at the edge of the cut as well as on the liver surface where the mesothelial cell sheet expresses several cytokines. Notably, in human liver Erk1/2 was also activated under the mesothelial cell sheet shortly after liver resections. Furthermore, in in vitro liver slice culture immediate early genes (IEGs) were upregulated within 1-2 h and the S phase marker proliferation-cell-nuclear-antigen (PCNA) appeared 24 h after injury. Although Erk1/2 was activated after injury, in MK2 depleted liver a set of IEGs, such as Dusp1, Cox2, or c-Myc and proliferation marker gene Ki67 were not induced. In addition, in immortalized hepatocyte cells, THLE-2, the same subset of genes was upregulated upon stimulation with lipopolysaccharide (LPS), but not in the presence of MK2 inhibitor. The protein level of tristetraprolin (TTP), a substrate for MK2 that plays a role in mRNA degradation, was increased in the presence of MK2 inhibitor. In this context, the depletion of TTP gene rescued Dusp1, Cox2, or c-Myc upregulation in the presence of MK2 inhibitor. These data imply that MK2 pathway is positively involved in Erk1/2 induced IEG response after liver injury. These data also suggest that in vitro liver culture may be a useful tool for measuring the proliferation potential of hepatocytes in individual liver.
Collapse
Affiliation(s)
- Doan Duy Hai Tran
- Institut fuer Biochemie, OE4310, Medizinische Hochschule Hannover, Carl-Neuberg-Str. 1, D-30623 Hannover, Germany
| | - Alexandra Koch
- Institut fuer Biochemie, OE4310, Medizinische Hochschule Hannover, Carl-Neuberg-Str. 1, D-30623 Hannover, Germany
| | - Shashank Saran
- Institut fuer Biochemie, OE4310, Medizinische Hochschule Hannover, Carl-Neuberg-Str. 1, D-30623 Hannover, Germany
| | - Marcel Armbrecht
- Institut fuer Biochemie, OE4310, Medizinische Hochschule Hannover, Carl-Neuberg-Str. 1, D-30623 Hannover, Germany
| | - Florian Ewald
- Department of Hepatobiliary and Transplant Surgery, University Medical Center Eppendorf, Martinistrasse 52, 20256, Hamburg, Germany
| | - Martina Koch
- Department of Hepatobiliary and Transplant Surgery, University Medical Center Eppendorf, Martinistrasse 52, 20256, Hamburg, Germany
| | - Tom Wahlicht
- Model Systems for Infection and Immunity (MSYS), Helmholtz Centre for Infection Research, Inhoffenstraße 7, 38124 Braunschweig, Germany
| | - Dagmar Wirth
- Model Systems for Infection and Immunity (MSYS), Helmholtz Centre for Infection Research, Inhoffenstraße 7, 38124 Braunschweig, Germany
| | - Armin Braun
- Fraunhofer Institut für Toxikologie und Experimentelle Medizin Atemwegspharmakologie, Nikolai-Fuchs-Str.1, D-30625 Hannover, Germany
| | - Björn Nashan
- Department of Hepatobiliary and Transplant Surgery, University Medical Center Eppendorf, Martinistrasse 52, 20256, Hamburg, Germany
| | - Matthias Gaestel
- Institut fuer Biochemie, OE4310, Medizinische Hochschule Hannover, Carl-Neuberg-Str. 1, D-30623 Hannover, Germany
| | - Teruko Tamura
- Institut fuer Biochemie, OE4310, Medizinische Hochschule Hannover, Carl-Neuberg-Str. 1, D-30623 Hannover, Germany.
| |
Collapse
|
20
|
Depletion of three combined THOC5 mRNA export protein target genes synergistically induces human hepatocellular carcinoma cell death. Oncogene 2015; 35:3872-9. [PMID: 26549021 DOI: 10.1038/onc.2015.433] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2015] [Revised: 10/01/2015] [Accepted: 10/11/2015] [Indexed: 12/15/2022]
Abstract
Hepatocellular carcinoma (HCC) is a frequent form of cancer with a poor prognosis and with limited possibilities of medical intervention. It has been shown that over 100 putative driver genes are associated with multiple recurrently altered pathways in HCC, suggesting that multiple pathways will need to be inhibited for any therapeutic method. mRNA processing is regulated by a complex RNA-protein network that is essential for the maintenance of homeostasis. THOC5, a member of mRNA export complex, has a role in less than 1% of mRNA processing, and is required for cell growth and differentiation, but not for cell survival in normal fibroblasts, hepatocytes and macrophages. In this report, we show that 50% depletion of THOC5 in human HCC cell lines Huh7 and HepG2 induced apoptosis. Transcriptome analysis using THOC5-depleted cells revealed that 396 genes, such as transmembrane BAX inhibitor motif containing 4 (TMBIM4), transmembrane emp24-like trafficking protein 10 (Tmed10) and D-tyrosyl-tRNA deacylase 2 (Dtd2) genes were downregulated in both cell lines. The depletion of one of these THOC5 target genes in Huh7 or HepG2 did not significantly induce cell death, suggesting that these may be fine tuners for HCC cell survival. However, the depletion of a combination of these genes synergistically increased the number of TUNEL (terminal deoxynucleotidyl transferase dUTP nick end labeling)-positive HCC. It must be noted that the depletion of these genes did not induce cell death in the hepatocyte cell line, THLE-2 cells. THOC5 expression was enhanced in 78% of cytological differentiation grading G2 and G3 tumor in primary HCC. Furthermore, the expression of a putative glycoprotein, Tmed10, is correlated to THOC5 expression level in primary HCCs, suggesting that this protein may be a novel biomarker for HCC. These data imply that the suppression of the multiple THOC5 target genes may represent a novel strategy for HCC therapy.
Collapse
|
21
|
Koch A, Saran S, Tran DDH, Klebba-Färber S, Thiesler H, Sewald K, Schindler S, Braun A, Klopfleisch R, Tamura T. Murine precision-cut liver slices (PCLS): a new tool for studying tumor microenvironments and cell signaling ex vivo. Cell Commun Signal 2014; 12:73. [PMID: 25376987 PMCID: PMC4226874 DOI: 10.1186/s12964-014-0073-7] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2014] [Accepted: 10/23/2014] [Indexed: 11/29/2022] Open
Abstract
Background One of the most insidious characteristics of cancer is its spread to and ability to compromise distant organs via the complex process of metastasis. Communication between cancer cells and organ-resident cells via cytokines/chemokines and direct cell-cell contacts are key steps for survival, proliferation and invasion of metastasized cancer cells in organs. Precision-cut liver slices (PCLS) are considered to closely reflect the in vivo situation and are potentially useful for studying the interaction of cancer cells with liver-resident cells as well as being a potentially useful tool for screening anti-cancer reagents. Application of the PCLS technique in the field of cancer research however, has not yet been well developed. Results We established the mouse PCLS system using perfluorodecalin (PFD) as an artificial oxygen carrier. Using this system we show that the adherence of green fluorescent protein (GFP) labeled MDA-MB-231 (highly invasive) cells to liver tissue in the PCLS was 5-fold greater than that of SK-BR-3 (less invasive) cells. In addition, we generated PCLS from THOC5, a member of transcription/export complex (TREX), knockout (KO) mice. The PCLS still expressed Gapdh or Albumin mRNAs at normal levels, while several chemokine/growth factor or metalloprotease genes, such as Cxcl12, Pdgfa, Tgfb, Wnt11, and Mmp1a genes were downregulated more than 2-fold. Interestingly, adhesion of cancer cells to THOC5 KO liver slices was far less (greater than 80% reduction) than to wild-type liver slices. Conclusion Mouse PCLS cultures in the presence of PFD may serve as a useful tool for screening local adherence and invasiveness of individual cancer cells, since single cells can be observed. This method may also prove useful for identification of genes in liver-resident cells that support cancer invasion by using PCLS from transgenic liver.
Collapse
Affiliation(s)
- Alexandra Koch
- Institut fuer Biochemie, OE4310, Medizinische Hochschule Hannover, Carl-Neuberg-Str. 1, D-30623, Hannover, Germany.
| | - Shashank Saran
- Institut fuer Biochemie, OE4310, Medizinische Hochschule Hannover, Carl-Neuberg-Str. 1, D-30623, Hannover, Germany.
| | - Doan Duy Hai Tran
- Institut fuer Biochemie, OE4310, Medizinische Hochschule Hannover, Carl-Neuberg-Str. 1, D-30623, Hannover, Germany.
| | - Sabine Klebba-Färber
- Institut fuer Biochemie, OE4310, Medizinische Hochschule Hannover, Carl-Neuberg-Str. 1, D-30623, Hannover, Germany.
| | - Hauke Thiesler
- Institut fuer Biochemie, OE4310, Medizinische Hochschule Hannover, Carl-Neuberg-Str. 1, D-30623, Hannover, Germany.
| | - Katherina Sewald
- Fraunhofer Institut für Toxikologie und Experimentelle Medizin Atemwegspharmakologie, Nikolai-Fuchs-Str.1, D-30625, Hannover, Germany.
| | - Susann Schindler
- Fraunhofer Institut für Toxikologie und Experimentelle Medizin Atemwegspharmakologie, Nikolai-Fuchs-Str.1, D-30625, Hannover, Germany.
| | - Armin Braun
- Fraunhofer Institut für Toxikologie und Experimentelle Medizin Atemwegspharmakologie, Nikolai-Fuchs-Str.1, D-30625, Hannover, Germany.
| | - Robert Klopfleisch
- Institute of Veterinary Pathology, Freie Universitaet Berlin, Robert-von-Ostertag- Str. 15, D-14163, Berlin, Germany.
| | - Teruko Tamura
- Institut fuer Biochemie, OE4310, Medizinische Hochschule Hannover, Carl-Neuberg-Str. 1, D-30623, Hannover, Germany.
| |
Collapse
|
22
|
Tran DDH, Saran S, Williamson AJK, Pierce A, Dittrich-Breiholz O, Wiehlmann L, Koch A, Whetton AD, Tamura T. THOC5 controls 3'end-processing of immediate early genes via interaction with polyadenylation specific factor 100 (CPSF100). Nucleic Acids Res 2014; 42:12249-60. [PMID: 25274738 PMCID: PMC4231767 DOI: 10.1093/nar/gku911] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Transcription of immediate early genes (IEGs) in response to extrinsic and intrinsic signals is tightly regulated at multiple stages. It is known that untranslated regions of the RNA can play a role in these processes. Here we show that THOC5, a member of the TREX (transcription/export) complex, plays a role in expression of only a subset of constitutively active genes, however transcriptome analysis reveals that more than 90% of IEG were not induced by serum in THOC5 depleted cells. Furthermore, THOC5 depletion does not influence the expression of the most rapidly induced IEGs, e.g. Fos and Jun. One group of THOC5 target genes, including Id1, Id3 and Wnt11 transcripts, were not released from chromatin in THOC5 depleted cells. Genes in another group, including Myc and Smad7 transcripts, were released with shortening of 3′UTR by alternative cleavage, and were spliced but export was impaired in THOC5 depleted cells. By interactome analysis using THOC5 as bait, we show that upon stimulation with serum THOC5 forms a complex with polyadenylation-specific factor 100 (CPSF100). THOC5 is required for recruitment of CPSF100 to 3′UTR of THOC5 target genes. These data suggest the presence of a novel mechanism for the control of IEG response by THOC5 via 3′end-processing.
Collapse
Affiliation(s)
- Doan Duy Hai Tran
- Institut fuer Biochemie, OE4310, Medizinische Hochschule Hannover, Carl-Neuberg-Strasse 1, D-30623 Hannover, Germany
| | - Shashank Saran
- Institut fuer Biochemie, OE4310, Medizinische Hochschule Hannover, Carl-Neuberg-Strasse 1, D-30623 Hannover, Germany
| | - Andrew J K Williamson
- Stem Cell and Leukaemia Proteomics Laboratory, The University of Manchester, Manchester Academic Health Science Centre, 27 Palatine Road, Withington Manchester, M20 3LJ UK
| | - Andrew Pierce
- Stem Cell and Leukaemia Proteomics Laboratory, The University of Manchester, Manchester Academic Health Science Centre, 27 Palatine Road, Withington Manchester, M20 3LJ UK
| | - Oliver Dittrich-Breiholz
- Institut fuer Biochemie, OE4310, Medizinische Hochschule Hannover, Carl-Neuberg-Strasse 1, D-30623 Hannover, Germany
| | - Lutz Wiehlmann
- Pädiatrische Pneumologie OE6710 Medizinische Hochschule Hannover, Carl-Neuberg-Strasse 1, D-30623 Hannover, Germany
| | - Alexandra Koch
- Institut fuer Biochemie, OE4310, Medizinische Hochschule Hannover, Carl-Neuberg-Strasse 1, D-30623 Hannover, Germany
| | - Anthony D Whetton
- Stem Cell and Leukaemia Proteomics Laboratory, The University of Manchester, Manchester Academic Health Science Centre, 27 Palatine Road, Withington Manchester, M20 3LJ UK
| | - Teruko Tamura
- Institut fuer Biochemie, OE4310, Medizinische Hochschule Hannover, Carl-Neuberg-Strasse 1, D-30623 Hannover, Germany
| |
Collapse
|
23
|
Pagani IS, Spinelli O, Mattarucchi E, Pirrone C, Pigni D, Amelotti E, Lilliu S, Boroni C, Intermesoli T, Giussani U, Caimi L, Bolda F, Baffelli R, Candi E, Pasquali F, Lo Curto F, Lanfranchi A, Porta F, Rambaldi A, Porta G. Genomic quantitative real-time PCR proves residual disease positivity in more than 30% samples with negative mRNA-based qRT-PCR in Chronic Myeloid Leukemia. Oncoscience 2014; 1:510-21. [PMID: 25594053 PMCID: PMC4278316 DOI: 10.18632/oncoscience.65] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2014] [Accepted: 07/23/2014] [Indexed: 12/20/2022] Open
Abstract
Imatinib mesylate (IM) is the first line therapy against Chronic Myeloid Leukemia, effectively prolonging overall survival. Because discontinuation of treatment is associated with relapse, IM is required indefinitely to maintain operational cure. To assess minimal residual disease, cytogenetic analysis is insensitive in a high background of normal lymphocytes. The qRT-PCR provides highly sensitive detection of BCR-ABL1 transcripts, but mRNA levels are not directly related to the number of leukemic cells, and undetectable results are difficult to interpret. We developed a sensitive approach to detect the number of leukemic cells by a genomic DNA (gDNA) Q-PCR assay based on the break-point sequence, with a formula to calculate the number of Ph-positive cells. We monitored 8 CML patients treated with IM for more than 8 years. We tested each samples by patient specific gDNA Q-PCR in parallel by the conventional techniques. In all samples positive for chimeric transcripts we showed corresponding chimeric gDNA by Q-PCR, and in 32.8% (42/128) of samples with undetectable levels of mRNA we detected the persistence of leukemic cells. The gDNA Q-PCR assay could be a new diagnostic tool used in parallel to conventional techniques to support the clinician's decision to vary or to STOP IM therapy.
Collapse
Affiliation(s)
- Ilaria S Pagani
- Department of Experimental and Clinical Medicine, Insubria University, Varese, Italy ; Department of Experimental Medicine and Surgery, Tor Vergata University, Rome, Italy
| | - Orietta Spinelli
- Hematology laboratory, USC Hematology, Papa Giovanni XXIII Hospital, Bergamo, Italy
| | - Elia Mattarucchi
- Department of Experimental and Clinical Medicine, Insubria University, Varese, Italy
| | - Cristina Pirrone
- Department of Experimental and Clinical Medicine, Insubria University, Varese, Italy
| | - Diana Pigni
- Department of Experimental and Clinical Medicine, Insubria University, Varese, Italy
| | - Elisabetta Amelotti
- Department of Experimental and Clinical Medicine, Insubria University, Varese, Italy
| | - Silvia Lilliu
- Hematology laboratory, USC Hematology, Papa Giovanni XXIII Hospital, Bergamo, Italy
| | - Chiara Boroni
- Hematology laboratory, USC Hematology, Papa Giovanni XXIII Hospital, Bergamo, Italy
| | - Tamara Intermesoli
- Hematology laboratory, USC Hematology, Papa Giovanni XXIII Hospital, Bergamo, Italy
| | - Ursula Giussani
- Laboratory of Medical Genetics, Papa Giovanni XXIII Hospital, Bergamo, Italy
| | - Luigi Caimi
- Department of Molecular and Translational Medicine, University of Brescia, Brescia, Italy
| | - Federica Bolda
- Laboratory of chemical-clinical analysis, Section of Hematology and blood coagulation, Stem Cells laboratory, Spedali Civili of Brescia, Brescia, Italy
| | - Renata Baffelli
- Laboratory of chemical-clinical analysis, Section of Hematology and blood coagulation, Stem Cells laboratory, Spedali Civili of Brescia, Brescia, Italy
| | - Eleonora Candi
- Department of Experimental Medicine and Surgery, Tor Vergata University, Rome, Italy
| | - Francesco Pasquali
- Department of Experimental and Clinical Medicine, Insubria University, Varese, Italy
| | - Francesco Lo Curto
- Department of Experimental and Clinical Medicine, Insubria University, Varese, Italy
| | - Arnalda Lanfranchi
- Laboratory of chemical-clinical analysis, Section of Hematology and blood coagulation, Stem Cells laboratory, Spedali Civili of Brescia, Brescia, Italy
| | - Fulvio Porta
- Laboratory of chemical-clinical analysis, Section of Hematology and blood coagulation, Stem Cells laboratory, Spedali Civili of Brescia, Brescia, Italy
| | - Alessandro Rambaldi
- Hematology laboratory, USC Hematology, Papa Giovanni XXIII Hospital, Bergamo, Italy
| | - Giovanni Porta
- Department of Experimental and Clinical Medicine, Insubria University, Varese, Italy
| |
Collapse
|
24
|
Pitzonka L, Ullas S, Chinnam M, Povinelli BJ, Fisher DT, Golding M, Appenheimer MM, Nemeth MJ, Evans S, Goodrich DW. The Thoc1 encoded ribonucleoprotein is required for myeloid progenitor cell homeostasis in the adult mouse. PLoS One 2014; 9:e97628. [PMID: 24830368 PMCID: PMC4022742 DOI: 10.1371/journal.pone.0097628] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2014] [Accepted: 04/22/2014] [Indexed: 12/15/2022] Open
Abstract
Co-transcriptionally assembled ribonucleoprotein (RNP) complexes are critical for RNA processing and nuclear export. RNPs have been hypothesized to contribute to the regulation of coordinated gene expression, and defects in RNP biogenesis contribute to genome instability and disease. Despite the large number of RNPs and the importance of the molecular processes they mediate, the requirements for individual RNP complexes in mammalian development and tissue homeostasis are not well characterized. THO is an evolutionarily conserved, nuclear RNP complex that physically links nascent transcripts with the nuclear export apparatus. THO is essential for early mouse embryonic development, limiting characterization of the requirements for THO in adult tissues. To address this shortcoming, a mouse strain has been generated allowing inducible deletion of the Thoc1 gene which encodes an essential protein subunit of THO. Bone marrow reconstitution was used to generate mice in which Thoc1 deletion could be induced specifically in the hematopoietic system. We find that granulocyte macrophage progenitors have a cell autonomous requirement for Thoc1 to maintain cell growth and viability. Lymphoid lineages are not detectably affected by Thoc1 loss under the homeostatic conditions tested. Myeloid lineages may be more sensitive to Thoc1 loss due to their relatively high rate of proliferation and turnover.
Collapse
Affiliation(s)
- Laura Pitzonka
- Department of Pharmacology & Therapeutics, Roswell Park Cancer Institute, Buffalo, New York, United States of America
| | - Sumana Ullas
- Department of Pharmacology & Therapeutics, Roswell Park Cancer Institute, Buffalo, New York, United States of America
| | - Meenalakshmi Chinnam
- Department of Pharmacology & Therapeutics, Roswell Park Cancer Institute, Buffalo, New York, United States of America
| | - Benjamin J. Povinelli
- Department of Immunology, Roswell Park Cancer Institute, Buffalo, New York, United States of America
| | - Daniel T. Fisher
- Department of Immunology, Roswell Park Cancer Institute, Buffalo, New York, United States of America
| | - Michelle Golding
- Department of Immunology, Roswell Park Cancer Institute, Buffalo, New York, United States of America
| | - Michelle M. Appenheimer
- Department of Immunology, Roswell Park Cancer Institute, Buffalo, New York, United States of America
| | - Michael J. Nemeth
- Department of Immunology, Roswell Park Cancer Institute, Buffalo, New York, United States of America
| | - Sharon Evans
- Department of Immunology, Roswell Park Cancer Institute, Buffalo, New York, United States of America
| | - David W. Goodrich
- Department of Pharmacology & Therapeutics, Roswell Park Cancer Institute, Buffalo, New York, United States of America
- * E-mail:
| |
Collapse
|
25
|
Nuclear trafficking in health and disease. Curr Opin Cell Biol 2014; 28:28-35. [PMID: 24530809 DOI: 10.1016/j.ceb.2014.01.007] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2013] [Revised: 01/12/2014] [Accepted: 01/19/2014] [Indexed: 01/07/2023]
Abstract
In eukaryotic cells, the cytoplasm and the nucleus are separated by a double-membraned nuclear envelope (NE). Thus, transport of molecules between the nucleus and the cytoplasm occurs via gateways termed the nuclear pore complexes (NPCs), which are the largest intracellular channels in nature. While small molecules can passively translocate through the NPC, large molecules are actively imported into the nucleus by interacting with receptors that bind nuclear pore complex proteins (Nups). Regulatory factors then function in assembly and disassembly of transport complexes. Signaling pathways, cell cycle, pathogens, and other physiopathological conditions regulate various constituents of the nuclear transport machinery. Here, we will discuss several findings related to modulation of nuclear transport during physiological and pathological conditions, including tumorigenesis, viral infection, and congenital syndrome. We will also explore chemical biological approaches that are being used as probes to reveal new mechanisms that regulate nucleocytoplasmic trafficking and that are serving as starting points for drug development.
Collapse
|
26
|
Tran DDH, Koch A, Tamura T. THOC5, a member of the mRNA export complex: a novel link between mRNA export machinery and signal transduction pathways in cell proliferation and differentiation. Cell Commun Signal 2014; 12:3. [PMID: 24410813 PMCID: PMC3899923 DOI: 10.1186/1478-811x-12-3] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2013] [Accepted: 01/06/2014] [Indexed: 11/10/2022] Open
Abstract
Cell growth, differentiation, and commitment to a restricted lineage are guided by a timely expressed set of growth factor/cytokine receptors and their down-stream transcription factor genes. Transcriptional control mechanisms of gene expression during differentiation have been mainly studied by focusing on the cis- and trans-elements in promoters however, the role of mRNA export machinery during differentiation has not been adequately examined. THO (Suppressors of the transcriptional defects of hpr1 delta by overexpression) complex 5 (THOC5) is a member of THO complex which is a subcomplex of the transcription/export complex (TREX). THOC5 is evolutionarily conserved in higher eukaryotes, however the exact roles of THOC5 in transcription and mRNA export are still unclear. In this review, we focus on recently uncovered aspects of the role of THOC5 in signal transduction induced by extracellular stimuli. THOC5 is phosphorylated by several protein kinases at multiple residues upon extracellular stimuli. These include stimulation with growth factors/cytokines/chemokines, or DNA damage reagents. Furthermore, THOC5 is a substrate for several oncogenic tyrosine kinases, suggesting that THOC5 may be involved in cancer development. Recent THOC5 knockout mouse data reveal that THOC5 is an essential element in the maintenance of stem cells and growth factor/cytokine-mediated differentiation/proliferation. Furthermore, depletion of THOC5 influences less than 1% of total mRNA export in the steady state, however it influences more than 90% of growth factor/cytokine induced genes. THOC5, thereby contributes to the 3' processing and/or export of immediate-early genes induced by extracellular stimuli. These studies bring new insight into the link between the mRNA export complex and immediate-early gene response. The data from these studies also suggest that THOC5 may be a useful tool for studying stem cell biology, for modifying the differentiation processes and for cancer therapy.
Collapse
Affiliation(s)
| | | | - Teruko Tamura
- Institut fuer Biochemie, OE4310, Medizinische Hochschule Hannover, Carl-Neuberg-Str, 1, D-30623, Hannover, Germany.
| |
Collapse
|
27
|
Saran S, Tran DDH, Klebba-Färber S, Moran-Losada P, Wiehlmann L, Koch A, Chopra H, Pabst O, Hoffmann A, Klopfleisch R, Tamura T. THOC5, a member of the mRNA export complex, contributes to processing of a subset of wingless/integrated (Wnt) target mRNAs and integrity of the gut epithelial barrier. BMC Cell Biol 2013; 14:51. [PMID: 24267292 PMCID: PMC4222586 DOI: 10.1186/1471-2121-14-51] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2013] [Accepted: 11/19/2013] [Indexed: 11/26/2022] Open
Abstract
Background THO (Suppressors of the transcriptional defects of hpr1 delta by overexpression) complex 5 (THOC5), an mRNA export protein, is involved in the expression of only 1% of all genes. Using an interferon inducible knockout mouse system, we have previously shown that THOC5 is an essential element in the maintenance of hematopoietic stem cells and cytokine-mediated hematopoiesis in adult mice. Here we interrogate THOC5 function in cell differentiation beyond the hematopoietic system and study pathological changes caused by THOC5 deficiency. Results To examine whether THOC5 plays a role in general differentiation processes, we generated tamoxifen inducible THOC5 knockout mice. We show here that the depletion of THOC5 impaired not only hematopoietic differentiation, but also differentiation and self renewal of the gut epithelium. Depletion of the THOC5 gene did not cause pathological alterations in liver or kidney. We further show that THOC5 is indispensable for processing of mRNAs induced by Wnt (wingless/integrated) signaling which play key roles in epithelial cell differentiation/proliferation. A subset of Wnt target mRNAs, SRY-box containing gene 9 (Sox9), and achaete-scute complex homolog 2 (Ascl2), but not Fibronectin 1 (Fn1), were down-regulated in THOC5 knockout intestinal cells. The down-regulated Wnt target mRNAs were able to bind to THOC5. Furthermore, pathological alterations in the gastrointestinal tract induced translocation of intestinal bacteria and caused sepsis in mice. The bacteria translocation may cause Toll-like receptor activation. We identified one of the Toll-like receptor inducible genes, prostaglandin-endoperoxidase synthase 2 (Ptgs2 or COX2) transcript as THOC5 target mRNA. Conclusion THOC5 is indispensable for processing of only a subset of mRNAs, but plays a key role in processing of mRNAs inducible by Wnt signals. Furthermore, THOC5 is dispensable for general mRNA export in terminally differentiated organs, indicating that multiple mRNA export pathways exist. These data imply that THOC5 may be a useful tool for studying intestinal stem cells, for modifying the differentiation processes and for cancer therapy.
Collapse
Affiliation(s)
- Shashank Saran
- Institut fuer Biochemie, Medizinische Hochschule Hannover, OE4310 Carl-Neuberg-Str, 1, Hannover D-30623, Germany.
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|