1
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Kramárek M, Souček P, Réblová K, Grodecká L, Freiberger T. Splicing analysis of STAT3 tandem donor suggests non-canonical binding registers for U1 and U6 snRNAs. Nucleic Acids Res 2024; 52:5959-5974. [PMID: 38426935 PMCID: PMC11162779 DOI: 10.1093/nar/gkae147] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Revised: 02/02/2024] [Accepted: 02/16/2024] [Indexed: 03/02/2024] Open
Abstract
Tandem donor splice sites (5'ss) are unique regions with at least two GU dinucleotides serving as splicing cleavage sites. The Δ3 tandem 5'ss are a specific subclass of 5'ss separated by 3 nucleotides which can affect protein function by inserting/deleting a single amino acid. One 5'ss is typically preferred, yet factors governing particular 5'ss choice are not fully understood. A highly conserved exon 21 of the STAT3 gene was chosen as a model to study Δ3 tandem 5'ss splicing mechanisms. Based on multiple lines of experimental evidence, endogenous U1 snRNA most likely binds only to the upstream 5'ss. However, the downstream 5'ss is used preferentially, and the splice site choice is not dependent on the exact U1 snRNA binding position. Downstream 5'ss usage was sensitive to exact nucleotide composition and dependent on the presence of downstream regulatory region. The downstream 5'ss usage could be best explained by two novel interactions with endogenous U6 snRNA. U6 snRNA enables the downstream 5'ss usage in STAT3 exon 21 by two mechanisms: (i) binding in a novel non-canonical register and (ii) establishing extended Watson-Crick base pairing with the downstream regulatory region. This study suggests that U6:5'ss interaction is more flexible than previously thought.
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Affiliation(s)
- Michal Kramárek
- Centre for Cardiovascular Surgery and Transplantation, 656 91 Brno, Czech Republic
- Faculty of Medicine, Masaryk University, 625 00 Brno, Czech Republic
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, 62500 Brno, Czech Republic
| | - Přemysl Souček
- Centre for Cardiovascular Surgery and Transplantation, 656 91 Brno, Czech Republic
- Faculty of Medicine, Masaryk University, 625 00 Brno, Czech Republic
| | - Kamila Réblová
- Centre of Molecular Biology and Genetics, University Hospital and Masaryk University, Brno, Czech Republic
| | - Lucie Kajan Grodecká
- Centre for Cardiovascular Surgery and Transplantation, 656 91 Brno, Czech Republic
| | - Tomáš Freiberger
- Centre for Cardiovascular Surgery and Transplantation, 656 91 Brno, Czech Republic
- Faculty of Medicine, Masaryk University, 625 00 Brno, Czech Republic
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2
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Adesoye T, Tripathy D, Hunt KK, Keyomarsi K. Exploring Novel Frontiers: Leveraging STAT3 Signaling for Advanced Cancer Therapeutics. Cancers (Basel) 2024; 16:492. [PMID: 38339245 PMCID: PMC10854592 DOI: 10.3390/cancers16030492] [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: 10/18/2023] [Revised: 12/21/2023] [Accepted: 12/25/2023] [Indexed: 02/12/2024] Open
Abstract
Signal Transducer and Activator of Transcription 3 (STAT3) plays a significant role in diverse physiologic processes, including cell proliferation, differentiation, angiogenesis, and survival. STAT3 activation via phosphorylation of tyrosine and serine residues is a complex and tightly regulated process initiated by upstream signaling pathways with ligand binding to receptor and non-receptor-linked kinases. Through downstream deregulation of target genes, aberrations in STAT3 activation are implicated in tumorigenesis, metastasis, and recurrence in multiple cancers. While there have been extensive efforts to develop direct and indirect STAT3 inhibitors using novel drugs as a therapeutic strategy, direct clinical application remains in evolution. In this review, we outline the mechanisms of STAT3 activation, the resulting downstream effects in physiologic and malignant settings, and therapeutic strategies for targeting STAT3. We also summarize the pre-clinical and clinical evidence of novel drug therapies targeting STAT3 and discuss the challenges of establishing their therapeutic efficacy in the current clinical landscape.
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Affiliation(s)
- Taiwo Adesoye
- Department of Breast Surgical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA;
| | - Debasish Tripathy
- Department of Breast Medical Oncology, Division of Cancer Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA;
| | - Kelly K. Hunt
- Department of Breast Surgical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA;
| | - Khandan Keyomarsi
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
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3
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Berta D, Girma M, Melku M, Adane T, Birke B, Yalew A. Role of RNA Splicing Mutations in Diffuse Large B Cell Lymphoma. Int J Gen Med 2023; 16:2469-2480. [PMID: 37342407 PMCID: PMC10278864 DOI: 10.2147/ijgm.s414106] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2023] [Accepted: 06/08/2023] [Indexed: 06/22/2023] Open
Abstract
Ribonucleic acid splicing is a crucial process to create a mature mRNA molecule by removing introns and ligating exons. This is a highly regulated process, but any alteration in splicing factors, splicing sites, or auxiliary components affects the final products of the gene. In diffuse large B-cell lymphoma, splicing mutations such as mutant splice sites, aberrant alternative splicing, exon skipping, and intron retention are detected. The alteration affects tumor suppression, DNA repair, cell cycle, cell differentiation, cell proliferation, and apoptosis. As a result, malignant transformation, cancer progression, and metastasis occurred in B cells at the germinal center. B-cell lymphoma 7 protein family member A (BCL7A), cluster of differentiation 79B (CD79B), myeloid differentiation primary response gene 88 (MYD88), tumor protein P53 (TP53), signal transducer and activator of transcription (STAT), serum- and glucose-regulated kinase 1 (SGK1), Pou class 2 associating factor 1 (POU2AF1), and neurogenic locus notch homolog protein 1 (NOTCH) are the most common genes affected by splicing mutations in diffuse large B cell lymphoma.
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Affiliation(s)
- Dereje Berta
- Department of Hematology and Immunohematology, School of Biomedical and Laboratory Sciences, College of Medicine and Health Sciences, University of Gondar, Gondar, Ethiopia
| | - Mekonnen Girma
- Department of Quality Assurance and Laboratory Management, School of Biomedical and Laboratory Sciences, College of Medicine and Health Sciences, University of Gondar, Gondar, Ethiopia
| | - Mulugeta Melku
- Department of Hematology and Immunohematology, School of Biomedical and Laboratory Sciences, College of Medicine and Health Sciences, University of Gondar, Gondar, Ethiopia
- College of Medicine and Public Health, Flinders University, Adelaide, SA, Australia
| | - Tiruneh Adane
- Department of Hematology and Immunohematology, School of Biomedical and Laboratory Sciences, College of Medicine and Health Sciences, University of Gondar, Gondar, Ethiopia
| | - Bisrat Birke
- Department of Hematology and Immunohematology, School of Biomedical and Laboratory Sciences, College of Medicine and Health Sciences, University of Gondar, Gondar, Ethiopia
| | - Aregawi Yalew
- Department of Hematology and Immunohematology, School of Biomedical and Laboratory Sciences, College of Medicine and Health Sciences, University of Gondar, Gondar, Ethiopia
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4
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Choi S, Cho N, Kim KK. The implications of alternative pre-mRNA splicing in cell signal transduction. Exp Mol Med 2023; 55:755-766. [PMID: 37009804 PMCID: PMC10167241 DOI: 10.1038/s12276-023-00981-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2022] [Revised: 01/05/2023] [Accepted: 01/27/2023] [Indexed: 04/04/2023] Open
Abstract
Cells produce multiple mRNAs through alternative splicing, which ensures proteome diversity. Because most human genes undergo alternative splicing, key components of signal transduction pathways are no exception. Cells regulate various signal transduction pathways, including those associated with cell proliferation, development, differentiation, migration, and apoptosis. Since proteins produced through alternative splicing can exhibit diverse biological functions, splicing regulatory mechanisms affect all signal transduction pathways. Studies have demonstrated that proteins generated by the selective combination of exons encoding important domains can enhance or attenuate signal transduction and can stably and precisely regulate various signal transduction pathways. However, aberrant splicing regulation via genetic mutation or abnormal expression of splicing factors negatively affects signal transduction pathways and is associated with the onset and progression of various diseases, including cancer. In this review, we describe the effects of alternative splicing regulation on major signal transduction pathways and highlight the significance of alternative splicing.
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Affiliation(s)
- Sunkyung Choi
- Department of Biochemistry, College of Natural Sciences, Chungnam National University, Daejeon, 34134, Republic of Korea
| | - Namjoon Cho
- Department of Biochemistry, College of Natural Sciences, Chungnam National University, Daejeon, 34134, Republic of Korea
| | - Kee K Kim
- Department of Biochemistry, College of Natural Sciences, Chungnam National University, Daejeon, 34134, Republic of Korea.
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5
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Diallo M, Herrera F. The role of understudied post-translational modifications for the behavior and function of Signal Transducer and Activator of Transcription 3. FEBS J 2021; 289:6235-6255. [PMID: 34235865 DOI: 10.1111/febs.16116] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Revised: 06/16/2021] [Accepted: 07/07/2021] [Indexed: 12/19/2022]
Abstract
The Signal Transducer and Activator of Transcription (STAT) family of transcription factors is involved in inflammation, immunity, development, cancer, and response to injury, among other biological phenomena. Canonical STAT signaling is often represented as a 3-step pathway involving the sequential activation of a membrane receptor, an intermediate kinase, and a STAT transcription factor. The rate-limiting phosphorylation at a highly conserved C-terminal tyrosine residue determines the nuclear translocation and transcriptional activity of STATs. This apparent simplicity is actually misleading and can hardly explain the pleiotropic nature of STATs, the existence of various noncanonical STAT pathways, or the key role of the N-terminal domain in STAT functions. More than 80 post-translational modifications (PTMs) have been identified for STAT3, but their functions remain barely understood. Here, we provide a brief but comprehensive overview of these underexplored PTMs and their role on STAT3 canonical and noncanonical functions. A less tyrosine-centric point of view may be required to advance our understanding of STAT signaling.
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Affiliation(s)
- Mickael Diallo
- Faculdade de Ciências da Universidade de Lisboa, Cell Structure and Dynamics Laboratory, BioISI - Instituto de Biosistemas e Ciências integrativas, Lisbon, Portugal.,MOSTMICRO Research Unit, Instituto de Tecnologia Química e Biológica (ITQB-NOVA), Universidade Nova de Lisboa, Oeiras, Portugal
| | - Federico Herrera
- Faculdade de Ciências da Universidade de Lisboa, Cell Structure and Dynamics Laboratory, BioISI - Instituto de Biosistemas e Ciências integrativas, Lisbon, Portugal.,MOSTMICRO Research Unit, Instituto de Tecnologia Química e Biológica (ITQB-NOVA), Universidade Nova de Lisboa, Oeiras, Portugal
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6
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STAT3 Activation and Oncogenesis in Lymphoma. Cancers (Basel) 2019; 12:cancers12010019. [PMID: 31861597 PMCID: PMC7016717 DOI: 10.3390/cancers12010019] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2019] [Revised: 12/13/2019] [Accepted: 12/17/2019] [Indexed: 12/26/2022] Open
Abstract
Signal transducer and activator of transcription 3 (STAT3) is an important and the most studied transcription factor in the Janus kinase (JAK)/STAT signaling pathway. STAT3 mediates the expression of various genes that play a critical role in many cellular and biological processes, such as cell proliferation, survival, differentiation, migration, angiogenesis, and inflammation. STAT3 and associated JAKs are activated and tightly regulated by a variety of cytokines and growth factors and their receptors in normal immune responses. However, abnormal expression of STAT3 leads to its constitutive activation, which promotes malignant transformation and tumor progression through oncogenic gene expression in numerous human cancers. Human lymphoma is a heterogeneous malignancy of T and B lymphocytes. Constitutive signaling by STAT3 is an oncogenic driver in several types of B-cell lymphoma and most of T-cell lymphomas. Aberrant STAT3 activation can also induce inappropriate expression of genes involved in tumor immune evasion such as PD-L1. In this review, we focus on the oncogenic role of STAT3 in human lymphoma and highlight potential therapeutic intervention by targeting JAK/STAT3 signaling.
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7
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Zhang R, Lin P, Yang X, He RQ, Wu HY, Dang YW, Gu YY, Peng ZG, Feng ZB, Chen G. Survival associated alternative splicing events in diffuse large B-cell lymphoma. Am J Transl Res 2018; 10:2636-2647. [PMID: 30210700 PMCID: PMC6129525] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2018] [Accepted: 07/25/2018] [Indexed: 06/08/2023]
Abstract
Growing evidence has revealed that the initiation of various malignancies is closely associated with alternative splicing (AS) events in certain key oncogenes. However, in diffuse large B-cell lymphoma (DLBCL), there is still a great deal to learn about AS variants. In this study, 33,724 AS variant profiles were obtained from 16,278 genes in 48 DLBCL cases. A total of 10 AS variants were identified as overall survival (OS)- related events via multivariate Cox regression analysis. Notably, alternative donor (AD) sites in AS events in the low-risk group showed a significantly better outcome in DLBCL patients than in the high-risk group (P=0.0002). The area under the curve (AUC) of the receiver-operator characteristic curve (ROC) for ADs in DLBCL was 0.746. Furthermore, 66 related splicing factors were obtained to investigate their potential correlations with AS events. Factors SF1, HNRNPC, HNRNPD, and HNRNPH3 were significantly involved in different OS-related AS variants. Collectively, we constructed valuable prognostic predictors for DLBCL patients and mapped novel splicing networks for further investigation of the underlying mechanisms related to AS variants in DLBCLs.
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Affiliation(s)
- Rui Zhang
- Department of Pathology, First Affiliated Hospital of Guangxi Medical University6 Shuangyong Road, Nanning 530021, Guangxi Zhuang Autonomous Region, China
| | - Peng Lin
- Department of Ultrasonography, First Affiliated Hospital of Guangxi Medical University6 Shuangyong Road, Nanning 530021, Guangxi Zhuang Autonomous Region, China
| | - Xia Yang
- Department of Pathology, First Affiliated Hospital of Guangxi Medical University6 Shuangyong Road, Nanning 530021, Guangxi Zhuang Autonomous Region, China
| | - Rong-Quan He
- Department of Medical Oncology, First Affiliated Hospital of Guangxi Medical University6 Shuangyong Road, Nanning 530021, Guangxi Zhuang Autonomous Region, China
| | - Hua-Yu Wu
- Department of Cell Biology and Genetics, Guangxi Medical University22 Shuangyong Road, Nanning 530021, Guangxi Zhuang Autonomous Region, China
| | - Yi-Wu Dang
- Department of Pathology, First Affiliated Hospital of Guangxi Medical University6 Shuangyong Road, Nanning 530021, Guangxi Zhuang Autonomous Region, China
| | - Yong-Yao Gu
- Department of Pathology, First Affiliated Hospital of Guangxi Medical University6 Shuangyong Road, Nanning 530021, Guangxi Zhuang Autonomous Region, China
| | - Zhi-Gang Peng
- Department of Medical Oncology, First Affiliated Hospital of Guangxi Medical University6 Shuangyong Road, Nanning 530021, Guangxi Zhuang Autonomous Region, China
| | - Zhen-Bo Feng
- Department of Pathology, First Affiliated Hospital of Guangxi Medical University6 Shuangyong Road, Nanning 530021, Guangxi Zhuang Autonomous Region, China
| | - Gang Chen
- Department of Pathology, First Affiliated Hospital of Guangxi Medical University6 Shuangyong Road, Nanning 530021, Guangxi Zhuang Autonomous Region, China
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8
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Turton KB, Wilkerson EM, Hebert AS, Fogerty FJ, Schira HM, Botros FE, Coon JJ, Mosher DF. Expression of novel "LOCGEF" isoforms of ARHGEF18 in eosinophils. J Leukoc Biol 2018; 104:135-145. [PMID: 29601110 DOI: 10.1002/jlb.2ma1017-418rr] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2017] [Revised: 02/27/2018] [Accepted: 02/28/2018] [Indexed: 12/26/2022] Open
Abstract
Genomic, transcriptomic and proteomic databases indicate that the N-terminal 322 residues encoded by the presumptive LOC100996504 gene, which is adjacent to the ARHGEF18 guanine nucleotide exchange factor gene on chromosome 19, constitute the N-terminal portion of a 1361-residue isoform of ARHGEF18, dubbed LOCGEF-X3. LOCGEF-X3 arises from the use of a leukocyte-specific alternative transcriptional start site and splicing that bypasses the initial noncoding exon of the canonical 1015-residue ARHGEF18 isoform, p114. Eosinophil LOCGEF-X3 was amplified and cloned, recombinant LOCGEF-X3 was expressed, and anti-ARHGEF18 antibody was found to recognize a band in immunoblots of eosinophil lysates that co-migrates with recombinant LOCGEF-X3. PCR of eosinophils revealed minor amounts of transcripts for X4 and X5 isoforms of LOCGEF that arise from differential splicing and differ from the X3 isoform at their extreme N-termini. No p114 transcript or protein band was detected in eosinophils. Immunostaining with anti-ARHGEF18 antibody revealed relocalization of LOCGEF and RHOA from the periphery of round unstimulated eosinophils to the 2 poles of eosinophils polarized by treatment with IL5, CCL11, or IL33 in suspension. Canonical p114 ARHGEF18 has been implicated in maintenance of epithelial cell polarity. We suggest that the "LOC" portion of LOCGEF, which is unlike any other protein domain, has unique functions in control of polarity in activated eosinophils and other leukocytes.
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Affiliation(s)
- Keren B Turton
- Department of Biomolecular Chemistry, University of Wisconsin, Madison, Wisconsin, USA
| | - Emily M Wilkerson
- Department of Chemistry, University of Wisconsin, Madison, Wisconsin, USA
| | - Alex S Hebert
- Department of Chemistry, University of Wisconsin, Madison, Wisconsin, USA
| | - Frances J Fogerty
- Department of Biomolecular Chemistry, University of Wisconsin, Madison, Wisconsin, USA.,Department of Medicine, University of Wisconsin, Madison, Wisconsin, USA
| | - Hazel M Schira
- Department of Biomolecular Chemistry, University of Wisconsin, Madison, Wisconsin, USA
| | - Fady E Botros
- Department of Biomolecular Chemistry, University of Wisconsin, Madison, Wisconsin, USA
| | - Joshua J Coon
- Department of Biomolecular Chemistry, University of Wisconsin, Madison, Wisconsin, USA.,Department of Chemistry, University of Wisconsin, Madison, Wisconsin, USA
| | - Deane F Mosher
- Department of Biomolecular Chemistry, University of Wisconsin, Madison, Wisconsin, USA.,Department of Medicine, University of Wisconsin, Madison, Wisconsin, USA
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9
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Mosher DF, Wilkerson EM, Turton KB, Hebert AS, Coon JJ. Proteomics of Eosinophil Activation. Front Med (Lausanne) 2017; 4:159. [PMID: 29034237 PMCID: PMC5626809 DOI: 10.3389/fmed.2017.00159] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2017] [Accepted: 09/13/2017] [Indexed: 12/30/2022] Open
Abstract
We recently identified and quantified >7,000 proteins in non-activated human peripheral blood eosinophils using liquid chromatography coupled to tandem mass spectrometry (LC-MS/MS) and described phosphoproteomic changes that accompany acute activation of eosinophils by interleukin-5 (IL5) (1). These data comprise a treasure trove of information about eosinophils. We illustrate the power of label-free LC-MS/MS quantification by considering four examples: complexity of eosinophil STATs, contribution of immunoproteasome subunits to eosinophil proteasomes, complement of integrin subunits, and contribution of platelet proteins originating from platelet-eosinophil complexes to the overall proteome. We describe how isobaric labeling enables robust sample-to-sample comparisons and relate the 220 phosphosites that changed significantly upon treatment with IL5 to previous studies of eosinophil activation. Finally, we review previous attempts to leverage the power of mass spectrometry to discern differences between eosinophils of healthy subjects and those with eosinophil-associated conditions and point out features of label-free quantification and isobaric labeling that are important in planning future mass spectrometric studies.
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Affiliation(s)
- Deane F Mosher
- Department of Biomolecular Chemistry, University of Wisconsin, Madison, WI, United States.,Department of Medicine, University of Wisconsin, Madison, WI, United States
| | - Emily M Wilkerson
- Department of Chemistry, University of Wisconsin, Madison, WI, United States
| | - Keren B Turton
- Department of Biomolecular Chemistry, University of Wisconsin, Madison, WI, United States
| | - Alexander S Hebert
- Department of Chemistry, University of Wisconsin, Madison, WI, United States
| | - Joshua J Coon
- Department of Biomolecular Chemistry, University of Wisconsin, Madison, WI, United States.,Department of Chemistry, University of Wisconsin, Madison, WI, United States
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10
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Turton KB, Esnault S, Delain LP, Mosher DF. Merging Absolute and Relative Quantitative PCR Data to Quantify STAT3 Splice Variant Transcripts. J Vis Exp 2016. [PMID: 27768061 PMCID: PMC5092172 DOI: 10.3791/54473] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Human signal transducer and activator of transcription 3 (STAT3) is one of many genes containing a tandem splicing site. Alternative donor splice sites 3 nucleotides apart result in either the inclusion (S) or exclusion (ΔS) of a single residue, Serine-701. Further downstream, splicing at a pair of alternative acceptor splice sites result in transcripts encoding either the 55 terminal residues of the transactivation domain (α) or a truncated transactivation domain with 7 unique residues (β). As outlined in this manuscript, measuring the proportions of STAT3's four spliced transcripts (Sα, Sβ, ΔSα and ΔSβ) was possible using absolute qPCR (quantitative polymerase chain reaction). The protocol therefore distinguishes and measures highly similar splice variants. Absolute qPCR makes use of calibrator plasmids and thus specificity of detection is not compromised for the sake of efficiency. The protocol necessitates primer validation and optimization of cycling parameters. A combination of absolute qPCR and efficiency-dependent relative qPCR of total STAT3 transcripts allowed a description of the fluctuations of STAT3 splice variants' levels in eosinophils treated with cytokines. The protocol also provided evidence of a co-splicing interdependence between the two STAT3 splicing events. The strategy based on a combination of the two qPCR techniques should be readily adaptable to investigation of co-splicing at other tandem splicing sites.
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Affiliation(s)
- Keren B Turton
- Department of Biomolecular Chemistry, University of Wisconsin-Madison;
| | | | | | - Deane F Mosher
- Department of Biomolecular Chemistry, University of Wisconsin-Madison; Department of Medicine, University of Wisconsin-Madison
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11
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Wilkerson EM, Johansson MW, Hebert AS, Westphall MS, Mathur SK, Jarjour NN, Schwantes EA, Mosher DF, Coon JJ. The Peripheral Blood Eosinophil Proteome. J Proteome Res 2016; 15:1524-33. [PMID: 27005946 DOI: 10.1021/acs.jproteome.6b00006] [Citation(s) in RCA: 60] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
A system-wide understanding of biological processes requires a comprehensive knowledge of the proteins in the biological system. The eosinophil is a type of granulocytic leukocyte specified early in hematopoietic differentiation that participates in barrier defense, innate immunity, and allergic disease. The proteome of the eosinophil is largely unannotated with under 500 proteins identified. We now report a map of the nonstimulated peripheral blood eosinophil proteome assembled using two-dimensional liquid chromatography coupled with high-resolution mass spectrometry. Our analysis yielded 100,892 unique peptides mapping to 7,086 protein groups representing 6,813 genes as well as 4,802 site-specific phosphorylation events. We account for the contribution of platelets that routinely contaminate purified eosinophils and report the variability in the eosinophil proteome among five individuals and proteomic changes accompanying acute activation of eosinophils by interleukin-5. Our deep coverage and quantitative analyses fill an important gap in the existing maps of the human proteome and will enable the strategic use of proteomics to study eosinophils in human diseases.
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Affiliation(s)
| | | | - Alexander S Hebert
- Genome Center of Wisconsin, University of Wisconsin , 425 Henry Mall, Madison, Wisconsin 53706, United States
| | - Michael S Westphall
- Genome Center of Wisconsin, University of Wisconsin , 425 Henry Mall, Madison, Wisconsin 53706, United States
| | - Sameer K Mathur
- Department of Medicine, University of Wisconsin , Madison, Wisconsin 53792, United States
| | - Nizar N Jarjour
- Department of Medicine, University of Wisconsin , Madison, Wisconsin 53792, United States
| | - Elizabeth A Schwantes
- Department of Medicine, University of Wisconsin , Madison, Wisconsin 53792, United States
| | - Deane F Mosher
- Department of Medicine, University of Wisconsin , Madison, Wisconsin 53792, United States
| | - Joshua J Coon
- Genome Center of Wisconsin, University of Wisconsin , 425 Henry Mall, Madison, Wisconsin 53706, United States
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12
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Zheng M, Turton KB, Zhu F, Li Y, Grindle KM, Annis DS, Lu L, Drennan AC, Tweardy DJ, Bharadwaj U, Mosher DF, Rui L. A mix of S and ΔS variants of STAT3 enable survival of activated B-cell-like diffuse large B-cell lymphoma cells in culture. Oncogenesis 2016; 4:e184. [PMID: 26727576 PMCID: PMC4728674 DOI: 10.1038/oncsis.2015.44] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2015] [Revised: 10/29/2015] [Accepted: 11/12/2015] [Indexed: 12/13/2022] Open
Abstract
Activated B-cell-like diffuse large B-cell lymphoma (ABC DLBCL) is characterized by increased expression and activator of signal transducer and activator of transcription 3 (STAT3). ABC DLBCL cells require STAT3 for growth in culture. In ABC DLBCL cells, eosinophils and perhaps all cells, four variant STAT3 mRNAs (Sα, ΔSα, Sβ and ΔSβ) are present as a result of two alternative splicing events, one that results in the inclusion of a 55-residue C-terminal transactivation domain (α) or a truncated C-terminal domain with 7 unique residues (β) and a second that includes (S) or excludes (ΔS) the codon for Ser-701 in the linker between the SH2 and C-terminal domains. A substantial literature indicates that both α and β variants are required for optimal STAT3 function, but nothing is known about functions of ΔS variants. We used a knockdown/re-expression strategy to explore whether survival of ABC DLBCL cells requires that the four variants be in an appropriate ratio. No single variant rescued survival as well as STAT3Sα-C, Sα with activating mutations (A661C and N663C) in the SH2 domain. Better rescue was achieved when all four variants were re-expressed or Sα and ΔSα or Sβ and ΔSβ were re-expressed in pairs. Rescue correlated with expression of STAT3-sensitive genes NFKBIA and NFKBIZ. We consider a variety of explanations why a mix of S and ΔS variants of STAT3 should enable survival of ABC DLBCL cells.
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Affiliation(s)
- M Zheng
- Division of Hematology-Oncology, Department of Medicine, Carbone Cancer Center, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, USA.,Department of Hematology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - K B Turton
- Department of Biomolecular Chemistry, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, USA
| | - F Zhu
- Division of Hematology-Oncology, Department of Medicine, Carbone Cancer Center, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, USA
| | - Y Li
- Division of Hematology-Oncology, Department of Medicine, Carbone Cancer Center, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, USA
| | - K M Grindle
- Division of Hematology-Oncology, Department of Medicine, Carbone Cancer Center, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, USA
| | - D S Annis
- Department of Biomolecular Chemistry, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, USA
| | - L Lu
- Division of Hematology-Oncology, Department of Medicine, Carbone Cancer Center, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, USA
| | - A C Drennan
- Division of Hematology-Oncology, Department of Medicine, Carbone Cancer Center, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, USA
| | - D J Tweardy
- Department of Internal Medicine, MD Anderson Cancer Center, Houston, TX, USA
| | - U Bharadwaj
- Department of Internal Medicine, MD Anderson Cancer Center, Houston, TX, USA
| | - D F Mosher
- Division of Hematology-Oncology, Department of Medicine, Carbone Cancer Center, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, USA.,Department of Biomolecular Chemistry, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, USA
| | - L Rui
- Division of Hematology-Oncology, Department of Medicine, Carbone Cancer Center, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, USA
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