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Ranek JS, Stallaert W, Milner JJ, Redick M, Wolff SC, Beltran AS, Stanley N, Purvis JE. DELVE: feature selection for preserving biological trajectories in single-cell data. Nat Commun 2024; 15:2765. [PMID: 38553455 PMCID: PMC10980758 DOI: 10.1038/s41467-024-46773-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Accepted: 03/07/2024] [Indexed: 04/02/2024] Open
Abstract
Single-cell technologies can measure the expression of thousands of molecular features in individual cells undergoing dynamic biological processes. While examining cells along a computationally-ordered pseudotime trajectory can reveal how changes in gene or protein expression impact cell fate, identifying such dynamic features is challenging due to the inherent noise in single-cell data. Here, we present DELVE, an unsupervised feature selection method for identifying a representative subset of molecular features which robustly recapitulate cellular trajectories. In contrast to previous work, DELVE uses a bottom-up approach to mitigate the effects of confounding sources of variation, and instead models cell states from dynamic gene or protein modules based on core regulatory complexes. Using simulations, single-cell RNA sequencing, and iterative immunofluorescence imaging data in the context of cell cycle and cellular differentiation, we demonstrate how DELVE selects features that better define cell-types and cell-type transitions. DELVE is available as an open-source python package: https://github.com/jranek/delve .
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Affiliation(s)
- Jolene S Ranek
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Computational Medicine Program, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Wayne Stallaert
- Department of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, PA, USA
| | - J Justin Milner
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA
| | - Margaret Redick
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Computational Medicine Program, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Samuel C Wolff
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Computational Medicine Program, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Adriana S Beltran
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Human Pluripotent Cell Core, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA
| | - Natalie Stanley
- Computational Medicine Program, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
- Department of Computer Science, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
| | - Jeremy E Purvis
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
- Computational Medicine Program, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
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2
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Kwon MJ. Role of epithelial splicing regulatory protein 1 in cancer progression. Cancer Cell Int 2023; 23:331. [PMID: 38110955 PMCID: PMC10729575 DOI: 10.1186/s12935-023-03180-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2023] [Accepted: 12/12/2023] [Indexed: 12/20/2023] Open
Abstract
As aberrant alternative splicing by either dysregulation or mutations of splicing factors contributes to cancer initiation and progression, splicing factors are emerging as potential therapeutic targets for cancer therapy. Therefore, pharmacological modulators targeting splicing factors have been under development. Epithelial splicing regulatory protein 1 (ESRP1) is an epithelial cell-specific splicing factor, whose downregulation is associated with epithelial-mesenchymal transition (EMT) by regulating alternative splicing of multiple genes, such as CD44, CTNND1, ENAH, and FGFR2. Consistent with the downregulation of ESRP1 during EMT, it has been initially revealed that high ESRP1 expression is associated with favorable prognosis and ESRP1 plays a tumor-suppressive role in cancer progression. However, ESRP1 has been found to promote cancer progression in some cancers, such as breast and ovarian cancers, indicating that it plays a dual role in cancer progression depending on the type of cancer. Furthermore, recent studies have reported that ESRP1 affects tumor growth by regulating the metabolism of tumor cells or immune cell infiltration in the tumor microenvironment, suggesting the novel roles of ESRP1 in addition to EMT. ESRP1 expression was also associated with response to anticancer drugs. This review describes current understanding of the roles and mechanisms of ESRP1 in cancer progression, and further discusses the emerging novel roles of ESRP1 in cancer and recent attempts to target splicing factors for cancer therapy.
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Affiliation(s)
- Mi Jeong Kwon
- Vessel-Organ Interaction Research Center (MRC), College of Pharmacy, Kyungpook National University, Daegu, Republic of Korea.
- BK21 FOUR KNU Community-Based Intelligent Novel Drug Discovery Education Unit, College of Pharmacy and Research Institute of Pharmaceutical Sciences, Kyungpook National University, 80 Daehak-ro, Buk-gu, Daegu, 41566, Republic of Korea.
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3
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Advani R, Luzzi S, Scott E, Dalgliesh C, Weischenfeldt J, Munkley J, Elliott DJ. Epithelial specific splicing regulator proteins as emerging oncogenes in aggressive prostate cancer. Oncogene 2023; 42:3161-3168. [PMID: 37752235 PMCID: PMC10589096 DOI: 10.1038/s41388-023-02838-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Revised: 08/31/2023] [Accepted: 09/05/2023] [Indexed: 09/28/2023]
Abstract
Prostate cancer progression is connected to the activity of conventional oncogenes and tumour suppressors and driven by circulating steroid hormones. A key issue has been how to identify and care for aggressively developing prostate tumours. Here we discuss how expression of the splicing regulators ESRP1 and ESRP2, and how their role as "masterminds" of epithelial splicing patterns, have been identified as markers of aggressively proliferating prostate primary tumours. We suggest that the origin of prostate cancer within epithelial cells, and the subsequent association of ESRP1 and ESRP2 expression with more aggressive disease progression, identify ESRP1 and ESRP2 as lineage survival oncogenes. To move this field on in the future it will be important to identify the gene expression targets controlled by ESRP1/2 that regulate prostate cancer proliferation. Potential future therapies could be designed to target ESRP1 and ESRP2 protein activity or their regulated splice isoforms in aggressive prostate tumours. Design of these therapies is potentially complicated by the risk of producing a more mesenchymal splicing environment that might promote tumour metastasis.
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Affiliation(s)
- Rahul Advani
- Newcastle University Biosciences Institute (NUBI) and Newcastle University Cancer Centre, Newcastle University, Newcastle Upon Tyne, NE1 3BZ, United Kingdom
| | - Sara Luzzi
- Newcastle University Biosciences Institute (NUBI) and Newcastle University Cancer Centre, Newcastle University, Newcastle Upon Tyne, NE1 3BZ, United Kingdom
| | - Emma Scott
- Newcastle University Biosciences Institute (NUBI) and Newcastle University Cancer Centre, Newcastle University, Newcastle Upon Tyne, NE1 3BZ, United Kingdom
| | - Caroline Dalgliesh
- Newcastle University Biosciences Institute (NUBI) and Newcastle University Cancer Centre, Newcastle University, Newcastle Upon Tyne, NE1 3BZ, United Kingdom
| | - Joachim Weischenfeldt
- Biotech Research & Innovation Centre (BRIC), The Finsen Laboratory, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark
| | - Jennifer Munkley
- Newcastle University Biosciences Institute (NUBI) and Newcastle University Cancer Centre, Newcastle University, Newcastle Upon Tyne, NE1 3BZ, United Kingdom
| | - David J Elliott
- Newcastle University Biosciences Institute (NUBI) and Newcastle University Cancer Centre, Newcastle University, Newcastle Upon Tyne, NE1 3BZ, United Kingdom.
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4
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Derham JM, Kalsotra A. The discovery, function, and regulation of epithelial splicing regulatory proteins (ESRP) 1 and 2. Biochem Soc Trans 2023; 51:1097-1109. [PMID: 37314029 PMCID: PMC11298080 DOI: 10.1042/bst20221124] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Revised: 06/01/2023] [Accepted: 06/05/2023] [Indexed: 06/15/2023]
Abstract
Alternative splicing is a broad and evolutionarily conserved mechanism to diversify gene expression and functionality. The process relies on RNA binding proteins (RBPs) to recognize and bind target sequences in pre-mRNAs, which allows for the inclusion or skipping of various alternative exons. One recently discovered family of RBPs is the epithelial splicing regulatory proteins (ESRP) 1 and 2. Here, we discuss the structure and physiological function of the ESRPs in a variety of contexts. We emphasize the current understanding of their splicing activities, using the classic example of fibroblast growth factor receptor 2 mutually exclusive splicing. We also describe the mechanistic roles of ESRPs in coordinating the splicing and functional output of key signaling pathways that support the maintenance of, or shift between, epithelial and mesenchymal cell states. In particular, we highlight their functions in the development of mammalian limbs, the inner ear, and craniofacial structure while discussing the genetic and biochemical evidence that showcases their conserved roles in tissue regeneration, disease, and cancer pathogenesis.
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Affiliation(s)
- Jessica M. Derham
- Department of Biochemistry, University of Illinois Urbana-Champaign, Urbana, IL, USA
| | - Auinash Kalsotra
- Department of Biochemistry, University of Illinois Urbana-Champaign, Urbana, IL, USA
- Cancer Center @ Illinois, University of Illinois Urbana-Champaign, Urbana, IL, USA
- Carl R. Woese Institute of Genomic Biology, University of Illinois Urbana-Champaign, Urbana, IL, USA
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5
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Shivalingappa PKM, Singh DK, Sharma V, Arora V, Shiras A, Bapat SA. RBM47 is a Critical Regulator of Mouse Embryonic Stem Cell Differentiation. Stem Cell Rev Rep 2023; 19:475-490. [PMID: 35986129 PMCID: PMC9391069 DOI: 10.1007/s12015-022-10441-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/03/2022] [Indexed: 02/07/2023]
Abstract
RNA-binding proteins (RBPs) are pivotal for regulating gene expression as they are involved in each step of RNA metabolism. Several RBPs are essential for viable growth and development in mammals. RNA-binding motif 47 (RBM47) is an RRM-containing RBP whose role in mammalian embryonic development is poorly understood yet deemed to be essential since its loss in mouse embryos leads to perinatal lethality. In this study, we attempted to elucidate the significance of RBM47 in cell-fate decisions of mouse embryonic stem cells (mESCs). Downregulation of Rbm47 did not affect mESC maintenance and the cell cycle but perturbed the expression of primitive endoderm (PrE) markers and increased GATA4 + PrE-like cells. However, the PrE misregulation could be reversed by either overexpressing Rbm47 or treating the knockdown mESCs with the inhibitors of FGFR or MEK, suggesting an implication of RBM47 in regulating FGF-ERK signaling. Rbm47 knockdown affected the multi-lineage differentiation potential of mESCs as it regressed teratoma in NSG mice and led to a skewed expression of differentiation markers in serum-induced monolayer differentiation. Further, lineage-specific differentiation revealed that Rbm47 is essential for proper differentiation of mESCs towards neuroectodermal and endodermal fate. Taken together, we assign a hitherto unknown role(s) to RBM47 in a subtle regulation of mESC differentiation.
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Affiliation(s)
| | - Divya Kumari Singh
- National Centre for Cell Science, Savitribai Phule Pune University, Ganeshkhind, Pune, 411007, India
| | - Vaishali Sharma
- National Centre for Cell Science, Savitribai Phule Pune University, Ganeshkhind, Pune, 411007, India
| | - Vivek Arora
- National Centre for Cell Science, Savitribai Phule Pune University, Ganeshkhind, Pune, 411007, India
| | - Anjali Shiras
- National Centre for Cell Science, Savitribai Phule Pune University, Ganeshkhind, Pune, 411007, India
| | - Sharmila A Bapat
- National Centre for Cell Science, Savitribai Phule Pune University, Ganeshkhind, Pune, 411007, India.
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Bone Marrow Mesenchymal Stromal/Stem Cell-Derived Extracellular Vesicles Promote Corneal Wound Repair by Regulating Inflammation and Angiogenesis. Cells 2022; 11:cells11233892. [PMID: 36497151 PMCID: PMC9736484 DOI: 10.3390/cells11233892] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Revised: 11/22/2022] [Accepted: 11/28/2022] [Indexed: 12/05/2022] Open
Abstract
Severe corneal damage leads to complete vision loss, thereby affecting life quality and impinging heavily on the healthcare system. Current clinical approaches to manage corneal wounds suffer from severe drawbacks, thus requiring the development of alternative strategies. Of late, mesenchymal stromal/stem cell (MSC)-derived extracellular vesicles (EVs) have become a promising tool in the ophthalmic field. In the present study, we topically delivered bone-marrow-derived MSC-EVs (BMSC-EVs), embedded in methylcellulose, in a murine model of alkali-burn-induced corneal damage in order to evaluate their role in corneal repair through histological and molecular analyses, with the support of magnetic resonance imaging. Our data show that BMSC-EVs, used for the first time in this specific formulation on the damaged cornea, modulate cell death, inflammation and angiogenetic programs in the injured tissue, thus leading to a faster recovery of corneal damage. These results were confirmed on cadaveric donor-derived human corneal epithelial cells in vitro. Thus, BMSC-EVs modulate corneal repair dynamics and are promising as a new cell-free approach for intervening on burn wounds, especially in the avascularized region of the eye.
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Jones MK, Agarwal D, Mazo KW, Chopra M, Jurlina SL, Dash N, Xu Q, Ogata AR, Chow M, Hill AD, Kambli NK, Xu G, Sasik R, Birmingham A, Fisch KM, Weinreb RN, Enke RA, Skowronska-Krawczyk D, Wahlin KJ. Chromatin Accessibility and Transcriptional Differences in Human Stem Cell-Derived Early-Stage Retinal Organoids. Cells 2022; 11:3412. [PMID: 36359808 PMCID: PMC9657268 DOI: 10.3390/cells11213412] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Revised: 10/19/2022] [Accepted: 10/21/2022] [Indexed: 02/08/2023] Open
Abstract
Retinogenesis involves the specification of retinal cell types during early vertebrate development. While model organisms have been critical for determining the role of dynamic chromatin and cell-type specific transcriptional networks during this process, an enhanced understanding of the developing human retina has been more elusive due to the requirement for human fetal tissue. Pluripotent stem cell (PSC) derived retinal organoids offer an experimentally accessible solution for investigating the developing human retina. To investigate cellular and molecular changes in developing early retinal organoids, we developed SIX6-GFP and VSX2-tdTomato (or VSX2-h2b-mRuby3) dual fluorescent reporters. When differentiated as 3D organoids these expressed GFP at day 15 and tdTomato (or mRuby3) at day 25, respectively. This enabled us to explore transcriptional and chromatin related changes using RNA-seq and ATAC-seq from pluripotency through early retina specification. Pathway analysis of developing organoids revealed a stepwise loss of pluripotency, while optic vesicle and retina pathways became progressively more prevalent. Correlating gene transcription with chromatin accessibility in early eye field development showed that retinal cells underwent a clear change in chromatin landscape, as well as gene expression profiles. While each dataset alone provided valuable information, considering both in parallel provided an informative glimpse into the molecular nature eye development.
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Affiliation(s)
- Melissa K. Jones
- Viterbi Family Department of Ophthalmology, Shiley Eye Institute, University of California San Diego, La Jolla, CA 92093, USA
| | - Devansh Agarwal
- Viterbi Family Department of Ophthalmology, Shiley Eye Institute, University of California San Diego, La Jolla, CA 92093, USA
- Department of Bioengineering, University of California San Diego, La Jolla, CA 92093, USA
| | - Kevin W. Mazo
- Viterbi Family Department of Ophthalmology, Shiley Eye Institute, University of California San Diego, La Jolla, CA 92093, USA
| | - Manan Chopra
- Viterbi Family Department of Ophthalmology, Shiley Eye Institute, University of California San Diego, La Jolla, CA 92093, USA
| | - Shawna L. Jurlina
- Viterbi Family Department of Ophthalmology, Shiley Eye Institute, University of California San Diego, La Jolla, CA 92093, USA
| | - Nicholas Dash
- Viterbi Family Department of Ophthalmology, Shiley Eye Institute, University of California San Diego, La Jolla, CA 92093, USA
| | - Qianlan Xu
- Center for Translational Vision Research, University of California Irvine, Irvine, CA 92617, USA
| | - Anna R. Ogata
- Viterbi Family Department of Ophthalmology, Shiley Eye Institute, University of California San Diego, La Jolla, CA 92093, USA
| | - Melissa Chow
- Viterbi Family Department of Ophthalmology, Shiley Eye Institute, University of California San Diego, La Jolla, CA 92093, USA
| | - Alex D. Hill
- Viterbi Family Department of Ophthalmology, Shiley Eye Institute, University of California San Diego, La Jolla, CA 92093, USA
| | - Netra K. Kambli
- Viterbi Family Department of Ophthalmology, Shiley Eye Institute, University of California San Diego, La Jolla, CA 92093, USA
- Department of Biotechnology, California State University Channel Islands, Camarillo, CA 93012, USA
| | - Guorong Xu
- Center for Computational Biology and Bioinformatics, University of California San Diego, La Jolla, CA 92093, USA
| | - Roman Sasik
- Center for Computational Biology and Bioinformatics, University of California San Diego, La Jolla, CA 92093, USA
| | - Amanda Birmingham
- Center for Computational Biology and Bioinformatics, University of California San Diego, La Jolla, CA 92093, USA
| | - Kathleen M. Fisch
- Center for Computational Biology and Bioinformatics, University of California San Diego, La Jolla, CA 92093, USA
- Department of Obstetrics, Gynecology & Reproductive Sciences, University of California San Diego, La Jolla, CA 92037, USA
| | - Robert N. Weinreb
- Viterbi Family Department of Ophthalmology, Shiley Eye Institute, University of California San Diego, La Jolla, CA 92093, USA
| | - Ray A. Enke
- Department of Biology, James Madison University, Harrisonburg, VA 22807, USA
| | | | - Karl J. Wahlin
- Viterbi Family Department of Ophthalmology, Shiley Eye Institute, University of California San Diego, La Jolla, CA 92093, USA
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Duran-Arqué B, Cañete M, Castellazzi CL, Bartomeu A, Ferrer-Caelles A, Reina O, Caballé A, Gay M, Arauz-Garofalo G, Belloc E, Mendez R. Comparative analyses of vertebrate CPEB proteins define two subfamilies with coordinated yet distinct functions in post-transcriptional gene regulation. Genome Biol 2022; 23:192. [PMID: 36096799 PMCID: PMC9465852 DOI: 10.1186/s13059-022-02759-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Accepted: 08/12/2022] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND Vertebrate CPEB proteins bind mRNAs at cytoplasmic polyadenylation elements (CPEs) in their 3' UTRs, leading to cytoplasmic changes in their poly(A) tail lengths; this can promote translational repression or activation of the mRNA. However, neither the regulation nor the mechanisms of action of the CPEB family per se have been systematically addressed to date. RESULTS Based on a comparative analysis of the four vertebrate CPEBs, we determine their differential regulation by phosphorylation, the composition and properties of their supramolecular assemblies, and their target mRNAs. We show that all four CPEBs are able to recruit the CCR4-NOT deadenylation complex to repress the translation. However, their regulation, mechanism of action, and target mRNAs define two subfamilies. Thus, CPEB1 forms ribonucleoprotein complexes that are remodeled upon a single phosphorylation event and are associated with mRNAs containing canonical CPEs. CPEB2-4 are regulated by multiple proline-directed phosphorylations that control their liquid-liquid phase separation. CPEB2-4 mRNA targets include CPEB1-bound transcripts, with canonical CPEs, but also a specific subset of mRNAs with non-canonical CPEs. CONCLUSIONS Altogether, these results show how, globally, the CPEB family of proteins is able to integrate cellular cues to generate a fine-tuned adaptive response in gene expression regulation through the coordinated actions of all four members.
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Affiliation(s)
- Berta Duran-Arqué
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, 08028 Barcelona, Spain
| | - Manuel Cañete
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, 08028 Barcelona, Spain
| | - Chiara Lara Castellazzi
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, 08028 Barcelona, Spain
| | - Anna Bartomeu
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, 08028 Barcelona, Spain
| | - Anna Ferrer-Caelles
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, 08028 Barcelona, Spain
| | - Oscar Reina
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, 08028 Barcelona, Spain
| | - Adrià Caballé
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, 08028 Barcelona, Spain
| | - Marina Gay
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, 08028 Barcelona, Spain
| | - Gianluca Arauz-Garofalo
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, 08028 Barcelona, Spain
| | - Eulalia Belloc
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, 08028 Barcelona, Spain
| | - Raúl Mendez
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, 08028 Barcelona, Spain
- Institució Catalana de Recerca I Estudis Avançats (ICREA), 08010 Barcelona, Spain
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9
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Endo Y, Kamei KI, Hasegawa K, Okita K, Ito H, Terada S, Inoue-Murayama M. Generation and gene expression profiles of Grevy's zebra induced Pluripotent Stem Cells. Stem Cells Dev 2022; 31:250-257. [PMID: 35316100 DOI: 10.1089/scd.2021.0253] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Induced pluripotent stem cells (iPSCs) can serve as a biological resource for functional and conservation research for various species. This realisation has led to the generation of iPSCs from many species, including those identified as endangered. However, the understanding of species variation in mammalian iPSCs remains largely unknown. To gain insight into species variation in iPSCs, we generated iPSCs from a new species Grevy's zebra (Equus grevyi; gz-iPSCs), which has been listed as endangered in the IUCN (International Union for Conservation of Nature) Red List. We isolated primary fibroblast cells from an individual and successfully reprogrammed them into iPSCs. The generated gz-iPSCs continued to grow under primed-type culture condition and showed pluripotency and differentiation potential. To describe the molecular characteristics of gz-iPSCs, we performed RNA sequencing analysis. The gz-iPSC transcriptome showed robust expression of pluripotency associated genes reported in human and mouse, suggesting evolutionary conservation among the species. This study provides insight into the iPSCs from a rare species and helps the understanding of the gene expression basis underlying mammalian PSCs.
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Affiliation(s)
| | - Ken-Ichiro Kamei
- Kyoto University - Yoshida Campus, 12918, Kyoto, Japan, 606-8501;
| | | | | | | | - Shiho Terada
- Kyoto University - Yoshida Campus, 12918, Kyoto, Japan;
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10
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The RNA-Binding Protein ESRP1 Modulates the Expression of RAC1b in Colorectal Cancer Cells. Cancers (Basel) 2021; 13:cancers13164092. [PMID: 34439247 PMCID: PMC8392041 DOI: 10.3390/cancers13164092] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Revised: 08/03/2021] [Accepted: 08/09/2021] [Indexed: 12/14/2022] Open
Abstract
Simple Summary Colorectal cancer (CRC) ranks third for incidence and second for number of deaths among cancer types worldwide. Poor patient survival due to inadequate response to currently available treatment regimens points to the urgent requirement for personalized therapy in CRC patients. Our aim was to provide mechanistic insights into the pro-tumorigenic role of the RNA-binding protein ESRP1, which is highly expressed in a subset of CRC patients. We show that, in CRC cells, ESRP1 binds to and has the same trend in expression as RAC1b, a well-known tumor promoter. Thus, RAC1b may be a potential therapeutic target in ESRP1-overexpressing CRC. Abstract RNA binding proteins are well recognized as critical regulators of tumorigenic processes through their capacity to modulate RNA biogenesis, including alternative splicing, RNA stability and mRNA translation. The RNA binding protein Epithelial Splicing Regulatory Protein 1 (ESRP1) can act as a tumor suppressor or promoter in a cell type- and disease context-dependent manner. We have previously shown that elevated expression of ESRP1 in colorectal cancer cells can drive tumor progression. To gain further insights into the pro-tumorigenic mechanism of action of ESRP1, we performed cDNA microarray analysis on two colorectal cells lines modulated for ESRP1 expression. Intriguingly, RAC1b was highly expressed, both at mRNA and protein levels, in ESRP1-overexpressing cells, while the opposite trend was observed in ESRP1-silenced CRC cells. Moreover, RAC1 and RAC1b mRNA co-immunoprecipitate with ESRP1 protein. Silencing of RAC1b expression significantly reduced the number of soft agar colonies formed by ESRP1-overexpressing cells, suggesting that ESRP1 acted, at least partially, through RAC1b in its tumor-promoting activities in CRC cells. Thus, our data provide molecular cues on targetable candidates in CRC cases with high ESRP1 expression.
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11
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Wang X, Ping C, Tan P, Sun C, Liu G, Liu T, Yang S, Si Y, Zhao L, Hu Y, Jia Y, Wang X, Zhang M, Wang F, Wang D, Yu J, Ma Y, Huang Y. hnRNPLL controls pluripotency exit of embryonic stem cells by modulating alternative splicing of Tbx3 and Bptf. EMBO J 2021; 40:e104729. [PMID: 33349972 PMCID: PMC7883296 DOI: 10.15252/embj.2020104729] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2020] [Revised: 11/15/2020] [Accepted: 11/16/2020] [Indexed: 11/09/2022] Open
Abstract
The regulatory circuitry underlying embryonic stem (ES) cell self-renewal is well defined, but how this circuitry is disintegrated to enable lineage specification is unclear. RNA-binding proteins (RBPs) have essential roles in RNA-mediated gene regulation, and preliminary data suggest that they might regulate ES cell fate. By combining bioinformatic analyses with functional screening, we identified seven RBPs played important roles for the exit from pluripotency of ES cells. We characterized hnRNPLL, which mainly functions as a global regulator of alternative splicing in ES cells. Specifically, hnRNPLL promotes multiple ES cell-preferred exon skipping events during the onset of ES cell differentiation. hnRNPLL depletion thus leads to sustained expression of ES cell-preferred isoforms, resulting in a differentiation deficiency that causes developmental defects and growth impairment in hnRNPLL-KO mice. In particular, hnRNPLL-mediated alternative splicing of two transcription factors, Bptf and Tbx3, is important for pluripotency exit. These data uncover the critical role of RBPs in pluripotency exit and suggest the application of targeting RBPs in controlling ES cell fate.
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Affiliation(s)
- Xue Wang
- State Key Laboratory of Medical Molecular BiologyInstitute of Basic Medical SciencesChinese Academy of Medical SciencesSchool of Basic Medicine Peking Union Medical CollegeBeijingChina
- Department of Medical GeneticsInstitute of Basic Medical SciencesChinese Academy of Medical SciencesSchool of Basic Medicine Peking Union Medical CollegeBeijingChina
| | - Changyun Ping
- State Key Laboratory of Medical Molecular BiologyInstitute of Basic Medical SciencesChinese Academy of Medical SciencesSchool of Basic Medicine Peking Union Medical CollegeBeijingChina
- Key Laboratory of RNA Regulation and HematopoiesisDepartment of Biochemistry and Molecular BiologyInstitute of Basic Medical SciencesChinese Academy of Medical SciencesSchool of Basic Medicine Peking Union Medical CollegeBeijingChina
- Present address:
Department of PathologyHenan Provincial People's HospitalPeople's Hospital of Zhengzhou UniversityZhengzhouHenanChina
| | - Puwen Tan
- Department of BioinformaticsSchool of Basic Medical SciencesSouthern Medical UniversityGuangzhouChina
| | - Chenguang Sun
- State Key Laboratory of Medical Molecular BiologyInstitute of Basic Medical SciencesChinese Academy of Medical SciencesSchool of Basic Medicine Peking Union Medical CollegeBeijingChina
- Key Laboratory of RNA Regulation and HematopoiesisDepartment of Biochemistry and Molecular BiologyInstitute of Basic Medical SciencesChinese Academy of Medical SciencesSchool of Basic Medicine Peking Union Medical CollegeBeijingChina
| | - Guang Liu
- State Key Laboratory of Medical Molecular BiologyInstitute of Basic Medical SciencesChinese Academy of Medical SciencesSchool of Basic Medicine Peking Union Medical CollegeBeijingChina
- Department of Medical GeneticsInstitute of Basic Medical SciencesChinese Academy of Medical SciencesSchool of Basic Medicine Peking Union Medical CollegeBeijingChina
| | - Tao Liu
- State Key Laboratory of Medical Molecular BiologyInstitute of Basic Medical SciencesChinese Academy of Medical SciencesSchool of Basic Medicine Peking Union Medical CollegeBeijingChina
- Department of Obstetrics and GynecologyThe Third Affiliated Hospital of Chongqing Medical University (General Hospital)ChongqingChina
| | - Shuchun Yang
- State Key Laboratory of Medical Molecular BiologyInstitute of Basic Medical SciencesChinese Academy of Medical SciencesSchool of Basic Medicine Peking Union Medical CollegeBeijingChina
- Department of Medical GeneticsInstitute of Basic Medical SciencesChinese Academy of Medical SciencesSchool of Basic Medicine Peking Union Medical CollegeBeijingChina
| | - Yanmin Si
- State Key Laboratory of Medical Molecular BiologyInstitute of Basic Medical SciencesChinese Academy of Medical SciencesSchool of Basic Medicine Peking Union Medical CollegeBeijingChina
- Key Laboratory of RNA Regulation and HematopoiesisDepartment of Biochemistry and Molecular BiologyInstitute of Basic Medical SciencesChinese Academy of Medical SciencesSchool of Basic Medicine Peking Union Medical CollegeBeijingChina
| | - Lijun Zhao
- State Key Laboratory of Medical Molecular BiologyInstitute of Basic Medical SciencesChinese Academy of Medical SciencesSchool of Basic Medicine Peking Union Medical CollegeBeijingChina
- Key Laboratory of RNA Regulation and HematopoiesisDepartment of Biochemistry and Molecular BiologyInstitute of Basic Medical SciencesChinese Academy of Medical SciencesSchool of Basic Medicine Peking Union Medical CollegeBeijingChina
| | - Yongfei Hu
- Department of BioinformaticsSchool of Basic Medical SciencesSouthern Medical UniversityGuangzhouChina
| | - Yuyan Jia
- State Key Laboratory of Medical Molecular BiologyInstitute of Basic Medical SciencesChinese Academy of Medical SciencesSchool of Basic Medicine Peking Union Medical CollegeBeijingChina
- Department of Medical GeneticsInstitute of Basic Medical SciencesChinese Academy of Medical SciencesSchool of Basic Medicine Peking Union Medical CollegeBeijingChina
| | - Xiaoshuang Wang
- State Key Laboratory of Medical Molecular BiologyInstitute of Basic Medical SciencesChinese Academy of Medical SciencesSchool of Basic Medicine Peking Union Medical CollegeBeijingChina
- Key Laboratory of RNA Regulation and HematopoiesisDepartment of Biochemistry and Molecular BiologyInstitute of Basic Medical SciencesChinese Academy of Medical SciencesSchool of Basic Medicine Peking Union Medical CollegeBeijingChina
| | - Meili Zhang
- State Key Laboratory of Medical Molecular BiologyInstitute of Basic Medical SciencesChinese Academy of Medical SciencesSchool of Basic Medicine Peking Union Medical CollegeBeijingChina
- Department of Medical GeneticsInstitute of Basic Medical SciencesChinese Academy of Medical SciencesSchool of Basic Medicine Peking Union Medical CollegeBeijingChina
| | - Fang Wang
- State Key Laboratory of Medical Molecular BiologyInstitute of Basic Medical SciencesChinese Academy of Medical SciencesSchool of Basic Medicine Peking Union Medical CollegeBeijingChina
- Key Laboratory of RNA Regulation and HematopoiesisDepartment of Biochemistry and Molecular BiologyInstitute of Basic Medical SciencesChinese Academy of Medical SciencesSchool of Basic Medicine Peking Union Medical CollegeBeijingChina
| | - Dong Wang
- Department of BioinformaticsSchool of Basic Medical SciencesSouthern Medical UniversityGuangzhouChina
- Dermatology HospitalSouthern Medical UniversityGuangzhouChina
- Center for Informational BiologyUniversity of Electronic Science and Technology of ChinaChengduChina
| | - Jia Yu
- State Key Laboratory of Medical Molecular BiologyInstitute of Basic Medical SciencesChinese Academy of Medical SciencesSchool of Basic Medicine Peking Union Medical CollegeBeijingChina
- Key Laboratory of RNA Regulation and HematopoiesisDepartment of Biochemistry and Molecular BiologyInstitute of Basic Medical SciencesChinese Academy of Medical SciencesSchool of Basic Medicine Peking Union Medical CollegeBeijingChina
| | - Yanni Ma
- State Key Laboratory of Medical Molecular BiologyInstitute of Basic Medical SciencesChinese Academy of Medical SciencesSchool of Basic Medicine Peking Union Medical CollegeBeijingChina
- Key Laboratory of RNA Regulation and HematopoiesisDepartment of Biochemistry and Molecular BiologyInstitute of Basic Medical SciencesChinese Academy of Medical SciencesSchool of Basic Medicine Peking Union Medical CollegeBeijingChina
| | - Yue Huang
- State Key Laboratory of Medical Molecular BiologyInstitute of Basic Medical SciencesChinese Academy of Medical SciencesSchool of Basic Medicine Peking Union Medical CollegeBeijingChina
- Department of Medical GeneticsInstitute of Basic Medical SciencesChinese Academy of Medical SciencesSchool of Basic Medicine Peking Union Medical CollegeBeijingChina
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12
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Alternative splicing modulates cancer aggressiveness: role in EMT/metastasis and chemoresistance. Mol Biol Rep 2021; 48:897-914. [PMID: 33400075 DOI: 10.1007/s11033-020-06094-y] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2020] [Accepted: 12/15/2020] [Indexed: 12/11/2022]
Abstract
Enhanced metastasis and disease recurrence accounts for the high mortality rates associated with cancer. The process of Epithelial-Mesenchymal Transition (EMT) contributes towards the augmentation of cancer invasiveness along with the gain of stem-like and the subsequent drug-resistant behavior. Apart from the well-established transcriptional regulation, EMT is also controlled post-transcriptionally by virtue of alternative splicing (AS). Numerous genes including Fibroblast Growth Factor receptor (FGFR) as well as CD44 are differentially spliced during this trans-differentiation process which, in turn, governs cancer progression. These splicing alterations are controlled by various splicing factors including ESRP, RBFOX2 as well as hnRNPs. Here, we have depicted the mechanisms governing the splice isoform switching of FGFR and CD44. Moreover, the role of the splice variants generated by AS of these gene transcripts in modulating the metastatic potential and stem-like/chemoresistant behavior of cancer cells has also been highlighted. Additionally, the involvement of splicing factors in regulating EMT/invasiveness along with drug-resistance as well as the metabolic properties of the cells has been emphasized. Tumorigenesis is accompanied by a remodeling of the cellular splicing profile generating diverse protein isoforms which, in turn, control the cancer-associated hallmarks. Therefore, we have also briefly discussed about a wide variety of genes which are differentially spliced in the tumor cells and promote cancer progression. We have also outlined different strategies for targeting the tumor-associated splicing events which have shown promising results and therefore this approach might be useful in developing therapies to reduce cancer aggressiveness in a more specific manner.
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13
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RNA-Seq analysis reveals pluripotency-associated genes and their interaction networks in human embryonic stem cells. Comput Biol Chem 2020; 85:107239. [DOI: 10.1016/j.compbiolchem.2020.107239] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2019] [Revised: 02/19/2020] [Accepted: 02/19/2020] [Indexed: 12/25/2022]
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14
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Li D, Kishta MS, Wang J. Regulation of pluripotency and reprogramming by RNA binding proteins. Curr Top Dev Biol 2020; 138:113-138. [PMID: 32220295 DOI: 10.1016/bs.ctdb.2020.01.003] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Embryonic stem cells have the capacities of self-renewal and pluripotency. Pluripotency establishment (somatic cell reprogramming), maintenance, and execution (differentiation) require orchestrated regulatory mechanisms of a cell's molecular machinery, including signaling pathways, epigenetics, transcription, translation, and protein degradation. RNA binding proteins (RBPs) take part in every process of RNA regulation and recent studies began to address their important functions in the regulation of pluripotency and reprogramming. Here, we discuss the roles of RBPs in key regulatory steps in the control of pluripotency and reprogramming. Among RNA binding proteins are a group of RNA helicases that are responsible for RNA structure remodeling with important functional implications. We highlight the largest family of RNA helicases, DDX (DEAD-box) helicase family and our current understanding of their functions specifically in the regulation of pluripotency and reprogramming.
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Affiliation(s)
- Dan Li
- Department of Cell, Developmental and Regenerative Biology; The Black Family Stem Cell Institute; Icahn School of Medicine at Mount Sinai, New York, NY, United States; The Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Mohamed S Kishta
- Hormones Department, Medical Research Division, National Research Centre, Cairo, Egypt; Stem Cell Lab., Center of Excellence for Advanced Sciences, National Research Centre, Cairo, Egypt; Department of Medicine, Columbia Center for Human Development, Columbia University Irving Medical Center, New York, NY, United States
| | - Jianlong Wang
- Department of Cell, Developmental and Regenerative Biology; The Black Family Stem Cell Institute; Icahn School of Medicine at Mount Sinai, New York, NY, United States; The Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, United States; Department of Medicine, Columbia Center for Human Development, Columbia University Irving Medical Center, New York, NY, United States.
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15
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Teles SP, Oliveira P, Ferreira M, Carvalho J, Ferreira P, Oliveira C. Integrated Analysis of Structural Variation and RNA Expression of FGFR2 and Its Splicing Modulator ESRP1 Highlight the ESRP1amp- FGFR2norm- FGFR2-IIIchigh Axis in Diffuse Gastric Cancer. Cancers (Basel) 2019; 12:cancers12010070. [PMID: 31881796 PMCID: PMC7017189 DOI: 10.3390/cancers12010070] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2019] [Revised: 12/15/2019] [Accepted: 12/23/2019] [Indexed: 01/11/2023] Open
Abstract
Gastric Cancer (GC) is one of the most common and deadliest types of cancer in the world. To improve GC prognosis, increasing efforts are being made to develop new targeted therapies. Although FGFR2 genetic amplification and protein overexpression in GC have been targeted in clinical trials, so far no improvement in patient overall survival has been found. To address this issue, we studied genetic and epigenetic events affecting FGFR2 and its splicing regulator ESRP1 in GC that could be used as new therapeutic targets or predictive biomarkers. We performed copy number variation (CNV), DNA methylation, and RNA expression analyses of FGFR2/ESRP1 across several cohorts. We discovered that both genes were frequently amplified and demethylated in GC, resulting in increased ESRP1 expression and of a specific FGFR2 isoform: FGFR2-IIIb. We also showed that ESRP1 amplification in GC correlated with a significant decreased expression of FGFR2-IIIc, an alternative FGFR2 splicing isoform. Furthermore, when we performed a survival analysis, we observed that patients harboring diffuse-type tumors with low FGFR2-IIIc expression revealed a better overall survival than patients with FGFR2-IIIc high-expressing diffuse tumors. Our results encourage further studies on the role of ESRP1 in GC and support FGFR2-IIIc as a relevant biomarker in GC.
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Affiliation(s)
- Sara Pinto Teles
- Ipatimup—Institute of Molecular Pathology and Immunology, University of Porto, Rua Júlio Amaral de Carvalho 45, 4200-135 Porto, Portugal
- i3S—Instituto de Investigação e Inovação em Saúde, University of Porto, Rua Alfredo Allen 208, 4200-135 Porto, Portugal
- Master in Oncology, Institute of Biomedical Sciences Abel Salazar, University of Porto (ICBAS-UP), 4050-313 Porto, Portugal
| | - Patrícia Oliveira
- Ipatimup—Institute of Molecular Pathology and Immunology, University of Porto, Rua Júlio Amaral de Carvalho 45, 4200-135 Porto, Portugal
- i3S—Instituto de Investigação e Inovação em Saúde, University of Porto, Rua Alfredo Allen 208, 4200-135 Porto, Portugal
| | - Marta Ferreira
- Ipatimup—Institute of Molecular Pathology and Immunology, University of Porto, Rua Júlio Amaral de Carvalho 45, 4200-135 Porto, Portugal
- i3S—Instituto de Investigação e Inovação em Saúde, University of Porto, Rua Alfredo Allen 208, 4200-135 Porto, Portugal
| | - Joana Carvalho
- Ipatimup—Institute of Molecular Pathology and Immunology, University of Porto, Rua Júlio Amaral de Carvalho 45, 4200-135 Porto, Portugal
- i3S—Instituto de Investigação e Inovação em Saúde, University of Porto, Rua Alfredo Allen 208, 4200-135 Porto, Portugal
| | - Pedro Ferreira
- Ipatimup—Institute of Molecular Pathology and Immunology, University of Porto, Rua Júlio Amaral de Carvalho 45, 4200-135 Porto, Portugal
- i3S—Instituto de Investigação e Inovação em Saúde, University of Porto, Rua Alfredo Allen 208, 4200-135 Porto, Portugal
- Department of Computer Science, Faculty of Sciences, University of Porto, Rua Campo Alegre 1021/1055, 4169-007 Porto, Portugal
| | - Carla Oliveira
- Ipatimup—Institute of Molecular Pathology and Immunology, University of Porto, Rua Júlio Amaral de Carvalho 45, 4200-135 Porto, Portugal
- i3S—Instituto de Investigação e Inovação em Saúde, University of Porto, Rua Alfredo Allen 208, 4200-135 Porto, Portugal
- Department Pathology and Oncology Faculty of Medicine University of Porto, Alameda Prof. Hernâni Monteiro, 4200-319 Porto, Portugal
- Correspondence:
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16
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Singh B, Sarli VN, Kinne HE, Shamsnia A, Lucci A. Evaluation of 6-mercaptopurine in a cell culture model of adaptable triple-negative breast cancer with metastatic potential. Oncotarget 2019; 10:3681-3693. [PMID: 31217902 PMCID: PMC6557209 DOI: 10.18632/oncotarget.26978] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2018] [Accepted: 05/13/2019] [Indexed: 02/07/2023] Open
Abstract
Progenitor-like cancer cells that can survive in reversible quiescence when faced with various challenges in the body are often behind disease progression. A lack of glutamine in culture medium, which eliminates >99.9% of proliferating SUM149 triple-negative breast cancer cells, selects such adaptable, pan-resistant cells. Our data support the hypothesis that a lack of glutamine forces the selection of an epigenetic state that does not require a high level of TET2, thus selecting an “undifferentiated” therapy-resistant phenotype as seen in TET2-mutant cancers. Our data suggesting that highly adaptable cells are generated through reprograming of the epigenome and transcriptome led us to evaluate low-dose 6-mercaptopurine as a potential therapy in our model. We found that a long treatment with low-dose 6-mercaptopurine inhibited the proliferation of these adaptable cells to a greater extent than it inhibited parental cells. Importantly, a small percentage of adaptable cells survived a low-dose 6-mercaptopurine treatment in a reversible quiescence, analogous to the persistence of abnormal progenitor-like cells in inflammatory bowel disease, which stays in a durable remission with a 6-mercaptopurine treatment. Based on a biomarkers analysis, a long treatment with 6-mercaptopurine or aspirin partially reversed epithelial to mesenchymal transition in adaptable cancer cells. A cell culture model of adaptable cancer cells that persist in the body will help in discovering superior therapies that can be offered before the disease advances to metastasis.
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Affiliation(s)
- Balraj Singh
- Department of Breast Surgical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.,Morgan Welch Inflammatory Breast Cancer Research Program and Clinic, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Vanessa N Sarli
- Department of Breast Surgical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.,Morgan Welch Inflammatory Breast Cancer Research Program and Clinic, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Hannah E Kinne
- Department of Breast Surgical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.,Morgan Welch Inflammatory Breast Cancer Research Program and Clinic, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Anna Shamsnia
- Department of Breast Surgical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.,Morgan Welch Inflammatory Breast Cancer Research Program and Clinic, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Anthony Lucci
- Department of Breast Surgical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.,Morgan Welch Inflammatory Breast Cancer Research Program and Clinic, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
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17
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Kim YD, Kim HS, Lee J, Choi JK, Han E, Jeong JE, Cho YS. ESRP1-Induced CD44 v3 Is Important for Controlling Pluripotency in Human Pluripotent Stem Cells. Stem Cells 2018; 36:1525-1534. [DOI: 10.1002/stem.2864] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2018] [Revised: 05/15/2018] [Accepted: 05/19/2018] [Indexed: 01/12/2023]
Affiliation(s)
- Young-Dae Kim
- Stem Cell Research Laboratory; Immunotherapy Convergence Research Center, Korea Research Institute of Bioscience and Biotechnology; Daejeon 34141 Republic of Korea
| | - Han-Seop Kim
- Stem Cell Research Laboratory; Immunotherapy Convergence Research Center, Korea Research Institute of Bioscience and Biotechnology; Daejeon 34141 Republic of Korea
| | - Jungwoon Lee
- Stem Cell Research Laboratory; Immunotherapy Convergence Research Center, Korea Research Institute of Bioscience and Biotechnology; Daejeon 34141 Republic of Korea
| | - Jung-Kyun Choi
- Stem Cell Research Laboratory; Immunotherapy Convergence Research Center, Korea Research Institute of Bioscience and Biotechnology; Daejeon 34141 Republic of Korea
- Department of Bioscience; KRIBB School, University of Science & Technology; Daejeon Republic of Korea
| | - Enna Han
- Stem Cell Research Laboratory; Immunotherapy Convergence Research Center, Korea Research Institute of Bioscience and Biotechnology; Daejeon 34141 Republic of Korea
- Department of Bioscience; KRIBB School, University of Science & Technology; Daejeon Republic of Korea
| | - Ji E. Jeong
- Stem Cell Research Laboratory; Immunotherapy Convergence Research Center, Korea Research Institute of Bioscience and Biotechnology; Daejeon 34141 Republic of Korea
| | - Yee S. Cho
- Stem Cell Research Laboratory; Immunotherapy Convergence Research Center, Korea Research Institute of Bioscience and Biotechnology; Daejeon 34141 Republic of Korea
- Department of Bioscience; KRIBB School, University of Science & Technology; Daejeon Republic of Korea
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18
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The RNA-binding protein ESRP1 promotes human colorectal cancer progression. Oncotarget 2018; 8:10007-10024. [PMID: 28052020 PMCID: PMC5354637 DOI: 10.18632/oncotarget.14318] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2016] [Accepted: 12/01/2016] [Indexed: 02/06/2023] Open
Abstract
Epithelial splicing regulatory protein 1 (ESRP1) is an epithelial cell-specific RNA binding protein that controls several key cellular processes, like alternative splicing and translation. Previous studies have demonstrated a tumor suppressor role for this protein. Recently, however, a pro-metastatic function of ESRP1 has been reported. We thus aimed at clarifying the role of ESRP1 in Colorectal Cancer (CRC) by performing loss- and gain-of-function studies, and evaluating tumorigenesis and malignancy with in vitro and in vivo approaches. We found that ESRP1 plays a role in anchorage-independent growth of CRC cells. ESRP1-overexpressing cells grown in suspension showed enhanced fibroblast growth factor receptor (FGFR1/2) signalling, Akt activation, and Snail upregulation. Moreover, ESRP1 promoted the ability of CRC cells to generate macrometastases in mice livers. High ESRP1 expression may thus stimulate growth of cancer epithelial cells and promote colorectal cancer progression. Our findings provide mechanistic insights into a previously unreported, pro-oncogenic role for ESRP1 in CRC, and suggest that fine-tuning the level of this RNA-binding protein could be relevant in modulating tumor growth in a subset of CRC patients.
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19
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Walser TC, Jing Z, Tran LM, Lin YQ, Yakobian N, Wang G, Krysan K, Zhu LX, Sharma S, Lee MH, Belperio JA, Ooi AT, Gomperts BN, Shay JW, Larsen JE, Minna JD, Hong LS, Fishbein MC, Dubinett SM. Silencing the Snail-Dependent RNA Splice Regulator ESRP1 Drives Malignant Transformation of Human Pulmonary Epithelial Cells. Cancer Res 2018; 78:1986-1999. [PMID: 29431637 DOI: 10.1158/0008-5472.can-17-0315] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2017] [Revised: 02/28/2017] [Accepted: 01/30/2018] [Indexed: 12/31/2022]
Abstract
Epithelial-to-mesenchymal transition (EMT) is organized in cancer cells by a set of key transcription factors, but the significance of this process is still debated, including in non-small cell lung cancer (NSCLC). Here, we report increased expression of the EMT-inducing transcription factor Snail in premalignant pulmonary lesions, relative to histologically normal pulmonary epithelium. In immortalized human pulmonary epithelial cells and isogenic derivatives, we documented Snail-dependent anchorage-independent growth in vitro and primary tumor growth and metastatic behavior in vivo Snail-mediated transformation relied upon silencing of the tumor-suppressive RNA splicing regulatory protein ESRP1. In clinical specimens of NSCLC, ESRP1 loss was documented in Snail-expressing premalignant pulmonary lesions. Mechanistic investigations showed that Snail drives malignant progression in an ALDH+CD44+CD24- pulmonary stem cell subset in which ESRP1 and stemness-repressing microRNAs are inhibited. Collectively, our results show how ESRP1 loss is a critical event in lung carcinogenesis, and they identify new candidate directions for targeted therapy of NSCLC.Significance: This study defines a Snail-ESRP1 cancer axis that is crucial for human lung carcinogenesis, with implications for new intervention strategies and translational opportunities. Cancer Res; 78(8); 1986-99. ©2018 AACR.
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Affiliation(s)
- Tonya C Walser
- Division of Pulmonary and Critical Care Medicine, David Geffen School of Medicine at UCLA, Los Angeles, California.,Department of Medicine, David Geffen School of Medicine at UCLA, Los Angeles, California.,Lung Cancer Research Program, Jonsson Comprehensive Cancer Center at UCLA, Los Angeles, California
| | - Zhe Jing
- Division of Pulmonary and Critical Care Medicine, David Geffen School of Medicine at UCLA, Los Angeles, California.,Department of Medicine, David Geffen School of Medicine at UCLA, Los Angeles, California.,Lung Cancer Research Program, Jonsson Comprehensive Cancer Center at UCLA, Los Angeles, California
| | - Linh M Tran
- Division of Pulmonary and Critical Care Medicine, David Geffen School of Medicine at UCLA, Los Angeles, California.,Department of Medicine, David Geffen School of Medicine at UCLA, Los Angeles, California.,Lung Cancer Research Program, Jonsson Comprehensive Cancer Center at UCLA, Los Angeles, California
| | - Ying Q Lin
- Division of Pulmonary and Critical Care Medicine, David Geffen School of Medicine at UCLA, Los Angeles, California.,Department of Medicine, David Geffen School of Medicine at UCLA, Los Angeles, California.,Lung Cancer Research Program, Jonsson Comprehensive Cancer Center at UCLA, Los Angeles, California
| | - Natalie Yakobian
- Division of Pulmonary and Critical Care Medicine, David Geffen School of Medicine at UCLA, Los Angeles, California.,Department of Medicine, David Geffen School of Medicine at UCLA, Los Angeles, California.,Lung Cancer Research Program, Jonsson Comprehensive Cancer Center at UCLA, Los Angeles, California
| | - Gerald Wang
- Division of Pulmonary and Critical Care Medicine, David Geffen School of Medicine at UCLA, Los Angeles, California.,Department of Medicine, David Geffen School of Medicine at UCLA, Los Angeles, California.,Lung Cancer Research Program, Jonsson Comprehensive Cancer Center at UCLA, Los Angeles, California
| | - Kostyantyn Krysan
- Division of Pulmonary and Critical Care Medicine, David Geffen School of Medicine at UCLA, Los Angeles, California.,Department of Medicine, David Geffen School of Medicine at UCLA, Los Angeles, California.,Lung Cancer Research Program, Jonsson Comprehensive Cancer Center at UCLA, Los Angeles, California
| | - Li X Zhu
- Division of Pulmonary and Critical Care Medicine, David Geffen School of Medicine at UCLA, Los Angeles, California.,Department of Medicine, David Geffen School of Medicine at UCLA, Los Angeles, California.,Lung Cancer Research Program, Jonsson Comprehensive Cancer Center at UCLA, Los Angeles, California.,VA Greater Los Angeles Health Care System, Los Angeles, California
| | - Sherven Sharma
- Division of Pulmonary and Critical Care Medicine, David Geffen School of Medicine at UCLA, Los Angeles, California.,Department of Medicine, David Geffen School of Medicine at UCLA, Los Angeles, California.,Lung Cancer Research Program, Jonsson Comprehensive Cancer Center at UCLA, Los Angeles, California.,VA Greater Los Angeles Health Care System, Los Angeles, California
| | - Mi-Heon Lee
- Department of Surgery, David Geffen School of Medicine at UCLA, Los Angeles, California
| | - John A Belperio
- Division of Pulmonary and Critical Care Medicine, David Geffen School of Medicine at UCLA, Los Angeles, California.,Department of Medicine, David Geffen School of Medicine at UCLA, Los Angeles, California.,Lung Cancer Research Program, Jonsson Comprehensive Cancer Center at UCLA, Los Angeles, California
| | - Aik T Ooi
- Lung Cancer Research Program, Jonsson Comprehensive Cancer Center at UCLA, Los Angeles, California.,Department of Pediatrics, David Geffen School of Medicine at UCLA, Los Angeles, California.,Mattel Children's Hospital at UCLA, Los Angeles, California
| | - Brigitte N Gomperts
- Lung Cancer Research Program, Jonsson Comprehensive Cancer Center at UCLA, Los Angeles, California.,Department of Pediatrics, David Geffen School of Medicine at UCLA, Los Angeles, California.,Mattel Children's Hospital at UCLA, Los Angeles, California
| | - Jerry W Shay
- Department of Cell Biology, The University of Texas Southwestern Medical Center, Dallas, Texas
| | - Jill E Larsen
- QIMR Berghofer Medical Research Institute, Brisbane, Australia
| | - John D Minna
- Hamon Center for Therapeutic Oncology Research, The University of Texas Southwestern Medical Center, Dallas, Texas
| | - Long-Sheng Hong
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine at UCLA, Los Angeles, California
| | - Michael C Fishbein
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine at UCLA, Los Angeles, California
| | - Steven M Dubinett
- Division of Pulmonary and Critical Care Medicine, David Geffen School of Medicine at UCLA, Los Angeles, California. .,Department of Medicine, David Geffen School of Medicine at UCLA, Los Angeles, California.,Lung Cancer Research Program, Jonsson Comprehensive Cancer Center at UCLA, Los Angeles, California.,VA Greater Los Angeles Health Care System, Los Angeles, California.,Department of Pathology and Laboratory Medicine, David Geffen School of Medicine at UCLA, Los Angeles, California.,Department of Molecular and Medical Pharmacology, David Geffen School of Medicine at UCLA, Los Angeles, California
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20
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Voena C, Varesio LM, Zhang L, Menotti M, Poggio T, Panizza E, Wang Q, Minero VG, Fagoonee S, Compagno M, Altruda F, Monti S, Chiarle R. Oncogenic ALK regulates EMT in non-small cell lung carcinoma through repression of the epithelial splicing regulatory protein 1. Oncotarget 2017; 7:33316-30. [PMID: 27119231 PMCID: PMC5078097 DOI: 10.18632/oncotarget.8955] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2015] [Accepted: 03/29/2016] [Indexed: 11/25/2022] Open
Abstract
A subset of Non-Small Cell Lung Carcinoma (NSCLC) carries chromosomal rearrangements involving the Anaplastic Lymphoma Kinase (ALK) gene. ALK-rearranged NSCLC are typically adenocarcinoma characterized by a solid signet-ring cell pattern that is frequently associated with a metastatic phenotype. Recent reports linked the presence of ALK rearrangement to an epithelial-mesenchymal transition (EMT) phenotype in NSCLC, but the extent and the mechanisms of an ALK-mediated EMT in ALK-rearranged NSCLC are largely unknown. We found that the ALK-rearranged H2228 and DFCI032, but not the H3122, cell lines displayed a mesenchymal phenotype. In these cell lines, oncogenic ALK activity dictated an EMT phenotype by directly suppressing E-cadherin and up-regulating vimentin expression, as well as expression of other genes involved in EMT. We found that the epithelial splicing regulatory protein 1 (ESRP1), a key regulator of the splicing switch during EMT, was repressed by EML4-ALK activity. The treatment of NSCLC cells with ALK tyrosine kinase inhibitors (TKIs) led to up-regulation of ESRP1 and E-cadherin, thus reverting the phenotype from mesenchymal to epithelial (MET). Consistently, ESRP1 knock-down impaired E-cadherin up-regulation upon ALK inhibition, whereas enforced expression of ESRP1 was sufficient to increase E-cadherin expression. These findings demonstrate an ALK oncogenic activity in the regulation of an EMT phenotype in a subset of NSCLC with potential implications for the biology of ALK-rearranged NSCLC in terms of metastatic propensity and resistance to therapy.
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Affiliation(s)
- Claudia Voena
- Department of Molecular Biotechnology and Health Sciences, University of Torino, Torino, Italy.,Center for Experimental Research and Medical Studies (CERMS), Città della Salute e della Scienza, Torino, Italy.,Department of Pathology, Children's Hospital and Harvard Medical School, Boston, MA, USA
| | - Lydia M Varesio
- Department of Molecular Biotechnology and Health Sciences, University of Torino, Torino, Italy.,Center for Experimental Research and Medical Studies (CERMS), Città della Salute e della Scienza, Torino, Italy
| | - Liye Zhang
- Section of Computational Biomedicine, Boston University School of Medicine, Boston, MA, USA
| | - Matteo Menotti
- Department of Molecular Biotechnology and Health Sciences, University of Torino, Torino, Italy.,Center for Experimental Research and Medical Studies (CERMS), Città della Salute e della Scienza, Torino, Italy
| | - Teresa Poggio
- Department of Molecular Biotechnology and Health Sciences, University of Torino, Torino, Italy.,Center for Experimental Research and Medical Studies (CERMS), Città della Salute e della Scienza, Torino, Italy
| | - Elena Panizza
- Department of Molecular Biotechnology and Health Sciences, University of Torino, Torino, Italy.,Center for Experimental Research and Medical Studies (CERMS), Città della Salute e della Scienza, Torino, Italy
| | - Qi Wang
- Department of Pathology, Children's Hospital and Harvard Medical School, Boston, MA, USA
| | - Valerio G Minero
- Department of Molecular Biotechnology and Health Sciences, University of Torino, Torino, Italy.,Center for Experimental Research and Medical Studies (CERMS), Città della Salute e della Scienza, Torino, Italy
| | - Sharmila Fagoonee
- Department of Molecular Biotechnology and Health Sciences, University of Torino, Torino, Italy.,Molecular Biotechnology Center, University of Torino, Torino, Italy
| | - Mara Compagno
- Department of Molecular Biotechnology and Health Sciences, University of Torino, Torino, Italy.,Center for Experimental Research and Medical Studies (CERMS), Città della Salute e della Scienza, Torino, Italy.,Department of Pathology, Children's Hospital and Harvard Medical School, Boston, MA, USA
| | - Fiorella Altruda
- Department of Molecular Biotechnology and Health Sciences, University of Torino, Torino, Italy.,Molecular Biotechnology Center, University of Torino, Torino, Italy
| | - Stefano Monti
- Section of Computational Biomedicine, Boston University School of Medicine, Boston, MA, USA
| | - Roberto Chiarle
- Department of Molecular Biotechnology and Health Sciences, University of Torino, Torino, Italy.,Center for Experimental Research and Medical Studies (CERMS), Città della Salute e della Scienza, Torino, Italy.,Department of Pathology, Children's Hospital and Harvard Medical School, Boston, MA, USA
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21
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Rohacek AM, Bebee TW, Tilton RK, Radens CM, McDermott-Roe C, Peart N, Kaur M, Zaykaner M, Cieply B, Musunuru K, Barash Y, Germiller JA, Krantz ID, Carstens RP, Epstein DJ. ESRP1 Mutations Cause Hearing Loss due to Defects in Alternative Splicing that Disrupt Cochlear Development. Dev Cell 2017; 43:318-331.e5. [PMID: 29107558 PMCID: PMC5687886 DOI: 10.1016/j.devcel.2017.09.026] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2016] [Revised: 08/15/2017] [Accepted: 08/26/2017] [Indexed: 12/30/2022]
Abstract
Alternative splicing contributes to gene expression dynamics in many tissues, yet its role in auditory development remains unclear. We performed whole-exome sequencing in individuals with sensorineural hearing loss (SNHL) and identified pathogenic mutations in Epithelial Splicing-Regulatory Protein 1 (ESRP1). Patient-derived induced pluripotent stem cells showed alternative splicing defects that were restored upon repair of an ESRP1 mutant allele. To determine how ESRP1 mutations cause hearing loss, we evaluated Esrp1-/- mouse embryos and uncovered alterations in cochlear morphogenesis, auditory hair cell differentiation, and cell fate specification. Transcriptome analysis revealed impaired expression and splicing of genes with essential roles in cochlea development and auditory function. Aberrant splicing of Fgfr2 blocked stria vascularis formation due to erroneous ligand usage, which was corrected by reducing Fgf9 gene dosage. These findings implicate mutations in ESRP1 as a cause of SNHL and demonstrate the complex interplay between alternative splicing, inner ear development, and auditory function.
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Affiliation(s)
- Alex M Rohacek
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Clinical Research Building, Room 463, 415 Curie Boulevard, Philadelphia, PA 19104, USA
| | - Thomas W Bebee
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Richard K Tilton
- Division of Human Genetics, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Caleb M Radens
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Clinical Research Building, Room 463, 415 Curie Boulevard, Philadelphia, PA 19104, USA
| | - Chris McDermott-Roe
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Natoya Peart
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Maninder Kaur
- Division of Human Genetics, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Michael Zaykaner
- Division of Human Genetics, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Benjamin Cieply
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Kiran Musunuru
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Yoseph Barash
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Clinical Research Building, Room 463, 415 Curie Boulevard, Philadelphia, PA 19104, USA
| | - John A Germiller
- Division of Pediatric Otolaryngology, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Ian D Krantz
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Clinical Research Building, Room 463, 415 Curie Boulevard, Philadelphia, PA 19104, USA; Division of Human Genetics, The Children's Hospital of Philadelphia, Philadelphia, PA, USA.
| | - Russ P Carstens
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
| | - Douglas J Epstein
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Clinical Research Building, Room 463, 415 Curie Boulevard, Philadelphia, PA 19104, USA.
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22
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Mager LF, Koelzer VH, Stuber R, Thoo L, Keller I, Koeck I, Langenegger M, Simillion C, Pfister SP, Faderl M, Genitsch V, Tcymbarevich I, Juillerat P, Li X, Xia Y, Karamitopoulou E, Lyck R, Zlobec I, Hapfelmeier S, Bruggmann R, McCoy KD, Macpherson AJ, Müller C, Beutler B, Krebs P. The ESRP1-GPR137 axis contributes to intestinal pathogenesis. eLife 2017; 6:28366. [PMID: 28975893 PMCID: PMC5665647 DOI: 10.7554/elife.28366] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2017] [Accepted: 09/25/2017] [Indexed: 12/19/2022] Open
Abstract
Aberrant alternative pre-mRNA splicing (AS) events have been associated with several disorders. However, it is unclear whether deregulated AS directly contributes to disease. Here, we reveal a critical role of the AS regulator epithelial splicing regulator protein 1 (ESRP1) for intestinal homeostasis and pathogenesis. In mice, reduced ESRP1 function leads to impaired intestinal barrier integrity, increased susceptibility to colitis and altered colorectal cancer (CRC) development. Mechanistically, these defects are produced in part by modified expression of ESRP1-specific Gpr137 isoforms differently activating the Wnt pathway. In humans, ESRP1 is downregulated in inflamed biopsies from inflammatory bowel disease patients. ESRP1 loss is an adverse prognostic factor in CRC. Furthermore, generation of ESRP1-dependent GPR137 isoforms is altered in CRC and expression of a specific GPR137 isoform predicts CRC patient survival. These findings indicate a central role of ESRP1-regulated AS for intestinal barrier integrity. Alterations in ESRP1 function or expression contribute to intestinal pathology.
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Affiliation(s)
- Lukas Franz Mager
- Institute of Pathology, University of Bern, Bern, Switzerland.,Graduate School for Cellular and Biomedical Sciences, University of Bern, Bern, Switzerland
| | | | - Regula Stuber
- Institute of Pathology, University of Bern, Bern, Switzerland
| | - Lester Thoo
- Institute of Pathology, University of Bern, Bern, Switzerland.,Graduate School for Cellular and Biomedical Sciences, University of Bern, Bern, Switzerland
| | - Irene Keller
- Department of BioMedical Research, University of Bern, Bern, Switzerland.,Interfaculty Bioinformatics Unit and Swiss Institute of Bioinformatics, University of Bern, Bern, Switzerland
| | - Ivonne Koeck
- Institute of Pathology, University of Bern, Bern, Switzerland.,Graduate School for Cellular and Biomedical Sciences, University of Bern, Bern, Switzerland.,Department of BioMedical Research, University of Bern, Bern, Switzerland
| | | | - Cedric Simillion
- Department of BioMedical Research, University of Bern, Bern, Switzerland.,Interfaculty Bioinformatics Unit and Swiss Institute of Bioinformatics, University of Bern, Bern, Switzerland
| | - Simona P Pfister
- Graduate School for Cellular and Biomedical Sciences, University of Bern, Bern, Switzerland.,Institute for Infectious Diseases, University of Bern, Bern, Switzerland
| | - Martin Faderl
- Institute of Pathology, University of Bern, Bern, Switzerland.,Graduate School for Cellular and Biomedical Sciences, University of Bern, Bern, Switzerland
| | - Vera Genitsch
- Institute of Pathology, University of Bern, Bern, Switzerland
| | - Irina Tcymbarevich
- Division of Gastroenterology and Hepatology, University Hospital Zurich, Zurich, Switzerland
| | - Pascal Juillerat
- Department of Gastroenterology, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland
| | - Xiaohong Li
- Center for Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, United States
| | - Yu Xia
- Department of Genetics, The Scripps Research Institute, La Jolla, United States
| | | | - Ruth Lyck
- Theodor Kocher Institute, University of Bern, Bern, Switzerland
| | - Inti Zlobec
- Institute of Pathology, University of Bern, Bern, Switzerland
| | | | - Rémy Bruggmann
- Interfaculty Bioinformatics Unit and Swiss Institute of Bioinformatics, University of Bern, Bern, Switzerland
| | - Kathy D McCoy
- Department of BioMedical Research, University of Bern, Bern, Switzerland
| | - Andrew J Macpherson
- Department of BioMedical Research, University of Bern, Bern, Switzerland.,Department of Gastroenterology, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland
| | | | - Bruce Beutler
- Center for Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, United States
| | - Philippe Krebs
- Institute of Pathology, University of Bern, Bern, Switzerland
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23
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Neumann DP, Goodall GJ, Gregory PA. Regulation of splicing and circularisation of RNA in epithelial mesenchymal plasticity. Semin Cell Dev Biol 2017; 75:50-60. [PMID: 28789987 DOI: 10.1016/j.semcdb.2017.08.008] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2017] [Revised: 07/28/2017] [Accepted: 08/03/2017] [Indexed: 12/13/2022]
Abstract
Interconversions between epithelial and mesenchymal states, often referred to as epithelial mesenchymal transition (EMT) and its reverse MET, play important roles in embryonic development and are recapitulated in various adult pathologies including cancer progression. These conversions are regulated by complex transcriptional and post-transcriptional mechanisms including programs of alternative splicing which are orchestrated by specific splicing factors. This review will focus on the latest developments in our understanding of the splicing factors regulating epithelial mesenchymal plasticity associated with cancer progression and the induction of pluripotency, including potential roles for circular RNAs (circRNAs) which have been recently implicated in these processes.
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Affiliation(s)
- Daniel P Neumann
- Centre for Cancer Biology, University of South Australia and SA Pathology, Adelaide, SA, 5000, Australia
| | - Gregory J Goodall
- Centre for Cancer Biology, University of South Australia and SA Pathology, Adelaide, SA, 5000, Australia; Discipline of Medicine, The University of Adelaide, Adelaide, SA 5005, Australia; School of Molecular and Biomedical Science, The University of Adelaide, Adelaide, SA 5005, Australia
| | - Philip A Gregory
- Centre for Cancer Biology, University of South Australia and SA Pathology, Adelaide, SA, 5000, Australia; Discipline of Medicine, The University of Adelaide, Adelaide, SA 5005, Australia.
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24
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Chen Q, Hu G. Post-transcriptional regulation of the pluripotent state. Curr Opin Genet Dev 2017; 46:15-23. [PMID: 28654825 DOI: 10.1016/j.gde.2017.06.010] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2017] [Revised: 04/17/2017] [Accepted: 06/08/2017] [Indexed: 12/20/2022]
Abstract
Pluripotency describes the developmental capacity to give rise to all cell types in the adult body. A comprehensive understanding of the molecular mechanisms that regulate pluripotency is important for both basic and translational research. While earlier studies mostly focused on signaling pathways, transcriptional regulation, and epigenetic modifications, recent investigations showed that RNA binding proteins, RNA processing machineries, and regulatory RNA molecules also play essential roles. Here, we provide a concise review on the latest findings and developments in post-transcriptional regulation of the pluripotent state.
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Affiliation(s)
- Qing Chen
- Epigenetics and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, RTP, NC, United States.
| | - Guang Hu
- Epigenetics and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, RTP, NC, United States.
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25
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Alternative splicing regulates distinct subcellular localization of Epithelial splicing regulatory protein 1 (Esrp1) isoforms. Sci Rep 2017. [PMID: 28634384 PMCID: PMC5478600 DOI: 10.1038/s41598-017-03180-3] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
Abstract
Epithelial-Splicing-Regulatory-Protein 1 (Esrp1) is a cell-type specific RNA-binding protein (RBP) that is essential for mammalian development through maintenance of epithelial cell properties including barrier function. Esrp1 also regulates splicing during the epithelial to mesenchymal transition (EMT). It contains three highly conserved RNA recognition motifs (RRMs) in the absence of other clearly defined protein domains. Esrp1 itself is also alternatively spliced to produce multiple protein isoforms. Here we determined that two competing alternative 5' splice sites in exon 12 yield Esrp1 isoforms with differential nucleocytoplasmic localization. We carried out a detailed characterization of the Esrp1 peptide that is sufficient to confer nuclear localization. Furthermore, we identified splice variants encoding distinct nuclear and cytoplasmic isoforms of fusilli, the D. Melanogaster Esrp1 ortholog. Our observations demonstrate that the production of both nuclear and cytoplasmic Esrp1 isoforms through alternative splicing is phylogenetically conserved; strongly suggesting it is biologically significant. Thus, while previous studies have described extensive regulation by nuclear Esrp1 to promote epithelial specific splicing, it will be of great interest to study the contribution of cytoplasmic Esrp1 in maintenance of epithelial cell functions.
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26
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Kim YD, Lee J, Kim HS, Lee MO, Son MY, Yoo CH, Choi JK, Lee SC, Cho YS. The unique spliceosome signature of human pluripotent stem cells is mediated by SNRPA1, SNRPD1, and PNN. Stem Cell Res 2017; 22:43-53. [PMID: 28595116 DOI: 10.1016/j.scr.2017.05.010] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/15/2017] [Revised: 05/25/2017] [Accepted: 05/26/2017] [Indexed: 12/21/2022] Open
Abstract
Spliceosomes are the core host of pre-mRNA splicing, allowing multiple protein isoforms to be produced from a single gene. Herein, we reveal that spliceosomes are more abundant in human pluripotent stem cells (hPSs), including human embryonic stem cells (hESs) and human induced pluripotent stem cells (hiPSs), than non-hPSs, and their presence is associated with high transcriptional activity. Supportively, spliceosomal components involved in the catalytically active pre-mRNA splicing step were mainly co-localized with hPS spliceosomes. By profiling the gene expression of 342 selected splicing factors, we found that 71 genes were significantly altered during the reprogramming of human somatic cells into hiPSs. Among them, SNRPA1, SNRPD1, and PNN were significantly up-regulated during the early stage of reprogramming, identified as hub genes by interaction network and cluster analysis. SNRPA1, SNRPD1, or PNN depletion led to a pronounced loss of pluripotency and significantly blocked hiPS generation. SNRPA1, SNRPD1, and PNN co-localized with the hPS spliceosomes, physically interacted with each other, and positively influenced the appearance of hPS spliceosomes. Our data suggest that SNRPA1, SNRPD1, and PNN are key players in the regulation of pluripotency-specific spliceosome assembly and the acquisition and maintenance of pluripotency.
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Affiliation(s)
- Young-Dae Kim
- Stem Cell Research Laboratory, Immunotherapy Convergence Research Center, Korea Research Institute of Bioscience and Biotechnology, 125 Gwahak-ro, Yuseong-gu, Daejeon, Republic of Korea
| | - Jungwoon Lee
- Stem Cell Research Laboratory, Immunotherapy Convergence Research Center, Korea Research Institute of Bioscience and Biotechnology, 125 Gwahak-ro, Yuseong-gu, Daejeon, Republic of Korea
| | - Han-Seop Kim
- Stem Cell Research Laboratory, Immunotherapy Convergence Research Center, Korea Research Institute of Bioscience and Biotechnology, 125 Gwahak-ro, Yuseong-gu, Daejeon, Republic of Korea
| | - Mi-Ok Lee
- Stem Cell Research Laboratory, Immunotherapy Convergence Research Center, Korea Research Institute of Bioscience and Biotechnology, 125 Gwahak-ro, Yuseong-gu, Daejeon, Republic of Korea
| | - Mi-Young Son
- Stem Cell Research Center, Korea Research Institute of Bioscience and Biotechnology, 125 Gwahak-ro, Yuseong-gu, Daejeon, Republic of Korea
| | - Chae Hwa Yoo
- Stem Cell Research Laboratory, Immunotherapy Convergence Research Center, Korea Research Institute of Bioscience and Biotechnology, 125 Gwahak-ro, Yuseong-gu, Daejeon, Republic of Korea
| | - Jung-Kyun Choi
- Stem Cell Research Laboratory, Immunotherapy Convergence Research Center, Korea Research Institute of Bioscience and Biotechnology, 125 Gwahak-ro, Yuseong-gu, Daejeon, Republic of Korea; Department of Bioscience, KRIBB School, University of Science & Technology, 113 Gwahak-ro, Yuseong-gu, Daejeon 34113, Republic of Korea
| | - Sang Chul Lee
- Research Center for Metabolic Regulation, Korea Research Institute of Bioscience and Biotechnology, 125 Gwahak-ro, Yuseong-gu, Daejeon, Republic of Korea
| | - Yee Sook Cho
- Stem Cell Research Laboratory, Immunotherapy Convergence Research Center, Korea Research Institute of Bioscience and Biotechnology, 125 Gwahak-ro, Yuseong-gu, Daejeon, Republic of Korea; Department of Bioscience, KRIBB School, University of Science & Technology, 113 Gwahak-ro, Yuseong-gu, Daejeon 34113, Republic of Korea.
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27
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Sagnol S, Marchal S, Yang Y, Allemand F, de Santa Barbara P. Epithelial Splicing Regulatory Protein 1 (ESRP1) is a new regulator of stomach smooth muscle development and plasticity. Dev Biol 2016; 414:207-18. [PMID: 27108394 DOI: 10.1016/j.ydbio.2016.04.015] [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: 02/11/2016] [Revised: 04/08/2016] [Accepted: 04/19/2016] [Indexed: 12/22/2022]
Abstract
In vertebrates, stomach smooth muscle development is a complex process that involves the tight transcriptional or post-transcriptional regulation of different signalling pathways. Here, we identified the RNA-binding protein Epithelial Splicing Regulatory Protein 1 (ESRP1) as an early marker of developing and undifferentiated stomach mesenchyme. Using a gain-of-function approach, we found that in chicken embryos, sustained expression of ESRP1 impairs stomach smooth muscle cell (SMC) differentiation and FGFR2 splicing profile. ESRP1 overexpression in primary differentiated stomach SMCs induced their dedifferentiation, promoted specific-FGFR2b splicing and decreased FGFR2c-dependent activity. Moreover, co-expression of ESRP1 and RBPMS2, another RNA-binding protein that regulates SMC plasticity and Bone Morphogenetic Protein (BMP) pathway inhibition, synergistically promoted SMC dedifferentiation. Finally, we also demonstrated that ESRP1 interacts with RBPMS2 and that RBPMS2-mediated SMC dedifferentiation requires ESRP1. Altogether, these results show that ESRP1 is expressed also in undifferentiated stomach mesenchyme and demonstrate its role in SMC development and plasticity.
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Affiliation(s)
- Sébastien Sagnol
- PhyMedExp, INSERM U1046, CNRS UMR 9214, University of Montpellier, 34295 Montpellier cedex 5, France
| | - Stéphane Marchal
- PhyMedExp, INSERM U1046, CNRS UMR 9214, University of Montpellier, 34295 Montpellier cedex 5, France
| | - Yinshan Yang
- Centre de Biochimie Structurale, CNRS UMR 5048, INSERM U1054, University of Montpellier, 34295 Montpellier cedex 5, France
| | - Frédéric Allemand
- Centre de Biochimie Structurale, CNRS UMR 5048, INSERM U1054, University of Montpellier, 34295 Montpellier cedex 5, France
| | - Pascal de Santa Barbara
- PhyMedExp, INSERM U1046, CNRS UMR 9214, University of Montpellier, 34295 Montpellier cedex 5, France.
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28
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Hayakawa A, Saitoh M, Miyazawa K. Dual Roles for Epithelial Splicing Regulatory Proteins 1 (ESRP1) and 2 (ESRP2) in Cancer Progression. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2016; 925:33-40. [DOI: 10.1007/5584_2016_50] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
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29
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Abstract
Stem cells are pivotal for development and tissue homeostasis of multicellular animals, and the quest for a gene toolkit associated with the emergence of stem cells in a common ancestor of all metazoans remains a major challenge for evolutionary biology. We reconstructed the conserved gene repertoire of animal stem cells by transcriptomic profiling of totipotent archeocytes in the demosponge Ephydatia fluviatilis and by tracing shared molecular signatures with flatworm and Hydra stem cells. Phylostratigraphy analyses indicated that most of these stem-cell genes predate animal origin, with only few metazoan innovations, notably including several partners of the Piwi machinery known to promote genome stability. The ancestral stem-cell transcriptome is strikingly poor in transcription factors. Instead, it is rich in RNA regulatory actors, including components of the "germ-line multipotency program" and many RNA-binding proteins known as critical regulators of mammalian embryonic stem cells.
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30
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Abstract
Establishment, maintenance, and exit from pluripotency require precise coordination of a cell's molecular machinery. Substantial headway has been made in deciphering many aspects of this elaborate system, particularly with respect to epigenetics, transcription, and noncoding RNAs. Less attention has been paid to posttranscriptional regulatory processes such as alternative splicing, RNA processing and modification, nuclear export, regulation of transcript stability, and translation. Here, we introduce the RNA binding proteins that enable the posttranscriptional regulation of gene expression, summarizing current and ongoing research on their roles at different regulatory points and discussing how they help script the fate of pluripotent stem cells.
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Affiliation(s)
- Julia Ye
- The Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, Center for Reproductive Sciences, University of California, San Francisco, San Francisco, CA 94143, USA; Department of Urology, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Robert Blelloch
- The Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, Center for Reproductive Sciences, University of California, San Francisco, San Francisco, CA 94143, USA; Department of Urology, University of California, San Francisco, San Francisco, CA 94143, USA.
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31
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Abstract
The expression of gamma-glutamyl transpeptidase (GGT) is essential to maintaining cysteine levels in the body. GGT is a cell surface enzyme that hydrolyzes the gamma-glutamyl bond of extracellular reduced and oxidized glutathione, initiating their cleavage into glutamate, cysteine (cystine), and glycine. GGT is normally expressed on the apical surface of ducts and glands, salvaging the amino acids from glutathione in the ductal fluids. GGT in tumors is expressed over the entire cell membrane and provides tumors with access to additional cysteine and cystine from reduced and oxidized glutathione in the blood and interstitial fluid. Cysteine is rate-limiting for glutathione synthesis in cells under oxidative stress. The induction of GGT is observed in tumors with elevated levels of intracellular glutathione. Studies in models of hepatocarcinogenesis show that GGT expression in foci of preneoplastic hepatocytes provides a selective advantage to the cells during tumor promotion with agents that deplete intracellular glutathione. Similarly, expression of GGT in tumors enables cells to maintain elevated levels of intracellular glutathione and to rapidly replenish glutathione during treatment with prooxidant anticancer therapy. In the clinic, the expression of GGT in tumors is correlated with drug resistance. The inhibitors of GGT block GGT-positive tumors from accessing the cysteine in extracellular glutathione. They also inhibit GGT activity in the kidney, which results in the excretion of GSH in the urine and a rapid decrease in blood cysteine levels, leading to depletion of intracellular GSH in both GGT-positive and GGT-negative tumors. GGT inhibitors are being developed for clinical use to sensitize tumors to chemotherapy.
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Affiliation(s)
- Marie H Hanigan
- Department of Cell Biology, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma, USA.
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32
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Abstract
Embryonic stem cell maintenance, differentiation, and somatic cell reprogramming require the interplay of multiple pluripotency factors, epigenetic remodelers, and extracellular signaling pathways. RNA-binding proteins (RBPs) are involved in a wide range of regulatory pathways, from RNA metabolism to epigenetic modifications. In recent years we have witnessed more and more studies on the discovery of new RBPs and the assessment of their functions in a variety of biological systems, including stem cells. We review the current studies on RBPs and focus on those that have functional implications in pluripotency, differentiation, and/or reprogramming in both the human and mouse systems.
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33
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Ishii H, Saitoh M, Sakamoto K, Kondo T, Katoh R, Tanaka S, Motizuki M, Masuyama K, Miyazawa K. Epithelial splicing regulatory proteins 1 (ESRP1) and 2 (ESRP2) suppress cancer cell motility via different mechanisms. J Biol Chem 2014; 289:27386-99. [PMID: 25143390 DOI: 10.1074/jbc.m114.589432] [Citation(s) in RCA: 119] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
ESRP1 (epithelial splicing regulatory protein 1) and ESRP2 regulate alternative splicing events associated with epithelial phenotypes of cells, and both are down-regulated during the epithelial-mesenchymal transition. However, little is known about their expression and functions during carcinogenesis. In this study, we found that expression of both ESRP1 and ESRP2 is plastic: during oral squamous cell carcinogenesis, these proteins are up-regulated relative to their levels in normal epithelium but down-regulated in invasive fronts. Importantly, ESRP1 and ESRP2 are re-expressed in the lymph nodes, where carcinoma cells metastasize and colonize. In head and neck carcinoma cell lines, ESRP1 and ESRP2 suppress cancer cell motility through distinct mechanisms: knockdown of ESRP1 affects the dynamics of the actin cytoskeleton through induction of Rac1b, whereas knockdown of ESRP2 attenuates cell-cell adhesion through increased expression of epithelial-mesenchymal transition-associated transcription factors. Down-regulation of ESRP1 and ESRP2 is thus closely associated with a motile phenotype of cancer cells.
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Affiliation(s)
- Hiroki Ishii
- From the Departments of Biochemistry, Otolaryngology, Head and Neck Surgery, and
| | | | - Kei Sakamoto
- the Section of Oral Pathology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Bunkyo-ku, Tokyo 113-0034, Japan
| | - Tetsuo Kondo
- Human Pathology, Interdisciplinary Graduate School of Medicine and Engineering, University of Yamanashi, Yamanashi 409-3898 and
| | - Ryohei Katoh
- Human Pathology, Interdisciplinary Graduate School of Medicine and Engineering, University of Yamanashi, Yamanashi 409-3898 and
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34
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How chemistry supports cell biology: the chemical toolbox at your service. Trends Cell Biol 2014; 24:751-60. [PMID: 25108565 DOI: 10.1016/j.tcb.2014.07.002] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2014] [Revised: 06/10/2014] [Accepted: 07/10/2014] [Indexed: 01/07/2023]
Abstract
Chemical biology is a young and rapidly developing scientific field. In this field, chemistry is inspired by biology to create various tools to monitor and modulate biochemical and cell biological processes. Chemical contributions such as small-molecule inhibitors and activity-based probes (ABPs) can provide new and unique insights into previously unexplored cellular processes. This review provides an overview of recent breakthroughs in chemical biology that are likely to have a significant impact on cell biology. We also discuss the application of several chemical tools in cell biology research.
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