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Acosta-Cárdenas J, Jiménez-García LF, Cruz-Gómez SDJ, Mendoza-von der Borch AP, Segura-Valdez MDL. Microscopic Analysis of Nuclear Speckles in a Viviparous Reptile. Int J Mol Sci 2024; 25:5281. [PMID: 38791320 PMCID: PMC11120696 DOI: 10.3390/ijms25105281] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2024] [Revised: 05/10/2024] [Accepted: 05/10/2024] [Indexed: 05/26/2024] Open
Abstract
Nuclear speckles are compartments enriched in splicing factors present in the nucleoplasm of eucaryote cells. Speckles have been studied in mammalian culture and tissue cells, as well as in some non-mammalian vertebrate cells and invertebrate oocytes. In mammals, their morphology is linked to the transcriptional and splicing activities of the cell through a recruitment mechanism. In rats, speckle morphology depends on the hormonal cycle. In the present work, we explore whether a similar situation is also present in non-mammalian cells during the reproductive cycle. We studied the speckled pattern in several tissues of a viviparous reptile, the lizard Sceloporus torquatus, during two different stages of reproduction. We used immunofluorescence staining against splicing factors in hepatocytes and oviduct epithelium cells and fluorescence and confocal microscopy, as well as ultrastructural immunolocalization and EDTA contrast in Transmission Electron Microscopy. The distribution of splicing factors in the nucleoplasm of oviductal cells and hepatocytes coincides with the nuclear-speckled pattern described in mammals. Ultrastructurally, those cell types display Interchromatin Granule Clusters and Perichromatin Fibers. In addition, the morphology of speckles varies in oviduct cells at the two stages of the reproductive cycle analyzed, paralleling the phenomenon observed in the rat. The results show that the morphology of speckles in reptile cells depends upon the reproductive stage as it occurs in mammals.
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Affiliation(s)
- Jeniffer Acosta-Cárdenas
- Laboratorio de Nanobiología Celular, Departamento de Biología Celular, Facultad de Ciencias, Universidad Nacional Autónoma de México—UNAM, Mexico City 04510, Mexico; (J.A.-C.); (L.F.J.-G.); (S.d.J.C.-G.); (A.P.M.-v.d.B.)
- Posgrado en Ciencias Biológicas, Universidad Nacional Autónoma de México, Mexico City 04510, Mexico
| | - Luis Felipe Jiménez-García
- Laboratorio de Nanobiología Celular, Departamento de Biología Celular, Facultad de Ciencias, Universidad Nacional Autónoma de México—UNAM, Mexico City 04510, Mexico; (J.A.-C.); (L.F.J.-G.); (S.d.J.C.-G.); (A.P.M.-v.d.B.)
| | - Sarai de Jesús Cruz-Gómez
- Laboratorio de Nanobiología Celular, Departamento de Biología Celular, Facultad de Ciencias, Universidad Nacional Autónoma de México—UNAM, Mexico City 04510, Mexico; (J.A.-C.); (L.F.J.-G.); (S.d.J.C.-G.); (A.P.M.-v.d.B.)
| | - Ana Paulina Mendoza-von der Borch
- Laboratorio de Nanobiología Celular, Departamento de Biología Celular, Facultad de Ciencias, Universidad Nacional Autónoma de México—UNAM, Mexico City 04510, Mexico; (J.A.-C.); (L.F.J.-G.); (S.d.J.C.-G.); (A.P.M.-v.d.B.)
| | - María de Lourdes Segura-Valdez
- Laboratorio de Nanobiología Celular, Departamento de Biología Celular, Facultad de Ciencias, Universidad Nacional Autónoma de México—UNAM, Mexico City 04510, Mexico; (J.A.-C.); (L.F.J.-G.); (S.d.J.C.-G.); (A.P.M.-v.d.B.)
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Alexander KA, Yu R, Skuli N, Coffey NJ, Nguyen S, Faunce C, Huang H, Dardani IP, Good AL, Lim J, Li C, Biddle N, Joyce EF, Raj A, Lee D, Keith B, Simon MC, Berger SL. Nuclear speckles regulate HIF-2α programs and correlate with patient survival in kidney cancer. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.14.557228. [PMID: 37745397 PMCID: PMC10515914 DOI: 10.1101/2023.09.14.557228] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/26/2023]
Abstract
Nuclear speckles are membrane-less bodies within the cell nucleus enriched in RNA biogenesis, processing, and export factors. In this study we investigated speckle phenotype variation in human cancer, finding a reproducible speckle signature, based on RNA expression of speckle-resident proteins, across >20 cancer types. Of these, clear cell renal cell carcinoma (ccRCC) exhibited a clear correlation between the presence of this speckle expression signature, imaging-based speckle phenotype, and clinical outcomes. ccRCC is typified by hyperactivation of the HIF-2α transcription factor, and we demonstrate here that HIF-2α drives physical association of a select subset of its target genes with nuclear speckles. Disruption of HIF-2α-driven speckle association via deletion of its speckle targeting motifs (STMs)-defined in this study-led to defective induction of speckle-associating HIF-2α target genes without impacting non-speckle-associating HIF-2α target genes. We further identify the RNA export complex, TREX, as being specifically altered in speckle signature, and knockdown of key TREX component, ALYREF, also compromises speckle-associated gene expression. By integrating tissue culture functional studies with tumor genomic and imaging analysis, we show that HIF-2α gene regulatory programs are impacted by specific manipulation of speckle phenotype and by abrogation of speckle targeting abilities of HIF-2α. These findings suggest that, in ccRCC, a key biological function of nuclear speckles is to modulate expression of a specific subset of HIF-2α-regulated target genes that, in turn, influence patient outcomes. We also identify STMs in other transcription factors, suggesting that DNA-speckle targeting may be a general mechanism of gene regulation.
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Affiliation(s)
- Katherine A. Alexander
- Penn Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Department of Cell and Developmental Biology, Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Ruofan Yu
- Penn Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Department of Cell and Developmental Biology, Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Nicolas Skuli
- Department of Cell and Developmental Biology, Perelman School of Medicine, Philadelphia, PA 19104, USA
- Stem Cell and Xenograft Core, Department of Medicine – Division of Hematology and Oncology, University of Pennsylvania, Philadelphia, PA 19104, USA
- Abramson Family Cancer Research Institute, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Nathan J. Coffey
- Department of Cell and Developmental Biology, Perelman School of Medicine, Philadelphia, PA 19104, USA
- Abramson Family Cancer Research Institute, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Son Nguyen
- Penn Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Christine Faunce
- Penn Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Department of Cell and Developmental Biology, Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Hua Huang
- Penn Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Department of Cell and Developmental Biology, Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Ian P. Dardani
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Austin L. Good
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Joan Lim
- Penn Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Department of Cell and Developmental Biology, Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Catherine Li
- Penn Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Department of Cell and Developmental Biology, Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Nicholas Biddle
- Penn Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Department of Cell and Developmental Biology, Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Eric F. Joyce
- Penn Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Arjun Raj
- Penn Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Daniel Lee
- Division of Urology, Department of Surgery, Perelman School of Medicine, University of Pennsylvania, Philadelphia PA 19104, USA
| | - Brian Keith
- Department of Cell and Developmental Biology, Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - M. Celeste Simon
- Department of Cell and Developmental Biology, Perelman School of Medicine, Philadelphia, PA 19104, USA
- Abramson Family Cancer Research Institute, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Shelley L. Berger
- Penn Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Department of Cell and Developmental Biology, Perelman School of Medicine, Philadelphia, PA 19104, USA
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Department of Biology, School of Arts and Sciences, University of Pennsylvania, Philadelphia, PA 19104, USA
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Dreher RD, Theisen ER. Lysine specific demethylase 1 is a molecular driver and therapeutic target in sarcoma. Front Oncol 2023; 12:1076581. [PMID: 36686841 PMCID: PMC9846348 DOI: 10.3389/fonc.2022.1076581] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Accepted: 12/07/2022] [Indexed: 01/05/2023] Open
Abstract
Sarcomas are a diverse group of tumors with numerous oncogenic drivers, and display varied clinical behaviors and prognoses. This complexity makes diagnosis and the development of new and effective treatments challenging. An incomplete understanding of both cell of origin and the biological drivers of sarcomas complicates efforts to develop clinically relevant model systems and find new molecular targets. Notably, the histone lysine specific demethylase 1 (LSD1) is overexpressed in a number of different sarcomas and is a potential therapeutic target in these malignancies. With the ability to modify histone marks, LSD1 is a key player in many protein complexes that epigenetically regulate gene expression. It is a largely context dependent enzyme, having vastly different and often opposing roles depending on the cellular environment and which interaction partners are involved. LSD1 has been implicated in the development of many different types of cancer, but its role in bone and soft tissue sarcomas remains poorly understood. In this review, we compiled what is known about the LSD1 function in various sarcomas, to determine where knowledge is lacking and to find what theme emerge to characterize how LSD1 is a key molecular driver in bone and soft tissue sarcoma. We further discuss the current clinical landscape for the development of LSD1 inhibitors and where sarcomas have been included in early clinical trials.
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Affiliation(s)
- Rachel D. Dreher
- Abigail Wexner Research Institute, Center for Childhood Cancer and Blood Diseases, Nationwide Children’s Hospital, Columbus, OH, United States
- Biomedical Sciences Graduate Program, College of Medicine, the Ohio State University, Columbus, OH, United States
| | - Emily R. Theisen
- Abigail Wexner Research Institute, Center for Childhood Cancer and Blood Diseases, Nationwide Children’s Hospital, Columbus, OH, United States
- Biomedical Sciences Graduate Program, College of Medicine, the Ohio State University, Columbus, OH, United States
- Department of Pediatrics, College of Medicine, The Ohio State University, Columbus, OH, United States
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Shaath H, Vishnubalaji R, Elango R, Kardousha A, Islam Z, Qureshi R, Alam T, Kolatkar PR, Alajez NM. Long non-coding RNA and RNA-binding protein interactions in cancer: Experimental and machine learning approaches. Semin Cancer Biol 2022; 86:325-345. [PMID: 35643221 DOI: 10.1016/j.semcancer.2022.05.013] [Citation(s) in RCA: 38] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Revised: 05/16/2022] [Accepted: 05/20/2022] [Indexed: 01/27/2023]
Abstract
Understanding the complex and specific roles played by non-coding RNAs (ncRNAs), which comprise the bulk of the genome, is important for understanding virtually every hallmark of cancer. This large group of molecules plays pivotal roles in key regulatory mechanisms in various cellular processes. Regulatory mechanisms, mediated by long non-coding RNA (lncRNA) and RNA-binding protein (RBP) interactions, are well documented in several types of cancer. Their effects are enabled through networks affecting lncRNA and RBP stability, RNA metabolism including N6-methyladenosine (m6A) and alternative splicing, subcellular localization, and numerous other mechanisms involved in cancer. In this review, we discuss the reciprocal interplay between lncRNAs and RBPs and their involvement in epigenetic regulation via histone modifications, as well as their key role in resistance to cancer therapy. Other aspects of RBPs including their structural domains, provide a deeper knowledge on how lncRNAs and RBPs interact and exert their biological functions. In addition, current state-of-the-art knowledge, facilitated by machine and deep learning approaches, unravels such interactions in better details to further enhance our understanding of the field, and the potential to harness RNA-based therapeutics as an alternative treatment modality for cancer are discussed.
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Affiliation(s)
- Hibah Shaath
- Translational Cancer and Immunity Center (TCIC), Qatar Biomedical Research Institute (QBRI), Hamad Bin Khalifa University (HBKU), Qatar Foundation (QF), PO Box 34110, Doha, Qatar
| | - Radhakrishnan Vishnubalaji
- Translational Cancer and Immunity Center (TCIC), Qatar Biomedical Research Institute (QBRI), Hamad Bin Khalifa University (HBKU), Qatar Foundation (QF), PO Box 34110, Doha, Qatar
| | - Ramesh Elango
- Translational Cancer and Immunity Center (TCIC), Qatar Biomedical Research Institute (QBRI), Hamad Bin Khalifa University (HBKU), Qatar Foundation (QF), PO Box 34110, Doha, Qatar
| | - Ahmed Kardousha
- College of Health & Life Sciences, Hamad Bin Khalifa University (HBKU), Qatar Foundation (QF), PO Box 34110, Doha, Qatar
| | - Zeyaul Islam
- Diabetes Research Center (DRC), Qatar Biomedical Research Institute (QBRI), Hamad Bin Khalifa University (HBKU), Qatar Foundation, PO Box 34110, Doha, Qatar
| | - Rizwan Qureshi
- College of Science and Engineering, Hamad Bin Khalifa University (HBKU), Qatar Foundation, PO Box 34110, Doha, Qatar
| | - Tanvir Alam
- College of Science and Engineering, Hamad Bin Khalifa University (HBKU), Qatar Foundation, PO Box 34110, Doha, Qatar
| | - Prasanna R Kolatkar
- College of Health & Life Sciences, Hamad Bin Khalifa University (HBKU), Qatar Foundation (QF), PO Box 34110, Doha, Qatar; Diabetes Research Center (DRC), Qatar Biomedical Research Institute (QBRI), Hamad Bin Khalifa University (HBKU), Qatar Foundation, PO Box 34110, Doha, Qatar
| | - Nehad M Alajez
- Translational Cancer and Immunity Center (TCIC), Qatar Biomedical Research Institute (QBRI), Hamad Bin Khalifa University (HBKU), Qatar Foundation (QF), PO Box 34110, Doha, Qatar; College of Health & Life Sciences, Hamad Bin Khalifa University (HBKU), Qatar Foundation (QF), PO Box 34110, Doha, Qatar.
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Faber GP, Nadav-Eliyahu S, Shav-Tal Y. Nuclear speckles - a driving force in gene expression. J Cell Sci 2022; 135:275909. [PMID: 35788677 DOI: 10.1242/jcs.259594] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Nuclear speckles are dynamic membraneless bodies located in the cell nucleus. They harbor RNAs and proteins, many of which are splicing factors, that together display complex biophysical properties dictating nuclear speckle formation and maintenance. Although these nuclear bodies were discovered decades ago, only recently has in-depth genomic analysis begun to unravel their essential functions in modulation of gene activity. Major advancements in genomic mapping techniques combined with microscopy approaches have enabled insights into the roles nuclear speckles may play in enhancing gene expression, and how gene positioning to specific nuclear landmarks can regulate gene expression and RNA processing. Some studies have drawn a link between nuclear speckles and disease. Certain maladies either involve nuclear speckles directly or dictate the localization and reorganization of many nuclear speckle factors. This is most striking during viral infection, as viruses alter the entire nuclear architecture and highjack host machinery. As discussed in this Review, nuclear speckles represent a fascinating target of study not only to reveal the links between gene positioning, genome subcompartments and gene activity, but also as a potential target for therapeutics.
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Affiliation(s)
- Gabriel P Faber
- The Mina and Everard Goodman Faculty of Life Sciences , Bar-Ilan University, Ramat Gan 5290002, Israel.,Institute of Nanotechnology , Bar-Ilan University, Ramat Gan 5290002, Israel
| | - Shani Nadav-Eliyahu
- The Mina and Everard Goodman Faculty of Life Sciences , Bar-Ilan University, Ramat Gan 5290002, Israel.,Institute of Nanotechnology , Bar-Ilan University, Ramat Gan 5290002, Israel
| | - Yaron Shav-Tal
- The Mina and Everard Goodman Faculty of Life Sciences , Bar-Ilan University, Ramat Gan 5290002, Israel.,Institute of Nanotechnology , Bar-Ilan University, Ramat Gan 5290002, Israel
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