1
|
Parajuli P, Craig DB, Gadgeel M, Bagla S, Wright RE, Chu R, Shanti CM, Thirunagari R, Grover SK, Ravindranath Y. Defective monocyte plasticity and altered cAMP pathway characterize USB1-mutated poikiloderma with neutropenia Clericuzio type. Br J Haematol 2024; 204:683-693. [PMID: 37779259 DOI: 10.1111/bjh.19128] [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: 06/13/2023] [Revised: 08/22/2023] [Accepted: 09/15/2023] [Indexed: 10/03/2023]
Abstract
Poikiloderma with neutropenia (PN) Clericuzio type (OMIM #604173) is a rare disease with areas of skin hyper- and hypopigmentation caused by biallelic USB1 variants. The current study was spurred by poor healing of a perianal tear wound in one affected child homozygous for c.266-1G>A (p.E90Sfster8) mutation, from a family reported previously. Treatment with G-CSF/CSF3 or GM-CSF/CSF2 transiently increased neutrophil/monocytes count with no effect on wound healing. Analysis of peripheral blood revealed a lack of non-classical (CD14+/- CD16+ ) monocytes, associated with a systemic inflammatory cytokine profile, in the two affected brothers. Importantly, despite normal expression of cognate receptors, monocytes from PN patients did not respond to M-CSF or IL-34 in vitro, as determined by cytokine secretion or CD16 expression. RNAseq of monocytes showed 293 differentially expressed genes, including significant downregulation of GATA2, AKAP6 and PDE4DIP that are associated with leucocyte differentiation and cyclic adenosine monophosphate (cAMP) signalling. Notably, the plasma cAMP was significantly low in the PN patients. Our study revealed a novel association of PN with a lack of non-classical monocyte population. The defects in monocyte plasticity may contribute to disease manifestations in PN and a defective cAMP signalling may be the primary effect of the splicing errors caused by USB1 mutation.
Collapse
Affiliation(s)
- Prahlad Parajuli
- Department of Pharmaceutical and Health Sciences, Eugene Applebaum College of Pharmacy, Wayne State University, Detroit, Michigan, USA
- Barbara Ann Karmanos Cancer Institute, Michigan, Detroit, USA
| | - Douglas B Craig
- Barbara Ann Karmanos Cancer Institute, Michigan, Detroit, USA
- Department of Pediatrics, Wayne State University School of Medicine, Detroit, Michigan, USA
| | - Manisha Gadgeel
- Children's Hospital of Michigan, Detroit Medical Center, Detroit, Michigan, USA
- Central Michigan University, Mt. Pleasant, Michigan, USA
| | - Shruti Bagla
- Department of Pediatrics, Wayne State University School of Medicine, Detroit, Michigan, USA
| | - Robert E Wright
- Department of Pharmaceutical and Health Sciences, Eugene Applebaum College of Pharmacy, Wayne State University, Detroit, Michigan, USA
| | - Roland Chu
- Children's Hospital of Michigan, Detroit Medical Center, Detroit, Michigan, USA
- Central Michigan University, Mt. Pleasant, Michigan, USA
| | - Christina M Shanti
- Children's Hospital of Michigan, Detroit Medical Center, Detroit, Michigan, USA
| | - Rajeev Thirunagari
- Children's Hospital of Michigan, Detroit Medical Center, Detroit, Michigan, USA
| | - Sudershan K Grover
- Children's Hospital of Michigan, Detroit Medical Center, Detroit, Michigan, USA
| | - Yaddanapudi Ravindranath
- Barbara Ann Karmanos Cancer Institute, Michigan, Detroit, USA
- Department of Pediatrics, Wayne State University School of Medicine, Detroit, Michigan, USA
- Children's Hospital of Michigan, Detroit Medical Center, Detroit, Michigan, USA
| |
Collapse
|
2
|
Martínez-Balsalobre E, García-Castillo J, García-Moreno D, Naranjo-Sánchez E, Fernández-Lajarín M, Blasco MA, Alcaraz-Pérez F, Mulero V, Cayuela ML. Telomerase RNA-based aptamers restore defective myelopoiesis in congenital neutropenic syndromes. Nat Commun 2023; 14:5912. [PMID: 37737237 PMCID: PMC10516865 DOI: 10.1038/s41467-023-41472-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Accepted: 09/06/2023] [Indexed: 09/23/2023] Open
Abstract
Telomerase RNA (TERC) has a noncanonical function in myelopoiesis binding to a consensus DNA binding sequence and attracting RNA polymerase II (RNA Pol II), thus facilitating myeloid gene expression. The CR4/CR5 domain of TERC is known to play this role, since a mutation of this domain found in dyskeratosis congenita (DC) patients decreases its affinity for RNA Pol II, impairing its myelopoietic activity as a result. In this study, we report that two aptamers, short single-stranded oligonucleotides, based on the CR4/CR5 domain were able to increase myelopoiesis without affecting erythropoiesis in zebrafish. Mechanistically, the aptamers functioned as full terc; that is, they increased the expression of master myeloid genes, independently of endogenous terc, by interacting with RNA Pol II and with the terc-binding sequences of the regulatory regions of such genes, enforcing their transcription. Importantly, aptamers harboring the CR4/CR5 mutation that was found in DC patients failed to perform all these functions. The therapeutic potential of the aptamers for treating neutropenia was demonstrated in several preclinical models. The findings of this study have identified two potential therapeutic agents for DC and other neutropenic patients.
Collapse
Affiliation(s)
- Elena Martínez-Balsalobre
- Grupo de Telomerasa, Cáncer y Envejecimiento, Hospital Clínico Universitario Virgen de la Arrixaca, 30120, Murcia, Spain
- Instituto Murciano de Investigación Biosanitaria (IMIB) Pascual Parrilla, 30120, Murcia, Spain
- Departamento de Biología Celular e Histología, Facultad de Biología, Universidad de Murcia, 30100, Murcia, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), ISCIII, 28029, Madrid, Spain
| | - Jesús García-Castillo
- Grupo de Telomerasa, Cáncer y Envejecimiento, Hospital Clínico Universitario Virgen de la Arrixaca, 30120, Murcia, Spain
- Instituto Murciano de Investigación Biosanitaria (IMIB) Pascual Parrilla, 30120, Murcia, Spain
| | - Diana García-Moreno
- Grupo de Telomerasa, Cáncer y Envejecimiento, Hospital Clínico Universitario Virgen de la Arrixaca, 30120, Murcia, Spain
- Instituto Murciano de Investigación Biosanitaria (IMIB) Pascual Parrilla, 30120, Murcia, Spain
- Departamento de Biología Celular e Histología, Facultad de Biología, Universidad de Murcia, 30100, Murcia, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), ISCIII, 28029, Madrid, Spain
| | - Elena Naranjo-Sánchez
- Grupo de Telomerasa, Cáncer y Envejecimiento, Hospital Clínico Universitario Virgen de la Arrixaca, 30120, Murcia, Spain
- Instituto Murciano de Investigación Biosanitaria (IMIB) Pascual Parrilla, 30120, Murcia, Spain
- Departamento de Biología Celular e Histología, Facultad de Biología, Universidad de Murcia, 30100, Murcia, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), ISCIII, 28029, Madrid, Spain
| | - Miriam Fernández-Lajarín
- Grupo de Telomerasa, Cáncer y Envejecimiento, Hospital Clínico Universitario Virgen de la Arrixaca, 30120, Murcia, Spain
- Instituto Murciano de Investigación Biosanitaria (IMIB) Pascual Parrilla, 30120, Murcia, Spain
- Departamento de Biología Celular e Histología, Facultad de Biología, Universidad de Murcia, 30100, Murcia, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), ISCIII, 28029, Madrid, Spain
| | - María A Blasco
- Telomeres and Telomerase Group, Molecular Oncology Program, Spanish National Cancer Centre (CNIO), Melchor Fernández Almagro 3, 28029, Madrid, Spain
| | - Francisca Alcaraz-Pérez
- Grupo de Telomerasa, Cáncer y Envejecimiento, Hospital Clínico Universitario Virgen de la Arrixaca, 30120, Murcia, Spain.
- Instituto Murciano de Investigación Biosanitaria (IMIB) Pascual Parrilla, 30120, Murcia, Spain.
- Departamento de Biología Celular e Histología, Facultad de Biología, Universidad de Murcia, 30100, Murcia, Spain.
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), ISCIII, 28029, Madrid, Spain.
| | - Victoriano Mulero
- Instituto Murciano de Investigación Biosanitaria (IMIB) Pascual Parrilla, 30120, Murcia, Spain.
- Departamento de Biología Celular e Histología, Facultad de Biología, Universidad de Murcia, 30100, Murcia, Spain.
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), ISCIII, 28029, Madrid, Spain.
| | - María L Cayuela
- Grupo de Telomerasa, Cáncer y Envejecimiento, Hospital Clínico Universitario Virgen de la Arrixaca, 30120, Murcia, Spain.
- Instituto Murciano de Investigación Biosanitaria (IMIB) Pascual Parrilla, 30120, Murcia, Spain.
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), ISCIII, 28029, Madrid, Spain.
| |
Collapse
|
3
|
Huynh TN, Parker R. The PARN, TOE1, and USB1 RNA deadenylases and their roles in non-coding RNA regulation. J Biol Chem 2023; 299:105139. [PMID: 37544646 PMCID: PMC10493513 DOI: 10.1016/j.jbc.2023.105139] [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: 05/13/2023] [Revised: 07/28/2023] [Accepted: 07/29/2023] [Indexed: 08/08/2023] Open
Abstract
The levels of non-coding RNAs (ncRNAs) are regulated by transcription, RNA processing, and RNA degradation pathways. One mechanism for the degradation of ncRNAs involves the addition of oligo(A) tails by non-canonical poly(A) polymerases, which then recruit processive sequence-independent 3' to 5' exonucleases for RNA degradation. This pathway of decay is also regulated by three 3' to 5' exoribonucleases, USB1, PARN, and TOE1, which remove oligo(A) tails and thereby can protect ncRNAs from decay in a manner analogous to the deubiquitination of proteins. Loss-of-function mutations in these genes lead to premature degradation of some ncRNAs and lead to specific human diseases such as Poikiloderma with Neutropenia (PN) for USB1, Dyskeratosis Congenita (DC) for PARN and Pontocerebellar Hypoplasia type 7 (PCH7) for TOE1. Herein, we review the biochemical properties of USB1, PARN, and TOE1, how they modulate ncRNA levels, and their roles in human diseases.
Collapse
Affiliation(s)
- Thao Ngoc Huynh
- Department of Biochemistry, University of Colorado Boulder, Boulder, Colorado, USA
| | - Roy Parker
- Department of Biochemistry, University of Colorado Boulder, Boulder, Colorado, USA; Howard Hughes Medical Institute, Chevy Chase, Maryland, USA.
| |
Collapse
|
4
|
Love SL, Emerson JD, Koide K, Hoskins AA. Pre-mRNA splicing-associated diseases and therapies. RNA Biol 2023; 20:525-538. [PMID: 37528617 PMCID: PMC10399480 DOI: 10.1080/15476286.2023.2239601] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/18/2023] [Indexed: 08/03/2023] Open
Abstract
Precursor mRNA (pre-mRNA) splicing is an essential step in human gene expression and is carried out by a large macromolecular machine called the spliceosome. Given the spliceosome's role in shaping the cellular transcriptome, it is not surprising that mutations in the splicing machinery can result in a range of human diseases and disorders (spliceosomopathies). This review serves as an introduction into the main features of the pre-mRNA splicing machinery in humans and how changes in the function of its components can lead to diseases ranging from blindness to cancers. Recently, several drugs have been developed that interact directly with this machinery to change splicing outcomes at either the single gene or transcriptome-scale. We discuss the mechanism of action of several drugs that perturb splicing in unique ways. Finally, we speculate on what the future may hold in the emerging area of spliceosomopathies and spliceosome-targeted treatments.
Collapse
Affiliation(s)
- Sierra L. Love
- Genetics Training Program, University of Wisconsin-Madison, Madison, WI, USA
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, USA
| | - Joseph D. Emerson
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA, USA
| | - Kazunori Koide
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA, USA
| | - Aaron A. Hoskins
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, USA
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, USA
| |
Collapse
|
5
|
Unsupervised generative and graph representation learning for modelling cell differentiation. Sci Rep 2020; 10:9790. [PMID: 32555334 PMCID: PMC7300092 DOI: 10.1038/s41598-020-66166-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2019] [Accepted: 02/10/2020] [Indexed: 12/22/2022] Open
Abstract
Using machine learning techniques to build representations from biomedical data can help us understand the latent biological mechanism of action and lead to important discoveries. Recent developments in single-cell RNA-sequencing protocols have allowed measuring gene expression for individual cells in a population, thus opening up the possibility of finding answers to biomedical questions about cell differentiation. In this paper, we explore unsupervised generative neural methods, based on the variational autoencoder, that can model cell differentiation by building meaningful representations from the high dimensional and complex gene expression data. We use disentanglement methods based on information theory to improve the data representation and achieve better separation of the biological factors of variation in the gene expression data. In addition, we use a graph autoencoder consisting of graph convolutional layers to predict relationships between single-cells. Based on these models, we develop a computational framework that consists of methods for identifying the cell types in the dataset, finding driver genes for the differentiation process and obtaining a better understanding of relationships between cells. We illustrate our methods on datasets from multiple species and also from different sequencing technologies.
Collapse
|
6
|
Congenital neutropenia and primary immunodeficiency diseases. Crit Rev Oncol Hematol 2019; 133:149-162. [DOI: 10.1016/j.critrevonc.2018.10.003] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2017] [Revised: 10/09/2018] [Accepted: 10/09/2018] [Indexed: 02/06/2023] Open
|
7
|
Abstract
PURPOSE OF REVIEW The term osteopetrosis refers to a group of rare skeletal diseases sharing the hallmark of a generalized increase in bone density owing to a defect in bone resorption. Osteopetrosis is clinically and genetically heterogeneous, and a precise molecular classification is relevant for prognosis and treatment. Here, we review recent data on the pathogenesis of this disorder. RECENT FINDINGS Novel mutations in known genes as well as defects in new genes have been recently reported, further expanding the spectrum of molecular defects leading to osteopetrosis. Exploitation of next-generation sequencing tools is ever spreading, facilitating differential diagnosis. Some complex phenotypes in which osteopetrosis is accompanied by additional clinical features have received a molecular classification, also involving new genes. Moreover, novel types of mutations have been recognized, which for their nature or genomic location are at high risk being neglected. Yet, the causative mutation is unknown in some patients, indicating that the genetics of osteopetrosis still deserves intense research efforts.
Collapse
Affiliation(s)
- Eleonora Palagano
- Humanitas Clinical and Research Institute, via Manzoni 113, 20089, Rozzano, MI, Italy
- Department of Medical Biotechnologies and Translational Medicine, University of Milan, Milan, Italy
| | - Ciro Menale
- Humanitas Clinical and Research Institute, via Manzoni 113, 20089, Rozzano, MI, Italy
- Milan Unit, CNR-IRGB, Milan, Italy
| | - Cristina Sobacchi
- Humanitas Clinical and Research Institute, via Manzoni 113, 20089, Rozzano, MI, Italy.
- Milan Unit, CNR-IRGB, Milan, Italy.
| | - Anna Villa
- Humanitas Clinical and Research Institute, via Manzoni 113, 20089, Rozzano, MI, Italy
- Milan Unit, CNR-IRGB, Milan, Italy
| |
Collapse
|
8
|
Experimental approaches to studying the nature and impact of splicing variation in zebrafish. Methods Cell Biol 2016; 135:259-88. [PMID: 27443930 DOI: 10.1016/bs.mcb.2016.02.006] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
From a fixed number of genes carried in all cells, organisms create considerable diversity in cellular phenotype through differential regulation of gene expression. One prevalent source of transcriptome diversity is alternative pre-mRNA splicing, which is manifested in many different forms. Zebrafish models of splicing dysfunction due to mutated spliceosome components provide opportunity to link biochemical analyses of spliceosome structure and function with whole organism phenotypic outcomes. Drawing from experience with two zebrafish mutants: cephalophŏnus (a prpf8 mutant, isolated for defects in granulopoiesis) and caliban (a rnpc3 mutant, isolated for defects in digestive organ development), we describe the use of glycerol gradient sedimentation and native gel electrophoresis to resolve components of aberrant splicing complexes. We also describe how RNAseq can be employed to examine relatively rare alternative splicing events including intron retention. Such experimental approaches in zebrafish can promote understanding of how splicing variation and dysfunction contribute to phenotypic diversity and disease pathogenesis.
Collapse
|
9
|
A zebrafish model of Poikiloderma with Neutropenia recapitulates the human syndrome hallmarks and traces back neutropenia to the myeloid progenitor. Sci Rep 2015; 5:15814. [PMID: 26522474 PMCID: PMC4629135 DOI: 10.1038/srep15814] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2014] [Accepted: 09/22/2015] [Indexed: 01/27/2023] Open
Abstract
Poikiloderma with Neutropenia (PN) is an autosomal recessive genodermatosis characterized by early-onset poikiloderma, pachyonychia, hyperkeratosis, bone anomalies and neutropenia, predisposing to myelodysplasia. The causative C16orf57/USB1 gene encodes a conserved phosphodiesterase that regulates the stability of spliceosomal U6-RNA. The involvement of USB1 in splicing has not yet allowed to unveil the pathogenesis of PN and how the gene defects impact on skin and bone tissues besides than on the haematological compartment. We established a zebrafish model of PN using a morpholino-knockdown approach with two different splicing morpholinos. Both usb1-depleted embryos displayed developmental abnormalities recapitulating the signs of the human syndrome. Besides the pigmentation and osteochondral defects, usb1-knockdown caused defects in circulation, manifested by a reduced number of circulating cells. The overall morphant phenotype was also obtained by co-injecting sub-phenotypic dosages of the two morpholinos and could be rescued by human USB1 RNA. Integrated in situ and real-time expression analyses of stage-specific markers highlighted defects of primitive haematopoiesis and traced back the dramatic reduction in neutrophil myeloperoxidase to the myeloid progenitors showing down-regulated pu.1 expression. Our vertebrate model of PN demonstrates the intrinsic requirement of usb1 in haematopoiesis and highlights PN as a disorder of myeloid progenitors associated with bone marrow dysfunction.
Collapse
|
10
|
Shchepachev V, Wischnewski H, Soneson C, Arnold AW, Azzalin CM. Human Mpn1 promotes post-transcriptional processing and stability of U6atac. FEBS Lett 2015. [PMID: 26213367 DOI: 10.1016/j.febslet.2015.06.046] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Mpn1 is an exoribonuclease that modifies the spliceosomal small nuclear RNA (snRNA) U6 by trimming its oligouridine tail and introducing a cyclic phosphate group (>p). Mpn1 deficiency induces U6 3' end misprocessing, accelerated U6 decay and pre-mRNA splicing defects. Mutations in the human MPN1 gene are associated with the genodermatosis Clericuzio-type poikiloderma with neutropenia (PN). Here we present the deep sequencing of the >p-containing transcriptomes of mpn1Δ fission yeast and PN cells. While in yeast U6 seems to be the only substrate of Mpn1, human Mpn1 also processes U6atac snRNA. PN cells bear unstable U6atac species with aberrantly long and oligoadenylated 3' ends. Our data corroborate the link between Mpn1 and snRNA stability suggesting that PN could derive from pre-mRNA splicing aberrations.
Collapse
Affiliation(s)
- Vadim Shchepachev
- Institute of Biochemistry (IBC), Eidgenössische Technische Hochschule Zürich (ETHZ), Zürich CH-8093, Switzerland
| | - Harry Wischnewski
- Institute of Biochemistry (IBC), Eidgenössische Technische Hochschule Zürich (ETHZ), Zürich CH-8093, Switzerland
| | - Charlotte Soneson
- Bioinformatics Core Facility, SIB Swiss Institute of Bioinformatics, Lausanne CH-1015, Switzerland
| | - Andreas W Arnold
- Dermatologische Universitätsklinik, Universitätsspital Basel, Basel CH-4031, Switzerland
| | - Claus M Azzalin
- Institute of Biochemistry (IBC), Eidgenössische Technische Hochschule Zürich (ETHZ), Zürich CH-8093, Switzerland.
| |
Collapse
|