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Sharma G, Paganin M, Lauria F, Perenthaler E, Viero G. The SMN-ribosome interplay: a new opportunity for Spinal Muscular Atrophy therapies. Biochem Soc Trans 2024; 52:465-479. [PMID: 38391004 PMCID: PMC10903476 DOI: 10.1042/bst20231116] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Revised: 02/12/2024] [Accepted: 02/13/2024] [Indexed: 02/24/2024]
Abstract
The underlying cause of Spinal Muscular Atrophy (SMA) is in the reduction of survival motor neuron (SMN) protein levels due to mutations in the SMN1 gene. The specific effects of SMN protein loss and the resulting pathological alterations are not fully understood. Given the crucial roles of the SMN protein in snRNP biogenesis and its interactions with ribosomes and translation-related proteins and mRNAs, a decrease in SMN levels below a specific threshold in SMA is expected to affect translational control of gene expression. This review covers both direct and indirect SMN interactions across various translation-related cellular compartments and processes, spanning from ribosome biogenesis to local translation and beyond. Additionally, it aims to outline deficiencies and alterations in translation observed in SMA models and patients, while also discussing the implications of the relationship between SMN protein and the translation machinery within the context of current and future therapies.
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Paganin M, Tebaldi T, Lauria F, Viero G. Visualizing gene expression changes in time, space, and single cells with expressyouRcell. iScience 2023; 26:106853. [PMID: 37250782 PMCID: PMC10220493 DOI: 10.1016/j.isci.2023.106853] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Revised: 05/05/2023] [Accepted: 05/05/2023] [Indexed: 05/31/2023] Open
Abstract
The last decade has witnessed massive advancements in high-throughput techniques capable of producing increasingly complex gene expression datasets across time and space and at the resolution of single cells. Yet, the large volume of big data available and the complexity of experimental designs hamper an easy understanding and effective communication of the results. We present expressyouRcell, an easy-to-use R package to map the multi-dimensional variations of transcript and protein levels in dynamic cell pictographs. expressyouRcell visualizes gene expression variations as pictographic representations of cell-type thematic maps. expressyouRcell visually reduces the complexity of displaying gene expression and protein level changes across multiple measurements (time points or single-cell trajectories) by generating dynamic representations of cellular pictographs. We applied expressyouRcell to single cell, bulk RNA sequencing (RNA-seq), and proteomics datasets, demonstrating its flexibility and usability in the visualization of complex variations in gene expression. Our approach improves the standard quantitative interpretation and communication of relevant results.
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Affiliation(s)
| | - Toma Tebaldi
- Yale Comprehensive Cancer Center, Yale University School of Medicine, New Haven, CT, USA
- Department CIBIO, University of Trento, Trento, Italy
| | - Fabio Lauria
- Institute of Biophysics, CNR Unit Trento, Trento, Italy
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Serafin V, Lissandron V, Buldini B, Bresolin S, Paganin M, Grillo F, Andriano N, Palmi C, Cazzaniga G, Marmiroli S, Conter V, Basso G, Accordi B. Phosphoproteomic analysis reveals hyperactivation of mTOR/STAT3 and LCK/Calcineurin axes in pediatric early T-cell precursor ALL. Leukemia 2017; 31:1007-1011. [PMID: 28082737 DOI: 10.1038/leu.2017.13] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- V Serafin
- Department of Woman's and Child's Health, University of Padova, Padova, Italy
| | - V Lissandron
- Department of Woman's and Child's Health, University of Padova, Padova, Italy
| | - B Buldini
- Department of Woman's and Child's Health, University of Padova, Padova, Italy
| | - S Bresolin
- Department of Woman's and Child's Health, University of Padova, Padova, Italy
| | - M Paganin
- Department of Woman's and Child's Health, University of Padova, Padova, Italy
| | - F Grillo
- Department of Woman's and Child's Health, University of Padova, Padova, Italy
| | - N Andriano
- Centro Ricerca Tettamanti, Department of Pediatrics, University of Milano-Bicocca, Fondazione MBBM, Monza, Italy
| | - C Palmi
- Centro Ricerca Tettamanti, Department of Pediatrics, University of Milano-Bicocca, Fondazione MBBM, Monza, Italy
| | - G Cazzaniga
- Centro Ricerca Tettamanti, Department of Pediatrics, University of Milano-Bicocca, Fondazione MBBM, Monza, Italy
| | - S Marmiroli
- Department of Surgery, Medicine, Dentistry and Morphology, University of Modena and Reggio Emilia, Modena, Italy
| | - V Conter
- Center of Hemato-Oncology, Department of Pediatrics, University of Milano-Bicocca, Fondazione MBBM, Ospedale San Gerardo, Monza, Italy
| | - G Basso
- Department of Woman's and Child's Health, University of Padova, Padova, Italy
| | - B Accordi
- Department of Woman's and Child's Health, University of Padova, Padova, Italy
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Bronzini I, Aresu L, Paganin M, Marchioretto L, Comazzi S, Cian F, Riondato F, Marconato L, Martini V, Te Kronnie G. DNA methylation and targeted sequencing of methyltransferases family genes in canine acute myeloid leukaemia, modelling human myeloid leukaemia. Vet Comp Oncol 2016; 15:910-918. [PMID: 27098563 DOI: 10.1111/vco.12231] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2015] [Revised: 02/11/2016] [Accepted: 03/11/2016] [Indexed: 01/13/2023]
Abstract
Tumours shows aberrant DNA methylation patterns, being hypermethylated or hypomethylated compared with normal tissues. In human acute myeloid leukaemia (hAML) mutations in DNA methyltransferase (DNMT3A) are associated to a more aggressive tumour behaviour. As AML is lethal in dogs, we defined global DNA methylation content, and screened the C-terminal domain of DNMT3 family of genes for sequence variants in 39 canine acute myeloid leukaemia (cAML) cases. A heterogeneous pattern of DNA methylation was found among cAML samples, with subsets of cases being hypermethylated or hypomethylated compared with healthy controls; four recurrent single nucleotide variations (SNVs) were found in DNMT3L gene. Although SNVs were not directly correlated to whole genome DNA methylation levels, all hypomethylated cAML cases were homozygous for the deleterious mutation at p.Arg222Trp. This study contributes to understand genetic modifications of cAML, leading up to studies that will elucidate the role of methylome alterations in the pathogenesis of AML in dogs.
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Affiliation(s)
- I Bronzini
- Oncohematology Laboratory, Department of Women's and Children's Health, University of Padova, Padova, Italy
| | - L Aresu
- Department of Comparative Biomedicine and Food Science, University of Padova, Padova, Italy
| | - M Paganin
- Oncohematology Laboratory, Department of Women's and Children's Health, University of Padova, Padova, Italy
| | - L Marchioretto
- Department of Cellular Biotechnology and Hematology, Sapienza University of Rome, Rome, Italy
| | - S Comazzi
- Department of Veterinary Science and Public Health, University of Milan, Milano, Italy
| | - F Cian
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - F Riondato
- Department of Veterinary Sciences, University of Turin, Turin, Italy
| | - L Marconato
- Centro Oncologico Veterinario, Sasso Marconi, Bologna, Italy
| | - V Martini
- Department of Veterinary Science and Public Health, University of Milan, Milano, Italy
| | - G Te Kronnie
- Oncohematology Laboratory, Department of Women's and Children's Health, University of Padova, Padova, Italy
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Durum SK, Li W, Zenatti P, Ribeiro D, Zuurbier L, Silva M, Paganin M, Tritapoe J, Hixon J, Silveira A, Cardoso B, Sarmento L, Correia N, Toribio M, Kobarg J, Horstmann M, Pieters R, Brandalise S, Ferrando A, Meijerink J, Yunes J, Barata J. 74. Cytokine 2013. [DOI: 10.1016/j.cyto.2013.06.077] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Durum S, Li W, Zenatti P, Ribeiro D, Zuurbier L, Silva M, Paganin M, Tritapoe J, Hixon J, Silveira A, Cardoso B, Sarmento L, Correia N, Toribio M, Kobarg J, Horstmann M, Pieters R, Brandalise S, Ferrando A, Meijerink J, Yunes J, Barata J. O023 Oncogenic IL-7R gain-of-function mutations in childhood T-ALL. Cytokine 2012. [DOI: 10.1016/j.cyto.2012.06.055] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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Durum SK, Li W, Zenatti P, Ribeiro D, Zuurbier L, Silva M, Paganin M, Tritapoe J, Hixon J, Silveira A, Cardoso B, Sarmento L, Correia N, Toribio M, Kobarg J, Horstmann M, Pieters R, Brandalise S. CS07-7. Oncogenic IL-7R gain-of-function mutations in childhood T-ALL. Cytokine 2011. [DOI: 10.1016/j.cyto.2011.07.344] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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Paganin M, Zecca M, Fabbri G, Polato K, Biondi A, Rizzari C, Locatelli F, Basso G. Minimal residual disease is an important predictive factor of outcome in children with relapsed ‘high-risk’ acute lymphoblastic leukemia. Leukemia 2008; 22:2193-200. [DOI: 10.1038/leu.2008.227] [Citation(s) in RCA: 72] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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Zaccaroni M, Ciuffreda M, Paganin M, Beani L. Does an early aversive experience to humans modify antipredator behaviour in adult Rock partridges? ETHOL ECOL EVOL 2007. [DOI: 10.1080/08927014.2007.9522561] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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Mann G, Cazzaniga G, van der Velden VHJ, Flohr T, Csinady E, Paganin M, Schrauder A, Dohnal AM, Schrappe M, Biondi A, Gadner H, van Dongen JJM, Panzer-Grümayer ER. Acute lymphoblastic leukemia with t(4;11) in children 1 year and older: The ‘big sister’ of the infant disease? Leukemia 2007; 21:642-6. [PMID: 17287854 DOI: 10.1038/sj.leu.2404577] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
The t(4;11)-positive acute lymphoblastic leukemia (ALL) is a rare disease in children above the age of 1 year. We studied the clinical and biological characteristics in 32 consecutively diagnosed childhood cases (median age 10.0 years, range 1.0-17.1 years). Immunophenotyping revealed a pro-B and a pre-B stage in 24 and eight cases, respectively. IGH genes were rearranged in 84% of leukemias with a predominance of incomplete DJ(H) joints. Whereas IGK-Kde and TCRD rearrangements were rare, TCRG rearrangements were present in 50% of cases and involved mainly Vgamma11 or Vgamma9 together with a Jgamma1.3./2.3 gene segment, an unusual combination among t(4;11)-negative B-cell precursor ALL. Oligoclonality was found in about 30% as assessed by heterogeneous IGH and TCRG rearrangements. Our data are in line with transformation of a precursor cell at an early stage of B-cell development but retaining the potential to differentiate to the pre-B cell stage in vivo. Although a distinct difference between infant and older childhood cases with t(4;11) became evident, no age-related biological features were found within the childhood age group. In contrast to infants with t(4;11)-positive ALL, childhood cases had a relatively low cumulative incidence of relapse of 25% at 3.5 years with BFM-based high-risk protocols.
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Affiliation(s)
- G Mann
- St. Anna Kinderspital, Department of Pediatric Hematology/Oncology, Vienna, Austria
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Germano G, del Giudice L, Lo Nigro L, Polato K, Giarin E, Paganin M, Basso G. Comparative sequence analysis of incomplete DJH and TCR gene rearrangements in children with relapses of T-ALL. Leukemia 2005; 19:1687-9. [PMID: 16015384 DOI: 10.1038/sj.leu.2403878] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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