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Torices L, Nunes-Xavier CE, Mingo J, Luna S, Erramuzpe A, Cortés JM, Pulido R. Induction of Translational Readthrough on Protein Tyrosine Phosphatases Targeted by Premature Termination Codon Mutations in Human Disease. Methods Mol Biol 2024; 2743:1-19. [PMID: 38147205 DOI: 10.1007/978-1-0716-3569-8_1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2023]
Abstract
Nonsense mutations generating premature termination codons (PTCs) in various genes are frequently associated with somatic cancer and hereditary human diseases since PTCs commonly generate truncated proteins with defective or altered function. Induced translational readthrough during protein biosynthesis facilitates the incorporation of an amino acid at the position of a PTC, allowing the synthesis of a complete protein. This may evade the pathological effect of the PTC mutation and provide new therapeutic opportunities. Several protein tyrosine phosphatases (PTPs) genes are targeted by PTC in human disease, the tumor suppressor PTEN being the more prominent paradigm. Here, using PTEN and laforin as examples, two PTPs from the dual-specificity phosphatase subfamily, we describe methodologies to analyze in silico the distribution and frequency of pathogenic PTC in PTP genes. We also summarize laboratory protocols and technical notes to study the induced translational readthrough reconstitution of the synthesis of PTP targeted by PTC in association with disease in cellular models.
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Affiliation(s)
- Leire Torices
- Biobizkaia Health Research Institute, Barakaldo, Spain
| | - Caroline E Nunes-Xavier
- Biobizkaia Health Research Institute, Barakaldo, Spain
- Institute for Cancer Research, Oslo University Hospital, The Norwegian Radium Hospital, Oslo, Norway
| | - Janire Mingo
- Biobizkaia Health Research Institute, Barakaldo, Spain
| | - Sandra Luna
- Biobizkaia Health Research Institute, Barakaldo, Spain
| | - Asier Erramuzpe
- Biobizkaia Health Research Institute, Barakaldo, Spain
- Ikerbasque, The Basque Foundation for Science, Bilbao, Spain
| | - Jesús M Cortés
- Biobizkaia Health Research Institute, Barakaldo, Spain
- Ikerbasque, The Basque Foundation for Science, Bilbao, Spain
- Cell Biology and Histology Department, University of the Basque Country (UPV/EHU), Leioa, Spain
| | - Rafael Pulido
- Biobizkaia Health Research Institute, Barakaldo, Spain.
- Ikerbasque, The Basque Foundation for Science, Bilbao, Spain.
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2
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Torices L, Nunes-Xavier CE, López JI, Pulido R. Novel anti-PTEN C2 domain monoclonal antibodies to analyse the expression and function of PTEN isoform variants. PLoS One 2023; 18:e0289369. [PMID: 37527256 PMCID: PMC10393154 DOI: 10.1371/journal.pone.0289369] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Accepted: 07/17/2023] [Indexed: 08/03/2023] Open
Abstract
PTEN is a major tumor suppressor gene frequently mutated in human tumors, and germline PTEN gene mutations are the molecular diagnostic of PTEN Hamartoma Tumor Syndrome (PHTS), a heterogeneous disorder that manifests with multiple hamartomas, cancer predisposition, and neurodevelopmental alterations. A diversity of translational and splicing PTEN isoforms exist, as well as PTEN C-terminal truncated variants generated by disease-associated nonsense mutations. However, most of the available anti-PTEN monoclonal antibodies (mAb) recognize epitopes at the PTEN C-terminal tail, which may introduce a bias in the analysis of the expression of PTEN isoforms and variants. We here describe the generation and precise characterization of anti-PTEN mAb recognizing the PTEN C2-domain, and their use to monitor the expression and function of PTEN isoforms and PTEN missense and nonsense mutations associated to disease. These anti-PTEN C2 domain mAb are suitable to study the pathogenicity of PTEN C-terminal truncations that retain stability and function but have lost the PTEN C-terminal epitopes. The use of well-defined anti-PTEN mAb recognizing distinct PTEN regions, as the ones here described, will help to understand the deleterious effects of specific PTEN mutations in human disease.
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Affiliation(s)
- Leire Torices
- Biobizkaia Health Research Institute, Barakaldo, Spain
| | - Caroline E Nunes-Xavier
- Biobizkaia Health Research Institute, Barakaldo, Spain
- Institute for Cancer Research, Oslo University Hospital, Oslo, Norway
| | - José I López
- Biobizkaia Health Research Institute, Barakaldo, Spain
| | - Rafael Pulido
- Biobizkaia Health Research Institute, Barakaldo, Spain
- Ikerbasque, The Basque Foundation for Science, Bilbao, Spain
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3
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Torices L, Mingo J, Rodríguez-Escudero I, Fernández-Acero T, Luna S, Nunes-Xavier CE, López JI, Mercadillo F, Currás M, Urioste M, Molina M, Cid VJ, Pulido R. Functional analysis of PTEN variants of unknown significance from PHTS patients unveils complex patterns of PTEN biological activity in disease. Eur J Hum Genet 2023; 31:568-577. [PMID: 36543932 PMCID: PMC10172195 DOI: 10.1038/s41431-022-01265-w] [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: 06/16/2022] [Revised: 12/01/2022] [Accepted: 12/06/2022] [Indexed: 12/24/2022] Open
Abstract
Heterozygous germline mutations in PTEN gene predispose to hamartomas and tumors in different tissues, as well as to neurodevelopmental disorders, and define at genetic level the PTEN Hamartoma Tumor Syndrome (PHTS). The major physiologic role of PTEN protein is the dephosphorylation of phosphatidylinositol (3,4,5)-trisphosphate (PIP3), counteracting the pro-oncogenic function of phosphatidylinositol 3-kinase (PI3K), and PTEN mutations in PHTS patients frequently abrogate PTEN PIP3 catalytic activity. PTEN also displays non-canonical PIP3-independent functions, but their involvement in PHTS pathogeny is less understood. We have previously identified and described, at clinical and genetic level, novel PTEN variants of unknown functional significance in PHTS patients. Here, we have performed an extensive functional characterization of these PTEN variants (c.77 C > T, p.(Thr26Ile), T26I; c.284 C > G, p.(Pro95Arg), P95R; c.529 T > A, p.(Tyr177Asn), Y177N; c.781 C > G, p.(Gln261Glu), Q261E; c.829 A > G, p.(Thr277Ala), T277A; and c.929 A > G, p.(Asp310Gly), D310G), including cell expression levels and protein stability, PIP3-phosphatase activity, and subcellular localization. In addition, caspase-3 cleavage analysis in cells has been assessed using a C2-domain caspase-3 cleavage-specific anti-PTEN antibody. We have found complex patterns of functional activity on PTEN variants, ranging from loss of PIP3-phosphatase activity, diminished protein expression and stability, and altered nuclear/cytoplasmic localization, to intact functional properties, when compared with PTEN wild type. Furthermore, we have found that PTEN cleavage at the C2-domain by the pro-apoptotic protease caspase-3 is diminished in specific PTEN PHTS variants. Our findings illustrate the multifaceted molecular features of pathogenic PTEN protein variants, which could account for the complexity in the genotype/phenotype manifestations of PHTS patients.
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Affiliation(s)
- Leire Torices
- Biocruces Bizkaia Health Research Institute, Barakaldo, Spain
| | - Janire Mingo
- Biocruces Bizkaia Health Research Institute, Barakaldo, Spain
| | - Isabel Rodríguez-Escudero
- Departamento de Microbiología y Parasitología, Facultad de Farmacia, UCM & Instituto Ramón y Cajal de Investigaciones Sanitarias (IRYCIS), Madrid, Spain
| | - Teresa Fernández-Acero
- Departamento de Microbiología y Parasitología, Facultad de Farmacia, UCM & Instituto Ramón y Cajal de Investigaciones Sanitarias (IRYCIS), Madrid, Spain
| | - Sandra Luna
- Biocruces Bizkaia Health Research Institute, Barakaldo, Spain
| | - Caroline E Nunes-Xavier
- Biocruces Bizkaia Health Research Institute, Barakaldo, Spain
- Institute for Cancer Research, Oslo University Hospital, Oslo, Norway
| | - José I López
- Biocruces Bizkaia Health Research Institute, Barakaldo, Spain
- Department of Pathology, Cruces University Hospital, Barakaldo, Spain
| | - Fátima Mercadillo
- Familial Cancer Clinical Unit, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
| | - María Currás
- Familial Cancer Clinical Unit, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
| | - Miguel Urioste
- Familial Cancer Clinical Unit, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
| | - María Molina
- Departamento de Microbiología y Parasitología, Facultad de Farmacia, UCM & Instituto Ramón y Cajal de Investigaciones Sanitarias (IRYCIS), Madrid, Spain
| | - Víctor J Cid
- Departamento de Microbiología y Parasitología, Facultad de Farmacia, UCM & Instituto Ramón y Cajal de Investigaciones Sanitarias (IRYCIS), Madrid, Spain
| | - Rafael Pulido
- Biocruces Bizkaia Health Research Institute, Barakaldo, Spain.
- Ikerbasque, The Basque Foundation for Science, Bilbao, Spain.
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4
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Alaña L, Nunes-Xavier CE, Zaldumbide L, Martin-Guerrero I, Mosteiro L, Alba-Pavón P, Villate O, García-Obregón S, González-García H, Herraiz R, Astigarraga I, Pulido R, García-Ariza M. Identification and Functional Analysis of a Novel CTNNB1 Mutation in Pediatric Medulloblastoma. Cancers (Basel) 2022; 14:cancers14020421. [PMID: 35053583 PMCID: PMC8773623 DOI: 10.3390/cancers14020421] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Revised: 01/10/2022] [Accepted: 01/11/2022] [Indexed: 12/10/2022] Open
Abstract
Simple Summary We have analyzed a panel of 88 pediatric medulloblastoma tumors for exon 3 mutations from the CTNNB1 gene and identified eight missense point-mutations and one in-frame deletion. We describe and functionally characterize a novel CTNNB1 in-frame deletion (c.109-111del, pSer37del, ΔS37) found in a pediatric patient with a classic medulloblastoma, WNT-activated grade IV (WHO 2016). To the best of our knowledge, this mutation has not been previously reported in medulloblastoma, and it is uncertain its role in the disease development and progression. Our analysis discloses gain-of-function properties for the new ΔS37 β-catenin variant. Abstract Medulloblastoma is the primary malignant tumor of the Central Nervous System (CNS) most common in pediatrics. We present here, the histological, molecular, and functional analysis of a cohort of 88 pediatric medulloblastoma tumor samples. The WNT-activated subgroup comprised 10% of our cohort, and all WNT-activated patients had exon 3 CTNNB1 mutations and were immunostained for nuclear β-catenin. One novel heterozygous CTNNB1 mutation was found, which resulted in the deletion of β-catenin Ser37 residue (ΔS37). The ΔS37 β-catenin variant ectopically expressed in U2OS human osteosarcoma cells displayed higher protein expression levels than wild-type β-catenin, and functional analysis disclosed gain-of-function properties in terms of elevated TCF/LEF transcriptional activity in cells. Our results suggest that the stabilization and nuclear accumulation of ΔS37 β-catenin contributed to early medulloblastoma tumorigenesis.
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Affiliation(s)
- Lide Alaña
- Pediatric Oncology Group, Biocruces Bizkaia Health Research Institute, Plaza de Cruces 12, 48903 Barakaldo, Spain; (I.M.-G.); (P.A.-P.); (O.V.); (S.G.-O.); (I.A.); (M.G.-A.)
- Correspondence: ; Tel.: +34-946-006-000 (ext. 2401)
| | - Caroline E. Nunes-Xavier
- Biomarkers in Cancer Unit, Biocruces Bizkaia Health Research Institute, Plaza de Cruces 12, 48903 Barakaldo, Spain; (C.E.N.-X.); (R.P.)
- Department of Tumor Biology, Institute for Cancer Research, Oslo University Hospital, The Norwegian Radium Hospital, 0310 Oslo, Norway
| | - Laura Zaldumbide
- Department of Pathology, Hospital Universitario de Cruces, Osakidetza, Plaza de Cruces 12, 48903 Barakaldo, Spain; (L.Z.); (L.M.)
| | - Idoia Martin-Guerrero
- Pediatric Oncology Group, Biocruces Bizkaia Health Research Institute, Plaza de Cruces 12, 48903 Barakaldo, Spain; (I.M.-G.); (P.A.-P.); (O.V.); (S.G.-O.); (I.A.); (M.G.-A.)
- Department of Genetics, Physical Anthropology and Animal Pathology, Faculty of Science and Technology, University of the Basque Country, UPV/EHU, 48940 Leioa, Spain
| | - Lorena Mosteiro
- Department of Pathology, Hospital Universitario de Cruces, Osakidetza, Plaza de Cruces 12, 48903 Barakaldo, Spain; (L.Z.); (L.M.)
| | - Piedad Alba-Pavón
- Pediatric Oncology Group, Biocruces Bizkaia Health Research Institute, Plaza de Cruces 12, 48903 Barakaldo, Spain; (I.M.-G.); (P.A.-P.); (O.V.); (S.G.-O.); (I.A.); (M.G.-A.)
| | - Olatz Villate
- Pediatric Oncology Group, Biocruces Bizkaia Health Research Institute, Plaza de Cruces 12, 48903 Barakaldo, Spain; (I.M.-G.); (P.A.-P.); (O.V.); (S.G.-O.); (I.A.); (M.G.-A.)
| | - Susana García-Obregón
- Pediatric Oncology Group, Biocruces Bizkaia Health Research Institute, Plaza de Cruces 12, 48903 Barakaldo, Spain; (I.M.-G.); (P.A.-P.); (O.V.); (S.G.-O.); (I.A.); (M.G.-A.)
- Department of Physiology, Faculty of Medicine and Nursing, Campus de Leioa, University of the Basque Country, UPV/EHU, 48940 Leioa, Spain
| | - Hermenegildo González-García
- Oncohematology Pediatric Unit, Department of Pediatrics, Hospital Universitario de Valladolid, C/Ramon y Cajal n°3, 47003 Valladolid, Spain; (H.G.-G.); (R.H.)
| | - Raquel Herraiz
- Oncohematology Pediatric Unit, Department of Pediatrics, Hospital Universitario de Valladolid, C/Ramon y Cajal n°3, 47003 Valladolid, Spain; (H.G.-G.); (R.H.)
| | - Itziar Astigarraga
- Pediatric Oncology Group, Biocruces Bizkaia Health Research Institute, Plaza de Cruces 12, 48903 Barakaldo, Spain; (I.M.-G.); (P.A.-P.); (O.V.); (S.G.-O.); (I.A.); (M.G.-A.)
- Pediatric Oncohematology Unit, Pediatrics Department, Hospital Universitario Cruces, Osakidetza, Plaza de Cruces 12, 48903 Barakaldo, Spain
- Pediatrics Department, Faculty of Medicine and Nursing, University of the Basque Country, UPV/EHU, Plaza de Cruces 12, 48903 Barakaldo, Spain
| | - Rafael Pulido
- Biomarkers in Cancer Unit, Biocruces Bizkaia Health Research Institute, Plaza de Cruces 12, 48903 Barakaldo, Spain; (C.E.N.-X.); (R.P.)
- IKERBASQUE, Basque Foundation for Science, 48009 Bilbao, Spain
| | - Miguel García-Ariza
- Pediatric Oncology Group, Biocruces Bizkaia Health Research Institute, Plaza de Cruces 12, 48903 Barakaldo, Spain; (I.M.-G.); (P.A.-P.); (O.V.); (S.G.-O.); (I.A.); (M.G.-A.)
- Pediatric Oncohematology Unit, Pediatrics Department, Hospital Universitario Cruces, Osakidetza, Plaza de Cruces 12, 48903 Barakaldo, Spain
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5
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Luna S, Torices L, Mingo J, Amo L, Rodríguez-Escudero I, Ruiz-Ibarlucea P, Erramuzpe A, Cortés JM, Tejada MI, Molina M, Nunes-Xavier CE, López JI, Cid VJ, Pulido R. A global analysis of the reconstitution of PTEN function by translational readthrough of PTEN pathogenic premature termination codons. Hum Mutat 2021; 42:551-566. [PMID: 33600059 DOI: 10.1002/humu.24186] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Revised: 01/15/2021] [Accepted: 02/14/2021] [Indexed: 12/29/2022]
Abstract
The PTEN tumor suppressor gene is mutated with high incidence in tumors and in the germline of patients with cancer predisposition or with macrocephaly associated with autism. PTEN nonsense mutations generating premature termination codons (PTC) and producing nonfunctional truncated PTEN proteins are frequent in association with human disease. However, there are no studies addressing the restoration of full-length PTEN proteins from the PTC-mutated PTEN gene by translational readthrough. Here, we have performed a global translational and functional readthrough analysis of the complete collection of PTEN PTC somatic or hereditary mutations found in tumors or in the germline of patients (disease-associated PTEN PTCome), and we set standards for the analysis of the potential of readthrough functional reconstitution in disease-relevant genes. Our analysis indicates that prevalent pathogenic PTEN PTC mutations are susceptible to PTEN functional restoration in response to readthrough-inducing compounds. Comprehensive readthrough analyses of disease-associated PTComes will be valuable tools for the implementation of readthrough-based precision interventions in specific groups of patients.
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Affiliation(s)
- Sandra Luna
- Biocruces Bizkaia Health Research Institute, Barakaldo, Spain
| | - Leire Torices
- Biocruces Bizkaia Health Research Institute, Barakaldo, Spain
| | - Janire Mingo
- Biocruces Bizkaia Health Research Institute, Barakaldo, Spain
| | - Laura Amo
- Biocruces Bizkaia Health Research Institute, Barakaldo, Spain
| | - Isabel Rodríguez-Escudero
- Departamento de Microbiología y Parasitología, Facultad de Farmacia, UCM & Instituto Ramón y Cajal de Investigaciones Sanitarias (IRYCIS), Madrid, Spain
| | | | - Asier Erramuzpe
- Biocruces Bizkaia Health Research Institute, Barakaldo, Spain
| | - Jesús M Cortés
- Biocruces Bizkaia Health Research Institute, Barakaldo, Spain.,Ikerbasque, The Basque Foundation for Science, Bilbao, Spain
| | - María I Tejada
- Biocruces Bizkaia Health Research Institute, Barakaldo, Spain
| | - María Molina
- Departamento de Microbiología y Parasitología, Facultad de Farmacia, UCM & Instituto Ramón y Cajal de Investigaciones Sanitarias (IRYCIS), Madrid, Spain
| | - Caroline E Nunes-Xavier
- Biocruces Bizkaia Health Research Institute, Barakaldo, Spain.,Institute for Cancer Research, Oslo University Hospital, Oslo, Norway
| | - José I López
- Biocruces Bizkaia Health Research Institute, Barakaldo, Spain.,Department of Pathology, Cruces University Hospital, Barakaldo, Spain
| | - Víctor J Cid
- Departamento de Microbiología y Parasitología, Facultad de Farmacia, UCM & Instituto Ramón y Cajal de Investigaciones Sanitarias (IRYCIS), Madrid, Spain
| | - Rafael Pulido
- Biocruces Bizkaia Health Research Institute, Barakaldo, Spain.,Ikerbasque, The Basque Foundation for Science, Bilbao, Spain
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6
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Torices L, de las Heras J, Arango-Lasprilla JC, Cortés JM, Nunes-Xavier CE, Pulido R. MMADHC premature termination codons in the pathogenesis of cobalamin D disorder: Potential of translational readthrough reconstitution. Mol Genet Metab Rep 2021; 26:100710. [PMID: 33552904 PMCID: PMC7847965 DOI: 10.1016/j.ymgmr.2021.100710] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Accepted: 12/31/2020] [Indexed: 11/21/2022] Open
Abstract
Mutations in the MMADHC gene cause cobalamin D disorder (cblD), an autosomal recessive inborn disease with defects in intracellular cobalamin (cbl, vitamin B12) metabolism. CblD patients present methylmalonic aciduria (MMA), homocystinuria (HC), or combined MMA/HC, and usually suffer developmental delay and cognitive deficits. The most frequent MMADHC genetic alterations associated with disease generate MMADHC truncated proteins, in many cases due to mutations that create premature termination codons (PTC). In this study, we have performed a comprehensive and global characterization of MMADHC protein variants generated by all annotated MMADHC PTC mutations in cblD patients, and analyzed the potential of inducible translational PTC readthrough to reconstitute MMADHC biosynthesis. MMADHC protein truncation caused by disease-associated PTC differentially affected the alternative usage of translation initiation sites, protein abundance, and subcellular localization of MMADHC. Aminoglycoside compounds induced translational PTC readthrough of MMADHC truncated variants, allowing the biosynthesis of full-length MMADHC in a PTC-specific manner. Our results suggest that translational PTC readthrough-based interventions could complement current therapies for cblD patients carrying specific MMADHC PTC mutations.
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Affiliation(s)
- Leire Torices
- Biocruces Bizkaia Health Research Institute, Barakaldo, Spain
| | - Javier de las Heras
- Biocruces Bizkaia Health Research Institute, Barakaldo, Spain
- Division of Pediatric Metabolism (CIBER-ER), Cruces University Hospital, Barakaldo, Spain
- Department of Pediatrics, University of the Basque Country (UPV/EHU), Leioa, Spain
| | - Juan Carlos Arango-Lasprilla
- Biocruces Bizkaia Health Research Institute, Barakaldo, Spain
- Department of Cell Biology and Histology, University of the Basque Country (UPV/EHU), Leioa, Spain
- Ikerbasque, The Basque Foundation for Science, 48013 Bilbao, Spain
| | - Jesús M. Cortés
- Biocruces Bizkaia Health Research Institute, Barakaldo, Spain
- Department of Cell Biology and Histology, University of the Basque Country (UPV/EHU), Leioa, Spain
- Ikerbasque, The Basque Foundation for Science, 48013 Bilbao, Spain
| | - Caroline E. Nunes-Xavier
- Biocruces Bizkaia Health Research Institute, Barakaldo, Spain
- Institute of Cancer Research, Oslo University Hospital Radiumhospitalet, N-0424 Oslo, Norway
| | - Rafael Pulido
- Biocruces Bizkaia Health Research Institute, Barakaldo, Spain
- Ikerbasque, The Basque Foundation for Science, 48013 Bilbao, Spain
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7
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Baghban R, Farajnia S, Ghasemi Y, Hoseinpoor R, Safary A, Mortazavi M, Zarghami N. Mutational Analysis of Ocriplasmin to Reduce Proteolytic and Autolytic Activity in Pichia pastoris. Biol Proced Online 2020; 22:25. [PMID: 33308171 PMCID: PMC7734836 DOI: 10.1186/s12575-020-00138-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Accepted: 12/01/2020] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Ocriplasmin (Jetrea) is using for the treatment of symptomatic vitreomacular adhesion. This enzyme undergoes rapid inactivation and limited activity duration as a result of its autolytic nature after injection within the eye. Moreover, the proteolytic activity can cause photoreceptor damage, which may result in visual impairment in more serious cases. RESULTS The present research aimed to reduce the disadvantages of ocriplasmin using site-directed mutagenesis. To reduce the autolytic activity of ocriplasmin in the first variant, lysine 156 changed to glutamic acid and, in the second variant for the proteolytic activity reduction, alanine 59 mutated to threonine. The third variant contained both mutations. Expression of wild type and three mutant variants of ocriplasmin constructs were done in the Pichia pastoris expression system. The mutant variants were analyzed in silico and in vitro and compared to the wild type. The kinetic parameters of ocriplasmin variants showed both variants with K156E substitution were more resistant to autolytic degradation than wild-type. These variants also exhibited reduced Kcat and Vmax values. An increase in their Km values, leading to a decreased catalytic efficiency (the Kcat/Km ratio) of autolytic and mixed variants. Moreover, in the variant with A59T mutation, Kcat and Vmax values have reduced compared to wild type. The mix variants showed the most increase in Km value (almost 2-fold) as well as reduced enzymatic affinity to the substrate. Thus, the results indicated that combined mutations at the ocriplasmin sequence were more effective compared with single mutations. CONCLUSIONS The results indicated such variants represent valuable tools for the investigation of therapeutic strategies aiming at the non-surgical resolution of vitreomacular adhesion.
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Affiliation(s)
- Roghayyeh Baghban
- Medical Biotechnology Department, Faculty of Advanced Medical Science, Tabriz University of Medical Sciences, Tabriz, Iran
- Research Committee, Tabriz University of Medical Sciences, Tabriz, Iran
- Poostchi Ophthalmology Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
- Biotechnology Research Center, Tabriz University of Medical Sciences, Daneshgah Ave, Tabriz, Iran
| | - Safar Farajnia
- Biotechnology Research Center, Tabriz University of Medical Sciences, Daneshgah Ave, Tabriz, Iran.
- Drug Applied Research Center, Tabriz University of Medical Sciences, Tabriz, Iran.
| | - Younes Ghasemi
- Department of Pharmaceutical Biotechnology, Faculty of Pharmacy and Pharmaceutical Sciences Research Center, Shiraz University of Medical Science, Shiraz, Iran
| | - Reyhaneh Hoseinpoor
- Department of Biotechnology, School of Advanced Technologies in Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Azam Safary
- Connective Tissue Diseases Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Mojtaba Mortazavi
- Department of Biotechnology, Institute of Science and High Technology and Environmental Science, Graduate University of Advanced Technology, Kerman, Iran
| | - Nosratollah Zarghami
- Medical Biotechnology Department, Faculty of Advanced Medical Science, Tabriz University of Medical Sciences, Tabriz, Iran
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8
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De Las Heras J, Diez I, Jimenez-Marin A, Cabrera A, Ramos-Usuga D, Diaz-Fernandez MV, Torices L, Nunes-Xavier CE, Pulido R, Arango-Lasprilla JC, Cortes JM. Brain Circuit Alterations and Cognitive Disability in Late-Onset Cobalamin D Disorder. J Clin Med 2020; 9:E990. [PMID: 32252256 PMCID: PMC7231091 DOI: 10.3390/jcm9040990] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2020] [Revised: 03/21/2020] [Accepted: 04/01/2020] [Indexed: 12/13/2022] Open
Abstract
Neuroimaging studies describing brain circuits' alterations in cobalamin (vitamin B12)-deficient patients are limited and have not been carried out in patients with inborn errors of cobalamin metabolism. The objective of this study was to assess brain functionality and brain circuit alterations in a patient with an ultra-rare inborn error of cobalamin metabolism, methylmalonic aciduria, and homocystinuria due to cobalamin D disease, as compared with his twin sister as a healthy control (HC). We acquired magnetic resonance imaging (including structural, functional, and diffusion images) to calculate brain circuit abnormalities and combined these results with the scores after a comprehensive neuropsychological evaluation. As compared with HC, the patient had severe patterns of damage, such as a 254% increment of ventricular volume, pronounced subcortical and cortical atrophies (mainly at striatum, cingulate cortex, and precuneus), and connectivity alterations at fronto-striato-thalamic circuit, cerebellum, and corpus callosum. In agreement with brain circuit alterations, cognitive deficits existed in attention, executive function, inhibitory control, and mental flexibility. This is the first study that provides the clinical, genetic, neuroanatomical, neuropsychological, and psychosocial characterization of a patient with the cobalamin D disorder, showing functional alterations in central nervous system motor tracts, thalamus, cerebellum, and basal ganglia, that, as far as we know, have not been reported yet in vitamin B12-related disorders.
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Affiliation(s)
- Javier De Las Heras
- Division of Pediatric Metabolism, Cruces University Hospital, 48903 Barakaldo, Spain; (J.D.L.H.); (M.V.D.-F.)
- Inborn Errors of Metabolism Group, Biocruces Bizkaia Health Research Institute, 48903 Barakaldo, Spain
- Department of Pediatrics, University of the Basque Country (UPV/EHU), 48940 Leioa, Spain
| | - Ibai Diez
- Gordon Center for Medical Imaging, Department of Radiology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02115, USA;
- Athinoula A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02129, USA
- Neurotechnology Laboratory, Tecnalia Health Department, 48160 Derio, Spain
| | - Antonio Jimenez-Marin
- Computational Neuroimaging Group, Biocruces Bizkaia Health Research Institute, 48903 Barakaldo, Spain;
- Biomedical Research Doctorate Program, University of the Basque Country (UPV/EHU), 48940 Leioa, Spain;
| | | | - Daniela Ramos-Usuga
- Biomedical Research Doctorate Program, University of the Basque Country (UPV/EHU), 48940 Leioa, Spain;
- Biocruces Bizkaia Health Research Institute, 48903 Barakaldo, Spain
| | | | - Leire Torices
- Biomarkers in Cancer Unit, Biocruces Bizkaia Health Research Institute, 48903 Barakaldo, Spain; (L.T.); (C.E.N.-X.); (R.P.)
| | - Caroline E. Nunes-Xavier
- Biomarkers in Cancer Unit, Biocruces Bizkaia Health Research Institute, 48903 Barakaldo, Spain; (L.T.); (C.E.N.-X.); (R.P.)
- Department of Tumor Biology, Institute for Cancer Research, Oslo University Hospital Radiumhospitalet, 0424 Oslo, Norway
| | - Rafael Pulido
- Biomarkers in Cancer Unit, Biocruces Bizkaia Health Research Institute, 48903 Barakaldo, Spain; (L.T.); (C.E.N.-X.); (R.P.)
- IKERBASQUE. Basque Foundation for Science, 48013 Bilbao, Spain
| | - Juan Carlos Arango-Lasprilla
- Biocruces Bizkaia Health Research Institute, 48903 Barakaldo, Spain
- IKERBASQUE. Basque Foundation for Science, 48013 Bilbao, Spain
- Department of Cell Biology and Histology, University of the Basque Country (UPV/EHU), 48940 Leioa, Spain
| | - Jesus M. Cortes
- Computational Neuroimaging Group, Biocruces Bizkaia Health Research Institute, 48903 Barakaldo, Spain;
- IKERBASQUE. Basque Foundation for Science, 48013 Bilbao, Spain
- Department of Cell Biology and Histology, University of the Basque Country (UPV/EHU), 48940 Leioa, Spain
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9
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Precise definition of PTEN C-terminal epitopes and its implications in clinical oncology. NPJ Precis Oncol 2019; 3:11. [PMID: 30993208 PMCID: PMC6465295 DOI: 10.1038/s41698-019-0083-4] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2018] [Accepted: 03/05/2019] [Indexed: 02/07/2023] Open
Abstract
Anti-PTEN monoclonal antibodies (mAb) are arising as important tools for immunohistochemistry (IHC) and protein quantification routine analysis in clinical oncology. Although an effort has been made to document the reliability of tumor tissue section immunostaining by anti-PTEN mAb, and to standardize their IHC use in research and in the clinical practice, the precise topological and biochemical definition of the epitope recognized by each mAb has been conventionally overlooked. In this study, six commercial anti-PTEN mAb have been validated and characterized for sensitivity and specificity by IHC and FISH, using a set of prostate and urothelial bladder tumor specimens, and by immunoblot, using PTEN positive and PTEN negative human cell lines. Immunoblot precise epitope mapping, performed using recombinant PTEN variants and mutations, revealed that all mAb recognized linear epitopes of 6–11 amino acid length at the PTEN C-terminus. Tumor-associated or disease-associated mutations at the PTEN C-terminus did not affect subcellular localization or PIP3 phosphatase activity of PTEN in cells, although resulted in specific loss of reactivity for some mAb. Furthermore, specific mimicking-phosphorylation mutations at the PTEN C-terminal region also abolished binding of specific mAb. Our study adds new evidence on the relevance of a precise epitope mapping in the validation of anti-PTEN mAb for their use in the clinics. This will be substantial to provide a more accurate diagnosis in clinical oncology based on PTEN protein expression in tumors and biological fluids.
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10
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A pathogenic role for germline PTEN variants which accumulate into the nucleus. Eur J Hum Genet 2018; 26:1180-1187. [PMID: 29706633 DOI: 10.1038/s41431-018-0155-x] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2017] [Revised: 03/27/2018] [Accepted: 03/30/2018] [Indexed: 11/08/2022] Open
Abstract
The PTEN gene encodes a master regulator protein that exerts essential functions both in the cytoplasm and in the nucleus. PTEN is mutated in the germline of both patients with heterogeneous tumor syndromic diseases, categorized as PTEN hamartoma tumor syndrome (PHTS), and a group affected with autism spectrum disorders (ASD). Previous studies have unveiled the functional heterogeneity of PTEN variants found in both patient cohorts, making functional studies necessary to provide mechanistic insights related to their pathogenicity. Here, we have functionally characterized a PTEN missense variant [c.49C>G; p.(Gln17Glu); Q17E] associated to both PHTS and ASD patients. The PTEN Q17E variant displayed partially reduced PIP3-catalytic activity and normal stability in cells, as shown using S. cerevisiae and mammalian cell experimental models. Remarkably, PTEN Q17E accumulated in the nucleus, in a process involving the PTEN N-terminal nuclear localization sequence. The analysis of additional germline-associated PTEN N-terminal variants illustrated the existence of a PTEN N-terminal region whose targeting in disease causes PTEN nuclear accumulation, in parallel with defects in PIP3-catalytic activity in cells. Our findings highlight the frequent occurrence of PTEN gene mutations targeting PTEN N-terminus whose pathogenicity may be related, at least in part, with the retention of PTEN in the nucleus. This could be important for the implementation of precision therapies for patients with alterations in the PTEN pathway.
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11
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Abstract
Directed evolution has emerged as one of the most effective protein engineering methods in basic research as well as in applications in synthetic organic chemistry and biotechnology. The successful engineering of protein activity, allostery, binding affinity, expression, folding, fluorescence, solubility, substrate scope, selectivity (enantio-, stereo-, and regioselectivity), and/or stability (temperature, organic solvents, pH) is just limited by the throughput of the genetic selection, display, or screening system that is available for a given protein. Sometimes it is possible to analyze millions of protein variants from combinatorial libraries per day. In other cases, however, only a few hundred variants can be screened in a single day, and thus the creation of smaller yet smarter libraries is needed. Different strategies have been developed to create these libraries. One approach is to perform mutational scanning or to construct "mutability landscapes" in order to understand sequence-function relationships that can guide the actual directed evolution process. Herein we provide a protocol for economically constructing scanning mutagenesis libraries using a cytochrome P450 enzyme in a high-throughput manner. The goal is to engineer activity, regioselectivity, and stereoselectivity in the oxidative hydroxylation of a steroid, a challenging reaction in synthetic organic chemistry. Libraries based on mutability landscapes can be used to engineer any fitness trait of interest. The protocol is also useful for constructing gene libraries for deep mutational scanning experiments.
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Affiliation(s)
- Carlos G Acevedo-Rocha
- Department of Biocatalysis, Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470, Mülheim an der Ruhr, Germany.
- Department of Chemistry, Philipps-Universität Marburg, Marburg, 35032, Germany.
- Biosyntia ApS, 2100, Copenhagen, Denmark.
| | - Matteo Ferla
- Department of Biochemistry, Oxford University, Oxford, OX1 3QU, UK
| | - Manfred T Reetz
- Department of Biocatalysis, Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470, Mülheim an der Ruhr, Germany
- Department of Chemistry, Philipps-Universität Marburg, Marburg, 35032, Germany
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12
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Luna S, Mingo J, Amo L, Rodríguez-Escudero I, Erramuzpe A, Molina M, Nunes-Xavier C, Tejada I, López J, Cortés J, Cid V, Pulido R. Readthrough response of pathogenic premature termination codons at PTEN gene: implications in precision therapy for PHTS patients. Ann Oncol 2017. [DOI: 10.1093/annonc/mdx508.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
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13
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Mingo J, Luna S, Gaafar A, Ruiz R, Carracedo A, Guerra I, López J, Pulido R. The relevance of precision epitope mapping for accurate oncologic diagnostic based on PTEN protein expression in tumours. Ann Oncol 2017. [DOI: 10.1093/annonc/mdx508.018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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14
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Ipe J, Swart M, Burgess KS, Skaar TC. High-Throughput Assays to Assess the Functional Impact of Genetic Variants: A Road Towards Genomic-Driven Medicine. Clin Transl Sci 2017; 10:67-77. [PMID: 28213901 PMCID: PMC5355973 DOI: 10.1111/cts.12440] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2016] [Accepted: 01/03/2017] [Indexed: 01/08/2023] Open
Affiliation(s)
- J Ipe
- Indiana University School of Medicine, Department of Medicine, Division of Clinical Pharmacology, Indianapolis, Indiana, USA
| | - M Swart
- Indiana University School of Medicine, Department of Medicine, Division of Clinical Pharmacology, Indianapolis, Indiana, USA
| | - K S Burgess
- Indiana University School of Medicine, Department of Medicine, Division of Clinical Pharmacology, Indianapolis, Indiana, USA.,Indiana University School of Medicine, Department of Pharmacology and Toxicology, Indianapolis, Indiana, USA
| | - T C Skaar
- Indiana University School of Medicine, Department of Medicine, Division of Clinical Pharmacology, Indianapolis, Indiana, USA
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