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      Novel application of luciferase assay for the in vitro functional assessment of KAL1 variants in three females with septo-optic dysplasia (SOD)

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          Abstract

          KAL1 is implicated in 5% of Kallmann syndrome cases, a disorder which genotypically overlaps with septo-optic dysplasia (SOD). To date, a reporter-based assay to assess the functional consequences of KAL1 mutations is lacking. We aimed to develop a luciferase assay for novel application to functional assessment of rare KAL1 mutations detected in a screen of 422 patients with SOD.

          Quantitative analysis was performed using L6-myoblasts stably expressing FGFR1, transfected with a luciferase-reporter vector containing elements of the FGF-responsive osteocalcin promoter.

          The two variants assayed [p.K185N, p.P291T], were detected in three females with SOD (presenting with optic nerve hypoplasia, midline and pituitary defects). Our novel assay revealed significant decreases in transcriptional activity [p.K185N: 21% (p < 0.01); p.P291T: 40% (p < 0.001)].

          Our luciferase-reporter assay, developed for assessment of KAL1 mutations, determined that two variants in females with hypopituitarism/SOD are loss-of-function; demonstrating that this assay is suitable for quantitative assessment of mutations in this gene.

          Highlights

          • We identified variations in X-linked KAL1 in three girls with septo-optic dysplasia.

          • We developed a luciferase assay for novel functional assessment of these variants.

          • Variants were loss of function but variably penetrant; other genes may be involved.

          • Cellular secretion of one of the mutant KAL1 proteins was partially disrupted.

          • We identified KAL1 expression in developing human pituitary by in situ hybridisation.

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          Most cited references45

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          The Protein Data Bank.

          The Protein Data Bank (PDB; http://www.rcsb.org/pdb/ ) is the single worldwide archive of structural data of biological macromolecules. This paper describes the goals of the PDB, the systems in place for data deposition and access, how to obtain further information, and near-term plans for the future development of the resource.
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            Comparative protein modelling by satisfaction of spatial restraints.

            We describe a comparative protein modelling method designed to find the most probable structure for a sequence given its alignment with related structures. The three-dimensional (3D) model is obtained by optimally satisfying spatial restraints derived from the alignment and expressed as probability density functions (pdfs) for the features restrained. For example, the probabilities for main-chain conformations of a modelled residue may be restrained by its residue type, main-chain conformation of an equivalent residue in a related protein, and the local similarity between the two sequences. Several such pdfs are obtained from the correlations between structural features in 17 families of homologous proteins which have been aligned on the basis of their 3D structures. The pdfs restrain C alpha-C alpha distances, main-chain N-O distances, main-chain and side-chain dihedral angles. A smoothing procedure is used in the derivation of these relationships to minimize the problem of a sparse database. The 3D model of a protein is obtained by optimization of the molecular pdf such that the model violates the input restraints as little as possible. The molecular pdf is derived as a combination of pdfs restraining individual spatial features of the whole molecule. The optimization procedure is a variable target function method that applies the conjugate gradients algorithm to positions of all non-hydrogen atoms. The method is automated and is illustrated by the modelling of trypsin from two other serine proteinases.
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              A coding-independent function of gene and pseudogene mRNAs regulates tumour biology

              The canonical role of messenger RNA (mRNA) is to deliver protein-coding information to sites of protein synthesis. However, given that microRNAs bind to RNAs, we hypothesized that RNAs possess a biological role in cancer cells that relies upon their ability to compete for microRNA binding and is independent of their protein-coding function. As a paradigm for the protein-coding-independent role of RNAs, we describe the functional relationship between the mRNAs produced by the PTEN tumour suppressor gene and its pseudogene (PTENP1) and the critical consequences of this interaction. We find that PTENP1 is biologically active as determined by its ability to regulate cellular levels of PTEN, and that it can exert a growth-suppressive role. We also show that PTENP1 locus is selectively lost in human cancer. We extend our analysis to other cancer-related genes that possess pseudogenes, such as oncogenic KRAS. Further, we demonstrate that the transcripts of protein coding genes such as PTEN are also biologically active. Together, these findings attribute a novel biological role to expressed pseudogenes, as they can regulate coding gene expression, and reveal a non-coding function for mRNAs.
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                Author and article information

                Contributors
                Journal
                Mol Cell Endocrinol
                Mol. Cell. Endocrinol
                Molecular and Cellular Endocrinology
                North Holland Publishing
                0303-7207
                1872-8057
                05 December 2015
                05 December 2015
                : 417
                : 63-72
                Affiliations
                [a ]Section of Genetics and Epigenetics in Health and Disease, Genetics and Genomic Medicine Programme, UCL Institute of Child Health, London, UK
                [b ]Kinghorn Centre for Clinical Genomics, Garvan Institute of Medical Research, Darlinghurst, NSW, Australia
                [c ]St Vincent's Clinical School, UNSW Australia, Sydney, NSW, Australia
                [d ]Centre for Neuroendocrinology, Royal Free Hospital and University College Medical School, University College London, London, UK
                [e ]Department of Anaesthesiology, Nanjing Medical University First Affiliated Hospital, Jiangsu Province Hospital, Nanjing 210029, China
                [f ]Neural Development Unit, UCL Institute of Child Health, London, UK
                [g ]Centre for Endocrinology, William Harvey Research Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, John Vane Science Centre, Charterhouse Square, London, UK
                [h ]Division of Mathematical Biology, National Institute for Medical Research, London, UK
                [i ]University of Cambridge, Addenbrookes Hospital, Cambridge, UK
                [j ]Princess Margaret Hospital for Children, Subiaco, Western Australia, Australia
                Author notes
                []Corresponding author. UCL-Institute of Child Health 30 Guilford St London, WC1N 1EH, UK. m.dattani@ 123456ucl.ac.uk
                [1]

                The first two authors contributed equally to the work.

                Article
                S0303-7207(15)30076-9
                10.1016/j.mce.2015.09.010
                4646839
                26375424
                95b25796-1e6d-4986-ba72-73ae65f6fc9a
                © 2015 The Authors

                This is an open access article under the CC BY license (http://creativecommons.org/licenses/by/4.0/).

                History
                : 21 March 2015
                : 10 September 2015
                : 10 September 2015
                Categories
                Article

                Endocrinology & Diabetes
                luciferase assay,septo-optic dysplasia,kal1,kallmann syndrome,females
                Endocrinology & Diabetes
                luciferase assay, septo-optic dysplasia, kal1, kallmann syndrome, females

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