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López-Rivera JJ, Rodríguez-Salazar L, Soto-Ospina A, Estrada-Serrato C, Serrano D, Chaparro-Solano HM, Londoño O, Rueda PA, Ardila G, Villegas-Lanau A, Godoy-Corredor M, Cuartas M, Vélez JI, Vidal OM, Isaza-Ruget MA, Arcos-Burgos M. Structural Protein Effects Underpinning Cognitive Developmental Delay of the PURA p.Phe233del Mutation Modelled by Artificial Intelligence and the Hybrid Quantum Mechanics–Molecular Mechanics Framework. Brain Sci 2022; 12:brainsci12070871. [PMID: 35884678 PMCID: PMC9313109 DOI: 10.3390/brainsci12070871] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Revised: 06/21/2022] [Accepted: 06/24/2022] [Indexed: 02/06/2023] Open
Abstract
A whole-exome capture and next-generation sequencing was applied to an 11 y/o patient with a clinical history of congenital hypotonia, generalized motor and cognitive neurodevelopmental delay, and severe cognitive deficit, and without any identifiable Syndromic pattern, and to her parents, we disclosed a de novo heterozygous pathogenic mutation, c.697_699del p.Phe233del (rs786204835)(ACMG classification PS2, PM1, PM2, PP5), harbored in the PURA gene (MIM*600473) (5q31.3), associated with Autosomal Dominant Mental Retardation 31 (MIM # 616158). We used the significant improvement in the accuracy of protein structure prediction recently implemented in AlphaFold that incorporates novel neural network architectures and training procedures based on the evolutionary, physical, and geometric constraints of protein structures. The wild-type (WT) sequence and the mutated sequence, missing the Phe233, were reconstructed. The predicted local Distance Difference Test (lDDT) for the PURAwt and the PURA–Phe233del showed that the occurrence of the Phe233del affects between 220–320 amino acids. The distortion in the PURA structural conformation in the ~5 Å surrounding area after the p.Phe233del produces a conspicuous disruption of the repeat III, where the DNA and RNA helix unwinding capability occurs. PURA Protein–DNA docking corroborated these results in an in silico analysis that showed a loss of the contact of the PURA–Phe233del III repeat domain model with the DNA. Together, (i) the energetic and stereochemical, (ii) the hydropathic indexes and polarity surfaces, and (iii) the hybrid Quantum Mechanics–Molecular Mechanics (QM–MM) analyses of the PURA molecular models demarcate, at the atomic resolution, the specific surrounding region affected by these mutations and pave the way for future cell-based functional analysis. To the best of our knowledge, this is the first report of a de novo mutation underpinning a PURA syndrome in a Latin American patient and highlights the importance of predicting the molecular effects in protein structure using artificial intelligence algorithms and molecular and atomic resolution stereochemical analyses.
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Affiliation(s)
- Juan Javier López-Rivera
- INPAC Research Group, Fundación Universitaria Sanitas, Bogotá 111321, Colombia;
- Grupo de Genética Médica, Clínica Universitaria Colombia y Clínica Pediátrica Colsanitas, Bogotá 111321, Colombia; (C.E.-S.); (D.S.); (H.M.C.-S.); (O.L.)
- Correspondence: (J.J.L.-R.); (M.A.-B.)
| | - Luna Rodríguez-Salazar
- Grupo de Bioinformática, Laboratorio de Clínica Colsanitas, Bogotá 110221, Colombia; (L.R.-S.); (P.A.R.); (G.A.)
| | - Alejandro Soto-Ospina
- Genética Molecular (GenMol), Facultad de Ciencias Exactas y Naturales, Universidad de Antioquia, Medellín 050012, Colombia; (A.S.-O.); (A.V.-L.)
| | - Carlos Estrada-Serrato
- Grupo de Genética Médica, Clínica Universitaria Colombia y Clínica Pediátrica Colsanitas, Bogotá 111321, Colombia; (C.E.-S.); (D.S.); (H.M.C.-S.); (O.L.)
| | - David Serrano
- Grupo de Genética Médica, Clínica Universitaria Colombia y Clínica Pediátrica Colsanitas, Bogotá 111321, Colombia; (C.E.-S.); (D.S.); (H.M.C.-S.); (O.L.)
| | - Henry Mauricio Chaparro-Solano
- Grupo de Genética Médica, Clínica Universitaria Colombia y Clínica Pediátrica Colsanitas, Bogotá 111321, Colombia; (C.E.-S.); (D.S.); (H.M.C.-S.); (O.L.)
| | - Olga Londoño
- Grupo de Genética Médica, Clínica Universitaria Colombia y Clínica Pediátrica Colsanitas, Bogotá 111321, Colombia; (C.E.-S.); (D.S.); (H.M.C.-S.); (O.L.)
| | - Paula A. Rueda
- Grupo de Bioinformática, Laboratorio de Clínica Colsanitas, Bogotá 110221, Colombia; (L.R.-S.); (P.A.R.); (G.A.)
| | - Geraldine Ardila
- Grupo de Bioinformática, Laboratorio de Clínica Colsanitas, Bogotá 110221, Colombia; (L.R.-S.); (P.A.R.); (G.A.)
| | - Andrés Villegas-Lanau
- Genética Molecular (GenMol), Facultad de Ciencias Exactas y Naturales, Universidad de Antioquia, Medellín 050012, Colombia; (A.S.-O.); (A.V.-L.)
- Grupo de Neurociencias de Antioquia (GNA), Facultad de Medicina, Universidad de Antioquia, Medellín 050012, Colombia
| | | | - Mauricio Cuartas
- Grupo de Investigación Estudios en Psicología, Departamento de Psicología, Escuela de Humanidades, Universidad EAFIT, Medellín 050022, Colombia;
| | - Jorge I. Vélez
- Universidad del Norte, Barranquilla 080001, Colombia; (J.I.V.); (O.M.V.)
| | - Oscar M. Vidal
- Universidad del Norte, Barranquilla 080001, Colombia; (J.I.V.); (O.M.V.)
| | | | - Mauricio Arcos-Burgos
- Grupo de Investigación en Psiquiatría (GIPSI), Departamento de Psiquiatría, Instituto de Investigaciones Médicas, Facultad de Medicina, Universidad de Antioquia, Medellín 050012, Colombia
- Correspondence: (J.J.L.-R.); (M.A.-B.)
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Identification of Potential Prognostic Biomarkers for Breast Cancer Based on lncRNA-TF-Associated ceRNA Network and Functional Module. BIOMED RESEARCH INTERNATIONAL 2021; 2020:5257896. [PMID: 32802855 PMCID: PMC7411464 DOI: 10.1155/2020/5257896] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Revised: 06/23/2020] [Accepted: 06/29/2020] [Indexed: 11/17/2022]
Abstract
Breast cancer leads to most of cancer deaths among women worldwide. Systematically analyzing the competing endogenous RNA (ceRNA) network and their functional modules may provide valuable insight into the pathogenesis of breast cancer. In this study, we constructed a lncRNA-TF-associated ceRNA network via combining all the significant lncRNA-TF ceRNA pairs and TF-TF PPI pairs. We computed important topological features of the network, such as degree and average path length. Hub nodes in the lncRNA-TF-associated ceRNA network were extracted to detect differential expression in different subtypes and tumor stages of breast cancer. MCODE was used for identifying the closely connected modules from the ceRNA network. Survival analysis was further used for evaluating whether the modules had prognosis effects on breast cancer. TF motif searching analysis was performed for investigating the binding potentials between lncRNAs and TFs. As a result, a lncRNA-TF-associated ceRNA network in breast cancer was constructed, which had a scale-free property. Hub nodes such as MDM4, ZNF410, AC0842-19, and CTB-89H12 were differentially expressed between cancer and normal sample in different subtypes and tumor stages. Two closely connected modules were identified to significantly classify patients into a low-risk group and high-risk group with different clinical outcomes. TF motif searching analysis suggested that TFs, such as NFAT5, might bind to the promoter and enhancer regions of hub lncRNAs and function in breast cancer biology. The results demonstrated that the synergistic, competitive lncRNA-TF ceRNA network and their functional modules played important roles in the biological processes and molecular functions of breast cancer.
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Daniel DC, Johnson EM. PURA, the gene encoding Pur-alpha, member of an ancient nucleic acid-binding protein family with mammalian neurological functions. Gene 2017; 643:133-143. [PMID: 29221753 DOI: 10.1016/j.gene.2017.12.004] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2017] [Revised: 12/04/2017] [Accepted: 12/04/2017] [Indexed: 12/20/2022]
Abstract
The PURA gene encodes Pur-alpha, a 322 amino acid protein with repeated nucleic acid binding domains that are highly conserved from bacteria through humans. PUR genes with a single copy of this domain have been detected so far in spirochetes and bacteroides. Lower eukaryotes possess one copy of the PUR gene, whereas chordates possess 1 to 4 PUR family members. Human PUR genes encode Pur-alpha (Pura), Pur-beta (Purb) and two forms of Pur-gamma (Purg). Pur-alpha is a protein that binds specific DNA and RNA sequence elements. Human PURA, located at chromosome band 5q31, is under complex control of three promoters. The entire protein coding sequence of PURA is contiguous within a single exon. Several studies have found that overexpression or microinjection of Pura inhibits anchorage-independent growth of oncogenically transformed cells and blocks proliferation at either G1-S or G2-M checkpoints. Effects on the cell cycle may be mediated by interaction of Pura with cellular proteins including Cyclin/Cdk complexes and the Rb tumor suppressor protein. PURA knockout mice die shortly after birth with effects on brain and hematopoietic development. In humans environmentally induced heterozygous deletions of PURA have been implicated in forms of myelodysplastic syndrome and progression to acute myelogenous leukemia. Pura plays a role in AIDS through association with the HIV-1 protein, Tat. In the brain Tat and Pura association in glial cells activates transcription and replication of JC polyomavirus, the agent causing the demyelination disease, progressive multifocal leukoencephalopathy. Tat and Pura also act to stimulate replication of the HIV-1 RNA genome. In neurons Pura accompanies mRNA transcripts to sites of translation in dendrites. Microdeletions in the PURA locus have been implicated in several neurological disorders. De novo PURA mutations have been related to a spectrum of phenotypes indicating a potential PURA syndrome. The nucleic acid, G-rich Pura binding element is amplified as expanded polynucleotide repeats in several brain diseases including fragile X syndrome and a familial form of amyotrophic lateral sclerosis/fronto-temporal dementia. Throughout evolution the Pura protein plays a critical role in survival, based on conservation of its nucleic acid binding properties. These Pura properties have been adapted in higher organisms to the as yet unfathomable development of the human brain.
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Affiliation(s)
- Dianne C Daniel
- Department of Microbiology and Molecular Cell Biology, Eastern Virginia Medical School, Norfolk, VA 23507, USA
| | - Edward M Johnson
- Department of Microbiology and Molecular Cell Biology, Eastern Virginia Medical School, Norfolk, VA 23507, USA.
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Bida O, Gidoni M, Ideses D, Efroni S, Ginsberg D. A novel mitosis-associated lncRNA, MA-linc1, is required for cell cycle progression and sensitizes cancer cells to Paclitaxel. Oncotarget 2016; 6:27880-90. [PMID: 26337085 PMCID: PMC4695032 DOI: 10.18632/oncotarget.4944] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2015] [Accepted: 07/31/2015] [Indexed: 11/25/2022] Open
Abstract
Long noncoding RNAs (lncRNAs) are major regulators of many cellular processes including cell cycle progression and tumorigenesis. In this study, we identify a novel lncRNA, MA-linc1, and reveal its effects on cell cycle progression and cancer growth. Inhibition of MA-linc1 expression alters cell cycle distribution, leading to a decrease in the number of G1 cells and a concomitant increase in all other stages of the cell cycle, and in particular G2/M, suggesting its involvement in the regulation of M phase. Accordingly, knock down of MA-linc1 inhibits M phase exit upon release from a mitotic block. We further demonstrate that MA-linc1 predominantly functions in cis to repress expression of its neighboring gene, Purα, which is often deleted in human cancers and whose ectopic expression inhibits cell cycle progression. Knock down of Purα partially rescues the MA-linc1 dependent inhibition of M phase exit. In agreement with its suggested role in M phase, inhibition of MA-linc1 enhances apoptotic cell death induced by the antimitotic drug, Paclitaxel and this enhancement of apoptosis is rescued by Purα knockdown. Furthermore, high levels of MA-linc1 are associated with reduced survival in human breast and lung cancer patients. Taken together, our data identify MA-linc1 as a novel lncRNA regulator of cell cycle and demonstrate its potential role in cancer progression and treatment.
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Affiliation(s)
- Or Bida
- The Mina and Everard Goodman Faculty of Life Science, Bar Ilan University, Ramat Gan 52900, Israel
| | - Moriah Gidoni
- The Mina and Everard Goodman Faculty of Life Science, Bar Ilan University, Ramat Gan 52900, Israel
| | - Diana Ideses
- The Mina and Everard Goodman Faculty of Life Science, Bar Ilan University, Ramat Gan 52900, Israel
| | - Sol Efroni
- The Mina and Everard Goodman Faculty of Life Science, Bar Ilan University, Ramat Gan 52900, Israel
| | - Doron Ginsberg
- The Mina and Everard Goodman Faculty of Life Science, Bar Ilan University, Ramat Gan 52900, Israel
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Li S, Wang L, Fu B, Dorf ME. Trim65: a cofactor for regulation of the microRNA pathway. RNA Biol 2015; 11:1113-21. [PMID: 25483047 DOI: 10.4161/rna.36179] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
MicroRNA (miRNA) comprise a large family of non-protein coding transcripts which regulate gene expression in diverse biological pathways of both plants and animals. We recently used a systematic proteomic approach to generate a protein interactome map of the human miRNA pathway involved in miRNA biogenesis and processing. The interactome expands the number of candidate proteins in the miRNA pathway and connects the network to other cellular processes. Functional analyses identified TRIM65 and at least 3 other proteins as novel regulators of the miRNA pathway. Biochemical studies established that TRIM65 forms stable complexes with TNRC6 proteins and these molecules co-localize in P-body-like structures. Gain of function and RNAi analyses reveal that TRIM65 negatively regulates miRNA-driven suppression of mRNA translation by targeting TNRC6 proteins for ubiquitination and degradation. The potential molecular mechanisms which regulate TRIM65 catalytic activity are discussed.
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Key Words
- AGO, Argonaute
- AP-MS, Affinity purification coupled with mass spectrometry
- DGCR8, DiGeorge syndrome critical region gene 8
- HCIP, High confidence interacting protein
- IMP-1, IGF2 mRNA-binding protein 1
- MOV10, Moloney leukemia virus 10
- MiRNA, microRNA
- PDCD4, Programmed cell death 4
- PTEN, Phosphatase and tensin homolog
- RISC, RNA-induced silencing complex
- RNA-induced silencing complex
- TARBP2, TAR (HIV-1) RNA binding protein 2
- TNRC6
- TNRC6, Trinucleotide repeat containing 6
- TRIM65, Tripartite Motif-Containing 65
- interactome
- proteomics
- tripartite motif proteins
- ubiquitin E3 ligase
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Affiliation(s)
- Shitao Li
- a Department of Microbiology & Immunobiology; Harvard Medical School; Boston , MA USA
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Jutras BL, Chenail AM, Carroll DW, Miller MC, Zhu H, Bowman A, Stevenson B. Bpur, the Lyme disease spirochete's PUR domain protein: identification as a transcriptional modulator and characterization of nucleic acid interactions. J Biol Chem 2013; 288:26220-26234. [PMID: 23846702 PMCID: PMC3764826 DOI: 10.1074/jbc.m113.491357] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
The PUR domain is a nucleic acid-binding motif found in critical regulatory proteins of higher eukaryotes and in certain species of bacteria. During investigations into mechanisms by which the Lyme disease spirochete controls synthesis of its Erp surface proteins, it was discovered that the borrelial PUR domain protein, Bpur, binds with high affinity to double-stranded DNA adjacent to the erp transcriptional promoter. Bpur was found to enhance the effects of the erp repressor protein, BpaB. Bpur also bound single-stranded DNA and RNA, with relative affinities RNA > double-stranded DNA > single-stranded DNA. Rational site-directed mutagenesis of Bpur identified amino acid residues and domains critical for interactions with nucleic acids, and it revealed that the PUR domain has a distinct mechanism of interaction with each type of nucleic acid ligand. These data shed light on both gene regulation in the Lyme spirochete and functional mechanisms of the widely distributed PUR domain.
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Affiliation(s)
- Brandon L Jutras
- From the Department of Microbiology, Immunology, and Molecular Genetics and
| | - Alicia M Chenail
- From the Department of Microbiology, Immunology, and Molecular Genetics and
| | - Dustin W Carroll
- the Graduate Center for Toxicology, University of Kentucky College of Medicine, Lexington, Kentucky 40536
| | - M Clarke Miller
- the James Graham Brown Cancer Center, University of Louisville, Louisville, Kentucky 40202, and
| | - Haining Zhu
- the Department of Molecular and Cellular Biochemistry, University of Kentucky College of Medicine, Lexington, Kentucky 40536
| | - Amy Bowman
- From the Department of Microbiology, Immunology, and Molecular Genetics and
| | - Brian Stevenson
- From the Department of Microbiology, Immunology, and Molecular Genetics and.
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