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Marom R, Zhang B, Washington ME, Song IW, Burrage LC, Rossi VC, Berrier AS, Lindsey A, Lesinski J, Nonet ML, Chen J, Baldridge D, Silverman GA, Sutton VR, Rosenfeld JA, Tran AA, Hicks MJ, Murdock DR, Dai H, Weis M, Jhangiani SN, Muzny DM, Gibbs RA, Caswell R, Pottinger C, Cilliers D, Stals K, Eyre D, Krakow D, Schedl T, Pak SC, Lee BH. Dominant negative variants in KIF5B cause osteogenesis imperfecta via down regulation of mTOR signaling. PLoS Genet 2023; 19:e1011005. [PMID: 37934770 PMCID: PMC10656020 DOI: 10.1371/journal.pgen.1011005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2023] [Revised: 11/17/2023] [Accepted: 10/03/2023] [Indexed: 11/09/2023] Open
Abstract
BACKGROUND Kinesin motor proteins transport intracellular cargo, including mRNA, proteins, and organelles. Pathogenic variants in kinesin-related genes have been implicated in neurodevelopmental disorders and skeletal dysplasias. We identified de novo, heterozygous variants in KIF5B, encoding a kinesin-1 subunit, in four individuals with osteogenesis imperfecta. The variants cluster within the highly conserved kinesin motor domain and are predicted to interfere with nucleotide binding, although the mechanistic consequences on cell signaling and function are unknown. METHODS To understand the in vivo genetic mechanism of KIF5B variants, we modeled the p.Thr87Ile variant that was found in two patients in the C. elegans ortholog, unc-116, at the corresponding position (Thr90Ile) by CRISPR/Cas9 editing and performed functional analysis. Next, we studied the cellular and molecular consequences of the recurrent p.Thr87Ile variant by microscopy, RNA and protein analysis in NIH3T3 cells, primary human fibroblasts and bone biopsy. RESULTS C. elegans heterozygous for the unc-116 Thr90Ile variant displayed abnormal body length and motility phenotypes that were suppressed by additional copies of the wild type allele, consistent with a dominant negative mechanism. Time-lapse imaging of GFP-tagged mitochondria showed defective mitochondria transport in unc-116 Thr90Ile neurons providing strong evidence for disrupted kinesin motor function. Microscopy studies in human cells showed dilated endoplasmic reticulum, multiple intracellular vacuoles, and abnormal distribution of the Golgi complex, supporting an intracellular trafficking defect. RNA sequencing, proteomic analysis, and bone immunohistochemistry demonstrated down regulation of the mTOR signaling pathway that was partially rescued with leucine supplementation in patient cells. CONCLUSION We report dominant negative variants in the KIF5B kinesin motor domain in individuals with osteogenesis imperfecta. This study expands the spectrum of kinesin-related disorders and identifies dysregulated signaling targets for KIF5B in skeletal development.
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Affiliation(s)
- Ronit Marom
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
- Texas Children’s Hospital, Houston, Texas, United States of America
| | - Bo Zhang
- Department of Pediatrics, Washington University School of Medicine, St Louis, Missouri, United States of America
| | - Megan E. Washington
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
| | - I-Wen Song
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
| | - Lindsay C. Burrage
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
- Texas Children’s Hospital, Houston, Texas, United States of America
| | - Vittoria C. Rossi
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
- Texas Children’s Hospital, Houston, Texas, United States of America
| | - Ava S. Berrier
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
| | - Anika Lindsey
- Department of Pediatrics, Washington University School of Medicine, St Louis, Missouri, United States of America
| | - Jacob Lesinski
- Department of Pediatrics, Washington University School of Medicine, St Louis, Missouri, United States of America
| | - Michael L. Nonet
- Department of Neuroscience, Washington University School of Medicine, St Louis, Missouri, United States of America
| | - Jian Chen
- Department of Genetics, Washington University School of Medicine, St Louis, Missouri, United States of America
| | - Dustin Baldridge
- Department of Pediatrics, Washington University School of Medicine, St Louis, Missouri, United States of America
| | - Gary A. Silverman
- Department of Pediatrics, Washington University School of Medicine, St Louis, Missouri, United States of America
| | - V. Reid Sutton
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
- Texas Children’s Hospital, Houston, Texas, United States of America
| | - Jill A. Rosenfeld
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
| | - Alyssa A. Tran
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
| | - M. John Hicks
- Texas Children’s Hospital, Houston, Texas, United States of America
- Department of Pathology & Immunology, Baylor College of Medicine, Houston, Texas, United States of America
| | - David R. Murdock
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
| | - Hongzheng Dai
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
| | - MaryAnn Weis
- Department of Orthopaedics and Sports Medicine, University of Washington, Seattle, Washington, United States of America
| | - Shalini N. Jhangiani
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
| | - Donna M. Muzny
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
| | - Richard A. Gibbs
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
| | - Richard Caswell
- Exeter Genomics Laboratory, Royal Devon University Healthcare NHS Foundation Trust, Exeter, United Kingdom
| | - Carrie Pottinger
- All Wales Medical Genomics Service, Wrexham Maelor Hospital, Wrexham, UK
| | - Deirdre Cilliers
- Oxford Centre for Genomic Medicine, Oxford University Hospitals NHS Foundation Trust, Oxford, United Kingdom
| | - Karen Stals
- Exeter Genomics Laboratory, Royal Devon University Healthcare NHS Foundation Trust, Exeter, United Kingdom
| | | | - David Eyre
- Department of Orthopaedics and Sports Medicine, University of Washington, Seattle, Washington, United States of America
| | - Deborah Krakow
- Human Genetics, Obstetrics & Gynecology, Orthopedic Surgery, University of California, Los Angeles, California, United States of America
| | - Tim Schedl
- Department of Genetics, Washington University School of Medicine, St Louis, Missouri, United States of America
| | - Stephen C. Pak
- Department of Pediatrics, Washington University School of Medicine, St Louis, Missouri, United States of America
| | - Brendan H. Lee
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
- Texas Children’s Hospital, Houston, Texas, United States of America
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2
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Yanaizu M, Adachi H, Araki M, Kontani K, Kino Y. Translational regulation and protein-coding capacity of the 5' untranslated region of human TREM2. Commun Biol 2023; 6:616. [PMID: 37291187 PMCID: PMC10250343 DOI: 10.1038/s42003-023-04998-6] [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: 09/08/2022] [Accepted: 05/30/2023] [Indexed: 06/10/2023] Open
Abstract
TREM2 is a transmembrane receptor expressed in microglia and macrophages. Elevated TREM2 levels in these cells are associated with age-related pathological conditions, including Alzheimer's disease. However, the regulatory mechanism underlying the protein expression of TREM2 remains unclear. In this study, we uncover the role of the 5' untranslated region (5'-UTR) of human TREM2 in translation. An upstream start codon (uAUG) in the 5'-UTR of TREM2 is specific to some primates, including humans. The expression of the conventional TREM2 protein, starting from the downstream AUG (dTREM2), is repressed by the 5'-UTR in a uAUG-mediated manner. We also detect a TREM2 protein isoform starting from uAUG (uTREM2) that is largely degraded by proteasomes. Finally, the 5'-UTR is essential for the downregulation of dTREM2 expression in response to amino acid starvation. Collectively, our study identifies a species-specific regulatory role of the 5'-UTR in TREM2 translation.
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Affiliation(s)
- Motoaki Yanaizu
- Department of Bioinformatics and Molecular Neuropathology, Meiji Pharmaceutical University, 2-522-1, Noshio, Kiyose-shi, Tokyo, 204-8588, Japan
- Department of RNA Pathobiology and Therapeutics, Meiji Pharmaceutical University, 2-522-1, Noshio, Kiyose-shi, Tokyo, 204-8588, Japan
| | - Haruka Adachi
- Department of Bioinformatics and Molecular Neuropathology, Meiji Pharmaceutical University, 2-522-1, Noshio, Kiyose-shi, Tokyo, 204-8588, Japan
| | - Makoto Araki
- Department of Biochemistry, Meiji Pharmaceutical University, 2-522-1, Noshio, Kiyose-shi, Tokyo, 204-8588, Japan
| | - Kenji Kontani
- Department of Biochemistry, Meiji Pharmaceutical University, 2-522-1, Noshio, Kiyose-shi, Tokyo, 204-8588, Japan
| | - Yoshihiro Kino
- Department of Bioinformatics and Molecular Neuropathology, Meiji Pharmaceutical University, 2-522-1, Noshio, Kiyose-shi, Tokyo, 204-8588, Japan.
- Department of RNA Pathobiology and Therapeutics, Meiji Pharmaceutical University, 2-522-1, Noshio, Kiyose-shi, Tokyo, 204-8588, Japan.
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3
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Fedorova AD, Kiniry SJ, Andreev DE, Mudge JM, Baranov PV. Thousands of human non-AUG extended proteoforms lack evidence of evolutionary selection among mammals. Nat Commun 2022; 13:7910. [PMID: 36564405 PMCID: PMC9789052 DOI: 10.1038/s41467-022-35595-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Accepted: 12/12/2022] [Indexed: 12/24/2022] Open
Abstract
The synthesis of most proteins begins at AUG codons, yet a small number of non-AUG initiated proteoforms are also known. Here we analyse a large number of publicly available Ribo-seq datasets to identify novel, previously uncharacterised non-AUG proteoforms using Trips-Viz implementation of a novel algorithm for detecting translated ORFs. In parallel we analyse genomic alignment of 120 mammals to identify evidence of protein coding evolution in sequences encoding potential extensions. Unexpectedly we find that the number of non-AUG proteoforms identified with ribosome profiling data greatly exceeds those with strong phylogenetic support suggesting their recent evolution. Our study argues that the protein coding potential of human genome greatly exceeds that detectable through comparative genomics and exposes the existence of multiple proteins encoded by the same genomic loci.
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Affiliation(s)
- Alla D Fedorova
- School of Biochemistry and Cell Biology, University College Cork, Cork, Ireland.
- SFI Centre for Research Training in Genomics Data Science, University College Cork, Cork, Ireland.
| | - Stephen J Kiniry
- School of Biochemistry and Cell Biology, University College Cork, Cork, Ireland
| | - Dmitry E Andreev
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, RAS, Moscow, Russia
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Jonathan M Mudge
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Pavel V Baranov
- School of Biochemistry and Cell Biology, University College Cork, Cork, Ireland.
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4
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Wang Z, Zhang L, Tang F, Yang Z, Wang M, Jia J, Wang D, Yang L, Zhong S, Yuan G. Transcriptome analysis of peripheral blood mononuclear cells in patients with type 1 diabetes mellitus. Endocrine 2022; 78:270-279. [PMID: 35976509 DOI: 10.1007/s12020-022-03163-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/10/2022] [Accepted: 08/03/2022] [Indexed: 12/01/2022]
Abstract
PURPOSE Type 1 diabetes mellitus (T1DM) is a chronic autoimmune disease characterized by the destruction of pancreatic β cells. The goal of this study was to explore potential biological biomarkers for T1DM. METHODS Two microarray datasets (GSE55098 and GSE156035) about human peripheral blood mononuclear cells (PBMCs) were systematically extracted from the Gene Expression Omnibus (GEO) database. Common genes were identified from the perspective of differentially expressed genes (DEGs) and weighted gene co-expression network analysis (WGCNA) respectively, and hub genes were identified by least absolute shrinkage and selection operator (LASSO) analysis. We also observed the expression of these hub genes in some common autoimmune diseases and predicted transcription factors (TFs) that might be associated with these genes. RESULTS Seven hub genes (DDIT4, ESCO2, SH3BP4, PRICKLE1, EPM2AIP1, KCNJ15 and GRM8) were finally identified. Receiver operating characteristic (ROC) analysis showed that the high expression of these genes could well predict the occurrence of T1DM. Gene set enrichment analysis (GSEA) suggested that most of these hub genes may be mainly involved in the changes of biological functions such as inflammation, infection, immunity, cancer, and apoptosis. Further, compared with the control group, the expression levels of these hub genes also changed in some other autoimmune diseases, such as rheumatoid arthritis (RA), systemic lupus erythematosus (SLE), primary biliary cholangitis (PBC), etc., indicating that they might be the common targets of these autoimmune diseases. CONCLUSIONS The present study identified novel genes associated with T1DM from the PBMCs perspective that might provide new ideas for the early diagnosis, monitoring, evaluation, and prediction of T1DM.
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Affiliation(s)
- Zhaoxiang Wang
- Department of Endocrinology, Affiliated Hospital of Jiangsu University, Zhenjiang, Jiangsu, 212001, China
| | - Li Zhang
- Department of Endocrinology, Affiliated Kunshan Hospital of Jiangsu University, Kunshan, Jiangsu, 215300, China
| | - Fengyan Tang
- Department of Endocrinology, Affiliated Kunshan Hospital of Jiangsu University, Kunshan, Jiangsu, 215300, China
| | - Zhongming Yang
- Department of Endocrinology, Affiliated Hospital of Jiangsu University, Zhenjiang, Jiangsu, 212001, China
| | - Mengzhu Wang
- Department of Endocrinology, Affiliated Hospital of Jiangsu University, Zhenjiang, Jiangsu, 212001, China
| | - Jue Jia
- Department of Endocrinology, Affiliated Hospital of Jiangsu University, Zhenjiang, Jiangsu, 212001, China
| | - Dong Wang
- Department of Endocrinology, Affiliated Hospital of Jiangsu University, Zhenjiang, Jiangsu, 212001, China
| | - Ling Yang
- Department of Endocrinology, Affiliated Hospital of Jiangsu University, Zhenjiang, Jiangsu, 212001, China
| | - Shao Zhong
- Department of Endocrinology, Affiliated Kunshan Hospital of Jiangsu University, Kunshan, Jiangsu, 215300, China.
| | - Guoyue Yuan
- Department of Endocrinology, Affiliated Hospital of Jiangsu University, Zhenjiang, Jiangsu, 212001, China.
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5
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Cole S, Giri N, Alter BP, Gianferante DM. Variable Clinical Features in a Large Family With Diamond Blackfan Anemia Caused by a Pathogenic Missense Mutation in RPS19. Front Genet 2022; 13:914141. [PMID: 35923690 PMCID: PMC9340065 DOI: 10.3389/fgene.2022.914141] [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: 04/06/2022] [Accepted: 06/10/2022] [Indexed: 11/17/2022] Open
Abstract
Introduction: Diamond Blackfan anemia (DBA) is an autosomal dominant ribosomopathy caused predominantly by pathogenic germline variants in ribosomal protein genes. It is characterized by failure of red blood cell production, and common features include congenital malformations and cancer predisposition. Mainstays of treatment are corticosteroids, red blood cell transfusions, and hematologic stem cell transplantation (HSCT). Despite a better understanding of the genotype of DBA, the biological mechanism resulting in the clinical phenotype remains poorly understood, and wide heterogeneity can be seen even within a single family as depicted here. Case Description: Thirty family members enrolled in the National Cancer Institute inherited bone marrow failure syndromes study were evaluated with detailed medical questionnaires and physical examinations, including 22 in the family bloodline and eight unrelated partners. Eight participants had been previously told they had DBA by clinical criteria. Targeted germline RPS19 testing was done on all family members. A pathogenic heterozygous missense mutation in RPS19 (p.R62Q, c.185G > A) was detected in ten family members, including one person previously presumed unaffected. Eight family members presented with macrocytic anemia in infancy; all of whom were responsive to prednisone. Four family members became treatment independent; however, one individual became transfusion-dependent 36 years later following an episode of pneumonia. One prednisone responsive individual electively discontinued steroid treatment, and lives with severe anemia. One prednisone responsive individual died at age 28 from a stroke. Two family members developed colorectal cancer in their fifties; one had never required treatment for anemia. None had major congenital anomalies. Discussion: This large family with DBA demonstrates the heterogeneity of phenotypes that can be seen within the same genotype. Most family members presented with steroid-responsive anemia in infancy and subtle congenital malformations, findings consistent with recent genotype-phenotype studies of RPS DBA. However, two family members were relatively unaffected, underscoring the importance of further studies to assess modifier genes, and epigenetic and/or environmental factors which may result in normal erythropoiesis despite underlying ribosome dysfunction. This large, multigenerational family highlights the need for individualized treatment, the importance of early cancer surveillance even in individuals with clinically mild phenotypes, and the benefit of long-term follow-up to identify late complications.
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Affiliation(s)
- Sarah Cole
- Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, United States
- Walter Reed National Military Medical Center, Bethesda, MD, United States
| | - Neelam Giri
- Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, United States
| | - Blanche P. Alter
- Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, United States
| | - D. Matthew Gianferante
- Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, United States
- *Correspondence: D. Matthew Gianferante,
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6
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Fedorova D, Ovsyannikova G, Kurnikova M, Pavlova A, Konyukhova T, Pshonkin A, Smetanina N. De novo TP53 germline activating mutations in two patients with the phenotype mimicking Diamond-Blackfan anemia. Pediatr Blood Cancer 2022; 69:e29558. [PMID: 35084091 DOI: 10.1002/pbc.29558] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/10/2021] [Revised: 12/19/2021] [Accepted: 12/20/2021] [Indexed: 11/09/2022]
Abstract
Diamond-Blackfan anemia (DBA) is an inherited bone marrow failure syndrome, associated with mutations in ribosomal protein (RP) genes. Growing data on mutations in non-RP genes in patients with DBA-like phenotype became available over recent years. We describe two patients with the phenotype of DBA (onset of macrocytic anemia within the first year of life, paucity of erythroid precursors in bone marrow) and germline de novo variants in the TP53 gene. Both patients became transfusion independent, probably due to L-leucine therapy. The possible role of TP53 variants should be considered in patients with DBA-like phenotype and no mutations in RP genes.
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Affiliation(s)
- Daria Fedorova
- Dmitry Rogachev National Research Medical Center of Pediatric Hematology, Oncology and Immunology, Moscow, Russian Federation
| | - Galina Ovsyannikova
- Dmitry Rogachev National Research Medical Center of Pediatric Hematology, Oncology and Immunology, Moscow, Russian Federation
| | - Maria Kurnikova
- Dmitry Rogachev National Research Medical Center of Pediatric Hematology, Oncology and Immunology, Moscow, Russian Federation
| | - Anna Pavlova
- Dmitry Rogachev National Research Medical Center of Pediatric Hematology, Oncology and Immunology, Moscow, Russian Federation
| | - Tatiana Konyukhova
- Dmitry Rogachev National Research Medical Center of Pediatric Hematology, Oncology and Immunology, Moscow, Russian Federation
| | - Alexey Pshonkin
- Dmitry Rogachev National Research Medical Center of Pediatric Hematology, Oncology and Immunology, Moscow, Russian Federation
| | - Nataliya Smetanina
- Dmitry Rogachev National Research Medical Center of Pediatric Hematology, Oncology and Immunology, Moscow, Russian Federation
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7
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Mfarej MG, Skibbens RV. Genetically induced redox stress occurs in a yeast model for Roberts syndrome. G3 (BETHESDA, MD.) 2022; 12:6460337. [PMID: 34897432 PMCID: PMC9210317 DOI: 10.1093/g3journal/jkab426] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Accepted: 11/01/2021] [Indexed: 12/31/2022]
Abstract
Roberts syndrome (RBS) is a multispectrum developmental disorder characterized by severe limb, craniofacial, and organ abnormalities and often intellectual disabilities. The genetic basis of RBS is rooted in loss-of-function mutations in the essential N-acetyltransferase ESCO2 which is conserved from yeast (Eco1/Ctf7) to humans. ESCO2/Eco1 regulate many cellular processes that impact chromatin structure, chromosome transmission, gene expression, and repair of the genome. The etiology of RBS remains contentious with current models that include transcriptional dysregulation or mitotic failure. Here, we report evidence that supports an emerging model rooted in defective DNA damage responses. First, the results reveal that redox stress is elevated in both eco1 and cohesion factor Saccharomyces cerevisiae mutant cells. Second, we provide evidence that Eco1 and cohesion factors are required for the repair of oxidative DNA damage such that ECO1 and cohesin gene mutations result in reduced cell viability and hyperactivation of DNA damage checkpoints that occur in response to oxidative stress. Moreover, we show that mutation of ECO1 is solely sufficient to induce endogenous redox stress and sensitizes mutant cells to exogenous genotoxic challenges. Remarkably, antioxidant treatment desensitizes eco1 mutant cells to a range of DNA damaging agents, raising the possibility that modulating the cellular redox state may represent an important avenue of treatment for RBS and tumors that bear ESCO2 mutations.
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Affiliation(s)
- Michael G Mfarej
- Department of Biological Sciences, Lehigh University, Bethlehem, PA 18015, USA
| | - Robert V Skibbens
- Department of Biological Sciences, Lehigh University, Bethlehem, PA 18015, USA
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8
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Zaheed O, Kiniry SJ, Baranov PV, Dean K. Exploring Evidence of Non-coding RNA Translation With Trips-Viz and GWIPS-Viz Browsers. Front Cell Dev Biol 2021; 9:703374. [PMID: 34490252 PMCID: PMC8416628 DOI: 10.3389/fcell.2021.703374] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Accepted: 07/12/2021] [Indexed: 11/21/2022] Open
Abstract
Detection of translation in so-called non-coding RNA provides an opportunity for identification of novel bioactive peptides and microproteins. The main methods used for these purposes are ribosome profiling and mass spectrometry. A number of publicly available datasets already exist for a substantial number of different cell types grown under various conditions, and public data mining is an attractive strategy for identification of translation in non-coding RNAs. Since the analysis of publicly available data requires intensive data processing, several data resources have been created recently for exploring processed publicly available data, such as OpenProt, GWIPS-viz, and Trips-Viz. In this work we provide a detailed demonstration of how to use the latter two tools for exploring experimental evidence for translation of RNAs hitherto classified as non-coding. For this purpose, we use a set of transcripts with substantially different patterns of ribosome footprint distributions. We discuss how certain features of these patterns can be used as evidence for or against genuine translation. During our analysis we concluded that the MTLN mRNA, previously misannotated as lncRNA LINC00116, likely encodes only a short proteoform expressed from shorter RNA transcript variants.
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Affiliation(s)
- Oza Zaheed
- School of Biochemistry and Cell Biology, University College Cork, Cork, Ireland
| | - Stephen J Kiniry
- School of Biochemistry and Cell Biology, University College Cork, Cork, Ireland
| | - Pavel V Baranov
- School of Biochemistry and Cell Biology, University College Cork, Cork, Ireland.,Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, RAS, Moscow, Russia
| | - Kellie Dean
- School of Biochemistry and Cell Biology, University College Cork, Cork, Ireland
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9
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van Dooijeweert B, Broeks MH, van Beers EJ, Verhoeven-Duif NM, van Solinge WW, Nieuwenhuis EES, Jans JJ, van Wijk R, Bartels M. Dried blood spot metabolomics reveals a metabolic fingerprint with diagnostic potential for Diamond Blackfan Anaemia. Br J Haematol 2021; 193:1185-1193. [PMID: 33997957 PMCID: PMC8251760 DOI: 10.1111/bjh.17524] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Accepted: 03/18/2021] [Indexed: 02/06/2023]
Abstract
The diagnostic evaluation of Diamond Blackfan Anaemia (DBA), an inherited bone marrow failure syndrome characterised by erythroid hypoplasia, is challenging because of a broad phenotypic variability and the lack of functional screening tests. In this study, we explored the potential of untargeted metabolomics to diagnose DBA. In dried blood spot samples from 18 DBA patients and 40 healthy controls, a total of 1752 unique metabolite features were identified. This metabolic fingerprint was incorporated into a machine‐learning algorithm, and a binary classification model was constructed using a training set. The model showed high performance characteristics (average accuracy 91·9%), and correct prediction of class was observed for all controls (n = 12) and all but one patient (n = 4/5) from the validation or ‘test’ set (accuracy 94%). Importantly, in patients with congenital dyserythropoietic anaemia (CDA) – an erythroid disorder with overlapping features – we observed a distinct metabolic profile, indicating the disease specificity of the DBA fingerprint and underlining its diagnostic potential. Furthermore, when exploring phenotypic heterogeneity, DBA treatment subgroups yielded discrete differences in metabolic profiles, which could hold future potential in understanding therapy responses. Our data demonstrate that untargeted metabolomics in dried blood spots is a promising new diagnostic tool for DBA.
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Affiliation(s)
- Birgit van Dooijeweert
- Central Diagnostic Laboratory-Research, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands.,Department of Paediatric Haematology, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands
| | - Melissa H Broeks
- Section Metabolic Diagnostics, Department of Genetics, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands
| | - Eduard J van Beers
- Van Creveldkliniek, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Nanda M Verhoeven-Duif
- Section Metabolic Diagnostics, Department of Genetics, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands
| | - Wouter W van Solinge
- Central Diagnostic Laboratory-Research, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands
| | - Edward E S Nieuwenhuis
- Department of Paediatric Haematology, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands
| | - Judith J Jans
- Section Metabolic Diagnostics, Department of Genetics, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands
| | - Richard van Wijk
- Central Diagnostic Laboratory-Research, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands
| | - Marije Bartels
- Department of Paediatric Haematology, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands.,Van Creveldkliniek, University Medical Center Utrecht, Utrecht, the Netherlands
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10
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Vlachos A, Atsidaftos E, Lababidi ML, Muir E, Rogers ZR, Alhushki W, Bernstein J, Glader B, Gruner B, Hartung H, Knoll C, Loew T, Nalepa G, Narla A, Panigrahi AR, Sieff CA, Walkovich K, Farrar JE, Lipton JM. L-leucine improves anemia and growth in patients with transfusion-dependent Diamond-Blackfan anemia: Results from a multicenter pilot phase I/II study from the Diamond-Blackfan Anemia Registry. Pediatr Blood Cancer 2020; 67:e28748. [PMID: 33025707 PMCID: PMC8273758 DOI: 10.1002/pbc.28748] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Revised: 09/17/2020] [Accepted: 09/18/2020] [Indexed: 01/23/2023]
Abstract
BACKGROUND Diamond-Blackfan anemia (DBA) is an inherited bone marrow failure syndrome characterized by anemia, short stature, congenital anomalies, and cancer predisposition. Most cases are due to mutations in genes encoding ribosomal proteins (RP) leading to RP haploinsufficiency. Effective treatments for the anemia of DBA include chronic red cell transfusions, long-term corticosteroid therapy, or hematopoietic stem cell transplantation. In a small patient series and in animal models, there have been hematologic responses to L-leucine with amelioration of anemia. The study objectives of this clinical trial were to determine feasibility, safety, and efficacy of L-leucine in transfusion-dependent patients with DBA. PROCEDURE Patients ≥2 years of age received L-leucine 700 mg/m2 orally three times daily for nine months to determine a hematologic response and any improvement in growth (NCT01362595). RESULTS This multicenter, phase I/II study enrolled 55 subjects; 43 were evaluable. There were 21 males; the median age at enrollment was 10.4 years (range, 2.5-46.1 years). No significant adverse events were attributable to L-leucine. Two subjects had a complete erythroid response and five had a partial response. Nine of 25, and 11 of 25, subjects experienced a positive weight and height percentile change, respectively, at the end of therapy. CONCLUSIONS L-leucine is safe, resulted in an erythroid response in 16% of subjects with DBA, and led to an increase in weight and linear growth velocity in 36% and 44% of evaluable subjects, respectively. Further studies will be critical to understand the role of L-leucine in the management of patients with DBA.
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Affiliation(s)
- Adrianna Vlachos
- Feinstein Institutes for Medical Research, Northwell Health, Manhasset, NY;,Division of Hematology/Oncology and Cellular Therapy, Cohen Children’s Medical Center, Northwell Health, New Hyde Park, NY
| | - Evangelia Atsidaftos
- Feinstein Institutes for Medical Research, Northwell Health, Manhasset, NY;,Division of Hematology/Oncology and Cellular Therapy, Cohen Children’s Medical Center, Northwell Health, New Hyde Park, NY
| | | | - Ellen Muir
- Feinstein Institutes for Medical Research, Northwell Health, Manhasset, NY;,Division of Hematology/Oncology and Cellular Therapy, Cohen Children’s Medical Center, Northwell Health, New Hyde Park, NY
| | - Zora R. Rogers
- University of Texas Southwestern Medical Center at Dallas, Dallas, TX
| | - Waseem Alhushki
- Cure 4 The Kids Foundation, Pediatric Hematology Oncology, Las Vegas, NV
| | - Jonathan Bernstein
- Cure 4 The Kids Foundation, Pediatric Hematology Oncology, Las Vegas, NV; presently at Penn State Health Milton S. Hershey Medical Center, Hershey, PA
| | - Bertil Glader
- Division of Pediatric Hematology/Oncology, Stanford University School of Medicine, Stanford, CA
| | - Barbara Gruner
- Division of Pediatric Hematology/Oncology, University of Missouri, Columbia, MO
| | - Helge Hartung
- Division of Hematology, The Children’s Hospital of Philadelphia, Philadelphia, PA
| | - Christine Knoll
- The Center for Cancer and Blood Disorders, Phoenix Children’s Hospital, Phoenix, AZ
| | - Thomas Loew
- Division of Pediatric Hematology/Oncology, University of Missouri, Columbia, MO, presently at University of Kansas Medical Center, Kansas City, KS
| | - Grzegorz Nalepa
- Department of Pediatric Hematology-Oncology, Indiana University School of Medicine, Indianapolis, IN
| | - Anupama Narla
- Division of Pediatric Hematology/Oncology, Stanford University School of Medicine, Stanford, CA
| | - Arun R. Panigrahi
- University of Louisville, Louisville, KY, presently at University of California Davis, Sacramento, CA
| | - Colin A. Sieff
- Harvard Medical School, Dana-Farber and Boston Children’s, Cancer and Blood Disorders Center, Boston, MA
| | - Kelly Walkovich
- Division of Hematology/Oncology, C.S. Mott Children’s Hospital, Ann Arbor, MI
| | - Jason E. Farrar
- Pediatric Hematology/Oncology, Arkansas Children’s Research Institute & University of Arkansas for Medical Sciences, Little Rock, AR
| | - Jeffrey M. Lipton
- Feinstein Institutes for Medical Research, Northwell Health, Manhasset, NY;,Division of Hematology/Oncology and Cellular Therapy, Cohen Children’s Medical Center, Northwell Health, New Hyde Park, NY
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11
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Mfarej MG, Skibbens RV. An ever-changing landscape in Roberts syndrome biology: Implications for macromolecular damage. PLoS Genet 2020; 16:e1009219. [PMID: 33382686 PMCID: PMC7774850 DOI: 10.1371/journal.pgen.1009219] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Roberts syndrome (RBS) is a rare developmental disorder that can include craniofacial abnormalities, limb malformations, missing digits, intellectual disabilities, stillbirth, and early mortality. The genetic basis for RBS is linked to autosomal recessive loss-of-function mutation of the establishment of cohesion (ESCO) 2 acetyltransferase. ESCO2 is an essential gene that targets the DNA-binding cohesin complex. ESCO2 acetylates alternate subunits of cohesin to orchestrate vital cellular processes that include sister chromatid cohesion, chromosome condensation, transcription, and DNA repair. Although significant advances were made over the last 20 years in our understanding of ESCO2 and cohesin biology, the molecular etiology of RBS remains ambiguous. In this review, we highlight current models of RBS and reflect on data that suggests a novel role for macromolecular damage in the molecular etiology of RBS.
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Affiliation(s)
- Michael G. Mfarej
- Department of Biological Sciences, Lehigh University, Bethlehem, Pennsylvania, United States of America
| | - Robert V. Skibbens
- Department of Biological Sciences, Lehigh University, Bethlehem, Pennsylvania, United States of America
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12
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Cellai F, Bonassi S, Cristaudo A, Bonotti A, Neri M, Ceppi M, Bruzzone M, Milić M, Munnia A, Peluso M. Chromatographic Detection of 8-Hydroxy-2'-Deoxyguanosine in Leukocytes of Asbestos Exposed Workers for Assessing Past and Recent Carcinogen Exposures. Diagnostics (Basel) 2020; 10:E239. [PMID: 32326213 PMCID: PMC7235992 DOI: 10.3390/diagnostics10040239] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2020] [Revised: 04/15/2020] [Accepted: 04/18/2020] [Indexed: 11/16/2022] Open
Abstract
Asbestos fibers include a group of silicate minerals that occur in the environment and are widely employed in occupational settings. Asbestos exposure has been associated to various chronic diseases; such as pulmonary fibrosis; mesothelioma; and lung cancer; often characterized by a long period of latency. Underlying mechanisms that are behind the carcinogenic effect of asbestos have not been fully clarified. Therefore; we have conducted an epidemiological study to evaluate the relationship between 8-hydroxy-2'-deoxyguanosine (8-oxodG), one of the most reliable biomarkers of oxidative stress and oxidative DNA damage; and asbestos exposure in the peripheral blood of residents in Tuscany and Liguria regions; Italy; stratified by occupational exposure to this carcinogen. Levels of 8-oxodG were expressed such as relative adduct labeling (RAL); the frequency of 8-oxodG per 105 deoxyguanosine was significantly higher among exposed workers with respect to the controls; i.e., 3.0 ± 0.2 Standard Error (SE) in asbestos workers versus a value of 1.3 ± 0.1 (SE) in unexposed controls (p < 0.001). When the relationship with occupational history was investigated; significant higher levels of 8-oxodG were measured in current and former asbestos workers vs. healthy controls; 3.1 ± 0.3 (SE) and 2.9 ± 0.2 (SE), respectively. After stratification for occupational history; a significant 194% excess of adducts was found in workers with 10 or more years of past asbestos exposure (p < 0.001). 8-oxodG can be used for medical surveillance programs of cohorts of workers with past and recent exposures to carcinogens for the identification of subjects requiring a more intense clinical surveillance.
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Affiliation(s)
- Filippo Cellai
- Cancer Risk Factor Branch, Regional Cancer Prevention Laboratory, ISPRO-Study, Prevention and Oncology Network Institute, 50139 Florence, Italy; (F.C.); (A.M.)
| | - Stefano Bonassi
- Clinical and Molecular Epidemiology, IRCCS San Raffaele Pisana, 00166 Rome, Italy; (S.B.); (M.N.)
- Department of Human Sciences and Quality of Life Promotion, San Raffaele University, 00166 Rome, Italy
| | - Alfonso Cristaudo
- Department of Translational Research and New Technologies in Medicine and Surgery, University of Pisa, 56010 Pisa, Italy;
- Occupational Medicine Unit, University of Pisa, 56010 Pisa, Italy;
| | | | - Monica Neri
- Clinical and Molecular Epidemiology, IRCCS San Raffaele Pisana, 00166 Rome, Italy; (S.B.); (M.N.)
| | - Marcello Ceppi
- Unit of Clinical Epidemiology, IRCCS Ospedale Policlinico San Martino, 16131 Genoa, Italy; (M.C.); (M.B.)
| | - Marco Bruzzone
- Unit of Clinical Epidemiology, IRCCS Ospedale Policlinico San Martino, 16131 Genoa, Italy; (M.C.); (M.B.)
| | - Mirta Milić
- Mutagenesis Unit, Institute for Medical Research and Occupational Health, 10000 Zagreb, Croatia;
| | - Armelle Munnia
- Cancer Risk Factor Branch, Regional Cancer Prevention Laboratory, ISPRO-Study, Prevention and Oncology Network Institute, 50139 Florence, Italy; (F.C.); (A.M.)
| | - Marco Peluso
- Cancer Risk Factor Branch, Regional Cancer Prevention Laboratory, ISPRO-Study, Prevention and Oncology Network Institute, 50139 Florence, Italy; (F.C.); (A.M.)
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13
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Michel AM, Kiniry SJ, O'Connor PBF, Mullan JP, Baranov PV. GWIPS-viz: 2018 update. Nucleic Acids Res 2019; 46:D823-D830. [PMID: 28977460 PMCID: PMC5753223 DOI: 10.1093/nar/gkx790] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2017] [Accepted: 08/29/2017] [Indexed: 12/15/2022] Open
Abstract
The GWIPS-viz browser (http://gwips.ucc.ie/) is an on-line genome browser which is tailored for exploring ribosome profiling (Ribo-seq) data. Since its publication in 2014, GWIPS-viz provides Ribo-seq data for an additional 14 genomes bringing the current total to 23. The integration of new Ribo-seq data has been automated thereby increasing the number of available tracks to 1792, a 10-fold increase in the last three years. The increase is particularly substantial for data derived from human sources. Following user requests, we added the functionality to download these tracks in bigWig format. We also incorporated new types of data (e.g. TCP-seq) as well as auxiliary tracks from other sources that help with the interpretation of Ribo-seq data. Improvements in the visualization of the data have been carried out particularly for bacterial genomes where the Ribo-seq data are now shown in a strand specific manner. For higher eukaryotic datasets, we provide characteristics of individual datasets using the RUST program which includes the triplet periodicity, sequencing biases and relative inferred A-site dwell times. This information can be used for assessing the quality of Ribo-seq datasets. To improve the power of the signal, we aggregate Ribo-seq data from several studies into Global aggregate tracks for each genome.
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Affiliation(s)
- Audrey M Michel
- School of Biochemistry and Cell Biology, University College Cork, Cork, Ireland
| | - Stephen J Kiniry
- School of Biochemistry and Cell Biology, University College Cork, Cork, Ireland
| | | | - James P Mullan
- School of Biochemistry and Cell Biology, University College Cork, Cork, Ireland
| | - Pavel V Baranov
- School of Biochemistry and Cell Biology, University College Cork, Cork, Ireland
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14
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Sheu SJ, Chen JL, Bee YS, Lin SH, Shu CW. ERBB2-modulated ATG4B and autophagic cell death in human ARPE19 during oxidative stress. PLoS One 2019; 14:e0213932. [PMID: 30870514 PMCID: PMC6417729 DOI: 10.1371/journal.pone.0213932] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2018] [Accepted: 03/04/2019] [Indexed: 01/12/2023] Open
Abstract
Age-related macular degeneration (AMD) is an ocular disease with retinal degeneration. Retinal pigment epithelium (RPE) degeneration is mainly caused by long-term oxidative stress. Kinase activity could be either protective or detrimental to cells during oxidative stress; however, few reports have described the role of kinases in oxidative stress. In this study, high-throughput screening of kinome siRNA library revealed that erb-b2 receptor tyrosine-protein kinase 2 (ERBB2) knockdown reduced reactive oxygen species (ROS) production in ARPE-19 cells during oxidative stress. Silencing ERBB2 caused an elevation in microtubule associated protein light chain C3-II (MAP1LC3B-II/I) conversion and sequesterone (SQSTM)1 protein level. ERBB2 deprivation largely caused an increase in autophagy-regulating protease (ATG4B) expression, a protease that negatively recycles MAP1LC3-II at the fusion step between the autophagosome and lysosome, suggesting ERBB2 might modulate ATG4B for autophagy induction in oxidative stress-stimulated ARPE-19 cells. ERBB2 knockdown also caused an accumulation of nuclear factor erythroid 2-related factor 2 (NRF2) and enhanced its transcriptional activity. In addition, ERBB2 ablation or treatment with autophagy inhibitors reduced oxidative-induced cytotoxic effects in ARPE-19 cells. Furthermore, ERBB2 silencing had little or no additive effects in ATG5/7-deficient cells. Taken together, our results suggest that ERBB2 may play an important role in modulating autophagic RPE cell death during oxidative stress, and ERBB2 may be a potential target in AMD prevention.
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Affiliation(s)
- Shwu-Jiuan Sheu
- Department of Ophthalmology, Kaohsiung Veterans General Hospital, Kaohsiung, Taiwan
- School of Medicine, National Yang-Ming University, Taipei, Taiwan
| | - Jiunn-Liang Chen
- Department of Ophthalmology, Kaohsiung Veterans General Hospital, Kaohsiung, Taiwan
- School of Medicine, National Yang-Ming University, Taipei, Taiwan
- Department of Optometry, Shu-Zen Junior College of Medicine and Management, Kaohsiung, Taiwan
| | - Youn-Shen Bee
- Department of Ophthalmology, Kaohsiung Veterans General Hospital, Kaohsiung, Taiwan
- Yuh-Ing Junior College of Health Care and Management, Kaohsiung, Taiwan
- National Defense Medical Center, Taipei, Taiwan
| | - Shi-Han Lin
- Department of Ophthalmology, Kaohsiung Veterans General Hospital, Kaohsiung, Taiwan
| | - Chih-Wen Shu
- School of Medicine for International Students, I-Shou University, Kaohsiung, Taiwan
- Institute of Biomedical Sciences, National Sun Yat-Sen University, Kaohsiung, Taiwan
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15
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Hetman M, Slomnicki LP. Ribosomal biogenesis as an emerging target of neurodevelopmental pathologies. J Neurochem 2018; 148:325-347. [PMID: 30144322 DOI: 10.1111/jnc.14576] [Citation(s) in RCA: 59] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2018] [Revised: 08/15/2018] [Accepted: 08/21/2018] [Indexed: 12/17/2022]
Abstract
Development of the nervous system is carried out by complex gene expression programs that are regulated at both transcriptional and translational level. In addition, quality control mechanisms such as the TP53-mediated apoptosis or neuronal activity-stimulated survival ensure successful neurogenesis and formation of functional circuitries. In the nucleolus, production of ribosomes is essential for protein synthesis. In addition, it participates in chromatin organization and regulates the TP53 pathway via the ribosomal stress response. Its tight regulation is required for maintenance of genomic integrity. Mutations in several ribosomal components and trans-acting ribosomal biogenesis factors result in neurodevelopmental syndromes that present with microcephaly, autism, intellectual deficits and/or progressive neurodegeneration. Furthermore, ribosomal biogenesis is perturbed by exogenous factors that disrupt neurodevelopment including alcohol or Zika virus. In this review, we present recent literature that argues for a role of dysregulated ribosomal biogenesis in pathogenesis of various neurodevelopmental syndromes. We also discuss potential mechanisms through which such dysregulation may lead to cellular pathologies of the developing nervous system including insufficient proliferation and/or loss of neuroprogenitors cells, apoptosis of immature neurons, altered neuronal morphogenesis, and neurodegeneration.
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Affiliation(s)
- Michal Hetman
- Departments of Neurological Surgery, Kentucky Spinal Cord Injury Research Center, Louisville, Kentucky, USA.,Pharmacology and Toxicology, University of Louisville, Louisville, Kentucky, USA
| | - Lukasz P Slomnicki
- Departments of Neurological Surgery, Kentucky Spinal Cord Injury Research Center, Louisville, Kentucky, USA
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16
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Andreev DE, Arnold M, Kiniry SJ, Loughran G, Michel AM, Rachinskii D, Baranov PV. TASEP modelling provides a parsimonious explanation for the ability of a single uORF to derepress translation during the integrated stress response. eLife 2018; 7:32563. [PMID: 29932418 PMCID: PMC6033536 DOI: 10.7554/elife.32563] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2017] [Accepted: 06/21/2018] [Indexed: 12/13/2022] Open
Abstract
Translation initiation is the rate-limiting step of protein synthesis that is downregulated during the Integrated Stress Response (ISR). Previously, we demonstrated that most human mRNAs that are resistant to this inhibition possess translated upstream open reading frames (uORFs), and that in some cases a single uORF is sufficient for the resistance. Here we developed a computational model of Initiation Complexes Interference with Elongating Ribosomes (ICIER) to gain insight into the mechanism. We explored the relationship between the flux of scanning ribosomes upstream and downstream of a single uORF depending on uORF features. Paradoxically, our analysis predicts that reducing ribosome flux upstream of certain uORFs increases initiation downstream. The model supports the derepression of downstream translation as a general mechanism of uORF-mediated stress resistance. It predicts that stress resistance can be achieved with long slowly decoded uORFs that do not favor translation reinitiation and that start with initiators of low leakiness.
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Affiliation(s)
- Dmitry E Andreev
- School of Biochemistry and Cell Biology, University College Cork, Cork, Ireland.,Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Maxim Arnold
- Department of Mathematical Sciences, The University of Texas at Dallas, Richardson, United States
| | - Stephen J Kiniry
- School of Biochemistry and Cell Biology, University College Cork, Cork, Ireland
| | - Gary Loughran
- School of Biochemistry and Cell Biology, University College Cork, Cork, Ireland
| | - Audrey M Michel
- School of Biochemistry and Cell Biology, University College Cork, Cork, Ireland
| | - Dmitrii Rachinskii
- Department of Mathematical Sciences, The University of Texas at Dallas, Richardson, United States
| | - Pavel V Baranov
- School of Biochemistry and Cell Biology, University College Cork, Cork, Ireland
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17
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Meier M, Grant J, Dowdle A, Thomas A, Gerton J, Collas P, O'Sullivan JM, Horsfield JA. Cohesin facilitates zygotic genome activation in zebrafish. Development 2018; 145:dev156521. [PMID: 29158440 DOI: 10.1242/dev.156521] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2017] [Accepted: 11/07/2017] [Indexed: 02/01/2023]
Abstract
At zygotic genome activation (ZGA), changes in chromatin structure are associated with new transcription immediately following the maternal-to-zygotic transition (MZT). The nuclear architectural proteins cohesin and CCCTC-binding factor (CTCF) contribute to chromatin structure and gene regulation. We show here that normal cohesin function is important for ZGA in zebrafish. Depletion of the cohesin subunit Rad21 delays ZGA without affecting cell cycle progression. In contrast, CTCF depletion has little effect on ZGA, whereas complete abrogation is lethal. Genome-wide analysis of Rad21 binding reveals a change in distribution from pericentromeric satellite DNA and other locations, including the miR-430 locus (the products of which are responsible for maternal transcript degradation), to genes, as embryos progress through the MZT. After MZT, a subset of Rad21 binding overlaps the pioneer factor Pou5f3, which activates early expressed genes. Rad21 depletion disrupts the formation of nucleoli and RNA polymerase II foci, suggestive of global defects in chromosome architecture. We propose that Rad21/cohesin redistribution to active areas of the genome is key to the establishment of chromosome organization and the embryonic developmental program.
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Affiliation(s)
- Michael Meier
- Department of Pathology, University of Otago, Dunedin 9016, New Zealand
| | - Jenny Grant
- Department of Pathology, University of Otago, Dunedin 9016, New Zealand
| | - Amy Dowdle
- Department of Pathology, University of Otago, Dunedin 9016, New Zealand
| | - Amarni Thomas
- Department of Pathology, University of Otago, Dunedin 9016, New Zealand
| | - Jennifer Gerton
- Stowers Institute for Medical Research, 1000 E 50th Street, Kansas City, MO 64110, USA
- Department of Biochemistry and Molecular Biology, University of Kansas Medical Center, Kansas City, KS 66160, USA
| | - Philippe Collas
- Department of Molecular Medicine, Institute of Basic Medical Sciences, Faculty of Medicine, University of Oslo, Oslo 0316, Norway
| | - Justin M O'Sullivan
- Liggins Institute, The University of Auckland, Private Bag 92019, Auckland 1023, New Zealand
- Maurice Wilkins Centre for Molecular Biodiscovery, The University of Auckland, Private Bag 92019, Auckland 1010, New Zealand
| | - Julia A Horsfield
- Department of Pathology, University of Otago, Dunedin 9016, New Zealand
- Maurice Wilkins Centre for Molecular Biodiscovery, The University of Auckland, Private Bag 92019, Auckland 1010, New Zealand
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18
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Banerji R, Skibbens RV, Iovine MK. How many roads lead to cohesinopathies? Dev Dyn 2017; 246:881-888. [PMID: 28422453 DOI: 10.1002/dvdy.24510] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2016] [Revised: 03/10/2017] [Accepted: 04/11/2017] [Indexed: 12/16/2023] Open
Abstract
Genetic mapping studies reveal that mutations in cohesion pathways are responsible for multispectrum developmental abnormalities termed cohesinopathies. These include Roberts syndrome (RBS), Cornelia de Lange Syndrome (CdLS), and Warsaw Breakage Syndrome (WABS). The cohesinopathies are characterized by overlapping phenotypes ranging from craniofacial deformities, limb defects, and mental retardation. Though these syndromes share a similar suite of phenotypes and arise due to mutations in a common cohesion pathway, the underlying mechanisms are currently believed to be distinct. Defects in mitotic failure and apoptosis i.e. trans DNA tethering events are believed to be the underlying cause of RBS, whereas the underlying cause of CdLS is largely modeled as occurring through defects in transcriptional processes i.e. cis DNA tethering events. Here, we review recent findings described primarily in zebrafish, paired with additional studies in other model systems, including human patient cells, which challenge the notion that cohesinopathies represent separate syndromes. We highlight numerous studies that illustrate the utility of zebrafish to provide novel insights into the phenotypes, genes affected and the possible mechanisms underlying cohesinopathies. We propose that transcriptional deregulation is the predominant mechanism through which cohesinopathies arise. Developmental Dynamics 246:881-888, 2017. © 2017 Wiley Periodicals, Inc.
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Affiliation(s)
- Rajeswari Banerji
- Department of Biological Science, Lehigh University, Bethlehem, Pennsylvania
| | - Robert V Skibbens
- Department of Biological Science, Lehigh University, Bethlehem, Pennsylvania
| | - M Kathryn Iovine
- Department of Biological Science, Lehigh University, Bethlehem, Pennsylvania
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19
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Drummond MJ, Reidy PT, Baird LM, Dalley BK, Howard MT. Leucine Differentially Regulates Gene-Specific Translation in Mouse Skeletal Muscle. J Nutr 2017; 147:1616-1623. [PMID: 28615380 PMCID: PMC5572492 DOI: 10.3945/jn.117.251181] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2017] [Revised: 04/26/2017] [Accepted: 05/12/2017] [Indexed: 01/06/2023] Open
Abstract
Background: Amino acids, especially leucine, are particularly effective in promoting protein synthesis. Leucine is known to increase the rate of protein synthesis in skeletal muscle through the mechanistic target of rapamycin complex 1-dependent, as well as -independent, signaling pathways. However, the overall translation program is poorly defined, and it is unknown how the activation of these pathways differentially controls the translation of specific mRNAs.Objective: Ribosome profiling and RNA sequencing were used to precisely define the translational program activated by an acute oral dose of leucine.Methods: Adult male C57BL/6 mice were deprived of food overnight before the delivery of an acute dose of l-leucine (9.4 mg) (n = 6) or vehicle (n = 5) and tissues collected 30 min later. Ribosome footprints and total RNA were isolated and subjected to deep sequencing. Changes in gene-specific mRNA abundance and ribosome occupancy were determined between the leucine-treated and control groups by aligning sequence reads to Reference Sequence database mRNAs and applying statistical features of the Bioconductor package edgeR.Results: Our data revealed mRNA features that confer translational control of skeletal muscle mRNAs in response to an acute dose of leucine. The subset of skeletal muscle mRNAs that are activated consists largely of terminal oligopyrimidine mRNAs (false discovery rate: <0.05), whereas those with reduced translation had 5' untranslated regions with increased length. Only the small nuclear RNAs, which are required for ribosome biogenesis, were significantly altered in RNA abundance. The inferred functional translational program activated by dietary leucine includes increased protein synthesis capacity and energy metabolism, upregulation of sarcomere-binding proteins, modulation of circadian rhythm, and suppression of select immune components.Conclusions: These results clarify the translation program acutely stimulated by leucine in mouse skeletal muscle and establish new methodologies for use in future studies of skeletal muscle disease or aging and further examination of downstream effects of leucine on gene expression.
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Affiliation(s)
| | | | | | - Brian K Dalley
- Huntsman Cancer Institute, University of Utah, Salt Lake City, UT
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20
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Henson E, Chen Y, Gibson S. EGFR Family Members' Regulation of Autophagy Is at a Crossroads of Cell Survival and Death in Cancer. Cancers (Basel) 2017; 9:cancers9040027. [PMID: 28338617 PMCID: PMC5406702 DOI: 10.3390/cancers9040027] [Citation(s) in RCA: 68] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2017] [Revised: 03/15/2017] [Accepted: 03/21/2017] [Indexed: 12/14/2022] Open
Abstract
The epidermal growth factor receptor (EGFR) signaling pathways are altered in many cancers contributing to increased cell survival. These alterations are caused mainly through increased expression or mutation of EGFR family members EGFR, ErbB2, ErbB3, and ErbB4. These receptors have been successfully targeted for cancer therapy. Specifically, a monoclonal antibody against ErbB2, trastuzumab, and a tyrosine kinase inhibitor against EGFR, gefitinib, have improved the survival of breast and lung cancer patients. Unfortunately, cancer patients frequently become resistant to these inhibitors. This has led to investigating how EGFR can contribute to cell survival and how cancer cells can overcome inhibition of its signaling. Indeed, it is coming into focus that EGFR signaling goes beyond a single signal triggering cell proliferation and survival and is a sensor that regulates the cell’s response to microenvironmental stresses such as hypoxia. It acts as a switch that modulates the ability of cancer cells to survive. Autophagy is a process of self-digestion that is inhibited by EGFR allowing cancer cells to survive under stresses that would normally cause death and become resistant to chemotherapy. Inhibiting EGFR signaling allows autophagy to contribute to cell death. This gives new opportunities to develop novel therapeutic strategies to treat cancers that rely on EGFR signaling networks and autophagy. In this review, we summarize the current understanding of EGFR family member regulation of autophagy in cancer cells and how new therapeutic strategies could be developed to overcome drug resistance.
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Affiliation(s)
- Elizabeth Henson
- Research Institute in Oncology and Hematology, CancerCare Manitoba, 675 McDermot Ave., Winnipeg, MB R3E 0V9, Canada.
| | - Yongqiang Chen
- Research Institute in Oncology and Hematology, CancerCare Manitoba, 675 McDermot Ave., Winnipeg, MB R3E 0V9, Canada.
| | - Spencer Gibson
- Research Institute in Oncology and Hematology, CancerCare Manitoba, 675 McDermot Ave., Winnipeg, MB R3E 0V9, Canada.
- Department of Biochemistry and Medical Genetics, Faculty of Health Sciences, University of Manitoba, Winnipeg, MB R3E 0V9, Canada.
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A novel spiroindoline targets cell cycle and migration via modulation of microtubule cytoskeleton. Mol Cell Biochem 2017; 429:11-21. [DOI: 10.1007/s11010-016-2932-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2016] [Accepted: 12/23/2016] [Indexed: 10/20/2022]
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22
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Tumor Microenvironment, a Paradigm in Hepatocellular Carcinoma Progression and Therapy. Int J Mol Sci 2017. [PMID: 28216578 DOI: 10.3390/ijms18020405.] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Abstract
Hepatocellular carcinoma (HCC) is among the most lethal and prevalent cancers in the human population. Different etiological factors such as hepatitis B and C virus, alcohol and diabetes cause liver injury followed by inflammation, necrosis and hepatocytes proliferation. Continuous cycles of this destructive-regenerative process culminates in liver cirrhosis which is characterized by regenerating nodules that progress to dysplastic nodules and ultimately HCC. Despite its significance, there is only an elemental understanding of the pathogenetic mechanisms, and there are only limited therapeutic options. Therefore, the study of the involved molecular mechanisms can open a new insight to define more effective treatment strategies. A variety of alterations have been reported in HCC patients, particularly the cancer-associated microenvironment components including immune cells, fibroblast cells, endothelial cells and extracellular matrix can support the neoplastic cells to proliferate, growth and invade. This review summarizes the current state of knowledge and highlights the principal challenges that are relevant to controlling this milieu.
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Tahmasebi Birgani M, Carloni V. Tumor Microenvironment, a Paradigm in Hepatocellular Carcinoma Progression and Therapy. Int J Mol Sci 2017; 18:ijms18020405. [PMID: 28216578 PMCID: PMC5343939 DOI: 10.3390/ijms18020405] [Citation(s) in RCA: 111] [Impact Index Per Article: 15.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2016] [Revised: 02/02/2017] [Accepted: 02/08/2017] [Indexed: 12/12/2022] Open
Abstract
Hepatocellular carcinoma (HCC) is among the most lethal and prevalent cancers in the human population. Different etiological factors such as hepatitis B and C virus, alcohol and diabetes cause liver injury followed by inflammation, necrosis and hepatocytes proliferation. Continuous cycles of this destructive–regenerative process culminates in liver cirrhosis which is characterized by regenerating nodules that progress to dysplastic nodules and ultimately HCC. Despite its significance, there is only an elemental understanding of the pathogenetic mechanisms, and there are only limited therapeutic options. Therefore, the study of the involved molecular mechanisms can open a new insight to define more effective treatment strategies. A variety of alterations have been reported in HCC patients, particularly the cancer-associated microenvironment components including immune cells, fibroblast cells, endothelial cells and extracellular matrix can support the neoplastic cells to proliferate, growth and invade. This review summarizes the current state of knowledge and highlights the principal challenges that are relevant to controlling this milieu.
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Affiliation(s)
- Maryam Tahmasebi Birgani
- Department of Medical Genetics, School of Medicine, Ahvaz Jundishapur University of Medical Sciences, Ahvaz 63461, Iran.
| | - Vinicio Carloni
- Department of Experimental and Clinical Medicine, University of Florence, Largo Brambilla 3, Florence 50134, Italy.
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24
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3-(2-deoxy-β-d-erythro-pentafuranosyl)pyrimido[1,2-α]purin-10(3H)-one deoxyguanosine adducts of workers exposed to asbestos fibers. Toxicol Lett 2017; 270:1-7. [PMID: 28188891 DOI: 10.1016/j.toxlet.2017.02.008] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2016] [Revised: 01/30/2017] [Accepted: 02/06/2017] [Indexed: 01/25/2023]
Abstract
Asbestos is the commercial name for a group of silicate minerals naturally occurring in the environment and widely used in the industry. Asbestos exposure has been associated with pulmonary fibrosis, mesothelioma, and malignancies, which may appear after a period of latency of 20-40 years. Mechanisms involved in the carcinogenic effects of asbestos are still not fully elucidated, although the oxidative stress theory suggests that phagocytic cells produce large amounts of reactive oxygen species, due to their inability to digest asbestos fiber. We have conducted a mechanistic study to evaluate the association between 3-(2-deoxy-β-d-erythro-pentafuranosyl)pyrimido[1,2-α]purin-10(3H)-one deoxyguanosine (M1dG) adducts, a biomarker of oxidative stress and lipid peroxidation, and asbestos exposure in the peripheral blood of 327 subjects living in Tuscany and Liguria, Italy, stratified by occupational exposure to asbestos. Adduct frequency was significantly greater into exposed subjects with respect to the controls. M1dG per 108 normal nucleotides were 4.0±0.5 (SE) in 156 asbestos workers, employed in mechanic, naval, petrochemical, building industries, and in pottery and ceramic plants, versus a value of 2.3±0.1 (SE) in 171 controls (p<0.001). After stratification for occupational history, the effects persisted in 54 current asbestos workers, mainly employed in building renovation industry (2.9±0.3 (SE)), and in 102 former asbestos workers (4.5±0.7 (SE)), with p-values of 0.033, and <0.001, respectively. A significant effect of smoking on heavy smokers was found (p=0.005). Our study gives additional support to the oxidative stress theory, where M1dG may reflect an additional potential mechanism of asbestos-induced toxicity.
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25
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Lysyl Oxidase and the Tumor Microenvironment. Int J Mol Sci 2016; 18:ijms18010062. [PMID: 28036074 PMCID: PMC5297697 DOI: 10.3390/ijms18010062] [Citation(s) in RCA: 105] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2016] [Revised: 12/20/2016] [Accepted: 12/23/2016] [Indexed: 12/14/2022] Open
Abstract
The lysyl oxidase (LOX) family of oxidases contains a group of extracellular copper-dependent enzymes that catalyze the cross-linking of collagen and elastin by oxidation, thus maintaining the rigidity and structural stability of the extracellular matrix (ECM). Aberrant expression or activation of LOX alters the cellular microenvironment, leading to many diseases, including atherosclerosis, tissue fibrosis, and cancer. Recently, a number of studies have shown that LOX is overexpressed in most cancers and that it is involved in the regulation of tumor progression and metastasis. In contrast, a few reports have also indicated the tumor-suppressing role of LOX. In this short review, we discuss recent research on the correlations between LOX and cancer. Further, the role of LOX in tumor microenvironment remodeling, tumorigenesis, and metastasis and the underlying mechanisms have also been elucidated.
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26
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Zhou Y, Ren J, Song T, Peng J, Wei H. Methionine Regulates mTORC1 via the T1R1/T1R3-PLCβ-Ca 2+-ERK1/2 Signal Transduction Process in C2C12 Cells. Int J Mol Sci 2016; 17:ijms17101684. [PMID: 27727170 PMCID: PMC5085716 DOI: 10.3390/ijms17101684] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2016] [Revised: 09/20/2016] [Accepted: 09/27/2016] [Indexed: 12/13/2022] Open
Abstract
The mammalian target of rapamycin complex 1 (mTORC1) integrates amino acid (AA) availability to support protein synthesis and cell growth. Taste receptor type 1 member (T1R) is a G protein-coupled receptor that functions as a direct sensor of extracellular AA availability to regulate mTORC1 through Ca2+ stimulation and extracellular signal-regulated kinases 1 and 2 (ERK1/2) activation. However, the roles of specific AAs in T1R1/T1R3-regulated mTORC1 are poorly defined. In this study, T1R1 and T1R3 subunits were expressed in C2C12 myotubes, and l-AA sensing was accomplished by T1R1/T1R3 to activate mTORC1. In response to l-AAs, such as serine (Ser), arginine (Arg), threonine (Thr), alanine (Ala), methionine (Met), glutamine (Gln), and glycine (Gly), Met induced mTORC1 activation and promoted protein synthesis. Met also regulated mTORC1 via T1R1/T1R3-PLCβ-Ca2+-ERK1/2 signal transduction. Results revealed a new role for Met-regulated mTORC1 via an AA receptor. Further studies should be performed to determine the role of T1R1/T1R3 in mediating extracellular AA to regulate mTOR signaling and to reveal its mechanism.
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Affiliation(s)
- Yuanfei Zhou
- Department of Animal Nutrition and Feed Science, College of Animal Science and Technology, Huazhong Agriculture University, Wuhan 430070, Hubei, China.
- The Cooperative Innovation Center for Sustainable Pig Production, Wuhan 430070, Hubei, China.
| | - Jiao Ren
- Department of Animal Nutrition and Feed Science, College of Animal Science and Technology, Huazhong Agriculture University, Wuhan 430070, Hubei, China.
| | - Tongxing Song
- Department of Animal Nutrition and Feed Science, College of Animal Science and Technology, Huazhong Agriculture University, Wuhan 430070, Hubei, China.
| | - Jian Peng
- Department of Animal Nutrition and Feed Science, College of Animal Science and Technology, Huazhong Agriculture University, Wuhan 430070, Hubei, China.
- The Cooperative Innovation Center for Sustainable Pig Production, Wuhan 430070, Hubei, China.
| | - Hongkui Wei
- Department of Animal Nutrition and Feed Science, College of Animal Science and Technology, Huazhong Agriculture University, Wuhan 430070, Hubei, China.
- The Cooperative Innovation Center for Sustainable Pig Production, Wuhan 430070, Hubei, China.
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Zhang XJ, Jia SS. Fisetin inhibits laryngeal carcinoma through regulation of AKT/NF-κB/mTOR and ERK1/2 signaling pathways. Biomed Pharmacother 2016; 83:1164-1174. [PMID: 27551764 DOI: 10.1016/j.biopha.2016.08.035] [Citation(s) in RCA: 59] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2016] [Revised: 07/26/2016] [Accepted: 08/11/2016] [Indexed: 02/09/2023] Open
Abstract
Targeting cancer cells is crucial for improving the efficiency of laryngeal cancer treatment. However, the signaling pathway and therapeutic strategy, related to the tumor, still need further research. Dietary flavonoid fisetin (3,3',4',7-tetrahydroxyflavone) found in many fruits and vegetables has been shown in preclinical studies to inhibit cancer growth through regulating cell cycle, apoptosis, angiogenesis, invasion and metastasis without causing any toxicity to normal cells. PI3K/AKT and ERK1/2 have been known as essential signaling pathways to modulate cell proliferation, apoptosis as well as autophagy via mTOR, Caspase-3 and NF-κB signals. In our study, flow cytometry and western blot assays suggested that apoptosis was induced by fisetin administration, promoting Caspase-3 expressions by regulating PI3K/AKT/NF-κB. Additionally, fisetin suppressed TU212 cells proliferation, which was linked with ERK1/2 inactivation. Further, the activation of PI3K/AKT-regulated mTOR was inhibited by fisetin, leading to transcription suppression and proliferation inhibition of TU212 cells. In vivo studies also showed that the tumor volume and weight of nude mice were reduced for fisetin use with KI-67 decrease and LC3II increase in tumor tissue samples. Together, our data indicated that fisetin had a potential role in controlling human laryngeal cancer through inhibiting tumor cell proliferation, inducing apoptosis and autophagy regulated by ERK1/2 and AKT/NF-κB/mTOR signaling pathways, which might provide a therapeutic strategy for laryngeal cancer inhibition in future.
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Affiliation(s)
- Xi-Jun Zhang
- Department of Otolaryngology-Head and Neck Surgery, The Fourth Affiliated Hospital of Harbin Medical University, No. 37 Yiyuan Street, Nangang District, Harbin 150001, China
| | - Shen-Shan Jia
- Department of Otolaryngology-Head and Neck Surgery, Harbin Medical University Cancer Hospital, No. 150 Haping Road, Nangang District, Harbin 150001, China.
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Non-Invasive Methods to Monitor Mechanisms of Resistance to Tyrosine Kinase Inhibitors in Non-Small-Cell Lung Cancer: Where Do We Stand? Int J Mol Sci 2016; 17:ijms17071186. [PMID: 27455248 PMCID: PMC4964555 DOI: 10.3390/ijms17071186] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2016] [Revised: 06/28/2016] [Accepted: 07/15/2016] [Indexed: 12/22/2022] Open
Abstract
The induction of resistance mechanisms represents an important problem for the targeted therapy of patients with non-small-cell lung cancer (NSCLC). The best-known resistance mechanism induced during treatment with epidermal growth factor receptor (EGFR)-tyrosine kinase inhibitors (TKIs) is EGFR T790M mutation for which specific drugs are have been developed. However, other molecular alterations have also been reported as induced resistance mechanisms to EGFR-TKIs. Similarly, there is growing evidence of acquired resistance mechanisms to anaplastic lymphoma kinase (ALK)-TKI treatment. A better understanding of these acquired resistance mechanisms is essential in clinical practice as patients could be treated with specific drugs that are active against the induced alterations. The use of free circulating tumor nucleic acids or circulating tumor cells (CTCs) enables resistance mechanisms to be characterized in a non-invasive manner and reduces the need for tumor re-biopsy. This review discusses the main resistance mechanisms to TKIs and provides a comprehensive overview of innovative strategies to evaluate known resistance mechanisms in free circulating nucleic acids or CTCs and potential future orientations for these non-invasive approaches.
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Knockdown of AMPKα2 Promotes Pulmonary Arterial Smooth Muscle Cells Proliferation via mTOR/Skp2/p27(Kip1) Signaling Pathway. Int J Mol Sci 2016; 17:ijms17060844. [PMID: 27258250 PMCID: PMC4926378 DOI: 10.3390/ijms17060844] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2016] [Revised: 05/06/2016] [Accepted: 05/24/2016] [Indexed: 12/11/2022] Open
Abstract
It has been shown that activation of adenosine monophosphate-activated protein kinase (AMPK) suppresses proliferation of a variety of tumor cells as well as nonmalignant cells. In this study, we used post-transcriptional gene silencing with small interfering RNA (siRNA) to specifically examine the effect of AMPK on pulmonary arterial smooth muscle cells (PASMCs) proliferation and to further elucidate its underlying molecular mechanisms. Our results showed that knockdown of AMPKα2 promoted primary cultured PASMCs proliferation; this was accompanied with the elevation of phosphorylation of mammalian target of rapamycin (mTOR) and S-phase kinase-associated protein 2 (Skp2) protein level and reduction of p27(Kip1). Importantly, prior silencing of mTOR with siRNA abolished AMPKα2 knockdown-induced Skp2 upregulation, p27(Kip1) reduction as well as PASMCs proliferation. Furthermore, pre-depletion of Skp2 by siRNA also eliminated p27(Kip1) downregulation and PASMCs proliferation caused by AMPKα2 knockdown. Taken together, our study indicates that AMPKα2 isoform plays an important role in regulation of PASMCs proliferation by modulating mTOR/Skp2/p27(Kip1) axis, and suggests that activation of AMPKα2 might have potential value in the prevention and treatment of pulmonary arterial hypertension.
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Role of Mitochondrial DNA Copy Number Alteration in Human Renal Cell Carcinoma. Int J Mol Sci 2016; 17:ijms17060814. [PMID: 27231905 PMCID: PMC4926348 DOI: 10.3390/ijms17060814] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2016] [Revised: 05/09/2016] [Accepted: 05/10/2016] [Indexed: 12/19/2022] Open
Abstract
We investigated the role of mitochondrial DNA (mtDNA) copy number alteration in human renal cell carcinoma (RCC). The mtDNA copy numbers of paired cancer and non-cancer parts from five resected RCC kidneys after radical nephrectomy were determined by quantitative polymerase chain reaction (Q-PCR). An RCC cell line, 786-O, was infected by lentiviral particles to knock down mitochondrial transcriptional factor A (TFAM). Null target (NT) and TFAM-knockdown (TFAM-KD) represented the control and knockdown 786-O clones, respectively. Protein or mRNA expression levels of TFAM; mtDNA-encoded NADH dehydrogenase subunit 1 (ND1), ND6 and cytochrome c oxidase subunit 2 (COX-2); nuclear DNA (nDNA)-encoded succinate dehydrogenase subunit A (SDHA); v-akt murine thymoma viral oncogene homolog 1 gene (AKT)-encoded AKT and v-myc myelocytomatosis viral oncogene homolog gene (c-MYC)-encoded MYC; glycolytic enzymes including hexokinase II (HK-II), glucose 6-phosphate isomerase (GPI), phosphofructokinase (PFK), and lactate dehydrogenase subunit A (LDHA); and hypoxia-inducible factors the HIF-1α and HIF-2α, pyruvate dehydrogenase kinase 1 (PDK1), and pyruvate dehydrogenase E1 component α subunit (PDHA1) were analyzed by Western blot or Q-PCR. Bioenergetic parameters of cellular metabolism, basal mitochondrial oxygen consumption rate (mOCRB) and basal extracellular acidification rate (ECARB), were measured by a Seahorse XFe-24 analyzer. Cell invasiveness was evaluated by a trans-well migration assay and vimentin expression. Doxorubicin was used as a chemotherapeutic agent. The results showed a decrease of mtDNA copy numbers in resected RCC tissues (p = 0.043). The TFAM-KD clone expressed lower mtDNA copy number (p = 0.034), lower mRNA levels of TFAM (p = 0.008), ND1 (p = 0.007), and ND6 (p = 0.017), and lower protein levels of TFAM and COX-2 than did the NT clone. By contrast, the protein levels of HIF-2α, HK-II, PFK, LDHA, AKT, MYC and vimentin; trans-well migration activity (p = 0.007); and drug resistance to doxorubicin (p = 0.008) of the TFAM-KD clone were significantly higher than those of the NT clone. Bioenergetically, the TFAM-KD clone expressed lower mOCRB (p = 0.009) but higher ECARB (p = 0.037) than did the NT clone. We conclude that a reduction of mtDNA copy number and decrease of respiratory function of mitochondria in RCC might be compensated for by an increase of enzymes and factors that are involved in the upregulation of glycolysis to confer RCC more invasive and a drug-resistant phenotype in vitro.
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Cell and Signal Components of the Microenvironment of Bone Metastasis Are Affected by Hypoxia. Int J Mol Sci 2016; 17:ijms17050706. [PMID: 27187355 PMCID: PMC4881528 DOI: 10.3390/ijms17050706] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2016] [Revised: 04/28/2016] [Accepted: 05/03/2016] [Indexed: 12/27/2022] Open
Abstract
Bone metastatic cells release bone microenvironment proteins, such as the matricellular protein SPARC (secreted protein acidic and rich in cysteine), and share a cell signaling typical of the bone metabolism controlled by Runx2. The megakaryocytes in the bone marrow engrafted by the metastases seem to be one of the principal microenvironment sources of the biological stimuli, implicated in the formation of an osteoblastic niche, and affecting metastasis phenotype and colonization. Educated platelets in the circulation might derive from megakaryocytes in bone metastasis. The evaluation of predictive markers in the circulating platelets might be useful for the stratification of patients for therapeutic purposes. The hypoxic environment in bone metastasis is one of the key regulators of the network of the biological soluble and structural components of the matrix. In bone metastatic cells under hypoxia, similar patterns of Runx2 and SPARC are observed, both showing downregulation. Conversely, hypoxia induces Endothelin 1, which upregulates SPARC, and these biological stimuli may be considered prognostic markers of bone metastasis in breast carcinoma patients.
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Maroni P, Bendinelli P, Resnati M, Matteucci E, Milan E, Desiderio MA. The Autophagic Process Occurs in Human Bone Metastasis and Implicates Molecular Mechanisms Differently Affected by Rab5a in the Early and Late Stages. Int J Mol Sci 2016; 17:443. [PMID: 27023526 PMCID: PMC4848899 DOI: 10.3390/ijms17040443] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2016] [Revised: 03/09/2016] [Accepted: 03/09/2016] [Indexed: 12/14/2022] Open
Abstract
Autophagy favours metastatic growth through fuelling energy and nutrients and resistance to anoikis, typical of disseminated-tumour cells. The autophagic process, mediated by a unique organelle, the autophagosome, which fuses with lysosomes, is divided into three steps. Several stages, especially early omegasome formation and isolation-membrane initiation, remain controversial; molecular mechanisms involve the small-GTPase Rab5a, which regulates vesicle traffic for autophagosome formation. We examined Rab5a involvement in the function of key members of ubiquitin-conjugation systems, Atg7 and LC3-lipidated, interacting with the scaffold-protein p62. Immunohistochemistry of Rab5a was performed in human specimens of bone metastasis and pair-matched breast carcinoma; the autophagic-molecular mechanisms affected by Rab5a were evaluated in human 1833 bone metastatic cells, derived from breast-carcinoma MDA-MB231 cells. To clarify the role of Rab5a, 1833 cells were transfected transiently with Rab5a-dominant negative, and/or stably with the short-hairpin RNA Atg7, were exposed to two inhibitors of autolysosome function, and LC3II and p62 expression was measured. We showed basal autophagy in bone-metastatic cells and the pivotal role of Rab5a together with Beclin 1 between the early stages, elongation of isolation membrane/closed autophagosome mediated by Atg7, and the late-degradative stages. This regulatory network might occur in bone-metastasis and in high-grade dysplastic lesions, preceding invasive-breast carcinoma and conferring phenotypic characteristics for dissemination.
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Affiliation(s)
- Paola Maroni
- Istituto Ortopedico Galeazzi, Scientific Institute for Research, Hospitalization and Health Care (IRCCS), Milano 20161, Italy.
| | - Paola Bendinelli
- Dipartimento di Scienze Biomediche per la Salute, Molecular Pathology Laboratory, Università degli Studi di Milano, Milano 20133, Italy.
| | - Massimo Resnati
- San Raffaele Scientific Institute, Division of Genetics and Cell Biology, Milano 20133, Italy.
| | - Emanuela Matteucci
- Dipartimento di Scienze Biomediche per la Salute, Molecular Pathology Laboratory, Università degli Studi di Milano, Milano 20133, Italy.
| | - Enrico Milan
- San Raffaele Scientific Institute, Division of Genetics and Cell Biology, Milano 20133, Italy.
| | - Maria Alfonsina Desiderio
- Dipartimento di Scienze Biomediche per la Salute, Molecular Pathology Laboratory, Università degli Studi di Milano, Milano 20133, Italy.
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