1
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Choi WH, Cho Y, Cha JH, Lee DH, Jeong JG, Jung SH, Song JJ, Lee JH, Lee SY. Functional pathogenicity of ESRRB variant of uncertain significance contributes to hearing loss (DFNB35). Sci Rep 2024; 14:21215. [PMID: 39261511 PMCID: PMC11390957 DOI: 10.1038/s41598-024-70795-8] [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: 01/24/2024] [Accepted: 08/21/2024] [Indexed: 09/13/2024] Open
Abstract
Advances in next-generation sequencing technologies have led to elucidation of sensorineural hearing loss genetics and associated clinical impacts. However, studies on the functional pathogenicity of variants of uncertain significance (VUS), despite their close association with clinical phenotypes, are lacking. Here we identified compound heterozygous variants in ESRRB transcription factor gene linked to DFNB35, specifically a novel splicing variant (NM_004452.4(ESRRB): c.397 + 2T>G) in trans with a missense variant (NM_004452.4(ESRRB): c.1144C>T p.(Arg382Cys)) whose pathogenicity remains unclear. The splicing variant (c.397 + 2T>G) caused exon 4 skipping, leading to premature stop codon formation and nonsense-mediated decay. The p.(Arg382Cys) variant was classified as a VUS due to its particularly higher allele frequency among East Asian population despite disease-causing in-silico predictions. However, functional assays showed that p.(Arg382Cys) variant disrupted key intramolecular interactions, leading to protein instability. This variant also reduced transcriptional activity and altered expression of downstream target genes essential for inner ear function, suggesting genetic contribution to disease phenotype. This study expanded the phenotypic and genotypic spectrum of ESRRB in DFNB35 and revealed molecular mechanisms underlying ESRRB-associated DFNB35. These findings suggest that variants with high allele frequencies can also possess functional pathogenicity, providing a breakthrough for cases where VUS, previously unexplored, could be reinterpreted by elucidating their functional roles and disease-causing characteristics.
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Affiliation(s)
- Won Hoon Choi
- Department of Otorhinolaryngology-Head and Neck Surgery, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Yeijean Cho
- Seoul National University College of Medicine, Seoul, South Korea
| | - Ju Hyuen Cha
- Department of Otorhinolaryngology-Head and Neck Surgery, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Dae Hee Lee
- CTCELLS, Inc., 21, Yuseong-Daero, 1205 Beon-Gil, Yuseong-Gu, Daejeon, Republic of Korea
| | - Jong Gwan Jeong
- CTCELLS, Inc., 21, Yuseong-Daero, 1205 Beon-Gil, Yuseong-Gu, Daejeon, Republic of Korea
| | - Sung Ho Jung
- Department of Otorhinolaryngology-Head and Neck Surgery, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Jae-Jin Song
- Department of Otorhinolaryngology-Head and Neck Surgery, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Jun Ho Lee
- Department of Otorhinolaryngology-Head and Neck Surgery, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Sang-Yeon Lee
- Department of Otorhinolaryngology-Head and Neck Surgery, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Republic of Korea.
- Sensory Organ Research Institute, Seoul National University Medical Research Center, Seoul, Republic of Korea.
- Department of Genomic Medicine, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Republic of Korea.
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2
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Polla DL, Fard MAF, Tabatabaei Z, Habibzadeh P, Levchenko OA, Nikuei P, Makrythanasis P, Hussain M, von Hardenberg S, Zeinali S, Fallah MS, Schuurs-Hoeijmakers JHM, Shahzad M, Fatima F, Fatima N, Kaat LD, Bruggenwirth HT, Fleming LR, Condie J, Ploski R, Pollak A, Pilch J, Demina NA, Chukhrova AL, Sergeeva VS, Venselaar H, Masri AT, Hamamy H, Santoni FA, Linda K, Ahmed ZM, Kasri NN, de Brouwer APM, Bergmann AK, Hethey S, Yavarian M, Ansar M, Riazuddin S, Riazuddin S, Silawi M, Ruggeri G, Pirozzi F, Eftekhar E, Sheshdeh AT, Bahramjahan S, Mirzaa GM, Lavrov AV, Antonarakis SE, Faghihi MA, van Bokhoven H. Biallelic variants in TMEM222 cause a new autosomal recessive neurodevelopmental disorder. Genet Med 2021; 23:1246-1254. [PMID: 33824500 PMCID: PMC8725574 DOI: 10.1038/s41436-021-01133-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Revised: 02/12/2021] [Accepted: 02/16/2021] [Indexed: 01/25/2023] Open
Abstract
PURPOSE To elucidate the novel molecular cause in families with a new autosomal recessive neurodevelopmental disorder. METHODS A combination of exome sequencing and gene matching tools was used to identify pathogenic variants in 17 individuals. Quantitative reverse transcription polymerase chain reaction (RT-qPCR) and subcellular localization studies were used to characterize gene expression profile and localization. RESULTS Biallelic variants in the TMEM222 gene were identified in 17 individuals from nine unrelated families, presenting with intellectual disability and variable other features, such as aggressive behavior, shy character, body tremors, decreased muscle mass in the lower extremities, and mild hypotonia. We found relatively high TMEM222 expression levels in the human brain, especially in the parietal and occipital cortex. Additionally, subcellular localization analysis in human neurons derived from induced pluripotent stem cells (iPSCs) revealed that TMEM222 localizes to early endosomes in the synapses of mature iPSC-derived neurons. CONCLUSION Our findings support a role for TMEM222 in brain development and function and adds variants in the gene TMEM222 as a novel underlying cause of an autosomal recessive neurodevelopmental disorder.
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Affiliation(s)
- Daniel L. Polla
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behavior, Radboud University Medical Center, Nijmegen, The Netherlands.,CAPES Foundation, Ministry of Education of Brazil, Brasília, Brazil.,These authors contributed equally: Daniel L. Polla, Mohammad Ali Farazi Fard
| | - Mohammad Ali Farazi Fard
- Persian BayanGene Research and Training Center, Shiraz University of Medical Sciences, Shiraz, Fars, Iran.,These authors contributed equally: Daniel L. Polla, Mohammad Ali Farazi Fard
| | - Zahra Tabatabaei
- Persian BayanGene Research and Training Center, Shiraz University of Medical Sciences, Shiraz, Fars, Iran
| | - Parham Habibzadeh
- Persian BayanGene Research and Training Center, Shiraz University of Medical Sciences, Shiraz, Fars, Iran
| | | | - Pooneh Nikuei
- Molecular Medicine Research Center, Hormozgan Health Institute, Hormozgan University of Medical Sciences, Bandar Abbas, Iran
| | - Periklis Makrythanasis
- Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva, Switzerland.,Present address: Biomedical Research Foundation Academy of Athens, Athens, Greece
| | - Mureed Hussain
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behavior, Radboud University Medical Center, Nijmegen, The Netherlands
| | | | - Sirous Zeinali
- Department of Molecular Medicine, Biotechnology Research Center, Pasteur Institute of Iran, Tehran, Iran
| | | | - Janneke H. M. Schuurs-Hoeijmakers
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behavior, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Mohsin Shahzad
- Department of Otorhinolaryngology Head & Neck Surgery, School of Medicine, University of Maryland, Baltimore, MD, USA.,Department of Molecular Biology, Shaheed Zulfiqar Ali Bhutto Medical University, Islamabad, Pakistan.,Jinnah Burn and Reconstructive Surgery Center, Allama Iqbal Medical Research Center, University of Health Sciences, Lahore, Pakistan
| | - Fareeha Fatima
- Center for Excellence in Molecular Biology, University of Punjab, Lahore, Pakistan
| | - Neelam Fatima
- Center for Excellence in Molecular Biology, University of Punjab, Lahore, Pakistan
| | - Laura Donker Kaat
- Department of Clinical Genetics, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands
| | - Hennie T. Bruggenwirth
- Department of Clinical Genetics, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands
| | - Leah R. Fleming
- St. Luke’s Children’s Genetics and Metabolic Clinic, Boise, ID, USA
| | - John Condie
- St Luke’s Pediatric Neurology Clinic, Boise, ID, USA
| | - Rafal Ploski
- Department of Medical Genetics, Warsaw Medical University, Warsaw, Poland
| | - Agnieszka Pollak
- Department of Medical Genetics, Warsaw Medical University, Warsaw, Poland
| | - Jacek Pilch
- Department of Pediatric Neurology, Medical University of Silesia, Katowice, Poland
| | | | | | | | - Hanka Venselaar
- Center for Molecular and Biomolecular Informatics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Amira T. Masri
- Faculty of Medicine, Pediatric Department Division of Child Neurology, The University of Jordan, Amman, Jordan
| | - Hanan Hamamy
- Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva, Switzerland
| | - Federico A. Santoni
- Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva, Switzerland.,Department of Endocrinology Diabetes and Metabolism, Lausanne University Hospital, Lausanne, Switzerland
| | - Katrin Linda
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behavior, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Zubair M. Ahmed
- Department of Otorhinolaryngology Head & Neck Surgery, School of Medicine, University of Maryland, Baltimore, MD, USA
| | - Nael Nadif Kasri
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behavior, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Arjan P. M. de Brouwer
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behavior, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Anke K. Bergmann
- Department of Human Genetics, Hannover Medical School, Hanover, Germany
| | - Sven Hethey
- Department of Neuropediatrics, Children’s and Youth Hospital Auf der Bult, Hanover, Germany
| | - Majid Yavarian
- Persian BayanGene Research and Training Center, Shiraz University of Medical Sciences, Shiraz, Fars, Iran
| | - Muhammad Ansar
- Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva, Switzerland.,Institute of Molecular and Clinical Ophthalmology Basel, Basel, Switzerland
| | - Saima Riazuddin
- Department of Otorhinolaryngology Head & Neck Surgery, School of Medicine, University of Maryland, Baltimore, MD, USA
| | - Sheikh Riazuddin
- Department of Molecular Biology, Shaheed Zulfiqar Ali Bhutto Medical University, Islamabad, Pakistan.,Jinnah Burn and Reconstructive Surgery Center, Allama Iqbal Medical Research Center, University of Health Sciences, Lahore, Pakistan
| | - Mohammad Silawi
- Persian BayanGene Research and Training Center, Shiraz University of Medical Sciences, Shiraz, Fars, Iran
| | - Gaia Ruggeri
- Center for Integrative Brain Research, Seattle Children’s Research Institute, Seattle, WA, USA
| | - Filomena Pirozzi
- Center for Integrative Brain Research, Seattle Children’s Research Institute, Seattle, WA, USA
| | - Ebrahim Eftekhar
- Molecular Medicine Research Center, Hormozgan Health Institute, Hormozgan University of Medical Sciences, Bandar Abbas, Iran
| | - Afsaneh Taghipour Sheshdeh
- Persian BayanGene Research and Training Center, Shiraz University of Medical Sciences, Shiraz, Fars, Iran
| | - Shima Bahramjahan
- Persian BayanGene Research and Training Center, Shiraz University of Medical Sciences, Shiraz, Fars, Iran
| | - Ghayda M. Mirzaa
- Center for Integrative Brain Research, Seattle Children’s Research Institute, Seattle, WA, USA.,Department of Pediatrics, University of Washington, Seattle, WA, USA.,Brotman Baty Institute for Precision Medicine, Seattle, WA, USA
| | | | - Stylianos E. Antonarakis
- Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva, Switzerland.,Medigenome, Swiss Institute of Genomic Medicine, Geneva, Switzerland
| | - Mohammad Ali Faghihi
- Persian BayanGene Research and Training Center, Shiraz University of Medical Sciences, Shiraz, Fars, Iran.,Department of Psychiatry & Behavioral Sciences, Hussman Institute for Human Genomics, University of Miami, Miami, FL, USA
| | - Hans van Bokhoven
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behavior, Radboud University Medical Center, Nijmegen, The Netherlands.
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3
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De Novo Variants in SPOP Cause Two Clinically Distinct Neurodevelopmental Disorders. Am J Hum Genet 2020; 106:405-411. [PMID: 32109420 DOI: 10.1016/j.ajhg.2020.02.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2019] [Accepted: 02/05/2020] [Indexed: 12/20/2022] Open
Abstract
Recurrent somatic variants in SPOP are cancer specific; endometrial and prostate cancers result from gain-of-function and dominant-negative effects toward BET proteins, respectively. By using clinical exome sequencing, we identified six de novo pathogenic missense variants in SPOP in seven individuals with developmental delay and/or intellectual disability, facial dysmorphisms, and congenital anomalies. Two individuals shared craniofacial dysmorphisms, including congenital microcephaly, that were strikingly different from those of the other five individuals, who had (relative) macrocephaly and hypertelorism. We measured the effect of SPOP variants on BET protein amounts in human Ishikawa endometrial cancer cells and patient-derived cell lines because we hypothesized that variants would lead to functional divergent effects on BET proteins. The de novo variants c.362G>A (p.Arg121Gln) and c. 430G>A (p.Asp144Asn), identified in the first two individuals, resulted in a gain of function, and conversely, the c.73A>G (p.Thr25Ala), c.248A>G (p.Tyr83Cys), c.395G>T (p.Gly132Val), and c.412C>T (p.Arg138Cys) variants resulted in a dominant-negative effect. Our findings suggest that these opposite functional effects caused by the variants in SPOP result in two distinct and clinically recognizable syndromic forms of intellectual disability with contrasting craniofacial dysmorphisms.
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4
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van den Akker WMR, Brummelman I, Martis LM, Timmermans RN, Pfundt R, Kleefstra T, Willemsen MH, Gerkes EH, Herkert JC, van Essen AJ, Rump P, Vansenne F, Terhal PA, van Haelst MM, Cristian I, Turner CE, Cho MT, Begtrup A, Willaert R, Fassi E, van Gassen KLI, Stegmann APA, de Vries BBA, Schuurs-Hoeijmakers JHM. De novo variants in CDK13 associated with syndromic ID/DD: Molecular and clinical delineation of 15 individuals and a further review. Clin Genet 2019; 93:1000-1007. [PMID: 29393965 DOI: 10.1111/cge.13225] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2017] [Revised: 01/03/2018] [Accepted: 01/24/2018] [Indexed: 01/06/2023]
Abstract
De novo variants in the gene encoding cyclin-dependent kinase 13 (CDK13) have been associated with congenital heart defects and intellectual disability (ID). Here, we present the clinical assessment of 15 individuals and report novel de novo missense variants within the kinase domain of CDK13. Furthermore, we describe 2 nonsense variants and a recurrent frame-shift variant. We demonstrate the synthesis of 2 aberrant CDK13 transcripts in lymphoblastoid cells from an individual with a splice-site variant. Clinical characteristics of the individuals include mild to severe ID, developmental delay, behavioral problems, (neonatal) hypotonia and a variety of facial dysmorphism. Congenital heart defects were present in 2 individuals of the current cohort, but in at least 42% of all known individuals. An overview of all published cases is provided and does not demonstrate an obvious genotype-phenotype correlation, although 2 individuals harboring a stop codons at the end of the kinase domain might have a milder phenotype. Overall, there seems not to be a clinically recognizable facial appearance. The variability in the phenotypes impedes an à vue diagnosis of this syndrome and therefore genome-wide or gene-panel driven genetic testing is needed. Based on this overview, we provide suggestions for clinical work-up and management of this recently described ID syndrome.
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Affiliation(s)
- W M R van den Akker
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - I Brummelman
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - L M Martis
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - R N Timmermans
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - R Pfundt
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - T Kleefstra
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - M H Willemsen
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - E H Gerkes
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - J C Herkert
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - A J van Essen
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - P Rump
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - F Vansenne
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - P A Terhal
- Department of Genetics, University Medical Centre Utrecht, Utrecht, The Netherlands
| | - M M van Haelst
- Department of Genetics, University Medical Centre Utrecht, Utrecht, The Netherlands.,Department of Clinical Genetics, AMC/VUmc, Amsterdam, The Netherlands
| | - I Cristian
- Division of Genetics and Metabolism, Department of Pediatrics, Nemours Children's Hospital Orlando, Orlando, Florida
| | - C E Turner
- Department of Genetics, Walter Reed National Military Medical Center, Bethesda, Maryland
| | - M T Cho
- GeneDx, Gaithersburg, Maryland
| | | | | | - E Fassi
- Division of Genetics and Genomic Medicine, Department of Pediatrics, Washington University School of Medicine, St Louis, Missouri
| | - K L I van Gassen
- Department of Genetics, University Medical Centre Utrecht, Utrecht, The Netherlands
| | - A P A Stegmann
- Department of Human Genetics, Maastricht University Hospital, Maastricht, The Netherlands
| | - B B A de Vries
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
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5
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Milanesi E, Voinsky I, Hadar A, Srouji A, Maj C, Shekhtman T, Gershovits M, Gilad S, Chillotti C, Squassina A, Potash JB, Schulze TG, Goes FS, Zandi P, Kelsoe JR, Gurwitz D. RNA sequencing of bipolar disorder lymphoblastoid cell lines implicates the neurotrophic factor HRP-3 in lithium's clinical efficacy. World J Biol Psychiatry 2019; 20:449-461. [PMID: 28854847 DOI: 10.1080/15622975.2017.1372629] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Objectives: Lithium remains the oldest and most effective treatment for mood stabilisation in bipolar disorder (BD), even though at least half of patients are only partially responsive or do not respond. This study aimed to identify biomarkers associated with lithium response in BD, based on comparing RNA sequencing information derived from lymphoblastoid cell lines (LCLs) of lithium-responsive (LR) versus lithium non-responsive (LNR) BD patients, to assess gene expression variations that might bear on treatment outcome. Methods: RNA sequencing was carried out on 24 LCLs from female BD patients (12 LR and 12 LNR) followed by qPCR validation in two additional independent cohorts (41 and 17 BD patients, respectively). Results: Fifty-six genes showed nominal differential expression comparing LR and LNR (FC ≥ |1.3|, P ≤ 0.01). The differential expression of HDGFRP3 and ID2 was validated by qPCR in the independent cohorts. Conclusions: We observed higher expression levels of HDGFRP3 and ID2 in BD patients who favourably respond to lithium. Both of these genes are involved in neurogenesis, and HDGFRP3 has been suggested to be a neurotrophic factor. Additional studies in larger BD cohorts are needed to confirm the potential of HDGFRP3 and ID2 expression levels in blood cells as tentative favourable lithium response biomarkers.
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Affiliation(s)
- Elena Milanesi
- Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of Medicine, Tel Aviv University , Tel Aviv , Israel.,Genetics Unit, IRCCS, San Giovanni di Dio, Fatebenefratelli , Brescia , Italy
| | - Irena Voinsky
- Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of Medicine, Tel Aviv University , Tel Aviv , Israel
| | - Adva Hadar
- Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of Medicine, Tel Aviv University , Tel Aviv , Israel
| | - Ala Srouji
- Institute of Psychiatric Phenomics and Genomics, Ludwig-Maximilians-University Munich , Munich , Germany.,Department of Genetic Epidemiology in Psychiatry, Central Institute of Mental Health , Mannheim , Germany
| | - Carlo Maj
- Genetics Unit, IRCCS, San Giovanni di Dio, Fatebenefratelli , Brescia , Italy
| | - Tatyana Shekhtman
- Department of Psychiatry, University of California , San Diego , CA , USA
| | - Michael Gershovits
- The Nancy & Stephen Grand Israel National Center for Personalized Medicine, Weizmann Institute of Science , Rehovot , Israel
| | - Shlomit Gilad
- The Nancy & Stephen Grand Israel National Center for Personalized Medicine, Weizmann Institute of Science , Rehovot , Israel
| | - Caterina Chillotti
- Unit of Clinical Pharmacology, University Hospital of Cagliari , Cagliari , Italy
| | - Alessio Squassina
- Section of Neurosciences and Clinical Pharmacology, Department of Biomedical Sciences, School of Medicine, University of Cagliari , Cagliari , Italy
| | - James B Potash
- Department of Psychiatry, University of Iowa Carver College of Medicine , Iowa City , IA , USA
| | - Thomas G Schulze
- Institute of Psychiatric Phenomics and Genomics, Ludwig-Maximilians-University Munich , Munich , Germany.,Department of Genetic Epidemiology in Psychiatry, Central Institute of Mental Health , Mannheim , Germany.,Department of Psychiatry and Psychotherapy, University Medical Center Georg-August-University , Göttingen , Germany
| | - Fernando S Goes
- Department of Psychiatry, Johns Hopkins University , Baltimore , MD , USA
| | - Peter Zandi
- Department of Psychiatry, Johns Hopkins University , Baltimore , MD , USA
| | - John R Kelsoe
- Department of Psychiatry, University of California , San Diego , CA , USA
| | - David Gurwitz
- Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of Medicine, Tel Aviv University , Tel Aviv , Israel
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6
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Hadar A, Milanesi E, Walczak M, Puzianowska-Kuźnicka M, Kuźnicki J, Squassina A, Niola P, Chillotti C, Attems J, Gozes I, Gurwitz D. SIRT1, miR-132 and miR-212 link human longevity to Alzheimer's Disease. Sci Rep 2018; 8:8465. [PMID: 29855513 PMCID: PMC5981646 DOI: 10.1038/s41598-018-26547-6] [Citation(s) in RCA: 82] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2018] [Accepted: 05/15/2018] [Indexed: 01/13/2023] Open
Abstract
Alzheimer's Disease (AD) is the most common cause of dementia in the elderly. Centenarians - reaching the age of >100 years while maintaining good cognitive skills - seemingly have unique biological features allowing healthy aging and protection from dementia. Here, we studied the expression of SIRT1 along with miR-132 and miR-212, two microRNAs known to regulate SIRT1, in lymphoblastoid cell lines (LCLs) from 45 healthy donors aged 21 to 105 years and 24 AD patients, and in postmortem olfactory bulb and hippocampus tissues from 14 AD patients and 20 age-matched non-demented individuals. We observed 4.0-fold (P = 0.001) lower expression of SIRT1, and correspondingly higher expression of miR-132 (1.7-fold; P = 0.014) and miR-212 (2.1-fold; P = 0.036), in LCLs from AD patients compared with age-matched healthy controls. Additionally, SIRT1 expression was 2.2-fold (P = 0.001) higher in centenarian LCLs compared with LCLs from individuals aged 56-82 years; while centenarian LCLs miR-132 and miR-212 indicated 7.6-fold and 4.1-fold lower expression, respectively. Correlations of SIRT1, miR-132 and miR-212 expression with cognitive scores were observed for AD patient-derived LCLs and postmortem AD olfactory bulb and hippocampus tissues, suggesting that higher SIRT1 expression, possibly mediated by lower miR-132 and miR-212, may protect aged individuals from dementia and is reflected in their peripheral tissues.
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Affiliation(s)
- A Hadar
- Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, 69978, Israel
| | - E Milanesi
- Department of Cellular and Molecular Medicine, Victor Babes National Institute of Pathology, Bucharest, Romania
| | - M Walczak
- Institute of Genetics and Animal Breeding, Polish Academy of Sciences, Warsaw, Poland
| | - M Puzianowska-Kuźnicka
- Department of Human Epigenetics, Mossakowski Medical Research Centre, Warsaw, Poland
- Department of Geriatrics and Gerontology, Medical Centre of Postgraduate Education, Warsaw, Poland
| | - J Kuźnicki
- The International Institute of Molecular and Cell Biology, Warsaw, Poland
| | - A Squassina
- Department of Biomedical Sciences, University of Cagliari, Cagliari, Italy
| | - P Niola
- Department of Biomedical Sciences, University of Cagliari, Cagliari, Italy
| | - C Chillotti
- Unit of Clinical Pharmacology, University Hospital of Cagliari, Cagliari, Italy
| | - J Attems
- Institute of Neuroscience and Newcastle University Institute of Ageing, Newcastle University, Newcastle upon Tyne, UK
| | - I Gozes
- Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, 69978, Israel.
- Adams Super Center for Brain Studies, Sagol School of Neuroscience, Tel Aviv University, Tel Aviv, Israel.
| | - D Gurwitz
- Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, 69978, Israel.
- Adams Super Center for Brain Studies, Sagol School of Neuroscience, Tel Aviv University, Tel Aviv, Israel.
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7
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Colombo M, Lòpez‐Perolio I, Meeks HD, Caleca L, Parsons MT, Li H, De Vecchi G, Tudini E, Foglia C, Mondini P, Manoukian S, Behar R, Garcia EBG, Meindl A, Montagna M, Niederacher D, Schmidt AY, Varesco L, Wappenschmidt B, Bolla MK, Dennis J, Michailidou K, Wang Q, Aittomäki K, Andrulis IL, Anton‐Culver H, Arndt V, Beckmann MW, Beeghly‐Fadel A, Benitez J, Boeckx B, Bogdanova NV, Bojesen SE, Bonanni B, Brauch H, Brenner H, Burwinkel B, Chang‐Claude J, Conroy DM, Couch FJ, Cox A, Cross SS, Czene K, Devilee P, Dörk T, Eriksson M, Fasching PA, Figueroa J, Fletcher O, Flyger H, Gabrielson M, García‐Closas M, Giles GG, González‐Neira A, Guénel P, Haiman CA, Hall P, Hamann U, Hartman M, Hauke J, Hollestelle A, Hopper JL, Jakubowska A, Jung A, Kosma V, Lambrechts D, Le Marchand L, Lindblom A, Lubinski J, Mannermaa A, Margolin S, Miao H, Milne RL, Neuhausen SL, Nevanlinna H, Olson JE, Peterlongo P, Peto J, Pylkäs K, Sawyer EJ, Schmidt MK, Schmutzler RK, Schneeweiss A, Schoemaker MJ, See MH, Southey MC, Swerdlow A, Teo SH, Toland AE, Tomlinson I, Truong T, van Asperen CJ, van den Ouweland AM, van der Kolk LE, Winqvist R, Yannoukakos D, Zheng W, Dunning AM, Easton DF, Henderson A, Hogervorst FB, Izatt L, Offitt K, Side LE, van Rensburg EJ, EMBRACE S, HEBON S, McGuffog L, Antoniou AC, Chenevix‐Trench G, Spurdle AB, Goldgar DE, de la Hoya M, Radice P. The BRCA2 c.68-7T > A variant is not pathogenic: A model for clinical calibration of spliceogenicity. Hum Mutat 2018; 39:729-741. [PMID: 29460995 PMCID: PMC5947288 DOI: 10.1002/humu.23411] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2017] [Revised: 02/06/2018] [Accepted: 02/10/2018] [Indexed: 12/12/2022]
Abstract
Although the spliceogenic nature of the BRCA2 c.68-7T > A variant has been demonstrated, its association with cancer risk remains controversial. In this study, we accurately quantified by real-time PCR and digital PCR (dPCR), the BRCA2 isoforms retaining or missing exon 3. In addition, the combined odds ratio for causality of the variant was estimated using genetic and clinical data, and its associated cancer risk was estimated by case-control analysis in 83,636 individuals. Co-occurrence in trans with pathogenic BRCA2 variants was assessed in 5,382 families. Exon 3 exclusion rate was 4.5-fold higher in variant carriers (13%) than controls (3%), indicating an exclusion rate for the c.68-7T > A allele of approximately 20%. The posterior probability of pathogenicity was 7.44 × 10-115 . There was neither evidence for increased risk of breast cancer (OR 1.03; 95% CI 0.86-1.24) nor for a deleterious effect of the variant when co-occurring with pathogenic variants. Our data provide for the first time robust evidence of the nonpathogenicity of the BRCA2 c.68-7T > A. Genetic and quantitative transcript analyses together inform the threshold for the ratio between functional and altered BRCA2 isoforms compatible with normal cell function. These findings might be exploited to assess the relevance for cancer risk of other BRCA2 spliceogenic variants.
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Affiliation(s)
- Mara Colombo
- Unit of Molecular Bases of Genetic Risk and Genetic TestingDepartment of ResearchFondazione IRCCS (Istituto di Ricovero e Cura a Carattere Scientifico) Istituto Nazionale dei Tumori (INT)MilanItaly
| | - Irene Lòpez‐Perolio
- Molecular Oncology Laboratory CIBERONCHospital Clinico San CarlosIdISSC (Instituto de Investigación Sanitaria del Hospital Clínico San Carlos)MadridSpain
| | - Huong D. Meeks
- Huntsman Cancer InstituteUniversity of UtahSalt Lake CityUtah
| | - Laura Caleca
- Unit of Molecular Bases of Genetic Risk and Genetic TestingDepartment of ResearchFondazione IRCCS (Istituto di Ricovero e Cura a Carattere Scientifico) Istituto Nazionale dei Tumori (INT)MilanItaly
| | - Michael T. Parsons
- Department of Genetics and Computational BiologyQIMR Berghofer Medical Research InstituteBrisbane, QLD 4006Australia
| | - Hongyan Li
- Huntsman Cancer InstituteUniversity of UtahSalt Lake CityUtah
| | - Giovanna De Vecchi
- Unit of Molecular Bases of Genetic Risk and Genetic TestingDepartment of ResearchFondazione IRCCS (Istituto di Ricovero e Cura a Carattere Scientifico) Istituto Nazionale dei Tumori (INT)MilanItaly
| | - Emma Tudini
- Department of Genetics and Computational BiologyQIMR Berghofer Medical Research InstituteBrisbane, QLD 4006Australia
| | - Claudia Foglia
- Unit of Molecular Bases of Genetic Risk and Genetic TestingDepartment of ResearchFondazione IRCCS (Istituto di Ricovero e Cura a Carattere Scientifico) Istituto Nazionale dei Tumori (INT)MilanItaly
| | - Patrizia Mondini
- Unit of Molecular Bases of Genetic Risk and Genetic TestingDepartment of ResearchFondazione IRCCS (Istituto di Ricovero e Cura a Carattere Scientifico) Istituto Nazionale dei Tumori (INT)MilanItaly
| | - Siranoush Manoukian
- Unit of Medical GeneticsDepartment of Medical Oncology and HematologyFondazione IRCCS (Istituto di Ricovero e Cura a Carattere Scientifico) Istituto Nazionale dei Tumori (INT)MilanItaly
| | - Raquel Behar
- Molecular Oncology Laboratory CIBERONCHospital Clinico San CarlosIdISSC (Instituto de Investigación Sanitaria del Hospital Clínico San Carlos)MadridSpain
| | - Encarna B. Gómez Garcia
- Department of Clinical Genetics and GROWSchool for Oncology and Developmental BiologyMUMCMaastrichtThe Netherlands
| | - Alfons Meindl
- Department of Obstetrics and GynecologyUniversity HospitalLMU MunichGermany
| | - Marco Montagna
- Immunology and Molecular Oncology UnitVeneto Institute of Oncology IOV ‐ IRCCSPaduaItaly
| | - Dieter Niederacher
- Department of Gynaecology and ObstetricsUniversity Hospital DüsseldorfHeinrich‐Heine UniversityDuesseldorfGermany
| | - Ane Y. Schmidt
- Center for Genomic MedicineRigshospitaletUniversity of CopenhagenCopenhagenDenmark
| | | | - Barbara Wappenschmidt
- Center for Hereditary Breast and Ovarian CancerUniversity Hospital of CologneCologneGermany
- Center for Integrated Oncology (CIO)Medical FacultyUniversity Hospital of CologneCologneGermany
| | - Manjeet K. Bolla
- Centre for Cancer Genetic EpidemiologyDepartment of Public Health and Primary CareUniversity of CambridgeCambridgeUK
| | - Joe Dennis
- Centre for Cancer Genetic EpidemiologyDepartment of Public Health and Primary CareUniversity of CambridgeCambridgeUK
| | - Kyriaki Michailidou
- Centre for Cancer Genetic EpidemiologyDepartment of Public Health and Primary CareUniversity of CambridgeCambridgeUK
- Department of Electron Microscopy/Molecular PathologyThe Cyprus Institute of Neurology and GeneticsNicosiaCyprus
| | - Qin Wang
- Centre for Cancer Genetic EpidemiologyDepartment of Public Health and Primary CareUniversity of CambridgeCambridgeUK
| | - Kristiina Aittomäki
- Department of Clinical GeneticsHelsinki University HospitalUniversity of HelsinkiHelsinkiFinland
| | - Irene L. Andrulis
- Fred A. Litwin Center for Cancer GeneticsLunenfeld‐Tanenbaum Research Institute of Mount Sinai HospitalTorontoOntario
- Department of Molecular GeneticsUniversity of TorontoTorontoCanada
| | - Hoda Anton‐Culver
- Department of EpidemiologyUniversity of California IrvineIrvineCalifornia
| | - Volker Arndt
- Division of Clinical Epidemiology and Aging ResearchGerman Cancer Research Center (DKFZ)HeidelbergGermany
| | - Matthias W. Beckmann
- Department of Gynaecology and ObstetricsUniversity Hospital Erlangen, Friedrich‐Alexander University Erlangen‐NurembergComprehensive Cancer Center Erlangen‐EMNErlangenGermany
| | - Alicia Beeghly‐Fadel
- Division of EpidemiologyDepartment of MedicineVanderbilt Epidemiology CenterVanderbilt‐Ingram Cancer CenterVanderbilt University School of MedicineNashvilleTennessee
| | - Javier Benitez
- Human Cancer Genetics ProgramSpanish National Cancer Research CentreMadridSpain
- Centro de Investigación en Red de Enfermedades Raras (CIBERER)ValenciaSpain
| | - Bram Boeckx
- VIB Center for Cancer BiologyVIBLeuvenBelgium
- Laboratory for Translational GeneticsDepartment of Human GeneticsUniversity of LeuvenLeuvenBelgium
| | - Natalia V. Bogdanova
- Department of Radiation OncologyHannover Medical SchoolHannoverGermany
- Gynaecology Research UnitHannover Medical SchoolHannoverGermany
- N.N. Alexandrov Research Institute of Oncology and Medical RadiologyMinskBelarus
| | - Stig E. Bojesen
- Copenhagen General Population StudyHerlevand Gentofte HospitalCopenhagen University HospitalHerlevDenmark
- Department of Clinical BiochemistryHerlev and Gentofte HospitalCopenhagen University HospitalHerlevDenmark
- Faculty of Health and Medical SciencesUniversity of CopenhagenCopenhagenDenmark
| | - Bernardo Bonanni
- Division of Cancer Prevention and GeneticsIstituto Europeo di OncologiaMilanItaly
| | - Hiltrud Brauch
- Dr. Margarete Fischer‐Bosch‐Institute of Clinical PharmacologyStuttgartGermany
- University of TübingenTübingenGermany
- German Cancer Consortium (DKTK)German Cancer Research Center (DKFZ)HeidelbergGermany
| | - Hermann Brenner
- Division of Clinical Epidemiology and Aging ResearchGerman Cancer Research Center (DKFZ)HeidelbergGermany
- German Cancer Consortium (DKTK)German Cancer Research Center (DKFZ)HeidelbergGermany
- Division of Preventive OncologyGerman Cancer Research Center (DKFZ) and National Center for Tumor Diseases (NCT)HeidelbergGermany
| | - Barbara Burwinkel
- Department of Obstetrics and GynecologyUniversity of HeidelbergHeidelbergGermany
- Molecular Epidemiology GroupC080German Cancer Research Center (DKFZ)HeidelbergGermany
| | - Jenny Chang‐Claude
- Division of Cancer EpidemiologyGerman Cancer Research Center (DKFZ)HeidelbergGermany
- Research Group Genetic Cancer EpidemiologyUniversity Cancer Center Hamburg (UCCH)University Medical Center Hamburg‐EppendorfHamburgGermany
| | - Don M. Conroy
- Centre for Cancer Genetic EpidemiologyDepartment of OncologyUniversity of CambridgeCambridgeUK
| | - Fergus J. Couch
- Department of Laboratory Medicine and PathologyMayo ClinicRochesterNew York
| | - Angela Cox
- Sheffield Institute for Nucleic Acids (SInFoNiA)Department of Oncology and MetabolismUniversity of SheffieldSheffieldUK
| | - Simon S. Cross
- Academic Unit of PathologyDepartment of NeuroscienceUniversity of SheffieldSheffieldUK
| | - Kamila Czene
- Department of Medical Epidemiology and BiostatisticsKarolinska InstitutetStockholmSweden
| | - Peter Devilee
- Department of PathologyLeiden University Medical CenterLeidenThe Netherlands
- Department of Human GeneticsLeiden University Medical CenterLeidenThe Netherlands
| | - Thilo Dörk
- Gynaecology Research UnitHannover Medical SchoolHannoverGermany
| | - Mikael Eriksson
- Department of Medical Epidemiology and BiostatisticsKarolinska InstitutetStockholmSweden
| | - Peter A. Fasching
- Department of Gynaecology and ObstetricsUniversity Hospital Erlangen, Friedrich‐Alexander University Erlangen‐NurembergComprehensive Cancer Center Erlangen‐EMNErlangenGermany
- David Geffen School of MedicineDepartment of Medicine Division of Hematology and OncologyUniversity of California at Los AngelesLos AngelesCalifornia
| | - Jonine Figueroa
- Usher Institute of Population Health Sciences and InformaticsThe University of Edinburgh Medical SchoolEdinburghUK
- Division of Cancer Epidemiology and GeneticsNational Cancer InstituteRockvilleMaryland
| | - Olivia Fletcher
- The Breast Cancer Now Toby Robins Research CentreThe Institute of Cancer ResearchLondonUK
| | - Henrik Flyger
- Department of Breast SurgeryHerlev and Gentofte HospitalCopenhagen University HospitalHerlevDenmark
| | - Marike Gabrielson
- Department of Medical Epidemiology and BiostatisticsKarolinska InstitutetStockholmSweden
| | | | - Graham G. Giles
- Cancer Epidemiology & Intelligence DivisionCancer Council VictoriaMelbourneAustralia
- Centre for Epidemiology and BiostatisticsMelbourne School of Population and Global healthThe University of MelbourneMelbourneAustralia
| | - Anna González‐Neira
- Human Cancer Genetics ProgramSpanish National Cancer Research CentreMadridSpain
| | - Pascal Guénel
- Cancer & Environment GroupCenter for Research in Epidemiology and Population Health (CESP)INSERMUniversity Paris‐SudUniversity Paris‐SaclayVillejuifFrance
| | - Christopher A. Haiman
- Department of Preventive MedicineKeck School of MedicineUniversity of Southern CaliforniaLos AngelesCalifornia
| | - Per Hall
- Department of Medical Epidemiology and BiostatisticsKarolinska InstitutetStockholmSweden
| | - Ute Hamann
- Molecular Genetics of Breast CancerDeutsches Krebsforschungszentrum (DKFZ)HeidelbergGermany
| | - Mikael Hartman
- Saw Swee Hock School of Public HealthNational University of SingaporeSingaporeSingapore
- Department of SurgeryNational University Health SystemSingaporeSingapore
| | - Jan Hauke
- Center for Hereditary Breast and Ovarian CancerUniversity Hospital of CologneCologneGermany
- Center for Integrated Oncology (CIO)Medical FacultyUniversity Hospital of CologneCologneGermany
- Center for Molecular Medicine Cologne (CMMC)University of CologneCologneGermany
| | - Antoinette Hollestelle
- Department of Medical OncologyFamily Cancer ClinicErasmus MC Cancer InstituteRotterdamThe Netherlands
| | - John L. Hopper
- Centre for Epidemiology and BiostatisticsMelbourne School of Population and Global healthThe University of MelbourneMelbourneAustralia
| | - Anna Jakubowska
- Department of Genetics and PathologyPomeranian Medical UniversitySzczecinPoland
| | - Audrey Jung
- Division of Cancer EpidemiologyGerman Cancer Research Center (DKFZ)HeidelbergGermany
| | - Veli‐Matti Kosma
- Translational Cancer Research AreaUniversity of Eastern FinlandKuopioFinland
- Institute of Clinical MedicinePathology and Forensic MedicineUniversity of Eastern FinlandKuopioFinland
- Imaging CenterDepartment of Clinical PathologyKuopio University HospitalKuopioFinland
| | - Diether Lambrechts
- VIB Center for Cancer BiologyVIBLeuvenBelgium
- Laboratory for Translational GeneticsDepartment of Human GeneticsUniversity of LeuvenLeuvenBelgium
| | - Loid Le Marchand
- Epidemiology ProgramUniversity of Hawaii Cancer CenterHonoluluHawaii
| | - Annika Lindblom
- Department of Molecular Medicine and SurgeryKarolinska InstitutetStockholmSweden
| | - Jan Lubinski
- Department of Genetics and PathologyPomeranian Medical UniversitySzczecinPoland
| | - Arto Mannermaa
- Translational Cancer Research AreaUniversity of Eastern FinlandKuopioFinland
- Institute of Clinical MedicinePathology and Forensic MedicineUniversity of Eastern FinlandKuopioFinland
- Imaging CenterDepartment of Clinical PathologyKuopio University HospitalKuopioFinland
| | - Sara Margolin
- Department of Clinical Science and Education SödersjukhusetKarolinska InstitutetStockholmSweden
| | - Hui Miao
- Saw Swee Hock School of Public HealthNational University of SingaporeSingaporeSingapore
| | - Roger L. Milne
- Cancer Epidemiology & Intelligence DivisionCancer Council VictoriaMelbourneAustralia
- Centre for Epidemiology and BiostatisticsMelbourne School of Population and Global healthThe University of MelbourneMelbourneAustralia
| | - Susan L. Neuhausen
- Department of Population SciencesBeckman Research Institute of City of HopeDuarteCalifornia
| | - Heli Nevanlinna
- Department of Obstetrics and GynecologyHelsinki University HospitalUniversity of HelsinkiHelsinkiFinland
| | - Janet E. Olson
- Department of Health Sciences ResearchMayo ClinicRochesterNew York
| | - Paolo Peterlongo
- IFOMThe FIRC (Italian Foundation for Cancer Research) Institute of Molecular OncologyMilanItaly
| | - Julian Peto
- Department of Non‐Communicable Disease EpidemiologyLondon School of Hygiene and Tropical MedicineLondonUK
| | - Katri Pylkäs
- Laboratory of Cancer Genetics and Tumor BiologyCancer and Translational Medicine Research UnitBiocenter OuluUniversity of OuluOuluFinland
- Laboratory of Cancer Genetics and Tumor BiologyNorthern Finland Laboratory Centre OuluOuluFinland
| | | | - Marjanka K. Schmidt
- Division of Molecular PathologyThe Netherlands Cancer Institute – Antoni van Leeuwenhoek HospitalAmsterdamThe Netherlands
- Division of Psychosocial Research and EpidemiologyThe Netherlands Cancer Institute – Antoni van Leeuwenhoek hospitalAmsterdamThe Netherlands
| | - Rita K. Schmutzler
- Center for Hereditary Breast and Ovarian CancerUniversity Hospital of CologneCologneGermany
- Center for Integrated Oncology (CIO)Medical FacultyUniversity Hospital of CologneCologneGermany
- Center for Molecular Medicine Cologne (CMMC)University of CologneCologneGermany
| | - Andreas Schneeweiss
- Department of Obstetrics and GynecologyUniversity of HeidelbergHeidelbergGermany
- National Center for Tumor DiseasesUniversity of HeidelbergHeidelbergGermany
| | | | - Mee Hoong See
- Breast Cancer Research UnitCancer Research InstituteUniversity Malaya Medical CentreKuala LumpurMalaysia
| | | | - Anthony Swerdlow
- Division of Genetics and EpidemiologyThe Institute of Cancer ResearchLondonUK
- Division of Breast Cancer ResearchThe Institute of Cancer ResearchLondonUK
| | - Soo H. Teo
- Breast Cancer Research UnitCancer Research InstituteUniversity Malaya Medical CentreKuala LumpurMalaysia
- Cancer Research MalaysiaSubang JayaSelangorMalaysia
| | - Amanda E. Toland
- Department of Molecular VirologyImmunology and Medical GeneticsComprehensive Cancer CenterThe Ohio State UniversityColumbusOhio
| | - Ian Tomlinson
- Wellcome Trust Centre for Human Genetics and Oxford NIHR Biomedical Research CentreUniversity of OxfordOxfordUK
| | - Thérèse Truong
- Cancer & Environment GroupCenter for Research in Epidemiology and Population Health (CESP)INSERMUniversity Paris‐SudUniversity Paris‐SaclayVillejuifFrance
| | | | | | - Lizet E. van der Kolk
- Family Cancer ClinicThe Netherlands Cancer Institute ‐ Antoni van Leeuwenhoek hospitalAmsterdamThe Netherlands
| | - Robert Winqvist
- Laboratory of Cancer Genetics and Tumor BiologyCancer and Translational Medicine Research UnitBiocenter OuluUniversity of OuluOuluFinland
- Laboratory of Cancer Genetics and Tumor BiologyNorthern Finland Laboratory Centre OuluOuluFinland
| | - Drakoulis Yannoukakos
- Molecular Diagnostics LaboratoryINRASTESNational Centre for Scientific Research “Demokritos”AthensGreece
| | - Wei Zheng
- Division of EpidemiologyDepartment of MedicineVanderbilt Epidemiology CenterVanderbilt‐Ingram Cancer CenterVanderbilt University School of MedicineNashvilleTennessee
| | | | - Alison M. Dunning
- Centre for Cancer Genetic EpidemiologyDepartment of OncologyUniversity of CambridgeCambridgeUK
| | - Douglas F. Easton
- Centre for Cancer Genetic EpidemiologyDepartment of Public Health and Primary CareUniversity of CambridgeCambridgeUK
- Centre for Cancer Genetic EpidemiologyDepartment of OncologyUniversity of CambridgeCambridgeUK
| | - Alex Henderson
- Institute of Genetic MedicineCentre for LifeNewcastle Upon Tyne Hospitals NHS TrustNewcastle upon TyneUK
| | - Frans B.L. Hogervorst
- Family Cancer ClinicThe Netherlands Cancer Institute ‐ Antoni van Leeuwenhoek hospitalAmsterdamThe Netherlands
| | - Louise Izatt
- Clinical GeneticsGuy's and St. Thomas’ NHS Foundation TrustLondonUK
| | - Kenneth Offitt
- Clinical Genetics Research LaboratoryDept. of MedicineCancer Biology and GeneticsMemorial Sloan‐Kettering Cancer CenterNew YorkNew York
| | - Lucy E. Side
- Wessex Clinical Genetics ServiceMailpoint 627, Princess Anne Hospital, Coxford Road, Southampton, SO16 5YA
| | | | - Study EMBRACE
- Centre for Cancer Genetic EpidemiologyDepartment of Public Health and Primary CareUniversity of CambridgeStrangeways Research LaboratoryWorts CausewayCambridgeUK
| | - Study HEBON
- The Hereditary Breast and Ovarian Cancer Research Group Netherlands (HEBON)Coordinating center: Netherlands Cancer InstituteAmsterdamThe Netherlands
| | - Lesley McGuffog
- Centre for Cancer Genetic EpidemiologyDepartment of Public Health and Primary CareUniversity of CambridgeCambridgeUK
| | - Antonis C. Antoniou
- Centre for Cancer Genetic EpidemiologyDepartment of Public Health and Primary CareUniversity of CambridgeCambridgeUK
| | - Georgia Chenevix‐Trench
- Department of Genetics and Computational BiologyQIMR Berghofer Medical Research InstituteBrisbane, QLD 4006Australia
| | - Amanda B. Spurdle
- Department of Genetics and Computational BiologyQIMR Berghofer Medical Research InstituteBrisbane, QLD 4006Australia
| | | | - Miguel de la Hoya
- Molecular Oncology Laboratory CIBERONCHospital Clinico San CarlosIdISSC (Instituto de Investigación Sanitaria del Hospital Clínico San Carlos)MadridSpain
| | - Paolo Radice
- Unit of Molecular Bases of Genetic Risk and Genetic TestingDepartment of ResearchFondazione IRCCS (Istituto di Ricovero e Cura a Carattere Scientifico) Istituto Nazionale dei Tumori (INT)MilanItaly
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8
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Verkerk AJMH, Zeidler S, Breedveld G, Overbeek L, Huigh D, Koster L, van der Linde H, de Esch C, Severijnen LA, de Vries BBA, Swagemakers SMA, Willemsen R, Hoogeboom AJM, van der Spek PJ, Oostra BA. CXorf56, a dendritic neuronal protein, identified as a new candidate gene for X-linked intellectual disability. Eur J Hum Genet 2018; 26:552-560. [PMID: 29374277 DOI: 10.1038/s41431-017-0051-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2017] [Revised: 11/20/2017] [Accepted: 11/23/2017] [Indexed: 11/09/2022] Open
Abstract
Intellectual disability (ID) comprises a large group of heterogeneous disorders, often without a known molecular cause. X-linked ID accounts for 5-10% of male ID cases. We investigated a large, three-generation family with mild ID and behavior problems in five males and one female, with a segregation suggestive for X-linked inheritance. Linkage analysis mapped a disease locus to a 7.6 Mb candidate region on the X-chromosome (LOD score 3.3). Whole-genome sequencing identified a 2 bp insertion in exon 2 of the chromosome X open reading frame 56 gene (CXorf56), resulting in a premature stop codon. This insertion was present in all intellectually impaired individuals and carrier females. Additionally, X-inactivation status showed skewed methylation patterns favoring the inactivation of the mutated allele in the unaffected carrier females. We demonstrate that the insertion leads to nonsense-mediated decay and that CXorf56 mRNA expression is reduced in the impaired males and female. In murine brain slices and primary hippocampal neuronal cultures, CXorf56 protein was present and localized in the nucleus, cell soma, dendrites, and dendritic spines. Although no other families have been identified with pathogenic variants in CXorf56, these results suggest that CXorf56 is the causative gene in this family, and thus a novel candidate gene for X-linked ID with behavior problems.
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Affiliation(s)
- Annemieke J M H Verkerk
- Department of Bioinformatics, Erasmus Medical Center, Rotterdam, The Netherlands. .,Department of Internal Medicine, Erasmus Medical Center, Rotterdam, The Netherlands.
| | - Shimriet Zeidler
- Department of Clinical Genetics, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Guido Breedveld
- Department of Clinical Genetics, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Lydia Overbeek
- Department of Clinical Genetics, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Daphne Huigh
- Department of Bioinformatics, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Linda Koster
- Department of Bioinformatics, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Herma van der Linde
- Department of Clinical Genetics, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Celine de Esch
- Department of Clinical Genetics, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Lies-Anne Severijnen
- Department of Clinical Genetics, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Bert B A de Vries
- Department of Human Genetics, Radboud Medical Center, Nijmegen, The Netherlands.,Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands
| | | | - Rob Willemsen
- Department of Clinical Genetics, Erasmus Medical Center, Rotterdam, The Netherlands
| | | | - Peter J van der Spek
- Department of Bioinformatics, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Ben A Oostra
- Department of Clinical Genetics, Erasmus Medical Center, Rotterdam, The Netherlands
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9
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Hadar A, Milanesi E, Squassina A, Niola P, Chillotti C, Pasmanik-Chor M, Yaron O, Martásek P, Rehavi M, Weissglas-Volkov D, Shomron N, Gozes I, Gurwitz D. RGS2 expression predicts amyloid-β sensitivity, MCI and Alzheimer's disease: genome-wide transcriptomic profiling and bioinformatics data mining. Transl Psychiatry 2016; 6:e909. [PMID: 27701409 PMCID: PMC5315547 DOI: 10.1038/tp.2016.179] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/06/2016] [Revised: 05/26/2016] [Accepted: 06/15/2016] [Indexed: 12/30/2022] Open
Abstract
Alzheimer's disease (AD) is the most frequent cause of dementia. Misfolded protein pathological hallmarks of AD are brain deposits of amyloid-β (Aβ) plaques and phosphorylated tau neurofibrillary tangles. However, doubts about the role of Aβ in AD pathology have been raised as Aβ is a common component of extracellular brain deposits found, also by in vivo imaging, in non-demented aged individuals. It has been suggested that some individuals are more prone to Aβ neurotoxicity and hence more likely to develop AD when aging brains start accumulating Aβ plaques. Here, we applied genome-wide transcriptomic profiling of lymphoblastoid cells lines (LCLs) from healthy individuals and AD patients for identifying genes that predict sensitivity to Aβ. Real-time PCR validation identified 3.78-fold lower expression of RGS2 (regulator of G-protein signaling 2; P=0.0085) in LCLs from healthy individuals exhibiting high vs low Aβ sensitivity. Furthermore, RGS2 showed 3.3-fold lower expression (P=0.0008) in AD LCLs compared with controls. Notably, RGS2 expression in AD LCLs correlated with the patients' cognitive function. Lower RGS2 expression levels were also discovered in published expression data sets from postmortem AD brain tissues as well as in mild cognitive impairment and AD blood samples compared with controls. In conclusion, Aβ sensitivity phenotyping followed by transcriptomic profiling and published patient data mining identified reduced peripheral and brain expression levels of RGS2, a key regulator of G-protein-coupled receptor signaling and neuronal plasticity. RGS2 is suggested as a novel AD biomarker (alongside other genes) toward early AD detection and future disease modifying therapeutics.
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Affiliation(s)
- A Hadar
- Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - E Milanesi
- Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - A Squassina
- Department of Biomedical Sciences, University of Cagliari, Cagliari, Italy
| | - P Niola
- Department of Biomedical Sciences, University of Cagliari, Cagliari, Italy
| | - C Chillotti
- Unit of Clinical Pharmacology, University Hospital of Cagliari, Cagliari, Italy
| | - M Pasmanik-Chor
- Bioinformatics Unit, George Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
| | - O Yaron
- The Genomic Analysis Laboratory, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - P Martásek
- Department of Pediatrics and Adolescent Medicine, First Faculty of Medicine, Charles University in Prague and General University Hospital in Prague, Prague, Czech Republic
| | - M Rehavi
- Department of Physiology and Pharmacology, Sackler Faculty of Medicine, Tel Aviv University, Ramat Aviv, Tel Aviv, Israel
| | - D Weissglas-Volkov
- Department of Cell and Developmental Biology, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - N Shomron
- Department of Cell and Developmental Biology, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel,Adams Super Center for Brain Studies, Sagol School of Neuroscience, Tel Aviv University, Tel Aviv, Israel
| | - I Gozes
- Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel,Adams Super Center for Brain Studies, Sagol School of Neuroscience, Tel Aviv University, Tel Aviv, Israel,Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv 69978, Israel. E-mail: or
| | - D Gurwitz
- Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel,Adams Super Center for Brain Studies, Sagol School of Neuroscience, Tel Aviv University, Tel Aviv, Israel,Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv 69978, Israel. E-mail: or
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10
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Tomas-Roca L, Tsaalbi-Shtylik A, Jansen JG, Singh MK, Epstein JA, Altunoglu U, Verzijl H, Soria L, van Beusekom E, Roscioli T, Iqbal Z, Gilissen C, Hoischen A, de Brouwer APM, Erasmus C, Schubert D, Brunner H, Pérez Aytés A, Marin F, Aroca P, Kayserili H, Carta A, de Wind N, Padberg GW, van Bokhoven H. De novo mutations in PLXND1 and REV3L cause Möbius syndrome. Nat Commun 2015; 6:7199. [PMID: 26068067 PMCID: PMC4648025 DOI: 10.1038/ncomms8199] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2014] [Accepted: 04/17/2015] [Indexed: 11/17/2022] Open
Abstract
Möbius syndrome (MBS) is a neurological disorder that is characterized by paralysis of the facial nerves and variable other congenital anomalies. The aetiology of this syndrome has been enigmatic since the initial descriptions by von Graefe in 1880 and by Möbius in 1888, and it has been debated for decades whether MBS has a genetic or a non-genetic aetiology. Here, we report de novo mutations affecting two genes, PLXND1 and REV3L in MBS patients. PLXND1 and REV3L represent totally unrelated pathways involved in hindbrain development: neural migration and DNA translesion synthesis, essential for the replication of endogenously damaged DNA, respectively. Interestingly, analysis of Plxnd1 and Rev3l mutant mice shows that disruption of these separate pathways converge at the facial branchiomotor nucleus, affecting either motoneuron migration or proliferation. The finding that PLXND1 and REV3L mutations are responsible for a proportion of MBS patients suggests that de novo mutations in other genes might account for other MBS patients. lt has been debated for decades if there is a genetic aetiology underlying Möbius syndrome, a neurological disorder characterized by facial paralysis. Here Tomas-Roca et al. use exome sequencing and identify de novo mutations in PLXND1 and REV3L, representing converging pathways in hindbrain development.
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Affiliation(s)
- Laura Tomas-Roca
- Department of Human Genetics, Radboud University Medical Center, Donders Institute for Brain, Cognition and Behaviour, PO Box 9101, Nijmegen 6500 HB, The Netherlands.,Department of Human Anatomy and Psychobiology, School of Medicine, University of Murcia, 30100 Espinardo (Murcia), Spain
| | - Anastasia Tsaalbi-Shtylik
- Department of Human Genetics, Leiden University Medical Center, P.O. Box 9600, 2300 RC Leiden, The Netherlands
| | - Jacob G Jansen
- Department of Human Genetics, Leiden University Medical Center, P.O. Box 9600, 2300 RC Leiden, The Netherlands
| | - Manvendra K Singh
- Department of Cell and Developmental Biology, Cardiovascular Institute, Perelman School of Medicine at the University of Pennsylvania, 9-105 SCTR, 3400 Civic Center Boulevard, Philadelphia, Pennsylvania 19104, USA.,Signature Research Program in Cardiovascular and Metabolic Disorders, Duke-NUS Graduate Medical School Singapore, National Heart Center Singapore, 8 College Road, Singapore 169857, Singapore
| | - Jonathan A Epstein
- Department of Cell and Developmental Biology, Cardiovascular Institute, Perelman School of Medicine at the University of Pennsylvania, 9-105 SCTR, 3400 Civic Center Boulevard, Philadelphia, Pennsylvania 19104, USA
| | - Umut Altunoglu
- Medical Genetics Department, Istanbul Medical Faculty, Istanbul University, Millet Caddesi, Capa, Fatih 34093, Turkey
| | - Harriette Verzijl
- Department of Neurology, Radboud University Medical Center, Donders Institute for Brain, Cognition and Behaviour, PO Box 9101, Nijmegen 6500 HB, The Netherlands
| | - Laura Soria
- Department of Human Genetics, Radboud University Medical Center, Donders Institute for Brain, Cognition and Behaviour, PO Box 9101, Nijmegen 6500 HB, The Netherlands
| | - Ellen van Beusekom
- Department of Human Genetics, Radboud University Medical Center, Donders Institute for Brain, Cognition and Behaviour, PO Box 9101, Nijmegen 6500 HB, The Netherlands
| | - Tony Roscioli
- Department of Human Genetics, Radboud University Medical Center, Donders Institute for Brain, Cognition and Behaviour, PO Box 9101, Nijmegen 6500 HB, The Netherlands.,The Kinghorn Centre for Clinical Genomics, Garvan Institute of Medical Research, Sydney, New South Wales 2010, Australia
| | - Zafar Iqbal
- Department of Human Genetics, Radboud University Medical Center, Donders Institute for Brain, Cognition and Behaviour, PO Box 9101, Nijmegen 6500 HB, The Netherlands
| | - Christian Gilissen
- Department of Human Genetics, Radboud University Medical Center, Donders Institute for Brain, Cognition and Behaviour, PO Box 9101, Nijmegen 6500 HB, The Netherlands
| | - Alexander Hoischen
- Department of Human Genetics, Radboud University Medical Center, Radboud Institute for Molecular Life Sciences (RIMLS), PO Box 9101, Nijmegen 6500 HB, The Netherlands
| | - Arjan P M de Brouwer
- Department of Human Genetics, Radboud University Medical Center, Donders Institute for Brain, Cognition and Behaviour, PO Box 9101, Nijmegen 6500 HB, The Netherlands
| | - Corrie Erasmus
- Department of Neurology, Radboud University Medical Center, Donders Institute for Brain, Cognition and Behaviour, PO Box 9101, Nijmegen 6500 HB, The Netherlands
| | - Dirk Schubert
- Department of Cognitive Neuroscience, Radboud University Medical Center, Donders Institute for Brain, Cognition and Behaviour, PO Box 9101, Nijmegen 6500 HB, The Netherlands
| | - Han Brunner
- Department of Human Genetics, Radboud University Medical Center, Donders Institute for Brain, Cognition and Behaviour, PO Box 9101, Nijmegen 6500 HB, The Netherlands.,Department of Clinical Genetics, Maastricht University Medical Center, PO Box 5800, Maastricht 6200AZ, The Netherlands
| | - Antonio Pérez Aytés
- Dysmorphology and Reproductive Genetics Unit, Moebius Syndrome Foundation of Spain, University Hospital LA FE, Valencia 46540, Spain
| | - Faustino Marin
- Department of Human Anatomy and Psychobiology, School of Medicine, University of Murcia, 30100 Espinardo (Murcia), Spain
| | - Pilar Aroca
- Department of Human Anatomy and Psychobiology, School of Medicine, University of Murcia, 30100 Espinardo (Murcia), Spain
| | - Hülya Kayserili
- Medical Genetics Department, Istanbul Medical Faculty, Istanbul University, Millet Caddesi, Capa, Fatih 34093, Turkey
| | - Arturo Carta
- Ophthalmology Unit, Department of Biomedical, Biotechnological and Translational Sciences (S.Bi.Bi.T.), University of Parma, via Gramsci 14, 43126, Parma, Italy
| | - Niels de Wind
- Department of Human Genetics, Leiden University Medical Center, P.O. Box 9600, 2300 RC Leiden, The Netherlands
| | - George W Padberg
- Department of Neurology, Radboud University Medical Center, Donders Institute for Brain, Cognition and Behaviour, PO Box 9101, Nijmegen 6500 HB, The Netherlands
| | - Hans van Bokhoven
- Department of Human Genetics, Radboud University Medical Center, Donders Institute for Brain, Cognition and Behaviour, PO Box 9101, Nijmegen 6500 HB, The Netherlands
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11
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Latent Membrane Protein LMP2A Impairs Recognition of EBV-Infected Cells by CD8+ T Cells. PLoS Pathog 2015; 11:e1004906. [PMID: 26067064 PMCID: PMC4465838 DOI: 10.1371/journal.ppat.1004906] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2014] [Accepted: 04/22/2015] [Indexed: 01/04/2023] Open
Abstract
The common pathogen Epstein-Barr virus (EBV) transforms normal human B cells and can cause cancer. Latent membrane protein 2A (LMP2A) of EBV supports activation and proliferation of infected B cells and is expressed in many types of EBV-associated cancer. It is not clear how latent EBV infection and cancer escape elimination by host immunity, and it is unknown whether LMP2A can influence the interaction of EBV-infected cells with the immune system. We infected primary B cells with EBV deleted for LMP2A, and established lymphoblastoid cell lines (LCLs). We found that CD8+ T cell clones showed higher reactivity against LMP2A-deficient LCLs compared to LCLs infected with complete EBV. We identified several potential mediators of this immunomodulatory effect. In the absence of LMP2A, expression of some EBV latent antigens was elevated, and cell surface expression of MHC class I was marginally increased. LMP2A-deficient LCLs produced lower amounts of IL-10, although this did not directly affect CD8+ T cell recognition. Deletion of LMP2A led to several changes in the cell surface immunophenotype of LCLs. Specifically, the agonistic NKG2D ligands MICA and ULBP4 were increased. Blocking experiments showed that NKG2D activation contributed to LCL recognition by CD8+ T cell clones. Our results demonstrate that LMP2A reduces the reactivity of CD8+ T cells against EBV-infected cells, and we identify several relevant mechanisms. Epstein-Barr virus (EBV) is carried by most humans. It can cause several types of cancer. In healthy infected people, EBV persists for life in a "latent" state in white blood cells called B cells. For infected persons to remain healthy, it is crucial that they harbor CD8-positive "killer" T cells that recognize and destroy precancerous EBV-infected cells. However, this protection is imperfect, because the virus is not eliminated from the body, and the danger of EBV-associated cancer remains. How does the virus counteract CD8+ T cell control? Here we study the effects of latent membrane protein 2A (LMP2A), which is an important viral molecule because it is present in several types of EBV-associated cancers, and in latently infected cells in healthy people. We show that LMP2A counteracts the recognition of EBV-infected B cells by antiviral killer cells. We found a number of mechanisms that are relevant to this effect. Notably, LMP2A disturbs expression of molecules on B cells that interact with NKG2D, a molecule on the surface of CD8+ T cells that aids their activation. In this way, LMP2A weakens important immune responses against EBV. Similar mechanisms may operate in different types of LMP2A-expressing cancers caused by EBV.
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Pen AE, Nyegaard M, Fang M, Jiang H, Christensen R, Mølgaard H, Andersen H, Ulhøi BP, Østergaard JR, Væth S, Sommerlund M, de Brouwer APM, Zhang X, Jensen UB. A novel single nucleotide splice site mutation in FHL1 confirms an Emery-Dreifuss plus phenotype with pulmonary artery hypoplasia and facial dysmorphology. Eur J Med Genet 2015; 58:222-9. [PMID: 25724586 DOI: 10.1016/j.ejmg.2015.02.003] [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] [Received: 08/13/2014] [Accepted: 02/12/2015] [Indexed: 10/24/2022]
Abstract
We describe a Danish family with an, until recently, unknown X-linked disease with muscular dystrophy (MD), facial dysmorphology and pulmonary artery hypoplasia. One patient died suddenly before age 20 and another was resuscitated from cardiac arrest at the age of 28. Linkage analysis pointed to a region of 25 Mb from 123.6 Mb to 148.4 Mb on chromosome X containing over 100 genes. Exome sequencing identified a single nucleotide splice site mutation c.502-2A > T, which is located 5' to exon 6 in the gene encoding four and a half LIM domain 1 (FHL1) protein. FHL1 expresses three main splice variants, known as FHL1A, FHL1B and FHL1C. In healthy individuals, FHL1A is the predominant splice variant and is mainly found in skeletal and cardiac muscle. The FHL1 transcript profiles from two affected individuals were investigated in skin fibroblasts with quantitative real-time PCR. This demonstrated loss of isoform A and B, and an almost 200-fold overexpression of isoform C confirming that lack of FHL1A and overexpression of FHL1C results in an extended phenotype of EDMD as recently shown by Tiffin et al. [2013].
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Affiliation(s)
- Anja E Pen
- Department of Clinical Genetics, Aarhus University Hospital, Skejby, Denmark
| | - Mette Nyegaard
- Department of Biomedicine, Aarhus University, Aarhus, Denmark
| | | | - Hui Jiang
- BGI-Shenzhen, Shenzhen 518083, China; Shenzhen Key Laboratory of Genomics, Shenzhen 518083, China; The Guangdong Enterprise Key Laboratory of Human Disease Genomics, Shenzhen 518083, China
| | - Rikke Christensen
- Department of Clinical Genetics, Aarhus University Hospital, Skejby, Denmark
| | - Henning Mølgaard
- Department of Cardiology, Aarhus University, Aarhus, Denmark; Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
| | - Henning Andersen
- Department of Neurology, Aarhus University, Aarhus, Denmark; Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
| | | | - John R Østergaard
- Department of Clinical Medicine, Aarhus University, Aarhus, Denmark; Centre for Rare Diseases, Aarhus University Hospital, Aarhus, Denmark
| | - Signe Væth
- Department of Clinical Genetics, Aarhus University Hospital, Skejby, Denmark; Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
| | - Mette Sommerlund
- Department of Dermatology, Aarhus University, Aarhus, Denmark; Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
| | - Arjan P M de Brouwer
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, Holland
| | - Xiuqing Zhang
- BGI-Shenzhen, Shenzhen 518083, China; Shenzhen Key Laboratory of Genomics, Shenzhen 518083, China; The Guangdong Enterprise Key Laboratory of Human Disease Genomics, Shenzhen 518083, China
| | - Uffe B Jensen
- Department of Clinical Genetics, Aarhus University Hospital, Skejby, Denmark; Department of Clinical Medicine, Aarhus University, Aarhus, Denmark.
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13
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Gómez-Herreros F, Schuurs-Hoeijmakers JHM, McCormack M, Greally MT, Rulten S, Romero-Granados R, Counihan TJ, Chaila E, Conroy J, Ennis S, Delanty N, Cortés-Ledesma F, de Brouwer APM, Cavalleri GL, El-Khamisy SF, de Vries BBA, Caldecott KW. TDP2 protects transcription from abortive topoisomerase activity and is required for normal neural function. Nat Genet 2014; 46:516-21. [PMID: 24658003 DOI: 10.1038/ng.2929] [Citation(s) in RCA: 109] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2013] [Accepted: 02/28/2014] [Indexed: 12/12/2022]
Abstract
Topoisomerase II (TOP2) removes torsional stress from DNA and facilitates gene transcription by introducing transient DNA double-strand breaks (DSBs). Such DSBs are normally rejoined by TOP2 but on occasion can become abortive and remain unsealed. Here we identify homozygous mutations in the TDP2 gene encoding tyrosyl DNA phosphodiesterase-2, an enzyme that repairs 'abortive' TOP2-induced DSBs, in individuals with intellectual disability, seizures and ataxia. We show that cells from affected individuals are hypersensitive to TOP2-induced DSBs and that loss of TDP2 inhibits TOP2-dependent gene transcription in cultured human cells and in mouse post-mitotic neurons following abortive TOP2 activity. Notably, TDP2 is also required for normal levels of many gene transcripts in developing mouse brain, including numerous gene transcripts associated with neurological function and/or disease, and for normal interneuron density in mouse cerebellum. Collectively, these data implicate chromosome breakage by TOP2 as an endogenous threat to gene transcription and to normal neuronal development and maintenance.
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Affiliation(s)
- Fernando Gómez-Herreros
- 1] Genome Damage and Stability Centre, School of Biological Sciences, University of Sussex, Sussex, UK. [2]
| | - Janneke H M Schuurs-Hoeijmakers
- 1] Department of Human Genetics, Radboud University Nijmegen Medical Centre, Nijmegen, The Netherlands. [2] Department of Cognitive Neurosciences, Donders Institute for Brain Cognition and Behaviour, Radboud University Medical Centre, Nijmegen, The Netherlands. [3]
| | - Mark McCormack
- 1] Molecular and Cellular Therapeutics, The Royal College of Surgeons in Ireland, Dublin, Ireland. [2]
| | - Marie T Greally
- National Centre for Medical Genetics, Our Lady's Children's Hospital, Crumlin, Dublin, Ireland
| | - Stuart Rulten
- Genome Damage and Stability Centre, School of Biological Sciences, University of Sussex, Sussex, UK
| | - Rocío Romero-Granados
- Centro Andaluz de Biología Molecular y Medicina Regenerativa (CABIMER), Departamento de Genética, CSIC (Centro Superior de Investigaciones Científicas)-Universidad de Sevilla, Sevilla, Spain
| | | | - Elijah Chaila
- Division of Neurology, Beaumont Hospital, Dublin, Ireland
| | - Judith Conroy
- School of Medicine and Medical Science, University College Dublin, Dublin, Ireland
| | - Sean Ennis
- School of Medicine and Medical Science, University College Dublin, Dublin, Ireland
| | - Norman Delanty
- 1] Molecular and Cellular Therapeutics, The Royal College of Surgeons in Ireland, Dublin, Ireland. [2] Division of Neurology, Beaumont Hospital, Dublin, Ireland
| | - Felipe Cortés-Ledesma
- Centro Andaluz de Biología Molecular y Medicina Regenerativa (CABIMER), Departamento de Genética, CSIC (Centro Superior de Investigaciones Científicas)-Universidad de Sevilla, Sevilla, Spain
| | - Arjan P M de Brouwer
- 1] Department of Human Genetics, Radboud University Nijmegen Medical Centre, Nijmegen, The Netherlands. [2] Department of Cognitive Neurosciences, Donders Institute for Brain Cognition and Behaviour, Radboud University Medical Centre, Nijmegen, The Netherlands
| | - Gianpiero L Cavalleri
- Molecular and Cellular Therapeutics, The Royal College of Surgeons in Ireland, Dublin, Ireland
| | - Sherif F El-Khamisy
- 1] Kreb's Institute, Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield, UK. [2] Center of Genomics, Helmy Institute, Zewail City of Science and Technology, Giza, Egypt
| | - Bert B A de Vries
- 1] Department of Human Genetics, Radboud University Nijmegen Medical Centre, Nijmegen, The Netherlands. [2] Department of Cognitive Neurosciences, Donders Institute for Brain Cognition and Behaviour, Radboud University Medical Centre, Nijmegen, The Netherlands
| | - Keith W Caldecott
- Genome Damage and Stability Centre, School of Biological Sciences, University of Sussex, Sussex, UK
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14
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Boraldi F, Annovi G, Bartolomeo A, Quaglino D. Fibroblasts from patients affected by Pseudoxanthoma elasticum exhibit an altered PPi metabolism and are more responsive to pro-calcifying stimuli. J Dermatol Sci 2014; 74:72-80. [PMID: 24461675 DOI: 10.1016/j.jdermsci.2013.12.008] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2013] [Revised: 12/13/2013] [Accepted: 12/19/2013] [Indexed: 01/31/2023]
Abstract
BACKGROUND Pseudoxanthoma elasticum (PXE) is a genetic disorder characterized by progressive calcification of soft connective tissues. The pathogenesis is still hard to pin down. In PXE dermal fibroblasts, in addition to impaired carboxylation of the vitamin K-dependent inhibitor matrix Gla protein (MGP), we have also demonstrated an up-regulation of alkaline phosphatase activity. In the light of these data we have suggested that both calcium and phosphate metabolism might be locally altered, both pathways acting in synergy on the occurrence of matrix calcification. OBJECTIVE This study aims to better explore if cultured PXE fibroblasts, compared to control cells, exhibit a modified inorganic pyrophosphate (PPi) metabolism and are more responsive to pro-calcifying stimuli. METHODS Primary human dermal fibroblasts isolated from healthy individuals and from PXE patients were cultured for different time points in standard and in pro-calcifying media. The expression of ANKH/ANKH, ENPP1/PC1, ALPL/TNAP, SPP1/OPN was evaluated by qRT-PCR and Western blot, respectively. TNAP activity was measured by spectrophotometric analyses, whereas calcification was investigated by light and electron microscopy as well as by micro-analytical techniques. RESULTS In the presence of pro-calcifying stimuli, dermal fibroblasts alter their phenotype favouring matrix mineralization. In particular, ENPP1/PC1 and SPP1/OPN expression, as well as TNAP activity, was differently expressed in control and in PXE fibroblasts. Moreover, in pathologic cells the ratio between factors favouring and reducing PPi availability exhibits a more pronounced shift towards a pro-calcifying balance. CONCLUSION PXE fibroblasts are more susceptible to pro-calcifying stimuli and in these cells an altered PPi metabolism contributes to matrix calcification.
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Affiliation(s)
- Federica Boraldi
- Department of Life Sciences, University of Modena and Reggio Emilia, Modena, Italy
| | - Giulia Annovi
- Department of Life Sciences, University of Modena and Reggio Emilia, Modena, Italy
| | - Angelica Bartolomeo
- Department of Life Sciences, University of Modena and Reggio Emilia, Modena, Italy
| | - Daniela Quaglino
- Department of Life Sciences, University of Modena and Reggio Emilia, Modena, Italy.
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15
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Oud MM, van Bon BW, Bongers EMHF, Hoischen A, Marcelis CL, de Leeuw N, Mol SJJ, Mortier G, Knoers NVAM, Brunner HG, Roepman R, Arts HH. Early presentation of cystic kidneys in a family with a homozygous INVS mutation. Am J Med Genet A 2014; 164A:1627-34. [PMID: 24677454 DOI: 10.1002/ajmg.a.36501] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2013] [Accepted: 01/27/2014] [Indexed: 11/07/2022]
Abstract
Nephronophthisis (NPHP) is an autosomal recessive cystic kidney disease that is the most frequent monogenic cause of end-stage renal disease in children. Infantile NPHP, often in combination with other features like situs inversus, are commonly caused by mutations in the INVS gene. INVS encodes the ciliary protein inversin, and mutations induce dysfunction of the primary cilia. In this article, we present a family with two severely affected fetuses that were aborted after discovery of grossly enlarged cystic kidneys by ultrasonography before 22 weeks gestation. Exome sequencing showed that the fetuses were homozygous for a previously unreported nonsense mutation, resulting in a truncation in the IQ1 domain of inversin. This mutation induces nonsense-mediated RNA decay, as suggested by a reduced RNA level in fibroblasts derived from the fetus. However, a significant amount of mutant INVS RNA was present in these fibroblasts, yielding mutant inversin protein that was mislocalized. In control fibroblasts, inversin was present in the ciliary axoneme as well as at the basal body, whereas in the fibroblasts from the fetus, inversin could only be detected at the basal body. The phenotype of both fetuses is partly characteristic of infantile NPHP and Potter sequence. We also identified that the fetuses had mild skeletal abnormalities, including shortening and bowing of long bones, which may expand the phenotypic spectrum associated with INVS mutations.
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Affiliation(s)
- Machteld M Oud
- Department of Human Genetics, Radboud University Medical Centre, Nijmegen, The Netherlands; Radboud Institute for Health Sciences, Radboud University Medical Centre, Nijmegen, The Netherlands; Radboud Institute for Molecular Life Sciences, Radboud University Nijmegen, Nijmegen, The Netherlands
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16
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17
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de Brouwer APM, Nabuurs SB, Verhaart IEC, Oudakker AR, Hordijk R, Yntema HG, Hordijk-Hos JM, Voesenek K, de Vries BBA, van Essen T, Chen W, Hu H, Chelly J, den Dunnen JT, Kalscheuer VM, Aartsma-Rus AM, Hamel BCJ, van Bokhoven H, Kleefstra T. A 3-base pair deletion, c.9711_9713del, in DMD results in intellectual disability without muscular dystrophy. Eur J Hum Genet 2013; 22:480-5. [PMID: 23900271 DOI: 10.1038/ejhg.2013.169] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2012] [Revised: 05/21/2013] [Accepted: 07/02/2013] [Indexed: 11/09/2022] Open
Abstract
We have identified a deletion of 3 base pairs in the dystrophin gene (DMD), c.9711_9713del, in a family with nonspecific X-linked intellectual disability (ID) by sequencing of the exons of 86 known X-linked ID genes. This in-frame deletion results in the deletion of a single-amino-acid residue, Leu3238, in the brain-specific isoform Dp71 of dystrophin. Linkage analysis supported causality as the mutation was present in the 7.6 cM linkage interval on Xp22.11-Xp21.1 with a maximum positive LOD score of 2.41 (MRX85 locus). Molecular modeling predicts that the p.(Leu3238del) deletion results in the destabilization of the C-terminal domain of dystrophin and hence reduces the ability to interact with β-dystroglycan. Correspondingly, Dp71 protein levels in lymphoblastoid cells from the index patient are 6.7-fold lower than those in control cell lines (P=0.08). Subsequent determination of the creatine kinase levels in blood of the index patient showed a mild but significant elevation in serum creatine kinase, which is in line with impaired dystrophin function. In conclusion, we have identified the first DMD mutation in Dp71 that results in ID without muscular dystrophy.
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Affiliation(s)
- Arjan P M de Brouwer
- 1] Department of Human Genetics, Nijmegen Centre for Molecular Life Sciences, Radboud University Nijmegen Medical Centre, Nijmegen, The Netherlands [2] Institute of Genetic and Metabolic Disease, Radboud University Nijmegen Medical Centre, Nijmegen, The Netherlands [3] Department of Cognitive Neuroscience, Donders Institute for Brain, Cognition and Behaviour, Radboud University Nijmegen, Nijmegen, The Netherlands
| | - Sander B Nabuurs
- Centre for Molecular and Biomolecular Informatics, Nijmegen Centre for Molecular Life Sciences, Radboud University Nijmegen, Nijmegen, The Netherlands
| | - Ingrid E C Verhaart
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Astrid R Oudakker
- 1] Department of Human Genetics, Nijmegen Centre for Molecular Life Sciences, Radboud University Nijmegen Medical Centre, Nijmegen, The Netherlands [2] Department of Cognitive Neuroscience, Donders Institute for Brain, Cognition and Behaviour, Radboud University Nijmegen, Nijmegen, The Netherlands
| | - Roel Hordijk
- Department of Genetics, University Medical Center Groningen, Groningen, The Netherlands
| | - Helger G Yntema
- Department of Human Genetics, Nijmegen Centre for Molecular Life Sciences, Radboud University Nijmegen Medical Centre, Nijmegen, The Netherlands
| | - Jannet M Hordijk-Hos
- Department of Genetics, University Medical Center Groningen, Groningen, The Netherlands
| | - Krysta Voesenek
- Department of Human Genetics, Nijmegen Centre for Molecular Life Sciences, Radboud University Nijmegen Medical Centre, Nijmegen, The Netherlands
| | - Bert B A de Vries
- 1] Department of Human Genetics, Nijmegen Centre for Molecular Life Sciences, Radboud University Nijmegen Medical Centre, Nijmegen, The Netherlands [2] Institute of Genetic and Metabolic Disease, Radboud University Nijmegen Medical Centre, Nijmegen, The Netherlands
| | - Ton van Essen
- Department of Genetics, University Medical Center Groningen, Groningen, The Netherlands
| | - Wei Chen
- Department Human Molecular Genetics, Max Planck Institute for Molecular Genetics, Ihnestrasse 73, Berlin, Germany
| | - Hao Hu
- Department Human Molecular Genetics, Max Planck Institute for Molecular Genetics, Ihnestrasse 73, Berlin, Germany
| | - Jamel Chelly
- Institut Cochin, INSERM Unité 1016, CNRS UMR 8104, Paris, France
| | - Johan T den Dunnen
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Vera M Kalscheuer
- Department Human Molecular Genetics, Max Planck Institute for Molecular Genetics, Ihnestrasse 73, Berlin, Germany
| | | | - Ben C J Hamel
- Department of Human Genetics, Nijmegen Centre for Molecular Life Sciences, Radboud University Nijmegen Medical Centre, Nijmegen, The Netherlands
| | - Hans van Bokhoven
- 1] Department of Human Genetics, Nijmegen Centre for Molecular Life Sciences, Radboud University Nijmegen Medical Centre, Nijmegen, The Netherlands [2] Department of Cognitive Neuroscience, Donders Institute for Brain, Cognition and Behaviour, Radboud University Nijmegen, Nijmegen, The Netherlands
| | - Tjitske Kleefstra
- 1] Department of Human Genetics, Nijmegen Centre for Molecular Life Sciences, Radboud University Nijmegen Medical Centre, Nijmegen, The Netherlands [2] Institute of Genetic and Metabolic Disease, Radboud University Nijmegen Medical Centre, Nijmegen, The Netherlands [3] Department of Cognitive Neuroscience, Donders Institute for Brain, Cognition and Behaviour, Radboud University Nijmegen, Nijmegen, The Netherlands
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Granese B, Scala I, Spatuzza C, Valentino A, Coletta M, Vacca RA, De Luca P, Andria G. Validation of microarray data in human lymphoblasts shows a role of the ubiquitin-proteasome system and NF-kB in the pathogenesis of Down syndrome. BMC Med Genomics 2013; 6:24. [PMID: 23830204 PMCID: PMC3717290 DOI: 10.1186/1755-8794-6-24] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2013] [Accepted: 06/29/2013] [Indexed: 11/25/2022] Open
Abstract
BACKGROUND Down syndrome (DS) is a complex disorder caused by the trisomy of either the entire, or a critical region of chromosome 21 (21q22.1-22.3). Despite representing the most common cause of mental retardation, the molecular bases of the syndrome are still largely unknown. METHODS To better understand the pathogenesis of DS, we analyzed the genome-wide transcription profiles of lymphoblastoid cell lines (LCLs) from six DS and six euploid individuals and investigated differential gene expression and pathway deregulation associated with trisomy 21. Connectivity map and PASS-assisted exploration were used to identify compounds whose molecular signatures counteracted those of DS lymphoblasts and to predict their therapeutic potential. An experimental validation in DS LCLs and fetal fibroblasts was performed for the most deregulated GO categories, i.e. the ubiquitin mediated proteolysis and the NF-kB cascade. RESULTS We show, for the first time, that the level of protein ubiquitination is reduced in human DS cell lines and that proteasome activity is increased in both basal conditions and oxidative microenvironment. We also provide the first evidence that NF-kB transcription levels, a paradigm of gene expression control by ubiquitin-mediated degradation, is impaired in DS due to reduced IkB-alfa ubiquitination, increased NF-kB inhibitor (IkB-alfa) and reduced p65 nuclear fraction. Finally, the DSCR1/DYRK1A/NFAT genes were analysed. In human DS LCLs, we confirmed the presence of increased protein levels of DSCR1 and DYRK1A, and showed that the levels of the transcription factor NFATc2 were decreased in DS along with a reduction of its nuclear translocation upon induction of calcium fluxes. CONCLUSIONS The present work offers new perspectives to better understand the pathogenesis of DS and suggests a rationale for innovative approaches to treat some pathological conditions associated to DS.
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Affiliation(s)
- Barbara Granese
- Department of Pediatrics, Federico II University, Naples 80131, Italy
| | - Iris Scala
- Department of Pediatrics, Federico II University, Naples 80131, Italy
| | - Carmen Spatuzza
- Department of Biotechnological Sciences, Federico II University, Naples 80131, Italy
| | - Anna Valentino
- Department of Pediatrics, Federico II University, Naples 80131, Italy
| | - Marcella Coletta
- Department of Pediatrics, Federico II University, Naples 80131, Italy
| | - Rosa Anna Vacca
- Institute of Biomembranes and Bioenergetics, National Council of Research, Bari 70126, Italy
| | - Pasquale De Luca
- Stazione Zoologica “A. Dohrn”, c/o BioGeM, Via Camporeale, Ariano Irpino 83031, Italy
| | - Generoso Andria
- Department of Pediatrics, Federico II University, Naples 80131, Italy
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Vincent M, Oved K, Morag A, Pasmanik-Chor M, Oron-Karni V, Shomron N, Gurwitz D. Genome-wide transcriptomic variations of human lymphoblastoid cell lines: insights from pairwise gene-expression correlations. Pharmacogenomics 2012; 13:1893-904. [DOI: 10.2217/pgs.12.179] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Aims: Human lymphoblastoid cell lines (LCLs) are a rich resource of information on human interindividual genomic, transcriptomic, proteomic and phenomic variations, and are therefore gaining popularity for pharmacogenomic studies. In the present study we demonstrate that genome-wide transcriptomic data from a small LCL panel from unrelated individuals is sufficient for detecting pairs of genes that exhibit highly correlated expression levels and may thus convey insights about coregulated genes. Materials & methods: RNA samples were prepared from LCLs representing 12 unrelated healthy adult female Caucasian donors. Transcript levels were determined with the Affymetrix Human Gene arrays. Expression-level correlations were searched using Partek® Genomics Suite™ and the R environment. Sequences of detected correlated gene pairs were compared for shared conserved 3´-UTR miRNA binding. Results: Most of the approximately 33,000 transcripts covered by the Affymetrix arrays showed closely similar expression levels in LCLs from unrelated donors. However, the expression levels of some transcripts showed large inter-individual variations. When comparing the expression levels of each of the top 1000 genes showing the largest interindividual expression variations against the others, two sets containing 156 and 4438 correlated gene pairs with false-discovery rates of 0.01 and 0.05 were detected, respectively. Similar analysis of another gene-expression data set from LCLs (GSE11582) indicated that 61 and 39% of identified pairs matched the pairs detected from our transcriptomic data, respectively. Shared conserved 3´-UTR miRNA binding sites were noted for 14–17% of the top 100 gene pairs, suggesting that regulation by miRNA may contribute to their coordinated expression. Conclusion: Probing genome-wide transcriptomic data sets of LCLs from unrelated individuals may detect coregulated genes, adding insights on cellular regulation by miRNAs. Original submitted 11 July 2012; Revision submitted 4 September 2012
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Affiliation(s)
- Marc Vincent
- Université Paris Descartes, INSERM UMRS775, Paris, France
| | - Keren Oved
- Department of Human Molecular Genetics & Biochemistry, Sackler Faculty of Medicine, Tel-Aviv University, Israel
- Department of Cell & Developmental Biology, Sackler Faculty of Medicine, Tel-Aviv University, Israel
| | - Ayelet Morag
- Department of Human Molecular Genetics & Biochemistry, Sackler Faculty of Medicine, Tel-Aviv University, Israel
| | - Metsada Pasmanik-Chor
- Bioinformatics Unit, George Wise Faculty of Life Sciences, Tel-Aviv University, Israel
| | - Varda Oron-Karni
- Bioinformatics Unit, George Wise Faculty of Life Sciences, Tel-Aviv University, Israel
| | - Noam Shomron
- Department of Cell & Developmental Biology, Sackler Faculty of Medicine, Tel-Aviv University, Israel
| | - David Gurwitz
- Department of Human Molecular Genetics & Biochemistry, Sackler Faculty of Medicine, Tel-Aviv University, Israel
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20
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Jochum S, Moosmann A, Lang S, Hammerschmidt W, Zeidler R. The EBV immunoevasins vIL-10 and BNLF2a protect newly infected B cells from immune recognition and elimination. PLoS Pathog 2012; 8:e1002704. [PMID: 22615564 PMCID: PMC3355093 DOI: 10.1371/journal.ppat.1002704] [Citation(s) in RCA: 122] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2011] [Accepted: 04/02/2012] [Indexed: 11/24/2022] Open
Abstract
Lifelong persistence of Epstein-Barr virus (EBV) in infected hosts is mainly owed to the virus' pronounced abilities to evade immune responses of its human host. Active immune evasion mechanisms reduce the immunogenicity of infected cells and are known to be of major importance during lytic infection. The EBV genes BCRF1 and BNLF2a encode the viral homologue of IL-10 (vIL-10) and an inhibitor of the transporter associated with antigen processing (TAP), respectively. Both are known immunoevasins in EBV's lytic phase. Here we describe that BCRF1 and BNLF2a are functionally expressed instantly upon infection of primary B cells. Using EBV mutants deficient in BCRF1 and BNLF2a, we show that both factors contribute to evading EBV-specific immune responses during the earliest phase of infection. vIL-10 impairs NK cell mediated killing of infected B cells, interferes with CD4+ T-cell activity, and modulates cytokine responses, while BNLF2a reduces antigen presentation and recognition of newly infected cells by EBV-specific CD8+ T cells. Together, both factors significantly diminish the immunogenicity of EBV-infected cells during the initial, pre-latent phase of infection and may improve the establishment of a latent EBV infection in vivo.
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Affiliation(s)
- Simon Jochum
- Research Unit Gene Vectors, Helmholtz Center, Munich, Germany
| | - Andreas Moosmann
- Clinical Cooperation Group Immunooncology, Helmholtz Center, Munich, Germany
| | - Stephan Lang
- Department of Otorhinolaryngology, Universitätsklinikum Essen, Essen, Germany
| | | | - Reinhard Zeidler
- Ludwig-Maximilians-Universität, Department of Otorhinolaryngology, Munich, Germany
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21
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Guillard M, Morava E, de Ruijter J, Roscioli T, Penzien J, van den Heuvel L, Willemsen MA, de Brouwer A, Bodamer OA, Wevers RA, Lefeber DJ. B4GALT1-congenital disorders of glycosylation presents as a non-neurologic glycosylation disorder with hepatointestinal involvement. J Pediatr 2011; 159:1041-3.e2. [PMID: 21920538 DOI: 10.1016/j.jpeds.2011.08.007] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/03/2011] [Revised: 07/05/2011] [Accepted: 08/02/2011] [Indexed: 10/17/2022]
Abstract
The clinical phenotype of congenital disorders of glycosylation is heterogeneous, mostly including a severe neurological involvement and multisystem disease. We identified a novel patient with a galactosyltransferase deficiency with mild hepatopathy and coagulation anomalies, but normal psychomotor development. The tissue-specific expression of the defective B4GALT1 gene correlated with the clinical phenotype.
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Affiliation(s)
- Maïlys Guillard
- Department of Laboratory Medicine, Institute for Genetic and Metabolic Disease, Radboud University Nijmegen Medical Centre, Nijmegen, The Netherlands
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22
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Genetic CD21 deficiency is associated with hypogammaglobulinemia. J Allergy Clin Immunol 2011; 129:801-810.e6. [PMID: 22035880 DOI: 10.1016/j.jaci.2011.09.027] [Citation(s) in RCA: 156] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2011] [Revised: 08/25/2011] [Accepted: 09/07/2011] [Indexed: 11/22/2022]
Abstract
BACKGROUND Complement receptor 2 (CR2/CD21) is part of the B-cell coreceptor and expressed by mature B cells and follicular dendritic cells. CD21 is a receptor for C3d-opsonized immune complexes and enhances antigen-specific B-cell responses. OBJECTIVE Genetic inactivation of the murine CR2 locus results in impaired humoral immune responses. Here we report the first case of a genetic CD21 deficiency in human subjects. METHODS CD21 protein expression was analyzed by means of flow cytometry and Western blotting. CD21 transcripts were quantified by using real-time PCR. The CD21 gene was sequenced. Wild-type and mutant CD21 cDNA expression was studied after transfection of 293T cells. Binding of EBV-gp350 or C3d-containing immune complexes and induction of calcium flux in CD21-deficient B cells were analyzed by means of flow cytometry. Antibody responses to protein and polysaccharide vaccines were measured. RESULTS A 28-year-old man presented with recurrent infections, reduced class-switched memory B cells, and hypogammaglobulinemia. CD21 receptor expression was undetectable. Binding of C3d-containing immune complexes and EBV-gp350 to B cells was severely reduced. Sequence analysis revealed a compound heterozygous deleterious mutation in the CD21 gene. Functional studies with anti-immunoglobulin- and C3d-containing immune complexes showed a complete loss of costimulatory activity of C3d in enhancing suboptimal B-cell receptor stimulation. Vaccination responses to protein antigens were normal, but the response to pneumococcal polysaccharide vaccination was moderately impaired. CONCLUSIONS Genetic CD21 deficiency adds to the molecular defects observed in human subjects with hypogammaglobulinemia.
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23
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The lytic phase of epstein-barr virus requires a viral genome with 5-methylcytosine residues in CpG sites. J Virol 2011; 86:447-58. [PMID: 22031942 DOI: 10.1128/jvi.06314-11] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
Epstein-Barr virus (EBV) is a human herpesvirus which has been studied intensively for its role in certain human tumors. It also serves as a model of herpesviral latency because it establishes an immediate, latent infection in human B cells. When EBV infects quiescent, primary B cells it induces their continuous proliferation to yield growth-transformed B-cell lines in vitro. The lytic or productive phase of EBV's life cycle is induced by the expression of the viral BZLF1 gene in latently infected cells. The BZLF1 protein is a transactivator, which selectively binds to two classes of distinct DNA sequence motifs. One class is similar to the motifs that are bound by members of the AP-1 transcription factor family to which BZLF1 belongs. The second class, which contains CpG motifs, is predominant in viral promoters of early lytic genes and is BZLF1's preferred or exclusive target sequence when methylated. The BZLF1 gene is transiently expressed in newly infected B cells but fails to induce EBV's lytic cycle, potentially because the virion DNA is unmethylated. Here we report that the lack of 5-methylcytosine residues in CpG sites of virion DNA prevents the expression of essential lytic genes indispensable for viral DNA amplification during productive infection. This finding indicates that BZLF1 transactivates these promoters in a methylation-dependent fashion and explains how progeny virus synthesis is abrogated in newly infected B cells. Our data also reveal that viral lytic DNA synthesis precludes CpG methylation of virion DNA during EBV's lytic, productive cycle, which can be overcome by the ectopic expression of a prokaryotic cytosine methyltransferase to yield CpG-methylated virion DNA. Upon infection of B cells, randomly CpG-methylated virion DNA induces high expression of essential lytic genes in contrast to virion DNA free of 5-methylcytosine residues. Our data suggest that unmethylated virion DNA is part of EBV's strategy to prevent the viral lytic phase in newly infected B cells, allowing it to establish its characteristic latent infection in them.
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24
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Coene KLM, Mans DA, Boldt K, Gloeckner CJ, van Reeuwijk J, Bolat E, Roosing S, Letteboer SJF, Peters TA, Cremers FPM, Ueffing M, Roepman R. The ciliopathy-associated protein homologs RPGRIP1 and RPGRIP1L are linked to cilium integrity through interaction with Nek4 serine/threonine kinase. Hum Mol Genet 2011; 20:3592-605. [PMID: 21685204 DOI: 10.1093/hmg/ddr280] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
Recent studies have established ciliary dysfunction as the underlying cause of a broad range of multi-organ phenotypes, known as 'ciliopathies'. Ciliopathy-associated proteins have a common site of action in the cilium, however, their overall importance for ciliary function differs, as implied by the extreme variability in ciliopathy phenotypes. The aim of this study was to gain more insight in the function of two ciliopathy-associated protein homologs, RPGR interacting protein 1 (RPGRIP1) and RPGRIP1-like protein (RPGRIP1L). Mutations in RPGRIP1 lead to the eye-restricted disease Leber congenital amaurosis, while mutations in RPGRIP1L are causative for Joubert and Meckel syndrome, which affect multiple organs and are at the severe end of the ciliopathy spectrum. Using tandem affinity purification in combination with mass spectrometry, we identified Nek4 serine/threonine kinase as a prominent component of both the RPGRIP1- as well as the RPGRIP1L-associated protein complex. In ciliated cells, this kinase localized to basal bodies, while in ciliated organs, the kinase was predominantly detected at the ciliary rootlet. Down-regulation of NEK4 in ciliated cells led to a significant decrease in cilium assembly, pointing to a role for Nek4 in cilium dynamics. We now hypothesize that RPGRIP1 and RPGRIP1L function as cilium-specific scaffolds that recruit a Nek4 signaling network which regulates cilium stability. Our data are in line with previously established roles in the cilium of other members of the Nek protein family and define NEK4 as a ciliopathy candidate gene.
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Affiliation(s)
- Karlien L M Coene
- Department of Human Genetics (855), Radboud University Nijmegen Medical Centre, PO Box9101, 6500 HB Nijmegen, The Netherlands
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25
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Morag A, Pasmanik-Chor M, Oron-Karni V, Rehavi M, Stingl JC, Gurwitz D. Genome-wide expression profiling of human lymphoblastoid cell lines identifies CHL1 as a putative SSRI antidepressant response biomarker. Pharmacogenomics 2011; 12:171-84. [PMID: 21332311 DOI: 10.2217/pgs.10.185] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
AIMS Selective serotonin reuptake inhibitors (SSRIs) are the most commonly used class of antidepressants for treating major depression. However, approximately 30% of patients do not respond sufficiently to first-line antidepressant drug treatment and require alternative therapeutics. Genome-wide studies searching for SSRI response DNA biomarkers or studies of candidate serotonin-related genes so far have given inconclusive or contradictory results. Here, we present an alternative transcriptome-based genome-wide approach for searching antidepressant drug-response biomarkers by using drug-effect phenotypes in human lymphoblastoid cell lines (LCLs). MATERIALS & METHODS We screened 80 LCLs from healthy adult female individuals for growth inhibition by paroxetine. A total of 14 LCLs with reproducible high and low sensitivities to paroxetine (seven from each phenotypic group) were chosen for genome-wide expression profiling with commercial microarrays. RESULTS The most notable genome-wide transcriptome difference between LCLs displaying high versus low paroxetine sensitivities was a 6.3-fold lower (p = 0.0000256) basal expression of CHL1, a gene coding for a neuronal cell adhesion protein implicated in correct thalamocortical circuitry, schizophrenia and autism. The microarray findings were confirmed by real-time PCR (36-fold lower CHL1 expression levels in the high paroxetine sensitivity group). Several additional genes implicated in synaptogenesis or in psychiatric disorders, including ARRB1, CCL5, DDX60, DDX60L, ENDOD1, ENPP2, FLT1, GABRA4, GAP43, MCTP2 and SPRY2, also differed by more than 1.5-fold and a p-value of less than 0.005 between the two paroxetine sensitivity groups, as confirmed by real-time PCR experiments. CONCLUSION Genome-wide transcriptional profiling of in vitro phenotyped LCLs identified CHL1 and additional genes implicated in synaptogenesis and brain circuitry as putative SSRI response biomarkers. This method might be used as a preliminary tool for searching for potential depression treatment biomarkers.
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Affiliation(s)
- Ayelet Morag
- Department of Human Molecular Genetics & Biochemistry, Sackler Faculty of Medicine, Tel-Aviv University, Israel
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26
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Chiocchetti A, Pakalapati G, Duketis E, Wiemann S, Poustka A, Poustka F, Klauck SM. Mutation and expression analyses of the ribosomal protein gene RPL10 in an extended German sample of patients with autism spectrum disorder. Am J Med Genet A 2011; 155A:1472-5. [PMID: 21567917 DOI: 10.1002/ajmg.a.33977] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2010] [Accepted: 01/22/2011] [Indexed: 11/11/2022]
Affiliation(s)
- A Chiocchetti
- Division of Molecular Genome Analysis, German Cancer Research Center, Heidelberg, Germany
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27
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Morava E, Wevers RA, Cantagrel V, Hoefsloot LH, Al-Gazali L, Schoots J, van Rooij A, Huijben K, van Ravenswaaij-Arts CMA, Jongmans MCJ, Sykut-Cegielska J, Hoffmann GF, Bluemel P, Adamowicz M, van Reeuwijk J, Ng BG, Bergman JEH, van Bokhoven H, Körner C, Babovic-Vuksanovic D, Willemsen MA, Gleeson JG, Lehle L, de Brouwer APM, Lefeber DJ. A novel cerebello-ocular syndrome with abnormal glycosylation due to abnormalities in dolichol metabolism. ACTA ACUST UNITED AC 2010; 133:3210-20. [PMID: 20852264 DOI: 10.1093/brain/awq261] [Citation(s) in RCA: 79] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
Cerebellar hypoplasia and slowly progressive ophthalmological symptoms are common features in patients with congenital disorders of glycosylation type I. In a group of patients with congenital disorders of glycosylation type I with unknown aetiology, we have previously described a distinct phenotype with severe, early visual impairment and variable eye malformations, including optic nerve hypoplasia, retinal coloboma, congenital cataract and glaucoma. Some of the symptoms overlapped with the phenotype in other congenital disorders of glycosylation type I subtypes, such as vermis hypoplasia, anaemia, ichtyosiform dermatitis, liver dysfunction and coagulation abnormalities. We recently identified pathogenic mutations in the SRD5A3 gene, encoding steroid 5α-reductase type 3, in a group of patients who presented with this particular phenotype and a common metabolic pattern. Here, we report on the clinical, genetic and metabolic features of 12 patients from nine families with cerebellar ataxia and congenital eye malformations diagnosed with SRD5A3-congenital disorders of glycosylation due to steroid 5α-reductase type 3 defect. This enzyme is necessary for the reduction of polyprenol to dolichol, the lipid anchor for N-glycosylation in the endoplasmic reticulum. Dolichol synthesis is an essential metabolic step in protein glycosylation. The current defect leads to a severely abnormal glycosylation state already in the early phase of the N-glycan biosynthesis pathway in the endoplasmic reticulum. We detected high expression of SRD5A3 in foetal brain tissue, especially in the cerebellum, consistent with the finding of the congenital cerebellar malformations. Based on the overlapping clinical, biochemical and genetic data in this large group of patients with congenital disorders of glycosylation, we define a novel syndrome of cerebellar ataxia associated with congenital eye malformations due to a defect in dolichol metabolism.
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Affiliation(s)
- Eva Morava
- Radboud University Nijmegen Medical Centre, Institute for Genetic and Metabolic Disease, P.O. Box 9101, 6500 HB Nijmegen, The Netherlands.
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CDK19 is disrupted in a female patient with bilateral congenital retinal folds, microcephaly and mild mental retardation. Hum Genet 2010; 128:281-91. [PMID: 20563892 PMCID: PMC2921488 DOI: 10.1007/s00439-010-0848-x] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2010] [Accepted: 06/03/2010] [Indexed: 12/13/2022]
Abstract
Microcephaly, mental retardation and congenital retinal folds along with other systemic features have previously been reported as a separate clinical entity. The sporadic nature of the syndrome and lack of clear inheritance patterns pointed to a genetic heterogeneity. Here, we report a genetic analysis of a female patient with microcephaly, congenital bilateral falciform retinal folds, nystagmus, and mental retardation. Karyotyping revealed a de novo pericentric inversion in chromosome 6 with breakpoints in 6p12.1 and 6q21. Fluorescence in situ hybridization analysis narrowed down the region around the breakpoints, and the breakpoint at 6q21 was found to disrupt the CDK19 gene. CDK19 was found to be expressed in a diverse range of tissues including fetal eye and fetal brain. Quantitative PCR of the CDK19 transcript from Epstein–Barr virus-transformed lymphoblastoid cell lines of the patient revealed ~50% reduction in the transcript (p = 0.02), suggesting haploinsufficiency of the gene. cdk8, the closest orthologue of human CDK19 in Drosophila has been shown to play a major role in eye development. Conditional knock-down of Drosophila cdk8 in multiple dendrite (md) neurons resulted in 35% reduced dendritic branching and altered morphology of the dendritic arbour, which appeared to be due in part to a loss of small higher order branches. In addition, Cdk8 mutant md neurons showed diminished dendritic fields revealing an important role of the CDK19 orthologue in the developing nervous system of Drosophila. This is the first time the CDK19 gene, a component of the mediator co-activator complex, has been linked to a human disease.
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Hurtado del Pozo C, Calvo RM, Vesperinas-García G, Gómez-Ambrosi J, Frühbeck G, Corripio-Sánchez R, Rubio MA, Obregon MJ. IPO8 and FBXL10: new reference genes for gene expression studies in human adipose tissue. Obesity (Silver Spring) 2010; 18:897-903. [PMID: 19876011 DOI: 10.1038/oby.2009.374] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Housekeeping genes frequently used in gene expression studies are highly regulated in human adipose tissue. To ensure a correct interpretation of results, it is critical to select appropriate reference genes. Subcutaneous (SC) and omental (OM) adipose tissue expression was analyzed from lean and obese subjects using whole genome complementary DNA (cDNA) microarrays to identify stably expressed genes and commercial TaqMan low density arrays (LDAs), with 16 common control genes. The best candidate gene from microarrays analysis was F-box and leucine-rich repeat protein-10 (FBXL10) (fold-change 10(-3) P < 0.01), an ubiquitous nucleolar protein evolutionarily conserved. Hypoxanthine phosphoribosyltransferase 1 (HPRT1) and importin 8 (IPO8), were the best reference genes among the 16 genes in the LDAs with coefficient of variation (CV) of 4.51 and 4.55%, respectively. However, when the LDAs data were further analyzed by the geNorm and NormFinder softwares, IPO8, a nuclear protein mediating import of proteins, was the first and the third better reference gene, respectively. IPO8 and FBXL10 were further validated by real-time PCR in additional OM and SC fat samples and primary cultured preadipocytes. According to their CV, IPO8 resulted more suitable than FBXL10 in both adipose tissue depots and SC preadipocytes, whereas FBXL10 performed better than IPO8 in OM cultured preadipocytes. Both genes expression levels did not change throughout adipogenesis. Thus, we provide clear evidence that IPO8 and FBXL10 are good candidates to use as reference genes in gene expression studies in human OM and SC adipose tissues as well as differentiated primary preadipocytes.
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Affiliation(s)
- Carmen Hurtado del Pozo
- Instituto de Investigaciones Biomedicas, Consejo Superior de Investigaciones Cientificas-UAM, Madrid, Spain
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Lugtenberg D, Zangrande-Vieira L, Kirchhoff M, Whibley AC, Oudakker AR, Kjaergaard S, Vianna-Morgante AM, Kleefstra T, Ruiter M, Jehee FS, Ullmann R, Schwartz CE, Stratton M, Raymond FL, Veltman JA, Vrijenhoek T, Pfundt R, Schuurs-Hoeijmakers JHM, Hehir-Kwa JY, Froyen G, Chelly J, Ropers HH, Moraine C, Gècz J, Knijnenburg J, Kant SG, Hamel BCJ, Rosenberg C, van Bokhoven H, de Brouwer APM. Recurrent deletion of ZNF630 at Xp11.23 is not associated with mental retardation. Am J Med Genet A 2010; 152A:638-45. [PMID: 20186789 DOI: 10.1002/ajmg.a.33292] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
ZNF630 is a member of the primate-specific Xp11 zinc finger gene cluster that consists of six closely related genes, of which ZNF41, ZNF81, and ZNF674 have been shown to be involved in mental retardation. This suggests that mutations of ZNF630 might influence cognitive function. Here, we detected 12 ZNF630 deletions in a total of 1,562 male patients with mental retardation from Brazil, USA, Australia, and Europe. The breakpoints were analyzed in 10 families, and in all cases they were located within two segmental duplications that share more than 99% sequence identity, indicating that the deletions resulted from non-allelic homologous recombination. In 2,121 healthy male controls, 10 ZNF630 deletions were identified. In total, there was a 1.6-fold higher frequency of this deletion in males with mental retardation as compared to controls, but this increase was not statistically significant (P-value = 0.174). Conversely, a 1.9-fold lower frequency of ZNF630 duplications was observed in patients, which was not significant either (P-value = 0.163). These data do not show that ZNF630 deletions or duplications are associated with mental retardation.
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Affiliation(s)
- Dorien Lugtenberg
- Department of Human Genetics, Nijmegen Centre for Molecular Life Sciences and Donders Institute for Brain, Cognition and Behaviour, Radboud University Nijmegen Medical Centre, Nijmegen, The Netherlands
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31
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Mortensen DM, Røge R, Øzbay A, Koefoed-Nielsen PB, Jørgensen KA. Gene expression analysis of calcineurin isoforms in T-lymphocytes--a method applied on kidney-transplant recipients. Transpl Immunol 2010; 23:24-7. [PMID: 20226242 DOI: 10.1016/j.trim.2010.02.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2009] [Revised: 01/15/2010] [Accepted: 02/26/2010] [Indexed: 11/16/2022]
Abstract
BACKGROUND Tacrolimus exerts its immunosuppressive effect through inhibition of the intracellular enzyme calcineurin phosphatase (CaN). In this study, we set-up a validated real-time PCR method to measure the gene expression of the two major isoforms of the catalytic subunit of CaN in T-lymphocytes. METHODS 20 stable kidney-transplant recipients, 10 early kidney-transplant recipients and 10 healthy non-medicated subjects had blood drawn and T-lymphocytes were isolated using E-rosette gradient centrifugation method. The cell counts were analyzed by DNA quantification using Hoeschst 33285. Gene expressions were analyzed using real-time PCR for CaN Aalpha, CaN Abeta and the reference genes CD3E and PPIB. RESULTS The real-time PCR method was found to be with high efficiencies and low intra- and inter-assay variabilities. No statistically significant differences were found in the gene expression levels of the two reference genes among the three groups. The two major isoforms of CaN A were expressed in equal amounts in the T-lymphocytes. CONCLUSION We found no significant difference in the reference genes between the three groups, but looking at the data there was a trend towards an up-regulation of CD3E. PPIB appears to be the more stable of the two reference genes tested in our study.
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Affiliation(s)
- D M Mortensen
- Research Laboratory C, Department of Renal Medicine C, Aarhus University Hospital, Skejby, Brendstrupgaardsvej 100, DK 8200 Aarhus N, Denmark.
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Toll-like receptor agonists synergistically increase proliferation and activation of B cells by epstein-barr virus. J Virol 2010; 84:3612-23. [PMID: 20089650 DOI: 10.1128/jvi.01400-09] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Epstein-Barr virus (EBV) efficiently drives proliferation of human primary B cells in vitro, a process relevant for human diseases such as infectious mononucleosis and posttransplant lymphoproliferative disease. Human B-cell proliferation is also driven by ligands of Toll-like receptors (TLRs), notably viral or bacterial DNA containing unmethylated CpG dinucleotides, which triggers TLR9. Here we quantitatively investigated how TLR stimuli influence EBV-driven B-cell proliferation and expression of effector molecules. CpG DNA synergistically increased EBV-driven proliferation and transformation, T-cell costimulatory molecules, and early production of interleukin-6. CpG DNA alone activated only memory B cells, but CpG DNA enhanced EBV-mediated transformation of both memory and naive B cells. Ligands for TLR2 or TLR7/8 or whole bacteria had a weaker but still superadditive effect on B-cell transformation. Additionally, CpG DNA facilitated the release of transforming virus by established EBV-infected lymphoblastoid cell lines. These results suggest that the proliferation of EBV-infected B cells and their capability to interact with immune effector cells may be directly influenced by components of bacteria or other microbes present at the site of infection.
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Coene KL, Roepman R, Doherty D, Afroze B, Kroes HY, Letteboer SJ, Ngu LH, Budny B, van Wijk E, Gorden NT, Azhimi M, Thauvin-Robinet C, Veltman JA, Boink M, Kleefstra T, Cremers FP, van Bokhoven H, de Brouwer AP. OFD1 is mutated in X-linked Joubert syndrome and interacts with LCA5-encoded lebercilin. Am J Hum Genet 2009; 85:465-81. [PMID: 19800048 DOI: 10.1016/j.ajhg.2009.09.002] [Citation(s) in RCA: 144] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2009] [Revised: 08/23/2009] [Accepted: 09/04/2009] [Indexed: 12/12/2022] Open
Abstract
We ascertained a multi-generation Malaysian family with Joubert syndrome (JS). The presence of asymptomatic obligate carrier females suggested an X-linked recessive inheritance pattern. Affected males presented with mental retardation accompanied by postaxial polydactyly and retinitis pigmentosa. Brain MRIs showed the presence of a "molar tooth sign," which classifies this syndrome as classic JS with retinal involvement. Linkage analysis showed linkage to Xpter-Xp22.2 and a maximum LOD score of 2.06 for marker DXS8022. Mutation analysis revealed a frameshift mutation, p.K948NfsX8, in exon 21 of OFD1. In an isolated male with JS, a second frameshift mutation, p.E923KfsX3, in the same exon was identified. OFD1 has previously been associated with oral-facial-digital type 1 (OFD1) syndrome, a male-lethal X-linked dominant condition, and with X-linked recessive Simpson-Golabi-Behmel syndrome type 2 (SGBS2). In a yeast two-hybrid screen of a retinal cDNA library, we identified OFD1 as an interacting partner of the LCA5-encoded ciliary protein lebercilin. We show that X-linked recessive mutations in OFD1 reduce, but do not eliminate, the interaction with lebercilin, whereas X-linked dominant OFD1 mutations completely abolish binding to lebercilin. In addition, recessive mutations in OFD1 did not affect the pericentriolar localization of the recombinant protein in hTERT-RPE1 cells, whereas this localization was lost for dominant mutations. These findings offer a molecular explanation for the phenotypic spectrum observed for OFD1 mutations; this spectrum now includes OFD1 syndrome, SGBS2, and JS.
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Jacobs JFM, van Bokhoven H, van Leeuwen FN, Hulsbergen-van de Kaa CA, de Vries IJM, Adema GJ, Hoogerbrugge PM, de Brouwer APM. Regulation of MYCN expression in human neuroblastoma cells. BMC Cancer 2009; 9:239. [PMID: 19615087 PMCID: PMC2720985 DOI: 10.1186/1471-2407-9-239] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2009] [Accepted: 07/18/2009] [Indexed: 12/04/2022] Open
Abstract
Background Amplification of the MYCN gene in neuroblastoma (NB) is associated with a poor prognosis. However, MYCN-amplification does not automatically result in higher expression of MYCN in children with NB. We hypothesized that the discrepancy between MYCN gene expression and prognosis in these children might be explained by the expression of either MYCN-opposite strand (MYCNOS) or the shortened MYCN-isoform (ΔMYCN) that was recently identified in fetal tissues. Both MYCNOS and ΔMYCN are potential inhibitors of MYCN either at the mRNA or at the protein level. Methods Expression of MYCN, MYCNOS and ΔMYCN was measured in human NB tissues of different stages. Transcript levels were quantified using a real-time reverse transcriptase polymerase chain reaction assay (QPCR). In addition, relative expression of these three transcripts was compared to the number of MYCN copies, which was determined by genomic real-time PCR (gQPCR). Results Both ΔMYCN and MYCNOS are expressed in all NBs examined. In NBs with MYCN-amplification, these transcripts are significantly higher expressed. The ratio of MYCN:ΔMYCN expression was identical in all tested NBs. This indicates that ΔMYCN and MYCN are co-regulated, which suggests that ΔMYCN is not a regulator of MYCN in NB. However, the ratio of MYCNOS:MYCN expression is directly correlated with NB disease stage (p = 0.007). In the more advanced NB stages and NBs with MYCN-amplification, relatively more MYCNOS is present as compared to MYCN. Expression of the antisense gene MYCNOS might be relevant to the progression of NB, potentially by directly inhibiting MYCN transcription by transcriptional interference at the DNA level. Conclusion The MYCNOS:MYCN-ratio in NBs is significantly correlated with both MYCN-amplification and NB-stage. Our data indicate that in NB, MYCN expression levels might be influenced by MYCNOS but not by ΔMYCN.
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Affiliation(s)
- Joannes F M Jacobs
- Department of Human Genetics, Radboud University Nijmegen Medical Centre, Nijmegen Centre for Molecular Life Sciences, Donders Institute for Brain, Cognition and Behaviour, P.O. Box 9101, 6500 HB Nijmegen, the Netherlands.
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Doreau A, Belot A, Bastid J, Riche B, Trescol-Biemont MC, Ranchin B, Fabien N, Cochat P, Pouteil-Noble C, Trolliet P, Durieu I, Tebib J, Kassai B, Ansieau S, Puisieux A, Eliaou JF, Bonnefoy-Bérard N. Interleukin 17 acts in synergy with B cell-activating factor to influence B cell biology and the pathophysiology of systemic lupus erythematosus. Nat Immunol 2009; 10:778-85. [PMID: 19483719 DOI: 10.1038/ni.1741] [Citation(s) in RCA: 368] [Impact Index Per Article: 24.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2009] [Accepted: 04/16/2009] [Indexed: 01/28/2023]
Abstract
Studies have suggested involvement of interleukin 17 (IL-17) in autoimmune diseases, although its effect on B cell biology has not been clearly established. Here we demonstrate that IL-17 alone or in combination with B cell-activating factor controlled the survival and proliferation of human B cells and their differentiation into immunoglobulin-secreting cells. This effect was mediated mainly through the nuclear factor-kappaB-regulated transcription factor Twist-1. In support of the relevance of our observations and the potential involvement of IL-17 in B cell biology, we found that the serum of patients with systemic lupus erythematosus had higher concentrations of IL-17 than did the serum of healthy people and that IL-17 abundance correlated with the disease severity of systemic lupus erythematosus.
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Affiliation(s)
- Agnès Doreau
- Université de Lyon, Institut Fédératif de Recherche 128, Lyon, France
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David D, Marques B, Ferreira C, Vieira P, Corona-Rivera A, Ferreira JC, van Bokhoven H. Characterization of two ectrodactyly-associated translocation breakpoints separated by 2.5 Mb on chromosome 2q14.1-q14.2. Eur J Hum Genet 2009; 17:1024-33. [PMID: 19223936 DOI: 10.1038/ejhg.2009.2] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
Split hand-split foot malformation or ectrodactyly is a heterogeneous congenital defect of digit formation. The aim of this study is the mapping of the breakpoints and a detailed molecular characterization of the candidate genes for an isolated and syndromic form of ectrodactyly, both associated with de novo apparently balanced chromosome translocations involving the same chromosome 2 band, [t(2;11)(q14.2;q14.2)] and [t(2;4)(q14.1;q35)], respectively. Breakpoints were mapped by fluorescence in situ hybridization using bacterial artificial chromosome clones. Where possible, these breakpoints were further delimited. Candidate genes were screened for pathogenic mutations and the expression levels of two of them analysed. The isolated bilateral split foot malformation-associated chromosome 2 breakpoint was localized at 120.9 Mb, between the two main candidate genes, encoding GLI-Kruppel family member GLI2 and inhibin-betaB. The second breakpoint associated with holoprosencephaly, hypertelorism and ectrodactyly syndrome was mapped 2.5 Mb proximal at 118.4 Mb and the candidate genes identified from this region were the insulin-induced protein 2 and the homeobox protein engrailed-1. No clear pathogenic mutations were identified in any of these genes. The breakpoint between INHBB and GLI2 coincides with a previously identified translocation breakpoint associated with ectrodactyly. We propose a mechanism by which translocations in the 2q14.1-q14.2 region disrupt the specific arrangement of long-range regulatory elements that control the tight quantitative spatiotemporal expression of one or more genes from the breakpoint region.
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Affiliation(s)
- Dezso David
- Department of Genetics, National Institute of Health Dr Ricardo Jorge, Lisboa, Portugal.
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Pilbrow AP, Ellmers LJ, Black MA, Moravec CS, Sweet WE, Troughton RW, Richards AM, Frampton CM, Cameron VA. Genomic selection of reference genes for real-time PCR in human myocardium. BMC Med Genomics 2008; 1:64. [PMID: 19114010 PMCID: PMC2632664 DOI: 10.1186/1755-8794-1-64] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2008] [Accepted: 12/29/2008] [Indexed: 11/26/2022] Open
Abstract
Background Reliability of real-time PCR (RT-qPCR) data is dependent on the use of appropriate reference gene(s) for normalization. To date, no validated reference genes have been reported for normalizing gene expression in human myocardium. This study aimed to identify validated reference genes for use in gene expression studies of failed and non-failed human myocardium. Methods Bioinformatic analysis of published human heart gene expression arrays (195 failed hearts, 16 donor hearts) was used to identify 10 stable and abundant genes for further testing. The expression stability of these genes was investigated in 28 failed and 28 non-failed human myocardium samples by RT-qPCR using geNorm software. Results Signal recognition particle 14 kDa (SRP14), tumor protein, translationally-controlled 1 (TPT1) and eukaryotic elongation factor 1A1 (EEF1A1) were ranked the most stable genes. The commonly used reference gene, glyceraldehyde-3-phosphate dehydrogenase (GAPDH) was ranked the least stable of the genes tested. The normalization strategy was tested by comparing RT-qPCR data of both normalized and raw expression levels of brain natriuretic peptide precursor (NPPB), a gene known to be up-regulated in heart failure. Non-normalized levels of NPPB exhibited a marginally significant difference between failed and non-failed samples (p = 0.058). In contrast, normalized NPPB expression levels were significantly higher in heart-failed patients compared with controls (p = 0.023). Conclusion This study used publicly available gene array data to identify a strategy for normalization involving two reference genes in combination that may have broad application for accurate and reliable normalization of RT-qPCR data in failed and non-failed human myocardium.
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Affiliation(s)
- Anna P Pilbrow
- Christchurch Cardioendocrine Research Group, Department of Medicine, University of Otago-Christchurch, PO Box 4345, Christchurch 8014, New Zealand.
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Balogh A, Paragh G, Juhász A, Köbling T, Törocsik D, Mikó E, Varga V, Emri G, Horkay I, Scholtz B, Remenyik E. Reference genes for quantitative real time PCR in UVB irradiated keratinocytes. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY B-BIOLOGY 2008; 93:133-9. [PMID: 18789713 DOI: 10.1016/j.jphotobiol.2008.07.010] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/09/2008] [Revised: 07/25/2008] [Accepted: 07/31/2008] [Indexed: 11/18/2022]
Abstract
Real time quantitative reverse transcription-polymerase chain reaction (qRT-PCR) is a sensitive and highly reproducible method often used for determining mRNA levels. To enable proper comparison of gene expression genes expressed at stabile levels within the cells in the studied experimental system need to be identified and used as reference. Ultraviolet B (UVB) radiation is an exogenous carcinogenic stimulus in keratinocytes, and UVB elicited changes have extensively been studied by qRT-PCR, yet a comparison of commonly used reference genes in UVB treatment is lacking. To find the best genes for compensating slight inter-sample variations in keratinocytes in UVB experiments and to understand the potential effects of improper reference gene (RG) selection we have analyzed the mRNA expression of 10 housekeeping genes in neonatal human epidermal keratinocytes (NHEK) after UVB treatment. The biological effect of the used UVB light source was validated by trypane blue exclusion, MTT and comet assays. 20-40mJ/cm(2) dose was chosen for the experiments. The stability of the 10 RGs was assessed by the GeNorm and Normfinder software tools. Regardless of their slightly different algorithm the programs found succinate dehydrogenase complex subunit A (SDHA) to be the best individual RG and SDHA and phosphoglycerate kinase-1 (PGK1) as the most suitable combination. Analysis of the expression of tumor necrosis factor alpha (TNFalpha) and vascular endothelial growth factor (VEGF) found that while the perception of changes in TNF-alpha, a gene undergoing marked upregulation after UVB irradiation is independent of the used RG, changes seen in the more modestly upregulated VEGF are greatly effected by reference gene selection. These findings highlight the importance of reference gene selection in UVB irradiation experiments, and provide evidence that using SDHA or the combination of SDHA and PGK1 as standards could be a reliable method for normalizing qRT-PCR results in keratinocytes after UVB treatment.
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Affiliation(s)
- Attila Balogh
- Department of Dermatology, Medical and Health Science Center, University of Debrecen, Debrecen, Hungary Nagyerdei Körut 98, H-4032 Debrecen, Hungary
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Schraders M, Jares P, Bea S, Schoenmakers EFPM, van Krieken JHJM, Campo E, Groenen PJTA. Integrated genomic and expression profiling in mantle cell lymphoma: identification of gene-dosage regulated candidate genes. Br J Haematol 2008; 143:210-21. [PMID: 18699851 DOI: 10.1111/j.1365-2141.2008.07334.x] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Mantle cell lymphoma (MCL) is characterized by the t(11;14)(q13;q32) translocation and several other cytogenetic aberrations, including heterozygous loss of chromosomal arms 1p, 6q, 11q and 13q and/or gains of 3q and 8q. The common intervals of chromosomal imbalance have been narrowed down using array-comparative genomic hybridization (CGH). However, the chromosomal intervals still contain many genes potentially involved in MCL pathogeny. Combined analysis of tiling-resolution array-CGH with gene expression profiling on 11 MCL tumours enabled the identification of genomic alterations and their corresponding gene expression profiles. Only subsets of genes located within given cytogenetic anomaly-intervals showed a concomitant change in mRNA expression level. The genes that showed consistent correlation between DNA copy number and RNA expression levels are likely to be important in MCL pathology. Besides several 'anonymous genes', we also identified various fully annotated genes, whose gene products are involved in cyclic adenosine monophosphate-regulated pathways (PRKACB), DNA damage repair, maintenance of chromosome stability and prevention of rereplication (ATM, ERCC5, FBXO5), energy metabolism (such as genes that are involved in the synthesis of proteins encoded by the mitochondrial genome) and signal transduction (ARHGAP29). Deregulation of these gene products may interfere with the signalling pathways that are involved in MCL tumour development and maintenance.
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Affiliation(s)
- Margit Schraders
- Department of Pathology, Radboud University Nijmegen Medical Centre, Nijmegen, The Netherlands
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Dubos A, Pannetier S, Hanauer A. Inactivation of theCDKL3gene at 5q31.1 by a balanced t(X;5) translocation associated with nonspecific mild mental retardation. Am J Med Genet A 2008; 146A:1267-79. [DOI: 10.1002/ajmg.a.32274] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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Allen D, Winters E, Kenna PF, Humphries P, Farrar GJ. Reference gene selection for real-time rtPCR in human epidermal keratinocytes. J Dermatol Sci 2007; 49:217-25. [PMID: 18061409 DOI: 10.1016/j.jdermsci.2007.10.001] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2007] [Revised: 09/21/2007] [Accepted: 10/11/2007] [Indexed: 11/26/2022]
Abstract
BACKGROUND RNA interference represents a powerful tool with which to achieve suppression of specific target mRNA. Real-time rtPCR is a useful technique for assessing levels of mRNA expression. Critically, for real-time rtPCR to yield meaningful results, it is necessary to normalise expression of the gene of interest to stably expressed endogenous control genes. OBJECTIVES The study involved establishing expression profiles for 11 housekeeping genes in human epidermal keratinocyte cell lines determining their relative stability. Furthermore, the effect of the presence of shRNA on these expression profiles has been established. METHODS Keratinocytes were transfected using lipid-based transfection or AMAXA nucleofection. Real-time rtPCR was used to establish RNA expression levels. Data analysis was carried out using geNORM. RESULTS When using HaCaT or adult NHEK cells any combination of 8 of the housekeeping genes would be appropriate for normalisation. In contrast, with juvenile NHEK cells only 4 of the housekeeping genes were found to be sufficiently stable to be deemed appropriate for normalisation of expression data. Furthermore data demonstrated that the expression of housekeeping genes may sometimes be affected by the induction of the RNAi pathway. CONCLUSIONS The data obtained highlight the importance of characterising housekeeping gene expression profiles in each specific cell type prior to choosing a set of housekeeping genes for expression studies. The results from this study are applicable to researchers working with human epidermal keratinocytes and the experimental approach is more broadly applicable to any researcher carrying out real-time rtPCR.
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Affiliation(s)
- Danny Allen
- Department of Genetics, Trinity College Dublin, Dublin 2, Ireland.
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de Brouwer APM, Williams KL, Duley JA, van Kuilenburg ABP, Nabuurs SB, Egmont-Petersen M, Lugtenberg D, Zoetekouw L, Banning MJG, Roeffen M, Hamel BCJ, Weaving L, Ouvrier RA, Donald JA, Wevers RA, Christodoulou J, van Bokhoven H. Arts syndrome is caused by loss-of-function mutations in PRPS1. Am J Hum Genet 2007; 81:507-18. [PMID: 17701896 PMCID: PMC1950830 DOI: 10.1086/520706] [Citation(s) in RCA: 63] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2007] [Accepted: 06/04/2007] [Indexed: 11/03/2022] Open
Abstract
Arts syndrome is an X-linked disorder characterized by mental retardation, early-onset hypotonia, ataxia, delayed motor development, hearing impairment, and optic atrophy. Linkage analysis in a Dutch family and an Australian family suggested that the candidate gene maps to Xq22.1-q24. Oligonucleotide microarray expression profiling of fibroblasts from two probands of the Dutch family revealed reduced expression levels of the phosphoribosyl pyrophosphate synthetase 1 gene (PRPS1). Subsequent sequencing of PRPS1 led to the identification of two different missense mutations, c.455T-->C (p.L152P) in the Dutch family and c.398A-->C (p.Q133P) in the Australian family. Both mutations result in a loss of phosphoribosyl pyrophosphate synthetase 1 activity, as was shown in silico by molecular modeling and was shown in vitro by phosphoribosyl pyrophosphate synthetase activity assays in erythrocytes and fibroblasts from patients. This is in contrast to the gain-of-function mutations in PRPS1 that were identified previously in PRPS-related gout. The loss-of-function mutations of PRPS1 likely result in impaired purine biosynthesis, which is supported by the undetectable hypoxanthine in urine and the reduced uric acid levels in serum from patients. To replenish low levels of purines, treatment with S-adenosylmethionine theoretically could have therapeutic efficacy, and a clinical trial involving the two affected Australian brothers is currently underway.
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Affiliation(s)
- Arjan P M de Brouwer
- Departments of Human Genetics, Radboud University Nijmegen Medical Centre, Nijmegen, The Netherlands.
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Bergen AW, Baccarelli A, McDaniel TK, Kuhn K, Pfeiffer R, Kakol J, Bender P, Jacobs K, Packer B, Chanock SJ, Yeager M. Cis sequence effects on gene expression. BMC Genomics 2007; 8:296. [PMID: 17727713 PMCID: PMC2077339 DOI: 10.1186/1471-2164-8-296] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2007] [Accepted: 08/29/2007] [Indexed: 11/10/2022] Open
Abstract
Background Sequence and transcriptional variability within and between individuals are typically studied independently. The joint analysis of sequence and gene expression variation (genetical genomics) provides insight into the role of linked sequence variation in the regulation of gene expression. We investigated the role of sequence variation in cis on gene expression (cis sequence effects) in a group of genes commonly studied in cancer research in lymphoblastoid cell lines. We estimated the proportion of genes exhibiting cis sequence effects and the proportion of gene expression variation explained by cis sequence effects using three different analytical approaches, and compared our results to the literature. Results We generated gene expression profiling data at N = 697 candidate genes from N = 30 lymphoblastoid cell lines for this study and used available candidate gene resequencing data at N = 552 candidate genes to identify N = 30 candidate genes with sufficient variance in both datasets for the investigation of cis sequence effects. We used two additive models and the haplotype phylogeny scanning approach of Templeton (Tree Scanning) to evaluate association between individual SNPs, all SNPs at a gene, and diplotypes, with log-transformed gene expression. SNPs and diplotypes at eight candidate genes exhibited statistically significant (p < 0.05) association with gene expression. Using the literature as a "gold standard" to compare 14 genes with data from both this study and the literature, we observed 80% and 85% concordance for genes exhibiting and not exhibiting significant cis sequence effects in our study, respectively. Conclusion Based on analysis of our results and the extant literature, one in four genes exhibits significant cis sequence effects, and for these genes, about 30% of gene expression variation is accounted for by cis sequence variation. Despite diverse experimental approaches, the presence or absence of significant cis sequence effects is largely supported by previously published studies.
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Affiliation(s)
- Andrew W Bergen
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD USA
- Center for Health Sciences, Policy Division, SRI International, Menlo Park, CA USA
| | - Andrea Baccarelli
- School of Public Health, Harvard University, Boston, MA USA
- Molecular Epidemiology and Genetics, EPOCA Epidemiology Center, Maggiore Hospital, Mangiagalli and Regina Elena IRCCS Foundation & University of Milan, Milan, Italy
| | | | | | - Ruth Pfeiffer
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD USA
| | | | | | - Kevin Jacobs
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD USA
- Core Genotyping Facility, National Cancer Institute, Gaithersburg, MD USA
| | - Bernice Packer
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD USA
- Core Genotyping Facility, National Cancer Institute, Gaithersburg, MD USA
- Science Applications International Corporation-National Cancer Institute (NCI), NCI-FCRDC, Frederick, MD USA
| | - Stephen J Chanock
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD USA
- Core Genotyping Facility, National Cancer Institute, Gaithersburg, MD USA
| | - Meredith Yeager
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD USA
- Core Genotyping Facility, National Cancer Institute, Gaithersburg, MD USA
- Science Applications International Corporation-National Cancer Institute (NCI), NCI-FCRDC, Frederick, MD USA
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Identification of new reference genes for the normalisation of canine osteoarthritic joint tissue transcripts from microarray data. BMC Mol Biol 2007; 8:62. [PMID: 17651481 PMCID: PMC1976117 DOI: 10.1186/1471-2199-8-62] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2007] [Accepted: 07/25/2007] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Real-time reverse transcriptase quantitative polymerase chain reaction (real-time RT-qPCR) is the most accurate measure of gene expression in biological systems. The comparison of different samples requires the transformation of data through a process called normalisation. Reference or housekeeping genes are candidate genes which are selected on the basis of constitutive expression across samples, and allow the quantification of changes in gene expression. At present, no reference gene has been identified for any organism which is universally optimal for use across different tissue types or disease situations. We used microarray data to identify new reference genes generated from total RNA isolated from normal and osteoarthritic canine articular tissues (bone, ligament, cartilage, synovium and fat). RT-qPCR assays were designed and applied to each different articular tissue. Reference gene expression stability and ranking was compared using three different mathematical algorithms. RESULTS Twelve new potential reference genes were identified from microarray data. One gene (mitochondrial ribosomal protein S7 [MRPS7]) was stably expressed in all five of the articular tissues evaluated. One gene HIRA interacting protein 5 isoform 2 [HIRP5]) was stably expressed in four of the tissues evaluated. A commonly used reference gene glyceraldehyde-3-phosphate dehydrogenase (GAPDH) was not stably expressed in any of the tissues evaluated. Most consistent agreement between rank ordering of reference genes was observed between Bestkeeper(c) and geNorm, although each method tended to agree on the identity of the most stably expressed genes and the least stably expressed genes for each tissue. New reference genes identified using microarray data normalised in a conventional manner were more stable than those identified by microarray data normalised by using a real-time RT-qPCR methodology. CONCLUSION Microarray data normalised by a conventional manner can be filtered using a simple stepwise procedure to identify new reference genes, some of which will demonstrate good measures of stability. Mitochondrial ribosomal protein S7 is a new reference gene worthy of investigation in other canine tissues and diseases. Different methods of reference gene stability assessment will generally agree on the most and least stably expressed genes, when co-regulation is not present.
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Ayers D, Clements DN, Salway F, Day PJR. Expression stability of commonly used reference genes in canine articular connective tissues. BMC Vet Res 2007; 3:7. [PMID: 17484782 PMCID: PMC1884148 DOI: 10.1186/1746-6148-3-7] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2006] [Accepted: 05/07/2007] [Indexed: 12/16/2022] Open
Abstract
Background The quantification of gene expression in tissue samples requires the use of reference genes to normalise transcript numbers between different samples. Reference gene stability may vary between different tissues, and between the same tissue in different disease states. We evaluated the stability of 9 reference genes commonly used in human gene expression studies. Real-time reverse transcription PCR and a mathematical algorithm were used to establish which reference genes were most stably expressed in normal and diseased canine articular tissues and two canine cell lines stimulated with lipolysaccaride (LPS). Results The optimal reference genes for comparing gene expression data between normal and diseased infrapatella fat pad were RPL13A and YWHAZ (M = 0.56). The ideal reference genes for comparing normal and osteoarthritic (OA) cartilage were RPL13A and SDHA (M = 0.57). The best reference genes for comparing normal and ruptured canine cranial cruciate ligament were B2M and TBP (M = 0.59). The best reference genes for normalising gene expression data from normal and LPS stimulated cell lines were SDHA and YWHAZ (K6) or SDHA and HMBS (DH82), which had expression stability (M) values of 0.05 (K6) and 0.07 (DH82) respectively. The number of reference genes required to reduce pairwise variation (V) to <0.20 was 4 for cell lines, 5 for cartilage, 7 for cranial cruciate ligament and 8 for fat tissue. Reference gene stability was not related to the level of gene expression. Conclusion The reference genes demonstrating the most stable expression within each different canine articular tissue were identified, but no single reference gene was identified as having stable expression in all different tissue types. This study underlines the necessity to select reference genes on the basis of tissue and disease specific expression profile evaluation and highlights the requirement for the identification of new reference genes with greater expression stability for use in canine articular tissue gene expression studies.
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Affiliation(s)
- Duncan Ayers
- Centre for Integrated Genomic Medical Research, The Manchester Interdisciplinary Biocentre, University of Manchester, M1 7ND, UK
| | - Dylan N Clements
- Centre for Integrated Genomic Medical Research, The Manchester Interdisciplinary Biocentre, University of Manchester, M1 7ND, UK
- Musculoskeletal Diseases Research Group, Faculty of Veterinary Science, University of Liverpool. UK
| | - Fiona Salway
- Centre for Integrated Genomic Medical Research, The Manchester Interdisciplinary Biocentre, University of Manchester, M1 7ND, UK
| | - Philip JR Day
- Centre for Integrated Genomic Medical Research, The Manchester Interdisciplinary Biocentre, University of Manchester, M1 7ND, UK
- ISAS – Institute for Analytical Sciences, Bunsen-Kirchhoff-Str. 11, 44139 Dortmund, Germany
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