1
|
Gokhale S, Victor E, Tsai J, Spirollari E, Matracz B, Takatsuka S, Jung J, Kitamura D, Xie P. Upregulated Expression of the IL-9 Receptor on TRAF3-Deficient B Lymphocytes Confers Ig Isotype Switching Responsiveness to IL-9 in the Presence of Antigen Receptor Engagement and IL-4. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2023; 210:1059-1073. [PMID: 36883978 PMCID: PMC10073299 DOI: 10.4049/jimmunol.2200563] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Accepted: 02/06/2023] [Indexed: 03/09/2023]
Abstract
The pleiotropic cytokine IL-9 signals to target cells by binding to a heterodimeric receptor consisting of the unique subunit IL-9R and the common subunit γ-chain shared by multiple cytokines of the γ-chain family. In the current study, we found that the expression of IL-9R was strikingly upregulated in mouse naive follicular B cells genetically deficient in TNFR-associated factor 3 (TRAF3), a critical regulator of B cell survival and function. The highly upregulated IL-9R on Traf3-/- follicular B cells conferred responsiveness to IL-9, including IgM production and STAT3 phosphorylation. Interestingly, IL-9 significantly enhanced class switch recombination to IgG1 induced by BCR crosslinking plus IL-4 in Traf3-/- B cells, which was not observed in littermate control B cells. We further demonstrated that blocking the JAK-STAT3 signaling pathway abrogated the enhancing effect of IL-9 on class switch recombination to IgG1 induced by BCR crosslinking plus IL-4 in Traf3-/- B cells. Our study thus revealed, to our knowledge, a novel pathway that TRAF3 suppresses B cell activation and Ig isotype switching by inhibiting IL-9R-JAK-STAT3 signaling. Taken together, our findings provide (to our knowledge) new insights into the TRAF3-IL-9R axis in B cell function and have significant implications for the understanding and treatment of a variety of human diseases involving aberrant B cell activation such as autoimmune disorders.
Collapse
Affiliation(s)
- Samantha Gokhale
- Department of Cell Biology and Neuroscience, Rutgers University, Piscataway, New Jersey 08854
- Graduate Program in Cellular and Molecular Pharmacology, Rutgers University, Piscataway, New Jersey 08854
| | - Eton Victor
- Department of Cell Biology and Neuroscience, Rutgers University, Piscataway, New Jersey 08854
| | - Jemmie Tsai
- Department of Cell Biology and Neuroscience, Rutgers University, Piscataway, New Jersey 08854
| | - Eris Spirollari
- Department of Cell Biology and Neuroscience, Rutgers University, Piscataway, New Jersey 08854
| | - Brygida Matracz
- Department of Cell Biology and Neuroscience, Rutgers University, Piscataway, New Jersey 08854
| | - Shogo Takatsuka
- Division of Molecular Biology, Research Institute for Biomedical Sciences (RIBS), Tokyo University of Science, Noda, Japan
| | - Jaeyong Jung
- Department of Cell Biology and Neuroscience, Rutgers University, Piscataway, New Jersey 08854
- Graduate Program in Cellular and Molecular Pharmacology, Rutgers University, Piscataway, New Jersey 08854
| | - Daisuke Kitamura
- Division of Molecular Biology, Research Institute for Biomedical Sciences (RIBS), Tokyo University of Science, Noda, Japan
| | - Ping Xie
- Department of Cell Biology and Neuroscience, Rutgers University, Piscataway, New Jersey 08854
- Rutgers Cancer Institute of New Jersey
| |
Collapse
|
2
|
Cheung S, Xie P, Rosenwaks Z, Palermo GD. Profiling the male germline genome to unravel its reproductive potential. Fertil Steril 2023; 119:196-206. [PMID: 36379263 PMCID: PMC9898105 DOI: 10.1016/j.fertnstert.2022.11.006] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Revised: 10/28/2022] [Accepted: 11/07/2022] [Indexed: 11/15/2022]
Abstract
OBJECTIVE To identify specific germline mutations related to sperm reproductive competence, in couples with unexplained infertility. DESIGN In this retrospective study, couples were divided according to whether they had successful intracytoplasmic sperm injection outcomes (fertile) or not (infertile). Ancillary sperm function tests were performed on ejaculates, and whole exome sequencing was performed on spermatozoal DNA. Sperm aneuploidy and gene mutation profiles were compared between the 2 cohorts as well as according to the specific reasons for reproductive failure. SETTING Center for reproductive medicine at a major academic medical center. PATIENT(S) Thirty-one couples with negative infertility workups and normal semen parameters. INTERVENTION(S) Couples with mutations on fertilization- or embryo development-related genes were subsequently treated by assisted gamete treatment or microfluidics, respectively. MAIN OUTCOME MEASURE(S) Intracytoplasmic sperm injection cycle outcomes including fertilization, clinical pregnancy, and delivery rates. RESULT(S) Sperm aneuploidy was lower in the fertile group (4.0% vs. 8.4%). Spermatozoa from both cohorts displayed mutations associated with sperm-egg fusion (ADAM3A) and acrosomal development (SPACA1), regardless of reproductive outcome. The infertile cohort was then categorized according to the reasons for reproductive failure: absent fertilization, poor early embryo development, implantation failure, or pregnancy loss. Spermatozoa from the fertilization failure subgroup (n = 4) had negligible PLCζ presence (10% ± 9%) and gene mutations (PLCZ1, PIWIL1, ADAM15) indicating a sperm-related oocyte-activating deficiency. These couples were successfully treated by assisted gamete treatment in their subsequent cycles. Spermatozoa from the poor early embryo development subgroup (n = 5) had abnormal centrosomes (45.9% ± 5%), and displayed mutations impacting centrosome integrity (HAUS1) and spindle/microtubular stabilization (KIF4A, XRN1). Microfluidic sperm processing subsequently yielded a term pregnancy. Spermatozoa from the implantation failure subgroup (n = 7) also had abnormal centrosomes (53.1% ± 13%) and carried mutations affecting embryonic implantation (IL9R) and microtubule and centrosomal integrity (MAP1S, SUPT5H, PLK4), whereas those from the pregnancy loss subgroup (n = 5) displayed mutations on genes involved in trophoblast development (NLRP7), cell cycle regulation (MARK4, TRIP13, DAB2IP, KIF1C), and recurrent miscarriage (TP53). CONCLUSION(S) By assessing the sperm genome, we identified specific germline mutations related to various reproductive processes. This information may clarify elusive factors underlying reproductive competence and enhance treatment for couples with unexplained infertility.
Collapse
Affiliation(s)
- Stephanie Cheung
- The Ronald O. Perelman and Claudia Cohen Center for Reproductive Medicine, Weill Cornell Medicine, New York, New York
| | - Philip Xie
- The Ronald O. Perelman and Claudia Cohen Center for Reproductive Medicine, Weill Cornell Medicine, New York, New York
| | - Zev Rosenwaks
- The Ronald O. Perelman and Claudia Cohen Center for Reproductive Medicine, Weill Cornell Medicine, New York, New York
| | - Gianpiero D Palermo
- The Ronald O. Perelman and Claudia Cohen Center for Reproductive Medicine, Weill Cornell Medicine, New York, New York.
| |
Collapse
|
3
|
Xp;Yq Unbalanced Translocation with Pseudoautosomal Region Aberrations in a Natural Two-Generation Transmission. BIOMED RESEARCH INTERNATIONAL 2020; 2020:4976204. [PMID: 33344636 PMCID: PMC7732387 DOI: 10.1155/2020/4976204] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Revised: 11/12/2020] [Accepted: 11/23/2020] [Indexed: 12/03/2022]
Abstract
Translocations involving X and Y chromosomes rarely occur in humans and may affect reproductive function. We investigated an Xp:Yq unbalanced translocation with pseudoautosomal region (PAR) aberrations in a natural two-generation transmission. We report the case of an azoospermic male and his fertile mother without any other abnormal clinical phenotypes, except for short stature. Cytogenetic methods, including karyotyping and fluorescence in situ hybridization (FISH), revealed the translocation. Chromosomal microarray comparative genomic hybridization (array-CGH) was used to investigate the regions of Xp partial deletion and Yq partial duplication. Final chromosome karyotypes in the peripheral blood of the infertile male and his mother were 46,Y,der(X)t(X;Y)(p22.33;q11.22) and 46,X,der(X)t(X;Y)(p22.33;q11.22), respectively. Short-stature-homeobox gene deletion was responsible for the short stature in both subjects. PAR aberrations and AZFc duplication may be a direct genetic risk factor for spermatogenesis. This report further supports the use of routine karyotype analysis, FISH-based technology, and array-CGH analysis to identify derivative chromosomes in a complex rearrangement.
Collapse
|
4
|
Kwapisz M, Morillon A. Subtelomeric Transcription and its Regulation. J Mol Biol 2020; 432:4199-4219. [PMID: 32035903 PMCID: PMC7374410 DOI: 10.1016/j.jmb.2020.01.026] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2019] [Revised: 01/14/2020] [Accepted: 01/14/2020] [Indexed: 12/13/2022]
Abstract
The subtelomeres, highly heterogeneous repeated sequences neighboring telomeres, are transcribed into coding and noncoding RNAs in a variety of organisms. Telomereproximal subtelomeric regions produce non-coding transcripts i.e., ARRET, αARRET, subTERRA, and TERRA, which function in telomere maintenance. The role and molecular mechanisms of the majority of subtelomeric transcripts remain unknown. This review depicts the current knowledge and puts into perspective the results obtained in different models from yeasts to humans.
Collapse
Affiliation(s)
- Marta Kwapisz
- Laboratoire de Biologie Moléculaire Eucaryote, Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, UPS, France
| | - Antonin Morillon
- ncRNA, Epigenetic and Genome Fluidity, CNRS UMR 3244, Sorbonne Université, PSL University, Institut Curie, Centre de Recherche, 26 rue d'Ulm, 75248, Paris, France.
| |
Collapse
|
5
|
Young E, Abid HZ, Kwok PY, Riethman H, Xiao M. Comprehensive Analysis of Human Subtelomeres by Whole Genome Mapping. PLoS Genet 2020; 16:e1008347. [PMID: 31986135 PMCID: PMC7004388 DOI: 10.1371/journal.pgen.1008347] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Revised: 02/06/2020] [Accepted: 10/15/2019] [Indexed: 12/03/2022] Open
Abstract
Detailed comprehensive knowledge of the structures of individual long-range telomere-terminal haplotypes are needed to understand their impact on telomere function, and to delineate the population structure and evolution of subtelomere regions. However, the abundance of large evolutionarily recent segmental duplications and high levels of large structural variations have complicated both the mapping and sequence characterization of human subtelomere regions. Here, we use high throughput optical mapping of large single DNA molecules in nanochannel arrays for 154 human genomes from 26 populations to present a comprehensive look at human subtelomere structure and variation. The results catalog many novel long-range subtelomere haplotypes and determine the frequencies and contexts of specific subtelomeric duplicons on each chromosome arm, helping to clarify the currently ambiguous nature of many specific subtelomere structures as represented in the current reference sequence (HG38). The organization and content of some duplicons in subtelomeres appear to show both chromosome arm and population-specific trends. Based upon these trends we estimate a timeline for the spread of these duplication blocks.
Collapse
Affiliation(s)
- Eleanor Young
- School of Biomedical Engineering, Drexel University, Philadelphia, PA, United States of America
| | - Heba Z. Abid
- School of Biomedical Engineering, Drexel University, Philadelphia, PA, United States of America
| | - Pui-Yan Kwok
- Cardiovascular Research Institute, University of California–San Francisco, San Francisco, CA, United States of America
- Department of Dermatology, University of California–San Francisco, San Francisco, CA, United States of America
- Institute for Human Genetics, University of California–San Francisco, San Francisco, CA, United States of America
| | - Harold Riethman
- Medical Diagnostic & Translational Sciences, Old Dominium University, Norfolk, VA, United States of America
| | - Ming Xiao
- School of Biomedical Engineering, Drexel University, Philadelphia, PA, United States of America
- Institute of Molecular Medicine and Infectious Disease in the School of Medicine, Drexel University, Philadelphia, PA, United States of America
| |
Collapse
|
6
|
Molecular Characterization of Mosaicism for a Small Supernumerary Marker Chromosome Derived from Chromosome Y in an Infertile Male with Apparently Normal Phenotype: A Case Report and Literature Review. BIOMED RESEARCH INTERNATIONAL 2019; 2019:9398275. [PMID: 31828149 PMCID: PMC6885818 DOI: 10.1155/2019/9398275] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/09/2019] [Revised: 10/14/2019] [Accepted: 11/01/2019] [Indexed: 01/31/2023]
Abstract
Small supernumerary marker chromosomes (sSMCs), equal in size or smaller than chromosome 20 of the same metaphase, can hardly be identified through traditional banding technique. They are usually associated with intelligent disability, growth retardation, and infertility, but the genotype-phenotype correlations are still complicated for their complex origins and constitutions. Herein, we identified a 26-year-old Chinese infertile male who carried a mosaic sSMC and was diagnosed as severe oligospermia. The G-banding analysis initially described his karyotype as mos 47, XY, +mar[32]/46, XY[18]. The chromosomal microarray analysis results showed a 25.5 Mb gain in Yp11.31q11.23 and a 0.15 Mb loss in Yq12. Two SRY signals were discovered in the “seemingly” normal chromosome Y in both cell lines using SRY probe: one normal SRY was located on the distal tip of the short arm of chromosome Y while the other SRY was located on the terminal of long arm in the same chromosome Y. The sSMC(Y) was finally identified as der(Y) (pter ⟶ q11.23) (SRY-). To our knowledge, the chromosomal Y anomalies, SRY gene translocated from der(Y) (pter ⟶ q11.23) to qter of normal chromosome Y, were not reported before. Our findings indicated that the mosaic presence of sSMC(Y) may be the main cause of severe oligospermia although no other apparent abnormalities were observed in the proband. Further research on association between sSMC(Y) and spermatogenesis impairment should be investigated. It is recommended measures of traditional and molecular cytogenetic analysis should be taken to determine the origins and constitutions of sSMC so as to offer more appropriate genetic counseling for the infertile sSMC carriers.
Collapse
|
7
|
Lin JX, Leonard WJ. The Common Cytokine Receptor γ Chain Family of Cytokines. Cold Spring Harb Perspect Biol 2018; 10:cshperspect.a028449. [PMID: 29038115 DOI: 10.1101/cshperspect.a028449] [Citation(s) in RCA: 112] [Impact Index Per Article: 18.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Interleukin (IL)-2, IL-4, IL-7, IL-9, IL-15, and IL-21 form a family of cytokines based on their sharing the common cytokine receptor γ chain (γc), which was originally discovered as the third receptor component of the IL-2 receptor, IL-2Rγ. The IL2RG gene is located on the X chromosome and is mutated in humans with X-linked severe combined immunodeficiency (XSCID). The breadth of the defects in XSCID could not be explained solely by defects in IL-2 signaling, and it is now clear that γc is a shared receptor component of the six cytokines noted above, making XSCID a disease of defective cytokine signaling. Janus kinase (JAK)3 associates with γc, and JAK3-deficient SCID phenocopies XSCID, findings that served to stimulate the development of JAK3 inhibitors as immunosuppressants. γc family cytokines collectively control broad aspects of lymphocyte development, growth, differentiation, and survival, and these cytokines are clinically important, related to allergic and autoimmune diseases and cancer as well as immunodeficiency. In this review, we discuss the actions of these cytokines, their critical biological roles and signaling pathways, focusing mainly on JAK/STAT (signal transducers and activators of transcription) signaling, and how this information is now being used in clinical therapeutic efforts.
Collapse
Affiliation(s)
- Jian-Xin Lin
- Laboratory of Molecular Immunology and the Immunology Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland 20892-1674
| | - Warren J Leonard
- Laboratory of Molecular Immunology and the Immunology Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland 20892-1674
| |
Collapse
|
8
|
Young E, Pastor S, Rajagopalan R, McCaffrey J, Sibert J, Mak ACY, Kwok PY, Riethman H, Xiao M. High-throughput single-molecule mapping links subtelomeric variants and long-range haplotypes with specific telomeres. Nucleic Acids Res 2017; 45:e73. [PMID: 28180280 PMCID: PMC5605236 DOI: 10.1093/nar/gkx017] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2016] [Accepted: 02/07/2017] [Indexed: 01/22/2023] Open
Abstract
Accurate maps and DNA sequences for human subtelomere regions, along with detailed knowledge of subtelomere variation and long-range telomere-terminal haplotypes in individuals, are critical for understanding telomere function and its roles in human biology. Here, we use a highly automated whole genome mapping technology in nano-channel arrays to analyze large terminal human chromosome segments extending from chromosome-specific subtelomere sequences through subtelomeric repeat regions to terminal (TTAGGG)n repeat tracts. We establish detailed maps for subtelomere gap regions in the human reference sequence, detect many new large subtelomeric variants and demonstrate the feasibility of long-range haplotyping through segmentally duplicated subtelomere regions. These features make the method a uniquely valuable new tool for improving the quality of genome assemblies in complex DNA regions. Based on single molecule mapping of telomere-terminal DNA fragments, we provide proof of principle for a novel method to estimate telomere lengths linked to distinguishable telomeric haplotypes; this single-telomere genotyping method may ultimately enable delineation of human cis elements involved in telomere length regulation.
Collapse
Affiliation(s)
- Eleanor Young
- Drexel University, School of Biomedical Engineering, Philadelphia, PA, 19104 USA
| | - Steven Pastor
- Drexel University, School of Biomedical Engineering, Philadelphia, PA, 19104 USA
| | | | - Jennifer McCaffrey
- Drexel University, School of Biomedical Engineering, Philadelphia, PA, 19104 USA
| | - Justin Sibert
- Drexel University, School of Biomedical Engineering, Philadelphia, PA, 19104 USA
| | - Angel C Y Mak
- Cardiovascular Research Institute, University of California, San Francisco, CA, 94158 USA
| | - Pui-Yan Kwok
- Cardiovascular Research Institute, University of California, San Francisco, CA, 94158 USA
| | - Harold Riethman
- Old Dominion University, Medical Diagnostic and Translational Sciences, Norfolk, VA, 23529 USA
| | - Ming Xiao
- Drexel University, School of Biomedical Engineering, Philadelphia, PA, 19104 USA.,Institute of Molecular Medicine and Infectious Disease, School of Medicine, Drexel University, Philadelphia, PA, 19102 USA
| |
Collapse
|
9
|
Behjati F, Ghasemi Firouzabadi S, Sajedi F, Kahrizi K, Najafi M, Ebrahimizade Ghasemlou B, Shafeghati Y, Behnia F, Mohammadi Arya AR, Karimi H, Hadipour F, Hadipour Z, Jamali P, Kariminejad R, Darvish H, Bahman I, Bagherizadeh E, Najmabadi H, Vameghi R. Identification of Chromosome Abnormalities in Subtelomeric Regions Using Multiplex Ligation Dependent Probe Amplification (MLPA) Technique in 100 Iranian Patients With Idiopathic Mental Retardation. IRANIAN RED CRESCENT MEDICAL JOURNAL 2014; 15:e8221. [PMID: 24693374 PMCID: PMC3950786 DOI: 10.5812/ircmj.8221] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 10/09/2012] [Accepted: 06/14/2013] [Indexed: 11/16/2022]
Abstract
Background Mental retardation/Developmental delay (MR/DD) is present in 1 - 3% of the general
population (1, 2). MR is defined as a significant impairment of both cognitive (IQ <
70) and social adaptive functions, with onset before 18 years of age. Objectives The purpose was to determine the results of subtelomeric screening by the Multiplex
Ligation Dependent Probe Amplification (MLPA) Technique in 100 selected patients with
idiopathic mental retardation (IMR) in Iran. Materials and Methods A number of 100 patients with IMR, normal karyotypes and negative fragile-X and
metabolic tests were screened for subtelomeric abnormalities using MLPA technique. Results Nine of 100 patients showed subtelomeric abnormalities with at least one of the two
MLPA kits. Deletion in a single region was found in 3 patients, and in two different
subtelomeric regions in 1 patient. Duplication was only single and was present in 2
patients. Three patients were found to have both a deletion and duplication.MLPA testing
in the parental samples of 7 patients which was accessible showed that 4 patients were
de novo, 2 patients had inherited from a clinically normal mother, and one had inherited
from a clinically normal father. Screening with the two MLPA kits (SALSA P036 and SALSA
P070) proved abnormality in only five of the 9 patients. Conclusions So, the prevalence rate of abnormal subtelomeres using MLPA technique in patients with
idiopathic MR in our study was 5 - 9%, the higher limit referring to the positive
results of one of the two MLPA kits, and the lower limit representing the results of
positive double-checking with the two MLPA kits.
Collapse
Affiliation(s)
- Farkhondeh Behjati
- Genetics Research Center, University of Social Welfare and
Rehabilitation Sciences, Tehran, IR Iran
| | | | - Firoozeh Sajedi
- Pediatric Neurorehabilitation Research Center, University
of Social Welfare and Rehabilitation Sciences, Tehran, IR Iran
| | - Kimia Kahrizi
- Genetics Research Center, University of Social Welfare and
Rehabilitation Sciences, Tehran, IR Iran
| | - Mostafa Najafi
- Genetics Research Center, University of Social Welfare and
Rehabilitation Sciences, Tehran, IR Iran
| | | | - Yousef Shafeghati
- Genetics Research Center, University of Social Welfare and
Rehabilitation Sciences, Tehran, IR Iran
- Sarem Cell Research Center, Sarem Hospital, Tehran, IR
Iran
| | - Fatemeh Behnia
- Department of Occupational Therapy, University of Social
Welfare and Rehabilitation Sciences, Tehran, IR Iran
| | | | | | | | - Zahra Hadipour
- Sarem Cell Research Center, Sarem Hospital, Tehran, IR
Iran
| | | | | | - Hossein Darvish
- Department of Medical Genetics, Shahid Beheshti University
of Medical Sciences, Tehran, IR Iran
| | - Ideh Bahman
- Genetics Research Center, University of Social Welfare and
Rehabilitation Sciences, Tehran, IR Iran
| | | | - Hossein Najmabadi
- Genetics Research Center, University of Social Welfare and
Rehabilitation Sciences, Tehran, IR Iran
| | - Roshanak Vameghi
- Pediatric Neurorehabilitation Research Center, University
of Social Welfare and Rehabilitation Sciences, Tehran, IR Iran
- Corresponding author: Roshanak Vameghi, Pediatric
Neurorehabilitation Research Center, University of Social Welfare and Rehabilitation
Sciences, Tehran, IR Iran. Tel/Fax: +9821-22180099, E-mail:
| |
Collapse
|
10
|
Heim D, Cornils K, Schulze K, Fehse B, Lohse AW, Brümmendorf TH, Wege H. Retroviral insertional mutagenesis in telomerase-immortalized hepatocytes identifies RIPK4 as novel tumor suppressor in human hepatocarcinogenesis. Oncogene 2014; 34:364-72. [DOI: 10.1038/onc.2013.551] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2013] [Revised: 09/30/2013] [Accepted: 11/03/2013] [Indexed: 12/28/2022]
|
11
|
Abstract
CD4(+) T helper (Th) cells act as important regulators of the mammalian adaptive immune response. CD4(+) Th cells were originally characterized as either Th1 or Th2 types, based on the cytokines they produce. Over the past two decades, however, we have attained a much more detailed understanding of CD4(+) T-cell differentiation, functions, and gene expression profiles, which led to the identification of additional types, such as the Th17 and induced regulatory T cells. Recently, researchers have characterized yet another novel and distinct population that exists among these immune-modulatory cells. The 'Th9' cells were first identified as a Th2 subpopulation that produced exceptionally large quantities of the Th2-specific cytokine interleukin 9. However, experimental analysis revealed that Th9 cells had divergent regulatory capabilities and were critically involved in different immune processes. In particular, we now know that Th9 acts as a major contributor to the onset and progression of allergies, especially asthma. Here, we will review the heterogeneity and biology of CD4(+) Th cells and summarize the characteristics known to date of interleukin 9 and Th9 cells to build a framework for better understanding of their roles in disease processes, especially in allergy-induced asthma.
Collapse
Affiliation(s)
- Junchao Xing
- Institute of Immunology PLA, Third Military Medical University, Chongqing 400038, PR China
| | | | | |
Collapse
|
12
|
IL-9: basic biology, signaling pathways in CD4+ T cells and implications for autoimmunity. J Neuroimmune Pharmacol 2009; 5:198-209. [PMID: 20020328 DOI: 10.1007/s11481-009-9186-y] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2009] [Accepted: 11/20/2009] [Indexed: 01/11/2023]
Abstract
CD4(+) T cell subsets play an important role in the adaptive immune response in human autoimmune diseases and in animal models of autoimmunity. In recent years, our knowledge of CD4(+) T cell differentiation has increased significantly, and new subsets continue to be recognized. Of significant importance is the recent discovery of Th9 cells, the CD4 + T cell subset that produces Interleukin-9. IL-9 has largely been regarded as a Th2 cytokine; however, it is now known that under specific conditions, Tregs, Th1, Th17 and the Th9 subset of T cells also produce IL-9. The STAT family of proteins plays a major role in the signaling pathways of these CD4(+)T subsets. Biological actions of IL-9 and the STATs signaling pathways in autoimmune diseases are continuing to be clarified. Investigation of IL-9-producing CD4(+)T cells, and elucidation of the mechanisms of IL-9-induced STATs signaling, in concert with other transcription factors, will provide a better understanding of the pathogenesis of various autoimmune diseases.
Collapse
|
13
|
Bottarelli L, Azzoni C, Necchi F, Lagrasta C, Tamburini E, D'Adda T, Pizzi S, Sarli L, Rindi G, Bordi C. Sex chromosome alterations associate with tumor progression in sporadic colorectal carcinomas. Clin Cancer Res 2007; 13:4365-70. [PMID: 17671117 DOI: 10.1158/1078-0432.ccr-06-2736] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
PURPOSE The X and Y chromosomes have been associated with malignancy in different types of human tumors. This study attempts to determine the involvement of X chromosome and pseudoautosomal regions (PAR) in sporadic colorectal carcinogenesis. EXPERIMENTAL DESIGN An allelotyping of X chromosome in 20 premalignant and 22 malignant sporadic colorectal tumors (CRC) from female patients and an analysis of losses [loss of heterozygosity (LOH)] on PARs from 44 CRCs and 12 adenomas of male patients were carried out. In male tumors, a fluorescence in situ hybridization analysis was done to identify which sex chromosome was possibly lost. RESULTS The LOH frequency in female CRCs was 46% with higher incidence in patients with tumor recurrence than in those who were disease-free (P < 0.01) and with a significant difference from adenomas (11%; P < 0.0001). The LOH rate of PARs in male CRCs was 37% with a frequency significantly higher in patients with recurrence (P < 0.03). These results were maintained also when data from PARs of all 66 male and female patients were cumulated (P < 0.05). LOH in PARs was significantly correlated with LOH at 5q (P < 0.01) and 18q (P < 0.01), early and late events, respectively, in colorectal carcinogenesis. Fluorescence in situ hybridization analysis in male patients with extensive PAR LOH revealed a preferential loss of the Y chromosome. CONCLUSIONS Our data suggest a role for sex chromosome deletions in the malignant progression of sporadic CRCs and support the presence in the PARs of putative tumor suppressor genes involved in the progression of human sporadic CRCs.
Collapse
Affiliation(s)
- Lorena Bottarelli
- Department of Pathology and Laboratory Medicine, Medical School, Parma University, Parma, Italy
| | | | | | | | | | | | | | | | | | | |
Collapse
|
14
|
Velagaleti GVN, Robinson SS, Rouse BM, Tonk VS, Lockhart LH. Subtelomeric rearrangements in idiopathic mental retardation. Indian J Pediatr 2005; 72:679-85. [PMID: 16131774 DOI: 10.1007/bf02724077] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/08/2022]
Abstract
OBJECTIVE To estimate the frequency of subtelomeric rearrangements in patients with sporadic and non-syndromic idiopathic mental retardation (IMR). METHODS A total of 18 IMR patients were taken for the study. Selection criteria included no known syndromes or chromosomes abnormalities and known causes of IMR. All patients signed an informed consent to participate. Chromosome analysis was carried out on all patients to rule out gross chromosome abnormalities. Lymphocyte cultures were initiated and harvested using standard protocols. For fluorescence in situ hybridization (FISH), Chromoprobe Multiprobe-T system was used. This system consists of 24 embossed areas with each area having one reversibly bound subtelomere probe for a specific chromosome. The subtelomere probes were differentially labeled with green fluorescence for short arm and orange for the long arm. Hybridization, washing and staining are done using standard protocols. A minimum of 5 metaphases were analyzed per chromosome per patient. RESULTS A total of 2 subtelomeric rearrangements were detected (11.1%). Case 1 involved a 17-year-old with severe MR, profound deafness and dysmorphic features with reciprocal translocation t(3;7)(q26.2; p15.1). The second case involved a 4.6-year-old with mild developmental delay and a terminal deletion of the long arm of chromosome 2, del(2) (q37.3). The frequency of abnormalities detected in our study is in agreement with published reports. CONCLUSION Subtelomeric screening with FISH is a useful tool for investigation of IMR, however, it is not cost effective in all cases. Conventional chromosome analysis coupled with targeted FISH testing might be the optimal strategy for investigation of IMR.
Collapse
|
15
|
|
16
|
Tufarelli C, Hardison R, Miller W, Hughes J, Clark K, Ventress N, Frischauf AM, Higgs DR. Comparative analysis of the alpha-like globin clusters in mouse, rat, and human chromosomes indicates a mechanism underlying breaks in conserved synteny. Genome Res 2004; 14:623-30. [PMID: 15060003 PMCID: PMC383306 DOI: 10.1101/gr.2143604] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
We have sequenced and fully annotated a 65,871-bp region of mouse Chromosome 17 including the Hba-ps4 alpha-globin pseudogene. Comparative sequence analysis with the functional alpha-globin loci at human Chromosome 16p13.3 and mouse Chromosome 11 shows that this segment of mouse Chromosome 17 contains a group of three alpha-like pseudogenes (Hba-psm-Hba-ps4-Hba-q3), similar to the duplicated sets found at the functional mouse cluster on Chromosome 11. In addition, exons 7 to 12 of the mLuc7L gene are present just downstream from the pseudogene cluster, indicating that this clone contains the region in which human 16p13.3 switches in synteny between mouse Chromosomes 11 and 17. Comparison of the sequences around the alpha-like clusters on the two mouse chromosomes reveals the presence of conserved tandem repeats. We propose that these repetitive elements have played a role in the fragmentation of the mouse alpha cluster during evolution.
Collapse
Affiliation(s)
- Cristina Tufarelli
- MRC Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, Headington, Oxford OX3 9DS, UK
| | | | | | | | | | | | | | | |
Collapse
|
17
|
Dennehey BK, Gutches DG, McConkey EH, Krauter KS. Inversion, duplication, and changes in gene context are associated with human chromosome 18 evolution. Genomics 2004; 83:493-501. [PMID: 14962675 DOI: 10.1016/j.ygeno.2003.08.017] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2003] [Accepted: 08/19/2003] [Indexed: 12/11/2022]
Abstract
Human chromosome 18 differs from its homologues in the great apes by a pericentric inversion. We have identified a chimpanzee bacterial artificial chromosome that spans a region where a break is likely to have occurred in a human progenitor and have characterized the corresponding regions in both chimpanzees and humans. Interspecies sequence comparisons indicate that the ancestral break occurred between the genes ROCK1 and USP14. In humans, the inversion places ROCK1 near centromeric heterochromatin and USP14 adjacent to highly repetitive subtelomeric repeats. In addition, we provide evidence for a human segmental duplication that may have provided a mechanism for the inversion.
Collapse
Affiliation(s)
- Briana K Dennehey
- Department of Molecular, Cellular and Developmental Biology, University of Colorado, Boulder, CO 80309, USA
| | | | | | | |
Collapse
|
18
|
Riethman H, Ambrosini A, Castaneda C, Finklestein J, Hu XL, Mudunuri U, Paul S, Wei J. Mapping and initial analysis of human subtelomeric sequence assemblies. Genome Res 2004; 14:18-28. [PMID: 14707167 PMCID: PMC314271 DOI: 10.1101/gr.1245004] [Citation(s) in RCA: 80] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Physical mapping data were combined with public draft and finished sequences to derive subtelomeric sequence assemblies for each of the 41 genetically distinct human telomere regions. Sequence gaps that remain on the reference telomeres are generally small,well-defined,and for the most part,restricted to regions directly adjacent to the terminal (TTAGGG)n tract. Of the 20.66 Mb of subtelomeric DNA analyzed, 3.01 Mb are subtelomeric repeat sequences (Srpt),and an additional 2.11 Mb are segmental duplications. The subtelomeric sequence assemblies are enriched >25-fold in short,internal (TTAGGG)n-like sequences relative to the rest of the genome; a total of 114 (TTAGGG)n-like islands were found,55 within Srpt regions,35 within one-copy regions,11 at one-copy/Srpt or Srpt/segmental duplication boundaries,and 13 at the telomeric ends of assemblies. Transcripts were annotated in each assembly,noting their mapping coordinates relative to their respective telomere and whether they originate in duplicated DNA or single-copy DNA. A total of 697 transcripts were found in 15.53 Mb of one-copy DNA,76 transcripts in 2.11 Mb of segmentally duplicated DNA,and 168 transcripts in 3.01 Mb of Srpt sequence. This overall transcript density is similar (within approximately 10%) to that found genome-wide. Zinc finger-containing genes and olfactory receptor genes are duplicated within and between multiple telomere regions.
Collapse
Affiliation(s)
- Harold Riethman
- The Wistar Institute, Philadelphia, Pennsylvania 19104, USA.
| | | | | | | | | | | | | | | |
Collapse
|
19
|
Frints SGM, Jun L, Fryns JP, Devriendt K, Teulingkx R, Van den Berghe L, De Vos B, Borghgraef M, Chelly J, Des Portes V, Van Bokhoven H, Hamel B, Ropers HH, Kalscheuer V, Raynaud M, Moraine C, Marynen P, Froyen G. Inv(X)(p21.1;q22.1) in a man with mental retardation, short stature, general muscle wasting, and facial dysmorphism: clinical study and mutation analysis of the NXF5 gene. Am J Med Genet A 2003; 119A:367-74. [PMID: 12784308 DOI: 10.1002/ajmg.a.20195] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
We describe a 59-year-old male (patient A059) with moderate to severe mental retardation (MR) and a pericentric inversion of the X-chromosome: inv(X)(p21.1;q22.1). He had short stature, pectus excavatum, general muscle wasting, and facial dysmorphism. Until now, no other patients with similar clinical features have been described in the literature. Molecular analysis of both breakpoints led to the identification of a novel "Nuclear RNA export factor" (NXF) gene cluster on Xq22.1. Within this cluster, the NXF5 gene was interrupted with subsequent loss of gene expression. Hence, mutation analysis of the NXF5 and its neighboring homologue, the NXF2 gene was performed in 45 men with various forms of syndromic X-linked MR (XLMR) and in 70 patients with nonspecific XLMR. In the NXF5 gene four nucleotide changes: one intronic, two silent, and one missense (K23E), were identified. In the NXF2 gene two changes (one intronic and one silent) were found. Although none of these changes were causative mutations, we propose that NXF5 is a good candidate gene for this syndromic form of XLMR, given the suspected role of NXF proteins is within mRNA export/transport in neurons. Therefore, mutation screening of the NXF gene family in phenotypically identical patients is recommended.
Collapse
MESH Headings
- Abnormalities, Multiple/diagnosis
- Abnormalities, Multiple/genetics
- Active Transport, Cell Nucleus
- Base Sequence
- Chromosome Breakage
- Chromosome Inversion
- Chromosomes, Human, X
- Cloning, Molecular
- Gene Expression
- Humans
- In Situ Hybridization, Fluorescence
- Male
- Mental Retardation, X-Linked/genetics
- Mental Retardation, X-Linked/metabolism
- Middle Aged
- Molecular Sequence Data
- Mutation/genetics
- Nuclear Proteins/genetics
- Nucleocytoplasmic Transport Proteins
- RNA/metabolism
- RNA-Binding Proteins/genetics
- Sequence Homology, Nucleic Acid
- Syndrome
Collapse
Affiliation(s)
- Suzanna G M Frints
- Human Genome Laboratory and Flanders Interuniversity Institute for Biotechnology, University of Leuven, Leuven, Belgium
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
20
|
Charchar FJ, Svartman M, El-Mogharbel N, Ventura M, Kirby P, Matarazzo MR, Ciccodicola A, Rocchi M, D'Esposito M, Graves JAM. Complex events in the evolution of the human pseudoautosomal region 2 (PAR2). Genome Res 2003; 13:281-6. [PMID: 12566406 PMCID: PMC420362 DOI: 10.1101/gr.390503] [Citation(s) in RCA: 55] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
The 320-kb human pseudoautosomal region 2 (PAR2) at the tips of the long arms of the X and Y chromosomes is thought to have been duplicated onto the Y chromosome recently in primate evolution. The four genes within PAR2 have been proposed to constitute two zones with different base ratios and transcription, one of which was added recently to the X chromosome. To test this hypothesis, we cloned and mapped PAR2 genes in other species, the lemur, the cat, and a marsupial, the tammar wallaby. None of the human PAR2 genes colocalized with human PAR1 genes in the marsupial genome, confirming that the human PAR1 and PAR2 evolved independently. Of the four PAR2 genes, only SYBL1 was located on the X chromosome in all species, including marsupials, so it was part of the ancient X. HSPRY3 localized to the X in all the eutherians, but not marsupial, so it must have been added to the X 80-130 million years ago. CXYorf1 was present on the X in primates and also in mouse, but autosomal in wallaby, suggesting a later addition 70-130 million years ago, and IL9R was on the X only in primate, suggesting addition 60-70 million years ago. The results therefore demonstrate that at least two independent additions were necessary for PAR2 evolution. The present gene order on the human X also requires two inversions. The complicated evolutionary pathway supports the hypothesis that terminal interchromosomal rearrangements are common in regions unpaired at meiosis.
Collapse
Affiliation(s)
- Fadi J Charchar
- Department of Genetics, La Trobe University, Bundoora, Victoria 3086, Australia.
| | | | | | | | | | | | | | | | | | | |
Collapse
|
21
|
de Ravel TJL, Fryns JP, Van Driessche J, Vermeesch JR. Complex chromosome re-arrangement 45,X,t(Y;9) in a girl with sex reversal and mental retardation. ACTA ACUST UNITED AC 2003; 124A:259-62. [PMID: 14708098 DOI: 10.1002/ajmg.a.20372] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
A girl with mental retardation and multiple minor anomalies was found to have a complex chromosome 9p re-arrangement comprising a deleted, translocated Y chromosome, a deletion of the sex reversal gene region (DMRT1) at 9p, together with an inverted duplication of the more proximal part of 9p. The karyotype was 45,X,der(Y;9)(Ypter-->Yq12::9p21.1-->9p22.2::9p22.2-->9qter) de novo. The karyotypic male, phenotypic female had a dysgerminoma of the left dysplastic ovary. The patient had typical 'trisomy 9p' syndrome, and we propose that the critical region for this phenotype is located between 9p22.1 and 9p22.2.
Collapse
Affiliation(s)
- T J L de Ravel
- Center for Human Genetics, University of Leuven, Belgium
| | | | | | | |
Collapse
|
22
|
van Geel M, Dickson MC, Beck AF, Bolland DJ, Frants RR, van der Maarel SM, de Jong PJ, Hewitt JE. Genomic analysis of human chromosome 10q and 4q telomeres suggests a common origin. Genomics 2002; 79:210-7. [PMID: 11829491 DOI: 10.1006/geno.2002.6690] [Citation(s) in RCA: 100] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
The subtelomeric region of human chromosome 4q contains the locus for facioscapulohumeral muscular dystrophy (FSHD). The FSHD mutation is a deletion within an array of 3.3-kb tandem repeats (D4Z4). The disease mechanism is unknown but is postulated to involve position effect. A closely related 3.3-kb array on chromosome 10qter, in contrast, is not associated with a disease phenotype. We show here that the 4q homology on chromosome 10 is not confined to the 3.3-kb repeats but extends both proximally (42 kb) and distally to include the telomere. We have also identified the most distal expressed gene on 10q known so far, mapping only 96 kb from the 3.3-kb repeat array. A 4q variant has also been identified; there is 92%nucleotide identity between the two 4q forms, 4qA and 4qB. The 4qter and 10qter forms show homology to other chromosome ends, including 4p, 21q, and 22q, and these regions may represent a relatively common subtelomeric domain.
Collapse
Affiliation(s)
- Michel van Geel
- Department of Cancer Genetics, Roswell Park Cancer Institute, Buffalo, New York 14263, USA
| | | | | | | | | | | | | | | |
Collapse
|
23
|
Abstract
Subtelomeres are extraordinarily dynamic and variable regions near the ends of chromosomes. They are defined by their unusual structure: patchworks of blocks that are duplicated near the ends of multiple chromosomes. Duplications among subtelomeres have spawned small gene families, making inter-individual variation in subtelomeres a potential source of phenotypic diversity. The ectopic recombination that occurs between subtelomeres might also have a role in reconstituting telomeres in the absence of telomerase. However, the propensity for subtelomeres to interchange is a double-edged sword, as extensive subtelomeric homology can mediate deleterious rearrangements of the ends of chromosomes to cause human disease.
Collapse
Affiliation(s)
- Heather C Mefford
- Division of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA
| | | |
Collapse
|
24
|
van Geel M, Eichler EE, Beck AF, Shan Z, Haaf T, van der Maarel SM, Frants RR, de Jong PJ. A cascade of complex subtelomeric duplications during the evolution of the hominoid and Old World monkey genomes. Am J Hum Genet 2002; 70:269-78. [PMID: 11731935 PMCID: PMC419983 DOI: 10.1086/338307] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2001] [Accepted: 10/23/2001] [Indexed: 11/03/2022] Open
Abstract
Subtelomeric duplications of an obscure tubulin "genic" segment located near the telomere of human chromosome 4q35 have occurred at different evolutionary time points within the last 25 million years of the catarrhine (i.e., hominoid and Old World monkey) evolution. The analyses of these segments reported here indicate an exceptional level of evolutionary instability. Substantial intra- and interspecific differences in copy number and distribution are observed among cercopithecoid (Old World monkey) and hominoid genomes. Characterization of the hominoid duplicated segments reveals a strong positional bias within pericentromeric and subtelomeric regions of the genome. On the basis of phylogenetic analysis from predicted proteins and comparisons of nucleotide-substitution rates, we present evidence of a conserved b-tubulin gene among the duplications. Remarkably, the evolutionary conservation has occurred in a nonorthologous fashion, such that the functional copy has shifted its positional context between hominoids and cercopithecoids. We propose that, in a chimpanzee-human common ancestor, one of the paralogous copies assumed the original function, whereas the ancestral copy acquired mutations and eventually became silenced. Our analysis emphasizes the dynamic nature of duplication-mediated genome evolution and the delicate balance between gene acquisition and silencing.
Collapse
Affiliation(s)
- Michel van Geel
- Department of Cancer Genetics, Roswell Park Cancer Institute, Buffalo, NY, USA
| | | | | | | | | | | | | | | |
Collapse
|
25
|
Mah N, Stoehr H, Schulz HL, White K, Weber BH. Identification of a novel retina-specific gene located in a subtelomeric region with polymorphic distribution among multiple human chromosomes. BIOCHIMICA ET BIOPHYSICA ACTA 2001; 1522:167-74. [PMID: 11779631 DOI: 10.1016/s0167-4781(01)00328-1] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The human retina is comprised of a large number of cell types with highly specialized functions that depend on the action of countless genes, many of which are exclusively expressed in the retina. We have isolated a novel retinal gene, termed F379. The transcript was initially identified as a cluster of ESTs derived predominantly from retinal cDNA libraries and its retinal transcription confirmed by Northern blot and RT-PCR. Screening of retinal cDNA libraries yielded four clones that were assembled into a 1188 bp consensus sequence. The putative open reading frame includes an unusual configuration of Alu and MIR repeats and encodes a putative 85 aa peptide with no significant homology to any known protein sequence outside of the Alu and MIR elements. Comparison with genomic sequence determined that F379 consists of three exons and maps to multiple locations throughout the genome, a finding confirmed by PCR screening of a somatic cell hybrid mapping panel. F379 appears to be contained within a region of subtelomeric DNA that is duplicated in a polymorphic distribution to multiple chromosomes. Comparison of interchromosomal sequence variation with the sequences of expressed transcripts suggests that the gene is transcribed in the human retina from at least four different chromosomes.
Collapse
Affiliation(s)
- N Mah
- Institut fuer Humangenetik, Biozentrum, Universitaet Wuerzburg, D-97074, Wuerzburg, Germany
| | | | | | | | | |
Collapse
|
26
|
Abstract
Asthma is a triad of intermittent airway obstruction, bronchial smooth muscle cell hyperreactivity to bronchoconstrictors, and chronic bronchial inflammation. From an aetiological standpoint, asthma is a heterogeneous disease, but often appears as a form of immediate hypersensitivity. Many patients with asthma have other manifestations of atopy, such as rhinitis or eczema. Even among non-atopic patients with asthma, the pathophysiology of airway constriction is similar, raising the hypothesis that alternative mechanisms of mast cell degranulation may underlie the disease. The primary inflammatory lesion of asthma consists of accumulation of CD4(+) T helper type 2 (TH2) lymphocytes and eosinophils in the airway mucosa. TH2 cells orchestrate the asthmatic inflammation through the secretion of a series of cytokines, particularly interleukin 4 (IL-4), IL-13, IL-5, and IL-9. IL-4 is the major factor regulating IgE production by B cells, and is required for optimal TH2 differentiation. However, blocking IL-4 is not sufficient to inhibit the development of asthma in experimental models. In contrast, inhibition of IL-13, another TH2 cytokine whose signal transduction pathway overlaps with that of IL-4, completely blocks airway hyperreactivity in mouse asthma models. IL-5 is a key factor for eosinophilia and could therefore be responsible for some of the tissue damage seen in chronic asthma. IL-9 has pleiotropic activities on allergic mediators such as mast cells, eosinophils, B cells and epithelial cells, and might be a good target for therapeutic interventions. Finally, chemokines, which can be produced by many cell types from inflamed lungs, play a major role in recruiting the mediators of asthmatic inflammation. Genetic studies have demonstrated that multiple genes are involved in asthma. Several genome wide screens point to chromosome 5q31--33 as a major susceptibility locus for asthma and high IgE values. This region includes a cluster of cytokine genes, and genes encoding IL-3, IL-4, IL-5, IL-9, IL-13, granulocyte macrophage colony stimulating factor, and the beta chain of IL-12. Interestingly, for some of these cytokines, a linkage was also established between asthma and their receptor. Another susceptibility locus has been mapped on chromosome 12 in a region that contains other potential candidate cytokine genes, including the gene encoding interferon gamma, the prototypical TH1 cytokine with inhibitory activities for TH2 lymphocytes. Taken together, both experimental and genetic studies point to TH2 cytokines, such as IL-4, IL-13, IL-5, and IL-9, as important targets for therapeutic applications in patients with asthma.
Collapse
Affiliation(s)
- J C Renauld
- Ludwig Institute for Cancer Research and Experimental Medicine Unit, Université Catholique de Louvain, B-1200 Brussels, Belgium.
| |
Collapse
|
27
|
Abstract
The human Y chromosome is strictly paternally inherited and, in most of its length, does not recombine during male meiosis. These features make the Y a very useful genetic marker for different purposes. In the last decade, the Y has been increasingly used to investigate the evolution, migrations and range expansions of modern humans. The possibility to construct highly informative Y chromosome haplotypes has also had a significant impact in forensic studies and paternity testing. All these studies assume that the Y chromosome markers used are selectively neutral. However, recent experimental and statistical analyses suggest that both positive and negative selection are acting on the Y chromosome and, consequently, may influence Y chromosome haplotype distribution in the general population. Current data suggest that the effects of selection on patterns of Y chromosome distribution are minimal, however as interest focuses on biological functions of the Y chromosome which have a major impact on male fitness such as fertility, these assumptions may be challenged. This review briefly describes the genes and biological functions of the human Y chromosome and its use in disentangling the origin and history of human populations. An overview of the role of selection acting on the Y chromosome from the perspective of human population histories and disease is given.
Collapse
Affiliation(s)
- L Quintana-Murci
- Unité d'Immunogénétique Humaine, Institut Nationale de la Santé et de la Recherche Médicale (INSERM) E0021, Institut Pasteur, 25-28 rue du Dr. Roux, 75724 Cedex 15, Paris, France.
| | | | | |
Collapse
|
28
|
Frints SG, Fryns J, Lagae L, Syrrou M, Marynen P, Devriendt K. Xp22.3; Yq11.2 chromosome translocation and its clinical manifestations. ANNALES DE GENETIQUE 2001; 44:71-6. [PMID: 11522244 DOI: 10.1016/s0003-3995(01)01071-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
We report clinical and molecular investigations in a boy with karyotype 46,Y,der(X)t(X;Y)(qter-->p22.3::q11.21-->qter) and his mother with karyotype 46,X,der(X)t(X;Y)(qter-->p22.3::q11.21-->qter). Haplo-insufficiency for the Xp22.3-->pter chromosomal region in the boy resulted in postnatal growth retardation, developmental delay, partial ichthyosis and facial dysmorphism, but normal external genitals. His mother has a normal phenotype with normal stature and gonadal function but borderline intelligence. FISH-analysis showed a duplication of the Y-heterochromatin probe in the proband and a deletion of the Y933D4 probe in his mother. Molecular investigations situated the Xp22.3 breakpoint between DXS278 and the KAL gene and the Yq11.21 breakpoint between the DYS391 and DYS390 in the proband and his mother. X-inactivation study was performed by analysis of the polymorphic CAG-repeat in the androgen-receptor gene as described showing a normal random (40% versus 60%) inactivation pattern in the mother. The manifestations in male and female with loss of the Xp22.3-->pter and gain of the Yq11.21-->qter chromosomal region are discussed.
Collapse
Affiliation(s)
- S G Frints
- Center for Human Genetics, University of Leuven, Belgium
| | | | | | | | | | | |
Collapse
|
29
|
Soussi-Gounni A, Kontolemos M, Hamid Q. Role of IL-9 in the pathophysiology of allergic diseases. J Allergy Clin Immunol 2001; 107:575-82. [PMID: 11295641 DOI: 10.1067/mai.2001.114238] [Citation(s) in RCA: 75] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Considerable evidence from both human and animal studies indicates that CD4(+) cells are the predominant cell type involved in the regulation of airway inflammation through the expression of T(H)2-type cytokines. The effects of T(H)2-type cytokines, particularly IL-4 and IL-5, on inflammatory and structural cells in airways have been studied in great detail. They were shown to be important for inflammatory cell maturation, activation and proliferation, IgE production, chemokine expression, mucus secretion, and bronchial hyperresponsiveness. Recent work has shown the potential importance of another T(H)2-type cytokine, IL-9. The development of transgenic mice overexpressing IL-9 has suggested a key role for this cytokine in the development of the asthmatic phenotype, including eosinophilic inflammation, bronchial hyperresponsiveness, elevated IgE levels, and increased mucus secretion. IL-9 has been shown to act on many cell types involved in asthma, including T cells, B cells, mast cells, eosinophils, neutrophils, and epithelial cells, and thus might be important in the pathophysiology of allergic asthma.
Collapse
Affiliation(s)
- A Soussi-Gounni
- Meakins-Christie Laboratories, McGill University, 3626 St Urbain St., Montreal, Quebec, Canada HX2 2P2
| | | | | |
Collapse
|
30
|
Quintana-Murci L, Fellous M. The Human Y Chromosome: The Biological Role of a "Functional Wasteland". J Biomed Biotechnol 2001; 1:18-24. [PMID: 12488622 PMCID: PMC79676 DOI: 10.1155/s1110724301000080] [Citation(s) in RCA: 63] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
"Functional wasteland," "Nonrecombining desert" and "Gene-poor chromosome" are only some examples of the different definitions given to the Y chromosome in the last decade. In comparison to the other chromosomes, the Y is poor in genes, being more than 50% of its sequence composed of repeated elements. Moreover, the Y genes are in continuous decay probably due to the lack of recombination of this chromosome. But the human Y chromosome, at the same time, plays a central role in human biology. The presence or absence of this chromosome determines gonadal sex. Thus, mammalian embryos with a Y chromosome develop testes, while those without it develop ovaries (Polani, 1981). What is responsible for the male phenotype is the testis-determining SRY gene (Sinclair, 1990) which remains the most distinguishing characteristic of this chromosome. In addition to SRY, the presence of other genes with important functions has been reported, including a region associated to Turner estigmata, a gene related to the development of gonadoblastoma and, most important, genes related to germ cell development and maintenance and then, related with male fertility (Lahn and Page, 1997). This paper reviews the structure and the biological functions of this peculiar chromosome.
Collapse
|
31
|
Voet T, Vermeesch J, Carens A, Dürr J, Labaere C, Duhamel H, David G, Marynen P. Efficient male and female germline transmission of a human chromosomal vector in mice. Genome Res 2001; 11:124-36. [PMID: 11156621 PMCID: PMC311020 DOI: 10.1101/gr.159901] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
A small accessory chromosome that was mitotically stable in human fibroblasts was transferred into the hprt(-) hamster cell line CH and developed as a human chromosomal vector (HCV) by the introduction of a selectable marker and the 3' end of an HPRT minigene preceded by a loxP sequence. This HCV is stably maintained in the hamster cell line. It consists mainly of alphoid sequences of human chromosome 20 and a fragment of human chromosome region 1p22, containing the tissue factor gene F3. The vector has an active centromere, and telomere sequences are lacking. By transfecting a plasmid containing the 5' end of HPRT and a Cre-encoding plasmid into the HCV(+) hamster cell line, the HPRT minigene was reconstituted by Cre-mediated recombination and expressed by the cells. The HCV was then transferred to male mouse R1-ES cells and it did segregate properly. Chimeras were generated containing the HCV as an independent chromosome in a proportion of the cells. Part of the male and female offspring of the chimeras did contain the HCV. The HCV(+) F1 animals harbored the extra chromosome in >80% of the cells. The HCV was present as an independent chromosome with an active centromere and the human F3 gene was expressed from the HCV in a human-tissue-specific manner. Both male and female F1 mice did transmit the HCV to F2 offspring as an independent chromosome with properties similar to the original vector. This modified small accessory chromosome, thus, shows the properties of a useful chromosomal vector: It segregates stably as an independent chromosome, sequences can be inserted in a controlled way and are expressed from the vector, and the HCV is transmitted through the male and female germline in mice.
Collapse
MESH Headings
- Animals
- Cell Adhesion Molecules, Neuronal/biosynthesis
- Cell Adhesion Molecules, Neuronal/genetics
- Cell Line
- Chimera/genetics
- Chromosomes, Artificial/genetics
- Chromosomes, Human/genetics
- Chromosomes, Human/virology
- Contactins
- Cricetinae
- Crosses, Genetic
- Embryo, Mammalian
- Female
- Fibroblasts
- Gene Transfer Techniques
- Genetic Vectors/biosynthesis
- Genetic Vectors/genetics
- Humans
- Hypoxanthine Phosphoribosyltransferase/genetics
- Integrases/genetics
- Male
- Mice
- Mice, Inbred C57BL
- Mice, Transgenic
- Mitosis/genetics
- Mutagenesis, Insertional
- Recombination, Genetic
- Simian virus 40/genetics
- Stem Cells/physiology
- Viral Proteins
Collapse
Affiliation(s)
- T Voet
- Human Genome Laboratory, Leuven, Belgium
| | | | | | | | | | | | | | | |
Collapse
|
32
|
Knight SJ, Flint J. Perfect endings: a review of subtelomeric probes and their use in clinical diagnosis. J Med Genet 2000; 37:401-9. [PMID: 10851249 PMCID: PMC1734614 DOI: 10.1136/jmg.37.6.401] [Citation(s) in RCA: 153] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Chromosomal rearrangements involving the ends of chromosomes (telomeres) are emerging as an important cause of human genetic diseases. This review describes the development of first and second generation sets of telomere specific clones, together with advances in fluorescence in situ hybridisation (FISH) technology, which have made the prospect of screening for telomeric rearrangements a realistic goal. Initial FISH studies using the telomere specific clones indicate that they will be a valuable diagnostic tool for the investigation of mental retardation, the characterisation of known abnormalities detected by conventional cytogenetic analysis, spontaneous recurrent miscarriages, infertility, haematological malignancies, and preimplantation diagnosis, as well as other fields of clinical interest. In addition, they may help investigate telomere structure and function and can be used in the identification of dosage sensitive genes involved in human genetic disease.
Collapse
Affiliation(s)
- S J Knight
- Institute of Molecular Medicine, John Radcliffe Hospital, Headington, Oxford OX3 9DS, UK
| | | |
Collapse
|
33
|
Matarazzo MR, Cuccurese M, Strazzullo M, Vacca M, Curci A, Miano MG, Cocchia M, Mercadante G, Torino A, D'Urso M, Ciccodicola A, D'Esposito M. Human and mouse SYBL1 gene structure and expression. Gene 1999; 240:233-8. [PMID: 10564831 DOI: 10.1016/s0378-1119(99)00375-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
SYBL1 is a gene in the 320kb human pseudo-autosomal region at the terminus of Xq and Yq. In contrast to other pseudoautosomal genes, SYBL1 is inactivated on one X in every female cell, and is also inactive on the Y of male cells. Hypermethylation of the CpG island associated with the human gene is involved in this phenomenon. In an attempt to further examine its regulation, the genomic organization of the X-linked mouse Sybl1 homolog was analyzed and compared with the human gene. Human and mouse show the same exon number, exon-intron junctions and a highly conserved basal promoter. The structural and functional conservation of basal regulatory regions suggests that inactivation is imposed by similar auxiliary epistatic regulatory mechanism.
Collapse
Affiliation(s)
- M R Matarazzo
- International Institute of Genetics and Biophysics, CNR, 80125, Naples, Italy
| | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
34
|
van Geel M, Heather LJ, Lyle R, Hewitt JE, Frants RR, de Jong PJ. The FSHD region on human chromosome 4q35 contains potential coding regions among pseudogenes and a high density of repeat elements. Genomics 1999; 61:55-65. [PMID: 10512680 DOI: 10.1006/geno.1999.5942] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The distal end of chromosome 4q contains the locus involved in facioscapulohumeral muscular dystrophy (FSHD1). Specific genomic deletions within a tandem DNA repeat (D4Z4) are associated with the disease status, but no causal genes have yet been discovered. In a systematic search for genes, a 161-kb stretch of genomic DNA proximal to D4Z4 was sequenced, analyzed for homologies, and subjected to gene prediction programs. A major fraction (45%) of the subtelomeric region is composed of repeat sequences attributable mainly to LINE-1 elements. Apart from the previously identified FRG1 and TUB4q sequences, several additional potential coding regions were identified by analyzing the sequence with exon prediction programs. So far, we have been unable to demonstrate transcripts by RT-PCR or cDNA library hybridization. However, several retrotransposed pseudogenes were identified. The high density of pseudogenes and repeat elements is consistent with the subtelomeric location of this region and explains why previous transcript identification studies have been problematic.
Collapse
Affiliation(s)
- M van Geel
- Department of Cancer Genetics, Roswell Park Cancer Institute, Buffalo, New York 14263, USA
| | | | | | | | | | | |
Collapse
|
35
|
Abstract
Comparative gene mapping and chromosome painting permit the tentative reconstruction of ancestral karyotypes. The modern human karyotype is proposed to differ from that of the most recent common ancestor of catarrhine primates by two major rearrangements. The first was the fission of an ancestral chromosome to produce the homologues of human chromosomes 14 and 15. This fission occurred before the divergence of gibbons from humans and other apes. The second was the fusion of two ancestral chromosomes to form human chromosome 2. This fusion occurred after the divergence of humans and chimpanzees. Moving further back in time, homologues of human chromosomes 3 and 21 were formed by the fission of an ancestral linkage group that combined loci of both human chromosomes, whereas homologues of human chromosomes 12 and 22 were formed by a reciprocal translocation between two ancestral chromosomes. Both events occurred at some time after our most recent common ancestor with lemurs. Less direct evidence suggests that the short and long arms of human chromosomes 8, 16 and 19 were unlinked in this ancestor. Finally, the most recent common ancestor of primates and artiodactyls is proposed to have possessed a chromosome that combined loci from human chromosomes 4 and 8p, a chromosome that combined loci from human chromosomes 16q and 19q, and a chromosome that combined loci from human chromosomes 2p and 20.
Collapse
Affiliation(s)
- D Haig
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA.
| |
Collapse
|
36
|
Wong AC, Shkolny D, Dorman A, Willingham D, Roe BA, McDermid HE. Two novel human RAB genes with near identical sequence each map to a telomere-associated region: the subtelomeric region of 22q13.3 and the ancestral telomere band 2q13. Genomics 1999; 59:326-34. [PMID: 10444334 DOI: 10.1006/geno.1999.5889] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Two closely related genes have been identified at 2q13 and 22q13.3. These genes show similarity to members of the RAB family of small GTPases. RABL2A and RABL2B differ by three conservative amino acid changes over a total of 228 residues. Both are expressed in all tissues tested. Northern analysis showed that a 2.5-kb transcript is expressed in all tissues tested while a 1.4-kb transcript is specifically expressed only in muscle. The size difference between these two transcripts is the result of differential splicing of an intron within the 3' UTR. RABL2B is located within the subtelomeric region of 22q13.3. RABL2A maps to 2q13, the site of an ancestral telomere fusion event, suggesting that it also may be a subtelomeric gene.
Collapse
Affiliation(s)
- A C Wong
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta, T6G 2E9, Canada
| | | | | | | | | | | |
Collapse
|
37
|
Abstract
The human Y chromosome has long been recognized as being responsible for sex determination. In fact, it also encodes more than 30 genes and gene families that participate in a variety of cellular functions, including bone development, tooth growth, and spermatogenesis. De-novo deletion of Y chromosome segments that contain spermatogenesis genes occurs frequently, resulting in low sperm production and male infertility. This article reviews our current knowledge of the structure and function of the Y chromosome is reviewed.
Collapse
Affiliation(s)
- P H Yen
- Division of Medical Genetics, Harbor-UCLA Medical Center, Torrance, California 90502-2064, USA.
| |
Collapse
|
38
|
Grasso L, Huang M, Sullivan CD, Messler CJ, Kiser MB, Dragwa CR, Holroyd KJ, Renauld JC, Levitt RC, Nicolaides NC. Molecular analysis of human interleukin-9 receptor transcripts in peripheral blood mononuclear cells. Identification of a splice variant encoding for a nonfunctional cell surface receptor. J Biol Chem 1998; 273:24016-24. [PMID: 9727018 DOI: 10.1074/jbc.273.37.24016] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Genetic studies on mouse models of asthma have identified interleukin-9 (IL9) as a determining factor in controlling bronchial hyperresponsiveness, a hallmark of the disease. Recently, the human IL9 receptor (hIL9R) gene locus has also been implicated in determining susceptibility to bronchial hyperresponsiveness and asthma. In order to evaluate the structure and function of the encoded product, we analyzed receptor transcripts derived from peripheral blood mononuclear cells of 50 unrelated donors. Sequence analysis of the entire coding region identified a splice variant that contains an in frame deletion of a single residue at codon 173 (DeltaQ). This variant could be permanently expressed in a cytokine-dependent murine T-cell line but lacked the ability to induce proliferation in response to human IL9. In situ analyses of cells expressing the wild-type and DeltaQ receptors found both forms to be expressed at the cell surface, but the DeltaQ receptor was unable to bind hIL9 and could not be recognized by N-terminal specific antibodies. These findings demonstrate that hIL9RDeltaQ presents an altered structure and function and suggests its potential role in down-regulating IL9 signaling in effector cells and associated biological processes.
Collapse
Affiliation(s)
- L Grasso
- Magainin Institute of Molecular Medicine, Magainin Pharmaceuticals, Inc., Plymouth Meeting, Pennsylvania 19462, USA
| | | | | | | | | | | | | | | | | | | |
Collapse
|
39
|
Demoulin JB, Renauld JC. Interleukin 9 and its receptor: an overview of structure and function. Int Rev Immunol 1998; 16:345-64. [PMID: 9505195 DOI: 10.3109/08830189809043001] [Citation(s) in RCA: 101] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Interleukin-9 (IL-9) is a multifunctional cytokine produced by activated TH2 clones in vitro and during TH2-like T cell responses in vivo. Although IL-9 was initially described as a T cell growth factor, its role in T cell responses is still unclear. While freshly isolated normal T cells do not respond to IL-9, this cytokine induces the proliferation of murine T cell lymphomas in vitro, and in vivo overexpression of IL-9 results in the development of thymic lymphomas. In the human, the existence of an IL-9 mediated autocrine loop has been suggested for some malignancies such as Hodgkin's disease. Various observations indicate that IL-9 is actively involved in mast cells responses by inducing the proliferation and differentiation of these cells. Other potential biological targets for IL-9 include B lymphocytes, and hematopoietic progenitors, for which higher responses were observed with foetal or transformed cells as compared to normal adult progenitors. The IL-9 receptor is a member of the hemopoietin receptor superfamily and interacts with the gamma chain of the IL-2 receptor for signaling. Signal transduction studies have stressed the role of the Jak-STAT pathway in various IL-9 bioactivities, whereas the 4PS/IRS2 adaptor protein might also play a significant role in IL-9 signaling.
Collapse
Affiliation(s)
- J B Demoulin
- Ludwig Institute for Cancer Research and Experimental Medicine Unit, Catholic University of Louvain, Brussels, Belgium
| | | |
Collapse
|
40
|
Trask BJ, Friedman C, Martin-Gallardo A, Rowen L, Akinbami C, Blankenship J, Collins C, Giorgi D, Iadonato S, Johnson F, Kuo WL, Massa H, Morrish T, Naylor S, Nguyen OT, Rouquier S, Smith T, Wong DJ, Youngblom J, van den Engh G. Members of the olfactory receptor gene family are contained in large blocks of DNA duplicated polymorphically near the ends of human chromosomes. Hum Mol Genet 1998; 7:13-26. [PMID: 9384599 DOI: 10.1093/hmg/7.1.13] [Citation(s) in RCA: 164] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
We have identified three new members of the olfactory receptor (OR) gene family within a large segment of DNA that is duplicated with high similarity near many human telomeres. This segment is present at 3q, 15q, and 19p in each of 45 unrelated humans sampled from various populations. Additional copies are present polymorphically at 11 other subtelomeric locations. The frequency with which the block is present at some locations varies among populations. While humans carry seven to 11 copies of the OR-containing block, it is located in chimpanzee and gorilla predominantly at a single site, which is not orthologous to any of the locations in the human genome. The observation that sequences flanking the OR-containing segment are duplicated on larger and different sets of chromosomes than the OR block itself demonstrates that the segment is part of a much larger, complex patchwork of subtelomeric duplications. The population analyses and structural results suggest the types of processes that have shaped these regions during evolution. From its sequence, one of the OR genes in this duplicated block appears to be potentially functional. Our findings raise the possibility that functional diversity in the OR family is generated in part through duplications and inter-chromosomal rearrangements of the DNA near human telomeres.
Collapse
Affiliation(s)
- B J Trask
- Department of Molecular Biotechnology, Box 357730, University of Washington, Seattle, WA 98195, USA.
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
41
|
D'Esposito M, Matarazzo MR, Ciccodicola A, Strazzullo M, Mazzarella R, Quaderi NA, Fujiwara H, Ko MS, Rowe LB, Ricco A, Archidiacono N, Rocchi M, Schlessinger D, D'Urso M. Differential expression pattern of XqPAR-linked genes SYBL1 and IL9R correlates with the structure and evolution of the region. Hum Mol Genet 1997; 6:1917-23. [PMID: 9302271 DOI: 10.1093/hmg/6.11.1917] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
The recently discovered second pseudoautosomal region (XqPAR) contains at least two genes, IL9R and SYBL1. Recent findings show that, like XpPAR genes, IL9R escapes X inactivation and its Y allele is also expressed, but SYBL1 seems to act like an X-linked gene, expressed from the active X chromosome but not from the inactive X or Y. Here we show that differences are also seen in the evolution of the sex chromosome locations of IL9R and SYBL1. IL9R is known to be autosomal in mice, and is X-linked only in primates. SYBL1, however, has been found to be on the X chromosome in all mammals tested, from marsupials to humans. Both genes were duplicated on the Y homologue of the terminal portion of the X chromosome during the evolution of Homo sapiens from other higher primates. The inactivation pattern of SYBL1 may be correlated with its longer history of X linkage, and at a more centromeric chromosomal position during evolution; the more recent X linkage and more telomeric position of the IL9R gene may explain its autosomal, 'uninactivated' transcriptional status.
Collapse
Affiliation(s)
- M D'Esposito
- International Institute of Genetics and Biophysics, CNR, Naples, Italy
| | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
42
|
Affiliation(s)
- H Riethman
- The Wistar Institute, Molecular Genetics, Philadelphia, Pennsylvania 19104, USA
| |
Collapse
|
43
|
Guo J, Apiou F, Mellerin MP, Lebeau B, Jacques Y, Minvielle S. Chromosome mapping and expression of the human interleukin-13 receptor. Genomics 1997; 42:141-5. [PMID: 9177784 DOI: 10.1006/geno.1997.4628] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Interleukin-13 (IL-13) is a cytokine secreted by activated T cells and shares most but not all biological activities with interleukin-4 (IL-4). Both cytokines play an important role as a switch factor directing synthesis of IgE; they act on monocytes and endothelial cells, but unlike IL-4, IL-13 does not act on T cells. These cytokines have both common and distinct components in their respective receptors. Based on sequence similarity shared by cytokine receptor family members, we have identified a cDNA encoding the human IL-13 receptor (IL-13R). This cDNA was used to examine the pattern of IL-13R mRNA expression by Northern blot analyses of poly(A)+ RNA purified from different human tissues and cell lines. Among several myeloma cell lines analyzed, the U266 cell line was the only one found to express IL-13R transcripts. This cell line is also the only one described as producing IgE. The IL-13R gene was mapped to chromosome Xq24 by in situ hybridization. Interestingly, this locus is near that of the CD40 ligand gene, the product of which is also involved, like IL-13, in proliferation and IgE isotype switching of human B cells. The human IL-13R gene maps between two cytokine receptor genes located on the chromosome arm Xq region: the interleukin-2 receptor gamma chain gene (Xq13.1) and the interleukin-9 receptor gene (Xq28). The lack of nucleotide sequence similarity suggests unrelated evolutionary pathways between these receptor genes.
Collapse
MESH Headings
- Amino Acid Sequence
- Base Sequence
- Cell Line
- Chromosome Mapping
- DNA, Complementary/genetics
- Evolution, Molecular
- Gene Expression
- Humans
- In Situ Hybridization, Fluorescence
- Interleukin-13/metabolism
- Interleukin-13 Receptor alpha1 Subunit
- Interleukin-9/metabolism
- Molecular Sequence Data
- Multiple Myeloma/genetics
- Multiple Myeloma/immunology
- RNA, Messenger/genetics
- RNA, Messenger/metabolism
- Receptors, Interleukin/genetics
- Receptors, Interleukin-13
- Receptors, Interleukin-2/genetics
- Receptors, Interleukin-9
- Tissue Distribution
- Tumor Cells, Cultured
- X Chromosome/genetics
Collapse
Affiliation(s)
- J Guo
- INSERM U211, Institut de Biologie, Nantes, France
| | | | | | | | | | | |
Collapse
|
44
|
Flint J, Thomas K, Micklem G, Raynham H, Clark K, Doggett NA, King A, Higgs DR. The relationship between chromosome structure and function at a human telomeric region. Nat Genet 1997; 15:252-7. [PMID: 9054936 DOI: 10.1038/ng0397-252] [Citation(s) in RCA: 117] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
We have sequenced a contiguous 284,495-bp segment of DNA extending from the terminal (TTAGGG)n repeats of the short arm of chromosome 16, providing a full description of the transition from telomeric through subtelomeric DNA to sequences that are unique to the chromosome. To complement and extend analysis of the primary sequence, we have characterized mRNA transcripts, patterns of DNA methylation and DNase I sensitivity. Together with previous data these studies describe in detail the structural and functional organization of a human telomeric region.
Collapse
Affiliation(s)
- J Flint
- MRC Molecular Haematology Unit, John Radcliffe Hospital, Headington, Oxford, UK
| | | | | | | | | | | | | | | |
Collapse
|
45
|
Gläser B, Hierl T, Taylor K, Schiebel K, Zeitler S, Papadopoullos K, Rappold G, Schempp W. High-resolution fluorescence in situ hybridization of human Y-linked genes on released chromatin. Chromosome Res 1997; 5:23-30. [PMID: 9088640 DOI: 10.1023/a:1018437301461] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Genes within the differential region of the human Y chromosome do not recombine, and therefore the determination of their location depends on physical mapping. Yeast artificial chromosome (YAC) contigs spanning the euchromatic region of the human Y have become a powerful tool for the generation of an overlapping clone map. With this approach, however, complete physical mapping is difficult in Y euchromatic regions that are rich in repetitive sequences. We have, therefore, made use of the fluorescence in situ hybridization technique as an alternative strategy for physically mapping the PRKY and AMELY genes as well as the TSPY, RBM and DAZ gene families to human Y chromosomes in prometaphase and to extended Y chromatin in interphase. From our results, the following order of gene sequences in interval 3 of the short arm of the human Y chromosome is suggested: TSPY major with few RBM sequences interspersed-PRKY-AMELY-TSPY minor with few RBM sequences interspersed-cen. On the long arm, RBM sequences appear to be distributed over wide regions of intervals 5 and 6 with few TSPY sequences interspersed. Distal to an RBM signal cluster, a large cluster of DAZ signals is located with only a few DAZ and RBM signals overlapping in between the two clusters.
Collapse
Affiliation(s)
- B Gläser
- Institute of Human Genetics and Anthropology, University of Freiburg, Germany
| | | | | | | | | | | | | | | |
Collapse
|
46
|
Rogner UC, Heiss NS, Kioschis P, Wiemann S, Korn B, Poustka A. Transcriptional analysis of the candidate region for incontinentia pigmenti (IP2) in Xq28. Genome Res 1996; 6:922-34. [PMID: 8908511 DOI: 10.1101/gr.6.10.922] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
The hereditary form of incontinentia pigmenti (IP2) is a rare disorder characterized by abnormalities of the tissues and organs derived from the ectoderm and neuroectoderm and has been linked to Xq28 distal to the factor VIII gene (F8C). Four YAC clones covering the 1.1-Mb candidate region at the telomere of Xq28 were subjected to direct cDNA selection and Alu long-range PCR. The products of both methods were subsequently used to isolate 154 cosmid clones that were assembled into five cosmid contigs. This first-generation cosmid map covered the region almost entirely and was used as a basis for constructing a transcript map that was in turn integrated with the physical YAC and cosmid maps. To isolate specifically coding sequences, exon trapping and cDNA selection methods were combined. Exon trapping was carried out on YAC Alu-PCR products, YAC Alu long-range PCR products, and on pools of cosmids. The region-specific enriched cDNA library was then screened by using the exon trap products as complex probes. To ensure a more complete analysis, the products from cDNA selection experiments were also used to screen conventional oligo(dT) primed cDNA libraries. Twenty overlapping cDNA contigs were assembled and computer analyses were performed to identify EST hits, open reading frames, protein motifs, and protein sequence homologies. Five of the cDNA contigs corresponded to known sequences such as the factor VIII, c6.1A, and c6.1B. genes, and both distal copies of the factor VIII intron 22 repeat sequence. Expression patterns of the 15 new cDNA contigs were analyzed by Northern blot and RT-PCR studies and these data were integrated with expression data obtained from known EST sequences. Although a more detailed analysis of this 1.1-Mb region with respect to the structure and function of the genes will only ultimately be possible by a global sequencing approach, an analysis of all novel transcripts as candidate genes for incontinentia pigmenti is already in progress.
Collapse
Affiliation(s)
- U C Rogner
- Deutsches Krebsforschungszentrum, Abteilung Molekulare Genomanalyse, Heidelberg, Germany
| | | | | | | | | | | |
Collapse
|
47
|
D'Esposito M, Ciccodicola A, Gianfrancesco F, Esposito T, Flagiello L, Mazzarella R, Schlessinger D, D'Urso M. A synaptobrevin-like gene in the Xq28 pseudoautosomal region undergoes X inactivation. Nat Genet 1996; 13:227-9. [PMID: 8640232 DOI: 10.1038/ng0696-227] [Citation(s) in RCA: 58] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
The X and Y chromosomes that maintain human dimorphism are thought to have descended from a single progenitor, with the Y chromosome becoming largely depleted of genes. A number of genes, however, retain copies on both X and Y chromosomes and escape the inactivation that affects most X-linked genes in somatic cells. Many of those genes are present in two pseudoautosomal regions (PARs) at the termini of the short (p) and long (q) arms of the sex chromosomes. For both PARs, pairing facilitates the exchange of information, ensuring the homogenisation of X and Y chromosomal material in these regions. We report here a strikingly different regulation of expression of a gene in Xq PAR. Unlike all Xp PAR genes studied so far, a synaptobrevin-like gene, tentatively named SYBL1, undergoes X inactivation. In addition, it is also inactive on the Y chromosome, thereby maintaining dosage compensation in an unprecedented way.
Collapse
Affiliation(s)
- M D'Esposito
- International Institute of Genetics and Biophysics, CNR, Naples, Italy
| | | | | | | | | | | | | | | |
Collapse
|