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Cerecedo-Lopez CD, Bernstock JD, Dmytriw AA, Chen JA, Chalif JI, Gupta S, Driver J, Huang K, Stanley SE, Li JZ, Chi J, Lu Y. Spontaneous intramedullary abscesses caused by Streptococcus anginosus: two case reports and review of the literature. BMC Infect Dis 2022; 22:141. [PMID: 35144555 PMCID: PMC8830018 DOI: 10.1186/s12879-022-07099-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Accepted: 01/27/2022] [Indexed: 01/24/2023] Open
Abstract
BACKGROUND Intramedullary abscesses are rare infections of the spinal cord. Intramedullary abscesses often have a complex presentation, making a high index of suspicion essential for prompt diagnosis and management. CASE PRESENTATION We present two cases of intramedullary abscesses referred to and ultimately managed at our institution. Delayed diagnosis occurred in both instances due to the rarity of intramedullary abscesses and their propensity to mimic other pathologies. For both patients, prompt surgical management and the rapid institution of broad-spectrum antibiotics were critical in preventing further neurological decline. CONCLUSIONS Although rare, it is critical to consider intramedullary abscesses on the differential for any MRI lesions that are hyperintense on T2 and peripherally enhancing on T1 post-contrast sequences, as even short delays in treatment can lead to severe neurological damage.
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Affiliation(s)
- Christian D. Cerecedo-Lopez
- grid.38142.3c000000041936754XDepartment of Neurosurgery, Brigham and Women’s Hospital, Harvard Medical School, 75 Francis Street, Boston, 02120 MA USA
| | - Joshua D. Bernstock
- grid.38142.3c000000041936754XDepartment of Neurosurgery, Brigham and Women’s Hospital, Harvard Medical School, 75 Francis Street, Boston, 02120 MA USA
| | - Adam A. Dmytriw
- grid.38142.3c000000041936754XDepartment of Neuroradiology, Brigham and Women’s Hospital, Harvard Medical School, MA Boston, USA
| | - Jason A. Chen
- grid.38142.3c000000041936754XDepartment of Neurosurgery, Brigham and Women’s Hospital, Harvard Medical School, 75 Francis Street, Boston, 02120 MA USA
| | - Joshua I. Chalif
- grid.38142.3c000000041936754XDepartment of Neurosurgery, Brigham and Women’s Hospital, Harvard Medical School, 75 Francis Street, Boston, 02120 MA USA
| | - Saksham Gupta
- grid.38142.3c000000041936754XDepartment of Neurosurgery, Brigham and Women’s Hospital, Harvard Medical School, 75 Francis Street, Boston, 02120 MA USA
| | - Joseph Driver
- grid.38142.3c000000041936754XDepartment of Neurosurgery, Brigham and Women’s Hospital, Harvard Medical School, 75 Francis Street, Boston, 02120 MA USA
| | - Kevin Huang
- grid.38142.3c000000041936754XDepartment of Neurosurgery, Brigham and Women’s Hospital, Harvard Medical School, 75 Francis Street, Boston, 02120 MA USA
| | - Susan E. Stanley
- grid.38142.3c000000041936754XDepartment of Medicine, Division of Infectious Diseases, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA USA
| | - Jonathan Z. Li
- grid.38142.3c000000041936754XDepartment of Medicine, Division of Infectious Diseases, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA USA
| | - John Chi
- grid.38142.3c000000041936754XDepartment of Neurosurgery, Brigham and Women’s Hospital, Harvard Medical School, 75 Francis Street, Boston, 02120 MA USA
| | - Yi Lu
- grid.38142.3c000000041936754XDepartment of Neurosurgery, Brigham and Women’s Hospital, Harvard Medical School, 75 Francis Street, Boston, 02120 MA USA
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Gaysinskaya V, Stanley SE, Adam S, Armanios M. Synonymous Mutation in DKC1 Causes Telomerase RNA Insufficiency Manifesting as Familial Pulmonary Fibrosis. Chest 2020; 158:2449-2457. [PMID: 32710892 DOI: 10.1016/j.chest.2020.07.025] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2020] [Revised: 07/11/2020] [Accepted: 07/13/2020] [Indexed: 11/28/2022] Open
Abstract
BACKGROUND Idiopathic pulmonary fibrosis (IPF) is the most common of short telomere phenotypes. Familial clustering of IPF is common, but the genetic basis remains unknown in more than one-half of cases. We identified a 65-year-old man with familial IPF, short telomere length, and low telomerase RNA levels. He was diagnosed with a short telomere syndrome after developing hematologic complications post-lung transplantation, but no mutations were identified in a clinical testing pipeline. RESEARCH QUESTION What is the molecular basis underlying the familial IPF and low telomerase RNA levels in this patient? STUDY DESIGN AND METHODS We analyzed whole-genome sequence data and performed functional molecular studies on cells derived from the patient and his family. RESULTS We identified a previously unreported synonymous variant c.942G>A p.K314K in DKC1, the gene encoding the dyskerin ribonucleoprotein, which is required for telomerase RNA biogenesis. The mutation created a competing de novo exonic splicing enhancer, and the misspliced product was degraded by nonsense-mediated decay causing an overall dyskerin deficiency in mutation carriers. In silico tools identified other rare silent DKC1 variants that warrant functional evaluation if found in patients with short telomere-mediated disease. INTERPRETATION Our data point to silent mutation in telomere maintenance genes as a mechanism of familial pulmonary fibrosis. In contrast to DKC1 missense mutations, which primarily manifest in children as dyskeratosis congenita, hypomorphic mutations affecting dyskerin levels likely have a predilection to presenting in adults as pulmonary fibrosis.
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Affiliation(s)
- Valeriya Gaysinskaya
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD; Telomere Center, Johns Hopkins University School of Medicine, Baltimore, MD
| | - Susan E Stanley
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD; Telomere Center, Johns Hopkins University School of Medicine, Baltimore, MD
| | - Soheir Adam
- Department of Medicine, Duke University School of Medicine, Durham, NC
| | - Mary Armanios
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD; Sidney Kimmel Comprehensive Cancer, Johns Hopkins University School of Medicine, Baltimore, MD.
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Gable DL, Gaysinskaya V, Atik CC, Talbot CC, Kang B, Stanley SE, Pugh EW, Amat-Codina N, Schenk KM, Arcasoy MO, Brayton C, Florea L, Armanios M. ZCCHC8, the nuclear exosome targeting component, is mutated in familial pulmonary fibrosis and is required for telomerase RNA maturation. Genes Dev 2019; 33:1381-1396. [PMID: 31488579 PMCID: PMC6771387 DOI: 10.1101/gad.326785.119] [Citation(s) in RCA: 70] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2019] [Accepted: 08/15/2019] [Indexed: 11/25/2022]
Abstract
In this study, Gable et al. follow a family with early onset pulmonary fibrosis and report the discovery of a new genetic cause of pulmonary fibrosis. They use multidimensional analysis methods, involving molecular studies, mouse model, and transcriptome-wide studies to show that heterozygous loss-of-function of the exosomal targeting protein ZCCHC8 to identify a novel cause of telomerase insufficiency in human disease. Short telomere syndromes manifest as familial idiopathic pulmonary fibrosis; they are the most common premature aging disorders. We used genome-wide linkage to identify heterozygous loss of function of ZCCHC8, a zinc-knuckle containing protein, as a cause of autosomal dominant pulmonary fibrosis. ZCCHC8 associated with TR and was required for telomerase function. In ZCCHC8 knockout cells and in mutation carriers, genomically extended telomerase RNA (TR) accumulated at the expense of mature TR, consistent with a role for ZCCHC8 in mediating TR 3′ end targeting to the nuclear RNA exosome. We generated Zcchc8-null mice and found that heterozygotes, similar to human mutation carriers, had TR insufficiency but an otherwise preserved transcriptome. In contrast, Zcchc8−/− mice developed progressive and fatal neurodevelopmental pathology with features of a ciliopathy. The Zcchc8−/− brain transcriptome was highly dysregulated, showing accumulation and 3′ end misprocessing of other low-abundance RNAs, including those encoding cilia components as well as the intronless replication-dependent histones. Our data identify a novel cause of human short telomere syndromes-familial pulmonary fibrosis and uncover nuclear exosome targeting as an essential 3′ end maturation mechanism that vertebrate TR shares with replication-dependent histones.
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Affiliation(s)
- Dustin L Gable
- Medical Scientist Training Program, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA.,Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, Maryland 21287, USA.,Telomere Center, Johns Hopkins University School of Medicine, Baltimore, Maryland 21287, USA
| | - Valeriya Gaysinskaya
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, Maryland 21287, USA.,Telomere Center, Johns Hopkins University School of Medicine, Baltimore, Maryland 21287, USA
| | - Christine C Atik
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, Maryland 21287, USA.,Telomere Center, Johns Hopkins University School of Medicine, Baltimore, Maryland 21287, USA
| | - C Conover Talbot
- Institute for Basic Biomedical Sciences, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA
| | - Byunghak Kang
- Department of Comparative and Molecular Pathobiology, Johns Hopkins University School of Medicine, Baltimore, Maryland 21287, USA
| | - Susan E Stanley
- Medical Scientist Training Program, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA.,Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, Maryland 21287, USA.,Telomere Center, Johns Hopkins University School of Medicine, Baltimore, Maryland 21287, USA
| | - Elizabeth W Pugh
- Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland 21287, USA
| | - Nuria Amat-Codina
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, Maryland 21287, USA.,Telomere Center, Johns Hopkins University School of Medicine, Baltimore, Maryland 21287, USA
| | - Kara M Schenk
- Osler Medical Housestaff Training Program, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA
| | - Murat O Arcasoy
- Department of Medicine, Duke University School of Medicine, Durham, North Carolina 27708, USA
| | - Cory Brayton
- Department of Comparative and Molecular Pathobiology, Johns Hopkins University School of Medicine, Baltimore, Maryland 21287, USA
| | - Liliana Florea
- Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland 21287, USA
| | - Mary Armanios
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, Maryland 21287, USA.,Telomere Center, Johns Hopkins University School of Medicine, Baltimore, Maryland 21287, USA.,Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland 21287, USA.,Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland 21287, USA
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Stanley SE, Gable DL, Wagner CL, Carlile TM, Hanumanthu VS, Podlevsky JD, Khalil SE, DeZern AE, Rojas-Duran MF, Applegate CD, Alder JK, Parry EM, Gilbert WV, Armanios M. Loss-of-function mutations in the RNA biogenesis factor NAF1 predispose to pulmonary fibrosis-emphysema. Sci Transl Med 2017; 8:351ra107. [PMID: 27510903 DOI: 10.1126/scitranslmed.aaf7837] [Citation(s) in RCA: 141] [Impact Index Per Article: 20.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2016] [Accepted: 07/14/2016] [Indexed: 12/23/2022]
Abstract
Chronic obstructive pulmonary disease and pulmonary fibrosis have been hypothesized to represent premature aging phenotypes. At times, they cluster in families, but the genetic basis is not understood. We identified rare, frameshift mutations in the gene for nuclear assembly factor 1, NAF1, a box H/ACA RNA biogenesis factor, in pulmonary fibrosis-emphysema patients. The mutations segregated with short telomere length, low telomerase RNA levels, and extrapulmonary manifestations including myelodysplastic syndrome and liver disease. A truncated NAF1 was detected in cells derived from patients, and, in cells in which the frameshift mutation was introduced by genome editing, telomerase RNA levels were reduced. The mutant NAF1 lacked a conserved carboxyl-terminal motif, which we show is required for nuclear localization. To understand the disease mechanism, we used CRISPR (clustered regularly interspaced short palindromic repeats)/Cas9 (CRISPR-associated protein-9 nuclease) to generate Naf1(+/-) mice and found that they had half the levels of telomerase RNA. Other box H/ACA RNA levels were also decreased, but rRNA pseudouridylation, which is guided by snoRNAs, was intact. Moreover, first-generation Naf1(+/-) mice showed no evidence of ribosomal pathology. Our data indicate that disease in NAF1 mutation carriers is telomere-mediated; they show that NAF1 haploinsufficiency selectively disturbs telomere length homeostasis by decreasing the levels of telomerase RNA while sparing rRNA pseudouridylation.
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Affiliation(s)
- Susan E Stanley
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA. Medical Scientist Training Program, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Dustin L Gable
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA. Medical Scientist Training Program, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Christa L Wagner
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Thomas M Carlile
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Vidya Sagar Hanumanthu
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Joshua D Podlevsky
- Department of Chemistry and Biochemistry, Arizona State University, Tempe, AZ 85277, USA
| | - Sara E Khalil
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Amy E DeZern
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA. Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA. Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Maria F Rojas-Duran
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Carolyn D Applegate
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA. Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA. McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Jonathan K Alder
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Erin M Parry
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA. Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Wendy V Gilbert
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Mary Armanios
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA. Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA. McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA.
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Parry EM, Gable DL, Stanley SE, Khalil SE, Antonescu V, Florea L, Armanios M. Germline Mutations in DNA Repair Genes in Lung Adenocarcinoma. J Thorac Oncol 2017; 12:1673-1678. [PMID: 28843361 DOI: 10.1016/j.jtho.2017.08.011] [Citation(s) in RCA: 51] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2017] [Revised: 07/31/2017] [Accepted: 08/05/2017] [Indexed: 12/13/2022]
Abstract
INTRODUCTION Although lung cancer is generally thought to be environmentally provoked, anecdotal familial clustering has been reported, suggesting that there may be genetic susceptibility factors. We systematically tested whether germline mutations in eight candidate genes may be risk factors for lung adenocarcinoma. METHODS We studied lung adenocarcinoma cases for which germline sequence data had been generated as part of The Cancer Genome Atlas project but had not been previously analyzed. We selected eight genes, ATM serine/threonine kinase gene (ATM), BRCA2, DNA repair associated gene (BRCA2), checkpoint kinase 2 gene (CHEK2), EGFR, parkin RBR E3 ubiquitin protein ligase gene (PARK2), telomerase reverse transcriptase gene (TERT), tumor protein p53 gene (TP53), and Yes associated protein 1 gene (YAP1), on the basis of prior anecdotal association with lung cancer or genome-wide association studies. RESULTS Among 555 lung adenocarcinoma cases, we detected 14 pathogenic mutations in five genes; they occurred at a frequency of 2.5% and represented an OR of 66 (95% confidence interval: 33-125, p < 0.0001 [chi-square test]). The mutations fell most commonly in ATM (50%), followed by TP53, BRCA2, EGFR, and PARK2. Most (86%) of these variants had been reported in other familial cancer syndromes. Another 12 cases (2%) carried ultrarare variants that were predicted to be deleterious by three protein prediction programs; these most frequently involved ATM and BRCA2. CONCLUSIONS A subset of patients with lung adenocarcinoma, at least 2.5% to 4.5%, carry germline variants that have been linked to cancer risk in Mendelian syndromes. The genes fall most frequently in DNA repair pathways. Our data indicate that patients with lung adenocarcinoma, similar to other solid tumors, include a subset of patients with inherited susceptibility.
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Affiliation(s)
- Erin M Parry
- Osler Medical Housestaff Training Program, Johns Hopkins University School of Medicine, Baltimore, Maryland; Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Dustin L Gable
- Medical Scientist Training Program, Johns Hopkins University School of Medicine, Baltimore, Maryland; Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, Maryland; McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Susan E Stanley
- Medical Scientist Training Program, Johns Hopkins University School of Medicine, Baltimore, Maryland; Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, Maryland; McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Sara E Khalil
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, Maryland; McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Valentin Antonescu
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland; McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Liliana Florea
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland; McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Mary Armanios
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, Maryland; McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland; Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland.
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Lee M, Roos P, Sharma N, Atalar M, Evans TA, Pellicore MJ, Davis E, Lam ATN, Stanley SE, Khalil SE, Solomon GM, Walker D, Raraigh KS, Vecchio-Pagan B, Armanios M, Cutting GR. Systematic Computational Identification of Variants That Activate Exonic and Intronic Cryptic Splice Sites. Am J Hum Genet 2017; 100:751-765. [PMID: 28475858 DOI: 10.1016/j.ajhg.2017.04.001] [Citation(s) in RCA: 57] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2016] [Accepted: 03/30/2017] [Indexed: 12/30/2022] Open
Abstract
We developed a variant-annotation method that combines sequence-based machine-learning classification with a context-dependent algorithm for selecting splice variants. Our approach is distinctive in that it compares the splice potential of a sequence bearing a variant with the splice potential of the reference sequence. After training, classification accurately identified 168 of 180 (93.3%) canonical splice sites of five genes. The combined method, CryptSplice, identified and correctly predicted the effect of 18 of 21 (86%) known splice-altering variants in CFTR, a well-studied gene whose loss-of-function variants cause cystic fibrosis (CF). Among 1,423 unannotated CFTR disease-associated variants, the method identified 32 potential exonic cryptic splice variants, two of which were experimentally evaluated and confirmed. After complete CFTR sequencing, the method found three cryptic intronic splice variants (one known and two experimentally verified) that completed the molecular diagnosis of CF in 6 of 14 individuals. CryptSplice interrogation of sequence data from six individuals with X-linked dyskeratosis congenita caused by an unknown disease-causing variant in DKC1 identified two splice-altering variants that were experimentally verified. To assess the extent to which disease-associated variants might activate cryptic splicing, we selected 458 pathogenic variants and 348 variants of uncertain significance (VUSs) classified as high confidence from ClinVar. Splice-site activation was predicted for 129 (28%) of the pathogenic variants and 75 (22%) of the VUSs. Our findings suggest that cryptic splice-site activation is more common than previously thought and should be routinely considered for all variants within the transcribed regions of genes.
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Affiliation(s)
- Melissa Lee
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | | | - Neeraj Sharma
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Melis Atalar
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Taylor A Evans
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Matthew J Pellicore
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Emily Davis
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Anh-Thu N Lam
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Susan E Stanley
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Sara E Khalil
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - George M Solomon
- Division of Pulmonary, Allergy, and Critical Care Medicine, University of Alabama at Birmingham, Birmingham, AL 35233 USA
| | - Doug Walker
- Pediatric Pulmonary Medicine, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Karen S Raraigh
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Briana Vecchio-Pagan
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Mary Armanios
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Garry R Cutting
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.
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Gorgy AI, Jonassaint NL, Stanley SE, Koteish A, DeZern AE, Walter JE, Sopha SC, Hamilton JP, Hoover-Fong J, Chen AR, Anders RA, Kamel IR, Armanios M. Hepatopulmonary syndrome is a frequent cause of dyspnea in the short telomere disorders. Chest 2016; 148:1019-1026. [PMID: 26158642 DOI: 10.1378/chest.15-0825] [Citation(s) in RCA: 70] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
BACKGROUND Telomere syndromes have their most common manifestation in idiopathic pulmonary fibrosis and emphysema. The short telomere defect in these patients may manifest systemically as bone marrow failure and liver disease. We sought to understand the causes of dyspnea in telomerase and telomere gene mutation carriers who have no parenchymal lung disease. METHODS Clinical and pathologic data were reviewed as part of a Johns Hopkins-based natural history study of short telomere syndromes including dyskeratosis congenita. RESULTS Hepatopulmonary syndrome (HPS) was diagnosed in nine of 42 cases (21%). Their age at presentation was significantly younger than that of cases initially presenting with pulmonary fibrosis and emphysema (median, 25 years vs 55 years; P < .001). Cases had evidence of intra- and extrapulmonary arteriovascular malformations that caused shunt physiology. Nodular regenerative hyperplasia was the most frequent histopathologic abnormality, and it was seen in the absence of cirrhosis. Dyspnea and portal hypertension were progressive, and the median time to death or liver transplantation was 6 years (range, 4-10 years; n = 6). In cases that underwent liver transplantation, dyspnea and hypoxia improved, but pulmonary fibrosis subsequently developed. CONCLUSIONS This report identifies HPS as a frequent cause of dyspnea in telomerase and telomere gene mutation carriers. While it usually precedes the development of parenchymal lung disease, HPS may also co-occur with pulmonary fibrosis and emphysema. Recognizing this genetic diagnosis is critical for management, especially in the lung and liver transplantation setting.
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Affiliation(s)
| | | | - Susan E Stanley
- Department of Oncology, Baltimore, MD; McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD
| | | | - Amy E DeZern
- Department of Oncology, Baltimore, MD; Department of Medicine, Baltimore, MD
| | - Jolan E Walter
- Department of Division of Allergy and Immunology, Massachusetts General Hospital for Children, Boston, MA
| | | | | | - Julie Hoover-Fong
- Department of Pediatrics, Baltimore, MD; McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD
| | | | | | | | - Mary Armanios
- Department of Oncology, Baltimore, MD; Department of Pathology, Baltimore, MD; McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD.
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Pauerstein PT, Sugiyama T, Stanley SE, McLean GW, Wang J, Martín MG, Kim SK. Dissecting Human Gene Functions Regulating Islet Development With Targeted Gene Transduction. Diabetes 2015; 64:3037-49. [PMID: 25901096 PMCID: PMC4512220 DOI: 10.2337/db15-0042] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/10/2015] [Accepted: 04/09/2015] [Indexed: 01/19/2023]
Abstract
During pancreas development, endocrine precursors and their progeny differentiate, migrate, and cluster to form nascent islets. The transcription factor Neurogenin 3 (Neurog3) is required for islet development in mice, but its role in these dynamic morphogenetic steps has been inferred from fixed tissues. Moreover, little is known about the molecular genetic functions of NEUROG3 in human islet development. We developed methods for gene transduction by viral microinjection in the epithelium of cultured Neurog3-null mutant fetal pancreas, permitting genetic complementation in a developmentally relevant context. In addition, we developed methods for quantitative assessment of live-cell phenotypes in single developing islet cells. Delivery of wild-type NEUROG3 rescued islet differentiation, morphogenesis, and live cell deformation, whereas the patient-derived NEUROG3(R107S) allele partially restored indicators of islet development. NEUROG3(P39X), a previously unreported patient allele, failed to restore islet differentiation or morphogenesis and was indistinguishable from negative controls, suggesting that it is a null mutation. Our systems also permitted genetic suppression analysis and revealed that targets of NEUROG3, including NEUROD1 and RFX6, can partially restore islet development in Neurog3-null mutant mouse pancreata. Thus, advances described here permitted unprecedented assessment of gene functions in regulating crucial dynamic aspects of islet development in the fetal pancreas.
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Affiliation(s)
- Philip T Pauerstein
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA
| | - Takuya Sugiyama
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA
| | - Susan E Stanley
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA
| | - Graeme W McLean
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA
| | - Jing Wang
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA
| | - Martín G Martín
- Department of Pediatrics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA
| | - Seung K Kim
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA
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9
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Alder JK, Stanley SE, Wagner CL, Hamilton M, Hanumanthu VS, Armanios M. Exome sequencing identifies mutant TINF2 in a family with pulmonary fibrosis. Chest 2015; 147:1361-1368. [PMID: 25539146 DOI: 10.1378/chest.14-1947] [Citation(s) in RCA: 121] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
BACKGROUND Short telomeres are a common defect in idiopathic pulmonary fibrosis, yet mutations in the telomerase genes account for only a subset of these cases. METHODS We identified a family with pulmonary fibrosis, idiopathic infertility, and short telomeres. RESULTS Exome sequencing of blood-derived DNA revealed two mutations in the telomere-binding protein TINF2. The first was a 15-base-pair deletion encompassing the exon 6 splice acceptor site, and the second was a missense mutation, Thr284Arg. Haplotype analysis indicated both variants fell on the same allele. However, lung-derived DNA showed predominantly the Thr284Arg allele, indicating that the deletion seen in the blood was acquired and may have a protective advantage because it diminished expression of the missense mutation. This mosaicism may represent functional reversion in telomere syndromes similar to that described for Fanconi anemia. No mutations were identified in over 40 uncharacterized pulmonary fibrosis probands suggesting that mutant TINF2 accounts for a small subset of familial cases. However, similar to affected individuals in this family, we identified a history of male and female infertility preceding the onset of pulmonary fibrosis in 11% of TERT and TR mutation carriers (five of 45). CONCLUSIONS Our findings identify TINF2 as a mutant telomere gene in familial pulmonary fibrosis and suggest that infertility may precede the presentation of pulmonary fibrosis in a small subset of adults with telomere syndromes.
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Affiliation(s)
- Jonathan K Alder
- Department of Oncology and Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD; Department of Physiology and Developmental Biology, Brigham Young University, Provo, UT
| | - Susan E Stanley
- Department of Oncology and Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD; McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD
| | - Christa L Wagner
- Department of Oncology and Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD; McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD
| | - Makenzie Hamilton
- Department of Physiology and Developmental Biology, Brigham Young University, Provo, UT
| | - Vidya Sagar Hanumanthu
- Department of Oncology and Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD; McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD
| | - Mary Armanios
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD.
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Stanley SE, Armanios M. The short and long telomere syndromes: paired paradigms for molecular medicine. Curr Opin Genet Dev 2015; 33:1-9. [PMID: 26232116 DOI: 10.1016/j.gde.2015.06.004] [Citation(s) in RCA: 82] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2015] [Revised: 06/10/2015] [Accepted: 06/16/2015] [Indexed: 01/26/2023]
Abstract
Recent advances have defined a role for abnormally short telomeres in a broad spectrum of genetic disorders. They include rare conditions such as dyskeratosis congenita as well pulmonary fibrosis and emphysema. Now, there is new evidence that some familial cancers, such as melanoma, are caused by mutations that lengthen telomeres. Here, we examine the significance of these short and long telomere length extremes for understanding the molecular basis of age-related disease and cancer.
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Affiliation(s)
- Susan E Stanley
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD 21287, United States; Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, United States; Medical Scientist Training Program, Johns Hopkins University School of Medicine, Baltimore, MD 21287, United States
| | - Mary Armanios
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD 21287, United States; Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, United States; McKusick Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21287, United States.
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11
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Parry EM, Gable DL, Stanley SE, Armanios MY. Rare germline TP53 variants in lung adenocarcinoma. J Clin Oncol 2015. [DOI: 10.1200/jco.2015.33.15_suppl.1548] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Affiliation(s)
- Erin Michelle Parry
- Osler Medical Housestaff Training Program, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD
| | - Dustin L Gable
- Medical Scientist Training Program, Johns Hopkins University School of Medicine, Baltimore, MD
| | - Susan E Stanley
- Medical Scientist Training Program, Johns Hopkins University School of Medicine, Baltimore, MD
| | - Mary Y. Armanios
- Department of Oncology and Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD
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Stanley SE, Chen JJL, Podlevsky JD, Alder JK, Hansel NN, Mathias RA, Qi X, Rafaels NM, Wise RA, Silverman EK, Barnes KC, Armanios M. Telomerase mutations in smokers with severe emphysema. J Clin Invest 2014; 125:563-70. [PMID: 25562321 DOI: 10.1172/jci78554] [Citation(s) in RCA: 129] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2014] [Accepted: 11/25/2014] [Indexed: 11/17/2022] Open
Abstract
Mutations in the essential telomerase genes TERT and TR cause familial pulmonary fibrosis; however, in telomerase-null mice, short telomeres predispose to emphysema after chronic cigarette smoke exposure. Here, we tested whether telomerase mutations are a risk factor for human emphysema by examining their frequency in smokers with chronic obstructive pulmonary disease (COPD). Across two independent cohorts, we found 3 of 292 severe COPD cases carried deleterious mutations in TERT (1%). This prevalence is comparable to the frequency of alpha-1 antitrypsin deficiency documented in this population. The TERT mutations compromised telomerase catalytic activity, and mutation carriers had short telomeres. Telomerase mutation carriers with emphysema were predominantly female and had an increased incidence of pneumothorax. In families, emphysema showed an autosomal dominant inheritance pattern, along with pulmonary fibrosis and other telomere syndrome features, but manifested only in smokers. Our findings identify germline mutations in telomerase as a Mendelian risk factor for COPD susceptibility that clusters in autosomal dominant families with telomere-mediated disease including pulmonary fibrosis.
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Newberry EP, Kennedy SM, Xie Y, Luo J, Stanley SE, Semenkovich CF, Crooke RM, Graham MJ, Davidson NO. Altered hepatic triglyceride content after partial hepatectomy without impaired liver regeneration in multiple murine genetic models. Hepatology 2008; 48:1097-105. [PMID: 18697204 PMCID: PMC2577767 DOI: 10.1002/hep.22473] [Citation(s) in RCA: 92] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
UNLABELLED Liver regeneration is impaired following partial hepatectomy (PH) in mice with genetic obesity and hepatic steatosis and also in wild-type mice fed a high-fat diet. These findings contrast with other data showing that liver regeneration is impaired in mice in which hepatic lipid accumulation is suppressed by either pharmacologic leptin administration or by disrupted glucocorticoid signaling. These latter findings suggest that hepatic steatosis may actually be required for normal liver regeneration. We have reexamined this relationship using several murine models of altered hepatic lipid metabolism. Liver fatty acid (FA) binding protein knockout mice manifested reduced hepatic triglyceride (TG) content compared to controls, with no effect on liver regeneration or hepatocyte proliferation. Examination of early adipogenic messenger RNAs revealed comparable induction in liver from both genotypes despite reduced hepatic steatosis. Following PH, hepatic TG was reduced in intestine-specific microsomal TG transfer protein deleter mice, which fail to absorb dietary fat, increased in peroxisome proliferator activated receptor alpha knockout mice, which exhibit defective FA oxidation, and unchanged (from wild-type mice) in liver-specific FA synthase knockout mice in which endogenous hepatic FA synthesis is impaired. Hepatic TG increased in the regenerating liver in all models, even in animals in which lipid accumulation is genetically constrained. However, in no model -- and over a >90-fold range of hepatic TG content -- was liver regeneration significantly impaired following PH. CONCLUSION Although hepatic TG content is widely variable and increases during liver regeneration, alterations in neither exogenous or endogenous lipid metabolic pathways, demonstrated to promote or diminish hepatic steatosis, influence hepatocyte proliferation.
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Affiliation(s)
| | - Susan M. Kennedy
- Department of Medicine, School of Medicine, Washington University, St. Louis, MO
| | - Yan Xie
- Department of Medicine, School of Medicine, Washington University, St. Louis, MO
| | - Jianyang Luo
- Department of Medicine, School of Medicine, Washington University, St. Louis, MO
| | - Susan E. Stanley
- Department of Medicine, School of Medicine, Washington University, St. Louis, MO
| | - Clay F. Semenkovich
- Department of Medicine, School of Medicine, Washington University, St. Louis, MO
| | | | | | - Nicholas O. Davidson
- Department of Medicine, School of Medicine, Washington University, St. Louis, MO
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15
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Lu J, Chen M, Stanley SE, Li E. Effect of heterodimer partner RXRalpha on PPARgamma activation function-2 helix in solution. Biochem Biophys Res Commun 2007; 365:42-6. [PMID: 17980149 DOI: 10.1016/j.bbrc.2007.10.143] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2007] [Accepted: 10/22/2007] [Indexed: 12/01/2022]
Abstract
The structural mechanism of allosteric communication between retinoid X receptor (RXR) and its heterodimer partners remains controversial. As a first step towards addressing this question, we report a nuclear magnetic resonance (NMR) study on the GW1929-bound peroxisome proliferator-activated receptor gamma (PPARgamma) ligand-binding domain (LBD) with and without the 9-cis-retinoic acid (9cRA)-bound RXRalpha LBD. Sequence-specific 13C(alpha), 13C(beta), and 13CO resonance assignments have been established for over 95% of the 275 residues in the PPARgamma LBD monomer. The 1HN, 15N, and 13CO chemical shift perturbations induced by the RXRalpha LBD binding are located at not only the heterodimer interface that includes the C-terminal residue Y477 but also residues Y473 and K474 in the activation function-2 (AF-2) helix. This result suggests that 9cRA-bound RXRalpha can affect the PPARgamma AF-2 helix in solution and demonstrates that NMR is a powerful new tool for studying the mechanism of allosteric ligand activation in RXR heterodimers.
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Affiliation(s)
- Jianyun Lu
- Department of Internal Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA.
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16
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Abstract
Rapid advances in genome sequencing and gene expression microarray technologies are providing unprecedented opportunities to identify specific genes involved in complex biological processes, such as development, signal transduction, and disease. The vast amount of data generated by these technologies has presented new challenges in bioinformatics. To help organize and interpret microarray data, new and efficient computational methods are needed to: (1) distinguish accurately between different biological or clinical categories (e.g., malignant vs. benign), and (2) identify specific genes that play a role in determining those categories. Here we present a novel and simple method that exhaustively scans microarray data for unambiguous gene expression patterns. Such patterns of data can be used as the basis for classification into biological or clinical categories. The method, termed the Characteristic Attribute Organization System (CAOS), is derived from fundamental precepts in systematic biology. In CAOS we define two types of characteristic attributes ('pure' and 'private') that may exist in gene expression microarray data. We also consider additional attributes ('compound') that are composed of expression states of more than one gene that are not characteristic on their own. CAOS was tested on three well-known cancer DNA microarray data sets for its ability to classify new microarray samples. We found CAOS to be a highly accurate and robust class prediction technique. In addition, CAOS identified specific genes, not emphasized in other analyses, that may be crucial to the biology of certain types of cancer. The success of CAOS in this study has significant implications for basic research and the future development of reliable methods for clinical diagnostic tools.
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Affiliation(s)
- I N Sarkar
- Department of Medical Informatics, College of Physicians and Surgeons, Columbia University, New York, NY 10032, USA
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17
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Stephens JC, Schneider JA, Tanguay DA, Choi J, Acharya T, Stanley SE, Jiang R, Messer CJ, Chew A, Han JH, Duan J, Carr JL, Lee MS, Koshy B, Kumar AM, Zhang G, Newell WR, Windemuth A, Xu C, Kalbfleisch TS, Shaner SL, Arnold K, Schulz V, Drysdale CM, Nandabalan K, Judson RS, Ruano G, Vovis GF. Haplotype variation and linkage disequilibrium in 313 human genes. Science 2001; 293:489-93. [PMID: 11452081 DOI: 10.1126/science.1059431] [Citation(s) in RCA: 562] [Impact Index Per Article: 24.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
Variation within genes has important implications for all biological traits. We identified 3899 single nucleotide polymorphisms (SNPs) that were present within 313 genes from 82 unrelated individuals of diverse ancestry, and we organized the SNPs into 4304 different haplotypes. Each gene had several variable SNPs and haplotypes that were present in all populations, as well as a number that were population-specific. Pairs of SNPs exhibited variability in the degree of linkage disequilibrium that was a function of their location within a gene, distance from each other, population distribution, and population frequency. Haplotypes generally had more information content (heterozygosity) than did individual SNPs. Our analysis of the pattern of variation strongly supports the recent expansion of the human population.
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Affiliation(s)
- J C Stephens
- Genaissance Pharmaceuticals, Inc., Five Science Park, New Haven, CT 06511, USA.
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18
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Planet PJ, DeSalle R, Siddall M, Bael T, Sarkar IN, Stanley SE. Systematic analysis of DNA microarray data: ordering and interpreting patterns of gene expression. Genome Res 2001; 11:1149-55. [PMID: 11435396 DOI: 10.1101/gr.187601] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Affiliation(s)
- P J Planet
- Department of Microbiology, Columbia University College of Physicians and Surgeons, New York, New York 10032, USA
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19
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Broughton RE, Stanley SE, Durrett RT. Quantification of homoplasy for nucleotide transitions and transversions and a reexamination of assumptions in weighted phylogenetic analysis. Syst Biol 2000; 49:617-27. [PMID: 12116430 DOI: 10.1080/106351500750049734] [Citation(s) in RCA: 55] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022] Open
Abstract
Nucleotide transitions are frequently down-weighted relative to transversions in phylogenetic analysis. This is based on the assumption that transitions, by virtue of their greater evolutionary rate, exhibit relatively more homoplasy and are therefore less reliable phylogenetic characters. Relative amounts of homoplastic and consistent transition and transversion changes in mitochondrial protein coding genes were determined from character-state reconstructions on a highly corroborated phylogeny of mammals. We found that although homoplasy was related to evolutionary rates and was greater for transitions, the absolute number of consistent transitions greatly exceeded the number of consistent transversions. Consequently, transitions provided substantially more useful phylogenetic information than transversions. These results suggest that down-weighting transitions may be unwarranted in many cases. This conclusion was supported by the fact that a range of transition: transversion weighting schemes applied to various mitochondrial genes and genomic partitions rarely provided improvement in phylogenetic estimates relative to equal weighting, and in some cases weighting transitions more heavily than transversions was most effective.
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Affiliation(s)
- R E Broughton
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, New York 14853-2701, USA
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Affiliation(s)
- GB Nunn
- Department of Ornithology, American Museum of Natural History, Central Park West at 79th Street, New York, NY 10024, USA
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21
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Abstract
Patterns of molecular evolution in birds have long been considered anomalous. Compared with other vertebrates, birds have reduced levels of genetic divergence between groups of similar taxonomic ranks for a variety of nuclear and mitochondrial markers. This observation led to the avian constraint hypothesis, which identifies increased functional constraint on avian proteins as the cause for the reduction in genetic divergence. Subsequent investigations provided additional support for the avian constraint hypothesis when rates of molecular evolution were found to be slower in birds than in mammals in a variety of independent calibrations. It is possible to test the avian constraint hypothesis as an explanation for this avian slowdown by comparing DNA sequence data from protein-coding regions in birds and homologous regions in mammals. The increased selective constraints should lead to a reduction in the proportion of amino acid replacement substitutions. To test for such a decrease, we calculated the numbers of amino acid replacement substitutions per replacement site (dN) and silent substitutions per silent site (dS) for the complete mitochondrial cytochrome b gene using 38 avian and 43 mammalian comparisons that were phylogenetically independent. We find that dN/dS is significantly smaller in birds than in mammals. This difference cannot be explained by differences in codon bias affecting dS values. We suggest that the avian slowdown can be explained, at least in part, by a decreased tolerance for amino acid substitutions in avian species relative to mammalian species.
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Affiliation(s)
- S E Stanley
- Section of Ecology and Systematics, Cornell University, USA.
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22
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Abstract
Variation in rates of molecular evolution now appears to be widespread. The demonstration that body size is correlated with rates of molecular evolution suggests that physiological and ecological factors may be involved in molecular rate variation, but large-scale comparative studies are still lacking. Here, we use complete cytochrome b sequences from 85 species of tube-nosed seabirds (order Procellariiformes) and 5 outgroup species of penguins (order Sphenisciformes) to test for an association between body mass and rates of molecular evolution within the former avian order. Cladistic analysis of the 90 sequences estimates a phylogeny largely consistent with the traditional taxonomy of the Procellariiformes. The Diomedeidae, Procellariidae, and Pelecanoididae are monophyletic, while the Hydrobatidae are basal and paraphyletic. However, the two subfamilies within the Hydrobatidae (Hydrobatinae and Oceanitinae) are monophyletic. A likelihood ratio test detects significant deviation from clocklike evolution in our data. Using a sign test for an association between body mass and branch length in the seabird phylogeny, we find that larger taxa tend to have shorter terminal branch lengths than smaller taxa. This observation suggests that rates of mitochondrial DNA evolution are slower for larger taxa. Rate calibrations based on the fossil record reveal concordant body size effects. We interpret these results as evidence for a metabolic rate effect, as the species in this order exhibit large differences in metabolic rates, which are known to be highly correlated with body mass in this group. Our results support previous findings of body size effects and show that this effect can be significant even within a single avian order. This suggests that even lineage-specific molecular clocks may not be tenable if calibrations involve taxa with different metabolic rates.
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Affiliation(s)
- G B Nunn
- Department of Ornithology, American Museum of Natural History, New York, New York, USA
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Affiliation(s)
- S E Stanley
- Section of Ecology and Systematics, Corson Hall, Cornell University, Ithaca, NY 14853-2701, USA
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