51
|
Otten RA, Ellenberger DL, Adams DR, Fridlund CA, Jackson E, Pieniazek D, Rayfield MA. Identification of a window period for susceptibility to dual infection with two distinct human immunodeficiency virus type 2 isolates in a Macaca nemestrina (pig-tailed macaque) model. J Infect Dis 1999; 180:673-84. [PMID: 10438354 DOI: 10.1086/314968] [Citation(s) in RCA: 38] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022] Open
Abstract
The potential to establish dual retroviral infections was investigated in this study. Groups of macaques infected with human immunodeficiency virus type 2 (HIV-2) isolate (either GB122 or CDC77618) were exposed to the other virus at 2, 4, 8, 12, 14, or 72 weeks after primary inoculation. Dual infections were established in macaques simultaneously exposed to both viruses. In other groups, secondary infections were observed only if challenge occurred at early intervals after primary infection but before a full seroconversion. Polymerase chain reaction and virus-isolation data demonstrated that challenges at 8, 12, 14, or 72 weeks after infection with the initial isolate failed to result in a dual infection. Anti-HIV-2 serologic titers, CD4 levels, virus burden, and the ability to superinfect peripheral blood mononuclear cells in vitro were not correlated with susceptibility to or protection from secondary challenges in this investigation. These findings demonstrate a window period for susceptibility to dual infection and indicate that protection from retroviral infection may be achievable.
Collapse
|
|
26 |
38 |
52
|
Lam C, Golas GA, Davids M, Huizing M, Kane MS, Krasnewich DM, Malicdan MCV, Adams DR, Markello TC, Zein WM, Gropman AL, Lodish MB, Stratakis CA, Maric I, Rosenzweig SD, Baker EH, Ferreira CR, Danylchuk NR, Kahler S, Garnica AD, Bradley Schaefer G, Boerkoel CF, Gahl WA, Wolfe LA. Expanding the clinical and molecular characteristics of PIGT-CDG, a disorder of glycosylphosphatidylinositol anchors. Mol Genet Metab 2015; 115:128-140. [PMID: 25943031 PMCID: PMC6341466 DOI: 10.1016/j.ymgme.2015.04.007] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/06/2015] [Revised: 04/28/2015] [Accepted: 04/29/2015] [Indexed: 11/28/2022]
Abstract
PIGT-CDG, an autosomal recessive syndromic intellectual disability disorder of glycosylphosphatidylinositol (GPI) anchors, was recently described in two independent kindreds [Multiple Congenital Anomalies-Hypotonia-Seizures Syndrome 3 (OMIM, #615398)]. PIGT encodes phosphatidylinositol-glycan biosynthesis class T, a subunit of the heteropentameric transamidase complex that facilitates the transfer of GPI to proteins. GPI facilitates attachment (anchoring) of proteins to cell membranes. We describe, at ages 7 and 6 years, two children of non-consanguineous parents; they had hypotonia, severe global developmental delay, and intractable seizures along with endocrine, ophthalmologic, skeletal, hearing, and cardiac anomalies. Exome sequencing revealed that both siblings had compound heterozygous variants in PIGT (NM_015937.5), i.e., c.918dupC, a novel duplication leading to a frameshift, and c.1342C > T encoding a previously described missense variant. Flow cytometry studies showed decreased surface expression of GPI-anchored proteins on granulocytes, consistent with findings in previous cases. These siblings further delineate the clinical spectrum of PIGT-CDG, reemphasize the neuro-ophthalmologic presentation, clarify the endocrine features, and add hypermobility, low CSF albumin quotient, and hearing loss to the phenotypic spectrum. Our results emphasize that GPI anchor-related congenital disorders of glycosylation (CDGs) should be considered in subjects with early onset severe seizure disorders and dysmorphic facial features, even in the presence of a normal carbohydrate-deficient transferrin pattern and N-glycan profiling. Currently available screening for CDGs will not reliably detect this family of disorders, and our case reaffirms that the use of flow cytometry and genetic testing is essential for diagnosis in this group of disorders.
Collapse
|
Case Reports |
10 |
38 |
53
|
Ochiai K, Takita S, Eiraku T, Kojima A, Iwase K, Kishi T, Fukuchi K, Yasue T, Adams DR, Allcock RW, Jiang Z, Kohno Y. Phosphodiesterase inhibitors. Part 3: Design, synthesis and structure–activity relationships of dual PDE3/4-inhibitory fused bicyclic heteroaromatic-dihydropyridazinones with anti-inflammatory and bronchodilatory activity. Bioorg Med Chem 2012; 20:1644-58. [DOI: 10.1016/j.bmc.2012.01.033] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2011] [Revised: 01/19/2012] [Accepted: 01/19/2012] [Indexed: 11/24/2022]
|
|
13 |
37 |
54
|
Donges CE, Duffield R, Guelfi KJ, Smith GC, Adams DR, Edge JA. Comparative effects of single-mode vs. duration-matched concurrent exercise training on body composition, low-grade inflammation, and glucose regulation in sedentary, overweight, middle-aged men. Appl Physiol Nutr Metab 2013; 38:779-88. [DOI: 10.1139/apnm-2012-0443] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
|
|
12 |
37 |
55
|
Baker EH, Sloan JL, Hauser NS, Gropman AL, Adams DR, Toro C, Manoli I, Venditti CP. MRI characteristics of globus pallidus infarcts in isolated methylmalonic acidemia. AJNR Am J Neuroradiol 2014; 36:194-201. [PMID: 25190203 DOI: 10.3174/ajnr.a4087] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
BACKGROUND Bilateral infarcts confined to the globus pallidus are unusual and occur in conjunction with only a few disorders, including isolated methylmalonic acidemia, a heterogeneous inborn error of metabolism. On the basis of neuroradiographic features of metabolic strokes observed in a large cohort of patients with methylmalonic acidemia, we have devised a staging system for methylmalonic acidemia-related globus pallidus infarcts. MATERIALS AND METHODS Forty patients with isolated methylmalonic acidemia and neurologic symptoms underwent clinical brain MR imaging studies, which included 3D-T1WI. Infarcted globus pallidus segments were neuroanatomically characterized, and infarct volumes were measured. RESULTS Globus pallidus infarcts were present in 19 patients; all were bilateral, and most were left-dominant. A neuroanatomic scoring system based on the infarct patterns was devised; this revealed a 5-stage hierarchical susceptibility to metabolic infarct, with the posterior portion of the globus pallidus externa being the most vulnerable. Globus pallidus infarct prevalence by methylmalonic acidemia class was the following: cblA (5/7, 71%), cblB (3/7, 43%), mut(o) (10/22, 45%), and mut- (1/4, 25%). Tiny lacunar infarcts in the pars reticulata of the substantia nigra, previously unrecognized in methylmalonic acidemia, were found in 17 patients, 13 of whom also had a globus pallidus infarct. CONCLUSIONS The staged pattern of globus pallidus infarcts in isolated methylmalonic acidemia suggests a nonuniform, regionally specific cellular susceptibility to metabolic injury, even for patients having milder biochemical phenotypes. In support of this hypothesis, the delineation of lacunar infarcts in the pars reticulata of the substantia nigra, a tissue functionally and histologically identical to the globus pallidus interna, supports the concept of cell-specific pathology.
Collapse
|
Research Support, N.I.H., Intramural |
11 |
35 |
56
|
|
|
42 |
33 |
57
|
Christian F, Anthony DF, Vadrevu S, Riddell T, Day JP, McLeod R, Adams DR, Baillie GS, Houslay MD. p62 (SQSTM1) and cyclic AMP phosphodiesterase-4A4 (PDE4A4) locate to a novel, reversible protein aggregate with links to autophagy and proteasome degradation pathways. Cell Signal 2010; 22:1576-96. [PMID: 20600853 DOI: 10.1016/j.cellsig.2010.06.003] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2010] [Accepted: 06/15/2010] [Indexed: 02/07/2023]
Abstract
Chronic challenge of cyclic AMP phosphodiesterase-4A4 (PDE4A4) with certain PDE4 selective inhibitors causes it to reversibly form intracellular aggregates that are not membrane-encapsulated. These aggregates are neither stress granules (SGs) nor processing bodies (PBs) as they contain neither PABP-1 nor Dcp1a, respectively. However, the PDE4 inhibitor rolipram decreases arsenite-induced SGs and increases the amount of PBs, while arsenite challenge ablates rolipram-induced PDE4A4 aggregates. PDE4A4 aggregates are neither autophagic vesicles (autophagosomes) nor aggresomes, although microtubule disruptors ablate PDE4A4 aggregate formation. PDE4A4 constitutively co-immunoprecipitates with p62 protein (sequestosome1, SQSTM1), which locates to both PDE4A4 aggregates and autophagosomes in cells constitutively challenged with rolipram. The mTor inhibitor, rapamycin, activates autophagy, prevents PDE4A4 from forming intracellular aggregates and triggers the loss of bound p62 from PDE4A4. siRNA-mediated knockdown of p62 attenuates PDE4A4 aggregate formation. The p62-binding protein, light chain 3 (LC3), is not found in PDE4A4 aggregates. Blockade of proteasome activity and activation of autophagy with MG132 both increases the level of ubiquitinated proteins found associated with PDE4A4 and inhibits PDE4A4 aggregate formation. Activation of autophagy with either thapsigargin or ionomycin inhibits PDE4A4 aggregate formation. Inhibition of autophagy with either wortmannin or LY294002 activates PDE4A4 aggregate formation. The protein kinase C inhibitors, RO 320432 and GO 6983, and the ERK inhibitors UO 126 and PD 98059 all activated PDE4A4 aggregate formation, whilst roscovitine, thalidomide and the tyrosine kinase inhibitors, genistein and AG17, all inhibited this process. We suggest that the fate of p62-containing protein aggregates need not necessarily be terminal, through delivery to autophagic vesicles and aggresomes. Instead, we propose a novel regulatory mechanism where a sub-population of p62-containing protein aggregates would form in a rapid, reversible manner so as to sequester specific cargo away from their normal, functionally important site(s) within the cell. Thus an appropriate conformational change in the target protein would confer reversible recruitment into a sub-population of p62-containing protein aggregates and so provide a regulatory function by removing these cargo proteins from their functionally important site(s) in a cell.
Collapse
|
Research Support, Non-U.S. Gov't |
15 |
33 |
58
|
Burke EA, Frucht SJ, Thompson K, Wolfe LA, Yokoyama T, Bertoni M, Huang Y, Sincan M, Adams DR, Taylor RW, Gahl WA, Toro C, Malicdan MCV. Biallelic mutations in mitochondrial tryptophanyl-tRNA synthetase cause Levodopa-responsive infantile-onset Parkinsonism. Clin Genet 2018; 93:712-718. [PMID: 29120065 PMCID: PMC5828974 DOI: 10.1111/cge.13172] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2017] [Revised: 10/30/2017] [Accepted: 11/05/2017] [Indexed: 12/30/2022]
Abstract
Mitochondrial aminoacyl‐tRNA synthetases (mtARSs) are essential, ubiquitously expressed enzymes that covalently attach amino acids to their corresponding tRNA molecules during translation of mitochondrial genes. Deleterious variants in the mtARS genes cause a diverse array of phenotypes, many of which involve the nervous system. Moreover, distinct mutations in mtARSs often cause different clinical manifestations. Recently, the gene encoding mitochondrial tryptophanyl tRNA synthetase (WARS2) was reported to cause 2 different neurological phenotypes, a form of autosomal recessive intellectual disability and a syndrome of severe infantile‐onset leukoencephalopathy. Here, we report the case of a 17‐year‐old boy with compound heterozygous mutations in WARS2 (p.Trp13Gly, p.Ser228Trp) who presented with infantile‐onset, Levodopa‐responsive Parkinsonism at the age of 2 years. Analysis of patient‐derived dermal fibroblasts revealed decreased steady‐state WARS2 protein and normal OXPHOS content. Muscle mitochondrial studies suggested mitochondrial proliferation without obvious respiratory chain deficiencies at the age of 9 years. This case expands the phenotypic spectrum of WARS2 deficiency and emphasizes the importance of mitochondrial protein synthesis in the pathogenesis of Parkinsonism.
Collapse
|
Research Support, Non-U.S. Gov't |
7 |
33 |
59
|
Mochel F, Sedel F, Vanderver A, Engelke UFH, Barritault J, Yang BZ, Kulkarni B, Adams DR, Clot F, Ding JH, Kaneski CR, Verheijen FW, Smits BW, Seguin F, Brice A, Vanier MT, Huizing M, Schiffmann R, Durr A, Wevers RA. Cerebellar ataxia with elevated cerebrospinal free sialic acid (CAFSA). ACTA ACUST UNITED AC 2009; 132:801-9. [PMID: 19153153 DOI: 10.1093/brain/awn355] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
In order to identify new metabolic abnormalities in patients with complex neurodegenerative disorders of unknown aetiology, we performed high resolution in vitro proton nuclear magnetic resonance spectroscopy on patient cerebrospinal fluid (CSF) samples. We identified five adult patients, including two sisters, with significantly elevated free sialic acid in the CSF compared to both the cohort of patients with diseases of unknown aetiology (n = 144; P < 0.001) and a control group of patients with well-defined diseases (n = 91; P < 0.001). All five patients displayed cerebellar ataxia, with peripheral neuropathy and cognitive decline or noteworthy behavioural changes. Cerebral MRI showed mild to moderate cerebellar atrophy (5/5) as well as white matter abnormalities in the cerebellum including the peridentate region (4/5), and at the periventricular level (3/5). Two-dimensional gel analyses revealed significant hyposialylation of transferrin in CSF of all patients compared to age-matched controls (P < 0.001)--a finding not present in the CSF of patients with Salla disease, the most common free sialic acid storage disorder. Free sialic acid content was normal in patients' urine and cultured fibroblasts as were plasma glycosylation patterns of transferrin. Analysis of the ganglioside profile in peripheral nerve biopsies of two out of five patients was also normal. Sequencing of four candidate genes in the free sialic acid biosynthetic pathway did not reveal any mutation. We therefore identified a new free sialic acid syndrome in which cerebellar ataxia is the leading symptom. The term CAFSA is suggested (cerebellar ataxia with free sialic acid).
Collapse
|
Research Support, Non-U.S. Gov't |
16 |
32 |
60
|
Johnston KA, Allcock RW, Jiang Z, Collier ID, Blakli H, Rosair GM, Bailey PD, Morgan KM, Kohno Y, Adams DR. Concise routes to pyrazolo[1,5-a]pyridin-3-yl pyridazin-3-ones. Org Biomol Chem 2008; 6:175-86. [DOI: 10.1039/b713638b] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
|
|
17 |
32 |
61
|
Kanca O, Andrews JC, Lee PT, Patel C, Braddock SR, Slavotinek AM, Cohen JS, Gubbels CS, Aldinger KA, Williams J, Indaram M, Fatemi A, Yu TW, Agrawal PB, Vezina G, Simons C, Crawford J, Lau CC, Chung WK, Markello TC, Dobyns WB, Adams DR, Gahl WA, Wangler MF, Yamamoto S, Bellen HJ, Malicdan MCV, Acosta MT, Adams DR, Agrawal P, Alejandro ME, Allard P, Alvey J, Andrews A, Ashley EA, Azamian MS, Bacino CA, Bademci G, Baker E, Balasubramanyam A, Baldridge D, Bale J, Barbouth D, Batzli GF, Bayrak-Toydemir P, Beggs AH, Bejerano G, Bellen HJ, Bernstein JA, Berry GT, Bican A, Bick DP, Birch CL, Bivona S, Bohnsack J, Bonnenmann C, Bonner D, Boone BE, Bostwick BL, Botto L, Briere LC, Brokamp E, Brown DM, Brush M, Burke EA, Burrage LC, Butte MJ, Carey J, Carrasquillo O, Chang TCP, Chao HT, Clark GD, Coakley TR, Cobban LA, Cogan JD, Cole FS, Colley HA, Cooper CM, Cope H, Craigen WJ, D'Souza P, Dasari S, Davids M, Dayal JG, Dell'Angelica EC, Dhar SU, Dorrani N, Dorset DC, Douine ED, Draper DD, Duncan L, Eckstein DJ, Emrick LT, Eng CM, Esteves C, Estwick T, Fernandez L, Ferreira C, Fieg EL, Fisher PG, Fogel BL, Forghani I, Fresard L, Gahl WA, Godfrey RA, Goldman AM, Goldstein DB, Gourdine JPF, Grajewski A, Groden CA, Gropman AL, Haendel M, Hamid R, Hanchard NA, Hayes N, High F, Holm IA, Hom J, Huang A, Huang Y, Isasi R, Jamal F, Jiang YH, Johnston JM, Jones AL, Karaviti L, Kelley EG, Kiley D, Koeller DM, Kohane IS, Kohler JN, Krakow D, Krasnewich DM, Korrick S, Koziura M, Krier JB, Kyle JE, Lalani SR, Lam B, Lanpher BC, Lanza IR, Lau CC, Lazar J, LeBlanc K, Lee BH, Lee H, Levitt R, Levy SE, Lewis RA, Lincoln SA, Liu P, Liu XZ, Longo N, Loo SK, Loscalzo J, Maas RL, Macnamara EF, MacRae CA, Maduro VV, Majcherska MM, Malicdan MCV, Mamounas LA, Manolio TA, Mao R, Markello TC, Marom R, Marth G, Martin BA, Martin MG, Martínez-Agosto JA, Marwaha S, May T, McCauley J, McConkie-Rosell A, McCormack CE, McCray AT, Metz TO, Might M, Morava-Kozicz E, Moretti PM, Morimoto M, Mulvihill JJ, Murdock DR, Nath A, Nelson SF, Newberry JS, Newman JH, Nicholas SK, Novacic D, Oglesbee D, Orengo JP, Pace L, Pak S, Pallais JC, Palmer CG, Papp JC, Parker NH, Phillips JA, Posey JE, Postlethwait JH, Potocki L, Pusey BN, Quinlan A, Raja AN, Renteria G, Reuter CM, Rives L, Robertson AK, Rodan LH, Rosenfeld JA, Rowley RK, Ruzhnikov M, Sacco R, Sampson JB, Samson SL, Saporta M, Schaechter J, Schedl T, Schoch K, Scott DA, Shakachite L, Sharma P, Shashi V, Shields K, Shin J, Signer R, Sillari CH, Silverman EK, Sinsheimer JS, Sisco K, Smith KS, Solnica-Krezel L, Spillmann RC, Stoler JM, Stong N, Sullivan JA, Sutton S, Sweetser DA, Tabor HK, Tamburro CP, Tan QKG, Tekin M, Telischi F, Thorson W, Tifft CJ, Toro C, Tran AA, Urv TK, Velinder M, Viskochil D, Vogel TP, Wahl CE, Walley NM, Walsh CA, Walker M, Wambach J, Wan J, Wang LK, Wangler MF, Ward PA, Waters KM, Webb-Robertson BJM, Wegner D, Westerfield M, Wheeler MT, Wise AL, Wolfe LA, Woods JD, Worthey EA, Yamamoto S, Yang J, Yoon AJ, Yu G, Zastrow DB, Zhao C, Zuchner S. De Novo Variants in WDR37 Are Associated with Epilepsy, Colobomas, Dysmorphism, Developmental Delay, Intellectual Disability, and Cerebellar Hypoplasia. Am J Hum Genet 2019; 105:413-424. [PMID: 31327508 PMCID: PMC6699142 DOI: 10.1016/j.ajhg.2019.06.014] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2018] [Accepted: 06/14/2019] [Indexed: 12/16/2022] Open
Abstract
WD40 repeat-containing proteins form a large family of proteins present in all eukaryotes. Here, we identified five pediatric probands with de novo variants in WDR37, which encodes a member of the WD40 repeat protein family. Two probands shared one variant and the others have variants in nearby amino acids outside the WD40 repeats. The probands exhibited shared phenotypes of epilepsy, colobomas, facial dysmorphology reminiscent of CHARGE syndrome, developmental delay and intellectual disability, and cerebellar hypoplasia. The WDR37 protein is highly conserved in vertebrate and invertebrate model organisms and is currently not associated with a human disease. We generated a null allele of the single Drosophila ortholog to gain functional insights and replaced the coding region of the fly gene CG12333/wdr37 with GAL4. These flies are homozygous viable but display severe bang sensitivity, a phenotype associated with seizures in flies. Additionally, the mutant flies fall when climbing the walls of the vials, suggesting a defect in grip strength, and repeat the cycle of climbing and falling. Similar to wall clinging defect, mutant males often lose grip of the female abdomen during copulation. These phenotypes are rescued by using the GAL4 in the CG12333/wdr37 locus to drive the UAS-human reference WDR37 cDNA. The two variants found in three human subjects failed to rescue these phenotypes, suggesting that these alleles severely affect the function of this protein. Taken together, our data suggest that variants in WDR37 underlie a novel syndromic neurological disorder.
Collapse
|
Research Support, N.I.H., Extramural |
6 |
32 |
62
|
Werner L, Machara A, Adams DR, Cox DP, Hudlicky T. Synthesis of Buprenorphine from Oripavine via N-Demethylation of Oripavine Quaternary Salts. J Org Chem 2011; 76:4628-34. [DOI: 10.1021/jo200567n] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
|
|
14 |
32 |
63
|
Myerson J, Adams DR, Hale S, Jenkins L. Analysis of group differences in processing speed: Brinley plots, Q-Q plots, and other conspiracies. Psychon Bull Rev 2003; 10:224-37. [PMID: 12747512 DOI: 10.3758/bf03196489] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Researchers in a growing number of areas (including cognitive development, aging, and neuropsychology) use Brinley plots to compare the processing speed of different groups. Ratcliff, Spieler, and McKoon (2000) argued that a Brinley plot is a quantile-quantile (Q-Q) plot and that therefore Brinley plot regression slopes measure standard deviation ratios rather than relative speed of processing. We show that this argument is incorrect. Brinley plots, by definition, are not Q-Q plots; the former are based on unranked data and the latter are based on ranked data. Furthermore, the relationship between standard deviation ratios and slopes is a general property of regression lines and has no implications for the use of Brinley plot regression slopes as processing speed measures. We also show that the relative speed interpretation of Brinley plot slopes is strongly supported by converging evidence from a metaanalysis of visual search, mental rotation, and memory scanning in young and older adults. As to Ratcliff et al.'s hypothesis that age differences in response time are attributable to greater cautiousness on the part of the elderly, rather than true processing speed differences, this hypothesis has been extensively tested in previous studies and found wanting.
Collapse
|
Comparative Study |
22 |
32 |
64
|
Terry R, Cheung YF, Praestegaard M, Baillie GS, Huston E, Gall I, Adams DR, Houslay MD. Occupancy of the catalytic site of the PDE4A4 cyclic AMP phosphodiesterase by rolipram triggers the dynamic redistribution of this specific isoform in living cells through a cyclic AMP independent process. Cell Signal 2003; 15:955-71. [PMID: 12873709 DOI: 10.1016/s0898-6568(03)00092-5] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
In cells transfected to express wild-type PDE4A4 cAMP phosphodiesterase (PDE), the PDE4 selective inhibitor rolipram caused PDE4A4 to relocalise so as to form accretion foci. This process was followed in detail in living cells using a PDE4A4 chimera formed with Green Fluorescent Protein (GFP). The same pattern of behaviour was also seen in chimeras of PDE4A4 formed with various proteins and peptides, including LimK, RhoC, FRB and the V5-6His tag. Maximal PDE4A4 foci formation, occurred over a period of about 10 h, was dose-dependent on rolipram and was reversible upon washout of rolipram. Inhibition of protein synthesis, using cycloheximide, but not PKA activity with H89, inhibited foci generation. Foci formation was elicited by Ro20-1724 and RS25344 but not by either Ariflo or RP73401, showing that not all PDE4 selective inhibitors had this effect. Ariflo and RP73401 dose-dependently antagonised rolipram-induced foci formation and dispersed rolipram pre-formed foci as did the adenylyl cyclase activator, forskolin. Foci formation showed specificity for PDE4A4 and its rodent homologue, PDE4A5, as it was not triggered in living cells expressing the PDE4B2, PDE4C2, PDE4D3 and PDE4D5 isoforms as GFP chimeras. Altered foci formation was seen in the Deltab-LR2-PDE4A4 construct, which deleted a region within LRZ, showing that appropriate linkage between the N-terminal portion of PDE4A4 and the catalytic unit of PDE4A4 was needed for foci formation. Certain single point mutations within the PDE4A4 catalytic site (His505Asn, His506Asn and Val475Asp) were shown to ablate foci formation but still allow rolipram inhibition of PDE4A4 catalytic activity. We suggest that the binding of certain, but not all, PDE4 selective inhibitors to PDE4A4 induces a conformational change in this isoform by 'inside-out' signalling that causes it to redistribute in the cell. Displacing foci-forming inhibitors with either cAMP or inhibitors that do not form foci can antagonise this effect. Specificity of this effect for PDE4A4 and its homologue PDE4A5 suggests that interplay between the catalytic site and the unique N-terminal region of these isoforms is required. Thus, certain PDE4 selective inhibitors may exert effects on PDE4A4 that extend beyond simple catalytic inhibition. These require protein synthesis and may lead to redistribution of PDE4A4 and any associated proteins. Foci formation of PDE4A4 may be of use in probing for conformational changes in this isoform and for sub-categorising PDE4 selective inhibitors.
Collapse
|
|
22 |
31 |
65
|
Adams DR, Sincan M, Fuentes Fajardo K, Mullikin JC, Pierson TM, Toro C, Boerkoel CF, Tifft CJ, Gahl WA, Markello TC. Analysis of DNA sequence variants detected by high-throughput sequencing. Hum Mutat 2012; 33:599-608. [PMID: 22290882 DOI: 10.1002/humu.22035] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2011] [Accepted: 12/02/2011] [Indexed: 12/18/2022]
Abstract
The Undiagnosed Diseases Program at the National Institutes of Health uses high-throughput sequencing (HTS) to diagnose rare and novel diseases. HTS techniques generate large numbers of DNA sequence variants, which must be analyzed and filtered to find candidates for disease causation. Despite the publication of an increasing number of successful exome-based projects, there has been little formal discussion of the analytic steps applied to HTS variant lists. We present the results of our experience with over 30 families for whom HTS sequencing was used in an attempt to find clinical diagnoses. For each family, exome sequence was augmented with high-density SNP-array data. We present a discussion of the theory and practical application of each analytic step and provide example data to illustrate our approach. The article is designed to provide an analytic roadmap for variant analysis, thereby enabling a wide range of researchers and clinical genetics practitioners to perform direct analysis of HTS data for their patients and projects.
Collapse
|
Research Support, N.I.H., Intramural |
13 |
31 |
66
|
Adams DR, Jones AM, Plopper CG, Serabjit-Singh CJ, Philpot RM. Distribution of cytochrome P-450 monoxygenase enzymes in the nasal mucosa of hamster and rat. THE AMERICAN JOURNAL OF ANATOMY 1991; 190:291-8. [PMID: 2048556 DOI: 10.1002/aja.1001900309] [Citation(s) in RCA: 31] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Deposition of inhaled particulates onto the respiratory mucosa is relatively great in that portion of the nasal cavity unprotected by ciliated, goblet, or keratinized superficial cells. The cytochrome P-450 system is an important enzyme system involved in the biotransformation of xenobiotics into metabolites that are more readily absorbed. To examine the transitional region caudal to the nasal vestibule, nasal tissues of hamster and rat were prepared for immunocytochemistry. Blocks of tissue representing four levels along the long axis of the nasal cavity were examined. Paraffin sections were processed through the avidin-biotin peroxidase procedure, with diaminobenzidine tetrahydrochloride as the chromagen. Enzyme localization was accomplished through the use of antibodies for three rabbit cytochrome P-450 isozymes; 2, 5, and 6 (subfamilies IIB, IVB, and IA, respectively); and for rabbit NADPH-cytochrome P-450 reductase. Enzyme distribution was similar in both hamster and rat nasal tissues except in cells of striated and intercalated ducts of nasal glands and in cells of the nasolacrimal duct where immunoreactivity was greater in the hamster. Immunoreactivity for reductase and isozyme 2 was intense in nonciliated cells lining the nonolfactory epithelium, in sustentacular cells of the olfactory epithelium, and in acinar cells of olfactory glands. Distribution of reaction products to isozyme 5 and 6 were similar to but not so intense as those of reductase and isozyme 2. Reaction products for reductase and isozyme 2 occurred generally in the same cellular and intracellular regions with the following exceptions: isozyme 2 was more concentrated in cells of striated ducts and of the nasolacrimal duct, and reductase was more abundant in intercalated ducts of nasal glands.(ABSTRACT TRUNCATED AT 250 WORDS)
Collapse
|
Comparative Study |
34 |
31 |
67
|
Day JP, Lindsay B, Riddell T, Jiang Z, Allcock RW, Abraham A, Sookup S, Christian F, Bogum J, Martin EK, Rae RL, Anthony D, Rosair GM, Houslay DM, Huston E, Baillie GS, Klussmann E, Houslay MD, Adams DR. Elucidation of a Structural Basis for the Inhibitor-Driven, p62 (SQSTM1)-Dependent Intracellular Redistribution of cAMP Phosphodiesterase-4A4 (PDE4A4). J Med Chem 2011; 54:3331-47. [DOI: 10.1021/jm200070e] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
|
|
14 |
30 |
68
|
Hartley T, Lemire G, Kernohan KD, Howley HE, Adams DR, Boycott KM. New Diagnostic Approaches for Undiagnosed Rare Genetic Diseases. Annu Rev Genomics Hum Genet 2020; 21:351-372. [DOI: 10.1146/annurev-genom-083118-015345] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Accurate diagnosis is the cornerstone of medicine; it is essential for informed care and promoting patient and family well-being. However, families with a rare genetic disease (RGD) often spend more than five years on a diagnostic odyssey of specialist visits and invasive testing that is lengthy, costly, and often futile, as 50% of patients do not receive a molecular diagnosis. The current diagnostic paradigm is not well designed for RGDs, especially for patients who remain undiagnosed after the initial set of investigations, and thus requires an expansion of approaches in the clinic. Leveraging opportunities to participate in research programs that utilize new technologies to understand RGDs is an important path forward for patients seeking a diagnosis. Given recent advancements in such technologies and international initiatives, the prospect of identifying a molecular diagnosis for all patients with RGDs has never been so attainable, but achieving this goal will require global cooperation at an unprecedented scale.
Collapse
|
|
5 |
30 |
69
|
El Buri A, Adams DR, Smith D, Tate RJ, Mullin M, Pyne S, Pyne NJ. The sphingosine 1-phosphate receptor 2 is shed in exosomes from breast cancer cells and is N-terminally processed to a short constitutively active form that promotes extracellular signal regulated kinase activation and DNA synthesis in fibroblasts. Oncotarget 2018; 9:29453-29467. [PMID: 30034630 PMCID: PMC6047680 DOI: 10.18632/oncotarget.25658] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2018] [Accepted: 06/04/2018] [Indexed: 12/21/2022] Open
Abstract
We demonstrate here that the G protein-coupled receptor (GPCR), sphingosine 1-phosphate receptor 2 (S1P2, Mr = 40 kDa) is shed in hsp70+ and CD63+ containing exosomes from MDA-MB-231 breast cancer cells. The receptor is taken up by fibroblasts, where it is N-terminally processed to a shorter form (Mr = 36 kDa) that appears to be constitutively active and able to stimulate the extracellular signal regulated kinase-1/2 (ERK-1/2) pathway and DNA synthesis. An N-terminally truncated construct of S1P2, which may correspond to the processed form of the receptor generated in fibroblasts, was found to be constitutively active when over-expressed in HEK293 cells. Analysis based on the available crystal structure of the homologous S1P1 receptor suggests that, in the inactive-state, the N-terminus of S1P2 may tension TM1 so as to maintain a compressive action on TM7. This in turn may stabilise a closed basal state interface between the intracellular ends of TM7 and TM6. Cleavage and removal of the S1P2 N-terminal peptide is postulated to facilitate relaxation of TM1 and accompanying separation of TM6 and TM7. The latter transition is one of the key elements of G protein engagement and is required to open the intracellular coupling interface beneath the GPCR helix bundle. Therefore, removal at the N-terminus of S1P2 is likely to enhance G protein coupling. These findings provide the first evidence that S1P2 is released from breast cancer cells in exosomes and is processed by fibroblasts to promote ERK signaling and proliferation of these cells.
Collapse
|
Journal Article |
7 |
29 |
70
|
Adams DR, McFarland LZ. Septal olfactory organ in Peromyscus. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY. A, COMPARATIVE PHYSIOLOGY 1971; 40:971-4. [PMID: 4400102 DOI: 10.1016/0300-9629(71)90285-4] [Citation(s) in RCA: 29] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
|
|
54 |
29 |
71
|
Arbabi A, Adams DR, Fidler S, Brudno M. Identifying Clinical Terms in Medical Text Using Ontology-Guided Machine Learning. JMIR Med Inform 2019; 7:e12596. [PMID: 31094361 PMCID: PMC6533869 DOI: 10.2196/12596] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2018] [Revised: 02/20/2019] [Accepted: 03/29/2019] [Indexed: 01/22/2023] Open
Abstract
Background Automatic recognition of medical concepts in unstructured text is an important component of many clinical and research applications, and its accuracy has a large impact on electronic health record analysis. The mining of medical concepts is complicated by the broad use of synonyms and nonstandard terms in medical documents. Objective We present a machine learning model for concept recognition in large unstructured text, which optimizes the use of ontological structures and can identify previously unobserved synonyms for concepts in the ontology. Methods We present a neural dictionary model that can be used to predict if a phrase is synonymous to a concept in a reference ontology. Our model, called the Neural Concept Recognizer (NCR), uses a convolutional neural network to encode input phrases and then rank medical concepts based on the similarity in that space. It uses the hierarchical structure provided by the biomedical ontology as an implicit prior embedding to better learn embedding of various terms. We trained our model on two biomedical ontologies—the Human Phenotype Ontology (HPO) and Systematized Nomenclature of Medicine - Clinical Terms (SNOMED-CT). Results We tested our model trained on HPO by using two different data sets: 288 annotated PubMed abstracts and 39 clinical reports. We achieved 1.7%-3% higher F1-scores than those for our strongest manually engineered rule-based baselines (P=.003). We also tested our model trained on the SNOMED-CT by using 2000 Intensive Care Unit discharge summaries from MIMIC (Multiparameter Intelligent Monitoring in Intensive Care) and achieved 0.9%-1.3% higher F1-scores than those of our baseline. The results of our experiments show high accuracy of our model as well as the value of using the taxonomy structure of the ontology in concept recognition. Conclusion Most popular medical concept recognizers rely on rule-based models, which cannot generalize well to unseen synonyms. In addition, most machine learning methods typically require large corpora of annotated text that cover all classes of concepts, which can be extremely difficult to obtain for biomedical ontologies. Without relying on large-scale labeled training data or requiring any custom training, our model can be efficiently generalized to new synonyms and performs as well or better than state-of-the-art methods custom built for specific ontologies.
Collapse
|
Journal Article |
6 |
28 |
72
|
Adams DR, Tollinche LE, Yeoh CB, Artman J, Mehta M, Phillips D, Fischer GW, Quinlan JJ, Sakai T. Short-term safety and effectiveness of sugammadex for surgical patients with end-stage renal disease: a two-centre retrospective study. Anaesthesia 2019; 75:348-352. [PMID: 31721151 DOI: 10.1111/anae.14914] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/15/2019] [Indexed: 12/17/2022]
Abstract
Sugammadex is a novel reversal agent for aminosteroid neuromuscular blocking drugs, especially rocuronium. Given its renal excretion, sugammadex is not recommended for patients with end-stage renal disease; however, reports exist of its use in this group of patients. This two-institutional retrospective observational study aimed to review the safety profile and effectiveness of sugammadex in surgical patients with end-stage renal disease who required pre-operative renal replacement therapy. Adult surgical patients with end-stage renal disease requiring pre-operative renal replacement therapy, who received sugammadex between April 2016 and January 2019, were studied. The primary outcome was the incidence of postoperative tracheal re-intubation within 48 h. The secondary outcome was the incidence of deferred tracheal extubation in the operating theatre. One hundred and fifty-eight patients were identified from 125,653 surgical patients: 48 patients (30%) underwent renal transplantation and 110 (70%) underwent non-renal transplantation procedures. There were 22 instances (14%) of deferred tracheal extubation due to surgical and/or pre-existing medical conditions. Out of the 136 patients who had the tracheal tube removed at the end of the procedure, three patients had their trachea re-intubated within 48 h: two patients developed pulmonary oedema resulting from volume overload; and one patient had worsening sepsis. No incidence of recurrence of neuromuscular blockade was observed. Of note, 24 (18%) patients were found to have incomplete neuromuscular blockade reversal with neostigmine but administration of sugammadex led to successful tracheal extubation. In conclusion, sugammadex appears to be safe and effective in adult patients with end-stage renal disease receiving pre-operative renal replacement therapy.
Collapse
|
Research Support, Non-U.S. Gov't |
6 |
28 |
73
|
Baynam GS, Groft S, van der Westhuizen FH, Gassman SD, du Plessis K, Coles EP, Selebatso E, Selebatso M, Gaobinelwe B, Selebatso T, Joel D, Llera VA, Vorster BC, Wuebbels B, Djoudalbaye B, Austin CP, Kumuthini J, Forman J, Kaufmann P, Chipeta J, Gavhed D, Larsson A, Stojiljkovic M, Nordgren A, Roldan EJA, Taruscio D, Wong-Rieger D, Nowak K, Bilkey GA, Easteal S, Bowdin S, Reichardt JKV, Beltran S, Kosaki K, van Karnebeek CDM, Gong M, Shuyang Z, Mehrian-Shai R, Adams DR, Puri RD, Zhang F, Pachter N, Muenke M, Nellaker C, Gahl WA, Cederroth H, Broley S, Schoonen M, Boycott KM, Posada M. A call for global action for rare diseases in Africa. Nat Genet 2020; 52:21-26. [PMID: 31873296 DOI: 10.1038/s41588-019-0552-2] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
|
Research Support, Non-U.S. Gov't |
5 |
28 |
74
|
Lin KM, Ternent CA, Adams DR, Thorson AG, Blatchford GJ, Christensen MA, Watson P, Lynch HT. Colorectal cancer in hereditary breast cancer kindreds. Dis Colon Rectum 1999; 42:1041-5. [PMID: 10458128 DOI: 10.1007/bf02236700] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
PURPOSE This study compared characteristics of colorectal cancer between families with dominant breast cancer inheritance and the general population. The cumulative incidence of colorectal cancer was also studied in genetically determined breast cancer syndrome subjects with BRCA1 and BRCA2 mutations and compared with the general population. METHODS Subjects included 42 patients with colorectal cancer from 32 clinically determined hereditary breast cancer kindreds based on the autosomal dominant inheritance of breast cancers and early age of onset. The general population colorectal cancer cohort was composed of 755 patients from a tumor registry. Lifetime risk of colorectal cancer was determined in 164 BRCA1 and 88 BRCA2 gene mutation carriers and compared with the general population. Mean age of colorectal cancer onset, anatomic site distribution, histologic stage at presentation, and five year stage-stratified survival rates were compared between clinically determined hereditary breast cancer family members and the general population. RESULTS The lifetime risk of colorectal cancer in male BRCA1 and BRCA2 mutation carriers was 5.6 percent, which was not different from 6 percent in males from the general population. Likewise, the lifetime colorectal cancer risk in female BRCA1 and BRCA2 mutation carriers was 3.2 percent, which was not different from 5.9 percent in females from the general population. Mean age of onset +/- standard error for patients with colorectal cancer was 60 +/- 2 years for hereditary breast cancer kindreds compared with 67 +/- 0.4 years for the general population (P = 0.0004). Colorectal cancer site distribution did not vary between hereditary breast cancer and the general population. Overall colorectal cancer stage distribution was significantly different, with more Stage I and fewer Stage IV cancers in subjects with hereditary breast cancer compared with the general population (P = 0.01). Overall five year stage-stratified colorectal cancer survival rate +/- standard error was 66 +/- 8 percent for hereditary breast cancer kindreds and 46 +/- 2 percent for the general population (P = 0.023). CONCLUSION Lifetime cumulative colorectal cancer incidence in subjects with BRCA1 and BRCA2 gene mutations was not different from the general population. However, significant differences in colorectal cancer were noted between hereditary breast cancer family members and the general population. Hereditary breast cancer-associated colorectal cancer had an earlier age of onset, lower tumor stage, and better survival rate than the general population. Except for age of onset, colorectal cancer in hereditary breast cancer kindreds exhibited more favorable characteristics than colorectal cancer in the general population.
Collapse
|
|
26 |
27 |
75
|
Yalla K, Elliott C, Day JP, Findlay J, Barratt S, Hughes ZA, Wilson L, Whiteley E, Popiolek M, Li Y, Dunlop J, Killick R, Adams DR, Brandon NJ, Houslay MD, Hao B, Baillie GS. FBXW7 regulates DISC1 stability via the ubiquitin-proteosome system. Mol Psychiatry 2018; 23:1278-1286. [PMID: 28727686 PMCID: PMC5984089 DOI: 10.1038/mp.2017.138] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/28/2016] [Revised: 05/12/2017] [Accepted: 05/15/2017] [Indexed: 01/27/2023]
Abstract
Disrupted in schizophrenia 1 (DISC1) is a multi-functional scaffolding protein that has been associated with neuropsychiatric disease. The role of DISC1 is to assemble protein complexes that promote neural development and signaling, hence tight control of the concentration of cellular DISC1 in neurons is vital to brain function. Using structural and biochemical techniques, we show for we believe the first time that not only is DISC1 turnover elicited by the ubiquitin proteasome system (UPS) but that it is orchestrated by the F-Box protein, FBXW7. We present the structure of FBXW7 bound to the DISC1 phosphodegron motif and exploit this information to prove that disruption of the FBXW7-DISC1 complex results in a stabilization of DISC1. This action can counteract DISC1 deficiencies observed in neural progenitor cells derived from induced pluripotent stem cells from schizophrenia patients with a DISC1 frameshift mutation. Thus manipulation of DISC1 levels via the UPS may provide a novel method to explore DISC1 function.
Collapse
|
Research Support, N.I.H., Extramural |
7 |
26 |