Publications by authors named "Smita Patel"

249 Publications

Highly efficient 5' capping of mitochondrial RNA with NAD and NADH by yeast and human mitochondrial RNA polymerase.

Elife 2018 12 12;7. Epub 2018 Dec 12.

Department of Genetics and Waksman Institute, Rutgers University, United States.

Bacterial and eukaryotic nuclear RNA polymerases (RNAPs) cap RNA with the oxidized and reduced forms of the metabolic effector nicotinamide adenine dinucleotide, NAD and NADH, using NAD and NADH as non-canonical initiating nucleotides for transcription initiation. Here, we show that mitochondrial RNAPs (mtRNAPs) cap RNA with NAD and NADH, and do so more efficiently than nuclear RNAPs. Direct quantitation of NAD- and NADH-capped RNA demonstrates remarkably high levels of capping in vivo: up to ~60% NAD and NADH capping of yeast mitochondrial transcripts, and up to ~15% NAD capping of human mitochondrial transcripts. The capping efficiency is determined by promoter sequence at, and upstream of, the transcription start site and, in yeast and human cells, by intracellular NAD and NADH levels. Our findings indicate mtRNAPs serve as both sensors and actuators in coupling cellular metabolism to mitochondrial transcriptional outputs, sensing NAD and NADH levels and adjusting transcriptional outputs accordingly.
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http://dx.doi.org/10.7554/eLife.42179DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6298784PMC
December 2018

RIG-I Uses an ATPase-Powered Translocation-Throttling Mechanism for Kinetic Proofreading of RNAs and Oligomerization.

Mol Cell 2018 10 27;72(2):355-368.e4. Epub 2018 Sep 27.

Department of Biochemistry and Molecular Biology, Robert Wood Johnson Medical School, Rutgers University, Piscataway, NJ 08854, USA. Electronic address:

RIG-I has a remarkable ability to specifically select viral 5'ppp dsRNAs for activation from a pool of cytosolic self-RNAs. The ATPase activity of RIG-I plays a role in RNA discrimination and activation, but the underlying mechanism was unclear. Using transient-state kinetics, we elucidated the ATPase-driven "kinetic proofreading" mechanism of RIG-I activation and RNA discrimination, akin to DNA polymerases, ribosomes, and T cell receptors. Even in the autoinhibited state of RIG-I, the C-terminal domain kinetically discriminates against self-RNAs by fast off rates. ATP binding facilitates dsRNA engagement but, interestingly, makes RIG-I promiscuous, explaining the constitutive signaling by Singleton-Merten syndrome-linked mutants that bind ATP without hydrolysis. ATP hydrolysis dissociates self-RNAs faster than 5'ppp dsRNA but, more importantly, drives RIG-I oligomerization through translocation, which we show to be regulated by helicase motif IVa. RIG-I translocates directionally from the dsRNA end into the stem region, and the 5'ppp end "throttles" translocation to provide a mechanism for threading and building a signaling-active oligomeric complex.
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http://dx.doi.org/10.1016/j.molcel.2018.08.021DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6434538PMC
October 2018

Use of an Electronic Medical Record to Track Adherence to the Mediterranean Diet in a US Neurology Clinical Practice.

Mayo Clin Proc Innov Qual Outcomes 2018 Mar 1;2(1):49-59. Epub 2018 Feb 1.

NorthShore Neurological Institute, NorthShore University HealthSystem, Evanston, IL.

Objective: We describe our experience with routinely capturing and analyzing Mediterranean diet data via structured clinical documentation support tools built into the electronic medical record and describe adherence to the Mediterranean diet in patients at risk for either stroke or dementia in a US neurology clinical practice.

Patients And Methods: The Mediterranean diet is associated with a reduced risk of stroke and dementia. The Department of Neurology at NorthShore University HealthSystem routinely evaluates patients at initial and annual outpatient visits using structured clinical documentation support (SCDS) tools built into the electronic medical record (EMR). For patient evaluations in our Vascular Neurology and Brain Health subspecialty clinics, SCDS tools in the EMR include the validated 14-item questionnaire for Mediterranean diet adherence (PREvención con DIeta MEDiterránea [PREDIMED]) that autoscores, auto-interprets, writes to the progress note, and electronically captures data. Our study population includes patients seen at these clinics from July 1, 2015, through November 29, 2017.

Results: At their initial office visit, 25.5% (95/373) of Brain Health patients scored 10 or more points ("strongly adherent") on the PREDIMED (median, 8; range, 0-14) whereas 6.7% (55/829) of Vascular Neurology patients achieved a score of 10 or more points (median, 6; range, 0-12). By contrast, 34.7% (2586/7447) of individuals in the original PREDIMED cohort were strongly adherent to the Mediterranean diet.

Conclusion: PREDIMED scores can be electronically captured to tailor nutrition interventions by assessing baseline adherence at the time of their initial neurology clinic visit. Patients in our Midwestern US clinics were weakly adherent to the Mediterranean diet. This suggests a major opportunity for nutrition intervention and education in US neurology clinical practices, toward preserving and improving brain health.
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http://dx.doi.org/10.1016/j.mayocpiqo.2017.12.003DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6124331PMC
March 2018

Hypomorphic caspase activation and recruitment domain 11 (CARD11) mutations associated with diverse immunologic phenotypes with or without atopic disease.

J Allergy Clin Immunol 2019 04 28;143(4):1482-1495. Epub 2018 Aug 28.

Department of Paediatric Immunology and ID, Our Lady's Children's Hospital, Crumlin, Dublin, Ireland.

Background: Caspase activation and recruitment domain 11 (CARD11) encodes a scaffold protein in lymphocytes that links antigen receptor engagement with downstream signaling to nuclear factor κB, c-Jun N-terminal kinase, and mechanistic target of rapamycin complex 1. Germline CARD11 mutations cause several distinct primary immune disorders in human subjects, including severe combined immune deficiency (biallelic null mutations), B-cell expansion with nuclear factor κB and T-cell anergy (heterozygous, gain-of-function mutations), and severe atopic disease (loss-of-function, heterozygous, dominant interfering mutations), which has focused attention on CARD11 mutations discovered by using whole-exome sequencing.

Objectives: We sought to determine the molecular actions of an extended allelic series of CARD11 and to characterize the expanding range of clinical phenotypes associated with heterozygous CARD11 loss-of-function alleles.

Methods: Cell transfections and primary T-cell assays were used to evaluate signaling and function of CARD11 variants.

Results: Here we report on an expanded cohort of patients harboring novel heterozygous CARD11 mutations that extend beyond atopy to include other immunologic phenotypes not previously associated with CARD11 mutations. In addition to (and sometimes excluding) severe atopy, heterozygous missense and indel mutations in CARD11 presented with immunologic phenotypes similar to those observed in signal transducer and activator of transcription 3 loss of function, dedicator of cytokinesis 8 deficiency, common variable immunodeficiency, neutropenia, and immune dysregulation, polyendocrinopathy, enteropathy, X-linked-like syndrome. Pathogenic variants exhibited dominant negative activity and were largely confined to the CARD or coiled-coil domains of the CARD11 protein.

Conclusion: These results illuminate a broader phenotypic spectrum associated with CARD11 mutations in human subjects and underscore the need for functional studies to demonstrate that rare gene variants encountered in expected and unexpected phenotypes must nonetheless be validated for pathogenic activity.
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http://dx.doi.org/10.1016/j.jaci.2018.08.013DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6395549PMC
April 2019

Is It Safe to Switch From Intravenous Immunoglobulin to Subcutaneous Immunoglobulin in Patients With Common Variable Immunodeficiency and Autoimmune Thrombocytopenia?

Front Immunol 2018 19;9:1656. Epub 2018 Jul 19.

Center for Chronic Immunodeficiency, University Hospital, Medical Faculty, Albert-Ludwigs University, Freiburg, Germany.

Background: A significant amount of common variable immunodeficiency (CVID) patients manifest with autoimmunity. Particularly, autoimmune thrombocytopenia (AITP) is commonly seen. Intravenous immunoglobulins (IVIG) are an established treatment option for both, CVID and AITP. Nonetheless, due to fewer systemic side effects, immunoglobulins are increasingly applied subcutaneously (SCIG).

Objective: To compare the efficacy and safety of IVIG and SCIG treatment in patients with both CVID and clinical relevant thrombocytopenia in the prevention of AITP bouts.

Methods: Patients with both CVID and AITP were enrolled at the Centre for Chronic Immunodeficiency in Freiburg, Germany and at the Royal Free Hospital, London, UK. Clinical and laboratory features of patients were collected and analyzed.

Results: This retrospective study recruited 61 adult patients between 19 and 71 years of age who had a diagnosis of CVID and at least one bout of thrombocytopenia defined as a platelet count of <50,000/μl if bleeding episodes occurred, or a platelet count of <20,000/μl without bleeding. Thirty patients received immunoglobulin through IVIG, and 31 patients were on SCIG replacement. One patient of the IVIG-group was excluded, because of a diffuse large B-cell lymphoma. We did not find a higher occurrence of thrombocytopenic events in CVID patients who received SCIG, compared to CVID patients who had IVIG, but we identified a low IgG through level as a risk factor for AITP bouts.

Conclusion: SCIG is at least as safe as IVIG for patients with CVID and concomitant AITP. However, an IgG through level under 7 g/l is a key factor for the development of AITP.
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http://dx.doi.org/10.3389/fimmu.2018.01656DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6060403PMC
July 2018

Aberrant T-cell antigen expression in a plasma cell neoplasm.

Blood 2018 07;132(3):341

Columbia University Medical Center.

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http://dx.doi.org/10.1182/blood-2018-04-843730DOI Listing
July 2018

Helicase promotes replication re-initiation from an RNA transcript.

Nat Commun 2018 06 13;9(1):2306. Epub 2018 Jun 13.

Howard Hughes Medical Institute, Cornell University, Ithaca, NY, 14853, USA.

To ensure accurate DNA replication, a replisome must effectively overcome numerous obstacles on its DNA substrate. After encountering an obstacle, a progressing replisome often aborts DNA synthesis but continues to unwind. However, little is known about how DNA synthesis is resumed downstream of an obstacle. Here, we examine the consequences of a non-replicating replisome collision with a co-directional RNA polymerase (RNAP). Using single-molecule and ensemble methods, we find that T7 helicase interacts strongly with a non-replicating T7 DNA polymerase (DNAP) at a replication fork. As the helicase advances, the associated DNAP also moves forward. The presence of the DNAP increases both helicase's processivity and unwinding rate. We show that such a DNAP, together with its helicase, is indeed able to actively disrupt a stalled transcription elongation complex, and then initiates replication using the RNA transcript as a primer. These observations exhibit T7 helicase's novel role in replication re-initiation.
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http://dx.doi.org/10.1038/s41467-018-04702-xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5997990PMC
June 2018

Correlating Transcription Initiation and Conformational Changes by a Single-Subunit RNA Polymerase with Near Base-Pair Resolution.

Mol Cell 2018 05;70(4):695-706.e5

Department of Physics and Center for the Physics of Living Cells, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA; Howard Hughes Medical Institute, Baltimore, MD 21205, USA; Departments of Biophysics and Biophysical Chemistry, Biophysics, and Biomedical Engineering, Johns Hopkins University, MD 21205, USA. Electronic address:

We provide a comprehensive analysis of transcription in real time by T7 RNA Polymerase (RNAP) using single-molecule fluorescence resonance energy transfer by monitoring the entire life history of transcription initiation, including stepwise RNA synthesis with near base-pair resolution, abortive cycling, and transition into elongation. Kinetically branching pathways were observed for abortive initiation with an RNAP either recycling on the same promoter or exchanging with another RNAP from solution. We detected fast and slow populations of RNAP in their transition into elongation, consistent with the efficient and delayed promoter release, respectively, observed in ensemble studies. Real-time monitoring of abortive cycling using three-probe analysis showed that the initiation events are stochastically branched into productive and failed transcription. The abortive products are generated primarily from initiation events that fail to progress to elongation, and a majority of the productive events transit to elongation without making abortive products.
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http://dx.doi.org/10.1016/j.molcel.2018.04.018DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5983381PMC
May 2018

Correlation between computer tomography-derived scar topography and critical ablation sites in postinfarction ventricular tachycardia.

J Cardiovasc Electrophysiol 2018 03 5;29(3):438-445. Epub 2018 Mar 5.

Division of Cardiovascular Medicine, Department of Radiology, University of Michigan, Ann Arbor, MI, USA.

Background: Myocardial wall thickness (WT) in patients with a prior myocardial infarction has been used to indicate scarring. However, the correlation of WT with sites critical to ventricular tachycardia (VT) has not been previously investigated. The purpose of this study was to correlate electroanatomic mapping data obtained during VT ablation with WT determined by cardiac computed tomography (CT).

Methods And Results: Cardiac CTs were performed in 15 consecutive patients (mean age 63 ± 10 years, 86% male, left ventricular ejection fraction 27 ± 12%) with a prior infarct referred for VT ablation. The CTs were registered to the electroanatomic maps obtained during the mapping procedure. Pacing was performed throughout the scar at sites with fractionated electrograms and isolated potentials. Ablation sites were identified by pace-mapping or entrainment-mapping and these sites were correlated with WT. Bipolar and unipolar voltage amplitude and bipolar electrogram width correlated with WT (correlation coefficient: 0.63, 0.65, and 0.41, respectively, P < 0.001). Ablation target sites were identified for 58 of 113 inducible VTs. The ablation target sites were located on CT-defined ridges (WT: 4.2 ± 1.2 mm) bordered by areas of thinning (WT: 2.6 ± 1.1 mm, P < 0.0001) in 14 of 15 patients. Ablation targets were found on ridges in 49 of 58 VTs (84%) for which target sites were identified. A total of 70 ridges were localized in the 15 patients. VT became noninducible postablation in 11 of 15 patients (73%).

Conclusion: WT measured by CT identifies ridges of myocardial tissue that often are critical for postinfarction VT and that can be appropriate target sites for ablation.
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http://dx.doi.org/10.1111/jce.13441DOI Listing
March 2018

Familial Parkinson's point mutation abolishes multiple system atrophy prion replication.

Proc Natl Acad Sci U S A 2018 01 26;115(2):409-414. Epub 2017 Dec 26.

Institute for Neurodegenerative Diseases, Weill Institute for Neurosciences, University of California, San Francisco, CA 94158;

In the neurodegenerative disease multiple system atrophy (MSA), α-synuclein misfolds into a self-templating conformation to become a prion. To compare the biological activity of α-synuclein prions in MSA and Parkinson's disease (PD), we developed nine α-synuclein-YFP cell lines expressing point mutations responsible for inherited PD. MSA prions robustly infected wild-type, A30P, and A53T α-synuclein-YFP cells, but they were unable to replicate in cells expressing the E46K mutation. Coexpression of the A53T and E46K mutations was unable to rescue MSA prion infection in vitro, establishing that MSA α-synuclein prions are conformationally distinct from the misfolded α-synuclein in PD patients. This observation may have profound implications for developing treatments for neurodegenerative diseases.
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http://dx.doi.org/10.1073/pnas.1719369115DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5777081PMC
January 2018

Kinetics of Human Mutant Tau Prion Formation in the Brains of 2 Transgenic Mouse Lines.

JAMA Neurol 2017 12;74(12):1464-1472

Institute for Neurodegenerative Diseases, Weill Institute for Neurosciences, University of California, San Francisco.

Importance: Accumulation of the protein tau is a defining characteristic of several neurodegenerative diseases. Thorough assessment of transgenic (Tg) mouse lines that replicate this process is critical for establishing the models used for testing anti-tau therapeutics in vivo.

Objective: To define a consistent mouse model of disease for use in future compound efficacy studies.

Design, Setting, And Participants: In this time course study, cohorts of Tg and control mice were euthanized at defined intervals. Collected brains were bisected down the midline. One half was frozen and used to measure the tau prion content, while the other half was fixed for immunostaining with anti-tau antibodies. All mice were maintained at the Hunters Point Animal Facility at the University of California, San Francisco, and all experiments were performed at the Mission Bay Campus of the University of California, San Francisco. Study animals were PS19, homozygous and hemizygous Tg(MAPT*P301S), and B6/J mice. The study dates were August 9, 2010, to October 3, 2016.

Main Outcomes And Measures: Tau prions were measured using a cell-based assay. Neuropathology was measured by determining the percentage area positive for immunostaining in defined brain regions. A separate cohort of mice was aged until each mouse developed neurological signs as determined by trained animal technicians to assess mortality.

Results: A total of 1035 mice were used in this time course study. These included PS19 mice (51.2% [126 of 246] male and 48.8% [120 of 246] female), Tg(MAPT*P301S+/+) mice (52.3% [216 of 413] male, 43.8% [181 of 413] female, and 3.9% [16 of 413] undetermined), Tg(MAPT*P301S+/-) mice (51.8% [101 of 195] male and 48.2% [94 of 195] female), and B6/J mice (49.7% [90 of 181] male and 50.3% [91 of 181] female). While considerable interanimal variability in neuropathology, disease onset, and tau prion formation in the PS19 mice was observed, all 3 measures of disease were more uniform in the Tg(MAPT*P301S+/+) mice. Comparing tau prion formation in Tg(MAPT*P301S+/+) mice with B6/J controls, the 95% CIs for the 2 mouse lines diverged before age 5 weeks, and significant (P < .05) neuropathology in the hindbrain of 24-week-old mice was quantifiable.

Conclusions And Relevance: The assessment of disease progression using 3 criteria showed that disease onset in PS19 mice is too variable to obtain reliable measurements for drug discovery research. However, the reproducibility of tau prion formation in young Tg(MAPT*P301S+/+) mice establishes a rapid assay for compound efficacy in vivo.
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http://dx.doi.org/10.1001/jamaneurol.2017.2822DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5822201PMC
December 2017

Megakaryocytic blast crisis in chronic myeloid leukemia: A primary presentation.

Indian J Pathol Microbiol 2017 Jul-Sep;60(3):445-447

Department of Pathology, Medical College Baroda, SSG Hospital, Vadodara, Gujarat, India.

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http://dx.doi.org/10.4103/IJPM.IJPM_841_16DOI Listing
October 2018

Transcriptional fidelities of human mitochondrial POLRMT, yeast mitochondrial Rpo41, and phage T7 single-subunit RNA polymerases.

J Biol Chem 2017 11 7;292(44):18145-18160. Epub 2017 Sep 7.

From the Department of Biochemistry and Molecular Biology, Robert Wood Johnson Medical School and

Single-subunit RNA polymerases (RNAPs) are present in phage T7 and in mitochondria of all eukaryotes. This RNAP class plays important roles in biotechnology and cellular energy production, but we know little about its fidelity and error rates. Herein, we report the error rates of three single-subunit RNAPs measured from the catalytic efficiencies of correct and all possible incorrect nucleotides. The average error rates of T7 RNAP (2 × 10), yeast mitochondrial Rpo41 (6 × 10), and human mitochondrial POLRMT (RNA polymerase mitochondrial) (2 × 10) indicate high accuracy/fidelity of RNA synthesis resembling those of replicative DNA polymerases. All three RNAPs exhibit a distinctly high propensity for GTP misincorporation opposite dT, predicting frequent A→G errors in RNA with rates of ∼10 The A→C, G→A, A→U, C→U, G→U, U→C, and U→G errors mostly due to pyrimidine-purine mismatches were relatively frequent (10-10), whereas C→G, U→A, G→C, and C→A errors from purine-purine and pyrimidine-pyrimidine mismatches were rare (10-10). POLRMT also shows a high C→A error rate on 8-oxo-dG templates (∼10). Strikingly, POLRMT shows a high mutagenic bypass rate, which is exacerbated by TEFM (transcription elongation factor mitochondrial). The lifetime of POLRMT on terminally mismatched elongation substrate is increased in the presence of TEFM, which allows POLRMT to efficiently bypass the error and continue with transcription. This investigation of nucleotide selectivity on normal and oxidatively damaged DNA by three single-subunit RNAPs provides the basic information to understand the error rates in mitochondria and, in the case of T7 RNAP, to assess the quality of transcribed RNAs.
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http://dx.doi.org/10.1074/jbc.M117.797480DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5672038PMC
November 2017

MSA prions exhibit remarkable stability and resistance to inactivation.

Acta Neuropathol 2018 01 28;135(1):49-63. Epub 2017 Aug 28.

Institute for Neurodegenerative Diseases, Weill Institute for Neurosciences, University of California, 675 Nelson Rising Lane, San Francisco, CA, 94158, USA.

In multiple system atrophy (MSA), progressive neurodegeneration results from the protein α-synuclein misfolding into a self-templating prion conformation that spreads throughout the brain. MSA prions are transmissible to transgenic (Tg) mice expressing mutated human α-synuclein (TgM83), inducing neurological disease following intracranial inoculation with brain homogenate from deceased patient samples. Noting the similarities between α-synuclein prions and PrP scrapie (PrP) prions responsible for Creutzfeldt-Jakob disease (CJD), we investigated MSA transmission under conditions known to result in PrP transmission. When peripherally exposed to MSA via the peritoneal cavity, hind leg muscle, and tongue, TgM83 mice developed neurological signs accompanied by α-synuclein prions in the brain. Iatrogenic CJD, resulting from PrP prion adherence to surgical steel instruments, has been investigated by incubating steel sutures in contaminated brain homogenate before implantation into mouse brain. Mice studied using this model for MSA developed disease, whereas wire incubated in control homogenate had no effect on the animals. Notably, formalin fixation did not inactivate α-synuclein prions. Formalin-fixed MSA patient samples also transmitted disease to TgM83 mice, even after incubating in fixative for 244 months. Finally, at least 10% sarkosyl was found to be the concentration necessary to partially inactivate MSA prions. These results demonstrate the robustness of α-synuclein prions to denaturation. Moreover, they establish the parallel characteristics between PrP and α-synuclein prions, arguing that clinicians should exercise caution when working with materials that might contain α-synuclein prions to prevent disease.
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http://dx.doi.org/10.1007/s00401-017-1762-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5756500PMC
January 2018

Hematopoietic stem cell transplantation in 29 patients hemizygous for hypomorphic /NEMO mutations.

Blood 2017 09 5;130(12):1456-1467. Epub 2017 Jul 5.

Department of Pediatrics and.

X-linked recessive ectodermal dysplasia with immunodeficiency is a rare primary immunodeficiency caused by hypomorphic mutations of the gene encoding the nuclear factor κB essential modulator (NEMO) protein. This condition displays enormous allelic, immunological, and clinical heterogeneity, and therapeutic decisions are difficult because NEMO operates in both hematopoietic and nonhematopoietic cells. Hematopoietic stem cell transplantation (HSCT) is potentially life-saving, but the small number of case reports available suggests it has been reserved for only the most severe cases. Here, we report the health status before HSCT, transplantation outcome, and clinical follow-up for a series of 29 patients from unrelated kindreds from 11 countries. Between them, these patients carry 23 different hypomorphic mutations. HSCT was performed from HLA-identical related donors (n = 7), HLA-matched unrelated donors (n = 12), HLA-mismatched unrelated donors (n = 8), and HLA-haploidentical related donors (n = 2). Engraftment was documented in 24 patients, and graft-versus-host disease in 13 patients. Up to 7 patients died 0.2 to 12 months after HSCT. The global survival rate after HSCT among NEMO-deficient children was 74% at a median follow-up after HSCT of 57 months (range, 4-108 months). Preexisting mycobacterial infection and colitis were associated with poor HSCT outcome. The underlying mutation does not appear to have any influence, as patients with the same mutation had different outcomes. Transplantation did not appear to cure colitis, possibly as a result of cell-intrinsic disorders of the epithelial barrier. Overall, HSCT can cure most clinical features of patients with a variety of mutations.
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http://dx.doi.org/10.1182/blood-2017-03-771600DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5609334PMC
September 2017

Anomalous Coronary Arteries That Need Intervention: Review of Pre- and Postoperative Imaging Appearances.

Radiographics 2017 May-Jun;37(3):740-757. Epub 2017 Apr 7.

From the Department of Radiology (P.P.A., S.P.), Department of Internal Medicine, Division of Cardiology (T.L.), and Department of Cardiac Surgery (B.Y.), University of Michigan Health System, 1500 E Medical Center Dr, Ann Arbor, MI 48109; Department of Radiology, University of Ottawa, Ottawa, Ont, Canada (C.D., E.P.); and Department of Radiology, University of Toronto, Toronto, Ont, Canada (E.N.).

Coronary artery anomalies constitute a diverse group of abnormalities, ranging from anatomic variants to those having hemodynamic consequences. This review focuses on major anomalies that have clinical implications requiring treatment, including anomalous origin of the coronary artery from the opposite sinus with interarterial course specifically with an intramural course, coronary artery origin from the pulmonary artery, and coronary artery fistula. Comprehensive imaging evaluation is necessary to precisely delineate the anatomy as well as pathophysiologic aspects of the anomaly before determining treatment options for a specific patient. Coronary computed tomographic angiography provides elegant depiction of coronary arterial anatomy and the relationship of the vessel to the adjacent structures, with the ability to perform three-dimensional reconstructions. Magnetic resonance (MR) imaging is emerging as an alternative noninvasive imaging strategy, particularly in young individuals, due to the lack of ionizing radiation and avoidance of iodinated contrast agents. This review describes the roles and recent technical advancements in computed tomography and MR imaging pertinent to coronary artery imaging. Additionally, this article will familiarize readers with the cross-sectional imaging appearance of clinically relevant coronary anomalies, hemodynamic considerations, and complex decision making. The different management strategies used for these anomalies, such as coronary unroofing, reimplantation, bypass grafting, Takeuchi repair, and surgical and interventional closure of fistulas, as well as specific posttreatment complications, are also discussed. RSNA, 2017.
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http://dx.doi.org/10.1148/rg.2017160124DOI Listing
November 2017

British Lung Foundation/United Kingdom Primary Immunodeficiency Network Consensus Statement on the Definition, Diagnosis, and Management of Granulomatous-Lymphocytic Interstitial Lung Disease in Common Variable Immunodeficiency Disorders.

J Allergy Clin Immunol Pract 2017 Jul - Aug;5(4):938-945. Epub 2017 Mar 25.

Department of Cellular Pathology, Barts Health NHS Trust, London, United Kingdom.

A proportion of people living with common variable immunodeficiency disorders develop granulomatous-lymphocytic interstitial lung disease (GLILD). We aimed to develop a consensus statement on the definition, diagnosis, and management of GLILD. All UK specialist centers were contacted and relevant physicians were invited to take part in a 3-round online Delphi process. Responses were graded as Strongly Agree, Tend to Agree, Neither Agree nor Disagree, Tend to Disagree, and Strongly Disagree, scored +1, +0.5, 0, -0.5, and -1, respectively. Agreement was defined as greater than or equal to 80% consensus. Scores are reported as mean ± SD. There was 100% agreement (score, 0.92 ± 0.19) for the following definition: "GLILD is a distinct clinico-radio-pathological ILD occurring in patients with [common variable immunodeficiency disorders], associated with a lymphocytic infiltrate and/or granuloma in the lung, and in whom other conditions have been considered and where possible excluded." There was consensus that the workup of suspected GLILD requires chest computed tomography (CT) (0.98 ± 0.01), lung function tests (eg, gas transfer, 0.94 ± 0.17), bronchoscopy to exclude infection (0.63 ± 0.50), and lung biopsy (0.58 ± 0.40). There was no consensus on whether expectant management following optimization of immunoglobulin therapy was acceptable: 67% agreed, 25% disagreed, score 0.38 ± 0.59; 90% agreed that when treatment was required, first-line treatment should be with corticosteroids alone (score, 0.55 ± 0.51).
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http://dx.doi.org/10.1016/j.jaip.2017.01.021DOI Listing
January 2018

Tau prions from Alzheimer's disease and chronic traumatic encephalopathy patients propagate in cultured cells.

Proc Natl Acad Sci U S A 2016 12 28;113(50):E8187-E8196. Epub 2016 Nov 28.

Institute for Neurodegenerative Diseases, Weill Institute for Neurosciences, University of California, San Francisco, CA 94143;

Tau prions are thought to aggregate in the central nervous system, resulting in neurodegeneration. Among the tauopathies, Alzheimer's disease (AD) is the most common, whereas argyrophilic grain disease (AGD), corticobasal degeneration (CBD), chronic traumatic encephalopathy (CTE), Pick's disease (PiD), and progressive supranuclear palsy (PSP) are less prevalent. Brain extracts from deceased individuals with PiD, a neurodegenerative disorder characterized by three-repeat (3R) tau prions, were used to infect HEK293T cells expressing 3R tau fused to yellow fluorescent protein (YFP). Extracts from AGD, CBD, and PSP patient samples, which contain four-repeat (4R) tau prions, were transmitted to HEK293 cells expressing 4R tau fused to YFP. These studies demonstrated that prion propagation in HEK cells requires isoform pairing between the infecting prion and the recipient substrate. Interestingly, tau aggregates in AD and CTE, containing both 3R and 4R isoforms, were unable to robustly infect either 3R- or 4R-expressing cells. However, AD and CTE prions were able to replicate in HEK293T cells expressing both 3R and 4R tau. Unexpectedly, increasing the level of 4R isoform expression alone supported the propagation of both AD and CTE prions. These results allowed us to determine the levels of tau prions in AD and CTE brain extracts.
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http://dx.doi.org/10.1073/pnas.1616344113DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5167200PMC
December 2016

Human mitochondrial transcription factors TFAM and TFB2M work synergistically in promoter melting during transcription initiation.

Nucleic Acids Res 2017 01 29;45(2):861-874. Epub 2016 Nov 29.

Department of Biochemistry and Molecular Biology, Rutgers, Robert Wood Johnson Medical school, Piscataway, NJ 08854, USA

Human mitochondrial DNA is transcribed by POLRMT with the help of two initiation factors, TFAM and TFB2M. The current model postulates that the role of TFAM is to recruit POLRMT and TFB2M to melt the promoter. However, we show that TFAM has 'post-recruitment' roles in promoter melting and RNA synthesis, which were revealed by studying the pre-initiation steps of promoter binding, bending and melting, and abortive RNA synthesis. Our 2-aminopurine mapping studies show that the LSP (Light Strand Promoter) is melted from -4 to +1 in the open complex with all three proteins and from -4 to +3 with addition of ATP. Our equilibrium binding studies show that POLRMT forms stable complexes with TFB2M or TFAM on LSP with low-nanomolar K values, but these two-component complexes lack the mechanism to efficiently melt the promoter. This indicates that POLRMT needs both TFB2M and TFAM to melt the promoter. Additionally, POLRMT+TFB2M makes 2-mer abortives on LSP, but longer RNAs are observed only with TFAM. These results are explained by TFAM playing a role in promoter melting and/or stabilization of the open complex on LSP. Based on our results, we propose a refined model of transcription initiation by the human mitochondrial transcription machinery.
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http://dx.doi.org/10.1093/nar/gkw1157DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5314767PMC
January 2017

An unusual case of fatty posterior mediastinal ganglioneuroma.

BJR Case Rep 2017 26;3(2):20150482. Epub 2016 Nov 26.

Department of Radiology, George Washington University, Washington, DC, USA.

Ganglioneuromas, which arise from neural crest cells, are typically seen in adolescent and young adults. We describe an unusual case of posterior mediastinal ganglioneuroma with a large fatty component in a middle-aged male. This imaging feature has only been reported in five published manuscripts in the English literature.
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http://dx.doi.org/10.1259/bjrcr.20150482DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6159259PMC
November 2016

The diagnostic challenge of the sequelae of acute pancreatitis on CT imaging: a pictorial essay.

Abdom Radiol (NY) 2017 04;42(4):1199-1209

Department of Radiology, George Washington University Hospital, 900 23rd St. NW, Washington, DC, 20037, USA.

Purpose: The purpose of the study was to present a pictorial review of the long-term sequelae of acute pancreatitis on CT imaging as these findings can cause diagnostic confusion in the absence of a proper clinical history and/or prior CT imaging.

Methods: We retrospectively identified 81 patients who had an episode of acute pancreatitis with diagnostic findings on CT and also underwent one or more follow-up CT scans at least 1 month beyond the acute episode. The residual findings on all follow-up CT scans were tabulated, including the time interval since the initial bout of acute pancreatitis.

Result: Residual inflammatory changes were present in 19.8% of cases, with a median time period lasting 86 days since the initial episode of acute pancreatitis. Residual fluid collections were seen in 27.2% and persisted for a median of 132 days. Three patients had residual solid-appearing inflammatory masses, which could be mistaken for neoplasms. Other long-term sequelae were also tabulated, including pancreatic ductal dilatation, pancreatic atrophy, new or increased pancreatic calcifications, biliary tract dilatation, central portal venous occlusion, and pseudoaneurysm formation. These residual findings and long-term complications are presented as a pictorial essay.

Conclusion: Recognizing the spectrum of residual findings of acute pancreatitis, some of which can be long term, is important in the correct interpretation of a pancreatic CT. These findings can mimic acute pancreatitis or a pancreatic/peripancreatic neoplasm and often cause diagnostic confusion, especially in the absence of prior CT imaging.
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http://dx.doi.org/10.1007/s00261-016-0986-2DOI Listing
April 2017

Overcoming a nucleosomal barrier to replication.

Sci Adv 2016 Nov 11;2(11):e1601865. Epub 2016 Nov 11.

Fox Chase Cancer Center, Philadelphia, PA 19111, USA.; Faculty of Biology, Lomonosov Moscow State University, Moscow, Russia.

Efficient overcoming and accurate maintenance of chromatin structure and associated histone marks during DNA replication are essential for normal functioning of the daughter cells. However, the molecular mechanisms of replication through chromatin are unknown. We have studied traversal of uniquely positioned mononucleosomes by T7 replisome in vitro. Nucleosomes present a strong, sequence-dependent barrier for replication, with particularly strong pausing of DNA polymerase at the +(31-40) and +(41-65) regions of the nucleosomal DNA. The exonuclease activity of T7 DNA polymerase increases the overall rate of progression of the replisome through a nucleosome, likely by resolving nonproductive complexes. The presence of nucleosome-free DNA upstream of the replication fork facilitates the progression of DNA polymerase through the nucleosome. After replication, at least 50% of the nucleosomes assume an alternative conformation, maintaining their original positions on the DNA. Our data suggest a previously unpublished mechanism for nucleosome maintenance during replication, likely involving transient formation of an intranucleosomal DNA loop.
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http://dx.doi.org/10.1126/sciadv.1601865DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5106197PMC
November 2016

DNA looping mediates nucleosome transfer.

Nat Commun 2016 11 3;7:13337. Epub 2016 Nov 3.

Department of Physics-Laboratory of Atomic and Solid State Physics, Cornell University, Ithaca, New York 14853, USA.

Proper cell function requires preservation of the spatial organization of chromatin modifications. Maintenance of this epigenetic landscape necessitates the transfer of parental nucleosomes to newly replicated DNA, a process that is stringently regulated and intrinsically linked to replication fork dynamics. This creates a formidable setting from which to isolate the central mechanism of transfer. Here we utilized a minimal experimental system to track the fate of a single nucleosome following its displacement, and examined whether DNA mechanics itself, in the absence of any chaperones or assembly factors, may serve as a platform for the transfer process. We found that the nucleosome is passively transferred to available dsDNA as predicted by a simple physical model of DNA loop formation. These results demonstrate a fundamental role for DNA mechanics in mediating nucleosome transfer and preserving epigenetic integrity during replication.
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http://dx.doi.org/10.1038/ncomms13337DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5097161PMC
November 2016

Lakes of Extramedullary Hematopoiesis in a Renal Hemangioma With Extensive Nephrocalcinosis.

Int J Surg Pathol 2017 Feb 24;25(1):61-62. Epub 2016 Sep 24.

1 Rush University Medical Center, Chicago, IL, USA.

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http://dx.doi.org/10.1177/1066896916666320DOI Listing
February 2017

Variable phenotype and discrete alterations of immune phenotypes in CTP synthase 1 deficiency: Report of 2 siblings.

J Allergy Clin Immunol 2016 12 14;138(6):1722-1725.e6. Epub 2016 Jul 14.

Clinical Immunology Group, Oxford NIHR Biomedical Research Centre, United Kingdom.

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http://dx.doi.org/10.1016/j.jaci.2016.04.059DOI Listing
December 2016

Prognosis of Good syndrome: mortality and morbidity of thymoma associated immunodeficiency in perspective.

Clin Immunol 2016 Oct 4;171:12-17. Epub 2016 Aug 4.

Nijmegen Center for Immunodeficiency and Autoinflammation (NCIA), Department of Internal Medicine, Radboud University Medical Centre, Nijmegen, The Netherlands.

Good syndrome (GS) or thymoma-associated immunodeficiency, is a rare condition that has only been studied in retrospective case series. General consensus was that GS has a worse prognosis than other humoral immunodeficiencies. In this study, physicians of GS patients completed two questionnaires with a two year interval with data on 47 patients, 499 patient years in total. Results on epidemiology, disease characteristics, and outcome are presented. Mean age at diagnosis was 60years and median follow-up from onset of symptoms was 9years. There was a high frequency of respiratory tract infections due to encapsulated bacteria. Median survival was 14years. Survival was reduced compared to age-matched population controls (5-year survival: 82% versus 95%, p=0.008). In this cohort survival was not associated with gender (HR 0.9, 95% CI 0.3-3.0), autoimmune diseases (HR 2.9, 95% CI 0.8-10.1) or immunosuppressive use (HR 0.3, 95% CI: 0.1-1.2).
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http://dx.doi.org/10.1016/j.clim.2016.07.025DOI Listing
October 2016

Guinea Pig Prion Protein Supports Rapid Propagation of Bovine Spongiform Encephalopathy and Variant Creutzfeldt-Jakob Disease Prions.

J Virol 2016 11 14;90(21):9558-9569. Epub 2016 Oct 14.

Institute for Neurodegenerative Diseases, University of California, San Francisco, San Francisco, California, USA Department of Neurology, University of California, San Francisco, San Francisco, California, USA Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, California, USA

The biochemical and neuropathological properties of bovine spongiform encephalopathy (BSE) and variant Creutzfeldt-Jakob disease (vCJD) prions are faithfully maintained upon transmission to guinea pigs. However, primary and secondary transmissions of BSE and vCJD in guinea pigs result in long incubation periods of ∼450 and ∼350 days, respectively. To determine if the incubation periods of BSE and vCJD prions could be shortened, we generated transgenic (Tg) mice expressing guinea pig prion protein (GPPrP). Inoculation of Tg(GPPrP) mice with BSE and vCJD prions resulted in mean incubation periods of 210 and 199 days, respectively, which shortened to 137 and 122 days upon serial transmission. In contrast, three different isolates of sporadic CJD prions failed to transmit disease to Tg(GPPrP) mice. Many of the strain-specified biochemical and neuropathological properties of BSE and vCJD prions, including the presence of type 2 protease-resistant PrP, were preserved upon propagation in Tg(GPPrP) mice. Structural modeling revealed that two residues near the N-terminal region of α-helix 1 in GPPrP might mediate its susceptibility to BSE and vCJD prions. Our results demonstrate that expression of GPPrP in Tg mice supports the rapid propagation of BSE and vCJD prions and suggest that Tg(GPPrP) mice may serve as a useful paradigm for bioassaying these prion isolates.

Importance: Variant Creutzfeldt-Jakob disease (vCJD) and bovine spongiform encephalopathy (BSE) prions are two of the prion strains most relevant to human health. However, propagating these strains in mice expressing human or bovine prion protein has been difficult because of prolonged incubation periods or inefficient transmission. Here, we show that transgenic mice expressing guinea pig prion protein are fully susceptible to vCJD and BSE prions but not to sporadic CJD prions. Our results suggest that the guinea pig prion protein is a better, more rapid substrate than either bovine or human prion protein for propagating BSE and vCJD prions.
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http://dx.doi.org/10.1128/JVI.01106-16DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5068510PMC
November 2016

Towards authentic transgenic mouse models of heritable PrP prion diseases.

Acta Neuropathol 2016 10 28;132(4):593-610. Epub 2016 Jun 28.

Institute for Neurodegenerative Diseases, University of California, San Francisco, 675 Nelson Rising Lane, San Francisco, CA, 94143-0518, USA.

Attempts to model inherited human prion disorders such as familial Creutzfeldt-Jakob disease (CJD), Gerstmann-Sträussler-Scheinker (GSS) disease, and fatal familial insomnia (FFI) using genetically modified mice have produced disappointing results. We recently demonstrated that transgenic (Tg) mice expressing wild-type bank vole prion protein (BVPrP) containing isoleucine at polymorphic codon 109 develop a spontaneous neurodegenerative disorder that exhibits many of the hallmarks of prion disease. To determine if mutations causing inherited human prion disease alter this phenotype, we generated Tg mice expressing BVPrP containing the D178N mutation, which causes FFI; the E200K mutation, which causes familial CJD; or an anchorless PrP mutation similar to mutations that cause GSS. Modest expression levels of mutant BVPrP resulted in highly penetrant spontaneous disease in Tg mice, with mean ages of disease onset ranging from ~120 to ~560 days. The brains of spontaneously ill mice exhibited prominent features of prion disease-specific neuropathology that were unique to each mutation and distinct from Tg mice expressing wild-type BVPrP. An ~8-kDa proteinase K-resistant PrP fragment was found in the brains of spontaneously ill Tg mice expressing either wild-type or mutant BVPrP. The spontaneously formed mutant BVPrP prions were transmissible to Tg mice expressing wild-type or mutant BVPrP as well as to Tg mice expressing mouse PrP. Thus, Tg mice expressing mutant BVPrP exhibit many of the hallmarks of heritable prion disorders in humans including spontaneous disease, protease-resistant PrP, and prion infectivity.
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http://dx.doi.org/10.1007/s00401-016-1585-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5152593PMC
October 2016

The Yeast Mitochondrial RNA Polymerase and Transcription Factor Complex Catalyzes Efficient Priming of DNA Synthesis on Single-stranded DNA.

J Biol Chem 2016 08 16;291(32):16828-39. Epub 2016 Jun 16.

From the Department of Biochemistry and Molecular Biology, Rutgers University, Robert Wood Johnson Medical School, Piscataway, New Jersey 08854,

Primases use single-stranded (ss) DNAs as templates to synthesize short oligoribonucleotide primers that initiate lagging strand DNA synthesis or reprime DNA synthesis after replication fork collapse, but the origin of this activity in the mitochondria remains unclear. Herein, we show that the Saccharomyces cerevisiae mitochondrial RNA polymerase (Rpo41) and its transcription factor (Mtf1) is an efficient primase that initiates DNA synthesis on ssDNA coated with the yeast mitochondrial ssDNA-binding protein, Rim1. Both Rpo41 and Rpo41-Mtf1 can synthesize short and long RNAs on ssDNA template and prime DNA synthesis by the yeast mitochondrial DNA polymerase Mip1. However, the ssDNA-binding protein Rim1 severely inhibits the RNA synthesis activity of Rpo41, but not the Rpo41-Mtf1 complex, which continues to prime DNA synthesis efficiently in the presence of Rim1. We show that RNAs as short as 10-12 nt serve as primers for DNA synthesis. Characterization of the RNA-DNA products shows that Rpo41 and Rpo41-Mtf1 have slightly different priming specificity. However, both prefer to initiate with ATP from short priming sequences such as 3'-TCC, TTC, and TTT, and the consensus sequence is 3'-Pu(Py)2-3 Based on our studies, we propose that Rpo41-Mtf1 is an attractive candidate for serving as the primase to initiate lagging strand DNA synthesis during normal replication and/or to restart stalled replication from downstream ssDNA.
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http://dx.doi.org/10.1074/jbc.M116.740282DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4974394PMC
August 2016