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1.
Hum Mol Genet ; 29(9): 1417-1425, 2020 06 03.
Artículo en Inglés | MEDLINE | ID: mdl-32167558

RESUMEN

Amelogenesis is the process of enamel formation. For amelogenesis to proceed, the cells of the inner enamel epithelium (IEE) must first proliferate and then differentiate into the enamel-producing ameloblasts. Amelogenesis imperfecta (AI) is a heterogeneous group of genetic conditions that result in defective or absent tooth enamel. We identified a 2 bp variant c.817_818GC>AA in SP6, the gene encoding the SP6 transcription factor, in a Caucasian family with autosomal dominant hypoplastic AI. The resulting missense protein change, p.(Ala273Lys), is predicted to alter a DNA-binding residue in the first of three zinc fingers. SP6 has been shown to be crucial to both proliferation of the IEE and to its differentiation into ameloblasts. SP6 has also been implicated as an AI candidate gene through its study in rodent models. We investigated the effect of the missense variant in SP6 (p.(Ala273Lys)) using surface plasmon resonance protein-DNA binding studies. We identified a potential SP6 binding motif in the AMBN proximal promoter sequence and showed that wild-type (WT) SP6 binds more strongly to it than the mutant protein. We hypothesize that SP6 variants may be a very rare cause of AI due to the critical roles of SP6 in development and that the relatively mild effect of the missense variant identified in this study is sufficient to affect amelogenesis causing AI, but not so severe as to be incompatible with life. We suggest that current AI cohorts, both with autosomal recessive and dominant disease, be screened for SP6 variants.


Asunto(s)
Amelogénesis Imperfecta/genética , Proteínas de Unión al ADN/genética , Proteínas del Esmalte Dental/genética , Factores de Transcripción de Tipo Kruppel/genética , Proteínas Adaptadoras Transductoras de Señales/genética , Ameloblastos/metabolismo , Ameloblastos/patología , Amelogénesis Imperfecta/patología , Proteínas Relacionadas con la Autofagia/genética , Diferenciación Celular/genética , Proliferación Celular/genética , Esmalte Dental/crecimiento & desarrollo , Esmalte Dental/patología , Femenino , Predisposición Genética a la Enfermedad , Haplotipos , Humanos , Masculino , Mutación Missense/genética , Linaje , Regiones Promotoras Genéticas/genética , Diente/crecimiento & desarrollo , Diente/patología , Secuenciación del Exoma
2.
Chembiochem ; 22(1): 232-240, 2021 01 05.
Artículo en Inglés | MEDLINE | ID: mdl-32961017

RESUMEN

The BCL-2 family is a challenging group of proteins to target selectively due to sequence and structural homologies across the family. Selective ligands for the BCL-2 family regulators of apoptosis are useful as probes to understand cell biology and apoptotic signalling pathways, and as starting points for inhibitor design. We have used phage display to isolate Affimer reagents (non-antibody-binding proteins based on a conserved scaffold) to identify ligands for MCL-1, BCL-xL , BCL-2, BAK and BAX, then used multiple biophysical characterisation methods to probe the interactions. We established that purified Affimers elicit selective recognition of their target BCL-2 protein. For anti-apoptotic targets BCL-xL and MCL-1, competitive inhibition of their canonical protein-protein interactions is demonstrated. Co-crystal structures reveal an unprecedented mode of molecular recognition; where a BH3 helix is normally bound, flexible loops from the Affimer dock into the BH3 binding cleft. Moreover, the Affimers induce a change in the target proteins towards a desirable drug-bound-like conformation. These proof-of-concept studies indicate that Affimers could be used as alternative templates to inspire the design of selective BCL-2 family modulators and more generally other protein-protein interaction inhibitors.


Asunto(s)
Proteína 1 de la Secuencia de Leucemia de Células Mieloides/análisis , Proteína bcl-X/análisis , Apoptosis , Humanos , Ligandos , Modelos Moleculares , Proteína 1 de la Secuencia de Leucemia de Células Mieloides/metabolismo , Unión Proteica , Conformación Proteica , Proteína bcl-X/metabolismo
3.
Genet Med ; 23(11): 2171-2177, 2021 11.
Artículo en Inglés | MEDLINE | ID: mdl-34230635

RESUMEN

PURPOSE: The availability of genetic test data within the electronic health record (EHR) is a pillar of the US vision for an interoperable health IT infrastructure and a learning health system. Although EHRs have been highly investigated, evaluation of the information systems used by the genetic labs has received less attention-but is necessary for achieving optimal interoperability. This study aimed to characterize how US genetic testing labs handle their information processing tasks. METHODS: We followed a qualitative research method that included interviewing lab representatives and a panel discussion to characterize the information flow models. RESULTS: Ten labs participated in the study. We identified three generic lab system models and their relevant characteristics: a backbone system with additional specialized systems for interpreting genetic results, a brokering system that handles housekeeping and communication, and a single primary system for results interpretation and report generation. CONCLUSION: Labs have heterogeneous workflows and generally have a low adoption of standards when sending genetic test reports back to EHRs. Core interpretations are often delivered as free text, limiting their computational availability for clinical decision support tools. Increased provision of genetic test data in discrete and standard-based formats by labs will benefit individual and public health.


Asunto(s)
Sistemas de Información en Laboratorio Clínico , Comunicación , Registros Electrónicos de Salud , Pruebas Genéticas , Humanos , Investigación Cualitativa
4.
Genet Med ; 23(11): 2178-2185, 2021 11.
Artículo en Inglés | MEDLINE | ID: mdl-34429527

RESUMEN

PURPOSE: Genetic laboratory test reports can often be of limited computational utility to the receiving clinical information systems, such as clinical decision support systems. Many health-care interoperability (HC) standards aim to tackle this problem, but the perceived benefits, challenges, and motivations for implementing HC interoperability standards from the labs' perspective has not been systematically assessed. METHODS: We surveyed genetic testing labs across the United States and conducted a semistructured interview with responding lab representatives. We conducted a thematic analysis of the interview transcripts to identify relevant themes. A panel of experts discussed and validated the identified themes. RESULTS: Nine labs participated in the interview, and 24 relevant themes were identified within five domains. These themes included the challenge of complex and changing genetic knowledge, the motivation of competitive advantage, provided financial incentives, and the benefit of supporting the learning health system. CONCLUSION: Our study identified the labs' perspective on various aspects of implementing HC interoperability standards in producing and communicating genetic test reports. Interviewees frequently reported that increased adoption of HC standards may be motivated by competition and programs incentivizing and regulating the incorporation of interoperability standards for genetic test data, which could benefit quality control, research, and other areas.


Asunto(s)
Laboratorios , Motivación , Atención a la Salud , Pruebas Genéticas , Humanos , Informática , Estados Unidos
5.
J Virol ; 90(20): 9543-55, 2016 10 15.
Artículo en Inglés | MEDLINE | ID: mdl-27512077

RESUMEN

UNLABELLED: Kaposi's sarcoma-associated herpesvirus (KSHV) is the causative agent of commonly fatal malignancies of immunocompromised individuals, including primary effusion lymphoma (PEL) and Kaposi's sarcoma (KS). A hallmark of all herpesviruses is their biphasic life cycle-viral latency and the productive lytic cycle-and it is well established that reactivation of the KSHV lytic cycle is associated with KS pathogenesis. Therefore, a thorough appreciation of the mechanisms that govern reactivation is required to better understand disease progression. The viral protein replication and transcription activator (RTA) is the KSHV lytic switch protein due to its ability to drive the expression of various lytic genes, leading to reactivation of the entire lytic cycle. While the mechanisms for activating lytic gene expression have received much attention, how RTA impacts cellular function is less well understood. To address this, we developed a cell line with doxycycline-inducible RTA expression and applied stable isotope labeling of amino acids in cell culture (SILAC)-based quantitative proteomics. Using this methodology, we have identified a novel cellular protein (AT-rich interacting domain containing 3B [ARID3B]) whose expression was enhanced by RTA and that relocalized to replication compartments upon lytic reactivation. We also show that small interfering RNA (siRNA) knockdown or overexpression of ARID3B led to an enhancement or inhibition of lytic reactivation, respectively. Furthermore, DNA affinity and chromatin immunoprecipitation assays demonstrated that ARID3B specifically interacts with A/T-rich elements in the KSHV origin of lytic replication (oriLyt), and this was dependent on lytic cycle reactivation. Therefore, we have identified a novel cellular protein whose expression is enhanced by KSHV RTA with the ability to inhibit KSHV reactivation. IMPORTANCE: Kaposi's sarcoma-associated herpesvirus (KSHV) is the causative agent of fatal malignancies of immunocompromised individuals, including Kaposi's sarcoma (KS). Herpesviruses are able to establish a latent infection, in which they escape immune detection by restricting viral gene expression. Importantly, however, reactivation of productive viral replication (the lytic cycle) is necessary for the pathogenesis of KS. Therefore, it is important that we comprehensively understand the mechanisms that govern lytic reactivation, to better understand disease progression. In this study, we have identified a novel cellular protein (AT-rich interacting domain protein 3B [ARID3B]) that we show is able to temper lytic reactivation. We showed that the master lytic switch protein, RTA, enhanced ARID3B levels, which then interacted with viral DNA in a lytic cycle-dependent manner. Therefore, we have added a new factor to the list of cellular proteins that regulate the KSHV lytic cycle, which has implications for our understanding of KSHV biology.


Asunto(s)
Proteínas de Unión al ADN/genética , Herpesvirus Humano 8/genética , Sarcoma de Kaposi/virología , Proteínas Virales/genética , Línea Celular Tumoral , Inmunoprecipitación de Cromatina/métodos , Replicación del ADN/genética , ADN Viral/genética , Regulación Viral de la Expresión Génica/genética , Humanos , Proteínas Inmediatas-Precoces/genética , Linfoma de Efusión Primaria/genética , Linfoma de Efusión Primaria/virología , ARN Interferente Pequeño/genética , Transactivadores/genética , Activación Viral/genética , Latencia del Virus/genética , Replicación Viral/genética
6.
PLoS Pathog ; 11(3): e1004771, 2015 Mar.
Artículo en Inglés | MEDLINE | ID: mdl-25794275

RESUMEN

Kaposi's sarcoma-associated herpesvirus (KSHV) is the causative agent of Kaposi's sarcoma (KS) and primary effusion lymphoma (PEL), which are aggressive malignancies associated with immunocompromised patients. For many non-viral malignancies, therapeutically targeting the ubiquitin proteasome system (UPS) has been successful. Likewise, laboratory studies have demonstrated that inhibition of the UPS might provide a promising avenue for the treatment of KSHV-associated diseases. The largest class of E3 ubiquitin ligases are the cullin-RING ligases (CRLs) that are activated by an additional ubiquitin-like protein, NEDD8. We show that pharmacological inhibition of NEDDylation (using the small molecule inhibitor MLN4924) is cytotoxic to PEL cells by inhibiting NF-κB. We also show that CRL4B is a novel regulator of latency as its inhibition reactivated lytic gene expression. Furthermore, we uncovered a requirement for NEDDylation during the reactivation of the KSHV lytic cycle. Intriguingly, inhibition prevented viral DNA replication but not lytic cycle-associated gene expression, highlighting a novel mechanism that uncouples these two features of KSHV biology. Mechanistically, we show that MLN4924 treatment precluded the recruitment of the viral pre-replication complex to the origin of lytic DNA replication (OriLyt). These new findings have revealed novel mechanisms that regulate KSHV latency and reactivation. Moreover, they demonstrate that inhibition of NEDDylation represents a novel approach for the treatment of KSHV-associated malignancies.


Asunto(s)
Ciclopentanos/farmacología , Regulación Viral de la Expresión Génica/efectos de los fármacos , Herpesvirus Humano 8/fisiología , Pirimidinas/farmacología , Sarcoma de Kaposi/tratamiento farmacológico , Ubiquitinas/metabolismo , Activación Viral/efectos de los fármacos , Línea Celular Tumoral , Replicación del ADN/efectos de los fármacos , ADN Viral/biosíntesis , ADN Viral/genética , Células HEK293 , Humanos , Proteína NEDD8 , FN-kappa B/antagonistas & inhibidores , FN-kappa B/genética , FN-kappa B/metabolismo , Sarcoma de Kaposi/genética , Sarcoma de Kaposi/metabolismo , Ubiquitinas/genética , Activación Viral/genética
7.
PLoS Pathog ; 10(5): e1004098, 2014 May.
Artículo en Inglés | MEDLINE | ID: mdl-24788796

RESUMEN

Kaposi's sarcoma-associated herpesvirus (KSHV) is an oncogenic herpesvirus associated with multiple AIDS-related malignancies. Like other herpesviruses, KSHV has a biphasic life cycle and both the lytic and latent phases are required for tumorigenesis. Evidence suggests that KSHV lytic replication can cause genome instability in KSHV-infected cells, although no mechanism has thus far been described. A surprising link has recently been suggested between mRNA export, genome instability and cancer development. Notably, aberrations in the cellular transcription and export complex (hTREX) proteins have been identified in high-grade tumours and these defects contribute to genome instability. We have previously shown that the lytically expressed KSHV ORF57 protein interacts with the complete hTREX complex; therefore, we investigated the possible intriguing link between ORF57, hTREX and KSHV-induced genome instability. Herein, we show that lytically active KSHV infected cells induce a DNA damage response and, importantly, we demonstrate directly that this is due to DNA strand breaks. Furthermore, we show that sequestration of the hTREX complex by the KSHV ORF57 protein leads to this double strand break response and significant DNA damage. Moreover, we describe a novel mechanism showing that the genetic instability observed is a consequence of R-loop formation. Importantly, the link between hTREX sequestration and DNA damage may be a common feature in herpesvirus infection, as a similar phenotype was observed with the herpes simplex virus 1 (HSV-1) ICP27 protein. Our data provide a model of R-loop induced DNA damage in KSHV infected cells and describes a novel system for studying genome instability caused by aberrant hTREX.


Asunto(s)
Transformación Celular Viral/genética , Inestabilidad Genómica/fisiología , Herpesvirus Humano 8/fisiología , Transporte de ARN/genética , Proteínas Virales/fisiología , Roturas del ADN de Doble Cadena , Células HEK293 , Infecciones por Herpesviridae/genética , Infecciones por Herpesviridae/virología , Interacciones Huésped-Patógeno/genética , Humanos , Complejos Multiproteicos/fisiología , ARN Mensajero/metabolismo , ARN Viral/metabolismo , Sarcoma de Kaposi/genética , Sarcoma de Kaposi/virología , Transducción de Señal/genética
8.
BMC Womens Health ; 16: 41, 2016 07 22.
Artículo en Inglés | MEDLINE | ID: mdl-27449775

RESUMEN

BACKGROUND: To assess the demographic and attitudinal factors associated with HPV vaccine initiation and completion among 18-26 year old women in Utah. METHOD: Between January 2013 and December 2013, we surveyed 325 women from the University of Utah Community Clinics about their HPV vaccine related beliefs and behaviors. Odds ratios (ORs) were estimated from logistic regression models to identify variables related to HPV vaccine initiation and series completion. RESULTS: Of the 325 participants, 204 (62.8 %) had initiated the vaccine and 159 (48.9 %) had completed the 3-dose series. The variables associated with HPV vaccine initiation were lower age (OR = 1.18 per year); being unmarried (OR = 3.62); not practicing organized religion (OR = 2.40); knowing how HPV spreads (OR = 6.29); knowing the connection between HPV and cervical cancer (OR = 3.90); a belief in the importance of preventive vaccination (OR = 2.45 per scale unit); strength of doctor recommendation (OR = 1.86 per scale unit); and whether a doctor's recommendation was influential (OR = 1.70 per scale unit). These variables were also significantly associated with HPV vaccine completion. CONCLUSION: The implications of these findings may help inform policies and interventions focused on increasing HPV vaccination rates among young women. For example, without this information, programs might focus on HPV awareness; however, the results of this study illustrate that awareness is already high (near saturation) in target populations and other factors, such as strong and consistent physician recommendations, are more pivotal in increasing likelihood of vaccination. Additionally, our findings indicate the need for discussions of risk assessment be tailored to the young adult population.


Asunto(s)
Conocimientos, Actitudes y Práctica en Salud , Infecciones por Papillomavirus/prevención & control , Vacunas contra Papillomavirus/uso terapéutico , Mujeres/psicología , Adolescente , Adulto , Análisis Factorial , Femenino , Humanos , Vacunas contra Papillomavirus/farmacología , Medición de Riesgo/métodos , Encuestas y Cuestionarios , Utah , Neoplasias del Cuello Uterino/prevención & control
9.
Prenat Diagn ; 35(5): 440-6, 2015 May.
Artículo en Inglés | MEDLINE | ID: mdl-25273838

RESUMEN

OBJECTIVE: The aim of this article is to determine the cost effectiveness of cell free DNA (cfDNA) as a replacement for integrated screening using a societal cost perspective. METHOD: This study used Monte-Carlo simulation with one-way and probabilistic sensitivity analysis. RESULTS: Cell free DNA is more effective and less costly than integrated screening. The incremental cost-effectiveness ratio for cfDNA relative to the integrated test was -$277 955 per case detected (95th percent confidence interval -$881 882 to $532 785). CONCLUSION: Cell free DNA screening is a cost-effective replacement for maternal serum screening when the lifetime costs of Down syndrome live births are considered. The adoption of cfDNA screening would save approximately $277 955 for each additional case detected over integrated screening.


Asunto(s)
Aborto Inducido/economía , ADN/sangre , Síndrome de Down/economía , Diagnóstico Prenatal/economía , Análisis Costo-Beneficio , Síndrome de Down/sangre , Síndrome de Down/diagnóstico , Femenino , Humanos , Método de Montecarlo , Embarazo
10.
EMBO J ; 29(11): 1851-64, 2010 Jun 02.
Artículo en Inglés | MEDLINE | ID: mdl-20436455

RESUMEN

Kaposi's sarcoma-associated herpesvirus (KSHV) expresses numerous intronless mRNAs that are unable to access splicing-dependent cellular mRNA nuclear export pathways. To circumvent this problem, KSHV encodes the open reading frame 57 (ORF57) protein, which orchestrates the formation of an export-competent virus ribonucleoprotein particle comprising the nuclear export complex hTREX, but not the exon-junction complex (EJC). Interestingly, EJCs stimulate mRNA translation, which raises the intriguing question of how intronless KSHV transcripts are efficiently translated. Herein, we show that ORF57 associates with components of the 48S pre-initiation complex and co-sediments with the 40S ribosomal subunits. Strikingly, we observed a direct interaction between ORF57 and PYM, a cellular protein that enhances translation by recruiting the 48S pre-initiation complex to newly exported mRNAs, through an interaction with the EJC. Moreover, detailed biochemical analysis suggests that ORF57 recruits PYM to intronless KSHV mRNA and PYM then facilitates the association of ORF57 and the cellular translation machinery. We, therefore, propose a model whereby ORF57 interacts directly with PYM to enhance translation of intronless KSHV transcripts.


Asunto(s)
Proteínas Portadoras/metabolismo , Herpesvirus Humano 8/metabolismo , Sistemas de Lectura Abierta/fisiología , ARN Mensajero/metabolismo , Transporte Activo de Núcleo Celular/genética , Proteínas Portadoras/genética , Citoplasma/genética , Citoplasma/metabolismo , Exones , Herpesvirus Humano 8/genética , Humanos , Empalme del ARN , Transporte de ARN/genética , ARN Mensajero/genética , Ribosomas/genética , Ribosomas/metabolismo , Virión/genética , Virión/metabolismo
11.
J Virol ; 87(24): 13853-67, 2013 Dec.
Artículo en Inglés | MEDLINE | ID: mdl-24109239

RESUMEN

Merkel cell carcinoma (MCC) is a highly aggressive nonmelanoma skin cancer arising from epidermal mechanoreceptor Merkel cells. In 2008, a novel human polyomavirus, Merkel cell polyomavirus (MCPyV), was identified and is strongly implicated in MCC pathogenesis. Currently, little is known regarding the virus-host cell interactions which support virus replication and virus-induced mechanisms in cellular transformation and metastasis. Here we identify a new function of MCPyV small T antigen (ST) as an inhibitor of NF-κB-mediated transcription. This effect is due to an interaction between MCPyV ST and the NF-κB essential modulator (NEMO) adaptor protein. MCPyV ST expression inhibits IκB kinase α (IKKα)/IKKß-mediated IκB phosphorylation, which limits translocation of the NF-κB heterodimer to the nucleus. Regulation of this process involves a previously undescribed interaction between MCPyV ST and the cellular phosphatase subunits, protein phosphatase 4C (PP4C) and/or protein phosphatase 2A (PP2A) Aß, but not PP2A Aα. Together, these results highlight a novel function of MCPyV ST to subvert the innate immune response, allowing establishment of early or persistent infection within the host cell.


Asunto(s)
Antígenos Virales de Tumores/metabolismo , Carcinoma de Células de Merkel/metabolismo , Quinasa I-kappa B/metabolismo , Poliomavirus de Células de Merkel/metabolismo , Infecciones por Polyomavirus/metabolismo , Infecciones Tumorales por Virus/metabolismo , Antígenos Virales de Tumores/genética , Carcinoma de Células de Merkel/genética , Carcinoma de Células de Merkel/inmunología , Carcinoma de Células de Merkel/virología , Línea Celular , Humanos , Quinasa I-kappa B/genética , Quinasa I-kappa B/inmunología , Inmunidad Innata , Poliomavirus de Células de Merkel/genética , FN-kappa B/genética , FN-kappa B/inmunología , Fosforilación , Infecciones por Polyomavirus/genética , Infecciones por Polyomavirus/inmunología , Infecciones por Polyomavirus/virología , Unión Proteica , Infecciones Tumorales por Virus/genética , Infecciones Tumorales por Virus/inmunología , Infecciones Tumorales por Virus/virología
12.
Arch Pathol Lab Med ; 2024 Sep 20.
Artículo en Inglés | MEDLINE | ID: mdl-39299704

RESUMEN

CONTEXT.­: Technology companies and research groups are increasingly exploring applications of generative artificial intelligence (GenAI) in pathology and laboratory medicine. Although GenAI holds considerable promise, it also introduces novel risks for patients, communities, professionals, and the scientific process. OBJECTIVE.­: To summarize the current frameworks for the ethical development and management of GenAI within health care settings. DATA SOURCES.­: The analysis draws from scientific journals, organizational websites, and recent guidelines on artificial intelligence ethics and regulation. CONCLUSIONS.­: The literature on the ethical management of artificial intelligence in medicine is extensive but is still in its nascent stages because of the evolving nature of the technology. Effective and ethical integration of GenAI requires robust processes and shared accountability among technology vendors, health care organizations, regulatory bodies, medical professionals, and professional societies. As the technology continues to develop, a multifaceted ecosystem of safety mechanisms and ethical oversight is crucial to maximize benefits and mitigate risks.

13.
Appl Clin Inform ; 2024 Oct 03.
Artículo en Inglés | MEDLINE | ID: mdl-39362293

RESUMEN

OBJECTIVES: Empirically investigate current practices and analyze ethical dimensions of clinical data sharing by healthcare organizations for uses other than treatment, payment, and operations. Make recommendations to inform research and policy for healthcare organizations to protect patients' privacy and autonomy when sharing data with unrelated third parties. METHODS: Semi-structured interviews and surveys involving 24 informatics leaders from 22 US healthcare organizations, accompanied by thematic and ethical analyses. RESULTS: We found considerable heterogeneity across organizations in policies and practices. Respondents understood "data sharing" and "research" in very different ways. Their interpretations of these terms ranged from making data available for academic and public health uses, and to HIEs; to selling data for corporate research, to contracting with aggregators for future resale or use. The nine interview themes were that healthcare organizations: (1) share clinical data with many types of organizations, (2) have a variety of motivations for sharing data, (3) do not make data sharing policies readily available, (4) have widely varying data sharing approval processes, (5) most commonly rely on HIPAA de-identification to protect privacy, (6) were concerned about clinical data use by electronic health record vendors, (7) lacked data sharing transparency to the general public, (8) allowed individual patients little control over sharing of their data, and (9) had not yet changed data sharing practices within the year following the US Supreme Court 2022 decision denying rights to abortion. CONCLUSIONS: Our analysis identified gaps between ethical principles and healthcare organizations' data sharing policies and practices. To better align clinical data sharing practices with patient expectations and biomedical ethical principles, we recommend: updating HIPAA, including re-identification and upstream sharing restrictions in data sharing contracts, better coordination across data sharing approval processes, fuller transparency and opt-out options for patients, and accountability for data sharing and consequent harms.

14.
PLoS Pathog ; 7(1): e1001244, 2011 Jan 06.
Artículo en Inglés | MEDLINE | ID: mdl-21253573

RESUMEN

The herpesvirus proteins HSV-1 ICP27 and HVS ORF57 promote viral mRNA export by utilizing the cellular mRNA export machinery. This function is triggered by binding to proteins of the transcription-export (TREX) complex, in particular to REF/Aly which directs viral mRNA to the TAP/NFX1 pathway and, subsequently, to the nuclear pore for export to the cytoplasm. Here we have determined the structure of the REF-ICP27 interaction interface at atomic-resolution and provided a detailed comparison of the binding interfaces between ICP27, ORF57 and REF using solution-state NMR. Despite the absence of any obvious sequence similarity, both viral proteins bind on the same site of the folded RRM domain of REF, via short but specific recognition sites. The regions of ICP27 and ORF57 involved in binding by REF have been mapped as residues 104-112 and 103-120, respectively. We have identified the pattern of residues critical for REF/Aly recognition, common to both ICP27 and ORF57. The importance of the key amino acid residues within these binding sites was confirmed by site-directed mutagenesis. The functional significance of the ORF57-REF/Aly interaction was also probed using an ex vivo cytoplasmic viral mRNA accumulation assay and this revealed that mutants that reduce the protein-protein interaction dramatically decrease the ability of ORF57 to mediate the nuclear export of intronless viral mRNA. Together these data precisely map amino acid residues responsible for the direct interactions between viral adaptors and cellular REF/Aly and provide the first molecular details of how herpes viruses access the cellular mRNA export pathway.


Asunto(s)
ADN-(Sitio Apurínico o Apirimidínico) Liasa/metabolismo , Herpesvirus Humano 1/metabolismo , Proteínas Inmediatas-Precoces/metabolismo , ARN Mensajero/metabolismo , ARN Viral/metabolismo , Proteínas Represoras/metabolismo , Transactivadores/metabolismo , Secuencia de Aminoácidos , Sitios de Unión , ADN-(Sitio Apurínico o Apirimidínico) Liasa/química , Exodesoxirribonucleasas/metabolismo , Herpesvirus Humano 1/genética , Humanos , Proteínas Inmediatas-Precoces/química , Datos de Secuencia Molecular , Fosfoproteínas/metabolismo , Unión Proteica , Mapeo de Interacción de Proteínas , ARN Viral/química , Proteínas Represoras/química , Transactivadores/química
15.
PLoS Pathog ; 7(7): e1002138, 2011 Jul.
Artículo en Inglés | MEDLINE | ID: mdl-21814512

RESUMEN

The hTREX complex mediates cellular bulk mRNA nuclear export by recruiting the nuclear export factor, TAP, via a direct interaction with the export adaptor, Aly. Intriguingly however, depletion of Aly only leads to a modest reduction in cellular mRNA nuclear export, suggesting the existence of additional mRNA nuclear export adaptor proteins. In order to efficiently export Kaposi's sarcoma-associated herpesvirus (KSHV) intronless mRNAs from the nucleus, the KSHV ORF57 protein recruits hTREX onto viral intronless mRNAs allowing access to the TAP-mediated export pathway. Similarly however, depletion of Aly only leads to a modest reduction in the nuclear export of KSHV intronless mRNAs. Herein, we identify a novel interaction between ORF57 and the cellular protein, UIF. We provide the first evidence that the ORF57-UIF interaction enables the recruitment of hTREX and TAP to KSHV intronless mRNAs in Aly-depleted cells. Strikingly, depletion of both Aly and UIF inhibits the formation of an ORF57-mediated nuclear export competent ribonucleoprotein particle and consequently prevents ORF57-mediated mRNA nuclear export and KSHV protein production. Importantly, these findings highlight that redundancy exists in the eukaryotic system for certain hTREX components involved in the mRNA nuclear export of intronless KSHV mRNAs.


Asunto(s)
Núcleo Celular/metabolismo , Herpesvirus Humano 8/metabolismo , Proteínas Nucleares/metabolismo , ARN Mensajero/metabolismo , ARN Viral/metabolismo , Proteínas de Unión al ARN/metabolismo , Proteínas Virales/metabolismo , Transporte Activo de Núcleo Celular/genética , Núcleo Celular/genética , Núcleo Celular/virología , Células HEK293 , Herpesvirus Humano 8/genética , Humanos , Proteínas Nucleares/genética , ARN Mensajero/genética , ARN Viral/genética , Proteínas de Unión al ARN/genética , Proteínas Virales/genética
17.
J Gen Intern Med ; 28(12): 1565-72, 2013 Dec.
Artículo en Inglés | MEDLINE | ID: mdl-23645451

RESUMEN

BACKGROUND: Interpretation of a diagnostic test result requires knowing what proportion of patients with a "similar" result has the condition in question. This information is often not readily available from the medical literature, or may be based on different clinical populations that make it nonapplicable. In certain settings, where correlated screening parameters and diagnostic data are available in electronic medical records, a representation of diagnostic test performance on "patients like my patient" can be obtained. OBJECTIVE: We sought to integrate patient demographic and physician practice information using a simplified nearest neighbor algorithm. We used this method to illustrate the relationship between tTG IgA test result and duodenal biopsy for celiac disease in a local diagnostic context. PARTICIPANTS: We used a data set of 1,461 paired tissue transglutaminase (tTG) IgA and definitive duodenal biopsy results from Intermountain Healthcare with data on patient age and ordering physician specialty. This was split into a discovery set of 1,000 and a validation set of 461 paired results. MAIN MEASURES: Accuracy of the local discovery data set in predicting probability of positive duodenal biopsy and confidence intervals around predicted probability in the test data compared to probabilities of positive biopsy implied from published logistic regression and from published sensitivity and specificity studies. KEY RESULTS: The near-neighbor method could estimate probability of clinical outcomes with predictive performance equivalent to other methods while adjusting probability estimates and confidence intervals to fit specific clinical situations. CONCLUSIONS: Data from clinical encounters obtained from electronic medical records can yield prediction estimates that are tailored to the individual patient, local population, and healthcare delivery processes. Local analysis of diagnostic probability may be more clinically meaningful than probabilities inferred from published studies. This local utility may come at the expense of external validity and generalizability.


Asunto(s)
Algoritmos , Enfermedad Celíaca/sangre , Enfermedad Celíaca/diagnóstico , Sistemas de Apoyo a Decisiones Clínicas , Modelos Estadísticos , Adolescente , Sistemas de Apoyo a Decisiones Clínicas/normas , Proteínas de Unión al GTP/sangre , Humanos , Inmunoglobulina A/sangre , Persona de Mediana Edad , Proteína Glutamina Gamma Glutamiltransferasa 2 , Estudios Retrospectivos , Transglutaminasas/sangre , Adulto Joven
18.
Anal Biochem ; 442(1): 51-61, 2013 Nov 01.
Artículo en Inglés | MEDLINE | ID: mdl-23928048

RESUMEN

Many proteins involved in DNA repair systems interact with DNA that has structure altered from the typical B-form helix. Using magnetic beads to immobilize DNAs containing various types of structures, we evaluated the in vitro binding activities of two well-characterized DNA repair proteins, Escherichia coli MutS and human p53. E. coli MutS bound to double-stranded DNAs, with higher affinity for a G/T mismatch compared to a G/A mismatch and highest affinity for larger non-B-DNA structures. E. coli MutS bound best to DNA between pH 6 and 9. Experiments discriminated between modes of p53-DNA binding, and increasing ionic strength reduced p53 binding to nonspecific double-stranded DNA, but had minor effects on binding to consensus response sequences or single-stranded DNA. Compared to nonspecific DNA sequences, p53 bound with a higher affinity to mismatches and base insertions, while binding to various hairpin structures was similar to that observed to its consensus DNA sequence. For hairpins containing CTG repeats, the extent of p53 binding was proportional to the size of the repeat. In summary, using the flexibility of the magnetic bead separation assay we demonstrate that pH and ionic strength influence the binding of two DNA repair proteins to a variety of DNA structures.


Asunto(s)
ADN/química , Proteínas de Escherichia coli/química , Proteína MutS de Unión a los Apareamientos Incorrectos del ADN/química , Proteína p53 Supresora de Tumor/química , Secuencia de Aminoácidos , Escherichia coli , Humanos , Conformación de Ácido Nucleico , Concentración Osmolar
19.
Prenat Diagn ; 33(12): 1201-6, 2013 Dec.
Artículo en Inglés | MEDLINE | ID: mdl-24027169

RESUMEN

OBJECTIVES: In maternal serum screening for Down syndrome, a cutoff of 1 : 270 is often used as a decision point to recommend invasive confirmatory testing. However, it has not been established how well this or any other cutoff relates to patient preferences, that is, the values that pregnant women attach to various screening outcomes. The purpose of this study was to examine the clinical and economic tradeoffs of a wide range of risk cutoffs for the quadruple screen. METHODS: Screening costs and outcomes for multiple risk cutoffs were modeled using a Monte Carlo simulation. RESULTS: The optimal cutoff for maternal serum screening depends on the relative values placed by the patient on different outcomes. Total societal costs were similar across the range of cutoffs. CONCLUSIONS: Given that different screening outcomes are optimized by different cutoff values, a one-size-fits-all approach may not be appropriate.


Asunto(s)
Síndrome de Down/diagnóstico , Diagnóstico Prenatal/métodos , Aborto Espontáneo/etiología , Adulto , Amniocentesis/efectos adversos , Gonadotropina Coriónica/sangre , Costos y Análisis de Costo , Síndrome de Down/sangre , Estriol/sangre , Femenino , Edad Gestacional , Humanos , Inhibinas/sangre , Edad Materna , Método de Montecarlo , Embarazo , Diagnóstico Prenatal/economía , Factores de Riesgo , alfa-Fetoproteínas
20.
Arch Pathol Lab Med ; 2023 Sep 11.
Artículo en Inglés | MEDLINE | ID: mdl-37694955

RESUMEN

CONTEXT.­: Clinician feedback is an important source of information for laboratory quality improvement programs. OBJECTIVE.­: To pilot a program for nearly real-time solicitation and analysis of physician feedback regarding clinical laboratory services. DESIGN.­: Laboratories distributed either electronic or paper survey forms to physicians. Results were tabulated by College of American Pathologists staff. Free-text comments were shared promptly with the participating laboratories to facilitate follow-up. RESULTS.­: Forty-seven clinical laboratories participated in the study and submitted results for 987 physician surveys, including both paper and electronic forms. Of 694 responses submitted electronically within the study period, 460 (66.3%) included at least 1 free-text entry, for a total of 951 free-text comments. CONCLUSIONS.­: Point-of-service solicitation of physician feedback regarding clinical laboratory services is feasible and can provide a substantial quantity of potentially useful information regarding laboratory performance from the customer perspective.

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