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PubMed · 14582908

Diagnostic tools in tuberculous pleurisy: a direct comparative study.

Abstract

Thoracoscopy is the most accurate yet most expensive tool for establishing the diagnosis of tuberculous (TB) pleurisy. However, most high TB-incidence regions have limited financial resources, lack the infrastructure needed for routine thoracoscopy and require an alternative, cost-effective diagnostic approach for pleural effusions. Altogether, 51 patients with undiagnosed exudative pleural effusions were recruited for a prospective, direct comparison between bronchial wash, pleural fluid microbiology and biochemistry (adenosine deaminase (ADA) and cell count), closed needle biopsy, and medical thoracoscopy. The final diagnosis was TB in 42 patients (82%), malignancy in five (10%) and idiopathic in four patients (8%). Sensitivity of histology, culture and combined histology/culture was 66, 48 and 79%, respectively for closed needle biopsy and 100, 76 and 100%, respectively for thoracoscopy. Both were 100% specific. Pleural fluid ADA of > or = 50 U x L(-1) was 95% sensitive and 89% specific. Combined ADA, lymphocyte/neutrophil ratio > or = 0.75 plus closed needle biopsy reached 93% sensitivity and 100% specificity. A combination of pleural fluid adenosine deaminase, differential cell count and closed needle biopsy has a high diagnostic accuracy in undiagnosed exudative pleural effusions in areas with high incidences of tuberculosis and might substitute medical thoracoscopy at considerably lower expense in resource-poor countries.

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BibTeXRIS

A H Diacon, B W Van de Wal, C Wyser, J P Smedema, J Bezuidenhout, C T Bolliger, G Walzl. 2003. Diagnostic tools in tuberculous pleurisy: a direct comparative study.. https://doi.org/10.1183/09031936.03.00017103a

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A contextual activity score (CAS) for inferring ADAR-associated transcriptional activity across RNA-seq, single-cell, and spatial transcriptomics.

BACKGROUND AND OBJECTIVE: Adenosine-to-inosine RNA editing, catalyzed by Adenosine Deaminases Acting on RNA (ADARs), is a widespread modification involved in neural function, immune regulation, and cancer. The Alu Editing Index (AEI) is the standard metric to estimate ADAR activity but requires raw sequencing reads and is poorly suited for single-cell and spatial transcriptomic data. This study aimed to develop an alternative framework for inferring ADAR-associated transcriptional activity from gene expression data across diverse transcriptomic technologies. METHODS: We developed the Contextual Activity Score (CAS), a framework based on transcriptional signatures from ADAR perturbation experiments. Context-specific signatures were generated for human neurons, mouse neurons, and cancer models to infer ADAR1 and ADAR2 activity. CAS was computed from normalized gene expression matrices using regulon-based enrichment analysis. Performance was evaluated by comparing with the Alu Editing Index across bulk RNA sequencing datasets, simulated sequencing depths, and library preparation protocols. RESULTS: CAS showed strong concordance with the Alu Editing Index across multiple datasets, while remaining robust to reduced sequencing depth and different library protocols. Unlike the Alu Editing Index, CAS can be applied to single-cell and spatial transcriptomic data and enables the independent assessment of ADAR2 activity. In cancer and neuronal contexts, CAS captured biologically meaningful variations in ADAR-associated transcriptional activity at sample, cell-type, and spatial levels. CONCLUSION: CAS provides a scalable approach applicable across multiple RNA-seq protocols for estimating ADAR-associated transcriptional activity using gene expression data. This method, implemented in an open-source R package for broad adoption, expands the ability to study ADAR-associated transcriptional activity across transcriptomic modalities where direct editing quantification is challenging, such as single-cell and spatial transcriptomics.

Adenosine Deaminase↗

5',8-cyclo-dAdo and 8-oxo-dAdo DNA Lesions Are Both Substrates of Adenosine Deaminase: A Preliminary Study.

Genetic information, whether inside or outside the nucleus, is exposed to a variety of harmful physico-chemical factors. Although DNA damage repair systems have been extensively studied, little information about post-repair and non-genomic DNA damage metabolism is available in the literature. Adenosine deaminase (ADA) is an abundant enzyme found on both sides of the cell membrane that regulates the concentration of adenine derivatives. In this article, it has been shown that 7,8-dihydro-8-oxo-2'-deoxyadenosine (OXOdAdo) and (5'R/S) 5',8-cyclo-2'-deoxyadenosine ((5'R/S)cdAdo) are suitable substrates for ADA. For this purpose, theoretical Density Functional Tight Binding and RP-HPLC analyses were applied. The products of ADA activity, i.e., OXOdIno (7,8-dihydro-8-oxo-2'-deoxyinosine) and (5'R/S) cdIno ((5'R/S) 8-cyclo-2'-deoxyinosine), were identified and confirmed by high-resolution mass spectroscopy. Although the (5'R) and (5'S)cdAdo enzymatic deamination processes are much slower (34% and 32% after 168 h, respectively) than the process observed for dAdo, 5',8-cyclo-2'-deoxyinosine should be considered when monitoring cyclopurine levels in physiological fluids. The same should be considered in the case of OXOdAdo, which is completely converted to OXOdIno within one minute and may therefore be less visible than OXOdGuo during mass spectroscopy analysis. Both these observations are important, given the abundance of 2'-deoxyadenosine on both sides of the cell membrane and its potential conversion into OXOdAdo and (5'R/S)cdAdo. They may also explain why the observed level of OXOdAdo is much lower than that of OXOdGuo in cells and physiological fluids, even though their difference in ionisation potential is only 0.25 eV. Future studies are needed to further investigate the metabolism of DNA damage and to identify the enzymes involved in nucleic acid biochemistry.

Adenosine Deaminase↗

A high resolution A-to-I editing map in the mouse identifies editing events controlled by pre-mRNA splicing.

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Adenosine Deaminase↗