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      Diagnosis and biomarkers for ocular tuberculosis: From the present into the future

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          Abstract

          Tuberculosis is an airborne disease caused by Mycobacterium tuberculosis (Mtb) and can manifest both pulmonary and extrapulmonary disease, including ocular tuberculosis (OTB). Accurate diagnosis and swift optimal treatment initiation for OTB is faced by many challenges combined with the lack of standardized treatment regimens this results in uncertain OTB outcomes. The purpose of this study is to summarize existing diagnostic approaches and recently discovered biomarkers that may contribute to establishing OTB diagnosis, choice of anti-tubercular therapy (ATT) regimen, and treatment monitoring. The keywords ocular tuberculosis, tuberculosis, Mycobacterium, biomarkers, molecular diagnosis, multi-omics, proteomics, genomics, transcriptomics, metabolomics, T-lymphocytes profiling were searched on PubMed and MEDLINE databases. Articles and books published with at least one of the keywords were included and screened for relevance. There was no time limit for study inclusion. More emphasis was placed on recent publications that contributed new information about the pathogenesis, diagnosis, or treatment of OTB. We excluded abstracts and articles that were not written in the English language. References cited within the identified articles were used to further supplement the search.

          We found 10 studies evaluating the sensitivity and specificity of interferon-gamma release assay (IGRA), and 6 studies evaluating that of tuberculin skin test (TST) in OTB patients. IGRA (Sp = 71-100%, Se = 36-100%) achieves overall better sensitivity and specificity than TST (Sp = 51.1-85.7%; Se = 70.9-98.5%). For nuclear acid amplification tests (NAAT), we found 7 studies on uniplex polymerase chain reaction (PCR) with different Mtb targets, 7 studies on DNA-based multiplex PCR, 1 study on mRNA-based multiplex PCR, 4 studies on loop-mediated isothermal amplification (LAMP) assay with different Mtb targets, 3 studies on GeneXpert assay, 1 study on GeneXpert Ultra assay and 1 study for MTBDRplus assay for OTB. Specificity is overall improved but sensitivity is highly variable for NAATs (excluding uniplex PCR, Sp = 50-100%; Se = 10.5-98%) as compared to IGRA. We also found 3 transcriptomic studies, 6 proteomic studies, 2 studies on stimulation assays, 1 study on intraocular protein analysis and 1 study on T-lymphocyte profiling in OTB patients. All except 1 study evaluated novel, previously undiscovered biomarkers. Only 1 study has been externally validated by a large independent cohort.

          Future theranostic marker discovery by a multi-omics approach is essential to deepen pathophysiological understanding of OTB. Combined these might result in swift, optimal and personalized treatment regimens to modulate the heterogeneous mechanisms of OTB. Eventually, these studies could improve the current cumbersome diagnosis and management of OTB.

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          Most cited references183

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          A programmable dual-RNA-guided DNA endonuclease in adaptive bacterial immunity.

          Clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated (Cas) systems provide bacteria and archaea with adaptive immunity against viruses and plasmids by using CRISPR RNAs (crRNAs) to guide the silencing of invading nucleic acids. We show here that in a subset of these systems, the mature crRNA that is base-paired to trans-activating crRNA (tracrRNA) forms a two-RNA structure that directs the CRISPR-associated protein Cas9 to introduce double-stranded (ds) breaks in target DNA. At sites complementary to the crRNA-guide sequence, the Cas9 HNH nuclease domain cleaves the complementary strand, whereas the Cas9 RuvC-like domain cleaves the noncomplementary strand. The dual-tracrRNA:crRNA, when engineered as a single RNA chimera, also directs sequence-specific Cas9 dsDNA cleavage. Our study reveals a family of endonucleases that use dual-RNAs for site-specific DNA cleavage and highlights the potential to exploit the system for RNA-programmable genome editing.
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            CRISPR-Cas12a target binding unleashes indiscriminate single-stranded DNase activity

            CRISPR-Cas12a (Cpf1) proteins are RNA-guided enzymes that bind and cut DNA as components of bacterial adaptive immune systems. Like CRISPR-Cas9, Cas12a has been harnessed for genome editing based on its ability to generate targeted, double-stranded DNA (dsDNA) breaks. Here we show that RNA-guided DNA binding unleashes indiscriminate single-stranded DNA (ssDNA) cleavage activity by Cas12a that completely degrades ssDNA molecules. We find that target-activated, non-specific ssDNase cleavage is also a property of other type V CRISPR-Cas12 enzymes. By combining Cas12a ssDNase activation with isothermal amplification, we create a method termed DNA Endonuclease Targeted CRISPR Trans Reporter (DETECTR), which achieves attomolar sensitivity for DNA detection. DETECTR enables rapid and specific detection of human papillomavirus in patient samples, thereby providing a simple platform for molecular diagnostics.
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              CRISPR interference: RNA-directed adaptive immunity in bacteria and archaea.

              Sequence-directed genetic interference pathways control gene expression and preserve genome integrity in all kingdoms of life. The importance of such pathways is highlighted by the extensive study of RNA interference (RNAi) and related processes in eukaryotes. In many bacteria and most archaea, clustered, regularly interspaced short palindromic repeats (CRISPRs) are involved in a more recently discovered interference pathway that protects cells from bacteriophages and conjugative plasmids. CRISPR sequences provide an adaptive, heritable record of past infections and express CRISPR RNAs - small RNAs that target invasive nucleic acids. Here, we review the mechanisms of CRISPR interference and its roles in microbial physiology and evolution. We also discuss potential applications of this novel interference pathway.
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                Author and article information

                Journal
                Theranostics
                Theranostics
                thno
                Theranostics
                Ivyspring International Publisher (Sydney )
                1838-7640
                2023
                1 April 2023
                : 13
                : 7
                : 2088-2113
                Affiliations
                [1 ]Lee Kong Chian School of Medicine, Nanyang Technological University of Singapore, Singapore.
                [2 ]Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.
                [3 ]National Healthcare Group Eye Institute, Tan Tock Seng Hospital, Singapore, Singapore.
                [4 ]Department of Ophthalmology, Faculty of Medicine Universitas Indonesia - CiptoMangunkusmoKirana Eye Hospital, Jakarta, Indonesia.
                [5 ]Laboratory Medical Immunology, Department of Immunology, ErasmusMC, UniversityMedical Centre, Rotterdam, the Netherlands.
                [6 ]Department of Internal Medicine, Division of Clinical Immunology, Erasmus MC, University Medical Center, Rotterdam, The Netherlands.
                [7 ]Department of Ophthalmology, Erasmus MC, University Medical Center, Rotterdam, The Netherlands.
                [8 ]Immunology Programme, Life Sciences Institute, National University of Singapore, Singapore, Singapore.
                [9 ]Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore.
                [10 ]Department of Biochemistry, Post Graduate Institute of Medical Education and Research, Chandigarh, India.
                [11 ]A*SATR Infectious Diseases Labs (A*STAR ID Labs), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore.
                [12 ]Singapore Immunology Network (SIgN), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore.
                [13 ]University of Indonesia Hospital (RSUI), Depok, West Java, Indonesia.
                [14 ]Advanced Eye Centre, Post-Graduate Institute of Medical Education and Research (PGIMER), Chandigarh, India.
                [15 ]Duke NUS Medical School, Singapore, Singapore.
                [16 ]Singapore Eye Research Institute, Singapore, Singapore.
                [17 ]National Institute for Health Research Biomedical Research Centre, Moorfields Eye Hospital, London, UK.
                [18 ]School of Pharmacy, Nantong University, Nantong, P. R. China.
                [19 ]Department of Mechanical Engineering, University College London, London, United Kingdom.
                Author notes
                ✉ Corresponding author: A/Prof (Dr) Rupesh Agrawal, Senior Consultant, National Healthcare Group Eye Institute, Tan Tock Seng Hospital, Singapore 308433, Email: Rupesh_agrawal@ 123456ttsh.com.sg .

                Competing Interests: The authors have declared that no competing interest exists.

                Article
                thnov13p2088
                10.7150/thno.81488
                10157737
                37153734
                99ed77b4-d8d3-42f3-a51b-ffaed586638f
                © The author(s)

                This is an open access article distributed under the terms of the Creative Commons Attribution License ( https://creativecommons.org/licenses/by/4.0/). See http://ivyspring.com/terms for full terms and conditions.

                History
                : 2 December 2022
                : 19 March 2023
                Categories
                Review

                Molecular medicine
                ocular tuberculosis,molecular diagnostic techniques,biomarkers,multi-omic,precision medicine

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