Aptamer-based Proteomic Signature of Intensive Phase Treatment Response in Pulmonary Tuberculosis
New drug regimens of greater efficacy and shorter duration are needed for tuberculosis (TB) treatment. The identification of accurate, quantitative, non-culture based markers of treatment response would improve the efficiency of Phase 2 TB drug testing.
In an unbiased biomarker discovery approach, we applied a highly multiplexed, aptamer-based, proteomic technology to analyze serum samples collected at baseline and after 8 weeks of treatment from 39 patients with pulmonary TB from Kampala, Uganda enrolled in a Centers for Disease Control and Prevention (CDC) TB Trials Consortium Phase 2B treatment trial.
We identified protein expression differences associated with 8-week culture status, including Coagulation Factor V, SAA, XPNPEP1, PSME1, IL-11 Rα, HSP70, Galectin-8, α2-Antiplasmin, ECM1, YES, IGFBP-1, CATZ, BGN, LYNB, and IL-7. Markers noted to have differential changes between responders and slow-responders included nectin-like protein 2, EphA1 (Ephrin type-A receptor 1), gp130, CNDP1, TGF-b RIII, MRC2, ADAM9, and CDON. A logistic regression model combining markers associated with 8-week culture status revealed an ROC curve with AUC=0.96, sensitivity=0.95 and specificity=0.90. Additional markers showed differential changes between responders and slow-responders (nectin-like protein), or correlated with time-to-culture-conversion (KLRK1).
Serum proteins involved in the coagulation cascade, neutrophil activity, immunity, inflammation, and tissue remodeling were found to be associated with TB treatment response. A quantitative, non-culture based, five-marker signature predictive of 8-week culture status was identified in this pilot study.
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ABSTRACT: Tuberculosis differs from most other bacterial infectious diseases by a very long duration of combination antibiotic therapy required to achieve relapse-free cure. While the standard recommended "short-course" treatment length for tuberculosis is 6 months, the World Health Organization recommends duration of 20 months for the treatment of patients with multidrug-resistant (MDR) and extensively drug-resistant tuberculosis (XDR-TB). Apart from the long duration of antituberculosis therapy, treatment of M/XDR-TB is very expensive and often associated with adverse drug events. The optimal duration for treatment of tuberculosis likely differs between individuals and depends on a variety of variables, such as the extent of the disease, the immune status of the host and the virulence and the drug-resistance of the causative strain of M. tuberculosis. Some patients with M/XDR-TB may have to be treated with currently available anti-tuberculosis drug regimens for more than 20 months while much shorter treatment durations may be possible to achieve cure for the majority of patients with M/XDR-TB. Personalization of the duration of treatment for tuberculosis, especially for patients with M/XDR-TB, would be highly desired. In recent years much progress has been made in the identification of bio-signatures that could eventually lead to individual recommendations for the duration of antituberculosis therapy for tuberculosis patients. This pulmonary perspective reviews the knowledge on clinical and radiological scores, host- and pathogen disease-related profiles, molecules and signatures that are currently explored as biomarkers to personalize the duration of therapy in tuberculosis.American Journal of Respiratory and Critical Care Medicine 06/2014; DOI:10.1164/rccm.201402-0363PP · 13.00 Impact Factor
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ABSTRACT: Limited chemical diversity of nucleic acid libraries has long been suspected to be a major constraining factor in the overall success of SELEX (Systematic Evolution of Ligands by EXponential enrichment). Despite this constraint, SELEX has enjoyed considerable success over the past quarter of a century as a result of the enormous size of starting libraries and conformational richness of nucleic acids. With judicious introduction of functional groups absent in natural nucleic acids, the "diversity gap" between nucleic acid-based ligands and protein-based ligands can be substantially bridged, to generate a new class of ligands that represent the best of both worlds. We have explored the effect of various functional groups at the 5-position of uracil and found that hydrophobic aromatic side chains have the most profound influence on the success rate of SELEX and allow the identification of ligands with very low dissociation rate constants (named Slow Off-rate Modified Aptamers or SOMAmers). Such modified nucleotides create unique intramolecular motifs and make direct contacts with proteins. Importantly, SOMAmers engage their protein targets with surfaces that have significantly more hydrophobic character compared with conventional aptamers, thereby increasing the range of epitopes that are available for binding. These improvements have enabled us to build a collection of SOMAmers to over 3,000 human proteins encompassing major families such as growth factors, cytokines, enzymes, hormones, and receptors, with additional SOMAmers aimed at pathogen and rodent proteins. Such a large and growing collection of exquisite affinity reagents expands the scope of possible applications in diagnostics and therapeutics.Molecular Therapy - Nucleic Acids 10/2014; 3(10):e201. DOI:10.1038/mtna.2014.49 · 4.51 Impact Factor
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ABSTRACT: Aptamers have been increasingly applied in biomedical field as a class of biorecognition elements that possess many advantages such as high specificity and binding affinity, easy synthesis, easy modification, small size, non-toxicity and good stability. Many diseases like cancer exhibit cellular aberrations at morphological and molecular levels. Medical diagnosis based on molecular features can be highly specific and extremely sensitive when proper recognition molecule and an efficient signal transduction system are employed. However, bioanalysis of human diseases at the molecular level is an extremely challenging field because effective probes to identify and recognize biomarkers of diseases are not readily available. Traditional bio-recognition molecule, antibody has been exploited to develop excellent diagnosis assays in many formats, but antibodies are insufficient to match the requirements of fast and portable biosensors for point-of-care applications, which are at high demand in pathogenic bacteria detection as well as other diseases like cancer. Aptamers are short single-stranded oligonucleotides, which can be selected from random combinatorial library by SELEX in vitro. This relatively new biorecognition agent has superior intrinsic characteristics for biosensor development. In this review, we first present major aptamer selection technologies and the main formats of biosensors, which were frequently employed in aptasensor development. Then, the current state of aptamers as applied to medical diagnosis was discussed for specifically cancer and pathogen diagnosis. Finally, an overview of aptamer-nanomaterials conjugates was presented in many applications such as diagnosis, bioimaging, and theranostics.Current topics in medicinal chemistry 04/2015; 15(12). DOI:10.2174/1568026615666150413154233 · 3.40 Impact Factor