Elucidating Novel Serum Biomarkers Associated with Pulmonary Tuberculosis Treatment

Abstract

In an unbiased approach to biomarker discovery, we applied a highly multiplexed proteomic technology (SOMAscan, SomaLogic, Inc, Boulder, CO) to understand changes in proteins from paired serum samples at enrollment and after 8 weeks of TB treatment from 39 patients with pulmonary TB from Kampala, Uganda enrolled in the Center for Disease Control and Prevention’s Tuberculosis Trials Consortium (TBTC) Study 29. This work represents the first large-scale proteomic analysis employing modified DNA aptamers in a study of active tuberculosis (TB). We identified multiple proteins that exhibit significant expression differences during the intensive phase of TB therapy. There was enrichment for proteins in conserved networks of biological processes and function including antimicrobial defense, tissue healing and remodeling, acute phase response, pattern recognition, protease/anti-proteases, complement and coagulation cascade, apoptosis, immunity and inflammation pathways. Members of cytokine pathways such as interferon-gamma, while present, were not as highly represented as might have been predicted. The top proteins that changed between baseline and 8 weeks of therapy were TSP4, TIMP-2, SEPR, MRC-2, Antithrombin III, SAA, CRP, NPS-PLA2, LEAP-1, and LBP. The novel proteins elucidated in this work may provide new insights for understanding TB disease, its treatment and subsequent healing processes that occur in response to effective therapy.

Non-helical DNA Triplex Forms a Unique Aptamer Scaffold for High Affinity Recognition of Nerve Growth Factor

“…Such chemically modified aptamers are particularly well-suited to selection schemes that favor long-lived complexes; hence, we refer to this class of aptamers as SOMAmers (slow off-rate modified aptamers). SOMAmers have transformed the landscape of proteomics, leading to a sensitive and highly multiplexed platform with applications in biomarker discovery and early-stage disease detection (De Groote et al, 2013;Gold et al, 2010Gold et al, , 2012Loffredo et al, 2013;Lollo et al, 2014;Mehan et al, 2012Mehan et al, , 2013Ostroff et al, 2010Ostroff et al, , 2012, as well as sandwich-based single analyte detection assays (Ochsner et al, , 2014, rapid histochemistry tools (Gupta et al, 2011), and therapeutic applications (Gelinas et al, 2014;Gupta et al, 2014).…”

Serum biomarkers of treatment response within a randomized clinical trial for pulmonary tuberculosis

“…BD Vacutainer® SST™ Tubes were centrifuged within 2 hours of collection and processed according to manufacturer recommendations. All sites conducted collection, processing and storage of sera according to a standardized manual of operating procedures that has been confirmed to provide quality samples free of processing errors[33]. Serum was aliquoted (minimum of 500ul volume) into 1.2 ml cryovials on site in Kampala, Uganda, then frozen at -70°C.…”

Latent tuberculosis infection – Revisiting and revising concepts

“…We have shown [150] that IL-10 and TGF-b in supernatants of Mtb-stimulated PBMC are found at higher levels in TB patients when compared to healthy subjects with LTBI. Other promising approaches include proteomics [151], metabolomics [152], and serodiagnosis [153].…”