Serum siderocalin levels in patients with tuberculosis and HIV infection

From simple to complex: Protein-based biomarker discovery in tuberculosis

Tuberculosis (TB) is a deadly infectious disease that affects millions of people globally. TB proteomics signature discovery has been a rapidly growing area of research that aims to identify protein biomarkers for the early detection, diagnosis, and treatment monitoring of TB. In this review, we have highlighted recent advances in this field and how it is moving from the study of single proteins to high-throughput profiling and from only using proteomics to include additional types of data in multi-omics studies. We have further covered the different sample types and experimental technologies used in TB proteomics signature discovery, focusing on studies of HIV-negative adults. The published signatures were defined as either coming from hypothesis-based protein targeting or from unbiased discovery approaches. The methodological approaches influenced the type of proteins identified and were associated with the circulating protein abundance. However, both approaches largely identified proteins involved in similar biological pathways, including acute-phase responses and T-helper type 1 and type 17 responses. By analysing the frequency of proteins in the different signatures, we could also highlight potential robust biomarker candidates. Finally, we discuss the potential value of integration of multi-omics data and the importance of control cohorts and signature validation.

Expression and Analyses of CXCL9/10/11 and CXCR3 in Ulcerative Cutaneous Tuberculosis

We explored the biological functions, signaling pathways, potential inflammation, and immune biomarkers involved in ulcerative cutaneous tuberculosis (UCT). Mycobacterium tuberculosis-infected tissues from UCT patients and patients with noncutaneous tuberculous ulcers (NCTUs) were studied using transcriptomic analysis. Functional enrichment determined using the Gene Ontology database and enrichment of signaling pathways was ascertained using the Kyoto Encyclopedia of Genes and Genomes database. Protein-protein interaction (PPI) networks were analyzed to determine the hub genes. A total of 4,396 differentially expressed genes (DEGs) were identified. DEGs were enriched in CXCR3 chemokine receptor binding, chemokine activity, and cytokine-cytokine receptor interaction and other aspects. Analyses of PPI networks identified 15 hub genes. Expression of chemokine (C-X-C motif) ligand 9 (CXCL9)/10/11 messenger RNA (mRNA) and C-X-C motif chemokine receptor 3 (CXCR3) mRNA in the lesions of patients with UCT increased compared with that in NCTU cases. Expression of CXCL9 mRNA and CXCL10 mRNA in plasma also increased, which was consistent with other test results. We discovered a novel plasma CXC chemokine signature that could be used to differentiate UCT from NCTU. Our study (1) provides a reference for UCT diagnosis and selection of diagnostic markers and (2) lays the foundation for further elucidation of UCT pathogenesis.

rpoB gene mutations in rifampin-resistant Mycobacterium tuberculosis isolates from rural areas of Zhejiang, China

Objective

The aim was to analyze genetic mutations in the rpoB gene of rifampin-resistant Mycobacterium tuberculosis isolates (RIF^R-MTB) from Zhejiang, China.

Methods

We prospectively analyzed RIF^R-associated mutations in 13 rural areas of Zhejiang. Isolates were subjected to species identification, phenotype drug susceptibility testing (DST), DNA extraction, and rpoB gene sequencing.

Results

A total of 103 RIF^R isolates were identified by DST (22 RIF^R only, 14 poly-drug resistant, 49 multidrug resistant, 13 pre-extensively drug resistant [pre-XDR], and 5 extensively drug resistant [XDR]) from 2152 culture-positive sputum specimens. Gene sequencing of rpoB showed that the most frequent mutation was S450L (37.86%, 39/103); mutations P280L, E521K, and D595Y were outside the rifampicin resistance-determining region (RRDR) but may be associated with RIF^R. Mutations associated with poly-drug resistant, pre-XDR, and XDR TB were mainly located at codon 445 or 450 in the RRDR.

Conclusions

The frequency of rpoB RRDR mutation in Zhejiang is high. Further studies are needed to clarify the relationships between RIF^R and the TTC insertion at codon 433 in the RRDR and the P280L and D595Y mutations outside the RRDR.

Scavenging Bacterial Siderophores with Engineered Lipocalin Proteins as an Alternative Antimicrobial Strategy

Iron acquisition mediated by siderophores, high-affinity chelators for which bacteria have evolved specific synthesis and uptake mechanisms, plays a crucial role in microbiology and in host-pathogen interactions. In the ongoing fight against bacterial infections, this area has attracted biomedical interest. Beyond several approaches to interfere with siderophore-mediated iron uptake from medicinal and immunochemistry, the development of high-affinity protein scavengers that tightly complex the siderophores produced by pathogenic bacteria has appeared as a novel strategy. Such binding proteins have been engineered based on siderocalin-also known as lipocalin 2-an endogenous human scavenger of enterobactin and bacillibactin that controls the systemic spreading of commensal bacteria such as Escherichia coli. By using combinatorial protein design, siderocalin was reshaped to bind several siderophores from Pseudomonas aeruginosa and, in particular, petrobactin from Bacillus anthracis, none of which is recognized by the natural protein. Such engineered versions of siderocalin effectively suppress the growth of corresponding pathogenic bacteria by depriving them of their iron supply and offer the potential to complement antibiotic therapy in situations of acute or persistent infection.