Genome-wide microRNAs analysis of peripheral blood mononuclear cells reveals elevated miR-142-3p expression as a potential biomarker for secondary syphilis
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ABSTRACT:
ORGANISM(S): synthetic construct Homo sapiens
PROVIDER: GSE156421 | GEO | 2020/08/19
REPOSITORIES: GEO
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Project description:Treponema pallidum (Tp) infection evokes vigorous immune responses, resulting in tissue damage. The immune mechanism after Treponema pallidum infection is still not clear. MicroRNAs (miRNAs) have been shown, however, to influence immune cell function and consequently the generation of antibody responses during other microbe infections, but these values are unknown for Tp. In this study, we performed a comprehensive analysis of differentially expressed miRNAs in healthy persons, untreated patients with syphilis, patients in the serofast state, and serologically cured patients. MiRNAs were profiled from patient peripheral blood obtained at the time of serological diagnosis. There were 89 differentially regulated miRNA identified in total. Then both the target sequence analysis on these different miRNAs and pathway analysis were performed to identify important immune and cell signaling pathways. Following RT-qPCR confirmation, three miRNAs (hsa-miR-195-5p, hsa-miR-223-3p, hsa-miR-589-3p) showed significant difference among serofast state, and serological cure (P<0.05). Two miRNAs (hsa-miR-195-5p, hsa-miR-1204) showed significant differences among untreated patients and healthy individuals. This is the first study of miRNA expression difference in PBMC in different stages of T. pallium infection. Our study suggests that the combination of three miRNAs has great potential to serve as non-invasive biomarkers of Treponema pallidum infections, which will facilitate better diagnosis and treat of T. pallium infections.
2019-12-28 | GSE142676 | GEO
Project description:Proteome-wide analysis of the syphilis spirochete, Treponema pallidum ssp. pallidum (Nichols strain). Treponemes were in vitro-cultured.
2023-12-07 | MSV000093603 | MassIVE
Project description:Proteome-wide analysis of the syphilis spirochete, Treponema pallidum ssp. pallidum (Nichols strain). Treponemes were cultured in, and isolated from, New Zealand white rabbits.
2023-05-24 | MSV000092028 | MassIVE
Project description:Treponema pallidum ssp. pallidum, the causative agent of syphilis, can now be cultured continuously in vitro utilizing a tissue culture system, and the multiplication rates are similar to those obtained in experimental infection of rabbits. In this study, the RNA transcript profiles of the T. pallidum Nichols during in vitro culture and rabbit infection were compared to examine whether gene expression patterns differed in these two environments. To this end, RNA preparations were converted to cDNA and subjected to RNA-seq using high throughput Illumina sequencing; reverse transcriptase quantitative PCR was also performed on selected genes for validation of results. The transcript profiles in the in vivo and in vitro environments were remarkably similar, exhibiting a high degree of concordance overall. However, transcript levels of 94 genes (9%) out of the 1,063 predicted genes in the T. pallidum genome were significantly different during rabbit infection versus in vitro culture, varying by up to 8-fold in the two environments. Genes that exhibited significantly higher transcript levels during rabbit infection included those encoding multiple ribosomal proteins, several prominent membrane proteins, glycolysis-associated enzymes, replication initiator DnaA, rubredoxin, thioredoxin, two putative regulatory proteins, and proteins associated with solute transport. In vitro cultured T. pallidum had higher transcript levels of DNA repair proteins, cofactor synthesis enzymes, and several hypothetical proteins. The overall concordance of the transcript profiles may indicate that these environments are highly similar in terms of their effects on T. pallidum physiology and growth, and may also reflect a relatively low level of transcriptional regulation in this reduced genome organism.
2021-10-12 | GSE185709 | GEO
Project description:Background A molecular diagnostic test that could directly evaluate Treponema pallidum subspecies pallidum antigens in urine would greatly facilitate the prompt diagnosis of syphilis. Methods A multi-platform high resolution shotgun proteomics approach was used to investigate the presence of T. pallidum proteins in male urine samples collected from individuals with and without syphilis. Study participants were included in an observational cohort study conducted at the Institute of Tropical Medicine, Antwerp, Belgium from 2014 to 2017. In total, N = 60 individuals were included in this sub-study, including n = 36 with early symptomatic stage (primary/secondary), n = 13 early latent and n = 5 late latent stage and n = 6 controls. Almost all participants were HIV-positive (56/60; 93 %) and identified as men who have sex with men (MSM) (59/60; 98 %). Sixteen (27 %) individuals were serum PCR positive for T. pallidum at the time of diagnosis. Ten pools containing urine from six participants (±1.5 mL per individual) were created based on clinical staging. Urine protein was extracted from the pools by a two-step molecular weight cut-off centrifugal filtration to remove large proteins and non-protein material. Samples were digested, subjected to multi-dimensional liquid chromatographic separation based on hydrophobicity and were analysed with matrix-assisted laser desorption/ionization time of flight (MALDI-TOF) and/or liquid chromatography- electrospray ionization quadruple ion mobility time-of-flight high-definition mass spectrometry (LC/ESI-Q-IM-TOF) in data dependent (MALDI-TOF/TOF) and data independent HDMSE (ESI-IM-Q-TOF) acquisition modes. Results In total, 26 peptides corresponding to four unique T. pallidum proteins were uncovered in four different pooled urine samples, from n = 3 symptomatic (primary/secondary stage; PSS) and n = 1 latent stage pool. Peptides from GTPase Obg (Tp0742) were detected in two separate PSS pooled samples. Protein designations are listed as in the currently annotated T. pallidum proteome available at the UniProt database (Proteome ID: UP000014259) which is related to the genome assembly and annotation ID GCA_000410535.2 listed on the European Nucleotide Archive. Eleven peptides from an uncharacterized protein (Tp0369) and 8 peptides from a protein annotated as the Borrelia-like p83/100 protein (Tp0486) were detected in two different PSS pooled samples. A protein annotated as an ABC superfamily transport protein (Tp0804) was uncovered in a latent stage pooled sample. BLAST analyses revealed low peptide sequence similarity with other pathogenic and commensal prokaryotes and human proteins. Conclusions High resolution mass spectrometric analyses of protein extracts from pooled urine samples resulted in the detection of four T. pallidum proteins. This is the first successful account of applying proteomics approaches to detect treponemal antigens in clinical samples. These proteins could represent potential biomarkers for downstream diagnostic applications.
2018-10-18 | PXD009707 | Pride
Project description:In this project, we investigated whether diverse spirochete species contain lysinoalanine cross-linkages between conserved residues in their flagellar hook proteins (FlgE). We examined the following species: Treponema denticola¸ Borreliella burgdorferi, Treponema phagedenis, Treponema pallidum, Brachyspira hyodysenteriae, Leptospira interrogans. For each bacterial species, we examined a variety of different sample types, including recombinantly produced FlgE, polyhooks purified from flik knock-out strains, and wild-type periplasmic filaments. Overall, our data suggests that lysinoalanine crosslinking in a conserved FlgE post-translational modification in spirochetes and is required for the unique motility of these organisms. For more information, please see the following manuscript: https://doi.org/10.1101/2023.06.13.544825.
2024-01-26 | PXD045997 | Pride
Project description:Purpose, aims and objectives: Bovine digital dermatitis (BDD) is a painful and ulcerative, inflammatory, infectious disease of digital skin in dairy and beef cattle and is one of the most economically important causes of severe cattle lameness worldwide. A polytreponemal aetiology has been consistently implicated in BDD pathogenesis with three key phylogroups implicated globally: Treponema medium, Treponema phagedenis and Treponema pedis. This study aimed to investigate the hypothesis that the three Treponema phylogroups implement distict mechanisms of pathogenesis within cells of the bovine foot skin tissue during infection. Using a next generation RNA sequencing (RNA-Seq) approach, the dysregulation of global mRNA expression was investigated in primary bovine foot skin fibroblasts following challenge with representative strains of the three predominant BDD Treponema phylogroups (T19, T320A and T3552B respectively). Transcriptome profiles were compared to that of a commensal treponeme, Treponema ruminis strain Ru1, in attempts to identify pathogenic signatures. Results and conclusions: Here, for the first time, we implicate fibroblasts as a likely source of interleukin-8 dysregulation in BDD lesions. Despite treponemes reportedly having atypical LPS, a strong pro-inflammatory response was elicited by the BDD treponemes in a similar manner to the Gram-negative LPS control, which appeared to be mediated through interleukin-17 signalling. Along with interleukin-17, several interesting gene targets were identified which may help to inform and drive future vaccine development and therapeutic approaches; particularly those of RGS16, GRO1, MAFF and ZC3H12A, which were only stimulated by BDD treponemes. Interestingly, the three BDD treponemes were found to elicit very distinct mechanisms of pathogenesis in fibroblasts. T. phagedenis and T. pedis spirochaetes were found to upregulate several genes associated with apoptosis. Both T. medium and T. pedis spirochaetes, but notably not T. phagedenis, stimulated genes associated with actin rearrangement and a loss of cell adhesion, which may promote their persistence and deeper invasion within host tissues. The upregulation of antimicrobial peptide precursor, DEFB123, by T. phagedenis spirochaetes may present a microbial ecological advantage to all treponemes within BDD infected tissue, explaining their dominance within lesions. Interestingly, T. medium phylogroup was the least stimulatory and appeared to induce immunosuppression via the dysregulation of genes such as TSC22D3. Together with findings that the commensal, T. ruminis, significantly dysregulated over three times the number of host genes compared to each BDD treponeme; this suggests that, alike the syphilis pathogen (Treponema pallidum), BDD treponemes have evolved to become “stealth pathogens” and avoid triggering a substantial host immune/inflammatory response to promote persistence and facilitate invasion of host tissues. Overall, this study has highlighted the complexities of BDD pathogenesis; three key Treponema phylogroups appear to elicit very distinct mechanisms of pathogenesis in bovine foot skin cells. Several interesting gene targets have been identified from this study which may help to inform and drive future vaccine development and therapeutic approaches.
2019-09-26 | GSE138011 | GEO
Project description:Phagocytosis requires the activation of a plethora of mechanisms that include the activation of the actin cytoskeleton guided by the Arp2/3 complex. These are promoted by activators such as the Wiskott Aldrich Syndrome Protein (WASP) family members. In order to further understand the molecular mechanisms involved in the early events leading the phagocytosis of the pathogenic Mycobacterium tuberculosis, we set out to examine potential roles of miRNAs in phagocytosis using genome-wide expression profiling to identify miRNAs differentially regulated following mycobacterial infection. One of the miRNAs activated upon infection of mouse macrophages with the non-pathogenic Mycobacterium smegmatis, the widely conserved miR-142-3p, was predicted and confirmed to target the Neural-WASP (N-WASP). Upregulating of miR-142-3p in mouse macrophages inversely correlated with levels of N-WASP, upon infection with live pathogenic and non-pathogenic mycobacteria, suggesting an active role of Mycobacterium tuberculosis on the regulation of phagocytosis, at the post-transcriptional level, in host cells. The reduction of N-WASP correlated with a reduced internalization of bacteria per macrophage, independently of the phagocytosis index. Furthermore, the downregulation of WASP levels accompanied those of N-WASP, at early but not at late time points, suggesting a closely regulatory mechanism among both family members, dependent on the time frame of the phagocytosis. Additionally, upregulating of miR-142-3p promoted the change in the protein levels of another predicted and confirmed target, the Cofilin2 protein, in a phagocytosis-independent fashion. Downregulation experiments promoted aberrant morphologic phenotypes in macrophages, similar to observed by others in PBMCs of humans with Wiskott Aldrich Syndrome, suggesting the strong involvement of miR-142-3p on the regulation of the actin machinery in macrophages. Altogether these results show for the first time that miRNAs are involved in the regulation of actin-mediated phagocytosis of pathogenic bacteria and that these are direct targets of Mycobacterium tuberculosis. Expression analysis of mouse macrophage cell line J774A.1 in response to infection with Mycobacterium smegmatis mc2155 EGFP. Three biological replicates each for uninfected and infected samples.
2013-06-16 | E-GEOD-23429 | biostudies-arrayexpress