Integrated single-cell transcriptome and T cell receptor profiling reveals defects of T cell exhaustion in pulmonary tuberculosis.

Tuberculosis-affected lungs with chronic inflammation harbor abundant immunosuppressive immune cells but the nature of such inflammation is unclear. Dysfunction in T cell exhaustion, while implicated in chronic inflammatory diseases, remains unexplored in tuberculosis. Given that immunotherapy targeting exhaustion checkpoints exacerbates tuberculosis, we speculate that T cell exhaustion is dysfunctional in tuberculosis. Using integrated single-cell RNA sequencing and T cell receptor profiling we reported defects in exhaustion responses within inflamed tuberculosis-affected lungs. Tuberculosis lungs demonstrated significantly reduced levels of exhausted CD8+ T cells and exhibited diminished expression of exhaustion-related transcripts among clonally expanded CD4+ and CD8+ T cells. Additionally, clonal expansion of CD4+ and CD8+ T cells bearing T cell receptors specific for CMV was observed. Expanded CD8+ T cells expressed the cytolytic marker GZMK. Hence, inflamed tuberculosis-affected lungs displayed dysfunction in T cell exhaustion. Our findings likely hold implications for understanding the reactivation of tuberculosis observed in patients undergoing immunotherapy targeting the exhaustion checkpoint.

Corneal subbasal nerve plexus reinnervation and stromal cell morphology with different cap thicknesses in small incision lenticule extraction.

PURPOSE: The corneal cap thickness is a vital parameter designed in small incision lenticule extraction (SMILE). The purpose was to investigate the changes in corneal subbasal nerve plexus (SNP) and stromal cells with different cap thicknesses and evaluate the optimized design for the surgery. METHODS: In this prospective, comparative, non-randomized study, a total of 108 eyes of 54 patients who underwent SMILE were allocated into three groups with different corneal cap thicknesses (110 µm, 120 µm or 130 µm group). The SNP and stromal cell morphological changes obtained from in vivo corneal confocal microscopy (IVCCM) along with their refractive outcomes were collected at 1 week, 1 month, 3 months and 6 months postoperatively. One-way analysis of variance (ANOVA) was used to compare the parameters among the three groups. RESULTS: The SNPs in the three groups all decreased after surgery and revealed a gradual increasing trend during the 6-month follow-up. The values of the quantitative nerve metrics were significantly lower in the 110 µm group than in the 120 µm and 130 µm groups, especially at 1 week postoperatively. No difference was detected between the 120 µm and 130 µm groups at any time point. Both Langerhans cells and keratocytes were activated after surgery, and the activation was alleviated during the follow-up. CONCLUSIONS: The SMILE surgeries with 110 µm, 120 µm or 130 µm cap thickness design achieved good efficacy, safety, accuracy and stability for moderate to high myopic correction while the thicker corneal cap was more beneficial for corneal nerve regeneration.

The consensus guideline of perioperative antiviral therapy for AIDS patients in China based on clinical practice.

The prevalence of human immunodeficiency virus (HIV) and acquired immune deficiency syndrome (AIDS) has emerged as a major public health concern in China. When patients with HIV infection undergo surgical treatment, there are two main challenges. Firstly, medical staff face a high risk of HIV infection due to occupational exposure. Secondly, the patient's immune function is impaired, increasing the risk of opportunistic infections and postoperative complications. The surgical treatment of such patients is unique, and the risk of occupational exposure during the operation primarily depends upon the viral load of HIV/AIDS patients. Therefore, perioperative antiretroviral therapy is of paramount importance in order to standardize the perioperative antiretroviral therapy (ART) for HIV/AIDS patients. The Surgery Group of the Chinese Association of STD and AIDS Prevention and Control, in collaboration with the Treatment Association, and Surgery Group of the Chinese Medical Association of Tropical Diseases and Parasitology, has developed an expert consensus on perioperative antiretroviral therapy for HIV/AIDS patients. This consensus encompasses various aspects, including surgical risk assessment, selection of perioperative antiretroviral therapy regimens, prevention of opportunistic infections, and the crucial focus on rapid preoperative viral load reduction and immune function reconstruction for HIV/AIDS patients.

Corneal metabolic biomarkers for moderate and high myopia in human.

This study aimed to identify the corneal metabolic biomarkers for moderate and high myopia in human. We enrolled 221 eyes from 221 subjects with myopia to perform the femtosecond laser small incision lenticule extraction (SMILE) surgery. Among these, 71 eyes of 71 subjects were enrolled in the low myopic group, 75 eyes of 75 subjects in the moderate myopic group and 75 eyes of 75 subjects in the high myopic group. The untargeted metabolomics analysis was performed to analyze the corneal tissues extracted during the SMILE surgery using an ultra-high-performance liquid chromatography (UHPLC) coupled to a quadrupole time-of-flight (Q-TOF) mass spectrometry (MS). The one-way analysis of variance (ANOVA) was used to identify the different metabolites among the three myopic groups, the orthogonal partial least-squares discriminant analysis (OPLS-DA) model was used to reveal the different metabolites between moderate myopia and low myopia, and between high myopia and low myopia. The Venn gram was used to find the overlapped metabolites of the three datasets of the different metabolites. The stepwise multiple linear regression analysis was used to determine the metabolic molecules associated with manifest refractive spherical equivalents (MRSE). The Receiver Operating Characteristics (ROC) analysis was performed to reveal the corneal biomarkers for moderate and high myopia. The hub biomarker was further selected by the networks among different metabolites created by the Cytoscape software. A total of 1594 metabolites were identified in myopic corneas. 321 metabolites were different among the three myopic groups, 106 metabolites were different between high myopic corneas and low myopic corneas, 104 metabolites were different between moderate myopic corneas and low myopic corneas, and 30 metabolic molecules overlapped among the three datasets. The multivariate linear regression analysis revealed the myopic degree was significantly influenced by the corneal levels of azelaic acid, arginine-proline (Arg-Pro), 1-stearoyl-2-myristoyl-sn-glycero-3-phosphocholine, and hypoxanthine. The ROC curve analysis showed that azelaic acid, Arg-Pro and hypoxanthine were effective in discriminating low myopia from moderate to high myopia with the area under the curve (AUC) values as 0.982, 0.991 and 0.982 for azelaic acid, Arg-Pro and hypoxanthine respectively. The network analysis suggested that Arg-Pro had the maximum connections among these three biomarkers. Thus, this study identified azelaic acid, Arg-Pro and hypoxanthine as corneal biomarkers to discriminate low myopia from moderate to high myopia, with Arg-Pro serving as the hub biomarker for moderate and high myopia.

Effect of 3% Diquafosol Sodium on Dry Eye After Femtosecond Laser-Assisted In Situ Keratomileusis and Small Incision Lenticule Extraction Surgery in High-Myopic Eyes.

PURPOSE: To evaluate the effect of 3% diquafosol sodium eye drop on dry eye after femtosecond laser-assisted in situ keratomileusis (FS-LASIK) and small incision lenticule extraction (SMILE) in high-myopic eyes. METHODS: Eighty-one cases with high myopia (162 eyes) who received FS-LASIK or SMILE were divided into four groups by surgical design and tear film stability: D-FS-LASIK (5s

Single-cell RNA-sequencing reveals heterogeneity and intercellular crosstalk in human tuberculosis lung.

Lung inflammation indicated by 18F-labeled fluorodeoxyglucose (FDG) in patients with tuberculosis is associated with disease severity and relapse risk upon treatment completion. We revealed the heterogeneity and intercellular crosstalk in lung tissues with 18F-FDG avidity and adjacent uninvolved tissues from 6 tuberculosis patients by single-cell RNA-sequencing. Tuberculous lungs had an influx of regulatory T cells (Treg), exhausted CD8 T cells, immunosuppressive myeloid cells, conventional DC, plasmacytoid DC, and neutrophils. Immune cells in inflamed lungs showed general up-regulation of ATP synthesis and interferon-mediated signaling. Immunosuppressive myeloid and Treg cells strongly displayed transcriptions of genes related to tuberculosis disease progression. Intensive crosstalk between IL4I1-expressing myeloid cells and Treg cells involving chemokines, costimulatory molecules, and immune checkpoints, some of which are specific in 18F-FDG-avid lungs, were found. Our analysis provides insights into the transcriptomic heterogeneity and cellular crosstalk in pulmonary tuberculosis and guides unveiling cellular and molecular targets for tuberculosis therapy.

Comparison of total corneal power measurements obtained with different devices after myopic keratorefractive surgery.

AIM: To analyze the differences, agreements, and correlation among total corneal power parameters generated by different instruments after myopic keratorefractive surgery. METHODS: The prospective cross-sectional study included patients who underwent myopic keratorefractive surgery and received measurements of corneal power 3mo after surgery. Automated keratometer was used for the measurement of simulated keratometry (SimK), swept-source optical coherence tomography (SS-OCT) based biometer for total keratometry (TK), anterior segment-OCT for real keratometry (RK), and Scheimpflug keratometer for the true net power (TNP), the total corneal refractive power (TCRP) and equivalent K-readings (EKR). The differences among these parameters were analyzed, and the agreements and correlation between SimK and other total corneal power parameters were investigated. RESULTS: A total of 70 eyes of 70 patients after myopic keratorefractive surgery were included. The evaluated corneal power parameters were as follows: SimK 38.32±1.93 D, TK 37.54±2.12 D, RK 36.64±2.09 D, TNP 36.56±1.97 D, TCRP 36.70±2.01 D, and EKR 37.55±2.00 D. Pairwise comparison showed that there were significant differences (P<0.001) among all parameters except for between TK and EKR, RK and TNP, RK and TCRP (P=1.000, 1.000, 1.000, respectively). The limits of agreement between SimK and TK, RK, TNP, TCPR, and EKR were 1.08, 1.08, 1.43, 1.48, and 1.73 D, respectively. All parameters showed good correlation with SimK, and the correlation coefficients were 0.995, 0.994, 0.983, 0.982, and 0.975. CONCLUSION: Among the corneal power parameters after myopic keratorefractive surgery, the value of SimK is the largest, followed by TK and EKR, with TCRP, RK, and TNP being the smallest. The differences among the parameters may be attributable to the different calculation principles. Correct understanding and evaluation of corneal power parameters can provide a theoretical basis for taking advantage of the total corneal power to improve the accuracy of intraocular lens calculation after keratorefractive surgery.

Evaluation of the IP-10 mRNA release assay for diagnosis of TB in HIV-infected individuals.

HIV-infected individuals are susceptible to Mycobacterium tuberculosis (M.tb) infection and are at high risk of developing active tuberculosis (TB). Interferon-gamma release assays (IGRAs) are auxiliary tools in the diagnosis of TB. However, the performance of IGRAs in HIV-infected individuals is suboptimal, which limits clinical application. Interferon-inducible protein 10 (IP-10) is an alternative biomarker for identifying M.tb infection due to its high expression after stimulation with M.tb antigens. However, whether IP-10 mRNA constitutes a target for the diagnosis of TB in HIV-infected individuals is unknown. Thus, we prospectively enrolled HIV-infected patients with suspected active TB from five hospitals between May 2021 and May 2022, and performed the IGRA test (QFT-GIT) alongside the IP-10 mRNA release assay on peripheral blood. Of the 216 participants, 152 TB patients and 48 non-TB patients with a conclusive diagnosis were included in the final analysis. The number of indeterminate results of IP-10 mRNA release assay (13/200, 6.5%) was significantly lower than that of the QFT-GIT test (42/200, 21.0%) (P = 0.000026). IP-10 mRNA release assay had a sensitivity of 65.3% (95%CI 55.9% - 73.8%) and a specificity of 74.2% (95%CI 55.4% - 88.1%), respectively; while the QFT-GIT test had a sensitivity of 43.2% (95%CI 34.1% - 52.7%) and a specificity of 87.1% (95%CI 70.2% - 96.4%), respectively. The sensitivity of the IP-10 mRNA release assay was significantly higher than that of QFT-GIT test (P = 0.00062), while no significant difference was detected between the specificities of these two tests (P = 0.198). The IP-10 mRNA release assay showed a lower dependence on CD4+ T cells than that of QFT-GIT test. This was evidenced by the fact that the QFT-GIT test had a higher number of indeterminate results and a lower sensitivity when the CD4+ T cells counts were decreased (P < 0.05), while no significant difference in the number of indeterminate results and sensitivity were observed for the IP-10 mRNA release assay among HIV-infected individuals with varied CD4+T cells counts (P > 0.05). Therefore, our study suggested that M.tb specific IP-10 mRNA is a better biomarker for diagnosis of TB in HIV-infected individuals.

Effects of riboflavin/ultraviolet-A scleral collagen cross-linking on regional scleral thickness and expression of MMP-2 and MT1-MMP in myopic guinea pigs.

OBJECTIVE: To investigate the effects of scleral collagen cross-linking (SXL) using riboflavin and ultraviolet A (UVA) light on the scleral thickness of different regions and expression of matrix metalloproteinase 2 (MMP-2) and membrane-type MMP-1 (MT1-MMP) in guinea pigs with lens-induced myopia. METHODS: Forty-eight 4-week-old guinea pigs were assigned to three groups (n = 16 per group): SXL group, lens-induced myopia (LIM) group, and control group. The sclera of the right eye of the guinea pig in the SXL group was surgically exposed, riboflavin was dropped on the treatment area for 10 minutes before the 30-minute UVA irradiation. The same surgical procedure was performed in the LIM group without UVA irradiation. The -10.00 D lenses were then placed on the right eyes of guinea pigs in the SXL and LIM groups for six weeks. The control group received no treatment. The left eyes were untreated in all groups. The ocular axial length (AXL) and refraction were measured at 4 weeks and 10 weeks of age. 10-week-old guinea pigs were sacrificed, and the right eyes were enucleated and evenly divided for preparation of hematoxylin and eosin (HE) stained sections, quantitative real-time polymerase chain reaction (qPCR) and western blotting. The scleral thickness of different regions was measured on HE stained sections. The temporal half of the sclera was harvested to measure the expression of MMP-2 and MT1-MMP by qPCR and western blotting. RESULTS: The AXL was significantly shorter, and the degree of myopic refraction was significantly lower in the SXL group than those in the LIM group at 10 weeks of age. The scleral thickness of the cross-linked area was significantly greater in the SXL group than that of the corresponding area in the LIM group, while the scleral thickness of the untreated nasal side was not significantly different between the SXL group and the LIM group. The expression of MMP-2 and MT1-MMP of the cross-linked sclera was significantly downregulated compared with that of the corresponding area in the LIM group. CONCLUSION: Riboflavin/UVA SXL could slow myopia progression and thicken the cross-linked sclera in guinea pigs, which might be related to the downregulation of MMP-2 and MT1-MMP expression during the scleral remodeling process.

Corneal biomechanical characteristics following small incision lenticule extraction for myopia and astigmatism with 3 different cap thicknesses.

BACKGROUND: The design of cap thickness for small incision lenticule extraction (SMILE) plays a role in post-laser vision correction (post-LVC) corneal biomechanics. This study aimed to compare the corneal biomechanical characteristics following SMILE with different cap thicknesses of 110 µm, 120 µm, and 130 µm for myopia and myopic astigmatism correction. METHODS: Seventy-five patients (146 eyes) who underwent SMILE with designed cap thickness of 110 µm, 120 µm, and 130 µm were recruited at the Eye Center of Beijing Tongren Hospital between August 2020 and November 2021. Visual acuity, refraction, and corneal biomechanical parameters were measured preoperatively, 1 week and 1, 3, 6 months postoperatively. One-way analysis of variances (ANOVA) with Bonferroni correction or Kruskal-Wallis test was performed to compare the parameters among different groups. Repeated-measures analysis of variance with Bonferroni correction or Friedman test was applied for comparing the parameters within different follow-up times. RESULTS: Uncorrected distance visual acuity of 110-µm group was better only at 1-week and 1-month postoperatively (P = 0.012, 0.037). There were no significant differences in spherical equivalent, nor in Corvis biomechanical index-laser vision correction (CBI-LVC). All the parameters reached stability at 3-month postoperatively. Integrated radius (IR) and deformation amplitude ratio 2 mm (DA ratio 2 mm) in 120-µm and 130-µm groups were higher than 110-µm group at 1-month postoperatively (P = 0.019, 0.002). So was Ambrósio relational thickness (ARTh) at 6-month postoperatively (P = 0.011). Stiffness parameter at applanation A1 (SP-A1), stress-strain index (SSI), biomechanically corrected intraocular pressure (bIOP) and central corneal thickness (CCT) were highest in 130-µm group, followed by 120-µm group, then 110-µm group at 3-month (P<0.001, P = 0.030, P = 0.027, P = 0.008) and 6-month (P<0.001, P = 0.002, P = 0.0023, P = 0.001) postoperatively. CONCLUSIONS: The corneal stiffness following SMILE was greatest with 130-µm cap, followed by 120-µm cap, then 110-µm cap. 130-µm cap might have advantages in terms of corneal biomechanics and retreatment option. The SMILE-designed protocol should be customized in practice.

Scleral Remolding-Related Gene Expression After Scleral Collagen Cross-Linking Using Ultraviolet A and Riboflavin in Myopic Guinea Pig Model.

PURPOSE: This study was conducted to evaluate scleral remolding-related gene expression after scleral collagen cross-linking (SCXL) using ultraviolet A (UVA) and riboflavin in lens-induced myopia (LIM) guinea pigs. METHODS: A total of 100 4-week-old pigmented guinea pigs were randomly divided into five groups (n = 20): SCXL + LIM, LIM, SCXL, Sham, and Control. Refraction, anterior chamber depth (ACD), lens thickness (LT), vitreous chamber depth (VCD), and axial length (AL) were measured using streak retinoscope and A-scan ultrasonography. SCXL was performed using 0.1% riboflavin solution and 365 nm UVA irradiation. Lens-induced myopia was achieved by wearing -10 D concave lenses. Quantitative real-time PCR (qPCR) and western blot were used to measure mRNA and protein levels, respectively. RESULTS: Myopia was successfully induced in the LIM group, while myopic refraction was higher and ACD and AL were shorter in SCXL + LIM compared with LIM, suppressing myopia progression. The scleral COL1A1 mRNA levels were significantly decreased and MMP2 and ACTA2 mRNA levels were significantly increased in LIM compared with other groups, while COL1A1 mRNA levels were increased and MMP2 and ACTA2 mRNA levels were decreased in SCXL + LIM compared with LIM. The scleral COL1A1 protein levels were significantly increased at 1 week and 4 weeks and MMP2 protein levels were significantly decreased at 1 week in SCXL compared with SCXL + LIM, LIM and Control. MMP2 protein levels were significantly decreased in SCXL + LIM and SCXL compared with LIM at 4 weeks. The differences in TGFB1, BMP2, CCN2, ITGA2, and ITGB1 mRNA levels and ACTA2 protein levels between the five groups were not significantly different. CONCLUSION: SCXL using UVA and riboflavin could influence the expression of scleral remolding-related genes, including COL1A1, MMP2, TIMP2, and ACTA2, and thus contribute to improving collagen synthesis and reducing collagen degradation and might have an effect on slowing myopia progression.

Identification of unique transcriptomic signatures and key genes through RNA sequencing and integrated WGCNA and PPI network analysis in HIV infected lung cancer.

With the widespread use of highly active antiretroviral therapy (HARRT), the survival time of AIDS patients has been greatly extended. However, the incidence of lung cancer in HIV-infected patients is increasing and has become a major problem threatening the survival of AIDS patients. The aim of this study is to use Weighted Gene Co-expression Network Analysis (WGCNA) and differential gene analysis to find possible key genes involved in HIV-infected lung cancer. In this study, using lung tissue samples from five pairs of HIV-infected lung cancer patients, second-generation sequencing was performed and transcriptomic data were obtained. A total of 132 HIV-infected lung cancer-related genes were screened out by WGCNA and differential gene expression analysis methods. Based on gene annotation analysis, these genes were mainly enriched in mitosis-related functions and pathways. In addition, in protein-protein interaction (PPI) analysis, a total of 39 hub genes were identified. Among them, five genes (ASPM, CDCA8, CENPF, CEP55, and PLK1) were present in both three hub gene lists (intersection gene, DEGs, and WCGNA module) suggesting that these five genes may become key genes involved in HIV-infected lung cancer.

Comparing Standard Keratometry and Total Keratometry Before and After Myopic Corneal Refractive Surgery With a Swept-Source OCT Biometer.

Background: More recently, the swept-source OCT biometer-IOLMaster 700 has provided direct total corneal power measurement, named total keratometry. This study aims to evaluate whether standard keratometry (SK) and total keratometry (TK) with IOLMaster 700 can accurately reflect the corneal power changes induced by myopic corneal refractive surgery. Methods: In this study, the biometric data measured with the swept-source OCT biometer-IOLMaster 700 before and 3 months after the myopic corneal refractive surgery were recorded. The changes of biological parameters, including SK, posterior keratometry (PK), and TK, and the difference between SK and TK were compared. In addition, the changes of SK and TK induced by the surgery were compared with the changes of spherical equivalent at the corneal plane (ΔSEco). Results: A total of 74 eyes (74 patients) were included. The changes of SK, PK, TK, axial length, anterior chamber depth, and lens thickness after refractive surgery were all statistically significant (all p < 0.01), while the change of white-to-white was not (p = 0.075). The difference between SK and TK was -0.03 ± 0.10D before the corneal refractive surgery and increased to -0.78 ± 0.26D after surgery. The changes of SK and the changes of TK induced by the surgery had a good correlation with the changes of SEco (r = 0.97). ΔSK was significantly smaller than ΔSEco, with a difference of -0.65 ± 0.54D (p < 0.01). However, the difference between ΔTK and ΔSEco (0.10 ± 0.50D) was not statistically significant (p = 0.08). Conclusions: Using SK to reflect the changes induced by the myopic corneal refractive surgery may lead to underestimation, while TK could generate a more accurate result. The new parameter, TK, provided by the IOLMaster 700, appeared to provide an accurate, objective measure of corneal power that closely tracked the refractive change in corneal refractive surgery.

Rapid GPR183-mediated recruitment of eosinophils to the lung after Mycobacterium tuberculosis infection.

Influx of eosinophils into the lungs is typically associated with type II responses during allergy and fungal and parasitic infections. However, we previously reported that eosinophils accumulate in lung lesions during type I inflammatory responses to Mycobacterium tuberculosis (Mtb) in humans, macaques, and mice, in which they support host resistance. Here we show eosinophils migrate into the lungs of macaques and mice as early as one week after Mtb exposure. In mice this influx is CCR3 independent and instead requires cell-intrinsic expression of the oxysterol receptor GPR183, which is highly expressed on human and macaque eosinophils. Murine eosinophils interact directly with bacilli-laden alveolar macrophages, which upregulate the oxysterol-synthesizing enzyme Ch25h, and eosinophil recruitment is impaired in Ch25h-deficient mice. Our findings show that eosinophils are among the earliest cells from circulation to sense and respond to Mtb infection of alveolar macrophages and reveal a role for GPR183 in the migration of eosinophils into lung tissue.

Identification of Key CircRNAs Related to Pulmonary Tuberculosis Based on Bioinformatics Analysis.

Pulmonary tuberculosis (TB) is a chronic infectious disease that is caused by respiratory infections, principally Mycobacterium tuberculosis. Increasingly, studies have shown that circular (circ)RNAs play regulatory roles in different diseases through different mechanisms. However, their roles and potential regulatory mechanisms in pulmonary TB remain unclear. In this study, we analyzed circRNA sequencing data from adjacent normal and diseased tissues from pulmonary TB patients and analyzed the differentially expressed genes. We then constructed machine learning models and used single-factor analysis to identify hub circRNAs. We downloaded the pulmonary TB micro (mi)RNA (GSE29190) and mRNA (GSE83456) gene expression datasets from the Gene Expression Omnibus database and performed differential expression analysis to determine the differentially expressed miRNAs and mRNAs. We also constructed a circRNA-miRNA-mRNA interaction network using Cytoscape. Gene Ontology enrichment analysis and Kyoto Encyclopedia of Genes and Genomes pathway analysis were used to predict the biological functions of the identified RNAs and determine hub genes. Then, the STRING database and cytoHubba were used to construct protein-protein interaction networks. The results showed 125 differentially expressed circRNAs in the adjacent normal and diseased tissues of pulmonary TB patients. Among them, we identified three hub genes associated with the development of pulmonary TB: hsa_circ_0007919 (upregulated), hsa_circ_0002419 (downregulated), and hsa_circ_0005521 (downregulated). Through further screening, we determined 16 mRNAs of potential downstream genes for hsa-miR-409-5p and hsa_circ_0005521 and established an interaction network. This network may have important roles in the occurrence and development of pulmonary TB. We constructed a model with 100% prediction accuracy by machine learning and single-factor analysis. We constructed a protein-protein interaction network among the top 50 hub mRNAs, with FBXW7 scoring the highest and SOCS3 the second highest. These results may provide a new reference for the identification of candidate markers for the early diagnosis and treatment of pulmonary TB.

Comprehensive Genetic Analysis of Tuberculosis and Identification of Candidate Biomarkers.

Purpose: The purpose of this study is to use the data in the GEO database to analyze, screen biomarkers that can diagnose tuberculosis, and verification of candidate biomarkers. Materials and methods: GSE158767 dataset were used to process WGCNA analysis, differential gene analysis, Gene ontology and KEGG analysis, protein-protein network analysis and hub genes analysis. Based on our previous study, the intersect between WGCNA and differential gene analysis could be used as candidate biomarkers. Then, the enzyme-linked immunosorbent assay was used to validate candidate biomarkers, and receiver operating characteristic was used to assess diagnose ability of candidate biomarkers. Results: A total of 412 differential genes were screened. And we obtained 105 overlapping genes between DEGs and WGCNA. GO and KEGG analysis showed that most of the differential genes were significantly enriched in innate immunity. A total of 15 hub genes were screened, and four of them were verified by Enzyme-linked immunosorbent assay. CCL5 performed well in distinguishing the healthy group from the TB group (AUC = 0.723). And CCL19 performed well in distinguishing the TB group from the ORD groups (AUC = 0.811). Conclusion: CCL19, C1Qb, CCL5 and HLA-DMB may play important role in tuberculosis, which indicated four genes may become effective biomarkers and could be conveniently used to facilitate the individual tuberculosis diagnosis in Chinese people.

Identification of Hub Genes Associated With Tuberculous Pleurisy by Integrated Bioinformatics Analysis.

Improving the understanding of the molecular mechanism of tuberculous pleurisy is required to develop diagnosis and new therapy strategies of targeted genes. The purpose of this study is to identify important genes related to tuberculous pleurisy. In this study, the expression profile obtained by sequencing the surgically resected pleural tissue was used to explore the differentially co-expressed genes between tuberculous pleurisy tissue and normal tissue. 29 differentially co-expressed genes were screened by weighted gene co-expression network analysis (WGCNA) and differential gene expression analysis methods. According to the functional annotation analysis of R clusterProfiler software package, these genes are mainly enriched in nucleotide-sugar biosynthetic process (biological process), ficolin-1-rich granule lumen (cell component), and electron transfer activity (molecular function). In addition, in the protein-protein interaction (PPI) network, 20 hub genes of DEGs and WCGNA genes were identified using the CytoHubba plug-in of Cytoscape. In the end, RPL17 was identified as a gene that can be the biomarker of tuberculous pleurisy. At the same time, there are seven genes that may have relationship with the disease (UBA7, NDUFB8, UQCRFS1, JUNB, PSMC4, PHPT1, and MAPK11).

Prediction of the Complication Risk in Drug-Resistant Tuberculosis After Surgery: Development and Assessment of a Novel Nomogram.

Background: Surgery is increasingly accepted as an adjunctive approach to treat multidrug-resistant tuberculosis (MDR-TB) or extensively drug-resistant tuberculosis (XDR-TB). However, a model that includes all factors to predict the risk of postoperative complications is lacking. Methods: We developed a prediction model based on 138 patients who had undergone surgery as treatment for drug-resistant tuberculosis (DR-TB) after 24 months. Clinical features on the lesion type (L), treatment history (T), physiologic status of the body (B), and surgical approach (S) were evaluated. Multivariable logistic regression analysis was conducted by clinical features selected in the least absolute shrinkage and selection operator (LASSO) to build a nomogram. The discrimination, calibration, and clinical usefulness of the nomogram were assessed using the C-Index, calibration plots, and decision curves. Internal validation was assessed using bootstrapping. Results: The nomogram contained the features L, B, T, cavitary, recurrent chest infection (RCI) and MDR-TB/XDR-TB. The model displayed good discrimination with a C-Index of 0.879 (95% CI: 0.799-0.967). A high C-Index of 0.824 was achieved in the interval validation. Decision-curve analysis showed that the nomogram was clinically useful if intervention was decided at the non-adherence possibility threshold of 4%. Conclusion: Our novel nomogram could be used conveniently to predict postoperative complication risk in DR-TB patients.

Eosinophils are part of the granulocyte response in tuberculosis and promote host resistance in mice.

Host resistance to Mycobacterium tuberculosis (Mtb) infection requires the activities of multiple leukocyte subsets, yet the roles of the different innate effector cells during tuberculosis are incompletely understood. Here we uncover an unexpected association between eosinophils and Mtb infection. In humans, eosinophils are decreased in the blood but enriched in resected human tuberculosis lung lesions and autopsy granulomas. An influx of eosinophils is also evident in infected zebrafish, mice, and nonhuman primate granulomas, where they are functionally activated and degranulate. Importantly, using complementary genetic models of eosinophil deficiency, we demonstrate that in mice, eosinophils are required for optimal pulmonary bacterial control and host survival after Mtb infection. Collectively, our findings uncover an unexpected recruitment of eosinophils to the infected lung tissue and a protective role for these cells in the control of Mtb infection in mice.

IRF1 as a potential biomarker in Mycobacterium tuberculosis infection.

Pulmonary tuberculosis (PTB) is a major global public health problem. The purpose of this study was to find biomarkers that can be used to diagnose tuberculosis. We used four NCBI GEO data sets to conduct analysis. Among the four data sets, GSE139825 is lung tissue microarray, and GSE83456, GSE19491 and GSE50834 are blood microarray. The differential genes of GSE139825 and GSE83456 were 68 and 226, and intersection genes were 11. Gene ontology (GO) analyses of 11 intersection genes revealed that the changes were mostly enriched in regulation of leucocyte cell-cell adhesion and regulation of T-cell activation. Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis of DEGs revealed that the host response in TB strongly involves cytokine-cytokine receptor interactions and folate biosynthesis. In order to further narrow the range of biomarkers, we used protein-protein interaction to establish a hub gene network of two data sets and a network of 11 candidate genes. Eventually, IRF1 was selected as a biomarker. As validation, IRF1 levels were shown to be up-regulated in patients with TB relative to healthy controls in data sets GSE19491 and GSE50834. Additionally, IRF1 levels were measured in the new patient samples using ELISA. IRF1 was seen to be significantly up-regulated in patients with TB compared with healthy controls with an AUC of 0.801. These results collectively indicate that IRF1 could serve as a new biomarker for the diagnosis of pulmonary tuberculosis.