Identifying autophagy-related genes as potential targets for immunotherapy in tuberculosis.

PURPOSE: Identifying of host-directed targets and molecular markers of immune response for tuberculosis (TB) immunotherapy is urgent and meaningful. Previous studies have demonstrated an important role of autophagy in the course and pathophysiology of TB and is associated with the efficacy of TB treatment. However, its role in TB immunotherapy is still incomplete. METHODS: The effect of autophagy on intracellular bacteria load was examined in sulforaphane (SFN)-treated THP-1 cells. The immune infiltration was assessed based on public databases. Functional enrichment analysis revealed the pathways involved. LASSO Cox regression analysis was employed to identify hub genes. Moreover, machine learning analysis was used to obtain important targets of TB immunotherapy. Finally, the relationship between hub genes and immune infiltration was assessed, as well as the relevance of chemokines. RESULTS: We found that SFN reduced intracellular bacteria load by enhancing autophagy in THP-1 cells. Thirty-two autophagy-related genes (ARGs) were identified, three types of immune cells (macrophages, neutrophils, and DC cells) were significantly enriched in TB patients, and 6 hub genes (RAB5A, SQSTM1, MYC, MAPK8, MAPK3, and FOXO1) were closely related to TB immune infiltration. The 32 ARGs were mainly involved in autophagy, apoptosis, and tuberculosis pathways. FOXO1, SQSTM1, and RAB5A were identified as important target genes according to the ranking of variable importance, with FOXO1 being a potential autophagy-related target of TB immunotherapy. CONCLUSION: This study highlights the association between autophagy-related genes and immune infiltration in TB. Three key genes, especially FOXO1, regulated by SFN, will provide new insights into diagnostic and immunotherapy strategies for clinical tuberculosis.

Mining biomarkers from routine laboratory tests in clinical records associated with air pollution health risk assessment.

Clinical laboratory in hospital can produce amounts of health data every day. The purpose of this study was to mine biomarkers from clinical laboratory big data associated with the air pollution health risk assessment using clinical records. 13, 045, 629 clinical records of all 27 routine laboratory tests in Changsha Central Hospital, including ALB, TBIL, ALT, DBIL, AST, TP, UREA, UA, CREA, GLU, CK, CKMB, LDL-C, TG, TC, HDL-C, CRP, WBC, Na, K, Ca, Cl, APTT, PT, FIB, TT, RBC and those daily air pollutants concentration monitoring data of Changsha, including PM2.5, PM10, SO2, NO2, CO, and O3 from 2014 to 2016, were retrieved. The moving average method was used to the biological reference interval was established. The tests results were converted into daily abnormal rate. After data cleaning, GAM statistical model construction and data analysis, a concentration-response relationship between air pollutants and daily abnormal rate of routine laboratory tests was observed. Our study found that PM2.5 had a stable association with TP (lag07), ALB (lag07), ALT (lag07), AST (lag07), TBIL (lag07), DBIL (lag07), UREA (lag07), CREA (lag07), UA (lag07), CK (lag 06), GLU (lag07), WBC (lag07), Cl (lag07) and Ca (lag07), (P < 0.05); O3 had a stable association with AST (lag01), CKMB (lag06), TG (lag07), TC (lag05), HDL-C (lag07), K (lag05) and RBC (lag07) (P < 0.05); CO had a stable association with UREA (lag07), Na (lag7) and PT (lag07) (P < 0.05); SO2 had a stable association with TP (lag07) and LDL-C (lag0) (P < 0.05); NO2 had a stable association with APTT (lag7) (P < 0.05). These results showed that different air pollutants affected different routine laboratory tests and presented different pedigrees. Therefore, biomarkers mined from routine laboratory tests may potentially be used to low-cost assess the health risks associated with air pollutants.

Characterization and phylogenetic analysis of the complete chloroplast genome of Tulipa patens (Liliaceae).

The chloroplast genome and evolutionary relationship analysis of Tulipa patens could provide fundamental genetic reference for its molecular breeding and biological research. The complete chloroplast genome of T. patens was sequenced and reported here. The genome was 152,050 bp in length, containing a pair of inverted repeated regions (26,330 bp) which were separated by a large single copy region of 82,184 bp, and a small single copy region of 17,206 bp. A total of 133 functional genes were annotated, including 87 protein-coding genes, 38 tRNA genes, and eight rRNA genes. The phylogenetic relationships of 10 species indicated that T. patens was closely related to Tulipa sylvestris.

Emergence of nontuberculous mycobacteria infections during bedaquiline-containing regimens in multidrug-resistant tuberculosis patients.

OBJECTIVES: The World Health Organization recommends the use of bedaquiline (BDQ) to formulate efficacious combination regimens against multidrug-resistant tuberculosis (MDR-TB). This study reports, for the first time, a case series of MDR-TB patients treated with BDQ who experienced sputum culture reconversion due to emergence of nontuberculous mycobacteria (NTM) infections. METHODS: A multicentre case series was established, including patients who started treatment for laboratory-confirmed MDR-TB between January 1, 2018 and March 31, 2020. The study included patients with positive cultures that had no expression of tuberculosis-specific MPT64 protein. Multilocus sequence analysis was used to perform rapid species identification. Susceptibility to BDQ was detected using Thermo Fisher frozen microtiter plates by the laboratory staff at Beijing Chest Hospital. RESULTS: Among the 286 patients receiving BDQ regimens included in this study, the emergence of NTM isolations was reported in nine cases (3.1%). After exposure to BDQ, seven out of these nine patients achieved culture conversion by 4 weeks. The median time for reported NTM infection was 12 weeks (range: 4-24 weeks). Of these, seven were rapidly growing mycobacteria, and two were slow growing. The most frequent NTM species was M. abscessus (five isolates), followed by M. fortuitum (two isolates), M. avium (one isolate), and M. intracellulare (one isolate). In addition, three patients showed resistance to BDQ at baseline. CONCLUSION: In conclusion, our results demonstrated the emergence of novel NTM populations in MDR-TB patients during BDQ therapy. The notably rapid development of NTM infections underlines the need for systematic species identification during the follow-up period.

Association between fine particle exposure and common test items in clinical laboratory: A time-series analysis in Changsha, China.

Most studies on the health effects of PM2.5 (fine particulate matter with diameter smaller than 2.5 µm) use indirect indicators, such as mortality and number of hospital visits. Recent research shows that biomarkers can also be used to evaluate the health effects of PM2.5; however, these biomarkers are not very common. Clinical laboratories can provide a significant amount of test data that have been proven to have important diagnostic value. Therefore, we use big data analysis methods to find the associations between clinical laboratory common test items and PM2.5 exposure. Data related to air pollution and meteorological information between 2014 and 2016 were obtained from the China National Environmental Monitoring Centre and the China National Meteorological Information Center. Additionally, data of 27 common test items from the same period were collected from Changsha Central Hospital. Primary analyses included a generalized additive model to analyze the associations between PM2.5 concentration and common test items; the model was adjusted for time trends, weather conditions (temperature and humidity), and days of the week. Furthermore, we adjusted the effects of other air pollutants, such as PM10, SO2, NO2, CO, and O3. 17 items such as TP, ALB, ALT, AST, TBIL, DBIL, UREA, CREA, UA, GLU, LDL, WBC, K, Cl, Ca, TT, and FIB were significantly positively associated with PM2.5 concentration (P< 0.05) and have concentration-response relationship. After adjusting the effect of PM10+SO2+NO2+CO+O3, TP, ALB, ALT, AST, TBIL, DBIL, UREA, CREA, UA, GLU, WBC, Cl, and Ca were still significantly associated with PM2.5 concentration (P< 0.05). This current study suggested that clinical laboratory common test items may be used to assess and predict the health effects of PM2.5 on the population.

Complete chloroplast genome of Tulipa buhseana (Liliaceae).

The complete chloroplast genome of Tulipa buhseana was sequenced and reported here. The circular genome of T. buhseana is 152,062 bp in length and contains 133 functional genes consisting of 87 coding sequences, 38 tRNA genes, and 8 rRNA genes. With 1 species from Smilacaceae and 1 species from Alstroemeriaceae as outgroup, phylogenetic relationships of 8 Liliaceae species based on their chloroplast genomes indicated that T. buhseana is closest to T. altaica.

Characterization of the complete chloroplast genome of Tulipa iliensis (Liliaceae).

The chloroplast genome and evolutionary relationship analysis of Tulipa gesneriana L. could provide fundamental genetic reference for its molecular breeding and biological research. The complete chloroplast genome of Tulipa iliensis was sequenced and reported here. Its chloroplast genome was 151,744 bp in length, containing a pair of inverted repeated regions (26,354 bp) which were separated by a large single copy region of 81,794 bp, and a small single copy region of 17,242 bp. Moreover, a total of 133 functional genes were annotated, including 87 mRNA, 38 tRNA genes, and 8 rRNA genes.The phylogenetic relationships of 16 species indicated that T. iliensis was closely related to T. altaica.

RNA-binding protein HuR regulates hsa-let-7c expression by its RNA recognition motif.

MicroRNAs (miRNAs) are small noncoding RNAs that control diverse cellular and developmental events through repression of large sets of target mRNAs. miRNAs expressions were mainly regulated at two levels: transcriptional and post-transcriptional. Transcriptional regulation of miRNA-encoding genes produce specific expression patterns of individual miRNA. However, the mechanism of post-transcriptional regulation of miRNAs remains largely unknown. The present study was aimed to clarify whether HuR, an evolutionary conserved AU-rich binding protein, could regulate miRNAs expressions. By means of a computational screen for AUUUA motifs within pri-miRNAs, we found that the downstream of hsa-let-7c but not hsa-miR-21 was enriched of AUUUA motifs. Then we transfected HuR and mutant HuR lacking RNA recognition motif 3 (RRM3) respectively into HEK293T cells. And HuR protein and miRNAs expressions were detected by Western blot and real-time PCR, respectively. The results showed that the overexpression of HuR promoted mature hsa-let-7c expression but not hsa-miR-21 expression. Furthermore, overexpression of HuR deletion mutant lacking RRM3 did not promote hsa-let-7c expression. These results suggest that RRM3 is crucial for HuR mediating mature hsa-let-7c expression. Collectively, these findings proposed a novel role of HuR in biogenesis of miRNAs, possibly by way of post-transcriptional regulation of miRNAs.