Jie Zhang’s research while affiliated with Sichuan University and other places

Plant growth-promoting rhizobacteria (PGPR) are beneficial bacteria residing in the rhizosphere and are capable of enhancing plant growth through various mechanisms. Streptomyces sp. GD-4 is a plant growth-promoting bacterium isolated from the rhizosphere soil of Leymus secalinus. To further elucidate the molecular mechanisms underlying the beneficial effects of the strain on plant growth, we evaluated the growth-promoting effects of Streptomyces sp. GD-4 on forage grasses and conducted comprehensive genome mining and comparative genomic analysis of the strain. Strain GD-4 effectively colonized the rhizosphere of three forages and significantly promoted the growth of both plant roots and leaves. Genome sequence functional annotation of GD-4 revealed lots of genes associated with nitrogen, phosphorus, and sulfur metabolism. Additionally, genes potentially involved in plant growth promotion such as indole-3-acetic acid (IAA) biosynthesis, trehalose production, siderophore production, and phosphate solubilization were annotated. Whole-genome analysis revealed that GD-4 may possess molecular mechanisms involved in soil nutrient cycling in rhizosphere soil and plant growth promotion. The bacteria also possess genes associated with adaptability to abiotic stress conditions, further supporting the ability of Streptomyces sp. GD-4 to colonize nutrient-poor soils. These findings provide a foundation for further research into soil remediation technologies in plateau regions.

Objective MiRNAs and lncRNAs are important regulators in the process of skin photoaging. In this study, we investigated the expression changes and interactions between miR4298 and lncKRTAP5-6-3 in chronically UVB-damaged human keratinocyte cell line (HaCaT) cells and explored miR4298-MAPK/ERK signaling pathway-Cathepsin D-lncKRTAP5-6-3 mechanisms in photoaging cells. Methods HaCaT cells were irradiated with 12 mJ/cm² UVB once a day for 7 days. miR-4298 mimics and miR-4298 inhibitors were transfected into HaCaT cells by lipo3000 transfection reagent, and the HaCaT cells were divided into three groups: blank control group; UVB-damaged group; and UVB damage+miR-4298 regulation (overexpression or inhibition) group. The expression levels of miR4298 and lncKRTAP5-6-3 were quantitatively analyzed using RT-PCR, while the expression of Cathepsin D and MAPK/ERK signaling pathway proteins was detected using Western blot. Results After 7 consecutive days of UVB irradiation, the expression of miR-4298 decreased by 0.64 ± 0.06 (P < 0.001) compared to the un-irradiated HaCaT cells, and the expression of the KRTAP5-6-3 decreased by 0.80 ± 0.13 (P < 0.001) compared to the control group. The expression of p-ERK signaling was increased by 0.9437 ± 0.1186 (P < 0.0001), and Cathepsin D was decreased by 0.6163 ± 0.075 (P < 0.0001). In HaCaT cells transfected with miR-4298 mimics and then irradiated by UVB for 7 days, the expression of lncKRTAP5-6-3 was increased to 0.5114 ± 0.1438 (P < 0.05)-fold, and the phosphorylation level of ERK signaling was decreased by 0.3880 ± 0.1185 (P < 0.01), while Cathepsin D expression was increased by 0.2617 ± 0.0749 (P < 0.0001) compared to the UVB-damaged group. In HaCaT cells transfected with miR-4298 inhibitors and then irradiated by UVB for 7 days, lncKRTAP5-6-3 was decreased by 0.1697 ± 0.1383, the phosphorylation level of ERK signaling was increased by 1.096 ± 0.7836 (P < 0.05), while Cathepsin D expression was decreased by 0.05197 ± 0.24827 compared to the UVB-damaged group. Conclusion The synergistic effects of miR4298 and lncKRTAP5-6-3 play important roles in chronic UVB-damaged HaCaT cells by regulating the MAPK/ERK signaling pathway and Cathepsin D expression. This study presents novel targets for intervening in chronic ultraviolet damage (photoaging) skin and UV-related dermatoses.

Background Inflammation and lipids are both involved in the pathogenesis of coronary heart disease (CHD). However, the mediation effect of lipoproteins on the association between inflammation and recurrent coronary events in CHD patients remains unclear. Methods This was a retrospective study including CHD patients hospitalized in the Department of Cardiovascular Medicine in Sun Yat-sen Memorial Hospital between January 2011 and December 2012 with the endpoint of recurrent coronary events. The study calculated inflammatory score based on six serum inflammatory markers, including complement C3, complement C4, hyper-sensitive CRP, fibrinogen, D-dimer, and white blood cell count. Logistic regression analysis, subgroup analysis and mediation analysis were performed to assess the associations between inflammatory score and recurrent coronary events in different subpopulations and the identification of mediators. Inflammatory cytokine expression, cholesterol efflux capacity, and hepatic cholesterol influx were performed in additional CHD patients and healthy controls. Results There were 191 CHD patients included in the analysis with a median inflammatory score of −0.78 (−2.17, 1.35) and 63 cases of recurrent coronary events. Subgroup logistic regression analysis demonstrated that inflammatory score was positively associated with recurrent coronary events only in the diabetic subgroup [OR: 1.241 (1.004, 1.534), P < 0.046]. HDL-cholesterol (HDL-C): non-HDL-C performed 46.74 % of negative mediation effect on this association. CHD patients had lower cholesterol efflux capacity than healthy controls, which was mediated by HDL: non-HDL ratio of 0.4. No difference was found in hepatic cholesterol influx between the two groups. Conclusion Inflammatory score was associated with recurrent coronary events mediated by HDL-C: non-HDL-C ratio in diabetic CHD patients, indicating that lipoproteins might aggravate the inflammatory effect on atherosclerosis under hyperglycemia. Our findings suggested that anti-inflammatory and lipid-lowering therapies might be beneficial for this population.

Background Nude mouse has been widely used to study photoaging induced by long-term chronic UV exposure. Circular RNAs (circRNAs) have been previously identified in several diseases. However, the roles of circRNAs in photoaging and potential regulatory mechanisms remain unclear. Objectives To identify specific circRNAs differentially expressed in photoaged skin and investigate their potential role in aging. Materials and Methods In this study, we screened out the microarray data to profile the expression of circRNAs. The circRNAs were analyzed by Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) biological pathway. Results 36 circRNAs were identified to be differentially expressed between the UV group and control group (fold change > 1.5; P < 0.05), including 6 upregulated and 30 downregulated circRNAs. GO and KEGG biological pathway analyses indicated that the changes in circRNAs were associated with cancer, inflammation, oxidative stress, and metabolism. Conclusions This present study revealed a circRNAs expression profiling in vivo. These findings not only provide a new possibility to prevent the occurrence of photoaging but also have therapeutic values for photoaging and associated skin diseases.

Background The previous study investigated whether the functions of small, medium, and large high density lipoprotein (S/M/L-HDL) are correlated with protein changes in mice. Herein, the proteomic and functional analyses of high density lipoprotein (HDL) subclasses were performed in humans and rats. Methods After purifying S/M/L-HDL subclasses from healthy humans (n = 6) and rats (n = 3) using fast protein liquid chromatography (FPLC) with calcium silica hydrate (CSH) resin, the proteomic analysis by mass spectrometry was conducted, as well as the capacities of cholesterol efflux and antioxidation was measured. Results Of the 120 and 106 HDL proteins identified, 85 and 68 proteins were significantly changed in concentration among the S/M/L-HDL subclasses in humans and rats, respectively. Interestingly, it was found that the relatively abundant proteins in the small HDL (S-HDL) and large HDL (L-HDL) subclasses did not overlap, both in humans and in rats. Next, by searching for the biological functions of the relatively abundant proteins in the HDL subclasses via Gene Ontology, it was displayed that the relatively abundant proteins involved in lipid metabolism and antioxidation were enriched more in the medium HDL (M-HDL) subclass than in the S/L-HDL subclasses in humans, whereas in rats, the relatively abundant proteins associated with lipid metabolism and anti-oxidation were enriched in M/L-HDL and S/M-HDL, respectively. Finally, it was confirmed that M-HDL and L-HDL had the highest cholesterol efflux capacity among the three HDL subclasses in humans and rats, respectively; moreover, M-HDL exhibited higher antioxidative capacity than S-HDL in both humans and rats. Conclusions The S-HDL and L-HDL subclasses are likely to have different proteomic components during HDL maturation, and results from the proteomics-based comparison of the HDL subclasses may explain the associated differences in function.

Background Leymus secalinus is a pioneer plant grown in the Zoige desertified alpine grassland and it is also one of the dominant plant species used for environmental remediation. L. secalinus plays a large role in vegetation reconstruction in sandy land, but the abundance and diversity of its endophytes have not yet been investigated. Objectives This study was performed to investigate the changes in the endophytic bacterial community structure of L. secalinus under different ecological environments and to analyze the effects of environmental changes and different plant tissues on the L. secalinus endophytic bacteria. Methods Leaf, stem, and root tissue samples of L. secalinus were collected from Zoige Glassland (Alpine sandy land) and an open field nursery (Control). DNA was extracted and the 16S ribosomal DNA was amplified. The sequence library was sequenced on an Illumina MiSeq platform and clustered by operational taxonomic units (OTUs). α -diversity and β -diversity analyses, species diversity analyses, functional prediction, and redundancy (RDA) analyses for the soil physicochemical properties were conducted. Results α -diversity and β -diversity analyses showed that the endophytic bacteria in L. secalinus varied in different areas and tissues. The abundance of Allorhizobium-Neorhizobium-Pararhizobium-Rhizobium , which is related to nitrogen fixation, increased significantly in the L. secalinus found in the Zoige Grassland. Moreover, the abundance of nutrition metabolism and anti-stress abilities increased in functional prediction in the desert samples. The soil physicochemical properties had an insignificant influence on bacterial diversity. Conclusion The changes in the endophytic bacterial community structure in L. secalinus were significant and were caused by environmental alterations and plant choice. The endophytic bacteria in L. secalinus grown in alpine sandy land may have greater anti-stress properties and the ability to fix nitrogen, which has potential value in environmental remediation and agricultural production.

Background Impaired glycolipid metabolism can induce vascular injury and plaque formation. It is important to investigate the associations between carotid plaque progression and lipid-lowering goal achievement and cardiovascular disease. Methods Diabetic patients who underwent at least 2 carotid ultrasound scans with intervals ≥0.5 years and were hospitalized in the Department of Endocrinology at Sun Yat-sen Memorial Hospital were included. Patients were divided into 3 groups based on carotid plaque progression: the persistent plaque absence, new-onset plaque and persistent plaque presence groups. The primary outcomes were CHD and stroke, while the secondary outcomes were low-density lipoprotein cholesterol (LDL-C) and non-high-density lipoprotein cholesterol (non-HDL-C) goal achievement. Results There were 304 diabetic patients included, with a median follow-up period of 2.15 years. In multivariable logistic regression analysis, persistent plaque presence was positively associated with a 2.285-fold increase in coronary heart disease (CHD) prevalence, while new-onset plaque was associated with a 3.225-fold increase in stroke prevalence compared to persistent plaque absence in patients with follow-up periods ≥ 0.5 years. The association remained significant in patients with a follow-up period ≥ 1 year and ≥2 years. The velocity of average plaque length change was independently associated with increased ΔLDL-C (last – goal) (β = 0.073, P = 0.048). Conclusion Carotid plaque progression had long-term association with CHD and stroke starting from 0.5 years, while the velocity of average plaque length associated with increased ΔLDL-C (last – goal) might reflect patient response to statins. Repeated carotid plaque measurements might guide lipid-lowering therapies.

Background Accumulating evidence has suggested the impact of cellular senescence on tumorigenesis, development, and immune modulation in cancers. However, the prognostic value of cellular senescence-related genes (SRGs) and their association with immunotherapy response remain unexplored in skin cutaneous melanoma (SKCM) patients. Methods In this study, we explored the expression profiles of 279 SRGs in 469 SKCM patients included from TCGA database. The univariate and least absolute shrinkage and selection operator (LASSO) were conducted to construct a cellular senescence-related signature (SRS), and Kaplan–Meier survival curves as well as ROC curve were used to validate the predictive capability. The GSE65904 dataset was further used to validate the predictive ability of prognostic signature. Moreover, we explored the correlations of the SRS with tumor-infiltrating immune cells and response to immunotherapy. The expression levels of prognosis related SRGs were validated based on immunohistochemistry. In addition, consensus clustering analysis was performed to stratify SKCM patients into different clusters and compared them in OS. Results We developed a prognostic prediction SRS for patients with SKCM and verified patients in low-risk group were associated with better prognosis. Moreover, the correlation analysis showed that the SRS could predict the infiltration of immune cells and immune status of the immune microenvironment in SKCM, and patients with low-risk score might benefit from immunotherapy. In addition, all the SKCM patients in this study were classified into three clusters based on the mRNA expression profiles of 113 SRGs, which revealed that cluster 1 suffered poorer outcomes relative to clusters 2 and 3. Conclusions The SRS developed in this study could be used as a prediction tool in survival assessment and immunotherapy for SKCM patients.

Skin cutaneous melanoma (SKCM) is a skin cancer type characterized by a high degree of immune cell infiltration. The potential function of lactate, a main metabolic product in the tumor microenvironment (TME) of SKCM, remains unclear. In this study, we systemically analyzed the predictive value of lactate-related genes (LRGs) for prognosis and response to immune checkpoint inhibitors (ICIs) in SKCM patients included from The Cancer Genome Atlas (TCGA) database. Cluster 3, by consensus clustering for 61 LRGs, manifested a worse clinical outcome, attributed to the overexpression of malignancy marks. In addition, we created a prognostic prediction model for high- and low-risk patients and verified its performance in a validation cohort, GSE65904. Between TME and the risk model, we found a negative relation of the immunocyte infiltration levels with patients’ risk scores. The low-risk cases had higher ICI expression and could benefit better from ICIs relative to the high-risk cases. Thus, the lactate-related prognosis risk signature may comprehensively provide a basis for future investigations on immunotherapeutic treatment for SKCM.