Single-cell transcriptome analyses reveal critical roles of RNA splicing during leukemia progression.

Leukemogenesis is proposed to be a multistep process by which normal hematopoietic stem and progenitor cells are transformed into full-blown leukemic cells, the details of which are not fully understood. Here, we performed serial single-cell transcriptome analyses of preleukemic and leukemic cells (PLCs) and constructed the cellular and molecular transformation trajectory in a Myc-driven acute myeloid leukemia (AML) model in mice, which represented the transformation course in patients. We found that the Myc targets were gradually up-regulated along the trajectory. Among them were splicing factors, which showed stage-specific prognosis for AML patients. Furthermore, we dissected the detailed gene network of a tipping point for hematopoietic stem and progenitor cells (HSPCs) to generate initiating PLCs, which was characterized by dramatically increased splicing factors and unusual RNA velocity. In the late stage, PLCs acquired explosive heterogeneity through RNA alternative splicing. Among them, the Hsp90aa1hi subpopulation was conserved in both human and mouse AML and associated with poor prognosis. Exon 4 skipping of Tmem134 was identified in these cells. While the exon skipping product Tmem134ß promoted the cell cycle, full-length Tmem134α delayed tumorigenesis. Our study emphasized the critical roles of RNA splicing in the full process of leukemogenesis.

Identifying STRN3-RARA as a new fusion gene for acute promyelocytic leukemia.

Here we report a new fusion gene, STRN3-RARA, in acute promyelocytic leukemia (APL). It cooperates with UTX deficiency to drive full-blown APL in mice. Although STRN3-RARA leukemia quickly relapses after all-trans retinoic acid treatment, it can be restrained by cepharanthine.

AFF4 regulates cellular adipogenic differentiation via targeting autophagy.

Transcriptional elongation is a universal and critical step during gene expression. The super elongation complex (SEC) regulates the rapid transcriptional induction by mobilizing paused RNA polymerase II (Pol II). Dysregulation of SEC is closely associated with human diseases. However, the physiological role of SEC during development and homeostasis remains largely unexplored. Here we studied the function of SEC in adipogenesis by manipulating an essential scaffold protein AF4/FMR2 family member 4 (AFF4), which assembles and stabilizes SEC. Knockdown of AFF4 in human mesenchymal stem cells (hMSCs) and mouse 3T3-L1 preadipocytes inhibits cellular adipogenic differentiation. Overexpression of AFF4 enhances adipogenesis and ectopic adipose tissue formation. We further generate Fabp4-cre driven adipose-specific Aff4 knockout mice and find that AFF4 deficiency impedes adipocyte development and white fat depot formation. Mechanistically, we discover AFF4 regulates autophagy during adipogenesis. AFF4 directly binds to autophagy-related protein ATG5 and ATG16L1, and promotes their transcription. Depleting ATG5 or ATG16L1 abrogates adipogenesis in AFF4-overepressing cells, while overexpression of ATG5 and ATG16L1 rescues the impaired adipogenesis in Aff4-knockout cells. Collectively, our results unveil the functional importance of AFF4 in regulating autophagy and adipogenic differentiation, which broaden our understanding of the transcriptional regulation of adipogenesis.

The potential causal association between systemic lupus erythematosus and endocrine and metabolic disorders in the East Asian population: A bidirectional two-sample Mendelian randomization study.

OBJECTIVES: Observational studies indicate a significant correlation between systemic lupus erythematosus (SLE) and endocrine and metabolic disorders, but the causal association between SLE and endocrine and metabolic disorders remains unclear due to the reverse causality and confounding biases commonly presented in conventional observational research. This study endeavors to uncover the causal association between SLE and three common endocrine and metabolic disorders, including Graves' disease (GD), type 2 diabetes mellitus (T2DM), and osteoporosis (OP). METHODS: We used genome-wide association study data for SLE and three endocrine and metabolic disorders in an East Asian population, employing bidirectional two-sample Mendelian randomization (MR) analysis and sensitivity analysis to ascertain the causal association between SLE and endocrine and metabolic disorders. RESULTS: A multiplicative random-effect inverse-variance weighted approach revealed a significant positive correlation between SLE and an elevated risk of GD with an odds ratio (OR) of 1.12 (95% CI: 1.04-1.22, p < .01), and inverse-variance weighted (IVW) analysis also indicated that SLE increased the risk of OP with an OR of 1.035 (95% CI: 1.003-1.068, p < .05). Additionally, GD causally affected SLE in an IVW analysis after Bonferroni correction, with an OR of 1.33 (95% CI: 1.19-1.49, p < .05/3), but the application of multivariable MR analysis resulted in the absence of a causal association of GD on SLE (OR 1.047, 95% CI: 0.952-1.151, p > .05). Lastly, the robustness and validity of the findings were verified through a sensitivity analysis. CONCLUSIONS: We confirmed that SLE has a causal effect on GD as well as OP, but no evidence exists to substantiate a causal link between SLE and T2DM. Our study offers valuable contributions for uncovering the etiology of SLE and endocrine and metabolic disorders and furthering disease risk research while providing potential targets for disease monitoring and therapeutic intervention.

Nocardioides jiangxiensis sp. nov., a novel actinobacterium isolated from lakeside soil, exhibiting the biosynthesis potential of mycofactocin.

A Gram-stain-positive, rod-shaped, non-spore-forming and non-motile bacterium, designated WY-20T, was isolated from a lakeside soil sample collected in Jiangxi Province, PR China. Growth was observed at 20-42 °C (optimum 30 °C), pH 5.0-8.0 (optimum pH 7.0) and salinity of 0-3.0% (w/v; optimum 0.5%). Phylogenetic analysis based on the 16S rRNA gene sequences indicated that strain WY-20T belongs to the genus Nocardioides and showed the highest sequence similarity (98.1%) to N. phosphati WYH11-7T, followed by N. cavernaquae K1W22B-1T (97.8%), N. marmoriterrae JOS5-1T (97.2%) and N. jensenii NBRC 14755T (97.1%). The average nucleotide identity and digital DNA-DNA hybridization values between strains WY-20T and N. phosphati WYH11-7T were 83.5% and 26.2%, respectively. The predominant fatty acids (≥ 10% of the total fatty acids) were C18:1ω9c, C17:0, C16:0, summed feature 8 (C18:1ω7c and/or C18: 1ω6c) and C17:1ω9c. The major menaquinone was MK-8 (H4). The major polar lipids were diphosphatidylglycerol, phosphatidylglycerol and two unidentified phospholipids. In addition, meso-diaminopimelic acid was the diagnostic diamino acid in the cell-wall peptidoglycan. Based on phenotypic, genotypic and phylogenetic pieces of evidence, strain WY-20T represents a novel species in the genus Nocardioides, for which the name Nocardioides jiangxiensis sp. nov. is proposed. The type strain is WY-20T (= GDMCC 4.317T = KACC 23379T).

Sphingomonas caeni sp. nov., a phenolic acid-degrading bacterium isolated from activated sludge.

A Gram-stain-negative, rod-shaped, polar flagellated or stalked and non-spore-forming bacterium, designated LB-2T, was isolated from activated sludge. Growth was observed at 20-30 °C (optimum 28 °C), pH 6.0-8.0 (optimum pH 7.0) and salinity of 0-0.5% (w/v; optimum 0.5%). Phylogenetic analysis based on the 16S rRNA gene indicated that strain LB-2T belongs to the genus Sphingomonas and showed the highest sequence similarity (96.7%) and less than 96.7% similarities to other type strains. The genome size of strain LB-2T was 4.10 Mb, with 66.8 mol% G + C content. The average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values between strains LB-2T and S. canadensis FWC47T were 77.8% and 21%, respectively. The predominant cellular fatty acids were summed feature 8 (C18:1ω7c and/or C18 : 1ω6c) and C16:0. The major polar lipids were aminolipid, glycolipid, sphingoglycolipid, phosphatidylcholine, phosphatidylglycerol, four unidentified lipids, glycophospholipid, phosphatidylethanolamine and diphosphatidylglycerol. The predominant respiratory quinone was Q-10 and the major polyamine was sym-homospermidine. On the basis of phenotypic, genotypic and phylogenetic evidences, strain LB-2T represents a novel species in the genus Sphingomonas, for which the name Sphingomonas caeni sp. nov. is proposed. The type strain is LB-2T (GDMCC 1.3630T = NBRC 115,102T).

Association between dietary intake of flavonoids and hyperuricemia: a cross-sectional study.

BACKGROUND: Previous research has demonstrated flavonoid intake was closely related to hyperuricemia. The purpose of this study was to examine whether flavonoid intake was associated with serum uric acid and hyperuricemia in U.S. adults. METHODS: The study sample consisted of 8,760 participants enrolled in the National Health and Nutrition Examination Survey (NHANES) from 2007 to 2010. Flavonoid consumption was measured using a two-day recall questionnaire on dietary intake. Hyperuricemia was defined based on the serum uric acid levels, determined as ≥ 7 mg/dL for males and ≥ 6 mg/dL for females. The study utilized multivariate linear regression to determine the correlation between flavonoid consumption and serum uric acid levels. Additionally, analyses involving multivariate logistic regression and restricted cubic splines (RCS) were conducted to evaluate the potential link between flavonoid consumption and hyperuricemia. All analyses were adjusted for possible confounding variables. RESULTS: The study revealed a negative correlation between serum uric acid levels and elevated levels of anthocyanidins and flavanones, with significant p-trends of < 0.001 and 0.02 respectively. The multivariate analysis showed that anthocyanidins and flavanones intake had a significant negative association with the risk of hyperuricemia, with p-trend value being < 0.001 and 0.01, respectively. Flavan-3-ols, flavonols, and all flavonoids exhibited a non-linear association with the incidence of hyperuricemia, with significant p-nonlinear values of < 0.001, 0.04, and 0.01 respectively. CONCLUSION: Our study demonstrated that individuals who follow a diet rich in anthocyanins and flavanones had significantly lower serum uric acid levels and a lower incidence of hyperuricemia.

Nivolumab treatment of relapsed/refractory Epstein-Barr virus-associated hemophagocytic lymphohistiocytosis in adults.

Epstein-Barr virus (EBV)-associated hemophagocytic lymphohistiocytosis (EBV-HLH) is a life-threatening hyperinflammatory syndrome triggered by EBV infection. It often becomes relapsed or refractory (r/r), given that etoposide-based regimens cannot effectively clear the virus. r/r EBV-HLH is invariably lethal in adults without allogeneic hematopoietic stem cell transplantation. Here, we performed a retrospective analysis of 7 r/r EBV-HLH patients who were treated with nivolumab on a compassionate-use basis at West China Hospital. All 7 patients tolerated the treatment and 6 responded to it. Five of them achieved and remained in clinical complete remission with a median follow-up of 16 months (range, 11.4-18.9 months). Importantly, both plasma and cellular EBV-DNAs were completely eradicated in 4 patients. Single-cell RNA-sequencing analysis showed that HLH syndrome was associated with hyperactive monocytes/macrophages and ineffective CD8 T cells with a defective activation program. Nivolumab treatment expanded programmed death protein-1-positive T cells and restored the expression of HLH-associated degranulation and costimulatory genes in CD8 T cells. Our data suggest that nivolumab, as a monotherapy, provides a potential cure for r/r EBV-HLH, most likely by restoring a defective anti-EBV response.

Proteome analysis guided genetic engineering of Corynebacterium glutamicum S9114 for tween 40-triggered improvement in L-ornithine production.

BACKGROUND: L-ornithine is a valuable amino acid with a wide range of applications in the pharmaceutical and food industries. However, the production of L-ornithine by fermentation cannot compete with other methods, because of the low titers produced with this technique. Development of fermentation techniques that result in a high yield of L-ornithine and efficient strategies for improving L-ornithine production are essential. RESULTS: This study demonstrates that tween 40, a surfactant promoter of the production of glutamate and arginine, improves L-ornithine production titers in engineered C. glutamicum S9114. The intracellular metabolism under tween 40 triggered fermentation conditions was explored using a quantitative proteomic approach, identifying 48 up-regulated and 132 down-regulated proteins when compared with the control. Numerous proteins were identified as membrane proteins or functional proteins involved in the biosynthesis of the cell wall. Modulation of those genes revealed that the overexpression of CgS9114_09558 and the deletion of CgS9114_13845, CgS9114_02593, and CgS9114_02058 improved the production of L-ornithine in the engineered strain of C. glutamicum Orn8. The final strain with all the exploratory metabolic engineering manipulations produced 25.46 g/L of L-ornithine, and a yield of 0.303 g L-ornithine per g glucose, which was 30.6% higher than that produced by the original strain (19.5 g/L). CONCLUSION: These results clearly demonstrate the positive effect of tween 40 addition on L-ornithine accumulation. Proteome analysis was performed to examine the impact of tween 40 addition on the physiological changes in C. glutamicum Orn8 and the results showed several promising modulation targets for developing L-ornithine-producing strains.

Role of the ClpX from Corynebacterium crenatum involved in stress responses and energy metabolism.

ClpX and ClpP are involved in many important functions, including stress responses and energy metabolism, in microorganisms. However, the ClpX and ClpP of microbes used in industrial scale have rarely been studied. Industrial bacterial fermentation experiences a variety of stresses, and energy metabolism is extremely important for industrial bacteria. Thus, the role played by the ClpX and ClpP of industrial bacteria in fermentation should be investigated. Most microorganisms have a single clpP gene, while Corynebacterium crenatum AS 1.542 possesses two clpPs. Herein, the clpX, clpP1, and clpP2 of C. crenatum were cloned, and its fusion protein was expressed and characterized. We also constructed clpX deletion mutant and complementation strain. Results indicate that ClpX serves an important function in thermal, pH, and ethanol stresses. It is also involved in NADPH synthesis and glucose consumption during fermentation.

Plasmonic ELISA based on DNA-directed gold nanoparticle growth for Cronobacter detection in powdered infant formula samples.

The traditional gold nanoparticle (AuNP) growth-based plasmonic ELISA (pELISA) strictly and directly controlled by reducing reagents can achieve high sensitivity, but it remains fragile toward the surrounding environment. This work developed a sandwich pELISA for Cronobacter detection in powdered infant formula samples by mediating AuNP growth through DNA. In this assay, DNA adsorbed on the surface of gold nanoseeds guided the anisotropic crystal growth with hydroxylamine as a reducing reagent, and the catalase-hydrogen peroxide (Cat-H2O2) system was introduced to bridge the DNA-directed AuNP growth and pELISA, as such DNA can be cleaved into fragments by the hydroxyl radical generated from oxidation of H2O2 through Fenton reagents. Under optimized conditions, the proposed pELISA can qualitatively detect Cronobacter species (Cronobacter muytjensii ATCC 51329) by the naked eye with a cut-off limit of 3 × 105 cfu/mL. This method also revealed a good linear range (3 × 102 to 3 × 107 cfu/mL) for quantitative detection of C. muytjensii ATCC 51329 with a limit of detection of 1.6 × 102 cfu/mL, which is approximately 162.5 times lower than that of horseradish peroxidase-based conventional ELISA (2.6 × 104 cfu/mL). By taking advantage of highly stable DNA-directed AuNP growth, the proposed method shows a good performance in powdered infant formula samples spiked with different concentrations of C. muytjensii ATCC 51329 with average recoveries ranging from 90.79 to 119.09% and coefficient of variation ranging from 4.24 to 9.55%. These values corresponded to an acceptable accuracy and precision for the proposed method. In brief, this work shows potential for screening other analytes in food safety, clinical diagnostics, and environmental monitoring.

Quantum bead-based fluorescence-linked immunosorbent assay for ultrasensitive detection of aflatoxin M1 in pasteurized milk, yogurt, and milk powder.

Herein, we reported a novel direct competitive fluorescence-linked immunosorbent assay (dcFLISA) for the ultrasensitive detection of aflatoxin M1 (AFM1) in pasteurized milk, yogurt, and milk powder using 150-nm quantum dot beads (QB) as the carrier of competing antigen. Large QB were applied to decrease the binding affinity of the competing antigen to antibody and enhance the fluorescent signal intensity. The aflatoxin B1 molecule was used as the surrogate of AFM1 to label with BSA on the surface of QB because of its 63% cross reaction to anti-AFM1 mAb. The binding affinity of the competing antigen to mAb was tuned by changing the labeled molar ratios of aflatoxin B1 to BSA. Through combining the advantages of QB as the carrier of the competing antigen, including low binding affinity to mAb and highly fluorescent signal output, the proposed dcFLISA exhibited an ultrahigh sensitivity for AFM1 detection, with a half-maximal inhibitory concentration of 3.15 pg/mL in 0.01 M phosphate-buffered saline solution (pH 7.4), which is substantially lower than that of the traditional horseradish peroxidase-based ELISA. The proposed method also exhibited very low detection limitations of 0.5, 0.6, and 0.72 pg/mL for real pasteurized milk, yogurt, and milk powder, respectively. These values are considerably below the maximum permissible level of the European Commission standard for AFM1 in dairy products. In summary, the proposed dcFLISA offers a novel strategy with an ultrahigh sensitivity for the routine monitoring of AFM1 in various dairy products.

[Fluorescence immunosorbent assay for quantitative detection of Listeria monocytogenes].

OBJECTIVE: Establishment of fuorescence immunosorbent assay for quantitative detection of Listeria monocytogenes. METHODS: The coupled mAbs named 10 E7 H6 and 10 A11 were screened from seven strains of anti-L. monocytogenes mAbs using a sandwich enzyme-linked immunosorbent assay(ELISA). The fluorescent immunoassay was established for L. monocytogenes detection by using biotinylated 10 A11 mAbs as detection antibody, 10 E7 H6 mAbs as capture antibody, and streptavidin-labeled fluorescent microspheres as detection probes, respectively. RESULTS: The optimum concentrations of capture and detection antibodies were 10 µg/mL and 5 µg/mL, respectively, and the optimum reaction pH was 7. 4. Under these conditions, the limit of detection of the proposed method for L. monocytogenes detection was 10~5 CFU/mL, which improved by two orders of magnitude compared to conventional ELISA; and it has a certain cross-reaction with several other Listeria but no significant cross-reactivity with other pathogenic bacteria. CONCLUSION: The method can be used for the detection of L. monocytogenes in pure culture solution, and can also be used for rapid immunological screening test of several other Listeria species in the genus Listeria.

Effective Removal of Tetracycline from Aqueous Solution by Organic Acid-Coated Magnetic Nanoparticles.

Self-assembled iron oxide nanocomposites are good magnetic nano-adsorbents that can be prepared using simple methods. Four types of organic acid-functionalised (oleic acid, undecenoic acid, caprylic acid or hexanoic acid) magnetic nanoparticles (MNPs) were synthesised through a one-pot chemisorption method for the removal of tetracycline (TC) from aqueous solution. The undecenoic acid-coated MNPs (UA-MNPs) exhibited the highest adsorption efficiency and can be easily retrieved with a low-gradient magnetic separator (0.4 Tesla) at pH 5.0 aqueous solution. The TC adsorption process on the UA-MNPs followed the Langmuir isotherm and the maximum adsorption capacities increased from 86.96 mg g(-1) to 222.2 mg g(-1) with the increase in temperature from 288 K to 318 K. The kinetics of adsorption fits pseudo-second-order model perfectly with a rate constant, 5.946 g mg(-1) min(-1) at 298 K. The positive values of the enthalpy (AH) and the negative value of the free energy (AG) indicated an endothermic and spontaneous adsorption process of TC on the UA-MNPs. Moreover, the UA-MNPs possessed excellent ability to adsorb the other three major types of TC antibiotics, including chlortetracycline, oxytetracycline and doxycycline.

Effect of Tween 40 and DtsR1 on L-arginine overproduction in Corynebacterium crenatum.

BACKGROUND: L-Glutamate is an important precursor in the L-arginine (L-Arg) biosynthetic pathway. Various methods, including polyoxyethylene sorbitan monopalmitate (Tween 40) addition and dtsR1 disruption, have been widely used to induce L-glutamate overproduction in Corynebacterium glutamicum. In this study, a novel strategy for L-Arg overproduction through Tween 40 trigger and ΔdtsR1 mutant were proposed in Corynebacterium crenatum. RESULTS: Corynebacterium crenatum mutant (CCM01) was selected as a host strain, whose argR was lethal via mutagenesis screening, the proB gene was knocked out, and argB was replaced by argB M4 (E19R, H26E, D311R, and D312R) to release L-Arg feedback resistance. After Tween 40 trigger in the logarithmic period, L-Arg production increased from 15.22 to 17.73 g/L in CCM01 strain. When NCgl1221 and dtsR1 disruption (CCM03), L-Arg production drastically increased to 27.45 g/L and then further to 29.97 g/L after Tween 40 trigger. Moreover, the specific activity of α-oxoglutarate dehydrogenase complex (ODHC) decreased, whereas the regeneration of NADP(+)/NADPH significantly increased after dtsR1 disruption and Tween 40 trigger. Results of real-time PCR showed that the transcriptional levels of odhA, sucB, and lpdA (encoding three subunits of the ODHC complex) were downregulated after Tween 40 trigger or dtsR1 disruption. By contrast, zwf transcription (encoding glucose-6-phosphate dehydrogenase) showed no significant difference among CCM01, CCM02 (ΔNCgl1221), and CCM03 (ΔNCgl1221ΔdtsR1) strains without Tween 40 trigger but evidently increased by 5.50 folds after Tween 40 trigger. CONCLUSION: A novel strategy for L-Arg overproduction by dtsR1 disruption and Tween 40 trigger in C. crenatum was reported. Tween 40 addition exhibited a bifunctional mechanism for L-Arg overproduction, including reduced ODHC activity and enhanced NADPH pools accumulation by downregulated dtsR1 expression and upregulated zwf expression, respectively.

[Effect of FarR on transcriptional levels of arginine biosynthetic genes in Corynebacterium crenatum AS 1.542 and its relationship with ArgR].

OBJECTIVE: The FarR protein was involved in the regulation of arginine biosynthetic pathway in corynebacterium, but the regulation mechanism of FarR protein and its relationship with the negative regulator ArgR have never been reported. In this work, we constructed two deletion mutants: C. crenatum delta farR and C. crenatum delta argR delta farR, and investigated the FarR function and its relationship with ArgR through the determination of transcriptional levels of arginine biosynthetic genes in four strains, including C. crenatum delta argR constructed in previous work. METHODS: We used marker-less knockout technology to construct C. crenatum delta farR and C. crenatum delta argR delta farR, and compared the transcriptional levels of the arginine biosynthetic genes in three mutant strains with those of the wild type strain using real-time fluorescence quantitative PCR. RESULTS: The results of RT-qPCR indicate that, in the absence of ArgR, FarR acted as a positive regulator. When farR gene was knockout alone, the transcriptional levels of arginine biosynthetic genes appeared up-regulated, down-regulated or no influence. CONCLUSION: FarR and ArgR are involved together in the regulation of arginine biosynthetic pathway of C. crenatum.

Moxibustion ameliorates osteoarthritis by regulating gut microbiota via impacting cAMP-related signaling pathway.

BACKGROUND: Osteoarthritis (OA) is a prevalent progressive disorder. Moxibustion has found widespread use in clinical practice for OA, while its underlying mechanism remains elusive. OBJECTIVE: To investigate whether moxibustion can ameliorate OA by influencing the metabolic processes in OA and to elucidate the specific metabolic mechanisms involved. METHODS: C57BL/6J WT mice were randomly assigned to one of three groups: the SHAM group, the ACLT group, and the ACLT+M group. In the ACLT+M group, mice underwent moxibustion treatment at acupoints Shenshu (BL23) and Zusanli (ST36) for a continuous period of 28 days, with each session lasting 20 min. We conducted a comprehensive analysis to assess the impact of moxibustion on OA, focusing on pathological changes, intestinal flora composition, and serum metabolites. RESULTS: Moxibustion treatment effectively mitigated OA-related pathological changes. Specifically, moxibustion treatment resulted in the amelioration of articular cartilage damage, synovial inflammation, subchondral bone sclerosis when compared to the ACLT group. Moreover, 16S rDNA sequencing analysis revealed that moxibustion treatment positively influenced the composition of the flora, making it more similar to that of the SHAM group. Notably, moxibustion treatment led to a reduction in the abundance of Ruminococcus and Proteobacteria in the intestine. In addition, non-targeted metabolomics analysis identified 254 significantly different metabolites between the groups. Based on KEGG pathway analysis and the observed impact of moxibustion on OA-related inflammation, moxibustion therapy is closely associated with the cAMP-related signaling pathway. CONCLUSION: Moxibustion can relieve OA by regulating intestinal flora and via impacting cAMP-related signaling pathway.

Copper Resistance Mechanism and Copper Response Genes in Corynebacterium crenatum.

Heavy metal resistance mechanisms and heavy metal response genes are crucial for microbial utilization in heavy metal remediation. Here, Corynebacterium crenatum was proven to possess good tolerance in resistance to copper. Then, the transcriptomic responses to copper stress were investigated, and the vital pathways and genes involved in copper resistance of C. crenatum were determined. Based on transcriptome analysis results, a total of nine significantly upregulated DEGs related to metal ion transport were selected for further study. Among them, GY20_RS0100790 and GY20_RS0110535 belong to transcription factors, and GY20_RS0110270, GY20_RS0100790, and GY20_RS0110545 belong to copper-binding peptides. The two transcription factors were studied for the function of regulatory gene expression. The three copper-binding peptides were displayed on the C. crenatum surface for a copper adsorption test. Furthermore, the nine related metal ion transport genes were deleted to investigate the effect on growth in copper stress. This investigation provided the basis for utilizing C. crenatum in copper bioremediation.

Comparison of different genetic testing modalities applied in paediatric patients with steroid-resistant nephrotic syndrome.

BACKGROUND: Steroid-resistant nephrotic syndrome (SRNS) are monogenic in some cases, however, there are still no clear guidelines on genetic testing in the clinical practice of SRNS in children. METHODS: Three hundred thirty-two children were diagnosed with SRNS, and all children underwent genetic testing, including gene panels and/or whole-exome/genome sequencing (WES/WGS), during treatment. We analysed the relationship between clinical manifestation and genotype, and compared different genetic testing methods' detection rates and prices. RESULTS: In this study, 30.12% (100/332) of children diagnosed with SRNS had monogenic causes of the disease. With 33.7% (122/332) of children achieving complete remission, 88.5% (108/122) received steroids combined with tacrolimus (TAC). In detectability, WES increased by 8.69% (4/46) on gene panel testing, while WGS increased by 4.27% (5/117) on WES, and WES was approximately 1/7 of the price of WGS for every further 1% increase in pathogenicity. CONCLUSIONS: We verified that steroids combined with TAC were the most effective option in paediatric SRNS. In detection efficiency, we found that WGS was the highest, followed by WES. The panel was the lowest, but the most cost-effective method when considering the economic-benefit ratio, and thus it should be recommended first in SRNS.

A genomic association study revealing subphenotypes of childhood steroid-sensitive nephrotic syndrome in a larger genomic sequencing cohort.

Dissecting the genetic components that contribute to the two main subphenotypes of steroid-sensitive nephrotic syndrome (SSNS) using genome-wide association studies (GWAS) strategy is important for understanding the disease. We conducted a multicenter cohort study (360 patients and 1835 controls) combined with a GWAS strategy to identify susceptibility variants associated with the following two subphenotypes of SSNS: steroid-sensitive nephrotic syndrome without relapse (SSNSWR, 181 patients) and steroid-dependent/frequent relapse nephrotic syndrome (SDNS/FRNS, 179 patients). The distribution of two single-nucleotide polymorphisms (SNPs) in ANKRD36 and ALPG was significant between SSNSWR and healthy controls, and that of two SNPs in GAD1 and HLA-DQA1 was significant between SDNS/FRNS and healthy controls. Interestingly, rs1047989 in HLA-DQA1 was a candidate locus for SDNS/FRNS but not for SSNSWR. No significant SNPs were observed between SSNSWR and SDNS/FRNS. Meanwhile, chromosome 2:171713702 in GAD1 was associated with a greater steroid dose (>0.75 mg/kg/d) upon relapse to first remission in patients with SDNS/FRNS (odds ratio = 3.14; 95% confidence interval, 0.97-9.87; P = 0.034). rs117014418 in APOL4 was significantly associated with a decrease in eGFR of greater than 20% compared with the baseline in SDNS/FRNS patients (P = 0.0001). Protein-protein intersection network construction suggested that HLA-DQA1 and HLA-DQB1 function together through GSDMA. Thus, SSNSWR belongs to non-HLA region-dependent nephropathy, and the HLA-DQA/DQB region is likely strongly associated with disease relapse, especially in SDNS/FRNS. The study provides a novel approach for the GWAS strategy of SSNS and contributes to our understanding of the pathological mechanisms of SSNSWR and SDNS/FRNS.