Super-enhancers conserved within placental mammals maintain stem cell pluripotency.

Despite pluripotent stem cells sharing key transcription factors, their maintenance involves distinct genetic inputs. Emerging evidence suggests that super-enhancers (SEs) can function as master regulatory hubs to control cell identity and pluripotency in humans and mice. However, whether pluripotency-associated SEs share an evolutionary origin in mammals remains elusive. Here, we performed comprehensive comparative epigenomic and transcription factor binding analyses among pigs, humans, and mice to identify pluripotency-associated SEs. Like typical enhancers, SEs displayed rapid evolution in mammals. We showed that BRD4 is an essential and conserved activator for mammalian pluripotency-associated SEs. Comparative motif enrichment analysis revealed 30 shared transcription factor binding motifs among the three species. The majority of transcriptional factors that bind to identified motifs are known regulators associated with pluripotency. Further, we discovered three pluripotency-associated SEs (SE-SOX2, SE-PIM1, and SE-FGFR1) that displayed remarkable conservation in placental mammals and were sufficient to drive reporter gene expression in a pluripotency-dependent manner. Disruption of these conserved SEs through the CRISPR-Cas9 approach severely impaired stem cell pluripotency. Our study provides insights into the understanding of conserved regulatory mechanisms underlying the maintenance of pluripotency as well as species-specific modulation of the pluripotency-associated regulatory networks in mammals.

FifBase: a comprehensive fertility-associated indicators factor database for domestic animals.

Fertility refers to the ability of animals to maintain reproductive function and give birth to offspring, which is an important indicator to measure the productivity of animals. Fertility is affected by many factors, among which environmental factors may also play key roles. During the past years, substantial research studies have been conducted to detect the factors related to fecundity, including genetic factors and environmental factors. However, the identified genes associated with fertility from countless previous studies are randomly dispersed in the literature, whereas some other novel fertility-related genes are needed to detect from omics-based datasets. Here, we constructed a fertility index factor database FifBase based on manually curated published literature and RNA-Seq datasets. During the construction of the literature group, we obtained 3301 articles related to fecundity for 13 species from PubMed, involving 2823 genes, which are related to 75 fecundity indicators or 47 environmental factors. Eventually, 1558 genes associated with fertility were filtered in 10 species, of which 1088 and 470 were from RNA-Seq datasets and text mining data, respectively, involving 2910 fertility-gene pairs and 58 fertility-environmental factors. All these data were cataloged into FifBase (http://www.nwsuaflmz.com/FifBase/), where the fertility-related factor information, including gene annotation and environmental factors, can be browsed, retrieved and downloaded with the user-friendly interface.

Direct and indirect photodegradation of bisphenol A in the presence of natural water components.

The impacts and mechanisms of natural water constituents, such as humic acid (HA), nitrates, iron and chloride ions, to the photodegradation of bisphenol A (BPA) were investigated in aqueous media under UV light irradiation. Due to the contributions of ·OH, 1O2, O2- and BPA* to BPA photodegradation in pure water in 13.4, 7.7, 22.9 and 47.9%, respectively, BPA was attenuated through the reaction pathway of direct photodegradation more than self-sensitized photodegradation. About indirect photodegradation, BPA photolysis through inhibitory effect from HA was mainly by light screening effect and quenching effect was insignificant. NO- 3 and NO- 2 both showed inhibitory effect but due to different reactive oxidization species (ROS). The photodegradation of BPA was significantly enhanced by the addition of iron from the formation of ·OH and H2O2, due to iron-assisted indirect photolysis for the degradation process. A dual effect of chloride depending on the different concentration levels involved quenching and promotion effect on reactive photo-induced species (RPS). A simple linear model revealed that BPA photodegradation was significantly impacted by the interaction of the above factors. In natural water, the decreased photolytic rate of BPA was mainly attributed to triple-excited dissolved organic matter (3DOM*), indicating that indirect photolysis was the primary transformation pathway of BPA. The detected photolysis products, such as nitrate and chlorinated products, suggest that there might be potential ecological risk of BPA photodegradation.

The Association of Low Hemoglobin Levels with IgA Nephropathy Progression: A Two-Center Cohort Study of 1,828 Cases.

AIM: To investigate the relationship between hemoglobin levels and the progression of IgA nephropathy (IgAN). METHODS: In a two-center cohort of 1,828 cases with biopsy-proven IgAN, we examined the association of hemoglobin levels with the primary outcome of a composite of all-cause mortality or kidney failure defined as a 40% decline in eGFR, or ESKD (defined as eGFR <15 mL/min/1.73 m2 or need for kidney replacement therapy including hemodialysis, peritoneal dialysis, or kidney transplantation), or the outcome of kidney failure, assessed using Cox and logistic regression models, respectively, with adjustment for confounders. RESULTS: At baseline, mean age, eGFR, and hemoglobin levels were 33.75 ± 11.03 years, 99.70 ± 30.40 mL/min/1.73 m2, and 123.47 ± 18.36 g/L, respectively. During a median of approximately 7-year follow-up, 183 cases reached the composite outcome. After adjustment for demographic and IgAN-specific covariates and treatments, a lower quartile of hemoglobin was nonlinearly associated with an increased risk of the primary outcome or kidney failure in the Cox proportional hazards models (primary outcome: HR for quartile 3 vs. 4, 1.37; 95% CI, 0.83-2.25; HR for quartile 2 vs. 4, 1.18; 95% CI, 0.68-2.07; HR for quartile 1 vs. 4, 1.91; 95% CI, 1.15-3.17; kidney failure: HR for quartile 3 vs. 4, 1.39; 95% CI, 0.84-2.31; HR for quartile 2 vs. 4, 1.20; 95% CI, 0.68-2.11; HR for quartile 1 vs. 4, 1.83; 95% CI, 1.09-3.07) in the fully adjusted model. Then, hemoglobin levels were transformed to a binary variable for fitting the model according to the criteria for anemia of 110 g/L in the women and 120 g/L in men in China. The participants in the anemia group had an increased risk of developing outcomes compared with the nonanemia group in both genders (primary outcome: male: HR, 1.64; 95% CI, 1.01-2.68; female: HR, 1.68; 95% CI, 1.02-2.76; kidney failure: male: HR, 1.60; 95% CI, 0.97-2.64; female: HR, 1.58; 95% CI, 0.95-2.61) in the fully adjusted model. CONCLUSIONS: A low level of hemoglobin was nonlinearly associated with IgAN progression. The anemic IgAN patients presented a higher risk of developing poor outcomes compared with the nonanemic patients.

Association of weight-adjusted waist index and diabetic kidney disease in type 2 diabetes mellitus.

Objective: The aim of this study was to investigate the relationship between weight-adjusted-waist index (WWI) and diabetic kidney disease in individuals afflicted with type 2 diabetes. Methods: Comprehensive data were ascertained from the National Health and Nutrition Examination Survey in 2013-March 2020. Weighted univariate, multivariate logistic regression models, subgroup analyses and tests for interaction were performed. Additionally, we employed smooth curve fitting to assess linear correlations and the threshold effects were calculated by applying a binary linear regression model. Breakpoints are identified by a model with maximum likelihood ratio and a two-step recursive approach. Receiver operating characteristic curve (ROC) along with the area under the curve (AUC) value predict the capability of WWI and body mass index for diabetic kidney disease. Results: A total of 10,661 individuals diagnosed with type 2 diabetes were included, and the overall prevalence of diabetic kidney disease was 20.74%. WWI exhibited a positive correlation with the likelihood of diabetic kidney disease in type 2 diabetes patients (OR: 1.17, 95% CI: 1.03-1.33). The results of subgroup analysis showed significant interaction for gender (P < 0.05). Among female patients, U-shaped correlations were observed with a breakpoint at 11.48. Additionally, weight-adjusted waist index (AUC = 0.664) proved to be a more effective predictor of diabetic kidney disease compared to body mass index (AUC = 0.555). Conclusion: In patients with type 2 diabetes, increased weight-adjusted-waist index is implicated with an increased risk of diabetic kidney disease. WWI can be used as a new anthropometric index to predict diabetic kidney disease, and its predictive ability is stronger than body mass index.

Study on the relationship between lipoprotein (a) and diabetic kidney disease.

OBJECTIVE: Little is currently known about the role of lipid metabolism in diabetic kidney disease (DKD), warranting further study. The present study sought to investigate the correlation between lipid metabolism and renal function as well as renal pathological grade/score in DKD patients. METHODS: A total of 224 patients diagnosed with DKD by pathological examination were retrospectively analyzed, of which 74 patients were further evaluated by DKD pathological grade/score. ANOVA was used to investigate serum lipoprotein (a) [Lp (a)] levels in DKD patients with different chronic kidney disease (CKD) stages. Spearman correlation analysis was used to evaluate the relationship between Lp (a) and renal function-related indicators. The DKD pathological grade/score was also evaluated with this method. The receiver operating characteristic (ROC) curve was used to analyze the value of Lp (a) in assessing renal function and pathological changes. RESULTS: There were significant differences in Lp (a) levels among different CKD stages (H = 17.063, p = 0.002) and glomerular grades (H = 12.965, p = 0.005). Lp (a) levels correlated with serum creatinine (p = 0.000), blood urea nitrogen (p = 0.000), estimated glomerular filtration rate (p = 0.000), 24-h proteinuria (24hUPro, p = 0.000), urine microalbumin (p = 0.000), urine albumin creatinine ratio (p = 0.000), glomerular basement membrane thickness (p = 0.003), and glomerular grade (p = 0.039). ROC curve demonstrated good performance of Lp (a) as an indicator to assess CKD stage 4-5 (AUC = 0.684, p = 0.000), 24hUPro > 3.5 g (AUC = 0.720, p = 0.000), and glomerular grade III-IV (AUC = 0.695, p = 0.012). CONCLUSIONS: Elevated levels of Lp (a) are associated with decreased GFR, increased proteinuria, and renal pathological progression, suggesting they could be used to monitor changes in DKD patients.

Association between weight-adjusted-waist index and the risk of hyperuricemia in adults: a population-based investigation.

Objective: This investigation sought to elucidate the potential correlation between a recently characterized adiposity metric, termed the Weight-Adjusted-Waist Index (WWI) and hyperuricemia. Methods: A cross-sectional design was employed in this study, featuring both hyperuricemic and non-hyperuricemic subjects with complete WWI data, sourced from the National Health and Nutrition Examination Survey (NHANES) spanning 2017 to March 2020. WWI was calculated utilizing the formula which involves the division of waist circumference (WC) by the square root of the body weight. In order to determine the relationship between WWI and hyperuricemia, both univariate and multivariate logistic regression models, appropriately weighted, were employed in the analysis. The linearity of relationships was validated using smooth curve fitting. Additionally, subgroup evaluations and interaction assessments were conducted. Results: The study sample comprised 7437 subjects, yielding a hyperuricemia prevalence of 18.22%. Stratifying WWI into tertiles, a progressive rise in hyperuricemia prevalence was evident with increasing WWI (Tertile 1: 11.62%, Tertile 2: 17.91%, Tertile 3: 25.13%). The odds ratio (OR) demonstrated that individuals within the highest WWI tertile were significantly more prone to hyperuricemia than those in the lowest tertile (OR = 2.41, 95% CI: 1.88-3.08). Conclusion: This study provides evidence that an elevated WWI is correlated with an increased risk of hyperuricemia in the adult population of the United States. These results suggest that WWI may serve as a viable anthropometric indicator for predicting hyperuricemia.

SCM is potential resource for non-invasive preimplantation genetic testing based on human embryos single-cell sequencing.

The ongoing development of assisted reproductive technologies has provided hope to individuals struggling with infertility, promising the potential for a healthy pregnancy. One significant innovation in field of pre-implantation genetic screening (PGS) requires the biopsy of embryos or oocytes, which has potential implications for the health and development of the resultant offspring. Therefore, a non-invasive approach to preimplantation genetic screening is highly sought after. The clinical application of non-invasive preimplantation genetic testing (ni-PGT) is currently limited, with its sensitivity and specificity requiring further investigation. In this study, we used 218 human embryos for single-cell whole genome amplification (WGA), along with ni-PGT of blastocoele fluid (BF) and spent culture medium (SCM). Whole blastocyst (WB), trophectoderm biopsy (TB), and inner cell mass (ICM) from embryo biopsies were used as controls to track genomic signal alterations. Our results showed that the overall genome similarity between SCM and ICM was higher than that of BF. Apart from the Y chromosome, both SCM and ICM demonstrated numerous variant sites across other chromosomes.Further categorization of gene variants in these two sample types revealed that missense variants were the most prevalent, single nucleotide polymorphisms were more common than insertions or deletions, and C > T was the dominant single nucleotide variants in both ICM and SCM. Lastly, we found that the mutant genes in SCM and ICM had different biological functions and pathways. This study indicates that SCM provides a more effective source of embryonic DNA for preimplantation genetic screening, offering a novel reference point for genetic screening research.

Single-cell transcriptome analysis of Bisphenol A exposure reveals the key roles of the testicular microenvironment in male reproduction.

Testicular development during juvenile is crucial for subsequent male reproductive function. However, it remains poorly understood about the contribution of the testis microenvironment to human germ cell maturation. Therefore, we systematically analyzed scRNA-seq transcriptome and found the dramatic changes in cell-type composition in human testis during puberty. Then we constructed cell-cell communication networks between germ cells and somatic cells in the juvenile testis, which may be achieved via immune-related pathways. Our results showed that maturation-promoting factors are the switches of the Sertoli cells that drive sperm maturation. Furthermore, we found that Bisphenol A(BPA) enhanced the maturation and growth of germ cells through the Sertoli cell's secretory protein. Finally, our results indicate Bisphenol A would lead to the dysregulation of secreted protein expression in Sertoli cells during spermatogenesis, which in turn has direct cytotoxicity to Sertoli cells. Bisphenol A is one of the underlying causes of non-obstructive azoospermia (NOA). In summary, our results reveal the reproductive toxicity and molecular mechanism of Bisphenol A in Sertoli cells and male reproduction. Provide a reference for the toxicity of Bisphenol A to human reproduction.

Prognostic evaluation model of diabetic nephropathy patients.

BACKGROUND: Diabetic nephropathy (DN) affects about 40% of diabetes mellitus (DM) patients and is the leading cause of chronic kidney disease (CKD) and end-stage renal disease (ESRD) globally, especially in advanced countries. We aimed to explore the risk factors affecting the prognosis of DN, and to establish a prognostic evaluation line map. METHODS: We analyzed 471 cases of DN from December 2011 to April 2020, and extracted the basic clinical factors, including gender, age, and history of diabetes. Analysis included that of associations between DN and hypertension, creatinine (CR), body mass index (BMI), and fundus lesions. Statistical analysis was performed using R software and the related R package. The above clinical factors were analyzed by both single- and multiple-factor Cox regression. The participants were divided into two groups, including a high risk and a low risk group. A Kaplan-Meier curve was drawn for survival analysis of the high and low risk groups, and the log-rank method was used for statistical testing. A receiver operating characteristic (ROC) curve was drawn with the area under the curve (AUC) calculated to evaluate the predictive effectiveness of the line map. RESULTS: This study initially included 471 patients; however, 33 patients (7.0%) were lost to follow-up due to inaccessibility. A total of 93 cases (21.2%) died during the follow-up. The 3-year and 5-year renal survival rates were 74.5% and 22.6%, respectively. Single factor Cox analysis showed that the course of diabetes, fundus lesions, BMI, and grade of hypertension were risk factors for renal survival, and had adverse effects on prognosis (P<0.05). Multivariate Cox regression analysis showed that BMI and grade of hypertension were independent risk factors for survival of DKD, and had adverse effects on prognosis (P<0.05). Survival analysis showed that low risk group participants had significantly better survival rates than high risk group participants (P<0.05). The AUC was 0.742, which meant that the line map could accurately predict the survival rate of DN patients. CONCLUSIONS: The influence of risk factors on prognosis can be accurately evaluated by line diagram which can provide a basis for clinical decision making.

TET2 mediated demethylation is involved in the protective effect of triptolide on podocytes.

The epithelial-mesenchymal transition (EMT) is usually considered the central mechanism of podocyte injury that eventually leads to proteinuria. We used an in vitro TGF-ß1 induced podocyte EMT model and an in vivo rat focal segmental glomerulosclerosis (FSGS) model to uncover the mechanism underlying the protective effect of triptolide (TP) on podocytes. We found that TP could reverse the podocyte EMT process and upregulate the expression of TET2 in the TGF-ß1-induced podocyte injury model. Bisulfite amplicon sequencing (BSAS) showed TP could alter the methylation status at some specific sites of the medium CpG density region in the promoters of NEPH1 and nephrin, two main markers of the podocyte slit diaphragm. Knockdown of TET2 with shRNA lentivirus (Lv) leads to high methylation of the promoters of NEPH1 and nephrin such that their expression can not return to normal levels, even after treatment with TP. In vivo, we found that TP could protect against podocyte injury in the FSGS rat and increase TET2 expression. These results suggested TET2-mediated DNA demethylation may be partly involved in podocyte injury. We believe these findings can help uncover a novel molecular mechanism of TP in alleviating podocyte-associated glomerular diseases.

Anti-apoptosis mechanism of triptolide based on network pharmacology in focal segmental glomerulosclerosis rats.

Triptolide (TPL), the active component of Tripterygium wilfordii, exhibits anti-cancer and antioxidant functions. We aimed to explore the anti-apoptosis mechanism of TPL based on network pharmacology and in vivo and in vitro research validation using a rat model of focal segmental glomerulosclerosis (FSGS). The chemical structures and pharmacological activities of the compounds reported in T. wilfordii were determined and used to perform the network pharmacology analysis. The Traditional Chinese Medicine Systems Pharmacology Database (TCMSP) was then used to identify the network targets for 16 compounds from Tripterygium wilfordii. Our results showed that 47 overlapping genes obtained from the GeneCards and OMIM databases were involved in the occurrence and development of FSGS and used to construct the protein-protein interaction (PPI) network using the STRING database. Hub genes were identified via the MCODE plug-in of the Cytoscape software. IL4 was the target gene of TPL in FSGS and was mainly enriched in the cell apoptosis term and p53 signaling pathway, according to Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses. TPL inhibited FSGS-induced cell apoptosis in rats and regulated IL4, nephrin, podocin, and p53 protein levels via using CCK8, TUNEL, and Western blot assays. The effects of IL4 overexpression, including inhibition of cell viability and promotion of apoptosis, were reversed by TPL. TPL treatment increased the expression of nephrin and podocin and decreased p53 expression in rat podocytes. In conclusion, TPL inhibited podocyte apoptosis by targeting IL4 to alleviate kidney injury in FSGS rats.

Jixuecao (Herba Centellae Asiaticae) alleviates mesangial cell proliferation in IgA nephropathy by inducing mitofusin 2 expression.

OBJECTIVE: To investigate the effect of mitofusin 2 (Mfn2) and its downstream signaling pathway on glomerular mesangial cells (GMCs) proliferation in IgA nephropathy (IgAN), as well as the mechanism of action of Jixuecao (Herba Centellae Asiaticae, HCA) in the treatment of IgAN. METHODS: Adenovirus-mediated Mfn2 gene transfection and Mfn2 expression were analyzed by real-time polymerase chain reaction (PCR) and Western blotting. IgA1 induced the proliferation of GMCs, which were then treated with HCA. Cell proliferation was detected with cell counting kit-8 (CCK-8), and Mfn2 expression was analyzed by real-time PCR and western blotting. An IgAN animal model was also established and treated with HCA. GMCs proliferation was detected by hematoxylin-eosin staining, mitochondrial structure was analyzed by electron microscopy, mitochondrial function was determined by the Clark oxygen electrode method, and the expression of Mfn2, Phospho-extracellular regulated protein kinases1/2 (P-ERK1/2), Cyclin-dependent kinase 2 (CDK2), Phospho-p27 (p-p27), and cyclin A was analyzed by Western blotting. RESULTS: In vitro, HCA inhibited GMCs in a concentration-dependent manner in association with the upregulation of Mfn2 expression. The overexpression of Mfn2 inhibited IgA1-induced GMCs proliferation and elevated the effect of HCA. In vivo, treatment with HCA could alleviate albuminuria and creatinine and GMCs proliferation. These effects were related to the upregulation of Mfn2, p-p27 and inhibition of p-ERK1/2, CDK2, and cyclinA. Mitochondrial swelling, vacuolar degeneration, and reduction of respiratory control rate were identified in IgAN, but HCA could improve the mitochondrial structure and function. CONCLUSION: HCA inhibited GMCs proliferation via the upregulation Mfn2 and the inhibition of Ras-Raf-ERK/MAPK. We revealed that changes of mitochondrial structure and function are associated with IgAN, but that HCA can improve these mitochondrial features.

Synthetic self-assembled homogeneous network hydrogels with high mechanical and recoverable properties for tissue replacement.

Development of hydrogels with high mechanical and recoverable properties under physiological conditions is of great importance for broadening and improving their potential applications in load-bearing artificial soft tissues. Inspired by the self-assembly of chemical entities, homogeneous network hydrogels, which contain over 90 wt% water, were synthesized via covalent cross-linking of poly(vinyl alcohol) (PVA) and poly(vinyl pyrrolidone) (PVP) triggered by microwave-assisted treatment. A structurally homogeneous network results in an evenly distributed stress that endures high strains with minimal energy dissipation, which enable the hydrogels to withstand up to 1.16 MPa of tensile stress, over seven-fold stretch length with negligible hysteresis, and sustain cyclic compression following high amplitude deformation. It is of importance for tissue replacement that the hydrogels retain these excellent properties under physiological conditions.