TEAD2 initiates ground-state pluripotency by mediating chromatin looping

The transition of mouse embryonic stem cells (ESCs) between serum/LIF and 2i(MEK and GSK3 kinase inhibitor)/LIF culture conditions serves as a valuable model for exploring the mechanisms underlying ground and confused pluripotent states. Regulatory networks comprising core and ancillary pluripotency factors drive the gene expression programs defining stable naïve pluripotency. In our study, we systematically screened factors essential for ESC pluripotency, identifying TEAD2 as an ancillary factor maintaining ground-state pluripotency in 2i/LIF ESCs and facilitating the transition from serum/LIF to 2i/LIF ESCs. TEAD2 exhibits increased binding to chromatin in 2i/LIF ESCs, targeting active chromatin regions to regulate the expression of 2i-specific genes. In addition, TEAD2 facilitates the expression of 2i-specific genes by mediating enhancer-promoter interactions during the serum/LIF to 2i/LIF transition. Notably, deletion of Tead2 results in reduction of a specific set of enhancer-promoter interactions without significantly affecting binding of chromatin architecture proteins, CCCTC-binding factor (CTCF), and Yin Yang 1 (YY1). In summary, our findings highlight a novel prominent role of TEAD2 in orchestrating higher-order chromatin structures of 2i-specific genes to sustain ground-state pluripotency.

Effects of particulate matter exposure on the risk of type 2 diabetes: a Mendelian randomization study

OBJECTIVE

The impact of particulate matter (PM) on the risk of type 2 diabetes (T2D) remains inconclusive. The purpose of this study was to assess the causal relationship between PM and T2D using Mendelian randomization (MR) analysis.

MATERIALS AND METHODS

Single nucleotide polymorphisms (SNPs) for PM2.5, PM10, and T2D were obtained from the UK Biobank and FinnGen datasets. Inverse variance weighted, MR-Egger, and weighted median were utilized to examine the causal relationship between exposure and outcome. MR-Egger intercept analysis, Cochran's Q test, and leave-one-out sensitivity analysis were used to assess horizontal pleiotropy, heterogeneity, and robustness of the results, respectively.

RESULTS

The MR analysis revealed a significant association between PM2.5 and increased risk of T2D (OR: 1.159, 95% CI: 1.003 to 1.339, p = 0.045), while no significant association was found between PM10 and T2D risk (OR: 1.031, 95% CI: 0.788 to 1.350, p = 0.822). MR-Egger intercept analysis and Cochran's Q test indicated no evidence of horizontal pleiotropy or heterogeneity in these results. Sensitivity analysis demonstrated the robustness of the results.

CONCLUSIONS

This MR analysis suggests that PM2.5, rather than PM10, is associated with an increased risk of T2D. The use of air purifiers and anti-smog masks may potentially help reduce the risk of T2D. Further research is needed to elucidate the specific effects and underlying mechanisms of PM2.5 and PM10 on T2D.

A Mendelian randomization study of the effect of selenium on autoimmune thyroid disease

OBJECTIVE

The impact of selenium on autoimmune thyroid disease (AITD) is a subject of ongoing debate. This study aimed to analyze the causal correlations of selenium with autoimmune thyroiditis (AIT), autoimmune hyperthyroidism (AIH), and Graves' disease (GD) by Mendelian randomization (MR).

MATERIALS AND METHODS

Single nucleotide polymorphisms related to selenium, AIT, AIH, and GD were sourced from the IEU Open GWAS project and FinnGen. Exposure-outcome causality was assessed using inverse variance weighted, MR-Egger, and weighted median. Horizontal pleiotropy was examined using the MR-Egger intercept, heterogeneity was evaluated with Cochran's Q test, and the robustness of the results was confirmed via leave-one-out sensitivity analysis.

RESULTS

The MR analysis revealed that selenium did not exhibit a causal relationship with AIT (OR 0.993, 95% CI 0.786 to 1.108, p=0.432), AIH (OR 1.066, 95% CI 0.976 to 1.164, p=0.154), or GD (OR 1.052, 95% CI 0.984 to 1.126, p=0.138). Moreover, the MR-Egger intercept and Cochran's Q test demonstrated the absence of horizontal pleiotropy or heterogeneity in these results (p>0.05). Sensitivity analysis affirmed the robustness of these results.

CONCLUSIONS

This MR analysis concluded that selenium was not linked to AIT, AIH, or GD risk. Therefore, indiscriminate selenium supplementation is not advisable for AITD patients without concurrent selenium deficiency.

Is polyethylene glycol loxenatide 100 μg the preferred glucagon-like peptide-1 receptor agonist for type 2 diabetes mellitus? A meta-analysis and trial sequential analysis

OBJECTIVE

This study aimed to systematically evaluate the efficacy, safety and optimal dose of polyethylene glycol loxenatide (PEX168) for treating type 2 diabetes mellitus (T2DM).

MATERIALS AND METHODS

Clinical trials of PEX168 for T2DM were identified in 8 databases, with a build time limit of January 2023. Included studies were subjected to meta-analysis and trial sequential analysis (TSA).

RESULTS

On the efficacy endpoint, the meta-analysis showed that PEX168 100 μg significantly reduced 0.86% glycated hemoglobin type A1c (HbA1c) (MD -0.86, 95% CI -1.02 - -0.70,  p<0.00001), 1.11 mmol/L fasting plasma glucose (FPG) (MD -1.11, 95% CI -1.49 - -0.74, p<0.00001) and 1.91 mmol/L 2h postprandial glucose (PPG) (MD -1.91, 95% CI -3.35 - -0.46, p=0.01) compared with placebo. The TSA showed that all these benefits were conclusive. On safety endpoints, total adverse events (AEs), gastrointestinal (GI) AEs, serious AEs, and hypoglycemia were comparable to placebo for PEX168 100 μg (p>0.05). In the dose comparison, the HbA1c, FPG, and 2h PPG of PEX168 200 μg were comparable to 100 μg (p>0.05), while GI AEs were significantly higher than 100 μg (RR=2.84, 95% CI 1.64-4.93,  p=0.0002).

CONCLUSIONS

PEX168 100 μg can significantly lower blood glucose and does not increase the risk of total AEs, GI AEs, and hypoglycemia, which may be a preferred glucagon-like peptide-1 receptor agonist for type 2 diabetes mellitus.

Functional dissection of PRC1 subunits RYBP and YAF2 during neural differentiation of embryonic stem cells

Polycomb repressive complex 1 (PRC1) comprises two different complexes: CBX-containing canonical PRC1 (cPRC1) and RYBP/YAF2-containing variant PRC1 (vPRC1). RYBP-vPRC1 or YAF2-vPRC1 catalyzes H2AK119ub through a positive-feedback model; however, whether RYBP and YAF2 have different regulatory functions is still unclear. Here, we show that the expression of RYBP and YAF2 decreases and increases, respectively, during neural differentiation of embryonic stem cells (ESCs). Rybp knockout impairs neural differentiation by activating Wnt signaling and derepressing nonneuroectoderm-associated genes. However, Yaf2 knockout promotes neural differentiation and leads to redistribution of RYBP binding, increases enrichment of RYBP and H2AK119ub on the RYBP-YAF2 cotargeted genes, and prevents ectopic derepression of nonneuroectoderm-associated genes in neural-differentiated cells. Taken together, this study reveals that RYBP and YAF2 function differentially in regulating mESC neural differentiation.

Bibliometric analysis of intestinal microbiota in diabetic nephropathy

OBJECTIVE

The purpose of this study is to use bibliometrics to explore the research overview and research hotspots.

MATERIALS AND METHODS

The relevant literature on intestinal flora and diabetic nephropathy in the Web of Science Core Collection was sorted out, and VOSviewer, CiteSpace, Scimago Graphica and other software were used to conduct data visualization analysis on the number of publications, countries, institutions, journals, authors, keywords and citations.

RESULTS

A total of 124 relevant literatures were included. From 2015 to 2022, the number of published papers increased every year. The countries, institutions and journals that published the most articles in this field are China, Isfahan University Medical Science and Frontiers in Pharmacology. Liu Bicheng and Mirlohi Maryam are the authors with the most published articles in this field. The main keywords of research in this field are obesity, inflammation, oxidative stress, indoxyl sulfate, short-chain fatty acids (SCFAs) and Chinese herbal medicine.

CONCLUSIONS

This is the first bibliometric analysis of diabetic nephropathy and gut microbiota, reporting hot spots and emerging trends. Obesity, inflammation, oxidative stress, indoxyl sulfate, SCFAs and Chinese herbal medicine are the main keywords of current research, and SCFAs and Chinese herbal medicine may be the hotspots of future research.

Efficacy and safety of iguratimod combined with methylprednisolone for primary Sjögren's syndrome: a meta-analysis and trial sequential analysis

OBJECTIVE

The purpose of this study is to evaluate the combination of iguratimod (IGU) and methylprednisolone (MP) for the efficacy and safety of primary Sjögren's syndrome (pSS) by a meta-analysis and a trial sequential analysis (TSA).

MATERIALS AND METHODS

Clinical studies of IGU combined with MP for pSS were searched through eight databases. Revman 5.3 and TSA 0.9.5.10 Beta were used for the meta-analysis and TSA.

RESULTS

In terms of efficacy endpoints, compared with "HCQ+MP" group, "IGU+MP" group decreased erythrocyte sedimentation rate (ESR) [mean difference (MD)=-5.15, 95% confidence interval (CI)=(-7.37, -2.93), p<0.0001], immunoglobulin G (IgG) [MD=-3.38, 95% CI=(-4.13, -2.64), p<0.00001], immunoglobulin M (IgM) [MD=-0.64, 95% CI=(-1.19, -0.09), p=0.02], Immunoglobulin A (IgA) [MD=-1.16, 95% CI=(-1.92, -0.39), p=0.003], EULAR Sjögren's Syndrome Disease Activity Index (ESSDAI) [MD=-1.62, 95% CI=(-2.07, -1.17), p<0.0001], EULAR Sjögren's Syndrome Patient Reported Index (ESSPRI) [MD=-2.07, 95% CI=(-2.54, -1.59), p<0.0001], increase platelet (PLT) [MD=13.21, 95% CI=(9.77,16.65), p<0.00001], and improve Schirmer I test (SIT) [MD=1.86, 95% CI=(1.40, 2.32), p<0.0001]. TSA presented that these benefits observed with the current information volume were all conclusive, except for IgM. In terms of safety endpoints, the total adverse event rates (AEs), leucopenia, gastrointestinal (GI) AEs, skin diseases, and liver dysfunction of the "IGU+MP" group and the "HCQ+MP" group were comparable. And TSA indicated that the results need to be confirmed by additional studies. Harbord regression showed no publication bias (p=0.986).

CONCLUSIONS

IGU combined with MP effectively attenuates autoimmune responses (IgG, IgM, IgA), reduces clinical symptoms and disease activity (ESR, PLT, ESSPRI, ESSDAI), and improves the exocrine gland functional status (SIT) in patients with pSS. IGU combined with MP does not increase the risk of adverse events, which means that IGU combined with MP may be a safe and effective strategy for the treatment of pSS and has value for further research exploration.

Is tirzepatide 15 mg the preferred treatment strategy for type 2 diabetes? A meta-analysis and trial-sequence-analysis

OBJECTIVE

The study aims to evaluate tirzepatide's efficacy and safety in treating type 2 diabetes by meta-analysis and trial-sequential-analysis (TSA).

MATERIALS AND METHODS

Eight databases were searched for clinical trials on tirzepatide for type 2 diabetes with a time limit of November 2022. Revman5.3 and TSA 0.9.5.10 Beta were selected for meta-analysis and TSA.

RESULTS

Compared with placebo, the meta-analysis demonstrated that tirzepatide 15 mg reduced hemoglobin-type-A1C (HbA1c) (p<0.00001), fasting-serum-glucose (FSG) (p<0.00001), and weight (p<0.00001). Compared with insulin, tirzepatide 15 mg reduced HbA1c (p<0.00001), FSG (p<0.00007), and weight (p<0.00001). Compared with glucagon-like-peptide-1 receptor-agonist (GLP-1 RA), tirzepatide 15 mg reduced HbA1c (p=0.00004), FSG (p=0.001), and weight (p<0.00001). In safety endpoints, the meta-analysis revealed that adverse events (AEs) of placebo, insulin and GLP-1 RA were comparable to tirzepatide 15 mg. The total AEs (p=0.02) and gastrointestinal (GI) AEs (p=0.03) were higher in tirzepatide 15 mg than in the placebo, while hypoglycemia (<54 mg/dl) was comparable. The major adverse cardiovascular events-4 (MACE-4) (p=0.03) and hypoglycemia (<54 mg/dl) (p<0.00001) of tirzepatide 15 mg were lower when compared to insulin, while total AEs (p=0.03) were increased. Compared with GLP-1 RA, tirzepatide 15 mg was comparable in safety endpoints in total AEs and GI AEs, while hypoglycemia (<54 mg/dl) (p=0.04) was higher. TSA indicated that HgA1c, FSG, and weight benefits were conclusive. In safety endpoints, only MACE-4 and hypoglycemia (<54 mg/dl) of Tirzepatide 15 mg vs. Insulin were conclusive. Harbord regression of AEs suggested no evident publication bias (p=0.618).

CONCLUSIONS

Tirzepatide 15 mg reduced HbA1c and weight more effectively than placebo, insulin, and GLP-1 RA. Total AEs were higher than placebo and insulin but comparable to GLP-1 RA. Tirzepatide 15 mg is a kind of optimal strategy to treat type 2 diabetes. However, there is a need to focus on GI AEs.

[Importance of comprehensive management of anastomotic site after ultra-low anal sphincter-preservation surgery]

Intersphincteric resection (ISR) surgery increases the rate of anal sphincter preservation in patients with ultra-low rectal cancers. However, the anastomotic site of ISR surgery is at risk for structural healing complications such as anastomotic leakage, anastomotic dehiscence, secondary anastomotic stenosis, chronic presacral sinus, rectovaginal fistula, and rectourethral fistula, which can lead to a persistent defunctioning ostomy or a secondary permanent colostomy. This article systematically describes the preoperative high-risk factors and characteristics of anastomotic site structural healing complications after ISR surgery, as well as the management of the anastomotic site during various stages including hospitalization, from discharge to one month after surgery, from one month after surgery to before stoma reversal, and after stoma reversal. This is to provide a clearer understanding of the risks associated with the anastomotic site at different stages of the healing process and to timely detect and actively manage related complications, thereby reducing the rate of permanent colostomy and truly achieving the dual goals of "survival benefit" and "quality of life improvement" in ISR surgery.

RBBP4 is an epigenetic barrier for the induced transition of pluripotent stem cells into totipotent 2C-like cells

Cellular totipotency is critical for whole-organism generation, yet how totipotency is established remains poorly illustrated. Abundant transposable elements (TEs) are activated in totipotent cells, which is critical for embryonic totipotency. Here, we show that the histone chaperone RBBP4, but not its homolog RBBP7, is indispensable for maintaining the identity of mouse embryonic stem cells (mESCs). Auxin-induced degradation of RBBP4, but not RBBP7, reprograms mESCs to the totipotent 2C-like cells. Also, loss of RBBP4 enhances transition from mESCs to trophoblast cells. Mechanistically, RBBP4 binds to the endogenous retroviruses (ERVs) and functions as an upstream regulator by recruiting G9a to deposit H3K9me2 on ERVL elements, and recruiting KAP1 to deposit H3K9me3 on ERV1/ERVK elements, respectively. Moreover, RBBP4 facilitates the maintenance of nucleosome occupancy at the ERVK and ERVL sites within heterochromatin regions through the chromatin remodeler CHD4. RBBP4 depletion leads to the loss of the heterochromatin marks and activation of TEs and 2C genes. Together, our findings illustrate that RBBP4 is required for heterochromatin assembly and is a critical barrier for inducing cell fate transition from pluripotency to totipotency.

3D genome perspective on cell fate determination, organ regeneration, and diseases

The nucleosome is the fundamental subunit of chromatin. Nucleosome structures are formed by the combination of histone octamers and genomic DNA. Through a systematic and precise process of folding and compression, these structures form a 30-nm chromatin fibre that is further organized within the nucleus in a hierarchical manner, known as the 3D genome. Understanding the intricacies of chromatin structure and the regulatory mode governing chromatin interactions is essential for unravelling the complexities of cellular architecture and function, particularly in relation to cell fate determination, regeneration, and the development of diseases. Here, we provide a general overview of the hierarchical structure of chromatin as well as of the evolution of chromatin conformation capture techniques. We also discuss the dynamic regulatory changes in higher-order chromatin structure that occur during stem cell lineage differentiation and somatic cell reprogramming, potential regulatory insights at the chromatin level in organ regeneration, and aberrant chromatin regulation in diseases.

[Laparoscopic versus open pelvic exenteration for locally advanced rectal cancer: analysis of short- and long-term effects]

Objective: To explore the feasibility, safety, and short- and long-term efficacy of laparoscopic pelvic exenteration (LPE) in treating locally advanced rectal cancer. Methods: The clinical data of 173 patients who had undergone pelvic exenteration (PE) for locally advanced rectal cancer that had been shown by preoperative imaging or intraoperative exploration to have invaded beyond the mesorectal excision plane and adjacent organs in the Cancer Hospital, Chinese Academy of Medical Sciences (n=64) and Peking University First Hospital (n=109) from 2010 January to 2021 December were collected retrospectively. Laparoscopic PE (LPE) had been performed on 82 of these patients and open PE (OPE) on 91. Short- and long-term outcomes (1-, 3-, and 5-year overall and disease-free survival and 1- and 3-year cumulative local recurrence rates) were compared between these groups. Results: The only statistically significant difference in baseline data between the two groups (P>0.05) was administration of neoadjuvant therapy. Compared with OPE, LPE had a significantly shorter operative time (319.3±129.3 minutes versus 417.3±155.0 minutes, t=4.531, P<0.001) and less intraoperative blood loss (175 [20-2000] ml vs. 500 [20-4500] ml, U=2206.500, P<0.001). The R0 resection rates were 98.8% and 94.5%, respectively (χ²=2.355, P=0.214). At 18.3% (15/82), and the incidence of perioperative complications was lower in the LPE group than in the OPE group (37.4% [34/91], χ²=7.727, P=0.005). The rates of surgical site infection were 7.3% (6/82) and 23.1% (21/91) in the LPE and OPE group, respectively (χ²=8.134, P=0.004). The rates of abdominal wound infection were 0 and 12.1% (11/91) (χ²=10.585, P=0.001), respectively, and of urinary tract infection 0 and 6.6% (6/91) (χ²=5.601, P=0.030), respectively. Postoperative hospital stay was shorter in the LPE than OPE group (12 [4-60] days vs. 15 [7-87] days, U=2498.000, P<0.001). The median follow-up time was 40 (2-88) months in the LPE group and 59 (1-130) months in the OPE group. The 1-, 3-, and 5-year overall survival rates were 91.3%, 76.0%, and 62.5%, respectively, in the LPE group, and 91.2%, 68.9%, and 57.6%, respectively, in the OPE group. The 1, 3, and 5-year disease-free survival rates were 82.8%, 64.9%, and 59.7%, respectively, in the LPE group and 76.9%, 57.8%, and 52.7%, respectively, in the OPE group. The 1- and 3-year cumulative local recurrence rates were 5.1% and 14.1%, respectively, in the LPE group and 8.0% and 15.1%, respectively, in the OPE group (both P>0.05). Conclusions: In locally advanced rectal cancer patients, LPE is associated with shorter operative time, less intraoperative blood loss, fewer perioperative complications, and shorter hospital stay compared with OPE. It is safe and feasible without compromising oncological effect.

Identification of ovarian endometriotic cysts in cystic lesions of the ovary by amide proton transfer-weighted imaging and R2∗ mapping

AIM

To investigate the value of amide proton transfer weighted (APTw) imaging and R2∗ mapping of cystic fluid in differentiating ovarian endometriotic cysts (OE) from other ovarian cystic (OOC) lesions.

MATERIALS AND METHODS

A total of 42 patients who underwent 3 T pelvic magnetic resonance imaging (MRI) were enrolled. Nineteen lesions were OE and 27 lesions were OOC. The APTw imaging and R2∗ values of the cystic fluid were measured and compared between the two groups using the independent sample t-test or Mann-Whitney U-test. Receiver operating characteristic (ROC) curves were used to evaluate the diagnostic efficacy of different parameters. The area under ROC curves (AUCs) was compared using the Delong test. Spearman's correlation analysis was used to assess the correlation between APTw imaging and R2∗ values.

RESULTS

APTw imaging values of OE were lower, while R2∗ values were higher in OE than those in OOC (p=0.001 and < 0.001). The AUCs of APTw imaging and R2∗ values to identify OE from OOC were 0.910 and 0.975. The AUC increased to 0.990 when combining APTw imaging and R2∗ values, yet without a significant difference to the APTw imaging or R2∗ value alone (p=0.229 and 0.082, respectively). APTw imaging values were negatively correlated with R2∗ values (r=-0.522, p<0.001).

CONCLUSION

Both APTw imaging and R2∗ values of OE are significantly different from other ovarian cystic lesions. APTw imaging combined with R2∗ values show excellent diagnostic efficacy to differentiate between OE and OOC.

[Risk factor and nomogram for predicting the probability of a permanent stoma after laparoscopic intersphincteric resection for ultralow rectal cancer]

Objective: A permanent stoma can seriously affect patients' quality of life. Clinicians need to consider the risk of a permanent stoma when making clinical decisions. This study analyzed preoperative predictors of a permanent stoma after laparoscopic intersphincteric resection for low rectal cancer (LISR), and a prediction model was constructed validated. Methods: This was a retrospective study that analyzed clinical data of 331 ultralow rectal cancer patients who were diagnosed with primary rectal adenocarcinoma by endoscopy and pathology, including 218 males and 113 female, (58.8±11.2) years and (23.7±3.1) kg/m². The patients underwent LISR with a preventive stoma from January 2012 to December 2020. Patients with multiple primary colorectal cancers, who underwent emergency surgery for intestinal obstruction or bleeding or perforation, and did not complete 18 months follow up were exclucled. R software was used to randomly select 234 patients as the modeling group with a ratio of approximately 7:3, and the remaining 97 patients comprised the validation group. The stoma site was determined by the surgeon before the operation, and the ileum 30 cm from the ileocecal valve was selected. The rates of a permanent stoma for the entire group and the preoperative clinical factors that may affect the permanency of a stoma in the modeling group were determined. A permanent stoma was defined as failure to close the stoma at 18 months after surgery. Multivariate logistic regression analysis was used to analyze the preoperative independent risk factors for a permanent stoma after LISR. R software was used to create the nomogram model, and the predictive ability of the nomogram model was evaluated by receiver operating characteristic (ROC) curve analysis. Results: Among the 331 patients who underwent LISR, 37 (26 cases in the modeling group and 11 cases in the validation group, 11.2%) developed a permanent stoma for the following reasons: anastomotic stenosis due to leakage (16 cases, 43.2%), distant metastasis (16 cases, 43.2%), intolerant to stoma closure surgery (3 cases, 8.1%), stenosis due to postoperative radiation (1 case, 2.7%), and poor recovery of anorectal function (1 case, 2.7%). Univariate analysis showed that preoperative neoadjuvant chemoradiotherapy, poorly differentiated tumor, cT3 stage, and distant metastasis were associated with a permanent stoma. Multivariate logistic regression analysis showed that neoadjuvant chemoradiotherapy [OR=3.078, 95% confidence interval (CI): 1.326-7.147; P=0.009], cT3 stage (OR=2.257, 95%CI: 1.001-5.091; P=0.049), and stage IV cancer (OR=16.180, 95%CI: 2.753-95.102; P=0.002) were independent risk factors for permanent stoma after LISR. Based on the selected risk factors, a nomogram model for predicting permanent stoma was constructed. The area under the ROC curve of the modeling group was 0.793, the optimal cut-off value was 0.890, the sensitivity was 0.577, and the specificity was 0.885. The area under the ROC curve of the validation group was 0.953. The corrected curves of the modeling group and the validation group showed a good degree of fit. Conclusion: Neoadjuvant chemoradiotherapy, cT3 stage, and distant metastasis are independent predictors of a permanent stoma after LISR, and the nomogram model is helpful to predict the probability of a permanent stoma. Patients with high-risk factors should be adequately informed of the risk of a permanent stoma before colorectal surgery.

CTCF acetylation at lysine 20 is required for the early cardiac mesoderm differentiation of embryonic stem cells

The CCCTC-binding factor (CTCF) protein and its modified forms regulate gene expression and genome organization. However, information on CTCF acetylation and its biological function is still lacking. Here, we show that CTCF can be acetylated at lysine 20 (CTCF-K20) by CREB-binding protein (CBP) and deacetylated by histone deacetylase 6 (HDAC6). CTCF-K20 is required for the CTCF interaction with CBP. A CTCF point mutation at lysine 20 had no effect on self-renewal but blocked the mesoderm differentiation of mouse embryonic stem cells (mESCs). The CTCF-K20 mutation reduced CTCF binding to the promoters and enhancers of genes associated with early cardiac mesoderm differentiation, resulting in diminished chromatin accessibility and decreased enhancer-promoter interactions, impairing gene expression. In summary, this study reveals the important roles of CTCF-K20 in regulating CTCF genomic functions and mESC differentiation into mesoderm.

YY1 safeguard multidimensional epigenetic landscape associated with extended pluripotency

Although extended pluripotent stem cells (EPSCs) have the potential to form both embryonic and extraembryonic lineages, how their transcriptional regulatory mechanism differs from that of embryonic stem cells (ESCs) remains unclear. Here, we discovered that YY1 binds to specific open chromatin regions in EPSCs. Yy1 depletion in EPSCs leads to a gene expression pattern more similar to that of ESCs than control EPSCs. Moreover, Yy1 depletion triggers a series of epigenetic crosstalk activities, including changes in DNA methylation, histone modifications and high-order chromatin structures. Yy1 depletion in EPSCs disrupts the enhancer-promoter (EP) interactions of EPSC-specific genes, including Dnmt3l. Yy1 loss results in DNA hypomethylation and dramatically reduces the enrichment of H3K4me3 and H3K27ac on the promoters of EPSC-specific genes by upregulating the expression of Kdm5c and Hdac6 through facilitating the formation of CCCTC-binding factor (CTCF)-mediated EP interactions surrounding their loci. Furthermore, single-cell RNA sequencing (scRNA-seq) experiments revealed that YY1 is required for the derivation of extraembryonic endoderm (XEN)-like cells from EPSCs in vitro. Together, this study reveals that YY1 functions as a key regulator of multidimensional epigenetic crosstalk associated with extended pluripotency.

CTCF functions as an insulator for somatic genes and a chromatin remodeler for pluripotency genes during reprogramming

CTCF mediates chromatin insulation and long-distance enhancer-promoter (EP) interactions; however, little is known about how these regulatory functions are partitioned among target genes in key biological processes. Here, we show that Ctcf expression is progressively increased during induced pluripotency. In this process, CTCF first functions as a chromatin insulator responsible for direct silencing of the somatic gene expression program and, interestingly, elevated Ctcf expression next ensures chromatin accessibility and contributes to increased EP interactions for a fraction of pluripotency-associated genes. Therefore, CTCF functions in a context-specific manner to modulate the 3D genome to enable cellular reprogramming. We further discover that these context-specific CTCF functions also enlist SMARCA5, an imitation switch (ISWI) chromatin remodeler, together rewiring the epigenome to facilitate cell-fate switch. These findings reveal the dual functions of CTCF in conjunction with a key chromatin remodeler to drive reprogramming toward pluripotency.

[Research progress of micronucleus visualization analysis and artificial intelligence detection strategy]

The micronucleomics test can comprehensively display a variety of harmful endpoints, such as DNA damage and repair, chromosome breakage or loss and cell growth inhibition, with fast, simple and economical feature. Micronucleomics is not only widely used in the comprehensive assessment of the types and modes of genetic action of exogenous chemicals (such as drugs, food additives, cosmetics, environmental pollutants, etc.), but also plays an important role in the screening and risk assessment of cancer population at high risk. However, the traditional micronucleomics image counting method has the characteristics of time-consuming, low accuracy, and high cost, which cannot meet the current analysis requirements of large-scale, multi-index, rapidity, high precision and visualization. In recent years, with the rapid development of the era of precision medicine based on big data, visualized analysis of new micronucleomics based on machine learning and detection strategies based on deep learning have shown a good application prospect. This review, based on the application value of micronucleomics, systematically compares the traditional and new artificial intelligence counting of micronucleus images, and discusses the future direction of micronucleus image detection.

Establishment of prediction models for COVID-19 patients in different age groups based on Random Forest algorithm

BACKGROUND

Coronavirus disease 2019 (COVID-19) has rapidly become a global pandemic. Age is an independent factor in death from the disease, and predictive models to stratify patients according to their mortality risk are needed.

AIM

To compare the laboratory parameters of the younger (≤70) and the elderly (>70) groups, and develop death prediction models for the two groups according to age stratification.

DESIGN

A retrospective, single-center observational study.

METHODS

This study included 437 hospitalized patients with laboratory-confirmed COVID-19 from Tongji Hospital in Wuhan, China, 2020. Epidemiological information, laboratory data and outcomes were extracted from electronic medical records and compared between elderly patients and younger patients. First, recursive feature elimination (RFE) was used to select the optimal subset. Then, two random forest (RF) algorithms models were built to predict the prognoses of COVID-19 patients and identify the optimal diagnostic predictors for patients' clinical prognoses.

RESULTS

Comparisons of the laboratory data of the two age groups revealed many different laboratory indicators. RFE was used to select the optimal subset for analysis, from which 11 variables were screened out for the two groups. The RF algorithm were built to predict the prognoses of COVID-19 patients based on the best subset, and the area under ROC curve (AUC) of the two groups is 0.874 (95% CI: 0.833-0.915) and 0.842 (95% CI: 0.765-0.920).

CONCLUSION

Two prediction models for COVID-19 were developed in the patients with COVID-19 based on random forest algorithm, which provides a simple tool for the early prediction of COVID-19 mortality.

[Controversy and prospect of transanal total mesorectal excision]

As a novel surgical technique, taTME has developed rapidly in recent years. TaTME inevitably attracts some skepticism on safety, efficacy, and indication. First, the controversies over taTME are mainly reflected on the safety and effectiveness of taTME. On one hand, the increase of surgical complications, such as urethral injury, CO2 embolism, anastomotic leakage and pelvic infection, has raised concerns about the safety of taTME. Second, the poor quality of taTME specimens, the increased local recurrence rate and the impaired anal function after taTME, also make people question the effectiveness of taTME. Third, there are more or less controversies in the selection of taTME cases, surgical procedures and cost-effectiveness. However, it can not be denied that taTME has a promising future in view of both surgical theory and clinical practice. Furthermore, taTME is a relatively safe and effective supplementary surgical procedure, especially for patients with low rectal cancer. We should attach more importance to structured training for beginners and conduct high-quality clinical studies in the future development of taTME in China, so as to ensure the safe implementation of taTME and obtain high-level evidence-based medicine evidence, and then standardize the clinical practice of taTME.

Notoginsenoside R1 protects hypoxia-reoxygenation deprivation-induced injury by upregulation of miR-132 in H9c2 cells

BACKGROUND

Myocardial ischemia/reperfusion injury (IRI) is a common perioperative complication of heart and great vessels surgery, aggravating the original myocardial damage and seriously affecting the postoperative recovery of cardiac function. The aim of this study was to reveal the functional effects and potential mechanisms of notoginsenoside R1 (NG-R1) in myocardial cells injured by hypoxia-reoxygenation (H/R).

METHODS

The rat cardiomyocyte line H9c2 was subjected to H/R with or without NG-R1 treatment. The levels of miR-132 and HBEGF in the cell were altered by microRNA or short-hairpin RNA transfection. Cell viability, apoptosis, lactate dehydrogenase (LDH) and malondialdehyde (MDA) were monitored. Dual luciferin was used to detect the relationship between miR-132 and HBEGF.

RESULTS

NG-R1 (20 μM) had no impact on H9c2 cells, but cell viability was significantly reduced at 80 μM. NG-R1 (20 μM) protected H9c2 cells against H/R-induced cell damage, accompanied by increased cell viability, reduced cell apoptosis, and downregulation of LDH and MDA. Furthermore, the level of miR-132 was decreased in response to H/R exposure but then increased after NG-R1 treatment. When miR-132 was overexpressed, H/R-induced cell damage could be recovered. Downregulation of miR-132 limited the protective effect of NG-R1 on H/R damage. We also found that HBEGF was a direct target of miR-132. The expression of HBEGF was increased upon H/R damage, and this increase was reversed after NG-R1 treatment.

CONCLUSIONS

This study demonstrated that NG-R1 markedly protected H9c2 cells against H/R-induced damage via upregulation of miR-132 and downregulation of its target protein HBEGF.

RNA helicase DDX5 acts as a critical regulator for survival of neonatal mouse gonocytes

OBJECTIVES

Mammalian spermatogenesis is a biological process of male gamete formation. Gonocytes are the only precursors of spermatogonial stem cells (SSCs) which develop into mature spermatozoa. DDX5 is one of DEAD-box RNA helicases and expresses in male germ cells, suggesting that Ddx5 plays important functions during spermatogenesis. Here, we explore the functions of Ddx5 in regulating the specification of gonocytes.

MATERIALS AND METHODS

Germ cell-specific Ddx5 knockout (Ddx5-/- ) mice were generated. The morphology of testes and epididymides and fertility in both wild-type and Ddx5-/- mice were analysed. Single-cell RNA sequencing (scRNA-seq) was used to profile the transcriptome in testes from wild-type and Ddx5-/- mice at postnatal day (P) 2. Dysregulated genes were validated by single-cell qRT-PCR and immunofluorescent staining.

RESULTS

In male mice, Ddx5 was expressed in germ cells at different stages of development. Germ cell-specific Ddx5 knockout adult male mice were sterile due to completely devoid of germ cells. Male germ cells gradually disappeared in Ddx5-/- mice from E18.5 to P6. Single-cell transcriptome analysis showed that genes involved in cell cycle and glial cell line-derived neurotrophic factor (GDNF) pathway were significantly decreased in Ddx5-deficient gonocytes. Notably, Ddx5 ablation impeded the proliferation of gonocytes.

CONCLUSIONS

Our study reveals the critical roles of Ddx5 in fate determination of gonocytes, offering a novel insight into the pathogenesis of male sterility.