Protein lysine β-hydroxybutyrylation (Kbhb) is a newly discovered post-translational modification associated with a wide range of biological processes. Identifying Kbhb sites is critical for a better understanding of its mechanism of action. However, biochemical experimental methods for probing Kbhb sites are costly and have a long cycle. Therefore, a feature embedding learning method based on the Transformer encoder was proposed to predict Kbhb sites. In this method, amino acid residues were mapped into numerical vectors according to their amino acid class and position in a learnable feature embedding method. Then the Transformer encoder was used to extract discriminating features, and the bidirectional long short-term memory network (BiLSTM) was used to capture the correlation between different features. In this paper, a benchmark dataset was constructed, and a Kbhb site predictor, AutoTF-Kbhb, was implemented based on the proposed method. Experimental results showed that the proposed feature embedding learning method could extract effective features. AutoTF-Kbhb achieved an area under curve (AUC) of 0.87 and a Matthews correlation coefficient (MCC) of 0.37 on the independent test set, significantly outperforming other methods in comparison. Therefore, AutoTF-Kbhb can be used as an auxiliary means to identify Kbhb sites.
Protein Processing, Post-Translational ; Lysine/chemistry* ; Proteins/chemistry* ; Machine Learning ; Algorithms

Protein liquid-liquid phase separation (LLPS), a pivotal phenomenon intricately linked to cellular processes, is regulated by various other proteins. However, there is still a lack of high-throughput methods for screening protein regulators of LLPS in target proteins. Here, we developed a CRISPR/Cas9-based screening method to identify protein phase separation regulators by integrating bimolecular fluorescence complementation (BiFC) and fluorescence-activated cell sorting (FACS). Using this newly developed method, we screened the RNA-binding proteins that regulate PABPN1 phase separation and identified the tumor suppressor QKI as a promoter of PABPN1 phase separation. Furthermore, QKI exhibits decreased expression levels and diminished nuclear localization in colorectal cancer cells, resulting in reduced PABPN1 phase separation, which, in turn, promotes alternative polyadenylation (APA), cell proliferation, and migration in colorectal cancer.
Humans ; Colorectal Neoplasms/genetics* ; RNA-Binding Proteins/genetics* ; Poly(A)-Binding Protein I/genetics* ; CRISPR-Cas Systems ; Flow Cytometry ; Cell Proliferation ; Cell Line, Tumor ; Cell Movement

Pelvic organ prolapse (POP), whose etiology is influenced by genetic and clinical risk factors, considerably impacts women's quality of life. However, the genetic underpinnings in non-European populations and comprehensive risk models integrating genetic and clinical factors remain underexplored. This study constructed the first polygenic risk score (PRS) for POP in the Chinese population by utilizing 20 disease-associated variants from the largest existing genome-wide association study. We analyzed a discovery cohort of 576 cases and 623 controls and a validation cohort of 264 cases and 200 controls. Results showed that the case group exhibited a significantly higher PRS than the control group. Moreover, the odds ratio of the top 10% risk group was 2.6 times higher than that of the bottom 10%. A high PRS was significantly correlated with POP occurrence in women older than 50 years old and in those with one or no childbirths. As far as we know, the integrated prediction model, which combined PRS and clinical risk factors, demonstrated better predictive accuracy than other existing PRS models. This combined risk assessment model serves as a robust tool for POP risk prediction and stratification, thereby offering insights into individualized preventive measures and treatment strategies in future clinical practice.
Humans ; Female ; Pelvic Organ Prolapse/epidemiology* ; Middle Aged ; Risk Assessment/methods* ; China/epidemiology* ; Multifactorial Inheritance ; Aged ; Risk Factors ; Genome-Wide Association Study ; Genetic Predisposition to Disease ; Case-Control Studies ; Adult ; Polymorphism, Single Nucleotide ; Genetic Risk Score ; East Asian People

BackgroundPatients with depressive disorder often exhibit impaired decision-making functions. However， the relationship between decision-making abilities and depressive and anxiety symptoms in these patients remains unclear. ObjectiveTo explore the characteristics of decision-making behavior in patients with depressive disorder， and to analyze its relationship with clinical symptoms. MethodsA total of 48 patients diagnosed with depressive disorder according to the Diagnostic and Statistical Manual of Mental Disorders， fourth edition （DSM-IV） were recruited from the Department of Psychosomatic Medicine of the Affiliated Hospital of Southwest Medical University from October 2020 to May 2023. Concurrently， 52 healthy individuals matched for age and gender were recruited from Luzhou as the control group. Beck Depression Inventory （BDI） and Beck Anxiety Inventory （BAI） were used for assessment， and decision-making behavior was evaluated using Probabilistic Reversal Learning （PRL） task. Indicators assessed included the number of trials to criterion， perseverative errors， win-stay rate and lose-shift rate. Spearman correlation analysis was used to assess the correlation between BDI and BAI scores and PRL task indicators. ResultsThe depression group showed a significantly higher lose-shift rate compared with the control group （t=3.684， P<0.01）. There were no statistically significant differences between two groups in trials to criterion， perseverative errors and win-stay rate （t=0.329， 0.132， 0.609， P>0.05）. In depression group， BDI and BAI scores were positively correlated with the win-stay rate（r=0.450， 0.398， P<0.01）. ConclusionPatients with depressive disorder are more likely to change their decision-making strategies following negative outcomes. Furthermore， the severity of depressive and anxiety symptoms is associated with a greater propensity to maintain existing decisions after receiving positive feedback. ［Funded by 2019 Joint Project of Luzhou Science and Technology Bureau-Southwest Medical University （number， 2019LZXNYDJ39］

BACKGROUND:Human periodontal stem cells have a certain inhibitory effect on the pro-inflammatory function of M1-type macrophages,and it is not clear whether icariin,which has anti-inflammatory and other pharmacological activities,can enhance the inhibitory effect of human periodontal stem cells on M1-type macrophages. OBJECTIVE:To investigate the effect of icariin on M1 macrophages after pretreatment of human periodontal stem cells. METHODS:Primary human periodontal stem cells were isolated,cultured and characterized.THP-1 was induced and M1-type macrophages were identified by immunofluorescence staining and PCR.Human periodontal stem cells were cultured with α-MEM complete medium containing concentrations of 10-7,10-6,10-5,and 10-4 mol/L icariin,and the cytotoxicity of Icariin on human periodontal stem cells was detected by the CCK-8 assay at 1,3,5,and 7 days,respectively.α-MEM complete medium,untreated α-MEM conditioned medium for human periodontal stem cells and α-MEM conditioned medium for human periodontal stem cells pretreated with icariin for 24 hours were conditioned with RPMI-1640 complete medium in a 1:1 ratio for M1-type macrophages in the control,untreated,and pretreated groups,and 24 hours later,the mRNA expression of inflammatory factors in M1 macrophages was detected by RT-PCR.The protein expression of inflammatory factors in M1 macrophages was detected by ELISA.The expression of surface markers and nuclear factor-κB pathway-related proteins in M1/M2 macrophages was detected by western blot assay. RESULTS AND CONCLUSION:(1)CCK-8 assay results showed that 10-7,10-6,10-5,10-4 mol/L icariin was not cytotoxic to the human periodontal stem cells,and from day 5 onwards,all the concentrations increased the cell viability,and promoted the cell proliferation.10-4 mol/L icariin was selected for follow-up experiment.(2)RT-PCR and ELISA results showed that compared with the control group,the untreated group and the pretreated group both decreased the expression and secretion of interleukin-1β,interleukin-6,and tumor necrosis factor-α of M1-type macrophages(P<0.05),and the pretreated group was lower than the untreated group(P<0.05).(3)Western blot assay results showed that compared with the untreated group,the expression of CD86 was significantly lower in the pretreated group(P<0.05);compared with the control group,the expression of CD206,a surface marker of M2-type macrophages,was elevated in both the untreated and pretreated groups(P<0.01),and it was significantly higher in the pretreated group than in the untreated group(P<0.01).In M1-type macrophages after 24 hours of conditioned culture,compared with the control group,the expression of nuclear factor-κB/P65 was decreased in the untreated group and the pretreated group(P<0.01),and the expression of p-IκBα was decreased only in the pretreated group(P<0.01);the expression of both nuclear factor-κB/P65 and p-IκBα was significantly reduced in the pretreated group compared with the untreated group(P<0.05),while the difference of IκBα in the three groups was not statistically significant.(4)These results indicated that icariin enhanced the inhibitory effect of human periodontal stem cells on M1-type macrophages,and this effect may be related to the inhibition of the nuclear factor-κB signaling pathway of macrophages.

ObjectiveTo investigate whether there are differences in the efficacy of Gegen Qinliantang with different contents of Puerariae Lobatae Radix on the acute enteritis （AE） model mice and provide a scientific basis for the interpretation of Gegen Qinliantang in the treatment of "Xie Re Li". MethodsA total of 112 male BALB/c mice were randomly divided into a blank group，model group，single Puerariae Lobatae Radix group，non-Puerariae Lobatae Radix group，regular dose Gegen Qinliantang group （regular dose group），half-dose Puerariae Lobatae Radix group，and doubled-dose Puerariae Lobatae Radix group， with 16 mice in each group. Hematoxylin-eosin （HE） staining was used to observe the pathological changes of the colon tissue. Western blot was employed to detect the expression of ZO-1 （a protein in the tight junction） and Occludin in the colon tissue， as well as the changes of tumor necrosis factor-α （TNF-α） and interleukin-1β （IL-1β）. ResultsCompared with the blank group，the DAI scores of the mice in the model group were significantly higher （P<0.05），and the histopathological sections of their colon tissues showed mucosal damage，glandular atrophy，disordered arrangement，and a large number of inflammatory cells infiltration，and the expression of ZO-1 and Occludin proteins in their colon tissues was significantly down-regulated （P<0.05，P<0.01）. The expression of inflammatory factors TNF-α and IL-1β was significantly up-regulated （P<0.05，P<0.01）. Compared with the model group，the DAI scores of mice in all dosing groups decreased significantly （P<0.05），with the most significant effect in the regular dose group. After 7 d of drug administration，the regular dose group had the best impact on the repair of colonic mucosa in the AE mouse model. The regular dose group significantly down-regulated the expression of TNF-α （P<0.05） and significantly up-regulated the expression of ZO-1 protein （P<0.05）. The doubled-dose Puerariae Lobatae Radix group significantly down-regulated the expression of IL-1β protein （P<0.01），and there was no significant difference between all dosing groups and the model group in terms of the expression of Occludin protein. After 14 d of drug administration，the best effect on the repair of colonic mucosa in the AE mouse model was observed in the doubled dose Puerariae Lobatae Radix group. All groups except the non-Puerariae Lobatae Radix group significantly down-regulated the expression of TNF-α （P<0.01）. Meanwhile，the regular dose group and doubled-dose Puerariae Lobatae Radix group significantly elevated the expression level of Occludin protein （P<0.01）. The doubled-dose Puerariae Lobatae Radix group also significantly inhibited the expression of IL-1β protein （P<0.05） and up-regulated ZO-1 protein expression （P<0.05）. ConclusionGegen Qinliantang can reduce the pathological damage of colon tissue， protect the barrier function and structure of intestinal epithelial cells， and reduce the expression of inflammatory factors， so as to achieve the therapeutic effect of AE model mice. When comparing the therapeutic efficacy of Gegen Qinliantang containing different Gegen contents， Gegen Qinliantang with the proportion of the original formula of Zhongjing was the most effective in AE model mice.

ObjectiveTo investigate whether there are differences in the efficacy of Gegen Qinliantang with different contents of Puerariae Lobatae Radix on the acute enteritis （AE） model mice and provide a scientific basis for the interpretation of Gegen Qinliantang in the treatment of "Xie Re Li". MethodsA total of 112 male BALB/c mice were randomly divided into a blank group，model group，single Puerariae Lobatae Radix group，non-Puerariae Lobatae Radix group，regular dose Gegen Qinliantang group （regular dose group），half-dose Puerariae Lobatae Radix group，and doubled-dose Puerariae Lobatae Radix group， with 16 mice in each group. Hematoxylin-eosin （HE） staining was used to observe the pathological changes of the colon tissue. Western blot was employed to detect the expression of ZO-1 （a protein in the tight junction） and Occludin in the colon tissue， as well as the changes of tumor necrosis factor-α （TNF-α） and interleukin-1β （IL-1β）. ResultsCompared with the blank group，the DAI scores of the mice in the model group were significantly higher （P<0.05），and the histopathological sections of their colon tissues showed mucosal damage，glandular atrophy，disordered arrangement，and a large number of inflammatory cells infiltration，and the expression of ZO-1 and Occludin proteins in their colon tissues was significantly down-regulated （P<0.05，P<0.01）. The expression of inflammatory factors TNF-α and IL-1β was significantly up-regulated （P<0.05，P<0.01）. Compared with the model group，the DAI scores of mice in all dosing groups decreased significantly （P<0.05），with the most significant effect in the regular dose group. After 7 d of drug administration，the regular dose group had the best impact on the repair of colonic mucosa in the AE mouse model. The regular dose group significantly down-regulated the expression of TNF-α （P<0.05） and significantly up-regulated the expression of ZO-1 protein （P<0.05）. The doubled-dose Puerariae Lobatae Radix group significantly down-regulated the expression of IL-1β protein （P<0.01），and there was no significant difference between all dosing groups and the model group in terms of the expression of Occludin protein. After 14 d of drug administration，the best effect on the repair of colonic mucosa in the AE mouse model was observed in the doubled dose Puerariae Lobatae Radix group. All groups except the non-Puerariae Lobatae Radix group significantly down-regulated the expression of TNF-α （P<0.01）. Meanwhile，the regular dose group and doubled-dose Puerariae Lobatae Radix group significantly elevated the expression level of Occludin protein （P<0.01）. The doubled-dose Puerariae Lobatae Radix group also significantly inhibited the expression of IL-1β protein （P<0.05） and up-regulated ZO-1 protein expression （P<0.05）. ConclusionGegen Qinliantang can reduce the pathological damage of colon tissue， protect the barrier function and structure of intestinal epithelial cells， and reduce the expression of inflammatory factors， so as to achieve the therapeutic effect of AE model mice. When comparing the therapeutic efficacy of Gegen Qinliantang containing different Gegen contents， Gegen Qinliantang with the proportion of the original formula of Zhongjing was the most effective in AE model mice.

ObjectiveTo investigate the intervention effects and mechanisms of the flavonoid hyperoside （Hyp） on lipopolysaccharide （LPS）-induced inflammation in the zebrafish model. MethodsZebrafish larvae were either microinjected with 0.5 g·L^-1 LPS or immersed in 1 g·L^-1 LPS for the modeling of inflammation. The larvae were then treated with Hyp at 25， 50， and 100 mg·L^-1 through immersion for four consecutive days. The inflammatory phenotypes were assessed by analyzing the mortality rate， malformation rate， body length， and yolk sac area ratio. Behavioral tests were conducted to evaluate the inflammatory stress responses， and macrophage migration was observed by fluorescence microscopy. Additionally， the mRNA levels of inflammation-related genes， including interleukin-1β （IL-1β）， interleukin-6 （IL-6）， chemokine C-C motif ligand 2 （CCL2）， chemokine C-X3-C motif receptor 1 （CX3CR1）， chemokine C-C motif receptor 2 （CCR2）， and genes associated with the Toll-like receptor 4 （TLR4）/myeloid differentiation factor 88 （MyD88）/nuclear factor-kappa B （NF-κB） signaling pathway， were measured by Real-time quantitative polymerase chain reaction（Real-time PCR）. ResultsCompared with the pure water injection group， the model group exhibited increased mortality， malformation rates and yolk sac area ratio （P0.01）， reduced body length （P0.01）， increased total swimming distance and high-speed swimming duration （P0.01）， and up-regulated mRNA levels of TLR4， MyD88， NF-κB， IL-1β， IL-6， CCL2， CX3CR1， and CCR2 （P0.01）. Hyp at low， medium and high doses， as well as aspirin， reduced the mortality and malformation rates （P0.05，P0.01）， increased the body length （P0.05，P0.01）， decreased the yolk sac area ratio （P0.01）， reduced the high-speed swimming duration （P0.01）， and down-regulated the mRNA levels of TLR4， MyD88， NF-κB， IL-1β， IL-6， CCL2， CX3CR1， and CCR2 （P0.05，P0.01） compared with the model group. ConclusionHyp may modulate the TLR4/MyD88/NF-κB pathway to ameliorate inflammatory phenotypes and alleviate stress conditions in zebrafish， thereby exerting the anti-inflammatory effect.

Prostate cancer (PCa) ranks as the second most prevalent malignancy among men worldwide. Early diagnosis, personalized treatment, and prognosis prediction of PCa play a crucial role in improving patients' survival rates. The advancement of artificial intelligence (AI), particularly the utilization of deep learning (DL) algorithms, has brought about substantial progress in assisting the diagnosis, treatment, and prognosis prediction of PCa. The introduction of the foundation model has revolutionized the application of AI in medical treatment and facilitated its integration into clinical practice. This review emphasizes the clinical application of AI in PCa by discussing recent advancements from both pathological and imaging perspectives. Furthermore, it explores the current challenges faced by AI in clinical applications while also considering future developments, aiming to provide a valuable point of reference for the integration of AI and clinical applications.
Humans ; Prostatic Neoplasms/diagnosis* ; Male ; Artificial Intelligence ; Deep Learning ; Prognosis