Mapping the epitope of PD-L1 to the paratope of the antibody durvalumab using molecular dynamics simulation.

OBJECTIVES: Durvalumab, a human monoclonal antibody that stops PD-L1 from attaching itself to CD80 and PD-1, was approved by the Food and Drug Administration for use in cancer therapy. An essential stage in antibody optimization is mapping paratope residues to epitope residues. In this study, our earlier computer-aided method based on molecular dynamics (MD) simulations was used to observe the paratope residues on durvalumab and their companions on PD-L1. METHODS: The durvalumab/PD-L1 complex model was obtained from the Protein Data Bank and used in a rectangular box for solvation. On durvalumab, the paratope residues and their companions on PD-L1 were identified using MD simulations. The interface residues were ranked on the basis of their contributions to the binding of durvalumab and PD-L1 by assessing the stability of hydrogen bonds and salt bridges. This assessment was conducted using free and guided MD simulations. RESULTS: Seventeen residues, including ASP26, GLU58, GLU60, ASP61, ARG113, ARG125, and THR127 on PD-L1 and H31ARG, H52LYS, H53GLN, H57GLU, H99GLU, H103PHE, H113ARG, L28ARG, L31SER, and L92TYR on durvalumab, were expected to be necessary for the binding of durvalumab to PD-L1. ASP26, ARG113, and ARG125 on PD-L1 were essential for its binding to PD-1. Eight residues (GLU60, ASP61, and THR127 on PD-L1 and L31SER, H99GLU, H53GLU, H31ARG, and H113ARG on durvalumab) were newly found, and two residues (LYS124 on PD-L1 and L94SER on durvalumab) proven nonessential for complexation, compared to the findings from the examined crystal structure. CONCLUSIONS: The antithrombotic antibody of durvalumab's paratope may be effectively mapped to the PD-L1 epitope using the existing computer method. This information will help optimize durvalumab.

Potassium sodium hydrogen citrate intervention on gut microbiota and clinical features in uric acid stone patients.

The high recurrence rate of renal uric acid stone (UAS) poses a significant challenge for urologists, and potassium sodium hydrogen citrate (PSHC) has been proven to be an effective oral dissolution drug. However, no studies have investigated the impact of PSHC on gut microbiota and its metabolites during stone dissolution therapy. We prospectively recruited 37 UAS patients and 40 healthy subjects, of which 12 patients completed a 3-month pharmacological intervention. Fasting vein blood was extracted and mid-stream urine was retained for biochemical testing. Fecal samples were collected for 16S ribosomal RNA (rRNA) gene sequencing and short chain fatty acids (SCFAs) content determination. UAS patients exhibited comorbidities such as obesity, hypertension, gout, and dyslipidemia. The richness and diversity of the gut microbiota were significantly decreased in UAS patients, Bacteroides and Fusobacterium were dominant genera while Subdoligranulum and Bifidobacterium were poorly enriched. After PSHC intervention, there was a significant reduction in stone size accompanied by decreased serum uric acid and increased urinary pH levels. The abundance of pathogenic bacterium Fusobacterium was significantly downregulated following the intervention, whereas there was an upregulation observed in SCFA-producing bacteria Lachnoclostridium and Parasutterella, leading to a significant elevation in butyric acid content. Functions related to fatty acid synthesis and amino acid metabolism within the microbiota showed upregulation following PSHC intervention. The correlation analysis revealed a positive association between stone pathogenic bacteria abundance and clinical factors for stone formation, while a negative correlation with SCFAs contents. Our preliminary study revealed that alterations in gut microbiota and metabolites were the crucial physiological adaptation to PSHC intervention. Targeted regulation of microbiota and SCFA holds promise for enhancing drug therapy efficacy and preventing stone recurrence. KEY POINTS: • Bacteroides and Fusobacterium were identified as dominant genera for UAS patients • After PSHC intervention, Fusobacterium decreased and butyric acid content increased • The microbiota increased capacity for fatty acid synthesis after PSHC intervention.

Comparative Analysis of Super-Mini Percutaneous Nephrolithotomy Combined with Flexible Ureteroscopic Lithotripsy versus Flexible Ureteroscopic Lithotripsy Alone for Treating Complex Kidney Stones: A Retrospective Study of 205 Patients.

BACKGROUND This retrospective study aimed to compare outcomes from super-mini percutaneous nephrolithotomy (SMP) combined with flexible ureteroscopic lithotripsy (FURL) and FURL alone in 205 patients with 2.5-4.2 cm diameter complex kidney stones. MATERIAL AND METHODS Between January 2018 and December 2022, 92 patients were treated with SMP combined with FURL (group A), and 113 patients were treated with FURL alone (group B). The stone-free rate (SFR), retreatment ratio, operation time, mean decline in hemoglobin level, postoperative pain visual analogue scale (VAS), and postoperative hospitalization time and complications were analyzed and compared between the 2 groups. RESULTS The SFR 3 days after the operation was 85.87% in group A, which was significantly higher than that in group B (72.57%) (P=0.021). The rate of retreatment in group A (3.26%) was significantly lower than that in group B (10.62%) (P=0.044). The SFR after 90 days was higher in group A (94.57%) than in group B (90.27%) (P=0.254). The mean decrease in hemoglobin, postoperative hospitalization duration, and VAS score 6 hours after the operation were all significantly higher in group A than in group B (P<0.05). However, there was no significant difference in operation time, VAS score at 12 and 24 hours after the operation, and complication rate. CONCLUSIONS In the treatment of complex renal stones, compared with FURL, SMP combined with FURL in the oblique supine lithotomy position has the advantages of a higher early SFR with no increased risk of complications.

A functional MMP-9-1562C>T polymorphism, MMP-9 serum levels and nephrolithiasis risk in a southern Chinese population.

Background: The role of matrix metalloproteinase 9 (MMP-9) in the pathophysiology of chronic kidney disease (CKD), which is associated with a nearly two-fold greater risk for urinary calculi compared to people without CKD, has been demonstrated. The aim of the research is to evaluate the association between MMP-9-1562C>T polymorphism, MMP-9 serum levels and nephrolithiasis risk. Methods: A hospital-based case-control study involving 302 kidney stone patients and 408 controls without kidney stone from southern China was conducted. Sanger sequencing was used to genotype the MMP-9-1562C>T polymorphism. The serum MMP-9 was measured in 105 kidney stone patients and 77 controls by enzyme-linked immunosorbent assay. Results: Compared to the control group, the CT genotype was more frequent in nephrolithiasis patients (adjusted OR = 1.60, 95% CI = 1.09-2.37: the risk of developing nephrolithiasis in individuals with CT genotype compared to CC genotype). Moreover, there was also a higher frequency of CT/TT genotypes among patients with nephrolithiasis (adjusted OR = 1.49, 95% CI = 1.02-2.19: the risk of developing nephrolithiasis in individuals with CT/TT genotypes compared to CC genotype). The risk remained for the subgroups of patients aged >53, smokers with pack-years of smoking >20, non-drinkers, non-diabetic patients, patients with hypertension, recurrent episodes and calcium oxalate stones (OR = 2.26, 95% CI = 1.31-3.91; OR = 5.47, 95% CI = 1.10-27.30; OR = 1.76, 95% CI = 1.14-2.72; OR = 1.54, 95% CI = 1.03-2.30; OR = 1.97, 95% CI = 1.01-3.82; OR = 1.67, 95% CI = 1.06-2.62; OR = 1.54, 95% CI = 1.02-2.32, respectively). Biochemical parameters did not differ between genotypes. Compared to controls (18.57 ± 5.80 ng/mL), nephrolithiasis patients had significantly higher serum MMP-9 levels (30.17 ± 6.78 ng/mL, p < 0.001). The serum MMP-9 levels of patients with CT/TT genotypes of MMP-9-1562C>T were significantly higher than those with CC genotype (32.00 ± 6.33 vs. 29.13 ± 6.85 ng/mL, p = 0.037). Conclusion: The MMP-9-1562C>T polymorphism in association with its soluble protein increased the risk of kidney stone, thus suggesting it could be used as a susceptibility biomarker for nephrolithiasis. Further functional studies and larger studies that include environmental exposure data are needed to confirm the findings.

ATRA treatment slowed P-selectin-mediated rolling of flowing HL60 cells in a mechano-chemical-dependent manner.

All-trans retinoic acid (ATRA)-induced differentiation of acute promyelocytic leukemia (APL) toward granulocytes may trigger APL differentiation syndrome (DS), but there is less knowledge about the mechano-chemical regulation mechanism of APL DS under the mechano-microenvironment. We found that ATRA-induced changes in proliferation, morphology, and adhesive molecule expression levels were either dose or stimulus time dependent. An optimal ATRA stimulus condition for differentiating HL60 cells toward neutrophils consisted of 1 × 10-6 M dose and 120 h of stimulus time. Under wall shear stresses, catch-slip bond transition governs P-selectin-mediated rolling for neutrophils and untreated or ATRA-treated (1 × 10-6 M, 120 h) HL60 cells. The ATRA stimuli slowed down the rolling of HL60 cells on immobilized P-selectin no matter whether ICAM-1 was engaged. The ß2 integrin near the PSGL-1/P-selectin axis would be activated within sub-seconds for each cell group mentioned above, thus contributing to slow rolling. A faster ß2 integrin activation rate and the higher expression levels of PSGL-1 and LFA-1 were assigned to induce the over-enhancement of ATRA-treated HL60 adhesion in flow, causing APL DS development. These findings provided an insight into the mechanical-chemical regulation for APL DS development via ATRA treatment of leukemia and a novel therapeutic strategy for APL DS through targeting the relevant adhesion molecules.

Association between Dyslipidemia and Nephrolithiasis Risk in a Chinese Population.

PURPOSE: To evaluate the association between dyslipidemia and nephrolithiasis risk in a Chinese population. MATERIALS AND METHODS: Fasting plasma lipid profiles were measured in a case-control study of 540 nephrolithiasis cases and 656 kidney stone-free controls. RESULTS: Triglycerides (TG) levels were significantly higher, but total cholesterol (TC), high-density lipoprotein cholesterol (HDL-C) and low-density lipoprotein cholesterol (LDL-C) levels were significantly lower in nephrolithiasis patients than those in the control group (each p < 0.05). Similar associations were found in both primary and recurrent nephrolithiasis patients except for TC levels. Significantly lower TC and LDL-C levels were found in all patients except those with uric acid stones. Patients with calcium oxalate (CaOx) and uric acid stones had significantly higher TG levels. Individuals with hypertriglyceridemia and low HDL-cholesterolemia were associated with increased risk of nephrolithiasis (OR 1.31, 95% CI 1.01-1.71 and OR 7.57, 95% CI 5.64-10.17, respectively). Conversely, those with hypercholesterolemia and high LDL-cholesterolemia were associated with decreased nephrolithiasis risk (OR 0.60, 95% CI 0.46-0.79 and OR 0.61, 95% CI 0.42-0.90, respectively). The risk remained in patients with CaOx stones. CONCLUSIONS: Our results suggest that dyslipidemia was associated with nephrolithiasis risk in a Chinese population, especially in patients with CaOx stones.

Calcium-Sensing Receptor Genetic Polymorphisms and Risk of Developing Nephrolithiasis in a Chinese Population.

OBJECTIVE: To evaluate the association between calcium-sensing receptor (CaSR) Arg990Gly (rs1042636, A > G), Ala986Ser (rs1801725, G > T) polymorphisms, and urolithiasis risk. METHODS: Polymorphisms mentioned above were genotyped in a hospital-based case-control study of 615 patients diagnosed with nephrolithiasis and 315 kidney stone-free controls in a Chinese population using the SNaPshot method. RESULTS: The results indicated a significantly increased risk associated with CaSR Arg990Gly GG genotypes (OR 1.64, 95% CI 1.08-2.50) compared with the AA genotype. The CaSR Arg990Gly G carriers (AG/GG) had an adjusted OR (95% CI) of 1.45 (1.04-2.03, p = 0.021) compared with the wild genotype in the dominant model. In the stratified analyses, the risk remained for the subgroup of patients with age >48, never smokers and patients with hypertension and calcium oxalate stones (OR 1.78, 95% CI 1.02-3.09; OR 1.54, 95% CI 1.03-2.30; OR 2.83, 95% CI 1.32-6.07; OR 1.60, 95% CI 1.12-2.28, respectively). CONCLUSION: Our results provide evidences that the CaSR Arg990Gly polymorphism is associated with the risk of nephrolithiasis development in a Chinese population.

Expression and significance of TIMP-3, PACAP and VIP in vaginal wall tissues of patients with stress urinary incontinence.

The objective of the present study was to investigate whether tissue inhibitor of metalloproteinase-3 (TIMP-3), pituitary adenylate cyclase-activating polypeptide (PACAP), and vasoactive intestinal peptide (VIP) participate in the occurrence of female stress urinary incontinence (SUI) by measuring the expression levels of TIMP-3, PACAP, and VIP in the vaginal wall and analyzing their correlation to understand the pathogenesis of female SUI. Forty female patients who were admitted to our hospital for tension-free obturator tape surgery for treatment of SUI from April, 2012 to December, 2015 were selected as the study group. Forty patients who underwent vaginal or total abdominal hysterectomy for treatment of non-estrogen-related diseases during the same period were selected as the control group. Tissue samples from the anterior vaginal wall, located at twelve o'clock, were taken from both groups. The expression levels of TIMP-3, PACAP and VIP were detected by immunohistochemistry, and the correlation of integral optical density (IOD) among expressions of TIMP-3, PACAP, and VIP was investigated. The expression of TIMP-3 in vaginal wall tissues of the study group was lower than that of the control group (P<0.05). The expression of PACAP and VIP in vaginal tissues of the study group were lower than those of the control group (P<0.05). In the study group, the IOD of PACAP expression was significantly and positively correlated with that of VIP (r=0.873, P<0.05), the IOD of PACAP expression was significantly and positively correlated with that of TIMP-3 (r=0.802, P<0.05), and the IOD of VIP expression was significantly and positively correlated with that of TIMP-3 (r=0.716, P<0.05). In conclusion, TIMP-3, PACAP and VIP jointly participate in the occurrence of female SUI. Increasing the expression of TIMP-3, PACAP, and VIP, repairing neurons, and enhancing the elasticity of vaginal wall tissues may become a new way to treat female SUI.

The interleukin-10 promoter polymorphism rs1800872 (-592C>A), contributes to cancer susceptibility: meta-analysis of 16,785 cases and 19,713 controls.

Interleukin-10 (IL-10) is a multifunctional cytokine which participates in the development and progression of various malignant tumors. To date, a number of case-control studies were conducted to detect the association between IL-10-592C>A polymorphism and cancer risk in humans. However, the results of these studies on the association remain conflicting. In an effort to solve this controversy, we performed a meta-analysis based on 70 case-control studies from 65 articles, including 16 785 cancer cases and 19 713 controls. We used odds ratios (ORs) with 95% confidence intervals (CIs) to assess the strength of the association. The overall results suggested that the variant homozygote genotype AA of the IL-10-592C>A polymorphism was associated with a moderately decreased risk of all cancer types (OR = 0.90, 95% CI = 0.83-0.98 for homozygote comparison, OR = 0.92, 95% CI = 0.86-0.98 for recessive model). In the stratified analyses, the risk remained for studies of smoking-related cancer, Asian populations and hospital-based studies. These results suggested that the IL-10-592C>A polymorphism might contribute to the cancer susceptibility, especially in smoking-related cancer, Asians and hospital-based studies. Further studies are needed to confirm the relationship.

Interleukin-10-819C>T polymorphism contributed to cancer risk: evidence from 29 studies.

Cytokines are important modulators in the interactions between the host immune system and malignant tumor. Of these, Interleukin-10 (IL-10) is an important immunoregulatory cytokine mainly produced by macrophages and T lymphocytes. To date, a number of studies investigated the role of the IL-10-819C>T polymorphism in the aetiology of cancers of various organs. However, the results of these studies remain inconclusive. So, we carried out a meta-analysis on all eligible case-control studies to estimate the overall cancer risk of IL-10-819C>T polymorphism as well as to quantify the between-study heterogeneity and potential bias. This meta-analysis, including 8157 cases and 10473 controls from 29 published case-control studies, explored the association between a potentially functional polymorphism, -819C>T within the IL-10 promoter region and cancer risk. We used odds ratios (ORs) with 95% confidence intervals (CIs) to assess the strength of the association. The results provided evidence that the IL-10-819C>T polymorphism was associated with a significant decrease in overall cancer risk. In the stratified analyses, the risk remained for studies of "other cancer", smoking-related cancer, Asian populations and hospital-based studies. This meta-analysis identified an evidence of the association between the IL-10-819C>T and cancer risk, especially in "other cancer", smoking-related cancers, Asians and hospital-based studies. Further large case-control studies, especially studies in African population were needed to validate our results.

Using the theory of coevolution to predict protein-protein interactions in non-small cell lung cancer.

Systems biology has become an effective approach for understanding the molecular mechanisms underlying the development of lung cancer. In this study, sequences of 100 non-small cell lung cancer (NSCLC)-related proteins were downloaded from the National Center for Biotechnology Information (NCBI) databases. The Theory of Coevolution was then used to build a protein-protein interaction (PPI) network of NSCLC. Adopting the reverse thinking approach, we analyzed the NSCLC proteins one at a time. Fifteen key proteins were identified and categorized into a special protein family F(K), which included Cyclin D1 (CCND1), E-cadherin (CDH1), Cyclin-dependent kinase inhibitor 2A (CDKN2A), chemokine (C-X-C motif) ligand 12 (CXCL12), epidermal growth factor (EGF), epidermal growth factor receptor (EGFR), TNF receptor superfamily, member 6(FAS), FK506 binding protein 12-rapamycin associated protein 1 (FRAP1), O-6-methylguanine-DNA methyltransferase (MGMT), parkinson protein 2, E3 ubiquitin protein ligase (PARK2), phosphatase and tensin homolog (PTEN), calcium channel voltage-dependent alpha 2/delta subunit 2 (CACNA2D2), tubulin beta class I (TUBB), SWI/SNF-related, matrix-associated, actin-dependent regulator of chromatin, subfamily a, member 2 (SMARCA2), and wingless-type MMTV integration site family, member 7A (WNT7A). Seven key nodes of the sub-network were identified, which included PARK2, WNT7A, SMARCA2, FRAP1, CDKN2A, CCND1, and EGFR. The PPI predictions of EGFR-EGF, PARK2-FAS, PTEN-FAS, and CACNA2D2-CDH1 were confirmed experimentally by retrieving the Biological General Repository for Interaction Datasets (BioGRID) and PubMed databases. We proposed that the 7 proteins could serve as potential diagnostic molecular markers for NSCLC. In accordance with the developmental mode of lung cancer established by Sekine et al., we assumed that the occurrence and development of lung cancer were linked not only to gene loss in the 3p region (WNT7A, 3p25) and genetic mutations in the 9p region but also to similar events in the regions of 1p36.2 (FRAP1), 6q25.2-q27 (PARK2), and 11q13 (CCND1). Lastly, the invasion or metastasis of lung cancer happened.