PARP inhibitors suppress tumours via centrosome error-induced senescence independent of DNA damage response.

BACKGROUND: Poly(ADP-ribose) polymerase (PARP) inhibitors have emerged as promising chemotherapeutic drugs primarily against BRCA1/2-associated tumours, known as synthetic lethality. However, recent clinical trials reported patients' survival benefits from PARP inhibitor treatments, irrelevant to homologous recombination deficiency. Therefore, revealing the therapeutic mechanism of PARP inhibitors beyond DNA damage repair is urgently needed, which can facilitate precision medicine. METHODS: A CRISPR-based knock-in technology was used to establish stable BRCA1 mutant cancer cells. The effects of PARP inhibitors on BRCA1 mutant cancer cells were evaluated by biochemical and cell biological experiments. Finally, we validated its in vivo effects in xenograft and patient-derived xenograft (PDX) tumour mice. FINDINGS: In this study, we uncovered that the majority of clinical BRCA1 mutations in breast cancers were in and near the middle of the gene, rather than in essential regions for DNA damage repair. Representative mutations such as R1085I and E1222Q caused transient extra spindle poles during mitosis in cancer cells. PAR, which is synthesized by PARP2 but not PARP1 at mitotic centrosomes, clustered these transient extra poles, independent of DNA damage response. Common PARP inhibitors could effectively suppress PARP2-synthesized PAR and induce cell senescence by abrogating the correction of mitotic extra-pole error. INTERPRETATION: Our findings uncover an alternative mechanism by which PARP inhibitors efficiently suppress tumours, thereby pointing to a potential new therapeutic strategy for centrosome error-related tumours. FUNDING: Funded by National Natural Science Foundation of China (NSFC) (T2225006, 82272948, 82103106), Beijing Municipal Natural Science Foundation (Key program Z220011), and the National Clinical Key Specialty Construction Program, P. R. China (2023).

Reliability and minimal detectable change of the Short Physical Performance Battery in older adults with mild cognitive impairment.

OBJECTIVES: Reliability of the Short Physical Performance Battery (SPPB) are rarely examined among older adults with mild cognitive impairment (MCI). This study aimed to investigate the test-retest reliability and minimal detectable change (MDC) of the SPPB in older adults with MCI. METHODS: Participants included 100 older adults with MCI. The SPPB was assessed with the first 2 assessments separated by a 20-min interval and the third separated by a 1-week interval. The intraclass correlation coefficient (ICC) and MDC values were estimated. RESULTS: The intraday ICC was 0.73 for the SPPB score, 0.90 for the 4-m walk time (4mwt), and 0.95 for the 5-times chair stand time (5cst); the corresponding interday ICC values were 0.76, 0.89, and 0.91, respectively. The MDC values ranged from 1.1 to 1.2 for the SPPB score, from 0.77 to 0.80 s for the 4mwt, and from 1.32 to 1.77 for the 5cst. CONCLUSIONS: The SPPB had satisfactory reliability among older adults with MCI. The test-retest reliability of the SPPB is sufficient (>0.7) for group comparisons. Moreover, the test-retest reliability for the 4mwt and 5cst subscale performances is acceptable (> 0.9) for individual-level measurements over time.

Association between dietary magnesium intake and gallstones: the mediating role of atherogenic index of plasma.

BACKGROUND: Dyslipidemia and abnormalities in cholesterol metabolism are commonly observed in individuals with gallstone disease. Previous research has demonstrated that dietary magnesium can influence lipid metabolism. The atherogenic index of plasma (AIP) has emerged as a novel lipid marker. This study aimed to examine the possible correlation between dietary magnesium intake and gallstones and the potential mediating role of AIP in US adults. METHODS: A total of 4,841 adults were included in this study from the National Health and Nutrition Examination Survey (NHANES) conducted from 2017 to 2020. A variety of statistical techniques such as logistic regression, subgroup analysis, smoothed curve fitting, and causal mediation analysis were utilized to analyze the information collected from the participants. RESULTS: In the fully adjusted model, a statistically noteworthy inverse relationship was observed between dietary magnesium intake and the presence of gallstones, as indicated by an odds ratio (OR) of 0.58 and a 95% confidence interval (CI) of (0.42, 0.81). Causal intermediary analysis revealed that the association between magnesium intake and gallstones was partially mediated by AIP, with a mediation ratio of 3.2%. CONCLUSION: According to this study, dietary magnesium intake had a significant linear negative association with the prevalence of gallstones, in which AIP played a mediating role. This discovery offers novel perspectives on the prevention and management of gallstones.

Switching GoÌ -Martini for Investigating Protein Conformational Transitions and Associated Protein-Lipid Interactions.

Proteins are dynamic biomolecules that can transform between different conformational states when exerting physiological functions, which is difficult to simulate using all-atom methods. Coarse-grained (CG) Go̅-like models are widely used to investigate large-scale conformational transitions, which usually adopt implicit solvent models and therefore cannot explicitly capture the interaction between proteins and surrounding molecules, such as water and lipid molecules. Here, we present a new method, named Switching Go̅-Martini, to simulate large-scale protein conformational transitions between different states, based on the switching Go̅ method and the CG Martini 3 force field. The method is straightforward and efficient, as demonstrated by the benchmarking applications for multiple protein systems, including glutamine binding protein (GlnBP), adenylate kinase (AdK), and ß2-adrenergic receptor (ß2AR). Moreover, by employing the Switching Go̅-Martini method, we can not only unveil the conformational transition from the E2Pi-PL state to E1 state of the type 4 P-type ATPase (P4-ATPase) flippase ATP8A1-CDC50 but also provide insights into the intricate details of lipid transport.

Sea Cucumber Polysaccharide from Stichopus japonicu and Its Photocatalytic Degradation Product Alleviate Acute Alcoholic Liver Injury in Mice.

To prevent alcoholic liver disease, the addition of bioactive substances to the alcoholic drink Baijiu has been considered a feasible option. In the present study, the hepatoprotective effects of a sea cucumber sulfated polysaccharide (SCSP) isolated from Stichopus japonicu were investigated. Moreover, in order to enhance its solubility in an alcohol solution, it was depolymerized using a photocatalytic reaction, and the photocatalytic degradation products (dSCSPs) with an average molecular weight of less than 2 kDa were studied and compared with SCSP. They were characterized by a series of chemical and spectroscopy methods and the oligosaccharide fragments in the dSCSP were further identified by HPLC-MSn analysis. Then, the in vivo experiment showed that the addition of SCSP or dSCSP to Baijiu could alleviate alcoholic liver injury in mice. Further analysis also revealed their protective effect in reducing oxidative stress damage and their regulation of the metabolism of phosphatidylcholine (PC) and phosphatidylethanolamine (PE) in the liver. Of note, dSCSP was more effective at reducing the level of malondialdehyde in the liver. These findings indicate that the addition of sea cucumber polysaccharide or its low-molecular-weight derivative in Baijiu has the potential to alleviate alcoholic liver injury.

Prevalence and molecular characterization of multi-resistant Escherichia coli isolates from clinical bovine mastitis in China.

Different antibiotics are used to treat mastitis in dairy cows that is caused by Escherichia coli (E. coli). Antimicrobial resistance in food-producing animals in China has been monitored since 2000. Surveillance data have shown that the prevalence of multiresistant E. coli in animals has increased significantly. This study aimed to investigate the occurrence and molecular characteristics of resistance determinants in E. coli strains (n = 105) obtained from lactating cows with clinical bovine mastitis (CBM) in China. A total of 220 cows with clinical mastitis, which has swollen mammary udder with reduced and red or gangrenous milk, were selected from 5000 cows. The results showed 94.3% of the isolates were recognized as multidrug resistant. The isolates (30.5%) were positive for the class I integrase gene along with seven gene cassettes that were accountable for resistance to trimethoprim resistance (dfrA17, dfr2d and dfrA1), aminoglycosides resistance (aadA1 and aadA5) and chloramphenicol resistance (catB3 and catB2), respectively. The blaTEM gene was present in all the isolates, and these carried the blaCTX gene. A double mutation in gyrA (i.e., Ser83Leu and Asp87Asn) was observed in all fluoroquinolone-resistant isolates. In total, nine fluoroquinolone-resistant E. coli isolates were identified with five different types of mutations in parC. In four (44.4%) isolates, Ser458Ala was present in parE, and in all nine (9/9) fluoroquinolone-resistant isolates, Pro385Ala was present in gyrB. Meanwhile, fluoroquinolone was observed as highly resistant, especially in isolates with gyrA and parC mutations. In summary, the findings of this research recognize the fluoroquinolone resistance mechanism and disclose integron prevalence and ESBLs in E. coli isolates from lactating cattle with CBM.

Prognostic factors for surgical site infection in patients with spinal metastases and following surgical treatment.

There were few articles reviewed prognostic factors of surgical site infection (SSI) in patients with spinal metastases following surgery. The purpose of the present study was to systematically: (1) investigate the incidence rates of SSI following spinal metastases surgery; (2) identify the factors which were independently associated with postoperative wound infection. One hundred sixty-seven consecutive adult patients with spinal metastases and underwent surgical treatment were retrospectively enrolled from January 2011 to February 2022. Demographic data, disease and operation-related indicators were extracted and analyzed. Univariate and multivariate logistic analysis model were performed respectively to determine independent risk factors of SSI. 17 cases infection were collected in this study. The overall incidence of SSI after surgery of spinal metastases patients was 10.2%. Univariate regression analysis showed that age (P = .028), preoperative ALB level (P = .024), operation time (P = .041), intraoperative blood loss (P = .030), Karnofsky Performance Status score (P = .000), body mass index (P = .013), American Society of Anesthesiologists > 2 (P = .010), Tobacco consumption (P = .035), and number of spinal levels involved in surgical procedure (P = .007) were associated with wound infection. Finally, the multivariate logistic model demonstrated that body mass index (P = .043; OR = 1.038), preoperative ALB level (P = .018; OR = 1.124), and number of spinal levels (P = .003; OR = 1.753) were associated with SSI occurrence. Surgery on multiple vertebral levels for spinal metastases significantly increases the risk of SSI and weight management, nutritional support and palliative surgery have the positive significance in reducing wound complications. Orthopedist should focus on identifying such high-risk patients and decrease the incidence of wound infection by formulating comprehensive and multi-disciplinary care strategy.

DNA Methylation-Based Diagnosis and Treatment of Breast Cancer.

DNA methylation is a key epigenetic modifier involved in tumor formation, invasion, and metastasis. The development of breast cancer is a complex process, and many studies have now confirmed the involvement of DNA methylation in breast cancer. Moreover, the number of genes identified as aberrantly methylated in breast cancer is rapidly increasing, and the accumulation of epigenetic alterations becomes a chronic factor in the development of breast cancer. The combined effects of external environmental factors and the internal tumor microenvironment promote epigenetic alterations that drive tumorigenesis. This article focuses on the relevance of DNA methylation to breast cancer, describing the role of detecting DNA methylation in the early diagnosis, prediction, progression, metastasis, treatment, and prognosis of breast cancer, as well as recent advances. The reversibility of DNA methylation is utilized to target specific methylation aberrant promoters as well as related enzymes, from early prevention to late targeted therapy, to understand the journey of DNA methylation in breast cancer with a more comprehensive perspective. Meanwhile, methylation inhibitors in combination with other therapies have a wide range of prospects, providing hope to drug-resistant breast cancer patients.

Amide proton transfer-weighted imaging and stretch-exponential model DWI based 18F-FDG PET/MRI for differentiation of benign and malignant solitary pulmonary lesions.

OBJECTIVES: To differentiate benign and malignant solitary pulmonary lesions (SPLs) by amide proton transfer-weighted imaging (APTWI), mono-exponential model DWI (MEM-DWI), stretched exponential model DWI (SEM-DWI), and 18F-FDG PET-derived parameters. METHODS: A total of 120 SPLs patients underwent chest 18F-FDG PET/MRI were enrolled, including 84 in the training set (28 benign and 56 malignant) and 36 in the test set (13 benign and 23 malignant). MTRasym(3.5 ppm), ADC, DDC, α, SUVmax, MTV, and TLG were compared. The area under receiver-operator characteristic curve (AUC) was used to assess diagnostic efficacy. The Logistic regression analysis was used to identify independent predictors and establish prediction model. RESULTS: SUVmax, MTV, TLG, α, and MTRasym(3.5 ppm) values were significantly lower and ADC, DDC values were significantly higher in benign SPLs than malignant SPLs (all P < 0.01). SUVmax, ADC, and MTRasym(3.5 ppm) were independent predictors. Within the training set, the prediction model based on these independent predictors demonstrated optimal diagnostic efficacy (AUC, 0.976; sensitivity, 94.64%; specificity, 92.86%), surpassing any single parameter with statistical significance. Similarly, within the test set, the prediction model exhibited optimal diagnostic efficacy. The calibration curves and DCA revealed that the prediction model not only had good consistency but was also able to provide a significant benefit to the related patients, both in the training and test sets. CONCLUSION: The SUVmax, ADC, and MTRasym(3.5 ppm) were independent predictors for differentiation of benign and malignant SPLs, and the prediction model based on them had an optimal diagnostic efficacy.

Osiris17 is essential for stable integrin localization and function during insect wing epithelia remodeling.

The dynamic adhesion between cells and their extracellular matrix is essential for the development and function of organs. During insect wing development, two epithelial sheets contact each other at their basal sites through the interaction of ßPS integrins with the extracellular matrix. We report that Osiris17 contributes to the maintenance of ßPS integrins localization and function in developing wing of Drosophila and locust. In flies with reduced Osiris17 expression the epithelia sheets fail to maintain the integrity of basal cytoplasmic junctional bridges and basal adhesion. In contrast to the continuous basal integrin localization in control wings, this localization is disrupted during late stages of wing development in Osiris17 depleted flies. In addition, the subcellular localization revealed that Osiris17 co-localizes with the endosomal markers Rab5 and Rab11. This observation suggests an involvement of Osiris17 in endosomal recycling of integrins. Indeed, Osiris17 depletion reduced the numbers of Rab5 and Rab11 positive endosomes. Moreover, overexpression of Osiris17 increased co-localization of Rab5 and ßPS integrins and partially rescued the detachment phenotype in flies with reduced ßPS integrins. Taken together, our data suggest that Osiris17 is an endosome related protein that contributes to epithelial remodeling and morphogenesis by assisting basal integrins localization in insects.

Free-hand technique of C7 pedicle screw insertion using a simply defined entry point without fluoroscopic guidance for cervical spondylotic myelopathy patients with C3 to C6 instrumented by lateral mass screws: a retrospective cohort study.

BACKGROUND: Nowadays, both lateral mass screw (LMS) and pedicle screw were effective instrumentation for posterior stabilization of cervical spine. This study aims to evaluate the feasibility of a new free-hand technique of C7 pedicle screw insertion without fluoroscopic guidance for cervical spondylotic myelopathy (CSM) patients with C3 to C6 instrumented by lateral mass screws. METHODS: A total of 53 CSM patients underwent lateral mass screws instrumentation at C3 to C6 levels and pedicle screw instrumentation at C7 level were included. The preoperative 3-dimenional computed tomography (CT) reconstruction images of cervical spine were used to determine 2 different C7 pedicle screw trajectories. Trajectory A passed through the axis of the C7 pedicle while trajectory B selected the midpoint of the base of C7 superior facet as the entry point. All these 53 patients had the C7 pedicle screw inserted through trajectory B by free-hand without fluoroscopic guidance and the postoperative CT images were obtained to evaluate the accuracy of C7 pedicle screw insertion. RESULTS: Trajectory B had smaller transverse angle, smaller screw length, and smaller screw width but both similar sagittal angle and similar pedicle height when compared with trajectory A. A total of 106 pedicle screws were inserted at C7 through trajectory B and only 8 screws were displaced with the accuracy of screw placement as high as 92.5%. CONCLUSION: In CSM patients with C3 to C6 instrumented by LMS, using trajectory B for C7 pedicle screw insertion is easy to both identify the entry point and facilitate the rod insertion.

NCSP-PLM: An ensemble learning framework for predicting non-classical secreted proteins based on protein language models and deep learning.

Non-classical secreted proteins (NCSPs) refer to a group of proteins that are located in the extracellular environment despite the absence of signal peptides and motifs. They usually play different roles in intercellular communication. Therefore, the accurate prediction of NCSPs is a critical step to understanding in depth their associated secretion mechanisms. Since the experimental recognition of NCSPs is often costly and time-consuming, computational methods are desired. In this study, we proposed an ensemble learning framework, termed NCSP-PLM, for the identification of NCSPs by extracting feature embeddings from pre-trained protein language models (PLMs) as input to several fine-tuned deep learning models. First, we compared the performance of nine PLM embeddings by training three neural networks: Multi-layer perceptron (MLP), attention mechanism and bidirectional long short-term memory network (BiLSTM) and selected the best network model for each PLM embedding. Then, four models were excluded due to their below-average accuracies, and the remaining five models were integrated to perform the prediction of NCSPs based on the weighted voting. Finally, the 5-fold cross validation and the independent test were conducted to evaluate the performance of NCSP-PLM on the benchmark datasets. Based on the same independent dataset, the sensitivity and specificity of NCSP-PLM were 91.18% and 97.06%, respectively. Particularly, the overall accuracy of our model achieved 94.12%, which was 7~16% higher than that of the existing state-of-the-art predictors. It indicated that NCSP-PLM could serve as a useful tool for the annotation of NCSPs.

Structure-activity relationship of Caulerpa lentillifera polysaccharide in inhibiting lipid digestion.

Caulerpa lentillifera polysaccharide (CLP) has been characterized as a sulfated polysaccharide which can effectively inhibit lipid digestion. However, little information was known regarding its inhibitory mechanisms. In the present study, desulfation and degradation were conducted to prepare the derivatives of CLP, and a series of chemical and spectroscopic methods were used to elucidate the structure-activity relationship of CLP on the inhibitory effect of lipid digestion. Results revealed that CLP possessed excellent binding capacities for sodium cholate, sodium glycocholate, and sodium taurocholate. In addition, CLP can effectively inhibit lipase activity by quenching the fluorescence intensity, changing the secondary structure, and decreasing the UV-Vis absorbance. Of note, sulfate groups in CLP took a vital role in inhibiting lipase activity, while the molecular weight of CLP showed a positive correlation with the binding activities of bile acids. Furthermore, adding CLP into the whey protein isolate (WPI) emulsion system also impeded lipid digestion, indicating that CLP can be a potential reduced-fat nutraceutical used in food emulsion systems.

Diabetes Mellitus Mediates the Relationship Between Atherogenic Index of Plasma and Gallstones: A Population-Based Cross-Sectional Study.

Purpose: Previous studies have shown a correlation between diabetes mellitus and gallstone formation. The atherogenic index of plasma (AIP) is associated with many metabolic diseases. However, insufficient evidence still exists to elucidate the association between AIP and gallstones. The primary objective of this study was to investigate the correlation between AIP and gallstones in US adults, and the secondary objective was to analyze whether diabetes plays a mediating role in the association. Patients and Methods: Using data from the National Health and Nutrition Survey (NHANES) conducted between 2017 and March 2020, this study investigated the association between AIP and gallstone incidence in US adults. A variety of statistical methods were used to analyze the data in this study, including multivariate logistic regression, subgroup analyses, restricted cubic spline curves (RCS), and mediation effects analysis. In addition, two-stage linear regression was used to detect possible threshold and saturation effects. Results: A total of 6952 subjects were enrolled in the trial, of which 748 patients were diagnosed with gallstones. A significant positive association between AIP and gallstones was observed by fully adjusted multivariate logistic regression analysis, with an odds ratio (OR) of 1.45 and a 95% confidence interval (CI) of (1.09, 1.93). In addition, a non-linear positive association and saturation effect between AIP and gallstones were found, with an inflection point of 0.2246. Mediation analysis showed that diabetes had a mediating effect of 16.9% in the association between AIP and gallstones. Conclusion: This study suggests that elevated levels of AIP are linked to an augmented vulnerability to gallstone development, with diabetes serving as a mediating factor. These findings present a novel perspective on clinical approaches to prevent and manage gallstones.

Exploring the Alternative Conformation of a Known Protein Structure Based on Contact Map Prediction.

The rapid development of deep learning-based methods has considerably advanced the field of protein structure prediction. The accuracy of predicting the 3D structures of simple proteins is comparable to that of experimentally determined structures, providing broad possibilities for structure-based biological studies. Another critical question is whether and how multistate structures can be predicted from a given protein sequence. In this study, analysis of tens of two-state proteins demonstrated that deep learning-based contact map predictions contain structural information on both states, which suggests that it is probably appropriate to change the target of deep learning-based protein structure prediction from one specific structure to multiple likely structures. Furthermore, by combining deep learning- and physics-based computational methods, we developed a protocol for exploring alternative conformations from a known structure of a given protein, by which we successfully approached the holo-state conformations of multiple representative proteins from their apo-state structures.

Tumor-associated astrocytes promote tumor progression of Sonic Hedgehog medulloblastoma by secreting lipocalin-2.

Sonic Hedgehog (SHH) subgroup of medulloblastoma (MB) accounts for about 25% of all subgroups of MB. Tumor microenvironment (TME) may play a key role in the tumor progression and therapeutic resistance. Tumor-associated astrocytes (TAAs) are reshaped to drive tumor progression through multiple paracrine signals. However, the mechanism by which TAAs modulate MB cells remains elusive. Here, we illuminated that TAAs showed a specific and dynamic pattern during SHH-MB development. Most TAAs gathered to the tumor margin during the tumor progression, rather than evenly distributed in the early-stage tumors. We further demonstrated that lipocalin-2 (LCN2) secreted by TAAs could promote the tumor growth and was correlated with the poor prognosis of MB patients. Knocking down LCN2 in TAAs in vitro impeded the proliferation and migration abilities of MB cells. In addition, we identified that TAAs accelerated the tumor growth by secreting LCN2 via STAT3 signaling pathway. Accordingly, blockade of STAT3 signaling by its inhibitor WP1066 and AAV-Lcn2 shRNA, respectively, in TAAs abrogated the effects of LCN2 on tumor progression in vitro and in vivo. In summary, we for the first time clarified that LCN2, secreted by TAAs, could promote MB tumor progression via STAT3 pathway and has potential prognostic value. Our findings unveiled a new sight in reprogramming the TME of SHH-MB and provided a potential therapeutic strategy targeting TAAs.

Nanoscale one-dimensional close packing of interfacial alkali ions driven by water-mediated attraction.

The permeability and selectivity of biological and artificial ion channels correlate with the specific hydration structure of single ions. However, fundamental understanding of the effect of ion-ion interaction remains elusive. Here, via non-contact atomic force microscopy measurements, we demonstrate that hydrated alkali metal cations (Na+ and K+) at charged surfaces could come into close contact with each other through partial dehydration and water rearrangement processes, forming one-dimensional chain structures. We prove that the interplay at the nanoscale between the water-ion and water-water interaction can lead to an effective ion-ion attraction overcoming the ionic Coulomb repulsion. The tendency for different ions to become closely packed follows the sequence K+ > Na+ > Li+, which is attributed to their different dehydration energies and charge densities. This work highlights the key role of water molecules in prompting close packing and concerted movement of ions at charged surfaces, which may provide new insights into the mechanism of ion transport under atomic confinement.