Integrated single-cell and bulk RNA-sequencing data reveal molecular subtypes based on lactylation-related genes and prognosis and therapeutic response in glioma.

Objectives: Glioma, the most common and aggressive form of brain cancer, possesses a complex biology, which makes elucidating its underlying mechanisms and developing effective treatment strategies challenging. Lactylation is a recently discovered post-translational modification and has emerged as a novel research target to understand its role in various biological processes and diseases. Herein, we explored the role of lactylation in gliomas. Methods: Single-cell RNA-sequencing (scRNA-seq) data were downloaded from the Tumour Immune Single-Cell Hub database. The R package 'Seurat' was used for processing the scRNA-seq data. Lactylation-related genes were identified from published literature and the Molecular Signatures Database. An unsupervised clustering method was used to identify glioma subtypes based on identified lactylation-related genes. Differences among the various clusters were examined, including clinical features, differentially expressed genes (DEGs), enriched pathways and immune cell infiltrates. A lactylation score was generated to predict the overall survival (OS) of patients with glioma using DEGs between the two clusters. Results: The lactylation-related genes were obtained from the scRNA-seq data, identifying two molecular subtypes, and a prognostic signature was established to stratify patients with glioma into high- and low-score groups. Analysis of the tumour immune microenvironment revealed that patients in the high-score group exhibited increased immune cell infiltration, chemokine expression and immune checkpoint expression but exhibited worse OS and better response to immunotherapy. Conclusions: Altogether, we established a novel signature based on lactylation-related clusters for robust survival prediction and immunotherapeutic response in gliomas.

Spatiotemporal Concurrent PARP Inhibitor Sensitization Based on Radiation-Responsive Nanovesicles for Lung Cancer Chemoradiotherapy.

The implementation of chemoradiation combinations has gained great momentum in clinical practices. However, the full utility of this paradigm is often restricted by the discordant tempos of action of chemotherapy and radiotherapy. Here, a gold nanoparticle-based radiation-responsive nanovesicle system loaded with cisplatin and veliparib, denoted as CV-Au NVs, is developed to augment the concurrent chemoradiation effect in a spatiotemporally controllable manner of drug release. Upon irradiation, the in situ generation of •OH induces the oxidation of polyphenylene sulfide from being hydrophobic to hydrophilic, resulting in the disintegration of the nanovesicles and the rapid release of the entrapped cisplatin and veliparib (the poly ADP-ribose polymerase (PARP) inhibitor). Cisplatin-induced DNA damage and the impairment of the DNA repair mechanism mediated by veliparib synergistically elicit potent pro-apoptotic effects. In vivo studies suggest that one-dose injection of the CV-Au NVs and one-time X-ray irradiation paradigm effectively inhibit tumor growth in the A549 lung cancer model. This study provides new insight into designing nanomedicine platforms in chemoradiation therapy from a vantage point of synergizing both chemotherapy and radiation therapy in a spatiotemporally concurrent manner.

CDK4/6 inhibition sensitizes MEK inhibition by inhibiting cell cycle and proliferation in pancreatic ductal adenocarcinoma.

Pancreatic ductal adenocarcinoma (PDAC) is not sensitive to most chemotherapy drugs, leading to poor chemotherapy efficacy. Recently, Trametinib and Palbociclib have promising prospects in the treatment of pancreatic cancer. This article aims to explore the effects of Trametinib on pancreatic cancer and address the underlying mechanism of resistance as well as its reversal strategies. The GDSC (Genomics of Drug Sensitivity in Cancer) and CTD2 (Cancer Target Discovery and Development) were utilized to screen the potential drug candidate in PDAC cell lines. The dose-increase method combined with the high-dose shock method was applied to induce the Trametinib-resistant PANC-1 and MIA PaCa-2 cell lines. The CCK8 proliferation assay, colony formation assay, flow cytometry, and western blot were conducted to verify the inhibitory effect of Trametinib and Palbociclib. RNA-seq was performed in resistant PDAC cell lines to find the differential expression genes related to drug resistance and predict pathways leading to the reversal of Trametinib resistance. The GDSC and CTD2 database screening revealed that Trametinib demonstrates a significant inhibitory effect on PDAC. We found that Trametinib has a lower IC50 than Gemcitabine in PDAC cell lines. Both Trametinib and Gemcitabine can decrease the proliferation capacity of pancreatic cells, induce cell cycle arrest, and increase apoptosis. Simultaneously, the phosphorylation of the AKT and ERK pathways were inhibited by the treatment of Trametinib. In addition, the RNA-seq of Trametinib-induced resistance PDAC cell lines reveals that the cyclin-dependent kinase (CDK)-RB-E2F regulatory axis and G2/M DNA damage checkpoint might lead the drug resistance. Besides, the combination of Trametinib with Palbociclib could inhibit the proliferation and cell cycle of both resistant cells lines and also restore the sensitivity of drug-resistant cells to Trametinib. Last but not least, the interferon-α and interferon-γ expression were upregulated in resistance cell lines, which might lead to the reversal of drug resistance. The study shows Trametinib has a critical inhibitory effect on PDAC. Besides, the combination of Trametinib with Palbociclib can inhibit the proliferation of PDAC-resistant cells.

Potential Strategy to Control the Organic Components of Condensable Particulate Matter: A Critical Review.

More and more attention has been paid to condensable particulate matter (CPM) since its emissions have surpassed that of filterable particulate matter (FPM) with the large-scale application of ultralow-emission reform. CPM is a gaseous material in the flue stack but instantly turns into particles after leaving the stack. It is composed of inorganic and organic components. Organic components are an important part of CPM, and they are an irritant, teratogenic, and carcinogenic, which triggers photochemical smog, urban haze, and acid deposition. CPM organic components can aggravate air pollution and climate change; therefore, consideration should be given to them. Based on existing methods for removing atmospheric organic pollutants and combined with the characteristics of CPM organic components, we provide a critical overview from the aspects of (i) fundamental cognition of CPM, (ii) common methods to control CPM organic components, and (iii) catalytic oxidation of CPM organic components. As one of the most encouraging methods, catalytic oxidation is discussed in detail, especially in combination with selective catalytic reduction (SCR) technology, to meet the growing demands for multipollutant control (MPC). We believe that this review is inspiring for a fuller understanding and deeper exploration of promising approaches to control CPM organic components.

Expression of concern: Gadolinium embedded iron oxide nanoclusters as T1-T2 dual-modal MRI-visible vectors for safe and efficient siRNA delivery.

Expression of concern for 'Gadolinium embedded iron oxide nanoclusters as T1-T2 dual-modal MRI-visible vectors for safe and efficient siRNA delivery' by Xiaoyong Wang et al., Nanoscale, 2013, 5, 8098-8104, https://doi.org/10.1039/C3NR02797J.

Synthetic Leaves Based on Crystalline Olefin-Linked Covalent Organic Frameworks for Efficient CO2 Photoreduction with Water.

We report, for the first time, a new synthetic strategy for the preparation of crystalline two-dimensional olefin-linked covalent organic frameworks (COFs) based on aldol condensation between benzodifurandione and aromatic aldehydes. Olefin-linked COFs can be facilely crystallized through either a pyridine-promoted solvothermal process or a benzoic anhydride-mediated organic flux synthesis. The resultant COF leaf with high in-plane π-conjugation exhibits efficient visible-light-driven photoreduction of carbon dioxide (CO2) with water (H2O) in the absence of any photosensitizer, sacrificial agents, or cocatalysts. The production rate of carbon monoxide (CO) reaches as high as 158.1 µmol g-1 h-1 with near 100% CO selectivity, which is accompanied by the oxidation of H2O to oxygen. Both theoretical and experimental results confirm that the key lies in achieving exceptional photoinduced charge separation and low exciton binding. We anticipate that our findings will facilitate new possibilities for the development of semiconducting COFs with structural diversity and functional variability.

Comparison of traditional and suctioning ureteral access sheath during retrograde intrarenal surgery in the treatment of renal calculi.

PURPOSE: This study aims to compare the efficiency and clinical outcomes between the suctioning ureteral access sheath (UAS) group and the traditional UAS group during retrograde intrarenal surgery (RIRS) for kidney stones and explore the impact of suctioning UAS on postoperative infectious complications. METHODS: We retrospectively reviewed the clinical data of 162 patients with kidney stones who underwent RIRS with a traditional UAS (n = 74) or a suctioning UAS (n = 71) between March 2021 and May 2023. RESULTS: The mean operative time in suctioning UAS group (39.03 ± 18.01 s) was significantly shorter than that (49.73 ± 20.77 s) in the traditional UAS group (P = 0.037). The mean postoperative hospital stay was significantly shorter in the suctioning UAS group (1.57 ± 0.82d) compared with the traditional UAS group (2.30 ± 1.6 2 d) (P = 0.032). The instant SFRs were significantly higher in the suctioning UAS group (88.73%) than in the traditional UAS group (75.68%) (P = 0.040). The overall SFR in suctioning UAS group (92.96%) was slightly higher than the traditional UAS group (85.14%). The incidence of overall complications was significantly higher in the traditional UAS group (35.14%) than in the suctioning UAS group (16.90%) (P = 0.013). In multivariate analysis, female patients (OR 0.053, P = 0.018), positive urine WBC (OR 10.382, P = 0.034), operative time > 60 min (OR 20.231, P = 0.032), and the application of traditional UAS (OR 0.042, P = 0.017) were independent risk factors associated with infectious complications. CONCLUSION: We demonstrated that suctioning UAS provided a higher instant SFR and fewer postoperative infectious complications during RIRS, and patients with predictable risk factors for infectious complications could potentially benefit from the use of the suctioning UAS.

Coassembly Nanomedicine Mediated by Intermolecular Interactions Between Methotrexate and Baricitinib for Improved Rheumatoid Arthritis Treatment.

The combination of anti-rheumatoid arthritis (RA) drugs methotrexate (MTX) and baricitinib (BTN) has been reported to improve RA treatment efficacy. However, study on the strategy of combination is elusive when considering the benefit of the synergy between MTX and BTN. In this study, we found that the N-heterocyclic rings in the MTX and BTN offer hydrogen bonds and π-π stacking interactions, driving the formation of exquisite vesicular morphology of nanovesicles, denoted as MB NVs. The MB NVs with the MTX/BTN weight ratio of 2:1, MB NVs (2:1), showed an improved anti-RA effect through the synergy between the anti-inflammatory and antiproliferative responses. This work presents that the intermolecular interactions between drug molecules could mediate the coassembly behavior into nanomedicine as well as the therapy synergy both in vitro and in vivo, which may provide further understanding on the rational design of combination nanomedicine for therapeutic purposes.

The effect of multiple factors on changes in organic-inorganic fractions of condensable particulate matter during coal combustion.

Condensable particulate matter (CPM) from coal combustion is the focus of current pollutant emission studies, and CPM can be divided into inorganic and organic fractions according to the component characteristics. At present, the effects of different factors in the combustion process on the organic and inorganic components of CPM have not been discussed systematically. Here, we conducted combustion experiments collected the generated CPM on a well-controlled drip tube furnace, and investigated the effects of different factors on the generation of organic and inorganic components of CPM by varying the furnace wall insulation temperature, the ratio of gas supply components and the water vapor content in the flue gas. The results showed that the increase in combustion temperature (1300-1500 °C) and oxygen concentration (15-25%) reduced the total CPM generation by 9.8% and 19.98%, respectively, and the intervention of water vapor increased the ability of the whole CPM sampling device to capture ultrafine condensable particles. The generation of CPM organic components decreased with the enhancement of combustion temperature and oxygen content on combustion characteristics, and alkanes shifted to low carbon content. The amount of CPM inorganic components increased with the increase of water vapor content in the flue gas, and this change was dominated by SO42-. The above results provide a feasible idea for the next step of the precise reduction of CPM components.

Functional analysis reveals calcium-sensing receptor gene regulating cell-cell junction in renal tubular epithelial cells.

PURPOSE: Calcium-sensing receptor (CASR) influences the expression pattern of multiple genes in renal tubular epithelial cells. The objective of this inquiry was to explore the molecular mechanisms of CASR in renal tubular epithelial cells and nephrolithiasis. METHODS: HK-2 cells were transfected with lentiviruses carrying either CASR (named CASR) or an empty vector negative control (named NC), as well as shRNA intended to target CASR (named shCASR) or its corresponding negative control (named shNC). CCK-8 assay was used to detect the effect of CASR on the proliferation of HK-2 cells. RNA-Sequencing was applied to explore potential pathways regulated by CASR in HK-2 cells. RESULTS: PCR and western blot results showed that CASR expression was significantly increased in CASR cells and was decreased in shCASR cells when compared to their corresponding negative control, respectively. CCK-8 assay revealed that CASR inhibited the proliferation of HK-2 cells. RNA-Sequencing results suggested that the shCASR HK-2 cells exhibited a significant up-regulation of 345 genes and a down-regulation of 366 genes. These differentially expressed genes (DEGs) were related to cell apoptosis and cell development. In CASR HK-2 cells, 1103 DEGs primarily functioned in mitochondrial energy metabolism, and amino acid metabolism. With the Venn diagram, 4 DEGs (Clorf116, ENPP3, IL20RB, and CLDN2) were selected as the hub genes regulated by CASR. Enrichment analysis revealed that these hub genes were involved in cell-cell junction, and epithelial cell development. CONCLUSIONS: In summary, our investigation has the potential to offer novel perspectives on CASR regulating cell-cell junction in HK-2 cells.

METTL16 suppressed the proliferation and cisplatin-chemoresistance of bladder cancer by degrading PMEPA1 mRNA in a m6A manner through autophagy pathway.

N6-methyladenosine (m6A) is important in the physiological processes of many species. Methyltransferase-like 16 (METTL16) is a novel discovered m6A methylase, regulating various tumors in an m6A-dependent manner. However, its function in bladder cancer (BLCA) remains largely unclear. In the present study, we found that low expression of METTL16 predicted poor survival in BLCA patients. METTL16 inhibited the proliferation and cisplatin-resistance function of bladder cancer cells in vitro and in vivo. In addition, METTL16 reduced the mRNA stability of prostate transmembrane protein androgen induced-1 (PMEPA1) via binding to its m6A site in the 3'-UTR, thereby inhibited the proliferation of bladder cancer cells and increased the sensitivity of cisplatin through PMEPA1-mediated autophagy pathway. Finally, we found that hypoxia-inducible factor 2α (HIF-2α) exerted its tumor-promoting effect by binding the METTL16 promoter region to repress its transcription. Taken together, High expression of METTL16 predicted better survival in BLCA. METTL16 significantly inhibited bladder cancer cell proliferation and sensitized bladder cancer cells to cisplatin via HIF-2α-METTL16-PMEPA1-autophagy axis in a m6A manner. These findings might provide fresh insights into BLCA therapy.

Stop moving: MR motion correction as an opportunity for artificial intelligence.

Subject motion is a long-standing problem of magnetic resonance imaging (MRI), which can seriously deteriorate the image quality. Various prospective and retrospective methods have been proposed for MRI motion correction, among which deep learning approaches have achieved state-of-the-art motion correction performance. This survey paper aims to provide a comprehensive review of deep learning-based MRI motion correction methods. Neural networks used for motion artifacts reduction and motion estimation in the image domain or frequency domain are detailed. Furthermore, besides motion-corrected MRI reconstruction, how estimated motion is applied in other downstream tasks is briefly introduced, aiming to strengthen the interaction between different research areas. Finally, we identify current limitations and point out future directions of deep learning-based MRI motion correction.

Synergistic removal performance and mechanism of Cd(II) and As(III) from irrigation water by iron sulfide-based porous biochar.

Since Cd(II) and As(III) have extremely opposite chemical characteristics, it is a huge challenging to simultaneously remove these two ions from aqueous solutions. Therefore, a novel iron sulfide-based porous biochar (FSB) was synthesized and used to evaluate its Cd(II) and As(III) removal performance and mechanisms. The characterization and batch experiments results indicated that FeS was successfully loaded on the surface of biochar and increased its adsorption sites. The iron sulfide-based porous biochar was very favorable for the removal of Cd(II) and As(III) in the weakly acidic environment. The maximum adsorption of Cd(II) and As(III) by FSB was 108.8 mg g-1 and 76.3 mg g-1, respectively, according to the Langmuir and Freundlich isothermal adsorption model, and the adsorption equilibrium time was 12 h and 4 h, respectively, according to the pseudo-second-order kinetic model. In the coexisting ion system, Cd(II) adsorption was suppressed by Ca2+, Mg2+, and humic acid, but enhanced by PO43- and As(III). As(III) adsorption was inhibited by PO43- and humic acid. Precipitation and complexation are the predominant adsorption mechanisms of Cd(II) and As(III), which contribute to the formation of Cd-O, Fe-O-Cd, As-O, Fe-O-As, ternary complex Cd-Fe-As, and stable compounds FeAsO4·2H2O and CdS. Therefore, The iron sulfide-based porous biochar can be an efficient and environmentally friendly candidate for the treatment of Cd(II) and As(III) co-polluted irrigation water.

Identification of Hub Genes and Physiological Effects of Overexpressing the Photosynthesis-Related Gene Soly720 in Tomato under High-CO2 Conditions.

Changes in the atmospheric CO2 concentration influence plant growth and development by affecting the morphological structure and photosynthetic performance. Despite evidence for the macro-effects of elevated CO2 concentrations on plant morphology and yield in tomato, the gene regulatory network and key genes related to cross-regulation have not been reported. To identify the hub genes and metabolic pathways involved in the response of tomato to CO2 enrichment, weighted gene co-expression network analysis was conducted using gene expression profiles obtained by RNA sequencing. The role of the photosynthesis-related gene Soly720 (Solyc01g007720) in CO2-enriched tomato plants was explored. Tomato plants responded to CO2 enrichment primarily through RNA-related pathways and the metabolism of amino acids, fatty acids, and carbohydrates. The hub genes in co-expression networks were associated with plant growth and development, including cellular components and photosynthesis. Compared to wild-type plants, transgenic plants overexpressing the Soly720 gene exhibited 13.4%, 5.5%, 8.9%, and 4.1% increases in plant height, stem diameter, leaf length, and leaf width, respectively, under high-CO2 conditions. The morphological improvements in transgenic plants were accompanied by enhancement of photosynthetic performance in terms of chlorophyll contents, photosynthetic characteristics, and key enzyme activities. This study elucidates the response network of tomato to CO2 enrichment and demonstrates the regulatory role of Soly720 in photosynthesis under high-CO2 conditions.

Predicting pathological complete response to neoadjuvant systemic therapy for triple-negative breast cancers using deep learning on multiparametric MRIs.

We trained and validated a deep learning model that can predict the treatment response to neoadjuvant systemic therapy (NAST) for patients with triple negative breast cancer (TNBC). Dynamic contrast enhanced (DCE) MRI and diffusion-weighted imaging (DWI) of the pre-treatment (baseline) and after four cycles (C4) of doxorubicin/cyclophosphamide treatment were used as inputs to the model for prediction of pathologic complete response (pCR). Based on the standard pCR definition that includes disease status in either breast or axilla, the model achieved areas under the receiver operating characteristic curves (AUCs) of 0.96 ± 0.05, 0.78 ± 0.09, 0.88 ± 0.02, and 0.76 ± 0.03, for the training, validation, testing, and prospective testing groups, respectively. For the pCR status of breast only, the retrained model achieved prediction AUCs of 0.97 ± 0.04, 0.82 ± 0.10, 0.86 ± 0.03, and 0.83 ± 0.02, for the training, validation, testing, and prospective testing groups, respectively. Thus, the developed deep learning model is highly promising for predicting the treatment response to NAST of TNBC.Clinical Relevance- Deep learning based on serial and multiparametric MRIs can potentially distinguish TNBC patients with pCR from non-pCR at the early stage of neoadjuvant systemic therapy, potentially enabling more personalized treatment of TNBC patients.

Magnetic Resonance Imaging Nanoprobe Quantifies Nitric Oxide for Evaluating M1/M2 Macrophage Polarization and Prognosis of Cancer Treatments.

Macrophages play a crucial role in immune activation and provide great value in the prognosis of cancer treatments. Current strategies for prognostic evaluation of macrophages mainly target the specific biomarkers to reveal the number and distribution of macrophages in the tumors, whereas the phenotypic change of M1 and M2 macrophages in situ is less understood. Here, we designed an ultrasmall superparamagnetic iron oxide nanoparticle-based molecular imaging nanoprobe to quantify the repolarization of M2 to M1 macrophages by magnetic resonance imaging (MRI) using the redox-active nitric oxide (NO) as a vivid chemical target. The nanoprobe equipped with O-phenylenediamine groups could react with the intracellular NO molecules during the repolarization of M2 macrophages to the M1 phenotype, leading to electrical attraction and colloidal aggregation of the nanoprobes. Consequently, the prominent changes of the T1 and T2 relaxation in MRI allow for the quantification of the macrophage polarization. In a 4T1 breast cancer model, the MRI nanoprobe was able to reveal macrophage polarization and predict treatment efficiency in both immunotherapy and radiotherapy paradigms. This study presents a noninvasive approach to monitor the phenotypic changes of M2 to M1 macrophages in the tumors, providing insight into the prognostic evaluation of cancer treatments regarding macrophage-mediated immune responses.

Membrane Proteins and Membrane Curvature: Mutual Interactions and a Perspective on Disease Treatments.

The pathogenesis of various diseases often involves an intricate interplay between membrane proteins and membrane curvature. Understanding the underlying mechanisms of this interaction could offer novel perspectives on disease treatment. In this review, we provide an introduction to membrane curvature and its association with membrane proteins. Furthermore, we delve into the impact and potential implications of this interaction in the context of disease treatment. Lastly, we discuss the prospects and challenges associated with harnessing these interactions for effective disease management, aiming to provide fresh insights into therapeutic strategies.

Longitudinal dynamic contrast-enhanced MRI radiomic models for early prediction of response to neoadjuvant systemic therapy in triple-negative breast cancer.

Early prediction of neoadjuvant systemic therapy (NAST) response for triple-negative breast cancer (TNBC) patients could help oncologists select individualized treatment and avoid toxic effects associated with ineffective therapy in patients unlikely to achieve pathologic complete response (pCR). The objective of this study is to evaluate the performance of radiomic features of the peritumoral and tumoral regions from dynamic contrast-enhanced magnetic resonance imaging (DCE-MRI) acquired at different time points of NAST for early treatment response prediction in TNBC. This study included 163 Stage I-III patients with TNBC undergoing NAST as part of a prospective clinical trial (NCT02276443). Peritumoral and tumoral regions of interest were segmented on DCE images at baseline (BL) and after two (C2) and four (C4) cycles of NAST. Ten first-order (FO) radiomic features and 300 gray-level-co-occurrence matrix (GLCM) features were calculated. Area under the receiver operating characteristic curve (AUC) and Wilcoxon rank sum test were used to determine the most predictive features. Multivariate logistic regression models were used for performance assessment. Pearson correlation was used to assess intrareader and interreader variability. Seventy-eight patients (48%) had pCR (52 training, 26 testing), and 85 (52%) had non-pCR (57 training, 28 testing). Forty-six radiomic features had AUC at least 0.70, and 13 multivariate models had AUC at least 0.75 for training and testing sets. The Pearson correlation showed significant correlation between readers. In conclusion, Radiomic features from DCE-MRI are useful for differentiating pCR and non-pCR. Similarly, predictive radiomic models based on these features can improve early noninvasive treatment response prediction in TNBC patients undergoing NAST.

Enhancing maize's nitrogen-fixing potential through ZmSBT3, a gene suppressing mucilage secretion.

Maize (Zea mays) requires substantial amounts of nitrogen, posing a challenge for its cultivation. Recent work discovered that some ancient Mexican maize landraces harbored diazotrophic bacteria in mucilage secreted by their aerial roots. To see if this trait is retained in modern maize, we conducted a field study of aerial root mucilage (ARM) in 258 inbred lines. We observed that ARM secretion is common in modern maize, but the amount significantly varies, and only a few lines have retained the nitrogen-fixing traits found in ancient landraces. The mucilage of the high-ARM inbred line HN5-724 had high nitrogen-fixing enzyme activity and abundant diazotrophic bacteria. Our genome-wide association study identified 17 candidate genes associated with ARM across three environments. Knockouts of one candidate gene, the subtilase family gene ZmSBT3, confirmed that it negatively regulates ARM secretion. Notably, the ZmSBT3 knockout lines had increased biomass and total nitrogen accumulation under nitrogen-free culture conditions. High ARM was associated with three ZmSBT3 haplotypes that were gradually lost during maize domestication, being retained in only a few modern inbred lines such as HN5-724. In summary, our results identify ZmSBT3 as a potential tool for enhancing ARM, and thus nitrogen fixation, in maize.