DNA hypomethylation patterns and their impact on the tumor microenvironment in colorectal cancer.

BACKGROUND: Recent research underscores the pivotal role of immune checkpoints as biomarkers in colorectal cancer (CRC) therapy, highlighting the dynamics of resistance and response to immune checkpoint inhibitors. The impact of epigenetic alterations in CRC, particularly in relation to immune therapy resistance, is not fully understood. METHODS: We integrated a comprehensive dataset encompassing TCGA-COAD, TCGA-READ, and multiple GEO series (GSE14333, GSE37892, GSE41258), along with key epigenetic datasets (TCGA-COAD, TCGA-READ, GSE77718). Hierarchical clustering, based on Euclidean distance and Ward's method, was applied to 330 primary tumor samples to identify distinct clusters. The immune microenvironment was assessed using MCPcounter. Machine learning algorithms were employed to predict DNA methylation patterns and their functional enrichment, in addition to transcriptome expression analysis. Genomic mutation profiles and treatment response assessments were also conducted. RESULTS: Our analysis delineated a specific tumor cluster with CpG Island (CGI) methylation, termed the Demethylated Phenotype (DMP). DMP was associated with metabolic pathways such as oxidative phosphorylation, implicating increased ATP production efficiency in mitochondria, which contributes to tumor aggressiveness. Furthermore, DMP showed activation of the Myc target pathway, known for tumor immune suppression, and exhibited downregulation in key immune-related pathways, suggesting a tumor microenvironment characterized by diminished immunity and increased fibroblast infiltration. Six potential therapeutic agents-lapatinib, RDEA119, WH.4.023, MG.132, PD.0325901, and AZ628-were identified as effective for the DMP subtype. CONCLUSION: This study unveils a novel epigenetic phenotype in CRC linked to resistance against immune checkpoint inhibitors, presenting a significant step toward personalized medicine by suggesting epigenetic classifications as a means to identify ideal candidates for immunotherapy in CRC. Our findings also highlight potential therapeutic agents for the DMP subtype, offering new avenues for tailored CRC treatment strategies.

Rational Design of an In-Situ Polymer-Inorganic Hybrid Solid Electrolyte Interphase for Realising Stable Zn Metal Anode under Harsh Conditions.

The in-depth understanding of the composition-property-performance relationship of solid electrolyte interphase (SEI) is the basis of developing a reliable SEI to stablize the Zn anode-electrolyte interface, but it remains unclear in rechargeable aqueous zinc ion batteries. Herein, a well-designed electrolyte based on 2 M Zn(CF3SO3)2-0.2 M acrylamide-0.2 M ZnSO4 is proposed. A robust polymer (polyacrylamide)-inorganic (Zn4SO4(OH)6.xH2O) hybrid SEI is in situ constructed on Zn anodes through controllable polymerization of acrylamide and coprecipitation of SO4 2- with Zn2+ and OH-. For the first time, the underlying SEI composition-property-performance relationship is systematically investigated and correlated. The results showed that the polymer-inorganic hybrid SEI, which integrates the high modulus of the inorganic component with the high toughness of the polymer ingredient, can realize high reversibility and long-term interfacial stability, even under ultrahigh areal current density and capacity (30 mA cm-2~30 mAh cm-2). The resultant Zn||NH4V4O10 cell also exhibits excellent cycling stability. This work will provide a guidance for the rational design of SEI layers in rechargeable aqueous zinc ion batteries.

Liver metastases across cancer types sharing tumor environment immunotolerance can impede immune response therapy and immune monitoring.

BACKGROUND: Hepatic immune tolerance might contribute to the development of therapeutic resistance to immunotherapy. However, addressing this issue is challenging since the efficacy of immunotherapy in the context of liver metastasis (LM) remains poorly studied. Here, we aimed to establish an LM common immune feature (LMCIF) score to quantify the characteristics of LM immunotolerance across cancer types for assisting clinical disease management. METHODS: Large-scale clinical data were collected to identify the prognosis of LM. Multi-omics datasets of metastatic cancers with LM special immune-related pathways (LMSIPs) from the Molecular Signatures Database (MSigDB)were used to obtain an LMCIF cluster. Based on differential expression genes (DEGs), a novel LMCIF score for the LMCIF cluster was constructed. In addition, multi-omics, and immunohistochemistry (IHC) data from the public and in-house cohorts were used to explore the features of LM, and LMCIF score. RESULTS: Patients with LM had a worse prognosis and significantly lower infiltration of immune cells than patients with metastasis to other organs when analyzed with combined clinical and RNA sequencing data. After extracting the LMCIF cluster from 373 samples by utilizing 29 LMSIPs and validating them in a microarray cohort, an LMCIF score was established to confirm the role of the immunosuppressive environment as a contributor to the poor prognosis of LM across cancer types. Moreover, this LMCIF score could be used to predict the immune response of cancer patients undergoing immunotherapy. Finally, we identified that the majority of the 31 LMCIF genes exhibited a negative correlation with TME cells in LM patients, one of them, KRT19, which possessed the strongest positive correlation with LMCIF score, was confirmed to have an immunosuppressive effect through IHC analysis. CONCLUSIONS: Our results suggest that LM across cancer types share similar immunological profiles that induce immunotolerance and escape from immune monitoring. The novel LMCIF score represents a common liver metastasis immune cluster for predicting immunotherapy response, the results of which might benefit clinical disease management.

Localised degradation within sulfide-based all-solid-state electrodes visualised by Raman mapping.

The distribution of degradation products, before and after cycling, within common sulfide-based solid electrolytes (ß-Li3PS4, Li6PS5Cl and Li10GeP2S12) was mapped using Raman microscopy. All composite electrodes displayed the appearance of side reaction products after the initial charge-discharge cycle, located at the site of a LiNi0.6Mn0.2Co0.2O2 particle.

Understanding the Influence of Li7La3Zr2O12 Nanofibers on Critical Current Density and Coulombic Efficiency in Composite Polymer Electrolytes.

Composite polymer electrolytes (CPEs) are attractive materials for solid-state lithium metal batteries, owing to their high ionic conductivity from ceramic ionic conductors and flexibility from polymer components. As with all lithium metal batteries, however, CPEs face the challenge of dendrite formation and propagation. Not only does this lower the critical current density (CCD) before cell shorting, but the uncontrolled growth of lithium deposits may limit Coulombic efficiency (CE) by creating dead lithium. Here, we present a fundamental study on how the ceramic components of CPEs influence these characteristics. CPE membranes based on poly(ethylene oxide) and lithium bis(trifluoromethanesulfonyl)imide (PEO-LiTFSI) with Li7La3Zr2O12 (LLZO) nanofibers were fabricated with industrially relevant roll-to-roll manufacturing techniques. Galvanostatic cycling with lithium symmetric cells shows that the CCD can be tripled by including 50 wt % LLZO, but half-cell cycling reveals that this comes at the cost of CE. Varying the LLZO loading shows that even a small amount of LLZO drastically lowers the CE, from 88% at 0 wt % LLZO to 77% at just 2 wt % LLZO. Mesoscale modeling reveals that the increase in CCD cannot be explained by an increase in the macroscopic or microscopic stiffness of the electrolyte; only the microstructure of the LLZO nanofibers in the PEO-LiTFSI matrix slows dendrite growth by presenting physical barriers that the dendrites must push or grow around. This tortuous lithium growth mechanism around the LLZO is corroborated with mass spectrometry imaging. This work highlights important elements to consider in the design of CPEs for high-efficiency lithium metal batteries.

Photosensitisation of inkjet printed graphene with stable all-inorganic perovskite nanocrystals.

All-inorganic perovskite nanocrystals (NCs) with enhanced environmental stability are of particular interest for optoelectronic applications. Here we report on the formulation of CsPbX3 (X is Br or I) inks for inkjet deposition and utilise these NCs as photosensitive layers in graphene photodetectors, including those based on single layer graphene (SLG) as well as inkjet-printed graphene (iGr) devices. The performance of these photodetectors strongly depends on the device structure, geometry and the fabrication process. We achieve a high photoresponsivity, R > 106 A W-1 in the visible wavelength range and a spectral response controlled by the halide content of the perovskite NC ink. By utilising perovskite NCs, iGr and gold nanoparticle inks, we demonstrate a fully inkjet-printed photodetector with R ≈ 20 A W-1, which is the highest value reported to date for this type of device. The performance of the perovskite/graphene photodetectors is explained by transfer of photo-generated charge carriers from the perovskite NCs into graphene and charge transport through the iGr network. The perovskite ink developed here enabled realisation of stable and sensitive graphene-based photon detectors. Compatibility of inkjet deposition with conventional Si-technologies and with flexible substrates combined with high degree of design freedom provided by inkjet deposition offers opportunities for partially and fully printed optoelectronic devices for applications ranging from electronics to environmental sciences.

Multiomics characterization and verification of clear cell renal cell carcinoma molecular subtypes to guide precise chemotherapy and immunotherapy.

Clear cell renal cell carcinoma (ccRCC) is a heterogeneous tumor with different genetic and molecular alterations. Schemes for ccRCC classification system based on multiomics are urgent, to promote further biological insights. Two hundred and fifty-five ccRCC patients with paired data of clinical information, transcriptome expression profiles, copy number alterations, DNA methylation, and somatic mutations were collected for identification. Bioinformatic analyses were performed based on our team's recently developed R package "MOVICS." With 10 state-of-the-art algorithms, we identified the multiomics subtypes (MoSs) for ccRCC patients. MoS1 is an immune exhausted subtype, presented the poorest prognosis, and might be caused by an exhausted immune microenvironment, activated hypoxia features, but can benefit from PI3K/AKT inhibitors. MoS2 is an immune "cold" subtype, which represented more mutation of VHL and PBRM1, favorable prognosis, and is more suitable for sunitinib therapy. MoS3 is the immune "hot" subtype, and can benefit from the anti-PD-1 immunotherapy. We successfully verified the different molecular features of the three MoSs in external cohorts GSE22541, GSE40435, and GSE53573. Patients that received Nivolumab therapy helped us to confirm that MoS3 is suitable for anti-PD-1 therapy. E-MTAB-3267 cohort also supported the fact that MoS2 patients can respond more to sunitinib treatment. We also confirm that SETD2 is a tumor suppressor in ccRCC, along with the decreased SETD2 protein level in advanced tumor stage, and knock-down of SETD2 leads to the promotion of cell proliferation, migration, and invasion. In summary, we provide novel insights into ccRCC molecular subtypes based on robust clustering algorithms via multiomics data, and encourage future precise treatment of ccRCC patients.

Surface Analysis of Pristine and Cycled NMC/Graphite Lithium-Ion Battery Electrodes: Addressing the Measurement Challenges.

Lithium-ion batteries are the most ubiquitous energy storage devices in our everyday lives. However, their energy storage capacity fades over time due to chemical and structural changes in their components, via different degradation mechanisms. Understanding and mitigating these degradation mechanisms is key to reducing capacity fade, thereby enabling improvement in the performance and lifetime of Li-ion batteries, supporting the energy transition to renewables and electrification. In this endeavor, surface analysis techniques are commonly employed to characterize the chemistry and structure at reactive interfaces, where most changes are observed as batteries age. However, battery electrodes are complex systems containing unstable compounds, with large heterogeneities in material properties. Moreover, different degradation mechanisms can affect multiple material properties and occur simultaneously, meaning that a range of complementary techniques must be utilized to obtain a complete picture of electrode degradation. The combination of these issues and the lack of standard measurement protocols and guidelines for data interpretation can lead to a lack of trust in data. Herein, we discuss measurement challenges that affect several key surface analysis techniques being used for Li-ion battery degradation studies: focused ion beam scanning electron microscopy, X-ray photoelectron spectroscopy, Raman spectroscopy, and time-of-flight secondary ion mass spectrometry. We provide recommendations for each technique to improve reproducibility and reduce uncertainty in the analysis of NMC/graphite Li-ion battery electrodes. We also highlight some key measurement issues that should be addressed in future investigations.

Typing characteristics of metabolism-related genes in osteoporosis.

Objective: Osteoporosis is a common musculoskeletal disease. Fractures caused by osteoporosis place a huge burden on global healthcare. At present, the mechanism of metabolic-related etiological heterogeneity of osteoporosis has not been explored, and no research has been conducted to analyze the metabolic-related phenotype of osteoporosis. This study aimed to identify different types of osteoporosis metabolic correlates associated with underlying pathogenesis by machine learning. Methods: In this study, the gene expression profiles GSE56814 and GSE56815 of osteoporosis patients were downloaded from the GEO database, and unsupervised clustering analysis was used to identify osteoporosis metabolic gene subtypes and machine learning to screen osteoporosis metabolism-related characteristic genes. Meanwhile, multi-omics enrichment was performed using the online Proteomaps tool, and the results were validated using external datasets GSE35959 and GSE7429. Finally, the immune and stromal cell types of the signature genes were inferred by the xCell method. Results: Based on unsupervised cluster analysis, osteoporosis metabolic genotyping can be divided into three distinct subtypes: lipid and steroid metabolism subtypes, glycolysis-related subtypes, and polysaccharide subtypes. In addition, machine learning SVM identified 10 potentially metabolically related genes, GPR31, GATM, DDB2, ARMCX1, RPS6, BTBD3, ADAMTSL4, COQ6, B3GNT2, and CD9. Conclusion: Based on the clustering analysis of gene expression in patients with osteoporosis and machine learning, we identified different metabolism-related subtypes and characteristic genes of osteoporosis, which will help to provide new ideas for the metabolism-related pathogenesis of osteoporosis and provide a new direction for follow-up research.

Chemical constituents, antibacterial activity and mechanism of Paeonia suffruticosa Andr. buds extract against Staphylococcus aureus and Escherichia coli O157:H7.

Sixteen chemical constituents of Paeonia suffruticosa Andr. buds extract (PSABE) were identified by UHPLC-PDA-Q/TOF-MS, belonging to phenolic acids, flavonoids, monoterpene glycosides and gallotannins. PSABE exhibited significant antibacterial activity against six tested microorganisms. Particularly, it showed the most efficient antibacterial effect against Staphylococcus aureus and Escherichia coli O157:H7, which the minimum inhibition concentration (MIC) and minimum bactericide concentration (MBC) both were 1.56 mg/mL and 6.25 mg/mL, respectively. The results showed that PSABE induced obvious alterations in membrane fatty acid composition of S. aureus and E. coli O157:H7, such as the decrease of unsaturated fatty acids, leading to the reduce of membrane fluidity. Membrane integrity was destroyed and cell morphology was obviously changed with PSABE. Furthermore, the transcription level of virulence factors was inhibited in the presence of PSABE. These results indicated that PSABE mainly exerted antibacterial effect by damaging cell membrane and inhibiting transcription level of virulence factors.[Figure: see text].

Structure and Ion Dynamics in Imidazolium-Based Protic Organic Ionic Plastic Crystals.

A fundamental understanding of the structure and dynamics of organic ionic plastic crystal (OIPC) materials allows for a more rational design of molecular chemistry toward improved mechanical and electrochemical performances. This Letter investigates the solid-state structure and ion dynamics of two imidazolium-based protic organic ionic plastic crystals as well as the ion-transport properties in both compounds. A combination of DSC, conductivity, NMR, and synchrotron X-ray studies revealed that a subtle change in cation chemistry results in substantial differences in the thermal phase behavior, crystalline structures, as well as the ion conduction mechanisms in the protic plastic crystal compounds. Whereas most of the research nowadays has been focused on the optimization of chemistry of cations and anions, this work highlights the importance of microstructures on the ion transport rate and pathways of the OIPC materials.

The influence of anion chemistry on the ionic conductivity and molecular dynamics in protic organic ionic plastic crystals.

Proton conductors are widely used in different electrochemical devices including fuel cells and redox flow batteries. Compared to conventional proton conducting polymer membranes, protic organic ionic plastic crystal (POIPC) is a novel solid-state proton conductor with high proton conductivity even under anhydrous conditions. In this work, different organic protic salts based on the same parent di-functional cation with different anions were synthesized and characterized. It is found that the di-protonated cation plays an important role in defining the thermal properties, leading to stronger plastic crystal behavior and a higher melting point. Static solid-state NMR and the synchrotron XRD results show that the di-protonated cation allows greater dynamics in the crystal in contrast to the mono-protonated counterparts. The 1-(N,N-dimethylammonium)-2-(ammonium)ethane triflate ([DMEDAH2][Tf]2) has the highest ionic conductivity of 1.1 × 10-4 S cm-1 at 50 °C, whereas the bis(trifluoromethanesulfonyl)amide counterpart [DMEDAH2][TFSA]2 has the lowest ionic conductivity (2.8 × 10-7 S cm-1 at 50 °C) with no measureable mobile ion component at this temperature. The fraction of mobile species is significantly suppressed in the TFSA containing salts as against the Tf systems.

Solid-State Lithium Conductors for Lithium Metal Batteries Based on Electrospun Nanofiber/Plastic Crystal Composites.

Organic ionic plastic crystals (OIPCs) are a class of solid-state electrolytes with good thermal stability, non-flammability, non-volatility, and good electrochemical stability. When prepared in a composite with electrospun polyvinylidene fluoride (PVdF) nanofibers, a 1:1 mixture of the OIPC N-ethyl-N-methylpyrrolidinium bis(fluorosulfonyl)imide ([C2 mpyr][FSI]) and lithium bis(fluorosulfonyl)imide (LiFSI) produced a free-standing, robust solid-state electrolyte. These high-concentration Li-containing electrolyte membranes had a transference number of 0.37(±0.02) and supported stable lithium symmetric-cell cycling at a current density of 0.13 mA cm-2 . The effect of incorporating PVdF in the Li-containing plastic crystal was investigated for different ratios of PVdF and [Li][FSI]/[C2 mpyr][FSI]. In addition, Li|LiNi1/3 Co1/3 Mn1/3 O2 cells were prepared and cycled at ambient temperature and displayed a good rate performance and stability.

N-ethyl-N-methylpyrrolidinium bis(fluorosulfonyl)imide-electrospun polyvinylidene fluoride composite electrolytes: characterization and lithium cell studies.

Using the organic ionic plastic crystal N-ethyl-N-methylpyrrolidinium bis(fluorosulfonyl)imide ([C2mpyr][FSI]) with electrospun nanofibers, LiFSI doped [C2mpyr][FSI]-PVdF composites were developed as solid state, self-standing electrolyte membranes. Different lithium salt concentration were investigated, with 10 mol% LiFSI found to be optimal amongst those assessed. Composites with different weight ratios of plastic crystal and polymer were prepared and 10 wt% polymer gave the highest conductivity. In addition, the effects of PVdF incorporation on the morphological, thermal, and structural properties of the organic ionic plastic crystal were investigated. Ion mobilities were also studied using solid-state nuclear magnetic resonance techniques. The electrolytes were then assembled into lithium symmetric cells and cycled galvanostatically at 0.13 mA cm-2 at both ambient temperature and at 50 °C, for more than 500 cycles.