Isovalerylspiramycin I suppresses small cell lung cancer proliferation via ATR/CHK1 mediated DNA damage response and PERK/eIF2α/ATF4/CHOP mediated ER stress.

Small cell lung cancer (SCLC) urgently needs new therapeutic approaches. We found that the antibiotic-derived compound Isovalerylspiramycin I (ISP-I) has potent anti-tumor activity against SCLC cell lines H1048 and DMS53 both in vitro and in vivo. ISP-I induced apoptosis, G2/M phase cell cycle arrest, and mitochondrial respiratory chain dysfunction in both cell lines. Comprehensive RNA sequencing revealed that the anti-SCLC effects of ISP-I were primarily attributed to ATR/CHK1-mediated DNA damage response and PERK/eIF2α/ATF4/CHOP-mediated ER stress. Importantly, the induction of DNA damage, ER stress, and apoptosis by ISP-I was mitigated by the reactive oxygen species (ROS) scavenger N-acetyl-L-cysteine (NAC), underscoring the critical role of ROS in the anti-SCLC mechanism of ISP-I. Moreover, ISP-I treatment induced immunogenic cell death (ICD) in SCLC cells, as evidenced by increased adenosine triphosphate (ATP) secretion, elevated release of high-mobility group box 1 (HMGB1), and enhanced exposure of calreticulin (CRT) on the cell surface. Additionally, network pharmacology analysis, combined with cellular thermal shift assay (CETSA) and cycloheximide (CHX) chase experiments, demonstrated that ISP-I acted as a ligand for apurinic/apyrimidinic endonuclease 1 (APEX1) and promoted its degradation, leading to the accumulation of ROS. In conclusion, our findings elucidate the multifaceted mechanisms underlying the anti-cancer effects of ISP-I, highlighting its potential as a promising therapeutic candidate for SCLC treatment.

A hierarchical porous hard carbon@Si@soft carbon material for advanced lithium-ion batteries.

Silicon (Si) is considered as one of the most potential commercial materials for the next-generation lithium-ion batteries (LIBs) owing to its high theoretical capacity and low voltage platform. However, the severe volume expansion and poor electric conductivity of Si anodes limit the practical application. Herein, a hierarchical porous hard carbon@Si@soft carbon (PHC@Si@SC) material was prepared by a chemical vapor deposition (CVD) and following calcination process. The differences in capacities and initial Coulombic efficiencies (ICEs) resulting from variations in silane deposition are demonstrated using PHC@Si as a model. To improve the cycling performance, a cheap pitch-derived soft carbon was introduced to protect the nano-Si to suppress the volume expansion. The formed PHC@Si@SC anode delivers a high capacity of 1625 mAh g-1 and a high ICE of 86.8%, attributed to the excellent cooperation of hard and soft carbon. The capacity retention is 55% after 100 cycles with a harsh N/P ratio of 1.1 in a PHC@Si@SC||NCM811 full cell. This work provides a strategy, which is easy to scale up for practical application.

Prediction of gestational diabetes mellitus by multiple biomarkers at early gestation.

BACKGROUND: It remains unclear which early gestational biomarkers can be used in predicting later development of gestational diabetes mellitus (GDM). We sought to identify the optimal combination of early gestational biomarkers in predicting GDM in machine learning (ML) models. METHODS: This was a nested case-control study including 100 pairs of GDM and euglycemic (control) pregnancies in the Early Life Plan cohort in Shanghai, China. High sensitivity C reactive protein, sex hormone binding globulin, insulin-like growth factor I, IGF binding protein 2 (IGFBP-2), total and high molecular weight adiponectin and glycosylated fibronectin concentrations were measured in serum samples at 11-14 weeks of gestation. Routine first-trimester blood test biomarkers included fasting plasma glucose (FPG), serum lipids and thyroid hormones. Five ML models [stepwise logistic regression, least absolute shrinkage and selection operator (LASSO), random forest, support vector machine and k-nearest neighbor] were employed to predict GDM. The study subjects were randomly split into two sets for model development (training set, n = 70 GDM/control pairs) and validation (testing set: n = 30 GDM/control pairs). Model performance was evaluated by the area under the curve (AUC) in receiver operating characteristics. RESULTS: FPG and IGFBP-2 were consistently selected as predictors of GDM in all ML models. The random forest model including FPG and IGFBP-2 performed the best (AUC 0.80, accuracy 0.72, sensitivity 0.87, specificity 0.57). Adding more predictors did not improve the discriminant power. CONCLUSION: The combination of FPG and IGFBP-2 at early gestation (11-14 weeks) could predict later development of GDM with moderate discriminant power. Further validation studies are warranted to assess the utility of this simple combination model in other independent cohorts.

Connexin 25 maintains self-renewal and functions of airway basal cells for airway regeneration.

BACKGROUND: The formation of stem cell clones enables close contact of stem cells inside. The gap junctions in such clone spheres establish a microenvironment that allows frequent intercellular communication to maintain self-renewal and functions of stem cells. Nevertheless, the essential gap junction protein for molecular signaling in clones is poorly known. METHODS: Primary human airway basal cells (hBCs) were isolated from brushing samples through bronchoscopy and then cultured. A tightly focused femtosecond laser was used to excite the local Ca2+ in an individual cell to initiate an internal Ca2+ wave in a clone to screen gap junction proteins. Immunoflourescence staining and clonogenicity assay were used to evaluate self-renewal and functions. RNA and protein levels were assessed by PCR and Western blot. Air-liquid interface assay was conducted to evaluate the differentiation potential. A Naphthalene injury mouse model was used to assess the regeneration potential. RESULTS: Herein, we identify Connexin 25 (Cx25) dominates intercellular Ca2+ communications in clones of hBCs in vitro to maintain the self-renewal and pluripotency of them. The self-renewal and in vitro differentiation functions and in vivo regeneration potential of hBCs in an airway damage model are both regulated by Cx25. The abnormal expression of Cx25 is validated in several diseases including IPF, Covid-19 and bronchiectasis. CONCLUSION: Cx25 is essential for hBC clones in maintaining self-renewal and functions of hBCs via gap junctions.

Supramolecular H-Aggregates of Squaraines with Enhanced Type I Photosensitization for Combined Photodynamic and Photothermal Therapy.

Combined photodynamic and photothermal therapy (PDT and PTT) can achieve more superior therapeutic effects than the sole mode by maximizing the photon utilization, but there remains a significant challenge in the development of related single-molecule photosensitizers (PSs), particularly those with type I photosensitization. In this study, self-assembly of squaraine dyes (SQs) is shown to be a promising strategy for designing PSs for combined type I PDT and PTT, and a supramolecular PS (TPE-SQ7) has been successfully developed through subtle molecular design of an indolenine SQ, which can self-assemble into highly ordered H-aggregates in aqueous solution as well as nanoparticles (NPs). In contrast to the typical quenching effect of H-aggregates on reactive oxygen species (ROS) generation, our results encouragingly manifest that H-aggregates can enhance type I ROS (•OH) generation by facilitating the intersystem crossing process while maintaining a high PTT performance. Consequently, TPE-SQ7 NPs with ordered H-aggregates not only exhibit superior combined therapeutic efficacy than the well-known PS (Ce6) under both normoxic and hypoxic conditions but also have excellent biosafety, making them have important application prospects in tumor phototherapy and antibacterial fields. This study not only proves that the supramolecular self-assembly of SQs is an effective strategy toward high-performance PSs for combined type I PDT and PTT but also provides a different understanding of the effect of H-aggregates on the PDT performance.

Organic Materials with Ultrabright Phosphorescence at Room Temperature under Physiological Conditions for Bioimaging.

In contrast to the high efficiency of room temperature phosphorescence in crystal states, the generally utilized nanoparticles of organic materials in bioimaging demonstrated sharply decreased performance by orders of magnitude under physiological conditions, badly limiting the realization of their unique advantages. This case, especially for organic red/near-infrared (NIR) phosphorescence materials, is not only the challenge present in reality but more importantly, for the theoretical problem of deeply understanding and avoiding the quenching effect by oxygen and water toward excited triplet states. Herein, thanks to the intelligent molecular design by the introduction of abundant hydrophobic chains and highly-branched structures, bright and persistent red/NIR phosphorescence under physiological conditions has been realized, which demonstrated the shielding effect towards oxygen, and strengthened the intermolecular interactions to suppress the non-radiative transitions. Accordingly, the record phosphorescence intensity of nanoparticles in bioimage, up to 8.21 ± 0.36 × 108 p s-1 cm-2 sr-1, was achieved, to realize the clear phosphorescence imaging of liver and tumors in living mice, even lymph nodes in rabbit models with high SBRs. This work afforded an efficient way to achieve the bright red/NIR phosphorescence nanoparticles, guiding their further applications in biology and medicine.

Urchin-like NiCo-based bimetallic hydroxide decorated with DOPO as highly hydrophobic flame retardant for remarkably reducing fire hazard of poly (L-lactic acid).

Designing high-performance flame retardants for poly (L-lactic acid) (PLA) materials and exploring a simple and scalable strategy have been hot topics in research. In this work, a novel and highly efficient flame retardant, that is, 9,10-dihydro-9-oxa-10-phosphaphenanthrene-10-oxide (DOPO) decorated urchin-like NiCo-based bimetallic hydroxide (NiCo-BH@DOPO), was synthesized and incorporated into PLA to prepare PLA and NiCo-BH@DOPO (PLA/NiCo-BH@DOPO) composite. Benefiting from the DOPO organic modification, NiCo-BH@DOPO had superb hydrophobicity and presented excellent dispersion in the PLA matrix. When 20 wt% NiCo-BH@DOPO was added, the LOI value of PLA/NiCo-BH@DOPO composites reached 33.2 %, passed the V-0 level of UL-94 grade, and its maximum peak heat release rate (PHRR) and total heat release (THR) were reduced by 13.2 % and 17.3 %, respectively, compared with PLA/NiCo-BH composites. Furthermore, the residue of PLA/NiCo-BH@DOPO at 800 °C reached 19.8 wt% and the T10% (temperature at 10 % weight loss) increased by 33 °C. More importantly, the residual PLA/NiCo-BH@DOPO char exhibits a significantly reduced presence of large cracks compared to PLA/NiCo-BH, indicating a more compact formation of residual char. NiCo-BH@DOPO endowed PLA with outstanding flame retardancy, thermal stability and carbonization properties, which were owing to the multi-coordinating effect transition metal (NiCo-BH) catalyzed the char formation to form a char layer barrier and DOPO free radicals captured to inhibit the combustion reaction chain. This investigation provided a facile strategy for the novel multi-function NiCo-based bimetallic hydroxide flame retardant, expanding NiCo-BH potential applications in PLA.

A real-world pharmacovigilance study using disproportionality analysis of United States Food and Drug Administration Adverse Event Reporting System events for vinca alkaloids: comparing vinorelbine and Vincristine.

BACKGROUND: Vinca alkaloids are widely used in cancer treatment for their ability to target microtubule dynamics. While their efficacy in treating certain cancers is well-established, the full spectrum of their adverse event profiles remains an area of ongoing research. METHODS: We analyzed AEs related to vinorelbine and vincristine using a retrospective case/non-case approach with data from the FDA Adverse Event Reporting System (FAERS). We applied various algorithms to detect AE signals: the reporting odds ratio (ROR) and proportional reporting ratio (PRR) measured disproportionality and association strength; the Bayesian confidence propagation neural network (BCPNN) calculated the Information Component (IC) for associations against background rates; and the multi-item gamma Poisson shrinker (MGPS) yielded empirical Bayes geometric mean (EBGM) values, accounting for reporting variability. RESULTS: Both medications significantly involve the blood and lymphatic systems, with vinorelbine reporting 401 cases in this System Organ Class (SOC), exhibiting a ROR of 17.4, PRR of 12.4, IC of 3.63, and EBGM of 12.38. An intersection analysis of Preferred Terms (PTs) has uncovered previously unreported AEs shared by both drugs, including posterior reversible encephalopathy syndrome and inappropriate antidiuretic hormone secretion. CONCLUSIONS: This analysis highlights the need for ongoing research of the risks associated with vinorelbine and vincristine.

Aging-associated atrial fibrillation: A comprehensive review focusing on the potential mechanisms.

Atrial fibrillation (AF) has been receiving a lot of attention from scientists and clinicians because it is an extremely common clinical condition. Due to its special hemodynamic changes, AF has a high rate of disability and mortality. So far, although AF has some therapeutic means, it is still an incurable disease because of its complex risk factors and pathophysiologic mechanisms, which is a difficult problem for global public health. Age is an important independent risk factor for AF, and the incidence of AF increases with age. To date, there is no comprehensive review on aging-associated AF. In this review, we systematically discuss the pathophysiologic evidence for aging-associated AF, and in particular explore the pathophysiologic mechanisms of mitochondrial dysfunction, telomere attrition, cellular senescence, disabled macroautophagy, and gut dysbiosis involved in recent studies with aging-associated AF. We hope that by exploring the various dimensions of aging-associated AF, we can better understand the specific relationship between age and AF, which may be crucial for innovative treatments of aging-associated AF.

Engineering Shewanella oneidensis-Carbon Felt Biohybrid Electrode Decorated with Bacterial Cellulose Aerogel-Electropolymerized Anthraquinone to Boost Energy and Chemicals Production.

Interfacial electron transfer between electroactive microorganisms (EAMs) and electrodes underlies a wide range of bio-electrochemical systems with diverse applications. However, the electron transfer rate at the biotic-electrode interface remains low due to high transmembrane and cell-electrode interfacial electron transfer resistance. Herein, a modular engineering strategy is adopted to construct a Shewanella oneidensis-carbon felt biohybrid electrode decorated with bacterial cellulose aerogel-electropolymerized anthraquinone to boost cell-electrode interfacial electron transfer. First, a heterologous riboflavin synthesis and secretion pathway is constructed to increase flavin-mediated transmembrane electron transfer. Second, outer membrane c-Cyts OmcF is screened and optimized via protein engineering strategy to accelerate contacted-based transmembrane electron transfer. Third, a S. oneidensis-carbon felt biohybrid electrode decorated with bacterial cellulose aerogel and electropolymerized anthraquinone is constructed to boost the interfacial electron transfer. As a result, the internal resistance decreased to 42 Ω, 480.8-fold lower than that of the wild-type (WT) S. oneidensis MR-1. The maximum power density reached 4286.6 ± 202.1 mW m-2, 72.8-fold higher than that of WT. Lastly, the engineered biohybrid electrode exhibited superior abilities for bioelectricity harvest, Cr6+ reduction, and CO2 reduction. This study showed that enhancing transmembrane and cell-electrode interfacial electron transfer is a promising way to increase the extracellular electron transfer of EAMs.

Engineering PTS-based glucose metabolism for efficient biosynthesis of bacterial cellulose by Komagataeibacter xylinus.

Bacterial cellulose (BC) is a renewable biomaterial that has attracted significant attention due to its excellent properties and wide applications. Komagataeibacter xylinus CGMCC 2955 is an important BC-producing strain. It primarily produces BC from glucose while simultaneously generating gluconic acid as a by-product, which acidifies the medium and inhibits BC synthesis. To enhance glucose uptake and BC synthesis, we reconstructed the phosphoenolpyruvate-dependent glucose phosphotransferase system (PTSGlc) and strengthened glycolysis by introducing heterologous genes, resulting in a recombinant strain (GX08PTS03; Δgcd::ptsHIcrrE. coli::ptsGE. coli::pfkAE. coli). Strain GX08PTS03 efficiently utilized glucose for BC production without accumulating gluconic acid. Subsequently, the fermentation process was systematically optimized. Under optimal conditions, strain GX08PTS03 produced 7.74 g/L of BC after 6 days of static fermentation, with a BC yield of 0.39 g/g glucose, which were 87.41 % and 77.27 % higher than those of the wild-type strain, respectively. The BC produced by strain GX08PTS03 exhibited a longer fiber diameter along with a lower porosity, significantly higher solid content, crystallinity, tensile strength, and Young's modulus. This study is novel in reporting that the engineered PTSGlc-based glucose metabolism could effectively enhance the production and properties of BC, providing a future outlook for the biopolymer industry.

Deliberation concerning the role of M1-type macrophage subset in oral carcinogenesis.

Over the last decade, accumulating evidence has suggested that tumor-associated macrophages (TAMs) play a significant role in the tumor development. This commentary wishes to highlight the findings by You, et al. that M1-like TAMs could cascade a mesenchymal/stem-like phenotype of oral squamous cell carcinoma (OSCC) via the IL6/Stat3/THBS1 feedback loop. These unprecedented findings identified M1-like TAMs-regulated processes as potentially tumor-promotion in the context of OSCC immunomicroenvironment.

Phenotyping of FGF12AV52H mutation in mouse implies a complex FGF12 network.

Pathogenic missense mutation of the FGF12 gene is responsible for a variable disease phenotypic spectrum. Disease-specific therapies require precise dissection of the relationship between different mutations and phenotypes. The lack of a proper animal model hinders the investigation of related diseases, such as early-onset epileptic encephalopathy. Here, an FGF12AV52H mouse model was generated using CRISPR/Cas9 technology, which altered the A isoform without affecting the B isoform. The FGF12AV52H mice exhibited seizure susceptibility, while no spontaneous seizures were observed. The increased excitability in dorsal hippocampal CA3 neurons was confirmed by patch-clamp recordings. Furthermore, immunostaining showed that the balance of excitatory/inhibitory neurons in the hippocampus of the FGF12AV52H mice was perturbed. The increases in inhibitory SOM+ neurons and excitatory CaMKII+ neurons were heterogeneous. Moreover, the locomotion, anxiety levels, risk assessment behavior, social behavior, and cognition of the FGF12AV52H mice were investigated by elevated plus maze, open field, three-chamber sociability, and novel object tests, respectively. Cognition deficit, impaired risk assessment, and social behavior with normal social indexes were observed, implying complex consequences of V52H FGF12A in mice. Together, these data suggest that the function of FGF12A in neurons can be immediate or long-term and involves modulation of ion channels and the differentiation and maturation of neurons. The FGF12AV52H mouse model increases the understanding of the function of FGF12A, and it is of great importance for revealing the complex network of the FGF12 gene in physiological and pathological processes.

Chemosynthetic alphaproteobacterial diazotrophs reside in deep-sea cold-seep bottom waters.

Nitrogen (N)-fixing organisms, also known as diazotrophs, play a crucial role in N-limited ecosystems by controlling the production of bioavailable N. The carbon-dominated cold-seep ecosystems are inherently N-limited, making them hotspots of N fixation. However, the knowledge of diazotrophs in cold-seep ecosystems is limited compared to other marine ecosystems. In this study, we used multi-omics to investigate the diversity and catabolism of diazotrophs in deep-sea cold-seep bottom waters. Our findings showed that the relative abundance of diazotrophs in the bacterial community reached its highest level in the cold-seep bottom waters compared to the cold-seep upper waters and non-seep bottom waters. Remarkably, more than 98% of metatranscriptomic reads aligned on diazotrophs in cold-seep bottom waters belonged to the genus Sagittula, an alphaproteobacterium. Its metagenome-assembled genome, named Seep-BW-D1, contained catalytic genes (nifHDK) for nitrogen fixation, and the nifH gene was actively transcribed in situ. Seep-BW-D1 also exhibited chemosynthetic capability to oxidize C1 compounds (methanol, formaldehyde, and formate) and thiosulfate (S2O32-). In addition, we observed abundant transcripts mapped to genes involved in the transport systems for acetate, spermidine/putrescine, and pectin oligomers, suggesting that Seep-BW-D1 can utilize organics from the intermediates synthesized by methane-oxidizing microorganisms, decaying tissues from cold-seep benthic animals, and refractory pectin derived from upper photosynthetic ecosystems. Overall, our study corroborates that carbon-dominated cold-seep bottom waters select for diazotrophs and reveals the catabolism of a novel chemosynthetic alphaproteobacterial diazotroph in cold-seep bottom waters. IMPORTANCE: Bioavailable nitrogen (N) is a crucial element for cellular growth and division, and its production is controlled by diazotrophs. Marine diazotrophs contribute to nearly half of the global fixed N and perform N fixation in various marine ecosystems. While previous studies mainly focused on diazotrophs in the sunlit ocean and oxygen minimum zones, recent research has recognized cold-seep ecosystems as overlooked N-fixing hotspots because the seeping fluids in cold-seep ecosystems introduce abundant bioavailable carbon but little bioavailable N, making most cold seeps inherently N-limited. With thousands of cold-seep ecosystems detected at continental margins worldwide in the past decades, the significant role of cold seeps in marine N biogeochemical cycling is emphasized. However, the diazotrophs in cold-seep bottom waters remain poorly understood. Through multi-omics, this study identified a novel alphaproteobacterial chemoheterotroph belonging to Sagittula as one of the most active diazotrophs residing in cold-seep bottom waters and revealed its catabolism.

Research on the mechanism of threefold discrepancy in thermal conductivity between room temperature and phase transition temperature for 1,3,5,7-tetranitro-1,3,5,7-tetrazocine (HMX) crystals.

Cracks originating from thermal expansion and thermally induced phase transitions significantly hinder thermal conduction in certain energetic materials. For 1,3,5,7-tetranitro-1,3,5,7-tetrazocine (HMX) crystals, a classic explosive, their temperature-dependent thermal conductivity serves as a crucial parameter determining safety and stability. In this work, the thermal conductivity of HMX single crystals before and after thermal damage under different heating conditions was measured and calculated, as well as the thermal conductivity of different regions of each single crystal. A threefold discrepancy in thermal conductivity was observed between room temperature and the phase transition temperature of the HMX crystal. The different effects of different types of damage and cracks, characterized by using 3D X-ray computed tomography (CT), on the thermal conduction process of the crystal were further analyzed. The results indicate that different heating methods influence the phase transformation of the crystals and the distributions of fast cracks and small cracks. The strong directivity of the fast cracks will significantly impact the thermal conductivity along two horizontal directions, whereas small cracks exert the greatest influence on the primary direction of heat conduction. The relevant conclusions were also verified by finite element analysis (FEA) modeling.

Interactions between microbial communities and polymers in hydraulic fracturing water cycle: A review.

Hydraulic fracturing (HF) has substantially boosted global unconventional hydrocarbon production but has also introduced various environmental and operational challenges. Understanding the interactions between abundant and diverse microbial communities and chemicals, particularly polymers used for proppant delivery, thickening, and friction reduction, in HF water cycles is crucial for addressing these challenges. This review primarily examined the recent studies conducted in China, an emerging area for HF activities, and comparatively examined studies from other regions. In China, polyacrylamide (PAM) and its derivatives products became key components in hydraulic fracturing fluid (HFF) for unconventional hydrocarbon development. The microbial diversity of unconventional HF water cycles in China was higher compared to North America, with frequent detection of taxa such as Shewanella, Marinobacter, and Desulfobacter. While biodegradation, biocorrosion, and biofouling were common issues across regions, the mechanisms underlying these microbe-polymer interactions differed substantially. Notably, in HF sites in the Sichuan Basin, the use of biocides gradually decreased its efficiency to mitigate adverse microbial activities. High-throughput sequencing proved to be a robust tool that could identify key bioindicators and biodegradation pathways, and help select optimal polymers and biocides, leading to more efficient HFF systems. The primary aim of this study is to raise awareness about the interactions between microorganisms and polymers, providing fresh insights that can inform decisions related to enhanced chemical use and biological control measures at HF sites.

GloEC: a hierarchical-aware global model for predicting enzyme function.

The annotation of enzyme function is a fundamental challenge in industrial biotechnology and pathologies. Numerous computational methods have been proposed to predict enzyme function by annotating enzyme labels with Enzyme Commission number. However, the existing methods face difficulties in modelling the hierarchical structure of enzyme label in a global view. Moreover, they haven't gone entirely to leverage the mutual interactions between different levels of enzyme label. In this paper, we formulate the hierarchy of enzyme label as a directed enzyme graph and propose a hierarchy-GCN (Graph Convolutional Network) encoder to globally model enzyme label dependency on the enzyme graph. Based on the enzyme hierarchy encoder, we develop an end-to-end hierarchical-aware global model named GloEC to predict enzyme function. GloEC learns hierarchical-aware enzyme label embeddings via the hierarchy-GCN encoder and conducts deductive fusion of label-aware enzyme features to predict enzyme labels. Meanwhile, our hierarchy-GCN encoder is designed to bidirectionally compute to investigate the enzyme label correlation information in both bottom-up and top-down manners, which has not been explored in enzyme function prediction. Comparative experiments on three benchmark datasets show that GloEC achieves better predictive performance as compared to the existing methods. The case studies also demonstrate that GloEC is capable of effectively predicting the function of isoenzyme. GloEC is available at: https://github.com/hyr0771/GloEC.

AFP: Finding pathways accounting for stoichiometry along with atom group tracking in metabolic network.

Automatically finding novel pathways plays an important role in the initial designs of metabolic pathways in synthetic biology and metabolic engineering. Although path-finding methods have been successfully applied in identifying valuable synthetic pathways, few efforts have been made in fusing atom group tracking into building stoichiometry model to search metabolic pathways from arbitrary start compound via Mixed Integer Linear Programming (MILP). We propose a novel method called AFP to find metabolic pathways by incorporating atom group tracking into reaction stoichiometry via MILP. AFP tracks the movements of atom groups in the reaction stoichiometry to construct MILP model to search the pathways containing atom groups exchange in the reactions and adapts the MILP model to provide the options of searching pathways from an arbitrary or given compound to the target compound. Combining atom group tracking with reaction stoichiometry to build MILP model for pathfinding may promote the search of well-designed alternative pathways at the stoichiometric modeling level. The experimental comparisons to the known pathways show that our proposed method AFP is more effective to recover the known pathways than other existing methods and is capable of discovering biochemically feasible pathways producing the metabolites of interest.

TARDBP is a candidate diagnostic biomarker promoting tumor progression via impacting tumor immunity and tumor microenvironment.

In the realm of cancer research, particularly hepatocellular carcinoma (HCC), TAR DNA-binding protein (TARDBP) has transitioned from being associated with neurodegenerative diseases to emerging as a significant molecule in oncology due to its aberrant expression in HCC and other malignancies. This shift underlines the versatility of TARDBP and its critical role in tumorigenesis. Our study illuminates TARDBP's universal upregulation across various cancers, indicating its involvement in fundamental oncogenic processes and potential impact on genomic instability. The relationship between TARDBP expression and tumor mutational burden (TMB) across several cancers highlights its influence on a key hallmark of cancer progression. Additionally, TARDBP's interaction with immune and inflammatory factors within the tumor microenvironment, including its association with immune-stimulatory factors and inverse relationship with immune inhibitors, suggests its role in modulating immune evasion. Clinically, TARDBP's aberrant expression correlates with adverse patient outcomes in HCC, making it a promising candidate for therapeutic targeting. The study concludes that TARDBP holds significant potential as a novel therapeutic target in HCC and possibly other malignancies, meriting further exploration to integrate TARDBP-targeted therapies into cancer treatment protocols, thereby advancing the field of precision medicine.