Essential Pathways Research Articles

Identification of novel vesicular monoamine transporter 2 (VMAT2) inhibitors: A structure-based approach

The Vesicular Monoamine Transporter 2 (VMAT2) is responsible for transporting monoamine neurotransmitters such as serotonin, dopamine, and norepinephrine from the cytoplasm into synaptic vesicles. This VMAT2 mediated transport governs essential brain pathways, controlling functions like movement, sleep, and mood regulation. Dysfunction in these pathways is implicated in various psychiatric or neurodegenerative disorders, making VMAT2 a promising drug target. This study utilized a structure-based approach to identify novel VMAT2 inhibitor candidates. Initially, molecular docking identified several promising compounds when compared to standard inhibitors. Three novel compounds (S31, S42, and S48) that bind to VMAT2′s active site were further evaluated using molecular dynamics (MD) simulations, and their binding-free energies were calculated. Among these, S42 formed the most stable complex with VMAT2, exhibiting the lowest binding free energy and interacting with key residues such as Val-232 and Leu-37, which may confer selectivity. Additionally, S42 demonstrated superior binding strength in pulling simulations relative to other candidates and standard molecules. Umbrella sampling simulations further supported S42 as a strong candidate for VMAT2 inhibition. In conclusion, S42 warrants further investigation to fully explore its therapeutic potential.

Therapeutic role of naringin in cancer: molecular pathways, synergy with other agents, and nanocarrier innovations.

Naringin, a flavanone glycoside found abundantly in citrus fruits, is well-known for its various pharmacological properties, particularly its significant anticancer effects. Research, both in vitro and in vivo, has shown that naringin is effective against several types of cancer, including liver, breast, thyroid, prostate, colon, bladder, cervical, lung, ovarian, brain, melanoma, and leukemia. Its anticancer properties are mediated through multiple mechanisms, such as apoptosis induction, inhibition of cell proliferation, cell cycle arrest, and suppression of angiogenesis, metastasis, and invasion, all while exhibiting minimal toxicity and adverse effects. Naringin's molecular mechanisms involve the modulation of essential signaling pathways, including PI3K/Akt/mTOR, FAK/MMPs, FAK/bads, FAKp-Try397, IKKs/IB/NF-κB, JNK, ERK, β-catenin, p21CIPI/WAFI, and p38-MAPK. Additionally, it targets several signaling proteins, such as Bax, TNF-α, Zeb1, Bcl-2, caspases, VEGF, COX-2, VCAM-1, and interleukins, contributing to its wide-ranging antitumor effects. The remarkable therapeutic potential of naringin, along with its favorable safety profile, highlights its promise as a candidate for cancer treatment. This comprehensive review examines the molecular mechanisms behind naringin's chemopreventive and anticancer effects, including its pharmacokinetics and bioavailability. Furthermore, it discusses advancements in nanocarrier technologies designed to enhance these characteristics and explores the synergistic benefits of combining naringin with other anticancer agents, focusing on improved therapeutic efficacy and drug bioavailability.

Exploring Gene Expression and Alternative Splicing in Duck Embryonic Myoblasts via Full-Length Transcriptome Sequencing

The duck industry is vital for supplying high-quality protein, making research into the development of duck skeletal muscle critical for improving meat and egg production. In this study, we leveraged Oxford Nanopore Technologies (ONT) sequencing to perform full-length transcriptome sequencing of myoblasts harvested from the leg muscles of duck embryos at embryonic day 13 (E13), specifically examining both the proliferative (GM) and differentiation (DM) phases. Our analysis identified a total of 5797 novel transcripts along with 2332 long non-coding RNAs (lncRNAs), revealing substantial changes in gene expression linked to muscle development. We detected 3653 differentially expressed genes and 2246 instances of alternative splicing, with key genes involved in essential pathways, such as ECM–receptor interaction and Notch signaling, prominently featured. Additionally, we constructed a protein–protein interaction network that highlighted critical regulators—MYOM3, MYL2, MYL1, TNNI2, and ACTN2—associated with the processes of proliferation and differentiation in myoblasts. This extensive transcriptomic investigation not only sheds light on the intricate molecular mechanisms driving skeletal muscle development in ducks but also provides significant insights for future breeding strategies aimed at enhancing the efficiency of duck production. The results emphasize the efficacy of ONT sequencing in uncovering complex regulatory networks within avian species, ultimately contributing to progress in animal husbandry.

Bioinformatics analysis of the Microsporidia sp. MB genome: a malaria transmission-blocking symbiont of the Anopheles arabiensis mosquito

BackgroundThe use of microsporidia as a disease-transmission-blocking tool has garnered significant attention. Microsporidia sp. MB, known for its ability to block malaria development in mosquitoes, is an optimal candidate for supplementing malaria vector control methods. This symbiont, found in Anopheles mosquitoes, can be transmitted both vertically and horizontally with minimal effects on its mosquito host. Its genome, recently sequenced from An. arabiensis, comprises a compact 5.9 Mbp.ResultsHere, we analyze the Microsporidia sp. MB genome, highlighting its major genomic features, gene content, and protein function. The genome contains 2247 genes, predominantly encoding enzymes. Unlike other members of the Enterocytozoonida group, Microsporidia sp. MB has retained most of the genes in the glycolytic pathway. Genes involved in RNA interference (RNAi) were also identified, suggesting a mechanism for host immune suppression. Importantly, meiosis-related genes (MRG) were detected, indicating potential for sexual reproduction in this organism. Comparative analyses revealed similarities with its closest relative, Vittaforma corneae, despite key differences in host interactions.ConclusionThis study provides an in-depth analysis of the newly sequenced Microsporidia sp. MB genome, uncovering its unique adaptations for intracellular parasitism, including retention of essential metabolic pathways and RNAi machinery. The identification of MRGs suggests the possibility of sexual reproduction, offering insights into the symbiont’s evolutionary strategies. Establishing a reference genome for Microsporidia sp. MB sets the foundation for future studies on its role in malaria transmission dynamics and host-parasite interactions.

The crowding-out effect of physical fitness activities on medical expenditure in the aged group.

China is facing the challenge of "deep aging", and promoting healthy aging has become a key research topic. Both medical care and physical exercise are important for health, but while medical services focus on treating illness, physical fitness activities focus on prevention, making them a more effective approach for promoting healthy aging. This study uses data from the China Health and Retirement Longitudinal Study (CHARLS), focusing on individuals aged 60 to 80, to investigate the relationship between physical fitness activities and medical expenditures. A Tobit model was employed to analyze the data. (1) Active participation in physical fitness activities significantly improves the health of older adults, making physical activity an essential pathway to achieve healthy aging. (2) Participation in sports and fitness activities leads to a crowding-out effect on medical expenditures, significantly reducing healthcare costs for participants. (3) High-intensity physical activities are most suitable for individuals aged 60-65, moderate-intensity activities for those aged 66-70, and low-intensity activities for those aged 71-80. (1) Policies should focus on raising awareness of physical fitness benefits among older adults, encouraging regular physical activity to improve health and reduce medical costs. (2) A shift from treatment to prevention in health management is needed, promoting exercise as a cost-effective way to reduce healthcare spending. (3) Age-specific fitness guidelines should be developed to provide tailored exercise recommendations for different older aldult age groups.

Peroxisome proliferator-activated receptor agonists as an adjuvant for cancer therapy: A review

Cancer is now one of the leading diseases responsible for the highest mortality rates worldwide. Cancer treatment is extremely intricate and is often associated with less targeted effects and more side effects. In the last few years, two significant revolutions in cancer treatment have altered treatment paradigms: immuno-oncology and the pursuit of actionable changes in oncogene-driven cancers. Significant obstacles continue to exist in both areas of cancer treatment. Next-generation sequencing technologies for molecular prescreening in clinical research are advancing, but their widespread clinical use is hindered by challenges related to the clinical interpretation of large genomic data. Moreover, cancer mono-chemotherapy is associated with issues such as inadequate efficacy, drug resistance, and systemic toxicity. It is not possible to administer cytotoxic drugs limitlessly. Combination therapy was developed in response to this circumstance, with the expectation of achieving high therapeutic efficacy at lower dosages of medication. Peroxisome proliferator-activated receptors (PPARs) are a group of essential lipid sensors and metabolic pathway regulators. In addition, they possess the ability to modulate immunity, inflammation, and endothelial nitric oxide synthase activation. Alongside their well-established functions, new insights into the roles of PPAR agonists in cancer research are emerging. After reviewing current research, it is evident that PPAR modulators have significant potential for managing cancer. This review aims to consolidate the functions of PPAR ligands alongside other cancer therapies. We provide a comprehensive perspective on the applicability of PPAR ligands in cancer treatment as an adjuvant.

Enhanced biosynthesis of poly(3-hydroxybutyrate) in engineered strains of Pseudomonas putida via increased malonyl-CoA availability.

Malonyl-coenzyme A (CoA) is a key precursor for the biosynthesis of multiple value-added compounds by microbial cell factories, including polyketides, carboxylic acids, biofuels, and polyhydroxyalkanoates. Owing to its role as a metabolic hub, malonyl-CoA availability is limited by competition in several essential metabolic pathways. To address this limitation, we modified a genome-reduced Pseudomonas putida strain to increase acetyl-CoA carboxylation while limiting malonyl-CoA utilization. Genes involved in sugar catabolism and its regulation, the tricarboxylic acid (TCA) cycle, and fatty acid biosynthesis were knocked-out in specific combinations towards increasing the malonyl-CoA pool. An enzyme-coupled biosensor, based on the rppA gene, was employed to monitor malonyl-CoA levels invivo. RppA is a type III polyketide synthase that converts malonyl-CoA into flaviolin, a red-colored polyketide. We isolated strains displaying enhanced malonyl-CoA availability via a colorimetric screening method based on the RppA-dependent red pigmentation; direct flaviolin quantification identified four engineered strains had a significant increase in malonyl-CoA levels. We further modified these strains by adding a non-canonical pathway that uses malonyl-CoA as precursor for poly(3-hydroxybutyrate) biosynthesis. These manipulations led to increased polymer accumulation in the fully engineered strains, validating our general strategy to boost the output of malonyl-CoA-dependent pathways in P. putida.

Genome-wide screening reveals essential roles for HOX genes and imprinted genes during caudal neurogenesis of human embryonic stem cells

Mapping the essential pathways for neuronal differentiation can uncover new therapeutics and models for neurodevelopmental disorders. We thus utilized a genome-wide loss-of-function library in haploid human embryonic stem cells, differentiated into caudal neuronal cells. We show that essential genes for caudal neurogenesis are enriched for secreted and membrane proteins and that a large group of neurological conditions, including neurodegenerative disorders, manifest early neuronal phenotypes. Furthermore, essential transcription factors are enriched with homeobox (HOX) genes demonstrating synergistic regulation and surprising non-redundant functions between HOXA6 and HOXB6 paralogs. Moreover, we establish the essentialome of imprinted genes during neurogenesis, demonstrating that maternally expressed genes are non-essential in pluripotent cells and their differentiated germ layers, yet several are essential for neuronal development. These include Beckwith-Wiedemann syndrome- and Angelman syndrome-related genes, for which we suggest a novel regulatory pathway. Overall, our work identifies essential pathways for caudal neuronal differentiation and stage-specific phenotypes of neurological disorders.

Boosting Droplet Transport for Fog Harvest.

Wedge-shaped superhydrophilic tracks have been considered as one of the most effective ways to transport droplets for diverse cutting-edge applications, e.g., energy harvesting and lab-on-a-chip devices. Although significant progress, such as serial wedge-shaped tracks with curved edges, has evolved to advance the liquid transport, the ultrafast and long-distance transporting of drop-shaped liquid remains challenging. Here, inspired by the cactus spine that enables fast droplet transport and the serial spindle knot of spider silk, which is capable of collecting condensate from a wide range of distances, we created serial wedge-shaped superhydrophilic patterns and optimized their side edges with a convex brachistochrone curve to boost the acceleration. The junctions of the serial patterns were meanwhile reformed into concave brachistochrone curves to lower the energy barrier for sustained transport. For transporting the liquid in drop shapes to the long distance at high velocity, the wedge-shaped tracks were slenderized to the greatest extent to suppress the liquid spreading and thus prevent the degradation of the Laplace driving force. Moreover, the junction that determines the energy barrier of droplet striding was carefully designed based on the principle of minimizing momentum loss. The exquisite architecture design pushed the droplet transport to a maximum instantaneous velocity of 207.7 mm·s-1 and an outermost transport distance of 120.5 mm, exceeding most wettability or geometric gradient based reports. The transported volume of the droplets can be readily regulated by simply scaling the created architectures. The enhanced droplet transport facilitates the motion and departure of the cohered droplets, enabling a 1.9-fold rise of the water collection rate and 12-fold increase of the heat transfer coefficient during the fog harvest test. This scalable, controllable, and easily fabricatable surface design provides an essential pathway in realizing high-performance manipulation of droplets and possibly pioneers substantial innovative applications in multidisciplinary fields. Those include but are not limited to energy harvesting, lab-on-a-chip devices, and MEMS systems.

Identification of a divalent metal transporter required for cellular iron metabolism in malaria parasites

Plasmodium falciparum malaria parasites invade and multiply inside red blood cells (RBCs), the most iron-rich compartment in humans. Like all cells, P. falciparum requires nutritional iron to support essential metabolic pathways, but the critical mechanisms of iron acquisition and trafficking during RBC infection have remained obscure. Parasites internalize and liberate massive amounts of heme during large-scale digestion of RBC hemoglobin within an acidic food vacuole (FV) but lack a heme oxygenase to release porphyrin-bound iron. Although most FV heme is sequestered into inert hemozoin crystals, prior studies indicate that trace heme escapes biomineralization and is susceptible to nonenzymatic degradation within the oxidizing FV environment to release labile iron. Parasites retain a homolog of divalent metal transporter 1 (DMT1), a known mammalian iron transporter, but its role in P. falciparum iron acquisition has not been tested. Our phylogenetic studies indicate that P. falciparum DMT1 (PfDMT1) retains conserved molecular features critical for metal transport. We localized this protein to the FV membrane and defined its orientation in an export-competent topology. Conditional knockdown of PfDMT1 expression is lethal to parasites, which display broad cellular defects in iron-dependent functions, including impaired apicoplast biogenesis and mitochondrial polarization. Parasites are selectively rescued from partial PfDMT1 knockdown by supplementation with exogenous iron, but not other metals. These results support a cellular paradigm whereby PfDMT1 is the molecular gatekeeper to essential iron acquisition by blood-stage malaria parasites and suggest that therapeutic targeting of PfDMT1 may be a potent antimalarial strategy.

TLR4 promotes smooth muscle cell-derived foam cells formation by inducing receptor-independent macropinocytosis.

Foam cells are primarily formed through scavenger receptors that mediate the uptake of various modified low-density lipoproteins (LDL) into cells. In addition to the receptor-dependent pathway, macropinocytosis is an essential non-receptor endocytic pathway for vascular smooth muscle cells (VSMCs) to take up lipids. However, the molecular mechanisms underlying this process remain unclear. Primary cultured VSMCs were stimulated with 200 ng/ml lipopolysaccharide (LPS) and 200 μg/ml native LDL (nLDL). We observed a significant increase in TLR4 protein expression and a significant activation of macropinocytosis, which correlated with the highest uptake of nLDL and intracellular lipid deposition in WT VSMCs. However, macropinocytosis was inhibited and lipid accumulation decreased after treatment with macropinocytosis inhibitors and Syk inhibitors in WT VSMCs. Consistently, TLR4 knockout significantly suppressed macropinocytosis and lipid droplets accumulation in VSMCs. Taken together, our findings suggest a critical role of TLR4/Syk signaling in promoting receptor-independent macropinocytosis leading to VSMC-derived foam cells formation.

Two critical membranes. How does the chloroplast envelope affect plant acclimation properties?

Chloroplasts play a pivotal role in the metabolism of leaf mesophyll cells, functioning as a cellular hub that orchestrates molecular reactions in response to environmental stimuli. These organelles contain complex protein machinery for energy conversion and are indispensable for essential metabolic pathways. Proteins located within the chloroplast envelope membranes facilitate bidirectional communication with the cell and connect essential pathways, thereby influencing acclimation processes to challenging environmental conditions such as temperature fluctuations and light intensity changes. Despite their importance, a comprehensive overview of the impact of envelope-located proteins during acclimation to environmental changes is lacking. Understanding the role of these proteins in acclimation processes could provide insights into enhancing stress tolerance under increasingly challenging environments. This review highlights the significance of envelope-located proteins in plant acclimation.

Synthesis and mechanistic investigation of BPA fluorescent probes targeting BPA for potential application in Boron Neutron Capture Therapy (BNCT)

Boronic acid analogs are crucial in modern organic chemistry and drug development, serving as versatile reagents and intermediates with significant therapeutic applications. This area has gained increased interest with the recent development of the drug 4-boron-L-phenylalanine (L-BPA) for boron neutron capture therapy (BNCT). Fluorescent probe technology offers an essential pathway for imaging drugs in vitro and in vivo, providing high sensitivity with great spatial and temporal resolution for both disease diagnosis and drug development. In this paper, we designed and investigated three fluorescent probes—W-1-NN, W-2-NS and W-3-NO—for sensing 4-boron-L-phenylalanine (L-BPA). Among these, only W-1-NN reacts with L-BPA, resulting in a spectral blue-shift change. This probe can “ratiometrically” and specifically detect L-BPA among various metals, with a limit of detection (LOD) of 7.11 μM. Mechanistic studies revealed that the addition of L-BPA disrupts the inherent ESIPT mechanism of W-1-NN in protonic solutions, resulting in the appearance of a new peak at 372 nm. Additionally, theoretical computational studies have also demonstrated that the complexation of W-1-NN with L-BPA triggers a change in the resonance structure, resulting in a larger energy gap and causing a blue shift in the spectrum. Furthermore, W-1-NN has been successfully applied to the detection of L-BPA in human urine. Therefore, the template probe with N/O as the target and the introduction of N atoms can specifically detect L-BPA. This template probe lays the foundation for the detection of L-BPA, and provides great possibilities for the future realization of the template probe to be connected with different fluorophores to make it emit at long wavelengths to reach the target of the near-infrared.

Dynamic and Stable R&D Strategies for Green Technology Based on Cooperative Differential Games

As the “carbon neutrality” strategy is implemented, green technology R&D, a core competitive strength for sustainable enterprise development, is an essential pathway for China’s transformation and green growth. Green technology, a breakthrough over traditional production technologies, involves lengthy and costly R&D processes with high risks typically beyond the reach of a single enterprise. It requires the heterogeneous functions of enterprises, universities, and research institutions to complement each other’s advantages and establish an “industry–university–research” collaborative innovation alliance for green technologies. This paper constructs differential game models for non-cooperative and cooperative green technology R&D involving a green manufacturer and a research institution. We solve and compare the profits for both parties under these scenarios, apply a time-consistent payment distribution mechanism to allocate cooperative profits, and ensure that neither party deviates from the optimal cooperative trajectory over a prolonged period, achieving Pareto improvement and enhancing social welfare.

Research on the Role of E-commerce Vocational Skills Competitions in Cultivating Students' Innovation and Entrepreneurship Abilities

In the context of globalization and rapid advancements in information technology, e-commerce has become a significant force driving economic development. To enhance students' practical abilities and qualities for innovation and entrepreneurship, e-commerce vocational skills competitions have emerged, gradually becoming an important means of cultivating students' comprehensive capabilities. This paper explores the definitions and types of e-commerce vocational skills competitions and analyzes their specific role in fostering students' innovative and entrepreneurial abilities. The focus lies on how competitions impact the cultivation of innovative thinking, improvement of technical application skills, and enhancement of entrepreneurial awareness and management capabilities. The research results indicate that e-commerce vocational skills competitions not only effectively improve students' innovative abilities but also significantly enhance their entrepreneurial awareness and practical skills, providing essential pathways for universities to nurture competitive, innovative talents.

TMT-based quantitative proteomics unveils the protective mechanism of Polygonatum sibiricum polysaccharides on septic acute liver injury

Polygonatum sibiricum polysaccharides (PSP) has been shown to possess multiple pharmacological functions. Our previous study found that PSP could protect against acute liver injury during sepsis via inhibiting inflammatory response. However, the underlying molecular mechanism by which PSP alleviates septic acute liver injury (SALI) remains unknown. Herein, TMT-based quantitative proteomics was utilized to explore the essential pathways and proteins involved in the protective effects of PSP on SALI. The results revealed that 632 and 176 differentially expressed proteins (DEPs) were identified in Model_vs_Control and PSP_vs_Model, respectively. GO annotation showed similar trends, suggesting that these DEPs were primarily involved in the cellular anatomical entity in Cellular Component, the cellular processe and the biological regulation in Biological Process, the binding and the catalytic activity in Molecular Function. Meanwhile, KEGG enrichment analysis implied that four common pathways, including the NF-κB signaling pathway, the IL-17 signaling pathway, the TNF signaling pathway and the Toll-like receptor signaling pathway, were closely associated with the pathogenesis of sepsis among the top 20 remarkably enriched pathways in Model_vs_Control_up and PSP_vs_Model_down. Moreover, the levels of several common DEPs, including TLR2, IKKi, JunB and CXCL9, were validated by WB, which was in line with the results of proteomics. Therefore, the protective effects of PSP on SALI might exert via blocking the above-mentioned inflammation pathways.Significance: PSP, recognized as a key component of Polygonatum sibiricum, exhibits a range of pharmacological functions. Our previous study found that PSP could protect against SALI, yet failing to clarify the mechanism of action. To reveal the underlying molecular mechanism involved in the protective effects of PSP on SALI, a TMT-based quantitative proteomic analysis was performed to detect and analyse the DEPs in liver tissue among the control group, the model group and the PSP group in this study. The results provide theoretical references for exploring the action mechanism of drugs and facilitate the comprehensive utilization of PSP. SignificancePSP have been identified as the most crucial components of Polygonatum sibiricum with various pharmacological functions. Our previous study found that PSP could protect against SALI, but the mechanism of action remains unknown. To reveal the underlying molecular mechanism involved in the protective effects of PSP on SALI, a TMT-based quantitative proteomic analysis was performed to detect and analyse the DEPs in liver tissue among the control group, the model group and the PSP group in this study. The results provide theoretical references for exploring the action mechanism of drugs and facilitate the comprehensive utilization of PSP.

Small archaea may form intimate partnerships to maximize their metabolic potential.

DPANN archaea have characteristically small cells and unique genomes that were long overlooked in diversity surveys. Their reduced genomes often lack essential metabolic pathways, requiring symbiotic relationships with other archaeal and bacterial hosts for survival. Yet a long-standing question remains, what is the advantage of maintaining ultrasmall cells. A recent study by Zhang et al. examined genomes of DPANN archaea from marine oxygen deficient zones (ODZs) (I. H. Zhang, B. Borer, R. Zhao, S. Wilbert, et al., mBio 15:e02918-23, 2024, https://doi.org/10.1128/mbio.02918-23). Surprisingly, these genomes contain a broad array of metabolic pathways including genes predicted to be involved in nitrous oxide (N2O) reduction. However, N2O levels are likely too low in ODZs to make this metabolically feasible. Modeling co-localization of DPANN archaea (N2O consumers) with other larger cells (N2O producers) demonstrates that N2O uptake rates can be optimized by maximizing the producer-to-consumer size ratio and proximity of consumer cells to producers. This may explain why such a diversity of archaea maintain extremely small cell sizes.

HIV-1 Vpr-induced DNA damage activates NF-κB through ATM-NEMO independent of cell cycle arrest.

Lentiviruses encode a number of multi-functional accessory proteins, however, the primary role of the accessory protein Vpr remains unclear. As Vpr engages the host DNA damage response (DDR) at multiple steps, modulation of the DDR is considered central to the function(s) of Vpr. Vpr activates ataxia telangiectasia and Rad3 (ATR)-mediated DDR signaling, resulting in cell cycle arrest. However, the cellular consequences of Vpr-induced DNA damage, and the connection of Vpr-induced DNA damage to other Vpr functions, are unknown. Here, we determined that HIV-1 Vpr-induced DNA damage activates the ATM-NF-κB essential modulator (NEMO) pathway and alters cellular transcription via NF-κB/RelA. Through RNA-sequencing (RNA-seq) of cells expressing Vpr or mutants that separate the ability of Vpr to induce DNA damage from other DDR phenotypes, we identified that Vpr alters the transcriptome independent of cell cycle arrest. In tissue-cultured U2OS cells and primary human monocyte-derived macrophages (MDMs), we showed Vpr activates both ataxia telangiectasia mutated (ATM) and NF-κB/RelA signaling cascades. While inhibition of NEMO did not affect Vpr-induced DNA damage, it prevented NF-κB activation by Vpr, highlighting the importance of NEMO in Vpr-mediated transcriptional reprogramming. Virion-delivered Vpr was sufficient to induce DNA damage and activate ATM-NEMO dependent NF-κB transcription, suggesting that engagement of the DDR and transcriptional changes can occur early during viral replication. Together, our data uncover cellular consequences of Vpr-induced DNA damage and provide a mechanism for how Vpr activates NF-κB through DNA damage and ATM-NEMO signaling, which occur independent of cell cycle arrest. We propose this is essential to overcoming restrictive environments, such as in macrophages, to enhance viral replication.IMPORTANCEThe HIV accessory protein Vpr is multi-functional and required for viral replication in vivo, yet how Vpr enhances viral replication is unknown. Emerging literature suggests that a conserved function of Vpr is the engagement of the host DNA damage response (DDR). For example, Vpr activates DDR signaling, causes DDR-dependent cell cycle arrest, promotes degradation of various DDR proteins, and alters cellular consequences of DDR activation. However, a central understanding of how these phenotypes connect and how they affect HIV-infected cells remains unknown. Here, we found that Vpr-induced DNA damage alters the host transcriptome by activating an essential transcription pathway, NF-κB. This occurs early during the infection of primary human immune cells, suggesting NF-κB activation and transcriptome remodeling are important for establishing productive HIV-1 infection. Together, our study provides novel insights into how Vpr alters the host environment through the DDR, and what roles Vpr and the DDR play to enhance HIV replication.

Effects of BYL-719 (alpelisib) on human breast cancer stem cells to overcome drug resistance in human breast cancer.

Breast cancer continues to be a major health concern and is currently the most commonly diagnosed cancer worldwide. Relapse, metastasis, and therapy resistance are major clinical issues that doctors need to address. We believe BYL-719, which is PI3 kinase p110а inhibitor, could also inhibit the breast cancer stem cell phenotype and epithelial-to-mesenchymal transition (EMT). In addition to the PI3K/AKT signaling pathway, BYL-719 can also inhibit essential cancer-related signaling pathways, all of which would ultimately act on the microenvironment of cancer stem cells, which is quite complicated and regulates the characteristics of tumors. These include the stemness and resistance of malignant tumors, plasticity of cancer stem cells, and anti-apoptotic features. A three-dimensional (3D) mammosphere culture method was used in vitro to culture and collect breast cancer stem cells (BCSCs). MTT, clonogenic, and cell apoptosis assays were used to detect cell viability, self-renewal, and differentiation abilities. A sphere formation assay under 3D conditions was used to detect the mammophore inhibition rate of BYL-719. The subpopulation of CD44+CD24- was detected using flow cytometry analysis while EMT biomarkers and essential signaling pathways were detected using western blotting. All the data were analyzed using GraphPad Prism 9 software. BCSC-like cells were obtained by using the 3D cell culture method in vitro. We confirmed that BYL-719 could inhibit BCSC-like cell proliferation in 3D cultures and that the stemness characteristics of BCSC-like cells were inhibited. The PI3K/AKT/mTOR signaling pathway could be inhibited by BYL-719, and the Notch, JAK-STAT and MAPK/ERK signaling pathways which have crosstalk in the tumor microenvironment (TME) are also inhibited. By comparing eribulin-resistant breast cancer cell lines, we confirmed that BYL-719 could effectively overcome drug resistance. The 3D cell culture is a novel and highly effective method for enriching BCSCs in vitro. Furthermore, the stemness and EMT of BCSCs were inhibited by BYL-719 by acting on various signaling pathways. Finally, we believe that drug resistance can be overcome by targeting the BCSCs. Conjugation of BYL-719 with other anti-neoplastic agents may be a promising treatment for this in clinic.

Identification and interaction analysis of molecular markers in myocardial infarction by bioinformatics and next-generation sequencing data analysis

BackgroundCardiovascular diseases are prevalent worldwide with any age, and it is characterized by sudden blockage of blood flow to heart and permanent damage to the heart muscle, whose cause and underlying molecular mechanisms are not fully understood. This investigation aimed to explore and identify essential genes and signaling pathways that contribute to the progression of MI.MethodsThe aim of this investigation was to use bioinformatics and next-generation sequencing (NGS) data analysis to identify differentially expressed genes (DEGs) with diagnostic and therapeutic potential in MI. NGS dataset (GSE132143) was downloaded from the Gene Expression Omnibus (GEO) database. DEGs between MI and normal control samples were identified using the DESeq2 R bioconductor tool. The gene ontology (GO) and REACTOME pathway enrichment analyses of the DEGs were performed using g:Profiler. Next, four kinds of algorithms in the protein–protein interaction (PPI) were performed to identify potential novel biomarkers. Next, miRNA-hub gene regulatory network analysis and TF-hub gene regulatory network were constructed by miRNet and NetworkAnalyst database, and Cytoscape software. Finally, the diagnostic effectiveness of hub genes was predicted by receiver operator characteristic curve (ROC) analysis and AUC more than 0.800 was considered as having the capability to diagnose MI with excellent specificity and sensitivity.ResultsA total of 958 DEGs were identified, consisting of 480 up-regulated genes and 478 down-regulated genes. The enriched GO terms and pathways of the DEGs include immune system, neuronal system, response to stimulus and multicellular organismal process. Ten hub genes (namely cftr, cdk1, rps13, rps15a, rps27, notch1, mrpl12, nos2, ccdc85b and atn1) were obtained via protein–protein interaction analysis results. MiRNA-hub gene regulatory network and TF-hub gene regulatory network showed that hsa-mir-409-3p, hsa-mir-3200-3p, creb1 and tp63 might play an important role in the MI.ConclusionsAnalysis of next-generation sequencing dataset combined with global network information and validation presents a successful approach to uncover the risk hub genes and prognostic markers of MI. Our investigation identified four risk- and prognostic-related gene signatures, including cftr, cdk1, rps13, rps15a, rps27, notch1, mrpl12, nos2, ccdc85b and atn1. This gene sets contribute a new perspective to improve the diagnostic, prognostic, and therapeutic outcomes of MI.