Identification of molecular subtypes and a prognostic signature based on m6A/m5C/m1A-related genes in lung adenocarcinoma.

Lung cancer, specifically the histological subtype lung adenocarcinoma (LUAD), has the highest global occurrence and fatality rate. Extensive research has indicated that RNA alterations encompassing m6A, m5C, and m1A contribute actively to tumorigenesis, drug resistance, and immunotherapy responses in LUAD. Nevertheless, the absence of a dependable predictive model based on m6A/m5C/m1A-associated genes hinders accurately predicting the prognosis of patients diagnosed with LUAD. In this study, we collected patient data from The Cancer Genome Atlas (TCGA) and identified genes related to m6A/m5C/m1A modifications using the GeneCards database. The "ConsensusClusterPlus" R package was used to produce molecular subtypes by utilizing genes relevant to m6A/m5C/m1A identified through differential expression and univariate Cox analyses. An independent prognostic factor was identified by constructing a prognostic signature comprising six genes (SNHG12, PABPC1, IGF2BP1, FOXM1, CBFA2T3, and CASC8). Poor overall survival and elevated expression of human leukocyte antigens and immune checkpoints were correlated with higher risk scores. We examined the associations between the sets of genes regulated by m6A/m5C/m1A and the risk model, as well as the immune cell infiltration, using algorithms such as ESTIMATE, CIBERSORT, TIMER, ssGSEA, and exclusion (TIDE). Moreover, we compared tumor stemness indices (TSIs) by considering the molecular subtypes related to m6A/m5C/m1A and risk signatures. Analyses were performed based on the risk signature, including stratification, somatic mutation analysis, nomogram construction, chemotherapeutic response prediction, and small-molecule drug prediction. In summary, we developed a prognostic signature consisting of six genes that have the potential for prognostication in patients with LUAD and the design of personalized treatments that could provide new versions of personalized management for these patients.

High-order sensory processing nanocircuit based on coupled VO2 oscillators.

Conventional circuit elements are constrained by limitations in area and power efficiency at processing physical signals. Recently, researchers have delved into high-order dynamics and coupled oscillation dynamics utilizing Mott devices, revealing potent nonlinear computing capabilities. However, the intricate yet manageable population dynamics of multiple artificial sensory neurons with spatiotemporal coupling remain unexplored. Here, we present an experimental hardware demonstration featuring a capacitance-coupled VO2 phase-change oscillatory network. This network serves as a continuous-time dynamic system for sensory pre-processing and encodes information in phase differences. Besides, a decision-making module for special post-processing through software simulation is designed to complete a bio-inspired dynamic sensory system. Our experiments provide compelling evidence that this transistor-free coupling network excels in sensory processing tasks such as touch recognition and gesture recognition, achieving significant advantages of fewer devices and lower energy-delay-product compared to conventional methods. This work paves the way towards an efficient and compact neuromorphic sensory system based on nano-scale nonlinear dynamics.

VO2 memristor-based frequency converter with in-situ synthesize and mix for wireless internet-of-things.

Wireless internet-of-things (WIoT) with data acquisition sensors are evolving rapidly and the demand for transmission efficiency is growing rapidly. Frequency converter that synthesizes signals at different frequencies and mixes them with sensor datastreams is a key component for efficient wireless transmission. However, existing frequency converters employ separate synthesize and mix circuits with complex digital and analog circuits using complementary metal-oxide semiconductor (CMOS) devices, naturally incurring excessive latency and energy consumption. Here we report a highly uniform and calibratable VO2 memristor oscillator, based on which we build memristor-based frequency converter using 8[Formula: see text]8 VO2 array that can realize in-situ frequency synthesize and mix with help of compact periphery circuits. We investigate the self-oscillation based on negative differential resistance of VO2 memristors and the programmability with different driving currents and calibration resistances, demonstrating capabilities of such frequency converter for in-situ frequency synthesize and mix for 2 ~ 8 channels with frequencies up to 48 kHz for low frequency transmission link. When transmitting classical sensor data (acoustic, vision and spatial) in an end-to-end WIoT experimental setup, our VO2-based memristive frequency converter presents up to 1.45× ~ 1.94× power enhancement with only 0.02 ~ 0.21 dB performance degradations compared with conventional CMOS-based frequency converter. This work highlights the potential in solving frequency converter's speed and energy efficiency problems in WIoT using high crystalline quality epitaxially grown VO2 and calibratable VO2-based oscillator array, revealing a promising direction for next-generation WIoT system design.

MiR-3529-3p from PDGF-BB-induced cancer-associated fibroblast-derived exosomes promotes the malignancy of oral squamous cell carcinoma.

AIMS: This study aims to explore the role of exosomes from cancer-associated fibroblasts (CAFs) induced by PDGF-BB in promoting the malignancy of oral squamous cell carcinoma (OSCC) and provide new insight into the mechanism of OSCC progression and its treatment. MAIN METHODS: Exosomes were extracted from human oral mucosa fibroblasts (hOMFs) and CAFs. Differentially expressed miRNAs of exosomes between hOMFs and CAFs were analysed using high-throughput sequencing and self-programmed R software. Cal-27, a human tongue squamous carcinoma cell line, was treated with exosomes. Differentially expressed miRNAs between clinical cancer tissues and adjacent tissues and between hOMF and CAF exosomes were verified by qRT‒PCR. The effect of miR-3529-3p on Cal-27 cells was clarified by overexpressing or knocking down miR-3529-3p in Cal-27 cells. Sample expression and differentially expressed miRNA expression were compared between cancer and paracarcinoma tissues. KEY FINDINGS: We found that exosomes from CAFs (CAF-Exos) were internalized by tongue squamous carcinoma cells and promoted their proliferation, migration, invasion, and antiapoptotic effects. MiR-3529-3p was a significant differentially expressed miRNA between CAF-Exos and exosomes from hOMFs (hOMF-Exos). The overexpression of miR-3529-3p promoted proliferation, migration, and invasion and inhibited apoptosis of Cal-27 cells. SIGNIFICANCE: This study explores the role of PDGF-BB-induced CAFs in promoting malignancy in OSCC. This study will provide new insight into the mechanism of OSCC progression and its treatment.

Identification of cancer stemness and M2 macrophage-associated biomarkers in lung adenocarcinoma.

Objective: Cancer stemness and M2 macrophages are intimately linked to the prognosis of lung adenocarcinoma (LUAD). For this reason, this investigation sought to identify the key genes relevant to cancer stemness and M2 macrophages, explore the relationship between these genes and clinical characteristics, and determine the potential mechanism. Methods: LUAD transcriptomic data was analyzed from The Cancer Genome Atlas (TCGA) as well as the Gene Expression Omnibus databases. Differential expression analysis was performed to discern abnormally expressed genes between LUAD and control samples in TCGA cohort. The Cell type Identification by Estimating Relative Subsets of RNA Transcripts (CIBERSORT) algorithm was applied to determine varyingly infiltrated immune cells in LUAD compared with the control samples in TCGA cohort. Weighted correlation network analysis (WGCNA) was performed to identify genes associated with mRNA expression-based stemness index (mRNAsi) and M2 macrophages. Least absolute shrinkage and selection operator (LASSO), RandomForest (RF) and support vector machine-recursive feature elimination (SVM-RFE) machine learning methods were conducted to detect gene signatures. Global survival evaluation (Kaplan-Meier curve) was applied to investigate the relationship between gene signatures and the survival time of LUAD patients. Receiver operating characteristic (ROC) curves were produced to define biomarkers relevant to diagnosis. Gene Set Enrichment Analysis (GSEA) was performed to probe the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways related to diagnostic biomarkers. The public single-cell dataset of LUAD (GSE123902) was used to investigate the expression differences of diagnostic biomarkers in various cell types in LUAD. Real-time quantitative PCR (qRT-PCR) was performed to confirm key genes in lung adenocarcinoma cells. Results: A total of 5,410 differentialy expressed genes (DEGs) as well as 15 differentially infiltrated immune cells were identified between LUAD and control sepcimens in TCGA cohort. Thirty-seven DEGs were associated with both M2 macrophages and mRNAsi according to the WGCNA analysis. Sixteen common gene signatures were obtained using three diverse algorithms. CBFA2T3, DENND3 and FCAMR were correlated to overall and disease-free survival of LUAD patients. ROC curves revealed that CBFA2T3 and DENND3 expression accurately classified LUAD and control samples. The results of single cell related analysis showed that two diagnostic biomarkers expressions were differed between the different tissue sources in M2-like macrophages. QRT-PCR demonstrated the mRNA expressions of CBFA2T3 and DENND3 were upregulated in lung adenocarcinoma cells A549 and H2122. Conclusion: Our study identified CBFA2T3 and DENND3 as key genes associated with mRNAsi and M2 macrophages in LUAD and investigated the potential molecular mechanisms underlying this relationship.

VEGF-modified PLA/HA nanocomposite fibrous membrane for cranial defect repair in rats.

A major obstacle to bone tissue repair is the difficulty in establishing a rapid blood supply areas of bone defects. Vascular endothelial growth factor (VEGF)-infused tissue-engineered scaffolds offer a possible therapeutic option for these types of injuries. Their role is to accelerate angiogenesis and improve bone healing. In this study, we used electrostatic spinning and biofactor binding to construct polylactic acid (PLA)/hydroxyapatite (HA)-VEGF scaffold materials and clarify their pro-vascular role in bone defect areas for efficient bone defect repair. PLA/HA nanocomposite fibrous membranes were manufactured by selecting suitable electrostatic spinning parameters. Heparin and VEGF were bound sequentially, and then the VEGF binding and release curves of the fiber membranes were calculated. A rat cranial defect model was constructed, and PLA/HA fiber membranes bound with VEGF and unbound with VEGF were placed for treatment. Finally, we compared bone volume recovery and vascular recovery in different fibrous membrane sites. A VEGF concentration of 2.5 µg/mL achieved the maximum binding and uniform distribution of PLA/HA fibrous membranes. Extended-release experiments showed that VEGF release essentially peaked at 14 days. In vivo studies showed that PLA/HA fibrous membranes bound with VEGF significantly increased the number of vessels at the site of cranial defects, bone mineral density, bone mineral content, bone bulk density, trabecular separation, trabecular thickness, and the number of trabeculae at the site of defects in rats compared with PLA/HA fibrous membranes not bound with VEGF. VEGF-bound PLA/HA fibrous membranes demonstrate the slow release of VEGF. The VEGF binding process does not disrupt the morphology and structure of the fibrous membranes. The fibrous membranes could stimulate both osteogenesis and angiogenesis. Taken together, this research provides a new strategy for critical-sized bone defects repairing.

Multi-omics analysis of LAMB3 as a potential immunological and biomarker in pan-cancer.

Laminin Subunit Beta 3 (LAMB3) is a transcription factor and participates in the coding of laminin. It plays an important role in cell proliferation, adhesion, and transfer by regulating various target genes and signaling pathways. However, the role of LAMB3 in human pan-cancer immunology and prognosis is still poorly understood. The TCGA, GTEx, CCLE, and HPA databases were utilized for the analysis of LAMB mRNA and protein expression. The expression of LAMB3 in various immune and molecular subtypes of human cancer was examined using the TISIDB database. The prognostic significance of LAMB3 in various cancers and clinical subtypes was investigated using Kaplan-Meier and Cox regression analysis. The relationship between LAMB3 expression, various immune cell infiltration, immune checkpoints, tumor mutational load, microsatellite instability, and DNA methylation was examined using the TCGA database. Clinical samples of four lung cancer cell lines and eight lung cancer cases were collected to confirm the expression of mRNA in lung cancer. In 17 cancers, the mRNA for LAMB3 is expressed differently and has good diagnostic and prognostic value in 22 cancers. Cox regression and Nomogram analysis show that LAMB3 is an independent risk factor for 15 cancers. LAMB3 is implicated in a variety of tumorigenesis and immune-related signaling pathways, according to GO, KEGG, and GSEA results. LAMB3 expression was associated with TMB in 33 cancer types and MSI in 32 cancer types, while in lung cancer LAMB3 expression was strongly associated with immune cell infiltration and negatively correlated with all seven methylated CpG islands. Cellular experiments demonstrated that LAMB3 promotes malignant behavior of tumor cells. Preliminary mechanistic exploration revealed its close association with PD-L1, CTLA4, cell stemness gene CD133 and ß-catenin-related signaling pathways. Based on these findings, it appears that LAMB3 could be a potential therapeutic target for immunotherapy and tumor prognosis. Our findings reveal an important role for LAMB3 in different cancer types.

Analysis of mRNA-miRNA interaction network reveals the role of CAFs-derived exosomes in the immune regulation of oral squamous cell carcinoma.

BACKGROUND: Cancer-associated fibroblasts (CAFs) have significant tumor regulatory functions, and CAFs-derived exosomes (CAFs-Exo) released from CAFs play an important role in the progression of oral squamous cell carcinoma (OSCC). However, a lack of comprehensive molecular biological analysis leaves the regulatory mechanisms of CAFs-Exo in OSCC unclear. METHODS: We used platelet derived growth factor-BB (PDGF-BB) to induce the transformation of human oral mucosa fibroblast (hOMF) into CAFs, and extracted exosomes from the supernatant of CAFs and hOMF. We validated the effect of CAFs-Exo on tumor progression by exosomes co-culture with Cal-27 and tumor-forming in nude mice. The cellular and exosomal transcriptomes were sequenced, and immune regulatory genes were screened and validated using mRNA-miRNA interaction network analysis in combination with publicly available databases. RESULTS: The results showed that CAFs-Exo had a stronger ability to promote OSCC proliferation and was associated with immunosuppression. We discovered that the presence of immune-related genes in CAFs-Exo may regulate the expression of PIGR, CD81, UACA, and PTTG1IP in Cal-27 by analyzing CAFs-Exo sequencing data and publicly available TCGA data. This may account for the ability of CAFs-Exo to exert immunomodulation and promote OSCC proliferation. CONCLUSIONS: CAFs-Exo was found to be involved in tumor immune regulation through hsa-miR-139-5p, ACTR2 and EIF6, while PIGR, CD81, UACA and PTTG1IP may be potentially effective targets for the treatment of OSCC in the future.

Glucose-independent insulin and glucagon secreted from ventral pancreas sharing a similar pattern in healthy adult rat.

Elevated blood glucose concentration due to food intake will trigger insulin secretion from the dorsal pancreas has been extensively studied. This increased intracellular insulin level can stimulate glucagon release from intra-islets. However, the interaction between glucagon and insulin under a fasting state is unknown. To explore the relationship, we partially removed the ventral and dorsal pancreas on wild-type adult rats. The glucose tolerance test was conducted to measure influence of the surgery on the integrity function of the pancreas. The fasting insulin/glucagon level before and after surgery were measured by the ELISA kit. The statistical analyses indicated that the ventral removal of the pancreas had higher fasting glucose than that of dorsal removal. And only the ventral removal group showed significantly increased basal insulin and basal glucagon levels. Our findings showed differential role of the ventral pancreas in response to a glucose-free stimulus and also provided the possible in vitro target for developing the anti-hyperglycemic drugs.

Untargeted Metabolomics Reveal the Protective Effect of Bone Marrow Mesenchymal Stem Cell Transplantation Against Ovariectomy-Induced Osteoporosis in Mice.

Bone marrow mesenchymal stem cell transplantation (BMSCT) is a potential treatment for osteoporosis, capable of contributing to bone tissue repair. BMSCT has demonstrated osteoinductive effects and the ability to regulate microenvironmental metabolism; however, its role and mechanisms in bone loss due to reduced estrogen levels remain unclear. In this study, the effect of BMSCT on ovariectomy (OVX)-induced osteoporosis in mice was assessed, and liquid chromatography-mass spectrometry (LC-MS) metabolomic studies of bone tissue were conducted to identify potential metabolic molecular markers. The results revealed that BMSCT reduces OVX-induced bone loss in mice while improving the mechanical properties of mouse femurs and increasing the expression of osteogenic markers in peripheral blood. In a metabolomic study, 18 metabolites were screened as potential biomarkers of the anti-osteoporotic effect of BMSCT. These metabolites are mainly involved in arachidonic acid metabolism, taurine and hypotaurine metabolism, and pentose and glucuronate interconversions. Collectively, these results illustrate the correlation between metabolites and the underlying mechanisms of osteoporosis development and are important for understanding the role and mechanisms of exogenous bone marrow mesenchymal stem cells (BMSCs) in osteoporosis management. This study lays the foundation for research on BMSCs as a treatment strategy for osteoporosis.

Mesenchymal stem cells prevent ovariectomy-induced osteoporosis formation in mice through intraosseous vascular remodeling.

Mesenchymal stem cells (MSCs) can promote osteogenesis and are a promising therapy for postmenopausal osteoporosis. However, the relationship between improved intraosseous microcirculation and increased bone mass induced by MSCs in postmenopausal osteoporosis remains unclear. After the primary MSCs were characterized, they were transplanted into ovariectomized mice. MSCs transplantation enhanced the trabecular number, trabecular bone volume/total volume, and trabecular bone mineral density in ovariectomized mice. To determine the role of MSCs in vascular repair, mice were subjected to femoral artery ligation. Through laser speckle flowmetry, vascular perfusion and femoral trabecular bone and cortical bone analyses, we determined the effects of MSCs in promoting intraosseous angiogenesis and preventing osteoporosis in mice. MSCs effectively prevented postmenopausal osteoporosis development, which is associated with the involvement of MSCs in reestablishment of microcirculation within the skeleton.

Does Supplemental Nutrition Assistance Program Reduce Food Insecurity among Households with Children? Evidence from the Current Population Survey.

The Supplemental Nutrition Assistance Program (SNAP) is designed to improve household diet and food security-a pressing problem confronting low-income families in the United States. Previous studies on the issue often ignored the methodological issue of endogenous program participation. We revisit this important issue by estimating a simultaneous equation system with ordinal household food insecurity. Data are drawn from the 2009-2011 Current Population Survey Food Security Supplement (CPS-FSS), restricted to SNAP-eligible households with children. Our results add to the stocks of empirical findings that SNAP participation ameliorates food insecurity among adults only, but increases the probabilities of low and very low food security among children. These contradictory results indicate that our selection approach with a single cross section is only partially successful, and that additional efforts are needed in further analyses of this complicated issue, perhaps with longitudinal data. Socio-demographic variables are found to affect food-secure households and food-insecure households differently, but affect SNAP nonparticipants and participants in the same direction. The state policy tools, such as broad-based categorical eligibility (BBCE) and simplified reporting, can encourage SNAP participation and thus ameliorate food insecurity. Our findings can inform policy deliberations.

Transiently chaotic simulated annealing based on intrinsic nonlinearity of memristors for efficient solution of optimization problems.

Optimization problems are ubiquitous in scientific research, engineering, and daily lives. However, solving a complex optimization problem often requires excessive computing resource and time and faces challenges in easily getting trapped into local optima. Here, we propose a memristive optimizer hardware based on a Hopfield network, which introduces transient chaos to simulated annealing in aid of jumping out of the local optima while ensuring convergence. A single memristor crossbar is used to store the weight parameters of a fully connected Hopfield network and adjust the network dynamics in situ. Furthermore, we harness the intrinsic nonlinearity of memristors within the crossbar to implement an efficient and simplified annealing process for the optimization. Solutions of continuous function optimizations on sphere function and Matyas function as well as combinatorial optimization on Max-cut problem are experimentally demonstrated, indicating great potential of the transiently chaotic memristive network in solving optimization problems in general.

Spiking neurons with spatiotemporal dynamics and gain modulation for monolithically integrated memristive neural networks.

As a key building block of biological cortex, neurons are powerful information processing units and can achieve highly complex nonlinear computations even in individual cells. Hardware implementation of artificial neurons with similar capability is of great significance for the construction of intelligent, neuromorphic systems. Here, we demonstrate an artificial neuron based on NbOx volatile memristor that not only realizes traditional all-or-nothing, threshold-driven spiking and spatiotemporal integration, but also enables dynamic logic including XOR function that is not linearly separable and multiplicative gain modulation among different dendritic inputs, therefore surpassing neuronal functions described by a simple point neuron model. A monolithically integrated 4 × 4 fully memristive neural network consisting of volatile NbOx memristor based neurons and nonvolatile TaOx memristor based synapses in a single crossbar array is experimentally demonstrated, showing capability in pattern recognition through online learning using a simplified δ-rule and coincidence detection, which paves the way for bio-inspired intelligent systems.

Different material factors affect the proliferation and osteogenic differentiation of bone marrow mesenchymal stem cells / 中国组织工程研究

BACKGROUND: In the treatment of bone defect or bone injury by tissue engineering, biomaterials affect the survival rate, proliferation and differentiation of bone marrow mesenchymal stem cells. OBJECTIVE: To review the research progress regarding how biomaterials affect the proliferation and osteogenic differentiation of bone marrow mesenchymal stem cells, and to guide the rational application of biomaterials. METHODS: A computer-based online search of CNKI, PubMed, Web of Science, and Wanfang database with the search terms “Bone marrow mesenchymal stem cells, Osteogenic differentiation, Biological materials, The microstructure”. The eligible literatures regarding the effects of different biomaterials on the proliferation and osteogenic differentiation of bone marrow mesenchymal stem cells were included. RESULTS AND CONCLUSION: (1) Metallic materials have the advantages of good biocompatibility, bone conductivity, and mechanical performance. Non-metallic materials exhibit good biocompatibility, bone conductivity, reabsorption, and three-dimensional shaping. (2) There are many factors that affect the surface microstructure of the biomaterial. As for the same biomaterial, greater surface energy/ wettability leads to better proliferation and osteogenic differentiation of bone marrow mesenchymal stem cells; greater roughness better promotes the proliferation, adhesion, and differentiation of bone marrow mesenchymal stem cells; larger pore diameter and lower pore diameter rate are more prone to promote the osteogenic differentiation of bone marrow mesenchymal stem cells; greater substrate rigidity and elastic modulus better facilitate the osteogenic differentiation of bone marrow mesenchymal stem cells. The abovementioned factors of the biomaterials affect the proliferation and osteogenic differentiation of bone marrow mesenchymal stem cells. These findings help promote the application of biomaterials seeded with bone marrow mesenchymal stem cells in the clinic.