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Yellow plumage is common in chickens, especially in breeds such as the Huiyang Bearded chicken, which is indigenous to China. We evaluated plumage colour distribution in F1, F2, and F3 populations of an Huiyang Bearded chicken × White Leghorn chicken cross, the heredity of the yellow plumage trait was distinguished from that of the gold plumage and other known plumage colours. Microscopic analysis of the feather follicles indicated that pheomelanin particles were formed in yellow but not in white feathers. To screen genes related to formation of the pheomelanin particles, we generated transcriptome data from yellow and white feather follicles from 7- and 11-week-old F3 chickens using RNA-seq. We identified 27 differentially expressed genes (DEGs) when comparing the yellow and white feather follicles. These DEGs were enriched in the Gene Ontology classes 'melanosome' and 'melanosome organization' related to the pigmentation process. Down-regulation of TYRP1, DCT, PMEL, MLANA, and HPGDS, verified using quantitative reverse transcription PCR, may lead to reduced eumelanin and increased pheomelanin synthesis in yellow plumage. Owing to the presence of the Dominant white locus, both white and yellow plumage lack eumelanin, and white feathers showed no pigments. Our results provide an understanding of yellow plumage formation in chickens.

The failure to maintain the viability of ischemic myocardium is one of the mechanisms that causes ischemic heart dysfunction after revascularization. Hibernating myocardium is considered to be able to maintain long-term viability during chronic hypoperfusion. Pigment epithelium-derived factor (PEDF) decreases the contractility of hypoxic cardiomyocytes and protects cardiomyocytes against ischemic injury, which is strikingly similar to the pathophysiologic characteristics of hibernating myocardium. It was therefore postulated that PEDF may induce acute ischemic myocardium into a "hibernating-like" state to maintain its viability. Adult Sprague-Dawley rat models of acute myocardial infarction were surgically established. Lentiviral vectors carrying the PEDF gene (PEDF-LVs) were delivered into myocardium with infarction to overexpress PEDF locally. It was found that PEDF local overexpression significantly reduced myocardial infarct size and cardiomyocytes necrosis but did not improve cardiac function at rest. The contractile reserve assessed by low-dose dobutamine stress echocardiography and "perfusion-metabolism mismatch" assessed by positron emission tomography, which are the characteristics of viable myocardium in hibernation, were observed in the PEDF overexpressed ischemic heart. Ultrastructural changes observed by electron microscopy and glycogen deposition explored by Periodic acid-Schiff staining were similar to the histological characteristics of hibernating myocardium. Moreover, PEDF overexpression protected the cardiomyocytes against anoxic injury and retained their functional recovery potential after reoxygenation in vitro . PEDF local overexpression may induce acute ischemic myocardium into a "hibernating-like" state and maintain its viability. This novel effect of PEDF presents an important clinical approach to enhance functional recovery after revascularization therapy in acute myocardial infarction.

ADMATS-7 is known to play an important role in the pathogenesis of various diseases, including cartilaginous diseases. IL-17A is an inflammatory cytokine detected in degenerative disc tissues. However, the interplay between IL-17A and ADMATS-7 in human disc degeneration is still unknown. Samples collected from 50 patients were divided into three groups according to MRI degeneration grading system score. Immunohistochemistry, RT-PCR and western Blotting were used to investigate the expression of ADAMTS-7 in NP tissues. Furthermore, a rat disc degeneration model was established, and the expression level of ADAMTS-7 was assayed using immunohistochemistry, RT-PCR and western Blotting. The human NP cells were cultured in the presence and absence of IL-17A stimulation. RNA extracts were collected, and real-time PCR was performed to determine the expression of ADAMTS-7. Moreover, ADAMTS-7 concentrations were detected in human NP cell culture supernatants by ELISA. After culturing NP cells with IL-17A (with or without Etanercept), ADAMTS-7 levels were detected in each group. ADAMTS-7 expression was dramatically elevated in both human and rat degenerative NP tissues compared with normal controls. The RT-PCR and ELISA results revealed that IL-17A could enhance the production of ADAMTS-7, while ADAMTS-7 expression dramatically decreased in the IL-17A + Etanercept group in comparison to the IL-17A alone group. Our results indicate the presence of ADAMTS-7 in human NP cells and imply its potential role in disc degeneration. Additionally, our results indicate that IL-17A induced ADAMTS-7 expression via TNF-α, which may form a molecular axis in human NP cells.

Objective: To explore the clinical significance of interleukin (IL)-32 in the treatment of rheumatoid arthritis (RA) patients and analyze the correlations of IL-32 with C-reactive protein (CRP), erythrocyte sedimentation rate (ESR), and rheumatoid factor (RF)., Methods: A total of 97 patients with RA and 36 patients with non-RA connective tissue diseases (CTD) were included. The mRNA levels of IL-32 and TNF-α in peripheral blood mononuclear cells (PBMCs) were determined using a quantitative real-time polymerase chain reaction. The plasma concentrations of IL-32 and TNF-α were determined using enzyme-linked immunosorbent assays. Data were analyzed using one-way ANOVA and Spearman's method., Results: The mRNA levels of IL-32 and TNF-α in the active RA groups were significantly higher than those in the healthy control, stable RA, and non-RA CTD groups (P < 0.01). There was no significant difference between the stable RA, healthy control, and non-RA CTD groups (P > 0.05). The concentrations of IL-32 and TNF-α in the active RA groups were significantly higher than those in the stable RA and control groups (P < 0.01). IL-32 expression was positively correlated with TNF-α, ESR, CRP, RF, and DAS28 in patients with RA (P < 0.01). CONCLUSION The levels of IL-32 and TNF-α in the peripheral blood of patients with active RA are significantly higher than in that of patients with stable RA and healthy people. The IL-32 level in peripheral blood may provide a reference for the detection of RA activity.

Background: c-Jun/AP-1 has been linked to invasive properties of aggressive breast cancer. Recently, it has been reported that overexpression of c-Jun in breast cancer cell line MCF-7 resulted in increased AP-1 activity, motility and invasiveness of the cells in vitro and tumor formation in nude mice. However, the role of c-Jun in metastasis of human breast cancer in vivo is currently unknown., Methods: To further investigate the direct involvement of c-Jun in tumorigenesis and metastasis, in the present study, the effects of c-Jun overexpression were studied in both in vitro and in nude mice., Results: Ectopic overexpression of c-Jun promoted the growth of MCF-7 cells and resulted in a significant increase in the percentage of cells in S phase and increased motility and invasiveness. Introduction of c-Jun gene alone into weakly invasive MCF-7 cells resulted in the transfected cells capable of metastasizing to the nude mouse liver following tail vein injection., Conclusion: The present study confirms that overexpression of c-Jun contributes to a more invasive phenotype in MCF-7 cells. It indicates an interesting relationship between c-Jun expression and increased property of adhesion, migration and in vivo liver metastasis of MCF-7/c-Jun cells. The results provide further evidence that c-Jun is involved in the metastasis of breast cancer. The finding also opens an opportunity for development of anti-c-Jun strategies in breast cancer therapy.

Background: Esophageal squamous cell carcinoma (ESCC) is often diagnosed at advanced stages due to the inherent limitations of current screening methodologies. Central to evaluating tumor invasion and prognostic assessment in ESCC is the integrity of the basement membrane (BM). However, current research on the implications of BM-related genes (BMRGs) in diagnosing ESCC remains sparse. Methods: We performed a comprehensive analysis using single-cell RNA-sequencing (scRNA-seq) data from the Gene Expression Omnibus (GEO) database, alongside gene expression profiles acquired from GEO and The Cancer Genome Atlas (TCGA) databases. This identified differentially expressed BMRGs in ESCC. Employing LASSO, RF, and SVM-RFE, we selected potential BM biomarkers and crafted a diagnostic nomogram for ESCC, validated by ROC curves and AUC values. We also explored immune infiltration and biological mechanisms through consensus clustering and GSVA, and utilized single cell trajectory analysis and GSCALite to study gene distributions and pathways. In vitro experiments further elucidated the role of these genes in ESCC carcinogenesis. Results: Here, we discovered that ESCC cell types exhibited markedly elevated BM-related scores. Our analysis pinpointed seven BM genes upregulated and linked to immune infiltration, showcasing unique gene expression profiles and varying immune cell densities across the BM-related subtypes. Furthermore, a robust positive correlation was observed between these genes expression and EMT activity. The knockdown of BGN significantly suppressed cell proliferation, migration, invasion, while also augmenting cell viability following chemotherapy drug treatment. Conclusion: Our study identified seven key BMRGs (BGN, LAMB3, SPARC, MMP1, LUM, COL4A1, and NELL2) and established a diagnostic nomogram for ESCC. Of noteworthy significance is the discovery of BGN as a promising drug target, indicating a novel strategy for future clinical combination therapies in ESCC. [ABSTRACT FROM AUTHOR]

The secreted phospholipase A2 (sPLA2) isoform, sPLA2-IIA, has been implicated in a variety of diseases and conditions, including bacteremia, cardiovascular disease, COVID-19, sepsis, adult respiratory distress syndrome, and certain cancers. Given its significant role in these conditions, understanding the regulatory mechanisms impacting its levels is crucial. Genome-wide association studies (GWAS) have identified several single nucleotide polymorphisms (SNPs), including rs11573156, that are associated with circulating levels of sPLA2-IIA. The work in the manuscript leveraged 4 publicly available datasets to investigate the mechanism by which rs11573156 influences sPLA2-IIA levels via bioinformatics and modeling analysis. Through genotype-tissue expression (GTEx), 234 expression quantitative trait loci (eQTLs) were identified for the gene that encodes for sPLA2-IIA, PLA2G2A. SNP2TFBS was used to ascertain the binding affinities between transcription factors (TFs) to both the reference and alternative alleles of identified eQTL SNPs. Subsequently, candidate TF-SNP interactions were cross-referenced with the ChIP-seq results in matched tissues from ENCODE. SP1-rs11573156 emerged as the significant TF-SNP pair in the liver. Further analysis revealed that the upregulation of PLA2G2A transcript levels through the rs11573156 variant was likely affected by tissue SP1 protein levels. Using an ordinary differential equation based on Michaelis-Menten kinetic assumptions, we modeled the dependence of PLA2G2A transcription on SP1 protein levels, incorporating the SNP influence. Collectively, our analysis strongly suggests that the difference in the binding dynamics of SP1 to different rs11573156 alleles may underlie the allele-specific PLA2G2A expression in different tissues, a mechanistic model that awaits future direct experimental validation. This mechanism likely contributes to the variation in circulating sPLA2-IIA protein levels in the human population, with implications for a wide range of human diseases. [ABSTRACT FROM AUTHOR]

Background: Lung cancer is the most common malignant tumor. In the present study, we identified a long non‐coding RNA (lncRNA) AC100826.1 (simplify to Lnc1), which was highly expressed in non‐small cell lung cancer (NSCLC) tissues compared with the paracancerous tissues. We also observed the critical role of Lnc1 in regulating the metastasis ability of NSCLC cells. Methods: RNA sequencing was performed to detect differential expression levels of lncRNAs in NSCLC tissues and its paracancerous tissues. Effects of Lnc1 on cell proliferation, invasion, and migration were determined by CCK‐8, transwell and scratch assays. The xenograft experiment confirmed the effect of Lnc1 on NSCLC cells proliferation and migration abilities in vivo. RT‐qPCR and western blots were performed to determine the expression levels of mRNAs and proteins. Results: The expression level of Lnc1 was related to multiple pathological results, knockdown of Lnc1 can inhibit the proliferation and metastasis abilities of NSCLC cells. silencing phospholipase C, β1(PLCB1) can reverse the promoting effects of overexpression Lnc1 on NSCLC cells proliferation and migration abilities. In addition, the Rap1 signaling pathway was implicated in the regulation of Lnc1 in NSCLC metastasis. Conclusion: Our results suggest that Lnc1 regulated the metastatic ability of NSCLC cells through targeting the PLCB1/Rap1 signal pathway. [ABSTRACT FROM AUTHOR]

Hepatocellular carcinoma (HCC) results in the abnormal regulation of cellular metabolic pathways. Constraint-based modeling approaches can be utilized to dissect metabolic reprogramming, enabling the identification of biomarkers and anticancer targets for diagnosis and treatment. In this study, two genome-scale metabolic models (GSMMs) were reconstructed by employing RNA sequencing expression patterns of hepatocellular carcinoma (HCC) and their healthy counterparts. An anticancer target discovery (ACTD) framework was integrated with the two models to identify HCC targets for anticancer treatment. The ACTD framework encompassed four fuzzy objectives to assess both the suppression of cancer cell growth and the minimization of side effects during treatment. The composition of a nutrient may significantly affect target identification. Within the ACTD framework, ten distinct nutrient media were utilized to assess nutrient uptake for identifying potential anticancer enzymes. The findings revealed the successful identification of target enzymes within the cholesterol biosynthetic pathway using a cholesterol-free cell culture medium. Conversely, target enzymes in the cholesterol biosynthetic pathway were not identified when the nutrient uptake included a cholesterol component. Moreover, the enzymes PGS1 and CRL1 were detected in all ten nutrient media. Additionally, the ACTD framework comprises dual-group representations of target combinations, pairing a single-target enzyme with an additional nutrient uptake reaction. Additionally, the enzymes PGS1 and CRL1 were identified across the ten-nutrient media. Furthermore, the ACTD framework encompasses two-group representations of target combinations involving the pairing of a single-target enzyme with an additional nutrient uptake reaction. Computational analysis unveiled that cell viability for all dual-target combinations exceeded that of their respective single-target enzymes. Consequently, integrating a target enzyme while adjusting an additional exchange reaction could efficiently mitigate cell proliferation rates and ATP production in the treated cancer cells. Nevertheless, most dual-target combinations led to lower side effects in contrast to their single-target counterparts. Additionally, differential expression of metabolites between cancer cells and their healthy counterparts were assessed via parsimonious flux variability analysis employing the GSMMs to pinpoint potential biomarkers. The variabilities of the fluxes and metabolite flow rates in cancer and healthy cells were classified into seven categories. Accordingly, two secretions and thirteen uptakes (including eight essential amino acids and two conditionally essential amino acids) were identified as potential biomarkers. The findings of this study indicated that cancer cells exhibit a higher uptake of amino acids compared with their healthy counterparts. [ABSTRACT FROM AUTHOR]

Background: Sepsis, an infection-triggered inflammatory syndrome, poses a global clinical challenge with limited therapeutic options. Our study is designed to identify potential diagnostic biomarkers of sepsis onset in critically ill patients by bioinformatics analysis. Methods: Gene expression profiles of GSE28750 and GSE74224 were obtained from the Gene Expression Omnibus (GEO) database. These datasets were merged, normalized and de-batched. Weighted gene co-expression network analysis (WGCNA) was performed and the gene modules most associated with sepsis were identified as key modules. Functional enrichment analysis of the key module genes was then conducted. Moreover, differentially expressed gene (DEG) analysis was conducted by the "limma" R package. Protein-protein interaction (PPI) network was created using STRING and Cytoscape, and PPI hub genes were identified with the cytoHubba plugin. The PPI hub genes overlapping with the genes in key modules of WGCNA were determined to be the sepsis-related key genes. Subsequently, the key overlapping genes were validated in an external independent dataset and sepsis patients recruited in our hospital. In addition, CIBERSORT analysis evaluated immune cell infiltration and its correlation with key genes. Results: By WGCNA, the greenyellow module showed the highest positive correlation with sepsis (0.7, p = 2e − 19). 293 DEGs were identified in the merged datasets. The PPI network was created, and the CytoHubba was used to calculate the top 20 genes based on four algorithms (Degree, EPC, MCC, and MNC). Ultimately, LTF, LCN2, ELANE, MPO and CEACAM8 were identified as key overlapping genes as they appeared in the PPI hub genes and the key module genes of WGCNA. These sepsis-related key genes were validated in an independent external dataset (GSE131761) and sepsis patients recruited in our hospital. Additionally, the immune infiltration profiles differed significantly between sepsis and non-sepsis critical illness groups. Correlations between immune cells and these five key genes were assessed, revealing that plasma cells, macrophages M0, monocytes, T cells regulatory, eosinophils and NK cells resting were simultaneously and significantly associated with more than two key genes. Conclusion: This study suggests a critical role of LTF, LCN2, ELANE, MPO and CEACAM8 in sepsis and may provide potential diagnostic biomarkers and therapeutic targets for the treatment of sepsis. [ABSTRACT FROM AUTHOR]

Tumour‐associated macrophages (TAMs), encompassing M1 and M2 subtypes, exert significant effects on osteosarcoma (OS) progression and immunosuppression. However, the impacts of TAM‐derived biomarkers on the progression of OS remains limited. The GSE162454 profile was subjected to single‐cell RNA (scRNA) sequencing analysis to identify crucial mediators between TAMs and OS cells. The clinical features, effects and mechanisms of these mediators on OS cells and tumour microenvironment were evaluated via biological function experiments and molecular biology experiments. Phosphodiesterase 4C (PDE4C) was identified as a pivotal mediator in the communication between M2 macrophages and OS cells. Elevated levels of PDE4C were detected in OS tissues, concomitant with M2 macrophage level, unfavourable prognosis and metastasis. The expression of PDE4C was observed to increase during the conversion process of THP‐1 cells to M2 macrophages, which transferred the PDE4C mRNA to OS cells through exosome approach. PDE4C increased OS cell proliferation and mobility via upregulating the expression of collagens. Furthermore, a positive correlation was observed between elevated levels of PDE4C and increased TIDE score, decreased response rate following immune checkpoint therapy, reduced TMB and diminished PDL1 expression. Collectively, PDE4C derived from M2 macrophages has the potential to enhance the proliferation and mobility of OS cells by augmenting collagen expression. PDE4C may serve as a valuable biomarker for prognosticating patient outcomes and response rates following immunotherapy. [ABSTRACT FROM AUTHOR]

Cancer is one of the leading causes of deaths worldwide. Survival analysis and prediction of cancer patients is of great significance for their precision medicine. The robustness and interpretability of the survival prediction models are important, where robustness tells whether a model has learned the knowledge, and interpretability means if a model can show human what it has learned. In this paper, we propose a robust and interpretable model SurvConvMixer, which uses pathways customized gene expression images and ConvMixer for cancer short-term, mid-term and long-term overall survival prediction. With ConvMixer, the representation of each pathway can be learned respectively. We show the robustness of our model by testing the trained model on absolutely untrained external datasets. The interpretability of SurvConvMixer depends on gradient-weighted class activation mapping (Grad-Cam), by which we can obtain the pathway-level activation heat map. Then wilcoxon rank-sum tests are conducted to obtain the statistically significant pathways, thereby revealing which pathways the model focuses on more. SurvConvMixer achieves remarkable performance on the short-term, mid-term and long-term overall survival of lung adenocarcinoma, lung squamous cell carcinoma and skin cutaneous melanoma, and the external validation tests show that SurvConvMixer can generalize to external datasets so that it is robust. Finally, we investigate the activation maps generated by Grad-Cam, after wilcoxon rank-sum test and Kaplan–Meier estimation, we find that some survival-related pathways play important role in SurvConvMixer. [ABSTRACT FROM AUTHOR]

Background: Congenital heart disease (CHD) is a prevalent congenital cardiac malformation, which lacks effective early biological diagnosis and intervention. MicroRNAs, as epigenetic regulators of cardiac development, provide potential biomarkers for the diagnosis and treatment of CHD. However, the mechanisms underlying miRNAs-mediated regulation of cardiac development and CHD malformation remain to be further elucidated. This study aimed to explore the function of microRNA-20b-5p (miR-20b-5p) in cardiac development and CHD pathogenesis. Methods and results: miRNA expression profiling identified that miR-20b-5p was significantly downregulated during a 12-day cardiac differentiation of human embryonic stem cells (hESCs), whereas it was markedly upregulated in plasma samples of atrial septal defect (ASD) patients. Our results further revealed that miR-20b-5p suppressed hESCs-derived cardiac differentiation by targeting tet methylcytosine dioxygenase 2 (TET2) and 5-hydroxymethylcytosine, leading to a reduction in key cardiac transcription factors including GATA4, NKX2.5, TBX5, MYH6 and cTnT. Additionally, knockdown of TET2 significantly inhibited cardiac differentiation, which could be partially restored by miR-20b-5p inhibition. Conclusions: Collectively, this study provides compelling evidence that miR-20b-5p functions as an inhibitory regulator in hESCs-derived cardiac differentiation by targeting TET2, highlighting its potential as a biomarker for ASD. [ABSTRACT FROM AUTHOR]

Castration-resistant prostate cancer (CRPC) represents one type of advanced prostate cancer (PCa) with a median survival time of 1–2 years. Currently, there is a lack of reliable gene panels in predicting hormone treatment (HT) responses due to limited knowledge of CRPC-specific tumor-microenvironment (TME) characteristics. In this study, we first screened for up-regulated genes in CRPC samples using bulk-sequencing data retrieved from TCGA online database, and further investigated the expression status of these genes in four sets of downloaded single-cell RNA sequencing (scRNAseq) data: GSE117403 containing 16 normal human prostate samples; GSE141445 containing 13 PCa samples; GSE176031 containing 11 PCa samples and GSE137829 containing 6 CRPC samples. We identified a series of CRPC-specific TME characteristics including an enriched number of PEG10+ neuroendocrine cells, elevated expression of PPIB/CCDC74A/GAPDH/AR genes in tumor cells, increased expression of FAP/TGFB1 in cancer-associated fibroblasts (CAFs), suppressed immune environment featured by enhanced M2 macrophage polarization, T cell exhaustion and increased number of regulatory B cells. We further established a 12-gene panel using these characteristics and showed that this panel could separate CRPC samples from PCa samples (AUC of 0.78), and CRPC patients with higher panel scores tended to have treatment failure or progression (R = −0.47, p = 0.019). Based on these unique TME characteristics of CRPC, we established a prediction tool for estimating the duration of HT responses in PCa treatment. Our results suggest mechanisms by which prostate cancer becomes castrate resistant. Further study of PEG10 (and/or others) to evaluate therapeutic efficacy should be considered. Increased number of PEG10+ neuroendocrine cells is associated with recurrence of HT PCa patients A 12-gene panel could be used to predict duration of HT responses in PCa treatment [ABSTRACT FROM AUTHOR]

We utilized scRNA-seq, a well-established technology, to uncover the gene expression characteristics of IL34+ CAFs within HCC. We analyzed the related mechanisms through in vitro and in vivo assays. To begin, we acquired scRNA-seq datasets about HCC, which enabled us to identify distinct cell subpopulations within HCC tissues. We conducted a differential analysis to pinpoint DEGs associated with normal fibroblasts (NFs) and CAFs. Subsequently, we isolated NFs and CAFs, followed by the sorting of IL34+ CAFs. These IL34+ CAFs were then co-cultured with T cells and HCC cells to investigate their potential role in Tregs infiltration, CD8+ T cell toxicity, and the biological processes of HCC cells. We validated our findings in vivo using a well-established mouse model. Our analysis of HCC tissues revealed the presence of seven primary cell subpopulations, with the most significant disparities observed within fibroblast subpopulations. Notably, high IL34 expression was linked to increased expression of receptor proteins and enhanced proliferative activity within CAFs, with specific expression in CAFs. Furthermore, we identified a substantial positive correlation between IL34 expression and the abundance of Tregs. Both in vitro and in vivo experiments demonstrated that IL34+ CAFs promoted Tregs infiltration while suppressing CD8+ T cell toxicity. Consequently, this promoted the growth and metastasis of HCC. In summary, our study affirms that IL34+ CAFs play a pivotal role in augmenting the proliferative activity of CAFs, facilitating Tregs infiltration, and inhibiting CD8+ T cell toxicity, ultimately fostering the growth and metastasis of HCC. [ABSTRACT FROM AUTHOR]

This study aimed to explore the role and mechanism of DYRK1a regulating ferroptosis of cardiomyocytes during myocardial ischemia–reperfusion injury (MIRI). H9c2 cells treated with oxygen–glucose deprivation/reoxygenation (OGD/R) were used as MIRI cell models and transfected with sh‐DYRK1a or/and erastin. Cell viability, apoptosis, and DYRK1a mRNA/protein expression were measured accordingly. The levels of reactive oxygen species (ROS), iron, malondialdehyde (MDA), and glutathione (GSH) were determined. The expression of ferroptosis‐related proteins (GPX4, SLC7A11, ACSL4, and TFR1) was detected using western blotting. The MIRI rat model was established to explore the possible role of DYRK1a suppression in cell injury and ferroptosis. OGD/R cells showed elevated mRNA and protein expression for DYRK1a. OGD/R cells transfected with sh‐DYRK1a showed elevated cell viability, GSH content, increased GPX4 and SLC7A11 expression, suppressed iron content, MDA, ROS, ACSL4, and TFR1 expression, and reduced apoptosis rate, whereas co‐transfection of sh‐DYRK1a with erastin reversed the attenuation of sh‐DYRK1a on MIRI. The suppressive effect of sh‐DYRK1a on MI/R injury was confirmed in an MIRI rat model. DYRK1a mediates ferroptosis of cardiomyocytes to deteriorate MIRI progression. [ABSTRACT FROM AUTHOR]

Simple Summary: N7-methylguanosine (m7G) methylation plays an important role in the development of pancreatic adenocarcinoma (PDAC). Among the 29 regulatory genes of m7G methylation, they can be roughly divided into three categories: methyltransferase (writer), demethylase (eraser), and binding protein (reader) according to their functions. In this study, we explore the role of m7G reader NCBP2 in PDAC progression: NCBP2 activates MEK/ERK signaling by upregulating c-JUN, thereby promoting PDAC cell proliferation. In summary, we identify a novel potential therapeutic target for PDAC, which sheds new light on the treatment of PDAC patients. PDAC is one of the most common malignant tumors worldwide. The difficulty of early diagnosis and lack of effective treatment are the main reasons for its poor prognosis. Therefore, it is urgent to identify novel diagnostic and therapeutic targets for PDAC patients. The m7G methylation is a common type of RNA modification that plays a pivotal role in regulating tumor development. However, the correlation between m7G regulatory genes and PDAC progression remains unclear. By integrating gene expression and related clinical information of PDAC patients from TCGA and GEO cohorts, m7G binding protein NCBP2 was found to be highly expressed in PDAC patients. More importantly, PDAC patients with high NCBP2 expression had a worse prognosis. Stable NCBP2-knockdown and overexpression PDAC cell lines were constructed to further perform in-vitro and in-vivo experiments. NCBP2-knockdown significantly inhibited PDAC cell proliferation, while overexpression of NCBP2 dramatically promoted PDAC cell growth. Mechanistically, NCBP2 enhanced the translation of c-JUN, which in turn activated MEK/ERK signaling to promote PDAC progression. In conclusion, our study reveals that m7G reader NCBP2 promotes PDAC progression by activating MEK/ERK pathway, which could serve as a novel therapeutic target for PDAC patients. [ABSTRACT FROM AUTHOR]

Background: Long noncoding RNAs (lncRNAs) have been reported to play vital roles in the development and progression of cancer. However, their biological significance and functional mechanisms in non-small cell lung cancer (NSCLC) are mostly unclear. Methods: We performed RNA-sequencing to predict the differential expression of lncRNAs in clinical NSCLC and paired paracancerous lung tissues. To identify lncRNA expression, quantitative polymerase chain reaction (qPCR) was used. Using both cell and mouse models, We studied lncRNA AC016727.1's function in NSCLC growth and metastasis. Western blot assays, dual luciferase reporter assays, and chromatin immunoprecipitation were used to analyze the functional mechanism of lncRNA AC016727.1. Results: Our larger NSCLC cohorts validated that the lncRNA AC016727.1 was upregulated in 94 paired NSCLC tissues and correlated with poor survival. Functionally, lncRNA AC016727.1 downregulation inhibited NSCLC cell proliferation, aerobic glycolysis, EMT, and migration, inducing apoptosis. Conversely, upregulated lncRNA AC016727.1 expression exhibited the opposite effect, promoting NSCLC cell survival. Importantly, lncRNA AC016727.1 knockdown inhibited lung cancer growth and slowed the progression of lung metastasis in nude mouse models. Mechanistically, lncRNA AC016727.1 upregulated BACH1 target gene expression by acting as a sponge for miR-98-5p, thereby functioning as a competing endogenous RNA. The function of lncRNA AC016727.1 is mediated by the miR-98-5p/BACH1 axis in NSCLC cells. Meanwhile, the transcription factor HIF-1α can bind to the promoter and activate lncRNA AC016727.1 transcription. lncRNA AC016727.1 regulates HIF-1α expression via BACH1 in NSCLC and forms the lncRNA AC016727.1/BACH1/HIF-1α signaling loop under hypoxic conditions. Conclusion: Our study reveals a novel lncRNA AC016727.1/BACH1/HIF-1α signaling loop in the progression of NSCLC under hypoxic conditions, suggesting that lncRNA AC016727.1 could act as a useful biomarker for NSCLC and a new therapeutic target. [ABSTRACT FROM AUTHOR]

Maize, the most widely planted and highest yielding of the three major crops in the world, requires the development and breeding of new varieties to accommodate the shift towards mechanized harvesting. However, the moisture content of kernels during harvest poses a significant challenge to mechanized harvesting, leading to seed breakage and increased storage costs. Previous studies highlighted the importance of LEA (Late Embryogenesis Abundant) members in regulating kernel dehydration. In this study, we aimed to gain a better understanding of the relationship between the LEA family and grain dehydration in maize. Through expression pattern analysis of maize, we identified 52 LEA genes (ZmLEAs) distributed across 10 chromosomes, organized into seven subgroups based on phylogenetic analysis, gene structure, and conserved motifs. Evolutionary and selective pressure analysis revealed that the amplification of ZmLEA genes primarily resulted from whole-genome or fragment replication events, with strong purifying selection effects during evolution. Furthermore, the transcriptome data of kernels of two maize inbred lines with varying dehydration rates at different developmental stages showed that 14 ZmLEA genes were expressed differentially in the two inbreds. This suggested that the ZmLEA genes might participate in regulating the kernel dehydration rate (KDR) in maize. Overall, this study enhances our understanding of the ZmLEA family and provides a foundation for further research into its role in regulating genes associated with grain dehydration in maize. [ABSTRACT FROM AUTHOR]

Nucleoporins (NUPs) comprise nuclear pore complexes, gateways for nucleocytoplasmic transport. As primary human keratinocytes switch from the progenitor state towards differentiation, most NUPs are strongly downregulated, with NUP93 being the most downregulated NUP in this process. To determine if this NUP downregulation is accompanied by a reduction in nuclear pore numbers, we leveraged Stochastic Optical Reconstruction Microscopy. No significant changes in nuclear pore numbers were detected using three independent NUP antibodies; however, NUP reduction in other subcellular compartments such as the cytoplasm was identified. To investigate how NUP reduction influences keratinocyte differentiation, we knocked down NUP93 in keratinocytes in the progenitor-state culture condition. NUP93 knockdown diminished keratinocytes' clonogenicity and epidermal regenerative capacity, without drastically affecting nuclear pore numbers or permeability. Using transcriptome profiling, we identified that NUP93 knockdown induces differentiation genes related to both mechanical and immune barrier functions, including the activation of known NF-κB target genes. Consistently, keratinocytes with NUP93 knockdown exhibited increased nuclear localization of the NF-κB p65/p50 transcription factors, and increased NF-κB reporter activity. Taken together, these findings highlight the gene regulatory roles contributed by differential NUP expression levels in keratinocyte differentiation, independent of nuclear pore numbers. Nucleoporins (NUPs) compose the nuclear pores. As skin epidermal cells switch from the progenitor state to differentiation, NUPs are downregulated without changing pore numbers. Downregulation of NUP93 is further connected to NF-kB activation. [ABSTRACT FROM AUTHOR]

Inorganic phosphate (Pi) is actively taken up by Pi transporters (PTs) from the soil and transported into the plant. Here, we functionally characterized the Brassica napus gene BnaPT37, which belongs to the PHT1 family. BnaPT37 is a plasma membrane-localized protein containing 534 amino acids. Expression of BnaPT37 increased significantly under Pi deficiency in various tissues, especially in fully expanded leaves. Expression of the β-glucuronidase reporter gene driven by the BnaPT37 promoter showed that BnaPT37 is expressed in the root, stem, calyx, and leaf under Pi deficiency. BnaPT37 can complement a yeast mutant strain defective in five Pi transporters and can restore the growth of the Arabidopsis atpt1/2 double mutant under Pi deprivation. Overexpression of BnaPT37 in rapeseed significantly increased Pi translocation from root to shoot. Moreover, the movement of Pi from fully expanded leaves to new leaves and roots was enhanced in the transgenic lines compared to the wild type. However, the overexpression of BnaPT37 inhibited the flowering time, plant height, and Pi accumulation in seeds. In conclusion, BnaPT37 functions as a plasma membrane-localized Pi transporter and might be involved in Pi translocation from root to shoot and Pi distribution from source to sink in B. napus. [ABSTRACT FROM AUTHOR]

Magnaporthe oryzae Oryzae (MoO) pathotype is a devastating fungal pathogen of rice; however, its pathogenic mechanism remains poorly understood. The current research is primarily focused on single-omics data, which is insufficient to capture the complex cross-kingdom regulatory interactions between MoO and rice. To address this limitation, we proposed a novel method called Weighted Gene Autoencoder Multi-Omics Relationship Prediction (WGAEMRP), which combines weighted gene co-expression network analysis (WGCNA) and graph autoencoder to predict the relationship between MoO–rice multi-omics data. We applied WGAEMRP to construct a MoO–rice multi-omics heterogeneous interaction network, which identified 18 MoO small RNAs (sRNAs), 17 rice genes, 26 rice mRNAs, and 28 rice proteins among the key biomolecules. Most of the mined functional modules and enriched pathways were related to gene expression, protein composition, transportation, and metabolic processes, reflecting the infection mechanism of MoO. Compared to previous studies, WGAEMRP significantly improves the efficiency and accuracy of multi-omics data integration and analysis. This approach lays out a solid data foundation for studying the biological process of MoO infecting rice, refining the regulatory network of pathogenic markers, and providing new insights for developing disease-resistant rice varieties. [ABSTRACT FROM AUTHOR]

SWEET proteins play important roles in plant growth and development, sugar loading in phloem and resistance to abiotic stress through sugar transport. In this study, 13 BpSWEET genes were identified from birch genome. Collinearity analysis showed that there were one tandem repeating gene pair (BpSWEET1b/BpSWEET1c) and two duplicative gene pairs (BpSWEET17a/BpSWEET17b) in the BpSWEET gene family. The BpSWEET gene promoter regions contained several cis-acting elements related to stress resistance, for example: hormone-responsive and low-temperature-responsive cis-elements. Analysis of transcriptome data showed that BpSWEET genes were highly expressed in several sink organs, and the most BpSWEET genes were rapidly up-regulated under cold stress. BpSWEET1c, which was highly expressed in cold stress, was selected for further analysis. It was found that BpSWEET1c was located on the cell membrane. After 6 h of 4 °C stress, sucrose content in the leaves and roots of transient overexpressed BpSWEET1c was significantly higher than that of the control. MDA content in roots was significantly lower than that of the control. These results indicate that BpSWEET1c may play a positive role in the response to cold stress by promoting the metabolism and transport of sucrose. In conclusion, 13 BpSWEET genes were identified from the whole genome level. Most of the SWEET genes of birch were expressed in the sink organs and could respond to cold stress. Transient overexpression of BpSWEET1c changed the soluble sugar content and improved the cold tolerance of birch. [ABSTRACT FROM AUTHOR]

Background: Histone methyltransferases are crucial regulators in non‐small cell lung cancer (NSCLC) development. This study explored the mechanism of histone methyltransferase SET domain containing 1A (SETD1A)‐mediated H3K4me2 methylation in NSCLC cell ferroptosis and provides novel targets for NSCLC treatment. Methods: Upon downregulation of SETD1A in NSCLC cell lines, cell proliferation potential, malondialdehyde (MDA), superoxide dismutase (SOD) and glutathione (GSH) activities, iron content, and SETD1A, long noncoding RNA HOXC cluster antisense RNA 3 (lncRNA HOXC‐AS3), E1A binding protein p300 (EP300), glutathione peroxidase 4 (GPX4) expressions were determined via cell counting kit‐8, ELISA, iron assay kits, RT‐qPCR, and western blot. Enrichment levels of SETD1A and H3K4me3 in the HOXC‐AS3 promotor were measured via chromatin immunoprecipitation, and the binding of HOXC‐AS3 and EP300 was analyzed via RNA immunoprecipitation. Rescue experiments were performed to confirm their roles in NSCLC cell ferroptosis. Xenograft tumor models were established to validate the role of SETD1A in vivo. Results: SETD1A, H3K4me3, HOXC‐AS3, and EP300 were highly‐expressed in NSCLC cells. Silencing SETD1A inhibited NSCLC cell proliferation, increased MDA and iron levels, and decreased SOD, GSH, and GPX4 levels. SETD1A downregulation reduced H3K4me3 level, HOXC‐AS3 expression, the binding of HOXC‐AS3 to EP300, and EP300 stability. Overexpression of HOXC‐AS3 or EP300 reversed the promotion of silencing SETD1A on NSCLC cell ferroptosis. Silencing SETD1A reduced tumor volume and weight and positive rate of ki67 and increased ferroptosis through the HOXC‐AS3/EP300 axis. Conclusion: SETD1A‐mediated H3K4me2 methylation promoted HOXC‐AS3 expression, binding of HOXC‐AS3 to EP300, and EP300 stability, thereby suppressing NSCLC cell ferroptosis. [ABSTRACT FROM AUTHOR]

Background: Hepatocellular carcinoma still has a high incidence and mortality rate worldwide, and further research is needed to investigate its occurrence and development mechanisms in depth in order to identify new therapeutic targets. Ferritinophagy is a type of autophagy and a key factor in ferroptosis that could influence tumor onset and progression. Although, the potential role of ferritinophagy-related genes (FRGs) in liver hepatocellular carcinoma (LIHC) is unknown. Methods: Single-cell RNA sequencing (scRNA-seq) data of LIHC were obtained from the Gene Expression Omnibus (GEO) dataset. In addition, transcriptome and clinical follow-up outcome data of individuals with LIHC were extracted from the The Cancer Genome Atlas (TCGA) dataset. FRGs were collected through the GeneCards database. Differential cell subpopulations were distinguished, and differentially expressed FRGs (DEFRGs) were obtained. Differential expression of FRGs and prognosis were observed according to the TCGA database. An FRG-related risk model was constructed to predict patient prognosis by absolute shrinkage and selection operator (LASSO) and COX regression analyses, and its prognosis predictive power was validated. Ultimately, the association between risk score and tumor microenvironment (TME), immune cell infiltration, immune checkpoints, drug sensitivity, and tumor mutation burden (TMB) was analyzed. We also used quantitative reverse transcription polymerase chain reaction (qRT-PCR) to validate the expression of key genes in normal liver cells and liver cancer cells. Results: We ultimately identified 8 cell types, and 7 differentially expressed FRGs genes (ZFP36, NCOA4, FTH1, FTL, TNF, PCBP1, CYB561A3) were found among immune cells, and we found that Monocytes and Macrophages were closely related to FRGs genes. Subsequently, COX regression analysis showed that patients with high expression of FTH1, FTL, and PCBP1 had significantly worse prognosis than those with low expression, and our survival prediction model, constructed based on age, stage, and risk score, showed better prognostic prediction ability. Our risk model based on 3 FRGs genes ultimately revealed significant differences between high-risk and low-risk groups in terms of immune infiltration and immune checkpoint correlation, drug sensitivity, and somatic mutation risk. Finally, we validated the key prognostic genes FTH1, FTL, using qRT-PCR, and found that the expression of FTH1 and FTL was significantly higher in various liver cancer cells than in normal liver cells. At the same time, immunohistochemistry showed that the expression of FTH1, FTL in tumor tissues was significantly higher than that in para-tumor tissues. Conclusion: This study identifies a considerable impact of FRGs on immunity and prognosis in individuals with LIHC. The collective findings of this research provide new ideas for personalized treatment of LIHC and a more targeted therapy approach for individuals with LIHC to improve their prognosis. [ABSTRACT FROM AUTHOR]

Background: Peanut is an economically-important oilseed crop and needs a large amount of calcium for its normal growth and development. Calcium deficiency usually leads to embryo abortion and subsequent abnormal pod development. Different tolerance to calcium deficiency has been observed between different cultivars, especially between large and small-seed cultivars. Results: In order to figure out different molecular mechanisms in defensive responses between two cultivars, we treated a sensitive (large-seed) and a tolerant (small-seed) cultivar with different calcium levels. The transcriptome analysis identified a total of 58 and 61 differentially expressed genes (DEGs) within small-seed and large-seed peanut groups under different calcium treatments, and these DEGs were entirely covered by gene modules obtained via weighted gene co-expression network analysis (WGCNA). KEGG enrichment analysis showed that the blue-module genes in the large-seed cultivar were mainly enriched in plant-pathogen attack, phenolic metabolism and MAPK signaling pathway, while the green-module genes in the small-seed cultivar were mainly enriched in lipid metabolism including glycerolipid and glycerophospholipid metabolisms. By integrating DEGs with WGCNA, a total of eight hub-DEGs were finally identified, suggesting that the large-seed cultivar concentrated more on plant defensive responses and antioxidant activities under calcium deficiency, while the small-seed cultivar mainly focused on maintaining membrane features to enable normal photosynthesis and signal transduction. Conclusion: The identified hub genes might give a clue for future gene validation and molecular breeding to improve peanut survivability under calcium deficiency. [ABSTRACT FROM AUTHOR]

Porcine epidemic diarrhea virus (PEDV) has led to significant economic losses in the global porcine industry since the emergence of variant strains in 2010. The high mutability of coronaviruses endows PEDV with the ability to evade the host immune response, which impairs the effectiveness of vaccines. In our previous study, we generated a highly cell-passaged PEDV strain, CT-P120, which showed promise as a live attenuated vaccine candidate by providing satisfactory protection against variant PEDV infection in piglets. However, the mechanism by which the attenuated CT-P120 adapts to cells during passage, resulting in increased replication efficiency, remains unclear. To address this question, we conducted a comparative transcriptomic analysis of Vero E6 cells infected with either the original parental strain (CT-P10) or the cell-attenuated strain (CT-P120) of PEDV at 6, 12, and 24 h post-infection. Compared to CT-P10, CT-P120 infection resulted in a significant decrease in the number of differentially expressed genes (DEGs) at each time point. Functional enrichment analysis of genes revealed the activation of various innate immune-related pathways by CT-P10, notably attenuated during CT-P120 infection. To validate these results, we selected eight genes (TRAF3, IRF3, IFNL1, ISG15, NFKB1, MAP2K3, IL1A, and CCL2) involved in antiviral processes and confirmed their mRNA expression patterns using RT-qPCR, in line with the transcriptomic data. Subsequent protein-level analysis of selected genes via Western blotting and enzyme-linked immunosorbent assay corroborated these results, reinforcing the robustness of our findings. Collectively, our research elucidates the strategies underpinning PEDV attenuation and immune evasion, providing invaluable insights for the development of effective PEDV vaccines. [ABSTRACT FROM AUTHOR]

Due to their unique biochemical and spectroscopic properties, both heme and phycocyanobilin are widely applied in the medical and food industries. Synechocystis sp. PCC 6803 contains both heme and phycocyanin, and is capable of synthesizing phycocyanin using heme as a precursor. The aim of this study was to uncover viable metabolic targets in the porphyrin pathway from Synechocystis sp. PCC 6803 to promote the accumulation of heme and phycocyanin in the recombinant strains of microalgae. A total of 10 genes related to heme synthesis pathway derived from Synechococcus elongatus PCC 7942 and 12 genes related to endogenous heme synthesis were individually overexpressed in strain PCC 6803. The growth rate and pigment content (heme, phycocyanin, chlorophyll a and carotenoids) of 22 recombinant algal strains were characterized. Quantitative real-time PCR technology was used to investigate the molecular mechanisms underlying the changes in physiological indicators in the recombinant algal strains. Among the 22 mutant strains, the mutant overexpressing the haemoglobin gene (glbN) of strain PCC 6803 had the highest heme content, which was 2.5 times higher than the wild type; the mutant overexpressing the gene of strain PCC 7942 (hemF) had the highest phycocyanin content, which was 4.57 times higher than the wild type. Overall, the results suggest that genes in the porphyrin pathway could significantly affect the heme and phycocyanin content in strain PCC 6803. Our study provides novel crucial targets for promoting the accumulation of heme and phycocyanin in cyanobacteria. [ABSTRACT FROM AUTHOR]

Background: Accurately classifying complex diseases is crucial for diagnosis and personalized treatment. Integrating multi-omics data has been demonstrated to enhance the accuracy of analyzing and classifying complex diseases. This can be attributed to the highly correlated nature of the data with various diseases, as well as the comprehensive and complementary information it provides. However, integrating multi-omics data for complex diseases is challenged by data characteristics such as high imbalance, scale variation, heterogeneity, and noise interference. These challenges further emphasize the importance of developing effective methods for multi-omics data integration. Results: We proposed a novel multi-omics data learning model called MODILM, which integrates multiple omics data to improve the classification accuracy of complex diseases by obtaining more significant and complementary information from different single-omics data. Our approach includes four key steps: 1) constructing a similarity network for each omics data using the cosine similarity measure, 2) leveraging Graph Attention Networks to learn sample-specific and intra-association features from similarity networks for single-omics data, 3) using Multilayer Perceptron networks to map learned features to a new feature space, thereby strengthening and extracting high-level omics-specific features, and 4) fusing these high-level features using a View Correlation Discovery Network to learn cross-omics features in the label space, which results in unique class-level distinctiveness for complex diseases. To demonstrate the effectiveness of MODILM, we conducted experiments on six benchmark datasets consisting of miRNA expression, mRNA, and DNA methylation data. Our results show that MODILM outperforms state-of-the-art methods, effectively improving the accuracy of complex disease classification. Conclusions: Our MODILM provides a more competitive way to extract and integrate important and complementary information from multiple omics data, providing a very promising tool for supporting decision-making for clinical diagnosis. [ABSTRACT FROM AUTHOR]

Coronavirus disease 2019 (COVID-19) seriously threatens human health and has been disseminated worldwide. Although there are several treatments for COVID-19, its control is currently suboptimal. Therefore, the development of novel strategies to treat COVID-19 is necessary. Ion channels are located on the membranes of all excitable cells and many intracellular organelles and are key components involved in various biological processes. They are a target of interest when searching for drug targets. This study aimed to reveal the relevant molecular features of ion channel genes in COVID-19 based on bioinformatic analyses. The RNA-sequencing data of patients with COVID-19 and healthy subjects (GSE152418 and GSE171110 datasets) were obtained from the Gene Expression Omnibus (GEO) database. Ion channel genes were selected from the Hugo Gene Nomenclature Committee (HGNC) database. The RStudio software was used to process the data based on the corresponding R language package to identify ion channel-associated differentially expressed genes (DEGs). Based on the DEGs, Gene Ontology (GO) functional and pathway enrichment analyses were performed using the Enrichr web tool. The STRING database was used to generate a protein–protein interaction (PPI) network, and the Cytoscape software was used to screen for hub genes in the PPI network based on the cytoHubba plug-in. Transcription factors (TF)–DEG, DEG–microRNA (miRNA) and DEG–disease association networks were constructed using the NetworkAnalyst web tool. Finally, the screened hub genes as drug targets were subjected to enrichment analysis based on the DSigDB using the Enrichr web tool to identify potential therapeutic agents for COVID-19. A total of 29 ion channel-associated DEGs were identified. GO functional analysis showed that the DEGs were integral components of the plasma membrane and were mainly involved in inorganic cation transmembrane transport and ion channel activity functions. Pathway analysis showed that the DEGs were mainly involved in nicotine addiction, calcium regulation in the cardiac cell and neuronal system pathways. The top 10 hub genes screened based on the PPI network included KCNA2, KCNJ4, CACNA1A, CACNA1E, NALCN, KCNA5, CACNA2D1, TRPC1, TRPM3 and KCNN3. The TF–DEG and DEG–miRNA networks revealed significant TFs (FOXC1, GATA2, HINFP, USF2, JUN and NFKB1) and miRNAs (hsa-mir-146a-5p, hsa-mir-27a-3p, hsa-mir-335-5p, hsa-let-7b-5p and hsa-mir-129–2-3p). Gene-disease association network analysis revealed that the DEGs were closely associated with intellectual disability and cerebellar ataxia. Drug-target enrichment analysis showed that the relevant drugs targeting the hub genes CACNA2D1, CACNA1A, CACNA1E, KCNA2 and KCNA5 were gabapentin, gabapentin enacarbil, pregabalin, guanidine hydrochloride and 4-aminopyridine. The results of this study provide a valuable basis for exploring the mechanisms of ion channel genes in COVID-19 and clues for developing therapeutic strategies for COVID-19. [ABSTRACT FROM AUTHOR]

Rose plants are widely cultivated as cut flowers worldwide and have economic value as sources of natural fragrance and flavoring. Rosa 'Crimson Glory', whose petals have a pleasant fragrance, is one of the most important cultivars of edible rose plants. Flower storage at low-temperature is widely applied in production to maintain quality; however, chilling results in a decrease in aromatic volatiles. To determine the molecular basis underlying the changes in aromatic volatile emissions, we investigated the changes in volatile compounds, DNA methylation patterns, and patterns of the transcriptome in response to chilling temperature. The results demonstrated that chilling roses substantially reduced aromatic volatile emissions. We found that these reductions were correlated with the changes in the methylation status of the promoters and genic regions of the genes involved in volatile biosynthesis. These changes mainly occurred for CHH (H = A, T, or C) which accounted for 51% of the total methylation. Furthermore, transcript levels of scent-related gene Germacrene D synthase (RhGDS), Nudix hydrolase 1 (RhNUDX1), and Phenylacetaldehyde reductase (RhPAR) of roses were strikingly depressed after 24 h at low-temperature and remained low-level after 24 h of recovery at 20 °C. Overall, our findings indicated that epigenetic regulation plays an important role in the chilling tolerance of roses and lays a foundation for practical significance in the production of edible roses. [ABSTRACT FROM AUTHOR]

The unique and tailorable physicochemical features of zinc oxide nanoparticles (ZnO-NPs) synthesized from green sources make them attractive for use in cancer treatment. Hydroponic-cultured ginseng-root-synthesized ZnO-NPs (HGRCm-ZnO NPs) were coated with O-carboxymethyl chitosan (CMC) polymer, which stabilized and enhanced the biological efficacy of the nanoparticles. Nanoparticles were characterized by X-ray diffraction (XRD), UV-Vis spectroscopy, transmission electron microscopy (TEM), Fourier-transform infrared spectroscopy (FT-IR), and energy-dispersive X-ray spectroscopy (EDS). The flower-shaped nanoparticles were crystalline in nature with a particle size of 28 nm. To evaluate if these NPs had anti-lung cancer activity, analysis was performed on a human lung carcinoma cell line (A549). HGRCm-ZnO nanoparticles showed less toxicity to normal keratinocytes (HaCaTs), at concentrations up to 20 µg/mL, than A549 cancer cells. Additionally, these NPs showed dose-dependent colony formation and cell migration inhibition ability, which makes them more promising for lung cancer treatment. Additionally, Hoechst and propidium iodide dye staining also confirmed that the NP formulation had apoptotic activity in cancer cells. Further, to evaluate the mechanism of cancer cell death via checking the gene expression, HGRCm ZnO NPs upregulated the BAX and Caspase 3 and 9 expression levels but downregulated Bcl-2 expression, indicating that the nanoformulation induced mitochondrial-mediated apoptosis. Moreover, these preliminary results suggest that HGRCm ZnO NPs can be a potential candidate for future lung cancer treatment. [ABSTRACT FROM AUTHOR]

The advent of single-cell RNA-sequencing (scRNA-seq) provides an unprecedented opportunity to explore gene expression profiles at the single-cell level. However, gene expression values vary over time and under different conditions even within the same cell. There is an urgent need for more stable and reliable feature variables at the single-cell level to depict cell heterogeneity. Thus, we construct a new feature matrix called the delta rank matrix (DRM) from scRNA-seq data by integrating an a priori gene interaction network, which transforms the unreliable gene expression value into a stable gene interaction/edge value on a single-cell basis. This is the first time that a gene-level feature has been transformed into an interaction/edge-level for scRNA-seq data analysis based on relative expression orderings. Experiments on various scRNA-seq datasets have demonstrated that DRM performs better than the original gene expression matrix in cell clustering, cell identification and pseudo-trajectory reconstruction. More importantly, the DRM really achieves the fusion of gene expressions and gene interactions and provides a method of measuring gene interactions at the single-cell level. Thus, the DRM can be used to find changes in gene interactions among different cell types, which may open up a new way to analyze scRNA-seq data from an interaction perspective. In addition, DRM provides a new method to construct a cell-specific network for each single cell instead of a group of cells as in traditional network construction methods. DRM's exceptional performance is due to its extraction of rich gene-association information on biological systems and stable characterization of cells. [ABSTRACT FROM AUTHOR]

Simple Summary: Insulin-like growth factor 1 (IGF1) promotes mammalian development and growth. The poly(dA:dT) tract usually acts as a promoter element to regulate gene transcription. In this study, it was found that the length of a poly(dA:dT) tract in the porcine IGF1 promoter can regulate gene expression in vivo. Moreover, this polymorphism is associated with porcine growth traits (days to 115 kg and average daily gain). These results suggest that the poly(dA:dT) tract is a genetic marker for porcine growth traits. Insulin-like growth factor 1 (IGF1) is an important regulator of body growth, development, and metabolism. The poly(dA:dT) tract affects the accessibility of transcription factor binding sites to regulate transcription. Therefore, this study assessed the effects of two poly(dA:dT) tracts on the transcriptional activity of porcine IGF1. The luciferase assay results demonstrated that the poly(dA:dT) tract 2 (−264/−255) was a positive regulatory element for IGF1 gene expression, and the activities between the different lengths of the poly(dA:dT) tract 2 were significant ( p < 0.01 ). The transcription factor C/EBPα inhibited the transcription of IGF1 by binding to tract 2, and the expression levels between the lengths of tract 2 after C/EBPα binding were also statistically different ( p < 0.01 ). Only the alleles 10T and 11T were found in the tract 2 in commercial pig breeds, while the 9T, 10T, and 11T alleles were found in Chinese native pig breeds. The allele frequencies were in Hardy–Weinberg equilibrium in all pig breeds. The genotypes of tract 2 were significantly associated with the growth traits (days to 115 kg and average daily gain) ( p < 0.05 ) in commercial pig breeds. Based on these findings, it can be concluded that the tract 2 mutation could be applied as a candidate genetic marker for growth trait selection in pig breeding programs. [ABSTRACT FROM AUTHOR]

Many basic Helix-Loop-Helix (bHLH) transcription factors precisely regulate the expression of Fe uptake and translocation genes to control iron (Fe) homeostasis, as both Fe deficiency and toxicity impair plant growth and development. In rice, three clade IVc bHLH transcription factors have been characterised as positively regulating Fe-deficiency response genes. However, the function of OsbHLH057, another clade IVc bHLH transcription factor, in regulating Fe homeostasis is unknown. Here, we report that OsbHLH057 is involved in regulating Fe homeostasis in rice. OsbHLH057 was highly expressed in the leaf blades and lowly expressed in the roots; it was mainly expressed in the stele and highly expressed in the lateral roots. In addition, OsbHLH057 was slightly induced by Fe deficiency in the shoots on the first day but was not affected by Fe availability in the roots. OsbHLH057 localised in the nucleus exhibited transcriptional activation activity. Under Fe-sufficient conditions, OsbHLH057 knockout or overexpression lines increased or decreased the shoot Fe concentration and the expression of several Fe homeostasis-related genes, respectively. Under Fe-deficient conditions, plants with an OsbHLH057 mutation showed susceptibility to Fe deficiency and accumulated lower Fe concentrations in the shoot compared with the wild type. Unexpectedly, the OsbHLH057-overexpressing lines had reduced tolerance to Fe deficiency. These results indicate that OsbHLH057 plays a positive role in regulating Fe homeostasis, at least under Fe-sufficient conditions. [ABSTRACT FROM AUTHOR]

Background: Breast cancer (BC) is the most common malignant tumor worldwide. Apoptosis and hypoxia are involved in the progression of BC, but reliable biomarkers for these have not been developed. We hope to explore a gene signature that combined apoptosis and hypoxia‐related genes (AHGs) to predict BC prognosis and immune infiltration. Methods: We collected the mRNA expression profiles and clinical data information of BC patients from The Cancer Genome Atlas database. The gene signature based on AHGs was constructed using the univariate Cox regression, least absolute shrinkage and selection operator, and multivariate Cox regression analysis. The associations between risk scores, immune infiltration, and immune checkpoint gene expression were studied using single‐sample gene set enrichment analysis. Besides, gene signature and independent clinicopathological characteristics were combined to establish a nomogram. Finally, Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) were performed on the potential functions of AHGs. Results: We identified a 16‐AHG signature (AGPAT1, BTBD6, EIF4EBP1, ERRFI1, FAM114A1, GRIP1, IRF2, JAK1, MAP2K6, MCTS1, NFKBIA, NFKBIZ, NUP43, PGK1, RCL1, and SGCE) that could independently predict BC prognosis. The median score of the risk model divided the patients into two subgroups. By contrast, patients in the high‐risk group had poorer prognosis, less abundance of immune cell infiltration, and expression of immune checkpoint genes. The gene signature and nomogram had good predictive effects on the overall survival of BC patients. GO and KEGG analyses revealed that the differential expression of AHGs may be closely related to tumor immunity. Conclusion: We established and verified a 16‐AHG BC signature which may help predict prognosis, assess potential immunotherapy benefits, and provide inspiration for future research on the functions and mechanisms of AHGs in BC. [ABSTRACT FROM AUTHOR]

Objective. This paper aims to explore novel ferroptosis-related biomarkers for acute kidney injury (AKI). Methods. Various bioinformatic methods, such as differential expression analysis, functional annotation analysis, machine learning, and chemical-gene network analysis, were used in this study. Furthermore, the expression and proferroptotic role of RPS7 were validated with further bioinformatics analysis and biochemical experiments. Results. GSE30718 dataset and GSE139061 dataset were used, and the differentially expressed genes (DEGs) were screened. The DEGs were overlapped with ferroptosis-related genes and genes associated with AKI, which led to the identification of four candidate genes. Machine learning and ROC curve analysis were conducted, and RPS7 and TRIB3 were selected for diagnostic model analysis and functional analysis. Finally, the upregulation of RSP7 in cisplatin-induced AKI was validated in cisplatin-induced AKI, and its proferroptotic role was confirmed in cisplatin-treated proximal tubular cells. Conclusion. Our results indicated that RPS7 might present as a novel ferroptosis-related biomarker for AKI, and it derived ferroptosis to accentuate cisplatin-induced AKI. [ABSTRACT FROM AUTHOR]

Objective: The focus of this study was the six-transmembrane epithelial antigen of the prostate 4 (STEAP4) gene, on the basis of the cloned goat STEAP4 gene sequence. Its molecular and expression characteristics were analyzed, and its influence on the differentiation of goat subcutaneous adipocytes was explored through overexpression. Method: Reverse-transcription PCR (RT-PCR) was used to clone the goat STEAP4 sequence, and online tools were used to analyze the molecular characteristic. Real-time quantitative PCR (qPCR) was used to detect the expression level of STEAP4 in goat tissues and subcutaneous adipocyte differentiation. Liposome transfection, BODIPY, Oil Red O staining, and qPCR were used to explore the effect of overexpression of STEAP4 on adipocyte differentiation. Results: The cloned goat STEAP4 gene sequence was 1388 bp, and the complete coding sequence (CDS) region was 1197 bp, which encoded a total of 398 amino acids. Compared with the predicted sequence (XM_005679300.3), there were three base mutations in the CDS region of goat STEAP4, A188G, T281C, and A507G. Among them, A507G changed the amino acid at position 170 from Ile to Val. Analysis of the physical and chemical properties of the protein showed that STEAP4 was a stable hydrophilic basic protein. STEAP4 gene expression level was highest in goat liver tissue (P<0.01), followed by lung and back subcutaneous adipose tissue. STEAP4 showed different expression levels in goat subcutaneous adipocytes at different times during the induction of differentiation. The expression in the late stage of differentiation was higher than that before differentiation and lowest at 12 h (P<0.01). Overexpression of STEAP4 promoted the accumulation of intracellular lipid droplets; C/EBP β (CCAAT enhancer binding protein) was extremely significantly up-regulated (P<0.01), and aP2 (fatty acid binding protein) was significantly up-regulated (P<0.05). Conclusion: Overexpression of STEAP4 could promote the differentiation of goat subcutaneous preadipocytes. This study lays the foundation for an in-depth study of the role of STEAP4 in goat lipid deposition. [ABSTRACT FROM AUTHOR]

To further determine how BHE affected the growth of HCC cells, the proportion of each cell cycle phase was explored in HCC cells by flow cytometry. Blue honeysuckle (Lonicera caerulea L.) is a species of bush that grows in eastern Russia. Blue honeysuckle extract (BHE) is rich in bioactive phytochemicals which can inhibit the proliferation of tumor cells. The mechanism underlying the anticancer activity of BHE in primary liver cancer is poorly understood. The purpose of this study was to evaluate the growth inhibition mechanism of bioactive substances from blue honeysuckle on hepatocellular carcinoma (HCC) cells and to explore its protein and gene targets. The compounds in BHE were determined by high-performance liquid chromatography (HPLC) and liquid chromatography-mass spectrometry (LC-MS). Cell counting kit-8 (CCK8) assay was used to evaluate the effects of BHE on HCC cell proliferation, and flow cytometry assay (FCA) was used to determine how BHE arrested the proportion of each cell cycle phase in HCC cells. Western blot (WB) was performed to determine the expression of cell cycle-related proteins in HCC cells treated with different concentrations of BHE. The xenograft tumor animal models were established by HCC cell implantation. The results showed that cyanidin-3-o-glucoside and cyanidin-3-o-sophoroside which are the main biologically active components were detected in BHE. BHE is highly effective in inhibiting the proliferation of HCC cells by arresting the HCC cell cycle in the G2/M phase. BHE also downregulated the expression of conventional or classical dendritic cells-2 (cDC2) and cyclin B1 by promoting the expression of myelin transcription factor 1 (MyT1) in HCC cells. The weight and volume of xenografts were significantly decreased in the BHE treated groups when compared to the control group. BHE increased the expression of MyT1 in xenograft tissues. These findings showed that blue honeysuckle extract inhibits proliferation in vivo and in vitro by downregulating the expression of cDC2 and cyclin B1 and upregulating the expression of MyT1 in HCC cells. [ABSTRACT FROM AUTHOR]

Simple Summary: Esophageal squamous cell carcinoma (ESCC) is a familiar lethal malignance. Increasing evidence has disclosed that lncRNA is involved in tumorgenesis and progression in various tumor types. However, the current understanding of angiogenesis-related lncRNAs (ARlncRNAs) involved in ESCC remains evasive. We developed and validated a six-DEARlncRNA risk score system among the GSE53624 and GSE53622 set, aiming to identify the novel prognostic targets for ESCC. Our results showed that the six-DEARlncRNA could be used as an effective independent prognostic factor of ESCC. Furthermore, the six-DEARlncRNA biomarkers mainly participated in regulation of the skin and epidermis development, and these processes protected the body from environmental insults and may have been involved in the progression of ESCC. In conclusion, this study showed that the six-DEARlncRNA signature could be used as an independent prognostic factor and may be a valuable target for treatment options in ESCC. Esophageal squamous cell carcinoma (ESCC) is a lethal gastrointestinal malignancy worldwide. We aimed to identify an angiogenesis-related lncRNAs (ARlncRNAs) signature that could predict the prognosis in ESCC. The GSE53624 and GSE53622 datasets were derived from the GEO database. The differently expressed ARlncRNAs (DEARlncRNAs) were retrieved by the weighted gene co-expression network analysis (WGCNA), differential expression analysis, and correlation analysis. Optimal lncRNA biomarkers were screened from the training set and the six-DEARlncRNA signature comprising AP000696.2, LINC01711, RP11-70C1.3, AP000487.5, AC011997.1, and RP11-225N10.1 could separate patients into high- and low-risk groups with markedly different survival. The validation of the reliability of the risk model was performed by the Kaplan-Meier test, ROC curves, and risk curves in the test set and validation set. Predictive independence analysis indicated that risk score is an independent prognostic biomarker for predicting the prognosis of ESCC patients. Subsequently, a ceRNA regulatory network and functional enrichment analysis were performed. The IC50 test revealed that patients in the high-risk group were resistant to Gefitinib and Lapatinib. Finally, the six DEARlncRNAs were detected by qRT-PCR. In conclusion, we demonstrated a novel ARlncRNA signature as an independent prognostic factor to distinguish the risk of ESCC patients and benefit the personalized clinical applications. [ABSTRACT FROM AUTHOR]

Glucose metabolism reprogramming is an important reason for the functional remodeling, growth, and migration of vascular smooth muscle cells (VSMCs). It is also an important basis for the occurrence and development of aortic dissection (AD), but the specific regulatory factors are not clear. Noncoding RNA activated by DNA damage (NORAD) is dysfunctional in many diseases, but the role of NORAD in AD etiology is unclear. We first established a vascular remodeling cell model of AD, and the expression of NORAD in VSMCs was significantly increased. Functional experiments showed that inhibition of NORAD could downregulate the proliferation and migration of VSMCs. Meanwhile, silencing NORAD could also inhibit the flux of glycolysis, suggesting that NORAD may aggravate AD by promoting glycolysis. In addition, mechanism studies have shown that NORAD can exert VSMCs-regulating function by recruiting LIN28B to bind to TGF-β mRNA, which subsequently facilitates the expression of TGF-β1 (transforming growth factor β1). The recovery experiment also showed that overexpression of TGF-β could reverse the inhibitory effect of NORAD knockdown on VSMCs in terms of proliferation, migration, and glycolysis. Collectively, these results indicated that the NORAD/LIN28B/TGF-β axis promoted cell proliferation and migration through regulating aerobic glycolysis in VSMCs. Therefore, NORAD may regulate the occurrence of AD by affecting the reprogramming of glucose metabolism, and NORAD can be recognized as a good target for VSMC phenotypic intervention and AD treatment. [ABSTRACT FROM AUTHOR]

Background. Herpes simplex virus type 2 (HSV-2) infestation was the most widespread STD (sexually transmitted diseases) among humans and was the leading cause of infectious recurrent genital herpes. Existing therapies against HSV-2 did incompletely restrain the comeback of activated HSV-2 infestation. Geranium wilfordii Maxim had long been used as traditional Chinese medicine for treating the diseases owing to its anti-inflammatory and antiviral effects. Herein, the study was designed to investigate the antiviral activity of G.wilfordii and its potential effect in regulating the host's immune response. Methods. To identify the stage of infection at which the compounds inhibited HSV-2, we performed virucidal, therapeutic, and prophylactic assays. The antiviral efficacy was evaluated by the analysis of viral components HSV-2 gD and VP16. The antiviral activities of these compounds were also evaluated by phenotypic analysis, such as cell proliferation and apoptosis. Molecular docking studies on candidate compounds were done to indicate binding interactions between the compounds and adopted compound targets. Results. Quercetin, corilagin, and geraniin inhibited the replication of HSV-2, with geraniin showing greater TI. The obtained IC50 value of quercetin was 204.7 μM and TI (IC50/EC50) was 5.1, whereas the obtained IC50 value of corilagin was 118.0 μg/ml and TI was 4.05. Geraniin exhibited prominent antiviral activity with an IC50 of 212.4 μM and an EC50 of 18.37 μM, resulting in a therapeutic index (TI) of 11.56. Geraniin showed important in vitro virucidal activity through blocking viral attachment. Compared with the virus group, the apoptosis rates in quercetin-, corilagin-, and geraniin-treated groups were significantly decreased (p < 0.001).The expressions at the transcription genes of virus own replication key factors (including HSV-2 gD and VP16) and cytokines (including TBK1) of infected cells treated with quercetin, corilagin, and geraniin were inhibited. The in silico approaches demonstrated a high number of potential strong intermolecular interactions as hydrogen bonds between geraniin, corilagin, and the activity site of HSV-2 gD. Molecular docking studies demonstrated the effects of corilagin by targeting TBK1. Conclusions. Together, these results highlighted the importance of G.wilfordii treatment in HSV-2 infection and underscored its therapeutic potential. However, additional in vitro and in vivo research was required to validate our findings. [ABSTRACT FROM AUTHOR]

Lung cancer is the leading cause of the cancer deaths. Therefore, predicting the survival status of lung cancer patients is of great value. However, the existing methods mainly depend on statistical machine learning (ML) algorithms. Moreover, they are not appropriate for high-dimensionality genomics data, and deep learning (DL), with strong high-dimensional data learning capability, can be used to predict lung cancer survival using genomics data. The Cancer Genome Atlas (TCGA) is a great database that contains many kinds of genomics data for 33 cancer types. With this enormous amount of data, researchers can analyze key factors related to cancer therapy. This paper proposes a novel method to predict lung cancer long-term survival using gene expression data from TCGA. Firstly, we select the most relevant genes to the target problem by the supervised feature selection method called mutual information selector. Secondly, we propose a method to convert gene expression data into two kinds of images with KEGG BRITE and KEGG Pathway data incorporated, so that we could make good use of the convolutional neural network (CNN) model to learn high-level features. Afterwards, we design a CNN-based DL model and added two kinds of clinical data to improve the performance, so that we finally got a multimodal DL model. The generalized experiments results indicated that our method performed much better than the ML models and unimodal DL models. Furthermore, we conduct survival analysis and observe that our model could better divide the samples into high-risk and low-risk groups. [ABSTRACT FROM AUTHOR]

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Background. Cardiac fibrosis (CF) is major myocardial change in diabetic cardiomyopathy (DCM). Yangxinshi as a Chinese medicine formula is used to treat cardiovascular diseases. However, the exact effective mechanism of Yangxinshi on CF is still uncertain. Hence, based on the pharmacological network, predicting the active components, potential targets and pathways of Yangxinshi on diabetic fibrosis require to be further studied. Materials and Methods. By using Cytoscape 3.6.0 Bisogenet plug-in, the active components of Yangxinshi were obtained and screened through TCMSP, and the PPI network of DCM-CF was constructed and then screened by CytoNCA plug-in. GO analysis and KEGG pathway enrichment analysis were carried out by Cluego plug-in. Combined with the results of network pharmacological analysis, cells in vitro were performed to verify the CF stimulated with high glucose or intervence with Yangxinshi, and the expressions of Cbl-b, p-smad2, and α-SMA were detected. Results. Yangxinshi might play a key role in reversing cardiac fibrosis in individuals with DCM by regulating the signal pathway of CBL and promoted the expression of Cbl-b and inhibited the expression of p-smad2 and α-SMA, verifying some predictive work via network pharmacology. Conclusion. Based on network pharmacology, this study demonstrates that the beneficial effect of Yangxinshi on CF is related to the Cbl-b/smad2 pathway, providing an idea for the therapeutic effect of Yangxinshi on cardiac fibrosis in DCM. [ABSTRACT FROM AUTHOR]