Differential Analysis Research Articles

ANO7 expression in the prostate modulates mitochondrial function and lipid metabolism

BackgroundProstate cancer (PrCa) is a significant health concern, ranking as the second most common cancer in males globally. Genetic factors contribute substantially to PrCa risk, with up to 57% of the risk being attributed to genetic determinants. A major challenge in managing PrCa is the early identification of aggressive cases for targeted treatment, while avoiding unnecessary interventions in slow-progressing cases. Therefore, there is a critical need for genetic biomarkers that can distinguish between aggressive and non-aggressive PrCa cases. Previous research, including our own, has shown that germline variants in ANO7 are associated with aggressive PrCa. However, the function of ANO7 in the prostate remains unknown.MethodsWe performed RNA-sequencing (RNA-seq) on RWPE1 cells engineered to express ANO7 protein, alongside the analysis of a single-cell RNA-sequencing (scRNA-seq) dataset and RNA-seq from prostate tissues. Differential gene expression analysis and gene set enrichment analysis (GSEA) were conducted to identify key pathways. Additionally, we assessed oxidative phosphorylation (OXPHOS), glycolysis, and targeted metabolomics. Image analysis of mitochondrial morphology and lipidomics were also performed to provide further insight into the functional role of ANO7 in prostate cells.ResultsANO7 expression resulted in the downregulation of metabolic pathways, particularly genes associated with the MYC pathway and oxidative phosphorylation (OXPHOS) in both prostate tissue and ANO7-expressing cells. Measurements of OXPHOS and glycolysis in the ANO7-expressing cells revealed a metabolic shift towards glycolysis. Targeted metabolomics showed reduced levels of the amino acid aspartate, indicating disrupted mitochondrial function in the ANO7-expressing cells. Image analysis demonstrated altered mitochondrial morphology in these cells. Additionally, ANO7 downregulated genes involved in fatty acid metabolism and induced changes in lipid composition of the cells, characterized by longer acyl chain lengths and increased unsaturation, suggesting a role for ANO7 in regulating lipid metabolism in the prostate.ConclusionsThis study provides new insights into the function of ANO7 in prostate cells, highlighting its involvement in metabolic pathways, particularly OXPHOS and lipid metabolism. The findings suggest that ANO7 may act as a key regulator of cellular lipid metabolism and mitochondrial function in the prostate, shedding light on a previously unknown aspect of ANO7’s biology.

APNet, an explainable sparse deep learning model to discover differentially active drivers of severe COVID-19.

Computational analyses of bulk and single-cell omics provide translational insights into complex diseases, such as COVID-19, by revealing molecules, cellular phenotypes, and signalling patterns that contribute to unfavourable clinical outcomes. Current in silico approaches dovetail differential abundance, biostatistics, and machine learning, but often overlook non-linear proteomic dynamics, like post-translational modifications, and provide limited biological interpretability beyond feature ranking. We introduce APNet, a novel computational pipeline that combines differential activity analysis based on SJARACNe co-expression networks with PASNet, a biologically-informed sparse deep learning model, to perform explainable predictions for COVID-19 severity. The APNet driver-pathway network ingests SJARACNe co-regulation and classification weights to aid result interpretation and hypothesis generation. APNet outperforms alternative models in patient classification across three COVID-19 proteomic datasets, identifying predictive drivers and pathways, including some confirmed in single-cell omics and highlighting under-explored biomarker circuitries in COVID-19. APNet's R, Python scripts and Cytoscape methodologies are available at https://github.com/BiodataAnalysisGroup/APNet. Supplementary information can be accessed in Zenodo (10.5281/zenodo.14680520).

Mechanistic elucidation of human pancreatic acinar development using single-cell transcriptome analysis on a human iPSC differentiation model

Few effective treatments have been developed for intractable pancreatic exocrine disorders due to the lack of suitable disease models using human cells. Pancreatic acinar cells differentiated from human induced pluripotent stem cells (hiPSCs) have the potential to solve this issue. In this study, we aimed to elucidate the developmental mechanisms of pancreatic exocrine acinar lineages to establish a directed differentiation method for pancreatic acinar cells from hiPSCs. hiPSC-derived pancreatic endoderm cells were spontaneously differentiated into both pancreatic exocrine and endocrine tissues by implantation into the renal subcapsular space of NOD/SCID mice. Single-cell RNA-seq analysis of the retrieved grafts confirmed the differentiation of pancreatic acinar lineage cells and identified REG4 as a candidate marker for pancreatic acinar progenitor cells. Furthermore, differential gene expression analysis revealed upregulated pathways, including cAMP-related signals, involved in the differentiation of hiPSC-derived pancreatic acinar lineage cells in vivo, and we found that a cAMP activator, forskolin, facilitates the differentiation from hiPSC-derived pancreatic endoderm into pancreatic acinar progenitor cells in our in vitro differentiation culture. Therefore, this platform contributes to our understanding of the developmental mechanisms of pancreatic acinar lineage cells and the establishment of differentiation methods for acinar cells from hiPSCs.

Endoplasmic reticulum stress-related CLIP4 plays a procarcinogenic role in hepatocellular carcinoma: an integrated analysis

ObjectiveTo explore the potential of endoplasmic reticulum stress (ERS)-associated protein CLIP4 as a biomarker for hepatocellular carcinoma (HCC) and the underlying mechanism.MethodsTCGA public database and a tissue microarray were used to investigate the molecular characteristics of CLIP4 and its association with disease. TCGA-LIHC dataset was used for single-gene differential expression analysis, single-gene correlation analysis, functional enrichment analysis, immune infiltration analysis, and DNA methylation analysis. RNA-seq, immunohistochemistry, western blotting, and RT-qPCR were used to verify the effect of ERS on CLIP4 expression. Public databases and miRNA-seq data were used to explore the TF-miRNA-CLIP4 regulatory network. CCK-8, colony formation, EdU staining, wound-healing, Transwell, western blotting and RT-qPCR were used to detect the effects of CLIP4 on the proliferation, migration and epithelial-mesenchymal transition (EMT) of HCC cells.ResultsAnalysis of TCGA datasets and tissue microarrays demonstrated that elevated CLIP4 expression was associated with poor prognosis in HCC. Enrichment analysis revealed that CLIP4 is involved in the immune response, cell adhesion, and EMT. There was a positive correlation between CLIP4 expression and the infiltration of the majority of immune cells, immunomodulators, and chemokines. Furthermore, the DNA methylation pattern of CLIP4 was found to have significant prognostic value. ERS was found to significantly upregulate CLIP4 expression. In addition, the ERS-RELA-miR-222-5p-CLIP4 transcriptional network was constructed to clarify the role of CLIP4. Cell function experiments confirmed that it promotes the proliferation, migration, and EMT of HCC cells.ConclusionsCLIP4 is a potential immune-related oncogenic molecule in HCC. ERS regulates the expression of CLIP4, and CLIP4 promotes the proliferation, migration, and EMT of HCC cells.

Identification of Interleukin-Related Genes Signature for Prognosis Prediction in Head and Neck Squamous Cell Carcinoma Patients.

This study focused on identifying the interleukin (IL)-related genes that influence the head and neck squamous cell carcinoma (HNSCC) patients' prognosis and response to anticancer therapy in patients with HNSCC. We developed a risk model that included three gene signatures, IL Enhancer Binding Factor 2 (ILF2), IL 36 alpha (IL36A), and IL10, based on differential expression analysis, survival analysis, Least Absolute Shrinkage and Selection Operator (LASSO) analysis, and Cox regression analysis. We found that the low-risk group was scored with higher immune cell infiltration, higher expression of human leukocyte antigen (HLA) family genes and immune checkpoint genes, higher cytolytic activity (CYT), tertiary lymphoid structures (TLS), and CD8A/PD-L1 ratio. In contrast, the high-risk group was scored with higher tumor immune dysfunction and exclusion (TIDE), which implied worse response to immunotherapy and worse prognosis. The results above indicated that the low-risk group had stronger antitumor immunity and better responsiveness to immunotherapy. We also observed a significantly enriched pattern of cancer-related pathways and immune pathways in the comparison of the high-risk and low-risk groups. Furthermore, the high-risk group had higher sensitivity to chemotherapy drugs, which suggested that they might benefit from chemotherapy treatment. Following the results above, we confirmed in HNSCC cell lines and clinical specimens that the level of ILF2 in tumors was significantly higher than that in adjacent tumor tissues. Besides, in vivo and in vitro results both showed that silencing ILF2 might depress tumor growth, invasion, and migration. This study not only provided novel perspectives into the immunological and molecular mechanisms of HNSCC and uncovered IL-related gene signatures for predicting HNSCC patients' prognosis and response to chemotherapy and immunotherapy, but also preliminarily suggested that ILF2 might be an important target in the treatment of HNSCC.

Deciphering Regulatory Networks Governing Seedling Emergence in Deep-Sown Direct-Seeded Rice Cultivation

The rise of direct-seeded rice cultivation as a suitable alternative to transplanted puddled rice depends on developing genotypes with high seedling emergence under deep sown conditions. Two rice genotypes (IRGC 128442 and PR126) were screened for contrasting seedling emergence and subjected to high-throughput RNA sequencing under varying sowing depths (4 cm and 10 cm) and time intervals (5, 10, and 15 days after sowing). On average, a total of 2702 differentially expressed genes were identified across twelve inter- and intra-genotypic pairwise differential expression analyses, with a false discovery rate ≤ 0.05 and log2 fold change ≥ ± 2. The DEGs specifically showing differential expression under deep-sowing stress were prioritized and further refined based on their corresponding gene ontology terms, gene set enrichment analysis and KEGG and plant reactome pathway. From this pool of DEGs, 24 genes were validated using qRT-PCR. Among these, two genes (LOC_Os04g51460 and LOC_Os02g45450) contribute to cell wall remodelling and membrane stability, while three genes (LOC_Os04g48484, LOC_Os06g04399, and LOC_Os07g15440) play key roles in mitigating abiotic stress. Transcriptional regulators (LOC_Os06g33940 and LOC_Os01g45730) drive stress responses and growth. Notably, high fold changes in LOC_Os03g22720 and LOC_Os07g01960 underscore their importance in early stress responses and metabolic adjustments. The transcriptome analysis also highlighted the role of 29 heat shock proteins in response to deep sowing stress. Differential expression of key components in the abscisic acid (ABA)-mediated signalling pathway such as OsABI5 (LOC_Os01g64000), phosphatase 2C-like (PP2C) (LOC_Os09g15670) and OsPYL (LOC_Os06g36670) indicated downregulation of ABA signalling in the genotype IRGC 128442. Additionally, a role for miRNA-mediated regulation of auxin response factors was hypothesized in seedling emergence regulation. The study brings us closer to understanding the genetic control of seedling emergence under deep sown conditions. Functional validation of the key candidate genes and pathways could provide new targets for genetic improvement, potentially contributing to the development of rice cultivars optimized for direct-seeded rice cultivation.

Newly isolated halotolerant Gordonia terrae S-LD serves as a microbial cell factory for the bioconversion of used soybean oil into polyhydroxybutyrate

Polyhydroxybutyrate (PHB) is a class of biodegradable polymers generally used by prokaryotes as carbon sources and for energy storage. This study explored the feasibility of repurposing used soybean oil (USO) as a cost-effective carbon substrate for the production of PHB by the strain Gordonia terrae S-LD, marking the first report on PHB biosynthesis by this rare actinomycete species. This strain can grow under a broad range of temperatures (25–40 ℃), initial pH values (4–10), and salt concentrations (0–7%). The findings indicate that this strain can synthesize PHB at a level of 2.63 ± 0.6 g/L in a waste-containing medium containing 3% NaCl within a 3 L triangular flask, accounting for 66.97% of the cell dry weight. Furthermore, 1H NMR, 13C NMR, and GC–MS results confirmed that the polymer was PHB. The thermal properties of PHB, including its melting (Tm) and crystallization (Tc) temperatures of 176.34 °C and 56.12 °C respectively, were determined via differential scanning calorimetry analysis. The produced PHB was characterized by a weight-average molecular weight (Mw) of 5.43 × 105 g/mol, a number-average molecular weight (Mn) of 4.00 × 105 g/mol, and a polydispersity index (PDI) of 1.36. In addition, the whole genome was sequenced, and the PHB biosynthetic pathway and quantitative expression of key genes were delineated in the novel isolated strain. In conclusion, this research introduces the first instance of polyhydroxyalkanoate (PHA) production by Gordonia terrae using used soybean oil as the exclusive carbon source, which will enrich strain resources for future PHB biosynthesis.

Identification and study of mood-related biomarkers and potential molecular mechanisms in type 2 diabetes mellitus.

A significant correlation between type 2 diabetes mellitus (T2DM) and mood has been reported. However, the specific mechanism of mood's role in T2DM is unclear. This study aims to discover mood-related biomarkers in T2DM and further elucidate their underlying molecular mechanisms. The GSE81965 and GSE55650 datasets were sourced from public databases, and mood-related genes (MRGs) were retrieved from previous literature. Initially, differentially expressed MRGs (DE-MRGs) were obtained by combining differential expression analysis and weighted gene co-expression network analysis (WGCNA). Subsequently, the DE-MRGs were incorporated into the LASSO and SVM to identify diagnostic biomarkers for T2DM. Four machine learning methods were utilized to construct the diagnostic models in T2DM, and the model with the optimal algorithm was screened. Further, based on biomarkers, functional enrichment, immune infiltration, and regulatory network analyses were conducted to excavate deeper into the pathogenesis of T2DM. In vivo experiments were used to validate the expression of the biomarkers. A total of 23 DE-MRGs were identified by overlapping 723 DEGs and 64 key modules, and there were strong positive correlations between these DE-MRGs. Afterward, KCTD16, SLC8A1, RAB11FIP1, and RASGEF1B were identified as biomarkers associated with mood in T2DM, and they had favorable diagnostic performance. Meanwhile, the RF diagnostic model constructed based on biomarkers was performed optimally and had high diagnostic accuracy for T2DM patients. Animal experiments indicated that expression levels of SLC8A1, RAB11FIP1, and RASGEF1B in T2DM were consistent with the microarray results.In conclusion, KCTD16, SLC8A1, RAB11FIP1, and RASGEF1B were identified as biomarkers related to mood in T2DM.

Unveiling prognostic value of JAK/STAT signaling pathway related genes in colorectal cancer: a study of Mendelian randomization analysis

BackgroundColorectal cancer (CRC) ranks among the frequently occurring malignant neoplasms affecting the gastrointestinal tract. This study aimed to explore JAK-STAT signaling pathway related genes in CRC and establish a new prognostic model.MethodsThe data set used in this study is from a public database. JAK-STAT-differentially expressed genes (DEGs) were identified through differential expression analysis and weighted gene co-expression network analysis (WGCNA). Prognostic genes were selected from JAK-STAT-DEGs through Mendelian randomization (MR), univariate Cox regression, and least absolute shrinkage and selection operator (LASSO) analyses. The expressions of prognostic genes were verified by RT-qPCR. Then, a risk model was built and validated by the GSE39582. Independent prognostic factors were screened underlying risk scores and different clinical indicators, resulting in the construction of a nomogram. Additionally, immune infiltration, immune scores and immune checkpoint inhibitors analyses and gene set enrichment analysis (GSEA) were carried out.ResultsThe 3,668 JAK-STAT-DEGs were obtained by intersection of 5826 CRC-DEGs and 9766 JAK-STAT key module genes. Five prognostic genes were selected (ANK3, F5, FAM50B, KLHL35, MPP2), and their expressions were significantly different between CRC and control groups. A risk model was constructed according to prognostic genes and verified by GSE39582. In addition, the nomogram exhibited superior predictive accuracy for CRC. Furthermore, immune analysis results indicated a notable positive correlation between risk score and the scores of immune (R = 0.486), stromal (R = 0.309), and ESTIMATE (R = 0.422). Immune checkpoint inhibitor ADORA2A (Cor = 0.483263) exhibited the strongest positive correlation with risk score. And MPP2 exhibited the most potent activating influence on the cell cycle pathway, whereas ANK3 demonstrated the most significant inhibitory effect within the apoptosis pathway.ConclusionsA new JAK-STAT related CRC prognostic model was constructed and validated, which possessed an underlying predictive potential for CRC patients’ prognosis and could potentially enhance tailored guidance for immunotherapy.

TMT-label comparative proteomics reveals the vernalization mechanism in Wucai (Brassica campestris L.).

To investigate the molecular basis of vernalization in Wucai [Brassica campestris L. (Syn. Brassica rapa L.) ssp. chinensis var. rosularis Tsen], we performed differential proteomic analysis using a tandem mass tags (TMT)-based approach. Proteins from shoot apices subjected to 0, 15, and 30 days of vernalization (V0, V15, and V30) were analyzed to identify differentially abundant proteins (DAPs). A total of 8066 proteins were obtained, and 507 shared DAPs were involved in both initiation and progression of vernalization. Gene Ontology (GO) and Gene Ontology (KEGG) annotations revealed functional enrichment in cellular processes, metabolic pathways, and translation-related activities, including photosynthesis, glucosinolate biosynthesis, and flavonoid biosynthesis. Proteomic data showed reduced abundance of photosynthesis-related proteins and upregulation of flavonoid biosynthesis during vernalization. Transcriptional validation of 24 proteins across metabolic and regulatory pathways corroborated proteomic findings, with notable peaks in genes associated with flavonoid biosynthesis at 15 days of vernalization, such as VESR1,CH13, CHS1, FHT, and FLS1. The functions of these genes in vernalization will be further analyzed. SIGNIFICANCE: Wucai is prone to premature bolting and flowering under cold conditions, as vernalization plays a key role in controlling flowering time in Chinese cabbage crops. However, the proteomic basis of vernalization remains poorly understood. In this study, TMT-based proteomic analysis identified DAPs associated with vernalization. Pathway enrichment analysis highlighted key DAPs and their roles in significantly enriched pathways relevant to vernalization. Notably, genes in the flavonoid biosynthesis pathway genes, including VESR1, CH13, CHS1, FHT, and FLS1, respond to vernalization. These findings offer novel insights into the molecular mechanisms underlying flowering time regulation in Wucai.

Skin microbiome differences in pancreatic adenocarcinoma, other cancers, and healthy controls: a pilot study

IntroductionMany studies have reported the importance of the human microbiome in relationship to the overall health of its host. While recent studies have explored the microbiome’s role in various types of cancer compared to healthy patients, this pilot study is the first to investigate differences in the skin microbiome composition among pancreatic adenocarcinoma patients, individuals with other cancers, and cancer-free controls.MethodsThe study characterizes the skin microbiome’s potential associations with cancer status by analyzing skin swabs from the forehead and cheek of 58 participants using Next Generation Sequencing (NGS), differential abundance analysis, and machine learning techniques.ResultsThe study results indicated that the cancer group displayed a significantly higher mean alpha diversity compared to the control group. Additionally, a machine learning classification model achieved a mean F1 Score of 0.943 in predicting cancer status, indicating measurable differentiation in the skin microbiome between the study groups. This differentiation is supported by differential abundance methods, including ANCOM-BC and MaAsLin2.DiscussionThis pilot study suggests that skin microbiome profiling could serve as a non-invasive biomarker for cancer detection and monitoring, which warrants a larger, longitudinal study to validate these results.

Identification of serum phosphatidylinositol glycan anchor biosynthesis class U protein as diagnostic biomarker for breast cancer.

Finding markers of breast cancer that are strong specificity and high. Sensitivity is important. The expression of phosphatidylinositol U（PIGU） protein is increased in a variety of tumor cells, but the role of its secreted fragment in breast cancer is lacking. Differential expression analysis was performed in breast cancer patients by bioinformatics method. Univariate survival analysis and ROC curve plotting were used to explore the correlation between serum PIGU and the prognosis of breast cancer patients. ELISA was used to detect serum PIGU level. Electrochemiluminescence immunoassay was used to determine serum carcinoembryonic antigen (CEA), carbohydrate antigen-153(CA153) and carbohydrate antigen-125 (CA125) levels. The expression level of PIGU protein in breast cancer tumor tissues was higher than that in normal tissues, and PIGU expression level was a prognostic risk factor for breast cancer patients (HR > 1, p < 0.05) and had good predictive power (AUC = 0.8941). Compared with healthy individuals, the serum PIGU level of breast cancer patients was significantly highly expressed (p < 0.01), and the serum PIGU expression level was weakly positively correlated with CEA (r = 0.3270), but not significantly correlated with CA153 and CA125 (p > 0.05). PIGU has the potential to be a predictive prognostic marker for breast cancer.

Differentiating balance and harmony through natural language analysis: a cross-national exploration of two understudied wellbeing-related concepts

ABSTRACT Although the concepts of balance and harmony are increasingly appreciated as important in research on wellbeing, their precise meaning is often vague or unclear. This paper aims to elucidate these ideas by exploring responses by 15,275 people across 154 nations to two open-ended questions embedded after the online VIA Inventory of Strengths: ‘What does balance mean to you?’ and ‘What does harmony mean to you?’, together with an item on which people prefer. Strikingly, while harmony was analysed as more positively valenced, people tended to prefer balance. This is perhaps because, using differential language-based analyses, we found people interpret harmony as mostly about relationships working well in synchrony, whereas balance seems to convey proportionality across most life domains, and hence may have more applicability and impact. The paper offers suggestions for future work on these topics, such as exploration of the relevance of culture and economics.

Activating PKC-ε induces HIV expression with improved tolerability.

Despite suppressive antiretroviral therapy (ART), HIV-1 persists in latent reservoirs that seed new HIV infections if ART is interrupted, necessitating lifelong therapy for people with HIV. Activation of latent HIV during ART could improve recognition and elimination of infected cells by the immune system. Protein kinase C (PKC) isozymes increase HIV transcription and hence are potential latency reversal agents. However, the clinical utility of PKCs for this application is limited due to toxicity, which is poorly understood. Our studies showed that PKC activation with multiple classes of agonists leads to widespread platelet activation, consistent with disseminated intravascular coagulation, at concentrations that were similar to those required for T-cell activation. Differential expression analysis indicated that PKC-ε and PKC-η isoforms are expressed at high levels in human CD4+ T cells but not in platelets. Using structure-based drug design, we developed a novel PKC agonist, C-233, with increased selectivity for PKC-ε. C-233 increased both supernatant HIV RNA and p24 expression ex vivo after treatment of CD4+ T cells from ART-suppressed people with HIV. C-233 was 5-fold more potent for T-cell activation relative to platelet activation. Our studies support the use of structure-based drug design to create selective novel PKC agonists for the safe activation of HIV reservoirs and improved tolerability.

Effect of intestinal microbiota on adaptation to overcrowding stress in grouper (Epinephelus fuscoguttatus♀×E. lanceolatus♂).

Density is an important aquaculture parameter. When the pearl gentian grouper (Epinephelus fuscoguttatus♀×E. lanceolatus♂) is farmed intensively, it could lead to a degradation in genetic resources and an increase in disease outbreaks. The composition of the intestinal microbiota plays a key role in creating a specific intestinal microecosystem, which is essential for the survival, growth, and immune response of the host under environmental stress like overcrowding. This study utilized 16S rRNA sequencing and metabolomics analysis techniques to investigate the differences in intestinal microbial community stability of grouper under different stocking time and density pressure conditions. The research results showed that compared to the low-density group, the high-density group of groupers experienced an increase in mortality rate and feed coefficient in the early stages of culture, while the weight gain rate decreased. Differential analysis of intestinal microbial communities revealed significant differences in the gut microbiota of grouper between different density groups after 10 days of culture, but no significant differences were observed after 20 days of culture. At the same time, intestinal histopathology showed that the high-density group of groupers exhibited a reduction in intestinal villi length and thickness of the intestinal wall after 10 days of culture. However, the intergroup differences had reduced after 20 days of culture. Furthermore, high density cultivation upregulated the expression of inflammatory factors like IL-1β, TNF-α, IL-8, and IL-6 in the intestinal tract of groupers after 10 days of culture. However, after 20 days of culture, the expression levels of intestinal inflammatory factors in both the high-density and low-density groups of groupers were significantly reduced, and the differences between the intergroup diminished. Through correlation analysis of differential metabolites and species in the intestine, multiple metabolites significantly upregulated and associated with the upregulation of the Staphylococcus genus were identified in the intestinal tract of groupers after 20 days of high-density cultivation. The selected four associated metabolites (including creatine, fosinopril, 4-aminobutyric acid, and guanidinopropanoic acid) were validated to significantly reduce the expression of cellular inflammatory factors using the self-established grouper head kidney (HK) cell line. In conclusion, density pressure in the early culture period could affect the stability of the intestinal microbial environment of grouper. As aquaculture time increases, the intestinal microbial community of grouper drives the body's anti-inflammatory response and enhanced its adaptation to density pressure by regulating own structure and secretion of metabolites.

Deciphering adenosine signaling in hepatocellular carcinoma: pathways, prognostic models, and therapeutic implications.

Hepatocellular carcinoma (HCC) is a highly lethal cancer due to its aggressive nature and poor prognosis. Adenosine, a key metabolic regulator in the tumor microenvironment (TME), plays a crucial role in cancer progression. In this review, we first described adenosine triphosphate (ATP)-adenosine metabolism in the TME and summarize its effects on tumor growth, immune suppression, angiogenesis, and metastasis in HCC. Given the limited number of clinical studies on adenosine signaling in HCC, we conducted Lasso-Cox analysis using the TCGA-LIHC cohort to develop a prognostic risk model composed of eight adenosine signaling-related genes. This model stratified the patients into low- and high-risk groups, with Kaplan‒Meier survival analysis revealing poorer overall survival in the high-risk group. Additionally, differential gene expression analysis between the two groups identified 24 enriched signaling pathways for further investigation. Immune infiltration and single cell RNA-seq analyses revealed a correlation between adenosine and immunosuppressive activity in the TME, with a particularly strong association observed in macrophages, dendritic cells, and monocytes. Finally, we provided an overview of the advancements of antagonists that target adenosine receptors progress in both preclinical research and clinical trials. In conclusion, this review aims to deepen our understanding of the biological role of adenosine and highlights emerging therapeutic strategies that may improve treatment outcomes for HCC.

Age-related changes in DNA methylation in a sample of elderly Brazilians

BackgroundAge-related changes in DNA methylation (DNAm) play a critical role in regulating gene expression. However, most epigenome-wide association studies have predominantly focused on individuals of European descent. This study aims to characterize longitudinal changes in DNAm patterns in a cohort of elderly Brazilian participants.MethodsDNAm profiles were collected approximately nine years apart from 23 elderly Brazilian individuals using the Illumina Infinium MethyationEPIC BeadChip. Using mixed-effects models, we examined changes in DNAm patterns using both quantitative age and binary timepoint (e.g., baseline vs. follow-up) as predictors of interest to identify differentially methylated positions (DMPs). Significant DMPs were compared with a list of previously identified age-related DMPs. Differentially methylated regions (DMRs) were also identified using DMRcate. Gene ontology (GO) pathway enrichment analyses were performed to explore the functional significance of identified DMPs and DMRs.ResultsOf the 586,229 autosomal probes included in the differential methylation analyses, 2768 significant (FDR < 0.05) age-associated DMPs (aDMPs) and 2757 significant (FDR < 0.05) timepoint-associated DMPs (tpDMPs) were identified. Of the 2768 aDMPs, 1471 were replicated from previous studies. Of the 1297 non-replicated CpGs, 77.4% were exclusive to the EPIC array. The DMR analyses identified 305 age-associated DMRs (aDMRs) and 372 timepoint-associated DMRs (tpDMRs). Both aDMPs and aDMRs exhibited age-related hypermethylation within CpG islands and promoter regions of the genome, whereas hypomethylation predominantly occurred in interCGI and intergenic regions and introns. The GO enrichment analyses identified several neurological and cognition-related pathways enriched for hypermethylated CpG islands, many of which were mapped near transcription start sites and first exon regions.ConclusionsThis longitudinal study identified age-associated and timepoint-associated DMPs and DMRs in a sample of elderly Brazilians. Most of the non-replicated CpGs were found to be on the new EPIC array, suggesting that more age-related studies using the EPIC array are required to validate these CpGs. The GO pathway enrichment analyses identified age-related enrichment of several gene sets related to cognitive and physical decline in elderly populations. The enrichment of these sites could provide evidence for age-related neurodegeneration and cognitive decline in elderly populations.

Cancer multi-omics-based differential expression analysis and prognostic potential of identified hub targets of myco-metabolites for breast carcinoma and lung carcinoma

BackgroundBreast carcinoma (BC) and lung carcinoma (LC) have the highest incidence and mortality rates worldwide. In prior work, studied sample hub targets contributing to anticancer potential against BC and LC were identified through network pharmacology. In the present work, web servers UALCAN, GEPIA2, and KM plotter were used to explore the genomic and proteomic expression of these hub targets, along with their prognosis potential in BC and LC.ResultsDifferential hub targets SRC, MAPK3, PTPN11, JAK2, ESR1, and HAP900A1 for BC and PTPN11, JAK2, ESR1, EGFR, and MAPK3 for LC, showed good prognostic potentials. Collectively, PTPN11, JAK2, and ESR1 were overlapped differential expressed hub targets involved in the significantly good prognosis of both carcinoma.ConclusionThese differentially expressed hub targets may be taken into account for future BC and LC treatments due to their strong prognostic potential.

Damsels in Disguise: Development of Ultraviolet Sensitivity and Colour Patterns in Damselfishes (Pomacentridae).

Damselfishes (Pomacentridae) are widespread and highly abundant on tropical coral reefs. They exhibit diverse body colouration within and between the ~250 species and across ontogenetic stages. In addition to human-visible colours (i.e., 400-700 nm), most adult damselfishes reflect ultraviolet (UV, 300-400 nm) colour patches. UV sensitivity and UV colour signals are essential for feeding and form the basis for a secret communication channel invisible to the many UV-blind predatory fish on the reef; however, how these traits develop across ontogenetic stages and their distribution across the damselfish family is poorly characterised. Here, we used UV photography, phylogenetic reconstructions of opsin genes, and differential gene expression analysis (DGE) of retinal samples to investigate the development of UV vision and colour patterns in three ontogenetic stages (pre-settlement larval, juvenile, and adult) of 11 damselfish species. Using DGE, we found similar gene expression between juveniles and adults, which strongly differed from larvae. All species and all stages expressed at least one UV-sensitive sws1 opsin gene. However, UV body colour patterns only started to appear at the juvenile stage. Moreover, Pomacentrus species displayed highly complex UV body patterns that were correlated with the expression of two sws1 copies. This could mean that some damselfishes can discriminate colours that change only in their UV component. We demonstrate dramatic shifts in both UV sensitivity and UV colouration across the development stages of damselfish while highlighting the importance of considering ontogeny when studying the coevolution of visual systems and colour signals.

Transcriptome analysis reveals hypoxic response key genes and modules as well as adaptive mechanism of crucian carp (Carassius auratus) gill under hypoxic stress

Fish gill tissue is a primary organ responsive to acute oxygen deprivation or dissolved oxygen (DO) fluctuations in aquatic environments. However, the adaptive mechanism of crucian carp to hypoxic stress remains largely unknown. Here, we investigated gill physiological and transcriptomic changes of crucian carp exposed to hypoxic conditions (dissolved oxygen concentration of 0.6 ± 0.3 mg/L) for different durations (0 d, 1 d, 2d, 3d, 4 d, and 5d). Transcriptomic analysis revealed that the hypoxia group (0.6 ± 0.3 mg/L DO) exhibited a reduction in interlamellar cell mass (ILCM) on the gill filaments, compared with the control group (6.6 ± 0.3 mg/L DO). With prolonged hypoxia stress, the epithelial cells in the gill lamellae became sparse at 3 d to 5 d, and gill vacuoles were increased. A total of 3,502 differentially expressed genes (DEGs) were identified, and 3 hypoxia-specific modules were screened through differential expression analysis, weighted gene co-expression network analysis (WGCNA), and Bayesian network analysis. The apoptosis, necroptosis, efferocytosis and FoxO signaling pathways were significantly enriched based on the KEGG enrichment pathway analysis. The VEGF pathway genes are significantly expressed, enhancing the generation of microvessels in the gill filaments, and improving the capacity to carry oxygen, thus enabling the crucian carp to adapt to hypoxia stress. Hypoxia activated glycolysis, enhanced anaerobic metabolism, promoted β-oxidation of fatty acids, providing energy and maintaining normal physiological metabolism, eventually improving antioxidant and immune capabilities in crucian carp. In summary, this study reveals the molecular mechanism by which crucian carp adapt to hypoxic stress. Our findings provide valuable references for promoting the healthy aquaculture of hypoxic-sensitive fish and breeding hypoxia-tolerant fish varieties.