Gene Expression Profiles Of Cells Research Articles

Leveraging Artificial Intelligence and Gene Expression Analysis to Identify Some Potential Bovine Coronavirus (BCoV) Receptors and Host Cell Enzymes Potentially Involved in the Viral Replication and Tissue Tropism

Bovine coronavirus (BCoV) exhibits dual tissue tropism, infecting both the respiratory and enteric tracts of cattle. Viral entry into host cells requires a coordinated interaction between viral and host proteins. However, the specific cellular receptors and co-receptors facilitating BCoV entry remain poorly understood. Similarly, the roles of host proteases such as Furin, TMPRSS2, and Cathepsin-L (CTS-L), known to assist in the replication of other coronaviruses, have not been extensively explored for BCoV. This study aims to identify novel BCoV receptors and host proteases that modulate viral replication and tissue tropism. Bovine cell lines were infected with BCoV isolates from enteric and respiratory origins, and the host cell gene expression profiles post-infection were analyzed using next-generation sequencing (NGS). Differentially expressed genes encoding potential receptors and proteases were further assessed using in-silico prediction and molecular docking analysis. These analyses focused on known coronavirus receptors, including ACE2, NRP1, DPP4, APN, AXL, and CEACAM1, to identify their potential roles in BCoV infection. Validation of these findings was performed using the qRT-PCR assays targeting individual genes. We confirmed the gene expression profiles of these receptors and enzymes in some BCoV (+/−) lung tissues. Results revealed high binding affinities of 9-O-acetylated sialic acid and NRP1 to BCoV spike (S) and hemagglutinin-esterase (HE) proteins compared to ACE2, DPP4, and CEACAM1. Additionally, Furin and TMPRSS2 were predicted to interact with the BCoV-S polybasic cleavage site (RRSRR|A), suggesting their roles in S glycoprotein activation. This is the first study to explore the interactions of BCoV with multiple host receptors and proteases. Functional studies are recommended to confirm their roles in BCoV infection and replication.

Nuclear talin-1 provides a bridge between cell adhesion and gene expression.

Talin-1 (TLN1) is best known to activate integrin receptors and transmit mechanical stimuli to the actin cytoskeleton at focal adhesions. However, the localization of TLN1 is not restricted to focal adhesions. By utilizing both subcellular fractionations and confocal microscopy analyses, we show that TLN1 localizes to the nucleus in several human cell lines, where it is tightly associated with the chromatin. Importantly, small interfering RNA (siRNA)-mediated depletion of endogenous TLN1 triggers extensive changes in the gene expression profile of human breast epithelial cells. To determine the functional impact of nuclear TLN1, we expressed a TLN1 fusion protein containing a nuclear localization signal. Our findings revealed that the accumulation of nuclear TLN1 alters the expression of a subset of genes and impairs the formation of cell-cell clusters. This study introduces an additional perspective on the canonical view of TLN1 subcellular localization and function.

Single-cell transcriptome reveals three types of adipocytes associated with intramuscular fat content in pigs.

Intramuscular fat is an essential component of muscle tissue, and understanding its contribution to skeletal muscle fat infiltration and meat quality, together with the underlying genetic mechanisms, is a major topic in pig husbandry. However, the composition of cell types and gene expression profiles essential for this purpose remain largely unexplored. Here, we performed single-cell transcriptome analysis on muscle tissue from adult pigs and identified 15 cell types, including three previously uncharacterized types of adipocytes: Adipocyte 1, Adipocyte 2, and Aregs. Phenotypic analysis showed their proportions correlated closely with intramuscular fat content. Based on integrated analysis of ATAC-seq with RNA-seq data, Adipocyte 1 and Aregs have gene expression profiles and transcription factor (TF) motif enrichment typical of adipocytes. On the other hand, myogenic TF motifs were enriched in marker gene promoters in Adipocyte 2, suggesting that these cells originate from muscle cells. Moreover, the marker gene promoters and lineage-specific TF expression in these three adipocyte types were conserved between pigs and humans. These findings provide deep insights towards understanding the complexity of mammalian intramuscular adipocyte types and the gene regulation underlying their organization and function.

WDR26 depletion alters chromatin accessibility and gene expression profiles in mammalian cells.

WD-repeat containing protein 26 (WDR26) is an essential component of the CTLH E3 ligase complex. Mutations in WDR26 lead to Skraban-Deardorff, an intellectual disability syndrome with clinical features resembling other disorders arising from defects in transcriptional regulation and chromatin structure. However, the role of WDR26 and its associated CTLH complex in regulating chromatin or transcription has not been elucidated. Here, we assessed how loss of WDR26 affects chromatin accessibility and gene expression. Transcriptome analysis of WDR26 knockout HeLa cells revealed over 2000 differentially expressed genes, while ATAC-Seq analysis showed over 32,000 differentially accessible chromatin regions, the majority mapping to intergenic and intronic regions and 13 % mapping to promoters. Above all, we found that WDR26 loss affected expression of genes regulated by AP-1 and NF-1 transcription factors and resulted in dramatic changes in their chromatin accessibility. Overall, our analyses implicate WDR26 and the CTLH complex in chromatin regulation.

Integrative single-cell and multi-omics analyses reveal ferroptosis-associated gene expression and immune microenvironment heterogeneity in gastric cancer

Gastric cancer (GC), a prevalent malignancy worldwide, encompasses a multitude of biological processes in its progression. Recently, ferroptosis, a novel mode of cell demise, has become a focal point in cancer research. The microenvironment of gastric cancer is composed of diverse cell populations, yet the specific gene expression profiles and their association with ferroptosis are not well understood. Our study employed single-cell RNA sequencing to thoroughly investigate the transcriptomic profiles and identify differential gene expression in gastric cancer, offering fresh insights into the cellular diversity and underlying molecular mechanisms of this disease. We discovered a set of significantly differentially expressed genes in GC, which may serve as valuable leads for future functional investigations. Subsequent analyses, including gene set intersection and functional enrichment, pinpointed genes implicated in ferroptosis and conducted comprehensive Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses to elucidate their biological roles. In the gene selection and model validation section, critical genes were identified using machine learning algorithms, constructing a model with high predictive accuracy. Besides, distorted immune landscapes were further identified in RBL using ssGSEA analysis such that the complex association of gene expression features and its interaction networks as well as infiltration by various types of immune cells can be more clearly understood. Correlation analysis with different immune cell subtypes showed CTSB as an important regulator in the distributions of cancer infiltrating cells. Single-cell RNA sequencing analysis was utilized to map the cellular composition and gene expression profiles of cells in the gastric cancer microenvironment, which provide critical information for elucidating cellular heterogeneity as well as tumor microenvironment regulation in GC. Moreover, the distribution of FTH1, ZFP36 and CIRBP at different expression levels show new research prospects for functional information of these promoters in tumor microenvironment. In summary, the present study augments our knowledge of molecular mechanisms underlying gastric tumorigenesisa and provide scientific basis for identifing new targets and biomarkers in therapeutic diagnosis.

The Genetic Expression Difference of A2058 Cells Treated by Plasma Direct Exposure and Plasma-Treated Medium and the Appropriate Treatment Strategy.

Background/Objectives: Cold atmospheric plasma (CAP) has been demonstrated as an adjustable device to generate various combinations of short-lived reactive oxygen and nitrogen species (RONS) and as a promising appliance for cancer therapy. This study investigated the effects of direct and indirect treatments of Argon-based CAP to cancer cells (A2058, A549, U2OS and BCC) and fibroblasts (NIH3T3 and L929) on cell viability. We also aimed to understand whether plasma-generated RONS were involved in this process using genetic evidence. Methods: The intensity of reactive species in the plasma gas and the concentrations of RONS in phosphate-buffered saline (PBS) and cell culture medium were measured. A viability assay was performed after the cells were treated by plasma in PBS and medium with various volumes to realize the lethal effects of plasma under different conditions. Diverse cells were treated in the same solution to compare the sensitivities of different cells to plasma treatments. The gene expression profiles of A2058 cells after the direct and indirect treatments were analyzed by next generation gene sequencing. Accordingly, we discovered the advantages of sequential treatments on cancer therapy. Results: The cumulative concentration of hydroxyterephthalic acid (HTA) revealed that the pre-existing OH radical (•OH) in PBS increased with the treatment durations. However, there was no significant increase in the concentration of HTA in culture medium. HTA was detected in the treatment interface of PBS but not medium, showing the penetration of •OH through PBS. The concentrations of H2O2 and NO2- increased with the treatment durations, but that of NO3- was low. The direct treatments caused stronger lethal effects on cancer cells under certain conditions. The fibroblasts showed higher tolerance to plasma treatments. From gene expression analysis, the initial observations showed that both treatments influenced transcription-related pathways and exhibited shared or unique cellular stress responses. The pre-treatments, especially of direct exposure, revealed better cancer inhibition. Conclusions: The anti-cancer efficiency of plasma could be enhanced by pre-treatments and by adjusting the liquid interfaces to avoid the rapid consumption of short-lived RONS in the medium. To achieve better therapeutic effects and selectivity, more evidence is necessary to find optional plasma treatments.

Genetic Analysis of Retinal Cell Types in Neuropsychiatric Disorders

As an accessible part of the central nervous system, the retina provides a unique window to study pathophysiological mechanisms of brain disorders in humans. Imaging and electrophysiological studies have revealed retinal alterations across several neuropsychiatric and neurological disorders, but it remains largely unclear which specific cell types and biological mechanisms are involved. To determine whether specific retinal cell types are affected by genomic risk for neuropsychiatric and neurological disorders and to explore the mechanisms through which genomic risk converges in these cell types. This genetic association study combined findings from genome-wide association studies in schizophrenia, bipolar disorder, major depressive disorder, multiple sclerosis, Parkinson disease, Alzheimer disease, and stroke with retinal single-cell transcriptomic datasets from humans, macaques, and mice. To identify susceptible cell types, Multi-Marker Analysis of Genomic Annotation (MAGMA) cell-type enrichment analyses were applied and subsequent pathway analyses performed. The cellular top hits were translated to the structural level using retinal optical coherence tomography (acquired between 2009 and 2010) and genotyping data in the large population-based UK Biobank cohort study. Data analysis was conducted between 2022 and 2024. Cell type-specific enrichment of genetic risk loading for neuropsychiatric and neurological disorder traits in the gene expression profiles of retinal cells. Expression profiles of amacrine cells (interneurons within the retina) were robustly enriched in schizophrenia genetic risk across mammalian species and in different developmental stages. This enrichment was primarily driven by genes involved in synapse biology. Moreover, expression profiles of retinal immune cell populations were enriched in multiple sclerosis genetic risk. No consistent cell-type associations were found for bipolar disorder, major depressive disorder, Parkinson disease, Alzheimer disease, or stroke. On the structural level, higher polygenic risk for schizophrenia was associated with thinning of the ganglion cell inner plexiform layer, which contains dendrites and synaptic connections of amacrine cells (B, -0.09; 95% CI, -0.16 to -0.03; P = .007; n = 36 349; mean [SD] age, 57.50 [8.00] years; 19 859 female [54.63%]). Higher polygenic risk for multiple sclerosis was associated with increased thickness of the retinal nerve fiber layer (B, 0.06; 95% CI, 0.02 to 0.10; P = .007; n = 36 371; mean [SD] age, 57.51 [8.00] years; 19 843 female [54.56%]). This study provides novel insights into the cellular underpinnings of retinal alterations in neuropsychiatric and neurological disorders and highlights the retina as a potential proxy to study synaptic pathology in schizophrenia.

The Role of Glial Cells in Autism Spectrum Disorder: Molecular Mechanisms and Therapeutic Approaches.

Autism Spectrum Disorder (ASD) is a neurodevelopmental condition characterized by social communication deficits and repetitive behaviors. Emerging evidence highlights the significant role of glial cells, particularly astrocytes and microglia, in the pathophysiology of ASD. Glial cells are crucial for maintaining homeostasis, modulating synaptic function, and responding to neural injury. Dysregulation of glial cell functions, including altered cytokine production, impaired synaptic pruning, and disrupted neuroinflammatory responses, has been implicated in ASD. Molecular mechanisms underlying these disruptions involve aberrant signaling pathways, such as the mTOR pathway, and epigenetic modifications, leading to altered gene expression profiles in glial cells. Moreover, microglial activation and reactive astrocytosis contribute to an inflammatory environment that exacerbates neural circuit abnormalities. Understanding these molecular mechanisms opens avenues for therapeutic interventions. Current therapeutic approaches targeting glial cell dysfunction include anti-inflammatory agents, modulators of synaptic function, and cell-based therapies. Minocycline and ibudilast have shown potential for modulating microglial activity and reducing neuroinflammation. Additionally, advancements in gene editing and stem cell therapy hold promise for restoring normal glial function. This abstract underscores the importance of glial cells in ASD. It highlights the need for further research to elucidate the complex interactions between glial dysfunction and ASD pathogenesis, aiming to develop targeted therapies that can ameliorate the clinical manifestations of ASD.

A minority of Th1 and Tfh effector cells express survival genes shared by memory cell progeny that require IL-7 or TCR signaling to persist.

It is not clear how CD4+ memory Tcells are formed from a much larger pool of earlier effector cells. We found that transient systemic bacterial infection rapidly generates several antigen-specific T helper (Th)1 and T follicular helper (Tfh) cell populations with different tissue residence behaviors. Although most cells of all varieties had transcriptomes indicative of cell stress and death at the peak of the response, some had already acquired a memory cell signature characterized by expression of genes involved in cell survival. Each Th1 and Tfh cell type was maintained long term by interleukin (IL)-7, except germinal center Tfh cells, which depended on a Tcell antigen receptor (TCR) signal. The results indicate that acute infection induces rapid differentiation of Th1 and Tfh cells, a minority of which quickly adopt the gene expression profile of memory cells and survive by signals from the IL-7 receptor or TCR.

Single-Cell RNA-Sequencing of Zebrafish Olfactory Epithelium Identifies Odor-Responsive Candidate Olfactory Receptors.

Single-cell RNA-sequencing (scRNA-seq) is a powerful method to comprehensively overlook gene expression profiles of individual cells in various tissues, providing fundamental datasets for classification of cell types and further functional analyses. Here we adopted scRNA-seq analysis for the zebrafish olfactory sensory neurons which respond to water-borne odorants and pheromones to elicit various behaviors crucial for survival and species preservation. Firstly, a single-cell dissociation procedure of the zebrafish olfactory rosettes was optimized by using cold-active protease, minimizing artifactual neuronal activation. Secondly, various cell types were classified into distinct clusters, based on the expressions of well-defined marker genes. Notably, we validated non-overlapping expressions of different families of olfactory receptors among the clusters of olfactory sensory neurons. Lastly, we succeeded in estimating candidate olfactory receptors responding to a particular odor stimulus by carefully scrutinizing correlated expressions of immediate early genes. Thus, scRNA-seq is a useful measure for the analysis of olfactory sensory neurons not only in classifying functional cell types but also in identifying olfactory receptor genes for given odorants and pheromones.

Genome-wide transcriptome analysis of gene expression profiles in Goose Astrovirus-infected GEF cells.

As a novel emerging pathogen, mainly causing visceral and articular gout in goslings, the pathogenesis of goose astrovirus (GAstV) remains unclear, seriously impeding the development of effective prevention and control methods. To better understand the reprogrammed cellular genes due to GAstV infection, a high-throughput transcriptome analysis was performed with primary goose embryo fibroblasts (GEF) at 48 h after infection. A total of 2324 differentially expressed genes (DEGs) were identified, and Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis showed that most DEGs were closely associated with immune signal pathway and metabolic process. Subsequently, several immune and metabolic related genes, such as Mx, OAS, STAT1, IFIT5, and ADA, were identified and further validated via quantitative real-time PCR and western blot. This was the first study using GEF as the cell model to explore the host response to GAstV infection, which will undoubtedly provide a solid foundation to elucidate the pathogenesis of GAstV.

Differentiating multiple sclerosis with predominant spinal cord and optic nerve involvement from other autoimmune demyelinating diseases using B cell immunophenotyping and gene expression profiling.

Multiple sclerosis (MS) may present with predominant involvement of the spinal cord and optic nerve (MS/w-SCON) and mimic other autoimmune inflammatory demyelinating disorders (AIDD) such as neuromyelitis optica spectrum disorder (NMOSD), and relapsing inflammatory optic neuritis (RION). Thus, biomarkers are required for effective differential diagnosis of AIDD. Patients with MS/w-SCON (n = 20), MS without involvement of SCON (MS/wo-SCON) (n = 22), NMOSD (n = 16), RION (n = 15) and healthy individuals (n = 21) were included. Peripheral blood cell immunophenotypes were analyzed by flow cytometry and gene expression levels of isolated B cells were assessed by microarray analysis and quantitative real-time PCR. Significantly increased Breg, plasmablast, and plasma cell ratios distinguished MS/w-SCON from other groups. Most differentially expressed B cell genes were subjected to protein-protein interaction yielding a network of 13 immune mediators (IL18, IL18R1, P2RY12, CSF3R, TNFSF4, TNFRSF13C, TNFRSF1A, CCL20, CCL5, CCR4, CCL4L2, CXCL5, CXCL10). CCL4L2 and CCR4 expression levels distinguished MS/w-SCON. IL18/IL18R1 and CCL5 were distinguishing factors for NMOSD and RION, respectively. Peripheral blood B cell expression levels of CCL4L2, CCR4, IL18, IL18R1 and CCL5 are candidate biomarkers for differential diagnosis of AIDD of CNS. Our results substantiate the significance of B cells in the pathogenesis of these disorders.

Dual inhibition of MAPK/ERK and BMP signaling induces entorhinal-like identity in mouse ESC-derived pallial progenitors.

The mechanisms that determine distinct embryonic pallial identities remain elusive. The central role of Wnt signaling in directing dorsal telencephalic progenitors to the isocortex or hippocampus has been elucidated. Here, we show that timely inhibition of MAPK/ERK and BMP signaling in neuralized mouse embryonic stem cells (ESCs) specifies a cell identity characteristic of the allocortex. Comparison of the global gene expression profiles of neural cells generated by MAPK/ERK and BMP inhibition (MiBi cells) with those of cells from early postnatal encephalic regions reveals a pallial identity of MiBi cells, distinct from isocortical and hippocampal cells. MiBi cells display a unique pattern of gene expression and connectivity, and share molecular and electrophysiological features with theentorhinal cortex. Our results suggest that early changes in cell signaling can specify distinct pallial fates that are maintained by specific neuronal lineages independent of subsequent embryonic morphogenetic interactions and can determine their functional connectivity.

Canid alphaherpesvirus 1 infection alters the gene expression and secretome profile of canine adipose-derived mesenchymal stem cells in vitro

BackgroundCanine adipose-derived mesenchymal stem cells (cAD-MSCs) demonstrate promising tissue repair and regeneration capabilities. However, the procurement and preservation of these cells or their secreted factors for therapeutic applications pose a risk of viral contamination, and the consequences for cAD-MSCs remain unexplored. Consequently, this research sought to assess the impact of canid alphaherpesvirus 1 (CHV) on the functional attributes of cAD-MSCs, including gene expression profiles and secretome composition.MethodsTo this end, abdominal adipose tissue from 12 healthy dogs was harvested to isolate cAD-MSCs. These samples were tested for CHV contamination before introducing a wild-type CHV strain via serial passages. Following CHV infection, real-time reverse transcription-polymerase chain reaction array and liquid chromatography with tandem mass spectrometry assessments enabled analyses of gene expression and secretome’s proteomic profile, respectively.ResultsThis study showed that the initial cAD-MSC populations were devoid of CHV. cAD-MSCs showed susceptibility to infection with wild-type CHV, leading to notable modifications in gene expression and secretome profile. The observed genomic variations in gene expression indicate potential impacts on the stemness, migration, and other functional properties of cAD-MSCs, highlighting the need for further studies to evaluate their functional capacity post-infection. Moreover, gene expression and secretome analyses suggest a shift in stem cell differentiation toward an adipogenic phenotype.ConclusionTo the best of our knowledge, this is the first study of the effects of virus infection on gene expression and secretome composition in cAD-MSCs. The outcomes of our study underscore the imperative of routine viral screening prior to the therapeutic use of cAD-MSCs. Moreover, these findings provide novel insights into the pathogenic mechanisms of CHV and pave the way for future canine stem cell and virus research.

Comparison of the Efficacy of Photodynamic Therapy Versus Cisplatin Application

Introduction: Photodynamic therapy (PDT) is a photochemical treatment that involves the use of light and photosensitizer. This method is applied as a therapeutic approach against several types of cancer. The main aim of this study is to compare the efficacy of PDT with that of cisplatin (a well-known chemotherapy agent) through protein-protein interaction (PPI) network analysis. Methods: Gene expression profiles of human melanoma A375 cells from the Gene Expression Omnibus (GEO) were selected for analysis via directed PPI network analysis. The significant differentially expressed genes (DEGs) were identified and assessed based on co-expression interactions. The critical DEGs were introduced by considering out-degree and in-degree values. Results: Two directed PPI networks for upregulated and downregulated DEGs were constructed. TP53 was identified as a critical upregulated gene in response to cisplatin in comparison with PDT. EGFR, PPARG, MMP9, PTGS2, FOXO1, and RUNX2 were highlighted as the crucial downregulated genes due to the effect of cisplatin on the gene expression of the treated cells. Conclusion: Cisplatin directly targets key cellular functions such as cell growth, differentiation, migration, and invasion. It seems that the combination of cisplatin and PDT is a suitable method for treating cancers because cisplatin targets the key genes responsible for cancer development, while PDT intensifies the effect of cisplatin and reduces its side effects.

SQLE-mediated squalene metabolism promotes tumor immune evasion in pancreatic cancer

BackgroundSqualene epoxidase (SQLE) is a key enzyme in cholesterol biosynthesis and has been shown to negatively affect tumor immunity and is associated with poor outcomes of immunotherapy in various cancers. While most research in this area has focused on the impact of cholesterol on immune functions, the influence of SQLE-mediated squalene metabolism within the tumor immune microenvironment (TIME) remains unexplored.MethodsWe established an immune-competent mouse model (C57BL/6) bearing mouse pancreatic cancer xenografts (KPC cells) with or without stable SQLE-knockdown (SQLE-KD) to evaluate the impact of SQLE-mediated metabolism on pancreatic cancer growth and immune functions. The effect of squalene on tumor growth and immune cells was tested by direct administration of squalene to C57BL/6 mice bearing KPC tumors. Flow cytometry analysis and immunohistochemical (IHC) staining of immune cells from the tumor tissues were performed to evaluate changes in immune function. We also employed RNA-sequencing to analyze the gene expression profiles in pancreatic cancer cells (PANC-1) treated with or without squalene. RT-PCR and Western blot analyses were used to investigate the relevant molecular mechanisms.ResultsWe show that SQLE is significantly overexpressed in pancreatic cancer, and abrogation of SQLE results in a significant increase in squalene accumulation within tumor cells. The elevated squalene inhibits CXCL1 transcription through its impact on the NF-κB pathway via p65, and thus reduces the recruitment of myeloid-derived suppressor cells (MDSCs) and tumor-associated macrophages (TAMs) into the tumor microenvironment. Silencing of SQLE also leads to an increased proportion of CD8+ T cells in the tumor tissues and suppresses tumor growth in vivo. Importantly, direct administration of squalene, the metabolic substrate of SQLE, to immune-competent mice bearing KPC pancreatic cancer tumors causes a substantial decrease in CD206+ TAMs and MDSCs, thus releasing immune suppression and inhibiting tumor growth.ConclusionOur study shows that squalene is an important immune-modulating metabolite that inhibits the infiltration of immune-suppressive cells in TIME, and that SQLE exerts its tumor immune evasion effect by metabolic removal of squalene. Thus, SQLE-mediated squalene metabolic pathway could be a potential target to enhance antitumor immunity in pancreatic cancer.

Gene expression profiles in human dental pulp stem cells treated short-term with lipopolysaccharides before and after osteoinduction.

Dental pulp stem cells (DPSCs) are essential for reparative dentinogenesis following damage or infection. DPSCs surrounding the blood vessels in the central region of the dental pulp actively proliferate after tooth injury and differentiate into new odontoblast-like cells or odontoblasts to form reparative dentin. However, the signaling pathways involved in undifferentiated and osteodifferentiated DPSCs under inflammatory conditions remain unclear. This study aimed to compare the expression profiles of immortalized undifferentiated and osteo-differentiated human DPSCs (hDPSCs) treated with and without lipopolysaccharide (LPS) to elucidate the molecular regulatory mechanisms involved in inflammatory conditions. We investigated the differences between undifferentiated and osteodifferentiated hDPSCs in response to LPS. RNA-seq analyses of undifferentiated and osteodifferentiated hDPSCs were performed with and without LPS. Whole-transcriptome profiling revealed distinct differences in the expression patterns of LPS-treated undifferentiated and osteodifferentiated DPSCs. Death-associated protein kinase 1 levels downregulated in LPS-treated osteodifferentiated cells, inhibiting apoptosis and enhancing cell survival. After LPS treatment, osteodifferentiated DPSCs exhibited higher expression levels of various inflammatory cytokines and chemokines than undifferentiated DPSCs. This study provides valuable transcriptomic data as a critical resource for uncovering potential therapeutic targets to enhance cell survival and regulate inflammation within the dental pulp. By elucidating the key molecular mechanisms and identifying specific gene expression changes linked to inflammatory and immune responses, these findings provide significant insights into osteo-differentiated hDPSCs.

NADPH oxidase expression profile and PBMC immunophenotypic changes in anti-TNF-treated rheumatoid arthritis patients

The aim of this research was to prospectively evaluate the impact of NOX2 gene expression profile (including NCF1, NCF2 and NCF4 genes) in peripheral blood mononuclear cells (PBMCs) on immune signatures, clinical characteristics and responsiveness to anti-TNFα treatment in RA patients. Blood specimens were collected from 31 rheumatoid arthritis (RA) patients and 25 healthy controls, and 16 RA patients were followed at two timepoints during anti-TNF treatment. mRNA expression levels of selected genes and immunoregulatory cytokines concentrations were determined. We observed the significant upregulation of NCF4 and CD14 expression in RA group. The mRNA levels of NCF1 and CD14 positively correlated both in groups of RA patients and healthy controls. NOX2 gene expression profile was not associated with anti-TNFα responsiveness, nor with RA clinical features. TNFα inhibition has not influenced NOX2 expression either. Notably, this study indicate the novel links between expression levels of NCF1 and monocyte differentiation antigen CD14.

A comprehensive analysis of gene expression and the immune landscape in gastric cancer through single-cell and multi-omics approaches

Gastric cancer (GC) is a common malignant tumor worldwide, characterized by complex biological processes. The distribution of various cell types and gene expression profiles in the GC microenvironment remains unclear. This study uses single-cell RNA sequencing to explore gene expression patterns and identify differentially expressed genes in GC samples, offering new insights into cellular diversity and potential molecular mechanisms. We conducted temporal and clustering analyses with single-cell sequencing, followed by Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses to clarify their functions. Using machine learning, we identified relevant genes to create highly accurate prediction models. Additionally, ssGSEA analysis provided detailed insights into the immunosuppressive tumor microenvironment, revealing complex gene expression interactions and diverse immune infiltrates in cancer. Correlation analysis highlighted TIMP1 as having significant prognostic value across different immune cell subtypes. Single-cell RNA sequencing revealed the cellular landscape and gene expression profiles of the GC microenvironment, offering crucial data on how cell heterogeneity is regulated in relation to the tumor microenvironment. Moreover, new insights into the expression levels of AGT, INHBA, and TIMP1 showed distinct sex-biased gene functions within the tumor microenvironment. These findings enhance our understanding of the molecular mechanisms associated with gastric cancer development and may lay the groundwork for identifying novel therapeutic targets and diagnostic strategies.

Deep learning in integrating spatial transcriptomics with other modalities.

Spatial transcriptomics technologies have been extensively applied in biological research, enabling the study of transcriptome while preserving the spatial context of tissues. Paired with spatial transcriptomics data, platforms often provide histology and (or) chromatin images, which capture cellular morphology and chromatin organization. Additionally, single-cell RNA sequencing (scRNA-seq) data from matching tissues often accompany spatial data, offering a transcriptome-wide gene expression profile of individual cells. Integrating such additional data from other modalities can effectively enhance spatial transcriptomics data, and, conversely, spatial transcriptomics data can supplement scRNA-seq with spatial information. Moreover, the rapid development of spatial multi-omics technology has spurred the demand for the integration of spatial multi-omics data to present a more detailed molecular landscape within tissues. Numerous deep learning (DL) methods have been developed for integrating spatial transcriptomics with other modalities. However, a comprehensive review of DL approaches for integrating spatial transcriptomics data with other modalities remains absent. In this study, we systematically review the applications of DL in integrating spatial transcriptomics data with other modalities. We first delineate the DL techniques applied in this integration and the key tasks involved. Next, we detail these methods and categorize them based on integrated modality and key task. Furthermore, we summarize the integration strategies of these integration methods. Finally, we discuss the challenges and future directions in integrating spatial transcriptomics with other modalities, aiming to facilitate the development of robust computational methods that more comprehensively exploit multimodal information.