Unique Expression Pattern Research Articles

Spatiotemporal characterization of cyclooxygenase pathway enzymes during vertebrate embryonic development

Vertebrate development is regulated by several complex well-characterized morphogen signaling pathways, transcription factors, and structural proteins, but less is known about the enzymatic pathways that regulate early development. We have identified that factors from the inflammation-mediating cyclooxygenase (COX) signaling pathway are expressed at early stages of development in avian embryos. Using Gallus gallus (chicken) as a research model, we characterized the spatiotemporal expression of a subset of genes and proteins in the COX pathway during early neural development stages. Specifically, here we show expression patterns of COX-1, COX-2, and microsomal prostaglandin E synthase-2 (mPGES-2) as well as the genes encoding these enzymes (PTGS1, PTGS2, and PTGES-2). Unique expression patterns of individual players within the COX pathway suggest that they may play non-canonical/non-traditional roles in the embryo compared to their roles in the adult. Future work should examine the function of the COX pathway in tissue specification and morphogenesis and determine if these expression patterns are conserved across species.

Regional homogeneity patterns reveal the genetic and neurobiological basis of State-Trait Anxiety

ObjectiveState anxiety and trait anxiety are differentially mapped in brain function. However, the genetic and neurobiological basis of anxiety-related functional changes remain largely unknown.MethodsParticipants aged 18–30 from the community underwent resting-state fMRI and were assessed with the State-Trait Anxiety Inventory. Using a general linear regression model, we analyzed the effects of state and trait anxiety, as well as their sum and difference (delta), on regional homogeneity (ReHo) in cortical areas. ReHo patterns denote the spatial distribution of ReHo associated with anxiety scores. We further explored the spatial correlations between ReHo patterns and neuromaps, including gene expression, neurotransmitter receptor density, myelination, and functional connectivity gradients, to elucidate the genetic and molecular substrates of these ReHo patterns.ResultsOur findings demonstrated robust spatial correlations between whole-brain ReHo patterns for state and trait anxiety, with trait anxiety and the delta value exhibiting stronger network correlations, notably in the dorsal attention, salience, visual, and sensorimotor networks. Genes highly correlated with ReHo patterns exhibited unique spatiotemporal expression patterns, involvement in oxidative stress, metabolism, and response to stimuli, and were expressed in specific cell types. Furthermore, ReHo patterns significantly correlated with neuromaps of neurotransmitter receptor density, myelination, and functional connectivity gradients.ConclusionsThe ReHo patterns associated with anxiety may be driven by genetic and neurobiological traits. Our findings contribute to a deeper understanding of the pathogenesis of anxiety from a genetic and molecular perspective.

IMMU-07. THE IMMUNE LANDSCAPE OF PEDIATRIC BRAIN TUMORS: A TRANSCRIPTOMIC ANALYSIS

Abstract Despite standard-of-care therapy, pediatric brain tumors are now the leading cause of cancer-related death in children, highlighting an urgent need for the development of new treatments. Immunotherapy is actively being evaluated as a therapeutic approach to pediatric brain tumors, however, more research is needed to reveal additional antigenic targets that exist in these malignancies. In this study, our team performed a transcriptomic analysis of pediatric brain tumor RNA sequencing data within the Children’s Brain Tumor Network (CBTN) to identify intra and extracellular antigens that are highly expressed across major tumor types. Interestingly, our team observed that most tumors had high gene expression of a group of antigens that were unique to that specific tumor type. Specifically, our analysis revealed that diffuse midline gliomas (DMGs) highly expressed the extracellular antigens CA9, CTCFL, and ST8SIA1, whereas atypical rhabdoid tumors (ATRTs) highly expressed MUC1 and TEK. Other tumors that displayed high gene expression for a variety of antigenic targets included H3-wildtype high-grade gliomas (HGGs), and ependymomas (EPNs). Strikingly, we observed minimal difference in antigen expression in primary tumors when compared to patient-matched recurrences. Beyond antigen expression, we evaluated the expression of antigen processing machinery (APM) which includes major histocompatibility complexes (MHCs). Our findings revealed that DMGs had the lowest level of APM expression, however, these tumors uniquely expressed high levels of the immune checkpoints ADORA2A, CD276, and KLRC1. Contrarily, ATRTs showed a high expression of immune checkpoints CD274 (PD-L1), PVR, and CD80. Other tumors included in our analysis had unique expression patterns of antigen, as well as APM and immune checkpoints. Our findings illustrate that pediatric brain tumors have distinct expression patterns of antigens, APM, and immune checkpoints that are specific to tumor type, emphasizing diverse, rather than general, immunotherapeutic approaches must be considered for childhood brain tumors.

CCDC28A deficiency causes head-tail coupling defects and immotility in murine spermatozoa

Male infertility presents a substantial challenge in reproductive medicine, often attributed to impaired sperm motility. The present study investigates the role of CCDC28A, a protein expressed specifically in male germ cells, whose paralog CCDC28B has been implicated in ciliogenesis. We identify unique expression patterns for CCDC28A and CCDC28B within the mouse testes, where CCDC28A is expressed in germ cells, whereas CCDC28B is expressed in supporting somatic cells. Through knockout mouse models and histological analyses, we reveal that CCDC28A deficiency results in diminished sperm motility and structural aberrations in sperm tails, notably affecting the head-tail coupling apparatus (HTCA), thereby causing male infertility. Fine structural analyses by transmission electron microscopy reveal disruptions at the capitulum-basal plate junction of the HTCA in the CCDC28A mutants. This results in the bending of the head within the neck region, often accompanied by thickening of the tail midpiece. Our discovery demonstrates that CCDC28A plays an essential role in male fertility and sperm tail morphogenesis through the formation of HTCA.

Whole Blood Transcriptome Analysis in Congenital Anemia Patients.

Congenital anemias include a broad range of disorders marked by inherent abnormalities in red blood cells. These abnormalities include enzymatic, membrane, and congenital defects in erythropoiesis, as well as hemoglobinopathies such as sickle cell disease and thalassemia. These conditions range in presentation from asymptomatic cases to those requiring frequent blood transfusions, exhibiting phenotypic heterogeneity and different degrees of severity. Despite understanding their different etiologies, all of them have a common pathophysiological origin with congenital defects of erythropoiesis. We can find different types, from congenital sideroblastic anemia (CSA), which is a bone marrow failure anemia, to hemoglobinopathies as sickle cell disease and thalassemia, with a higher prevalence and clinical impact. Recent efforts have focused on understanding erythropoiesis dysfunction in these anemias but, so far, deep gene sequencing analysis comparing all of them has not been performed. Our study used Quant 3' mRNA-Sequencing to compare transcriptomic profiles of four sickle cell disease patients, ten thalassemia patients, and one rare case of SLC25A38 CSA. Our results showed clear differentiated gene map expressions in all of them with respect to healthy controls. Our study reveals that genes related to metabolic processes, membrane genes, and erythropoiesis are upregulated with respect to healthy controls in all pathologies studied except in the SLC25A38 CSA patient, who shows a unique gene expression pattern compared to the rest of the congenital anemias studied. Our analysis is the first that compares gene expression patterns across different congenital anemias to provide a broad spectrum of genes that could have clinical relevance in these pathologies.

Type-1-to-type-2 transition of brain microvascular pericytes induced by cytokines and disease-associated proteins: Role in neuroinflammation and blood-brain barrier disruption.

While the concept of pericyte heterogeneity in the brain microvasculature is becoming more widely accepted, little is known about how they arise, or their functional contributions to the blood-brain barrier (BBB). We therefore set out to examine the distribution of subtypes of pericytes at the BBB and sought to elucidate some of their functional characteristics by examining their unique mRNA expression patterns. We demonstrate that type-1 pericytes (PC1) that are associated with young healthy brains and BBB homeostasis, can transition into type-2 pericytes (PC2) that are associated with disease and BBB breakdown, both in vitro and in vivo, in the presence of both endogenous and disease associated ligands. We identified PC1 and PC2 in single-cell RNA-sequencing from vascular enriched mouse brain and identified transcriptional differences between PC1 and PC2. PC2 showed increased expression of genes associated with phagocytosis and peripheral immune cell infiltration. On the contrary, PC1 displayed increased expression of genes involved in hedgehog signaling, which is known to promote tight junction formation at the BBB. Our data support the PC1-to-PC2 transition as an origin of PC diversity and suggest a functional role for PC1 in maintaining BBB homeostasis and PC2 in responding to pathological conditions.

Comprehensive single-cell profiling of monocytes in HLA-B27-positive ankylosing spondylitis with acute anterior uveitis.

Acute anterior uveitis (AAU) is a common extra-articular manifestation of ankylosing spondylitis (AS), particularly in patients positive for the human leucocyte antigen (HLA)-B27 genetic marker. To explore the underlying mechanisms of HLA-B27+ AS-associated AAU, we employed single-cell RNA sequencing to profile the transcriptomes of peripheral blood mononuclear cells in three HLA-B27+ AS-associated AAU patients and three healthy controls (HCs). We identified 11 distinct immune cell clusters, with a particular focus on monocytes, revealing six subsets, including three previously unidentified subsets, namely, GTPase immune-associated proteins, Th17-related, and lncRNA monocytes, with unique gene expression patterns. Significant differences in monocyte composition, activation states, and gene expression were observed between patients and HCs, particularly within HLA monocyte subpopulations. Notably, enhanced expression of X-inactive specific transcript and myeloid cell nuclear differentiation antigen genes was validated across monocyte subclusters in patients. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes analysis highlighted significant enrichment in antigen processing and presentation pathways, shedding light on the disease's molecular mechanisms. These findings provide novel insights into the molecular mechanisms of HLA-B27+ AS-associated AAU and may contribute to the development of targeted diagnostic and therapeutic strategies. Further clinical validation is essential.

Genetic Adaptations of Soybean to Cold Stress Reveal Key Insights Through Transcriptomic Analysis.

Low temperatures greatly restrict the development, growth, and productivity of soybeans, with their effects differing across various cultivars. The present work investigated the transcriptome and physiological reactions of two soybean cultivars, namely "KD52" exhibiting cold tolerance and "DS17" displaying cold sensitivity, to cold stress across a precisely defined period. The soybean plants were subjected to cold treatment at 6 °C for durations of 0, 2, 4, and 8 h. A comparative physiological marker study revealed distinct reactions to cold stress in the two cultivars. The findings showed that increased malondialdehyde levels provided evidence of DS17's heightened vulnerability to lipid peroxidation and membrane degradation. In contrast, the KD52 cultivar exhibited increased activities of antioxidant enzymes, including peroxidase and superoxide dismutase, in response to cold exposure, suggesting a strong antioxidant defense system against oxidative stress. The transcriptomic analysis revealed dynamic responses, mapping 54,532 genes. Within this group, a total of 234 differentially expressed genes (DEGs) were found to be consistently changed at several time intervals, showing unique expression patterns across the two cultivars. Analysis of the association between these important DEGs and the physiological indicators revealed candidate genes that may be involved in controlling oxidative damage and antioxidant defenses. Some key genes showed a progressive rise in expression over time in both cultivars, with a more significant acceleration in KD52, and are probably involved in promoting adaptation processes during extended periods of cold exposure. The identification of improved defense mechanisms in KD52, together with the identification of crucial genes, offers great prospects for enhancing the cold stress resilience of soybean.

Genomic identification, characterization, and stress-induced expression profiling of glyoxalase and D-lactate dehydrogenase gene families in Capsicum annuum

BackgroundCapsicum annuum, a significant agricultural and nutritional crop, faces production challenges due to its sensitivity to various abiotic stresses. Glyoxalase (GLY) and D-lactate dehydrogenase (D-LDH) enzymes play vital roles in mitigating these stresses by detoxifying the stress-induced cytotoxin, methylglyoxal (MG).MethodsA genome-wide study was conducted to identify and characterize glyoxalase I (GLYI), glyoxalase II (GLYII), unique glyoxalase III or DJ-1 (GLYIII), and D-LDH gene candidates in Capsicum annuum. The identified members were evaluated based on their evolutionary relationships with known orthologues, as well as their gene and protein features. Their expression patterns were examined in various tissues, developmental stages, and in response to abiotic stress conditions using RNA-seq data and qRT-PCR.ResultsA total of 19 GLYI, 9 GLYII, 3 DJ-1, and 11 D-LDH members were identified, each featuring characteristic domains: glyoxalase, metallo-β-lactamase, DJ-1_PfpI, and FAD_binding_4, respectively. Phylogenetic analysis revealed distinct clades depending on functional diversification. Expression profiling demonstrated significant variability under stress conditions, underscoring their potential roles in stress modulation. Notably, gene-specific responses were observed with CaGLYI-2, CaGLYI-7, CaGLYII-6, CaDJ-1 A, and CaDLDH-1 showed upregulation under salinity, drought, oxidative, heat, and cold stresses, while downregulation were shown for CaGLYI-3, CaGLYII-1, CaDJ-1B, and CaDJ-1 C. Remarkably, CaGLYI-1 presented a unique expression pattern, upregulated against drought and salinity but downregulated under oxidative, heat, and cold stress.ConclusionThe identified GLY and D-LDH gene families in Capsicum annuum exhibited differential expression patterns under different abiotic stresses. Specifically, CaGLYI-2, CaGLYI-7, CaGLYII-6, CaDJ-1 A, and CaDLDH-1 were upregulated in response to all five analyzed abiotic stressors, highlighting their critical role in stress modulation amidst climate change. This study enhances our understanding of plant stress physiology and opens new avenues for developing stress-resilient crop varieties, crucial for sustainable agriculture.

Spatial transcriptomics of a parasitic flatworm provides a molecular map of drug targets and drug resistance genes

The spatial organization of gene expression dictates tissue functions in multicellular parasites. Here, we present the spatial transcriptome of a parasitic flatworm, the common liver fluke Fasciola hepatica. We identify gene expression profiles and marker genes for eight distinct tissues and validate the latter by in situ hybridization. To demonstrate the power of our spatial atlas, we focus on genes with substantial medical importance, including vaccine candidates (Ly6 proteins) and drug resistance genes (glutathione S-transferases, ABC transporters). Several of these genes exhibit unique expression patterns, indicating tissue-specific biological functions. Notably, the prioritization of tegumental protein kinases identifies a PKCβ, for which small-molecule targeting causes parasite death. Our comprehensive gene expression map provides unprecedented molecular insights into the organ systems of this complex parasitic organism, serving as a valuable tool for both basic and applied research.

Expression and its clinical significance of cell-cycle dependent kinase 1 in malignant peripheral nerve sheath tumors

To explore the role and clinical significance of cell-cycle dependent kinase 1 (CDK1) and its upstream and downstream molecules in the development of malignant peripheral nerve sheath tumor (MPNST) through the analysis of clinical tissue samples. A total of 56 tumor samples from MPNST patients ("Tianjin" dataset) who underwent surgical resection, confirmed by histology and pathology between September 2011 and March 2020, along with 17 normal tissue samples, were selected as the research subjects. MPNST-related hub genes were identified through transcriptome sequencing, bioinformatics analysis, immunohistochemistry staining, and survival analysis, and their expression levels and prognostic associations were analyzed. Transcriptome sequencing and bioinformatics analysis revealed that upregulated genes in MPNST were predominantly enriched in cell cycle-related pathways, with CDK1 occupying a central position among all differentially expressed genes. Further differential analysis demonstrated that CDK1 mRNA expression in sarcoma tissues was significantly higher than in normal tissues [based on searching the cancer genome atlas (TCGA) dataset, P<0.05]. In MPNST tissues, CDK1 mRNA expression was not only significantly higher than in normal tissues (based on Tianjin, GSE141438 datasets, P<0.05), but also significantly higher than in neurofibromatosis (NF) and plexiform neurofibromas (PNF) (based on GSE66743 and GSE145064 datasets, P<0.05). Immunohistochemical staining results indicated that the expression rate of CDK1 protein in MPNST tissues was 40.31%. Survival analysis results demonstrated that CDK1 expression was associated with poor prognosis. The survival time of MPNST patients with high CDK1 mRNA expression was significantly lower than that of the low expression group ( P<0.05), and the overall survival trend of patients with positive CDK1 protein expression was worse than that of patients with negative CDK1 expression. Additionally, differential analysis of CDK family genes (CDK1-8) revealed that only CDK1 was significantly upregulated in MPNST, NF, and PNF. Increased expression of CDK1 is associated with poor prognosis in MPNST patients. Compared to other CDK family members, CDK1 exhibits a unique expression pattern, suggesting its potential as a therapeutic target for MPNST.

Microglia Signatures: A Cause or Consequence of Microglia-Related Brain Disorders?

Microglia signatures refer to distinct gene expression profiles or patterns of gene activity that are characteristic of microglia. Advances in gene expression profiling techniques, such as single-cell RNA sequencing, have allowed us to study microglia at a more detailed level and identify unique gene expression patterns that are associated, but not always, with different functional states of these cells. Microglial signatures depend on the developmental stage, brain region, and specific pathological conditions. By studying these signatures, it has been possible to gain insights into the underlying mechanisms of microglial activation and begin to develop targeted therapies to modulate microglia-mediated immune responses in the CNS. Historically, the first two signatures coincide with M1 pro-inflammatory and M2 anti-inflammatory phenotypes. The first one includes upregulation of genes such as CD86, TNF-α, IL-1β, and iNOS, while the second one may involve genes like CD206, Arg1, Chil3, and TGF-β. However, it has long been known that many and more specific phenotypes exist between M1 and M2, likely with corresponding signatures. Here, we discuss specific microglial signatures and their association, if any, with neurodegenerative pathologies and other brain disorders.

Quantitative and spatially resolved detection of multiplexed microRNA from plant tissue via hybridization to hydrogel-bound DNA probes in nanoliter well arrays

Understanding complex regulatory networks in plant systems requires elucidating the roles of various gene regulators under a spatial landscape. MicroRNA are key regulators that impart high information value through their tissue specificity and stability when using expression patterns for evaluating network outcomes. However, current techniques that utilize spatial multiplexing and quantitation of microRNA are limited to primarily mammalian systems. Here, we present a method to spatially resolve and quantify multiple endogenous microRNA in situ using ethanol fixed, paraffin embedded model plant species. This method utilizes target-specific microRNA capture along with universal ligating and labelling, all within functionalized hydrogel posts containing DNA probes in nanoliter well arrays. We demonstrate the platform’s multiplexing capabilities through analyzing three endogenous microRNA in Arabidopsis thaliana rosettes which provide useful answers to fundamental plant growth and development from the unique expression patterns. The spatial tissue technique is also validated using non-spatial small RNA assays to demonstrate the versatility of the well array platform. Our new platform expands the toolkit of spatial omics technologies for plants.

Comprehensive transcriptomic analysis identifies three distinct subtypes of pituitary adenomas: insights into tumor behavior, prognosis, and stem cell characteristics

BackgroundPituitary adenomas (PAs) are the second most common intracranial tumor. While current diagnostic practices rely primarily on histological testing, they often fail to capture the molecular complexities of pituitary adenomas, underscoring the need for a molecular-based classification to refine therapeutic strategies and prognostic assessments. This study aims to provide a molecularly unbiased classification of pituitary adenomas and explore their unique gene expression patterns and clinical features.MethodsWe performed unsupervised hierarchical clustering of the gene expression profiles of 117 PA samples to identify three distinct molecular subtypes. Subsequently, we analyzed the compiled transcriptomic profiles of each individual subtype for pathway enrichment. We also validated the new classification with a validation set containing 158 PAs and 24 pituitary adenoma stem cells (PASCs).ResultsConsensus clustering of transcriptomic data from 117 pituitary adenoma (PA) samples identified three distinct molecular subtypes, each showing unique gene expression patterns and associated biological processes: Group I is enriched in signaling pathways, such as the cAMP signaling pathway and the calcium signaling pathway. Group II is primarily related to metabolic processes, including nitrogen metabolism and arginine biosynthesis in cancer. Group III predominantly shows enrichment in immune responses and potential malignant transformation of the disease, especially through cancer-related pathways such as the JAK–STAT signaling pathway and the PI3K–Akt signaling pathway. The immune profiling revealed distinct patterns for each subtype: Group I had higher dendritic cells and fewer CD8+ T cells, Group II had more monocytes and macrophages, and Group III had elevated levels of T cells. Additionally, there were differences in clinical characteristics and prognosis among the subtypes, with Group III having a worse prognosis, despite the smaller tumor size compared to other groups. Notably, differences in PASCs correlated with the molecular subtypes, with Group III stem cells being enriched in tumorigenesis pathways, PI3K–Akt signaling pathway and Ras signaling pathway.ConclusionOur study introduces a novel molecular classification for pituitary adenomas, independent of traditional histological methods. Each subtype features distinct genetic, molecular, and immunological profiles. We have isolated pituitary adenoma stem-like cells (PASCs), pairing them with tumor tissues for detailed transcriptomic analysis. These PASCs exhibit diverse molecular traits consistent with the new classification.

Investigating the expression profiles of cysteine string proteins (CSPs) in cochlear tissue

ObjectiveThis study aims to explore the expression patterns of cysteine string protein alpha (CSPα) and cysteine string protein beta (CSPβ) in the mammalian inner ear, with an emphasis on their temporal dynamics during the developmental stages of C57BL/6 mice. MethodsWe utilized immunofluorescence staining to assess the localization and distribution of CSPα and CSPβ within the inner ears of C57BL/6 mice and miniature pigs. Additionally, this method facilitated the investigation of their temporal expression profiles. ResultsIn adult C57BL/6 mice and miniature pigs, CSPα and CSPβ were identified in the cytoplasm of inner hair cells and spiral ganglion cells, yet were absent in outer hair cells. Both proteins were found to colocalize with Ctbp2 on the basal side of the cytoplasm in inner hair cells' basilar membrane. Expression of CSPα was observed at the nerve fiber termini at the basilar membrane's base of inner and outer hair cells 10 days postnatally in C57BL/6 mice. Notably, expression of both CSPα and CSPβ in the cytoplasm of inner hair cells emerged on the 12th day post-birth, aligning with the timeline for registering cochlear potentials. The expression levels of both proteins increased with age, but were consistently absent in outer hair cells. Contrastingly, expression of CSPα and CSPβ was present in the cytoplasm of inner hair cells in miniature pigs as early as one day post-birth, yet remained absent in the three rows of outer hair cells. ConclusionCSPα and CSPβ exhibit predominant and specific expression in inner hair cells and spiral ganglion cells. A unique expression pattern was observed for CSPα, which was also present at the nerve fiber endings of both inner and outer hair cells. The developmental expression trajectory of CSPα and CSPβ in mouse inner hair cells is characterized by an initial absence, followed by a gradual increase. Moreover, the timing of expression onset between mice and miniature pigs indicates distinct temporal dynamics, suggesting a potential role in auditory development.

Liver Fatty Acid-Binding Protein as a Diagnostic Marker for Non-Alcoholic Fatty Liver Disease

Abstract Background NAFLD is the most common cause of chronic liver disease in the developed world and represents a spectrum of diseases with some patients developing cirrhosis and hepatocellular carcinoma. Fatty acid-binding proteins (FABPs) are a family of small and highly conserved lipid chaperone molecules with highly varied functions. Different members of the FABP family exhibit unique patterns of tissue expression and are expressed most abundantly in tissues involved in active lipid metabolism in hepatocytes, adipocytes and cardiac myocytes, where fatty acids are prominent substrates for lipid biosynthesis, storage or breakdown, the respective FABPs make up between 1% and 5% of all soluble cytosolic proteins. In the hepatic lobule, L-FABP is expressed in hepatocytes in a declining gradient from portal to central location. L-FABP is a protein involved in multiple biologic functions, such as intracellular fatty acid transport, cholesterol and phospholopid metabolism, which plays an important facilitative role in hepatic fatty acid oxidation. Some studies reported that L-FABP level is increased in NAFLD. Therefore, it is preferable to use effective noninvasive methods in clinical practice for identifying NAFLD, tracking disease processes, and monitoring treatment effects. Many studies demonstrated that serological markers are beneficial as noninvasive tools for diagnosis of NAFLD. This study was conducted to determine whether serum L-FABP has a diagnostic value as a marker for NAFLD. Patients and Methods We enrolled in this study 80 consecutive patients with NAFLD who were diagnosed with Ultrasonography and Fibroscan with CAP. The control group consisted of 20 healthy control subjects matched for age and gender. Serum levels of L-FABP were determined by enzyme-linked immunosorbent assay. Results L-FABP levels in NAFLD patients were higher than in the control group (p &amp;lt; 0.05). Conclusion Serum L-FABP could be considered as a reliable non-invasive marker for detection of NAFLD.

A high-throughput gene expression analysis software tool for developmental time series and gene signature analysis of human cardiomyocyte differentiation

Publicly available high-throughput gene expression data enable the investigation of biological processes by the scientific community. Although several bioinformatics tools offer methodologies for basic differential gene expression analysis, difficulties arise in the analysis of multiple sample groups comprising a developmental time series, especially when the identification and classification of unique gene expression patterns is the primary goal of the study. Data analysis using these tools requires programming experience, which limits the accessibility of these tools to the broader community. To streamline developmental time-series investigations, we created the Developmental Gene Expression Analysis (devGEA) tool. This environment can be implemented locally or via web browsers to expedite differential gene expression analysis. This tool provides gene signature determination methods that can classify differentially expressed genes based on their correlation with gene expression patterns. devGEA was used to characterize cardiac development gene expression signatures from high-throughput RNA-seq datasets profiling small-molecule directed cardiomyocyte differentiation of human pluripotent stem cell lines (hiPSCs). After pre-processing, discrete gene expression criteria-based expected changes were used to classify the genes into developmental signatures. Several cardiomyocyte differentiation markers and candidate cardiac genes representing different developmental signatures were experimentally validated using the GIBCOTM hiPSC line. This method was then compared to a gene signature correlation approach that classified expressed genes based on their degree of similarity with key cardiac developmental signatures representing the stages of cardiomyocyte differentiation. Therefore, devGEA provides a robust workflow for investigator-driven analysis of developmental time series, allowing for the identification of differentially expressed genes and gene signatures for extensive experimental investigation. We also introduced a method for classifying genes by their correlation with genes or developmental patterns of interest. Our correlation-based method takes advantage of a priori knowledge of an experiment and is conceptually simpler than unsupervised clustering approaches.

Endogenous retroviral ERVH48-1 promotes human urine cell reprogramming

Endogenous retroviruses (ERVs), once thought to be mere remnants of ancient viral integrations in the mammalian genome, are now recognized for their critical roles in various physiological processes, including embryonic development, innate immunity, and tumorigenesis. Their impact on host organisms is significant driver of evolutionary changes, offering insight into evolutionary mechanisms. In our study, we explored the functionality of ERVs by examining single-cell transcriptomic profiles from human embryonic stem cells and urine cells. This led to the discovery of a unique ERVH48-1 expression pattern between these cell types. Additionally, somatic cell reprogramming efficacy was enhanced when ERVH48-1 was overexpressed in a urine cell-reprogramming system. Induced pluripotent stem cells (iPSCs) generated with ERVH48-1 overexpression recapitulated the traits of those produced by traditional reprogramming approaches, and the resulting iPSCs demonstrated the capability to differentiate into all three germ layers in vitro. Our research elucidated the role of ERVs in somatic cell reprogramming.

Genome-wide identification, characterization, and expression analysis of the transient receptor potential gene family in mandarin fish Siniperca chuatsi

BackgroundTemperature is a crucial environmental determinant for the vitality and development of teleost fish, yet the underlying mechanisms by which they sense temperature fluctuations remain largely unexplored. Transient receptor potential (TRP) proteins, renowned for their involvement in temperature sensing, have not been characterized in teleost fish, especially regarding their temperature-sensing capabilities.ResultsIn this study, a genome-wide analysis was conducted, identifying a total of 28 TRP genes in the mandarin fish Siniperca chuatsi. These genes were categorized into the families of TRPA, TRPC, TRPP, TRPM, TRPML, and TRPV. Despite notable variations in conserved motifs across different subfamilies, TRP family members shared common structural features, including ankyrin repeats and the TRP domain. Tissue expression analysis showed that each of these TRP genes exhibited a unique expression pattern. Furthermore, examination of the tissue expression patterns of ten selected TRP genes following exposure to both high and low temperature stress indicated the expression of TRP genes were responsive to temperatures changes. Moreover, the expression profiles of TRP genes in response to mandarin fish virus infections showed significant upregulation for most genes after Siniperca chuatsi rhabdovirus, mandarin fish iridovirus and infectious spleen and kidney necrosis virus infection.ConclusionsThis study characterized the TRP family genes in mandarin fish genome-wide, and explored their expression patterns in response to temperature stress and virus infections. Our work will enhance the overall understanding of fish TRP channels and their possible functions.

Single Cell Droplet-Based Efficacy and Transcriptomic Analysis of a Novel Anti-KLRG1 Antibody for Elimination of Autoreactive T Cells.

Progress in developing improvements in the treatment of autoimmune disease has been gradual, due to challenges presented by the nature of these conditions. Namely, the need to suppress a patient's immune response while maintaining the essential activity of the immune system in controlling disease. Targeted treatments to eliminate the autoreactive immune cells driving disease symptoms present a promising new option for major improvements in treatment efficacy and side effect management. Monoclonal antibody therapies can be applied to target autoreactive immune cells if the cells possess unique surface marker expression patterns. Killer cell lectin like receptor G1 (KLRG1) expression on autoreactive T cells presents an optimal target for this type of cell depleting antibody therapy. In this study, we apply a variety of in vitro screening methods to determine the efficacy of a novel anti-KLRG1 antibody at mediating specific natural killer (NK) cell mediated antibody-dependent cellular cytotoxicity (ADCC). The methods include single-cell droplet microfluidic techniques, allowing timelapse imaging and sorting based on cellular interactions. Included in this study is the development of a novel method of sorting cells using a droplet-sorting platform and a fluorescent calcium dye to separate cells based on CD16 recognition of cell-bound antibody. We applied this novel sorting method to visualize transcriptomic variation between NK cells that are or are not activated by binding the anti-KLRG1 antibody using RNA sequencing. The data in this study reveals a reliable and target-specific cytotoxicity of the cell depleting anti-KLRG1 antibody, and supports our droplet-sorting calcium assay as a novel method of sorting cells based on receptor activation.