Differential Expression Patterns Research Articles

Exploring the Biological Effects of Polystyrene Nanoplastics on Spermatogenesis: Insights From Transcriptomic Analysis in Mouse Spermatocytes.

The presence of polystyrene plastics in the human testis has raised concerns, yet their biological activity remains poorly characterized. This study aimed to investigate the biological effects and potential regulatory genes of polystyrene nanoplastics on spermatocyte line, GC-2spd(ts). After a 24-h exposure to polystyrene nanoplastics, the results indicated cell membrane disruption, impairment of mitochondrial membrane potential, increased levels of reactive oxygen species (ROS), and induced DNA damage. Furthermore, a comprehensive transcriptomic analysis was conducted, revealing differential gene expression patterns in GC-2spd(ts) cells in response to polystyrene nanoplastics. A total of 134 differentially expressed genes (DEGs) were identified, with 48 genes upregulated and 86 genes downregulated. The Gene Ontology analysis highlighted the involvement of these genes in various spermatogenesis-related biological processes, including acrosome reaction, sperm mitochondrial organization, sperm annulus, and outer acrosomal membrane. Subsequently, the quantification of gene expression through qRT-PCR identified five key genes (NSUN7, SEPTIN4, TRIM36, EQTN, and SYT8) screened from the DEGs. In conclusion, this study provides valuable insights into the biological effects of polystyrene nanoplastics on mouse spermatocytes using comprehensive transcriptomic analysis, contributing to the establishment of a foundation for future investigations into these relevant pathways.

Clinicopathological significance of SOX2 and FOXG1 expression patterns in ovarian immature teratomas

Objective: To investigate the relationship between the expression patterns of SOX2 and FOXG1 and the differentiation/development level of neural components in immature teratoma and to determine the clinical significance and potential application of this correlation in a clinical setting. Methods: We conducted a comprehensive whole transcriptome sequencing analysis to identify differentially expressed genes (DEGs) across various subtypes of ovarian germ cell tumors. Additionally, immunohistochemical staining of paraffin-embedded tissue sections was employed to assess the nuclear staining pattern of SOX2 and FOXG1 proteins within the tumor tissues. Results: The transcriptome sequencing data showed that transcription factors SOX2 and FOXG1 exhibited high levels of expression typically in immature teratoma and occupied a pivotal position within the protein-protein interaction network. Immunohistochemical staining revealed the absence of both SOX2 and FOXG1 protein expression in dysgerminoma and yolk sac tumor samples. In immature teratoma, immunohistochemical staining demonstrated diffuse expression of SOX2 and FOXG1 proteins within the inner layer of densely-arranged primitive neuroepithelial tubules. This pattern of expression suggested the presence of stem cell-like properties within these tumor cells. In the sparsely peripheral neurogliocytes, FOXG1 maintained a diffuse nuclear staining pattern resembling that of neuroepithelial cells, while SOX2 exhibited a scattered pattern of positive staining, hinting at a neural lineage differentiation potential. This spatial differential expression pattern of SOX2 and FOXG1 proteins in immature teratoma suggested that primitive neural components within these tumors often recapitulated the trajectory of neural formation and cortical development that was typically observed during embryogenesis. The primitive neural tube acted as the center that constantly moved from inside to outside, with a dynamic shift from the interior to the exterior, paralleled by the sequential differentiation of cell lineages from primitive neuroepithelial stem cells to radial glia, intermediate progenitor cells, and ultimately to precursor glia. Conclusions: This spatial expression pattern of SOX2 and FOXG1 proteins observed in immature teratoma mirrors the lineage differentiation and migration trajectories of primitive neuroepithelial components typically seen in embryonic neurogenesis and cortical development. In daily practice, the combined application of SOX2 and FOXG1 SOX2 and FOXG1 helps identify the primitive neuroepithelial components in immature teratoma, avoid misjudgment of similar morphologies, and thereby assist in the histological grading and clinical decision-making.

Human liver organoids are susceptible to Plasmodium vivax infection

BackgroundThe eradication of Plasmodium vivax malaria is complicated due to the presence of hypnozoites, the hidden dormant form of the parasite that is present in the liver. Currently available drug regimens are effective at killing hypnozoites but cause side effects and are difficult to administer. Studies testing drugs for liver-stage malaria remain rare and mainly rely on the use of cancerous or immortalized hepatic cells and primary hepatocytes.MethodsOrganoids were used as platform to model liver-stage vivax malaria. Hepatic endoderm cells, endothelial progenitor cells and mesenchymal cells were generated from human induced pluripotent stem cells and self-assembled into liver organoids on top of Matrigel layer. Liver characteristic and maturity were examined through genes and proteins expression of liver markers, and liver functional tests before infected with Plasmodium vivax sporozoites. The infection was then verified by the detection of parasitophorous vacuole membrane proteins, Upregulated in Infectious Sporozoite 4 (UIS4), and blood-stage infection following co-culture with human reticulocytes.ResultsGenerated liver organoids showed upregulation of liver specific transcripts including hepatic nuclear factor 4A (HNF4A), alpha-fetoprotein (AFP), and albumin (ALB) which also confirmed by the protein expression. Furthermore, those organoids resembled mature hepatocytes in terms of albumin secretion, fat and glycogen storage and cytochrome activity. Following invasion of P. vivax sporozoites, PvUIS4 was detected and the hepatic merozoites could develop into ring-stage and early trophozoites in human reticulocytes. Moreover, differential expression patterns of genes involved in lipid and cholesterol synthesis were also detected.ConclusionsStem cell-derived liver organoids resemble mature liver cells in terms of liver functions and are susceptible to infection with P. vivax sporozoites, paving the way for studies on the mechanism of hypnozoite formation and testing of possible hypnozoitocidal drugs.

Crosstalk Between Cancer-associated Fibroblasts and Myeloid Cells Shapes the Heterogeneous Microenvironment of Gastric Cancer.

Targeted therapies have improved the clinical outcomes of most patients with cancer. However, the heterogeneity of gastric cancer remains a major hurdle for precision treatment. Further investigations into tumor microenvironment heterogeneity are required to resolve these problems. In this study, bioinformatic analyses, including metabolism analysis, pathway enrichment, differentiation trajectory inference, regulatory network construction, and survival analysis, were applied to gain a comprehensive understanding of tumor microenvironment biology within gastric cancer using single-cell RNA-seq and public datasets and experiments were carried out to confirm the conclusions of these analyses. We profiled heterogeneous single-cell atlases and identified eight cell populations with differential expression patterns. We identified two cancer-associated fibroblasts (CAFs) subtypes, with particular emphasis on the role of inflammatory cancer-associated fibroblasts (iCAFs) in EMT and lipid metabolic crosstalk within the tumor microenvironment. Notably, we detected two differentiation states of iCAFs that existed in different tissues with discrepant expression of genes involved in immuno-inflammation or ECM remodeling. Moreover, investigation of tumor-infiltrating myeloid cells has revealed the functional diversity of myeloid cell lineages in gastric cancer. Of which a proliferative cell lineage named C1QC+MKI67+TAMs was recognized with high immunosuppressive capacities, suggesting it has immune suppression and cell proliferation functions in the tumor niche. Finally, we explored regulatory networks based on ligand-receptor pairs and found crucial pro-tumor crosstalk between CAFs and myeloid cells in the tumor microenvironment (TME). These findings provide insights for future cancer treatments and drug discovery.

Full-length transcriptome reveals alternative splicing regulation pattern of skin color variant in red tilapia (Oreochromis spp.)

The hybrid species red tilapia (Oreochromis spp.) is favored in aquaculture for its bright color, rapid growth, and high market value. However, color variation hinders market development, which is influenced by both genetic and environmental factors. We aim to identify candidate genes and pathways related to pigmentation, uncovering the molecular basis of these color variations in red tilapia by employing third-generation full-length transcriptome sequencing combined with second-generation transcriptome analysis. Our analysis focused on three distinct phenotypic classes: whole pink, pink with black blotch, and whole black. Pigment cell and pigment composition analysis highlighted that the pigment pattern in red tilapia is primarily determined by the distribution and interaction of various pigment cells, including melanophores, xanthophores, erythrophores, and iridophores. The whole pink individuals were characterized by an absence of melanophores and a high concentration of carotenoids, while the whole black individuals exhibited active melanogenesis. Transcriptomic data indicated that genes associated with melanin synthesis (wnt, fzd7, lef, tcf7, tyrp1, oca2, pmel, bmp2, cbs) were up-regulated in whole black individuals, while genes related to carotenoid uptake and deposition (scarb1, ldlr, ttc39b, stard5, stard10, plin2, fitm2, bscl2), as well as pteridine synthesis (gch1, ptps), were more actively expressed in whole pink individuals. Retinol metabolism was identified as a mediator of the interaction between melanin synthesis and carotenoid deposition. Further, alternative splicing (AS) act as a crucial post-transcriptional mechanism regulating body coloration, beyond transcriptional differences. Analysis of AS events identifies multiple splice variants of pigment-related genes (scarb1, pax7, ctnnb1, rxrb, bscl2, gjb10, bmp4, frzb) that exhibit differential expression and splicing patterns across different color phenotypes. Notably, AS events of the scarb1 gene, related to carotenoid deposition, and the polr2d gene, associated with the transcription machinery, may significantly influence pigment deposition patterns in red tilapia. Our work not only deepens the genetic understanding of pigmentation in red tilapia but also establishes a solid foundation for improving color stability through selective breeding and genetic improvement programs across various hybrid species in aquaculture, which is crucial for marketability and consumer attraction.

Transcriptome Analysis Reveals the lncRNA-mRNA Co-expression Network Regulating the Aestivation of Sea Cucumber.

LncRNAs are long non-coding RNAs that are widely recognized as crucial regulators of gene expression and metabolic control, involved in numerous dormancy-related processes. Aestivation is a common hypometabolism strategy of sea cucumber (Apostichopus japonicus) in response to high-temperature conditions and is typically characterized by the degradation of the intestine and respiratory tree. Although the aestivation process has been extensively studied in sea cucumbers, the role of lncRNAs in the context of aestivation states remains a conspicuous knowledge gap. Here, we identified and characterized 14,711 lncRNAs in A. japonicus and analyzed their differential expression patterns during the aestivation process in the intestine and respiratory tree. The results revealed the physiological differences, especially the metabolic processes, between the intestine and respiratory tree during the aestivation. The co-expression network of lncRNA-mRNA suggested the dominant role of lncRNA in regulating the differential response of the intestine and respiratory trees. Differentially co-expressed factors were significantly enriched in the deep-aestivation stage-specific modules. Conserved co-expressed factors included several transcription factors known to be involved in rhythm regulation, such as Klf2 and Egr1. Furthermore, a specific trans-acting lncRNA (lncrna.1393.1) was identified as a potential regulator of Klf2 and Egr1. Overall, the systematic identification, characterization, and expression analysis of lncRNAs in A. japonicus enhanced our knowledge of long non-coding regulation of aestivation in sea cucumber and provided new clues for understanding the common "toolkit" of dormancy regulatory mechanisms.

The Lifespan Evolution of Individualized Neurophysiological Traits.

This study examines how brain activity reflects the development of individuality across a person's life. Using magnetoencephalography to capture brief recordings of spontaneous brain activity, the researchers distinguished between over 1,000 individuals, spanning ages 4 to 89. They found that the brain regions most associated with individuality change with age: sensory and motor regions become increasingly distinctive in early adulthood, highlighting their role in shaping a person's unique characteristics of brain activity. The study also revealed that changes in brain activity across different ages correspond to specific patterns of gene expression, shedding light on how genetics influence brain individuality. These findings deepen our understanding of the biological foundations of inter-individual differences and how it evolves over the lifespan.

CosGeneGate selects multi-functional and credible biomarkers for single-cell analysis.

Selecting representative genes or marker genes to distinguish cell types is an important task in single-cell sequencing analysis. Although many methods have been proposed to select marker genes, the genes selected may have redundancy and/or do not show cell-type-specific expression patterns to distinguish cell types. Here, we present a novel model, named CosGeneGate, to select marker genes for more effective marker selections. CosGeneGate is inspired by combining the advantages of selecting marker genes based on both cell-type classification accuracy and marker gene specific expression patterns. We demonstrate the better performance of the marker genes selected by CosGeneGate for various downstream analyses than the existing methods with both public datasets and newly sequenced datasets. The non-redundant marker genes identified by CosGeneGate for major cell types and tissues in human can be found at the website as follows: https://github.com/VivLon/CosGeneGate/blob/main/marker gene list.xlsx.

A multi-class support vector machine classification model based on 14 microRNAs for forensic body fluid identification

MicroRNAs (miRNAs) are promising biomarkers for forensic body fluid identification owing to their small size, stability against degradation, and differential expression patterns. However, the expression of most body fluid-miRNAs is relative (differentially expressed in certain body fluids) rather than absolute (exclusively expressed in a specific body fluid). Moreover, different body fluids contain heterogeneous cell types, complicating their identification. Therefore, appropriate normalization strategies to eliminate non-biological variations and robust models to interpret expression levels accurately are necessary prerequisites for applying miRNAs in body fluid identification. In this study, the expression stability of six candidate reference genes (RGs) across five body fluids was validated using geNorm, NormFinder, BestKeeper and RankAggreg, and the most suitable combination of RGs (hsa-miR-484 and hsa-miR-191–5p) was identified under our experimental conditions. Subsequently, we systematically evaluated the expression patterns of the 28 most promising body fluid-specific miRNA markers using TaqMan RT-qPCR and selected the optimal combination of markers (12 miRNAs) to establish a multi-class support vector machine (MSVM) classification model. An independent test set (60 samples) was used to validate the accuracy of the proposed classification model, while an additional 30 casework samples were used to assess its robustness. The MSVM model accurately predicted the body fluid origin for almost all (59/60) single-source samples. Moreover, this model demonstrated the capability to identify aged forensic samples and to predict the primary components of mixed stains to a certain extent. In summary, this study presented a miRNA-based MSVM classification model for forensic body fluid identification using the qPCR platform. However, extensive validation, especially inter-laboratory collaborative exercises, is necessary before miRNA can be routinely applied in forensic identification practice.

Wnt signaling aberrant activation drives ameloblastoma invasion and recurrence: bioinformatics and in vitro insights

ObjectiveThis study aims to explore the regulatory mechanisms of Wnt signaling in the invasion and recurrence of ameloblastoma (AM) to provide a new theoretical basis for its treatment.MethodsBulk RNA sequencing was employed to analyze samples from AM patients, and identify differentially expressed genes. Subsequently, bioinformatics methods such as Weighted Gene Co-Expression Network Analysis (WGCNA), DESeq2, and KEGG enrichment analysis were utilized to construct gene co-expression networks and identify pathways associated with invasion and recurrence. Furthermore, in vitro experiments, including Cell Counting Kit-8 (CCK-8), Wound healing assays, Western blotting, and qPCR were conducted to validate the effects of Wnt signaling on AM biological functions and the expression of related genes and proteins.ResultsBioinformatics analysis revealed significant activation of the Wnt signaling pathway during AM invasion and recurrence, and differential gene analysis identified specific gene expression patterns associated with the Wnt signaling pathway. In vitro experiments further demonstrated that the standard Wnt/β-catenin pathway activator, Laduviglusib significantly activated Wnt signaling, leading to a marked increase in the mRNA and protein expression levels of TCF7, β-catenin, WNT2B, and LEF1, thereby enhancing the proliferation and migration capabilities of AM cells.ConclusionThis study reveals the critical role of aberrant Wnt signaling activation in AM proliferation and migration, identifying it as a key driver of AM invasion and recurrence. The findings provide new insights into the mechanisms underlying AM invasion and recurrence, laying the foundation for developing novel therapeutic strategies.

PDLIM1, a novel miR-3940-5p target, regulates the malignant progression of diffuse large B-cell lymphoma

ABSTRACT Background PDZ And LIM domain protein 1 (PDLIM1), a protein-coding gene, has been widely reported to exhibit differential expression patterns across various human cancers, including hematological malignancies. This study aimed to investigate PDLIM1 expression pattern and its functional role in diffuse large B-cell lymphoma (DLBCL) both in vitro and in vivo. Methods PDLIM1 expression patterns were reanalyzed using data from the Gene Expression Omnibus, and the results were subsequently validated in patient tissue samples and a panel of four DLBCL cell lines. MicroRNA-3940-5p (miR-3940-5p) was identified as an upstream regulator of PDLIM1. The interaction between PDLIM1 and miR-3940-5p and its effects on DLBCL cellular activities and cancer development were further explored using a DLBCL mouse model. Results Elevated PDLIM1 expression was observed in DLBCL cells and tissues. Reduced cell proliferation and increased DLBCL cell apoptosis were observed following the knockdown of this gene. Furthermore, short hairpin RNA (shRNA)-mediated PDLIM1 knockdown diminished tumorigenesis of DLBCL cells in nude mice. miR-3940-5p was identified as an upstream regulator of PDLIM1. PDLIM1 expression and function were negatively modulated by the upregulation of miR-3940-5p, consequently affecting the malignant phenotype of DLBCL cells. Conclusion These findings suggest that the miR-3940-5p/PDLIM1 axis may play a crucial role in DLBCL pathogenesis and could potentially be exploited for therapeutic interventions.

Expression of the Hippo pathway effector, TEAD1, within the developing murine forebrain

The Hippo pathway is a critical regulator of animal development. Activation of the Hippo pathway causes a cascade of phosphorylation events that culminate in the phosphorylation of the transcriptional co-factors YAP and TAZ, which limits their entry into the nucleus. When the Hippo pathway is ‘off’, however, YAP and TAZ can enter the nucleus, where they interact with the transcription factors of the TEA Domain (TEAD) family to regulate transcriptional activity. Despite the importance of the Hippo pathway for development, including within the nervous system, the expression of the TEAD family remains poorly defined in mammals. Here, we mapped the expression of TEAD1 in the developing mouse brain. We find that TEAD1 expression is confined to progenitor cells during embryonic development, namely radial glia and intermediate progenitor cells. TEAD1 expression is not evident in post-mitotic neurons of the cortical plate. We also identify expression of TEAD1 in developing and mature ependymal cells of the lateral and third ventricle, including within the subcommissural organ, as well as by cells within the choroid plexuses and the forebrain neurogenic niches. Finally, we find that adult mice conditionally heterozygous for Tead1 in the central nervous system exhibit a significantly smaller brain. Collectively, these findings reveal a specific pattern of expression for TEAD1 during telencephalic development and implicate this factor in regulating neural progenitor cell proliferation.

Physiological, transcriptomic, and metabolomic analyses of the chilling stress response in two melon (Cucumis melo L.) genotypes

BackgroundChilling stress is a key abiotic stress that severely restricts the growth and quality of melon (Cucumis melo L.). Few studies have investigated the mechanism of response to chilling stress in melon.ResultsWe characterized the physiological, transcriptomic, and metabolomic response of melon to chilling stress using two genotypes with different chilling sensitivity (“162” and “13-5A”). “162” showed higher osmotic regulation ability and antioxidant capacity to withstand chilling stress. Transcriptome analysis identified 4395 and 4957 differentially expressed genes (DEGs) in “162” and “13-5A” under chilling stress, respectively. Metabolome analysis identified 615 and 489 differential enriched metabolites (DEMs) were identified in “162” and “13-5A” under chilling stress condition, respectively. Integrated transcriptomic and metabolomic analysis showed enrichment of glutathione metabolism, and arginine (Arg) and proline (Pro) metabolism, with differential expression patterns in the two genotypes. Under chilling stress, glutathione metabolism-related DEGs, 6-phosphogluconate dehydrogenase (G6PDH), glutathione peroxidase (GPX), and glutathione s-transferase (GST) were upregulated in “162,” and GSH conjugates (L-gamma-glutamyl-L-amino acid and L-glutamate) were accumulated. Additionally, “162” showed upregulation of DEGs encoding ornithine decarboxylase, Pro dehydrogenase, aspartate aminotransferase, pyrroline-5-carboxylate reductase, and spermidine synthase and increased Arg, ornithine, and Pro. Furthermore, the transcription factors (TFs), MYB, ERF, MADS-box, and bZIP were significantly upregulated, suggesting their crucial role in chilling tolerance of melon.ConclusionsThese findings elucidate the molecular response mechanism to chilling stress in melon and provide insights for breeding chilling-tolerant melon.

Transcriptome profiling uncovers differentially expressed genes linked to nutritional quality in vegetable soybean.

Vegetative soybean (maodou or edamame) serves as a nutrient-rich food source with significant potential for mitigating global nutritional deficiencies. This study undertook a thorough examination of the nutritional profiles and transcriptomic landscapes of six soybean cultivars, including three common cultivars (Heinong551, Heinong562, and Heinong63) and three fresh maodou cultivars (Heinong527, HeinongXS4, and HeinongXS5). Nutrient analysis of the seeds disclosed notable differences in the levels of protein, fat, soluble sugars, vitamin E, calcium, potassium, magnesium, manganese, iron, and zinc across the cultivars. Through comparative transcriptome profiling and RNA sequencing, distinct variations in differentially expressed genes (DEGs) were identified between fresh and traditional maodou cultivars. Functional enrichment analyses underscored the involvement of DEGs in critical biological processes, such as nutrient biosynthesis, seed development, and stress responses. Additionally, association studies demonstrated robust correlations between specific DEG expression patterns and seed nutrient compositions across the different cultivars. Sankey diagrams illustrated that DEGs are strongly linked with seed quality traits, revealing potential molecular determinants that govern variations in nutritional content. The identified DEGs and their relationships with nutritional profiles offer valuable insights for breeding programs focused on developing cultivars with improved nutritional quality, tailored to specific dietary needs or industrial applications.

Abstract B062: Transcriptomic analysis of whole blood samples from prostate cancer patients: A comparative study of patients from geographically diverse populations

Abstract Introduction: Prostate cancer is the most frequently diagnosed cancer across 112 countries. Among American men, an estimated 299, 010 new cases and 35,250 deaths are projected for 2024. In this study, the transcriptomic profile of prostate cancer patients from geographically and ethnically diverse cohorts (USA-Caucasian, RSA-Black) were compared to identify gene expression patterns associated with prostate cancer. Methods: Whole blood samples were collected from PCa and controls. Controls had the same age-range as PCa with no clinical indication of prostatic disease and serum PSA levels below 1.5 ng/ml. RNA was isolated, sequencing was carried out on Novaseq 6000, and data analyzed using PartekFlow to identify differential gene expression patterns (RSA-PCa: 6, RSA-Control: 6, USA-PCa: 7, USA-Control: 11). qRT-PCR was undertaken on a cohort of 27 biomarkers (PROSTest) related to PCa in whole blood. Results: Differential expression analysis identified distinct patterns in USA and RSA groups. In the USA PCa cohort, 2,193 genes were differentially expressed compared to the controls with fold change (FC) >1, p-value (p) <0.05, while in the RSA PCa cohort, 1,627 genes were differentially expressed compared to the controls. Pathway analyses identified enrichment for immune responsive genes in the RSA cohorts. We identified that 26 of 27 Wren’s PROSTest genes detectable in both groups. RNAseq and normalized PCR gene expression were well- correlated (r=0.44, p=0.0012, n=30 pairs). Conclusion: Based on this RNAseq study, there may be geographic differences related to ethnicity in overall blood RNA gene expression. We specifically identified alterations in immune function gene expression between the USA and RSA. Importantly, PROSTest genes were detected in both populations and exhibited a significant correlation. Development of gene signatures for biomarker discovery should, however, consider specific ethnicities and geographical regions. Citation Format: Srinivas V Koduru, Mark Kidd, Ané Pieters, S E Nagel, Robert P Millar, Abdel B Halim. Transcriptomic analysis of whole blood samples from prostate cancer patients: A comparative study of patients from geographically diverse populations [abstract]. In: Proceedings of the AACR Special Conference: Liquid Biopsy: From Discovery to Clinical Implementation; 2024 Nov 13-16; San Diego, CA. Philadelphia (PA): AACR; Clin Cancer Res 2024;30(21_Suppl):Abstract nr B062.

Genome-wide identification of the OVATE gene family and revelation of its expression profile and functional role in eight tissues of Rosa roxburghii Tratt

BackgroundThe OVATE gene family is a new class of transcriptional repressors, which play an important regulatory role in plant growth and development. Many studies have proved that the OVATE gene family can regulate the development of plant tissues and organs and resist stress, but its quantity and functional role in Rosa roxburghii remain unknown.ResultsIn this study, 14 OVATE family members were identified by re-annotating the genome of Rosa roxburghii, and these members were unevenly distributed on 6 chromosomes. Evolutionary analysis indicated that these family members were classified into three groups. In their promoter regions, many hormone-related cis-acting elements such as ABA, GA, and MeJA were identified. Segmental duplication is an important driving force for the expansion of the OVATE family in Rosa roxburghii. Transcriptome sequencing and RT-qPCR analysis showed that OVATE gene family had a specific tissue expression pattern in Rosa roxburghii. For instance, the expression level of gene Rr602241 in leaves was more than 4 times that of other tissues. The gene Rr101515 was highly expressed in FR1 and FR4 stages of fruit tree development, and was highly homologous to the gene regulating fruit shape in tomatoes. These results suggest that members of the OVATE gene family may have diverse functions in different tissues. Furthermore, based on the transcriptome data of eight tissues, a transcriptional regulatory co-expression network of different transcription factors and 14 OVATE genes was constructed.ConclusionIn conclusion, our study provides the expression profiles of the OVATE family and reveals the potential functional roles of different members in the growth and development of Rosa roxburghii Tratt.

Abstract 4142799: Central role of LIM domain binding 3 (LDB3) protein in Tetralogy of Fallot assessed by single-nuclei multiome profiling of paediatric right ventricular samples

Background and aims: Tetralogy of Fallot (TOF; EC: 1565/2019) is the most common cyanotic congenital heart defect with a world-wide incidence of 0.02–0.04%. The pathophysiological mechanisms driven by variable genetic background are poorly understood. We applied the single-nuclei multiome profiling, composed of ATAC and RNA-seq from the same nuclei, of right ventricular samples of children with TOF. The final aim was to define cell types and characterize gene regulation states in different cell clusters including activation and maturation. Methods: Right ventricular samples were prospectively gathered during routinely performed cardiac surgery for TOF correction (EC: 1565/2019). In total, six paediatric patient samples were processed, and on average ~1,500 nuclei were sequenced per sample. Data was analysed using Scanpy to cluster and annotate cells, pycisTopic to identify cell stats and cis-regulatory topics, and SCENIC+ for enhancer-driven gene Regulatory network (eRegulon) construction. Results: Through manual annotation, using published markers, we identified cell types including cardiomyocyte, fibroblast, endothelial, pericyte, immune and neuronal cells. From this, we observed cell type specific expression, with overexpression of decorin in fibroblasts, PTPRC in immune cells, and neurexin genes in neuronal cells found. Differential expression analysis highlighted patient specific patterns of expression, of which gene set enrichment showed enrichment for genes associated with actomyosin structure organisation, dilated cardiomyopathy and cardiac muscle contraction. Integration of the gene expression data with the ATAC-seq data, across all patients, allowed for the construction of eRegulons networks. In detail, in the cardiomyocyte-annotated clusters, we identified enrichment of MEF2, MEIS2 and EPAS1 family enhancers with a central role of LIM domain binding 3 protein (LDB3, associated with cytoskeletal actin and muscle alpha-actin binding) (Fig. 1). Conclusion: Single nuclei multiome profiling of paediatric right ventricular TOF samples identified several patient specific patterns of expression and regulatory networks, related to the development of cyanotic congenital heart disease, and sheds light to the potential drivers of TOF.

RADT-06. IDENTIFICATION OF NEW RADIATION RESPONSE PREDICTOR GENES FOR GLIOBLASTOMACRUCIAL CONTRIBUTION OF THE LUNATIC FRINGE GENE (LFNG)

Abstract Glioblastoma (GBM) is adults’ most common aggressive primary intracranial tumor. The current standard of care involves maximal safe surgery followed by radiochemotherapy. OBJECTIVE our study was to identify genes that predict response to radiochemotherapy. MATERIALS AND METHODS We collected molecular and clinical data, including primary glioma mRNA expression, from two international online databases - TCGA and CCGA. A total of 76 cases were examined, with 41 patients in the TCGA cohort and 35 in the CCGA cohort. The patients were divided into two groups before assessing the data. Group 1 included patients who were alive at the time of the analysis, and Group 2 included patients who had passed away. Then, we performed a single-center Moroccan transcriptomic study involving 28 cases to assess the impact of the individualized gene in our environment. RESULTS The following genes, namely SRPX, S100A16, LFNG, CD5, CMBL, and TCTN2, are among the top genes co-overexpressed in TCGA and CGGA patients. We conducted a multivariate COX survival test, taking into account known prognostic clinical parameters, and found that the LFNG gene is the only marker of poor prognosis independent of other clinical markers in TCGA and CGGA patients treated with radiotherapy. Our results indicate that patients who overexpress LFNG have elevated IFNg levels and low granzyme B levels, while the levels of perforin and granzyme A remain unaffected by LFNG variation. Furthermore, our results demonstrate positive correlations between LFNG gene expression and four immune checkpoints (PD1, PDL1, CTLA4, and VISTA), but negative correlations only with TIM3. CONCLUSION Our findings suggest that LFNG could serve as a useful biomarker for identifying patients with poor prognosis and that LFNG expression may be associated with specific immune checkpoint expression patterns. These results have important implications for the development of new therapeutic approaches in the treatment of TCGA and CGGA patients.

Multi-omics approaches define novel aphid effector candidates associated with virulence and avirulence phenotypes

BackgroundCompatibility between plant parasites and their hosts is genetically determined {Citation}both interacting organisms. For example, plants may carry resistance (R) genes or deploy chemical defences. Aphid saliva contains many proteins that are secreted into host tissues. Subsets of these proteins are predicted to act as effectors, either subverting or triggering host immunity. However, associating particular effectors with virulence or avirulence outcomes presents challenges due to the combinatorial complexity. Here we use defined aphid and host genetics to test for co-segregation of expressed aphid transcripts and proteins with virulent or avirulent phenotypes.ResultsWe compared virulent and avirulent pea aphid parental genotypes, and their bulk segregant F1 progeny on Medicago truncatula genotypes carrying or lacking the RAP1 (Resistance to Acyrthosiphon pisum 1) resistance quantitative trait locus. Differential gene expression analysis of whole body and head samples, in combination with proteomics of saliva and salivary glands, enabled us to pinpoint proteins associated with virulence or avirulence phenotypes. There was relatively little impact of host genotype, whereas large numbers of transcripts and proteins were differentially expressed between parental aphids, likely a reflection of their classification as divergent biotypes within the pea aphid species complex. Many fewer transcripts intersected with the equivalent differential expression patterns in the bulked F1 progeny, providing an effective filter for removing genomic background effects. Overall, there were more upregulated genes detected in the F1 avirulent dataset compared with the virulent one. Some genes were differentially expressed both in the transcriptome and in the proteome datasets, with aminopeptidase N proteins being the most frequent differentially expressed family. In addition, a substantial proportion (27%) of salivary proteins lack annotations, suggesting that many novel functions remain to be discovered.ConclusionsEspecially when combined with tightly controlled genetics of both insect and host plant, multi-omics approaches are powerful tools for revealing and filtering candidate lists down to plausible genes for further functional analysis as putative aphid effectors.

The potential of ESCO2 as a prognostic and immunotherapeutic marker of pan-cancer and its role in anti-PD1 treatment of bladder cancer.

Background Establishment of sister chromatid cohesion N-acetyltransferase 2 (ESCO2), a member of the EFO2 family, is implicated in the pathogenesis and progression of various cancers. However, there has been limited comprehensive pan-cancer analysis conducted on ESCO2 thus far. Methods Publicly available databases, such as the UCSC Xena database, were utilized to examine differential expression patterns across various cancer types. In addition, variations in expression levels were investigated across distinct clinical stages. Univariate Cox regression and Kaplan-Meier survival analyses were conducted to evaluate the impact on overall survival (OS), disease-specific survival (DSS), disease-free interval (DFI), and progression-free interval (PFI) at a pan-cancer level. The correlation between ESCO2 expression and immune cell infiltration was examined to gain insight into the tumor microenvironment in different cancers. The results of the bioinformatic analysis were validated using immunotherapy clinical trials and pathological specimens. CCK-8 and transwell assay experiments were performed to investigate the biological function of ESCO2. Results ESCO2 expression was found to be up-regulated in most cancers, with a correlation to TNM stages. Prognostic analysis indicated that overexpression of ESCO2 was associated with poor prognosis in various cancers. Furthermore, the correlation between ESCO2 expression and immune cell infiltration suggested its potential as a predictor for immunotherapy efficacy. Notably, ESCO2 expression showed positive associations with immunoinhibitor, immnostimulator, MHC molecule, chemokine receptor, tumor mutation burden (TMB) and microsatellite instability (MSI) levels in bladder cancer (BLCA). The validation cohort for immunotherapy corroborated these findings and substantiated that ESCO2 could function as an autonomous prognostic biomarker and a promising target for cancer treatment via immunotherapy. In addition, in vitro experiments confirmed the role of ESCO2 in influcing the proliferation, invasion and migration of BLCA cells. Conclusion ESCO2 participates in regulating the immune infiltration and affecting the prognosis of patients in many cancers, especially in BLCA. ESCO2 may serve as a prognostic and immunotherapy biomarker in future treatment of human cancer.