Comparative Gene Expression Analysis Research Articles

Expression and clinical significance of pattern recognition receptor-associated genes in hand, foot and mouth disease

Objective: To explore which pattern recognition receptors (PRRs) play a key role in the development of hand, foot, and mouth disease (HFMD) by analyzing PRR-associated genes. Methods: We conducted a comparative analysis of PRR-associated gene expression in human peripheral blood mononuclear cells (PBMCs) infected with enterovirus 71 (EV-A71) which were derived from patients with HFMD of different severities and at different stages. A total of 30 PRR-associated genes were identified as significantly upregulated both over time and across different EV-A71 isolates. Subsequently, ELISA was employed to quantify the expression of the six most prominent genes among these 30 identified genes, specifically, BST2, IRF7, 1FI16, TRIM21, MX1, and DDX58. Results: Compared with those at the recovery stage, the expression levels of BST2 (P=0.027), IFI16 (P=0.016), MX1 (P=0.046) and DDX58 (P=0.008) in the acute stage of infection were significantly upregulated, while no significant difference in the expression levels of IRF7 (P=0.495) and TRIM21 (P=0.071) was found between different stages of the disease. The expression levels of BST2, IRF7, IFI16 and MX1 were significantly higher in children infected with single pathogen than those infected with mixed pathogens, and BST2, IRF7, IFI16 and MX1 expression levels were significantly lower in coxsackie B virus (COXB) positive patients than the negative patients. Expression levels of one or more of BST2, IRF7, IFI16, TRIM21, MX1 and DDX58 genes were correlated with PCT levels, various white blood cell counts, and serum antibody levels that reflect disease course of HFMD. Aspartate aminotransferase was correlated with BST2, MX1 and DDX58 expression levels. Conclusions: PRR-associated genes likely initiate the immune response in patients at the acute stage of HFMD.

Comparative analysis of gene expression between mice and humans in acetaminophen-induced liver injury by integrating bioinformatics analysis

ObjectiveMice are routinely utilized as animal models of drug-induced liver injury (DILI), however, there are significant differences in the pathogenesis between mice and humans. This study aimed to compare gene expression between humans and mice in acetaminophen (APAP)-induced liver injury (AILI), and investigate the similarities and differences in biological processes between the two species.MethodsA pair of public datasets (GSE218879 and GSE120652) obtained from GEO were analyzed using “Limma” package in R language, and differentially expressed genes (DEGs) were identified, including co-expressed DEGs (co-DEGs) and specific-expressed DEGS (specific-DEGs). Analysis of Gene Set Enrichment Analysis (GSEA), Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) were performed analyses for specific-DEGs and co-DEGs. The co-DEGs were also used to construct transcription factor (TF)-gene network, gene-miRNA interactions network and protein-protein interaction (PPI) network for analyzing hub genes.ResultsMouse samples contained 1052 up-regulated genes and 1064 down-regulated genes, while human samples contained 1156 up-regulated genes and 1557 down-regulated genes. After taking the intersection between the DEGs, only 154 co-down-regulated and 89 co-up-regulated DEGs were identified, with a proportion of less than 10%. It was suggested that significant differences in gene expression between mice and humans in drug-induced liver injury. Mouse-specific-DEGs predominantly engaged in processes related to apoptosis and endoplasmic reticulum stress, while human-specific-DEGs were concentrated around catabolic process. Analysis of co-regulated genes reveals showed that they were mainly enriched in biosynthetic and metabolism-related processes. Then a PPI network which contains 189 nodes and 380 edges was constructed from the co-DEGs and two modules were obtained by Mcode. We screened out 10 hub genes by three algorithms of Degree, MCC and MNC, including CYP7A1, LSS, SREBF1, FASN, CD44, SPP1, ITGAV, ANXA5, LGALS3 and PDGFRA. Besides, TFs such as FOXC1, HINFP, NFKB1, miRNAs like mir-744-5p, mir-335-5p, mir-149-3p, mir-218-5p, mir-10a-5p may be the key regulatory factors of hub genes.ConclusionsThe DEGs of AILI mice models and those of patients were compared, and common biological processes were identified. The signaling pathways and hub genes in co-expression were identified between mice and humans through a series of bioinformatics analyses, which may be more valuable to reveal molecular mechanisms of AILI.

Abstract 876: spatialGE: Empowering researchers to study the tumor microenvironment leveraging spatial transcriptomics

Abstract The use of single-cell RNA-seq (scRNA-seq) to understand the complexity of the tumor microenvironment (TME) has been pivotal in advancing cancer research and treatment strategies. Nevertheless, locating the individual TME components in their spatial contexts is essential to understanding the complexity of the TME, tumorigenesis, metastasis, and drug response. The recent popularity of spatially resolved transcriptomics (SRT) allows researchers to describe the TME and their spatial neighborhoods; however, SRT data analysis can be challenging for non-data scientists. Thus, we have developed spatialGE, a point-and-click web application designed to empower researchers in the analysis of SRT data. Our application offers a suite of functionalities, including the visualization of spatial gene expression activity maps, quantification of the spatial heterogeneity, testing of pathway-level spatial aggregation, tissue domain/niche detection, detection of spatial gradients in expression patterns, and differential expression analysis. Furthermore, spatialGE allows direct comparative analysis of gene expression with the morphology in tissue images, as well as methods for cell/domain phenotyping. Data input has been streamlined and made flexible to receive outputs from multiple SRT platforms. Analyses and results are stored within user-defined projects to facilitate accessibility at any time. We demonstrate the usefulness of spatialGE through its application to leptomeningeal metastatic melanoma (LMM) tissues assayed with the Visium platform. The gene expression tissue domain detection and gradient analysis in spatialGE indicated that SERPINA3 expression is higher in tumor regions closer to stroma. This finding led to cell culture experiments indicating that knocking down SERPINA3 results in the sensitization of tumors to MAPK-targeting therapy. These results highlight the utility of spatialGE for exploring SRT data and the empowerment of cancer researchers to explore the spatial architecture of the TME. Citation Format: Oscar Ospina, Roberto Manjarres-Betancur, Guillermo Gonzalez-Calderon, Alex C. Soupir, Inna Smalley, Kenneth Tsai, Joseph Markowitz, Anders Berglund, Xiaoqing Yu, Brooke L. Fridley. spatialGE: Empowering researchers to study the tumor microenvironment leveraging spatial transcriptomics [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 876.

Comparative analysis of differential gene expression reveals novel insights into the heteroblastic foliage functional traits of Pinus massoniana seedlings

Pinus massoniana needles, rich in medicinal polysaccharides and flavonoids, undergo heteroblastic foliage, transitioning from primary needles (PN) to secondary needles (SN) during growth, resulting in altered functional traits. Despite its significance, the molecular regulatory mechanisms governing these traits remain unclear. This study employs Iso-Seq and RNA-Seq analyses to explore differentially expressed genes (DEGs) associated with functional traits throughout the main growth season of heteroblastic foliage. Co-expression network analysis identified 34 hub genes and 17 key transcription factors (TFs) influencing light-harvesting antenna, photosystem I and II, crucial in photosynthesis regulation. Additionally, 14 genes involved in polysaccharide metabolism pathways, synthesizing sucrose, glucose, UDP sugars, and xylan, along with four genes in flavonoid biosynthesis pathways, regulating p-coumaroyl-CoA, quercetin, galangin, and myricetin production, exhibited differential expression between PN and SN. Further analysis unveils a highly interconnected network among these genes, forming a pivotal cascade of TFs and DEGs. Therefore, heteroblastic changes significantly impact needle functional traits, potentially affecting the pharmacological properties of PN and SN. Thus, these genomic insights into understanding the molecular-level differences of heteroblastic foliage, thereby establishing a foundation for advancements in the pharmaceutical industry related to needle-derived products.

Genetic diversity promotes resilience in a mouse model of Alzheimer's disease.

Alzheimer's disease (AD) is a neurodegenerative disorder with multifactorial etiology, including genetic factors that play a significant role in disease risk and resilience. However, the role of genetic diversity in preclinical AD studies has received limited attention. We crossed five Collaborative Cross strains with 5xFAD C57BL/6J female mice to generate F1 mice with and without the 5xFAD transgene. Amyloid plaque pathology, microglial and astrocytic responses, neurofilament light chain levels, and gene expression were assessed at various ages. Genetic diversity significantly impacts AD-related pathology. Hybrid strains showed resistance to amyloid plaque formation and neuronal damage. Transcriptome diversity was maintained across ages and sexes, with observable strain-specific variations in AD-related phenotypes. Comparative gene expression analysis indicated correlations between mouse strains and human AD. Increasing genetic diversity promotes resilience to AD-related pathogenesis, relative to an inbred C57BL/6J background, reinforcing the importance of genetic diversity in uncovering resilience in the development of AD. Genetic diversity's impact on AD in mice was explored. Diverse F1 mouse strains were used for AD study, via the Collaborative Cross. Strain-specific variations in AD pathology, glia, and transcription were found. Strains resilient to plaque formation and plasma neurofilament light chain (NfL) increases were identified. Correlations with human AD transcriptomics were observed.

Abstract 1676 Comparative Analysis of Differential Gene Expression of Cultured Cell Lines Exposed to Bisphenol-A and Taxol

Abstract 1676 Comparative Analysis of Differential Gene Expression of Cultured Cell Lines Exposed to Bisphenol-A and Taxol

Comparative Analysis of Quantitative Gene Expression of TGF-β in Patients with Recurrent Vulvovaginal Candidiasis and the Normal Population

Background: Recurrent vulvovaginal candidiasis (RVVC) is a widespread opportunistic gynecological condition resulting from infections by Candida albicans and non-C. albicans (NAC) species. Transforming growth factor-beta (TGF-β), a significant cytokine involved in cell-mediated immunity (CMI), plays a crucial role in vaginal infections. Objectives: The current study was conducted to evaluate the differences in TGF-β gene expression between patients with RVVC and healthy individuals using real-time polymerase chain reaction (PCR). Methods: This case-control study involved 124 patients diagnosed with RVVC and 225 age-matched healthy individuals as controls. The mRNA expression of the TGF-β gene was measured using quantitative real-time PCR (QRT-PCR). Data analysis and the creation of graphs were carried out using SPSS and GraphPad PRISM software. Results: The QRT-PCR findings showed higher TGF-β expression in RVVC patients compared to the control group, though the difference was not statistically significant (P = 0.2538). Conclusions: Our study revealed that the expression of the TGF-β1 isoform was elevated in patients with clinical manifestations in the vagina, although the increase was not statistically significant. Based on this outcome, further in vivo studies are necessary to elucidate the precise role of TGF-β isoforms in the vaginal tract of patients with RVVC.

Functional Analysis of Genes Specifically Expressed during Aerial Hyphae Collapse as a Potential Signal for Perithecium Formation Induction in Fusarium graminearum.

Fusarium graminearum, the causal agent of Fusarium head blight (FHB) in cereal crops, employs the production of sexual fruiting bodies (perithecia) on plant debris as a strategy for overwintering and dissemination. In an artificial condition (e.g., carrot agar medium), the F. graminearum Z3643 strain was capable of producing perithecia predominantly in the central region of the fungal culture where aerial hyphae naturally collapsed. To unravel the intricate relationship between natural aerial hyphae collapse and sexual development in this fungus, we focused on 699 genes differentially expressed during aerial hyphae collapse, with 26 selected for further analysis. Targeted gene deletion and quantitative real-time PCR analyses elucidated the functions of specific genes during natural aerial hyphae collapse and perithecium formation. Furthermore, comparative gene expression analyses between natural collapse and artificial removal conditions reveal distinct temporal profiles, with the latter inducing a more rapid and pronounced response, particularly in MAT gene expression. Notably, FGSG_09210 and FGSG_09896 play crucial roles in sexual development and aerial hyphae growth, respectively. Taken together, it is plausible that if aerial hyphae collapse occurs on plant debris, it may serve as a physical cue for inducing perithecium formation in crop fields, representing a survival strategy for F. graminearum during winter. Insights into the molecular mechanisms underlying aerial hyphae collapse provides offer potential strategies for disease control against FHB caused by F. graminearum.

OP21 Spatial Transcriptomics of Pre-treatment Biopsies Revealing Molecular Maturation State and Chronic Crypt Damage, Reflecting Histological Severity, as Predictors of Primary Responsiveness to TNF-α Inhibitors in Bio-naive Ulcerative Colitis Patients

Abstract Background Biologic therapies, particularly tumor necrosis factor-alpha inhibitors (TNFi), have greatly advanced the treatment of ulcerative colitis (UC), yet significant number of patients still do not respond to these treatments. For UC management, achieving both histologic and molecular healing is crucial, highlighting the need for more comprehensive therapeutic strategies. Despite extensive research, there is a significant gap in studies that simultaneously assess histologic and molecular changes at both the crypt and lamina propria (LP) levels. Our study addresses this gap by investigating TNFi-resistant UC patients, utilizing spatial transcriptomics to discern specific cell types within histologic sections and integrating these insights to enhance understanding of UC treatment responses. Methods We evaluated 56 patients categorized into test (n=23), validation (n=31), and healthy control groups (n=2). Each underwent biopsies at the same sites before (preTx) and after treatment (postTx), as shown in Figure 1A. This study focused on a 3-month follow-up of patients who were administered TNFi as a primary biologic therapy following resistance to conventional treatments. We used digital spatial profiling to analyze gene expression in the crypt and LP, as seen in Figures 1B and 1C. We then correlated molecular data with morphological characteristics and quantitatively evaluated histologic factors, especially crypt distortion and atrophy, reported as percentages (%). Results Among the study participants, 29 were classified as responders (R) to TNFi, while 25 were non-responders (non-R). A comparative analysis of gene expression between R and non-R groups revealed a differential expression pattern: 72 genes in the crypt and 105 genes in the LP across varying histologies, as shown in Figure 1D and 1E. Notably, in the preTx samples of non-R, crypts displayed significantly lower expression of genes associated with the maturation of colonocytes, including BEST4, C10orf99, CA2, CA4, CA7, PHGR1, SLC26A2, SLC26A3, LYPD8, CLCA1, and SCNN1, compared to the R group (Figure 1F). Furthermore, when correlating spatial transcriptomic data with histomorphological features, we observed that crypt distortion and atrophy were significantly more pronounced in the non-R group than in the R group in the preTx biopsy samples (Figures 1G and 1H). Conclusion Our study's spatial profiling unveils distinct molecular and histologic features between R and non-R to TNFi among bio-naive UC patients. The evaluation of chronic histological features such as crypt distortion, and molecular maturation status, in predicting TNFi response highlights the potential of early histologic assessment in guiding biologic therapy in the UC treatment pathway.

Does Size Matter? Small and Large Larvae of Pikeperch (Sander lucioperca) in a Comparative Gene Expression Analysis

Size differences are common in the aquaculture of fishes. In the larviculture of cannibalistic species such as pikeperch, they majorly influence mortality rates and consequently provoke losses in the aquaculture industry. With this study, we aim to reveal molecular differences between small and large pikeperch of the same age using a set of 20 genes associated with essential developmental processes. Hereby, we applied a general study design to early and late larval pikeperch before the onset of piscivory to explore the causes of growth differences in these developmental groups. The analysis of the expression levels showed developmental but not size-related differences in PGC1A, TGFB1, MYOD1, MRF4, and the collagens COL1A1 and COL1A2. Furthermore, increased head lengths were found in larger late larvae compared to their smaller conspecifics. While no uniquely size-related expression differences were found, the expression patterns of PGC1A in combination with TGFB1 as regulators of the citric acid cycle indicate a possible influence of mitochondrial energy metabolism. Furthermore, expression differences of MYOD1 and MRF4 point out possible temporal advantages of myogenetic processes in the larger late larval group and hypothesise growth advantages of the larger late larvae resulting from various influences, which provide a promising target for future research.

Identification of common and specific fibrosis-related genes in three common chronic kidney diseases

Background Kidney fibrosis is the common final pathway of virtually all advanced forms of chronic kidney disease (CKD) including diabetic nephropathy (DN), IgA nephropathy (IgAN) and membranous nephropathy (MN), with complex mechanism. Comparative gene expression analysis among these types of CKD may shed light on its pathogenesis. Therefore, we conducted this study aiming at exploring the common and specific fibrosis-related genes involved in different types of CKD. Methods Kidney biopsy specimens from patients with different types of CKD and normal control subjects were analyzed using the NanoString nCounter® Human Fibrosis V2 Panel. Genes differentially expressed in all fibrotic DN, IgAN and MN tissues compared to the normal controls were regarded as the common fibrosis-related genes in CKD, whereas genes exclusively differentially expressed in fibrotic DN, IgAN or MN samples were considered to be the specific genes related to fibrosis in DN, IgAN and MN respectively. Quantitative real-time PCR (qRT-PCR) was performed to validate the expression of the selected genes. Results Protein tyrosine phosphatase receptor type C (PTPRC), intercellular cell adhesion molecule-1 (ICAM1), vascular cell adhesion molecule-1 (VCAM1), interleukin 10 receptor alpha (IL10RA) and CC chemokine receptor 2 (CCR2) were identified as the potential common genes for kidney fibrosis in different types of CKD, while peroxisome proliferator-activated receptor alpha (PPARA), lactate oxidase (LOX), secreted phosphoprotein 1 (SPP1) were identified as the specific fibrosis-associated genes for DN, IgAN and MN respectively. qRT-PCR demonstrated that the expression levels of these selected genes were consistent with the NanoString analysis. Conclusions There were both commonalities and differences in the mechanisms of fibrosis in different types of CKD, the commonalities might be used as the common therapeutic targets for kidney fibrosis in CKD, while the differences might be used as the diagnostic markers for DN, IgAN and MN respectively. Inflammation was highly relevant to the pathogenesis of fibrosis. This study provides further insight into the pathophysiology and treatment of fibrotic kidney disease.

Expression of RASSF1A, DIRAS3, and AKAP9 Genes in Thyroid Lesions: Implications for Differential Diagnosis and Prognosis of Thyroid Carcinomas.

Thyroid carcinoma is the primary endocrine malignancy worldwide. The preoperative examination of thyroid tissue lesion is often unclear. Approximately 25% of thyroid cancers cannot be diagnosed definitively without post-surgery histopathological examination. The assessment of diagnostic and differential markers of thyroid cancers is needed to improve preoperative diagnosis and reduce unnecessary treatments. Here, we assessed the expression of RASSF1A, DIRAS3, and AKAP9 genes, and the presence of BRAF V600E point mutation in benign and malignant thyroid lesions in a Polish cohort (120 patients). We have also performed a comparative analysis of gene expression using data obtained from the Gene Expression Omnibus (GEO) database (307 samples). The expression of RASSF1A and DIRAS3 was decreased, whereas AKAP9's was increased in pathologically changed thyroid compared with normal thyroid tissue, and significantly correlated with e.g., histopathological type of lesion papillary thyroid cancer (PTC) vs follicular thyroid cancer (FTC), patient's age, tumour stage, or its encapsulation. The receiver operating characteristic (ROC) analysis for the more aggressive FTC subtype differential marker suggests value in estimating RASSF1A and AKAP9 expression, with their area under curve (AUC), specificity, and sensitivity at 0.743 (95% CI: 0.548-0.938), 82.2%, and 66.7%; for RASSF1A, and 0.848 (95% CI: 0.698-0.998), 54.8%, and 100%, for AKAP9. Our research gives new insight into the basis of the aggressiveness and progression of thyroid cancers, and provides information on potential differential markers that may improve preoperative diagnosis.

Fibroblast Growth Factor 23 is a Potential Prognostic Biomarker in Uterine Sarcoma.

Uterine sarcoma (US) is a highly malignant cancer with poor prognosis and high mortality in women. In this study, we evaluated the expression of human fibroblast growth factor 23 (FGF23) in different US subtypes and the relationship between survival and clinicopathological characteristics. We conducted a comparative analysis of FGF23 gene expression in different pathological types of US. Utilizing a cohort from The Cancer Genome Atlas of 57 patients, a 50-patient microarray dataset (GSE119043) from the Gene Expression Omnibus and a Suining cohort of 44 patients, we analyzed gene expression profiles and corresponding clinicopathological information. Immunohistochemistry was used to examine the expression level of FGF23 in four US subtypes. Survival analysis was used to assess the relationship between FGF23 expression and prognosis in US patients. Compared with uterine normal smooth muscle and uterine leiomyoma, FGF23 expression was significantly upregulated in US and was differentially expressed in four US subtypes. Uterine carcinosarcoma exhibited the highest expression of FGF23 among the subtypes. Survival analysis revealed no correlation between FGF23 expression and either overall survival or progression-free survival in US (P > 0.05). Similar results were obtained from the validation cohorts. Univariate and multivariate analyses showed no significant correlation between FGF23 expression and the US prognosis. Tumor stage, CA125, and tumor recurrence were independent prognostic factors for survival of US patients. FGF23 was highly expressed in US and was promising as a novel potential biomarker for the diagnosis and prognosis of US.

Comparative analyses of erythroblast transformation specific-1 related gene expression before and after neoadjuvant bevacizumab therapy for newly diagnosed glioblastoma

Comparative analyses of erythroblast transformation specific-1 related gene expression before and after neoadjuvant bevacizumab therapy for newly diagnosed glioblastoma

Comparative Gene-Expression Analysis of the Ligamentum Flavum of Patients with Lumbar Spinal Canal Stenosis: Comparison between the Dural and Dorsal Sides of the Thickened Ligamentum Flavum.

Thickening of the ligamentum flavum is the main factor in the development of lumbar spinal canal stenosis (LSCS). Although previous studies have reported factors related to ligamentum flavum thickening, its etiology has not been clarified. Furthermore, it is often difficult to set proper controls to investigate the pathologies of thickening due to differences in patient characteristics, such as age, sex, obesity, and comorbidities. This study aimed to elucidate the pathologies of ligamentum flavum thickening by comparing the dural and dorsal sides of the thickened ligamentum flavum in patients with LSCS. Ligamentum flavum samples were collected from 19 patients with LSCS. The samples were divided into the dural and dorsal sides. The dural side was used as a control to assess the pathologies occurring on the dorsal side. Elastic Masson staining was used to assess the elastic fibres. Gene expression levels were comprehensively assessed using quantitative reverse transcription polymerase chain reaction and DNA microarray analyses. Gene ontology analysis was used to identify biological processes associated with differentially expressed genes. The elastic fibres were significantly decreased on the dorsal side of the thickened ligamentum flavum. Genes related to fibrosis, inflammation, tissue repair, remodeling, and chondrometaplasia, such as COL1A2, COL3A1, COL5A1, TGFB1, VEGFA, TNFA, MMP2, COL10A1, and ADAMTS4, were highly expressed on the dorsal side of the thickened ligamentum flavum. The biological processes occurring on the dorsal side of the thickened ligamentum flavum were extracellular matrix organization, cell adhesion, extracellular matrix disassembly, and proteolysis.These are considered important pathologies of ligamentum flavum thickening.

Exploring the mechanism of blindness physiopathy in Brassica oleracea var italica L. by comprehensive transcriptomics and metabolomics analysis

Blindness is a physiopathy characterized by apical abortion that particularly affects the Brassica family. The occurrence of blindness has been related to exposure to low temperatures during early developmental stages. However, the causes of this selective sensitivity and how they affect the correct development remain unknown. In this study, we investigated the mechanisms involved in the occurrence of blindness in broccoli plants. The analysis of RNAseq, focused on membrane transporters and the synthesis pathways of glucosinolates and phenolics, was related with physiological changes in nutrient and water uptake, gas exchange, and metabolism. Comparative gene expression analysis between control and blindness-affected broccoli plants revealed distinct regulation patterns in roots and shoots, leading to reduced synthesis of glucosinolates and phenolics. Additionally, the expression levels of aquaporins and potassium transporters were found to be associated with mineral and water transport. In this way, our results revealed the causes of blindness by identifying differentially expressed genes, highlighting those related to secondary metabolism, as well as genes involved in water and nutrient uptake and transport as the crucial involved in the physiopathy appearance.

Comparative Transcriptome Analysis of Gene Expression and Regulatory Characteristics Associated with Different Bolting Periods in Spinacia oleracea.

Bolting is a symbol of the transition from vegetative to reproductive growth in plants. Late bolting can effectively prolong the commercial value of spinach and is of great importance for spinach breeding. Bolting has complex regulatory networks, and current research on spinach bolting is relatively weak, with specific regulatory pathways and genes unclear. To clarify the regulatory characteristics and key genes related to bolting in spinach, we conducted a comparative transcriptome analysis. In this study, 18 samples from three periods of bolting-tolerant spinach material 12S3 and bolting-susceptible material 12S4 were analyzed using RNA-seq on, resulting in 10,693 differentially expressed genes (DEGs). Functional enrichment and co-expression trend analysis indicated that most DEGs were enriched in the photoperiod pathway, the hormone signaling pathway, and the cutin, suberin, and wax biosynthetic pathways. According to the weighted gene co-expression network analysis (WGCNA), SpFT (SOV4g003400), SOV4g040250, and SpGASA1 (SOV6g017600) were likely to regulate bolting through the gibberellin and photoperiod pathways, and SpELF4 (SOV1g028600) and SpPAT1 (SOV4g058860) caused differences in early and late bolting among different cultivars. These results provide important insights into the genetic control of bolting in spinach and will help elucidate the molecular mechanisms of bolting in leafy vegetables.

Gene expression plasticity facilitates different host feeding in Ips sexdentatus (Coleoptera: Curculionidae: Scolytinae)

Host shift is ecologically advantageous and a crucial driver for herbivore insect speciation. Insects on the non-native host obtain enemy-free space and confront reduced competition, but they must adapt to survive. Such signatures of adaptations can often be detected at the gene expression level. It is astonishing how bark beetles cope with distinct chemical environments while feeding on various conifers. Hence, we aim to disentangle the six-toothed bark beetle (Ips sexdentatus) response against two different conifer defences upon host shift (Scots pine to Norway spruce). We conducted bioassay and metabolomic analysis followed by RNA-seq experiments to comprehend the beetle’s ability to surpass two different terpene-based conifer defence systems. Beetle growth rate and fecundity were increased when reared exclusively on spruce logs (alternative host) compared to pine logs (native host). Comparative gene expression analysis identified differentially expressed genes (DEGs) related to digestion, detoxification, transporter activity, growth, signalling, and stress response in the spruce-feeding beetle gut. Transporter genes were highly abundant during spruce feeding, suggesting they could play a role in pumping a wide variety of endogenous and xenobiotic compounds or allelochemicals out. Trehalose transporter (TRET) is also up-regulated in the spruce-fed beetle gut to maintain homeostasis and stress tolerance. RT-qPCR and enzymatic assays further corroborated some of our findings. Taken together, the transcriptional plasticity of key physiological genes plays a crucial role after the host shift and provides vital clues for the adaptive potential of bark beetles on different conifer hosts.

Comparative gene expression and pathway analysis of neuroendocrine neoplasms in relation to clinical outcomes and tumor location

Comparative gene expression and pathway analysis of neuroendocrine neoplasms in relation to clinical outcomes and tumor location

PEO: Plant Expression Omnibus - a comparative transcriptomic database for 103 Archaeplastida.

The Plant Expression Omnibus (PEO) is a web application that provides biologists with access to gene expression insights across over 100 plant species, ~60 000 manually annotated RNA-seq samples, and more than 4 million genes. The tool allows users to explore the expression patterns of genes across different organs, identify organ-specific genes, and discover top co-expressed genes for any gene of interest. PEO also provides functional annotations for each gene, allowing for the identification of genetic modules and pathways. PEO is designed to facilitate comparative kingdom-wide gene expression analysis and provide a valuable resource for plant biology research. We provide two case studies to demonstrate the utility of PEO in identifying candidate genes in pollen coat biosynthesis in Arabidopsis and investigating the biosynthetic pathway components of capsaicin in Capsicum annuum. The database is freely available at https://expression.plant.tools/.