Transcriptome Expression Profiles Research Articles

Undifferentiated Melanoma: A Clinicopathologic and Gene Expression Analysis Study With Identification of HMGA2 as a Diagnostic Marker.

Undifferentiated melanoma poses a unique diagnostic challenge as, by definition, it lacks expression of the melanocytic markers S100 protein, Sox10, Mart1, and HMB45. Despite this aberrant phenotype, undifferentiated melanoma is characterized by known melanoma driver alterations, including BRAF and NRAS mutations. Due to variable morphologic features and a lack of melanocytic differentiation, molecular diagnostics are often required for the identification of melanoma-compatible driver alterations to support the diagnosis. Here, we describe a cohort of 27 undifferentiated melanomas and employ gene expression profiling to compare undifferentiated melanoma to conventional melanoma in both matched cases arising in the same patients and unmatched cases. The histologic spectrum of undifferentiated melanoma was variable and included tumors composed of epithelioid, spindled, pleomorphic, rhabdoid and balloon cells, often with necrosis. Notably, a subset of undifferentiated melanomas demonstrated a prominent stroma, including myxoid and vascular components. We demonstrate that the histologic category is the main determinant of differential gene expression between conventional and undifferentiated melanoma. In addition, undifferentiated melanomas show several significantly upregulated gene expression pathways, including those associated with epithelial-mesenchymal transition. These data provide novel insights into the transcriptomic expression profile of undifferentiated melanoma and offer potential explanations for the unusual phenotype. Notably, HMGA2 was found to be the most significantly up-regulated gene in the undifferentiated melanoma cohort, with immunohistochemical studies demonstrating that HMGA2 is a sensitive and specific marker for the diagnosis of undifferentiated melanoma and for its distinction from mimics which show overlapping morphologic features and lack melanocytic differentiation.

Palmitoylation regulators drive the progression of clear cell renal cell carcinoma through Inhibition of cuproptosis: insights into the role of ZDHHC18

BackgroundProtein palmitoylation is a reversible post-translational modification that increases protein hydrophobicity, which can affect protein localization, stability, and function. Although palmitoylation is frequently observed in various cancers, the specific mechanisms by which it influences clear cell renal cell carcinoma (ccRCC) are still not well understood.MethodsThis study used transcriptome expression profiles and clinical characteristics of clear cell renal cell carcinoma (ccRCC) obtained from The Cancer Genome Atlas (TCGA) and the Gene Expression Omnibus (GEO) databases. Kaplan-Meier (KM) survival analysis was performed to evaluate patient survival. Consensus clustering was applied to identify tumor palmitoylation patterns. A total of 101 different machine learning methods were used to develop predictive models. Functional enrichment analyses were conducted using Gene Ontology (GO) analysis, Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis, and Gene Set Variation Analysis (GSVA).ResultsOf the 34 prognosis-related palmitoylation-related genes (PRGs), 29 were used to cluster patients in the TCGA-KIRC cohort, leading to the identification of four palmitoylation clusters. We developed a risk model and a nomogram based on palmitoylation scores to enhance risk classification. Functional analysis indicated that high-risk patients exhibited disrupted fatty acid metabolism. Correlation analysis identified ZDHHC18 as a potential hub gene associated with impaired fatty acid metabolism and cuproptosis. Finally, we validated the role of ZDHHC18 in ccRCC proliferation through in vitro experiments.ConclusionOur research demonstrated that PRGs play a crucial role in the development of clear cell renal cell carcinoma (ccRCC). A nomogram based on palmitoylation scores may accurately predict the prognosis of ccRCC patients. Furthermore, the palmitoylation regulator ZDHHC18 affects cuproptosis in ccRCC, which in turn impacts patient survival.

Comparative Analysis of ICS Combined with LABA versus Addition of Omalizumab on Transcriptomic Expression Profiles in Patients with Allergic Asthma

IntroductionAsthma causes airway inflammation, leading to symptoms that impair patients’ quality of life, making it a significant global public health issue. Inhaled corticosteroids (ICS) with long-acting beta-agonists therapy (LABA) is commonly used to manage moderate to severe asthma. For patients unresponsive to ICS with LABA, omalizumab may be added to improve asthma control. Understanding transcriptomic expressions is crucial as it provides insights into the molecular mechanisms underlying treatment. However, the impact of omalizumab on transcriptomic expressions remains unclear. Therefore, this study aims to investigate the transcriptomic expression profiles and clinical outcomes between patients receiving ICS with LABA therapy and those adding omalizumab.Materials and MethodsThis is a prospective, real-world study that enrolled 26 participants, divided into three groups: Group 1, ICS with LABA (n=10); Group 2, ICS with LABA plus omalizumab (n=12); and Group 3, healthy controls (n=4). Assessments included transcriptomic expression profiles, and bioinformatics analysis, IgE, airborne allergen test, pulmonary function test, blood tests, and asthma control test (ACT).ResultsACT scores were significantly higher in Group 1 and 2 compared to Group 3. IgE levels, dust mite sensitivity, and dynamic pulmonary function changes after bronchodilator administration were notably higher in Group 2. In these patients, down-regulated genes included those related to immune response, NOD-like receptor signaling, RIG-I signaling, IL-17 signaling, and antioxidant activity. Conversely, up-regulated genes were found in the cGMP-PKG signaling pathway, cardiomyopathy-related pathways, and voltage-gated calcium channel activity.ConclusionPatients receiving ICS with LABA plus omalizumab still exhibited more dynamic airway changes and higher IgE levels. Downregulation of immune and inflammatory pathways suggests its potential as an add-on treatment for severe asthma. However, upregulated genes were observed in the cGMP-PKG signaling pathway, cardiomyopathy-related pathways, and voltage-gated calcium channel activity.

Placental whole transcriptome expression profile in patients with early-onset, late-onset preeclampsia and gestational diabetes mellitus

Preeclampsia (PE) and gestational diabetes mellitus (GDM) are significant pregnancy complications with complex pathogenesis. Therefore, we conducted a comprehensive investigation using whole-transcriptome sequencing of placental samples. The results revealed dysregulation of key pathways in early-onset-PE (OE-PE), including Wnt signaling, PI3K-Akt signaling, MAPK signaling, FoxO signaling, and TNF signaling, along with downregulation of genes related to Ca2 + conduction and hormone pathways. In late-onset-PE (LO-PE) and GDM, abnormalities were observed in immune pathways including chemokine signaling pathway and IL-17 signaling pathway, with differing immune cell infiltration patterns. EO-PE was associated with reduced T cells and B cells, while LO-PE had increased plasmacytoid dendritic and CD56bright natural killer cells. In GDM, a notable increase in the infiltration of various immune cells— including central memory CD8 T cells, monocytes, B cells, T cells, and central memory CD4 T cells — was observed. Additionally, downregulation of HLA-A and HLA-F, particularly in EO-PE, suggests immune dysregulation. CCL26-has-miR-618-has-circ-0001776 could potentially contribute to the progression of EO-PE, while CREB1-has-miR-373-3p-has-circ-0003793/has-circ-0001146 may be implicated in the LO-PE development. Additionally, GZMB-has-miR-199a-5p/has-miR-199b-5p-has-circ-0008959/novel-circ_0008792 may mediate the disease progression of GDM. In summary, genes related to placental cell functions are inhibited in PE, while autoimmune abnormalities may play a role in LO-PE and GDM pathogenesis.

Transcriptomic Insights and Quantification of Free Amino Acids in Auricularia heimuer Cultivated on Corncob Substrate

Substrate type exerts a critical influence on the growth, development, and nutritional quality of Auricularia heimuer. In this study, agricultural waste-derived corncob was used as the treatment group (T1), with sawdust serving as the control (CK), to systematically investigate the variation in free amino acid (FAA) content and transcriptomic expression profiles in fruiting bodies of A. heimuer under the two substrate conditions. Principal component analysis (PCA) revealed a clear separation between CK and T1 samples in terms of FAA composition, indicating that substrate type significantly affects FAA profiles. The corncob substrate notably increased the total FAA content in A. heimuer (2624.57 mg/kg), representing an 11.4% elevation compared to the sawdust group (2355.86 mg/kg), and markedly enhanced the proportion of flavor-associated amino acids (49.2% vs. 42.6%). In particular, the umami amino acid content was 74% higher than in the CK group. Transcriptome analysis identified 20 differentially expressed genes associated with FAA biosynthesis and degradation, including key enzymes involved in umami amino acid metabolism, such as aspartate decarboxylase (ADC), glutamate decarboxylase (GAD), and glutamate N-acetyltransferase (GNA), which were downregulated in T1. This suggests that glutamate and aspartate may have accumulated due to suppressed catabolism. KEGG (Kyoto Encyclopedia of Genes and Genomes) pathway enrichment analysis further indicated that the differentially expressed genes were significantly enriched in pathways related to branched-chain amino acid metabolism, carbon metabolism, and secondary metabolism. Collectively, these findings demonstrate that corncob substrate significantly alters the accumulation and metabolic profile of FAAs in A. heimuer by modulating the expression of key metabolic enzymes, providing a theoretical foundation for the efficient cultivation of A. heimuer using agricultural waste and for enhancing its flavor quality.

Comparative transcriptomic analysis reveals the reactive oxygen species metabolism involving in melatonin-alleviated chilling injury in postharvest banana fruit.

Comparative transcriptomic analysis reveals the reactive oxygen species metabolism involving in melatonin-alleviated chilling injury in postharvest banana fruit.

Identification of Mitochondrial and Succinylation Modification-Related Gene Signature in Ischemic Stroke.

Ischemic stroke (IS) is a leading cause of death and disability worldwide, often associated with immune dysregulation, mitochondrial dysfunction, and altered protein succinylation. This study aimed to identify mitochondrial and succinylation-related gene signatures with diagnostic potential in IS. Differentially expressed genes (DEGs) associated with IS were identified using transcriptome expression profiles from merged GSE16561 and GSE58294 GEO datasets. Functional enrichment and WGCNA identified hub genes. Mitochondrial and succinylation-related gene expression was assessed via ssGSEA. Feature genes were selected using machine learning. A prognostic nomogram was constructed. PPI networks were generated using GeneMANIA. Immune infiltration was assessed through ssGSEA. Drug-gene interactions were explored using DGIdb. qRT-PCR validation was performed on blood samples from IS patients and controls. We identified 317 DEGs enriched in immune response and inflammation pathways in 108 IS patients and 47 healthy controls using data from the merged datasets. WGCNA identified 101 hub genes in the yellow module and 65 in the brown module. Seven overlapping genes related to mitochondrial and succinylation processes were identified. Feature gene analysis revealed six key genes (MRPL41, NGRN, SLC25A42, SPTLC2, TUBB, and TXN) with robust diagnostic potential across both the merged and individual datasets (all AUCs > 0.7). Nomogram integration demonstrated predictive reliability. Feature genes exhibited significant correlations with immune cell infiltration. qRT-PCR validation confirmed the differential expression of four feature genes. TUBB and TXN showed interactions with various drugs. Mitochondrial and succinylation-related genes have diagnostic significance in IS, providing insights into disease pathogenesis and clinical applications.

Abstract 6605: Spatially-resolved single-cell transcriptome landscape of response and resistance to CDK4/6 inhibitors in patients with hormone receptor-positive metastatic breast cancer

Abstract Cyclin-dependent kinase 4/6 inhibitors (CDK4/6i) have significantly improved the treatment of hormone receptor (HR+) positive breast cancer. Clinical trials have demonstrated that addition of CDK4/6i to endocrine therapy (ET) improves both progression-free and overall survival in patients with HR+ metastatic breast cancer (MBC). Nevertheless, their impact remains limited by the eventual development of resistance. While a number of resistance mechanisms have been identified using both preclinical model systems and translational interrogation of patient specimens, these are not apparent in all cases. As part of the Human Tumor Atlas Network, we integrated genomic (whole-exome sequencing; n=47), single-nucleus transcriptomic (snRNA-seq; n=56), and spatial expression profiling (MERFISH and multiplex immunofluorescence; n=22 and n=17, respectively) from 58 clinically annotated MBC biopsy specimens collected before or after treatment with CDK4/6i plus ET to dissect the roles of tumor-intrinsic programs and the tumor microenvironment (TME) in CDK4/6i resistance. Transcriptomic analysis of the tumor cell compartment with snRNA-seq not only extended prior findings including an association between expression of cell-cycle programs and CDK4/6i resistance, but importantly identified additional programs associated with response and resistance including ciliogenesis, immune evasion, and inflammation. Additionally, tumor-intrinsic gene programs related to epithelial-to-mesenchymal transition had a decreased activity in ESR1 mutant biopsies, a mutational feature of CDK4/6i-resistant MBC associated with upregulated estrogen receptor pathway activity. In the TME, CD8+ T cells were depleted in the CDK4/6i-resistant biopsies, both before and after treatment. In contrast, the CDK4/6i-sensitive biopsies displayed pro-inflammatory features including an increased number of CXCL9+/CXCL10+ macrophages and clustering of CD8+ T cells in the vicinity of the malignant cells spatially. Notably, MERFISH also demonstrated an association between spatial architecture and CDK4/6i response, with the malignant cells in the CDK4/6i-resistant biopsies dispersed spatially compared to the sensitive biopsies. In summary, to the best of our knowledge, this study represents the largest spatially-resolved single-cell MBC cohort with curated CDK4/6i response status established to date. Our findings offer insights into potential biomarkers for CDK4/6i response based on tumor-intrinsic and tumor-microenvironment mechanisms, as well as therapeutic opportunities. Citation Format: Junko Tsuji, Jorge Gómez Tejeda Zañudo, Timothy R. Blosser, Ha T. Vu, Danielle Firer, Nick Maus, Kathleen L. Pfaff, Billie A. Porter, Jason L. Weirather, Anne Carlisle, Allison M. Frangieh, Elliot Boblitt, Aaron R. Thorner, Karla E. Helvie, Isabella E. Kallassy, Laura K. DelloStritto, Ragnhild Laursen, François Aguet, Mendy Miller, Melissa E. Hughes, Nancy U. Lin, Sara M. Tolaney, Eliezer M. Van Allen, Samouil L. Farhi, Xiaowei Zhuang, Barbara Engelhardt, Scott J. Rodig, Alex K. Shalek, Aviv Regev, Bruce E. Johnson, Nikhil Wagle, Gad Getz, Daniel L. Abravanel. Spatially-resolved single-cell transcriptome landscape of response and resistance to CDK4/6 inhibitors in patients with hormone receptor-positive metastatic breast cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2025; Part 1 (Regular Abstracts); 2025 Apr 25-30; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2025;85(8_Suppl_1):Abstract nr 6605.

Abstract 2895: Efficacy of DNA-PK inhibitor as maintenance strategy after cisplatin induction in SCLC

Abstract Given the aggressive nature of small cell lung cancer (SCLC) and the frequent relapse after initial chemotherapy, this work aims to identify novel approaches to enhance the immune response. DNA-dependent protein kinase (DNA-PK) is a targetable enzyme involved in non-homologous end joining (NHEJ) and antiviral responses. DNA-PK plays a role during cGAS/STING dependent and independent viral DNA sensing pathway. Thus, we investigated the role of DNA-PK inhibition (DNA-PKi) as a maintenance strategy following cisplatin treatment in SCLC patients, focusing on its ability to enhance antitumor immune responses. We included different models of SCLC, in particular SCLC patient-derived peripheral blood mononuclear cells (PBMCs), SCLC cell lines and cocultures of PBMCs with SCLC cells and SCLC tumor spheroids. SCLC cells were treated in vitro with low-dose cisplatin (0.5 µM), and blood was collected from SCLC patients on day 3 of cisplatin treatment. SCLC cells and PBMCs were subjected to transcriptomic sequencing and gene expression profiling to assess the effect of DNA-PKi on PBMC subsets (CD8+ T cells, NK cells and monocytes). Gene set enrichment analysis (GSEA) of RNA-seq data revealed that cisplatin treatment enriched several DDR pathways and upregulated immune-related pathways in both SCLC cell lines and patient-derived PBMCs. Sequential treatment with DNA-PKi after cisplatin significantly activated CD8+ T-cell and NK-cell pathways, as well as enhancing interferon-related pathways and gene signatures associated with viral infections. In vitro treatment with DNA-PKi resulted in increased expression of pro-inflammatory markers in PBMCs, promoting M1 polarization of macrophages (TNF-α, IL-6 and CXCL10) while inhibiting M2 polarization (IL-10, IL4 and CCL22). This shift towards an anti-tumor phenotype was confirmed by enhanced NK cell-mediated cytotoxicity against SCLC cell lines. In addition, combination therapy with DNA-PKi and anti-PD-L1 resulted in increased immune cell infiltration into tumor spheroids, demonstrating a synergistic effect on anti-tumor immunity. In conclusion, our data suggests that DNA-PKi may improve immune responsiveness and potentially prolong antitumor effects in SCLC patients. Future investigations are warranted to further elucidate these mechanisms and to evaluate the clinical applicability of DNA-PKi in combination with existing therapies for SCLC. Citation Format: Luisa Amato, Caterina De Rosa, Concetta Tuccillo, Francesca Iommelli, Viviana De Rosa, Virginia Tirino, Federica Papaccio, Kavya Ramkumar, Qi Wang, Jing Wang, Alberto Servetto, Floriana Morgillo, Lauren Averett Byers, Fortunato Ciardiello, Carminia Maria Della Corte. Efficacy of DNA-PK inhibitor as maintenance strategy after cisplatin induction in SCLC [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2025; Part 1 (Regular Abstracts); 2025 Apr 25-30; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2025;85(8_Suppl_1):Abstract nr 2895.

Abstract 2931: AXL-directed surface targeting approaches in recalcitrant pulmonary high-grade neuroendocrine carcinomas

High-grade neuroendocrine carcinomas of the lung (hgNECs), which include small cell lung cancer (SCLC) and pulmonary large-cell neuroendocrine carcinoma (LCNEC), are characterized by poor prognoses, limited treatment options and rapid emergence of resistance. While recent surfaceome-directed approaches targeting DLL3, SEZ6, and TROP2 using chimeric antigen receptor T cells (CAR-Ts), bispecific T cell engagers (BiTEs) and antibody drug conjugates (ADCs) show considerable promise in hgNECs, novel strategies to target the heterogenous resistant disease are needed. AXL, a TAM family receptor tyrosine kinase, is known to mediate resistance to chemotherapy, radiation and targeted therapies in SCLC and other cancers, through its roles in epithelial to mesenchymal transition (EMT), DNA damage repair and replication stress tolerance. We hypothesize that targeting cell surface AXL would provide an effective therapeutic strategy in hgNECs, especially for relapsed disease. We analyzed the transcriptomic (bulk and single-cell RNA sequencing) and proteomic (immunohistochemistry) expression profiles of AXL in treatment-naïve and relapsed SCLC, LCNEC and other extrapulmonary hgNECs patient tumors. High levels of AXL expression were seen in distinct tumor subsets. Notably, AXL-high tumors exhibited molecular signatures associated with resistance (higher EMT scores, lower replication stress and cisplatin response). To evaluate AXL as a viable surface target in hgNECs, we generated a preclinical CAR T cell against AXL. Anti-AXL CAR T cells were effective at inducing cytotoxicity in AXL-expressing SCLC and LCNEC cell lines. Similarly, an anti-AXL ADC also showed selective and potent cytotoxicity in AXL-positive models. These findings establish AXL as both a valuable biomarker and a promising target for the drug-resistant hgNECs, supporting the development of AXL-directed therapeutics such as anti-AXL CAR T cells and anti-AXL ADCs. Citation Format: Kavya Ramkumar, C. Allison Stewart, Yan Yang, Bingnan Zhang, Qi Wang, Yuanxin Xi, Runsheng Wang, Alejandra G. Serrano, Luisa M. Solis Soto, Jing Wang, John V. Heymach, Carl M. Gay, Lauren A. Byers. AXL-directed surface targeting approaches in recalcitrant pulmonary high-grade neuroendocrine carcinomas [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2025; Part 1 (Regular Abstracts); 2025 Apr 25-30; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2025;85(8_Suppl_1):Abstract nr 2931.

Integration Analysis of Circle-Sequencing and Transcriptome Reveals Extrachromosomal Circular DNA Is Involved in the Regulation of Vascular Cambium Annual Cycle in Chinese Pine.

Extrachromosomal circular DNA (eccDNA) has been reported to play important roles in regulating genome replication, immune response and cellular communications in humans and animals. Recently, the presence of eccDNA has also recently been discovered in Arabidopsis, Amaranthus palmeri and Oryza sativa. Nevertheless, whether eccDNA exists and has roles in woody plants remains enigmatic. Here, we conducted a comprehensive analysis of morphological imaging, transcriptome and eccDNA expression profiles during different development stages of vascular cambium in Chinese pine (Pinus tabuliformis (P. tabuliformis)). It was found that eccDNA existed in the different development stages of vascular cambium and derived from each chromosome of P. tabuliformis. Further analysis revealed that eccDNA was not entirely random but rather exhibited a certain preference in exon regions. We also identified a high frequency of AA/AT/TT/TA dinucleotide repeats at the junctions of eccDNA and found that the length distribution of eccDNA was clustered between 158 and 316 bp. Notably, integration analysis revealed that differentially expressed eccDNAs and their annotated genes exhibited more significant dynamic changes in the dormant stage as compared with other stages. Taken together, our results provide new insights into the important mechanisms by which eccDNA influences vascular cambium development, enhancing our understanding of its role in tree plasticity.

Differential expression and correlation analysis of global transcriptome for obstructive sleep apnea hypopnea syndrome.

In order to investigate the gene expression patterns and molecular regulatory mechanisms of obstructive sleep apnea hypopnea syndrome (OSAHS), the global transcriptome expression profiles of OSAHS patients and healthy people were analyzed using transcriptome sequencing technology. Differential expression of circular RNA, microRNA, long noncoding RNA, and messenger RNA was investigated between the two groups. To further explore the role of differentially expressed genes in OSAHS, we functionally annotated the differentially expressed genes using enrichment analysis of GO and KEGG pathways. Finally, the ceRNA regulatory network of OSAHS was constructed. And validate the differentially expressed mRNA through qRT-PCR analysis. The results showed that 349 circRNAs,552 lncRNAs,205 miRNAs, 502 mRNAs were differentially expressed in patients with OSAHS compared with the healthy population. Terms such as centrosome, positive regulation of execution phase of apoptosis, oxidoreductase activity, regulation of Th 17 cell differentiation and immune response, neutrophil mediated cytotoxicity were enriched in the GO list, suggesting a potential correlation with OSAHS. Pathway analysis showed that Ferroptosis, Herpes simplex virus 1 infection, Pathways in cancer, Hematopoietic cell lineage and other pathways play an important role in OSAHS. By constructing a ternary network, two circRNAs and four lncRNAs were screened as ceRNAs to compete with miRNAs in the co-expression network, and associated with OSAHS by regulating the function of mRNAs in the network. By constructing a quaternary network miR-8485 and miR-6089 were found to be the top two ranked miRNAs most closely associated with OSAHS. Both qRT-PCR and transcriptome sequencing analysis showed similar trends. This provides more theoretical basis for exploring the complex molecular mechanisms of global transcriptome in the development of OSAHS.

Transcriptome analysis reveals the key roles of TaSMP1 and ABA signaling pathway in wheat seed dormancy and germination.

This study analyzed dynamic transcriptome profiles to reveal differential expression patterns of ABA related and LEA protein family genes and verified that TaSMP1 affects seed germination by interacting with TaABI5. Seed dormancy is a crucial survival strategy for plants to cope with environmental stresses. High levels of seed dormancy result in uneven germination, while low levels of seed dormancy increase the risk of pre-harvest sprouting (PHS), which threatens crop yield and quality. Therefore, achieving the optimal balance between seed dormancy and germination is vital for maximum potential crop yield and quality. This study constructed dynamic transcriptome expression profiles of the germination process for the weakly dormant wheat variety Jing 411 (J411) and the strongly dormant landrace variety Hongsuibai (HSB), revealing the temporal expression of differentially expressed genes. Plant hormone-related genes played a crucial role in the early germination response, particularly the abscisic acid (ABA) signaling gene TaABI5 and the ABA catabolism gene TaCYP707A1. The late embryogenesis abundant (LEA) protein family genes exhibited differential expression patterns during the germination of seeds with varying levels of dormancy. The TaSMP1 gene, a member of the LEA protein family, was identified as a negative regulator of seed dormancy, interacting directly with the key transcription factor TaABI5 in the ABA signaling pathway and influencing the expression of the seed germination gene TaDOG1L1. This study provides essential insights into the molecular mechanisms balancing seed dormancy and germination, offering potential targets for enhancing wheat resistance to PHS.

Functional validation to explore the protective role of miR-223 in Staphylococcus aureus-induced bovine mastitis

BackgroundMastitis caused by Staphylococcus aureus (S. aureus) is one of the most intractable problems for the dairy industry, causing significantly reduced milk yields and early slaughter of cows worldwide. MicroRNAs (miRNAs) can post-transcriptionally regulate gene expression and studies in recent years have shown the importance of miRNA-associated gene regulation in S. aureus-induced mastitis.ResultsIn this study, to investigate the role of miR-223 in mastitis, we performed experiments to overexpress and suppress miR-223 in an immortalized bovine mammary epithelial cell line (MAC-T) infected with S. aureus. Overexpression of miR-223 in MAC-T cells repressed cell apoptosis and necrosis induced by S. aureus infection, whereas suppression of miR-223 had the opposite effect. Transcriptome expression profiling with weighted gene co-expression network analysis (WGCNA) and gene set variation analysis (GSVA) showed that miR-223 affects apoptosis and inflammation-related pathways. Furthermore, differentially expressed (DE) genes were evaluated, and genes exhibiting contrasting expression trends in the miR-223 overexpressed and suppressed groups were assessed as potential target genes of miR-223. Potential target genes, including CDC25B, PTPRF, DCTN1, and DPP9, were observed to be associated with apoptosis and necroptosis. Finally, through integrative analysis of genome-wide association study (GWAS) data and the animal quantitative trait loci (QTL) database, we determined that target genes of miR-223 were significantly enriched in single-nucleotide polymorphisms (SNP) and QTLs related to somatic cell count (SCC) and mastitis.ConclusionIn summary, miR-223 has an inhibitory effect on S. aureus-induced cell apoptosis and necrosis by regulating PTPRF, DCTN1, and DPP9. These genes were significantly enriched in QTL regions associated with bovine mastitis resistance, underscoring their relevance in genetic regulation of disease resilience. Our findings provide critical genetic markers for enhancing mastitis resistance, particularly S. aureus-induced mastitis, through selective breeding. This work offers valuable insights for developing cattle with improved resistance to mastitis via targeted genetic selection.

Descriptive Comparative Transcriptomic Analysis of Genotype IV SHEV ORF3-Expressing HepG2 Cells.

Background: Swine hepatitis E (HEV) is a zoonotic infectious disease caused by the swine hepatitis E virus (SHEV). Open reading frame 3 (ORF3) is a key virulence factor in swine HEV, playing a crucial role in the release of viral particles, the modulation of the host innate immune response, and regulation of autophagy and apoptosis, etc. However, its main function and pathogenic mechanism remain incompletely understood. Results: In our study, adenoviruses ADV4-ORF3 and ADV4-GFP were successfully constructed and mediated the overexpression of enhanced green fluorescent protein (EGFP)-ORF3 and EGFP in HepG2 cells. A total of 217 differentially expressed messenger RNAs (mRNAs) were screened by high-throughput sequencing, and 27 statistically significant differentially expressed genes were screened for further quantitative real-time reverse transcription (qRT-PCR) verification by functional enrichment (Gene Ontology [GO] and Kyoto Encyclopedia of Genes and Genomes [KEGG]). They are mainly involved in six pathways: the cellular response to unfolded protein, inflammatory response, cytokine activity, TNF signaling pathway, influenza A, and pathways in cancer. In a comparative analysis of transcriptome and mRNA expression profiles of lncRNA sequencing, the results showed that 3 mRNAs of GPX1, MDM4, and CLDN and 39 transcripts overlapped and have been identified. Conclusions: Eight differential genes, HSPA1A, HSPA1B, PLD3, RELA, GPI, SAMHD1, RPS6KA4, and PIK3CB, were successfully verified. Comparing and analyzing the results of the two sequencing methods indicated that the 3 mRNAs of GPX1, MDM4, and CLDN and 39 transcripts overlapped and have been identified in SHEV ORF3-expressing HepG2 cells, which has laid a genetic foundation for the physiological function and mechanism of SHEV ORF3.

Wnt/β-catenin signalling underpins juvenile Fasciola hepatica growth and development.

Infection by the liver fluke, Fasciola hepatica, places a substantial burden on the global agri-food industry and poses a significant threat to human health in endemic regions. Widespread resistance to a limited arsenal of chemotherapeutics, including the frontline flukicide triclabendazole (TCBZ), renders F. hepatica control unsustainable and accentuates the need for novel therapeutic target discovery. A key facet of F. hepatica biology is a population of specialised stem cells which drive growth and development - their dysregulation is hypothesised to represent an appealing avenue for control. The exploitation of this system as a therapeutic target is impeded by a lack of understanding of the molecular mechanisms underpinning F. hepatica growth and development. Wnt signalling pathways govern a myriad of stem cell processes during embryogenesis and drive tumorigenesis in adult tissues in animals. Here, we identify five putative Wnt ligands and five Frizzled receptors in liver fluke transcriptomic datasets and find that Wnt/β-catenin signalling is most active in juveniles, the most pathogenic life stage. FISH-mediated transcript localisation revealed partitioning of the five Wnt ligands, with each displaying a distinct expression pattern, consistent with each Wnt regulating the development of different cell/tissue types. The silencing of each individual Wnt or Frizzled gene yielded significant reductions in juvenile worm growth and, in select cases, blunted the proliferation of neoblast-like cells. Notably, silencing FhCTNNB1, the key effector of the Wnt/β-catenin signal cascade led to aberrant development of the neuromuscular system which ultimately proved lethal - the first report of a lethal RNAi-induced phenotype in F. hepatica. The absence of any discernible phenotypes following the silencing of the inhibitory Wnt/β-catenin destruction complex components is consistent with low destruction complex activity in rapidly developing juvenile worms, corroborates transcriptomic expression profiles and underscores the importance of Wnt signalling as a key molecular driver of growth and development in early-stage juvenile fluke. The putative pharmacological inhibition of Wnt/β-catenin signalling using commercially available inhibitors phenocopied RNAi results and provides impetus for drug repurposing. Taken together, these data functionally and chemically validate the targeting of Wnt signalling as a novel strategy to undermine the pathogenicity of juvenile F. hepatica.

Genome-Wide Identification and Expression Analysis of TCP Transcription Factors Responding to Multiple Stresses in Arachis hypogaea L.

The TEOSINTE-BRANCHED1/CYCLOIDEA/PROLIFERATING-CELL-FACTOR (TCP) gene family, a plant-specific transcription factor family, plays pivotal roles in various processes such as plant growth and development regulation, hormone crosstalk, and stress responses. However, a comprehensive genome-wide identification and characterization of the TCP gene family in peanut has yet to be fully elucidated. In this study, we conducted a genome-wide search and identified 51 TCP genes (designated as AhTCPs) in peanut, unevenly distributed across 17 chromosomes. These AhTCPs were phylogenetically classified into three subclasses: PCF, CIN, and CYC/TB1. Gene structure analysis of the AhTCPs revealed that most AhTCPs within the same subclade exhibited conserved motifs and domains, as well as similar gene structures. Cis-acting element analysis demonstrated that the AhTCP genes harbored numerous cis-acting elements associated with stress response, plant growth and development, plant hormone response, and light response. Intraspecific collinearity analysis unveiled significant collinear relationships among 32 pairs of these genes. Further collinear evolutionary analysis found that peanuts share 30 pairs, 24 pairs, 33 pairs, and 100 pairs of homologous genes with A. duranensis, A. ipaensis, Arabidopsis thaliana, and Glycine max, respectively. Moreover, we conducted a thorough analysis of the transcriptome expression profiles in peanuts across various tissues, under different hormone treatment conditions, in response to low- and high-calcium treatments, and under low-temperature and drought stress scenarios. The qRT-PCR results were in accordance with the transcriptome expression data. Collectively, these studies have established a solid theoretical foundation for further exploring the biological functions of the TCP gene family in peanuts, providing valuable insights into the regulatory mechanisms of plant growth, development, and stress responses.

Investigating the Role of Osteopontin (OPN) in the Progression of Breast, Prostate, Renal and Skin Cancers

Background/Objectives: Cancer is caused by disruptions in the homeostatic state of normal cells, which results in dysregulation of the cell cycle, and uncontrolled growth and proliferation in affected cells to form tumors. Successful development of tumorous cells proceeds through the activation of pathways promoting cell development and functionality, as well as the suppression of immune signaling pathways; thereby providing these cells with proliferative advantages, which subsequently metastasize into surrounding tissues. These effects are primarily caused by the upregulation of oncogenes, of which SPP1 (secreted phosphoprotein 1), a non-collagenous bone matrix protein, is one of the most well-known. Methods: In this study, we conducted a further examination of the transcriptomic expression profile of SPP1 (Osteopontin) during the progression of cancer in four human tissues, breast, prostate, renal and skin, in order to understand the circumstances conducive to its activation and dysregulation, the biological pathways and other mechanisms involved as well as differences in its splicing patterns influencing its expression and functionality. Results: A significant overexpression of SPP1, as well as a set of other highly correlated genes, was seen in most of these tissues, indicating their extensive implication in cancer. Increased expression was observed with higher tumor stages, especially in renal and skin cancer, while applying therapeutic modalities targeting these genes dampened this effect in breast, prostate and skin cancer. Pathway analyses showed gene signatures related to cell growth and development enriched in tumorigenic conditions and earlier cancer stages, while later stages of cancer showed pathways associated with weakened immune response, in all cancers studied. Moreover, the utilization of therapeutic methods showed the activation of immunogenic pathways in breast, prostate and skin cancer, thereby confirming their viability. Further analyses of differential transcript expression levels in these oncogenes showed their exonic regions to be selectively overexpressed similarly in tumorigenic samples in all cancers studied, while also displaying significant differences in exon selectivity between constituent transcripts, providing a basis for their high degree of multifunctionality in cancer. Conclusions: Overall, this study corroborates the entrenched role of SPP1 in the progression of these four types of cancer, as confirmed by its overexpression and activation of related oncogenes, their co-involvement in key cellular pathways, and predisposition to exhibit differential splicing between their transcripts, while the above effects were found to be highly inhibitable through treatment methods, thereby highlighting its promising role in therapeutic development.

Comprehensive Analysis of Programmed Cell Death-Related Genes in Diagnosis and Synovitis During Osteoarthritis Development: Based on Bulk and Single-Cell RNA Sequencing Data.

Synovitis is one of the key pathological feature driving osteoarthritis (OA) development. Diverse programmed cell death (PCD) pathways are closely linked to the pathogenesis of OA, but few studies have explored the relationship between PCD-related genes and synovitis. The transcriptome expression profiles of OA synovial samples were obtained from the Gene Expression Omnibus (GEO) database. Using machine learning algorithms, Hub PCD-related differentially expressed genes (Hub PCD-DEGs) were identified. The expression of Hub PCD-DEGs was validated in human OA samples by qRT-PCR. A diagnostic model for OA was constructed based on the expression levels of Hub PCD-DEGs. Unsupervised consensus clustering analysis and weighted correlation network analysis (WGCNA) were employed to identify differential clustering patterns of PCD-related genes in OA patients. The molecular characteristics of Hub PCD-DEGs, their role in synovial immune inflammation, and their association with the immune microenvironment were investigated through functional enrichment analysis and ssGSEA immune infiltration analysis. Single-cell RNA sequencing analysis provided insights into the characteristics of distinct cell clusters in OA synovial tissues and their interactions with Hub PCD-DEGs. We identified five Hub PCD-DEGs: TNFAIP3, JUN, PPP1R15A, INHBB, and DDIT4. qRT-PCR analysis confirmed that all five genes were significantly downregulated in OA synovial tissue. The diagnostic model constructed based on these Hub PCD-DEGs demonstrated diagnostic efficiency in distinguishing OA tissues as well as progression of OA. Additionally, a correlation was observed between the expression levels of Hub PCD-DEGs, immune cell infiltration, and inflammatory cytokine levels. We identified two distinct PCD clusters, each exhibiting unique molecular and immunological characteristics. Single-cell RNA sequencing further revealed dynamic and complex cellular changes in OA synovial tissue, with differential expression of Hub PCD-DEGs across various immune cell types. Our study suggests that PCD-related genes may be involved in development of OA synovitis. The five screened Hub PCD-DEGs (TNFAIP3, JUN, PPP1R15A, INHBB and DDIT4) could be explored as candidate biomarkers or therapeutic targets for OA.

M2 macrophages regulate nucleus pulposus cell extracellular matrix synthesis through the OPN-CD44 axis in intervertebral disc degeneration.

M2 macrophages regulate nucleus pulposus cell extracellular matrix synthesis through the OPN-CD44 axis in intervertebral disc degeneration.