Comprehensive Transcriptome Analysis Research Articles

Ectopic expression of a truncated NLR gene from wild Arachis enhances resistance to Fusarium oxysporum

Fusarium oxysporum causes devastating vascular wilt diseases in numerous crop species, resulting in substantial yield losses. The Arabidopsis thaliana-F. oxysporum f.sp. conglutinans (FOC) model system enables the identification of meaningful genotype–phenotype correlations and was applied in this study to evaluate the effects of overexpressing an NLR gene (AsTIR19) from Arachis stenosperma against pathogen infection. AsTIR19 overexpression (OE) lines exhibited enhanced resistance to FOC without any discernible phenotype penalties. To elucidate the underlying resistance mechanisms mediated by AsTIR19 overexpression, we conducted whole transcriptome sequencing of an AsTIR19-OE line and non-transgenic wild-type (WT) plants inoculated and non-inoculated with FOC using Illumina HiSeq4000. Comparative analysis revealed 778 differentially expressed genes (DEGs) attributed to transgene overexpression, while fungal inoculation induced 434 DEGs in the OE line, with many falling into defense-related Gene Ontology (GO) categories. GO and KEGG enrichment analysis showed that DEGs were enriched in the phenylpropanoid and flavonoid pathways in the OE plants. This comprehensive transcriptomic analysis underscores how AsTIR19 overexpression reprograms transcriptional networks, modulating the expression of stress-responsive genes across diverse metabolic pathways. These findings provide valuable insights into the molecular mechanisms underlying the role of this NLR gene under stress conditions, highlighting its potential to enhance resistance to Fusarium oxysporum.

CTNI-78. PNOC008: A PILOT TRIAL TESTING THE CLINICAL BENEFIT OF USING MOLECULAR PROFILING TO DETERMINE AN INDIVIDUALIZED TREATMENT PLAN IN CHILDREN AND YOUNG ADULTS WITH NEWLY DIAGNOSED HIGH-GRADE GLIOMA (EXCLUDING DIFFUSE INTRINSIC PONTINE GLIOMA)

Abstract BACKGROUND Despite multiple clinical trials in young patients with newly diagnosed high grade gliomas (HGG), survival remains poor. PNOC008 is a single-arm, multi-center pilot trial, investigating the feasibility, toxicity, and efficacy of a molecularly guided individualized treatment approach following radiotherapy. METHODS Patients aged ≤21 years with newly diagnosed, localized, hemispheric HGG (Stratum A) or non DIPG, diffuse midline glioma (DMG) (Stratum B) were eligible. Comprehensive molecular profiling (targeted gene panel, whole exome, and whole transcriptome sequencing) was performed on primary tumor tissue. The molecular data was reviewed by a dedicated tumor board that recommended an individualized treatment plan combining up to four FDA approved drugs. Patients were followed for toxicity and efficacy. Circulating tumor DNA (ctDNA), imaging, and quality of life (QOL) measures were collected at multiple timepoints. RESULTS Fifty-five HGG patients enrolled between 2018 and 2023 (median age 11 years [range 2-20], n=31 female, n=29 Stratum A), including H3K27-altered (n=17), H3/IDH-wildtype diffuse pediatric-type (n=16), and H3G34-mutant diffuse hemispheric glioma (n=12). In 44 patients that followed the recommended treatment, median overall survival (OS) from time of study enrollment was 26.5 months in Stratum A (lower 95% CI: 18.5) and 23.6 months in Stratum B (lower 95% CI: 16.8), and 30 months in H3G34-mutant patients (n=10, lower 95% CI:24.6) with median follow-up of 34.5 months for all patients (lower 95% CI: 32.2). The treatment recommendations most commonly included alkylator with targeted therapy combinations. The often novel drug combinations were generally well tolerated with grade 3 or 4 treatment-related adverse events being mostly hematologic. Central imaging, ctDNA, and QOL analyses are underway. CONCLUSIONS A personalized treatment approach using comprehensive transcriptomic and genomic analysis is feasible and well tolerated with encouraging survival data in children and young adults with HGG. Further analyses of molecular subgroups and correlatives are ongoing.

A combined analysis of transcriptome and proteome reveals the regulation mechanism of alginate oligosaccharides on alleviating energy deficit in postharvest strawberry

Strawberry exhibits a very short shelf life due to its rapid softening and decay, resulting in postharvest loss. Our previous study showed that AOS, an eco-friendly nontoxic natural product, plays a role in preserving the freshness of strawberries by regulating ABA content and its signaling pathway. Considering the critical role that energy deficit plays in the senescence process of fruits, coupled with the potential influence of plant hormones on energy metabolism. In this study, the molecular mechanism of strawberry postharvest senescence in response to AOS treatment was further explored from the perspective of energy metabolism regulation. This was achieved through a two-layered approach, integrating the direct determination of energy-related substances with a comprehensive joint analysis of transcriptome and proteome data. AOS treatment significantly delayed the loss of ATP, ADP, and AMP contents compared to control fruit, implying that maintaining cell energy is a crucial factor in AOS postponing senescence in strawberry. Subsequently, the mechanisms were further revealed by transcriptome and proteome analysis. Overall, 255 DEGs were screened from the AOS group, mainly related to carbohydrate and energy metabolism, defense, plant hormone, and secondary metabolism. Additionally, A total of 227 proteins were identified that were differentially expressed in the AOS group, and the majority were related to carbohydrate and energy metabolism (85 proteins). Two omics data implied that AOS could effectively regulate the energy metabolism system to maintain the cellular energy level of harvested strawberry during storage, ultimately leading to longer shelf life. Therefore, our findings provide comprehensive information regarding the molecular mechanism underlying the postharvest storage of strawberry treated with AOS. From our results, it can be concluded that AOS postharvest treatment is very useful for keeping fruit quality and extending shelf life by maintaining a higher energy level.

Co-Colorectal cancer stem cells employ the FADS1/DDA axis to evade NK cell-mediated immunosuppression after co-cultured with NK cells under hypoxia

Colorectal cancer (CRC) ranks as China’s second most common cancer and fifth top cancer death cause. The study highlights the role of Natural Killer (NK) cells in targeting cancer stem cells (CSCs) that evade immune responses in CRC. Colorectal cancer stem cells (CCSCs) were stem from HT-29 cells and co-cultured with NK cells under normoxic or hypoxic conditions. The impact of this co-culture was evaluated using CCK8 assays for NK cell viability, ELISA for cytokine level changes, and flow cytometry for assessing NK cell apoptosis and activation. Comprehensive metabolomic and transcriptomic analyses were also performed to identify key genes and metabolites involved in the interaction between CCSCs and NK cells Co-culture of CCSCs with NK cells under hypoxia reduced NK cytotoxicity, increased NK apoptosis, and altered cytokine secretion by decreasing IFN-γ and TNF-α levels while increasing IL-6. Transcriptomic and metabolomic analysis identified 4 genes (FADS1, ALDH3A2, GCSH, MTCL1) and 3 metabolites (glyoxylic acid, spermine, DDA) as significant. Interfering with FADS1 counteracted the suppression of IFN-γ and TNF-α induced by CSC cells. Curiously, this inhibition caused by si-FADS1 could be neutralized by the addition of exogenous DDA. Co-culturing with NK cells notably increased spermine levels. Exogenous spermine resulted in a significant reduction in HT-29 cell death rates at 32 µM, 64 µM, and 128 µM, compared to NK cells without spermine. Our research explored CCSCs employed the FADS1/DDA axis to evade NK cell-mediated immunosuppression after co-cultured with NK cells under hypoxia.

Genome-wide analysis of the R2R3-MYB gene family and identification of candidate genes that regulate isoflavone biosynthesis in red clover (Trifolium pratense)

Red clover (Trifolium pratense) is a perennial legume with high feeding and medicinal value attributed to its abundant isoflavone content. Previous studies reported that R2R3-MYB transcription factors are involved in the biosynthesis of isoflavones; however, their specific role in red clover remains poorly understood. Through comprehensive genome-wide and transcriptome analyses, a total of 138 TpR2R3-MYB genes were identified and classified into 30 distinct subgroups within a phylogenetic tree. Importantly, six of these subgroups showed associations with isoflavone biosynthesis in red clover. The majority of segmental duplication events (Ka/Ks < 1) indicated that the TpR2R3-MYB gene underwent strong purifying selection during evolution. The qRT-PCR analysis demonstrated high expression levels of TpMYB79 and TpMYB53 in Minshan red clover at full flowering stage, consistent with the trend for isoflavone content determination, suggesting that TpMYB79 and TpMYB53 might be important regulators of isoflavone biosynthesis in red clover. Additionally, we observed nucleus and vacuole membrane localization of TpMYB53 and TpMYB79, with TpMYB53 primarily exerting transcriptional activation through its C-terminal activation motifs while TpMYB79 exhibited no transcriptional activity. These findings provided a foundation for the study of the biological function of R2R3-MYB transcription factors in red clover.

Inflammasome-targeted therapy might prevent adverse perinatal outcomes of recurrent chronic intervillositis of unknown etiology

Chronic histiocytic intervillositis of unknown origin (CHI) is a rare placental disorder associated with adverse pregnancy outcomes, frequent recurrence, and a lack of effective preventive strategies. Recent insights indicate a potential link between CHI-associated inflammatory lesions and the inflammasome pathway, suggesting innovative therapeutic avenues. Here we show a potential role of the inflammasome pathway in CHI through comprehensive transcriptomic analysis of grade 2 or 3 histopathologic CHI samples, paired with placental controls. Additionally, we present case studies of three individuals with recurrent CHI, who have undergone treatment with anakinra and colchicine throughout pregnancy, resulting in improved perinatal outcomes. Notably, all cases are characterized by the birth of healthy, full-term infants, with reduced or absent intervillositis recurrence. Placental assessment unveils heightened activation of the NLRP3-PYCARD inflammasome pathway and IL-1β processing in CHI samples, with downregulation observed in treated pregnancy samples, devoid of intervillositis. Collectively, these findings suggest a potential therapeutic role for targeting the inflammasome pathway in preventing recurrent CHI in pregnant individuals.

The Molecular Classification of Pheochromocytomas and Paragangliomas: Discovering the Genomic and Immune Landscape of Metastatic Disease.

Pheochromocytomas (PCCs) and paragangliomas (PGLs, together PPGLs) are the most hereditary tumors known. PPGLs were considered benign, but the fourth edition of the World Health Organisation (WHO) classification redefined all PPGLs as malignant neoplasms with variable metastatic potential. The metastatic rate differs based on histopathology, genetic background, size, and location of the tumor. The challenge in predicting metastatic disease lies in the absence of a clear genotype-phenotype correlation among the more than 20 identified genetic driver variants. Recent advances in molecular clustering based on underlying genetic alterations have paved the way for improved cluster-specific personalized treatments. However, despite some clusters demonstrating a higher propensity for metastatic disease, cluster-specific therapies have not yet been widely adopted in clinical practice. Comprehensive genomic profiling and transcriptomic analyses of large PPGL cohorts have identified potential new biomarkers that may influence metastatic potential. It appears that no single biomarker alone can reliably predict metastatic risk; instead, a combination of these biomarkers may be necessary to develop an effective prediction model for metastatic disease. This review evaluates current guidelines and recent genomic and transcriptomic findings, with the aim of accurately identifying novel biomarkers that could contribute to a predictive model for mPPGLs, thereby enhancing patient care and outcomes.

Fungal Methane Production Under High Hydrostatic Pressure in Deep Subseafloor Sediments

Fungi inhabiting deep subseafloor sediments have been shown to possess anaerobic methane (CH4) production capabilities under atmospheric conditions. However, their ability to produce CH4 under in situ conditions with high hydrostatic pressure (HHP) remains unclear. Here, Schizophyllum commune 20R-7-F01, isolated from ~2 km below the seafloor, was cultured in Seawater Medium (SM) in culture bottles fitted with sterile syringes for pressure equilibration. Subsequently, these culture bottles were transferred into 1 L stainless steel pressure vessels at 30 °C for 5 days to simulate in situ HHP and anaerobic environments. Our comprehensive analysis of bioactivity, biomass, and transcriptomics revealed that the S. commune not only survived but significantly enhanced CH4 production, reaching approximately 2.5 times higher levels under 35 MPa HHP compared to 0.1 MPa standard atmospheric pressure. Pathways associated with carbohydrate metabolism, methylation, hydrolase activity, cysteine and methionine metabolism, and oxidoreductase activity were notably activated under HHP. Specifically, key genes involved in fungal anaerobic CH4 synthesis, including methyltransferase mct1 and dehalogenase dh3, were upregulated 7.9- and 12.5-fold, respectively, under HHP. Enhanced CH4 production under HHP was primarily attributed to oxidative stress induced by pressure, supported by intracellular reactive oxygen species (ROS) levels and comparative treatments with cadmium chloride and hydrogen peroxide. These results may provide a strong theoretical basis and practical guidance for future studies on the contribution of fungi to global CH4 flux.

Characterization of Superoxide Dismutase (SOD) Gene Family and Their Responses to Salinity Stress and Fruit Development in Octoploid Strawberry

Superoxide dismutases (SODs), as the first line of defense against reactive oxygen species (ROS), play an essential role in protecting plants from adverse elicitors during plant growth and development. However, little is known about the SOD gene family and their response to salinity stress and fruit development in cultivated strawberries (Fragaria × ananassa). In this study, 32 SOD genes consisting of 16 Cu/ZnSODs, 11 FeSODs, and 5 MnSOD were identified, which presented three well-resolved clades in the phylogenetic tree. Each clade had similar motifs, and exon–intron structures, which in turn supported the evolutionary classification. Cis-acting element analysis suggested that FaSOD genes might be involved in the plant response to abiotic and biotic stresses, hormones, and light. The analysis of previously published transcriptome data revealed that FaSOD genes are expressed variably under salt stress. Among these SODs, FaMSD5 was expressed at relatively high levels in strawberry root and leaf, and its transcript abundance significantly increased after salt treatment. Some transcription factors related to photomorphogenesis, hormone signaling pathways, and hyperosmotic salinity response were predicted to bind to the FaMSD5 promoter. These outcomes implied that FaMSD5 might play an important role in protection against salt stress. In addition, the comprehensive transcriptome analysis of FaSOD genes in strawberry fruit showed that almost all FaCSDs and FaMSDs were more highly expressed than FaFSDs at different developmental stages, and the expression patterns of FaCSD1, FaCSD2, FaCSD7, FaCSD8, and FaCSD10 suggested that they were likely to be involved in fruit development and ripening. This study provides a basis for further exploration of the function of the FaSOD gene family in strawberry and provides candidate FaSOD genes for enhancing salinity tolerance and regulating fruit development and ripening.

The full transcription map of cottontail rabbit papillomavirus in tumor tissues.

Cottontail rabbit papillomavirus (CRPV), the first papillomavirus associated with tumor development, has been used as a powerful model to study papillomavirus pathogenesis for more than 90 years. However, lack of a comprehensive analysis of the CRPV transcriptome has impeded the understanding of CRPV biology and molecular pathogenesis. Here, we report the construction of a complete CRPV transcription map from Hershey CRPV-induced skin tumor tissues. By using RNA-seq in combination with long-reads PacBio Iso-seq, 5' and 3' RACE, primer-walking RT-PCR, Northern blot, and RNA in situ hybridization, we demonstrated that the CRPV genome transcribes its early and late RNA transcripts unidirectionally from at least five distinct major promoters (P) and polyadenylates its transcripts at two major polyadenylation (pA) sites. The viral early transcripts are primarily transcribed from three "early" promoters, P90, P156, and P907 and polyadenylated at nt 4368 by using an early polyadenylation signal (PAS) at nt 4351. Like other low-risk human papillomaviruses and animal papillomaviruses, CRPV E6 and E7 transcripts are transcribed from three separate early promoters. Transcripts from two "late" promoters, P7525, and P1225, utilize either an early PAS for E1^E4 or a late PAS at 7399 for L2 and L1 RNA polyadenylation at nt 7415 to express capsid L2 and L1 proteins respectively. By using the mapped four 5' splice sites and three 3' splice sites, CRPV RNA transcripts undergo extensive alternative splicing to produce more than 33 viral RNA isoforms for production of at least 12 viral proteins, some of which without codon optimization are expressible in rabbit RK13 and human HEK293T cells. The constructed full CRPV transcription map in this study for the first time will enhance our understanding of the structures and expressions of CRPV genes and their contribution to molecular pathogenesis and tumorigenesis.

Identification of putative genes for caffeoylated flavonoid glycoside biosynthesis in Pseudognaphalium affine

Pseudognaphalium affine (D. Don) Anderberg, commonly found in East Asia, has extensive applications as both a traditional medicine and a vegetable in China. The caffeoylated flavonoid glycosides produced by P. affine exhibit remarkable anti-complement activities. Although these compounds have potential therapeutic value, the biosynthetic pathway responsible for their production remains largely unknown. To elucidate the key catalytic steps involved in caffeoylated flavonoid glycoside biosynthesis, we conducted a comprehensive analysis of the full-length transcriptome of P. affine. Further phylogenetic tree analysis predicted potential UDP glycosyltransferase (UGT) and BAHD acyltransferase (BAHD-AT) related with caffeoylated flavonoid glycoside biosynthesis. Subsequently, enzyme assay led to the discovery of PaUGT23 as a key enzyme responsible for the glycosylation of hydroxy groups in flavonoids, resulting in the formation of luteolin-4′-O-glucoside, luteolin-7-O-glucoside, quercetin-4′-O-glucoside, quercetin-7-O-glucoside, and apigenin-7-O-glucoside, while PaBAHD21 was found to catalyze the caffeoylation of flavonoid glycosides, resulting in the formation of luteolin 4′-O-β-D-(6″-E-caffeoyl)-glucopyranoside, quercetin 4′-O-β-D-(6″-E-caffeoyl)-glucopyranoside, apigenin 4′-O-β-D-(6″-E-caffeoyl)-glucopyranoside and apigenin 7-O-β-D-(6″-E-caffeoyl)-glucopyranoside. Moreover, their catalytic activities were verified in vivo by transient transfection experiment. This study presents the first comprehensive analysis of the full-length transcriptome in P. affine, providing significant insights into the biosynthesis and accumulation mechanisms of bioactive caffeoylated flavonoid glycosides.

Effects of Electroacupuncture at Varied Frequencies on Analgesia and Mechanisms in Sciatic Nerve Cuffing-Induced Neuropathic Pain Mice

Addressing the intricate challenge of chronic neuropathic pain has significant implications for the physical and psychological well-being of patients, given its enduring nature. In contrast to opioids, electroacupuncture (EA) may potentially provide a safer and more efficacious therapeutic alternative. Our objective is to investigate the distinct analgesic effects and potential mechanisms of EA at frequencies of 2 Hz, 100 Hz, and 18 kHz in order to establish more precise frequency selection criteria for clinical interventions. Analgesic efficacy was evaluated through the measurement of mice’s mechanical and thermal pain thresholds. Spinal cord inflammatory cytokines and neuropeptides were quantified via Quantitative Real-time PCR (qRT-PCR), Western blot, and immunofluorescence. Additionally, RNA sequencing (RNA-Seq) was conducted on the spinal cord from mice in the 18 kHz EA group for comprehensive transcriptomic analysis. The analgesic effect of EA on neuropathic pain in mice was frequency-dependent. Stimulation at 18 kHz provided superior and prolonged relief compared to 2 Hz and 100 Hz. Our research suggests that EA at frequencies of 2 Hz, 100 Hz, and 18 kHz significantly reduce the release of inflammatory cytokines. The analgesic effects of 2 Hz and 100 Hz stimulation are due to frequency-dependent regulation of opioid release in the spinal cord. Furthermore, 18 kHz stimulation has been shown to reduce spinal neuronal excitability by modulating the serotonergic pathway and downstream receptors in the spinal cord to alleviate neuropathic pain.

Revealing the Diversity of Sequences, Structures, and Targets of Peptides from South China Sea Macrodactyla doreensis Based on Transcriptomics.

The South China Sea is rich in sea anemone resources, and the protein and peptide components from sea anemone toxins comprise an important treasure trove for researchers to search for leading compounds. This study conducted a comprehensive transcriptomic analysis of the tentacles and column of Macrodactyla doreensis and explored the distribution and diversity of proteins and peptides in depth using bioinformatics, initially constructing a putative protein and peptide database. In this database, typical peptide families are identified through amino acid sequence analysis, and their 3D structures and potential biological activities are revealed through AlphaFold2 modeling and molecular docking. A total of 4239 transcripts were identified, of which the putative protein accounted for 81.53%. The highest content comprised immunoglobulin and a variety of proteases, mainly distributed in the column and related to biological functions. Importantly, the putative peptide accounted for 18.47%, containing ShK domain and Kunitz-type peptides, mainly distributed in the tentacles and related to offensive predatory behavior. Interestingly, 40 putative peptides belonging to eight typical peptide families were identified, and their structures and targets were predicted. This study reveals the diversity and complexity of Macrodactyla doreensis toxins and predicts their structure and targets based on amino acid sequences, providing a feasible approach for research regarding the discovery of peptides with potentially high activity.

Metastatic organotropism in small cell lung cancer.

Metastasis is the leading cause of cancer-related deaths, yet its regulatory mechanisms are not fully understood. Small-cell lung cancer (SCLC) is the most metastatic form of lung cancer, with most patients presenting with widespread disease, making it an ideal model for studying metastasis. However, the lack of suitable preclinical models has limited such studies. We utilized well-annotated rapid autopsy-derived tumors to develop xenograft models that mimic key features of SCLC, including histopathology, rapid and widespread development of metastasis to the liver, brain, adrenal, bone marrow, and kidneys within weeks, and response to chemotherapy. By integrating in vivo lineage selection with comprehensive transcriptomic and epigenomic analyses, we identified critical cellular programs driving metastatic organotropism to the liver and brain, the most common sites of SCLC metastasis. Our findings reveal the key role of nuclear-cytoskeletal interactions in SCLC liver metastasis. Specifically, the loss of the nuclear envelope protein lamin A/C, encoded by the LMNA gene, increased nuclear deformability and significantly increased the incidence of liver metastasis. Human liver metastases exhibited reduced LMNA expression compared to other metastatic sites, correlating with poorer patient outcomes and increased mortality. This study introduces novel preclinical models for SCLC metastasis and highlights pathways critical for organ-specific metastasis, offering new avenues for the development of targeted therapies to prevent or treat metastatic disease.

ARR1 and ARR12 modulate arsenite toxicity responses in Arabidopsis roots by transcriptionally controlling the actions of NIP1;1 and NIP6;1.

Cytokinin is central to coordinating plant adaptation to environmental stresses. Here, we first demonstrated the involvement of cytokinin in Arabidopsis responses to arsenite [As(III)] stress. As(III) treatment reduced cytokinin contents, while cytokinin treatment repressed further primary root growth in Arabidopsis plants under As(III) stress. Subsequently, we revealed that the cytokinin signaling members ARR1 and ARR12, the type-B ARABIDOPSIS RESPONSE REGULATORs, participate in cytokinin signaling-mediated As(III) responses in plants as negative regulators. A comprehensive transcriptome analysis of the arr1 and arr12 single and arr1,12 double mutants was then performed to decipher the cytokinin signaling-mediated mechanisms underlying plant As(III) stress adaptation. Results revealed important roles for ARR1 and ARR12 in ion transport, nutrient responses, and secondary metabolite accumulation. Furthermore, using hierarchical clustering and regulatory network analyses, we identified two NODULIN 26-LIKE INTRINSIC PROTEIN (NIP)-encoding genes, NIP1;1 and NIP6;1, potentially involved in ARR1/12-mediated As(III) uptake and transport in Arabidopsis. By analyzing various combinations of arr and nip mutants, including high-order triple and quadruple mutants, we demonstrated that ARR1 and ARR12 redundantly function as negative regulators of As(III) tolerance by acting upstream of NIP1;1 and NIP6;1 to modulate their function in arsenic accumulation. ChIP-qPCR, EMSA, and transient dual-LUC reporter assays revealed that ARR1 and ARR12 transcriptionally activate the expression of NIP1;1 and NIP6;1 by directly binding to their promoters and upregulating their expression, leading to increased arsenic accumulation under As(III) stress. These findings collectively provide insights into cytokinin signaling-mediated plant adaptation to excessive As(III), contributing to the development of crops with low arsenic accumulation.

Investigation of the preharvest arginine spraying mechanism on antioxidant system in postharvest broccoli via transcriptomics and metabolomics

According to our previous study, preharvest spraying of arginine for 1 day enhanced the antioxidant capacity of postharvest broccoli, but the underlying molecular mechanisms remain unclear. We here performed a comprehensive transcriptome and metabolome analysis to investigate the effects of arginine sprayed 1 day before harvest on the antioxidant capacity and yellowing of broccoli as well as the related action mechanisms. In total, 67 differentially expressed genes and 12 key differentially accumulated metabolites were identified in broccoli at 4 and 8 days during storage. Herein, the gene expression of superoxide dismutase, catalase, and the corresponding peroxisome protein Mpv17 (MPV17) was upregulated, consequently enhancing the scavenging of reactive oxygen species. Genes encoding glucosinolate synthesis- and metabolism-related enzymes were upregulated, and among them, the gene ST5b_c was upregulated by 8.23-fold, which promoted the accumulation of its metabolites. Expression of lignin- and flavonoid biosynthesis-related genes (CAD, POD, CHI, and CHS) was elevated. Flavonoid and lignin accumulation was promoted, with a greater antioxidant capacity at 4 and 8 days, respectively, in the arginine-sprayed broccoli. Additionally, the ascorbate–glutathione cycle was promoted in broccoli at 4 days, GLCAK and APX genes were upregulated by more than 2-fold, and broccoli exhibited a higher tolerance level because of the notably stimulated ascorbic acid and glutathione accumulation. This study offers new insights into the mechanisms through which preharvest spraying of arginine regulates the antioxidant capacity of postharvest broccoli.

Elucidating the downstream pathways triggered by H2S signaling in Arabidopsis thaliana under drought stress via transcriptome analysis

ABSTRACT Hydrogen sulfide (H2S) is a crucial signaling molecule in plants. Recent studies have shown that H2S plays an equally important role as nitric oxide (NO) and hydrogen peroxide (H2O2) in plant signaling. Previous studies have demonstrated the involvement of H2S in regulating drought and other stressful environmental conditions, but the exact downstream molecular mechanisms activated by the H2S signaling molecule remain unclear. In this study, we conducted a comprehensive genome-wide transcriptomic analysis of both wild type (WT) and double mutant (lcd/des1). Arabidopsis thaliana plants were exposed to 40% polyethylene glycol (PEG) to induce drought stress and 20 µM sodium hydrosulfide (NaHS). The resulting transcriptome data were analyzed for differentially significant genes and their statistical enrichments in the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways. The results indicated significant upregulation of genes related to photosynthesis, carbon fixation, plant secondary metabolite biosynthesis, inositol and phosphatidylinositol signaling pathways, and stress-responsive pathways in mutant plants under drought stress. Mutant plants with impaired H2S signaling mechanisms displayed greater susceptibility to drought stress compared to wild-type plants. In summary, all findings highlight the pivotal role of H2S signaling in stimulating other drought-responsive signaling pathways.

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

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

Whole-blood RNA biomarkers for predicting survival in non-human primates following thoracic radiation

Radiation injury, either from radiotherapy or a mass-casualty event requires a health care system that can efficiently allocate resources to patients. We conducted a comprehensive transcriptome analysis of whole blood from a nonhuman primate model that received upper thoracic radiation (9.8–10.7 Gy). Blood samples were collected at multiple time points, extending up to 270 days post-irradiation with a minimum n = 6 for initial time points (Day 3-Day 40) and a total number of n = 28 primates. No males receiving the higher dose survived to Day 270. Using the Elastic Net model in R we found that pooling biomarkers from Day 3–21 increased our accuracy in discerning survival time, pleural effusion or dose compared to using biomarkers specific to a single day. For survival data, in predicting short term (less than 90 day), medium term (Day 91–269) or long-term survival (Day 270), prediction accuracy using only Day 3 data was 0.14 (95% Confidence Interval (CI) 0.1, 0.19) while pooled data for Male and Female was 0.76 (CI 0.69, 0.82). When pooled data was divided by biological sex, accuracy was 0.7 (CI 0.58, 0.8) for pooled data from Males and 0.84 (CI 0.76, 0.91) for Females. The development of RNA biomarkers as a tool to aid in clinical decision-making could significantly improve patient care in cases of radiation injury, whether from radiotherapy or mass-casualty events. Further validation and clinical translation of these findings could lead to improved patient care and management strategies in cases of radiation exposure.

Transcriptome analysis provides new insights into the response of canine intestinal epithelial cells treated by sulforaphane: a natural product of cruciferous origin.

This study presents a comprehensive transcriptome analysis of canine intestinal epithelial cells following treatment with sulforaphane (SFN), a naturally occurring compound found in cruciferous vegetables with established anti-inflammatory and antioxidant properties. Through high-throughput sequencing, we identified 29,993 genes, among which 1,612 were differentially expressed, with 792 up-regulated and 820 down-regulated in response to SFN treatment. Our analysis revealed significant enrichment of genes in pathways associated with the inflammatory response, lipid metabolism, oxidative stress response, and T-cell mediated immunity, suggesting SFN's potential in modulating these biological processes. Notably, the PPARγ gene, which plays a crucial role in the body's oxidative stress and inflammatory response, was highly up-regulated, indicating its possible centrality in SFN's effects. Gene-gene interaction analysis further supported SFN's role in alleviating inflammation through PPARγ, with key genes in oxidative stress and inflammatory response pathways showing significant correlations with PPARγ. Overall, our findings provide molecular evidence for SFN's protective effects on canine intestinal health, potentially through the modulation of inflammatory and oxidative stress pathways, with PPARγ emerging as a critical mediator.