Comprehensive Expression Profiling Research Articles

A liquid biopsy analysis of exosomal miRNA to detect lymph node metastasis in early gastric cancer.

469 Background: Additional surgical resection is required to achieve a complete cure in patients with early gastric cancer (EGC) due to the potential risk for lymph node metastasis (LNM) after pathological analysis. However, LNM is estimated to occur in approximately 10% of patients with high-risk EGC. In this study, we investigated a blood-based liquid biopsy assay of exosomal miRNA for the noninvasive detection of LNM in patients with high-risk EGC. Methods: Two genome-wide miRNA expression profiling datasets (GSE164174 and TCGA) were analyzed to prioritize biomarkers in pretreatment plasma samples from clinical training and validation cohorts of GC patients. An integrated exosomal miRNA panel was developed and a risk stratification model combining the miRNA panel with clinical risk factors was established. Results: Using comprehensive expression profiling of public datasets, we identified a transcriptomic panel of four miRNAs (miR-34b, miR-130a, miR-375, and miR-627) that robustly identified patients with LNM [area under the curve (AUC) = 0.86, 95% confidence interval (CI) = 0.77-0.92]. We assessed panel performance in a training cohort (AUC=0.86, 95% CI=0.67-0.96) and validated it in an independent validation cohort (AUC=0.84, 95% CI=0.64-0.95). Our risk stratification model was more accurate than the panel and was an independent predictor of LNM identification (AUC=0.97). Conclusions: A novel noninvasive, liquid biopsy-based method for patients with EGC may predict those traditionally classified as high-risk patients with LNM who are unlikely to benefit from surgical resection.

The Icarian flight of antibody-drug conjugates: target selection amidst complexity and tackling adverse impacts.

Antibody-drug conjugates (ADCs) represent a promising class of targeted cancer therapeutics that combine the specificity of monoclonal antibodies with the potency of cytotoxic payloads. Despite their therapeutic potential, the use of ADCs faces significant challenges, including off/on-target toxicity and resistance development. This review examines the current landscape of ADC development, focusing on the critical aspects of target selection and antibody engineering. We discuss strategies to increase ADC efficacy and safety, including multitarget approaches, pH-dependent antibodies, and masked peptide technologies. The importance of comprehensive antigen expression profiling in both tumor and normal tissues is emphasized, highlighting the role of advanced technologies, such as single-cell sequencing and artificial intelligence (AI), in optimizing target selection. Furthermore, we explore combination therapies and innovations in linker‒payload chemistry, which may provide approaches for expanding the therapeutic window of ADCs. These advances pave the way for the development of more precise and effective cancer treatments, potentially extending ADC applications beyond oncology.

Comprehensive Identification and Expression Profiling of Lipoxygenase Genes in Sweet Cherry During Fruit Development

Lipoxygenase (LOX) is involved in the oxidation of fatty acids in plants and is a ubiquitous oxygenase that plays an important role in the process of plant resistance to adversity. In this study, the LOX gene family in the sweet cherry genome was identified by bioinformatics methods, the chromosomal mapping of different LOX genes was carried out, and the homology alignment and functional domain analysis of the encoded proteins were performed. The results showed that there were nine LOX gene sequences in the sweet cherry LOX gene family, and the subcellular localization was mainly located in the cytoplasm, chloroplast, or plasma membrane, and was concentrated on chromosomes 1, 2, 3, 4, 6, and 8. During the ripening process of sweet cherry fruits, the LOX gene family showed five different expression patterns, the expression peak of different LOX genes reached the peak of expression at a specific development period, all LOX genes jointly promoted the growth and development of fruits, the enzyme activities of LOX in different varieties of early and late ripening cherries exhibited great differences during the development process, and the results of volatile content in the later stages also showed that different varieties of cherries had their specificity. The results of this study provide a theoretical basis for further revealing the specific functions of LOX gene family members in sweet cherry.

Inflammation alters the expression and activity of the mechanosensitive ion channels in periodontal ligament cells.

Periodontal ligament cells (PDLCs) possess mechanotransduction capability, vital in orthodontic tooth movement (OTM) and maintaining periodontal homeostasis. The study aims to elucidate the expression profiles of mechanosensitive ion channel (MIC) families in PDLCs and how the inflammatory mediator alters their expression and function, advancing the understanding of the biological process of OTM. Human PDLCs were cultured and exposed to TNF-α. RNA sequencing was conducted to explore the mRNA transcriptome of both normal and TNF-α-treated PDLCs. Differentially expressed MICs were identified and analyzed. The functional expressions of TRPA1 and TRPM8 were further validated by RT-qPCR, Western blot, and calcium influx assays. All 10 identified MIC families or subfamilies were expressed in PDLCs, with the TRP family being the most abundant. KCNK2, PIEZO1, TMEM87A, and PKD2 were the most expressed ion channels in PDLCs. TNF-α altered the expression of the MIC families, resulting in increased expression of PIEZO, K2P, TRP, TMEM63, and TMEM87 families and decreased expression of ENaC/ASIC, TMC/TMHS/TMIE, TMEM150, TMEM120, and L/T/N-Type calcium channel families. Furthermore, 17 DEMICs were identified (false discovery rate < 0.05), with the top five (fold change ≥ 2), including upregulated TRPA1 and TRPM8. The functional expressions of TRPA1 and TRPM8 were verified, suggesting that TNF-α significantly increased their expression and sensitized their activities. The study provides comprehensive expression profiles of the MICs in PDLCs and reveals how inflammation alters the expression and activities of the MICs. Treatments targeting these MICs may offer promising strategies for improving OTM and preventing complications in inflammatory environments, ultimately leading to more effective and safer orthodontic practices.

Comprehensive Genome-Wide Identification and Expression Profiling of bHLH Transcription Factors in Areca catechu Under Abiotic Stress.

The basic helix-loop-helix (bHLH) transcription factor (TF) family, the second-largest among eukaryotes, is known for its evolutionary and functional diversity across plant species. However, bHLH genes have not yet been characterized in Areca catechu. In this study, we identified 76 AcbHLH genes, which exhibit a variety of physicochemical properties. Phylogenetic analysis revealed evolutionary relationships between Arabidopsis thaliana bHLH genes (AtbHLH) and their counterparts in A. catechu (AcbHLH). These analyses also highlighted conserved amino acid motifs (S, R, K, P, L, A, G, and D), conserved domains, and evolutionary changes, such as insertions, deletions, and exon gains or losses. Promoter analysis of AcbHLH genes revealed 76 cis-elements related to growth, phytohormones, light, and stress. Gene duplication analysis revealed four tandem duplications and twenty-three segmental duplications, while AcbHLH63 in the Areca genome exhibited significant synteny with bHLH genes from A. thaliana, Vitis vinifera, Solanum lycopersicum, Brachypodium distachyon, Oryza sativa, and Zea mays. Furthermore, relative expression analysis showed that under drought stress (DS), AcbHLH22, AcbHLH39, AcbHLH45, and AcbHLH58 showed distinct upregulation in leaves at specific time points, while all nine AcbHLH genes were upregulated in roots. Under salt stress (SS), AcbHLH22, AcbHLH39, AcbHLH45, and AcbHLH58 were upregulated in leaves, and AcbHLH22, AcbHLH34, and AcbHLH39 exhibited differential expression in roots at various time points. This study provides valuable insights into the bHLH superfamily in A. catechu, offering a solid foundation for further investigation into its role in responding to abiotic stresses.

Genome-Wide Identification and Expression Profiles of Nuclear Factor Y A Transcription Factors in Blueberry Under Abiotic Stress.

Nuclear Factor Y A (NF-YA) transcription factors are widely involved in multiple plant biological processes, such as embryogenesis, abscisic acid signaling, and abiotic stress response. This study presents a comprehensive genome-wide identification and expression profiling of NF-YA transcription factors in blueberry (Vaccinium corymbosum), an important economic crop with good adaptability, under abiotic stress conditions. Given the economic significance and health benefits of blueberries, understanding their responses to environmental stresses, such as salt, drought, and temperature extremes, is crucial. A total of 24 NF-YA transcription factors were identified through bioinformatics analyses, including sequence alignment, phylogenetic tree construction, and conserved motif analysis. The expression patterns of these NF-YA genes were evaluated in various tissues (roots, stems, and leaves) and under different stress treatments (abscisic acid, salt, and cold) using quantitative real-time PCR (qRT-PCR). The results indicated that most VcNF-YA genes exhibited higher expression levels in stems and leaves compared to roots. Most VcNF-YAs were responsive to the stress treatment. Furthermore, cis-acting element analysis revealed that the promoters of VcNF-YAs were enriched with elements responsive to abiotic stress, suggesting their pivotal role in stress adaptation. This research unveils the expressional responses of NF-YA transcription factors in blueberry upon abiotic stresses and lays the groundwork for future studies on improving crop adaptation.

Pituitary whole transcriptome analysis reveals key genes regulating reproduction in Hy-Line Brown hens and the construction of their ceRNA molecular regulatory network

BackgroundThe development and egg-laying performance of hens are precisely regulated by hormones secreted by the pituitary. In this study, we performed comprehensive transcriptome sequencing of pituitary from Hy-Line Brown hens at 15, 20, 30 and 68 W of age. Through association analysis, we identified key genes and ceRNA regulatory networks related to pituitary development and egg production.ResultsBased on the comprehensive transcriptome data, we identified 470 differentially expressed lncRNAs (DE-lncRNAs), 38 differentially expressed miRNAs (DE-miRNAs), and 2,449 differentially expressed mRNAs (DE-mRNAs). Time-series analysis pinpointed genes and signaling pathways that significantly influence pituitary hormone secretion at various stages. At 15 W, the high expression of GHRHR, NPY1R, and TSHR in the pituitary supports growth. At 20 and 30 W, elevated GNRHR expression sustains continuous egg production. In the late laying period, the expression of PRL may lead to a decline in egg production. Additionally, association analysis enabled the construction of a ceRNA regulatory network involving non-coding RNAs that regulate the development and reproduction of hens.ConclusionThis study elucidated the comprehensive transcriptome expression profiles of the pituitary gland during the development and egg-laying processes in Hy-Line Brown hens and constructed the associated molecular regulatory networks. These findings lay the foundation for investigating the mechanisms by which non-coding RNAs regulate pituitary hormone secretion.

Abstract B008: Exploring the Dual Roles of RNAs as Oncogenic Drivers and Therapeutic Targets in Cancer: A Cross-Sectional Study

Abstract RNAs have emerged as pivotal molecules in the complex landscape of cancer biology, acting as both drivers of oncogenesis and therapeutic targets. This cross-sectional experimental design research explores the dual roles of RNAs, particularly focusing on the interplay between non-coding RNAs (ncRNAs), messenger RNAs (mRNAs), and their regulatory networks in various cancer types. The study systematically analyzes RNA expression profiles across a broad spectrum of cancer samples, employing high-throughput sequencing technologies combined with bioinformatics tools to identify key RNA species that contribute to tumorigenesis. The experimental design includes the collection of tumor and adjacent normal tissues from patients diagnosed with breast, lung, and colorectal cancers. RNA extraction and sequencing are performed to generate comprehensive expression profiles. Differential expression analysis is conducted to pinpoint RNAs that are significantly dysregulated in cancerous tissues compared to their normal counterparts. Subsequently, functional assays, including RNA interference (RNAi) and CRISPR/Cas9-mediated gene editing, are utilized to validate the oncogenic or tumor-suppressive roles of these RNAs in cancer cell lines. To further elucidate the mechanistic pathways, the study integrates data from RNA-binding protein immunoprecipitation (RIP) and crosslinking immunoprecipitation (CLIP) assays, providing insights into the RNA-protein interactions that influence cancer progression. Additionally, the research evaluates the therapeutic potential of targeting these RNAs, using small interfering RNAs (siRNAs) and antisense oligonucleotides (ASOs) in preclinical cancer models. Preliminary findings highlight the significance of long non-coding RNAs (lncRNAs) and micro RNAs (miRNAs) in modulating key signaling pathways involved in cell proliferation, apoptosis, and metastasis. This study underscores the importance of RNA-based diagnostics and therapeutics, paving the way for innovative treatment strategies in cancer management. Citation Format: Fathelrahman M Gameel. Exploring the Dual Roles of RNAs as Oncogenic Drivers and Therapeutic Targets in Cancer: A Cross-Sectional Study [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: RNAs as Drivers, Targets, and Therapeutics in Cancer; 2024 Nov 14-17; Bellevue, Washington. Philadelphia (PA): AACR; Mol Cancer Ther 2024;23(11_Suppl):Abstract nr B008.

PATH-63. M6A REGULATOR-BASED MOLECULAR CLASSIFICATION AND HUB GENES ASSOCIATED WITH IMMUNE INFILTRATION CHARACTERISTICS AND CLINICAL OUTCOMES IN DIFFUSE GLIOMAS

Abstract BACKGROUND m6A methylation modification is a new regulatory mechanism involved in tumorigenesis and tumor-immunity interaction. However, its impact on glioma immune microenvironment and clinical outcome remains unclear. METHODS Comprehensive expression profiles of 18 m6A regulators were used to identify molecular subtypes exhibiting distinct m6A modification patterns in 1673 glioma samples sourced from public datasets. A multi-genes signature was constructed for predicting clinical outcome and response to immunotherapy in glioma patients. Immunohistochemistry and cellular experiments were performed for validation. RESULTS Two m6A subtypes of gliomas were identified. The m6A-low-risk subtype was characterized by paucity of immune infiltrates; Whereas the m6A-high-risk subtype had higher abundances of multiple immune cells including lymphocyte and macrophage as well as increased expression of PD-L1, corresponding to an immunosuppressive phenotype. The m6A-high-risk subtype had poorer survival than the m6A-low-risk subtype in both the glioblastoma and lower grade gliomas cohorts. Eight m6A-related hub genes of high prognostic significances were identified and selected for developing a scoring signature termed as m6Ascore. Elevated m6Ascore indicated worse survival for glioma patients under standard care, but showed enhanced response to immunotherapy. Moreover, we demonstrated that overexpression of FTO, a m6A demethylase, inhibited the expressions of m6A-related hub genes (PTX3, SPAG4), impaired glioma cell viability and reduced macrophage chemotaxis. CONCLUSION This work develops an immune- and clinical-relevant m6A subtyping and a scoring model, which enhances our understanding of the role of m6A modification in regulating immune infiltration microenvironment in gliomas and helps to identify patients who are more likely to benefit from immunotherapy.

Molecular identification and expression patterns of sweet cherry HIPPs and functional analysis of PavHIPP16 in cold stress.

The HIPP proteins are involved in low-temperature stress, the growth of sweet cherry, and may be potential targets for genetic improvement. PavHIPP16 improved cold resistance in Arabidopsis. In response to abiotic stressors, the heavy metal-associated isoprenylated plant protein (HIPP) proteins play a crucial regulatory role. Although the function of HIPP has been identified in some plants, there have been fewer systematic studies conducted on sweet cherry (Prunus avium L.). Therefore, we performed a comprehensive analysis and expression profiling of PavHIPPs using bioinformatics, RT-PCR, and qRT-PCR techniques. Our findings revealed that 28 PavHIPP genes were unevenly distributed across eight chromosomes. We predicted nine motifs in PavHIPP proteins and observed similar gene structures among highly homologous proteins. The promoter sequences of PavHIPPs contained numerous regulatory elements associated with an adversity of stress. The expression levels of some members showed varying degrees of change under low-temperature treatment. These genes were differentially expressed during flower and fruit development. Arabidopsis overexpressing the PavHIPP16 (OE) gene showed significantly lower relative conductivity and malondialdehyde (MDA) content compared with the wild-type (WT) plants under cold environment. Conversely, peroxidase (POD) activity, superoxide dismutase (SOD) activity, and proline content were significantly higher in OE Arabidopsis than in WT plants. Overall, our results suggest that PavHIPP16 OE Arabidopsis thaliana exhibited enhanced adaptability compared to WT plants under cold conditions. This study provides a foundation for future investigations of the pathways regulating sweet cherry growth and development mediated by the HIPP genes.

Comprehensive Genome-Wide Analysis and Expression Profiling of the HVA22 Gene Family Unveils Their Potential Roles in Soybean Responses to Abiotic Stresses

Comprehensive Genome-Wide Analysis and Expression Profiling of the HVA22 Gene Family Unveils Their Potential Roles in Soybean Responses to Abiotic Stresses

Comprehensive Annotation and Expression Profiling of C2H2 Zinc Finger Transcription Factors across Chicken Tissues.

As the most abundant class of transcription factors in eukaryotes, C2H2-type zinc finger proteins (C2H2-ZFPs) play critical roles in various biological processes. Despite being extensively studied in mammals, C2H2-ZFPs remain poorly characterized in birds. Recent accumulation of multi-omics data for chicken enables the genome-wide investigation of C2H2-ZFPs in birds. The purpose of this study is to reveal the genomic occurrence and evolutionary signature of chicken C2H2-ZFPs, and further depict their expression profiles across diverse chicken tissues. Here, we annotated 301 C2H2-ZFPs in chicken genome, which are associated with different effector domains, including KRAB, BTB, HOMEO, PHD, SCAN, and SET. Among them, most KRAB-ZFPs lack orthologues in mammals and tend to form clusters by duplication, supporting their fast evolution in chicken. We also annotated a unique and previously unidentified SCAN-ZFP, which is lineage-specific and highly expressed in ovary and testis. By integrating 101 RNA-seq datasets for 32 tissues, we found that most C2H2-ZFPs have tissue-specific expression. Particularly, 74 C2H2-ZFPs-including 27 KRAB-ZFPs-show blastoderm-enriched expression, indicating their association with early embryo development. Overall, this study performs comprehensive annotation and expression profiling of C2H2 ZFPs in diverse chicken tissues, which gives new insights into the evolution and potential function of C2H2-ZFPs in avian species.

Common principles of macrophage biology in blood–tissue barriers

AbstractBlood–tissue barriers play crucial roles in specialized tissues such as the central nervous system (CNS), eye, testis, and placenta. Tissue‐resident macrophages in these tissues are indispensable for maintaining tissue homeostasis and responding to pathological conditions. Recent advances in high‐throughput and high‐dimensional single‐cell analysis techniques, coupled with fate‐mapping tools, have revealed a remarkable diversity of tissue‐resident macrophages at the blood–tissue barrier. However, while comprehensive expression profiling has revealed the heterogeneity of macrophages within individual tissues, the commonalities of macrophages across anatomically similar structures like blood–tissue barriers remain poorly understood. This review focuses on the diversity and functional specialization of macrophages in tissues with blood–tissue barriers, highlighting recent insights into their anatomical distribution, developmental origins, phenotypic characteristics, and roles in maintaining tissue homeostasis. These findings may deepen our understanding of macrophage adaptation mechanisms in tissues with blood–tissue barriers, potentially leading to improved therapies for related disorders. Furthermore, examining the similarities and differences of macrophages across tissues may elucidate the molecular underpinnings of tissue‐specific adaptation mechanisms and functional specialization.

Comprehensive genomic analysis and expression profiling of the cytochrome P450 genes during abiotic stress and flavonoid biosynthesis in potato (Solanum tuberosum)

The research focused on the cytochrome P450 (CYP) superfamily, a prominent enzyme family involved in plant metabolism. A total of 253 StCYP genes from the potato genome were investigated and characterized through various methods, including phylogentic analysis, physical and chemical characterization, chromosome localization, gene structure and conserved protein domain classification, gene duplication occurrences, collinearity and expression pattern analysis. The 253 StCYPs were classified into seven clans and 33 families, distributed unevenly across 12 chromosomes. Collinearity analysis revealed 28 pairs of orthologous genes between potato StCYPs and Arabidopsis AtCYPs. Moreover, the expression of the StCYPs in various tissue parts of doubled haploid (DM) potatoes under abiotic stress and exogenous hormone treatment was investigated by using RNA-seq data from the PGSC database. It was discovered that one StCYP gene likely contributes to drought stress response through the ABA-dependent pathway. Furthermore, RNA-seq analysis of pigmented tuber flesh from three potato clones at three developmental stages enabled the identification of StCYPs potentially implicated in the flavonoid biosynthesis in potato tubers. In particular, StCYP705A-like was further validated for its potential role in this process. Employing Gfanno software in conjunction with RNA-seq data, seven StCYP genes (Two StC4H, three StF3′H, one StFNS Ⅱ and one StF3′5′H) were identified as flavonoid biosynthetic pathway genes in potato. Additionally, five StCYPs in CYP 71 clan demonstrated a strong association with flavonoid biosynthesis. These findings lay a groundwork for a more comprehensive understanding of the StCYP gene family and further exploration of the functions of StCYP genes in potato abiotic stress tolerance and flavonoids biosynthesis.

Comprehensive characterization and expression profiling of BBX gene family in soybean in response to UV-B stress

The BBX gene family encodes transcription factors that regulate several biological processes, such as plant growth, development, and stress response. They have been identified and thoroughly studied in numerous plant species. The functional role of the BBX gene family against UV-B stress in soybean has not been well documented. Herein, this study focused on a comprehensive investigation of the GmBBX genes in soybean and their expression patterns in response to UV-B exposure. A total of 184 BBX genes were identified and analyzed to determine the conserved domain. Single and double B-box and CCT domains were found across these proteins, indicating potential functional diversity. The protein physicochemical properties showcased diverse characteristics, highlighting molecular size, stability, and hydrophobicity. Phylogenetic analysis revealed five distinct clades, showcasing a non-uniform distribution of GmBBX genes. Chromosomal mapping showed a non-uniform distribution of GmBBX genes across the 20 chromosomes of soybean. The highest number of genes (26) were found on chromosome 13, whereas chromosomes 5 and 15 displayed the lowest number of genes (3 genes each). Gene structure analysis revealed variations in exon-intron patterns, while motif composition analysis unveiled conserved motifs among GmBBX proteins. Gene duplication indicated that the expansion of the GmBBX genes was linked with tandem and dispersed duplications. Gene ontology analysis revealed enrichment of terms associated with light stimulus, response to abiotic stress, and molecular functions such as zinc ion binding. The promoter region reveals cis-acting elements related to hormones, light, and stress responses. The GmBBX genes exhibited differential expression in response to UV-B stress, suggesting their possible role in plant defense against UV-B stress. This study will provide a solid foundation for further analysis of the molecular mechanisms of GmBBX genes in soybean against UV-B stress.

A comprehensive characterization and expression profiling of defensin family peptides in Arabidopsis thaliana with a focus on their abiotic stress-specific transcriptional modulation

In addition to defensins, plants possess an array of defensin-like peptides that share many of their characteristics, as well as a role in plant’s innate immunity. Their involvement in the response to pathogens is well-known but the contribution in the plant response to abiotic stimuli is not fully understood. We have undertaken an in silico analysis to characterize all defensin family genes hitherto found in Arabidopsis, including genes encoding for defensin-like peptides, by detecting several peptides as candidates for further studies aiming to decipher specific responses to biotic and abiotic stresses, as well as to their crosstalk. We performed several analyses, including co-expression and cis-regulatory elements analyses, using transcriptomic data obtained from the ARS database, which integrates more than 20,000 Arabidopsis RNA-seq libraries.In silico analysis showed that jasmonates and ABA, together with transcription factors belonging to WRKY and AP2/EREBP families, modulate defensin and defensin-like gene expression. Indeed, the analysis performed in this study allowed to extract and organize omics data, which finally supported the inducible nature of defensins under both abiotic and biotic stresses. Moreover, in vivo expression analyses confirmed the heat and drought responsiveness of PDF1.4, ATTI1, PDF1.1, DEFL 206, defensin family genes selected for being upregulated by several abiotic conditions, at transcriptional level. Finally, the co-expression analysis provided information on other biological processes that may be correlated to the defensin induction, such as maintaining ROS homeostasis. Combining the comprehensive analysis of different transcriptional datasets with the integration of in vivo analyses emerged as a robust methodological approach to assess the proposed multi-stress responsive nature of defensin family genes.

Identification of apoptosis-related long non-coding RNAs expression profiles in patient with cervical intraepithelial neoplasia 3.

Long non-coding RNAs (lncRNAs) play an essential role in cancer biology. Cervical intraepithelial neoplasia grade 3 (CIN3) is the most severe precancerous lesion of cervical cancer. However, the mechanism of multiple lncRNAs in CIN3 has not been studied in-depth and is worth exploring. This study aims to summarize the lncRNA expression profile in CIN 3 and screen for lncRNAs with potential oncogenic effects. To further clarify the role of lncRNAs in the development of CIN3, this study collected cancer tissue and para-cancer tissue specimens from three CIN3 patients. The RNA sequencing (RNA-Seq) analysis was used to construct expression profiles of lncRNAs and confirmed by real-time reverse transcription PCR (real-time RT-PCR) methods. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) were performed with computational methods. We obtained their possible target genes through the cis- and trans-regulatory analysis of the lncRNAs. In addition, this study predicted new transcripts and lncRNAs by Cufflinks analysis and coding potential identification (Coding Potential Calculator) analysis to discover new tumor regulatory molecules. The differential expressions of 1 555 genes, 1 562 mRNAs, 241 ncRNAs, and 6 616 new predicted-lncRNAs were found. The most prominently up-regulated and down-regulated lncRNAs were NR_145433.1 and ENST00000513672.1, respectively. KEGG analysis revealed that lncRNA-targeted genes were closely related to apoptosis, metabolic, p53 signaling pathway, and other cancer-related pathways. The real-time RT-PCR validation results of 5 apoptosis-related lncRNAs (NR_145433.1, ENST00000510610.2, UC001Kfo, ENST00000602964.1, and NR_123733.1) in cervical cancer were consistent with the sequencing results. This study provides a comprehensive expression profile of lncRNAs in CIN3 patients, particularly the apoptosis-related expression profile of lncRNAs, and provides direction and clues for the study of cervical cancer and the search for potential therapeutic targets.

Construction of a Cancer Stem Cell Marker Genes-Related 22-Gene Signature for Overall Survival Prediction in High-Risk Wilms’ Tumor

Background: This study aimed to investigate the comprehensive expression profile of cancer stem cell (CSC)-related genes and construct a prognostic signature for overall survival (OS) prediction in high-risk Wilms’ tumor (WT). Materials and methods: Gene expression and survival data from 120 high-risk WT cases in the Therapeutically Applicable Research to Generate Effective Treatments (TARGET)-WT were used. Results: In total, 229 CSC-related genes were found to be significantly dysregulated in WT compared to tumor-adjacent normal tissues, among which 34 were associated with OS. Using LASSO regression, a 22-gene signature was developed, which exhibited excellent performance in 3-, 5-, and 10-year OS predictions (AUC > 0.86). The high-risk score group showed markedly poorer OS compared to the low-risk score group (median separation, HR = 6.41, 95% CI: 3.18–12.92, p = 3.2e − 9). The 22-gene signature was an independent prognostic factor for OS (HR = 5.086, 95% CI: 3.019–8.568, p < 0.001). Conclusion: This study identified a robust prognostic signature that can effectively support OS prediction.

Comprehensive Identification and Expression Profiling of Epidermal Pattern Factor (EPF) Gene Family in Oilseed Rape (Brassica napus L.) under Salt Stress.

Rapeseed is a crucial oil crop globally, and in recent years, abiotic stress has increasingly affected its growth, development, yield, and quality. Salt stress is a significant abiotic factor that restricts crop production. The EPF gene family is vital in managing salt stress by controlling stomatal development and opening, which reduces water loss and increases plant salt tolerance. To explore the features of the EPF gene family in Brassica napus and their expression under salt stress, this study utilized Arabidopsis EPF protein sequences as seed sequences, including their PF17181 and PF16851 domains. A total of 27 members of the EPF gene family were detected within the rapeseed genome. The study examined the physicochemical properties, gene structure, phylogenetic relationships, and collinearity of BnEPFs. Through transcriptomes, we employed the qPCR method to determine the relative expression levels of BnEPF genes potentially associated with rapeseed stress resistance under both non-salt and salt stress conditions. Subsequently, we assessed their influence on rapeseed plants subjected to salt stress. During salt stress conditions, all BnEPF genes displayed a downregulation trend, indicating their potential impact on stomatal development and signal transduction pathways, consequently improving rapeseed's resistance to salt stress. The study findings establish a basis for exploring the roles of BnEPFs and offer candidate genes for breeding stress-resistant varieties and enhancing the yield in rapeseed.

Comprehensive genomic screening and expression profiling of trihelix family in pearl millet under abiotic stresses with emphasis on functional insights of PgTHX24

The trihelix transcription factors (THX TFs) play a crucial role in light responses and are involved in plant growth, development, and stress responses. In this study, we have identified 35 trihelix TFs in pearl millet (Pennisetum glaucum), which is one of the most widely grown C4 cereal crops in tropical semi-arid regions. Identified PgTHXs (Trihelix members of P. glaucum) were classified into 5 subgroups (GT1, GT2, GTγ, SH4, and SIP1) based on phylogenetic analysis, and these subgroup members shared similar gene structure and motif distribution pattern. Collinearity analysis exhibited gene duplication events of trihelix family members in pearl millet across the genome. Gene ontology (GO) annotation and cis-regulatory elements (CREs) analysis of PgTHXs suggested their involvement in diverse biological and molecular functions associated with plant growth, development, and stress responses. RNA sequencing data and expression profile displayed differential expression patterns of PgTHXs under abiotic stress and phytohormone treatments. The induced expression pattern of the PgTHX4, PgTHX5, PgTHX24, and PgTHX30 suggested their potential involvement in abiotic stress responses through phytohormonal signalling pathways. Among these, PgTHX24, a GT-3b member, was localized in the nucleus with self-transactivation ability. Overexpression of PgTHX24 positively regulated expression of stress-related markers in transformed pearl millet calli under drought stress conditions. Promoter activity analysis also highlighted the stress-inducible nature of PgTHX24’s promoter. Overall, our findings provide a comprehensive understanding of PgTHXs with a framework for further functional characterization to understand their regulatory role in pearl millet’s growth, development, and stress responses. Key messageThirty-five trihelix TFs were identified in pearl millet, and a comprehensive expression profile highlighted their functional diversity. Overexpression of PgTHX24 exhibited its potential involvement in abiotic stress responses.