Expression Patterns Research Articles

Chromatin structure and 3D architecture define the differential functions of PU.1 regulatory elements in blood cell lineages

The precise spatiotemporal expression of the hematopoietic ETS transcription factor PU.1, a key determinant of hematopoietic cell fates, is tightly regulated at the chromatin level. However, how chromatin signatures are linked to this dynamic expression pattern across different blood cell lineages remains uncharacterized. Here, we performed an in-depth analysis of the relationships between gene expression, chromatin structure, 3D architecture, and trans-acting factors at PU.1 cis-regulatory elements (PCREs). By identifying phylogenetically conserved DNA elements within chromatin-accessible regions in primary human blood lineages, we discovered multiple novel candidate PCREs within the upstream region of the human PU.1 locus. A subset of these elements localizes within an 8-kb-wide cluster exhibiting enhancer features, including open chromatin, demethylated DNA, enriched enhancer histone marks, present enhancer RNAs, and PU.1 occupation, presumably mediating PU.1 autoregulation. Importantly, we revealed the presence of a common 35-kb-wide CTCF-flanked insulated neighborhood that contains the PCRE cluster (PCREC), forming a chromatin territory for lineage-specific and PCRE-mediated chromatin interactions. These include functional PCRE-promoter interactions in myeloid and B cells that are absent in erythroid and T cells. By correlating chromatin structure and 3D architecture with PU.1 expression in various lineages, we were able to attribute enhancer versus silencer functions to individual elements. Our findings provide mechanistic insights into the interplay between dynamic chromatin structure and 3D architecture in the chromatin regulation of PU.1 expression. This study lays crucial groundwork for additional experimental studies that validate and dissect the role of PCREs in epigenetic regulation of normal and malignant hematopoiesis.

Comprehensive Analysis and Experimental Validation of HEPACAM2 as a Potential Prognosis Biomarker and Immunotherapy Target in Colorectal Cancer.

The role of HEPACAM family member 2 (HEPACAM2) is unclear in colorectal cancer (CRC). The objective of this study was to perform an extensive examination of HEPACAM2 and validate it experimentally in CRC. This study investigated the significance of HEPACAM2 in CRC and its potential diagnostic utility utilizing data from the Cancer Genome Atlas (TCGA) database. Additionally, the study examined potential regulatory networks involving HEPACAM2, including its associations with immune infiltration, immune checkpoint genes, tumor mutational burden (TMB), microsatellite instability (MSI), mRNA expression-based stemness index (mRNAsi), and drug sensitivity in CRC. The expression of HEPACAM2 was further validated using the GSE89076 dataset, and quantitative reverse transcription PCR (qRT-PCR) was employed to confirm HEPACAM2 expression levels in six pairs of CRC tissue samples. HEPACAM2 exhibited abnormal expression patterns in various types of cancer, including CRC. A decrease in HEPACAM2 expression levels in CRC was found to be significantly correlated with the T stage (p < 0.001). Reduced HEPACAM2 expression in CRC patients was also linked to poorer overall survival (OS) (p = 0.007). The expression levels of HEPACAM2 in CRC patients were identified as an independent prognostic factor (p = 0.016). Furthermore, HEPACAM2 was associated with TCF-dependent signaling in response to WNT, G2/M checkpoints, and other pathways. The expression of HEPACAM2 in CRC was found to be associated with immune infiltration, immune checkpoint genes, TMB / MSI, and mRNAsi. Additionally, the expression of HEPACAM2 in CRC was significantly and inversely correlated with the drug sensitivities to gw772405x and 6-phenyl-6h-indeno[1,2-c]isoquinoline-5,11-dione. qRT-PCR confirmed that the expression level of HEPACAM2 was found to be lowly expressed in CRC tissues. These findings suggest that HEPACAM2 may serve as a potential prognostic biomarker and immunotherapeutic target for CRC patients.

Comprehensive studies of the serine carboxypeptidase-like (SCPL) gene family in Carya cathayensis revealed the roles of SCPL4 in epigallocatechin-3-gallate (EGCG) synthesis and drought tolerance

Hickory (Carya cathayensis) nuts are rich in epigallocatechin-3-gallate (EGCG) with multiple health functions. EGCG also regulates plant growth, development and stress responses. However, research on the synthesis mechanism of EGCG and its function in hickory is currently limited. Herein, 44 serine carboxypeptidase-like (SCPL) members were identified from the hickory genome and classified into three major categories: SCPL-I, SCPL-II, and SCPL-III. In the CcSCPLs-IA branch, CcSCPL3/4/5/8/9/11/13 showed differential expression patterns in various tissues, especially with relatively high expression levels in plant roots, female flowers and seed coat. These proteins have a catalytic triad composed of serine (Ser), aspartic acid (Asp) and histidine (His). Ser-His in the triad and arginine (Arg) mediated the docking of CcSCPL3/4/5/11 with 1-O-galloyl-β-d-glucose (βG) and epigallocatechin (EGC), whereas the Asp of the triad did not. CcSCPL4 was further confirmed to promote the synthesis of EGCG in tobacco leaves. CcSCPL4 may function as monomer and be mainly localized within cellular structures outside the nucleus. Notably, the expression level of CcSCPL4 significantly changed after drought, cold, and salt stress, with the highest expression level under drought stress. Meanwhile CcSCPL4 over-expression could enhance the drought resistance of Saccharomyces cerevisiae and Arabidopsis. This study elucidates key enzymes for EGCG synthesis and their role in drought resistance, providing insights into the EGCG synthesis pathway and molecular breeding of hickory in future.

Magnesium-Doped Carbon Quantum Dot Nanomaterials Alleviate Salt Stress in Rice by Scavenging Reactive Oxygen Species to Increase Photosynthesis.

Salt stress has strongly impacted the long-term growth of eco-friendly farming worldwide. By targeting the oxidative stress induced by salt, the utilization of biomass-derived carbon dots (CDs) that possess high-efficiency antioxidant properties, are nontoxic, and have excellent biocompatibility represents a viable and effective approach for enhancing the salt tolerance of plants. In this study, we blended magnesium oxide nanoparticles with carbon sources derived from durian shells to construct Mg-doped carbon dots (Mg-CDs) through a hydrothermal reaction. We demonstrated that the foliar application of 150 μg/mL Mg-CDs to rice plants after treatment with 100 mM salt effectively increased the plant height (9.52%), fresh weight (22.41%), dry weight (33.33%), K+ content (21.46%), chlorophyll content (36.21%), and carotenoid content (16.21%); decreased the malondialdehyde (MDA) (9.43%), Na+ (25.75%), H2O2 (17.50%), and O2•- contents (37.99%); and promoted the photosynthetic system and antioxidant activity. Transcriptome analysis revealed that Mg-CD pretreatment triggered transcriptional reprogramming in rice seedlings. The enrichment analysis of the Kyoto Encyclopedia of Genes and Genomes pathways based on trend groups of gene expression patterns of Profile 8 and Profile 15 indicated that priming with Mg-CDs activated stress signaling- and defense-related pathways, such as metabolic pathways, biosynthesis of secondary metabolites, and photosynthesis pathways. These activations subsequently prompted the expression of genes related to the mitogen-activated protein kinase signaling pathway, hormone signal transduction, the oxidative stress response, and the photosynthetic system. This study demonstrated that the use of Mg-CDs represents a potential strategy to increase plant salt tolerance, creating the possibility for the regulation of crop salinity stress and offering valuable advancements in sustainable agriculture.

A luminal non-coding RNA-based genomic classifier confirms favourable outcomes in patients with clinically organ-confined bladder cancer treated with radical cystectomy.

To further evaluate a genomic classifier (GC) in a cohort of patients undergoing radical cystectomy (RC), as long non-coding RNA (lncRNA)-based genomic profiling has suggested utility in identifying a distinct tumour subgroup corresponding to a favourable prognosis in patients with bladder cancer. Transcriptome-wide expression profiling using Decipher Bladder was performed on transurethral resection of bladder tumour samples from a cohort of patients with high-grade, clinically organ-confined (cTa-T2N0M0) urothelial carcinoma (UC) who subsequently underwent RC without any neoadjuvant therapy (n = 226). The lncRNA-based luminal favourable status was determined using a previously developed GC. The primary endpoint was overall survival (OS) after RC. Secondary endpoints included cancer-specific mortality and upstaging at RC. In the study, 134 patients were clinical non-muscle-invasive bladder cancer (cTa/Tis/T1) and 92 patients were cT2. We identified 60 patients with luminal favourable subtype, all of which showed robust gene expression patterns associated with less aggressive bladder cancer biology. On multivariate analysis, patients with the luminal favourable subtype (vs without) were significantly associated with lower odds of upstaging to pathological (p)T3+ disease (odds ratio [OR] 0.32, 95% confidence interval [CI] 0.12-0.82; P = 0.02), any upstaging (OR 0.41, 95% CI 0.20-0.83; P = 0.01), and any upstaging and/or pN+ (OR 0.50, 95% CI 0.25-1.00; P = 0.05). Luminal favourable bladder cancer was significantly associated with better OS (hazard ratio 0.33, 95% CI 0.15-0.74; P = 0.007). This study validates the performance of the GC for identifying UCs with a luminal favourable subtype, harbouring less aggressive tumour biology.

Molecular characterization, spatio-temporal expression patterns of crtc2 gene and its immune roles in yellow catfish (Pelteobagrus fulvidraco)

cAMP response element binding (CREB) protein 2 (CRTC2) is a transcriptional coactivator of CREB and plays an important role in the immune system. Thus far, the physiological roles of Crtc2 in teleost are still poorly understood. In this study, the crtc2 gene was identified and characterized from yellow catfish (Pelteobagrus fulvidraco; therefore, the gene is termed as pfcrtc2), and its evolutionary and molecular characteristics as well as potential immunity-related roles were investigated. Our results showed that the open reading frame of pfcrtc2 was 2,346 bp in length, encoding a protein with 781 amino acids. Gene structure analysis revealed its existence of 14 exons and 13 introns. A phylogenetic analysis proved that the tree of crtc2 was clustered into five groups, exhibiting a similar evolutionary topology with species evolution. Multiple protein sequence alignment demonstrated high conservation of the crtc2 in various vertebrates with similar structure. Syntenic and gene structural comparisons further established that crtc2 was highly conserved, implying its similar roles in diverse vertebrates. Tissue distribution pattern detected by quantitative real-time PCR showed that the pfcrtc2 gene was almost expressed in all detected tissues except for eyes, with the highest expression levels in the gonad, indicating that Crtc2 may play important roles in various tissues. In addition, pfcrtc2 was transcribed at all developmental stages in yellow catfish, showing the highest expression levels at 12 h after fertilization. Finally, the transcriptional profiles of crtc2 were significantly increased in yellow catfishes injected with Aeromonas hydrophila or Poly I:C, which shared a consistent change pattern with four immune-related genes including IL-17A, IL-10, MAPKp38, and NF-κBp65, suggesting pfCrtc2 may play critical roles in preventing both exogenous bacteria and virus invasion. Anyway, our findings lay a solid foundation for further studies on the functions of pfcrtc2, and provide novel genetic loci for developing new strategies to control disease outbreak in teleost.

Transcriptomics-guided optimization of vitamins to enhance erythromycin yield in saccharopolyspora erythraea

Comparative transcriptomics uncovered distinct expression patterns of genes associated with cofactor and vitamin metabolism in the high-yielding mutant strain Saccharopolyspora erythraea HL3168 E3, as compared to the wild-type NRRL 2338. An in-depth analysis was conducted on the effects of nine vitamins, and it was determined that thiamine pyrophosphate (TPP), vitamin B2, vitamin B6, vitamin B9, vitamin B12, and hemin are key enhancers in erythromycin production in E3, increasing the erythromycin titer by 7.96–12.66%. Then, the Plackett-Burman design and the path of steepest ascent were applied to further optimize the vitamin combination for maximum production efficiency, enhancing the erythromycin titer in shake flasks by 39.2%. Otherwise, targeted metabolomics and metabolic flux analysis illuminated how vitamin supplementation modulates the central carbon metabolism with notable effects on the TCA cycle and methionine synthesis to augment the provision of energy and precursors essential for erythromycin synthesis. This work highlights the capacity for precise vitamin supplementation to refine metabolic pathways, thereby boosting erythromycin production, and provides valuable directions for application on an industrial scale.Graphical

Systematical characterization of Rab7 gene family in Gossypium and potential functions of GhRab7B3-A gene in drought tolerance

BackgroundCotton serves as a primary source of natural fibers crucial for the textile industry. However, environmental elements such as drought have posed challenges to cotton cultivation, resulting in adverse impacts on both production and fiber quality. Improving cotton’s resilience to drought could mitigate yield losses and foster the expansion of cotton farming. Rab7 protein, widely present in organisms, controls the degradation and recycling of cargo, and has a potential role in biotic and abiotic tolerance. However, comprehensive exploration of the Rab7 gene family in Gossypium remains scarce.ResultsHerein, we identified a total of 10, 10, 20, and 20 Rab7 genes through genome-wide analysis in Gossypium arboreum, Gossypium raimondii, Gossypium hirsutum, and Gossypium barbadense, respectively. Collinearity analysis unveiled the pivotal role of whole genome or segmental duplication events in the expansion of GhRab7s. Study of gene architecture, conserved protein motifs, and domains suggested the conservation of structure and function throughout evolution. Exploration of cis-regulatory elements revealed the responsiveness of GhRab7 genes to abiotic stress, corroborated by transcriptome analysis under diverse environmental stresses. Notably, the greatly induced expression of GhRab7B3-A under drought treatment prompted us to investigate its function through virus-induced gene silencing (VIGS) assays. Silencing GhRab7B3-A led to exacerbated dehydration and wilting compared with the control. Additionally, inhibition of stomatal closure, antioxidant enzyme activities and expression patterns of genes responsive to abiotic stress were observed in GhRab7B3-A silenced plants.ConclusionsThis study sheds light on Rab7 members in cotton, identifies a gene linked to drought stress, and paves the way for additional investigation of Rab7 genes associated with drought stress tolerance.

The phenotypic and genotypic spectrum of individuals with mono- or biallelic ANK3 variants.

ANK3 encodes ankyrin-G, a protein involved in neuronal development and signaling. Alternative splicing gives rise to three ankyrin-G isoforms comprising different domains with distinct expression patterns. Mono- or biallelic ANK3 variants are associated with non-specific syndromic intellectual disability in 14 individuals (seven with monoallelic and seven with biallelic variants). In this study, we describe the clinical features of 13 additional individuals and review the data on a total of 27 individuals (16 individuals with monoallelic and 11 with biallelic ANK3 variants) and demonstrate that the phenotype for biallelic variants is more severe. The phenotypic features include language delay (92%), autism spectrum disorder (76%), intellectual disability (78%), hypotonia (65%), motor delay (68%), attention deficit disorder (ADD) or attention deficit hyperactivity disorder (ADHD) (57%), sleep disturbances (50%), aggressivity/self-injury (37.5%), and epilepsy (35%). A notable phenotypic difference was presence of ataxia in three individuals with biallelic variants, but in none of the individuals with monoallelic variants. While the majority of the monoallelic variants are predicted to result in a truncated protein, biallelic variants are almost exclusively missense. Moreover, mono- and biallelic variants appear to be localized differently across the three different ankyrin-G isoforms, suggesting isoform-specific pathological mechanisms.

Transcriptome and WGCNA Analyses Reveal Key Genes Regulating Anthocyanin Biosynthesis in Purple Sprout of Pak Choi (Brassica rapa L. ssp. chinensis)

Chinese cabbage is rich in vitamins, fibre, and nutrients and is one of the primary vegetables consumed in autumn and winter in South Asia. ‘Purple pak choi’ sprouts are particularly rich in anthocyanins and are favoured by consumers. However, reports on the regulation of anthocyanin synthesis in purple pak choi sprouts do not exist. In this study, we examined the phenotypic development of purple pak choi sprouts after germination. The total anthocyanin content increased from 0.02 to 0.52 mg/g FW from days 0 to 6. RNA-seq data analysis revealed an increase in differentially expressed genes corresponding to the development of purple pak choi sprouts. Expression pattern analysis of genes associated with the anthocyanin biosynthesis pathway revealed a significant upregulation of structural genes during the purple phase, suggesting that the transcription factors PAP2 and MYBL2 may play crucial regulatory roles. BraPAP2.A03, BraTT8.A09, and BraMYBL2.A07 exhibited strong interactions with key genes in the anthocyanin biosynthesis pathway, specifically BraDFR.A09. Furthermore, the expression of BraPAP2.A03 aligned with the expression patterns of most anthocyanin biosynthesis-related genes, whereas those of BraTT8.A09 and BraMYBL2.A07 corresponded with the expression pattern of BraDFR.A09. These results provide valuable insights into regulatory mechanisms underlying anthocyanin synthesis in purple pak choi sprouts.

LncRNA HAGLROS: A Vital Oncogenic Propellant in Various Human Cancers.

HAGLR Opposite Strand lncRNA (HAGLROS) is a long non-coding RNA (lncRNA) located on the long arm of human chromosome 2 at locus 2q31.1. Emerging evidence highlights HAGLROS as a pivotal player in human cancers, characterized by its significant upregulation across multiple malignancies where it functions as an oncogenic driver. Its aberrant expression is closely linked to the initiation and progression of 13 distinct cancer types, notably correlating with adverse clinical outcomes and reduced overall survival rates in 9 of these cancer types. Mechanistically, HAGLROS is under the regulatory influence of the transcription factor STAT3, exerts competitive binding to 9 miRNAs, activates 5 signaling pathways pivotal for cancer cell proliferation and metastasis, as well as intricately modulates gene expression profiles. Given its multifaceted roles, HAGLROS emerges as a promising candidate for cancer diagnostics and prognostics. Moreover, its potential as a therapeutic target holds considerable promise for novel treatment strategies in oncology. This review synthesizes current research on HAGLROS, covering its expression patterns, biological roles, and clinical significance in cancer. By shedding light on these aspects, this review aims to contribute new perspectives that advance our understanding of cancer biology, enhance diagnostic accuracy, refine prognostic assessments, and pave the way for targeted therapeutic interventions.

Identification of Target Gene and Interacting Protein of Two LaSCL6 Alternative Splicing Variants Provides Novel Insights into Larch Somatic Embryogenesis

Somatic embryogenesis is valuable for clonal propagation and genetic improvement, and it also serves as an ideal system for studying plant development mechanisms. In Larix kaempferi, microRNA171 and its target gene L. kaempferi SCARECROW-LIKE6 (LaSCL6), which has two alternative splicing variants, can regulate somatic embryogenesis; however, the underlying molecular mechanism is still unknown. In this study, we overexpressed these two LaSCL6 variants in Oryza sativa and Arabidopsis thaliana and then used the RNA-Seq method to screen genes from O. sativa and A. thaliana, whose expression patterns are related to those of LaSCL6 variants. The screened genes were then used to search L. kaempferi proteins to identify the candidate target genes of LaSCL6. After yeast one-hybrid and dual- luciferase transcriptional activity assays, cytochrome P450, family 89, subfamily A, polypeptide 5 (CYP89A5), and wall-associated receptor kinase-like 20 (WAKL20) were confirmed to be the target genes of LaSCL6-var1; in addition, WAKL20 and UDP-glycosyltransferase 85A3 (UGT85A3) were confirmed to be the target genes of LaSCL6-var2. Moreover, APETALA2-like protein 2, a transcription factor from the AP2/ERF family, was shown to interact with LaSCL6-var1 and LaSCL6-var2. Taken together, our results suggest a regulatory network of miR171-LaSCL6. The findings presented here not only provide novel insights into the regulation of the miR171-LaSCL6 module but also explain the mechanism underlying larch somatic embryogenesis and other biological processes.

Genome-wide analysis of the Amorphophallus konjac AkCSLA gene family and its functional characterization in drought tolerance of transgenic arabidopsis

BackgroundAmorphophallus konjac (A. konjac), a perennial tuberous plant, is widely cultivated for its high konjac glucomannan (KGM) content, a heteropolysaccharide with diverse applications. The cellulose synthase-like (CSL) gene family is known to be a group of processive glycan synthases involved in the synthesis of cell-wall polysaccharides and plays an important role in the biological process of KGM. However, in A. konjac the classification, structure, and function of the AkCSLA superfamily have been studied very little.ResultsBioinformatics methods were used to identify the 11 AkCSLA genes from the whole genome of Amorphophallus konjac and to systematically analyze their characteristics, phylogenetic evolution, promoter cis-elements, expression patterns, and subcellular locations. Phylogenetic analysis revealed that the AkCSLA gene family can be divided into three subfamilies (Groups I- III), which have close relationships with Arabidopsis. The promoters of most AkCSLA family members contain MBS elements and ABA response elements. Analysis of expression patterns in different tissues showed that most AkCSLAs are highly expressed in the corms. Notably, PEG6000 induced down-regulation of the expression of most AkCSLAs, including AkCSLA11. Subcellular localization results showed that AkCSLA11 was localized to the plasma membrane, Golgi apparatus and endoplasmic reticulum. Transgenic Arabidopsis experiments demonstrated that overexpression of AkCSLA11 reduced the plant’s drought tolerance. This overexpression also inhibited the expression of drought response genes and altered the sugar components of the cell wall. These findings provide new insights into the response mechanisms of A. konjac to drought stress and may offer potential genetic resources for improving crop drought resistance.ConclusionIn conclusion, the study reveals that the AkCSLA11 gene from A. konjac negatively impacts drought tolerance when overexpressed in Arabidopsis. This discovery provides valuable insights into the mechanisms of plant response to drought stress and may guide future research on crop improvement for enhanced resilience.

Genome-Wide Characterization of Shi-Related Sequence Gene Family and Its Roles in Response to Zn2+ Stress in Cucumber

Shi-related sequence (SRS) proteins, which consist of the RING-like zinc finger domain and IGGH domain, are plant-specific transcription factors that have been well-studied in several plant species. However, information about SRS genes and their roles in cucumber (Cucumis sativus L.) is limited. Therefore, we performed detailed bioinformatic analysis of the SRS gene family, including gene numbers and positions, genes structures, conserved motif distribution patterns, phylogenetic analysis, and promoter cis-element analysis. Eight SRS genes were identified in cucumber and distributed on all seven cucumber chromosomes. SRS genes are conserved in plants and divided into two groups in cucumber based on their protein sequence. In silico analysis predicted that most genes may function in response to abiotic stresses and phytohormones. Gene ontology analysis predicted the possible involvement of genes in development and reproduction, and DNA and protein binding on a molecular level. Furthermore, the differential expression pattern of SRS genes in leaf, stem and root under the condition of Zn2+ stress suggested their roles in response to Zn2+ stress. Furthermore, our metal tolerance assay suggested that CsSRS2 and CsSRS5 mediated enhanced tolerance to Zn2+ stress in Escherichia coli cells. Our study provides a foundation for the functional study of SRS genes in cucumber.

Isolation and Identification of Alkaloid Genes from the Biomass of Fritillaria taipaiensis P.Y. Li

Background/Objectives: Fritillaria taipaiensis P.Y. Li is a valuable traditional Chinese medicinal herb that utilizes bulbs as medicine, which contain multiple alkaloids. Biomass, as a sustainable resource, has promising applications in energy, environmental, and biomedical fields. Recently, the biosynthesis and regulatory mechanisms of the main biomass components of biomass have become a prominent research topic. Methods: In this article, we explored the differences in the heterosteroidal alkaloid components of F. taipaiensis biomass using liquid chromatography–mass spectrometry and high-throughput transcriptome sequencing. Results: The experimental results demonstrated significant differences in the eight types of heterosteroidal alkaloid components among the biomass of F. taipaiensis, including peimisine, imperialine, peimine, peiminine, ebeinone, ebeiedine, ebeiedinone, and forticine. Transcriptomic analysis revealed substantial significant differences in gene expression patterns in the various samples. Three catalytic enzyme-coding genes, 3-hydroxy-3-methylglutaryl coenzyme A synthase (HMGS), 3-hydroxy-3-methylglutaryl coenzyme A reductase (HMGR), and terpene synthase (TPS), were speculated to contribute to the regulation of the differential accumulation of alkaloid synthesis in F. taipaiensis bulbs. A strong positive correlation was observed between the transcriptional level of the TPS gene and the alkaloid content of F. taipaiensis biomass, suggesting that TPS may be a key gene in the biosynthesis pathway of alkaloids. This finding can be used for subsequent gene function verification and molecular regulatory network analysis. Conclusions: This work provides fundamental data and novel insights for the subsequent research on alkaloid biosynthesis in F. taipaiensis.

Clinical and prognostic significance of Hec1 expression in patients with Cervical Cancer

ObjectiveHec1 is a component of the Ndc80 kinetochore complex and is frequently upregulated in various cancers. However, the clinical significance of Hec1 in cervical cancer remains largely unknown. This study aimed to investigate the expression patterns of Hec1 in cervical cancer and its relationship with the clinicopathological characteristics of patients diagnosed with the disease.MethodsImmunohistochemistry was used to assess the expression of Hec1 in 136 cervical cancer tissue samples and 82 normal cervical tissue samples. The relationship between Hec1 protein expression and the clinicopathological characteristics of cervical cancer patients was analyzed using the Chi-square test. Additionally, the association between Hec1 protein expression and patient survival was examined using Kaplan-Meier survival curves. Independent risk factors affecting the prognosis of cervical cancer patients were analyzed using the Cox proportional hazards regression model.ResultsThe positive expression rate of Hec1 protein in cervical cancer tissues was 83.82%, significantly higher than the 7.31% in normal cervical tissues. Compared to patients with negative Hec1 expression, those with positive expression exhibited significantly higher FIGO staging, increased lymph node metastasis, greater depth of tumor stromal infiltration, and larger tumor diameter. Multivariable analysis using the Cox proportional hazards regression model indicated that Hec1 positive expression was an independent risk factor for both overall survival (HR = 2.79, 95% CI: 1.65–4.05, p = 0.012) and progression-free survival (HR = 1.81, 95% CI: 1.22-3.18, p = 0.002) in cervical cancer patients. Kaplan-Meier survival curve analysis showed that patients with positive Hec1 expression experienced a lower overall survival (HR: 2.72, 95% CI: 1.15–4.52, p = 0.004) and progression-free survival (HR: 3.12, 95% CI: 1.62–5.03, p = 0.002) when compared to those with negative Hec1 expression.ConclusionHec1 is significantly upregulated in cervical cancer tissues and associated with poor prognosis in cervical cancer patients. Therefore, Hec1 could be a novel biomarker, not only for the diagnosis and treatment evaluation of cervical cancer but also as an indicator for predicting the prognosis of cervical cancer patients.

Whole Blood Transcriptome Analysis in Congenital Anemia Patients

Congenital anemias include a broad range of disorders marked by inherent abnormalities in red blood cells. These abnormalities include enzymatic, membrane, and congenital defects in erythropoiesis, as well as hemoglobinopathies such as sickle cell disease and thalassemia. These conditions range in presentation from asymptomatic cases to those requiring frequent blood transfusions, exhibiting phenotypic heterogeneity and different degrees of severity. Despite understanding their different etiologies, all of them have a common pathophysiological origin with congenital defects of erythropoiesis. We can find different types, from congenital sideroblastic anemia (CSA), which is a bone marrow failure anemia, to hemoglobinopathies as sickle cell disease and thalassemia, with a higher prevalence and clinical impact. Recent efforts have focused on understanding erythropoiesis dysfunction in these anemias but, so far, deep gene sequencing analysis comparing all of them has not been performed. Our study used Quant 3′ mRNA-Sequencing to compare transcriptomic profiles of four sickle cell disease patients, ten thalassemia patients, and one rare case of SLC25A38 CSA. Our results showed clear differentiated gene map expressions in all of them with respect to healthy controls. Our study reveals that genes related to metabolic processes, membrane genes, and erythropoiesis are upregulated with respect to healthy controls in all pathologies studied except in the SLC25A38 CSA patient, who shows a unique gene expression pattern compared to the rest of the congenital anemias studied. Our analysis is the first that compares gene expression patterns across different congenital anemias to provide a broad spectrum of genes that could have clinical relevance in these pathologies.

Lamin A and Emerin Protein Expression Remains Consistently Low and Nuclear Size is Unchanged in Normal Endometrium, Precancerous Lesions, and Endometrioid Carcinoma.

Nuclear laminar or inner nuclear membrane proteins, including lamin A, B1, and B2 and emerin, are involved in maintaining nuclear morphology. However, their expression patterns vary among tumors and remain incompletely understood. Endometrioid carcinoma (EC) exhibits mild nuclear atypia, although the underlying reasons have not been thoroughly explored. In this study, we quantitatively analyzed emerin and lamin A, B1, and B2 expression levels in normal endometrium (NE), precancerous lesions, and EC using computer-assisted image analysis to assess the proteins' roles in nuclear morphologic change during tumorigenesis. From NE to EC, nuclear size remained unchanged, and lamin A and emerin were consistently expressed at low levels, whereas lamin B1 and B2 expression gradually decreased. Given the association between lamin A and emerin as well as their roles in nuclear morphology, these results indicate that their consistent low expression may underlie the preservation of nuclear size and shape in EC relative to NE. Conversely, lamin B1 and B2 are implicated in tumor progression rather than nuclear morphology maintenance. As lamin A and emerin are expressed in many organs and tumors, the consistently low expression of these proteins from NE to EC highlights a notable feature of the endometrium and endometrial carcinogenesis.

Comprehensive circular RNA profiling in various sheep tissues

Despite the scientific relevance of circular RNAs (circRNAs), the study of these RNAs in non-model organisms, especially in sheep, is still in its infancy. On the other hand, while some studies have focused on sheep circRNA identification in a limited number of tissues, there is a lack of comprehensive analysis that profile circRNA expression patterns across the tissues not yet investigated. In this study, 61 public RNA sequencing datasets from 12 different tissues were uniformly analyzed to identify circRNAs, profile their expression and investigate their various characteristics. We reported for the first time a circRNA expression landscape with functional annotation in sheep tissues not yet investigated including hippocampus, BonMarrowMacrophage, left-ventricle, thymus, ileum, reticulum and 23-day-embryo. A stringent computational pipeline was employed and 8919 exon-derived circRNAs with high confidence were identified, including 88 novel circRNAs. Tissue-specificity analysis revealed that 3059 circRNAs were tissue-specific, which were also more specific to the tissues than linear RNAs. The highest number of tissue-specific circRNAs was found in kidney, hippocampus and thymus, respectively. Co-expression analysis revealed that expression of circRNAs may not be affected by their host genes. While most of the host genes produced more than one isoform, only one isoform had dominant expression across the tissues. The host genes of the tissue-specific circRNAs were significantly enriched in biological/pathways terms linked to the important functions of their corresponding tissues, suggesting potential roles of circRNAs in modulating physiological activity of those tissues. Interestingly, functional terms related to the regulation and various signaling pathways were significantly enriched in all tissues, suggesting some common regulatory mechanisms of circRNAs to modulate the physiological functions of tissues. Finding of the present study provide a valuable resource for depicting the complexity of circRNAs expression across tissues of sheep, which can be useful for the field of sheep genomic and veterinary research.

Antibody Preparation, Protein Expression, and Function Analysis of Cyp19a1b in Ovarian Differentiation in a Natural Triploid Teleost Qi River Crucian Carp (Carassius auratus)

Estrogen is an essential sex steroid that functions in numerous biological systems including female reproduction, neuroendocrine, vascular, skeletal, and immune systems. The synthesis of estrogen is controlled by the rate-limiting enzyme, which has been confirmed to exist in two different forms, named brain aromatase and ovary aromatase, and encoded by cyp19a1a and cyp19a1b respectively in teleosts. However, existing studies have primarily focused on the expression and function of cyp19a1b in the brain and cyp19a1a in the gonad, the roles of cyp19a1b in the female gonad of teleosts are largely unknown. In our previous study, we cloned the full length of the cyp19a1b gene from a natural triploid teleost Qi River crucian carp (Carassius auratus), andthe spatial and temporal expression patterns of cyp19a1b mRNA were detected. To further clarify the roles of cyp19a1b in the ovarian differentiation of Qi River crucian carp, we produced a polyclonal antibody of Cyp19a1b in this study. Western blotting results showed that Cyp19a1b was mainly expressed in the brain and then in the ovary, heart, liver, and muscle. During embryogenesis, Cyp19a1b was abundantly expressed in the neurula stage. Immunohistochemistry demonstrated that Cyp19a1b was expressed in the radioactive glial cells (RGCs) of the brain from 20 days after hatching (dah) and the somatic cells of the ovaries from 30 dah, the critical period of ovarian differentiation in Qi River crucian carp. With the treatment of letrozole, an inhibitor of the aromatase, the expression of Cyp19a1b was downregulated both in the brain and gonad. Our results suggested that Cyp19a1b might be involved in the development of the nervous system and also participate in the ovarian differentiation of Qi River crucian carp.