Specific Transcription Research Articles

TEFM facilitates transition from RNA synthesis to DNA synthesis at H-strand replication origin of mtDNA

Transcription of human mitochondrial DNA (mtDNA) begins from specific transcription promoters. In strand-asynchronous mtDNA replication, transcripts from the light-strand promoter serve as primers for leading-strand synthesis at the origin of the H-strand replication (OH). A 7S DNA strand, a presumed aborted replication product, is also synthesized from OH. Transition from RNA synthesis to DNA synthesis at OH is crucial for balancing replication with transcription, yet the mechanism remains unclear. Herein, we examine the role of mitochondrial transcription elongation factor (TEFM) in this process. TEFM knockout results in decreased 7S DNA, strand-asynchronous replication intermediates, and mtDNA copy number, all of which are concordant with downregulation of RNA-to-DNA transition at OH. Conversely, levels of tRNAs encoded near transcription promoters increase, indicating enhanced transcription initiation frequency. Taken together, we propose that, in addition to conferring processivity to the mitochondrial RNA polymerase, TEFM plays a crucial role in maintaining the balance between mitochondrial transcription and replication.

Regulation of NK cell development, maturation, and antitumor responses by the nuclear receptor NR2F6

Natural killer (NK) cell development and functionality rely on precise regulation by specific transcription factors (TFs). Our study demonstrates that the nuclear orphan receptor NR2F6 represses the expression of the activating receptor NKp46, an established key player in NK cell-mediated cytotoxicity during infection and tumor rejection. Despite normal NK cell development in the bone marrow, germline Nr2f6-deficient mice exhibit impaired terminal maturation of NK cells in the periphery. Short-term NK cell responses to lipopolysaccharide (LPS) activation, independent of NKp46, are subsequently reduced in Nr2f6-deficient mice. Conventional type 1 dendritic cells (cDC1) and macrophage populations are decreased in spleens of Nr2f6-deficient mice, subsequently, IL-15-dependent NK cell priming is limited. Administration of exogenous IL-15 in vitro and as IL-15 complex in vivo can compensate for these deficits, promoting terminal maturation of NK cells in Nr2f6-deficient mice. Subsequent transcriptome analysis reveals significant changes in gene expression profiles of NK cells from IL-15 complex treated Nr2f6-deficient mice, with notable alterations in essential NK genes such as Klrg1, Prdm1, Stat5a, Zeb2, and Prf1. Consequently, Nr2f6-deficient IL-15 complex-treated NK cells raise enhanced effector responses of IFNγ, Perforin, and Granzyme B upon ex vivo activation. Of importance, Nr2f6-deficient mice are protected against MHC-I negative B16-F10 melanoma lung metastasis formation, especially with IL-15 complex treatment, indicating the potential of NR2F6 to affect NKp46-dependent NK cell-mediated tumor surveillance. The therapeutic targeting of NR2F6 may be a promising strategy for boosting NKp46-dependent NK-cell-mediated tumor surveillance and metastasis.

Transcriptome and chromatin accessibility landscape of ovarian development at different egg-laying stages in taihe black-bone silky fowls.

Taihe Black-Bone Silky Fowl (SF) is a famous local breed in China, known for its high nutritional and medicinal value. However, its low egg-laying rate significantly limits its economic benefits. This study aims to explore the ovarian development status, as well as the changes in the transcriptome and chromatin accessibility landscape at different egg-laying stages of SF, in order to reveal the epigenetic regulatory mechanisms underlying ovarian development in laying hens. The results showed that during peak egg-laying, serum levels of follicle stimulating hormone (FSH), luteinizing hormone (LH), estradiol (E2), and progesterone (P4) in the SF were higher than in the other laying periods. Meanwhile, the serum and ovarian matrix total antioxidant capacity (T-AOC) level decreased with increasing age, whereas the ovarian matrix malondialdehyde (MDA) level showed the opposite trend. Compared to the late laying period, several genes related to ovarian development and reproductive hormone secretion, including TDRD5, CCNO, CYP17A1, BMP15, and STAR, were upregulated during the peak egg-laying period. Additionally, we identified key transcription factors (TF) associated with different egg-laying periods. Specific TF, such as Fli1, Etv2, and AT2G15740, linked to the peak egg-laying period, play significant roles in cell and tissue development. The specific transcription factor Nr5a2, associated with the late laying period, has been shown to inhibit E2 production. Furthermore, genes related to poultry reproductive performance, such as STAR and WNT4, were found to be regulated by specific distal enhancers in open chromatin regions (OCR). In conclusion, this study elucidated the dynamic changes in the transcriptome and chromatin accessibility landscape during ovarian development in SF at different egg-laying stages and highlighted key TF, including Fli1, Etv2, and Nr5a2, as well as essential genes like STAR and WNT4 that regulate ovarian development. These findings provide valuable insights into the regulatory mechanisms influencing egg-laying performance in SF and offer new strategies for improving ovarian follicle development and egg production performance in poultry.

Mechanism of ABA in Plants Exposed to Cold Stress

Abscisic acid (ABA) is a natural hormone produced in plants, which plays an important role in plant growth and development and in response to adversity. Increasing research indicates that ABA is involved in plant response to cold stress and enhances the cold tolerance of plants through various pathways. Therefore, the roles, regulator mechanisms and regulator pathways of ABA in plant response to cold stress are summarized. In this paper, we first discuss the mechanism of cold damage in plants. Second, we review the important roles of ABA in enhancing plant cold tolerance, including the interactions between endogenous and exogenous ABA, ABA and other substances, ABA and specific genes and transcription factors, and ABA and phosphorylation. On the whole, the involvement of ABA in the plant’s response to cold stress constitutes a complex and multi-dimensional system. ABA interacts with various factors, including hormones, enzymes, genes and so on, to establish a regulatory network that enhances plant resistance to cold injury. Finally, we also provide some perspectives for future research on plant ABA, and we hope that this paper can provide some lessons for future research on the mechanism of ABA involvement in plant adversity stress.

Region and cell-type resolved multi-omic altas of the heart.

The heart is a vital muscular organ in vertebrate animals, responsible for maintaining blood circulation through rhythmic contraction. Although previous studies have investigated the heart proteome, the full hierarchical molecular network at cell-type and region resolved level, illustrating the specialized roles and crosstalk among different cell types and regions, remains unclear. Here, we presented an atlas of cell-type resolved proteome for mouse heart and region resolved proteome for both mouse and human hearts. In-depth proteomic analysis identified 11,794 proteins across four cell types and 11,995 proteins across six regions of the mouse heart. To further illustrate protein expression patterns in both physiological and pathological conditions, we conducted proteomic analysis on human heart samples from four regions with dilated cardiomyopathy (DCM). We quantified 8,201 proteins in DCM tissue and 8,316 proteins in adjacent unaffected myocardium (AUM) tissue across the four human heart regions. Notably, we found that the retinoic acid synthesis pathway was significantly enriched in the DCM-affected left ventricle, and functional experiments demonstrated that all-trans retinoic acid (atRA) efficiently rescued Ang II-induced myocardial hypertrophy and transverse aorta constriction (TAC)- induced heart failure. In conclusion, our datasets uncovered the functional features of different cell types and their synergistic cooperation centered by cell-type specific transcription factors (ctsTF) in different regions, while these TF-TG (target gene) axes were significantly altered in DCM. Additionally, atRA was demonstrated to be an efficient treatment for heart failure. This work presented a panoramic heart proteome map, offering a valuable resource for future cardiovascular research.

Identification of a Novel QTL on LG16 Associated with Acute Salt Tolerance in Red Tilapia (Oreochromis spp.) Using GWAS.

Culturing saline tilapia has become a new trend in the aquaculture due to the scarcity of freshwater resources. In this study, the genetic basis controlling for salt tolerance were investigated by using a ddRAD-seq-based GWAS in 288 individuals with extreme salt tolerant traits from half-sib families of red tilapia. 12 genome-wide significant SNPs and 6 chromosome-wide significant SNPs associated with acute salt tolerance were identified. Two QTLs on LG18:25,593,701-7009020 and on LG16:19,735,164-21,231,391 were defined. It is noteworthy that the QTL on LG16 is a novel QTL associated with acute salt stress. Near the significant SNP sites, we identified candidate genes sik1, ltb4r2b, pnp5b and kirrel1b with differential transcript expression under salt stress. Furthermore, significant physiological differences in serum osmolality and ion concentrations were confirmed between the tolerant group and sensitive group under 4.5h of 22 ppt stress. The sensitive group had much higher serum osmolality (osmolality: 642.20 ± 6.30mOsm/kg) and higher concentrations of sodium and chloride ions (sodium: 317.67 ± 5.03mmol/L and chloride: 316.43 ± 8.28mmol/L) than the tolerant group (547.60 ± 15.44mOsm/kg, p osmolality = 0.0002; sodium: 280.53 ± 9.13 mmol/L, p sodium < 0.0242; chloride: 266.00 ± 12.00 mmol/L, p chloride < 0.0184). However, the lowest bicarbonate concentration was detected in the sensitive group at 22 ppt (2.53 ± 0.30mmol/L), which was significantly different from both the sensitive group at 0 ppt (p = 0.0008) and the tolerant group at 22 ppt (p = 0.0164). Our research laid the foundation for exploring the genetic mechanisms of acute salt tolerance and osmoregulation in red tilapia and for developing strains of red tilapia adapted to saltwater.

Bayesian identification of differentially expressed isoforms using a novel joint model of RNA-seq data.

We develop a Bayesian approach, BayesIso, to identify differentially expressed isoforms from RNA-seq data. The approach features a novel joint model of the sample variability and the deferential state of isoforms. Specifically, the within-sample variability and the between-sample variability of each isoform are modeled by a Poisson-Lognormal model and a Gamma-Gamma model, respectively. Using a Bayesian framework, the differential state of each isoform and the model parameters are jointly estimated by a Markov Chain Monte Carlo (MCMC) method. Extensive studies using simulation and real data demonstrate that BayesIso can effectively detect isoforms of less differentially expressed and differential transcripts for genes with multiple isoforms. We applied the approach to breast cancer RNA-seq data and uncovered a unique set of isoforms that form key pathways associated with breast cancer recurrence. First, PI3K/AKT/mTOR signaling and PTEN signaling pathways are identified as being involved in breast cancer development. Further integrated with protein-protein interaction data, pathways of Jak-STAT, mTOR, MAPK and Wnt signaling are revealed in association with breast cancer recurrence. Finally, several pathways are activated in the early recurrence of breast cancer. In tumors that occur early, members of pathways of cellular metabolism and cell cycle (such as CD36 and TOP2A) are upregulated, while immune response genes such as NFATC1 are downregulated.

Temporal transcriptional profiling of host cells infected by a veterinary alphaherpesvirus using nanopore sequencing

In our research, we performed temporal transcriptomic profiling of host cells infected with Equid alphaherpesvirus 1 (EHV-1) by utilizing direct cDNA sequencing based on nanopore MinION technology. The sequencing reads were harnessed for transcript quantification at various time points. Viral infection-induced differential gene expression was identified through the edgeR package. The identified genes were segmented into six groups based on their kinetic characteristics. The initial three clusters encompass immediate-early response genes, typically transcription factors and elements of antiviral signaling pathways. These genes were either upregulated (cluster 1) or downregulated (clusters 2 and 3) during the early infection phase. The remaining three clusters include late response genes. In these categories, it is challenging to determine whether changes in gene expression are directly connected to the viral infection or merely side effects of the infection. A study of gene associations using the STRINGDB software revealed several gene networks that might be directly impacted by the virus. We also explored whether gene co-expression could be a result of their collective regulation by upstream transcription factors using the Gene Regulatory Network database. Finally, our differential transcript usage (DTU) analysis identified a number of genes that exhibited altered proportions of transcript isoforms in comparison to non-infected cells. Thus, our analysis revealed that EHV-1 infection not only alters host gene expression but also leads to differential use of transcript isoforms, particularly splice variants.

Differential Gene Expression Analysis of Whole Blood Transcriptome Between Young and Old Border Collie Dogs

Aging is the most significant risk factor for many diseases and increased mortality, and it is influenced by both genetic and environmental factors. In this study, our primary goal was to investigate age-related gene expression changes in whole blood samples collected from dogs and identify potential biomarkers of healthy aging. We sequenced the mRNA fraction of whole blood samples from five young and five old border collie dogs and performed differential gene expression and differential transcript usage analyses. The raw sequencing data exhibited high quality. Multidimensional scaling analysis failed to differentiate age clusters. Moreover, we identified only a limited number of differentially expressed genes (n = 61) and 30 genes with differential transcript usage between the blood transcriptomes of young and old dogs. Our results align with publicly available data on dogs. However, studies on other species, such as wolves, have identified more significant age-related genes. In conclusion, while some of our findings are promising, further research is needed to standardize environmental factors affecting blood gene expression levels in dogs. Additionally, we recommend implementing pre-sequencing hemoglobin depletion to improve the analysis of whole blood in future studies.

Unlocking a Decade of Research on Embryo-Derived Extracellular Vesicles: Discoveries Made and Paths Ahead.

Over the past decade, research on embryo-derived extracellular vesicles (EVs) has unveiled their critical roles in embryonic development and intercellular communication. EVs secreted by embryos are nanoscale lipid bilayer vesicles that carry bioactive cargo, including proteins, lipids, RNAs, and DNAs, reflecting the physiological state of the source cells. These vesicles facilitate paracrine and autocrine signaling, influencing key processes such as cell differentiation, embryo viability, and endometrial receptivity. Studies reveal that EVs can traverse the zona pellucida, transferring molecular signals that enhance blastocyst formation and support embryo-maternal crosstalk. EVs have emerged as non-invasive biomarkers for embryo quality, with their cargo providing insights into genetic integrity and developmental competence. Advances in isolation and characterization techniques have identified specific microRNA (miRNAs) and transcription factors within EVs, offering potential for use in preimplantation genetic screening (PGS) and sex determination. Moreover, EV-mediated interactions with the maternal environment are critical for successful implantation, as they modulate gene expression and immune responses in endometrial and oviductal cells. Despite these advancements, challenges persist, including the standardization of EV isolation methods and the low yield of EVs DNA from spent culture media. Future research should aim to refine analytical techniques, explore EV-miRNA profiling, and investigate the mechanisms underlying EV-mediated signaling. By addressing these gaps, EVs could revolutionize embryo selection and reproductive technologies, offering new strategies to improve outcomes in assisted reproduction and animal breeding.

Genetic susceptibility and potential therapeutic targets of unruptured intracranial aneurysms: A genome-wide study based on Mendelian randomization.

At present, although some studies have offered certain insights into the genetic factors related to unruptured intracranial aneurysms (uIAs), the potential genetic targets associated with uIAs remain largely unknown. Thus, this research adopted Mendelian randomization (MR) analysis to study two genome-wide association studies on uIAs, aiming to determine the reliable genetic susceptibility and potential therapeutic targets for uIAs. This study summarizes the data of expression quantitative trait loci (eQTL) as exposure data. The outcome data of uIAs were derived from the study by Bakker et al. and the FinnGen Biobank (version R10). The reliable genetic susceptibility and potential therapeutic targets of uIAs were identified by means of Mendelian randomization (MR) methods, with the inverse variance weighting (IVW) method as the primary analytical approach. Simultaneously, sensitivity and pleiotropy analyses were carried out, and the results were visualized. Subsequently, drug predictions and molecular docking were conducted for the potential gene targets to verify their reliability. The MR analysis of the training cohort identified 100 targets related to uIAs. Then, these 100 gene targets and eQTL data were verified by MR Analysis again with the testing cohort. Finally, 7 gene targets were selected, namely MTMR3, SERINC1, CITED2, NKX3-1, ATOX1, MYADM and SLC20A1-DT.GO/KEGG enrichment analysis confirmed that the 7 gene targets mainly participate in the process Biological functions and pathways such as art development, cellular response to hypoxia, male Gonad development, RNA polymerase II specific DNA binding transcription factor binding, DNA binding transcription factor binding, Mineral absorption, Inositol phase metabolism, Photoshatidylinositol signaling system, etc.The protein-protein interaction（PPI） network describes the interactions between seven gene targets and related proteins.The molecular docking diagram shows good binding between candidate drugs and proteins related to gene targets. The study identified 7 reliable gene susceptibility and potential therapeutic targets associated with uIAs, offering new insights for clinical diagnosis and treatment of uIAs, and suggesting novel research directions for understanding the etiology and molecular mechanisms of uIAs.

The expression of transcription factors in the human fetal subthalamic nucleus suggests its origin from the first hypothalamic prosomere.

In this study, we analyzed the spatio-temporal pattern of expression of specific transcription factors (PITX2, FOXA1, BARHL1, FOXP1, FOXP2) in the human fetal subthalamic nucleus and its neighboring structures from 11 postconceptional weeks (PCW) to 3 postnatal months. We found that all analyzed transcription factors are expressed already during the early fetal period (at 11 PCW). Both FOXP1- and FOXP2-immunoreactive cells were found in the subthalamic nucleus as well as in the striatum, thalamus, reticular nucleus, but not in the zona incerta. FOXP2-ir cells were also found in the lateral hypothalamic-supramamillary area (LHA-SMA) and internal pallidal segment.On the other hand, PITX2, FOXA1 and BARHL1 were expressed exclusively in the subthalamic nucleus and LHA-SMA, from 11 PCW until the birth, the only exception being gradual loss of BARHL1 expression in the LHA-SMA during the late fetal period.Our findings present the first evidence in the human fetal brain that neurons of the subthalamic nucleus do not originate in the diencephalon, as was proposed by classical histological studies, but instead share a common hypothalamic (hp1 prosomere) origin with neurons of the LHA-SMA group, as proposed by the prosomeric model of brain development.

SmERF6 Promotes the Expression of Terpenoid Pathway in Salvia officinalis and Improves the Production of High Value Abietane Diterpenes, Carnosol and Carnosic acid.

Carnosol (CO) and carnosic acid (CA) are pharmaceutically important diterpenes predominantly produced in members of Lamiaceae, Salvia officinalis (garden sage), Salvia fruticosa and Rosmarinus officinalis. Nevertheless, availability of these compounds in plant system is very low. In an effort to improve the in planta content of these diterpenes in garden sage, SmERF6 (Salvia miltiorrhiza Ethylene Responsive Factor 6) transcription factor was expressed heterologously. Bai et al. (2018) proved that SmERF6 binds to the promoter regions of Copalyl pyrophosphate synthase (CPS) and Kaurene synthase like (KSL) genes, and improves transcription, thereby, augmenting ferruginol levels, a common precursor for abietane diterpenes in Salvia genus, moreover, transgenic hairy roots of S. miltiorrhiza displayed four fold improved tanshinone content. In our study, heterologous transient expression of SmERF6 in S. officinalis exhibited inter-specific activity in promoting differential accumulation of diterpenes. Overexpression studies showed elevation in the levels of CO (2-fold) and CA (5-fold). Further, in infiltrated leaves levels of ferruginol (50%) and CA derivatives (rosmanol, epirosmanol, methyl carnosic acid) were significantly upregulated along with the other signature terpenes. Finally, stable transgenic lines of S. officinalis developed through Agrobacterium mediated in planta genetic transformation accumulated significant amounts of CO (4-folds), CA (3-folds) as compared to wild plants. Overall, the present study is the first report on improving the content of pharmaceutically important diterpenes in S. officinalis by overexpressing pathway specific transcription factors. The current findings showed convincing evidence for the concept of improving specialized metabolite(s) content in medicinal plants by manipulating the expression of transcriptional regulators.

GTS-21 modulates rheumatoid arthritis Th17 and Th2 lymphocyte subset differentiation through the ɑ7nAch receptor.

Previous research has demonstrated ɑ7nAch receptor (ɑ7nAchR) agonists to provide benefit for rheumatoid arthritis (RA) patients. However, the immunological mechanism of action for these ɑ7nAchR agonists has not been elucidated. Herein, the effect of GTS-21, a selective ɑ7nAchR agonist, on the differentiation of Th17 and Th2 cells was assessed. CD4 + T cells were obtained from the peripheral blood mononuclear cells (PBMCs) of RA patients and healthy donors. CD4 + T cells were separately differentiated into Th2 or Th17 cells with or without GTS-21 and with or without alpha-bungarotoxin (ɑBgt) (a ɑ7nAchR antagonist). The proportions of Th17 and Th2 cells were assessed by flow cytometry. Levels of the T cell cytokines, IL-17A and IL-4, were assessed by ELISA. Specific transcription factors, retinoic orphan receptor c (RORc), and GATA Binding Protein 3 (GATA-3) were detected by western blot. GTS-21 reduced IL-17A and increased IL-4 production by RA PBMCs. GTS-21 reduced the percentage of Th17 cells and increased the percentage of Th2 cells during Th17 and Th2 differentiation, respectively. GTS-21 downregulated RA CD4 + T cells RORc levels and reduced the secretion of IL-17A during Th17 differentiation. GTS-21 upregulated RA CD4 + T cells GATA3 and promoted IL-4 production during Th2 differentiation. ɑ-Bgt blocked the effects of GTS-21 during Th17 and Th2 differentiation. These results demonstrated that GTS-21 suppressed RA Th17 differentiation and promoted Th2 differentiation. As such, the use of GTS-21 may be a new therapeutic approach by which to treat RA patients. Key Points • GTS-21 suppressed RA Th17 differentiation and promoted Th2 differentiation via acting on ɑ7nAchR. • The protective effect of GTS-21 on RA may be related to its regulation of Th cell subsets.

Global DNA methylomes reveal oncogenic-associated 5-hydroxylmethylated cytosine (5hmC) signatures in the cell-free DNA of cancer patients.

Characterization of tumor epigenetic aberrations is integral to understanding the mechanisms of tumorigenesis and provide diagnostic, prognostic, and predictive information of high clinical relevance. Among the different tumor-associated epigenetic signatures, 5 methyl-cytosine (5mC) and 5-hydroxymethylcytosine (5hmC) are the two most well-characterized DNA methylation alterations linked to cancer pathogenesis. 5hmC has a tissue-specific distribution and its abundance is subjected to changes in tumor DNA, making it a promising biomarker. Detecting tumor-related DNA methylation alterations in tissues is highly invasive, while the analysis of the cell-free DNA (cfDNA) is poised to supplement, if not replace, surgical biopsies. Despite many studies attempted to identify new epigenetic targets for liquid biopsy assays, little is known about the regulatory roles of 5hmC, its impacts on the molecular phenotypes in tumors. Most importantly, whether the oncogenic-associated 5hmC signatures found in tumor tissues can be recapitulated in patients' cfDNA. In this study, we performed the unbiased and simultaneous detection of 5mC and 5hmC whole-genome DNA modifications at base-resolution from two distinct cancer cohorts, from patients with bladder cancer or B-Cell lymphoma, their corresponding normal tissues, and cfDNAs from plasma. We analyzed tissue-specific methylation patters and searched for signatures in gene coding and regulatory regions linked to cancerous states. We then looked for methylation signatures in patients' cfDNA to determine if they were consistent with the tumor-specific patterns. We determined the functional significance of 5hmC in tissue specific transcription and uncovered hundreds of tumor-associated 5hmC signatures. These tumor-associated 5hmC changes, particularly in genes and enhancers, were functionally significant in tumorigenesis pathways and correlated with tumor specific gene expression. To investigate if cfDNA is a faithful surrogate for tumor-associated 5hmC, we devised a targeted capture strategy to examine the alterations of 5hmC in cfDNA from patients with bladder cancer and lymphoma with sufficient sensitivity and specificity and confirmed that they recapitulated the patterns we observed in tumor tissues. Our results provide analytic validation of 5hmC as a cancer-specific biomarker. The methods described here for systematic characterization of 5hmC at functional elements open new avenues to discover epigenetic markers for non-invasive diagnosis, monitoring, and stratifying cancer.

RNA sequencing reveals key factors modulating TNFα-stimulated odontoblast-like differentiation of dental pulp stem cells.

Inflammation is a complex host response to harmful infections or injuries, playing both beneficial and detrimental roles in tissue regeneration. Notably, clinical dentinogenesis associated with caries development occurs within an inflammatory environment. Reparative dentinogenesis is closely linked to intense inflammation, which triggers the recruitment and differentiation of dental pulp stem cells (DPSCs) into the dentin lineage. Understanding how inflammatory responses influence DPSCs is essential for elucidating the mechanisms underlying dentin and pulp regeneration. Given the limited data on this process, a broad approach is employed here to gain a deeper understanding of the complex mechanisms involved and to identify downstream signaling targets. This study aims to investigate the role of inflammation and the complement receptor C5L2 in the odontoblastic differentiation of DPSCs and the associated transcriptomic changes using poly-A RNA sequencing (RNA-seq). RNA-seq techniques provide insight into the transcriptome of a cell, offering higher coverage and greater resolution of its dynamic nature. Following inflammatory stimulation, DPSCs exhibit significantly altered gene profiles, including marked upregulation of key odontogenic genes, highlighting the critical role of inflammation in dentinogenesis. We demonstrate that TNFα-treated odontoblast-like differentiating DPSCs, under C5L2 modulation, exhibit significant differential gene expression and transcriptomic changes. The data presented may provide new avenues for experimental approaches to uncover pathways in dentinogenesis by identifying specific transcription factors and gene profiles.

N6-methyladenosine RNA modification regulates the transcription of SLC7A11 through KDM6B and GATA3 to modulate ferroptosis

BackgroundRecent studies indicate that N6-methyladenosine (m6A) RNA modification may regulate ferroptosis in cancer cells, while its molecular mechanisms require further investigation.MethodsLiquid Chromatography-Tandem Mass Spectrometry (HPLC/MS/MS) was used to detect changes in m6A levels in cells. Transmission electron microscopy and flow cytometry were used to detect mitochondrial reactive oxygen species (ROS). RNA sequencing (RNA-seq) was employed to analyze the factors regulating ferroptosis. Chromatin immunoprecipitation (ChIP) was used to assess the binding of regulatory factors to the SLC7A11 promoter, and a Dual-Luciferase reporter assay measured promoter activity of SLC7A11. The dm6ACRISPR system was utilized for the demethylation of specific transcripts. The Cancer Genome Atlas Program (TCGA) database and immunohistochemistry validated the role of the METTL3/SLC7A11 axis in cancer progression.ResultsThe m6A methyltransferase METTL3 was upregulated during cancer cell ferroptosis and facilitated erastin-induced ferroptosis by enhancing mitochondrial ROS. Mechanistic studies showed that METTL3 negatively regulated the transcription and promoter activity of SLC7A11. Specifically, METTL3 induced H3K27 trimethylation of the SLC7A11 promoter by suppressing the mRNA stability of H3K27 demethylases KDM6B. Furthermore, METTL3 suppressed the expression of GATA3, which regulated SLC7A11 transcription by binding to the putative site at − 597 to − 590 of the SLC7A11 promoter. METTL3 decreased the precursor mRNA stability of GATA3 through m6A/YTHDF2-dependent recruitment of the 3′-5′ exoribonuclease Dis3L2. Targeted demethylation of KDM6B and GATA3 m6A using the dm6ACRISPR system significantly increased the expression of SLC7A11. Moreover, the transcription factor YY1 was responsible for erastin-induced upregulation of METTL3 by binding to its promoter-proximal site. In vivo and clinical data supported the positive roles of the METTL3/SLC7A11 axis in tumor growth and progression.ConclusionsMETTL3 regulated the transcription of SLC7A11 through GATA3 and KDM6B to modulate ferroptosis in an m6A-dependent manner. This study provides a novel potential strategy and experimental support for the future treatment of cancer.

Research on the Direct Conversion of Human Skin Cells into Nerve Cells

The direct conversion of human skin cells into nerve cells is an emerging field with potential applications in regenerative medicine. This study investigates the conversion of Human Skin-Derived Progenitor Cells (hSKPs) and Human Dermal Fibroblasts (hDFs) into neural cells using specific transcription factors or molecular cocktails. A review of the literature was conducted to inform the design of a research study employing a combination of in vitro and in vivo experiments and molecular biology techniques to induce neural differentiation in skin-derived cells. The findings demonstrate that both hSKPs and hDFs can successfully differentiate into neural cells, displaying neuronal morphology and electrophysiological functionality. These studies conclude that skin cells possess significant potential for direct reprogramming into functional neurons, providing a direct approach for studying neurological diseases and developing therapeutic strategies. However, challenges regarding the efficiency and safety of the reprogramming process persist, necessitating further optimization prior to clinical application

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

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

EdgeR v4: powerful differential analysis of sequencing data with expanded functionality and improved support for small counts and larger datasets.

edgeR is an R/Bioconductor software package for differential analyses of sequencing data in the form of read counts for genes or genomic features. Over the past 15years, edgeR has been a popular choice for statistical analysis of data from sequencing technologies such as RNA-seq or ChIP-seq. edgeR pioneered the use of the negative binomial distribution to model read count data with replicates and the use of generalized linear models to analyze complex experimental designs. edgeR implements empirical Bayes moderation methods to allow reliable inference when the number of replicates is small. This article announces edgeR version 4, which includes new developments across a range of application areas. Infrastructure improvements include support for fractional counts, implementation of model fitting in C and a new statistical treatment of the quasi-likelihood pipeline that improves accuracy for small counts. The revised package has new functionality for differential methylation analysis, differential transcript expression, differential transcript and exon usage, testing relative to a fold-change threshold and pathway analysis. This article reviews the statistical framework and computational implementation of edgeR, briefly summarizing all the existing features and functionalities but with special attention to new features and those that have not been described previously.