Modification Patterns Research Articles

Prediction of gene expression using histone modification patterns extracted by Particle Swarm Optimization.

Histone modifications play an important role in transcription regulation. Although the general importance of some histone modifications for transcription regulation has been previously established, the relevance of others and their interaction is subject to ongoing research. By training Machine Learning models to predict a gene's expression and explaining their decision making process, we can get hints on how histone modifications affect transcription. In previous studies, trained models were either hardly explainable or the models were trained solely on the abundance of histone modifications. Based on other studies, which used histone modification patterns, rather than their abundance, to identify potential regulatory elements, we hypothesize the histone modification pattern in a gene's promoter to be more predictive for gene expression. We used an optimisation algorithm to extract predictive histone modification profiles. Our algorithm called PatternChrome achieved an average AUC score of 0.9029 over 56 samples for binary classification, outperforming all previous algorithms for the same task. We explained the models decisions to deduce the effect of specific features, certain histone modifications or promoter positions on transcription regulation. Although the predictive histone modification patterns were extracted for each sample separately, they can be used to predict gene expression in other samples, implying that the created patterns are largely generalizable. Interestingly, the impact of histone modifications on gene regulation appears predominantly indifferent to cellular specificity. Through explanation of the classifier's decisions, we substantiate established literature knowledge while concurrently revealing novel insights into the intricate landscape of transcriptional regulation via histone modification. The code for the PatternChrome algorithm, the scripts for the analyses and the required data can be found at (https://gitlab.gwdg.de/MedBioinf/generegulation/patternchrome). Supplementary data are available at Bioinformatics online.

Comprehensive analysis of the transcriptome-wide m6A Methylome in sheep testicular development.

N6-methyladenosine (m6A) modification of RNA is a critical post-transcriptional modification, that dynamically contributes to testicular development and spermatogenesis. Nevertheless, the investigation into the role of m6A in testicular development of sheep remains insufficient. Herein, we conducted a comprehensive analysis of the m6A transcriptome landscape in the testes of F1 hybrid Southdown × Hu sheep across M0 (0 months old, newborn), M3 (3 months old, sexually immature), M6 (6 months old, sexually mature), and Y1 (1 years old, adult). By profiling the m6A signatures across the transcriptome, we observed distinct differences in m6A modification patterns during sheep testicular development. Our cross-analysis of m6A and mRNA expression revealed that the expression of 743 genes and their m6A modification were concurrent. Notably, the combined analysis of the two comparative groups, M0 vs. M6 and M0 vs. Y1, exhibited a positive correlation, with 30 candidate genes each located within the largest protein-protein interaction network. Intriguingly, eight key hub genes (VEGFA, HDAC9, ZBTB40, KDM5B, MTRR, EAPS1, TSSK3, and BMP4) were identified to be associated with the regulation of sheep testicular development and spermatogenesis. These findings contribute to a deeper understanding of the dynamic role of m6A modification in sheep testicular biology. This study to map RNA m6A modification in sheep testes at different ages, providing novel insights into m6A topology and the molecular mechanisms associated with spermatogenesis in Southdown × Hu sheep F1 hybrids and laying the foundation for further investigations of mammalian spermatogenesis.

Characterization and functional analysis of conserved non-coding sequences among poaceae: insights into gene regulation and phenotypic variation in maize

BackgroundConserved non-coding sequences (CNS) are islands of non-coding sequences conserved across species and play an important role in regulating the spatiotemporal expression of genes. Identification of CNS provides valuable information about potentially functional genomic elements, regulatory regions, and helps to gain insights into the genetic basis of crop agronomic traits.ResultsHere, we comprehensively analyze CNS in maize, by comparing the genomes of maize inbred line B73 (Zea mays ssp. mays), its close wild relative Zea mays spp. mexicana, and other grasses in Poaceae, including sorghum (Sorghum bicolor), foxtail millet (Setaria italica) and two adlay (Coix lacryma) cultivars. There were 289,931 CNS found in two syntenic gene pairs, while 51,701 CNS were conserved within at least three species. To explore the regulatory characteristics of the CNS identified, the flanking regions of CNS were compared with the peaks called using both transposase-accessible chromatin with high-throughput sequencing (ATAC-seq) and chromatin immunoprecipitation with high-throughput sequencing (ChIP-Seq) data of histone modifications. It was found that CNS in maize were enriched in open chromatin regions compared with randomly selected non-coding regions of similar length. A significant enrichment of transcription factor binding sites was found within CNS sequences, including different transcription factors involved in abiotic stress response, such as OBP (OBF-BINDING PROTEIN) family and Adof1 (Encodes dof zinc finger protein). To investigate the epigenetic modification patterns in CNS, ChIP-Seq data for histone modifications H3K9ac, H3K4me3, H3K36me3, H3K9me3, and H3K27ac were further analyzed to depict the changes along CNS. Our findings revealed significantly elevated levels of transcription-promoting histone modifications in the CNS regions compared to randomly selected non-coding sequences with an equal number and similar length. Notably, CNS were also identified on both Vgt1 (Vegetative to generative transition 1) and ZmCCT10. In addition, CNS with potential functions were identified based on SNPs within CNS significantly associated with various agronomic traits in maize, which holds potential utility in molecular breeding for maize.ConclusionsIn summary, we identified and characterized CNS in maize through genomic comparative analysis, which provides valuable insights into their potential regulatory effects on gene expression and phenotypic variation.

Multiplexed siRNA Immunoassay Unveils Spatial and Quantitative Dimensions of siRNA Function, Abundance, and Localization In Vitro and In Vivo.

Small interfering RNAs (siRNAs) have been successfully used as therapeutics to silence disease-causing genes when conjugated to ligands or formulated in lipid nanoparticles to target relevant cell types for efficacy while sparing other cells for safety. To support the development of new methods for delivery of siRNA therapeutics, we developed and characterized a panel of antibodies generated against chemically modified nucleotides used in therapeutic siRNA molecules, identifying a monoclonal antibody that detects a broad range of siRNA representing distinct sequences and modification patterns. By integrating this anti-siRNA antibody with additional reagents, we created a multiplex siRNA immunoassay that simultaneously quantifies siRNA uptake, trafficking, and silencing activity. Using immunohistochemistry (IHC), we applied our method on tissues from mice treated with unconjugated, GalNAc-conjugated, or cholesterol-conjugated siRNAs and quantitatively assessed the biodistribution and activity of siRNAs in various organs. In addition, we used high-content imaging (HCI) and applied our multiplex siRNA immunoassay in tissue culture to enable simultaneous quantification of siRNA uptake, activity, and intracellular colocalization with endosome markers. These methods provide a robust platform for testing nucleic acid delivery methods in vitro and in vivo, allowing precise analysis and visualization of the pharmacokinetics and pharmacodynamics of siRNA therapeutics with cellular and subcellular resolution.

Dynamic histone modification patterns coordinating DNA processes.

Significant effort has been spent attempting to unravel the causal relationship between histone post-translational modifications and fundamental DNA processes, including transcription, replication, and repair. However, less attention has been paid to understanding the reciprocal influence-that is, how DNA processes, in turn, shape the distribution and patterns of histone modifications and how these changes convey information, both temporally and spatially, from one process to another. Here, we review how histone modifications underpin the widespread bidirectional crosstalk between different DNA processes, which allow seemingly distinct phenomena to operate as a unified whole.

Decoding Codon Bias: The Role of tRNA Modifications in Tissue-Specific Translation.

The tRNA epitranscriptome has been recognized as an important player in mRNA translation regulation. Our knowledge of the role of the tRNA epitranscriptome in fine-tuning translation via codon decoding at tissue or cell levels remains incomplete. We analyzed tRNA expression and modifications as well as codon optimality across seven mouse tissues. Our analysis revealed distinct enrichment patterns of tRNA modifications in different tissues. Queuosine (Q) tRNA modification was most enriched in the brain compared to other tissues, while mitochondrial tRNA modifications and tRNA expression were highest in the heart. Using this observation, we synthesized, and delivered in vivo, codon-mutated EGFP for Q-codons, where the C-ending Q-codons were replaced with U-ending codons. The protein levels of mutant EGFP were downregulated in liver, which is poor in Q, while in brain EGFP, levels did not change. These data show that understanding tRNA modification enrichments across tissues is not only essential for understanding codon decoding and bias but can also be utilized for optimizing gene and mRNA therapeutics to be more tissue-, cell-, or condition-specific.

Integration of histone modification-based risk signature with drug sensitivity analysis reveals novel therapeutic strategies for lower-grade glioma.

Lower-grade glioma (LGG) exhibits significant heterogeneity in clinical outcomes, and current prognostic markers have limited predictive value. Despite the growing recognition of histone modifications in tumor progression, their role in LGG remains poorly understood. This study aimed to develop a histone modification-based risk signature and investigate its relationship with drug sensitivity to guide personalized treatment strategies. We performed single-cell RNA sequencing analysis on LGG samples (n = 4) to characterize histone modification patterns. Through integrative analysis of TCGA-LGG (n = 513) and CGGA datasets (n = 693 and n = 325), we constructed a histone modification-related risk signature (HMRS) using machine learning approaches. The model's performance was validated in multiple independent cohorts. We further conducted comprehensive analyses of molecular mechanisms, immune microenvironment, and drug sensitivity associated with the risk stratification. We identified distinct histone modification patterns across five major cell populations in LGG and developed a robust 20-gene HMRS from 129 candidate genes that effectively stratified patients into high- and low-risk groups with significantly different survival outcomes (training set: AUC = 0.77, 0.73, and 0.71 for 1-, 3-, and 5-year survival; P < 0.001). Integration of HMRS with clinical features further improved prognostic accuracy (C-index >0.70). High-risk tumors showed activation of TGF-β and IL6-JAK-STAT3 signaling pathways, and distinct mutation profiles including TP53 (63% vs 28%), IDH1 (68% vs 85%), and ATRX (46% vs 20%) mutations. The high-risk group demonstrated significantly elevated immune and stromal scores (P < 0.001), with distinct patterns of immune cell infiltration, particularly in memory CD4+ T cells (P < 0.001) and CD8+ T cells (P = 0.001). Drug sensitivity analysis revealed significant differential responses to six therapeutic agents including Temozolomide and targeted drugs (P < 0.05). Our study establishes a novel histone modification-based prognostic model that not only accurately predicts LGG patient outcomes but also reveals potential therapeutic targets. The identified associations between risk stratification and drug sensitivity provide valuable insights for personalized treatment strategies. This integrated approach offers a promising framework for improving LGG patient care through molecular-based risk assessment and treatment selection.

The PARPscore system using poly (ADP-ribose) polymerase (PARP) family features and tumor immune microenvironment in glioma

The immune response plays a pivotal role in tumor progression and therapy. However, the influence of protein PAR polymerases (PARPs) modifications on cell infiltration within the tumor microenvironment (TME) remains insufficiently understood. In this study, the Clinical and RNA sequencing data we performed a comprehensive analysis of PARPs modification patterns, exploring their associations with TME cell infiltration were acquired from the Cancer Genome Atlas (TCGA) and Chinese Glioma Genome Atlas (CGGA) database. To quantify PARPs modification in individual tumors, we developed a novel metric, the PARPscore, derived using principal component analysis. Our findings revealed three distinct PARPs modification patterns, each correlated with unique TME infiltration characteristics and tumor immunophenotypes. These patterns demonstrated predictive value for various clinical parameters, including inflammation stage, tumor subtypes, TME matrix activity, genetic variations, and patient prognosis. Notably, the high PARPscore subtype exhibited features of stromal activation and reduced immune infiltration, indicative of a non-inflamed, immune-excluded TME phenotype, and was associated with poorer survival outcomes. Conversely, lower PARPscore subtypes corresponded to substantial therapeutic benefits and improved outcomes in two independent immunotherapy cohorts. This study underscores the critical role of PARPs modification in shaping the diverse and dynamic TME. By delineating tumor-specific PARPs modification patterns, we provide valuable insights into TME complexity and its implications for immunotherapy.

Влияние обогащенных рационов на состав и функциональный профиль микробиома рубца баранчиков

The gastrointestinal microbiome of ruminants is a complex ecological system. It ferments feed components and protects the body from opportunistic and pathogenic microflora. The interaction between the microbiota and the host organism depends on the diet, which complicates the scientific understanding of their impact on digestive processes, immunity, and yield. The article describes the composition and functional profile of microbiome in the rumen of young Edilbay rams fed with organic additives based on essential microelements. The samples were obtained from seven-month-old Edilbay rams, which received Ioddar-Zn and DAFS-25 feed additives. The study involved four groups of animals: control (no additives), experimental group I (Yoddar-Zn), experimental group II (DAFS-25), and experimental group III (Yoddar-Zn + DAFS-25). The composition and functional profile of the microbiome were studied using the NGS sequencing. The bioinformatics data analysis involved Qiime2 ver. 2020.8 and standard statistical methods. The feed additives had a positive effect on the growth and development of the rams. The highest live weight indicators belonged to experimental group III, which received Yoddar-Zn and DAFS-25. The ratio of Firmicutes and Bacteroidetes phylum changed, indicating a potential shift in metabolic processes towards an increase in the ratio of volatile fatty acids (acetate / propionate). The greatest changes were observed in animals that consumed the selenium additive DAFS-25, both separately and with Ioddar-Zn. The additives did not increase the count of Proteobacteria, Mycoplasma, and Escherichia-Shigella, which are associated with inflammatory processes. The feed additives affected the functional profile of rumen microbiome in young rams: they improved the carbohydrate and energy metabolism, as well as the synthesis of vitamins and cofactors. In addition, the research revealed some patterns of microbiome modification, which indicated a positive effect of the additives on metabolic processes, resulting in a more efficient digestion of feed ingredients and, eventually, in increased meat yield.

Comparative Analysis of Human Brain RNA-seq Reveals the Combined Effects of Ferroptosis and Autophagy on Alzheimer's Disease in Multiple Brain Regions.

Ferroptosis and autophagy are closely associated with Alzheimer's disease (AD). Elevated ferric ion levels can induce oxidative stress and chronic inflammatory responses, resulting in brain tissue damage and further neurological cell damage. Autophagy in Alzheimer's has a dual role. On one hand, it protects neurons by removing β-amyloid and cellular damage products caused by oxidative stress and inflammation. On the other hand, abnormal autophagy is linked to neuronal apoptosis and neurodegeneration. However, the intricate interplay between ferroptosis and autophagy in AD remains insufficiently explored. This study focuses on the roles of ferroptosis and autophagy in AD and their interconnection through bioinformatics analysis, shedding light on the disease. Ferroptosis and autophagy significantly correlate with the development and course of AD. Using PPI network analysis and unsupervised consistency clustering analysis, we uncovered a complex network of interactions between ferroptosis and autophagy during disease progression, demonstrating a significant congruence in their modification patterns. Functional analyses further demonstrated that ferroptosis and autophagy together affect the immunological status and synaptic regulation in hippocampal regions in patients with AD, which significantly impacts the start and progression of the disease.

Dementia with lewy bodies patients with high tau levels display unique proteome profiles

BackgroundClinical studies have long observed that neurodegenerative disorders display a range of symptoms and pathological features and, in some cases, overlap, suggesting that these diseases exist on a spectrum. Dementia with Lewy Bodies (DLB), a synucleinopathy, is a prominent example, where symptomatic similarities with tauopathy, Alzheimer’s disease, are observed. Although tau pathology has been observed in DLB, the interplay between tau and α-synuclein is poorly understood at a molecular level.MethodsQuantitative mass spectrometry analysis was used to measure protein abundance in the insoluble fraction from cortical brain tissue from pathologically diagnosed DLB subjects (n = 30) and age-matched controls (n = 29). Using tau abundance, we stratified the DLB subjects into two subgroups termed DLBTau+ (higher abundance) and DLBTau− (lower abundance). We conducted proteomic analysis to characterize and compare the cortical proteome of DLB subjects exhibiting elevated tau, as well as the molecular modifications of tau and α-synuclein to explore the dynamic between tau and α-synuclein pathology in these patients.ResultsProteomic analyses revealed distinct global protein dysregulations in DLBTau+ and DLBTau− subjects when compared to controls. Notably, DLBTau+ patients exhibited increased levels of tau, along with ubiquitin, and APOE, indicative of cortical proteome alterations associated with elevated tau. Comparing DLBTau+ and DLBTau− groups, we observed significant upregulation of cytokine signaling and metabolic pathways in DLBTau− patients, while DLBTau+ subjects showed increases in protein ubiquitination processes and regulation of vesicle-mediated transport. Additionally, we examined the post-translational modification patterns of tau and α-synuclein. Our analysis revealed distinct phosphorylation and ubiquitination sites on α-synuclein between groups. Moreover, we observed increased modifications on tau specifically within the DLBTau+ subgroup.ConclusionThis molecular-level data supports the idea of neurodegenerative disease as a continuum of diseases with distinct PTM profiles DLBTau+ and DLBTau− patients in comparison to AD. These findings further emphasize the importance of identifying specific and tailored therapeutic approaches targeting the involved proteopathies in the neurodegenerative disease spectrum.

Integrative analysis of the 3D genome and epigenome in mouse embryonic tissues.

While a rich set of putative cis-regulatory sequences involved in mouse fetal development have been annotated recently on the basis of chromatin accessibility and histone modification patterns, delineating their role in developmentally regulated gene expression continues to be challenging. To fill this gap, here we mapped chromatin contacts between gene promoters and distal sequences across the genome in seven mouse fetal tissues and across six developmental stages of the forebrain. We identified 248,620 long-range chromatin interactions centered at 14,138 protein-coding genes and characterized their tissue-to-tissue variations and developmental dynamics. Integrative analysis of the interactome with previous epigenome and transcriptome datasets from the same tissues revealed a strong correlation between the chromatin contacts and chromatin state at distal enhancers, as well as gene expression patterns at predicted target genes. We predicted target genes of 15,098 candidate enhancers and used them to annotate target genes of homologous candidate enhancers in the human genome that harbor risk variants of human diseases. We present evidence that schizophrenia and other adult disease risk variants are frequently found in fetal enhancers, providing support for the hypothesis of fetal origins of adult diseases.

Decoding the prognostic landscape of LUAD: the interplay between N6-methyladenosine modification and immune microenvironment

BackgroundTo determine the role of N6-methyladenosine (m6A) modification in the tumor immune microenvironment (TIME), as well as their association with lung adenocarcinoma (LUAD).MethodsConsensus clustering was performed to identify the subgroups with distinct immune or m6A modification patterns using profiles from TCGA. A risk score model was constructed using least absolute shrinkage and selection operator regression and validated in two independent cohorts and LUAD tissue microarrays. For experimental validation, the regulation of METTL3/m6A axis in the expression of candidate genes by RIP-qPCR assay in A549 and H460 cell lines. Co-culture experiments with human T cells were performed to evaluate the impact of METTL3 on the enhancement of anti-tumor immunity through in vitro experiments.ResultsWe identified 282 m6A regulator genes and 955 immune-related genes, selecting seven key genes (SFTPC, CYP24A1, KRT6A, PTTG1, S100P, FAM83A, and ANLN) to develop a risk score model using Lasso regression. High-risk patients, determined by this model, exhibited poorer prognosis, increased immune infiltration, higher tumor mutational burden, more neoantigens, and elevated PD-L1 expression. These findings were validated by two independent databases and LUAD tissue microarrays. METTL3 was found to impact the mRNA expression of these genes, with METTL3 deficiency abolishing these interactions. Inhibition of METTL3 enhanced anti-tumor immunity, T cell activation, exhaustion, and infiltration in vitro.ConclusionThis risk score system shows promise for prognostic prediction and the development of personalized treatment strategies for LUAD patients.

The Archaeology of Cannibalism: a Review of the Taphonomic Traits Associated with Survival and Ritualistic Cannibalism

Taphonomic studies of osteoarchaeological human assemblages have mainly focused on establishing recognisable markers that allow us to discriminate between humanly induced modifications from natural causes, or how to differentiate cannibalism from secondary burial. Less attention has been dedicated to recognise specific taphonomic patterns associated with the different motivations for cannibalism. In this paper, I present a review of archaeological human assemblages whose induced modifications have been interpreted either as survival or ritualistic cannibalism, based on their association with historic and ethnographic evidence. The broad range of different butchery and modification patterns observed for these assemblages suggests that the osteological evidence and the frequency of taphonomic traits alone cannot be used to unequivocally identify different forms of cannibalism. However, the environmental, historical and archaeological contexts can offer indications on the type of cannibalism practiced. In particular, the strongest arguments for cannibalism as a survival event are found within the environmental context and the opportunistic behaviour associated with the cannibalistic act. On the other hand, evidence for ritualistic cannibalism comes from its recurrent appearance within a historical context, as a widespread activity over time and as an established customary behaviour for the group involved.

The diverse landscape of RNA modifications in cancer development and progression.

RNA modifications, a central aspect of epitranscriptomics, add a regulatory layer to gene expression by modifying RNA function without altering nucleotide sequences. These modifications play vital roles across RNA species, influencing RNA stability, translation, and interaction dynamics, and are regulated by specific enzymes that add, remove, and interpret these chemical marks. This review examines the role of aberrant RNA modifications in cancer progression, exploring their potential as diagnostic and prognostic biomarkers and as therapeutic targets. We focus on how altered RNA modification patterns impact oncogenes, tumor suppressor genes, and overall tumor behavior. We performed an in-depth analysis of recent studies and advances in RNA modification research, highlighting key types and functions of RNA modifications and their roles in cancer biology. Studies involving preclinical models targeting RNA-modifying enzymes were reviewed to assess therapeutic efficacy and potential clinical applications. Aberrant RNA modifications were found to significantly influence cancer initiation, growth, and metastasis. Dysregulation of RNA-modifying enzymes led to altered gene expression profiles in oncogenes and tumor suppressors, correlating with tumor aggressiveness, patient outcomes, and response to immunotherapy. Notably, inhibitors of these enzymes demonstrated potential in preclinical models by reducing tumor growth and enhancing the efficacy of existing cancer treatments. RNA modifications present promising avenues for cancer diagnosis, prognosis, and therapy. Understanding the mechanisms of RNA modification dysregulation is essential for developing targeted treatments that improve patient outcomes. Further research will deepen insights into these pathways and support the clinical translation of RNA modification-targeted therapies.

Single-cell transcriptome profiling of m6A regulator-mediated methylation modification patterns in elderly acute myeloid leukemia patients

Millions of people worldwide die of acute myeloid leukaemia (AML) each year. Although N6-methyladenosine (m6A) modification has been reported to regulate the pathogenicity of AML, the mechanisms by which m6A induces dysfunctional hematopoietic differentiation in elderly AML patients remain elusive. This study elucidates the mechanisms of the m6A landscape and the specific roles of m6A regulators in hematopoietic cells of elderly AML patients. Notably, fat mass and obesity-associated protein (FTO) was found to be upregulated in hematopoietic stem cells (HSCs), myeloid cells, and T-cells, where it inhibits their differentiation via the WNT signaling pathway. Additionally, elevated YT521-B homology domain family proteins 2 (YTHDF2) expression in erythrocytes was observed to negatively regulate differentiation through oxidative phosphorylation, resulting in leukocyte activation. Moreover, IGF2BP2 was significantly upregulated in myeloid cells, contributing to an aberrant chromosomal region and disrupted oxidative phosphorylation. m6A regulators were shown to induce abnormal cell-cell communication within hematopoietic cells, mediating ligand-receptor interactions across various cell types through the HMGB1-mediated pathway, thereby promoting AML progression. External validation was conducted using an independent single-cell RNA sequencing (scRNA-Seq) dataset. The THP-1 and MV411 cell lines were utilized to corroborate the m6A regulator profile; in vitro experiments involving short hairpin RNA (shRNA) targeting FTO demonstrated inhibition of cell proliferation, migration, and oxidative phosphorylation, alongside induction of cell cycle arrest and apoptosis. In summary, these findings suggest that the upregulation of m6A regulators in HSCs, erythrocytes, myeloid cells, and T-cells may contribute to the malignant differentiation observed in AML patients. This research provides novel insights into the pathogenesis of AML in elderly patients and identifies potential therapeutic targets.

Design, Screening and Development of Asymmetric siRNAs Targeting the MYC Oncogene in Triple-Negative Breast Cancer.

Triple-negative breast cancer (TNBC) is a subtype of breast cancer that lacks hormone receptor and Her2 (ERBB2) expression, leaving chemotherapy as the only treatment option. The urgent need for targeted therapy for TNBC patients has led to the investigation of small interfering RNAs (siRNAs), which can target genes in a sequence-specific manner, unlike other drugs. However, the clinical translation of siRNAs has been hindered by the lack of an effective delivery system, except in the case of liver diseases. The MYC oncogene is commonly overexpressed in TNBC compared to other breast cancer subtypes. In this study, we used siRNA to target MYC in MDA-MB-231, MDA-MB-157, MDA-MB-436 and Hs-578T cells. We designed various symmetric and asymmetric (asiRNAs), screened them for in vitro efficacy, modified them for enhanced nuclease resistance and reduced off-target effects, and conjugated them with cholesterol (ChoL) and docosanoic acid (DCA) as a delivery system. DCA was conjugated to the 3' end of asiRNA by a cleavable phosphodiester linker for in vivo delivery. Our findings demonstrated that asiRNA-VP and Mod_asiRNA10-6 efficiently downregulated MYC and its downstream targets, including RRM2, RAD51 and PARP1. Moreover, in a tumor xenograft model, asiRNA-VP-DCA effectively knocked down MYC mRNA and protein expression. Remarkably, durable knockdown persisted for at least 46 days postdosing in mouse tumor xenografts, with no visible signs of toxicity, underscoring the safety of DCA-conjugated asiRNAs. In conclusion, this study developed novel asiRNAs, design platforms, validated modification patterns, and in vivo delivery systems specifically targeting MYC in TNBC.

Low-input CUT&Tag for efficient epigenomic profiling of zebrafish stage I oocytes.

Histone modification signatures mark sites of transcriptional regulatory elements and regions of gene activation and repression. These sites vary among cell types and undergo dynamic changes during development and in diseases. Oocytes produce numerous maternal factors essential for early embryonic development, which are significantly influenced by epigenetic modifications. The profiling of epigenetic modifications during oogenesis remains uniquely challenging due to the presence of numerous tightly wrapped granulosa cells. Here, we successfully established a low-input CUT&Tag (Cleavage Under Targets and Tagmentation) method tailored for zebrafish stage I oocytes. This advanced technique enables high-resolution profiling of histone modifications and DNA-binding proteins, critical for understanding chromatin dynamics in developing oocytes. In this study, we detailed the workflow for this technique, including the isolation of pure stage I oocytes without somatic cells, library construction and quality monitoring. Our results demonstrate the method's efficacy by identifying distinct histone modification patterns and analyzing differentially expressed genes in oocytes with and without granulosa cells. We also successfully profiled divergent histone modifications in oocytes derived from wild-type and huluwa mutants. These advancements overcome technical challenges in epigenetic research on zebrafish oocytes and establish a solid foundation for exploring the epigenetic regulatory mechanisms of maternal contribution.

Harnessing m1A modification: a new frontier in cancer immunotherapy.

N1-methyladenosine (m1A) modification is an epigenetic change that occurs on RNA molecules, regulated by a suite of enzymes including methyltransferases (writers), demethylases (erasers), and m1A-recognizing proteins (readers). This modification significantly impacts the function of RNA and various biological processes by affecting the structure, stability, translation, metabolism, and gene expression of RNA. Thereby, m1A modification is closely associated with the occurrence and progression of cancer. This review aims to explore the role of m1A modification in tumor immunity. m1A affects tumor immune responses by directly regulating immune cells and indirectly modulating tumor microenvironment. Besides, we also discuss the implications of m1A-mediated metabolic reprogramming and its nexus with immune checkpoint inhibitors, unveiling promising avenues for immunotherapeutic intervention. Additionally, the m1AScore, established based on the expression patterns of m1A modification, can be used to predict tumor prognosis and guide personalized therapy. Our review underscores the significance of m1A modification as a burgeoning frontier in cancer biology and immuno-oncology, with the potential to revolutionize cancer treatment strategies.

Identification of lethality-related m7G methylation modification patterns and the regulatory features of immune microenvironment in sepsis

ObjectivesN7-methylguanosine (m7G) modification is closely related to the occurrence of human diseases, but its roles in sepsis remain unclear. This study aimed to explore the patterns of lethality-related m7G regulatory factor-mediated RNA methylation modification and immune microenvironment regulatory features in sepsis. MethodsThree sepsis-related datasets (E-MTAB-4421 and E-MTAB-4451 as training sets and GSE185263 as a validation set) were collected, and differentially expressed m7G-related genes were analyzed between survivors and non-survivors. Lethality-related m7G signature genes were then screened using machine learning methods, followed by the construction of a survival recognition model. Additionally, differences in immune cell distribution were determined and differentially expressed genes (DEGs) between different subtypes were analyzed. Weighted gene co-expression network analysis (WGCNA) was used to select important modules and related hub genes. ResultsIn total, 10 differentially expressed m7G-related genes were identified between the survivors and non-survivors, and after further analysis, EIF4G3, EIF4E3, NSUN2, NUDT4, and GEMIN5 were identified as the optimal lethality-related m7G genes. A survival status diagnostic model was then constructed with a combined AUC of 0.678. Fifteen types of immune cells were significantly different between survivors and non-survivors. Sepsis samples were classified into two subtypes, with 22 types of immune cells showing significant differences. Subsequently, 1707 DEGs were identified between the two subtypes, which were significantly enriched in 91 GO terms and 16 KEGG pathways. Finally, the green module with |correlation| > 0.3 was found to be closely related to the subtypes and survival status; further, the top10 hub genes were obtained. ConclusionThe constructed survival status diagnostic model based on the five lethality-related m7G signature genes may help predict the survival status of patients, and the 10 hub genes obtained may be potential therapeutic targets for sepsis.