Activation Of Transcription Factors Research Articles

Chromatin accessibility is associated with therapeutic response in prostate cancer.

Treatment of advanced prostate cancer is challenging due to a lack of effective therapies. Therefore, it is important to understand the molecular mechanisms underlying therapeutic resistance in prostate cancer and to identify promising drug targets offering significant clinical advantages. Given the pivotal role of dysregulated transcriptional programs in the therapeutic response, it is essential to prioritize translational efforts targeting cancer-associated transcription factors (TFs). The present study investigated whether chromatin accessibility was associated with therapeutic resistance in prostate cancer using Assay for Transposase-Accessible Chromatin with sequencing (ATAC-seq) data. The bioinformatics analysis identified differences in chromatin accessibility between the drug response (Remission) and drug resistance (Disease) groups. Additionally, a significant association was observed between chromatin accessibility, transcriptional output and TF activity. Among TFs, forkhead box protein M1 (FOXM1) was identified as a TF with high activity and expression in the Disease group. Notably, the results of the computational analysis were validated by FOXM1 knockdown experiments, which resulted in suppressed cell proliferation and enhanced therapeutic sensitivity in prostate cancer cells. The present findings demonstrated that chromatin accessibility and TF activity may be associated with therapeutic resistance in prostate cancer. Additionally, these results provide the basis for future investigations aimed at understanding the molecular mechanisms of drug resistance and developing novel therapeutic approaches for prostate cancer.

WRKY Transcription Factors in Response to Metal Stress in Plants: A Review.

Heavy metals in soil can inflict direct damage on plants growing within it, adversely affecting their growth height, root development, leaf area, and other physiological traits. To counteract the toxic impacts of heavy metals on plant growth and development, plants mitigate heavy metal stress through mechanisms such as metal chelation, vacuolar compartmentalization, regulation of transporters, and enhancement of antioxidant functions. WRKY transcription factors (TFs) play a crucial role in plant growth and development as well as in responses to both biotic and abiotic stresses; notably, heavy metal stress is classified as an abiotic stressor. An increasing number of studies have highlighted the significant role of WRKY proteins in regulating heavy metal stress across various levels. Upon the entry of heavy metal ions into plant root cells, the production of reactive oxygen species (ROS) is triggered, leading to the phosphorylation and activation of WRKY TFs through MAPK cascade signaling. Activated WRKY TFs then modulate various physiological processes by upregulating or downregulating the expression of downstream genes to confer heavy metal tolerance to plants. This review provides an overview of the research advancements regarding WRKY TFs in regulating heavy metal ion stress-including cadmium (Cd), arsenic (As), copper (Cu)-and aluminum (Al) toxicity.

Poly (ADP-Ribose) Polymerase-1 (PARP-1) Inhibitors in Diabetic Retinopathy: An Attractive but Elusive Choice for Drug Development.

Owing to its promiscuous roles, poly (ADP-ribose) polymerase-1 (PARP-1) is involved in various neurological disorders including several retinal pathologies. Diabetic retinopathy (DR) is the most common microvascular complication of diabetes mellitus affecting the retina. In the present review, we highlight the importance of PARP-1 participation in pathophysiology of DR and discuss promising potential inhibitors for treatment. A high glucose level enhances PARP-1 expression; PARP inhibitors have gained attention due to their potential therapeutic effects in DR. They target different checkpoints (blocking nuclear transcription factor (NF-κB) activation; oxidative stress protection, influence on vascular endothelial growth factor (VEGF) expression, impacting neovascularization). Nowadays, there are several improved clinical PARP-1 inhibitors with different allosteric effects. Combining PARP-1 inhibitors with other compounds is another promising option in DR treatments. Besides pharmacological inhibition, genetic disruption of the PARP-1 gene is another approach in PARP-1-initiated therapies. In terms of future treatments, the limitations of single-target approaches shift the focus onto combined therapies. We emphasize the importance of multi-targeted therapies, which could be effective not only in DR, but also in other ischemic conditions.

Seasonal influence on miRNA expression dynamics of extracellular vesicles in equine follicular fluid.

Ovarian follicular fluid (FF) is a dynamic environment that changes with the seasons, affecting follicle development, ovulation, and oocyte quality. Cells in the follicles release tiny particles called extracellular vesicles (EVs) containing vital regulatory molecules, such as microRNAs (miRNAs). These miRNAs are pivotal in facilitating communication within the follicles through diverse signaling and information transfer forms. EV-coupled miRNA signaling is implicated to be associated with ovarian function, follicle and oocyte growth and response to various environmental insults. Herein, we investigated how seasonal variations directly influence the ovulatory and anovulatory states of ovarian follicles and how are they associated with follicular fluid EV-coupled miRNA dynamics in horses. Ultrasonographic monitoring and follicular fluid aspiration of preovulatory follicles in horses during the anovulatory (spring: non-breeding) and ovulatory (spring, summer, and fall: breeding) seasons and subsequent EV isolation and miRNA profiling identified significant variation in EV-miRNA cargo content. We identified 97 miRNAs with differential expression among the groups and specific clusters of miRNAs involved in the spring transition (miR-149, -200b, -206, -221, -328, and -615) and peak breeding period (including miR-143, -192, -451, -302b, -100, and let-7c). Bioinformatic analyses showed enrichments in various biological functions, e.g., transcription factor activity, transcription and transcription regulation, nucleic acid binding, sequence-specific DNA binding, p53 signaling, and post-translational modifications. Cluster analyses revealed distinct sets of significantly up- and down-regulated miRNAs associated with spring anovulatory (Cluster 1) and summer ovulation-the peak breeding season (Clusters 4 and 6). The findings from the current study shed light on the dynamics of FF-EV-coupled miRNAs in relation to equine ovulatory and anovulatory seasons, and their roles in understanding the mechanisms involved in seasonal shifts and ovulation during the breeding season warrant further investigation.

Biochemical Defence of Plants against Parasitic Nematodes.

Plant parasitic nematodes (PPNs), such as Meloidogyne spp., Heterodera spp. and Pratylenchus spp., are obligate parasites on a wide range of crops, causing significant agricultural production losses worldwide. These PPNs mainly feed on and within roots, impairing both the below-ground and the above-ground parts, resulting in reduced plant performance. Plants have developed a multi-component defence mechanism against diverse pathogens, including PPNs. Several natural molecules, ranging from cell wall components to secondary metabolites, have been found to protect plants from PPN attack by conferring nematode-specific resistance. Recent advances in omics analytical tools have encouraged researchers to shed light on nematode detection and the biochemical defence mechanisms of plants during nematode infection. Here, we discuss the recent progress on revealing the nematode-associated molecular patterns (NAMPs) and their receptors in plants. The biochemical defence responses of plants, comprising cell wall reinforcement; reactive oxygen species burst; receptor-like cytoplasmic kinases; mitogen-activated protein kinases; antioxidant activities; phytohormone biosynthesis and signalling; transcription factor activation; and the production of anti-PPN phytochemicals are also described. Finally, we also examine the role of epigenetics in regulating the transcriptional response to nematode attack. Understanding the plant defence mechanism against PPN attack is of paramount importance in developing new, effective and sustainable control strategies.

UV-induced reactive oxygen species and transcriptional control of 3-deoxyanthocyanidin biosynthesis in black sorghum pericarp.

Black pericarp sorghum has notable value due to the biosynthesis of 3-deoxyanthocyanidins (3-DOAs), a rare class of bioactive polyphenols valued as antioxidant food additives and as bioactive compounds with cytotoxicity to human cancer cells. A metabolic and transcriptomic study was conducted to ascertain the cellular events leading to the activation of 3-DOA biosynthesis in black sorghum pericarp. Prolonged exposure of pericarp during grain maturation to high-fluence ultraviolet (UV) light resulted in elevated levels of reactive oxygen species (ROS) and the activation of 3-DOA biosynthesis in pericarp tissues. In conjunction with 3-DOA biosynthesis was the transcriptional activation of specific family members of early and late flavonoid biosynthesis pathway genes as well as the downstream activation of defense-related pathways. Promoter analysis of genes highly correlated with 3-DOA biosynthesis in black pericarp were enriched in MYB and HHO5/ARR-B motifs. Light microscopy studies of black pericarp tissues suggest that 3-DOAs are predominantly localized in the epicarp and are associated with the cell wall. A working model of UV-induced 3-DOA biosynthesis in black pericarp is proposed that shares features of plant immunity associated with pathogen attack or mechanical wounding. The present model depicts ROS accumulation, the transcriptional activation of receptor kinases and transcription factors (TFs) including NAC, WRKY, bHLH, AP2, and C2H2 Zinc finger domain. This study identified key biosynthetic and regulatory genes of 3-DOA accumulation in black pericarp and provided a deeper understanding of the gene networks and cellular events controlling this tissue-and genotype-specific trait.

STAT3/p-STAT3 expression is correlated with clinicopathological characteristics and prognosis in non-small cell lung cancer.

Signal transducer and activator of transcription factor 3 (STAT3)/phosphorylated STAT3 (p-STAT) play a critical role in tumorigenesis, however, there is limited information on its prognostic value in non-small cell lung cancer (NSCLC). To address this question, 239 lung cancer and 71 normal lung tissue samples were obtained in this study. Immunohistochemistry was applied to detect STAT3/p-STAT3 expression. Pearson's Chi-squared test and the Kaplan-Meier method were conducted to evaluate associations with patients' clinical characteristics and survival. According to our results, STAT3/p-STAT3 was significantly upregulated in lung cancer tissue (p<0.001). Moreover, p-STAT3 expression was significantly correlated with age (p=0.046) and pathological types (p=0.037). In survival analysis, STAT3 positivity was negatively associated with survival in patients older than 60 years (p=0.043) but failed to be an independent prognostic factor in multivariate analysis (p=0.083). Therefore, STAT3/p-STAT3 may serve as a critical biomarker in NSCLC.

A20 intrinsically influences human effector T-cell survival and function by regulating both NF-κB and JNK signaling.

A20 is a dual-function ubiquitin-editing enzyme that maintains immune homeostasis by restraining inflammation. Although A20 serves a similar negative feedback function for T-cell receptor (TCR) signaling, the molecular mechanisms utilized and their ultimate impact on human T-cell function remain unclear. TCR engagement triggers the assembly of the CARD11-BCL10-MALT1 (CBM) protein complex, a signaling platform that governs the activation of downstream transcription factors including NF-κB and c-Jun/AP-1. Utilizing WT and A20 knockout Jurkat T cells, we found that A20 is required to negatively regulate NF-κB and JNK. Utilizing a novel set of A20 mutants in NF-κB and AP-1-driven reporter systems, we discovered the ZnF7 domain is crucial for negative regulatory capacity, while deubiquitinase activity is dispensable. Successful inactivation of A20 in human primary effector T cells congruently conferred sustained NF-κB and JNK signaling, including enhanced upregulation of activation markers, and increased secretion of several cytokines including IL-9. Finally, loss of A20 in primary human T cells resulted in decreased sensitivity to restimulation-induced cell death and increased sensitivity to cytokine withdrawal-induced death. These findings demonstrate the importance of A20 in maintaining T-cell homeostasis via negative regulation of both NF-κB and JNK signaling.

Transcriptome analysis of Dendrobium officinale exposed to high temperature stress

This study aims to mine the genes of Dendrobium officinale in response to high temperature stress and explore the molecular mechanism underlying the heat tolerance of D. officinale. In this study, the D. officinale variety &quot;Dahongshe&quot; was exposed to high temperature for 0, 2, 6, and 12 h, and then transcriptome analysis and qPCR were carried out. The transcriptome of each sample was analyzed by high-throughput sequencing. A total of 14 639 transcripts were obtained after the assembly by StringTie, with the lengths ranging from 500 bp to 2 000 bp. A total of 1 858 differentially expressed genes(DEGs) under high temperature stress in D. officinale, including 1 085 genes with upregulated expression and 773 with downregulated expression. The number of DEGs gradually increased over the time of high temperature treatment. GO enrichment analysis showed that the DEGs were mainly concentrated in transmembrane transport, responses to light, temperature, and radiation stimuli, and activity of transcription factors. The KEGG enrichment analysis revealed that the DEGs responding to high temperature stress were mainly in the pathways of endoplasmic reticulum protein processing, phytohormone signaling pathways, and plant-pathogen interaction. qPCR was performed for 12 randomly selected DEGs, and the outcomes proved that the transcriptome data were accurate and reliable. The results provide a theoretical basis for future work on the molecular mechanism of heat tolerance and the breeding of heat-tolerant varieties of D. officinale.

Transcription Factor Analysis to Investigate Immunosenescence in Rheumatoid Arthritis Patients.

Rheumatoid arthritis (RA) is linked to various signs of advanced aging, such as premature immunosenescence which occurs due to decline in regenerative ability of T cells. RA T cells develop a unique aggressive inflammatory senescent phenotype with an imbalance of Th17/T regulatory (Treg) cell homeostasis and presence of CD28- T cells. The phenotypic analysis and characterization of T cell subsets become necessary to ascertain if any functional deficiencies exist within with the help of transcription factor (TF) analysis. These subset-specific TFs dictate the functional characteristics of T-cell populations, leading to the production of distinct effector cytokines and functions. Examining the expression, activity, regulation, and genetic sequence of TFs not only aids researchers in determining their importance in disease processes but also aids in immunological monitoring of patients enrolled in clinical trials, particularly in evaluating various T-cell subsets [Th17 (CD3+CD4+IL17+RORγt+) cells and T regulatory (Treg) (CD3+CD4+CD25+CD127-FOXP3+) cells], markers of T-cell aging [aged Th17 cells (CD3+CD4+IL17+RORγt+CD28-), and aged Treg cells (CD3+CD4+CD25+CD127-FOXP3+CD28-)]. In this context, we propose and outline the protocols for assessing the expression of TFs in aged Th17 and Treg cells, highlighting the crucial aspects of this cytometric approach.

Context transcription factors establish cooperative environments and mediate enhancer communication

Many enhancers control gene expression by assembling regulatory factor clusters, also referred to as condensates. This process is vital for facilitating enhancer communication and establishing cellular identity. However, how DNA sequence and transcription factor (TF) binding instruct the formation of high regulatory factor environments remains poorly understood. Here we developed a new approach leveraging enhancer-centric chromatin accessibility quantitative trait loci (caQTLs) to nominate regulatory factor clusters genome-wide. By analyzing TF-binding signatures within the context of caQTLs and comparing episomal versus endogenous enhancer activities, we discovered a class of regulators, ‘context-only’ TFs, that amplify the activity of cell type-specific caQTL-binding TFs, that is, ‘context-initiator’ TFs. Similar to super-enhancers, enhancers enriched for context-only TF-binding sites display high coactivator binding and sensitivity to bromodomain-inhibiting molecules. We further show that binding sites for context-only and context-initiator TFs underlie enhancer coordination, providing a mechanistic rationale for how a loose TF syntax confers regulatory specificity.

Exploration of key ferroptosis-related genes as therapeutic targets for sepsis based on bioinformatics and the depiction of their immune profiles characterization

To explore the characteristics of key ferroptosis-related genes as therapeutic targets for sepsis based on bioinformatics analysis, and describe their immune characteristics. The transcriptome datasets GSE57065, GSE9960, GSE28750, and GSE137340 were downloaded from the Gene Expression Omnibus (GEO) database, immune-related gene (IRG) were obtained from ImmPort and InnateDB databases, and ferroptosis-related gene (FRG) were downloaded from the FerrDb database. The datasets GSE57065, GSE9960, and GSE28750 were integrated into an analysis dataset by the surrogate variable analysis (SVA) package and analyzed this analysis dataset by using the "limma" package to obtain differentially expressed gene (DEG), then the intersection set of DEG, FRG, and IRG were considered as ferroptosis and immune-related DEG (FImDEG). Gene ontology (GO) functional annotation and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses were performed using "ClusterProfiler" to understand the biological function of FImDEG. The key genes were screened by protein-protein interaction (PPI) network, least absolute shrinkage and selection operator (LASSO) regression algorithms, and support vector machine (SVM) analyses, and Logistic regression model was built based on above key genes. Receiver operator characteristics curve (ROC curve) was plotted to evaluate the diagnostic efficacy of the key genes alone or combinative. The degree of infiltration of 22 immune cells was assessed using the "CIBERSORT" package, and the correlation between the expressions of key genes and infiltration degree of immune cells was analyzed. Dataset GSE137340 was used to verify these key genes. A dataset consisting of 146 sepsis samples and 61 healthy control samples was obtained by processing the database and removing batch effect. A total of 4 537 DEG were obtained, including 2 066 up-regulated genes and 2 471 down-regulated genes. 2 519 IRG and 855 FRG were obtained from the relevant database. Using the intersection of DEG, IRG and FRG, 34 FImDEG were obtained, including 20 up-regulated genes and 14 down-regulated genes. GO functional annotation showed that the biological functions of 34 FImDEG were mainly inhibition of transferase activity, regulation of DNA-binding transcription factor activity and cell response to stimulation. In terms of molecular function, it was mainly related to RNA polymerase II-specific DNA-binding transcription factor binding and various protein ligase binding. Changes in cell composition occurred mainly in promyelocytic leukemia protein and chromatin silencing complexes. Enrichment analysis of KEGG pathway showed that the major pathways involved in 34 FImDEG included cell aging, expression of programmed death-ligand 1 (PD-L1) and programmed death-1 (PD-1) checkpoint pathways in cancer, interleukin-17 (IL-17) signaling pathway, lipid and atherosclerosis, and NOD-like receptor signaling pathway. Four key genes, including cytochrome b-245 β chain (CYBB), mitogen-activated protein kinase 14 (MAPK14), prostaglandin-endoperoxide synthase 2 (PTGS2) and V-relreticuloendotheliosis viral oncogene homology A (RELA), were screened through PPI network and LASSO and SVM machine learning. ROC curve analysis showed that the area under ROC curve (AUC) of the four key genes for diagnosing sepsis was all greater than 0.65, and the AUC of MAPK14 was 0.911. Logistic regression model was constructed based on four key genes, and the AUC was 0.956. Immunoinfiltration analysis showed that compared with healthy control samples, the infiltration degree of neutrophils and macrophages M0 was significantly increased in sepsis samples, while the infiltration degree of resting natural killer cell (NK cell), naive CD4+ T cell and CD8+ T cell was significantly lowered. Correlation analysis showed that the positive correlation between MAPK14 expression and the infiltration degree of neutrophils was the highest. Validation results in the GSE137340 dataset showed that compared with healthy control samples, the expressions of CYBB and MAPK14 in sepsis samples were significantly up-regulated, however, the expressions of PTGS2 and RELA were significantly down-regulated, similar to the expression trend in the above analysis dataset. Four key genes, including CYBB, MAPK14, PTGS2, and RELA, in the development of sepsis were identified through bioinformatics analysis, which play an important role in the immune process, and MAPK14 may be an important target for immune intervention.

Collaborative role of two distinct cilium-specific cytoskeletal systems in driving Hedgehog-responsive transcription factor trafficking.

Calibrated transcriptional outputs in cellular signaling require fine regulation of transcription factor activity. In vertebrate Hedgehog (Hh) signaling, the precise output of the final effectors, the GLI (Glioma-associated-oncogene) transcription factors, depends on the primary cilium. In particular, the formation of the activator form of GLI upon pathway initiation requires its concentration at the distal cilium tip. However, the mechanisms underlying this critical step in Hh signaling are unclear. We developed a real-time imaging assay to visualize GLI2, the primary GLI activator isoform, at single particle resolution within the cilium. We observed that GLI2 is a cargo of Intraflagellar Transport (IFT) machinery and is transported with anterograde bias during a restricted time window following pathway activation. Our findings position IFT as a crucial mediator of transcription factor transport within the cilium for vertebrate Hh signaling, in addition to IFT's well-established role in ciliogenesis. Surprisingly, a conserved Hh pathway regulator, the atypical non-motile kinesin KIF7, is critical for the temporal control of GLI2 transport by IFT and the spatial control of GLI2 localization at the cilium tip. This discovery underscores the collaborative role of a motile and a non-motile cilium-specific cytoskeletal system in determining the transcriptional output during Hh signaling.

Genome-Wide Association Studies of Hair Whorl in Pigs.

In pigs, a hair whorl refers to hairs that form a ring of growth around the direction of the hair follicle at the dorsal hip. In China, a hair whorl is considered a negative trait that affects marketing, and no studies have been conducted to demonstrate whether hair whorl affects pig performance and provide an explanation for its genetic basis. Performance-measured traits and slaughter-measured traits of hair whorl and non-hair whorl pigs were differentially analyzed, followed by genome-wide association analysis (GWAS) and copy number variation (CNV) methods to investigate the genetic basis of hair whorl in pigs. Differential analysis of 2625 pigs (171 hair whorl and 2454 non-hair whorl) for performance measures showed that hair whorl and non-hair whorl pigs differed significantly (p < 0.05) in traits such as live births, total litter size, and healthy litter size (p < 0.05), while differential analysis of carcass and meat quality traits showed a significant difference only in the 45 min pH (p = 0.0265). GWAS identified 4 SNP loci significantly associated with the hair whorl trait, 2 of which reached genome-significant levels, and 23 candidate genes were obtained by annotation with the Ensembl database. KEGG and GO enrichment analyses showed that these genes were mainly enriched in the ErbB signaling, endothelial apoptosis regulation, and cell proliferation pathways. In addition, CNV analysis identified 652 differential genes between hair whorl and non-hair whorl pigs, which were mainly involved in the signal transduction, transcription factor activity, and nuclear and cytoplasmic-related pathways. The candidate genes and copy number variation differences identified in this study provide a new theoretical basis for pig breeding efforts.

Beneficial Effects of Tyrosol and Oleocanthal from Extra Virgin Olive Oil on Liver Health: Insights into Their Mechanisms of Action.

The Mediterranean diet and consumption of EVOO are associated with multiple beneficial effects for human health, e.g. reduction in cardiovascular risk and mortality, improvement in the lipid profile, and the prevention of chronic diseases, such as cancers and neurodegenerative diseases. In EVOO, more than 30 different phenolic-derived compounds have been identified, representing one of the most promising bioactive classes in olive oil. This review explores the hepatoprotective properties of two of these compounds, tyrosol and oleocanthal, focusing on their mechanisms of action. Recent studies have shown that these compounds, which share a similar chemical structure with a hydroxyl group attached to an aromatic hydrocarbon ring, can potentially mitigate chronic liver diseases, such as MASLD and liver fibrosis, as well as their progression to liver cancer. Consequently, they deserve attention for future pharmacological drug development. In vitro and in vivo studies have suggested that these compounds exert these effects through the regulation of cellular pathways involved in antioxidant response, lipid metabolism, transcription factor activity, and NF-κB signaling. Understanding the mechanisms underlying the hepatoprotective properties of tyrosol and oleocanthal may provide valuable information for the development of therapeutic agents based on their chemical structures capable of targeting chronic liver diseases.

Candidate Genes for Brown Fiber in Cotton Revealed Among the R2R3-Myb and bHLH-Myc Gene Families

ABSTRACT Naturally colored cotton varieties attract investigators due to their eco-friendly and hypoallergenic properties. Genetic mechanisms, determining control of pigment biosynthesis pathway in cotton fiber, are being intensively studied nowadays. However, the knowledge, explaining control of proanthocyanidins accumulation in cotton fiber by the MBW complex (R2R3-Myb, bHLH-Myc and WD40), is insufficient. In this connection, we focused on the regulatory genes from a number of the most likely ones involved in proanthocyanidins biosynthesis. We used the Sanger sequencing approach to reveal the allelic diversity of the R2R3-Myb and bHLH-Myc genes among contrast genotype accessions including various fiber shades and hypocotyl color. Having used the number of bioinformatics tools, we concluded that the replacement of conserved tryptophan residue abolished the DNA-binding activity of the GhMYB10-A transcription factor and this, probably, can be associated with the light brown fiber phenotype. Deeper studies are required to definitely establish the GhMYB10-A function. However, our achievements can be practically applied in marker-assisted breeding of cotton varieties with naturally colored fiber.

Characterization of non-coding variants associated with transcription factor binding through ATAC-seq-defined footprint QTLs in liver.

Non-coding variants discovered by genome-wide association studies (GWAS) are enriched in regulatory elements harboring transcription factor (TF) binding motifs, strongly suggesting a connection between disease association and the disruption of cis-regulatory sequences. Occupancy of a TF inside a region of open chromatin can be detected in ATAC-seq where bound TFs block the transposase Tn5, leaving a pattern of relatively depleted Tn5 insertions known as a "footprint". Here, we sought to identify variants associated with TF-binding, or "footprint quantitative trait loci" (fpQTLs) in ATAC-seq data generated from 170 human liver samples. We used computational tools to scan the ATAC-seq reads to quantify TF binding likelihood as "footprint scores" at variants derived from whole genome sequencing generated in the same samples. We tested for association between genotype and footprint score and observed 693 fpQTLs associated with footprint-inferred TF binding (FDR < 5%). Given that Tn5 insertion sites are measured with base-pair resolution, we show that fpQTLs can aid GWAS and QTL fine-mapping by precisely pinpointing TF activity within broad trait-associated loci where the underlying causal variant is unknown. Liver fpQTLs were strongly enriched across ChIP-seq peaks, liver expression QTLs (eQTLs), and liver-related GWAS loci, and their inferred effect on TF binding was concordant with their effect on underlying sequence motifs in 80% of cases. We conclude that fpQTLs can reveal causal GWAS variants, define the role of TF binding site disruption in disease and provide functional insights into non-coding variants, ultimately informing novel treatments for common diseases.

Integrating network pharmacology, molecular docking and non-targeted serum metabolomics to illustrate pharmacodynamic ingredients and pharmacologic mechanism of Haizao Yuhu Decoction in treating hyperthyroidism.

To explore the pharmacodynamic ingredients and pharmacologic mechanism of Haizao Yuhu Decoction (HYD) in treating hyperthyroidism via an analysis integrating network pharmacology, molecular docking, and non-targeted serum metabolomics. Therapeutic targets of hyperthyroidism were searched through multi-array analyses in the Gene Expression Omnibus (GEO) database. Hub genes were subjected to the construction of a protein-protein interaction (PPI) network, and GO and KEGG enrichment analyses. Targets of active pharmaceutical ingredients (APIs) in HYD and those of hyperthyroidism were intersected to yield hub genes, followed by validations via molecular docking and non-targeted serum metabolomics. 112 hub genes were identified by intersecting APIs of HYD and therapeutic targets of hyperthyroidism. Using ultra-high performance liquid chromatography with quadrupole time-of-flight mass spectrometry (UPLC-Q-TOF-MS) in both negative and positive ion polarity modes, 279 compounds of HYD absorbed in the plasma were fingerprinted. Through summarizing data yielded from network pharmacology and non-targeted serum metabolomics, 214 common targets were identified from compounds of HYD absorbed in the plasma and therapeutic targets of hyperthyroidism, including PTPN11, PIK3CD, EGFR, HRAS, PIK3CA, AKT1, SRC, PIK3CB, and PIK3R1. They were mainly enriched in the biological processes of positive regulation of gene expression, positive regulation of MAPK cascade, signal transduction, protein phosphorylation, negative regulation of apoptotic process, positive regulation of protein kinase B signaling and positive regulation of MAP kinase activity; and molecular functions of identical protein binding, protein serine/threonine/tyrosine kinase activity, protein kinase activity, RNA polymerase II transcription factor activity, ligand-activated sequence-specific DNA binding and protein binding. A total of 185 signaling pathways enriched in the 214 common targets were associated with cell proliferation and angiogenesis. HYD exerts a pharmacological effect on hyperthyroidism via inhibiting pathological angiogenesis in the thyroid and rebalancing immunity.

Predicting bacterial fitness in Mycobacterium tuberculosis with transcriptional regulatory network-informed interpretable machine learning.

Mycobacterium tuberculosis (Mtb) is the causative agent of tuberculosis disease, the greatest source of global mortality by a bacterial pathogen. Mtb adapts and responds to diverse stresses such as antibiotics by inducing transcriptional stress-response regulatory programs. Understanding how and when these mycobacterial regulatory programs are activated could enable novel treatment strategies for potentiating the efficacy of new and existing drugs. Here we sought to define and analyze Mtb regulatory programs that modulate bacterial fitness. We assembled a large Mtb RNA expression compendium and applied these to infer a comprehensive Mtb transcriptional regulatory network and compute condition-specific transcription factor activity profiles. We utilized transcriptomic and functional genomics data to train an interpretable machine learning model that can predict Mtb fitness from transcription factor activity profiles. We demonstrated that this transcription factor activity-based model can successfully predict Mtb growth arrest and growth resumption under hypoxia and reaeration using only RNA-seq expression data as a starting point. These integrative network modeling and machine learning analyses thus enable the prediction of mycobacterial fitness under different environmental and genetic contexts. We envision these models can potentially inform the future design of prognostic assays and therapeutic intervention that can cripple Mtb growth and survival to cure tuberculosis disease.

The role of dietary fibre in intestinal heat shock protein regulation

SummaryThe gastrointestinal tract serves as a pivotal physical barrier that prevents the translocation of exogenous substances from the intestinal lumen into the systemic circulation. Dysfunction of intestinal barrier function has been implicated in the pathogenesis of several diseases, such as metabolic disorders. Heat shock proteins (HSPs) play a critical role in maintaining the resilience and viability of epithelial cells when exposed to stressors. Evidence suggests that dietary fibre (DF), a known inducer of HSP production, may be a promising candidate for strengthening the intestinal barrier. Understanding the regulation of intestinal HSPs and the protective effect of DF is critical to defending against environmental threats and preserving human health. To date, six DFs—pectin, chicory, psyllium, guar gum, partially hydrolysed guar gum, and xylooligosaccharide—have been reported to have promotive effects on intestinal HSP induction. DF promotes intestinal HSP induction through gut microbiota‐dependent and independent mechanisms. DF is fermented by gut microbiota to produce short‐chain fatty acids, specifically butyrate and propionate, to promote HSP production. Meanwhile, DF also promotes intestinal HSP induction through direct interaction with intestinal epithelial cells, independent of gut microbiota activity, although the precise mechanism is still unclear. Regulation of intestinal HSP occurs by transcriptional modulation through activation of heat shock transcription factors, primarily heat shock factor 1, or at the post‐transcriptional level by modulation of the translation process. This review highlights recent advances in understanding the role of DF in improving intestinal barrier function, with particular emphasis on the regulatory mechanisms of intestinal HSPs.