JASPAR 2020: update of the open-access database of transcription factor binding profiles

Indole-3-lactic acid suppresses colorectal cancer via metabolic reprogramming

Research indicates that abnormal gut microbiota metabolism is linked to colorectal cancer (CRC) progression, but the role of microbiota-related tryptophan metabolism disruption remains unclear. Using metagenomic sequencing and targeted Trp metabolomics, our research identified that CRC patients had abnormal indole-3-lactic acid (ILA) levels, which were related to tumor malignancy. Exogenous ILA administration suppressed CRC development in AOM/DSS induced and xenograft mice models. Furthermore, in vitro experiments demonstrated that ILA inhibits tumor cell proliferation, migration, and anti-apoptotic capabilities. Mechanistically, ILA appears to directly occupy the phosphorylation sites of STAT3, leading to a reduction in intracellular phosphorylated STAT3 (p-STAT3) levels and the inhibition of the HK2 pathway, thereby downregulating glucose metabolism in cancer cells. Notably, this inhibition is independent of the aryl hydrocarbon receptor (AHR). In conclusion, our research findings demonstrate that alterations in tryptophan metabolism among CRC patients can influence tumor progression and reveal a novel mechanism through which ILA exerts its inhibitory effects on CRC. These findings offer new insights into the role of gut microbiota in CRC and identify potential clinical therapeutic targets.

Screening potential diagnostic biomarkers for PLA2R‑associated idiopathic membranous nephropathy by WGCNA analysis and LASSO algorithm

Adult nephrotic syndrome is primarily caused by membranous nephropathy (MN), with idiopathic membranous nephropathy (IMN) being a prominent subtype. The onset of phospholipase A2 receptor (PLA2R1)-associated IMN is critically linked to M-type PLA2R1 exposure, yet the mechanism underlying glomerular injury remains unclear. In this study, membranous nephropathy datasets (GSE115857, GSE200828) were retrieved from GEO. Differential gene expression was analyzed using the 'limma' R package. WGCNA filtered PLA2R-related modules and intersected genes. LASSO regression, evaluated by ROC analysis, identified characteristic genes. Binomial logistic regression assessed their association with IMN. Validation was performed in the GSE133288 dataset. IHC and qRT-PCR detected characteristic gene expression in PLA2R-positive patients. This study identified elevated PLA2R expression in IMN patients among 117 DEGs. PPI analysis suggested enrichment in Golgi membranes, co-regulation, and glucocorticoid responsiveness, implicating the PPAR pathway by KEGG. WGCNA revealed a 440-gene brown module associated with IMN-PLA2R, with ECM1, SLC19A2, RASD1, FOSB, KDELR3, ZFP36, and ELF4 highlighted as diagnostic markers by ROC analysis. Clinical validation confirmed ECM1 upregulation increased IMN risk, while upregulation of SLC19A2, ZFP36, RASD1, and FOSB decreased it. ECM1 positively correlated with PLA2R, whereas SLC19A2, ZFP36, and FOSB negatively correlated. IHC analysis demonstrated consistent gene expression patterns in IMN tissues, with podocyte exposure to PLA2R-positive serum reducing viability and increasing apoptosis. Functional studies, prompted by RASD1 downregulation, revealed enhanced cell activity and reduced apoptosis upon RASD1 overexpression compared to the Serum + Ov-NC control. Collectively, this study identified diagnostic markers for PLA2R-related IMN, offering novel therapeutic targets for the treatment of IMN.

Role of PRC2 in the stochastic expression of Aire target genes and development of mimetic cells in the thymus

The transcriptional targets of Aire and the mechanisms controlling their expression in medullary thymic epithelial cells (mTECs) need to be clarified to understand Aire's tolerogenic function. By using a multi-omics single-cell approach coupled with deep scRNA-seq, we examined how Aire controls the transcription of a wide variety of genes in a small fraction of Aire-expressing cells. We found that chromatin repression by PRC2 is an important step for Aire to achieve stochastic gene expression. Aire unleashed the silenced chromatin configuration caused by PRC2, thereby increasing the expression of its functional targets. Besides this preconditioning for Aire's gene induction, we demonstrated that PRC2 also controls the composition of mTECs that mimic the developmental trait of peripheral tissues, i.e., mimetic cells. Of note, this action of PRC2 was independent of Aire and it was more apparent than Aire. Thus, our study uncovered the essential role of polycomb complex for Aire-mediated promiscuous gene expression and the development of mimetic cells.

Precision targeting of β-catenin induces tumor reprogramming and immunity in hepatocellular cancers

First-line immune checkpoint inhibitor (ICI) combinations show responses in subsets of hepatocellular carcinoma (HCC) patients. Nearly half of HCCs are Wnt-active with mutations in CTNNB1 (encoding for β-catenin), AXIN1/2, or APC, and demonstrate heterogeneous and limited benefit to ICI due to an immune excluded tumor microenvironment. We show significant tumor responses in multiple β-catenin-mutated immunocompetent HCC models to a novel siRNA encapsulated in lipid nanoparticle targeting CTNNB1 (LNP-CTNNB1). Both single-cell and spatial transcriptomics reveal cellular and zonal reprogramming, along with activation of immune regulatory transcription factors IRF2 and POU2F1, re-engaged type I/II interferon signaling, and alterations in both innate and adaptive immunity upon β-catenin suppression with LNP-CTNNB1 at early- and advanced-stage disease. Moreover, ICI enhances response to LNP-CTNNB1 in advanced-stage disease by preventing T cell exhaustion and through formation of lymphoid aggregates (LA). In fact, expression of an LA-like gene signature prognosticates survival for patients receiving atezolizumab plus bevacizumab in the IMbrave150 phase III trial and inversely correlates with CTNNB1-mutatational status in this patient cohort. In conclusion, LNP-CTNNB1 is efficacious as monotherapy and in combination with ICI in CTNNB1-mutated HCCs through impacting tumor cell-intrinsic signaling and remodeling global immune surveillance, providing rationale for clinical investigations.

Revealing long-range heterogeneous organization of nucleoproteins with 6mA footprinting by ipdTrimming

Enabled by long-read sequencing technologies, particularly Single Molecule, Real-Time sequencing, N6-methyladenine (6mA) footprinting is a transformative methodology for revealing the heterogenous and dynamic distribution of nucleosomes and other DNA-binding proteins. Here, we present ipdTrimming, a novel 6mA-calling pipeline that outperforms existing tools in both computational efficiency and accuracy. Utilizing this optimized experimental and computational framework, we are able to map nucleosome positioning and transcription factor occupancy in nuclear DNA and establish high-resolution, long-range binding events in mitochondrial DNA. Our study highlights the potential of 6mA footprinting to capture coordinated nucleoprotein binding and to unravel epigenetic heterogeneity.

Identification of cell specific biomarkers for intellectual disability via single cell RNA sequencing and transcriptomic bioinformatics approaches

Limitations in cognitive functioning and adaptive behavior are hallmarks of Intellectual Disability (ID), a neurodevelopmental disease. Specific genetic disorders that result in ID can also have immune system anomalies, such as changes in T (CD4+ and CD8+) cell activity. This work aimed to compare single-cell RNA-sequencing (scRNA-seq) and transcriptome data to find biomarkers linked to T cells that could potentially be utilized for the diagnosis and assessment of ID. After integrating genes and performing a comparative analysis 196 genes were identified as differentially expressed genes (DEGs). Furthermore, the DAVID online platform and FunRich software were utilized to detect signal transduction and translation, immune response, MHC (Major Histocompatibility Complex) class II, antigen processing and presentation, allograft rejection and important pathways of type I diabetes mellitus. In this investigation, six ribosomal proteins (RPS27A, RPS21, RPS18, RPS7, RPS5, and RPL9) have been identified as the hub genes of ID from PPI. Additionally, eleven topological algorithms discovered only one hub protein, namely RPS27A from the protein-protein interaction (PPI) network. Through the analysis of the regulatory network, we have identified several crucial transcriptional factors (TFs) including FOXC1, FOXL1, and GATA2; microRNAs such as mir-92a-3p, and mir-16-5p were investigated by procedural data analysis. This study used scRNA-seq and transcriptomics data analysis to define unique biomarkers associated with T cell types throughout the progression of ID. Ongoing research on the activity of ID genes is contributing to a greater understanding of the pathophysiology of ID and will become more scientific and research-based in future.

SP1 promotes triple-negative breast cancer progression by targeting USP5

BACKGROUND

Triple-negative breast cancer (TNBC) is characterized by the absence of targeted therapies and a dismal prognosis, necessitating a critical exploration of the molecular mechanisms driving TNBC pathogenesis and the identification of novel therapeutic targets. While dysregulated USP5 expression has been observed in various malignancies, its specific functions and mechanisms in TNBC remain poorly understood.

METHODS

The study utilized a combination of TCGA database analysis, immunohistochemistry staining (IHC), quantitative RT-PCR, and western blotting assay to investigate the expression of USP5 and SP1 in TNBC. Furthermore, the study examined the role of the SP1-USP5 axis and the USP5 inhibitor periplocin in TNBC progression through CCK-8 assay, colony formation assay, EDU incorporation assay, and tumor xenograft experiments. Additionally, the study explored the underlying mechanisms involved in the regulation of USP5 expression in TNBC using luciferase assay, ChIP-qPCR, quantitative RT-PCR, and western blotting assay. In order to ascertain potential inhibitors of USP5 activity, a combination of the Molecular Operating Environment (MOE) multi-functional docking platform, cellular thermal shift assay, and in vitro USP5 activity assay were utilized.

RESULTS

In the current investigation, it was observed that the expression of USP5 was elevated in TNBC and was significantly correlated with decreased overall survival rates among patients. The upregulation of USP5 was found to be mediated by the transcription factor SP1 through its binding to the USP5 promoter, consequently facilitating the progression of TNBC. Notably, the natural compound periplocin was identified as a promising inhibitor of USP5, demonstrating potential efficacy in impeding the advancement of TNBC.

CONCLUSIONS

Our research findings indicate that the SP1-USP5 signaling pathway is significantly involved in the advancement of TNBC, and periplocin's ability to target USP5 presents a potential therapeutic approach for managing TNBC. These results offer valuable insights for the development of novel treatment strategies for TNBC patients.

High temporal-resolution transcriptome landscape reveals the biological process and regulatory genes of melanin deposition in breast muscle of Silkie chickens during embryonic development

BACKGROUND

Abnormal deposition of melanin in skeletal muscle is an interesting phenomenon and the Silkie is the most typical example. Melanin deposition involves multiple steps such as neural crest cell migration, melanocyte differentiation, melanosome assembly and melanin biosynthesis, which have already occurred during the embryonic stage of Silkies. However, there is no comprehensive understanding of the dynamic changes in the biological processes and regulatory mechanism underlying melanin deposition in skeletal muscle during chicken embryonic development.

RESULTS

In this study, high-performance liquid chromatography (HPLC) was used to accurately measure the melanin content in breast muscle across 13 embryonic time points. There was no melanin in breast muscle on embryonic day 8 (E08) to E10, a trace amount of melanin on E11 to E16 and a large amount of melanin on E17 to E21. According to melanin content and deposition pattern, the melanin deposition process in breast muscle was further divided into five stages, including E08 to E10, E11 to E14, E15 to E16, E17 to E18, and E19 to E21. High temporal-resolution transcriptome analysis was performed in the breast muscle of Silkies across 13 embryonic time points. The protein-coding genes (PCGs) and transcriptional factors (TFs) significantly specifically expressed at these five stages were identified. Among these stage-specific genes, stage-specific DEGs between Silkies and Wenchang chickens without melanosis were further screened at each stage. During E08 to E10, three stage-specific DEGs and one stage-specific TF act on neural crest cell migration and melanocyte stem cell differentiation. During E17 to E21, nine stage-specific DEGs and one stage-specific TF act on melanosome assembly and melanin biosynthesis. During E19 to E21, one stage-specific DEG enhances melanin biosynthesis. These stage-specific DEGs and TFs all affect the final melanin content of breast muscle.

CONCLUSIONS

This study reveals the critical stage of melanin deposition in breast muscle during the embryonic development, and identified the biological processes and functional genes at each stage. This study provides novel insights into the biological process and regulatory mechanism of melanin deposition in skeletal muscle and provides a reference for breeding Silkies with high muscle melanin content.

Intragenic viral silencer element regulates HTLV-1 latency via RUNX complex recruitment

Retroviruses integrate their genetic material into the host genome, enabling persistent infection. Human T cell leukaemia virus type 1 (HTLV-1) and human immunodeficiency virus type 1 (HIV-1) share similarities in genome structure and target cells, yet their infection dynamics differ drastically. While HIV-1 leads to high viral replication and immune system collapse, HTLV-1 establishes latency, promoting the survival of infected cells and, in some cases, leading to leukaemia. The mechanisms underlying this latency preference remain unclear. Here we analyse blood samples from people with HTLV-1 and identify an open chromatin region within the HTLV-1 provirus that functions as a transcriptional silencer and regulates transcriptional burst. The host transcription factor RUNX1 binds to this open chromatin region, repressing viral expression. Mutation of this silencer enhances HTLV-1 replication and immunogenicity, while its insertion into HIV-1 suppresses viral production. These findings reveal a strategy by which HTLV-1 ensures long-term persistence, offering potential insights into retroviral evolution and therapeutic targets.

Single-cell multiomic analysis unveils the immune landscape dynamics of graves' ophthalmopathy

Graves' ophthalmopathy (GO) is an autoimmune disease that occurs concurrently with Graves' disease, potentially leading to facial disfigurement and irreversible vision loss. However, the molecular characteristics of cellular changes in the peripheral immune environment of GO patients remain unclear. This study presents a multi-omics single-cell analysis of peripheral blood from GO patients and healthy controls, revealing key molecular alterations in immune cell subpopulations. We identify increased chromatin accessibility and regulatory activity of pro-inflammatory factors, such as FOS and NF-κB family. Immune repertoire analysis shows enhanced diversity in GO patients. Notably, GO-specific clonal expansions are enriched in CD8 effector T (CD8 Te) cells, which exhibit signs of enhanced T cell chemotaxis and exhaustion. Multi-omics integration analysis reveals that changes in SLC35G1 and IDNK expression in CD8 Te are linked to disease phenotypes, with trends aligning with experimental results. We find that this cell cluster could infiltrate into orbital tissues and upregulate fibrosis-related pathways associated with fibroblasts in GO. These findings indicate its potential role in driving disease progression. Our study reveals the epigenetic and transcriptomic landscape in the peripheral blood of GO patients, enhancing the understanding of the pathogenic molecular mechanisms and offering potential directions for prevention and treatment.

Chromatin state origins of uterine leiomyoma

Aberrations in the regulatory genome play a pivotal role in population-level disease predisposition. Annotation of the regulatory regions using appropriate primary tissues - instead of cell lines affected by selection and other confounding factors - could shed new light into mechanisms underlying common conditions. We test this approach in uterine leiomyomas, highly prevalent benign neoplasms of the myometrium, by creating 15-state chromatin annotations for myometrium and uterine leiomyomas. Integration with RNA-seq, ATAC-seq, HiChIP and methylation data enables us to compare the epigenomes of myometrium and ULs with distinct driver mutations, highlighting the role of bivalent regions in the neoplastic process. Subsequently, a genome wide association study meta-analysis is performed, using three different cohorts. Disease association loci are enriched at active chromatin, especially at enhancers, and harbor tumor- and driver mutation-specific chromatin states. At SATB2 locus we show the effect of the risk genotype already in the normal tissue. Integration of genome-wide association studies and deep regulatory genomics data from the correct tissue type represents a powerful approach in understanding population-level disease predisposition.

Sinularin induces autophagy-dependent cell death by activating ULK1 and enhancing FOXO3-ATG4A axis in prostate cancer cells

Sinularin is a natural product extracted from soft coral and is shown to exhibit antitumor effects against multiple human cancers. We previously showed that Sinularin induces apoptotic cell death via stabilizing the FOXO3 protein in prostate cancer cells. In this study, we demonstrated that Sinularin triggers autophagy via two different mechanisms in prostate cancer cells. First, Sinularin reduced the S757 phosphorylation of ULK1 protein, which was mediated by mTOR, leading to ULK1 activation and autophagy initiation. Second, Sinularin enhanced the expression of autophagic protein ATG4A, which is the key regulator in the formation of autophagosome, through a FOXO3-dependent transcriptional mechanism. Next, we identified that ATG4A is a new target gene of the transcription factor FOXO3. Additionally, we also found that Sinularin-induced autophagy promoted survivin degradation and led to cell apoptosis. Taken together, these findings suggest that Sinularin induces prostate cancer cell autophagy by promoting autophagy initiation through activation of ULK1 and formation of autophagosome through the FOXO3-ATG4A pathway.

A unified analysis of atlas single-cell data

Recent efforts to generate atlas-scale single-cell data provide opportunities for joint analysis across tissues and modalities. Existing methods use cells as the reference unit, hindering downstream gene-based analysis and removing genuine biological variation. Here we present GIANT, an integration method designed for atlas-scale gene analysis across cell types and tissues. GIANT converts data sets into gene graphs and recursively embeds genes without additional alignment. Applying GIANT to two recent atlas data sets yields unified gene-embedding spaces across human tissues and data modalities. Further evaluations demonstrate GIANT's usefulness in discovering diverse gene functions and underlying gene regulation in cells from different tissues.

Quasi-spatial single-cell transcriptome based on physical tissue properties defines early aging associated niche in liver

Aging is associated with the accumulation of senescent cells, which are triggered by tissue injury response and often escape clearance by the immune system. The specific traits and diversity of these cells in aged tissues, along with their effects on the tissue microenvironment, remain largely unexplored. Despite the advances in single-cell and spatial omics technologies to understand complex tissue architecture, senescent cell populations are often neglected in general analysis pipelines due to their scarcity and the technical bias in current omics toolkits. Here we used the physical properties of tissue to enrich the age-associated fibrotic niche and subjected them to single-cell RNA sequencing and single-nuclei ATAC sequencing (ATAC-seq) analysis and named this method fibrotic niche enrichment sequencing (FiNi-seq). Fibrotic niche of the tissue was selectively enriched based on its resistance to enzymatic digestion, enabling quasi-spatial analysis. We profiled young and old livers of male mice using FiNi-seq, discovered Wif1- and Smoc1-producing mesenchymal cell populations showing senescent phenotypes, and investigated the early immune responses within this fibrotic niche. Finally, FiNi-ATAC-seq revealed age-associated epigenetic changes enriched in fibrotic niche cells. Thus, our quasi-spatial, single-cell profiling method allows the detailed analysis of initial aging microenvironments, providing potential therapeutic targets for aging prevention.

A transcription factor module mediating C2 photosynthesis in the Brassicaceae

C4 photosynthesis has arisen from the ancestral C3 state in over sixty lineages of angiosperms. It is widely accepted that an early step in C4 evolution is associated with the appearance of so-called C2 photosynthesis caused by loss of glycine decarboxylase activity from mesophyll cells followed by activation in the bundle sheath. Although changes in cis to a distal enhancer upstream of the P-subunit of GLYCINE DECARBOXYLASE (GLDP) from C2 Moricandia enable loss of expression from mesophyll cells, the mechanism then allowing GLDP expression in the bundle sheath is not known. Here we identify a MYC-MYB transcription factor module previously associated with the control of glucosinolate biosynthesis as the basis of this foundational event in the evolution of C2 photosynthesis. Specifically, we find that in the C3 state this MYC-MYB module already patterns GLDP expression to bundle sheath cells. As a consequence, when GLDP expression is lost from the mesophyll, the MYC-MYB dependent expression in the bundle sheath is revealed. Evolution of C2 photosynthesis is thus associated with a MYC-MYB based transcriptional network already present in the C3 state. This work identifies a molecular genetic mechanism underlying the bundle sheath accumulation of glycine decarboxylase required for C2 photosynthesis and thus a fundamental step in the evolution of C4 photosynthesis.

Multi-omic and spatial analysis of mouse kidneys highlights sex-specific differences in gene regulation across the lifespan

There is a sex bias in the incidence and progression of many kidney diseases. To better understand such sexual dimorphism, we integrated data from six platforms, characterizing 76 kidney samples from 68 mice at six developmental and adult time points, creating a molecular atlas of the mouse kidney across the lifespan for both sexes. We show that proximal tubules have the most sex-biased differentially expressed genes emerging after 3 weeks of age and are associated with hormonal regulations. We reveal potential mechanisms involving both direct and indirect regulation by androgens and estrogens. Spatial profiling identifies distinct sex-biased spatial patterns in the cortex and outer stripe of the outer medulla. Additionally, older mice exhibit more aging-related gene alterations in loops of Henle, proximal tubules and collecting ducts in a sex-dependent manner. Our results enhance the understanding of spatially resolved gene expression and hormone regulation underlying kidney sexual dimorphism across the lifespan.

Characterizing somatic mutations in ovarian cancer germline risk regions

Epithelial ovarian cancer (EOC) genetics research has been focused on germline or somatic mutations independently. Emerging evidence suggests that the somatic mutational landscape can be shaped by the germline genetic background. In this study, we aim to unravel the role of somatic alterations within EOC germline susceptibility regions by incorporating functional annotations. We investigate somatic events, including mutational signatures, point mutations, copy number alterations, and transcription factor binding disruptions, within 33 EOC germline susceptibility regions. Our analysis identifies significant associations between candidate germline susceptibility genes and somatic mutational signatures known to be key risk factors for EOC, such as mismatch repair deficiency, age-related mutagenesis, and homologous recombination deficiency. In addition, we find somatic point mutations and copy number alterations are significantly enriched in histotype-specific active enhancers and promoters within EOC risk loci. Furthermore, we examine the impact of germline variants and somatic mutations on transcription factor binding sites, identifying cancer developmental transcription factor motifs frequently affected by both types of mutations. Overall, our study highlights the importance of integrating germline and somatic mutations with regulatory and epigenomic data to gain insights into the genetic basis of EOC.

NR2F2 regulation of interstitial cell fate in the embryonic mouse testis and its impact on differences of sex development

Testicular fetal Leydig cells produce androgens essential for male reproductive development. Impaired fetal Leydig cell differentiation leads to differences of sex development including hypospadias, cryptorchidism, and infertility. Despite fetal Leydig cells are thought to originate from proliferating progenitor cells in the testis interstitium, the precise mechanisms governing the interstitial cells to fetal Leydig cell transition remain elusive. Using mouse models and single-nucleus multiomics, we find that fetal Leydig cells arise from a Nr2f2-positive interstitial population. Embryonic deletion of Nr2f2 in mouse testes results in differences of sex development, including dysgenic testes, Leydig cell hypoplasia, cryptorchidism, and hypospadias. By combining single-nucleus multiomics and NR2F2 ChIP-seq we find that NR2F2 promotes the progenitor fate while suppresses Leydig cell differentiation by modulating key transcription factors and downstream genes. Our findings establish Nr2f2 as a crucial regulator of fetal Leydig cell differentiation and provide molecular insights into differences of sex development linked to Nr2f2 mutations.

scMultiMap: Cell-type-specific mapping of enhancers and target genes from single-cell multimodal data

Mapping enhancers and target genes in disease-related cell types provides critical insights into the functional mechanisms of genome-wide association studies (GWAS) variants. Single-cell multimodal data, which measure gene expression and chromatin accessibility in the same cells, enable the cell-type-specific inference of enhancer-gene pairs. However, this task is challenged by high data sparsity, sequencing depth variation, and the computational burden of analyzing a large number of pairs. We introduce scMultiMap, a statistical method that infers enhancer-gene association from sparse multimodal counts using a joint latent-variable model. It adjusts for technical confounding, permits fast moment-based estimation and provides analytically derived p-values. In blood and brain data, scMultiMap shows appropriate type I error control, high statistical power, and computational efficiency (1% of existing methods). When applied to Alzheimer's disease (AD) data, scMultiMap gives the highest heritability enrichment in microglia and reveals insights into the regulatory mechanisms of AD GWAS variants.

Variant-specific disruption to notch signalling in PAX6 microphthalmia and aniridia patient-derived hiPSC optic cup-like organoids

The homeobox-containing transcription factor PAX6 is a key regulator of eye development. Pathogenic heterozygous PAX6 variants lead to variable ocular phenotypes, most commonly haploinsufficiency-induced aniridia. Missense variants are typically associated with milder ocular conditions, although variants in the DNA-binding paired domain which alter target binding lead to severe ocular phenotypes including bilateral microphthalmia, similar to SOX2-anophthalmia syndrome. However, the variant-specific pathway disruption resulting in phenotypic heterogeneity is not well understood. To investigate pathogenic mechanisms of PAX6 variants, transcriptomic and chromatin accessibility analysis was performed on hiPSC derived 3D optic cup-like organoids generated from patients with variants (i) PAX6N124K displaying combined microphthalmia, aniridia and optic nerve coloboma, and (ii) PAX6R261X exhibiting typical aniridia. Total RNA sequencing analysis revealed downregulation of SOX2 in missense PAX6N124K cups compared to both wildtype and PAX6R261X haploinsufficient aniridia controls, along with Notch signalling components and markers of proliferation and differentiation. Transcription factor binding motifs of Notch-related genes were also found to be differentially bound in PAX6N124K cups through ATACseq footprinting analysis. Our analysis of PAX6-related oculopathies using in vitro models reveals disruption to DNA binding perturbs SOX2 and Notch signalling, contributing to severe ocular phenotypes in patients with missense changes in the paired domain. This work reveals a previously unestablished role for PAX6 in SOX2 and Notch signalling regulation during early oculogenesis, as well as illuminating disease mechanisms underlying variant-specific ocular phenotypes and genotype-phenotype correlations. These novel insights can influence clinical care, and provide valuable data on potential therapeutic targets, which can guide future translational research.

DNA sequence analysis landscape: a comprehensive review of DNA sequence analysis task types, databases, datasets, word embedding methods, and language models

Deoxyribonucleic acid (DNA) serves as fundamental genetic blueprint that governs development, functioning, growth, and reproduction of all living organisms. DNA can be altered through germline and somatic mutations. Germline mutations underlie hereditary conditions, while somatic mutations can be induced by various factors including environmental influences, chemicals, lifestyle choices, and errors in DNA replication and repair mechanisms which can lead to cancer. DNA sequence analysis plays a pivotal role in uncovering the intricate information embedded within an organism's genetic blueprint and understanding the factors that can modify it. This analysis helps in early detection of genetic diseases and the design of targeted therapies. Traditional wet-lab experimental DNA sequence analysis through traditional wet-lab experimental methods is costly, time-consuming, and prone to errors. To accelerate large-scale DNA sequence analysis, researchers are developing AI applications that complement wet-lab experimental methods. These AI approaches can help generate hypotheses, prioritize experiments, and interpret results by identifying patterns in large genomic datasets. Effective integration of AI methods with experimental validation requires scientists to understand both fields. Considering the need of a comprehensive literature that bridges the gap between both fields, contributions of this paper are manifold: It presents diverse range of DNA sequence analysis tasks and AI methodologies. It equips AI researchers with essential biological knowledge of 44 distinct DNA sequence analysis tasks and aligns these tasks with 3 distinct AI-paradigms, namely, classification, regression, and clustering. It streamlines the integration of AI into DNA sequence analysis tasks by consolidating information of 36 diverse biological databases that can be used to develop benchmark datasets for 44 different DNA sequence analysis tasks. To ensure performance comparisons between new and existing AI predictors, it provides insights into 140 benchmark datasets related to 44 distinct DNA sequence analysis tasks. It presents word embeddings and language models applications across 44 distinct DNA sequence analysis tasks. It streamlines the development of new predictors by providing a comprehensive survey of 39 word embeddings and 67 language models based predictive pipeline performance values as well as top performing traditional sequence encoding-based predictors and their performances across 44 DNA sequence analysis tasks.

Active regulatory elements recruit cohesin to establish cell specific chromatin domains

As the 3D structure of the genome is analysed at ever increasing resolution it is clear that there is considerable variation in the 3D chromatin architecture across different cell types. It has been proposed that this may, in part, be due to increased recruitment of cohesin to activated cis-elements (enhancers and promoters) leading to cell-type specific loop extrusion underlying the formation of new sub-TADs. Here we show that cohesin correlates well with the presence of active enhancers and that this varies in an allele-specific manner with the presence or absence of polymorphic enhancers which vary from one individual to another. Using the alpha globin cluster as a model, we show that when all enhancers are removed, peaks of cohesin disappear from these regions and the erythroid specific sub-TAD is no longer formed. Re-insertion of the major alpha globin enhancer (R2) is associated with re-establishment of recruitment and increased interactions. In complementary experiments insertion of the R2 enhancer element into a "neutral" region of the genome recruits cohesin, induces transcription and creates a new large (75 kb) erythroid-specific domain. Together these findings support the proposal that active enhancers recruit cohesin, stimulate loop extrusion and promote the formation of cell specific sub-TADs.

Genomics guiding personalized first-line immunotherapy response in lung and bladder tumors

BACKGROUND

Immune checkpoint inhibitors (ICI) have revolutionized cancer treatment, particularly in advanced non-small cell lung cancer (NSCLC) and muscle-invasive bladder cancer (MIBC). However, identifying reliable predictive biomarkers for ICI response remains a significant challenge. In this study, we analyzed real-world cohorts of advanced NSCLC and MIBC patients treated with ICI as first-line therapy.

METHODS

Tumor samples underwent Whole Genome Sequencing (WGS) to identify specific somatic variants and assess tumor mutational burden (TMB). Additionally, mutational signature extraction and pathway enrichment analyses were performed to uncover the underlying mechanisms of ICI response. We also characterized HLA-I haplotypes and investigated LINE-1 retrotransposition.

RESULTS

Distinct mutation patterns were identified in patients who responded to treatment, suggesting potential biomarkers for predicting ICI effectiveness. In NSCLC, tumor mutational burden (TMB) did not differ significantly between responders and non-responders, while in MIBC, higher TMB was linked to better responses. Specific mutational signatures and HLA haplotypes were associated with ICI response in both cancers. Pathway analysis showed that NSCLC responders had active inflammatory and immune pathways, while pathways enriched in non-responders related to FGFR3 and neural crest differentiation, associated to resistance mechanisms. In MIBC, responders had alterations in DNA repair, leading to more neoantigens and a stronger ICI response. Importantly, for the first time, we found that LINE-1 activation was positively linked to ICI response, especially in MIBC.

CONCLUSION

These findings reveal promising biomarkers and mechanistic insights, offering a new perspective on predicting ICI response and opening up exciting possibilities for more personalized immunotherapy strategies in NSCLC and MIBC.

Exploring bioactive natural products for treating neurodegenerative diseases: a computational network medicine approach targeting the estrogen signaling pathway in amyotrophic lateral sclerosis and Parkinson's disease

Amyotrophic lateral sclerosis (ALS) and Parkinson's disease (PD) share overlapping molecular mechanisms, including estrogen signaling dysregulation, oxidative stress, and neuroinflammation. Standard treatments often lead to adverse effects due to unintended cross-talk with the estrogen signaling pathway. Identifying key regulatory genes and bioactive plant-derived compounds that modulate estrogen signaling without interfering with standard therapies offers a promising neuroprotective strategy. A network medicine and systems biology approach was used, beginning with the screening of 29 medicinal plants for ALS and 49 for PD, identifying 12 shared plants with neuroprotective potential. Bioactive compounds were screened for gene, protein, and pathway interactions, leading to target prediction (846 ALS-related and 690 PD-related targets) and disease association mining, which identified 93 overlapping genes (OGs). Protein-protein interaction (PPI) network analysis and MCODE clustering revealed ESR1, EGFR, and SRC as key hub-bottleneck (HB) genes, further validated via differential gene expression analysis. Gene ontology (GO) and pathway enrichment analyses revealed significant enrichment in estrogen signaling confirming the involvement of HB genes in neurodegenerative disease progression. Differential expression analysis confirmed ESR1 upregulation in ALS but downregulation in PD, suggesting a converse disease-specific regulatory pattern. Gene regulatory network (GRN) analysis identified hsa-miR-145-5p (ALS) and hsa-miR-181a-5p (PD) as key regulators, while FOXC1, GATA2, and TP53 emerged as crucial transcription factors (TFs) influencing disease progression. Molecular docking and MD simulations validated strong and stable interactions of Eupalitin (CYP19A1, -9.0 kcal/mol), Hesperetin (ESR1, -8.1 kcal/mol), and Sumatrol (PIK3CA, -8.9 kcal/mol). These phytochemicals, derived from Rosmarinus officinalis, Artemisia scoparia, Ocimum tenuiflorum, and Indigofera tinctoria, maintained stable hydrogen bonding and hydrophobic interactions for over 30% of a 25 ns simulation, supporting their therapeutic potential. The identification of ESR1, EGFR, and SRC as key targets, alongside estrogen signaling involvement, highlights the need for targeted nutraceutical interventions. These findings pave the way for safer, plant-based therapies that mitigate neurodegeneration while preserving estrogen signaling integrity, offering a promising adjuvant strategy alongside existing treatments.

Single-nucleus multi-omics implicates androgen receptor signaling in cardiomyocytes and NR4A1 regulation in fibroblasts during atrial fibrillation

The dysregulation of gene expression programs in the human atria during persistent atrial fibrillation (AF) is not completely understood. Here, we reanalyze bulk RNA-sequencing datasets from two studies (N = 242) and identified 755 differentially expressed genes in left atrial appendages of individuals with persistent AF and non-AF controls. We combined the bulk RNA-sequencing differentially expressed genes with a left atrial appendage single-nucleus multi-omics dataset to assign genes to specific atrial cell types. We found noncoding genes at the IFNG locus (LINC01479, IFNG-AS1) strongly dysregulated in cardiomyocytes. We defined a gene expression signature potentially driven by androgen receptor signaling in cardiomyocytes from individuals with AF. Cell-type-specific gene expression modules suggested an increase in T cell and a decrease in adipocyte and neuronal cell gene expression in AF. Lastly, we showed that reducing NR4A1 expression, a marker of a poorly characterized human atrial fibroblast subtype, fibroblast activation markers, extracellular matrix remodeling and cell proliferation decreased.

Loss of ARID1A accelerates prostate tumourigenesis with a proliferative collagen-poor phenotype through co-operation with AP1 subunit cFos

BACKGROUND

Prostate cancer (PC) is the commonest male visceral cancer, and second leading cause of cancer mortality in men in the Western world.

METHODS

Using a forward-mutagenesis Sleeping Beauty (SB) transposon-based screen in a Probasin Cre-Recombinase (Pb-Cre) Pten-deficient mouse model of PC, we identified Arid1a loss as a driver in the development of metastatic disease.

RESULTS

The insertion of transposon in the Arid1a gene resulted in a 60% reduction of Arid1a expression, and reduced tumour free survival (SB:Ptenfl/fl Arid1aINT median 226 days vs SB:Ptenfl/fl Arid1aWT 293 days, p = 0.02),with elevated rates of metastasis (SB:Ptenfl/fl Arid1aINT 75% lung metastasis rate vs 17% SB:Ptenfl/fl Arid1aWT, p < 0.001). We further generated a Pb-Cre Pten- and Arid1a-deficient mouse model, in which loss of Arid1a demonstrated a profound acceleration in tumorigenesis in Ptenfl/fl mice compared to Pten loss alone (Pb-Cre Ptenfl/flArid1a+/+ median survival of 267 days vs Pb-Cre Ptenfl/fl Arid1afl/fl 103 days, p < 0.0001).

CONCLUSION

Our data revealed homozygous Arid1a loss is required to dramatically accelerate prostate tumourigenesis. Analysis of RNA and ChIP -Sequencing data suggests Arid1a loss enhanced the function of AP-1 subunit cFos. In clinical PC cohort, ARID1A and cFos levels stratified an aggressive subset of PC with a poor survival outcome with a median of only 30 months.

SIMVI disentangles intrinsic and spatial-induced cellular states in spatial omics data

Spatial omics technologies enable analysis of gene expression and interaction dynamics in relation to tissue structure and function. However, existing computational methods may not properly distinguish cellular intrinsic variability and intercellular interactions, and may thus fail to reliably capture spatial regulations. Here, we present Spatial Interaction Modeling using Variational Inference (SIMVI), an annotation-free deep learning framework that disentangles cell intrinsic and spatial-induced latent variables in spatial omics data with rigorous theoretical support. By this disentanglement, SIMVI enables estimation of spatial effects at a single-cell resolution, and empowers various downstream analyses. We demonstrate the superior performance of SIMVI across datasets from diverse platforms and tissues. SIMVI illuminates the cyclical spatial dynamics of germinal center B cells in human tonsil. Applying SIMVI to multiome melanoma data reveals potential tumor epigenetic reprogramming states. On our newly-collected cohort-level CosMx melanoma data, SIMVI uncovers space-and-outcome-dependent macrophage states and cellular communication machinery in tumor microenvironments.

DeltaC and DeltaD ligands play different roles in the segmentation clock dynamics

The vertebrate segmentation clock drives periodic somite segmentation during embryonic development. Her1 and Her7 clock proteins generate oscillatory expression of their own genes as well as that of deltaC in zebrafish. In turn, DeltaC and DeltaD ligands activate Notch signaling, which then activates transcription of clock genes in neighboring cells. While DeltaC and DeltaD proteins form homo- and heterodimers, only DeltaC-containing oscillatory dimers were expected to be functional. To investigate the contributions of DeltaC and DeltaD proteins on the transcription of her1 and her7 segmentation clock genes, we counted their transcripts by performing single molecule fluorescent in situ hybridization imaging in different genetic backgrounds of zebrafish embryos. Surprisingly, we found that DeltaD homodimers are also functional. We further found that Notch signaling promotes transcription of both deltaC and deltaD genes, thereby creating a previously unnoticed positive feedback loop. Our computational model highlighted the intriguing differential roles of DeltaC and DeltaD dimers on the clock synchronization and transcript numbers, respectively. We anticipate that a mechanistic understanding of the Notch signaling pathway will not only shed light on the mechanism driving robust somite segmentation but also inspire similar quantitative studies in other tissues and organs.

Rapidly evolved genomic regions shape individual language abilities in present-day humans

1Minor genetic changes have produced profound differences in cognitive abilities between humans and our closest relatives, particularly in language. Despite decades of research, ranging from single-gene studies to broader evolutionary analyses[1, 2, 3, 4, 5], key questions about the genomic foundations of human language have persisted, including which sequences are involved, how they evolved, and whether similar changes occur in other vocal learning species. Here we provide the first evidence directly linking rapidly evolved genomic regions to language abilities in contemporary humans. Through extensive analysis of 65 million years of evolutionary events in over 30,000 individuals, we demonstrate that Human Ancestor Quickly Evolved Regions (HAQERs)[5] - sequences that rapidly accumulated mutations after the human-chimpanzee split - specifically influence language but not general cognition. These regions evolved to shape language development by altering binding of Forkhead domain transcription factors, including FOXP2. Strikingly, language-associated HAQER variants show higher prevalence in Neanderthals than modern humans, have been stable throughout recent human history, and show evidence of convergent evolution across other mammalian vocal learners. An unexpected pattern of balancing selection acting on these apparently beneficial alleles is explained by their pleiotropic effects on prenatal brain development contributing to birth complications, reflecting an evolutionary trade-off between language capability and reproductive fitness. By developing the Evolution Stratified-Polygenic Score analysis, we show that language capabilities likely emerged before the human-Neanderthal split - far earlier than previously thought[3, 6, 7]. Our findings establish the first direct link between ancient genomic divergence and present-day variation in language abilities, while revealing how evolutionary constraints continue to shape human cognitive development.

Distinct gene regulatory dynamics drive skeletogenic cell fate convergence during vertebrate embryogenesis

Cell type repertoires have expanded extensively in metazoan animals, with some clade-specific cells being crucial to evolutionary success. A prime example are the skeletogenic cells of vertebrates. Depending on anatomical location, these cells originate from three different precursor lineages, yet they converge developmentally towards similar cellular phenotypes. Furthermore, their 'skeletogenic competency' arose at distinct evolutionary timepoints, thus questioning to what extent different skeletal body parts rely on truly homologous cell types. Here, we investigate how lineage-specific molecular properties are integrated at the gene regulatory level, to allow for skeletogenic cell fate convergence. Using single-cell functional genomics, we find that distinct transcription factor profiles are inherited from the three precursor states and incorporated at lineage-specific enhancer elements. This lineage-specific regulatory logic suggests that these regionalized skeletogenic cells are distinct cell types, rendering them amenable to individualized selection, to define adaptive morphologies and biomaterial properties in different parts of the vertebrate skeleton.

DNA methylation dynamics in the small intestine of egg-selected laying hens along egg production stages

Decades of artificial selection have markedly enhanced egg production efficiency, yet the epigenetic underpinnings, notably DNA methylation dynamics in the gut, remain largely unexplored. Here, we investigate how breeds and developmental stages influence DNA methylation profiles in laying hens, and their potential relationship to laying performance and gut health. We compared two highly selected laying hen strains, Lohmann Brown-Classic (LB) and Lohmann Selected Leghorn-Classic (LSL), which exhibited similar egg production but divergent physiological, metabolic, and immunological characteristics. Our sampling encompassed key developmental stages: the pullet stage (10 and 16 wk old), peak production (24 and 30 wk old), and later stage (60 wk old) (n = 99; 10 per group), allowing us to elucidate the temporal dynamics of epigenetic regulation. Our findings highlight a crucial window of epigenetic modulation during the prelaying period, characterized by stage-specific methylation alterations and the involvement of predicted transcription factor motifs within methylated regions. This observation was consistent with the expression patterns of DNA methyltransferases (DNMTs), including DNMT1, DNMT3A, and DNMT3B. In addition, a higher methylation level was observed in specific loci or regions in the LSL compared with the LB strain. Notably, we uncover strain-specific differences in methylation levels, particularly pronounced in genomic regions associated with intestinal integrity, inflammation, and energy homeostasis. Our research contributes to the multidisciplinary framework of epigenetics and egg-laying performance, offering valuable implications for poultry production and welfare.NEW & NOTEWORTHY Our study reveals key methylation changes in the jejunum mucosa of laying hens across developmental stages and between strains, with implications for gut health, immune function, and egg production. These findings highlight a crucial role of epigenetic regulation in optimizing performance.

The endocannabinoid anandamide mediates anti-inflammatory effects through activation of NR4A nuclear receptors

BACKGROUND AND PURPOSE

Endocannabinoids are lipid mediators, which elicit complex biological effects that extend beyond the central nervous system. Tissue concentrations of endocannabinoids increase in atherosclerosis, and for the endocannabinoid N-arachidonoyl-ethanolamine (anandamide, AEA), this has been linked to an anti-inflammatory function. In this study, we set out to determine the anti-inflammatory mechanism of action of AEA, specifically focusing on vascular smooth muscle cells.

EXPERIMENTAL APPROACH

RNA-sequencing, RT-qPCR, LC-MS/MS, NanoBit, ChIP, microscale thermophoresis, NMR structural footprinting, Gal4 reporter gene assays and loss of function approaches in cell and ex vivo organ culture were used.

KEY RESULTS

AEA pretreatment attenuated the cytokine-mediated induction of inflammatory gene expression such as CCL2. This effect was also observed in preparations obtained from cannabinoid receptor knockout mice and after pertussis toxin treatment. The anti-inflammatory effect of AEA required preincubation, suggesting an effect through gene induction. AEA increased the expression of the nuclear receptors NR4A1 and NR4A2. Knockdown and knockout of these receptors blocked the AEA-mediated anti-inflammatory effect in cell culture and aortic organ culture, respectively. Conversely, NR4A agonists (CsnB, C-DIM12) attenuated inflammatory gene expression. AEA binds to NR4A, and mutations in NR4A attenuated this effect. The interaction of AEA with NR4A caused recruitment of the nuclear corepressor NCoR1 to the CCL2 promoter, resulting in gene suppression.

CONCLUSION AND IMPLICATIONS

By binding to NR4A, AEA elicits an anti-inflammatory response in vascular smooth muscle cells. NR4A-binding by AEA analogues may represent novel anti-inflammatory agents.

Peony Seed Oil Inhibited Neuroinflammation by PPAR/RXR Signaling Pathway in D-Gal Induced Mice

Essential fatty acids could regulate inflammation, especially n-3 PUFA (n-3 polyunsaturated fatty acids), which are considered to have a protective effect to inhibit neuroinflammation. Peony seed oil is one of the most abundant n-3 PUFAs in oils. but the mechanism of peony seed oil affecting inflammation in mice brains is still lacking convincing evidence. Sixty male C57BL/6J mice were randomly allocated into four groups: D-gal (D-galactose) induced model group, FO (D-gal + fish oil), PSO (D-gal + peony seed oil). After 10 weeks, the fatty acid composition in liver and brain tissues and potentially related genes were examined. Docosahexaenoic acid (DHA) was significantly higher, while arachidonic acid (AA) was significantly lower in both in the PSO and FO groups than that in the model group in the brain and liver. In the PSO and FO groups, the relative mRNA levels of Fads1/2, Elovl2, and Acaa1a were significantly up-regulated, but Acox1 and Acox3 were significantly down-regulated compared to the model group. In the PSO and FO groups, the relative protein levels of PPARG, RXRA, and IL-10 were significantly up-regulated, and the expressions of AGERs, TNF-α, PLA2, and PGF2α were significantly down-regulated compared to the model group. The phosphorylation-tau of total tau protein ratio was significantly lower in the PSO and FO groups than in the model group. Peony seed oil, rich in n-3 PUFA, inhibited neuroinflammation and rescued the disruption of alternative splicing of the Mapt gene by activating the PPAR/RXR signaling pathway and promoting n-3/n-6 biosynthesis.

A distal convoluted tubule-specific isoform of murine SLC41A3 extrudes magnesium

BACKGROUND

The distal convoluted tubule (DCT) plays an indispensable role in magnesium (Mg2+) reabsorption in the kidney. Yet, the extrusion mechanism of Mg2+ has not been identified. The solute carrier 41A3 (SLC41A3) has been suggested to be involved in Mg2+ extrusion, but this has never been conclusively demonstrated.

METHODS

Using available RNA-sequencing data and real-time quantitative PCR, expression of two alternative Slc41a3 transcripts, encoding isoform (Iso) 1 or 2, were assessed in kidney and isolated DCT tubules. HEK293 or HAP1 cells were transfected with plasmids expressing either of the isoforms, followed by 25Mg2+ transport studies. Identification of cis-regulatory elements (CRE) was achieved by combining data from publicly available ATAC sequencing data and luciferase assays.

RESULTS

Gene expression studies revealed a distinct transcript of Slc41a3 in the DCT with an alternative promoter, leading to a protein with a unique N-terminus; SLC41A3-Iso 2. HEK293 cells overexpressing SLC41A3-Iso 2, but not -Iso 1, exhibited 2.7-fold and 1.6-fold higher 25Mg2+ uptake and extrusion, compared to mock, respectively. The transport was independent of Na+, of the Mg2+ channel TRPM7 or of transporters CNNM3 and -4. We identified a CRE accessible in the DCT, ±2.8kb upstream of the transcript. The presence of the CRE increased the Slc41a3-Iso 2 promoter activity 3.8-fold following luciferase assays, indicating the CRE contains an enhancer function.

CONCLUSION

In conclusion, we identified two alternative transcripts of Slc41a3 in mouse. Slc41a3-Iso 2 is enriched within the DCT using specific gene regulatory elements. We speculate that specifically in the DCT, SLC41A3-Iso 2 orchestrates Mg2+ extrusion.

Identification of glycolysis-related gene signatures for prognosis and therapeutic targeting in idiopathic pulmonary fibrosis

Background

Glycolysis plays a crucial role in fibrosis, but the specific genes involved in glycolysis in idiopathic pulmonary fibrosis (IPF) are not well understood.

Methods

Three IPF gene expression datasets were obtained from the Gene Expression Omnibus (GEO), while glycolysis-related genes were retrieved from the Molecular Signatures Database (MsigDB). Differentially expressed glycolysis-related genes (DEGRGs) were identified using the "limma" R package. Diagnostic glycolysis-related genes (GRGs) were selected through least absolute shrinkage and selection operator (LASSO) regression regression and support vector machine-recursive feature elimination (SVM-RFE). A prognostic signature was developed using LASSO regression, and time-dependent receiver operating characteristic (ROC) curves were generated to evaluate predictive performance. Single-cell RNA sequencing (scRNA-seq) data were analyzed to examine GRG expression across various cell types. Immune infiltration analysis, Gene Set Enrichment Analysis (GSEA), and Gene Set Variation Analysis (GSVA) were performed to elucidate potential molecular mechanisms. A bleomycin (BLM)-induced pulmonary fibrosis mouse model was used for experimental validation via reverse transcription-quantitative polymerase chain reaction (RT-qPCR).

Results

14 GRGs (VCAN, MERTK, FBP2, TPBG, SDC1, AURKA, ARTN, PGP, PLOD2, PKLR, PFKM, DEPDC1, AGRN, CXCR4) were identified as diagnostic markers for IPF, with seven (ARTN, AURKA, DEPDC1, FBP2, MERTK, PFKM, SDC1) forming a prognostic model demonstrating predictive power (AUC: 0.831-0.793). scRNA-seq revealed cell-type-specific GRG expression, particularly in macrophages and fibroblasts. Immune infiltration analysis linked GRGs to imbalanced immune responses. Experimental validation in a bleomycin-induced fibrosis model confirmed the upregulation of GRGs (such as AURKA, CXCR4). Drug prediction identified inhibitors (such as Tozasertib for AURKA, Plerixafor for CXCR4) as potential therapeutic agents.

Conclusion

This study identifies GRGs as potential prognostic biomarkers for IPF and highlights their role in modulating immune responses within the fibrotic lung microenvironment. Notably, AURKA, MERTK, and CXCR4 were associated with pathways linked to fibrosis progression and represent potential therapeutic targets. Our findings provide insights into metabolic reprogramming in IPF and suggest that targeting glycolysis-related pathways may offer novel pharmacological strategies for antifibrotic therapy.

The repression of the lipolytic inhibitor G0s2 enhancers affects lipid metabolism

The G0/G1 switch gene 2 (G0s2) is a selective inhibitor of adipose triglyceride lipase (ATGL) which is the rate-limiting enzyme for triglycerides (TGs) hydrolysis in adipocytes, and regulates the mobilization of TGs in adipocytes and hepatocytes. The expression and functional disorders of G0S2 are associated with various metabolic diseases and related pathological states, such as obesity and metabolic syndrome and non-alcoholic fatty liver disease (NAFLD). However, the extent to which the transcriptional regulatory mechanisms mediated by the interaction between the G0s2 gene promoter and enhancer regions are involved remains unknown. Here, through the analysis of epigenomic data (H3K27ac, H3K4me1, and DHS-seq) and luciferase reporter assays, we identified three active enhancers of G0s2 in 3 T3-L1 adipocytes. Subsequently, using the dCas9-KRAB system for epigenetic inhibition of G0S2-En2, -En4, and -En5 revealed the functional role of these enhancers in regulating G0s2 expression and lipid droplet biosynthesis. Additionally, transcriptome analyses revealed that inhibition of G0S2-En5 downregulated pathways associated with lipid metabolism and lipid biosynthesis. Furthermore, overexpression of transcription factors (TFs) and motif mutation experiments identified that PPARG and RXRA regulate the activity of G0S2-En5. Taken together, we identified functional enhancers regulating G0s2 expression and elucidated the important role of the G0S2-En5 in lipid droplet biogenesis.

Identifying Therapeutic Targets and Potential Drugs for Diabetic Retinopathy: Focus on Oxidative Stress and Immune Infiltration

Background

Diabetic retinopathy (DR), a microvascular disorder linked to diabetes, is on the rise globally. Oxidative stress and immune cell infiltration are linked to illness initiation and progression, according to recent study. This study investigated biomarkers connected to DR and oxidative stress and their connection with immune cell infiltration using bioinformatics analysis and found possible therapeutic medications.

Methods

The Gene Expression Omnibus (GEO) database was used to obtain the gene expression data for DR. Differentially expressed genes (DEGs) and oxidative stress (OS)-related genes were intersected. The Enrichment analyses concentrate on OS-related differentially expressed genes (DEOSGs). Analysis of protein-protein interaction (PPI) networks and machine learning algorithms were used to identify hub genes. Single-gene Gene Set Enrichment Analysis (GSEA) identified biological functions, while nomograms and ROC curves assessed diagnostic potential. Immune infiltration analysis and regulatory networks were constructed. Drug prediction was validated through molecular docking, and hub gene expression was confirmed in dataset and animal models.

Results

Compared to the control group, 91 DEOSGs were found. Enrichment analyses showed that these DEOSGs were largely connected to oxidative stress response, PI3K/Akt pathway, inflammatory pathways, and immunological activation. Four hub genes were found via PPI networks and machine learning. These hub genes were diagnostically promising according to nomogram and ROC analysis. Analysis of immune cell infiltration highlighted the role of immune cells. Gene regulatory networks for transcription factor (TF) and miRNA were created. Using structural data, molecular docking shows potential drugs and hub genes have high binding affinity. Dataset analysis, Real-Time Quantitative Polymerase Chain Reaction (RT-qPCR) and Western Blot (WB) confirmed the CCL4 expression difference between DR and controls.

Conclusion

CCL4 was identified as potential oxidative stress-related biomarker in DR, providing new insights for DR diagnosis and treatment.

The transcription factor combination MEF2 and KLF7 promotes axonal sprouting in the injured spinal cord with functional improvement and regeneration-associated gene expression

BACKGROUND

Axon regeneration after injury to the central nervous system (CNS) is limited by an inhibitory environment but also because injured neurons fail to initiate expression of regeneration associated genes (RAGs). The potential of strong RAG expression to promote regeneration in the CNS is exemplified by the conditioning lesion model, whereby peripheral nerve injury promotes regeneration of centrally projecting branches of the injured neurons. RAG expression could potentially be induced by delivery of the right set of transcription factors (TFs). We here aim to identify TF combinations that activate this program.

METHODS

We first analysed binding site motifs in promoters of the RAG program to identify nine candidate growth-promoting TFs. These were systematically screened in vitro to identify combinations that had potent neurite-growth promoting activity. Next, adeno-associated viral vectors were used to express these TF combinations in vivo in L4/L5 dorsal root ganglia to test whether they would promote regeneration in a spinal cord injury model (dorsal column lesion) in female rats. To determine whether they could activate the RAG program we carried out gene expression profiling on laser-dissected dorsal root ganglion neurons specifically expressing these TF combinations, and of DRG neurons that had been axotomized.

RESULTS

Promoter analysis identified ATF3, Jun, CEBPD, KLF7, MEF2, SMAD1, SOX11, STAT3 and SRF as candidate RAG-activating TFs. In vitro screening identified two TF combinations, KLF7/MEF2 and ATF3/KLF7/MEF2, that had potent neurite-growth promoting activity, the latter being the more powerful. In vivo, KLF7/MEF2, but not ATF3/KLF7/MEF2 or KLF7 or MEF2 alone, promoted axonal sprouting into the dorsal column lesion site and led to improved functional recovery. Gene expression profiling revealed that unexpectedly, the MEF2-VP16 construct used had little transcriptional activity in vivo, suggesting additional steps may be required to achieve full MEF2 activity. All combinations except MEF2 alone induced RAG expression mirroring that induced by axotomy to significant extents, while ATF3/KLF7/MEF2, KLF7 and ATF3, but not KLF7/MEF2 also induced apoptosis-related genes which may hinder regeneration.

CONCLUSIONS

The TF combination KLF7/MEF2 partially mimics the conditioning lesion effect, inducing axonal sprouting into a dorsal column lesion and driving significant RAG expression, and also promotes functional improvement.

Multi-locus CRISPRi targeting with a single truncated guide RNA

A critical goal in functional genomics is evaluating which non-coding elements contribute to gene expression, cellular function, and disease. Functional characterization remains a challenge due to the abundance and complexity of candidate elements. Here, we develop a CRISPRi-based approach for multi-locus screening of putative transcription factor binding sites with a single truncated guide. A truncated guide with hundreds of sequence match sites can reliably disrupt enhancer activity, which expands the targeting scope of CRISPRi while maintaining repressive efficacy. We screen over 13,000 possible CTCF binding sites with 24 guides at 10 nucleotides in spacer length. These truncated guides direct CRISPRi-mediated deposition of repressive H3K9me3 marks and disrupt transcription factor binding at most sequence match target sites. This approach can be a valuable screening step for testing transcription factor binding motifs or other repeated genomic sequences and is easily implemented with existing tools.

EDF1 accelerates ganglioside GD3 accumulation to boost CD52-mediated CD8+ T cell dysfunction in neuroblastoma

BACKGROUND

Heterogeneous clinical features and prognosis in neuroblastoma (NB) children are frequently dominated by immune elements. Dysfunction and apoptosis in immune cells result from the exposure to continuous tumor-related antigen stimulation and coinhibitory signals. To date, key factors pointing to the restriction of NB-specific CD8+ T cells remain elusive.

METHODS

We performed bulk-RNA sequencing and lipidomic analyses of children with mediastinal NB. Bioinformatics analysis and biological validation were applied to uncover the underlying mechanism.

RESULTS

Three subtypes were identified using nonnegative matrix factorization (NMF), among which we highlighted an apoptotic status of infiltrated CD8+ T cells, along with the highest CD52 and EDF1 expression in Cluster3 (C3) subtypes. It was verified that high EDF1 expression in NB cells led to Lactosylceramide (LacCer) accumulation, as well as downstream ganglioside-GD3, which subsequently increased the expression of CD52 and immune checkpoint genes, chemotaxis, and apoptosis-related events in activated CD8+T cells. Mechanistically, EDF1 was recruited as a coactivator to form the NF-κB/RelA/EDF1 complex, which further prevented the promoter region methylation of ST8SIA1, to elevate its transcription.

CONCLUSION

These findings characterize abundant GD3 in NB cells, which regulated by the EDF1/RelA/ST8SIA1 axis, is responsible for CD8+ T cell dysfunction. Inhibition of EDF1 may reduce suppressive factors and prevent immune escape of NB cells. Modulating NB-associated GD3 levels through metabolic intervention is beneficial for tuning the depth and duration of responses to current NB therapies. The integration of transcriptomic and lipidomic data offers a more comprehensive understanding of the interaction between LacCer metabolites and the immune status in NB.

Spatial integration of multi-omics single-cell data with SIMO

Technical limitations in spatial and single-cell omics sequencing pose challenges for capturing and describing multimodal information at the spatial scale. To address this, we develop SIMO, a computational method designed for the Spatial Integration of Multi-Omics datasets through probabilistic alignment. Unlike previous tools, SIMO not only integrates spatial transcriptomics with single-cell RNA-seq but expands beyond, enabling integration across multiple single-cell modalities, such as chromatin accessibility and DNA methylation, which have not been co-profiled spatially before. We benchmark SIMO on simulated datasets, demonstrating its high accuracy and robustness. Further application on biological datasets reveals SIMO's ability to detect topological patterns of cells and their regulatory modes across multiple omics layers. Through comprehensive analysis of real-world data, SIMO uncovers multimodal spatial heterogeneity, offering deeper insights into the spatial organization and regulation of biological molecules. These findings position SIMO as a powerful tool for advancing spatial biology by revealing previously inaccessible multimodal insights.

A rare PRIMER cell state in plant immunity

Plants lack specialized and mobile immune cells. Consequently, any cell type that encounters pathogens must mount immune responses and communicate with surrounding cells for successful defence. However, the diversity, spatial organization and function of cellular immune states in pathogen-infected plants are poorly understood1. Here we infect Arabidopsis thaliana leaves with bacterial pathogens that trigger or supress immune responses and integrate time-resolved single-cell transcriptomic, epigenomic and spatial transcriptomic data to identify cell states. We describe cell-state-specific gene-regulatory logic that involves transcription factors, putative cis-regulatory elements and target genes associated with disease and immunity. We show that a rare cell population emerges at the nexus of immune-active hotspots, which we designate as primary immune responder (PRIMER) cells. PRIMER cells have non-canonical immune signatures, exemplified by the expression and genome accessibility of a previously uncharacterized transcription factor, GT-3A, which contributes to plant immunity against bacterial pathogens. PRIMER cells are surrounded by another cell state (bystander) that activates genes for long-distance cell-to-cell immune signalling. Together, our findings suggest that interactions between these cell states propagate immune responses across the leaf. Our molecularly defined single-cell spatiotemporal atlas provides functional and regulatory insights into immune cell states in plants.

Oncofetal reprogramming drives phenotypic plasticity in WNT-dependent colorectal cancer

Targeting cancer stem cells (CSCs) is crucial for effective cancer treatment, yet resistance mechanisms to LGR5+ CSC depletion in WNT-driven colorectal cancer (CRC) remain elusive. In the present study, we revealed that mutant intestinal stem cells (SCs) depart from their canonical identity, traversing a dynamic phenotypic spectrum. This enhanced plasticity is initiated by oncofetal (OnF) reprogramming, driven by YAP and AP-1, with subsequent AP-1 hyperactivation promoting lineage infidelity. The retinoid X receptor serves as a gatekeeper of OnF reprogramming and its deregulation after adenomatous polyposis coli (APC) loss of function establishes an OnF 'memory' sustained by YAP and AP-1. Notably, the clinical significance of OnF and LGR5+ states in isolation is constrained by their functional redundancy. Although the canonical LGR5+ state is sensitive to the FOLFIRI regimen, an active OnF program correlates with resistance, supporting its role in driving drug-tolerant states. Targeting this program in combination with the current standard of care is pivotal for achieving effective and durable CRC treatment.

Inhibition of triglyceride metabolism-associated enhancers alters lipid deposition during adipocyte differentiation

Triglyceride (TG) metabolism is a complex and highly coordinated biological process regulated by a series of genes, and its dysregulation can lead to the occurrence of disorders in lipid metabolism. However, the transcriptional regulatory mechanisms of crucial genes in TG metabolism mediated by enhancer-promoter interactions remain elusive. Here, we identified candidate enhancers regulating the Agpat2, Dgat1, Dgat2, Pnpla2, and Lipe genes in 3T3-L1 adipocytes by integrating epigenomic data (H3K27ac, H3K4me1, and DHS-seq) with chromatin three-dimensional interaction data. Luciferase reporter assays revealed that 11 enhancers exhibited fluorescence activity. The repression of enhancers using the dCas9-KRAB system revealed the functional roles of enhancers of Dgat2 and Pnpla2 in regulating their expression and TG metabolism. Furthermore, transcriptome analyses revealed that inhibition of Dgat2-En4 downregulated pathways associated with lipid metabolism, lipid biosynthesis, and adipocyte differentiation. Additionally, overexpression and motif mutation experiments of transcription factor found that two TFs, PPARG and RXRA, regulate the activity of Agpat2-En1, Dgat2-En4, and Pnpla2-En5. Our study identified functional enhancers regulating TG metabolism and elucidated potential regulatory mechanisms of TG deposition from enhancer-promoter interactions, providing insights into understanding lipid deposition.

FSTL1 and TLR4 interact with PEDV structural proteins to promote virus adsorption to host cells

Infection with porcine epidemic diarrhea virus (PEDV) results in enormous economic damage to the global swine industry. PEDV starts its life cycle by binding to the receptors of host cells and adsorbing onto the cellular surfaces. However, it is still unknown how PEDV adsorbs onto the surface of host cells and the mechanism beneath the interplay of host cell transmembrane protein with PEDV proteins. FSTL1, which is a secreted glycoprotein, participates in diverse pathological and physiological processes, including immune modulation and cell proliferation and differentiation. The transmembrane protein, TLR4, serves as a pattern recognition receptor recognizing a broad spectrum of pathogens, which exerts a crucial effect on the host immune system. In this study, we identified that FSTL1 promoted PEDV infection. Further studies demonstrated the interactive relationship between FSTL1 and PEDV structural proteins (N and S2). In addition, we also confirmed that TLR4 interacted with FSTL1 and PEDV N, S1, and S2 proteins on the cell surface. Moreover, FSTL1 promoted the interaction of TLR4 and PEDV and induced viral adsorption to host cells. This study offers explicit evidence that FSTL1 and TLR4 act as mediators for host cell adsorption of PEDV by interacting with PEDV N/S proteins.IMPORTANCEAs a highly infectious porcine epidemic diarrhea virus (PEDV)-induced intestinal condition of swine, porcine epidemic diarrhea (PED) results in a 100% death rate among suckling piglets and poses a serious economic burden to global swine farming. Therefore, it is essential to investigate the mechanism of virus infection, replication, and proliferation. Virus begins its life cycle by binding to the receptor of host cells and adsorbing onto the cellular surfaces. However, it remains unclear how PEDV adsorbs onto the host cell surfaces. This study revealed that host protein FSTL1 interacted with the PEDV N and S2 proteins, while TLR4 interacted with the FSTL1 and PEDV proteins (N, S1, and S2). Moreover, we thoroughly and methodically demonstrated that FSTL1 was engaged in the PEDV internalization and attachment processes by promoting the recognition of PEDV N\S proteins by TLR4 and induced the viral adsorption to host cells.

Thermodynamic principles link in vitro transcription factor affinities to single-molecule chromatin states in cells

The molecular details governing transcription factor (TF) binding and the formation of accessible chromatin are not yet quantitatively understood - including how sequence context modulates affinity, how TFs search DNA, the kinetics of TF occupancy, and how motif grammars coordinate binding. To resolve these questions for a human TF, erythroid Krüppel-like factor (eKLF/KLF1), we quantitatively compare, in high throughput, in vitro TF binding rates and affinities with in vivo single molecule TF and nucleosome occupancies across engineered DNA sequences. We find that 40-fold flanking sequence effects on affinity are consistent with distal flanks tuning TF search parameters and captured by a linear energy model. Motif recognition probability, rather than time in the bound state, drives affinity changes, and in vitro and in nuclei measurements exhibit consistent, minutes-long TF residence times. Finally, pairing in vitro biophysical parameters with thermodynamic models accurately predicts in vivo single-molecule chromatin states for unseen motif grammars.

ROS-regulated SUR1-TRPM4 drives persistent activation of NLRP3 inflammasome in microglia after whole-brain radiation

Delayed radiation-induced brain injury (RIBI) characterized by progressive cognitive decline significantly impacts patient outcomes after radiotherapy. The activation of NLRP3 inflammasome within microglia after brain radiation is involved in the progression of RIBI by mediating inflammatory responses. We have previously shown that sulfonylurea receptor 1-transient receptor potential M4 (SUR1-TRPM4) mediates microglial NLRP3-related inflammation following global brain ischemia. However, the role of SUR1-TRPM4 in RIBI remains unclear. Here, we found that whole-brain radiation induced up-regulation and assembly of SUR1-TRPM4, which further activated the NLRP3 inflammasome in microglia and caused persistent neuroinflammation in mice. Blocking SUR1-TRPM4 by glibenclamide or gene deletion of Trpm4 effectively prevented NLRP3-mediated neuroinflammation and alleviated RIBI. Utilizing the mouse model of RIBI and irradiated BV2 cells, we further demonstrated that irradiation caused mitochondrial damage to microglia, leading to violent release of reactive oxygen species (ROS), which enhanced the transcription of SUR1, TRPM4, and NLRP3 inflammasome-related molecules. Moreover, ROS up-regulated ten-eleven translocation 2 (TET2) to enhance TRPM4 expression by mediating the demethylation of the gene promoter, thereby facilitating the assembly of SUR1-TRPM4 in microglia. In summary, this study deciphers that SUR1-TRPM4 crucially mediates the persistent activation of microglial NLRP3 inflammasome under the action of ROS after whole-brain radiation, offering novel therapeutic strategies for delayed RIBI as well as other NLRP3-related neurological disorders involving excessive ROS production.

Genetic coupling of enhancer activity and connectivity in gene expression control

Gene enhancers often form long-range contacts with promoters, but it remains unclear if the activity of enhancers and their chromosomal contacts are mediated by the same DNA sequences and recruited factors. Here, we study the effects of expression quantitative trait loci (eQTLs) on enhancer activity and promoter contacts in primary monocytes isolated from 34 male individuals. Using eQTL-Capture Hi-C and a Bayesian approach considering both intra- and inter-individual variation, we initially detect 19 eQTLs associated with enhancer-eGene promoter contacts, most of which also associate with enhancer accessibility and activity. Capitalising on these shared effects, we devise a multi-modality Bayesian strategy, identifying 629 "trimodal QTLs" jointly associated with enhancer accessibility, eGene promoter contact, and gene expression. Causal mediation analysis and CRISPR interference reveal causal relationships between these three modalities. Many detected QTLs overlap disease susceptibility loci and influence the predicted binding of myeloid transcription factors, including SPI1, GABPB and STAT3. Additionally, a variant associated with PCK2 promoter contact directly disrupts a CTCF binding motif and impacts promoter insulation from downstream enhancers. Jointly, our findings suggest an inherent genetic coupling of enhancer activity and connectivity in gene expression control relevant to human disease and highlight the regulatory role of genetically determined chromatin boundaries.

Epigenetic mechanisms regulating CD8+ T cell senescence in aging humans

Aging leads to the decline of immunity, rendering the elderly susceptible to infection and disease. In the CD8+ T cell compartment, aging leads to a substantial increase of cells with high levels of senescence-associated ß-galactosidase activity (SA-ßGal) and other senescence characteristics, including a pro-inflammatory transcriptome and impaired proliferative potential. Using senescent cell isolation coupled with multiomic profiling, here we characterized the epigenetic mechanisms regulating CD8+ T cell senescence in a cohort of younger and older donors. High levels of SA-ßGal activity defined changes to global transcriptomes and chromatin accessibility landscapes, with a minor effect of age. Widespread enhancer remodeling was required for the repression of functional CD8+ T cell genes and upregulation of inflammatory and secretory pathway genes. Mechanistically, the senescence program in CD8+ T cells was controlled by chromatin state-specific transcription factor (TF) networks whose composition was largely insensitive to donor age. Pharmacological inhibition of TF network nodes AP1, KLF5, and RUNX2 modulated the transcriptional output, demonstrating the feasibility of TF network perturbation as an approach to modulate CD8+ T cell senescence. Further, CD8+ T cell senescence gene signatures faithfully predicted refractoriness to chimeric antigen receptor (CAR) T-cell therapy in a cohort of diffuse large B cell lymphomas and were highly enriched in the transcriptomes of peripheral CD8+ T cells of individuals with active systemic lupus erythematosus. Collectively, our findings demonstrate the potential of multiomic profiling in identifying key regulators of senescence across cell types and suggest a critical role of senescent CD8+ T cells in disease progression.

Single-nucleus CUT&RUN elucidates the function of intrinsic and genomics-driven epigenetic heterogeneity in head and neck cancer progression

Interrogating regulatory epigenetic alterations during tumor progression at the resolution of single cells has remained an understudied area of research. Here we developed a highly sensitive single-nucleus CUT&RUN (snCUT&RUN) assay to profile histone modifications in isogenic primary, metastatic, and cisplatin-resistant head and neck squamous cell carcinoma (HNSCC) patient-derived tumor cell lines. We find that the epigenome can be involved in diverse modes to contribute toward HNSCC progression. First, we demonstrate that gene expression changes during HNSCC progression can be comodulated by alterations in both copy number and chromatin activity, driving epigenetic rewiring of cell states. Furthermore, intratumor epigenetic heterogeneity (ITeH) may predispose subclonal populations within the primary tumor to adapt to selective pressures and foster the acquisition of malignant characteristics. In conclusion, snCUT&RUN serves as a valuable addition to the existing toolkit of single-cell epigenomic assays and can be used to dissect the functionality of the epigenome during cancer progression.