STAR: ultrafast universal RNA-seq aligner

Development of a Caco-2-based intestinal mucosal model to study intestinal barrier properties and bacteria-mucus interactions

The intestinal mucosal barrier is a dynamic system that allows nutrient uptake, stimulates healthy microbe-host interactions, and prevents invasion by pathogens. The mucosa consists of epithelial cells connected by cellular junctions that regulate the passage of nutrients covered by a mucus layer that plays an important role in host-microbiome interactions. Mimicking the intestinal mucosa for in vitro assays, particularly the generation of a mucus layer, has proven to be challenging. The intestinal cell-line Caco-2 is widely used in academic and industrial laboratories due to its capacity to polarize, form an apical brush border, and reproducibly grow into confluent cell layers in different culture systems. However, under normal culture conditions, Caco-2 cultures lack a mucus layer. Here, we demonstrate for the first time that Caco-2 cultures can form a robust mucus layer when cultured under air-liquid interface (ALI) conditions on Transwell inserts with addition of vasointestinal peptide (VIP) in the basolateral compartment. We demonstrate that unique gene clusters are regulated in response to ALI and VIP single stimuli, but the ALI-VIP combination treatment resulted in a significant upregulation of multiple mucin genes and proteins, including secreted MUC2 and transmembrane mucins MUC13 and MUC17. Expression of tight junction proteins was significantly altered in the ALI-VIP condition, leading to increased permeability to small molecules. Commensal Lactiplantibacillus plantarum bacteria closely associated with the Caco-2 mucus layer and differentially colonized the surface of the ALI cultures. Pathogenic Salmonella enterica were capable of invading beyond the mucus layer and brush border. In conclusion, Caco-2 ALI-VIP cultures provide an accessible and straightforward way to culture an in vitro intestinal mucosal model with improved biomimetic features. This novel in vitro intestinal model can facilitate studies into mucus and epithelial barrier functions and in-depth molecular characterization of pathogenic and commensal microbe-mucus interactions.

Single and multi-omic characterization of a porcine model of ethanol-induced hepatic fibrosis

Cirrhosis is a form of end-stage liver disease characterized by extensive hepatic fibrosis and loss of liver parenchyma. It is most commonly the result of long-term alcohol abuse in the United States. Large animal models of cirrhosis, as well as of one of its common long-term sequelae, HCC, are needed to study novel and emerging therapeutic interventions. In the present study, liver fibrosis was induced in the Oncopig cancer model, a large animal HCC model, via intrahepatic, intra-arterial ethanol infusion. Liver sections from five fibrosis induced and five age-matched controls were harvested for RNA-seq (mRNA and lncRNA), small RNA-seq (miRNA), and reduced representation bisulfite sequencing (RRBS; DNA methylation). Single- and multi-omic analysis was performed to investigate the transcriptomic and epigenomic mechanisms associated with fibrosis deposition in this model. A total of 3,439 genes, 70 miRNAs, 452 lncRNAs, and 7,715 methylation regions were found to be differentially regulated through individual single-omic analysis. Pathway analysis indicated differentially expressed genes were associated with collagen synthesis and turnover, hepatic metabolic functions such as ethanol and lipid metabolism, and proliferative and anti-proliferative pathways including PI3K and BAX/BCL signaling pathways. Multi-omic latent variable analysis demonstrated significant concordance with the single-omic analysis. lncRNA's associated with UHRF1BP1L and S1PR1 genes were found to reliably discriminate the two arms of the study. These genes were previously implicated in human cancer development and vasculogenesis, respectively. These findings support the validity and translatability of this model as a useful preclinical tool in the study of alcoholic liver disease and its treatment.

E. coli genetically modified for purine nucleobase release promotes butyrate generation and colonic wound healing during DSS insult

The gut microbiota transforms energy stored as undigestible carbohydrates into a remarkable number of metabolites that fuel intestinal bacterial communities and the host tissue. Colonic epithelial cells at the microbiota-host interface depend upon such microbiota-derived metabolites (MDMs) to satisfy their energy requisite. Microbial dysbiosis eliciting MDM loss contributes to barrier dysfunction and mucosal disease. Recent work has identified a role for microbiota-sourced purines (MSPs), notably hypoxanthine, as an MDM salvaged by the colonic epithelium for nucleotide biogenesis and energy balance. Here, we investigated the role of MSPs in mice during disease-modeled colonic energetic stress using a strain of E. coli genetically modified for enhanced purine nucleobase release (E. coli Mutant). E. coli Mutant colonization protected against DSS-induced tissue damage and permeability while promoting proliferation for wound healing. Metabolite and metagenomic analyses suggested a colonic butyrate-purine nucleobase metabolic axis, wherein the E. coli Mutant provided purine substrate for Clostridia butyrate production and host purine salvage, altogether supplying the host substrate for efficient nucleotide biogenesis and energy balance.

Novel immunodominant neoepitope in a KPC mouse model of pancreatic cancer allowing identification of tumor-specific T cells

The 4662 KPC model is one of the most widely used mouse models of pancreatic cancer. It represents an excluded immune phenotype and closely recapitulates the pathophysiology of pancreatic cancer in humans. We set out to identify the endogenous neoepitopes present in 4662 cells. By combining whole-exome and RNA-sequencing and a bioinformatic neoantigen prediction pipeline, we have identified 15 potential candidate neoantigen epitopes. Ten more highly expressed were selected for validation in an in vivo vaccination study with 4662-tumor bearing mice. The Mrps35-derived neoantigen was found to be immunogenic as we have identified endogenous T-cells responding to this neoepitope, and the response was significantly increased upon vaccination with a synthetic peptide and upon PD1-IL2v therapy. Dextramers based on this peptide were validated and can be used to monitor endogenous tumor-specific CD8+ T-cells in response to immunotherapy. This will support the development of novel therapies for this highly unmet medical need indication.

RNA Pol-II transcripts in nucleolar associated domains of cancer cell nucleoli

We performed a comparative study of the non-ribosomal gene content of nucleoli from seven cancer cell lines, using identical methods of purification and analysis. We identified unique chromosomal domains associated with the nucleolus (NADs) and genes within these domains (NAGs). Four cell lines have relatively few NAGs, which appears mostly transcriptionally inactive, consistent with literature. The remaining three lines formed a separate group with nucleoli with unique features and NADS. They constitute larger number of common NAGs, marked by ATAC-seq and having accessible promoters, with histone markers for transcriptional activity and detectable RNA Pol II bound at their promoters. The transcripts of these genes are almost entirely exported from the nucleolus. These results indicate that RNA Pol II dependent transcription in NADs can vary widely in different cell types, presumably dependent on the cell's developmental stage. Nucleolus-associated genes are likely to be distinguished marks reflecting the cell's metabolism.

The immune checkpoint LAG-3 is expressed by melanoma cells and correlates with clinical progression of the melanoma

Immune checkpoint blockers have substantially improved prognosis of melanoma patients, nevertheless, resistance remains a significant problem. Here, intrinsic and extrinsic factors in the tumor microenvironment are discussed, including the expression of alternative immune checkpoints such as lymphocyte activation gene 3 (LAG-3) and T-cell immunoglobulin and mucin domain-containing protein 3 (TIM-3). While most studies focus on immune cell expression of these proteins, we investigated their melanoma cell intrinsic expression by immunohistochemistry in melanoma metastases of 60 patients treated with anti-programmed cell death protein 1 (PD-1) and/or anti-cytotoxic T-lymphocyte-associated protein 4 (CTLA-4) therapy, and correlated it with the expression of potential ligands, RNA sequencing data and clinical outcome. LAG-3 and TIM-3 were commonly expressed in melanoma cells. In the stage IV cohort, expression of LAG-3 was associated with M1 stage (p < 0.001) and previous exposure to immune checkpoint inhibitors (p = 0.029). Moreover, in the anti-PD-1 monotherapy treatment group patients with high LAG-3 expression by tumor cells tended to have a shorter progression-free survival (p = 0.088), whereas high expression of TIM-3 was associated with a significantly longer overall survival (p = 0.007). In conclusion, we provide a systematic analysis of melanoma cell intrinsic LAG-3 and TIM-3 expression, highlighting potential implications of their expression on patient survival.

Human macrophage response to the emerging enteric pathogen Aeromonas veronii: Inflammation, apoptosis, and downregulation of histones

This study investigated the pathogenic mechanisms of Aeromonas veronii in macrophages. THP-1 derived macrophages were used as a human macrophage model and were treated with A. veronii strain AS1 isolated from intestinal biopsies of an IBD patient, or Escherichia coli strain K-12. RNA was extracted and subjected to RNA sequencing and comparative transcriptomic analyses. Protein levels of IL-8, IL-1β, IL-18, and TNFα were measured using ELISA, and apoptosis was assessed using caspase 3/7 assays. Both A. veronii AS1 and E. coli K-12 significantly upregulated the expression of many genes involving inflammation. At the protein level, A. veronii AS1 induced significantly higher levels of IL-8, TNFα, mature IL-18 and IL-1β than E. coli K-12, and led to greater elevation of caspase 3/7 activities. Both A. veronii AS1 and E. coli K-12 upregulated the expression of CASP5, but not other caspase genes. A. veronii AS1 significantly downregulated the expression of 20 genes encoding histone proteins that E. coli K-12 did not. The more profound pathogenic effects of A. veronii in inducing inflammation and apoptosis in macrophages than E. coli K-12 are consistent with its role as a human enteric pathogen. The upregulated expression of CASP5 and increased release of IL-1β and IL-18 support the role of CASP5 in activation of non-canonical inflammasome. The downregulation of histone genes by A. veronii suggests a unique impact on host cell gene expression, which may represent a novel virulence strategy. These findings advance the understanding of pathogenic mechanisms of the emerging human enteric pathogen A. veronii.

Identification of key factors causing ketosis in dairy cows with low feed intake

Ketosis is a common metabolic disease in high-yield dairy cows. Key genes affecting ketosis need to be further explored by new methods. The gene expression profiling and clinical data of GSE92398, GSE104079, and GSE4304 were obtained from the gene expression omnibus (GEO) database. Core modules and genes associated with RFI (residual feed intake) and ADF (alternate day fasting) were identified by weighted gene co-expression network analysis (WGCNA). Subsequently, the key genes related to ketosis and RFI were determined by protein-protein interaction (PPI) networks, ROC curves, functional enrichment, and differential expression analysis, respectively. The results showed that the genes of ACACA, ELOVL6 and XPO7 could be used as regulators of ketosis induced by low feed intake in dairy cows. At the same time, three genes (HRFI, STAT3 and IFNAR1) were retained as additional RFI biomarkers that could be considered. We identified three key factors as candidate genes and biomarkers of ketosis and RFI, respectively. These factors may provide a theoretical basis for targeted therapy of ketosis in dairy cows.

Cardiometabolic risk factor burden associates with an immature platelet profile

Cardiometabolic risk factors, obesity, diabetes and hyperlipidemia contribute to cardiovascular disease (CVD). While platelets are involved in CVD pathogenesis, the relationship between risk factor burden on platelet indices and the platelet transcriptome remains uncertain. Blood was collected from CVD-free adults, measuring platelet count, mean platelet volume (MPV), immature platelet fraction (IPF), and absolute immature platelet fraction (AIPF) by hemogram. Platelets were isolated and analyzed via RNA sequencing. Participants were stratified by number of cardiometabolic risk factors (diabetes, obesity, hyperlipidemia). We calculated median (IQR) values of platelet indices and p-for-trend via linear regression across risk factor burden. To evaluate the association between risk factor burden and platelet transcripts, we performed multivariable linear regression adjusting for age, sex, and race/ethnicity. Among 141 participants, (50.5 ± 14.8 years, 42% male, 26% Black) risk factor burden was associated with increasing platelet size, IPF, and AIPF but not platelet count. Platelet RNA sequencing identified 100 differentially expressed transcripts (p < .01; 66 upregulated, 34 downregulated). Gene ontology enrichment analysis demonstrated upregulated pathways of secondary metabolic processes (NES = 1.96, p < .01), and hematopoietic stem cell proliferation (NES = 1.95, p < .01). Greater cardiometabolic risk factor burden is associated with increased platelet size and immaturity and suggesting novel platelet-mediated mechanisms linking risk factor burden with CVD.

Integrative metagenomics and metabolomics reveal age-associated gut microbiota and metabolite alterations in a hamster model of COVID-19

Aging is a key contributor of morbidity and mortality during acute viral pneumonia. The potential role of age-associated dysbiosis on disease outcomes is still elusive. In the current study, we used high-resolution shotgun metagenomics and targeted metabolomics to characterize SARS-CoV-2-associated changes in the gut microbiota from young (2-month-old) and aged (22-month-old) hamsters, a valuable model of COVID-19. We show that age-related dysfunctions in the gut microbiota are linked to disease severity and long-term sequelae in older hamsters. Our data also reveal age-specific changes in the composition and metabolic activity of the gut microbiota during both the acute phase (day 7 post-infection, D7) and the recovery phase (D22) of infection. Aged hamsters exhibited the most notable shifts in gut microbiota composition and plasma metabolic profiles. Through an integrative analysis of metagenomics, metabolomics, and clinical data, we identified significant associations between bacterial taxa, metabolites and disease markers in the aged group. On D7 (high viral load and lung epithelial damage) and D22 (body weight loss and fibrosis), numerous amino acids, amino acid-related molecules, and indole derivatives were found to correlate with disease markers. In particular, a persistent decrease in phenylalanine, tryptophan, glutamic acid, and indoleacetic acid in aged animals positively correlated with poor recovery of body weight and/or lung fibrosis by D22. In younger hamsters, several bacterial taxa (Eubacterium, Oscillospiraceae, Lawsonibacter) and plasma metabolites (carnosine and cis-aconitic acid) were associated with mild disease outcomes. These findings support the need for age-specific microbiome-targeting strategies to more effectively manage acute viral pneumonia and long-term disease outcomes.

Smooth muscle extracellular matrix modified small intestinal submucosa conduits promote peripheral nerve repair

Challenges still exist to develop an ideal cell-free nerve guidance conduit (NGC) providing a favorable microenvironment for rapid and successful nerve regeneration. Proteomic analysis revealed that extracellular matrix (ECM) derived from smooth muscle cells (SMCs) was abundant in nerve-related active proteins and significantly enriched signaling pathways involved in nerve regeneration. However, whether NGCs based on SMCs-derived ECM modification strategy promote nerve regeneration remains unclear. In the study, we investigated the neuroregenerative effect of SMCs-derived ECM and developed a novel NGC (MyoNerve) by coating small intestinal submucosa (SIS) with SMCs-derived ECM. The SMCs-ECM was rich in neurotrophic factors, which endowed MyoNerve with remarkable neuroregenerative capabilities by promoting the expression of genes implicated in aspects of neuronal maintenance and activating signaling pathways involved in nerve regeneration. In vitro, MyoNerve exhibited excellent bioactivity for accelerating angiogenesis, regulating macrophages polarization, promoting the proliferation, migration and elongation of Schwann cells, enhancing differentiation of PC12 cells, and inducing the neurite outgrowth of dorsal root ganglia. In the model of rat sciatic nerve 10 mm defect, MyoNerve showed great potential for functional nerve regeneration by promoting angiogenesis, proliferation and migration of Schwann cells and neuron, axonal regeneration, remyelination, and neurological functional recovery.

The inflammasome adaptor pycard is essential for immunity against Mycobacterium marinum infection in adult zebrafish

Inflammasomes regulate the host response to intracellular pathogens including mycobacteria. We have previously shown that the course of Mycobacterium marinum infection in adult zebrafish (Danio rerio) mimics the course of tuberculosis in human. To investigate the role of the inflammasome adaptor pycard in zebrafish M. marinum infection, we produced two zebrafish knockout mutant lines for the pycard gene with CRISPR/Cas9 mutagenesis. Although the zebrafish larvae lacking pycard developed normally and had unaltered resistance against M. marinum, the loss of pycard led to impaired survival and increased bacterial burden in the adult zebrafish. Based on histology, immune cell aggregates, granulomas, were larger in pycard-deficient fish than in wild-type controls. Transcriptome analysis with RNA sequencing of a zebrafish haematopoietic tissue, kidney, suggested a role for pycard in neutrophil-mediated defence, haematopoiesis and myelopoiesis during infection. Transcriptome analysis of fluorescently labelled, pycard-deficient kidney neutrophils identified genes that are associated with compromised resistance, supporting the importance of pycard for neutrophil-mediated immunity against M. marinum. Our results indicate that pycard is essential for resistance against mycobacteria in adult zebrafish.

Neonatal microbiota colonization primes maturation of goblet cell-mediated protection in the pre-weaning colon

Regulated host-microbe interactions are a critical aspect of lifelong health. Colonic goblet cells protect from microorganisms via the generation of a mucus barrier structure. Bacteria-sensing sentinel goblet cells provide secondary protection by orchestrating mucus secretion when microbes breach the mucus barrier. Mucus deficiencies in germ-free mice implicate a role for the microbiota in programming barrier generation, but its natural ontogeny remains undefined. We now investigate the mucus barrier and sentinel goblet cell development in relation to postnatal colonization. Combined in vivo and ex vivo analyses demonstrate rapid and sequential microbiota-dependent development of these primary and secondary goblet cell protective functions, with dynamic changes in mucus processing dependent on innate immune signaling via MyD88 and development of functional sentinel goblet cells dependent on the NADPH/dual oxidase family member Duox2. Our findings identify new mechanisms of microbiota-goblet cell regulatory interaction and highlight the critical importance of the pre-weaning period for the normal development of protective systems that are key legislators of host-microbiota interaction.

BCOR and ZC3H12A suppress a core stemness program in exhausted CD8+ T cells

In chronic viral infections, sustained CD8+ T cell response relies on TCF1+ precursor-exhausted T cells (TPEX) exhibiting stem-like properties. TPEX self-renew and respond to PD-1 blockade, underscoring their paramount importance. However, strategies for effectively augmenting TPEX remain limited. Here, we demonstrate that ZC3H12A deficiency initiates a stemness program in TPEX but also increases cell death, whereas BCOR deficiency predominantly promotes TPEX proliferation. Consequently, co-targeting of both BCOR and ZC3H12A imparts exceptional stemness and functionality to TPEX, thereby enhancing viral control. Mechanistically, BCOR and ZC3H12A collaboratively suppress a core stemness program in TPEX characterized by heightened expression of ∼216 factors. While TCF1 plays a role, this core stemness program relies on novel factors, including PDZK1IP1, IFIT3, PIM2, LTB, and POU2F2. Crucially, overexpressing POU2F2 robustly boosts TPEX and enhances antiviral immunity. Thus, a core stemness program exists in exhausted T cells, jointly repressed by BCOR and ZC3H12A, robustly controlling TPEX differentiation and providing new targets for addressing T cell exhaustion.

Environmentally relevant concentrations of individual per- and polyfluoroalkyl substances (PFAS) and a PFAS mixture impact proliferation, migration, and gene transcription in a human myometrial cell line

Per- and polyfluoroalkyl substances (PFAS) are persistent environmental contaminants linked to adverse health effects. Epidemiological studies have linked PFAS with an increased risk of uterine diseases including fibroids however, the mechanisms involved remain to be elucidated. This study examined the impact of individual PFAS, such as legacy compounds [perfluorooctanoic acid (PFOA), perfluorooctanesulfonic acid (PFOS)] and alternative short-chain compounds [GENX/HFPO-DA and perfluorobutanesulfonic acid (PFBS)], along with a PFAS mixture, on the function and transcriptome of immortalized human myometrial cells (UT-TERT). Exposure to these PFAS resulted in increased cell viability and proliferation. Flow cytometry showed that PFOS and the PFAS mixture altered cell cycle progression, while migration assays indicated significant enhancement of cell migration following PFOS and mixture exposure. Moreover, PFOA, PFBS, and the PFAS mixture impaired gap junction intercellular communication (GJIC), suggesting possible disruptions in cellular communication in the uterine environment. Transcriptomic analysis identified extensive changes in gene expression after exposure to environmentally relevant PFAS levels, revealing common molecular pathways involved in cell signaling, lipid metabolism, and cell survival. These findings provide crucial insights into how PFAS may contribute to reproductive health risks, warranting further investigation into the long-term effects of PFAS on uterine function and overall reproductive health.

Loss of SPHK1 fuels inflammation to drive KRAS-mutated lung adenocarcinoma

Inflammation is a widely recognized key contributor to KRAS-driven lung adenocarcinoma (LUAD). Tumor-associated macrophages (TAM) are an integral part of the tumor microenvironment and create a supportive niche that sustains inflammation-driven tumorigenesis. In the present study, we unravel a dual role of sphingosine kinase 1 (SPHK1) in KRAS-driven LUAD. While SPHK1 promotes tumorigenesis in in vitro experimental models, it paradoxically suppresses tumorigenesis in in vivo models of KRAS-mutated LUAD. Mechanistically, tumor-intrinsic loss of SPHK1 leads to disrupted lipid homeostasis, increased inflammation and infiltration by TAM, ultimately driving tumor progression. Thus, our study suggests that clinically targeting the SPHK1/S1P axis could potentially result in increased tumor progression, possibly by rewiring the tumor microenvironment toward a more inflammatory and pro-tumorigenic state.

Essential Roles of Conserved Pseudouridines in Helix 69 for Ribosome Dynamics in Translation

The widespread distribution of pseudouridine (Ψ), an isomer of the canonical uridine base, in RNA indicates its functional importance to the cell. In eukaryotes, it is estimated that around 2% of ribosomal RNA nucleotides are pseudouridines, most of which are located in functional regions of the ribosome. Defects in RNA pseudouridylation induce a range of detrimental effects from compromised cellular protein biosynthesis to disease phenotypes in humans. However, genome-wide changes to mRNA translation profiles by ribosomes lacking specific conserved pseudouridines have not been extensively studied. Here, using a new genomic method called 5PSeq and in vitro biochemistry, we investigated changes in ribosome dynamics and cellular translation profiles upon loss of Ψ2258 and Ψ2260 in helix 69, the two most conserved pseudouridines in the ribosome in yeast cells. We found that inhibiting the formation of these two pseudouridines challenges ribosomes to maintain the correct open reading frame and causes generally faster ribosome dynamics in translation. Furthermore, mutant ribosomes are more prone to pause while translating a subset of GC-rich codons, especially rare codons such as Arg (CGA) and Arg (CGG). These results demonstrate the presence of Ψ2258 and Ψ2260 contributes to the dynamics of the H69 RNA stem-loop, and helps to maintain functional interactions with the tRNAs as they move within the ribosome. The optimality of this ribosome-tRNA interaction is likely to be more critical for those limited tRNAs that decode rare codons. Consistent with the changes in ribosome dynamics, we observe that IRES-mediated translation is compromised in the mutant ribosome. These results explain the importance of Ψ2258 and Ψ2260 in H69 to maintain cellular fitness. The strong conservation of Ψ2258 and Ψ2260 in the ribosomes from bacteria to humans indicates their functional significance in modulating ribosome functions. It's likely that the identified functions of these covalent modifications are conserved across species.

Gap-App: A sex-distinct AI-based predictor for pancreatic ductal adenocarcinoma survival as a web application open to patients and physicians

In this study, using RNA-Seq gene expression data and advanced machine learning techniques, we identified distinct gene expression profiles between male and female pancreatic ductal adenocarcinoma (PDAC) patients. Building on this insight, we developed sex-specific 3-year survival predictive models alongside a single comprehensive model. Despite smaller sample sizes, the sex-specific models outperformed the general model. We further refined our models by selecting the most important features from the initial models. The refined sex-specific predictive models achieved higher accuracy and consistently outperformed the refined comprehensive model, highlighting the value of sex-specific analysis. To ensure robustness, all refined sex-specific models were calibrated and then evaluated using an independent dataset. Random Forest models emerged as the most effective predictors, achieving accuracies of 90.33 % for males and 90.40 % for females on the training dataset, and 81.25 % for males and 89.47 % for females on the independent test dataset. These top-performing models were integrated into Gap-App, a web application that leverages individual gene expression profiles and sex information for personalized survival predictions. As the first online tool bridging complex genomic data with clinical application, Gap-App facilitates more precise, individualized cancer care, marking a significant step in personalized prognosis prediction. This study underscores the importance of incorporating sex differences in predictive modeling and sets the stage for the shift from traditional one-size-fits-all to more personalized and targeted medicine. The Gap-App service is freely available for patients and clinicians at www.gap-app.org.

Intestinal estrogen receptor beta modulates the murine colon tumor immune microenvironment

Chronic inflammation contributes to the development of colorectal cancer, partly through its regulation of the microenvironment and antitumor immunity. Interestingly, women have a lower incidence of colorectal cancer, and estrogen treatment has been shown to reduce the occurrence of colorectal tumors. While intestinal estrogen receptor beta (ERβ, Esr2) can protect against colitis and colitis-induced cancer in mice, its role in shaping the tumor microenvironment remains unknown. In this study, we performed RNA sequencing to analyze the transcriptome of colonic epithelia and tumors from azoxymethane/dextran sulfate sodium-treated wild-type and intestinal ERβ knockout (ERβKOVil) mice and vehicle-treated controls. This revealed significant differences in gene expression and enriched biological processes influenced by sex and genotype, with immune-related responses being overrepresented. Deconvolution supported differential immune cell abundance and immunostaining showed that tumors from ERβKOVil mice displayed significantly increased macrophage infiltration, decreased T cell infiltration, and impaired natural killer cell infiltration. Further, ERβ mRNA levels in clinical colorectal tumors correlated with immune signaling profiles and better survival. Our findings indicate that intestinal ERβ promotes an antitumor microenvironment and could potentially affect the effectiveness of immunotherapy. These insights highlight the importance of ERβ in modulating antitumor immunity and underscore its therapeutic potential in colorectal cancer.

Oligodendrocyte-derived IL-33 regulates self-reactive CD8+ T cells in CNS autoimmunity

In chronic inflammatory disorders of the central nervous system (CNS), tissue-resident self-reactive T cells perpetuate disease. The specific tissue factors governing the persistence and continuous differentiation of these cells remain undefined but could represent attractive therapeutic targets. In a model of chronic CNS autoimmunity, we find that oligodendrocyte-derived IL-33, an alarmin, is key for locally regulating the pathogenicity of self-reactive CD8+ T cells. The selective ablation of IL-33 from neo-self-antigen-expressing oligodendrocytes mitigates CNS disease. In this context, fewer self-reactive CD8+ T cells persist in the inflamed CNS, and the remaining cells are impaired in generating TCF-1low effector cells. Importantly, interventional IL-33 blockade by locally administered somatic gene therapy reduces T cell infiltrates and improves the disease course. Our study identifies oligodendrocyte-derived IL-33 as a druggable tissue factor regulating the differentiation and survival of self-reactive CD8+ T cells in the inflamed CNS. This finding introduces tissue factors as a novel category of immune targets for treating chronic CNS autoimmune diseases.

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.

Microglia and CD8+ T cell activation precede neuronal loss in a murine model of spastic paraplegia 15

In central nervous system (CNS) diseases characterized by late-onset neurodegeneration, the interplay between innate and adaptive immune responses remains poorly understood. This knowledge gap is exacerbated by the prolonged protracted disease course as it complicates the delineation of brain-resident and infiltrating cells. Here, we conducted comprehensive profiling of innate and adaptive immune cells in a murine model of spastic paraplegia 15 (SPG15), a complicated form of hereditary spastic paraplegia. Using fate-mapping of bone marrow-derived cells, we identified microgliosis accompanied by infiltration and local expansion of T cells in the CNS of Spg15-/- mice. Single-cell analysis revealed an expansion of disease-associated microglia (DAM) and effector CD8+ T cells prior to neuronal loss. Analysis of potential cell-cell communication pathways suggested bidirectional interactions between DAM and effector CD8+ T cells, potentially contributing to disease progression in Spg15-/- mice. In summary, we identified a shift in microglial phenotypes associated with the recruitment and expansion of T cells as a new characteristic of Spg15-driven neuropathology.

DNA methylation predicts infection risk in kidney transplant recipients

Kidney transplantation (KTx) is the method of choice for treating kidney failure. Identifying biomarkers predictive of transplant (Tx) outcomes is critical to optimize KTx; however, the immunosuppressive therapies required after KTx must also be considered. We applied targeted bisulfite sequencing (TBS-seq) to PBMCs isolated from 90 patients, with samples collected pre- and post-Tx (day 90), to measure DNA methylation changes. Our findings indicate that the PBMC DNA methylome is significantly affected by induction immunosuppression with anti-thymocyte globulin (ATG). We discovered that the risk of infection can be predicted using DNA methylation profiles, but not gene expression profiles. Specifically, 515 CpG loci associated with 275 genes were significantly impacted by ATG induction, even after accounting for age, sex, and cell-type composition. Notably, ATG-associated hyper-methylation down-regulates genes critical for immune response. In conclusion, this clinical omics study reveals that the immunosuppressant ATG profoundly impacts the DNA methylome of KTx recipients and identifies biomarkers that could be used in pre-Tx screening of patients vulnerable to infection, thereby informing immunosuppression strategies post-Tx.

Induction of immune priming against white spot syndrome in Procambarus clarkii through oral administration of transgenic Synechococcus sp. PCC7942: Insights from transcriptome analysis

White Spot Syndrome Virus (WSSV) poses a significant threat to aquaculture, particularly affecting the red swamp crayfish (Procambarus clarkii). This study explores the efficacy of oral administration of transgenic Synechococcus sp. PCC7942, engineered to express WSSV envelop protein VP19 and VP (19 + 28), in inducing immune priming in red swamp crayfish. Our results demonstrate that the transgenic cyanobacteria significantly enhance the immune responses of crayfish, as evidenced by the upregulation of immune-related genes and increased survival rates post-WSSV challenge. Furthermore, the immune-stimulating activity of these proteins is maintained even after fragmentation into polypeptides during digestion. These findings highlight the potential of using genetically modified algae as a sustainable and effective strategy for disease management in aquaculture. Additionally, the molecular mechanism of immune priming effect of crayfish was explained, which provided theoretical support for long-term protection of aquatic economic species against virus.

Effect of Low-Intensity Pulsed Ultrasound on Post-Traumatic Intra-Articular Knee Adhesions in Rats

OBJECTIVE

Intra-articular adhesions (IAA) caused by trauma or surgical invasion commonly elicit pain and motor dysfunction. However, effective treatments for preventing IAA remain elusive. This study investigated the effects of low-intensity pulsed ultrasound (LIPUS) therapy on IAA after immobilization following trauma.

METHODS

A knee adhesion model was established in male Wistar rats, which were divided into LIPUS and sham groups. LIPUS was applied for 20 min/d (30 mW/cm2 [spatial average temporal average], 1 MHz, duty cycle 20%, 5 times/wk, for 1, 2 and 3 wk). Another group of rats was treated with the same parameters for 3 or 7 d. After the treatment period, we evaluated the range of motion (ROM) of the knee joint, the length of the adhesion and the posterior knee joint capsule. RNA-seq and RT-quantitative polymerase chain reaction were performed to investigate the molecular mechanisms underlying the effects of LIPUS.

RESULTS

The knee ROM was significantly improved, and the adhesion length was reduced in the LIPUS group. RNA-seq identified 113 and 776 differentially expressed genes on days 3 and 7, respectively, highlighting pathways related to inflammatory, immune and fibrotic responses. IL-6 mRNA in the LIPUS group was significantly upregulated on day 3 and significantly downregulated at 1 wk. The TNFα, TGFβ and HIF1α levels did not differ between all groups. COL1A1 expression in the sham group significantly increased on day 7.

CONCLUSION

These results indicate that LIPUS therapy may affect inflammatory and fibrotic pathways and may serve as a rehabilitation approach to prevent the development of IAA.

STAT5B leukemic mutations, altering SH2 tyrosine 665, have opposing impacts on immune gene programs

STAT5B is a vital transcription factor for lymphocytes. Here, the function of two STAT5B mutations from human T-cell leukemias: one substituting tyrosine 665 with phenylalanine (STAT5BY665F) and the other with histidine (STAT5BY665H), was interrogated. In silico modeling predicted divergent energetic effects on homodimerization with a range of pathogenicity. In primary T cells in vitro, STAT5BY665F showed gain-of-function, whereas STAT5BY665H demonstrated loss-of-function. Introducing the mutation into the mouse genome illustrated that the gain-of-function Stat5b Y665F mutation resulted in accumulation of CD8+ effector and memory and CD4+ regulatory T cells, altering CD8+/CD4+ ratios. In contrast, STAT5BY665H "knock-in" mice showed diminished CD8+ effector and memory and CD4+ regulatory T cells. In contrast to WT STAT5B, the STAT5BY665F variant displayed greater STAT5 phosphorylation, DNA binding, and transcriptional activity after cytokine activation, whereas the STAT5BY665H variant resembled a null. The work exemplifies how joining in silico and in vivo studies of single nucleotides deepens our understanding of disease-associated variants, revealing structural determinants of altered function, defining mechanistic roles, and, specifically here, identifying a gain-of-function variant that does not directly induce hematopoietic malignancy.

Assessment of the effects of estetrol and 17α-ethinylestradiol on zebrafish (Danio rerio) metamorphosis: a morphological and transcriptomic approach

17α-ethinylestradiol (EE2) is a synthetic estrogen widely used in combined oral contraceptives (COCs) for years. Estetrol (E4), a natural estrogen synthesized by the fetal liver during pregnancy, is the estrogenic component of a new COC. While E4 is thought to have a limited environmental impact in comparison to EE2, its effects on non-reproductive functions in aquatic species remain underexplored. This study compared the impact of EE2 and E4 on the metamorphosis of zebrafish (Danio rerio), a vital life cycle process. Larvae were exposed to concentrations ranging from 10 to 10,000 times the measured (0.1 ng/L) or predicted (32 ng/L) environmental concentrations of EE2 and E4 respectively. Samples were collected at 14, 22, and 30 days post-fertilization (dpf) to assess morphological traits and perform transcriptomic analysis. EE2 exposure at 1,000 ng/L exhibited developmental delays from the onset of metamorphosis, with most traits affected at 22 dpf. The effects intensified at 30 dpf, with notable impacts at both EE2 100 and 1,000 ng/L. At 100 ng/L, modulations in the expression of genes involved in macronutrient metabolism, crucial to the developmental process, were observed throughout metamorphosis. Additionally, an upregulation of estrogen-specific responses and drug metabolism was noted. In contrast, no notable changes in traits were detected for the concentrations of E4 tested. Although gene expression related to cell structure and adhesion, peptidase activity, and muscle structure and contraction was altered at E4 32,000 ng/L, no metamorphosis-related pathways were affected. These results suggest that E4 presents a greater safety margin and may therefore be more environmentally friendly than EE2.

Human iPS cell-derived respiratory organoids as a model for respiratory syncytial virus infection

Respiratory syncytial virus (RSV) is a seasonal respiratory pathogen that primarily affects young children, potentially causing severe lower respiratory tract disease. Despite the high disease burden, understanding of RSV pathophysiology remains limited. To address this, advanced RSV infection models are needed. Whereas HEp-2 cells are widely used because of their high susceptibility to RSV, they do not accurately reflect the host response of the human respiratory tract. In this study, we evaluated human-induced pluripotent stem cell-derived respiratory organoids, which contain respiratory epithelial cells, immune cells, fibroblasts, and vascular endothelial cells, for their potential to model RSV infection and support pharmaceutical research. RSV-infected organoids exhibited high viral genome and protein expression, epithelial layer destruction, and increased collagen accumulation. Pro-inflammatory cytokine levels in culture supernatants also increased post-infection. Furthermore, RSV infection was significantly inhibited by monoclonal antibodies (nirsevimab, palivizumab, suptavumab, or clesrovimab), although ribavirin showed limited efficacy. These findings highlight the utility of respiratory organoids for RSV research.

Transcriptomic analyses of human brains with Alzheimer's disease identified dysregulated epilepsy-causing genes

BACKGROUND & OBJECTIVE

Alzheimer's Disease (AD) patients at multiple stages of disease progression have a high prevalence of seizures. However, whether AD and epilepsy share pathophysiological changes remains poorly defined. In this study, we leveraged high-throughput transcriptomic data from sporadic AD cases at different stages of cognitive impairment across multiple independent cohorts and brain regions to examine the role of epilepsy-causing genes.

METHODS

Epilepsy-causing genes were manually curated, and their expression levels were analyzed across bulk transcriptomic data from three AD cohorts and three brain regions. RNA-seq data from sporadic AD and control cases from the Knight ADRC, MSBB, and ROSMAP cohorts were processed and analyzed under the same analytical pipeline. An integrative clustering approach employing machine learning and multi-omics data was employed to identify molecularly defined profiles with different cognitive scores.

RESULTS

We found several epilepsy-associated genes/pathways significantly dysregulated in a group of AD patients with more severe cognitive impairment. We observed 15 genes consistently downregulated across the three cohorts, including sodium and potassium channels genes, suggesting that these genes play fundamental roles in cognitive function or AD progression. Notably, we found 25 of these genes dysregulated in earlier stages of AD and become worse with AD progression.

CONCLUSION

Our findings revealed that epilepsy-causing genes showed changes in the early and late stages of AD progression, suggesting that they might be playing a role in AD progression. We can not establish directionality or cause-effect with our findings. However, changes in the epilepsy-causing genes might underlie the presence of seizures in AD patients, which might be present before or concurrently with the initial stages of AD.

Reproductive adaptation of Astyanax mexicanus under nutrient limitation

Reproduction is a fundamental biological process for the survival and continuity of species. Examining changes in reproductive strategies offers valuable insights into how animals have adapted their life histories to different environments. Since reproduction is one of the most energy-intensive processes in female animals, nutrient scarcity is expected to interfere with the ability to invest in gametes. Lately, a new model to study adaptation to nutrient limitation has emerged; the Mexican tetra Astyanax mexicanus. This fish species exists as two different morphs, a surface river morph and a cave-dwelling morph. The cave-dwelling morph has adapted to the dark, lower biodiversity, and nutrient-limited cave environment and consequently evolved an impressive starvation resistance. However, how reproductive strategies have adapted to nutrient limitations in this species remains poorly understood. Here, we compared breeding activities and maternal contributions between laboratory-raised surface fish and cavefish. We found that cavefish produce different clutch sizes of eggs with larger yolk compared to surface fish, indicating a greater maternal nutrient deposition in cavefish embryos. To systematically characterize yolk compositions, we used untargeted proteomics and lipidomics approaches to analyze protein and lipid profiles in 2-cell stage embryos and found an increased proportion of sphingolipids in cavefish compared to surface fish. Additionally, we generated transcriptomic profiles of surface fish and cavefish ovaries using a combination of single cell and bulk RNA sequencing to examine differences in maternal contribution. We found that genes essential for hormone regulation were upregulated in cavefish follicular somatic cells compared to surface fish. To evaluate whether these differences contribute to their reproductive abilities under natural-occurring stress, we induced breeding in starved female fish. Remarkably, cavefish maintained their ability to breed under starvation, whereas surface fish largely lost this ability. We identified insulin-like growth factor 1a receptor (igf1ra) as a potential candidate gene mediating the downregulation of ovarian development genes, potentially contributing to the starvation-resistant fertility of cavefish. Taken together, we investigated the female reproductive strategies in Astyanax mexicanus, which will provide fundamental insights into the adaptations of animals to environments with extreme nutrient deficit.

TRAIL induces cytokine production via the NFkB2 pathway promoting neutrophil chemotaxis and neutrophil-mediated immune-suppression in triple negative breast cancer cells

Tumor necrosis factor-related apoptosis-inducing ligand (TRAIL) is a potential cancer therapeutic that induces apoptosis in cancer cells while sparing the non-malignant cells in preclinical models. However, its efficacy in clinical trials has been limited, suggesting unknown mechanisms modulating TRAIL activity in patients. We hypothesized that TRAIL treatment elicits transcriptional changes in triple negative breast cancer (TNBC) cells that alter the immune milieu. RNAseq analysis of MDA-MB-231 cells along with validation in additional cell lines demonstrated that TRAIL induced cytokines such as CXCLs 1, 2, 3, 8,11 and IL-6, which are known to modify neutrophil function. Mechanistically, TRAIL dependent induction of the cytokines was predominantly mediated by death receptor 5, caspase-8 and the non-canonical NFKB2 pathway. These cytokines produced by TRAIL-treated TNBC cells enhanced chemotaxis of normal human donor isolated neutrophils. Using TNBC xenograft models, TRAIL induced activation of NFkB2 pathway, cytokine production and increased neutrophil recruitment into the tumors. Moreover, preincubation of neutrophils in supernatants from TRAIL-treated TNBC cells significantly impaired neutrophil function as measured by reduced respiratory burst and cytotoxic effect against TNBC cells. Transcriptomic analysis of neutrophils incubated with either TRAIL alone or supernatant of TRAIL-treated TNBC cells revealed increased expression of inflammatory cytokines, immune modulatory genes, immune checkpoint genes, and genes implicated in delayed neutrophil apoptosis. Functional studies showed that these neutrophils suppress T cell proliferation and augment Treg suppressive phenotype. Collectively, our study demonstrates a novel role of TRAIL-induced NFKB2-dependent cytokine production that promotes neutrophil chemotaxis and neutrophil-mediated immune suppression.

Single-cell transcriptomic analysis identifies tissue-specific fibroblasts as the main modulators of myeloid cells in peritoneal metastasis of different origin

Colorectal cancer (CRC) peritoneal metastasis (CPM) is related to limited therapy options and poor prognosis. Although stromal cells heavily infiltrate most CPMs, interactions between different cell types in their microenvironment remain unclear. Here, we investigated tumor and distant normal tissue from CPM and CRC patients using single-cell RNA sequencing. Investigating the incoming and outgoing signals between cells revealed that fibroblasts dominate the CPM signaling landscape with myeloid cells as their strongest interaction partner. Using immunohistochemistry, we confirmed that fibroblasts co-localize with macrophages in the CPM microenvironment. A fibroblast sub-population detected only in CPM and normal peritoneum demonstrated immunoregulatory properties in co-culture experiments, and was further detected in additional peritoneal malignancies derived from ovarian and gastric origin. This novel fibroblast type and its communication with macrophages could be attractive targets for therapeutic interventions in CPM and potentially peritoneal surface malignancies in general.

IPMK depletion influences genome-wide DNA methylation

Inositol polyphosphate multikinase (IPMK) is emerging as a critical regulator of nuclear functions. While earlier studies in yeast and cell lines linked IPMK to gene expression, recent work reveals its role in modulating histone acetylation through the activation of histone deacetylases 1/3 (HDAC1/3). Interestingly, HDAC1/3 interact with DNA methyltransferase 1 (DNMT1), stabilizing DNMT1 and promoting DNA methylation. As an HDAC1/3 activator, IPMK may thereby influence DNA methylation dynamics. This study investigates how the genetic depletion of IPMK influences DNA methylation, though the role of its kinase activity remains untested. Using long-read Oxford nanopore sequencing, we conducted methylation analysis for >28 millions of CpG sites and discovered that IPMK deletion results in over 22,000 differentially methylated regions (DMRs). Integrating affected genes by DMRs and RNA-seq data, we found that 35 genes show an inverse correlation between methylation in promoter regions and gene expression. Pathway analysis revealed that genes related to tissue remodeling and hematopoiesis are affected. Notably, MMP14 and LIF showed significant methylation changes in promoter regions under IPMK deletion, resulting in decreased mRNA and protein expression. Collectively, this study identifies IPMK as a novel regulator of DNA methylation. While this study did not investigate the role of IPMK's kinase activity in regulating DNA methylation, future studies will determine whether IPMK's effects on DNA methylation are driven by its kinase activity or by kinase-independent mechanisms.

Response of astrocytes and their interaction with surrounding brain cells after acute ischemia-reperfusion analyzed by single-cell transcriptome sequencing

Astrocytes play a key role in the occurrence and development of ischemic stroke. However, reactive astrocytes have both detrimental and protective roles in ischemic stroke. Regrettably, the stimulation signals associated with the transformation of astrocytes into different subclusters lack systemic analysis, and the mechanism by which astrocytes produce multiple effects is not entirely clear. We investigated the heterogeneity of mouse astrocytes 12 h after cerebral ischemia-reperfusion via Single-cell RNA sequencing and verified gene expressions by reverse transcription-polymerase chain reaction. We acquired astrocyte subclusters' transcriptional characteristics involved in diversified functions. To explore what stimulus signals cause astrocyte heterogeneity, we present a blueprint for cellular communication between astrocyte subclusters and other surrounding brain cells 12 h after ischemia-reperfusion, and identified 9 genes which are potential and promising for being therapeutic targets and 6 genes were specific to astrocyte subcluster 2 that tend to resist ischemia-reperfusion injury. At 12 h after ischemia-reperfusion, each subcluster of astrocytes is characteristic in terms of function and communication with surrounding cells, which is based on the activation genes and transcription molecules that we have revealed with subcluster characteristics. Our results provide a basis for revealing the anti-injury response of astrocytes to cerebral ischemia-reperfusion, which involves coordination of different subclusters and the coordination of astrocytes with surrounding brain cells.

Development and validation of a transcription factor regulatory network-based signature for individualized prognostic risk in lung adenocarcinoma

Despite significant progress in diagnostic and therapeutic modalities, lung adenocarcinoma (LUAD) still exhibits a high recurrence risk and a low 5-year survival rate. Reliable prognostic signatures are imperative for risk stratification in LUAD patients. This study encompassed 2740 patients from 23 LUAD cohorts, including one single-cell RNA sequencing (scRNA-seq) dataset, five bulk RNA-seq datasets, and 17 microarray datasets. Using scRNA-seq dataset, we defined a group of epithelial-specific transcription factors significantly over-represented in the epithelial-to-mesenchymal transition (EMT) gene set (enrichment ratio [ER] = 5.80, Fisher's exact test p < .001), and the corresponding target genes were significantly enriched in the cancer driver gene set (ER = 2.74, p < .001), indicating of their crucial roles in the EMT process and tumor progression. We constructed a single-cell gene pairs (scGPS) signature, composed of 3521 gene pairs derived from the epithelial cell-specific transcription factor regulatory network, to predict overall survival (OS) of LUAD. High-risk patients identified by scGPS in the discovery cohort exhibited significantly worse OS compared to low-risk patients (Hazard ratio [HR] = 1.78, 95% CI: 1.29-2.46, log-rank p = 1.80 × 10-4). The scGPS outperformed other established gene signatures and demonstrated robust prognostic stratification across various independent datasets, including microarray data and even early-stage LUAD patients. It remained an independent prognostic factor after adjusting for clinical and pathologic factors. In addition, combining scGPS with tumor stage further enhanced prognostic accuracy compared to using stage alone. The scGPS signature offers individualized prognosis estimations, showing significant potential for practical application in clinical settings.

Inhibition of the LINE1-derived MET transcript induces apoptosis and oncoprotein knockdown in cancer cells

The expression of intragenic long interspersed nuclear elements 1 (LINE1s) can generate chimeric sequences disrupting host gene transcription. Among these, L1-MET, within mesenchymal epithelial transition (MET) oncogene, is particularly interesting, as its expression has been associated with the acquisition of tumorigenic phenotypes and cancer progression. We investigated the effects of targeting L1-MET in eight cancer cell lines derived from breast, lung, and gastrointestinal cancers, as well as in non-transformed human fibroblasts and lymphocytes, using specifically developed modified antisense oligonucleotides. Inhibition of L1-MET resulted in decreased cell viability, increased apoptosis, and gene expression profile reprogramming in cancer cells, including significant downregulation of MET and epidermal growth factor receptor (EGFR) proteins. These effects were related to the L1-MET/MET expression levels and the type of cellular addiction, with pronounced impacts in cells harboring MET gene amplification and EGFR-activating mutations. They were also detectable, though less pronounced, in cancer cells with steady-state levels of MET and EGFR proteins or addiction to other oncogenes. We demonstrate that targeting L1-MET can knockdown MET and EGFR protein. The restricted expression of L1-MET to cancer cells suggests that its inhibition could be an effective strategy to induce death in oncogene-addicted tumor cells and offers a potential means to overcome the limitations of conventional targeted therapies.

FUBP3 enhances HIV-1 transcriptional activity and regulates immune response pathways in T cells

Far-upstream element-binding protein 3 (FUBP3) was identified at actively transcribing HIV promoters through chromatin affinity purification and mass spectrometry. Known for regulating cellular processes such as transcription and translation by binding to DNAs and RNAs, FUBP3's role in HIV transcriptional regulation was previously unrecognized. This study reveals that FUBP3 enhances HIV-1 transcriptional activation by interacting with Tat and trans-activation response (TAR)-RNA, critical for boosting viral transcription through recruitment of activating factors that promote RNA polymerase II (RNAPII) elongation. Transcriptomic analysis, chromatin immunoprecipitation, and biochemical assays demonstrated that FUBP3 associates with and stabilizes TAR-RNA, in a Tat-dependent manner, and enhances Tat steady-state levels via interaction with Tat's basic domain. Suppressing FUBP3 decreased HIV-1 transcription and altered expression of host genes linked to T cell activation and inflammation, underscoring its broad regulatory impact. Additionally, FUBP3 was enriched at active promoters, confirming its role in transcriptional regulation at specific genomic locations. These findings highlight FUBP3's critical role in the HIV-1 life cycle and suggest its potential as a therapeutic target in HIV-1 infection. Additionally, this study expands our understanding of FUBP3's functions in oncogenic and inflammatory pathways.

Dominant interfering CARD11 variants disrupt JNK signaling to promote GATA3 expression in T cells

Several "primary atopic disorders" are linked to monogenic defects that attenuate TCR signaling, favoring T helper type 2 (TH2) cell differentiation. Patients with CARD11-associated atopy with dominant interference of NF-κB signaling (CADINS) disease suffer from severe atopy, caused by germline loss-of-function/dominant interfering (LOF/DI) CARD11 variants. The CARD11 scaffold enables TCR-induced activation of NF-κB, mTORC1, and JNK signaling, yet the function of CARD11-dependent JNK signaling in T cells remains nebulous. Here we show that CARD11 is critical for TCR-induced activation of JNK1 and JNK2, as well as canonical JUN/FOS AP-1 family members. Patient-derived CARD11 DI variants attenuated WT CARD11 JNK signaling, mirroring effects on NF-κB. Transcriptome profiling revealed JNK inhibition upregulated TCR-induced expression of GATA3 and NFATC1, key transcription factors for TH2 cell development. Further, impaired CARD11-JNK signaling was linked to enhanced GATA3 expression in CADINS patient T cells. Our findings reveal a novel intrinsic mechanism connecting impaired CARD11-dependent JNK signaling to enhanced GATA3/NFAT2 induction and TH2 cell differentiation in CADINS patients.

A chromosome-scale and haplotype-resolved genome assembly of tetraploid blackberry (Rubus L. subgenus Rubus Watson)

Blackberries (Rubus spp.) are globally consumed and well known for their rich anthocyanin and antioxidant content and distinct flavors. Improving blackberries has been challenging due to genetic complexity of traits and limited genomic resources. The blackberry genome has been particularly challenging to assemble due to its polyploid nature. Here, we present the first chromosome-scale and haplotype-phased assembly for the primocane-fruiting, thornless tetraploid blackberry selection BL1 (Rubus L. subgenus Rubus Watson). The genome assembly was generated using Oxford Nanopore Technology and Hi-C scaffolding, resulting in a 919 Mb genome distributed across 27 pseudochromosomes, with an N50 of 35.73 Mb. This assembly covers >92% of the genome length and contains over 98% of complete BUSCOs. Approximately, 58% of the assembly consists of repetitive sequences, with long terminal repeats being the most abundant class. A total of 87,968 protein-coding genes were predicted, of which, 82% were functionally annotated. Genome mining and RNA-Seq analyses identified possible candidate genes and transcription factors related to thornlessness and the key structural genes and transcription factors for anthocyanin biosynthesis. Activator genes including PAP1 and TTG1 and repressor genes such as ANL2 and MYBPA1 play an important role in the fine tuning of anthocyanin production during blackberry development. Resequencing of seven tetraploid blackberry cultivars/selections with different horticultural characteristics revealed candidate genes that could impact fruiting habit and disease resistance/susceptibility. This tetraploid reference genome should provide a valuable resource for accelerating genetic analysis of blackberries and facilitating the development of new improved cultivars with enhanced horticultural and nutritional traits.

Effects of sunlight exposure on tire tread particle leachates: Chemical composition and toxicity in aquatic systems

Tire tread particles (TTP) are small micro- or nano-particles resulting from the friction of tire tread against roadways. These secondary microplastics have been found in waterways, arriving through airborne means or runoff. Due to their abundance and persistence in aquatic environments, TTP pose a potential hazard to wildlife. Natural degradation processes like photoirradiation can potentially worsen this by transforming leached TTP chemicals. In this study, we assessed the toxicity and chemical composition of TTP leachates produced over 1 or 6 days in either dark or photoirradiated conditions. For toxicity studies, zebrafish embryos were exposed to leachates over a range of concentrations and from 0 to 4 days post fertilization. TTP exposures impaired survival and hatching, induced embryonic defects, and modulated detoxification by the enzyme ethyoxyresorufin-O-deethylase. RNA sequencing revealed divergent effects based on photoirradiation, including impacts on glycolysis, lipid metabolism, and mitochondrial function. For chemical analysis, leachates were assessed using comprehensive two-dimensional gas chromatography coupled to time-of-flight mass spectrometry (GC × GC/TOF-MS) and chromatographic features were annotated. In total, 546 chromatographic features were detected across all samples, and clustering showed unique chemical profiles based on photoirradiation during leaching. Several compounds were in high abundance in 1-day irradiated leachates, including 1,3-diphenylguanidine, aniline, and 1H-benzotriazole, though their relative abundance was reduced in 6-day leachates. Overall, this research compounds on the existing literature defining TTPs as toxic microplastics in the environment, and we show novel chemical and toxicological data that demonstrates how photoirradiation in the natural environment may exacerbate toxicity.

Defective Processing of Cytoplasmic and Chloroplast Ribosomal RNA in the Absence of Arabidopsis DXO1

Decapping 5'-3' exoribonucleases from the DXO/Rai1 family are highly conserved among eukaryotes and exhibit diverse enzymatic activities depending on the organism. The biochemical and structural properties of the plant DXO1 differ from the yeast and animal counterparts, which is reflected in the in vivo functions of this enzyme. Here we show that Arabidopsis DXO1 contributes to the efficient processing of rRNA precursors in both nucleolar/cytosolic and chloroplast maturation pathways. However, the processing defects in DXO1-deficient plants do not depend on the catalytic activity of the enzyme but rely on its plant-specific N-terminal extension, which is responsible for the interaction with the mRNA cap methyltransferase RNMT1. Our RNA sequencing analyses show that the dxo1 mutation deregulates the expression of many ribosomal protein genes, most likely leading to inefficient or delayed pre-rRNA maturation. These phenotypes are partially suppressed by RNMT1 overexpression, suggesting that defective cap synthesis may be responsible, at least to some extent, for the observed effects.

Serum exosomal hsa-miR-142-5p, hsa-miR-1908-5p, and hsa-miR-450b-5p as candidate biomarkers for recurrent depressive disorder diagnosis and ECT treatment response: A preliminary investigation

PURPOSE

This study investigated the differential expression of serum exosomal miRNAs in female patients with recurrent depressive disorder (RDD) before and after non-convulsive electroconvulsive therapy (ECT), aiming to explore potential diagnostic and therapeutic biomarkers.

METHOD

Serum samples were collected from three groups: healthy female volunteers aged 30-50, female patients with RDD prior to ECT, and female patients post-ECT who had achieved remission. Exosomes were isolated from serum, identified through transmission electron microscopy, nanoparticle tracking analysis, and Western blot analysis of exosomal markers. Total RNA was extracted from exosomes, and miRNA sequencing was conducted to identify differentially expressed miRNAs. Gene target prediction, Gene Ontology, and KEGG pathway enrichment analyses were also performed.

RESULTS

miRNA sequencing revealed significant differences in exosomal miRNA profiles among the three groups. Compared to controls, 69 miRNAs were upregulated and 98 downregulated in the model group, while the recovery group showed 41 upregulated and 51 downregulated miRNAs compared to the model group. Furthermore, the recovery group exhibited 35 upregulated and 59 downregulated miRNAs compared to controls. Analysis identified hsa-miR-142-5p, hsa-miR-1908-5p, and hsa-miR-450b-5p as potential biomarkers for RDD diagnosis and ECT treatment response, with functional roles likely related to inflammation, neurotransmission, and synaptic plasticity.

CONCLUSION

Serum exosomal miRNAs, particularly hsa-miR-142-5p, hsa-miR-1908-5p, and hsa-miR-450b-5p, emerged as promising candidates for further investigation as biomarkers for RDD diagnosis and treatment monitoring. Larger, multi-center studies are warranted to validate these findings.

Size Matters: Influence of Available Soil Volume on the Root Architecture and Plant Response at Transcriptomic and Metabolomic Levels in Barley

Pot size is a critical factor in plant growth experiments, influencing root architecture, nutrient uptake, and overall plant development as well as sensing of stress. In controlled environments, variation in pot size can impact phenotypic and molecular outcomes and may bias experimental results. Here, we investigated how pot size affects the root system architecture and molecular responses of two barley genotypes, the landrace BERE and the modern elite CONCERTO, through assessment of shoot and root traits and by using X-ray computed tomography complemented by transcriptomic and metabolomic analyses. The two genotypes showed distinctly different adaptations to changes in pot size. The landrace showed greater stability and adaptability with consistent root traits and enhanced accumulation of osmoprotectant metabolites across different pot sizes with respect to CONCERTO. Conversely, the elite line was more sensitive to pot size variations, particularly showing altered root architecture and transcriptomic responses. Overall, this study highlights the importance of selecting an appropriate pot size for plant growth experiments, particularly when focused on root traits, and highlights the importance of considering the physiological and molecular changes due to growth environment choice in experimental design in barley.

Cholesterol sulfate as a negative regulator of cellular cholesterol homeostasis

Cholesterol sulfate (CS), one of the most abundant cholesterol derivatives, recently emerged as a key regulatory molecule in several physiological processes. Here, we demonstrate multiple mechanisms by which CS reduces intracellular cholesterol levels. CS promotes the proteasomal degradation of 3-hydroxy-3-methylglutaryl-CoA reductase reductase by enhancing insulin-induced gene-mediated ubiquitination, thereby inhibiting cholesterol synthesis. In addition, CS blocks low-density lipoprotein receptor endocytosis, reducing low-density lipoprotein cholesterol uptake. CS further suppresses the proteolytic activation of sterol regulatory element-binding protein 2, a master transcription factor governing cholesterol synthesis and uptake. Using in vitro and in vivo models, we show that CS lowers cholesterol by targeting both the cholesterol synthesis and uptake pathways, while also modulating an important feedback loop via sterol regulatory element-binding protein 2. These findings highlight the potential of CS as a modulator of cholesterol metabolism, offering new therapeutic insights into cholesterol-related disorders.

Transcriptomic profiling of blood platelets identifies a diagnostic signature for pancreatic cancer

BACKGROUND

Pancreatic cancer (PaCa) is a deadly malignancy that is often diagnosed at an advanced stage, limiting treatment and reducing survival. There is an urgent need for convenient and accurate diagnostic markers for the early detection of PaCa.

METHODS

In this multicenter case-control study, we performed transcriptome analysis of 673 platelet samples from different in-house and public cohorts. RNA sequencing and RT-qPCR were used to discover and validate potential platelet biomarkers. A multi-gene signature was developed using binomial generalized linear model and independently validated in multicenter cohorts.

RESULTS

Two platelet RNAs, SCN1B and MAGOHB, consistently showed robust altered expression patterns between PaCa and healthy controls across cohorts, as confirmed by both RNA sequencing and RT-qPCR. The diagnostic two-RNA signature, PLA2Sig, demonstrated remarkable performance in detecting PaCa, with area under the receiver operating characteristic curve (AUC) values of 0.808, 0.900, 0.783, and 0.830 across multicenter cohorts. Furthermore, PLA2Sig effectively identified resectable stage I&II PaCa cases with an AUC of 0.812. Notably, PLA2Sig outperformed the traditional serum markers carcinoembryonic antigen and carbohydrate antigen 19-9 in distinguishing PaCa from healthy controls, and is complementary to established blood-based screening biomarkers.

CONCLUSION

These findings provide preliminary but promising evidence for the potential utility of platelet RNAs as an alternative non-invasive liquid biopsy tool for the early detection of PaCa.

Involvement of TGF-β signaling pathway-associated genes in the corneal endothelium of patients with Fuchs endothelial corneal dystrophy

This study investigated the involvement of TGF-β signaling pathway-associated genes in the pathogenesis of Fuchs endothelial corneal dystrophy (FECD). The RNA-sequencing analysis of corneal endothelial cells (CECs) from FECD patients revealed significant alterations in multiple TGF-β superfamily genes, with 9 genes upregulated (including BMP6, GDF5, and TGF-β2) and 10 genes downregulated (including BMP2, NOG, and INHBA) compared to controls. Quantitative PCR validation confirmed the elevated expression of GDF5 (3.35-fold in non-expanded and 7.66-fold in expanded TCF4), TGF-β2 (6.17-fold and 11.5-fold), and TGF-β1 (1.78-fold and 1.58-fold) in FECD patients with and without TCF4 trinucleotide repeat expansion. Ex-vivo experiments using donor corneas demonstrated that TGF-β2 stimulation significantly increased the expression of extracellular matrix (ECM) components associated with guttae formation, including fibronectin, types I and VI collagens, and other matrix proteins. Immunofluorescence confirmed increased fibronectin protein expression in the corneal endothelium following TGF-β1 or TGF-β2 treatment. This study provides the first comprehensive analysis of TGF-β superfamily involvement in FECD and suggests that GDF5, found to be upregulated in FECD, may contribute to the disease process. These findings further indicate that dysregulation of TGF-β signaling pathways drives the characteristic ECM accumulation in FECD, potentially offering new therapeutic targets for this progressive corneal disease involving fibrosis-related alterations. Future research is warranted to clarify GDF5's specific role and mechanistic impact on FECD pathogenesis.

Uncovering hepatic transcriptomic and circulating proteomic signatures in MASH: A meta-analysis and machine learning-based biomarker discovery

BACKGROUND

Metabolic-associated steatohepatitis (MASH), the progressive form of metabolic-associated steatotic liver disease (MASLD), poses significant risks for liver fibrosis and cardiovascular complications. Despite extensive research, reliable biomarkers for MASH diagnosis and progression remain elusive. This study aimed to identify hepatic transcriptomic and circulating proteomic signatures specific to MASH, and to develop a machine learning-based biomarker discovery model.

METHODS

A systematic review of RNA-Seq and proteomic datasets was conducted, retrieving 7 hepatic transcriptomics and 3 circulating proteomics studies, encompassing 483 liver samples and 169 serum/plasma samples, respectively. Differential gene and protein expression analyses were performed, and pathways were enriched using gene set enrichment analysis. A machine learning (ML) model was developed to identify MASH-specific biomarkers, utilizing biologically significant protein ratios.

KEY FINDINGS

Hepatic transcriptomic analysis identified 5017 differentially expressed genes (DEGs), with significant enrichment of extracellular matrix (ECM) pathways. Serum proteomics revealed six differentially expressed proteins (DEPs), including complement-related proteins. Integration of transcriptomic and proteomic data highlighted the complement cascade as a key pathway in MASH, with discordant regulation between the liver and circulation. The ML-based biomarker discovery model, utilizing protein ratios, achieved an F1 scores of 0.83 and 0.64 in the training sets and 0.67 in an external validation set.

CONCLUSION

Our findings indicate ECM deregulation and complement system involvement in MASH progression. The novel ML model incorporating protein ratios offers a potential tool for MASH diagnosis. However, further refinement and validation across larger and more diverse cohorts is needed to generalize these results.

Identification of FLYWCH1 as a regulator of platinum-resistance in epithelial ovarian cancer

Platinum-based combination chemotherapy remains the backbone of first-line treatment for patients with advanced epithelial ovarian cancer (EOC). While most patients initially respond well to the treatment, patients with relapse ultimately develop platinum resistance. This study identified FLYWCH-type zinc finger-containing protein 1 (FLYWCH1) as an important regulator in the resistance development process. We showed that the loss of FLYWCH1 promotes platinum resistance in EOC cells, and the low FLYWCH1 expression is correlated with poor prognosis of EOC patients. In platinum-sensitive cells, FLYWCH1 colocalizes with H3K9me3, but this association is significantly reduced when cells acquire resistance. The suppression of FLYWCH1 induces gene expression changes resulting in the deregulation of pathways associated with resistance. In line with its connection to H3K9me3, FLYWCH1 induces gene silencing in a synthetic reporter assay and the suppression of FLYWCH1 alters H3K9me3 at promoter regions and repeat elements. The loss of FLYWCH1 leads to the derepression of LTR and Alu repeats, thereby increasing transcriptional plasticity and driving the resistance development process. Our data highlight the importance of FLYWCH1 in chromatin biology and acquisition of platinum resistance through transcriptional plasticity and propose FLYWCH1 as a potential biomarker for predicting treatment responses in EOC patients.

Super pan-genome-wide analysis of Hordeum WOX genes and identification of key members conferring salt stress tolerance

The WUSCHEL-related homeobox (WOX) is a transcription factor family specific to plants, playing a key role in the initiation and maintenance of meristematic tissue, organ formation and response to abiotic stress. Here we identified 14-15 WOX genes in four Hordeum species, conducted their phylogenetic tree, determined their chromosome locations and gene structures, and analyzed their collinearity and cis-acting elements in promoters. Presence Absence Variation (PAV) analysis revealed that certain WOX genes in the four Hordeum species were lost and expanded. Duplication analysis discovered five types of duplications contributing to the formation of WOX genes, with dispersed duplication (DSD) being the main type in four Hordeum species. WOXs belonging to DSD exhibited a high number of long terminal repeat retrotransposons (LTR-RTs), indicating the potential role of LTR-RTs in the formation of WOX genes of the DSD type. Evaluation of Ka/Ks values showed that all WOX genes have undergone purification selection, with varying degrees among different clades of WOX genes. Furthermore, through pan-transcriptome analysis and quantitative experiments, we identified a common gene clade and the WOX13 co-expression networks responding to saline stress. Survival ratio statistics of Arabidopsis thaliana complementation lines under salt treatment suggested that HvWOX13 may play a crucial role in regulating salt tolerance. These findings provide new insights into evolutionary studies of WOX gene family and offer valuable gene resources for breeding crops with enhanced salt stress resistance.

Tape-strip profiling identifies unique immune and lipid dysregulation in patients with seborrheic dermatitis

BACKGROUND

Seborrheic dermatitis (SD) is a common, chronic inflammatory skin disease with limited understanding of its pathophysiology. Molecular profiling has been limited by invasiveness of sampling methods.

OBJECTIVE

To analyze the molecular skin profile of adult patients with SD using tape strips.

METHODS

Tape-strips obtained from facial lesions of 26 adult SD patients and 18 demographically matched healthy controls were evaluated with RNA sequencing.

RESULTS

SD molecular skin fingerprint was characterized by strong and significant upregulation of interleukin (IL)23/T-helper (Th)17 and Th22 (i.e. IL23A, IL22, PI3, LL37, S100A8, S100A12), some Th1 skewing (OASL, STAT1, CXCL9), and limited Th2 modulation. A parallel downregulation of barrier markers (CLDN1/8, FA2H, ELOVL3) was also observed.

LIMITATIONS

Limited representation of mild and severe SD patients.

CONCLUSION

These data deepen our understanding of SD suggesting that it has robust Th17/Th22, some Th1 skewing, and minimal Th2 activation, and associated skin barrier alterations. This provides rationale for novel immunomodulatory treatment approaches for SD patients targeting IL23/Th17 and/or Th22 pathways.