title: Tumor cells with cholangiocytic phenotype form oncogenic niches with fibroblasts in hepatocellular carcinoma

city: Taipei City

first: Li-Wen

last: Chiou

address: Chung Shan S. Rd.

country: Taiwan

institute: National Taiwan University

summary: Background: A subset of hepatocellular carcinoma (HCC) exhibits cholangiocytic features associated with aggressive behavior, poor prognosis, and treatment resistance, but the underlying mechanisms remain unclear. We investigated the characteristics of duct-like (DL) tumor cells and their interactions with fibroblasts in HCC. Methods: Single-cell RNA sequencing data from 40 primary HCC samples were integrated to identify tumor subpopulations and signaling networks. Spatial transcriptomic datasets were analyzed to assess colocalization of DL cells and fibroblasts. Functional studies were performed using liver cancer cell lines cultured on collagen I or treated with cancer-associated fibroblast (CAF)-conditioned medium, followed by molecular analyses. Results: A distinct DL tumor cell population expressing cholangiocytic and stem-like markers was identified. DL cells showed activation of Wnt, MAPK, Notch, and Hippo pathways, whereas non-duct-like cells retained hepatocytic metabolic programs.   Fibroblasts preferentially interacted with DL cells through extracellular matrix ligands, especially collagens and fibronectin, binding integrins and syndecans. Spatial transcriptomics demonstrated close colocalization of DL cells and fibroblasts in regions with high oncogenic pathway activity. SPP1 emerged as a major mediator of DL-to-fibroblast signaling. In vitro, collagen I and CAF-conditioned medium promoted cholangiocytic features and suppressed hepatocytic differentiation. Conclusion: DL tumor cells form a reciprocal oncogenic niche with fibroblasts that promotes HCC progression and therapeutic resistance

overall_design: In this study, we applied single-cell RNA sequencing (scRNA-Seq) and spatial transcriptomics to comprehensively delineate the cellular composition, lineage trajectories, and intercellular signaling networks of HCC with cholangiocytic phenotype.

first: Liwen

first: Yulin

last: Jhuang

first: Zhongzhe

last: Lin

first: Chingyao

last: Yang

first: Yungming

last: Jeng


title: Epigenome and Chromatin Analyses Uncover SPATC1L-COL6A as a Novel Causal Locus in Childhood Obesity

status: Public on May 04 2026

city: L'Hospitalet

first: Josep

last: Jimenez-Chillaron

state: Barcelona

address: c/ Feixa Llarga s/n, Pavello de Govern, 4a planta, Biophysics Unit

department: Physiological Sciences

country: Spain

institute: University of Barcelona

type: Methylation profiling by genome tiling array

summary: Childhood obesity is a major public health challenge, that increases the risk of comorbidities such as type 2 diabetes and cardiovascular disease, which collectively reduce life expectancy. Epigenetic mechanisms have been proposed as contributors to obesity-related long-term metabolic dysfunction.  We performed DNA methylation profiling in whole blood from prepubertal children with obesity and normal weight controls, and identified 109 CpG sites associated with obesity. Two of these sites showed evidence of playing a causal role in mediating childhood obesity, as supported by two-sample Mendelian randomization test. Strikingly, both CpGs mapped within the same gene: Spermatogenesis and Centriole Associated 1 Like (SPATC1L). Further, we validated the causal CpGs in an independent clinical cohort. Together, these data suggest the SPATC1L locus might be a novel potential region playing a causal role on obesity development.   To functionally confirm causality, we performed CRISPR/Cas9-mediated editing of these CpG sites. Their modification downregulated SPATC1L and neighbouring collagen genes (COL6A1, COL6A2), previously implicated in childhood obesity, and promoted higher lipid accumulation and insulin resistance in vitro. Following CpG editing, activating histone marks (H3K27Ac, H3K4me3) were reduced at the promoters of these genes, suggesting that these CpG sites regulate their expression through chromatin-mediated mechanisms.  n summary, our study identifies the SPATC1L–COL locus as a novel causal region in childhood obesity and highlights mechanistic links between CpG methylation, histone modifications, deregulation of collagen gene expression, and metabolic dysfunction.

overall_design: We aimed to profile global DNA methylation profile in peripheral cells of prepubertal children with obesity and a group of age-matched lean controls. Specifically, the cohort (Barcelona, Spain) consisted of 38 pre-pubertal children (26 with obesity and 12 with normal weight) .

middle: C


title: RXRα Suppression Drives Hepatic Metabolic and Immune Dysfunction in Sepsis: Gene induction by BEX in Sham & CLP (8h)

city: Gent

first: Steven

last: Timmermans

address: Technologiepark 71

country: Belgium

institute: VIB-UGent

type: Expression profiling by high throughput sequencing

summary: Sepsis is a life-threatening condition where a dysregulated host response to infection causes organ dysfunction and the collapse of metabolic and immune functions. Here, we identify hepatocyte Retinoid X Receptor α (RXRα) as a central integrator of host resilience during polymicrobial sepsis. We show that hepatic Rxra expression is transcriptionally dependent on the upstream regulator Hepatocyte Nuclear Factor 4 α (HNF4α), and that sepsis rapidly suppresses RXRα abundance at both the mRNA and protein levels. Transcriptomic profiling further reveals that the septic liver develops partial resistance to pharmacological RXR activation by its agonist Bexarotene (Bex). Despite this, prophylactic treatment with Bex preserves metabolic stability, enhances bacterial clearance, and improves survival. Using hepatocyte-specific inducible RXRα-deficient mice (RXRαiAlbKO), we demonstrate that this protective effect is strictly dependent on hepatocyte RXRα. Mechanistically, the loss of RXRα in hepatocytes leads to a profound reduction in the liver-resident macrophage, Kupffer cells (KC), resulting in uncontrolled bacterial dissemination and increased mortality. This defect is phenocopied by selective KC depletion. These findings establish that hepatocyte RXRα is essential for maintaining the hepatic macrophage niche, thereby linking hepatocellular transcriptional competence to systemic antibacterial defense.

overall_design: RNA-seq expression profiling of male C57BL/6J mice 8 hours after CLP or sham, the mice were given either DMSO or Bexarotene 6h after the surgery and sampled 2 hours later for a total time of 8 hours. 3 biological replicates were used per condition

first: Matyas

last: Jelinek

first: Jolien

last: Vandewalle

first: Marah

last: Heyerick

first: Tineke

last: Vanderhaeghen

first: Céline

last: Van Dender

first: Madeleine

last: Hellemans

first: Daria

last: Fijalkowska

first: Martin

last: Guilliams

first: Karolien

last: De Bosscher

first: Claude

last: Libert


title: Ubiquitin-Proteasome System Dysregulation in Alzheimer's Disease Impacts Protein Abundance

city: Watertown

first: Mahlon

last: Collins

state: MA

address: 490 Arsenal Way Suite 110

country: USA

institute: Parallel Squared Technology Institute

summary: Alzheimer's disease (AD) is a relentlessly progressive, fatal neurodegenerative disorder that results in widespread protein dysfunctions.  However, the full extent of aberrant proteomic changes in AD and their impact on cellular physiology remains unknown.  This is, in part, because of the challenges of comprehensively measuring the proteome.  Here, we used plexDIA, an approach that provides deep proteomic coverage and high throughput by parallelizing the acquisition of peptides and samples, to characterize proteomic changes in AD. Using human dorsolateral prefrontal cortex tissue, we identified 281 differentially abundant proteins in AD.  By systematically analyzing compartment and protein complex-specific shifts in protein abundance, we identified an AD-specific decrease in levels of the 20S proteasome, the catalytic core of the cell's primary protein degradation pathway.  This alteration was accompanied by widespread decreases in proteasome subunit stoichiometries.  Many proteasome substrate proteins were negatively correlated with 20S levels and increased in AD, suggesting that reduced 20S levels leads to abnormal protein accumulation. By analyzing proteins increased in AD, we identify key properties of such proteins: They have fast degradation rates, they contain signal sequences that allow them to be targeted for proteasomal degradation, and they are targeted by quality control pathways that recognize mislocalized proteins.  Changes in these gene products at the protein and mRNA levels were highly discordant, providing additional evidence for increased protein abundance driven by impaired clearance.  We also identified coherent sets of ubiquitin system enzymes, proteins that target substrates for proteasomal degradation, whose levels robustly discriminate AD from non-AD samples.  One subset exhibited consistent increases in AD, while another, which contained the tau E3 ligase Cul5, exhibited consistent decreases, revealing complex changes in the ubiquitin system in AD.  Taken together, our results suggest that decreased ubiquitin-proteasome system capacity and impaired clearance of short-lived and mislocalized proteins contribute substantially to proteopathic burden in AD.

overall_design: RNA-seq of Brodmann area 9 of the dorsolateral prefrontal cortex in 24 samples spanning the Braak stages of AD progression.

first: Collins

last: Mahlon

first: Friedrich

last: Corinna

first: Elcheikhali

last: Megan

first: Stewart

last: Peyton

first: Derks

last: Jason

first: Connors-Stewart

last: Theresa

first: Altig

last: Kirstin

first: Melloni

last: Alexandra

first: Petelski

last: Aleksandra

first: Oakley

last: Derek

first: Hyman

last: Bradley

first: Slavov

last: Nikolai


title: Contrasting transcriptional responses and genetic determinants underlie Zymoseptoria tritici adaptation mechanisms to simulated host defense environments

city: Zurich

first: Cecile

last: Lorrain

state: Zurich

address: Universistätstrasse 2

department: Plant PAthology

country: Switzerland

institute: ETH Zurich

summary: Successful colonization of the wheat apoplast requires that Zymoseptoria tritici tolerate host-derived stresses, but the mechanisms underlying this adaptation remain poorly understood. We combined phenotypic assays, transcriptomics, and genome-wide association analyses to characterize fungal responses to acidic pH, salicylic acid, gibberellic acid, and oxidative stress. Exposure to salicylic acid inhibited in vitro growth across a global collection of 411 Z. tritici strains, whereas acidic pH promoted growth, illustrating contrasting effects on pathogen performance of environments simulating host-defense responses. At the transcriptional level, acidic pH and oxidative stress induced the strongest and most similar responses, while salicylic acid elicited a more distinct transcriptional program and gibberellic acid caused only limited transcriptional changes. Although the sets of differentially expressed genes were largely condition specific, overlapping enrichment of transport- and redox-related functions across conditions indicated shared transcriptional responses. K-mer based genome-wide association mapping identified five candidate loci associated with growth under acidic pH, gibberellic acid and salicylic acid, including four loci specific to a single growth condition. These loci colocalized with genes implicated in cell wall remodeling, nitrogen metabolite regulation, proteostasis, and ubiquitin-related processes. This study highlights the multifaceted strategies employed by Z. tritici to navigate environments simulating host-defense responses, involving shared and environment-specific adaptations. We provide new insights into the genetic and molecular basis of fungal resilience, with implications for understanding pathogen-host interactions.

overall_design: The pre-culture of the reference strain IPO323 (Goodwin et al. 2011) was prepared as previously described for plant defense response phenotyping. To assess the transcriptomic response, we prepared 25 mL spore suspensions (2.5 x 105 spores/mL) for each treatment, maintaining the same environmental conditions used for the phenotyping. These suspensions were incubated for 90 hours at 18°C in the dark, with three biological replicates per condition. For hydrogen peroxide, due to its rapid degradation, a spore suspension of the hydrogen peroxide treatment and another spore suspension for the control were prepared and incubated for only 15 hours at 18°C. After incubation, 2 mL of each spore suspension was transferred and centrifuged at approximately 9400 x g for 2 minutes to remove the media. The resulting spore pellets were immediately flash-frozen and stored at -80°C. Frozen samples were sent to Biomarker Technologies GmbH (BMKgene, Münster, Germany) for RNA extraction and sequencing. Sequencing was performed using Illumina NovaSeq X, with paired-end 150 bp reads.  Sequencing adapters and reads shorter than 50 bp were trimmed using Trimmomatic v.0.38 (Bolger et al. 2014) with the following parameters: ILLUMINACLIP:${adapters}:2:30:10 LEADING:15 TRAILING:15 SLIDINGWINDOW:5:15 MINLEN:50. The trimmed reads were aligned to the Z. tritici IPO323 transcriptome reference (Lapalu et al. 2023), and transcript abundances were quantified using Kallisto v0.46.1 (Bray et al. 2016) with default parameters for paired-end reads. Read counts were summarized using tximport v1.32.0 (Soneson et al. 2016). Differential gene expression analysis was conducted using the R package DESeq2 (Love et al. 2014). Principal component analysis (PCA) was performed on the DESeq2 r-log transformed normalized counts. Genes were considered differentially expressed if the adjusted p-value was < 0.05 and the log2 fold change was > 1.5 (upregulated) or < -1.5 (downregulated)(Love et al. 2014).

first: Silvia

last: Miñana-Posada

first: Alice

last: Feurtey

first: Bruce

middle: A

last: McDonald

first: Cécile


title: Functional reconstitution of adrenocortical transdifferentiation from human pluripotent stem cells

status: Public on May 05 2026

city: Philadelphia

first: Eoin

middle: Christopher

last: Whelan

state: PA

address: 3800 Spruce St

department: Biomedical Sciences

institute: University of Pennsylvania School of Veterinary Medicine

summary: Proper prenatal adrenal cortex development is essential to prevent life-threatening adrenal insufficiency. This process relies on self-renewing progenitor cells within a capsule (Cap)-derived niche of the definitive zone (DZ) and trans-differentiation into cortisol-producing transitional and androgen-producing fetal zones. However, species-specific limitations in rodent models hinder mechanistic insights. To address this, we developed a human iPSC-derived organoid system that mimics prenatal adrenal development. Our advanced platform efficiently generates DZ-like cells (DZLCs) and Cap-like cells (CapLCs), revealing that DZLCs arise from adrenal primordium-like cells (APLCs) and are sustained via CapLC-derived RSPO3/WNT signaling. These DZLCs trans-differentiate into transitional and fetal zone-like cells (FZLCs) through ACTH and RSPO3 signaling. Notably, NR0B1 loss impairs DZLC specification while driving direct APLC-to-FZLC conversion, recapitulating NR0B1 mutation-associated X-linked adrenal hypoplasia congenita. Notably, DZLCs encapsulated with CapLCs form ACTH-responsive, cortisol-producing cortical tissue in vivo, demonstrating therapeutic potential. These organoid models offer a powerful platform for adrenal research and lay the groundwork for cell-based therapies for adrenal insufficiency.

overall_design:
The experimental design for the single-cell RNA sequencing portion of this paper involved assaying the transcriptomes of prepubertal and adult adrenal cortical cells, along with capsular cells, isolating those cells and comparing them to iPSC-derived cortical cells (APLCs, DZLCs, TZLCs, FZLCs).

***************************************************************
Raw files for human/patient samples were not submitted to GEO due to concerns about submitting personally identifiable sequence data for open access.
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first: Michinori

last: Mayama

first: Takeshi

last: Sato

first: Adrian

middle: N

last: Leu

first: Jerome

middle: F

last: Strauss

first: Richard

middle: J

last: Auchus

first: Kotaro

last: Sasaki


title: RXRα Suppression Drives Hepatic Metabolic and Immune Dysfunction in Sepsis: RXRα KO in CLP/SHAM

first: Steven

last: Timmermans

overall_design: RNA-seq expression profiling of RXRα KO mice and WT littermates after CLP or SHAM. Livers ere sampled 24h after the CLP or SHAM surgery

first: Matyas

last: Jelinek

first: Jolien

last: Vandewalle

first: Marah

last: Heyerick

first: Tineke

last: Vanderhaeghen

first: Céline

last: Van Dender

first: Madeleine

last: Hellemans

first: Daria

last: Fijalkowska

first: Martin

last: Guilliams

first: Karolien

last: De Bosscher

first: Claude

last: Libert


title: Exploring the Mechanism of Rapamycin in Attenuating Renal Ischemia-Reperfusion Injury

city: Kunming

first: bo

last: yuan

address: No. 295 Xichang Road, Wuhua District

country: China

institute: The First Affiliated Hospital of Kunming Medical University

summary: To investigate the protective effect and mechanism of rapamycin on renal ischemia-reperfusion injury, we established rat models with sham, I/R, and rapamycin treatment.We then performed gene expression profiling analysis using RNA-seq data of kidney tissues from 3 groups of rats with 3 biological replicates each.

overall_design: Healthy male Sprague-Dawley rats were randomly divided into three groups: sham operation group, renal I/R model group, and rapamycin treatment group. I/R injury was induced by clamping the left renal artery for 45 minutes followed by reperfusion. Rapamycin was administered intraperitoneally at 1 mg/kg/day. After reperfusion, renal tissues were collected for total RNA extraction and transcriptome sequencing. Quality control, sequence alignment, gene quantification, and differential expression analysis were performed to screen key genes and pathways.

first: Bo

last: Yuan

first: Zhenlei

last: Fan

first: Caini

last: Liang

first: Yuntong

last: Jia

first: Qiang

last: Tang

first: Tao

last: Liu

first: Min

last: Zhang


title: Spatial and Bulk Transcriptomic Profiling Defines the Molecular Evolution of Cutaneous Squamous Cell Carcinoma and Reveals Stage-Specific Biomarkers of Clinical Relevance [GeoMx]

city: Bordeaux

first: Hamid-Reza

last: Rezvani

address: 2 Rue Dr Hoffmann Martinot

country: France

institute: Bordeaux Institute of Oncology (BRIC)

summary: Background: Cutaneous squamous cell carcinoma (cSCC) is among the most common skin cancers and can be associated with poor prognosis in aggressive cases, with a median overall survival of approximately two years. Despite its well-described stepwise progression from actinic keratosis to invasive disease, robust molecular markers that discriminate disease stages and inform clinical decision-making remain limited. Objectives: This study aimed to delineate progression continuum and stage-related transcriptional programs underlying cSCC evolution, identify candidate biomarkers for risk stratification and invasion, and assess the broader relevance of these molecular signatures across human cancers. Methods: We applied bulk RNA sequencing (HTG EdgeSeq) and spatial transcriptomics (GeoMx DSP) to profile skin biopsies from 8 patients recruited in collaboration with Bordeaux University Hospital. Importantly, each patient simultaneously presented four stages (healthy skin, pre-malignant lesion, tumor core, and invasive front) providing a unique framework to interrogate the full molecular trajectory of cSCC progression within individuals. Results: Spatial transcriptomic analyses identified more than 2,000 differentially expressed genes (adjusted p < 0.01) whose expression in squamous cells changed across disease stages. These genes were organized into 18 coordinated expression programs reflecting progressive biological rewiring during tumor evolution. Pathways related to cellular stress responses, proliferation, extracellular matrix remodeling, and inflammation were progressively upregulated, whereas differentiation programs and lipid and amino acid metabolism were consistently downregulated.  In contrast, peritumoral macrophages showed increased expression of genes involved in purine metabolism, glycolysis, and pyruvate metabolism across progression. To assess the broader clinical relevance of the progression-associated gene programs, we developed a Snakemake-based pipeline to systematically screen 32 solid and hematological malignancies from The Cancer Genome Atlas. This workflow is designed to be fully reproducible and readily extensible, enabling other researchers to perform similar progression and survival analyses across cancer types. Notably, we defined a cSCC-progression signature which significantly correlated with poor overall survival (p  < 0.05) in 10 additional cancer types. Furthermore , we last identified 12 cSCC stage-specific biomarkers, whose expression was confirmed to be stage-specific via Visium HD. Conclusions: Together, this study provides a spatially resolved and stage-aware transcriptomic map of cSCC progression, identifies coordinated gene programs underlying disease evolution, and defines progression-associated signatures with prognostic relevance across multiple cancers, highlighting their potential clinical utility.

overall_design: GeoMx Digital Spatial Profiler (spatial transcriptomics) profiling of 3 patients bearing cutaneous squamous cell carcinoma tumors. Each patient has been biopsied for the invasive front, tumor, actinic keratosis/in situ lesion, peritumoral area, and healthy skin. Captured areas were divided based on GeoMx staining for CD68 (macrophages), PanCK (squamous cells) and VIM+PanCK (tumor invasive front).

first: Sergio

last: Oterino-Sogo

first: Fatima

last: Naji

first: Jean-Philippe

last: Guegan

first: Marie

last: Beylot-Barry

first: Léa

last: Dousset

first: Macha

last: Nikolski

last: Redvani


title: NOVEL HEXOKINASE-2 ASSOCIATED INFLAMMATORY PROCESSES IN THE GLIOBLASTOMA TUMOUR MICROENVIRONMENT

city: Wolverhampton

first: Christopher

last: Edwards

address: Wulfruna Street

country: United Kingdom

institute: University of Wolverhampton

summary: Deregulation of cellular metabolism is a hallmark of cancer, in which tumour cells upregulate glycolysis and preferentially ferment glucose to lactate (rather than pyruvate) in the 'Warburg effect'. Tumour-specific upregulation of hexokinase 2 (HK2), which catalyses the first rate-limiting step of glycolysis, has been established as key to this Warburg metabolism. Interrogating the impact of HK2 expression inhibition upon the glioblastoma transcriptome has the potential to uncover a number of novel canonical/non-canonical relationships that could serve as future co-therapeutic targets. To investigate this, we employed RNAseq to compare the expression profiles of glioblastoma cell cultures transfected with either HK2-targeted or non-targeting negative-control siRNA, thereby identifying genes differentially expressed specifically following HK2KD. Gene ontology category enrichment (GOSeq, Enrichment map) and STRING protein-protein interaction analysis of genes identified to be differentially expressed post HK2 knockdown (HK2KD) highlighted potential non-canonical roles for HK2 in regulating inflammatory, immune and angiogenesis-related processes within the glioblastoma tumour microenvironment.

overall_design: RNAseq profiling of glioblastoma cell lines (U87-MG) and glioblastoma patient derived cell cultures (IN859, IN2045) that received HK2KD or non-targeting negative control.

first: Edwards

last: Christopher

first: Taylor

last: Richards

first: Katherine

last: Karakoula


title: Ketogenic regulation of histone modification by CDK4 promotes leukemogenesis [ChIP-seq]

city: Wuhan

first: Jin

last: Xu

address: 115 East Lake Road, Wuhan, Hubei, 430071, P. R. China

institute: Wuhan university

type: Genome binding/occupancy profiling by high throughput sequencing

summary: While ketogenic nutrition shows promise as an adjunct to conventional cancer therapies, its efficacy varies depending on the type of cancer and its specific metabolic characteristics. How ketone bodies affect tumorigenesis and how the ketogenic pathway becomes deregulated in cancer remain to be fully understood. Using T-cell acute lymphoblastic leukemia (T-ALL) as a model, we here demonstrate that ketogenic metabolite β-hydroxybutyrate (BHB) plays a remarkable pro-leukemogenic role in mice. T-ALL cells generally exhibited greater expression of β-hydroxybutyrate dehydrogenase (BDH1), the metabolic enzyme that leads to cell autonomous synthesis of BHB. Mechanistically, aberrant CDK4 activation enables direct phosphorylation of BDH1 at the serine 296 residue and enhances its protein stability. Importantly, BDH1 deficiency leads to robust growth inhibition and cell death of human T-ALL cells, and markedly impedes NOTCH1-induced T-ALL progression in mice. BDH1-mediated production of BHB enhances the histone modification of β-hydroxybutyrylation (Kbhb), thereby leading to transcriptional activation of pro-leukemogenic genes MYC and NKX3.1. These findings shed light on how oncogenic CDK4 deregulates ketogenesis and promotes leukemia progression via an epigenetic mechanism. Therefore, ketogenic diets or ketone supplements should be taken with caution by cancer patients. Therapeutic interventions targeting key ketogenic enzymes may hold great promise for leukemia treatment.

overall_design: Fragmentation of the genome of Jurkat was achieved using ultrasonication, followed by immunoprecipitation with H3K9bhb and H3K9ac antibodies

first: Guoliang

last: Qing

first: Hudan


title: Trajectories of maternal epigenetic aging measures across pregnancy and postpartum

city: University Park

first: Laura

last: Etzel

address: Health and Human Development Building

institute: Penn State

summary: Pregnancy has been proposed as a biological “stress test” that may transiently accelerate maternal biological aging, followed by partial recovery in the postpartum period; however, longitudinal evidence characterizing these trajectories remains limited. This longitudinal study followed 130 women across mid to late pregnancy, early postpartum (6–9 months), and later postpartum (36–43 months) to characterize nonlinear changes in multiple markers of biological aging. Biological aging was assessed using complementary indicators, including telomere length, DNA methylation–based epigenetic aging measures, and pace-of-aging metrics. Genome-wide DNA methylation data were generated from maternal biospecimens using the Illumina Infinium MethylationEPIC v2.0 BeadChip to support derivation of epigenetic aging measures and evaluation of longitudinal methylation dynamics. Generalized additive mixed models were used to examine within-person changes over time. Results indicated relative stability or slowing of biological aging during early postpartum, followed by marker-specific patterns of stabilization or decline during later postpartum. Subsequent pregnancy during the later postpartum period was associated with shorter telomere length and altered recovery trajectories, including accelerated pace of aging among women who became pregnant again. Together, these findings suggest that while partial recovery of biological aging markers may occur following pregnancy, such recovery may be sensitive to additional reproductive demands. The DNA methylation data deposited here support longitudinal analyses of maternal biological aging across pregnancy and postpartum and provide a resource for future studies examining reproductive influences on epigenetic aging processes. Additional study data available via figshare at: https://doi.org/10.6084/m9.figshare.30005287

overall_design: This submission includes longitudinal maternal saliva-derived DNA samples collected from women followed across pregnancy and the postpartum period. Samples were obtained at up to three time points per participant: mid to late pregnancy, early postpartum (approximately 6–9 months after delivery), and later postpartum (approximately 36–43 months after delivery). The dataset enables comparison of DNA methylation patterns and derived epigenetic aging measures across time points within individuals, as well as between individuals who did and did not experience a subsequent pregnancy during follow-up. No experimental manipulation was performed; all samples were collected observationally under naturalistic conditions. Raw Illumina IDAT files were imported into R using the Bioconductor package minfi. Detection p-values were calculated from raw red and green channel intensities using minfi::detectionP. Background correction and normalization were performed using Illumina’s control-based method as implemented in minfi::preprocessIllumina (background correction enabled, control normalization). Processed beta values (proportion methylated) were extracted using minfi::getBeta.  The processed data table was generated containing, for each probe (ID_REF), the processed beta value and the corresponding detection p-value for each sample.

first: Idan

last: Shalev

first: Patricia

last: Garrett-Peters


title: Cetuximab or panituximab differentially impact miRNA expression and potential signaling pathway in cancer colon HCT116 or HT29 cells in vitro

city: Tours

first: FREDERIC

last: PICOU

address: 10 blvd Tonnelle

department: Hematology

institute: CHU de Tours

type: Non-coding RNA profiling by high throughput sequencing

summary: Aiming to understaned resistance to monocolonal antibodies (Cetuximab, Ctx or Panituximab, Pani) in colon cancer cells, miRNA were studies in both HT29 cells(B-RAF mutated, moderattely-sensitive to Ctx) and HCT116 (K-RAS mutated, highly resistant to Ctx)

overall_design: HCT116 or HT29 colon cancer cells model are exposed to 10 or 100µg/ml of Cituximab or Panituximab for 48 hours in vitro. MiRNA expression were quantified by NGS (IlluminaNextSeq550).

first: laetitia

last: Corset

first: Frederic

last: Picou

first: Frauke

last: Beilstein

first: Sadija

last: Ibrahim

first: Romain

last: Chautard

first: William

last: Raoul


title: Tcf21 deletion from podocyte precursors as a model for congenital nephrotic syndrome

city: Chicago

first: Yalu

last: Zhou

state: IL

address: 303 E Superior St

department: Department of Medicine

institute: Northwestern University

summary: Here, we establish a mouse model of congenital nephrotic syndrome (NS) by genetic deletion of transcription factor 21 (Tcf21), a gene required for normal podocyte development, selectively from early podocyte precursors. Single cell transcriptomics of kidneys from these mice capture glomerular and tubulointerstitial changes that occur early in the course of NS and provide additional insights into: 1) the regulation of podocyte development and function by TCF21, 2) the effects of podocyte injury on other glomerular cells, and 3) the tubulointerstitial changes that occur in response to the glomerular dysfunction and associated massive proteinuria of podocytopathies.

overall_design: Tcf21 was deleted specifically from podocyte precursors via a Pax8 driven Cre recombinase. 2 male mice without Tcf21 expression in podocytes (Tcf21-KO mice) along with 2 control male mice (1 Cre positive control and 1 Cre negative control) were euthanized between 2-3 weeks of age and kidneys were harvested and digested into a single cell suspension for scRNAseq.

first: Vidhi

last: Dalal

first: Susan

last: Quaggin


title: Myeloid-derived WNTs impairs anti-tumor immune responses in pancreatic cancer

city: Seoul

first: Yi Rang

address: 101 Daehak-ro, Jongno-gu

country: South Korea

institute: Seoul National University Hospital

summary: We performed single-cell RNA sequencing on tumor-infiltrating cells isolated from orthotopic KPC pancreatic tumors at day 21 post-implantation. The objective was to determine how macrophage-specific ablation of WNT secretion (Csf1r-Cre;Porcnfl/fl) reshapes the PDAC immune microenvironment.

overall_design: At day 21 after orthotopic implantation of KPC pancreatic cancer cells, KPC tumors were harvested from Csf1r-Cre;Porcnfl/fl (macrophage-specific Porcn knockout) mice and littermate control mice. Tumors were dissociated into single-cell suspensions, and live cells were processed for single-cell RNA sequencing (scRNA-seq) to profile transcriptional changes across the entire tumor microenvironment associated with abrogation of myeloid WNT secretion. Libraries were prepared using the Chromium Next GEM Single Cell 3′ RNA kit v3.1 (10x Genomics) and sequenced on an Illumina NovaSeq 6000.

first: Na Hyun

last: Kim

first: Young Min

last: Song

first: San Sung

last: Kwon

first: Sang Hyub

last: Lee

first: Eun Na

first: Seung Hyeok

last: Seok


title: Multimodal profiling of Her2/neu-specific TCR-T cells reveals clonotype-dependent activation programs underlying differential cytotoxic efficacy

city: Yerevan

first: Roman

middle: Yurievich

last: Perik-Zavodskii

state: Yerevan

address: Khorenatsi 1

department: Research and Development

country: Armenia

institute: PerikLab

summary: Adoptive T cell therapy targeting tumor-associated antigens offers a promising avenue for cancer immunotherapy, yet the mechanisms underlying functional heterogeneity among T cell receptors (TCR) recognizing the same antigen remain poorly understood. Here, we comprehensively profile three Her2/neu-specific TCR constructs using integrated multimodal analysis that combines cytotoxicity assays, single-cell multiomics, bulk transcriptomics, cytokine profiling, and in vivo tumor modeling. Despite identical antigen specificity, the constructs exhibit a functional hierarchy: Construct #3 displays potent cytotoxicity in vitro and potent tumor regression in vivo, whereas Constructs #1 and #2 were less effective. Single-cell proteotranscriptomic analysis shows that tumor cell encounter drives activation of cytotoxic CD8⁺ T effector cells and transdifferentiation of NKT cells into APC-like cells. Interactomics also revealed high communication probability between APC-like NKT cells and CD4⁺ T cells, potentially forming a cooperative activation network that sustains effector function. Bulk transcriptomic and secretomic profiling showed that Construct #3 couples cytolytic gene expression with the secretion of anti-tumor cytokines and effector molecules. Together, these findings establish a mechanistic link between anti-Her2/neu TCR-driven transcriptional programming and therapeutic efficacy, illustrating how multi-omic approaches can inform the rational design of potent TCR therapies for solid tumors.

overall_design: Peripheral blood CD3+ T cells from healthy HLA-A*02:01 donors were isolated and activated ex vivo. Cells were transduced with lentiviral vectors encoding for Her2/neu-specific TCRs or kept non-transduced. After co-culture with Her2/neu-expressing tumor cells for 20 hours, TCR T-cells and non-trancduced T-cells were stained with SampleTag and AbSeq antibodies and processed using the BD Rhapsody single-cell workflow.

first: Saleh

last: Alrhmoun

first: Olga

last: Perik-Zavodskaia


title: Murine splenic CD45+ Erythroid cells display transcriptomic signatures of antigen-presenting cells

summary: We performed single-cell RNA sequencing using the BD Rhapsody platform to profile CD45+ cell from murine spleen.

overall_design: Spleen mononuclear cells were isolated from intact mice by tissue disaggregation and Ficoll density gradient centrifugation. CD45+ cells were isolated from the spleen mononuclear cells using CD45 magnetic sorting. The resulting cells were then loaded into a BD Rhapsody Express.


title: Sphingosine Kinase-2 Inhibition Increases Acetyl-CoA Carboxylase Activity and Phosphatidylcholine Levels to Program Immunogenicity in Myeloid-Derived Suppressor Cells [ATAC-seq]

city: Charleston

first: Vamsi

last: Gangaraju

address: 173 Ashley Ave

institute: Medical University of South Carolina

summary: Myeloid-derived suppressor cells (MDSCs) in the tumor microenvironment (TME) are a major barrier to adoptive T cell therapy, underscoring the need to enhance T cell efficacy by overcoming immunosuppression. Here, we investigated how sphingosine-1-phosphate (S1P), an abundant signaling lipid in the TME, regulates the programming and function of MDSCs. We show that inhibition of sphingosine kinase-2 (SphK2), which generates S1P in MDSCs, reduces their suppressive activity and enhances antigen presentation. Pharmacological inhibition of SphK2 improved the response to anti-PD1 therapy in preclinical models of checkpoint-resistant breast, bladder, and melanoma cancers by mitigating MDSCmediated suppression, thereby limiting tumor progression. Mechanistically, S1P directly interacts with Acetyl-CoA Carboxylase 1 (ACC1) to inhibit its activity, altering fatty acid and glycolytic pathways. Lowering intracellular S1P restores ACC activity and promotes phosphatidylcholine synthesis, reducing the immunosuppressive phenotype of MDSCs. These findings highlight the SphK2/ACC/phospholipid axis as a promising therapeutic target in cancer immunotherapy.

overall_design: We performed assay for transposase-accessible chromatin using sequencing (ATAC-seq) as described previously (PMID: 35454405) with modification as described below. EL4 tumor cells were injected into WT and Sphk2 KO mice. After 14 days, tumor-derived MDSCs (FACS-sorted Gr1+CD11b+ cells from ascitic fluid) were collected from WT and Sphk2 KO mice and used for making ATAC-seq libraries. We used 2 x 10^4 MDSCs and modified the concentration of the Tn5 enzyme for the transposase reaction. ATAC-seq libraries with 40% of the recommended Tn5 per reaction were prepared as described before (PMID: 35454405).

first: Paramita

last: Chakraborty

first: Shikhar

last: Mehrotra


title: Probing RNA-protein interactions in the early embryo

city: Worcester

first: Oliver

last: Rando

address: 364 Plantation St.

department: BMB

institute: UMass Chan Medical School

summary: The union of two germ cells to form a zygote, and subsequent early embryo development, are marked by radical remodeling of virtually every major class of biomolecules as the specialized germline states give way to the rapid and active growth that marks early development. In recent years, advances in ultra-low input genome-wide methods have enabled systematic analyses of mRNA abundance, and of chromatin organization, throughout early development in a variety of model systems. Here, we extend these efforts to the study of RNA binding protein (RBP) function in early mouse embryos, adapting REMORA based on fusing an RNA-editing enzyme to an RBP of interest – for use in early embryos. We benchmark our approach for several well-studied RBPs, successfully recovering expected features of their RNA cargos, and overall surveyed the RNA cargos for 17 RBPs of interest for early gene regulation. Analysis of changes in mRNA metabolism following knockdowns of the RBPs surveyed here allowed us to define direct regulatory functions for a subset of RBPs in the early mammalian embryo, including an unanticipated role for the RNA export factor Alyref in control of 3’ polyadenylation sites. Together, our data provide a proof of concept resource for systematically exploring RBP functions in mammalian embryogenesis.

overall_design: Smart-seq3 RNA sequencing of 2-cell and 4-cell stage mouse embryos, with A-to-I RNA editing or siRNA mediated gene knockdown, mRNA and/or siRNA microinjected into zygotes.

first: Bora

last: Pablo

first: Rando

last: Oliver


title: Transcriptome and Hormone Regulations Shape Drought Stress-Dependent Fusarium Head Blight Susceptibility in Different Barley Genotypes

city: Freising

first: Ralph

last: Hückelhoven

address: Emil-Ramann-Str. 2

department: Chair of Phytopathology

country: Germany

institute: Technische Universität München

summary: This dataset comprises 3'RNAseq data from a greenhouse experiment investigating the transcriptional responses of four spring barley genotypes (Avalon, Barke, Morex, and Palmella Blue) to Fusarium culmorum infection and drought stress. Plants were grown under controlled conditions and subjected to four treatment combinations: watered + mock (WM), watered + Fusarium (WFc), drought + mock (DM), and drought + Fusarium (DFc). Samples were collected at 4 and 7 days post-inoculation (dpi) from spikes and used for RNA extraction.

overall_design: RNA was extracted from barley spikes collected at  4 and 7 days post-inoculation (dpi) from four spring barley genotypes (Hordeum vulgare: Avalon, Barke, Morex, and Palmella Blue) under four treatment conditions: watered + mock (WM), watered + Fusarium culmorum (WFc), drought + mock (DM), and drought + Fusarium culmorum (DFc). Each sample represents a pool of four spikes from different pots, with four biological replicates per condition and time point. The experiment was designed to investigate the interaction between drought stress and Fusarium culmorum infection in barley, focusing on genotype-specific transcriptional responses. Plants were spray-infected with a Fusarium culmorum spore solution or mock-treated with water, and covered with plastic bags for 48 hours to ensure high humidity and promote successful infection. RNA was extracted from flash-frozen spike tissue and used for transcriptome profiling via RNA sequencing.

first: Sophia

last: Hein

first: Felix

last: Hoheneder

first: Christina

middle: E

last: Steidele

first: Christine

last: Wurmser


title: TRMT5/NES Coordinated Activity Drives Pancreatic Cancer Growth and Metastasis [Ribo-seq]

city: Cambridge

first: Francisco

middle: Jose

last: Campos-Laborie

address: Tennis Court Rd

department: The Gurdon Institute

institute: University of Cambridge

summary: Pancreatic cancer is a disease of urgent unmet clinical need with a 94% death rate, predicted to become the second leading cause of cancer-related death by 2030. Despite increased efforts, effective therapies have not materialised. Here, we uncover a new molecular pathway underpinning pancreatic carcinogenesis, involving TRMT5, an RNA m1G methyltransferase. We show that TRMT5 is overexpressed in primary pancreatic adenocarcinomas (PDACs), and its expression is associated with worse patient survival. High levels of TRMT5 expression positively correlate with the tumorigenic capacity of pancreatic cell lines and of human pancreatic cancer organoids. Using an unbiased multiple screening approach, we identify a new axis involving TRMT5 and Nestin (NES) in pancreatic cancer and define NES mRNA as a substrate of TRMT5. We demonstrate that NES expression, a key cancer regulator, rescues the growth defect of TRMT5 depleted PDAC cells. We pinpoint a site of TRMT5-mediated m1G modification to a G-quadruplex structure within the protein coding region of NES mRNA. Functionally, m1G destabilizes the G-quadruplex structure to promote translation of NES. Finally, we demonstrate that TRMT5 is essential for the metastatic capacity of PDAC cells, significantly promotes the growth of patient-derived PDAC organoids and increases the survival rate of PDAC patient-derived xenografts. Our findings establish the TRMT5/NES axis as a new vulnerability in PDAC and they provide the foundation for innovative combinatorial clinical approaches, targeting an RNA-modification pathway in pancreatic cancer.

overall_design: To further explore the role of TRMT5-dependent m1G in mRNA, and identify mRNAs translationally regulated by TRMT5, we performed ribosome profiling followed by deep sequencing (Ribo-seq) of RNA from control and TRMT5 depleted (for 4 days) PANC-1 cells. This dataset includes paired samples, such as input RNA and ribo-protected fragments samples from the same replicate (e.g., replicate 1 and 2).

first: Carlos

last: Melo


title: Native long-read RNA sequencing of human monocytes reveals activation-induced alternative splicing toward functional isoforms

city: Utrecht

first: Jorg

last: van Loosdregt

address: Lundlaan 6

country: Netherlands

institute: UMC Utrecht

summary: Alternative splicing is a key mechanism for expanding transcriptomic and proteomic complexity, yet its role in innate immune activation remains incompletely understood. Here, we applied Oxford Nanopore native RNA sequencing to generate an isoform-level transcriptome of primary human monocytes before and after activation with lipopolysaccharide (LPS). We identify over 24,000 expressed isoforms, including thousands of previously unannotated variants. Activation with LPS induced widespread isoform-specific expression changes, leading to extensive isoform switching events, which were validated using matched short-read RNA-Seq. These activation-induced shifts enhanced transcript immune-regulatory functions: activated monocytes preferentially express longer, coding-competent isoforms with complete open reading frames, fewer retained introns, and increased domain complexity. By integrating matched Ribo-seq and proteomic data, we demonstrate that these isoform modulations are associated with enhanced translation of immune effector proteins. Together, our findings position alternative splicing as a dynamic and functional regulator of monocyte activation, emphasizing the need for isoform-level resolution to fully understand immune cell function and inflammation.

overall_design: Short-read bulk RNA-Seq data of monocytes from 8 healthy volunteers and nanopore native long-read RNA-Seq data of monocytes from 3 healthy volunteers in two different conditions: ex vivo and 3h in vitro LPS stimulation.


title: A Conserved NLRC5 Signaling Pathway in Developing Human Cortical Neurons is Required for Interferon Gamma Driven Changes in HLA Class I Expression and Neural Activity

city: Stanford

first: Michelle

middle: Katherine

last: Drews

state: CALIFORNIA

address: 318 Campus Drive, W150

department: Biology

institute: Stanford University

summary: Maternal infection and inflammation are linked to increased risk of neurodevelopmental disorders. Here we show that MHC Class I molecules (human: HLA I), which play key roles in brain development, are expressed in neurons in human cortical organoids (hCOs) and human cerebral cortex. These HLA I molecules are significantly upregulated by interferon gamma (IFNg) exposure. Inflammatory mediators downstream of IFNg, including the HLA I enhancer NLRC5, are mechanistically implicated in this upregulation by RNA sequencing IsHhHHLA. NLRC5 KO hCOs fail to undergo developmental increases in neuronal HLA I expression, as well as IFNg-driven HLA I upregulation. Functionally, IFNg exposure lowers spontaneous neural activity in hCOs, which is prevented in NLRC5 KO.  These observations link IFNg to human neuronal HLA I expression via NLRC5 and demonstrate a functional consequence on spontaneous activity in a developing neural circuit.  Changes in levels and patterns of neural activity associated with elevated HLA I may contribute to the increased risk of altered cortical development and suggest that targeting NLRC5 could mitigate consequences of neuroinflammation.

overall_design: Bulk RNAseq analysis of RNA extracted from day 250 human cortical organoids from two lines (Line C and Line D) from 3 independent differentiations after being treated with 48 hours of 100 ng/mL interferon gamma or an equivalent volume of 0.1% BSA control in PBS.

middle: K

first: Jimena

last: Andersen

first: Ji-il

last: Kim

first: Melissa

last: Stafford

first: Anca

middle: M

last: Pasca

first: Sergiu

middle: P

first: Carla

last: Shatz


title: Analysis of mouse livers fed with high cholesterol diet and alcohol by spatial transcriptomics

city: Kansas City

first: Irina

last: Tikhanovich

state: Kansas

address: 3901 Rainbow blvd

institute: University of Kansas Medical Center

summary: Background & Aims: Alcohol-associated liver disease (ALD) heavily contributes to global alcohol related mortality. Alcohol can synergize with other causes of liver disease such as metabolic syndrome induced by western diet (high fat, high fructose, high cholesterol). However, the role of individual western diet components in ALD development is not fully understood. We aimed to study the role of cholesterol in alcohol pathogenesis. Previous studies have shown that hepatic cholesterol metabolism is dysregulated with alcohol use resulting in altered lipoprotein levels. We aimed to study the role of cholesterol in ALD development using a mouse model.  Approach and results: 8-week-old male mice were fed ad libitum with low fat high cholesterol diet (Research Diets, cat# D24120501, 1% cholesterol) in combination with 20% EtOH in the drinking water for 10 weeks. Compared to high-cholesterol diet alone, alcohol treated mice showed elevated levels of serum ALT and AST, INR/PT, increased liver inflammation, fibrosis, ductular reaction and signs of liver failure such as reduced HNF4α and albumin production.  To assess the mechanism of alcohol-induced pathology, we performed spatial transcriptomic analysis using 5k gene Xenium panel (10x Genomics). We found that the liver adapted to high cholesterol diet by increasing cholesterol metabolism in hepatocytes. In contrast, alcohol impaired liver adaptation to high cholesterol diet by reducing cholesterol metabolism, HDL production, and hepatic cholesterol secretion, thus driving inflammation and fibrosis. Hepatocyte specific Kdm5b knockout mice were partially protected from alcohol effects by restoring cholesterol secretion in part through an upregulation of Abcg8. Accordingly, these mice were protected against alcohol-induced fibrosis development and inflammation.  Conclusion: In summary, alcohol impairs liver adaptation to high cholesterol diet. Increasing liver cholesterol secretion by KDM5B inhibition protects liver from ALD development.

overall_design: Mice were fed high cholesterol diet  and 20% alcohol in the drinking water. Kdm5b floxed mice received AAV-control, AAV-TBG-Cre or AAV-Krt19-Cre at the begining of alcohol feeding. Liver samples from one mouse in each group were  analyzed on the same Xenium slide.

first: Michael

last: Schonfeld


title: Histone Demethylase KDM6B Promotes Postnatal Oligodendrocyte Development and Cortical Myelination

city: East Lansing

first: Jin

last: He

state: Michigan

address: 603 Wilson Road, Biochem Bldg. Rm. 410

institute: Michigan State Univeristy

summary: Myelination in the postnatal cortex requires epigenetic programs that activate oligodendrocyte gene networks. Here we show that the histone H3K27me3 demethylase KDM6B promotes this process in vivo. Conditional Kdm6b deletion (Kdm6b-cKO) in Emx1⁺ dorsal telencephalic progenitors caused delayed cortical myelination. Lineage-specific RNA-seq revealed that the oligodendrocyte master regulator Sox10 was significantly reduced, as well as myelination effectors, indicating impaired oligodendrocyte maturation. Chromatin immunoprecipitation assays of the same lineage showed increased H3K27me3 at promoter-proximal regions of Sox10, consistent with loss of KDM6B-mediated de-repression. Temporally controlled Sox10 induction partially rescued myelination in Kdm6b-cKO mice. These findings define a KDM6B→SOX10 axis that licenses oligodendrocyte development and cortical myelination by removing repressive H3K27me3 and sustaining active chromatin, with implications for KDM6B-related neurodevelopmental disorders.

overall_design: Examination of differential gene expression between wild-type and Kdm6b-deleted cortical neural cells derived from Emx1⁺ progenitors


title: Paracrine Signals from HIV-1 Infected Immune Cells Reprogram Cervical Cancer Pathways

city: Accra

first: Charles

middle: Ochieng'

last: Olwal

address: WACCBIP, Volta Road, University Of Ghana

department: Department of Biochemistry, Cell and Molecular Biology

country: Ghana

institute: West African Centre for Cell Biology of Infectious Pathogens

summary: Persistent infection with human papillomavirus (HPV) is the primary cause of cervical cancer worldwide. Notably, women co-infected with HPV and human immunodeficiency virus type 1 (HIV-1) have a six-fold higher lifetime risk of developing cervical cancer compared to those without HIV, even when adhering to antiretroviral therapy (ART) and achieving T-cell reconstitution. While chronic HIV-1 infection is known to cause inflammation, how paracrine signals from immune cells alter signaling in cervical cells remain poorly understood. To address this, we conducted global transcriptomics analysis on cervical swabs from Kenyan women with HPV, stratified by HIV-1 and cancer status. Strikingly, women with HIV-1 showed cancer-like gene expression patterns in non-cancerous cervical epithelial cells. Complementary global mass spectrometry (MS) proteomics of cervical cells exposed to the secretome of HIV-1–infected primary CD4+ T-cells revealed altered expression of proteins in MAPK, PI3K-AKT, and β-catenin signaling pathways. Integrative network analyses of transcriptomic and proteomic datasets revealed that HIV-1 altered gene expression in key pathways known to drive cervical cancer, including genes commonly mutated in HIV-1-naïve disease. Notably, IRS-1, a key PI3K-AKT pathway activator, was found to be consistently upregulated in both participant samples and cell culture models, as were interferon-stimulated genes. Phosphoproteomics MS analysis confirmed PI3K-AKT pathway activation in cervical cells exposed to conditioned media from HIV-1-infected T-cells. Together, our findings uncover how HIV-1 reshapes cervical cell signaling via paracrine mechanisms and highlights the PI3K pathway as a potential therapeutic target in HIV-associated cervical cancer.

overall_design: RNA-seq profiling of cervical samples from HIV-infected and HIV-uninfected Kenyan women who have normal cervix, precancerous cervical lesions or invasive cervical carcinoma

middle: O

first: Ujjwal

last: Rathore

first: Sara

last: Makanani

first: Prashant

last: Kaushal

first: Immy

last: Ashley

first: Manisha

middle: R

last: Ummadi

first: Vincent

last: Appiah

first: Alexandra

middle: L

last: DjomkamZune

first: Sophie

last: Blanc

first: Declan

last: Winters

first: Yennifer

last: Delgado

first: Kapten

last: Muthoka

first: Jacqueline

last: Fabius

first: Manon

last: Eckhardt

first: Robyn

last: Kaake

first: Maureen

last: Su

first: Oliver

last: Fregoso

first: Judd

last: Hultquist

first: Elkanah

last: Orang’o

first: Danielle

last: Swaney

first: George

last: Boateng

first: Nevan

last: Krogan

first: Peter

last: Quashie

first: Yaw

last: Bediako

first: Mehdi

last: Bouhaddou


title: TRMT5/NES Coordinated Activity Drives Pancreatic Cancer Growth and Metastasis [RIP-seq II]

first: Francisco

last: Campos-Laborie

overall_design: To identify potential m1G containing mRNAs that may contribute to the observed early cellular effects, we performed meRIP experiments, followed by deep sequencing of polyA+ enriched RNA isolated from control and TRMT5 depleted (for 4 days) PANC-1 cells. To gain depth, this experiment was repeated with different number of replicates per experiment and per condition.

first: Carlos

last: Melo


title: Transcriptomic profiling of cancer-associated fibroblasts (CAFs)/activated-hepatic stellate cells (HSCs) of murine cholangiocarcinoma (CCA) by NanoString GeoMX DSP.

city: Austin

first: Ningling

last: Kang

state: Minnesota

address: 801 16th AVE NE

department: tumor microenvironment and metastasis

institute: the Hormel Institute

summary: To study whether targeting Cd274/PD-L1 of HSCs by Cre/loxP approach in mice altered HSC transcriptome, HSC activation into CAFs, CCA/HSC interactions, and CCA growth, portal vein injection of SB mouse CCA cells (1 million cells per mouse) was performed on two months old Cd274+/+Col1A1Cre mice and two months old Cd274F/FCol1A1Cre mice. Murine CCA sections were prepared for transcriptomic profiling with the NanoString GeoMix DSP

overall_design: Cryo-sections of murine CCA were fixed with formalin, hybridized with the NanoString mouse whole transcriptome atlas, followed  by immunofluorescence staining with anti-desmin to label CAFs/activated-HSCs, anti-CD45 to label Immune cells, and SYTO3 staining for cell nuclei. Regions of Interest (ROIs) were selected for data requisition and analysis. Desmin+ CD45- cells in each ROI (CAFs) were collected for transcriptomic profiling. AOIs 14, 15, 16 were selected from CCA of Cd274+/+Col1A1Cre mice and AOIs 11, 12, 13 were selected from CCA of Cd274F/FCol1A1Cre mice. 12 sequencing data were generated for the CAFs of murine CCA due to dual_indexing primers_based sequencing.

first: Kang

last: Ningling

first: Bai

last: Bing


title: Gene expression profiling of human DLD-1 cells after instant depletion of TREX2 subunits

city: Bethesda

first: Caroline

last: Esnault

state: md

address: 9000 Rockville Pike,

institute: NICHD NIH

summary: We used the RNA-sequencing approach to distinguish the roles of TREX2 subunits in transcription, mRNA processing and RNA export. AID-mediated depletion of TREX2 subunits caused rapid changes in transcriptomic profiles and alternatively shaped cells’ transcriptomes. The transcriptomic changes associated with GANP and PCID2 loss appeared closely related. Meanwhile, the loss of ENY2 produced a distinctly different transcriptomic profile compared to the loss of GANP and PCID2. The loss of CETNs had minimal impact on the cell transcriptome.

overall_design: We performed high throughput RNA sequencing on human DLD-1 cell line where we specifically depleted GANP, PCID2, ENY2, CETN2, CETN2/3, SAC3D1, and LENG8 using Auxin-Inducible Degron system.

first: Vasilisa

last: Aksenova

first: James

last: Iben

first: Tianwei

last: Li

first: Mary

last: Dasso


title: RNA-seq in aortic smooth muscle cells from a mice lacking Arg1 expression in erytrhrocytes (RBC.ARG1-KO) and their litter mate controls (RBC.ARG1-WT) after culture in standard DMEM or foam cell medium (DIAM)

first: Franziska

last: Greulich

address: Gregor-Mendel-Str. 2

department: Metabolic Programming

institute: TU München

summary: Endothelial dysfunction is an early event in atherosclerosis development and centrally linked with insufficient endothelial nitric oxide (NO) production. However, supraphysiological chronically increased NO levels, including from other cellular sources, also may induce endothelial dysfunction, and may play a role. Here, we studied how chronically elevated NO production from erythrocytes, achieved by genetic deletion of arginase-1 (ARG1), impacts smooth muscle cell (SMC) lipid accumulation and atherosclerosis progression.

overall_design: Mice lacking ARG1 in the red blood cell (RBC) lineage were generated by crossing erythropoietin receptor (EpoR or Er) Cre recombinase transgenic mice (ErCre tg) with ARG1 flox/flox transgenic mice (RRID:IMSR_JAX:008817). Primary SMCs were isolated from the aorta of RBC.ARG1 wildtype (WT) and RBC.ARG1 knockout (KO) mice and cultured in DMEM containing 10% fetal bovine serum (FBS; Gibco), 100 U/mL penicillin and 100 µg/mL streptomycin (Gibco). To promote lipid accumulation, SMCs (at 80% confluency) were switched to DMEM supplemented with dexamethasone (0.1 µM; Sigma), insulin (1 µM; Sigma) and L-ascorbic acid (50 µg/mL; Sigma) for 10 days. Total RNA-seq was performed in 4 biological replicates of smooth muscle cells and the effect of the genotype and medium analysed

first: Beichen

last: Sun

first: Rajinikanth

last: Gogiraju

first: Katrin

last: Schäfer


title: TRMT5/NES Coordinated Activity Drives Pancreatic Cancer Growth and Metastasis [RIP-seq I]


title: Cytotoxic Tissue-Resident NK Cells Infiltrate and Control Solid Epithelial Tumor Growth [ATAC-Seq]

city: STANFORD

first: Imran

middle: Ahammad

last: Mohammad

state: CA

address: lokey stem cell research building, 2165, 265 Campus Drive, Palo Alto, CA 94305

department: OHNS

summary: Human tissue-resident natural killer (trNK) cells – broadly defined by markers of tissue-residency, such as CD49a (integrin alpha1, ITGA1) and CD103 (integrin alpha E, ITGAE) – are increasingly recognized for their immunoregulatory role in host control of infection, malignancy, and autoimmunity. Although the importance of transforming growth factor beta (TGFβ) in trNK cell differentiation has been demonstrated, the context in which the differentiation of CD49a+CD103+ trNK cells occurs can result in either an immunosuppressive phenotype or a highly cytotoxic one. To understand this dichotomy better, we utilized a multiomics approach to molecularly characterize these cells and identified a highly cytotoxic trNK (ctrNK) cell phenotype, characterized by the expression of CD39.

overall_design: 50,000 sorted NK cells from different conditions  (CTRL, HNSCC-induced double negative, HNSCC-induced double positive, and TGF-β induced double positive NK cells) were processed using the Diagenode ATAC-seq kit.

first: John

middle: B

last: Sunwoo

first: Jennifer

last: Foltz


title: Simvastatin Reprograms Lipid Metabolism in B16.F10 Melanoma Cells to Favor an Early Resistant Phenotype

city: Cluj-Napoca

first: Giorgiana

last: Negrea

state: Cluj

address: Clinicilor street

country: Romania

institute: Babes-Bolyai University

summary: Our previous studies demonstrated that simvastatin (SIM) inhibited B16.F10 murine melanoma cell proliferation in vivo and in vitro via strong suppressing the production of subunit α of hypoxia inducible factor 1 (HIF-1) (HIF-1 α) - a key regulator of cancer cell adaptation to hypoxia. However, beyond its known role in hypoxia, normoxic expression of HIF-1α in melanoma has been linked to increased cancer cell aggressiveness, underscoring its broader impact on tumor biology. Since the translation of HIF-1α is modulated by Akt, SIM effects on both regulatory factors in relation to cancer cell metabolism under normoxia were investigated. SIM effects on cell metabolism were analyzed at mRNA and at protein level. Our data suggested that SIM reprogrammed glucose metabolism to ensure replenishment of tricarboxylic acid (TCA) cycle, favoring its biosynthetic role over its energy role. This shift supported lipid-derived signaling molecules synthesis including isoprenoids and prostaglandins, favoring associated with cell survival and aggressiveness. Our results have important clinical implications, as they emphasize the potential of targeting key lipid metabolic pathways to overcome the adaptive mechanisms driven by normoxic HIF-1α expression. Thus, our data offer promise for novel combination therapies which disrupt the metabolic plasticity of melanoma, to ultimately improve therapeutic outcomes.

overall_design: RNA-sequencing profiling of B16.F10 melanoma cells treated with Simvastatin for 24h compared to control (3 biological replicates/sample).

middle: G

first: Loredana

last: Balacescu

first: Ilie

last: Pavel

first: Alina

last: Sesarman

first: Manuela

last: Banciu


title: [NanoString nCounter]: Characterization of the transcriptional landscape of mouse lung epithelial cells treated with synergistic immunostimulatory ligands followed by MHV coronavirus infection.

city: Houston

first: Scott

last: Evans

state: TX

address: 6565 MD Anderson Blvd, Unit 1059

department: Pulmonary Medicine

institute: University of Texas MD Anderson Cancer Center

summary: Coronaviruses can cause serious disease in humans and animals. They are often difficult to study due to the variability of disease as well as safety concerns related to biosafety requirements. Here, we use a BSL2-compatible murine betacoronavirus (MHV-A59) which infects multiple organs to study the respiratory phase of disease and subsequent systemic dissemination. We asked whether inducible epithelial resistance, activated by the combination of pattern recognition receptor agonists Pam2+ODN, can limit both pulmonary infection and systemic spread of disease. Prophylactic exposure with Pam2+ODN improves survival and reduces extrapulmonary viral burden, including in the liver, consistent with limited systemic spread. Stopping the infection at the level of the lungs is associated with improved physiological outcomes and increased protection for the mice. We further characterize the response of the epithelial cells to infection and treatment and demonstrate modulation of epithelial gene expression, including attenuation of virus-induced responses, to better understand the mechanisms of protection and how these responses may be leveraged against future infectious agents.

overall_design: Gene expression changes of MLE-15 cells were profiled after Pam2+ODN (4+1 μM) or PBS pretreatment followed by MHV infection (MOI 0.1), with RNA collected at 24 hours post-infection and analyzed using the nCounter Mouse Host Response Panel (NanoString).

first: Michael

last: Longmire

first: Jezreel

last: Pantaleón García


title: Pivotal Role of the NuRD Complex in Remodeling Chromatin Environment and Maintaining Genome Architecture at CTCF Sites [mESC Bisulfite-seq]

city: Hong Kong

first: Jian

last: Yan

state: Hong Kong Special Administrative Region

address: 83 Tat Chee Avenue, Kowloon

department: Department of Biomedical Sciences

institute: City University of Hong Kong

type: Methylation profiling by high throughput sequencing

summary: CCCTC-binding factor (CTCF) is an evolutionarily conserved transcription factor with diverse regulatory roles. Around stable CTCF binding sites, nucleosomes are highly ordered and DNA methylation is reduced, yet the mechanisms establishing and maintaining this epigenetic environment remain unclear. Utilizing an innovative eBioID method, we identified that virtually all subunits of the nucleosome remodeling and deacetylase (NuRD) complex are associated with CTCF in cells. Further analyses revealed that the NuRD complex is necessary for the chromatin binding of CTCF, and emerges as a novel regulator of the genome architecture. Additionally, we discovered that MBD3-NuRD facilitates the recruitment of TET demethylases to CTCF sites, initiating local DNA demethylation essential for the activation of adjacent gene expression. Embryonic stem cells deficient in the NuRD complex showed impaired lineage commitment. In summary, this study elucidates a mechanism illustrating the interplay between CTCF binding and the epigenome including 3D genome organization and DNA methylation, with the NuRD complex serving as an indispensable mediator.

overall_design: CTCF is closely related to the three-dimensional structure of the genome, and its stable binding site shows a low level of DNA methylation. Through eBioID experiments for CTCF and TET1/2/3, we found that multiple components of NuRDComplex appeared simultaneously in the list of CTCF and TETs interacting proteins. We performed BS-Seq and CTCF ChIP-Seq on mESCWT/SKO/TKO cells and found that genomic methylation had no significant effect on CTCF binding. We also performed HiC sequencing in BPK25-treated mESCs, and combined with published mESC WT/CTCF-AID HiC data, analyzed and compared the effects of CTCF or NuRD complex degradation on the three-dimensional structure of the genome. We performed a series of treatments on HEK293T cells, including DMSO, IAA(degraded CTCF), BPK25(degraded NuRD complex), etc., and then conducted RNA-Seq, ChIP-Seq, and BS-Seq experiments respectively. Explore the dependencies between CTCF, NuRD complex, and TET1/2/3. In addition, to investigate the biological significance of NuRD complexes in reshaping the chromatin environment and maintaining genomic structure around CTCF binding sites, we performed differentiation experiments on human embryonic stem cells (hESC) and mouse embryonic stem cells (mESC). During differentiation, we specifically target CTCF or NuRD complexes for knockout. To assess the impact of these gene knockdowns, We analyzed genome-wide methylation levels, gene expression profiles, and changes in CTCF, MBD2/3, and TET1/2/3 binding sites by BS-Seq, RNA-Seq, and CHI-SEQ, respectively, to clarify the important role of MBD3-NuRD, TET, and CTCF interaction regulatory axis in stem cell differentiation and development. In this SubSeries, we performed BS-Seq on mESC WT, SKO (sextuple knockout for Dnmt1/3a/3b and Tet1/2/3), and TKO (triple knockout for Tet1/2/3) cells to analyze genome-wide methylation levels across these three cell types.

first: Xi

last: Wang

first: Wenju

last: Wu


title: Developmental manganese, but not concurrent lead exposure, alters social processing selectively in male mice

city: Catania

first: Grete Francesca

last: Privitera

address: Via Santa Sofia

department: Department of Clinical and Experimental Medicine

country: Italy

institute: University of Catania

summary: Exposure to environmental pollutants, including heavy metals, during fetal life and early childhood, represents a major public health concern. While the health effects of exposure to a single metal have been well documented, real-life scenarios including simultaneous exposure to multiple metals have not yet been extensively investigated. In this study, we investigated the neurobehavioral effects and hippocampal transcriptomic alterations in mouse offspring developmentally exposed to lead (Pb), manganese (Mn), or their combination. Female mice were exposed to environmentally relevant low doses of Pb (100 ppm), Mn (2g/L), or both, via drinking water beginning two weeks prior to conception and continuing throughout gestation and lactation. Offspring of both sexes were assessed at multiple developmental stages using a comprehensive behavioral test battery to identify age- and sex-specific effects of exposure. For transcriptomic analysis, one male and one female (two month-old) from six litters per group (naive siblings of behaviorally tested mice) were euthanized for hippocampal tissue collection. Our novel finding was a specific deficit in social recognition in adult males developmentally exposed to Mn, an effect not observed in the Pb+Mn co-exposure group. To explore potential molecular mechanisms underlying the Mn-associated behavioral phenotype in males, we focused on differentially expressed genes (DEGs) with |logFC| > 1.5 and p < 0.01. Among these, Mup3 (major urinary protein 3) emerged as particularly notable due to its role in pheromonal communication and its potential link to the altered social investigation behaviors observed in Mn-exposed males. Overall, our behavioral data suggest that developmental exposure to Pb or Mn alone, but not in combination, elicits adverse neurobehavioral outcomes, particularly in males. Importantly, the pronounced effects of individual metal exposure, along with the apparent antagonistic interaction in the combined exposure group, were mirrored at the transcriptomic level.

overall_design: Hippocampal RNAseq profiles of 2-month-old mice developmentally exposed to Pb, Mn or their combination (from two weeks before conception till weaning, 8 weeks)

first: Anna Maria

last: Tartaglione

first: Oyku

last: Dinckol

first: Giorgia

last: Macchioni

first: Ettore

last: Meccia

first: Byron

last: Fuentes

first: Eleonora

last: Parlanti

first: Anna

last: Pino

first: Alfredo

last: Pulvirenti

first: Laura

last: Ricceri

first: Gemma

last: Calamandrei


title: NAT10-mediated mRNA N4-acetylcytidine Modifications in Mouse Oocytes Constitute a Checkpoint of Ovarian Follicle Development [NAT10-smart-seq2]

city: Hangzhou

first: Heng-yu

last: Fan

state: Zhejiang

address: Yuhangtang Road

institute: Life Sciences  Institute

summary: During mammalian follicular development, the correct establishment of the epitranscriptome in oocytes is essential for precise gene repression and the acquisition of developmental competence. N4-acetylcytidine (ac4C) is a conserved posttranscriptional RNA modification catalyzed by the only known “writer”, N-acetyltransferase 10 (NAT10). NAT10-targeted transcripts in oocytes and their functions in supporting folliculogenesis are poorly understood. In this study, we showed that oocyte-specific knockout of Nat10 resulted in retardation of oocyte growth with defective follicular development, premature ovarian failure, and female sterility. We profiled the ac4C landscape in the ovarian transcriptome and identified many folliculogenesis-related oocyte genes with ac4C modifications. Loss of Nat10 in oocytes eliminated ac4C signals, resulting in the downregulation of numerous oocyte-derived transcripts with reduced stability. Moreover, Nat10-deletion in oocytes or mutations in these ac4C sites led to decreased levels of protein translation, whereas the introduction of ac4C into these mRNAs increased their translational efficiencies. In addition, our data showed that the distinct gene expression patterns in granulosa cells within arrested secondary follicles were disrupted, and the identity of granulosa cells was altered by Nat10 deletion in oocytes. Taken together, these findings provide evidence that NAT10-mediated ac4C modification is a crucial regulatory factor in the maintenance of oocyte competence and that it constitutes a checkpoint for ovarian folliculogenesis beyond the secondary follicle stage.

overall_design: ac4C-RIP-seq was performed as previously described[12], with minor modifications. Briefly, poly(A)-RNA was isolated from ovaries as described above, and an anti-ac4C antibody (1 μg) or rabbit monoclonal IgG Isotype control (1 μg) were pre-coupled to 300 μg of Protein G Dynabeads (ThermoFisher Scientific) in PBS for 1 h at room temperature. Approximately 8 μg of DNase-treated poly(A)-RNA was spiked with 10 pg (1:10–1:5) or 1 pg (1:10–1:6) of ac4C RNA and analyzed by immunoprecipitation using an anti-ac4C antibody or rabbit monoclonal IgG isotype control in 100 mL of acetylated RNA immunoprecipitation (acRIP) buffer. After immunoprecipitation, the beads were washed five times in acRIP buffer and RNA was eluted using RNase-free proteinase K (50 mg, Thermo Fisher Scientific) digestion in 100 mL of buffer containing 50 mM Tris-HCl [pH7.5], 75 mM NaCl, 6.25 mM EDTA, and 1% SDS for 1 h at 37 °C. RNA was extracted using phenol:chloroform [pH 4.5] and precipitated with ethanol, 0.3 M sodium acetate [pH 5.5], and 15 mg/mL linear acrylamide. RNA in the acRIPs was reverse transcribed using the Superscript III system and a reverse primer specific for mouse b-globin (Table S7) according to the manufacturer’s suggestions. Barcoded libraries were pooled and sequenced on a HiSeq X Ten platform (Illumina, San Diego, CA, USA) in the 150 bp paired-end mode.

first: Wenjing

first: Yuke

first: Lu

last: Chen

first: Shaoyuan

last: Liu

first: Hengyu


title: Pivotal Role of the NuRD Complex in Remodeling Chromatin Environment and Maintaining Genome Architecture at CTCF Sites [mESC ChIP-seq]

first: Jian

last: Yan

overall_design: CTCF is closely related to the three-dimensional structure of the genome, and its stable binding site shows a low level of DNA methylation. Through eBioID experiments for CTCF and TET1/2/3, we found that multiple components of NuRDComplex appeared simultaneously in the list of CTCF and TETs interacting proteins. We performed BS-Seq and CTCF ChIP-Seq on mESCWT/SKO/TKO cells and found that genomic methylation had no significant effect on CTCF binding. We also performed HiC sequencing in BPK25-treated mESCs, and combined with published mESC WT/CTCF-AID HiC data, analyzed and compared the effects of CTCF or NuRD complex degradation on the three-dimensional structure of the genome. We performed a series of treatments on HEK293T cells, including DMSO, IAA(degraded CTCF), BPK25(degraded NuRD complex), etc., and then conducted RNA-Seq, ChIP-Seq, and BS-Seq experiments respectively. Explore the dependencies between CTCF, NuRD complex, and TET1/2/3. In addition, to investigate the biological significance of NuRD complexes in reshaping the chromatin environment and maintaining genomic structure around CTCF binding sites, we performed differentiation experiments on human embryonic stem cells (hESC) and mouse embryonic stem cells (mESC). During differentiation, we specifically target CTCF or NuRD complexes for knockout. To assess the impact of these gene knockdowns, We analyzed genome-wide methylation levels, gene expression profiles, and changes in CTCF, MBD2/3, and TET1/2/3 binding sites by BS-Seq, RNA-Seq, and CHI-SEQ, respectively, to clarify the important role of MBD3-NuRD, TET, and CTCF interaction regulatory axis in stem cell differentiation and development. In this subset, we carried out CTCF ChIP-Seq in three types of mESC cells (WT/SKO/TKO) to analyze the effect of DNA methylation on CTCF binding.

first: Xi

first: Wenju

last: Sun


title: Pivotal Role of the NuRD Complex in Remodeling Chromatin Environment and Maintaining Genome Architecture at CTCF Sites [HEK293T ChIP-seq]

overall_design: CTCF is closely related to the three-dimensional structure of the genome, and its stable binding site shows a low level of DNA methylation. Through eBioID experiments for CTCF and TET1/2/3, we found that multiple components of NuRDComplex appeared simultaneously in the list of CTCF and TETs interacting proteins. We performed BS-Seq and CTCF ChIP-Seq on mESCWT/SKO/TKO cells and found that genomic methylation had no significant effect on CTCF binding. We also performed HiC sequencing in BPK25-treated mESCs, and combined with published mESC WT/CTCF-AID HiC data, analyzed and compared the effects of CTCF or NuRD complex degradation on the three-dimensional structure of the genome. We performed a series of treatments on HEK293T cells, including DMSO, IAA(degraded CTCF), BPK25(degraded NuRD complex), etc., and then conducted RNA-Seq, ChIP-Seq, and BS-Seq experiments respectively. Explore the dependencies between CTCF, NuRD complex, and TET1/2/3. In addition, to investigate the biological significance of NuRD complexes in reshaping the chromatin environment and maintaining genomic structure around CTCF binding sites, we performed differentiation experiments on human embryonic stem cells (hESC) and mouse embryonic stem cells (mESC). During differentiation, we specifically target CTCF or NuRD complexes for knockout. To assess the impact of these gene knockdowns, We analyzed genome-wide methylation levels, gene expression profiles, and changes in CTCF, MBD2/3, and TET1/2/3 binding sites by BS-Seq, RNA-Seq, and CHI-SEQ, respectively, to clarify the important role of MBD3-NuRD, TET, and CTCF interaction regulatory axis in stem cell differentiation and development. In this subset, we used DMSO, IAA and BPK25 to treat HEK293T cells and then conducted ChIP-Seq experiments of CTCF, MBD2/3 and TET1 to analyze the effects of degradation of CTCF and NuRD complex on the binding sites of these proteins.

last: Wang

last: Wu


title: ALK4R–Stimulated Glutaminolysis and mTOR-C/EBPbeta Signaling Drives the Differentiation of Novel IL-10-Producing Regulatory T Cells

city: Kyoto

first: Masaki

last: Tajima

address: Yoshidakonoe cho

country: Japan

institute: Kyoto University

summary: Here we report that Dectin-1-stimulated dendritic cells (DCs) induce unique IL-10-producing T cells with strong regulatory function during fungal infection or experimental asthma.These T cells, which we call Dectin-10 T cells, are induced by DC-initiated signaling that sets in motion two complementary mechanisms of IL-10-producing T cell differentiation. The first involves induction of nascent Dect-10 T cell IL-4 synthesis and attendant GATA3 production, the latter a factor that exerts canonical and epigenetic transcriptional function at separate IL-10 promoter sites. The second involves TGFbetaR-family(ActRIB(ALK4)) signaling associated with induction of glutaminolysis and generation of alpha-ketoglutarate, a factor that induces rapamycin-sensitive TORC1 activation; the latter, in turn, causes translation of the LIP isoform of C/EBPbeta and binding LIP to CREB1 to form a CREB1-LIP complex that binds to adjacent sites on the IL- 10 promoter and transactivation of the IL10 gene. Dect-10 T cell regulatory function is manifest by its capacity to down-regulate normally protective immune responses to hyphal C. albicans renal infection.  In addition, Dect-10 T cells, in accord with their IL-4-dependent genesis, suppress dust mite-induced experimental asthma.

overall_design: RNAseq was conducted on bone marrow derived dendritic cells (BMDCs) treated with Zymosan Depleted, heat killed C. albicans (Yeast), or heat killed C. albicans (Hyphae).

first: Warren

last: Strober


title: Pivotal Role of the NuRD Complex in Remodeling Chromatin Environment and Maintaining Genome Architecture at CTCF Sites [BPK25 Hi-C]

overall_design:
CTCF is closely related to the three-dimensional structure of the genome, and its stable binding site shows a low level of DNA methylation. Through eBioID experiments for CTCF and TET1/2/3, we found that multiple components of NuRD Complex appeared simultaneously in the list of CTCF and TETs interacting proteins. We performed BS-Seq and CTCF ChIP-Seq on mESC WT/SKO/TKO cells and found that genomic methylation had no significant effect on CTCF binding. We also performed HiC sequencing in BPK25-treated mESCs, and combined with published mESC WT/CTCF-AID HiC data, analyzed and compared the effects of CTCF or NuRD complex degradation on the three-dimensional structure of the genome. We performed a series of treatments on HEK293T cells, including DMSO, IAA(degraded CTCF), BPK25(degraded NuRD complex), etc., and then conducted RNA-Seq, ChIP-Seq, and BS-Seq experiments respectively. Explore the dependencies between CTCF, NuRD complex, and TET1/2/3. In addition, to investigate the biological significance of NuRD complexes in reshaping the chromatin environment and maintaining genomic structure around CTCF binding sites, we performed differentiation experiments on human embryonic stem cells (hESC) and mouse embryonic stem cells (mESC). During differentiation, we specifically target CTCF or NuRD complexes for knockout. To assess the impact of these gene knockdowns, We analyzed genome-wide methylation levels, gene expression profiles, and changes in CTCF, MBD2/3, and TET1/2/3 binding sites by BS-Seq, RNA-Seq, and ChIP-Seq, respectively, to clarify the important role of MBD3-NuRD, TET, and CTCF interaction regulatory axis in stem cell differentiation and development.
In this SubSeries, we performed Hi-C experiments after mESC treatment with BPK25 to evaluate the effect of NuRD complex degradation on the three-dimensional structure of the genome.


title: A novel Plasmodium cytosolic protein regulates parasite fitness, gametocytogenesis, and transmission

city: Lucknow

first: Dr Satish

last: Mishra

state: Uttar Pradesh

address: Sector 10 jankipuram extension

department: Molecular Microbiology and Immunology

country: India

institute: CSIR- Central Drug Research Institute Lucknow

summary: Understanding the transcriptional changes upon PFTP gene knockout in Plasmodium berghei parasite in comparison to wild-type parasites. We were interested in looking for the parasite's gametocytes transcripomic analysis.

overall_design: Enriched gametocytes were purified and subject to RNA sequencing and analysis.

first: Aastha

last: Varshney

first: Nirdosh

last: Nirdosh

first: Satish


title: Species-specific oxygen sensing governs the initiation of vertebrate limb regeneration

city: Tübingen

first: Can

last: Aztekin

address: Max-Planck-Ring 9

department: TheFriedrich Miescher Laboratory

institute: The Max Planck Society for Biology

summary: Why mammals cannot regenerate limbs, unlike amphibians, presents a longstanding puzzle in biology. We show that exposing ex vivo amputated embryonic mouse limbs to subatmospheric oxygen environment, or stabilizing oxygen-sensitive HIF1A enables not only rapid wound healing, but alters cellular mechanics, and reshapes the histone landscape to prime regenerative fates. Conversely, regenerative Xenopus tadpole limbs display low oxygen-sensing capacity, robust wound healing, a regenerative histone landscape, and glycolytic programs even under high oxygen. This reduced oxygen-sensing capacity, in stark contrast to mammals, associates with decreased HIF1A-regulating gene expressions. Our findings thus uncover species-specific oxygen sensing as a unifying mechanism for limb regeneration initiation across vertebrates, reveal how aquatic subatmospheric habitats may enhance regenerative capabilities, and identify targetable barriers to unlock latent limb regenerative programs in adult mammals.

overall_design: ATAC-seq datasets at 1 dpa in mouse explants cultured under either 96-well or ALI conditions.

first: Georgios

last: Tsissios

first: Marion

last: Leleu

first: Kelly

last: Hu


title: NAT10-mediated mRNA N4-acetylcytidine Modifications in Mouse Oocytes Constitute a Checkpoint of Ovarian Follicle Development [RIP-Seq]

first: Heng-yu

overall_design: The oocytes were harvested from 6W mature WT and Gdf9-cre Nat10 conditional knockout female mice 32-48h after PMSG and washed by 0.2% containing PBS for 3 times, then 10 oocytes per sample were lysed in lysis buffer (containing 0.2% Triton X-100 and Recombination RNase Inhibitor) and prceeded for cDNA library constribution following the workflow of Smart-seq2. And for each sample, ERCC (1:1000, 0.2μl/sample) were added as spike-in for further calibration.

first: Wenjing

first: Yuke


title: Pivotal Role of the NuRD Complex in Remodeling Chromatin Environment and Maintaining Genome Architecture at CTCF Sites [HEK293T_siNURD_CTCF_ChIP_Seq]

overall_design:
CTCF is closely related to the three-dimensional structure of the genome, and its stable binding site shows a low level of DNA methylation. Through eBioID experiments for CTCF and TET1/2/3, we found that multiple components of NuRD Complex appeared simultaneously in the list of CTCF and TETs interacting proteins. We performed BS-Seq and CTCF ChIP-Seq on mESC WT/SKO/TKO cells and found that genomic methylation had no significant effect on CTCF binding. We also performed HiC sequencing in BPK25-treated mESCs, and combined with published mESC WT/CTCF-AID HiC data, analyzed and compared the effects of CTCF or NuRD complex degradation on the three-dimensional structure of the genome. We performed a series of treatments on HEK293T cells, including DMSO, IAA(degraded CTCF), BPK25(degraded NuRD complex), etc., and then conducted RNA-Seq, ChIP-Seq, and BS-Seq experiments respectively. Explore the dependencies between CTCF, NuRD complex, and TET1/2/3. In addition, to investigate the biological significance of NuRD complexes in reshaping the chromatin environment and maintaining genomic structure around CTCF binding sites, we performed differentiation experiments on human embryonic stem cells (hESC) and mouse embryonic stem cells (mESC). During differentiation, we specifically target CTCF or NuRD complexes for knockout. To assess the impact of these gene knockdowns, We analyzed genome-wide methylation levels, gene expression profiles, and changes in CTCF, MBD2/3, and TET1/2/3 binding sites by BS-Seq, RNA-Seq, and ChIP-Seq, respectively, to clarify the important role of MBD3-NuRD, TET, and CTCF interaction regulatory axis in stem cell differentiation and development.
In this SubSeries, we used siRNA to knock down NuRD complex components such as CHD3/4/5 and MBD2/3 in HEK293T cells, respectively, and then performed ChIP-Seq with CTCF antibodies to evaluate the effect of knocking down different components of the NuRD complex on CTCF binding sites.


title: Pivotal Role of the NuRD Complex in Remodeling Chromatin Environment and Maintaining Genome Architecture at CTCF Sites [mESC_BPK25_HiC batch 2]

overall_design: CTCF is closely related to the three-dimensional structure of the genome, and its stable binding site shows a low level of DNA methylation. Through eBioID experiments for CTCF and TET1/2/3, we found that multiple components of NuRDComplex appeared simultaneously in the list of CTCF and TETs interacting proteins. We performed BS-Seq and CTCF ChIP-Seq on mESCWT/SKO/TKO cells and found that genomic methylation had no significant effect on CTCF binding. We also performed HiC sequencing in BPK25-treated mESCs, and combined with published mESC WT/CTCF-AID HiC data, analyzed and compared the effects of CTCF or NuRD complex degradation on the three-dimensional structure of the genome. We performed a series of treatments on HEK293T cells, including DMSO, IAA(degraded CTCF), BPK25(degraded NuRD complex), etc., and then conducted RNA-Seq, ChIP-Seq, and BS-Seq experiments respectively. Explore the dependencies between CTCF, NuRD complex, and TET1/2/3. In addition, to investigate the biological significance of NuRD complexes in reshaping the chromatin environment and maintaining genomic structure around CTCF binding sites, we performed differentiation experiments on human embryonic stem cells (hESC) and mouse embryonic stem cells (mESC). During differentiation, we specifically target CTCF or NuRD complexes for knockout. To assess the impact of these gene knockdowns, We analyzed genome-wide methylation levels, gene expression profiles, and changes in CTCF, MBD2/3, and TET1/2/3 binding sites by BS-Seq, RNA-Seq, and CHI-SEQ, respectively, to clarify the important role of MBD3-NuRD, TET, and CTCF interaction regulatory axis in stem cell differentiation and development. In this SubSeries, we performed Hi-C experiments after mESC treatment with BPK25 to evaluate the effect of NuRD complex degradation on the three-dimensional structure of the genome.


title: Pivotal Role of the NuRD Complex in Remodeling Chromatin Environment and Maintaining Genome Architecture at CTCF Sites [mESC_d0246_DMSO_BPK25_IAA_RNA_Seq]

overall_design:
CTCF is closely related to the three-dimensional structure of the genome, and its stable binding site shows a low level of DNA methylation. Through eBioID experiments for CTCF and TET1/2/3, we found that multiple components of NuRD Complex appeared simultaneously in the list of CTCF and TETs interacting proteins. We performed BS-Seq and CTCF ChIP-Seq on mESC WT/SKO/TKO cells and found that genomic methylation had no significant effect on CTCF binding. We also performed HiC sequencing in BPK25-treated mESCs, and combined with published mESC WT/CTCF-AID HiC data, analyzed and compared the effects of CTCF or NuRD complex degradation on the three-dimensional structure of the genome. We performed a series of treatments on HEK293T cells, including DMSO, IAA(degraded CTCF), BPK25(degraded NuRD complex), etc., and then conducted RNA-Seq, ChIP-Seq, and BS-Seq experiments respectively. Explore the dependencies between CTCF, NuRD complex, and TET1/2/3. In addition, to investigate the biological significance of NuRD complexes in reshaping the chromatin environment and maintaining genomic structure around CTCF binding sites, we performed differentiation experiments on human embryonic stem cells (hESC) and mouse embryonic stem cells (mESC). During differentiation, we specifically target CTCF or NuRD complexes for knockout. To assess the impact of these gene knockdowns, We analyzed genome-wide methylation levels, gene expression profiles, and changes in CTCF, MBD2/3, and TET1/2/3 binding sites by BS-Seq, RNA-Seq, and ChIP-Seq, respectively, to clarify the important role of MBD3-NuRD, TET, and CTCF interaction regulatory axis in stem cell differentiation and development.
In this SubSeries, we treated mESC during induced differentiation with DMSO, BPK25 and IAA respectively, resulting in the degration of CTCF or NuRD complex during differentiation. Then, RNA was collected at d0246 days for RNA-SEQ sequencing. Finally, the expression profiles of the same treatment at different time points and different treatment groups at the same time points were compared.


title: Pivotal Role of the NuRD Complex in Remodeling Chromatin Environment and Maintaining Genome Architecture at CTCF Sites [CTCF_MBD2_HT_Me_CAP_SELEX]

overall_design:
CTCF is closely related to the three-dimensional structure of the genome, and its stable binding site shows a low level of DNA methylation. Through eBioID experiments for CTCF and TET1/2/3, we found that multiple components of NuRD Complex appeared simultaneously in the list of CTCF and TETs interacting proteins. We performed BS-Seq and CTCF ChIP-Seq on mESC WT/SKO/TKO cells and found that genomic methylation had no significant effect on CTCF binding. We also performed HiC sequencing in BPK25-treated mESCs, and combined with published mESC WT/CTCF-AID HiC data, analyzed and compared the effects of CTCF or NuRD complex degradation on the three-dimensional structure of the genome. We performed a series of treatments on HEK293T cells, including DMSO, IAA(degraded CTCF), BPK25(degraded NuRD complex), etc., and then conducted RNA-Seq, ChIP-Seq, and BS-Seq experiments respectively. Explore the dependencies between CTCF, NuRD complex, and TET1/2/3. In addition, to investigate the biological significance of NuRD complexes in reshaping the chromatin environment and maintaining genomic structure around CTCF binding sites, we performed differentiation experiments on human embryonic stem cells (hESC) and mouse embryonic stem cells (mESC). During differentiation, we specifically target CTCF or NuRD complexes for knockout. To assess the impact of these gene knockdowns, We analyzed genome-wide methylation levels, gene expression profiles, and changes in CTCF, MBD2/3, and TET1/2/3 binding sites by BS-Seq, RNA-Seq, and ChIP-Seq, respectively, to clarify the important role of MBD3-NuRD, TET, and CTCF interaction regulatory axis in stem cell differentiation and development.
In this subset, CTCF and MBD2 proteins were expressed and purified in vitro, and HT-SELEX and Methyl-SELEX experiments were carried out on the two proteins respectively. And we have developed a new CAP-Methyl-SELEX method by combining the published CAP-HT-SELEX and Methyl-SELEX techniques.The CAP-HT-SELEX and CAP-Methyl-SELEX experiments were carried out on CTCF-MBD2. Three replicates were designed for all experiments, and four cycles were performed for each. By analyzing the proportion of dinucleotides (especially CG) in the SELEX sequencing data with the number of cycles, the methylation preference of individual CTCF, MBD2 and their dimers was inferred.


title: Bulk RNA-sequencing of A549 cells transduced with Ad5 empty vector (GFP) or Ad5 expressing SARS-CcV-2 nucleocapsid (AdN)

city: Wuhan

first: Haiyun

last: Yu

state: other

address: 13 Hangkong Road, Baofeng Street

department: Department of Pathogen Biology

institute: Huazhong University of Science and Technology Tongji Medical College

summary: To investigate how the abundant expression of SARS-CoV-2 nucleocapsid might change the transcriptome, A549 human lung carcinoma cells were transduced with replication-deficient recombinant human adenovirus type‐5 expressing SARS-CcV-2 nucleocapsid (AdN) or the empty vetor (GFP). Twenty-four hours later, the transduced cells were subjected to bulk RNA sequencing.

overall_design: To mimic the abundant expression of human-infecting coronaviruse nucleocapsid protein in infected cells, replication-deficient recombinant human adenovirus type‐5 was used as the vector. Recombinant adenovirus type‐5 expressing FLAG-tagged SARS-CoV-2 nucleocapsid (GeneBank: MN908947.3) or empty vector were obtained from Vigenebio (Jinan, China). A549 human lung carcinoma cells were used as the cell model and were transduced with 100 MOI (multiplicity of infection) of the above adenoviruses. Twenty-four hours later, cells were subjected to bulk RNA sequencing.

first: Chaohong


title: Pivotal Role of the NuRD Complex in Remodeling Chromatin Environment and Maintaining Genome Architecture at CTCF Sites [hESC_H9_d049_RNA_Seq]

first: Jian

overall_design: CTCF is closely related to the three-dimensional structure of the genome, and its stable binding site shows a low level of DNA methylation. Through eBioID experiments for CTCF and TET1/2/3, we found that multiple components of NuRD Complex appeared simultaneously in the list of CTCF and TETs interacting proteins. We performed BS-Seq and CTCF ChIP-Seq on mESC WT/SKO/TKO cells and found that genomic methylation had no significant effect on CTCF binding. We also performed HiC sequencing in BPK25-treated mESCs, and combined with published mESC WT/CTCF-AID HiC data, analyzed and compared the effects of CTCF or NuRD complex degradation on the three-dimensional structure of the genome. We performed a series of treatments on HEK293T cells, including DMSO, IAA(degraded CTCF), BPK25(degraded NuRD complex), etc., and then conducted RNA-Seq, ChIP-Seq, and BS-Seq experiments respectively. Explore the dependencies between CTCF, NuRD complex, and TET1/2/3. In addition, to investigate the biological significance of NuRD complexes in reshaping the chromatin environment and maintaining genomic structure around CTCF binding sites, we performed differentiation experiments on human embryonic stem cells (hESC) and mouse embryonic stem cells (mESC). During differentiation, we specifically target CTCF or NuRD complexes for knockout. To assess the impact of these gene knockdowns, We analyzed genome-wide methylation levels, gene expression profiles, and changes in CTCF, MBD2/3, and TET1/2/3 binding sites by BS-Seq, RNA-Seq, and ChIP-Seq, respectively, to clarify the important role of MBD3-NuRD, TET, and CTCF interaction regulatory axis in stem cell differentiation and development.

first: Xi