title: VGLL1 contributes to both the transcriptome and epigenome of the developing trophoblast compartment [ATAC-Seq]

first: Robert

last: Morey

address: 2880 Torrey Pines Scenic Dr

department: Pathology

institute: UCSD

summary: The trophectoderm (TE), the outer layer of the blastocyst, is the first lineage specified during mammalian development. It initiates attachment and implantation into the maternal endometrium and gives rise to trophoblasts, the epithelial cells of the placenta that support development in utero.  Animal models have identified key signaling pathways, including BMP, WNT, and HIPPO, that regulate extra-embryonic ectoderm development, but species-specific differences in regulatory networks underlying TE specification and placental development emphasize the need for human-specific models. We were the first to previously identify Vestigial-like Family Member 1 (VGLL1), a coactivator of the TEAD family of transcription factors, as a human-specific placental marker highly expressed in first trimester trophoblast progenitors. The HIPPO signaling pathway effector TEAD4 in complex with YAP1 regulates initial TE specification by acting on key TE transcription factors (TEtra factors): GATA2, GATA3, TFAP2A, and TFAP2C. Pluripotent stem cells (PSCs) represent a unique resource to study species-specific genetic and epigenetic mechanisms of TE and trophoblast development. Here, we use a PSC model in which BMP4 treatment and WNT inhibition (via IWP2) induce TE-like cells. We examined BMP4-dependent chromatin accessibility during the transition from PSC to TE-like cells in relation to gene expression and WNT activation. We found that BMP4 drives chromatin remodeling toward a trophoblast identity and that mesoderm genes are only transiently expressed with canonical WNT activation. Using this model, we determined that, while VGLL1 expression activation is temporally downstream of the TEtra factors, it is necessary for complete trophoblast differentiation by regulating EGFR expression and reinforcing GATA3 activation through positive feedback.  We also found that VGLL1 enhanced canonical WNT signaling by directly regulating WNT receptors and effector genes. Furthermore, we identified KDM6B as a direct target of VGLL1. As a chromatin remodeler, KDM6B removes the repressive H3K27me3 at bivalent promoters, enabling the transcriptional activation of TE markers. These findings establish a mechanistic framework that determine the lineage outcomes at the interplay of three developmentally important signaling pathways, HIPPO, BMP, and WNT, positioning VGLL1 at the center of the genetic and epigenetic mechanisms supporting the maintenance and differentiation of human TE and trophoblast cells, key aspects of early placental development.

overall_design: ATAC-seq of WA09/H9 at day 0, day 2, and day 4 of trophectoderm(TE)-like cell differentiation with BMP4 or BMP4/IWP2.

first: Ruben

middle: I

last: Calderon

first: Nirvay

last: Sah

first: Molly

last: Huang

first: Ryan

last: Kittle

first: Walee

middle: B

last: Shaik

first: Jennifer

last: Chousal

first: Sampada

last: Kallol

first: Tony

last: Bui

first: Alexandra

last: Mitre

first: Norah

middle: M

last: Fogarty

first: Claudia

last: Gerri

first: Claire

last: Zheng

first: Peter

last: DeHoff

first: Pratik

last: Home

first: Kathy

last: Niakan

first: Heidi

last: Cook-Andersen

first: Kathleen

last: Fisch

first: Soumen

last: Paul

first: Francesca

last: Soncin


title: Endothelial cells in sepsis - batch 1

status: Public on Nov 10 2025

city: Münster

first: Klaus

last: Schughart

address: Von-Esmarch-Str 56

department: Virology

country: Germany

institute: University Münster

type: Expression profiling by high throughput sequencing

summary: Differentially expressed genes were identified in lung endothelial cells of CLP-treated mice compared to sham-treated controls and after treatment with sitagliptin. Sitagliptin strongly reduced the inflamatory response.

overall_design: Sepsis was induced in mice by CLP (Cecal Ligation Puncture). Some mice were treated with sitagliptin. Endothelial cells from the lungs of CLP-treated, CLP plus sitagliptin, sham-treated and untreated mice were isolated and subjected to RNAseq analysis. Analysis was done in two batches, this is batch 1.

first: Nana-Maria

last: Wagner

first: Laura

last: Brabenec

first: Katharina

middle: E

last: Hellenthal


title: Neuronal conversion of pre-labeled astrocyte using adeno-asociated viruses in vivo

status: Public on Nov 09 2025

city: Toronto

first: Hussein

last: Ghazale

state: Ontario

address: 2075 Bayview Ave, North York

department: Biological Sciences

country: Canada

institute: Sunnybrook Research Institute

summary: Neuronal reprogramming using adeno-associated viruses (AAVs) carrying a GFAP mini-promoter to drive neurogenic transcription factor expression in astrocytes in vivo were refuted due to off-target neuronal expression. Here, we show successful neuronal conversion of pre-labeled astrocytes using AAV-GFAP to express phospho-deficient Ascl1SA6, and demonstrate that miR124 target sites reduce off-target neuronal expression. Finally, single cell transcriptomic and pseudotime trajectory analyses confirmed Ascl1SA6-driven astrocyte-to-neuron conversion, and more limited oligodendrocyte conversion events

overall_design: Following AAV injection into the motor cortex of C57/BL6 male mice, brains were harvested 7 and 50 days post injection. Cortex was microdissected under the microscope and single cell suspension was prepared for single cell analysis using scRNA-seq.

first: Carol

last: Schuurmans


title: Single cell analysis of epidermis from nickel-challenged skin

city: Copenhagen

first: Kelvin

last: Yeung

address: Blegdamsvej 3B

country: Denmark

institute: LEO SIC

summary: In this study, we investigated the consequences of repetitive nickel challenge at previously nickel-challenged skin sites in allergic participants. Repeated challenge with nickel resulted in progressive worsening allergic skin reactions in nearly all participants (11 out of 12). To investigate the immunopathogenesis of nickel in allergic contact dermatitis (ACD), clinically cleared epidermal skin taken 21 days after each challenge was analyzed by immunohistochemistry, flow cytometry and single-cell RNA sequencing (scRNA-seq). Correlating with the worsening skin reactions, an expanding pool of epidermal CD4+ and CD8+ tissue-resident memory T (TRM) cells was seen locally in the challenged skin. Using scRNA-seq a broad subset of TRM cells with various effector phenotypes was identified, which included a predominant population of type 2 T helper (TH2) and KIR+CD8+ TRM cells that expanded with repeated challenge. We observed, broad clonal expansion after nickel challenge with interindividual variations, and clonally related clusters of less differentiated cells which may supply more developed effector TRM cells. Furthermore, repetitive challenge resulted in an increasing population of exhausted regulatory T (Treg) cells that showed lesser clonal expansion. Collectively, our data suggests that repeated challenge to nickel leads to aggravation of eczema and is supported by the increased numbers of effector TRM cells, phenotype differentiation, clonal expansion, and exhaustion of Treg cells in the challenged skin.

overall_design:
Analysis of epidermal skin cells obtained by punch biopsies from preiovusly nickel- or vehicle-challenged clinically cleared skin taken 21 days after each challenge. The exact same skin sites were challenged with nickel for a total of three times with 21 days between challenges.
>>>Submitter declares that raw data are unvailable due to patient privacy concerns<<<


title: The effect of Slc6a6 loss on MSC function.

city: Rochester

first: Cameron

last: Baker

state: NY

address: 601 Elmwood Ave

country: USA

institute: University of Rochester

summary: RNA sequencing analysis was performed on MSCs isolated from age and sex matched Slc6a6 WT/KO mice.

overall_design: Long bones from TauT WT/KO mice were harvested and CD45- MSC cultures were magnetically sorted and processed for RNA-sequencing.

first: Christina

last: Kaszuba

middle: D

first: Jeevisha

last: Bajaj


title: Characterizing Hypoxia-Orchestrated Post-Stroke Changes in Oligodendrocyte Precursor Cells for Improved Stroke Cell Therapy

city: Kyoto

first: Kazuto

last: Tsukita

state: Kyoto

address: 54 Shogoin-Kawaharacho

country: Japan

institute: Kyoto university

summary: Oligodendrocyte precursor cells (OPCs) are traditionally known for their role in differentiating into oligodendrocytes, thereby contributing to myelination. Additionally, it has been increasingly recognized that OPCs actively modify their characteristics in response to the surrounding environment, exhibiting various other functions. However, how and when OPCs change their characteristics after acute ischemic stroke, and the contribution of these changes to post-stroke recovery, are not well understood. In this study, we aimed to transcriptionally characterize the changes in OPCs during acute ischemic stroke and develop therapies to support these changes. For this purpose, we first leveraged mouse single-cell RNA sequencing (scRNAseq) datasets to create a “middle cerebral artery occlusion (MCAO) atlas.” Crucially, we identified the distinct appearance of “angiogenic” OPCs in the subacute phase and “oligogenic” OPCs in the chronic phase after MCAO, contributing to angiogenesis and remyelination, respectively. Furthermore, we successfully induced OPCs ex vivo with similar functional characteristics to “angiogenic” OPCs through severe hypoxic preconditioning. The intravenous transplantation of these hypoxia-preconditioned OPCs more efficiently promoted post-stroke angiogenesis, reduced infarct size, and improved neurological function after MCAO compared to normally treated OPCs. Finally, we demonstrated that mild hypoxia at least partially contributes to the generation of “oligogenic” OPCs. Therefore, following acute ischemic stroke, OPCs sense oxygen levels and undergo phenotypic changes to exhibit functions required at specific times. Importantly, therapies supporting these phenotypic changes hold great promise for improving recovery from damage caused by acute ischemic stroke, for which current available treatments focus on quickly restoring blood flow.

overall_design: To investigate the effect of a mild hypoxic preconditioning on ex vivo POCs, we conducted comparative bulk RNAseq of these mild hypoxic-preconditioned OPCs and normally-treated OPCs.

first: Ken

last: Yasuda

first: Takakuni

last: Maki

first: Yasuhiro

last: Kuwata


title: RNA-seq profiling in dorsal root ganglian (DRG) after fracture surgery and Protectin DX treatment

status: Public on Nov 07 2025

city: Durham

first: Sharat

last: Chandra

state: NC

address: 3 Genome Court

department: Department of Anesthesiology

institute: Duke University

summary: This study investigates the molecular mechanisms by which Protectin DX (PDX), a specialized pro-resolving mediator derived from docosahexaenoic acid, alleviates fracture-induced postoperative pain through GPR37 receptor signaling. The bulk RNA-sequencing experiment was conducted on L3-L5 dorsal root ganglia (DRG) tissues collected from CD1 mice three days after tibial fracture surgery, comparing gene expression profiles between PDX-treated and vehicle-treated groups. The primary goals are to identify differentially expressed genes regulated by PDX treatment, with particular focus on macrophage/neutrophil signaling, cytokine responses, and neuronal excitability pathways that contribute to pain resolution. This transcriptomic analysis aims to elucidate the molecular basis of PDX's superior analgesic efficacy compared to conventional anti-inflammatory treatments, and to understand how PDX promotes rather than delays the resolution of postoperative pain. The findings have significant clinical relevance for developing safer, non-opioid therapeutic strategies for postoperative pain management, particularly in orthopedic surgery patients, where current treatments often remain inadequate despite multimodal approaches.

overall_design: RNA-seq profiling of L3-L5 dorsal root ganglia (DRG) from vehicle- and PDX-treated CD1 mice at day 3 post-tibial fracture surgery. Sample size: n=6 per group (3 males and 3 females)

first: Yize

last: Li

first: Sangsu

last: Bang

first: Jasmine

last: Ji

first: Jing

last: Xu

first: Min

last: Lee

first: Charles

middle: N

last: Serhan

first: Ru-Rong


title: Cannabidiol exerts antiinflammatory effects but maintains T effector memory cell differentiation in humans

city: Indianapolis

first: Michael

middle: T

last: Eadon

state: IN

address: 950 West Walnut Street Room 402 Room 402

institute: Indiana University School of Medicine

summary: Cannabidiol is widely available and often used for pain management. Individuals with kidney disease or renal allografts  have limited analgesia options. We conducted a Phase 1 healthy volunteer study to compare the peripheral immune cell  distribution before (pre-cannabidiol) and after exposure to cannabidiol at steady state (post-cannabidiol).  This study included specimens from  12 participants who received oral cannabidiol (up to 5 mg/kg twice daily)  for 12 days. Lymphocytes were isolated and stimulated with anti-CD3/CD28 antibodies, with or without tacrolimus.  Understanding the clinical safety of cannabidiol use is important given the paucity of pain control options available for  immunocompromised transplant populations. Each individual has three conditions that are sequenced for the phase No CD3/CD28, CD3/CD28 and CD3/CD28 +Tacrolimus across two phases: pre-CBD and post-CBD.

overall_design:
PBMCs were collected from each participant at Day 1 (pre-CBD) and Day 12 (post-CBD). Cells were cultured ex vivo for 72 h under six conditions that combine T-cell stimulation (±CD3/CD28), cannabidiol (±CBD), and tacrolimus (±TAC). After culture, cells were processed for single-cell RNA-seq using the 10x Genomics Chromium 3′ v3.1 workflow and sequenced on an Illumina NovaSeq 6000. In total, 59 libraries (6 conditions × 2 time-points × participants) capture transcriptomic effects of CBD, TAC, and T-cell activation:
1 - No CD3/CD28, No CBD, No Tacrolimus;
2 - CD3/CD28, No CBD; No Tacrolimus;
3 - CD3/CD28, No CBD, Tacrolimus;
4 - No CD3/CD28, CBD; No Tacrolimus;
5 - CD3/CD28, CBD; No Tacrolimus;
6 - CD3/CD28, CBD; Tacrolimus;

first: Debora

middle: L

last: Gisch


title: Analysis of the Cercospora zeina transciptome in the early, mid and late stages of gray leaf spot disease on maize

status: Public on Nov 08 2025

city: Hatfield

first: Dave

middle: Kenneth

last: Berger

state: Gauteng

address: Plant Sciences Complex, Entrance 11 - Corner Lunnon Road & Herold Street

department: Dept. Plant and Soil Sciences, Forestry and Agricultural Biotechnology Institute (FABI)

country: South Africa

institute: University of Pretoria

summary: Cercospora zeina is a fungal pathogen that causes gray leaf spot (GLS) disease on maize (Zea mays L.) in South Africa. Upon landing on a maize leaf, the pathogen rapidly enters through the stomata and continues to develop asymptomatically for up to 28 days before symptoms are seen. As previous work has yet to adequately determine how the pathogen behaves during its infective period, we used transcriptomics to gain insights about the in-planta development of the pathogen and explore how it uses its effectors to facilitate this process. Samples from B73 maize inbreds infected with C. zeina were harvested in a time course experiment and used for RNA sequencing. We used reads mapped to the C. zeina genome as a proxy for biomass accumulation. At the end of the latent period, C. zeina was found to rapidly accumulate biomass and showed a nearly 50-fold increase in biomass as symptoms appeared. There were two distinct transcriptional waves occurring across the infection period. The first wave showed expression of genes for cellular growth, maintenance and immune avoidance, whereas the second wave was enriched with genes involved in detoxification and carbohydrate catabolism. A total of 140 putative effector genes were differentially expressed over the time-courses, with most up-regulated during the mid stage when the switch to necrotrophy occurs. Transient expression of three of these C. zeina effectors (CzEcp2, CzNis1a, CzNis1b) induced plant immunity in Nicotiana spp. resulting in the development of a hypersensitive response. This suggests that a cohort of C. zeina effectors expressed at this time have functions for which receptors have evolved in non-host species like tobacco. Altogether, this work suggests C. zeina behaves as a latent necrotroph during infection and provides a foundation for future research into the infection biology of C. zeina on maize.

sample_organism:
Zea mays
Cercospora zeina

platform_organism:
Zea mays
Cercospora zeina

overall_design: Infection trials were set up by inoculating B73 maize plants with the C. zeina CMW 25467 strain. Samples were harvested at three timepoints: 23, 30 and 44-days post infection (dpi) with four replicates harvested per timepoint. Mock-inoculated plants inoculated with Tween 20 (0.02%) were used as a control for the experiment.

first: Trystan

middle: R

last: Nadasen

first: Ingo

last: Hein

middle: K


title: Control of gene output by intron RNA structure

city: Worcester

first: Leonard

last: Schärfen

state: MA

address: 368 Plantation Street

department: RNA Therapeutics Institute

institute: UMass Chan Medical School

summary: Intron removal through pre-mRNA splicing is a central step in gene expression across Eukarya. The process initiates with the recognition of intronic sequence elements (splice sites) by highly conserved RNA-protein components of the spliceosome. Intron sequences themselves are not generally conserved  beyond the splice sites, yet intronic mutations are often associated with genetic disease. Here we systematically test if and how  intron RNA structure formation modulates gene output. We generated intron variant libraries that measure the impact of base pairing at every position across a natural intron. Using a massively parallel reporter assay (MPRA), we find that base pairing involving the splice sites modulates splicing across orders of magnitude. An additional intron region upstream of the branch site was also sensitive to structure, suggesting steric hindrance. Combining thermodynamic structure prediction with libraries designed to sequester splice sites in structures of varying stability, we show that machine learning models can nearly fully explain observed gene output. Informed by this, designed alterations in intron sequence that modulate base pairing are shown to improve inefficient splicing of human β-globin IVS1. Finally, intronic mutations that alter RNA structure emerge rapidly under selection pressure, providing eukaryotes with a simple  evolutionary strategy to fine-tune gene output.

overall_design: We used Sort-seq to assay the gene output of thousands of intron variants. Introns were either designed to form specific structures, or were randomly generated and then integrated in high-throughput into the yeast genome. Yeast libraries were then sorted using FACS into bins of different fluorescence levels. From each bin, genomic dna was isolated and the intron region amplified. This library was then sequenced. Identifying the frequency with which each variant is found in each bin allows us to estimate the original fluorescence value of every intron variant. In addition to Sort-seq for several different library designs, we also performed a selection experiment to estimate mutation rates of yeast clones that survive evolutionary pressure against a stem loop at the 5'SS. We generated amplicon sequencing libraries to measure mutation rates after mutagenesis and selection.

first: Pernille

last: Bech

first: Paulina

last: Podszywałow-Bartnicka

first: Karla

last: Neugebauer


summary: Cannabidiol is widely available and often used for pain management. Individuals with kidney disease or renal allografts  have limited analgesia options. We conducted a Phase 1 healthy volunteer study to compare the peripheral immune cell  distribution before (pre-cannabidiol) and after exposure to cannabidiol at steady state (post-cannabidiol).  This study included specimens from participants who received oral cannabidiol (up to 5 mg/kg twice daily)  for 12 days. Lymphocytes were isolated and stimulated with anti-CD3/CD28 antibodies, with or without tacrolimus.  Understanding the clinical safety of cannabidiol use is important given the paucity of pain control options available for  immunocompromised transplant populations. Each individual has three conditions that are sequenced for the phase No CD3/CD28, CD3/CD28 and CD3/CD28 +Tacrolimus across two phases: pre-CBD and post-CBD.

overall_design: PBMCs were collected from each participant at Day 1 (pre-CBD) and Day 12 (post-CBD). Cells were cultured ex vivo for 72 h under six conditions that combine T-cell stimulation (±CD3/CD28), cannabidiol (±CBD), and tacrolimus (±TAC). After culture, cells were processed  for single-nucleos RNA-seq using the Chromium Next GEM Single Cell Multiome ATAC + Gene Expression (v.1.0)  workflow and sequenced on an Illumina NovaSeq 6000. In total, 2 libraries (1 condition × 1 time-point × participants) capture transcriptomic effects of CBD, and T-cell activation.


title: EZH2 directs breast cancer progression through the modulation of epithelial cellular plasticity [RNA-Seq]

city: Montreal

first: William

last: Muller

state: Quebec

address: 1160 Av des Pins O

department: Biochemistry

institute: McGill University

summary: Breast cancer remains a leading cause of death among women, encompassing diverse molecular subtypes with distinct clinical outcomes. The HER2+ subtype is particularly aggressive, with many patients eventually developing resistance to HER2-targeted therapies, underscoring the urgent need for alternative treatment strategies. Enhancer of Zeste Homolog 2 (EZH2), the catalytic subunit of Polycomb Repressive Complex 2, represses the expression of genetic programs crucial for differentiation, control of proliferation, and apoptosis through histone H3 lysine 27 trimethylation (H3K27me3). To investigate the role of EZH2 in HER2+ tumor progression, we crossed a genetically engineered mouse model (GEMM) of HER2-driven breast cancer with a conditional Ezh2 knockout strain. The results showed that Ezh2 is essential for accelerating tumor initiation and metastatic dissemination in HER2-driven breast cancer. Combined bulk and single cell RNA sequencing analyses revealed a significant downregulation of basal cell populations in the absence of Ezh2, characterized by the loss of Tp63 expression, and an upregulation of luminal progenitor cell populations, driven by crucial transcription factors such as Esr1, thereby driving luminal lineage commitment. Further, inhibition of EZH2 in vitro resulted in increased expression of ER in HER2+ human breast cancer cell lines and rendered them susceptible to tamoxifen. Altogether, these findings demonstrate that EZH2 dictates breast cancer plasticity through control of cellular identity and provides rationale for combining EZH2 inhibitors with endocrine therapies to improve outcomes in HER2+ breast cancer.

overall_design: RNA-seq profiling of wildtype EIC/EZH2 tumor cells and  EIC/EZH2 knockout tumor cells obtained from mice, 5 biological samples for each group

first: Linshan

last: Liu

first: Ellie

last: Massey

first: Dongmei

last: Zuo

first: Alain

last: Pacis

first: Mert

last: Demirdizen

first: Jessica

last: Cinkornpumin

first: Yu

last: Gu

first: Elizabeth

last: Podleszanski

first: Hailey

last: Proud

first: Virginie

last: Sanguin-Gendreau

first: Vasilios

last: Papavasiliou

first: Zhengze

last: Jiang

first: Harvey W.

last: Smith

last: Pastor

first: Paolo

last: Ceppi

first: William J.


first: Michael

last: Eadon

summary: This SuperSeries is composed of the SubSeries listed below.

overall_design: Refer to individual Series

first: Debora

last: Gisch


title: Location and etiology modulate fibroblast activation in the failing human heart

city: Leuven

first: Hywel

middle: Llewelyn

last: Roderick

address: Herestraat 49

department: Cardiovascular Sciences

country: Belgium

institute: Katholieke Universiteit Leuven

summary: Cardiac fibrosis is a major contributor to heart failure (HF), yet its therapeutic targeting remains limited due to the complexity of fibrosis types and distributions. This study investigates fibroblast heterogeneity and spatial organization in the left ventricle of human hearts from non-failing donors and HF patients with ischemic or dilated cardiomyopathy. Using single-nucleus RNA sequencing and spatial transcriptomics, distinct fibroblast subpopulations were identified, with resident fibroblasts being depleted in HF and replaced by disease-associated states. Differences in activation ligands, transcriptional trajectories, and spatial localization revealed divergent fibroblast transitions between scar and interstitial fibrosis, and between HF subtypes. These results provide insight into fibroblast dynamics and offer potential targets to modulate fibrosis in heart failure.

overall_design: Nuclei from snap frozen human cardiac tissue was sequenced using 10x technology in 3 batches. 4 non-failing samples included (each 2 in one 10x lane). 6 samples from DCM, 5 samples from ICM (non-scar), and 5 samples form ICM-scar were included.

first: Mohamad

last: Youness

first: Samaneh

last: Ekhteraei-Tousi

first: Rosa

last: Doñate Puertas

first: Chandan

last: Nagaraju

first: Karin

last: Sipido


title: Characterisation of human in vitro tumour-associated macrophage models to define translational relevance

city: Barcelona

first: Clara

last: Alsinet

address: Diagonal 615

country: Spain

institute: AstraZeneca

summary: Tumour-associated macrophages (TAMs) are key components of the tumour microenvironment with a demonstrated ability to modulate anti-tumour T-cell responses and immunotherapy outcomes. With increasing realisation that the M1/M2 paradigm does not reflect the complexity of macrophage phenotypes in cancer patients, an urgent need has arisen to develop improved, translatable in vitro models for human TAMs. To address this gap, we have screened conditioned media from a panel of tumour cell lines for their ability to induce suppressive marker upregulation on human monocyte-derived macrophages (hMDMs), as well as active T-cell immunosuppression. We performed secretome characterization of these tumour-conditioned media (TCM) to shed light on cancer cell-derived soluble factors that may contribute to TAM polarisation. Furthermore, we characterized the proteomic and transcriptomic signatures of macrophages exposed to either TCM or primary ascites fluid from ovarian cancer patients and performed bioinformatics analysis to determine the most translationally relevant models of TAMs. In summary, our work provides mechanistic insights on tumour-macrophage crosstalk in the context of establishing suppressive TAM phenotypes and addresses the long-standing gap of defining translationally relevant human in vitro TAM models.

overall_design: RNAseq profiling of in vitro differentiated macrophages from freshly isolated CD14+ monocytes. Monocytes were differentiated for 6 days in 50ng/ml of M-CSF with tumor conditioned media from cancer cell lines cultures or ascites fluid from ovarian cancer patients.

first: Arthur

last: Dyer

first: Rebecca

last: Dudley

first: Shreya

last: Ahuja

first: Pawan

last: Poudel

first: Georgina

last: Bowyer

first: Kalvin

last: Sahota

first: Saly

last: Songvilay

first: Des

last: Jones

first: Matthew

last: Glover

first: Sonja

last: Hess

first: Elina

last: Timosenko

first: Simon

middle: J

last: Dovedi


title: The exit of naïve pluripotency contains a metabolism-induced checkpoint for telomere homeostasis.

city: London

first: Veronique

last: Azuara

state: London

address: Institute of Reproductive and Developmental Biology, Hammersmith Hospital Campus

department: Metabolism, Digestion and Reproduction

country: United Kingdom

institute: Imperial College London

summary: During peri-implantation development, the pluripotent tissue of the early embryo undergoes profound cellular and biochemical reprogramming. These transformations are essential for subsequent development, yet how they are coordinated with the preservation of genome integrity remains poorly understood. Here, we uncover a telomere length checkpoint that is elicited by metabolic remodeling as mouse embryonic stem cells (ESCs) transition from the naïve to formative pluripotent state. We show that the exit of naïve pluripotency is marked by accelerated mitochondrial respiration and de novo lipogenesis, fueling lipid droplet accumulation required for tissue remodeling. Unexpectedly, these acute metabolic shifts trigger transient telomere shortening and activate ZSCAN4, a pluripotency-associated regulator of telomeres, followed by telomere re-elongation as cells adopt a more glycolytic metabolic profile. Our findings reveal a feedback mechanism in which metabolism-induced telomere stress engages ZSCAN4 as a protective response, thereby linking metabolic state to telomere homeostasis during early developmental progression.

first: Roshni

middle: A

last: de Souza


title: SOX2 is a dispensable modulator of NUT carcinoma oncogenesis in mouse

city: East Lansing

first: Bin

last: Gu

state: MI

address: 755 Woodlot Drive

department: OBGYN

institute: Michigan State University

summary: NUT Carcinoma (NC) is an aggressive and lethal malignancy driven by BRD4::NUTM1 and other NUTM1 fusion oncogenes, which aberrantly activate transcription factors (TFs) linked to poorly differentiated squamous cell carcinoma (SCC) phenotypes. Among these, SOX2 has been proposed as a critical driver. However, its roles in NC initiation and progression have not been investigated in vivo. Here, using a genetically engineered mouse model (GEMM) that faithfully recapitulates human NC, we performed lineage-specific conditional deletion of Sox2 in both squamous and non-squamous tissues during NC oncogenesis. We found that SOX2 is dispensable for NC initiation and progression, and that tumors lacking SOX2 retain characteristic histological features and expression of key oncogenic drivers, including BRD4::NUTM1, MYC, and TP63. Bulk RNA sequencing revealed only modest transcriptional changes in SOX2-deficient tumors, primarily affecting metabolic and biosynthetic pathways, without disrupting core oncogenic programs. These findings challenge the assumption that SOX2 is universally required for NC oncogenesis and highlight the autonomy of BRD4::NUTM1 in establishing and maintaining the NC phenotype. Our results suggest that SOX2-targeted therapies may have limited utility as monotherapy and provide a refined framework for prioritizing  therapeutic targets for this devastating cancer.

overall_design: RNA-seq profiling of wildtype and Sox2 KO tumors from oral cavity and pancreas

first: Chenxiang

last: Luo


title: Multi-Omics Elucidation of KDM5C, KDM6A, and KMT2B Roles in Cancer Epigenetic Dysregulation and Transcriptional Reprogramming [ATAC-seq]

city: Shanghai

first: Tengjiao

last: Li

address: No.800, Dongchuan Road, Minhang District, Shanghai, China Address in Chinese

department: School of Pharmaceutical Sciences

country: China

institute: Shanghai Jiao Tong University

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Histone-modifying enzymes (HMEs) are critical regulators of tumorigenesis through epigenetic reprogramming. While mutations in HMEs are recognized drivers of cancer epigenome dysregulation, systematic comparative analyses of their mutational impacts and functional divergence across malignancies remain underexplored. This study addresses this gap by investigating three HMEs—KDM5C (H3K4me3 demethylase), KMT2B (H3K4me3 methyltransferase), and KDM6A (H3K27me3 demethylase)—frequently mutated in diverse cancers. Using CRISPR/Cas9 knockout cell lines, we performed integrated multi-omics profiling encompassing genome-wide chromatin accessibility, transcriptomics, and chromatin-bound proteomics. Contrary to expectations that KMT2B loss (H3K4me3 depletion) and KDM5C loss (H3K4me3 accumulation) would induce opposing transcriptional programs, or that KDM6A deficiency (H3K27me3 accumulation) would exhibit distinct regulatory effects, our analyses revealed striking discrepancies between transcriptional outputs and chromatin-associated proteomic states across all three knockouts. Notably, each HME knockout elicited distinct transcriptional regulatory patterns, challenging conventional assumptions about their antagonistic or synergistic functions. These findings highlight context-dependent functional hierarchies among HMEs and underscore the necessity of multi-dimensional profiling to resolve epigenetic regulatory complexity. Our work advances the mechanistic understanding of cancer epigenetics and provides a framework for elucidating tumorigenic vulnerabilities linked to HME dysregulation.

overall_design: ATAC-seq: 50,000 cell nuclei were collected from each cell line. Resuspend cell nuclei in 50 ul of transposition mixture (25 ul 2× TD buffer, 2.5 ul transposase (100nM final), 16.5 ul PBS, 0.5 ul 1% digitonin, 0.5 ul 10% Tween-20, 5 ul H2O) by pipetting up and down 6 times. Incubate reaction at 37°C for 30 minutes in a HUXImixer (HUXI, shanghai) with 1000 RPM mixing. Transposition reactions were cleaned up with a UNIQ-10 Column MicroDNA Gel Extraction Kit (Songon Biotech, shanghai). Libraries were amplified with Illumina Nextera sequencing primers.


title: Multi-Omics Elucidation of KDM5C, KDM6A, and KMT2B Roles in Cancer Epigenetic Dysregulation and Transcriptional Reprogramming [RNA-seq]

overall_design: RNA-seq profiling of wildtype HEK293T cells and their knockout derivatives (sgKDM5C, sgKDM6A, and sgKMT2B).


title: RhCMV Expands CCR5 Memory T Cells and promotes SIV reservoir seeding in the Gut Mucosa

city: Covington

first: Joseph

last: Mudd

state: LA

address: 18703 Three Rivers Road

department: Division of Immunology

institute: TNPRC

summary: Cytomegalovirus (CMV) is a prevalent β-herpesvirus that persists asymptomatically in immunocompetent hosts. In people with HIV-1 (PWH), CMV is associated with HIV-1 persistence and particular inflammatory-related co-morbidities. The true causative role of CMV in HIV-associated pathologies however remains unclear given that nearly all PWH are coinfected with CMV. In this study, we examined acute phase immune and virological dynamics in cohorts of SIV-infected rhesus macaques (RMs) that were naturally seropositive or -negative for rhesus CMV (RhCMV). We observed prior to SIV, RhCMV expanded a polyclonal population of target CCR5+CD4+ T cells in gut and lymph nodes (LN) that expressed the chemotactic receptor CXCR3 and were largely not specific for RhCMV. Upon SIV infection, RhCMV+ RMs exhibited higher peak viremia and elevated levels of SIV DNA in the upper and lower intestine. Greater seeding of SIV DNA was associated with a maintenance of CCR5-expressing CD4+ T cells that were enriched within the RhCMV+ gut along a CXCR3-CXCL9 chemotactic axis. Overall, the data suggest that RhCMV can promote SIV susceptibility within a diverse, polyclonal pool of CD4 T cells that are not entirely RhCMV-specific.

overall_design: Bulk RNA TCR-seq was performed on sorted CD4+CCR5+ and CD4+CMV-specific T cells from 5 rhesus macaques. CMV-specific T cells were identified and sorted using an activation-induced marker assay following in vitro stimulation with CMV lysate.

first: Chrysostomos

last: Perdios

first: Naveen Suresh

last: Babu

first: Celeste D.

last: Coleman

first: Anna T.

last: Brown

first: Shevon N.

last: Alexander

first: Matilda J.

last: Mostrom

first: Carolina

last: Allers

first: Lara

last: Doyle-Meyers

first: Christine M.

last: Fennessey

first: Lori A.

last: Rowe

first: Brandon F.

last: Keele

first: Amitinder

last: Kaur

first: Michael L.

last: Freeman

first: Joseph C.


title: PLAMseq enables the simultaneous proteo-genomic characterization of chromatin-associated proteins and protein interactions in a single workflow.

city: Sevilla

first: Román

last: González-Prieto

address: Americo Vespucio 24

institute: CABIMER

summary:
Chromatin Immunoprecipitation (ChIP) and Co-Immunoprecipitation (CoIP) assays are the most common approaches to characterize the genomic localization and protein interactors, respectively for a protein of interest. However, these approaches require the use of specific antibodies, which are costly reagents that often face sensitivity and specificity issues. Based on TurboID, we developed PLAMseq (Proximity Labelled Affinity-purified Mass spectrometry plus sequencing), after a short biotin pulse, DNA-protein crosslinks are induced by formaldehyde and the interactors of a protein of interest together with their associated DNA sequences are purified simultaneously and identified by mass spectrometry-based proteomics and Next Generation Sequencing, respectively.
To validate PLAMseq, we performed the proteo-genomic characterization of two proteins which genomic loci are very well characterized, namely, RNA polymerase II and CTCF with excellent robustness and reproducibility. Next, we applied PLAMseq to characterize Histone H1 SUMOylation, a histone post-translational modification which study has remained elusive due to the lack of specific reagents. SETDB1 binds to SUMOylated histone H1 and, accordingly, SUMOylated histone H1 colocalize with H3K9me3 at repetitive regions of the genome.

overall_design: PLAMseq (Proximity Labelled Affinity-purified Mass spectrometry plus sequencing) was performed in CTCF-TurboID, POL2RI-TurboID, TurboID-H1.2, TurboID-H1.4, TurboID-H1.0, NTurboID-H1.2 + CTurboID-SUMO1, NTurboID-H1.2 + CTurboID-SUMO2, NTurboID-H1.4 + CTurboID-SUMO1, NTurboID-H1.4 + CTurboID-SUMO2, NTurboID-H1.0 + CTurboID-SUMO1, NTurboID-H1.0 + CTurboID-SUMO2, TurboID-only and Wild Type HeLa cell lines after 10 minutes biotin 1x exposure. All experiments were done in triplicate.

first: Lourdes

last: González-Vinceiro

first: Carmen

last: Espejo-Serrano

first: María Eugenia

last: Soler-Oliva

first: María Luisa

last: Mateos-Martín

first: Daniel

last: Rico

first: Cristina

last: González-Aguilera


title: LHPP expression in triple-negative breast cancer promotes tumor growth and metastasis by modulating the tumor microenvironment

city: La Jolla

first: Jeffrey

last: Reina

state: CA

address: 10010 N Torrey Pines Rd

institute: Salk Institute for Biological Studies

summary: Triple-negative breast cancer (TNBC) is a highly aggressive and metastatic form of breast cancer that lacks an effective targeted therapy. To identify potential therapeutic targets, we investigated the phosphohistidine phosphatase, LHPP, which has been implicated in the development of several types of cancer. However, the full significance of LHPP in cancer progression remains unclear due to our limited understanding of its molecular mechanism. We found that levels of the LHPP phosphohistidine phosphatase were significantly increased in human breast cancer patients compared to normal adjacent tissues, with the highest levels in the TNBC subtype. When LHPP was knocked out in the MDA-MB-231 human TNBC cell line, cell proliferation, wound healing capacity, and invasion were significantly reduced. However, LHPP knockout in TNBC cells did not significantly affect overall phosphohistidine protein levels. Interestingly, LHPP knockout in MDA-MB-231 cells delayed tumor growth and reduced metastasis when orthotopically transplanted into mouse mammary glands. To investigate LHPP’s role in breast cancer progression, we used next-generation sequencing and proximity-labeling proteomics, and found that LHPP regulates gene expression in chemokine-mediated signaling and actin cytoskeleton organization. Depletion of LHPP reduced the presence of tumor-infiltrating macrophages in mouse xenografts. Our results support a tumor promoter role for LHPP phosphohistidine phosphatase in MDA-MB-231TNBC cells and suggest that targeting LHPP phosphatase could be a potential therapeutic strategy for TNBC.

overall_design: To understand the molecular pathways regulated by LHPP, RNAseq was performed on human breast cancer cells with and without LHPP expression. LHPP was genetically depleted in the MDA-MB-231 and MCF7 cell lines via CRISPR-Cas9, generating LHPP knockout (KO) and wild-type (WT) control cells. RNA was extracted from both cell types, followed by library preparation and RNA sequencing to capture differences in gene expression profiles when LHPP is depleted. Three replicates for each cell type were used

first: Queralt

last: Vallmajo-Martin

first: Jia

last: Ning

first: Aubrey

last: Michi

first: Kay

last: Yeung

first: Geoffrey

last: Wahl

first: Tony

last: Hunter


title: The methyl-CpG-binding protein 2 inhibits cGAS-associated signaling

city: Montpellier

first: Nadine

last: LAGUETTE

address: 1919 Rte de Mende

country: France

institute: Institut de Génétique Moléculaire de Montpellier

summary: We analyzed the impact of dsDNA stimulation on transcriptomics and retrotranscriptomics profiles in murine cell lines (Mouse Embryonic Fribroblasts and RAW264.7).

overall_design: WT-RAW264.7  and WT-MEF were transfected (or not: Mock) with dsDNA prior to RNA or DNA extraction respectively.  WT and Mecp2 KO RAW264.7 cells were subjected to RNA extraction. All experiemtns were performed in triplicates.

first: Hanane

last: Chamma

first: Soumyabrata

last: Guha

first: Roger Junior

last: Eloiflin

first: Adeline

last: Augereau

first: Pierre

last: Le Hars

first: Moritz

last: Schüssler

first: Yasmine

last: Messaoud-Nacer

first: Mohammad

last: Salma

first: Joe

last: McKellar

first: Joanna

last: Re

first: Morgane

last: Chemarin

first: Arnaud

last: Carrier

first: Michael

last: Disyak

first: Clara

last: Taffoni

first: Robin

last: Charpentier

first: Zoé

last: Husson

first: Emmanuel

last: Valjent

first: Charlotte

last: Andrieu-Soler

first: Eric

last: Soler

first: Maria

middle: H

last: Christensen

first: Søren

last: Paludan

first: Florian

last: Schmidt

first: Daniela

last: Tropea

first: Karim

last: Majzoub

first: Isabelle

last: Vila

last: Laguette


title: Single cell (sc) RNAseq reveals transcriptional states of transgenic MAGE-A1 specific TCR-T CD4+ and CD8+ cells in NSG tumor model

city: Seattle

first: Aude

last: Chapuis

state: WA

address: 1100 Fairview Ave

institute: Fred Hutchinson Cancer Center

summary: We have studied the efficacy of MAGE-A1 specific transgenic T cells against A375F NSG model by flow cytometry and IHC analysis. We then employed a scRNAseq approach to characterize the transcriptional states of transgenic CD4+ and CD8+ TCR-T cells that infiltrated into A375F tumor by extracting these cells from tumors. This scRNAseq study allow us to compare the transcriptional differences between our groups ( T-TCR-MA1-CD8ab, T-TCR-MA1-CD8/28)

overall_design: CD4+ and CD8+ T-TCR-MA1-CD8ab, T-TCR-MA1-CD8/28 were infused into in vivo murine models with A375F tumor cell line as described in methods.  Four  of the following group were compared: CD4+  T-TCR-MA1-CD8ab only , CD8+  T-TCR-MA1-CD8ab only, CD4+ and CD8+ T-TCR-MA1-CD8ab combo, and  CD4+ and CD8+ T-TCR-MA1-CD8/28 combo. Tumors (n=6) were digested and CD4+ and CD8+ T cells were sorted from single cell suspension.  CD4+ only and CD8+ only T-TCR-MA1-CD8ab (pooled as one sample) (NSG_CD8_4), CD4+ and CD8+ T-TCR-MA1-CD8ab combo(NSG_WT), and CD4+ and CD8+ T-TCR-MA1-CD8/28 combo(NSG_G) were then continued for scRNA seq library prep.

first: Shihong

last: Zhang

first: Tzu-Hao

last: Tang

first: Sinead

last: Kinsella

first: Francesco

last: Mazziotta

first: Lauren

last: Martin

first: Bo

last: Lee


title: Integrated stress response inhibition prolongs the lifespan of a Pelizaeus-Merzbacher disease mouse model by increasing oligodendrocyte survival.

city: Chicago

first: Brian

last: Popko

state: IL

address: 7601 Morton Medical Research Building, 320 East Superior Street

department: Neurology

institute: Northwestern Feinberg School of Medicine

summary: The leukodystrophy Pelizaeus-Merzbacher disease (PMD) is caused by myelin protein proteolipid protein gene (PLP1) mutations. PMD is characterized by oligodendrocyte death and CNS hypomyelination; thus, increasing oligodendrocyte survival and enhancing myelination could provide therapeutic benefit. Here, we use the PMD mouse model Jimpy to determine the impact of the integrated stress response (ISR) on the oligodendrocyte response to mutant PLP expression. Male Jimpy animals in which the ISR-triggering eukaryotic initiation factor (eIF) 2α kinase, protein kinase-like endoplasmic reticulum kinase (PERK), is inactivated have an extended lifespan that correlates with increased oligodendrocyte survival and enhanced CNS myelination. Inactivation of downstream components of the ISR pathway, in contrast, does not rescue oligodendrocytes or myelin. Phosphorylated eIF2α inhibits the exchange factor eIF2B, resulting in diminished protein synthesis. Treatment with small molecule eIF2B activators 2BAct and ISRIB increases oligodendrocyte survival, CNS myelination, and doubled the Jimpy lifespan. These results suggest that ISR modulation could provide therapeutic benefit to PMD patients.

overall_design: We have two distinct sets of samples. One is from mice in which the ISR gene Perk is inactivated specifically in oligodendrocytes: we have samples from WT mice (control and Perk mutants) as well as Jimpy mice (control and Perk mutants). The other set of samples is from WT and Jimpy mice treated with the ISR inhibitor 2BAct at three different developmental time points P7, P14, and P21.

first: Yanan

last: Chen

first: Rejani

last: Kunjamma

first: Karin

last: Lin

first: Caitlin

last: Connellly

first: Carmela

last: Sidrauski


title: UMP functions as an endogenous regulator of NR4A1 to control gastric cancer progression [ChIP-Seq]

city: Guangzhou

first: Guodi

last: Cai

state: Guangdong Province

address: 132, Waihuandonglu, Daxue Cheng

department: School Of Pharmaceutical Sciences

institute: Sun Yat-Sen university

summary: Nucleotide metabolism reprogramming drives tumor progression, yet how tumor cells sense nucleotide levels remain unclear. Here we identified UMP as an endogenous regulator of the orphan nuclear receptor NR4A1 in gastric cancer (GCa). Under UMP-sufficiency, UMP directly binds to NR4A1, inhibiting its tumor-suppressive function and promoting GCa progression. Conversely, UMP deficiency resulting from disrupted pyrimidine biosynthesis derepresses NR4A1, which suppresses GCa cell survival and progression by both increasing NR4A1 occupancy at super‑enhancers to reprogram survival‑gene expression and enhancing NR4A1’s pro‑apoptotic activity at the mitochondria. NR4A1 loss was sufficient to rescue the effects of pyrimidine nucleotide stress on GCa cells in vitro and in vivo. NR4A1 agonists suppressed the pyrimidine salvage pathway triggered by de novo pyrimidine biosynthesis (DNPB) inhibition. Co-targeting DNPB and NR4A1 induced synergistic tumor lethality in GCa xenograft models. Together, our results establish UMP as an endogenous regulator of NR4A1 and provide an effective therapeutic strategy for GCa.

overall_design: AGS cells were treated with vehicle, BAY (5 nM) or BAY (5 nM) plus Uridine (100 μM) for 24 h before harvested. Cell preparation, crosslinking, nuclei preparation and chromatin shearing was following truChIP® Chromatin Shearing Kit (Covaris), according to the manufacturer’s instruction. Chromatin fragments were precipitated by using specific antibodies and Protein G beads, washed, and treated with Proteinase K and RNAse A. Purified ChIP DNA was then used for library generation. Libraries were quantified with the Bioanalyzer 2100 (Agilent) and sequenced in single-end 50-bp mode on the MGISEQ2000 (BGI, Wuhan, China). Antibodies used were against H3K27ac (Abcam; ab4729).

first: Junjian

last: Wang

first: Zhenhua


title: UMP functions as an endogenous regulator of NR4A1 to control gastric cancer progression

overall_design: AGS cells were treated with vehicle or DHODH inhibitors BAY (5 nM) or Ach-A (0.75 μM), or the combination of BAY (5 nM) and uridine (100 μM), or NR4A1 agonists Csn-B (40 μM) for 48 h before RNA extraction. RNA-seq libraries from 1 μg total RNA were prepared using Illumina Tru-Seq RNA Sample, according to the manufacturer’s instructions. Libraries were validated with an Agilent Bioanalyzer (Agilent Technologies, Palo Alto, CA). Sequencing was performed on the BGISEQ platform at BGI Tech (Wuhan, China). The FASTQ-formatted sequence data were analyzed by using a standard BWA–Bowtie–Cufflinks workflow. Sequence reads were mapped to GRCh38/hg38 assembly with BWA and Biotie software. The Cufflinks package was used for transcript assembly, quantification of normalized gene and isoform expression, and analysis of different expression. Gene Set Enrichment Analysis (GSEA v.3.0) was applied to rank genes based on the shrunken limma log2 fold changes. The GSEA tool was used in “pre-ranked” model with default parameters.


title: Alteration of Autophagy and Glial Activity in Nilotinib-Treated Huntington’s Disease Patients

city: Washington, DC

first: Max

last: Stevenson

state: DC

address: 3970 Reservoir Rd. NW

institute: Georgetown University

type: Non-coding RNA profiling by high throughput sequencing

summary: We explored the effects of a low dose of nilotinib (150 mg) on behavioral changes and motor symptoms in manifest HD patients and examined the effects of nilotinib on several brain mechanisms, including dopamine transmission and gene expression via cerebrospinal fluid (CSF) miRNA sequencing. Nilotinib, 150 mg, did not result in any behavioral changes, although it significantly attenuated HVA levels, suggesting reduction of dopamine catabolism. There was no significant change in HTT, phosphorylated neuro-filament and inflammatory markers in the CSF and plasma via immunoassays. Whole miRNA genome sequencing of the CSF revealed significant longitudinal changes in miRNAs that control specific genes associated with autophagy, inflammation, microglial activity and basal ganglia neurotransmitters, including dopamine and serotonin.

overall_design: We performed whole genome miRNA sequencing in the CSF (n = 5) collected at baseline and 3 months from each individual patient to allow us to measure longitudinal miRNA changes. miRNAs inversely regulate mRNA, and they do not necessarily require large changes to affect their targets, therefore, we assessed all miRNA that met p < 0.05 between 3 months and baseline

first: Rency

last: Varghese

first: Charbel

last: Moussa


title: Convergent evolution of scavenger cell development at vertebrate brain borders

city: Melbourne

first: Michelle

last: Meier

address: 305 Grattan Street

country: Australia

institute: Peter MacCallum Cancer Centre

summary: The vertebrate central nervous system (CNS) is protected by the blood brain barrier (BBB) and meningeal membranes, which ensure immune privilege. In the mammalian brain, microglia and border associated macrophages (BAMs) provide immune surveillance and scavenge wastes, yet how evolution shaped immune-cell diversity and function is not understood. In zebrafish, a vascular-derived mural lymphatic endothelial cell (muLEC) lineage fulfils scavenger cell functions at CNS borders. Here, we identify the transcription factor odd-skipped related 2 (osr2) as a specific marker and regulator of muLEC differentiation and maintenance. osr2 controls the transition of muLECs from interconnected endothelial cells to individual scavenger cells in part via control of cadherin-6 (cdh6). muLECs are more transcriptionally similar to BAMs than to other mammalian meningeal cells and share several functions in tissue homeostasis. However, BAMs are absent from zebrafish and muLECs from mice and humans. Analysis of osr2, LEC and BAM markers in diverse vertebrate species reveals muLECs as an ancient lineage and BAMs a recent mammalian specialisation. muLECs and BAMs share functional analogies but are not homologous, providing an example of convergent evolution. This highlights the physiological importance of meningeal scavenger cells and the developmental plasticity of LECs in generating specialised cell types throughout evolution.

sample_organism:
Danio rerio
Mus musculus

platform_organism:
Danio rerio
Mus musculus

overall_design: This study contains three datasets from two species (zebrafish and mouse). 1. Cells of transgenic WT zebrafish heads (7dpf) were isolated using fluorescence activated cell sorting (FACS) according to the presence or absence of kdrl (+). 2. Cells of transgenic WT and osr2-/- zebrafish heads (30dpf) were isolated using fluorescence activated cell sorting (FACS) according to the presence or absence of fli1a (+) and lyve1b (+) 3. Cells of 488acLDL uptake enriched cells of the mouse meningeal layer (3 months) were isolated using FACS, according to presence of absence of 488acLDL. scRNA-seq analysis was performed both within and across species and datasets.

first: Andrea

last: U Gaudi

first: Oguzhan

middle: F

last: Baltaci

first: Sayali

last: Chowdhary

first: Frank

last: Tulenko

first: Stefanie

last: Dudczig

first: Sebastian-Alexander

last: Stamatis

first: Scott

last: Paterson

first: Hujun

last: Yu

first: Maria Cristina

last: Rondon Galeano

first: Elizabeth

last: Mason

first: Lee

last: Miles

first: Robert

last: Bryson-Richardson

first: Andrew

last: Pask

first: Jana

last: Vukovic

first: Anne

last: Lagendijk

first: Kelly

last: Smith

first: Jan

last: Kaslin

first: Michael

last: Harrison

first: Peter

last: Currie

first: Neil

last: Bower

first: Benjamin

last: Hogan


title: Non-canonical functions of UGT2B17 promote castrate-resistant prostate cancer progression

city: Vancour

first: Xuesen

last: Dong

address: 276 - 2660 Oak Street

institute: Vancour Prostate Cancer

summary: When prostate cancer (PCa) overcomes the androgen receptor (AR) target therapy and progresses to the castrate-resistant prostate cancer (CRPC) stage, it becomes curable. UDP glucuronosyltransferase 2B17 (UGT2B17) is the key enzyme determining androgen bioavailability to AR inside PCa cells. However, whether UGT2B17 promotes CRPC progression remains poorly understood. Here, we report that anti-AR therapy increases UGT2B17 protein stability. UGT2B17 is localized in both the cytoplasm and nucleus to exert multiple non-enzymatic functions. In the cytoplasm, UGT2B17 activates unfolded protein response (UPR) to counteract endoplasmic reticulum (ER) stress for cell survival. UGT2B17 can exert its nuclear functions by stimulating c-Src kinase to activate AR in the absence of androgens. The UGT2B17-Src axis confers PCa cells resistant to DNA damage and promotes cell cycling by passing the G2 checkpoints through de-activating ATM and ATR kinases. We conclude that these non-enzymatic functions of UGT2B17 activate multiple survival pathways to allow CRPC progression.

overall_design: RNA-seq analysis comparing the transcriptome between LNCaP95(UGT2B17 KO) and LNCaP95(UGT2B17 KO) transfected with UGT2B17WT UGT2B17Mut SRCK259M or SRCY530F


title: Genome-wide CRISPR Knockout Screen in HAP1 MTHFD1-K56R cells to identify genes which confer to resistance to adenosine toxicity

status: Public on Nov 06 2025

city: Vienna

first: Stefan

last: Kubicek

address: Lazarettgasse 14

country: Austria

institute: CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences

summary: This dataset contains sequencing data from a pooled CRISPR knockout screen performed in HAP1 MTHFD1K56R (i.e. harbouring a K56R mutation in MTHFD1) cells. Cells were transduced with a lentiviral genome-wide sgRNA knockout library (Brunello, Addgene #73179) followed by puromycin selection. The screen was then performed in IMDM medium with dialysed FBS supplemented with 50µM adenosine (ADE). Under these conditions, HAP1 MTHFD1K56R usually die. Dialysed medium (DIA) was used as control conditions. Cells were expanded for 14 days and surviving cells were collected for subsequent sequencing analyses. The screen aimed to identify genes whose loss would confer to adenosine resistance in HAP1 MTHFD1-K56R cells. Sequencing was performed to identify sgRNA abundances between adenosine treatment and control. Data was analyzed using PinAPL-Py.

overall_design: MTHFD1-K56R cells were transduced with Brunello sgRNA KO library (MOI approx. 1, >500x sgRNA coverage), selected for puromycin and cultured for 14days in total in dialysed media -+ 50µM adenosine. Experiments were performed in duplicates (2x DIA = CTRL, 2x ADE)

first: Jung-Ming George

last: Lin


title: A chromatin-linked CPL2–PHD2/3 module sustains multiple DNA methylation pathways and Polycomb silencing [WGBS]

city: Shenzhen

first: Jian-Kang

last: Zhu

state: Guangdong

address: 1088 Xueyuan Blvd, Nanshan

department: Institute of Advanced Biotechnology, Institute of Homeostatic Medicine, and School of Medicine

institute: Southern University of Science and Technology

type: Methylation profiling by high throughput sequencing

summary: While multiple chromatin-based epigenetic pathways are well characterized, their genome-wide coordination and hierarchical interplay remain poorly understood. We previously identified the BAH–PHD–CPL2 complex, where AIPP3 binds H3K27me3 via its BAH domain and, in concert with PHD2 and PHD3 (PHD2/3), recruits CPL2 to repress transcription by dephosphorylating RNA Polymerase II. Here, we show that CPL2 and PHD2/3 form a distinct module (CPL2–PHD2/3) that safeguards CHH DNA methylation and silences CHH-methylated sites at transposable elements (TEs) through engagement of multiple DNA methylation pathways. The CPL2–PHD2/3 module physically associates with SUVH4 and SUVH5 (SUVH4/5) to preserve SUVH4/5–CMT2-mediated CHH methylation at a subset of H3K9me2-marked regions. Chromatin enrichment of PHD3 likewise enables the module to sustain RNA-directed DNA methylation (RdDM)-mediated CHH DNA methylation at sites bearing H3K9me2, H3K27me3, or neither. Thus, CPL2–PHD2/3 emerges as a previously underappreciated, multifunctional regulator of plant DNA methylation networks. Unexpectedly, its gene repression function is uncoupled from DNA methylation. CPL2–PHD2/3 represses Polycomb-marked genes by interacting with LHP1 or recognizing hypomethylated H3K4. While it cooperates with LHP1 at a subset of targets, it also independently silences many more genes that LHP1 alone cannot repress, both sets of genes being critical for proper development. This dual, yet largely LHP1-insufficient, repression mode singles out CPL2–PHD2/3 as the essential executor of Polycomb silencing. Together, our findings establish CPL2–PHD2/3 as a chromatin-responsive integrator that spans DNA methylation and Polycomb-associated repression, providing a unifying mechanism for epigenetic control of both TEs and genes across diverse chromatin landscapes.

overall_design: To investigate whether the CPL2–PHD2/3 module regulates DNA methylation and how it interacts with SUVH–CMT-mediated methylation maintenance loops and/or RdDM-dependent de novo pathways, we generated single-base resolution DNA methylome maps for Col-0, cpl2-2, phd2-1, phd3-1, as well as CRISPR (C) knockout lines of the double mutants phd2/3C11 (hereafter referred to as phd2phd3C11 in library names) and phd2/3C19 (phd2phd3C19). To further assess transcriptional consequences associated with DNA methylation or Polycomb silencing, we performed RNA sequencing on the same set of genotypes.

first: Lingrui

last: Zhang

first: Kai

last: Tang


title: A chromatin-linked CPL2–PHD2/3 module sustains multiple DNA methylation pathways and Polycomb silencing [RNA-seq]


title: A chromatin-linked CPL2–PHD2/3 module sustains multiple DNA methylation pathways and Polycomb silencing.

summary: This SuperSeries is composed of the SubSeries listed below.

overall_design: Refer to individual Series


title: Inhibition of heme biosynthesis triggers cuproptosis in acute myeloid leukemia

first: Emily

last: Gruber

state: VIC

address: 305 Grattan St

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus


title: Sprint interval exercise drives a unique transcriptional mitochondrial stress response in humans

first: Javier

last: Botella

address: Ballarat road

institute: Victoria University

summary: The molecular mechanisms by which different exercise prescriptions dictate mitochondrial remodelling are poorly understood in humans. Here, we show that, compared to moderate-intensity continuous exercise (MICE), sprint-interval exercise (SIE) – a known time-efficient high-intensity exercise – leads to mitochondrial stress and transcriptionally activates the mitochondrial unfolded protein response (UPRmt).

overall_design: Baseline (Pre), post-exercise (+2.5h), post-recovery (+24h)

first: David

last: Bishop


title: Endothelial Cells retain inflammatory memory through chromatin remodeling II

city: Albany

first: Ramon

last: Bossardi Ramos

state: Ny

address: 43 New Scotland Avenue

department: Department of Molecular and Cellular Physiology

institute: Albany Medical College

summary: Sepsis survivors exhibit long-term endothelial dysfunction, increasing susceptibility to secondary infections such as pneumonia. To investigate the epigenetic and transcriptional basis of endothelial inflammatory memory, we performed transcriptomic profiling of primary human endothelial cells exposed to sequential inflammatory stimuli in a two-hit in vitro model. IL-6 priming induced sustained transcriptional reprogramming and heightened responsiveness to a secondary LPS challenge, indicative of a memory-like state. To mechanistically dissect this response, we silenced the AP-1 transcription factor JunB using siRNA during the priming phase and evaluated its role in shaping the inflammatory memory response. These studies provide insight into the molecular circuitry maintaining endothelial memory and identify JunB as a potential regulator of this process.

overall_design: Primary human umbilical vein endothelial cells (HUVECs) were treated with IL-6 (50 ng/mL) or PBS for 72 hours (first hit)

last: Bossardi-Ramos


title: Endothelial Cells retain inflammatory memory through chromatin remodeling [RNA-Seq 2]

summary: Sepsis survivors exhibit long-term endothelial dysfunction, increasing susceptibility to secondary infections such as pneumonia. To investigate the molecular basis of endothelial inflammatory memory, we performed transcriptomic profiling of lung and kidney endothelial cells isolated from a murine two-hit sepsis model. This model incorporates cecal ligation and puncture (CLP) as the primary inflammatory event, followed by a secondary intranasal challenge with Streptococcus pneumoniae.

overall_design: RNA was extracted from lung and kidney endothelial cells isolated from mice subjected to a two-hit model of sepsis. The first hit involved cecal ligation and puncture (CLP) or sham surgery, followed by recovery. The second hit consisted of a secondary intranasal challenge with Streptococcus pneumoniae (SP) or PBS. Endothelial cells were isolated at defined time points and RNA-seq was performed using the Illumina NovaSeq 6000 platform (paired-end). A total of 54 samples representing various treatment groups across lung and kidney tissues were analyzed to identify gene expression signatures associated with endothelial inflammatory memory.


title: Endothelial Cells retain inflammatory memory through chromatin remodeling [ATAC-seq]

summary: Sepsis survivors exhibit long-term endothelial dysfunction, increasing susceptibility to secondary infections such as pneumonia. To investigate the epigenetic and transcriptional basis of endothelial inflammatory memory, we employed transcriptomic profiling of primary endothelial cells exposed to inflammatory stimuli in a two-hit model. This study reveals persistent transcriptional reprogramming following IL-6 exposure and identifies a primed endothelial state that amplifies responses to secondary challenges.

overall_design: Primary endothelial cells were treated with IL-6 or PBS for 72 hours (first hit), followed by a 48-hour washout phase. Nuclei were isolated for ATAC-seq from cells collected at two timepoints: immediately after the 72-hour treatment (IL6_72h, PBS_72h) and after the 48-hour washout (IL6_72h_W48h, PBS_72h_W48h). Each group included two or three biological replicates


title: Endothelial Cells retain inflammatory memory through chromatin remodeling

overall_design: Primary endothelial cells were treated with IL-6 or PBS for 72 hours (first hit), followed by a 48-hour washout phase. Cells were then challenged with either LPS or PBS for 6 hours (second hit). Total RNA was extracted from 18 samples across six experimental conditions: IL6_72h, IL6_72h_W48h, IL672h_W48h_LPS, PBS_72h, PBS_72h_W48h, and PBS72h_W48h_LPS, each with three biological replicates. RNA-seq was performed using the Illumina NovaSeq 6000 platform (paired-end). The resulting data were analyzed to identify genes associated with inflammatory memory.


title: AT3 RNA-seq

city: Barcelona

first: Toni

last: Celià-Terrassa

address: C/ del Dr. Aiguader, 88, Ciutat Vella,

institute: Hospital del Mar Research Institute

summary: ER+ breast cancer is the most prevalent subtype of the disease with improved prognosis thanks to advances in target therapies against the main driver of proliferation, estrogen receptor (ER). Despite all the advances in the study of this subtype, murine models that allow to study the interaction of tumor cells with the stromal compartment are merely absent. In this study we aimed to ectopically overexpresse the protein ER in AT3 murine cell line and check the ability to resemble ER+ breast cancer cells. We compared the transcriptomic profile of ER-OE cells versus control.

overall_design: AT3 cells were transduced with vector control or ER overexpressing construct. Both cell lines were treated with 10 nm of E2 during 24 h. Cell pellets were lysed and RNA extracted for RNA sequencing. Transcriptomic changes upon ER overexpression together with E2 treatment were analyzed.

first: José Ángel

last: Palomeque


title: Endothelial Cells retain inflammatory memory through chromatin remodeling [ATAC]

overall_design: Kidney endothelial cells isolated from mice subjected to a two-hit model of sepsis. The first hit involved cecal ligation and puncture (CLP) or sham surgery, followed by recovery. The second hit consisted of a secondary intranasal challenge with Streptococcus pneumoniae (SP) or PBS.


title: Synaptic proteins that aggregate and degrade slower with aging accumulate in microglia

city: Stanford

first: Ian

last: Guldner

address: 290 Jane Stanford Way

department: Neuro

institute: Stanford University

summary: As part of our study, we sorted CD11b+ cells (microglia) from the brain. To assess the purity of the sorted cells, we performed RNA-seq on them. As a relative comparison, we also performed RNA-seq on whole brain homogenate.

overall_design: 400,000 CD11b+ cells (microglia) from the mouse brain were sorted and subjected to preparation for RNA-seq. Hemi brains were also subjected to preparation for RNA-seq. All samples were obtained from young male C57BL/6 mice.

first: Wyss-Coray

last: Tony


title: Suprachiasmatic nucleus regulation of brown fat thermogenesis via ADRB3-S100B axis

city: suzhou

first: Yizhun

last: Zeng

address: renai road NO.199

institute: schoow university

summary: The suprachiasmatic nucleus (SCN), the central circadian pacemaker, orchestrates daily metabolic rhythms, yet its role in substrate selection and thermogenic adaptation remains insufficiently understood. Here, we show that SCN lesioning abolishes the adaptive suppression of brown adipose tissue (BAT) thermogenesis typically observed during time-restricted feeding in subthermoneutral environments (TRF-STE), a condition that imposes concurrent nutrient and thermal challenges. Contrary to wild-type responses, SCN-lesioned mice maintain elevated BAT thermogenic activity, driven by enhanced sympathetic tone and β3-adrenergic receptor (ADRB3) signaling. This compensatory response promotes a shift from lipid oxidation to glucose utilization, enabling heat production despite impaired lipolysis. Mechanistically, we identify a SCN-regulated ADRB3-S100B signaling axis underlying this metabolic reprogramming. S100B, a nutrient-sensitive protein calcium-binding protein, is upregulated in BAT following SCN disruption, where it enhances thermogenic capacity by stimulating brown adipocyte proliferation and suppressing senescence. Functional studies reveal that S100B is both necessary and sufficient for sustaining BAT thermogenesis under TRF-STE. Furthermore, diverse SCN disruption models, including light-induced circadian arrhythmia, N - Methyl - D - aspartic acid (NMDA) excitotoxicity, and Caspase-3-mediated ablation, consistently elevates S100B expression in BAT, reinforcing its role as a convergent effector of SCN-regulated metabolic adaptation. These findings uncover a previously unrecognized role of the SCN in coordinating thermogenic flexibility and fuel partitioning under stress. The identification of the ADRB3-S100B axis as a key mediator of this adaptation provides new mechanistic insight into the neural regulation of energy balance, with potential therapeutic relevance for circadian misalignment, obesity, and resistance to diet-induced weight loss.

overall_design: After two days of TRF or ad libitum at 21℃ for both sham and SCNx mice, their interscapular brown adipose tissue was collected at ZT4 and ZT16 on day two for RNA-seq.

first: Ying

last: Xu

first: Qi

last: Chen

first: Xiaopeng

last: Song

first: Yue

last: Gu

first: Antonio

last: Vidal-Puig

first: Jie


title: MCF7 and MDA-MB-231 RNA-seq

summary: LCOR is a corepressor of activated nuclear receptors that inhibits the transcriptional activity of these proteins. Recently, LCOR was described to act also as a transcription activator by DNA direct binding through its HTH domain of genes involved in antigen presentation. This double transcriptional role of LCOR is determined by the expression of nuclear receptor. We overexpressed LCOR and performed RNA-seq in breast cancer cell lines of nuclear receptor positive subtype (MCF7) and nuclear receptor absent (MDA-MB-231). This analysis allows to compare transcriptional regulation of LCOR depending on the presence of nuclear receptors.

overall_design: MCF7 and MDA-MB-231 were transduced with inducible LCOR construct. After antibiotic selection, cells were treated with vehicle or 1 ug/ml of doxycycline. After 24 h of induction, cells were lysed following Qiagen RNA extraction protocol. RNA was submitted for RNA-sequencing and study the transcriptional changes occurring when LCOR is overexpressed in both breast cancer cell lines.


title: RNA-seq analysis of canine thyroid carcinomas.

city: Fort Collins

first: Sunetra

last: Das

state: CO

address: 300 W Drake Rd

department: Clinical Sciences

institute: Colorado State University

summary: Thyroid tumors represent 1-3% of canine cancers with most tumors classified as follicular carcinomas and less frequently as medullary carcinomas. A cohort of canine thyroid carcinomas underwent RNASeq exploration (n=30). Clustering of tumor transcriptomes produced 2 groups; T1 and T2 clusters comprised of follicular thyroid carcinomas (FTC) and medullary thyroid carcinomas (MTC), respectively. Tumors were histologically typed as follicular, compact, and follicular-compact on blinded review, with most MTC classified as compact with rare follicular-compact appearance, while FTC displayed all 3 patterns. FTC samples had significantly elevated levels of ERBB2 and HER2 protein and RET signaling was up-regulated in MTC. Elevated HER2 protein staining was associated with shorter progression free survival (PFI). Additional studies are warranted to explore the utility of these biomarkers to improve diagnosis and treatment of thyroid carcinoma in dogs.

overall_design: We ran  gene expression profiling analysis,  hirerchical clustering, and differential expression between in silico clusters, using data obtained from RNA-seq.

first: Dawn

last: Duval


title: GW9662 , a Peroxisome proliferator-activated receptor γ (PPARγ) inhibitor, impairs early embryonic development in zebrafish

city: Clemson

first: Subham

last: Dasgupta

state: South Carolina

address: 142 Long Hall

institute: Clemson University

summary: Peroxisome proliferator-activated receptor γ (PPARγ) functions as a nuclear transcription factor with primary roles in lipid and glucose metabolism and adipocyte differentiation. Despite intensive research in metabolic contexts, its role during early vertebrate development remains underexplored. Our study focused on understanding PPARγ's developmental role by administering a PPARγ antagonist called GW9662 (GW) to block its activity in zebrafish embryos during early development from 6 hours post-fertilization (hpf) to 24 hpf. The first phenotypic screening found that ventralization occurred along with an expanded blood island region, a structure that is involved in early blood cell development. Transcriptomic analysis demonstrated that exposure to GW led to dysregulation of multiple biological pathways, including cytoskeletal organization, lipid biosynthesis, and epithelial-to-mesenchymal transition (EMT). Immunohistochemistry further validated these findings, demonstrating increased lipid accumulation, cytoskeletal disruption, and altered EMT markers. Our findings suggest that PPARγ plays a crucial role in multiple processes  during early embryogenesis, and this disruption can lead to profound morphological and molecular alterations.

overall_design: Zebrafish embryos were exposed to GW-9662, followed by phenotyping, RNA seq, immunohistochemistry and Nile Red stain

first: Sunil

last: Sharma

first: Kanchaka

last: Pathiraja

first: Tyler

last: Johnson

first: Jabez

last: Battu


title: Dynamics of the Spanish fir transcriptome in nature: Metabolic pathways and gene networks involved in the response to climate stress

city: Malaga

first: Vanessa

middle: Viviana

last: Castro Rodriguez

state: Malaga

address: Universidad de Malaga

institute: Universidad de Malaga

summary: Mediterranean forests such as those integrated by Spanish firs in southern Spain are extremely sensitive to the effects of climate climate-driven stresses. Recurrent periods of drought and prolonged warming in the last few years are major factors involves in the current vulnerability of local populations. In this work, physiological and transcriptional analyses were combined to assess the response of trees growing in the forest under natural conditions. The results show a modulation of the transcriptome in response to climatic stress with substantial changes in the expression of genes involved in water stress, aromatic amino acid metabolism, and transcription factors associated with the transcriptional regulation of the observed patterns of gene expression. Roots were determined to be the primary organs involved in the transcriptional response to stress which may be mediated by a gene-network including interactions among structural and regulatory genes. Interactive elements comprise genes encoding stress-related proteins of the ApLEA family, ApADH, the first committed enzyme in tyrosine biosynthesis, and root-specific transcription factors implicated in stress regulation belonging to the ApERF, ApYABBY and ApNAC superfamilies. Data provide new insights to understand the response of Spanish firs to current climatic disturbances by the identification of individual genes and gene-networks potentially involved in local adaptation. This new knowledge will facilitate comparative studies of gene variation in the Spanish fir populations using the identified genes as molecular markers for selection of the best adapted genotypes in the response of climate stress.

overall_design: In this study, needles and roots from adult Abies pinsapo trees (30–50 years old) were analyzed. To examine the effect of climatic variations on the tree transcriptome dynamics, tissue samples were collected from two different organs (needles and roots) at both sites (YUN and RON) and during both seasons, spring (SPR) and autumn (AUT). On each occasion, needles and roots were harvested at midday from ten randomly selected adult individuals (30-50 yr-old trees) of A. pinsapo.

first: Irene

last: Blanca-Reyes

first: María

last: Torés-España

first: Víctor

last: Lechuga

first: María Teresa

last: Llebrés

first: Fernando N

last: de la Torre

first: José A

last: Carreira

first: Concepción

last: Ávila

first: Francisco M

last: Cánovas

last: Castro-Rodriguez


title: Integration of metabolomic and transcriptomic analyses reveals novel regulatory functions of the ChREBP transcription factor in energy metabolism

city: Houston

first: Mark

last: Herman

state: Texas

address: 1 Baylor Plaza

institute: Baylor College of Medicine

summary: Carbohydrate Response Element-Binding Protein (ChREBP) is a transcription factor that activates key genes involved in glucose, fructose, and lipid metabolism in response to carbohydrate feeding, but its other potential roles in metabolic homeostasis have not been as well studied. We used liver-selective GalNAc-siRNA technology to suppress expression of ChREBP in rats fed a high fat/high sucrose diet and characterized hepatic and systemic responses by integrating transcriptomic and metabolomic analyses. GalNAc-siChREBP-treated rats had lower levels of multiple short-chain acyl CoA metabolites compared to rats treated with GalNAc-siCtrl containing a non-targeting siRNA sequence.  These changes were related to a sharp decrease in free CoA levels in GalNAc-siChREBP treated-rats, accompanied by lower expression of transcripts encoding enzymes and transporters involved in CoA biosynthesis. These activities of ChREBP likely contribute to its complex effects on hepatic lipid and energy metabolism. While core enzymes of fatty acid (FA) oxidation are induced by ChREBP knockdown, accumulation of liver acylcarnitines and circulating ketones indicate diversion of acetyl CoA to ketone production rather than complete oxidation in the TCA cycle.  Despite strong suppression of pyruvate kinase and activation of pyruvate dehydrogenase, pyruvate levels were maintained, likely via increased expression of pyruvate transporters, and decreased expression of lactate dehydrogenase and alanine transaminase. GalNAc-siChREBP treatment increased hepatic citrate and isocitrate levels while decreasing levels of distal TCA cycle intermediates.  The drop in free CoA levels, needed for the 2-ketoglutarate dehydrogenase reaction, as well as a decrease in transcripts encoding the anaplerotic enzymes pyruvate carboxylase, glutamate dehydrogenase, and aspartate transaminase likely contributed to these effects.  GalNAc-siChREBP treatment caused striking increases in PRPP and ZMP/AICAR levels, and decreases in GMP, IMP, AMP, NaNM, NAD(P), and NAD(P)H levels, accompanied by reduced expression of enzymes that catalyze late steps in purine and NAD synthesis.  ChREBP suppression also increased expression of a set of plasma membrane amino acid transporters, possibly as an attempt to replenish TCA cycle intermediates. In sum, combining transcriptomic and metabolomic analyses has revealed regulatory functions of ChREBP that go well beyond its canonical roles in control of carbohydrate and lipid metabolism to now include mitochondrial metabolism and cellular energy balance.

overall_design: All procedures were approved by Duke University Institutional Animal Care and Use Committee and performed according to the regulations of the committee. Breeding pairs of Obese Prone CD (OP/CD) Sprague Dawley rats were gifts from Dr. Warren Grill and Dr. Eric Gonzalez, Duke University, and a colony was established and maintained by Duke Laboratory Animal Resources (DLAR). Starting at 4 weeks of age, male OP/CD rats were single-housed with a light cycle of 7 AM on/7 PM off, and fed ad libitum with a high-fat/high-sucrose (HF/HS) diet (D12451i, Research Diets) containing 47% fat (kcal) and 17% sucrose (kcal).  Body weight and food intake were monitored weekly. After 9 weeks of feeding of the HF/HS diet, plasma samples were collected via saphenous vein bleeding. One week later, animals received an initial subcutaneous injection of one of two GalNAc-siRNA constructs at a dose of 9 mg/kg body weight, or an equal volume of the diluent (PBS), (see below for description of the two GalNAc-siRNA reagents).  Additional doses of each GalNAc-siRNA construct were injected at 10, 18 and 25 days after the first injection. Animals were fasted overnight one day after the third injection (day 19), and subjected to an intraperitoneal glucose tolerance test (IPGTT) on the following day. Animals were weighed and a glucose solution (1g/kg body weight) was administered via intraperitoneal injection.  Tail blood samples were obtained and glucose levels measured with a blood glucose meter (CVSHealth) immediately before and at 30,60, 90, 120, and 180 minutes after bolus injection of glucose.  One day after the fourth GalNAc-siRNA or saline injection on day 25, plasma samples were collected via saphenous vein bleeding.  A bolus of deuterium oxide (D2O, 10 ml/kg body weight, Sigma Aldrich) was then given by intraperitoneal injection and followed by free access to drinking water supplemented with 4% D2O for the rest of the experimental period. Saphenous plasma samples were collected again one day after the bolus delivery of D2O (day 27).  On day 28 between 8 AM-noon, animals were anesthetized with Nembutal (250 mg/kg) by intraperitoneal injection and sacrificed for collection of plasma and liver samples that were rapidly frozen in liquid nitrogen and stored at -80oC for further analyses.

first: Jie

last: An

first: Inna

last: Astapova

first: Guofang

last: Zhang

first: Andrew

last: Cangelosi

first: Olga

last: Ilkayeva

first: Hannah

last: Marchuk

first: Miachael

last: Muehlbauer

first: Tabitha

last: George

first: Joseph

last: Brozinick

first: Christopher

last: Newgard


title: Gene expression data from patients with peripheral arterial disease stenosis grade 1 vs 4 and 5

city: Atlanta

first: Luke

last: Brewster

state: GA

address: 101 Woodruff Circle

department: Surgery

institute: Emory University

summary:
Human PAD arteries were obtained from patients undergoing amputation. This is an extension of a previously published data set from Dr. Lawson's lab. In total 39 arterial samples from 27 patients undergoing amputation were collected, including posterior tibial artery, anterior tibial artery, superficial femoral artery, peroneal artery, and popliteal artery. Histologic sections were graded for the degree of stenosis as follows: zero – none, one - 1-25%, two – 26-50%, three – 51-75%, four – 76-95%, five – 96-100%. The protocol was approved by the Duke University Health System Institutional Review Board and all the donors gave their permission by written consent.
We used microarrays to detail the global programme of gene expression underlying peripheral arterial disaes specifically in high-stenosis vessels vs. non-stenotic vessels.

overall_design: About 150 mg tissues were collected for RNA extraction using the standard TRIzol protocol and RNA quality was assessed by electropherogram using an Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA). Complementary DNA probes were generated without amplification and hybridized to Affymetrix U133A microarrays (Affymetrix, Santa Clara, CA) and signal intensity were processed by the GeneChip scanner.

first: Jeffery

last: Lawson


title: Spatial transcriptomics of 12 tumor tissues from colorectal cancer

city: Lille, Cedex

first: Bernadette

last: Neve

address: Bâtiment ONCOLille, Bld du Professeur Jules Leclercq

department: CANTHER

institute: ONCOLille

summary: To studied how transcript expression was distributed in heterogenous colorectal tumor tissues, we performed spatial transcriptome analysis of 12 CRC tumor samples. The OrgaRES consortium study includes tissues samples from patients at the university hospital of Lille (CHU Lille, France) obtained with the approval of the institutional review board and the Lille ALLIANCE-CANCER biobank. All patients gave their informed consent and signed a non-opposition statement to research use of a biological sample.

overall_design: Visium spatial expression analysis of 12 cryo-preserved colorectal cancer tissues

first: Elsa

last: Hadj Bachir

first: Belinda

last: Duchêne

first: Isabelle

last: Van Seuningen

first: Emmanuelle

last: Leteurtre

first: Charlotte

last: Dufour

first: Shéhérazade

last: Sebda

first: Martin

last: Figeac

first: Jean-Pascal

last: Meneboo

first: Audrey

last: Vincent


title: Long non-coding RNA UCA1 modulates chromatin remodeling via SMARCA2-containing SWI/SNF complex in human colorectal cancer

summary: Differential lncRNA expression has been correlated to clinical characteristics of colorectal cancers (CRC), which are the second leading cause of cancer-related deaths. LncRNA UCA1 plays a role in epigenetic gene regulation in diverse cancers. We studied CRC cell properties in CRISPR/Cas9 HT29-derived models and, interestingly, UCA1-depleted HT29 cells presented an increased stem-cell phenotype. We show that loss of UCA1 modulates SWI/SNF chromatin remodeling complexes, which were previously shown to be involved in maintaining stem-cell properties. Not only was UCA1 permissive for induced SWI/SNF subunit SMARCA2 (BRM) expression upon chemo-drug treatment, but it also affected subunit compositions of SWI/SNF complexes by direct interaction of UCA1 with both ATP helicase BRM and BRG1. UCA1 is known to stimulate proliferation and decrease apoptosis, and we here show that it can restrain cells from a stem cell phenotype. The dual action of UCA1 revealed in this study highlights the complex actions of lncRNAs in cancer.

overall_design: RNAseq analysis of control ICP, dUCA1E1 and dUCA1E2 cells treated for 72h with or without 2 µM 5-Fluorouracil (5-FU).

first: Mouloud

last: Souidi

first: Nicolas

last: Jonckheere


title: MCF7 ChIP-seq

first: Toni

last: Celià-Terrassa

summary: LCOR is a corepressor of activated nuclear receptors that inhibits the transcriptional activity of these proteins. Recently, LCOR was described to act also as a transcription activator by DNA direct binding through its HTH domain of genes involved in antigen presentation. This double transcriptional role of LCOR is determined by the expression of nuclear receptor. Here we performed ChiP-seq analysis of LCOR in MCF-7 cells which expressed the nuclear receptor estrogen receptor. In paralel we treated the cells with an estrogen receptor degrader (fulvestrant) or ectopic expression of the LCOR without the nuclear receptor binding domain (LSKAA). This analysis allows to compare the genome wide distribution of LCOR depending on the presence of nuclear receptor and the ability to interact.

overall_design: MCF7 cells were transduced with control, LCOR and LSKAA inducible overexpressing plasmids. MCF7-LCOR OE cells were induced with 1 ug/ml of doxycycline and treated with vehicle or 1 uM of fulvestrant. MCF7-LSKAA OE were induced with doxycycline. After 24 h, cells were croslinked and chromatin extracts were obtained for immunoprecipitation of LCOR. Isolated DNA bound to LCOR was submitted for sequencing. After alignment and analysis of sequenced DNA, conditions were compared to check the different prefferentially bound motif of LCOR in each condition

first: José Ángel

last: Palomeque


title: Tungsten is Utilized for Lactate Consumption and SCFA Production by a Dominant Human Gut Microbe Eubacterium limosum

city: Athens

first: Michael

middle: W. W.

last: Adams

address: 120 East Green St.

department: Molecular Biology and Biochemistry

institute: University of Georgia

summary: Eubacterium limosum is a dominant member of the human gut microbiome and produces short-chain fatty acids (SCFAs). These promote immune system function and inhibit inflammation, making this microbe important for human health. Lactate is a primary source of gut SCFAs but its utilization by E. limosum has not been explored. We show that E. limosum growing on lactate takes up added tungstate rather than molybdate and produces the SCFAs acetate and butyrate, but not propionate. The genes encoding an electron bifurcating, tungsten-containing oxidoreductase (WOR1) and a tungsten-containing formate dehydrogenase (FDH), along with an electron bifurcating lactate dehydrogenase (LCT), lactate permease and enzymes of the propanediol pathway, are all up-regulated on lactate compared to growth on glucose. Lactate metabolism is controlled by a GntR-family repressor (LctR) and two global regulators, Rex and CcpA, where Rex in part controls W storage and tungstopyranopterin (Tuco) biosynthesis. Tuco-dependent riboswitches, along with CcpA, also control two iron transporters, consistent with the increased iron demand for many iron-containing enzymes, including WOR1 and FDH, involved in SCFA production. From intracellular aldehyde concentrations and the substrate specificity of WOR1, we propose that WOR1 is involved in detoxifying acetaldehyde produced during lactate degradation. Lactate to SCFA conversion by E. limosum is clearly highly tungstocentric and tungsten might be an overlooked micronutrient in the human microbiome and in overall human health.

overall_design: To investigate the effect of tungsten (W) and lactate on E. limosum and metabolic pathways, RNA sequencing was done comparing lactace vs glucose under conditions with and without additional W added.

first: Saisuki

last: Putumbaka

first: Gerrit

last: Schut

middle: P

last: Thorgersen

first: Farris

last: Poole

first: Nana

last: Shao

first: Dmitry

last: Rodionov

middle: W


title: Transcriptional architecture of promoters and enhancers and the rapid unleash of heat shock response in Canis lupus familiaris [mRNA-seq]

city: Stockholm

first: Anniina

last: Vihervaara

address: Tomtebodavägen 23A, 17165 Solna, Sweden

department: Department of Gene Technology

country: Sweden

institute: Science for Life Laboratory, KTH Royal Institute of Technology

summary: Dogs exhibit high genetic diversity due to extensive breeding, and provide a versatile model for genetics, evolution, and complex traits. While RNA synthesis and transcriptional architecture of promoters and enhancers have been extensively analyzed in human, mouse, and fly, little is known about the mechanisms that coordinate gene and enhancer transcription in dog. Here, we combine precision run-on sequencing (PRO-seq) and strand-specific mRNA-seq (mRNA-seq) to measure nascent transcription, mRNA expression and mRNA stability in golden retriever macrophage (DH82) cells. Tracking transcription at nucleotide-resolution uncovers the precise transcription start nucleotides (TSN) genome-wide, identifies the exact locations of promoters and transcribed enhancers, and quantifies transcription machineries at initiation, promoter proximal pause, gene bodies, and termination windows. Moreover, we trigger an instant transcriptional reprogramming using heat shock, and track at nucleotide-resolution, how dog cells coordinate RNA synthesis and mRNA expression across the genome. Taken together, this study describes the transcriptional landscape at nucleotide-resolution, measures RNA synthesis, mRNA expression and mRNA-stability, and identifies mechanisms of gene and enhancer reprogramming in Canis lupus familiaris.

overall_design: RNA sequencing (RNA-seq) of macrophage-like cells from golden retriever (DH82) under normal growth conditions and heat shock.

first: Samu

middle: V

last: Himanen


title: Comparative transcriptomics analysis of fatty acid-secreting Yarrowia lipolytica reveals importance of cell wall proteins

city: Gent

first: Inge

middle: N. A.

last: Van Bogaert

address: Coupure Links, 653

department: Department of Biotechnology

institute: Ghent University

summary: Yarrowia lipolytica has been considered one of the most promising platforms for the microbial production of fatty acids and derived products. The deletion of the faa1 gene coding for an acyl-CoA synthetase leads to the accumulation and secretion of free fatty acids (FFAs) into the extracellular space. The secretion of products is beneficial for the development of microbial cell factories to avoid intracellular inhibitory effects and reduce downstream processing costs. However, the mechanism behind the secretion of fatty acids is not well known. In this research, we compared the transcriptome of this mutant showing FFA secretion to a wildtype-like strain not showing this phenotype. Both toxicity and growth assays, as well as deletion and overexpression mutants of candidate genes were used to assess the effects of candidate genes on the export of FFAs. Although no clear transporter of fatty acids was identified, the analysis of the transcriptomic data revealed an overrepresentation of cell wall-related proteins. Based on this results, a literature search allowed to retrieve proteins related to the cell wall previously associated to lipid. Experiments performed on these candidates proved their involvement in resistance to FFAs toxicity, with one of them being a potential acyl-CoA export protein.

overall_design: Quintuplates were analysed, comparing a wild-type strain with a mutant (faa1 knockout) able to secrete fatty acids when growing in high C/N ratio

first: Jose

middle: M

last: Salvador Lopez

first: Filip

last: Van Nieuwerburgh

first: Dieter

last: Deforce


title: ColoStem, a core transcriptional signature that identifies poor prognosis fetal-type colorectal tumors

first: Lluis

last: Espinosa

state: Barcelona

address: Dr. Aiguader 88

department: Institut Municipal d'Investigacions Mèdiques, (IMIM)

institute: Hospital del Mar

summary: We have previously shown that non-curative chemotherapy imposes fetal conversion and high metastatic capacity to cancer cells. Analysis of public colorectal cancer datasets confirms the existence of a fetal signature consisting of 28 upregulated and 8 downregulated genes that stratify patients with worse prognosis. We have analyzed a metacohort generated by the integration of several colorectal cancer datasets and performed qPCR analysis of paraffin-embedded and plasma samples from our in-house cohort of colorectal cancer tumors. We uncovered a core fetal signature, which we have called ColoStem, composed of 5 genes upregulated and 3 genes downregulated that display prognosis value in a multivariate analysis. We also define EpiColostem as a purer epithelial signature with comparable prognosis value as ColoStem. By qPCR analysis of RNA extracted from paraffin-embedded tissues, we demonstrated the actual possibility of using ColoStem and EpiColoStem to refine the prognostication of CRC patients with a simple an affordable method. Initial analysis of plasma samples indicates that both signatures could be adapted for its use in liquid biopsy. Our results reveal ColoStem and EpiColoStem tests as valuable tools for the identification of fetal-type CRC tumors thus refining patient prognosis.

overall_design: We analyzed bulk RNAseq samples obtained from colorectal cancer Patient-Derived Organoids: 3xnon-fetal (PDO4, PDO10 and PDO66) and 3xfetal (PDO5, PDO27 and PDO127B), plus 2xtreated with 5-FU+Irinotecan (PDO66), each in triplicates.

first: Laura

last: Solé

first: Eric

last: Canton

first: María

last: Maqueda

first: Teresa

last: Lobo-Jarne

first: Antonio

last: Barbáchano

first: Ferran

last: Torres

first: Julia-Jié

last: Cabré-Romans

first: Ángela

last: Montoto

first: Lierni

last: Fernández-Ibarrondo

first: Daniel

last: Martínez-Garcia

first: Marta

last: Guix

first: Mónica

last: Larrubia-Loring

first: Clara

last: Montagut

first: Alberto

last: Muñoz

first: Anna

last: Bigas

first: Mar

last: Iglesias

first: Beatriz

last: Bellosillo

first: Lluís


title: Transcriptional architecture of promoters and enhancers and the rapid unleash of heat shock response in Canis lupus familiaris [PRO-seq]

first: Anniina

last: Vihervaara

overall_design: Precision run-on sequencing (PRO-seq) of macrophage-like cells from golden retriever (DH82) under normal growth conditions and heat shock.

first: Samu

last: Himanen


title: Molecular Insights into HIV-associated Cardiac Dysfunction

city: Boston

first: Boston University

last: Microarray and Sequencing Resource

state: MA

address: 72 East Concord Street, E631

department: Microarray and Sequencing Resource

institute: Boston University

summary: Antiretroviral therapy (ART) in human immunodeficiency virus (HIV) improved life expectancy in people living with HIV (PLWH) but cardiac diseases have emerged as a leading cause of death in this population. There is a notable increase in diastolic dysfunction and HF with preserved ejection fraction (HFpEF) attributed to the altered metabolic milieu seen in PLWH on ART. However, the specific role(s) that HIV itself, and/or ART may have on the cardiomyocyte phenotype is unknown. We investigated molecular pathways altered in cardiomyocytes in vitro in response to serum from ART-naïve and after ART-treated patients. Cardiomyocytes were treated for 24 hours with serum obtained longitudinally from HIV patients before and after receiving ART for 6 months. RNA sequencing revealed that differences between pre- and post-treatment with ART were related to processes involving cell death, cardiomyocyte calcium handling, and adverse remodeling. Apoptotic death was increased in cardiomyocytes treated with serum obtained from ART naïve HIV patients whereas those treated with serum from the same patients 6 months after ART presented changes in calcium-handling proteins and profibrotic markers, indicating altered contraction and relaxation, and adverse remodeling. These findings demonstrate altered molecular pathways in cardiomyocytes in response to active viremia and ART.

overall_design: Cardiomyocytes were treated for 24 hours with serum obtained longitudinally from HIV patients before and after receiving ART for 6 months, followed by RNA sequencing.

first: Maria

last: Munoz

first: Eng

last: Saw

first: Flora

last: Sam