title: Bromodomain of CREBBP/EP300 cooperates with BNC2 to reprogram cell state in breast cancer

city: Singapore

first: Li Ping

last: Toh

address: 61 Biopolis Drive, Proteos, #06-14

country: Singapore

institute: IMCB

summary: The plasticity of cancer cells influences their phenotypic and functional diversity. Understanding the mechanisms underlying cell state transitions, particularly the epithelial-mesenchymal transition (EMT) and its reverse process – mesenchymal-epithelial transition (MET), can provide insights into therapeutic strategies that control tumor progression and metastasis. Epigenetic reprogramming governs cellular plasticity. To survey epigenetic inhibitors capable of inducing MET, we employ a high-throughput small-molecule library screen coupled to a cell state reporter assay. We identify CREBBP/EP300 bromodomain inhibitor as a potent MET promoter, which specifically induces cell state transition in basal-like breast cancer but not luminal breast cancer. CREBBP/EP300 bromodomain inhibition leads to a gain in luminal characteristics and a reduction in stem-like properties. Strikingly, inhibiting the bromodomain of CREBBP/EP300, rather than its HAT domain, is more effective in promoting MET, decreasing tumorigenicity, and impeding metastasis. This underscores the finding that CREBBP/EP300 mediated cell state reprogramming is not attributed to changes in histone acetylation but likely converges on effector genes recognized by the bromodomain. Through transcriptomic and ChIP-Seq analyses, we find the zinc finger protein basonuclin-2 (BNC2) as a potential transcription factor involved in cell state regulation. Its interaction with CREBBP/EP300 bromodomain is essential for regulating super-enhancer-associated genes that maintain the mesenchymal cell state. These findings provide a new functional role for the bromodomain in epigenetic regulation and suggest strategies for therapeutic intervention in mesenchymal breast cancer.

overall_design: To evaluate the transcriptional reprogramming that could be respobsible for mesenchymal-epithelial transitions, we treated NAMEC8 cells with SGC-CBP30 and A-485. We then performed gene expression profiling analysis using data obtained from RNA-seq of NAMEC8 that has been treated with SGC-CBP30 and A-485 for seven days in duplicates. Comparative gene expression profiling analysis of RNA-seq data for NAMEC8 treated with DMSO and SGC-CBP30, as well as DMSO and A-485, were done.

first: Cheryl

last: Phua


title: High-resolution immune atlas of murine healthy prostate and prostate cancer from neoplasia to adenocarcinoma stage in the inducible PTEN(i)pe-/- mice

status: Public on Sep 30 2025

city: Marseille

first: Lionel

last: Spinelli

address: Avenue de Luminy

country: France

institute: CIML

type: Expression profiling by high throughput sequencing

summary: Prostate cancer (PCa) is the most commonly diagnosed cancer and the second leading cause of cancer-related mortility among men in western societies. PCa exhibits a protracted progression, initiating as Prostatic Intraepithelial Neoplasia (PIN), advancing to adenocarcinoma, and eventually culminating in metastatic dissemination. The advent of Immune Checkpoint Inhibitors (ICI) has been revolutionized the field of cancer immunology. However, the efficacy of immunotherapy in PCa has been limited, and the role of immune cells in prostate tumorigenesis has only recently been explored. In this study, we performed an in-depth characterization of immune cells in healthy murine prostate and during PCa progression in PTEN(i)pe-/- mice. In this model, the PTEN gene is selectively ablated in prostatic luminal epithelial cells at adulthood (PSA-CreERT2), closely mimicking human PCa development. Notably, tumor progression in this model is gradual, with the PIN stage manifesting at 3 months post-gene invalidation and the adenocarcinoma stage at 9 months. The strict temporal control of PTEN depletion coupled with the slow tumor progression, makes the PTEN(i)pe-/- mouse model an invaluable tool for delineating immune infiltration during tumor development and evaluating therapeutic interventions.  Here we performed scRNAseq on CD45+ immune cells residing in the dorsolateral lobes of prostate at respectively 3 and 9 months post tamoxifen treatment of PTEN(i)pe-/- and control mice, allowing to establish a high-resolution immune atlas of murine PCa from neoplasia to adenocarcinoma. Our findings reveal significant heterogeneity among mononuclear phagocytes (dendritic cells and macrophages), neutrophils and lymphoid immune cells in the prostate. Various neutrophil clusters exhibit an immunosuppressive signature from the PIN stage onward. We observed the recruitment of Trem2+ tumor-associated macrophage subset during PCa, potentially contributing to tumorigenesis. Additionally, there was an increase in CD8+ T lymphocytes in PCa, which exhibited an activated/exhausted phenotype. Our study elucidates the intricate dynamics of immune cell behavior in PCa from early to late stages. These insights pave the way for novel immunotherapeutic strategies to treat prostate cancer, thereby advancing the field of tumor immunology.

overall_design: To establish a high-resolution immune atlas of healthy prostate and prostate cancer we performed scRNA-seq on sorted tissue resident CD45+ immune cells from the inducible adult PTEN(i)pe-/- mice at the Prostatic Intraepithelila Neoplasia stage (PIN) and Adenocarcinoma stages, and age-matched healthy PTENL2/L2 control individuals at 3months and 9months post tamoxifen administration respectively. Few minutes prior sacrifice, mice were injected intravenously with fluorescent anti-CD45.2 antibodies to perform blood/tissue partitioning, allowing to exclude cells present in the vasculature and ensure to study solely the immune cells present in prostate parenchyma. Cells were extracted from DLV prostate lobes by enzymatic digestion. Prostate samples from three PTEN(i)pe-/- mice at 3months post tamoxifen were pooled prior to sorting. Similarly, prostate samples from five  sex-matched PTENL2/L2 control littermates at 3months post-tamoxifen were also pooled prior to sorting. The same approach was applied for the 9months samples of PTEN(i)pe-/- and control mice respectively. Tissue resident CD45+ immune cells were sorted by fluorescence-activated cell sorting (FACS). As we found previously that neutrophils were prevalent within the leukocyte infiltrate from PIN to adenocarcinoma stages of Pten(i)pe-/-prostate, neutrophils were sorted separately from the other CD45+ immune cells and cells were mixed again at a 25% ratio of neutrophils with 75% of CD45+ non neutrophil immune cells prior 10X Genomics Chromium System encapsulation and scRNAsequencing. We included 8 independent samples encompassing 2 replicates of PtenL2/L2 control 3 months, PtenL2/L2 control 9 months, Pten(i)pe-/- 3 months PIN and Pten(i)pe-/- 9 months adenocarcinoma.

first: Despoina

last: Pervizou

first: Joanna

last: De Chiara

last: Chasson

first: Frédéric

last: Fiore

first: Marc

last: Bajénoff

first: Bernard

last: Malissen

first: Daniel

last: Metzger

first: Gilles

last: Laverny

first: Sandrine

last: Henri


title: scRNA-seq analysis of mouse utricular sensory epithelium at embryonic day 14 and postnatal day 2

city: SHANGHAI

first: yunzhong

last: zhang

state: SHANGHAI

address: 83 fenyang road, xuhui district

department: Department of ENT Institute and Otorhinolaryngology

country: China

institute: Eye & ENT Hospital of Fudan University

summary: To determine the BMP4 expression levels during inner ear development, we performed a single-cell RNA sequencing (scRNA-seq) analysis of mouse utricular sensory epithelium at embryonic day 14 (E14) and postnatal day 2 (P2).

overall_design: Utricles were harvested from E14 and P2 mice, followed by the careful mechanical removal of the otolithic membranes. Subsequently, the tissues were incubated with thermolysin to facilitate the detachment of the sensory epithelium.


title: Single Cell Transcriptional Perturbome in Pluripotent Stem Cell Models

city: Torino

first: Elisa

last: Balmas

address: via Nizza 52

department: Department of molecular biotechnology and life sciences

country: Italy

institute: University of Torino

summary: Functional genomics screens in human induced pluripotent stem cell (hiPSC) models offer immense potential yet remain challenging. We developed iPS2-seq: iPS-optimized inducible Postranscriptional Silencing in pool deconvoluted by single cell sequencing. This method allows phenotype-agnostic screens in hPSCs and their derivatives through loss-of-function perturbations that are mRNA-depleting (bypassing genotoxicity), clonally traced (controlling genetic and epigenetic variability), single cell aware (accounting for asyncronous and heterogeneous differentiation), isogenic engineered (preventing silencing), inducible and reversible (enabling stage-specific studies and robust control-treatment paired analyses). iPS2-seq is compatible with both commercial microfluidics and homebrew split-pool scRNA-seq protocols, enabling screens with different scales, costs, and input materials. A dedicated bioinformatics pipeline, catcheR, supports iPS2-seq design and analysis. We demonstrate this by studying congenital heart disease-associated genes in hiPSC-derived monolayer cardiomyocytes and cardiac organoids, identifying a key role for SMAD2 in cardiomyogenesis. iPS2-seq strengthens and democratizes access to functional single cell genomics in and beyond hiPSC-derived organoids.

overall_design: Proof of principle and testing experiments on sci-RNAseq iPS2-seq have been performed on two batches of hPSC-derived cardiomyocytes at day 21 and 25, respectively. Cells have been treated with Tetracycline throughout differentiation. For this experiment it was used a 2-level of indexing sci-RNAseq protocol (Cao J. et. al, Science 2017). During RT and PCR indexing steps, additional primers have been used to enrich for UCI and shRNA barcodes for the iPS-2 seq pipeline. Sequencing has been performed on a NextSeq 500 with a High Output kit 75 cycles. Read1, 18 cycles; Index1, 10 cycles; Index2, 10 cycles, Read2, 52 cycles.

first: Maria

middle: L

last: Ratto

first: Alessandro

last: Bertero

first: Kirsten

last: Snijders


title: BMP4 regulates transcriptomic changes in mouse utricle

summary: Transcriptomic sequencing data encompassing the process of inner ear vestibular hair cell regeneration under the regulatory effects of BMP4.

overall_design: To explore the molecular mechanism through which BMP4 functions in inner ear progenitor cells, we performed bulk RNA-sequencing to assess changes in downstream transcriptional networks.


title: RB modulates chromatin organization by regulating cohesin-dependent loops and enhancer-promoter interactions [HiChIP]

city: Boston

first: Hanjun

last: Lee

state: Massachusetts

address: 77, Avenue Louis Pasteur

department: Department of Genetics

country: USA

institute: Harvard Medical School

type: Genome binding/occupancy profiling by high throughput sequencing

summary: The retinoblastoma protein (RB) is a well-characterized repressor of E2F transcriptional activity that controls genes involved in cell proliferation during the G1-phase. Here, we examine the effect of RB on chromatin organization and uncover a non-canonical role for RB in which it promotes the removal of cohesin from insulators and thereby induces the expression of adjacent genes. We identify that RB colocalizes with cohesin across the human genome. During mitosis, RB facilitates the removal of cohesin from CTCF sites, with this effect persisting into early G1, impacting loop formation and extrusion at topologically associating domain (TAD) boundaries. Chromosome conformation capture assays revealed that RB reduces insulation at TAD boundaries and promotes enhancer-promoter interactions marked by histone 3 lysine 27 acetylation. In this way, RB enhances the transcription of hundreds of genes beyond the E2F transcriptional program, expanding our understanding of this key tumor suppressor and cell cycle regulator.

overall_design: H3K27ac HiChIP for RB WT or RB KO hTERT1-RPE1 cells that are synchronized in G1 via contact inhibition

first: Ioanna-Maria

last: Gkotinakou

first: Michael

middle: S

last: Lawrence

first: Ioannis

last: Sanidas


title: Histone methyltransferase PRDM9 promotes survival of drug-tolerant persister cells in glioblastoma [RNA-seq]

city: Camperdown

first: George

middle: Louis

last: Joun

state: NSW

address: John Hopkins Drive

department: School of Medical Sciences

country: Australia

institute: The University of Sydney

summary: Chemotherapy often kills a large fraction of cancer cells but leaves behind a small population of drug-tolerant persister cells. These persister cells survive drug treatments through reversible, non-genetic mechanisms and cause tumour recurrence upon cessation of therapy. Here, we report a drug tolerance mechanism regulated by the germ-cell-specific H3K4 methyltransferase PRDM9. Through histone proteomic, transcriptomic, lipidomic, and ChIP-sequencing studies combined with CRISPR knockout and phenotypic drug screen, we identified that chemotherapy-induced PRDM9 upregulation promotes metabolic rewiring in glioblastoma stem cells, leading to chemotherapy tolerance. Mechanistically, PRDM9-dependent H3K4me3 at cholesterol biosynthesis genes enhances cholesterol biosynthesis, which persister cells rely on to maintain homeostasis under chemotherapy-induced oxidative stress and lipid peroxidation. PRDM9 inhibition, combined with chemotherapy, resulted in strong anti-cancer efficacy in preclinical glioblastoma models, significantly enhancing the magnitude and duration of the antitumor response by eliminating persisters. These findings demonstrate a previously unknown role of PRDM9 in promoting metabolic reprogramming that enables the survival of drug-tolerant persister cells.

overall_design: Drug Treated glioblastoma stem cell line RKI1, followed by RNA sequencing. Treatment with tubulin inhibitor CMPD1 (10uM) +/- PRDM9 inhibitor MRK-740 (3uM) for 72 hours, to check changes in gene expression that may be underlying DTP response

first: Lenka

last: Munoz


title: Characterization of extracellular vesicle miRNA cargos from mouse bone

city: Nantes Cedex 1

first: Laura

last: ENTZ

address: Faculté d'Odontologie 1 place Alexis Ricordeau

institute: INSERM UMR 1229 - RMeS

type: Non-coding RNA profiling by high throughput sequencing

summary: EVs are known to play an important role in communication between bone cells. However, few studies have been carried out on EVs derived from osteocytes. The main aim of this project was to collect, characterize and evaluate the potential osteogenic properties of EVs derived from bone, composed of 95% osteocytes. Two subpopulations of EVs, large EVs (lEVs) and small EVs (sEVs), were isolated by differential centrifugation from Swiss male mouse long bone cortices and were characterized from a physico-chemical and functional point of view. Identification of protein and miRNA cargos associated with lEVs and sEVs was carried out by proteomics and small RNA-Seq respectively.

overall_design: EVs were collected from tibias and femurs of 8 weeks old Swiss-CD1 mice. Total RNA from three replicate of lEVs and sEVs was extracted and analyzed using smallRNA-Seq.

last: Entz

first: Benjamin

last: SaintPierre

first: Angélique

last: Galvani

first: Valérie

last: Geoffroy


title: RB modulates chromatin organization by regulating cohesin-dependent loops and enhancer-promoter interactions

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

overall_design: Refer to individual Series


title: Designed macrocyclic peptide rescues behavioral impairment and brain pathology in an Alzheimer’s disease mouse model

city: Munich

first: Peter

last: Androvic

state: Bavaria

address: Feodor-Lynen-Strasse 17

country: Germany

institute: LMU Hospital, Institute for Stroke and Dementia Research

summary: Alzheimer's disease (AD) is a neurodegenerative disorder hallmarked by the accumulation of extracellular amyloid-β (Aβ) plaques, with currently limited therapeutic options. We explored the potential of a macrocyclic peptide, 2E, designed to robustly inhibit Aβ self-aggregation by mimicking the interaction surface of islet amyloid polypeptide (IAPP) with Aβ. Our findings from two treatment paradigms in 5XFAD female and male mice revealed a significant reduction in cortical amyloid deposition, decreased neuronal damage, and enhanced astrocytic activation upon 2E administration. Furthermore, treated mice displayed improvements in memory and motor functions without any alterations in anxiety or stress responses, as evidenced by behavioral tests. Notably, RNA-seq analyses highlighted 2E's ability to bolster astrocytic activation while reversing AD-associated neuronal gene expression changes. Importantly, following intraperitoneal injection, 2E's presence in the brain attests to its biodistribution capability. Thus, the macrocyclic peptide 2E, either as a standalone or combined with other anti-amyloid strategies, emerges as a promising candidate to combat Aβ-driven AD pathogenesis.

overall_design: To study the effect of 2E treatment on cellular responses, RNA for bulk RNA-Seq was isolated from PFA-fixed micro-dissected brain tissue from wild-type, saline-treated 5xFAD mice and 2E-treated 5xFAD mice using optimized protocol. Samples were collected from four brain regions (cortex, hippocampus, brain stem, and cortex+hippocampus). RNA-Seq libraries were prepared using SmartSeq2 protocol.

first: Ozgun

last: Gokce


title: RB modulates chromatin organization by regulating cohesin-dependent loops and enhancer-promoter interactions [Mnase-Seq]

overall_design: MNase-seq for RB WT or RB KO hTERT1-RPE1 cells


title: PriOmics: integration of high_throughput proteomic data with complementary omics layers using mixed graphical modeling with group priors

city: Ulm

first: Emil

last: Chteinberg

address: Albert-Einstein-Allee 11

institute: Ulm University Medical Center

summary: Mass spectrometry (MS)_based high_throughput proteomics data cover abundances of 1,000s of proteins and facilitate the study of co_ and post_translational modifications (CTMs/PTMs) such as acetylation, ubiquitination, and phosphorylation. Yet, it remains an open question how to holistically explore such data and their relationship to complementary omics layers (including the HTG EdgeSeq Pan B_Cell Lymphoma Panel) or phenotypical information. Network inference methods aim for a holistic analysis of data to reveal relationships between molecular variables and to resolve underlying regulatory mechanisms. Among those, graphical models have received increased attention as they can distinguish direct from indirect relationships, aside from their generalizability to diverse data types. We propose PriOmics as a graphical modeling approach to integrate proteomics data with complementary omics layers and pheno_ and genotypical information. PriOmics models intensities of individual peptides and incorporates their protein affiliation as prior knowledge in order to resolve statistical relationships between proteins and CTMs/PTMs. We show in simulation studies that PriOmics improves the recovery of statistical associations compared to the state of the art and demonstrate that it can disentangle regulatory effects of protein modifications from those of respective protein abundances. These findings are substantiated in a dataset of Diffuse Large B-Cell Lymphomas (DLBCLs) where we integrate SWATH_MS_based proteomics data with the HTG EdgeSeq Pan B_Cell Lymphoma transcriptional Panel and phenotypic information.

overall_design: Three hundred sixty difisue large B_cell lymphoma (DLBCL) FFPE tissue samples were analyzed by HTG EdgeSeq Pan B_Cell Lymphoma Panel. For each FFPE sample, a total of 6 µm2 area was collected.

first: Robin

last: Kosch

first: Katharina

last: Limm

first: Annette

middle: M

last: Staiger

first: Nadine

last: Kurz

first: Nicole

last: Seifert

first: Bence

last: Oláh

first: Stefan

last: Solbrig

first: Marita

last: Ziepert

first: Rainer

last: Spang

first: Helena

middle: U

last: Zacharias

first: German

last: Ott

middle: J

last: Oefner

last: Altenbuchinger

first: Reiner

last: Siebert


first: Hanjun

last: Lee

overall_design: ATAC-seq for RB WT or RB KO hTERT1-RPE1 cells that are asynchronous or synchronized in G1 or S phase or for hTERT1-RPE1 cells that expressed constitutively active RB for 0 h, 24 h, or 72 h

first: Ioanna-Maria

last: Gkotinakou

first: Michael

last: Lawrence

first: Ioannis

last: Sanidas


title: Single ooplasm biopsy RNA-Seq reveals important and distinct pathways linked to oocyte competence

city: Pirassununga

first: Flavio

middle: Vieira

last: Meirelles

state: Sao Paulo

address: Duque de caxias

department: Veterinary Medicine

country: Brazil

institute: University of Sao Paulo

type: Methylation profiling by high throughput sequencing

summary: Oocyte competence is a complex process that is directly associated with the ability of oocyte to develop a newborn. The generation of a viable gamete has a multifactorial origin directly related to follicle and oocyte growth. Several dynamic changes in the follicle have driven the oocyte to success or failure, such as storage of metabolites, epigenetic modifications, and maternal RNAs, among others. However, little is known about the precise factors of maternal RNAs associated with oocyte competence, once these RNAs are consumed during maternal embryonic transition. To investigate the oocyte transcriptome landscape, we used a biopsy method to remove ~1.5% of ooplasm followed by a Single-ooplasm-biopsy RNA-Seq approach after retrospectively tracking the oocyte fate. We identified factors driving competence and the feasibility of the technique in obtaining enough amount of sample and high-quality sequencing results, enabling the model establishment. Furthermore, we integrated data from granulosa and cumulus cell transcriptome. Besides that, the first polar body methylation showed high similarities with pathways enriched in the ooplasm-biopsy transcriptome. In granulosa and ooplasm-biopsy with high-competence, we found MAPK and Oxytocin signaling enriched, while the process of necroptosis and ferroptosis were associated with low-competence oocytes. Deep analysis in the ooplasm-biopsy transcriptome, shows MYC as the highest up-regulated gene, and GNAS as a central hub gene in the network analysis. In addition, TIMP1, APOA1, EZR1, and STAT1 were key genes in the low-competence group of oocytes. Importantly, we found that metabolic alteration in the low-low-competence group was constantly found in all transcriptomes data, suggesting a metabolic disturbance inherited since the follicle environment which is amplified in cumulus cells after oocyte maturation.

overall_design: Granulosa cells from bovine oocytes were collected individually from each follicle. The respective COCs were matured in vitro where we collected an ooplasm biopsy, the first polar body, and cumulus cells. All samples were sequenced using RNA-Seq or WGBS to investigate the groups that reached the blastocyst stage or were arrested in the cleavage step.

first: Dewison

last: Ricardo Ambrizi

first: Ricardo

last: Perecin Nociti

first: Lawrence

middle: C

last: Smith

last: Vieira Meirelles


title: Inflammasome-resistant IPSC-derived myeloid-derived suppressor cells (iMDSCs)  ameliorate xenogeneic GVHD

city: Minneapolis

last: Zaiken

state: MN

address: East River Parkway

department: Pediatrics

institute: University of Minnesota

summary: Acute graft versus host disease (aGVHD) is considered a major complication of allogeneic hematopoietic stem cell transplant (aHSCT). Front-line pharmaceutical treatment is not uniformly effective and has toxic side effects. Myeloid-derived suppressor cells (MDSCs) are a heterogeneous population of immature myeloid cells with potent immunosuppressive functions. Their potential to control GVHD has been proven in different rodent models. However, a high MDSC to T cell ratio and multiple doses of MDSCs are needed to achieve maximum effectiveness. Clinical translation of in vitro MDSC generation limits its clinical usage by a relatively low yield and need for personalized patient products, especially challenging for multiple treatment courses. Therefore, we developed an in vitro method to generate MDSCs on a large scale from a human induced pluripotent stem cell (iPSC)-derived CD34+ cells. iMDSCs shared a similar morphology, phenotype, and suppressive function with peripheral blood (PB)-MDSCs. In striking contrast to PB-MDSCs, iMDSCs retained 95% of suppressor function when exposed to the damage-associated molecular pattern stimuli, LPS + ATP, released during GVHD. RNAseq analysis and gene knockdown studies revealed that inflammasome-resistant iMDSCs maintained expression of phosphoglycerate dehydrogenase, an enzyme involved in purine metabolism. Consistent with the retention of suppressor function during lethal xenogeneic GVHD-induced tissue injury, recipients of human iMDSCs and peripheral blood mononuclear cells (PBMC) experienced therapeutic benefits. Together, these data provide a platform for translating in vitro generated, off-the-shelf iMDSCs into the clinic for suppressing GVHD and other adverse immune responses.

overall_design: Human myeloid derived suppressor cells were differentiated from PBMC and iPSC. For inflammasome study, PBMC derived MDSCs (PB MDSC) and iPSC derived MDSCs (iMDSC) were treated with/without LPS and ATP to induce the inflammasome and then frozen down with lysis buffer for RNAseq. For iMDSCs subtypes(CD14- vs CD14+) comparison, cells were flow sorted by the CD14 expression and frozen down with lysis buffer for RNAseq.

first: Lie

last: Ma

last: Zeikan

first: Matthew

last: Denholtz

first: Bahram

last: Valamehr

first: Bruce

last: Blazar


title: Investigating the inter-relationship of SRPK1 and HRV infection

city: Glasgow

first: Sheila

middle: Veronica

last: Graham

state: Glasgow City

address: 464 Bearsden Road, Garscube Estate

department: MRC-UoG CVR

country: United Kingdom

institute: University of Glasgow

summary: Human rhinoviruses (HRV) are a leading cause of the common cold, but can often lead to respiratory complications in immunocompromised groups, evidently in a species-associated manner. There has been a growing interest in what underlies the variability in the severity of induced disease between HRV A, B and C strains. Koo et al. investigated this at the transcriptomic level in respiratory epithelial cells harvested from children, hospitalised with acute wheezing episodes. (https://doi.org/10/4049/j.immunol.1800178). Interestingly, this study revealed significant alterations in the expression of key host cell splicing factors between some HRV-infected children and uninfected controls, mainly the Serine/Arginine Protein Kinase 1 (SRPK1) and several Serine/Arginine rich Splicing Factors (SRSFs).   As these splicing factors regulate host splicing and translation, we hypothesise that HRV infection regulates the kinase SRPK1 and its substrates SRSFs to either dysregulate the splicing of host mRNAs performing antiviral functions and/or to alter the translation of viral proteins. We initiated this investigation by exploring HRV-A infections in-vitro using the strain HRV16. Here, we show that the pharmacological inhibition as well as the overexpression of SRPK1 has a direct and opposing effect on HRV16 infection in primary bronchial epithelial cells. In the same system, HRV16 infection led to significant downregulation at the gene, protein and phosphorylation levels of SRPK1 as well as of SRSF1, SRSF3 and SRSF6. Transcriptomic and alternative splicing (AS) bioinformatic analysis was performed using a physiologically relevant primary bronchial epithelial 3D model. This revealed the significantly altered AS of 1228 host genes during infection, with subsequent pathway analysis enriching the vast majority of these genes in cilia development and function networks. The impact of this effect has been demonstrated here, with HRV16 infection leading to significantly decreased cilia length and total numbers in our primary bronchial epithelial 3D model. Overall, this investigation has unravelled novel networks implemented during HRV infection and provided insights into the association of recurrent HRV infections at an early age with respiratory complications during development.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for primary bronchial epithelial cells (HRV16 infected vs mock infected, 3 technical replicates per condition)

first: Christoforos

last: Rozario

middle: V

first: Quan

last: Qu

first: Rose

last: Maciewicz


title: CircFTO, a c-Myc induced circRNA, sustains cell growth under Serine and Glycine deprivation

city: Hefei

first: Qidong

last: Li

state: Anhui

address: 443 Huangshan Road, Shushan district

institute: Lianxin Liu Lab

summary: Metabolic reprogramming is recognized as a hallmark of cancer and plays a pivotal role in sustaining cell growth under metabolic stress. However, the precise mechanisms are not completely understood. Here we dissect how circFTO, a circular RNA (circRNA), reinforces the serine biosynthesis pathway (SSP) through facilitating the expression of c-Myc. We found that circFTO expression was frequently overexpressed in hepatocellular carcinoma (HCC)-derived cell lines and tissues compared to their normal hepatic cell counterparts. In the context of HCC, we showed circFTO acts as ligand to bind and stabilize IGF2BPs, then elevated c-Myc expression through prolonging c-Myc mRNA half-life. In response to SG deprivation (Serine&Glycine deprivation), circFTO was transcriptionally induced by c-Myc, thus formed a circFTO-c-Myc positive feedback loop. In consequence, SSP components including PHGDH, PSAT1, PSPH, SHMT1 and SHMT2 are upregulated though the circFTO-c-Myc feedback loop. Intriguingly, some evidences showed the circFTO-c-Myc feedback loop is able to shift glucose metabolic flux towards SSP. Manipulating circFTO elicited robust effects on SSP associated genes with marked changes in HCC growth in vitro and in xenograft models under both normal and SG deprivation condition, indicative of the significant contribution of circFTO to tumorigenic phenotypes. Moreover, circFTO level is positively related to c-Myc expression in hepatocellular carcinoma tissues. Together, this work identifies circFTO as an integral element of SSP-regulated metabolic reprogramming under SG deprivation and implicitly highlights the potential of targeting circFTO to selectively counter the cancers.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for HepG2 cells with circFTO Knockdown

first: Yichun

last: Wang

first: Hanhui

last: Yao

first: Mian

last: Wu

first: Lianxin

last: Liu


title: Spatially resolved multi-omic profiling of human hippocampus reveals region-specific alterations in major depressive disorder [ATAC-seq]

city: New York

first: Kam

last: Leong

state: NY

address: 3600 Broadway, RM450C

department: Biomedical Engineering

institute: Columbia University

summary: The human hippocampus, a center of learning and memory, has a complex architecture with high cellular and molecular heterogeneity. We present the first spatially resolved atlas of human hippocampus at the genome scale. Spatial transcriptome sequencing on 10 hippocampi identified the hippocampal sub-fields and cell types in the dentate gyrus and the cornu Ammonis regions. We deconvoluted the cellular composition in each pixel to build a gene expression landscape of each cell subtype. Psychiatrically healthy brains were compared with brains from subjects with major depressive disorder (MDD) to identify differentially modulated pathogenic genes and pathways in a region-specific manner. We observed surprisingly high variability of RNA splicing in MDD compared with control. RNA velocity analysis suggested a model for how transcriptomic instability in MDD contributes to a high inter-patient heterogeneity particularly in the pyramidal neurons. Spatially resolved chromatin accessibility profiling further identified potential epigenetic underpinnings implicated in MDD molecular neuropathology.

overall_design: Ten human hippocampi were sequenced with DBiT-seq at 50 um resolution.

first: Xiao

last: Yang

first: Su

first: Fan

last: Rong

first: Leong

last: Kam


title: Spatially resolved multi-omic profiling of human hippocampus reveals region-specific alterations in major depressive disorder [RNA-seq]


title: SMAD4 regulates the progression of cholangiocarcinoma (CCA) by modulating the expression of STING1

city: JiNan

first: Anda

last: Shi

address: Culture West Road num 107

institute: Qilu Hospital

summary: SMAD4 regulates the expression of STING1 through its transcription  regulating function. Dual low expression of STING1 and SMAD4 had more power in  predicting patient survival. These results indicate that SMAD4-silenced CCA may  downregulate its STING1 expression to adapt to the immune system.

overall_design: Genome expression after SMAD4 knockdown in cholangiocarcinoma cells.

first: Zongli

last: Zhang

first: Kangshuai


title: Multi-modal Spatial Cellular Taxonomy of Human Hippocampus  Reveals Region-Specific Activity and States


title: A functional link between Enhanced Disease Susceptibility 1 and GH3.12/avrPphB susceptible 3 in pattern-triggered immunity in plants

city: Meguro

first: Kei

last: Hiruma

state: Tokyo

address: 3-8-1 Komaba,

department: Life Sciences

country: Japan

institute: The University of Tokyo

summary: Pattern recognition receptors (PRRs) recognize microbial molecular patterns to enhance plant defenses through pattern-triggered immunity (PTI). In Arabidopsis, EFR and FLS2 provide PRRs for bacterial EF-Tu (elf18 epitope) and flagellin (flg22 epitope), respectively. Whether and how PRRs are diverged in defense signaling downstream of receptor complexes is unknown. Here we report that ENHANCED DISEASE SUSCEPTIBILITY 1 (EDS1) is required for EFR- but not FLS2-mediated immunity against Pseudomonas syringae pv. tomato DC3000. Genome-wide profiling of elf18-induced transcriptional reprograming reveals defense-related genes that are deregulated in eds1 plants and rsw3, a dysfunctional glucosidase II± allele, which is specifically impaired in elf18-induced sustained defense activation. Negatively influenced elf18-inducible genes in eds1 and rsw3 plants include PBS3, encoding GH3 acyl adenylase. PBS3 also identifies a critical component in EFR-triggered immunity. Our findings point to a critical role for EDS1-mediated PBS3 induction in PTI and separate requirements between the EFR and FLS2 pathways.

overall_design: Three plant genotypes, three treatments including the control, and four time points were tested. For each condition, three biological replicates were made.

first: Tatsuya

last: Nobori

first: Annegret

last: Ross

first: Kenichi

last: Tsuda

first: Yusuke

last: Saijo


title: RB modulates chromatin organization by regulating cohesin-dependent loops and enhancer-promoter interactions [RNA-Seq]

first: Hanjun

last: Lee

overall_design: RNA-seq for RB WT or RB KO hTERT1-RPE1 cells synchronized in G1 or S phase

first: Ioanna-Maria

last: Gkotinakou

first: Michael

last: Lawrence

first: Ioannis

last: Sanidas


title: Maternal nutritional protein deficiency reduces nephron endowment at birth via disruption of nephron progenitor trajectory and branching morphogenesis

city: Clayton

first: Kieran

last: Short

address: 19 Innovation Walk

institute: Monash University

summary: Nephron number in the mouse kidney is lowered when maternal protein intake is reduced to 6-8% down from 20% (normal diet). We used single cell sequencing to study the transcriptional response to maternal low protein diet in the mouse embryonic kidney at days E14.5 and P0 (birth).

overall_design: Females were fed a low protein diet for 2 weeks prior to conception, through to birth. Kidneys were dissected from offspring at E14.5 and at P0 and processed for single cell (E14.5) or single nuclear (P0) RNA sequencing.

first: Giovane

last: Tortelote

first: Fabiola

last: Diniz

first: Samir

last: El-Dahr

first: Ian

last: Smyth


title: Bojungikki-tang ameliorates psoriasis-like dermatitis: Network analysis and transcriptomics with experimental validation

status: Public on Sep 29 2025

city: Daejeon

first: Bu-Yeo

last: Kim

address: 1672 Yuseongdae-ro, Yuseong-gu

department: Herbal Medicine Research Division

country: South Korea

institute: Korea Institute of Oriental Medicine

summary: Psoriasis is a chronic and complex disease characterized by itching, burning, and soreness with scaly plaques and erythematous lesions. we evaluated the effect of Bojungikki-tang (BJT, Buzhong-Yiqi-Tang in traditional Chinese medicine and Hochu-ekki-to in Kampo medicine) as a combination of medicinal herbs against psoriasis. Network analysis from transcriptomics was used to determine the effective phytochemical constituents of BJT.

overall_design: To identify the protective effect of BJT on psoriasis-like skin inflammation, topical imiquimod (IMQ)-applied mice were administered with BJT (250, 500, or 1000 mg/kg/day) or MTX (1 mg/kg/day) orally for 7 days.

first: Yun Hee


title: RB modulates chromatin organization by regulating cohesin-dependent loops and enhancer-promoter interactions [ChIP-Seq]

overall_design: ChIP-seq (SMC3, acSMC3, H3K27ac, H3K27me3) for RB WT or RB KO hTERT1-RPE1 cells that are asynchronous or synchronized in G1 or S phase or for hTERT1-RPE1 cells that expressed constitutively active RB


title: Chromatin structure dynamics directs neuronal cell fate acquisition

city: Antwerp

first: Valeriya

last: Malysheva

state: Select State

address: Universiteitsplein 1, Building V

country: Belgium

institute: VIB Center for Molecular Neurology

summary: Here we reveal the governing role of the chromatin interactome in the commitment and propagation of the initiating signal in early neurogenesis by reconstructing dynamic Gene Regulatory Networks (GRNs) that integrate transcriptome, chromatin accessibility and long-range chromatin interactions in a temporal dimension.

overall_design: Examination of chromatin structure during ATRA-induced early neurogenesis


title: Combinatorial interactions between viral proteins expand the potential functional landscape of the tomato yellow leaf curl virus proteome

city: Tübingen

first: Rosa

last: Lozano-Durán

address: Auf der Morgenstelle 32

institute: University of Tübingen

summary: Viruses manipulate the cells they infect in order to replicate and spread. Due to strict size restrictions, viral genomes have reduced genetic space; how the action of the limited num- ber of viral proteins results in the cell reprogramming observed during the infection is a long- standing question. Here, we explore the hypothesis that combinatorial interactions may expand the functional landscape of the viral proteome. We show that the proteins encoded by a plant-infecting DNA virus, the geminivirus tomato yellow leaf curl virus (TYLCV), physi- cally associate with one another in an intricate network, as detected by a number of protein- protein interaction techniques. Importantly, our results indicate that intra-viral protein-protein interactions can modify the subcellular localization of the proteins involved. Using one partic- ular pairwise interaction, that between the virus-encoded C2 and CP proteins, as proof-of- concept, we demonstrate that the combination of viral proteins leads to novel transcriptional effects on the host cell. Taken together, our results underscore the importance of studying viral protein function in the context of the infection. We propose a model in which viral pro- teins might have evolved to extensively interact with other elements within the viral prote- ome, enlarging the potential functional landscape available to the pathogen

overall_design: RNA-seq profiling of Nicotiana benthamiana leaves transiently expressing C2, CP and C2+CP TYLCV genes, and infected with TYLCV, TYLCV-C2 mutant and TYLCV-CP mutant

first: Liping

last: Wang

first: Huang

last: Tan

first: Laura

last: Medina-Puche

first: Mengshi

last: Wu

first: Borja

last: Garnelo Gomez

first: Man

last: Gao

first: Chaonan

last: Shi

first: Tamara

last: Jimenez-Gogonra

first: Pengfei

last: Fan

first: Xue

last: Ding

first: Dan

last: Zhang

first: Yi

first: Tábata

last: Rosas-Díaz

first: Yujing

last: Liu

first: Emmanuel

last: Aguilar

first: Xing

last: Fu


title: System biology reveals a mechanism associated with protection by the co-immunization of DNA and protein in the same anatomical site (LN)

city: Chicago

first: Slim

last: Fourati

state: Illinois

address: 300 E Superior St

department: Medicine

institute: Northwestern University

summary: System immunology was used to identify the mechanisms linked to the immunogenicity and protective efficacy of an HIV vaccine comprised of Env and Gag DNA and Env proteins by co-administration of the vaccine components in the same muscles or by separate administration of DNA and protein in contralateral sites in female rhesus macaques. Interestingly, only macaques in the co-administration vaccine group were protected against SHIV CH505 acquisition after repeated low-dose intravaginal challenge and showed 67% risk reduction per exposure. Macaques in the co-administration group developed higher migratory monocytes (CXCR4+ monocytes with increased LYN expression) from blood to lymph nodes. The heightened frequency of those migratory monocytes was associated with heightened ADCC pre-challenge and with decreased risk of acquisition. These data suggest that monocytes migration is key to the simultaneous recognition, processing and presentation of DNA+Env protein in the same draining lymph nodes to confer protective immunity.

overall_design: Lymph node bulk RNA-seq (paired-end strand-specific) for 60 samples. Samples were collected from 18 rhesus macaques that receive DNA and protein in both legs and 18 rhesus animals that received DNA and protein in different legs

first: Michael

last: Gale

first: Rafick-Pierre

last: Sekaly

first: Barbara

middle: B

last: Felber

first: George

middle: N

last: Pavlakis


title: RNA alterations induced by influenza infection

city: Jinan

first: Ran

last: Wei

state: Shandong

address: No. 23788, Gongye North Road, Licheng District, Jinan City, Shandong Province, China

institute: Poultry Institute, Shandong Academy of Agricultural Sciences, Ji’nan, China

summary: The H13N2 subtype avian influenza virus (AIV) is a virus with cross-species transmission capability, which was previously known to mainly infect waterfowl. However, recent studies have confirmed that this virus can also infect poultry and mammals. This cross-species transmission ability has raised widespread concerns about its potential public health threat. In this study, we used the human lung epithelial cell line A549 as a model to investigate the changes in RNA expression after 24 hours of infection with H13N2 virus. These findings provide important insights into the cross-species transmission mechanism of H13N2 virus and its impact on host cells, while also offering a scientific basis for assessing its potential public health risks and developing prevention strategies.

overall_design: RNA-seq were performed for A549 cell lines with or without H1N1 or H13N2 infection

first: Zhijun

last: Yu


title: VH gene accessibility in pro-B cells

first: Amy

last: Kenter

state: IL

address: 835 S Wolcott

institute: UIC

summary: The generation of a diverse immunoglobulin repertoire is essential for humoral immunity and requires the participation of all V genes in V(D)J recombination.  Efficient repertoire formation depends on the access of approximately 100 functional VH genes spread over 2.4 Mb of the Igh locus to the DH and JH segment clusters located in the recombination center (RC) with the intronic Em enhancer.  A process termed locus contraction is thought to generate proximity of the distal VH genes to the RC.  Here, we explore the function of newly discovered novel enhancers and a highly transcribed VH promoter and their impact on VH gene accessibility in chromatin.  We demonstrate that these transcriptional elements determines regional Igh gene transcription but have little impact on chromatin accessibility.

overall_design: ATAC-seq was performed on BM derived Rag2-/-, Rag2-/-SiteI.3Pr-/- and Rag1-/-NE1-/-  murine pro-B cells following 5 days of ex vivo IL7 expansion.

first: Ellen

last: Drake

first: Sarah

last: Naiyer


title: The GBS data of 275 recombinant inbred lines derived from inbreds Ji846 and Ye3189

city: Beijing

first: Xin

last: Lu

address: Zhongguancun South Street,Haidian District

institute: Chinese Academy of Agricultural Sciences

type: Genome variation profiling by high throughput sequencing

summary: An ultra-high density accurate linkage map for a set of maize RILs was constructed using a GBS strategy. This map will facilitate identification of genes and exploration of QTL for complex architecture in maize. It will also be helpful for further research into the mechanisms that control complex architecture while also providing a basis for marker-assisted selection

overall_design: we employed a genotyping-by-sequencing strategy to construct an ultra-high-resolution linkage map  for 275 recombinant inbred lines (RILs) derived from a high-PC female Ji846 and low-PC male Ye3189.

first: Zhiqiang

last: Zhou

first: Yu

first: Xinhai

last: Li


title: Screening of target genes for the drug histamine.

first: Anda

last: Shi

summary: To explore histamine target genes,we used CRISPR-PoolTMKOUT-Human-Single vector to build GeCKO(genome-scale CRISPR-Cas9 knockout) human library.Then Genome-wide CRISPR screen was used to detect target genes in cholangiocarcinoma cells.

overall_design: After GeCKO library was successfully constructed using lentivirus in human cholangiocarcinoma cell lines, the nuclear genome was extracted for PCR(Polymerase Chain Reaction) purification and amplification, then the PCR amplification products were detected by Genome-wide CRISPR screen.

first: Zongli

last: Zhang

first: Yunfei

last: Xu


title: Voluntary exercise alleviates neural functional deficits in Parkinson’s disease mice by inhibiting microglial ferroptosis via SLC7A11/ALOX12 axis

city: Guangzhou

first: Jinghui

state: Guangdong

address: NO. 600,Tianhe Road

department: Department of Rehabilitation Medicine

institute: the Third Affiliated Hospital of Sun Yat-sen University

summary: Microglia are more susceptible to ferroptosis compared to neurons and astrocytes, which may compromise their phagocytic and clearance capabilities of α-synuclein (α-syn) in Parkinson’s disease (PD). While the beneficial effects of physical exercise (PE) on reducing α-syn deposition in PD have been highlighted, the role of PE in modulating microglial ferroptosis remains unclear. This study focuses on the impact of exercise on inhibiting microglial ferroptosis and mitigating α-syn accumulation. We demonstrate that voluntary exercise effectively inhibits microglial ferroptosis. Mechanistically, PE-induced upregulation of SLC7A11 inhibits microglial ferroptosis by suppressing ALOX12, thereby enhancing microglial phagocytosis and clearance of α-syn, which is paralleled by improvements in neurological function in PD mice. Collectively, these findings not only underscore the critical role of microglial ferroptosis in the pathological progression of PD but also elucidate the molecular mechanism by which PE attenuates microglial ferroptosis via the SLC7A11/ALOX12 axis.

overall_design:
The substantial nigra tissues (from three mice in corresponding group, specially) used for sequencing were prepared with RNase-free instruments. RNA-seq of profiling of aforementioned brain tissues was performed.
Mice in “M” group (which means “MPTP” group) received intraperitoneal injection of MPTP-HCl (Sigma, Italy) that dissolved in saline at a dose of 20 mg/kg twice weekly for 5 weeks.
Mice in “P” group (which means “MPTP+ PE” group) received intraperitoneal injection of MPTP-HCl (Sigma, Italy) that dissolved in saline at a dose of 20 mg/kg twice weekly for 5 weeks.  After the first MPTP injection, mice in MPTP + PE group underwent two months of voluntary wheel exercise.
Mice in “V” group (which means “Vehicle” group) received saline injections twice weekly for 5 weeks.

first: Xiaofei

last: He

first: Lili


title: Cancer-associated fibroblasts promote esophageal carcinogenesis and lung metastasis by CDH11-mediated extracellular matrix environment remodeling [RNA-Seq]

city: fujian xiamen

first: yangfan

address: 55 Zhenhai Road, Siming District, Xiamen, Fujian Province

institute: The First Affiliated Hospital of Xiamen University

summary: Lung metastasis is a major cause of death in patients with esophageal squamous cell carcinoma (ESCC) and its tumor microenvironment (TME) is highly complex; however, the molecular mechanisms of ESCC lung metastasis are unclear. In this study, the first comprehensive single-cell atlas of ESCC lung metastasis is established using single-cell RNA sequencing of 11 patient samples. The findings highlight the dynamic evolutionary patterns of the TME and distinct characteristics of key cellular subpopulations. The immune microenvironment exhibited significant alterations, with a subpopulation of pro-carcinogenic cancer-associated fibroblasts (CAFs) in primary ESCC foci and lung metastases. Notably, calreticulin CDH11 is exclusively expressed in these CAFs and upregulated in conjunction with lung metastasis of ESCC. CDH11 modulates the AKT-related signaling pathway through its interaction with FGFR1, influencing CAF-mediated extracellular matrix remodeling, thereby facilitating metastatic progression. Application of the CDH11 inhibitor, celecoxib, presents a promising new strategy for targeting lung metastasis in ESCC. The molecular mechanisms underlying the lung metastatic microenvironment of ESCC, which are expected to improve the molecular typing accuracy of ESCC lung metastasis to the single-cell level contribute to the development of a precision therapeutic system based on the modulation of the stromal microenvironment, with significant clinical translational potential.

overall_design: We conducted scRNA-seq on tissue samples from 11 patients. This cohort included paraneoplastic tissues from five patients who underwent surgical resection for ESCC, primary ESCC tissues from three patients who underwent endoscopic clamping, and biopsy tissues from three patients with lung metastases arising from ESCC

first: Qin

last: Lin

first: Haojun

last: Chen


title: Nucleophosmin supports WNT-driven hyperproliferation and tumour initiation

first: Kathryn

last: Gilroy

address: Garscube

institute: CRUK Scotland Institute

summary: Nucleophosmin (NPM1), a nucleolar protein frequently mutated in haematopoietic malignancies, is overexpressed in several solid tumours with poorly understood functional roles. Here, we demonstrate that Npm1 is upregulated following APC loss in WNT-responsive tissues and supports WNT-driven intestinal and liver tumourigenesis. Mechanistically, NPM1 loss induces ribosome pausing and accumulation at the 5’-end of coding sequences, triggering a protein synthesis stress response and p53 activation, which mediate this anti-tumourigenic effect. Collectively, our data identify NPM1 as a critical WNT effector that sustains WNT-driven hyperproliferation and tumourigenesis by attenuating the integrated stress response (ISR) and p53 activation. Notably, NPM1 expression correlates with elevated WNT signalling and proliferation in human colorectal cancer (CRC), while CRCs harbouring NPM1 deletions exhibit preferential TP53 inactivation, underscoring the clinical relevance of our findings. Being dispensable for adult epithelial homeostasis, NPM1 represents a promising therapeutic target in p53-proficient WNT-driven tumours, including treatment-refractory KRAS-mutant CRC, and hepatic cancers.

overall_design: Bulk RNAseq expression data from mouse small intestine and colon tissues, with genetic modifications in combinations of the genes Apc, Kras, Braf, p53, Alk5, and Notch1.

first: Georgios

last: Kanellos

first: Mark

last: White

first: Megan

last: Mills

first: Andrew

middle: D

last: Campbell

first: Owen

last: Sansom


title: Curcumin mitigated aflatoxin B1 induced endoplasmic reticulum stress and gut-kidney axis damage in sheep via regulating the ATF6/GRP78 and IL-1β/NF-κB signaling pathways

city: Changchun

first: qi

middle: Chuan

last: Wang

address: No. 5333 Xian Load

institute: Jilin university

summary: Curcumin regulated ATF6/GRP78 and IL-1β/NF-κB to alleviate kidney damage

overall_design: CON, AFB1_CUR, AFB1

first: Ting

first: Chuanqi


title: Cancer-associated fibroblasts promote esophageal carcinogenesis and lung metastasis by CDH11-mediated extracellular matrix environment remodeling [scRNA-Seq]


title: Impact of hyaluronic acid coating of collagen membranes: RNAseq of gingival fibroblasts

city: Vienna

first: Reinhard

last: Gruber

address: Sensengasse 2a

country: Austria

institute: Medical University Vienna

summary: Collagen membranes are commonly used biomaterials in clinical dentistry that can be coated with hyaluronic acid (HA). To investigate fibroblast responses, gingival fibroblasts were seeded on porcine-derived membranes originating from dermis (Mucoderm®) and pericardium (Collafleece®) —with or without lyophilized HA, followed by bulk RNA sequencing. Mucoderm® and Collafleece® elicited a significant transcriptional response compared to fibroblasts grown on tissue culture surfaces. Compared to Mucoderm®, Collafleece® increased the expression of extracellular matrix genes CCN1, CCN2, COL1A1, POSTN, SPARC, TAGLN, FBN2, CCDC80 and CREB3L1. Decreased genes included the proteases MMP3 and MMP10 but also detoxifying genes MT1E, MT2A, HMOX1, NQO1. RNA sequencing further revealed that HA coating increased IL24 in Mucoderm®, but no increasing changes was observed in Collafleece®. These data suggest that Collafleece® has a comparably stronger positive impact on extracellular matrix formation by in gingival fibroblast than Mucoderm®. The results further imply that HA coating does consistently impact fibroblast behavior.

overall_design: We exposed gingival fibroblasts on porcine-derived membranes originating from dermis (Mucoderm®) and pericardium (Collafleece®) —with or without lyophilized HA, followed by bulk RNA sequencing, to identify changes in the genetic signatures of fibroblasts.

first: Panahipour

last: Layla

first: Xiaoyu

last: Huang


title: RNA-seq of  Chara braunii NIES 1604 and S276

city: Praha 6

first: Karel

last: Muller

address: Rozvojová 263

department: Lab. of hormonal regulations in plants

country: Czech Republic

institute: Institute of Experimenal Botany of the Czech Academy of Sciences

summary: To investigate gene expression in different cells of Chara braunii we performed RNA sequencing of whole thali with rhizoids and thalli without rhizoids in strains NIES 1604 and S276.

overall_design: Analysis included whole Chara braunii plants (in 3 repetitions) of strain S276, then the collected samples included thalli with rhizoids and without rhizoid from two strains of Chara braunii (NIES 1604 and S276).

first: Stanislav

last: Vosolsobě

last: Müller

first: Katarina

last: Kurtović

first: Jan

last: Petrášek


title: RNA Expression of TH10785 treated human T cells

city: Magdebrug

first: Dimitrios

last: Mougiakakos

address: Leipziger Str. 44

department: Universitätsklinik für Hämatologie, Onkologie und Zelltherapie

institute: Universitätsklinikum  Magdeburg A.ö.R.

summary: To investigate the transcriptomic effects of the OGG1 agonist TH10785, we treated T cells with the compound and analyzed gene expression profiles. Our aim was to evaluate the potential of OGG1 activation as a strategy to restore and preserve T cell function under conditions of oxidative stress.

overall_design: Isolated human T cells untreated  (Sample6,7,29,30) or treated (Sample6_10785,Sample7_10785,Sample29_10785,Sample30_10785) with TH10785 at a concentration of  7.5 μM. T cells were co-cultured with Nalm6 and CD19xCD3. RNA was isolated on day 10.

first: Domenica

last: Saul

first: Christopher

last: Lischer

first: Heiko

last: Bruns

first: Nicole

last: Ziegler

first: Aimo

last: Kannt

first: Maruice

last: Michel


title: Genomic stress and STING activation in oligodendroytes drives Alzheimer's Disease

city: Gainesville

first: Stefan

last: Prokop

state: FL

address: 1275 Center Dr

department: Pathology

institute: University of Florida

summary: Oligodendrocytes are a vital yet understudied cell type, especially in the case of neurodegeneration. This is despite their potential to mitigate neuronal degeneration through axonal structural support and metabolic supplementation, which may be pivotal in reinforcing neurons in times of cellular stress. Neuronal degeneration runs rampant in Alzheimer’s Disease (AD), which is the most common form of dementia. Exhaustive research into AD pathogenesis has yet to yield safe and effective treatment. Even the most recent amyloid monoclonals do little to slow progression of disease and indeed any improvement seems to be clinically indiscernible. Additionally, these drugs carry a significant risk of vascular events. While amyloid-beta and tau accumulation and neuronal pathology are main hallmarks of AD, a wide cascade of cellular events are also present. Demyelination is a prominent pathological hallmark of AD and has even been shown to occur in the preclinical phase of disease. Studies have suggested that oligodendrocyte and myelin deficits precede tau and Aβ accumulation, perhaps playing their own role in precipitating neurodegeneration and neuronal/axonal decline. The mechanisms of oligodendrocyte dysfunction in AD remain unknown. DNA damage has been increasingly linked to AD progression, and markers of DNA damage have been shown to be upregulated in oligodendrocytes in particular within both AD patients and animal models. This DNA damage can activate the nucleic-acid sensing pathway mediated by stimulator of interferon related genes (STING) as well as the Type I interferon response, further impacting oligodendrocyte homeostasis. DNA damage in oligodendrocytes and its ramifications could deprive neurons of crucial support, thereby accelerating degeneration. Indeed, DNA damage in oligodendrocytes as well as the role its resulting cascade of pathways have in the AD brain have not yet been explored.

overall_design: spatial transcriptomic profiling of Olig2+ cells in AD patient tissue (from normal aging, prelinical disease, and AD as identified by Braak score) costained with beta-amyloid. White matter, grey matter regions as well as regions with plaque and devoid of plaque were identified and sequenced using the GeoMx platform.

first: Raghavan

last: Tula

first: Li

last: Sihan

first: Tsering

last: Wangchen


title: TP53 deficiency in AML induces resistance to T-cell engagers through an immunosuppressive secretome

city: München

first: Kieron

last: White

address: Genzentrum, Feodor-Lynen-Straße 25

department: Gene Center

institute: LMU

summary: Bispecific T-cell engagers (BiTEs) have transformed the treatment of B-cell malignancies, yet clinical activity in AML has been modest at best, irrespective of the target antigen. Resistance is driven in part by the genetic heterogeneity of AML, most notably TP53 mutations, present in 10-15% of de novo and up to 25% of therapy-related AML. These mutations confer resistance to T-cell-based therapies, consistent with the dismal outcomes observed after allogeneic HSCT. Thus, we hypothesized that TP53 aberrations in AML contribute to cellintrinsic and extrinsic resistance against T-cell-based immunotherapy. To investigate this, we utilized the BiTE molecule AMG 330 (CD3×CD33) in co-cultures with primary AML cells (pAML) harboring TP53 deletions (DEL) and AML cell lines with a TP53 knockdown (KD). Cytotoxicity against TP53 DEL pAML and TP53 KD cell lines was reduced in co-cultures with T cells. In addition, T-cell proliferation and proinflammatory cytokine secretion was impaired in cocultures with TP53 KD cells. Transwell assays identified the secretome of TP53 KD AML cells as a key contributor to the observed immunosuppressive effect. Furthermore, proteomic analysis revealed TGF-β1 in TP53 KD co-cultures as a mediator of T-cell suppression. Lastly, RNA sequencing of T cells co-cultured with TP53 KD cells uncovered a transcriptional shift toward a senescent cell cycle profile. Our data collectively identify the immunosuppressive secretome of TP53-deficient AML as a key barrier to T-cell-engaging immunotherapies, underscoring an unmet clinical need for strategies able to restore T-cell function in TP53 KD AML.

overall_design: RNA bulk sequencing profile of AML cell lines after 3-day co-culture with human T cells

first: Winter

last: Lis

first: White

last: Kieron

first: Marion

last: Subklewe


title: Epigenetic heterogeneity and state-specific transcriptional programs determine differential drug response in osteosarcoma [CUT&Run]

city: San Francisco

first: Alex

middle: G

last: Lee

state: CA

address: 1550 4th Street

institute: UCSF

summary: Osteosarcoma is a genomically complex tumor with structural rearrangements, aneuploidy, and chromosomal alterations, resulting in significant intertumoral heterogeneity. This complexity hampers the identification of key oncogenic pathways and subtypes. We hypothesized that chromatin accessibility could uncover molecular features to clarify their transcriptional programs, suggesting new therapies. Using ATAC-seq, H3K27ac profiling, and single-cell multiome analysis, we identified two distinct cellular states in osteosarcoma driven by unique transcription factor networks linked to normal bone development. These subtypes can be detected in patient samples via a specific gene expression signature with prognostic value.

overall_design: Osteosarcoma cell lines derived from xenographs were used in this study. H3K27ac was profiled by CUT&RUN. IgG was used as control per sample. 2-5 replicates were performed per sample.

first: Eunice

last: López-Fuentes

first: Alejandro

last: Sweet-Cordero


title: Epigenetic and transcriptional heterogeneity define osteosarcoma subtypes and establish targetable vulnerabilities [multiomics]

overall_design: We utilized multiomic analysis single-nucleus  (snRNAseq + snATACseq) on five samples from patient-derived xenografts to investigate the heterogeneity and transcriptional/epigenetic landscape of osteosarcoma. This study specifically aimed to address the enrichment of early osteoblast derived (EOD) and late osteoblast derived (LOD) clusters.


title: Transcriptome changes in BeWo cells under chemically induced hypoxia

city: Moscow

first: Ivan

last: Antipenko

address: 11 Pokrovksy Bulvar, Moscow, 109028, Russia

country: Russia

institute: HSE University

summary: Hypoxia is an important condition in placental biology, required for trophoblast differentiation but also associated with various placental pathologies. To model hypoxic response, BeWo b30 choriocarcinoma cells were treated with cobalt chloride (CoCl₂) or an oxyquinoline derivative (4896-3212), both chemical inducers of the HIF1α signaling pathway. Transcriptome profiling was performed to identify gene expression changes under these conditions compared to untreated controls. The dataset provides information on hypoxia-induced transcriptional reprogramming, including genes involved in metabolism, lipid homeostasis, and HIF1α-regulated signaling pathways. These results may contribute to understanding molecular mechanisms of placental adaptation to hypoxia and its role in pathological states.

overall_design: RNA-seq profiling of BeWo b30 cells after 24 h exposure to cobalt (II) chloride or oxyquinoline derivative 4896-3212, both chemical inducers of the HIF-1α signaling pathway

first: Evgeny

last: Knyazev

first: Timur

last: Kulagin

first: Alexander

last: Tonevitsky


title: Methamphetamine Induces Metallothionein 1 Expression and an Inflammatory Phenotype in Primary Human HIV-infected Macrophages [JW81_JW82_JW84]

city: Bronx

first: Jessica

last: Weiselberg

address: 1300 Morris Park Avenue, Forchheimer 727

institute: Albert Einstein College of Medicine

summary: HIV associated neurocognitive impairment (HIV-NCI), a comorbidity of HIV infection, affects up to 50% of people with HIV (PWH). HIV-infected monocytes that transmigrate across the blood brain barrier and differentiate into macrophages establish a CNS viral reservoir that activates and infects parenchymal cells, contributing to neuronal damage that characterizes HIV-NCI. Methamphetamine (meth) use is prevalent in PWH and further impairs cognitive functioning. To examine whether meth-mediated dysregulation of macrophage functions may contribute to increased HIV-NCI, we characterized differential gene expression in primary human HIV-infected macrophages treated daily with meth for five days by RNA-sequencing. We identified increases in multiple gene isoforms of metallothionein 1 (MT1), a heavy metal binding protein involved in protective mechanisms against metal toxicity and oxidative stress. Nuclear localization of MT1 protein was previously shown to either positively or negatively affect NF-κB activity in a cell type specific manner, with nuclear MT1 contributing to LPS-induced TNF-α and IL-6 in macrophages. We found that daily meth treatment for one to five days increased nuclear localization of MT1 in macrophages acutely infected with HIV which was associated with increased LPS-induced CXCL8 and CCL8, and a trend towards increased basal and/or LPS-induced expression of other cytokines/chemokines, including TNF-α and IL-6, that was donor specific. ROS levels were not changed with meth treatment although there was a donor specific trend towards increased ROS with multiple days of meth treatment. These data indicate that repeated exposure of macrophages to meth in the context of HIV increases nuclear MT1 localization, which is associated with increased inflammatory mediator production, and therefore may be a mechanism that contributes to meth-mediated exacerbation of HIV-NCI.

overall_design:
Primary human macrophages were obtained from culturing monocytes from healthy individuals and were infected with HIV or left uninfected. After three days of infection, HIV-infected macrophages were treated daily with meth for five days. Uninfected samples were treated daily with emth begining at the same timepoint.

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

first: Meng

last: Niu

first: Cristian

middle: A

last: Hernandez

first: Howard

last: Fox

first: Tina

last: Calderon

first: Joan

middle: W

last: Berman


title: Methamphetamine Induces Metallothionein 1 Expression and an Inflammatory Phenotype in Primary Human HIV-infected Macrophages [JW98_JW100]


title: ZFAS1 suppression in HepG2 cells

city: Ottawa

first: Ruth

last: McPherson

state: Ontario

address: 40 Ruskin

country: Canada

institute: UOHI

summary: Cultured HepG2 hepatoblastoma cells were treated with ZFAS1 targeting gapmer oligonucleotides

overall_design: Four different passages of HepG2 cells (p12, p13, p19 and p20) were treated for 48 h with pairs of antisense oligonucleotides targeting three exons of of ZFAS1 variants  ENST00000618800 (ASO 3+4, ASO 5+6) and ENST00000620594 (ASO 7+8), or a control ASO (CTLASO)

first: S

last: Soubeyrand

first: R


title: Macrophages display spatiotemporal specificity in intrahepatic cholangiocarcinoma and drive tumour progression via OSM and THBS1

city: zhengzhou

first: tingjie

last: wang

state: Henan

address: dongming road

institute: zzu

summary: scRNAseq for AKT1/NICD1 ICC mouse model

overall_design: scRNAseq for AKT1/NICD1 ICC mouse model

first: Tingjie

last: Wang

first: Chuanrui

last: Xu

first: Ruitao

last: Long


title: Biomimetic fractal topography enhances podocyte maturation in vitro

city: Toronto

first: Milica

last: Radisic

address: 160 College St

institute: University of Toronto

summary: Cells and tissues in their native environment are organized into intricate fractal structures, which are rarely recapitulated in their culture in vitro. The extent to which fractal patterns that resemble complex topography in vivo influence cell maturation, and the cellular responses to such shape stimulation remain inadequately elucidated. Yet, the application of fractal cues (topographical stimulation via self-similar patterns) as an external input may offer a much-needed solution to the challenge of improving the differentiated cell phenotype in vitro. Here, we established fractality in the kidney glomerulus and podocytes, branching highly differentiated kidney cells within the glomerulus. Biomimetic fractal patterns derived from glomerular histology were used to generate topographical (2.5-D) substrates for cell culture. Podocytes grown on fractal topography expressed higher levels of functional markers and exhibited enhanced cell polarity. To track morphological complexities of differentiated podocytes, we employed a fluorescent labelling assay where labelled individual cells are tracked within otherwise optically silent confluent cell monolayer to reveal single-cell borders. RNAseq analysis suggested enhanced ECM deposition and remodeling in podocytes grown on fractal substrates versus flat surfaces, and enhanced maturation accompanied by stress in podocytes grown on fractal versus non-fractal topography. The incorporation of fractal topography into standard tissue culture well plates as demonstrated here may serve as a user-friendly bioengineered platform for high-fidelity cell culture.

overall_design: RNA-seq profiling of E11 murine porodyctes cultured on polydimethylsiloxane (PDMS) substrates with No Topography (NT), Round Topography (RT), and High Fractal (HF) topography where NT and RT serve as non-fractal non-topographic control and non-fractal topographic control groups, respectively, and HF refers to a biomimetic high fractal topographic group derived from healthy histological glomerular tracing

first: Chuan

last: Liu

first: Praful

last: Aggarwal

first: Karl

middle: T

last: Wagner

first: Shira

last: Landau

first: Teng

last: Cui

first: Xin

last: Song

first: Laleh

last: Shamaei

first: Naimeh

last: Rafatian

first: Yimu

last: Zhao

first: Sonia

last: Rodriguez-Ramirez

first: Keith

last: Morton

first: Elizabeth

last: Virlee

first: Chen Yu

last: Li

first: Dawn

last: Bannerman

first: Simon

last: Pascual-Gil

first: Sargol

last: Okhovatian

first: Anastasia

first: Sergi

last: Clotet-Freixas

first: Teodor

last: Veres

first: Mohtada

last: Sadrzadeh

first: Tobin

last: Filleter

first: Ulrich

last: Broeckel

first: Ana

last: Konvalinka


title: Differentiation and Dexamethasone Atrophy on C2C12 myotubes

city: Berlin

first: Suzuka

last: Nakagawa

address: Robert-Rössle Str. 10

institute: MDC

summary: Skeletal muscle atrophy and weakness are major contributors to morbidity, prolonged recovery, and long-term disability across a wide range of diseases. Atrophy is caused by breakdown of sarcomeric proteins resulting in loss of muscle mass and strength. Molecular mechanism underlying the onset of muscle atrophy and its progression have been analysed in patients, mice, and cell culture but the complementarity of these model systems remains to be explored. Here, we applied deep-coverage transcriptomic and proteomic profiling to characterize dynamic changes during dexamethasone-induced atrophy in the widely used murine skeletal muscle cell line C2C12. Comparison with published datasets confirmed that muscle differentiation is well recapitulated in C2C12 myotubes. Under dexamethasone-induced treatment, this model was particularly suited to capture early atrophy events, prior to disassembly and degradation of sarcomeric proteins. We also identified alterations in mitochondrial gene expression and differential alternative splicing events during early-stage myotube atrophy. This dataset complements existing in vivo data and provides novel insights into the regulatory processes during skeletal muscle wasting.

overall_design: mRNA-seq of undifferentiated C2C12 cells (day 0), differentiated cells (day 7), vehicle treated controls (day 8, day 10) and 100 µM Dexamethasone treated cells (day 8, day 10)

first: Aristotelis

last: Misios

first: Dermot

last: Harnett


title: Urine stem cells as a bona fide model to study cartilage associated disease [RNA-Seq]

city: Erlangen

first: Steffen

last: Uebe

address: Kussmaulallee 4

department: Humangenetisches Institut

institute: Uniklinikum Erlangen

summary: Non-invasive cellular models for genetic growth disorders affecting cartilage and bone remain rare, hampering mechanistic studies and the development of personalized therapies. Here, we present urine-derived stem cells (USCs), as a robust in vitro system for human chondrogenesis. Single-cell RNA sequencing of undifferentiated USCs revealed distinct clusters, of which a subset had high stem cell character. After differentiation, USCs underwent osteogenic and chondrogenic lineage with positive marker expression, confirmed by bulk-RNA-Seq. Single cell transcriptomic comparisons with healthy cartilage revealed a healthy cartilage mimicking, chondrocyte-like subcluster. Pseudotime analysis revealed multiple chondrogenic trajectories.

overall_design: RNA-seq analysis of osteogenically and chondrogenically induced (14 days) and differentiated urinary stem cells

first: Alexander

last: Schulz

first: Christian

last: Thiel

first: Emily

last: Brockmann

first: Arif

last: Ekici

first: André

last: Reis


title: 4R-Tau Seeding Activity Reveals Molecular Subtypes in Progressive Supranuclear Palsy

city: London

first: Tallulah

middle: Suzanne

last: Andrews

address: 1151 Richmond St.

institute: University of Western Ontario

summary: Progressive Supranuclear Palsy (PSP) is a clinically heterogeneous 4-repeat (4R)-tauopathy marked by variable progression and phenotypic diversity. We examined the distribution of high-molecular-weight tau (HMW-tau) species and 4R-tau seeding capacity across 25 PSP cases and 20 brain regions. HMW-tau levels varied regionally, with the temporal and motor cortices exhibiting the highest abundance. Using size-exclusion chromatography (SEC) and 4R-tau seed amplification assays (SAAs), we identified that HMW-tau fractions exhibit the greatest seeding activity. Proteomic and spatial transcriptomic analyses of the primary motor cortex revealed dysregulated adaptive immunity and metabolic pathways in high-seeder cases. Neuropathological clustering confirmed distinct profiles associated with tau seeding activity. These findings suggest that evaluating tau seeding capacity may offer valuable insights into the heterogeneity of PSP and its underlying molecular drivers.

overall_design: Post-mortem tissue sections from the motor cortex of four patients with Progressive Supranuclear Palsy (PSP) (2 high seeders, 2 low seeders) were selected for spatial transcriptomics based on distinct 4R-tau seeding capacities identified via seed amplification assays. These cases showed comparable PSP stage, phenotype, and co-pathologies. They were also used in neuropathological and proteomic analyses. Tissue quality (DV200 > 50%) ensured suitability for Visium profiling.

first: Ivan

last: Martinez Valbuena

first: Gabor

last: Kovacs


title: DNA methylation patterns of neuroendocrine neoplasms

city: Heidelberg

first: Stephanie

last: Roessler

address: Im Neuenheimer Feld 224

institute: Heidelberg University Hospital

type: Methylation profiling by genome tiling array

summary: Neuroendocrine neoplasms (NEN) are thought to originate from diffuse endocrine networks and therefore most frequently occur in the gastrointestinal tract and lungs. The liver is a frequent site of metastasis of NEN but also the presence of primary hepatic NEN (PHNEN) has been proposed. Due to the impact on disease management, it is urgently required to discriminate the origin of hepatic NEN metastases and to identify clinically relevant subgroups.

overall_design: A set of 15 PHNEN was analyzed by Illumina DNA methylation.

first: Reka

last: Toth


title: Derivation of embryonic stem cells from cloned blastocysts using improved somatic cell nuclear transfer in common marmoset

city: Tsukuba

first: Inoue

last: Kimiko

state: Ibaraki

address: 3-1-1 Koyadai

department: BioResource Research Center

institute: RIKEN

summary: The common marmoset (Callithrix jacchus) is a genetically modifiable non-human primate increasingly used in biomedical research. However, methods to preserve or expand valuable genetic resources in this species remain underdeveloped. Here, we established a method for deriving embryonic stem cells (ESCs) from blastocysts generated by somatic cell nuclear transfer (SCNT) in the marmoset. Injection of mRNA encoding the histone demethylase Kdm4d enabled efficient reprogramming of somatic nuclei, allowing blastocyst formation in 14.5% from fibroblasts. However, nuclear transfer ESCs (ntESCs) were not established from these blastocysts. Combining this method with a G9a histone methyltransferase inhibitor (RK-701) improved blastocyst quality and allowed derivation of ntESC lines, including wildtype and GFP-transgenic lines. These ntESCs exhibited normal karyotypes and pluripotency both in vitro and in vivo. Nuclear and mitochondrial DNA analyses confirmed their nuclear donor origin and cytoplasmic inheritance from recipient oocytes. Transcriptome analysis identified abnormally expressed genes in ntESCs present in a line-dependent and -independent manner, suggesting partial reprogramming resistance that may inform future optimization of SCNT in primates. Our study establishes marmoset SCNT method enabling derivation of ntESCs which may provide a new platform for preserving and engineering marmoset genetic resources.

overall_design: Comparative analysis of gene expression in ESCs derived from IVF, naturally fertilizaed (NAT), and SCNT in common marmoset.

first: Shogo

last: Matoba

first: Satoshi

last: Funaya


title: CK1α in Sertoli cells is essential for testicular development and spermatogenesis in mice

city: Yangzhou

first: Hongzhou

last: Guo

state: Jiangsu

address: No. 12, Wenhui East Road, Hanjiang District

institute: COLLEGE OF VETERINARY MED-LIB

summary: Our recent study indicated that CK1α is expressed in both germ cells and somatic cells within the mouse testes, exerting regulatory control over spermatogenesis.

overall_design: TRIzol reagent (TaKaRa, Dalian, China) was used to extract total RNA from E16.5 mouse testes. Totally, 3cKO mice and 3WT mice was performed.

first: Mingyue

last: Wang

first: Sheng

last: Cui

first: Di

last: Zhang

first: Jinglin

first: Yewen

last: zhou

first: Kemian

last: Gou


title: Methamphetamine Induces Metallothionein 1 Expression and an Inflammatory Phenotype in Primary Human HIV-infected Macrophages

first: Jessica

last: Weiselberg

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

overall_design: Refer to individual Series


title: IG-DMR escapes from global hypomethylation during adult neural stem cells reprogramming [MeDIP-seq]

city: Valencia

first: Jordi

last: Planells

state: Valencia

address: Doctor Moliner, 50 street

department: Biologia celular, biologia funcional y antropologia fisica

country: Spain

institute: Universitat de València

summary: Genomic imprinting is an epigenetic mechanism that causes monoallelic expression of genes depending on their parental origin. Loss of imprinting (LOI) is associated with cancer progression and human imprinting disorders (IDs), impacting foetal development, metabolism and cognition. Imprinted genes, organized in clusters, rely on methylation at imprint control regions (ICRs), which are differentially methylated regions (DMRs) on both parental chromosomes. Somatic cell reprogramming into induced pluripotent stem cells (iPSCs) is a valuable tool to understand the mechanisms associated with pluripotency and holds promise for generating patient-specific stem cells for therapeutical applications to treat different pathologies such as IDs. Here, we conduct genome-wide RNA-seq and MeDIP-seq analysis on mouse iPSCs derived from adult neural stem cells (NSCs). Our findings reveal a comprehensive alteration in iPSCs transcriptome profile, aligning with DNA hypomethylation. This correlation is pivotal in discerning which modifications in genomic imprinting during the reprogramming process represent undesirable epigenetic abnormalities that could compromise the quality of iPSCs. Simultaneously, it helps identify genuine epigenetic modifications that are inherently linked to pluripotency, thus ensuring a clearer understanding of the factors influencing iPSC quality and pluripotent potential

overall_design:
Gene imprinting is a molecular mechanism by which the expression of a gene is limited in a parent-of-origin manner. It has been shown that methylation in imprinting control regions (ICRs) is crucial for monoallelic expression. We isolated neural stem cells (NSCs) from the sub-ventricular zone of adult mouse brains. We then reprogrammed adult NSCs to iPSCs by co-transfection of Oct4 and Klf4 plasmids in retroviral vectors.
We have profiled the methylome genome-wide with  Methylated DNA immunoprecipitation sequencing (MeDIP-seq) in NSCs (n = 3) and reprogrammed adults NSCs (iPSCs) (n = 3) to compare the methylation profiles, with particular attention to imprinted genes.

first: Laura

last: Lázaro-Carot

first: Esteban

last: Jiménez-Villalba

first: Anna

last: Lozano-Ureña

first: Raquel

last: Montalbán-Loro

first: Jennifer

last: Díaz-Moncho

first: Adela

last: Lleches-Pradilla

first: Martina

last: Kirstein

first: Mitsuteru

last: Ito

first: Elisabeth J.

last: Radford

first: Sacri R.

last: Ferrón


title: Mapping the thymic hematopoietic antigen presenting cell network

city: Fitzroy

first: Mark

last: Chong

state: Victoria

address: 9 Princes Street

institute: St Vincent's Institute of Medical Research

summary: To characterize thymic APCs in an unbiased manner, we generated a scRNA-seq atlas of thymic antigen presenting cells (APCs) isolated from thymic rosettes, cellular complexes of physically interacting thymocytes and APCs. Around 8,000 APCs were captured, mostly haematopoietic in origin, consisting of B cell, dendritic cell and macrophage lineages.

overall_design: Thymic rosettes were isolated from three C57Bl/6 female mice and dissociated into single cell suspension using trypsin. CD11b+CD11c+EpCAM+B220+Gr-1+SiglecH+F4/80+ cells and remaining CD90.2- non-thymocytes were sorted by fluorescence activated cell sorting (FACS) for single cell RNA sequencing on the 10X Genomics platform.

first: Yi

last: Wang

first: Xin

last: Liu


title: Epigenetic heterogeneity and state-specific transcriptional programs determine differential drug response in osteosarcoma. [ATAC-Seq, cell line]

first: Alex

last: Lee

overall_design: Patient derived xenographs (PDX), patient samples, PDX-cell lines and comercially available cell lines including the non-cancer hFOB1.19 osteoblast cell line were used. Nuclei was isolated and transposition was performed to generate the ATAC-seq libraries.

first: López-Fuentes

last: Eunice

first: Sweet-Cordero

last: Alejandro

first: Lee

last: Alex


title: IG-DMR escapes from global hypomethylation during adult neural stem cells reprogramming [RNA-seq]

first: Jordi

last: Planells

overall_design:
Gene imprinting is a molecular mechanism by which the expression of a gene is limited in a parent-of-origin manner. It has been shown that methylation in imprinting control regions (ICRs) is crucial for monoallelic expression. We isolated neural stem cells (NSCs) from the sub-ventricular zone of adult mouse brains. We then reprogrammed adult NSCs to iPSCs by co-transfection of Oct4 and Klf4 plasmids in retroviral vectors.
We have profiled the methylome genome-wide with  Methylated DNA immunoprecipitation sequencing (MeDIP-seq) in NSCs (n = 3) and reprogrammed adults NSCs (iPSCs) (n = 2) to compare the methylation profiles, with particular attention to imprinted genes.

first: Laura

last: Lázaro-Carot


title: Urine stem cells as a bona fide model to study cartilage associated disease

first: Steffen

last: Uebe

overall_design: single cell RNA-seq analysis of  chondrogenically induced (14 days) and differentiated urinary stem cells

first: Alexander

last: Schulz

first: Christian

last: Thiel

first: Emily

last: Brockmann

first: Arif

last: Ekici

first: André

last: Reis


title: Eif1ad3 as a key regulator during zygotic genome activation

first: Zongliang

last: Jiang

address: 2033 Mowry Rd

department: Animal Sciences

summary: Eif1ad3 with its homologs, including Eif1ad4, Eif1ad6, Eif1ad7, etc., which are barely studied before, are found to be highly translated during ZGA and regulating the translational activity of critical genes, especially for ribosome assembly. Knocking down Eif1ad3 leads to defective ZGA and further preimplantation development. These data identified Eif1ad3 as an indispensable factor governing mouse embryo development at ZGA.

overall_design: For Eif1ad3 and its variance knockdown experiments, 1-Cell embryo were collected from CF1 (envigo) microinjected with control (only RfxCas13d-IVT mRNA) or Eif1adKD (gRNA+RfxCas13d-IVT mRNA). Embryos from control and knockdown groups were further cultured until blastocyst to observe the development.  For RNA-Seq, 2-cell stage (control and knockdown groups) were collected. To generate Eif1ad3-6xHis mRNA, total RNA from 2-Cell embryos was extracted from a pool of mouse embryos, followed by first strand cDNA synthesis. To overexpress Eif1ad3, in vitro transcribed mRNAs (IVT-mRNAs) were microinjected into zygotes at final concentration of 200 ng/uL. RIP experiments were conducted using the EZ-Magna RIP Kit (Millipore Corporation, Billerica, MA). Briefly, 2-Cell stage embryos (over expressed 200 cells and control 200 cell per replicate) were harvested, lysed and then incubated with RIP buffer containing magnetic beads conjugated with anti-His tag antibody (Millipore) or corresponding negative control IgG (Millipore). After the antibody was recovered using protein A/G beads, the purified RNA were used to perform RNA-seq.

first: Z

first: H

last: Ming


title: Fructose specifically exacerbates pathogenic-Th17 cell differentiation and autoimmune diseases through ROS-EGFR signal

city: wuhan

first: xiaoyu

last: liu

state: 湖北 (Húběi)

address: Donghu Road, No. 115, Wuchang District, Wuhan, Hubei Province

institute: wuhan university

summary: Th17 cells are quite heterogeneous, with pathogenic roles in autoimmunity and non-pathogenic roles in maintaining tissue homeostasis. Although efforts have been made to study genetic and cellular factors in regulating Th17 cell differentiation, little is known about the role of environmental factors and their underlying mechanisms. Here, we revealed that high-fructose intake selectively enhanced the differentiation and function of IL1b+IL-6+IL-23-induced pathogenic Th17 cells (pTh17), without affecting TGFb1+IL-6-induced non-pTh17 cells, and exacerbated autoimmune diseases models. Notably, fructose enhanced both aerobic glycolysis and OXPHOS activity in pTh17 cells, leading to increased ROS production and subsequently promoting their differentiation. N-acetyl cysteine (NAC), a ROS scavenger, specifically impaired pTh17 cell immunity and mitigated autoimmune disease under high-fructose consumption. Mechanistically, ROS accumulation resulted in higher EGFR expression and activation, which subsequently translocated in nucleus to bind with STAT3, enhancing its transcriptional activity of CNS6 and CNS9 regions of Rorc. Taking together, we illustrated a previously unrecognized mechanism underlying the adverse effects of high-fructose intake in pTh17 cell-related pathologies and diseases.

overall_design: Naive CD4+ T cells, which were purified from spleen and lymph nodes, were cultured under pTh17 or βTH17 polarization conditions with or without 50 mM fructose for 2 or 4 days. Then, RNA was extracted from the pTh17 cells or βTH17 cells.

first: Xiaoyu

first: Wenhao

last: Hu

first: Jie

last: Sun

first: Bing

last: Wu


title: A Murine Model of Glioblastoma Initiating Cells and Human Brain Organoid Xenograft for Photodynamic Therapy Testing

city: Badalona

first: Mar

last: Mallo

address: Ctra de Can Ruti, s/n, camí de les escoles. Edifici IMPPC

institute: Josep Carreras Leukaemia Research Institute

summary: Despite decades of research, brain tumours remain among the deadliest of all forms of cancer. As recurrence in glioblastoma is locally generated around the resection cavity, the ability of these tumours to resist almost all conventional and novel treatments relates, in part, to the unique cell-intrinsic and microenvironmental properties of neural tissues. Photodynamic therapy (PDT) relies on photo-toxic effects induced by specific molecules (photosensitisers) upon absorption of photons from a light source. Such toxic effects are not specific to a particular molecular fingerprint of GBM, but rather depend on selective accumulation of the photosensitiser inside tumour cells and their sensitivity to the effects, triggered by light. Here we report four new GICs obtained in Hospital Clinic Barcelona, HCB-GICs, to optimize preclinical studies of PDT, and to explore neoadjuvant protocols for a more effective PDT and photodiagnostic visualization. HCB-GIC cells express the known “stemness” markers Nestin and SOX2, Vimentin and CD44, contributing to invasiveness and to infiltrative ability within brain organoids, properties associated also to mesenchymal phenotype.  HCB-GICs are susceptible to be treated with PDT, since the burden of cells into organoids decreased while increased cell death after irradiation. Moreover, we optimize an experimental in vivo model, able to assess the antitumoral effect of 5-ALA mediated PDT in engraftments of HCB-GICs co-cultures on the kidneys of high immunosupressed mice. In conclusion, we suggest that PDT might be an effective therapy to kill GICs with heterogeneous molecular fingerprint that achieve high levels of PPIX accumulation in tumor niche.

overall_design: Comparison of HCB-GICs (glioblastoma initiating cells) obtained by primary culture of GB biopsies and their original tumor (4 samples)

first: Angeles

last: Sierra


title: Histone methyltransferase PRDM9 promotes survival of drug-tolerant persister cells in glioblastoma

city: Camperdown

first: George

middle: Louis

last: Joun

state: NSW

address: John Hopkins Drive

department: School of Medical Sciences

institute: The University of Sydney


title: Ginseng nanoparticles inhibit lung cancer cell migration by direct cell surface interaction-associated mechanical stress

city: Gyeonggido

first: gunwoo

last: park

address: 206, World cup-ro, Yeongtong-gu, Suwon-si,

institute: ajou univ

summary: Consuming raw ginseng is a common practice, which allows for the intake of not only saponins but also a variety of other bioactive compounds. This suggests that biologically derived ginseng could serve as a promising avenue for developing novel ginseng-based materials. However, research on the development and efficacy of these biological materials remains limited.

overall_design: In this study, we fabricated nanoparticles from fresh ginseng seeds, leaves, stems, and roots through pulverization and serial extrusion methods, thereby simulating the forms that may potentially be generated during the consumption of raw ginseng. The nanoparticles were characterized using zeta sizer and zeta potential analyses, with their morphology confirmed via scanning electron microscopy (SEM). The efficacy of these nanoparticles in inhibiting cell proliferation and migration was evaluated across various cancer cell lines, including lung carcinoma H1299, metastatic melanoma B16F10, breast cancer MD, and fibrosarcoma HT1080. To further elucidate the mechanisms of action, RNA sequencing and Western blotting were employed to analyze migration-related transcriptomes and proteins. The interactions between nanoparticles and cancer cells were examined using real-time holotomography.

first: Sofia

last: Brito

first: Gunwoo

last: Park

first: Ji-Hwan

first: Bum-Ho

last: Bin


title: Therapeutic JAK1 inhibition reverses lupus nephritis in a mouse model and demonstrates transcriptional changes consistent with human disease

city: Wocester

first: Rachel

middle: E

last: Twomey

state: MA

address: 100 Research Drive

department: Immunology

institute: AbbVie

summary: Janus kinase family members are essential for signaling by multiple cytokines, including many implicated in SLE pathogenesis. To test whether inhibition of JAK1 signaling can be efficacious in SLE, we used a JAK1-selective inhibitor (ABT-317) and evaluated its ability to ameliorate disease in murine SLE.

overall_design: 48 NZB/W-F1 mice were treated with anti-CD40 or anti-JAK1 and kidney and salivary gland tissue were used for NA extraction. Young mice and baseline (disease onset) mice were used as controls.


title: Conserved and dynamic ESR1 signaling in developing cortex mediates early postnatal social behavior [snATAC-seq]

city: San Diego

first: Yuejia

last: Liu

state: California

address: DNC 210, The Scripps Research Institute, 9060 Activity Road, Unit F

institute: The Scripps Research Institute

summary: To dissect the genomic function of Esr1 in neonatal cortical neurons, we performed estradiol benzoate or vehicle treatment on P1 Esr1-Cre;LSL-Sun1-GFP animals and harvested the neocortex to perform single-nucleus assay for transposase-accessible chromatin using sequencing (snATAC-seq) with the GFP+ cells.

overall_design: Esr1-Cre;LSL-Sun1-GFP pups at P1, 6hr post treatment of either vehicle or estradiol-benzoate injection, were used for this experiment. After tissue dissection and nuclei isolation, GFP+ and 7-AAD+ nuclei in each condition were collected into cold PBS with 0.1% BSA using Fluorescence-activated cell sorting (FACS). Collected nuclei were enriched with ConA beads and proceed to 10X single nuclei ATAC-seq (V2)

first: Xinhe

last: Zheng

first: Xin

last: Jin

first: Longzhi

last: Tan


title: Conserved and dynamic ESR1 signaling in developing cortex mediates early postnatal social behavior [scRNA-seq]

summary: To define the cell types expressing Esr1 in the developing mouse cortex, we applied scRNA-seq from P1 neocortex expressing the transgenic reporter. Droplet-based scRNA-seq was performed with both GFP+ (cellular lineages expressing Esr1) and unsorted, whole populations.

overall_design: Esr1-Cre;LSL-Sun1-GFP pups at P1 were used for this experiment. The entire neocortex was dissected - cells were isolated by Fluorescence-activated cell sorting (FACS) with only DAPI as the unsorted population; or isolated by FACS with DAPI and GFP to enrich for the Esr1+ population only. Cells collected from each condition were processed and analyzed using scRNA-seq


title: Lack of dystrophin disrupts fetal muscle stem cell polarity and commitment during secondary myogenesis

city: Ottawa

first: Theodore

last: Perkins

state: ON

address: 501 Smyth Rd.

department: Cellular and Molecular Medicine

institute: Ottawa Hospital Research Institute

summary: No cure exists for Duchenne Muscular Dystrophy (DMD), a devastating and fatal muscle degenerative disease caused by a loss-of-function mutations to the DMD gene which encode the large cytoskeleton protein dystrophin. Conventionally, the disease is thought to manifest around 3-5 years of age when fragile myofibers become damaged from patient ambulation. However, we find that perturbation in fetal muscle stem cell (fMuSC) commitment and polarity occur during secondary myogenesis in the mdx mouse, a model of DMD. To study the cell state and the transcriptomic profileof mdx fMuSCs, we conducted single cell RNA-sequencing of myogenic cells derived from the limbs of E17.5 Pax7-nGFP embryos on the C57BL/10ScSnJ and mdx backgrounds.

overall_design: Fetal muscle stem cells were FACS-isolated from the limbs of the limbs of E17.5 Pax7-nGFP embryos on the C57BL/10ScSnJ and mdx backgrounds.The experiment was performed on biological duplicates.

first: Marie

last: Esper

first: Alexander

middle: Y

last: Lin

first: Dallas

last: Bennett

first: Michael

last: Rudnicki


title: Effect of temozolomide resistant on gene expression in mouse neuroblastoma tumor [ChIPseq]

city: Belmont

first: Evon

last: Poon

state: Surrey

address: 15, Cotswold Road, Godstone Road

department: Clinical Studies

institute: Institute of Cancer Research

summary: Advances in preclinical models that recapitulate chemorefractory and relapsed disease are needed to better predict the efficacy of an expanding and promising armamentarium of drug candidates being tested in early-phase pediatric clinical trials. Here, we used longitudinal magnetic resonance imaging to design an individualized, dose-escalating treatment regimen that induces evolution of neuroblastoma in the Th-MYCN genetically-engineered mouse model, concomitant with the acquisition of resistance to Temozolomide, a standard chemotherapy used in treatment of refractory, relapsed neuroblastoma patients within European early-phase clinical trials. MRI longitudinally identified the development of intra-tumoral heterogeneity. Molecular profiling of expanding, treatment-refractory regions identified prominent up-regulation of the nor-adrenergic core regulatory signature and deregulation of the CDK2 pathway. Treatment with the CDK2/9 inhibitor fadraciclib led to significant response and an overall survival benefit in temozolomide-resistant Th-MYCN tumors and allografts generated from these resistant tumors. These findings demonstrate the utility of genetically-engineered mouse models as platforms to dissect the evolution of chemoresistance in neuroblastoma and they provide a mechanistic rationale to support the evaluation of fadraciclib in ongoing paediatric phase I studies of chemotherapy combined with Temozolomide in relapsed, treatment refractory neuroblastoma patients.

overall_design: We used longitudinal magnetic resonance imaging to design an individualized, dose-escalating treatment regimen that induces evolution of neuroblastoma in the Th-MYCN genetically-engineered mouse model, concomitant with the acquisition of resistance to Temozolomide

first: Tong

last: Liang

first: Louis

last: Chesler

first: Charles


title: Effect of temozolomide resistant on gene expression in mouse neuroblastoma tumor [RNA-seq]