title: High-Throughput Transcriptomics Analysis of Chemical Effects on Zebrafish Liver (ZFL) and Embryonic (ZEM2S) Cells

city: RTP

first: Monique

last: Hazemi

address: 109 T.W. Alexander Dr

institute: US EPA

summary: With thousands of chemicals in commerce and the environment with incomplete ecotoxicity information, rapid identification of potential hazards is a critical need. Molecular profiling assays such as high-throughput transcriptomics (HTTr) provides an efficient means of screening chemicals for bioactivity and potential hazards in cell lines derived from ecological species. Information from HTTr screening can be used to identify concentrations of test chemicals that perturb cellular biology, as the basis for mechanistic prediction and to group chemicals based on bioactivity patterns. In this study, a set of chemicals, including drugs and chemicals found in consumer products, were tested in eight-point concentration series in two zebrafish cell lines: the ZFL liver cell line (ATCC CRL-2643) and the ZEM2S embryonic cell line (ATCC CRL-2147). At total of 42 unique chemicals were tested in each cell line. The experimental design also included vehicle control wells and reference chemicals tested in either eight-point concentration series or at a single concentration in order to assess assay performance.

overall_design:
ZFL and ZEM2S cell lysates in 384-well format were created 24 hours following chemical exposure by adding 10 µL of 2X BioSpyder Enhanced lysis buffer to 10 µL of residual phosphate buffered saline remaining in each assay well following two rounds of washing.  Lysates were created inside of a PCR hood. Plates were shipped to BioSpyder, Inc. frozen (on dry ice) using overnight shipping. Lysates were then analyzed by BioSpyder using the Zebrafish S1500+ Surrogate assay (v1.0) with standard attenuation. 2 µL of each lysate was hybridized with 2 µL of detector oligos from the assay using the following thermal cycler protocol: 10 min at 70 °C, followed by gradual decrease to 45 °C over 49 min, then incubating at 45 °C for 16-24 h. Excess oligos were then removed via nuclease digestion (90 min at 37 °C), and hybridized detector oligos were ligated (1 h at 37 °C) following respective additions of 24 µL TempO-Seq nuclease and ligation mixes. RNA/DNA duplexes were then heat-denatured, and 10 µL of each ligation product was transferred to an amplification microplate containing 10 µL of PCR master mix per well. Ligation products were then uniquely labeled during product amplification with well coordinate-specific “barcoded” primer pairs containing universal adapters for sequencing.  Samples were pooled into sequencing libraries and sequenced on an Illumina NovaSeq X Sequencing System (Illumina, San Diego, CA).  The target read depth for each test sample was 1.7 x 10^6 mapped reads.

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The table below lists SRA accessions for raw data already submitted to SRA under PRJNA1289737.
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first: Peter

last: Schumann

first: Joseph

middle: L

last: Bundy

first: Derik

last: Haggard

first: Logan

middle: J

last: Everett

first: Joshua

last: Harrill

first: Felix

last: Harris

first: David

last: Ryoo

first: Jacob

last: Collins

first: Claudia

last: Rivetti

first: Bruno

last: Campos

first: Geoff

last: Hodges

first: Carlie

last: LaLone


title: Extrachromosomal DNA Associates with Nuclear Condensates and Reorganizes Chromatin Structures to Enhance Oncogenic Transcription [ChIP-seq]

status: Public on Sep 18 2025

city: Seattle

first: Chia-Lin

last: Wei

state: WA

address: 3720 15th Ave NE

department: The Northwest Genomics Center (NWGC)

country: USA

institute: University of Washington

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Extrachromosomal, circular DNA (ecDNA) is a prevalent and significant oncogenic alteration in cancer genomes. Its frequency is associated with aggressive tumor behavior and poor patient outcome. To understand how ecDNA promotes oncogenesis, we map ecDNA-associated chromatin complexes at single-molecule resolution in three well-characterized ecDNA+ cancer models that harbor different oncogenes. Using a suite of 3D genome mapping and imaging analyses, we determined ecDNA nuclear organization and uncovered that ecDNA hubs are part of MED1-mediated condensates that can be rapidly disrupted by agents perturbing liquid-liquid phase separation (LLPS). The functional relevance of ecDNA condensates was demonstrated by inhibition of LLPS which led to hub dispersal, the reduction of MED1 co-activator binding, inhibition of oncogenic transcription and selectively increase cell death of ecDNA-containing cells across a broad range of cancer models. Robust epigenetically silencing of the regulatory modules within ecDNAs effectively disrupts ecDNA’s mode of actions and demonstrates the causality between ecDNA enhancer function, chromosomal contacts, transcription and cellular proliferation, which directly corroborate ecDNA’s trans-activator activity. Our findings reveal that ecDNA drives tumor promotion activity through nuclear condensate and suggests that exploiting these nuclear structures may serve as a universal strategy against malignant tumors. Our work elucidates the structures, functions and regulation of ecDNA which is expected to transform the paradigm for studying cancer genomes and expand the current views of how oncogenes are regulated, from which new clinical strategies can be realized.

overall_design: Perform chromatin interaction assays including WGS, ChIA-Drop, ChIA-PET, ChIATAC, ChIP-seq, CUT&Tag, and RNA-seq to define genome-wide ecDNA-mediated chromatin interactomes and characterize their functional impact on transcription programs following 1,6-HD treatment and CRISPR-based epigenomic perturbations in cancers.

first: Harianto

last: Tjong

first: Chia-Hao

last: Tung

first: Aziz

last: Taghbalout

first: Ping

last: Wang


title: CARD14 signaling in intestinal epithelial cells induces intestinal inflammation and intestinal transit delay

status: Public on Sep 17 2025

city: Zwijnaarde

first: Aigerim

last: Aidarova

address: Technologiepark-Zwijnaarde 71

department: Center for Inflammation Research

country: Belgium

institute: VIB-Ghent University

type: Expression profiling by high throughput sequencing

summary: CARD14 is an intracellular NF-κB signaling mediator in the skin, and rare CARD14 variants have been associated with psoriasis and atopic dermatitis. CARD14 is also expressed in intestinal epithelial cells (IEC). However, its function in the intestine remains unknown. We demonstrate here that transgenic mice expressing the psoriasis associated gain-of-function human CARD14(E138A) mutant specifically in IEC, show mild intestinal inflammation, without epithelial damage. Moreover, CARD14(E138A)IEC mice show a drastic reduction in intestinal motility, often associated with rectal prolapse. Enteric neuronal survival and functionality is unaffected in CARD14(E138A)IEC mice. Transcriptome analysis of IEC from CARD14(E138A)IEC mice reveals decreased expression of antimicrobial peptides by Paneth cells, accompanied with microbial dysbiosis and increased susceptibility to enteric bacterial infection. Our findings suggest that gain-of-function CARD14 mutations may not only predispose patients to psoriasis, but also mild intestinal inflammation, reduced intestinal motility and increased sensitivity to intestinal infection. CARD14(E138A)IEC mice are a valuable tool for further investigation of IEC-intrinsic molecular processes involved in intestinal inflammation and motility disorders.

overall_design: This study compares gene expression profiles between control WT and CARD14(E138A) mice in two distinct intestinal regions: the small intestine and the colon. Intestinal epithelial cells were isolated separately from each region. The primary comparisons are cotnrol WT vs CARD14(E138A)  within the small intestine and control WT vs CARD14(E138A) within the colon. Each group includes 4 biological replicates. RNA was extracted and sequenced using Illumina technology to identify genotype-specific transcriptional changes in each intestinal compartment.


title: DNA topoisomerase II promotes N6-adenosine mRNA methylation [ChIPseq_Ser2P]

city: Seville

first: Silvia

last: Jimeno-González

address: Avda. Américo Vespucio 24

department: Genética

country: Spain

institute: Universidad de Sevilla

summary: Topoisomerase II (TOP2) is an enzyme that regulates of DNA topology, primarily by removing DNA supercoiling. This function is crucial during transcription, as the movement of RNA polymerase II (RNAPII) generates torsional stress. However, the specific role of TOP2 in the regulation of gene expression remains to be fully elucidated, as both TOP2 inhibitors and poisons have been shown to upregulate specific genes. In this study, we show that TOP2 poisoning negatively affects transcription elongation of genes repressed at the level of promoter-proximal pausing. Importantly, this effect is counteracted by a defective mRNA N6-adenosine methylation (m6A) which results in altered mRNA turnover and pre-mRNA splicing. We propose that TOP2 serves a dual function, supporting the maintenance of basal transcription elongation while simultaneously promoting m6A modification in pre-mRNAs to reduce the overall gene expression output.

overall_design: Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) for RBP1, the largest subunit of RNA polymerase II Ser2 phosphorylated.

first: Clara

last: Megías-Fernández

first: Irene

last: Delgado-Sainz

first: Alberto

last: León-Halcón

first: Valentina

last: Buglioni

first: Federica

last: Bruno

first: Cristina

last: González-Aguilera

first: Magdalena

middle: M

last: Maslon


title: Differentially expressed fusogens specify myocyte states to drive myogenesis

city: Montreal

first: Jean-Francois

last: Cote

state: Quebec

address: 110 pine avenue

country: Canada

institute: IRCM

summary: During myogenesis, myocyte fusion leads to the formation of multinucleated muscle fibers, but how exactly this process is initiated remains poorly understood. Here, we performed single-cell RNA-sequencing on mouse somites from E9.5-E11.5 embryos, revealing multiple differentiation states during primary myogenesis. Among these, we identified two unexpected myocyte populations: one expressing both myomaker (Mymk) and myomixer (Mymx) (termed Mc1) and another expressing only Mymk (termed Mc2). Fluorescence in situ hybridization demonstrated that both populations are mononucleated and co-exist within the same somites, with only Mc1 persisting during secondary myogenesis. Lineage tracing using Mymx:Cre; RosaTdT mice demonstrated that the Mc2 cells arise from the Mc1. Mechanistically, we show that Mef2 and Rxr factors positively and negatively regulate Mymx expression, respectively. Additionally, RXRG interacts with MYOD1 and MYOG, modulating their transcriptional activity in luciferase assays. Collectively, our findings uncover two populations among the myocytes that drive primary and secondary fiber formation, challenging the traditional view of vertebrate muscle precursor homogeneity.

overall_design: Pregnant C57BL/6 wild type mice were sacrificed at 9.5 days and 11.5 days Embryos were extracted and interlimb somites were dissected and dissociated and sent for analysis as described in the manuscript..

first: Sarah

last: Nahlé

last: Coté


title: PLETHORAs shape Arabidopsis phyllotaxis through modulation of patterning robustness and accelerated inflorescence development [RNA-seq]

city: Wageningen

first: Merijn

last: Kerstens

address: Droevendaalsesteeg 1

department: Plant Developmental Biology

country: Netherlands

institute: Wageningen University & Research

summary:
•	Phyllotaxis is the arrangement of lateral organs on a stem axis, which in Arabidopsis follows a spiral pattern. We previously described that loss of three PLETHORA (PLT) transcription factors shifts the phyllotactic spiral to novel metastable patterns, but the mechanism behind these shifts remained unclear.
•	In this study, we aimed to fill this knowledge gap by performing detailed analysis of phyllotaxis in plt rosettes, inflorescences and meristems. We supplement our quantitative measurements with transcriptomic profiling of plt3 plt7 meristems, genome-wide in vitro binding assays and an EMS enhancer screen in plt3 plt5 plt7.
•	Contrary to earlier beliefs, primordium positioning at the inflorescence meristem is only subtly noisier in plt3 plt5 plt7, which we attribute to loss of PLT-controlled regulation of auxin and cytokinin networks. However, the meristematic patterning defects alone cannot explain the large deviations from the spiral pattern in mature mutant inflorescences. Instead, accelerated inflorescence development of plt3 plt5 plt7 generates larger patterning deviations through joint action of meristem chirality and stem torsion. We demonstrate the importance of the relationship between chirality, torsion and internode length in tissue-twisting mutants.
•	We conclude that shoot meristematic PLTs provide robustness to primordium patterning and phyllotaxis through integration of developmental processes during bolting.

overall_design: RNA-seq profiling of Arabidopsis Col-0 and plt3 plt7 inflorescence meristems (31-33 dpg) and shoot apical meristems (7 dpg).

first: Freek

last: van der Klugt

first: Hugo

last: Hofhuis

first: Ben

last: Scheres

first: Viola

last: Willemsen


title: PLETHORAs shape Arabidopsis phyllotaxis through modulation of patterning robustness and accelerated inflorescence development [WGS]

summary:
•	Phyllotaxis is the arrangement of lateral organs on a stem axis, which in Arabidopsis follows a spiral pattern. We previously described that loss of three PLETHORA (PLT) transcription factors shifts the phyllotactic spiral to novel metastable patterns, but the mechanism behind these shifts remained unclear.
•	In this study, we aimed to fill this knowledge gap by performing detailed analysis of phyllotaxis in plt rosettes, inflorescences and meristems. We supplement our quantitative measurements with transcriptomic profiling of plt3 plt7 meristems, genome-wide in vitro binding assays and an EMS enhancer screen in plt3 plt5 plt7.
•	Contrary to earlier beliefs, primordium positioning at the inflorescence meristem is only subtly noisier in plt3 plt5 plt7, which we attribute to loss of PLT-controlled regulation of auxin and cytokinin networks. However, the meristematic patterning defects alone cannot explain the large deviations from the spiral pattern in mature mutant inflorescences. Instead, accelerated inflorescence development of plt3 plt5 plt7 generates larger patterning deviations through joint action of meristem chirality and stem torsion. We demonstrate the importance of the relationship between chirality, torsion and internode length in tissue-twisting mutants.

overall_design: Whole-genome sequencing (Arabidopsis) of the segregating backcross progeny of an EMS-induced phenotype in the plt3plt5plt7 background.


title: An RNA Splicing System that Excises DNA Transposons from Animal mRNAs [Illlumina]

city: Boston

first: Long-Wen

last: Zhao

state: Massachusetts

address: 77 Avenue  Louis Pasteur, NRB Room 266

department: Genetics

institute: Harvard Medical School

summary: All genomes harbor mobile genetic parasites called transposable elements (TEs). Here we describe a system, which we term SOS splicing, that protects C. elegans and human genes from DNA transposon-mediated disruption by excising these TEs from host mRNAs. SOS splicing, which appears to operate independently of the spliceosome, is a pattern recognition system triggered by base-pairing of inverted terminal repeat elements, which are a defining feature of DNA transposons. We identify three factors required for SOS splicing in both C. elegans and human cells; AKAP17A, which binds TE-containing mRNAs; the RNA ligase RTCB; and CAAP1, which bridges RTCB and AKAP17A, allowing RTCB to ligate mRNA fragments generated by TE excision. We propose that SOS splicing is a novel, conserved, and RNA structure-directed mode of mRNA splicing and that one function of SOS splicing is to genetically buffer animals from the deleterious effects of DNA-transposon-mediated gene perturbation.

overall_design: RNA-seq was performed on wild-type (YY2224) and akap-17(-) (YY2287) young adult C. elegans to examine transcriptomic changes in the absence of AKAP-17. RIP-seq was conducted to identify RNAs directly bound by AKAP-17.


title: PLETHORAs shape Arabidopsis phyllotaxis through modulation of patterning robustness and accelerated inflorescence development [DAP-seq]

overall_design: PLT3, PLT5 and PLT7 DAP-seq on gDNA derived from Arabidopsis shoot apical meristems and inflorescence meristems.


title: Toss GERALT into chloroplast to make it green: an age-dependent regulator of chloroplast biogenesis and chlorophyll biosynthesis.

city: Poznan

first: Andrzej

last: Pacak

address: Uniwersytetu Poznanskiego 6

country: Poland

institute: Adam Mickiewicz University, Poznan

summary: The studies were performed using Arabidopsis thaliana: wt Col (N6000) and SALK_116579 (geralt, GERMINATION ALBINO TRANSIENT) mutant. At2g47590 gene encodes GERALT protein. This protein was not characterized so far. It is localized in chloroplasts, influences chloroplast biogenesis and chlorophyll biosynthesis and its role decreases with the plant age.

overall_design: RNA was isolated from 100 mg of plant tissues derived from whole seedlings: wt and geralt mutant collected at two time-points: 5 day-old or 12 day-old. Plants were grown in in vitro culture in the culture chamber and were harvested approximately 4h after turn on the light. RNA-Seq was performed for 12 libraries (three biological replications for two time-points, wt and mutant plants).

first: Agnieszka

middle: K

last: Banaś

first: Joanna

last: Grzyb

first: Piotr

last: Zgłobicki

first: Beata

last: Myśliwa-Kurdziel

first: Katarzyna

last: Leja

first: Małgorzata

last: Kozieradzka-Kiszkurno

first: Kinga

last: Kłodawska

first: Robert

last: Konieczny

first: Maria

last: Pilarska

first: Ewa

last: Niewiadomska

first: Aneta

last: Bażant

first: Łukasz

last: Szewc

middle: B

last: Kowalska

first: Wojciech

last: Strzałka


title: Two closely related TRB-containing complexes cooperate to mediate H3K4me3 demethylation and transcriptional repression [RNA-seq]

city: Beijing

first: xinjian

last: He

address: No. 7, zhongguancun life science park road, changping district

country: China

institute: National Institute of Biological Sciences

summary: The telomere repeat binding factors TRB1, TRB2, and TRB3 (TRB1/2/3) in Arabidopsis thaliana not only function as components of the PEAT complex involved in histone acetylation and H2A deubiquitination but also interact with Polycomb Repressive Complex 2 (PRC2) involved in H3 lysine 27 trimethylation (H3K27me3). In this study, we demonstrate that TRB1/2/3 form two additional chromatin-associated complexes, which we term TRB1/2/3-HTH1/2/3 (TRHT) and TRB1/2/3-HISTONE-DEMETHYLASE (TRHD). The TRHT complex comprises TRB1/2/3, ICU11, and HTH1/2/3, whereas the TRHD complex is composed of TRB1/2/3, ICU11, ZDP2, JMJ14, and NAC050/052. The TRHT and TRHD (TRHT/TRHD) complexes occupy a common set of target genes and cooperate to mediate JMJ14-mediated H3K4me3 demethylation and transcriptional repression. Compared with PEAT and PRC2 target genes, which are characterized by high and low levels of H3K4me3, respectively, the TRHT/TRHD target genes exhibit low to medium levels of H3K4me3. At the whole-genome level, TRB1/2/3 repress transcription at TRHT/TRHD and PRC2 target genes, while facilitating transcription at PEAT target genes. At the TRHT/TRHD target genes, the TRHT/TRHD complexes mediate transcriptional repression through both H3K4me3 demethylation-dependent and –independent mechanisms. These findings reveal the molecular mechanisms by which how the TRHT/TRHD complexes are coordinated with the PEAT and PRC2 complex to ensure the orchestration of multiple histone modifications at the whole-genome level.

overall_design: Examination of the mRNA expression of 12-day-old wild type and five mutants in Arabidopsis

first: XinJian


title: The SMC Hinge is a Selective Gate for Obstacle Bypass

city: Ecublens VD

first: Hon-Wing

last: Liu

address: Le Biophore, CH-1015 Lausanne

country: Switzerland

institute: Université de Lausanne

summary: DNA loop-extruding SMC complexes play vital roles in genome maintenance and DNA immunity. However, the ability of these ring-shaped DNA motors to navigate large DNA-bound obstacles, such as DNA/RNA polymerases and ribosomes in prokaryotes, has remained unclear. Here, we demonstrate that a bacterial SMC Wadjet complex can efficiently bypass obstacles larger than the SMC coiled coil lumen if they are linked to the extruded DNA by single-stranded DNA (ssDNA). This process is mediated by the selective entrapment of the ssDNA linker within the SMC hinge channel, which acts as an obligate gate—permitting ssDNA passage while excluding double-stranded DNA (dsDNA). By threading the linker through the hinge gate as dsDNA is translocated through the SMC motor, the obstacle can follow a trajectory distinct from its associated dsDNA, remaining outside the SMC ring. This mechanism enables continuous dsDNA entrapment while successfully bypassing obstacles. We show that hinges of diverse SMC complexes including eukaryotic condensin and Smc5/6 also selectively accommodate ssDNA, suggesting that hinge bypass is a conserved feature across SMC proteins. We demonstrate that while the hinge domain is essential for obstacle bypass, it is dispensable for loop extrusion, showing that these functions are independent, provided by separate SMC modules. These findings uncover the long-sought function of the SMC hinge toroid and provide the first mechanistic explanation for how DNA-entrapping SMC complexes can extrude loops on chromosomal DNA densely populated with obstacles. Integrating hinge bypass into the DNA loop extrusion model, we propose that the hinge may also facilitate the passage of RNA and peptide, enabling bypass of transcription-associated ribonucleoprotein complexes and other SMC complexes.

overall_design: ChIP-seq of condensin complex Smc in B. subtilis strains (WT, hinge charge neutralizing mutant and ∆scpB). Cells were grown in minimal media until exponential phase before ChIP against KITE subunit ScpB

first: Hon Wing

first: Florian

last: Roisné-Hamelin

first: Michael

last: Taschner

first: James

last: Collier

first: Madhusudhan

last: Srinivasan

first: Stephan

last: Gruber


title: DNA topoisomerase II promotes N6-adenosine mRNA methylation [meRIPSEQ]

first: Silvia

last: Jimeno-González

overall_design: Study differential m6A methylation in control and etoposide treated cells. Two replicates were performed per condition.

first: Clara

last: Megías-Fernández

first: Irene

last: Delgado-Sainz

first: Alberto

last: León-Halcón

first: Valentina

last: Buglioni

first: Federica

last: Bruno

first: Cristina

last: González-Aguilera

first: Magdalena

last: Maslon


title: An RNA Splicing System that Excises DNA Transposons from Animal mRNAs [Nanopore]

first: Long-Wen

last: Zhao

sample_organism:
Caenorhabditis elegans
Homo sapiens

platform_organism:
Caenorhabditis elegans
Homo sapiens

overall_design: Nanopore long-read sequencing to characterize SOS splicing isoforms in C. elegans and HEK293T cell line.


title: DNA topoisomerase II promotes N6-adenosine mRNA methylation [ChrRNAseq]

overall_design: Study of the transcriptional outcome after chromatin replication by chromatin-associated RNA sequencing (ChrRNA). All experiments were done in duplicates.


title: DNA topoisomerase II promotes N6-adenosine mRNA methylation [TT-seq]


title: DNA topoisomerase II promotes N6-adenosine mRNA methylation [RNAseq]

overall_design: To study differences in RNA stability and gene expression under etoposide treatment, we performed a kinetic in which, under etoposide treatment, serum-starved RPE-1 cells were treated with triptolide to repress the transcription. RNA was collected at different times points and then we performed gene expression profiling analysis using data obtained from RNA-seq.


title: Regulation of ILC2s by Brg1 (ATAC-seq on WT and KO ILC2eff)

city: Shanghai

first: Ju

last: Qiu

address: 320 Yueyang Road

institute: Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences

summary: The alteration of chromatin status critically dictates the expansion and function of group 2 innate lymphoid cells (ILC2s), which have been shown to play a pathogenic role in allergic lung inflammation. In this study, we use multi-omics approaches to dissect the molecular mechanisms of how Brg1 regulates ILC2s in allergic lung diseases through a cell intrinsic manner. Our data indicate that Brg1 regulates ILC2 properties through orchestrating ILC2 energetic metabolism. These findings are enlightening for the understanding of ILC2-mediated pathogenesis in allergic lung inflammation and highlight Brg1 as a potential therapeutic target.

overall_design: Lung ILC2s (Lin−CD45+RFP+ cells) were purified from IL-33-treated Il5Cre/+Smarca4+/+(WT) and Il5Cre/+Smarcaf/f (KO) mice and subsequently subjected to ATAC-seq analysis.

first: Jupei

last: Tang

first: Jinxin


title: DNA topoisomerase II promotes N6-adenosine mRNA methylation

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

overall_design: Refer to individual Series


title: Creeping fat-derived mechanosensitive fibroblasts drive intestinal fibrosis in Crohn’s disease strictures [Xenium]

city: Stanford

first: Benjamin

last: Pham

state: CA

address: 257 Campus Drive

institute: Stanford University

summary: A significant complication of Crohn’s disease (CD) is intestinal fibrosis, which narrows the bowel lumen to cause a stricture. Creeping fat (CF) is the wrapping of mesenteric adipose tissue (MAT) around inflamed and fibrotic bowel, but its role in stricture progression in CD is unclear. In this study, we explore whether CF-derived fibroblasts, the cells primarily responsible for extracellular matrix (ECM) deposition, directly contribute to stricture progression.  By performing scRNA-seq, Visium and Xenium on pediatric CD strictures, we identified a CF-associated, mechanosensitive, CTHRC1+ fibroblast enriched for YAP/TAZ signaling that localized to the fibrotic CF-bowel wall interface within the stricture. We developed a novel mouse model of intestinal fibrosis that exhibited CF and used lineage tracing to show that Postn+ mouse fibroblasts, analogous to human CTHRC1+ fibroblasts, infiltrate fibrotic bowel and deposit ECM in a YAP/TAZ-dependent manner through scRNA-seq. Our findings identify mesenteric fat as a key source of pro-fibrotic fibroblasts that can be therapeutically targeted to limit intestinal fibrosis.

overall_design: Spatial transcriptomics of human bowel and mesenteric adipose tissue using the 10X Genomics Xenium platform with 470 custom gene probes.

first: Khristian

middle: E

last: Bauer-Rowe


title: Targeting a Galectin-3/EGR1 transcriptional complex inhibits the pro-metastatic signature in TRIM49-deficient gastric adenocarcinoma

city: Chong Qing

first: Xianfeng

last: Li

address: Da ping

department: Department of Gastroenterology, Daping Hospital

institute: Army Medical University (Third Military Medical University)

summary: Distal metastasis, driven by intracellular signaling rewiring, is a leading cause of cancer mortality. The role of post-translational modifications in metastasis remains unclear. A CRISPR screen in a gastric adenocarcinoma (GAC) mouse model identified TRIM49 as a metastasis suppressor. TRIM49 is downregulated in most advanced GACs, correlating with poor prognosis. Galectin-3, stabilized in TRIM49-deficient cells due to impaired degradation, forms a complex with EGR1, enhancing pro-metastatic gene expression. Disrupting this complex with GB1107 inhibits metastasis in mouse models. The Galectin-3/EGR1 complex in TRIM49-deficient GAC is a key driver of metastasis and a potential therapeutic target.

overall_design: Cut&Tag of EGR1 and Galectin-3 to identify the binding sites of key genes; RNA-Seq of inhibition of Galectin-3 and overexpression of TRIM49 for identifying their targets.

first: Zhongyi

last: Qin

first: Linrong

last: Che

first: Bin

last: Wang


title: Neuronal development shapes activity-dependent gene expression profiles in a stimulus-specific manner

city: CABA

first: Damian

last: Refojo

state: CABA

address: Godoy Cruz 2390

country: Argentina

institute: Biomedicine Research Institute of Buenos Aires (IBioBA)

summary: Neuronal activity-dependent gene expression is fundamental to a wide variety of brain functions. Transcriptional profile after in vitro stimulation has been assessed using different modalities to induce neuronal activity. In this work, we first investigate the influence of development on neuronal activity and activity-driven transcription. We used an RNA sequencing approach over 7 days in vitro (DIV) or mature 21 DIV neurons after neuronal depolarization with potassium chloride (KCl)compared to Biccuculine application, a synaptic modality to induce neuronal activity. To further investigate how different activity patterns influence gene transcription in mature neurons, we performed a comparative analysis of global gene expression in neurons treated with extensively used activation protocols KCl, Bic, and TTX withdrawal. Our results demonstrate that different patterns of neuronal activity not only induce different transcriptional profiles but also exhibit distinct temporal dynamics for the same genes. These findings offer novel insights into the complex relationship between neuronal activity and gene expression, shedding light on the context-dependent nature of activity-dependent transcriptional responses.

overall_design: We experimentally assessed developmental effects of activity-dependent gene expression programs using mice forebrain primary neuronal cultures. Neurons were cultured for 7 or 21 days and their activity-dependent gene expression profiles upon KCl and Bicuculine stimulation were compared by performing bulk transcriptomic analysis. Additionally, we then compare the effect of KCl, Bicuculline and TTX withdrawal on DIV21 neurons using the same approach

first: Jeronimo

last: Lukin

first: Maximiliano

last: Beckel

first: Ines

last: Patop

first: Sebastian

last: Kadener


title: Effect of propranolol on murine B16F10 metastasis-bearing lungs or on monocytes isolated from these lungs

city: Odense

first: Lars

last: Grøntved

address: Campusvej 55

department: Biochemistry and Molecular Biology

country: Denmark

institute: University of Southern Denmark

summary: We demonstrate that the β-blocker propranolol strongly reduces lung metastasis in multiple murine models, with the reduction being completely dependent on CD4+ T cells. To dissect the underlying mechanisms behind the anti-metastatic effect of propranolol, an experimental B16F10 lung metastasis model was combined with propranolol treatment. Total lung RNA or RNA from FACS-isolated lung monocytes and magnetic bead-isolated CD4+ T-cells were subjected to RNA sequencing.

overall_design: C57BL/6 mice were i.v. injected with B16F10 melanoma cells leading to the formation of lung metastasis. Total lung RNA or RNA from FACS-isolated lung monocytes and magnetic bead-isolated CD4+ T-cells were subjected to RNA sequencing.

first: Daniel

last: Hargbøl Madsen


title: Molecular Insights into the Role of Desmin Intermediate Filament Network  in Chromatin Landscape, Early Cardiogenic Commitment and  Cardiomyocyte Differentiation and Maturation  (RNA-Seq Kap)

city: Alexandroupolis

first: Panagiotis

last: Liakopoulos

address: Dragana

department: Molecular Biology and Genetics

country: Greece

institute: Democritus University of Thrace

summary: The cardiac cytoskeleton is essential for the proper intracellular and intercellular integration of structure and function, failure of which leads to heart disease. However, its role during development and cardiac differentiation is often overlooked. Here, we sought to understand the role of the desmin intermediate filament cytoskeletal network in cardiac cell differentiation and homeostasis during embryonic development, post birth, adulthood and upon different stimuli. We show that desmin is highly expressed in cardiac progenitor cell populations during embryogenesis. In addition, using direct cellular reprogramming of fibroblasts to induced cardiomyocytes, we demonstrated that ectopic desmin expression directly influences cardiomyogenesis through a timely transcriptional regulation of the Notch1 signaling pathway. On the contrary, the absence of desmin in induced cardiomyocytes leads to substantial perturbations in cardiac maturation by diminishing the expression and proper localization of cardiac specific proteins, impairing calcium homeostasis and delaying myofibril formation. RNA and ChIP sequencing, along with chromosome conformation capture (HiC) in desmin-depleted cardiomyocytes revealed that the observed gene expression changes reflect the identified corresponding changes in chromatin architecture that cause loss of genome organization and thus contributing to pathophysiological phenotype.

overall_design: total 2 samples:  induced cardiomycytes from WT (Des+/+)  fibrobllasts transduced with a viral cocktail containing: one sample Gata4,Mef2C, Tbx5 plus Desmin and second  Gata4,Mef2C, Tbx5 plus DsRED (control). RNAseq experiments were carried out in the Greek Genome Center (GGC) of the Biomedical Research Foundation of the Academy of Athens (BRFAA). RNAseq libraries were prepared with the illumina TruSeq RNA v2 kit using 1 μg of total RNA. Libraries were checked with the Agilent bioanalyzer DNA1000 chip, quantitated with the qubit HS spectrophotometric method and pooled in equimolar amounts for Sequencing. 100 bp Single-End reads were generated with the illumina NovaSeq sequencer. RNA-seq raw sequencing data were aligned to human genome version GCCh37/hg19 with the use of tophat (version 2.0.9) [39]  with the use of «--b2-very-sensitive» parameter.  Same tools (version 0.1.19) [40] were used for data filtering and file format conversion while HT-seq count (version 0.6.1p1) algorithm  was performed for assigning aligned reads into exons using the following command line «htseq-count –s no –m intersection -nonempty». Finally, differentially expressed genes were identified with the use of DESeq R package and genes with fold change cut off 1.5 and p-value<=0.05 were considered to be differentially expressed (DEGs). Gene ontology and pathway analysis was performed in the DEGs with DAVID knowledgebase and Ingenuity Pathway Analysis software (IPA). Only pathways and biological processes with p-value <=0.05 were considered to be significantly enriched.

first: Mary

last: Tsikitis

first: Petros

last: Kolovos


title: An epigenetic repressor TRIM66 dictates monogenic olfactory receptor expression, neural activity, and olfactory behavior

first: Yalei

last: Kong

address: No. 280, Chongqing South Road

institute: Shanghai Jiao Tong University

summary: Olfactory receptor gene choice is an extremely intricate example of monogenic and monoallelic expression, where one out of over 1,000 receptor genes is transcribed in each olfactory sensory neuron. This process involves expression of multiple olfactory receptor genes in immature neurons, followed by silencing of all but one receptor genes during maturation. However, the molecular identity of the repressors remains mysterious. Here, we discover TRIM66 as a key repressor. Multiple receptor genes are retained at low levels in most single mature OSNs after deletion of Trim66, leading to decreased expression of the vast majority of olfactory receptor genes. Mechanistically, TRIM66 can bind to, assembly, and repress olfactory receptor enhancers, thereby silencing extra olfactory receptor genes. Functionally, deletion of Trim66 leads to severe defects in the olfactory information processing and innate olfactory behaviors. Our study provides the missing link in understanding the transition from polygenic to monogenic olfactory receptor expression.

overall_design:
To examine the potential role of Trim66 in olfactory receptor (OR) expression, we generated KO and cKO mouse lines and assessed changes in receptor expression following Trim66 deletion (For bulk RNA-seq and scRNA-seq data).
To investigate the mechanisms of OR gene regulation by Trim66, we performed ChIP-seq in the MOE of WT mice using antibodies against TRIM66, ATF5, EZH2, and YY1 (For ChIP-seq data).
To evaluate changes in chromatin accessibility, We further performed ATAC-seq in the MOE of Trim66 knockout mice (For ATAC-seq data).
We further performed Hi-C in Trim66 knockout mice to investigate 3D genome organization (For Hi-C data).
Additionally, we carried out CUT&Tag experiments in Olfr1507-expressing OSNs isolated from Olfr1507-ires-tdTomato; Trim66 knockout mice using antibodies against H3K27ac and H3K27me3 to profile histone modifications (For H3K27ac, H3K4me1, H3K9me3, and H3K27me3 data).

first: Hongqiang

last: Bao

first: Qian


title: Molecular insights into the role of desmin intermediate filament network in chromatin landscape, cardiomyocyte differentiation, and maturation


title: Two closely related TRB-containing complexes cooperate to mediate H3K4me3 demethylation and transcriptional repression [ChIP-seq]

first: xinjian

last: He

overall_design: Examination of protein binding levels in transgenic plants; For H3K4me3 ChIP-seq, examination of H3K4me3 levels in wild type and four mutants.

first: XinJian


title: Molecular Insights into the Role of Desmin Intermediate Filament Network  in Chromatin Landscape, Early Cardiogenic Commitment and  Cardiomyocyte Differentiation and Maturation  (RNA-Seq)

overall_design: total 4 samples: adult Cardiomycytes (ACM) from WT (Des+/+) and Null (Des-/-) mouse hearts (2 samples), adult cardiomyocytes (ACM) from WT (Des+/+) and Null (Des-/-) hearts (2 samples) of mice that have undergone swimming stress exercise. RNAseq experiments were carried out in the Greek Genome Center (GGC) of the Biomedical Research Foundation of the Academy of Athens (BRFAA). RNAseq libraries were prepared with the Illumina TruSeq RNA v2 kit using 1 μg of total RNA. Libraries were checked with the Agilent bioanalyzer DNA1000 chip, quantitated with the qubit HS spectrophotometric method and pooled in equimolar amounts for Sequencing. 100 bp Single-End reads were generated with the Illumina NovaSeq sequencer.


title: DNA topoisomerase II promotes N6-adenosine mRNA methylation [ChIPseq]

first: Silvia

last: Jimeno-González

overall_design: Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) for RBP1, the largest subunit of RNA polymerase II, and METTL3 in serum-starved RPE-1 cells after 50 µM etoposide treatment.

first: Clara

last: Megías-Fernández

first: Irene

last: Delgado-Sainz

first: Alberto

last: León-Halcón

first: Valentina

last: Buglioni

first: Federica

last: Bruno

first: Cristina

last: González-Aguilera

first: Magdalena

last: Maslon


title: Fos binding in hippocampal chromain 1 h after peritoneal KA administration

city: San Juan de Alicante

first: Sergio

last: Niñerola

state: Alicante

address: Avenida Santiago Ramon y Cajal, s/n

department: Molecular Neurobiology and Neuropathology

institute: CSIC-Instituto de Neurociencias de Alicante

summary: Fos induction is the most commonly used marker of neuronal activation. Here, we investigate the binding profile of Fos in the adult mouse hippocampus using antibodies specific against this transcription factor and the chromatin Immunoprecipitation coupled to DNA-sequencing (ChIP-seq) method.  We generated profiles in basal conditions and 1 hour after neuronal stimulation. To trigger the syncronous activation of hippocampal exciatory neurons we treated the mice with kainic acid (KA) through peritoneal administration. This model of status epilepticus has been characterized in detail at the epigenomic level (Fernandez-Albert et al., 2019).

overall_design: Two-month-old C57BL/6J mice were treated with PBS (saline) of Kainic acid (KA, two consecutive intraperitoneal injections separated by 30 min at 10 mg/kg). One hour after the first kainate injection, mice with level 4 epileptic seizures were sacrificed with subsequent dissection of their hippocampi. A Dounce homogenizer was used to dissociate hippocampal tissue and the extract was incubated with anti-Fos antibody and used for ChIP-seq.

first: Beatriz

last: del Blanco

first: Angel

last: Barco


title: Molecular Insights into the Role of Desmin Intermediate Filament Network  in Chromatin Landscape, Early Cardiogenic Commitment and  Cardiomyocyte Differentiation and Maturation  (HiC)

first: Panagiotis

last: Liakopoulos

overall_design: 8 samples: induced cardiomycytes from WT (Des+/+) and Null (Des-/-) fibrobllasts (2samples), Neonatal Cardiomycytes (NCM) from WT (Des+/+) and Null (Des-/-) mouse hearts (2 samples),  adult Cardiomycytes (ACM) from WT (Des+/+) and Null (Des-/-) mouse hearts (2 samples), adult cardiomyocytes (ACM) from WT (Des+/+) and Null (Des-/-) hearts (2 samples) of mice that have undergone swimming stress exercise. HiC was performed per protocol in Diaz et al  (Diaz, N., K. Kruse, T. Erdmann, A.M. Staiger, G. Ott, G. Lenz, and J.M. Vaquerizas, Chromatin conformation analysis of primary patient tissue using a low input Hi-C method. Nat Commun, 2018. 9(1): p. 4938.). Analyzed by FAN-C

first: Mary

first: Petros


title: Regulation of ILC2s by Brg1 (ATAC-seq on WT and KO ILC2mem)

first: Ju

last: Qiu

overall_design: Lung ILC2s (Lin-CD45+RFP+ cells) were purified from the Il5Cre/+Smarca4+/+(WT) and Il5Cre/+Smarca4f/f (KO) mice, which were administered with 30 μg papain in 25 μl PBS every day for 3 days and rested for 2 months. Cells were subjected to ATAC-seq analysis.

first: Jupei

last: Tang

first: Jinxin


title: Allele-specific genomics decodes gene targets and mechanisms of the non-coding genome

city: Munich

first: Tim

last: Hasenbein

address: Biedersteiner Str. 29

department: Institute of Pharmacology and Toxicology

country: Germany

institute: Technical University Munich

summary: A substantial proportion of disease variants reside in non-coding RNAs (ncRNAs), which serve as important regulatory elements. However, most ncRNA targets remain unknown, hindering our understanding of complex diseases. We found allele-specific ncRNAs enriched near allelic protein-coding genes, suggesting that allele-specific expression could be used to predict ncRNA-targets. We applied this concept to mouse organs, revealing 397 enhancing or repressive ncRNA-to-target associations. Next, we applied this strategy to tissues from nearly 1,000 individuals (GTEx). Given the outbred nature of humans, each individual harbors a unique allele-specific landscape, allowing novel ncRNA-to-target discovery with each individual. We uncovered 2,291 ncRNA-to-targets along with their mechanisms, which we benchmarked against sample-matched eQTLs. Further GWAS integration assigned 30.59% of variants overlapping informative ncRNA to their protein-coding targets. As more sequencing data and risk variants become available, this strategy will continue to elucidate targets and mechanisms, ultimately decoding the entire cis-acting landscape of the non-coding genome.

overall_design: RNA-seq data from brain, heart, liver, lung, kidney, and spleen from 9-week-old F1 hybrid mice (BL6 x CAST)

first: Daniel

last: Andergassen


title: Molecular Insights into the Role of Desmin Intermediate Filament Network  in Chromatin Landscape, Early Cardiogenic Commitment and  Cardiomyocyte Differentiation and Maturation (ChIP-Seq)

overall_design: total 4 samples: adult Cardiomycytes (ACM) from WT (Des+/+) and Null (Des-/-) mouse hearts (2 samples), adult cardiomyocytes (ACM) from WT (Des+/+) and Null (Des-/-) hearts (2 samples) of mice that have undergone swimming stress exercise. ChIP was performed per protocol described in Katsouda, A., D. Valakos, G. Vatsellas, D. Thanos, and A. Papapetropoulos, An optimized protocol for chromatin immunoprecipitation from murine inguinal white adipose tissue. STAR Protoc, 2023. 4(4): p. 102594. H3K27Ac and LaminA/C chromatin immunoprecipitation was performed on isolated chromatin using 2ugs of antibody (H3K27Ac : Abcam ab4729 and LaminA/C:Millipore).Input and IP DNAs were quantified with qubit. 5-10 ng DNA from each sample were used as input for ChIPSeq library prep with the NEBNext Ultra II DNA library prep kit for Illumina, according to manufacturer’s instructions. QC of the final purified libraries was performed with qubit and Agilent bioanalyzer DNA1000 and sequencing was carried out in the Illumina Novaseq 6000 sequencer. Approximately 25 Million, 100 bp long Single End Reads were generated per sample. Quality control of the raw sequencing reads was performed with the FASTQC and FastxToolkit software. Raw reads from ChIP-Seq experiments were aligned to the GRCm38 (mm10) reference genome using the Bowtie2 aligner with default options .  SAM files were converted to sorted and indexed BAM files using Samtools [39]. Peak calling was performed using in-house scripts (https://github.com/supatt-lab/rChIPSeqTools/blob/master/sPeakDetection.R). Annotation of the peak lists was done using the ChIPseeker R package. Common and unique peak regions between ChIP-Seq experiments were computed using ChIPpeakAnno. Gene ontology analysis was performed using clusterProfiler.

last: Tsikitis

last: Kolovos


title: Regulation of ILC2s by Brg1 (RNA-seq on ILC2nav ILC2eff)

overall_design: ILC2s were purified from the lung of PBS-treated mice(ILC2nav) or papain-treated mice(ILC2eff). Cells were subjected to RNA-seq analysis.


title: Regulation of ILC2s by Brg1 (CUTandTag)

overall_design: Lung ILC2s isolated from naïve wild-type mice, IL-33-treated wild-type mice and Il5Cre/+Smarca4f/f mice as a negative control. Cells were subjected to Brg1 CUT&Tag analysis.


title: Requirements for Establishment and Epigenetic Stability of Mammalian Heterochromatin

first: Harleen

last: Saini

state: MA

address: 240 Longwood Avenue

overall_design: Refer to individual Series


title: Regulation of ILC2s by Brg1 (RNA-seq on WT and KO ILC2eff)

overall_design: ILC2s were purified from the lungs of IL-33-treated Il5Cre/+Smarca4+/+ (ILC2eff WT) and Il5Cre/+Smarca4f/f (ILC2eff KO) mice and subsequently subjected to RNA-seq analysis.


title: Regulation of ILC2s by Brg1 (ATAC-seq on ILC2nav ILC2eff ILC2mem)

overall_design: ILC2s were purified from mice treated with PBS (ILC2nav), papain (ILC2eff) and from mice treated with papain and rested for 2 months (ILC2mem). ILC2nav, ILC2eff and ILC2mem cells were then subjected to ATAC-seq analysis.


title: Adenine DNA methylation associated with transcriptionally permissive chromatin is widespread across eukaryotes

city: London

first: Alex

last: de Mendoza

address: Mile End Road. Fogg Building 5.14

department: School of Biological and Behavioural Sciences

country: United Kingdom

institute: Queen Mary University of London

summary: DNA methylation in the form of 5-methylcytosine (5mC) is widespread in eukaryotes, while the presence of N6-methyladenine (6mA) has sparked considerable debate. Methodological disparities in quantifying and mapping 6mA in genomic DNA have fueled this controversy. Yet, the distantly related early branching fungi, ciliates and the algae Chlamydomonas reinhardtii exhibit robust 6mA methylation patterns, but the origin and evolution of 6mA remain unknown. Here we use Oxford Nanopore modified base calling to profile 6mA at base pair resolution in 18 unicellular eukaryotes spanning all major eukaryotic supergroups. Our results reveal that only species encoding the adenine methyltransferase AMT1 display robust genomic 6mA patterns. Notably, 6mA consistently accumulates downstream of transcriptional start sites, aligning with H3K4me3-enriched nucleosomes, suggesting a conserved role in placing transcriptionally permissive nucleosomes. Intriguingly, the recurrent loss of the 6mA pathway across eukaryotes, particularly in major multicellular lineages, implies a convergent alteration in the dual methylation system of the Last Eukaryotic Common Ancestor, which featured transcription-associated 6mA and repression-associated 5mC.

sample_organism:
Acanthamoeba castellanii
Naegleria gruberi
Spizellomyces punctatus
Creolimax fragrantissima

overall_design: Profiling of histone H3K4me3 & H3K27ac by ChIP-seq in four eukaryotic species grown in axenic conditions, including Naegleria gruberi, Acanthamoeba castellanii, Creolimax fragrantissima and Spizellomyces punctatus. Additional mRNA-seq performed on N. gruberi and S. punctatus cultures grown / staged in different cell stages.

first: Pedro

last: Romero Charria

last: Navarrete

first: Arnau

last: Sebé-Pedrós


title: Nanoscale photoproximity labeling of c-Myc predicts cancer specific therapeutic targets

status: Public on Sep 16 2025

city: Jupiter

first: Ryan

middle: Raffaele

last: Milione

state: Florida

address: 130 Scripps Way, A-359

department: Chemistry

institute: UF Scripps Biomedical Research

summary: Transcription factors (TFs) have long been aspirational therapeutic targets for the treatment of diseases, as their dysregulation is a common mechanism for altered cell states. Despite this, many TFs implicated in disease have disordered structures and lack canonical binding pockets, rendering them non-trivial targets for small molecule-based therapies. Directly inhibiting TF function has proven difficult, but indirect inhibition by targeting the effector molecules that modulate TF function is a promising alternative strategy. Here we report a unified strategy for capturing cancer-specific protein-protein interactions using µMap photoproximity labeling. Using a recently reported intein-based strategy for catalyst conjugation in biochemically intact nuclei, we demonstrate that we can capture unique protein interactomes of c-Myc in androgen receptor dependent and independent prostate cancer cell lines, and that these unique interactors can be mined to identify druggable vulnerabilities. We find that a PC-3 specific Myc interactor, SLK, selectively promotes Myc stabilization and drives epithelial morphology only in androgen receptor negative prostate cancer.

overall_design: RNA-seq profiling of total mRNA in WPMY-1, LNCaP, and PC-3 wild-type cells. The goal of this experiment is to evaluate alternative splicing of SLK in each cell line. Additionally, PC-3 cells transfected with 0.75µg c-Myc-CfaN or c-Myc-V5-6xHis plasmids are compared against PC-3 wild-type mRNA profiles to validate that c-Myc target gene transcription is increased after transient transfection of both constructs.

middle: R

first: Feifei

last: Tong

first: Kelset

last: Wolfe

first: Pfizer

last: Pfizer

first: Michalina

last: Janiszewska

first: Ciaran

middle: P

last: Seath


title: Gene expression profiles modulated by lipophilic sea buckthorn (Hippophae rhamnoides L.) extract in BT-549 triple-negative breast cancer cells

city: Cluj-Napoca

first: Simona

last: Visan

state: Cluj

address: 34-36 Republicii

department: Functional Genomics, Proteomics and Experimental Pathology

country: Romania

institute: The Oncology Institute “Prof Dr. Ion Chiricuta”,

summary: Considering that dysregulation of cholesterol levels has been established as one of the hallmarks of cancer, moreover ferroptosis, autophagy, tumor cell,  immune cell stemness, and the cellular DNA damage response are regulated through cholesterol metabolism, while recent research studies have shown that dietary supplementation with sea buckthorn reduced total cholesterol only in people with abnormal lipid metabolism, the aim of this study was to identify, for the first time, the main signaling pathways, biological processes, cellular functions, and upstream regulators modulated by lipophilic sea buckthorn extract (LSBE) in BT-549 TNBC cell line.

overall_design: The experimental design of this study included the use of the human TNBC cell line BT-549 (ductal carcinoma, mesenchymal subtype, ER-, PR-, HER2-)  and lipophilic sea buckthorn extract (LSBE) charachterized and purified in our previous study (https://doi.org/10.3390/molecules28114486). 4 biological replicates were used for treated and untreated cells.

first: Loredana

last: Balacescu

first: Flaviu

last: Drigla

first: Ovidiu

first: Adela

last: Pintea


title: Protein palmitoylation and sphingolipid metabolism control regulated exocytosis in cytotoxic lymphocytes

city: Vienna

first: CCRI

last: BiCU

address: Zimmermannpl. 10

department: Bioinformatics Core Unit

country: Austria

institute: St. Anna Children's Cancer Research Institute

summary: Regulated exocytosis controls key cellular functions ranging from neurotransmitter release to the secretion of immune mediators and its disruption is associated with numerous pathologies. The cytotoxic activity of lymphocytes is particularly dependent on regulated and polarized lytic granule delivery towards infected or malignant cells. Although genetic and mechanistic studies have identified factors regulating exocytosis in cytotoxic lymphocytes, a systematic mapping of the relevant factors and their relationships is lacking. Through a genome-scale CRISPR knockout screen in a human natural killer cell line, we characterized a complex genetic network regulating cytotoxic granule exocytosis, with lipid metabolism and protein lipidation amongst the most prominent pathways. By combining global protein lipidation and membrane lipid composition studies, we found that ZDHHC17 drives palmitoylation of the core SNARE complex protein SNAP23 to target cytotoxic granules to GM1-rich lipid rafts whose assembly is controlled by serine palmitoyltransferase.

overall_design: Brunello pooled degranulation screen: 377.6 million NK-92 Cas9-BFP clone1 cells were transduced with Brunello lentivirus at an infection percentage of 19.637, yielding a total of 74.15 million infected cells and a calculated coverage of 925.89 cells per sgRNA determined as described above upon puromycin selection. NK-92 Cas9-BFP clone1 cells were transduced with the lentiGuide.Puro vector. In example, 0.8 million cells were distributed per well in 12-well plates containing 200µL of unconcentrated Brunello viral supernatant (1:1 mix of 48h and 72h viral harvest) in total 1mL growth medium supplemented with 6µM BX795 and 8µg/mL Protamine sulfate. Cell were spinfected at 1000rcf, 60min, 37°C and then incubated for 6 hours at 37°C, 5% CO2. Thereafter, plates were centrifuged at 300rcf 5min and supernatant was gently removed and replaced by adding 2ml fresh growth medium per well. Next day cells were pooled and evenly distributed to T175 cell culture flasks. On day 3 cells were selected for a total of 6 days with 2.5 µg/ml puromycin, changing and splitting cells every 2 days. After complete selection puromycin was removed and cells were maintained at always at pre-determined coverage for another 8 days. Finally, 400 million Brunello transduced NK-92 Cas9-BFP clone1 cells were used for a degranulation assay with PMA/Ionomycin stimulation. Fixed cells were pre-gated on CD56 positive cells and sorted using BD FACS Aria into CD107a negative (LAMP1 neg) and CD107a high (LAMP1 hi) populations. NK-92 RAB27a knockout cells deficient in degranulation were used as gating controls. Sorted cells were pelleted, snap-frozen in LN2 and stored at -80°C for further usage. An aliquot of unstimulated and unstained cells after puromycin selection were taken along as control to assess sgRNA presentation in Brunello transduced cells.

first: Artem

last: Kalinichenko

first: Jakob

last: Huemer

first: Kaan

last: Boztug


title: Requirements for Establishment and Epigenetic Stability of Mammalian Heterochromatin [CRISPR Screen]

first: Harleen

last: Saini

institute: Harvard Medical School

summary: Heterochromatic domains of DNA account for a large fraction of mammalian genomes and have critical roles in silencing of transposons and genes but the mechanisms that establish and maintain these domains are not fully understood. Here we use an inducible heterochromatin formation system combined with targeted CRISPR gene disruption to show that DNA sequence-independent and histone H3 lysine 9 methylation (H3K9me)-dependent heterochromatin can only be inherited during a limited number of cell divisions in mouse embryonic stem cells but becomes stable upon differentiation. We show that multiple H3K9 methyltransferases work together with DNA cytosine methyltransferases and other factors, including RNA processing proteins, to establish and maintain heterochromatin. In addition, we find that deletion of DHX9, an RNA/DNA helicase, results in defective heterochromatin maintenance associated with R-loop accumulation. Our findings suggest that components of H3K9 and DNA methylation pathways work in concert to ensure heterochromatin stability which additionally requires R-loop removal.

overall_design: CRISPR-Cas9 Screen to identify the molecular networks involved in establishment and maintenance of a silent state.

first: Antonis

last: Tatarakis

first: Danesh

last: Moazed


title: Plexin-B1 safeguards astrocyte agility and glial alignment to facilitate wound corralling and axon pathfinding after spinal cord injury

city: New York

first: Molly

middle: S

last: Estill

state: NY

address: 1 Gustave L. Levy Place

department: Neuroscience

institute: Mount Sinai School of Medicine

summary: Glial spatial organization is critical for neural repair after spinal cord injury (SCI). In response to injury, reactive astrocytes extend hypertrophic processes to corral the lesion core and sequester debris and inflammatory cells. How these long, arborized processes remain intact, and how astrocytes avoid collisions to assemble a glial bridge to guide axon pathfinding across lesion site remain unclear. Here we identify the guidance receptor Plexin‑B1 as a key regulator of membrane integrity, process plasticity, and astrocyte alignment. Live‑cell imaging revealed that Plexin‑B1 deletion triggers membrane shedding and slows extension and retraction of astrocytic processes. The loss of astrocyte agility disrupts contact‑dependent avoidance, leading to disorganized astrocytes and misguided axons in vitro and in vivo. Mice with astrocyte‑specific Plexin‑B1 deletion showed defective glial border, enlarged lesions, inflammatory spill‑over, and dysregulated astrocyte–microglia signaling. These defects resulted in impaired axon regeneration and poorer functional recovery after spinal‑cord injury. Thus, Plexin‑B1 mediated agility of astrocyte processes safeguards membrane integrity and spatial alignment, enabling effective wound corralling and axon pathfinding during neural repair following SCI.

overall_design: To understand how Plexin-B1 deletion affects astrocyte activation and glial interactions after SCI, we performed single-nucleus RNA sequencing (snRNA-seq) of uninjured and 7 dpi spinal cords from wildtype (WT) and Plxnb1-/- mice (n = 3 per condition; Fig. 5a) by Split-seq (Parse, Inc.)

first: Haofei

last: Ni

first: Zhilai

last: Zhou

first: Dalia

last: Halawani

first: Chrystian

last: Alves

first: Li

last: Shen

first: Ning

last: Xie

first: Roland

last: Friedel

first: Hongyan

last: Zou


title: Wild-type KRAS activation drives evasion of interferon-mediated immunity and resistance to immunotherapy in hepatocellular carcinoma

city: Hong Kong

first: Carmen

middle: Oi Ning

last: Leung

state: Please Select

address: Hung Hom

department: Applied Biology and Chemical Technology

country: Hong Kong

institute: The Hong Kong Polytechnic University

summary: Based on scRNA-seq analysis, we found that KRAS inhibited the expression of intrinsic interferon-mediated MHC-I and impaired extrinsic interferon-induced dendritic cell recruitment, resulting in a reduction of CD8+ T cell activity due to the suppression of CXCL9 through the EGFR/MEK/ERK signalling pathway.

overall_design: The tumor immune microenvironment of the c-MYC-lucOE/Tp53KO/EV and c-MYC-lucOE/Tp53KO/Kras mice were compared using scRNA-seq.

first: Martina

last: LEI

middle: O

last: LEUNG

first: Terence

last: LEE


title: Transcriptomic profiling of pulmonary vascular remodeling in MCT rat model treated with CM5480

city: 91400 Orsay

first: Florent

last: Dumont

state: Ile de France

address: 17 avenue des sciences

country: France

institute: Université Paris-Saclay

summary: To better understand the molecular mechanisms of CM5480 treatment in MCT rats, a RNA sequencing analysis was performed in lung tissues collected from 5 control-vehicle, 5 control-CM5480, 5 MCT-vehicle, 5 MCT-CM5480 rats.

overall_design: mRNA profiles of lung tissues from control and MCT rats treated with vehicle or CM5480

first: Fabrice

last: Antigny

first: Anaïs

last: Saint-Martin-Willer

first: Grégoire

last: Ruffenach


title: Genetic suppression of precocious transcription termination identifies mutations in essential subunits of the fission yeast cleavage and polyadenylation machinery

first: Ana

last: Sanchez

address: 430 E 67th Street, RRL-865

department: Molecular Biology

country: USA

institute: Memorial Sloan Kettering Cancer Center

summary: RNA-seq anaysis compares gene expression of each mutant (cft1-L249Q, msi2-G252E, pfs2-E104A, pfs2-V180F, pla1-Y86L, pta1-T524M, and ysh1-L74F) to the wild-type fission yeast (Schizosaccharomyces pombe)

overall_design: 7 test samples and 1 control sample were processed (each sample has 3 replicate experiments).

first: Aleksei

last: Innokentev

first: Lauren

last: Bednor

first: Jill

last: Babor

first: Beate

last: Schwer

first: Stewart

last: Shuman


title: Neutrophil-enriched gene signature correlates with teplizumab therapy resistance in different stages of type 1 diabetes

city: Leuven

first: Pierre

last: Lemaitre

address: Herestraat 49 - box 902

department: Department of Chronic Diseases, Metabolism and Ageing (CHROMETA)

country: Belgium

institute: KU Leuven

summary: Teplizumab, a humanized anti-CD3 monoclonal antibody, represents a major advancement in autoimmune type 1 diabetes (T1D) treatment, capable of delaying clinical onset in stage 2 and preserving beta cell function in early stage 3. However, therapeutic responses are heterogeneous. To better understand this variability, we applied single-cell transcriptomics to paired peripheral blood and pancreas samples from anti-mouse CD3-treated non-obese diabetic (NOD) mice. This analysis identified distinct gene signatures associated with therapy success or resistance, with consistent patterns across both compartments. Success-associated signatures were enriched in NK/CD8⁺ T cells as well as other immune cell types, whereas resistance signatures were predominantly expressed by neutrophils. The immune communities underlying these response signatures were largely confirmed in human whole-blood sequencing data from the AbATE study at 6 months, which assessed teplizumab therapy in stage 3 T1D. Furthermore, baseline expression profiling in both the human TN10 (stage 2) and AbATE (stage 3) cohorts identified immune signatures predictive of therapy response, T cell-enriched signatures in responders and neutrophil-enriched signatures in non-responders, highlighting the critical roles of both adaptive and innate immunity in determining teplizumab outcome. Using an elastic-net logistic regression model, we developed a 26-gene blood-based signature capable of predicting teplizumab response with high accuracy (average AUC = 0.97 across bootstrapped datasets). Together, these findings demonstrate the predictive potential of immune gene signatures and highlight the value of transcriptomic profiling in guiding individualized treatment strategies with teplizumab in T1D.

overall_design: CITE-seq: RO (Recent-Onset) diabetic NOD mice were treated for 5 consecutive days with 2.5 μg per day of hamster anti-mouse CD3 monoclonal antibody. Mice that returned to normoglycemia until 28 days after therapy start were considered R = Responders. Mice that did not return to normoglycemia after therapy start were considered NR = Non-Responders. Single-cell suspensions from NOD pancreases and blood were stained with CITE-seq antibody (ADTs and HTOs) and CD45+ cells were sorted by Fluorescence-activated cell sorting (FACS).

first: Gabriele

last: Sassi

first: Chantal

last: Mathieu

first: Conny

last: Gysemans


title: Foxi2 and Sox3 are master regulators controlling ectoderm germ layer specification in Xenopus [ChIP-Seq]

city: Santa Ana

first: Clark

last: Hendrickson

address: 17331 Grovemont

institute: University of California, Irvine

summary: In vertebrates, germ layer specification represents a critical transition where pluripotent cells acquire lineage-specific identities. We identify the maternal transcription factors Foxi2 and Sox3 to be pivotal master regulators of ectodermal germ layer specification in Xenopus. Ectopic coexpression of Foxi2 and Sox3 in prospective endodermal tissue induces the expression of ectodermal markers while suppressing mesendodermal markers. Transcriptomics analyses reveal that Foxi2 and Sox3 jointly and independently regulate hundreds of ectodermal target genes. During early cleavage stages, Foxi2 and Sox3 pre-bind to key cis-regulatory modules (CRMs), marking sites that later recruit Ep300 and facilitate H3K27ac deposition, thereby shaping the epigenetic landscape of the ectodermal genome. These CRMs are highly enriched within ectoderm-specific super-enhancers (SEs). Our findings highlight the pivotal role of ectodermal SE-associated CRMs in precise and robust ectodermal gene activation, establishing Foxi2 and Sox3 as central architects of ectodermal lineage specification.

overall_design: Foxi2 ChIP-seq: Developmentally synchronized embryos were harvested at stage 8, 9 and 10.5, then fixed with formaldehyde in biological duplicates. Chromatin immunoprecipitation was performed using anti-Foxi2 or anti-Sox3 antibodies and DNA was purified for sequencing.  P300, H3K27ac, H3K27me3 ChIP-seq analysis: Developmentally synchronized embryos were harvested at stage 10.5 and fixed with formaldehyde in biological duplicates. The presumptive ectoderm (animal) and endoderm (vegetal) tissues were dissected from the fixed embryos, and ChIP-seq was performed using anti-P300, anti-H3K27ac, and anti-H3K27me3 antibodies.  Previously published wild-type blastula and gastrula whole-embryo ChIP-seq of H3K27ac, H3K4me1 were ren-analyzed from GSE56000 and H3K27me3 from GSE67974.

first: Ken

middle: W

last: Cho


title: Foxi2 and Sox3 are master regulators controlling ectoderm germ layer specification in Xenopus [snRNA-Seq]

overall_design: Nuclei harvested at Stage 10.5 from developmentally synchronized embryos were isolated and fixed before combinatorial barcoding and high throughput sequencing.

first: KW


title: Glucocorticoids unleash immune-dependent melanoma control through inhibition of the GARP/TGFβ axis [scRNA-seq]

city: Manchester

first: Santiago

last: Zelenay

address: Wilmslow Rd, Manchester M20 4BX

institute: Cancer Research UK Manchester Institute

summary: Glucocorticoids were found to trigger immune-dependent control of an orthotopic melanoma model. We used scRNAseq to better understand the changes in tumour-infiltrating immune cells following glucocorticoid treatment.

overall_design: 10 mice were implanted with 20967 melanoma tumours intradermally. 5 mice were treated with control drug and 5 with glucocorticoid (clobetasol priopionate). These tumours were harvested, digested, pre-stained with anti-CD45 and HTO hashtags, and then the tumour-infiltrating immune cells were sorted, pooled, and subjected to scRNA sequencing.

first: Charles

middle: H

last: Earnshaw

first: Maria

middle: A

last: Koufaki

first: Richard

last: Reeves

first: Robert

last: Sellers

first: Sudhakar

last: Sahoo


title: A three-dimensional ex vivo model recapitulates in vivo features and unravels increased drug resistance in childhood acute lymphoblastic leukemia

city: Zurich

first: Magdalini

last: Kanari

address: Lengstrasse 30

department: Oncology

institute: University Children's Hospital Zurich

summary: Single cell RNA sequencing of ex vivo 3D cocultures with MSCs, ECs and ALL PDXs to evaluate their interdependance

overall_design: 3D ex vivo vascular-like structures(MSC-HUVEC) were co-cultured with acute lymphoblastic leukemic pateint-derived xenograft cells for 72hours


title: Characterizing subpopulation heterogeneity in childohood acute lymphoblastic leukemia

summary: Single cell RNA sequencing of patient derived xenografts ALL samples to decipher subtype based vulnerabilities

overall_design: PDXs were injected and left to fully engraft in NSG mice, following by their isolation for sinlgle cell RNA sequencing

first: Kanari

last: Magdalini

first: Iria

last: Jimenez Garcia


title: Requirements for Establishment and Epigenetic Stability of Mammalian Heterochromatin [ChIP-Seq]

city: Boston

first: Harleen

last: Saini

summary: Heterochromatic domains of DNA account for a large fraction of mammalian genomes and have critical roles in silencing of transposons and genes but the mechanisms that establish and maintain these domains are not fully understood. Here we use an inducible heterochromatin formation system combined with targeted CRISPR gene disruption to show that DNA sequence-independent and histone H3 lysine 9 methylation (H3K9me)-dependent heterochromatin can only be inherited during a limited number of cell divisions in mouse embryonic stem cells but becomes stable upon differentiation. We show that multiple H3K9 methyltransferases work together with DNA cytosine methyltransferases and other factors, including RNA processing proteins, to establish and maintain heterochromatin. Our findings suggest that components of H3K9 and DNA methylation pathways work in concert to ensure heterochromatin stability.

overall_design: Chromatin immunoprecipitation DNA sequencing (ChIP-seq) for H3K9me3 histone modification in wild-type and mutant mouse embryonic stem cells (mESCs). Chromatin immunoprecipitation DNA sequencing (ChIP-seq) for H3K9me3 histone modification in UHRF1 mutant mouse embryonic stem cells (mESCs).

first: Antonis

last: Tatarakis

first: Danesh

last: Moazed


title: Effect of muscle-specific Pex5 depletion on gene expression in gastrocnemius muscle in 18 months-old mice

city: Pozzuoli

first: Rossella

last: De Cegli

address: Via Campi Flegrei 34

country: Italy

institute: Tigem

summary: We generated a muscle-specific Pex5 KO mouse to investigate the consequences of peroxisomal dysfunction on muscle homeostasis. Our study reveals that peroxisomal impairment triggers early alterations in skeletal muscle lipid and amino acid metabolism and disrupts the physical interaction between peroxisomes and mitochondria, resulting in reduction of muscle force and exercise performance. Over time, these disruptions lead to metabolic changes that affect mitochondrial content, and function anticipating the development of age-related muscle dysfunction.

overall_design: Total RNA was extracted from n=7 control and n=7 Pex5-null gastrocnemius muscle

first: R

first: V

last: Romanello


title: Effect of muscle-specific Pex5 depletion on gene expression in gastrocnemius muscle in 9 months-old mice

overall_design: Total RNA was extracted from n=6 control and n=7 Pex5-null gastrocnemius muscle


title: Effect of muscle-specific Pex5 depletion on gene expression in gastrocnemius muscle in 3 months-old mice

overall_design: Total RNA was extracted from n=4 control and n=5 Pex5-null gastrocnemius muscle


title: Anti-cancer therapy induces endothelial dysfunction in the human microcirculation that is prevented by VEGF-B overexpression

city: Wauwatosa

first: Ibrahim

last: Vazirabad

state: Wisconsin

address: 8915 W Connell Ave

department: Physiology

institute: Medical College of Wisconsin

summary: The present study is the first to demonstrate longitudinal declines in microvascular endothelial function in breast cancer patients undergoing anti-cancer therapy.  Microvascular dysfunction persists for several months after treatment, which may have implications for elevated cardiovascular risk in cancer patients.  Therapies with a high risk of cardiotoxicity (doxorubicin and trastuzumab) induce vasomotor impairments in healthy arterioles ex vivo.   These findings highlight microvascular endothelial dysfunction as a consequence of anti-cancer therapy which may contribute to treatment-induced cardiotoxicity.  The microcirculation represents a potential therapeutic target for intervention to prevent or predict adverse cardiovascular outcomes in breast cancer patients.

overall_design: Endothelial cells were grown from adipose tissue collected from donors without known cardiovascular disease. Endothelial cells isolated from surgical discard tissue (sample table below) were cultured and used for gene expression profiling of the effects of 0.1µM doxorubicin (DOX), 10µg/ul trastuzumab (TZM), 1µM paclitaxel (PTX) and their respective controls (media only for DOX and TZM; DMSO for PTX).

first: Janée

middle: D

last: Terwoord

first: Laura

last: Norwood Toro

first: Shelby

middle: N

last: Hader

first: Joe

last: Hockenberry

first: Jasmine

last: Linn

middle: Y

first: Amanda

last: Kong

first: Alison

last: Kriegel

first: Riikka

last: Kivelä

first: Gillian

last: Murtagh

first: David

last: Gutterman

first: Andreas

last: Beyer

first: Joseph

middle: C

first: Ziqing

last: Liu


title: Effect of muscle-specific Pex5 depletion on gene expression in gastrocnemius muscle

first: Rossella

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

overall_design: Refer to individual Series


title: Single-nucleus multi-omics identifies shared and distinct pathways in Pick’s and Alzheimer’s disease

city: Irvine

first: Vivek

last: Swarup

state: California

address: Biological Sciences III, 3224

institute: UCI

summary: The study of transcriptomic and epigenomic variations in neurodegenerative diseases, particularly tauopathies like Pick’s disease (PiD) and Alzheimer’s disease (AD), offers insights into their underlying regulatory mechanisms. Here, we identified critical regulatory changes driving disease progression, revealing potential therapeutic targets. Our comparative analyses uncovered disease-enriched non-coding regions and genome-wide transcription factor (TF) binding differences, linking them to target genes. Notably, we identified a distal human-gained enhancer (HGE) associated with E3 ubiquitin ligase (UBE3A), highlighting disease-specific regulatory alterations. Additionally, fine-mapping of AD risk genes uncovered loci enriched in microglial enhancers and accessible in other cell-types. Shared and distinct TF binding patterns were observed in neurons and glial cells across PiD and AD. We validated our findings using CRISPR to excise a predicted enhancer region in UBE3A and developed an interactive database, scROAD, to visualize predicted single-cell TF occupancy and regulatory networks.

overall_design: Nuclei from human PFC tissue were isolated from 7 patients with Pick's disease, and 9 of their age-matched controls. snATAC-seq and snRNA-seq were performed to study the regulatory mechanisms and gene expression alternation.

first: Zechuan

last: Shi

first: Sudeshna

last: Das

first: Samuel

last: Morabito

first: Emily

last: Miyoshi

first: Elizabeth

last: Head


title: Human peripheral and tissue Foxp3-high regulatory T cells in patients with hepatocellular carcinoma [CITE-seq]

city: Taoyuan

first: Wei-Ting

last: Ku

address: No. 259, Wenhua 1st Rd., Guishan Dist.

country: Taiwan

institute: Chang Gung University

summary: CD4⁺ regulatory T cells (Tregs) are pivotal in hepatocellular carcinoma (HCC) progression, but systemic depletion risks autoimmunity. Using single-cell CITE-seq on tumor, non-tumor, and peripheral blood samples, we identified a peripheral Foxp3^high Treg subset that preferentially migrates to tumors via the CCR5–CCL5 axis, where they acquire a terminally differentiated, activated phenotype with elevated LAYN and TRM signatures, and further enhance Foxp3 expression and immunosuppressive activity in response to pro-inflammatory cytokines. The proportion of Foxp3^high Tregs in peripheral blood strongly correlated with their tumor infiltration, and a >3.5% Foxp3^high Tregs/CD4⁺ T cells ratio predicted poor survival and early recurrence (AUROC >0.75). These findings establish peripheral Foxp3^high Tregs as both key mediators of immunosuppression and a promising non-invasive biomarker for HCC prognosis.

overall_design: CITE-seq analysis was performed on 51,067 CD4+ T cells from eight HCC patients.

first: Chien-Hao

last: Huang

first: Jayashri

last: Mahalingam

first: Cheng-Heng

last: Wu

first: Tsung-Han

first: Jian-He

last: Fang

first: Chung-Wei

last: Su

first: Po-Ting

last: Lin

first: Chien-Wei

last: Peng

first: Chan-Keng

last: Yang

first: Wei

last: Teng

first: Wen-Juei

last: Jeng

last: Chen

first: Chen-Chun

first: Shi-Ming

first: I-Shyan

last: Sheen

first: Yung-Chang

first: Chun-Yen


title: HNF4G and FOXA1 are context-specific drivers of pancreatic cancer progression [RNA-seq]

city: Cambridge

first: Jason

last: Carroll

address: Li Ka Shing Centre, Robinson Way

institute: Cancer Research UK, Cambridge Institute

summary: Despite recent advances in the treatment of pancreatic adenocarcinoma (PDAC), clinical outcome remains poor. Previous work identified the pioneer transcription factor FOXA1 as a mediator of new regulatory elements that drive tumour progression in models of late-stage disease. Given the critical role of FOXA1 as a pioneer factor for nuclear receptor (NR) transcription factors (TF) in breast and prostate cancer (Estrogen Receptor and Androgen Receptor), we hypothesised that FOXA1 might function with a NR in PDAC. Using RIME, our unbiased approach for discovering endogenous protein complexes, we identified HNF4A and HNF4G as reproducible, FOXA1-associated proteins, a finding that was validated in clinical samples of PDAC. Using complex and diverse PDAC models, we show that gene transcription in the classical subtype of pancreatic cancer is regulated by FOXA1/GATA5/6 and HNF4G. We show that HNF4G drives primary disease, in part by recruiting the methyltransferase PRMT1 to regulatory regions. In a primary tumour context, HNF4G is the dominant protein and the presence of HNF4G masks FOXA1 activity, resulting in FOXA1 being present, but functionally redundant in primary disease. During the transition to metastasis however, HNF4G expression decreases, which unmasks FOXA1 activity, where it becomes transcriptionally active and a subsequent driver of metastasis. We provide new molecular insight into the key TFs in PDAC and the stage-specific activity of these proteins.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: RNAseq in the Control, HNF4G-KO, FOXA1 O.E, HNF4G-KO+FOXA1 tumours in the HPAF-II cells. KPC mouse derived cell lines of matched tumour and liver mets subjected to RNA seq

first: Rao

middle: V

last: Shalini

first: Chernukhin

last: Igor

first: Carroll

last: Jason


title: HNF4G and FOXA1 are context-specific drivers of pancreatic cancer progression


title: Foxi2 and Sox3 are master regulators controlling ectoderm germ layer specification in Xenopus [RNA-Seq]

first: Clark

last: Hendrickson

overall_design: High throughput RNA-seq profiling of developmentally synchronized Foxi2 and Sox3 morphants and wild-type Xenopus tropicalis embryos at blastula and early gastrula stages.  Previously published wild-type early gastrula dissection RNA-seq data was re-analyzed from GSE81458.  Previously published wild-type timecourse expression RNA-seq data was re-analyzed from GSE65785.

middle: L

first: KW

last: Cho


title: FRA1 (FOSL1) Suppresses Neoplastic Transformation and Modulates Radiation Responses via Transcriptional Control of Mitogenic and Stress-Responsive Networks

status: Public on Sep 15 2025

city: Sudbury

first: Sujeenthar

last: Tharmalingam

state: Ontario

address: 935 Ramsey Lake Road

country: Canada

institute: NOSM University

summary: Purpose: FOS-like antigen 1 (FRA1), encoded by FOSL1, is an inducible subunit of the AP-1 transcription factor complex and regulates gene expression in response to proliferative and environmental cues. Although FRA1 has been linked to cancer progression, its role in early transformation and radiation responses remains unclear. Methods: CRISPR-engineered human CGL1 cells—a hybrid of HeLa and normal fibroblasts—were used to evaluate the impact of FRA1 overexpression and knockout on neoplastic transformation. Transformation frequency, clonogenic survival, DNA damage recognition and repair, and cell cycle distribution were assessed following irradiation. Transcriptomic profiling was performed under baseline and serum-stimulated conditions. Results: FRA1 loss markedly increased both spontaneous and radiation-induced transformation frequency, while overexpression suppressed transformation under both conditions. FRA1-deficient cells were sensitized to radiation-induced cell killing, despite intact DNA damage recognition and repair. In contrast, FRA1 overexpression promoted G2/M accumulation post-irradiation, suggesting enhanced checkpoint activation. Transcriptomic profiling revealed that FRA1 remodels AP-1 complex composition and functions as a transcriptional repressor of mitogen- and stress-responsive genes. FRA1-mediated repression was observed across gene networks involved in extracellular matrix remodeling, hypoxia signaling, inflammation, and proliferation, under both baseline and serum-stimulated conditions. Conclusion: These findings establish FRA1 as a key modulator of neoplastic transformation and radiation response, acting primarily through transcriptional repression of pro-tumorigenic signaling pathways.

overall_design: RNA sequencing was performed on CGL1 cells with FRA1 knockout, FRA1 overexpression, and their respective control lines under baseline conditions and 2 hours following serum stimulation. This design allowed for the identification of differentially expressed genes regulated by FRA1 under resting and mitogen-stimulated states.


title: Anthracyclines induce global changes in chromatin accessibility in cardiomyocytes that overlap with cardiovascular disease loci

city: Galveston

first: Michelle

middle: C.

last: Ward

address: 301 University blvd.

institute: UTMB

summary: We performed chromatin immunoprecipitation followed by sequencing (ChIP-seq) in human iPSC-derived cardiomyocytes to map genome-wide binding sites of TOP2B. Libraries were prepared from ChIP and matched input DNA, sequenced using 40 bp paired-end reads. After quality control and alignment to the human reference genome (GRCh38), high-confidence reads were filtered and duplicate reads removed. Peak calling using MACS2 in broad mode identified 5,410 enriched genomic regions, enabling investigation of TOP2B-associated regulatory elements in human cardiomyocytes.

overall_design: Chromatin immunoprecipitation was performed to map endogenous TOP2B binding sites in untreated human iPSC-derived cardiomyocytes. ChIP and matched input DNA were collected from 40 million cells each, derived from a single female donor line (UCSD143i-87-1). Libraries were prepared from immunoprecipitated chromatin and sequenced using 40 bp paired-end reads.

first: Sayan

last: Paul

first: Elizabeth

last: Matthews


title: Notch coordinates self-organization of germ layers and axial polarity in cnidarian gastruloids

first: Juan

middle: Daniel

last: Montenegro

state: Vienna

address: Djerassiplatz 1

department: Department of neurobiology and developmental biology

institute: University of Vienna

summary: Dissociation and reaggregation experiments in several animal systems have revealed the stunning capacity of self-organization. Reaggregated early gastrula cells (here called gastruloids) of the sea anemone Nematostella vectensis are able to regenerate with only little delay whole organisms that are virtually indistinguishable from normal developing polyps. However, the molecular control underlying the restoration of body axis and germ layers remains largely unknown. To address this, we established a standardized protocol, which reproducibly generates gastruloids developing into polys with a single body axis. Here, we show that committed mesodermal and endodermal cells are sorted out  to the surface of the aggregate, where  mesodermal cells form clusters of about 30 cells. At a critical time point, one mesodermal cluster immigrates, along with peripherally attached endodermal cells. Thereby, the inner germ layer and the oral-aboral axis is established in one and the same process. Functional studies demonstrated that this polarization of the endodermal cells requires a feedback loop of Notch and Wnt signaling. The dissociation of the early embryo disrupts Notch signaling in the endodermal cells, which leads to transient adoption of an endomesodermal profile, marked by the expression of the mesodermal cadherin1 until the boundaries between the germ layer identities are re-established. Our results highlight distinct morphogenetic behaviors of mesodermal and endodermal cells and the hitherto unknown role of Notch signaling in germ layer boundary formation in self-organizing gastruloids. Conservation of Notch-mediated boundary formation between endoderm and mesoderm mirrors bilaterian mechanisms, demonstrating how adoption of ancestral regulatory networks governing morphogenesis likely enabled the diversification of metazoan body plans.

overall_design: (1) DMSO treated library: Embryos were raised until 24hpf and then treated from 24hpf to 48hpf with 50uM DMSO as control and then samples were collected for sequencing; (2) LY treated library: Embryos were raised until 24hpf and then treated from 24hpf to 48hpf with 50uM LY411575 as treatment and then samples were collected for sequencing; (3) Gastrula.ACME library: Embryos were raised until 24hpf and then samples were collected for sequencing; (4) 4, 12, 24 and 48 hpa Embryos were raised until 24h and then dissociated, reaggregated and allowed to develop until the specified time when samples were collected.

first: Ulrich

last: Technau

first: Narayanaswamy

last: Sanjay

first: Franziska

last: Haas

first: Emmanuel

last: Haillot

first: Elly

last: Tanaka


title: Transcriptomic analysis reveals the key role of inflammatory and immune signaling in the anti-perimenopausal depression effects of Bushen Shugan Huayu decoction

city: Beijing

first: Ziqin

last: Feng

address: Beijing xicheng district northern cabinet number five

institute: Guang'anmen Hospital, China Academy of Chinese Medical Sciences

summary: Five patients diagnosed with perimenopausal depression in Beijing were treated with the BSSGHY decoction and clinically observed. The severity of depression and associated symptoms was assessed using the HAMD, Kupperman, and PSQI scales before and after treatment, and serum levels of inflammatory factors were quantified using ELISA. Differentially expressed genes in PBMCs were identified through mRNA sequencing and subsequently analyzed using DESeq2 software.

overall_design: Transcriptome analysis of PBMC samples was conducted from 5 patients before and after treatment.

first: Xiaohan

last: Chen

first: Fengquan

last: Xu

first: Yicheng

last: Liu

first: Yu

last: Zheng


title: Auto-inhibition of PRC2 by the broadly expressed long isoform of AEBP2.

city: Dublin 2

first: Adrian

middle: P.

last: Bracken

state: Co. Dublin

address: Smurfit institute of Genetics, Lincoln Place, Trinity College Dublin

department: Smurfit Institute of Genetics

country: Ireland

institute: Trinity College Dublin

summary: Polycomb Repressive Complex 2 (PRC2) is an essential chromatin regulator responsible for mono-, di- and tri- methylating H3K27. Control of PRC2 activity is a critical process in development and disease. While PRC2 is inhibited in germinal cells, no inhibitory cofactor has been identified in somatic cells. Here we show that the alternative isoforms of its accessory subunit AEBP2, namely AEBP2 S (short) and AEBP2L (long), perform opposite functions in modulating PRC2 activity. While AEBP2S is predominantly expressed during early embryogenesis, AEBP2L is expressed throughout embryogenesis and adulthood. AEBP2L inhibits both DNA binding by PRC2 and its histone methyltransferase activity in vitro and impairs PRC2 binding to target genes in embryonic stem cells. In contrast, AEBP2S promotes the DNA-binding activity of PRC2 and is essential for de novo repression of target genes during the transition from naïve to primed pluripotency. Mechanistically, through high-resolution Cryo-EM and mutagenesis, we show that the recently evolved, negatively charged N-terminal region of AEBP2L inhibits PRC2. We propose a model in which the N-terminus of AEBP2L arose in vertebrates to restrain PRC2 activity in somatic cells.

overall_design:
To investigate the ability of AEBP2 isoforms to bind chromatin in cells, we ectopically expressed human AEBP2 isoforms in generated by us Aebp2 KO mouse embryonic stem cells (E14), and performed ChIP-Rx of AEBP2 and SUZ12. The cell lines included in this dataset are: WT E14, Aebp2 KOs, Aebp2 KO+AEBP2L (AL) and Aebp2 KO+AEBP2S (AS).
To determine the transcriptional activity of the AEBP2 promoters in mouse embryonic stem cells, we performed 3 replicates of RNA-Seq in WT E14 mESCs.
To evaluate the genome-wide localisation of AEBP2, SUZ12, JARID2 and H3K27me3, we performed ChIP-Seq/Rx (proteins), or Cut&Run (H3K27me3) in our Aebp2 knock-out ESC line panel: WT E14, AEBP2L KO (LKO), AEBP2S KO (SKO) and complete Aebp2 KO (AEBP2KO).
To determine the contributions of the AEBP2 isoforms to de novo gene repression, we performed 3 replicates of QuantSeq in ESCs and Epiblast-like cells (D0 and D2 samples, respectively) in the four KO cell lines (WT, LKO, SKO, Aebp2 KO).

first: Marlena

last: Mucha


title: HNF4G and FOXA1 are context-specific drivers of pancreatic cancer progression [ATAC-seq]

first: Jason

last: Carroll

overall_design: ATAC-seq in pancreatic cancer cell lines of human and mouse origin

first: Rao

last: Shalini

first: Chernukhin

last: Igor

first: Carroll

last: Jason


title: Creatine Kinase B Regulates Glycolysis and de novo Lipogenesis Pathways to Control Lipid Accumulation During Adipogenesis

city: Stockholm

first: Salwan

last: Maqdasy

address: Norra Stationsgatan 69

department: Medicine

country: Sweden

institute: Karolinska Institute

summary: White adipocyte differentiation involves precise coordination between metabolic sensing and transcriptional regulation to ensure appropriate lipid storage. While creatine and its associated kinases have been implicated in adipose energy buffering and inflammation, the cell-intrinsic roles of the cytosolic (CKB) and mitochondrial (CKMT2) creatine kinases in adipogenesis remain insufficiently defined. In this study, we identified CKB and CKMT2 as progressively upregulated during white adipocyte differentiation. Loss- and gain-of-function studies revealed that CKB constrains de novo lipogenesis (DNL), in part by limiting the activation of the carbohydrate-responsive element-binding protein (ChREBP), a key transcriptional regulator of lipogenic gene expression. Mechanistically, we found that CKB physically interacts with AKT and appears to regulate its activation in response to insulin. Loss of CKB persistently activated AKT-mTORC1 signaling, which fueled glycolytic flux and, in turn, enhanced ChREBP activation, thereby channeling glucose-derived carbons into lipid synthesis. Taken together, our findings suggest that CKB serves as a metabolic rheostat linking creatine metabolism, insulin signaling, and nutrient-responsive transcription to control lipid accumulation during adipocyte differentiation. We propose CKB-AKT-ChREBP as a regulatory axis contributing to the metabolic remodeling underlying lipid homeostasis during adipogenesis.

overall_design: in vitro differentiated human white adipocytes transfected one day prior to adipogenic induction with siRNA targeting Creatine Kinase B (CKB), Mitochondrial Creatine Kinase 2 (CKMT2) and non-targeting control, harvested in triplicates at day ten of differentiation.

first: Gianluca

last: Renzi

first: Roamne

last: Higos

first: Ivan

last: Vlassakev

first: Abdoul

last: Bello

first: Muhmmad

last: Omar-Hmeadi

first: Mattias

last: Hansen

first: Fatiha

last: Merabtene

first: Christine

last: Rouault

first: Ondrej

last: Hodek

first: Lucas

last: Massier

first: Bruno

last: Antonny

first: Genevieve

last: Marcelin

first: Janane

middle: F

last: Rahbani

first: Simon

last: Lecoutre


title: Transcriptome analysis of DEHP-treated breast cancer cells

city: Taichung

first: Wei-Chien

last: Huang

address: 9F, No.6, Hsueh-Shih Road

department: Graduate Institute of Cancer Biology

institute: China Medical University

summary: This dataset contains RNA-seq profiles of breast cancer cells treated with di(2-ethylhexyl) phthalate (DEHP) or control vehicle. The study aims to characterize transcriptomic changes induced by DEHP exposure. RNA was extracted from treated cells, sequenced, and analyzed to assess gene expression differences between DEHP-treated and control conditions. The dataset provides information on genes responsive to DEHP and may serve as a resource for studies on environmental chemical effects on breast cancer cells.

overall_design: Breast epithelial cells MCF-10A were treated with DEHP or control vehicle.  Cells were incubated for 24 hours prior to RNA extraction using TRIzol reagent. The resulting RNA-seq data were used to identify gene expression changes induced by DEHP exposure.

first: Shu-Wei

last: Hu


title: ARID1A and ARID1B preserve B cell identity, prevent myeloid transformation and reveal therapeutic vulnerabilities

city: St. Louis

first: George

last: Souroullas

state: MO

address: 660 S. Euclid Av

institute: Washington University School of Medicine

summary: Chromatin remodeling by the SWI/SNF complex is essential for hematopoietic lineage commitment and differentiation.  While core subunits ARID1A and ARID1B are frequently mutated in B cell malignancies, their specific roles in B cell development and transformation remain poorly understood. Here, we investigated the function of these SWI/SNF components using conditional knockout mice with CD19-Cre–mediated deletion, initiated at the pro-B cell stage. Loss of either Arid1a or Arid1b led to a partial block in B cell differentiation in the bone marrow and impaired germinal center formation following antigen exposure.  Double deletion of Arid1a and Arid1b resulted in a more severe phenotype, with marked reduction in peripheral B cells, shortened overall survival, and development of an aggressive leukemia. Surprisingly, the malignancy was of myeloid origin, arising from a small subset of CD19-expressing multipotent progenitors (MPPs). These Arid1a/Arid1b-deficient MPPs exhibited abnormal expansion, defective differentiation in methylcellulose assays, and transcriptional dysregulation of key self-renewal programs driven by CBFA2T3 (ETO2) and Fli1.  In established B cell lymphoma cells in vitro, loss of ARID1A and ARID1B together mildly affected cell growth, while loss of ARID1A increased sensitivity to pharmacological EZH2 inhibition. Collectively, our findings reveal stage-specific and compensatory roles for ARID1A and ARID1B in B cell development, uncover a previously unrecognized mechanism by which SWI/SNF loss in early progenitors can drive transformation towards myeloid leukemia, and identified possible therapeutic vulnerabilities in patients with ARID1A mutations.

overall_design: RNA sequencing performed on SUDHL6 cells targeted using CRISPR/Cas9 to inactivate expression of ARID1A, ARID1B or both.  Non-target sgRNA used to generate stable control cell line clones.  Mouse primary multipotent progenitors (MPPs) were harvested from bone marrow, sorted using FACS, and processed for RNA isolation right after.

first: Phyo Nay

last: Lin

middle: P


title: Rapeseed NAC-type transcription factor BnNAC038 manipulates the trade-off between drought response and growth [DAP-seq]

first: Jingrui

last: Li

address: Yuanmingyuan West Road No.2

country: China

institute: China Agricultural Universtiy

summary: Drought stress significantly impairs plant growth. In response to this stress, plants have evolved adaptive strategies to effectively allocate their limited resources, thereby ensuring both survival and growth under drought conditions. However, the regulatory mechanisms that govern this adaptive response and the key regulatory factors involved in the trade-off remain poorly understood. In this study, we identified a Brassica napus NAC transcription factor, BnNAC038, which functions as a central regulator in balancing drought tolerance and yield in the oil crop rapeseed. Loss-of-function analysis demonstrated that BnNAC038 knockout plants exhibited enhanced drought tolerance, characterized by higher survival rates, reduced water loss, increased sensitivity to ABA-induced stomatal closure, and elevated leaf temperature. Additionally, DAPseq and RNAseq analyses provided a more comprehensive understanding of the regulatory mechanisms involved. Taken together, our results offer compelling evidence for a novel strategy to develop drought-resilient crops with minimal yield penalties for sustainable agriculture, achieved through the targeted manipulation of negative regulators of drought responses.

overall_design: DAP-seq of BnNAC038 was conducted with genomic DNA library.

first: Daojie

last: Wang


title: HNF4G and FOXA1 are context-specific drivers of pancreatic cancer progression [HiChIP-Seq]

first: Jason

last: Carroll

overall_design: Hi-ChIP in Pancreatic Cancer clinical samples and cell lines of human and mouse origin

first: Rao

last: Shalini

first: Chernukhin

last: Igor

first: Carroll

middle: S

last: Jason


title: Rapeseed NAC-type transcription factor BnNAC038 manipulates the trade-off between drought response and growth [RNA-seq]

overall_design: RNA-seq profiling was conducted on wild-type, knockout lines (BnNAC038-KO-1), and overexpression lines (BnNAC038-OE-1, BnNAC038-OE-2) under treatment with 50 μM ABA and 20% PEG.


title: HNF4G and FOXA1 are context-specific drivers of pancreatic cancer progression [ChIP-seq]

overall_design: ChIP-seq in Pancreatic Cancer clinical samples and cell lines of human and mouse origin