title: Pivotal Role of the NuRD Complex in Remodeling Chromatin Environment and Maintaining Genome Architecture at CTCF Sites [mESC_d0246_RNA_Seq]

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

first: Wenju


title: Dispensable role of RPB1 CTD in co-transcriptional splicing in mouse ESC (Fraction chrRNA-seq)

status: Public on May 04 2026

city: Beijing

first: Yajing

last: Hao

address: NO.1 Beichen West Road, Chaoyang District

department: Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences

country: China

institute: Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation

summary: To define the function of CTD on co-transcriptional splicing, we used auxin-inducible CTD degron system in mouse embryonic stem cells (mESCs) with auxin treatment for 3 hours to sufficiently deplete Rpb9. To measure co-transcriptional splicing, we fractionated mESCs cells (spiked in with Drosophila S2 cells for data normalization) into cytosolic (Cyt), nucleoplasm (NP), and chromatin/particle (Chr) fractions. We purified total RNA from Chr compartment, depleted ribosomal RNAs, and constructed two independent libraries for RNA-seq, which showed excellent reproducibility.

overall_design: Characterization of co-transcriptional splcing after degradation of CTD in mESC cells

first: Changwei

last: Shao

first: Xiang-Dong

last: Fu


title: Pivotal Role of the NuRD Complex in Remodeling Chromatin Environment and Maintaining Genome Architecture at CTCF Sites [HEK293T_BPK25_BS_Seq]

city: Hong Kong

first: Jian

last: Yan

state: Hong Kong Special Administrative Region

address: 83 Tat Chee Avenue, Kowloon

department: Department of Biomedical Sciences

institute: City University of Hong Kong

type: Methylation profiling by high throughput sequencing

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

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

first: Xi

last: Wang

last: Sun

last: Wu


title: Pivotal Role of the NuRD Complex in Remodeling Chromatin Environment and Maintaining Genome Architecture at CTCF Sites [HEK293T_siNURD_TET1_ChIP_Seq]

type: Genome binding/occupancy profiling by high throughput sequencing

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


title: mTOR inhibition enhances the antitumor efficacy of RAF dimer-MEK blockade by inhibiting the ATF4-MTHFD2 pathway

city: Montreal

first: Sonia

middle: Victoria

last: del Rincon

state: QC

address: E-537, 3755 Chemin de la Côte-Ste-Catherine

country: Canada

institute: McGill University

type: Expression profiling by high throughput sequencing

summary: RAF monomer inhibitors are clinically approved for the treatment of BRAFV600-mutant melanoma in combination with a MEK inhibitor, but ineffective in other melanoma subtypes. Moreover, RAF dimer inhibitors, such as belvarafenib, when combined with MEK inhibitors (cobimetinib) have promising but limited efficacy in non-BRAF-mutant melanomas. Here, we report that the mTOR inhibitor sapanisertib improves the efficacy of combined belvarafenib and cobimetinib therapy in NRAS, NF1, and KIT-mutant melanomas. Mechanistically, sapanisertib combined with belvarafenib and cobimetinib suppressed ATF4 expression and its target gene MTHFD2 while inducing DNA damage, revealing a previously underappreciated role of the ATF4-MTHFD2 axis in DNA damage repair and drug response. Human and murine models resistant to combined belvarafenib and cobimetinib exhibited elevated levels of ATF4 and MTHFD2 and were sensitive to sapanisertib. This study provides novel treatment opportunities for patients with non-BRAF-mutant melanomas, or those who relapse following belvarafenib and cobimetinib combination therapy.

overall_design: We treated NRAS-mutant WM3406 melanoma cell lines with belvarafenib (25 nM), cobimetinib (50 nM), and the mTOR inhibitor sapanisertib (INK128, 25 nM) and we performed RNA sequencing analysis after 24 h.

first: Feiyang

last: Cai

first: Fan

last: Huang

first: Christophe

last: Goncalves

first: Harinee

last: Srikannan

first: Natascha

last: Gagnon

first: Elizabeth

middle: M

last: Guettler

first: Léa

last: Mukeba-Harchies

first: Jennifer

last: Maxwell

first: Jie

last: Su

first: Krikor

last: Bijian

first: Fabrice

last: Journe

first: April

last: Rose

first: Alexandre

last: Orthwein

middle: V

last: del Rincón

first: Wilson

middle: H

last: Miller Jr.


title: Pivotal Role of the NuRD Complex in Remodeling Chromatin Environment and Maintaining Genome Architecture at CTCF Sites [HEK293T_IAA72h_ChIP_Seq]

first: Jian

last: Yan

last: Wang

first: Wenju

last: Sun

last: Wu


title: H3K4me3 ChIPmentation-seq, human primary fibroblasts

city: Charlestown

first: Gian Paolo

last: Dotto

state: MA

address: 149 13th Street

department: Cutaneous Biology Research Center

country: USA

institute: Massachusetts General Hsopital

summary: Chromatin immunoprecipitation coupled with tagmentation followed by next-generation sequencing (ChIPmentation-seq) for histone H3 lysine 4 trimethylation (H3K4me3) was performed in human primary fibroblasts. H3K4me3 is a mark of active promoters and was used to identify open, transcriptionally active chromatin in primary dermal fibroblasts isolated from healthy donors.

overall_design: CHIPmentation-seq profiling of H3K4me3 in a healthy donor derived primary dermal fibroblasts.

first: Jovan

last: Isma

first: Emery

last: Di Cicco

first: Gian-Paolo


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

first: Xi


title: Pivotal Role of the NuRD Complex in Remodeling Chromatin Environment and Maintaining Genome Architecture at CTCF Sites [HEK293T_BPK25_ChIP_Seq]


title: RNAseq to profile transcriptomes of alveolar macrophage from wild type and HDAC1-2 cKO mice

first: wenlong

last: Lai

address: Tsinghua university

department: School of medicine

institute: Tsinghua University

summary: We performed the transcriptomic analysis of alveolar macrophage(AM) isolated from wild type and HDAC1-2 cKO mice. AM (CD45+CD11c+F4/80+) were sorted from the lung of 2-weeks-old mice. Total RNA from AM was extracted by Trizol reagent according to the manufacturer’s instructions. Library construction and data processing were performed by Beijing Genomics Institute. Libraries were sequenced on Illumina Hiseq4000.

overall_design: mRNA profiles of alveolar macrophage from wild type and HDAC1-2 cKO mice were generated by RNA-sequencing analysis

first: Wenlong


title: Light sensitive short hypocotyl (LSH) confer symbiotic nodule identity in the legume Medicago truncatula

city: Cologne

first: Tak

last: Lee

address: Carl-von-Linne weg 10

country: Germany

institute: Max Planck Institute for Plant Breeding Research

summary: Legumes produce specialized root nodules that are distinct from lateral roots in morphology and function, with nodules intracellularly hosting nitrogen-fixing bacteria. We have previously shown that a lateral root program underpins nodule initiation, but there must be additional developmental regulators that confer nodule identity. Here, we show two members of the LIGHT SENSITIVE SHORT HYPOCOTYL (LSH) transcription factor family, predominantly known to define shoot meristem complexity and organ boundaries, function as regulators of nodule organ identity. In parallel to the root initiation program, LSH1/LSH2 recruit a program into the root cortex that mediates the divergence into nodules, in particular with cell divisions in the mid cortex. This includes regulation of auxin and cytokinin, promotion of NODULE ROOT1/2 and Nuclear Factor Y-A1 and suppression of the lateral root program. A principal outcome of LSH1/LSH2 function is the production of cells able to accommodate nitrogen-fixing bacteria, a key feature unique to nodules.

overall_design: Proteins NIN and LSH were overexpressed with LjUBI promoter, to search for their binding sites

first: Katharina

last: Schiessl


title: scRNA analysis of inflamed and uninflamed colon tissues of Crohn's disease patients

status: Public on May 03 2026

city: Changzhou

first: Jie

last: Zhao

state: Jiangsu

address: No.68 Gehu Road

institute: The Third Affiliated Hospital of Nanjing Medical University

summary: Single-cell RNA sequencing was performed on colonic tissues from Crohn’s disease patients, comparing inflammatory and non-inflammatory regions. The dataset characterizes cell-type composition and inflammation-associated transcriptional changes at single-cell resolution.

overall_design: Colonic tissue samples were collected from inflammatory and non-inflammatory regions of Crohn’s disease patients and subjected to single-cell RNA sequencing. After quality control, data were analyzed for cell clustering, marker gene identification, and functional enrichment to compare transcriptional profiles between the two regions.


title: ELF5 regulates epithelial integrity independently of EHF

city: Philadelphia

first: Alekh

last: Paranjapye

state: Pennsylvania

address: 3400 Civic Center Blvd

department: Genetics

institute: University of Pennsylvania

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

overall_design: Refer to individual Series


title: ELF5 regulates epithelial integrity independently of EHF [ChIP-seq]

summary: E74-like ETS transcription factor 5 (ELF5) is one of three epithelial ETS family transcription factors. The ELF5 gene maps to chr11p13 where it is located adjacent to another epithelial ETS factor gene, ETS homologous factor (EHF). This genomic interval is associated with lung disease. The functions of ELF5 in the airway epithelium are not well studied, in large part due to a lack of cellular models expressing the gene. Using scRNA-seq data from primary human bronchial (HBE) and nasal (HNE) epithelial cells we show ELF5 expression in subsets of ciliated and secretory cells, implicating a role for this factor in the airway epithelium. Next, we generate cistrome and transcriptome data for ELF5 in another epithelial cell type with abundant ELF5, and use bioinformatic tools to reveal the potential functions of this factor in the airway epithelium. ELF5 has a strong repressive function in epithelial cells, where it has a profound impact on organization of the extracellular matrix. Activation of ELF5 expression in primary HBE cells using CRISPRa enhanced transepithelial resistance (TER) and wound repair. These results illustrate an important role for ELF5 in maintaining airway epithelial integrity, which is critical to lung health. Furthermore, ELF5 can act independently from EHF and exhibits opposite effects in the airway epithelium.

overall_design: Three ChIP-seq replicates

first: Jey

last: Sabith Ebron

first: Monali

last: NandyMazumdar

first: Ann

last: Harris


title: Pivotal Role of the NuRD Complex in Remodeling Chromatin Environment and Maintaining Genome Architecture at CTCF Sites [hESC_H9_d049_ChIP_Seq]


title: ELF5 regulates epithelial integrity independently of EHF [RNA-seq]

first: Hannah

last: Swahn

middle: S

last: Ebron

first: James

last: Browne


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

first: Jian

last: Yan

summary: The currently available data of CTCF binding in mammalian cells are exclusively obtained with ChIP-seq. In order to fully retain the dynamic information of CTCF binding, we have developed a new method called GpC-Methylation Assisted Tracing (G-MAT) of a nuclear protein, which leverages DNA cytosine methylation to record the footprints of a protein within a given period of time.

overall_design: In principle, endogenous CTCF proteins are coupled with a cytosine methyltransferase M.CviPI cloned from Chlorella virus NYs-1 that covalently adds a methyl-group on carbon 5 (C5) of cytosine at the GpC dinucleotides that is un-erasable by any known demethylase. As a result, GpC adjacent to CTCF interacting sites can be permanently methylated, enabling genome-wide tracing the trajectory of CTCF footprints on chromatin using the whole genome bisulfite sequencing (WGBS). To enhance the methylation efficiency for improved signal-to-noise ratio in footprint detection, we took advantage of the SunTag system8 in fusion with endogenous CTCF proteins that recruited up to 10 copies of M.CviPI proteins fused with a single chain antibody fragment (scFv).

last: Wang

first: Wenju


title: Effect of grape pomace skin colonic ferments on  differentiated monolayers of Caco-2 cells

city: Macul

first: Omar

last: Porras

state: Santiago

address: El libano 5524

department: INTA

country: Chile

institute: University of Chile

summary: Dietary fibre usually comes associated with phenolic compounds either trapped in a network formed by indigestible polysaccharides or, in some cases, bound to this matrix by covalent bonds. This natural association protects some phenolic compounds during their journey through the gastrointestinal tract, reaching the colon, where most polysaccharides undergo fermentation, weakening the matrix and promoting the release of these compounds to exert benefits by modulating intestinal function. Unfortunately, there are still difficulties in investigating the impact of the human microbiota on the release of phenolic compounds from the indigestible fraction and on their effects on the intestinal epithelium.   In this study, grape pomace skin was subjected to in vitro digestion to obtain an indigestible fraction, which was further incorporated into SHIME bioreactors with human colonic microbiota. Throughout these stages, we monitored the release of phenolic compounds using HPLC-DAD. We determined the impact of a phenolic-rich indigestible fraction on the fermentative capacity of human microbiota by measuring the short-chain fatty acids (SCFA) levels and the effect of the resulting colonic ferments on the barrier properties of differentiated monolayers of Caco-2 cells by monitoring the transepithelial electrical resistance and the transcriptomic profile by RNA sequencing.

overall_design: RNA-seq profiling of Caco-2 cells exposed to colonic ferments of grape pomace skin

first: Miltha

last: Hidalgo

first: Rodrigo

last: Pulgar

first: Francisca

last: Vera-Tamargo

first: Adriano

last: Costa de Camargo

first: Alina

last: Concepción-Alvarez

first: Bárbara

last: Railef

first: Carolina

last: Añazco

first: Elva

last: González

first: Igor

last: Pacheco

first: Jorge

last: Meneses-Pacheco

first: Karen

last: Fuenzalida

first: Macarena

last: Moreno

first: Martina

last: Oyarzún

first: Raquel

last: Bridi

first: Vanessa

last: Rubio


title: Epithelial Edar is Responsible for Dental Anomalies in HED

city: Shanghai

first: Wenyu

last: Xu

address: 500 Quxi Road

department: Department of second dental center

institute: Shanghai ninth people's hospital

summary: In this study, we generated epithelial-specific Edar knockout mouse models and reported that the epithelial Edar is responsible for ectodermal dysplasia, determines tooth size and influences tooth morphology and number. Ko is from K14cre;Edarfl/fl mice and ctrl is from Edarfl/fl mice. Single-cell RNA sequencing revealed that impaired differentiation from preameloblasts to early ameloblasts may underlie the observed enamel defect. Taken together, these findings reveal a critical role of epithelial EDAR in tooth development and, for the first time, provide evidence that its downregulated expression can lead to enamel formation defects, offering new insights into the pathogenic mechanisms of EDAR-related HED.

overall_design: These cells were isolated from the dental germ of the the mandible first molar from Edarfl/fl and K14cre;Edarfl/fl  newborn C57black/B6 mice.


title: Effect of co-culture with ETBF in NOZ cell line on gene expreesion difference

city: shanghai

first: Jun

last: Chen

state: shanghai

address: renji hostipial

institute: shanghai jiao tong university

summary: Enterotoxigenic bacteroides fragilis (ETBF), a strain of B.fragilis is enriched in gallbladder cancer (GBC), but its causative role and translational implications in GBC remain unclear. Here, we demonstrate that ETBF promotes GBC cell proliferation and metastasis both in vitro and in vivo. Mechanistically, ETBF adheres to GBC cells through its surface protein, Membrane-bound lytic murein transglycosylase D precursor (MltD precursor), which binds to the TMPRSS13 receptor on GBC cells, leading to the activation of JAK2-STAT3 signaling pathway. Blockade of the MltD precursor-TMPRSS13 interaction abolishes ETBF-driven protumorigenic effects and JAK2 and STAT3 phosphorylation. Additionally, ETBF secretes the metalloprotease, B. fragilis toxin-1 (BFT-1), which accelerates GBC progression via activating NF-κB signaling to increase secretion of the cytokine CXCL1 and recruit myeloid-derived suppressor cells (MDSCs) into tumors for angiogenesis. Collectively, our study elucidates an oncogenic mechanism driven by ETBF and identifies that the MltD precursor-TMPRSS13 interaction as a potential therapeutic target for GBC.

overall_design: RNA-seq profiling of wildtye NOZ cells and ETBF-infected NOZ cell after 6 hous of adipogenic differentiation


title: Atopic asthma lowers nasal mucosal sphingolipids

city: New York

first: Stefan

last: Worgall

state: New York

address: 413 East 69th Street

department: Pediatrics

institute: NewYork Presbyterian- Weill Cornell Medicine

summary: Genetic variations at the 17q21 asthma-risk locus regulate the expression of gasdermin B (GSDMB) and ORMDL3, influencing inflammatory responses and sphingolipid metabolism. While asthma-associated 17q21 variations are known to affect ORMDL3 expression in immune and airway smooth muscle cells, its role in airway epithelial sphingolipid metabolism remains unclear. We investigated whether asthma and 17q21 genetic variations influence sphingolipid composition in the upper respiratory tract and how immune vs. epithelial cells contribute to this process. Sphingolipid profiles were analyzed in nasal fluid and blood from children with and without asthma. We also examined gene expression and sphingolipid composition in nasal epithelial cells and PBMCs from healthy adults homozygous for the rs7216389 C/C and T/T (asthma-risk) genotypes. Children with atopic asthma exhibited lower nasal fluid sphingolipids, including sphinganine, dihydroceramides, and ceramides, independent of corticosteroid use or allergic rhinitis. Asthma was further associated with higher plasma sphingolipids and lower blood cell sphingolipids, the latter mirroring patterns in nasal fluid. In PBMCs, the T allele increased ORMDL3 expression, suppressing de novo sphingolipid synthesis. However, in nasal epithelial cells, the T allele mainly increased GSDMB and there was no effect on sphingolipid metabolism. These findings establish nasal fluid sphingolipid profiling as a potential marker for atopic asthma and provide evidence of a cell-type-specific effect of 17q21 genetic variants. While ORMDL3-mediated sphingolipid suppression occurs in PBMCs and not airway epithelial cells, its systemic effects may contribute to lower airway sphingolipids in asthma.

overall_design: RNA-seq profiling from nasal cells and PBMCs collected from 12 healthy adult volunteers homozygous for the 17q21 rs7216389 C/C and T/T (asthma risk) genotypes.

first: Zenna

last: Solomon

first: Rika

last: Gomi

first: Zoe

last: Verzani

first: Andrea

last: Heras

first: Perdita

last: Permaul

first: Uthra

last: Balaji

first: Jinghua

last: Gu

first: Sarah

last: Brown

first: Natalia

last: Huerta

first: Natalie

last: Gosnell

first: Paul

last: Christos

first: Jennie

middle: G

last: Ono

first: Tilla


title: SMART-seq profiling of the ascending aorta and aortic arch from male and female Wnt1-Cre;Rosa26-mTmG mice

city: Chongqing

first: Qing

middle: Rex

last: Lyu

state: Chongqing

address: #118 Xingguang Avenue

department: Affiliated Chongqing General Hospital

institute: Chongqing University

summary: Vascular smooth muscle cells (VSMCs) in the ascending aorta and aortic arch arise from two distinct embryonic origins: the second heart field (SHF) and the cardiac neural crest (CNC). Whether these populations exhibit sex-dependent differences remains unknown. Here, we used Wnt1-Cre;Rosa26-mTmG mice to genetically label CNC-derived VSMCs with GFP, while non-CNC-derived cells expressed tdTomato. The ascending aorta and aortic arch were dissected from male and female mice, and single-cell suspensions were generated by enzymatic digestion. Cells were then sorted by fluorescence-activated cell sorting (FACS) based on GFP or tdTomato expression. RNA-expression profiles for each group were obtained using the Smart-seq platform. Thi study revealed the differential expression of VSMCs from different embryonic origin in both sexes.

overall_design: Single-cell suspensions were prepared from the ascending aorta and aortic arch of Wnt1-Cre;Rosa26-mTmG mice. Two male samples were pooled, while one female sample was processed separately. GFP-positive and tdTomato-positive cells were isolated from these suspensions by fluorescence-activated cell sorting (FACS), followed by SMART-seq analysis to profile gene expression in each sample.

first: Yanzhi

last: Wang

first: Cheng

last: Luo

first: Songmao


title: RAS pathway activation and microenvironmental adaptation as hallmarks of myeloid sarcoma

first: Bettina

last: Nadorp

state: NY

address: 500 1st Ave

department: Medicine/Pathology

institute: NYU Langone Health

summary: Myeloid sarcoma, an aggressive extramedullary subtype of acute myeloid leukemia (AML), occurs in up to 20% of patients, and remains strikingly understudied in large-scale genomic and multiomic investigations. The key biological drivers of its tumor evolution are largely unknown, timely detection in asymptomatic patients poses a clinical challenge, and effective treatment options are limited as patients are often excluded from clinical trials, rendering it a largely neglected disease entity. Here, we demonstrate that myeloid sarcoma evolves from medullary AML but exhibits distinct site-specific clonal evolution patterns. This is supported by unique transcriptional signatures of myeloid sarcoma that reflect adaptation to the extramedullary microenvironment. Also, we establish a proof of concept that circulating tumor DNA sequencing can capture the molecular composition of myeloid sarcoma, offering a potential non-invasive approach for molecular profiling of extramedullary AML. Collectively, our findings highlight marked biologic differences between medullary AML and myeloid sarcoma, including universal molecular evolution and RAS pathway activation as hallmarks of the disease.

overall_design: Tumor-derived RNA was subjected to 0.8x SPRI bead cleanup and size selection prior to DNase treatment and ribo-depletion prior to using the NEBNext Ultra II Directional kit preparation. The library was constructed for whole transcriptome sequencing (RNA-seq).  Paired-end 151-bp reads were generated on the Illumina NovaSeq (Illumina, Inc.), and reads were aligned to the human genome reference sequence (GRCh38).

first: Saranga

last: Wijeratne

first: Elaine

last: Mardis

first: Alice

last: Mims

first: Ann-Kathrin

last: Eisfeld


title: Effect of TRIB3 overexpressing on the gene expression in NCM460 cells

first: jing

last: liu

address: tian qiao

institute: Institute of Materia Medica, Chinese Academy of Medical Sciences

summary: Inflammatory bowel disease (IBD), including ulcerative colitis (UC) and Crohn’s disease (CD), is a chronic and relapsing disorder with increased prevalence all over the world. Bile acids are small molecules synthesized from cholesterol by the liver, and their metabolic disorder has a positive correlation with IBD development. Here, we identified that GCA promotes DSS induced mouse colitis through downregulating Tribbles homolog 3 (TRIB3) to inhibit the function of intestinal stem cells, which suggested the potential harmful biological function of conjugated primary bile acid—GCA in IBD. Then we have demonstrated that TRIB3 is highly expressed in crypts, to maintain the ISCs stemness traits. Downregulation of TRIB3 in intestinal epithelium cells accelerated IBD progression. To decipher the molecular mechanisms of TRIB3 in maintaining intestinal stem cells renewal, we established the control and TRIB3 overexpressing NCM460 cells to perform this high-throughput mRNA sequencing.

overall_design:
To investigate the molecular mechanisms of TRIB3 in maintaining intestinal stem cell renewal, we established the control and TRIB3 overexpressing NCM460 cells by infecting lentivirus.
We then performed gene expression profiling analysis sing data obtained from RNA-seq of cells of two groups with 3 replicates separately at 24h.
Comparative gene expression profiling of RNA-seq data for control and TRIB3 overexpressing NCM460 cells.

first: Shuang

last: Shang

first: Jing

last: Liu

first: Fang

last: Hua


title: Transcriptomic profile of patient derived glioblastoma stem cells from recurrent and newly diagnosed background

city: Miami

first: Shanta

last: Dhar

state: Florida

address: 1011 NW 15th Street, Room 437

department: Biochemistry

institute: University of Miami

summary: Metabolic rewiring of neoplastic cells can fuel tumorigenicity of cancer stem cells contributing to tumor recurrence. One such cancer is glioblastoma for which tumor recurrence is universal. After first line therapy includes surgical resection, temozolomide chemotherapy, and radiotherapy. Tumorigenic fueling of glioblastoma stem cells (GSCs) which have invaded into distal brain parenchyma that are unresectable and/or resistant to standard chemo and radiation therapy promote recurrence. We wanted to focus on studying whether there is a correlaion between metabolic substrate utilization, stemness, and tumorigenicity of patient derived GSC populations. Leveraging the knowledge of metabolic substrate utilization by the GSCs and their stemness potential may be a promissory target to curb the aggressiveness of the GSCs. Thus we embark on a journey to investigate the transcriptomic profile of the patient derived GSCs from varied background. Considering the heterogeneity of the GSCs, it is of utmost important to study patient derived GSCs from varied bakground. Our pool of cells comprise of 2 recurrent patient derived GSCs and 2 newly diagnosed GSCs. Our long term goal being to design and develop alternative nanotherpaeutic approaches to target the otherwise hard-to-target GSCs in the brain, we concentrated on using patient derived cells to closely recapitulate the tumor characteristics whiich would have been difficult if conventional cell lines were used. Thereby, a complete understanding of the genomic profile of the GSCs from varied patient background would help us figure out the best possible target site for therpeutics against GSCs and as a result delay/stop the tumor recurrence.

overall_design: We performed HISAT2 based RNA sequencing analysis on patient derived glioblastoma stem cells (GSCs) from varied background. The pool of cells comprise of 2 patient derived GSCs from recurrent background and 2 patient derived GSCs from newly diagnosed background. We aim at understanding the differential genomic profile of the patient derived GSCs based on their metabolic and stemness features so that we can use this knowledge to design and develop non-ivasive and/or invasive therapeutic interventions to target this heterogenous cell population.

first: S

last: Sarkar

first: A

last: Ashokan

first: B

last: Surnar

first: D

last: Eichberg

first: T

middle: I

last: Slepak

first: M

middle: E

last: Ivan


title: Gene expression profile of various brain cells obtained from APP-KI mice

city: Singapore

first: James

middle: Alastair

last: Miller

address: 11 Mandalay Road

department: Lee Kong Chian School of Medicine

country: Singapore

institute: Nanyang Technological University

summary: Brain cells, such as, oligodendrocytes, and neurons, interact with each other to maintain brain homeostasis. Here, we utilize scRNAseq to investigate the significant phenotypic heterogeneity of different brain cell types under neurodegenerative disorders, based on their transcriptional profiles

overall_design: Whole brain cells were isolated from 6-month-old APP-KI mice, with FIT2-WT or FIT2-Mut, respectively, to study their transcriptome alterations when macrophagic Fit2 genes are disrupted in Alzheimer's disease

first: Ruedl

last: Christiane

first: Wu

last: Xiaoting

first: Miller

last: James A


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

first: Jian

last: Yan

summary: Interactions between nuclear proteins and chromatin are critical in transcriptional regulation. The state-of-the-art approaches provide merely snapshot information on their interactions, which impedes our understanding of the causality in the dynamic regulatory processes. Here, we developed a novel method termed G-MAT that profiles the footprints of a nuclear protein on chromatin and DNA methylome simultaneously in living mammalian cells. Utilizing G-MAT to transcription factor CTCF, we inferred that CTCF searches its binding sites in the genome through stochastic collision to the chromatin. Together with eBioID, which is an enhanced BioID method facilitated by the Suntag system, we found hundreds of proteins with distinct functions co-occupying CTCF binding sites on chromatin, including RNA splicing and chromatin remodeling. Intriguingly, two methyl-CpG binding domain (MBD) proteins were found as interacting partners of CTCF, largely leading CTCF to preferentially bound to methylated DNA segments, consistent with the co-occurrence of CTCF footprints and DNA hyper-methylation when analyzing the G-MAT data at the single-molecule resolution. MBD2, one of the MBD proteins shown to be associated with demethylases, could likely erase DNA methylation near CTCF binding sites, resulting in seemingly anti-correlations between CTCF binding and DNA methylation. Altogether, G-MAT has enabled us to investigate the causal relationship between CTCF target searching and DNA methylation at the single-molecule level, providing an important data resource and novel insights for advanced understanding of transcriptional regulation dynamics.

overall_design: In situ Hi-C of cultured HEK293T cells to identify chromatin long range interaction loops, Topologically associating domains, and Compartment A and B.

first: Xi

last: Wang

first: Wenju

last: Sun

last: Wu


title: Exosomal lncRNA Microarray Profiling

city: Hangzhou

first: Jingbo

last: Lai

address: Xihu district

institute: Zhejiang University

summary: Exosomes were isolated from the culture supernatants of lymphocytes in two groups, and lncRNAs within the exosomes were identified using microarray sequencing.

first: Ye

last: Chen


first: Bettina

last: Nadorp

overall_design: Single-cell RNA-seq / CITE-seq on bone marrow aspirates or peripheral blood of acute myeloid leukemia patients  with myeloid sarcoma, or  myeloid sarcoma. Spatial transcriptomics (10X Visium) on myeloid sarcoma in the skin.

first: Audrey

last: Lasry

first: Iannis

last: Aifantis

first: Ann-Kathrin

last: Eisfeld


title: RNA-seq analysis of tumor-infiltrating effector T cells isolated from subcutaneous mouse Lewis lung carcinoma (LLC) tumors

city: Barcelona

first: Cristina

last: Lopez-Rodriguez

address: Carrer Dr. Aiguader, 88

department: Medicine and Life Sciences

country: Spain

institute: Universitat Pompeu Fabra

summary: The goal of this study was to analyze differences in gene expression between tumor-infiltrating effector T cells with higher or lower uptake of the 2-deoxyglucose analog 2-NBDG in vivo. Mice bearing subcutaneous LLC tumors were injected intravenously with the 2-deoxyglucose analog 2-(N-(7-nitrobenz-2-oxa-1,3-diazol-4-yl) amino)-2-deoxyglucose (2-NBDG, Life Technologies, catalog: N13195). 2-NBDG was used at 25 mg/kg of mouse body weight; 3.33 mg/ml in PBS. 2-NBDG was allowed to circulate for 15 min before euthanizing the mice and excising the tumors to isolate effector (CD44+, CD62L-negative T cells) TILs. The 15% of effector CD4 or CD8 TILs with the highest 2-NBDG staining were sorted as 2-NBDG Hi cells, and the lowest 15% were sorted as 2-NBDG Lo. 4 independent mice were used. For each population, a pool of 2000 cells (500 cells per mouse) was done. RNA of the respective pools was extracted with the RNeasy Microkit (Qiagen, Catalog: 74004), and cDNA libraries were prepared from poly A RNA (mRNA) using the Smart-Seq2 single-cell protocol (Picelli, et al., 2014, Nat. Protoc. 9, 171–181) with some modifications.

overall_design: To investigate functional differences between TILs with higher or lower capacity to uptake a blood-transported 2-deoxyglucose analog (2-NBDG), 4 mice bearing subcutaneous LLC tumors were injected with intravenous 2-NBDG to label T cells with greater or lesser capacity to uptake the probe.


title: Inhibition of METTL3 by STC-15 induces RNA misprocessing that results in dsRNA formation and activates innate immunity [GLORI]

city: Cambridge

first: Harry

last: Fischl

address: Babraham Research Campus

country: United Kingdom

institute: Storm Therapeutics

summary: The RNA methyltransferase METTL3 is responsible for the generation of m6A, the most abundant modification mark on mRNA and long non-coding RNA. Accumulating evidence suggests numerous roles of METTL3 in cancer initiation and progression and highlights the potential for targeting this enzyme in oncology. STC-15 is a potent and selective METTL3 inhibitor and the first RNA modifying enzyme inhibitor to enter human clinical development. It is structurally related to the previously published tool inhibitors STM2457 and STM3675. We previously identified the induction of a cancer cell-intrinsic interferon response following pharmacological inhibition of METTL3, leading to activation of T-cell-mediated anti-tumour response. Here, we profiled m6A levels at nucleotide resolution using GLORI and characterised RNA changes following METTL3 inhibition with STC-15 or STM3675. Following loss of m6A, we uncovered aberrant mRNA transcripts arising from intron retention (IR) and transcriptional run-on (RO) events downstream of m6A-enriched exons in human cancer cells and in tumour samples in vivo. We found that these IR and RO events produce double-stranded RNA and are bound by the cytoplasmic dsRNA sensor MDA5.Using preclinical in vitro and in vivo models, we characterised in detail the anti-tumour immune responses induced by STC-15. Our study reveals how METTL3 inhibition leads to dsRNA accumulation, which triggers a type I interferon response and induces anti-tumour immunity. Together, these findings provide a mechanistic rationale for STC-15 as a novel anti-cancer drug both as monotherapy and in combination with anti-PD1 checkpoint inhibitors.

overall_design: GLORI on polyadenylated RNA from A549, CAOV3, COV644, EFO21, OE21 and SKOV3 treated with DMSO and CAOV3 cells treated with 1 uM STM3675 for 24h


title: Inhibition of METTL3 by STC-15 induces RNA misprocessing that results in dsRNA formation and activates innate immunity [RNA-Seq MC38]

overall_design: rRNA-depleted total RNA-seq on blood and tumour samples harvested from an MC38 in vivo mouse model at time points following the last 100 mg/kg STC-15 or vehicle treatment


title: Hyperosmotic stress induces a large-scale rewiring of 3D chromatin interactions

status: Public on May 02 2026

city: Chapel Hill

first: John Patrick

last: Flores

state: NC

address: 104 Manning Dr

institute: UNC Chapel Hill

summary: Cells rapidly adapt to hyperosmotic stress through coordinated molecular responses. To determine how three-dimensional (3D) chromatin structure and chromatin accessibility contribute to this process, we profiled chromatin interactions, architectural protein occupancy, open chromatin regions, and transcriptional dynamics in human cells exposed to sorbitol-induced hyperosmotic stress. We performed time-resolved Hi-C to measure stress-induced remodeling of chromatin loops and domains, CUT&Tag to quantify CTCF, RAD21, YAP1, and H3K27ac occupancy at loop anchors, ATAC-seq to map changes in chromatin accessibility before and after sorbitol treatment, and RNA-seq to capture stress-responsive transcriptional programs. These data reveal global loss of pre-existing chromatin contacts and concurrent formation of de novo, transient loops enriched for retained CTCF and cohesin, alongside widespread changes in chromatin accessibility and transcriptional responses that are temporally layered and largely decoupled from loop remodeling. This dataset provides a resource for investigating how nuclear architecture, chromatin accessibility, and transcriptional regulation respond to hyperosmotic stress.

overall_design: eGFP-YAP HEK293 cells were serum-starved for 1 hour and then exposed to 200 mM sorbitol to induce hyperosmotic stress. Chromatin organization was profiled by in situ Hi-C at eight time points (0 min, 10 min, 30 min, 1 h, 3 h, 6 h, 12 h, and 24 h) to capture the formation, loss, and recovery of chromatin interactions. To assess the generality of chromatin remodeling, additional Hi-C experiments were performed in HEK293 wild-type and HCT116 cells with and without 1 hour of sorbitol treatment. Chromatin accessibility was profiled by ATAC-seq in untreated and 1-hour sorbitol-treated eGFP-YAP HEK293 cells to identify changes in open chromatin regions. Transcriptional responses were measured by stranded RNA-seq across a time course (0 h, 1 h, 3 h, 6 h, 9 h, 12 h, and 24 h). To quantify changes in architectural protein occupancy, CUT&Tag for CTCF and RAD21 was performed in untreated and 1-hour sorbitol-treated HEK293 cells.

first: JP

first: Andrea A.

last: Perreault

first: Zack

last: Drum

first: Chenxi

last: Xu

first: Doris

last: Cruz Alonso

first: Gelila

last: Petros

first: Yijia

first: Ivana Y.

last: Quiroga-Barber

first: Isha

last: Sahasrabudhe

first: Justin

last: Demmerle

first: Gang Greg

first: Danfeng

last: Cai

first: Douglas

last: Phanstiel


title: Adaptive Hypothesis Testing of Body Color Polymorphism in Rana dybowskii: From Behavior to Transcription

city: Harbin

first: Yicheng

last: Duan

address: No.26 Hexing Road, Xiangfang District, Harbin, P.R.China

institute: Northeast Forestry University

summary: To explore the adaptive mechanisms and molecular basis of body color polymorphism in Rana dybowskii, we conducted body color plasticity experiments, color plate preference behavioral experiments, COI gene-based phylogenetic analysis, and multi-tissue transcriptome sequencing on red, black, and white body color morphs. The results showed that R. dybowskii exhibited significant background-dependent body color plasticity, with rapid darkening or lightening in response to black/white background stimulation. Behavioral experiments revealed that all three morphs displayed a significant active preference for black-colored environments (P<0.05), but contrary to the initial hypothesis, none showed a preference for the environment matching its own body color. Phylogenetic analysis indicated that the genetic distances of black and red morphs from the reference R. dybowskii sequence fell within the range of intraspecific variation, while the white morph showed some genetic differentiation; however, the overall degree of genetic differentiation was limited. Following stringent transcriptome screening (CV<0.8), only a small number of differentially expressed genes were retained. KEGG pathway enrichment analysis of these filtered genes revealed significant enrichment of specific pathways in pairwise comparisons, showing tissue-specific and inter-group differences. This study reveals the complexity of body color polymorphism in R. dybowskii across phenotypic, behavioral, genetic, and molecular levels, though the specific ecological and physiological roles of the three color morphs remain to be elucidated.

overall_design: RNA-seq profiling of skin, liver, and oviduct tissues from red, black, and white body color morphs of Rana dybowskii, with three biological replicates per morph per tissue.

first: Zhiyu

last: Guo

first: Jiajun

last: Zhang

first: Yinzi

last: Ye


title: Loop extrusion by cohesin plays a role in enhancer-activated gene expression early in differentiation (RNA-Seq, CapC)

city: Oxford

first: Felice

middle: Hoching

last: Tsang

state: Oxfordshire

address: John Radcliffe Hospital/Headley Way

department: Weatherall Institute of Molecular Medicine

institute: University of Oxford

summary: Enhancers and their target promoters often come into close physical proximity when activated. This may be explained by a variety of mechanisms, including cohesin-mediated chromatin loop extrusion. However, acute depletion of cohesin does not cause widespread changes in gene expression. We have tested the role of cohesin-mediated loop extrusion in gene expression at the mouse alpha-globin locus during erythropoiesis. Acute depletion of cohesin disrupts alpha-globin expression at early but not late stages of differentiation. Furthermore, when single or multiple CTCF sites, known to block cohesin, are placed between the alpha-globin enhancers and promoters, alpha-gene expression is disrupted. Importantly, the CTCF site’s orientation is critical, suggesting that within this activated domain, in definitive erythroid cells cohesin predominantly but not exclusively, translocates from the enhancers to the promoters. We find that loop extrusion does play an important role in establishing enhancer-promoter proximity and consequent expression of inducible genes during differentiation.

overall_design: NG CaptureC was performed for EB derived erythroid (CD71) cells, either in triplicate for RAD21-dTAG treated and control EB cells, Forward CTCF insertion (clones D2H3, D3F3, F2D3) and wild type) or duplicate (Reverse CTCF insertion(clones F2G6 and D3H2). Capture was performed with biotinylated oligonucleotides targeting sequences adjacent to DpnII sites. Probes were divided into pools targeting upstream CTCF sites (HS38/HS39), the main enhancers (R1/R2) and downstream CTCF sites (HS44/48), except for one reverse sample (F2G6) which was probed with a combined upstream CTCF/enhancer pool and a seperate downstream CTCF pool. Probes used in the RAD21-dTAG experiment are targeting the Hba-a1 promoter and the R2 enhancer region.

first: Rosa

middle: J

last: Stolper


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

city: Hong Kong

first: Jian

last: Yan

address: 83 Tat Chee Avenue, Kowloon

institute: City University of Hong Kong

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

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

first: Xi

last: Wang

first: Wenju

last: Sun

last: Wu


title: Bulk RNA-seq of head tissue from wild-type and twist mutant Nematostella vectensis

city: Vienna

first: Patricio

last: Ferrer Murguia

state: Vienna

address: Djerassiplatz 1

country: Austria

institute: University of Vienna

summary: The basic helix-loop-helix transcription factor Twist plays roles in mesodermal development and tissue morphogenesis. To assess transcriptional changes associated with loss of Twist function, we performed bulk RNA-seq on head tissue, including tentacles, from wild-type and twist mutant Nematostella vectensis animals exhibiting neoplasm-like development.

overall_design: Head tissue, including tentacles, was dissected from wild-type animals and twist mutant animals exhibiting neoplasm-like development. Three biological replicates per condition were collected and processed for paired-end bulk RNA sequencing. Gene-level counts were generated using featureCounts and differential gene expression was analysed using edgeR.

last: Ferrer Muguia

first: Ulrich

last: Technau


title: Integrated Transcriptome and Metabolome Analysis Dissecting the Interaction between Cultivated Solanum lycopersicum and Tomato Brown Rugose Fruit Virus

city: Baoding

first: jun

address: No. 437 Dongguan Street, Baoding City, Hebei Province, China

institute: Plant Protection Institute, Hebei Academy of Agriculture and Forestry Sciences

summary: Tomato brown rugose fruit virus (ToBRFV) is an emerging and destructive tobamovirus. To elucidate its interaction with tomato (Solanum lycopersicum), we performed an integrated transcriptomic and metabolomic analysis. Compared to mock-inoculated plants, we identified 4,477 differentially expressed genes and 91 differentially accumulated metabolites. Notably, L‑Histidine was significantly upregulated while the flavonol quercetin was downregulated in response to infection. Functional validation via exogenous application revealed that L‑Histidine enhanced the expression of defense-related genes and activated the ethylene signaling pathway, whereas quercetin treatment upregulated genes involved in the MAPK signaling cascade. Collectively, our integrated multi-omics analysis and functional validation reveal that L‑Histidine acts as a positive immune inducer while quercetin contributes to antiviral defense through distinct signaling pathways. These findings provide novel insights into the molecular basis of tomato-ToBRFV interaction and highlight potential targets for antiviral strategies.

overall_design: RNA-seq profiling of healthy tomato leaves (mock-inoculated) and ToBRFV-infected tomato leaves.

first: Jun

first: Dianping

last: Di

first: Fei

last: Yang

first: Aihong


title: Pregnancy induced TRM cells protect against breast cancer [scRNAseq]

city: Clayton

first: Wei

last: Shi

state: Victoria

address: 15 Innovation Walk

department: Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute

country: Australia

institute: Monash University

summary: Age and parity are well-known factors that influence breast cancer development (1-3). Epidemiological studies have shown that women who have had multiple pregnancies are at a lower risk of developing breast cancer than women who have no history of pregnancy (4, 5). However, mechanisms that link parity and cancer protection are unclear. We discovered that CD8+ T cells with a tissue-resident memory (TRM) phenotype enriched in the mammary glands of parous women and mice compared to their virgin counterparts. Developmental kinetics revealed that these cells seeded the mammary gland during early gestation but persisted post lactation and was specific to the mammary glands. While these CD8 T cells expressed the TRM specific transcription factor Hobit, single cell transcriptomics revealed expansion of transcriptionally distinct canonical and non-canonical TRM populations, including a novel Hobit+ innate T cells (ITCs) in the parous mammary gland compared to their virgin counterparts. Furthermore, imaging analysis uncovered that the TRM like cells were associated with mammary epithelial cells and impairment in mammary gland branching during pregnancy significantly affected their differentiation or population expansion. In keeping with their association with mammary epithelial cells, all TRM subsets, including the Hobit+ITCs commonly required the cytokines TGF-β and IL-15 for their differentiation. Notably, depletion of CD103+ T cells exacerbated tumour growth in parous mice and lineage tracing experiments revealed that the canonical TRM like cells switched to an effector phenotype in tumours and contributed to tumour control. Together, we show for the first time that parity induces novel and heterogenous TRM like populations in the mammary gland that are central in providing protection against breast cancer.

overall_design: Live CD8 T cells (CD45+ TCRB+ CD8a+) were sorted from virgin and parous 4th mammary fat pad.

first: Ajithkumar

last: Vasanthakumar

first: Tabinda

last: Hussain

first: Liam

last: Neil

first: Bhupinder

last: Pal

first: Adelynn

last: Tang

first: David

last: Chisanga

first: Axel

last: Kallies


title: Promoter strength and position govern promoter competition via transcript-dependent insulation

city: Stanford

first: Joanna

last: Wysocka

state: California

address: 265 Campus Drive

institute: Stanford University

summary: Competition between promoters within a shared regulatory landscape has been implicated in development and disease, but the determinants of promoter competition remain unclear. Here, we introduce diverse promoters into defined genomic sites within the Sox2 locus and measure how these insertions attenuate endogenous Sox2 expression. We find that the level of reduction in endogenous Sox2 transcription is correlated with the strength of the inserted promoter. Transcription from the inserted promoter is required for competition, with longer transcript resulting in more competition. The inserted active promoter and its associated transcriptional unit function as an insulator, rendering competition position-dependent. Finally, we observe HUSH-mediated silencing of the inserted promoters, which counteracts competition. Together, our work uncovers the rules governing promoter competition, highlights its impact on tuning gene expression levels and genome evolution, and suggests that transcripts of sufficient level and length can mediate insulation independently of CTCF and cohesin.

overall_design: ChIP-seq of RNA Polymerase II (Pol2) and cohesin subunit Rad21 on edited F123 mouse embyronic stem cells

first: Mervenaz

last: Koska

first: Masahiro

last: Nagano

first: Tomek

last: Swigut

first: Alistair

last: Boettiger

first: Anders

last: Hansen


title: Mitochondrial Fission Factor (MFF) regulates mitochondrial Ca2+ homeostasis and neuronal activity in AgRP neurons

city: Cologne

first: Jens

last: Brüning

address: Gleueler Str. 50

institute: Max Planck Institute for Metabolism Research

summary: Mitochondria represent central regulators of neuronal function, and their network is dynamically restructured via fission and fusion. The mitochondrial fission factor (MFF) serves as an adaptor protein that recruits and organizes the core fission machinery at the outer mitochondrial membrane. Here, we investigated the role of MFF in AgRP neurons of the arcuate nucleus of the hypothalamus (ARC) in their regulation of systemic energy homeostasis. We demonstrated that mice lacking MFF in AgRP neurons exhibited increased mitochondrial size, both in AgRP neuron somata and their axonal compartments. This translated into increased mitochondrial Ca2+ uptake capacity, increased mitochondrial membrane potential, and a shift toward a more reduced mitochondrial NAD(P)H redox state. Ultimately, these changes resulted in increased neuronal excitability and neurotransmitter release to functionally enhance dynamic food intake during energy state transitions. Collectively, MFF-dependent mitochondrial fission links cell type-specific neuronal mitochondrial dynamics via mitochondrial Ca2+-handling to control of systemic metabolism.

overall_design: TRAP-seq of AgRP neuron-specific Mff knockout hypothalamic arcuate nucleus tissue from 11–12-week-old mice, using pooled (n=3 mice/replicate, 3–4 replicates/group) control (Mff^wt/wt) and experimental (Mff^fl/fl) samples with GFP-tagged RpL10a immunoprecipitation for ribosome-associated mRNA enrichment.

first: Almudena

last: del Río-Martín


title: Impact of Intestinal Propionate Metabolism on Systemic Metabolic Homeostasis

city: Baltimore

first: Michael

middle: J.

last: Wolfgang

state: MD

address: 855 N Wolfe Street

department: Institute for Basic Biomedical Sciences

institute: The Johns Hopkins University School of Medicine

summary: Propionate is an abundant short-chain fatty acid in mammals, largely derived from gut microbiota production. Due to its abundance, propionate metabolism is essential to maintain systemic homeostasis. Inborn errors of essential metabolic enzymes in this pathway causes severe illness, such as the development of Propionic Acidemia in cases of Propionyl-CoA Carboxylase (PCC) deficiency. We and others have previously developed mouse models deficient in Pcca, encoding the alpha subunit of PCC, to study the systemic and liver-specific mechanisms of propionic acidemia. However, the role of PCC in the intestine, where propionate is primarily absorbed, is understudied. To investigate the gut-specific role of PCC, we developed a mouse knockout of Pcca using Villin-Cre (Pcca Vill) on a floxed Pcca (Pcca ff) background. Here, we demonstrate the phenotypes present in this model provided both a standard (chow) and high fat (HFD) diets.

overall_design: To examine the local impact of Pcca deficiency on colonic transcription, we collected colon samples from Villin-Cre Pcca knockouts and Pcca ff littermate controls fed standard chow or high fat diet. We also collected colon samples from chow-fed liver-specific Pcca knockouts (developed previously using Albumin-Cre). We assessed the transcriptional profile of these colon samples via RNAseq.

first: Jasmine

last: Encarnacion


title: Enhancer regulation of OSR2 in mandibular incisor agenesis susceptibility [RNA-Seq]

city: Nanjing

first: Liwen

last: Fan

address: Hanzhong Road 140

institute: Nanjing Medical University

summary: Mandibular incisors are the most frequently congenitally absent teeth in Asian populations, affecting mastication, speech, aesthetics, and oral and maxillofacial functions over the long term. However, the genetic etiology of mandibular incisor agenesis (MIA) remains obscure. In this study, we conducted the first genome-wide association study on MIA in a Chinese population and identified an enhancer variant rs71514987 associated with an increased risk of MIA (odds ratio = 2.18, 95% confidence interval = 1.83-2.58, P = 3.62×10-19). Functional characterization indicated that rs71514987 C allele reduced the binding affinity of GATA4 to the OSR2 promoter, leading to increased OSR2 expression via remote regulation. Notably, elevated OSR2 levels promoted cell proliferation but diminished cell differentiation, migration, and apoptosis capabilities in stem cells from human exfoliated eciduous teeth (SHED), as well as abnormal development of pharyngeal teeth in zebrafish models. Mechanistic experiments further revealed that OSR2 bound to the promoter region of CXCR4, promoting its transcription level in the GPCR pathway, thereby influencing odontogenic differentiation during tooth development. Our findings provide novel insights into the molecular etiology of MIA.

overall_design: Stem cells from human exfoliated deciduous teeth (SHED) at passages 2-4 were divided into two groups: (1) control SHED cells transduced with empty vector (control group), and (2) SHED cells with stable overexpression of OSR2 (OSR2-OE group). Each group contained three independent biological replicates (total n=6 samples). All cells were cultured in α-MEM supplemented with 10% fetal bovine serum and 1% penicillin/streptomycin at 37°C in a 5% CO₂ incubator. After 48 hours of culture, total RNA was extracted using an RNA isolation kit (Vazyme, China) and reverse-transcribed into cDNA. Sequencing was performed on an Illumina NovaSeq 6000 platform.

first: Xinyu

last: Zhang

first: Ji

last: Mao

first: Barbara

last: Vona

first: Xinze

last: Xu

first: Mulong

last: Du

first: Lan

last: Ma

first: Yongchu

last: Pan


title: Single-cell transcriptomic analysis of lipoprotein transport in yolk sac membrane endodermal epithelial cells of chicken embryos

status: Public on May 01 2026

city: Taipei

first: Jie Ci

last: Wu

address: Roosevelt Rd.

country: Taiwan

institute: National Taiwan Unviersity

summary: This study investigates the transcriptional landscape of yolk sac membrane (YSM) endodermal epithelial cells in chicken embryos using single-cell RNA sequencing. The yolk sac membrane plays a critical role in nutrient absorption and transport, particularly in lipoprotein metabolism during early embryonic development.  Single-cell RNA sequencing was performed on YSM samples collected at embryonic day 4 (E4) and embryonic day 7 (E7). After quality control filtering, high-quality cells were retained for downstream analysis. Clustering analysis identified distinct cellular populations, and gene expression profiles were analyzed to characterize functional differences across developmental stages.  The processed data include filtered gene expression matrices, cell barcode annotations, gene feature annotations, and cell-level metadata including clustering assignments. Raw sequencing data are available in the Sequence Read Archive (SRA).

overall_design: Yolk sac membrane (YSM) tissues were collected from chicken embryos at embryonic day 4 (E4) and embryonic day 7 (E7). Single-cell suspensions were prepared and processed using the BD Rhapsody system.  Sequencing reads were processed to generate gene expression count matrices. Quality control filtering was applied to remove low-quality cells based on gene counts and sequencing depth. The filtered dataset was used for downstream analysis including normalization, dimensionality reduction, and clustering.  Processed data submitted to GEO correspond to the filtered dataset used in the analysis.

first: Jie-Ci

first: Zhao-Qi

last: Hu

first: Yuan-Yu

last: Lin

first: Harry John

last: Mersmann

first: Shih-Torng

last: Ding


title: MRE11 suppresses germline mutagenesis at meiotic double-strand breaks in mice

city: Ann Arbor

first: Agnieszka

last: Lukaszewicz

address: 1241 East Catherine Street

department: Human Genetics

institute: University of Michigan Medical School

summary: SPO11 forms hundreds of double-strand breaks (DSBs) to initiate meiotic recombination that is normally error-free. However, SPO11 activity can be mutagenic when one chromatid incurs closely spaced DSBs (double cuts), especially when DSBs are dysregulated by loss of the ATM kinase. De novo indels and structural variants can arise via end joining at double cuts within a single hotspot (microdeletions) or at adjacent hotspots separated by at least 30 kb, as we now show, sometimes accompanied by ectopic insertions of double-cut fragments. Here, we investigate how meiotic DSB end processing influences end joining. In MRE11-deficient mouse spermatocytes, which do not resect their DSBs, deletions at double cuts occur readily, with end-joining breakpoint profiles closely matching SPO11 DSB profiles. Microdeletions suggest that two DSBs can be as close as ~21 bp. The tyrosyl DNA phosphodiesterase TDP2 contributes to both deletion formation and ectopic insertion of double-cut fragments, presumably by removing SPO11 from DNA ends prior to joining. Finally, observations suggest a cooperative role for MRE11 and ATM in locally regulating DSB distributions. Our findings provide insight into the mechanism of de novo mutation origin, emphasizing the role of meiotic DSBs in shaping genome evolution.

overall_design: Detection of deletions in the absence of MRE11 at a single mouse DSB hotspot on Chr1 using amplicon deep sequencing. Four overlapping amplicons across the hotspot were amplified.

first: Thomas

last: Wilson

first: Scott

last: Keeney

first: Maria

last: Jasin


title: Pivotal Role of the NuRD Complex in Remodeling Chromatin Environment and Maintaining Genome Architecture at CTCF Sites [mESC_d0246_CTCF_MBD3_ChIP_Seq]

first: Jian

last: Yan

state: Hong Kong Special Administrative Region

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

first: Xi

last: Wang

first: Wenju

last: Sun


title: Antigen-scaffolds loaded with hyper-stable Neoleukin-2/15 expand antigen-specific T cells with a favorable phenotype for adoptive cell therapy

city: Kgs. Lyngby

first: Kamilla Kjærgaard

last: Munk

address: Henrik Dams Allé, 204

department: Department of Health Technology

country: Denmark

institute: Technical University of Denmark

summary: Adoptive cell therapy (ACT) has shown promising results in cancer treatment, however, achieving effective ex vivo expansion of potent, functionally active, and cytotoxic T cells remains challenging. To address this challenge, we recently developed artificial antigen-presenting scaffolds (Ag-scaffolds) capable of expanding antigen-specific T cells with phenotypes favorable for ACT.  In this study, we compared the established technology using IL2/IL21-loaded Ag-scaffolds (Ag-IL2/21) with Neoleukin-2/15-loaded Ag-scaffolds (Ag-Neo2/15). Neoleukin-2/15 (Neo2/15) is an engineered cytokine that selectively binds to IL-2Rβ/γ receptors, enhancing CD8+ T cell proliferation while limiting regulatory T cell expansion. Based on its favorable signaling properties, we hypothesized that incorporating Neo2/15 as part of the Ag-scaffolds would improve the quality and functionality of expanded T cells.  We showed that Ag-Neo2/15 scaffolds promoted significant T-cell expansion, with frequencies of antigen-specific CD8+ T cells comparable to those achieved with Ag-IL2/21 scaffolds. The CD8+ T cells expanded with Ag-Neo2/15 scaffolds exhibited potent TNFα and IFNγ, potentially enhancing their therapeutic potential. T cells expanded with Ag-Neo2/15 scaffolds had superior and durable cytotoxicity against tumor target cells compared to T cells expanded with Ag-IL2/21 scaffolds. These findings were further supported by our single-cell analysis revealing that T cells expanded with Ag-Neo2/15 scaffolds had higher cytotoxic scores and lower dysfunctionality scores compared to T cells expanded with Ag-IL2/21 scaffolds. The single-cell analysis also indicated increased expression of genes linked to cell division and enhanced proliferative capacity in Ag-Neo2/15 expanded T cells. Furthermore, TCR clonality analysis demonstrated that Ag-Neo2/15 scaffolds promoted the expansion of functionally superior T-cell clones, as the top clones of CD8+ T cells expanded with Ag-Neo2/15 scaffolds exhibited a favorable phenotype, essential for effective antigen recognition and sustained T-cell mediated cytotoxicity.  Our findings suggest that Ag-Neo2/15 scaffolds represent an advancement in ACT by producing high-quality, functional antigen-specific T cells. This method has the potential to improve clinical outcomes in cancer therapy by generating large numbers of highly functional T cells, thereby optimizing the balance between cytotoxicity and proliferation capacity with less exhausted T-cells in expansion protocols.

overall_design: We performed a single-cell analysis using antigen-specific T cells from two healthy donors to investigate differences between cells expanded with Ag-Neo2/15 scaffolds and those expanded using conventional strategies. In this analysis, we examined the transcriptome, surface proteome, and T-cell clonality of both unexpanded T cells, as well as T cells expanded using free peptide, IL-2 and IL-21, Ag-IL2/21 scaffolds, and two different Ag-Neo2/15 scaffolds (Neo-3x and Neo-12x).

last: Ormhøj

first: Kamilla

middle: K

first: Siri

last: Tvingsholm

first: Keerthana

last: Ramanathan

first: Amalie

last: Bentzen

first: Georgios

last: Kladis

first: Gitte

middle: N

last: Aasbjerg

first: Grigorii

last: Nos

first: Tripti

last: Tamhane

first: Hólmfridur

middle: R

last: Halldórsdóttir

first: Søren

last: Jakobsen

first: Marcus

last: Frej

first: Kristoffer

last: Johansen

first: Mohammad

last: Kadivar

first: Sine

last: Hadrup


title: Comparative transcriptome analysis of Pantoea, Micrococcus, Pseudomonas, and Herbaspirillum under ferric chloride (FeCl3) treatment

city: Gunsan

first: Sang Eun

last: Jeong

state: Jeonbuk (Jeollabuk-do)

address: 558 Daehak-ro

country: South Korea

institute: Kunsan National University

summary: This study provides comparative RNA-seq datasets for four freshwater bacterial isolates, Pseudomonas sp. FBCC-B13192, Herbaspirillum sp. FBCC-B12834, Pantoea sp. FBCC-B5559, and Micrococcus sp. FBCC-B5738, cultured under iron-replete (+100 uM FeCl3) and iron-limited (no FeCl3) conditions. Iron availability is a key factor influencing bacterial fitness, and iron limitation is known to activate siderophore biosynthesis, iron transport, and homeostasis pathways.  A total of eight libraries generated in 2024 and 2025 were analyzed, comprising 349.9 million processed reads. Reference-guided mapping rates varied among strains, with higher mapping efficiency observed in Pseudomonas, Herbaspirillum, and Pantoea, while Micrococcus showed comparatively lower mapping rates under both conditions.  Differential expression analysis revealed strain-specific responses to iron limitation. Genes related to pyoverdine and ferrichrome uptake were enriched in Pseudomonas and Herbaspirillum, enterobactin-associated pathways were prominent in Pantoea, and genes associated with siderophore production, heme utilization, and Fe-S cluster assembly were identified in Micrococcus.  Raw sequencing data are available in the NCBI Sequence Read Archive under BioProject PRJNA1456794, and processed data are deposited in a public repository. These datasets provide a valuable resource for understanding bacterial adaptation to iron availability and for comparative transcriptomic analyses.

sample_organism: Pseudomonas Herbaspirillum Micrococcus Pantoea

overall_design: Four bacterial strains, Pseudomonas sp. FBCC-B13192, Herbaspirillum sp. FBCC-B12834, Pantoea sp. FBCC-B5559, and Micrococcus sp. FBCC-B5738, were cultured under two conditions: iron-replete (+100 uM FeCl3) and iron-limited (no FeCl3). Total RNA was extracted from each culture and used to construct cDNA libraries. Paired-end RNA sequencing was performed using an Illumina platform.  For each strain, transcriptomic profiles under FeCl3-treated and control conditions were compared to identify differential gene expression associated with iron availability. Reads were quality filtered and mapped to their respective reference genomes, and gene expression levels were quantified for downstream comparative analysis.

first: Hyo Jung

last: Lee


title: Transcriptome of mouse brain perivascular macrophages (PVM) by RNA-seq

city: Wuhan

first: Huang

last: Hongqing

address: 1095 Jiefang Avenue, Qiaokou District, Wuhan, Hubei, P.R. China

institute: Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology

summary: This project includes transcriptome sequencing (RNA-seq) data of perivasccular macrophages (PVM) isolated from mouse brain. The goal is to compare the gene expression of PVM between young adult and aged mice to investigate aging-related changes.

overall_design: Comparism of PVM gene expression between young adult (3 months) and aged (18 months) C57BL/mice. 5 biological replictaes for age group, 7 for young adult group.


title: Loop extrusion by cohesin plays a role in enhancer-activated gene expression early in differentiation (ChIP-Seq, Rad21 and Stag2)

first: Felice

last: Tsang

overall_design: To confirm binding of CTCF, RAD21, and STAG2 to the newly inserted site and confirm recruitment to existing sites, we performed ChIP-seq in erythroid (Ter119) fetal liver cells and EB derived erythroid (CD71) cells. Fetal liver data is biological triplicates and EB data is biological duplicates (independent ES clones (Fwd: D2H3, F2D3. Rev: D2D6, D3H2)/independent differentiations for WT).

first: Rosa

last: Stolper


title: Transcriptomic Insights into the Adaptive Colonization of Escherichia coli O157:H7 during Production and Storage of Alfalfa Sprout

city: COLUMBUS

first: Ahmed

middle: E.

last: Yousef

state: Ohio

address: 2015 Fyffe Road

department: Food Science and Technology

institute: the Ohio State University

summary: Shiga toxin-producing Escherichia coli (STEC) is a major foodborne pathogen associated with raw produce such as sprouts, where it encounters fluctuating nutrient, temperature, and oxidative stress. This study elucidated the global transcriptional adaptations of E. coli O157:H7 EDL933 during colonization and persistence on alfalfa sprouts under simulated commercial sprouting and refrigerated storage. RNA sequencing was used to compare STEC grown in tryptic soy broth (D0), colonizing fresh sprouts for 5 days (D5), and held during sprout refrigeration for additional 3 days (D8). Among 5,002 expressed genes, 782 and 826 were differentially expressed (DEGs; |log2FC| ≥ 2, adjusted p < 0.05) at D5 vs. D0, and D8 vs. D0, respectively, whereas 11 genes only differed in the D8 vs. D5 comparison, indicating that the STEC transcriptome was largely stabilized by the time sprouts reach maturity, with refrigeration inducing minimal further shifts.  Transition of STEC from nutrient rich broth to sprout tissues induced a profound metabolic reprograming, characterized by the up-regulation of de novo amino acid biosynthesis (e.g., hisA–H, leuABCD, and ilv operons), to compensate for nitrogen limitation within sprout tissues. STEC further adapted to sprout environment by inducing high-affinity uptake systems for potassium (kdpA/B/C/F), phosphorus (pstSCAB), and sulfur (tauABCD), alongside enterobactin-mediated iron acquisition. To survive sprout microenvironment, STEC elevated the transcription of acid resistance (gadA/C, cadA/B), oxidative stress defense (sodA, katE/G), and envelope protection (degP, pspA–D, baeS) genes. Although initial colonization at D5 involved the induction of flagellar components, the transition to a sessile biofilm-associated lifestyle at D8 was marked by the repression of motility genes and the strong induction of curli fimbriae (csg) and colanic acid (wca) loci. Functional enrichment at D5 and D8, compared to D0, indicated coordinated stress regulation and translation. The major transcriptional trends observed in RNA seq were confirmed using RT-qPCR. Collectively, these findings highlight a multi tiered molecular adaptation strategy, enabling STEC adaptation and persistence in sprout environment, thus, providing insights that could be translated into STEC risk mitigation during sprout production

overall_design: Comparing global gene expression profiles of STEC cells harvested after five days of growth on sprouting alfalfa followed by three days of refrigeration with those of cells grown in tryptic soy broth (TSB) to early stationary phase.

first: Mostafa

last: Ali

last: Abdelhamid


title: A suppressor screen uncovers flu as a weak mutant and chloroplastic 1O2 triggers EX1-independent stress responses in Arabidopsis

city: Beijing

first: Liangsheng

last: Wang

address: No. 2 Yuanmingyuan West Road

institute: China Agricultural University

summary:
•	Singlet oxygen (1O2) is the main ROS produced in chloroplasts, particularly under environmental stress conditions. Studies using the Arabidopsis conditional flu (flu1-1) mutant have shown that chloroplastic 1O2 acts as a signal, activating retrograde signaling that eventually leads to photoinhibition or cell death.
•	Through a forward genetic screen for suppressors using EMS-mutagenized Arabidopsis flu1-1/ex1 mutants, we isolated two suppressor mutants (mut1 and mut2) that restored 1O2-induced stress responses. Using combined methods of map-based cloning and high-throughput sequencing, we mapped the causal mutations in both mut1 and mut2 to the FLU gene again.
•	We verified that the widely used flu1-1 is not the long-recognized null mutant, but rather a weak allele, encoding a variant that binds weakly to GluTR1 and leads to partial shutdown of tetrapyrrole biosynthesis in darkness. We further found that the FLU-knockout mutants produce more 1O2, activating transcriptional changes, enzymatic lipid peroxidation, and PCD even in the absence of EX1. Overexpression of SAFE1 suppressed 1O2-induced PCD in mut2 in a dosage-dependent manner.
•	Collectively, our findings redefine the nature of the widely used flu1-1 mutant and reveal that excessive 1O2 can overwhelm the inhibitory effect of endogenous SAFE1 and induce stress responses independently of EX1.

overall_design: Six-day-old flu1-1/ex1 and flu1-5/ex1 seedlings were kept in the dark for 4 h, or kept in the dark for 4 h followed by reillumination for 1 h. Total RNAs were extracted and subjected to standard RNA-Seq process.

first: Fan

last: Zhang

first: Jingrui

last: Li


title: PGC-1alpha pathway dysregulation disrupts myofiber specification in a mouse model of SBMA

first: Andrew

middle: P

last: Lieberman

state: MI

address: 1150 W Medical Center Dr.

institute: University of Michigan

summary: Skeletal muscle pathology is a critical but poorly understood contributor to neuromuscular degeneration in spinal and bulbar muscular atrophy (SBMA), a CAG/polyglutamine (polyQ) expansion disorder caused by mutation in the androgen receptor (AR). Using a gene-targeted SBMA mouse model, we applied single-nucleus RNA sequencing to identify a previously unrecognized, disease-specific population of skeletal muscle myonuclei that replace normal myonuclear subtypes. This transition was driven by dysregulation of the PGC-1α pathway, a central regulator of myofiber specification and metabolic identity. PGC-1α dysfunction in SBMA muscle was age-, hormone-, and polyQ length–dependent and was partially rescued by subcutaneous delivery of AR-targeted antisense oligonucleotides. Integrated ChIP-seq and RNA-seq analyses revealed that aberrant PGC-1α activity promoted the expression of a distinct set of myofiber specification genes while downregulating those defining healthy Type IIb and Type IIx myonuclei. We propose a model in which this dysfunction arose downstream of polyQ-mediated sequestration of PGC-1α cofactors MEF2, CREB, and CBP, leading to transcriptional reprogramming and cellular dysfunction. These findings implicate PGC-1α dysregulation as a key event linking AR polyQ expansion to skeletal muscle degeneration and suggest a shared mechanism for polyQ-mediated muscle pathology across related neurodegenerative diseases.

overall_design: All mice used in this study were of the C57BL/6J strain. RNA was extracted and sequenced from male WT, R6/2 transgenic, or SCA1 Q154 mice. Tissue samples used were all skeletal muscle: tibialis anterior at 24 weeks for SCA1 Q154, quadriceps at 12 weeks for R6/2 transgenic, and an equal number of age- and tissue-matched controls from WT.

first: Curtis

last: Kuo

first: Laura

middle: B

last: Chopp

first: Zhigang

last: Yu

first: Luhan

last: Ni

first: Hien

middle: T

last: Zhao

first: Janghoo

last: Lim


title: NPAS3-regulated astrocyte mitochondria bioenergetics is required for cognition

city: Buffalo

first: Henry

middle: G.

last: Withers

address: Elm and Carlton Streets

department: Biostatistics and Bioinformatics

institute: Roswell Park Comprehensive Cancer Center

summary: The basic helix-loop-helix (bHLH) transcription factor neuronal PAS domain protein 3 (NPAS3) provides transcriptional regulation of metabolic pathways, and despite its name is highly expressed in astrocytes. NPAS3 variants have been associated with cognitive dysfunction in several neuropsychiatric conditions, but the underlying brain cell type-specific mechanisms remain obscure. Here, we report that NPAS3 is a key regulator of mitochondria bioenergetics in astrocytes. Selective deletion of Npas3 in mature murine astrocytes decreases expression of Slc25a18 and its protein product, mitochondrial glutamate carrier 2, leading to reduced oxidative phosphorylation and lactate production in astrocytes. This deficit subsequently causes reduced excitability, dendritic spine density, and dendritic arborization of medial prefrontal cortex pyramidal neurons. Mice with Npas3-deficient cortical astrocytes exhibit impaired trace fear conditioning, which is rescued by lactate treatment. Thus, the present study demonstrates a mechanistic link between NPAS3-dependent astrocyte mitochondria bioenergetics and cognitive function and provides insights for glia-targeting treatment of cognitive dysfunction in neuropsychiatric disease.

overall_design: To investigate the role of Npas3 in the regulation of energy metabolism in astrocytes, we utilized mouse model of constitutive knockout of Npas3. We then performed gene expression profiling analysis using data obtained from RNAseq of forebrain tissue from heterozygous Npas3+/- and wildtype Npas3+/+ mice at embryonic day 16-17.

first: Mikhail

middle: V

last: Pletnikov

first: Kateryna

last: Murlanova

first: Juhyun

last: Kim

first: Frederick

middle: C

last: Nucifora Jr

first: Russell

middle: L

last: Margolis

first: Dong

middle: W


title: RNA profiling of wild-type and hnRNP A1/A2B1-knockout splenic B cells

city: shenzhen

first: Zhijian

last: Zhu

state: guangdong

address: 1088 Xueyuan Blvd, Nanshan

institute: southern university of science and technology

summary: The production of high-affinity antibodies is crucial for the human body to defend against microbial infections. This process requires the germinal center (GC) reaction of B cells, which generates high-affinity plasma cells. The development of germinal center B (GCB) cells is tightly regulated at multiple levels, including transcriptional, post-transcriptional, and epigenetic mechanisms. Among these, alternative splicing (AS), a key post-transcriptional regulatory process, plays an essential role in mediating B cell development and differentiation. The heterogeneous nuclear ribonucleoprotein (hnRNP) family is a major group of regulators of alternative splicing. hnRNP A1 and hnRNP A2B1 are the two most abundantly expressed RNA-binding proteins in this family, yet their functions in B cells remain unclear. In this study, we generated CD19-Cre-mediated conditional knockout mice for hnRNP A1 and hnRNP A2B1, and performed RNA sequencing to analyze the mRNA expression and alternative splicing events regulated by hnRNP A1 and hnRNP A2B1 in splenic B cells.

overall_design: To investigate how hnRNP A1 and hnRNP A2B1 regulate the germinal center B cell response, we utilized a Cre-loxP-mediated double knockout (DKO) mouse model for hnRNP A1 and hnRNP A2B1. We examined the changes in global RNA expression and alternative splicing in splenic B cells from wild-type (WT) and DKO mice, both under basal conditions and upon stimulation with anti-CD40 and anti-IgM.

first: Xijun

last: Ou


title: The chloroplast translocon subunit TOC33 relays singlet oxygen-induced chloroplast-to-nucleus retrograde signaling in Arabidopsis

first: Liangsheng

last: Wang

summary: Chloroplasts engaged in oxygenic photosynthesis frequently overproduce reactive oxygen species (ROS) under stress conditions, with singlet oxygen (1O2) being particularly harmful due to its high reactivity and short lifespan. The nuclear-encoded chloroplast protein EXECUTER1 (EX1) senses elevated 1O2 levels through Trp643 oxidation and undergoes proteolysis, a process essential for activating 1O2-induced EX1-mediated chloroplast-to-nucleus retrograde signaling (1O2-EX1 signaling). However, the link between EX1 proteolysis and subsequent nuclear transcriptome changes remains unclear. In this study, we isolated SOF1 (suppressor of flu 1) through a forward genetic screen using EMS-mutagenized flu mutant seeds of Arabidopsis thaliana harboring Flag-fused EX1 driven by its native promoter (referred to as fluEX1). Like flu, fluEX1 plants conditionally produce 1O2 in chloroplasts upon a dark-to-light shift. In the fluEX1 sof1, all 1O2-induced stress responses are largely suppressed, despite 1O2 levels being similar to those in the fluEX1. SOF1 encodes the chloroplast outer envelope-anchored preprotein import receptor TOC33. While TOC33 loss does not affect EX1 import, abundance, localization, and 1O2-induced proteolysis in the chloroplast, it blocks 1O2-induced chloroplast-to-nucleus retrograde signaling. TOC33 interacts with the UVR domain of EX1 (EX1-UVR) in the chloroplast envelope, facilitating 1O2-induced decrease of the chloroplast EX1-UVR and increase of the nucleus EX1-UVR. Moreover, ectopic expression of EX1-UVR outside of the chloroplast bypasses the restrictive barrier imposed by the chloroplast envelope, activating 1O2 signaling and inducing stress responses. Our findings demonstrate that SOF1/TOC33 mediates 1O2-EX1 signaling from the chloroplast to the nucleus and that the EX1-UVR domain can substitute for full-length EX1 in this signaling pathway.

overall_design: Six-d-old flu and flu/toc33-1 seedlings were kept in the dark for 4 hours, or kept in the dark for 4 hour followed by reillumination for 1 hour. Total RNAs were extracted and subjected to standard RNA-Seq process.

first: Huan

first: Fan

last: Zhang

first: Jingrui


title: Innate and Acquired Transcriptional Programs Shape Heterogeneous Tumor Cell Responses to PARP, Akt, and CDK4/6 Inhibitors

city: Austin

first: Amy

last: Brock

state: Texas

address: 107 W Dean Keaton St.

department: Biomedical Engineering

institute: University of Texas at Austin

summary: Targeted therapies are increasingly utilized across cancer types, yet their efficacy in triple-negative breast cancer (TNBC) remains limited due to the disease’s high heterogeneity and aggressive nature. In a heterogeneous tumor, treatment failure can occur due to the presence of therapy-tolerant cells, which may either be innately drug-tolerant or readily adaptive to therapy cytotoxicity. To investigate how transcriptomic heterogeneity influences response and adaptation to targeted therapy in TNBC, this study leverages the ClonMapper cell barcoding system combined with single-cell RNA sequencing (scRNA-seq) to track differential responses of DNA barcoded clonal subpopulations during treatment with PARP-, Akt-, and CDK4/6-targeting therapy. For the three different targeted therapies, distinct innate and acquired gene signatures, unique to each therapy type, are shown to be predictive of a cell’s level of persistence during treatment. This work demonstrates that non-genetic heterogeneity plays a central role in response and resistance to targeted therapy, highlighting the need to consider tumor heterogeneity to guide effective use of targeted chemotherapy in TNBC.

overall_design: Three TNBC cell lines - UACC-2087, UACC-3199, and 885512-J2 296-R PDC, were barcoded with the ClonMapper barcoding technology. Each cell line was treated individually with the PARP inhibitor olaparib, AKT inhibitor ipatasertib, and CDK4/6 inhibitor palbociclib, and an untreated control condition, with three replicates each, generating 36 samples. Unbarcoded control samples from each cell line were included. Palbociclib-treated UACC-3199 failed to survive and were not included. scRNA-seq was performed with the Parse Biosciences Evercode library prep kit with added CRISPR-detect functionality. Because ClonMapper barcodes are expressed as CRISPR gRNA, the CRISPR-detect kit generated barcode reads for each cell in the dataset. Whole-transcriptome libraries are included with a WT_ prefix for raw .fastqs and as wt.h5ad for a processed annotated data matrix. Barcode counts for each cell, quantified from CRISPR-detect, are included with a CR_ prefix for raw .fastqs and as bc.h5ad for a processed annotated data matrix.

first: Michael

last: Cotner


title: Promoter strength and position govern promoter competition via transcript-dependent insulation [Micro-C]

first: Joanna

last: Wysocka

overall_design: Micro-C with capture of Sox2 locus in mouse embryonic stem cells, with different promoter integrations.

first: Mervenaz

last: Koska

first: Masahiro

last: Nagano

first: Tomek

last: Swigut

first: Alistair

last: Boettiger

first: Anders

middle: S

last: Hansen


title: Overexpression of galectin-1 promotes cell invasion of unique migratory glioblastoma subpopulation in tumor-brain mechanical interface model

first: Stephanie

last: Seidlits

address: 107 W. Dean Keeton Street Austin

institute: The University of Texas

summary: Glioblastoma (GBM) is the most common primary brain tumor characterized by extensive infiltration into peritumoral brain tissue. GBM tumors exhibit substantial intratumoral heterogeneity making it difficult to identify and target invasive cell subpopulations. In this study, an interface hydrogel model matching in vivo tissue stiffness was utilized to investigate transcriptomic changes in GBM clonal subpopulations as cells migrate across mechanical interfaces. Using single-cell RNA sequencing combined with clonal lineage tracing, unique migratory clonal subpopulations were identified that preferentially migrate at the interface. These cells exhibit a distinct pre-invasive transcriptomic profile characterized by overexpression of galectin-1, a β-galactosidase binding protein. Our findings reveal overexpression of galectin-1 is an innate characteristic of the migratory cells and that expression level is correlated to invasion rate. This study provides insight into the mechanobiological mechanisms underlying GBM invasion and potential therapeutic targets for the invasive population.

overall_design: ScRNAseq was used to investigate the effects of stiffness on the transcriptome of migratory and non-migratory cells in two GBM patient-derived cell lines. Patient-derived GBM cells were encapsulated into stiff, tumor-like hydrogels and interfaced with soft, brain-like hydrogels. A soft-soft interface hydrogel was used as a control. Cells were cultured in interface hydrogels for 14 days. After 14 days, the hydrogels were separated and cells were extracted. Four experimental groups were formed corresponding to the gel stiffness where the cells initially originated and the migration status of the cells; soft migrating, soft non-migrating, stiff migrating, and stiff non-migrating. Samples were prepared with 10X Chromium Single Cell 3ʹ v3 kit.

first: Talia

last: Sanazzaro

first: Neha

last: Arvinth