title: Liver macrophage changes during early adaptation to alcohol exposure

city: Kansas City

first: Sumedha

last: Gunewardena

state: Kansas

address: 2146 West 39th Avenue

department: Dept. of Molecular and Integrative Physiology

institute: University of kansas medical center

summary: Liver macrophages consist of both Kupffer cells (KCs) and infiltrating macrophages (IM), and both populations change during alcohol associated liver disease. It has been suggested that KCs undergo a pro-inflammatory change after alcohol exposure, but the extent to which a pro-inflammatory shift results from IMs rather than KC activation is unclear. The purpose of this study was to examine the early effects of alcohol exposure on KCs and IMs in a murine model and compare these effects to observations in human liver. Mice were fed the Lieber-Decarli ethanol diet and total liver macrophage, and KC specific phenotypes were examined by flow cytometry, ex vivo cell culture and KC single cell RNAseq. Liver tissues from autopsy and transplant patients with different alcohol phenotypes were assessed. Early alcohol exposure caused a shift in the properties of total liver macrophages with an initial pro-inflammatory effect that partially resolved by 10 days. KCs became steadily less inflammatory over the first 10 days of alcohol exposure. Alcohol exposure in the absence of liver disease also shifted macrophage phenotypes in human livers. These results show that early alcohol exposure is sufficient to cause KC adaptation in a way that maintains liver homeostasis and limits inflammation. Understanding the mechanisms of these changes and how to sustain them may help prevent the development of long-term liver injury.

overall_design: We performed scRNAseq of liver Kupffer cells from chow fed mice and mice fed the Lieber-DeCarli liquid diet with 5% ethanol for either 3 or 10 days (n=1 mouse for each condition. Total nonparenchymal cells (NPCs) were isolated by liver perfusion, and FACS sorted F4/80-high, CD11b-intermediate cells were sequenced. Sequencing yield averaged 3,000-5,000 cells per sample and results from all 3 animals were combined for initial clustering.

first: Kyle

last: Yuquimpo

first: Janice

last: Averilla

first: Zhuan

last: Li

first: Priyanka

last: Ghosh

first: Sheetalnath

last: Rooge

first: Isabel

last: Aranzazu Pulido Ruiz

first: Winston

last: Dunn

first: Ann

last: Wozniak

first: Irina

last: Tikhanovich

first: Steven

last: Weinman


title: Inhibition of Acetyl-CoA metabolic enzymes by EVT0185 impairs hepatic stellate cell activation and reverses MASH and fibrosis in mouse models.

status: Public on Nov 17 2025

city: Hamilton

first: Russta

last: Fayyazi

state: ON

address: 1280 Main St W

department: Medicine

country: Canada

institute: McMaster University

type: Expression profiling by high throughput sequencing

summary: Metabolic Dysfunction-Associated Steatohepatitis (MASH) is characterized by liver steatosis and inflammation which lead to fibrosis following hepatic stellate cell (HSC) activation. Acetyl-CoA is fundamental for de novo lipogenesis (DNL) and cholesterol synthesis and can be derived from citrate via ATP citrate lyase (ACLY), or from acetate via acetyl-CoA synthetase (ACSS2). Here, we find that EVT0185, an ACLY and ACSS2 inhibitor, leads to resolution of MASH and fibrosis while lowering insulin and glucose in four distinct mouse models. EVT0185 also reduces fibrosis alone and in combination with semaglutide and more effectively than bempedoic acid in a model not characterized by steatosis or insulin resistance. Spatial transcriptomic and scRNAseq reveal marked downregulation of cholesterol synthesis in HSCs with EVT0185 treatment in vivo and in vitro. These data indicate a critical role for ACLY and ACSS2 in HSCs and suggest further clinical evaluation of EVT0185 for reducing MASH and fibrosis may be warranted.

overall_design: To investigate transcriptomic effects of EVT0185 treatment on activated human hepatic stellate cells (HSCs), bulk RNA-seq data was obtained from LX-2 cells, a human HSC immortalized cell line. Two cell lines were generated from the LX-2 cells: One stably expressing an empty control vector (PRP-empty) or another expressing human SLC27A2 (PRP-SLC27A2). All cells were treated with TGFB1 to induce the activated HSC phenotype, and either DMSO or 30 µM EVT0185 for 24 hours. Overall, 4 experimental conditions of n = 3 replicates were generated: PRP-empty DMSO; PRP-empty EVT0185; PRP-SLC27A2 DMSO; PRP-SLC27A2 EVT0185.

first: Fiorella

last: Di Pastena

first: Jaya

last: Gautam

first: James

last: Lally

first: Estelle

last: Grasset

first: Gregory

middle: R

last: Steinberg


title: Antioxidant program of islet-resident macrophages preserves β cell physiology [dataset 3]

city: Paris

first: Nicolas

last: Venteclef

address: 156 rue de Vaugirard

country: France

institute: Institut Necker Enfants Malades, INSERM U1151

summary: Macrophages residing inside mouse pancreatic islets have an activated phenotype at steady-state. We revealed that they also harbor an antioxidant profile driven by the cystine/glutamate antiporter SLC7A11. We thus explored the role of SLC7A11 in islet-resident macrophages under steady-state.

overall_design: Islets were isolated and pooled from 6-8 myeloid Slc7a11-MacWT and MacKO (LysMCre/+Slc7a11fl/fl ) mice and dissociated into single cells to FACS-sort CD45+ immune cells. Cells were used for single cell RNA sequencing using 10X genomics.

first: E

last: Dalmas

first: A

last: Jalon

first: M

last: Diedisheim


title: Transcriptomic analysis of nanoceria treatment in light-induced retinal degeneration in rat

city: Messina

first: Luigi

last: Donato

state: Italy

address: via Consolare Valeria, 1

department: BIOMORF

country: Italy

institute: University of Messina

summary: Retinal neurodegenerative diseases such as Age-related Macular Degeneration (AMD) and Retinitis Pigmentosa cause irreversible vision loss due to the limited regenerative capacity of the mammalian retina. Cerium oxide nanoparticles (nanoceria) are emerging therapeutics against oxidative stress and inflammation, major drivers of photoreceptor degeneration, but their mechanisms remain incompletely understood. We performed retinal transcriptomic analysis in a rat AMD model induced by high-intensity light and treated intravitreally with nanoceria. Six groups were analyzed: control, light damage, vehicle, nanoceria, vehicle + light damage, and nanoceria + light damage. Light damage activated inflammatory and apoptotic programs, with upregulation of cytokines (Tnf, Il6, Il1b, Ccl2) and downregulation of photoreceptor genes (Rho, Pde6a/b, Gnat1). Nanoceria treatment counteracted these effects, suppressing pro-inflammatory mediators, restoring antioxidative genes (Nfe2l2, Gclc, Sod2), and enhancing neuroprotective factors (Bdnf, Cntf, Ngf). Pathway analyses revealed inhibition of TNF/NF-κB/IL-17 signaling and activation of PI3K-Akt, JAK-STAT, and neurotrophin pathways. Unexpectedly, nanoceria also modulated amino acid and insulin metabolism (Ass1, Cps1, Insr, Irs1, Slc2a4) and reactivated transcription factors (Ascl1, Sox2, Notch1) typically silent in adult retina. Our findings highlight nanoceria as a multifunctional therapeutic that mitigates retinal degeneration by coordinating oxidative, inflammatory, and regenerative responses, supporting its translational potential to preserve vision in retinal neurodegenerative disease.

overall_design: Six experimental groups were analyzed: control, light damage, vehicle, nanoceria, vehicle + light damage, and nanoceria + light damage (n = 6–7 animals per group). Retinal RNA-seq was performed on Rattus norvegicus (paired-end 150 bp, Illumina NovaSeq 6000). Differential expression and pathway analyses were conducted to assess the impact of nanoceria treatment.

first: Darin

last: Zerti

first: Ignacio

last: Babiloni-Chust

first: Matthias

last: Carl

first: Carmela

last: Rinaldi

first: Lucia

last: Poggi

first: Rosalia

last: D’Angelo

first: Rita

last: Maccarone


title: A disintegrin-like and metalloproteinase with thrombospondin motifs 18 (ADAMTS18) cleaves fibronectin and regulates its fibrillogenesis

city: Kuopio

first: Nihay

last: Laham Karam

address: Neulaniementie 2

department: A.I. Virtanen Institute

country: Finland

institute: University of Eastern Finland

summary: Remodelling of the extracellular matrix plays a crucial role in the development, maintenance and repair of all tissues. Therefore, identifying the regulators of this process is essential. Among these, A disintegrin and metalloproteinase with a thrombospondin motif 18 (ADAMTS18) has been implicated in fibronectin (FN) matrix regulation. Knockout of ADAMTS18, either in mouse models or in vitro, was shown to lead to FN accumulation, mutation in epithelial branching and reduction in endothelial sprouting. However, the mechanisms by which ADAMTS18 influences endothelial specific functions and the extracellular matrix, particularly in the regulation of FN fibrils remains unclear. In this study, using both siRNA-mediated knockdown and overexpression of ADAMTS18 in primary endothelial cells, we delineated some of these mechanisms.  Using global RNA sequencing of endothelial cells we demonstrated differential gene regulation of vessel-development and endothelial adhesion genes with ADAMTS18-siRNA knockdown, whereas cell matrix and cell cycle associated genes were affected by overexpression of ADAMTS18. Consistent with the later, we observed reduced endothelial cell proliferation and altered cell cycle with ADAMTS18 overexpression. Using mass spectrometry, we identified two sites in FN that are proteolytically cleaved by ADAMTS18, including a cleavage site in the linker FN-I5-6. Cleavage at this site generated FN molecules lacking the N-terminal FN-I1-5 (29kDa) fragment that is known to be essential for FN fibrillogenesis. Accordingly, ADAMTS18 overexpression greatly impaired FN fibrillogenesis in endothelial cultures and in co-culture with fibroblasts. Our results implicate ADAMTS18 in FN-associated extracellular matrix remodelling and suggest an important role for ADAMTS18 in endothelium biology.

overall_design: The aim of this study was to study the effects of siRNA knockdown of human ADAMTS18 on gene expression over time. Human umbillical endothelial cells (HUVECs) were transfected with siRNA to knockdown ADAMTS18. For siRNA knockdown, dicer-substrate oligonucleotides hs.Ri.ADAMTS18.13.1, hs.Ri.ADAMTS18.13.2, hs.Ri.ADAMTS18.13.3 and DsiRNA control (TriEFCTA Kit DsiRNA Duples; IDTDNA) were transfected into HUVECs at a concentration of 10nM using Oligofectamine (Thermo Fisher Scientific, #12252011). HUVECs were collected 24 or 96 hours after transfection and RNA isolated. The cDNA library and RNA sequencing were performed at AZENTA.

last: Laham-Karam

first: Maria

last: Barbiera

first: Seppo

last: Ylä-Herttuala

first: Mikko

last: Gynther

first: Tetsuya

last: Terasaki

first: Suvi

last: Jauhiainen

first: Johanna

middle: p

last: Laakkonen

first: Michael

last: Jeltsch


title: BRD2 Bromodomain-Mediated Regulation of Cell State Plasticity Modulates Therapy Response in Glioblastoma

city: San Diego

first: raghavendra

last: vadla

state: CA

address: sanford consortium for regenerative medicine, 2880 Torrey Pines Scenic Drive

country: USA

institute: UCSD

summary: Background: Glioblastoma (GBM) displays remarkable cell state plasticity, a major contributor to therapeutic resistance and tumor progression. While epigenetic mechanisms play a central role in driving this plasticity, the key regulators remain poorly understood, and developing effective therapeutic strategies targeting them has been challenging. Methods: We investigated the role of BRD2, a key regulator of NF-κB mediated mesenchymal (MES) transition, using GBM patient-derived xenograft (PDX) cell lines, CRISPR-mediated knock-in/knockout approaches, RNA-seq, and in vitro and in vivo modeling. BET inhibitors were employed to target MES gene expression and sensitize GBM to radiation therapy. Results: We found that PTEN loss induces RelA chromatin localization and acetylation-mediated recruitment of BRD2 to the MES gene promoters. BRD2 binding is essential for maintaining MES gene expression and phenotype. Genetic ablation or loss-of-function mutation of BRD2 bromodomains reverses MES transition, enhances radiation sensitivity, and improves survival in orthotopic xenograft models. Additionally, treatment with a brain-penetrant BD2-selective inhibitor suppresses the MES phenotype and increases radiation sensitivity of GBM stem cells in vitro. Conclusion: Our study identifies BRD2 as a key mediator of MES transition in GBM, with its bromodomains playing a crucial role in driving cell state plasticity. Targeting BRD2 with BD2-selective inhibitors offers a promising therapeutic strategy to overcome radiation resistance and improve outcomes for GBM patients.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: To investigate the role of the NF-κB/BRD2 signaling axis in regulating mesenchymal transition in glioblastoma (GBM), we utilized multiple patient-derived glioma stem cell (GSC) lines. We established the following experimental conditions: CRISPR/Cas9-mediated knock-in mutantion of RelA, shRNA-mediated knockdown lines for BRD2, GSCs expressing BRD2 bromodomain point mutants to dissect domain-specific functions and GSCs treated with GSK620, a BET bromodomain inhibitor, to assess pharmacologic perturbation effects. For transcriptomic profiling, RNA-seq was performed on all experimental conditions and their respective controls, with biological triplicates for each sample type.

first: Raghavendra

last: Vadla

first: Frank

last: Furnari


title: Bile acids regulate lipid metabolism through selective actions on fatty acid absorption

city: Los Angeles

first: Thomas

middle: Q

last: de Aguiar Vallim

address: MRL 3230/3240 675 Charles E. Young Drive South

department: Cardiology

institute: University of California, Los Angeles

summary: Intestinal lipid absorption, the entry-point for fats into the body, requires the coordinated actions of bile acids and lipases. Here, we uncover distinct yet cooperative roles of bile acids in driving the differential uptake of dietary fatty acids. We first decreased bile acid pool size by disrupting the rate-limiting enzyme in bile acid synthesis, Cyp7a1, using liver-directed gene editing in mice. Compared to lipase inhibition, reduced bile acids prevented diet-induced obesity, increased anorectic hormones, suppressed excessive eating, and improved systemic lipid metabolism. Remarkably, decreasing bile acids selectively decreased absorption of saturated fatty acids, but preserved polyunsaturated fatty acids. By targeting additional bile acid enzymes, we identified specific functions of individual bile acid species. Mechanistically, we show that cholic acid preferentially solubilizes polyunsaturated fatty acids into mixed micelles for intestinal uptake. Our studies demonstrate that bile acids can selectively control fatty acid uptake, revealing insights for future interventions in metabolic disease.

overall_design: RNA-seq profiling of livers obtained from control CRISPR and Cyp7a1 CRISPR mice fed Western diet for 8 weeks.

first: Alvin

middle: P

last: Chan

first: Kelsey

middle: E

last: Jarrett

first: Rochelle

middle: W

last: Lai

first: Madelaine

middle: C

last: Brearley-Sholto

first: Angela

middle: S

last: Cheng

middle: O

last: Taveras

first: Anne

middle: M

last: Iwata

first: Michelle

last: Steel

first: Andrew

last: Lau

first: Emily

last: Whang

first: John

last: Kennelly

first: Yajing

last: Gao

first: Gabriella

last: Rubert

first: Heidi

last: Schmidt

last: Smith

first: Baolong

last: Su

first: Kevin

middle: J

last: Williams

first: Elizabeth

last: Tarling


title: Transcriptomic Profiling of Escherichia coli and Salmonella enterica Reveals Regulatory Roles of the 3′ UTR-Derived sRNA UhpU Under Various Growth Conditions

city: Shanghai

first: Chuan

last: Wang

address: 131 # Dong An Road

country: China

institute: Fudan University

summary: To investigate the biological function and regulatory impact of the 3′ UTR-derived small RNA (sRNA) UhpU, we performed transcriptomic analyses in both Escherichia coli and Salmonella enterica under multiple growth conditions. These include short-term pulse expression of UhpU in minimal medium supplemented with glucose-6-phosphate (G6P) or LB medium, as well as a comparative transcriptomic analysis of wild-type and ΔuhpTU deletion strains during LB growth. This dataset provides insight into UhpU’s regulatory roles in metabolic adaptation and its evolutionary diversification across species.

sample_organism:
Escherichia coli
Salmonella enterica subsp. enterica

overall_design: Three sets of RNA-seq experiments were conducted: 1.Pulse Expression in S. enterica During G6P Metabolism: The 72-nt Salmonella UhpU sequence was cloned downstream of the arabinose-inducible PBAD promoter and expressed in a ΔuhpTU background strain. Cultures were grown in M9CA medium with 0.1% glucose-6-phosphate (G6P) to OD₆₀₀ ~0.5, induced with 0.2% L-arabinose for 10 minutes, and RNA was extracted. An empty vector control was included for comparison. Non-stranded RNA-seq libraries were generated after DNase I treatment. 2.Pulse Expression in E. coli During LB and G6P Growth: The 265-nt E. coli UhpU sequence was similarly cloned and expressed in a ΔuhpTU strain. Cultures were grown either in LB medium to OD₆₀₀ ~1.0 or in M9CA with 0.1% G6P to OD₆₀₀ ~0.5. UhpU expression was induced with 0.2% L-arabinose for 10 minutes. RNA was extracted and processed as above, with the empty vector serving as a negative control.3.Comparative Transcriptomics of Wild-Type and ΔuhpTU E. coli Strains: To assess the endogenous role of UhpU, RNA was isolated from wild-type and ΔuhpTU E. coli strains grown in LB (Miller) medium to OD₆₀₀ ~1.0. Stranded RNA-seq libraries were prepared after DNase I treatment to compare transcriptomic differences attributable to the absence of UhpU under standard conditions.

first: Cheng

last: Bei

first: Qian


title: Codon-mediated translational control of M. oryzae effectors

city: Lincoln

first: Richard

middle: A.

last: Wilson

state: NE

institute: University of Nebraska-Lincoln

summary: Magnaporthe oryzae, the fungus causing rice blast disease, deploys effectors to manipulate host immunity. Apoplastic effectors are secreted conventionally, whereas cytoplasmic effectors are deployed into the biotrophic interfacial complex (BIC) via the unconventional protein secretion (UPS) pathway. Using reverse genetics and live-cell imaging, we previously showed that the translation of cytoplasmic (but not apoplastic) effector mRNAs relies on efficient decoding of AA-ending codons by the Uba4-dependent thiolation of wobble uridine-34 (s2U34) in cognate tRNAs. Loss of UBA4 abolished cytoplasmic effector secretion. Synonymous AA- to AG-ending codon changes in PWL2 mRNA and (we show here) AVR-Pik mRNA restored cytoplasmic effector production and secretion in Δuba4 strains. In WT, expressing recoded PWL2 or AVR-Pik led to the loss of translational speed control, massive protein production, and super-secretion into the BIC, which destabilized, abolishing infection. In PWL2, mutational analysis shows only one AA-ending codon is required for optimizing translation speed and maintaining BIC integrity, highlighting how codon usage choice on fine scales underpins the success of the M. oryzae-host rice plant interaction. We also show here how cytoplasmic effector secretion from other host-infecting M. oryzae lineages is similarly subjected to Uba4-dependent codon control, indicating it is a conserved, fundamental principle of host infection shaping effector evolution.

overall_design: RNA-seq profiling of rice leaves infected with wild-type Magnaporthe oryzae at 36 hours post-inoculation (hpi), with mock-treated samples as controls.

first: Gang

last: Li


title: An unbiased whole- genome open -reading frame overexpression screen identifies B3GALT2, a novel inducer of cellular ASO activity

city: Basel

first: Roland

last: Schmucki

address: Grenzacherstrase

country: Switzerland

institute: F. Hoffmann - La Roche AG

summary: Antisense oligonucleotides (ASOs) are a promising class of therapeutics, made out of chemically modified synthetic single-stranded nucleic acid molecules, yet their clinical translation is often hindered by challenges in cellular uptake and delivery. Identifying cellular factors that modulate ASO activity is crucial for overcoming these limitations. Utilizing a whole-genome open-reading frame (ORF) overexpression screen with a genetic splice reporter system to identify genes that can increase or decrease ASOs activity, we identified B3GALT2 as the most significant hit for increasing ASO activity. Subsequent validation in HEK293 and U2OS cell lines demonstrated that B3GALT2 overexpression consistently and significantly enhances the activity of both splice-switching and mRNA-degrading ASOs across different targets (CD81, MALAT1, CERS2). Transcriptomic analysis of B3GALT2-overexpressing cells showed upregulation of endocytic scavenger receptors CUBN and SCARA5, and gene set enrichment analysis indicated an enrichment of proteins involved in clathrin-dependent endocytosis. Mechanistic investigations revealed that B3GALT2 overexpression leads to a significant increase in ASO uptake. These findings highlight B3GALT2 as a novel modulator of ASO cellular entry and establish a new avenue for potentially improving ASO-based therapeutic strategies.

overall_design: Comparison of transcriptomic profiles of HEK293 cells under three conditions: wild-type, cells with doxycycline-inducible B3GALT overexpression, and control cells carrying an empty vector. Induction with doxycycline (0 ng/mL) was performed for 72 hours, and RNA was extracted for sequencing. The key variable under investigation is the effect of B3GALT2 overexpression on gene expression.

first: Julia

last: Hesselmann

first: Liza

last: Malong

first: Fililp

last: Roudnicky


title: Impaired cortical development and translational control in a missense mouse model of DDX3X syndrome

city: Aurora

first: Nicole

middle: D

last: Moss

address: 1775 Aurora Ct

institute: University of Colorado

summary: Heterozygous mutations in the X-linked RNA helicase DDX3X cause DDX3X syndrome, a rare neurodevelopmental disorder associated with cortical malformation and autism. Amongst the ~200 known de novo DDX3X variants, half are missense while the others are predicted loss-of-function (LoF). LoF mouse models reveal DDX3X loss impairs progenitors’ ability to generate excitatory neurons. Yet, how missense mutations impact corticogenesis in vivo is unknown. Here, we generated a conditional mouse model of Ddx3xT532M, a clinically severe and recurrent DDX3X syndrome mutation found in females. Using Cre-mediated expression of Ddx3xT532M in cortical progenitors and their progeny, we show this mutation alters corticogenesis and translation. Ddx3xT532M conditional knock-in (KI) males have severe microcephaly and apoptosis. In contrast, Ddx3xT532M conditional heterozygous (cHet) females exhibit only mild reductions in cortical size and neurogenesis. Using polysome fractionation of Ddx3xT532M and Ddx3xLoF cHet female cortices, we discover that Ddx3xT532M affects translation of key targets, with qualitative differences from Ddx3xLoF cHet females. Collectively, these cellular and molecular findings suggest that, the clinically severe Ddx3xT532M variant in cHet females is phenotypically similar to, but molecularly distinct from, Ddx3x haploinsufficiency in corticogenesis. Our study establishes a new model for understanding how missense mutations may cause DDX3X syndrome.

overall_design: Polysome fractionation RNA-Seq from E14.5 mouse cortex comparing Ddx3x-LoF  (Emx1-Cre/+;Ddx3x lox/+) to control (Ddx3x lox/+) and Ddx3x-T532M (Emx1-Cre/+;Ddx3x-T532M lox/+) to control (Emx1-Cre/+).

first: Abigail

last: Poff

first: Debra

middle: L

last: Silver


title: Metabolic quiescence of naïve-like memory T cells precedes and maintains antigen-specific T-cell memory

city: Erlangen

first: Kilian

last: Schober

address: Wasserturmstraße 3/5

department: Mikrobiologisches Institut – Klinische Mikrobiologie, Immunologie und Hygiene

country: Germany

institute: Uniklinikum Erlangen/ Friedrich-Alexander-Universität Erlangen-Nürnberg

summary: Metabolic activity shapes cell fate but remains challenging to capture in vivo with high resolution. We performed longitudinal metabolic and phenotypic profiling of human antigen-specific CD8+ T cells after yellow-fever vaccination on the single-cell level. During the acute phase, T cells upregulated glycolysis to fuel anabolic needs of proliferation, but predominantly used oxidative phosphorylation for energy production, as assessed via protein translation rates. Central memory T cells were the most active subset, while effector cells underwent metabolic shut-down. In contrast, weakly differentiated naïve-like memory T cells showed minimal activity, relying solely on oxidative phosphorylation already during the acute phase. Reinforcing the link between cellular quiescence and longevity, naïve-like memory cells were preferentially maintained even 26 years post vaccination. This association between differentiation degree and metabolic activity was conserved after SARS-CoV-2 vaccination and in two murine infection models. Our study dissects the metabolic profile of antigen-specific T-cell responses ex vivo, highlighting quiescence as a key feature for long-term immunological memory formation in humans.

overall_design: Yellow Fever Virus (YFV)-specific CD8+ T cells from human blood before and after YFV-vaccination were were identified by DNA-baroded pMHC multimers (Dextramers) in three independent experiments. Cells were stained with DNA-barcoded CITEseq antibodies for surface markers (among them CD45RA,CD62L,CD95), cells from 27 different donors and  11 time-points were labelled with TotalSeq-C anti-human hashtag antibodies and samples were pooled for further processing. CD8+ T cells specific for eight different  YFV-epitopes (including the HLA-A2-restricted NS4B214 epitope)  and five different control-virus epitopes, as well as cells without dextramer staining were sort-isolated by FACS. Cells were subjected to 5' scRNAseq on a 10x Genomics platform including VDJ-sequencing and  CITEseq for Dextramers, hashtag and surface marker antibodies.

first: Sina

last: Frischholz

first: Ev-Marie

last: Schuster

first: Myriam

last: Grotz

first: Christine

last: Schülein

last: Benz

first: Katharina

last: Kocher

first: Lucia

last: Klotz

first: Szilard

last: Varga

first: Theresa

last: Hiltner

first: Rayya

last: Alsalameh

first: Jan

last: Esse

first: Johannes

last: Träger

first: Jürgen

last: Held

first: Frederik

last: Graw

last: Pahle

first: Bernd

last: Spriewald

first: Luca

last: Gattinoni

first: Veit

last: Buchholz

first: Felix

last: Drost

first: Benjamin

last: Schubert

first: Simon

last: Rothenfußer

first: Dirk

middle: H

last: Busch

first: Christian

last: Bogdan


title: ZFTA-RELA ependymomas produce itaconate as an oncometabolite to sustain pathogenic fusion expression [ATAC-Seq]

city: Ann Arbor

first: Arul

last: Chinnaiyan

state: MI

address: 1500 East Medical Center Dr

department: MCTP

institute: University of Michigan

type: Genome binding/occupancy profiling by high throughput sequencing

summary: ZFTA-RELA ependymomas are malignant brain tumors that are frequently lethal. They are defined by fusions formed between the putative chromatin remodeler ZFTA and the NFkB-mediator-RELA. We identified that ZFTA-RELA cells produced itaconate, a key macrophage-associated immunomodulator metabolite. However, itaconate production by tumor cells and its tumor-intrinsic role are not well-established. Itaconate is synthesized by the enzyme Aconitate Decarboxylase-1 (ACOD1) and the ZFTA-RELA fusion upregulated ACOD1 in an NFkB-dependent manner. Additionally, itaconate production enabled a feed-forward system that maintained pathogenic ZFTA-RELA fusion expression through epigenetic activation. To supply the metabolic fuel needed to generate itaconate, these tumors epigenetically activated PI3K/mTOR signaling to enhance glutaminolysis, which provided the carbons necessary for itaconate synthesis. Consequently, antagonizing glutamine metabolism lowered pathogenic ZFTA-RELA levels and was potently therapeutic in multiple in vivo models. Finally, combining glutamine antagonism with PI3K/mTOR inhibition abrogated spinal metastasis. Our data demonstrate that ZFTA-RELA ependymomas subvert a macrophage-like itaconate metabolic pathway to maintain expression of the ZFTA-RELA fusion driver, implicating itaconate as an oncometabolite. Taken together, our results position itaconate upregulation as a previously unappreciated driver of ZFTA-RELA ependymomas. This study therefore has implications for future drug development for children with this devastating brain tumor and will further our understanding of oncometabolites as a novel class of therapeutic dependencies in cancers.

overall_design: ZFTA-RELA fusion  mouse neural stem cells (mNSCs) were treated with Citraconate (ACOD1 antagonist) or an EZH2 inhibitor (GSK343)

first: Siva Kumar

last: Natarajan

first: Joanna

last: Lum

first: James

last: Haggerty-Skeans

first: Minal

last: Nenwani

first: Sanjana

last: Eyunni

first: Mateus

last: Mota

first: Jill

last: Bayliss

first: Akash

last: Deogharkar

first: Erin

middle: T

last: Hamanishi

first: Matthew

last: Pun

first: Stefan

last: Sweha

last: Hoffman

first: Eleanor

last: Young

first: Qiuyang

last: Zhang

first: Rijul

last: Mehta

first: Olamide

last: Animasahun

first: Pranav

last: Narayanan

first: Sushanth

last: Sunil

first: Abhijit

last: Parolia

first: Peter

last: Sajjakulnukit

first: Pooja

last: Panwalkar

first: Robert

last: Doherty

first: Madison

last: Clausen

first: Derek

last: Dang

first: Debra

last: Hawes

first: Fusheng

last: Yang

first: Mariarita

last: Santi

first: Alexander

last: Judkins

first: Yelena

last: Wilson

first: Thomas

last: Vigil

first: Andrea

last: Franson

first: Richard

last: Mortensen

first: Tatsuya

last: Ozawa

last: Griesinger

first: Eric

last: Holland

first: Nicholas

middle: K

last: Foreman

first: Kulandaimanuvel

last: Antony Michaelraj

first: Sameer

last: Agnihotri

first: Michael

last: Taylor

last: Gilbertson

first: Carl

last: Koschmann

first: Costas


title: Decoding cnidarian cell type gene regulation

city: Barcelona

first: Arnau

last: Sebe-Pedros

address: Dr. Aiguader 88

department: Systems Biology

country: Spain

institute: Centre for Genomic Regulation

summary: Animal cell types are defined by differential access to genomic information, yet the regulatory programs governing cell identity remain largely unexplored across the animal tree of life. We used scATAC-seq to map chromatin accessibility landscapes in ~60,000 cells from whole adult and gastrula stages of the sea anemone Nematostella vectensis. We quantified cell type-specific activity for ~112,000 cis-regulatory elements (CREs), revealing extensive combinatorial enhancer usage and distinct promoter architectures. To further decode regulatory motif grammars, we trained sequence-based models predicting CRE activity and studied ontogenetic relationships between cell types. Integrating sequence motifs with transcription factor expression and CRE accessibility, we reconstructed gene regulatory networks that define cnidarian cell identities. Our work uncovers the complexity and logic of cell type gene regulation in early-branching animals.

overall_design: Nuclei suspensions were obtained from whole adult and gastrula-stage Nematostella vectensis wild-type animals, or Fluorescent-activated cell sorting (FACS) isolated elav+ neurons from NvElav1::mOrange transgenic polyps. Single cell ATACseq (scATACseq) libraries were prepared using 10x Genomics platform

first: Elek

last: Anamaria

first: Iglesias

last: Marta

first: Sebé-Pedrós

last: Arnau


title: The Chromosome 19 miRNA Cluster Guards Trophoblasts Against Overacting Innate Immunity

city: Pittsburgh

first: Jean-Francois

last: Mouillet

state: PA

address: 204 Craft Ave

department: OBGYN

institute: University of Pittsburgh

summary: To maintain pregnancy health, the human placenta delicately balances protection of the developing fetus from invading pathogens with suppression of excessive inflammation that could lead to fetal and neonatal autoimmune disorders. Previous research, including our own, has shown that small RNA products of the Chromosome 19 MicroRNA Cluster (C19MC) utilize diverse pathways to promote viral resistance in non-trophoblastic cells. However, the role of C19MC products in placental trophoblasts remained unclear. Here, we analyzed chromatin accessibility in the C19MC enhancer and identified a previously unknown regulatory domain. Deletion of this domain silenced the expression of C19MC microRNA and Alu elements in trophoblasts. This silencing unexpectedly activated innate immunity interferon genes and markedly increased TLR3-mediated sensitivity to poly(I:C), a viral RNA mimic. Our data suggest that C19MC non-coding RNAs interfere with endosomal TLR3 activation in trophoblasts, preventing excessive innate immune activation.

overall_design: RNA-seq profiling of CRISPR-Cas9-edited BeWo cells at different locations of the C19MC promoter region, with or without poly(I:C) treatment.

first: Yingshi

last: Ouyang

first: Elena

last: Sadovsky

first: Heather

last: Sorenson

first: Logan

last: Badeau

first: Saumen

last: Sarkar

first: Tianjiao

last: Chu

first: Alexander

last: Sorkin

first: Yoel


title: Functional Comparison to Ezh2 Reveals PRC2-Independent Functions of Jarid2 in Hematopoietic Stem Cell Lineage Commitment

city: St Louis

first: Grant

middle: A

last: Challen

state: MO

address: 660 Euclid Avenue

institute: Washington University School of Medicine

summary: Our previous studies showed the Polycomb Repressive Complex 2 (PRC2) co-factor Jarid2 represses self-renewal transcriptional networks in mouse multipotent progenitor cells (MPPs).  But only a fraction of de-repressed HSC-specific genes were associated with loss of H3K27me3, implying Jarid2 may have non-canonical (PRC2-indpendent) in hematopoiesis.  Here we sought to delineate any PRC2-independnent functions by comparing stem and progenitor cells genetically deficient for either Jarid2 or Ezh2.  Loss of Ezh2 leads to increased myeloid differentiation in transplantation assays.  In contrast, loss of Jarid2 enhanced T-cell output.  Single cell transcriptomics showed while loss of Jarid2 had minimal impact across progenitor populations, loss of Ezh2 led to accumulation of lymphoid-biased MPP4 cells and B-cell progenitors in the bone marrow.  Functional assays confirmed a differentiation block at the pre-pro B-cell stage.  The maturational arrest of Ezh2-deficient B-cell progenitors contrasts with increased T-cell output from loss of Jarid2, suggesting Jarid2 has non-canonical functions in hematopoiesis.

overall_design: To explore the potentially divergent roles of the PRC2 co‑factor Jarid2 and its catalytic subunit Ezh2, we generated Mx1‑Cre conditional mouse models with floxed alleles of Jarid2 (Jarid2fl/fl) or Ezh2 (Ezh2fl/fl), enabling the targeted ablation of either gene. We then performed single-cell RNA-seq and single-cell multi-omics sequencing to dissect mechanistic differences between Jarid2 and Ezh2 loss-of-function. For Single Cell RNA-seq studies, primary recipient mice were euthanized 18 weeks post-transplant to collect cells, while two-month-old baseline mice were used for the single-cell multi-omics workflow.To further explore the potentially divergent effects of Jarid2 and Ezh2 loss of function on H3K27me3 repressive mark, we performed Cut and Tag analysis on KSL (c-Kit+, Sca1+, Lineage-) cells sorted from the 3 million WBM secondary transplanted recipients. We then assessed the whole genome and gene specific loci depletion of H3K27me3 repressive marker upon Jarid2 and Ezh2 loss of function.

first: Hassan

last: Bjeije

first: Wentao

last: Han

first: Shu

last: Lin

first: Nancy

last: Issa

first: Aishwarya

last: Krishnan

first: Infencia

last: Xavier Raj

first: Jason

last: Arand

first: Yanan

last: Li

first: Wei

last: Yang

first: Jeffrey

last: Magee


title: The LUMINIDEPENDENS protein is a general repressor of transcription in Arabidopsis [RNA-Seq 2]

city: GIF SUR YVETTE

first: Qingyi

last: Wang

address: 630 rue noeztlin

summary: Genomic integrity is constantly challenged by transcription/replication conflicts, a major source of replication stress and instability across all life forms. While extensive studies have uncovered transcription/replication conflicts resolution mechanisms in animals, yeast, and prokaryotes, their counterparts in plants remain largely unexplored. Through a forward genetic screen, we identified the LUMINIDEPENDENS (LD) protein, previously known for regulating the flowering repressor FLC, as a key player in mitigating replication stress in plants. Strikingly, transcriptomic analyses reveal that loss of LD results in the upregulation of over 13,000 genes, establishing LD as a global transcriptional repressor. Consistent with this role, LD binds a substantial portion of the Arabidopsis genome and interacts with the MED18 subunit of the Mediator complex to modulate RNA polymerase II phosphorylation. These findings uncover a fundamental function of LD in fine-tuning transcription genome-wide, with an additional role in suppressing transcription/replication conflicts by locally dampening transcription and promoting replication fork progression. Our work highlights a previously unrecognized genome-protective strategy in plants, opening new avenues for understanding transcription/replication conflict management in eukaryotic systems.

overall_design: The experimental design integrates two spike-in RNA-seq datasets (Dataset1: Arabidopsis thaliana 7-day-old plantlets of Col0, fld, and ld mutants; Dataset2: Col0, pol2a, ld, and ld pol2a mutants) and a classic RNA-seq dataset (shoot apices of Col0, ld, pol2a, and ld pol2a mutants), each with three biological replicates.

first: Clara

last: Bergis-Ser

first: Xiaoning

last: He

first: Maherun

last: Nisa

first: Vickie

last: Kaiser

first: Christelle

last: Mazubert

first: Jeannine

last: Drouin-Wahbi

first: Rim

last: Brik-Chaouche

first: Layla

last: Chmaiss

first: Jeele

last: Van Leene

first: Geert

last: de Jaeger

first: Jose

last: Gutierrez-Marcos

first: Catherine

last: Bergounioux

last: Richet-Bourbousse

first: David

last: Latrasse

first: Moussa

last: Benhamed

first: Cécile

last: Raynaud


title: The LUMINIDEPENDENS protein is a general repressor of transcription in Arabidopsis [LD ChIP-Seq]

last: Wang

overall_design: ChIP-seq samples from Arabidopsis thaliana whole plantlets of the Id mutant genotype expressing the pLD-LD-GFP fusion protein, with two biological replicates and their corresponding input controls. These samples aim to investigate the LD-GFP DNA binding under the Id mutant background. The design also incorporates RNA polymerase II phosphorylation states (S2P and SSP) and histone H3K9ac modification profiles in both wild-type (Col-0) and Id mutant genotypes, with input controls and replicates for each condition.


title: Robust classification of pediatric brain tumors from cell-free DNA methylomes

city: Memphis

first: Kyle

last: Smith

state: TN

address: 262 Danny Thomas Pl

institute: St. Jude Children's Research Hospital

type: Methylation profiling by genome tiling array

summary: Cerebrospinal fluid (CSF) liquid biopsies serve as a rich source of tumor-derived cell-free DNA (cfDNA) for evaluating patients with central nervous system (CNS) tumors. However, challenges stemming from trace cfDNA yields and low mutational burden have hindered sensitivity, whereas first-generation clinical assays have relied on genetic alterations as biomarkers. Leveraging the diagnostic utility of DNA methylation classification in CNS tumors, we developed M-PACT (Methylation-based Predictive Algorithm for CNS Tumors), a robust deep neural network that accurately classifies tumors from sub-nanogram input cfDNA methylomes acquired through enzymatic methylation sequencing. In addition to tumor classification, this workflow enables methylation-based cellular deconvolution and sensitive copy number variation (CNV) detection. We benchmark our methodology in pediatric CNS embryonal tumors and further demonstrate accurate classification of intra-operative CSF, balanced tumor genomes, and secondary malignancies. Altogether, we provide a blueprint for CNS tumor classification from low input cfDNA methylomes, motivating prospective validation for future clinical implementation.

overall_design: We aimed to profile the cell-free DNA (cfDNA) methylome of pediatric brain tumor patient and the corresponding primary tumors. Cerebral spinal fluid (CSF) cfDNA was analyzed using the Infinium MethylationEpic array.

first: Paul

last: Northcott


title: Antioxidant program of islet-resident macrophages preserves β cell physiology [dataset 4]

first: Nicolas

last: Venteclef

summary: Macrophages residing inside mouse pancreatic islets have an activated phenotype at steady-state. We revealed that they also harbor an antioxidant profile, expressing CD9. We therefore explored the transcriptomic signature of CD9high versus CD9low macrophages using single cell RNA sequencing.

overall_design: Islets were isolated and pooled from 6-8 myeloid WT mice and dissociated into single cells to FACS-sort CD45+ immune cells. Cells were used for single cell RNA sequencing using a TotalSeq-B0813 anti-mouse CD9 antibody (Biolegend Cat# 124823) and 10X genomics.

first: E

last: Dalmas

first: A

last: Jalon

first: M

last: Diedisheim


title: Targeted Antisense Oligonucleotide Treatment Rescues Developmental Alterations in Spinal Muscular Atrophy Organoids [bulk RNA-seq]

city: Rozzano

first: Simona

last: Lodato

address: via Manzoni 56

institute: IRCCS Humanitas Research Hospital

summary: Spinal muscular atrophy (SMA) is a severe neurological disease caused by mutations in the SMN1 gene, characterized by early onset and degeneration of lower motor neurons.Understanding early neurodevelopmental defects in SMA is crucial for optimizing therapeutic interventions. Using spinal cord and cerebral organoids generated from multiple SMA type I donors, we revealed widespread disease mechanisms beyond motor neuron degeneration. Single-cell transcriptomics uncovered pervasive alterations across neural populations, from progenitors to neurons, demonstrating SMN-dependent dysregulation of neuronal differentiation programs. Multi-electrode array analysis identified consistent hyperexcitability in both spinal and brain organoids, establishing altered electrical properties as a central nervous system-wide feature of pathogenesis. Early administration of an optimized antisense oligonucleotide (ASO) that restored SMN levels rescued morphological and functional deficits in spinal cord organoids across different genetic backgrounds. Importantly, this early intervention precisely corrected aberrant splicing in newly identified SMN1 targets enriched at critical nodes of neuronal differentiation. Our findings demonstrate that early developmental defects are core features of SMA pathogenesis that can be prevented by timely therapeutic intervention, providing new insights for optimizing treatment strategies.

overall_design: Spinal cord organoids (SCOs) after 2 months of in vitro differentiation from three wilde-type CTRL lines (n=3 lines, 3 individual replicates), two SMA lines (n=2 lines, 3 individual replicates) and SMA SCOs treated with r6-morpholino (MO) and r6-scrambled-MO, as negative control (n=2 lines, 4 individual replicates per each condition).

first: Irene

last: Faravelli

first: Paola

last: Rinchetti

first: Monica

last: Tambalo

first: Illia

last: Simutin

first: Lisa

last: Mapelli

first: Sara

last: Mancinelli

first: Matteo

last: Miotto

first: Mafalda

last: Rizzuti

first: Andrea

last: D’Angelo

first: Chiara

last: Cordiglieri

first: Giulia

last: Forotti

first: Clelia

last: Peano

first: Paolo

last: Kunderfranco

first: Luca

last: Calandriello

first: Giacomo

last: Comi

first: Elvezia

last: Paraboschi

first: Eleonora

last: Pali

first: Francesca

last: Beatrice

first: Egidio

first: Serge

last: Przedborski

last: Nizzardo

first: Stefania

last: Corti


title: BPTF regulstes androgen receptor activity by enhancing chromatin accessibility and stabilizing the AR-FOXA1 interaction [Cut&Run]

city: Baltimore

first: Jianfei

last: Qi

state: MD

address: 655W baltimore street

department: Biochemistry and Molecular Biology

institute: University of Maryland

summary: BPTF, the scaffolding subunit of the nucleosome remodeling factor (NURF) complex, has been implicated in the progression of various malignancies. However, its role in prostate cancer (PCa) remains poorly understood. Here, we demonstrate that BPTF is upregulated in castration-resistant prostate cancer (CRPC) and promotes disease progression. RNA-seq revealed that BPTF primarily upregulates the expression of androgen receptor (AR) target genes. ChIP-seq showed that BPTF facilitates AR binding to enhancers and super-enhancers, while ATAC-seq demonstrated that BPTF increases chromatin accessibility to facilitate AR binding, partly via SMARCA1, a catalytic subunit of the NURF complex. Notably, BPTF/AR shared ChIP-seq peaks are highly enriched for FOXA1 motifs but only weakly enriched for AR motifs. We find that BPTF interacts with both FOXA1 and AR to form a protein complex in which FOXA1 recruits BPTF-AR to chromatin, while BPTF stabilizes the AR–FOXA1 interaction. Importantly, BPTF interacts with AR through its bromodomain, and a BPTF bromodomain inhibitor disrupts this interaction, leading to impaired AR signaling and suppressed PCa cell growth. In summary, our findings establish BPTF as a critical regulator of AR activity by promoting chromatin accessibility and stabilizing the AR–FOXA1 complex, highlighting BPTF as a potential therapeutic target in prostate cancer.

overall_design: Cut&Run of BPTF, AR, and FOXA1 in Rv1 cells transduced with shControl, shBPTF, or shFOXA1. Cut&Run of BPTF and AR in Rv1 cells transduced with shControl or shAR. Cut&Run of H3K27ac, H3K4me1, and SMARCA1 in Rv1 cells transduced with shControl.

first: Hee-Young

last: Jeon


title: BPTF regulstes androgen receptor activity by enhancing chromatin accessibility and stabilizing the AR-FOXA1 interaction [RNA-Seq]

overall_design: RNA-seq profiling in Rv1 cells with knock down derivatives (shcontrol, shBPTF, shSMARCA1, shSMARCA5, and shFOXA1)


title: BPTF regulstes androgen receptor activity by enhancing chromatin accessibility and stabilizing the AR-FOXA1 interaction [ATAC-Seq]

overall_design: ATAC-seq of Rv1 cells transduced with shControl, shBPTF, or shSMARCA1.


title: Detecting the whole genomic binding of PARP1 in H1975 cells  with CUT&Tag assay.

city: Nanjing

first: Changying

last: Guo

state: Jiangsu

address: Longmian Avenue, No. 639

department: School of Life Science and Technology

institute: China Pharmaceutical university

summary: To elucidate the mechanism of EGFR-AS1 on PARP1-DNA binding at genome level, we examined PARP1 binding in response to etoposide stimulation through CUT&Tag technique in H1975 cells which overexpressing EGFR-AS1.

overall_design: Cleavage under targets and tagmentation (CUT&Tag) for PARP1 in EGFR-AS1 overexpressed H1975 cells with or without etoposide treatment.

first: Kun

last: Gao

first: Liang

last: Jin


title: A disintegrin-like and metalloproteinase with thrombospondin motifs 18 (ADAMTS18) cleaves fibronectin and regulates its fibrillogenesis

city: Kuopio

first: Nihay

last: Laham Karam

summary: Remodelling of the extracellular matrix plays a crucial role in the development, maintenance and repair of all tissues. Therefore, identifying the regulators of this process is essential. Among these, A disintegrin and metalloproteinase with a thrombospondin motif 18 (ADAMTS18) has been implicated in fibronectin (FN) matrix regulation. Knockout of ADAMTS18, either in mouse models or in vitro, was shown to lead to FN accumulation, mutation in epithelial branching and reduction in endothelial sprouting. However, the mechanisms by which ADAMTS18 influences endothelial specific functions and the extracellular matrix, particularly in the regulation of FN fibrils remains unclear. In this study, using both siRNA-mediated knockdown and overexpression of ADAMTS18 in primary endothelial cells, we delineated some of these mechanisms.  Using global RNA sequencing of endothelial cells we demonstrated differential gene regulation of vessel-development and endothelial adhesion genes with ADAMTS18-siRNA knockdown, whereas cell matrix and cell cycle associated genes were affected by overexpression of ADAMTS18. Consistent with the later, we observed reduced endothelial cell proliferation and altered cell cycle with ADAMTS18 overexpression. Using mass spectrometry, we identified two sites in FN that are proteolytically cleaved by ADAMTS18, including a cleavage site in the linker FN-I5-6. Cleavage at this site generated FN molecules lacking the N-terminal FN-I1-5 (29kDa) fragment that is known to be essential for FN fibrillogenesis. Accordingly, ADAMTS18 overexpression greatly impaired FN fibrillogenesis in endothelial cultures and in co-culture with fibroblasts. Our results implicate ADAMTS18 in FN-associated extracellular matrix remodelling and suggest an important role for ADAMTS18 in endothelium biology.

overall_design: To investigate the role of ADAMTS18 in endothelial cells, we over-expressed human ADAMTS18 in human umbilical vein endothelila cells (HUVEC) using a lentiviral vector (LV). In addition, to study the effect of knockdown of ADAMTS18 we reduced ADAMTS18 expression in HUVEC using siRNA. We then performed gene expression profiling based on data derinved from RNA-sequencing from 4 independent HUVEC cultures (pool of 3 donors) for each treatment. and harvested after 2 or 3 days. Comparitive gene expression profiling was performed for the over-expression of ADAMTS18 via comparison to control transduced cells over-expressing a reporter gene (green fluorescent protein; GFP) 3 days after transduction. For the knockdown study siADAMTS18 samples were compared to control siRNA (siCTRL) samples, generated 2 days following transfection.

last: Laham-Karam

first: Maria

last: Barbiera

first: Mikko

last: Gynther

first: Tetsuya

last: Terasaki

first: Suvi

last: Jauhiainen

first: Johanna

last: Laakkonen

first: Michael

last: Jeltsch

first: Seppo

last: Ylä-Herttuala


title: Nrf2 orchestrates epigenetic regulation and acts as the master regulator of KLF4 expression and activity during arsenic-induced cell transformation

city: Stony Brook

first: Fei

last: Chen

state: NY

address: 101 Nicolls Road, MART 8M-0501

institute: Stony Brook University

summary: Emerging evidence suggests that Nrf2 plays a pro-carcinogenic role in various cancers. Our previous study showed that arsenic-induced Nrf2 activation promotes metabolic reprogramming and cancer stem-like cell formation. Here, we identify KLF4, a key pluripotency factor, as a direct transcriptional target of Nrf2 in arsenic-exposed human bronchial epithelial cells. ChIP-seq revealed multiple Nrf2 binding peaks at the KLF4 gene locus, co-localizing with the enhancer markers H3K4me1 and H3K27Ac. Nrf2 knockout reduced KLF4 expression and decreased enhancer marker enrichment, alongside a genome-wide reduction in KLF4 binding in arsenic-treated BEAS-2B cells. In BEAS-2B cells with functional Nrf2, arsenic treatment significantly increased KLF4 binding on genes involved in several oncogenic pathways, including STAT3, SOX2, Nrf2, cell growth, Hedgehog, and epithelial-to-mesenchymal transition (EMT). We also found that KLF4 participates in a self-regulating feedback loop in response to arsenic-induced Nrf2 signaling. Co-occupancy of Nrf2 and KLF4 is crucial for establishing active enhancers, suggesting that Nrf2’s oncogenic effects are, at least in part, mediated by Nrf2-dependent self-amplification of KLF4 expression and function. Thus, co-targeting Nrf2 and KLF4 may represent a promising therapeutic strategy for eliminating cancer stem-like cells.

overall_design: BEAS-2B cells, with or without Nrf2 knockout, were treated with or without 1 μM As³⁺ for 6 hours, followed by ChIP-seq analysis.

first: Ziwei

last: Wang

first: Zhuoyue

last: Bi


title: A giant virus creates a subcellular environment to overcome the codon-tRNA mismatch [Ribo-seq]

city: Wako

first: Shintaro

last: Iwasaki

state: Saitama

address: 2-1, Hirosawa

department: Center for Pioneering Research

country: Japan

institute: RIKEN

summary: A codon usage consonant with the cellular tRNA pool is important for efficient translation. However, Mimivirus, a giant DNA virus, relies on the host translation system of amoeba yet exhibits a codon usage distinct from its host. How this virus copes with the mismatch between the demand and supply of tRNAs remains unknown. Here, we found that the virus generates a subcellular compartment to translate virus mRNAs efficiently. The combination of genome-wide Ribo-Seq and RNA-Seq reveals that ribosomes traversed along viral mRNAs without pausing, despite the codon usage incompatibility with the host mRNAs. Although the virus encodes tRNA genes in the genome, mim-tRNA-Seq shows that the expression does not impact the composition of the cellular tRNA pool during infection. Instead, we observed that through in situ labeling of newly synthesized proteins, viral protein synthesis locally occurs around the periphery region of the viral factory, likely creating a unique environment to facilitate viral translation. Our data provide a perspective on how local translation shapes viral replication overcoming the mismatch of tRNA supply and codon demand.

overall_design: To study the changes that occur in viral and host translation over the course of Acanthamoeba polyphaga mimivirus (APMV) infection, we applied ribosome profiling, and RNA-seq to Acanthamoeba castellanii str. Neff cells infected with APMV as well as mock infected cells. The cells were infected with APMV at a multiplicity of infection (MOI) of 10 and harvested at 2, 4, and 8 hours post infection (hpi). For each time point, ribosome-protected footprints as well as total RNA were sequenced. Two biological replicates were prepared for each time point. To characterize the changes in tRNA library composition during the course of APMV infection, we applied mim-tRNA-seq on A. castellanii cells infected with APMV as well as mock infected cells. The cells were infected at a MOI of 10 and harvested at 2, 4, and 8 hpi. Two biological replicates were prepared for each time point.

first: Ruixuan

last: Zhang

first: Hiroyuki

last: Hikida

first: Yuichi

last: Shichino

first: Mari

last: Mito

last: Ogata


title: A giant virus creates a subcellular environment to overcome the codon-tRNA mismatch [tRNA-seq]

type: Non-coding RNA profiling by high throughput sequencing


title: A giant virus creates a subcellular environment to overcome the codon-tRNA mismatch [RNA-seq]


title: ZFTA-RELA ependymomas produce itaconate as an oncometabolite to sustain pathogenic fusion expression [ChIP-Seq]

first: Arul

last: Chinnaiyan

overall_design: ZFTA-RELA fusion cells (EPN1425 and mouse neural stem cells (mNSCs)) were treated with Citraconate (ACOD1 antagonist) or an EZH2 inhibitor (GSK343)

first: Siva Kumar

last: Natarajan

first: Joanna

last: Lum

first: James

last: Haggerty-Skeans

first: Minal

last: Nenwani

first: Sanjana

last: Eyunni

first: Mateus

last: Mota

first: Jill

last: Bayliss

first: Akash

last: Deogharkar

first: Erin

last: Hamanishi

first: Matthew

last: Pun

first: Stefan

middle: R

last: Sweha

first: Simon

last: Hoffman

first: Eleanor

last: Young

first: Qiuyang

first: Rijul

last: Mehta

first: Olamide

last: Animasahun

first: Pranav

last: Narayanan

first: Sushanth

last: Sunil

first: Abhijit

last: Parolia

first: Peter

last: Sajjakulnukit

first: Pooja

last: Panwalkar

first: Robert

last: Doherty

first: Madison

last: Clausen

first: Derek

last: Dang

first: Debra

last: Hawes

first: Fusheng

last: Yang

first: Mariarita

last: Santi

first: Alexander

last: Judkins

first: Yelena

last: Wilson

first: Thomas

last: Vigil

first: Andrea

last: Franson

first: Richard

last: Mortensen

first: Tatsuya

last: Ozawa

last: Griesinger

first: Eric

last: Holland

first: Nicholas

last: Foreman

first: Kulandaimanuvel

last: Antony Michaelraj

first: Sameer

last: Agnihotri

last: Taylor

last: Gilbertson

first: Carl


title: Generation and Transcriptome Profiling of Bonobo Induced Pluripotent Stem Cells Using Stealth RNA Vectors: A Tripartite Comparative Study with Humans and Chimpanzees

city: Inuyama

first: Yusuke

last: Hamazaki

state: Aichi

institute: Center for the Evolutionary Origins of Human Behavior, Kyoto University

summary: Bonobos (Pan paniscus), which share a close evolutionary lineage with chimpanzees (Pan troglodytes) and humans, offer vital insights into the genetic and developmental propensities underlying human evolution. In this study, we established nine integration-free bonobo induced pluripotent stem cell (iPSC) lines from cryopreserved peripheral blood mononuclear cells using Sendai virus-derived RNA vectors. These iPSCs exhibited key pluripotency gene expression, normal karyotypes, and the capacity for differentiation into neural, mesodermal, and endodermal lineages, including the first successful induction of limb bud mesoderm cells from great ape iPSCs. Comprehensive transcriptome comparisons among bonobo, chimpanzee, and human iPSCs uncovered significant gene expression and retrotransposon divergence between Homo and Pan species, while highlighting minimal differences between bonobos and chimpanzees. Nevertheless, variation in the expression of mitochondrial metabolism-related genes was observed between the Pan species, suggesting potential interspecies differences in metabolic activity. This work provides a valuable platform for investigating the molecular and cellular mechanisms underlying species-specific developmental traits in closely related hominids and sheds light on the evolutionary origins of human characteristics.

sample_organism:
Pan paniscus
Pan troglodytes

platform_organism:
Pan paniscus
Pan troglodytes

overall_design: transcriptome profiles of bonobo and chimpanzee iPSCs

first: Hiroto

last: Akuta

first: Hikaru

last: Suzuki

first: Kenji

last: Ichiyanagi

first: Takuya

last: Imamura

first: Masanori


title: p53 mediates phospholipid headgroup scavenging [RNA-seq]

city: New York

first: Lydia

last: Finley

address: 430 E 67th St

department: Cell Biology Program

institute: Memorial Sloan Kettering Cancer Center

summary: A growing number of studies have shown that p53 modulates metabolic pathways to support diverse biological functions. Given that p53 is most widely known to act as a transcriptional activator, this raises the possibility that p53 transcriptional activity governs metabolic reprogramming. Here, we performed targeted metabolomics and lipidomic analysis which revealed an increase in the de novo biosynthesis of phosphatidylethanolamine (PE) upon p53 activation. Elevated levels of phosphoethanolamine (PEtn), the PE headgroup, in p53 active cells are sustained through PE headgroup recycling, which is partially mediated through the transcriptional activation of autophagy by p53. Disruption of phospholipid headgroup recycling through genetic perturbation of the CDP-ethanolamine pathway results in defects in cell-state specific perturbations in growth and gene expression. Notably, we observe restructuring of endoplasmic reticulum (ER)-mitochondria contacts in cells where headgroup recycling was abrogated, likely an attempt to maintain lipid homeostasis, and this reorganization is reversed when flux through the CDP-Etn pathway is restored. Together, these results suggest that lipid recycling to be an additional tool in the p53 arsenal supporting cellular fitness.

overall_design: KPnull cells engineered to express a doxycycline-inducible vector without cDNA (Vector) or various forms of p53 (WT, wild-type; TAD1m, TAD1 p53 mutant; TAD2m, TAD2 p53 mutant; TAD1/2m, TAD1/2 p53 mutant) cultured with or without doxycycline for two days. KPsh cells grown on or off doxycycline for ten days. Cells were collected in duplicate or triplicate, followed by total RNA extraction using TRIzol.

first: J

last: Yashinskie

first: K

middle: I

last: Paras

first: L


title: p53 mediates phospholipid headgroup scavenging [ChIP-seq]

overall_design: KPnull cells engineered to express a doxycycline-inducible vector without cDNA (Vector) or p53 cultured with or without doxycycline for two days. Chromatin immunoprecipitation DNA-sequencing (ChIP-Seq) for P53 was performed.


title: Targeted Antisense Oligonucleotide Treatment Rescues Developmental Alterations in Spinal Muscular Atrophy Organoids [scRNA-seq]

first: Simona

last: Lodato

overall_design: 2-month-old Spinal Cord Organoids (SCOs) from wilde-type CTRL organoids (n=2 C1, n=2 C3) and SMA organoids (n=2 S1, n=2 S3) were profiled by scRNA-seq.

first: Irene

last: Faravelli

first: Paola

last: Rinchetti

first: Monica

last: Tambalo

first: Illia

last: Simutin

first: Lisa

last: Mapelli

first: Sara

last: Mancinelli

first: Matteo

last: Miotto

first: Mafalda

last: Rizzuti

first: Andrea

last: D’Angelo

first: Chiara

last: Cordiglieri

first: Giulia

last: Forotti

first: Clelia

last: Peano

first: Paolo

last: Kunderfranco

first: Luca

last: Calandriello

first: Giacomo

middle: P

last: Comi

first: Elvezia

last: Paraboschi

first: Eleonora

last: Pali

first: Francesca

last: Beatrice

first: Egidio

first: Serge

last: Przedborski

last: Nizzardo

first: Stefania

last: Corti


title: Modified loop2 epegRNA improve prime editing efficiency

city: Hangzhou

first: Lijia

last: Ma

state: Zhejiang

address: Shilongshan Road No.18, Cloud Town, Xihu District

department: School of Life Sciences

institute: Westlake university

summary: Prime editor (PE) has wide application prospects in disease treatment due to its diversity of editing outcomes. However, the editing efficiency of PE still needs to be further improved for therapeutic applications. Here, we increase the probability of hybridization of the pegRNA primer binding site (PBS) to single-stranded DNA flap by adding additional PBS sequence and reverse transcription template (RTT) to the loop region of pegRNA. The selection of loop and the design of loop length are optimized. The resulting modified loop2 epegRNA (ML-epegRNA) showed higher prime editing efficiency than that of the epegRNA in HEK293T cells. In addition, we used ML-epegRNA for PE editing of multiple editing types in multiple cell lines, and the results showed a general improvement in editing efficiency. Overall, the ML-epegRNA expands the capabilities of genome editing tools.

overall_design: After the plasmid with PE protein components and designed pegRNA was transferred into the cells, the positive cells were separated by flow sorting and the genome was extracted. Use site-specific primers with second-generation sequencing adapters to amplify target sites via PCR for library construction. High-throughput sequencing by Illumina NovaSeq6000.

first: Bailun

last: Li

first: Zhike

last: Lu

first: Ting

last: Zhou

first: Huilin

last: Mou

first: Zhilin

last: Zou


title: Transcription factors PLT and chromatin regulators PRC2 and JMJ703 form nuclear condensates to maintain gene repression in bivalent domains controlling cell fate in rice root meristem

city: Wuhan

first: Qi

address: Lion Rock Street

department: Hongshan District

institute: Huazhong Agricultural University

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

overall_design: Refer to individual Series


title: HOXB13 alters chromatin accessibility in prostate cancer through interactions with the SWI/SNF complex

city: Vancouver

first: Nathan

last: Lack

state: British Columbia

address: 2260 Oak st.

institute: Vancouver Prostate Centre

first: Shreyas

last: Lingadahalli

first: Betul

last: Ersoy Fazlioglu

first: Umut Berkay

last: Altintas


title: Total flavone of Abelmoschus manihot Lmedic inhibits the metastasis of  colorectal cancer cells via inhibition of the STAT3/EMT signaling pathway by  up-regulating LncRNAAL137782

first: Qian

address: Xianlin Avenue 138

institute: Nanjing University of Traditional Chinese Medicine

summary: Total flavone of Abelmoschus manihot Lmedic (TFA) is a natural compound known for its  anti-inflammatory, analgesic, and antioxidant properties. Despite extensive investigations  into the therapeutic potential of TFA, there remains a paucity of reports regarding its impact on cancer treatment. This study aimed to elucidate the effects and mechanisms of TFA in CRC therapy. Subsequently, we employed RNA-seq technology to scrutinize differences in the gene expression profiles between TFA-treated and untreated CRC cells. Our findings underscore that TFA suppresses the growth, migration, and apoptosis of CRC cells. In animal models, TFA inhibits CRC cell growth and reduces hepatic metastasis. Mechanistically, we observed that TFA accomplishes this by upregulating long non-coding RNA AL137782, which, in turn, inhibits the EMT/STAT3 signaling pathway.

overall_design: In order to study the inhibitory effect of TFA on the malignant phenotype of colorectal cancer cells,  we used TGF-β-induced DLD-1 cells for 24 h, and then intervened with TFA to observe the  changes in cell migration and apoptosis.

first: Hui

last: Zhang

first: Yongshan

last: He

first: Conghui

last: Han


title: Tailoring a CRISPR/Cas-based Epigenome Editor for Programmable Chromatin Acylation and Decreased Cytotoxicity

city: Houston

first: Isaac

middle: B

last: Hilton

state: Texas

address: 6500 Main St., BRC Rm 660

institute: Rice University


title: Cholesterol efflux protein, ABCA1, supports anti-cancer functions of myeloid immune cells.

status: Public on Nov 16 2025

city: Urbana

first: Erik

middle: Russell

last: Nelson

state: IL

address: 407 S. Goodwin Ave

department: Molecular and Integrative Physiology

institute: University of Illinois at Urbana-Champaign

summary: Breast and other solid tumors respond poorly to immune therapy. Myeloid cells (MCs) such as macrophages contribute to resistance. Established clinical evidence links cholesterol to cancer outcomes, with MC function being regulated by cholesterol metabolism. We screened MC-expressed regulators of cholesterol homeostasis linked to survival and identified the cholesterol efflux protein ABCA1. ABCA1 activity increases anti-cancer functions of macrophages: enhancing tumor infiltration, decreasing angiogenic potential, reducing efferocytosis, and improving support of CD8+ T cell activity. Mechanistically, different AKT isoforms are involved, through both PI3K-dependent and independent mechanisms. Highlighting the clinical relevance of our findings are correlations between ABCA1 in macrophages and angiogenic potential, VEGFA, and CD8 T cell abundance and activity. The culmination of these activities was demonstrated through increased tumor growth and metastasis in mice lacking MC-expressed ABCA1. Tumors grown in these mice were also more resistant to immune therapy. Therefore, modulating ABCA1 activity within MCs may represent a novel approach to immune therapy.

overall_design: Bone marrow derived macrphages were transfected with either a control siRNA or siRNA against ABCA1. 48hrs post transfection cells were dissociated using Accutase (Thermo #A1110501)

first: Shruti

middle: V

last: Bendre

first: Rajendra

last: K C

first: Kevin

last: VanBortle


title: Conserved roles of GATA4 and its target gene TBX2 in regulation of human cardiogenesis

city: Cardiff

first: Peter

last: Kille

state: Caerdydd

address: The Sir Martin Evans Building, Museum Avenue

department: School of Biosciences

country: United Kingdom

institute: Cardiff University

summary: The transcription factor (TF) GATA4 is a key mediator of cardiogenesis. GATA4 regulates cardiogenesis through the expression of its target genes, only some of which have been identified. We have used a gain of function model based on pluripotent embryonic ectoderm explants from Xenopus embryos expressing GATA4, to identify a set of downstream targets of GATA4 which are also regulated by Nodal, a known cardiogenic signal. GATA4 was shown to be required for the expression of target genes Tbx2 and Prdm1 in vivo, likely acting in a direct fashion by interacting with their regulatory regions. In addition, Tbx2 and Prdm1 are shown to have roles of their own in vivo, as downregulation of Tbx2, a positive target, and overexpression of Prdm1, a negative target, interferes with cardiac development in Xenopus embryos.  The conservation of the GATA4-TBX2-PRDM1 regulatory relationship was shown in human iPSC-derived cardiomyocytes. Loss of function of GATA4 lead to downregulation of TBX2, upregulation of PRDM1 expression and failure of cardiogenesis. GATA4 deficient cells failed to form normal cardiomyocytes, with most cells likely adopting alternative fates such as smooth muscle cells and fibroblasts, and only a small minority expressing an aberrant cardiomyocyte phenotype.  Genome wide transcriptomic analysis documented severe reduction of cardiomyocyte and endothelial cell transcriptomes and upregulation of transcriptional profiles of smooth muscle cells and fibroblasts. Disruption of TBX2 function did not alter cardiomyocyte differentiation efficiency but led to the formation of abnormal, hypertrophic cardiomyocytes, characterised by defective sarcomeres and upregulation of cardiomyocyte Gene Ontology terms. In addition, we show that PRDM1 is not essential for formation of cardiomyocytes, implying suppression of alternative fates and fine-tuning the expression of the cardiomyocyte program.  The results presented establish a conserved regulatory relationship between GATA4 and its target genes TBX2 and PRDM1, expanding the cardiac GRN and providing further insight into how cardiogenesis proceeds

overall_design: This data set represents RNAseq data from WT and CRISPR-Cas9 manipulated human iPSC cells lines differentiated to represent cardiomyocytes. Genee diting was performed to generate homozygous GATA (GATA4 -/- ), PRDM1 (PRDM1-/-) or  TBX2 (Tbx2del/del). Time and batch matched controls were used for the analsyis.

first: Branko

last: Latinkic

first: Nick

last: Owens

first: Michael

last: Gilchrist

first: Ewan

last: Fowler

first: Ilya

last: Patrushev

first: Pavel

last: Kirilenko

first: Nicola

last: Graham


title: The role of EHMT2 in uveal melanoma progression

city: Birmingham

first: Narendra

last: Wajapeyee

state: AL

address: 720 20th Street South, Kaul 540A

department: Department of Biochemistry and Molecular Genetics

institute: University of Alabama at Birmingham


title: The impact of small molecule L-2-hydroxyglutarate

first: Sunil

last: Sudarshan

address: FOT 1120 -  510 20th Street South

type: Methylation profiling by high throughput sequencing


title: siRNA mediated knockdown of ABCA1 in murine bone marrow derived macrophages

summary: RNA sequencing of murine bone marrow derived macrophages after transfection with control siRNA or siRNA against ABCA1

overall_design: RNAseq profiling of murine bone marrow macrophages. Control siRNA versus siRNA against ABCA1


title: Transcriptomic effects of PFBA and PFHxA exposure on RPMI2650 cells

city: Shanghai

first: Ting

last: Xu

address: No. 1239 Road Siping

institute: Tongji University

summary: This study investigated the toxicological effects of two short-chain per- and polyfluoroalkyl substances (PFAS), including perfluorobutanoic acid (PFBA) and perfluorohexanoic acid (PFHxA), on the transcriptome of human nasal RPMI2650 cells. Gene annotation enrichment analysis highlighted neurofactor, synaptic, solute carrier, and ribosome signaling pathways in common pathways of widespread transcriptional changes in RPMI2650 cells. Systematic analysis of RNA-seq data revealed that PFAS-treated RPMI2650 cells are encoded to participate in cell proliferation (H3C14), nerve regeneration (L1CAM, P2RY1), and solute transport (SLC17A7, LRRK2). TOP 10 GO analysis showed that DEGs was mainly concentrated in synaptic regulation, cell division correlation and solute carrier transport. For example, in the PFBA treatment group, typical terms include synaptic vesicular membrane (GO:0030672), synaptic transmission, glutaminergic energy (GO:0035249), and interneuronal synaptic transmission (GO:0007270), while in the PFHxA treatment group, DEGs is mainly enriched in nucleosomes (GO:0000786). Microtubule binding (GO:0008017) and neuronal differentiation in the central nervous system (GO:0021953). In KEGG enrichment pathway, PFBA-treated differential genes were mainly concentrated in synaptic related pathways, such as serotonergic synapses (hsa04726), glycerophospholipid metabolism (hsa00564), and GABAergic synapses (hsa04727). In addition to neuron-related pathways, PFHxA processing enrichedneurotransmitter related pathways such as sphingolipid biosynthesis-Globo and isoglobo series (hsa00603), GABaergic synapses (hsa04727), and neuroactive ligand-receptor interactions (hsa04080).

overall_design: To investigate the transcriptomic effects of PFAS of different chain lengths on nasal epithelial cells, RPMI2650 cells cultured at the air-liquid interface were exposed to 1μM PFBA and PFHxA for 7 days, and the cells were collected for transcriptome sequencing.

first: Huan

last: Wang


title: Cellular and Molecular Profiling of Collagenous Gastritis

city: Boston

first: Stephanie

last: Dougan

address: 450 Brookline Ave

institute: Dana Farber Cancer Institute

summary: Collagenous gastritis (CG) is a rare disease characterized by thick bands of subepithelial collagen within the stomach and presents with a variety of symptoms ranging from anemia to vomiting. Gastric biopsies were collected from six CG patients, including one patient before and after glucocorticoid steroid treatment, and several matched controls. Single-cell RNA- and T-cell receptor (TCR)-sequencing was performed on gastric biopsies.

overall_design: Control or CG patient biopsies were processed fresh and unsorted or frozen and CD45+ live flow-sorted. Single cell suspensions where processed in the 10x Genomics pipeline for scRNA- and scTCR-sequencing.

last: Walsh

first: Lestat

last: Ali

first: Jamie

last: DiCarlo

first: Enoch

last: Chung

first: Li

last: Qiang

first: Jiao

last: Shen

first: C

middle: E

last: Keleher

first: Mary

last: Thompson

first: Keri

last: Sullivan


title: Activated-ATF6α is an ER stress-inducing oncoprotein metabolically restricting immunosurveillance [bulk RNA-seq of TG-AAV-GFP/CRE, DEN/HFD]

city: La Jolla

first: Randal

middle: J.

last: Kaufman

state: CA

address: 10901 North Torrey Pines Road

department: Cancer Metabolism and Microenvironment Program, Center for Genetic Disorders and Aging Research NCI-Designated Cancer Center

institute: Sanford Burnham Prebys Medical Discovery Institute

summary: Hepatocellular carcinoma (HCC) is the fastest growing cause of cancer-related mortality with limited therapies. While endoplasmic reticulum (ER)-stress and the unfolded protein response (UPR) are implicated in HCC, the involvement of the UPR-transducer activating transcription factor 6 alpha (ATF6α) remains unclear. In contrast to the well-characterized role of ATF6α-activation as an adaptive response to ER-stress, we here demonstrate its hitherto unknown function as an ER stress-inducing oncoprotein and metabolic master-regulator restricting cancer-immunosurveillance. In human HCC, ATF6α-activation significantly correlated with reduced patient-survival, tumor-progression, local immunosuppression, and higher recurrence rates of liver-cancer upon hepatectomy. Hepatocyte-specific ATF6α-activation in mice induced progressive hepatitis with ER-stress, immunosuppression, and hepatocyte-proliferation. Concomitantly, activated-ATF6α increased glycolysis and repressed gluconeogenic enzyme fructose-1,6-bisphosphatase 1 (FBP1). Restoring FBP1 expression prevented ATF6α-activation-related pathologies. Prolonged ATF6α-activation in hepatocytes triggered hepatocarcinogenesis, intratumoral T-cell infiltration, and nutrient-deprived immune-exhaustion. Immune-checkpoint blockade (ICB) efficiently restored immunosurveillance and dramatically reduced HCC. In line, HCC patients with a significantly higher ATF6α-activation signature presented complete response to ICB monotherapy. Targeting Atf6 via germline, hepatocyte-specific ablation, or therapeutic delivery of antisense-oligonucleotides dampened HCC in preclinical liver-cancer models. Thus, prolonged ATF6α-activation drives ER-stress, leading to aberrant glucose metabolism-dependent immunosuppression in liver cancer. Our findings propose persistently activated ATF6α as an oncoprotein, stratification-marker for liver-cancer ICB, and targetable therapeutic strategy against HCC.

overall_design: Gene expression analysis of TG-AAV-GFP/CRE, DEN/HFD mice using RNA-seq

first: Xin

last: Li

first: Cynthia

last: Lebeaupin

first: Mathias

last: Heikenwälder


title: Activated-ATF6α is an ER stress-inducing oncoprotein metabolically restricting immunosurveillance [bulk RNA-seq of Atf6 KO DEN/HFD]

overall_design: Gene expression analysis of Atf6 KO DEN/HFD mice using RNA-seq


title: Activated-ATF6α is an ER stress-inducing oncoprotein metabolically restricting immunosurveillance


title: Gene expression profile at single cell level of rotavirus specific CD4+ T cells

city: Toronto

first: Kei

last: Haniuda

state: Ontario

address: 1 King’s College Circle, MSB7310

department: Department of Immunology

institute: University of Toronto

summary: IgA is the dominant antibody isotype secreted into the mucosal lumen. Mucosa-resident IgA+ plasma cells (PCs) generated following enteric infection can persist as long-lived plasma cells (LLPCs) in the gut, ensuring durable protection against reinfection. However, little is known about how virus-specific IgA+ PCs are generated and maintained. Upon infection with mouse rotavirus (RV) via the oral route, we found that antigen (Ag)-specific IgG+ and IgA+ PCs are generated in a follicular helper T (TFH) cell-dependent manner that involves CD40 signaling and MHC class II (MHCII) restricted Ag-presentation by B cells. Unexpectedly, although the RV-specific IgG response requires Ag-presentation by conventional dendritic cells, Ag-presentation by B cells is sufficient for the generation of RV-specific IgA. The accumulation of RV-specific IgA+ PCs in the small intestinal lamina propria (SILP) was found to depend on a type 1 TFH (TFH1) cell subset, which requires B cell Ag-presentation for their development and co-expresses Bcl-6 and T-bet. IFNγ receptor signaling is required for the expression of CXCR3 on RV-specific IgA+ PCs, which in turn promotes their migration to the SILP. Moreover, TFH1 cells are also required for the optimal development of IgA+ LLPCs in the upper and lower respiratory tracts in response to intranasal influenza A virus (IAV) infection. However unlike with RV, expression of MHCII on B cells was not sufficient for generating an IAV-specific IgA response in the airways, suggesting the operation of mucosal site-specific priming mechanisms. Collectively, our data reveal that unconventionally primed TFH1 cells support IgA responses to mucosal viral infections.

overall_design: Following mouse RV ECw infection, VP4-specific, VP6-specific and total CD4+ T cells were purified from pooled Peyer's patches (PPs) and mesenteric lymph nodes (MLNs) by magnetic sorting and flow cytometric sorting, and analyzed using scRNA-seq.

first: Jennifer

last: Gommerman


title: Cdh1 and Trp53 Knockout organoid,  Cdh1, Trp53 and Smad4 Knockout organoid RNA sequencing

city: ChunCheon-si

first: Jun Won

last: Park

address: Division of Biomedical Convergence, College of Biomedical Science, Kangwon National University, Kangwondaehak-gil

country: South Korea

institute: kangwon national univercity

summary:
To investigate the function of Smad4, we established Cdh1 and Trp53 Knockout organoid,  Cdh1, Trp53 and Smad4 Knockout organoid lines
We then performed gene expression profiling analysis using data obtained from RNA-seq of 4 different cells at two time points.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for Cdh1 and Trp53 Knockout organoid,  Cdh1, Trp53 and Smad4 Knockout organoid

first: Jun

middle: W

first: Hyeok

last: An

first: Sang

last: Seok


title: ScRNAseq analysis of data from patients with T1D and healthy donors

status: Public on Nov 15 2025

city: Prague

first: Veronika

last: Niederlova

address: Videnska 1083

country: Czech Republic

institute: Institute of Molecular Genetics of the Czech Academy of Science

summary: Type 1 diabetes (T1D) arises from loss of immune tolerance to pancreatic β-cells, yet its immunologic drivers remain unclear. We performed single-cell transcriptomic profiling of peripheral T cells from children newly diagnosed with T1D, the same children one year later, and healthy controls. At diagnosis, T1D was marked by broadly reduced effector and cytotoxic programs and increased stemness-related signatures across multiple T cell subsets, alongside impaired regulatory features in both Tregs and TR3-56 cells. Flow cytometry from the same cohort and reanalysis of public datasets confirmed these patterns. Together, these data suggest that T1D involves defective T cell effector differentiation and compromised regulatory control, contributing to immune dysregulation and loss of self-tolerance.

overall_design:
Peripheral blood mononuclear cells (PBMCs) were collected from children newly diagnosed with T1D and from healthy donors. A subset of the same T1D patients was re-sampled one year after diagnosis to assess longitudinal changes. CD4 and CD8 T cells were sorted and subjected to single-cell RNA sequencing using the 10x Genomics Chromium platform (5' v2 chemistry). Libraries were prepared according to the manufacturer’s protocol and sequenced on an Illumina NovaSeq 6000 instrument. Raw sequencing data were processed with Cell Ranger (10x Genomics) for demultiplexing, alignment to the GRCh38 reference genome, and UMI counting. Downstream analyses, including clustering, differential gene expression, and gene set enrichment, were performed using Seurat and custom R scripts. Please see also the associated github: https://github.com/Lab-of-Adaptive-Immunity/dia and Zenodo: https://zenodo.org/records/17280190 .

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

first: Juraj

last: Michalik

first: Ondrej

last: Stepanek


title: Transcriptional profiling of Xap5, Nono, and Sox5 knockout mouse fibroblasts during primary ciliogenesis

first: Weihua

last: Wang

address: No.8, Sanjiaohu Rd

institute: Jianghan University

summary: The formation of primary cilia (ciliogenesis) is a fundamental process in mammalian development, governed by precise transcriptional programs. While the Rfx and Foxj1 transcription factors are known master regulators, the full scope of this control, particularly for primary cilia, is not completely understood. This study aims to define the transcriptional network downstream of the ancient, evolutionarily conserved factor Xap5, which we identified as a novel master regulator of primary ciliogenesis. To achieve this, we performed transcriptome analysis (RNA-seq) on wild-type (WT) NIH/3T3 mouse fibroblasts and derived knockout (KO) cell lines for Xap5, its interacting cofactor Nono, and a key downstream effector, Sox5. Cells were profiled following 24 hours of serum starvation, a condition that induces primary cilia formation and revealed a significant cilia elongation defect in all three knockout lines. Overall, this dataset provides a comprehensive resource for identifying the common and unique gene expression programs regulated by the Xap5-Nono-Sox5 transcriptional cascade, an Rfx-independent pathway essential for building the primary cilium.

overall_design: The goal of this study was to identify the transcriptional network regulated by the Xap5-Nono-Sox5 pathway during primary ciliogenesis. To achieve this, we performed RNA-sequencing on four groups of NIH/3T3 mouse fibroblasts: Wild-type (WT), Xap5 KO, Nono KO and Sox5 KO. All cell lines were cultured and induced to form primary cilia by serum starvation for 24 hours prior to RNA extraction. The transcriptomes of the three knockout lines were then compared to the wild-type control to identify commonly and uniquely dysregulated genes, thereby defining the downstream targets of this novel ciliogenic pathway.

first: Xiqi

last: Zhang

first: Yaxuan

last: Qiu

first: Zhangfeng

last: Hu


title: Multi-omic integration identifies mechanisms of Broad Drug Resistance and opportunities for therapeutic reprogramming cancer cells

city: Notre Dame

first: Ian

last: Mersich

state: Indiana

address: 54417 Leahy Dr, Notre Dame, IN 46556

department: Chemistry and Biochemistry

institute: University of Notre Dame

summary: Broad drug resistance in cancer arises through diverse transcriptional, metabolic, and genetic adaptations, yet the shared molecular programs that sustain cross-resistant phenotypes remain incompletely defined. This study integrates PRISM drug-response data with transcriptomic, metabolomic, and mutational profiles to characterize the molecular features associated with broad drug resistance and to identify compounds capable of reversing resistance-associated gene signatures. Resistant cell lines exhibited coordinated activation of extracellular matrix remodeling, stress-adaptation pathways, and survival signaling, with NFE2L2 emerging as a central regulatory hub linking upstream mutations to oxidative-stress transcriptional programs. Multi-omic integration further revealed metabolic reprogramming as a conserved hallmark of resistance, and analyses of clinical cohorts demonstrated that resistance-associated alterations were associated with reduced progression-free survival.  Computational perturbagen screening nominated compounds predicted to counteract resistance-associated transcriptional signatures. Experimental validation confirmed that rosiglitazone suppressed NFE2L2-associated gene expression programs and restored chemotherapy sensitivity in resistant models, supporting a scalable framework for rational phenotypic reprogramming.  This GEO submission provides raw RNA-seq data generated from compound-treated OE19 cells used to experimentally validate candidate re-sensitization strategies.

overall_design: OE19 esophageal adenocarcinoma cells were treated with 1 µM rosiglitazone, halcinonide, methylprednisolone or 0.1% DMSO (control) , each in biological duplicate, alongside two untreated control samples. Total RNA was extracted using the Qiagen RNeasy Mini Kit according to the manufacturer’s instructions. RNA-seq libraries were prepared by the University of Notre Dame Genomics Core and sequenced on an Illumina NextSeq 2000 platform (paired-end, PE50), generating ~30 million reads per sample. Raw FASTQ files were aligned to the GRCh38/hg38 reference genome using HISAT2, and gene-level read counts were produced using featureCounts. FASTQ files (R1 and R2 for each biological replicate) are provided as supplementary data to support reproducibility and downstream analysis.


title: Side-population trophoblasts from normal and abnormal pregnancies

city: Auckland

first: Teena

last: Gamage

state: Scotland

country: New Zealand

institute: Grafton

summary: Gene expression microarrays investigating the transcriptome of matched populations of human side-population trophoblasts and cytotrophoblasts isolated from third trimester placentae

overall_design: Matched primary uncultured third trimester side-population and cytotrophblasts trophoblasts were isolated using FACS from five uncomplicated fetal growth restricted (FGR) (<5th customised growth centile) and five gestation-matched control human placentae. RNA was extracted using Macherey-Nagel NucleoSpin® RNA XS kit. RNA content and quality of each sample was determined using the Agilent RNA 6000 Pico Kit. cDNA was generated using 2.6ng of RNA and amplified using a NuGEN Ovation Pico WTA system V2 kit in accordance with the manufacturer's instructions (NuGEN, San Carlos, CA, USA). Purified cDNA was biotin labelled and hybridised to Affymetrix PrimeView microarrays (Affymetrix, USA).

first: Vicky

last: Fan

first: Jasper

last: Perry

first: Lawrence

last: Chamley

first: Joanna

last: James


title: Activated-ATF6α is an ER stress-inducing oncoprotein metabolically restricting immunosurveillance [bulk RNAseq of TG-AAV-GFP/CRE/FBP1]

first: Randal

last: Kaufman

overall_design: Gene expression analysis of TG-AAV-GFP/CRE/FBP1 mice using RNA-seq

first: Xin

last: Li

first: Cynthia

last: Lebeaupin

middle: J

first: Mathias

last: Heikenwälder


title: TREM2+ Macrophage Infiltration Underlies Breast Cancer Lung Metastasis due to Paclitaxel Treatment

city: Beijing

first: Yuqi

last: Xing

state: Beijing

address: Peking University

institute: Peking University

summary: Metastasis is a major cause of breast-cancer-related death and frequently occurs following paclitaxel neoadjuvant chemotherapy failure. Tumor microenvironment contributes to metastasis, while the role of specific host cells in lung metastases induced by paclitaxel (PTX) treatment remains poorly understood. Here, we demonstrate that PTX neoadjuvant chemotherapy promotes triggering receptor expressed on myeloid cells-2 (TREM2)-positive macrophage infiltration in the breast cancer tissues of patients. Meanwhile, we also show that more TREM2-positive macrophage infiltrates in breast cancer tissues of patients with lung -metastasized. Genetic TREM2 deficiency decreases breast cancer lung metastases induced by PTX treatment in vivo, suggesting that TREM2-positive macrophages are essential for PTX-promoting lung metastasis of breast cancer. We further reveal that PTX promotes tumor cell secretion of fibroblast growth factor 2 (FGF2), triggering TREM2 transcription via upregulating its transcriptional factor early growth response-1 (EGR1) in macrophages. Increased TREM2 activates epithelial-mesenchymal transition (EMT)-related cytokine secretion in macrophages, inducing tumor cell lung metastases. Targeting TREM2 significantly suppressed lung metastasis in breast-cancer-bearing mice. Our findings establish that tumor-cell-derived FGF2 induced by paclitaxel treatment upregulates TREM2 in myeloid macrophages, which in turn promotes the EMT of neighboring tumor cells through cytokine secretion. Our results highlight TREM2 as a potential therapeutic target to mitigate lung metastasis due to PTX treatment.

overall_design: RNA-seq of BT549-D, BT549-P, SUM159-D, SUM159-P, MDA-MB-231-D and MDA-MB-231-P were harvested and analyzed

first: Hongquan

first: Jun

last: Zhan


title: Endothelial IL-36 receptor activation promotes vascular stability to limit pathological microvessel permeability in the CNS

city: Dublin 2

first: Jeffrey

last: O'Callaghan

state: Dublin

address: Smurfit Institute

country: Ireland

institute: Trinity College, Dublin

summary: Pathological increases in vascular permeability lead to edema and swelling, causing a host of retinal and neurological disorders. Few barrier-enhancing factors have been discovered to specifically promote barrier integrity and make blood vessels resistant to fluid leakage. In this study, we explore the effects of IL-36 receptor (IL-36R) activation on vascular permeability in vivo in adult mice, ex vivo in tissue explant and in vitro in primary mouse and human microvascular endothelial cells. Using a highly soluble and biologically active DEVD- modified recombinant IL-36β cytokine, we find that processed DEVDIL-36β enhances endothelial barrier function, reducing vascular leakage and thus limiting pathology. Specific knockdown of IL-36R on endothelial cells using the Cre/Lox system demonstrates it is IL-36R signaling in endothelial cells that is responsible for DEVDIL-36β’s barrier-promoting property. Analysis of IL-36R expression and localization on endothelial cells implies IL-36R is mobilized to the plasma membrane in response to loss of endothelial cell-cell contact, in keeping with the IL-1 family role in responding to tissue stress. Mechanistically, IL-36R signaling increases adherens and tight junctions and induces vasculoprotective processes that result in vessel remodeling and stabilization. These functional assays are further supported by RNA sequencing data. In summary, our data present IL-36R signaling as a novel regulator of vascular integrity, with barrier-enhancing properties that prevent pathological vascular leakage.

overall_design: RNA-Seq profiling of primary mouse brain microvascular endothelial cells (BMVECs) treated with DEVD mIL-36β (100 ng/ml) for either 24 hours or untreated.

first: Erin

last: Fahey

first: Lucia

last: Celkova

first: Valentina

last: Frezza

first: Graeme P.

last: Sullivan

first: Kieran

last: Byrne

first: Avril

last: Watson

first: Yasmina E.

last: Hernandez-Santana

first: Kieva

first: Rachel

last: Dalton

first: Hande

last: Efe-Cicek

first: Conor

last: Delaney

first: Ema

last: Ozaki

first: Patrick T.

last: Walsh

first: Seamus J.

last: Martin

first: Matthew

last: Campbell

first: Sarah L.

last: Doyle


title: Genome-wide mapping of Xap5 and Nono binding sites by CUT&Tag in NIH/3T3 cells

first: Weihua

last: Wang

summary: This study maps the genome-wide binding sites of the proteins Xap5 and Nono in murine NIH/3T3 cells using CUT&Tag (Cleavage Under Targets and Tagmentation) sequencing. By employing antibodies specific to Xap5 and Nono, we profiled their protein-DNA interactions. The results identify numerous common genomic targets, highlighting a significant overlap in the DNA-binding profiles of these two proteins.

overall_design: NIH/3T3 cells were subjected to starvation for 24 hours prior to the experiment. CUT&Tag was performed to map the genome-wide binding sites of Xap5 and Nono. The procedure strictly followed the manufacturer’s protocol for the Hyperactive Universal CUT&Tag Assay Kit for Illumina Pro (Vazyme).

first: Xiqi

last: Zhang

first: Zhangfeng

last: Hu