title: CD163 Expression Defines a Red Pulp Macrophage Subset Engaged in Crosstalk with Marginal Metallophilic Macrophages During Blood-Stage Malaria

city: Bonn

first: Elvira

last: Mass

address: Carl-Troll-Str. 31

department: Developmental Biology of the Immune System

institute: Life & Medical Sciences Institute, University of Bonn

summary: The spleen harbors distinct macrophage subsets that support circulatory homeostasis and initiate immune responses. Yet, the ontogeny and long-term dynamics of these populations remain incompletely understood. Here, we identify a transcriptionally and developmentally distinct CD163-expressing red pulp macrophage (CD163high RPM) population that arises from yolk sac progenitors and maintains CD163 expression under homeostatic conditions. Using fate-mapping models, we show that CD163- RPMs are progressively replenished by monocytes during ageing, whereas CD163high RPMs are rather self-maintaining and occupy a vascular-associated niche. During blood-stage malaria, CD163high RPMs are rapidly depleted and fail to recover despite clearance of parasitemia. Mechanistically, the loss of CD163 expression is driven by infection-induced hemolysis and iron depletion, not parasite persistence. Single-cell RNA sequencing reveals that CD163high RPMs act as dominant signaling hubs under steady state, but malaria disrupts these intercellular communication networks, including a previously unrecognized interaction with marginal metallophilic macrophages (MMMs). CD163 deficiency exacerbates structural disintegration of the marginal zone and selectively impairs MMM recovery, underscoring a CD163-dependent regulatory axis between RPMs and MMMs. This study provides a comprehensive ontogenetic and functional map of splenic macrophages, and reveals that the sustained loss of a specialized, yolk sac-derived CD163high RPM subset rewires splenic architecture and inter-macrophage crosstalk long after infection resolution.

overall_design: Mouse spleen tissue was used to analyze two conditions: 90 days post infection with P.chabaudi infected mices and PBS treated control mice. CD64⁺ cells were FACS-enriched, and CD45⁻ cells were negatively enriched using MACS. Each condition included two biological replicates.

first: Katharina

last: Mauel

first: Daria

last: Hirschmann

first: Nelli

last: Blank-Stein

first: Marie-Louise

last: Diefenbach-Wilke

first: Miguel

last: Soares

first: Florent

last: Ginhoux

first: William R.

last: Heath

first: Lynette

last: Beattie


title: Effect of DOT1L inhibition on gene expression in SW1990 pancreatic cancer cells

status: Public on Jul 28 2026

city: Changchun

first: Ziyu

last: Liu

address: 1 Xinmin Street

country: China

institute: Jilin University

type: Expression profiling by high throughput sequencing

summary: Histone methyltransferase DOT1L plays a critical role in the regulation of gene expression through methylation of histone H3 at lysine 79 (H3K79), a modification associated with active transcription. However, its function in pancreatic ductal adenocarcinoma (PDAC) remains incompletely understood. In this study, we investigated the transcriptional impact of DOT1L in SW1990 pancreatic cancer cells using EPZ-5676, a selective DOT1L inhibitor. Treatment with EPZ-5676 resulted in widespread transcriptional changes, indicating a key regulatory role of DOT1L in maintaining the gene expression profile of SW1990 cells. Through RNA-seq analysis, we identified differentially expressed genes between the untreated control and EPZ-5676-treated cells, implicating DOT1L in pathways involved in cell proliferation, differentiation, and tumor progression. These findings suggest that DOT1L-mediated H3K79 methylation contributes to the transcriptional landscape of pancreatic cancer cells and may represent a potential therapeutic target.

overall_design: RNA-seq profiling of SW1990 pancreatic cancer cells treated with DOT1L inhibitor EPZ-5676 and untreated controls to identify differentially expressed genes.

first: Feng

last: Wei


title: sepsis-secreted G6PD supports guanine generation and Histone H3K27 demethylation to Drive Inflammatory Macrophages

status: Public on Jul 29 2026

city: Wuhan

first: Yueyu

last: Kong

state: Hubei

address: Wuhan University

institute: Wuhan University

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Sepsis is a complex syndrome associated with physiological, pathological, and biochemical abnormalities resulted from infection. Sepsis is the major cause of acute respiratory distress syndrome (ARDS). Extracellular vesicles (EVs) are serving as new messengers to mediate cell-cell communication in vivo. The function of EVs in sepsis patients are not well defined. We found sepsis EV encapsulating G6PD induced pro-inflammatory effects in the lung tissue by reprogramming purine metabolism. Most notably, guanine accumulation led to EZH2-mediated H3K27Me3 level. Finally  Our study provides a novel mechanism  of how EV reviried puring metabolism in lung tissue and leading to acute lung damage.

overall_design: RAW264.7 was treaed with guanine (10μg/mL) for 24h.Then, Chip-seq analysis the gene expression in RAW264.7 cells

first: C

last: Wang

first: H

last: Du

first: W

last: Yan


title: The KDM1A and KDM7A lysine demethylases cooperate to regulate androgen receptor function in prostate cancer cells

city: Nottingham

first: Nigel

middle: P

last: Mongan

address: University Park

department: Biodiscovery Institute

country: United Kingdom

institute: University of Nottingham

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

overall_design: Refer to individual Series


title: Transcriptome analysis in the prefrontal cortex of Shank2 heterozygous mice treated with drug

city: Daejeon

first: Eunjoon

last: Kim

address: Kuseong-dong

department: Center for Synaptic Brain Dysfunctions/Department of Biological Sciences

country: South Korea

institute: IBS/KAIST

summary: Autism spectrum disorders (ASD) affect ~2.8% of the population, but the underlying biological mechanisms remain poorly understood, largely due to significant genetic heterogeneity. Mouse models have identified numerous candidate mechanisms; however, whether these can be grouped into functionally coherent subtypes remains unclear, limiting targeted, mechanism-based treatments. We analyzed prefrontal cortex transcriptomes from 17 distinct ASD mouse models, encompassing both sexes, under baseline and two separate drug-treatment conditions, totaling 1,008 mice across 204 groups.

overall_design: Shank2-HT and WT mice were analyzed on postnatal day 25 (P25), immediately following 3 weeks of drug treatment (P3-24) administered via maternal milk before weaning. Male and female mice were administered two different drugs (fluoxetine and lithium), and prefrontal cortex regions of the mice were dissected to perform RNA-seq.

first: Junyeop Daniel

last: Roh

first: Yukyung

last: Jun

first: Mihyun

last: Bae

first: Hyojin

last: Kang


title: Transcriptome analysis in the prefrontal cortex of Chd8-S62X heterozygous mice treated with drug

overall_design: Chd8-S62X and WT mice were analyzed on postnatal day 25 (P25), immediately following 3 weeks of drug treatment (P3-24) administered via maternal milk before weaning. Male and female mice were administered two different drugs (fluoxetine and lithium), and prefrontal cortex regions of the mice were dissected to perform RNA-seq.


title: Multi-omic proximity labeling in vivo with PRADA

city: singapore

first: YUE

last: WAN

address: 1, #20-10 Fusionopolis Way, Connexis, North Tower, 138632

country: Singapore

institute: Genome Institute of Singapore,A*STAR

summary: Understanding the spatial organization of biomolecules in living organisms is a central but challenging goal in biology. Here we introduce Peroxidase Reactions Activated by D-amino Acids (PRADA), which uses an engineered oxidase to convert non-proteinogenic D-amino acids into H2O2 for in situ activation of a genetically-fused peroxidase. PRADA enables versatile proximity-based chemistries, including protein labeling, RNA labeling, and functional polymer assembly, with minimal toxicity and background. We demonstrate that PRADA is broadly applicable inside living organisms, including flies, worms, fish, and mice. By further leveraging the unique RNA reactivity of PRADA, we developed a mutational profiling sequencing strategy for spatiotemporally-resolved mapping of RNA secondary structure. Application of this multifaceted PRADA platform in a mouse xenograft model offered insights into its mitochondrial proteome, transcriptome, and RNA structurome, revealing RNA folding as a regulatory mechanism in mitochondrial gene expression. Collectively, PRADA holds promise to uncover the intricate organization of biomolecules in vivo.

overall_design: Labeled and enriched MITO-PRADA cell lines cultured in vitro and xenograft tumors in vivo, followed by library preparation. Caco2 cells were infected with astrovirus HAstV1 viruses,followed by SHAPE-Map protocol and library preparation, which was used a structure benchmaker for PRADA.

first: Jiapeng

first: Jian

last: Han

first: Yue

last: Wan

first: Shuo


title: Integrative transcriptomic and proteomic analysis unveils dynamic molecular responses to single, dual, and triple plasmid transfection of HEK293 cells for recombinant adeno-associated virus vector production

city: Dublin

first: Mark

last: Smales

state: Co. Dublin

address: Fosters Avenue

department: Advanced Biotherapies and Cell Factory

country: Ireland

institute: National Institute for Bioprocessing Research and Training

summary: Despite clinical success, scalable and high-titer manufacturing of recombinant adeno-associated virus (rAAV) remains challenging, partially due to a limited understanding of the underlying cellular mechanisms and regulatory factors that govern production. We systemically investigate single, dual and the prevailing triple plasmid transfection process for rAAV production in human embryonic kidney (HEK293) cells and subsequently elucidate cellular molecular impacts of each approach through integrative transcriptomics, proteomics and chemometrics. Using a ‘high concentration, H’ single plasmid transfection process yielded increased rAAV titer (3-12-fold) compared to dual or triple transfection with 1556 differentially expressed genes (DEGs) identified. Single plasmid transfection activated fundamental processes intrinsic to transient transfection, including immune and defense response of the host cells, in addition to regulation of viral processes. Key pathways correlating with improved rAAV productivity were identified, including MYC targets, interferon responses, E2F targets, oxidative phosphorylation, G2M checkpoint, mitotic spindle, and WNT beta catenin signalling. The top 25 signature genes correlating with rAAV productivity and top 30 hub genes were also identified, which collectively serve as targeted genome and pathway engineering points for improved rAAV production. The data provides a rich repository of knowledge for the rational optimization of transient transfection strategies for tangible improvements in rAAV manufacturing.

overall_design: This study systemically investigated the transcriptional changes of single, dual and the prevailing triple plasmid transfection processes for rAAV production in HEK293 cells, with three independent biological replicates per condition.

first: Yongjing

last: Xie


title: Direct DNA-RNA interactions dynamically decorate core functional elements within the human genome

city: Illkirch-Graffenstaden

first: Maximiliano

middle: M.

last: Portal

state: Alsace

address: 1 rue Laurent Fries

department: Functional Genomics and Cancer

country: France

institute: IGBMC

summary: Half a century ago the rules that govern DNA-RNA interactions were thoroughly crafted. However, our understanding of the role played by these structures within the cell remains fragmentary. In that regard, early observations suggested that the human genome is decorated with RNA molecules in vivo, and though we cannot ascertain that those interactions are built through direct DNA-RNA contact, a large body of circumstantial evidence supports that DNA-RNA platforms play key roles in genome control. Conceptually, RNA molecules provide an exquisite targeting scaffold to interfere with biological processes or target protein complexes to specific genomic locations. However, due to the lack of a technological leap, only a handful of documented examples describing endogenous DNA-interacting RNAs have been reported. To tackle this issue we developed DNA-interacting RNA – Identification (DiR-ID) and DNA-interacting RNA – Footprint (DiR-F), versatile methods enabling the identification of DNA-interacting RNAs and retrieval of DNA-RNA interaction footprints at single nucleotide resolution and genome-wide scale. Notably, we observed that thousands of DNA-RNA platforms are scattered throughout the genome displaying a large overlap with core functional elements (active/inactive TSS/TTS, enhancers, and promoters, facultative and constitutive heterochromatin among others) suggesting that DNA-interacting RNA molecules play a role in chromatin organization and functionality. Indeed, by interfering with JHDM1D-AS1 non-coding RNA -a bona fide DNA-interacting RNA that binds to specific sites contained within facultative heterochromatin- we altered the local epigenetic landscape, thus indicating that DNA-RNA platforms contribute to the establishment/maintenance of functional chromatin states. Finally, we identified a large number of transcripts engaged into DNA-RNA platforms and demonstrated that their recruitment to DNA respond to biological cues. All in all, we show that coding and non-coding RNAs establish direct interactions with DNA decorating hitherto identified regulatory elements throughout the genome and glimpse at a genome-wide remodeling of the chromatin landscape as a result of the recruitment/dismissal of DNA-interacting RNAs to its specific binding sites.

overall_design: DNA-RNA direct interactions footprinting (DiR-F), DNA-interacting RNA identification (DiR-ID), ChIP-Seq, FAIRE-Seq and mNET-Seq in HeLa cells.

middle: M

first: Hinrich

last: Gronemeyer


title: Transcriptome analysis in the prefrontal cortex of Shank3 KI heterozygous mice treated with drug

overall_design: Shank3 KI HT and WT mice were analyzed on postnatal day 25 (P25), immediately following 3 weeks of drug treatment (P3-24) administered via maternal milk before weaning. Male and female mice were administered two different drugs (fluoxetine and lithium), and prefrontal cortex regions of the mice were dissected to perform RNA-seq.


title: PIWIL4 knockdown alters piRNA expression in RSV-infected immortalized small airway epithelial cells

city: Galveston

first: Tiziana

last: Corsello

address: 301 University Blvd

country: USA

institute: UTMB

summary: Respiratory syncytial virus (RSV) is a leading cause of acute lower respiratory tract infection in young children, the elderly, and immunocompromised hosts, and no effective vaccine or therapy exists for infants. PIWIL4, a member of the PIWI protein family that interacts with PIWI-interacting RNAs (piRNAs), was found to be induced by RSV infection in airway epithelial cells. To investigate the role of PIWIL4 in piRNA expression during RSV infection, immortalized small airway epithelial (iSAE) cells were transfected with either a non-targeting or a PIWIL4-targeting siRNA and then left uninfected or infected with RSV for 15 hours. piRNA expression was profiled using the Arraystar Human piRNA Microarray (HG19), which targets 23,677 unique piRNAs, to identify piRNAs differentially expressed upon PIWIL4 knockdown under basal and RSV-infected conditions.

overall_design: 4 samples, one array per condition. RNA pooled from a single experiment performed in triplicate wells was hybridized to one array per condition (no biological-replicate arrays); the same RNA samples used for the companion gene expression arrays (GPL28885) were used here. 2x2 factorial design: siRNA treatment (non-targeting control vs. PIWIL4-targeting siRNA, 300 nM) x infection status (uninfected control vs. RSV Long strain, MOI 5, 15 hours post-infection) in immortalized human small airway epithelial (iSAE) cells.

first: Tianshuang

last: Liu

first: Andrzej

middle: S

last: Kudlicki

first: Yuanyi

last: Zhang

first: Nicholas

last: Dillman

first: Sehar

last: Fazal

first: Roberto

last: Garofalo

first: Antonella

last: Casola


title: Transcriptome analysis in the prefrontal cortex of Tbr1+/K228E heterozygous mice treated with drug

first: Eunjoon

last: Kim

overall_design: Tbr1+/K228E HT and WT mice were analyzed on postnatal day 25 (P25), immediately following 3 weeks of drug treatment (P3-24) administered via maternal milk before weaning. Male and female mice were administered two different drugs (fluoxetine and lithium), and prefrontal cortex regions of the mice were dissected to perform RNA-seq.

first: Junyeop Daniel

last: Roh

first: Yukyung

last: Jun

first: Mihyun

last: Bae

first: Hyojin


title: Transcriptome analysis in the prefrontal cortex of different ASD mouse models treated with drug


title: NREP deficiency reshapes liver-adipose lipid metabolism and the inflammatory microenvironment of adipose tissue

city: Zunyi

first: Hongkun

last: Li

address: Campus No. 1 Road, Zunyi City, Guizhou Province, China.

institute: Zunyi Medical University

summary: Obesity and associated metabolic disorders, including metabolic syndrome, represent a major global health challenge, but their underlying molecular mechanisms remain incompletely understood. Here, we investigated the role of the neuronal regeneration related protein (NREP) gene in body weight regulation, systemic adipose accumulation and inflammatory remodeling of metabolic tissues. Using an integrative multi omics approach, we analyzed human hepatic transcriptome datasets, generated a CRISPR/Cas9 NREP knockout mouse model. Body weight, adipose and hepatic histology, circulating lipid profiles, liver and inguinal white adipose tissue transcriptomes, and selected metabolic genes were assessed. Gene-set enrichment and mMCP-counter analyses were used to explore inflammatory pathways and estimated immune and stromal cell populations. Clinical data analysis revealed significantly higher hepatic NREP expression in over weight individuals and in patients with nonalcoholic fatty liver disease and nonalcoholic steatohepatitis. Genetic ablation of NREP in mice resulted in reduced body weight, sex dependent remodeling of adipose tissue, and pronounced alterations in the serum lipidome. Transcriptomic profiling demonstrated that NREP deficiency reprograms hepatic lipid metabolic networks by promoting fatty acid oxidation and suppressing de novo lipogenesis. Differentially expressed genes were significantly enriched for long‑chain fatty acid metabolism, PPAR signaling, and pathways associated with tissue fibrosis. Simultaneously, NREP ablation reduced the enrichment of inflammation and immune related pathways in adipose tissue, improved the metabolic microenvironment, and induced a high turnover lipid metabolic state in peripheral adipose tissues. These findings identify NREP as a potential regulator of metabolic-inflammatory coupling, establish NREP as a key modulator of body weight and lipid metabolism, and provide mechanistic insights into the pathophysiology of obesity and related metabolic disorders.

overall_design: Bulk RNA sequencing was performed to characterize tissue-specific transcriptional changes induced by global Nrep deficiency. Wild-type C57BL/6 mice and global Nrep-knockout mice generated using CRISPR/Cas-mediated genome editing were maintained under specific-pathogen-free conditions on a standard maintenance diet with a 12-h light/dark cycle. Liver and inguinal white adipose tissue (iWAT) were collected at 16 weeks of age. Two tissue-specific genotype comparisons were conducted independently. The liver experiment included three wild-type biological replicates (ML1, ML2 and ML3) and three Nrep-knockout biological replicates (NL1, NL2, and NL3). The iWAT experiment included three wild-type biological replicates (WT3_1, WT3_2 and WT3_3) and three Nrep-knockout biological replicates (KO4_1, KO4_2 and KO4_3). Genotype was the primary experimental variable, and differential expression analyses were performed independently within each tissue. The study was not designed as a direct liver-versus-iWAT comparison.

first: Rui

last: Cao

first: Xingyan

first: Guangbo

last: Yuan

first: Wenhu

last: Jin

first: Guangchao

last: Xu


title: Transcriptome analysis in the prefrontal cortex of PTEN KI heterozygous mice treated with drug

overall_design: PTEN KI HT and WT mice were analyzed on postnatal day 25 (P25), immediately following 3 weeks of drug treatment (P3-24) administered via maternal milk before weaning. Male and female mice were administered two different drugs (fluoxetine and lithium), and prefrontal cortex regions of the mice were dissected to perform RNA-seq.

last: Kang


title: Transcriptome analysis in the prefrontal cortex of Tanc2 heterozygous mice treated with drug

overall_design: Tanc2 HT and WT mice were analyzed on postnatal day 25 (P25), immediately following 3 weeks of drug treatment (P3-24) administered via maternal milk before weaning. Male and female mice were administered two different drugs (fluoxetine and lithium), and prefrontal cortex regions of the mice were dissected to perform RNA-seq.


title: Transcriptome analysis in the prefrontal cortex of Kmt5b heterozygous mice treated with drug

overall_design: Kmt5b HT and WT mice were analyzed on postnatal day 25 (P25), immediately following 3 weeks of drug treatment (P3-24) administered via maternal milk before weaning. Male and female mice were administered two different drugs (fluoxetine and lithium), and prefrontal cortex regions of the mice were dissected to perform RNA-seq.


title: Transcriptome analysis in the prefrontal cortex of Shank3 delta C heterozygous mice treated with drug

overall_design: Shank3 delta C HT and WT mice were analyzed on postnatal day 25 (P25), immediately following 3 weeks of drug treatment (P3-24) administered via maternal milk before weaning. Male and female mice were administered two different drugs (fluoxetine and lithium), and prefrontal cortex regions of the mice were dissected to perform RNA-seq.


title: Transcriptome analysis in the prefrontal cortex of Myt1l heterozygous mice treated with drug

overall_design: Myt1l HT, WT mice were analyzed on postnatal day 25 (P25), immediately following 3 weeks of drug treatment (P3-24) administered via maternal milk before weaning. Male and female mice were administered two different drugs (fluoxetine and lithium), and prefrontal cortex regions of the mice were dissected to perform RNA-seq.


title: Transcriptome analysis in the prefrontal cortex of Scn2a heterozygous mice treated with drug

overall_design: Scn2a-HT and WT mice were analyzed on postnatal day 25 (P25), immediately following 3 weeks of drug treatment (P3-24) administered via maternal milk before weaning. Male and female mice were administered two different drugs (fluoxetine and lithium), and prefrontal cortex regions of the mice were dissected to perform RNA-seq.


title: Transcriptome analysis in the prefrontal cortex of Trip12 heterozygous mice treated with drug

overall_design: Trip12 HT and WT mice were analyzed on postnatal day 25 (P25), immediately following 3 weeks of drug treatment (P3-24) administered via maternal milk before weaning. Male and female mice were administered two different drugs (fluoxetine and lithium), and prefrontal cortex regions of the mice were dissected to perform RNA-seq.


title: Evolutionary decoupling of somatosensory circuit architecture and sensory neuron identity

city: New York

first: Hyemin

last: Lee

state: NY

address: 435 E 30th St

department: Neuroscience

institute: NYU Langone Medical Center

summary: Deeply conserved neural circuit architectures often depend on shared fate specification programs. The extent to which circuit evolution relies on the diversification of neuronal identities versus rewiring of existing populations remains poorly defined. We addressed this problem by examining the somatosensory system of the skate Leucoraja erinacea, leveraging its 420-million-year separation from mammals. We find that core somatosensory circuit features - including layering of the dorsal spinal cord and modality-specific targeting of sensory afferents - are deeply conserved, thus defining an ancestral vertebrate organization. Unexpectedly, the molecular programs specifying sensory subtypes diverge extensively from those in mammals. Although sensory neuron identity and spinal connectivity rely on target-derived cues, skates employ distinct and neurotrophin receptor and transcription factor identity codes. We propose that ancient spinal circuit organization functions as a scaffold that preserves system integrity while permitting diversification of sensory neuron regulatory programs, suggesting a general strategy for somatosensory circuit evolution.

overall_design: Single nuclei were extracted from spinal cords (pooled from 6 embryos) and dorsal root ganglia (pooled from 14 embryos), collected from stage 31 and 32 Leucoraja erinacea embryos, and used to prepare three single-nucleus RNA-seq libraries: two from dorsal root ganglia and one from spinal cord. Single nuclei were partitioned into pre-templated instant partitions (PIPs) following the manufacturer's instructions (Fluent BioSciences, now Illumina). Reverse transcription and library prep were then performed according to the manufacturer's protocol. Samples were sequenced on an Illumina NovaSeq X.

first: Paul

middle: W

last: Frazel

first: Elena

last: Singer-Freeman

first: Hanshin

middle: D

last: Shin

first: Heebal

first: Shane

middle: A

last: Liddelow

first: Myungin

last: Baek

first: Jeremy

last: Dasen


title: Transcriptome analysis in the prefrontal cortex of Naa15 heterozygous mice treated with drug

first: Eunjoon

last: Kim

overall_design: Naa15 HT and WT mice were analyzed on postnatal day 25 (P25), immediately following 3 weeks of drug treatment (P3-24) administered via maternal milk before weaning. Male and female mice were administered two different drugs (fluoxetine and lithium), and prefrontal cortex regions of the mice were dissected to perform RNA-seq.

first: Junyeop Daniel

first: Yukyung


title: Transcriptome analysis in the prefrontal cortex of Ash1l heterozygous mice treated with drug

overall_design: Ash1l HT and WT mice were analyzed on postnatal day 25 (P25), immediately following 3 weeks of drug treatment (P3-24) administered via maternal milk before weaning. Male and female mice were administered two different drugs (fluoxetine and lithium), and prefrontal cortex regions of the mice were dissected to perform RNA-seq.

last: Roh

first: Mihyun

first: Hyojin


title: Transcriptome analysis in the prefrontal cortex of Dyrk1a+/I48X heterozygous mice treated with drug

overall_design: Dyrk1a+/I48X and WT mice were analyzed on postnatal day 25 (P25), immediately following 3 weeks of drug treatment (P3-24) administered via maternal milk before weaning. Male and female mice were administered two different drugs (fluoxetine and lithium), and prefrontal cortex regions of the mice were dissected to perform RNA-seq.

last: Jun


title: Transcriptome analysis in the prefrontal cortex of Tbl1xr1 KI heterozygous mice treated with drug

overall_design: Tbl1xr1 KI HT and WT mice were analyzed on postnatal day 25 (P25), immediately following 3 weeks of drug treatment (P3-24) administered via maternal milk before weaning. Male and female mice were administered two different drugs (fluoxetine and lithium), and prefrontal cortex regions of the mice were dissected to perform RNA-seq.

last: Bae


title: Codon-Optimized Npc1 mRNA corrects Niemann-Pick Type C1 disease phenotypes in vitro and in vivo [RNA-Seq]

city: Oak Ridge

first: Alice

last: Townsend

state: TN

address: 1 Bethel Valley Rd

institute: ORNL

summary: Niemann-Pick type C1 disease is a lysosomal storage disorder caused by mutations in the NPC1 gene, resulting in the accumulation of unesterified cholesterol in multiple tissues. Despite its severity, therapeutic options remain limited. . Using codon-optimized Npc1 mRNA delivered by lipid nanoparticles (Co-Npc1:LNP), we achieved enhanced NPC1 protein expression and prolonged therapeutic activity in vitro, correcting both primary and secondary disease defects. In an Npc1-/- mouse model, a single intravenous injection of Co-Npc1:LNP restored hepatic NPC1 protein levels, normalized autophagic flux, improved lipid abnormalities, and altered markers of liver injury. To interpret transcriptional changes post-Co-Npc1:LNP administration, we performed bulk RNA sequencing and applied MENTOR, a network-based clustering algorithm, and MENTOR-IA, an unbiased functional annotation tool, and identified restored pathways including cholesterol metabolism, lysosomal and mitochondrial function, and liver homeostasis. Overall, Co-Npc1:LNP in the Npc1-/- mouse liver showed a transcriptional shift towards a more Npc1+/+ state. Integration of single-nucleus RNA sequencing with our bulk transcriptomics further revealed cell-type-specific correction of disease-associated gene expression across hepatic cell types. Together, we report the development and in vivo validation of the first mRNA-based therapeutic for Niemann-Pick type C1.

overall_design: To test whether a lipid particle (LP)-encapsulated mRNA therapy can treat Niemann-Pick type C1 disease, mice lacking Npc1 (Npc1-/-) were compared with healthy, wildtype controls (Npc1+/+) following delivery of a control (GFP) or therapeutic (Npc1) formulated within an LP. 3-week-old Npc1+/+ were treated with saline (n=5) and Npc1-/- mice were treated with GFP mRNA (GFP:LP) (n=4), or codon-optimized Npc1 mRNA (Co-Npc1:LP) (n=5). Livers were collected 48 hours after treatment and homogenized for bulk sequencing.

first: Ellen

middle: R

last: Koufer

first: Youngseo

first: Adele

middle: B

last: Correia

first: Noah

middle: K

last: Latham

first: Koralege

middle: C

last: Pathmasiri

first: Kyle

last: Sullivan

first: Troy

last: Halseth

first: Elizabeth

last: Phillippi

first: Matthew

middle: L

last: Lieberman

first: Stephanie

last: Cologna

first: Andrew

first: Daniel

last: Jacobson

first: Anna

last: Schwendeman

first: Mark

last: Schultz


title: Transcriptome analysis in the prefrontal cortex of Arid1b heterozygous mice treated with drug

first: Eunjoon

last: Kim

overall_design: Arid1b-HT and WT mice were analyzed on postnatal day 25 (P25), immediately following 3 weeks of drug treatment (P3-24) administered via maternal milk before weaning. Male and female mice were administered two different drugs (fluoxetine and lithium), and prefrontal cortex regions of the mice were dissected to perform RNA-seq.

first: Junyeop Daniel

first: Yukyung

first: Mihyun

last: Kang


title: Transcriptome analysis in the prefrontal cortex of Chd8+/N2373K heterozygous mice treated with drug

overall_design: Chd8+/N2373K and WT mice were analyzed on postnatal day 25 (P25), immediately following 3 weeks of drug treatment (P3-24) administered via maternal milk before weaning. Male and female mice were administered two different drugs (fluoxetine and lithium), and prefrontal cortex regions of the mice were dissected to perform RNA-seq.

last: Roh

last: Jun

first: Hyojin


title: Transcriptome analysis in the prefrontal cortex of Grin2b+/C456Y heterozygous mice treated with drug

overall_design: Grin2b+/C456Y and WT mice were analyzed on postnatal day 25 (P25), immediately following 3 weeks of drug treatment (P3-24) administered via maternal milk before weaning. Male and female mice were administered two different drugs (fluoxetine and lithium), and prefrontal cortex regions of the mice were dissected to perform RNA-seq.

last: Bae


city: Seoul

first: Hanshin

middle: David

last: Shin

address: 1 Gwanak-ro, Gwanak-gu,

department: Interdisciplinary Program in Bioinformatics

institute: Seoul National University

summary: The extent to which conserved neural circuit architectures depend on shared molecular specification programs remains unclear. Here, we address this problem in the vertebrate somatosensory system using the little skate (Leucoraja erinacea), an early-diverging vertebrate that retains ancestral features of both finned and limb-based body plans. Combining molecular profiling, spatial transcriptomics, and embryological manipulations, we show that core features of somatosensory circuit organization—including laminar organization of the dorsal spinal cord and modality-specific targeting of sensory afferents—are deeply conserved. In contrast, the molecular programs that define sensory neuron subtypes are extensively reconfigured, including divergent neurotrophin receptor and transcription factor codes. We demonstrate that target-derived cues regulate molecular programs and are required for sensory neuron differentiation and circuit assembly. Together, these findings support a model in which conserved circuit architectures provide a stable scaffold that leverages flexible molecular programs to enable the evolutionary diversification of sensory systems.

overall_design: Bulk RNA-seq was performed on spinal cord (SC) and dorsal root ganglia (DRG) dissected from stage 32 Leucoraja erinacea embryos (3 biological replicates each, each replicate pooled from 3-4 embryos). Differential expression analysis between SC and DRG tissues was used to define tissue-specific gene expression signatures. Data were analyzed using edgeR with TMM normalization. Results were integrated with single-nucleus RNA-seq (PIPseq) and 10x Genomics Xenium spatial transcriptomics to characterize somatosensory neuron identity and circuit organization. Embryological fin-bud ablation experiments were used to test the role of target-derived cues in sensory neuron specification and circuit assembly.

first: Jeremy

last: Dasen

first: Myungin

last: Baek

first: Shane

last: Liddelow

first: Heebal

first: Hyemin

last: Lee

first: Paul

last: Frazel

first: Elena

last: Singer-Freeman


title: Astrocyte-derived cholesterol drives synaptic gene expression in developing neurons and reciprocal astrocytic transcriptional programs

city: Helsinki

first: Olli

last: Pietilainen

address: Haartmaninkatu 8

country: Finland

institute: University of Helsinki

summary: Astrocytes participate in neuronal synaptic programs enriched for genetic associations in schizophrenia and autism spectrum disorders (ASD). To understand how these co-regulated cellular programs are induced during early neuronal development, we studied astrocytes and iPSC-derived neurons in co-cultures and mono-cultures across 16 time points spanning 0.5 hours to 8 days. We found that upregulation of astrocytic cholesterol biosynthesis genes preceded the activation of synaptic gene programs in neurons and upregulation of astrocytic Nrxn1. Neuronal knockdown of key cholesterol receptors led to downregulation of neuronal synaptic genes and induced a robust transcriptional response in astrocytes, including further upregulation of Nrxn1. This suggests that astrocyte-supplied cholesterol drives neuronal synaptic changes and that bi-directional signalling is occurring. The upregulated neuronal genes were enriched for deleterious variants associated with schizophrenia and neurodevelopmental disorders, suggesting that their pathogenic effect may be, in part, mediated by reduced neuronal buffering capacity against fluctuations in astrocyte-derived cholesterol supply. These findings highlight the critical role of astrocyte-neuron interactions in psychiatric and neurodevelopmental disorders, particularly in relation to lipid metabolism and synaptic plasticity.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design:
Bulk RNA-seq profiling of human independent experiments in co-culture and mono-culture of iPSC-derived neurons (4 human cell lines: WTC-11, 1827, 1828, 2450) and mouse astrocytes. For one cell line (WTC-11) 4 experimental replicates of independent differentitions in 15 times points, as well as 4 mono-culture experiments at 48 hours. For three cell lines (1827, 1828, 2450) 3 experimental replicates of independent differentitions in 4 times points. In addition, 36 CRISPRi experiments were carried out using 3 independent guide RNAs for LRP1 and LDLR and 3 non-targeting guide RNAs with 4 experimental replicates in each (human iPCS cell line WTC11_TO-NGN2_dCas9-BFP-KRAB).

Bulk RNA-seq profiling of human independent experiments in co-culture of iPSC-derived neurons (3 human cell lines 1827, 1828, 2450) and mouse astrocytes. 3 experimental replicates of independent differentitions in 4 times points.

first: Vartiainen

last: Emilia

first: Liyanage

last: Dhara

first: Xu

last: He Jax

first: Schultz

last: Carson

first: Mazureac

last: Ilinca

first: Battaglia

last: Rachel A.

first: Trontti

last: Kalevi

first: Tegtmeyer

last: Matthew

first: Laakkonen

last: Pirjo

first: Filppu

last: Pauliina

first: Räsänen

last: Noora

first: Vuokila

last: Veikko

first: Niemimaa

last: Nea

first: Sealock

last: Julia

first: McMarroll

last: Steven

first: Nehme

last: Ralda

first: Pietiläinen

last: Olli


title: Nuclear receptor Nur77 resolves the inflammatory response of macrophages primarily by cis- and trans-regulation of AP-1 target genes [RNA-Seq]

city: Amsterdam

first: Claudia

last: van Tiel

address: Meibergdreef 15

department: Medical Biochemistry

country: Netherlands

institute: Amsterdam UMC

summary:
The nuclear receptor Nur77 plays a crucial, protective role in chronic inflammatory diseases and deficiency of Nur77 in macrophages results in excessive pro-inflammatory cytokine secretion. Previous research suggested that Nur77's regulatory function in inflammation is due to repression of the pro-inflammatory transcription factor NF-ĸB, but the underlying mechanism remains unclear. To address this, we applied a genome-wide, multi-omics approach in LPS-stimulated RAW264.7 macrophages with inducible Nur77 expression. Key findings were validated in wild-type and Nur77-deficient bone marrow-derived macrophages. We show that Nur77 suppresses the expression of inflammatory genes through a dual mechanism wherein Nur77 acts as a repressor of AP-1 targets at two levels: First, Nur77 occupies regulatory elements proximal to AP-1 target genes through AP-1 motifs and second, Nur77 regulates the expression of AP-1 family members themselves. These repressive activities of Nur77 result in diminished RNA Pol II on AP-1 genes and their targets. The first zinc finger of the Nur77 DNA-binding domain is required to reduce AP-1 activity.
In summary, Nur77 represses macrophage inflammation through regulation of both immediate-early AP-1 expression, as well as inhibition of AP-1-driven gene programs.

overall_design: Comparison of gene expression in RAW cells stably transfected with Nur77 or GFP, stimulated with 500 ng/ml LPS for 0, 1 and 5 hours. (n=4 per group )

first: Sanne

last: Lith

first: Sebastian

last: Gregoricchio

first: Beatriz

last: Freire

first: Simon

last: Linder

first: Onno

last: Bleijerveld

first: Liesbeth

last: Hoekman

first: Guglielmo

last: Alonzo

first: Wilbert

last: Zwart

first: Marten

last: Hoeksema

first: Carlie

middle: J

last: de Vries


title: Nuclear receptor Nur77 resolves the inflammatory response of macrophages primarily by cis- and trans-regulation of AP-1 target genes [ATAC-Seq]

overall_design: Comparison of chromatin acessibilitiy in RAW cells stably transfected with Nur77 or GFP, stimulated with 500 ng/ml LPS for 0 and 1 hour (n=3 per group )


title: Transcriptome analysis in the prefrontal cortex of Adnp heterozygous mice treated with drug

first: Eunjoon

last: Kim

overall_design: Adnp HT and WT mice were analyzed on postnatal day 25 (P25), immediately following 3 weeks of drug treatment (P3-24) administered via maternal milk before weaning. Male and female mice were administered two different drugs (fluoxetine and lithium), and prefrontal cortex regions of the mice were dissected to perform RNA-seq.

first: Junyeop Daniel

last: Roh

first: Yukyung

last: Jun

first: Mihyun

last: Bae

first: Hyojin

last: Kang


title: Nuclear receptor Nur77 resolves the inflammatory response of macrophages primarily by cis- and trans-regulation of AP-1 target genes [ChIP-Seq]

overall_design: ChIP-seq for Nur77, RNA polymerase II and H3K27ac in RAW264.7 cells stably expressing HA-tagged Nur77 or GFP, stimulated with 500 ng/ml LPS for 0 and 1 hour. (n=2 or 3 per group )


title: Single-nucleus RNA-seq atlas of 17 ASD-risk mouse lines under early-postnatal fluoxetine or lithium exposure (4-plex On-Chip Multiplexed)

summary: Autism spectrum disorder (ASD) involves more than 1,000 risk genes, complicating mechanistic subtyping. To resolve the cellular basis of transcriptomic stratification, we generated single-nucleus RNA-seq (snRNA-seq) profiles from the prefrontal cortex of 17 mouse lines carrying ASD-associated synaptic, chromatin-regulatory, and signaling mutations, together with C57BL/6J wild-type controls. Both sexes were profiled under baseline and early-postnatal (P3-P25) fluoxetine or lithium exposure. Four mice were multiplexed per 10x Genomics GEM-X v4 4-plex On-Chip Multiplexing (OCM) library, yielding 53 sequencing libraries (tubes) covering 212 individual mice. After downstream QC, approximately 1,016,895 nuclei from 205 mice were retained at postnatal day 25.

overall_design: Four-plex On-Chip Multiplexing (OCM) design: 4 mice -> 1 GEM well -> 1 sequencing library (tube). 53 tubes / 212 mice total. Each GSM in this Series corresponds to one tube; per-sample MEX matrices for the 4 multiplexed mice are provided as supplementary files of that GSM. Tube <-> mouse mapping is provided in mouse_to_pool.tsv (Series-level supplementary file).


title: First-line Sintilimab with P-GEMOX chemotherapy in advanced Extranodal Natural Killer/T cell lymphoma (SPIRIT): a single-arm, multicenter, phase 2 trial

city: Guangzhou

first: Xiao-Peng

last: Tian

address: 651 Dong Feng RD East

department: Department of Medical Oncology

institute: Sun Yat-sen University Cancer Center

summary: The addition of anti-PD-1 antibody to pegaspargase, gemcitabine and oxaliplatin (P-GEMOX) showed promising activity as first-line therapy in patients with advanced extranodal natural killer/T cell lymphoma, nasal type (ENKTL) in our previous retrospective study. Here, we assessed the clinical outcomes and multi-omics tumor profiling of sintilimab plus P-GEMOX for patients with previously untreated advanced ENKTL in this phase 2 trial.

overall_design: This was a multi-center, single-arm, phase 2 study conducted in four medical centers across China (ClinicalTrials.gov identifier: NCT04127227). Patients received sintilimab in combination with pegaspargase, gemcitabine and oxaliplatin once every 3 weeks (Q3W) for up to six cycles, followed by sintilimab monotherapy maintenance for up two years. In the induction phase, patients received sintilimab (200 mg administered intravenously on day 1), pegaspargase (2000 U/m2 administered intramuscular on day 1), gemcitabine (1g/m2 administered intravenously on days 1 and 8), and oxaliplatin (130 mg/m2 administered intravenously on day 1) every 3 weeks for six cycles. In the maintenance phase, patients received sintilimab (200 mg) Q3W until progressive disease, unacceptable toxicity, withdrawal of consent, or a maximum of 2 years of treatment.


title: Microtubule-RAB5 mutual-influential system screening based on gene-regulatory networks map in Rab5 RNAi eye-degeneration model

city: Hangzhou

first: Yuyu

state: Zhejiang

address: 79 Qingchun Rd., Shangcheng District

institute: The First Affiliated Hospital, Zhejiang University School of Medicine

summary: Rabs are involved in neuronal development and protrusion formation. Existing studies support the notion that manipulation or mutation of Rab genes could lead to functional changes in neurons. However, whether Rabs gene-manipulation induced Drosophila eye-degeneration remains unknown. By down-regulating Rab5, but not Rab7, we first constructed a compound eye injury model in Drosophila. As the distribution, content, and even maturation of RAB5-positive endosomes are influenced by cytoskeletal proteins, like actin or tubulin-related proteins, the existence of a bidirectional regulatory relationship between RAB5 and the cytoskeleton is unclear and worth researching. Through complete transcriptome sequencing combined immunofluorescence testing, we confirmed that down-regulation of Rab5 affected the expression of α-Tub84B (alternatively named TubA84B) but not γ-tubulin. Based on Weighted Gene Co-Expression Network Analysis (WGCNA) and multi-tissue screening verification, this study proposes that the apoptosis-related factors–Rab5–TubA84B have conserved regulatory functions with cooperative expression. Gene-manipulation confirmed that apoptotic factors, especially rpr, strongly regulated RAB5, and may ultimately influence microtubule structure through extremely complicated routes, including the RAB5 variance and the intracellular configuration ratio of α-tubulin to Glyceraldehyde-3-phosphate dehydrogenase.

overall_design: To investigate the Rabs family members in the regulation of Microtubule assmbly and tubulin expression,we established Rab5 RNAi, Rab7 RNAi and control Drosophila lines with the former exhibits severe eye-degeneration

first: Jingjing

last: Lin

first: Zaiwa

last: Wei

first: Yufeng

last: Yang

first: Qinghua

last: Li


title: CTCFL(BORIS) contributes to the transcriptional program of ovarian cancer by relaxing CTCF-mediated three-dimensional genome organization

status: Public on Jul 27 2026

city: Bethesda

first: Elena

last: Pugacheva

state: MD

department: NIAID

institute: NIH

summary: Disruption of three-dimensional genome architecture is a major driver of cancer initiation and progression, and genetic or epigenetic alterations of CTCF- and cohesin-bound chromatin anchors are among the principal mechanisms underlying this process. These same chromatin loop anchors can also be occupied by the germ cell–specific CTCF paralog CTCFL (BORIS), which is aberrantly reactivated in multiple malignancies. Here, we show that in ovarian cancer cells, BORIS reactivation establishes a distinct transcriptional program that collapses upon BORIS knockout and is accompanied by widespread changes in CTCF and cohesin occupancy, histone modifications, and chromatin accessibility. These BORIS-dependent transcriptional alterations occur in long-range genomic clusters, resulting in the coordinated activation or repression of neighboring genes, including hormonally regulated gene families. BORIS loss also increases topologically associating domain (TAD) insulation, strengthens A/B compartment segregation and chromatin loop interactions, and results in a more compact and constrained chromatin architecture. Together, our findings suggest that aberrant BORIS activation promotes transcriptional reprogramming by weakening CTCF-mediated chromatin insulation and relaxing three-dimensional genome organization in ovarian cancer.

overall_design: Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) in combination with RNA-seq and Hi-C data

first: Dharmendra Nath

last: Bhatt


title: Transcriptomic sequencing of subcutaneous fat of Guangdong small-eared pigs (GS) and Yorkshire pigs (YK) at different ages（9d and 80d)

first: Delin

last: Mo

address: Xingang Road

institute: Sun Yat-sen University

summary: In order to study the formation mechanism of the different backfat thickness of fat pigs and lean pigs, we selected the subcutaneous adipose tissue of fat pigs (GS) and lean pigs (YK) at different ages (8d and 90d) for RNA-Seq analysis.

overall_design: We extracted RNA from the subcutaneous adipose tissue of the middle part of the back of pigs of GS and YK breeds at 9 days and 80 days after birth, and performed differential expression analysis on the data after the database was established.

first: Xiaoyu

last: Wang

first: Rong

last: Xu


title: Single-molecule m6A profiling reveals position-dependent mRNA regulation and non-canonical roles for Ythdf2 in early embryogenesis

city: Farmington

first: Jean-Denis

last: Beaudoin

state: CT

address: 400 Farmington Avenue

department: Genetics and Genome Sciences

institute: UConn Health Center

summary: The maternal-to-zygotic transition (MZT) requires coordinated clearance and deadenylation of maternally-deposited mRNAs, yet the underlying molecular mechanisms remain poorly understood. N6-methyladenosine (m6A) has emerged as a key regulator of maternal mRNA fate, but prior studies have mainly relied on population-averaged short-read methods that cannot resolve modification state, poly(A) tail length, or isoform identity on the same molecule. Here, we employ nanopore direct RNA sequencing across the zebrafish MZT to resolve the interplay between m6A deposition, mRNA clearance, and poly(A) tail dynamics at single-molecule resolution. We find that 78% of expressed maternal genes harbor m6A-modified isoforms, significantly exceeding prior bulk estimates. Within-isoform comparisons demonstrate that m6A promotes mRNA decay, with CDS m6A contributing more than 3’-UTR m6A. The positional context of m6A directs the temporal regulation of poly(A) tail lengths. CDS m6A constitutively suppresses tail length throughout MZT, while 3′-UTR m6A promotes shortening only after zygotic genome activation (ZGA). Transcriptomic analysis of ythdf2 knockout embryos revealed two unrecognized roles. Ythdf2 sets m6A stoichiometry at MZT onset, and maintains global poly(A) tail homeostasis prior to ZGA through an m6A-independent mechanism. Together, these findings identify the single-molecule logic by which m6A modifications shape transcript fate during vertebrate MZT.

overall_design: m6A RNA modification basecalled Nanopore direct RNA-sequencing of zebrafish embryos in a developmental timecourse at 2, 4, and 6 hours per fertilization and MZythdf2 mutant and sibling WT zebrafish embryos at 2 and 6 hours per fertilization.

first: Sarah

last: Alshawi

first: Anna

last: Delgado-Tejedor

first: Srihari

last: Madhavan

first: Laia

last: Llovera

first: Rebeca

last: Medina

first: Cassandra

last: Kontur

first: Eva Maria

last: Novoa


title: A Glycolysis-Calcineurin Regulatory Axis Orchestrates Titan Cell Formation in Cryptococcus neoformans

city: Hyderabad

first: Sriram

last: Varahan

state: Telangana

address: Habsiguda

department: Microbes and biology of infection

country: India

institute: CSIR-Centre for Cellular and Molecular Biology

summary: Cryptococcus neoformans is an opportunistic fungal pathogen that causes pulmonary infections and life-threatening meningoencephalitis in immunocompromised individuals. In addition to the polysaccharide capsule and melanin, titan cell formation is a key virulence trait that promotes immune evasion and disease progression. Despite the established role of titan cells in C. neoformans pathogenesis, the molecular mechanisms governing their formation remain poorly understood. Here, we demonstrate that glycolysis is critical for titan cell formation in C. neoformans. Pharmacological inhibition or genetic disruption of glycolysis significantly impaired titanization, whereas exogenous cAMP add-back restored the defect. To elucidate the underlying mechanism, we performed comparative RNA-seq analyses of wild-type,  hxk2Δ, and  hxk2Δ supplemented with cAMP under titan cell inducing conditions. Transcriptomic analyses revealed significant downregulation of a large subset of calcineurin-responsive genes in the  hxk2Δ mutant, many of which were restored upon cAMP supplementation. Consistent with these findings, pharmacological inhibition of calcineurin using FK506 or cyclosporin A markedly reduced titan cell formation, establishing an essential role for calcineurin signaling in this morphological transition. Furthermore, supplementation with calcium chloride rescued the titanization defect of the  hxk2Δ mutant, whereas chelation of extracellular calcium with EGTA significantly inhibited titanization in wild-type cells. Using the calcium-sensitive dye, we found that intracellular calcium levels were substantially reduced in the  hxk2Δ mutant and were restored by calcium chloride or cAMP supplementation. Collectively, our findings uncover a previously unrecognized glycolysis–calcineurin regulatory axis that governs titan cell formation and establishes a direct mechanistic link between central carbon metabolism, calcium homeostasis and fungal morphogenesis.

overall_design: Wild-type,  hxk2Δ (with and without exogenous supplementation of cAMP) strains of C. neoformans were cultured in TCM at cell density of 10^6 CFU per ml for 24 hours at 37 °C under 5% carbon dioxide. Total RNA was isolated from cells harvested after 24 hours of incubation using the hot acid-phenol method.

first: Pallavi

last: Phatak

first: Sudharsan

last: Mathivathanan

first: Dhrumi

last: Shah

first: Ishvarya

last: Suresh

first: Mary

last: Shejo

first: Santosh Kumar

last: Das


title: Heterogeneous epigenetic variation converges on splicing dysregulation in opioid addiction

city: Cambridge

first: Chesna

last: Apere

state: Massachusetts

address: 455 Main St

department: Biology

institute: Whitehead Institute for Biomedical Research

summary: Disease heterogeneity presents a major challenge for genetic and epigenetic dissection of complex traits such as opioid use disorder (OUD). Here, we leverage individual heterogeneity to identify epigenetic variation linked to opioid overdose by profiling H3K27ac ChIP-seq in nucleus accumbens (NAc) from 91 overdose cases and accidental death controls. Machine learning models built on combinations of peaks distinguished cases from controls with high accuracy (AUROC = 0.95) and were enriched for OUD genetic risk. We defined individual-specific H3K27ac changes as Variant Enhancer Loci (VEL) and observed four-fold greater convergence on shared target genes in NAc than in prefrontal cortex. Convergent VEL target genes were enriched in independent OUD cohorts, and RNA splicing emerged as the top-enriched ontology. Knockdown of the splicing regulator CELF5 in iPSC-derived medium spiny neurons disrupted extracellular matrix organization genes. Collectively, this study provides new insights into opioid addiction and a conceptual framework for dissecting heterogeneous disorders.

overall_design: RNA-seq of iPSC-derived medium spiny neurons treated with scrambled (SCR) control or CELF5 siRNA. The study included two independent cell lines with six biological replicates per treatment condition in each cell line.

first: Fatir

last: Qureshi

first: Chidera

last: Okeke

first: Bibi

last: Kassim

first: Marina

last: Iskhakova

first: Richard

last: Sallari

first: Maharshi

last: Chakraborty

first: Laura

last: Morgan

first: Zia

last: Barnard

first: Xochitl

last: Luna

first: Megan

middle: E

last: Madden

first: Pavana

middle: G

last: Rotti

first: Sofia

last: Agueldo-Viales

first: Yike

last: Huang

first: Yasmine

middle: N

last: Sami

first: Scott

last: McCallum

first: An

middle: T

last: Hoang

first: Hannah

last: Ramcharan

first: Bryan

last: Quach

first: Caryn

last: Willis

first: Brion

last: Maher

first: Deborah

last: Mash

first: Peter

last: Scacheri

first: Eric

middle: O

last: Johnson

first: Schahram

last: Akbarian

first: Olivia

last: Corradin


title: CHI3L1 promotes proliferation and metastasis of ovarian cancer cells

city: Shanghai

first: Yaodi

last: Shao

address: 2699 West Gaoke Road

institute: Shanghai First Maternity and Infant Hospital

summary: Adipocyte-tumor interaction plays a critical role in tumor microenvironment. Typically, high-grade serous ovarian carcinoma (HGSOC) preferentially metastasizes to the omentum, an adipocyte-rich tissue, and obesity correlates with worse patient prognosis. However, the underlying mechanisms remain poorly understood. Here, we identify a bidirectional adipocyte–cancer cell axis in which HGSOC cells stimulate lactate metabolism in adjacent adipocytes, leading to hypoxia-inducible factor 1α (HIF-1α) activation and subsequent secretion of chitinase 3-like 1 (CHI3L1). On the one hand, CHI3L1 acts as an inflammatory factor that promotes the secretion of additional cytokines, perpetuating omental inflammation, driving CD8⁺ T cell exhaustion, and shaping an immunosuppressive microenvironment that favors tumor metastasis. On the other hand, CHI3L1 binds to and stabilizes protein arginine methyltransferase 5 (PRMT5) in tumor cells, thereby enhancing its methyltransferase activity. This upregulation suppresses dual-specificity phosphatase 1 (DUSP1), a phosphatase of mitogen-activated protein kinase (MAPK), and sustains oncogenic MAPK signaling across multiple tumor models. Obesity amplifies this pathway by heightening HIF-1α activity and elevating CHI3L1 levels in adipose tissue, which drives both tumor progression and resistance to anti-angiogenic therapy. Pharmacological inhibition of CHI3L1 disrupts this signaling loop and restores therapeutic sensitivity, while also alleviating immune exhaustion in the tumor microenvironment. Collectively, our findings establish CHI3L1 as a key mediator of a unified mechanism that drives omental tropism and obesity-associated aggressive phenotypes, highlighting its potential as a prognostic biomarker and therapeutic target to improve anti-angiogenic therapy.

overall_design: RNA-seq analysis in CHI3L1-knockdown ovarian cancer cells


title: Distinct activation programs in naïve and memory CD8 T cells govern progeny stemness and effector persistence (single cell experiment, NupHox mice, LCMV-OVA infection, Day 3 and Day 5)

city: Prague

first: Juraj

last: Michalik

address: Vídeňská 1083

country: Czech Republic

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

summary: We longitudinally profiled gene expression in naive and central and effector memory CD8+ T cells across multiple models of acute cognate infection to reveal subset-specific activation programs. However, how prior antigen experience alters T-cell activation programs remains poorly understood. We longitudinally profiled gene expression in naive, central memory, and effector memory CD8+ T cells in response to cognate antigen across multiple models of acute infection. Naive T cells engaged TOX- and TCF7-centered programs and generated early stem-like central memory precursors. Their initially slow proliferation was followed by rapid expansion and the production of large numbers of effector cells. Central memory T cells rapidly triggered effector and proliferation programs while maintaining a smaller self-renewing population. Effector memory T cells expanded poorly and generated almost exclusively effector progeny. Effector progeny derived from both memory subsets survived contraction more efficiently than naive T-cell-derived progeny and established persistent effector memory populations. These data show that prior antigen experience does not simply accelerate CD8+ T-cell activation but redirects cell-intrinsic programs governing progeny fate and persistence. These distinct programs may reflect adaptation to different histories and anticipated patterns of antigen exposure.

overall_design: Here we compared different cell types (Tm and Tn) from multiple samples using single-cell analysis.

first: Eva

last: Salyova

first: Darina

last: Paprckova

first: Veronika

last: Niederlova

first: Ondrej

last: Stepanek


title: Magnolol triggers ferroptosis in triple-negative breast cancer through modulation of the ETS2/SLC7A11/GPX4 signaling axis

city: Bengbu City, Anhui Province

first: Bohan

last: Li

address: 安徽省蚌埠市东海大道2600号

department: School of Pharmacy

institute: Bengbu Medical University

summary: Background: Ferroptosis, an iron-dependent form of regulated cell death driven by lipid peroxidation (LPO), represents a promising therapeutic strategy. Magnolia officinalis, a traditional herb for resolving dampness and phlegm, is known to modulate cellular metabolism. While magnolol (MAG), a bioactive neolignan from Magnolia officinalis, shows anti-TNBC activity, its role in inducing ferroptosis remains unexplored. Methods: Anti-TNBC effects of MAG were assessed in MDA-MB-231 and 4T1 cells via viability, apoptosis, and ferroptosis assays (intracellular Fe²⁺, LPO, GSH). Target identification employed network pharmacology, RNA-seq, surface plasmon resonance, and pull-down assays. Mechanisms were validated using siRNA/overexpression, Co-IP, and immunofluorescence. In vivo efficacy was evaluated in xenograft models. Results: MAG inhibited proliferation and induced apoptosis and ferroptosis in TNBC cells, evidenced by elevated Fe²⁺ and lipid peroxidation, depleted GSH, downregulated SLC7A11/GPX4, and mitochondrial shrinkage effects reversed by ferroptosis inhibitors. MAG directly bound and suppressed transcription factor ETS2. ETS2 knockdown sensitized cells to MAG-induced ferroptosis, while its overexpression restored SLC7A11/GPX4 expression and conferred resistance. Mechanistically, ETS2 transcriptionally regulated SLC7A11, and MAG enhanced ETS2-SLC7A11 protein interaction. In vivo, MAG significantly suppressed tumor growth with low toxicity and downregulated ETS2, SLC7A11, and GPX4. Conclusions: MAG induces ferroptosis in MDA-MB-231 cells, which may be mediated by targeting the ETS2/SLC7A11/GPX4 signaling axis, providing mechanistic insights into its anti-TNBC activity.

overall_design: To gain the signaling pathways of MAG in triple-negative breast cancer and the key proteins involved in ferroptosis, we performed RNA‑sequencing on control, MAG‑treated cells.


title: Single-cell RNA sequencing of human iPSC-derived forebrain organoids following amyloid-β42 treatment, microglia co-culture, and maraviroc treatment

city: Shenzhen

first: Yilin

last: Feng

state: Please Choose

address: XILI Street

institute: Tsinghua University

summary: Human induced pluripotent stem cell (iPSC)-derived forebrain organoids were used to model Alzheimer's disease-associated pathology and investigate the effects of microglia co-culture and CCR5 inhibition. Day 60 forebrain organoids were assigned to four experimental groups: untreated control, amyloid-β42 (Aβ42)-treated, Aβ42-treated followed by co-culture with mature human iPSC-derived microglia, and Aβ42-treated followed by maraviroc treatment and co-culture with mature human iPSC-derived microglia. Single-cell RNA sequencing was performed using the MGI DNBelab C-TaiM4 platform to characterize transcriptional changes and cellular composition across the four experimental conditions.

overall_design: Human iPSC-derived forebrain organoids were differentiated to Day 60 and assigned to four experimental groups: (1) untreated control (CTR), (2) Aβ42-treated (AD), (3) Aβ42-treated followed by 48-hour co-culture with mature human iPSC-derived microglia (AD_mgL), and (4) Aβ42-treated with maraviroc followed by 48-hour co-culture with mature human iPSC-derived microglia (AD_mgL_mar). Two independent biological replicates were analyzed for each condition, with each biological replicate consisting of three pooled forebrain organoids. Following completion of the treatments, organoids were dissociated into single-cell suspensions and processed using the MGI DNBelab C-TaiM4 single-cell RNA sequencing platform. Gene expression libraries and oligo libraries were sequenced on the DNBSEQ-T7 platform in paired-end 100-bp mode (PE100). Raw sequencing data were processed to generate gene-by-cell expression matrices for downstream quality control, clustering, cell type annotation, and differential gene expression analyses.


title: Multi-species genome-wide CRISPR screens identify conserved suppressors of cold-induced cell death

first: Tara

last: Thakurta

state: MA

address: 455 Main Street

institute: Whitehead Institute

summary: Bulk RNA-seq was performed on a hamster cell line (BHK-21) and a human cell line (K562). Cells were maintained at 37 C and then exposed to 4 C - K562 for 24 hours and 5 days, BHK-21 for 4 days - with three biological replicates per condition.

sample_organism:
Homo sapiens
Mesocricetus auratus

platform_organism:
Homo sapiens
Mesocricetus auratus

overall_design: Bulk RNA-seq of hamster BHK-21 and human K562 cells at 37 C and after cold (4 C) exposure. BHK-21: 37 C and 4-day 4 C (three biological replicates each; 6 samples). K562: 37 C, 24-hour 4 C, and 5-day 4 C (three biological replicates each; 9 samples). Libraries were sequenced paired-end (2x50) on an Illumina NovaSeq 6000.

first: Breanna

last: Lam

first: Kathrin

middle: M

last: Kajderowicz

first: Sinisa

last: Hrvatin


title: Ca²⁺-induced lysosomal dysfunction promotes SR-derived vesicle accumulation and microtubule aster formation in PLN R14del cardiomyopathy

city: Utrecht

first: Iris

last: Gooijers

address: Uppsalalaan 8

institute: Hubrecht Institute

summary: The structural and functional integrity of long-lived cells, like cardiomyocytes, depends heavily on robust degradation mechanisms, and disruption of these mechanisms can drive protein accumulation and cellular degeneration. Genetic variants in phospholamban (PLN), the main inhibitor of the sarco/endoplasmic reticulum Ca²⁺-ATPase 2a (SERCA2a), cause inherited cardiomyopathy characterized by the abnormal perinuclear accumulation of PLN protein resulting in a progressive loss of cardiomyocytes. However, the nature of these PLN structures, the mechanisms driving their formation, and their role in disease progression remain largely unresolved. Using a plna R14del zebrafish model, left ventricular tissue from end-stage PLN R14del cardiomyopathy patients, and pharmacological inhibition of SERCA2a in wild type (WT) cardiac slices, we demonstrate that abnormal perinuclear accumulation of PLN represents clusters of sarcoplasmic reticulum (SR)-derived PLN-containing vesicle-like structures that form due to impaired SERCA2a activity and increased cytosolic Ca²⁺ levels. Furthermore, we show that these SR-derived vesicle-like structures often localize adjacent to lysosomes. Interestingly, Ca²⁺dysregulation in plna R14del hearts leads to reduced lysosomal function, resulting in the accumulation of SR-derived vesicle-like structures at the microtubule organizing center (MTOC). Strikingly, the accumulation of vesicle-like structures at the MTOC is accompanied by reorganization of the linear microtubule network into asters, ion-channel mislocalization, sarcomere disorganization, and nuclear deformation. Restoration of lysosomal function through Ca²⁺ buffering or fasting reduces vesicle accumulation, restores microtubule organization, and rescues cellular architecture. Collectively, our study defines a Ca²⁺-sensitive pathway linking the formation of SR-derived vesicle-like structures, lysosomal dysfunction, and microtubule remodeling to pathological cellular rearrangements.

overall_design: SORT-seq of cardiomyotyes obtained from hearts extracted from one year old WT and plna R14del zebrafish.

first: Aleksandra

last: Arning

first: Cecilia

last: de Heus

first: Ursula

last: Heins-Marroquin

first: Phong

last: Nguyen

first: Hessel

last: Honkoop

first: Tim

last: Verhagen

first: Mostafa

last: Mokhles

first: Anneline

last: te Riele

first: Magdalena

last: Harakalova

first: Gijs

last: van Haaften

first: Linda

last: van Laake

first: Lukas

last: Kapitein

first: Nalan

last: Liv

first: Jeroen

last: Bakkers


title: Mapping transcriptional responses to cellular perturbation dictionaries with RNA fingerprinting [K562_drug]

first: Isabella

last: Grabski

address: 101 Avenue of the Americas

institute: New York Genome Center

summary: Single-cell perturbation dictionaries systematically measure how cells respond to genetic and chemical perturbations, creating the opportunity to assign causal interpretations to observational data. We introduce RNA fingerprinting, a statistical framework that maps transcriptional responses from new experiments onto reference perturbation dictionaries. RNA fingerprinting learns representations of perturbations, or ``fingerprints," from single-cell data, then probabilistically assigns query cells to one or more candidate perturbations. We benchmark our method across ground-truth datasets, demonstrating accurate assignments at single-cell resolution, scalability to genome-wide screens, and the ability to resolve combinatorial perturbations. We demonstrate its broad utility across diverse biological settings: identifying context-specific regulators of p53 under ribosomal stress, characterizing drug mechanisms of action and dose-dependent off-target effects, and uncovering cytokine-driven B cell heterogeneity during secondary influenza infection in vivo. Together, these results establish RNA fingerprinting as a versatile framework for interpreting single-cell datasets by linking cellular states to the underlying perturbations which generated them.

overall_design:
A549 cells received siRNA knockdowns, followed by DMSO or nutlin-3a treatment, and were then profiled in a multiplexed fashion with FlexPlex.
K562 cells received pooled CRISPRi perturbations and were then profiled with 10x 3’ scRNA-seq.
K562 cells were treated with HDAC inhibitors across a range of doses and then profiled with a multiplexed fashion with FlexPlex.

first: Blair

last: John

first: Lee

last: Junsuk

first: Mascio

last: Isabella

first: Dalgarno

last: Carol

first: Bradu

last: Alexandra


title: Mapping transcriptional responses to cellular perturbation dictionaries with RNA fingerprinting [k562_crispri]


title: Mapping transcriptional responses to cellular perturbation dictionaries with RNA fingerprinting [scRNA-Seq]

overall_design: A549 cells received siRNA knockdowns, followed by DMSO or nutlin-3a treatment, and were then profiled in a multiplexed fashion with FlexPlex.


title: Polymicrobial-driven NLRP6 inflammasome regulates 1 IL-1b production and alveolar bone loss in a murine model of periodontitis

city: Buffalo

first: Jason

last: Kay

address: 3435 Main Street

institute: University at Buffalo

summary: Periodontal disease is a chronic inflammatory condition that develops in response to oral microbiome dysbiosis and host-microbiome immune response dysregulation. The innate immune system plays a major role in the development and persistence of disease in part by producing inflammatory cytokines. One of the major cytokines implicated in disease is interleukin-1b (IL-1b), which requires inflammasome activation. Much of the oral microbiome, including Streptococci, which are otherwise considered commensal, is required for the full development of periodontal disease. We have previously reported that inflammatory-activated macrophages and neutrophils counterintuitively allow survival of internalized Streptococcus gordonii over non-activated phagocytes. This internal bacterial survival leads to inflammasome activation via the cytoplasmic activator NLRP6, but not NLRP3, and subsequent increases in IL-1b release. Here, we test and find that the keystone pathogen Porphyromonas gingivalis can activate macrophages in a manner that allows for increased S. gordonii survival and IL-1b production above levels when P. gingivalis interacts with macrophages alone. We also use the mouse ligature-induced periodontal disease model to test the importance of NLRP6 in disease development. We found mice lacking NLRP6 had significantly reduced bone loss, IL-1b, and neutrophil infiltration following disease induced by P. gingivalis when S. gordonii or other mouse commensals were present, but had no effect when S. gordonii was inoculated alone. This work thus reveals an additional important inflammasome activation mechanism by which oral keystone pathogens may stimulate periodontal disease progression.

overall_design: RNA-seq profile of mouse oral gingival tissue, which was subjected to a 2-week ligature model and treated with nothing, sham, S.gordonii, P. gingivalis, or P. gingivalis + S. gordonii.

first: Sarah

last: Metcalfe

first: Rajenda

middle: P

last: Settem

first: Edwin

last: Ovalle

first: Michelle

last: Panasiewicz

first: Alejandro

last: Escobar


title: Dual host-pathogen RNA sequencing of wild-type and EZH2-deficient Hoxb8-derived macrophages during Mycobacterium tuberculosis infection

city: Ithaca

first: bom nae rin

last: lee

address: 930 Campus Road

department: Microbiology&Immunology

institute: Cornell university

summary: Polycomb repressive complex 2 (PRC2) and its catalytic subunit EZH2 regulate macrophage permissiveness to intracellular Mycobacterium tuberculosis (Mtb). To define the host and bacterial transcriptional responses associated with EZH2 loss, we performed dual host-pathogen RNA sequencing of parental Cas9-expressing Hoxb8-derived macrophages and CRISPR-generated EZH2-deficient macrophages under uninfected conditions and at 3 days after infection with Mtb Erdman smyc'::mCherry. Host and pathogen transcriptomes were quantified to identify macrophage programs associated with bacterial restriction and bacterial stress-adaptation responses.

sample_organism:
Mycobacterium tuberculosis
Mus musculus

platform_organism:
Mycobacterium tuberculosis
Mus musculus

overall_design: Analysis of the transcriptional profiles of both the host and M. tuberculosis in parental (WT) and Ezh2-deficient Hoxb8-derived macrophages under uninfected and Mtb-infected conditions. Three biological replicates were analyzed per condition.

first: Bom Nae Rin

last: Lee

first: David

last: Russell


title: AP2-HS and a GDV1 regulatory feedback loop mediate environmental induction of sexual conversion in Plasmodium falciparum [AP2-HS ChIP-seq]

city: Barcelona

first: Elisabet

last: Tinto-Font

address: c/Rossello 153

department: Malaria

country: Spain

institute: ISGlobal

summary: Transmission of Plasmodium spp. from a human host to a mosquito vector requires that some parasites abandon the asexual replicative cycle in the blood, associated with all clinical symptoms of malaria, and convert into non-replicative sexual precursors called gametocytes. The sexual conversion rate (i.e., the proportion of parasites that convert at each cycle) is variable, which enables parasites to adjust the balance between sexual and asexual development to the conditions of the human blood environment. Under some specific types of stress, parasites enhance sexual conversion rates to increase their relative investment in transmission. Sexual conversion is orchestrated by the master regulator AP2-G, a transcription factor of the ApiAP2 family. In Plasmodium falciparum, the species that produces the vast majority of human malaria cases and deaths, activation of ap2-g expression requires the GDV1 protein, which displaces heterochromatin from the ap2-g promoter. An antisense long noncoding RNA (lncRNA) encoded in the same locus as GDV1, named gdv1-as, is a negative regulator of GDV1 expression, but how the expression of this lncRNA is regulated or how specific types of stress enhance sexual conversion is not known. Here we show that environmental induction of sexual conversion is initiated by activation of gdv1 expression in a process dependent on the AP2-HS transcription factor, previously described as the activator of the malarial protective HS response. Next, GDV1 activates the expression of its own repressor, gdv1-as, by removing heterochromatin from its putative promoter. This positive-negative regulatory feedback loop limits GDV1 activation to a short burst of expression. This same mechanism operates for stimulation of sexual conversion by different environmental conditions, and AP2-HS is also needed for the activation of metabolic pathways that compensate depletion of phospholipid precursors. These findings provide new insight on the mechanisms underlying the fundamental developmental decision of malaria parasites and explain their plasticity to increase the investment in transmission when the conditions of the environment are unfavourable.

overall_design: AP2-HS ChIP-seq profiling of P. falciparum parasites exposed to choline depletion or control conditions.

first: Tintó-Font

last: Elisabet

first: Casas-Vila

last: Núria

first: Martínez-Guardiola

last: César

first: Pérez-Cantero

last: Alba

first: Ràfols

last: Neus

first: Nyarko

last: Prince B.

first: Cortés

last: Alfred


title: AI-enabled discovery and biochemical optimization of minibinders targeting cancer cell-surface proteins

city: Bonn

first: Bianca

last: Broske

address: Venusberg-Campus 1

department: Institute of Experimental Oncology

country: Germany

institute: University Hospital Bonn

summary: AI-based protein design can rapidly generate novel protein binders, but experimental validation and functional optimization remain bottlenecks. We present a scalable workflow to develop of AI-designed minibinders against cancer-associated surface proteins. Screening thousands of designs using mammalian cell-surface display identifies several high-affinity PD-L1 minibinders but far fewer for CD276 (B7-H3) and VTCN1 (B7-H4), highlighting substantial target dependence. Interface predicted template modeling (ipTM) scores generated by Chai-1 with ESM embeddings correlate with binding success and capture deleterious effects of interface mutations. Fluorophore-labeled AI-minibinders enable flow-cytometric staining comparable to conventional antibodies. However, as chimeric antigen receptors (CARs), some show poor cell-surface trafficking and limited CAR-T cell functionality. Redesign through a genetic algorithm-based diversification strategy that preserves the binding interface while changing non-binding surfaces reveals experimentally a defined pI window that improves CAR expression and enhances target-selective tumor cell killing while reducing off-target cytotoxicity. Our findings establish biochemical optimization beyond the binding interface as critical requirement for translating AI-minibinders into functional applications.

overall_design: HEK293T cells were transduced with plasmids encoding minibinder libraries. The plasmids encoded mNeon as control for transduction. HEK293T cells were stained with their target protein and subsequently sorted for target recognition by fluorescence-activated cell sorting (FACS). The total mNeon positive population served as a representation control. Sorted cells were lysed and subjected to barcoding PCRs for NGS to identify the underlying binders.

first: Michael

last: Hölzel


title: scRNA-seq of biophysically separated immune cells in atherosclerosis

city: Stockholm

first: Cenk

last: Gurdap

address: SciLifeLab, Tomtebodavägen 23

country: Sweden

institute: Karolinska Institute

summary: We developed new method to profile biophysical properties of immune cells. We performed this technique to healthy and atherosclerosis individuals. We selected very healthy and diseases 4 individuals for each catergory based on biophysics and performed 10x genomics.

overall_design: 10x single cell sequencing of 4 healthy and 4 atherosclerosis individuals.


title: Transcriptomics of chronic antibody-mediated rejection

city: Chengdu

first: Heng

last: Xu

state: Sichuan

address: 17#, section 3, South Renmin Road

institute: Sichuan University

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

overall_design: Refer to individual Series


title: CTCF regulates wild-type and recombinant AAV gene expression by shaping viral chromatin [CUT&Run]

city: Madison

first: Kinjal

last: Majumder

state: WI

address: 1525 Linden Drive

department: Oncology

institute: University of Wisconsin

summary: Recombinant Adeno-Associated Viruses (rAAV) gene therapy vectors have been engineered from wild-type AAV (wtAAV2) by inserting the viral telomeres (that serve as replication and packaging signals) on either side of therapeutic transgenes. However, efficient expression of rAAV transgenes require large doses, leading to sporadic toxic side effects.  We have identified a novel cis-acting element in wtAAV2 bound by the cellular architectural protein CTCF (CCCTC-binding Factor). This CTCF binding element is necessary for efficient wtAAV2 gene expression and is sufficient to enhance the efficiency of rAAV vector’s ability to express reporter transgenes. Chromatin profiling studies reveal that this CTCF binding element regulates the chromatin landscape of the virus and viral vectors. Our discovery of adding merely 19bp of AAV’s CTCF binding element has generated a promising new rAAV gene therapy platform with enhanced transgene expression without impacting vector packaging capacity.

overall_design: Identification of the cellular interaction site of Adeno-Associated Virus, and the localization of the resultant DNA damage response. Independent replicates of chromosome conformation capture (designated as V3C in the file name) have been performed. For each time-point or treatment, at least two independent replicates of the indicated assays have been performed.

first: Clairine

last: Larsen


title: RNA-seq profiling of aged high- and low-capacity runner rat soleus muscle at baseline and after voluntary running

city: Budapest

first: Zsolt

last: Radák

address: Budapest, Alkotás u. 42-48, 1123

department: Research Center for Molecular Exercise Science

country: Hungary

institute: University of sports science, Hungary

summary: Soleus muscle RNA-seq was performed in aged female selectively bred high-capacity runner (HCR) and low-capacity runner (LCR) rats to characterize baseline transcriptional differences associated with intrinsic aerobic capacity and exercise-associated transcriptional responses after voluntary wheel running.

overall_design: RNA-seq of soleus muscle from four groups: sedentary LCR (n=8), sedentary HCR (n=8), LCR + voluntary running (n=5), and HCR + voluntary running (n=5).

first: Lei

last: Zhou

first: Radak

last: Zsolt


title: Intestinal lipase inhibition uncouples diet-induced obesity from MASH by remodeling the hepatic lipidome

city: Los Angeles

first: Rochelle

middle: Wing-hin

last: Lai

state: CA

address: 675 Charles E. Young Drive South

department: Medicine

institute: University of California Los Angeles

summary: Dietary fatty acids exert distinct effects on hepatic metabolism. Intestinal lipase inhibition, used clinically for obesity, promotes weight loss by indiscriminately reducing dietary fat absorption, yet its impact on hepatic lipid metabolism in metabolic dysfunction-associated steatohepatitis (MASH) remains poorly defined. Here, we examined the metabolic consequences of lipase inhibition of fat absorption in MASH. To induce MASH, C57BL/6J mice were fed the high-fat Gubra-Amylin NASH (GAN) diet with or without the lipase inhibitor orlistat for 32 weeks. Orlistat protected against diet-induced obesity by promoting fat malabsorption but failed to prevent the progression of hepatomegaly, steatosis, and fibrosis across longitudinal ultrasound imaging, biochemical assessments, and endpoint histology. Despite limiting weight gain, orlistat unexpectedly exacerbated hepatic inflammation. Lipidomic analyses revealed that indiscriminate inhibition of fat absorption depleted the liver of essential polyunsaturated fatty acids while increasing saturated fatty acids. This shift was associated with increased hepatic lipogenesis and proinflammatory signaling, preventing protection from MASH. In summary, lipase inhibition of intestinal fat absorption uncouples obesity from liver disease progression by reshaping the hepatic lipidome. These findings underscore the importance of dietary fat and hepatic lipid composition as key drivers of MASH pathogenesis.

overall_design: RNA-seq profiling of livers obtained from control orlistat-treated mice fed high-fat Gubra-Amylin NASH diet for 32 weeks.

first: Alvin

last: Chan

first: Tomasz

last: Czernuszewicz

middle: W

first: Kelsey

last: Jarrett

first: Andrew

last: Lau

first: Anisa

last: Warshan

first: Angela

middle: S

last: Cheng

first: Michelle

last: Steel

first: Heidi

last: Schmidt

first: Jakeline

last: Larios

first: Isaiah

last: Little

first: Gabriella

last: Rubert

first: Madelaine

last: Brearley-Sholto

first: Zeinab

last: Mamouei

first: Jessica

last: Pesner

first: Christopher

last: Hamad

first: Kevin

last: Francis

first: Nicholas

last: Bernthal

first: Elizabeth

middle: F

last: Redente

first: Clara

last: Magyar

first: Samual

last: French

last: Wiliams

last: Tarling

first: Thomas

middle: Q

last: de Aguiar Vallim


title: Methylome profiling of intrinsic aerobic capacity signatures in aged rat skeletal muscle

first: Zsolt

last: Radák

type: Methylation profiling by high throughput sequencing

summary: This Series contains reduced representation bisulfite sequencing (RRBS) data generated from soleus muscle of aged selectively bred high-capacity runner (HCR) and low-capacity runner (LCR) rats. The dataset was used to characterize DNA methylation differences associated with intrinsic aerobic capacity in aged skeletal muscle.

overall_design: Soleus muscle samples were collected from 23-24 months old female selectively bred high- and low-running capacity rats (HCR/LCR; 44th generation). A total of 14 baseline samples were analyzed for DNA methylation using RRBS (HCR n=6, LCR n=8).

first: Lei

last: Zhou

first: Radak

last: Zsolt


title: Targeting Inhibition of Histone Lysine Demethylase Kdm5b Ameliorates Myocardial Ischemia-Reperfusion Injury by Restoring Brinp2 Expression [RNA-seq]

city: Guangzhou

first: Yage

last: Nie

address: No.74 Zhongshan Rd.2, Guangzhou

institute: Sun Yat-sen University

summary: Myocardial ischemia/reperfusion (I/R) injury remains a major clinical challenge lacking effective therapies, largely due to incomplete mechanistic understanding. While reactive oxygen species (ROS) overproduction is a central pathogenic event, direct antioxidant strategies have largely failed clinically. Epigenetic regulation, particularly histone methylation, has emerged as a critical player in cardiac stress responses, yet the role of specific histone demethylases in I/R remains largely unexplored. Here, we identify lysine-specific demethylase 5B (Kdm5b), an eraser of the active transcription mark H3K4me3, as a key pathogenic mediator and therapeutic target in myocardial I/R injury. Kdm5b is markedly upregulated in hypoxic cardiomyocytes, leading to reduced H3K4me3 levels. Pharmacological inhibition of Kdm5b with AS8351, or genetic knockdown, protects cardiomyocytes from hypoxia/reoxygenation-induced (H/R) cell death, oxidative stress, and mitochondrial dysfunction. In mice, post-reperfusion AS8351 administration improves cardiac function and reduces infarct size. Integrative transcriptomic and epigenomic analyses identify Brinp2 as a direct transcriptional target of Kdm5b. Kdm5b occupies the Brinp2 locus, and its inhibition restores H3K4me3 occupancy and Brinp2 expression. Notably, Brinp2 knockdown largely abolishes AS8351-mediated protection both in vitro and in vivo. Collectively, our findings reveal a previously unrecognized Kdm5b-H3K4me3- Brinp2 epigenetic axis governing cardiomyocyte survival during I/R stress and position Kdm5b as a promising therapeutic target for ischemic heart disease.

overall_design: RNA-seq profiling of NRCM cells under normoxia, H/R-DMSO, and H/R-AS8351 conditions.

first: Zhun

last: liu

first: Qingquan

last: Zhao


title: Targeting Inhibition of Histone Lysine Demethylase Kdm5b Ameliorates Myocardial Ischemia-Reperfusion Injury by Restoring Brinp2 Expression

overall_design:
CUT&Tag-seq profiling of the KDM5B in normoxia NRCM cells.
CUT&Tag-seq profiling of the H3K4me3 in NRCM cells under H/R-DMSO, and H/R-AS8351 conditions.


title: Rubicon modulates neuroimmune responses following traumatic brain injury

city: Baltimore

first: Marta

last: Lipinski

address: 685 W Baltimore St

department: STAR

institute: University of Maryland, Baltimore

summary: Traumatic brain injury (TBI) elicits robust neuroinflammation and oxidative stress, coupled with an acute inhibition of macro-autophagy (autophagy) in neurons and microglia. Rubicon (Rubcn), a Beclin1 interacting protein that suppresses autophagy and mediates LC3-associated phagocytosis and endocytosis (LAP/LANDO), influences inflammatory signaling in metabolic, neurodegenerative, and inflammaging diseases; yet its role in acquired brain injury has not been defined. Using a controlled cortical impact model, we investigated the role of Rubicon in acute neuroinflammatory responses following injury by comparing wild-type and Rubcn-mutant mice. Bulk-RNA sequencing of injured cortex revealed attenuated induction of inflammatory pathways and reduced activation of pro-inflammatory microglial/macrophage phenotype in injured Rubcn-mutant mice. Rubcn-mutant mice demonstrated less pronounced inhibition of autophagy during the acute phase of injury. Although the inflammatory differences were transient, Rubicon mutant mice exhibited improved motor coordination and gait stability during recovery. Proteomic analyses revealed the presence of a truncated Rubicon protein in the mutant mice and identified the negative regulator of reactive oxygen species (NRROS) as a novel interactor of Rubicon. Consistent with this interaction, Rubcn-mutant mice displayed markedly reduced oxidative damage, indicated by decreased lipid peroxidation after injury. Together, these findings indicate that Rubicon promotes acute neuroinflammatory and oxidative stress responses following TBI by modulating autophagy and ROS production. Rubicon mediated pathways may serve as therapeutic targets that offer a neuroprotective strategy to improve outcomes after TBI.

overall_design: Bulk RNA-Seq of ipsilateral cortices from wild-type and Rubicon mutant (JAX stock #032581) mice under sham conditions or at day 3 after moderate traumatic brain injury (n = 4-6 per group). Moderate TBI was induced using a controlled cortical impact device (impact velocity of 4 m/s, deformation depth of 1.5 mm and dwell time of 100 ms) after craniotomy. Sham mice were subjected to the same procedures excluding the craniotomy and impact.

first: Marta M

first: Sagarina

last: Thapa


title: Carboplatin induces optic nerve oligodendrocyte loss and impairs myelin sheath microstructure in a mouse model of neurofibromatosis type 1 (NF1)

city: Houston

first: Rajasekaran

last: Mahalingam

state: TX

address: 6565 MD Anderson Blvd

department: Symptom Research

institute: University of Texas MD Anderson Cancer Center

summary: Vision impairment is a significant concern for children with Neurofibromatosis type 1 (NF1)-associated optic pathway glioma (OPG). While carboplatin-containing chemotherapy is often first-line therapy for NF1-OPG, it does not consistently improve visual function. Furthermore, chemotherapy is associated with altered white matter microstructure in individuals with NF1-OPG, suggesting a detrimental effect on oligodendroglia. We analyzed the tumor-independent effects of carboplatin on oligodendrocytes in Nf1-mutant mice and evaluated pharmacological strategies for reducing this chemotherapy-associated toxicity. Carboplatin- or vehicle-treated Nf1+/- mice or Nf1-mutant optic glioma cells were employed to assess the effects of restorative interventions on optic nerve oligodendrocytes in vivo and tumor cell growth in vitro, respectively. Clinically relevant carboplatin dosing induced oligodendrocyte loss and impaired myelin sheath structure in the optic nerves of Nf1+/- mice, an effect not observed following MEK inhibitor (selumetinib) treatment. Carboplatin downregulates genes essential for cholesterol biosynthesis and decreases cholesterol levels in carboplatin-exposed Nf1+/- optic nerves, such that dietary cholesterol supplementation after carboplatin exposure restored oligodendrocyte numbers. Carboplatin also increases the density of monocytes (microglia/macrophages) in the Nf1+/- optic nerves. Using PLX5622 (a CSF1R inhibitor) to reduce monocytes numbers or using clemastine to promote the generation and survival of oligodendrocytes, alleviated the oligodendrocyte loss caused by carboplatin treatment. Notably, PLX5622 and clemastine reduced the viability of Nf1-mutant optic glioma tumor cells.

overall_design: RNA-seq profiling of NF1 control and NF1 mice treated with Carboplatin and Selumetinib

first: Benjamin

last: Aghoghovwia

first: Kechen

last: Ban

first: Dimitrios

last: Stavropoulos

first: Chi-Yu

last: Chen

first: Bo

last: Wei

first: Ava

last: Hamblett

first: Samer

last: Sharafaldin

first: Hana

last: El-Toukhy

first: Momo

last: Harris

first: Chhay

last: Hok

first: Varsha

middle: K

last: Chandramouli

first: Carlos

last: Martínez Cerda

first: Renae

last: Bertrand

first: Sama

last: Alnassiry

first: Philip

last: Lorenzi

first: David

middle: H

last: Gutmann

first: Kun-Che

last: Chang

first: Yuan

last: Pan


title: Comparative single-cell RNA sequencing brain atlas of larval Astyanax mexicanus surface and Pachón cavefish

city: Columbia

first: Wesley

middle: C

last: Warren

state: MO

address: 1201 Rollins St.

department: Bond Life Sciences Center

institute: University of Missouri

summary: Transcriptional changes underlie not only adaptations of animals to novel or changing environments, but also to human disease phenotypes, such as insomnia. Linking specific transcriptional variations to observable traits can reveal the genetic basis of adaptive trait evolution and disease. To link genetic variation to phenotypic differences, we constructed the first single nucleus RNA sequencing (snRNA seq) brain atlas in a uniquely suited model system, the Mexican tetra Astyanax mexicanus. We made comparisons between surface and cavefish A. mexicanus morphs, which despite having dramatically different life histories, physiologies, and morphologies, can nevertheless interbreed. Here we show a suite of genetic changes that underlie specific differences in phenotypes, including synaptic and neural rewiring, as well as circadian dysregulation between surface and cave-dwelling morphs that may underlie human sleep disorders. Our comprehensive snRNA seq brain atlas revealed widespread divergence in the abundance and molecular signatures of neurons and glia between surface and cavefish and establishes a platform for uncovering the genetic underpinnings of cavefish disease phenotypes.

overall_design: Single nuclei RNA sequencing of larval A. mexicanus brains, aged six days post fertilization (6 dpf), from the Río Choy surface population and the Pachón cave population. Brains were pooled into samples of ~100 per sample and flash frozen for a total of four samples per population.

first: Kathryn

last: Gallman

first: Edward

last: Ricemeyer

first: Aakriti

last: Rastogi

first: X

last: Maggs

first: Emilio

last: Mendez

first: Erik

middle: R

last: Duboué

first: Nicolas

last: Rohner

first: Harini

last: Iyer

first: Alex

last: Keene


title: PRMT5-mediated intron retention triggers innate and adaptive immunity against cancer

city: Oxford

first: Nicholas

last: La Thangue

state: Oxfordshire

address: Old Road Campus Research Building, Roosevelt Drive

department: Department of Oncology

institute: University of Oxford

summary: PRMT5 is expressed at high levels in many cancers, where it regulates diverse cellular pathways that contribute to oncogenesis. Here, we have defined a new role for PRMT5 in regulating and coordinating the interplay between the innate and adaptive immune response. This occurs through the influence of PRMT5 on RNA splicing and the presence of retained introns (RIs). We found that RIs, which occur upon PRMT5 inhibition, have a propensity to form double-stranded RNA structures which activate the innate immune response. Furthermore, many RIs contain cryptic open reading frames which can be translated and then processed into small peptides that assemble with the MHC class I complex. Significantly, RI-derived peptides are highly immunogenic and a murine cancer vaccine, carrying a string of antigenic RI peptides, delayed tumour growth and enhanced survival. RIs are present in human tumour cells, and we identified T lymphocytes in cancer patients with antigen specificity for RI-derived peptides that killed human tumour cells in vitro. Regulating intron retention thus offers a new therapeutic approach to regulate tumour immunogenicity.

overall_design: To investigate the role played by PRMT5 pathway in transcript translation, we performed the polysome fraction RNA-seq analysis. These cells were treated with DMSO or a PRMT5 inhibitor (T1-44) as required.

first: Wiktoria

last: Blaszczak

first: Wojciech

last: Barczak

first: Chuyue

last: Zhang

first: Garret

last: Rochford

first: Annalisa

last: Nicastri

first: Claire

last: Hutchings

first: Anastasia

last: Samsonova

first: Alexander

last: Kanapin

first: Nicola

last: Ternette

first: Paul

last: Klenerman

middle: B


title: snRNA-Seq from peripancreatic human adipose tissue.

city: orlando

first: Adeline

last: Divoux

state: FL

address: 301 E. Princeton St

department: Translational Research Institute

institute: Adventhealth

summary: Using single-nuclei RNA-Seq technology, we interrogated the transcriptional composition of peripancreatic adipose tissue

overall_design: snRNA-Seq on frozen peripancreatic adipose tissue from one healthy organ donor.

first: Casu

last: Anna


title: Transcriptome profile of peripancreatic adipose tissue in pancreatitis

summary: RNA-seq experiments revealed an peripancreatic adipose tissue selective gene expression signature between control, pancreatitis and type 2 diabetes organ donors.

overall_design: RNA was extracted from PAT snap frozen tissues of the 5 CTRL, 12 pancreatitis and 5 donors with T2D using the gentle MACS dissociator and the RNeasy lipid tissue kit (QIAGEN).  RNA-seq libraries were prepared and sequenced using standard Illumina protocols for a HiSeq 2500 instrument. Raw reads were aligned to the hg38 genome, with HISAT2 (2.2.1). FeatureCounts (2.0.6) was used to count the reads number mapped to each gene. The differentially expressed genes analyses between groups were performed using DESeq2 with the standard RNA-seq workflow, genes with counts <100 were filtered.