title: A PI3Kδ-Foxo1-FasL signaling amplification loop rewires CD4 T helper cell signaling and differentiation.

city: Bethesda

first: Behdad (Ben)

last: Afzali Khoshkbijari

state: MD

address: 10 Center Drive, 10/8D03

department: Kidney Diseases Branch

institute: National Institutes of Diabetes, Digestive, and Kidney Diseases

summary: While inputs regulating CD4+ T helper (Th) cell differentiation are well defined, the integration of downstream signaling with transcriptional and epigenetic programs that define Th lineage identity remains incompletely resolved. PI3K signaling is a critical regulator of T cell function; activating mutations affecting PI3Kδ result in an immunodeficiency with multiple T cell defects. Using mice expressing activated PI3Kδ, we found aberrant expression of proinflammatory Th1 signature genes under Th2-inducing conditions, both in vivo and in vitro. This dysregulation was driven by a PI3Kδ-IL-2-Foxo1 signaling amplification loop, fueling Foxo1 inactivation, loss of Th2 lineage restriction, and extensive epigenetic reprogramming. Surprisingly, ablation of Fasl, a Foxo1-repressed gene, normalized both Th2 differentiation and TCR signaling. BioID and imaging revealed Fas interactions with TCR signaling components, which were supported by Fas-mediated potentiation of TCR signaling that could occur in the absence of FADD. Our results highlight Fas-FasL signaling as a critical intermediate in phenotypes driven by activated PI3Kδ, thereby linking two key pathways of immune dysregulation.

overall_design: CTCF CUT&Tag of WT and Pik3cdE1020K mouse CD4+ T Cells

first: Daniel

last: Chauss

first: Dominic

middle: P

last: Golec

first: Behdad

last: Afzali

first: Pamela

last: Schwartzberg


title: Acute hormonal signaling-induced 3D chromatin loop reorganization controls adipocyte thermogenesis [ChIP-Seq mouse, H3K27ac, H3K4me3, H2AZ]

status: Public on Feb 17 2026

city: Boston

first: Kaifu

last: Chen

state: MA

address: 300 Longwood Ave

department: Cardiology

country: USA

institute: Boston Children's Hospital

type: Genome binding/occupancy profiling by high throughput sequencing

summary: β3-adrenergic receptor (β3-AR) hormonal signaling is imperative for adaptative thermogenesis, facilitating heat generation during cold exposure. This study explores how β3-AR signaling regulates thermogenic gene activation by altering the three-dimensional (3D) genome organization. Our findings reveal a rapid 3D genome reorganization in brown adipocytes following 4 hours of β3-AR stimulation, highlighted by high-resolution Micro-C analysis. This reorganization involves substantial dynamic changes in chromatin loops, coupled with activation of genes involved in thermogenesis. Mechanistically, β3-AR signaling promotes the p18Hamlet/SRCAP complex assembly, catalyzing the chromatin incorporation of the histone variant H2A.Z. H2A.Z incorporation enhances chromatin accessibility at loop anchors, facilitating loop formation. Disruption of H2A.Z impairs loop dynamics and thermogenic function of brown adipocytes, with implications for both mice and humans. Notably, human homologous loop anchors are associated with obesity-related genetic variants. This study underscores the critical role of 3D genome architecture in thermogenic regulation, offering new dimensions into obesity’s molecular underpinnings.

overall_design: Chromatin immunoprecipitation-sequencing  (ChIP-seq) for H3K4me3, H3K27ac, and H2A.Z  in vehicle-treated control, β3-AR-stimulated control, and β3-AR-stimulated H2A.Z knockdowon (KD) brown adipocyte.

first: Yang

last: Zhang

first: Rongbin

last: Zheng

first: Tadataka

last: Tsuji

first: Yu-Hang

last: Xing

first: Chih-Hao

last: Wang

first: Justin

last: Darcy

first: Matthew

middle: D

last: Lynes

first: Rui

last: Dong

first: Miguel

middle: N

last: Rivera

first: C. Ronald

last: Kahn

first: Ferenc

last: Győry

first: Xiangyu

last: Liu

first: Morten

last: Lundh

first: Rini

last: Arianti

first: Brice

last: Emanuelli

first: Endre

last: Kristóf

first: Yu-Hua

last: Tseng


title: An immunobiliary single-cell atlas resolves crosstalk between type 2 conventional dendritic cells and γδ T cells in cholangitis [RNA-seq]

city: Würzburg

first: Stefan

last: Thomann

address: Versbacher Strasse 9

country: Germany

institute: Würzburg Systems Immunology

type: Expression profiling by high throughput sequencing

summary: The liver biliary niche serves as a reservoir of tissue-resident immune cells and supports tissue fibrosis upon damage, yet the role of peribiliary immune cells during cholangitis remains poorly understood. Here, we induce cholestatic liver injury mirroring human biliary diseases with bile acid retention in mice to establish a spatial and multimodal single-cell RNA sequencing atlas of the liver and liver-draining lymph nodes (LN). We characterized a hepatic disease state trajectory from dendritic cell precursors (preDCs) to a mature subset of pro-inflammatory Mgl2+ type 2 conventional dendritic cells (cDC2B) and observed dynamic crosstalk with γδ  T cells inducing an Il17 response (γδ T17). Dissection of the cDC2B-γδ T cell communication node identified the Icosl-Icos pair as an important cell contact-dependent interaction, which was validated in vitro. In vivo, cDC2B depletion attenuated γδ T17 responses in cholestatic liver injury, and liver fibrosis was reduced in a model of inducible γδ T cell depletion and in an Il17-deficient background.  Our work demonstrates dynamic turnover of cDC2 within the biliary niche during cholestasis, and a profibrogenic function of γδ T cells contingent on the induction by peribiliary cDC2B, highlighting relevant disease determinants within the immunobiliary and liver-draining LN niche.

overall_design: Multimodal mouse and human scRNA seq data. 6 human liver samples to capture pseudonormal liver cells and identify niche interactions. Furthermore a DDC disease atlas consisting of 12 samples covering a control and 5 disease timepoints to analyse immune cell dynamics in the DDC model. Furthermore, scRNA-seq datasets covering inflammatory resolution after long-term DDC diet and a short term DDC diet in combination with a cDC2B depletion. A CITE-seq dataset from liver draining lymph nodes at a control and two disease timepoints for the analysis of cDC2 dynamics. Two  experiments of liver immune cells capturing transcriptome and genomic accessibility data modalities at steady state and early cholestasis (DDC D5). Finally, multiplexed scRNA seq data of liver and lymph node derived γδ T cells undergoing cholestasis/cholestasis resolution and disease after cDC2B cell depletion.

first: Dominic

last: Grün


title: To profile the transcriptomics of M.tb from Tuberculous Pleuritis (TBP) biopsy samples (n=4) in comparison to in-vitro grown Mycobacterium tuberculosis (M.tb H37Rv) culture

city: Chandigarh

first: Indu

last: Verma

state: Chandigarh

address: Lab 310, Research Block A, 3rd Floor

department: Biochemistry

country: India

institute: Post Graduate Institute of Medical Education and Research

summary: Whole genome microarray was carried out using biopsy sample from four TBP patients where 1856 genes were found to be differentially expressed (DEGs) as compared to in-vitro grown M.tb H37Rv. The number of upregulated genes (1365) was higher in comparison to downregulated genes (491).

sample_organism:
Mycobacterium tuberculosis
Homo sapiens

overall_design: 8 pack microarray slide format (Bar code ID: G2509F, Design ID: 026323) from LCGC Life Science LLP, Agilent Technologies (USA) was used.

first: Prabhdeep

last: Kaur


title: Cell Atlas and Novel Signal Processing Strategy in Primate Insular Cortex [Patch-seq]

status: Public on Feb 16 2026

city: Guangzhou

first: Ruifeng

state: Guangdong province

address: Jinsui Road, 7#

department: Zhongshan Ophthalmic Center

country: China

institute: Sun Yat-sen University

summary: The anterior insular cortex (AIC) is a critical hub integrating exteroceptive and interoceptive information into high-order cognition, yet its neural basis remains incompletely understood. Here, by combining whole-cell-based single-cell transcriptomics with Patch-seq recordings, we resolved and characterized 78 detailed cell types in the macaque AIC, revealing the diversity and specialization of this region in cell type, connectivity profile, signal-processing strategy, and metabolic characteristics. Among these, we identified two transcriptomically and morphoelectrically defined von Economo neuron (VEN) subtypes, DSG2-expressing VEN-L and POC5-expressing VEN-S, transcriptomically relating to extratelencephalic and corticothalamic projection neurons, respectively. We also uncovered a previously underappreciated signal-processing strategy in VENs, whereby the geometry of the dendrite-originating axon initial segment (AIS) reshapes action potential dynamics and enhances somatic responsiveness to deep-layer synaptic inputs. Together, this multimodal atlas establishes a molecular and functional framework for investigating the circuit principles underlying deep-layer projection neurons in the primate AIC.

overall_design: Here we employed a massively parallel 10X genomics single cell RNA-sequencing (scRNA-seq) analysis of the AIC to derive a molecular classification and then related each molecularly distinct cell type to well-established AIC cell types via Patch-seq.

first: Sheng


title: Astrocyte nuclear transcriptome from mouse cortex in Fmr1 KO and Smad4 conditional KO

city: La Jolla

first: James

last: Deng

state: CA

address: 1 Miramar St, 929133

department: Molecular Neurobiology

institute: Salk Institute

summary: Analysis of astrocyte gene expression at P26-28 in mouse cortex with and without Fmr1 KO as well as with and without astrocyte Smad4 conditional KO.

overall_design: Profiling of astrocyte nuclear RNA from the mouse cortex at P26-28 in the four genotypes (1) Fmr1 WT;Smad4 WT, (2) Fmr1 WT;Smad4 cKO, (3) Fmr1 KO;Smad4 WT, (4) Fmr1 KO;Smad4 cKO, with 4-6 biological replicates per genotype

first: Lara

last: Labarta-Bajo

first: Nicola

last: Allen


title: Localised negative feedback shapes genome-wide patterning of meiotic DNA breaks

city: Brighton

first: Jon

middle: Alexander

last: Harper

address: School of Life Sciences, John Maynard Smith Building, University of Sussex, Falmer

department: Genome Damage and Stability Centre

country: United Kingdom

institute: University of Sussex

summary: Genetic diversity within sexually reproducing species arises via the formation and repair of programmed DNA double-strand breaks (DSBs) created by the evolutionarily conserved topoisomerase-like enzyme, Spo11. Because DSBs threaten genome stability, their formation is tightly regulated in both space and time. In S. cerevisiae, Tel1, the orthologue of mammalian Ataxia Telangiectasia Mutated (ATM) kinase, suppresses nearby DSB formation through local inhibition known as DSB interference. However, whether such local inhibition reshapes the genome-wide DSB landscape remains unclear. Here, we develop a quantitative simulation framework to model how Tel1-mediated feedback shapes Spo11-DSB formation across the yeast genome. We demonstrate that innate chromosome-specific DSB patterns, when combined with interference, generate complex, population-level redistribution of DSBs. We define the spatial range over which interference propagates and provide evidence that this regulatory mechanism requires Tel1 recruitment to DSBs via Xrs2 and Tel1 kinase activity. Although the pro-DSB factor Rec114 contributes to DSB regulation, mutation of potential Rec114 phosphorylation sites indicates that it is not an essential target of Tel1. Together, these findings demonstrate how localised negative feedback can drive broad-scale, emergent patterning of a fundamental genome-modifying process, with the potential in meiosis to influence recombination initiation and, consequently, genetic variation across generations.

overall_design: CC-seq libraries from sae2D meiotic SK1 S. cerevisiae cells isolated at 6 hours after sporulation induction

first: Luz

middle: M

last: Lopez Ruiz

middle: A

last: Johnson

first: Rachal

last: Allison

first: William

middle: H

last: Gittens

first: George

middle: G

last: Brown

first: Matthew

middle: J

last: Neale


title: Microglia Mitochondria Support Neuronal Maturation via Metabolic and Transcriptional Reprogramming in Human 3D In Vitro Brain Model

city: Cincinnati

first: Volha

last: Liaudanskaya

state: Ohio

address: 3159 Eden Ave.

department: Biomedical Engineering

institute: University of Cincinnati

summary: Autism Spectrum Disorder (ASD) is a neurodevelopmental condition characterized by disrupted neuronal circuit maturation. Emerging evidence implicates microglial function and mitochondrial regulation as contributors to ASD-associated biology, yet the mechanisms linking these processes to neuronal development remain poorly defined. Neuronal maturation requires tightly coordinated metabolic and transcriptional remodeling, in which mitochondria play a central role in regulating the developmental tempo and metabolic identity, while microglia modulate neuronal synaptic network maturation; however, whether microglia influence neuronal development through direct mitochondrial contributions remains unknown. Here, using a 3D human in vitro brain model, we show that microglial mitochondria can act as transferable cues that promote metabolic, mitochondria-dynamic, and transcriptional aspects of neuronal maturation. Neurons treated with microglial mitochondria exhibited enhanced oxidative metabolism, improved mitochondrial dynamics, and activation of gene programs associated with nervous system development and neurogenesis. These effects were accompanied by increased expression of dendritic maturation markers, supporting the view that transferred mitochondria can contribute to the regulation of neuronal state. However, full structural and synaptic maturation required the combined action of microglia-derived mitochondria and secreted signaling factors. Together, this study identified microglial mitochondrial transfer as a contributor to neuronal maturation with potential relevance to developmental trajectories disrupted in ASD.

overall_design: RNA-seq profiling of NM (Neurons and Microglia co-cultures), NTr (microglia mitochondria-treated neurons), and NUnTr (untreated neurons). (N refers to mt-DsRed2 Induced Human Neural Stem Cells (hiNSCs) and M refers to -mt-EBFP2 HMC3 Microglia Cell Line )

first: Sydney

last: Sterben

first: Charitha

middle: C

last: Anamala

first: Sahan

middle: B

last: Kansakar

first: Vaishnavi

last: Koduri


title: Characterization of mtdsRNA levels in Non-Small Cell Lung Carcinoma (NSCLC)

city: Los Angeles

last: Krieger

address: 10833 Le Conte Avenue

institute: University of California Los Angeles

summary: Mitochondrial double-stranded RNA (mtdsRNA) is exported to the cytoplasm when mitochondrial RNA degradation is impaired, serving as a novel Damage-Associated Molecular Pattern (DAMP) for mitochondrial stress.  The mtdsRNA has been detected in certain cancers, but its prevalence and functional role remain largely unexplored.  Moreover, mtdsRNA is not readily detected in large computational datasets.  Here, we used comprehensive computational characterization of NSCLC cell lines and identified elevated light-strand transcription in a subset of cell lines, suggesting a potential for mtdsRNA formation. Our work allowed us to stratify NSCLC lines into groups with high and low mtdsRNA abundance. Despite high cytoplasmic mtdsRNA levels in some lines, we did not observe consistent activation of Type-I interferon (IFN-l) response or ADAR editing. RT-qPCR analysis revealed that only USP18 transcripts were significantly regulated in a subset of NSCLC lines, indicating a partial or suppressed IFN-I response. Strand-specific RT-qPCR also revealed no bias in mitochondrial gene expression to account for this phenomenon. These results suggest that basal mtdsRNA accumulation does not robustly activate IFN-I signaling and may be tolerated in NSCLC. The monoclonal J2 antibody, which detects mtdsRNA, consistently emerged as a reliable marker of intracellular dsRNA burden and could serve as a functional readout of mitochondrial RNA dysregulation. This approach may help stratify tumors based on its immunogenic potential, independent of genomic mutations. Importantly, we report that mtdsRNA is upregulated in a subset of NSCLC cell lines, representing a potential new marker for mitochondrial dysfunction in cancer.

overall_design: Experiment 1 was RIP-Seq of three different NSCLC cell lines (H1437, H23, PC9) in three replicates. Experiment 2 was RIP-seq of three different NSCLC cell lines (H1437, H23, PC9) with and without IMT1 treatment.  Experiment 3 was RIP-seq of the NSCLC cell line H23 with and without ADAR1 knockdown.

middle: R

first: Sandy Che-Eun

middle: S

last: Lee

first: Maya Cielo

last: Cornejo

first: Kevin

middle: L

last: He


title: Comprehensive analysis of plasma exosomal and non-exosomal microRNA profiles identifies potential early indicators of carcass traits in Japanese Black cattle

city: Kyoto

first: Norihide

last: Yokoi

state: Kyoto

address: Kitashirakawa Oiwake-cho, Sakyo-ku

department: Graduate School of Agriculture

country: Japan

institute: Kyoto University

type: Non-coding RNA profiling by high throughput sequencing

summary: Background: Plasma microRNAs (miRNAs), which exist in exosomal (EX) and non-exosomal free circulating (FC) fractions, can be utilized as blood biomarkers. To identify early indicators of carcass traits, we performed comprehensive analysis of plasma miRNAs separately on EX and FC fractions in Japanese Black cattle at 20, 25, and 30 months of age. Results: We found a total of 1,071 miRNAs including 39 novel miRNA candidates, in which 345 and 358 miRNAs exhibited in measurable amounts in EX and FC fractions, respectively. Profiles of these miRNAs were similar at 20 and 25 months, but collectively different from those at 30 months. We identified 86 and 80 differentially existed miRNAs (DE-miRNAs) between 25 and 30 months in EX and FC fractions, respectively. Among the DE-miRNAs, we revealed significant correlations of bta-miR-150 (EX and FC), -30b-5p (EX), -423-3p (EX), and -222 (FC) with several carcass traits including marbling score. Interestingly, target genes of these DE-miRNAs were functionally enriched in KEGG pathways such as PI3-Akt and MAPK signaling pathways, suggesting their functional relevance to carcass quality and quantity traits. Conclusions: We clarified changes in plasma EX and FC miRNA profiles during the fattening period and identified several miRNAs having correlations with carcass traits. These results could support the utility of plasma miRNAs as potential early indicators of carcass traits in Japanese Black cattle.

overall_design: Small RNA-seq of plasma miRNAs separately on EX and FC fractions in Japanese Black cattle at 20, 25, and 30 months of age.

middle: O

last: Amolo

first: Shota

last: Inagaki

first: Yuya

last: Adachi

first: Zeng

last: Yang

first: Shinichiro

last: Ogawa


title: Histone methyl-transferase G9a inhibition boosts the efficacy of immune checkpoint inhibitors in experimental hepatocellular carcinoma

city: Pamplona

first: Maite

last: Fernandez-Barrena

address: Pio XII 55

country: Spain

institute: CIMA

summary: Immune checkpoint inhibitors (ICIs) have improved cancer therapy, but their efficacy in hepatocellular carcinoma (HCC) remains limited, partly associated with tumor-intrinsic mechanisms of immune evasion. To investigate potential epigenetic drivers of immune resistance, this study evaluated transcriptional changes following pharmacological inhibition of the histone methyltransferase G9a (EHMT2). Bulk RNA sequencing was performed on the murine NM53 and human PLC/PRF/5 HCC cell lines treated with G9a inhibitors. NM53 cells were treated with CM272 with or without interferon gamma (IFN-gamma), and PLC/PRF/5 cells were treated with EZM8266. Gene-level expression was quantified for both cell lines, and transposable element (TE) family-level expression was quantified for NM53 samples.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Bulk RNA sequencing was performed on the NM53 mouse hepatocellular carcinoma (HCC) cell line, derived from MYC-driven tumors, and the human HCC cell line PLC/PRF/5. NM53 cells were treated with the epigenetic inhibitor CM272 (400 nM, 24 h), followed by IFN-gamma (75 U/mL, 24 h) or vehicle control. PLC/PRF/5 cells were treated with EZM8266 (5 uM, 48 h) or vehicle control. Three technical replicates were generated for each condition.

first: Elena

last: Adan-Villaescusa

first: Borja

last: Castello-Uribe

first: Iker

last: Uriarte

first: Eva

last: Santamaria

first: Roberto

last: Barbero

first: Miriam

last: Belzunce

first: Amaya

last: López-Pascual

first: Maria

last: Ujue Latasa

first: Jasmin

last: Elurbide

first: Emiliana

last: Valbuena-Goiricelaya

first: Agavni

last: Mesropian

first: Guillem

last: Cano-Segarra

first: Ana

last: Hernández de Sande

first: Lorenzo

last: Nevi

first: Simone

last: Carotti

first: Umberto

last: Vespasiani-Gentilucci

first: Felipe

last: Prosper

first: Antonio

last: Pineda-Lucena

first: Bruno

last: Sangro

first: Josepmaria

last: Argemi

first: Pedro

last: Berraondo

first: Pablo

last: Sarobe

first: Albert

last: Gris-Oliver

first: Roser

last: Pinyol

first: Josep M

last: Llovet

last: Arechederra

first: Carmen

last: Berasain

first: Alexis

last: Cocozaki

first: Veronica

last: Gibaja

first: Matias A

last: Avila

last: G Fernandez-Barrena


title: Homo sapiens bulk RNA-seq for iMGLs and iMGL-motor neuron co-cultures with cGAS inhibitor

city: New York

first: Yajing

last: Liu

state: NY

address: 455 Main Street, Apt 6V

institute: Weill cornell medicine

summary: This study investigates the role of cGAS signaling in amyotrophic lateral sclerosis using human microglial-like cells (iMGLs) and iMGL-motor neuron co-cultures. Bulk RNA sequencing was performed to assess transcriptional and RNA splicing changes associated with TDP-43 pathology and their modulation by pharmacological cGAS inhibition.

overall_design: RNA-seq profiling of iMGL-control, iMGL-HT-DNA, iMGL-HT-DNA-cGASi, coculture-control, coculture-HT-DNA, coculture-HT-DNA-cGASi.

first: Li

last: Fan

first: Abulimiti

last: Aikedan

first: Weixi

last: Feng


title: Multi-omics Reveal Vitamin D Regulation of Immune-Gut Microbiome Interactions and Tolerogenic Pathways in Inflammatory Bowel Disease [16S rRNA-seq]

city: Jacksonville

first: John

last: Gubatan

state: FL

address: Mayo Clinic Mangurian Building 5220, 4500 San Pablo Rd

institute: Mayo Clinic Florida

summary: Loss of immune tolerance to the gut microbiome plays a pathogenic role in inflammatory bowel disease (IBD). How dietary factors alter host immune-gut microbiome interactions in IBD is unclear. Here, we apply multi-omics (IgA-SEQ, IgG-SEQ, blood scRNA-seq and immune repertoire sequencing) to investigate the effects of 12 weeks of vitamin D on host immune microbe interactions in patients with IBD. Vitamin D treatment associates with decreased disease activity and inflammatory markers and increased IgA-bound and decreased IgG-bound gut microbiota. Vitamin D alters the profiles of IgA-bound (increased Lachnospiraceae, Blautia) and IgG-bound (decreased Proteobacteria, Enterococcaceae) gut bacteria. Vitamin D increases BAFF signaling between plasmacytoid dendritic cells and B cells, alters BCR and TCR clonotypes that associate with Ig-bound gut microbiota, and increases α4β7+ B and T regulatory cells. Our results demonstrate that vitamin D promotes immune tolerance to gut microbiota in patients with IBD. Clinical trial is registered under NCT04828031

overall_design: Stool IgA-Seq and IgG-seq (16S sequening) from 48 patients with inflammatory bowel disease before and after vitamin D intervention


title: Transcriptome data of larval zebrafish exposed to continuous sub- and supra-MCL sodium arsenite and depleted uranium

city: Flagstaff

first: Phillip

middle: Hua

last: Kalaniopio

state: Arizona

address: 617 S Beaver St.

department: Department of Biological Sciences

institute: Northern Arizona University

summary: Depleted uranium (DU) and arsenic (As) are both ubiquitous contaminants in the American southwest, posing risks to indigenous tribes, wildlife, and the environment. DU’s chronic effects and mechanisms of toxicity are poorly elucidated. Concomitant mixture exposure studies with geographically relevant environmental contaminants including both DU and As are also not available. Continuous low-dose (UL, AsL), high-dose (UH, AsH), and concomitant (AsU) exposures are investigated using the larval zebrafish (Danio rerio), with exposure paradigms lasting from embryo collection at 2-3 hours post fertilization until harvest at 5 days post fertilization. Herein, we describe differential gene expression analyses including gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment statistics.

overall_design: RNA-seq profiling of larval (5 days post-fertilization) zebrafish continuously exposed to: 1 or 10 µM sodium arsenite, 30 or 300 µg/L uranyl nitrate, or 1 µM sodium arsenite and 30 µg/L uranyl nitrate in combination.

first: Kalaniopio

last: Phillip

first: Allen

last: Ronald

first: Salanga

last: Matthew


title: Loss of meningeal lymphatic endothelial cells results in formation of a novel vascular network with scavenging function.

city: Huddinge

first: Lars

last: Muhl

address: Blickagången 6

department: MedH

country: Sweden

institute: Karolinska Institutet

summary: For an extended period of time, the meninges were believed to be devoid of lymphatic vessels. The recent discovery of lymphatic vessels in the dura mater of humans, mice, and zebrafish, and the identification and characterization of scavenging lymphatic endothelial cells in zebrafish leptomeninges have contributed to a better understanding of waste removal routes from the brain. Zebrafish brain lymphatic endothelial cells (BLECs), in particular, have a high propensity for particulate waste removal from the cerebrospinal fluid. To further understand the function of BLECs, we have established a protocol for specifically ablating this cell type during embryonic stages. We show that BLECs do not recover upon complete depletion, even at adult stages. The absence of BLECs results in detrimental effects on the meningeal blood vasculature and on arachnoid mater structure. We further report that, upon BLEC ablation, a novel vessel network forms, which shares characteristics with lymphatic vessels and is able to take up substances injected into the brain parenchyma, thus possibly providing compensatory functions in the absence of BLECs.

overall_design: Single-cell transcriptomes were generated from individual FACS-sorted cells captured from the meninges of adult zebrafish for single-cell RNA-sequencing (Smart-seq3).

first: Katharina

last: Uphoff

first: Andreas

last: van Impel

first: Martin

last: Stehling

first: Christer

last: Betsholtz

first: Stefan

last: Schulte-Merker


title: Multi-omics Reveal Vitamin D Regulation of Immune-Gut Microbiome Interactions and Tolerogenic Pathways in Inflammatory Bowel Disease

overall_design: scRNA-seq from peripheral blood mononuclear cells from 48 patients with inflammatory bowel disease before and after vitamin D intervention


title: Targeted delivery of TGF-β inhibitor via LHRH-NanoTi reverses the NAT10/ac4C-mediated cisplatin-induced immunosuppressive tumor microenvironment in ovarian cancer

city: Hangzhou

first: Lv

last: Fei

address: The First People's Hospital of Hangzhou, Zhejiang Province

institute: Zhejiang Chinese Medical University

summary:
Background: Platinum-based chemotherapy for ovarian cancer is frequently compromised by the development of resistance, a process often accompanied by an immunosuppressive tumor microenvironment. The molecular mechanisms linking cisplatin resistance to immune evasion remain poorly understood, hindering the development of effective combination therapies.
Results: This study reveals that cisplatin-induced immunosuppression and resistance are driven by a reduction in N-acetyltransferase 10 (NAT10)-mediated N4-acetylcytidine (ac4C) modification, which produces two parts of unfavorable effects: 1) activating the DNA damage repair pathway, thereby confers resistance to cisplatin; 2) enhancing the expression of TGF-β via NAT10's interaction with ribosomal proteins RPS3 and RPS6. The elevated TGF-β increases the infiltration of myeloid-derived suppressor cells (MDSCs), M2 macrophages, exhausted CD8+ T cells, and regulatory T cells (Tregs) within the tumor microenvironment. To target this pathway, we developed a LHRH receptor-targeted nanodelivery system for a TGF-β inhibitor, which synergized with cisplatin to achieve superior antitumor efficacy by effectively reversing the immunosuppressive microenvironment.
Conclusions: Our study defines the NAT10/ac4C–TGF-β axis as a pivotal mechanism coordinating cisplatin resistance and immunosuppression in ovarian cancer. These findings propose targeted inhibition of TGF-β signaling as a promising therapeutic strategy to overcome platinum resistance by revitalizing the antitumor immune response.

overall_design: To explore the role of NAT10/ac4C-mediated mRNA regulation under cisplatin treatment, we conducted acRIP-seq on cisplatin-treated ID8 cells.

first: Fei

last: Lv


title: RNA-seq profiling of Siniperca chuatsi MFF-1 cells under hypoxic conditions

city: Zhuhai

first: Mincong

last: Liang

state: Guangdong

address: No. 2 Daxue Road

department: School of Marine Sciences

summary: To investigate the molecular mechanisms underlying hypoxia adaptation in mandarin fish (Siniperca chuatsi), bulk RNA sequencing was performed on MFF-1 cells. The study compares the transcriptomic profiles of cells cultured under normoxic conditions (21% O2) versus those subjected to hypoxic stress (3% O2) for 72 hours.

overall_design: The experimental variable was the oxygen concentration in the culture environment: normoxia (21% O2) versus hypoxia (3% O2). Cells were maintained under these specific conditions for 72 hours prior to RNA extraction. Three biological replicates were generated for each condition to allow for statistical analysis of differential gene expression.

first: Yang

last: Yu

first: Shaoping

last: Weng

first: Jian

last: He

first: Jianguo

first: Changjun

last: Guo


first: John

last: Gubatan


title: PRMT5 Inhibition Promotes Cross-Species Spermatogonia Expansion and Suppresses Differentiation

city: guangzhou

first: kang

last: Tang

address: No. 1023 South Shatai Road, Baiyun District, Guangzhou, Guangdong, China

institute: Southern Medical University

summary: Spermatogonial stem cells (SSCs) hold great promise for treating male infertility, but their clinical translation is impeded by the lack of optimal conditions to maintain their undifferentiated state in vitro. In this study, we focused on epigenetic regulators upregulated during differentiation as potential targets. Through a small-molecule screen targeting such conserved regulators, we found that PRMT5 inhibition suppressed mouse SSC differentiation and enhanced their proliferation in a GDNF-deficient, differentiation-prone microenvironment in vitro. Using SSC transplantation assays, we confirmed that EPZ015666-treated SSCs retained their spermatogonial identity. This differentiation-inhibitory effect was reversible upon EPZ015666 withdrawal, allowing for the restoration of normal spermatogenesis. Notably, EPZ015666 also inhibited differentiation and promoted the proliferation of human and non-human primate spermatogonia in vitro. Mechanistically, EPZ015666 exerted this effect by inhibiting the enzymatic active site of PRMT5. These findings suggest that PRMT5 inhibition could provide a novel strategy for culturing human SSCs in vitro.

overall_design: To address this, we generated Prmt5-knockout mouse cultured SSCs from Prmt5 flox/flox; Rosa26-CreERT2 mice by treating them with 1 µM 4-hydroxytamoxifen (4OHT) in vitro (Dong et al, 2021). Compared to the ethanol-treated (EtOH) control group, the expression level of PRMT5 and DMRT1 dramatically reduced in these knockout SSCs treated with 4OHT


title: Irx3 ameliorates postmyocardial infarction cardiac dysfunction by regulating both inflammatory and fibrotic pathways

city: Changchun

first: BIng

last: Li

address: 130021, No. 1, Xinmin Street, Chaoyang District, Changchun, Jilin Province

institute: First Hospital of Jilin University

summary: The Iroquois homeobox transcription factor Irx3 is associated with metabolic and hematologic disorders, but its role in cardiac repair after myocardial infarction (MI) remains unclear. This study found that Irx3 expression is significantly downregulated in the hearts of wild-type mice post-MI and in human AC16 cardiomyocytes under oxygen-glucose deprivation (OGD) conditions. Overexpression of Irx3 improved cardiac function, reduced infarct size and myocardial fibrosis, attenuated inflammatory cell infiltration, prolonged survival in MI mice, and suppressed collagen synthesis and proinflammatory cytokine secretion in vitro. Mechanistically, Irx3 directly targets Srpx2 and Ppm1l: it downregulates Srpx2 to enhance AP-1 activity, increase SMAD7 expression, and inhibit TGF-β/SMAD signaling to limit fibrosis; it upregulates Ppm1l to interact with IKKβ, suppress NF-κB signaling, and reduce inflammatory cytokines (IL-1β, IL-6, TNF-α). RNA sequencing (RNA-seq) of mouse left ventricular tissues and Irx3-overexpressing AC16 cells identified differentially expressed genes enriched in extracellular matrix (ECM) remodeling and inflammation-related pathways, confirming Irx3’s coordinate regulation of profibrotic and proinflammatory pathways. These findings highlight Irx3 as a promising therapeutic target for post-MI cardiac repair and functional recovery.

overall_design: Left ventricular tissues from C57BL/6J mice assigned to three groups (AAV9-Ctrl + Sham, AAV9-Ctrl + MI, AAV9-Irx3 + MI; n=4 per group), with MI induced by left anterior descending (LAD) coronary artery ligation and samples collected 14 days post-surgery.

first: Yu

last: Fu

first: Bing


title: P21+TREM2+-Senescent Macrophages Fuel Inflammaging and Metabolic Dysfunction-Associated Steatotic Liver Disease [NAFLD_time_course]

first: Ivan

last: Salladay-Perez

address: 615 Charles E Young Dr S

department: Department of Microbiology Immunology and Molecular Genetics

institute: University of California, Los Angeles

summary: Cellular senescence drives chronic sterile inflammation during aging via the senescence-associated secretory phenotype (SASP); however, the cell types responsible for this pathology remain poorly defined. Here, we identify p21⁺Trem2⁺ senescent macrophages as a major source of inflammaging. Using primary mouse and human macrophages, we developed a model of DNA damage and cholesterol-induced senescence and applied multi-omic profiling to fully characterize senescent macrophages. We found that senescent macrophages exhibit a distinctive p21-TREM2 expression profile and SASP, driven in part by type-I interferon signaling via secreted mitochondrial DNA. We also found that senescent macrophage accumulation occurs in aged and MASLD mouse livers and is enriched in human cirrhotic liver tissue. Finally, senolytic treatment targeting senescent macrophages reduced liver inflammation and steatosis in both aged and MASLD mice. Together, these findings establish macrophage senescence as a central driver of chronic inflammation in aging and metabolic liver disease, highlighting a promising, tractable therapeutic target.

overall_design: APOE*Leiden-CETP mice were crossed with 3 genetically distinct strains of mice with known response to liver fibrosis48. These strains include: 129/SvJ (fibrosis resistant), C57BL/6J (Medium fibrosis), and BXD19/TyJ (fibrosis prone). Animals were maintained on a 12‐hour light–dark cycle with ad libitum access to water. Male mice (8‐10 weeks old) were fed a high fat high cholesterol diet (33 kcal% fat from cocoa butter and 1% cholesterol; Research Diets; catalog no. D10042101) for 16 weeks. At the end of the study, mice were fasted for 4 hours beginning at 10:00 am and sacrificed at 02:00 pm.

first: Anthony

last: Covarrubias

first: Chantle

last: Edillor


title: ApoE4 Drives Microglial Lipid Dysregulation in Alzheimer’s Disease via Epigenetic Reprogramming of the AsxL1/LXRα–H3K4me3 Axis

city: Fuzhou

first: lanyan

last: lin

state: Fujian

address: 134 Dongjie Road

department: Department of Geriatric Medicine

institute: Fuzhou University School of Medicine

summary: Background The ε 4 allele of apolipoprotein E gene (ApoE) stands as the greatest genetic risk factor for late-onset Alzheimer’s disease (AD). Although microglia accumulating lipid droplets (LDAM) have been implicated in AD pathogenesis, the mechanistic link between ApoE4 and microglial lipid dysregulation remains elusive. Methods We employed a multi-omics approach, combining snRNA-seq and locus-specific epigenetic analysis, alongside microglia-specific gene manipulation in ApoE-targeted replacement (TR) mice. Primary microglia were challenged with cholesterol to simulate lipid overload conditions. Results In mid-life ApoE4-TR mice, microglia within the dentate gyrus developed pronounced lipid droplet accumulation, concurrent with impaired Aβ clearance and a pro-inflammatory shift. snRNA-seq unveiled a unique microglial cluster in ApoE4 mice, enriched for lipid-metabolism genes and marked by the pronounced downregulation of the hub gene AsxL1. Mechanistically, ApoE4 attenuated the AsxL1–LXRα interaction, leading to reduced H3K4me3 occupancy at promoters of lipid-efflux genes such as Abca1. Crucially, CRISPR-mediated, microglia-specific overexpression of AsxL1 restored H3K4me3 levels, normalized cholesterol efflux, and rescued Aβ phagocytic deficits in vivo. Conclusions Our findings define an epigenetic pathway whereby ApoE4 drives microglial dysfunction via the AsxL1–LXRα–H3K4me3 axis, fostering the LDAM phenotype. Enhancing AsxL1 function presents a promising therapeutic avenue for countering ApoE4-mediated pathogenesis in AD.

overall_design: RNA-seq of mus brain from January to June


title: Predictability of progression free survival in ovarian cancer

city: Aurora

first: Benjamin

last: Bitler

state: Colorado

address: CU Anschutz Research Complex II  12700 East 19th Avenue  3400D

department: Cancer Biology

institute: University of Colorado-Anschutz

summary: Given the interrelated mechanisms by which changes to the tumor microenvironment (TME) may drive disease recurrence, we test a novel machine learning approach to identifying key genes that may be involved in the likelihood of recurrence. The ability to compare pre- and post- NACT samples from the same patient shows how chemotherapy drives changes in the TME. We also had the opportunity to employ machine learning methods to investigate whether patient progression-free survival can be prediced from the impact of chemotherapy on the tumor microenvironment.

overall_design:
83 patients with high grade serous ovarian cancer were included in this study. Matched tumor samples from treatment naive biopsies and interval debulking surgery following neoadjuvant chemotherapy (NACT) were obtained from each patients with appropriate clinical information. 95 of these samples were analyzed using the raw (RCC) files provided in GEO series accession numbers GSE201600 and GSE181597. These 166 matched samples were used to capture the gene expression changes that occur after treatment. NanoStriing nCounter Human PanCancer IO360 panel was used to analyze the tumor RNA for 750 genes associated with the tumor microenvironment for all samples. All raw RCC files (of new and previously published data) were analyzed together as described in the data processing steps below.

***************************************************************
see 'GSE319500_reanalysis_samples.xlsx' for GEO accessions reused/reanalyzed for this study.
***************************************************************

first: Lucy

last: Kleunen

first: Grace

last: Bowman

first: Sarah

middle: E

last: Stockman

first: Logan

last: Barrios

first: Hope

last: Townsend

first: Kimberly

last: Jordan

first: Rebecca

last: Wolsky

first: Kian

last: Behbakht

first: Matthew

last: Sikora

first: Aaron

last: Clauset


title: Gene expression profiling of familial Kallmann syndrome caused by a novel ANOS1 variant

city: Bydgoszcz

first: Katarzyna

last: Bilińska

address: M.Skłodowskiej-Curie 9

country: Poland

institute: Nicolaus Copernicus University

summary: This RNA-seq dataset contains whole blood transcriptome profiles from individuals with X-linked familial Kallmann syndrome associated with a new variant in the ANOS1 gene (c.452G>C). Samples were collected from two affected male siblings, their mother, and controls. Total RNA was extracted from whole blood, and ribosomal RNA was depleted prior to library preparation using the KAPA RNA HyperPrep Kit with RiboErase. Paired-end RNA sequencing was performed on the Illumina NovaSeq X Plus platform, generating approximately 100 million paired-end reads per sample. Sequencing utilized 1% of a 10B, 300-cycle flow cell, which produces up to 20 billion paired-end reads per flow cell. This dataset enables a comprehensive analysis of gene expression and splicing patterns associated with ANOS1-related Kallmann syndrome, providing a valuable resource for studying transcriptomic alterations in hypogonadotropic hypogonadism.

overall_design: Whole blood RNA-seq was performed on samples from five individuals, including two affected males with X-linked Kallmann syndrome (ages 9 and 15), one heterozygous female carrier (age 40), and two unaffected controls (one male aged 9 years and one female aged 38 years). The study design enables a comparison of transcriptomic profiles between affected individuals, carriers, and age- and sex-matched controls.

first: Angelika

last: Gajewska

first: Magdalena

last: Pasińska


title: In Vivo inhibition of TDO2 in fibroids results in widespread alteration in the tumor transcriptome

city: torrance

first: Omid

last: Khorram

address: 1124  w carson st

institute: The lundquist Institute at UCLA medical center

summary: This study aimed to characterize large and small RNA transcriptomic changes in fibroid xenografts from mice treated with the TDO2 inhibitor 680C91 for two months.

overall_design: Analysis of large and small RNA transcriptomic changes from RNA-seq data in three sets of fibroid xenografts treated with vehicle or the TDO2 inhibitor 680C91 for two months.

first: Tsai-Der

last: Chuang

first: Abigail

last: Wiseman

first: Gabriela

last: Alfaro

first: Sayna

last: Pejouhesh Jahromi

first: Sepideh

first: Daniel

last: Baghdasarian


title: Anatomy, Projectome and Functional Annotation of Mouse Spinal Cord Neural Diversity

city: Dallas

first: Allan-Hermann

last: Pool

state: TX

address: 6000 Harry Hines Blvd

department: Department of Neuroscience, Peter O'Donnell Brain Institute, Department of Anesthesia and Pain Management

institute: University of Texas Southwestern Medical Center

summary: Spinal cord gives rise to central somatosensation and orchestrates autonomic and motor control. How its cellular diversity achieves physiological functions across sex and along its longitudinal axis and links spinal cord to higher order brain centers remains poorly understood. Here we used retrograde viral tracing with spatial transcriptomics and multiomic profiling of >750k mouse spinal cord neurons to define its output logic and functional cellular repertoire. We identified 70 spinal projection neuron classes that link the spinal cord to hind-, mid-, and forebrain centers implicated in itch, touch, and pain revealing the output wiring logic of the spinal cord. Furthermore, we characterized >500 anatomically and transcriptomically distinct neuron types that revealed extensive (~50%) rostro-caudal cellular specialization as well as first sex specific neuron classes in the spinal cord.  Finally, we assembled a neuron-class-to-phenotype map of the structure based on genetically defined interventions. As a result, we deliver an anatomically and functionally annotated cellular atlas of the complete adult mouse spinal cord to guide future interrogation of the organ.

overall_design: Cervical, thoracic, lumbar and sacral spinal cords were harvested from adult (p56) C57Bl6J male and female mice. Nuclei were extracted and NeuN+ neuronal nuclei were isolated with FACS sorting. Resulting neuronal suspensions were profiled with Chromium Next GEM Single Cell Multiome ATAC + Gene Expression kits from 10x Genomics. Altogether 3 biological replicates were acquired from all four spinal cord regions with three technical replicates each.

first: Liliana

last: Cano Gomez

first: Helen

last: Poldsam


title: Whole transcriptome microarray gene expression profiling of human cerebral cortex specimens of glioblastoma patients (Group3)

city: Zurich

first: Ursula

last: Quitterer

address: Winterthurerstrasse 190

department: Molecular Pharmacology

country: Switzerland

institute: ETH Zurich

summary: A study was performed which analyzed the transcriptome of cerebral cortex specimens obtained during surgery from glioblastoma patients. Specimens from three groups of glioblastoma patients (Group1, Group2, Group3) were analyzed. This part of the project presents data from Group3. The transcriptome study of Group3 includes cerebral cortex specimens from 12 glioblastoma patients (Patient27-Patient38).

overall_design: Whole transcriptome profiling was performed of cerebral cortex specimens obtained during surgery for glioblastoma from 12 patients.

first: Joshua

last: Abd Alla


title: A molecular map of the human spinal dorsal and ventral horn defines arrangement of neuronal types and glial sex differences

summary: The submitted dataset contains multiomic (single-nucleus RNA-seq and scATAC-seq) data from adult (p56) mouse male and female lumbar spinal cords for cross-species analysis.

overall_design: Lumbar spinal cords were harvested from adult (p56) C57Bl6J male and female mice. Nuclei were extracted and NeuN+ neuronal nuclei were isolated with FACS sorting. Resulting neuronal suspensions were profiled with Chromium Next GEM Single Cell Multiome ATAC + Gene Expression kits from 10x Genomics.

first: Satoshi

last: Ishishita


title: SMARCA4 Promotes Lineage Plasticity and Enzalutamide Resistance in Prostate Cancer by Regulating PROX1 via H3K27 Acetylation [RNA-Seq]

city: guagnzhou

first: Chenwei

last: Wu

address: 南方医科大学高层学生公寓1635

institute: 南方医科大学

summary: Enzalutamide resistance is a dynamic process often culminating in the aggressive progression to neuroendocrine prostate cancer (NEPC). This lineage plasticity is hypothesized to be driven by underlying epigenetic alterations, yet the core molecular drivers remain unclear. Elucidating these factors is of significant clinical importance for overcoming resistance. To model this transition, we established a dynamic gradient-resistant cell model simulating the clinical response to enzalutamide, and found robust upregulation of the chromatin remodeling factor SMARCA4 in resistant cells. Both in vitro and in vivo experimental results demonstrated that inhibiting SMARCA4 effectively suppresses tumor progression and reverses neuroendocrine transformation. Mechanistically, integrated multi-omics analysis, correlation studies, and protein interaction experiments revealed the transcription factor PROX1 as a crucial downstream target of SMARCA4, where its inhibition alone was sufficient to reverse the aggressive malignancy and neuroendocrine characteristics of resistant cells. We further demonstrated that SMARCA4 enhances H3K27ac levels and chromatin accessibility at the PROX1 locus to regulate its expression. Importantly, the tumor-suppressive effect of SMARCA4 knockdown could be rescued by histone deacetylase inhibitors (HDACi), achieving a level of recovery comparable to PROX1 overexpression. In summary, this study defines a core epigenetic pathway, showing that increased SMARCA4 activity promotes luminal-to-neuroendocrine transformation by enhancing histone acetylation and chromatin accessibility at the PROX1 locus. Targeting the SMARCA4-PROX1 axis provides a valuable therapeutic strategy for combating enzalutamide resistance and NEPC progression.

overall_design: Expression profiling by high throughput sequencing. Genome binding/occupancy profiling by high throughput sequencing

first: Mayao

last: Luo

first: Shidong

last: Lv

first: Qiang

last: Wei


title: SMARCA4 Promotes Lineage Plasticity and Enzalutamide Resistance in Prostate Cancer by Regulating PROX1 via H3K27 Acetylation [ATAC-seq]

address: 南方医科大学高层学生公寓1635


title: Whole transcriptome microarray gene expression profiling of cerebral cortex specimens from glioblastoma patients (Group1)

summary: The prevalence of glioblastoma increases with age. Advanced age is also one of the best-established risk factors for sporadic Alzheimer's disease (AD). Previous histopathological studies detected the occurrence of AD features in frontal cortex specimens from glioblastoma patients. This study aimed to identify AD-related transcript changes in cerebral cortex specimens obtained during surgery for glioblastoma. The study analyzed cerebral cortex specimens from three groups of glioblastoma patients (Group1, Group2, Group3). The transcriptome study of this Group1 includes specimens from 10 glioblastoma patients (Patient1-Patient10).

overall_design: Whole transcriptome profiling was performed of cerebral cortex specimens obtained during surgery for glioblastoma from 10 patients.


title: Decoding and Rewiring Promoter Architecture Using Large Language Models and Diffusion Frameworks: High-Throughput Promoter Strength Sequencing Source Data

first: wang

last: xing

address: No. 382, Outer Ring East Road, Guangzhou University Town, Panyu District

institute: South China University of Technology

summary: High-performance promoters are essential tools for precisely regulating gene expres-sion, yet their rational design within the vast combinatorial sequence space remains a major challenge. Here, we present a hybrid framework that integrates a large lan-guage model (LLM) with a diffusion model to enable data-driven and interpretable promoter design. The fine-tuned LLM predicts promoter strength with high accuracy and, through pseudo-sequence mutations, identifies biologically essential core motifs. A diffusion model is then conditioned on these motifs to reconstruct non-core regions and generate complete promoter sequences. We experimentally validated this approach in E. coli by high-throughput barcoded promoter activity sequencing: over 90% of the generated promoters showed measurable activity, and the best variants achieved ap-proximately ∼20-fold higher expression than the benchmark promoter (BBa_J23119). By explicitly coupling interpretability with generative design, this strategy provides a generalizable path to accelerate synthetic biology efforts and advance large-scale regu-latory sequence engineering.

overall_design:
This study employs a high-throughput barcoded sequencing assay to quantify the transcriptional activities of a synthetic promoter library in Escherichia coli DH5[alpha]. Each promoter was cloned into a plasmid reporter construct and uniquely associated with a barcode. The pooled plasmid library was introduced into E. coli DH5α and cultured in LB medium supplemented with 50 µg/mL kanamycin at 37 °C with shaking. At a defined time point, cells from the same pooled cultures were harvested for parallel extraction of total RNA and plasmid DNA. Barcode abundances in RNA (after reverse transcription) and DNA were determined by high-throughput sequencing. Promoter activity was quantified based on normalized RNA/DNA barcode ratios across biological replicates.
Please note that the study represents a replicate experiment under the same research theme as GSE316915, but with a different sequencing method and minor optimizations to the experimental protocol. This work aims to validate and complement the previous GSE316915 results. Therefore, while the two studies share the same scientific question and overall objectives, they differ in the experimental methodology and data generation process.

first: Xin

last: Lei

first: Xing

last: Wang

first: Yuzhong

last: Liu

first: Yangyu

last: Zhang

first: Jiesheng

last: Huang

first: Tianjiao

last: Peng

first: Ce

last: Liang

first: Quhuan

last: Li

first: Huaiguang

last: Jiang

first: Wei

last: Xiong


title: Wildfire smoke particulate matter induces ovarian hyperandrogenism via aryl hydrocarbon receptor activation IV

city: Pitscataway

first: Shuo

last: Xiao

state: NJ

address: 170 Frelinghuysen Rd, Room 404

department: Pharmacology & Toxicology

institute: Rutgers University

summary: Wildfires have become more frequent and intense worldwide. Wildfire smoke particulate matter (WFPM) can be more toxic than urban background PM due to nanosized PM or WFPM0.1 and more polar organic compounds including polycyclic aromatic hydrocarbons (PAHs). While WFPM has been linked to cardiopulmonary diseases, its impact on female reproduction remains elusive. Here, we used an in vivo mouse intratracheal exposure model and a 3D ovarian follicle culture system, together with molecular, transcriptomics, and computational analyses, to examine the effects of lab-synthesized (LS) and Canadian real-world WFPM0.1 (C- WFPM0.1) on ovarian functions. Intratracheal exposure to LS-WFPM0.1 disrupted estrous cycles and elevated serum estradiol and testosterone concentrations in young adult female mice. RT-qPCR and single-follicle RNA-sequencing (RNA-seq) analysis analysis revealed altered steroidogenic genes, transcriptomic changes, and activation of aryl hydrocarbon receptor (AhR) in antral follicles of from LS-WFPM0.1-treated mice. In vitro exposure revealed thatto LS-WFPM0.1 increased testosterone secretion and induced genes related to androgen synthesis and AhR. Single-follicle and single-oocyte RNA-seq analysis identified differentially expressed genes (DEGs) related to inflammation in somatic cells and mitochondria and cell cycle in oocytes. Both real-world C-WFPM0.1 from the 2023 Canadian wildfires and benzo[a]pyrene, a high molecule weight PAH, reproduced these ovarian defects caused by LS-WFPM0.1. Mechanistically, AhR inhibition reversed hyperandrogenism induced by WFPM0.1. Together, our findings demonstrate that PAH-containing WFPM0.1  perturbs ovarian steroidogenesis and induces hyperandrogenism through AhR activation. These results are crucial for developing strategies to protect women’s reproductive health and tailor guidelines for women seeking for infertility treatment during wildfire seasons.

overall_design: RNA seq profiling of antral follicular somatic cells treated with vehicle or LS-WFPM0.1 using 3D encapsulated in-vitro follicle growth (eIVFG) system extracted on 6th day of culture

first: Kuhelika

last: Mali

first: Delong

first: Lila

last: Bazina

first: Elena

last: Abramova

first: Jiyang

first: Pawat

last: Pattarawat

first: Audrey

last: Gaskins

first: Andrew

last: Gow

first: Philip

last: Demokritou


title: Whole transcriptome microarray gene expression profiling of Tg2576 Alzheimer mice upon treatment with a GRK2 activity modulator

first: Ursula

last: Quitterer

summary: With increased aging of the global society, the prevalence of Alzheimer's Disease (AD) is on the rise worldwide. This study aimed to identify AD-related transcript changes in frontal cortex specimens of 18-month-old Tg2576 mice which were used as an experimental model of AD. This study analyzed frontal cortex specimens of two groups of 18-month-old Tg2576 AD mice. The first group was treated for 6 months with the GRK2 activity modulated, CPD10 [1-(1,3-Benzodioxol-5-yl)-4-(cyclopropanecarbonyl)-3-hydroxy-2-phenyl-2H-pyrrol-5-one] in drinking water (8 mg/kg/d) and the untreated control group of 18-month-old Tg2576 mice received tap water. The whole transcriptome microarray gene expression analysis identifies transcripts which were altered by treatment with the GRK2 activity modulator.

overall_design: Whole transcriptome profiling was performed of frontal cortex specimens isolated from 18-month-old Tg2576 mice treated for 6 months with CPD10 and from 18-month-old untreated Tg2576 control mice

first: Joshua

last: Abd Alla


title: Targeting HDAC and proteostasis to eradicate quiescent cancer cells

city: Pittsburgh

first: Hatice

middle: Ulku

last: Osmanbeyoglu

state: Pennsylvania

address: 5607 Baum Blvd

department: Biomedical Informatics

institute: University of Pittsburgh

summary: Chemotherapy remains the primary treatment for ovarian cancer (OvCa), and chemoresistance drives patient mortality. Cellular quiescence, reversible exit from the cell cycle, increases chemotherapy resistance as chemotherapies primarily target rapidly proliferating cells. Here, we report that CHD4 and MBD3, components of the nucleosome remodeling and deacetylase (NuRD) complex, are downregulated in quiescent OvCa cells (qOvCa). We find that either CHD4 or MBD3 knockdown or histone deacetylase inhibitors (HDACi), induce quiescence in OvCa cells. RNA-Seq and ATAC-seq analysis of HDACi-treated cells confirmed expression changes consistent with induction of quiescence. Additionally, HDACi treated cells revealed downregulation of the RHO/RAC pathways. Suggesting downregulation of the RAC pathway could play a role in HDACi-mediated quiescence, RAC inhibitors (RACi) similarly induced quiescence. Both HDACi and RACi resulted in nuclear-to-cytoplasmic shifting of the pro-proliferative transcription factor MRTFA. which has been linked to quiescence. Further analysis of HDACi qOvCa indicated multiple alterations in proteostasis, including increased proteasome activity and autophagy. We find qOvCa cells are dependent on these pathways for survival, such that there is profound synergistic OvCa cell death with HDACi and proteasome- or autophagy-inhibitor combination therapy. Combined, this work supports HDACi as pharmacologic means to induce a quiescent state in OvCa cells and sensitize them to proteostasis-targeting drugs.

overall_design: Ovarian cancer cells were treated with DMSO control or vorinostrat -3uM for 48 hours and then RNA harvested for RNA-Seq

first: Buckanovich

last: Ronald

first: Osmanbeyoglu

last: Hatice


title: Wildfire smoke particulate matter induces ovarian hyperandrogenism via aryl hydrocarbon receptor activation I

overall_design: SMART-Seq2 profiling of single oocyte extracted from follicles treated with vehicle or LS-WFPM0.1 using 3D encapsulated in-vitro follicle growth (eIVFG) system extracted on 6th day of culture

last: Zhang

first: Qiang


title: Whole transcriptome microarray gene expression profiling of cerebral cortex specimens from glioblastoma patients (Group2)

summary: The study performed whole genome microarray gene expression profiling of cerebral cortex specimens obtained during surgery from glioblastoma patients. The project analyzed specimens from three groups of glioblastoma patients (Group1, Group2, Group3). This part of the project presents data from Group2 and includes specimens from 16 glioblastoma patients (Patient11-Patient26).

overall_design: Whole transcriptome profiling was performed of cerebral cortex specimens obtained during surgery for glioblastoma from 16 patients


title: ZNF750 loss in junctional zone of hair follicle and sebaceous gland leads to severe seborrheic-like psoriasiform dermatitis [day 50]

city: San Diego

first: George

last: Sen

state: California

address: 9452 Medical Ctr Dr, La Jolla, CA

department: Department of Dermatology

institute: University of California San Diego

summary: Loss of Zfp750 in juctional zone of hair follicle of the mice skin increased the inflammatory gene expression.

overall_design: Skin cells from control and Zfp750 knockout mice expressing tdTomato were sorted.

first: Uyanga

last: Batzorig


title: Smarca4 coordinates chromatin accessibility and metabolic programs to sustain hematopoietic stem cell function

city: Chongqing

first: Yuanyuan

last: Liu

address: No. 1 Medical College Road, Yuzhong District, Chongqing, China

institute: Chongqing Medical Journal

summary: Hematopoietic stem cells (HSCs) sustain lifelong hematopoiesis by balancing quiescence, self-renewal, and differentiation. However, immunophenotypic definitions of HSCs often fail to capture their functional state, particularly under conditions of stress, aging, or disease, where phenotypic HSCs may accumulate despite profound defects in long-term reconstitution. Here, we identify the chromatin remodeling ATPase Smarca4 (BRG1) as a critical regulator of functional HSC integrity. Conditional deletion of Smarca4 in the adult hematopoietic system leads to rapid hematopoietic failure, characterized by an expansion of phenotypically defined HSCs with impaired durable self-renewal capacity. Mechanistically, Smarca4 cooperates with the lineage-associated transcription factor RUNX1 to maintain chromatin accessibility and enhancer activity at the Pparg locus. Loss of Smarca4 selectively disrupts enhancer-associated H3K27ac, rewires metabolic gene programs, and compromises cellular energy homeostasis in HSCs. Restoration of Pparg expression partially rescues metabolic features and early progenitor composition but fails to restore normal differentiation output. Together, our findings establish Smarca4 as an essential epigenetic coordinator that integrates chromatin architecture with metabolic programming to sustain functional hematopoietic stem cell identity.

overall_design: The HSC cells from Smarca4fl/fl mice and Smarca4-CKO mice were sorted and performed Cut&Tag, ATAC-seq in order to discover the role Smarca4 in hematopoietic  system.

first: Yu

last: Hou

first: Bijie

last: Yang

first: Jiankun

last: Fan

first: Lin

last: Zou


title: Wildfire smoke particulate matter induces ovarian hyperandrogenism via aryl hydrocarbon receptor activation II

first: Shuo

last: Xiao

overall_design: RNA seq profiling of antral follicular somatic cells from vehicle or LS-WFPM0.1 treated (443 ug) mice extracted on 7th day after exposure via intratracheal instillation

first: Kuhelika

last: Mali

first: Delong

first: Lila

last: Bazina

first: Elena

last: Abramova

first: Jiyang

first: Pawat

last: Pattarawat


title: NIK-Driven IL-23 Production by Myeloid Cells is a Key Factor in the Development of Autoimmune Inflammation [16S rRNA-seq]

city: Mainz

first: Matthias

last: Klein

address: Langenbeckstrasse 1

department: Inst. for Immunology

institute: University Medical Center Mainz

summary: This study investigates the role of NF-κB inducing kinase (NIK) in myeloid cells during the development of experimental autoimmune encephalomyelitis (EAE). While NIK expression in circulating myeloid cells was found to be crucial for EAE pathogenesis, influencing T cell priming and IL-23 production, we sought to determine if these effects were mediated by alterations in the gut microbiota. To test this, we performed 16S rRNA gene sequencing on faecal samples from NIKfl/fl and NIK^CX3CR1 mice. Our results showed no significant differences in microbial composition between genotypes, indicating that the observed immune phenotype is independent of steady-state changes in the gut microbiome.

overall_design: We have employed a 16s rRNA sequencing of Faecal samples  of naïve NIKfl/fl control mice and NIK^CX3CR1 mice  to study differences in the microbiome. DNA extraction, 16S rRNA library preparation, sequencing, and bioinformatic analysis were performed by Novogene (Cambridge, UK). Faecal samples were collected from the mice during steady-state.

first: Nishada

last: Ramphal

first: Rebecca

last: Jasser

first: Tommy

last: Regen


title: Wildfire smoke particulate matter induces ovarian hyperandrogenism via aryl hydrocarbon receptor activation III

overall_design: RNA seq profiling of antral follicular somatic cells treated with vehicle or C-WFPM0.1 using 3D encapsulated in-vitro follicle growth (eIVFG) system extracted on 6th day of culture

last: Zhang

first: Qiang

first: Audrey

last: Gaskins

first: Andrew

last: Gow

first: Philip

last: Demokritou


title: FGF21 inhibits the senescence of nucleus pulposus cells by activating mitophagy

city: Champaign

first: QIQI

last: XIE

state: IL

address: 2753-11 Hunters Pond Run, Champaign, IL 61820

institute: University of Illinois Urbana-Champaign

summary: This study employed third-generation RNA sequencing (RNA-seq) technology to analyze mRNA isolated from nucleus pulposus cell samples in the TBHP group (n=3) and the FGF21+TBHP intervention group (n=3). Pathway and network analysis based on Gene Ontology (GO) terms was conducted to identify the biological functions of differentially expressed mRNA. The results revealed that, based on the screening criteria for differentially expressed genes (|logFC|>1 and P<0.05), a total of 189 significantly differentially expressed genes (DEGs) were identified, including 100 significantly upregulated genes and 89 downregulated genes (Supplementary Table 1). The enriched functions of these differentially expressed genes were closely related to the cAMP signaling pathway, ion channels, and transport vesicles. Gene Set Enrichment Analysis (GSEA) indicated that these genes were closely associated with autophagy and selective autophagy. This study provides therapeutic targets and related pathways for FGF21 treatment of IDD, offering new insights and targets for medical or pharmacological intervention in IDD.

overall_design: Nucleus pulposus cells (NPCs) were isolated from male Sprague-Dawley rats. Cells were cultured in vitro. Samples were divided into two experimental groups. The model group was treated with tert-butyl hydroperoxide (TBHP) to induce senescence. The treatment group was co-treated with TBHP and recombinant FGF21. Each group consisted of three biological replicates. Total RNA was extracted from these six samples. High-throughput RNA sequencing was performed to identify differentially expressed genes.

first: Zuolong

last: Wu

first: Qiqi

last: Xie

first: Rui

last: Ran

first: Cong

first: Keping

last: Wang

first: Haihong


title: Integrative Single-Cell RNA and ATAC Sequencing Uncovers Dosage-Sensitive, Cluster-Specific Regulatory Dynamics in Glioblastoma

city: Los Angeles

first: Khoi

last: Huynh

address: 1441 Eastlake Ave

department: Radiation Oncology,Keck School of Medicine of USC

institute: University of Southern California

summary: Glioblastoma (GBM) is an aggressive brain tumor that inevitably recurs after radiation therapy, resulting in poor patient outcomes. Given GBM’s cellular heterogeneity, we hypothesized that radiation induces sub-population specific alterations to survive and adapt to radiation stress. We performed integrated single-cell RNA-seq and ATAC-seq analyses across multiple GBM models exposed to clinically relevant radiation doses. Radiation reshaped the cellular landscape, altering both cell type composition and GBM subtype distribution. Cluster-specific and shared transcriptional programs were induced in a dose-dependent manner, with differentially expressed genes enriching distinct biological pathways. Chromatin accessibility analyses revealed parallel cluster-specific remodeling, with both opening and closing of regulatory elements linked to functional pathway shifts. Notably, 2 Gy and 6 Gy exposures elicited conserved transcriptional profiles in RNA clusters across independent GBM lines. Together, these results highlight radiation-induced transcriptional and chromatin remodeling programs in GBM at single-cell resolution and identify conserved cluster-specific adaptations that may underlie therapeutic resistance.

overall_design: Following radiation treatment, GSC20 cells are harvested 3 hours post radiation. Harvested cells are analyzed using the 10x Genomics Multiomic kit, including scRNA-seq and scATAC-seq

first: Sara

last: Weissman

first: Cheol

last: Park

first: Maria

last: Quiloan

first: Blake

last: Change

first: Kelly

last: Street

first: Eric

last: Chang

first: David

last: Tran

first: Aram

last: Modrek


title: NGS-based analysis of i6A and ms2i6A modification levels on tRNATyr in Schizosaccharomyces pombe and Escherichia coli

city: Berlin

first: Yu

last: Sun

address: Philippstr. 13

department: Institut für Biologie

institute: Humboldt-Universität zu Berlin

summary: Queuosine (Q) is a complex tRNA modification found at position 34 of four tRNAs with a GUN anticodon, and it regulates the translational efficiency and fidelity of the respective codons that differ at the Wobble position. Previous studies have shown that the Q34 modification enhances m5C38 formation in tRNAAsp by DNMT2 in Schizosaccharomyces pombe, an evolutionarily conserved phenomenon also observed in other organisms. Notably, in tRNATyr, the relative positions of Q34 and i6A (in S. pombe) or ms2i6A37 (in Escherichia coli) within the anticodon loop mirror the spatial relationship between Q34 and m5C38 in tRNAAsp. This structural similarity prompted us to investigate whether Q34 and i6A/ms2i6A37 might participate in a comparable modification circuit, where the presence of abasence of Q34 influences the formation of i6A or ms2i6A. To address this question, we adapted an approach in which tRNATyr molecules were reverse-transcribed using an RT-active DNA polymerase variant (RT-KTq I614Y), followed by PCR amplification and next genetation sequencing (NGS). This method generates higher error rates at i6A/ms2i6A37-modified positions compared with canonical A37 residues, enabling sensitive detection of these modifications. We furthur validated the approach using calibration samples created by mixing tRNA containing or lacking i6A/ms2i6A37, establishing a quantitative relationship between RT-derived error rates and the relative abundance of these modification.

sample_organism:
Escherichia coli
Schizosaccharomyces pombe

overall_design: For E. coli, ms2i6A37 levels in tRNATyr were analyzed, including wild-type BW25113 (containing Q34 in tRNATyr), Δtgt (containing G34), ΔqueA (containing preQ134), ΔqueF (containing preQ034), ΔmiaA (containing Q34 and unmodified A37, used as a negative control), and ΔmiaA Δtgt (containing G34 and unmodified A37, also used as a negative control). All E. coli strains were cultivated at 37°C or 42°C to mid-log phase before RNA extraction. Calibration samples were generated by mixing small RNAs from the ΔmiaA strain, which lacks ms2i6A, with small RNAs from the wild-type strain, which contains ms2i6A at an unknown absolute level. These mixtures, consisting of 12.5%, 25%, 50%, and 75% wild-type RNA, were used to establish a relationship between RT-derived error rates and relative modification abundance. For Schizosaccharomyces pombe, i6A37 levels in tRNATyr were examined in wild-type cells grown with queuine supplementation, resulting in Q34-containing tRNATyr, and without queuine supplementation, producing G34-containing tRNATyr. In addition, tit1Δ mutant cells were analyzed under the same supplementation conditions; tit1Δ produces tRNATyr containing Q34 and unmodified A37 when supplemented with queuine, and G34 with unmodified A37 when cultivated without queuine. These tit1Δ samples served as negative controls for i6A37 detection. For calibration, mixtures of RNA isolated from wild type cells and from the tit1Δ strain grown without queuine supplementation were prepared, enabling the concersion of the obserced error rates into the relative i6A37 modificaton level with respect to the wild type.

first: Ann

last: Ehrenhofer-Murray


title: A Human RORγt Mutant Enhances Th17-Mediated Inflammation via Increased HIF-1α Recruitment

city: LA

first: Peixian

last: Dong

address: 1450 Biggy St, NRT 5514, LA. CA

institute: USC

summary: T helper 17 (Th17) cells play a central role in mucosal defense and autoimmune pathology, with their differentiation and effector function critically controlled by the transcription factor RORγt. While genome-wide association studies (GWAS) have identified variants in the RORC locus associated with inflammatory diseases, the functional impact of these variants remains largely unexplored. Here, we report the identification and characterization of a hyperactive RORγt point mutation, N277D (mouse homolog N275D), which enhances Th17 inflammatory potential through increased cooperation with the hypoxia-inducible factor HIF-1α. Using a combination of computational modeling, retroviral expression, and CRISPR-engineered knock-in mice, we demonstrate that RORγtN275D promotes IL-17A⁺IFN-γ⁺ Th17 cell differentiation and exacerbates colitis in a T cell transfer model without affecting T cell development or homeostasis. Transcriptomic and metabolomic profiling revealed upregulation of glycolytic and hypoxia-associated pathways in mutant Th17 cells. Consistent with enhanced RORγtN275D-HIF-1α interaction, RORγtN275D was recruited to HIF-1α binding site at the Pdk1 locus, which is required for the upregulation of IFN-γ production in mutant Th17 cells. These findings reveal a novel regulatory axis between RORγt and HIF-1α that links transcriptional and metabolic programming in pathogenic Th17 cells and suggest a framework for functionally interrogating autoimmune risk variants to uncover therapeutic targets.

overall_design: To gain mechanistic insight into how the RORγtN275D mutation enhances Th17 pathogenicity, we performed transcriptomic profiling of in vitro-differentiated Th17 cells. Our previous in vivo studies revealed that RORγtN275D does not affect the development or homeostasis of steady-state Th17 cells, such as those in the intestinal lamina propria, but instead promotes the emergence of highly inflammatory, IL-17A⁺IFN-γ⁺ Th17 cells under disease conditions. This suggested a mutation-specific effect under inflammatory, but not homeostatic, cues. Therefore, to mimic the inflammatory environment and uncover a broader range of transcriptional changes, we polarized naïve CD4⁺ T cells from WT and RORγtN275D mice using IL-6, IL-1β, and IL-23. This cytokine combination is known to promote the differentiation of highly inflammatory, pathogenic Th17 cells implicated in autoimmunity and tissue inflammation, and it aligns with the cytokine milieu used in our in vivo colitis mode

first: Dong

last: Peixian


title: ZNF750 loss in junctional zone of hair follicle and sebaceous gland leads to severe seborrheic-like psoriasiform dermatitis [day 36]

first: George

last: Sen

first: Uyanga

last: Batzorig


title: Endometrial cortisol level and its relationship with psychological stress, molecular tissue changes, and clinical outcomes in infertile women

city: Valencia

first: Patricia

last: Diaz-Gimeno

state: Valencia

address: EDIFICIO BIOPOLO - LA FE, Avenida Fernando Abril Martorell, 106 - Torre A, Planta 1ª

department: Genomics and Systems Reproductive Medicine

institute: IIS La Fe / IVIRMA Global Research Alliance

summary: This study aims to elucidate the effect of stress, measured by different approaches, in the endometrial function in In Vitro Fertilization treatments.

overall_design: Prospective cohort study, involving 60 IVF patients included the collection of endometrial biopsies during the mid-secretory phase.

first: Diana

last: Marti-Garcia

last: Sebastian-Leon


title: Impact of Alzheimer’s disease risk factors and local neuromelanin content on the transcriptomic landscape of the human locus coeruleus

city: Baltimore

first: Keri

last: Martinowich

state: Maryland

address: 855 N Wolfe St Suite 300

institute: Lieber Institute for Brain Development

summary: The locus coeruleus (LC) is a small noradrenergic nucleus in the dorsal pons that sends projections widely across the brain to regulate multiple functions including  sleep, memory, arousal, and cognition. The LC has several unique cellular features including the presence of neuromelanin (NM) and its accumulation of a precursor to Alzheimer’s Disease (AD) pathology, soluble phospho-tau (pTau), in virtually all individuals by adulthood. NM increases in LC during early life, plateauing in middle age, and eventually dissipating, coinciding with LC neuron degeneration, a process which is observed in healthy aging but accelerated in AD. NM-sensitive neuroimaging predicts clinical severity and future progression of AD. While these findings suggest an etiologic role for the LC in AD, data describing the molecular landscape of the LC in middle age,  preceding the clinical manifestation of sporadic AD, is lacking. Understanding the molecular state of the LC during this time period is critical to developing interventions that preserve this brain region and the cognitive functions it supports. Here, we performed Visium spatial transcriptomics on 85 tissue sections of human postmortem LC from a cohort of 33 middle-aged, neurotypical donors, balanced for epidemiologic AD risk factors including sex, African or European ancestry, and APOE genotypes (carriers of the E4/risk or E2/protective alleles). We find an unexpected male-bias in LC expression of cholesterol synthesis pathway genes, suggesting that intrinsic neuronal cholesterol synthesis may be protective against AD. Comparing across APOE genotypes, astrocytic gene expression differs in the immediate vicinity of LC neurons. Finally, we leverage histological images captured from the profiled tissue to associate gene expression to NM abundance, finding that APOE expression is associated with reduced NM content, and that NM-associated genes are enriched for aging-related pathways. These findings provide important information about how AD risk factors and NM content impact molecular correlates of resilience/susceptibility of the aging LC to degeneration. Data are freely available, including through visualization browsers to enable wide utilization of these tools for understanding LC biology in AD and other LC-related neurodegenerative disorders, including Parkinson’s disease.

overall_design: We obtained tissue blocks of postmortem human brain containing locus coeruleus (LC) from 33 neurotypical adult brain donors, balanced for age, sex, APOE2 and APOE4 carrier status (all donors had at least one copy of one of the two alleles), and predominant genomic ancestry (African Ancestry or European Ancestry). We used the 10x Genomics Visium platform to generate spatial transcriptomics from two sequential tissue sections containing LC for each donor, with a second pair of tissue sections collected for a subset of donors. Data were integrated and clustered, defining a robust LC cluster, two mixed non-LC neuron clusters, and several clusters labeling spots with mixed glial types contents. 77 samples from 30 donors with substantial LC content (≥10 spots per tissue section) were retained for downstream analyses. Differential expression (DE) analyses were then performed for the 5 clusters (of 9 total) with adequate count data, including LC, comparing expression between groups for each Alzheimer's risk variable of interest (sex, genomic ancestry, and APOE genotype). Additional analyses were performed for: 1) spatially variable expression within spots of the LC cluster; 2) comparing neuromelanin (NM)containing LC spots NM-negative LC spots; 3) modeling spot-level NM relationships to spot-level gene expression; 4) nonnegative matrix factorization of LC cluster gene expression to identify discrete expression programs; 5) gene set enrichment analyses of DE genes, NM-associated genes, and factorization-identfied LC gene groups.

first: Bernard

last: Mulvey

first: Heena R

last: Divecha

first: Madhavi

last: Tippani

first: Svitlana V

last: Bach

first: Rahul

last: Bharadwaj

first: Ishbel

last: del Rosario

first: Sarah

last: Maguire

first: Ryan A

last: Miller

first: Aaron J

last: Salisbury

first: Atharv

last: Chandra

first: Beau A

last: Oster

first: Kelsey D

last: Montgomery

first: Sang Ho

last: Kwon

first: Haya

last: Algrain

first: Alexis

last: Papariello

first: Joel E

last: Kleinman

first: Leonardo

last: Collado-Torres

first: Thomas M

last: Hyde

first: Shizhong

last: Han

first: Daniel R

last: Weinberger

first: Stephanie C

last: Hicks

first: Stephanie

last: Cerceo Page

first: Kristen R

last: Maynard


title: Schizophrenia-linked gene expression changes across cortical layers and cellular microenvironments in human prefrontal cortex [Visium]

first: Keri

last: Martinowich

summary: Molecular mechanisms underlying dorsolateral prefrontal cortex (dlPFC) dysfunction in schizophrenia (SCZ) are poorly understood. dlPFC cell types are spatially organized across the six layers into functional microcircuits, which regulate cognitive and emotional processes that are implicated in SCZ. While regional specificity across cortical layers and cell types has been demonstrated for some SCZ-linked genes, spatially-resolved transcriptomics (SRT) can more definitively map molecular associations of disease. We investigated spatial gene expression changes in the human dlPFC from neurotypical control (n=31) and SCZ (n=32) brain donors using the Visium platform with incorporation of immunostaining to label perineuronal nets, neurons and vasculature. SCZ-associated DEGs were then mapped across these labeled cellular microenvironments and cortical layers. Major transcriptional alterations were identified in synaptic and neuroimmune pathways, which we localized to neuropil and glia-enriched domains. Integrative analysis with bulk and single-cell RNA studies highlighted distinct roles for spatially-localized glial cell populations, and identified enrichment of novel DEGs in endothelial cells and microglia. These findings were supported by enrichment of SCZ genetic risk across similar domains, and association of laminae-specific transcription factors to SCZ risk variants. Cellular resolution SRT using Xenium extended laminar disease associations to spatially-organized cell types. The findings highlight unique advantages of SRT to identify novel SCZ-related biology, particularly for cellular populations and compartments that may be missed with alternative technologies. We provide data resources to enable sample-level visualization of the spatial transcriptomics data (Samui) and to explore SCZ-associated DEGs across spatial domains (iSEE-layer adjusted) and cellular microenvironments (iSEE-Neuropil, iSEE-Neuron, iSEE-vasculature, iSEE-PNNs).

overall_design: The study includes fresh-frozen postmortem human brain tissue sections obtained from the dorsolateral prefrontal cortex (DLPFC) of 32 donors with schizophrenia (SCZ)  and 31 neurotypical controls (NTC). A single 10-µm-thick cryosection per donor was analyzed using the 10x Genomics Visium spatial transcriptomics platform (v1, 3' Gene Expression), yielding a total of 63 samples. The primary comparison was made between diagnostic groups: 32 SCZ samples and 31 NTC samples.

first: Sang-Ho

first: Boyi

last: Guo

first: Cindy

last: Fang

first: Madhavi

last: Tippani

first: Svitlana

middle: V

last: Bach

first: Ryan

first: Sarah

last: Maguire

first: Madeline

last: Valentine

first: Seyun

last: Oh

first: Aarti

last: Jajoo

first: Artemis

last: Iatrou

first: Vijetha

last: Balakundi

first: Yufeng

last: Du

first: Annie

last: Nguyen

first: Ruth

last: Zhang

first: Uma

last: Kaipa

first: Heena

last: Divecha

first: Jashandeep

last: Lobana

first: Joel

last: E. Kleinman

first: Nikolaos

middle: P

last: Daskalakis

first: Thomas

last: Page

first: Kristen


title: Transcriptomic profiling of zebrafish mutants for orthologs of genes that increase schizophrenia risk

city: Worcester

first: Summer

last: Thyme

state: MA

address: 364 Plantation St

institute: UMass Chan Medical School

summary: In this study, we used CRISPR/Cas9 to knock out multiple orthologs of genes that increase risk for schizophrenia in humans. Gene sets included those from SCHEMA (exome sequencing), copy number variatns, and de novo mutations in childhood onset schizophrenia. Larval brain activity and behavior as assessed for all lines. The truncating sp4 and atp1a3a-v139m point mutation were selected for transcriptomic analysis.

overall_design: RNA-sequencing of dissected heads of larval zebrafish and dissected whole brains from adults. Two heterozygous parents were crossed together, and larvae from one clutch were dissected at 6 days post-fertilization or animals were grown until adulthood until dissection. Mutant and wild-type control sibling embryos were identified by genotyping after dissection for larvae, and 3-5 heads were pooled for each biological replicate. Genotypes of adults were identified by finclipping prior to dissection. At least five biological replicates were collected per genotype.

first: Thyme

last: Summer


title: High-fat diet rewires gut host-microbiota relationship to derive worse outcomes following Clostridioides difficile infection

city: Ann Arbot

first: Raymond

last: Yung

state: Michigan

address: 109 Zina Pitcher Pl

institute: University of Michigan

overall_design: RNAseq profiling of C. difficile infected (CDI) and anitbiotic-treated (mock) cecal samples obtained from normal diet and high-fed diet fed C57BL/6J  mice.

first: Kumar

last: Archit

first: Nguyen

last: Nhu T Q

first: O'Brien

last: Martin

first: Young

last: Vincent B

first: Yung

last: Raymond


title: A human-specific enhancer modulates chromosomal interactions to promote neurogenesis [human scRNA-seq]

city: Durham

first: Federica

last: Mosti

state: NC

address: 213 Research Dr

institute: Duke University

summary: Changes to the human genome have driven the evolution of human features including a larger neocortex and enhanced cognition. Human Accelerated Regions (HARs) are highly-conserved loci containing human-specific variants, which can be transcriptional enhancers during neurodevelopment. However, the neurodevelopmental functions of HARs and their mechanism of gene regulation are still largely unknown. Here, we show that the HAR1984 promotes neural progenitor cell identity and neurogenesis by influencing species-specific transcription and chromatin interactions. Humanized HAR1984 knock-in of chimpanzee cortical organoids increased intermediate progenitors and neurons, whereas chimpanzee HAR1984 knock-in  in human cortical organoids produced the opposite phenotype. Moreover, humanized HAR1984 knock-in mouse brains showed increased progenitor proliferation and neuron number, resulting in a thicker cortex with cortical folding. Hi-C data revealed a chromatin loop of HAR1984 with its target genes, ETV5 and TRA2B, present in human fetal brains, but reduced in chimpanzee, macaque or mouse neural cells. We show that human-specific mutations in HAR1984 promote chromatin looping and that human-specific ETV5 binding auto-regulates enhancer activity. This work demonstrates new molecular mechanisms underlying human-specific neurodevelopment, linking HARs to chromatin architecture, cortical cell identity and evolutionary expansion of  human brains.

overall_design: Comparative gene expression profiling analysis of scRNA-seq data for Hs-HAR1984(Hs/Hs) and Hs-HAR1984(Pt/Pt) day60 and day90 human cortical organoids.  2 control lines and 2 CRISPR KI lines were analyzed.

first: Debra

last: Silver


title: Epigenetic Atlas of Bladder Cancer Reveals Master Transcription Factors and Risk-Associated Regulatory Elements in Luminal and Basal-Squamous Molecular Subtypes

city: Boston

first: Elio

last: Adib

address: 20 Shattuck Street

institute: Brigham and Women's Hospital

summary: We performed histone ChIP-seq, the Assay for Transposase-Accessible Chromatin using sequencing (ATAC-seq), and RNA sequencing (RNA-seq) on 28 fresh frozen bladder/upper tract tumor samples. We integrated 64 unique data sets to gain a holistic view of gene regulation in bladder cancer expression/molecular subtypes and nominated candidate subtype-specific master transcription factors (TF) driving expression differences. We also integrated bladder GWAS risk SNPs with H3K27ac ChIP-seq and ATAC-seq data and revealed that risk variants were significantly enriched in genetically determined peaks

overall_design: We performed histone ChIP-seq, ATAC-seq, and RNA sequencing (RNA-seq) to annotate the epigenetic landscape then integrate that data to nominate candidate master TFs important to maintain cellular identity. We also GWAS risk loci with epigenetically marked peaks.

first: Amin H.

last: Nassar

first: Sarah

last: Abou Alaiwi

first: Toni K.

last: Choueiri

first: David J.

last: Kwiatkowski

first: Matthew L.

last: Freedman


title: Serum Response Factor (SRF) drives actin cytoskeletal organization in adipocytes to support adaptive hypertrophic expansion and tissue remodeling during obesity

city: Indianapolis

first: Jisun

last: So

state: IN

address: 635 Barnhill Drive

department: Biochemistry and Molecular Biology

institute: Indiana University School of Medicine

summary: Background: Adipocyte hypertrophy, the unique ability of adipocytes to expand in response to positive energy balance, is a key determinant of metabolic health during obesity. However, the molecular mechanisms that govern this adaptive growth are not fully understood. Methods: We performed super-enhancer profiling to identify transcriptional regulators activated in adipocytes under obesogenic conditions. Functional roles of the identified regulator were assessed through in vitro and in vivo analyses, including adipocyte-specific deletion of target gene and subsequent single-nucleus RNA sequencing. Results: Serum Response Factor (SRF) was identified as a pivotal driver of actin cytoskeletal remodeling in adipocytes during obesity. SRF was both necessary and sufficient for the expression of actin cytoskeletal genes in vitro. In vivo, adipocyte-specific SRF deletion reduced actin cytoskeletal gene expression, disrupted filamentous actin networks, and impaired adipocyte enlargement following high-fat diet feeding. Despite similar body weights, mice lacking adipocyte SRF exhibited exacerbated insulin resistance and ectopic lipid accumulation in the liver and brown adipose tissues, reflecting compromised adipocyte integrity and lipid storage capacity. Single-nucleus RNA-seq further revealed that defective actin cytoskeletons in adipocytes disrupted tissue homeostasis, resulting in impaired vascularization and elevated inflammation. Conclusion: These findings establish SRF as a central regulator of actin cytoskeletal organization in adipocytes, essential for supporting healthy hypertrophic expansion and proper tissue remodeling during obesity. SRF emerges as a critical determinant of metabolic health and a potential therapeutic target for obesity-related disorders.

overall_design: To investigate SRF binding motifs and regulatory pathways, we performed SRF ChIP-seq in differentiated 3T3-L1 adipocytes treated with TGFβ1. For in vivo functional analyses, we conducted a comparative analysis of bulk RNA-seq and snRNA-seq data from epididymal (eWAT) and inguinal white adipose tissues (iWAT) of adipocyte-specific SRF knockout (SRF-AKO) mice and wild type (WT) mice.

first: Hyun Cheol

last: Roh


title: Aberrant DNA Methylation Underlying Prenatal Exposures and Increased Newborn and Childhood Adiposity

city: Chicago

first: Jami

last: Josefson

state: Illinois

address: 225 E Chicago Avenue

institute: Ann & Robert H. Lurie Children's Hospital of Chicago

type: Methylation profiling by genome tiling array

summary: This study aimed to identify whether cord blood DNA methylation at specific loci is associated with neonatal adiposity, a key risk factor for childhood obesity. An epigenome-wide association study was conducted using the Hyperglycemia and Adverse Pregnancy Outcome (HAPO) Study as a discovery sample. Assays were performed with Illumina EPIC arrays (791,359 CpG sites after quality control). Replication was performed in an independent cohort, Genetics of Glucose regulation in Gestation and Growth (Gen3G).  In 2740 HAPO samples, significant associations were identified at 89 CpG sites after accounting for multiple testing (Bonferroni-adjusted p < 0.05). Replication analyses conducted in 139 Gen3G participants confirmed associations for seven CpG sites. These included IGF1R, which encodes a transmembrane receptor involved in cell growth and survival that binds insulin-like growth factor I and insulin, and KLF7, which encodes a regulator of cell proliferation and inhibitor of adipogenesis; both are key regulators of growth during fetal life.  These findings support epigenetic mechanisms in the developmental origins of neonatal adiposity and as potential biomarkers of metabolic disease risk.

first: Alan

last: Kuang

first: Catherine

last: Allard

first: Monica

last: Bianco

first: William

last: Lowe Jr

first: Denise

last: Scholtens

first: Luigi

last: Bouchard

first: Marie-France

last: Hivert


title: CBP-IDRs regulate acetylation and gene expression

city: Sheffield

first: Daniel

middle: Arun

last: Bose

state: South Yorkshire

address: University of Sheffield, Firth Court, Western Bank

department: Biosciences

institute: The University of Sheffield

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

overall_design: Refer to individual Series


title: Functional genomics analysis of developing zebrafish and human endoderm reveals highly conserved cis-regulatory modules controlling vertebrate organogenesis [RNA-seq]

city: Coventry

first: Andrew

last: Nelson

address: Gibbet Hill Road

department: School of Life Sciences

institute: University of Warwick

summary: While vertebrate species are superficially diverse, they share key commonalities in terms of overall morphology, and organ configuration and function. Maintenance of these traits during evolution is partially explained by conservation of critical genes governing embryonic development. However, for conserved genes to deliver consistent developmental outcomes between species, similar gene regulatory programmes and gene expression patterns must also be maintained. The endoderm germ layer makes major contributions to the respiratory and gastrointestinal tracts, and associated organs including liver and pancreas. We used functional genomics approaches to identify highly conserved endodermal cis-regulatory modules (CRMs) functioning across the 400 million years of evolution separating zebrafish and humans. Our analyses suggest that there are few endoderm-specific CRMs, with many CRMs governing pancreas developmental also likely acting within the nervous system. Furthermore, these highly conserved CRMs are strongly enriched for binding sites of “neuro-pancreatic” transcription factors governing both pancreas and nervous system development, potentially suggesting function across these distinct organ systems. Additionally, we identify highly conserved CRMs likely participating endodermal patterning of adjacent craniofacial structures and sensory tissues. The highly conserved CRMs we identify are characterised by conserved patterns of transcription factor binding site co-occurrence. However, they are not characterised by rigid arrangement of binding sites, suggesting more complex or individual grammatical rules. Overall, our analyses provide key insights into critical gene regulatory control during vertebrate endoderm organogenesis, and define a compendium of highly conserved CRMs that should be prioritised for analysis of neuro-pancreatic gene transcriptional control, and anterior embryonic patterning.

overall_design: RNA-seq and ATAC-seq analysis of cell populations isolated from zebrafish at 28 and 48 hours post-fertilisation using fluorescence activated cell sorting.  Samples are enriched based on sox17:GFP  reporter expression relative to endothelial and erythrocyte markers (kdrl:cherry and gata1a:dsRed respectively).  Sox17E is endoderm-enriched; sox17M is sox17+ hematovascular cells; sox17N is sox17-negative lineages.

first: Daniela

middle: M

last: Figiel

first: Randa

last: Elsayed

first: Mark

middle: D

last: Walsh


title: mRNA profiling upon knockdown of circRNA-HIPK2

city: Hannover

first: Maximilian

last: Fuchs

address: Carl-Neuberg-Str. 1

department: IMTTS

institute: Hanover Medical School

summary: Despite advances in drug development, global mortality rates following heart failure (HF) remain still high, underscoring the critical need for novel therapeutic strategies. Emerging evidence highlights cardiac macrophages as promising cellular targets for intervention. In our investigation, we identified a circular RNA-HIPK2 (circHIPK2.) exhibiting close association with macrophage polarization dynamics following myocardial infarction (MI). To elucidate its functional significance and associated transcriptomic alterations, we performed targeted knockdown of circHIPK2. in macrophage cells through siRNA transfection, comparing experimental groups (circHIPK2 siR) with controls (ctrl siR).

overall_design: Expression profiling by high throughput sequencing on Raw264.7 macrophages upon transfection with 100 nM circRNA-HIPK2 siRNA and scramble siRNA, followed by LPS (100nM/mL) stimulation. Total RNA was harvested, sequencing was performed in triplecates.

first: Thum

last: Thomas

first: Jung

last: Mira

first: Maximillian


title: Single cell analysis applied to study Pth1r related skull deformity

city: Suita

first: Daisuke

last: Motooka

state: Osaka

address: 3-1, Yamadaoka

institute: NGS core facility, Research Institute for Microbial Diseases, Osaka University

summary: We have employed single cell RNA sequencing approach using 10XGenomics scRNAseq to elucidate roles of Pth1r in skull development. Conditional knockout mice for Pth1r exhibited unambiguous craniomaxillofacial deformity. This analysis will help to understand the unique molecular mechanisms.

overall_design: Craniomaxillofacial tissues were removed from genotyped mice. The tissues were processed with enzymatic digestion. Tomato-positive single mesenchymal cells were isolated by FACS and subjected to analysis at single cell resolution.

first: Katsuhiko

last: Amano

last: Okuzaki