title: Single-cell atlas of black rockfish (Sebastes schlegelii) ovarian stroma across reproductive states

city: Qingdao

first: Xinlin

last: Yang

state: Shandong

address: Yushan

institute: Ocean University of China

summary: This project contains single-cell RNA sequencing (scRNA-seq) data of the ovarian stroma from the viviparous teleost, black rockfish (Sebastes schlegelii). To define how the ovarian stroma is reprogrammed across reproduction, we profiled stromal cells spanning three distinct biological states: unfertilized, normal-gestation, and abnormal-gestation (characterized by spontaneous embryonic mortality and avascularity). This dataset aims to characterize the stromal cell composition, developmental trajectories, and immune-vascular interactions critical for maintaining intraovarian gestation, providing insights into the evolutionary biology of teleost viviparity.

overall_design: Ovarian stroma tissues from black rockfish were collected across three distinct reproductive states: unfertilized, normal-gestation, and abnormal-gestation. Single-cell suspensions were prepared, and single-cell gene-expression libraries were constructed using the 10x Genomics Chromium Next GEM Single Cell 3′ v3.1 workflow. The resulting libraries were sequenced on an Illumina NovaSeq platform with 2x150 bp paired-end reads to profile the stromal cell composition and transcriptomic changes across reproduction.


title: H3K9 di-methylation dynamics underlies mouse minor zygotic genome activation [CATCH-seq of early embryo]

status: Public on Apr 19 2026

city: Suita-shi, Osaka

first: Ryo

last: Maeda

address: Yamadaoka 1-3

country: Japan

institute: The University of Osaka

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Minor zygotic genome activation (ZGA) is crucial for early development and totipotency acquisition, yet the regulatory mechanisms driving minor ZGA genes remain elusive. Here we show that dynamic regulation of H3K9me2 is essential for minor ZGA. H3K9me2 levels at minor ZGA gene loci are reduced at early 2-cell and are re-established by morula. Maternal depletion of the H3K9 demethylases KDM3A and KDM3B leads to increased H3K9me2 and impaired minor ZGA in early 2-cell, followed by developmental arrest at 2- to 4-cell. In mESCs, H3K9 at minor ZGA loci is highly di-methylated; combined loss of the H3K9 methyltransferases G9a and SETDB1 leads to synergistic de-repression of minor ZGA genes. Mechanistically, SETDB1 specifically targets Dux, while G9a broadly represses minor ZGA genes through H3K9 di-methylation linked to lamina-associated heterochromatin formation. These findings establish H3K9me2 dynamics as a key regulator for minor ZGA, highlighting the indispensable role of epigenetic control in early embryogenesis.

overall_design: ChIP-seq of early embryo

first: Shunsuke

last: Kuroki

first: Masahiro

last: Matsuwaka

first: Azusa

last: Inoue

first: Makoto

last: Tachibana


title: H3K9 di-methylation dynamics underlies mouse minor zygotic genome activation [spike-in ChIP-seq of mESC]

overall_design: Epigenome profiling by high throughput sequencing


title: H3K9 di-methylation dynamics underlies mouse minor zygotic genome activation [ChIP-seq of mESC]


title: Region- and cell type-specific changes in gene expression in the cerebellum after classical fear conditioning [snRNA-Seq]

city: Seoul

first: Jungeun

last: Ji

address: 145 Anam-ro

department: Department of Integrated Biomedical and Life Science

country: South Korea

institute: Korea University

type: Expression profiling by high throughput sequencing

summary: The cerebellum has recently been recognized for its role in non-motor functions, including classical fear conditioning. However, the molecular mechanisms underlying non-motor learning and memory remain largely unknown. Here, we investigate the transcriptional changes in the cerebellum associated with auditory fear conditioning. Spatial transcriptomic analysis revealed that in the deep cerebellar nuclei (DCN), an output region of the cerebellum, the expression of immediate early genes increased following fear learning and retrieval, suggesting that DCN may contribute to fear memory processing. As for the cerebellar cortex, robust and region-specific transcriptional changes were observed, with distinct expression patterns emerging across the Purkinje cell layer of vermis region. To further elucidate transcriptional changes in specific DCN cell types involved in fear processing, we performed single-nucleus RNA sequencing and identified prominent gene expression changes in Kit+ inhibitory neurons. Collectively, our findings highlight region- and cell-type-specific molecular adaptations in the cerebellum, providing insights into its contribution to non-motor learning.

overall_design: We performed spatial transcriptomics data analysis using 10X Visium data obtained from coronal mouse cerebellum sections of 3 groups (fear conditioned vs after auditory memory retrieval vs home cage). We performed single-nuclei RNA-sequencing data analysis using data obtained from mouse deep cerebellar nuclei (DCN) of 3 groups (fear conditioned vs after auditory memory retrieval vs home cage).

first: Jinhee

last: Baek

first: Kyoung-Doo

last: Hwang

first: Seunghwan

last: Choi

first: Junko

last: Kasuya

first: Ted

last: Abel

first: Joon-Yong

last: An

first: Yong-Seok

last: Lee


title: Exploring the immune environment of glioblastoma in humanized mouse models

city: Birmingham

first: Satoru

last: Osuka

state: Alabama

address: 1720 2nd Ave. South, WTI401

country: USA

institute: The University of Alabama at Birmingham

summary: Glioblastoma (GBM) is the deadliest primary brain tumor in adults, and progress in therapy development has been hindered by the lack of preclinical models that faithfully recapitulate interactions between human tumor cells and human immune cells, particularly in therapy-resistant disease. To address this limitation, we established a humanized mouse model of GBM using radiation-resistant patient-derived xenografts (PDXs) implanted into immunodeficient mice reconstituted with human hematopoietic stem progenitor cells derived from umbilical cord blood. For single-cell RNA sequencing, peripheral blood (PB), tumor-infiltrating immune cells (TILs), and tumor cells were collected from humanized NOG-EXL mice bearing EGFP-positive JX14P-RT tumors. Tumor cells from the same JX14P-RT model implanted into non-humanized naive NOG-EXL mice were also analyzed for comparison. Single-cell suspensions were prepared from tumor tissues, and CD45-positive immune cells and EGFP-positive tumor cells were isolated by cell sorting. Human CD45-positive cells in peripheral blood were purified separately. The dataset includes three TIL samples from humanized mice, three PB samples from humanized mice, three tumor-cell samples from humanized mice, and two tumor-cell samples from naive mice. Individual samples were labeled with hashtag oligonucleotide antibodies, pooled, and then analyzed separately by compartment as TIL, PB, and tumor groups. Libraries were generated using the 10x Genomics Chromium Single Cell 3' platform and sequenced on an Illumina NovaSeq 6000. The data show infiltration of diverse human immune populations, including T cells, natural killer cells, and myeloid lineage cells, and support the utility of this model for studying the immune microenvironment of recurrent and therapy-resistant GBM.

overall_design: We profiled recurrent GBM cells, tumor-infiltrating immune cells, and paired peripheral blood immune cells from CD34+ hematopoietic stem cell–reconstituted humanized NOG-EXL mice implanted with JX14P-RT tumors. For tumor cell analysis, we analyzed EGFP+ tumor cells from three humanized mice and two naive mice. For immune cell analysis, we analyzed tumor-infiltrating immune cells and paired peripheral blood immune cells from three humanized mice. Single-cell suspensions enriched for CD45+ immune cells or EGFP+ tumor cells by cell sorting were subjected to scRNA-seq using the 10x Genomics single-cell platform. We generated a 10x Genomics Gene Expression library together with a paired Antibody Capture library containing both HTO and ADT features. HTO was used for sample multiplexing, and HTO-to-sample correspondence is provided in the supplementary file HTO_samples.csv. ADT data were included in the integrated dataset. HTO and ADT feature definitions are provided in GBM_feature_reference.csv, TIL_feature_reference.csv, and PB_feature_reference.csv.

first: Jun

last: Takei

first: Ken

last: Furudate

first: Masakazu

last: Kamata


title: H3K9 di-methylation dynamics underlies mouse minor zygotic genome activation [RNA-seq of early embryo]

first: Ryo

last: Maeda

overall_design: Expression profiling by high throughput sequencing


title: Region- and cell type-specific changes in gene expression in the cerebellum after classical fear conditioning

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

overall_design: Refer to individual Series


title: Alveolar Macrophages Undergo a Postnatal Transition from a Hyperphagocytic and Proinflammatory Profile to a Tolerogenic Profile

city: He Fei

first: Yu

last: Hang

address: 宿松路

country: China

institute: 合肥综合性国家科学中心大健康研究院

summary: Alveolar Macrophages (AMs) are crucial for lung immunity and homeostasis. While the ontogeny of AMs is well characterized, their postnatal phenotypic and functional maturation remains unclear. Here, we developed a bronchoalveolar lavage (BAL) protocol across key developmental stages and systematically analyzed age-dependent changes in AMs. AM numbers increased with age, acquiring a mature phenotype alongside alveolar maturation.BAL-recovered AMs decreased in size and increased in roundness from day 3 onward and revealed distinct gene expression profiles across different ages. Functionally, phagocytic capacity peaked in 3-day-old mice. Furthermore, AMs from all ages beyond day 1 showed lower basal inflammatory cytokine expression and an attenuated response to LPS, indicating a postnatal transition toward a tolerant phenotype. The transition from a hyper-phagocytic, pro_x0002_inflammatory neonatal profile to a tolerogenic adult phenotype underscores the intrinsic adaptation of AMs to the immunotolerant microenvironment of the mature lung. Our study provides a comprehensive kinetic profile of postnatal AM development.

overall_design: Bronchoalveolar lavage fluid (BALF) was collected from mice at postnatal days 1, 3, 7, 21, and 49 (D1, D3, D7, D21, D49). AMs were pooled from 3-6 mice per time point. 1.5×10⁴ AMs were resuspended in 50 μL of DMEM medium supplemented with 10% fetal bovine serum and seeded into a 384-well untreated plate.The cells were then stimulated with lipopolysaccharide (LPS) at a concentration of 400 ng/mL (purchased from InvivoGen, catalog number tlrl-b5lps) or treated with LPS-free medium (served as control). After 4 hours of incubation, AMs from  were collected for subsequent RNA sequencing (RNA-seq) analysis.

first: Hang

last: Yu

first: Shengwen

last: Shang

first: Qing

last: Xu

first: Jiabing

last: Tong

first: Jian

last: Wang

first: Fengqi

last: Li


title: mRNA-based influenza vaccine expands the breadth of the B cell response in humans

status: Public on Apr 18 2026

city: St. Louis

first: Julian

last: Zhou

state: MO

address: 425 S. Euclid Ave.

department: Pathology & Immunology

institute: Washington University in St. Louis

summary: Eliciting durable antibody responses against rapidly evolving pathogens such as the influenza virus remains a formidable challenge. Conventional influenza virus vaccines are poorly immunogenic and induce antibody responses of limited breadth. Germinal center (GC) reactions in draining lymph nodes are key sites for antibody diversification and affinity maturation following vaccination. Whether an mRNA-based influenza virus vaccine can induce a superior GC response in humans compared to conventional vaccines remains unclear. We assessed B cell responses in an observational study of cohorts of healthy young adults receiving a licensed, split-virion or an investigative mRNA-based quadrivalent seasonal influenza virus vaccine over two consecutive seasons. mRNA-based vaccines consistently elicited higher antibody titers and frequencies of memory B cells. In the draining lymph nodes, mRNA vaccination stimulated sustained GC reactions that persisted for at least 26 weeks post vaccination in five of thirteen participants across the two seasons. To understand how sustained GC activity shapes the secreted serum IgG repertoire, we performed proteomic analysis of serum IgG repertoire. mRNA vaccination increased the number of vaccine-elicited serum IgG clonotypes and promoted intraclonal expansion within pre-existing clonotypes. B cell lineage analyses further indicated that expanded serum clonotypes map to GC B cell-associated subbranches, consistent with ongoing GC-driven evolution underlying intraclonal expansion. This repertoire remodeling was accompanied by increased binding breadth against antigenically divergent influenza viruses. These findings reveal a key role for persistent GC responses in broadening the repertoire of vaccine-induced antibodies.

overall_design: scRNA-seq was performed on ultrasound-guided fine needle aspirates (FNA) samples of axillary lymph nodes and blood samples sorted for plasmablasts and IgDlo B cells collected at various timepoints.

first: Hanover

middle: C

last: Matz

first: Tae-Geun

first: Kritika

last: Dixit

first: Caroline

last: Kikawa

middle: Q

first: Garazi

middle: P

last: Alzua

first: Lowrey

last: Peyton

first: Anders

last: Madsen

first: Fangjie

last: Han

first: Ariana

middle: G

last: Farrell

first: Robert

last: Hoelzl

first: Aaron

middle: J

last: Schmitz

first: Stephen

last: Horvath

first: Hunter

middle: K

last: Keplinger

first: Benjamin

middle: S

last: Strnad

first: Mark

last: Hoegger

first: William

middle: D

last: Middleton

first: Michael

last: Klebert

first: Nina

middle: H

last: Lin

first: Raffael

last: Nachbagauer

first: Florian

last: Krammer

last: Paris

first: Jesse

last: Bloom

first: Jackson

last: Turner

first: Rachel

middle: M

last: Presti

first: Jiwon

first: Ali

last: Ellebedy


title: H3K9 di-methylation dynamics underlies mouse minor zygotic genome activation [RNA-seq of mESC]

first: Ryo

last: Maeda

overall_design: RNA-seq of mESC

first: Makoto

last: Tachibana


title: MiT Fusions, TSC1–TSC2 Divergence, and Stem-like Programs Reveal Distinct Origins and Vulnerabilities in PEComa [Methylation]

city: Illkirch

first: Gabriel

last: Malouf

state: Grand Est

address: 1 rue Laurent Fries

country: France

institute: INSTITUT/GENETIQUE/BIOLOGIE MOLEC/CELL

type: Methylation profiling by genome tiling array

summary: Perivascular epithelioid cell neoplasms (PEComas) are ultra-rare mesenchymal tumors lacking a molecular classification to guide therapy. Here we perform comprehensive multi-omic profiling of an unselected PEComa cohort. We identify frequent MITF rearrangements involving actin gene partners (ACTA2, ACTG1 and ACTB). Anatomical stratification reveals cyclin-dependent kinase module mutations in gynecologic tumors, whereas soft tissue, gastrointestinal, and pelvic tumors lacked mTOR pathway alterations but are enriched for TFE3/MITF rearrangements. Transcriptomic analysis defines four subtypes with distinct lineage programs—melanocytic, mesenchymal, or adipogenic—as well as unique mutational patterns and clinical behaviors. Notably, an aggressive stem-like subtype enriched for TP53/RB1 mutations exhibits high proliferation, activation of embryonic and Hedgehog signaling, immune infiltration, and resistance to mTOR inhibitors, but potential responsiveness to immunotherapy. Single-nucleus RNA sequencing reveals intra-tumoral heterogeneity within this subtype, including divergent inflammatory states. Together, these findings establish a molecular classification framework and identify actionable vulnerabilities in PEComa.

overall_design:
DNA methylation profiling was performed on human PEComa tumor samples to characterize epigenetic alterations and to support integrative analysis of subtype-specific transcriptional programs and tumor heterogeneity.

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

first: Justine

last: Gantzer

first: Xiaofan

last: Lu


title: H3K9 di-methylation dynamics underlies mouse minor zygotic genome activation


title: MiT Fusions, TSC1–TSC2 Divergence, and Stem-like Programs Reveal Distinct Origins and Vulnerabilities in PEComa [RNA-seq]

overall_design:
RNA sequencing was performed on human PEComa tumor samples to define transcriptional programs and support integrative molecular subtyping and characterization of tumor heterogeneity.

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


title: Region- and cell type-specific changes in gene expression in the cerebellum after classical fear conditioning [Spatial Transcriptomics]

first: Jungeun

last: Ji

first: Jinhee

last: Baek

first: Kyoung-Doo

last: Hwang

first: Seunghwan

last: Choi

first: Junko

last: Kasuya

first: Ted

last: Abel

first: Joon-Yong

last: An

first: Yong-Seok

last: Lee


title: Tuning of the RBR1-E2F/DP transcriptional module bythe F- box protein FBL17

city: Gif Sur Yvette

first: Xiaoning

last: HE

address: 630,Rue Noetzlin

institute: universite-paris-saclay

summary: F-box proteins of SCF E3 ligases have been documented to control the abundance of numerous critical regulatoryproteins. In Arabidopsis, one of them, F-BOX- LIKE17 (FBL17), stands out for playing a key role in DNA replication,DNA damage, and, more recently, for the control of cell size. FBL17 null mutants exhibit severe cellular defectsleading to lethality. However, the molecular mechanisms by which FBL17 operate remain poorly understood.Here, we show that FBL17 interacts with different components of the RETINOBLASTOMA-RELATED1/E2F moduleand is involved in the protein turnover of E2Fa and E2Fb. However, mutations in E2Fa or E2Fb do not alleviate thesevere fbl17 phenotype but worsen it. By contrast, it is the accumulation of the transcriptional repressor E2Fc thatcauses fbl17 mutant lethality. Our results highlight a key role for FBL17 in modulating the transcriptional controlof E2F target genes ensuring precise control of cell cycle progression and avoiding uncontrolled DNA damage re-sponse.

overall_design: ChIP-seq profiling of E2Fc-GFP binding in 10-day-old Arabidopsis fbl17-/- mutant seedlings. Two biological replicates were immunoprecipitated with anti-GFP antibody, libraries were constructed, and sequenced at 75 bp on an Illumina NextSeq 500.

first: Juliette

last: Espanet

last: He

first: Ting

last: Pan

first: Cécile

last: Raynaud

first: Moussa

last: Benhamed

first: Sandra

last: Noir

first: Pascal

last: Genschik


title: Endothelial FGF13 impairs angiogenesis by accelerating oxygen-independent HIF-1α degradation [RNA-Seq]

city: Wenzhou

first: Zhaohang

last: Wu

address: Chashan

institute: Wenzhou Medical University

summary: Angiogenesis is a tightly regulated process essential for both development and disease, yet the role of fibroblast growth factor 13 (FGF13) in vascular remodeling has remained unclear. Here, we identify FGF13 as a key negative regulator of physiological and pathological angiogenesis. Using endothelial cell–specific knockout and overexpression mouse models, combined with retinal vascularization assays, hindlimb ischemia and myocardial infarction models, and in vitro endothelial cell functional assays, we demonstrate that loss of FGF13 enhances, whereas its overexpression impairs, neovascularization. Mechanistically, FGF13 binds to the PAS domain of HIF-1α and facilitates its interaction with RACK1, leading to oxygen-independent degradation of HIF-1α and suppression of downstream angiogenic signaling. Importantly, adenoviral overexpression of HIF-1α reversed the inhibitory effects of FGF13, confirming its essential role in mediating FGF13-driven angiogenic regulation. These findings reveal FGF13 as a critical endothelial-intrinsic brake on angiogenesis and suggest its potential as a therapeutic target in ischemic vascular disease.

overall_design: Total RNA from the cells was collected using RNAiso Plus and subjected to genome-wide transcriptomic analysis using Gene Denovo Biotechnology Co. (Guangzhou, China).

first: Weitao

last: Cong


title: MiT Fusions, TSC1–TSC2 Divergence, and Stem-like Programs Reveal Distinct Origins and Vulnerabilities in PEComa [scRNA-seq]

first: Gabriel

last: Malouf

overall_design:
Single-nucleus RNA sequencing was performed on selected PEComa tumor samples to characterize cellular heterogeneity and to validate transcriptomic subtype classification at single-cell resolution.

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

first: Justine

last: Gantzer

first: Xiaofan

last: Lu


title: Relationship between Mycobacterium tuberculosis response to nitric oxide stress and iron limitation

city: Boston

first: Shumin

last: Tan

state: MA

address: 150 Harrison Ave

department: Molecular Biology and Microbiology

institute: Tufts University School of Medicine

summary: The purpose of this study was to identify genes that are differentially expressed upon M. tuberculosis exposure to nitric oxide (NO) or iron limitation stresses, either individually or in combination.

overall_design: RNAseq profiling of M. tuberculosis CDC1551 wild type exposed for 4 hours to control, nitric oxide (NO), low iron, or nitric oxide + low iron conditions.

first: Natalia

middle: F

last: Quirk


title: RNA-seq profiling of LPS tolerance in monocytes, THP-1, fibroblasts, smooth muscle cells, and endothelial cells

city: Moscow

first: Svetlana

last: Verkhova

address: 8 Baltiyskaya Street

country: Russia

institute: Laboratory of Angiopathology, Institute of General Pathology and Pathophysiology

summary: Atherosclerosis – a chronic disease of the arteries characterized by lipid accumulation and chronic local inflammation – is the primary cause of most ischemic cardiovascular diseases. The inflammatory process can be limited by endotoxin tolerance. This study performed a comparative transcriptomic analysis of LPS tolerance in primary monocytes, the THP-1 monocyte line, fibroblasts, endothelial cells, and smooth muscle cells. To model LPS tolerance, single and double LPS stimulation was performed. Sequencing of libraries obtained from total RNA after poly(A) selection was performed on the Illumina NextSeq 2000 platform. Primary monocytes and smooth muscle cells developed LPS tolerance; fibroblasts showed partial, mediator-dependent tolerance; THP-1 cells showed limited tolerance primarily for TNF; endothelial cells did not show tolerance for IL-8/CCL2. No conserved transcriptional tolerance signature was observed across tolerant cell types; overlap was limited to three genes (OAS1, IFIT2, IFIT3).

overall_design: The study included five cell types: primary peripheral blood monocytes, the THP-1 monocyte line, the hTERT977 embryonic fibroblast line, the EA.hy926 endothelial-like cell line derived from HUVEC, and primary aortic intima-media smooth muscle cells. The cells were divided into 4 conditions: Control-Control (“C_C”), Control-LPS (“C_LPS”), LPS-Control (“LPS_C”), and LPS-LPS (“LPS_LPS”). In the first stage, the cells were incubated for 4 hours with control medium or LPS (1 μg/mL); after medium change, a second incubation was performed for 20 hours with control medium or LPS. For each cell type and condition, three independent experiments were performed. RNA sequencing was performed using the Illumina NextSeq 2000.

first: Nikita

last: Nikiforov

first: Alexander

last: Zhuravlev

first: Elena

middle: A

last: Pudova

first: Anastasiya

middle: V

last: Snezhkina

first: Yegor

middle: E

last: Yegorov

first: Khava

last: Vishnyakova

first: Mikhail

last: Popov

first: Andrey

last: Omelchenko

first: Daria

last: Borodko

last: Chegodaev

first: Daiana

middle: B

last: Erdyneeva

first: Anna

last: Kudryavtseva

first: Ulyana

last: Khovantseva

last: Markin

first: Denis

last: Breshenkov

first: Eduard

middle: R

last: Charchyan

middle: N

last: Orekhov


title: Transcriptome profiling reveals the molecular mechanism of cuticular wax (bloom) formation during blueberry fruit development.

city: Jilin

first: chen

last: shaopeng

address: 77 Hanlin Road, Economic and Technological Development Zone, Jilin City, Jilin Province

institute: Jilin Agricultural Science and Technology College

summary: The cuticular wax, commonly known as fruit bloom, plays a crucial role in the postharvest quality, shelf-life, and stress resistance of blueberries. However, the transcriptional regulatory networks underlying its formation during fruit maturation remain largely unknown. In this study, we performed comparative transcriptome sequencing (RNA-seq) on blueberry fruits at three critical developmental stages: the early green fruit stage (stage 1), the color-break stage (stage 2), and the mature stage (stage 3). A total of 9 cDNA libraries (three independent biological replicates per developmental stage) were constructed and sequenced. This dataset captures the dynamic transcriptional reprogramming during fruit development, specifically highlighting the spatiotemporal expression patterns of genes involved in lipid metabolism, very-long-chain fatty acid (VLCFA) elongation, triterpenoid biosynthesis, and ABC transporter-mediated secretion. The provided RNA-seq data offer valuable insights into the molecular mechanisms of blueberry cuticular wax formation and serve as a fundamental resource for discovering key candidate genes for fruit quality improvement and genetic breeding.

overall_design: This submission includes transcriptomic samples designed to investigate the molecular mechanisms and transcriptional reprogramming of cuticular wax formation during blueberry fruit development. The experimental design encompasses three distinct developmental stages as the primary variable: the early green fruit stage (stage 1, serving as the baseline reference/control), the color-break stage (stage 2), and the mature stage (stage 3). Fruit samples were collected for RNA-seq analysis with three independent biological replicates per stage, resulting in a total of 9 samples.

first: shaopeng

last: chen

first: qianqian

last: zhuang


title: Dose-dependent Effects of Estrogen on Genomic Regulation in Breast Cancer Cells [Hi-C]

city: Dallas

first: W. Lee

last: Kraus

state: TX

address: 5323 Harry Hines Blvd.

institute: UT Southwestern Medical Center

summary: Estrogen is the primary mitogen for ER+ BC cells. However, most studies prior to this examining the genomic effects of E2-regulated signaling in cell-based assays used supraphysiological levels of hormone. While this has allowed us to understand the extremes of E2 signaling, it has limited our ability to examine cellular functions which operate at lower hormone concentrations. In particular, the genomic actions of ligand-bound ERa through transcriptional enhancer formation and function are not understood at physiological E2 doses. Here, we use an integrated genomic approach with RNA-seq, PRO-seq, ChIP-seq,  ATAC-seq, and HiC to identify gene sets that express preferentially at either picomolar or nanomolar concentrations of E2. Expression of these genes is regulated mainly at the transcriptional level and is associated with distinct enhancer features, including chromatin accessibility and H3K27ac enrichment, as well as differential binding of FOXA1 and GATA3 co-transcription factors. These features are also spatially organized within TAD boundries.

overall_design: HiC of MCF-7 cells treated with a range of E2 concentrations (veh., 10 pM, 10 nM).

first: Kim

last: Hyung Bum

first: Nandu

last: Tulip

first: Kraus

last: W Lee


title: A maternal Polycomb imprint is maintained in early Drosophila development through lower-order methylation states

city: Evanston

first: Shelby

last: Blythe

state: IL

address: Northwestern University, Hogan Hall, 2205 Tech Drive

department: Molecular Biosciences

institute: Northwestern University

type: Genome variation profiling by high throughput sequencing

summary: In an associated manuscript, we have measured by ChIP-seq the genome-wide distribution of total Histone H3, and Histone H3 di- and trimethylated at Lysine 27 (H3K27me2, H3K27me3) in early Drosophila embryos to measure establishment and maintenance of these modifications during the maternal-to-zygotic transition. We measured occupancy of these histone states at two timepoints corresponding to early embryonic cleavages (nuclear cycles 1-10, (NC1-10)) and late in the nuclear cycle following large-scale zygotic genome activation (nuclear cycle 14 (NC14)). The experiment was performed in two batches, each with two biological replicates for a total of 4 replicates. Two of the replicates were performed on embryos expressing RpA70-EGFP, which facilitates staging of early embryos by nuclear density. The second set of replicates were performed on embryos collected from a cross between RpA70-EGFP mothers and OregonR fathers. This second batch of replicates allowed us to distinguish whether H3, H3K27me2, or H3K27me3 preferentially associates with maternal or paternal chromating through the mapping of single nucleotide polymorphisms present in either the maternal or paternal genotype. To define these SNPs, we also performed whole genome resequencing of both parental stocks. We find that H3K27me2/3 is asymmetrically present on maternally-derived chromatin at NC1-10, and that both marks equalize by late NC14. In the associated manuscript, evidence is provided that the H3K27me2 mark is maintained over cleavage divisions, and that H3K27me3 is passively diluted over this time.

overall_design: ChIP-seq for three targets (total H3, H3K27me2, or H3K27me3) at two developmental stages (NC1-10 or NC14). Experiment 1: RpA70-EGFP embryos were collected and fixed prior to hand sorting for NC1-10 or NC14 nuclear density/morphology by RpA70-EGFP epifluorescence. Two independent replicates of 150 embryos (NC1-10) or 10 embryos (NC14) were processed for Tn5-assisted ChIP. Experiment 2: embryos from a cross between RpA70-EGFP mothers and OregonR fathers were collected and processed as described for Experiment 1. To determine the distribution of SNPs in the parental genotypes, genomic DNA from male RpA70-EGFP and OregonR flies was prepared and prepped into sequencing libraries using Illumina Nextera reagents.

first: Eleanor

last: Degen


title: Exercise Metabolic Memory Halts Pathological Cardiac Hypertrophy via PDK4

city: Guangzhou

first: Cankun

last: Zheng

address: Guangzhou Avenue

institute: Nanfang Hospital

summary: Background Pathological cardiac hypertrophy remains a major contributor to heart failure, with impaired glucose metabolism playing a central role. Although exercise is known to enhance myocardial glucose utilization, the long-term metabolic reprogramming effects of exercise and their role in preventing pathological hypertrophy are poorly understood. This study elucidates the mechanisms underlying the sustained metabolic memory induced by exercise hypertrophic preconditioning (EHP) and its cardioprotective effects, with a focus on RNA methylation and arachidonic acid metabolism.  Methods We employed PET/CT to assess cardiac glucose uptake and bulk RNA sequencing to profile myocardial gene expression in sedentary (Sed) and EHP mice. Genetic manipulation of Pdk4 was achieved via adeno-associated virus mediated overexpression and tamoxifen-inducible, cardiac-specific knockout (Pdk4-CKO). Pressure overload was induced by transverse aortic constriction (TAC) in Pdk4-CKO and control (Myh6-CreER, MCM) mice. Epigenetic regulation of Pdk4 by EHP was investigated using pyrosequencing, SELECT-qPCR and dual-luciferase assays. Untargeted metabolomics and molecular docking, molecular dynamics simulation, and CETSA were performed on heart tissues and neonatal rat cardiomyocytes/fibroblasts to identify key metabolites and their mechanisms of action.  Results: EHP conferred sustained myocardial glucose preference even after regression of physiological hypertrophy, mediated through METTL3-dependent m6A RNA methylation that suppressed Pdk4 expression. Pdk4 overexpression abolished EHP-mediated cardioprotection, whereas Pdk4 deletion enhanced cardiac function and attenuated fibrosis under pressure overload. Metabolomic profiling identified arachidonic acid-derived metabolites 5-KETE, 12-keto-leukotriene B4, and 20-hydroxy-leukotriene B4 as novel inhibitors of hypertrophy and fibrosis. These metabolites attenuated cardiomyocyte hypertrophy and fibroblast trans-differentiation through inhibition of the ERK2/MAPK1 pathway.  Conclusions: This study establishes a unified mechanism by which EHP induces metabolic memory through RNA methylation-dependent suppression of Pdk4, leading to altered arachidonic acid metabolism and the accumulation of protective lipid mediators. These findings highlight the therapeutic potential of targeting the PDK4–arachidonic acid metabolites axis to mitigate pathological cardiac remodeling.

overall_design: One week after the three-week swimming training, total RNA was extracted from five cardiac tissues of mice in the EHP and Sed groups

first: Hairuo

last: Lin

first: Yingqi

last: Zhu


title: Macrophage CD163 Promotes Post-Infarction Cardiac Repair and Preserves Left Ventricular Function via Osteopontin

city: Xiamen

first: Binbin

last: Liu

state: Fujian

address: Jinshan Road

department: Xiamen Cardiovascular Hospital

institute: Xiamen University

summary:
Background: Cardiac macrophages have been implicated in myocardial repair following myocardial infarction (MI), yet their therapeutic potential in ischemic cardiomyopathy (ICM) remains limited by an incomplete understanding of their molecular regulation. CD163 is highly expressed in these macrophages, yet its functional role in regulating post-MI cardiac repair remains unknown.
Methods: A cross-sectional clinical study was conducted to assess the association between circulating soluble CD163 concentration and heart failure due to ICM. To investigate the functional contribution of CD163 in ICM, Wild-type (WT) and Cd163/ mice were subjected to permanent ligation of the left anterior descending coronary artery. Single-cell RNA sequencing was employed to analyze transcriptional changes in cardiac immune cells. Recombinant osteopontin (OPN) and CD163 were administered to assess their therapeutic effect in Cd163/ mice.
Results: Circulating soluble CD163 levels were markedly elevated in patients with ICM-induced heart failure compared with individuals without heart failure (median difference 34.5 ng/mL, IQR 13.6–54.6 ng/mL, P = 0.002) and showed a positive correlation with the extent of systolic dysfunction and left ventricular dilation. Cd163/ mice displayed aggravated left ventricular systolic dysfunction, reduced ejection fraction and fractional shortening, impaired myocardial strain, and reduced relative wall thickness post-MI. Recombinant CD163 protein could reverse systolic dysfunction and left ventricular dilation in Cd163/ mice after MI. CD163 was predominantly expressed in CCR2⁻ resident cardiac macrophages, and CD163 deficiency altered transcriptional programs of macrophages without affecting their polarization status, with enrichment in cytokine signaling and extracellular matrix-related pathways. Spp1 (OPN) expression was significantly downregulated in Cd163/ hearts under both sham and MI conditions. Administration of recombinant OPN improved systolic function, reduced ventricular dilation, decreased fibrotic scar size, and restored the elastin-to-collagen ratio in Cd163/ mice.
Conclusions: In cardiac macrophages, CD163 contributes to post-myocardial infarction repair by upregulating OPN expression, which in turn helps maintain systolic function.

overall_design: MI was induced in male mice by permanent ligation of the left anterior descending (LAD) coronary artery as reports. One day prior to surgery, chest hair was removed with depilatory cream. Mice were anesthetized with 2% isoflurane and placed on a heating pad to maintain body temperature. After disinfecting the skin with povidone-iodine, a 1.2 cm left thoracic incision was made to expose the fourth intercostal space. The pleura and pericardium were opened, and the heart was gently exteriorized. The left coronary artery (LCA) was ligated approximately 3 mm from its origin using a 6-0 silk suture, and successful ligation was confirmed by pallor of the anterior left ventricular wall. The heart was then returned to the thoracic cavity, residual air was evacuated, and the chest was closed. Mice typically recovered within 3–5 minutes under observation. Sham-operated mice underwent the same procedure without LCA ligation. Recombinant osteopontin (OPN) was dissolved in sterile phosphate-buffered saline (PBS) at 5 ng/μL. A total of 200 ng OPN (40 μL) or an equal volume of PBS was injected at three sites along the infarct border zone immediately after LAD ligation using a Hamilton syringe with a 30-gauge, 4 mm needle.

first: Jingyu

last: Chen

first: Cuilian

last: Dai


title: Dose-dependent Effects of Estrogen on Genomic Regulation in Breast Cancer Cells


title: PerturbPair: A Dual-Modality Platform Integrating Perturb-seq and Optical Pooled Screening to Map Cellular Responses and Enable Cross-Modal Inference

city: San Francisco

first: Romain

last: Lopez

state: California

address: 1396 Sanchez St

institute: New York University

summary: This dataset profiles transcriptional responses to genetic perturbations in primary bone marrow–derived macrophages (BMDMs) stimulated with lipopolysaccharide (LPS). Using a pooled CRISPR library targeting 1,030 genes (with ~4 sgRNAs per gene), we applied Perturb-seq to capture single-cell RNA sequencing (scRNA-seq) profiles at 9 hours post-LPS stimulation.

overall_design: Primary bone marrow–derived macrophages (BMDMs) were isolated from Cas9 transgenic mice and differentiated in vitro. Cells were transduced at low multiplicity of infection (MOI ~0.2) with a pooled CRISPR library targeting 1,030 genes (4 sgRNAs per gene plus olfactory receptor and non-targeting controls). After 7 days of differentiation, macrophages were stimulated with lipopolysaccharide (LPS, 100 ng/ml) for 9 hours. Single-cell transcriptomes were captured using the 10x Genomics GEM-X platform, generating 334,633 high-quality single-cell RNA-seq profiles assigned to individual perturbations.

first: Takamasa

last: Kudo

first: Aviv

last: Regev


title: Dose-dependent Effects of Estrogen on Genomic Regulation in Breast Cancer Cells [RNA-seq]

summary: Estrogen is the primary mitogen for ER+ BC cells. However, most studies prior to this examining the genomic effects of E2-regulated signaling in cell-based assays used supraphysiological levels of hormone. While this has allowed us to understand the extremes of E2 signaling, it has limited our ability to examine cellular functions which operate at lower hormone concentrations. In particular, the genomic actions of ligand-bound ERa through transcriptional enhancer formation and function are not understood at physiological E2 doses. Here, we use an integrated genomic approach with RNA-seq, PRO-seq, ChIP-seq, and ATAC-seq to identify gene sets that express preferentially at either picomolar or nanomolar concentrations of E2. Expression of these genes is regulated mainly at the transcriptional level and is associated with distinct enhancer features, including chromatin accessibility and H3K27ac enrichment, as well as differential binding of FOXA1 and GATA3 co-transcription factors.

overall_design: RNA-seq of MCF-7 cells treated with a range of E2 concentrations (veh., 10 pM, 100 pM, 1 nM, 10 nM).


title: RNA-Seq and BiFC joint analysis revealed that NtCISZOG regulates the expression of NtChlH and positively regulates chlorophyll content in tobacco

city: Guiyang

first: Qin

last: Tang

address: Jiaxiu South Road

institute: Guizhou university

summary: We identified NtCISZOG as a key regulator of chlorophyll content in tobacco, revealing its interaction with NtChlH, which provides a genetic basis for breeding tobacco varieties with centralized leaf maturation.

overall_design: this study used mutants K326-gk-8, KY-OE-31, and the wild type as experimental materials and conducted a transcriptomic analysis of tobacco leaves at the seedling stage to explore the mechanism through which NtCISZOG regulates chlorophyll content in tobacco plants.


title: Dose-dependent Effects of Estrogen on Genomic Regulation in Breast Cancer Cells [ATAC-seq]

overall_design: ATAC-seq of MCF-7 cells treated with a range of E2 concentrations (veh., 10 pM, 100 pM, 1 nM, 10 nM).


title: Effect of carnitine treatment on muscle gene expression in mice modeled on a high-fat diet

city: Lishui

first: Yahong

last: Lu

state: Zhejiang

address: No.289, Kuocang Road, Liandu District, Lishui City, Zhejiang Province, China

institute: The Fifth Affiliated Hospital of Wenzhou Medical University

summary: Skeletal muscle fatty infiltration has been shown to be strongly associated with sarcopenia. In this study，we constructed a high-fat diet mouse model and treated model mice with carnitine.Gene expression in skeletal muscle of different groups of mice was analyzed by RNA sequencing.

overall_design: Nine-week-old C57BL/6J mice were assigned to three groups, and after two weeks of acclimatization, mice in the control group were fed a regular chow (10% kcal of fat, D12450J, Research Diets), and mice in the other groups were fed a high-fat diet (60% kcal of fat, D12492, Research Diets). Mice in the HFD+CAR group was given 100 mg/kg/day L-carnitine through their drinking water (MCE; Shanghai, China). All the mice were fed for 8 weeks. Before sacrifice, the mice were fasted for 6 h, and tissues were collected according to the appropriate preparation method for each experiment.

first: Yu

last: Bai

first: Weiqing

last: Li

first: Zhiguo

last: Zhou

first: Heihuan

last: Lai

first: Xingyu

last: Hu

first: Tao

last: Yang

first: Chendi

last: Wang

first: Yitao

first: Keping

last: Gan

first: Kechi

first: Haiwei

last: Ma

first: Lin

last: Shen

first: Dengwei

last: He


title: Dose-dependent Effects of Estrogen on Genomic Regulation in Breast Cancer Cells [PRO-seq]

first: W. Lee

last: Kraus

overall_design: PRO-seq of MCF-7 cells treated with a range of E2 concentrations (veh., 10 pM, 100 pM, 1 nM, 10 nM).

first: Kim

last: Hyung Bum

first: Nandu

last: Tulip

first: Kraus

last: W Lee


title: IFN-γ induction of GBP1 drives aberrant macrophage activation in human skin granulomas

city: Baltimore

first: Immunometabolism

last: Department

state: Maryland

address: 1650 Orleans Street

department: Immunometabolism

institute: Johns Hopkins University

summary: Granuloma annulare (GA) and cutaneous sarcoidosis (cSAR), non-communicable skin conditions, possess an overlapping immunopathology, in which the aberrant activation of macrophages by IFN-γ constitutes a central driver of disease. Nevertheless, our understanding of the molecular events occurring in pathologically activated GA and cSAR macrophages remains limited. Here, we analyzed published single-cell RNA sequencing data of GA and cSAR and performed in-vitro experiments with primary human cells, allowing us to show that oxidative phosphorylation (OXPHOS) is a dominant metabolic pathway in IFN-γ-activated macrophages. Furthermore, we identify an IFN-γ-induced, OXPHOS-sensitive response network in human GA and cSAR macrophages. Within this network, GBP1 plays a central role in controlling IFN-γ-mediated macrophage activation. Meanwhile, inhibition of OXPHOS and GBP1 both promoted resolution of granulomas and prevented granuloma induction in a human in-vitro granuloma model. Taken together, our study suggests that OXPHOS and GBP1 represent therapeutic strategies for treating cutaneous granulomatous diseases.

overall_design: PBMC were obtained from buffy coats by density gradient centrifugation using Ficoll-Paque Plus (Cytiva, 17-1440-03) or Lymphoprep (STEMCELL Technologies, 07851) and monocytes were separate with CD14+ MACS technology (Miltenyi Biotec, 130-050-201), according to manufacturer´s protocol. To induce differentiation into macrophages, eluted CD14+ cells were cultured in RPMI 1640 medium (Life Technologies, 21875091 or 21875158) supplemented with 10% FBS/FCS (Pan-Biotech, P30-3302 or Thermo Fisher, 10099141), 1% Penicillin/streptomycin (Sigma, P0781 or  GIBCO, 15140-122) and M-CSF 50 ng/ml (Miltenyi Biotec, 130-096-492 or R&D Systems, 216-MC-500) for 5-10 days. Activation of MDM was achieved by a treatment with IFN-γ (BD Biosciences, 554617) or LPS at 1 ng/ml (Invivogen, tlrl-eblps) in complete RPMI with 10mM glucose or 10mM Galactose. PBMC were collected from 6 separate buffy coats.

first: Mario

last: Fabri

first: David

last: Sanin


title: Extracellular vesicles derived from Plasmodium falciparum-infected red blood cells transfer miR451a, disrupting neutrophil function and contributing to immune dysregulation

city: Fribourg

first: Pierre-Yves

last: Mantel

address: Route Albert Gockel 1

department: Department: Oncology, Microbiology and Immunology

country: Switzerland

institute: University of Fribourg

summary: Malaria, caused by Plasmodium falciparum, compromise innate immunity, yet the underlying mechanisms remain poorly understood. Here, we demonstrate that the malaria parasite utilizes extracellular vesicles (EVs) derived from infected red blood cells (iRBC-EVs) as a mechanism to transfer the host microRNA miR451a to primary human neutrophils, effectively suppressing their immune functions. Using primary human neutrophils and transduced Human leukemia cell (HL-60 cells) with a lentiviral expression vector containing miR451a (HL-60miR451a), we evaluated the effect of miR451a in neutrophil transcription and effector functions (ROS production, swarming and antimicrobial activity). The microfluidic assay shows that the transferred miR451a significantly reduces chemotaxis and swarming ability of both primary human neutrophils and HL-60miR451a when subsequently challenge with Candida albicans. Bulk and single cell transcriptomic analysis reveals that miR451a alters transcriptional regulation in primary both neutrophils and HL-60miR451a, further impairing their immune responses . Additionally, we demonstrate that phagocytosed iRBC-EVs blunt the production of reactive oxygen species (ROS) and reduce the anti-microbicidal activity of neutrophils upon Salmonella typhimurium challenge. These observed immunosuppressive mechanisms provide critical insights into the mechanism of increased susceptibility of malaria-infected individuals to invasive bacterial or fungal diseases. Our findings shed light on the molecular interactions between P. falciparum and the host immune system, highlighting how malaria-induced immunosuppression exacerbates vulnerability to severe bacterial infections by impairing neutrophil functions. This knowledge has significant implications for therapeutic strategies aimed at mitigating co-infections and sepsis in malaria-endemic regions.

overall_design: RNA-seq profiling of human neutrophils unstimulated or stimulated with extracellular vesicles (EVs) derived from infected-Red Blood Cells in the presence or abscence of LPS. RNA-seq profiling of HL-60 cell line overexpresing scramble or miR451a stimulated or not with LPS for 90 minutes and 180 minutes.

first: Paola

last: Martinez

first: Simone

last: Lucchesi

first: Maria

last: Novedrati

first: Giorgio

last: Montesi

first: Francesco

last: Santoro


title: Dose-dependent Effects of Estrogen on Genomic Regulation in Breast Cancer Cells [ChIP-seq]

overall_design: ERa, H3K27ac, FOXA1, or GATA3 ChIP-seq of MCF-7 cells treated with a range of E2 concentrations (veh., 10 pM, 100 pM, 1 nM, 10 nM).


title: Krüppel-like factor 2 programs early exhausted T cell states and restrains antiviral immunity [TCR-Seq]

city: 福建省 / 厦门市 / 翔安区

first: Zifeng

last: Li

address: 福建省厦门市厦门大学翔安校区

summary: A key challenge in improving T cell-mediated immunotherapies is defining the factors that regulate functional versus exhaustion T cell fates. Through multi-round in vivo CRISPR screens in chronic LCMV Clone 13 infection and transcription factor (TF) benchmarking, we identified KLF2 as a top TF driving CX3CR1⁺ effector-like exhausted cell (Texeff-like) differentiation. Overexpression of KLF2 converted CX3CR1⁻ cells into Texeff-like cells by direct engagement of key loci. Conversely, loss of KLF2 increased inhibitory receptor expression and redirected cells toward terminal exhaustion. However, early after infection, KLF2 deficiency yielded increased CD8+ T cell accumulation and improved viral control. This effect was, in part, mediated by TOX and improved T cell localization with dendritic cells. Additional deletion of PD-1 further enhanced viral control, but induced severe immunopathology. Collectively, these findings identify KLF2 as a central regulator of the Texeff-like program and underscore exhaustion features as checkpoints balancing antiviral immunity and immunopathology.

overall_design: CD44+PD-1+ or GP33 tetramer+ cells from GzmbCreKlf2wt or GzmbCreKlf2fl/fl mice were sorted at the indicated time points after LCMV Cl13 infection.

first: Shengjun

last: Geng

first: Hongling

last: Huang


title: Coordinated regulation of calcium homeostasis and pathogenicity by a dual-action transcriptional regulator Cas5 [RNA-Seq]

city: Shanghai

first: JIHONG

last: liu

state: Shanghai

address: No. 320 Yueyang Road, Shanghai

institute: siii

summary: As a clinically relevant opportunistic human fungal pathogen, C. albicans is able to rapidly sense and adapt to changing microenvironments within the host, a process that is essential for its successful invasion and survival. Although studies have shown that the transcription factor Crz1 is the master regulator of calcium (Ca2+) homeostasis, accumulating evidence supports a clear involvement of other participants in this biological process. Here, following a high-throughput genetic screen, we identified the transcription factor Cas5 as a novel positive regulator of Ca2+ homeostasis in C. albicans. Mechanistically, Cas5 modulates Crz1 dephosphorylation, nuclear localization and Crz1-dependent signaling pathway by inhibiting protein kinase Tpk1 to maintain Ca2+ homeostasis. Furthermore, our study confirms that the calcineurin-mediated virulence is dependent on transcription factor Cas5 in a Crz1-independent manner, complementing a long-standing knowledge gap in the regulation of virulence by calcineurin. Taken together, our findings elucidate that a dual-action transcriptional regulator Cas5 coordinates both Ca2+ homeostasis and pathogenicity of C. albicans in the host.

overall_design: Overnight culture of WT, cnb1Δ/Δ, crz1Δ/Δ and cas5Δ/Δ strains in YPD, the next day, Cell pellets were transfer to fresh YPD for the starting concentration of C. albicans OD600 is 0.1 and culture to the logarithmic phase of growth at 30 ℃; where the calcium ion treatment group is to add 0.2 M calcium and continue to incubate for 1 h. Each strain was cultured in three independent parallel groups for each condition at the same time. Take 2 OD C. albicans to remove the supernatant by rapid centrifugation at 4 ℃, frozen in liquid nitrogen, and then use the above total RNA extraction method for RNA extraction, extraction of RNA samples using 1.5% agarose gel electrophoresis identification. The total RNA samples were sent to Tianjin Novogene for quality control, and the subsequent sequencing of the samples was carried out. The final library construction and Illumina HiSeq2000 sequencing of the samples were done by Tianjin Novogene.


title: Krüppel-like factor 2 programs early exhausted T cell states and restrains antiviral immunity [ATAC-seq]

city: 福建省 / 厦门市 / 翔安区

address: 福建省厦门市厦门大学翔安校区

overall_design: For ATAC-seq in vitro, P14 cells were activated and transduced with pMIGII empty vector or pMIGII-Klf2. After in vitro culture for an additional 2.5 days, cells were sorted for ATAC-seq library preparation. For ATAC-seq at day 5.5, Cas9-expressing P14 cells transduced with sgNTC (GFP⁺) or sgKlf2 (GFP⁺) were mixed at a 1:1 ratio with sgNTC-transduced “spike” cells (Ametrine⁺) and transferred to Cas9-expressing hosts infected with LCMV Cl13.Donor-derived cells were sort  for ATAC-seq library preparation at day 5.5.


title: Mediator Subunit Med4 Enforces Metastatic Dormancy in Breast Cancer (Histone ChIP-seq_shMed4)

city: New York

first: Seongyeon

last: Bae

state: NY

institute: Columbia University

summary: Breast cancer metastatic relapse after a latency period, known as metastatic dormancy, involves dormant tumor cells within pre-metastatic niches. Through rigorous genetic screening in mice, we identified the mediator complex subunit 4 gene, Med4, as a novel tumor-cell intrinsic gatekeeper in metastatic reactivation. Med4 downregulation effectively awakened dormant breast cancer cells, prompting reactivation and macroscopic metastatic outgrowth in the lungs. Med4 depletion results in profound changes in nuclear size and three-dimensional (3D) chromatin architecture from compacted to relaxed states in contrast to the known canonical function of the Mediator complex. These changes rewire the expression of extracellular matrix (ECM) proteins, integrins, and signaling components resulting in integrin-mediated mechano-transduction and activation of YAP and MRTF. In parallel, assembly of stress fibers pulls on the nuclear membrane, and thereby contributes to mediating and reinforcing the overall chromatin modifications that occur subsequent to Med4 depletion. MED4 gene deletions were observed in patients with metastatic breast cancer, and reduced MED4 expression correlates with worse prognosis. Our findings unveil a unique function of MED4 and identify an innovative mechanism by which MED4 regulates the epigenetic control of integrin signaling, pivotal in the metastatic reactivation of breast cancer. Additionally, we propose MED4 and related gene signatures as novel biomarkers for stratifying patients prone to recurrence, thus identifying subsets of patients who will benefit from targeting effectors activated by MED4 loss.

overall_design: Comprehensive chromatin state profiling and analysis of metastatic breast cancer by performing ChIP-sequencing of 5 core histone modifications.

first: Seong-Yeon

first: Filippo

last: Giancotti


title: Coordinated regulation of calcium homeostasis and pathogenicity by a dual-action transcriptional regulator Cas5 [ChIP-Seq]

overall_design: Briefly, cells were cultured in 50 mL of YPD medium until the optical density reached 0.6, in which the calcium ion-treated group was supplemented with 0.2 M calcium and continued to incubate for 1 h. Subsequently, cells were crosslinked with 1% formaldehyde for 15 min at 30°C with gentle shaking, and then quenched by adding 0.125 M glycine for 5 min. After three rounds of cold phosphate buffer (PBS) washing, fungal cells were lysed using glass beads in low-salt buffer with added protease inhibitors. After cell lysis, the lysate was sonicated on ice to fragment the chromatin into fragments of 200 to 500 bp size. After removal of the cellular debris, chromatin fragments were captured using protein A/G magnetic beads by the addition of anti-Myc-Tag monoclonal antibody(Abmart, M20002L) or Normal Rabbit IgG (Cell signaling technology, 2729S). The beads were subsequently washed using buffers of different salt concentrations ( in sequence, low salt buffer, high salt buffer, lithium chloride buffer and tri-ethylenediaminetetraacetic acid (TE) buffer). Subsequently, a buffer containing sodium dodecyl sulfate (SDS) and sodium chloride was added and heated overnight at 65°C to promote the release of DNA fragments. The beads were then treated with RNAase and proteinase K sequentially, the supernatant was centrifuged and purified using a DNA purification kit (Thermo Fisher Scientific, K0702).


title: Mediator Subunit Med4 Enforces Metastatic Dormancy in Breast Cancer (ATAC-seq_shMed1)

overall_design: Bulk ATAC-seq of D2A1-d cells expressing either NTC or Med1 shRNAs.


title: Krüppel-like factor 2 programs early exhausted T cell states and restrains antiviral immunity [RNA-Seq]

city: 福建省 / 厦门市 / 翔安区

address: 福建省厦门市厦门大学翔安校区

overall_design: For RNA-seq in vitro, P14 cells were activated and transduced with pMIGII empty vector or pMIGII-Klf2. After in vitro culture for an additional 2.5 days, cells were analyzed by flow cytometry or sorted for RNA-seq library preparation. For RNA-seq of Texeff-like and Texterm, Cas9-expressing P14 cells transduced with sgNTC (GFP⁺) and transferred to Cas9-expressing hosts infected with LCMV Cl13.Donor-derived cells were sort for RNA-seq library preparation at day 7.5. For RNA-seq at day 5.5, Cas9-expressing P14 cells transduced with sgNTC (GFP⁺) or sgKlf2 (GFP⁺) were mixed at a 1:1 ratio with sgNTC-transduced “spike” cells (Ametrine⁺) and transferred to Cas9-expressing hosts infected with LCMV Cl13.Donor-derived cells were sort for RNA-seq library preparation at day 5.5. For another RNA-seq at day 5.5, Cas9-expressing P14 cells were transduced with sgNTC (mCherry⁺), sgKlf2 (GFP⁺), and sgRunx3 (Ametrine⁺). The cells were mixed in a 1:1:1 ratio and transferred into Cas9-expressing hosts infected with LCMV Cl13. At day 5.5, donor-derived cells were sorted for RNA-seq library preparation. The sorted populations included sgNTC (mCherry⁺), sgKlf2 (GFP⁺), sgRunx3 (Ametrine⁺), and sgKlf2 + sgRunx3 (GFP⁺ Ametrine⁺).


title: Mediator Subunit Med4 Enforces Metastatic Dormancy in Breast Cancer (ATAC-seq_shMed4)

overall_design: Bulk ATAC-seq of D2A1-d cells expressing either NTC or Med4 shRNAs. The sample names have been provided as below.


title: Mediator Subunit Med4 Enforces Metastatic Dormancy in Breast Cancer

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

overall_design: Refer to individual Series


title: HILPDA facilitates PHB1 mitochondrial localization in cardiomyocytes and its deficiency leads to dilated cardiomyopathy

first: ZHUO

last: LIU

address: Road Dongan NO.130

institute: Fudan University

summary: Through data screening and transgenic mouse phenotype verification, we found that HILPDA plays a potential role in the development of dilated cardiomyopathy. To investigate the specific effects of HILPDA on cardiomyocytes and dilated heart disease, we generated HILPDA deficient embryonic stem cells (escs) using Crispr cas9 and differentiated them into cardiomyocytes. We assessed global gene expression changes in cardiomyocytes derived from Human H7 embryonic stem cells on day 15 of differentiation after HILPDA knockout by microarray analysis using the Illumina Hiseq produced by Annorud. We found that the expression of genes involved in mitochondrial oxidative respiration and mitochondrial functional damage was significantly down-regulated after HILPDA knockout.

overall_design: Total RNA isolated from cardiomyocytes differentiated from human H7 embryonic stem cell line on day 15 and cardiomyocytes  differentiated from HIlPDA-deficient human H7 embryonic stem cell line on day 15.

first: Fei

last: Gao

first: Chen

last: Xu

first: Ning

last: Sun


title: Jag1-regulated hybrid-EMT state identifies a subset of CD9hi pancreatic tumour-initiating cells with enriched stemness

city: London

first: Axel

last: Behrens

address: 123 Old Brompton Road

country: United Kingdom

institute: Institute of Cancer Research

summary: We previously identified a pancreatic ductal adenocarcinoma (PDAC) subpopulation capable of initiating PDAC and giving rise to PDAC heterogeneity, marked by the tetraspanin CD91. PDAC shows great cellular heterogeneity, with pronounced epithelial and mesenchymal cancer cell populations, and it has been suggested that cancer cells with hybrid epithelial-mesenchymal transition (EMT) features peculiarly contribute to tumour aggressiveness2,3. Here, we identify a stable hybrid-EMT subpopulation that are highly enriched for tumour initiating cell (TIC) properties which constituted a subpopulation of CD9hi TICs1. Hybrid-EMT CD9hi TICs showed increased capacity to form organoids and generate epithelial and mesenchymal tumour cell progeny. Interestingly, in contrast to the majority of PDAC organoids with cystic morphology, hybrid-EMT organoids exhibited a solid morphology and were able to give rise to both cystic and filled organoids, implying a relationship between stemness and solid morphology. Cell depletion of hybrid-EMT cells led to gradual collapse of organoids formation capability, suggesting hybrid-EMT cells are required for long-term organoid formation. Mechanistically, hybrid-EMT cells upregulated Jag1, which promoted their self-renewal by activating the Notch signalling pathway. Thus, the hybrid EMT state is a defining feature of stem cells in PDAC.

overall_design: Pancreatic Ductal Adenocarcinoma (PDAC) cells were isolated from the KPFRR (Pdx1-Flp;KrasFSF-G12D/+;Trp53frt/frt;Rosa26FSF-creER;Rosa26mTmG) mouse model. Single-cell transcriptomics was performed on GFP+ live cells using the 10x chromium system. The StemID and slingshot algorithms were used to identify the clusters with highest cancer stem cell identity.

first: Linxiang

last: Lan

first: Huafu

first: Shiwei

last: Zhang

first: Cristina

last: Garrone

first: May

middle: Z

last: Thin

first: Yihang

last: Pan

first: Changhua

first: Yulong

last: He

first: Rocio

last: Sancho


title: Topical application of Urolithin A slows intrinsic skin aging and protects from UVB-mediated photodamage: Findings from Randomized Clinical Trials

city: Ecublens

first: Davide

last: D'Amico

address: EPFL Innovation Park, Building C

institute: Amazentis SA

summary: Urolithin A is a gut microbiome derived postbiotic that has been shown to stimulate mitophagy, and improve muscle and mitochondrial health when administered orally to humans. In three separate randomized trials, we have now investigated the effect of topical administration of Urolithin A on skin aging features and on UVB-mediated photodamaged skin. Post-menopausal women with evidence of skin aging such as > Grade 3 wrinkle formation were included in a split-face/arm study design in the first trial (aging study 1; n=48), followed by a second larger trial (aging study 2; n=108) in middle-aged men and women focusing on wrinkle reduction. Healthy participants were included in the placebo-controlled, randomized UVB-induced trial (photo-damage trial; n=22). Participants were randomized to receive topical supplementation with either 0.5% Urolithin A cream or placebo for 8-weeks in a low-dose arm or 1% Urolithin A cream or placebo in the high-dose arm in theaging study 1. In theaging study 2participants were randomized to receive 1% UA in a day-cream, a night cream and a serum, that were compared to the untreated site. For thephoto-damage trial,topical patches containing either 0.5% or 1% UA or placebo cream were applied for 24-hours following UVB irradiation. The primary outcome in theaging study 1was an impact on biological pathways linked to skin aging in skin biopsies, and an impact on skin barrier function after 8-weeks. Key secondary endpoints were a change in facial wrinkle appearance (crow’s feet area). Theaging study 2focused on wrinkle reduction as a primary outcome. In the UVB-mediatedphoto-damage study, the primary read-out was the change in erythema after application. Molecular analyses were conducted on skin biopsies and usingex-vivosystems to investigate the mechanism of action mediating skin protective effects of Urolithin A. In theaging study 1, Urolithin A at 1% significantly up-regulated collagen synthesis pathways in human skin biopsies and led to a decrease in wrinkle depth on facial wrinkles. The lower dose had no significant impact. There was no change on skin barrier function with both doses suggesting maintenance of a healthy skin barrier function. Inaging study 2, topical application of Urolithin A at the 1% dose in different formulations (day-cream, night cream and serum) led to significant wrinkle reduction compared to the untreated side, confirming the previous findings. Skin hydration was improved significantly as well. In the third trial, investigating impact on photodamaged skin, Urolithin A application led to a significant decrease in UV-induced erythema (∼14%) compared to the untreated area, while placebo and lower dose UA cream’s showed no benefits. Urolithin A topical administration was safe and well-tolerated in all studies. UA also inhibited collagen degrading and pro-inflammatory pathways and up-regulated gene expression of biomarkers linked to induction of mitophagy and autophagy in human skin cells. Taken together, these clinical studies support the topical use of Urolithin A to manage and prolong skin health longevity by acting at the cellular level, supporting collagen structure, reducing wrinkle appearance and protecting against photoaging.

overall_design: Goal: To investigate the biological impact of Urolithin A applied topically on human healthy skin for 4 months, compared to placebo. Topical formulation contaexperimental conditions: placebo baseline; placebo end of study; UA. Each participant was randomly assigned to the test products to apply on either the left or the right side of the face and arm in the case of the aging study 1, where skin biopsies were collected. The tested products  were a moisturizing skin base cream containing standardized excipients (vehicle, i.e. Placebo) and for the (active) arms containing 1% UA (MitopureTM) added in the base cream. We then performed RNA-seq fromarm skin biopsies to compared changes in gene expression by Urolithin A, comparing end of study to baseline and after normalizing over Placebo.

first: Julie

last: Faitg

first: Anurag

last: Singh

first: Dimitris

last: Konstantopoulos


title: Mediator Subunit Med4 Enforces Metastatic Dormancy in Breast Cancer (RNA-seq_shMed4)

first: Seongyeon

last: Bae

overall_design: Total RNA was isolated from murine breast cancer D2A1-d cells expressing either NTC or Med4 shRNAs and sent to BGI for RNA-seq. The sample name was annotated below.

first: Filippo

last: Giancotti


title: Immune-skewed stromal–immune axis defined by antigen-presenting-like adipose stromal cells in lymphedema

status: Public on Apr 17 2026

city: 종로구

first: Hyunsung

last: Nam

state: 서울특별시

address: 대학로 1

institute: Seoul National University

summary: Background Lymphedema, a chronic and progressive disease, is characterized by lymphatic dysfunction, persistent inflammation, fibrosis, and pathological adipose tissue remodeling. Although adipose-derived stromal cells (ASCs) are implicated in disease progression, the stromal cell states and stromal–immune interactions that sustain chronic fibro-inflammatory remodeling remain poorly defined.  Methods Single-cell RNA sequencing was performed of the stromal vascular fraction isolated from anatomically matched human subcutaneous adipose tissues. These tissues were obtained from patients with advanced-stage lymphedema and healthy individuals to delineate disease-associated stromal heterogeneity at single-cell resolution.  Results A disease-expanded ASC progenitor population (ASC_c2) that exhibits pronounced transcriptional reprogramming in lymphedema was identified. The ASC_c2 population segregated into two mutually exclusive pathological subsets: a VCAM1⁺ vascular-interacting stromal population (V-ASCs) associated with ECM remodeling and CD74⁺HLA class II–expressing subset (I-ASCs) with antigen-presentation-like features. I-ASCs displayed a robust interferon-responsive transcriptional program consistent with immune priming and preferentially expressed the CXCL14 chemokine. Ligand–receptor interaction analysis revealed biased stromal–immune interactions between I-ASCs and CD8⁺ T cells, suggesting a skewed immune microenvironment in lymphedematous adipose tissue.  Conclusions Our findings suggest an immune-skewed stromal–immune axis in lymphedema, driven by immune-primed, antigen-presentation-like ASCs. The study findings suggest a cellular framework linking stromal reprogramming to chronic immune dysregulation and fibrosis in human lymphedema, offering insights into potential therapeutic targets for interrupting pathological stromal–immune crosstalk.

overall_design: Single-cell RNA sequencing data of adipose tissue stromal vascular fraction (SVF) from limb fat of patients with lymphedema and normal controls

first: Nam

last: Hyunsung

first: Choi

last: Una

first: Ha

last: Eun Hee

first: Lee

last: Brian Hyohyong

first: Ko

last: Jaecheon

first: Kim

last: Hyun Je

first: Hong

last: Ki Yong


first: Linxiang

last: Lan

address: 237 Fulham Rd

institute: The Institute of Cancer Research

summary: We previously identified a pancreatic ductal adenocarcinoma (PDAC) subpopulation capable of initiating PDAC and giving rise to PDAC heterogeneity, marked by the tetraspanin CD9.  PDAC shows great cellular heterogeneity, with pronounced epithelial and mesenchymal cancer cell populations, and it has been suggested that cancer cells with hybrid epithelial-mesenchymal transition (EMT) features peculiarly contribute to tumour aggressiveness. Here, we identify a stable hybrid-EMT subpopulation that is highly enriched for tumour initiating cell (TIC) properties which constituted a subpopulation of CD9hi TICs1. Hybrid-EMT CD9hi TICs showed increased capacity to form organoids and generate epithelial and mesenchymal tumour cell progeny. Interestingly, in contrast to the majority of PDAC organoids with cystic morphology, hybrid-EMT organoids exhibited a solid morphology and were able to give rise to both cystic and solid organoids, implying a relationship between stemness and solid morphology. Cell depletion of hybrid-EMT cells led to gradual collapse of organoids formation capability, suggesting hybrid-EMT cells are required for long-term organoid formation. Mechanistically, hybrid-EMT cells upregulated Jag1, which promoted their self-renewal by activating the Notch signalling pathway. Thus, the hybrid EMT state is a defining feature of stem cells in PDAC.

overall_design: To evaluate the role of Jag1 in the regulation of hybrid-EMT CD9hi tumour initiating cells (TICs), we generated Jag1 knocked-down mouse PDAC organoids by lentiviral shRNA, and then performed transcriptomic profiling on control (shCtrl) and Jag1 knocked-down (shJag1_3) organoids by RNA-sequencing (RNA-seq). Three biological replicates for each group were used and comparative gene expression analysis was conducted.

first: Shiwei

last: Zhang

first: Axel

last: Behrens


title: Mediator Subunit Med4 Enforces Metastatic Dormancy in Breast Cancer (RNA-seq_shMed1)

overall_design: Total RNA was isolated from murine breast cancer D2A1-d cells expressing either NTC or Med1 shRNAs and sent to BGI for RNA-seq. The sample name was annotated below.


title: Modulation of the DNA/RNA Binding Protein ARID5A Regulates Microglial Activation and Response [RIP-Seq]

city: La Jolla

first: Brian

last: Yee

state: CA

address: 9500 Gilman Dr

department: Health

institute: UCSD

summary: RNA binding proteins (RBPs) shape cellular function in health and disease. However, the function of RBPs expressed specifically in the central nervous system (CNS) remain uncharacterized. Within the CNS, we identify ARID5A as a microglial-specific RBP and integrate multi-omics analyses of ARID5A's RNA, DNA, and protein interactions to uncover its RNA-mediated regulation of microglial functions. We show ARID5A regulates the splicing and translation of its RNA targets, many of which are integral to microglial functions. We find ARID5A modulates cytokine secretion, lysosome activity, and iron accumulation, as well as ferroptosis sensitivity in microglia and co-cultured neurons. We illustrate the neuroprotective potential of ARID5A modulation, in which knockdown restored dysregulated functions in TREM2 mutant microglia. Our results highlight the potential of leveraging ARID5A-RNA interactions to restore dysregulated pathways in neurodegeneration.

overall_design: The following are sequencing data for RNA sequencing experiment performed on ipsc-derived microglia comparing crispri-mediated knockdown of ARID5A to a nontargeting control. Total RNA sequencing was used in splicing analysis and for input comparison controls to ribosome-protected RNA footprints in ribosome profiling.

first: Danielle

last: Schafer

first: Steven

last: Blue

first: Shuhao

last: Xu

first: Orel

last: Mizrahi

first: Maya

middle: L

last: Gosztyla

first: Katherine

last: Rothamel

first: Gene

middle: W

last: Yeo


title: Disruption of the Brain-Spleen Axis Impairs Monocyte-Microglia Communication and Accelerates Disease Progression in a Mouse Model of Amyloidosis

city: Jerusalem

first: Hodaya

last: Polonsky

address: Givat Ram

department: Edmond & Lily Safra Center for Brain Sciences

country: Israel

institute: The Hebrew University of Jerusalem

summary: Alzheimer’s disease (AD) is characterized by a prolonged asymptomatic phase before cognitive decline emerges, yet the mechanisms driving symptom onset remain unclear. Here, we hypothesized that the transition from asymptomatic to symptomatic disease is linked to dysfunction of brain–immune communication. Retrograde neuronal tracing in the 5xFAD mouse model of amyloidosis revealed reduced brain–spleen connectivity at advanced disease stages. To probe the functional role of the brain–spleen axis in coping with disease, we denervated the splenic nerve at an early presymptomatic stage. This intervention accelerated cognitive decline, impaired splenic hematopoiesis, diminished monocyte recruitment to the brain, disrupted monocyte–microglia signaling networks, and reduced the transition of microglia from a homeostatic to the disease-associated (DAM) state. Conversely, enhancing splenic noradrenergic input increased hematopoiesis, restored monocyte homing to the brain, and delayed cognitive impairment. The protective role of splenic monocytes was independently validated in a retinal cytotoxic injury model, in which splenic denervation impaired post-insult retinal ganglion cell survival. Together, these findings identify an active brain–spleen circuit in regulating monocyte recruitment and establish peripheral monocytes as key drivers of microglial state transitions and disease Alzheimer’s disease (AD) is characterized by a prolonged asymptomatic phase before cognitive decline emerges, yet the mechanisms driving symptom onset remain unclear. Here, we hypothesized that the transition from asymptomatic to symptomatic disease is linked to dysfunction of brain–immune communication. Retrograde neuronal tracing in the 5xFAD mouse model of amyloidosis revealed reduced brain–spleen connectivity at advanced disease stages. To probe the functional role of the brain–spleen axis in coping with disease, we denervated the splenic nerve at an early presymptomatic stage. This intervention accelerated cognitive decline, impaired splenic hematopoiesis, diminished monocyte recruitment to the brain, disrupted monocyte–microglia signaling networks, and reduced the transition of microglia from a homeostatic to the disease-associated (DAM) state. Conversely, enhancing splenic noradrenergic input increased hematopoiesis, restored monocyte homing to the brain, and delayed cognitive impairment. The protective role of splenic monocytes was independently validated in a retinal cytotoxic injury model, in which splenic denervation impaired post-insult retinal ganglion cell survival. Together, these findings identify an active brain–spleen circuit in regulating monocyte recruitment and establish peripheral monocytes as key drivers of microglial state transitions and disease progression.

overall_design: Following splenic denervation, myeloid cells from whole brains of 5xFAD mice were isolated [1:10] by Flourescence-activated cell sorting (FACS) and analysed using scRNA-seq

first: Tommaso

last: Croese

first: Miguel

last: Abellanas

first: Michal

last: Arad

first: Javier

last: Peralta Ramos

first: Yuliya

last: Androsova

first: Serena

last: Riccitelli

first: Sedi

last: Medina

first: Francesca

last: Palmas

first: Romano

last: Strobel

first: Giulia

last: Castellani

first: Denise

last: Kviatcovsky

first: Sarah

last: Phoebeluc-Colaiuta

first: Miriam

last: Adam

first: Sama

last: Murad

first: Hannah

last: Partney

first: Daniel

last: Kitsberg

first: Alexander

last: Dieter

first: Tomer-Meir

last: Salame

last: Brandis

first: Tevie

last: Mehlman

first: Oded

last: Singer

last: Rivlin-Etzion

first: Simon

last: Wiegert

first: Yosef

last: Shaul

first: Oren

last: Kobiler

first: Ofer

last: Yizhar

first: Naomi

last: Habib

last: Schwartz


title: TET2-mutant clonal hematopoiesis prevents T-cell exhaustion and suppresses cancer metastasis

city: Tsukuba

first: AI NHAN THI

last: LE

state: Ibaraki Prefecture

address: 2-1-1 Amakubo, University of Tsukuba Global Village, 305-8575

department: Department of Hematology

institute: Graduate School of Comprehensive Human Sciences, University of Tsukuba

type: Methylation profiling by high throughput sequencing

summary: TET2-mutant clonal hematopoiesis (CH) is associated with reduced cancer metastasis in human cohorts. Whole genome bisulfite sequencing (WGBS) of PD-1+CD8+ tumor-infiltrating lymphocytes (TILs) sorted from liver metastatic tumors of Vav1CreTet2KO and Tet2fl/fl mice was performed to characterize genome-wide DNA methylation changes associated with TET2 loss in exhausted CD8+ T cells.

overall_design: PD-1+CD8+ TILs were isolated from liver metastatic tumors of Vav1CreTet2KO (n=3: KO45, KO46, KO55) and Tet2fl/fl control (n=3: WT25, WT49, WT50) mice. Genomic DNA was extracted and WGBS libraries were prepared using the post-bisulfite adaptor tagging (PBAT) protocol. Libraries were sequenced on the Illumina NovaSeq X platform at Macrogen (RRID: SCR_024569) and aligned to the mouse reference genome (GRCm39) using the Bismark pipeline.

first: Ai-Nhan

middle: T

last: Le

first: Mamiko

last: Sakata-Yanagimoto

first: Robert

last: Vanner

first: Miura

last: Fumihito

first: Hiromitsu

last: Araki

first: Tran

last: Nguyen


title: BPTF is essential for vaccine-induced germinal center B cell responses

city: St. Louis

first: Julian

last: Zhou

address: 425 S. Euclid Ave.

institute: Washington University in St. Louis

summary: Germinal centers (GCs) are microanatomical structures in which antigen-specific B cells undergo proliferation, somatic hypermutation, and affinity-based competition to select high affinity clones that differentiate into memory B cells (MBCs) and plasma cells (PCs). B cell progression through the GC is tightly regulated and the molecular determinants that modulate GC B cell proliferation and survival are still under investigation. Here, we use a conditional deletion mouse model to demonstrate that bromodomain PHD finger transcription factor (BPTF), a subunit of the nucleosome remodeling factor (NURF) chromatin remodeling complex, is required for robust GC B cell responses following vaccination. In GC B cells, Bptf loss induces a stress-like transcriptional profile and a shift towards PC identity-defining transcriptional programing, although this does not lead to accumulation of functional PCs. Rather, we show that BPTF-deficient GC B cells are prone to cell death. Cumulatively, our data demonstrate that BPTF is necessary for GC B cell maintenance and robust antigen-specific B cell responses.

overall_design: RNA-seq profiling of dark zone (DZ) and light zone (LZ) germinal center (GC) B cells of wildtype B6.129P2(Cg)-Ighg1_tm1(cre)Cgn/J mice and floxed Bptf mice following vaccination against SARS-CoV-2 WA1 spike protein.

first: Alexandria

middle: J

last: Sturtz

first: Birk

last: Evavold

first: Zarifeh

last: Rarani

first: Wafaa

last: Alsoussi

middle: Q

first: Hanover

last: Matz

first: Hiromi

last: Muramatsu

first: Wren

last: Simkins

first: Sameer

last: Kumar Malladi

first: Katherine

last: McIntire

first: Jishnu

last: Das

first: Jackson

last: Turner

first: Norbert

last: Pardi

first: Ali

last: Ellebedy


title: Molecular mechanisms of promoter silencing by transcriptional readthrough

city: Montréal

first: Jacek

last: Majewski

state: QC

address: 740 Av. du Docteur-Penfield

department: Human Genetics

country: Canada

institute: McGill University

summary: Transcriptional interference is defined as the in cis suppression of one transcriptional process by another. While most mammalian genes are well insulated from such interference through proper transcriptional termination and chromatin boundary elements, disruption of these safeguards can lead to durable changes in gene activity and, in some cases, heritable epigenetic silencing. Here, we developed a tractable experimental system to investigate the mechanistic consequences of antisense transcriptional readthrough. Using mouse mesenchymal progenitor cells and CRISPR-Cas9, we modeled the epi-cblC phenotype through targeted deletion of the Prdx1 intron 5 splice acceptor site, resulting in transcriptional readthrough across the Mmachc locus. This led to aberrant deposition of H3K36me3, the establishment of DNA methylation, and stable, mitotically heritable silencing of Mmachc. Through systematic perturbations of transcription, and the H3K36 and DNA methylation machinery, we deconstruct the epigenetic and transcriptional mechanisms that contribute to readthrough-mediated silencing. We demonstrate that antisense transcription is the primary driver of repression, while H3K36me3 contributes an intrinsic silencing component that is further required for the establishment of DNA methylation, which in turn confers long term stability. Together, these findings define a hierarchical silencing cascade in which transcriptional readthrough is converted into stable epigenetic memory across cell divisions, and establish transcription as an instructive regulatory process that is capable of reshaping local chromatin environments and gene expression.

overall_design: Bulk RNA-seq of CRISPR-engineered C3H10T1/2 cell lines (Prdx1 splice-site mutants and epigenetic regulator knockouts) to evaluate mechanisms underlying Mmachc silencing.

first: Gerry

last: Shipman

first: Erika

last: Walback

first: Andy

last: García González

first: Cynthia

last: Horth

first: Michel

last: Gravel

first: Eric

last: Bareke


title: TET2-mutant clonal hematopoiesis prevents T-cell exhaustion and suppresses cancer metastasis [RNA-seq]

first: AI NHAN THI

last: LE

summary: TET2-mutant clonal hematopoiesis (CH) is associated with reduced cancer metastasis in human cohorts. Using mouse models of colorectal cancer liver metastasis, we demonstrate that Tet2-deficient hematopoietic cells suppress metastatic tumor burden by preventing CD8+ T-cell exhaustion. Bulk RNA-seq of sorted CD4+ and CD8+ tumor-infiltrating lymphocytes (TILs) from Vav1CreTet2KO, Cd4CreTet2KO, and Tet2fl/fl control mice was performed to characterize transcriptional changes associated with Tet2 loss in tumor-infiltrating T cells.

overall_design: CD4+ and CD8+ tumor-infiltrating lymphocytes (TILs) were sorted by flow cytometry from liver metastatic tumors of Vav1CreTet2KO, Cd4CreTet2KO, and Tet2fl/fl control mice at day 30 post-intrasplenic injection of Venus-AKTPM/LOH colorectal cancer cells. Total RNA was extracted and sequenced on the Illumina HiSeq X platform (paired-end, 150 bp) (Macrogen, RRID: SCR_016385)

first: Tran

last: Nguyen

first: Ai-Nhan

last: Le

first: Mamiko

last: Sakata-Yanagimoto

first: Robert

last: Vanner


title: Stepwise DNA unwinding gates TnpB genome-editing activity

city: Berkeley

first: Marena

middle: Isabelle

last: Trinidad

address: 2151 Berkeley Way

institute: Innovative Genomics Institute

summary: TnpB is a compact RNA-guided endonuclease and evolutionary ancestor of CRISPR-Cas12 that offers a promising platform for genome engineering. However, the genome-editing activity of TnpBs remains limited and its underlying determinants are poorly understood. Here, we used biochemical and single-molecule assays to examine the DNA-unwinding mechanism of Youngiibacter multivorans TnpB (Ymu1 TnpB). DNA unwinding proceeds through formation of a partially unwound intermediate state to a fully unwound open state. The open state forms inefficiently and collapses readily in the absence of negative supercoiling. An optimized variant, Ymu1-WFR, stabilizes formation of both the intermediate and open states, resulting in enhanced DNA cleavage in vitro and increased genome editing in vivo. These findings identify the physical basis for the observed minimal activities of natural TnpBs, revealing how stabilizing specific unwinding states enables efficient DNA targeting.

overall_design: Small RNA sequencing was performed on purified Ymu1 TnpB RNP complexes expressed in E. coli to characterize reRNA expression from a 200-nt scaffold construct. SHAPE-MaP chemical probing was performed on purified RNP complexes carrying either the 127-nt (wild-type length) or short reRNA scaffold to determine RNA secondary structure and reactivity profiles.

first: Honglue

last: Shi

first: Kamakshi

last: Vohra

first: Zehan

last: Zhou

first: Conner

last: Langeberg

middle: I


title: Single-cell RNA sequencing of iALI epithelial cell derived from UHOMi003-A cell line

city: Montpellier

first: Said

last: Assou

state: Languedoc-Roussillon

address: 80 av Augustin fliche, IRMB

institute: IRMB, Hôpital Saint Eloi

summary: The goal of this study was to identifed specifically iALI epithelial cell clusters by using single-cell RNA-sequencing (10x Genomics Chromium). We enriched the epithelial cells based on EpCam cell level, and then used 10X Genomics Chromium technology to capture 10 000 cells. The analyse was then performed using Seurat, to identified each cell cluster. The results reveal all bronchial epithelial cell population on iALI model. This include ciliated cells, basal cells, neuroendocrine cells and secretory cells.

overall_design: Global transcriptomic profiling at single cell resolution of iPSC-derived cells. Cell epithelial clusters were analysed on Seurat based on literature specific markers and then visualized by Uniform Manifold Approximation and Projection (UMAP).

first: Arnaud

last: Bourdin

first: John

last: De Vos


title: ASCL2 drives sorafenib resistance through FSAN-mediated MDR1 palmitoylation

city: Guang Zhou

first: Tingting

last: Guo

state: Guang Dong

address: University Town Campus (South Campus): 382 Zhonghuan Road East, Panyu District, Guangzhou Higher Education Mega Centre,

institute: South China University of Technology

summary: Addressing sorafenib resistance—a major barrier to effective treatment of hepatocellular carcinoma (HCC)—this study utilized patient-derived liver cancer stem cell (LCSC) models to elucidate the pivotal role of the transcription factor ASCL2 in maintaining stemness and driving drug resistance. Through integrated transcriptomic and epigenomic analyses, we discovered that ASCL2 orchestrates a resistance program by directly activating the transcription of fatty acid synthase (FASN) alongside palmitoyltransferases (ZDHHC5/9) and the multidrug resistance protein (MDR1), thereby transcriptionally "coupling" lipogenesis to protein modification. Mechanistically, ASCL2 promotes MDR1 palmitoylation and its subsequent membrane localization via FASN-driven palmitate production, ultimately leading to sorafenib resistance; conversely, pharmacological inhibition of palmitoylation disrupted MDR1 membrane localization and restored drug sensitivity in patient-derived LCSCs. These findings delineate a novel mechanism by which ASCL2 coordinates lipid metabolic reprogramming with post-translational modifications to drive therapeutic resistance, providing a potential interventional strategy to overcome sorafenib resistance by targeting LCSCs in HCC.

overall_design: RNA sequencing of LCSC-15 cells following ASCL2 knockdown

first: Yuyou

last: Duan


title: Temporal gating dictates stress-induced transcript export from the nucleus

city: Ann Arbor

first: Stephanie

last: Moon

state: MI

address: 3734 Med Sci II 1241 E. Catherine St

institute: University of Michigan

summary: RNA-sequencing was performed to analyze 1) nuclear and cytoplasmic transcripts in unstressed and arsenite stressed cells, and 2) gene expression changes over time during arsenite stress.

overall_design: Pair-end rRNA depleted RNA-seq of nuclear, cytoplasmic, and total RNA from U-2 OS cells were from unstressed or arsenite-stressed (250 µM) for 105 minutes followed by nuclear and cytoplasmic fractionation. PolyA+-enriched total RNA-seq from U-2 OS cells treated with arsenite for 15, 30, 45, 75, or 105 minutes with an unstressed control.

first: Noah

middle: S

last: Helton

first: Ben

last: Dodd


title: Gene expression-based, individualized carcinogenesis for patients with gastric cancer

city: Nanchong

first: Zhen

last: Jiang

state: Sichuan Province

address: No. 234 Fujiang Road

institute: North Sichuan Medical College

type:
Expression profiling by array
Non-coding RNA profiling by array

summary: Individualized gene expression signatures prediction classifiers were successfully constructed through expression profiling of a total of 19,077 genes in 6 gastric adenocarcinoma cases

overall_design: In the study presented here,a well-defined cohort of 6 gastric adenocarcinoma cases was used to acquire expression profiles of a total of 19,077 unique genes


title: METTL3 modulates cell viability and motility in HCC1143 and MDA-MB-231 triple-negative breast cancer cell lines

city: Izmir

first: Bünyamin

last: Akgül

state: Urla

address: Gulbahce Campus

department: Molecular Biology and Genetics

country: Turkey

institute: Izmir Institute of Technology

summary: The m6A methyltransferase METTL3 functions as a critical oncogenic driver in triple negative breast cancer (TNBC). However, its specific downstream targets and mechanistic functions in less metastatic TNBC subtypes remain poorly characterized. To address this, we evaluated METTL3 expression and the phenotypic effects of its siRNA-mediated knockdown in healthy mammary epithelial (MCF10A), low-metastatic TNBC (HCC1143) and high-metastatic TNBC (MDA-MB-231) cell lines. We assessed global m6A levels, cell proliferation, cell cycle progression and migration. To uncover specific downstream pathways, transcriptomic profiling was performed on HCC1143 cells, followed by RT-qPCR validation and m6A site prediction. METTL3 depletion reduced global m6A levels and cell viability across all cell lines. Notably, in low-metastatic HCC1143 cells, METTL3 knockdown induced a pronounced G2/M cell cycle arrest and dramatically impaired migration capacity.  Transcriptomic analysis of HCC1143 revealed altered expression of genes associated with these observed phenotypic changes. Specifically, critical transcripts harboring predicted m6A motifs, including LIMK1, CCNB2 and CDH1, were significantly dysregulated, pointing to potential alterations in pathways governing cytoskeletal remodeling, actin organization, and cell-cell adhesion. Taken together, we propose that METTL3 promotes cellular proliferation and motility in low-metastatic TNBC by regulating key transcripts involved in cell cycle progression and actin dynamics.

overall_design: 4 × 10⁵ HCC1143 cells were seeded into 10 cm dishes and incubated overnight. The cells were transfected with 25 nM of METTL3 siRNA pool (si-METTL3) or a non-target negative control siRNA (si-NC) using Dharmafect. The transfected cells were then incubated for 72 hours in a humidified atmosphere of 5% CO₂ at 37°C prior to harvesting for subsequent experiments.

first: Buket

last: Saglam-Sen

first: Dilek Cansu

last: Gurer-Er

first: Bunyamin

last: Akgul


title: Differentiating naturally occurring and disease associated autoantibodies in MPO-ANCA vasculitis through immunogenomic and epitope comparisons

city: Chapel Hill

first: Office of Genomics Research

last: UNC Lineberger Comprehensive Cancer Center

state: NC

address: 125 Mason Farm Road, CB #7599 5105-5106 Marsico Hall

institute: University of North Carolina at Chapel Hill

summary: It has been established that there are naturally occurring autoantibodies including ANCAs that are found in healthy individuals. While ANCAs are pathogenic in patients with vasculitis, they can be present without active clinical disease. This raises the question of what is distinct about the autoantibodies which cause disease. We used highly sensitive methods to isolate autoantibody producing cells from healthy individuals and patients with MPO-ANCA to sequence the BCRs (autoantibodies). We also used serum samples to analyze the reactive epitopes from both groups. We found that the isolated autoantigen specific B cells from our patients (but not healthy individuals) produced high levels of detectable MPO-ANCAs. The BCRs from patient cells showed clonal expansion and significant overlap in the complementarity determining region 3 (CDR3). We also identified distinct epitopes bound by patient autoantibodies only. Our study highlights the differences in naturally occurring autoantibodies (from healthy individuals) compared to autoantibodies identified in patients with MPO-ANCA.

overall_design: Cryopreserved peripheral blood mononuclear cells (PBMCs) from patients and healthy individuals collected with consent were thawed and labeled with antigen specific tetramers to isolate antigen specifi B cells, the remaining cells were also collected. Additional subpopulation of B cells was isolated from the same individuals. Cells were cultured and collected for total BCR sequencing.

first: Dhruti

middle: P

last: Chen

first: Mark

middle: G

last: Woodcock

first: Benjamin

last: Vincent

first: Donna

middle: O

last: Bunch


title: IL-9 and Blimp-1 protect the transcriptional identity of group 2 innate lymphocytes in allergic asthma

city: Pittsburgh

first: Amanda

middle: Catherine

last: Poholek

state: Pennsylvania

address: 4401 Penn Ave., Rangos Research Center 8129

department: Pediatrics

institute: University of Pittsburgh

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

overall_design: Refer to individual Series


title: Single-molecule DNA replication dynamics under WEE1 inhibition in wild-type and TRESLIN-stabilized HCT116 cells

city: Oklahoma

first: Christopher

middle: Lee

last: Sansam

state: OK

address: 825 NE 13th Street

department: Cell Cycle and Cancer Biology Program

institute: Oklahoma Medical Research Foundation

summary: We profiled single-molecule DNA replication dynamics in human HCT116 cells to determine how WEE1 inhibition and stabilization of the origin-firing factor TRESLIN (TICRR) influence replication initiation, termination, and fork progression. We analyzed two engineered HCT116 lines expressing mClover-tagged TRESLIN from the endogenous locus: a wild-type TRESLIN allele and a stabilized ΔSBI TRESLIN mutant. Cells were treated with the WEE1 inhibitor MK-1775 (1 µM) or vehicle and sequentially pulse-labeled with EdU and BrdU, followed by a thymidine chase, to generate replication tracts for long-read nanopore sequencing. High–molecular weight genomic DNA was prepared and sequenced on an Oxford Nanopore PromethION platform, and reads were aligned to the human reference genome (hg38/GRCh38). Replication features (leftward/rightward forks, initiation events, and termination events) and tract lengths were inferred from EdU/BrdU segmentation using DNAscent forkSense, enabling quantification of fork directionality and fork rates across conditions.  Associated preprint: bioRxiv [Preprint]. 2025 Jun 11;2025.06.10.657920. doi:10.1101/2025.06.10.657920.

overall_design: Four conditions were profiled (each with 3 biological replicates): WT TRESLIN HCT116 ± MK-1775 and ΔSBI TRESLIN HCT116 ± MK-1775. Cells were sequentially labeled (EdU 10 min → BrdU 10 min) and chased with thymidine before high–molecular weight DNA extraction and Oxford Nanopore WGS. Reads were aligned to hg38/GRCh38 and replication tracts were segmented with DNAscent forkSense to call forks, initiation, and termination events and to measure tract lengths.

first: Md

last: Hossain


title: CD8⁺ T-cell exhaustion-like and mitochondrial dysfunction define immune dysregulation in feline chronic gingivostomatitis

city: Davis

first: Amir

last: Kol

address: One Shields Ave, Davis, CA 95616, USA

institute: UC Davis

summary: Feline chronic gingivostomatitis (FCGS) is a debilitating oral disease characterized by immune dysregulation and chronic inflammation. We hypothesized that CD8+ T cells from FCGS cats exhibit exhaustion features with suppressed mitochondrial pathways, and that mesenchymal stromal cell (MSC) therapy post-extractions might restore these programs. RNA sequencing was performed on peripheral CD8+ T cells from cats with active FCGS before (disease group, D) and after (treated group, M) clinical remission following full-mouth extractions and MSC therapy, with specific-pathogen-free cats as controls (control group, C). CD8+ T cells from active disease displayed terminal effector differentiation and exhaustion-like signatures, including upregulation of cytotoxic markers (GZMB, GZMK, GZMA), differentiation markers (KLRG1, IL18R1/IL18RAP), and exhaustion-associated genes (EOMES, CD244, TNFSF10, CCR5, PRDM1, RGS16). Gene set enrichment analysis confirmed exhaustion-like CD8+ T-cell phenotype enrichment in active disease, which resolved after treatment. Pathway analysis revealed marked downregulation of mitochondrial respiratory chain components, ATP synthesis, and protein import pathways in active FCGS, with partial post-treatment resolution. Immunofluorescence of draining lymph nodes showed significantly increased CTLA-4+CD3+ T cells in both FCGS groups versus controls, suggesting persistent immunoregulatory signaling despite clinical improvement. These findings identify overlapping T-cell exhaustion and mitochondrial dysfunction-associated transcriptomic signatures in FCGS, supporting therapeutic strategies targeting immune-metabolic pathways.

overall_design: CD8+ T cells were selected from feline peripheral blood. Blood was collected from healthy control cats (n=10), cas with active chronic gingivostomatitis (FCGS, n=8) and cats with FCGS in remission post treatemnt (n=4).

first: Kol

last: Amir