title: DNA Methylation Regulating Activation of the Hypothalamic-Piuitary-Gonadal Axis in Patients with Delayed Puberty

status: Public on Jul 31 2026

city: London

first: Sasha

last: Howard

address: JVSC Charterhouse Square

department: Endocrinology

country: United Kingdom

institute: Queen Mary University London

type: Methylation profiling by genome tiling array

summary: Delayed puberty in humans is frequently an inherited condition with a clear genetic basis, previously linked to coding region sequence variation in gonadotropin-releasing hormone (GnRH) pathways genes. However, many patients do not have an identifiable genetic variant responsible for their delayed puberty and the role of epigenetic modifiers of human pubertal timing has been minimally explored.  Robust evidence has been provided that the timing of puberty in animal models is regulated by an epigenetic mechanism of transcriptional repression. In view of the unique dynamic activity of the hypothalamic-pituitary-gonadal axis, changes in DNA methylation are highly likely to play a regulatory role in pubertal onset and timing. Genome wide DNA methylation was detected using the Illumina EPIC array, for patients (n=92) with delayed puberty who had no previously identified genetic cause for the condition, and related unaffected controls (n=20).This revealed differentially methylated CpG sites linked to key genes involved in upstream regulation of GnRH signaling, including TAC3, SIRT1, PDYN, KMT2A, NELL2 and KAT2B, all of which had increased DNA methylation, along with NOS1 and ZNF573 which had decreased methylation in individuals with delayed puberty compared to controls. These differentially methylated CpG sites were found in either enhancer or promoter regions of their corresponding genes. The top five differentially methylated enhancer or promoter associated CpG sites, defined by q value, identifed novel candidates genes involved in delayed puberty, including CADPS2. Over representation analysis identified multiple KEGG pathways previously associated with growth dysfunction as significantly altered. These included the cAMP pathway, the neuroactive ligand-receptor interaction pathway and growth hormone synthesis pathway. Differential methylation of genes related to BMI was observed in delayed compared to normal pubertal timing, but it was not specific to patients with low or high BMI. Subsequently, pathogenic exonic variants in the genes associated with the top 10 CpG enhancer and promoter sites were identified in patients from additional cohorts with delayed puberty. These findings support that changes in DNA methylation of key genes involved in GnRH regulation contribute to the phenotype of human delayed puberty.

first: Charlotte

middle: L

last: Hall

first: Jordan

middle: E

last: Read

first: Harit

middle: K

last: Kohli

first: Dimitria

last: Brempou

first: Rebecca

middle: J

last: Oakey

middle: R


title: RalA-driven CCN3 secretion amplifies inflammatory catabolism to promote temporomandibular joint osteoarthritis

city: 山西

first: Jie

last: Yuan

address: The Second Hospital of Shanxi Medical University

country: China

type: Expression profiling by high throughput sequencing

summary: This project investigates the role of RalA in temporomandibular joint osteoarthritis using a mouse MIA-induced TMJOA model and primary mouse temporomandibular joint condylar chondrocytes. Transcriptomic profiling of siNC- and siRalA-transfected chondrocytes was performed to identify RalA-regulated inflammatory and extracellular matrix remodeling pathways. The study identifies CCN3 as a RalA-regulated secreted mediator that amplifies inflammatory cytokine production and cartilage catabolism.


title: Effect of a novel genistein isoflavonoid alkaloids (GIA) on gene expression in HCT116 colorectal cancer cells under hypoxic conditions

city: Wenzhou

first: Ya

last: Zhang

state: Zhejiang

address: Fanhai road 101

institute: the first affiliated hospital of Wenzhou medical university

summary: To investigate the molecular mechanism of a novel genistein isoflavonoid alkaloids (GIA) in suppressing colorectal cancer, we performed gene expression profiling analysis using RNA-seq of HCT116 cells treated with GIA or DMSO control under hypoxic conditions. We identified differentially expressed genes and pathways associated with ferroptosis, HIF-1 signaling, and glutathione metabolism.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for HCT116 cells treated with GIA (10 µM) versus vehicle control (DMSO) under hypoxic conditions for 24 hours.

first: Yangwen

last: Ai

first: Changxiong

last: Wang


title: Single-cell RNA sequencing of knee joint synovium from mice with collagen- and antibody-induced arthritis (C&AIA)

city: Huzhou

first: Yunliang

last: Yao

address: 759 East Second Ring Road

department: Medical School

institute: Huzhou Normal University

summary: Rheumatoid arthritis (RA) is a chronic autoimmune disease characterized by synovial inflammation, immune cell infiltration, and progressive joint destruction. Commonly used mouse models each carry practical constraints: collagen-induced arthritis (CIA) is largely restricted to the DBA/1 strain, whereas collagen antibody-induced arthritis (CAIA) is limited by antibody cost. To combine strain flexibility with a robust and reproducible effector phase, we established collagen- and antibody-induced arthritis (C&AIA) on the C57BL/6 background. To characterize the synovial cellular landscape of this model, we performed droplet-based single-cell RNA sequencing on synovial tissue dissected from inflamed knee joints of arthritic C&AIA mice. This dataset resolves the immune and stromal compartments of the C&AIA synovium and enables cross-species comparison with human RA synovial single-cell data.

overall_design: Single-cell RNA sequencing was performed on knee joint synovium from mice with collagen- and antibody-induced arthritis (C&AIA) on the C57BL/6 background. Synovium was dissected from inflamed knee joints of six arthritic mice at the effector phase of disease. Tissue from the six mice was pooled two animals per sample, yielding three biological replicate samples (B1, B2, B3). Single-cell suspensions were prepared by enzymatic dissociation and profiled by droplet-based single-cell RNA sequencing.

first: Jiexun

last: Cai

first: Jiapeng

last: Gao


title: Chromatin accessibility profiling of wild-type and Slc31a1 conditional knockout mouse bone marrow stromal cells by ATAC-seq

city: Changchun

first: Yuhang

last: Jiang

state: Jilin

address: No.461 Xinjiang Road

department: Institute of Translational Medicine

institute: The First Hospital of Jilin University

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Age-associated bone loss is largely driven by impaired osteoblast generation from bone marrow stromal cells (BMSCs), but the metabolic and epigenetic mechanisms that constrain osteogenic commitment remain incompletely understood. This study identifies SLC31A1-mediated copper uptake as a cell-intrinsic metabolic checkpoint required for BMSC osteogenic differentiation and skeletal integrity. ATAC-seq was performed to profile genome-wide chromatin accessibility in wild-type and Slc31a1 conditional knockout mouse BMSCs. The analysis revealed altered chromatin accessibility in Slc31a1-deficient BMSCs, including increased accessibility at the Id1 locus, supporting a model in which copper-dependent mitochondrial metabolism epigenetically restrain Id1 expression to permit osteogenic commitment.

overall_design: ATAC-seq was performed on primary mouse bone marrow stromal cells (BMSCs) isolated from wild-type control mice and mesenchymal lineage-specific Slc31a1 conditional knockout mice. The experimental comparison was designed to determine how loss of SLC31A1-mediated copper uptake alters chromatin accessibility in BMSCs. Approximately 50,000 viable cells were used per sample for ATAC-seq library preparation. Genome-wide accessibility profiles were compared between WT and Slc31a1 cKO BMSCs, and differential accessibility analysis was performed to identify chromatin regions affected by Slc31a1 deletion. Genome browser tracks were generated to visualize accessibility changes, including at the Id1 locus.


title: Single-cell RNA-seq reveals that SLC31A1-dependent copper uptake regulates osteogenic commitment of mouse bone marrow stromal cells

summary: Age-associated bone loss is largely driven by impaired osteoblast generation from bone marrow stromal cells (BMSCs), but the metabolic constraints that limit osteogenic commitment remain incompletely defined. In this study, we identify SLC31A1-mediated copper uptake as a cell-intrinsic metabolic checkpoint for BMSC osteogenic differentiation and skeletal integrity. This single-cell RNA-seq dataset profiles adherent bone marrow stromal cells isolated from wild-type Slc31a1flox/flox mice and mesenchymal lineage-specific Slc31a1 conditional knockout mice (Prrx1-Cre+/-; Slc31a1flox/flox). Single-cell transcriptomic analysis resolved Prrx1-positive osteogenic-lineage populations, including BMSC subsets and pre-osteoblasts, and revealed that Slc31a1-deficient BMSCs accumulate in an ID1-high progenitor state and fail to efficiently transition toward osteogenic commitment. Together with functional, metabolic, and epigenomic analyses, these data support a copper-mitochondria-NAD-SIRT1-ID1 axis that links trace metal uptake to stem/progenitor cell fate decisions and identifies intracellular copper availability as a reversible metabolic vulnerability in skeletal aging.

overall_design: Adherent bone marrow stromal cells were isolated from wild-type Slc31a1flox/flox littermate controls and mesenchymal lineage-specific Slc31a1 conditional knockout mice (Prrx1-Cre+/-; Slc31a1flox/flox). Single-cell RNA-seq libraries were generated using the 10x Genomics Chromium Single Cell 3' Reagent Kits v3 workflow and sequenced as paired-end reads on an Illumina NovaSeq 6000 platform. The design compares WT and Slc31a1-cKO BMSCs to determine how loss of SLC31A1-mediated copper uptake alters stromal/osteogenic lineage composition, cell-state transitions, and transcriptional programs. Prrx1-positive mesenchymal lineage cells were subset and re-clustered to evaluate progression from BMSC states toward pre-osteoblast commitment.


title: RNA-seq analysis of molecular pathway changes across distinct microenvironments

city: Jinan

first: Lin

last: Han

address: Wenhuaxi Road #107

institute: Shandong University

summary: In this study, three distinct microenvironmental conditions were established to investigate transcriptomic changes associated with different microenvironments. Samples were treated with or without the indicated drug treatment, with four biological replicates included in each group. Bulk RNA sequencing was performed to evaluate changes in gene expression and molecular pathways across the different experimental conditions.

overall_design: Bulk RNA sequencing was performed to compare transcriptomic profiles across three distinct microenvironmental conditions with or without drug treatment. Each experimental group included four biological replicates. The study was designed to evaluate gene expression changes associated with different microenvironmental conditions and treatment status.

first: Miao

last: Huang


title: Bulk RNA sequencing of prostate cancer (PCa) primary tumors and metastases: Epworth Clinical Cohort

city: Melbourne

first: xin

last: liu

address: 305 Graattan St

country: Australia

institute: Peter mac

summary: Prostate cancer (PCa) frequently metastasizes to bone, marking incurable disease. This progression is driven by an immunologically cold bone tumor microenvironment that fosters resistance to therapy. To define the mechanisms underlying this uniquely immunosuppressive niche, we applied spatial single cell analyses across primary tumors and metastatic sites. Bone metastases showed marked suppression of tumor-intrinsic type I interferon (IFN-I) signaling and loss of antigen presentation, features that strongly predicted reduced bone metastasis-free survival. Tumor-intrinsic IFN-I expression correlated with memory T cell infiltration, whereas the bone myeloid compartment was enriched for protumor macrophages and showed reduced dendritic cell (DC) activation and antigen presentation. Digital spatial profiling of matched tumors revealed a broad loss of IFN-I-regulated immunostimulatory and checkpoint molecules. Notably, B7-H3, a putative negative regulator of IFN-I, was highly expressed in bone metastases and inversely associated with antigen presentation. These findings define bone-specific mechanisms of immune resistance and highlight therapeutic vulnerabilities that could inform precision strategies for PCa.

overall_design: Using PCa tissue from non-metastatic primary tumors (NBmRC; n = 15), bone-metastatic primary tumors (BmRC; n = 18), lymph node metastases (LN; n = 4) and bone metastases (Bone met; n = 11), we compared gene expression differences relating to myeloid-lineage populations and dendritic cell subsets across these four groups of interest. Defined gene set testing was performed as appears in Owen et al., 2026, "Spatial Profiling Reveals Immune Escape Pathways and Therapeutic Vulnerabilities in Prostate Cancer Bone Metastases".

first: Katie

last: Owen

first: Belinda

middle: S

last: Parker

first: Linden

last: Gearing

first: Niall

middle: M

last: Corcoran

first: Christopher

last: Hovens

first: Paul

last: Hertzog


title: In vivo CRISPR screens identify dual functions of DNMT3A in mediating tumor immune evasion

city: Wuhan

first: jianhong

last: zhao

state: Hubei

address: Donghu Road, No. 115

institute: Wuhan University

summary: Cancer immunotherapy has achieved remarkable clinical efficacy across multiple cancers, but it remains ineffective for most patients and the resistance mechanisms remain elusive. Epigenetic regulators play pivotal roles in both tumorigenesis and the modulation of antitumor immunity. Here, we performed in vivo CRISPR-Cas9 screens targeting epigenetic regulators and identified DNMT3A as a key driver of tumor immune evasion, exerting its effects through both methyltransferase activity-dependent and -independent mechanisms. Mechanistically, DNMT3A repressed the expression of TNFRSF1A and TNFRSF1B in a methyltransferase activity-dependent manner, enabling tumor cells to evade TNFα-induced killing. Importantly, DNMT3A exerted an additional noncanonical function by interacting with NFYA to activate cholesterol biosynthesis-related genes. This led to the accumulation of zymosterol in the tumor interstitial fluid, which directly impaired SREBP2 cleavage and enhanced HMGCR degradation in CD8⁺ T cells. Consequently, zymosterol-mediated suppression of cholesterol biosynthesis in CD8⁺ T cells compromised their activation and antitumor effector functions. Targeting DNMT3A’s multifaceted functions with antisense oligonucleotides (ASOs) effectively overcame resistance to immune checkpoint blockade (ICB) therapy. Collectively, our findings uncover a dual role of DNMT3A in tumor immune evasion and establish it as an integrated epigenetic and metabolic checkpoint, thus providing a potential target for immunotherapy.

overall_design: Total RNA was isolated from three sample sets for RNA sequencing (RNA-seq): tumor tissues harvested from C57BL/6 mice bearing sgNTC or sgDnmt3a MC38 tumors, MC38 cells treated with or without 2 μM 5-Aza for 24 h, and CD8⁺ T cells treated with or without 20 μM zymosterol.

first: Jianhong

last: Zhao

first: Yanrong

last: Deng

first: Haonan

last: Chen

first: Xiaojun

last: Zhou

first: Siyuan

last: Yin

first: Qun

last: Qian

first: Xiaoyu

last: Xie

first: Quanjiao

first: Jinfang

first: Lifang

last: Fan

first: Xianghai

last: Ren

first: Baoxiang

first: Congqing


title: Pseudopodia couple microenvironmental sensing to adaptive transcriptional reprogramming

city: La Jolla

first: Richard

middle: L.

last: Klemke

state: CA

address: 3120 Biomedical Sciences Wy

department: Pathology

country: USA

institute: University of California, San Diego

summary: Pseudopodia are actin-rich membrane extensions that allow cells to sense and respond to environmental cues, including hypoxia, inflammation, and chemotactic signals. Although these sensory structures are thought to transmit information from the cell periphery to the nucleus to regulate cell-state changes, including those involved in cancer progression, the underlying mechanisms remain poorly understood. To address this gap, we used a unique combination of intracellular spatial multiomics approaches to identify transcription factors and chromatin remodeling genes enriched within protrusions. Our findings reveal that these transcriptional regulators are selectively positioned for local translation in pseudopodia and subsequent transport to the nucleus, where they can drive rapid genetic reprogramming. These findings reveal a previously underappreciated function of pseudopodia as spatially organized genetic regulatory structures that enable cells, including cancer cells, to rapidly adapt to diverse microenvironmental stressors.

overall_design: Bulk RNA-seq profling of n=3 replicates of pseudopodia (PD) , cell body (CB) fractionations, and whole cell sample from hTERT-MSC (ATCC #SCRC-4000) after 1-hour 50 ng/mL PDGF-BB treatment

first: Kourosh

last: Kouhmareh

first: Thi

middle: H

last: Le


title: Spatial transcriptomic profiling of human gastric cancer FFPE specimens

city: Fuzhou

first: Guangtan

last: Lin

state: Fujian

address: No. 29 Xinquan Road

department: Department of Gastric Surgery

institute: Fujian Medical University Union Hospital

summary: Spatial transcriptomics mapped in-situ immune cell distribution and gene expression of FFPE gastric cancer, spatially confirming RASAL2 enrichment in immune-desert tumor regions and linking intratumoral heterogeneity to immune exclusion.

overall_design: FFPE gastric cancer tissues were processed with 10x Visium platform. Libraries were sequenced on NovaSeq 6000. Raw data was aligned to GRCh38 using Space Ranger v2.0.0. Seurat v5.3.0 was used for filtering, normalization, clustering and RCTD cell deconvolution to map spatial gene expression and immune distribution.

first: Longlong

last: Cao


title: miRNA sequencing profiling of paired colorectal cancer and adjacent non-tumor tissues

city: 广西

first: 晓倩

last: 赵

address: 南宁

institute: 广西中医药大学

type: Non-coding RNA profiling by high throughput sequencing

summary: This study performed microRNA sequencing on 16 human tissue samples from 8 paired primary colorectal adenocarcinoma and matched adjacent non-tumor tissues. The aim was to identify differentially expressed microRNAs associated with colorectal cancer and to provide sequencing evidence for downstream molecular validation. The analysis focused on miRNA-183-3p, which was found to be upregulated in colorectal cancer tissues and was further investigated for its relationship with ESR1 repression.

overall_design: MicroRNA sequencing was performed on 8 paired human primary colorectal adenocarcinoma tissues and matched adjacent non-tumor tissues, corresponding to 16 tissue samples. Each patient contributed one tumor tissue sample and one matched adjacent non-tumor tissue sample. Differential miRNA expression analysis was performed between colorectal cancer tissues and adjacent non-tumor tissues. Independent validation samples used for qRT-PCR and western blotting were not included in this GEO sequencing submission.

first: Xiaoqian

first: Dongping

last: Lai

first: Xin

last: Yao

first: Xuedong

last: Han

first: Weixuan

last: Lan

first: Yunsi

last: Huang

first: Yunlong

last: Sun

first: Hao

last: Li

first: Song

last: Wang

first: Tao

last: Zhang


title: Targeted ATAC-see (tATAC-see): A Visual Assay for Target-Specific Chromatin Profiling

city: Redwood City

first: Yihao

last: Yang

address: 2600 Bridge Parkway

institute: Altos Labs

summary: We present Targeted ATAC-see (tATAC-see), a visual genomics assay for site-specific chromatin profiling. By integrating the in situ visualization of ATAC-see with antibody-tethered tagmentation, tATAC-see captures chromatin states at defined protein-occupied domains with the simplicity of standard immunofluorescence. Modulating the spatial interaction radius of Tn5 via salt titration enables extended tagmentation of target-proximal chromatin local environments. We validated this imaging-based method by capturing the expanded chromatin neighborhoods of active euchromatin (H3K27ac, H3K4me3) alongside the dense structural Lamina-Associated Domains (LADs) of Lamin A/C and Lamin B1. Utilizing an HDAC inhibitor, we test the assay’s sensitivity to detect dynamic structural remodeling. We not only tracked chromatin decompaction, but also demonstrated the robust structural resistance of LADs. As a proof of principle biological application, we applied tATAC-see to models of replicative, chronological, and pathological (Hutchinson-Gilford Progeria Syndrome) aging to assess its ability to detect well-characterized peripheral heterochromatin and LAD remodeling. We observed divergent chromatin trajectories at the nuclear envelope reflective of the Lamin’s distinct roles. Lamin B1 domains exhibited increased local accessibility consistent with age-associated heterochromatin erosion, while Lamin A/C-associated domains physically detach from their scaffold. Ultimately, tATAC-see provides a robust, accessible platform for mechanistic and population-level studies to uncover spatial epigenome dynamics natively in single cells.

overall_design: BJ neonatal (ATCC, CRL-2522) and adult human dermal fibroblasts (GM05294, Coriell Institute) subjet to Targeted ATAC-see at 0 mM and 300 mM for H3K27ac, H3K4me3, Lamin A/C, Lamin B1 and IgG controls. One replicate each.

first: Natalie

last: Kirkland

first: Manuel

middle: A

last: Castro

first: Pura

last: Munoz-Canoves

first: Zachary

last: Levine


title: scRNA-sequencing of gastric tissues derived from eight inflamed-type and eight desert-type tumors

first: Guangtan

last: Lin

summary: This study reports single-cell RNA sequencing (scRNA-seq) data from 16 human gastric cancer tumor samples. The cohort includes 8 immune-inflamed-type and 8 immune-desert-type tumors, aiming to characterize the cellular and transcriptomic landscapes associated with distinct immune phenotypes in gastric cancer. The dataset provides high-resolution profiles of tumor and immune cell states, enabling the investigation of epithelial-intrinsic regulators and cell-type-specific programs regulating immune desertification.

overall_design: Human GC tissues were washed with PBS, cleared of blood and adjacent non-tumor tissue, minced, and enzymatically dissociated into single-cell suspensions,analyzed using scRNA-seq.

first: Longlong


title: Cohesin loading at regulatory elements shapes 3D genome folding during erythropoiesis [RNA-Seq]

city: Cambridge

first: Varshini

last: Ramanathan

state: Massachusetts

address: Building 56 Room 787B, 32 Vassar Street

department: Biological Engineering

institute: Massachusetts Institute of Technology

summary: During erythropoiesis, differentiating cells silence much of the genome while maintaining high expression of select genes. It remains unclear whether this transcriptional specialization is linked to specific changes in 3D genome organization. We generated deep Micro-C maps across human erythropoiesis to understand the relationship between cis-regulatory elements and cohesin-mediated loop extrusion during erythroid differentiation. Shifts in erythroid 3D genome structure during differentiation and under perturbations of transcription factors and cohesin subunits/cofactors indicates that a subset of CREs concentrate loop extrusion near key genes during erythroid differentiation.

overall_design: RNA-Seq was performed on CD34+ hematopoeitic stem and progenitor cells derived from the peripheral blood of healthy donors that were differentiated to day 13 (Phase 3).


title: Trypanosoma congolense Variant Surface Glycoprotein gene expression occurs in the absence of monoallelic transcription control

city: Antwerp

first: Pieter

last: Monsieurs

address: Nationalestraat 155

country: Belgium

institute: Institute of Tropical Medicine

summary: Antigenic variation is a very widespread process for pathogen evasion of mammalian adaptive immunity, involving the continuous change of exposed antigens. In many single-celled pathogens, antigen expression during antigenic variation is monoallelic: just a single gene from a large family is expressed in one cell at a time. In African trypanosomes, antigenic variation relies on expression of Variant Surface Glycoprotein (VSG), and in Trypanosoma brucei there is detailed understanding of the machinery that dictates that only one of approximately 15 VSG expression sites is actively transcribed at a time. In the closely related African trypanosome, T. congolense, which remains a significant blight on agriculture productivity in sub-Sharan Africa, we have no such understanding of VSG gene expression control or dynamics. Here, we have investigated the mechanics of antigenic variation in T. congolense, first examining the patterns of VSG expression at the transcript and protein level in small parasite populations in vitro. Surprisingly, this analysis revealed much greater VSG diversity than seen in T. brucei, with such expression diversity unaltered in mutants that impair homologous recombination. Using single cell transcriptomics, we explain this diversity, since we find no evidence for monoallelic transcription of T. congolense VSGs, but show instead that each parasite can dynamically express up to ~40 different VSGs in a single cell both in vitro and in vivo. VSG co-expression occurs from VSG genes distributed across the genome, indicating the lack of a dedicated locus for VSG transcription. Thus, comparing two trypanosome species that rely on the same class of surface antigen for immune evasion has revealed highly distinct mechanisms for controlling antigen gene expression, challenging the assumed common operation of antigenic variation across African trypanosome species.

overall_design: Mice were independently infected with T. congolense strain MSOROM7, and parasites were isolated from peripheral blood during the early phase of parasitemia. Two independent biological replicates were analyzed.

first: Lieve

last: Vermeiren

first: Jan

last: Van Den Abbeele


title: Visualizing the Epigenetic Landscape of Aging and Cellular Reprogramming: Optimized ATAC-see for cells and tissues

summary: Spatial chromatin organization dictates cellular function and resilience, yet scalable imaging methods to quantify chromatin states in situ across aging and interventions are lacking. While ATAC-see can visualize accessible chromatin, its broader application is hindered by protocol variability, low throughput, and incompatibility with complex tissues. Here, we systematically optimize the ATAC-see workflow for robust, high-throughput quantitative imaging in fixed, adherent mammalian cells and fresh-frozen tissues. We validate the platform's sensitivity to pharmacologic remodeling and apply it to replicative, chronological, and pathological aging in primary human fibroblasts, revealing progressive age-associated chromatin opening and heterochromatin remodeling. Furthermore, we demonstrate that our optimized ATAC-see captures rapid, reversible chromatin reorganization during OSK(M)-driven partial reprogramming of aged fibroblasts. Finally, we extend a cost-effective and accessible protocol to murine tissue sections, quantifying in situ age-dependent remodeling. This standardized framework establishes chromatin accessibility as a highly scalable, sequencing-compatible imaging biomarker for evaluating aging and rejuvenation.

overall_design: 6 replicates of BJ neonatal fibroblasts subject to light fixation, ATAC-see and reverse crosslinking prior to NGS

first: Bhargav

middle: D

last: Sanketi

first: Mohammad

last: Jaber

first: Veronica

last: Lamas-Alverez

first: Freiya

last: Malhotra

first: Juan Carlos

last: Izpisua Belmonte


title: Spatiotemporal Clonal Architecture of the Newborn Mouse Forebrain

city: San Francisco

first: Guohua

last: Yuan

address: 1651 4th St Fl 5 521A, Weill Neurosciences Building

institute: UCSF

summary: The mammalian forebrain contains diverse neural and glial cell types distributed across anatomically and functionally distinct regions, but their temporal and regional lineage relationships remain incompletely understood. Here, we generated a large-scale clonal atlas of mouse forebrain development by combining high-complexity lentiviral barcoding with single-cell RNA sequencing. The dataset captures major neurona and glial populations and enables analysis of lineage relationships across developmental stages, sub cell types, and forebrain regions.

overall_design: Molecularly barcoded lentiviral pools were injected into the lateral ventricles of mice at embryonic days E11–E17 or postnatal day P0, and brains were collected at P4. The rostral and caudal cortex, striatum, thalamus, hippocampus, and olfactory bulb were dissected separately, and reporter-positive cells were isolated by fluorescence-activated cell sorting. For each sample, separate transcriptome and lineage-barcode libraries were generated using the 10x Genomics platform and sequenced.

first: Marilyn

last: Steyert

first: Matthew

middle: G

last: Keefe

first: Tomasz

last: Nowakowski


title: Sustained activation of the integrated stress response is a mediator of Long Covid.

city: New York

first: Edmund

middle: C

last: Jenkins

state: NY

address: 1468 Madison Avenue

department: Heme/Onc

institute: Icahn School of Medicine at Mt. Sinai

summary: Why some individuals recover from COVID-19, while others do not, remains unknown. Mitochondrial dysfunction has been identified as a hallmark of Long COVID, however, multiple mitochondria haplotypes exist in the human population. Here, we used two mouse models that share the same nuclear genome but differ in mitochondrial genomes and compare their recovery rate after SARS-CoV-2 infection. While in one model, mice recovered, in the other model, male mice did not recover. RNAseq analysis, over a post-infection time course, revealed activation of the integrated stress response (ISR), which is known to be activated during acute viral infection through the PKR kinase. Therefore, and as expected, in recovered mice, activation of the ISR is transient and restricted to the acute phase of infection. However, in mice that did not recover, the ISR shows a sustained activation at time points where viral particles are no longer detectable. Rather, the activation of the ISR correlates with the up-regulation of endogenous mitochondria derived dsRNA, which were recently shown to be the preferred substrate of the PKR kinase. Sustained activation of the ISR was confirmed in 3 independent datasets of Long COVID patients in human. We show that treatment with the ISR inhibitor, ISRIB, correlates with recovery in mice affected by Long COVID. Since ISRIB is currently tested in clinical trials for other conditions and is reported to improve symptoms associated with Long COVID such as memory lost, gut inflammation and cardiomyopathy in preclinical models, our data opens the possibility to explore ISRIB as an intervention for the treatment of Long COVID.

overall_design: Here, we used mice that share the same nuclear genome in the C57BL/6 genetic background (BL/6) but differ in mitochondrial genomes either from the C57BL/6 background (BL/6C57) or NZB/OlaHsd background (BL/6NZB). We compare the response to SARS-Cov2 infection in males and females in both genotypes. We found that despite similar initial response to infection and complete clearance of virus in both genotypes, their recovery rates from SARS-Cov2 infections differ. BL/6NZB mice of both sexes recovered while the BL/6C57 males specifically fail to recover

first: Doris

last: Germain


title: Multi-omic analysis reveals maturation programs in human pluripotent stem cell-derived cardiomyocytes during long-term culture

city: Madison

first: Sean

middle: P.

last: Palecek

state: Wisconsin

address: 1415 Engineering Drive

department: Chemical and Biological Engineering

institute: University of Wisconsin-Madison

summary: Human pluripotent stem cell-derived cardiomyocytes (hPSC-CMs) hold tremendous promise for disease modeling, drug discovery, and cardiac regenerative therapies. However, the immature phenotype of hPSC-CMs remains a major barrier limiting their translational utility. Here, we performed integrated multi-omic profiling to identify molecular pathways and regulatory programs associated with hPSC-CM maturation during long-term culture. hPSC-CMs were cultured for 113 days and analyzed using metabolomics, proteomics, and transcriptomics across progressive stages of maturation. Long-term culture induced widespread multi-omic remodeling, including significant changes in 142/934 metabolites, 550/3,556 proteins, and 2,892/23,309 transcripts from Day 30 to Day 113. Metabolomic analyses revealed early increases in phospholipid biosynthesis and mitochondrial beta oxidation of fatty acids from Day 30 to Day 60, suggesting metabolic priming precedes later maturation events. In contrast, proteomic remodeling was more prominent during later stages of maturation and was characterized by enhanced calcium handling and cell cycle exit. Transcriptomic analyses demonstrated progressive increases in ion channel expression, t-tubule organization, fatty acid metabolism, creatine shuttle pathways, and cell cycle arrest programs. Transcriptomic and integrative multi-omic pathway analyses identified coordinated suppression of TGFβ, MAPK, Wnt, and Hedgehog signaling together with activation of integrin-related, respiratory electron transport, muscle contraction, and Slit-Robo signaling pathways during maturation. Moreover, multi-omic transcription factor activity analysis prioritized a GATA4-centered network of putative cardiomyocyte maturation regulators including SOX7, SOX18, TBX2, and ZFPM2 (FOG2). Together, these findings elucidate the degree and pace of hPSC-CM maturation during long-term culture and establish an integrated multi-omic framework for identifying strategies to accelerate hPSC-CM maturation.

overall_design: We differentiated human pluripotent stem cells (hPSCs) to cardiomyocytes (CMs) using small molecules CHIR99021 and IWP2 and confirmed high cardiomyocyte purity on Day 16 (cTnT+ cells by flow cytometry). Then, we cultured independent wells from a WTC11 hiPSC-CM differentiation and collected samples during long-term culture maturation. For the multi-omic collection experiment, we used the WTC11 hiPSC line and collected samples on Days 30, 60, and 113 for proteomics, metabolomics, and transcriptomics. Each replicate is a well replicate of one WTC11 hiPSC-CM differentiation.

first: Austin

last: Feeney

first: Aaron

last: Simmons

middle: P


title: Effect of SMALS-329 treatment on gene expression in ACHN renal carcinoma cells

first: John

last: Gordan

address: 1700 4th Street

institute: UC San Francisco

summary: LKB1 is a tumor suppressor kinase whose inactivation is associated with poor prognosis and therapeutic resistance in multiple cancer types. To investigate the transcriptional effects of pharmacological LKB1 activation with SMALS-329, we performed RNA sequencing of ACHN renal carcinoma cells following treatment with 8 mM SMALS-329 for 24 hours. Gene set enrichment analysis identified an enrichment of genes involved in cell adhesion/mobility (11 genes) and cell polarity (6 genes) as the key downregulated group of genes. Additionally, we noted significant regulation, both up and down, of several inflammatory mediators and components of the unfolded protein response (UPR). These findings are consistent with the known effects of LKB1, namely the regulation of metabolism, inflammation, cell adhesion/mobility and cell polarity and the UPR.

overall_design: Total RNA was extracted from ACHN cells using the RNEasy RNA Purification Kit (Qiagen), following the manufacturer’s instructions. Reverse transcription was performed using SuperScript II Reverse Transcriptase (Thermo Fisher Scientific). Library preparation was performed by using the NEBNext Ultra™ II DNA Library Prep Kit (New England Biolabs), with tagmentation reagents from the Nextera XT DNA Library Prep Kit (Illumina). Sequencing was performed on the Illumina NextSeq platform in the Ramani Lab (UCSF). Reads were aligned to the human genome, and normalization and differential gene expression analyses were performed using DESeq2.

first: Aidan

last: Keith

first: Vijay

last: Ramani

first: Dominique

last: Mitchell


title: Characterizing the tumor microenvironment at the single-cell level reveals the potential immune evasion mechanism in giant cell tumor of bone

city: chongqing

first: dongyang

last: zhang

address: No. 30, Gaotanyan Zhengjie, Shapingba District

institute: Department of Orthopedics, the First Affiliated Hospital of Army Medical University

summary: Giant cell tumor of bone (GCTB) is intermediate, locally aggressive primary bone tumor that are usually occur in long bones and typically present as lytic lesions, leading to cortical expansion or destruction with a soft-tissue component. At present, the main treatment of GCTB is surgical curettage and bone cement filling, but the recurrence rate is more than 20%. It is known that tumor recurrence and immune escape are closely related to the microenvironment. We need a deeper understanding of the complex tumor microenvironment, as well as the role of various immune cells in the development of GCTB, in order to achieve a comprehensive treatment of GCTB.

overall_design: In this study, GCTB tissue was isolated in vivo from two patients undergoing surgical GCTB, and tumor tissue and its associated immune cell subtypes were identified by single-cell RNA sequencing. In combination with previous studies, the role of Siglec15 in tumor immunosuppression and osteolytic destruction was determined, and validated with recombinant Siglec15 antibody. The results broaden the understanding of the immune-microenvironment of GCTB, and provide a new insight for reducing the recurrence by adjuvant therapy.

first: Dongyang

last: Zhang


title: Hippo pathway inhibition restores visual function in blind mice via Müller glia-derived photoreceptor regeneration

city: Hengyang

first: Houjian

state: Hunan

address: Shigu District Chuanshan Road

institute: The First Affiliated Hospital of University of South China

summary: Photoreceptor loss causes irreversible blindness, with no effective therapies due to the mammalian retina’s inability to regenerate. Extending our previous finding that targeting the core Hippo effector YAP drives limited Müller glia (MG)-to-inner retinal neuron transdifferentiation yet induced marked, transient MG migration toward the outer retina, even in an inner retinal injury model. These results indicate that YAP holds high potential to instruct photoreceptor fate from endogenous MG. Here, we show that Hippo pathway acts as a master regulator governing MG trans-differentiation into photoreceptors. Genetic and pharmacological modulation of YAP promotes MG proliferation and drives their commitment to a photoreceptor lineage in a mouse model of outer nuclear layer injury.A single intravitreal injection of TDI‑011536 delivered via GelMA‑encapsulated mesoporous silica nanoparticles achieves substantial photoreceptor regeneration and restores visual function in blind mice, without systemic toxicity. Our findings identify the Hippo pathway as a promising therapeutic target for photoreceptor degenerative diseases and establish this nanoparticle system as a viable platform for clinical translation.

overall_design: To characterize the types of neurons regenerated in TDI-011536-treated mice, we performed scRNA-seq on fluorescence-activated cell sorting (FACS)-purified MG and their neuronal progeny 1 month after sodium iodate and TDI-011536 treatment.

first: Wenxin

last: Sun

first: Yuli

last: Guo

first: Xuechun

last: Wang

first: Wei

last: Zha

first: Zuguo

last: Liu


title: Potassium restriction phenocopies caloric restriction to extend chronological lifespan in yeast

city: Shanghai

first: Jintao

last: Huang

address: 800 Dongchuan Road

institute: Shanghai Jiao Tong University

summary: Potassium, as an essential cation in yeast, regulates membrane potential, enzyme activity, and nutrient sensing pathways via transporters such as Trk1/2, and is crucial for cellular and tissue function. Here, we show that extracellular potassium instead acts as a primary nutritional cue in Saccharomyces cerevisiae, exerting strong control over growth behaviour and chronological lifespan (CLS). The results indicate that in standard glucose (2%) medium, potassium restriction (PR) significantly extends the lifespan. Notably, it exhibited calorie restriction (CR)-like phenotypes across all detection levels: both triggered synergistic downregulation of the HOG1 MAPK and TOR-Sch9 pathways, inducing highly overlapping transcriptional reprogramming, promoting vacuolar fusion into a single giant vacuole, strengthening cell wall and membrane structures, and reshaping metabolic networks, and comprehensively suppressing the production of aromatic amino acid metabolites and NAD⁺ degradation products while selectively accumulating protective purine and carnitine derivatives. The longevity-promoting effects of PR and CR strictly depend on the nutritional environment, exhibiting antagonism when both nutrients are severely depleted. This indicates that yeast perceives the balance between potassium and glucose rather than their absolute concentrations. These findings identify PR as an additional CR mimetic and suggest that potassium is a key ionic regulator of aging in yeast. This provides a basis for understanding how ionic nutritional status modulates lifespan across species boundaries.

overall_design: For each RNA-sequencing (RNA-Seq) condition, three independent biological replicates were included for each of the four conditions (2% glucose/1 mM K⁺, 2% glucose/7 mM K⁺, 0.5% glucose/1 mM K⁺, and 0.5% glucose/7 mM K⁺).

first: Liping

first: Ziyun

last: Wu


title: Distinct activation programs in naïve and memory CD8 T cells govern progeny stemness and effector persistence

city: Prague

first: Juraj

last: Michalik

address: Vídeňská 1083

country: Czech Republic

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

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

overall_design: Refer to individual Series


title: Multiple Argonaute complexes orchestrate epigenetic silencing in the Arabidopsis germline [Bisulfite-Seq]

city: Klosterneuburg

first: Xiaoqi

last: Feng

address: Am Campus 1

department: Cell Biology

country: Austria

institute: Institute of Science and Technology Austria

type: Methylation profiling by high throughput sequencing

summary: We report AGO4/5/6/9-bound sRNAs map to pol iv-dependent sRNA clusters in the Arabidopsis thaliana male sexual lineage that regulates gene expression in meiocytes. We found that AGO4/6/9 but not AGO5 participate in RdDM in meiocytes, and AGO5 plays a subtle role in repressing TEs silenced by AGO4/6/9 and Pol IV in meiocytes.

overall_design: Whole genome bisulfite sequencing, RIP-seq and RNA-seq of wild type and AGO mutant samples in Arabidopsis male sex cells.

first: Jincheng

last: Long

first: Chao

last: Yang

first: Shujuan

last: Xu

first: Joke

last: Jaeger-Braet

first: Wenjing

last: She

first: Seijiro

last: Ono

first: James

last: Walker

first: Ygor

last: Souza-Vieira

first: Arp

last: Schnittger


title: Transcriptomic dissection of an appendicularian larva at single cell resolution [scRNA-seq]

city: Bergen

first: Simon

last: Henriet

address: Thormøhlensgate 55

country: Norway

institute: University of Bergen

summary: Oikopleura dioica is a larvacean urochordate that has arisen as an emerging model due to its specific characteristics. Through single cell analysis, we have mapped the different cell populations that are present during its development, and instruct the formation of lineage-specific structures.

overall_design: Maturing O. dioica individual females and males were dissociated during the course of maturation. Cells were isolated and analyzed using scRNA-seq recommendations from 10xGenomics

first: Anthony

last: Leon

first: Daniel

last: Chourrout


title: Spatial atlas of the human brain vasculature reveals specialized cell ensembles

first: Jerry

last: Wang

address: 513 Parnassus Ave. HSE-860

department: Neurosurgery

institute: University of California, San Francisco

summary: 10x Genomics Xenium profiling of human temporal cortex and hippocampus with custom cerebrovascular-focused gene panel

overall_design: Spatial transcriptomics profiling of 20 sections of temporal cortex and hippocampus across 13 human control donors

first: Ethan

last: Winkler


title: Transcriptomic profiling of NO07G02030 knockout and overexpression mutants in Nannochloropsis oceanica

city: Qingdao

first: Yanhai

last: Gong

address: No.189 Songling Road

department: single cell center

institute: qibebt, cas

summary: Genetic perturbation through knockout (KO) and overexpression (OE) revealed that NO07G02030 predominantly promotes genome-wide H3K36me3 deposition and gene activation. Strikingly, it also represses H3K36me3 at a distinct subset of 509 genes, demonstrating dual-directional regulatory capacity.

overall_design: Gene expression profiling was conducted using RNA-seq data obtained from NO07G02030 knockout and overexpression mutants, as well as the wild-type strain, under both standard light and high light conditions.

first: Xueqian

last: Chen

first: Qintao

first: Jing

last: Ren

first: Lianhong

first: Jian

first: Luyang

last: Sun


title: Characterization of Human Umbilical Cord Plasma MicroRNAs at Birth and Their Association with Birth-Related Biological Factors, Maternal and Fetal Exposomes, and Factors Related to Early-Life Adiposity Programming

city: Sherbrooke

first: Luigi

last: Bouchard

country: Canada

institute: Université de Shebrooke

summary: To characterize the human umbilical cord plasma (UCP) microtranscriptome profile at birth, we sequenced microRNAs in UCP samples collected at delivery, between the 34th and the 42th weeks of pregnancy (mean gestationnal age at birth: 39.3 ± 1.3 weeks), from 286 newborns from the Gen3G cohort. We then performed association analyses to assess the microRNA profile correlation with birth-related biological factors, maternal and fetal exposomes as well as factors related to early-life adiposity programming.

overall_design: Complete microtranscriptome from 286 human UCP samples collected at birth between the 34th and the 42th weeks of pregnancy (286 biological replicates) was assessed by next-generation sequencing. All participants were of European descent. Out of the 286 mother-child dyads, 276 mothers consented to data sharing for herself and her newborn.

first: Marie-France

last: Hivert

first: Patrice

last: Perron

first: Véronique

last: Desgagné

first: Andrée-Anne

last: Clément

first: Kathrine

last: Thibeault

first: Lysanne

last: Girard


title: Genome-wide mapping of human H4K20me3 in the HN-SCC-151 HPV-negative head and neck squamous cell carcinoma cells treated with DMSO or the SUV420H1 inhibitor A-196/siNC (control) or siSUV420H1 siRNAs.

city: ROCKVILLE

first: Vassiliki

last: Saloura

state: MARYLAND

address: 11705 STONEWOOD LN

department: TGMB

institute: NCI

summary: We used CUT&RUN to evaluate the genome-wide mapping of human H4K20me3 in HN-SCC-151 cells treated with DMSO or the SUV420H1 inhibitor A-196/siNC (control) or siSUV420H1 siRNAs.

overall_design: HN-SCC-151 cells were cultured in-vitro in three separate 10cm dishes per condition and treated with DMSO or A-196 (2.5uM)/siNC or siSUV420H1 siRNAs for 6 days. They were then collected and 500,000 cells from each of the plates were obtained and processed per EpiCypher's CUT&RUN assay protocol.

first: Arfa

last: Moshiri

first: Sohyoung

last: Kim


title: H3K36me3 profiling of NO07G02030 knockout and overexpression mutants in Nannochloropsis oceanica

first: Yanhai

overall_design: H3K36me3 profiling was conducted using ChIP-seq data obtained from NO07G02030 knockout and overexpression mutants, as well as the wild-type strain, under both standard light and high light conditions.

last: Xu


title: Stathmin 1 regulates mitophagy and cellular function in hematopoietic stem and progenitor cells

city: Saint Louis

first: laura

last: schuettpelz

state: MO

address: 660 S. Euclid

institute: washington university

summary: Stathmin 1 is a cytoplasmic phosphoprotein that regulates microtubule dynamics via promotion of microtubule catastrophe and sequestration of free tubulin heterodimers. Stathmin expression is a feature of proliferating cells, and it is overexpressed in many cancers, including hematopoietic malignancies. In contrast to its roles in proliferating cells, considerably less is known of Stathmin 1 in quiescent  cells. Notably, Stathmin 1 is highly expressed in hematopoietic stem and progenitor cells (HSPCs), and herein we found that loss of Stathmin 1 is associated with altered microtubule architecture and markedly impaired HSPC function. Transcriptomic studies suggested alterations in oxidative phosphorylation in Stmn1-/- HSPCs, and further mechanistic studies revealed defective mitochondrial structure and function in the absence of Stathmin 1 with increased ROS production. Microtubules associate with mitochondria and lysosomes to facilitate autophagosome formation and mitophagy, and indeed we found that this critical mitochondrial quality control process is impaired in Stathmin 1-deficient HSPCs. Finally, stimulation of autophagy improved the colony forming ability of Stmn1-/- HSPCs. Together, these data identify a novel, non-proliferative role for Stathmin 1 in the regulation of HSPC mitochondrial quality control and cellular function.

overall_design: RNA-seq profiling of hematopoietic stem cells from wild-type and Stathmin 1 knockout cells

first: Luana

last: Chiquetto

first: Laura

last: Schuettpelz


title: Single-cell transcriptomic profiling of endothelial cells across four developmental stages of zebrafish larvae

city: NanTong

first: Xiaofeng

last: Lu

address: 9# Seyuan Road

institute: Nantong University

summary: The vascular endothelium, once considered a simple passive barrier, is now recognized as a highly dynamic and heterogeneous tissue that plays a crucial role in organ homeostasis, immunity, and disease pathogenesis. We performed scRNA-seq to systematically profile zebrafish endothelial cells at 1, 2, 4, and 8 dpf, mapping their developmental progression at single-cell resolution. This study delineates the transition of ECs from early specification to functional specialization,  and defined distinct EC subpopulations during early ontogeny.

overall_design: Zebrafish at 4 developmental stages, including 24 hpf (hours post fertilization), 48 hpf, 4 dpf (days post fertilization) and 8 dpf of transgenic zebrafish Tg(kdrl:EGFP) were collected and digested to obtain single-cell suspensions. GFP+ cells were sorted and analyzed using large-scale scRNA-seq (10X Genomics) platform.

first: Guanyun

last: Wei

first: Shu

last: Zhao

first: Gangcai

last: Xie

first: Dong

last: Liu


title: Comparative transcriptome analysis of resistant and susceptible Brassica juncea lines infected with Albugo candida reveal white rust defense mechanism

city: New Delhi

first: Prajjwal

last: Rai

state: New Delhi

address: IARI, Pusa campus

department: Division of Plant Pathology

country: India

institute: Indian Agricultural Research Institute

summary: In this study, we aim to elucidate the transcriptome of white rust resistance in contrasting resistant and susceptible Brassica juncea lines. We have taken Near-Isogenic lines (NILs) fpor our study. These NILs, sharing an almost identical genetic background but differing in the presence or absence of a resistance locus, provide an excellent system for investigating the mechanistic basis of resistance. So, activation of defense-related genes downstream of R-gene recognition further reinforces resistance and distinguishes resistant from susceptible interactions.

overall_design: Brassica juncea genotypes Varuna (susceptible) and Varuna WRR (resistant NIL) were used. Albugo candida spore suspension was inoculated on 21 days old plants in controlled conditions. Leaf samples for transcriptome profiling were collected at 48 hours post inoculation (hpi) and 96 hpi from both mock and pathogen infected plants. So, finally comparative transcriptome analysis was done usng RNA-seq approach.

first: Mahender

last: Saharan

first: Nitish

last: Bhardwajj


title: RNA-seq profiling of C.elegans treated with bromhexine and genipin

city: Singapore

first: Weihan

last: Huai

address: 10 Medical Dr

country: Singapore

institute: NUS

summary: Pharmacological interventions directly modulating ageing could potentially extend human healthspan. Such interventions should be efficacious in adults and ideally repurpose drugs known to be safe. In this dataset we showed the RNA-seq of worms treated with bromhexine or genipin, two compounds predicted from their effect on longevity-associated modules we identified.

first: Jan

last: Gruber

first: Brian K.

last: Kennedy


title: Micronanoplastics (MNPs) and Inflammation in Lungs of Children Undergoing Pulmonary Surgical Resection

city: Chongqing

first: Yuhao

last: Wu

address: No. 136, Zhongshan Second Road

institute: Children’s Hospital of Chongqing Medical University

summary: Samples of peri-lesional lung tissues were collected following resection of pulmonary lesions. We compared lung tissues from the low-concentration MNP exposure (LCME) versus high-concentration MNP exposure (HCME) groups. RNA-seq found that exposure to airborne MNPs may activate inflammatory responses in the lungs of children.

overall_design: Human lung tissues from the LCME and HCME groups were sent for RNA-seq

first: Lianju

last: Shen

first: Yue

last: Tang

first: Yunni

last: Ran

first: Haohui

first: Yonggang

last: Li


title: Genome-wide binding of ZFPOBI1/TRIM28 and linked H3K9me3 dynamics

city: Copenhagen N

first: Daniel

middle: Martin

last: Messerschmidt

state: Zealand

address: 3C Blegdamsvej, Building 18

department: Faculty of Health and Medical Sciences

country: Denmark

institute: University of Copenhagen

summary: This work describes the function and targets of a maternal KRAB-Zinc finger protein, ZFPOBI1, which specifically targets a subset of LTR retrotransposons during embryonic epigenetic reprogramming.

overall_design: HA-tagged ZFPOBI1 was overexpressed in mouse embryonic stem cells to identify genome-wide binding sites by ChIP-sequencing. In ZFPOBI1 overexpressing cells TRIM28/Kap1 recruitment and H3K9me3 dynamics were also assed by ChIP-sequencing.


title: Human HN-SCC-151 HPV-negative head and neck squamous cell carcinoma cells treated with DMSO or the SUV420H1 inhibitor A-196/siNC (control) or siSUV420H1 siRNAs.

first: Vassiliki

last: Saloura

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus


title: Aptamer-Mediated Multivalent Endogenous ADAR1 Recruitment for Highly Efficient RNA Editing

city: Tianjin

first: Shu-Lin

address: No.94 of Weijin Road

institute: Nankai University

summary: Adenosine-to-inosine (A-to-I) RNA editing mediated by endogenous ADAR enzymes represents a promising therapeutic strategy for correcting disease-causing mutations at the transcript level without permanent genomic modification. To improve endogenous ADAR1 recruitment and RNA editing efficiency, we developed MARRS (Multivalent ADAR1 Recruiting RNA-editing System), a programmable RNA editing platform that incorporates engineered multivalent RNA aptamers targeting the Zα domain of ADAR1 p150 within a circular RNA scaffold. RNA sequencing was performed to characterize transcriptome-wide gene expression changes associated with MARRS and CLUSTER systems compared with control samples. The dataset consists of three experimental groups (Control, CLUSTER, and MARRS), each represented by three biological replicates. These data provide a resource for investigating the molecular consequences of enhanced endogenous ADAR1 recruitment and evaluating the transcriptomic impact of programmable RNA editing strategies.

overall_design: MCF-7 cells were divided into three experimental groups: the control group (Con), the CLUSTER group, and the MARRS group. Each group included three independent biological replicates (n = 3). Total RNA was extracted from each sample and subjected to RNA sequencing. The aim of this study was to compare transcriptional changes and detect mutations among the control, CLUSTER, and MARRS groups.

first: Han

last: Zhu


title: FGF-2 signaling dominates in TGF-β1/FGF-2–primed nasoseptal chondrocytes for cartilage tissue engineering

city: Edmonton

first: Zhiyao

last: Ma

state: Alberta

institute: University of Alberta

summary: For nasal reconstruction and the repair of articular cartilage lesions, autologous nasal septal cartilage (NSC) is a promising cell source for engineering hyaline cartilage. However, the low cell yield and high variability of cartilage quality between patients limit clinical scalability. Human NSC were isolated from tissue by enzymatic digestion, and after two passages, were treated with 1 ng/mL transforming growth factor β1 (TGF-β1), 5 ng/mL fibroblast growth factor 2 (FGF-2), or both factors together. Some cells were collected for molecular analyses before 3 weeks of chondrogenic differentiation, after which pellets were subjected to morphological, mechanical, histological, immunofluorescence, and biochemical analyses. Dual-priming resulted in the highest cumulative population doubling, followed by FGF-2, then TGF-β1. Treatment-dependent differences in cartilage matrix-forming genes largely converged in 3D constructs and showed little correlation, demonstrating the profound influence of culture system on gene expression. FGF-2-treated cells formed larger pellets by area and wet weight, followed by dual-primed cells, with TGF-β1-treated cells forming the smallest pellets with slightly higher Safranin-O staining intensity by area. Between dual-primed and TGF-β1-primed cells, bulk, unbiased RNA sequencing reveals extensive modulation of genes involved in mitotic/chromosome/DNA-maintenance programs, ECM/adhesion/cytoskeletal rewiring, and cell signalling. Principal component analysis demonstrates that, compared to TGF-β1 treatment, dual-priming results in much greater transcriptomic similarity with FGF-2-treated cells. We discuss the interacting regulator effects between both growth factors in driving the phenotype observed under combined treatment. Altogether, our analysis of regulated intracellular signalling pathways and growth factor interactions at the molecular level provides novel, foundational insights into cartilage biology that are essential for advancing tissue engineering strategies and optimizing clinical outcomes.

overall_design: Human nasal chondrocytes from six donors were expanded to passage 2 under T1, F2, or T1F2 priming conditions. Passage 2 monolayer cells were analyzed by RT-qPCR and RNA-seq to define growth-factor-dependent transcriptional programs. In parallel, primed cells were differentiated as 3D microtissue pellets for 21 days and evaluated by histology, immunofluorescence, biochemical assays, mechanical testing, and RT-qPCR to determine how monolayer priming influenced subsequent cartilage-like tissue formation.

first: Kiarra

last: Grimes

first: Aillette

last: Mulet-Sierra

first: Melanie

last: Kunze

first: Adetola

last: Adesida


title: Gene expression changes of C.elegans during aging and in daf-16(mu86) mutants

first: Weihan

summary: Aging is characterized by continuous deterioration of resilience and an increase in risk of diseases, leading to a gradual decline in function and, ultimately, death. Most of the studies on aging transcriptome  focused on whether the interventions can reverse the aging transcriptome, while the dynamics of the aging transcriptome is overlooked. We generated a transcriptomic dataset to investigate the molecular dynamics of aging and the role of insulin/IGF-1 signaling in regulating age-associated gene expression changes. Using Caenorhabditis elegans, we performed RNA sequencing across multiple time points during adulthood in both wild-type (N2) and daf-16(mu86) mutant animals, which lack the key FOXO transcription factor downstream of insulin/IGF-1 signaling.This dataset captures temporal gene expression changes associated with physiological aging and enables comparison between normal aging and impaired stress-response signaling. Samples were collected at defined adult stages, and total RNA was extracted for high-throughput sequencing. Differential expression and downstream analyses can be used to identify aging-associated transcriptional programs, distinguish adaptive versus potentially causative gene expression changes, and characterize daf-16-dependent regulatory networks. These data provide a resource for studying the systems-level architecture of aging, benchmarking transcriptomic aging clocks, and identifying gene modules associated with longevity and stress responses.

overall_design: RNA-seq profiling of N2 C.elegans at day 6, 8, 11, 14, 18 and daf-16(mu86) mutants at day 6.

first: Li-Fang

last: Ng

first: Jan


title: Sacral Neural Crest-Derived Extracellular Vesicles Suppress Pyroptosis via the ANXA1-FPR2 Axis to Repair Pelvic Ganglia

city: Suzhou

first: Xiaoyu

last: Lin

address: No. 100, Chongwen Road, Suzhou Industrial Park

institute: Suzhou Institute of Systems Medicine

summary: Pelvic autonomic nerve injury is a major cause of postoperative bowel dysfunction, yet effective strategies for restoring damaged pelvic ganglia remain lacking. Here, we demonstrate that extracellular vesicles derived from human pluripotent stem cell–induced sacral neural crest cells (Sacral NC-EVs) promote pelvic neuroregeneration by suppressing oxidative stress–induced pyroptosis. In a rat model of major pelvic ganglion (MPG) injury, local administration of Sacral NC-EVs improved gastrointestinal motility and partially restored rectal neural innervation and epithelial barrier integrity. Mechanistically, MPG injury induced a hypoxia-associated oxidative microenvironment that activated the NLRP3–caspase-1–GSDMD pyroptosis pathway, whereas Sacral NC-EVs effectively attenuated oxidative stress and inhibited pyroptotic signaling. Comparative analyses showed that Sacral NC-EVs produced more pronounced overall therapeutic effects than mesenchymal stem cell–derived and vagal neural crest–derived EVs, highlighting a functional advantage of developmental lineage matching. Proteomic and functional studies identified annexin A1 (ANXA1) as an important EV-associated mediator that acts through FPR2 signaling to contribute to the antioxidant and anti-pyroptotic effects of Sacral NC-EVs. Collectively, our findings establish lineage-matched EVs as a mechanism-driven, cell-free strategy for neural repair by targeting the oxidative stress–pyroptosis axis.

first: Ting

last: Yang


title: Transcriptional changes in GV oocytes upon maternal ZFPOBI deletion.

summary: This work describes the transcriptional changes in GV oocytes upon the disruption of the KRAB-ZFP protein ZFPOBI1/TRIM28 repressive complex, with particular focus transposable elements and LTR induced transcripts (LITs).

overall_design: This dataset contains RNA-seq analysis of wildtype and ZFPObi1 knock out GV oocytes.


title: The proprotein convertases regulate cumulus-oocyte-complex matrix integrity and cumulus cell behavior via a GDF-9 dependent mechanism

city: Chicago

first: Caroline

middle: Elisabeth

last: Kratka

state: IL

address: 303 East Superior Street

department: OBGYN

institute: Northwestern University

summary: The proprotein convertases (PCSKs) are serine proteases with a wide range of biological substrates. Pcsk3, 5, and 6 expression is upregulated in the mouse follicle during ovulation, but their functions in the ovary are underexplored. Using an ex vivo ovulation assay, we observed that a PCSK inhibitor (PCI) impairs follicular rupture and reduces cumulus cell adherence to the (COC) matrix. PCI treatment of COCs matured in vitro recapitulated loss of cumulus cell adherence late in the maturation period (12h) and revealed that PCI does not affect COC viability or the morphokinetics of oocyte maturation. Therefore, we hypothesized that the PCSKs have a role in maintaining structural integrity of the COC matrix. We first sought to determine which PCSKs may regulate COC matrix integrity. Using multiple approaches to assess PCSK3, 5, and 6 RNA and/or protein in the COC, we identified PCSK5A as the most likely regulator of COC matrix organization. To determine which pathways are dysregulated by PCI treatment, we conducted bulk RNA sequencing comparing control and PCI-treated COCs collected 0, 4, 8, or 12h after onset of in vitro maturation. 8h PCI-treated COCs clustered with 12h control COCs, indicating that PCI accelerates the normal temporal expression profile of COCs. Pathway analysis revealed that PCI treatment upregulated pathways related to metabolism and cell motility, and downregulated pathways corresponding to ECM organization, cell adhesion, and TGF-beta signaling. We then conducted proteomics of CTL vs. PCI-treated COCs at 10h to determine potential PCSK substrates that are affected by PCI treatment. Proteomics detected 79 proteins altered by PCI treatment, with functions related to ECM remodeling, cell adhesion/migration, cell signaling pathways, and metabolism. Notably, the oocyte proteome was stable with PCI treatment, consistent with earlier findings that the effect of PCI appears to be specific to cumulus cells. To validate PCI-induced ECM changes, we evaluated the PCI-treated COC matrix with H&E and a hyaluronic acid binding protein assay, which confirmed disruption of COC matrix integrity with PCSK inhibition. We then validated the effect of PCI on cumulus cell migration first with scanning electron microscopy, which revealed increased plasma membrane blebbing on the surface of PCI-treated cumulus cells. Live tracking of COC expansion showed that compared to control cumulus cells, PCI-treated cumulus cells have an increased mean square displacement and dysregulated anomalous diffusion, consistent with changes to cumulus cell migration. Based on the dysregulation of ECM organization and TGF-beta signaling pathways observed we PCI-treatment, we identified GDF9 as a substrate of interest, as it is a TGF-beta ligand with known PCSK consensus sequences and roles in COC expansion. Supplementation of recombinant GDF9 fully rescued COC matrix integrity, suggesting that GDF9 likely acts downstream of the PCSKs to regulate matrix organization. In conclusion, this study utilized a multi-omics approach to identify novel roles and molecular targets of the PCSKs in the COC during ovulation, with implications on development of fertility therapeutics and non-hormonal contraceptives.

overall_design: Bulk RNA-seq profiling of CTL COCs and PCI-treated COCs at 0h, 4h, 8h, and 12h of in vitro maturation

first: Ruixu

last: Huang

first: Robin

last: Skory

first: Christina

last: King

first: Jeffrey

last: Pea

first: Jiyang

last: Zhang

last: Milner

first: Anthony

last: Day

first: Nicolas

last: Plachta

first: Shuo

last: Xiao

first: Birgit

last: Schilling

first: Darryl

last: Russell

first: Britt

last: Goods

first: Francesca

last: Duncan


title: Transcriptomic response of largemouth bass (Micropterus nigricans) gill and spleen to bacterial coinfection

city: Auburn

first: Timothy

middle: James

last: Bruce

state: AL

address: 203 Swingle Hall

department: School of Fisheries, Aquaculture and Aquatic Sciences

institute: Auburn University

summary: Largemouth bass (Micropterus salmoides) were challenged with Aeromonas veronii (Av), Aeromonas hydrophila (Ah), Flavobacterium columnare (Fc), and coinfections (AvFc, AhFc), alongside mock-challenged and pre-challenge controls. Gill and spleen tissues were sampled at 0h (pre-challenge baseline), 12h, and 24h post-challenge. RNA-Seq was performed on 161 samples (79 gill, 82 spleen; 6 biological replicates per treatment/timepoint group, 10 for pre-challenge). Three gill samples were excluded due to low mapping rates consistent with gDNA contamination (11B3G, 15J2G, 29R3G). Differential expression analysis was performed using DESeq2 across 72 pairwise contrasts per tissue.

overall_design: 161 RNA-Seq samples from largemouth bass gill and spleen. 7 treatment groups: Pre-challenge baseline (n=10/tissue), Mock sham injection, Aeromonas veronii (Av), Aeromonas hydrophila (Ah), Flavobacterium columnare (Fc), AvFc coinfection, AhFc coinfection (n=6/group/tissue). Timepoints: 12h and 24h post-challenge. 164 total FASTQs deposited; 3 excluded from analysis (gDNA contamination).

first: Bruce

last: Timothy

first: Schneider

last: Chandler

first: Ledford

last: Owen


title: Single-Cell RNA Sequencing Identifies Stem-Like Subpopulations and Their Gene Signature in Lung Adenocarcinoma Progression

city: 广州

first: 丽娟

last: 邵

state: 广东省

address: 梅花村街道

institute: 广东药科大学附属第一医院

summary: Lung adenocarcinoma (LUAD) exhibits substantial intra-tumor heterogeneity (ITH), contributing to disease progression and therapeutic challenges. This study utilized single-cell RNA sequencing (scRNA-seq) to profile cells from stage I and III LUAD tumors and matched normal tissues, aiming to delineate malignant cell states and identify tumor-propagating subpopulations. Unsupervised clustering revealed eight major cell lineages, with epithelial cells dominating in tumors and a shift toward immunosuppressive niches in advanced stages, including elevated T cell exhaustion and pro-angiogenic macrophages. Malignant cells formed 11 subclusters, with stage III tumors enriched for invasive and immunosuppressive states. Pseudotime analysis suggested evolutionary trajectories from alveolar-like to squamous and stress-responsive lineages. Using CytoTRACE to infer stemness without predefined markers, we identified sub-cancer stem cells (sub-CSCs) predominantly in stage III, characterized by high transcriptional diversity and a core signature involving cytoskeleton motility, immune modulation, metabolic reprogramming, and protein homeostasis. A four-gene panel demonstrated strong prognostic value in independent cohorts. These findings provide insights into stemness-driven progression in LUAD and nominate potential targets for addressing heterogeneity.

overall_design: Tumor tissues and matched adjacent normal lung tissues were collected from patients with stage I (n = 3) and stage III (n = 3) lung adenocarcinoma (LUAD). Single-cell suspensions were generated from fresh specimens, and scRNA-seq libraries were constructed using the 10× Genomics platform. Raw sequencing data were processed with Cell Ranger to obtain UMI count matrices. After quality control and doublet removal, data integration across patients was performed using Harmony. Unsupervised clustering identified major cell lineages, followed by subclustering of malignant cells. CytoTRACE was applied to infer cellular stemness without predefined markers, and pseudotime trajectories were reconstructed using Monocle2. Functional enrichment analyses were conducted using clusterProfiler. Prognostic and diagnostic utility of candidate gene signatures was evaluated in independent TCGA-LUAD cohorts.

first: Qian

last: He

first: Lijuan

last: Shao

first: Jiali

last: Guo

first: Size

last: Chen


title: Single-Cell Transcriptomics Reveals Neural Fate Reprogramming in RARS2-Related Pontocerebellar Hypoplasia

city: Chengdu

first: Xing

last: Wei

state: --- Select One ---

address: No. 20, Section 3, Renmin South Road

institute: West China Second University Hospital

summary: Pontocerebellar hypoplasia type 6 (PCH6) is a severe neurodevelopmental disorder caused by mutations in RARS2, which encodes mitochondrial arginyl-tRNA synthetase (mtArgRS). Although RARS2-related mitochondrial dysfunction has been linked to impaired brain development, the cellular and molecular mechanisms remain largely unknown. In this study, we established a zebrafish model of rars2 deficiency and combined single-cell RNA sequencing (scRNA-seq) with immunofluorescence, in situ hybridization, and electron microscopy to dissect neural lineage alterations. Our analyses revealed a marked disruption of neurogenesis, accompanied by activation of glial and extracellular matrix–related programs. Key neurogenic transcription factors, including neurod4, her6, and pou3f1, were significantly downregulated, whereas glial- and stress-associated regulators such as hmgb1a, fabp7a, and foxp1b were strongly upregulated. Pathway enrichment indicated defects in RNA splicing and mitochondrial translation, together with compensatory metabolic and inflammatory responses. Collectively, these findings demonstrate that rars2 deficiency drives neural fate imbalance and glial activation through mitochondrial and transcriptional dysregulation, providing new insights into the pathogenesis of PCH6 and potential molecular targets for future therapeutic exploration.

overall_design: Single-cell RNA sequencing was performed on zebrafish embryos at 48 hours post fertilization (hpf) from wild-type and rars2 mutant groups. Approximately 200 embryos per group were dissociated into single-cell suspensions and processed using the 10x Genomics Chromium platform. Libraries were generated using the Chromium Single Cell 3’ Reagent Kit (v3.1) and sequenced on an Illumina NovaSeq 6000. Raw data were processed with Cell Ranger (v6.0.1) against the zebrafish GRCz11 reference genome, and downstream analyses were conducted using Seurat (v4.1.0).

first: Jing

last: Wang

first: Yanyun

first: Cong

last: Zhou

first: Zhaoyi

first: Shanling

last: Liu

first: Huaqin

last: Sun

first: Bin

first: Lin

last: Zhang


title: RNA-seq of human HN-SCC-151 HPV-negative head and neck squamous cell carcinoma cells treated with DMSO or the SUV420H1 inhibitor A-196/siNC (control) or siSUV420H1 siRNAs.

first: Vassiliki

last: Saloura

summary: We used RNA-seq to evaluate the transcriptomic changes induced in HN-SCC-151 cells treated with DMSO or the SUV420H1 inhibitor A-196/siNC (control) or siSUV420H1 siRNAs.

overall_design: Bulk RNA-seq was performed to characterize transcriptional changes associated with SUV420H1 perturbation in HPV-negative HNSCC models. Human HPV-negative HN-SCC-151 cells were cultured in-vitro in three separate 10cm dishes per condition and were treated with SUV420H1-targeting siRNA or the SUV420H1 enzymatic inhibitor A-196 (2.5uM) for 6 days, and compared with matched non-targeting siRNA or DMSO-treated controls. In vivo, MOC1 control tumors (n=4) and Suv420h1 knockout MOC1 tumors (n=4) grown in C57BL/6 mice were analyzed by bulk RNA-seq.

first: Arfa

last: Moshiri

first: Sohyoung

last: Kim


title: Prophylactic inhibition of LATS1/2 prior to high-dose irradiation promotes the regeneration of the damaged intestinal epithelium through Yap-dependent and independent mechanisms

city: Durham

first: Christine

middle: E

last: Eyler

state: NC

address: 308 Research Dr, LSRC B327C

department: Department of Radiation Oncology

institute: Duke University

summary: Intestinal epithelial cells can respond to ionizing radiation (IR) injury through Yap-driven regenerative pathways that facilitate the regeneration and repopulation of the intestinal epithelium. Yap is a key effector of the Hippo signaling pathway but the impact of pharmacologic approaches manipulating Yap activity as a means of promoting intestinal IR response have not been thoroughly evaluated. This study evaluated a selective and potent small-molecule inhibitor of Yap’s upstream negative regulators LATS1 and LATS2 (LATS1/2) on small intestinal radiation response in vitro and in vivo. Transient administration of this compound prior to IR facilitated in vitro radioprotection using mouse-derived enteroids as well as an in vivo radioprotective effect when systemically administered to mice prior to doses of IR that normally result in gastrointestinal acute radiation syndrome (GI-ARS). Transient systemic treatment with NCGC-023 before IR decreased DNA-damage, pre-mitotic apoptosis, and aberrant mitosis in the crypt epithelium. Mechanistically, Lats1/2 inhibition with NCGC-023 prompted gene expression changes characteristic of both Yap-dependent regenerative responses and Yap-independent metallothionine stress responses.

overall_design: RNA-seq was performed on RNA isolated from intestinal crypts of mice treated with either 50 mg/kg NCGC-023 (Lats1/2 inhibitor) or vehicle (5% DMSO, 19% 2-hydroxypropyl-beta-cyclodextrin, in sterile 1X PBS) at 24 and 2 hours prior to harvest. Four mice (2 male, 2 female) were treated with each treatment.

first: Olivia

last: White

first: Lucy

last: Driver

first: Katherine

last: Harbaugh

first: Chang-Lung

last: Lee


title: Mechano-Hypoxia Programs a Coordinated Chondrogenic–Osteochondral Transcriptome in Co-Cultures of Human Nasal Chondrocytes and Bone Marrow–Derived Mesenchymal Stromal Cells

first: Zhiyao

last: Ma

summary: Nasal chondrocyte–bone marrow mesenchymal stromal/stem cell (NC-BMSC) co-culture can enhance cartilage matrix formation, but whether this response remains separated from hypertrophic or osteochondral maturation under combined hypoxic and mechanical stimulation is unclear. Here, human NCs and BMSCs were seeded onto type I collagen scaffolds as monocultures or 1:3 NC:BMSC co-cultures, cultured for 6 weeks under hypoxia in chondrogenic medium, and then subjected to 7 days of intermittent dynamic compression. Construct phenotype was assessed using histology, collagen immunofluorescence, glycosaminoglycan and DNA quantification, unconfined compression testing, RT-qPCR, and endpoint bulk RNA sequencing. Co-culture constructs retained strong Safranin O-positive matrix and collagen II staining, whereas BMSC monocultures showed loss of proteoglycan-rich matrix by the endpoint. Measured glycosaminoglycan content in co-culture significantly exceeded the weighted expected value from the corresponding monocultures, indicating chondro-induction beyond additive cell-source contributions. Co-culture also produced significantly higher equilibrium and peak compressive moduli than donor-matched NC monocultures. RT-qPCR showed increased ACAN and SOX9 expression in co-culture, but also increased COL10A1, indicating that hypertrophic features were not fully suppressed. Endpoint RNA sequencing separated co-culture from NC monoculture and identified overlapping proliferation-, extracellular matrix-, and differentiation-associated programs. Co-culture upregulated proteoglycan- and cartilage-associated genes together with mineralization-, angiogenesis-, and remodeling-associated genes including SPP1, IBSP, DMP1, ALPL, and VEGFA. Mechanotransduction-associated genes and immediate-early transcriptional regulators were also enriched under the applied loading regimen. These findings show that NC-BMSC co-culture under hypoxic dynamic compression enhances cartilage-like matrix formation and mechanical function, but the improved tissue phenotype remains coupled to an osteochondral remodeling transcriptome. Future optimization should focus on uncoupling matrix induction from hypertrophic and mineralization-associated maturation.

overall_design: Human NCs and BMSCs were seeded onto type I collagen scaffolds as NC monocultures, BMSC monocultures, or 1:3 NC:BMSC co-cultures and maintained for 6 weeks under hypoxic chondrogenic conditions. Constructs were then exposed to 7 days of intermittent dynamic compression under hypoxia, with four loading cycles per day. Baseline constructs were collected before loading, and endpoint constructs were analyzed by histology, collagen immunofluorescence, GAG/DNA quantification, unconfined compression testing, RT-qPCR, and bulk RNA-seq. Donor-matched NC and co-culture constructs were compared to determine whether co-culture enhanced cartilage-like matrix formation, mechanical properties, and endpoint transcriptomic programs.

first: Jaden

last: Majumdar

first: David

last: Li

first: Melanie

last: Kunze

first: Aillette

last: Mulet-Sierra

first: Adetola

last: Adesida


title: Absence of Clec1a in murine cDC1s decrease IFN responses to necrotic cells

city: Nantes

first: Elise

last: Chiffoleau

address: 30 Bd jean Monnet CHU

country: France

summary: Interferons (IFNs) are proteins that signal and play a critical role in health and disease. IFNs play a protective role gainst pathogens such as during  viral, bacteria and fungal infections, but can also mediate many inflammatory and autoimmune diseases. IFNs are characterized by time-dependent activities that can drive opposing outcomes so IFN responses need to be carefully balanced to prevent deleterious effects and for the return to homeostasis. We previously characterized the C-type lectin receptor CLEC-1 as a receptor of necrotic cells particularly expressed by cDC1s. Here, we showed that the absence of Clec1a in cDC1s decreases the IFN responses to necrotic cells but not to pathogen such as E. Coli. These results suggest that CLEC-1 in cDC1s potentiates IFN signaling in response to necrotic cells to finely regulate downstream immunity.

overall_design: To investigate the role of CLEC-1 in murine cDC1s, we performed bulkRNAsequencing on in vitro highly purified murine cDC1s incubated 6 hours with necrotic cells (6 mice in 4 technical replicares per condition).

first: Thomas

last: Ogor

first: Camille

last: Ligeron

first: Jeremie

last: Poschmann

first: Cynthia

last: Fourgeux


title: Identification of transcriptional changes in Human endothelial cell line after depletion of transcription factor Sox4 via siRNA.

city: Charlottesville

first: Pankaj

last: Kumar

state: VA

address: 1340 Jefferson Park Ave

institute: UVA

summary: To get a global perspective of SOX4 regulated genes, we performed RNA-seq in HUVECs. Using the cutoff criteria 1.3-fold change with 0.05 FDR, we identified 2500 genes, with roles in actin filament, circulatory system development, cell surface signaling, tube morphogenesis and lipid biosynthesis.

overall_design: HUVEC cell were cultured and SOX4 was depleted using siRNA. RNA was extracted 48 hours post siRNA treatment using TRIzol  as per manufacturer?s procedure. RNA was quantified using Qubit 4 and quality was assessed by Agilent Tape station at UVA GATC core. NGS library was prepared and 50-base paired-end bulk sequencing was performed using Illumina NextSeq 2000 sequencing system using UVA GATC core that generated between 100-140 million read per sample.

first: Sunil

middle: K

last: Verma

first: Muge

last: Kuyumcu-Martinez

first: Imrul

last: Chowdhury


title: Integrated Transcriptomic Profiling Reveals Immune and Molecular Stage-Specific Signatures of Colorectal Cancer in Hispanics Living in Puerto Rico

city: San Juan

first: Elba

last: Caraballo Rivera

state: Puerto Rico

address: Av. Jose Kiko Custodio

institute: University of Puerto Rico Comprehensive Cancer Center

summary: Colorectal Cancer (CRC) has become the second leading cause of death related to cancer worldwide and the third most common malignancy. CRC tumors are classified into stages to describe the cancer; early (stages I and II) and advanced (stages III and IV). Despite the available screening methods and the scientific efforts in the development of a universal biomarker pannel for CRC early detection, there still exists a gap in a reliable non-invasive screening method for the Hispanic community. We aimed to elucidate the most important pathways along with the differential gene expression in early and advanced CRC stages in Hispanics living in Puerto Rico (PRH).

overall_design:
RNA-seq profiling colorectal tissues, including early- and advanced-stage CRC, and its adjacent mucosal tissue to elucidate key mechanisms that modulate CRC progression from early- (stages I & II) to advanced-stage (III & IV) CRC.

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

middle: N

last: Zenón Meléndez

first: Sheila

last: López Acevedo

first: Josué

last: Pérez Santiago

first: Yakshi

last: Ortiz Maldonado

first: Gabriela

last: Chardón Galindez

first: Madeline

last: Mártir Ocasio

first: Hilmaris

last: Centeno Girona

middle: V


title: scRNAseq Dataset of lungs from WT and Clec1a KO mice following primary or secondary E. coli lung infection

last: Chiffoleau

summary: Pneumonia is associated with significant morbidity and mortality and is the leading cause of hospitalization and death worldwide. Sepsis exhibits phases of enhanced inflammation, alternating with immune suppression. Sepsis-induced immunosuppression is characterized by a deep remodelling of the myeloid immune compartment, leaving patients vulnerable to more severe forms of secondary infections. Pattern Recognition Receptors (PRRs), such as the C Type Lectin Receptors (CLRs) family, are able to respond to a wide variety of endogenous and exogenous ligands, modulating a plethora of innate responses. We previously described the CLR CLEC-1, as a receptor of necrotic cells expressed by myeloid cells such as conventional Dendritic Cells type I (cDC1), and able to limit antigen presentation and downstream T cell response. Therefore, we evaluated the role of this novel immune checkpoint during the initial pro-inflammatory phase, and in the later inflammation resolution phase of sepsis. To do so, we performed E. coli lung primary and secondary infections in C57BL6 Clec1a deficient mice and analysed the immune response at day 1 and 3 following infections by scRNAseq.

overall_design: We performed scRNAseq on the lungs digested by dispase in C57BL6 Wild Type and Clec1a deficient mice at day 1 and 3 following E. coli lung primary or secondary infections.

first: Cedric

last: Jacqueline


title: Rat hepatic genes in response to choline-deficient diet

city: Higashi-Hiroshima

first: Yanaka

last: Noriyuki

address: Kagamiyama 1-4-4

department: Graduate School of Biosphere Science

country: Japan

institute: Hiroshima University

summary: Transcriptional profiling of rat liver. The objective of this study is to explore gene expression profiles of rat liver in response to choline-deficient diet

overall_design: Two-condition experiment, liver of four choline-deficient diet rats at 7 weeks of age

first: Noriyuki

last: Yanaka


title: Host eicosanoid signals define a granuloma-associated fibroblast population coordinating mycobacterial containment II

first: David

last: Tobin

address: 207 Research Drive

summary: We used single-cell RNA sequencing to interrogate granulomas from Mycobacterium marinum infected zebrafish (Danio rerio) of a genetic mutant and matched WT siblings. Granulomas are comprised of several cell types and we sought to understand the consequences of genetic disruption of the gene apolipoprotein db (apodb) on granuloma cells types and cell-specific transcription.

overall_design: Granulomas were dissected from infected zebrafish adults. Single-cell suspensions were generated by brief digestion with trypsin and sent for 10X Genomics scRNAseq processing.

first: Erika

middle: J

last: Hughes


title: Nintedanib and Pirfenidone affect growth and differentiation of human alveolar type 2 cells

city: South San Francisco

last: Garfield

state: CA

address: 1 DNA Way

department: Center of Excellence for Computational Sciences

institute: Genentech

summary: Idiopathic pulmonary fibrosis (IPF) is a progressive fibrotic lung disease characterized by epithelial cell senescence. Pirfenidone and nintedanib are approved drugs for the treatment of IPF.  They significantly slow disease progression, but their mechanisms of action, especially on Alveolar type 2 (AT2) cells, are poorly understood. We addressed this question by evaluating colony formation and growth of human AT2 cells co-cultured with fibroblasts in organoid culture in the presence of pirfenidone and nintedanib.  We further evaluated molecular changes induced by these drugs via single cell RNA-seq of treated organoids. Results. AT2 cell organoids cultured in the presence of pirfenidone or nintedanib resulted in increased colony formation and, in the case of nintedanib, in larger colonies.  We observed that untreated or pirfenidone treated AT2 cells lost surfactant protein C (SFTPC) expression and acquired an expression profile consistent with keratin (KRT)17high/KRT5- basaloid cells, whereas a larger proportion of nintedanib treated cells retained SFTPC expression. In contrast, AT2 cells treated with TGFb inhibitor exhibited intermediate (SFTPC-/KRT17low) gene expression profile.  Conclusion. These results suggest that nintedanib prevents transdifferentiation of AT2  cells to KRT17+/KRT5- cells in culture and likely acts proximal to TGFb.

overall_design: AT2 cells isolated from normal donor lungs or IPF patients were mixed with human fibroblasts in 3D culture and grown in the absence or presence of pirfenidone or nintedanib.  After 14 days in culture, the number of organoids was quantified and cells extracted from Matrigel for single cell RNA-seq.

first: Alexey

last: Bazarov

first: Andrea

last: Serra-Marques

first: Jason

last: Rock

first: Paul

last: Wolters


title: in vivo proximity-based mapping of subcellular proteomes, transcriptomes, and RNA structuromes II

city: Shanghai

first: Jiapeng

last: Liu

address: Yueyang Road 320

department: SIBCB

institute: CEMCS, CAS

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

sample_organism:
Caenorhabditis elegans
Homo sapiens

platform_organism:
Caenorhabditis elegans
Homo sapiens

overall_design: Labeled and enriched MITO-PRADA cell lines cultured in vitro and xenograft tumors in vivo, followed by library preparation.

first: Shuo

last: Han


title: in vivo proximity-based mapping of subcellular proteomes, transcriptomes, and RNA structuromes


title: Environmental enrichment resilience the social stress induced anxiety-like behaviour and memory impairment through epigenetic regulation in wild mice Mus booduga

city: Tiruchirappalli

first: Koilmani

last: Emmanuvel Rajan

address: School of Life Sciences

department: Animal Science

institute: Bharathidasan University

summary: Earlier, we demonstrated that environmental enrichment (EE) confers resilience against anxiety- and depression-like behaviors and improves learning and memory in the wild mouse Mus booduga. The present study was designed to investigate whether EE can confer resilience against social stress–induced behavioral and molecular alterations in  M. booduga. Animals in the experimental groups were subjected to an object recognition memory task, followed by whole-transcriptome analysis of hippocampal tissue samples. We found that social isolation under chronic stress down-regulated genes involved in stress regulation and synaptic plasticity, whereas EE restored object recognition memory and normalized the expression of these genes

overall_design: Indian field mice (Mus booduga) were captured directly from the agricultural field using rodent trapper. After habituation, Direct wild (DW) animals were subjected to behavioural tests, and hippocampal region was collected for whole transcriptome analysis. Other animals were subjected to immobilization stress by placing them in a plastic cylindrical tube (5.5 cm diameter × 15 cm length) for 7 days (2h/ day) and randomly divided into (ii) Standard Condition (SC): animals were transferred to standard laboratory cages (1 animal/ cage) and housed for 30 days; (iii) Environmental Enrichment (EE): animals were transferred  to an environmentally enriched cage  (8 animal/ cage) and maintained for 30 days. Then, experimental group animals were subjected to behavioural test, and hippocampus tissue was dissected out for analysis.

first: Swamynathan

last: Sowndharya


title: Myasthenia thymus reprograms class switched B cells into BAFF dependent survivors

first: Yuanqing

last: Yan

address: 303 E Superior Street

summary: In Myasthenia gravis (MG), autoantibody titers and thymectomy outcomes often fail to predict disease severity, suggesting that autoreactive B cells bypass normal tolerance checkpoints. Our analysis of the largest MG thymus atlas to date reveals a checkpoint swap where pathological B cells transition from T cell-dependent selection to a BAFF-driven survival program. These B cells exhibit reduced antigen presentation and CD40 co-stimulation, instead upregulating TNFRSF17 to engage BAFF signals provided by specialized T follicular helper cells. This reprogramming allows polyclonal autoreactive populations to persist and seed peripheral sites independent of stringent selection, explaining longstanding clinical paradoxes. Consequently, the BAFF-BCMA axis emerges as a critical therapeutic target and a high-fidelity biomarker for monitoring MG disease activity.

overall_design: Fresh thymus samples were obtained for single-cell RNA sequencing (scRNA-seq) using the 10x Genomics Chromium Single Cell 3' v3 and Single Cell 5' chemistries (the latter including V(D)J sequencing). Libraries were sequenced on NextSeq 1000/2000 instruments (for 3' v3) or an Illumina NovaSeq 6000 (for 5'). Raw scRNA-seq reads were demultiplexed using Cell Ranger (v6.0.0 for 3' v3; v7.1.0 for 5') and mapped to the GRCh38 (hg38) human reference genome. For Visium HD spatial transcriptomics, FFPE samples were utilized, and libraries were sequenced on an Illumina NovaSeq X Plus. These reads were mapped to the human genome (GRCh38) using Space Ranger (v3.1.0)

first: Diego

last: Avellla patino

first: Yimeng

last: Zhao

first: Xin

last: Wu

first: G.R. Scott

last: Budinger

first: Ankit

last: Bharat


title: ATR Is a Critical Dependency Gene Supporting Uveal Melanoma Cell Survival

city: Nashville

first: Michael

middle: L

last: Freeman

address: 2220Pierce Ave

department: Radiation Oncology

institute: Vanderbilt University Medical Center

summary: GNAQ, GNA11, CYSLTR2, and PLCB4 are well-characterized oncogenic drivers of uveal melanoma (UM). The oncogenic stress induced by these mutations creates a reliance on specific dependency genes that support tumor cell proliferation and survival. However, the genes that broadly contribute to UM cell fitness remain incompletely defined. Using the Dependency Map (DepMap) and Sanger Cancer Dependency bioinformatic resources, we identified ATR (HGNC:882; ATR checkpoint kinase) as a key regulator of UM cell fitness. Pharmacologic inhibition of ATR with the selective inhibitor VE-822 in 92.1 and MP38 cells, established models of low-risk and high-risk UM respectively, resulted in DNA double-strand break formation, micronuclei accumulation, and a marked reduction in cell viability. RNA sequencing followed by pathway enrichment analysis was performed to characterize the transcriptional response to ATR inhibition. Transcriptomic profiles from both cell lines support the hypothesis that successful completion of S phase and mitotic progression are critical determinants of survival following ATR inhibition. Further support for the hypothesis that mitotic progression is key to survival for ATR inhibited cells was obtained by treating with VE-822, paclitaxel, or the combination. Combined ATR and microtubule inhibition produced significant synergistic cytotoxicity in both UM models. Collectively, these findings identify ATR as a potential therapeutic vulnerability in uveal melanoma.

overall_design: 92.1 and MP38 uveal melanoma cells were treated for 72 hrs with either DMSO or VE-822. The VE-822 concentration was adjusted to achieve approximately 40% viability immediately after exposure when cells were lysed in RNAProtect and the RNA processed for RNA sequencing.

first: Geri

last: Traver

first: Kaely

last: Tornek


title: In vivo treatment of HT-29 xenografts with MV-CD46-muPA, Minnelide, or combination and NanoString nCounter analysis

city: miami

first: RIMPI

last: KHURANA

state: FL

address: Room 6112B, Rosenstiel Medical Science Building (RMSB),1600 NW 10th Avenue

institute: University of miami

summary: HT-29 human colorectal cancer xenografts were treated with vehicle control, MV-CD46-muPA, Minnelide, or MV-CD46-muPA + Minnelide combination. Three biological replicates per treatment group. RNA was extracted and analyzed using the nCounter Human Tumor Signaling 360 panel. RCC files are provided as raw data. Data were processed with nSolver 4.0 Advanced Analysis module with standard normalization and Benjamini–Hochberg correction.

overall_design: Experimental design includes 4 treatment groups (Control, MV-CD46-muPA, Minnelide, Combination) with 3 biological replicates each. Raw data are RCC files. Data processing includes normalization and statistical analysis in nSolver 4.0.

first: Valery

last: Chavez

first: Melissa

last: Montero

first: Ngoc

last: Tran

first: Carolina

middle: M

last: Mendes

first: Yuguan

last: Ban

first: Rimpi

last: Khurana

first: Michelle

last: Ceccarelli

first: Jaime

middle: R

last: Merchan