title: Trajectory-resolved human kidney organoid model defines OPFR developmental toxicity linked to adult CKD

status: Public on May 05 2026

city: Shanghai

first: Chenke

last: Xu

address: No. 2005, Songhu Road, Northwest of Xiangjiangqu City, Yangpu District

country: China

institute: Fudan University

type: Expression profiling by high throughput sequencing

summary: Human kidneys are highly vulnerable to environmental insults from gestation into adulthood, yet causal links between fetal chemical exposure and adult chronic kidney disease (CKD) remain difficult to establish because of decades-long latency and pervasive confounding in epidemiological study. As nephrogenesis establishes nephron endowment underlying fetal-origin adult-onset CKD, we developed a scalable, nephron-enriched, and trajectory-resolved human kidney organoid model using simple suspension culture approach. Using this model, we took organophosphate flame retardants (OPFRs), ubiquitous environmental contaminants in human embryos, as a representative class of chemical that disrupt nephrogenesis by specifically impairing the critical developmental transition underlying pre-tubular aggregation. We modeled our findings in organoids by treating pregnant mice with OPFR and followed the CKD-like phenotypes of their progeny later in adulthood. Together, this study establishes a kidney organoid model for assessing toxicity of an environmental chemical or a drug in nephrogenesis through mechanistically anchored “in-a-dish” testing.

overall_design: Bulk RNA-seq. Since stage 4 (in which pre-tubular aggregated) was identified as the specific stage that EHDPP affected during the development of renal (show in Results), the organoids after 2-day EHDPP exposure in stage 4 were collected for RNA-seq (n = 3). The quality and concentration of RNA were detected by a Nanodrop ND-1000 spectrophotometer (Nanodrop Technologies). RNA integrity number (RIN) was detected by Agilent 2100, and the RIN of > 7 qualified were used on RNA-seq. RNA-seq was achieved by the Beijing Genomics Institute. Poly A species were used to enrich RNA samples, and the libraries were constructed on the BGISEQ-500 platform (BGI). Sequencing depth of each library was approximate 40 million reads. SOAPnuke (v1.5.2), a software for FASTQ file filtering developed by the Beijing Genomics Institute, was used to filter the sequencing data, which treated all species in the same way. HISAT2 (v2.0.4) and Bowtie2 (v2.2.5) were used to map the reads against GRCh38.p12. Expectation-Maximization (v1.2.8) was used to calculated the gene expression levels. This study performed Gene Set Enrichment Analysis (GSEA) based on all expressed genes between the control and each exposure group. Two human collections of the molecular signatures database, sub-collection of C2 (curated gene sets) and canonical pathways (CP), were used for GSEA enrichment analysis. Sc-RNA-seq. For sample preparation, organoids were digested with Accumax (STEMCELL, 07921) for 10 min. Then, cells underwent washing and were subsequently resuspended in calcium- and magnesium-free 1X phosphate-buffered saline supplemented with 0.04% bovine serum albumin. A total of 15,000 viable cells were then used for scRNA-seq library preparation via the Chromium Next GEM Single Cell 3’ Kit v3.1 (10x Genomics, Catalog No. PN-1000268) and the Chromium Next GEM Chip G Single Cell Kit (10x Genomics, Catalog No. PN-1000127) according to the manufacturer’s protocol. All the libraries were pooled and sequenced via the 150 bp paired-end Illumina NovaSeq 6000 platform. Alignment and transcript quantification of the scRNA sequencing data were executed using the CellRanger count pipeline (version 8.0.1) with the mm39 reference assembly. Downstream integration of scRNA-seq datasets and cellular clustering analyses were conducted using the Seurat toolkit within the R statistical computing environment.

first: Lei

first: Xianlei

last: Jiang

first: Cheng

first: Jianying

last: Hu


title: Structural survey of HIF-2α reveals regulation of its subcellular localization and protein interactome

city: Lund

first: Stina

last: Östenberg

address: Sölvegatan 19

country: Sweden

institute: Lund University

summary: Hypoxia‑inducible factor 2α (HIF‑2α) is a central regulator of cellular homeostasis and a known oncogenic driver in multiple cancers. Although HIF‑2α is canonically defined as a nuclear transcription factor, its cytoplasmic presence and potential non‑transcriptional functions remain poorly understood. Here, we dissect the structural determinants of HIF‑2α localization, stability, and activity using a deletion‑construct library, transcriptional assays, and in vivo xenograft models. We show that the oxygen‑dependent degradation domain (ODD), and N‑terminal intrinsically disordered region (IDR) and transactivation domain (NTAD) promote cytoplasmic localization, whereas the C‑terminal IDR drives nuclear accumulation. Notably, we demonstrate that HIF‑2α nuclear localization occurs independently of ARNT dimerization, resolving a long-standing question in the field. While both NTAD and C‑terminal (C)TAD contribute to transcriptional activation, only CTAD mediates hypoxia responsive element (HRE)   transactivation, and neither domain is required for tumor growth in vivo. These data suggest a dominant role for non‑canonical cytoplasmic mechanisms in HIF‑2α-driven tumorigenesis. Proteomic analyses reveal HIF‑2α interactions with regulators of mitochondrial function, translation initiation, RNA splicing, vesicular transport, and DNA replication. Together, these findings uncover previously unrecognized structural and functional complexity of HIF‑2α and expand its role beyond canonical transcriptional regulation

overall_design: RNA-seq profiling of SK-N-BE(2) wild‑type cells and of cells transfected with full‑length HIF‑2α, ΔN‑CTAD, or Δc‑IDR to examine how distinct HIF‑2α structural variants reshape the transcriptomic landscape.

first: Tomas

last: Gregor

first: Sinan

last: Karakaya

first: Anja

last: Zethraeus

first: Elina

last: Fredlund

first: Charlotte

last: Welinder

first: Emma

last: Hammarlund

first: Jenny

last: Hansson

first: Jared

last: Rosenblum

first: Sofie

last: Mohlin


title: Host-Botrytis co-transcriptomics reveals finely tuned interactions with closely related legumes

city: Davis

first: Daniel

middle: J

last: Kliebenstein

state: CA

address: One Shields Ave

country: USA

institute: University of California Davis

summary: Generalist pathogens infect diverse plants, yet how these interactions differ across hosts is poorly understood. Here, we conduct a molecular analysis of a generalist pathogen interacting with closely related hosts. A co-transcriptomic framework is used to dissect host–pathogen interactions between the generalist necrotroph Botrytis cinerea and two closely related legume hosts, common bean (Phaseolus vulgaris) and cowpea (Vigna unguiculata). Using 72 diverse Botrytis isolates, we quantified lesion development alongside host and pathogen gene expression. Although lesion formation was driven primarily by pathogen genetic variation, transcriptomic responses in both host and pathogen exhibited significant host x isolate interactions. This indicated that extensive, fine-scale transcriptional plasticity created similar disease outcomes. Botrytis genes showing host-specific expression were enriched for cell wall–modifying enzymes and some specialized metabolic genes, indicating greater host responsiveness of these core virulence mechanisms than previously appreciated. Co-expression network analysis in both host and pathogen further showed that in both organisms, gene membership for individual networks are restructured in response to genetic diversity. Both legume species exhibited extensive isolate-dependent transcriptional reprogramming, with approximately two-thirds of expressed host genes responding to pathogen diversity. While conserved defense pathways such as jasmonate/ethylene signaling and phenylpropanoid metabolism were upregulated in both hosts, the specific genes in the networks differed markedly, highlighting lineage-specific rewiring of defense strategies. These results suggest that generalist pathogen success is underpinned by pervasive gene expression plasticity in both host and pathogen, allowing similar phenotypic outcomes to emerge from highly divergent molecular states.

sample_organism:
Phaseolus vulgaris
Vigna unguiculata

platform_organism:
Phaseolus vulgaris
Vigna unguiculata

overall_design: Co-transcriptomic profiling of 72 Botrytis isolates on 1 genotype of common bean and 1 genotype of cowpea at 48 hours after inoculation.

first: Anna

last: Muhich

first: Ritu

last: Singh

first: Cloe

last: Tom

first: Celine

last: Caseys


title: Spatial Analysis of T Cell Clonality in Autoimmune Kidney Disease Using TRV Probes

city: Hamburg

first: Robin

last: Khatri

address: Falkenried 94

department: Institute of Medical Systems Biology

country: Germany

institute: University Medical Center Hamburg-Eppendorf

summary: Hypothesizing that the localization of T cell clones correlates with immune function, our goal was to develop an unbiased method to study the spatial distribution of T cells in tissues. We created an in situ hybridization panel with 248 probes that identify immune and tissue cell types, and 132 probes for all variable TRAV, TRBV, TRGV, and TRDV gene segments. Applying this approach to analyze renal biopsies from patients with autoimmune kidney disease, combinations of TRV segments reliably provided spatial information about T cell clonality. Confined clusters of clonally related αβ T cells were found in proximity to increased numbers of antigen-presenting cells, B cells, and other T cells, reflecting local immune cell interactions. γδ T cells were more frequently located outside or at their periphery of T cell infiltration areas. In conclusion, integrating spatial information with TCR clonotype analysis provided new insights into the organization of immune responses at the tissue level.

overall_design: 2 slides containing 13 samples (3 control and 10 ANCA patients) were analyzed with Xenium

first: Cedric

last: Ly

first: Darius

middle: P

last: Schaub

first: Zeba

last: Sultana

first: Annika

last: Boxnick

first: Zheng

last: Song

first: Tobias

last: Huber

first: Thorsten

last: Wiech

first: Eva

last: Tolosa

first: Ulf

last: Panze

first: Stefan

last: Bonn

first: Christian

last: Krebs

first: Immo

last: Prinz


title: RNA-seq data from gingival crevicular fluid of pregnant women for gestational diabetes mellitus (GDM) prediction

city: Santiago

first: Gino

last: Nardocci

address: Av. Mons. Álvaro del Portillo 12.455

country: Chile

institute: Universidad de los Andes

summary: Gingival crevicular fluid samples were collected from pregnant women during the first trimester to investigate early transcriptomic changes associated with gestational diabetes mellitus (GDM). RNA-seq was performed to profile the complete gene expression landscape and identify predictive molecular signatures

overall_design: This study involved RNA-sequencing of gingival crevicular fluid (GCF) samples collected during the first trimester from 10 pregnant women, including 5 who later developed gestational diabetes mellitus (GDM) and 5 healthy controls. Samples were analyzed to identify differentially expressed genes associated with early GDM risk. Total RNA was extracted, and libraries were prepared using the Collibri Stranded RNA Library Prep Kit. Sequencing was performed on an Illumina HiSeq platform.

first: Alejandra

last: Chaparro

first: Maria

last: Bendek

middle: L

last: Mizgier

first: Carolina

last: Rojas

first: Valeria

last: Ramirez

first: Fernando

last: Bustos

first: Mattew

middle: W

last: Kemp

first: Mahesh

last: Choolani

first: Sebastian

middle: E

last: Illanes


title: NanoString nCounter Mouse PanCancer Immune Profiling of B16F10 tumors treated with DC vaccines

city: Cleveland

first: Jin Muk

last: Kang

state: OH

address: 2103 Cornell rd WRB 3501

institute: University Hospitals Cleveland Medical Center

summary: To examine the effect of PROTEXI  vaccination on the immunosuppressive nature of the tumor microenvironment (TME), the transcriptional signature of B16F10 tumors in the PROTEXI group with that of the control and DCTAA-vaccinated groups were compared at day 13. Total RNA was extracted from the tumors and subjected to differential gene expression profiling using the NanoString PanCancer Immune Profiling panel, consisting of 755 genes.

overall_design: The aim of the study was to profile immune-related gene expression using NanoString technology on isolated B16F10 tumors treated with DC-Trp2 or PROTEXI. B16F10 mice bearing tumor were treated with DC vaccines at Day 3 and 10 and then tumors were collected at Day 13.

first: Seunghwan

last: Lim


title: Maternal obesity remodels nutrient transporttranscriptional programs in early mouse embryonic and extraembryonic cell lineages

city: Toronto

first: Paul

last: Delgado Olguin

state: Ontario

address: 686 Bay Street

department: Translational Medicine

country: Canada

institute: The Hospital for Sick Children

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Maternal obesity increases the risk of congenital anomalies and later-life metabolic disease in offspring. Still, underlying mechanisms remain unclear, particularly in extraembryonic lineages at the maternal-fetal interface, which remain poorly studied. We jointly profiled gene expression and chromatin accessibility in single nuclei from mouse embryos and extraembryonic tissues in a diet-induced obesity model at embryonic day 8.5, when multiple organogenesis programs are underway. This analysis generated an atlas of 36 cell lineages, including derivatives of all three germ layers and trophoblast populations. Lineage allocation was preserved in embryos from obese dams. However, transcription was widely dysregulated. Oxidative phosphorylation genes were broadly suppressed, and genes involved in hypoxia, cytoskeleton remodeling, and cell migration were enriched among upregulated pathways. Chromatin accessibility changed in a few lineages, most notably in extraembryonic visceral endoderm and parietal trophoblast giant cells. Differently accessible chromatin was enriched in binding motifs for retinoic acid receptors. Indeed, genes involved in retinol and lipoprotein transport were suppressed, and RNA in situ hybridization confirmed reduced expression of retinol transporters Ttr, Rbp4, and Stra6, and lipoprotein transporter Apoa1 in visceral yolk sac. Thus, obesity during pregnancy causes early transcriptional dysregulation that impairs retinoic acid and lipoprotein transport at the maternal-fetal interface, suggesting a mechanism through which maternal obesity could influence long-term developmental outcomes.

overall_design: Following euthanasia of female mice through cervical dislocation, uteri were collected in ice-cold 1X PBS. Embryos were immediately dissected, and after careful staging by counting 8-12 somites, they were placed in cryogenic storage vials. Vials were snap-frozen by placing them in liquid nitrogen and were stored in liquid nitrogen tanks. Four (4) to five (5) embryos from the same stage and the same litter were pooled as individual samples. Three (3) samples from CT dams and three (3) samples from HF dams were collected for single-nuclei analysis.

first: Amalia

last: Caballero

first: Lijun

last: Chi

last: Delgado-Olguín


title: Transcriptomic profiling of spleen tissue in a mouse model of psoriasiform inflammation

city: 长沙

first: 烁琦

last: 张

address: 解放中路199号湘雅二医院有色院研究生宿舍

institute: 中南大学

summary: This study aims to characterize transcriptomic changes in the spleen of psoriasis-like mouse models induced by different experimental approaches. Psoriasis is a chronic inflammatory disease associated with systemic immune dysregulation beyond the skin. In this study, female BALB/c mice were used to establish psoriasis-like inflammation models via topical application of imiquimod (IMQ) to the dorsal skin (PSO-D) or ear (PSO-E), as well as IL-23-induced ear inflammation. Control mice (Con) received vehicle treatment. Spleen tissues were collected for RNA sequencing (RNA-seq) to investigate systemic immune responses. Total RNA was extracted from spleen tissues and subjected to high-throughput sequencing. Clean reads were aligned to the mouse reference genome (GRCm39), and gene expression levels were quantified. Differential expression analysis and functional enrichment analyses (including Gene Ontology and KEGG pathways) were performed. This dataset provides a comprehensive resource for understanding systemic immune alterations in different psoriasis-like models and may help elucidate mechanisms underlying immune dysregulation.

overall_design: RNA-seq profiling of spleen tissues from female BALB/c mice: untreated control, IMQ-induced dorsal psoriasis, IMQ-induced ear psoriasis, and IL-23-induced ear inflammation models, with 3–4 biological replicates per condition.

first: Shuo-Qi

last: Zhang

first: An-Hui

last: Zha

first: Wei-Yun

last: Shen


title: Spatial and Bulk Transcriptomic Profiling Defines the Molecular Evolution of Cutaneous Squamous Cell Carcinoma and Reveals Stage-Specific Biomarkers of Clinical Relevance [RNA-Seq]

city: Bordeaux

first: Hamid-Reza

last: Rezvani

address: 2 Rue Dr Hoffmann Martinot

country: France

institute: Bordeaux Institute of Oncology (BRIC)

summary: Background: Cutaneous squamous cell carcinoma (cSCC) is among the most common skin cancers and can be associated with poor prognosis in aggressive cases, with a median overall survival of approximately two years. Despite its well-described stepwise progression from actinic keratosis to invasive disease, robust molecular markers that discriminate disease stages and inform clinical decision-making remain limited. Objectives: This study aimed to delineate progression continuum and stage-related transcriptional programs underlying cSCC evolution, identify candidate biomarkers for risk stratification and invasion, and assess the broader relevance of these molecular signatures across human cancers. Methods: We applied bulk RNA sequencing (HTG EdgeSeq) and spatial transcriptomics (GeoMx DSP) to profile skin biopsies from 8 patients recruited in collaboration with Bordeaux University Hospital. Importantly, each patient simultaneously presented four stages (healthy skin, pre-malignant lesion, tumor core, and invasive front) providing a unique framework to interrogate the full molecular trajectory of cSCC progression within individuals. Results: Spatial transcriptomic analyses identified more than 2,000 differentially expressed genes (adjusted p < 0.01) whose expression in squamous cells changed across disease stages. These genes were organized into 18 coordinated expression programs reflecting progressive biological rewiring during tumor evolution. Pathways related to cellular stress responses, proliferation, extracellular matrix remodeling, and inflammation were progressively upregulated, whereas differentiation programs and lipid and amino acid metabolism were consistently downregulated.  In contrast, peritumoral macrophages showed increased expression of genes involved in purine metabolism, glycolysis, and pyruvate metabolism across progression. To assess the broader clinical relevance of the progression-associated gene programs, we developed a Snakemake-based pipeline to systematically screen 32 solid and hematological malignancies from The Cancer Genome Atlas. This workflow is designed to be fully reproducible and readily extensible, enabling other researchers to perform similar progression and survival analyses across cancer types. Notably, we defined a cSCC-progression signature which significantly correlated with poor overall survival (p  < 0.05) in 10 additional cancer types. Furthermore , we last identified 12 cSCC stage-specific biomarkers, whose expression was confirmed to be stage-specific via Visium HD. Conclusions: Together, this study provides a spatially resolved and stage-aware transcriptomic map of cSCC progression, identifies coordinated gene programs underlying disease evolution, and defines progression-associated signatures with prognostic relevance across multiple cancers, highlighting their potential clinical utility.

overall_design: HTG EdgeSeq (bulk RNA-seq) profiling of 8 patients bearing cutaneous squamous cell carcinoma tumors. Each patient has been biopsied for the tumor, actinic keratosis/in situ lesion, and healthy skin.

first: Sergio

last: Oterino-Sogo

first: Fatima

last: Naji

first: Jean-Philippe

last: Guegan

first: Marie

last: Beylot-Barry

first: Léa

last: Dousset

first: Macha

last: Nikolski

last: Redvani


title: RFX5 Mediates High-order Structures to Regulate Cancer Progression-Associated Genes [RNA-Seq]

first: Xiao

last: Ge

address: No. 800 Dongchuan Road

institute: Shanghai JiaoTong University

summary: RFX5 is a DNA binding protein known to regulate MHC genes expressions with little studies on its role in maintaining 3D genome architecture. Recent studies have shown its potential in mediating long-range interactions in specific regions, though the underlying mechanism remains poorly understood. Here, using genes related to cancer progression as a paradigm, we studied the role of RFX5 and found that it specifically regulates these genes. It mediates interactions between gene promoters and their distal enhancers, which can be several hundreds of kilobases apart. We also found that RFX5 regulates higher-order structures of TADs and compartments, which become unstable upon loss of RFX5. Our findings elucidate the fundamental role of RFX5 in maintaining proper chromosome architecture and shed light on the relationship between chromatin loops and gene expression.

overall_design: RNA-seq experiments measuring gene expression levels in RFX5 deleted cells and their wildtype control

first: Ge

last: Xiao

first: Zhang

last: Yijun

first: Wang

last: Yongming


title: MAPT-derived circTau6 induces tau pathogenesis and neurodegeneration by encoding Tau variants

city: Xiamen

first: Guangtong

last: Jiang

address: Xiang'an Campus,4221 Xiang'an South Road, Xiang'an District, Xiamen,Fujian, China.

institute: Xiamen University

summary: Imbalanced accumulation of microtubule-associated protein tau containing three or four repeat domains (3R or 4R tau species) is a core feature of tauopathies, which may result from alternative splicing of the MAPT mRNA. However, specific mechanisms yielding the imbalance were underinvestigated. Here, we identify a circular RNA (circTau6) derived from the MAPT gene in the human brain. CircTau6 was rolling-translated into novel 4R tau variants containing the second microtubule-binding repeat, namely cTau4R. The cTau4R proteins were intrinsically hyperphosphorylated and promoted phosphorylation of naive tau proteins derived from linear MAPT mRNA. Upregulation of cTau4R led to deposition of 4R and phosphorylated tau forms in human MAPT knock-in mice (hMAPT mice), accompanied by neuronal and synaptic damages, neuroinflammation, and cognitive deficits. Further, CircTau6 overexpression partially recapitulated molecular signatures that were seen in human tauopathic brains, and its expression was directly regulated by tauopathy-associated MAPT mutations. These findings identify the circTau6/cTau4R as an important post-transcriptional mechanism modulating tauopathy, which may be therapeutically targeted.

overall_design: RNA-seq profiling of hMAPT mouse hippocampus after AAV-circTau6 injection 80 days.

first: Lin

last: Shao


title: A NOTCH2 Pathogenic Variant Alters the Osteoblast and Vascular Cell Transcriptome of Mouse Femurs

city: Farmington

first: Ernesto

last: Canalis

state: CT

address: 263 Farmington Avenue

department: Orthopaedic Surgery

institute: UConn Health

summary: Pathogenic variants of NOTCH2 that lead to a gain or loss of function are associated with serious clinical consequences. A recently reported novel NOTCH2 4006G>C variant was associated with decreased Notch signaling and skeletal fragility in humans and mouse (Notch2em1Ecan) lines. In the present study, we analyze the transcriptome of femoral bones from mature control and Notch2em1Ecan mice following the exclusion of hematological cells. Single cells were analyzed following microfluidic partitioning on a Chromium X instrument using a 3' gene expression library. Uniform manifold approximation and projection (UMAP) for non-linear dimensional reduction defined 15 different cell clusters comprised of macrophages, red blood cells, endothelial, vascular and smooth and striated muscle cells and cells of the osteoblast lineage. Notch2 and Hes1 were the prevalent Notch receptor and target gene in most clusters. Independent clustering analysis of transcriptomes from control and Notch2em1Ecan femurs revealed a 35 – 45% decrease in cells forming the osteogenic and a 50 – 55% decrease in cells comprising the vascular cluster in Notch2em1Ecan femurs. Expression of Hes1 was decreased in Notch2em1Ecan cells. Analysis of nascent transcripts (intron/exon sequences) using the scVelo pipeline revealed suppressed velocity in vascular and osteogenic clusters from Notch2em1Ecan cells implying decreased transcription of genes constituting these clusters. In conclusion, a novel NOTCH2 deleterious variant associated with skeletal fragility alters the osteogenic and vascular transcriptome in femurs from adult mice.

overall_design: Control and Notch2em1Ecan female whole femurs at 6-9 months were flushed for marrow, subjected to ACK lysis buffer, and sorted by FACs for CD45 and TER119 negative cells.

first: Lauren

last: Schilling

first: Emily

last: Denker


title: RFX5 Mediates High-order Structures to Regulate Cancer Progression-Associated Genes [Hi-C]

overall_design: Hi-C experiments measuring global contact frequencies in RFX5 deleted cells and their wildtype control


title: RFX5 Mediates High-order Structures to Regulate Cancer Progression-Associated Genes [4C-Seq]

overall_design: QHR-4C experiments to calculate contact frequencies between gene promoters and their upstream or downstream enhancer fragments


title: Differential Expression of LncRNAs in Diabetic Corneal Neuropathy and Its Implications in Pathogenesis

city: Wuhan

first: Yuan

last: Zhang

address: No.169 Eastern lake Road

institute: Zhongnan hospital of Wuhan university

summary: Diabetic corneal neuropathy (DCN) is a common ocular complication of diabetes mellitus. To investigate transcriptomic alterations associated with DCN, we performed RNA sequencing of trigeminal ganglia from streptozotocin-induced DCN mice and age-matched control mice. This study aimed to characterize gene and long non-coding RNA (lncRNA) expression changes and provide a resource for exploring the molecular mechanisms of DCN.

overall_design: Trigeminal ganglia tissues were obtained from STZ-induced DCN mice and age-matched control C57BL/6J mice 4 months after diabetes induction.

first: Shan

last: Hu

first: Jizhen

last: Huang


title: Single-cell multi-omics analysis of TNFR1 and TNFR2 expression in human T-cells

city: Yerevan

first: Roman

middle: Yurievich

last: Perik-Zavodskii

state: Yerevan

address: Khorenatsi 1

department: Research and Development

country: Armenia

institute: PerikLab

summary: Tumor Necrosis Factor Alpha is a known pro-inflammatory cytokine that plays a key role in the pathogenesis of rheumatoid arthritis. Anti-cytokine therapies targeting Tumor Necrosis Factor Alpha have greatly succeeded in treating rheumatoid arthritis in many patients. Despite these developments, many of the mechanisms of Tumor Necrosis Factor Alpha action have yet to be uncovered. In this study, we incubated CD3+ T-cells from healthy donors and rheumatoid arthritis patients with Tumor Necrosis Factor Alpha and then performed their single-cell multi-omics analysis via BD Rhapsody.

overall_design: Human mononuclear cells were isolated by Ficoll density gradient centrifugation. T cells were isolated from the mononuclear cells using CD3 magnetic sorting. The resulting cells were then incubated with TNF-alpha and loaded into a BD Rhapsody Express.

first: Saleh

last: Alrhmoun

first: Olga

last: Perik-Zavodskaia


title: Liver Endothelial Zonation Orchestrates Hepatic Steatosis Onset through Retinoic Acid-regulated FGF1

city: Xi'an

first: Zhiqiang

last: Fang

state: Shaanxi

address: No.169,Changle West Road

institute: Xijing Hospital

summary: The contribution of liver sinusoidal endothelial cell (LSEC) zonation to metabolic dysfunction-associated steatotic liver disease (MASLD) pathogenesis remains undefined. We identified selective lipid deposition in the pericentral zone during early MASLD. Multi-omics analyses confirmed enhanced pericentral lipid metabolism in both hepatocytes and LSECs. Mechanistically, pericentral LSEC marker c-Kit transcriptionally activated FGF1 via nuclear receptor RXRG, which suppressed hepatocellular lipid accumulation through FGFR4 signaling. Remarkably, retinoic acid (RXRG’s endogenous ligand and active vitamin A metabolite) phenocopied FGF1’s anti-steatotic effects. Clinical data revealed an inverse correlation between dietary vitamin A and MASLD severity, suggesting therapeutic potential of vitamin A supplementation for early intervention.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for primary c-Kit positive and c-Kit negative LSECs isolated from a 12-week HFD diet-induced MASLD mice liver using c-Kit immunomagnetic beads

last: Wang


title: Flow induced-endothelial phenotypic transition contributes to Intracranial Aneurysm

city: Chengdu

first: Du

last: Lingyu

state: Sichuan

address: Yulin Street

institute: Sixhuan University

summary: Rupture of intracranial aneurysms (IAs) represents a life-threatening cerebrovascular event associated with high morbidity and mortality. Elucidating the pathological mechanisms driving IA initiation and progression is critical for developing an effective therapeutic strategy. Endothelial cell (EC) dysfunction is known to contribute to IA pathogenesis. Hemodynamic force— particularly fluid shear stress (FSS) are well-established mediators of IA pathogenesis, yet the mechanisms by which FSS triggers endothelial injury remain incompletely understood. In this study, single-cell sequencing of human revealed that endothelial-to-mesenchymal transition (EndMT) as a hallmark feature of early-stage IA formation, whereas EndMT was markedly attenuated in ruptured aneurysms. Using a mouse IA model and an in vitro parallel-plate flow chamber system, we demonstrated that exposure to high laminar FSS (HSS) promotes EndMT in endothelial cells, concomitant with actin cytoskeletal reorganization and nuclear translocation of Yes-associated protein (YAP). In contrast, under low or vortex flow (VSS) conditions characteristic of advanced IA stages, endothelial cells undergo phenotypic reversion—evidenced by reduced expression of cytoskeletal proteins and cytoplasmic sequestration of YAP. Notably, endothelial inflammation escalates progressively throughout IA development and contributes directly to sustained endothelial dysfunction. Pharmacological inhibition of actin polymerization effectively suppressed EndMT in the early stage but failed to restore endothelial integrity during the late stage. Collectively, these findings identify FSS–cytoskeleton–YAP–EndMT axis as a stage-specific, druggable pathway with translational potential for early intervention in intracranial aneurysm disease.

overall_design: Cells cultured on glass coverslips were exposed to flow using a parallel-plate flow chamber system (CellShear™, Chengdu Lixiang Biotechnology Co., Ltd., China). By reviewing the literature, we determined the three mechanical magnitudes and methods involved in this study[30]. The PSS group represents the normal physiological cerebrovascular fluid shear force, with a laminar flow size of 10 dyne/cm2; the HSS group represents the early stage of IA, as IA often forms at vascular bifurcations, where there is a higher fluid shear force, so it is set at a laminar flow of 20 dyne/cm2; and the VSS group represents the late stage of IA, at which the tumor forms and enlarges, with a large amount of blood flowing into the tumor cavity in an irregular vortex state, and the shear force is significantly reduced, so it is set at a vortex of 0.5 - 2 dyne/cm2.

first: Yang

last: Shen

first: Fei

first: Guixue

first: Lingyu

last: Du


title: Astrocyte circadian regulation in neurodegeneration: in vivo BMAL1 occupancy mapping using MACS-Calling Cards

city: St. Louis

first: India

last: Reiss

state: Missouri

address: 660 S. Euclid Ave.

department: Genetics

institute: Washington University in St. Louis

summary: Astrocytes maintain neuronal homeostasis through cellular programs that are frequently disrupted early in neurodegenerative disease, many of which are regulated by the circadian clock. The core clock transcription factor BMAL1 is required for normal astrocyte function, yet whether its regulatory activity is altered during neurodegeneration remains unclear. BMAL1 expression changes in disease are often inconsistent, suggesting that transcription factor binding, rather than expression levels, may be a more informative readout of BMAL1 function. We used a CLN3Δex7/8 model of neurodegeneration, which exhibits early astrocyte dysfunction prior to widespread neuronal loss, to test whether degenerative pathology reprograms BMAL1 binding in astrocytes. We developed an in vivo strategy to record transcription factor genomic occupancy specifically in astrocytes (MACS-Calling Cards, MACS-CC) and used it to map BMAL1 binding in wild-type and CLN3Δex7/8 mice. BMAL1 binding was extensively redistributed, with comparable numbers of wild-type–specific and disease-specific sites. Wild-type-specific BMAL1 binding was enriched near genes involved in circadian regulation and astrocyte differentiation, whereas disease-specific sites lacked coherent functional enrichment. Consistent with these changes, RNA-seq of sorted astrocytes revealed reduced expression of mature astrocyte markers in CLN3Δex7/8 mice. To define the mechanisms underlying BMAL1 retargeting in CLN3Δex7/8 astrocytes, we tested whether changes in chromatin accessibility could explain disease-associated gains and losses of BMAL1 binding. Although chromatin accessibility was broadly remodeled, differential accessibility did not predict BMAL1 binding gains or losses. Instead, motif analyses supported a model in which loss of normal cooperative transcription factor partnerships contributes to BMAL1 retargeting. Together, these findings demonstrate that MACS-CC enables in vivo TF occupancy mapping in astrocytes and reveals the mechanisms behind early rewiring of circadian regulatory programs within a model of neurodegeneration.

overall_design: BMAL1 Calling Card, Mnase-seq, and RNA-seq datasets from astrocytes (enriched from MACS), as well as BMAL1 Calling Card datasets from HepG2 cells.


title: RFX5 as a regulator of spatial chromatin contacts and gene expression

first: Xiao

last: Ge

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

overall_design: Refer to individual Series


title: Dietary supplementation with ursolic acid preserves skeletal muscle mass and strength in mouse models of cancer cachexia [RNA-seq]

city: Gainesville

first: Andrew

middle: R

last: Judge

state: FL

address: 1275 Center Drive, Biomedical Sciences Building RM J303

institute: University of Florida

summary: Skeletal muscle atrophy is a devastating and defining feature of cancer cachexia that reduces quality of life, treatment tolerance, and survival, but cannot be prevented or reversed by current management strategies. Ursolic acid is a natural dietary compound that has been shown to inhibit atrophy-associated changes in skeletal muscle mRNA expression in rodents and dogs, leading to beneficial changes in skeletal muscle structure and function.  We hypothesized that dietary supplementation with ursolic acid might help support skeletal muscle mass and function during cancer.  To test this hypothesis, we investigated ursolic acid's effects in five in vivo mouse models of cancer cachexia that are driven by pancreatic, colon, and lung cancer cells of mouse and human origin.  We found that dietary supplementation with ursolic acid has broad-spectrum effects towards cancer-induced skeletal muscle atrophy, significantly preserving muscle mass in all five cancer cachexia models.  Ursolic acid's positive effects on muscle mass and muscle fiber size led to significant improvements in grip strength and muscle tetanic force, persisted in the presence of chemotherapy, and were not associated with discernable changes in food intake or tumor growth.  Ursolic acid appeared to generate its beneficial effects in skeletal muscle by acting directly on muscle cells, inhibiting catabolic effects of tumor-derived secreted factors, and inhibiting > 90% of cancer-induced changes in skeletal muscle mRNA expression.  These results strongly nominate ursolic acid as a promising potential nutritional approach for supporting muscle mass and function in individuals with cancer.

overall_design: To test the hypothesis that ursolic acid might have similar effects in skeletal muscle of mice with pancreatic cancer, we isolated tibialis anterior muscles from KPC tumor-bearing animals who had received either standard chow or standard chow supplemented with ursolic acid.  As a negative control, we isolated tibialis anterior muscles from tumor-free animals who had received standard chow lacking ursolic acid.  We then performed comprehensive transcriptomic analyses (RNA-Seq) on the muscles from the three groups of mice (cancer-free control animals, cachectic KPC tumor-bearing animals with cancer-induced muscle atrophy, and KPC tumor-bearing animals who received dietary supplementation with ursolic acid).

first: Jeremy

middle: B

last: Ducharme

first: Scott

middle: M

last: Ebert

first: Miles

last: Cameron

first: Martin

last: Schonk

first: Chandler

middle: S

last: Callaway

middle: C

last: D'Lugos

first: John

last: Talley

first: Sarah

first: Christopher

last: Adams


title: Sphingosine Kinase-2 Inhibition Increases Acetyl-CoA Carboxylase Activity and Phosphatidylcholine Levels to Program Immunogenicity in Myeloid-Derived Suppressor Cells [RNA-seq]

city: Charleston, SC

first: Paramita

last: Chakraborty

address: 171 Ashley Avenue

institute: Medical University of South Carolina

summary: Myeloid-derived suppressor cells (MDSCs) in the tumor microenvironment (TME) are a major barrier to adoptive T cell therapy, underscoring the need to enhance T cell efficacy by overcoming immunosuppression. Here, we investigated how sphingosine-1-phosphate (S1P), an abundant signaling lipid in the TME, regulates the programming and function of MDSCs. We show that inhibition of sphingosine kinase-2 (SphK2), which generates S1P in MDSCs, reduces their suppressive activity and enhances antigen presentation. Pharmacological inhibition of SphK2 improved the response to anti-PD1 therapy in preclinical models of checkpoint-resistant breast, bladder, and melanoma cancers by mitigating MDSC- mediated suppression, thereby limiting tumor progression. Mechanistically, S1P directly interacts with Acetyl-CoA Carboxylase 1 (ACC1) to inhibit its activity, altering fatty acid and glycolytic pathways. Lowering intracellular S1P restores ACC activity and promotes phosphatidylcholine synthesis, reducing the immunosuppressive phenotype of MDSCs. These findings highlight the SphK2/ACC/phospholipid axis as a promising therapeutic target in cancer immunotherapy.

overall_design: This study was designed to define the transcriptional programs regulated by sphingosine kinase 2 (SphK2) in tumor-induced myeloid-derived suppressor cells (MDSCs) in vivo. Sphk2 wild-type (WT) and Sphk2 knockout (KO) mice were challenged with EL4 tumor cells, and MDSCs were isolated from ascitic fluid 14 days after tumor implantation. Freshly flow-sorted MDSCs from tumor-bearing WT and Sphk2 KO mice were subjected to RNA sequencing to identify gene expression changes associated with SphK2 deficiency in the tumor microenvironment. This design enables direct comparison of genotype-dependent transcriptional programs that regulate immune suppression, metabolic adaptation, and inflammatory signaling in tumor-driven MDSCs.

first: Shikhar

last: Mehrotra


title: A conserved Notch-Meis1-Pbx cascade specifies secretory progenitors into spatially diverse intestinal best4+ cells

city: Bethesda

first: Jeffrey

middle: Allen

last: Farrell

state: MD

address: 6 Center Drive (6A/1A06)

department: Division of Developmental Biology

institute: National Institute of Child Health and Human Development

summary: best4+ cells are a recently described vertebrate intestinal epithelial cell type. best4+ cells are reduced in inflammatory bowel disease and transcriptionally altered in colorectal cancer, suggesting that stimulation of their homeostatic replenishment may have therapeutic potential. However, it is unclear what function best4+ cells perform or how they develop, which is crucial to understand to therapeutically manipulate them. Since best4+ cells are evolutionarily lost in mice, here we established zebrafish as a tractable in vivo model to observe, manipulate, and remove best4+ cells in an organismal context. We dissected best4+ cell developmental regulation in vivo from birth to differentiation and specialization, focusing on factors that we show are evolutionarily conserved in best4+ cells across vertebrates. We demonstrate with lineage tracing that best4+ cells arise from secretory progenitors, where Notch/Dll4 signaling mediates a decision between best4+ and enterochromaffin cells by triggering expression of meis1b. Following specification by meis1b, we identify a role for pbx3a in the spatial diversification of best4+ cells, which develop regional heterogeneity in gene expression and intracellular pH that implies potential functional specialization. Together, in vivo live imaging, in vivo removal of best4+ cells, and non-autonomous effects on goblet cells suggest these cells have a sensory or communicative function. Altogether, this study experimentally delineates a comprehensive best4+ cell developmental program and develops a genetic toolkit to dissect their function in vivo, both of which will be instrumental to understand how best4+ cells are altered in disease and to stimulate the birth of new best4+ cells in patients.

overall_design: To investigate the role of candidate transcription factors meis1b and pbx3a in best4+ cell development, we performed scRNAseq on dissected intestines from 6 dpf meis1b and pbx3a mutant zebrafish larvae and their wild-type (WT) siblings. Droplet emulsions of single cell capture were generated using the 10X Genomics Chromium controller with Single Cell 3’ v3.1 consumable reagents for pbx3ay731 mutant samples, and the 10X Genomics Chromium GEM–X platform with Single Cell 3’ v4 reagents for the meis1by730 mutant samples.

first: Abhinav

last: Sur


title: RFX5 Mediates High-order Structures to Regulate Cancer Progression-Associated Genes [ChIP-Seq]

city: Shanghai

overall_design: ChIP-seq experiments to test binding patterns of transcription factor CTCF, RAD21, RFX5 and active enhancer mark of H3K27ac

first: Ge

last: Xiao

first: Zhang

last: Yijun

first: Wang

last: Yongming


title: Lipodystrophy and recovery are mediated by the Wnt/lipogenesis axis during skin fibrosis.

city: Oklahoma City

first: Michael

middle: C.

last: Rudolph

state: OK

address: 975 NE 10th St. BRC North rm 364

department: Biochemistry and Physiology

institute: OUHC

summary:
Acquired lipodystrophy in the dermal white adipose tissue (DWAT) is an early phenotype of skin fibrosis, followed by accumulation of extracellular matrix (ECM). Lipodystrophy syndromes are estimated to affect 1 in 20,000 people and are associated with metabolic
comorbidities. Recently, we showed that fibrosis-associated lipodystrophy is dependent on sustained Wnt signaling, but the mechanisms remain unclear. Transcriptomic profiling of mature dermal adipocytes in vivo reveal that Wnt activation downregulates the de novolipogenesis (DNL) axis enzymes within 48 hours. We found that protein expression of Fatty Acid Synthase (FASN), a key DNL enzyme, is dependent on sustained Wnt activation in vitro and in vivo. In bleomycin model, human SSc (< 1year of disease) and  keloids, FASN is significantly downregulated. Remarkably, FASN inhibition in mouse during reversal from Wnt induced fibrosis impeded recovery of DWAT lipid content and ECM topography. All together, we demonstrate that acquired lipodystrophy in the context of skin fibrosis is mediated by a new role of the Wnt-DNL axis. These findings underscore the importance of this pathway in lipodystrophy and fibrosis, opening new avenues for therapeutic targets in skin fibrosis.

overall_design: Bulk RNA-Seq profiling of intradermal adipocytes isolated from the floating fraction of mouse dorsal skin collagenase digest at 0-days (control), 2-days and 5-days of beta-catenin/WNT activation in mice

first: Suneeti

last: Madhavan

first: Radhika

last: Atit


title: RFX5 Mediates High-order Structures to Regulate Cancer Progression-Associated Genes [ATAC-seq]

first: Xiao

last: Ge

overall_design: ATAC-seq experiments measuring chromatin accessibility in RFX5 deleted cells and their wildtype control


title: Engineered probiotics limit T-cell driven CNS autoimmunity by activating AHR-KLF4-FADS3 signaling in intestinal dendritic cells

city: Boston

first: Zhaorong

last: Li

address: 60 Fenwood Road

institute: Dana Farber Cancer Institute

summary: Dendritic cells (DCs) control the induction of effector immune responses and tolerance. The development and function of DCs is regulated by transcriptional, epigenetic and metabolic programs, but the mechanisms controlling DC metabolism and its impact on autoimmune diseases remain poorly understood. Here, using single-cell and bulk RNA-sequencing, in vivo DC-specific gene perturbations, multiple sclerosis (MS) clinical samples and preclinical models, we identified an aryl hydrocarbon receptor (AHR) - Krüppel-like factor 4 (KLF4) - fatty acid desaturase enzyme 3 (FADS3) axis which drives the production of docosahexaenoic acid (DHA) in DCs and limits effector T-cell responses and the development of experimental autoimmune encephalomyelitis (EAE). Furthermore, we used synthetic biology approaches to engineer a probiotic (EcNIAA) that produces the AHR agonist indole-3-acetic acid (IAA) as a tool to limit pathogenic inflammatory responses. EcNIAA administration activates AHR-KLF4-FADS3 signaling in intestinal DCs, increasing DHA production and suppressing encephalitogenic T cells that originate in the gut and migrate to the central nervous system to promote autoimmune pathology. Briefly, we identified a novel immunometabolic axis that operates in DCs to limit effector T-cell responses, and can be targeted with engineered probiotics to treat autoimmunity.

overall_design: Dendritic cells were sorted from CNS and spleen of FADS3 KO mice and WT mices

first: Carolina

last: Polonio

first: Francisco

last: Quintana


title: RNA-seq gene expression data for Synechococcus sp. WH8102 under continuous  high, mid, and low phosphorus treatments in laboratory EFB experiments in 2025

city: Tucson

first: ALBA

last: FILELLA FILELLA LOPEZ DE LAMADRID

state: Arizona

address: 1007 E Lowell St.

department: MCB

institute: The University of Arizona

summary: Polyphosphate (polyP) is a ubiquitous and evolutionarily conserved form of phosphorus (P) present in all living organisms, yet its role in cellular and biogeochemical P cycling remains poorly constrained. In P-depleted marine environments, polyP consistently represents a larger fraction of total particulate P (TPP) than in P-replete environments. This P deficiency response is paradoxical under the classical view of polyP as a luxury storage compound, highlighting a longstanding unresolved discrepancy. Whether the elevated polyP:TPP ratio reflects active accumulation under P stress or simply the persistence of this intracellular pool has never been directly tested under steady-state conditions. Using continuous cultures of the globally important marine cyanobacterium Synechococcus sp. WH8102, we address this knowledge gap. While P availability strongly affected growth rates, single-cell C:N:P stoichiometry and the expression of P-stress genes, polyP:TPP increased with decreasing growth rate, reproducing the pattern observed in oligotrophic marine environments. This shift was not driven by polyP accumulation; instead, cellular polyP concentrations remained relatively stable across growth rates (ANOVA, p = 0.16), while other intracellular P pools—including RNA, free Pi, ATP and phospholipids—were preferentially depleted with decreasing P availability (ranging from 2.6- to 11.8-fold, respectively), increasing the relative contribution of polyP to total cellular P. Gene expression analysis revealed  little transcription differences between polyP-metabolism associated genes. These results indicate that cellular polyP content is maintained independently of growth rate under steady-state conditions, suggesting that P deficiency responses observed in oligotrophic environments and various microorganisms in batch culture reflect slow-growing physiology (differential pool lability over selective polyP retention), with consequences for interpreting particulate P stoichiometry and export.

overall_design: Genome-wide transcriptional responses (RNA-Seq) of the marine picocyanobacterium Synechococcus sp. WH8102 under three steady-state phosphate regimes (Low-P 1 µM, Mid-P 5 µM, High-P 36 µM) using exponentially fed-batch cultures, to investigate how phosphorus availability shapes cellular physiology and P-related metabolic processes.

first: Alba

last: Filella

first: Solange

last: Duhamel

first: Julia

last: Diaz

first: Mariona

last: Segura-Noguera

first: Adriana

last: Gomez-Buckley

first: Paul

last: Carini


title: NeuID is a novel neuron-specific lncRNA that regulates neuronal function in Alzheimer’s disease [ChIP-seq]

city: Göttingen

first: Andre

last: Fischer

state: NDS

address: Von-Siebold-Str. 3a

department: Epigenetics and Systems Medicine in Neurodegenerative Diseases

institute: DZNE Göttingen

summary: Non-coding RNAs are transcripts that do not encode proteins and comprise 98.5% of the human transcriptome. Among these, long non-coding RNAs (lncRNAs) have been implicated in various biological functions, including the control of gene expression and translation. The central nervous system (CNS) harbors a diverse array of lncRNA transcripts, yet the functions of many remain largely unexplored. In this study, we employed FANS with total RNA-sequencing and single-nuclei RNA sequencing approaches using human and mouse brain tissue to identify novel lncRNAs specific to neurons, and potentially associated with neurodegenerative diseases. We discovered a novel brain-specific lncRNA, the we named 'NeuID', that is specifically expressed in neuronal cells in the mouse and human brains. NeuID expression was found to be reduced in the brains of Alzheimer’s disease (AD) patients. Knockdown (KD) of NeuID resulted in the downregulation of synaptic plasticity genes. Additionally, NeuID KD led to decreased dendritic spine density and reduced neuronal network activity in MEA recordings. Furthermore, we demonstrate that NeuID interacts with EZH2, a component of the PRC2 complex, and mediates the h3k27me3 levels of Olig2 transcription factor. Notably, CRISPRa mediated overexpression of NeuID resulted in the rescue of functional impairment caused by AD-related pathological Aβ oligomers. Overall, our findings identify a novel brain and neuron-exclusive lncRNA that regulates neuronal function, is dysregulated in AD, and might be a potential therapeutic target against neuronal pathology in AD.

overall_design: h3k27me3 ChIP-seq profiling from primary hippocampal neurons treated with either control gapmers or NeuID gapmers to knockdown NeuID

first: Ranjit

last: Pradhan

first: Sadman

last: Sakib

first: Iga

last: Grzadzielewska

first: Eren

last: Diniz

first: Dennis

last: Krueger

first: Sophie

last: Schroeder

first: Susanne

last: Burkhardt

first: Anna-Lena

last: Schuetz

first: Jelena

last: Radulovic

first: Farahnaz

last: Sananbenesi

first: André


title: Deoxynivalenol and Porcine Reproductive and Respiratory Syndrome Virus (PRRSV) co-exposure aggravated UPR response in Marc-145 cells through PERK-ATF4 pathway

city: Jinzhong

first: Ruiyan

last: Niu

address: Shanxi Agricultural University, Taigu District, Jinzhong City, Shanxi Province

institute: Shanxi Agricultural University

summary: The project focuses on investigating the mechanisms underlying the effects of co-exposure to DON and PRRSV on Marc-145 cells.

overall_design: Marc-145 cells were infected with a MOI of 1 for PRRSV. The inoculum was removed after a one-hour viral adsorption period, and the cells were thoroughly washed in PBS. Four experimental groups were created: Group C, which received only maintenance medium; Group D, treated with 15 μg/mL DON in anhydrous ethanol; Group V, treated with PRRSV and maintenance medium; and Group VD, treated with both 15 μg/mL DON and PRRSV for 48 hours.

first: Shaosan

last: Zhang

first: Jiahui

last: Mi


title: HSF1 and YTHDC1 facilitate DNA damage repair upon heat stress by promoting the expressions of repair related genes

city: Beijing

first: Qidong

last: Deng

address: No.5 Yiheyuan Road Haidian District, Beijing 100871 P.R. China

department: School of Life Sciences

institute: Peking university

summary: External stressors, especially heat stress, always lead to DNA damage and genome instability in cells. However, how cells rapidly response to these DNA damage remains largely unknown. In this study, we found that the major transcription factor in heat shock response, HSF1, activated several NHEJ pathway related genes, especially NHEJ1, through the puncta it formed, thereby promoting the NHEJ pathway, reducing the DNA double-strand break upon heat stress. Furthermore, RNA m6A modification and its reader YTHDC1 were also found to play a role in this process, promoting the splicing of the NHEJ1 gene. Depletion of HSF1 or YTHDC1 led to increased nuclear γH2AX intensities in the heat shocked cells, which was rescued by overexpression of NHEJ1. Besides, overexpression of HSF1 or YTHDC1 both caused increased NHEJ pathway level in the heat shocked cells, indicating the HSF1/YTHDC1 – NHEJ1 – DNA double-strand repair axis. Our findings investigate an approach through which cells repair their damaged DNAs in the heat shock response, offering a new insight of how cells maintain a bare-minimum genome stability when exposed to external stressors.

overall_design: To investigate the impact of m6A and YTHDC1 on the NHEJ pathway related genes during heat shock response, we performed RNA-seq for not-heat shocked (NHS) U2OS cells treated with siCtrl, heat shocked (HS) U2OS cells treated with siCtrl and HS U2OS cells treated with siYTHDC1, as well as methylated RNA immunoprecipitation sequencing (MeRIP-seq) for U2OS cells.

first: Wenqing

last: Ding

first: Tianyu

last: Wang


title: Deciphering molecular underpinnings of cell state and state transitions with a global cell-state manifold

city: Cambridge

first: Reuben

last: Saunders

state: MA

address: 455 Main St

institute: Whitehead Institute

summary: Mammalian organisms comprise numerous types of cells with distinct gene-expression states, which arise from single zygotes differentiating on a complex landscape of cell states. The surge of single-cell transcriptomic data from human and other animals offer the possibility of constructing a global cell-state map, which will be foundational for understanding the molecular basis of normal tissue functions and dysfunction in diseases. However, this challenging task requires computationally efficient integration of many large datasets and accurate removal of artifactual batch effects while preserving true biological variations. Here, we developed a contrastive learning model that combines the strong batch-correction power of pairwise integration with the computational scalability of deep learning and used this model to construct a global cell-state map from human and mouse single-cell transcriptomic data. This model outperforms other state-of-the-art foundation models for batch correction and dataset integration. The resulting global cell-state manifold enables projection and annotation of cell states, generation of cell-state trajectories, and prediction of causal genes driving cell-state transitions. To further illustrate its power for understanding the molecular basis of cell-state transitions, we performed genome-scale perturb-seq experiments on human embryonic stem cells and systematically mapped the cell states induced by genetic perturbations to the global cell-state manifold. We identified gene programs that are differentially regulated both under normal development and upon genetic perturbations and distinct classes of perturbation-induced cell-state transitions that are aligned with or orthogonal to normal cell differentiation. The global cell-state manifold and related computational tools provide a powerful resource for understanding cell states and transitions in health and disease.

overall_design: Genome-scale CRISPRi Perturb-seq experiment in hESCs. Cells were transduced with a lentiviral library targetting thousands of genes and were analyzed by scRNA-seq.

first: Xingjie

last: Pan

first: Joseph

last: Replogle

first: Jonathan

last: Weissman

first: Xiaowei

last: Zhuang


title: single-cell spatial analysis reveals molecular mechanisms underlying immune cell organization and cancer cell heterogeneity in HPV-associated oropharyngeal carcinoma [xenium]

first: Cem

last: Sievers

address: 10 Center Drive

institute: NIH

summary: We combined spatial gene expression profiling with single-cell RNA-sequencing to study cellular organization in HPV-associated oropharyngeal carcinoma. The single-cell spatial gene expression portion of the study is described and provided in this deposition.

overall_design: Clinical (tissue) specimens were collected from patients with newly diagnosed, previously untreated HPV-related OPSCC referred to the NIH Clinical Center for consideration of clinical trials or from patients undergoing standard of care procedures following verbal and written informed consent under an IRB-approved biospecimen protocol (NCT03429036) and subjected to spatial gene expression profiling using the 10x Genomics Xenium platform.

first: Clint

last: Allen

first: Charalampos

last: Floudas


title: Complement Factor H maintains macrophage homeostasis through TRPM7 signaling

city: Buffalo

first: Jessy

last: Alexander

state: NY

address: 875 Ellicott Street

department: Medicine

institute: University at Buffalo

summary: Factor H (FH) is a critical regulator of the alternative complement pathway preventing uncontrolled complement activation. Its role in mitigating complement-mediated injury is evident in diseases such as dense deposit disease and age related macular degeneration characterized by significant macrophage (Mo) infiltration. While primarily synthesized in the liver, FH is also produced by other cells, including monocytes and Mos. However, the influence of FH on these cells remains incompletely understood. This study explores the functions of FH in rodent bone marrow-derived Mos, revealing FH-dependent regulation of genes linked to proliferation and inflammation, including C3aR, the receptor for C3a generated on complement activation. Further, our findings demonstrate that intrinsic FH deficiency in Mos enhances proliferation, trafficking, migration, and reduces phagocytosis. FH-deficient Mos exhibit metabolic alterations characterized by reduced oxidative phosphorylation and glycolysis. Notably, our results show for the first time that FH in Mos influences non-canonical functions through downstream C3a/C3aR signaling, modulating calcium levels and the activity of transient receptor potential cation channel, subfamily M, member 7 (TRPM7). Inhibiting TRPM7 activity with FTY720 reduces Mo proliferation, and blocking C3a/C3aR signaling mitigates TRPM7-related alterations and proliferation in Mos. In summary, this study highlights FH's functional relevance in maintaining homeostasis in Mos, where it modulates functions in a cell-autonomous manner, regulating TRPM7 through C3a/C3aR signaling pathways, offering therapeutic avenues for kidney disease and other inflammatory conditions.

overall_design: We used cultured rodent bone marrow derived macrophages (Mos) from FH sufficient and deficient mice to investigate the role of FH (n=3/group).

first: Shane

last: Fraher

first: Hyndevi

last: Dokuri

first: Ramkumar

last: Thiyagarajan

first: Kathryn

middle: A

last: Hausknech

first: Matthew

last: Sartori

first: Roh-Yu

last: Shen

first: Daniel

last: Fisher

first: Sharon

last: Evans

first: Alexander

last: Jacob

middle: I

last: McSkimming

first: Richard

last: Quigg


title: Aberrant brain-type neuronal programs in large-cell pancreatic neuroendocrine carcinoma

city: Berlin

first: Michael

last: Sigal

address: Augustenburger Platz 1

department: Dept. Hepatology and Gastroenterology

institute: Charité Universitätsmedizin

summary: High-grade pancreatic neuroendocrine carcinoma (panNEC) is a rare, aggressive cancer with limited tissue availability. Single-nucleus transcriptomics of five large-cell panNECs revealed two interesting neuroendocrine cell states: one highly proliferative with an aberrant brain-specific neuronal differentiation program and another stress-responsive state enriched for heat stress, hypoxia, and glycolysis. Our findings suggest potential therapeutic vulnerabilities, highlighting the need to evaluate the efficacy of combination therapies.

overall_design:
Fresh-frozen tumors from human high-grade neuroendocrine tumors were selected and subjected to snRNA-seq

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Raw files for human/patient samples are being made available in EGA (https://www.ebi.ac.uk/ega/) for controlled access to the personally identifiable sequence data.
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first: Olivia

last: Debnath

first: Hilmar

last: Berger

first: Katharina

last: Detjen

first: Phillip

last: Kirchner

first: Ilaria

last: Mariononi

first: Thomas

last: Conrad

first: Bertram

last: Wiedenmann

first: Aurel

last: Perren

first: Naveed

last: Ishaque

first: Ines

last: Eichhorn

first: Felix

last: Bolduan


title: Transcriptional profiling of hippocampus from a zQ175 KI mouse model of Huntington's disease treated with either HTT-10150 siRNA targeting full-length HTT or combination of HTT-634 and HTT-486 siRNAs targeting HTT1a

city: Princeton

first: Jeff

last: Aaronson

state: New Jersey

address: 155 Village Boulevard, Suite 200

department: Discovery & Systems Biology

institute: CHDI

summary: In this study, we conducted a comprehensive transcriptional profiling of the hippocampus utilizing a zQ175 knock-in (KI) mouse model of Huntington's disease, which was treated with either HTT-10150 siRNA specifically designed to target the full-length huntingtin (Htt) mRNA or combination of HTT-634 and HTT-486 siRNAs targeting HTT1a. Our investigation aimed to assess the impact of this intervention across different time points.

overall_design: The study involved four treatment groups: untreated mice, mice treated with non-targeting siRNA (NTC), mice administered with HTT-10150 siRNA  and mice treated with both HTT-634 and HTT-486 siRNAs. Three distinct treatment strategies were employed: 2[4]6 - treatment at 2 months, tissue collection at 6 months; 6[4]10 -  treatment at 6 months, tissue collection at 10 months; 2+6[8]10 - treatment at 2 and 6 months, tissue collection at 10 months. Hippocampal samples were collected from both zQ175 and wild-type mice. In total 192 samples were analyzed: four mice for each genotype/gender/treatment group.

first: Aikaterini

last: Papadopoulou

first: Gillian

last: Bates


title: Transcriptional profiling of striatum from a zQ175 KI mouse model of Huntington's disease treated with HTT-10150 siRNA targeting full-length Htt

summary: In this study we conducted a comprehensive transcriptional profiling of the striatum utilizing a zQ175 knock-in (KI) mouse model of Huntington's disease, which was treated with HTT-10150 siRNA specifically designed to target the full-length huntingtin (Htt) mRNA. Our investigation aimed to assess the impact of this intervention across different time points.

overall_design: The study involved three treatment groups: untreated mice, mice treated with non-targeting siRNA (NTC), and mice administered with HTT-10150 siRNA. Three distinct treatment strategies were employed: 2[4]6 - treatment at 2 months, tissue collection at 6 months; 6[4]10 -  treatment at 6 months, tissue collection at 10 months; 2+6[8]10 - treatment at 2 and 6 months, tissue collection at 10 months. Mouse striatal tissue samples were collected from zQ175 and wild type mice. In total 143 samples were analyzed: four mice for each genotype/gender/reatment group with the exception of wild type mice treated with HTT-10150 2+6[8]10 (2 females, 5 males)


title: Single-cell transcriptomics of bronchoalveolar lavage reveals divergent macrophage subpopulations and trajectories in interstitial lung disease

city: Darlinghurst

first: Peter

last: Allen

state: New South Wales

address: 384 Victoria Street

country: Australia

institute: Garvan Institute of Medical Research

summary: RATIONALE: Interstitial lung diseases (ILDs) encompass a diverse range of fibrotic conditions and contribute to significant respiratory morbidity and mortality. Assessment of the cellular composition of bronchoalveolar lavage (BAL) fluid is an important diagnostic test in people presenting with ILD, but BAL cellularity remains relatively uncharacterized at single-cell resolution. OBJECTIVE: To characterize immune cell populations in BAL across different ILDs and investigate the impact of shortened peripheral blood leukocyte telomere length on BAL immune profiles. METHODS: Single-cell RNA sequencing and downstream analysis were performed on BAL samples from 25 patients with various ILDs, including idiopathic pulmonary fibrosis (IPF), hypersensitivity pneumonitis, sarcoidosis, and silicosis. Both normal-telomere and short-telomere patients were included. Additionally, we integrated our findings with IPF genome-wide association study (GWAS) data. RESULTS: We identified sixteen distinct cell populations in BAL with notable differences across ILD subtypes. Analysis revealed six monocyte-like macrophage (MLM) subclusters following divergent trajectories: inflammatory CXCL10hi MLMs predominated in hypersensitivity pneumonitis, while pro-fibrotic SPP1hi MLMs were significantly expanded in IPF. Short-telomere patients demonstrated an increased proportion of pro-fibrotic SPP1hi MLMs with enhanced expression of fibrotic genes compared to patients with normal telomere length. Integration with genomic data confirmed that SPP1hi and CCL2hi MLM subclusters harbour cells with the highest IPF disease relevance scores. CONCLUSION: BAL-derived transcriptomics reveals distinct myeloid subpopulations across ILD subtypes, with specific populations associated with disease pathogenesis. These findings provide insight into ILD pathogenesis, motivate the development of more sophisticated diagnostic tests using BAL sampling, and highlight specific myeloid subpopulations as potential therapeutic targets.

overall_design: Bronchoalveolar lavage fluid was extracted from the lungs of ILD patients and single cell RNA was sequenced using the 10x Genomics scRNA protocols.

first: Lai-Ying

last: Zhang

first: Viviana

last: Lutzky

first: Simon

middle: H

last: Apte

first: Penelope

last: Groves

first: Maxine

last: Tan

first: Tharushi

last: De Silva

first: Quan

last: Nguyen

first: Joseph

last: Powell

first: Daniel

last: Chambers

first: Brendan

last: O’Sullivan


title: Osteopontin links acquired resistance to hypoxia-inducing antiangiogenics with refractoriness to anti-PD-L1 agents in breast cancer [III]

city: Madrid

first: Jose Luis

last: Ruiz-Sepulveda

state: Madrid

address: C/ Melchor Fernández Almagro, 3

department: Translational Research

country: Spain

institute: CNIO

summary: Resistance to antiangiogenics is a major challenge in cancer therapy. These agents can either normalize or exacerbate tumor vascular abnormality and hypoxia. The mechanisms of resistance remain unclear in the latter setting. By integrating data from mouse models and clinical trials, we show that hypoxia-inducing anti-VEGF therapy upregulates programmed cell death ligand 1 (PD-L1), yet fails to sensitize tumors to PD-L1 blockade. Mechanistically, early hypoxic stress triggers epithelial osteopontin (Spp1) production, which recruits monocytes and skews macrophages toward M2 states, suppressing T-cell cytotoxicity. Pharmacologic Spp1 depletion impedes the development of hypoxia, M2 infiltration, restores T-cell activity and enables synergy between antiangiogenics and anti-PD-L1. Genetic dissection – tumor-epithelial Spp1 knockout grafts and bone-marrow chimeras generated by lethal irradiation and reconstitution with Spp1-/- or wild-type hematopoietic donors – show that myeloid Spp1 contributes only marginally compared with epithelial Spp1. These findings identify Spp1 as a central mediator of resistance to hypoxia-inducing antiangiogenics, contribute to a comprehensive model of antiangiogenic resistance, and support Spp1-targeted strategies to personalize immuno/antiangiogenic therapy according to tumor hypoxia.

overall_design: To investigate the effects of antiangiogenic mediated hypoxia on breast tumors, we trated 7-weeks old MMTV-PyMT spontaneous breast tumor mouse models with 5mg/kg anti-VEGF-A antibody clone B20-4.1.1 twice per week or isotype IgG2a. After 6 weeks of treatment mice where sacrified and tumor samples dissociated into single cell suspension. Debris and dead cells were excluded by sorting DAPI- cells in BD FACS ARIA. Subsequently, cell multiplexing oligo labeling was conducted using the 3’CellPlex Kit Set A (10xGenomics, cat no. 1000261), following manufacturer’s instructions. Next, a secondary sort of DAPI- cells was executed with the BD FACS ARIA to further enrich for viable cells. Multiplexed-single-cell suspensions sourced from three distinct tumors were processed together into one sample, which was drop encapsulated with Chromium device (10xGenomics). The generated libraries were later sequenced using Illumina Nextseq 550 (with v2.5 reagent kits) and post-processed by the Cell Ranger Software (10xGenomics) to obtain a single-cell RNA-seq expression matrix for each sample.

first: José

last: Ruiz-Sepúlveda

first: María

last: Bueno

first: Silvana

last: Mouron

first: Verónica

last: Jiménez-Renard

first: Manuel

last: Muñoz

last: Moradiellos

first: Leonardo

last: Garma

first: Luis

last: García-Jimeno

first: Adam

last: Watson

first: Ghassan

last: Mouneimne

first: Solip

last: Park

first: Rebeca

last: Jimeno

first: Miguel

last: Quintela-Fandino


title: single-cell spatial analysis reveals molecular mechanisms underlying immune cell organization and cancer cell heterogeneity in HPV-associated oropharyngeal carcinoma

first: Cem

last: Sievers

summary: We combined spatial gene expression profiling with single-cell RNA-sequencing to study cellular organization in HPV-associated oropharyngeal carcinoma. The single-cell RNA-sequencing portion of the study is described and provided in this deposition.

overall_design: Clinical (tissue) specimens were collected from patients with newly diagnosed, previously untreated HPV-related OPSCC referred to the NIH Clinical Center for consideration of clinical trials or from patients undergoing standard of care procedures following verbal and written informed consent under an IRB-approved biospecimen protocol (NCT03429036).

first: Clint

last: Allen

first: Charalampos

last: Floudas


title: Osteopontin links acquired resistance to hypoxia-inducing antiangiogenics with refractoriness to anti-PD-L1 agents in breast cancer [II]

last: Ruiz-Sepulveda

overall_design: To investigate the effects oh antiangiogenic mediated hypoxia on tumor cell compartment we trated 7-weeks old MMTV-PyMT spontaneous breast tumor mouse models  with 5mg/kg anti-VEGF-A antibody clone B20-4.1.1 twice per week. After 6 weeks of treatment mice where sacrfied and breast tumors extracted. Intratumoral CD45-EPCAM+ tumor cells were FACS-Sorted and RNA extracted to perform 3'RNA-seq experiment.


title: Transcriptional profiling of brain from a zQ175 KI mouse model of Huntington's disease

first: Jeff

last: Aaronson

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

overall_design: Refer to individual Series


title: Osteopontin links acquired resistance to hypoxia-inducing antiangiogenics with refractoriness to anti-PD-L1 agents in breast cancer

first: Jose Luis

last: Ruiz-Sepúlveda

last: Bueno


title: Bulk RNA-seq analysis of exhausted CD8 T cell subsets during LCMV clone 13 infection

city: Saint Louis

first: Sunnie

last: Hsiung

state: MO

address: 660 S Euclid Ave

institute: Washington University in St. Louis

summary: CD8+PD-1+Ly108– cells were sorted from Tcf7FF CD8-cre mice and wild-type mice 35 days after LCMV clone 13 infection.

overall_design: Four Tcf7FF CD8cre (Tcf7-cKO) mice and four wild-type (WT) mice were infected with LCMV clone 13. Splenocytes were harvested on day 35 post-infection, enriched for CD8+ T cells using MojoSort Mouse CD8 T Cell Isolation Kit and subjected to FACS. Two populations were isolated (TIM3+CX3CR1+, TIM3+CX3CR1–).

first: Takeshi

last: Egawa


title: Osteopontin links acquired resistance to hypoxia-inducing antiangiogenics with refractoriness to anti-PD-L1 agents in breast cancer [I]

overall_design: To investigate the effects oh antiangiogenic mediated hypoxia on tumor immune compartment we trated 7-weeks old MMTV-PyMT spontaneous breast tumor mouse models  with 5mg/kg anti-VEGF-A antibody clone B20-4.1.1 twice per week. After 6 weeks of treatment mice where sacrfied and breast tumors extracted. Intratumoral CD45+ immune cells were FACS-Sorted and RNA extracted to perform 3'RNA-seq experiment.

first: José

first: María

first: Silvana

last: Mouron

last: Jiménez-Renard

last: Muñoz

last: Moradiellos


title: The CDK4/6 inhibitors dephosphorylate RNF26 to stabilize TSC1 and increase the sensitivity of ccRCC to anti-angiogenesis drug

city: Changsha

first: Huaiyuan

last: Liang

address: 183 Renmin Middle Road

institute: Institute of Urological Cancer, Central South University

summary: Renal cancer is one of the three most common malignant tumors in the urinary system, and its incidence rate ranks among the top 10 human malignant tumors in the world. It has been reported that the combined use of CDK4/6 inhibitors and mTOR inhibitors has achieved some clinical success in renal cell carcinoma. Therefore, exploring the underlying mechanism of CDK4/6 pathway in cancer cells and the drug interaction of CDK4/6 inhibitors in combination therapy would helpful find new therapeutic strategies for ccRCC. In studies, we intended to explore the mechanism of how CDK4/6 inhibitors increased the protein expression of TSC1 in ccRCC. We demonstrated that the CDK4/6 inhibitors stabilized TSC1 in ccRCC cells. Then, we showed that e3 ligase RNF26 interacted with TSC1 to promote the degradation of TSC1 and activate the mTOR signaling pathway in ccRCC. Treatment of the CDK4/6 inhibitors dephosphorylated RNF26 and decreased the interaction between RNF26 and TSC1 to prevent the degradation of TSC1. Therefore, RNF26 is recognized to be an ideal candidate to modulate the sensitivity of the CDK4/6 inhibitors and mTOR inhibitors in ccRCC.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for the A498 cells after kncokdown of RNF26.

first: Xin

last: Jin


title: HOXB13 expression in T47D cells in presence/absence of estradiol

city: Charlestown

first: Dennis

last: Sgroi

department: Pathology

institute: MGH

summary: HOXB13 gene expression in human ER+ breast cancer predicts the likelihood of benefit from extended adjuvant hormonal therapy benefit.  However, the gene expression changes associated with ectopic HOXB13 expression is unknown.  Here, we provide gene expression data associated with ectopic HOXB13 expression and the changes to this expression profile by estradiol.

overall_design: To investigate the gene expression profile associated with the ectopic expression of HOXB13 in the human ER+ T47D cell line in the presence and absence of estradiol.  Gene expression was assessed 24 hrs after exposure to vehicle (ethanol) or 2nM estradiol.

first: Michael

last: Lawrence

first: Preshita

last: Dave


title: Differential Expression of microRNAs after Induction of Endometriosis in Baboons

status: Public on May 04 2026

city: New Haven

first: Ramanaiah

last: Mamillapalli

address: 310 Cedar Street

department: OBGYN

institute: Yale University

summary: Endometriosis is an inflammatory chronic gynecological condition that affects 10-15% of reproductive-age women which causes pelvic pain and infertility. The disease is characterized by the growth of endometrial tissue outside the uterine cavity. Currently, early diagnosis of endometriosis is difficult due to non-specific symptoms and the absence of reliable biomarkers. Understanding these early molecular alterations could support the development of diagnostic tools for timely detection and treatment. The objective of this study was to identify changes in circulating microRNA (miRNA) profiles during the initial stages of endometriosis using a longitudinal non-human primate baboon model. Endometriosis was induced in female baboons by laparoscopic inoculation of menstrual endometrial tissue and plasma was collected at various timepoints. Plasma miRNAs at 3, 6, 9, and 15 months were analyzed using RNA sequencing. A total of 2,731 miRNAs were detected, 76 of which showed significant differences at least at one time point. There are four, three, and one miRNA exclusively differentially expressed at 3-, 6- and 9-month timepoints respectively while several (68) miRNAs are significantly expressed at 15 months. Four miRNAs (miR-210-3p, miR-448, miR-1260a/1260b, and miR-1298-5p) exhibited significant alterations across all time points. Of these, miR-210-3p increased, while the others decreased significantly. Hierarchical clustering revealed separation between the early (pre-inoculation and three months) and late (nine and 15 months) stages, indicating progressive divergence of miRNA profiles. These findings identify candidate miRNAs that may provide insight into early pathophysiological mechanisms and represent candidate circulating biomarkers associated with temporal molecular changes following disease induction, warranting further validation.

overall_design: Endometriosis was induced in Baboons by inoculating menustrual fluid tissue into peritoneal cavity by laparoscopy surgery, confirmed the lesion development by laparoscopic and histological evaluation. Blood was drawn on at preincoculation, month 3, 6, 9 and 15th and serum was collected and processed for tRFs differential expression (RNA-sequence analysis) across all time-ppoints while proinoculation time point taken as basal expression of these tRFs.

first: Hanna

last: Surmann

first: Niraj

last: Joshi

first: Gregory

last: Burns

first: Asgerally

middle: T

last: Fazleabas

first: Hugh

last: Taylor


title: Transcriptomic of Visceral Adipose Tissue in HFD-induced obesity: evaluation of Resveratrol

city: Chilpancingo de los Bravo

first: Mónica

last: Espinoza-Rojo

state: Guerrero

address: Av. Lazaro Cardenas SN

department: Facultad de Ciencias Químico Biológicas

country: Mexico

institute: Universidad Autónoma de Guerrero

summary: Visceral adipose tissue (VAT) expansion during the development of obesity is a hallmark of metabolic syndrome, characterized by hypoxia, oxidative stress, and a shift toward a pro-inflammatory secretome. This series examines the transcriptomic profile of VAT in male C57BL/6 mice subjected to long-term obesity induced by a high-fat diet (HFD, 60% of kcal from fat). To investigate new therapeutic avenues, we evaluated the impact of daily resveratrol administration (2.25 mg/kg) for 28 days, beginning at week 16 of life (8 weeks on the HFD diet). Using a transcriptomic approach (RNA-seq), we mapped the expression changes associated with the transition from healthy to dysfunctional adipose tissue. This study provides a detailed molecular resource for understanding how obesity-induced adipocyte stress can be attenuated by natural bioactives.

overall_design: A total of 5 visceral adipose tissue samples were analyzed: 1) Control (Standard Diet, n=1); 2) Obesity (HFD, n=2); 3) Obesity + Resveratrol (V_OBRSV, n=2). Samples were collected after 12 weeks (8 weeks of HFD and 4 weeks of treatment).

first: Monica

first: Brenda

last: De la Cruz-Concepción

first: Yaccil Adilene

last: Flores-Cortez

first: Isela

last: Parra-Rojas

first: Juan Miguel

last: Mendoza-Bello


title: Transcriptomic profiling of Visceral Adipose Tissue (VAT) in a neonatal STZ-induced diabetes model: modulatory effects of Curcumin. [RNA-Seq]

summary: Visceral Adipose Tissue (VAT) plays a pivotal role in the systemic metabolic complications of Type 2 Diabetes, acting as a primary site for pro-inflammatory cytokine secretion and lipid storage failure. In this study, we utilized a combined neonatal Streptozotocin (nSTZ) and High-Fat Diet (HFD) model to simulate the progression of diabetic adipopathy in C57BL/6 mice. The objective was to characterize the transcriptomic response of VAT to chronic hyperglycemia and lipid overload, and to evaluate the potential of Curcumin (50 mg/kg) as a metabolic and inflammatory modulator. Following 28 days of daily treatment via oral gavage, VAT samples were collected for total RNA sequencing. These data contribute to the understanding of the molecular mechanisms underlying adipose tissue dysfunction in diabetes and highlight the role of Curcumin in modulating the transcriptomic profile landscape to improve metabolic health.

overall_design: A total of 5 visceral adipose tissue samples were analyzed, distributed as follows: 1) Control (Standard Diet, n=1); 2) Diabetes (nSTZ + HFD, n=2); and 3) Diabetes + Curcumin (nSTZ + HFD + CUR, n=2). The diabetes model was induced via neonatal STZ and maintained with HFD. Samples were collected after a 4-week treatment period.


title: Laser Interstitial Thermal Therapy Enhances Bidirectional Blood-Brain Barrier Permeability in Glioblastoma

city: St. Louis

first: Jason

last: Wong

address: Neuroscience Research Building

department: Neurosurgery

summary: Laser interstitial thermal therapy (LITT) is a minimally invasive treatment for glioblastoma that increases blood-brain barrier (BBB) permeability. However, the mechanisms and spatiotemporal features of this effect remain unclear. It is also unknown whether LITT promotes release of circulating tumor DNA (ctDNA).Using our previously developed LITT mouse model, we employed single-cell RNA sequencing (scRNAseq) to investigate gene expression changes in endothelial cells following LITT in naïve mouse brain. Brains were also harvested at multiple time points to assess LITT effects on tight junction (TJ) integrity and transcytosis via immunofluorescence and transmission electron microscopy. Human glioblastoma tissues were analyzed to monitor ambient caveolae-mediated transcytosis in tumor regions. Finally, ctDNA levels in mouse plasma were quantified using digital droplet PCR following LITT.LITT triggered downregulation of pathways related to cell-cell junctions and upregulation of transcytosis. LITT transiently disrupted TJ integrity for 7 days up to 100 µm away from the ablation zone. Further, LITT increased caveolae-mediated transcytosis in endothelial cells for 21 days, peaking at 14 days, in part due to suppression of the transcytosis inhibitor Mfsd2a. LITT facilitated ctDNA detection in mouse plasma at 1 hour, 3 days, 7 days, and 14 days post-procedure.Our study demonstrates that LITT transiently disrupts the BBB in the periphery of the ablation with endothelial TJ disruption and transcytosis upregulation following distinct time courses. LITT effects on the BBB are bidirectional and enhance ctDNA release in addition to enabling brain entry of agents.

overall_design: Cell lysis, first-strand, and cDNA synthesis were performed using the Smart-seq-2 protocol in 96-well formats. After cDNA amplification (23 cycles), cDNA concentrations were measured with a dye-fluorescence assay (Quant-iT dsDNA High Sensitivity kit; Thermo Fisher) on a SpectraMax i3x microplate reader (Molecular Devices). Sample plates were selected for downstream processing if the mean concentration of blanks (ERCC-containing, non-cell wells) was greater than 0 ng/µL, and, after linear regression of the values obtained from the Quant-iT dsDNA standard curve, the R2 value was greater than 0.98. Sample wells were then selected if their cDNA concentrations were at least one standard deviation greater than the mean concentration of the blanks. These wells were reformatted to a new 384-well plate at a concentration of 0.3 ng/µL and a final volume of 0.4 µL using an Echo 550 acoustic liquid dispenser (Labcyte). Libraries were prepared and pooled using the Illumina Nextera XT Library Sample Preparation kit. Libraries were then sequenced on the NovaSeq 6000 Sequencing System (Illumina) using 2 × 100 bp paired-end reads and 2 × 8 bp index reads with a 200-cycle kit (Illumina, 20012861). Samples were sequenced at an average of 7.5M reads per cell.

first: Ryan

last: Cleary

first: Yiwei

last: Fu

first: David

last: Giles

first: Albert

last: Kim


title: Transcriptomic profiling of the hypothalamus in a neonatal STZ-induced diabetes model: effects of Curcumin and Aged Garlic Extract.

summary: Type 2 Diabetes Mellitus (T2DM) is associated with a state of chronic low-grade inflammation that severely affects the central nervous system, particularly the hypothalamus, which acts as the master regulator of energy homeostasis. This study aimed to characterize the hypothalamic transcriptomic signature in a complex murine model of T2DM induced by neonatal administration of Streptozotocin (nSTZ, 70 mg/kg) followed by a chronic High-Fat Diet (HFD, 60% kcal from fat). Given the neuroprotective properties of natural polyphenols, we evaluated the modulatory effects of Curcumin (50 mg/kg) and Aged Garlic Extract (EAE, 200 mg/kg) administered daily via oral gavage for 28 days. By employing high-throughput RNA sequencing (RNA-seq), we identified differentially expressed genes (DEGs) and perturbed molecular pathways involved in neuroinflammation, synaptic plasticity and gabaergic system. Our findings provide a comprehensive map of the gene expression changes associated with diabetic neurodegeneration and the therapeutic potential of nutraceutical interventions to restore hypothalamic function.

overall_design: A total of 12 hypothalamic samples were analyzed, distributed into four experimental groups: 1) Control (Standard diet, n=3); 2) Diabetes (nSTZ + HFD, n=4); 3) Diabetes + Curcumin (nSTZ + HFD + CUR, n=3); and 4) Diabetes + Aged garlic extract (nSTZ + HFD + EAE, n=2). The diabetes model was established by neonatal injection of STZ followed by an 8-week HFD protocol starting at 3 weeks of age. Treatments were administered orally daily for 4 weeks after 11 weeks on the diet.

last: De la Cruz-Concepcion


title: Human iPSC-Derived Cardiac Progenitor Cells Recapitulate Endogenous CPC Function and Offer a Rejuvenated Cell Source for Cardiac Regeneration

city: London

first: Fiona

last: Lewis-McDougall

address: Charterhouse Square

country: United Kingdom

institute: Queen Mary University of London

summary: Cardiac progenitor cells (CPCs) derived from human induced pluripotent stem cells (hiPSCs) represent a promising alternative to CPC isolation from adult hearts avoiding the need for invasive myocardial biopsy and potentially overcoming the age-related decline in CPC function. Human iPSC-derived CPCs have previously been generated however current strategies are limited by the generation of developmentally immature and heterogeneous progenitor populations with restricted expansion capacity. A lack of donor-matched comparisons with native human CPCs has also limited insight into their developmental fidelity, functional competence, and translational relevance. Together, this study provides the first comprehensive donor-matched comparison of hiPSC-derived and native CPCs, establishing hiPSC-CPCs as an accessible, standardised, and rejuvenated progenitor source that closely mirrors native CPC identity and function. These findings support the potential application of hiPSC-CPCs for cardiac regenerative medicine applications.

overall_design: Here, we generate expandable hiPSC-CPCs using a novel cell selection strategy and perform a direct, side-by-side comparison with eCPCs isolated from the same donor. We collected RNA for sequencing and unbiased transcriptomics analyses reveal that hiPSC-CPCs cluster closely with eCPCs, indicating shared lineage identity.

first: Gowtham

last: Reddy Cheruku

first: Alia Hafiz

last: Abbas Gasim

first: Laura

last: Deelen

first: Mohammed

last: Elbadawi

first: Ken

last: Suzuki

first: Wael

last: Awad


title: Single-cell RNA analysis of allele-specific MHC expression in macaque PBMC after T cell activation or treatment with pro-inflammatory or anti-inflammatory cytokines

city: Madison

last: O'Connor

state: WI

address: 585 Science Drive

department: Pathology and Laboratory Medicine

institute: University of Wisconsin-Madison

summary: We have employed a single-cell sequencing approach using 10X Genomics 5'scRNAseq to study expression of the Major Histocompatibility Complex (MHC) in peripheral blood mononuclear cells (PBMC) from Mauritian-origin cynomolgus and Indian-origin rhesus macaques. The MHC region has undergone a complex series of duplications in macaques relative to humans. Steady-state RNA levels of macaque MHC class I and class II transcripts vary over several orders of magnitude in whole blood and bulk PBMC. In this study, we compared transcript levels in untreated control PBMC with transcript levels after T cell activation, treatment with pro-inflammatory cytokines, or treatment with anti-inflammatory cytokines. Transcript levels for several minor MHC alleles were preferentially induced in monocytes and dendritic cells after treatment with pro-inflammatory cytokines or T cell activation.

sample_organism:
Macaca fascicularis
Macaca mulatta

platform_organism:
Macaca fascicularis
Macaca mulatta

overall_design: 10X Genomics 5'scRNAseq results were compared between PBMC from two naive Mauritian-origin cynomolgus and two Indian-origin rhesus macaques after the following experimental conditions: 1) overnight incubation in control media, 2) treatment with pro-inflammatory cytokines, 3) treatment with anti-inflammatory cytokines, or 4) T cell activation with CD3/CD298 beads. Treatment groups for each animal were distinguished with BioLegend TotalSeq-C hashtag antibodies and the following surface antigens (CD4, CD8a, CD11b, CD14, CD16, CD20 and CD86) were detected with antibody-derived tags (ADT). Illumina NovaSeqX+ sequencing was performed with custom parameters to maximize sequences from the most informative exon 2 region for MHC allelic discrimination. Sequences for each treatment group from four macaques were analyzed with 10X Genomics Cell Ranger and Loupe software to quantify allele-specific MHC transcript levels in PBMC subsets.

first: Max

last: Ertl

first: Roger

last: Wiseman

first: Anthony

middle: J

last: Veltri

first: Julie

last: Karl

first: Miranda

last: Stauss

first: William

middle: K

last: Gardner

first: Nicholas

last: Minor


title: Metabolically and epigenetically reprogrammed splenic TRNP1hiCD8+ T cells exacerbate liver fibrosis

city: Shanghai

first: Liyuan

last: Zhang

state: China

address: Xiangyin road

department: National Key Laboratory of Medical Immunology & Institute of Immunology

institute: Naval medical university

type: Methylation profiling by high throughput sequencing


title: Targeted Degradation of SETDB1 by an Aptamer-CRBNL PROTAC as a Novel Therapeutic Strategy for Breast Cancer

city: 天津

first: yingge

last: Lv

state: 天津

address: 天津市和平区气象台路

department: 基础医学院

institute: 天津医科大学

summary: PROteolysis TArgeting Chimeras (PROTACs) represent a novel therapeutic strategy that leverages the ubiquitin-proteasome system for targeted protein degradation. Aptamers, with their high specificity and binding affinity, have recently been explored as alternative recognition elements in PROTAC design. Here, we developed an aptamer-based PROTAC targeting SET domain bifurcated histone lysine methyltransferase 1 (SETDB1), an epigenetic regulator implicated in breast cancer progression. The SETDB1-specific aptamer identified in our previous work was conjugated to a CRBN E3 ligase ligand via click chemistry, generating a serum-stable PROTAC, designated as P-SETDB1-4. P-SETDB1-4 effectively recruits CRBN to SETDB1, inducing proteasome-dependent degradation of SETDB1 in breast cancer cells. Consequently, P-SETDB1-4 significantly inhibits the proliferation and migration of breast cancer cells. Moreover, P-SETDB1-4 enhances the CD8+ T cells cytotoxicity against breast cancer cells and suppresses tumor growth in vivo. RNA sequencing analysis elucidates the molecular mechanism underlying P-SETDB1-4-mediated tumor suppression and promotion of CD8+ T cell-mediated killing. This study provides a promising therapeutic strategy for breast cancer and highlights the potential of aptamer-CRBNL PROTACs for targeting other challenging oncogenic proteins.

overall_design: Examination of gene expression changes in MCF‑7 cells transfected with control PROTAC and P‑SETDB1‑4


title: Mouse embryo transcriptomes after two-cell blastomere separation

city: jinan

first: Leoti Jiawei

last: Wang

state: Shandong

address: Wenhua xilu

institute: Shandong UNIVERSITY

summary: This study profiled mouse preimplantation embryos by Smart-seq2 RNA-seq to assess whether separation of late two-cell blastomeres alters the developmental transcriptomic program. The dataset includes control 8-cell embryos, split morula-stage embryos derived from two-cell blastomeres, control morula embryos, split blastocyst-stage embryos derived from two-cell blastomeres, and control blastocysts. The data were used to compare global transcriptomic similarity, developmental-stage effects, sample correlations, hierarchical clustering and pseudotime trajectories between split embryos and intact controls.

overall_design: Smart-seq2 RNA-seq was performed on individual mouse embryo samples across preimplantation development. The dataset includes four control 8-cell embryos, six split morula-stage embryos derived from three sister pairs of separated two-cell blastomeres, five control morula embryos, six split blastocyst-stage embryos derived from three sister pairs of separated two-cell blastomeres, and three control blastocysts. Samples were compared by developmental stage and embryo origin to evaluate transcriptomic convergence after blastomere separation.

first: Leoti

last: Jiawei Wang

first: Jingye

first: Jinzhu

last: Song

first: Chuanxin

first: Shiyu

last: Liu

first: Zhenzhen

last: Hou

first: Jiayin

last: Gao

first: Shuiying

last: Ma

first: Boyang

first: Keliang

last: Wu

first: Zijiang

last: Chen


title: RNAP-seq: in vitro genome-scale transcription reveals preferential RNA polymerase pausing on Clostridioides difficile antisense DNA

city: Dallas

first: Ping

last: Shen

state: Texas

address: 5323 Harry Hines Blvd

department: Microbiology

institute: UT Southwestern Medical Center

summary: Mechanistic dissection of gene transcription and its regulation in diverse organisms remains a central challenge for molecular biology. In vivo analyses using high-throughput DNA sequencing readouts (e.g., RNA-seq, Term-seq, and NET-seq) have revealed that transcriptional pausing by RNA polymerase (RNAP) underpins the regulation of gene transcription. However, these in vivo methods are difficult to apply in non-model organisms and lack the power of bottom-up biochemical analysis that can deconvolute the confounding effects of the cellular environment. Here we report a method for unbiased transcription of entire genomes in vitro called RNAP-seq, which is capable of defining pause, arrest, and termination sites with single-nucleotide resolution and of defining the regulatory contributions of cis-acting RNA and DNA sequences and dissociable transcription factors with complete control over transcription conditions. Using RNAP-seq to compare transcription by recombinant RNAPs from Clostridioides difficile (Cdf) and Escherichia coli (Eco), we discovered that Cdf RNAP exhibits pausing signatures distinct from Eco RNAP. Cdf RNAP pauses more frequently and more strongly at T-rich sequences, particularly on antisense regions of genes. We also defined the action of Cdf NusG at genome scale, revealing its preferential action in riboswitch control regions. These findings demonstrate lineage-specific pausing features and suggest that genome composition and RNAP co-evolve to shape gene expression. RNAP-seq is broadly adaptable to diverse bacterial species and offers a powerful framework for uncovering fundamental principles of transcription that govern gene expression.

sample_organism:
Escherichia coli
Clostridioides difficile

overall_design: We performed in vitro RNAP-seq to map transcriptional pausing and termination across genomes. E. coli and C. difficile RNA polymerases were assayed on matched DNA templates. Pausing sites were identified using a multi-round Z-score–based approach, and terminator-associated sites were defined based on proximity to in vivo termination sites. Strand-specific coverage and 3′ end signals were generated.

first: Michael

last: Wolfe

first: Xinyun

last: Cao