title: Gene expression profile at single nucleus level of hippocampal cells from APP-TG mice treated with Low-dose ∆9-THC and Celecoxib

city: San Antonio

first: Chu

last: Chen

state: Texas

address: 7703 Floyd Curl Dr

department: Cellular and Integrative Physiology

institute: UT Health San Antonio

summary: Delta-9-tetrahydrocannabinol (Δ9-THC) is reported to rescue cognitive and synaptic functions in Alzheimer's disease (AD) mice model. However, Δ9-THC treatment resulted in neuroinflammation via activating Cox2 in the brain. Our hypothesis is that inhibiting cox2 via celecoxib treatment could inhibit neuroinflammation and enhance the neuroprotective effects of Δ9-THC. Our results indicated that Cel-THC treatment inhibited spatial learning and memory impairments of APP-TG mice via water maze test. To investigate the molecular mechanisms, we performed single nucleus RNA sequence of hippocampal cells from WT-Veh, APP-TG-Veh, APP-TG-THC, APP-TG-Cel, and APP-TG-Cel-THC groups. Our results showed that Cel-THC treatment reversed changes of synaptic, inflammation-, and AD-related differentially expressed genes caused by beta amyloid accumulation.

overall_design: Single nucleus transcriptomics of hippocampus from WT and transgenic mice were analyzed by snRNA-seq.

first: Chen

last: Chu

first: Zhang

last: Jian

first: Hu

last: Mei

first: Zhu

last: Dexiao


title: Transcriptome and phenotype-based epistasis analysis in Caenorhabditis elegans reveal daf-16/FoxO-dependent and independent effects of daf-2/InsR in L1 arrest and recovery

status: Public on Dec 03 2025

city: Durham

first: Kinsey

middle: C

last: Fisher

state: NC

address: 124 Science Drive

department: Biology

country: USA

institute: Duke University

type: Expression profiling by high throughput sequencing

summary: Reduced insulin/IGF signaling (IIS) in C. elegans increases starvation resistance in daf-16/FoxO-dependent fashion, but it is unclear whether the effects of reduced IIS are entirely dependent on daf-16/FoxO or if another effector(s) of IIS may be involved. We used RNA sequencing (RNA-seq) and phenotypic analysis of L1 starvation resistance to assess epistasis between daf-2/InsR and daf-16/FoxO. Essentially all differential gene expression caused by disruption of daf-2/InsR during starvation is daf-16-dependent. The effects of daf-2/InsR on starvation survival also appear entirely dependent on daf-16/FoxO, and the effect of daf-2/InsR on growth following starvation is largely daf-16-dependent. However, we also show daf-16-independent effects on growth and reproduction following recovery from starvation. These results support the conclusion that the effects of reduced IIS during L1 starvation are essentially daf-16/FoxO-dependent, but that reduced IIS engages one or more additional effectors during development following starvation.

overall_design: RNA-seq of fed and starved (12 hrs after hatch) wild type (N2), as well as starved daf-2(e1370), daf-16(mgDf47), and daf-16(mgDf47); daf-2(e1370) mutants

first: Rojin

last: Chitrakar

first: Ryan

last: Baugh


title: Spatiotemporal remodeling of chromatin topology architecture and H3K27me3 redistribution underlies vascular pathology in Hutchinson-Gilford progeria syndrome [CUT&Tag]

status: Public on Dec 04 2025

city: Ottawa

first: William

middle: L

last: Stanford

state: ON

address: 501 Smyth Rd

country: Canada

institute: Ottawa Hospital Research Institute

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Hutchinson-Gilford progeria syndrome (HGPS) is a devastating premature aging disorder driven by the accumulation of progerin, leading to severe vascular pathology. While epigenetic alterations are implicated, the spatiotemporal reorganization of the higher-order chromatin and its functional impact on vascular smooth muscle cell (VSMC) transcription remain poorly defined. Through an integrated multi-omics approach combining in situ high-throughput chromosome conformation capture (Hi-C) and Cleavage Under Targets and Tagmentation (CUT&Tag) profiling of CTCF, SMC1A, H3K27me3, H3K27ac, and H3K36me3 with transcriptomic analyses from control and HGPS iPSC-derived VSMCs, we reveal that global topologically associating domain (TAD) architecture remains largely intact in HGPS. However, the internal chromatin states of TADs undergo dynamic, passage-specific remodeling, characterized by a progressive accumulation of broad H3K27me3-repressed domains. This is accompanied by a loss of A/B compartment segregation, as confirmed by DNA-FISH, indicating a collapse of higher-order chromatin organization in late passage. Crucially, we uncover widespread rewiring of enhancer-promoter (E-P) loops, which is linked to the dysregulation of genes critical for vascular development, extracellular matrix organization, and atherosclerosis. Our study demonstrates that spatiotemporal redistribution of repressive histone marks and reorganization of E-P interactions within a structurally resilient TAD framework underpin widespread transcriptional dysregulation in HGPS vascular pathogenesis. This uncovers a critical dissociation    between higher-order chromatin architecture and epigenetic statehistone modification landscape, providing a mechanistic basis for the failure of vascular homeostasis in progeria.

overall_design: Cleavage Under Targets and Tagmentation (CUT&Tag) profiling of CTCF, SMC1A, H3K27me3, H3K27ac, and H3K36me3 in vascular smooth muscle cell differentiated from patient-derived induced pluripotent stem cells

first: Mzwanele

last: Ngubo

first: Naveen

last: Ahuja

first: Rana

last: Karimpour

first: Amit

last: Shrestha

first: Michael

middle: J

last: Hendzel

first: Theodore

last: Perkins


title: Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) analysis of ZNF148 in chondrocytes

city: Nanchang

first: Jinghong

last: Yuan

state: Jiangxi

address: No.1 Minde Road

country: China

institute: The Secondly Affiliated Hospital of Nanchang University

summary: Chromatin Immunoprecipitation (ChIP) was performed by fixing chondrocytes with formaldehyde, lysing them, and fragmenting chromatin via sonication. Specific antibodies of ZNF148 (Santa Cruz, sc-398148X, 200碌g/0.1ml) were used to immunoprecipitate protein-DNA complexes, followed by washing, reverse crosslinking and DNA purification for subsequent RT-qPCR or ChIP-seq analysis

overall_design: Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) analysis targeting ZNF148 in chondrocytes

first: Yameng

last: Wang

first: Jingyu

last: Jia

first: Xijuan

last: Liu


title: A targetable developmental program co-regulates angiogenesis and immune evasion [Hi-C]

city: New York

first: Pietro

last: Berico

state: NY

address: 550 1st Ave Smilow 305

department: Pathology

institute: NYU Langone Health

summary: Ultraviolet (UV)-induced DNA mutations produce genetic drivers of cutaneous melanoma initiation and numerous neoantigens that can trigger anti-tumor immune responses in the host. Consequently, melanoma cells must rapidly evolve to evade immune detection by simultaneously modulating cell-autonomous epigenetic mechanisms and tumor-microenvironment interactions. Angiogenesis has been implicated in this process; although an increase of vasculature facilitates the immune response in normal tissue, solid tumors manage to somehow enhance blood flow while preventing immune cell infiltration. By comparing the expression of transcription factors (TFs) across early-stage melanoma, naevi, and other cancer types, we found the homeodomain-containing TF HOXD13 drives a melanoblast-like developmental program, which is upregulated in melanoma and strongly correlated with angiogenesis and immune cell exclusion. Using transcriptomics, 3D chromatin profiling, and in vivo models, we demonstrate that HOXD13 upregulation promotes tumor growth in vivo by concomitantly enhancing angiogenesis and suppressing T-cell infiltration. HOXD13 orchestrates 3D chromatin contacts between distal enhancers and promoters, simultaneously activating VEGFA, SEMA3A, and CD73. VEGFA and SEMA3A remodel the tumor vasculature and CD73 elevates extracellular levels of adenosine, a vasodilator and immune suppressor that binds adenosine receptors (AdR) on endothelial and T cells. In line with these findings, HOXD13-induced growth advantage in vivo was significantly reversed by the concomitant administration of VEGFR and AdR inhibitors. By revealing a dual pro-angiogenic and immunosuppressive HOXD13-CD73/VEGF gene regulatory axis, we identify a subset of patients who might benefit from combinations of AdR and VEGFR inhibitors which are currently being tested in clinical trials.

overall_design: Human melanoma cell lines with different HOXD13 expression levels were subject to HiC and H3K27ac Hi-ChIP.

first: Eva

last: Hernando


title: Effect of depletion of PNPLA1 in gene expression during keratinocyte differentiation on reconstructed human epidermis

city: Toulouse

first: Nathalie

last: JONCA

state: France

address: CHU Purpan

country: France

institute: INSERM UMR1291 - CNRS UMR 5051 - Université Toulouse III

summary: Congenital ichthyoses are rare and disabling genodermatoses caused by mutations in genes involved in the epidermal barrier. More than 60 genes are known to be involved. However, 5-10% of the genetic variants identified in those genes are rarely or not described and their pathogenicity not yet demonstrated. They are therefore classified as Variants of Uncertain Significance (VUS) that leave number of patients undiagnosed, precluding prognosis, counselling and treatment.  We report here, an experimental strategy to reclassify VUS identified in congenital ichthyosis-causing genes tested for PNPLA1 variants. PNPLA is a transacylase essential for the skin barrier formation. It catalyzes the biosynthesis of acylceramides (AcylCer) in the stratum granulosum by esterification of ω-hydroxy ceramides with linoleic acid. We successfully characterized three PNPLA1 VUS identified in three patients with congenital ichthyosis, opening the possibility to extend the approach to other ichthyosis-causing genes.

overall_design: We generated immortalized keratinocyte cell lines (N/TERT-2G) CrisprCas9-knockout (KO) for the ichthyosis-causing gene PNPLA1. Three PNPLA1 VUS were ectopically expressed in the corresponding KO cell line by lentiviral transduction and the resulting cells were used to produce reconstructed human epidermis (RHE). To further characterized the KO PNPLA1 icthyosis model, we performed gene expression profiling analysis using data obtained by RNAseq of WT reconstructed epidermis vs 3 PNPLA1 KO clones

first: Nuria

last: Pell

first: Severine

last: Courrech

last: Garnier

first: Anne-Alicia

last: Gonzalez

first: Emeline

last: Lhuillier


title: An mRNA cap-binding complex in giant viruses controls protein synthesis

city: Boston

first: Amy

middle: Si-Ying

last: Lee

state: MA

address: 450 Brookline Ave SM520

department: Cancer Immunology and Virology

institute: DFCI

summary: In contrast to living organisms, viruses lack the machinery necessary for protein synthesis, instead co-opting host factors to translate viral transcripts. Giant DNA viruses, which encode putative orthologs of translation factors, challenge this dogma and blur the line between cellular and acellular biology. Here, we discover a complete mRNA cap-binding complex in mimivirus that we name viral IF4F. This complex associates with host ribosomes to orchestrate the temporally regulated synthesis of structural proteins critical for assembly of viral progeny. The m7G cap-binding subunit of viral IF4F has evolved specificity for viral cap structures through additional interactions with methylated adenosines in mRNAs. Viral IF4F further facilitates dynamic gene expression required to evade host abiotic stresses that normally restrict viral replication. Our study thereby extends a paradigm of eukaryotic translation regulation to include viruses and illuminates a series of evolutionary innovations to a core process of life.

overall_design: Ribosome profiling (RNA-seq and RIBO-seq) of Acanthamoeba castellanii infected with APMV WT and mutant viruses lacking viral translation factors (APMV Δ4A, Δ4E, Δ4G). Samples were collected at early (4 h) and late (8 h) times of infection.

first: J Maximilian

last: Fels

first: Aidan

middle: B

last: Hill

first: Richard

last: Han

first: Chantal

last: Abergel

first: Philip

last: Kranzusch

middle: S


title: Immune profiling of the lung in Influenza-Associated Pulmonary Aspergillosis using CITE-seq

city: Zwijnaarde

first: VIB

last: Single Cell Core

address: Technologiepark-Zwijnaarde 71

department: VIB Single cell core

country: Belgium

institute: VIB

summary: Influenza-associated pulmonary aspergillosis (IAPA) is a severe fungal superinfection affecting critically ill influenza patients. Current treatments target pathogens but do not address the dysregulated host immune responses that drive morbidity. Host-directed immunotherapies could overcome this treatment gap. In this study, we used CITE-seq to compare transcriptional and surface antibody expression in immune cell populations within the lung tissue of mice with IAPA, influenza infection, Aspergillus infection, and healthy controls. This dataset provides comprehensive immune profiling, offering insights into the immune landscape of the lung during IAPA compared to single infections and healthy controls, which could aid in the development of targeted immunomodulatory therapies. These findings are part of a broader investigation, as detailed in the study "Anakinra restores the immunological misfiring that drives influenza-associated pulmonary aspergillosis." Here, we identified IL-1 inflammation, extensive neutrophil activation, and NET release as key features of IAPA pathogenesis. This inflammation led to an immunological imbalance that impaired neutrophil function, creating a permissive environment for Aspergillus. Blocking the IL-1 receptor with anakinra reduced inflammation, restored neutrophil function, and protected influenza-infected mice from invasive pulmonary aspergillosis and death. These results underscore the critical role of IL-1 inflammation in IAPA and suggest that anakinra could be a promising immunomodulatory therapy for IAPA patients.

overall_design: To further refine the different immune cell populations in the lung, we performed CITE-seq on CD45+ sorted lung cells from Healthy control (HC) (n=3), Aspergillus (n=3), influenza (n=4) and IAPA (n=4) mice on day 7

first: Laura

last: Seldeslachts

first: Sirima

last: Kraisin

first: Intan M.W.

last: Dewi

first: Simon

last: Feys

first: Frederik

last: Staels

first: Marina

last: Gkountzinopoulou

first: Cato

last: Jacobs

first: Birger

last: Tielemans

first: Eliane

last: Vanhoffelen

first: Agustin

last: Reséndiz-Sharpe

first: Lander

last: De Herdt

first: Oswin

last: Kwan

first: Niels

last: Vandamme

first: Jana

last: Roels

first: Julika

last: Neumann

first: Teresa

last: Prezzemolo

first: Bert

last: Malengier-Devlies

first: Mathias

last: Stroobants

first: Agostinho

last: Carvalho

first: Patrick

last: Matthys

first: Lieve

last: Naesens

first: Katrien

last: Lagrou

first: Mona

last: Khan

first: Peter

last: Mombaerts

first: Georgios

last: Chamilos

first: Erik

last: Verbeken

first: Kimberly

last: Martinod

first: Frank L.

last: van de Veerdonk

first: Joost

last: Wauters

first: Greetje

last: Vande Velde

first: Stephanie

last: Humblet-Baron


title: Spatial Transcriptomics of Patients with Kaposi Sarcoma Identifies Mechanisms of Immune Evasion

city: Bethesda

first: Joseph

middle: M

last: Ziegelbauer

state: MD

address: 10 Center Dr. 6N110

institute: NIH / National Cancer Institute

summary: We performed Visium Spatial on Seven Skin Samples with Kapiosi Sarcoma tumor. For four of the samples, we included custom probes for five KSHV genes that allowed us to measure human and KSHV expression patterns at the same time.

overall_design: Punch biopsies from (LANA-positive) Kaposi sarcoma skin lesions were fixed with FFPE. Sections were cut and placed on 10X Genomics Visium slides for spatial transcriptomics.

first: Bahman

last: Afsari

first: Daphne

last: Knudsen-Palmer


title: Methionine Restriction Alleviates Kidney Fibrosis through Epigenetic Repression of the TGF-β/Smad3/Hoxc8/P-TEFb Axis

city: Tianjin

first: Zhiheng

last: Liu

state: Tianjin

address: No.22 Qixiangtai Road

department: Tianjin Research Center for Basic Medical Science

institute: Tianjin Medical University

summary: Renal fibrosis is a hallmark of chronic kidney diseases (CKDs) and a key driver of disease progression. While low-protein diets have been shown to alleviate fibrosis and slow CKD progression, the specific amino acids responsible for these effects remain unclear, and such diets often lead to malnutrition due to the restriction of essential amino acids. In this study, we evaluated 15 amino acid-restricted diets in a unilateral ureteral obstruction (UUO) mouse model and found that methionine restriction (MetR) most effectively reduced renal fibrosis. We further confirmed the efficacy of MetR in alleviating renal fibrosis in the folic acid nephropathy (FAN) mouse model. Mechanistically, we identified Hoxc8 as a key transcription factor responsive to MetR, mediating TGF-β-induced fibrotic gene expression. Our findings suggest that TGF-β-Smad3 signaling activates Hoxc8 during myofibroblast activation, initiating a self-reinforcing feedback loop through Hoxc8 self-activation. Using affinity purification-mass spectrometry, we discovered that Hoxc8 interacts with P-TEFb transcription elongation complex to enhance the expression of fibrotic genes. MetR suppresses Hoxc8 expression by reducing histone modifications, specifically H3K4me3 and H3K36me3, thereby inhibiting the TGF-β/Smad3/Hoxc8/P-TEFb axis and downregulating fibrosis-related gene expression. Notably, elevated HOXC8 expression was observed in CKD patients with kidney fibrosis, while fibroblast-specific Hoxc8 knockout mice demonstrated significantly reduced fibrosis following UUO surgery. These findings establish the TGF-β/Smad3/Hoxc8/P-TEFb axis as a crucial regulator of fibrosis and highlight MetR as a promising therapeutic strategy for the treatment of renal fibrosis.

overall_design: NRK-49F cellls were treated with TGF-β  and/or methionine restriction, siHoxc8.

first: Yunjing

first: Lirong

last: Zhang


title: A targetable developmental program co-regulates angiogenesis and immune evasion [scRNAseq]

first: Pietro

last: Berico

overall_design: B16F10 tumors control or silenced for Hoxd13 were generated in syngeneic animals and CD45 positive and negative cells were processed for scRNAseq.

first: Eva

last: Hernando


title: A targetable developmental program co-regulates angiogenesis and immune evasion [ChIP-seq, ATACseq and CUT&Tag]

overall_design: Different human melanoma cell lines upon silencing or overexpression of HOXD13 were subjected to ChIP-seq, ATACseq and CUT&Tag.


title: In situ multi-modal characterization of pancreatic cancer reveals tumor cell identity as a defining factor of the surrounding microenvironment

city: Cambridge

first: Brian

last: Rabe

address: 250 Water St

institute: Bristol Myers Squibb

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

overall_design: Refer to individual Series


title: A targetable developmental program co-regulates angiogenesis and immune evasion [RNA-Seq]

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Different human and murine melanoma cell lines upon silencing or overexpression of HOXD13 were subjected to RNA-seq.


title: Deciphering the Sperm RNA Code of Aging with PANDORA-seq

city: Salt Lake City

first: Qi

last: Chen

state: Utah

department: Department of Human Genetics

institute: university of utah

type: Non-coding RNA profiling by high throughput sequencing

summary: Sperm aging impacts male fertility and offspring health, highlighting the need for reliable aging biomarkers to guide reproductive decisions. Using PANDORA-seq, a novel method to comprehensively profile small non-coding RNAs (sncRNAs), we identified an "aging cliff" in mouse sperm RNA profiles-a sharp age-specific transition marked by significant shifts in genomic and mitochondrial tRNA-derived small RNAs (tsRNAs) and rRNA-derived small RNAs (rsRNAs). Notably, rsRNAs embedded in sperm heads exhibited a transformative length shift, with longer rsRNAs increasing and shorter ones decreasing with age, suggesting altered biogenesis with age. Remarkably, this sperm rsRNA length shift was consistently observed in two independent human aging cohorts, highlighting its evolutionary significance. Moreover, a combination of tsRNAs and rsRNAs (tsRNA/rsRNA cocktails) resembling those in aged sperm induced transcriptomic changes in embryonic stem cells, impacting metabolism and neurodegeneration pathways, mirroring the phenotypes observed in offspring of aged sperm. These results reveal new insights of sperm aging, highlighting the conserved rsRNA length shift in mice and humans, with translational potential for fertility and intergenerational health

overall_design: Mature sperm and sperm heads were collected from the cauda epididymis of male C57BL/6J mice aged 10, 30, 50, 70, and 90 weeks. Between 3 and 4 replicates were sequenced for each sample using PANDORA-seq and traditional sncRNA-seq. For paried human sperm heads, 8 donors provided two semen samples each over a span of 6 to 23 years. All human sperm head samples were sequenced using PANDORA-seq. For non-paired 47 human sperm head(cross-sectional cohort), 47 donors provide semen samples, and the sperm heads were only sequenced using PANDORA-seq. For the RNA-seq experiment, mESCs were transfected with vector, young_comb sncRNA mixture and old_comb sncRNA mixture seperately, After 24 hours of transfection, the total RNA were harvested by Trizol reagent for transcriptome RNA sequencing through polyA enrichment strategy.

first: Junchao

last: Shi

first: Xudong

first: Tong

last: Zhou


title: c-di-AMP–DasR signaling axis mediates Mycobacterial acid resistance

city: Shanghai

first: Di

last: You

address: Meilong Road 130

institute: East China University of Science & Technology

summary: Genomic mapping of DasR binding sites in vivo.

overall_design: M. tuberculosis H37Ra strains grown in MB7H9 medium are subjected to ChIP-seq using a specific anti-DasR antibody

first: Yu

last: Fu

first: Xue-Qin

last: Xie

first: Yi-Fan

last: Liang

first: Zhan-Hui

last: Xu

first: Shi-Qi

last: Yang

first: Bang-Ce

last: Ye


title: A targetable developmental program co-regulates angiogenesis and immune evasion [Spatial Transcriptomics]

overall_design: Human acral melanoma samples were processed for Visium 10X spatial transcriptomics.

first: Markus

last: Schober

first: Iman

last: Osman

first: Robert

last: Stagnitta


title: Primary Keratinocyte Model of Actinic Keratosis Reveals UV-Induced DNA Damage Accumulation and Persistent Interferon Signaling

city: Hamburg

first: Leonardo

last: Elsbroek

address: Beiersdorfstraße 1-9

country: Germany

institute: Beiersdorf AG

summary: Actinic keratosis (AK) is a precancerous, UV-induced skin lesion that can progress to cutaneous squamous cell carcinoma (cSCC). While UV radiation is known to drive mutations and immunosuppression in the skin, keratinocyte-intrinsic responses to chronic, low-dose solar UV exposure have been insufficiently studied in AK. We established a patient-derived in vitro model using primary keratinocytes from AK lesions and age-matched, sun-exposed skin to investigate how repeated low-dose UV irradiation shapes keratinocyte stress responses. Integrating high-content morphological profiling, cyclobutane pyrimidine dimer (CPD) quantification and bulk RNA sequencing, we observed pronounced morphological remodeling and persistent DNA damage in AK keratinocytes despite activation of DNA repair and unfolded protein response pathways. Transcriptomic analyses revealed constitutive and UV-enhanced interferon signaling in AK cells, including upregulation of innate DNA sensing and ISGylation genes. Meta-analysis of five independent datasets confirmed interferon pathway activation as a conserved feature of AK, and IFN-α exposure further sensitized AK keratinocytes to UV-induced CPD formation. Our primary model thus uncovers sustained interferon signaling and attenuated DNA damage repair as key keratinocyte-intrinsic features of AK, suggesting that chronic interferon responses may modulate UV-induced damage and contribute to early photocarcinogenic processes.

overall_design: Primary AK and photo-exposed healthy facial epidermis keratinocytes (HEK) were irradiated with solar-simulated radiation (SSR) at 100 mJ/cm² UVB-equivalent, either once or daily for 3 days, and harvested 6 h after the final exposure for RNA-seq.


title: Prenatal Glucocorticoid Exposure Disrupts a Subcluster Microglia Maturation Leading to ASD-like Behavior

city: Hangzhou

first: Baixiu

last: Zheng

state: Zhejiang

address: Yuhangtanglu

institute: Zhejiang University

summary: Prenatal glucocorticoid exposure, whether due to pharmacological treatment or stress-induced maternal overproduction, has been associated with an increased risk of autism spectrum disorders (ASD), yet the underlying neurodevelopmental mechanisms remain poorly understood. Here, we report that late-pregnancy exposure to dexamethasone resulted in ASD-like behaviors in adolescent offsprings, accompanied by an increased density of immature dendritic spines and imbalance of neurotransmission in hippocampus. Single-cell RNA sequencing uncovered a significant expansion of MRC1+ microglia derived from border-associated macrophages (BAM) following prenatal exposure, with arrested maturation into homeostatic microglia. Strikingly, this population exhibited selective F13a1 upregulation. Early postnatal inhibition of F13A1 restored microglial maturation and ameliorated behavioral abnormalities and dendritic spine deficits. Elevated levels of F13A1 were also observed in the plasma of postnatal rats and in the umbilical cord blood of human females exposed to prenatal glucocorticoids, suggesting its potential value as a biomarker.

overall_design: Single-cell RNA sequencing of microglia isolated from hippocampus of rats' embryo on gestational day 20 with prenatal dexamethasone exposure or not. Each sample contained 7 male embryos.


title: Transcriptomic Profiling of Wild-Type C. elegans Exhibiting High and Low Exopher Production

city: Warsaw

first: Michal

last: Turek

address: Pwinskiego 5a

country: Poland

institute: Institute of Biochemistry and Biophysics Polish Academy of Sciences

summary: We performed RNA sequencing on age-synchronized wild-type C. elegans that produced either high numbers of exophers (>20 per animal) or low numbers of exophers (<2 per animal) on adulthood day 2. This approach mirrors strategies using natural transcriptional heterogeneity within isogenic populations to uncover molecular determinants of phenotypic variation. The transcriptomes of high- and low-exopher producers differed profoundly. In total, 609 genes were significantly upregulated and 665 genes were significantly downregulated in high-exopher animals (p adj < 0.05, |log₂FC| > 1). These results demonstrate that exopher production is associated with distinct transcriptional states, indicating that variation in exopher output reflects meaningful underlying molecular differences within genetically identical populations.

overall_design: This study investigates transcriptomic differences between wild-type age-synchronized C. elegans that produce high versus low numbers of exophers. Animals were synchronized and scored on adulthood day 2 based on the number of visible exophers per worm. Two phenotypic groups were defined: (1) high-exopher producers (more than 20 exophers per animal) and (2) low-exopher producers (fewer than 2 exophers per animal). These two groups represent the main experimental conditions and constitute the variables under investigation. For each condition, independent biological samples were generated from separate populations of worms classified into the high- or low-exopher group. The design therefore consists of comparative transcriptomic profiling of high- vs low-exopher wild-type animals. No additional genetic mutants or treatment conditions are included in this submission.

first: Michał

first: Wojciech

last: Pokrzywa


title: Transcription Factor 4 Maintains Endothelial Cell Identity by Inhibiting Endothelial to Mesenchymal Transition

first: Kaifu

last: Chen

address: 300 Longwood Ave

department: Cardiology

institute: Boston Children's Hospital

summary: Endothelial-to-mesenchymal transition (EndoMT) is essential for embryonic heart development and contributes to many disease-causal pathobiological processes. It is unclear how the balance between endothelial cell (EC) identity and EndoMT mediators is regulated to drive this transition. This study identifies TCF4 as a critical EC identity gene. TCF4 knockdown in ECs impairs EC phenotype and function, and induces EC identity transition towards mesenchymal-like state. This discovery suggests that TCF4 functions as a guardian of EC identity against EndoMT. Mechanistically, TCF4 binds directly to the promoter of TGFB1 and SNAI1, leading to the repression of their expression. TCF4 expression is consistently downregulated in three EndoMT models. TCF4 downregulation diminishes its inhibitory effect on the TGFB signaling pathway, leading to upregulation of SNAI1 and TGFB1, and subsequently enhancing EndoMT. This, in turn, further suppresses TCF4 expression. Consequently, the TCF4-TGFB1 feedback loop is formed to intensify the EndoMT process. We demonstrate that introducing exogenous TCF4 disrupts this TCF4-TGFB1 feedback loop of EndoMT, rescuing EC phenotype and function under TGFB1 stimulation, as well as ECs from heart failure patients. Our results reveal a key role of TCF4 in safeguarding EC identity and preventing EndoMT, suggesting a therapeutic potential of TCF4 for EndoMT-related cardiovascular diseases.

overall_design: CUT&RUN analysis of TCF4 and SNAI1 in HUVECs to identify their binding peaks.

first: Gaopeng

last: Xian

first: Rongbin

first: Lili

last: Zhang


title: Differential contribution of TFE3 isoforms to cell motility and invasion

first: Pablo

last: Contreras

address: 50 South Dr.

institute: NIH

summary: We and other have previously reported that TFE3 migrates as two distinct bands of approximately 72 and 82 kDa in SDS-PAGE. Interestingly, whereas the smaller form of TFE3 is always present in cell lysates, the higher molecular weight form appears only after specific stress conditions, such as prolonged starvation. A recent report suggested that the 82 kDa form does in fact corresponds to TFE3 full length (TFE3-L). It was proposed that the control of TFE3 stability may constitute the main mechanism of TFE3 regulation. There is, however, a critical question that remains to be addressed regarding the role of the 72 kDa TFE3 short isoform (TFE3-S). TFE3-S is expressed at high levels in most cell types and its expression remains constant both under control and stress conditions. Characterizing the nature and regulation of TFE3-S, as well as its potential transcriptional activity and selectivity, is therefore essential to fully understand TFE3 regulation.

overall_design: To investigate the transcriptional capability of TFE3-L and TFE3-S, we generated adenovirus (Ad) expressing either recombinant (r)TFE3-L or rTFE3-S. ARPE-19 cells were infected for 30 hours with Ad-rTFE3-L, or Ad-rTFE3-S or Ad-Null as a negative control to compare.

first: José

middle: A

last: Martina

first: Katie

last: Rollins

first: Euteum

last: Jeong

first: Alberto

last: Rissone

first: Rosa

last: Puertollano


title: In situ multi-modal characterization of pancreatic cancer reveals tumor cell identity as a defining factor of the surrounding microenvironment. [RNA-Seq]

first: Brian

last: Rabe

summary: Pancreatic ductal adenocarcinoma is heterogeneous, with low tumor purity, a prominent microenvironment, and complex architecture, which preclude the identification of shared tumor-intrinsic and stromal biology within and across patients. We overcame these challenges by achieving necessary resolution and context through the application of complimentary genomics, pathology and machine learning approaches to characterize primary untreated tumors from 39 patients. We capture 340K spatial low-bulk and 530K spatial single-cell transcriptomes and observe a spectrum of classical-to-basal tumor subtypes present within all patients. We find each subtype has distinct regulators, stromal neighborhoods, microenvironment, extracellular matrix and histology corresponding to multiple immunosuppressive and therapy resistance mechanisms. We define key tumor heterogeneity features including the presence of mixed KRAS mutations and tertiary lymphoid structures; identifying biomarkers that distinguish the latter from lymph nodes. Lastly, leveraging patient, cell and mouse data, we determine which aspects of tumor biology are recapitulated in bulk datasets and reductionist models.

overall_design: RNAseq characterization of Panc0203, Panc0403, Panc1, AsPC1, and PACADD-188 cells in normoxia vs hypoxia (1%O2) over the course of 14 days

first: Anna

last: Lyubetskaya

first: Andrew

last: Kavran

first: Yulong

last: Bai

last: Fisher

first: Alba

last: Font-Tello

first: Anne

last: Lewin

first: Hannah

last: Pliner

first: Yunfan

last: Fan

first: Lauren

last: Giampapa

first: Yelena

last: Cheng

first: Chao

last: Dai

first: Ruifeng

last: Hu

first: Tom

last: Lila

first: Alexandre

last: P Alloy

first: Mike

last: Mason

first: Constance

last: Brett

first: Todd

first: Fayaz

last: Seifuddin

first: Steven

last: Vasquez Grinnell

first: Soren

middle: R

last: Stahlschmidt

first: Yilin

last: Zhao

first: Ryan

last: Golhar

first: Isaac

last: Neuhaus

first: Daniel

last: Carrera

first: Carlos

last: Rios

first: Pradeep

last: Kar

first: Abhishek

last: Shukla

first: Rachael

last: Bashford-Rogers

first: Matthew

last: Meyer

first: Enas

last: Abu Shah

first: Lara

last: Heij

first: Shivan

last: Sivakumar

first: Jimena

last: Trillo Tinoco

first: Benjamin

first: Konstantinos

last: Mavrakis

first: Eugene

last: Drokhlyansky


title: The Retinal Determination Gene Network can confer chemoresistant properties to AML

city: Manchester

first: Georges

last: Lacaud

state: England

address: Wilmslow Raod

department: Stem Cell Biology

country: United Kingdom

institute: Cancer Research UK Manchester Institute

summary: HoxA9, Six1 and Eya1 are targets of MOZ-TIF2 and MLL-AF9 fusion proteins in murine models. Hoxa9 overexpression can induce AML in murine HSPCs with a latency of ~6-9 months. Co-overexpression of RDGN members Six1 or Eya1 with Hoxa9 can enhance the differentiation block and colony forming potential of HoxA9 alone in vitro. RNA-seq was carried out on these lines to establish genetic pathways responsible for these chages in leukemogenicity. Benzarone is a potent EYA1 inhibitor. We wanted to assess if this drug was able to reverse the leukemogenic properties that EYA1 adds to HOXA9.

overall_design: Murine c-Kit+ cells were isolated from the bone marrow of female C57BL/6 mice. Cells were maintained in MT2 media  for 1 day before being retrovirally transduced with flourescent reporter plasmids encoding HoxA9 alone, or together with Six1/Eya1. Lines were  established in methylcellulose culture for 3 weeks before being cell sorted for their reporter construct and squenced. HOXA9_EYA1 lines were treated with either 5ug Benzarone or a DMSO (vehicle) control for 72hrs before RNA was extracted and samples sent for sequencing. HOXA9 alone (4 samples), HOXA9+SIX1 (4 samples).

first: Liam

last: Clayfield

first: Divya

last: Mailk

first: Anne

last: Largeot

first: Renaud

last: Mevel

first: Muhammad

middle: Z

last: Fadlullah

first: Rahima

last: Patel

first: Martyna

last: Szpakowska

last: Maqbool

first: Michael

last: Lie-a-ling

first: Andy

last: Chevigne

first: Jessica

last: Whittle

first: Pascal

last: Maire

first: Tim

last: Somervaille

first: Heide

last: Ford

first: Valerie

last: Kouskoff


title: TSniffer: Unbiased de novo identification of RNA editing sites and quantification of editing activity in RNA-seq data

city: Rochester

first: Christian

middle: Karl

last: Pfaller

state: MN

address: 200 First Street SW

department: Molecular Medicine

institute: Mayo Clinic

summary: RNA editing by adenosine deaminases acting on RNA (ADARs) is an evolutionarily conserved posttranscriptional modification essential for organismal development and normal cell function. Three catalytically active ADARs are conserved in mammals: two isoforms of ADAR1 referred to as ADAR1-p150 and ADAR1-p110, as well as ADAR2. All recognize and edit double-stranded RNA (dsRNA) structures but demonstrate target specificity and selectivity that dictate the unique essential biological functions of the three enzymes. The editing activity of ADAR1-p150 suppresses autoimmune responses against self-RNA structures, whereas ADAR1-p110 and ADAR2 have other primary functions. To better understand the mechanism of target selection by ADARs, we developed TSniffer, which allows accurate de novo identification of edited transcripts and quantification of the extent of editing within each transcript. We found that 17-40% of protein coding transcripts in mice, ferrets, and humans are edited by ADARs. Individual transcripts can harbor hundreds and thousands of editing sites, mostly within inverted retrotransposable elements. For human transcripts, we found differential editing by ADAR1 and ADAR2, aligning with a supportive role for ADAR2, while some targets were dominantly edited by ADAR1. Relying only on RNA-seq data and reference genome, TSniffer represents a novel tool to decipher the role of ADAR editing in different physiological states including disease models. Its unbiased approach is suitable for any organism.

sample_organism:
Homo sapiens
Mustela putorius furo

platform_organism:
Homo sapiens
Mustela putorius furo

overall_design: We analyzed RNA-seq datasets from wild type (WT) and ADAR-deficient mouse and human samples, GTEx datasets of human brain, and of ferret PBMCs.

first: Maike

last: Herrmann

first: Yvonne

last: Krebs

first: Francisco

last: Acosta

first: Sebastian

last: Parusel

first: Oliver

last: Siering

first: Felix

middle: G

last: Andres

first: Biruhalem

last: Taye

first: Csaba

last: Miskey

middle: K


title: A spatially resolved atlas of gastric cancer characterises a lymphocyte aggregated region [scRNA-seq]

city: Beijing

first: Zemin

last: Zhang

address: No.5 Yiheyuan Road, Haidian District

institute: Peking University

summary: The tumour microenvironment (TME) is a focal point in cancer immunotherapy: its cellular composition and spatial organisation, especially the distribution of lymphocytes, can affect the clinical outcomes of cancer patients. In addition, the function of a cell differs depending on its spatial location and interaction with neighbouring cells. Here, by integrating single-cell transcriptomics with spatial transcriptomics, we survey how the spatial distribution of different cell types varies across diverse histological regions of gastric cancer. Notably, tertiary lymphoid structures (TLSs), a tissue architecture harbouring lymphocytes more than any other region within the TME, possess great potential in modulating anti-tumorigenic immunity by elevating an array of genes (FDCSP and CCL19) principally involved in lymphocyte recruitment and activation.  Our findings advance the understanding of TLSs in contributing to anti-tumorigenic immunity in a spatially resolved context, which could be further leveraged as a predictive marker for immunotherapy response.

overall_design:
We built a high-resolution single-cell transcriptomic atlas by sequencing cells derived from four different tissue sources, including surgically resected tumour (denoted as T), histologically normal adjacent tissue (N), lymphoid node (L), and peripheral blood (P), from a cohort of 27 treatment-naive donors with GC, covering two clinical phenotypes — subtype (diffuse, indeterminate, and intestinal) and stage (I, II, and III).
*** Submitters state that they are not permitted to submit raw data (to GEO) by Ministry of Science and Technology, China***

first: Sen

last: Gao


title: In situ multi-modal characterization of pancreatic cancer reveals tumor cell identity as a defining factor of the surrounding microenvironment [Spatial Transcriptomics]

first: Brian

last: Rabe

summary: Pancreatic Ductal Adenocarcinoma (PDAC) is heterogeneous with low tumor purity, prominent microenvironment and complex architecture, which preclude identification of shared tumor intrinsic biology within and across patients. We overcame these challenges by applying spatial omics approaches – providing necessary resolution and context – to primary untreated PDAC tumors from 39 patients capturing 340K low-bulk and 530K single-cell spatial transcriptomes. We observe a spectrum of classical-to-basal tumor subtypes present within all patients. We identify a distinct population of proliferative tumor cells enriched for the DNA synthesis-condensation-mitosis transcriptional network suggesting this subset disproportionately contribute to tumor growth. Furthermore, we characterize the microenvironment surrounding each tumor subtype and observe that basal identity is contextually defined by collagen, hypoxic adaptation and fibroblast neighbors expressing activated stroma and interferon stimulated gene therapy resistance signatures. Lastly, leveraging orthogonal patient, cell and mouse data, we determine which aspects of PDAC biology are recapitulated in bulk datasets and reductionist models.

overall_design: PDAC tumors, resected following FOLFIRINOX neoadjuvant treatment, were FFPE embedded, and sectioned for spatial transcriptomic analysis using Visium for FFPE (human probeset v2)

first: Anna

last: Lyubetskaya

first: Andrew

last: Kavran

first: Yulong

last: Bai

last: Fisher

first: Hannah

last: Pliner

first: Alba

last: Font-Tello

first: Anne

last: Lewin

first: Ruifeng

last: Hu

first: Alexandre

middle: P

last: Alloy

first: Yelena

last: Cheng

first: Chao

last: Dai

first: Yunfan

last: Fan

first: Constance

last: Brett

first: Todd

first: Lauren

last: Giampapa

first: Sören

last: Stahlschmidt

first: Fayaz

last: Seifuddin

first: Steven

last: Vasquez Grinnell

first: Daniel

last: Carrera

first: Carlos

last: Rios

first: Tom

last: Lila

first: Pradeep

last: Kar

first: Abhishek

last: Shukla

first: Rachael

last: Bashford-Rogers

first: Lara

last: Heij

first: Mike

last: Mason

first: Ryan

last: Golhar

first: Isaac

last: Neuhaus

first: Enas

last: Shah

first: Jimena

middle: T

last: Tinoco

first: Benjamin

last: Chen

first: Shivan

last: Sivakumar

first: Konstantinos

last: Mavrakis

first: Eugene

last: Drokhlyansky


title: The Retinal Determination Gene Network can confer chemoresistant properties to AML [THP1_chip_rna]

first: Georges

last: Lacaud

summary: SIX1 is a target of MLL-AF9 and MOZ-TIF2 fusions in murine models of AML. SIX1 is also expressed in a subset of human AML cell lines. Being a transcription factor we have studied the functional loss of SIX1 in this cell line.

overall_design: ChIP sequencing of  1x10^8 formaldehyde crosslinked WT THP1 cells, using IgG as an isotype control. CRISPR CAS9 generated THP1 cells were also transduced with two guides targeting exon 1 and 2 of the SIX1 gene. Cells were sorted for guide expression and sequenced at 24, 48 and 72hrs to understand the dynamic gene changes upon SIX1 loss.

first: Liam

last: Clayfield

first: Divya

last: Mailk

first: Anne

last: Largeot

first: Renaud

last: Mevel

first: Muhammad

last: Fadlullah

first: Rahima

last: Patel

first: Martyna

last: Szpakowska

last: Maqbool

first: Michael

last: Lie-a-ling

first: Andy

last: Chevigne

first: Jessica

last: Whittle

first: Pascal

last: Maire

first: Tim

last: Somervaille

first: Heide

last: Ford

first: Valerie

last: Kouskoff

last: Lacaud#


title: Single-nucleus multiomic profiling of mouse substantia nigra across age

city: San Diego

first: Kangli

last: Wang

address: 9500 Gilman Drive

institute: University of California San Diego

summary: We used single-nucleus multiomic sequencing (snRNA-seq + snATAC-seq) to analyze the dynamic transcriptional regulation in mouse substantia nigra cell types across aging.

overall_design: Chromium Single-Cell Multiome ATAC + Gene Expression for mouse substantia nigra in four age stages of 2, 6, 12, and 18 months.

first: Allen

first: Bing

last: Ren


title: TSniffer: Unbiased de novo identification of RNA editing sites and quantification of editing activity in RNA-seq data [re-analysis]

first: Christian

last: Pfaller

relation:
Reanalysis of: GSM3167406
Reanalysis of: GSM3167414
Reanalysis of: GSM2474527
Reanalysis of: GSM2474528
Reanalysis of: GSM2474529
Reanalysis of: GSM3854153
Reanalysis of: GSM3854154
Reanalysis of: GSM3854155

overall_design:
We analyzed RNA-seq datasets from wild type (WT) and ADAR-deficient mouse and human samples, GTEx datasets of human brain, and of ferret PBMCs.

The re-analysis details are provided in the 'readme_re-analysis_details.txt', 'sample_to_processed_data_file.txt' files.

***************************************************************
The table below lists GEO accessions reused/reanalyzed for this study.
***************************************************************

The following re-analyzed samples are from GTEx data series (dbGaP phs000424):

Sample title SRA Experiment BioSample BioProject
GTEx, human brain, donor 1 SRX1153214 SAMN03878157 PRJNA75899
GTEx, human brain, donor 2 SRX1153642 SAMN03877474 PRJNA75899
GTEx, human brain, donor 3 SRX1155861 SAMN03878313 PRJNA75899

first: Maike

last: Herrmann

first: Yvonne

last: Krebs

first: Francisco

last: Acosta

first: Sebastian

last: Parusel

first: Oliver

last: Siering

first: Felix

last: Andres

first: Biruhalem

last: Taye

first: Csaba

last: Miskey


title: In situ multi-modal characterization of pancreatic cancer reveals tumor cell identity as a defining factor of the surrounding microenvironment [Nanostring CosMx]

first: Brian

last: Rabe

overall_design: FFPE sections of treatment naïve PDAC tumor resections were characterized using the CosMx tecnology through the Nanostring technology access program (TAP, 1k universal RNA panel).

first: Anna

last: Lyubetskaya

first: Andrew

last: Kavran

first: Yulong

last: Bai

last: Fisher

first: Alba

last: Font-Tello

first: Anne

last: Lewin

first: Hannah

last: Pliner

first: Yunfan

last: Fan

first: Lauren

last: Giampapa

first: Yelena

last: Cheng

first: Chao

last: Dai

first: Ruifeng

last: Hu

first: Tom

last: Lila

first: Alexandre

last: Alloy

first: Mike

last: Mason

first: Constance

last: Brett

first: Todd

first: Fayaz

last: Seifuddin

first: Steven

last: Vasquez Grinnell

first: Soren

last: Stahlschmidt

first: Yilin

last: Zhao

first: Ryan

last: Golhar

first: Isaac

last: Neuhaus

first: Daniel

last: Carrera

first: Carlos

last: Rios

first: Pradeep

last: Kar

first: Abhishek

last: Shukla

first: Rachael

last: Bashford-Rogers

first: Matthew

last: Meyer

first: Enas

last: Abu Shah

first: Lara

last: Heij

first: Shivan

last: Sivakumar

first: Jimena

last: Trillo Tinoco

first: Benjamin

last: Chen

first: Konstantinos

last: Mavrakis

first: Eugene

last: Drokhlyansky


title: Open chromatin, HIF binding and mRNA expression analysis in primary tubule and ccRCC cells

city: Aachen

first: René

last: Krüger

address: Pauwelsstraße 20

department: Institute for Stem Cell Biology

institute: RWTH Aachen University Medical School

overall_design: Refer to individual Series

first: Johannes

last: Schödel


title: Hepatic GPNMB aggravates NASH through binding to RYK [RNA-Seq]

city: Wuhan

first: Yue

last: Xi

state: Hubei

address: 81 St

department: College of life sciences

institute: Wuhan University

summary: The goals of this study are to define the moelcular events in NASH and to determine the role of GPNMB and RYK in NASH development

overall_design: RNA-seq analysis on mouse livers treated with HFHC, AMLN or ND and on Huh7 cells stably transfected with RYK and treated with GPNMB ECD for 8 h

first: Waner

last: Zeng

first: Bao-Liang

last: Song


title: A spatially resolved atlas of gastric cancer characterises a lymphocyte aggregated region [bulk RNA-seq]

first: Zemin

last: Zhang

overall_design:
We built a high-resolution single-cell transcriptomic atlas by sequencing cells derived from four different tissue sources, including surgically resected tumour (denoted as T), histologically normal adjacent tissue (N), lymphoid node (L), and peripheral blood (P), from a cohort of 27 treatment-naive donors with GC, covering two clinical phenotypes — subtype (diffuse, indeterminate, and intestinal) and stage (I, II, and III). In addition, 19 tumour samples were assayed by 33 ST sections, covering three categories of sampling locations in the tumour (core, in-between, and edge).
After dichotomising tumour samples into Groups A and B based on their cellular composition using ST, we performed RNA-seq on the remaining tumour samples to verify the findings revealed by ST.
*** Submitters state that they are not permitted to submit raw data (to GEO) by Ministry of Science and Technology, China***

first: Sen

last: Gao


title: In vivo CRISPR screening identifies SAGA complex members as a key regulators of hematopoiesis [RNA]

status: Public on Dec 02 2025

city: Philadelphia

first: Michael

last: Haney

state: PA

address: 422 Curie Boulevard

institute: University of Pennsylvania, Perelman School of Medicine, Department of Pathology

summary: The biological mechanisms that sustain the vast blood production required for healthy life remain incompletely understood. To search for novel regulators of hematopoiesis, we performed a genome-wide in vivo hematopoietic stem and progenitor cell (HSPC)-based CRISPR knockout screen for regulators of hematopoiesis. We discovered SAGA complex members, including Tada2b and Taf5l, as key regulators of hematopoiesis. Loss of Tada2b or Taf5l strongly inhibited hematopoiesis in vivo, causing a buildup of immature hematopoietic cells in the bone marrow. The SAGA complex deposits histone H3 lysine 9 acetylation (H3K9ac) and removes histone H2B ubiquitination (H2Bub). Loss of Tada2b led to reductions in H3K9ac levels and altered H2Bub enrichment in HSPCs, implicating disruption of SAGA complex activity. This was associated with upregulation of interferon pathway genes, reduced mitochondrial activity, and increased megakaryocyte progenitor cell commitment. Loss of these factors also enhanced the cell outgrowth and the interferon pathway in an in vivo human myelodysplastic syndrome cell line model. In summary, this study has identified the SAGA complex as an important regulator of hematopoiesis.

overall_design: Bulk RNA-seq of HSPCs

first: Adam

last: Wilkinson

first: Leonid

last: Olender


title: Identification of differentially expressed genes associated with tracheal injury recovery in a rabbit model of septic shock

city: Shijiazhuang

first: pei

last: zhang

state: He

address: No. 215, Heping West Road, Xinhua District,

department: Intensive Care Unit of Department of Anesthesiology

institute: HeBei Medical University

summary: Our study results suggest that APOB and CD36 may be involved in the pathogenesis of tracheal injury recovery in septic shock patients treated with NE.

overall_design: Nine New Zealand white rabbits were randomized to control (CON), septic shock model (SS), and septic shock norepinephrine treatment (SSNE) groups (each group n = 3). The SS and SSNE groups were injected with lipopolysaccharide to induce septic shock. The SSNE group was administered Ringer lactate with norepinephrine to maintain normal blood pressure. All animals underwent cuffed endotracheal intubation for 2 h. The injured tracheal segment was harvested. RNA sequencing was performed to identify the DEGs, followed by bioinformatics analysis, and pathological staining (both HE and Masson) was performed for pathological evaluation. Bioinformatics analysis included principal component analysis (PCA), gene set enrichment analysis (GSEA), and protein-protein interaction (PPI) network construction. Key findings were validated by qRT-PCR and immunohistochemistry.

first: Pei

first: Huaihai

last: Lu

first: Xuze

last: Li

first: Ye

last: Tian

first: Wenbin

first: Shuxian

last: Ma

first: Chao

last: Liu

first: Xvefang

first: Lining

last: Huang


title: Investigating and correcting a rare pathogenic mutation in GDF11

city: West Hartford

first: Sean

last: Congdon

state: CT

address: 200 Bloomfield Rd

institute: University of Hartford

summary: Single nucleotide variants (SNVs) and small insertions or deletions (indels) underlie most rare monogenic disorders, yet therapeutic strategies to precisely correct these mutations remain limited. Prime Editing enables repair of such pathogenic variants without introducing double-stranded breaks. Here, we applied CRISPR Prime Editing to model and correct a de novo GDF11 nonsense mutation (Tyr336*) identified in a participant from the Undiagnosed Diseases Network (UDN) with growth delay and multisystem abnormalities. Using HEK293T cells, we generated heterozygous GDF11 Tyr336* clones, which exhibited reduced GDF11 protein levels due to post-translational degradation likely mediated by ER- and Golgi-associated quality control pathways.  These cells displayed marked Golgi abnormalities, including an increased number of compact, irregularly shaped Golgi structures, findings consistent with Golgi fragmentation and stress. Transcriptomic profiling of HET cells revealed broad dysregulation of gene networks, including downregulation of metabolic and Golgi-linked biosynthetic genes, and upregulation of cell-adhesion and extracellular matrix genes. These transcriptional shifts paralleled the participant’s developmental, neural, and cardiovascular phenotypes. To correct the mutation, we tested multiple bespoke Prime Editing strategies and identified PE7, in combination with a pegRNA designed by Pridict, as the most effective ribonucleoprotein complex for rescue. Editing efficiency was further enhanced by introducing an additional silent PAM-disrupting mutation, likely preventing both Cas9 re-binding and mismatch repair. Together, these findings support a haploinsufficiency mechanism for the GDF11 Tyr336* allele and establish a generalizable framework for disease modeling and allele-specific correction of pathogenic variants in human cells.

overall_design: This study used CRISPR prime editing in HEK293T cells to generate a heterozygous line carrying the GDF11 Tyr336* allele on two of the three chromosomes, and we compared its transcriptomic profile to that of wild-type HEK293T cells

first: John

last: Bennett

first: Rhoddean

last: Opinya

first: Amara

last: Agosto

first: Olivia

last: Dossias

first: Christopher

last: Kokko

first: Aime

last: Levesque

first: Andrew

middle: O

last: Koob

last: Silver

first: Cindy

last: Thomas-Charles


title: Tracing the molecular route to progression in miRNA biogenesis-defective thyroid lesions [InfiniumMethylationData]

status: Public on Dec 10 2025

city: Hospitalet de Llobregat

first: Barbara

last: Rivera

address: Granvia de l'Hospitalet de Llobregat, 199

country: Spain

institute: IDIBELL

type: Methylation profiling by genome tiling array

summary: Germline and somatic alterations in DICER1 and DGCR8 microprocessors confer risk of developing benign and malignant thyroid lesions, yet the molecular events driving malignant transformation remain unclear. We trace the molecular trajectories from benignity to malignancy in DICER1/DGCR8-mutated thyroid lesions using multi-omic profiling on 27 DICER1/DGCR8-mutated samples. Our findings reveal a progressive, specific, and linear accumulation of genetic alterations, which when combined with enhanced downregulation of miRNAs distinguished DICER1/DGCR8-malignant lesions from their benign counterparts. Compensatory hypomethylation of miRNA encoding genes characterised DICER1/DGCR8-benign lesions, but as the tumors progressed to malignancy, methylation was partly reimposed, reversing the attempts to activate miRNA-encoded genes and further compromising miRNA production. Transcriptomic analyses revealed mutation-specific effects on the microenvironment, whereby DICER1 mutations activated canonical thyroid cancer progression pathways, whereas altered DGCR8 associated with immune-related alterations. This work unveils specific molecular events underlying malignant progression of miRNA-biogenesis related thyroid tumors and identifies potential biomarkers and disease etiology mechanisms.

overall_design: Thyroid lesion-specific genome-wide DNA methylation profiling was investigated in 3 FFT and 9 FFPE samples (5 TFNDs, 4 FTCs, 1 FVPTC, and 2 PDTCs) using the Illumina HumanMethylation EPIC array at GenomeScan (Leiden, The Netherlands). The data from these samples was combined with data from 5 publicly available datasets from the Gene Expression Omnibus (GEO): GSE121377, GSE197860, GSE97466, and GSE77804 and GSE214568 (thyroid data only); and 1 publicly available dataset from ArrayExpress: E-MTAB-10906. All 6 datasets employed Illumina platforms, with four using the EPIC array and two using the Illumina 450K array. Four datasets were also derived from FFT samples while the other two datasets were derived from FFPE samples. From these 6 studies, we included a total of 277 thyroid samples: 21 FVPTCs; 4 PTC, not otherwise specified (PTC-NOS); 6 ATCs; 6 OTAs; 8 OTCs; 60 CPTCs; 57 normal thyroid tissues; 29 TFNDs; 20 FTAs; 8 tall-cell variant PTC; 26 FTCs; 3 PDTCs; 7 NIFTPs; and 22 nodular hyperplasias. Additionally, we included 2 DICER1-mutated FVPTCs and 2 DGCR8-mutated FVPTC from the TCGA-THCA project.

first: Chong

last: Anne-Sophie

first: Roca

last: Carla


title: Symptomatic SARS-CoV-2 breakthrough infections broaden the repertoire of Spike-reactive CD4 T cells

city: La Jolla

first: Emil

last: Johansson

state: California

address: 9420 Athena Cir

department: Center for Autoimmunity and Inflammation

institute: La Jolla Institute for Immunology

summary: SARS-CoV-2 breakthrough infections (BTI) are relatively common, but little is known in terms of differentiating responses associated with asymptomatic BTI (ABTI) versus symptomatic BTI (SBTI). Here, we investigated the impact of ABTI and SBTI on antibody and T cell responses towards Spike. SBTI donors had significantly higher plasma anti-Spike RBD IgG titers compared to both ABTI and SARS-CoV-2 vaccinated donors with no signs of previous infection (VAX) donors. While no impact of ABTI or SBTIs was found in the magnitude of Spike-specific CD4 and CD8 T cell responses, both ABTI and SBTI donors had significantly higher CD4 T cell responses towards non-Spike antigens. In-depth characterization of Spike-specific CD4 and CD8 T cells at scRNA/TCRseq level revealed that ABTI and SBTI induced different alterations of the CD4 compartment. These included a IFNGhigh skewed response among cytokine-producing cells, and a concurrent expansion of type II IFN-responsive TH17-like cells in SBTI. SBTI donors were further found to have an increased CD4 TCR repertoire diversity compared to VAX donors. ABTI-associated alterations of the Spike-specific compartment were intermediate between SBTI and VAX groups, likely reflecting lower antigen exposure and less inflammatory environment during ABTIs versus SBTIs.

overall_design: Here, we used single-cell RNA sequencing (scRNAseq) and T cell receptor sequencing (scTCRseq) to characterize Spike (S)-specific T cell responses in VAX, ABTIs, and SBTIs, to define distinct immunological signatures related to T cell functionality and T cell subsets responding to antigen stimulation. We performed scRNAseq and scTCRseq on S-reactive CD4 T cells by sorting AIM+ (OX40+CD137+) cells following S megapool  stimulation.

first: Johansson

last: Emil

first: da Silva Antunes

last: Ricardo

first: Sette

last: Alessandro


title: A transcriptomic signature that predicts pre-hypertension in adolescence and higher systolic blood pressure in childhood

first: Terence

last: Garner

address: St Mary's Hospital, Oxford Road

department: Division of Developmental Biology and Medicine

institute: University of Manchester

summary: Suboptimal fetal growth (SFG), being born small-for-gestational-age (SGA), and catch-up (CU) growth are individually and together linked to cardiometabolic (CM) risks. However not all develop adverse outcomes. This study aimed to validate a transcriptomic signature to identify individuals at greatest CM risk. Using National Heart Lung and Blood Institute criteria to define CM risk, healthy and prehypertensive 17-year-olds were identified in the ALSPAC (UK) childhood cohort. Epigenomic and transcriptomic differences were analysed. A hypernetwork identified functionally related genes, which were used in random forest classification to predict prehypertensive phenotypes. The BabyGRO (UK) cohort included 80 children aged 3–7 years, born at term following pregnancies with SFG risks. Anthropometric, CM markers and transcriptomic profiles were collected, fetal and childhood weight trajectories and their relationship to CM markers assessed, and transcriptome used for prediction. CU-SGA individuals in ALSPAC were 1.6 times more likely than all others to be prehypertensive at 17 years (p<1x10⁻⁵). A 42-gene hypernetwork cluster was highly predictive of prehypertension (AUC 0.984, error rate 5.4%). In BabyGRO, 20 of these genes accurately predicted higher systolic blood pressure (AUC 0.971, error rate 3.6%). This transcriptomic signature could help identify children with adverse pre- and postnatal growth who may develop prehypertension.

overall_design: RNA-seq profiling of blood samples from children aged three-to-seven following detection of risk of FGR

first: Reena

last: Perchard

first: Philip

last: Murray

first: Amirul

last: Roslan

first: Lucy

middle: E

last: Higgins

first: Edward

middle: D

last: Johnstone

first: Adam

last: Stevens

first: Peter

last: Clayton


title: Single-cell transcriptional profiling of cancer cells in hairy cell leukemia (HCL) patients

city: Bethesda

first: Chi-Ping

last: Day

state: Maryland

address: Bldg 15C1, NIH-Bethesda

department: National Cancer Institute

institute: National Institutes of HEalth

summary: This single-cell RNA sequencing (scRNA-seq) dataset profiles human HCL cells from two patients with Hairy Cell Leukemia (HCL) and varient subtype of HCL (HCLv), both expressing unmutated IGHV4-34. scRNA-seq was performed on isolated CD19⁺ and CD3⁺cells from peripheral blood mononuclear cells (PBMC) (n=2). The dataset enables the characterization of expressed mutation and transcriptional profiles of human HCL cells and supports investigations into cellular lineage and pathways associated with pathologic activation leading to HCL and variant form of HCL (HCLv).

overall_design: This study (protocol# 10C0066) was approved by the National Institutes of Health Institutional Review Board (IRB). Fresh peripheral blood were collected from 2 patients diagnosed with HCL undergoing standard-of-care therapeutic treatment. All patients signed IRB-approved informed consent permitting the use of their blood for research. PBMCs were purified from peripheral blood, and cells positive for either CD19 or CD3 were isolated for full-length single-cell sequencing. The expressed mutations and transcriptional profiles were analyzed for identifying the lienage and developmental state of the single cells.

first: Robert

last: Kreitman

first: Evgeny

last: Arons

first: Chih-Hao

last: Wu

first: Suleyman

middle: C

last: Sahinalp


title: Multi-omics integration identifies diverse transcripts and chromatin accessibility profiles in Monopterus albus gonads

first: Yuan

last: Zhao

address: Donghu Road 7th

institute: Institute of Hydrobiology, Chinese Academy of Sciences

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


title: A spatially resolved atlas of gastric cancer characterises a lymphocyte aggregated region [Spatial Transcriptomics]

first: Zemin

last: Zhang

overall_design:
Nineteen tumour samples were assayed by 33 ST sections, covering three categories of sampling locations in the tumour (core, in-between, and edge). In addition, we assayed 39 replicates from the main study cohort using ST.
*** Submitters state that they are not permitted to submit raw data (to GEO) by Ministry of Science and Technology, China***

first: Sen

last: Gao


title: Transcription termination counteracts DNA damage after WEE1 inhibition

city: Oslo

first: Randi

last: Gussgard Syljuåsen

address: Ullernchausseen 70

department: Department of Radiation Biology, Institute for Cancer Research

country: Norway

institute: Oslo University Hospital

summary: Transcription termination is a key regulatory step in transcription and a potential target for cancer therapy, but how it can be exploited for treatment is incompletely understood. Here we show that transcription termination plays a crucial role in mitigating DNA damage and cell death upon WEE1 inhibition by adavosertib. Depleting five different transcription termination factors (WDR82, PNUTS, XRN2, DDX5 or CPSF73) increased adavosertib-induced DNA damage in S-phase. Conversely, inhibiting active transcription with DRB or triptolide, or co-depleting CDC73, a component of the PAF1 transcription elongation complex, reduced such damage. Additionally, read-through transcription following WDR82 depletion was partially inhibited by co-depletion of CDC73, supporting that read-through transcription contributes to DNA damage in response to WEE1 inhibition. Moreover, combining adavosertib with the CPSF73 inhibitor JTE-607, an anticancer compound which promotes read-through transcription, increased DNA damage during S-phase. Elevated expression of CPSF73 is associated with aggressive disease in prostate cancer patients, and combining JTE-607 with adavosertib synergistically reduced prostate cancer cell survival. Our findings suggest that transcription termination helps prevent toxic conflicts between transcription and replication following increased replication initiation caused by WEE1 inhibition.

overall_design: chromatin RNA sequencing experiment of HeLa cells 48h after transfection with scr, siWDR82, siCDC73 and siWDR82 + siCDC73


title: RNAseq of gingival fibroblasts exposed to activated platelets

city: Vienna

first: Reinhard

last: Gruber

address: Sensengasse 2a

country: Austria

institute: Medical University Vienna

summary: Platelet-rich fibrin (PRF) contains not only platelets but also leucocytes and the coagulated plasmatic fraction of centrifuged blood. Conclusions about the contribution of platelets to the overall PRF activity are, therefore, indirect. To overcome this limitation, we have used washed leucocyte-depleted platelets in our bioassays. The platelets were activated with thrombin to release the contents of their granules into the serum-free culture medium. Gingival fibroblasts were exposed to this platelet-released supernatant (PRS), and transcriptional changes were identified by RNA sequencing. Under the strict criteria of a minimal 2.0-log2 fold-expression change and a significance level of 3.0-log10, we could identify 147 up-regulated and 39 down-regulated genes. Among the genes recently identified with PRF lysates were IL11 and CXCL8, and a series of genes that indicate the mitogenic activity of PRS such as centromere-associated proteins (CENPA, E, F, M, U, W), cell division cycle proteins (CDCA2, A3, A5, A8, 6, 20, 25A, 25C, 45), kinesin-like proteins (KIF11, 14, 18A, 18B, 20A, 23, 4A, C1), and shugoshin 1 and 2, as supported by gene ontology. Verification by RT-PCR and immunoassays further confirmed the significant increase of IL11 and CXCL8 when gingival fibroblasts were exposed to PRS. Consistently, PRS provokes TGF-β but not NF-κB signaling, based on Smad2/3 and p65 translocation, respectively. In summary, our in vitro data provide support for the contribution of platelets in PRF, independent of leukocytes and plasma components, to elicit a robust response from gingival fibroblasts.

overall_design: We used washed leucocyte-depleted platelets in our bioassays. The platelets were activated with thrombin to release the contents of their granules into the serum-free culture medium. Gingival fibroblasts were exposed to this platelet-released supernatant (PRS), and transcriptional changes were identified by RNA sequencing. Verification by RT-PCR and immunoassays further confirmed the significant increase of IL11 and CXCL8 when gingival fibroblasts were exposed to PRS.

first: Panahipour

last: Layla


title: Age-dependent transcriptomic effects of morphine in the frontal cortex of female mice

city: Boston

first: Jonathan

middle: David

last: Lee

address: 3 Blackfan Circle, Rm. 424

institute: BIDMC

summary: Increasing lifespans make health problems in the elderly such as opioid misuse a more prominent concern. Understanding the effects that opioids may have on the aged brain can help us address age-related concerns of opioid exposure. This study aimed to assess potential interactions between aging and opioid exposure. Three-month-old (young adult) and 19-month-old (aged) C57BL/6JN mice were assigned to either a morphine (3mg/kg, i.p.) or saline group. A conditioned placed preference (CPP) task was used to assess reward sensitivity, while rotarod and beam walk tests were used to assess sensorimotor coordination. To assess for potential age-dependent effects of morphine on gene expression, we performed RNA sequencing in the prefrontal cortex (PFC). We found that morphine induced CPP in both age groups. Our results indicate impaired motor coordination in aged mice; however, morphine did not significantly affect motor coordination in either age group, although a trend toward an increased number of slips was observed in morphine-treated aged mice. Transcriptomic analysis revealed more robust effects of morphine on gene expression in the aged brain compared to the young brain. Interestingly, we found limited overlap between morphine-regulated genes in young and old mice, suggesting that the molecular effects of morphine are age-dependent. Taken together, while we found no significant interactions between morphine (at the tested dose) and aging in the behavioral assays, morphine caused age-dependent gene expression changes. Our findings suggest that age should be considered when prescribing opioids and that age-specific therapeutics may help address opioid use disorder in the elderly.

overall_design: RNA-seq profiling of mouse prefrontal cortex; young adult or old female mice were treated with morphine (3mg/kg, i.p.) or saline

first: Maria

last: Mavrikaki

first: Frank

middle: J

last: Slack


title: Stiffness-mediated Paracrine Signaling Enhances Induction of EMT in Oral Squamous Cell Carcinoma

middle: Jeffrey

last: Engler

state: CA

address: 2880 Torrey Pines Scenic Dr

institute: UCSD

summary: Oral Squamous Cell Carcinoma (OSCC) contains diverse communities of cells within the oral mucosa. A subset of the epithelia is highly responsive to changing niche conditions, resulting in their loss of polarity, epithelial-to-mesenchymal transition (EMT), and invasion in tumor-adjacent stroma. Given the range of cell states, we sought to understand how cytokine-mediated signaling from mesenchymal SCC25 cells or stiffness induced-mesenchymal (simCal27) cells caused EMT in naïve Cal27 epithelial cells. Media conditioned by SCC25 enhanced Cal27 cell migration, nuclear localization of EMT markers, and caused transcriptomic changes related to cytokine response ontological terms. SCC and simCal27 cells have unique cytokine profiles–which when regressed against transcriptomic changes–suggested that higher expression of IL-1a, IL-6, IL-8, Angiogenin and PAI-1 in conditioned media could drive EMT; upregulation of these cytokines also appears impactful for overall survival and progression-free interval. However, depletion and supplementation assays clearly show that the presence of these specific cytokines is critical to induce a migratory phenotype and that naïve Cal27’s motility is regulated by MAPK and AKT signaling pathways; loss or inhibition of these pathways reduced migration. These data suggest that paracrine signals from stiffness induced-mesenchymal cells act via distinct kinase pathways and may be necessary for cooperative dissemination of OSCC.

overall_design: RNA from Cal27 cells cultured with SCC25-CM for 3 days versus those cultured with fresh DMEM/F12 1:1 media for a day.

first: So Youn

last: Moon

first: Marcelo

middle: L

last: Lamers


title: Construction of a single-cell transcriptome atlas for Pogostemon cablin embryoids reveals PcNAC048 as a dual regulator coordinating lateral root morphogenesis and patchouli alcohol biosynthesis

city: Guangzhou

first: xiaobing

last: wang

address: Higher Education Mega center, Panyu, Guangzhou

institute: Guangzhou University of Chinese Medicine

summary: We have employed a single cell sequencing approach using 10x Genomics scRNAseq to study the single-cell atlas of Pogostemon cablin globular somatic embryos (GSE) and cotyledonary somatic embryos (CSE). Pseudo-time analysis reconstructed the continuous differentiation trajectory of apical meristem cells and epidermal cells. Further research identified PcNAC048 as a potential transcription factor regulating embryonic cell differentiation, which promotes lateral root development and negatively regulates the biosynthesis of patchouli alcohol. Overall, this study provides theoretical support for the development of Pogostemon cablin germplasm resources and the regulation of medicinal compounds.

overall_design: Protoplasts of globular somatic embryos (GSE) and cotyledonic somatic embryos (CSE) in P. cablin were isolated by enzymatic hydrolysis and analyzed using ScRNA-seq

first: Xiaobing

last: Wang

first: Xiaojin

last: Ge

first: Wenxuan

last: Zhong

first: Daidi

first: Zhiye

last: Yang

first: Ruoting

last: Zhan

first: Likai

last: Chen

first: Hua

last: Li


title: Targeting Pre-existing Club-Like Cells in Prostate Cancer Potentiates Androgen Deprivation Therapy

first: Gilles

last: Laverny

address: 1 rue Laurent fries

institute: IGBMC

summary: A critical knowledge gap in prostate cancer research is understanding whether castration-tolerant progenitor-like cells that reside in treatment-naïve tumors play a direct role in therapy resistance and tumor progression. Herein, we reveal that the castration tolerance of LSCmed (Lin-, Sca-1+, CD49fmed) progenitor cells, the mouse equivalent of human prostatic Club cells, arises not from intrinsic properties but from significant transcriptional reprogramming. Utilizing single-cell RNA sequencing of LSCmed cells isolated from prostate-specific Pten-deficient (Ptenpc-/-) mice, we identify the emergence of castration-resistant LSCmed cells enriched in stem-like features, driven by the transcription factor Fosl1/AP-1. We demonstrate that cells exhibiting Ptenpc-/- LSCmed characteristics are prevalent in the aggressive mesenchymal stem-like prostate cancer (MSPC) subtype recently identified in human castration-resistant prostate cancer (CRPC). Furthermore, our findings show that the dual-targeting agents JQ-1 and CX-6258—focused on Fosl1/AP-1 and PIM kinases, respectively—effectively suppress both the progenitor properties and the growth of mouse and human MSPC surrogates in vitro and in vivo. Thus, early eradication of castration-tolerant Club-like cells presents a promising therapeutic strategy to mitigate prostate cancer progression toward CRPC.

overall_design: Two groups of experimental mice (n=8 each) were castrated and after 4-day recovery, we started treatment with JQ-1 (daily) and CX-6258 (bi-weekly) versus vehicle (Fig. 6C). After 28 days, mice were euthanized, then prostates were harvested, weighed, and processed for histopathological analyses or functional assays. Two mice per condition were used to perform digital spatial profiling using the GeoMx.

first: Vanessa

last: Friedrich

first: Jacques-Emmanuel

last: Guidotti

first: Vincent

last: Goffin

first: Tao

last: Ye


title: C13 bacterial consortium is sensitive to C. jejuni infection which impacts host-derived miRNAs targeting bacterial and host genes

city: Gainesville

first: Christian

last: Jobin

state: Florida

department: Medicine

institute: University of Florida

summary: C. jejuni infection altered C13 bacterial composition and modified host extracellular vesicle (EV)-derived miRNA expression profile, associated with changes in microbial virulence gene expression. Host-derived miRNAs may be an important component of host-microbiome communication.

overall_design: Three groups of Germ Free (GF) Il10-/- mice were used in this study: 1) mice colonized with a defined consortium of 13 bacterial isolates (C13) representing the four most prominent phyla in the mouse gut.  2) C13 plus Campylobacter jejuni (C. jejuni) 81-176 and 3) GF alone.

first: Siddhi

last: Chitre

first: Raad

last: Gharaibeh


title: Inducible CD147 up-regulation boosts persistent SARS-CoV-2 infection triggering severe COVID-19 independent of ACE2 [scRNA-seq]

city: Xi’an

first: Ping

last: Zhu

address: Changle Xi Road

institute: Fourth Military Medical University

summary: The high mortality caused by severe COVID-19 poses challenges to public health. However, the pathogenesis of severe cases remains a puzzle. Here, we find that SARS-CoV-2 infection boosts CD147 inducible up-regulation, causing persistent virus infection and severe pathological lesions. Specifically, inducible expression of CD147 is transcriptionally regulated by the aryl hydrocarbon receptor (AHR) upon virus infection, while membrane-bound ACE2 decreases, thus indicating that CD147 is a predominant receptor responsible for persistent virus infection. Meanwhile, SARS-CoV-2 infection triggers immune imbalance by promoting cell death of CD4+ T and B cells and abnormal cell communications in rhesus macaque model. Meplazumab, a humanized CD147 antibody, effectively inhibits virus entry and cytokine level, and restores immune balance. We further resolve the cryo-EM structure of CD147-spike complex, and validate five pairs of residues at the interaction interface, which is blocked by Meplazumab via steric hindrance effect. Our findings uncover the pathogenesis of severe COVID-19.

sample_organism:
Macaca mulatta
Mus musculus

platform_organism:
Macaca mulatta
Mus musculus

overall_design: The rhesus macaques (n=16) were challenged with 106 TCID50 SARS-CoV-2 (Beta strain) by intratracheal routes at 0 dpi and divided into four groups. At 1 dpi, the rhesus macaques were injected intravenously with MPZ or 3E8 antibody. The groups were listed as follows: Ctrl group (PBS), MPZ group (MPZ, 10 mg/kg), 3E8 group (3E8, 10 mg/kg), and MPZ+3E8 group (MPZ, 5 mg/kg; 3E8, 5 mg/kg). At 7 dpi, the rhesus macaques were euthanized to collect the lung tissues for scRNA-seq and spatial transcriptomics analysis. Meanwhile, the lung tissues from four healthy rhesus macaques were used as the control. The hCD147 mice (n=4) were also challenged with 105 TCID50 SARS-CoV-2 (Beta strain) intranasally at 0 dpi. At 3 dpi, the mice were euthanized to collect the lung tissues for scRNA-seq and spatial transcriptomics analysis.

first: Zhi-Nan

first: Huijie

last: Bian

first: Liang

first: Ke

first: Qiang

last: Huang


title: ILC1 quiescence confers protection against MCMV infections during undernutrition

city: Akita

first: Megumi

last: Tatematsu

department: Department of Medical Biology

country: Japan

institute: Akita University Graduate School of Medicine

summary: In the liver, group 1 innate lymphoid cells (ILCs) comprise 10–20% tissue-resident ILC1 cells and 80–90% conventional NK cells. Both cells contribute to early defense against virus infection by secreting IFN-γ. However, the distinct role of ILC1 cells in viral infections remains incompletely understood. Here, we identified that ILC1 cells outnumbered NK cells, constituting 80–90% of group 1 ILCs in the liver during undernutrition. Mechanistically, undernutrition significantly reduced NK cell numbers, while hepatic ILC1 cells entered a quiescent state that allowed them to survive in an mTORC1-dependent manner. Metabolically, quiescent ILC1 cells exhibited greater glucose uptake than NK cells and efficiently utilized it via oxidative phosphorylation, which was induced by mTORC1. Finally, ILC1-deficient mice succumbed to MCMV infection under undernourished conditions, but not when fed ad libitum. These findings suggest a non-redundant function of hepatic ILC1 cells in protecting the host against MCMV infection during undernutrition.

overall_design: RNA-seq profiling of NK cells and ILC1 cells from wild type mice and Rptor flox Ncr1-Cre mice fed ad libitum or calorie-restricted.


title: Inducible CD147 up-regulation boosts persistent SARS-CoV-2 infection triggering severe COVID-19 independent of ACE2 [Spatial Transcriptomics]

last: Wang


title: STING activation induces cytotoxic and immune responses in meningiomas via inflammatory cell death pathways

city: Chicago

first: Mark

last: Youngblood

state: IL

address: 676 N. St. Clair Street; Suite 2210

department: Department of Neurological Surgery

institute: Northwestern University

summary: Meningiomas are common tumors of the central nervous system that are typically treated with surgery but lack alternative treatment options. Activation of the stimulator of interferon genes pathway with an agonist such as 8803 can trigger anti-tumor immune responses. Using integrated molecular approaches, here we show this pathway is expressed in both neoplastic and immune populations within meningiomas associated with promoter hypomethylation and increased chromatin accessibility. Treatment of diverse patient meningiomas ex vivo with 8803 induces direct tumor cytotoxicity through pyroptosis and the induction of gasdermin D membrane pore formation. Direct tumor cytotoxicity triggered by 8803 activates macrophages and upregulates matrix metalloproteinase production facilitating degradation of tumor stroma collagen. Treatment of preclinical meningiomas with 8803 induces survival benefits, including in an immune competent orthotopic setting, through remodeling of the tumor microenvironment, immune infiltration, and down regulation of tumor-mediated immune suppression thereby nominating 8803 for treatment consideration in meningiomas.

overall_design: Ex-vivo, patient derived meningiomas were processed as single cell suspensions post resection. RNA-seq profiling was applied to each patient sample with both a control treatment, and an 8803 STING-agoinst treatment

middle: W

first: Shashwat

last: Tripathi

first: Hinda

last: Najem

first: Harrshavasan

last: Congivaram

first: Mateo

last: Gomez

first: Amy

middle: B

last: Heimberger


overall_design: Refer to individual Series


title: Precise Excision of Expanded GGC Repeats in NOTCH2NLC via CRISPR/Cas9 for Treating Neuronal Intranuclear Inclusion Disease

city: Changsha

first: Yongcheng

last: Pan

state: Hunan

address: 87 Xiangya Rd

institute: Key Laboratory of Hunan Province in Neurodegenerative Disorders, Xiangya Hospital, Central South University

summary: Neuronal intranuclear inclusion disease (NIID) is an adult-onset neurodegenerative disease caused by expanded GGC repeats in the 5’ untranslated region of the human-specific NOTCH2NLC gene. The high sequence similarity between NOTCH2NLC and its paralogs poses a significant challenge for precise gene editing. Here, we develop a CRISPR/spCas9-based gene-editing strategy that precisely excises the expanded GGC repeats in NOTCH2NLC without detectable off-target effects on the highly homologous NOTCH2/NOTCH2NL family genes (<2% sequence divergence at this locus). The efficacy, specificity and safety of this approach are rigorously validated across multiple experimental models, including human cell lines, NIID iPSCs, and our previously established transgenic NIID mouse model. Our results demonstrate that precise excision of the expanded GGC repeats effectively alleviates NIID-related neuropathological, molecular and behavioral abnormalities. This study establishes the proof of concept for genome editing as a therapeutic strategy for NIID and other related repeat expansion disorders.

overall_design: We analyzed transcriptomic changes in mouse tissues and human NPCs pre- and post-gene therapy using RNA-seq.

first: Qiong

last: Liu

first: Nina

last: Xie

first: Beisha

last: Tang


title: Syndecan-1-targeted therapeutic antibody inhibits macropinocytosis and induces antitumor immunity in pancreatic cancer

city: Houston

first: Anil

last: Sood

state: Texas

address: 1515 Holcombe Blvd

institute: M. D. Anderson Cancer Center

summary: Pancreatic ductal adenocarcinoma (PDAC) remains one of the deadliest malignancies, with a 5-year survival rate of just 13%. While the development and early clinical use of small molecules targeting oncogenic KRAS mutations, key drivers of PDAC, have shown promise, resistance to these targeted therapies remains a significant challenge. We recently identified Syndecan-1 (SDC1), a highly expressed heparan sulfate proteoglycan, as a critical KRAS effector protein that promotes nutrient salvage and tumor growth. Here, we report the development of a human-specific monoclonal antibody (anti-SDC1 mAb) that inhibits PDAC cell proliferation in vitro and suppresses PDAC tumor growth in vivo. Mechanistically, anti-SDC1 mAb blocks macropinocytosis and induces antibody-dependent cellular cytotoxicity (ADCC). In vivo, anti-SDC1 mAb synergizes with standard chemotherapy, KRAS* inhibitors, and immunotherapies, resulting in tumor regression and near-complete response. These findings highlight anti-SDC1 mAb as a promising therapeutic strategy for PDAC and potentially other KRAS* and SDC1-driven tumors.

overall_design: Human AsPC-1 PDAC cells were treated with isotype or 22B under 0.2mM Gln for 3 days. Total RNA was then extracted for mRNA-seq.

first: Madelaine S

last: Theardy

first: Mitsunobu

last: Takeda

first: Zecheng

last: Yang

first: Jun

last: Yao

first: Haoqiang

last: Ying

first: Wantong


title: Macropinocytosis and vascularization detrmine response to mTOR inhibitors in lung squamous cell carcinomas

city: Los Angeles

first: Milica

last: Momcilovic

address: 10833 LeConte Ave

institute: University of California Los Angeles

summary: Resistance to small molecule inhibitors targeting key metabolic pathways in lung tumors remains a significant challenge in personalized cancer therapy. In this study, we investigated the mechanisms of resistance to the small molecule mTOR inhibitor TAK228 across lung squamous cell carcinoma (LUSC) cell lines, xenograft models, and patient-derived xenografts (PDXs). Our findings reveal that LUSC cells adapt to mTOR inhibition by engaging macropinocytosis, a form of endocytosis that facilitates enhanced uptake of extracellular nutrients, thereby increasing amino acid availability. Co-inhibition of both mTOR and macropinocytosis using small molecule inhibitors effectively reduced tumor growth. Additionally, we identified angiogenesis as a key mechanism limiting the efficacy of mTOR inhibition in vivo. Notably, prolonged treatment of PDXs with TAK228 and the glutaminase inhibitor CB-839 led to upregulation of vascularization, which coincided with a rebound in tumor growth despite the continued presence of both inhibitors. These findings highlight adaptive mechanisms that contribute to resistance to targeted therapies and provide insight into potential clinical strategies to overcome resistance in lung cancer.

overall_design: RNA-Seq profiling of (a) H1703 xenografts treated with Vehicle or TAK228 or TAK228+EIPA; (b) H2170 xenografts treated with Vehicle or TAK228; (c) PDX005 treated with Vehicle or TAK228+CB839.


title: Oxidative stress and GPX2 control pancreatic vs non-pancreatic cell fate in human endoderm

city: Poznan

first: Katarzyna

last: Blaszczyk

state: Wielkopolska

address: ul. Uniwersytetu Poznańskiego 6/1.87

department: Faculty of Biology, Institute of Molecular Biology and Biotechnology, Department of Gene Expression

institute: Adam Mickiewicz University

summary: The role of oxidative stress in cell fate decisions during human endoderm development remains poorly understood. Here, we show that GPX2, a key enzyme in the reactive oxygen species (ROS) scavenging pathway, plays a crucial role in directing pancreatic versus non-pancreatic cell fate decisions during in vitro human endoderm differentiation. Using hPSCs with GPX2 loss-of- or gain-of-function, we observed that GPX2-deficient cells exhibit a strong propensity to differentiate into liver-like cells, even under pancreatic-promoting conditions. Single-cell RNA sequencing, ATAC sequencing, and follow-up analyses revealed that GPX2 deficiency disrupts posterior foregut patterning, leading to the emergence of multilineage progenitors capable of generating liver- and intestine-like lineages. Phenotype rescue experiments demonstrated that manipulating oxidative stress levels by either inhibiting or promoting ROS production could mimic or revert the effects of GPX2 deficiency, respectively. Our findings highlight the critical role of oxidative stress in modulating developmental trajectories and suggest that GPX2 acts as a gatekeeper of pancreatic cell fate by influencing the expression of PDX1 and other lineage-specifying factors.

overall_design: Comparative gene expression profiling analysis of RNA-seq, scRNA-seq and ATAC-seq data for hPSCs and its GPX2 KO derivative in different stages of differentiation towards stem cells derived beta cells.

first: Joanna

last: Szpotkowska

first: Wojciech

last: Szlachcic

first: Maja

last: Baginska

first: Magdalena

last: Socha

first: Malgorzata

last: Borowiak


title: Inhibition of integrated stress response promotes primordial follicle activation via the mTOR pathway

city: guangzhou

first: Weiyong Wang

last: Wang

address: 382 Outer Ring East Road, Guangzhou Higher Education Mega Center

institute: south china university of technology

summary: Background: The integrated stress response (ISR) is a conserved signaling network that enables cells to cope with stress and maintain homeostasis. Accumulating evidence from both human and animal studies suggests that chronic stress has been implicated as a significant factor in the development of premature ovarian insufficiency (POI). The aim of this study was to investigate the effects of targeted ISR inhibition by ISRIB on primordial follicle activation and explore its underlying mechanisms in a mouse model.  Methods: This study used intraperitoneal injection to investigate the effects of ISR activity and its inhibitor ISRIB on primordial follicle activation in vivo. Newborn ICR mice were randomly assigned to the Control, Corticosterone, ISRIB, and Corticosterone + ISRIB groups. Mouse and human ovarian tissues were cultured in vitro and treated with ISRIB and/or a proto-oncogenic receptor tyrosine kinase (KIT) inhibitor. Various methods were used to assess differences in follicle counting, ISR activity, cell proliferation, cell apoptosis, and the mTOR pathway.  Results: ISR activity was present in normal newborn mouse ovaries and significantly increased in corticosterone-induced stress mouse ovaries. Excessive ISR activity induced by corticosterone reduced the number of primordial follicles, which could be partially reversed by ISRIB. In vitro treatment with ISRIB inhibited the protein levels of p-eIF2α and ATF4, while promoting granulosa cell proliferation and primordial follicle activation, and increasing the levels of phosphorylated mTOR (p-mTOR), phosphorylated protein kinase B (p-Akt), and KIT ligand (KITL). The KIT inhibitor ISCK03 significantly decreased the phosphorylation levels of Akt and forkhead box O3a (FOXO3a), as well as the number of growing follicles induced by ISRIB. In both in vivo injection and in vitro ovarian tissue culture models, ISRIB promoted primordial follicle activation via the mTOR pathway in pre-granulosa cells.  Conclusion: The results suggest that inhibiting ISR can prevent primordial follicle depletion caused by excessive ISR activity. ISRIB has been shown to promote primordial follicle activation in mouse and human ovaries via the mTOR pathway. These results suggest that ISRIB may be a potential therapeutic option for infertility in stress-induced POI patients.

first: Tiantian

last: Hao

first: Weiyong

first: Ziyong

last: Zhao

first: Zehua

last: Deng

first: Yashuang

last: Weng

first: Meijia

last: Zhang

first: Yuezhou

last: Chen

first: Zhenyu

last: Zhou

first: Wenbo

first: Longwei

last: Gao

first: Hongwei

last: Wei

first: Wenjun

first: Shuang


title: STING activation induces cytotoxic and immune responses in meningiomas via inflammatory cell death pathways [scMulti-omics]

first: Mark

last: Youngblood

overall_design: Single nucleus multiome (RNA-seq + ATAC-seq) profiling of frozen meningioma specimens post resection.

first: Shashwat

last: Tripathi

first: Hinda

last: Najem

first: Harrshavasan

last: Congivaram

first: Mateo

last: Gomez

first: Amy

last: Heimberger


title: Epigenetic profiling across hematopoietic stages identifies genomic loci with conserved chromatin alterations after infection

first: Pamela

last: Luna

state: TX

address: One Baylor Plaza

department: Molecular and Human Genetics

institute: Baylor College of Medicine

summary: Infection leads to durable cell-autonomous changes in hematopoietic stem and progenitor cells (HSPCs), resulting in production of innate immune cells with heightened immune function. The mechanisms underlying this phenomenon, termed central trained immunity, remain poorly understood. We hypothesized that infection induces histone modifications in chromatin, leading to changes in chromatin accessibility that are passed down from HSPCs to myeloid progenitors, monocytes and macrophages. To test this hypothesis, we conducted genome-wide surveillance of activating histone marks H3K27Ac and H3K4me3 and transposon accessibility of chromatin in hematopoietic stem cells, multipotent progenitor 3, granulocyte-monocyte progenitors, monocytes and macrophages of naïve versus Mycobacterium avium infected mice. While activating histone marks and chromatin accessibility were increased broadly in biological responses to interferon and cytokine signaling. Consistent with this finding, transcription factor binding motifs related to interferon signaling, including IRFs, NF-kB, and CEBP, were highly enriched across cell types. However, activating histone marks and increased chromatin accessibility were commonly induced at only a few loci including Irf1 and Gbp6 across multiple stages of differentiation. In summary, processing of inflammatory signaling upon systemic infection leads to epigenetic changes in HSPCs, and these changes are conserved at a small number of genetic loci in downstream monocytes.

overall_design: To understand how the overall chromatin accessibility landscape is changed in myeloid cells and their progenitors upon M. avium infection, we performed single cell assay for transposase accessibility sequencing (scATAC-seq) on targeted HSPCs and downstream terminally differentiated cells, including Mo/Macs, neutrophils, and B cells, from pooled murine samples from M. avium infected and naïve mice.

middle: N

first: Brandon

last: Tran

first: Katherine

middle: Y

last: King


title: Excitation-contraction coupling, cardiomyocyte electrophysiology, and transcriptome changes in two translational HFpEF murine models: Aetiology and sex-dependent differences

city: Seattle

first: Jennifer

last: Davis

state: WA

address: 850 Republican St, Brotman #343

department: Lab Medicine and Pathology

institute: University of Washington

summary: Heart failure (HF) with preserved ejection fraction (HFpEF) comprises heterogenous clinical phenotypes and presence of various co-morbidities. Recent two-hit translational animal models, including the hypertensive, nitrosative-stressed mice fed with high-fat diet and L-NAME (HFD+L-NAME) and the obese-diabetic leptin receptor-deficient db/db mice with excess aldosterone (db/db+Aldo), may phenocopy select subgroups of HFpEF. We systematically compared mechanisms of excitation-contraction coupling (ECC), electrophysiology, and gene transcription in these key preclinical HFpEF models and between sexes to advance translation. We performed morphometry, echocardiography, cellular electrophysiology, intracellular Ca2+ imaging, and RNA-sequencing. The multiorgan HFpEF phenotype showed key differences between the 2 models, db/db+Aldo mice were markedly obese, had severe hyperglycaemia and hepatomegaly, whereas male HFD+L-NAME mice had more pronounced cardiac hypertrophy. Diastolic dysfunction was more severe in db/db+Aldo mice and worse in females therein, whereas female sex was protective in HFD+L-NAME. Marked proarrhythmic action potential (AP) changes (AP prolongation, increased short-term variability and alternans threshold) occurred in db/db+Aldo (in both sexes), these AP changes were less severe in male HFD+L-NAME and absent in female HFD+L-NAME. In line with these, differential ionic current and Ca2+ handling changes occurred between these two HFpEF models and between sexes in each model. RNA-sequencing revealed highly distinctive gene expression profiles between HFpEF models. We conclude that marked differences exist in cardiomyocyte ECC, electrophysiology, and gene expression between HFD+L-NAME and db/db+Aldo mice and between sexes. This indicates that a combination of translational HFpEF models that mimic select HFpEF sub-phenogroups are needed to better understand HFpEF mechanisms for therapeutic drug development.

overall_design: RNAseq of whole heart samples from two groups. The first group (HFD-LNAME group) has WT mice treated with normal chow (Control - HFD-LName) and WT mice treated with high fat diet (HFD) with L-NAME (Treated - HFD-Lname). The second group (DBDB-Aldo) has WT mice treated with SHAM minipumps (Control - DBDB Aldo) and db/db mice treated with aldosterone minipumps (Treated - DBDB Aldo).

first: Bers

last: Donald

first: Heygi

last: Bence

first: Bailey

last: Logan