title: GDF5 exacerbates tubulointerstitial injury by inducing partial epithelial-mesenchymal transition of tubular epithelial cells in diabetic kidney disease

city: Chongqing

first: linqiang

last: ma

address: Medical University, No. 1 Youyi St

institute: The First Affiliated Hospital of Chongqing Medical University, Chongqing, China

summary: Adipokines serve crucial functions in diabetic kidney disease (DKD) pathogenesis. Growth differentiation factor 5 (GDF5) is highly expressed in adipose tissue, but its specific role in DKD is unknown. In this study, we observed elevated GDF5 expression in both DKD patients and db/db mice, suggesting a potential association between GDF5 and DKD progression. Elevated plasma GDF5 levels are associated with an increased risk of incident CKD in patients with type 2 diabetes mellitus. In animal studies, adipose-specific overexpression of GDF5 increased circulating GDF5 and exacerbated renal injury in db/db mice, characterized by increased tubulointerstitial injury and inflammation infiltration. Conversely, adipose-specific knockdown reduced circulating GDF5 and alleviated renal injury. In vitro studies demonstrated that GDF5 induces partial epithelial-mesenchymal transition (pEMT) in renal tubular epithelial cells via activation of the SMAD1/5/8 signaling pathway, as evidenced by reduced E-cadherin expression and increased Snail1 levels. Notably, the supernatant from GDF5-treated injured HK-2 cells was found to enhance the secretion of pro-inflammatory cytokines by macrophages. These findings suggest that adipose-derived GDF5 acts as a novel mediator contributing to tubulointerstitial injury in DKD.

overall_design: RNA-seq profliling of wildtype HK-2 cells or treat with 100ng/ml GDF5 for 48hours


title: Hydrogel-Encapsulated Primed Mesenchymal Stem Cells Enhance Regeneration and Immune Modulation in Full-Thickness Burn Wounds

status: Public on Jun 30 2026

city: UC Irvine

first: Ronke

middle: Mojoyinola

last: Olabisi

state: California

address: 3105 Natural Sciences II

department: Biomedical Engineering

country: USA

institute: UC Irvine

type: Expression profiling by high throughput sequencing

summary: Severe burn injuries pose significant clinical challenges, with high risks of infection, excessive inflammation, and impaired wound healing. Mesenchymal stem cells (MSCs) have shown regenerative and antimicrobial potential; however, their therapeutic efficacy is constrained by poor survival and engraftment. Here, we demonstrate that priming MSCs with insulin-secreting cells (ISCs) and encapsulating them in hydrogels (HEMI) enhances their regenerative function, leading to accelerated healing of full-thickness burns in a porcine model. Wounds treated with HEMIs achieved 80% closure within five weeks, compared to 50% in MSC-only and 0% in standard-of-care controls. Histological analysis revealed complete epidermal and dermal regeneration with minimal fibrosis in HEMI-treated wounds. Single-cell RNA sequencing (scRNA-seq) and differentially abundant sequencing (DA-seq) analysis identified distinct MSC subpopulations transitioning from a proliferative to a tissue-remodeling phenotype, with insulin priming promoting pathways involved in extracellular matrix (ECM) stabilization, immune modulation, and oxidative stress resistance. Our findings suggest that insulin priming enhances MSC-mediated tissue repair via paracrine mechanisms, providing a clinically translatable strategy for improving burn treatment and regenerative medicine applications.

overall_design: Adult human bone marrow-derived MSCs (BMMSCs) were incubated for 3 days with insulin and then collected for analysis with scRNA-seq.

first: Kristopher

last: White

first: Rabab

last: Chalaby

first: Annie

last: Dinh


title: Metabolite-driven remodeling of hepatic lipid metabolism by the plasticizer di-isononyl phthalate

city: Kuopio

first: Sini

middle: Anniina

last: Pitkänen

address: Neulaniementie 2

department: A. I. Virtanen -institute

country: Finland

institute: University of Eastern Finland

summary: Phthalates are widely used as plasticizers and solvents in common consumer products and are suspected to be metabolism-disrupting chemicals (MDCs). Di-isononyl phthalate (DINP) is a commonly used phthalate, which has been shown to induce liver damage, but the mechanisms and human relevance remain unclear. The effects of DINP on hepatic lipid metabolism were studied using a diet-induced obesity model of C56BL/6J male mice. The mice were orally exposed to 0, 1.5, 15 or 150 mg/kg bw/d DINP for 20 weeks next to a high-fat diet (HFD) with 45% calories from fat (Research Diets D12451), followed by assessment of the liver transcriptome.

overall_design: From the age of 8 weeks, C57Bl/6J male mice were fed ad libitum HFD and orally exposed to DINP in 0, 1.5, 15 or 150 mg/kg bw/d doses for 20 weeks. Transcriptome profiling was conducted for the livers of these mice.

first: Jaana

last: Rysä

first: Anna-Liisa

last: Levonen


title: Spatial transcriptome of pre-invasive lung adenocarcinoma

city: Taipei

first: Chia-Lang

last: Hsu

address: No. 7, Zhongshan S. Rd.

department: Department of Medical Research

country: Taiwan

institute: National Taiwan University Hospital

summary: We observed distinct mutational patterns across stages: EGFR mutations increased with pathological stages, while non-V600E BRAF mutations were enriched in AAH and AIS, suggesting pre-invasive lesions harboring different drivers follow distinct evolutionary paths. Based on these differences, we derived 23-gene and 59-gene signatures that stratified pre-invasive lesions into aggressive and non-aggressive groups. The aggressive signature was associated with worse prognosis supported by five stage-I LUAD cohorts. Two aggressive signature genes, LPGAT1 and XPR1, were functionally validated to promote LUAD cell invasion. Compared to non-aggressive lesions, aggressive lesions exhibited higher tumor mutation burden, enrichment of proliferative and EMT-related pathways, and evidence of immune-stromal remodeling.

overall_design: Spatial transcriptomics on 22 samples was employed to examine the intralesional heterogeneity and the tumor microenvironment.


title: DEHP Disrupts Lipid Metabolism Through Autophagy Hyperactivation and Mitochondrial Dysfunction [RNA-Seq]

city: wuhan

first: neng

middle: bin

last: xie

address: 115 donghu road

country: China

institute: wuhan university

summary: Di(2-ethylhexyl) phthalate (DEHP) is a widely used industrial plasticizer, raising global concerns due to its potential endocrine-disrupting effects and environmental persistence. Human exposure to DEHP primarily occurs through the ingestion of contaminated food and water, inhalation of airborne particles, and dermal contact with products containing DEHP. Understanding the toxicological mechanisms of DEHP is essential for evaluating its health risks and developing effective strategies to mitigate its adverse effects. In this study, we conducted long-term exposure experiments to DEHP using both animal model and in vitro system to investigate the complex interplay among DNA methylation, hyperactivation of autophagy, mitochondrial dysfunction, and lipid accumulation induced by DEHP. The results reveal that DEHP exposure induces the degradation of DNA methyltransferase 1 (DNMT1) by enhancing its interaction with the autophagy-related protein sequestosome 1 (SQSTM1). DNMT1 degradation results in decreased methylation of the promoter regions of genes associated with autophagosome formation, subsequently increasing their expression. The resulting demethylation excessively activates autophagy, contributing to mitochondrial dysfunction and lipid accumulation in the liver. This study uncovers a previously unrecognized interplay among hyperactivation of autophagy, mitochondrial dysfunction, and lipid accumulation in the context of DEHP exposure. These findings enhance our understanding of DEHP's toxicity and underscore concerns about the long-term health effects of environmental pollutants, particularly regarding metabolic diseases.

overall_design: Single-base resolution mapping of 5-methylcytosine in cell line HepG2 with or without DEHP exposure by BS-seq.

first: Bifeng

last: Yuan

first: SiYu

last: Yu

first: Nengbin

last: Xie


title: DEHP Disrupts Lipid Metabolism Through Autophagy Hyperactivation and Mitochondrial Dysfunction [BS-Seq]

type: Methylation profiling by high throughput sequencing


title: Lactylation-driven NSUN2-mediated RNA m5C modification promotes perineural invasion in pancreatic cancer

city: Guangzhou

first: Tianhao

last: Huang

state: Guangdong

address: No.106 Zhong Shan Er Road

institute: Southern Medical University

summary: Lactylation, a metabolic stress-induced modification, plays a pivotal role in regulating diverse biological processes. Its involvement in perineural invasion (PNI) of pancreatic ductal adenocarcinoma (PDAC), however, has not been clearly defined. Our study demonstrates that patients with severe PNI exhibit significantly elevated levels of global lactylation and lactate, correlating with poorer prognosis. We identified NSUN2, a methyltransferase, as a crucial mediator of lactylation-driven PNI. Inhibition of lactylation or NSUN2 markedly reduced the neural infiltration capabilities of tumor cells. Mechanistically, lactate accumulation leads to the lactylation of NSUN2 at lysine 692 (K692), subsequently inhibiting its ubiquitination and degradation. lactylation of NSUN2 mediated m5C modification on CDCP1 and STC11 mRNA, enhanced their mRNA stability. Consistently, analyses using a KPC mouse model demonstrated that the lactylation of NSUN2/CDCP1/STC11 axis enhanced PNI through m5C modification. Our findings reveal that lactylation-driven NSUN2-mediated RNA m5C modification plays a pivotal role in promoting PNI and suggest that targeting NSUN2 could offer a promising therapeutic strategy for PDAC.

overall_design: PANC1_lac_IP, PANC1_lac_Input, PANC1_nc_IP, PANC1_nc_Input

first: Shangyou

last: Zheng

first: Rufu

last: Chen

first: Xuebiao

last: Wei

first: Chonghui

last: Hu

first: Huimou

first: Honghui

last: Jiang


title: Defective Autophagy in GNE Myopathy is Reversed by Inhibition of Supplementary mTOR Activation [organoids RNA-seq]

city: Seoul

first: Eun-Ji

last: Kwon

address: 1, Gwanak-ro

country: South Korea

institute: Seoul National University

summary: GNE myopathy, a recessive autosomal disease caused by mutations in Glucosamine-(UDP-N-Acetyl)-2-Epimerase/N-Acetylmannosamine Kinase (GNE), is characterized by deficient sialic acid (SA) production and the formation of rimmed vacuoles. Similar to other autophagic vacuolar myopathies, defective autophagy has been identified as a causative factor in GNE myopathy. However, the molecular mechanism underlying this defective autophagy has not been fully determined. Through transcriptome analysis of two GNE myoblast models derived from human pluripotent stem cells (hPSCs), several gene sets associated with autophagy were identified as pathogenic gene signatures of GNE myopathy. This prediction, along with subsequent biochemical validation using GNE knockout in C2C12 myoblasts (KO cells), revealed that high production of extracellular matrix promoted focal adhesion and subsequent activation of the AKT-mTORC axis, leading to inhibitory phosphorylation of ULK1 and impeding autophagy initiation in KO cells. Notably, transcriptome-based drug screening for candidates that inversely correlate with the pathogenic gene signature identified copanlisib, an FDA-approved PI3K inhibitor, as a potential therapeutic candidate for GNE myopathy. As predicted, copanlisib enhanced autophagy by inhibiting mTOR-dependent ULK1 phosphorylation. These results suggest that copanlisib could be a feasible therapeutic option for patients with GNE myopathy.

overall_design: To investigate the effects of the GNE I329T mutation, we aim to generate an isogenic pair in H9 cells using a base editor and subsequently form organoids.

first: Hyukjin

last: Cha


title: Short-Fiber Scaffold PGCL Stop Overgrowth for Endometrial Hyperplasia

city: Shanghai

first: Yan

last: Zhou

address: 197 Ruijin 2nd Road

department: Department of Reproductive Medical Center

institute: Ruijin Hospital, School of Medicine, Shanghai Jiao Tong University

summary: Endometrial hyperplasia (EH), a precursor to endometrial carcinoma, poses a major threat to women’s health. Current treatments are hindered by the poor adaptability of rigid levonorgestrel (LNG)-releasing intrauterine systems. To overcome this, By physically loading LNG into the base PGC scaffold, we constructed a drug-loaded PGCL scaffold with improved therapeutic function. To elucidate the underlying molecular mechanisms of PGCL scaffold therapy, we performed high-throughput RNA sequencing on Ishikawa cells treated with PGC and PGCL scaffolds, respectively.

overall_design: RNA-seq of human ishikawa cell in PGC and PGCL group


title: Targeting Thioredoxin Reductase 1 (TrxR1) Uncovers Ferroptosis-Linked Transcriptional Vulnerabilities in Lung Cancer

city: Charleston

first: Stefano

last: Berto

state: SC

address: 68 President Street, BE208

institute: MUSC

summary: Bulk RNA sequencing revealed that KRAS-WT and EGFR-MUT LC cells, which are sensitive to TrxR1 inhibitors (CS47 and auranofin), undergo extensive transcriptional reprogramming, unlike the treatment-resistant KRAS-mutant (KRAS-MUT) cells. TrxR inhibition triggers robust transcriptional activation of glutathione biosynthesis, antioxidant defenses, and iron metabolism in KRAS-WT lung cancer cells. This adaptive response, while aimed at maintaining redox balance, is ultimately overwhelmed, leading to ferroptotic cell death.

overall_design: To investigate the effect of the TrxR1 inhibition on human lung cancer cells with a different genetic background, we treated 4 KRAS-MUT,  4 KRAS-WT and 3 EGFR-MUT human lung cancer lines with our novel reversible  inhibitor (CS47), the FDA-approved covalent inhibitor auranofin (AURA) or vehicle (VEH, 0.5% DMSO). We then performed RNA-sequencing to analyze changes un their trasnscriptome.

first: Cristina

last: Andreani


title: Prefrontal-raphe-habenular circuit drives fear memory recall and updating

city: Budapest

first: <Up loaded by Bioinformatics core  facility>

last: <PI shown in the article>

address: Szigony st 43.

country: Hungary

institute: HUN-REN Institute of Experimental Medicine

summary: Fear memory recall is a vital defensive response, yet its underlying neuronal mechanism remains incompletely understood. Here, we identify a fear recall pathway. We found that hippocampal and amygdalar memory centers directly target a group of medial prefrontal cortex (mPFC) neurons, which are necessary for fear recall and directly target vesicular glutamate transporter 2 (vGluT2)-expressing neurons in the pontine median raphe region (MRRvGluT2 neurons) in mice. We found that MRRvGluT2 neurons are necessary for recalling contextual and cued fear memories, they exhibit scalable fear-dependent activity, bidirectionally regulate depression-like behaviors, and show prolonged activity after a fearful experience. During fear memory recall, MRRvGluT2 neurons activate the lateral habenula (LHb), a region implicated in major depression. MRRvGluT2 neurons are electrophysiologically and genetically diverse, and present in rodent and primate species. The identified mPFC–MRR–LHb pathway critically mediates fear memory recall, providing potential therapeutic targets for fear-related disorders.

overall_design: RNA-sequencing on virally labelled MRR vGluT2 glutamatergic neurons collected from vGluT2-Cre mice injected with AAVretro-EF1a-DIO-mCherry into bilateral LHb.

first: Boldizsár

middle: Z

last: Balog

first: Albert

middle: M

last: Barth

first: Krisztián

last: Zichó

first: Abel

last: Major

first: Zsuzsanna

last: Bardóczi

first: János

last: Brunner

first: Charlotte

last: Seng

first: Márta

last: Jelitai

first: Katalin

middle: E

last: Sos

first: Réka

last: Sebestény

first: András

last: Szőnyi

first: Nikolas

last: Karalis

first: Áron

last: Orosz

first: Eszter

last: Sipos

first: Erik

last: Misák

first: György

last: Cserey

first: Andreas

last: Lüthi

first: Viktor

last: Varga

first: Csaba

last: Földy

last: Szabadics

first: Gábor

last: Nyiri


title: Time-Resolved Single-Nucleus Transcriptomic Mapping of Neuro–Glial–Vascular Communication in the Hyperacute-to-Acute Stages of Optic Nerve Injury

first: Caiwen

last: Xiao

state: -- Select State/Province --

address: Zhizaoju Road

institute: Shanghai Ninth People's Hospital

summary: Single-nucleus RNA-seq across six early time points after optic-nerve injury reveals a rapid, week-long shift in neuro-glial-vascular signaling: Müller glia, endothelial cells, and microglia pivot from pro-inflammatory to reparative programs.

overall_design: adult C57BL/6J mice were subjected to unilateral optic-nerve crush (ONC) and their retinas collected at six hyper-acute–acute stages—0h, 2 h, 8 h, 1 d, 3 d and 7 d

first: Yi

last: Ding

first: Wenyue

last: Zhang


title: Revealing differential type I and type II IFN responses in different immune cells in various human diseases by a new IFNs transcriptomic atlas

city: Seattle

first: Allen Institute

last: For Immunology

state: Washington

address: 615 Westlake Ave N, Seattle, WA

institute: Allen Institute

summary: Interferons (IFNs) are key cytokines mediating broad immunological responses in diverse processes including host defense, autoimmune diseases, and cancer. To gain single cell resolution in response to different IFNs in different human immune cells, we generated a new single-cell transcriptomic dataset in various human immune cell subsets by stimulating with IFN-α, IFN-β, IFN-γ, and IFN-λ1. We not only found classical IFN stimulated genes (ISGs) highly elevated across multiple immune cell subsets, but each immune cell subset also displayed unique gene sets in response to IFN-α or IFN-γ stimulation. Furthermore, expression fold changes of many ISGs shared between IFN-α and IFN-γ were different, which prompted us to utilize those unique features to generate a new scoring method. To obtain a comprehensive view of type I & II IFN responses from many different human diseases, we applied our tool to several published scRNAseq datasets from patients with known elevated IFN responses. We also applied this to a new cohort of newly diagnosed multiple myeloma (NDMM) patients and ran a cross-sectional and a longitudinal analysis to explore IFN responses in NDMM compared to healthy and NDMM after induction therapies, with or without daratumumab. We found higher circulating protein levels of IFN-α2A, IFN-β, and IFN-γ, and higher type I and type II IFN scores across all circulating immune cells in NDMM. Induction therapies only decreased type I IFN responses, especially in CD14 monocytes, and circulating IFN-α. Both known ISGs and novel cell-type specific ISGs from our ex vivo dataset could be recapitulated in in vivo NDMM. Our work provides insights into immune cell-type specific responses to IFNs and a new level of clarity to dissect different IFN responses from human diseases. With our cloud-based explorers, this new tool can be easily used by many others to further expand human IFN research.

overall_design:
The HIRIS-Atlas dataset comprised various interferon responses in different immune cells from 5 healthy young adults aged 25-39 years old. Four major immune cell subsets, T cells, B cells, NK cells, and CD14 monocytes from each subject were enriched from frozen PBMC and then stimulated with various human IFNs for 21 hours. Cells were fixed and subjected to 10x Genomic fixed scRNA-seq.
Raw data were uploaded to SRA under BioProject PRJNA1303123. SRA Accessions are listed in Series supplementary file.

first: Nicholas

last: Moss

first: Catalina

last: Sakai

first: Saransh N.

last: Kaul

first: Erik D.

last: Layton

first: Paige

last: Bouvatte

first: Samir

last: Rachid Zaim

first: Tao

last: Peng

first: Marla C.

last: Glass

first: Peter J.

last: Wittig

first: Yudong D.

last: He

first: Lucas T.

last: Graybuck

first: Christian M.

last: LaFrance

first: Upaasana

last: Krishnan

first: Dakota

last: Newman

first: Mackenzie S.

last: Kopp

first: Melinda L.

last: Angus-Hill

last: Skene

first: Mikael

last: Sigvardsson

first: Xiao-Jun

last: Li

first: Troy R.

last: Torgerson

first: Emma L.

last: Kuan


title: Transcriptomic and metabolomic profiling of Staphylococcus aureus and Escherichia coli treated with AuPt@ZIF-8 + H₂O₂ + NIR or control

first: Hongrui

last: Chen

address: 639 Zhizaoju Road, Shanghai 200011, P.R.China.

department: Plastic and reconstruction surgery

institute: Shanghai ninth people's hospital

summary: To clarify the antibacterial mechanism of AuPt@ZIF-8 + H₂O₂ + NIR, we treated Escherichia coli and Staphylococcus aureus with/without AuPt@ZIF-8 + H₂O₂ + NIR and observed the changes in gene expression using high-throughput transcriptome sequencing.

sample_organism:
Escherichia coli
Staphylococcus aureus

platform_organism:
Escherichia coli
Staphylococcus aureus

overall_design: Group 1: E. coli treated with AuPt@ZIF-8 + H₂O₂ + NIR; Group 2: untreated E. coli; Group 3:  S. aureus treated with AuPt@ZIF-8 + H₂O₂ + NIR; Group 4: untreated S. aureus

first: Chen

last: Hua

first: Xiaoxi

last: Lin


title: The CARM1 Epigenetic Enzyme Inhibits Cross-presenting Dendritic Cell Function in Cancer Immunity [multiome]

city: Boston

first: Xixi

last: Zhang

state: Massachusetts

address: 450 Brookline Ave

institute: Dana-Farber Cancer Institute

type: Genome binding/occupancy profiling by high throughput sequencing

summary: The cancer-immunity cycle requires cross-presenting dendritic cells (cDC1) that induce T cell-mediated immunity, but therapeutic strategies for enhancing intratumoral cDC1 function are inadequate.  We discovered the epigenetic enzyme Carm1 as a selective negative regulator of cancer antigen presentation by cDC1s, but not cDC2s.  Carm1 inactivation promoted cDC1 antigen cross-presentation, activation, and accumulation in tumors; and a Carm1 inhibitor enhanced cDC1-mediated priming of T cells by a cancer vaccine.  Carm1 inhibition increased chromatin accessibility at BATF3-JUN and RELA sites critical for cDC1 function and activation.  Carm1 expression was regulated by TGF-beta, explaining why Carm1 inactivation enhanced intratumoral cDC1 function without altering cDC1 homeostasis.  These studies identify Carm1 as a therapeutic target for enhancing the anti-tumor function of murine and human cDC1.

overall_design: 10xmultiome analysis (scRNA-seq plus scATAC-seq) was performed to profile tumor-infiltrating XCR1+ cDC1s respectively harvested from tumor-bearing Carm1fl/fl and Carm1fl/flXcr1Cre mice

first: Sherin

last: Xirenayi


title: Drosha regulates adipogenesis by modulating miR-204/miR-15b in OP9 cells [RNA-Seq]

first: Xin

address: 132 Daxuecheng Outer Ring E Rd

department: School of Medicine

institute: Sun Yat-sen University

summary: Mesenchymal stem cells (MSCs), being multipotent progenitors, have received the most widespread regulatory approval for commercialization as off-the-shelf cell therapies. Understanding the key molecular mechanisms regulating MSC differentiation is crucial for advancing their clinical utilization. Drosha is a critical enzyme in miRNA biogenesis. Despite its established role in diverse physiological processes, the involvement of Drosha in the adipogenic differentiation of MSCs has not been previously characterized. Here the role of Drosha/microRNA pathway in regulating the adipogenesis of OP9, a MSC derived from mouse bone marrow stroma, is characterized. Knocking down Drosha in OP9 significantly reduced its adipogenic capacity. Small RNA-seq analysis revealed that miR-204 and miR-15b were significantly downregulated in the adipogenic process of OP9 cells upon Drosha removal. Further exploration showed that the activity of ERK1/2 was significantly increased in Drosha KO OP9 cells, which was proved can suppress the transcriptional activity of PPARγ. Introducing miR-204 or miR-15b into OP9 cells significantly enhanced their adipogenic capacity and partially rescued the adipogenic defects caused by Drosha knockout. Mechanistically, miR-15b regulates ERK mediated adpogenic differentiation via repressing NRP2. Our data demonstrate that the Drosha/miR-15/NRP2 axis regulates adipogenesis of MSCs by modulating the ERK/PPARγ pathway. This discovery unveils a previously unappreciated molecular mechanism governing MSC adipogenic differentiation and suggests new avenues for exploring the therapeutic potential of MSCs.

overall_design: RNA-seq profiling of wildtype OP9 cells and their knockout derivatives (Drosha KO) at Day 10 of adipogenic differentiation

first: Wenjun

last: Xiao

first: Haoyu

last: Wang

first: Jiaying

last: Liu

first: Weiqian

first: Chuwen

first: Xuan

last: Jiang


title: Single Cell RNA Sequencing of immune cell populations from WT and Cdh5-cre Myct1 fl/fl mice

city: St. Louis

first: Yoojung

last: Kwon

state: Missouri

address: 660 S Euclid Ave, BJCIH 8th floor, room 8302

department: Pathology and Immunology

institute: Washington University in St. Louis

summary: We have examined single-cell sequencing using 10x Genomics scRNA-seq to study changes in the immune cell population from tumor-bearing Cdh5-cre Myct1 f/f mice. Previously, we identified that Myct1 is expressed in endothelial cells, and Myct1 deficiency reduces tumor angiogenesis, thereby enhancing the anti-tumor immune environment. This scRNA-seq provides a transcriptomic analysis of immune cells in the tumor microenvironment, showing how tumor angiogenesis affects immune cells in the tumor.

overall_design: Immune cells were FACS sorted as GFP-CD45+ population from PYMT-BO1 transplant tumor bearing WT and Cdh-cre Myct1 fl/fl mice on day14 post tumor transplantation. Single-cell RNA-sequencing was performed and analyzed.

first: Kyunghee

last: Choi

first: Ashraf Ul

last: Kabir

first: Carisa

last: Zeng

first: Maxim

last: Artyomov


title: Analysis and statistics of mRNA interacting with Tau5-positive microtubule associating protein tau in human hippocampal Alzheimer’s Disease tissue.

city: Gainesville

first: John

last: Koren

state: FL

address: 1275 Center Dr

institute: University of Florida

summary: The microtubule associating protien tau, (MAPT, tau) is a primary pathologic factor in a number of neurodegenerative disorders, including Alzheimer's Disease. Tau can interact with RNA. These interactions have been proposed as initiating factors for the formation of the pathological forms of tau noted in diseases. Additionally, it has been suggested that the m6A-methylation state of RNA is a factor in the association of RNA to tau. This study uses enhanced crosslinking immunoprecipitation (eCLIP) techniques to 1) identify, quantify, a sequence the RNA species interacting with the tau protein isolated from Alzheimers disease human hippocampal tissue, 2) identify, quantify, and sequence the methylated RNA in Alzheimer's disease human hippocampal tissue, and 3) to look for associations between the RNAs that interact with tau and RNA methylation status.

overall_design: Tissue from four ApoE 3/3 donors with pathologies designated as intermediate Alzheimer's (ADI) or high Alzheimer's (ADH) underwent eCLIP processes to identify and sequence the RNA that were interacting with tau and the RNA that featured m6A methylation. The primary output, in a manuscript under preparation, was to simplify the associated RNA data to a list of their representative genes. These gene lists were then compared for methylation status, tau interaction, and signaling pathways. The raw RNA seq associated with these studies was also used to examine the transcriptome of ADI and ADH.

last: Koren III

first: Tristyn

middle: N

last: Garza

first: Jose

middle: F

last: Abisambra


title: Effect of glucose deprivation and silencing of transcription factors ATF4 and ATF6 on gene expression in human lung adenocarcinoma cell line A549

city: L'Hospitalet de Llobregat

first: Cristina

last: Muñoz-Pinedo

state: Barcelona

address: Hospital Duran i Reynals, 3a planta - Avinguda de la Gran Via, 199

department: ONCOBELL

country: Spain

institute: Institut d'Investigació Biomédica de Bellvitge

summary: Tumours grow faster than the local vasculature, resulting in a shortage of oxygen and nutrients. To explore how lung cancer cells cope with a low-glucose environment, we analysed transcriptional changes in glucose-starved A549 cells using RNA-sequencing. This showed downregulation of multiple pathways related to DNA replication and cell cycle, and regulation of metabolic gene sets. The most upregulated transcriptional response to glucose deprivation was the Unfolded Protein Response (UPR), which has been shown to promote adaptation to proteotoxic and endoplasmic reticulum stress. Glucose shortage robustly induced the three branches of the UPR in several non-small cell lung carcinoma cell lines, as indicated by ATF4 accumulation, XBP1 mRNA splicing and ATF6 cleavage. ATF6 and ATF4 silencing revealed that these factors cooperate to regulate multiple metabolic genes and pathways related to lipid synthesis and to amino acid synthesis and transport. ATF4 additionally regulated the transcriptional induction of mitochondrial OXPHOS-associated pathways.

overall_design: RNA-seq profiling of wild-type A549 cells (transfected with a non-targeting siRNA sequence) and A549 cells transfected with a specific sequence for ATF4 and ATF6 at 6h and 16h of glucose deprivation. Control conditions are at 25mM glucose media.

first: Mabel

last: Cruz Rodríguez

first: Lidia

last: Collado Rodríguez

first: Sara

last: Hijazo Pechero

first: Joaquim

last: Moreno Caceres


title: Defective LCN2–FN1 signaling impairs stromal–immune communication and underlies recurrent implantation failure

city: Jinan

first: Wenhao

last: Yu

address: Wenhuaxi road

institute: Shandong University

summary: Defective endometrial decidualization and dysregulated immune responses are key contributors to recurrent implantation failure (RIF), yet the underlying molecular mechanisms remain poorly defined. Here, we identify significantly reduced LCN2 levels in both mid-luteal endometrial tissue and serum of RIF patients compared to fertile controls. Using uterine-specific conditional knockout (CKO) mouse models, we demonstrate that loss of Lcn2 impairs embryo implantation and reduces pregnancy rates. Single-cell RNA sequencing of post-implantation uteri on pregnancy day 5 revealed that Lcn2 deficiency reduces the proportion of primary decidual stromal cells and suppresses the proliferation of tissue-resident natural killer (trNK) cells. Mechanistically, we show that stromal-derived LCN2 promotes trNK cell proliferation by activating C/EBPβ-dependent transcription of Fn1. Supplementation with recombinant LCN2 or FN1 restores trNK cell expansion and rescues implantation defects in Lcn2-deficient mice. Together, these findings define a previously unrecognized stromal–immune axis in the peri-implantation endometrium and identify LCN2 and FN1 as potential diagnostic markers and therapeutic targets for RIF.

overall_design: To explore the role of LCN2 in shaping the immune environment during implantation, we performed single-cell RNA sequencing (scRNA-seq) on pregnancy day 5 uteri from Lcn2f/fIrescre conditional knockout mice  (n=4) and Lcn2f/f  control mice (n=3). Using a 10× Genomics single-cell 3'v2 kit, a single-cell suspension was prepared to perform single-cell capture and pre-amplification on the GemCode instrument (10× Genomics). The Illumina × 10 platform was used to sequence the generated library, and the Cell Ranger pipeline (10× genomics) was used to align and analyze the sequencing data.

first: Tianxiang

last: Ni

first: Tingting

last: Zhou

first: Xianping

last: Hou

first: Yuhan

last: Shao

first: Qian

last: Zhang

first: Junhao

last: Yan


title: Vitamin C mitigates potassium perchlorate exposure-induced disruption of spermatogenesis in medaka

city: Columbia

first: Ramji

last: Bhandari

state: MO

address: 1200 University Ave

department: Division of Biological Sciences

institute: University of Missouri

summary: Potassium perchlorate (KClO4), widely used in industrial and military applications, is an emerging environmental contaminant known to disrupt thyroid function. However, its potential impact on male reproductive health remains underexplored. In this study, we investigated the testicular toxicity induced by chronic KClO4 exposure over one spermatogenic cycle of medaka (Oryzias latipes) and evaluated the ameliorative effects of vitamin C. Adult male medaka were treated with 0.01 mg/L, 10 mg/L KClO4 and 10 mg/L KClO4 plus vitamin C (3 mg/mL) for 21 days. Fertilization percentage, histological examination, and transcriptomic profiling of the testis were performed.  KClO4 exposure decreased fertilization success caused disorganization of seminiferous tubules, and dysregulated spermatogenic genes in the testis. Transcriptomic analysis revealed substantial dysregulation of genes involved in cadherin and tubulin binding, chromatin remodeling, oxidative stress response, and germ cell development. Co-administration of vitamin C mitigated these effects by restoring testicular morphology, restoring fertilization rates, and partially reversing gene expression changes disrupted by potassium perchlorate exposure. The present findings suggest that vitamin C provides protective effects against perchlorate-induced testicular toxicity and highlight the need for further exploration of antioxidant-based interventions to safeguard reproductive health from perchlorate exposure.

overall_design: RNA-seq profiling was performed on medaka testis samples following exposure to varying concentrations of KClO₄. The exposure groups included a control (0 mg/L), low (0.01 mg/L) and high (10 mg/L) KClO₄ concentrations, as well as a co-treatment group receiving 10 mg/L KClO₄ combined with 3 mg/L vitamin C. Each group consisted of three biological replicates.

first: Beh

last: Reh

first: Santosh

last: Anand

first: Sourav

last: Chakraborty


title: Gene expression profiling of the spinal dorsal horn from wild-type and LPA4 knockout rats after Spared Nerve Injury (SNI)

city: izunokuni mifuku

first: takahisa

last: shimoda

state: Shizuoka

country: Japan

institute: Asahi Kasei Pharma

summary: Gene expression in the lumbar spinal dorsal horn (L4-L6) was compared across four experimental groups. The groups were: (1) Sham-operated wild-type (WT) rats, (2) SNI-operated WT rats, (3) Sham-operated LPA4 knockout (KO) rats, and (4) SNI-operated LPA4 KO rats. Four biological replicates were analyzed for each of the four groups at 28 days post-surgery.

overall_design: RNAseq profiling of  lumber spinal drsal horn of sham/SNI-operated WT and LPA4-KO rats at 28 days post-surgery.

first: Takahisa

last: Shimoda

first: Tomoya

last: Tanaka

first: Simeng

last: Ma

first: Yoki

last: Nakamura

first: Kazue

last: Hisaoka-Nakashima

first: Norimitsu

last: Morioka


title: Target macrophage SPP1 promotes CD8 T cell infiltrations

city: Wuhan

first: Bingyi

last: Liu

address: 1037 Luoyu Road, Hongshan District

institute: Huazhong University of science and technology

summary: SPP1 in tumor associated macrophages (TAM) can inhibit the infiltration of CD8 T cells, promote tumor growth, and reduce the efficacy of ICI immunotherapy. RNA sequencing data showed diffrential expressed genes and enrichment pathway in the bone marrow derived macrophages from SPP1fl/fl-Lyz2-icre mice compared to control SPP1fl/fl mice.

overall_design: To further explore the effects of SPP1 on the macrophage , we performed RNA-seq on bone marrow derived macrophages  from control SPP1fl/fl mice and SPP1fl/fl-Lyz2-icre mice.

first: Juanjuan

last: Wang

first: Yi

last: Shi

first: Yunhuan

last: Gao

first: Rongcun

last: Yang


title: Profiling and Functional Analysis of Urinary Exosomal MicroRNAs in Pregnant Women with Systemic Lupus Erythematosus

first: Shule

last: Zhang

address: 107 Wenhua Xilu

institute: Qilu Hospital of Shandong University

type: Non-coding RNA profiling by high throughput sequencing

summary: Background: Pregnancy in Systemic Lupus Erythematosus (pSLE) is high-risk, necessitating non-invasive biomarkers for monitoring and predicting complications. Urinary exosomes, containing miRNAs, offer a promising source reflecting systemic and renal states, yet their profile in late gestation pSLE is less studied. Objective: This study aimed to investigate the profile of urinary exosomal miRNAs in pregnant women with SLE during late gestation compared to healthy pregnant controls and to explore their potential biological roles and pathways. Methods: Urinary exosomes were isolated from 6 pSLE patients and 5 controls. Exosomes were characterized, and miRNAs were sequenced. Bioinformatics analyses, including target gene prediction and functional enrichment (GO, KEGG), were performed. Results: Exosomes were successfully isolated. Sequencing identified 29 significantly downregulated miRNAs in pSLE exosomes. Enrichment analysis of these miRNAs and their target genes indicated involvement in metabolic and immune pathways, virus infection, and cellular senescence. Target genes also enriched in protein stability and transport, and high-level analysis showed broader roles in metabolic, immune, and cellular maintenance/stress processes. Targets of top differentially expressed miRNAs linked to mRNA regulation, AMPK, and senescence pathways. Conclusion: Our findings demonstrate that urinary exosomal miRNAs are significantly altered in pregnant women with SLE during late gestation. The functional enrichment analysis suggests their target genes are involved in critical biological processes relevant to pSLE pathophysiology and pregnancy complications, including metabolism, immunity, viral response, senescence, and cellular maintenance. This highlights the potential of urinary exosomal miRNAs as non-invasive biomarkers for monitoring and predicting risks in this high-risk population.


title: Heterozygous BRCA1 SNPs in the DNA Binding Domain Enhance Sensitivity to PARP Inhibition in Breast Cancer Cells

city: Taichung City

first: Ling

last: Chen

address: Rm. 7, 4F., No. 99, Jingke S. Rd., Nantun Dist.

institute: AllBio Life, Inc.

summary: Poly(ADP-ribose) polymerase (PARP) inhibitors show efficacy in breast cancer patients with BRCA1/2 mutations. However, certain BRCA1 single nucleotide polymorphisms (SNPs) may alter protein function without complete loss of activity. This study investigates whether specific BRCA1 SNPs within the DNA binding domain affect cellular sensitivity to PARP inhibition. We used breast cancer cell lines with heterozygous BRCA1 SNPs (CAMA-1: rs799917, rs16941, rs16942, rs1799966) or wild-type BRCA1 (T47D). Cell viability was assessed following olaparib treatment using MTT assay. Transcriptome sequencing and functional enrichment analyses were performed. CAMA-1 cells exhibited significantly enhanced olaparib sensitivity compared to T47D cells, with viability reduced to 45% versus 75% at 50 μM after 72 hours (p<0.001). Transcriptome analysis revealed 6,978 differentially expressed genes, with enrichment in DNA binding, transcriptional regulation, and cellular degradation pathways, suggesting conditional haploinsufficiency under PARP inhibition stress. Heterozygous BRCA1 SNPs in the DNA binding domain confer increased PARP inhibitor sensitivity without pathogenic mutations. This suggests potential expansion of PARP inhibitor therapy to patients with specific BRCA1 polymorphisms, representing a novel biomarker for personalized breast cancer treatment.

overall_design: RNA-seq profiling of wild-type BRCA1 (T47D) cells and breast cancer cell lines with heterozygous BRCA1 SNPs (CAMA-1: rs799917, rs16941, rs16942, rs1799966). In addition, MDA-MB-436 (MDA) cell lines were employed as experimental standards.

first: Ming-Hsin

last: Yeh

first: Chang Wei

last: Li

first: Ting Ying

last: Shih

first: Ya-Chi

last: Kang

first: Yu-Di

last: Chang


title: aPKC-ζ III promotes trophoblast fusion by altering Par-3 interactions with Hippo Signaling Kinase LATS1.

city: Edmonton

first: Meghan

last: Riddell

state: AB

country: Canada

institute: University of Alberta

summary: The first trimester of human pregnancy is a critical developmental period for the placenta. The maternal-facing exchange surface, a single giant multinucleate syncytium called the syncytiotrophoblast (ST), must form in preparation for the onset of blood flow at ~10-12 weeks gestation. The syncytium is formed and maintained by progenitor cytotrophoblasts (pCT) that differentiate and fuse into the multinucleate syncytium. The differentiation of pCT to ST is regulated by the Hippo signaling pathway. Hippo signaling co-transcription factor YAP1 promotes pCT maintenance and stemness in early pregnancy, however, the regulation of Hippo signaling in trophoblasts is unknown. We have identified a novel PRKCZ encoded aPKC isoform that promotes pCT to ST differentiation. This novel aPKC, aPKC-ζ III, alters the Hippo signaling cascade by outcompeting Hippo kinase LATS1 for Par-3 binding, resulting in LATS1 activation, YAP1 inactivation, allowing for pCT to ST differentiation. Our findings are the first to identify a modulator of Hippo signaling in human trophoblasts that is critical for first trimester syncytiotrophoblast differentiation.

overall_design: For bulk RNA sequencing, PRKCZ-targetting siRNA was transfected into trophoblast stem cells CT29 cell lines which were subsequently used to generate placental organoids. A total of three control and 3 knockdown organoids were sequenced. Regarding the single nuclei sequencing, one CT27 and one CT29 cell lines were ruptured and their nucleis were collected and sequenced for further analysis.

first: Sumaiyah

last: Shaha

first: Wendy

middle: K

last: Duan

first: Juan

last: Garcia Rivas

first: Ivan

last: Domingo


title: LPS-Mediated Transcriptional Changes in Myeloid Lineage Cells:  Macrophages and Osteoclasts

city: Saint Louis

first: Gabriel

last: Mbalaviele

address: 425 S. Euclid Ave., Steven & Susan Lipstein BJCIH, Floor: 11, Room 11203

institute: WashU School of Medicine

summary: The NLRP3 inflammasome is a key driver of bone resorption in various inflammatory conditions, ranging from low-grade to high-grade inflammation. This bone-resorptive activity is mediated by osteoclasts (OCs), which differentiate from macrophages upon exposure to RANKL. While the non-autonomous effects of the inflammasome on the osteoclast lineage are well characterized, its cell-intrinsic (autonomous) role within these cells remains poorly understood. To address this knowledge gap, we treated mouse bone marrow-derived macrophages (BMDMs) with RANKL and monitored NLRP3 expression during osteoclastogenesis. Surprisingly, NLRP3 expression progressively declined as cells differentiated into osteoclasts, but was restored upon LPS priming. When OC cultures were exposed to LPS followed by nigericin to assess NLRP3 inflammasome activation, we observed robust inflammasome assembly in undifferentiated BMDMs, as expected. However, this response was absent in mature OCs and their lineage-committed precursors. To uncover the mechanisms underlying this suppression of NLRP3 activation during differentiation, we performed transcriptomic analysis across the macrophage-to-osteoclast transition, aiming to identify regulatory genes and pathways that may inhibit inflammasome assembly in OCs

overall_design: RNA-seq profiling of macrophages and RANKL-treated osteoclasts in the presence and absence of 100 ng/mL lipopolysaccharide (LPS)

first: Khushpreet

last: Kaur

first: Yael

last: Alippe

first: Chun

first: Nicholas

middle: P

last: Semenkovich

first: Saumya

last: Bhagat

first: Kunjan

last: Khanna

first: Yongjia

first: Nitin

last: Pokhrel

first: Timothy

last: Peterson

first: Deborah

middle: J

last: Veis

first: Yousef

last: Abu-Amer

first: Roberta

last: Faccio


title: Repertoire FLEX (REFLEX) Enables High-Throughput Multiomic scRNAseq with AIR Detection

first: Allen Institute

last: For Immunology

summary: Profiling the vast diversity of the T-cell repertoire at single-cell resolution is challenging due to the scale and cost requirements involved. Current technologies capture TCR or perform single-cell sequencing at scale but struggle to combine both. Here, we utilize both neat and virally stimulated PBMCs to showcase “REFLEX”, a technological approach enabling highly scalable, low cost-per-cell profiling of TCR repertoire in parallel with epitope and gene expression. This combination of capabilities allows for high throughput, multi-omic profiling of rare T cell subsets and longitudinal study formats at scales that were previously unattainable.

overall_design: To showcase the capabilities of REFLEX, we designed experiments using cell lines as well as cultured and non cultured PBMCs. We used pooled Jurkat and Raji cell lines to evaluate TCR specificity for cell type as well as TCR identification. Using non cultured PBMCs we evaluated REFLEX compatibility with 16 sample barcodes as well as fixed, long term storage and the incorporation of custom FLEX probes. Using cultured PBMCs we profiled TCR in response to stimulation with CMV derived peptide pools in the presence of varied cytokine supplement or metabolic inhibitor.

first: Hart

last: Matt

first: Thomson

last: Zach

first: Kaul

last: Saransh N.

first: Ilcisin

last: Saskia M.

first: Stuckey

last: Tyanna

first: Wittig

last: Peter J.

first: Krishnan

last: Upaasana

first: Ott

last: Alina

first: Skene


title: Effect of YTHDC2 knockdown on gene expressions in CAL-27 cell line

city: xi'an

first: Liangliang

last: Shen

address: West changle road 169

institute: The fourth military medical university

summary: Oral squamous cell carcinoma (OSCC), a highly prevalent and poor-prognosis malignancy, is closely associated with tumor metabolic reprogramming, particularly the glutamine-dependent metabolic phenotype. This study systematically investigates the role of N6-methyladenosine (m6A) modification in OSCC through integrated bioinformatics analysis and functional experiments, focusing on the tumor-suppressive function of the m6A reader YTHDC2 and its regulation of glutamine metabolism. Analysis based on The Cancer Genome Atlas (TCGA) datasets revealed that YTHDC2 expression was significantly inversely correlated with OSCC malignancy and patient survival. Functional validation showed that YTHDC2 depletion promoted OSCC cell proliferation and stem-like properties, whereas YTHDC2 overexpression markedly suppressed these malignant phenotypes. Mechanistic studies demonstrated that YTHDC2 stabilized VHL mRNA by recognizing m6A modification sites, enhancing VHL protein expression. This promoted VHL-mediated ubiquitin-dependent degradation of HIF-1α, leading to transcriptional repression of its downstream target GLS1. Consequently, this blocked glutaminolysis, tricarboxylic acid (TCA) cycle-driven energy production, and glutathione (GSH)-mediated antioxidant pathways. Additionally, low YTHDC2 expression in OSCC tissues was closely associated with DNA hypermethylation at CpG islands (e.g., cg21815882) in its promoter, an epigenetic silencing mechanism that sustains the glutamine-addicted phenotype. This study first uncovers the core role of the YTHDC2/m6A/VHL/HIF-1α/GLS1 signaling axis in metabolic regulation of OSCC, providing new insights into the molecular basis of glutamine addiction. YTHDC2 not only serves as a prognostic biomarker for OSCC but also highlights its-mediated metabolic pathway as a theoretical basis for developing targeted therapies against glutaminolysis.

overall_design: To investigate the mechanism of action of YTHDC2 in oral squamous cell carcinoma, we established YTHDC2 knockdown CAL-27 cell line, and then we used RNA-seq data from CAL-27 cell line for gene expression profiling.

first: Yulin

last: An


title: Transcriptional and functional architecture of the whole neutrophil compartment [RNA-seq sorted_cells]

city: New Haven

first: Andrés

last: Hidalgo

address: 10 Amistad Street

institute: Yale University

summary: In this study, we present NeuMAP, a comprehensive single-cell analysis of neutrophils spanning over 40 anatomical, physiological, and pathological contexts in mice. NeuMAP confirms and expands previous models of neutrophil diversity, revealing the organization of neutrophils into distinct functional hubs under both normal and pathological conditions. Furthermore, we delineate prototypical trajectories as key organizers of granulopoiesis and examine neutrophil dynamics along these trajectories during acute inflammation and cancer. Integrating insights from fate mapping, mutant mouse models, and in vitro experiments, we identified immunological signals guiding neutrophil through these typical trajectories of granulopoiesis, that balance immune protection, tissue homeostasis and repair. Specifically, we identified IFNB, GMCSF, and TGFB as drivers of pro-inflammatory, cancer-associated, and mature neutrophil states, respectively and found that the transcription factor JUNB drives the angiogenic and immunosuppressive function of neutrophils. Additionally, we uncover conserved transcriptional signatures for human neutrophil states, validate their prognostic significance in cancer patients, and introduce a proof-of-concept strategy for exploring the diagnostic potential of neutrophil functional diversity across various diseases using single-cell transcriptomics of blood neutrophils. Our study provides a model that delineates the global architecture of the neutrophil compartment in mammals, and stablishes a robust framework for further exploration of neutrophil biology.

overall_design: Neutrophills were collected from the lungs of control, flu-infected or cancer bearing mice by FACS-sorting as Ly6G+CD11b+ cells and the described combination of markers associated to each sample. Briefly, lungs  were harvested, cut into small pieces, and digested with Liberase TM (Sigma) and DNase I (Sigma) for 30 minutes at 37°C. Following digestion, tissues were passed through 70 µm nylon mesh sieves using syringe plungers to obtain single-cell suspensions. All single-cell suspensions were lysed in RBC lysis buffer (eBioscience) for 4min and stained with the following antibodies: CD11b-PE (Clone M1/70, BioLegend, 1:200); Ly6G-AF647 (Clone 1A8, eBioscience, 1:200); DAPI (1:10,000), CD14 APC-CY7 (Sa14-2, BioLegend)  and CD274 BV421 (10F-9G2, BioLegend). Sorted neutrophils were used for sequencing.

first: Ivan

last: Ballesteros

first: Andrea

last: Rubio-Ponce

first: Jon

last: Sicilia


title: Hsa_circ_0000818 targets miR-484/HIPK1 axis to ameliorate liver fibrosis by inhibiting Wnt/β-catenin pathway

city: Shanghai

first: Gong

middle: Ke

last: Tao

address: Jimo Road 150#

institute: easthospital

summary: This study sought to identify circRNAs implicated in HF progression and clarify their mechanisms. hsa_circ_0000818 inhibits HF progression by sponging miR-484 and enhancing HIPK1 expression through inhibition of Wnt/β-catenin signaling, making hsa_circ_0000818/miR-484 and its downstream gene HIPK1 potential new therapeutic targets for HF.

overall_design: Ten human samples have been analyzed, including five hepatic fibrosis samples and five normal human liver tissues from liver transplantation.

first: Kegong

first: Yuanyuan

last: Luo

first: Binbin

last: Li

first: Xin

last: Zeng

first: Yong

last: Lin


title: Acyl-CoA Synthetase Short Chain Family Member 2 (ACSS2) is Required for Colorectal Cancer Progression and Serves as a Druggable Target for Colorectal Cancer Treatment

city: Chicago

first: Lu

last: Gao

state: IL

institute: University of Chicago

summary: Acyl-CoA synthetase short chain family member 2 (ACSS2) catalyzes the conversion of acetate to acetyl-CoA, a key metabolite required for de novo lipogenesis and protein acetylation. Here we show that ACSS2 expression is markedly elevated at all stages of human colorectal cancer (CRC), and Acss2 silencing or conditional genetic ablation leads to a marked reduction in CRC tumor loads in mouse tumor xenograft models and CRC models induced by colonic epithelial Apc mutation or azoxymethane (AOM)/dextran sodium sulfate (DSS) treatment. Tumors with ACSS2 depletion exhibit robust DNA damage and excessive apoptosis, leading to increased recruitment of macrophages and CD8+ T cells to the tumor microenvironment. Further studies confirm that ACSS2 promotes CRC growth by blocking DNA damage and apoptosis under nutritional stress commonly occurring in solid tumors, suggesting ACSS2 is a therapeutic target for CRC therapy. Indeed, treatment with a small molecule ACSS2 inhibitor (ACSS2i) markedly suppresses tumor growth in CRC xenograft models and Apc-mutation induced sporadic CRC models. Consistently, ACSS2i treatment increases DNA damage and induces apoptosis in the tumors. These observations indicate that the conversion of acetate to acetyl-CoA by ACSS2 is crucial for CRC progression, and ACSS2 is a druggable target for CRC management.

overall_design: MC38 cells were transduced with a control lentivirus or a lentivirus carrying Acss2-specific shRNA to knock down Acss2. The control MC38 cells with normal ACSS2 expression (wt) and MC38 cells with ACSS2 knockdown (kd) were used to generate xenograft tumors in C57BL/6 mice. Three wt tumors and 4 kd tumors were used to extract cellular RNA for RNA-seq analysis.

first: Lei

last: Wang

first: Yan Chun


title: How the spectral properties of dawns impact Arabidopsis developmental programmes

city: York

first: Gina

last: Vong

address: Wentworth Way

department: Biology

country: United Kingdom

institute: University of York

summary: Plants have evolved to adapt to the fluctuating and dynamic lighting conditions observed outdoors in nature. Our previous work identified a gene regulatory network governing a burst of transcriptional activity within minutes of lights being switched on, directed by developmental hub genes such as HY5 and BBX31 (Balcerowicz et al. 2021). However, indoor growth chamber experiments usually involve an unnatural binary on/off light treatment that may cause light stress in plants.  On the other hand, natural dawns expose outdoor plants to gradual changes in irradiance and spectral composition. To address this gap in knowledge, we present here a fine-scale time-series transcriptome where plants were grown under simulated natural dawns inside growth cabinets. By mimicking the gradual increase in light irradiance as well as the changing ratios of wavelengths observed in natural dawns, we can model the gene regulatory network of Arabidopsis as it adapts to dynamic light signals in the early morning. This will enable us to simulate how the spectral patterns of natural dawns influence adaptation to light.

overall_design: Arabidopsis thaliana (col-0, elf3-1, pifq) seedlings were grown for 7 days under 4 light regimes: a) linear dawn (T1)  b) extreme dawn (T2) c) 8h control (C1) and d) 7h control (C2). On the 7th day, the seedlings were sampled in the morning, starting at ZT-0.5 (30mins before lights turned on) and continuing every 0.5h until ZT3.

first: Hailey

last: Tan

first: Kayla

last: McCarthy

first: Daphne

last: Ezer


title: Drosha regulates adipogenesis by modulating miR-204/miR-15b in OP9 cells [miRNA-Seq]

city: Guangzhou

institute: Sun Yat-sen University

summary: Mesenchymal stem cells (MSCs), being multipotent progenitors, have received the most widespread regulatory approval for commercialization as off-the-shelf cell therapies. Understanding the key molecular mechanisms regulating MSC differentiation is crucial for advancing their clinical utilization. Drosha is a critical enzyme in miRNA biogenesis. Despite its established role in diverse physiological processes, the involvement of Drosha in the adipogenic differentiation of MSCs has not been previously characterized. Here the role of Drosha/microRNA pathway in regulating the adipogenesis of OP9, a MSC derived from mouse bone marrow stroma, is characterized. Knocking down Drosha in OP9 significantly reduced its adipogenic capacity. Small RNA-seq analysis revealed that miR-204 and miR-15b were significantly downregulated in the adipogenic process of OP9 cells upon Drosha removal. Further exploration showed that the activity of ERK1/2 was significantly increased in Drosha KO OP9 cells, which was proved can suppress the transcriptional activity of PPARγ. Introducing miR-204 or miR-15b into OP9 cells significantly enhanced their adipogenic capacity and partially rescued the adipogenic defects caused by Drosha knockout. Mechanistically, miR-15b regulates ERK mediated adpogenic differentiation via repressing NRP2. Our data demonstrate that the Drosha/miR-15/NRP2 axis regulates adipogenesis of MSCs by modulating the ERK/PPARγ pathway. This discovery unveils a previously unappreciated molecular mechanism governing MSC adipogenic differentiation and suggests new avenues for exploring the therapeutic potential of MSCs.

overall_design: RNA-seq profiling of wildtype OP9 cells and their knockout derivatives (Drosha KO) at Day 10 of adipogenic differentiation

first: Wenjun

last: Xiao

first: Haoyu

first: Jiaying

last: Liu

first: Weiqian

last: Chen

first: Chuwen

first: Xuan

last: Jiang


title: XBP1 and CREB3L Coordinate Organelle Architecture and Inter-Organelle Metabolic Flows for Mucin Production in High Endothelial and Goblet Cells

city: Palo Alto

first: Kevin

last: Brulois

state: CA

address: 3801 Miranda Ave

institute: Stanford University

summary: High endothelial cells (HECs) and intestinal goblet cells (GCs) are highly specialized through organelle expansion and metabolism for production of sulfated mucins essential for lymphocyte homing and mucosal defense, respectively. How these cells coordinate organelle architecture and biosynthetic pathways to support such demands remains poorly understood. Here, we show at single-cell resolution that HECs rely on gene regulatory networks driven by IRE1α-XBP1 and CREB3L1/2 transcription factors. These networks upregulate enzymes and transporters that control inter-organelle metabolic fluxes for the step-wise assembly of      sulfated O-glycan synthesis, while scaling the endoplasmic reticulum (ER) and Golgi apparatus, reinforcing cargo trafficking and organizing sequential  glycosyltransferase deployment. Genetic and pharmacological perturbations show that these transcriptional circuits sustain lymph node HEC morphology and function in lymphocyte homing, and drive ectopic induction of HEV during inflammation. Parallel transcriptional networks operate in GCs. Together, our findings define a conserved regulatory logic that integrates metabolic pathways and organelle architecture to enable committed sulfo-mucin cell specialization across distinct tissue contexts.

overall_design: Endothelial cells were isolated from peripheral and mesenteric lymp nodes from WT or Xbp1-KO mice. Sorted Ecs were then proecessed using 10x Genomics 3'v3 chemistry.

first: Yuhan

last: Bi

first: Eugene C.

last: Butcher


title: Epithelial interferon-stimulated gene programs modulate chemotherapy sensitivity in colorectal cancer via EPSTI1

city: Tampere

first: Toni

middle: T

last: Seppälä

address: Arvo Ylpön katu 34

institute: Tampere University

summary: Precision oncology research typically utilizes patient-derived tumor organoids (PDTO) to predict clinical outcomes, but such efforts are often not directed towards identification of molecular factors underlying differential responses to therapy. Here, we performed bulk RNA-sequencing on treatment-naive PDTOs and combined gene expression data with in vitro drug response data to identify transcriptomic features and programs associated with low chemosensitivity.

overall_design:
PDTOs were expanded in vitro until sufficient biomass was reached (P5 to P12). Prior to in vitro drug testing, PDTOs were harvested with Cell Recovery Solution and cell pellets were snap-frozen to be used in bulk RNA-sequencing.

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

first: Erdogan Pekcan

last: Erkan

first: Emmi

last: Hämäläinen

first: Toni T.


title: Translational Control of Splicing Factors Directs Hematopoietic Stem Cell Fate [scRNA-seq]

city: Warsaw

first: Vladyslava

last: Liudkovska

address: Flisa 6

country: Poland

institute: IMol Polish Academy of Sciences

summary: The transition of hematopoietic stem cells (HSCs) from quiescence to differentiation is essential for homeostasis. While transcriptomic control of this process has been extensively studied, the diversity of mRNA isoforms during exit from quiescence remains unexplored. Here, we identify a translationally regulated splicing program governing hematopoietic fate decisions. Splicing factors involved in branch point recognition show dynamic protein-level regulation during HSC differentiation. Among them, Sf1 is translationally controlled via a conserved, structured 5′ UTR. Disrupting translation regulation of Sf1 skews differentiation toward stem cell and erythroid programs. Sf1-dependent alternative splicing affects 5′ UTRs of hematopoietic and DNA damage response genes, altering their translation and impairing DNA damage resolution. These findings reveal an unrecognized link between translational control of spliceosome components, alternative splicing, and HSC fate decisions.

overall_design: Singe-cell RNA-seq of primary ex vivo-expanded murine hematopoietic stem and progenitor cells (HSPCs) with and without translational control of Sf1. Samples with CRISPR-Cas9-mediated deletion of nucleotides 51–100 in the Sf1 5′ UTR (del) are compared to unedited control cells.

first: Sandra

last: Binias

first: Bartosz

last: Wojtas

first: Maciej

last: Cieśla


title: Orphan drug nitisinone combined with sorafenib synergistically boosts anti-PD-1 efficacy in MSS Colorectal Cancer [RNA-Seq]

first: Xiaoxia

address: 26 Yuancun Erheng Road

department: The Sixth Affiliated Hospital

summary: We reveal nitisinone, an FDA-approved tyrosine catabolism inhibitor that targets the HPD enzyme, and sorafenib exert synergistic growth inhibition effects in MSS CRC cells, organoids and mouse xenografts. Using co-cultures of PBMCs with autologous tumor organoids, orthotopic transplant models, multiplex immunostaining and scRNA-seq, we verify that the combination of nitisinone and sorafenib synergistically enhances anti-PD-1 efficacy in a manner that is dependent on the mtDNA-cGAS-STING axis and recruits and activates NK cells. Collectively, the “Triplet” therapy (nitisinone+sorafenib+anti-PD-1) not only achieves an excellent therapeutic effect but also has a favorable safety profile, potentially facilitating expanded access indications of nitisinone in future MSS CRC treatment strategies.

overall_design: RNA-Seq Profiling of MSS Colorectal Cancer Cells Treated with Nitisinone plus Sorafenib versus DMSO Control

first: Minshan

last: Wu

first: Guannnan

last: Tang

first: Yanxin

last: Luo


title: The CARM1 Epigenetic Enzyme Inhibits Cross-presenting Dendritic Cell Function in Cancer Immunity [scRNA-seq]

city: Boston

first: Xixi

last: Zhang

address: 450 Brookline Ave

institute: Dana-Farber Cancer Institute

summary: The cancer-immunity cycle requires cross-presenting dendritic cells (cDC1) that induce T cell-mediated immunity, but therapeutic strategies for enhancing intratumoral cDC1 function are inadequate.  We discovered the epigenetic enzyme Carm1 as a selective negative regulator of cancer antigen presentation by cDC1s, but not cDC2s.  Carm1 inactivation promoted cDC1 antigen cross-presentation, activation, and accumulation in tumors; and a Carm1 inhibitor enhanced cDC1-mediated priming of T cells by a cancer vaccine.  Carm1 inhibition increased chromatin accessibility at BATF3-JUN and RELA sites critical for cDC1 function and activation.  Carm1 expression was regulated by TGF-beta, explaining why Carm1 inactivation enhanced intratumoral cDC1 function without altering cDC1 homeostasis.  These studies identify Carm1 as a therapeutic target for enhancing the anti-tumor function of murine and human cDC1.

overall_design: Single-cell RNA sequencing (scRNA-seq) was performed to profile tumor-infiltrating MHCII+CD11c+ DCs respectively harvested from tumor-bearing Carm1fl/fl ,Carm1fl/flXcr1Cre and Carm1fl/fl Zbtb46Cre mice

first: Yuyang

last: Han


title: Unveiling the small protein landscape of uropathogenic E. coli

city: Freiburg

first: Rick

last: Gelhausen

state: Baden Württemberg

address: Georges-Köhler-Allee 106

department: Department of Computer Science

country: Germany

institute: Albert-Ludwigs-University Freiburg

summary: Uropathogenic Escherichia coli (UPEC) is the predominant causative agent of urinary tract infections, responsible for millions of infection cases each year. The UPEC strain, CFT073, shares only about 40% of its protein-coding genes with the E. coli laboratory strain MG1655. Its mosaic genome contains 60 large genomic islands derived from horizontal gene transfer and mobile elements. Many of its virulence genes reside in these pathogenicity islands. In this study, we explored the small proteome of CFT073 using ribosomal profiling coupled with RNA sequencing, and identified 138 unannotated small open reading frames (sORFs) in intergenic regions. The translation efficiency of all these ORFs was greater than one, indicating that the mRNA transcripts were occupied by ribosomes and undergoing active translation. Thirty of the sORFs were annotated in other genomes; the remaining 108 sORFs encode hypothetical or novel proteins. Reanalysis of conventional proteomic data confirmed protein translation from five of these sORFs. The prediction of transmembrane helices indicated that 8 small proteins encoded by novel sORFs may be associated with lipid membranes. Notably, 5 out of 8 have their sORFs in pathogenicity islands of the genome. We tested their membrane localization using a cell-free system containing lipid sponge droplets. Our study revealed the small proteome of an extraintestinal pathogenic E. coli and provided a catalog of sORFs for further investigation.

overall_design: Ribo-seq and parallel RNA-seq experiment to study the translatome and the small proteome of E. coli UPEC strain CFT073 strain during LB growth condition

first: Wenting

last: Liu

first: Lisa

last: Werland

first: Elisabetta

last: Fiore

first: Eric

last: Mersinger

first: Camila

last: Cilveti

first: Timo

last: Glatter

first: Rolf

last: Backofen

first: Cynthia

last: Sharma

first: Jing

last: Yuan


title: Notch-Rbpj signaling restrains regulatory T cell exhaustion in tumors

city: Heraklion

first: Matthieu

middle: David

last: Lavigne

address: Nikolaou Plastira 100

country: Greece

institute: IMBB-FORTH

summary: Regulatory T cells (Treg cells) are vital for immune homeostasis and prevention of autoimmunity while they exert an essential role in promoting tumor development. Recent efforts to characterize the immunosuppressive circuits of tumor-infiltrating Treg cells (tTreg cells), identified dysfunctional cell states including “ex Tregs”, “fragile” or metabolically-rewired Treg cells with potent anti-tumor properties; yet therapeutic targeting of Treg cells in cancer remains a major unmet need, indicating that unappreciated mechanisms of Treg cell function operate in the tumor microenvironment (TME). A puzzling question that awaits to be addressed is why Treg cells remain functional in the hostile TME, while their lymphocytic effector counterparts become exhausted or senescent. Herein, we identified Notch-Rbpj signaling as a checkpoint pathway which hinders the induction of exhaustion in tTreg cells. Rbpj-ablated Treg cells demonstrated an exhausted-related transcriptome and chromatin landscape and exhibited increased PD1 expression which accounted for the anti-tumor immunity and inhibition of tumor development. In support, PD1 deletion in exhausted Treg cells, rescued their exhausted phenotype and reinvigorated their tumor-promoting function. Finally, therapeutic administration of novel small molecule Rbpj inhibitors promoted Treg cell exhaustion and tumor reduction. Our findings suggest the Notch-Rbpj axis as an immune checkpoint for Treg cell exhaustion which could be targeted therapeutically for cancer therapy.

overall_design: For Full lengrh strand specific mRNA-seq  and ATAC-seq we compared triplicates of FACS-sorted Treg cells (CD45+CD4+ Foxp3YFP+)  from melanoma tumors of Foxp3YFPcre or RbpjΔFoxp3a mice. For Quant-seq we compared triplicates of Treg cells from melanoma bearing Foxp3EGFP mice (tumor -T) with triplicates of Treg cells from tumor-draining lymph nodes (TDLNs or LT).

first: Miranta

last: Papadopoulou

first: Myrto

last: Mitletton

first: Domenico

last: La Tartaro

first: Panayotis

last: Verginis

middle: D


title: The CARM1 Epigenetic Enzyme Inhibits Cross-presenting Dendritic Cell Function in Cancer Immunity [ATAC-seq]

first: Xixi

last: Zhang

overall_design: ATAC-seq analysis of control and Carm1-KO bone marrow-derived cDC1s

first: Wen

last: Wang


title: [eCLIP-seq] The RNA helicase domain of NAT10 promotes the biogenesis of hypomodified ribosomes to enhance cancer cell proliferation

first: Daniel

last: Arango

address: 303 E Superior St, Office 7-119

institute: Northwestern University

summary: N-acetyltransferase 10 (NAT10) is a multifunctional enzyme that harbors RNA acetyltransferase and RNA helicase domains and has emerged as a therapeutic vulnerability in solid and hematological malignancies. By coupling Proteolysis Targeting Chimera-mediated degradation of NAT10 with a deep mutational scanning assay, followed by biochemical, cellular, and in vivo validations, we find that the RNA helicase domain of NAT10 enhances cancer cell proliferation and tumor growth. This proliferative function of NAT10 is independent of RNA acetylation but requires its RNA-binding activity. The RNA helicase domain of NAT10 is required for 18S rRNA binding, promoting biogenesis of the 40S ribosomal subunit, while simultaneously interfering with the deposition of the conserved 18S rRNA modification m¹acp³Ψ. Loss of m¹acp³Ψ in 18S rRNA enhances cancer cell proliferation, revealing that NAT10 promotes the biogenesis of hypomodified ribosomes to facilitate tumor growth. These findings uncover a previously unrecognized mechanism by which NAT10 promotes cancer cell proliferation and establish its RNA helicase domain as a potential therapeutic target.

overall_design: seCLIP-seq using anti-NAT0 antibodies in HEP3B cells expressing YFP [NAT10(-)], NAT10-WT, NAT10-E389L, or NAT10-K290V.

first: Sharath

last: Narayan

first: Hannah

last: Serio


title: The impact of BSCI exposure on labour in pregnant mice after IL1A induction

city: Toronto

first: Jennifer

last: Mitchell

state: Ontario

address: 25 Harbord Street

department: Cell and Systems Biology

institute: University of Toronto

summary: To examine changes in chromatin accessibility involved in BSCI-mediated prevention of IL-1α-induced labour in pregnant mice, we conducted ATAC-seq on mouse myometrial tissues from four groups: Vehicle, IL-1α, BSCI and combined IL-1α with BSCI. Specifically, IL-1α is a method of labour induction, while administration of BSCI prior to and after administration of IL-1α prevents labour onset in mice. These data enable dissection of cis-regulatory elements involved in labour onset in response to IL-1α labour induction, as well as understanding of how these regions are modified in response to BSCI to prevent labour induction.

overall_design: ATACseq of pregnant mouse myometrial tisssue following injection of vehicle control, BSCI, IL1A or BSCI and IL1A. Three samples for each condition were collected.

first: Zoe

last: Gillespie

middle: A


title: The CARM1 Epigenetic Enzyme Inhibits Cross-presenting Dendritic Cell Function in Cancer Immunity [RNA-seq]

overall_design: RNA-seq profiling of control and Carm1-KO bone marrow-derived cDC1s; RNA-seq profiling of MSR scaffolds harvested from mice vaccinated with control-vax and EZM2302-vax,respectively.


title: Target macrophage SPP1 promtes CD8 T cell infiltrations

city: Suzhou

first: Xiaoyu

last: Lin

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

institute: Suzhou Institute of Systems Medicine

summary: SPP1 in tumor associated macrophages (TAM) can inhibit the infiltration of CD8 T cells, promote tumor growth, and reduce the efficacy of ICI immunotherapy. Single cell (sc)-RNA sequencing data showed markedly increased CD8 T cells in the tumor tissues of SPP1fl/fl-Lyz2-icre mice compared to control SPP1fl/fl mice.

overall_design: To further determine the effects of macrophage SPP1 on the CRC, we performed scRNAseq on MC38 tumor from control SPP1fl/fl mice and SPP1fl/fl-Lyz2-icre mice.

first: Juanjuan

first: Yi

last: shi

first: Yunhuan

last: Gao

first: Rongcun

last: Yang


title: The CARM1 Epigenetic Enzyme Inhibits Cross-presenting Dendritic Cell Function in Cancer Immunity [CUT&RUN]

overall_design: Cut&run analysis of control and Carm1-KO bone marrow-derived cDC1s

first: Ye

last: Zhao


title: Analysis and statistics of mRNA interacting with 7F2-positive microtubule associating protein tau in human hippocampal Alzheimer’s Disease tissue.

city: Gainesville

first: John

last: Koren

address: 1275 Center Dr

institute: University of Florida

summary: The microtubule associating protien tau, (MAPT, tau) is a primary pathologic factor in a number of neurodegenerative disorders, including Alzheimer's Disease. Tau can interact with RNA. These interactions have been proposed as initiating factors for the formation of the pathological forms of tau noted in diseases. Additionally, it has been suggested that the m6A-methylation state of RNA is a factor in the association of RNA to tau. This study uses enhanced crosslinking immunoprecipitation (eCLIP) techniques to 1) identify, quantify, a sequence the RNA species interacting with the tau protein isolated from Alzheimers disease human hippocampal tissue, 2) identify, quantify, and sequence the methylated RNA in Alzheimer's disease human hippocampal tissue, and 3) to look for associations between the RNAs that interact with tau and RNA methylation status.

overall_design: Tissue from four ApoE 3/3 donors with pathologies designated as intermediate Alzheimer's (ADI) or high Alzheimer's (ADH) underwent eCLIP processes to identify and sequence the RNA that were interacting with tau and the RNA that featured m6A methylation. The primary output, in a manuscript under preparation, was to simplify the associated RNA data to a list of their representative genes. These gene lists were then compared for methylation status, tau interaction, and signaling pathways. The raw RNA seq associated with these studies was also used to examine the transcriptome of ADI and ADH.

last: Koren III

first: Tristyn

last: Garza

first: Jose

last: Abisambra


title: The critical role of the host endogenous immune compartment after intracerebroventricular CAR T cell therapy in recurrent GBM

city: Philadelphia

first: Nelson

last: Freeburg

state: PA

address: 421 Curie Blvd

department: Cancer Biology

institute: University of Pennsylvania

summary: Glioblastoma (GBM) is the most common primary malignant brain tumor in adults, with a median survival of under 15 months and no effective treatment after recurrence. A recent phase I trial of intracerebroventricular (ICV) bivalent CAR T cells in recurrent GBM showed promising responses, including tumor reduction and prolonged survival. However, relapse remains common. We performed in-depth profiling of longitudinal CSF and tumor samples from responders and non-responders to characterize immune dynamics following infusion. Our study reveals that while CAR T cells activate post-infusion across all patients, outcomes were defined by divergent remodeling of the endogenous immune landscape. Cytotoxic NK cell expansion characterized responders, whereas regulatory T cell expansion and abundant baseline immunosuppressive myeloid cells characterized non-responders. These findings indicate that host immune cells play a critical role in ICV CAR T cell therapy for GBM, suggesting that combinatorial strategies modulating the endogenous immune compartment could improve next-generation treatments.

overall_design:
Single cell RNA sequencing on CAR T cell infusion products (18 patients), and cerebrospinal fluid samples (9 patients) from patients in a phase I clinical trial for bivalent CAR T cell therapy targeting EGFR epitope 806 and IL13RA2 were subjected to single cell RNA and TCR sequencing,  Single-nucleus RNA sequencing on tumor samples pre and post- CAR T cell infusion (6 patients), Bulk RNA sequencing from FFPE tumor samples pre and post CAR T cell infusion (6 patients).
======================================
Note from submitter: GSM9543406-GSM9543478: patient data and cannot be placed in SRA. We are in the process of getting clearance to upload them to dbGaP.
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last: Chafamo

first: Gayathri

last: Konanur Gopikrishna

first: Regan

last: Murphy

first: Jacqueline

last: Peng

first: Shridhar

last: Parthasarathy

first: Sydney

last: Dumont

first: Edward

middle: G

last: Estrada

first: Meghan

last: Logun

first: Yusha

last: Sun

first: Xin

first: Paya

last: Grover

first: Jesse

middle: L

last: Rodriguez

first: Kristen

last: Park

first: Yao

last: Fu

first: Nadine

last: Ben Hamouda

first: Isaias

last: Hernandez-Verdin

first: Lamia

last: Lamrani

first: Kelly

last: Hicks

first: Natalie

last: Cooper

first: Christina

last: Ekwegbara

first: Emma Grace

last: Bawden

first: Joshua

last: Waterfall

first: Jaime

last: Fuentealba

first: Marion

last: Alcantara

last: Seykora

first: Stephen

last: Prouty

first: David

last: Barrett

first: Esha

last: Banerjee

first: Arin

last: Cox

first: Charles

last: Assenmacher

first: Camilla

last: Macia

first: Melinda

last: Yin

first: Erica

last: Carpenter

first: Guo-li

last: Ming

first: Catherine

last: Sautès-Fridman

first: Wolf

middle: H

last: Fridman

first: Eric

last: Tartour


title: Silencing the Storm: A Next-Generation Secretome (PRS CK STORM) Rewrites the Immune Response in Viral Acute Respiratory Distress Syndrome

city: Madrid

first: Daniel

last: Lapuente

address: Calle de Isabel Colbrand, 6, 4ª planta, Fuencarral-El Pardo

institute: Peaches Biotech

summary: PRS CK STORM is a complex biological drug composed of the secretome derived from co-cultures of alternatively activated M2 macrophages and adipose-derived mesenchymal stem cells (ASCs). The secretome encompasses the total set of proteins and bioactive molecules released into the extracellular space, including cytokines, chemokines, growth factors, enzymes and exosomes. Rather than representing a simple mixture of isolated components, PRS CK STORM captures the physiological complexity of immunological crosstalk induced by exposing these cell types to a controlled stress environment—an approach designed to activate regenerative immune programs through dynamic intercellular communication. This drug has demonstrated therapeutic efficacy in vivo by reducing lung inflammation, viral load, and tissue injury in murine models of acute respiratory distress syndrome (ARDS). In parallel, multi-omic mechanistic assays have shown that PRS CK STORM consistently inhibits key pro-inflammatory signaling pathways including NF-κB, NLRP3 inflammasome, and COX-2 activity, supporting its immunoregulatory mechanism of action. To assess whether the molecular composition of PRS CK STORM reflects its observed immunomodulatory effects, we profiled the exosomal microRNA (miRNA) content in five independent drug production batches, enabling the identification of the most abundant miRNAs likely to contribute to its biological activity.

overall_design: Exosomal microRNA sequencing (miRNA-seq) profiling was performed on five independent production batches of PRS CK STORM. In each batch, alternatively activated M2 macrophages used in the co-culture were derived from monocytes isolated from a distinct healthy donor.

first: Juan Pedro

first: Francesca

last: Sarno

first: Noelia

last: Mendoza


title: [18S direct RNA sequencing] The RNA helicase domain of NAT10 promotes the biogenesis of hypomodified ribosomes to enhance cancer cell proliferation

last: Arango

overall_design: Nanopore direct RNA sequencing of 18S rRNA in HEP3B wildtype, NAT10-FKBP, and NAT10's helicase domain mutants (K290A and E389L).

first: Mahmood

last: Dalhat

first: Hannah

last: Serio


title: Single-nuclei transcriptome of enteric neurons in α-synuclein overexpressing mice

city: Cambridge

first: Christopher

middle: Peter

last: Pukszta

state: MA

address: 455 Main St

institute: Massachusetts Institute of Technology

summary: Overexpression of the neuronal protein α-synuclein (αSyn) is a risk factor for Parkinson’s disease (PD), and αSyn aggregation promotes neurodegeneration and movement disorders. αSyn overexpressing mice (Thy1-ASO) reproduce many PD-associated phenotypes such as motor deficits and constipation, which impacts a majority of patients. We sought to gain insight into enteric nervous system function in Thy1-ASO mice by isolating neuronal nuclei from mouse intestines, which makes up less than 1% of cells, followed by transcriptomic analysis. To overcome the challenge of profiling gene expression in rare cell populations within complex tissues, we engineered an adeno-associated virus (AAV) that expresses a fluorescent protein in the nuclear membrane under the control of a constitutive neuronal promoter. We generated a high-quality single-nuclei gene expression dataset that revealed transcriptional heterogeneity reflecting populations of 4 putative excitatory motor neuron subtypes, 2 putative inhibitory motor neuron subtypes, 3 putative interneuron subtypes, and a putative sensory neuron gene cluster. There was little difference in expression of individual genes in neurons between wild-type and Thy1-ASO mice in the colon, under the conditions tested. However, pathway analysis revealed changes in the PI3K pathway in excitatory motor neurons (upregulated in Thy1-ASO), MAPK and androgen pathways in inhibitory motor neurons (upregulated in Thy1-ASO), and WNT (upregulated in Thy1-ASO) and p53 (downregulated in Thy1-ASO) pathways in interneurons. This dataset can be leveraged to understand the physiological basis of gut motility deficits in α-synuclein overexpressing mice.

overall_design: Single nucleus RNA sequencing of wild type Black 6 [C57BL/6J] and alpha-synuclein overexpressing (ASO) [B6;DBA-Tg(Thy1-SNCA)61Ema] colonic neurons. Nueronal nuclei from disaggregated tissue were sorted into individual wells of a 384 well plate, flash frozen, and sequenced with SMART-Seq2.

first: John

middle: W

last: Bostick

first: Delaney

last: Sullivan

first: Sarkis

last: Mazmanian


title: [DMS-Seq] - The RNA helicase domain of NAT10 promotes the biogenesis of hypomodified ribosomes to enhance cancer cell proliferation

overall_design: Unbiased deep mutagenesis scanning and nanopore sequencing of exogenous NAT10. Cells expressing NAT10-FKBP were treated with dTAGV-1 to deplete endogenous NAT10, then transduced with a site-saturation mutagenesis library of NAT10. Cells were sorted on Day 0 and Day 12 post-treatment, sequenced, and analyzed.


title: m6A-methylation analysis and statistics of mRNA interacting with microtubule associating protein tau in human hippocampal Alzheimer’s Disease tissue.

last: Koren

last: Koren III

first: Tristyn

last: Garza

first: Jose

last: Abisambra


title: The function of FTO in small cell lung cancer [RNA-seq]

city: Yiwu

first: Yixuan

last: Yu

address: 1575 Chouzhou North Road, Futian Street

institute: The Fourth Affiliated Hospital of School of Medicine, and International School of Medicine

summary: This study investigates the role of the fat mass and obesity-associated protein (FTO), an m6A RNA demethylase, in small cell lung cancer (SCLC). RNA sequencing was performed to evaluate the transcriptomic changes in SCLC cell lines H69 and H82 following treatment with two selective FTO inhibitors, CS2 and FB23-2. Cells were treated with the inhibitors under defined conditions, and total RNA was extracted using the TRIzol reagent. RNA-seq libraries were constructed and sequenced using the DNBSEQ-T7 platform. The resulting dataset provides valuable insight into the downstream molecular effects of FTO inhibition in SCLC and may contribute to the identification of potential therapeutic targets in this highly aggressive tumor type.

overall_design: Small cell lung cancer cell lines H69 and H82 were treated with FTO inhibitors CS2 and FB23-2. RNA was extracted after treatment, and RNA-seq was performed to assess transcriptomic changes induced by FTO inhibition. DMSO served as controls. Each condition was performed with biological replicates.


title: [MerR-seq] The RNA helicase domain of NAT10 promotes the biogenesis of hypomodified ribosomes to enhance cancer cell proliferation

overall_design: Mapping the ends of ribosomal RNA and sequencing (MErR-seq) in HEP3B wildtype, and NAT10's helicase domain mutants (E389L).


title: Fibrogenic macrophages drive cardiac fibrosis via MMP12-mediated tissue remodeling

city: Vienna

first: Thomas

last: Weichhart

address: Waehringerstraße 10

department: Center for Pathobiochemistry and Genetics

country: Austria

institute: Medical University of Vienna

summary: Fibrosis is a major contributor to mortality in various diseases, yet, it isunderlying mechanisms remain unclear. Here, we identified a mechanistic driver of fibrosis by investigating a fibrotic cardiac sarcoidosis mouse model. We demonstrate that mTORC1 induced a recently described fibrogenic macrophage population expressing Cd63, Spp1, Gpnmb, and Fabp5. sc-RNAseq analysis revealed a stepwise differentiation process of monocytes into fibrogenic macrophages via TGFβ signaling under mTORC1 control. Crucially, we uncovered matrix metalloproteinase 12 (MMP12) as the key effector that enables fibrogenic macrophages to mediate fibrosis. Pharmacologic inhibition of MMP12 diminished fibroblast activation, granulomatous inflammation, and resolved fibrotic lesions in the myocardium. Analysis of human cardiac sarcoidosis tissue and transcriptomics data from human liver and lung fibrotic diseases suggests MMP12-driven fibrotic remodeling by macrophages as conserved pathogenic mechanism. These findings provide a mechanistic basis for fibrogenic macrophage function and establish MMP12 as promising therapeutic target for fibrotic disease and cardiac sarcoidosis.

overall_design: Whole mouse hearts from 3 floxed controls, 3 vehicle treated mice, and 3 Linvemastat treated mice, were isolated and flushed with ice cold PBS, and kept on ice until further processing. Single cell suspension was made with a standard tissue digestion protocol for heart tissue. Immune cells were isolated from whole mouse hearts via fluorescence associated cell sorting (FACS) based on the presence of CD45+ signal with the inclusion of some CD45- cells, and sequenced using the Illumina NovaSeq 6000 platform.

first: Mario

last: Mazic

first: Clarice

last: Lim


title: An RNA sequencing-based comparison of adolescent-young adults and adult patients with synovial sarcoma

city: MILAN

first: Luca

last: Agnelli

address: Venezian 1

department: Department of Advanced Diagnostics

country: Italy

institute: IRCCS Istituto Nazionale dei Tumori

summary: Synovial sarcoma (SS) is a rare disease accounting for 5%-10% of all soft tissue sarcomas. SS affects younger adults and children with a peak incidence in the fourth decade of life and its molecular hallmark is the SS18::SSX translocation. adolescent and young adults (AYAs) with SS have better 5-year estimated survival rates than adults but the reason behind these differences in outcomes have been hardly investigated.             In this  retrospective survey, to investigate their potential transcriptomic differences, 14 AYAs and 8 adults SSs samples, were analyzed trough RNA sequencing (RNAseq). The enrichment of recently published transcriptional signatures of specific SSs tumoral and infiltrating cells were also investigated in our data. In terms of both, progression free and overall survival, AYAs patients showed a better clinical outcome but, RNAseq results, underscored that AYAs and adults are characterized by reduced transcriptional variability although a few number of genes (in particular RPL39 and GATA 3 among others), turned out to be differentially expressed. The similarity between AYAs and adults also resulted after the comparison with specific the SSs transcriptional signatures although adults  were characterized by the enrichment of cycling cells while half of our AYAs samples showed an enhancement of infiltrating macrophages.       Albeit in a context of reduced transcriptional variability, these findings evidenced some biological difference that can potentially contribute to the observed different clinical outcome of AYAs and adults SSs patients.

overall_design: We performed RNA sequencing to investigate the biological differences underlying Sinovial Sarcoma across age groups, in adolescents and young adults (AYAs), on primary tumor tissues. Transcriptional profiles from 14 patients under the age of 25 were compared to those from 8 adult patients (over 30).

first: Fabio

last: Bozzi

first: Alessia

last: Bertolotti

first: Elena

last: Conca

first: Andrea

last: Davecchi

first: Paola

last: Collini

first: Antonina

last: Parafioriti

first: Sandro

last: Pasquali

first: Federica

last: Perrone

last: Tamborini

first: Michela

last: Casnova

first: Stefano

last: Chiaravalli

first: Giancarlo

last: Pruneri

first: Patrizia

last: Gasparini

last: Ferrari


title: Antibody-trapping presents a widespread pitfall for microscopy and genomics in the nucleus

city: Berlin

first: Konrad

middle: Jakub

last: Chudzik

address: Hannoversche Str. 28

institute: MDC-BIMSB

summary: Chromatin has a complex 3D structure and diverse binding proteins that coordinate the genome's most essential functions. Many microscopy and genomics technologies that map chromatin proteins and modifications rely on the diffusion of antibodies (Abs) to target epitopes within whole nuclei. Here, we reveal a critical flaw in such methods that arises when Abs become trapped at the edge of nuclear structures and fail to reach internally-positioned epitopes. This “Ab-trapping” results in artifactual peripheral signal that fundamentally distorts the apparent positions of chromatin features across the genome and nucleus. Using computational modelling and experimental validation, we demonstrate that Ab-trapping is caused by a combination of three compounding factors - high epitope abundance, high Ab affinity, and low Ab diffusion rates. Ab-trapping can thus systematically misrepresent the localization of many prevalent chromatin features like histone modifications, transcription factors, nucleolar proteins, and protein tags. We also show this artifact manifests in multiple technologies, including immunofluorescence microscopy, more recent CUT&Tag-seq, and likely any method relying on Ab diffusion. Finally, we outline readily implementable strategies to identify and mitigate Ab-trapping. Combined, our work presents a previously unrecognized yet prevalent artifact in Ab-based chromatin mapping methods and the means to resolve it.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: CUT&Tag targeting H3K9ac, H3K9me2 (using three different antibodies), and LaminB1 was performed in mouse rod photoreceptor cells isolated by fluorescence-activated cell sorting (FACS), alongside corresponding rabbit and mouse IgG controls. LaminB1 was additionally targeted in mouse G4 embryonic stem cells (ESCs; XY, 129S6/SvEvTac × C57BL/6Ncr F1 hybrid), alongside matched rabbit IgG controls. All experiments were performed in two biological replicates; ESC LaminB1 experiments additionally included two technical replicates per biological replicate.

first: Yuko

last: Sato

first: Xingchi

last: Yan

first: Simon

last: Ullrich

first: Watanya

last: Trakarnphornsombat

first: Lothar

last: Schermelleh

first: Geoffrey

last: Fudenberg

first: Hiroshi

last: Kimura

first: Michael

middle: I

last: Robson

first: Irina

last: Solovei


title: Endometriosis and NLRP3 inflammasome activation: the role of the peritoneal fluid

city: São Paulo

first: Helena

last: Malvezzi

state: São Paulo

address: Av. Morumbi

department: Research

country: Brazil

institute: Hospital Israelita Albert Einstein

summary: Endometriosis is a chronic inflammatory disease characterized by the ectopic growth of endometrial-like tissue outside the uterus, leading to pelvic pain, infertility, and increased inflammation. This study focuses on peritoneal fluid (PF) NLRP3 inflammasome pathway expression in patients with endometriosis, evaluating PF’s influence on immune responses and cell proliferation. PF, which contains immune cells and secreted factors, plays a critical role in maintaining the inflammatory microenvironment associated with endometriosis. Through RNA extraction, gene expression, protein analyses, and cell culture this research investigated inflammasome-related markers in PF and stromal cells from endometriotic lesions, eutopic endometrium, and non-endometriosis. Results revealed significant alterations in the expression of key inflammasome-related genes, including increased levels of Caspase-1 and interferon gamma. However, it was not observed significant impact of PF on NLRP3 expression or cell proliferation on patient derived stromal cell. These findings suggest that while the inflammasome can play a crucial role in lesion development, PF may reflect rather than drive the cellular changes associated with endometriosis. The highlights the importance of inflammasome regulation in understanding endometriosis pathogenesis and its inflammatory mechanisms.

overall_design:
This initial case-control investigation took place at the Hospital Israelita Albert Einstein (HIAE) in São Paulo, Brazil. The study received ethical clearance from the Human Research Ethics Committee of HIAE (CAAE 05776919.3.0000.0071) in March 2019, and all participating patients provided written informed consent.
In total, 60 patients, were enrolled in this study, ensuring that they met the specific inclusion and exclusion criteria outlined below.
Patients underwent video laparoscopy for the resection of endometriotic lesions or the evaluation of pelvic pain and myomectomy for intramural fibroids only. Deep retrocervical endometriosis lesions (EL), as well as eutopic endometrium (EE) were collected from patients referred for laparoscopic surgery to excise endometriosis lesions, as well as samples of non-endometriosis endometrium (NEE) from patients without laparoscopic evidence of endometriosis. These women were referred for surgery to treat uterine fibroids, benign ovarian cysts or elective tubal ligation, with the absence of endometriosis confirmed during the surgical procedure. For both groups, endometrium was collected using a Recamier Weldon curette shortly after the patient was positioned for surgery.
All collected tissues used for in vivo studies were stored at −80 °C. After surgical removal, the tissues collected for cell culture were immersed in a culture medium and subsequently processed in the experimental laboratory. Peritoneal fluid samples from 27 patients, who were undergoing laparoscopic surgery to excise endometriosis lesions, were collected. We ensured that peritoneal fluid samples were collected at the start of the surgery through visual inspection of the cul de sac, thereby preventing any potential blood contamination. Endometrial biopsies were collected. Diagnosis was confirmed through histopathological examination. Additionally, peritoneal fluid samples from 23 patients who did not have endometriosis, were collected. The absence of endometriosis was verified via laparoscopic surgery.
Inclusion criteria involved women aged 18–50 with regular menstrual cycles, regardless of whether they were undergoing hormonal treatment. Exclusion criteria encompassed individuals who were smokers, had hydrosalpinx, endometrial polyps, or had previously been diagnosed with diabetes, endocrinopathies, cardiovascular diseases, dyslipidemia, systemic lupus erythematosus, or other autoimmune, inflammatory, or neoplastic conditions.

first: Bruna

last: Cestari

first: Felipe

last: Ravagnani

first: Helen

last: Mendes

first: Camila

last: Hernandes

first: Sergio

last: Podgaec


title: C57bl/6j mice categorized to ketamine responders (Res), and nonresponsive (NR) mice using novelty suppressed feeding and forced swimming test.

city: Cleveland

first: Wanpeng

last: Cui

state: OH

address: Room E765, Robbins Building,, 10900 Euclid Ave, Department of Neurosciences,

department: Neurosciences

institute: Case Western Reserve University

summary: To identify the mechanims or brain target of ketamine in antidepression. Comparison of differentially expressed genes in ketamine responders and nonresponders after ketamine injection

overall_design: Bulk RNA sequencing of NR and Res mice. Three mice for each group

first: Lin

last: Mei


title: RNA-seq of RA-FLS(siNC vs siFUNDC1)

city: Guangzhou

first: Yaxiong

last: FANG

address: No.1 Du Xue Rd, Nansha District

institute: HKUSTGZ

summary: Total RNA sequencing was performed on fibroblast-like synoviocytes isolated from synovial biopsy tissues of patients with rheumatoid arthritis before and after knockdown of FUNDC1.

overall_design: Six cases of primary fibroblast-like synoviocytes, each including siNC group and siFUNDC1 group.