title: Transcriptomic analyses identify TMPRSS4 as a shared biomarker in asthma and atopic dermatitis

city: Wuxi

first: qin

last: chu

address: Department of Respiratory, The Affiliated Wuxi People’s Hospital of Nanjing Medical University

department: Department of Respiratory

summary:
Asthma and atopic dermatitis (AD) are common chronic inflammatory diseases that often co-occur, but the underlying shared biological mechanisms remain elusive. In this study, we performed WGCNA analyses on GSE6012 and GSE67472 datasets and identified 24 genes associated with both AD and asthma.
We observed that transmembrane protease serine 4 (TMPRSS4) showed significant upregulation in both asthma and AD patients across two independent datasets (GSE6012/GSE67472) using Wilcoxon testing with high receiver operating characteristic (ROC) curve performance, suggesting it may serve as a common biological marker for the co-occurrence of asthma and AD. To elucidate the biological role of TMPRSS4, we first validated its expression profile using Reverse transcription quantitative PCR (RT-qPCR), western blotting and immunofluorescence in HaCaT and BEAS-2B cell models. Subsequently, we performed TMPRSS4 knockout in these two cell lines and conducted RNA-Seq analysis, which revealed that TMPRSS4 might be involved in signal transduction and immune response pathways. Further investigation into the closely related signal transducer and activator of transcription 3 (STAT3) signaling pathway showed that knockout of TMPRSS4 led to increased phosphorylation at the Ser727 site and decreased phosphorylation at the Tyr705 site of STAT3. Moreover, TMPRSS4-/- cells exhibited increased endoplasmic reticulum (ER)-mitochondrion contacts. These findings suggest that TMPRSS4 may exert its function through regulating ER-mitochondrial function. Our study provides novel insights into the role of TMPRSS4 in the pathogenesis of asthma and AD co-occurrence and highlights its potential as a therapeutic target.

overall_design:
TMPRSS4 knockout in two cell lines and conducted RNA-Seq analysis
HD: Human immortalized epidermal cells, control cells treated with TNFα + IFNγ.
BK: Human airway epithelial cells, TMPRSS4 knockout cells treated with house dust mite (HDM)
HK: Human immortalized epidermal cells, TMPRSS4 knockout cells treated with TNFα + IFNγ.
BD: Human airway epithelial cells, control cells treated with house dust mite (HDM).

first: Chu

last: Qin


title: MANF in the Lateral Septum Dynamically Regulates Endoplasmic Reticulum Function via Transcriptomic Remodeling in Chronic Social Defeat Stress Response

status: Public on Jun 23 2026

city: Shanghai

first: Jinmei

last: Ye

state: Shanghai

address: NO.600 Wanping Nan Road,Shanghai

country: China

institute: shanghai mental health center

type: Expression profiling by high throughput sequencing

summary: This study characterized the dynamic molecular adaptations in the lateral septum (LS), a key limbic hub for stress processing, during the transition from acute to chronic social defeat stress (CSDS) in male C57BL/6J mice. Longitudinal bulk RNA-seq of LS tissue at CSDS days 1,4,7,10 revealed a biphasic endoplasmic reticulum (ER) stress response, with mesencephalic astrocyte-derived neurotrophic factor (MANF) as a core regulator. Functional validation confirmed that LS-specific MANF manipulation bidirectionally modulates ER stress, synaptic plasticity, and depressive-like behaviors in mice. Our findings identify MANF as a pivotal mediator bridging ER stress adaptation to neural circuit dysfunction in stress-induced depression.

overall_design: Longitudinal bulk RNA-seq analysis of LS tissue from male C57BL/6J mice under CSDS at four time points (day1, day4, day7, day10) and age-matched unstressed controls

first: Daihui

last: Peng


title: Gene Expression Profiling of Recipient Immune Cells Induced by 7 × 19 CAR-T Cell Dosing in a Syngeneic Mouse Model [scRNA-Seq]

city: FUJISAWA

first: Yuumi

last: Okuzono

state: KANAGAWA

address: 26-Muraoka-higashi 2-chome

country: Japan

institute: Takeda Pharmaceutical Company Limited

summary: Chimeric antigen receptor (CAR)-T cell therapy is effective for hematologic malignancies; however, the response of solid tumors is limited because of the immunosuppressive tumor microenvironment, antigen heterogeneity, and lack of persistence of transferred T cells. To overcome these challenges, CAR-T cells expressing interleukin-7 and chemokine (C-C motif) ligand 19 (7 × 19 CAR-T) were generated to achieve potent antitumor efficacy through the recruitment and proliferation of CAR-T cells and endogenous immune cells. To elucidate the underlying mechanism of 7 × 19 CAR-T cells against solid tumors, we analyzed the cellular composition and gene expression profiles of host immune cells following CAR-T cell infusion in a murine solid tumor model.  Antihuman CD20 7 × 19 CAR-T cells were prepared using Thy 1.1 congenic mice and administered to C57BL/6N mice bearing subcutaneous MC38 tumors expressing human CD20. The tumors were harvested 4 days postinfusion to capture early immune responses before overt tumor regression. CD90.1- recipient immune cells were subjected to flow cytometry analysis, and transcriptomics changes were determined using AmpliSeq and single-cell RNA seq.  An increase in recipient CD8+ T cells and macrophages was observed in the tumor of mice treated with 7 × 19 CAR-T cells, but not with conventional CAR-T. The expression of chemokines and genes associated with the inflammatory pathway was upregulated only in recipient immune cells of the 7 × 19 CAR-T-treated mice. Single-cell RNA-seq analysis revealed upregulation of pro-inflammatory genes and chemokines in the dendritic cell and monocyte/macrophage populations. These results indicate that 7 × 19 CAR-T cells initiate the early recruitment and activation of host immune cells, which contributes to their superior antitumor activity compared with conventional CAR-T cells.

overall_design: Single-cell RNA-seq libraries were prepared using CD45+ tumor-infiltrating immune cells. Single-cell suspensions were prepared. CD45+ cells were isolated using the EasySep CD45 positive selection kit (STEMCELL Technologies). For CITE-seq analysis, the cells were labeled with TotalSeq-A0380 anti-rat CD90/mouse CD90.1 (Thy1.1) antibody (BioLegend). Single-cell libraries were prepared from tumor tissue using the Chromium Single Cell 3' Library Kit v2 (10X Genomics) following the manufacturer’s instructions. The libraries were sequenced on an Illumina HiSeq system at 100,000 reads per cell depth. The initial data was processed using the Cell Ranger pipeline (version 4, 10× Genomics)

first: Yo

last: Muraki

first: Rina

last: Kurisu

first: Akiko

last: Abiru

first: Yukimi

last: Sakoda

first: Koji

last: Tamada

first: Chihiro

last: Akimoto


title: Lifelong consumption of freeze-dried Parabacteroides distasonis improves gut barrier integrity and extends lifespan and health span in Drosophila melanogaster

city: Boston

first: Jimmy

middle: W.

last: Crott

state: Massachusetts

address: 670 Albany Street

department: Pathology and Laboratory Medicine

country: USA

institute: Boston University School of Medicine

summary: Chronic inflammation has been shown to be associated with aging. In Drosophila melanogaster, age-related inflammation in the gut results in a disruption of gut barrier integrity, which can lead to reduced intestinal function and death. The anaerobic bacterium Parabacteroides distasonis (Pd) has anti-inflammatory properties and can attenuate tumorigenesis and promote intestinal barrier integrity in a mouse model of colorectal cancer. Here, we show that administration of Pd to adult Drosophila significantly increases mean lifespan and promotes maintenance of climbing ability throughout adult life. Furthermore, it enhances gut barrier integrity in aged adults. RNA-Seq analysis of Pd treated adult guts indicates that the enhanced healthspan is accompanied by transcriptional upregulation of genes involved in DNA replication and maintenance of genome integrity. These results suggest that Pd can induce a transcriptional shift towards augmented DNA repair in aging gut that prevents the breakdown of gut barrier integrity and promotes healthy aging.

overall_design: Bulk RNA-seq profiling of dissected guts from 45-day-old virgin female w1118 Drosophila fed either Control or Parabacteroides distasonis diets to identify transcriptional changes underlying lifespan extension.

first: Vicki

last: Do

first: Mitch

last: McVey

middle: W


title: Feeder-free generation of CD4 single-positive helper T cells from human iPSCs via stage-specific modulation of Notch and TCR Signaling

city: Kyoto

first: Shin

last: Kaneko

state: Kyoto

address: 53 Kawahara-cho, Shogoin, Sakyo-ku

department: Center for iPS Cell Research and Applications

institute: Kyoto University

summary: Induced pluripotent stem cell (iPSC)-derived T cells (iPS-T cells) represent a promising platform for adoptive immunotherapy, offering an unlimited source of T cells amenable to gene editing and rigorous quality control. While feeder-free in vitro redifferentiation systems have been successfully developed for CD8+ cytotoxic T cells, the generation of CD4+ helper T cells under similar conditions has remained elusive—despite their essential role in sustaining long-term immune responses. In this study, we established a feeder-free culture system for the generation of CD4 single-positive (SP) helper T cells from iPSCs, under conditions that exclude TCR signaling, which otherwise biases differentiation toward the cytotoxic lineage. By precisely modulating Notch and integrin signaling in a stage-specific manner, we induced the differentiation of CD4 SP iPS-T cells expressing key helper-associated molecules, including CD40L and ThPOK, capable of promoting dendritic cell maturation. Notably, these cells also acquired cytotoxic activity upon repeated expansion while retaining robust proliferative capacity. Our findings provide a foundation for the scalable and consistent production of both CD4 SP helper and killer T cells from pluripotent stem cells, advancing the potential of iPSC-based immunotherapies.

overall_design: We performed single-cell RNA sequencing (scRNA-seq), T cell receptor (TCR) sequencing (scTCR-seq), and CITE-seq (Cellular Indexing of Transcriptomes and Epitopes) on iPSC-derived T cells. T-cell derived iPSCs (clone TKT3V1-7) were differentiated using two methods: (1) a modified Feeder-free (FF) culture system and (2) an Artificial Thymic Organ (ATO) culture system. Samples were collected at multiple time points during the DP-to-SP transition: Day 21, 29, 33, and 37 for Feeder-free culture, and Day 21, 35, and 49 for ATO culture. Libraries were prepared using the 10x Genomics Chromium Single Cell 5' v2 chemistry (for GEX and TCR) and Feature Barcoding technology (for CITE-seq). Sequencing was performed to analyze transcriptional profiles, surface protein expression, and TCR clonotypes.

first: Yohei

last: Kawai


title: Manipulation of Mitochondrial Metabolism Sensitizes AML to MCL-1 Inhibition

city: Memphis

first: Yong-Dong

last: Wang

state: TN

address: 262 Danny Thomas Pl, MS1135

institute: St. Jude Children's Research Hospital

summary: MCL-1 (myeloid cell leukemia-1) promotes survival and confers therapeutic resistance in acute myeloid leukemia (AML), particularly in high-risk subtypes such as those harboring KMT2A rearrangements (KMT2A-r). Clinical trials of MCL-1 inhibitors have been limited by modest efficacy and dose-limiting toxicity, underscoring the need for rational combination strategies. Here, we identify inhibition of electron transport chain complex I (CI) as a synthetic lethal partner for MCL-1 blockade. Mechanistically, CI suppression activates the mitochondrial stress arm of the integrated stress response (ISR), sensitizing leukemia cells to apoptosis upon MCL-1 inhibition. Co-targeting CI and MCL-1 synergistically reduces viability in AML cell lines and patient-derived xenograft (PDX) samples in vitro, while significantly prolonging survival in mice bearing PDX AML. These findings provide a mechanistic rationale and preclinical evidence for dual inhibition of MCL-1 and CI as a therapeutic strategy, offering a potential path to overcome resistance to single-agent MCL-1 inhibitors and improve outcomes for patients with high-risk AML.

overall_design: MV4-11 and THP1 cells were plated and treated with DMSO or 50 nM IACS-010759 for 8 or 24 h for three independent replicates, and gene expressions were comparied  between groups of treated sample and control sample.

first: Lauren

last: Brakefield-Laird

first: Amit

last: Budhraja

first: Peter

middle: M

last: Hall

first: Dixie

last: Brewington

first: Jamila

last: Moore

first: Josi

last: Lott

first: Yonghui

last: Ni

first: Dennis

last: Voronin

first: Oliver

last: Grant-Chapman

first: Tresor

last: Mukiza

first: Tristen

last: Wright

first: Sandi

last: Radko-Juettner

first: Shondra

last: Pruett-Miller

first: Stanley

last: Pounds

last: Vogel

first: Joseph

middle: T

last: Opferman


title: Independent cell type-specific expression and distal regulation of the 9p21 locus cell cycle regulators: p14ARF, p16INK4A, p15INK4A, and ANRIL

city: Cambridge

first: Neva

middle: Cherniavsky

last: Durand

state: MA

address: 75 Ames St

institute: Broad Institute

type: Genome binding/occupancy profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: Chimeric AGO2-miR-eCLIP analysis of LIMD1 deficient (CRISPR-Cas9 edited) human SAEC cells

city: London

first: Eleni

last: Maniati

address: John Vane Science Centre, Charterhouse Square

department: Barts Cancer Institute

country: United Kingdom

institute: Queen Mary University of London

summary: To assess AGO2:miRNA:target interactions under LIMD1 deficiency, we performed chimeric AGO2-miR-eCLIP on CRISPR-edited hSAECs. This technique ligates miRNAs to their AGO2-bound targets, capturing endogenous AGO2:miRNA:target complexes. After successful IP with anti-AGO2 antibody, post-processing mapped reads were identified as AGO2-miRNA, AGO2-mRNA, or chimeric peaks.

overall_design: We have performed CRISPR-Cas9 editing on wild type human SAEC cells to generate three groups of cell lines: Cas9 (control: LIMD1+/+), LIMD1-/- and LIMD1+/-. AGO2 chimeric miR-eCLIP was performed on three CRISPR-biological replicates per group, with two  replicates performed on one clone per grooup. This n=4 experiment enabled the profile of miRNAs, mRNAs, and miRNA:mRNA chimeras (pairs) bound to AGO2, with the ultimate aim of identifying differences between the  3 sample groups.

first: Alex

middle: F

last: Crozier

first: Kunal

last: Shah

first: Anisha

last: Thind

first: Jun

last: Wang

first: Tyson

middle: V

last: Sharp


title: Tedja et al: Transcriptional regulation of Candida auris morphogenesis [exp 3]

city: Clayton

first: Traude

last: Beilharz

state: VIC

address: Wellington Rd

department: Biomedicine Discovery Institute

country: Australia

institute: Monash University

summary: Experiment 3: This experiment concerns the comparison of wild-type and 3 transcription factor mutants and their impacts on gene expression on glucose and lactate media.

overall_design: RNA-seq comparing wild type and 3 transcription factor mutants; brg1, irf1 and ume6

first: Ana

last: Traven

first: Irma

last: Tedja

first: Harshini

last: Weerasinghe

first: Calvin

last: Kraupner-Taylor

first: Paul

last: Harrison


title: Tedja et al: Transcriptional regulation of Candida auris morphogenesis [exp 2]

summary: Experiment 2: This experiment concerns the comparison of smooth and wrinkled versus clinical isolates of Candida auris. RNA-seq experiments were performed to correlate differential gene expression in non-fermentable carbon sources to pathogenic traits.

overall_design: RNA-seq comparing transcriptional responses of Candida. auris Smooth and Rough 4070140 an other clinical isolates (470121k, B8441, B11205) grown in various conditions.


title: DNA methylation and transcriptomic profiles of Wilms tumour reveal new deregulated genes and epigenetic processes relevant for tumour stratification and management

city: Caserta

first: Abu

last: Saadat

state: Caserta

address: Via Vivaldi, 43

department: Department of Environmental, Biological and Pharmaceutical Sciences and Technologies

country: Italy

institute: Università degli Studi della Campania Luigi Vanvitelli

summary: Wilms tumour (WT), the most common kidney cancer in children, presents features of altered kidney development and frequently exhibits molecular alterations at the 11p15.5 imprinted locus, affecting the IGF2 and H19 genes, which contribute to tumour growth and may also act as predisposing events that require additional hits for tumour initiation. The epigenetic landscape beyond 11p15.5 suggests diagnostic and prognostic potential, but its link to transcriptomic changes is largely unexplored. We integrated methylomic and transcriptomic datasets of 27 primary tumours and matched non-neoplastic kidneys. DNA methylation profiling identified around 9,000 differentially methylated CpG sites distinguishing neoplastic from non-neoplastic tissue and other pediatric cancers, thus representing a novel WT-specific epigenetic signature. We found that cases with Imprinting Centre 1 (IC1) gain of methylation exhibited the most extensive epigenetic alterations, LOH tumours showed intermediate changes, whereas regressive tumours with largely normal 11p15.5 status displayed limited methylation abnormalities. Three methylation clusters corresponding to transcriptomic subtypes were identified, characterised by distinct tumour microenvironment and chemosensitivity predictions: a regressive-enriched group with high immune infiltration and predicted susceptibility to paclitaxel, a proliferative group with high tumour purity and predicted sensitivity to doxorubicin, and a stromal-like group with intermediate predicted sensitivity to both drugs. Combined analysis of methylation and expression data revealed more than 900 genes under epigenetic control, which contributed to defining the WT subtypes. Analysis of the IGF2/H19 locus uncovered multiple regulatory mechanisms underlying IGF2 activation, including imprinting defects at IC1, methylation changes at DMR0, differential promoter usage, and transcriptional modulation by PLAG1 and BAHD1. These findings define the epigenetic architecture of WT, encompassing genome-wide methylation changes, subtype-specific patterns, and their integration with gene expression, supporting stratification of cases for improved prognosis and therapeutic approaches.

overall_design: Wilms tumor (WT) and adjacent non-neoplastic kidney (NNK) tissues were collected and subjected to multi-omics profiling. Genome-wide DNA methylation was assessed using the Illumina Infinium MethylationEPIC BeadChip array (54 samples), and total RNA sequencing was performed using the Ovation SoLo RNA-seq library kit and sequenced in paired-end 150 bp mode on NovaSeq 6000 (45 samples). Raw data were processed using standard pipelines in R for normalization, quality control, and differential analysis.

first: Francesco

last: Cecere

first: Federica

last: Rossetti

first: Laura

last: Pignata

first: Emilia

last: D’Angelo

first: Carlo

last: Giaccari

first: Gaetano

last: Verde

first: Paola

last: Quarello

first: Franca

last: Fagioli

first: Josep

last: Roma

first: Manel

last: Esteller

first: Enrique

last: De Álava

first: Flavia

last: Cerrato

first: Andrea

last: Riccio

first: Angela

last: Sparago


title: Benzalkonium Chloride-Induced Nephrotoxicity in 2D Cultures and a Human Kidney-on-a-Chip System

city: Seattle

first: James

middle: William

last: MacDonald

state: WA

address: 4225 Roosevelt Way NE

department: Environmental and Occupational Health Sciences

institute: University of Washington

summary: Benzalkonium chlorides (BACs) are quaternary ammonium compounds widely used in various consumer products and industries due to their broad spectrum anti-antimicrobial properties. Their mechanism of action is proposed through the perturbation and disruption of a lipid membrane with its amphiphilic structure, in which BACs consist of a positively charged nitrogen head group and long aliphatic tail consisting of various lengths (Merchel Piovesan Pereira & Tagkopoulos, 2019). Because of this mechanism, they are used as active ingredients in disinfectant and cleaning solutions (sprays, wipes and hand sanitizers), medical products (eye drops and nasal sprays), cosmetic and hygiene products, and used as sanitization tools in the agricultural and food processing industries (Merchel Piovesan Pereira & Tagkopoulos, 2019). Detectable levels of BACs on various food products (The Federal Institute for Risk Assessment (BfR) of Germany, 2012) as well as topical exposure to BACs through disinfectant application to various surfaces and mediums can lead to chronic and systemic exposure to humans. Major routes of exposure include ingestion, inhalation and dermal/ocular/nasal contact (US EPA, 2006). The COVID-19 pandemic has led to a dramatic increase in the usage of cleaning and disinfectant solutions in businesses and households, increasing the amount of indoor exposure to these compounds (Zheng et al., 2020).

overall_design: RNA-Seq of kidney primary tubule epithelial cell (PTEC) cells that were grown in flat tissue culture flasks (2D culture) and in ‘organ-on-a-chip’ microphysiological systems (3D MPS culture), treated with BACs at various concentrations as well as a vehicle control.

first: Marie

middle: N

last: Brzoska

first: Ryan

middle: P

last: Seguin

first: Jade

last: Yang

first: Vanessa

last: Lopez

first: Sydney

last: Arnzen

first: Edward

middle: J

last: Kelly

first: Libin

last: Xu


title: Multi-omic analysis reveals distinct endothelial gene expression profiles induced by pathological flow

city: Newcastle upon Tyne

first: Graham

last: Smith

address: Framlington Place

department: Bioinformatics Support Unit

institute: Newcastle University

type: Non-coding RNA profiling by high throughput sequencing


title: Bulk mRNA-seq analysis of LIMD1 deficient (CRISPR-Cas9 edited) human SAEC cells.

first: Eleni

last: Maniati

summary: To understand mRNA abundance changes in LIMD1 deficient human SAEC cells, we performed bulk mRNA-seq on Ctrl, LIMD1 Het, and LIMD1 KO (CRISPR-Cas9 edited) hSAECs.

overall_design: We have performed CRISPR-Cas9 editing on wild type human SAEC cells to generate 3 groups of cell lines: Cas9 (control: LIMD1+/+), LIMD1-/- and LIMD1+/-. Bulk mRNA-seq was performed on n=3 CRISPR-biological replicates per group, with the ultimate aim of identifying differences in mRNA abundancies between the 3 sample groups.

first: Alex

last: Crozier

first: Kunal

last: Shah

first: Anisha

last: Thind

first: Jun

last: Wang

first: Tyson

last: Sharp


title: Multi-omic analysis reveals distinct endothelial gene expression profiles induced by pathological flow [RNA-Seq]

summary: Aims -Coronary artery disease (CAD) remains a leading cause of mortality globally. Atherosclerosis develops at arterial sites exposed to disturbed, low, or oscillatory shear stress, while acute coronary syndromes-triggered by plaque rupture or erosion predominantly occurs in regions subjected to elevated shear stress. While the response of endothelial cells to disturbed flow has received significant attention, the response to elevated flow is less well studied.  Methods and Results - To address this shortfall, we conducted a comprehensive multi-omic analysis of primary human coronary artery endothelial cells (HCAECs) cultured for 72 hours under oscillatory shear stress (OSS), physiological laminar shear stress (LSS), and elevated shear stress (ESS). This identified 2,175 shear-regulated genes, with 1,218 uniquely responsive to OSS and 665 to ESS. Both OSS and ESS induced significant changes in RNA isoform selection, affecting 580 and 848 genes respectively. Signalling pathways regulating CAD pathogenesis including HIPPO, TGFβ/BMP, and IRF, showed altered RNA isoform selection which may influence plaque development and plaque erosion. 65% of LD-filtered CAD-associated genetic variants from two recent multi-population meta-analyses contained at least one OSS or ESS-regulated gene within 250Kb. Proteomic analysis identified 289 proteins differentially expressed under OSS and 171 under ESS, with notable discordance between mRNA and protein changes observed in 28.7% (OSS vs LSS) and 16.6% (ESS vs LSS) genes. Additionally, 40 shear-responsive microRNAs were identified, potentially contributing to 71% of this discordance. Conclusion- Both oscillatory and elevated flow trigger distinct HCAEC gene expression programmes, affecting mRNA, microRNA, splicing, and protein expression, and modulating pathways central to CAD pathogenesis.

overall_design: Confluent monolayers of three independent batches of male HCAECs were exposed to oscillatory ±0.5Pa 1Hz (OSS), normal physiological laminar shear stress (1.5Pa LSS) and elevated laminar shear stress (7.5Pa ESS) for 72 hours using our established parallel plate flow chambers. In brief, low passage HCAECs were seeded at high density onto gelatin-coated slides and cultured for 72 hours to ensure confluence and allow stable cell-cell junctions to form and extracellular matrix deposition to occur. Subsequently these HCAECs were cultured under flow for 72 hours before lysis for either RNA or protein purification. The ability to run >25  flow chambers at a time allowed the samples for all analyses for each individual donor to be prepared in a single experiment, allowing direct comparison across the different omic analyses for each HCAEC donor.

first: Stephen

last: White

middle: R

first: Giulio

last: Vidotto

first: Robert

last: Beal

first: Sara

last: Luzzi

first: Jon

last: Humphries

first: Martin


title: Spatial tumour-immune ecosystems shape the efficacy of anti-PD1 immunotherapy in primary cutaneous melanoma [RNAseq]

city: LYON

first: Julie

last: CARAMEL

address: 28 Rue Laennec

country: France

institute: Cancer Research Center of Lyon

summary: Intra-tumoral heterogeneity in melanoma arises from dynamic cancer cell plasticity and underlies various mechanisms of immune escape. Here, we combined high-plex immunofluorescence imaging with spatially resolved transcriptomics to map the architecture of melanoma cell states and their interactions with the immune microenvironment in primary cutaneous tumours prior to adjuvant anti-PD1 immune checkpoint inhibitor (ICI) treatment. Computational analyses showed that melanoma cells organise into spatially restricted patches, with a preferential organisation of undifferentiated cells associated with poor ICI efficacy. Neighbouring immune cell composition varied according to cancer cell states, with a crucial involvement of specific subsets of tumour-associated macrophages, driven by signalling pathways involving tumour-derived and microenvironmental cues such as IFN-γ and hypoxia. Integrated spatial analyses further revealed tumour-immune ecosystems that stratify patient outcomes, delineating configurations either associated with ICI efficacy or metastatic relapse. These results uncover the spatial landscape of tumour ecosystems and identify signalling pathways as potential targets for improving the efficacy of ICI in melanoma.

overall_design: to study the resistance to immunotherapy anti PD1, we perfomed bulk RNAseq sequencing of 57 pre treatment samples of patients with stage III melanoma, as well as snRNA sequencinf of 2 metastases and visium sequencing for 4 primary tumors..

first: Félix

last: Pham

first: Marion

last: Dufeu

first: Valentin

last: Benboubker

first: Maxime

last: Grimont

first: Amélie

last: Lhorisson

first: Justine

last: Berthet

first: Marie

last: Donzel

first: Raphael

last: Schneider

first: Laurie

last: Tonon

first: Anne-Claire

last: Doffin

last: Boivin

first: Simon

last: Durand

first: Bertrand

last: Dubois

first: Jonathan

first: Christophe

last: Caux

first: Jenny

last: Valladeau-Guilemond

first: Anaïs

last: Eberhardt

first: Stéphane

last: Dalle

last: Caramel


title: Organoid modeling of lung branching morphogenesis and epithelial lineage specification [RNA-Seq]

city: Guangzhou

first: Ruifang

last: Zhang

state: Guangdong

address: Haizhu District

institute: Guangzhou Laboratory

summary: In this study, multi-level branching lung organoids (BLOs) were generated from primary tip epithelial cells. Single-cell RNA sequencing demonstrated that BLOs comprise proximal airway and distal alveolar epithelial cell populations, faithfully modeling the developmental trajectory of distal lung epithelial lineages in vitro.

overall_design: We generated multi-level branching lung organoids (BLOs) from primary tip epithelial cells and analyzed their transcriptional profiles using RNA sequencing (RNA-seq).


title: AP-1 mediated lineage memory shapes viral resistance barriers in human skin

city: Philadelphia

first: Arjun

last: Raj

state: PA

address: 415/420 Clinical Research Building (CRB)

institute: University of Pennsylvania

summary: Individual cells exhibit striking variability in viral susceptibility, but it remains unknown whether this heterogeneity reflects memories encoded into the cellular lineage or true probabilistic variability. We used multi-color lineage tracing in a human primary organotypic skin model to reveal that viral resistance is encoded within specific cellular lineages. These lineages create distinct boundaries that block viral spread. Our lineage analyses in vitro confirmed that viral susceptibility exhibits strong heritability across cell generations, with siblings and cousins displaying remarkably similar infection outcomes. ATAC and proteomics profiling of resistant and susceptible clones revealed distinct epigenomic and proteomic states, with the transcription factor AP-1 emerging as a central regulator of lineage-encoded viral resistance. Inducing AP-1 activity rendered cells resistant to viral infection, further confirming its role in mediating resistance memory. Our findings demonstrate that antiviral resistance in human skin cells is encoded within cellular lineages and preserved through cell divisions, revealing how cell memory may shape infection dynamics and viral containment in tissues.

overall_design: ATAC-seq profiling of resistant and nonresistant HDFn clones, untreated, uninfected.

first: Laura

middle: C

last: Van Eyndhoven

first: Grant

last: Kinsler

first: Aoife

last: O'Farrell

first: Jingchao

first: Rim

last: Abderrahim

first: Apurv

last: Srivastav

first: Catherine

middle: G

last: Triandafillou

first: Todd

last: Greco

first: Kenneth

middle: S

last: Zaret

first: Ileana

last: Cristea

first: Megan

middle: H

last: Orzalli

first: Nir

last: Drayman

first: Abhyudai

last: Singh


title: Characterizing circulating pharmacodynamic biomarkers of IFNβ-1a biologics [inter]

city: Silver Spring

first: Lakshmi Manasa

middle: Sakuntala

last: Chekka

state: Maryland

address: 10903 New Hampshire Avenue

department: DARS, CDER

institute: U.S. FDA

summary: The current project is designed to evaluate the utility of proteomics in identifying pharmacodynamic (PD) biomarkers for biosimilarity assessment. This is an extension of the data submitted in GSE207945 which profiled longitudinal plasma samples from healthy subjects treated with single therapeutic doses/high doses of IFNβ-1a (30 μg) or Pegylated IFNβ-1a (125 μg) or placebo, to identify candidate PD biomarkers for the two biologics (n=248 for IFNβ-1a and N=528 for pegIFNβ-1a). The current project is a continuation study profiling longitudinal plasma samples from healthy subjects treated with an intermediate/lower dose of IFNβ-1a (15 μg) and pegIFNβ-1a (62.5 μg).  Here, we reproduced the previous PD biomarker candidate responses at a lower dose, and further characterized their PD response using characteristics such as significant area under the effect curve, dose-response, temporal profile and return to baseline, variability and sensitivity of the biomarker with sensitive doses on the steep portion of the dose-response curve and mechanism of action using all three tested dose groups (high, intermediate and low).

overall_design: The study includes data on >580 proteins from 12 subjects treated with IFNβ-1a (15 µg), 12 with pegIFNβ-1a (62.5 µg). The 12 subjects on IFNβ-1a were tested at 10 timepoints over 6 days, and the rest were tested at 12 time points over 13 days. Replicates for 3 random samples were included on the array along with two covid covalacent plasma samples.

first: Lakshmi

last: Manasa Sakuntala Chekka

first: Paula

last: Hyland


title: Exploiting Androgen Receptor Cell Cycle Effects to Enhance CDK4/6 Inhibitor Efficacy in Estrogen Receptor Positive Metastatic Breast Cancer

city: Barcelona

first: Alba

last: Mas Malavila

address: Saturnino Calleja 11-13

country: Spain

institute: VHIO

summary: The androgen receptor (AR) is expressed in 75% of estrogen receptor-positive (ER+) breast cancers (BC). Selective AR modulators (SARMs), like EP0062, present a promising therapeutic strategy for ER+ BC, particularly in patients who cannot tolerate endocrine therapy (ET) or whose tumors have developed resistance. We aimed to study the antitumor activity of EP0062 in ER+ patient-derived xenograft (PDX) models. EP0062 displayed comparable antitumor efficacy as selective ER degraders (SERDs), including in PDXs with ESR1, PIK3CA, or PTEN mutations. Tumors sensitive to both SARM and SERDs were enriched in GATA3 mutations. EP0062 treatment induced AR-target genes across all models tested. A 122-gene signature of SARM sensitivity associated with good prognosis in patients with ER+ BC was developed. Mechanistically, EP0062 downmodulated S-phase cell cycle proteins in sensitive models. In EP0062-resistant, ER-driven tumors, the addition of palbociclib restored drug sensitivity thus providing a promising strategy for metastatic patients with acquired ET resistance.

overall_design: We leveraged bulk RNA sequencing to examine the transcriptomic profiles of resistant and sensitive tumors either to the SARM EP0062, the SERD camizestrant or the CDK4/6-inhibitor palbociclib untreated and treated, in order to identify the mechanism of action of SARMs.

first: Laia

last: Monserrat

first: Violeta

last: Serra

first: Lara

last: Nonell

last: Mas


title: Spatial tumour-immune ecosystems shape the efficacy of anti-PD1 immunotherapy in primary cutaneous melanoma [Spatial Transcriptomics]

first: Julie

last: CARAMEL

first: Pham

last: Félix

first: Dufeu

last: Marion

first: Benboubker

last: Valentin

first: Grimont

last: Maxime

first: Lhorisson

last: Amélie

first: Berthet

last: Justine

first: Donzel

last: Marie

first: Schneider

last: Raphael

first: Tonon

last: Laurie

first: Doffin

last: Anne-Claire

first: Boivin

first: Durand

last: Simon

first: Dubois

last: Bertrand

first: Lopez

last: Jonathan

first: Caux

last: Christophe

first: Valladeau-Guilemond

last: Jenny

first: Eberhardt

last: Anaïs

first: Dalle

last: Stéphane

first: Caramel

last: Julie


title: Methionine-supplemented Longevity diet increases GLP-1 and FGF21 to reduce frailty and promote healthspan

city: Los Angeles

first: Valentina

last: Villani

state: CA

address: 4661 Sunset blvd

department: Urology

institute: Children's Hospital Los angeles

summary: Southern European countries have some of the highest life expectancies in the world, yet they display high frailty. Here, we examined different diets to identify compositions that promote both healthspan and strength. In genetically diverse mice, the western and ketogenic diets increased fat mass, insulin resistance, and cholesterol levels. In contrast, a low-protein pescatarian Longevity Diet (LD), combining traditional Mediterranean and Okinawan features with moderate methionine supplementation (LDMM) or a fasting-mimicking diet (FMD), reduced fat mass and frailty while improving cardiometabolic markers. The normocaloric LDMM reduced IGF-1 while increasing growth hormone, GLP-1, and FGF21, which was crucial for diet-induced fat loss and improved insulin sensitivity. These findings indicate that high methionine intake may partially explain the major increase in overweight and diabetes in epidemiological studies of subjects who maintain a healthy lifestyle but consume a high animal protein diet, but not in those consuming a high plant protein diet.

overall_design: Bulk RNAseq profiling of liver samples from 25 months old female HET3 mice fed a Longevity diet (LD) after 5 months of dietary intervention compared to a control standard diet (SD).

first: Maura

last: Fanti

first: Laura

last: Perin

first: Valter

last: Longo


title: In vivo double knockout CAR-T screen identifies synergistic gene pairs that enhance anti-tumor immunity

city: West Haven

first: Sidi

last: Chen

state: CT

address: 850 West Campus Drive

department: Genetics

institute: Yale University School of Medicine

summary: Chimeric antigen receptor (CAR) T cell therapy has revolutionized the treatment of hematological malignancies. However, its efficacy is hindered by multifaceted negative regulatory mechanisms intrinsic to T cells. Here we perform a large-scale high-throughput in vivo double-knockout (DKO) CRISPR screen in human CAR-T cells, and identify multiple DKO gene pairs that are both effective and synergistic. The top pair NR4A1_SOCS3 DKO has multiple favorable immunological features. Whole-transcriptome profiling and in vivo single cell RNA sequencing reveal that NR4A1_SOCS3 DKO specifically upregulated metabolic pathways in CAR-T cells, which was demonstrated to have significant higher metabolic fitness and mitochondria activities. NR4A1_SOCS3 DKO CAR-T or T cells exhibit exceptionally potent anti-tumor efficacy long-term tumor control across different tumor models, without compromising safety features. NR4A1_SOCS3 DKO outperforms other T/CAR-T cell genetic modifications such as REGNASE1 KO, MED12 KO, RASA2 KO, TRAF6 KO and PD1_CTLA4 DKO. These data demonstrate high-throughput DKO screening for rapid discovery of combination targets, and establish NR4A1_SOCS3 as promising joint intracellular checkpoints to engineer high-performance CAR-T therapies against cancer.

overall_design: Cut&Run profiling of NR4A1 binding sites in the genome of CAR-T cells, comparing SOCS3 KO and GTC (gene targeting control) group.

first: Liqun

last: Zhou

first: Kaiyuan

last: Tang

first: Paul

last: Renauer


title: Effect of Tyrphostin-AG4178 on ex-vivo mouse ovarian follicles in eIVFG ovulation system

city: Hanover

first: Hannah

last: VanBenschoten

state: NH

address: 15 Thayer Dr

department: Thayer School of Engineering

institute: Dartmouth College

summary: Ovulation is a coordinated, multicellular process carried out in the antral follicle involving gonadotropin-stimulus, cumulos-oocyte complex expansion, follicle rupture, followed by luteinization. Ovulation can be prevented by targeted inhibition of upstream signalling molecules via tool compounds such as Tyrphostin-AG4178, which binds to EGFR and thus prevents downstream MEK/ERK, prostaglandin, and Pgr signaling. We exposed ex vivo mouse ovarian follicles grown in an encapsulated in-vitro follicle growth (eIVFG) system to Tyrphostin-AG4178 after stimulus with hCG and performed bulk-RNA sequencing on whole follicles to observe the transcriptomic response to targeted ovulation inhibition.

overall_design: Bulk RNA-seq profiling of 16-day-old CD1 mouse antral ovarian follicles exposed to hCG and 10 µM Tyrphostin-AG1478 for 4 hours after 8 days of follicle growth in the eIVFG system.

first: Jiyang

last: Zhang

first: Shuo

last: Xiao

first: Brittany

last: Goods


title: DVE-1 is a telomere-binding protein and links the NuRD complex to telomere regulation in C. elegans

city: Mainz

first: Jan

last: Padeken

address: Ackermannweg 4

country: Germany

institute: Institute of Molecular Biology

summary: Telomeres are repetitive DNA sequences at the end of linear chromosomes bound by specialized proteins. In our previous quantitative proteomics screen for telomere-binding proteins of Caenorhabditis elegans, we identified the homeobox protein DVE-1, a homolog of mammalian SATB proteins and transcription factor that plays a central role in the mitochondrial unfolded protein response, as a telomere repeat binding protein. Here, we validate DVE-1 as a telomere-binding protein in C. elegans, demonstrating in vitro binding of DVE-1 to the single-stranded C-rich telomeric sequence and in vivo co-localization with the known telomere binding protein POT-1 corroborated by ChIPseq analysis. RNA interference-mediated knockdown of DVE-1 resulted in reduced TERRA expression and enhanced compaction of telomeric chromatin. Subsequent transcriptomic and proteomic analyses suggest a role for DVE-1 in the regulation of telomeric chromatin organization. Finally, DVE-1 immunoprecipitation followed by mass spectrometry identified all core components of the nucleosome remodeling and deacetylase (NuRD) complex as interaction partners, implicating DVE-1 in the coordination of NuRD complex activity in the context of telomere organization.

overall_design: ATAC-seq in embryos isolated from C. elegans wild-type (N2 (Bristol)) grown from L1-to day1 of adulthood on RNAi bacteria against dve-1, or empty vector (L4440)

last: Sluka

first: Alexandra

last: Blake

first: Nadezda

last: Podvalnaya

first: Albert

last: Fradera-Sola

first: Sabrina

last: Dietz

first: Lars

last: Teschke

first: Alejandro

last: Ceron-Noriega

first: Rosa

last: Herrera-Rodriguez

first: Valerie

last: Arz

first: René

last: Ketting

first: Emily

last: Nischwitz

first: Falk

last: Butter


title: PLA2G2D in tumour-draining lymph nodes regulates anti-tumour immunity

city: Rotterdam

first: Anneloes

last: van Krimpen

state: Zuid-Holland

address: Doctor Molewaterplein 40

department: Pulmonary Medicine

country: Netherlands

institute: Erasmus MC

summary: Current cancer immunotherapies can induce tumor regression, although responses are often not durable for reasons that are incompletely understood. Apart from activating pre-existing tumor-infiltrating T cells, recent studies have highlighted the importance of enforcing a systemic immune response from tumor-draining lymph nodes (TDLNs). However, mechanisms driving immune suppression in TDLNs remain poorly studied. We applied spatial proteogenomics on melanoma TDLNs and identified striking regional differences in immune cell composition in lymph nodes from patients with long-term (>5 years) disease control compared to those with early (<2 years) disease recurrence. TDLNs from patients with a poor prognosis were characterized by the expansion of a specific cellular interaction network in the lymph node paracortex, consisting of regulatory T cells (Tregs), dendritic cells (DCs) and macrophages interacting with cytotoxic CD8+ T cells. Targeted transcriptomics of cell types within this spatial neighbourhood revealed immunoregulatory myeloid cell phenotypes engaging with CD8+ T cells poised for exhaustion. Macrophages in patients with early disease recurrence resided in a dysfunctional state bearing hallmarks of chronic interferon-signalling – frequently residing near CD8+ T-cell–DC dyads. Besides known immune-suppressive molecules such as IDO and PD-L1, paracortex macrophages and DCs in patients with recurrence expressed high levels of the secreted phospholipase PLA2G2D across different cancer types. In addition, PLA2G2D was upregulated in non-small cell lung cancer patients upon acquired resistance to anti-PD-1 immunotherapy. Importantly, PLA2G2D loss-of-function or therapeutic inhibition markedly improved survival in tumor-bearing mice and increased the efficacy of anti-PD-1 immunotherapy. Collectively, we show that in-depth spatial profiling of cancer patient TDLNs offers novel insights into systemic anti-tumor immunity and identifies PLA2G2D as a target for cancer immunotherapy.

overall_design: Targeted whole-transcriptome sequencing of CD8+, CD11c+ and CD68+ cells within the paracortex of stage III melanoma patients with long-term (>5 years) disease control or early (<2 years) disease recurrence.

first: Ralph

last: Stadhouders

first: Floris

last: Dammeijer

first: Anne

last: Onrust


title: Effects of norepinephrine(NE) and dexamethasone(DEX) exposure on signaling pathways in ciliary body cells

city: Fukuoka

first: Keisuke

last: Ikegami

address: Nishi-ku Motooka 744

institute: Kyushu University

summary: Aqueous humor production by the ciliary body is regulated in part by hormonal cues, including norepinephrine (NE) and dexamethasone (DEX), and its circadian variation is thought to reflect rhythmic changes in these signals. However, the transcriptional programs and molecular pathways through which NE and DEX influence human non-pigmented ciliary epithelial cells remain incompletely defined. In this study, we performed RNA-seq analysis of human non-pigmented ciliary epithelial cells exposed to NE or DEX for 1 or 2 hours, with vehicle-treated cells as controls, to identify stimulus-responsive genes and pathways associated with ciliary body function and aqueous humor production.

overall_design: Human non-pigmented ciliary epithelial cells (HNPCEpiC) were treated with norepinephrine (NE), dexamethasone (DEX), or vehicle control and analyzed by RNA-seq. DEX-treated cells were collected after 1 or 2 hours of exposure, NE-treated cells were collected after 1 hour of exposure, and vehicle-treated control cells were collected at matched time points. Three biological replicates were analyzed for each condition.


title: Crocin I effect on WI-38 cells

city: Hangzhou

first: Yicheng

last: Fu

state: Zhejiang

address: Gudun road

institute: Zhejiang hospital

summary: Analysis of WI-38 cells treated with Crocin I.  Crocin I is a major active component of saffron. Results provide insight into protective effect of  Crocin I against WI-38 cells senescence.

overall_design: Total RNA of WI-38 cells was extracted from young control, old group,  Crocin I group, and analyzed using RNA-seq.

first: Zhiwei

last: Ding

first: Yunchuang

last: Chang

first: Chunxia

last: Wu

first: Sanying

last: Wang

first: Genxiang

last: Mao

first: Huili

last: Su


title: BMAL1 and YAP cooperate to hijack enhancers and promote inflammation in the aged epidermis [ChIP-Seq 1]

first: Camille

last: Stephan Otto Attolini

state: Select a State or Province

address: Baldiri Reixac 10

department: Biostatistics and bioinformatics Unit

institute: IRB Barcelona

summary: Ageing is characterised by persistent low-grade inflammation that is linked to impaired tissue homeostasis and functionality. However, the molecular mechanisms driving age-associated inflammation remain poorly understood. The mammalian skin is a clinically relevant target of age-driven inflammation associated with compromised barrier function, inefficient wound healing, elevated oxidative stress, and DNA damage accumulation. Here, we show that upon ageing a previously uncharacterised BMAL1–YAP transcriptional complex is hijacked from chromatin regions associated with homeostatic genes in adult epidermis and redirected to inflammation-related enhancers, amplifying the transcription of their target genes. Independently of its known role as a core circadian clock component, BMAL1 partners with the mechanosensitive transcriptional cofactor YAP at enhancer regions to regulate epidermal identity genes. In contrast, in aged skin, BMAL1–YAP complexes bind to enhancers of inflammation-related genes, co-regulated by NF-κB. Interestingly, aged pro-inflammatory signals from the IL-17 pathway activate YAP in a Hippo-independent manner. These findings unveil a transcriptional mechanism underlying epidermal ageing, linking chromatin dynamics to inflammatory transcriptional programs through BMAL1–YAP-bound enhancer rewiring. By elucidating how ageing reprograms transcriptional networks, our work highlights potential strategies to counteract chronic inflammation and restore tissue homeostasis across age-related loss of functionality.

overall_design: ChIP-seq of H3K4me3 and H3K27ac of adult (18-25 weeks old) and aged (80-90 weeks old) mouse epidermis at Zeitgeber time 4 (ZT4).

first: Camile

first: Guiomar

last: Solanas

first: Júlia

last: Bonjoch


title: Positional grammar of transcription factor binding partitions developmental and stress-response regulation in plants

city: Berkeley

first: Abraham

last: Morales-Cruz

state: California

address: 1 Cyclotron Road

institute: Joint Genome Institute

summary: Understanding how transcription factor binding site (TFBS) location influences gene regulation remains a fundamental challenge in plants. Here we integrate conserved TFBS with single-nucleus chromatin accessibility and expression datasets to resolve how TFBS location relates to regulatory function. Although TF binding patterns are conserved and frequently enriched near the TSS, positional enrichment of TFBSs poorly predicts cell type-specific gene expression. Instead, cell type-specific gene expression aligns with conserved TFBSs that are embedded in cell type-restricted chromatin, which show TF family-specific distributions across distal promoter and genic regions. In contrast, TSS-proximal TFBSs are implicated in rapid, tissue-wide transcriptional stress responses, as supported by hormone-induced gene expression analysis. Finally, distal upstream regions contain conserved TF clusters that overlap rare cell type-specific accessible chromatin and are highly enriched for genes controlling embryonic and meristem patterning, including auxin and other hormone pathway components. This positional partitioning of regulatory function indicates that TFBS location encodes distinct regulatory programs for TFs.

sample_organism:
Arabidopsis thaliana
Brassica oleracea
Arabidopsis lyrata
Capsella rubella

overall_design: To map chromatin accessibility at cellular resolution, a high-depth single-nucleus ATAC-seq (snATAC-seq) atlas was generated across four Brassicaceae species (Arabidopsis thaliana, Arabidopsis lyrata, Capsella rubella, and Brassica oleracea). Nuclei were isolated from fresh seedling, mature leaf, and floral bud tissues synchronized via staggered planting to align developmental stages. Isolated nuclei were cleaned of chloroplast debris, quantified via flow cytometry, and processed using the 10x Genomics Chromium platform for single-nuclei barcoding and transposition, followed by paired-end sequencing on Illumina NovaSeq architectures to yield high-coverage fragment data. Downstream bioinformatic filtering retained high-quality cells meeting a threshold of 3,000 fragments and a three-fold transcription start site (TSS) enrichment, profiling 74,307 A. thaliana nuclei and over 10,000 nuclei per sister species. These accessibility matrices were integrated with reference single-nucleus RNA-seq datasets using deep generative modeling (scVI) to assign cell type labels, resolving up to 30 distinct cellular identities. MACS3 was then deployed to call accessible chromatin regions (ACRs) within individual cell types, creating a comparative epigenomic framework to evaluate the spatial relationship between conserved transcription factor binding sites and cell type-restricted chromatin.

first: Sharon

last: Greenblum

first: Peng

first: Leo

last: Baumgart

first: Ronan

last: O'Malley


title: ERK1/2 Inhibition Overcomes Resistance to Venetoclax in AML By Inhibiting Drp1 Dependent Mitochondrial Fission

city: Houston

first: Priyanka

last: Sharma

state: Texas

address: 1515 Holcombe Blvd.

department: Department of Leukemia

institute: University of Texas MD Anderson Cancer Center

summary: Acute myeloid leukemia (AML) is a fatal hematological malignancy for most patients, and (MAPK) cascade is activated in 70%-80% of AML patients owing to activating/inactivating mutations in RAS and upstream proteins. Mutations in the RAS pathway are associated with secondary clinical resistance to venetoclax (ABT199) and hypomethylating agents. We found that ERK1/2 inhibition leads to increased mitochondrial length as well as overcomes resistance to venetoclax. To identify the factors that contribute to synergy and overcome resistance, we perfomed transcriptome profiling of AML cells treated with ABT199, ERK1/2 inhibitor or the combination treatment.Transcriptome analysis revealed downregulation of DRP1, a fission GTPase and a direct downstream target of ERK1/2, in response to ERKi +/-ABT199.

overall_design: Transcriptome profiles of OCI-AML3 cells treated with ABT-199 and/or ERKi for 24 h. DMSO was used as control. RNA was isolated using RNAeasy kit with on-column DNA digestion.

first: Gautam

last: Borthakur


title: Matrix-Bound Nanovesicles in Alcohol-Related Liver Disease: Characterization and Therapeutic Application

city: Pittsburgh

first: Shuchang

last: Liu

address: 203 Lothrop Street

institute: University of Pittsburgh

summary:
Background & Aims:
Alcohol-related liver disease (ALD) lacks effective therapies, and understanding extracellular matrix (ECM) remodeling during disease progression may reveal novel therapeutic targets. Matrix-bound nanovesicles (MBVs), embedded within ECM, contain bioactive proteins and microRNAs and promote tissue repair in various injury models. However, MBVs remain unexplored in ALD. In the present study, we not only characterized how alcohol alters hepatic MBV composition, but also evaluated therapeutic effects of exogenous healthy MBVs in alcohol-induced liver injury.
Approach:
Using the NIAAA chronic-plus-binge ethanol model, we first isolated hepatic MBVs and performed LC-MS/MS proteomic analysis with pathway enrichment to define alcohol-induced cargo alterations. We then administered MBVs from healthy porcine urinary bladder matrix to ethanol-exposed mice and assessed therapeutic effects through histopathological evaluation and bulk RNA sequencing.
Results and Conclusions:
Ethanol exposure enriched hepatic MBVs for metabolic stress and detoxification proteins, indicating disease-associated cargo remodeling. Therapeutic administration of healthy MBVs reduced steatosis, lipid peroxidation, and fibrogenic gene expression while normalizing ethanol-induced transcriptional programs related to oxidative stress, inflammation, and metabolism. MBVs acted context-dependently. That is, they promoted mild ECM remodeling in healthy livers while attenuating pathological signaling in injured tissue, suggesting they stabilize hepatocyte homeostasis rather than directly suppressing immunity. These findings establish MBVs as both disease-responsive biomarkers and therapeutic modulators of the hepatic microenvironment in ALD.

overall_design: Four experimental conditions were measured in this study. PF: Control mice, pair-fed (PF), vehicle  treatment. EtOH: Mice fed with Ethanol-containing diet (according to the NIAAA model, chronic and binge drinking), vehicle  treatment. EtOH+MBV: Mice on Ethanol-containing diet (according to the NIAAA model, chronic and binge drinking), treatment with MBVs. PF+MBV: Pair-fed mice, treated with MBVs.

first: Yekatarina

last: Krutshenko

first: Bashar

last: Matour

first: Jiang

last: Li

first: Jia-Jun

first: Lorien

last: Walker

first: Sam

last: Taborski

first: Michael

last: Merchant

first: Silvia

first: George

last: Hussey

first: Stephen

last: Badylak

first: Gavin

last: Arteel

first: Melanie

last: Scott


title: Subclinical cholestasis is a hallmark of gut dysbiosis causing resistance to cancer immunotherapy

city: Villejuif

first: Miguel

last: Araujo-Voces

state: Île-de-France

address: 114 rue Edouard Vaillant

department: Microbiota and mucosal immunity for cancer immunotherapy

institute: Gustave Roussy

summary: Gut dysbiosis compromises cancer immunosurveillance by downregulating ileal mucosal addressin cell adhesion molecule 1 (MAdCAM-1) but the metabolic landscape associated with gut dysbiosis remains elusive. Here, we show that antibiotics (ABX) or ABX-associated Enterocloster species, lead to the loss of secondary cholic acid-derived bile acids, BA (DCA) and the accumulation of tauro-conjugated primary BA (TCDCA, T-abo-MCA) in the plasma of patients and mice. DCA/GDCA (glyco-DCA) compensated dysbiosis bile acid abnormalities and circumvented primary resistance to PD-1 blockade. GDCA curtailed ABX-induced MAdCAM-1 downregulation and seemed to have an impact on anti tumor immunity. The single cell RNA sequencing in a mouse model of MCA205 fibrosarcoma helped us to characterize the effect of GDCA or DCA on anti tumor immunity and showed a decrease in T cell exhaustion in the TME.

overall_design: Mice were treated with broad spectrum ABX during 14 days in drinking water (D-14 to D0). They were injected at D0 with 0.8x10^6 cell of MCA205.  At D2, D4, D6 and D8, they received 2 gavages: the 1st with BA: LCA, DCA, GDCA or corn oil (vehicule) and the 2nd with the bacteria Enterocloster clostridioformis. At D5 and D8, they received anti-PD-1 treatment. They were sacrificed at D11.

first: Marine

last: FIDELLE


title: Oxygenated perfusion enhances hepatocyte function in human iPSC-liver tissue

city: Minato-ku

first: Yoshiki

last: Kuse

address: Shirokanedai 4-6-1

institute: The University of Tokyo

summary: This study aimed to create functional and scalable tissue from hiPSC-derived liver organoids (hiPSC-LOs) by establishing an oxygenation system utilizing a decellularized liver (DL), which retains the parenchymal and vascular extracellular matrix to support cell adhesion and medium perfusion. An oxygenation system for hiPSC-LO-engrafted DLs (hiPSC-LT) was established using perfusion of oxygen-enriched medium containing artificial red blood cells. Perfusion with oxygenated medium containing artificial red blood cells suppressed cell death and promoted hepatic function of hiPSC-LTs by mimicking the physiological oxygen concentration found in the fetal liver. The oxygenation system using DLs and artificial red blood cells effectively supported the generation of transplantable, functional hiPSC-LT.

overall_design: RNA expression profiles of human iPSC-liver tissue

first: Kiyoshi

last: Yamaguchi


title: Characterize transcriptomic changes in the PFC and hippocampus from wild-type and PTENδ-/- mice

city: Beijing

first: Zhenyu

last: Zhu

state: Beijing

address: 38 Xueyuan Road, Haidian

institute: Peking University

summary: Knockout PTENδ in mice leads to autism-like behavior pattern with increased compulsive behaviors and lack of social novelty. To further understand the in vivo function of PTENδ, we next performed RNA sequencing to characterize transcriptomic changes in the PFC from PTENδ-/- mice.

overall_design: PFC and hippocampus from 8-week-old wild-type and PTENδ-/- mice were harvested for RNA-seq analysis.


title: Aortic valve stenosis serum IGFBP2 mediates female-specific Evogliptin resistance in valve myofibroblasts

city: La Jolla

first: Brian

middle: A

last: Aguado

address: 2880 Torrey Pines Scenic Dr

institute: University of California San Diego

summary: Aortic valve stenosis (AVS) is a sexually dimorphic cardiovascular disease characterized by fibro-calcification of the aortic valve leaflet. Sex differences in AVS arise in part from sexually dimorphic serum composition that differentially regulates valvular interstitial cell (VIC) myofibroblast activation. However, how individual serum factors contribute to sex-specific drug responses remains unknown. Here, we integrate serum proteomic profiling with in vitro drug screening using hydrogel biomaterials to identify sex-specific regulators of antifibrotic drug efficacy. We found that serum Insulin-like Growth Factor Binding Protein 2 (IGFBP2) mediates Evogliptin resistance in female VICs cultured with female AVS serum through the activation of Rho/ROCK and focal adhesion kinase signaling. Our findings highlight IGFBP2 as a candidate biomarker for stratifying female AVS patients for Evogliptin treatment, underscoring the need to incorporate sex as a biological variable in determining AVS treatments.

overall_design: Female porcine valvular interstitial cells were cultured on stiff hydrogels for two days

first: Brandon

last: Vogt

first: Rayyan

last: Gorashi


title: Gene Expression Profiling of Recipient Immune Cells Induced by 7 × 19 CAR-T Cell Dosing in a Syngeneic Mouse Model

city: FUJISAWA

first: Yuumi

last: Okuzono

state: KANAGAWA

address: 26-Muraoka-higashi 2-chome

institute: Takeda Pharmaceutical Company Limited

summary: Chimeric antigen receptor (CAR)-T cell therapy is effective for hematologic malignancies; however, the response of solid tumors is limited because of the immunosuppressive tumor microenvironment, antigen heterogeneity, and lack of persistence of transferred T cells. To overcome these challenges, CAR-T cells expressing interleukin-7 and chemokine (C-C motif) ligand 19 (7 × 19 CAR-T) were generated to achieve potent antitumor efficacy through the recruitment and proliferation of CAR-T cells and endogenous immune cells. To elucidate the underlying mechanism of 7 × 19 CAR-T cells against solid tumors, we analyzed the cellular composition and gene expression profiles of host immune cells following CAR-T cell infusion in a murine solid tumor model.  Antihuman CD20 7 × 19 CAR-T cells were prepared using Thy 1.1 congenic mice and administered to C57BL/6N mice bearing subcutaneous MC38 tumors expressing human CD20. The tumors were harvested 4 days postinfusion to capture early immune responses before overt tumor regression. CD90.1- recipient immune cells were subjected to flow cytometry analysis, and transcriptomics changes were determined using AmpliSeq and single-cell RNA seq.  An increase in recipient CD8+ T cells and macrophages was observed in the tumor of mice treated with 7 × 19 CAR-T cells, but not with conventional CAR-T. The expression of chemokines and genes associated with the inflammatory pathway was upregulated only in recipient immune cells of the 7 × 19 CAR-T-treated mice. Single-cell RNA-seq analysis revealed upregulation of pro-inflammatory genes and chemokines in the dendritic cell and monocyte/macrophage populations. These results indicate that 7 × 19 CAR-T cells initiate the early recruitment and activation of host immune cells, which contributes to their superior antitumor activity compared with conventional CAR-T cells.

overall_design: Single-cell suspensions of tumor-infiltrated lymphocytes were prepared. CD45+ cells were enriched using the CD45 EasySep positive selection kit (STEMCELL Technologies, Vancouver, Canada), followed by depletion of CD90.1+ cells. Total RNA was extracted from the remaining recipient immune cells, complementary DNA libraries were prepared using the AmpliSeq Mouse Gene Expression Kit (Thermo Fisher Scientific), and sequencing was done using the Ion S5 Sequencer (Thermo Fisher Scientific).

first: Yo

last: Muraki

first: Rina

last: Kurisu

first: Akiko

last: Abiru

first: Yukimi

last: Sakoda

first: Koji

last: Tamada

first: Chihiro

last: Akimoto


title: Spalt-related is a catabolic switch activated by prolonged starvation

city: Helsinki

first: Ville

last: Hietakangas

address: Viikinkaari 9

country: Finland

institute: University of Helsinki

summary: Nutrient intake is tightly linked to animal energy metabolism and growth. Inhibition of anabolic processes during nutrient deprivation is a critical stress response necessary for survival. However, how transient vs. prolonged nutrient deprivation is sensed by the key metabolic organs and which downstream pathways mediate metabolic regulation under these conditions remain insufficiently understood. Here we uncover an unexpected role for the transcription factor Spalt-related (Salr), a known to be involved in wing morphogenesis, as a regulator of growth and metabolism upon nutrient starvation. Specifically, we observed that Salr is necessary and sufficient to inhibit cellular and organismal growth as well as lipid storage in the Drosophila fat body. Our results indicate that Salr inhibits anabolic processes through the regulation of mTOR complex 1 activity as well as by directly controlling genes involved in lipid catabolism and autophagy. We discovered that Salr and FoxO, a known downstream target of insulin signalling, act on overlapping set of target genes, but are regulated in a sequential manner. While FoxO is activated transiently upon starvation, Salr displays delayed activation kinetics. In conclusion, our results reveal a novel starvation-activated catabolic switch in the fat body, which is closely interconnected with the insulin/mTOR pathway.

overall_design: Here we aim to discover the tissue specific effect of Salr by overexpressing or knocking down Salr in the fat body and comparing them with their respective controls

first: Onur

last: Deniz

first: Krista

last: Kokki


title: Viral-based individualized neoantigen vaccine as adjuvant treatment in resected head and neck squamous cell carcinoma: immunogenicity and efficacy from a randomized Phase I trial

city: PARIS

first: Anne-laure

last: Le gac

address: 26 rue d'ulm

institute: Institut Curie

summary: TG4050 is a personalized vaccine targeting point mutations of the tumors.. This study allows the characterization of transcriptome and vdj rearrangements of tumor antigen specific CD8+ T cells elicited by personalized vaccines.

overall_design: 5 patients were trated with their personalized vaccines. Blood withdrawal was 64 days after the onset of vaccination. T cells specific for vaccine epitopes were identified using barcoded tetramers. All the cells were mixed in 1 reaction

first: C

last: Ottensmeier

first: J-P

last: Delord

first: A

last: I. Lalanne

last: Jamet

first: A-l

last: Le Gac

first: K

last: Bidet Huang

first: O

last: Lantz

last: Le Tourneau


title: Single-cell transcriptomic and TCR profiling of long-term persisting CD19 CAR-T cells from patient peripheral blood

city: Philadelphia

first: Zhixuan

last: Zheng

state: Pennsylvania

address: 4258 chestnut st.

institute: Perelman School of Medicine at the University of Pennsylvania

summary: This study profiles patient peripheral blood mononuclear cells (PBMCs) enriched for CAR-T cells using the 10x Genomics Chromium Single Cell 5′ platform. Two PBMC samples — peak patient #21 and year 9.3 patient #21 — were analyzed. Both gene expression (GEX) and T cell receptor (TCR V(D)J) libraries were prepared and sequenced on the Illumina NextSeq 2000 system. Processed data include filtered count matrices and clonotype annotation tables for downstream reanalysis.

overall_design:
Frozen PBMCs were thawed, FACS-sorted for live CAR⁺ T cells, and processed using the 10x Genomics Chromium GEM-X 5′ kit v3. Gene expression and TCR V(D)J libraries were prepared according to manufacturer instructions and sequenced on the Illumina NextSeq 2000. Raw reads were processed with Cell Ranger v8.0.1 using the GRCh38 reference genome supplemented with the CAR transgene. Downstream analyses were performed with Seurat v5.2.1, scRepertoire v2.5.1, Harmony v1.2.3, and clusterProfiler v4.16.0.

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

first: Paruzzo

last: Luca

first: Zheng

last: Zhixuan

first: Ruella

last: Marco


title: Exercise intensity differentially modulates systemic molecular responses and predicted interorgan communication in humans

city: New York

first: Douglas

last: Barrows

state: NY

address: 1230 York Ave

institute: Rockefeller University

summary: Exercise is recognized as a first-line lifestyle therapy for many cardiometabolic diseases, including obesity, type 2 diabetes, and hypertension. Despite the abundant health-promoting effects of exercise, in-depth characterization of circulatory factors mediating these benefits remain understudied in humans. Moreover, how different modes of exercise uniquely regulate these processes is unclear. Here, we address these questions by conducting a multi-cohort human exercise intervention, incorporating sprint-interval exercise (SIE), moderate-intensity exercise (MIE), and treadmill exercise to exhaustion to analyze intensity-dependent regulation of adipocytes and bulk adipose tissue. We find that exercise intensity uniquely influences the plasma proteome and plasma metabolome, and culturing primary human adipocytes with these plasma samples results in robust intensity-dependent transcriptome changes. We confirm many of these genes are similarly regulated by intense exercise in vivo, via RNA-sequencing of bulk adipose tissue following treadmill exercise to exhaustion. These findings underscore intensity-dependent regulation of adipose tissue following exercise.

overall_design: RNA-seq profiling of primary human subcutaneous adipocytes and of bulk human subcutaneous adipose tissue before and after either exercise or treatment with "exercised" plasma.

first: Luke

last: Olsen

first: Paul

last: Cohen


title: Transcriptomic profiling of unsorted day-17 iPSC-derived megakaryocytic differentiation cultures carrying SLFN14 p.Q93W

status: Public on Jun 22 2026

city: Changsha

first: Feifeng

last: Wu

state: Hunan

address: No.139, FuRong Road(Middle)

institute: The Second Xiangya Hospital of Central South University

summary: This study investigated transcriptomic alterations associated with impaired megakaryocytic maturation in a patient-derived induced pluripotent stem cell (iPSC) model of SLFN14-related thrombocytopenia. Bulk RNA-seq was performed on iPSC-derived megakaryocytic cells from a control iPSC line and an SLFN14 p.Q93W carrier-derived iPSC line.

overall_design: Two bulk RNA-seq libraries were generated from day-17 iPSC-derived megakaryocytic differentiation cultures: one SLFN14 p.Q93W heterozygous sample (A11) and one control sample. Gene-level read counts were generated for all detected genes and used to explore transcriptional alterations associated with defective megakaryocytic maturation.

first: Chuan

last: Wen


title: Organoid modeling of lung branching morphogenesis and epithelial lineage specification

city: Guangzhou

first: Ruifang

last: Zhang

state: Guangdong

address: Haizhu District

institute: Guangzhou Laboratory

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

overall_design: Refer to individual Series


title: Transcriptional regulation of Candida auris morphogenesis

city: Clayton

first: Traude

last: Beilharz

state: VIC

address: Wellington Rd

institute: Monash University

summary: Experiment 1: This experiment aimed to transcriptionally characterise two phenotypically different colony morphologies (smooth and wrinkled ) from the C. auris 470140 strain. The smooth colonies are phenotypically round and in yeast yeast from, whereas the wrinkled colonies are made up of elongated pseudo-hyphal cells. The aim was to correlate transcriptomic differences with their respective pathogenic traits

overall_design: RNA-seq comparing smooth and wrinkled isolates of C.auris strain 4701490 grown on either Glucose or Lactate medai

first: Ana

last: Traven

first: Irma

last: Tedja

first: Harshini

last: Weerasinghe

first: Calvin

last: Kraupner-Taylor

last: Harrison


title: Macrophage-augmenting targeted chimaeras for extracellular protein degradation

first: Yi

last: Wang

address: Shangtang Road

institute: Zhejiang Provincial People's Hospital

summary: Extracellular targeted protein degradation (eTPD) systems typically function through passive endocytic trafficking mechanisms that direct extracellular proteins toward lysosomal degradation without actively modulating the functional state of the target cell. Here we report macrophage-augmenting targeted chimaeras (MATACs), a dual-effector eTPD platform inspired by macrophage-mediated efferocytosis. MATACs are constructed by conjugating target-binding antibodies with synthetic polyphosphoserine (PPS) polymers that mimic the polyvalent phosphatidylserine "eat-me" signals displayed on apoptotic cells. We show that PPS functions as a programmable macrophage-targeting ligand that induces macrophage-specific uptake, lysosomal activation, and M2-like immune repolarization. By leveraging this biology, MATACs simultaneously direct extracellular and membrane-associated proteins toward macrophage lysosomes for degradation while actively reprogramming the engulfing macrophages into enhanced degradative and anti-inflammatory states. We show that MATACs efficiently degrade multiple inflammatory targets, including tumor necrosis factor-alpha (TNF-alpha), granulocyte-macrophage colony-stimulating factor (GM-CSF), matrix metalloproteinase-9 (MMP-9), CD86, and CD40. Mechanistically, PPS engagement promotes feed-forward enhancement of macrophage phagocytic and lysosomal functions, establishing a self-amplifying degradation cascade distinct from existing eTPD systems. In murine models of rheumatoid arthritis and ulcerative colitis, TNF-alpha-targeted MATACs exhibit potent therapeutic efficacy, superior suppression of inflammatory signaling, and restoration of immune homeostasis relative to the conventional neutralizing antibody. Collectively, these findings establish MATACs as the first dual-effector extracellular degrader platform in which the effector ligand itself actively reprograms the degradative immune cell during target elimination.

overall_design: Following a 48-h treatment with either PBS (control) or MATAC (100 nM), BMDMs were harvested to prepare single-cell suspensions. scRNA-seq libraries were subsequently constructed using the SeekOne DD Single Cell 3' library preparation kit (SeekGene, Catalog No. K00202) following the manufacturer's protocol. Raw sequencing data were processed using SeekSoul tools (SeekGene, v1.2.1) to generate gene expression matrices, followed by downstream analysis using the Seurat R package (version 4.4). Potential doublets were identified and removed via DoubletFinder, and low-quality cells were excluded and low-quality cells were filtered out if the number of genes was <300 or the ratio of mitochondrial reads was >10%. After normalization and clustering, cell identities were annotated using the SingleR package in conjunction with classical marker genes. Specifically, macrophages were subdivided into unpolarized (M0), activated (activated_M), lipid-associated (LAM), and alternatively activated (M2a and M2c) subtypes. The canonical markers used were Lyz2 and Adgre1 for M0; Nos2, Mki67 for activated_M; Trem2, and Gpnmb for LAM; Arg1 and Chil3 for M2a; Mertk for M2c. Subpopulation proportions were then compared between the control and MATAC-treated groups to assess shifts in macrophage polarization. Finally, Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis was performed on the marker genes of the M2c cluster using clusterProfiler to elucidate its key functional pathways.

first: Qi

first: Jingwen

last: Xie

first: Yuping

last: Chen

first: Jingxing

last: Si

first: Yuxuan

first: Zhili

last: Guo

first: Gaoxia

last: Ma

first: Xiaobei

last: Deng

first: Yan

last: Xu

first: Yumiao

first: Xinyao

first: Jaixin

last: Miao

first: Yuxin

last: Liang

first: Bin

first: Zhong

last: Shao

first: Dahong

first: Youqing

last: Shen

first: Min

last: Xue

first: Shiqun


title: RNA-seq of Osimertinib-treated PC9 cells in specific cell cycle stages

city: Cambridge

first: Laura

last: Biggins

address: Babraham Research Campus

department: Bioinformatics

institute: The Babraham Institute

summary: Osimertinib is the current standard-of-care for treatment-naive patients with EGFR mutation-positive advanced/metastatic non-small cell lung cancer (NSCLC), however resistance inevitably emerges. Osimertinib does not eradicate all cancer cells even in culture, leaving a long-lasting sub-population of Drug Tolerant Persister (DTP) cells that is common to many chemotherapeutics. The DTP population is non-proliferative and seemingly dormant, but resistant clones eventually emerge from the DTP state. Here we show that extensive DNA replication occurs in the DTP state and cells frequently progress through the cell cycle, though cell death is also frequent, such that cell division and cell loss are balanced and the population remains approximately constant. Cell cycling occurs with aberrant gene expression and abnormal DNA replication pattern, leading to DNA damage, extrachromosomal circular DNA formation and mitotic defects, such that replicating DTP cells are hypersensitive to low doses of ATM and ATR inhibitors. Our findings suggest that the DTP state is highly mutagenic and that targeting DNA repair in DTP cells has the potential to prevent the emergence of resistance through de novo mutations.

overall_design: Here, PC9 cells transfected with a FUCCI reporter were treated with osimertinib for 28 days, then fixed with glyoxal and cell-sorted based on DAPI and FUCCI reporters for G1, S and G2.

first: Kieron

last: May

first: Matthew

last: Martin

first: Jonathan

last: Houseley


title: Pericyte KATP Channel Hyperactivity Redistributes Cortical Blood Flow in a CADASIL Mouse Model

city: Aurora

first: Eric

last: Prince

state: CO

address: 12800 E 19th AAve

department: Neurosurgery

institute: University of Colorado Anschutz Medical Campus

summary: Spatial transcriptomics on WT versus CADASIL mouse model with brain and isolated vasculature

overall_design: Spatial gene expression profiling of mouse brain and isolated cerebral vasculature comparing TgNotch3^WT (control) and TgNotch3^R169C (CADASIL model) transgenic mice, using 10x Genomics Visium CytAssist (FFPE, Mouse Transcriptome Probe Set v1.0, mm10-2020-A). 2023 batch: 4 standard Visium samples processed with Space Ranger 2.0.1 (cerebral vessel samples manually aligned). 2024 batch: 4 Visium HD samples processed with Space Ranger 3.1.1 (8 um bin submitted).

first: Danielle

last: Jeffrey

middle: W

first: Fabrice

last: Dabertrand


title: Mitochondrial coenzyme Q redox balance restrains dopaminergic neuron activity to promote early-life sleep in Drosophila

first: Jianing

last: Yang

address: 3400 Civic Blvd

department: Neuroscience

institute: University of Pennsylvania

summary: Sleep is especially abundant during early life, yet the cellular mechanisms that maintain elevated juvenile sleep drive remain poorly understood. To identify cell-intrinsic regulators of juvenile sleep, we profiled gene expression in Drosophila dopaminergic neurons (DANs) at different ages and performed a targeted RNAi screen of genes with enriched juvenile expression. We found that the magnitude of mitochondrial complex I (MCI) disruption produced strikingly distinct physiological outcomes. Severe MCI loss-of-function caused profound mitochondrial dysfunction, reduced dopaminergic activity, and locomotor impairment. In contrast, partial MCI inhibition left overall  mitochondrial function intact but instead reduced sleep, with disproportionately strong effects on juvenile sleep fragmentation and depth, consistent with a gain of dopaminergic signaling. Multiple genetic manipulations that deplete the reduced coenzyme Q pool (CoQH₂) converged on a phenotype of increased dopaminergic activity and wakefulness, indicating that coenzyme Q redox balance itself regulates dopaminergic output. These findings support a model in which CoQH2-driven reverse electron transfer (RET) at MCI restrains dopaminergic arousal. By dissociating mitochondrial redox signaling from catastrophic mitochondrial failure, our work identifies a physiological role for coenzyme Q-dependent signaling in the regulation of neural activity and behavioral state. More broadly, these findings suggest that sleep phenotypes may serve as sensitive indicators of emerging mitochondrial dysfunction and reveal a potential link between the regulation of early-life sleep and later dopaminergic vulnerability.

overall_design: RNAseq profiling of FACS-purified central brain dopaminergic neurons labeled by Th-GAL4 from juvenile (0-1 day old) and mature (6-10 days old) Drosophila melanogaster adult flies

first: Jeffrey

middle: B

last: Rosa

first: Jenny

last: Luong

last: Kayser


title: Effect of calcium oxalate microcrystals on kidney proximal tubule epithelial cell gene expression in microgravity

city: Seattle

first: James

last: MacDonald

state: WA

address: 4225 Roosevelt Way NE

institute: University of Washington

summary: We evaluated the impact of spaceflight on a microphysiologic model of calcium oxalate (CaOx) kidney stone disease. Proximal tubule epithelial cells cultured as confluent microtubules were exposed to CaOx crystals with or without potassium citrate (a potential countermeasure) to determine impact on gene expression. Nine genes were differentially expressed in response to CaOx crystal exposure during spaceflight. This project presents the use of microgravity as a unique environment to study kidney pathophysiology.

overall_design: RNA-Seq of kidney primary tubule epithelial cell (PTEC) cells that were grown in ‘organ-on-a-chip’ microphysiological systems (3D MPS culture), treated with potassium citrate or calcium oxalate in normal and reduced gravity.

first: Jones-Isaac

last: Kendan

first: Catherine

middle: K

last: Yeung

first: Bain

last: Jacelyn

first: Lidberg

last: Kevin

first: Yang

last: Jade

first: Wang

last: Lu

first: MacDonald

last: James

first: Bammler

last: Theo

first: Kenneth

middle: E

last: Thummel

first: Corn

last: Megan

first: Vela Ruiz

last: Micaela

first: Countryman

last: Stefanie

first: Koenig

last: Paul

first: Himmelfarb

last: Jonathan

first: Edward

last: Kelly


title: miRNA profiling of pooled serum circulating cell-free miRNA of Tn+ tumor-bearing mice

city: Sao Paulo

first: Alexis Germán

last: Murillo Carrasco

email: agmurilloc@gmail.com, agmurilloc@usp.br

state: Sao Paulo

address: Av. Dr. Arnaldo 251, Sao Paulo

country: Brazil

institute: ICESP

summary: To investigate the systemic impact of Tn+ tumor phenotypes, we conducted an analysis of circulating miRNAs in the serum of mice bearing Tn+- 4T1 tumors. The 4T1/Tn+ cell line was generated via CRISPR/Cas9 targeting of Cosmc, and tumors were established orthotopically in BALB/c mice. Tumor-bearing animals were monitored for primary growth and micrometastatic dissemination to the lungs, followed by serum collection at endpoint. Serum samples were pooled according to tumor Tn status (Tn+ or Tn–) for total RNA extraction, including small RNAs. Using the NanoString nCounter Mouse v1.5 miRNA assay, we profiled miRNA expression in three serum pools (two Tn+, one Tn–), followed by normalization and quality control via the nCounter Advanced Analysis Software. Expression values were normalized using geometric means of internal positive and negative controls, and only stable miRNA regions (CV < 15%) were retained for downstream analysis.

first: Roger

last: Chammas

first: Teresa

last: Freire

first: Mercedes

last: Landeira

first: Alexis

last: Murillo

first: Patricia

last: Pintor


title: Myeloid MMP14 Couples Extracellular Proteolysis to Inflammatory and Metabolic Remodeling During Obesity

city: Houston

first: Long

middle: Jiang

last: Shao

address: 1825 Pressler St, SRB 401L

department: Institute of Molecular Medicine

institute: The University of Texas Health

summary: Macrophages orchestrate tissue remodeling, inflammation, and metabolic dysfunction in obesity, yet how macrophage-intrinsic extracellular proteolysis integrates with immunometabolic reprogramming remains poorly defined. Matrix metalloproteinase-14 (MMP14), a membrane-anchored protease with broad matrix-remodeling capacity, is markedly induced during monocyte-to-macrophage differentiation and further upregulated in adipose tissue macrophages from high-fat diet (HFD)-fed mice. Pharmacologic inhibition or myeloid-specific deletion of Mmp14 impaired macrophage differentiation, proliferation, migration, and phagocytosis, and blunted pro-inflammatory activation in response to obese adipose tissue–derived cues. Mechanistically, MMP14 enhanced inflammatory programming in part by promoting endotrophin generation and amplifying TLR4-NF-κB signaling. In parallel, MMP14 reshaped macrophage lipid metabolism by suppressing lipolysis and fostering lipid accumulation, thereby modifying macrophage-derived metabolic signals to neighboring cells. In vivo, myeloid-specific Mmp14 deletion protected mice from HFD-induced insulin resistance, dyslipidemia, hepatic steatosis, and adipose tissue inflammation and fibrosis, while increasing energy expenditure and fatty acid utilization. Collectively, these findings identify macrophage MMP14 as a central node linking extracellular matrix remodeling to inflammatory and metabolic dysfunction in obesity.

overall_design: RNA-seq profiling of Raw264.7 treated with LPS(100 ng/mL), compared with LPS(100 ng/mL) plus MMP14 neutralization Ab 3A2(50 μg/mL) for 24 hours to investigate the transcriptional changes.

first: Long J.

first: Fathima

last: Elizondo

first: Feng

last: Gao

first: Elizabeth

last: L. Lieu

first: Bharati

last: Reddi

first: Maryam

first: Iqbal

last: Mahmud

first: Kristin

last: Eckel-Mahan

first: Philipp

last: E. Scherer

first: Xin

last: Ge

first: Huaizhu

last: Wu

first: Sean

last: Hartig

first: Kai

last: Sun


title: Single-cell CITE-seq of peritoneal exudate cells from C57BL/6J mice during acute Toxoplasma gondii infection

city: Indianapolis

first: Americo

middle: H.

last: Lopez-Yglesias

state: IN

address: 635 Barnhill Drive, MS 268

department: Microbiology and Immunology

institute: Indiana University School of Medicine

summary: C57BL/6J mice were infected intraperitoneally with 20 cysts of Toxoplasma gondii. Peritoneal exudate cells were harvested on day 5 post-infection and profiled by single-cell CITE-seq (10x Genomics) using the BioLegend TotalSeq-B Mouse Universal Cocktail v1.0 to jointly measure transcriptome and cell-surface protein expression. This dataset was used to characterize T-bet (Tbx21) expression across myeloid populations during acute toxoplasmosis.

overall_design: Single-cell gene expression (GEX) and antibody-derived tag (ADT) libraries were generated from peritoneal exudate cells of T. gondii-infected C57BL/6J mice (day 5 post-infection) using the 10x Genomics platform with the TotalSeq-B Mouse Universal Cocktail. This work was supported by the American Heart Association Career Development Award 858028 (A.H.L.-Y), the Indiana University School of Medicine Clinical and Translational Sciences Institute Research Enhancement Grant (A.H.L.-Y), the Indiana University School of Medicine Program to Launch those Underrepresented in Medicine toward Success (A.H.L.-Y), and National Institutes of Health Grants R01AI168056 (A.H.L.-Y), and R35GM142701 (L.C.).

first: Madison

middle: L

last: Schanz

first: Fengdi

last: Zhao

first: Kamryn

last: Zadeii

first: Li

last: Chen


title: Mitochondrial STAT3-mediated suppression of apoptosis constrains antimycobacterial immunity

city: Nashville

last: Patrick

state: Tennessee

department: Pathology, Microbiology, and Immunology (PMI)

institute: Vanderbilt University Medical Center

summary: Maintenance of mitochondrial homeostasis is required to balance the host-pathogen interface during Mycobacterium tuberculosis (Mtb) infection of macrophages. Here, we implicate the non-canonical TRIM family member TRIM14 in regulating mitochondrial health during Mtb infection. Specifically, we show that TRIM14 constrains apoptosis by maintaining a mitochondrial pool of STAT3. TRIM14-dependent mito-STAT3 limits mitochondrial permeability transition pore opening, thereby preserving mitochondrial integrity and raising the threshold for apoptotic commitment. In the absence of TRIM14, increased STAT3 Ser754 phosphorylation reduces mitochondrial STAT3 localization, promoting mPTP opening and apoptosis. In vivo, Trim14 deficiency enhances apoptosis during Mtb infection and is associated with increased CD8+ T cell activation, consistent with apoptotic cell-driven antimycobacterial immunity. Together, these findings define a TRIM14–mito-STAT3 axis that suppresses protective apoptosis during Mtb infection and pinpoint mito-STAT3 as a potential target for host-directed tuberculosis therapies.

overall_design: RNA-seq profiling of unifected and 4 hours post mycobacterium tuberculosis infected WT primary bone marrow derived macrophages and Trim14 KO primary bone marrow derived macrophages.

first: Cory

last: Mabry

first: Aja

last: Coleman

first: Mackenzie

last: Smith

first: Stacy

last: Hahn

first: Taylor

middle: M

last: Newbolt

first: Morgan

last: Chapman

first: Lauren

last: Stranahan

first: Chi

last: Weindel

first: Robert

middle: O

last: Watson


title: TrAEL-seq of osimertinib-treated PC9 cells in specific cell cycle stages

first: Laura

last: Biggins

overall_design: PC9 cells were treated with osimertinib for 7, 14 or 28 days, then processed for TrAEL-seq, compared to pre-treatment controls. Resistant lines were derived from single cell clones of PC9 that were maintained in 500nM Osimertinib until resistant, then passaged and maintained in 500 nM Osimertinib. Pre-treatment and resistant cells were harvested during normal growth, 28 day samples were harvested as is since these cultures are non-proliferative.

first: Kieron

last: May

first: Matthew

last: Martin

first: Jonathan

last: Houseley


title: FBX-DMEP suppresses hepatocellular carcinoma through tubulin-associated mitotic dysregulation

city: Qingdao

first: Runhua

last: Liu

address: State Key Laboratory of Microbial Technology, Shandong University, No. 72 Binhai Road, Qingdao 266237, P.R. China

institute: Shandong University

summary: To investigate the mechanism underlying the anti-hepatocellular carcinoma activity of FBX-DMEP, transcriptome sequencing was performed on HepG2 cells.

overall_design: Transcriptome sequencing and analysis were conducted on HepG2 cells treated with DMSO (Group A, samples HedEi, HedSi, HedTi) or 2.5 μM FBX-DMEP (Group B, samples Heb2Ti, Heb2Tii, Heb2Tiii) for 48 hours.


title: Transcriptomic effects of neprilysin inhibition during endothelin-1–induced hypertrophic stress in human iPSC-derived cardiomyocytes

city: Chicago

first: Jacob

middle: D

last: Cunningham

state: IL

address: 1500 W Monroe St. Unit 221

department: Cell & Molecular Physiology

institute: Loyola University Chicago

summary: Human induced pluripotent stem cell–derived cardiomyocytes were used to investigate the cardiomyocyte-intrinsic effects of neprilysin inhibition during hypertrophic stress. Cardiomyocytes were treated with endothelin-1, the neprilysin inhibitor sacubitrilat, a combination of endothelin-1 and sacubitrilat, or vehicle control. Bulk RNA sequencing was performed to characterize transcriptional remodeling induced by endothelin-1 and to determine whether neprilysin inhibition modifies this response.

overall_design: The experiment used a 2 × 2 factorial design consisting of endothelin-1 treatment and neprilysin inhibition with sacubitrilat. The four experimental groups were vehicle control, sacubitrilat alone, endothelin-1 alone, and endothelin-1 plus sacubitrilat. Each RNA-sequencing library was generated from an independent human iPSC-derived cardiomyocyte culture replicate. Primary comparisons included control versus endothelin-1 and endothelin-1 versus endothelin-1 plus sacubitrilat.

first: Cunningham

last: Jacob

first: Phillips

last: Taylor

first: Mazzenga

last: Alexis

first: Nagrani

last: Kush

first: Bui

last: Tuan

first: Barefield

middle: Y

last: David

first: Robia

last: Seth


title: DNA methylation and transcriptomic profiles of Wilms tumour reveal new deregulated genes and epigenetic processes relevant for tumour stratification and management

city: Caserta

first: Abu

last: Saadat

state: Caserta

address: Via Vivaldi, 43

department: Department of Environmental, Biological and Pharmaceutical Sciences and Technologies

institute: Università degli Studi della Campania Luigi Vanvitelli

type: Methylation profiling by genome tiling array

summary: Wilms tumour (WT), the most common kidney cancer in children, presents features of altered kidney development and frequently exhibits molecular alterations at the 11p15.5 imprinted locus, affecting the IGF2 and H19 genes, which contribute to tumour growth and may also act as predisposing events that require additional hits for tumour initiation. The epigenetic landscape beyond 11p15.5 suggests diagnostic and prognostic potential, but its link to transcriptomic changes is largely unexplored. We integrated methylomic and transcriptomic datasets of 27 primary tumours and matched non-neoplastic kidneys. DNA methylation profiling identified around 9,000 differentially methylated CpG sites distinguishing neoplastic from non-neoplastic tissue and other pediatric cancers, thus representing a novel WT-specific epigenetic signature. We found that cases with Imprinting Centre 1 (IC1) gain of methylation exhibited the most extensive epigenetic alterations, LOH tumours showed intermediate changes, whereas regressive tumours with largely normal 11p15.5 status displayed limited methylation abnormalities. Three methylation clusters corresponding to transcriptomic subtypes were identified, characterised by distinct tumour microenvironment and chemosensitivity predictions: a regressive-enriched group with high immune infiltration and predicted susceptibility to paclitaxel, a proliferative group with high tumour purity and predicted sensitivity to doxorubicin, and a stromal-like group with intermediate predicted sensitivity to both drugs. Combined analysis of methylation and expression data revealed more than 900 genes under epigenetic control, which contributed to defining the WT subtypes. Analysis of the IGF2/H19 locus uncovered multiple regulatory mechanisms underlying IGF2 activation, including imprinting defects at IC1, methylation changes at DMR0, differential promoter usage, and transcriptional modulation by PLAG1 and BAHD1. These findings define the epigenetic architecture of WT, encompassing genome-wide methylation changes, subtype-specific patterns, and their integration with gene expression, supporting stratification of cases for improved prognosis and therapeutic approaches.

overall_design: Wilms tumor (WT) and adjacent non-neoplastic kidney (NNK) tissues were collected and subjected to multi-omics profiling. Genome-wide DNA methylation was assessed using the Illumina Infinium MethylationEPIC BeadChip array (54 samples), and total RNA sequencing was performed using the Ovation SoLo RNA-seq library kit and sequenced in paired-end 150 bp mode on NovaSeq 6000 (45 samples). Raw data were processed using standard pipelines in R for normalization, quality control, and differential analysis.

first: Francesco

last: Cecere

first: Federica

last: Rossetti

last: Pignata

first: Emilia

last: D’Angelo

first: Carlo

last: Giaccari

first: Gaetano

last: Verde

first: Paola

last: Quarello

first: Franca

last: Fagioli

first: Josep

last: Roma

first: Manel

last: Esteller

first: Enrique

last: De Álava

first: Flavia

last: Cerrato

first: Andrea

last: Riccio

first: Angela

last: Sparago


title: ChIP-seq profiling of MNDA in iPSC-derived human Sertoli-like cells

city: Beijing

first: Haihan

last: Xiao

address: Building N5, Jinyu Intelligent Manufacturing Factory, Haidian District, Beijing, China

institute: Everlife Biomed Co. Ltd. China

summary: Sertoli cells play vital roles in sustaining normal spermatogenesis. To explore the genomic binding and regulatory capacity of MNDA in Sertoli cells, we used human induced pluripotent stem cell-derived Sertoli-like cells (hiSCs) as an in vitro human Sertoli cell model, whose preparation procedures were adapted from the previously reported study (Liang et al., eLife, 2019). MNDA expression was induced in hiSCs via IFNα stimulation, and ChIP-seq was conducted to capture genome-wide MNDA binding events. Bioinformatic analysis identified thousands of specific MNDA binding peaks throughout the genome. These peaks were distributed across diverse genomic regions, including intergenic regions, gene bodies and regulatory regions flanking transcription start sites. Collectively, these results indicated that MNDA binds to multiple types of genomic loci and may modulate the transcription of downstream target genes.

overall_design: ChIP-seq for MNDA in hiSCs stimulated with IFNα


title: Transcriptional profiles upon MNDA overexpression in iPSC-derived human Sertoli-like cells

summary: Sertoli cells play vital roles in sustaining normal spermatogenesis. To explore the regulatory roles of MNDA in Sertoli cell physiological function, we used human induced pluripotent stem cell-derived Sertoli-like cells (hiSCs) as an in vitro human Sertoli cell model, whose preparation procedures were adapted from the previously reported study (Liang et al., eLife, 2019). MNDA was overexpressed in hiSCs through lentiviral transduction, followed by RNA-seq profiling and bioinformatic analysis. The results showed that MNDA overexpression led to downregulation of genes enriched in glycoprotein biosynthesis, cell-matrix adhesion and basal plasma membrane, accompanied by upregulation of genes involved in rhythmic process and actin filament bundle organization. Collectively, these data revealed the effects of MNDA on Sertoli cell function at the transcriptional level.

overall_design: A lentiviral MNDA overexpression vector was constructed based on the p2k7 vector backbone and packaged into lentiviral particles. hiSCs were then transduced with the lentiviruses to achieve MNDA overexpression. Cells transduced with lentiviruses carrying the empty p2k7 vector served as the control group and processed in parallel. Two independent experiments were carried out, and RNA-seq profiling was performed on MNDA-overexpressing and control cells harvested from both independent replicates.