title: Impaired regulation by purinergic signaling axis contributes to CD8+ T cell dysregulation in STAT3 GOF

first: Montana

last: Knight

address: 3615 Civic Center Blvd

department: Department of Biomedical and Health Informatics

institute: Children's Hospital of Philadelphia

summary: Gain-of-function (GOF) variants in STAT3 cause a complex disorder characterized by early-onset autoimmunity, lymphoproliferation, recurrent infections, and immune dysregulation. In both primary human and mouse models of STAT3 GOF, CD8+ T cells have been implicated as pathogenic drivers of autoimmunity, though the exact mechanisms remain poorly understood. Here, we found that in patients with STAT3 GOF, CD8+ T cells exist in a phenotypically activated state. Functional assessment revealed that naïve CD8+ T cells have an increased capacity for IFN-g and TNF-a production, with evidence of a Type I/II IFN transcriptional signature. Changes in immunoregulatory pathways revealed dysregulation of the purinergic signaling axis on CD8+ T cells: while CD39 was increased, downstream purinergic family members, CD73 and the adenosine receptor, A2AR, were downregulated, impairing the potential to produce or sense immunosuppressive adenosine. Evaluation of the impact of precision therapy in the form of JAK inhibitors at a cellular and functional level revealed partial normalization of naïve CD8+ T cell dysregulation, including aberrant cytokine production in patients. Our study suggests that a dysregulated purinergic signaling axis plays a key role in CD8+ T cell dysregulation in STAT3 GOF and may have implications for other rare monogenic immune disorders and common inflammatory disorders.

overall_design: Samples of human cryopreserved PBMCs were prepared and sequenced at the single cell level. Multimodal data was collected for both gene expression (scRNA-seq) and VDJ (scTCR-seq) information. Data from both a healthy control (n=5) and experimental group (data from patients with STAT3 GOF, n=7) was assessed.

first: Jose

last: Campos Duran

first: Samir

last: Sayed

first: Megan

last: Dalalo

first: Andrea

last: Mauracher

first: Peyton

middle: E

last: Conrey

first: Aaron

last: Schultz

first: Ceire

last: Hay

last: Lindell

first: Eric

middle: D

last: Abrams

first: Erica

middle: G

last: Schmitt

first: Martin

last: Thelin

first: Christian

last: Howard

first: Sara

last: Bluestein

first: Christine

middle: M

last: Seroogy

first: Tamara

last: Pozos

first: Akaluck

last: Thatayatikom

first: Ingrid

last: Lundgren

first: Amelie

last: Gauthier

first: Scott

last: Canna

first: Helen

last: Su

first: Michael

last: Keller

first: Ottavia

last: Delmonte

first: Lisa

last: Forbes Satter

first: Steven

last: Holland

first: Jenna

last: Bergerson

first: Jennifer

last: Leiding

first: Neil

last: Romberg

first: Alexandra

last: Freeman

first: Alejandro

last: Villarino

first: Mark

last: Anderson

last: Cooper

first: Tiphanie

middle: P


title: EBV infection in epithelial malignancies induces resistance to the anti-tumor function of natural killer cells via CD73-mediated metabolism of AMP [NK cells]

status: Public on Jul 23 2026

city: Guangzhou

first: Shuo

last: Wan

state: Guangdong

address: No.601, West Huangpu Avenue

country: China

institute: Jinan University

type: Expression profiling by high throughput sequencing

summary: CD73 is a metabolic immune checkpoint that regulates the homeostatic balance of adenosine levels in the tumor microenvironment (TME). However, the regulation of CD73 abnormal expression by Epstein-Barr virus (EBV) in EBV-associated malignancies and its immune editing mechanism on natural killer (NK) cells remains unclear. In this study, we demonstrate that CD73 is upregulated in EBV-associated malignancies and is negatively correlated with the anti-tumor activity of NK cells. Mechanistically, the EBV latent protein LMP2A upregulates CD73 expression through the PI3K/AKT signaling pathway, and the metabolic product of CD73, adenosine, negatively regulates the anti-tumor function of NK cells through multiple signaling pathways. Furthermore, targeted knockout of CD73, small molecule inhibitor, or neutralizing antibody combined with adoptive transfer of NK cells significantly improved the treatment efficacy for EBV-positive nasopharyngeal carcinoma (NPC). Importantly, we also found abnormal upregulation of CD73 in EBV-positive lymphoma, gastric cancer and lung cancer. In summary, our research identifies the mechanism of immune evasion of NK cell anti-tumor function in EBV-associated malignancies through the abnormal expression of CD73, and targeting CD73 combined with adoptive transfer of NK cells may provide a new strategy for immunotherapy of EBV-related malignancies.

overall_design: To define a direct comparison between ADO and CD73 (catalyzing AMP to ADO) blockade on NK cell function, the NK cells cocultured with the supernatant of HK1+EBV cells treated with 10 ug/ml control/CD73 antibody for 2 h and then 500 ng/ml AMP, were subjected to RNA-seq to analyze the differentially expressed genes and enrichment signaling pathways within and between groups. We further overlaid the sets of transcripts induced or repressed by CD73 (|log₂FC| > 0.5, p < 0.05; pink- and blue-highlighted transcripts  on the volcano plot of ADO-treated NK cells. These data indicate that CD73 signaling is a key mediator in ADO-dependent regulation of NK cell function.

first: Xiaobing

last: Duan

first: Jiali

last: Hu

first: Qiong

last: Luo

first: Yuncong

last: Zhang

first: Guangyong

last: Feng

first: Miaoshan


title: Small RNA Sequencing of Exosomal MicroRNAs in Sera from Patients with Echinococcus granulosus Infection

status: Public on Jul 24 2026

city: Xinjiang

first: Xiumin

last: Ma

address: 137 South Liyushan Road

institute: Tumor Hospital Affiliated to Xinjiang Medical University

type: Non-coding RNA profiling by high throughput sequencing

summary: This project aimed to explore the potential roles of exosomal microRNAs (miRNAs) in cystic echinococcosis by extracting and analyzing exosomes and their cargo miRNAs from the sera of patients with Echinococcus granulosus infection. First, serum exosomes were isolated and purified via size-exclusion chromatography with strict quality control, followed by morphological identification of exosomes using negative-staining transmission electron microscopy. Subsequently, exosomal RNA was extracted, and small RNA libraries were constructed with the Illumina TruSeq Small RNA Kit for single-end 50 bp sequencing on the Illumina Hiseq 2000/2500 platform. Raw sequencing data were processed and analyzed through the ACGT101-miR pipeline, including clean data generation, sRNA length screening, database alignment for filtration, miRNA identification, and further analysis of differentially expressed miRNAs as well as their target gene prediction and functional enrichment. This study completed the entire workflow from exosome isolation and identification to small RNA sequencing and bioinformatics analysis, laying a solid foundation for investigating the functional mechanisms of exosomal miRNAs in cystic echinococcosis.

overall_design: To explore the potential role of serum exosomal microRNAs (miRNAs) in echinococcosis by analyzing the miRNA expression profile of serum exosomes from patients with Echinococcus granulosus infection.

first: Guowen


title: EBV infection in epithelial malignancies induces resistance to the anti-tumor function of natural killer cells via CD73-mediated metabolism of AMP [cell line]

overall_design: In order to study the differential expression of nasopharyngeal carcinoma cell genes caused by EBV infection, we infected two nasopharyngeal carcinoma cell lines CNE2 and HK1 with EBV, and then used RNA-seq to detect the expression of genes that were up-regulated after EBV infection.


title: Human milk oligosaccharide 2’-fucosyllactose and lacto-n-neo-tetraose attenuate early-weaning-induced intestinal barrier dysfunction via gut microbiota modulation in mice

city: Shanghai

first: Ru

last: Chen

address: 1665 Kong Jiang Road

department: Department of Pediatric Surgery

institute: Shanghai Institute for Pediatric Research

summary: Early weaning is a common practice among young mothers and is associated with an increased risk of gastrointestinal disorders. Human milk oligosaccharides (HMOs) play a critical role in maintaining gut barrier integrity and have been increasingly applied in infant formulas. However, the mechanisms of HMOs in maintaining gut function remain unclear. This study aimed to assess the effects of 2'-fucosyllactose (2'-FL) and Lacto-N-neotetraose (LNnT) in a mouse model of early weaning.

overall_design: Fourteen-day-old mouse pups were randomly assigned to five groups: (1) control (normal suckling); enthanized at postnatal day (PND) 21; (2) early weaning (EW; weaned at PND 15); (3) EW+HMOs (2'-FL+LNnT); (4) EW+2'-FL; (5) EW+LNnT. Body weight and energy intake were monitored, and intestinal permeability and inflammation-related markers were assessed post-euthanization. RNA sequencing of jejunal samples was conducted to investigate the transcriptomic profiles.

first: Chen

last: Ru


title: Transcriptome profiling of ILC2 co-stimulated by GITR signaling under Activation condition

city: Seoul

first: Young Gyun

last: Ko

address: 103, daehak-ro, Jongro-gu

country: South Korea

institute: Seuol National university

summary: Innate-lymphoid cells (ILCs) are key regulators of tissue homeostasis/immunity but their anti-tumor roles are poorly defined. Here, we identify the GITR-ILC2-IL-9-eosinophil axis as a key driver of anti-tumor immunity. Specifically, GITR co-stimulation of ILC2s in the tumor microenvironment (TME) induces ATF3-dependent chromatin remodeling that causes the ILC2s to produce IL-9 but not canonical ILC2 cytokines (e.g. IL-5 and IL-13). ILC2-derived IL-9 then promotes eosinophil cytotoxicity, as indicated by their elevated cytotoxic granule-associated gene expression and tumoricidal activity. The IL-9-stimulated eosinophils thus effect tumor control. These events are facilitated by TME-induced expression of IL-9 receptor on eosinophils. TCGA-data analysis showed that IL-9-signature expression associated with favorable prognosis in patients with melanoma and lung adenocarcinoma. Our findings thus establish the GITR-ILC2-IL-9 axis as a pivotal pathway that integrates innate lymphoid and granulocyte responses and drives tumor immunity. This pathway may be a promising therapeutic target for enhancing eosinophil-mediated tumor suppression.

overall_design: RNA-seq profiling of mouse lung ILC2 stimulated with isotype IgG2b and DTA-1 under IL-2, IL-7, IL-33 condtion at 24h

first: Jong-Ho

last: Ham

first: Jae-Moon

first: Juhyun

last: Kim

first: Han Byeol

first: Doo-Hyun

last: Chung

first: Chul-Hwan

last: Lee

first: Sung Ho

last: Park

first: Tae Soo

first: Hey-Young


title: Sequential Imatinib and Anti-PD-1 Therapy in KIT-Altered Melanoma: Mechanistic Insights and Clinical Benefit

city: Chengdu

first: Jing

last: Yu

state: Sichuan

address: No.17, Section 3, Renmin South Road

institute: Sichuan university

summary: KIT is a key oncogenic driver in triple-wildtype melanoma and represents a rational therapeutic target for KIT inhibitors such as imatinib. However, the tumor immune microenvironment in KIT-altered melanoma and optimal strategies to integrate immunotherapy remain poorly defined. In this study, we found that melanomas harboring KIT mutations or amplifications exhibited reduced CD8⁺ T cell infiltration, indicative of an immune-cold phenotype. Imatinib treatment reversed this Immunosuppressive microenvironment by enhancing CD8⁺ T cell infiltration and cytotoxic activity. Furthermore, imatinib upregulated O-GlcNAc transferase (OGT), which functions as a protein lactyltransferase and increased PD-L1 expression through lysine lactylation, thereby sensitizing tumors to anti–PD-1 therapy. Based on these findings, we conducted an open-label, single-arm phase II clinical trial in patients with advanced or metastatic KIT-altered melanoma. Patients received imatinib monotherapy as induction for six weeks, followed by combination therapy with toripalimab, an anti–PD-1 antibody. The combiniation therapy was well-tolerated and demonstrated encouraging clinical activity, with an objective response rate (ORR) of 59.4% in the overall cohort, 73.9% in patients with exon 11/13 mutations, and 100% in those with exon 11 mutation plus amplification—markedly higher than the ORRs of 23.3% with imatinib monotherapy and 25.7% with anti–PD-1 monotherapy. Median progression-free survival and overall survival were 8.2 months (95% CI, 6.5–9.9) and 15.1 months (95% CI, 13.1–20.8), respectively. These results support the use of imatinib as an immune-sensitizing induction therapy prior to PD-1 blockade in KIT-altered melanoma and highlight the therapeutic relevance of OGT-mediated PD-L1 regulation.

overall_design: RNA-seq profiling of wildtype M21/A2058 cell lines and their overexpression derivatives (KIT-Amplification, KIT-L576P, KIT-K642E) at 24h of 100nM imatinib.

first: Jie

last: Dai

first: Xian

last: Jiang


title: Transcriptional activity during seed imbibition is conserved, robust and required for germination. [chipseq]

city: Warsaw

first: Michal

last: Krzyszton

address: Pawinskiego 5a

country: Poland

institute: Institute of Biochemistry and Biophysics, Polish Academy of Sciences

type: Genome binding/occupancy profiling by high throughput sequencing

summary: In most plants, germination begins with the reactivation of metabolism during water uptake by the desiccated seed. Notably, Pol II transcription is hypothesised not to be required for early germination, as seeds appear to initially rely on stored mRNAs produced during their maturation. Here, we show that efficient blocking of Pol II transcription completely stops germination in Arabidopsis seeds. Pol II activity is initiated early and is widespread, following expression and Pol II binding patterns established during seed drying. Our findings suggest that the earliest transcriptional phase relies on pre-existing protein factors. The transcriptional programme initiated during water uptake is robust across diverse imbibition conditions and in seeds matured at different temperatures, and is conserved in rapeseed (Brassica napus). Only after the successful completion of this initial phase and the passing of the translation-dependent checkpoint do seeds activate genes that lead to germination. Our results redefine the role of transcription in seed germination and highlight a conserved pattern of early transcriptional activation.

overall_design: Pol II ChIP-seq was performed using chromatin isolated from dry and 6h imbibed seeds.

first: Szymon

last: Swiezewski


title: Chromatin accessibility of ILC2 co-stimulated by GITR signaling under Activation condition [ATAC-Seq]

overall_design: ATAC-seq of mouse lung ILC2 stimulated with isotype IgG2b and DTA-1 under IL-2, IL-7, IL-33 condtion at 24h


title: Role of GFI1 in gamma delta T cells in adult mice.

city: Montreal

first: Tarik

last: Moroy

state: QC

address: 110, West Pine Avenue, 597

country: Canada

institute: Institut de recherches cliniques de Montréal

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

overall_design: Refer to individual Series


title: Transcriptional activity during seed imbibition is conserved, robust and required for germination.

sample_organism:
Arabidopsis thaliana
Brassica napus

platform_organism:
Arabidopsis thaliana
Brassica napus


title: IGF2BP3 regulates RNA metabolism during unfolded protein response [IGF2BP3 cells]

city: Vienna

first: Aleksandra

middle: S

last: Anisimova

address: Dr. Bohr Gasse 9

country: Austria

institute: Max Perutz Labs, Vienna BioCenter, University of Vienna, Medical University of Vienna

summary: Accumulation of misfolded proteins in the endoplasmic reticulum (ER) perturbs cellular homeostasis and leads to pathological conditions termed ER stress. The Unfolded Protein Response (UPR) is a highly conserved signaling cascade that maintains ER homeostasis. While the transcriptional response is paramount for UPR signaling, several mRNAs are regulated at the posttranscriptional level, yet how this is achieved remains poorly understood. Here, we show that a highly conserved RNA-binding protein, IGF2BP3, interacts with transcripts encoding for the UPR target genes and regulates the UPR signaling. During ER stress, IGF2BP3 destabilized most of its targets, including the UPR target RNAs. On the other hand, IGF2BP3 stabilized a subset of mRNAs encoding for transcription regulators through this indirectly regulated transcription of the UPR target genes. This feedback loop allows IGF2BP3 to elevate the levels of stress response genes while leading to the degradation of other transcripts during ER stress. Our results reveal a novel IGF2BP3-driven gene regulatory network contributing to cellular adaptation to ER stress.

overall_design: SLAMseq of auxin-mediated depletion of mAID-IGF2BP3 in control and endoplasmic reticulum (ER) stress conditions. Depletion is induced by auxin (IAA) treatment in parental (WT) or mAID-IGF2BP3 cells.

first: Harald

last: Hornegger

first: Irmgard

last: Fischer

first: Gijs

last: Versteeg

first: Stefan

last: Ameres

first: Elif

last: Karagöz


title: Transcriptional activity during seed imbibition is conserved, robust and required for germination. [1h and 3h labelling]

overall_design: mRNAs labelled with 4-SU during 1h and 3h Arabidopsis seed imbibition were enriched. 3'RNA-seq was performed for enriched and input samples.


title: IGF2BP3 regulates RNA metabolism during unfolded protein response [Ribo-Seq]

overall_design: Ribo-Seq of HCT116 cells upon IGF2BP3 or IGF2BP2 siRNA knockdown knockout in control and endoplasmic reticulum (ER) stress conditions


title: IGF2BP3 regulates RNA metabolism during unfolded protein response [HCT116]

overall_design: SLAM-Seq of HCT116 cells upon IGF2BP3, IGF2BP2 and double IGF2BP3 and IGF2BP2 siRNA knockdown  in control and endoplasmic reticulum (ER) stress conditions


title: IGF2BP3 regulates RNA metabolism during unfolded protein response [RKO iCas9 cells]

overall_design: SLAMseq of doxycycline-inducible knockout and siRNA-mediated depletion of IGF2BP3 and IGF2BP2 in RKO iCas9 cells.


title: Single cell transcriptomic analysis of splenic gamma delta T cells, thymic gamma delta T cells and thymic DN1-DN2-DN3 cells from WT and GFI1 KO mice.

summary: GFI1 is a transcription factor known to be essential for hematopoiesis and lymphoid cell generation. We have recently found that gamma delta T cells express GFI1 and its absence can impact gamma delta T cell formation.  In order to identify how the lack of  GFI1 can affect the development of thegamma delta T cell subsets, we have performed a single cell sequencing approach using 10X genomics scRNAseq on splenic gamma delta T cells, thymic gamma delta T cells and a pool of  thymic DN1-2-3 (DN) cells from WT and GFI1 KO mice. The sc RNA-seq highlighted differential transcriptomic changes between WT and GFI1 KO cells showing enrichment or  absence of  specific subsets of gamma delta  cells and their thymic progenitors.

overall_design: Splenic gamma delta T cells were sorted  from WT or GFI1 KO adult mice using the ARIA III sorter after mechanical dissociation of the spleen and lyse of red blood cells. WT and KO splenic cells were differently tagged to pool the cells together (cell hashing procedure) before gene expression analysis (10x genomics).                                  Thymic gamma delta T cells were sorted in parallel of the pool of thymic DN1, DN2 and DN3 (DN) cells from the same adult WT or GFI1 KO mice by using the ARIA III sorter. Again, the thymus were mechanically dissociated before lysis of the red blood cells and washings. WT and KO cells from the thymus were also differently tagged to pool the cells together (cell hashing procedure) before gene expression analysis (10x genomics).

first: Jennifer

last: Fraszczak


title: Prostate-specific CRISPR knock-in of human SKP2 induces prostatic intraepithelial neoplasia and adenocarcinoma and reprograms prostate microenvironment.

city: Orange

first: Liankun

last: Song

state: California

address: 101 the city dr. south, bldg55, rm260

country: USA

institute: University of California, Irvine

summary: S-phase kinase associated protein 2 (SKP2), an oncogene and promising therapeutic target, required for spontaneous tumor development in the retinoblastoma protein (pRB), PTEN or p53 deficient mice. We therefore have established a prostate specific CRISPR human SKP2 (hSKP2) knock-in mouse model for studying its role in prostate carcinogenesis. Overexpression of hSKP2 which is driven by endogenous mouse probasin promoter induces prostatic lesions including hyperplasia, mouse prostate intraepithelial neoplasia (mPIN), and low-grade carcinoma and increase prostate weights. Transcriptional profiling by RNA-sequencing analysis revealed significant gene expression alterations in epithelial to mesenchymal transition (EMT), extracellular matrix and interferon signaling in the prostate of hSKP2 knock-in mice compared to wild-type mice. Single cell deconvolution showed an increase of fibroblasts population and a decrease of CD8+T cell and B cell populations in the prostates of hSKP2-knock-in mice. Consistently with these results, overexpression of hSKP2 in human prostate cancer PC3 cells markedly increased cell migration and invasion and induced the gene expression of EMT and interferon pathways, including FMOD, THY1, PFPK, USP18, IL15, etc. In addition, prostate organoids were derived from hSKP2 knock-in and wild -type mouse prostates. Known SKP2 inhibitors Flavokawain A (FKA) and C1 both selectively decrease the viability and alter the morphologies of hSKP2 knock-in versus wild-type prostate organoids. Our studies have provided a new well-characterized prostate-specific hSKP2 knock-in mouse model for testing novel SKP2 targeting agents and new mechanistic insights for understanding an oncogenic role of SKP2 on prostate microenvironment.

overall_design: RNAseq analysis of ventral prostates of hSKP2 knock in (KI) and wild type (WT) mice at 12 months.

first: Xiaolin

last: Zi


title: Single cell transcriptomic analysis of total lung cells from WT and GFI1 KO mice.

summary: GFI1 is a transcription factor known to be essential for the hematopoiesis and for the formation of immune cells. Immune cells represent an important part of the lung tissue so we decided to determine the impact of  the absence of GFI1 on lung populations, especially immune cells.  Lungs from WT or GFI1 KO adult mice were enzymatically dissociated, before being washed and live lung cells were sorted using the ARIA III sorter. The sorted cells were used for gene expression (10x genomics). The sc RNA-seq highlighted differential transcriptomic changes between the 2 conditions, lung cells from GFI1 KO mice and lung cells from WT mice.This experiment allows us to identify specific populations which were absent or over represented in GFI1 KO lungs.

overall_design: Examination of transcriptome via single cell RNA seq of FACS purified mouse live lung cells at the adult stage comparing cells expressing or not GFI1.

first: Virginie

last: Calderon


title: IGF2BP3 regulates RNA metabolism during unfolded protein response [RNA-Seq]

overall_design: RNA-Seq of HCT116 cells upon IGF2BP3 or IGF2BP2 siRNA knockdown knockout in control and endoplasmic reticulum (ER) stress conditions


title: IGF2BP3 regulates RNA metabolism during unfolded protein response [PAR-CLIP]

overall_design: IR-PAR-CLIP of IGF2BP3 in HCT116 cells in control, endoplasmic reticulum (ER) stress and sodium arsenite stress conditions


title: IGF2BP3 regulates RNA metabolism during unfolded protein response

overall_design: RNA-Seq of HCT116 cells upon IGF2BP3 or IGF2BP2 CRISPR/Cas9 knockout in control and endoplasmic reticulum (ER) stress conditions


title: IGF2BP3 regulates RNA metabolism during unfolded protein response [QuantSeq]

overall_design: transcriptome (QuantSeq) of HCT116 cells in control, endoplasmic reticulum (ER) and arsenite stress conditions matching IR-PAR-CLIP samples


title: Single-cell multiomics of peripheral blood monocytes in Crohn's Disease

city: London

first: Eve

last: Hornsby

address: 4 Newark St

department: Blizard Institue/CIB

country: United Kingdom

institute: QMUL

summary: Dysfunctional intestinal monocyte-derived macrophages contribute to pathology in Inflammatory Bowel Disease (IBD). Signals from the tissue micro-environment contribute to this dysfunction, however growing evidence suggests that monocytes can be primed for inflammatory function prior to tissue recruitment.  Here we use single-nucleus multiomics, comprising RNA sequencing (RNA-seq) and assay for transposase-accessible chromatin using sequencing (ATAC-seq) to identify regulatory elements underlying the altered transcriptional profile in monocytes from newly diagnosed, treatment naive Crohn’s disease patients.

overall_design: Single-nucleus multiomics was performed on CD14+ monocytes isolated by positive magnetic selection from the peripheral blood of 3 newly diagnosed, treatment naive Crohn's disease patients with active endoscopic disease and 3 healthy controls using the 10x Genomics Chromium Next GEM Single Cell Multiome ATAC + Gene Expression assay at a target capture rate of 2400 nuclei/sample and sequencing at ~50,000 reads/cell.

first: Andrew

middle: J

last: Stagg

first: James

middle: O

last: Lindsay


title: Nanodrug modified with engineered cancer cell membrane targets CDKs to activate PD-L1 antibody immunotherapy against liver metastasis of immune-desert colon cancer

first: Dongbing

last: Ding

address: 600 Tianhe Road, Tianhe District, Guangzhou City, Guangdong Province

institute: The Third Affiliated Hospital of Sun Yat-sen University

summary: Immunotherapy based on the PD-1/PD-L1 axis blockade has no benefit for patients diagnosed with colon cancer liver metastasis (CCLM) for the MSS/pMMR subtype, which is known as an immune-desert cancer featuring poor immunogenicity and insufficient CD8+ T cell infiltration in the tumor microenvironment. Thus, turning the tumor microenvironment immunologically hot is critical for activating a potent immunotherapy through immune checkpoint blockade (ICB) in this unique subtype accounting for 85% cases of total colon cancer. Here, a multifunctional nanodrug (NP-D@MP) carrying a cyclin-dependent kinase (CDK)1/2/5/9 inhibitor and PD-L1 antibody to boost the ICB-based immunotherapy against MSS/pMMR CCLM via reversing the immunosuppressive tumor microenvironment. To enhance the MSS/pMMR CCLM-targeting efficacy, we modified the nanodrug with PD-L1 knockout cell membrane of this colon cancer subtype. The nanodrug boosted the immunogenicity of tumor microenvironment, thus improving response rate of PD-L1 antibody treatment. First, CDK inhibitor (CDKi) delivered by nanodrug down-regulates phosphorylated retinoblastoma and phosphorylated RNA polymerase II and meanwhile arrests the G2/M cell cycle in CCLM to promote immunogenic signal release, stimulate dendritic cell maturation, and enhance CD8+ T cell infiltration. Moreover, CDKi suppresses the secretion of immunosuppressive cytokines in tumor-associated myeloid cells (TAMCs) sensitizing ICB therapy in CCLM of murine CT26 cell. Notably, the great efficacy to activate immune responses is demonstrated in the patient-derived xenograft (PDX) model and the patient-derived organoid (PDO) model as well, revealing a clinical application potential. Overall, our study represents a promising therapeutic approach for targeting liver metastasis, remolding the TIME, and enhancing the response of MSS/pMMR CCLM to boost ICB immunotherapy.

overall_design: To investigate the role of current biomimicking nanodrugs to TAMCs, the total RNA of TAMCs  treated with PBS, NP@M, NP-D@M, and NP-D@MP for 24 h was extracted for RNA seq.

first: Rongpu

last: Liang

first: Tan

last: Li

first: Tianyun

last: Lan


title: Novel Cellular Patterns and Gene Drivers of Relapse in Adult Acute Myelogenous Leukemia

city: Ann Arbor

first: Qianyi

last: Ma

state: MI

address: 1141 E Catherine St

department: Human Genetics

institute: University of Michigan

summary: Through the analysis of 20 paired AML specimens procured before and at relapse from therapy we have identified three cellular relapse patterns:  i) shift to immaturity; ii) proportional regrowth, and, iii) shift to monocyte-like cells. We traced AML driver mutations back into early HSC/MPP like cells.  We identify high confidence genes that are differentially expressed in matched cell types between AML cells at diagnosis versus relapse.  We credentialled a subset of these genes via CRISPR-Cas9 screens in ten AML cell lines.  Overall, we identify novel patterns and drivers of AML relapse.

overall_design: paired analysis of twenty human acute leukemia bone marrow and blood samples by sc-RNA-seq using the Drop-seq set-up (3' sequencing). Samples were procured before and after relapse from therapy.  Samples with  'Dx'  represent the time point "at Diagnosis". Samples with 'Re' represent the time point at Relapse.

first: Malek

middle: N

last: Sami


title: Systemic reprogramming of monocytes in Crohn’s disease promotes their intestinal inflammatory function

summary: Dysfunctional intestinal monocyte-derived macrophages contribute to pathology in Inflammatory Bowel Disease (IBD). Signals from the tissue micro-environment contribute to this dysfunction, however growing evidence suggests that monocytes can be primed for inflammatory function prior to tissue recruitment.  Here we use single cell RNA sequencing (scRNA-seq) to define blood monocyte heterogeneity in a cohort of newly diagnosed, treatment naive Crohn’s disease and Ulcerative Colitis patients and healthy controls, and to establish the scope of of IBD-associated transcriptional changes in monocyte populations prior to arrival in the intestine.

overall_design: scRNAseq was performed on total monocytes isolated by negative magnetic selection from the peripheral blood of 12 newly diagnosed, treatment naive IBD patients with active endoscopic disease (6 Crohn’s disease and 6 Ulcerative Colitis) and 8 healthy controls using the 10x Genomics Chromium 3’ assay at a target capture rate of 1000 cells/sample and sequencing at ~50,000 reads/cell.


title: Tumor Cell JAGGED-1 Promotes Lymph Node Metastasis and Predicts Recurrence in Lymph Node Positive Breast Cancer Patients

city: Chicago

first: Naiche

middle: L

last: Adler

address: 909 S Wolcott Ave, room 2160

institute: University of Illinois Chicago

overall_design: Refer to individual Series


title: RNA-seq profiling of 14 paired primary and recurrent glioma cases

status: Public on Jul 22 2026

city: Taipei

first: Wen-Bin

last: Yang

address: 250 Wu-Hsing Street

country: Taiwan

institute: Taipei Medical University

summary: Glioma recurrence remains a major clinical challenge and is associated with poor patient outcomes. To characterize transcriptomic alterations associated with tumor recurrence, we performed bulk RNA sequencing on paired primary and recurrent glioma tissue specimens from 14 patients. According to the 2021 World Health Organization (WHO) Classification of Central Nervous System Tumors, glioblastoma is defined as IDH-wildtype (IDH-wt), CNS WHO grade 4. Based on these criteria, 11 paired cases were classified as glioblastoma (IDH-wt, grade 4), while three paired cases with IDH-mutant, grade 3 gliomas were included as a comparison group. Differential gene expression analysis was performed between paired primary and recurrent tumors to identify recurrence-associated transcriptomic changes. Functional enrichment and pathway analyses were subsequently conducted to investigate the biological processes and signaling pathways associated with the identified differentially expressed genes (DEGs). This dataset provides a resource for exploring the molecular mechanisms underlying glioma recurrence and may facilitate the identification of potential therapeutic targets and biomarkers associated with disease progression.

overall_design: Bulk RNA sequencing was conducted on paired primary and recurrent glioma tissue specimens from 14 patients.

first: Jian-Ying

last: Chuang

first: Pin-Yuan

last: Chen

first: Kwang-Yu

last: Chang


title: Distinct activation programs in naïve and memory CD8 T cells govern progeny stemness and effector persistence (bulk experiment, NupHox mice, Lm-OVA infection)

city: Prague

first: Juraj

last: Michalik

address: Vídeňská 1083

country: Czech Republic

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

summary: We longitudinally profiled gene expression in naive and central and effector memory CD8+ T cells across multiple models of acute cognate infection to reveal subset-specific activation programs. However, how prior antigen experience alters T-cell activation programs remains poorly understood. We longitudinally profiled gene expression in naive, central memory, and effector memory CD8+ T cells in response to cognate antigen across multiple models of acute infection. Naive T cells engaged TOX- and TCF7-centered programs and generated early stem-like central memory precursors. Their initially slow proliferation was followed by rapid expansion and the production of large numbers of effector cells. Central memory T cells rapidly triggered effector and proliferation programs while maintaining a smaller self-renewing population. Effector memory T cells expanded poorly and generated almost exclusively effector progeny. Effector progeny derived from both memory subsets survived contraction more efficiently than naive T-cell-derived progeny and established persistent effector memory populations. These data show that prior antigen experience does not simply accelerate CD8+ T-cell activation but redirects cell-intrinsic programs governing progeny fate and persistence. These distinct programs may reflect adaptation to different histories and anticipated patterns of antigen exposure.

overall_design: Here we compared different cell types (Tm, Taim and Tn) from multiple samples.

first: Eva

last: Salyova

first: Darina

last: Paprckova

first: Veronika

last: Niederlova

first: Ondrej

last: Stepanek


title: Stimulation of Adult Muscle Stem Cells with BMPs Results in Direct Activation of Notch Pathway Genes [RNA-seq III]

city: Berlin

first: Markus

last: Schuelke

state: Berlin

address: Augustenburger Platz 1

department: Neuropediatrics

country: Germany

institute: Charite

summary: Muscle stem cells (MuSC) are the cellular source for generation and regeneration of skeletal muscle. To ensure correct muscle growth, MuSC self-renewal and differentiation need to be tightly regulated. Several signaling systems have been implicated in the control of MuSCs, among them Bone Morphogenetic Proteins (BMPs) and Notch, both of which promote MuSC proliferation and suppress differentiation. To better understand the mechanisms of function and the target genes regulated by BMP signaling in myogenesis, we investigated the transcriptional responses of adult mouse MuSCs to BMP6/4 using RNA-sequencing. BMP6/4-stimulation of freshly isolated MuSCs for one hour rapidly increased the expression of classical BMP target genes like Id1 and strongly induced expression of genes of the Notch pathway (Hes1, Hey1, Lfng, Snai1). In parallel, using Cleavage Under Targets and Tagmentation (CUT&Tag), we generated whole-genome binding profiles for the BMP pathway effectors pSMAD1/5/9 and SMAD4 and detected binding in promoters and potential regulatory elements of BMP targets and Notch pathway genes (Hes1, Hey1, Lfng, Snai1) indicating that BMP signaling directly influences Notch and that crosstalk between the two pathways regulates myogenesis.

overall_design: RNA-seq of BMP6-stimulated and control adult mouse muscle stem cells with Notch and protein synthesis inhibition, three biological replicates

first: Birthe

middle: K

last: Lange

first: Angelina

last: Georgieva

first: Carmen

last: Birchmeier


title: Fus-depleted oligodendrocytes reduce neuronal damage and Alzheimer’s disease progression in the AppNL-G-F mouse

city: Pittsburgh

first: Sudhagar

last: Babu

address: 200 Lothrop Street

institute: University of Pittsburgh School of Medicine

summary: Oligodendrocytes provide myelination and metabolic support to neurons, but their contribution to Alzheimer's disease (AD) progression remains incompletely understood. To investigate the molecular effects of oligodendrocyte-specific Fus deletion, we performed single-cell RNA sequencing of hippocampal cells from AppNL-G-F (AD), AppNL-G-F/ Fusfl/fl/Cnpcre/+ (AD/cKO), Fusfl/fl/Cnpcre/+ (cKO), and Fusfl/fl (WT) mice. This dataset defines cell type-specific transcriptional profiles of hippocampal cells and identifies transcriptional changes associated with oligodendrocyte-specific Fus deletion in the context of Alzheimer's disease. These data provide a resource for investigating molecular pathways underlying oligodendrocyte function, glial interactions, and Alzheimer's disease pathogenesis.

overall_design: Single-cell RNA sequencing was performed on hippocampal cells isolated from AppNL-G-F (AD), AppNL-G-F/ Fusfl/fl/Cnpcre/+ (AD/cKO), Fusfl/fl/Cnpcre/+ (cKO), and Fusfl/fl (WT) mice using the 10x Genomics Chromium Single Cell Gene Expression FLEX platform. WT and cKO mice served as age-matched controls, with the cKO group providing a genotype-specific control for the AD/cKO mice. Cell type-specific transcriptional profiles were compared across genotypes.

first: Te-Hsuan

last: Tung

first: Hansruedi

last: Mathys

first: Franca

last: Cambi


title: Integrated bulk and spatial transcriptomic analysis identifies progression-associated molecular signatures in biopsy-proven hypertensive nephropathy [Spatial Transcriptomics]

city: Bergen

first: Tony

address: Haukelandsveien 22

country: Norway

institute: Haukeland University Hospital

summary:
Hypertensive nephropathy (HN) is a leading cause of chronic kidney disease (CKD), but molecular mechanisms underlying disease progression remain poorly understood. We aimed to identify transcriptomic signatures associated with disease progression and to localize these signatures within renal architectures.
Patients with biopsy-proven HN were selected from the Norwegian Kidney Biopsy Registry and stratified after ≥5 years of follow-up into early stable (ES), early progressor (EP), late stable (LS) and late progressor (LP) based on baseline kidney function and annual eGFR decline. Bulk transcriptomic profiling was performed in a discovery cohort and validated in an independent cohort using nCounter profiling. Spatial transcriptomics was applied to map progression-associated signatures to nephron compartments.
Bulk RNA sequencing identified 415 differentially expressed genes (DEGs) between ES and EP, and 692 between LS and LP samples. ES was enriched in circadian rhythm pathways, with reduced NR1D1 and NR1D2 expression in EP. LP was associated with metabolic reprogramming including glutathione, retinol and amino acid metabolism. Random forest modelling identified NR1D1 gene expression as a key classifier, validated in an independent cohort. Spatial transcriptomics revealed nephron segment-specific expression patterns, including a proximal tubule cluster enriched in ferroptosis in LP. Comparative nephron-segment analyses across groups revealed progression-associated biomarkers, including CHGA, CCN2 and SFRP2 in glomeruli, and APOE in proximal tubules.
HN progression appears to involve stage-specific and compartmentalized molecular programs. Integration of bulk and spatial transcriptomics identifies candidate biomarkers and pathways, potentially supporting innovative prognostic stratification and therapeutic strategies.

overall_design: Hypertensive nephropathy were identified in the Norwegian Kidney Biopsy Registry These patients were labelled as progressor or stable, early or late depending on their clinical outcome, with at least 5 years of follow up. Three samples from each group (twelve in total) were assembled into one histological slide and subjected to spatial transcriptomic, performed accordingly to Visium Cytassist. Samples were sequenced with Novoseq 6000

first: Jessica

last: Furriol

first: Lea

middle: Z

last: Landolt

first: Henrik

last: Foshaug

first: Stein Ivar

last: Hallan

first: Marius

middle: A

last: Övrehus

first: Sabine

last: Leh

first: Hrafn

last: Weishaupt

first: Andreas

last: Scherer

first: Liv

last: Jacobsen

first: Leila

last: Barmoudeh

first: Yushu

last: Li

first: Hans Arnfinn

last: Karlsen

first: Thomas

last: Knoop

first: Hans-Peter

last: Marti

first: Öystein

last: Eikrem


title: Transcriptome profiling of WT and exa1-1 under normal, salt, and heat stresses

city: Weifang

first: Yingtang

last: Ma

address: No. 699 Binhu Road, Xiashan Ecological Economic Development Zone

institute: Peking University Institute of Advanced Agricultural Sciences

summary: To elucidate the role of EXA1 in response to abiotic stress, we conducted whole-genome transcriptome analysis using 9-day-old seedlings of both wild-type (WT) and exa1-1 mutant lines under normal, salt, and heat stress conditions. Our findings indicate that EXA1 functions as a key regulator of gene expression associated with both stress adaptation and plant growth.

overall_design: Total RNA was extracted from 9-day-old seedlings of both wild-type (Col-0) and exa1-1 mutant lines, which were treated for 60 min under the following conditions: normal (1/2 MS, 23 °C), salt stress (1/2 MS supplemented with 200 mM NaCl), and heat stress (1/2 MS, 39 °C). Paired-end RNA sequencing (PE-150) was performed on an Illumina HiSeq platform, with three independent biological replicates for each genotype and treatment combination.

first: Yu

last: Tang

first: Sen

last: Wang


title: Integrated bulk and spatial transcriptomic analysis identifies progression-associated molecular signatures in biopsy-proven hypertensive nephropathy [RNA-seq]

first: Tony

last: Chen

overall_design: Hypertensive nephropathy were identified in the Norwegian Kidney Biopsy Registry These patients were labelled as progressor or stable, early or late depending on their clinical outcome, with at least 5 years of follow up.  Samples were sequenced with Novoseq 6000

first: Jessica

last: Furriol

first: Lea

last: Landolt


title: Integrated bulk and spatial transcriptomic analysis identifies progression-associated molecular signatures in biopsy-proven hypertensive nephropathy [NanoString]

overall_design: Hypertensive nephropathy were identified in the Norwegian Kidney Biopsy Registry These patients were labelled as progressor or stable, early or late depending on their clinical outcome, with at least 5 years of follow up. Twentysix samples were obtained. Five to six with 3 um thick microtomed sections were used for nanostring ncounter.

first: Henrik

last: Foshaug

first: Stein Ivar

last: Hallan

first: Marius

last: Övrehus


title: WT and exa1 mutant whole-genome transcriptome analysis under normal, salt and heat stress

summary: Purpose: To elucidate the role of EXA1 in response to abiotic stress, we conducted whole-genome transcriptome analysis using 9-day-old seedlings of both wild-type (WT) and exa1-1 mutant lines under normal, salt, and heat stress conditions. Conclusions: Our findings indicate that EXA1 functions as a key regulator of gene expression associated with both stress adaptation and plant growth.


title: Polysome profiling of the translatome of WT and exa1-1 under normal, salt, and heat stresses

summary: Purpose: To elucidate the role of EXA1 in the response to abiotic stress, we examined the possible effects of salt and heat stresses on Arabidopsis translatome using polysome profiling. Conclusion: We found that the translatome is partly and rapidly reprogrammed in response to salt and heat stresses, and such translatome reprogramming is EXA1-dependent.

overall_design: High-throughput sequencing of polysome-bound mRNA from 9-day-old seedlings of both wild-type (Col-0) and exa1-1 mutant lines, which were treated for 60 min under the following conditions: normal (1/2 MS, 23 °C), salt stress (1/2 MS supplemented with 200 mM NaCl), and heat stress (1/2 MS, 39 °C). Paired-end RNA sequencing was performed on an Illumina HiSeq platform, with three independent biological replicates for each genotype and treatment combination.


title: Sustained Influences of Reactive Oxygen Species and Brassinosteroids on Photosynthetic Capability and Antioxidant Responses to Heat Stress in Wheat

city: Bozeman

first: Jennifer

last: Lachowiec

state: MT

address: 119 Plant Biosciences Building

institute: Montana State University

summary: Short-term brassinosteroid-induced antioxidant activity and photosynthetic capability increases are indicated across numerous plant species and stress conditions. However, the long-term implications of exogenous brassinosteroid (BR) treatment and its reliance on reactive oxygen species (ROS) is not well defined. We investigated how manipulating BR in germinating wheat alongside a ROS-inhibitor could affect yield component outcomes when plants were subjected to heat stress during reproduction. Inhibiting BR reduced superoxide dismutase (SOD) activity, increased lipid peroxidation, and correlated with multiple yield component losses compared to controls following heat stress. Despite a greater initial reduction in effective photochemical yield and SOD activity during heat stress for BR-treated plants compared to controls, BR-treated plants had sustained SOD activity and photochemical capability over prolonged heat stress compared to continued losses observed in control plants. The inhibition of ROS proliferation during BR treatment did not consistently affect the long-term response of antioxidant activity tested but did reduce BR induced photosynthetic resilience during reproductive heat stress. This research suggests a more limited role of ROS and BR for enduring antioxidant activity and highlights their persistent interaction for photosynthetic capability under heat stress conditions.

overall_design: RNAseq profiling of Triticum aestivum cultivar Vida seeds treated with 2,4 EBR or a control during germination. Seeds were grown to booting stage and exposed to a 29C heat stress or not. Tissue was sampled every 8 hours from right before heat exposure until 24 hours after heat exposure.

first: Chloe

last: Hinson

first: Drue

last: Erwin


title: Next Generation Sequencing of Wild Type and Gata2; Mx1-Cre Heterozygote HSCs

city: CARDIFF

first: Neil

last: Rodrigues

address: Maindy Road

department: The European Cancer Stem Cell Research Institute

institute: Cardiff University

summary: Clinical GATA2 deficiency syndromes arise from germline haploinsufficiency inducing mutations in GATA2, resulting in immunodeficiency that evolves to myelodysplastic syndrome (MDS)/acute myeloid leukemia (AML). How GATA2 haploinsufficiency disrupts the function and transcriptional network of hematopoietic stem/progenitors (HSCs/HSPCs) to facilitate the shift from immunodeficiency sequalae to pre-leukemia is poorly characterised. Using a conditional mouse model harboring a single allele deletion of Gata2 when HSCs emerge in utero, we identify pervasive defects in HSPC differentiation from young adult Gata2 haploinsufficient mice during B-cell maturation, early erythroid specification, megakaryocyte maturation to platelets and inflammatory cell generation. Gata2 haploinsufficiency abolishes HSC self-renewal and multi-lineage differentiation capacity following transplantation. These alterations closely associate with deregulated DNA damage responses and inflammatory signalling conveyed from Gata2 haploinsufficient HSCs. We also identify functional interplay between Gata2 and Asxl1, a driver of DNA damage and inflammation and, notably, a recurrent secondary mutation found in GATA2 haploinsufficiency disease progression to MDS/AML. shRNA mediated knockdown of Asxl1 in Gata2 haploinsufficient HSPCs led to a differentiation block in committed progenitor formation beyond that in Gata2 haploinsufficient HSPCs. By analysis of HSCs from young adult compound Gata2/Asxl1 haploinsufficient mice, we discover hyperproliferation of double haploinsufficent HSCs, which are also functionally compromised in transplantation compared to their single haploinsufficient counterparts. Through both Gata2/Asxl1 dependent and unique transcriptional programs, HSCs from young adult compound Gata2/Asxl1 haploinsufficient mice fortify deregulated DNA damage responses and inflammatory signalling in HSCs initiated in Gata2 haploinsufficient mice and establish a broad pre-leukemic program. Our data reveal how Gata2 haploinsufficiency initially drives deregulation of HSC genome integrity and suggest the mechanisms of how secondary mutations like ASXL1 take advantage of HSC genomic instability to nurture a pre-leukemic state in GATA2 haploinsufficiency syndromes.

overall_design:
Wild Type and Gata2; Mx1-Cre Heterozygote HSCs were isolated after administration of 6 doses of pIpC from 8-to-12-week old mice (4 mice per genotype)

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Submitter states that missing raw files are due to file loss.
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first: Ali

last: Abdelfattah

first: Peter

last: Giles


title: Effect of TENT2 knockdown on miRNA profiling in human lung endothelial cells

city: New Haven

first: Asawari

last: Korde

state: CT

address: 300 Cedar street, TAC S440, PO Box 208057

department: Internal Medicine, PCCSM section

institute: Yale University School of Medicine

summary: MiRNAs are generated through a finely tuned multi-step process that includes precise cropping and cleavage of their precursors. The mature miRNA is then loaded onto an argonaute (Ago) protein to form an RNA-induced silencing complex (RISC) and target messenger RNAs.  Most of the mechanisms of miRNA regulation target one of the steps in the biogenesis. However, through analysis of miR-1 precursors, we demonstrate that VEGF stimulation induces degradation (decay) of mature miR-1-3p without affecting its precursors. This analysis also identified a specific miRNA 3’-adenylation pathway that targets the guide strand after RISC loading. VEGF induced the expression of terminal nucleotidyl transferase 2 (TENT2, also known as PAPD4 or GLD2), one of the main enzymes that mediate 3’ miRNA adenylation, and knockdown of TENT2 inhibited miR-1 decay. We examined the biological significance of TENT2 in VEGF-mediated EC proliferation, its pathogenic role in murine NSCLC models, and its expression and clinical significance in human NSCLC.

overall_design: We transduced primary human lung endothelial cells (HPMEC) with TENT2 shRNA lentivirus or control (Ctrlsh) with 3 replicates in each group. Total RNA (1ug/sample) were extracted 36 hours after the transduction, followed b serum starvation and a 24-hour treatment with PBS. The RNA were then sent for library preparation and microRNA sequencing at the Yale Center for Genome Analysis (YCGA). The canonical miRNAs were detected, and differentially expressed miRNAs between TENT2sh and ctrlsh groups were obtained.

first: Shervin

last: Takyar


title: The stage- and sex-specific transcriptome of the striped flea beetle Phyllotreta striolata

city: Hangzhou

first: Yanyan

last: Zhou

address: Xueyuan street 258

institute: China Jiliang University

summary: The striped flea beetle (SFB), Phyllotreta striolata, is a globally devastating cruciferous pest. A key challenge to its control lies in its complex life cycle—with egg, larval, and pupal stages confined to soil, while adults infest aerial plant parts—coupled with distinct antennal differences between males and females that underpin sex-specific ecological traits. Transcriptomic profiling across developmental stages offers a powerful approach to decode the genetic basis of these stage- and sex-related traits and inform targeted pest management. Here, we present the first comprehensive transcriptomic atlas of P. striolata, encompassing four key life stages (egg, larva, pupa, adult) with separate male and female adult. RNA sequencing of 15 samples (biological triplicates per group) generated 334.5 million raw reads. Dataset reliability was robust, as validated by correlation analysis, principal component analysis, and qRT-PCR. Differential expression analysis and functional enrichment further confirmed the dataset’s utility in dissecting stage-specific developmental programs and sex-biased molecular signatures. These data provide valuable insights into the biology and developmental dynamics of P. striolata and lay a solid foundation for functional genetic studies, thereby facilitating the identification of target genes and the development of effective, sustainable control strategies against this pest.

overall_design: To identify stage- and sex-specific expressed genes in the striped flea beetle (Phyllotreta striolata), we performed RNA-seq on five distinct developmental stages and sexes: egg, larva, pupa, male adult, and female adult. Samples were collected and sequenced with biological replicates to analyze transcriptomic variations across different life stages and sexes.

first: Chenxue

last: Geng

first: Xin

last: Liu

first: Nianbin

first: Yongli

last: Zheng

first: Qian

last: Li


title: Tumour-targeted nitric oxide nanotherapy overcomes sorafenib resistance and reprograms antitumour immunity in hepatocellular carcinoma

city: Taipei City

first: Sheng

last: Yang

address: No. 128, Sec. 2, Academia Rd., Nangang Dist.

department: Bioengineering

institute: National Tsing Hua University

summary: Therapeutic responses in hepatocellular carcinoma (HCC) are often limited by resistance-associated survival signaling and immune escape. Resistance to sorafenib, a first-line tyrosine kinase inhibitor (TKI) for advanced HCC, has been associated with activation of the AKT–mTOR pathway, suggesting that suppression of this axis may improve therapeutic efficacy. Here, we developed NanoNOSOR, an HCC-targeted SP94 peptide-functionalized lipid–PLGA nanoplatform for tumor-targeted, pH-responsive co-delivery of the nitric oxide donor DNIC and sorafenib. DNIC sensitized murine and human HCC cells to sorafenib by suppressing AKT–mTOR signaling. Co-loading DNIC and sorafenib into SP94-functionalized nanoparticles enhanced HCC cell uptake, promoted pH-responsive payload release, and achieved synergistic AKT–mTOR pathway suppression and cytotoxicity in vitro. In orthotopic HCC-bearing mice, NanoNOSOR preferentially accumulated in tumors and showed superior antitumor activity over single-agent nanoparticle formulations, as indicated by suppression of primary tumor growth and lung metastasis, together with increased tumor cell apoptosis. This antitumor effect was accompanied by transcriptional remodeling of the tumor microenvironment, with reduced proliferation-associated programs and increased immune-activation pathways. In addition, NanoNOSOR-mediated AKT–mTOR axis suppression downregulated PD-L1 immune checkpoint expression and enhanced intratumoral CD8⁺ T-cell infiltration and activation, linking tumor-intrinsic pathway inhibition to reduced immune escape. Biosafety analysis showed no overt hepatotoxicity, nephrotoxicity, or major organ damage. Together, these findings establish NanoNOSOR as a tumor-targeted NO–TKI co-delivery strategy that enhances therapeutic response and reprograms the HCC tumor microenvironment, providing a potential nanotherapeutic platform for overcoming therapeutic resistance in HCC.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for murine HCC tumors with or without treatment of nanoparticles loaded with DNIC and sorafenib

first: Chen

last: Yunching

first: Yang

last: Sheng


title: Single-cell RNA-seq of synovial fluid cells from osteoarthritis control patients

city: Chengdu

first: Heng

last: Xu

address: 17#, section 3, South Renmin Road

institute: Sichuan University

summary: This dataset contains processed 10x Genomics single-cell RNA-seq data from synovial fluid cells of three treatment-naive osteoarthritis (OA) patients. These OA samples were used as controls in the published Nature Communications study "Single cell immunoprofile of synovial fluid in rheumatoid arthritis with TNF/JAK inhibitor treatment" (doi: 10.1038/s41467-025-57361-0), which profiled synovial fluid immune cells to characterize rheumatoid arthritis-associated cellular states and treatment-related immune remodeling.

overall_design:
Synovial fluid cells from three treatment-naive OA patients were collected as control samples and profiled by 10x Genomics single-cell RNA sequencing. Fresh synovial fluid was processed to generate single-cell suspensions, libraries were prepared using Chromium Single Cell 3' v3 chemistry, and sequencing was performed on an Illumina NovaSeq 6000 platform. The submitted files are sample-specific Cell Ranger processed feature-barcode matrix archives for OA_1_1, OA_2_1, and OA_3_1.

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

last: Xia

first: Chenjia

last: He

first: Zhinan

last: Xue

first: Yuelan

last: Wang

first: Yun

last: Qin

first: Zhixiang

last: Ren

first: Yupeng

last: Huang

first: Han

last: Luo

first: Hai-Ning

last: Chen

first: Wei-Han

last: Zhang

first: Li-Bin

first: Yunying

last: Shi

first: Yangjuan

last: Bai

first: Bei

last: Cai

first: Lanlan

first: Feng

first: Maoxiang

last: Qian

first: Wei

last: Shu

first: Geng

last: Yin

first: Qibing

last: Xie


title: Hepatic transcriptome profiling of wild-type mice treated with GalNAc-siRnf10

city: Tianjin

first: du

last: chunyuan

address: youyi road

institute: Tianjin Medical University

summary: This study aimed to investigate the hepatic transcriptomic effects of GalNAc-conjugated siRNA-mediated Rnf10 knockdown in vivo. Wild-type mice were maintained on a normal chow diet and treated with GalNAc-siNC or GalNAc-siRnf10 at the indicated time points. Liver tissues were collected at the end of the experiment and subjected to bulk RNA sequencing. Differential gene expression analysis was performed to identify genes and pathways altered by GalNAc-siRnf10 treatment. Seed match enrichment analysis was further used to evaluate potential off-target effects associated with the siRnf10 guide strand.

overall_design: Wild-type mice were maintained on a normal chow diet and treated with GalNAc-siNC or GalNAc-siRnf10 at the indicated time points. Liver tissues were collected at 17 weeks and used for bulk RNA sequencing. The experimental design included GalNAc-siNC-treated control mice and GalNAc-siRnf10-treated mice with biological replicates in each group. RNA-seq data were analyzed to compare hepatic gene expression profiles between control and Rnf10 knockdown groups.

first: Yongsheng

last: Chang

first: Chunyuan

last: Du


title: Severe long-COVID is driven by monocyte reprogramming and broad immune dysregulation linked to herpesvirus activation

city: Nijmegen

first: Niels

last: Velthuijs

address: Houtlaan 4

department: Cell Biology

country: Netherlands

institute: Radboud University

summary: Long-COVID (LC) continues to impose a significant burden on patients and society, yet its pathophysiology remains poorly understood. Here, we characterize the functional, transcriptomic, and epigenomic state of monocytes from 21 patients with severe LC (sLC) at a median of 3.4 years after primary infection, as well as the transcriptomic profiles of T and B-cells. Plasma proteomics revealed elevated chemokines and type-I interferon-associated proteins, alongside a reduction in circulating monocytes. Monocytes from sLC patients demonstrated markedly reduced cytokine secretion upon ex vivo LPS stimulation, a finding reproduced in an in vitro model of LC. ATAC-sequencing revealed an epigenomic state of immune dysfunction in monocytes, partially driven by a loss of AP-1 transcription factor binding motifs. Single-cell transcriptomics using STAMP across 113,000 peripheral blood mononuclear cells (PBMCs) confirmed the downregulation of activator protein 1 (AP-1) family members and pro-inflammatory signaling in monocytes, along with impaired antigen presentation, dysregulated viral signaling, and immunosuppressive gene upregulation. T and B-cells demonstrated similar immune dysfunction at the transcriptome level. Epigenomic and transcriptomic evidence of herpesvirus activity, combined with elevated HHV-6 IgG serology in sLC patients, points toward viral reactivation as a candidate mechanism underlying persistent immune dysfunction. Together, these findings suggest that sLC is characterized by a long-lived, infection-induced interferon-priming state that drives monocyte hyporesponsiveness through AP-1-mediated epigenetic reprogramming and implicate HHV-6 reactivation as a potential therapeutic target.

overall_design:
20-21 samples per group of Nonsymptomatic donors (recovered from SARS-CoV-2 infection), mild long-COVID and severe long-COVID

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

last: Röring

first: Laszlo

last: Groh


title: Extracellular vesicles underlie cell-type-specific crosstalk during human cortical development and disease

city: Planegg-Martinsried

first: Filippo M.

last: Cernilogar

address: Grosshaderner Strasse 9

department: Biomedical Center

institute: LMU Munich

summary: Cellular crosstalk is an essential process influenced by numerous factors including secreted vesicles that transfer nucleic acids, lipids, and proteins between cells. Extracellular vesicles (EVs) have been the center of many studies focusing on neuron-to-neuron communication but whether EVs display cell-type-specific features for cellular crosstalk during neurogenesis is unknown. Using human-derived cerebral organoids, neural progenitors, neurons and astrocytes, we characterized the protein content of EVs and showed their cell-type-specific dynamics and function during brain development. Moreover, as many proteins coded by genes associated with neurodevelopmental disorders were detected in EVs, we examined EVs from patients with myoclonic epilepsy and found alterations in size, composition and function. This study sheds new light on the biology of EVs during brain development.

overall_design: We performed RNA-seq analysis on neural progenitor cells (NPCs) acutely treated (12 hours) with Extracellular vesicles (EVs) purified by the conditioned medium of dorsally patterned and ventrally patterned  human spheroids originated from control-  or EPM1 epileptic patients- iPSCs cells. The aim of this experiments was to dissect if EV content leads to transcriptional changes on receiving cells.

first: Rossella

last: Di Giamo

first: Silvia

last: Cappello

first: Filippo

first: Fabrizia

last: Pippicelli


title: STAT3 SH2 Domain Aspartic Acid 661 Mutations Activate Immune Gene Programs

city: Maimi

first: Alejandro

last: Villarino

state: Florida

address: 1600 NW 10th Ave, Rosenstiel Medical Science Building (RMSB), Room 3152A

institute: University of Miami

summary: The conserved aspartic acid residue D661 within the STAT3 SH2 domain is a recurrent mutational hotspot in hematologic malignancies, including T-cell large granular lymphocytic leukaemia, myelodysplastic syndromes and acute lymphoblastic leukaemia. To define the functional consequences of distinct STAT3D661 variants, we integrated computational, structural and in vitro and in vivo genetic approaches. AlphaMissense and PolyPhen-2 classified all four STAT3D661 variants (D661Y, D661V, D661N and D661H) as pathogenic. ClinVar classified D661Y and D661V as variants of uncertain significance. AlphaFold 3-based modelling predicted that D661Y and D661V strongly promoted SH2-TAD-mediated dimerization, while D661N and D661H exerted weaker structural effects. Functional in vitro assays in Stat3-deficient T cells demonstrated a gain-of-function (GOF) hierarchy of the STAT3 variants (D661Y ≈ V > H > N) resulting in activation of canonical STAT3 target genes and immune transcriptional programs. In vivo, only STAT3D661H mice were viable, displaying reduced CD4+ T cells, expansion of memory CD8+ T cells and enhanced immune gene expression. Collectively, our findings define a gradient of STAT3 D661 GOF variants, consistent with in vitro and in vivo experiments. D661Y and D661V mutants exhibited stronger transcriptional activity in T cells with impaired viability of mice carrying these variants.

overall_design: bulk' RNA-seq analysis of transduced CD4+ and CD8+ T cells sourced from mice lacking STAT3

first: Hye Kyung

last: Lee

first: Gyuhyeok

last: Cho

first: Jichun

last: Chen

first: Aaron

middle: B

last: Schultz

first: Sung-Gwon

first: Chengyu

last: Liu

first: Priscilla

last: Furth

first: Neal

last: Young

first: Jungwook

last: Kim

first: Lothar

last: Hennighausen


title: Retina-specific glucocorticoid receptor deletion disrupts rhythmic gene expression in the mouse retina under constant dark conditions.

city: Fukuoka

first: Keisuke

last: Ikegami

address: Nishi-ku Motooka 744

country: Japan

institute: Kyushu University

summary: The ocular circadian clock has been thought to be regulated primarily by environmental light. In many peripheral tissues, however, circadian clocks are influenced by temporal information conveyed by adrenal glucocorticoids, while glucocorticoid-dependent regulation of the eye clock, a light-receptive organ, has remained unclear. To investigate this mechanism, we generated retina-specific Nr3c1 (glucocorticoid receptor; GR) knockout mice by crossing Chx10-Cre mice, in which Cre-recombinase is driven by the Chx10 promoter expressed in the developing optic cup, with Nr3c1 flox/flox mice. Using these mice, we performed time-course tissue collection under constant dark conditions followed by time-series RNA-seq analysis. The analysis showed that many rhythmic genes detected in control retina were lost in retina-specific Nr3c1-deficient mice, suggesting that glucocorticoid signaling contributes to rhythmic retinal gene expression.

overall_design: Male 12-week-old WT (Cre-) and retina-specific Nr3c1 cKO (Cre+) mice were maintained under 12 h light/12 h dark (12L:12D) conditions for 2 weeks, and then transfered to constant dark (DD) conditions. Whole eyes were collected every 4 hours at 2, 6, 10, 14, 18, and 22 hours after circadian time 0 (CT2, CT6, CT10, CT14, CT18 and CT22) at 2nd day of DD. At each time point, whole eyes were collected from three WT mice and three cKO mice. Each whole-eye sample was homogenized with a pestle, and total RNA was extracted. Equal amounts of RNA from the three individuals in each genotype/time-point group were pooled and subjected to RNA-seq analysis.


title: VRK1 phosphorylates SRRM2 for the regulation of splicing of DNA damage repair factors

first: jinghan

last: rong

state: Zhejiang

address: westlake university

institute: westlake university

summary: Vaccinia-related kinase 1 (VRK1) is a nuclear serine/threonine kinase that contributes to genome stability through the phosphorylation of diverse substrates. This study investigated whether VRK1 regulates pre-messenger RNA splicing through serine/arginine repetitive matrix protein 2 (SRRM2), a nuclear speckle-associated splicing scaffold. Messenger RNA sequencing was performed in control HEK293T cells, VRK1-knockout HEK293T cells, and SRRM2-depleted HEK293T cells. Alternative splicing events were analyzed using replicate Multivariate Analysis of Transcript Splicing. Most differential alternative splicing events detected following VRK1 knockout or SRRM2 depletion were skipped-exon events. A subset of skipped-exon events was shared between VRK1-knockout and SRRM2-depleted cells, and the corresponding genes were enriched in DNA repair-related pathways. These data support a role for the VRK1-SRRM2 regulatory axis in maintaining the efficient alternative splicing of DNA damage response-related transcripts.

overall_design: RNA sequencing profiling of wild-type, VRK1-knockout, and SRRM2-depleted HEK293T cells, with three biological replicates per condition. Differential alternative splicing events in VRK1-knockout and SRRM2-depleted cells relative to wild-type cells were analyzed using replicate Multivariate Analysis of Transcript Splicing (rMATS). In the rMATS_SE_all.txt files, IJC refers to inclusion junction read counts supporting exon inclusion, and SJC refers to skipping junction read counts supporting exon skipping.

first: Xiaochun

last: Yu

first: Jinghan

last: Rong


title: Chronic IL-1 exposure attenuates IL-1 response and alters gene expression regulation while maintaining therapeutic sensitivity in BCa cell lines [ChIP-seq]

city: Richardson

first: Nikki

last: Delk

address: 800 West Campbell Road

department: Biological Sciences

institute: University of Texas at Dallas

summary: Chronic inflammation is a hallmark of the breast cancer tumor microenvironment and is also known to be associated with disease progression and therapeutic response. Interleukin-1 (IL-1) signaling has been widely studied in breast cancer biology; however, the long-term effect of sustained IL-1 exposure on hormone receptor–positive breast cancer cells remain poorly understood. In this study, we investigated how chronic IL-1 exposure influences inflammatory response, hormone dependency, and therapeutic sensitivity in ERα+/PR+ breast cancer models, MCF7 and T47D. Chronic IL-1 exposure attenuated response to subsequent acute IL-1 treatment, but the chronically exposed cells remained sensitive to serum deprivation, retained dependence on estrogen or progesterone receptor signaling, and responded robustly to endocrine and chemotherapeutic treatments. Extensive changes in basal gene expression and histone modification revealed that chronic IL-1 exposure alters transcriptional reprogramming and chromatin remodeling. Together, these findings demonstrate that chronic IL-1 signaling drives selective inflammatory response in hormone receptor–positive MCF7 and T47D breast cancer cells. This work underscores the continued therapeutic relevance of hormone receptor–targeted strategies in chronically inflamed tumors and provides insight into how sustained inflammatory stress shapes tumor behavior and gene regulation predicted to promote tumor progression.

overall_design: We performed ChIP sequencing  and differential binding analysis for the MCF7 parental cell line (termed: MCF71) and the corresponding chronic IL-1 subline cells (termed: MCas1, MCbs1) grown in normal growth medium (DMEM/10% FBE) in T75 flasks until 80% confluent. Cells were then collected for ChIP sequencing analysis to assess basal histone marks. Histone marks assayed: H3K4me1, H3K4me3, H3K27ac, H3K27me3

first: Rafah

last: Falah

first: Roopal

last: Dhar

first: Stephanie

last: Yamauchi

first: Monica

last: Bautista

first: Mohammad

last: Kanchwala

first: Liu Yan

last: Yan

first: Dinesh

last: Raju

first: Linyi

last: Xu

first: Kylah

last: Reliford

first: Afshan

last: Nawas

first: Samrah

last: Ali

first: Justin

last: Fang

first: Ola

last: Olaleye

first: Jyotsna

last: Tera

first: Rana

last: Abdelaziz

first: Reshmika

last: Kanakala

first: Aniketh

last: Sudungunta

first: Subhash

last: Eedarapali

first: Emmalee

last: Burr

first: Basir

last: Mansoor

first: Nicole

last: Roos

first: Sydney

last: Diep

first: Hiba

last: Afaq

first: Niranjana Rajesh

last: Rajesh

first: Saanvi

last: Manohar

first: Jennifer

last: Odikpo

first: Abhinav K.

last: Jain

first: Zhenyu

last: Xuan

first: Chao

last: Xing


title: Ankyrins are essential for synapse development in the mouse outer retina

city: Los Angeles

first: Yi-Rong

last: Peng

state: CA

address: 100 Stein Plaza Driveway, B-133

department: Department of Ophthalmology

institute: University of California, Los Angeles

summary: Retinal circuit assembly relies on the precise timing and positioning of key molecules between neuronal partners to mediate proper synapse formation. In the outer retina, horizontal cells are important interneurons that make the first contacts to photoreceptors and begin to segregate visual information into two distinct pathways by selectively forming synapses to the distinct types of photoreceptors. Dendrites of horizontal cells synapse exclusively to cone photoreceptors whereas the axon terminal synapses to rod photoreceptors.  Failure to properly form these early connections disrupts the downstream connectivity of other post-synaptic neurons such as bipolar cells and leads to abnormal visual function. Although these early events are critical for proper synapse development, little is known about the molecular mechanisms that establish horizontal cell to photoreceptor connectivity during development. In the present study, we performed single cell RNA-sequencing and uncovered new molecules that are highly expressed in horizontal cells. These include different members of the cytoskeletal scaffolding family of Ankyrins that are known to form specialized regions within neurons by recruiting different molecules to the membrane and linking them to the cytoskeleton. Specifically, we found Ankyrin-B to be highly expressed in horizontal cells at early time points and Ankyrin-G to be expressed at later stages. Loss of both Ankyrin-B and Ankyrin-G leads to synaptic defects between horizontal cells and photoreceptors which then affects connectivity to their bipolar targets and disrupts in vivo retinal responses. In summary, our findings uncovered a new role for Ankyrins in setting up the early connections between horizontal cells and photoreceptors required for proper circuit assembly and normal visual function.

overall_design: Tg(Cx57icre;Ai14) mice were used to label and isolate horizontal cells. Retinas were dissociated using papain, followed by FACS sorting to isolate horizontal cells, then dissociated into a single-cell suspension for RNA sequencing with a targeted cell number of 10,000 cells using the Chromium™ Next GEM Single Cell, 3’ Kit v3.1 (10X Genomics). cDNA was amplified with 11 cycles, and cDNA libraries were sequenced on the Illumina NovaSeq S4 platform.

first: Elizabeth

last: Zuniga-Sanchez

first: Ross

last: Perez

first: Martina

last: Cavallini


title: Recipient interleukin-1β production is critical for lung allograft acceptance

city: Saint Louis

first: Daniel

last: Kreisel

state: MO

address: 660 S Euclid Ave

institute: Washington University School of Medicine

summary: Proinflammatory cytokines, including IL-1β, TNF-α, and IL-6 have been linked to graft rejection and protocols have been developed to target these in solid organ transplant recipients. Pathways regulating rejection and tolerance differ across organs and remain poorly understood in lungs. Here, we used a mouse lung transplantation model to examine the role of inflammatory cytokines in graft acceptance. We found that recipient IL-1β drove systemic granulocyte colony-stimulating factor (G-CSF) release early after transplantation and promoted allograft infiltration with neutrophils that express immunosuppressive gene signatures. IL-1β promoted inducible nitric oxide synthase (iNOS) expression in neutrophils and accumulation of nitric oxide (NO) in allografts, a pathway that is critical for the acceptance of transplanted lungs. We observed that human and mouse neutrophils from lung transplant recipients suppress T cell responses in an NO-dependent fashion. Finally, recipients deficient in Il1b, but not Tnfa or Il6, acutely rejected lung allografts despite receiving immunosuppression that results in tolerance when administered to wildtype hosts. Thus, contrary to the widely held notion that proinflammatory cytokines promote deleterious outcomes after transplantation, our findings uncovered a previously unknown role for recipient IL-1β as a critical mediator of pulmonary allograft acceptance. Our findings inform future studies developing lung-specific immunosuppressive strategies.

overall_design: Allografts were harvested 4 days after transplantation into wildtype vs Il1b-deficient recipients and single-cell suspensions were prepared. Cells were stained with DAPI (BD Biosciences), CD45.1 (Clone A20, Invitrogen), CD45.2 (Clone 104, BioLegend). Fluorescence-activated cell sorting was performed on a BD FACS Melody cell sorter, and recipient immune cells (DAPI-CD45.1-CD45.2+) were sorted from pooled single-cell suspensions from n = 2 recipient allografts from each experimental condition. Sorted cells were submitted for single-cell RNA sequencing.

first: Amit

middle: I

last: Bery

first: Yuhei

last: Yokoyama

first: Venkatrao

last: Nunna

first: Junedh

last: Amrute

first: Shinichi

last: Kawana

first: Wenjun

last: Li

first: Yuriko

last: Terada

first: Kohei

last: Hashimoto

first: Katsutaka

last: Mineura

first: Satona

last: Tanaka

first: Yun Zhu

last: Bai

first: Hailey

last: Shepherd

first: Alexander

last: Wein

first: Charles

middle: R

last: Liu

last: Jacobsen

first: Varun

last: Puri

first: Ramsey

last: Hachem

first: Jon

middle: H

last: Ritter

first: Isaiah

last: Turnbull

first: Kory

last: Lavine

last: Krupnick

first: Andrew

last: Gelman

first: Ruben

last: Nava


title: Developmental Patterning and Vessel-Wall Remodeling at the Neural Crest–Ductus–Aortic Isthmus Interface in Infantile Coarctation of the Aorta

city: Augsburg

first: Victoria

middle: Elisabeth

last: Fincke

address: Stenglinstraße 2

institute: Childens Cancer Center - University hospital Augsburg

summary:
Background: Coarctation of the aorta (CoA) is a congenital narrowing of the aortic isthmus, typically located near the ductus arteriosus or ligamentum arteriosum. Despite successful anatomical repair, affected individuals remain at risk of recoarctation, arterial hypertension, and diffuse aortopathy, suggesting that CoA involves intrinsic abnormalities of the vessel wall beyond a localized mechanical obstruction. The developmental and molecular mechanisms underlying this vascular phenotype remain incompletely understood.
Results: Transcriptomic profiling identified 402 transcripts separating CoA from control tissue. Canonical pathway analysis showed a dominant extracellular matrix and collagen-remodeling signature, including collagen biosynthesis and modification, collagen degradation, integrin-mediated cell–matrix interaction, wound-healing-associated signaling, and fibrosis-like remodeling programs. In parallel, developmental patterning pathways were retained, including RAR/RXR-associated signaling, anterior HOX developmental annotations, and a shared HOX/MEIS signature. Network and upstream regulator analyses supported convergence of extracellular matrix, collagen, cytoskeletal, and muscle-associated modules with developmental and epigenetic regulators, including KAT6A, KAT6B, RAR/RXR/retinoic acid, DNMT3B, KMT2A, and ARID1A. RT-qPCR follow-up demonstrated increased expression of EDN1, AGTR2, IRS4, and TFAP2B, whereas selected pathway-derived candidates, including TGFB, were not confirmed. Conclusions: Infantile CoA tissue displayed a dominant vessel-wall remodeling phenotype accompanied by RA/HOX/MEIS-associated developmental patterning, smooth muscle/cytoskeletal regulatory programs, and selected vascular signaling changes. These findings support a developmental-remodeling model in which retained or reactivated positional-identity programs at the neural crest-ductus-aortic isthmus interface coexist with postnatal extracellular matrix remodeling. The data provide a hypothesis-generating molecular framework for understanding CoA as a localized congenital vascular lesion with persistent developmental and remodeling features.

overall_design: Human aortic tissue samples were obtained from 8 male infants with CoA and 6 age- and sex-matched controls younger than 1 year. Total RNA was isolated, and gene expression profiling was performed using whole human genome oligo microarrays (Agilent). Functional pathway, network, and upstream regulator analyses were conducted using Ingenuity Pathway Analysis (QIAGEN; version 24.0.2). Selected candidate genes were assessed by RT-qPCR in independent verification sets not included in the microarray analysis.

first: Isabell

last: Robl

first: Robert

last: Cesnjevar

first: Arif

last: Ekici

first: Steffen

last: Uebe

first: Pascal

last: Johann

first: Maria

last: Ramirez

first: Fabian

last: Fahlbusch

first: Julia

last: Moosmann


title: Plasma Exosomes Associated with Growth Divergence as in High-Density Cultured Grass Carp (Ctenopharyngodon idella): miRNA-Protein Profiling Reveals Cross-Tissue Communication Networks

city: Qingdao

first: Tengfei

last: Zhu

state: Shandong

address: Nanjing Road 106, Qingdao 266071, China

institute: Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences

summary: Grass carp (Ctenopharyngodon idella) is a major freshwater aquaculture species in China, but its growth is limited under intensive high-density farming. This study aimed to investigate the role of plasma exosomes in growth regulation by isolating and characterizing exosomes from fast- and slow-growing grass carp after nine months of culture. Exosomes showed typical morphology and expressed characteristic markers (CD63, CD81, TSG101). Small RNA sequencing identified 3325 miRNAs, with 177 highly abundant miRNAs differentially expressed: immune-related miRNAs were upregulated, while development-inhibitory miRNAs were downregulated in fast-growing fish. Target gene enrichment highlighted pathways in neural and skeletal development and amino acid metabolism. Integrative analysis across tissues revealed 26 miRNAs with coordinated expression patterns between plasma exosomes and brain, liver, or muscle, validated by qPCR. DIA proteomics quantified 4203 proteins, identifying 843 differentially enriched proteins linked to immune response, energy metabolism, and endoplasmic reticulum stress. Notably, TYMP was upregulated in muscle and exosomes, while several proteins (e.g., GYG2, BHMT) showed coordinated downregulation across tissues and exosomes in large fish. These results provide comprehensive evidence of exosome-mediated cross-tissue communication in teleosts and suggest plasma exosomal miRNAs and proteins as non-invasive biomarkers for growth performance in aquaculture.

overall_design: miRNA-seq profiling of exosomes isolated from the plasma of 10-month-old grass carp with significant differences in growth divergence

first: Zhipeng

last: Zheng

first: Hao

last: Chen

first: Yingying

last: Yu

first: Huayang

last: Guo

first: Baosuo

last: Liu

first: Kecheng

last: Zhang

first: Lin

last: Xian

first: Shuhui

first: Yang

first: Songlin

first: Dianchang


title: Chronic IL-1 exposure attenuates IL-1 response and alters gene expression regulation while maintaining therapeutic sensitivity in BCa cell lines

first: Nikki

last: Delk

overall_design: We performed RNA sequencing (RNA-seq) and differential gene expression analysis for the parental (MCF71, T47D1) cells treated acutely with vehicle control, 25ng/mL IL-1α or 25ng/mL IL-1β for 4 days and for the chronic IL-1 sublines (MCas1, MCbs1, T47Das1, T47Dbs1) grown in vehicle control only.

first: Rafah

last: Falah

first: Roopal

last: Dhar

first: Stephanie

last: Yamauchi

first: Monica

last: Bautista

first: Mohammad

last: Kanchwala

first: Liu Yan

last: Yan

first: Dinesh

last: Raju

first: Linyi

last: Xu

first: Kylah

last: Reliford

first: Afshan

last: Nawas

first: Samrah

last: Ali

first: Justin

last: Fang

first: Ola

last: Olaleye

first: Jyotsna

last: Tera

first: Rana

last: Abdelaziz

first: Reshmika

last: Kanakala

first: Aniketh

last: Sudungunta

first: Subhash

last: Eedarapali

first: Emmalee

last: Burr

first: Basir

last: Mansoor

first: Nicole

last: Roos

first: Sydney

last: Diep

first: Hiba

last: Afaq

first: Niranjana Rajesh

last: Rajesh

first: Saanvi

last: Manohar

first: Jennifer

last: Odikpo

first: Abhinav K.

last: Jain

first: Zhenyu

last: Xuan

first: Chao

last: Xing


title: Single-Cell RNA Sequencing of the Human Endometrium in Healthy Controls and Patients with Polycystic Ovary Syndrome

city: GuangZhou

first: Tengfei

last: Wang

state: GuangDong

address: No. 9 Jinsui Road, Tianhe District

institute: Guangzhou Women and Children's Medical Center

summary: Polycystic ovary syndrome (PCOS) is a common endocrine disorder affecting reproductive-aged women and is associated with endometrial dysfunction, including reduced receptivity, increased miscarriage risk, and elevated endometrial cancer risk. However, the cellular and molecular heterogeneity of the endometrium in PCOS patients remains poorly understood. In this study, we performed single-cell RNA sequencing (scRNA-seq) on endometrial biopsies obtained from healthy control women and PCOS patients. Endometrial samples were collected during the proliferative phase. We analyzed endometrial cell composition and transcriptional profiles at single-cell resolution. Our findings reveal PCOS-specific alterations in endometrial cell type composition, as well as cell-type-specific gene expression changes associated with inflammation, progesterone resistance, and extracellular matrix remodeling. These results provide a comprehensive cellular atlas of the PCOS endometrium and identify potential molecular targets for future therapeutic intervention.

overall_design: Endometrial biopsies were collected from healthy control women and PCOS patients during the proliferative phase of the menstrual cycle. Patients were diagnosed according to Rotterdam criteria. Fresh endometrial tissues were dissociated into single-cell suspensions using enzymatic digestion (collagenase I and DNase I). Viable cells were enriched and subjected to droplet-based single-cell RNA sequencing using the 10× Genomics Chromium platform. Libraries were sequenced on an Illumina NovaSeq 6000 platform. Raw sequencing data were processed using the Cell Ranger pipeline (version 7.0) for alignment to the human reference genome (GRCh38), barcode counting, and feature-barcode matrix generation. Downstream analysis was performed using Seurat (version 5.0), including quality control, normalization, dimensionality reduction, clustering, and differential expression analysis.

first: Siliang

last: Xu


title: Single-cell sequencing reveals NK cell dysregulation during chronic HIV infection and identifies transitional NK cell cytotoxicity related to HIV reservoir decay

city: Beijing

first: Jin-Wen

last: Song

state: Beijing

address: No. 100, West Fourth Ring Road, Fengtai District

institute: Beijing 302 Hospital

summary: We performed scRNA-seq on NK cells from HCs and PLWH before/after ART. We identified ten subsets, including IFN-responding (c7) and proliferating (c8, c9) cells that expand in untreated PLWH. Cytotoxicity of the transitional NK before ART correlated with subsequent HIV-DNA decline. Our findings reveal NK cell heterogeneity during HIV infection, informing NK-based immunotherapies.

overall_design:
This study used scRNA-seq, FACS, cytokine profiling, and viral DNA quantification to characterize NK cell heterogeneity and function in PLWH before and after ART compared with HCs.

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

first: Wen-Jing

last: Cao

first: Bao-Peng

last: Yang


title: Melanoma-derived exosomal miRNAs and keratinocyte-derived LL-37 define an epidermal–tumor arms race in melanoma

city: Bunkyo-Ku

first: Ge

last: Peng

state: Tokyo

address: 2-1-1 Hongo

institute: Juntendo University Graduate School of Medicine

summary: Melanoma progression involves dynamic interactions between tumor cells and the surrounding epidermal microenvironment. The cathelicidin antimicrobial peptide LL-37, expressed by keratinocytes, has been implicated in tumor-host defense; however, its transcriptomic impact on melanoma cells and its in vivo relevance remain incompletely characterized. Here, we performed bulk RNA sequencing of LL-37-treated A375 human melanoma cells in vitro and of tumor-bearing dorsal skin from K14CreCampf/f  (cKO) and wild type mice (WT) subjected to topical imiquimod stimulation in vivo, to elucidate the transcriptomic landscape underlying LL-37-mediated suppression of melanoma progression.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: In vitro, to investigate the transcriptomic effects of LL-37 on melanoma cells, A375 human melanoma cells were treated with LL-37 at a concentration of 80 μg/mL or left untreated as controls for 24 hours. Each condition was performed in biological triplicate (n = 3), yielding a total of six samples (SAMPLE-1 to SAMPLE-6) submitted for bulk RNA sequencing. Total RNA was extracted from each sample and subjected to library preparation and paired-end sequencing. In vivo, A syngeneic melanoma mouse model was established using K14Cre Campf/f (n=2) and wild type (n=2) mice. B16-F0-Luc melanoma cells (2 × 10⁵ cells in 200 µL of PBS) were injected intradermally into the dorsal skin on Day 1. From Day 15 to Day 21, 30 mg imiquimod cream (Beselna®, Mochida Pharmaceutical Co., Ltd., Tokyo, Japan) was applied daily to the dorsal skin of all mice.  On Day 25, one piece of tumor-bearing dorsal skin was dissected from each mouse, yielding four samples (SAMPLE-7 to SAMPLE-10) in total. RNA was extracted from all samples and subjected to RNA-Seq library preparation.

first: Quan

last: Sun

first: François

last: Niyonsaba


title: Nasal resident memory CD8 T cells adopt antiviral transcriptional programs during viral transmission

city: Atlanta

first: Mark

middle: Elliott

last: Williams

address: 201 Dowman Dr

institute: Emory University

summary: Tissue resident memory T cell populations play a critical role in host defense against respiratory viral infections by surveilling the respiratory tract and mounting rapid antiviral responses to their cognate antigens. While previous studies focused on lung resident memory T cells in the context of direct intranasal infection models, we utilize a natural respiratory virus transmission model to examine the transcriptional changes in antigen-specific nasal resident memory CD8 T cells during their initial response to infection. Here, we demonstrate that during respiratory virus transmission, nasal resident memory CD8 T cells adopt antiviral transcriptional programs denoted by expression of classical CD8 T cell activation and effector function genes, further supporting the development of upper respiratory tract targeting vaccination strategies.

overall_design: In the Sendai virus transmission model, contact mice were intranasally primed with PR8-SenNP and co-housed with Sendai-Luciferase infected index mice 35 days later (D35+0). IV- SenNP+ CD8+ T cells were FACS sorted from the nasal compartment of contact mice at both 3 (D35+3) and 6 (D35+6) days post exposure and scRNA-seq was performed using the 10X Genomics platform.

middle: E

first: Jacob

last: Kohlmeier

first: Sarah

last: Michalets


title: Persistent TOP1 cleavage complexes drive adaptive resistance to EGFR-targeted therapies in lung cancer

city: Toulouse

first: Olivier

last: Sordet

address: 2 Avenue Hubert Curien

department: CRCT

country: France

institute: INSERM

summary: Resistance to targeted cancer therapies often arises from drug-tolerant cells (DTCs), which survive treatment by entering a non-proliferative state. Over time, DTCs can acquire mutations that contribute to cell reproliferation, but how non-proliferating DTCs accumulate such mutations remains unclear. Here, we show that EGFR inhibition in EGFR-mutated lung cancer transiently downregulates tyrosyl-DNA phosphodiesterase 1 (TDP1), a repair enzyme that resolves abortive topoisomerase I cleavage complexes (TOP1ccs). In DTCs, elevated reactive oxygen species promote TOP1cc trapping, while TDP1 downregulation impairs their repair, driving TOP1cc accumulation, resistance mutation acquisition, and cell reproliferation. We further find that TDP1 expression is absent in approximately 25% of EGFR-mutated lung cancers. In TDP1-deficient cells, combining EGFR inhibition with at sublethal concentrations of topotecan, which further increases TOP1ccs, abolishes cell reproliferation. Together, these findings identify TOP1cc accumulation as a mechanism linking drug tolerance to a mutagenic program that drives adaptive resistance, and reveal TDP1 loss as a targetable vulnerability in EGFR-mutated lung cancers.

overall_design: RNA-seq experiments were performed in PC9 cells derived from a previously described subclonal line (Figarol et al., 2024: PMID: 38937474), with three replicate cultures per condition, generated by splitting cells from a common initial flask and subsequently cultured independently. TDP1 wild-type (WT) cells were analyzed under untreated (NT) conditions and following treatment with 1 µM erlotinib for 7 days (drug-tolerant cells, DTC) and 28 days (drug-tolerant expanded cells, DTEC). TDP1 knockout (KO2) PC9 cells were analyzed under untreated (NT) conditions.

first: Mathéa

last: Geraud

first: Agnese

last: Cristini

first: Maïna

last: Vienne


title: 3D organoids containing endothelial and neural cells generation by serial inductions of differentiation on human iPSC-derived embryoid bodies

city: Bethesda

first: Kory

last: Johnson

state: MD

address: 35/GF-127, 9000 Rockville Pike

department: DIR IT & Bioinformatics

institute: NINDS/NIH

summary: 3D brain organoids have been widely used as a tool to study human brain development and disorders. Although endothelial cells play important roles in the brain development and pathogenesis in neurological disorders, most 3D brain organoids lack inherent endothelial cells and need either the addition of endothelial cells or to be transplanted to animals to reconstitute such vascular structures, likely missing the developmental interactions of endothelial cells and other cells in the human brain. In order to reconstitute a 3D organoid mimicking the in vivo neural and endothelial cells development, we cultured iPSC-derived embryoid bodies in sequentially applied endothelial and neuronal induction media along with Matrigel embedding. The resulting 3D organoid consists of both neural cells and endothelial cells with vascular like structures, as determined by immunostaining. With scRNA-Seq analysis, the brain organoid was confirmed to contain neural cell types similar with human brains, including a variety of excitatory and inhibitory neurons and glia. Furthermore, when compared with traditional cerebral organoids without endothelial cells using RNA-Seq analysis, the endothelial containing neural organoids (EC-neural organoids) showed difference in gene profiles and favored angiogenesis and vasculogenesis. Of the differentially expressed genes, KRBA2 expression was found higher in neural cells and its inhibition by siRNA treatment resulted in decreased transcriptions of a variety of genes such as neuronal differentiation specific genes but not in genes specific to pluripotent stem cells such as OCT4. The EC-neural organoids also express receptors to SARS-CoV-2 similar to human brains. This 3D model provides a useful tool to study the interactions of endothelial cells and neural cells in the brain development and neural infectious disorders where endothelial cells and pericytes play pivotal roles.

overall_design: Bulk RNA-Seq profiling of six human blood-based iPSC derived 3D organoid sample pairs representing endothelial containing neural organoids (E) and traditional cerebral organoids (N).

first: Tongguang

first: Anna

last: Bagnell

first: Valerie

last: McDonald

first: Benjamin

middle: D

last: Gastfriend

first: Joseph

last: Steiner

first: Abdel

middle: G

last: Elkahloun

first: Rebekah

last: Langston

last: Cookson

first: Avindra

last: Nath