title: Adipose tissue-derived microRNAs as epigenetic modulators of type 2 diabetes [DPDR_RNASEQ]

first: Heike

last: Vogel

summary: Diabetes-resistant and diabetes-prone female New Zealand Obese mice were assessed based on liver fat content and early blood glucose concentrations at 10 weeks of age before the onset of T2D. Transcriptome analysis of gonadal white adipose tissue revealed genes potentially regulated by epigenetic mechanisms such as miRNAs or DNA methylation.

overall_design: RNA-sequencing was performed in gonadal white adipose tissue of 15 diabetes resistant (DR) and 15 diabetes prone (DP) animals, DR animals are healthy animals and are considered as control group.

first: Annette


title: Adipose tissue-derived microRNAs as epigenetic modulators of type 2 diabetes [3T3_RNASeq]

status: Public on Dec 17 2025

city: Nuthetal

state: BRB

address: Arthur-Scheunert-Allee 114-116

department: Department of Experimental Diabetology

country: Germany

institute: German Institute of Human Nutrition Potsdam-Rehbruecke

type: Expression profiling by high throughput sequencing

summary: Diabetes-resistant and diabetes-prone female New Zealand Obese mice were assessed based on liver fat content and early blood glucose concentrations at 10 weeks of age before the onset of T2D. Analysis of the microRNA profile in gonadal white adipose tissue revealed miRNA-335-5p, which could contribute to systemic metabolic changes associated with the risk of developing T2D. Treatment of miR-335-5p mimic in 3T3-L1 cells led to elevated triglyceride accumulation on day 3 of adipogenesis. To elucidate the molecular mechanisms underlying the increased triglyceride accumulation, RNA sequencing was conducted at days 3 and 6 of cell differentiation. This analysis showed alterations in genes involved in lipid metabolism, glycolytic enzymes and ECM remodeling.

overall_design: Lipofection of non-targeting mimic or miR-335-5p mimic in 3T3-L1 fibroblasts. Additional differentiation of cells in mature adipocytes and analysis of trancriptome profile.

last: Schürmann

first: Neele

last: Haacke

first: Ratika

last: Sehgal

first: Markus

last: Jähnert


title: OR7A10 GPCR engineering boosts CAR-NK therapy against solid tumors [scRNA-Seq]

city: West Haven

first: Sidi

last: Chen

state: CT

address: 850 West Campus Drive

country: USA

institute: Yale University

summary: Chimeric antigen receptor (CAR)-natural killer (NK) cell therapies hold promise for solid tumors but remain limited by poor tumor infiltration, persistence, and resistance within the tumor microenvironment (TME). To identify gain-of-function (GOF) targets that enhance CAR-NK efficacy, we performed an unbiased in vivo Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) activation (CRISPRa) screen, followed by a barcoded targeted in vivo open reading frame (ORF) screen in primary human CAR-NK cells. We identified, and robustly validated OR7A10, a G protein-coupled receptor (GPCR), as the top candidate. Engineering CAR-NKs with OR7A10 cDNA, a CRISPR-independent method with simple manufacturing strategy, enhanced proliferation, activation, degranulation, cytokine production, death ligand expression, chemokine receptor expression, cytotoxicity, persistence, metabolic fitness, and TME resistance, while reducing exhaustion in primary human NK cells derived from multiple peripheral blood and cord blood donors. OR7A10-GOF CAR-NKs displayed robust in vivo efficacy across multiple solid tumor models, achieving a 100% complete response in an orthotopic breast cancer model with long term tumor control and survival benefit. These findings establish OR7A10-engineered CAR-NKs as a highly potent and scalable off-the-shelf therapeutic for solid tumors.

overall_design: Single-cell transcriptomics was performed by 10X Genomics sequencing on OR7A10-OE and OR7A10(STOP) control CAR-PBNK-hIL-15 cells that were extracted from in vivo xenograft models of HT29-GL in NSG mice after 3 days.

first: Paul

last: Renauer

first: Luojia

last: Yang

first: Kaiyuan

last: Tang


title: Anti-HER2/neu TCR-T Cells in Action: Linking Transcriptional Signatures, Secretomics, and In Vivo Tumor Suppression

city: Novosibirsk

first: Saleh

last: Alrhmoun

address: Yadrintscvskaya street 14

country: Russia

institute: Federal State Budgetary Scientific Institution Research Institute of Fundamental and Clinical Immunology

summary: We performed single-cell RNA sequencing using the BD Rhapsody platform to profile HER2/neu-specific TCR-engineered human T cells following antigen stimulation. TCR-T cells and non-transduced control T cells were analyzed after co-culture with HER2/neu-expressing tumor cells.

overall_design: Peripheral blood CD3+ T cells from healthy HLA-A*02:01 donors were isolated and activated ex vivo. Cells were transduced with a lentiviral vector encoding a HER2/neu-specific TCR or kept non-transduced (LV-neg). After co-culture with HER2/neu-expressing tumor cells for 16–18 hours, TCR-T and LV-neg cells were stained with SampleTag and processed using the BD Rhapsody single-cell workflow.

first: Roman

last: Perik-Zavodski


title: Clinical and Molecular Characterization of KRAS Mutations in Renal Cell Carcinoma

city: New York

first: Fengshen

last: Kuo

state: New York

address: 1275 York Ave

institute: Memorial Sloan Kettering Cancer Center

summary: KRAS mutations in renal cell carcinoma (RCC) are rare and are associated with the histologic subtype "papillary renal neoplasm with reverse polarity" (PRNRP). Despite this association, the broader clinical and molecular implications of KRAS mutation in RCC are not well understood. This study aimed to characterize the clinical and molecular features of KRAS-mutated RCC. KRAS-mutant RCC patients were identified within the Memorial Sloan Kettering-Integrated Mutation Profiling of Actionable Cancer Targets (MSK-IMPACT) and The Cancer Genome Atlas Kidney Renal Papillary Cell Carcinoma (TCGA-KIRP) repository. Fraction and allele-specific copy number estimates from tumor sequencing (FACETS) was performed to obtain copy number alterations. Available samples were used for immunohistochemistry and RNA-sequencing analysis. Seventeen patients were included. Three distinct KRAS-mutant RCC subtypes were identified: KRAS-mutant PRCC (35%), KRAS-mutant URCC (35%), and PRNRP (29%). Seven patients (41%) had metastatic disease; none were PRNRP. RNAseq-based deconvolution analysis revealed that PRNRP had enrichment in distal nephron components, whereas KRAS-mutant PRCC was enriched in proximal tubule cells (p = 0.02). IHC staining of L1CAM was positive in PRNRP but negative in KRAS-mutant PRCC, supporting their distinct cell-of-origin phenotypes. This study is limited by its cohort size, which influences the availability of tissue samples. PRNRP represents a distinct KRAS-mutant RCC subtype with unique metabolic and genomic features linked to its distal nephron origin. This contrasts with the genomic complexity and aggressive clinical behavior observed in KRAS-mutant PRCC and URCC, highlighting the need for subtype-specific diagnostic criteria and therapeutic strategies.

overall_design:
RNA-seq profiling of primary frozen tumor samples from renal cell carcinoma with KRAS mutations. 3 different histology subtypes present, all had at least 1 representative sample.

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

first: Andrea

last: Lopez Sanmiguel

first: Abraham

middle: A

last: Hakimi

first: Yash

middle: S

last: Khandwala

first: Mark

last: Dawidek

first: Daniel

last: Barbakoff

first: Lina

last: Posada Calderon

first: Maria

middle: I

last: Carlo

first: Jonathan

last: Coleman

first: Satish

middle: K

last: Tickoo

first: Ed

last: Reznik

first: Ying-Bei

first: Victor

middle: E

last: Reuter

last: Russo


title: Deep exploration of the TCR CDR3β repertoire specific for viral CD4 T cell epitopes inside the circulating T cell repertoire

city: Gif-sur-Yvette

first: Stephane

last: Hua

address: Porte Nord RD36

country: France

institute: Commissariat à l'Energie Atomique et aux Energies Renouvelables

summary: This study provides an in-depth analysis of the diversity of the CD4 TCR CDR3β repertoire specific to Influenza A (HA) and Epstein-Barr virus (EBNA) epitopes. Epitope-specific CD4 T cells from 13 healthy donors were enriched using a short-term culture step, isolated based on activation markers, and sequenced for their TCR CDR3β region using high-throughput sequencing. The frequency of each clonotype were then identified within the complete circulating CD4 T-cell CDR3β repertoire. For both epitopes, the clonotype distribution was markedly skewed, with a small number of highly expanded clones comprising approximately 60% of the repertoire, alongside numerous low-frequency clonotypes. VJ gene usage and motif preferences differed between the two peptides, highlighting epitope-specific TCR selectivity. The response was predominantly composed of private T-cell clonotypes. The proportion of public clonotypes can increase among donors sharing HLA class II molecules and reveals in HLA-unrelated donors the level of TCR promiscuity. Overall, our data demonstrate that CD4 T-cell responses to these viral epitopes are polyclonal and highly personalized. The modest overlap of clonotypes between donors, coupled with a long tail of low-frequency clones, suggests that the full diversity of the epitope-specific T-cell repertoire is likely broader than previously estimated.

overall_design: TCRseq of total and specific CD4 T cells

first: Gautier

last: Lhomme

first: Rémi

last: Giraudet

first: Valéria

last: Porcheddu

first: Evelyne

last: Correia

first: Robert

last: Olaso

first: Stéphane

first: Bernard

last: Maillère


title: OR7A10 GPCR engineering boosts CAR-NK therapy against solid tumors [Primary Screen]

first: Sidi

last: Chen

overall_design: α-HER2-CAR-NK92 cell were transduced with dCas9-VP64-Blast and MS2-P65-HSF1-Hygro (Addgene)  at MOI < 1 and selected with Hygromycin and Blastcidin for 5-7 days. After complete selection, 1.8e8 CAR-NK92 cells were transduced with the sgRNA library (Addgene) at MOI = 0.2 (0.2 infectivity * 1.8e8 cells / 70,290 sgRNAs = 512x coverage). After 7 days of selection with Zeocin, > 4e7 Library-infected CAR-NK92 cells were maintained in culture (4e7 cells / 70,290 sgRNAs = 569x, although the coverage was limited by the bottleneck of the smaller in the process, e.g. 512x coverage). Eight-to-twelve-week-old female NSG mice were inoculated with 1e6 HT29-GL cells through subcutaneous injection. On day 8, 5e6 library-infected CAR-NK92 cells were adoptively transferred into each tumor-bearing mouse via intravenous injection (5e6 / 70,290 sgRNAs = 71x coverage). To support CAR-NK92 cell activity, mice received daily intraperitoneal injections of 2.5 μg human IL-2 beginning on the day of NK cell transfer. On 13-day post-transfer, mice were euthanized, and tumors were harvested for the subsequent experiments.

first: Paul

last: Renauer

first: Luojia

last: Yang

first: Kaiyuan

last: Tang


title: Temporal Dynamics in Murine Cardiac Transcriptome following Myocardial Infarction

city: Louisville

first: Richa

last: Singhal

state: KY

address: 580 S Preston Street, Baxter II Building, Office 321B

department: Medicine

institute: University of Louisville

summary: Myocardial infarction (MI) is a leading cause of heart failure with reduced ejection fraction. To overcome limitations of prior studies restricted to single timepoints, sexes, or partial tissue sampling, we generated a comprehensive, sex-inclusive, time-resolved transcriptional resource of the murine heart after non-reperfused MI. Male and female C57BL/6J mice were analyzed at baseline and 1, 4, 7, and 28 days post-MI, with ventricular dilation confirmed by echocardiography. Whole-heart profiling, including infarct and scar regions, enables detailed study of fibrotic and inflammatory processes. This dataset provides a rigorous community resource for investigating cardiac remodeling after MI.

overall_design: Experimental design leveraged key/common timepoints and included both sexes with three biological replicates in each group. 15–20-week-old male and female C57BL/6J mice were subjected to no intervention (Day 0) or to non-reperfused myocardial infarction (MI) for 1, 4, 7, or 28 days. Echocardiography was performed before tissue harvest to confirm ventricular dilation. Harvested tissue was processed, snap frozen, and shipped for scRNA flex assay.

first: Steven

middle: P

last: Jones


title: Persistent and Dose-Dependent Neural and Metabolic Gene Expression Changes Induced by Transient Citalopram Exposure in Zebrafish

city: Bozeman

first: Christa

last: Merzdorf

state: Montana

address: 109 Lewis Hall

department: MCB

institute: Montana State University

summary: Citalopram, a common selective serotonin reuptake inhibitor (SSRI), has been increasingly detected in aquatic environments due to ineffective removal and improper disposal. Although developmental exposure to SSRIs is linked to neurotoxicity, little is known about the persistence of gene expression alterations following limited exposure periods. Zebrafish embryos were exposed from 2 to 24 hours post-fertilization (hpf) at concentrations of citalopram hydrobromide spanning surface water to therapeutic serum levels (0.03, 0.9, 50, and 250 µg/L), followed by removal of the citalopram and development until 48 hpf. Whole-embryo RNA sequencing at 48 hpf revealed a non-linear dose–response wherein the lowest dose resulted in the induction of the highest number of differentially expressed genes (DEGs). Gene set enrichment analyses (GSEA) and overrepresentation analyses (ORA) showed that 0.03 µg/L citalopram caused upregulation of metabolic and developmental pathway genes, but suppressed synaptic membrane genes, whereas 0.9 µg/L resulted in strong downregulation of key neurotransmitter receptors. At 50 µg/L, genes linked to oxidative stress (glutathione metabolism and ferroptosis) were upregulated, and at 250 µg/L, stress and apoptotic processes were increased, while glutamate receptor genes were repressed. All four citalopram doses suggested synaptic and neurotransmitter alterations, implying that persistent neurodevelopmental impacts resulted from a limited early window of exposure. These data highlight that transient, low-level SSRI exposures shape long-term embryonic gene expression.

overall_design: Zebrafish embryos were exposed to one of the following conditions: Citalopram Hydrobromide 0.03 ug/L, 0.9 ug/L, 50 ug/L, and 250 ug/L. Citalopram exposure occurred from 0 to 24 hpf in zebrafish embryos, embryos were washed at 24hpf and allowed to develop in non-citalopram solution until 48 hpf. At 48hpf, 50 embryos were sample were harvested for total RNA, cDNA library prep, and RNAseq.

first: Ryan

last: North

first: Gwendolyn

last: Cooper

first: Lucas

last: Mears

first: Brian

last: Bothner

first: Mensur

last: Dlakić


title: OR7A10 GPCR engineering boosts CAR-NK therapy against solid tumors [mini screen]

overall_design: This experimental data is a primary human CAR-NK barcoded ORF-UMI mini-screen. An ORF library was generated for the top 35 gene targets (cDNA length ≤ 1 kb) from the initial CRISPRa screen, along with five fluorescent reporter genes as null controls. The ORF library was synthesized as individual eBlocks (IDT), pooled at equimolar ratios, and amplified with primers containing four-nucleotide random barcodes (UMIs; NNNN) to introduce molecular redundancy targeting the same gene. The ORF expression vector plasmid was bought from Addgene (#145026). The barcoded ORF library was pool-cloned into the expression vector using Gibson assembly.  Primary human peripheral blood NK cells from two healthy donors were first transduced with HER2-CAR lentivirus and then with the ORF library lentivirus at an MOI of ~0.2. A total of 20 million library-transduced CAR-NK cells were injected into each HT29 tumor-bearing mouse (n = 5 mice for Donor 0957 and n = 3 for Donor 0958 for each time point). Genomic DNA was extracted from tumors at day 3 and 6 post-treatment, as well as from pre-injection cells, and subjected to NGS to quantify ORF and UMI barcode representations.  Note that each set of fastq files is demultiplexed by the reverse


title: A phase II study of sitravatinib combined with tislelizumab plus docetaxel for acquired resistance to PD-(L)1 in patients with advanced/metastatic non-small cell lung cancer

city: Chengdu

first: Panwen

last: Tian

address: No. 37 Guoxue Lane, Wuhou District

country: China

institute: West China Hospital

summary: In this phase Ⅱ study, 13 patients with stage III/Ⅳ immune checkpoint inhibitors (ICIs) - acquired resistant non-small cell lung cancer (NSCLC) were treated with tislelizumab, sitravatinib, and docetaxel. The primary endpoint is a 6-month progression-free survival (PFS) rate. Although the target enrollment was not reached, the 6-month PFS rate among the enrolled patients was 58.9% (95% CI 0.234 - 0.825), with a median PFS of 7.589 months (95% CI 1.873 - 14.423) and a median OS of 17.150 months (95% CI 1.873 - not reached). The ORR was 58.3% (7 of 12 patients, 1 not evaluable), and the DCR was 100% (12 of 12 patients). Following treatment with sitravatinib, T-cell diversity (+0.435, p = 0.5) and the PSI of CD4⁺ T cells tend to increase (+21.948, p = 0.8438), whereas the PSI of CD8+ T cells declines (-174.16, p = 0.0938). High CD4⁺ T cells ΔPSI (>40) was associated with a strong trend of longer PFS (14.400 vs 7.6 months, p = 0.0499). In conclusion, sitravatinib combination therapy demonstrated promising clinical benefit and manageable safety in NSCLC patients with acquired resistance to ICIs.

overall_design: Peripheral blood samples were collected to perform TCR sequencing from patients at two time points: prior to the initiation of treatment (cycle 1, day 1 [C1D1], C1D1_Plasma group) and on the first day of the third treatment cycle (C3D1, C3D1_Plasma group). Additionally, tumor tissue samples (formalin-fixed, paraffin-embedded, FFPE) were also collected from patients in two reference groups: before immunotherapy (treatment-naïve group) and the ICI-resistant group (C1D1 ICI-PD group).

first: Yalun

last: Li

first: Jin

last: Zhou

first: Hua

last: Xie

first: Li

last: Jiang

first: Zonglian

last: Gong

first: Ke

last: Wang

first: Yan

last: Zhang

first: Weimin


title: Lactate Is a Metabolic–Epigenetic Signal That Links HIIT to miRNA-Centered Remodeling of the Skeletal-Muscle Methylome and Transcriptome [Methylation BeadChip]

city: Budapest

first: Zsolt

last: Radák

address: Budapest, Alkotás u. 42-48, 1123

department: Research Center for Molecular Exercise Science

country: Hungary

institute: University of sports science, Hungary

summary: Lactate, a major exercise-derived metabolite, has been proposed to couple cellular metabolism to gene regulation, yet its direct impact on skeletal muscle remains unclear. Male mice underwent six-week interventions (Control, lactate, HIIT, MCT1/2 inhibition, or HIIT+inhibition). We profiled gastrocnemius DNA methylation, mRNA-seq and miRNA-seq, and assessed signaling proteins, metabolites, and running performance. Lactate and HIIT each induced broad, site-specific remodeling of the methylome and transcriptome with substantial overlap at promoter CpGs and among DEGs. Promoter methylation changes showed weak coupling to steady-state mRNA, whereas integrative analyses revealed robust anti-directional miRNA–mRNA networks and enriched for chromatin/epigenetic regulators, identifying a lactate-driven miRNA axis as a proximate regulator of transcriptional output. At the protein level, lactate selectively increased TET2 and DNMT3A and activated PAX7, VEGF, and AKT–S6 signaling, consistent with integrative miRNA–mRNA findings. HIIT increased TET1/2 and DNMT3A with DNMT3B reduction and uniquely enhanced mitochondrial/antioxidant signaling. Blocking MCT1/2 abrogated HIIT-induced methylome and miRNA remodeling and blunted transcriptomic and protein adaptation, demonstrating that intact lactate flux is required for exercise-evoked epigenetic and transcriptomic reprogramming. Despite molecular convergence, chronic lactate did not improve running performance, indicating that lactate is necessary but not sufficient for the full physiological adaptation of training. These findings position a lactate–miRNA axis linking metabolic perturbation to epigenetic and transcriptional remodeling in skeletal muscle.

overall_design: Genome-wide DNA methylation profiling (Illumina Mouse Methylation BeadChip ) of gastrocnemius muscle from male BALB/c mice after 6-week interventions. Groups: Control (PBS), Lactate administration (500 mg/kg i.p.), High-intensity interval training (HIIT, treadmill protocol), MCT1/2 inhibitor (AR-C155858, i.p.), and HIIT + inhibitor.

first: Lei

first: Radak

last: Zsolt


title: Lactate Is a Metabolic–Epigenetic Signal That Links HIIT to miRNA-Centered Remodeling of the Skeletal-Muscle Methylome and Transcriptome

type: Non-coding RNA profiling by high throughput sequencing

overall_design: Small RNA sequencing of gastrocnemius muscle from male BALB/c mice (~2 months old) after 6-week interventions. Groups: Control (PBS), Lactate administration (500 mg/kg i.p.), High-intensity interval training (HIIT, treadmill protocol), MCT1/2 inhibitor (AR-C155858, i.p.), and HIIT + inhibitor.


title: Gut microbiota promote immune tolerance at the maternal-fetal interface

first: Julia

last: Brown

address: 413 E 69th Street, 1252A

institute: Weill Cornell Medicine

summary: Immune tolerance at the maternal-fetal interface is required for fetal development. Excessive maternal interferon gamma (IFNγ) and interleukin-17 (IL-17) is linked to pregnancy complications, but the regulation of maternal IFNγ and IL-17 at the maternal-fetal interface (MFI) is poorly understood. Here we demonstrate a gut-placenta immune axis in pregnant mice in which the absence or perturbation of gut microbiota dysregulates maternal IFNγ and IL-17 responses at the MFI, resulting in fetal resorption. Microbiota-dependent tryptophan derivatives suppress IFNγ+ and IL-17+ T cells at the MFI by priming myeloid-derived suppressor cells (MDSCs) and gut-derived RORγt+ Tregs, respectively. The tryptophan derivative indole-3-carbinol, or tryptophan-metabolizing Lactobacillus murinus, rebalances the T cell response at the MFI and reduces fetal resorption in germ-free mice. Furthermore, MDSCs, RORγt+ Tregs, and microbiota-dependent tryptophan derivatives are dysregulated at the MFI in human recurrent miscarriage cases. Together, our findings identify microbiota-dependent immune tolerance mechanisms that promote fetal development.

overall_design: scRNA-seq of CD45+ cells from blood, placenta, and uterus of E16.5 pregnant SPF and germ-free mice

first: Mohammed

last: Amir

first: Shui

last: Yu

first: Daniel

last: Wong

first: Jinghua

last: Gu

first: Uthra

last: Balaji

first: Christopher

last: Parkhurst

first: Seunghee

last: Hong

first: Lucy

middle: R

last: Hart

first: Hannah

middle: C

last: Carrow

first: Mamadou

last: Bah

first: Aparna

last: Ananthanarayanan

first: Katherine

middle: Z

last: Sanidad

first: Mengze

last: Lyu

first: Anisa

last: Siddikova

first: Marina

last: Lima Silva Santos

first: Inna

last: Serganova

first: Gretchen

last: Diehl

first: Josef

last: Anrather

first: Naohiro

last: Inohara

first: Gregory

middle: F

last: Sonnenberg

first: Virginia

last: Pascual

first: Melody

middle: Y

last: Zeng


title: OR7A10 GPCR engineering boosts CAR-NK therapy against solid tumors

first: Sidi

last: Chen

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

overall_design: Refer to individual Series


title: ALFQ Adjuvanted HIV-1 Envelope Protein Vaccination Elicits Durable Functional Antibody and Cellular Responses in Nonhuman Primates

city: Silver Spring

first: Rasmi

last: Thomas

state: MD

address: 503 Robert Grant Avenue

department: MHRP

institute: Walter Reed Army Institute of Research

summary: Adjuvants play an important role in modulating antigen-specific immune responses. We conducted a comparative adjuvant immunogenicity study in Rhesus macaques using HIV-1 subtype B gp120 envelope protein, B.63521 formulated with aluminum hydroxide gel (AH), or a family of liposomal adjuvants known as Army Liposome Formulation (ALF) to determine their effect on immune responses. ALF comprises saturated phospholipids, cholesterol, and an immunostimulant, monophosphoryl lipid A. Inclusion of a second immunostimulant, a saponin QS-21, or adsorption of the antigen to AH, followed by the addition of ALF generates ALFQ and ALFA, respectively, while the presence of both immunostimulants generates ALFQA. Priming with canarypox vector ALVAC, followed by boosting with ALVAC and gp120 formulated with AH, ALFA, ALFQ or ALFQA resulted in the QS-21-containing liposomal vaccine formulations (ALFQ and ALFQA) outperforming AH-based vaccine formulations (AH, ALFA) by inducing (i) binding antibodies of higher magnitude, durability, and avidity; (ii) higher neutralizing and Fc effector functional antibodies; (iii) higher frequency of durable antigen-specific plasma cells in the bone marrow; (iv) robust Env-specific polyfunctional CD4+ and CD8+ T cell responses and IL-21 producing T follicular helper cells. Transcriptomic analyses revealed that ALFQ and ALFQA vaccine formulations upregulated antiviral and innate immune pathways, including interferon signaling genes. These findings highlight that ALFQ is a highly potent adjuvant that facilitates multifaceted strong durable immune responses in nonhuman primates. Based on these data, an HIV vaccine containing B.63521 and CRF01_AE proteins formulated in ALFQ is currently being evaluated for safety and immunogenicity in a phase 1 clinical trial (NCT05423418).

overall_design: Bulk RNA-seq profiling of peripheral blood cells at week 12 and week 24 from Rhesus macaques given different adjuvants.

first: Daina

last: Eiser

first: Gautam

last: Kundu

first: Jiae

last: Kim

first: Mangala

last: Rao


title: Tissue Block-Resolved Spatiotemporal Transcriptomic Atlas of Human Fetal Brainstem Reveals Gene Modules and Paradigms Linked to Neurological Disorders

city: Jinan

first: ChengXin

last: Liu

state: Shandong

address: No. 16766, Jingshi Road

department: Cheeloo College of Medicine

institute: Shandong University

summary: The brainstem serves as a critical structural and functional hub connecting cerebral and spinal regions, yet its gene regulatory dynamics during fetal development remain poorly characterized. This study employed RNA-seq to map spatiotemporal transcriptomes across 107 tissue blocks from 18 human fetal brainstems (gestational weeks 9-33). Weighted gene co-expression network analysis (WGCNA) identified 22 functionally annotated modules. We quantitatively assessed their spatiotemporal activity gradients across developmental stages and anatomical subdomains, systematically classifying genes with significant temporal trajectories by phase-specific signatures. Crucially, we validated expression patterns of neurodevelopmental disorder-associated genes (e.g., Parkinson's, ALS, schizophrenia) within fetal brainstem tissues. Our integrated approach constructs a developmental transcriptomic profile, revealing stage-specific regulatory networks and dynamic transcriptional trajectories governing ontogeny. This work advances understanding of brainstem development and provides a foundational resource for neurological disorder research.

overall_design: RNA-seq profiling of 107 tissue blocks from distinct anatomical regions of 18 human fetal brainstem samples across gestational weeks 9 to 33.

first: Chenxi

last: Sun

first: Shizhou

first: Jianfen

last: Jiao


title: Procyanidin B1 Conducted Transcriptional Reprogramming and Anti-inflammatory Response in Chicken HD11 Cells Through Transcription Factor STAT2 and HIF1A

city: Jingzhou

first: Tinghua

last: Huang

address: Jingmi Road #266

institute: Yangtze University

summary: We used LPS-stimulated chicken HD11 macrophage-like cell as a model to identify the key transcription factors involved in transcriptome regulation responsible for Procyanidin B1 treatment. RNA-seq identified 1,384 transcripts significantly differentially expressed between the Procyanidin B1 treated group and the control group, and 696 transcripts significantly differentially expressed between LPS+Procyanidin B1 and LPS treated group (FDR < 0.05, FDR > 1.5). Bioinformatic analysis revealed that five transcription factors, FOSL1::JUND, CREB1, ZNF467, STAT2, and HIF1A were candidate genes for transcriptome regulation in Procyanidin B1 treated HD11 cells.

overall_design: The samples for RNA-seq experiment were collected from four treatment groups with four replicates for each group, the Procyanidin B1, Procyanidin B1+LPS, LPS and Control.

first: Min

last: Yao


title: Synthetic DNA co-immunization with vaccine-aligned common consensus nucleoprotein and hemagglutinin protects mice against lethal influenza infection with a single immunization

city: Philadelphia

first: Priyankara

middle: J

last: Wickramasinghe

state: PA

address: 3601 Spruce Street

department: Bioinformatics

institute: The Wistar Institute

summary: There is an urgent need for influenza vaccine strategies that enhance protection against influenza virus drift and across different subtypes. The conserved viral nucleoprotein (NP) is the most abundant viral protein during replication, and a target for broadly protective cellular immune responses. Guided by annual WHO-recommended seasonal vaccine strains, we engineered synthetic DNA vaccine candidates encoding vaccine-aligned common consensus (VACC) immunogens designed to represent the immune diversity of seasonal H1N1 and H3N2 virus NP proteins (pVACC-NPH1; pVACC-NPH3). Both pVACC-NPH1 and pVACC-NPH3 DNA vaccines induced robust cellular immune responses in mice, including the induction of durable responses. Immunization with a single dose of either DNA vaccine 14 days prior to lethal A/California/2009 H1N1 virus challenge provided protection against mortality. Single dose co-administration of pVACC-NPH3 with an HA-expressing DNA vaccine (pHAH1) and plasmid-encoded adjuvant pIL-12 afforded improved protection against morbidity and mortality in a high-dose challenge model. These data highlight the potential of heterologous cellular immunity induced by engineered NP immunogens to complement HA-based approaches to significantly improve challenge outcomes.

overall_design:
Gene expression analysis was eprformed to understand the impact of novel synthetic DNA vaccines on lung transcriptomic signatures in the context of infection.
We evaluated gene expression in mice receiving DNA vaccines targeting the influenza hemagglutinin (HA) protein and the nucleoprotein (NP), called pHAH1 and pVACC-NPH3, respectively.
Total RNA was extracted from FFPE lung scrolls obtained from mock (unvaccinated, uninfected), naïve (unvaccinated, infected), and the two groups receiving synthetic DNA vaccines (vaccinated, infected).

first: Ami

last: Patel

first: Ebony

last: Gary


title: Urinary Clusterin as a Biomarker of Human Kidney Disease Progression and Response to the Endothelin Receptor Antagonist Atrasentan: An Exploratory Analysis from the SONAR Trail

city: Ann Arbor

first: Jennifer

last: Harder

state: Michigan

address: 1150 W. Medical Center Drive

department: Division of Nephrology

institute: The University of Michigan

summary: The endothelin receptor antagonist atrasentan improved kidney outcomes in the SONAR trial for type 2 diabetes and chronic kidney disease (NCT01858532), though individual responses varied. To identify molecular biomarkers of atrasentan response and outcome, we conducted a nested case-control proteomics study (N=180) within the SONAR trial population and identified urinary clusterin (uCLU) as the top candidate. Transcriptomic analyses of human kidney biopsies at tissue and single cell level from independent cohorts revealed higher CLU mRNA levels associated with worse kidney function and outcomes. An endothelin signaling activation score derived from pathway genes was reduced by atrasentan in mice with diabetic kidney disease. In the SONAR trial (N=3,060), higher uCLU predicted worse outcomes, while atrasentan reduced uCLU by 42.6% over six weeks. Early uCLU changes independently predict improved kidney outcomes. In summary, uCLU is associated with kidney disease progression and response to atrasentan treatment, supporting its potential as a pharmacodynamic biomarker to target therapy.

overall_design: Bulk RNAseq data obtained from kidney glomerular tissues from wild type (n=5), BTBR ob/ob mice with 6 wk of saline (n=5) or atrasentan (n=7) treatment, respectively

first: Wenjun

last: Ju

first: Viji

last: Nair

first: Priya

last: Vart

first: J

middle: D

last: Smeijer

first: Kelly

middle: L

last: Hudkins

first: Maria

last: Larkina

first: Paul

last: Perco

first: Fred

last: Burdet

first: Kerby

last: Shedden

first: Michael

last: Hwang

first: Edmond

last: Lee

first: Christopher

last: O’Connor

first: John

last: Hartman

first: Markus

last: Bitzer

first: Mark

last: Ibberson

first: Kevin

last: Duffin

last: Gomez

first: Charles

last: Alpers

first: Matthias

last: Kretzler

first: Hiddo

last: Heerspink


title: Experimentally induced myocardial infarction in mice - RNA Sequencing of kidneys

city: Freiburg

first: Diana

last: Lindner

address: Hugstetter Straße 55

department: University Heart Center Freiburg-Bad Krozingen

institute: University Hospital Freiburg

summary: To induce myocardial infarction, ligation of left anterior descending (LAD) coronary artery was performed for 5d and 28d. Kidneys were collected from MI mice and sham-operated mice (5d).

overall_design: Kidneys from mice with myocardial infarction (5d and 28d post-MI) were compared to sham operated mice (5d post-MI)

first: Lindner

last: Diana


title: Experimentally induced myocardial infarction in mice - RNA Sequencing of sham left ventricular tissue and infarct zones

summary: To induce myocardial infarction, ligation of left anterior descending (LAD) coronary artery was performed for 5d. After 5d heart tisse was collected from the infarct zone of MI-mice and left ventricular tissue of sham operated mice.

overall_design: LAD ligation was performed in mice for 5d to experimentally induce myocardial infarction (MI). Mice without LAD ligation were used as controls (sham operated). For MI mice, RNA was extracted from the infarct zone and compared to heart tisse from sham-operated mice.


title: Stromal Cells from Endometriosis Patients Reflect Lesion Type-Specific Heterogeneity

city: Zurich

first: Genome

last: Informatics

address: Winterthurerstrasse 190

department: Functional Genomics Center Zurich (FGCZ)

country: Switzerland

institute: ETH ZURICH / University of Zurich

summary: Endometriosis shows significant lesion heterogeneity, but pathophysiological mechanisms leading to differences in clinical presentation are poorly understood. Here we utilized primary stromal cells from different types of endometriotic lesions to better understand the molecular mechanisms that lead to endometriosis heterogeneity. For this project, endometrial stromal cells (ESCs) were obtained from eutopic endometrium (EU), endometrioma (OMA), superficial (SF) and deep (DE) endometriosis lesions and analyzed in vitro for their behavior regarding proliferation, migration, and contractility. RNA sequencing was performed to explore the molecular mechanism underlying the observed changes.

overall_design: RNASeq of endometrial stromal cells from eutopic endometrium (C), deep endometriosis (DE), endometrioma (OMA), and superficial endometriosis (SF).

first: Marianne

last: Spalinger

first: Daniel

last: Rodriguez Gutierrez

first: Alina

last: Astourian

first: Valentina

last: vongrad

first: Brigitte

last: Leeners


title: Transcriptomic analysis of gastric cancer cells under stress conditions

city: Wuhan

first: Qiangsong

last: Tong

state: Hubei

address: 1277 Jiefang Avenue

department: Department of Surgery

institute: Union Hospital of Tongji Medical College

summary: Gastric cancer is a highly aggressive malignancy and ranks as the second most prevalent contributor to global cancer-related death. However, the underlying mechanisms regulating gastric cancer progression remain to be determined. To investigate the mechanisms regulating tumorigenesis and aggressiveness, we employed the Illumina HiSeq X Ten as a discovery platform to analyze the transcriptome profiling changes of human gastric cancer AGS cells in response to serum deprivation. The results showed that 1220 and 967 genes were respectively elevated or reduced in AGS cells following serum deprivation. Furthermore, we validated the RNA-seq results by real-time RT-PCR with high identity. Overall, our results provided fundamental information about the transcriptomic changes in response to serum deprivation in human gastric cancer cells, and these findings will help us understand the pathogenesis of gastric cancer progression.

overall_design: RNA-seq profiling of human gastric cancer AGS cells treated with complete medium (CM) or serum deprivation (SD).

first: Liduan

last: Zheng


title: NAD+ enhanced mesenchymal stromal cells effect on muscle atrophy by improving SIRT1/PGC-1α-mediated mitochondrial function via NAMPT

first: Jia

last: Song

state: Select...

address: No.107 Wenhua Xi Road, Jinan,Shandong Province

institute: Qilu Hospital of Shandong University

summary: Background: Sarcopenia contributes to all-cause mortality in the elderly; however, there is no specific treatment. Mesenchymal stromal cells (MSCs) ameliorate age-related muscle loss and dysfunction, and are potential therapeutic candidates for sarcopenia. However, their activity is easily affected by the surrounding environment and they are prone to replicative senescence during in vitro culture. Therefore, a drug that delays aging and enhances its function is required. Here, we investigated whether nicotinamide adenine dinucleotide (NAD+) pretreatment enhances the therapeutic efficacy of MSCs on skeletal muscle atrophy and its underlying mechanism in a D-gal-induced aging model. Methods: C57BL/6J mice and C2C12-differentiated myotubes exposed to D-gal were used to explore the effects of MSCs/NAD+-MSCs on muscle atrophy. MSCs/NAD+-MSCs were injected into the skeletal muscles of the hind limbs every 7 days for six cycles. Treadmill running and grip strength tests were used to evaluate the muscle strength. Muscle weight and fiber cross-sectional area (CSA) were used to measure muscle mass. Multiomics analysis of quadriceps and NAD+-pretreated MSCs (NAD+-MSCs), western blotting of muscle atrophy signaling, including Atrogin 1 and MuRF1, the mitochondrial complex, fatty acid oxidation indicators, and Seahorse analysis were performed to explore the underlying mechanisms. Results: MSCs increased grip strength (p=0.0005), running endurance (p=0.0006), and muscle mass (p=0.0165 for tibialis anterior (TA) muscle, p=0.0049 for soleus (SO) muscle) in D-gal-treated mice, with elevated muscle fiber CSA (p<0.0001), and reduced Atrogin1 (p=0.0242) and MuRF1 expression (p=0.0009). NAD+ pretreatment increased the effect of MSCs on muscle atrophy (p=0.0009 for grip strength, p=0.0169 for running endurance, p=0.0506 for TA muscle weight, p=0.0238 for SO muscle weight, p=0.0002 for muscle fiber CSA, p=0.0005 for Atrogin1 expression and p=0.0223 for MuRF1 expression). MSCs/NAD+-MSCs activated the SIRT1/PGC-1α signaling, enhanced mitochondrial function and fatty acid oxidation in D-gal-induced mice and C2C12 myotubes. SIRT1 knockdown weakened the beneficial effects of MSCs/NAD+-MSCs on muscle atrophy. RNA-seq of MSCs/NAD+-MSCs and proteomic analysis of their supernatants revealed that NAD+ enhanced the therapeutic effect of MSCs by promoting NAMPT secretion. Conclusions: NAD+ enhances the therapeutic effect of MSCs on age-related muscle atrophy by promoting NAMPT secretion, which acts on the SIRT1 signaling pathway, and improves mitochondrial function and fatty acid oxidation in skeletal muscles. This study provides new insights and a theoretical basis for the clinical treatment of sarcopenia.

overall_design: The skeletal muscles of D-gal-induced mice treated with PBS or MSCs were subjected to RNA-seq.

first: Yuting

last: Sun

first: Wenjian

last: Zhang

first: Jun

last: Cheng


title: Laccaria bicolor adapts to phosphate deficiency at the developmental, metabolic and gene expression levels

city: Lausanne

first: Giovanna

last: Ambrosini

address: Station 19

institute: EPFL

summary: This study aimed to decipher how the free-living ECM Laccaria bicolor adapts to Pi deficiency. L. bicolor mycelium grown for 7 days in medium without Pi showed very low Pi and polyphosphate reserves and grew in less compact but larger colonies. Pi deficiency resulted in approximately 1500-2000 genes being up- and down-regulated more than 2-fold compared to the mycelium grown with abundant Pi, with most genes partially reverting their expression pattern in cultures spiked with Pi for 24 hours. Numerous genes involved in Pi mobilization from organic sources, such as phosphatases and ribonucleases, were induced by Pi deficiency, as well as genes involved in Pi transport, and such expression patterns were matched by increase enzymatic activities. Pi deficiency also induced the synthesis of the betaine lipid diacylglyceryl-N,N,N-trimethylhomoserine (DGTS). Several genes induced by mycorrhization, such as those encoding protease inhibitors belonging to the mycocytin family and Micorrhizae-Induced Small Secreted Peptides (MiSSP), were also induced by Pi deficiency.

overall_design: Dikaryotic strain L. bicolor S238N was grown in liquid P5 medium with 7 mM inorganic phosphate (HP samples) or without phosphate (LP samples) for 7days. One set of cultures grown without phosphate for 7 day was spiked with 7 mM phosphate and grown for one additional day (LPspike sample). For each set, three independent replicates were generated and analyzed by RNAseq.

first: Anita

last: Loha

first: Sami

last: Bouziri

first: Yves

last: Poirier


title: Dicer accumulates in cytoplasmic foci upon alphavirus infection and plays a proviral role in Myotis myotis bat cells

city: Strasbourg

first: Sébastien

last: Pfeffer

address: 2 allée Konrad Roentgen

department: UPR 9002 - Architecture et Réactivité de l'ARN

institute: CNRS - Institut de Biologie Moléculaire et Cellulaire (IBMC)

summary: Bats are reservoirs for many viruses that frequently cause epidemics in humans and animals. It is thus critical to better understand their immune system and mechanisms of antiviral immunity. Despite an increasing number of studies, much is still unknown about the molecular mechanisms that govern bat-virus interactions, especially given the large diversity of bat species. Dicer is a conserved ribonuclease with multiple activities that can modulate antiviral immunity, including the detection of viral RNA as part of the RNA interference (RNAi) pathway, the maturation of micro RNAs, and the direct inhibition of innate immunity in mouse and human cells. In view of these complex activities of Dicer, we tested its antiviral activity in Myotis myotis nasal epithelial cells. Surprisingly, we did not see strong evidence of RNAi in these cells, but instead saw a proviral effect of Dicer for two alphaviruses, Sindbis and Semliki forest virus. We also observed a striking relocalization of Dicer to cytoplasmic foci upon infection with these viruses, which did not occur in the several human cell lines we tested. These foci contained dsRNA and viral plus strand RNA, suggesting that they are sites of viral replication. Finally, we found that factors specific to M. myotis cells are needed for Dicer relocalization. Overall, we propose that Dicer can play different roles in different bat species and/or cell types, and is being repurposed by alphaviruses to promote viral replication.

sample_organism:
Homo sapiens
Myotis myotis

platform_organism:
Homo sapiens
Myotis myotis

overall_design: SmallRNA sequencing were performed in M. myotis nasal epithelial cells either infected with Sindbis virus (SINV) or Semliki forest virus (VSV). As control, the same procedure was applied with human HEK293T cells, previously showed for not displaying a very strong RNAi signature against SINV (Girardi et al., 2013). Reads were aligned against their respective host genomes and all sequences that failed to map were used for a new alignment against SINV-GFP or VSV-GFP genomes. siRNA signatures were research on 22nt viral reads.

first: Léa

last: Gaucherand

first: Hugo

last: Marie

first: Julie

last: Cremaschi


title: KIAA0319 plays a critical role in cortical neuronal maturation and synaptic development through a dyslexia-associated gene network

city: New Haven

first: Michael

last: Scandura

address: 464 Congress Ave

institute: Yale University

summary: Dyslexia is a common learning disorder defined as difficulty processing written language despite otherwise normal intelligence and access to adequate educational resources. To date, associations with reading performance have been replicated for nine genes, including KIAA0319. However, the specific role of KIAA0319 in the molecular mechanisms underlying dyslexia remains unclear. To investigate its function in neurodevelopment, we used CRISPR-Cas9 to generate KIAA0319 knockout (KIAA0319 -/-) human embryonic stem cells (hESCs), which were subsequently used to generate human cortical organoids (hCOs). Single-cell RNA sequencing revealed that KIAA0319 -/- neural progenitor cells favored a truncated radial glia (tRG) fate rather than a mature neuron fate. Transcriptomic analysis identified coordinated expression across multiple dyslexia-associated genes, suggesting that KIAA0319 operates within a broader regulatory network. This network was also implicated in regulating primary cilia formation, cortical organization, and synaptic connectivity, indicating that dyslexia-associated genes influence fundamental neurodevelopmental processes beyond their role in reading and language-related pathways.

overall_design: The samples were 5 WT cortical organoids from D43 pooled together and 5 KO cortical organoids from D43 pooled together. This was the only batch analyzed.

first: Mu Seog

last: Choe

first: Ferdi Ridvan

last: Kiral

first: Cynthia

last: Lo

first: Jonghun

last: Kim

first: Woo Sub

last: Yang

first: Caihong

last: Qiu

first: Yinghong

last: Ma

first: Jeffrey

last: Gruen

first: In-Hyun

last: Park


title: From subcutaneous to orthotopic: Bridging the gap to human disease in lung cancer research [human]

city: Pamplona

first: Karmele

last: Valencia

state: Navarra

address: Avenida Pío XII, 55

department: Innovación Terapéutica en Cáncer de Pulmón

country: Spain

institute: Centro de Investigación Médica Aplicada (CIMA), Universidad de Navarra

summary: Preclinical lung cancer models frequently fail to predict clinical outcomes due to their limited ability to replicate the complex tumor microenvironment and metastatic processes seen in patients. In this study, we establish and characterize a clinically relevant orthotopic lung cancer model in mice, offering a substantial advancement over conventional subcutaneous models. Using thoracotomy-based injection of luciferase-expressing lung adenocarcinoma cells, we consistently generate single, well-defined nodules within the lung parenchyma that closely mimic human primary tumors. Longitudinal monitoring with bioluminescence imaging and computed tomography enables accurate spatial and volumetric assessment of tumor progression, with tumor size correlating with the initial cell dose.  Comparative analyses demonstrate that orthotopic tumors exhibit enhanced vascularization, proliferation, and reduced hypoxic and stress markers (HIF-1α, γH2AX, p16, p21), alongside elevated Cyclin D1 expression-features reflecting a more physiologically relevant tumor environment. Importantly, orthotopic tumors display an enriched and organized immune infiltration, including enriched CD4⁺ and CD8⁺ T cells and dendritic cells, forming immune niches not present in subcutaneous models.   To model metastasis, we isolate and culture circulating tumor cells (CTCs) from orthotopic tumor-bearing mice. Intracardiac injection of these CTCs leads to organ-specific metastases (e.g., liver, brain, bone), recapitulating clinical dissemination patterns. Transcriptomic and proteomic profiling of metastatic sublines reveals both conserved pro-metastatic programs-including chemokine signaling, EMT, and immune evasion-and niche-specific adaptations, particularly in bone metastases.  This orthotopic model offers enhanced translational relevance for evaluating therapies and dissecting metastatic progression in lung cancer.

overall_design: RNA-seq profiling of A549 parental cells, circulating tumor cells isolated from circulation in murine models, and their metastasic sublines from adrenal gland and bone.

first: Valencia

last: Karmele

first: Rodríguez

last: Covadonga

first: Picabea

last: Beñat


title: MRPL37 promotes hepatocellular carcinoma progression through modulating mitochondrial energy metabolism

city: yichang

first: Hao

last: Deng

state: hubei

address: DAXUE Road No.8

institute: China Three Gorges University

summary: Mitochondrial ribosomal proteins of the large subunit (MRPLs) are critical for mitochondrial protein synthesis and cellular energy metabolism. The role of MRPL37, a member of the MRPL family, in hepatocellular carcinoma (HCC) progression was investigated using SNU-398 HCC cells. In this study, we performed RNA sequencing (RNA-seq) to characterize transcriptomic changes following shRNA-mediated knockdown of MRPL37. The dataset includes RNA profiles from SNU-398 cells with MRPL37 knockdown and corresponding control cells. This analysis aims to elucidate the molecular mechanisms by which MRPL37 regulates mitochondrial function and energy metabolism in HCC. These data provide insights into the role of MRPL37 in HCC progression and may facilitate the identification of novel therapeutic targets for liver cancer.

overall_design: SNU-398 hepatocellular carcinoma cells were cultured under standard conditions and subjected to lentiviral transduction with shRNA targeting MRPL37 (shMRPL37) to achieve gene knockdown. A non-targeting shRNA (shControl) was used as a negative control. After selection and validation of knockdown efficiency by qRT-PCR and/or Western blot, total RNA was extracted from both shMRPL37 and shControl cells. Each group included biological replicates (please specify the number of replicates, e.g., n=3 per group). RNA samples with high integrity were used for library preparation and subsequent high-throughput RNA sequencing. The experimental design enables the identification of differentially expressed genes and pathways regulated by MRPL37 in SNU-398 cells, providing insights into the molecular mechanisms underlying its role in mitochondrial function and hepatocellular carcinoma progression.

first: Yigan

last: Zhang

first: Yanbin

last: Dong


title: Study of the function of Hnrnpu in liver regeneration

first: Yachun

last: An

address: 44 Wenhua West Road, Lixia District, Jinan City

institute: Shandong university

summary: In this study, we explored the effects of RNA splicing on hepatocyte fate decision. We found spatial remodeling of hepatic lobule during liver regeneration by  spatial transcriptome analysis in regenerative and control mouse model. We also reported cell heterogeneity of hepatocyte-organoids and found that splicing factors reprogram hepatocytes from single-cell resolution. To explore the detailed function of splicing factors, splicing inhibitors (Pladienolide B) were used to treated organoids, then total RNA were harvest for bulk RNA sequence. In summary, we found that splicing factors can promote the transformation of hepatocytes from metabolic state to proliferative state by spatial transcriptome, single-cell RNA sequencing, and bulk RNA sequencing.

overall_design: To investigate function of RNA splicing factors Hnrnpu in  liver regeneration,  we then performed gene expression profiling analysis using data obtained from RNA-seq of 6 different samples containing 3 wt and 3 Hnrnpu hepatocyte-specific knockout mouse.

first: Wenjing

last: Wei

first: Huili

last: Hu


title: Transcriptome profiling based on the presence of PHF23 and amino acid starvation

city: Seoul

first: Young Suk

last: Yu

address: 1-Gwanak-ro, Gwanak-gu

country: South Korea

institute: Seoul National University

summary: Autophagy is a conserved self-digestion pathway essential for maintaining cellular homeostasis and catabolism. Under normal conditions, autophagic activity remains minimal but is rapidly upregulated in response to stresses such as nutrient deprivation. While the transcriptional and epigenetic activation of autophagy under nutrient deprived condition has been widely studied, less is known about the repression mechanisms of autophagy under normal conditions. Here, we identify PHF23 as an epigenetic repressor of autophagy through a CRISPR interference (CRISPRi) screening. PHF23 inhibits the expression of autophagy genes by recruiting the NuRD complex and reducing chromatin accessibility, particularly at enhancer regions. This repressive function of PHF23 requires an intact PHD domain and is attenuated under amino acid starvation or mTOR inhibition conditions. Notably, inhibiting PHF23 enhances the autophagic clearance of pathological protein aggregates including Tau and a1 antitrypsin Z variant (ATZ), underscoring its potential as a therapeutic target in diseases characterized by proteotoxic stress.

overall_design: To investigate the roles of PHF23 in the regulation of autophagy and lysosome, we performed mRNA expression profiles of  WT and PHF23 KO HeLa cells with normal media, or amino acid starvation media

first: Seon Ah

last: Choi

first: Jaebeom

first: Sung Hee

last: Baek


title: Genome binding/occupancy profiling of PHF23 and changes in H3K27ac based on the presence of PHF23

type: Genome binding/occupancy profiling by high throughput sequencing

overall_design: To determine where PHF23 is recruited, we performed ChIP-sequencing (ChIP-seq) in HeLa. To investigate the roles of PHF23 in the regulation of H3K27ac, we performed ChIP-seq using PHF23 WT and PHF23 KO HeLa cells

last: Kim


title: CRISPRi screen identifying epigenetic regulators of autophagic flux

overall_design: To systematically identify epigenetic regulators involved in the autophagy regulation, we conducted a CRISPR interference (CRISPRi) screen using a reporter cell line stably expressing the tandem fluorescent-tagged LC3B construct (mCherry-GFP-LC3B). We designed a CRISPRi sgRNA library targeting 613 epigenetic regulators with a total of 3,340 sgRNAs, and transduced it into the reporter cell line. Following transduction, cells were sorted using fluorescence-activated cell sorting (FACS) based on alterations in autophagic flux, and the distribution of sgRNAs was analyzed by next-generation sequencing.


title: From subcutaneous to orthotopic: Bridging the gap to human disease in lung cancer research [mouse]

overall_design: RNA-seq profiling of LLC parental cells, circulating tumor cells isolated from circulation in murine models, and their metastasic sublines from brain and bone.

first: Orive

last: Daniel


title: Removal of elastin from the cell surface of primary human hepatocytes

city: Setagaya-ku

first: Kazuaki

last: Nakamura

state: Tokyo

department: Department of Pharmacology

country: Japan

institute: National Center for Child Health and Development

summary:
Primary human hepatocytes exhibit variable adhesiveness to culture vessels, which limits their utility in drug screening and regenerative medicine. We investigated the cause of this unstable adhesiveness of primary human hepatocytes and observed that the extracellular matrix on the surface inhibits cell adhesion to culture vessels. Elastin was identified as one of the main components of the surface extracellular matrix of non-adhering cells. This discovery suggests a novel approach to enhance their stable adhesion.
Unstable adhesion of primary human hepatocytes to culture vessels significantly hinders their use in research. We discovered that extracellular matrix components on the cell surface inhibit their attachment. Specifically, we identified elastin as a key problematic component in non-adhering cells.

overall_design: Suspension primary human hepatocytes with or without treatment with elastase were collected immediately after elastase treatment or 24 hours after seeding. Total RNA was extracted from the collected cells and analyzed by microarray.

first: Kohji

last: Okamura


title: Human airway eptithelial cell subsets exhibit distinct transcriptional profiles in response to IFN-gamma derived from influenza specific CD8 T cells.

city: Atlanta

first: Chris

last: Scharer

state: GA

address: 1510 Clifton Rd, Suite 3086A

department: Microbiology and Immunology

institute: Emory University

summary: To evaluate the impact of IFNγ secretion by influenza-specific CD8⁺ T cells on human lung epithelial cells, we stimulated total primary human lung cells with influenza peptides in the presence or absence of an IFNγ-blocking antibody. Following stimulation, epithelial cells (CD45⁻, CD31⁻, CD326⁺) were isolated by FACS and analyzed by single-cell RNA sequencing. Three stimulation conditions were compared including unstimulated, stimulated with influenza peptides plus isotype control antibody, and stimulated with influenza peptides plus anti-IFNg antibody.

overall_design: scRNAseq of airway epithelial cells comparing three stimulation conditions. Total epithelial cells were divided into subsets based on key transcription factors post sequencing.

first: Christopher

first: Mark

last: Williams

first: Jacob

last: Kohlmeier

first: Cameron

last: Mattingly


title: Simultaneous Induction of Multiple Classes of Broadly Neutralizing Antibody Precursors via Combination Germline-Targeting Immunization

city: La Jolla

first: Shane

last: Crotty

state: California

address: 9420 Athena

institute: La Jolla Institute For Immunology

summary: Inducing broadly neutralizing antibodies (bnAbs) against HIV remains a key challenge in vaccine development. Germline targeting immunogens have successfully primed bnAb B cell lineages to individual HIV envelope epitopes in humans and non-human primates. However, eliciting consistent breadth will require the induction of multiple bnAb classes. We investigated whether immunization with a combination of germline-targeting immunogens could concurrently prime multiple bnAb lineages in non-human primates. Animals were immunized with three immunogens, targeting distinct epitopes: the V3-glycan/N332 supersite, the V2 Apex region and the membrane-proximal external region (MPER), either individually or in combinations of two or all three. Triple combination immunization transiently reduced V2 Apex and V3-glycan responses, but by 8 weeks post-boost bnAb-precursor lineages were observed to all three epitopes. Similar somatic hypermutation was observed across groups, indicative of permissive germinal center responses. These findings support combination germline-targeting immunization as a viable strategy to prime multiple bnAb lineages simultaneously.

overall_design: N332-GT5, Apex-GT6 and 10E8-GT12 -specific B cells from PBMCs were isolated by fluorescence-activated cell sorting (FACS) and analyzed by scRNA-seq, including VDJ and GEX libraries, using the 10X Genomics platform. Samples were multiplexed using TotalSeq™-C hashtag antibodies (BioLegend).

first: Henry

last: Sutton


title: Distinct Prognostic and Molecular Profiles of Fat versus Vein Invasion in T3a Renal Cell Carcinoma

first: Chang Ohk

last: Sung

address: Song-Pa gu,Pung-nap dong

department: Pathology

institute: Asan Medical Center

summary: pT3a renal cell carcinoma (RCC) encompasses three different types of progression features –perinephric fat invasion, sinus fat invasion and renal vein (branch) invasion, leading to persistent debate on prognostic heterogeneity and the need for reclassification. RNA sequencing was performed on representative tumor samples from radical nephrectomy specimens of 11 sinus fat invasion (SFI) and 12 renal vein invasion (RVI) patients with clear cell RCC to identify differentially expressed genes and pathway enrichments. Transcriptomic profiling revealed that SFI tumors were enriched for epithelial-mesenchymal transition, KRAS signaling, and extracellular matrix reprogramming, whereas RVI tumors exhibited hypoxia, oxidative phosphorylation, and DNA repair pathway activation suggesting an intrinsically disparate competencies directing the tumors to adopt different invasion mechanisms.

first: Cheryn

last: Song


title: Removal of extracellular matrix from the cell surface improves adhesion of primary human hepatocytes

summary:
While investigating the causes of unstable adhesiveness of primary human hepatocytes, we observed that non-adhering cells had some kind of extracellular matrix on their surface, and this extracellular matrix inhibited cell adhesion to culture vessels. Removal of the matrix from the cell surface of non-adhering cells improved cellular attachment to culture vessels. We also performed comparative gene expression analysis between adhering and non-adhering cells to elucidate the molecular basis of differential adhesion behavior.
We investigated the unstable adhesiveness of primary human hepatocytes and found that non-adhering cells had extracellular matrix on their surface that inhibited cell adhesion. We also observed that matrix removal improved cellular attachment.

overall_design: Three suspension lots of primary human hepatocytes were purchased. Non-adhered and adhered cells were collected from each lot, resulting in a total of six samples for analysis.


title: Similar activation-driven transcriptional programs in lung CMV- and flu- specific memory CD8+ T cells despite differences in tissue residency profiles

summary: To investigate whether virus-specific human lung memory CD8⁺ T cells exhibit distinct transcriptional responses based on viral tropism, we stimulated total human lung cells ex vivo with peptide pools from either influenza virus (epithelial-restricted) or cytomegalovirus (CMV, broader tropism). Antigen-specific CD8⁺ T cells were identified using activation-induced markers (CD25 and CD137) and sorted for bulk RNA sequencing. Despite differences in tissue residency phenotypes, influenza- and CMV-specific CD8⁺ T cells displayed highly similar activation-induced transcriptional programs across nine donors, with shared enrichment of inflammatory and T cell signaling pathways. These findings suggest that lung memory CD8⁺ T cells mount comparable responses to antigen stimulation, regardless of viral specificity or residency profile.

overall_design: Total human lung cells from n=9 donors were stimulated in vitro for 18 hours with peptide pools specific for either influenza virus or cytomegalovirus (CMV), or left unstimulated. Antigen-specific CD8⁺ T cells were identified using activation-induced markers (CD25 and CD137) and isolated by FACS for bulk RNA sequencing. A PMA/ionomycin-stimulated sample was included as a positive control to set sorting gates. Unstimulated memory CD8⁺CD69⁺ T cells were also sorted as a comparison population.


title: High-resolution mapping and transcriptional profiling of coronary-cardiomyocyte interactions during zebrafish heart development

city: Montreal

first: Rubén

last: Marín-Juez

address: 3175 Chem. de la Côte-Sainte-Catherine

country: Canada

institute: CHU Sainte-Justine

summary: We used a 10X Genomics single-cell RNA sequencing approach to study transcriptional profiling of coronary developmental stages in zebrafish comparing data from initiation (10 mm), establishment (14 mm), expansion (18 mm) and maturation (28 mm).

overall_design: One pool of ventricles per developmental stage, initiation (10 mm) 25 ventricles, establishment (14 mm) 18 ventricles, expansion (18 mm) 12 ventricles and maturation (28 mm) 5 ventricles were extracted for single-cell dissociation and library preparation.

last: Marin-Juez

first: Muhammad Abdul

last: Rouf

first: Gülsüm

last: Kayman-Kürekçi

first: Shaoqiu

last: Zhang

first: Stéphanie Larrivée

last: Vanier

first: Sarah M.

last: Kamel

first: Ann Nee

last: Lee


title: IFN-gamma signaling early during infection dramatically enhances antiviral programs in epithelial cells

summary: To examine the impact of IFNγ signaling on human airway epithelial cells during influenza virus infection, we used differentiated air–liquid interface (ALI) cultures of normal human bronchial epithelial cells. Cultures were infected with influenza A/Netherlands/602/2009 (H1N1) and treated with recombinant IFNγ 4 hours post-infection. At 18 hours post-infection, basal, secretory, and ciliated epithelial cells were separated by FACS and analyzed by bulk RNA sequencing. IFNγ treatment after infection induced a distinct transcriptional signature across all epithelial subsets compared to infection alone, with basal cells showing the strongest transcriptional response. These data provide insight into epithelial subset–specific responses to IFNγ in the context of viral infection and reveal how early cytokine signaling can enhance antiviral programs in the human airway epithelium.

overall_design: ALI cultures of NHBEs were infected apically with H1N1 (A/Netherlands/602/2009) at MOI 0.1. IFNγ (100 ng/mL) was added basolaterally 4 hours post-infection. At 18 hours post-infection, epithelial cells were separated by FACS into basal, secretory, and ciliated subsets for bulk RNA sequencing. Samples were collected from three treatment groups (uninfected, infection only, infection + IFNγ), with all three epithelial subsets analyzed per group.


title: SBFI inhibitors reprogram transcriptomic landscape of prostate cancer leading to cell death [SBFI-1143]

city: Stony Brook

first: Agnieszka

middle: B.

last: Bialkowska

address: HSC-T17 Room 090

department: Dept. of Medicine

institute: Stony Brook University

summary: Prostate cancer (PCa) remains the second leading cause of cancer-related deaths in the United States. Fatty acid-binding protein 5 (FABP5), a member of a class of intracellular lipid transporters, promotes PCa progression via enhanced lipid metabolism and trafficking of lipid ligands. Previous work from our group has shown that the small molecule FABP5 inhibitors based on the truxillic-acid monoester (TAMEs) scaffold reduce PCa growth. In the current study, we demonstrate that the third-generation FABP5 inhibitor SBFI-1143 significantly inhibited the viability and proliferation of PCa cells by arresting cells at the G0/G1 and G2/M phases of the cell cycle and inducing apoptosis and cell death compared to 1st and 2nd generation inhibitors. Stinkingly, SBFI-1143 efficiently inhibited the growth of PCa spheroids compared to its predecessor, SBFI-103. RNA sequencing and Gene Set Enrichment Analysis (GSEA) demonstrated that SBFI-1143 more effectively suppressed the activity of pathways involved in cell cycle progression, cell cycle division, and chromosome organization, while upregulated genes associated with the endoplasmic reticulum (ER) stress, responses to the topologically incorrect folded proteins, and regulating apoptosis compared to the SBFI-103. We further show that SBFI-1143 inhibits oxidative phosphorylation, a process on which PCa depends during cancer initiation and progression. Notably, SBFI-1143 treatment downregulated genes attributed to the subpopulation of PCa cells characterized by the lineage plasticity-related signature leading to trans-differentiation, recurrence, and poor cancer prognosis. Our findings demonstrate that SBFI-1143 significantly modifies the transcriptomic landscape of PCa and may serve as a potentially effective therapeutic option for PCa.

overall_design: To investigate the mechanism of action and efficacy of SBFI-1143 in vitro, we treated the human prostate cancer cell line, PC-3, with vehicle control (DMSO) and 15uM of SBFI-11143 for 24 and 48 hours. Total RNA was isolated and RNA-seq was conducted. We then performed differential gene expression analysis using RNA-seq data from three biological replicates of each treatment condition to characterize significant transcriptomic changes in response to treatments.

first: Shubhra

last: Rajput

first: Joseph F

last: LaComb

last: Gordon

first: Hehe

last: Wang

first: Martin

last: Kaczocha

first: Agnieszka B

first: Iwao

last: Ojima


title: MEK Inhibitors Enhance post-radiation anti-tumor Immunity in KRAS-Mutant Lung Cancer

city: jiann

first: Yawen

last: zheng

address: jiefang road No105

institute: jinan central hospital

summary: 24 hours after the designated treatment, the LLC cells in four groups cultured in a 60 mm dish underwent two washes with PBS. Subsequently, 1 ml of TRIzol reagent was introduced. The solution was pipetted until it appeared clear, after which the mixture was transferred to an EP tube and stored at -80°C. The samples were then transported to BGI on dry ice for gene sequencing. Sequencing commenced once the samples successfully passed quality control assessments.

overall_design: four groups: control, MEKi(trametinib 10 nmol/L), RT(8Gy/1f) and MEKi+RT

last: Zheng

first: Meili

last: Sun


title: RNA-RNA Interactome Approaches Provide in vivo Evidence for a Critical Role of the Hfq Rim Face in sRNA-mRNA Pairing [GRILseq]

city: Bethesda

first: Caroline

last: Esnault

state: md

address: 9000 Rockville Pike,

institute: NICHD NIH

summary: Most bacterial small regulatory RNAs (sRNAs) modulate gene expression by forming complementary base pairs with target mRNAs, a process that is heavily reliant on the RNA chaperone Hfq in many microbes. Hfq, with its three distinct RNA-binding faces (proximal, rim, and distal), facilitates the simultaneous binding of sRNAs and target mRNAs, with each face providing specific interactions to promote pairing. However, the precise contributions of each Hfq face to RNA binding and sRNA-mRNA annealing in vivo remain unclear. Here, we systematically examined the functional impact of point mutations in chromomally-encoded Flag-tagged Hfq using the RNA Interaction by Ligation and Sequencing (RIL-seq) approach. While substantial numbers of sRNA-mRNA chimeras were detected for most Hfq face mutants, the rim face mutant R16A exhibited a near-complete loss of chimeras, even though functional assays confirmed that Hfq R16A retains partial regulatory activity. Further RIL-seq analysis demonstrated that the addition of the Flag tag did not significantly alter chimera formation or contribute to the loss of chimeras in R16A, and RNA immunoprecipitation sequencing (RIP-seq) analysis showed that R16A maintains partial RNA-binding activity. Using intracellular RIL-seq (iRIL-seq), a method with fewer in vitro processing steps after Hfq immunoprecipitation, we identified significantly more sRNA-mRNA chimeras in R16A compared to standard RIL-seq, indicating that the rim face plays a key role in stabilizing RNA pairs on Hfq. Our findings provide a comprehensive analysis of how the RNA-binding faces of Hfq contribute to sRNA stability and pairing in vivo and the unique function of the rim face. Additionally, we highlight the strengths of different RNA ligation-based sequencing approaches, with RIL-seq effectively capturing stable Hfq-associated interactions, while iRIL-seq captured more transient RNA pairings.

overall_design: WT and hfq R16A mutant were transformed with either an empty vector or a T4 RNA Ligase I-expressing vector. Biological duplicates of each strain were processed for either Hfq IP followed by RNA isolation (iRIL-seq) or direct RNA extraction for total RNA sequencing (Hi-GRIL-seq)

first: Xing

last: Luo

first: Aixia

first: François

last: De Mets

first: Philip

last: Adams

first: Ryan

last: Dale

first: Gisela

last: Storz

first: Susan

last: Gottesman


title: Loss of Prom1 triggers RPE Degeneration in Atrophic AMD

city: Nashville

first: Sujoy

last: Bhattacharya

state: Tennessee

address: 1161 21st Avenue S

department: Ophthalmology and Visual Sciences

institute: Vanderbilt University Medical Center/ Vanderbilt Eye Institute

summary: The gap in our understanding of the pathobiology of atrophic AMD (aAMD) is a barrier to developing new and effective therapies for geographic atrophy (GA) of the retinal pigment epithelium (RPE). Age-related decline in phagocytic function and impaired autophagy flux in RPE cause oxidized lipid-protein accumulation, accelerating complement-mediated inflammation and leading to RPE cell damage and apoptosis. Prominin-1 (Prom1), a glycosylated membrane protein, is essential for photoreceptor (PR) disk biogenesis and outer segment (OS) structure. However, Prom1 mutations are primarily implicated in macular diseases such as Stargardt disease 4 and bull’s eye macular dystrophies. The physiological impact of Prom1 mutations in the retina is not clear. We have shown earlier that Prom1 is a central regulator of autophagy in human RPE and identified Prom1 as an emerging player in RPE homeostasis. We propose to build upon these salient findings by assessing the central hypothesis that Prom1 plays a cell-autonomous role in the RPE and that defects in Prom1-dependent mTORC1-TFEB signaling impair RPE autophagy and lysosomal function, triggering mRPE degeneration and induction of epithelial-mesenchymal transition (EMT). This study investigated whether Prom1 is required for mouse RPE (mRPE) autophagy and phagocytosis, which are cellular processes essential for photoreceptor survival. Prom1-KO decreases autophagy flux, activates mTORC1, and concomitantly decreases transcription factor EB (TFEB) and Cathepsin-D activities in mRPE cells. In addition, Prom1-KO reduces the clearance of bovine photoreceptor outer segments in mRPE cells due to increased mTORC1 and reduced TFEB activities. Dysfunction of Prom1-dependent autophagy correlates with both a decrease in ZO-1 and E-cadherin and a concomitant increase in Vimentin, SNAI1, and ZEB1 levels, consistent with induction of epithelial-mesenchymal transition (EMT) in Prom1-KO mRPE cells. Transcriptomic analysis of Prom1-KO mouse RPE cells by RNA sequencing showed a list of 15 DEGs with high statistical significance in Prom1-KO vs. WT mRPE cells. GSEA and NES show significant upregulation of cell-cycle transcription factors (E2F and MYC targets, G2M checkpoint), mTORC1 signaling, unfolded protein response, reactive oxygen species, TNFA signaling via NF-kappaB, DNA repair, and oxidative phosphorylation pathways; whereas significant downregulation of apical junction and EMT pathways in Prom1-KO vs. WT mRPE cells. Our results demonstrate that Prom1-mTORC1-TFEB signaling is a central driver of cell-autonomous mRPE homeostasis. We show that Prom1-KO in mRPE leads to RPE defects similar to those seen in atrophic age-related macular degeneration and opens new avenues of investigation targeting Prom1 in retinal degenerative diseases.

overall_design: In cultured mouse RPE cells, the Prom1 gene was deleted using CRISPR/Cas9-mediated gene editing. Prom1-KO was verified using genomic DNA analysis. To understand the effect of Prom1-KO in mouse RPE in situ, we used Cre-loxP-mediated gene targeting. We crossed Prom1fl/fl mice with RPE65-Cre mice to generate RPE-specific Prom1-KO in a mouse model. This mouse was gavaged with Tamoxifen to delete the Prom1 gene in the RPE but not in the photoreceptors. We used Prom1 IHC and RNAscope assays to confirm Prom1-KO in the RPE in situ. The mouse eyes were dissected, and the RPE/choroid samples from WT and RPE-specific Prom1-KO mice were used for bulk RNA sequencing. To explore the role of Prom1 in mRPE cells, we used CRISPR/Cas9-mediated gene editing to delete Prom1 in vitro. WT and Prom1-KO mRPE cells were used to perform RNAseq on the Illumina NovaSeq6000 sequencing system.


title: Transcriptomic changes underlying the anti-steatotic effects of DHA supplementation in aged obese female mice

first: María

middle: Jesús

last: Moreno-Aliaga

address: University of Navarra

department: Nutrition, Food Science and Physiology

institute: Centre for Nutrition Research

summary: The prevalence of metabolic dysfunction-associated steatotic liver disease (MASLD) increases with age and obesity. The aim of this study is to characterize the transcriptomic changes in liver underlying the beneficial effects of docosahexaenoic acid (DHA) supplementation on MASLD progression in aged obese female mice. Two-month-old C57BL/6J female mice were fed ad libitum with high fat saturated diet (HFD, 45%) for 4 months. These diet-induced obese (DIO) mice were divided into two groups: the DIO group that continued with HFD and the DIO + DHA mice fed up to 18 months with the HFD containing a DHA-rich concentrate. High quality RNA from liver was used to perform RNA sequencing analysis. Further functional and clustering analyses of differentially expressed genes (DEGs) in liver between treatments revealed that DHA regulated processes related to lipid metabolic processes such as fatty acid beta oxidation, lipid storage, fatty acid transport and lipid localization. DHA treatment also affects PPAR signaling pathway and the regulation of inflammatory response. These data suggest that long-term DHA supplementation ameliorates MASLD progression in aged obese female mice by promoting transcriptomic changes in genes related to lipid metabolism and inflammatory response.

overall_design: RNAseq profiling of livers from 18 month-old DIO and DIO+DHA female mice. Two months-old C57BL/6J mice  were fed ad libi-tum for 4 months with high fat diet (HFD) containing as energy: 20% proteins, 35% carbohydrates, and 45% lipids (D12451 diet, Research Diets, Inc., New Brunswick, NJ USA). Then, DIO mice were divided into two groups: (1) the DIO group  continued with the HFD up to 18 months and (2) the DIO + DHA group, which was fed up to 18 months with the HFD containing a DHA-rich n-3 PUFA concentrate obtained from fish oil, replacing 15% wt/wt of dietary lipids (Research Diets Inc., New Brunswick, NJ, USA). The DHA-rich n-3 PUFA concentrate contained 683.4 mg DHA/g, 46.7 mg EPA/g, with a total content of n-3 PUFA of 838.9 mg/g as triglycerides.

first: Álvaro

last: Pejenaute Martínez de Lizarrondo

first: Paula

last: Martín-Climent

last: Martínez-Rubio

first: Neira

last: Sáinz Amillo

first: Elisa

last: Félix-Soriano

first: Elizabeth

last: Guruceaga

first: M Pilar

last: Lostao

first: Pedro

last: González-Muniesa

first: María J


title: Impact of culture conditions used in in-vitro bovine production on embryo development and trophoblast gene expression.

city: JOUY-en-JOSAS

first: gilles

last: charpigny

state: ILe de France

address: domaine de Vilvert

department: Physiologie Animale Systeme Elevage

institute: INRAE

summary: The aim of this study was to determine the effect of culture conditions and environment on the bovine embryo at two stages of development. Day-8 embryos were produced in vitro. Day-15 embryos were harvested from the recipient mother's uterus after the day 8 blastocysts had been initially transferred to the mother. In this study, we specifically investigated the effect of in vitro culture on trophoblastic gene expression.

overall_design: Trophoblastic tissue samples were collected day-8 of in vitro embryo development and at day-15 of pregnancy. Day-8 embryos were produced in vitro. Day-15 conceptus were collected at day 15 of pregnancy after transfer of day-8 in vitro produced embryo.

first: Fabienne

last: Nuttinck

first: Gilles

last: Charpigny

first: Alice

last: Jouneau


title: RNA-RNA Interactome Approaches Provide in vivo Evidence for a Critical Role of the Hfq Rim Face in sRNA-mRNA Pairing [RILseq]

first: Caroline

last: Esnault

overall_design: RILseq sequencing of Hfq mutants K31A, D9A, R16A and Y25D and corresponding wild-types to identify RNA-RNA chimeric transcripts

first: Xing

last: Luo

first: Aixia

last: Zhang

first: François

last: De Mets

first: Philip

last: Adams

first: Ryan

last: Dale


title: Epigenetic Regulation of Serine Biosynthesis by PHF8 During Neurogenesis

city: Barcelona

first: Marta

middle: Artés

last: Hernández

address: Baldiri Reixac 15

institute: IBMB-CSIC

summary: During neurodevelopment, progenitor proliferation is a highly orchestrated process, involving precise epigenetic modifications and immense metabolic demands. Yet, the intricate interplay between epigenetics and metabolism remains largely unexplored. To investigate this, we utilized neural stem cells to examine the role of PHF8, a histone demethylase whose mutations are linked to Siderius-Hamel syndrome, a rare neurodevelopmental disorder. Through an integrated multi- omics approach—combining transcriptomics, epigenomics, and metabolomics—we identify PHF8 as a key driver of the serine biosynthesis pathway, safeguarding the intracellular serine pool essential for neural progenitor proliferation. PHF8 fine- tunes chromatin accessibility at promoters of metabolic genes, ensuring their activation during development. Notably, loss of PHF8 not only disrupts amino acid metabolism and mTORC1 signaling, but also blocks autophagic flux, and impairs vesicle formation—ultimately stalling proliferation and triggering replicative defects and DNA damage. In vivo, PHF8 deficiency in mouse embryos halts neurogenesis, affecting progenitor expansion and neuron generation in the developing brain. Altogether, our work positions PHF8 as a pivotal molecular node linking chromatin dynamics, metabolic regulation, and neural development. These findings not only deepen our understanding of brain development but also open new avenues for exploring the epigenetic basis of metabolic and neurodevelopmental disorders.

overall_design: Cells were infected with lentiviral shRNA either scramble (control) or against PHF8 (shPHF8), and then used for RNA extraction,  ChIP-seq or ATAC-seq

last: Artés

first: Simona

last: Iacobucci

first: María

last: Balladore

first: Paula

last: Caballeria

last: García

first: Alex

last: Pérez

first: Natalia

last: Padilla

first: Silvina

last: Natch

first: Guillermo

last: Vicent

last: Vaquero

first: Mariona

last: Arbonés

first: Xavier

last: de la Cruz

last: Nieto

first: Neus

last: Agell

last: Mauvezin

first: Marian

last: Martínez


title: Differential nucleosome organization in human interphase and metaphase chromosomes [ChemMap]

city: Evanston

first: Xiaozhong

last: Wang

state: IL

address: 2200 Campus Dr

department: Molecular Biosciences

institute: Northwestern University

summary: Mitosis induces profound changes in chromosome structure, impacting nucleosome organization. Here, we employed chemical mapping to achieve single-base-pair resolution of nucleosome positioning in human interphase and metaphase chromosomes, unveiling distinct organizing principles between the two states. During interphase, we observe greater variability in internucleosome spacing, with a higher abundance of shorter linkers compared to metaphase, reflecting the genome's adaptability in accommodating nucleosome arrays for gene expression. Local analyses further uncover differential nucleosome landscapes at key euchromatin landmarks, including promoters, enhancers, and insulators, in each state. Moreover, we analyzed the relationship between DNA cyclizability and dyad positioning during mitosis. Our results indicate that in metaphase, nucleosomes exhibit significantly higher cyclizability around the dyad, whereas during interphase, nucleosomes more frequently position DNA with higher cyclizability in the nucleosome shoulder near regulatory genomic regions. Together, this study offers novel insights into the intricate interplay between DNA mechanics and nucleosome dynamics during mitosis.

overall_design: Through PiggyBac transgenic expression of an shRNA directed against a shared DNA sequence present in all human H4 genes and RNAi-resistant H4S47C cDNA, we generated H4S47C-substituted HeLa S3 stable cell lines suitable for efficient chemical cleavage of nucleosomes. Using these cells, we performed chemical nucleosome mapping experiments in both interphase and synchronized mitotic cells, with two replicates for each condition.

first: Keren

last: Li

first: Irem

last: Unlu

first: Lilien

middle: N

last: Voong

first: Xiaotian

last: Ma

first: Yiren

last: Tu

first: Ji-ping


title: RNA-RNA Interactome Approaches Provide in vivo Evidence for a Critical Role of the Hfq Rim Face in sRNA-mRNA Pairing [RNA-seq]

first: Caroline

last: Esnault

overall_design: RNAseq profiling of Hfq mutants K31A, D9A, R16A and Y25D and corresponding wild-types.

first: Xing

last: Luo

first: Aixia

last: Zhang

first: François

last: De Mets

first: Philip

last: Adams

first: Ryan

last: Dale

first: Gisela

last: Storz

first: Susan

last: Gottesman


title: Differential nucleosome organization in human interphase and metaphase chromosomes [MNase-Seq]

overall_design: MNase digestion of nucleosomal DNA in interphase and metaphase HeLa S3 cells was performed as described previously.


title: SLC29A3 supports phagosomal antibacterial signaling, and promotes autophagy by activating TRPML1 in mouse dendritic cells

city: Philadelphia

first: Adriana

last: Mantegazza

address: 233 South 10th Street

institute: Thomas Jefferson University

summary: Solute carrier (SLC)29A3 exports nucleosides from lysosomes into the cytosol, maintaining solute homeostasis and providing metabolic intermediates for cellular processes. Loss-of-function mutations in SLC29A3 cause H syndrome, characterized by histiocytosis, hyperinflammation and immunodeficiency. While dysfunctions in several cell types contribute to H syndrome and to SLC29A3 deficiency in mice, the mechanisms driving hyperinflammation and immunodeficiency are incompletely understood. Notably, the possible role played by dendritic cells (DCs), the most efficient antigen presenting cells and the main link between innate and adaptive immune responses, remains unknown. We show that, in murine DCs, SLC29A3 is recruited to phagosomes after bacterial capture, maintains phagosomal pH homeostasis, and ensures optimal phagosomal signaling to the production of IL-6, IL-12, and CCL-22. In addition, SLC29A3 promotes Ag presentation on MHC-II molecules to initiate adaptive immune responses. Notably, SLC29A3 supports the activity of the lysosomal calcium channel TRPML1, promoting transcription factor TFEB nuclear translocation and inducing autophagy, a major anti-inflammatory mechanism. Overexpression of human SLC29A3, but not the transport mutant G437R, in SLC29A3-deficient murine DCs restores cytokine production in response to bacteria phagocytosis, suggesting that SLC29A3 transport activity is required to drive anti-bacterial phagosomal signaling. Our data suggest that SLC29A3 plays a dual role in supporting immune function by promoting effective anti-microbial signaling and Ag presentation in DCs and inducing autophagy to control inflammation. Our findings also uncover a novel TRPML1-dependent mechanism by which SLC29A3 activates TFEB and suggest that defects in phagosomal signaling, TFEB activation and autophagy may contribute to immunodeficiency and hyperinflammation in SLC29A3 disorders.

overall_design: WT and SLC29A3-/- splenic dendritic cells (DCs) were untreated or pulsed with attenuated Salmonella typhimurium (STmDfla) at MOI:10 for 30 minutes, washed and chased for 3 hours. Cell pellets were processed for RNA isolation and submitted to Novogene Corporation (Sacramento, CA) for library preparation and RNA sequencing.

first: Daniel

last: Netting

first: Cynthia

last: Lopez-Haber

first: Zachary

last: Hutchins

first: Jose

middle: A

last: Martina

first: Rosa

last: Puertollano


title: chromatin accessibility profiling by ATAC-seq based on the presence of PHF23

first: Young Suk

last: Yu

summary: Autophagy is a conserved self-digestion pathway essential for maintaining cellular homeostasis and catabolism. Under normal conditions, autophagic activity remains minimal but is rapidly upregulated in response to stresses such as nutrient deprivation. While the transcriptional and epigenetic activation of autophagy under nutrient deprived condition has been widely studied, less is known about the repression mechanisms of autophagy under normal conditions. Here, we identify PHF23 as an epigenetic repressor of autophagy through a CRISPR interference (CRISPRi) screening. PHF23 inhibits the expression of autophagy genes by recruiting the NuRD complex and reducing chromatin accessibility, particularly at enhancer regions. This repressive function of PHF23 requires an intact PHD domain and is attenuated under amino acid starvation or mTOR inhibition conditions. Notably, inhibiting PHF23 enhances the autophagic clearance of pathological protein aggregates including Tau and a1 antitrypsin Z variant (ATZ), underscoring its potential as a therapeutic target in diseases characterized by proteotoxic stress.

overall_design: To investigate the roles of PHF23 in the regulation of chromatin accessibility, we performed ATAC-seq using PHF23 WT and PHF23 KO HeLa cells

first: Seon Ah

last: Choi

first: Jaebeom

last: Kim

first: Sung Hee

last: Baek


title: LINE-1 locus transcription nucleates oncogenic chromatin architecture [RNA-Seq]

city: Memphis

first: Jian

last: Xu

address: 262 Danny Thomas Place, MS 345

institute: St. Jude Children's Research Hospital

summary: Retrotransposons are a prolific class of genomic parasites frequently upregulated in human cancers, where their spontaneous mobility can generate insertional mutations and structural variations. However, whether retrotransposon-derived gene products contribute to cancer beyond retrotransposition remains unclear. Here, we identify an oncogenic, chromatin-associated function of RNAs produced by Long Interspersed Element-1 (LINE-1), the only autonomous human retrotransposon. Sequencing analysis of subcellular fractions revealed that LINE-1 RNAs primarily exist as nascent transcripts expressed from full-length, cell type-specific genomic copies of evolutionarily young LINE-1 subfamilies. Through developing a long-read sequencing-based chromosome conformation assay, we uncovered a class of highly interactive LINE-1 loci essential for gene expression across cancer subtypes, establishing an unexpected regulatory link between LINE-1 locus transcription and oncogenic gene expression via long-range chromatin interactions. Depleting LINE-1 RNAs disrupted LINE-1-centric chromatin interactions, leading to the downregulation of associated genes, whereas inserting a LINE-1 element into an endogenous genomic locus induced de novo chromatin interactions in a transcription-dependent manner. Therefore, retrotransposons not only mutagenize linear genetic content but also regulate cancer gene expression through transcription-dependent nucleation of chromatin architecture.

overall_design: Chromatin RNA-sequencing (Chromatin RNA-seq) was performed on ten cancer cell lines, as well as on ER-positive and triple-negative breast cancer (TNBC) tissue samples. RNA-seq was conducted on MCF7 cells treated with either LINE-1-targeting ASO1, ASO2, or a scrambled ASO control. Both Chromatin RNA-seq and Cytosolic RNA-seq were performed on three cell lines. Additionally, mRNA-sequencing was carried out on MCF7 cells stably expressing Tet-inducible Cas9 and sgRNAs targeting either L1HS_175, L1HS_274, or the AAVS1 safe harbor locus.

first: Michael

last: Lee Jr.

first: Yuannyu


title: Transcriptional profiling of Mycobacterium abscessus under long-term stress conditions: PBS starvation and dormancy under potassium deficiency

city: Moscow

first: Artem

last: Grigorov

address: Ulitsa Miklukho-Maklaya, 16/10

department: Genomics and Postgenomic Technologies

institute: Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry

summary: This dataset presents the transcriptional profile of Mycobacterium abscessus exposed to long-term stress conditions that model physiological states encountered during persistent infection. RNA-seq analysis was performed on M. abscessus cultures subjected to PBS starvation and potassium (K⁺) deficiency, which simulate nutrient limitation and metabolic downregulation characteristic of dormant mycobacterial populations.

overall_design: Differential gene expression was examined in Mycobacterium abscessus under long-term stress conditions compared to actively growing controls. The study investigated two distinct stress conditions: (1) PBS starvation, where bacteria were transferred to phosphate-buffered saline to induce nutrient limitation, and (2) potassium (K⁺) deficiency, where bacteria were cultured in media lacking adequate potassium to induce dormancy. A single set of actively growing bacterial cultures in complete media served as the control group for both stress conditions. RNA-seq was performed to analyze transcriptional changes between stressed bacteria and the control. All experimental conditions, including the control, were conducted in biological triplicates

first: Elena

middle: G

last: Salina

first: Billy

last: Martini

first: Tatyana

last: Azhikina


title: Coordinate tumor-antigen uptake and dendritic cell activation by chimeric antigen receptors. [RNA-seq]

city: Lausanne

first: Nadine

last: Fournier

state: Vaud

address: Agora Cancer Research Center, Bugon 25A

institute: Agora Cancer Research Center & Swiss Institute of Bioinformatics

summary: Effective anti-tumor immunity requires dendritic cells (DCs) to internalize, process and present tumor antigens to T cells. Adoptive transfer of DCs loaded ex vivo with tumor antigens has been shown to stimulate anti-tumor immunity in patients with cancer, but clinical responses have been mixed. To address limitations of traditional DC-based therapies, we constructed and functionally screened a panel of chimeric antigen receptors (CARs) optimized for expression and activity in DCs. Through this screening, we identified key functional components that informed the design of an inducible platform centered on an instructive chimeric antigen receptor (iCAR). This platform enables the DCs to (i) recognize a surface molecule present on cancer cells or their extracellular vesicles (EVs), such as GD2 and HER2, thereby promoting the acquisition of tumor-derived material that contains putative tumor antigens; (ii) undergo immunostimulatory activation to prime antigen-specific T cells via both cross-dressing and cross-presentation; and (iii) transactivate the expression of a therapeutic gene (IL-12) in response to antigen uptake. The iCAR converted melanoma-derived EVs from immune-suppressive to stimulatory cues for DCs. Moreover, systemic administration of iCAR-DCs enhanced antigen-specific T cells, expanded low-frequency T cell clonotypes, and delayed tumor growth in immunotherapy-resistant melanoma models without the need for ex vivo antigen loading or cell maturation. iCAR-DCs provide a platform for antigen-agnostic cancer immunotherapy that integrates antigen uptake with programmable DC activation.

overall_design: Comparative gene expression profiling of MutuDCs (Ctrl-iCAR or iCAR) treated with GD2+ EVs or untreated.

first: Yahya

last: Mohammadzadeh

first: Michele

last: De Palma


title: LINE-1 locus transcription nucleates oncogenic chromatin architecture [ChIRP-seq]

overall_design: Chromatin Isolation by RNA Purification (ChIRP)-sequencing was peformed in MCF7 cells with biotinylated probes targeting the LINE-1 5’UTR, ORF1 or ORF2.

last: Zhang


title: Colorectal cancer organoids drive patient-specific inflammation, cytotoxicity and tissue-residency programs in NK cells

city: Mannheim

first: Carsten

last: Sticht

address: Theodor-Kutzer-Ufer

department: ZMF

institute: University Heidelberg

summary: Natural killer (NK) cells represent a promising strategy for cellular cancer immunotherapy, but it remains unclear which patients benefit by such therapies. Using co-cultures of primary human allogenic NK cells and patient-derived colon cancer organoids (PDOs), we could stratify PDOs into NK cell “highly susceptible” and “rather resistant” groups reflected by differential expression of NKG2D-ligands, MHC class I and CEACAM. RNA-seq unveiled that hypoxia- and TGF-β-related gene signatures were induced in NK cells after PDO co-culture. Deletion of hypoxia inducible factor (HIF)-2a in primary NK cells or blocking of TGF-β-R1 empowered NK cell-mediated PDO killing. We further demonstrate that upon PDO killing, NK cells adopted an activation/inflammationhigh, cytotoxicitylow, tissue-residencyhigh program as evidenced by CXCR6 and CD49a expression coinciding with a “hot” cytokine/chemokine-rich microenvironment. Since PDO-exposed NK cells largely resemble features of NK cells from CRC patient tissues, our NK cell/PDO platform could be highly relevant for the optimization of NK cell products for personalized medicine.

overall_design: RNA seq. profiling of NK cells only and NK cells after 4-day exposure to PDO7 and PDO22

first: Andreas

last: von Kries

first: Adelheid

last: Cerwenka


title: LINE-1 locus transcription nucleates oncogenic chromatin architecture [L1CaP-C]

overall_design: LINE-1 Capture Pore-C (L1CapC) was performed on wild-type MCF7, K562, and T47D cell lines. It was also conducted on MCF7 cells treated with either a scrambled antisense oligonucleotide (ASO) or a LINE-1-targeting ASO. Additionally, LINE-1 Capture Pore-C was carried out on MCF7 cells stably expressing either a transgenic LINE-1 element or an "empty vector" TagBFP, both integrated at the "Rogi2" safe harbor locus (chr3:22,746,757).


title: Differential nucleosome organization in human interphase and metaphase chromosomes [RNA-Seq]

first: Xiaozhong

last: Wang

overall_design: Total RNA-seq of 2 clones of Hela S3 cells were performed as a complimentary data for the analysis of nuclesome mapped by chemical mapping

first: Keren

last: Li

first: Irem

last: Unlu

first: Lilien

last: Voong

first: Xiaotian

last: Ma

first: Yiren

last: Tu

first: Ji-ping