title: TGFβ-elicited pericyte dysfunction in aggressive prostate cancer

city: Badalona

first: ANE

middle: MARTINEZ

last: LARRINAGA

state: Barcelona

address: Ctra de Can Ruti, Camí de les Escoles s/n

department: Genesis of Cancer

country: Spain

institute: Institut de Recerca contra la Leucèmia Josep Carreras

summary: Pericytes are intrinsic components of vessels that regulate vascular stability and permeability. Aberrant vascularization is a hallmark of cancer, although the contribution of pericytes to this process is poorly understood. Here, we undertook a combined computational and experimental strategy to identify the molecular reprogramming of prostate pericytes during cancer pathogenesis and progression. Analysis of human prostate cancer and murine mouse models showed that prostate tumors exhibit a disequilibrium between endothelial and pericyte content with prognostic potential. Deeper molecular analysis revealed that there is no overt loss of pericytes in prostate tumors, but rather a disfunction that is concomitant with altered expression of a subset of cellular markers. We translate this finding into a simplified signature that discriminates pericyte abundance versus function. Leveraging single-cell RNA sequencing data, we find that TGFβ governs the molecular changes that underlie pericyte disfunction in tumors. This mechanism is associated with reduced pericyte contractility, enlargement of vascular lumen and increased permeability in prostate cancer. Altogether, this study revisits the paradigm of reduced number of pericyte in favor of their disfunction in tumors, and the importance of paracrine signaling in this process.

overall_design: To unravel the biological and functional consequences of paracrine TGFβ signaling in brain pericytes, we performed bulk RNA sequencing on cultured pericytes treated with TGFβ1 (5 μg/mL, PeproTech, #167100-21-B) or vehicle for 48 hours. Bulk RNA-Seq was conducted to investigate the differential gene expression in pericyte cultures treated with TGFβ1. Eight primary pericyte cultures derived from brain tissue were used. Four cultures were treated with TGFβ1 for 48 hours, while the other four were treated with vehicle as controls.


title: H9c2 cells with or without lactate (1hr)

status: Public on Oct 03 2025

city: Salt Lake City

first: Jordan

middle: A

last: Berg

state: UT

address: 15 N Medical Drive East, Rm 5520

department: Biochemistry

country: USA

institute: University of Utah

type: Expression profiling by high throughput sequencing

summary: H9c2 cardiomyoblast cells grown in DMEM or HPLM in the presence and absence of lactate. 4 unique conditions.

overall_design: H9c2 rat cardiomyoblast cells were grown in either DMEM or HPLM, in the presence or absence of lactate for 1 hour. RNA was then extracted from each condition and sequenced.

first: Ahmad

last: Cluntun

first: Opal

last: Allen

first: Jared

last: Rutter


title: Characterization of excitotoxicity induced transcriptional dysregulation

city: Jena

first: Philipp

last: Koch

address: Beutenbergstraße 11

department: Core Facility Life Science Computing

country: Germany

institute: Leibniz Institute on Aging - Fritz Lipmann Institute

summary: We describe the dysregulation of neuronal-activity dependent genes during the condition of toxic glutamate concentrations in primary hippocampal neurons. Genes differed in their response towards the loss of neuronal activity and the active shut-off of transcription. The most shut-off genes also show more direct synaptic function than the passively downregulated genes hinting to functional relevance of the shut-off mechanism. Findings were confirmed in an in vivo excitotoxicty model of Huntington´s disease.

overall_design: Five independent primary hippocampal preparations were treated with the GABAA receptor inhibitor bicuculline to induce transcription of synaptic-activity dependent genes. Following different durations of bicuculline treatment the active transcription shut-off was introduced by NMDA application and the passive shut-off by TTX application.

first: Kristin

last: Oberländer

first: Karol

last: Szafranski

first: David

last: Ibberson


title: Transcriptomic effects of irrigation with magnetized water on tomato (Solanum lycopersicum L.) during plant development

city: Martonvásár

first: Norbert

middle: Tibor

last: Hidvégi

address: Brunszvik street 2.

department: Department of Biological Resources

country: Hungary

institute: HUN-REN Centre for Agricultural Research Agricultural Institute

summary: Altered growth and yield have been proven in numerous crops in response to irrigation with magnetized water but there is still a lack of studies reporting molecular-level changes underlying these physiological alterations of plants. This study is the first to reveal transcriptional changes occurred in seedlings, blooming plants, and plants with fully ripe berries in response to irrigation with magnetized water. A total of 21 differentially expressed genes (DEGs) identified in 3 phenological phases were mostly involved in metabolic processes (metabolisms of carbohydrate, glutathione, lipid, vitamin and cofactors, biosynthesis of phenolpropanoid and proline) and cellular processes (DNA synthesis, transcription, translation and their regulation). The processes were related to vegetative biomass, developing flowers and berries. Furthermore, expression intensities of DEGs encoding proteins participating in cell division and enlargement (xyloglucan endotransglucosylase/hydrolase, EXORDIUM like protein) and in regulating water flow and other transmembrane transport processes (B12D protein, aquaporins, and dehydrin) were affected.

overall_design: For the control and magnetized water treatment, we used three biological replicates. mRNA-seq method was used for analyse the transcriptome profile for control and treated samples.

first: Judit

last: Dobránszki

first: Dóra

last: Farkas

first: Andrea

last: Gulyás

first: Gábor

last: Bagyánszky

first: Károly

last: Szép


title: Expression Profiling of cardiac fibroblasts

city: Saitama

first: MANABU

last: SHIRAISHI

address: Omiya-ku

country: Japan

institute: Jichi Medical Unversity

summary:
Transcriptome analysis of  RNA samples from cultured cardiac fibroblasts
Excessive extracellular matrix accumulation in the myocardium is a poor prognostic factor for reduced left ventricular function. It is known that improvement of hemodynamic loading improves myocardial fibrosis, but in vitro models of the pathogenesis have not been established, and the potential mechanism of fibrosis resolution have not clarified. We reproduced normal myocardium, fibrotic myocardium following hemodynamic loading and myocardium with improved fibrosis following hemodynamic loading reduction in vitro. Fibroblasts were activated to αSMA+ fibroblasts on myocardium following hemodynamic loading. On myocardium following hemodynamic loading reduction, they were deactivated to αSMA- fibroblasts, and their phenotype changed to fibrinolytic cells expressing MMP2 and MMP9. Comprehensive gene expression analysis of fibroblasts in each in vitro model revealed that Selenbp1 is one of the genes responsible for regulation of phenotypic changes in fibroblasts. In vitro, knockdown of Selenbp1 using RNA interference enhanced fibroblast activation and inhibited conversion to the fibrinolytic form. In vivo, knockdown of Selenbp1 caused structural changes in the left ventricle associated with progressive tissue fibrosis and left ventricular diastolic failure. Selenbp1 is involved in the regulation of fibroblast phenotype and was found to be one of the major molecules regulating collagen turnover in cardiac fibrosis.

overall_design: We analyzed cultured cardiac fibroblasts  using the Affymetrix GeneChip Arrays platform with ClariomTM S Assyay, Rat platform. Array data was processed by Affymetrix  Array Computational Tool. Group I: Fibroblasts were cultured in a medium with an elastic modulus of 16 Kpa. Group K: Fibroblasts were cultured in medium with an elastic modulus of 64 KPa plus TGF-beta recombinant protein. Group L: Fibroblasts were cultured in 64 KPa modulus medium with TGF-beta recombinant protein and then transferred to 16 KPa medium.

first: Manabu

last: Shiraishi


title: Pericytes orchestrate a tumor-restraining microenvironment in glioblastoma [Spatial Transcriptomics]

city: Lund

first: Kristian

last: Pietras

address: Sheelevägen 2

department: Division of Translational Cancer Research

country: Sweden

institute: Lund University

summary: To functionally assess the role of pericytes in glioma development and progression, we study the effects of pericyte depletion in orthotopic and transgenic mouse models of high-grade glioma using single-cell and spatial transcriptomics. We present evidence that pericytes mitigate glioma development by orchestrating a tumor-suppressive microenvironment, challenging the concept of pericytes as merely pro-oncogenic cells, and underscoring the importance of pericyte preservation in future GBM therapies.

overall_design: High-grade gliomas were initiated by stereotactically delivering the glioma oncogenic drivers PDGFB and shp53 into the subventricular zone of transgenic adult Ntv-a mice that were either pericyte-poor (Pdgfbret/ret) or control (Pdgfbret/+). 4 Pdgfbret/+ and 4 Pdgfbret/ret mice were sacrificed when displaying severe symptoms. Spatial transcriptomics sequencing was performed using the 10X Genomics Visium system.

first: Sebastian

last: Braun

first: Paulina

last: Bolivar

first: Clara

last: Oudenaarden

first: Jonas

last: Sjölund

first: Matteo

last: Bocci

first: Katja

last: Harbst

first: Mehrnaz

middle: S

last: Talkhoncheh

first: Bengt

last: Phung

first: Eugenia

last: Cordero

first: Rebecca

last: Rosberg

first: Elinn

last: Johansson

first: Göran

last: Jönsson

first: Alexander


title: Antigen reactivity defines tissue-resident memory and exhausted T cells in tumours.

status: Public on Oct 02 2025

city: Melbourne

first: Lachlan

last: Dryburgh

state: Victoria

address: 792 Elizabeth Street

department: The Department of Microbiology and Immunology,  The University of Melbourne

country: Australia

institute: The Peter Doherty Institute for Infection and Immunity

summary: CD8+ T cells are a key weapon in the therapeutic armamentarium against cancer. While CD8+CD103+ T cells with a tissue-resident memory T (TRM) cell phenotype associate with favourable prognoses, the tumour microenvironment also contains dysfunctional exhausted T (TEX) cells that exhibit a myriad of TRM-like features. Here, we deconvolute TRM and TEX cells across human cancers, ascribing markers and gene signatures that distinguish these populations and enable their functional distinction. While TRM cells exhibit superior functionality and are associated with long-term survival post-tumour resection, they are not associated with responsiveness to immune checkpoint blockade. Tumour-associated TEX and TRM cells are clonally distinct, with the latter comprising tumour-independent bystanders and tumour-specific cells segregated from cognate antigen. Intratumoural TRM cells can be forced towards an exhausted fate when chronic antigen stimulation occurs, arguing that the presence or absence of continuous antigen exposure within the microenvironment is the key distinction between tumour-associated TEX and TRM populations. These results suggest unique roles for TRM and TEX cells in tumour control, underscoring the need for distinct strategies to harness these populations in novel cancer therapies.

overall_design: scRNA-seq with CITE-seq and V(D)J profiling of CD3⁺ T cells isolated from colorectal cancer liver metastases, distal non-cancerous liver, and liver from cancer-free donors. Samples were collected from four patients with liver metastases and two cancer-free donors. Cells were loaded across 3 lanes of 10x Genomics 5' v2 kit, with unrelated CD3+CD8+ cells from PBMCs spiked across all 3 lanes to permit any batch corrections if necessary.

first: Laura

middle: K

last: Mackay

first: Thomas

middle: N

last: Burn

first: Jan

last: Schroeder


title: Reprogramming effect of Neurog2-9SA on adult mouse Muller glial cells [mutliomics]

city: Ann arbor

first: Thanh

last: Hoang

state: Michigan

address: 1000 wall street

institute: University of Michigan ann arbor

type: Genome binding/occupancy profiling by high throughput sequencing

summary: This study examines the reprogramming effect of Neurog2-9SA on adult mouse Muller glial cells. Generated neurons were characterized using immunohistochemistry, single-cell omics and electrophysiology. We found that AAV-mediated expression of Neurog20-9SA induces reprogramming of Muller glia into bipolar, amacrine-like neurons, and small subset of cells expressing phototreceptor marker

overall_design: GFP+ Muller glia cells and derived neurons were isolated using FACS at multiple timepoints, then subjected to 10xGenomic scRNA-Seq V3 and 10xGenomic Multiomics. Gene expression matrix and ATAC fragment files were generated using Cell ranger

first: Mengling

last: Ying

first: Sherine

last: Awad


title: Targeting Truncated O-Glycan Elicits Dual T Cell Immunity and Overcomes MHC-I Heterogeneity to Design Effective Cancer Vaccine

city: Guangzhou

first: Jing

last: Liao

state: Guangdong

address: No.1 Xinzao Road, Xinzao, Panyu District

department: GMU-GIBH Joint School of Life Sciences

country: China

institute: Guangzhou Medical University

summary: Aberrant O-glycosylation is a hallmark of cancer, but its contribution to immune evasion is unclear. Using CRISPR–Cas9 to delete GalNAc-transferases, particularly Galnt7, in tumor cells, we reduced mucin-type O-glycan truncation. This remodeling activated dendritic cell– and T cell–dependent immunity, eradicating established tumors, preventing metastasis, and generating durable memory. It enhanced clearance of MHC class I–positive tumors via coordinated CD8⁺ and CD4⁺ T cell responses, and uniquely enabled CD4⁺ T cell–mediated elimination of MHC class I–deficient tumors, which evade cytotoxic T lymphocyte surveillance. Tumor cells with reduced O-glycan truncation served as potent whole-cell vaccines, with efficacy further improved by radiotherapy. These findings establish glycosylation as a central regulator of tumor immune evasion and define a broadly applicable vaccine platform that bypasses the limitations of neoantigen-based approaches for low-immunogenicity cancers.

overall_design: RNA-seq profiling was performed on: 1) Colorectal tumor tissues from the AOM/DSS-induced tumorigenesis model at day 70 (n = 4). 2) The MC38 cell line (n = 3). 3) Tumor tissues collected on day 8 from wild-type C57BL/6J mice subcutaneously injected with Ctrl or Galnt7⁻/⁻ MC38 cells (n = 3). 4) CD8⁺ T cells isolated on day 14 from the spleens of C57BL/6J mice inoculated with MC38-Ctrl or MC38-Galnt7⁻/⁻ cells (n = 3). TCR-seq profiling was performed on CD8⁺ T cells isolated on day 14 from the spleens of C57BL/6J mice inoculated with MC38-Ctrl or MC38-Galnt7⁻/⁻ cells.

first: Jun

last: Chen

first: Chengzhou

last: Mao

first: Zijin

last: Xia

first: Wenhao

last: Mai

first: Xinyu

last: Wang

first: Xiaoding

last: Xu


title: Investigation of the Regulatory Mechanism of Dhx37 in Sertoli Cells Using snRNA-seq

city: Luoyang

first: Yuqing

last: Jiang

state: China

address: No. 263, Kaiyuan Avenue, Luolong District

institute: The First Affiliated Hospital, and College of Clinical Medicine of Henan University of Science and Technology

summary: To investigate the regulatory mechanism of Dhx37 in Sertoli cells, snRNA-seq analysis was performed on testicular cells isolated from whole testes of wild-type and Dhx37-/- mice (CKO)at P60. After quality control, single-cell transcriptomes for both wild-type and Dhx37-/- mice were obtained. UMAP dimension reduction and visualization categorized the cells into ten distinct clusters: Round Spermatids, Elongating Spermatids, Spermatocytes, Spermatogonia, Leydig cells, Fibroblasts, Sertoli cells, Macrophages, Endothelial cells, and others, based on known marker genes.

overall_design: Testicular cells were isolated from 8-week-old wild-type and Dhx37-/- mice following the snRNA-seq  procedure.

first: Huifang

last: Peng

first: Hongwei


title: Reprogramming of disease tolerance is necessary for infection defense during aging

city: San Diego

first: April

middle: Elizabeth

last: Williams

state: California

address: 10010 N Torrey Pines Rd

department: IGC

institute: Salk Institute for Biological Studies

summary: Cardiac gene expression of old and young C57Bl/6 mice infected with the LD50 dose of polymicrobial sepsis and age-matched uninfected controls.

overall_design: 12- and 75-week-old B6 mice were infected with the LD50 dose of 1:1 mixture of E. coli and S. aureus. When the morbid mice reached maximal morbidity in each age group, the hearts were harvested from the morbid-infected, healthy-infected and age-matched uninfected control mice for RNAseq.

first: Karina

last: Sanchez

first: Justin

middle: L

last: McCarville

middle: E

first: Sarah

middle: J

last: Stengel

first: Janelle

last: Ayres


title: Antigen reactivity defines tissue-resident memory and exhausted T cells in tumours

first: Lachlan

last: Dryburgh

overall_design: scRNAseq of transgenic T cells (either OT-I or gBT-I) isolated from B16-gB, epicutaneous melanoma tumours, and surrounding peritumoural skin. Split across 2 lanes of a 10x genomics, chromium 5' v2 kit. Each T cell type (tissue x transgenic) was hashtagged individually. Naive T cells were uniquely hashtagged and spiked in to allow for normalisation across lanes if required.

first: Laura

last: Mackay

first: Thomas

last: Burn

first: Jan

last: Schroeder

first: Maleika

last: Osman


title: Effects of three SSRIs (fluoxetine, citalopram, sertraline) exposure on brain tissue cells of zebrafish

city: Nanjing

first: mengyuan

last: Zhu

address: Xianlin Campus, Nanjing University, No.163 Xianlin Avenue, Qixia District, Nanjing, Jiangsu Province, China

institute: Nanjing university

summary: This study employed scRNA-seq to systematically analyze cellular proportions, differential gene expression, and the expression of enriched functional pathways in zebrafish brain tissues following SSRI exposure. Results revealed that distinct SSRI compounds disrupted core regulatory pathways of the serotonin neurotransmitter system through specific mechanisms, leading to significant gene expression heterogeneity in zebrafish brain cell populations. This research comprehensively elucidated the impacts of environmentally relevant concentration SSRI exposure on zebrafish brain cell populations, providing novel insights into the neurotoxic mechanisms of SSRIs in aquatic organisms.

overall_design: After exposing adult zebrafish to multiple SSRIs, their brain tissues were homogenized, and a single-cell suspension was isolated via density gradient centrifugation. The single-cell suspension was then loaded onto a microfluidic chip, and magnetic bead sorting was applied for scRNA-seq analysis.

first: Mengyuan

first: Junyi

last: Yang

first: Zhongchao

first: Hongqiang

last: Ren

first: Bing

last: Wu

first: Ling

last: Chen


title: Single-cell transcriptomics of Osr1 positive cells from mouse second heart field

city: Houston

first: Ke

last: Zhang

state: TX

address: 2121 W Holcombe Blvd

department: Center for Epigenetics & Disease Prevention

institute: Texas A&M IBT

summary: Cells from second heart field of mice with mixed B6/129/SvEv background were isolated and single cell sequencing was performed for two stages: E9.5 and E10.5. After dissection, hearts were minced and subjected to cell dissociation using trypsin.

overall_design:
Second heart field were harvested from WT mice at E9.5 and E10.5.

***************************************************************
The raw data were generated by North Dakota IDeA Network of Biomedical Research Excellence Bioinformatic Core which does not share raw data.
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first: Jing

last: Li

first: Lin

last: Liu

first: Linglin

last: Xie


title: FXR splicing by SF3B3 promotes MYC-driven hepatocarcinogenesis

city: Honolulu

first: Xue

last: Wang

state: Hawaii

address: 701 Ilalo Street

institute: University of Hawaii Cancer Center

summary: BACKGROUND AND AIMS: Dysregulation of the MYC oncogene is a major genetic event in hepatocellular carcinoma (HCC). Farnesoid X receptor (FXR), a bile acid (BA) receptor, has emerged as a promising therapeutic target for various liver diseases. Both BA composition and FXR isoforms have been shown to be significantly altered in human HCCs. This study aimed to investigate their potential roles in MYC-driven hepatocarcinogenesis. APPROACH AND RESULTS: HCC was induced in mice by hydrodynamic injection with MYC and MCL1 oncogenes. UPLC-MS/MS analysis revealed elevated BA levels, particularly primary conjugated BAs, in both serum and livers of MYC-driven HCC mice. qPCR and western blot analyses demonstrated suppression of BSEP and dysregulation of FXR splicing in the livers of these mice. Using RNA antisense purification coupled with mass spectrometry (RAP-MS), the splicing factor SF3B3 was identified as a regulator of FXR splicing. Both in silico and in vitro studies confirmed that SF3B3 is a direct downstream target of MYC in mice and humans. Functionally, overexpression of Fxrα2 and Fxrα4 or deletion of Sf3b3 significantly impeded MYC-driven hepatocarcinogenesis in mice. Moreover, combination treatment with a SF3B inhibitor and an FXR agonist synergistically suppressed proliferation of HCC cells. Analysis of clinical HCC samples revealed a positive correlation between SF3B3 and the relative expression of FXRα2. Conclusions: SF3B3 is a key downstream effector of MYC-driven hepatocarcinogenesis and a critical regulator of FXR splicing. Both SF3B3 and FXR represent druggable vulnerabilities in MYC-amplified HCC.

overall_design: RNA-seq profiling of HCC3-4 cells with shSf3b3 knockdown (KD) and negative control (PLKO).

first: Youcai


title: Exploring Mechano-metabolomic Pathways in CAR T cells

city: Brooklyn

first: Ngoc

middle: Bao

last: Luu

state: NY

address: 6 Metrotech Center, RH 621

institute: New York University

summary: Mechanical force generation at the immunological synapse is a hallmark of CAR T cell cytotoxicity and a key indicator of functional potency, yet the underlying mechanisms are not fully understood. Here, we performed real-time single-cell analysis to quantify the spatiotemporal dynamics of synaptic force and metabolic activity in CAR T cells upon CD19 antigen engagement. We identified a Piezo1–Ca²⁺–Wnt signaling axis that integrates mechanical sensing with cytoskeletal remodeling and metabolic reprogramming. This mechano-metabolic coupling drives CAR T cell activation and varies across different CAR constructs, patient-derived products, and manufacturing conditions. Notably, functional heterogeneity among CAR T cells correlates with differences in their mechanical force profiles and energetic output. Our findings reveal a reciprocal relationship between mechanotransduction and metabolic switching, providing new insight into CAR T cell biology. This framework may inform the development of screening tools and engineering strategies to enhance CAR T cell mechanical fitness, energetic resilience, and therapeutic efficacy.

overall_design: CAR T cells were acitvated by anti-FMC63 Antibody μBeads for 24 hours.

first: Weiqiang


title: Effects of Moringa oleifera extracellular vesicles on human microRNAs involved in the HeLa cell tumorigenesis

city: Roma

first: antonella

last: minutolo

state: RM

address: Via montpellier 1

department: Experimental medicine

country: Italy

institute: university of rome tor vergata

summary: The effects of extracellular vesicles from Moringa oleifera on the modulation of tumour associated human-microRNAs profile in cervical cancer-derived HeLa cells were investigated.  Plant extracellular vesicles have been shown to carry a variety of bioactive compounds, such as proteins, lipids, phytochemicals (e.g., phenols and flavonoids), and RNAs, including nucleic acids (e.g., miRs), mediating the transfer of information to recipient cells and thus modulating their function and gene expression.

overall_design: To define the microRNA profile in EVs-treated and untreated HeLa, the expression of 84 human miRNAs involved in human cancer was investigated. Total RNA was isolated from the pellets of MOES-EVs treated and untreated HeLa cells by TRIzol extraction method, according to the manufacturer’s instructions (Invitrogen, CA, USA). RNA was quantified using a NanoDropTM light spectrophotometer (Thermo Fisher Scientific, MA; USA) and stored at -20 °C until use. cDNA was obtained from total RNA by cDNA Reverse Transcription Kit (Thermo Fisher Scientific, MA; USA) and the expression analyses using a miScriptTM miRNA PCR Array Human Cancer Pathway array (cat # MIHS-102Z, Qiagen, Hilden, Germany). The assays were performed in a Bio-rad instrument (CFX96 Real-Time System, Biorad, Hercules, California, USA) using SYBR Green chemistry (Fast QPCR Master Mix, SmoBio, Taiwan), following the manufacturer’s instructions.   The basal miRs expression detected in untreated HeLa cells was categorized in three groups with respect to Ct values: group n.1 from 15 to 20 Ct; group n.2 from 21 to 30 Ct; group n.3 >30 Ct.   Data were obtained by the application of the 2−ΔCt method, normalising for the housekeeping controls SNORD 61 and SNORD 96A. The fold change was calculated between 2−ΔCt of treated cells/untreated cells. The miRs with >1.5-fold change were considered over expressed and those with a value between 0.5 and 1.5 equally expressed, while the miRs with a fold change <0.5 as under expressed.

first: MARINA

last: POTESTÀ

first: VALENTINA

last: ROGLIA

first: ALESSANDRA

last: MINCHELLA

first: MARCO

last: CIOTTI

first: ANNA

last: CRISCUOLO

first: GABRIELE

last: DI MARCO

first: ANGELO

last: GISMONDI

first: ANTONELLA

last: CANINI

first: ALESSIA

last: D’AGOSTINO

last: MINUTOLO

first: CARLA

last: MONTESANO


title: Single-nucleus RNA sequencing elucidates DHM's therapeutic mechanisms against HFD-induced BAT dysfunction

city: Tianjin

first: shuran

last: yang

address: No. 10, Poyanghu Road, West District of Tuanbo New Town, Jinghai District, Tianjin

institute: Tianjin University of Traditional Chinese Medicine

summary: Obesity is associated with chronic diseases such as atherosclerosis and type 2 diabetes. In obesity, brown adipose tissue (BAT) activity declines, and lipid accumulation impairs its function. Dihydromyricetin (DHM) exhibits multiple biological functions, including inhibiting adipogenesis, promoting lipolysis, suppressing mitochondrial autophagy, and exerting anti-inflammatory and antioxidant effects, collectively demonstrating significant potential in obesity prevention and treatment. However, research on DHM's mechanisms in the BAT of obese mice remains limited.  In this study, we performed single-nucleus RNA sequencing (snRNA-seq) to systematically characterize obesity-induced BAT dysfunction and DHM's effects at single-cell resolution in high-fat diet (HFD)-fed C57BL/6J mice. The results demonstrated that DHM ameliorated HFD-induced brown adipocyte dysfunction by modulating energy balance in Ad3 and Ad5 adipocyte subpopulations, promoting lipolysis, suppressing pro-inflammatory factor expression, inhibiting extracellular matrix remodeling, and regulating adipocyte-perivascular cell interactions. These findings provide insights into DHM's role in preventing BAT dysfunction and support its clinical application for obesity.

overall_design: snRNA-seq was conducted on three groups: normal diet (ND), high-fat diet (HFD), and HFD with DHM treatment (DHM_HFD). Bioinformatics analyses included multi-sample integration, cell annotation, pathway enrichment, transcription factor networks, and cell-cell communication prediction. These analyses identified dysfunctional adipocyte subpopulations and elucidated DHM's regulatory mechanisms.

first: Shuran

last: Yang

first: Guanyu

last: Zhang

first: Shuai

last: Wu

first: Yibing

first: Yusha

first: Ting

last: Yi

first: Danfeng

first: Zhenyu

last: Zhao

first: Xi

last: Li


title: RNA microarray was performed from lung adenocarcinoma cell CL1-0 and CL1-5 that were manipulated LCRMP-1 expression.

city: Taipei

first: Yuan-Ling

last: Hsu

address: No.1 Jen Ai road section 1

country: Taiwan

institute: National Taiwan University, College of Medicine

summary: Transcriptomic profiling of CL1-0 and CL1-5 cells with altered LCRMP-1 expression revealed that LCRMP-1 promotes angiogenesis by regulating angiogenesis facotr transcription, implicating its role as a transcriptional co-regulator in lung cancer progression.

overall_design:
CL1-0 LCRMP-1 overexpressing cells (clone  1 and clone 2) were compared with CL1-0 Vector control cells. CL1-5 LCRMP-1 silencing cell was compared with CL1-5 Scramble control cell. Each experimental condition for all cell lines was performed with two biological replicates.
Please note that each sample data was generated from both replicates.

first: Pei-Fang

last: Hung

first: Chi-Chung

last: Wang

first: Yih-Leong

last: Chang

first: Chen-Tu

first: Pei-Shan

first: Xuan-Ren

last: Chen

first: Tse-Ming

last: Hong

first: Pan-Chyr

first: Szu-Hua

last: Pan


title: LRRK2-mediated neuroinflammation induced neuronal dysfunctions in a Parkinson’s and Alzheimer’s disease cellular model

city: Brescia

first: Paolo

last: Martini

address: viale Europa 11

department: Department of Molecular and Translational Medicine

institute: University of Brescia

summary: Dissect the transcriptional consequences of neuroinflammation and the role of the kinase LRRK2 in regulating neuronal responses in human induced pluripotent stem cell (hiPSC)-derived neurons exposed to pro-inflammatory conditions relevant to Parkinson’s disease (PD) and Alzheimer’s disease (AD).Dopaminergic neurons (PD context) and cholinergic neurons (AD context) were differentiated from hiPSCs and subsequently cultured in glial-conditioned medium containing either α-synuclein pre-formed fibrils (α-syn pffs) or amyloid-β (Aβ) fibrils, for PD and aAD respectively. Neuronal cultures were exposed to inflammed media to model chronic inflammatory stress.

overall_design: hiPSCs derived dopaminergic neurons were cultured under four experimental conditions: untreated controls (NT; N=4), exposure to α-synuclein pre-formed fibrils (α-syn pffss) for PD context (N=4), treatment with the LRRK2 inhibitor PF (PF; N=5), or treatment with the LRRK2 inhibitor MLi-2 (MLI2; N=4). hiPSCs derived colinergic neurons were cultured under four experimental conditions: untreated controls (NT; N=5), exposure to amyloid-β (Aβ) for AD context (N=5), treatment with the LRRK2 inhibitor PF (PF; N=5), or treatment with the LRRK2 inhibitor MLi-2 (MLI2; N=5).

first: Veronica

last: Mutti

first: Moira

last: Marizzoni

first: Isabella

last: Russo


title: Flt3L -expanded conventional type I dendritic cells formed in the tumor prime “stem-like” T cells in the draining lymph nodes to evoke enhanced responses to immunotherapy [2]

city: Perth

first: Jesse

middle: David

last: Armitage

state: WA

address: 35 Stirling Hwy, Crawley

department: School of Biomedical Sciences

institute: University of Western Australia

summary: Immune checkpoint blockade (ICB) evokes anti-tumor immunity through the reinvigoration of tumor-specific T cell responses but it is only effective in a subset of patients. T cell differentiation status is a critical determinant of response, with less differentiated cells demonstrating an enhanced capacity to proliferate following ICB. Given recent data indicating that conventional type 1 dendritic cells (cDC1) maintain precursor exhausted (TPEX) cells, we hypothesized that expansion of cDC1s could enhance responses to ICB. Treatment of mice with Flt3L simultaneously expanded cDC1s and CD62L+SLAMF6+CD8+ T cells in both tumors and draining lymph nodes. The formation of these CD62L+SLAMF6+ CD8+ T cells is dependent on the transcription factor Myb, CCR7+ XCR1+DCs and lymph node egress. Hence, we demonstrate that the lymph node is a critical site for the effect of Flt3L on T cell differentiation state. We hypothesized that the promotion of this phenotype would enable more effective responses to ICB. Indeed, the combination of Flt3L and anti-CTLA4 led to significantly enhanced therapeutic responses and was associated with the emergence of a unique CD8+ T cell subset characterized by the expression of IL-21R.

overall_design: Single cell RNA-TCR profiling of whole AT-3 or AT-3-FLT3L tumors, +/- aCTLA4 treatment. Matched draining lymph nodes (dLNs) were also harvested from a proportion of these mice. tumor (n=6 per group) and dLN samples (n=3 per group) were labelled lipid-modified oligonucleotides (LMOs) for cell hashing and pooled into 4 samples for sequencing.

middle: D


title: ATP-dependent remodeling of chromatin condensates reveals distinct mesoscale outcomes

city: San Francisco

first: Vijay

last: Ramani

state: CA

address: 1700 Owen Street

institute: Gladstone Institues

summary: ATP-dependent chromatin remodeling enzymes mobilize nucleosomes, but how such mobilization affects chromatin condensation is unclear. Here, we investigate effects of two major remodelers, ACF and RSC using chromatin condensates and single-molecule footprinting. We find that both remodelers inhibit the formation of condensed chromatin. However, the remodelers have distinct effects on pre-formed chromatin condensates. ACF spaces nucleosomes without de-condensing the chromatin, explaining how ACF maintains nucleosome organization in transcriptionally repressed genomic regions. In contrast, RSC catalyzes ATP-dependent de-condensation of chromatin.  RSC also drives micron-scale movements of entire chromatin condensates. These additional  activities of RSC may contribute to its central role in transcription. The biological importance of remodelers may thus reflect both their effects on nucleosome mobilization and the corresponding consequences on chromatin dynamics at the mesoscale.

overall_design: Chromatin  was assembled in vitro via salt gradient dialysis. Chromatin arrays were remodeled in vitro with ATP-dependent chromatin remodelers and visualized via microscopy. Chromatin was then profiled with m6A methyltransferase footprinting and SMRT long-read sequencing (SAMOSA-ChAAT). 36 in vitro chromatin samples were analyzed.

first: Camille

last: Moore

first: Emily

last: Wong

first: Upneet

last: Kaur

first: Un Seng

last: Chio

first: Ziling

last: Zhou

first: Megan

last: Ostrowski

first: Ke

first: Iryna

last: Irkliyenko

first: Sean

first: Geeta

last: Narlikar


title: ZAK activation at the collided ribosome

city: Baltimore

first: James

last: Saba

state: MD

address: 725 N Wolfe St, 714 PCTB

department: Molecular Biology and Genetics

institute: Johns Hopkins

summary: Ribosome collisions activate the ribotoxic stress response (RSR) mediated by the MAP3K ZAKα (ZAK), which in turn regulates downstream phosphorylation of the MAPKs JNK and p38 and cell fate consequences. Despite this critical role during cellular stress, a structural and mechanistic understanding of the ZAK-ribosome interaction and activation have remained elusive. Here, we combine biochemistry with cryo-electron microscopy (cryo-EM) to dissect ZAK interactions with ribosomes in various states both in vivo and in vitro. We identified regions of ZAK necessary for binding to ribosomes under normal and under stress-induced conditions. Moreover, we discovered how interactions between ZAK and the ribosomal protein RACK1 mediate ZAK activation by recognizing the collision-interface. Further, we provide insight into how this process can be negatively regulated to prevent constitutive ZAK activation. Characterizing novel variants as well as a known pathogenic variant of ZAK’s SAM domain supports a key role of this conserved domain in regulating kinase activity on and off the ribosome. Collectively, we show that ZAK directly binds at the collided ribosome interface giving molecular insight into kinase activity regulation at the ribosome.

overall_design: CLIP-seq of ZAK-KO HEK293T cells transfected with different ZAK constructs (Full-length (WT), Activation Loop mutant (ActLoopD), 1-649 truncation (RBRdel), overexpressed Activation Loop Mutant (OX-ActLoopD), or mock (ZAK-KO), treated with or without Anisomycin. Two replicates for each group.

first: Vienna

last: Huso

first: Shuangshuang

last: Niu

first: Roland

last: Beckmann

first: Rachel

last: Green


title: A bioinformatics screen identifies TCF19 as an aggressiveness-sustaining gene in prostate cancer

city: Derio

first: Ana

middle: Maria

last: Aransay

state: BIZKAIA

address: Parque tecnologico de Bizkaia, Building 801-A

department: Genome Analysis Platform

institute: CIC bioGUNE

summary: Prostate cancer is a prevalent tumor type that, despite being highly curable, progresses to metastatic disease in a fraction of patients, thus accounting for more than 350 000 annual deaths worldwide. In turn, uncovering the molecular insights of metastatic disease is instrumental in improving the survival rate of prostate cancer patients. By means of gene expression meta-analysis in multiple prostate cancer patient cohorts, we identified a set of genes that are differentially expressed in aggressive prostate cancer. Transcription factor 19 (TCF19) stood out as an unprecedented epithelial gene upregulated in metastatic disease, with prognostic potential and negatively associated with the activity of the androgen receptor. By combining computational and empirical approaches, our data revealed that TCF19 is required for full metastatic capacity, and its depletion influences core cancer-related processes, such as tumor growth and vascular permeability, supporting the role of this gene in the dissemination of prostate tumor cells.

overall_design: GFP-Luc PC3 cells expressing stable shRNAs against Scramble or TCF19 were injected into the ventral lobe of the prostates of immune-deficient nude mice. Prostate primary tumors were collected after 19 days and processed for transcriptomics analysis. 6 tumors per group were collected.

first: Amaia

last: Ercilla

first: Jana

middle: R

last: Crespo

first: Saioa

last: Garcia-Longarte

first: Natalia

last: Martin-Martin

first: Onintza

last: Carlevaris

first: Ianire

last: Astobiza

first: Sonia

last: Fernández-Ruiz

first: Marta

last: Fidalgo

first: Marc

last: Guiu

first: José-Ezequiel

last: Martín

first: Isabel

last: Mendizabal

middle: M

first: Roger

last: Gomis

first: Mariona

last: Graupera

first: Arkaitz

last: Carracedo


title: Context-dependent regulation of T follicular helper cell formation, expansion and differentiation into T-regulatory type 1 cells by multiple transcription factors

city: Barcelona

first: Josep

last: Garnica

address: Rosselló, 149

institute: IDIBAPS

summary: Differentiation of naïve T cell precursors into distinct T helper cell subsets, including T follicular helper (TFH) cells, is driven by the expression/repression of subset-specific transcription factors (TFs) that have well defined effects on the acquisition of alternative gene expression programs. Repetitive antigen encounters by TFH cells can trigger their differentiation into IL-10-producing Foxp3– and Foxp3+ T-regulatory type 1 (TR1) cells. Since TFH cells are epigenetically poised to differentiate into TR1 cells, we hypothesized that the cell conversion events underpinning this process are regulated at the transcriptional level. Here, we interrogate the role of 20 TFs that bind to motifs enriched in open chromatin regions along the TFH-TR1 cell axis, on the size and function of the pre-treatment TFH cell pool and the size and transcriptional make-up of the various antigen-specific TFH/TR1 cell subsets arising in vivo post repetitive antigen challenge. We find that certain TFH TFs, such as TCF-1 and TOX-2, contribute to TFH cell genesis and TFH cell function but are dispensable for antigen-specific TFH cell expansion and TR1 transdifferentiation. Eleven other TFs, including ATF-6, BATF, BCL-6, BHLHE40, BLIMP-1, ELK-4, IRF4, c-MAF, STAT-3, STAT-4 and T-BET, play distinct roles at different stages of this pathway in a context-dependent manner. Most of these TFs simultaneously promote and suppress different cell conversion events along the axis and promote the expression of subset-specific signature genes at specific cell stages while simultaneously suppressing the expression of such genes at other cell stages in the pathway. This indicates that differentiation of TFH cells into TR1 progeny is driven by a carefully orchestrated sequence of TF gene expression and silencing events that yields dynamic combinations of TFs that enable cell-to-cell transitions. The transcriptional context in which specific TFs are expressed determines their ability to either drive or suppress such transitions and promote or inhibit the expression of alternative gene expression programs at different cell states.

overall_design: Single-cell RNA sequencing (scRNA-seq) was performed on T cells deficient for 11 transcription factors to investigate their roles in the TFH-to-TR1 differentiation pathway. Samples from control and TF-deficient mice were included in each sequencing run to enable accurate cell annotation across the four Tet+ subpopulations (TFH, TR1.1, Foxp3– TR1.2, and Foxp3+ TR1.2).

first: Enric

last: Canut

first: Mireia

last: Palou

first: Pere

last: Santamaria


title: Flt3L -expanded conventional type I dendritic cells formed in the tumor prime “stem-like” T cells in the draining lymph nodes to evoke enhanced responses to immunotherapy [1]

first: Jesse

last: Armitage

overall_design: Single cell RNA profiling of whole 24JK or 24JK-FLT3L tumors. Harvested day 16, n=5 per group


title: Adipocyte-derived FABP4 promotes MASLD-induced hepatocellular carcinoma by driving ITGB1-mediated β-catenin activation [rhFABP4]

city: Shatin

first: Karl Kam Hei

last: So

state: New Territories

address: 608A, Lo Kwee-Seong Integrated Biomedical Sciences Building, The Chinese University of Hong Kong

country: Hong Kong

institute: The Chinese University of Hong Kong

summary: The mechanism underlying regulatory role of FABP4 in MASLD-HCC development was examined using bulk RNA sequencing.

overall_design: HCC cell line PLC/PRF/5 was pretreated with either 0ng/mL or 100ng/mL human recombinant FABP4 (rhFABP4) for 24 hours. RNA of treated cells was extracted for bulk RNA sequencing.

first: Carmen

middle: O

last: LEUNG

first: Shilpa

last: GURUNG

first: Katherine

middle: P

last: CHUNG

first: Karl

last: SO

first: Terence

last: LEE


title: Transcriptome profile of hepatocellular carcinoma in patients with atezolizumab plus bevacizumab therapy.

city: Chiba-shi

first: Hiroaki

last: Kanzaki

state: Chiba

address: 1-8-1 Inohana, Chuo-ku

department: Department of Gastroenterology

institute: Graduate School of Medicine, Chiba University

summary: Hepatocellular carcinoma (HCC) is a rapidly increasing and highly lethal cancer worldwide, with many patients diagnosed at advanced stages and early-stage patients often experiencing high recurrence rates. The combination of atezolizumab plus bevacizumab emerged as a groundbreaking immunotherapy, establishing a new standard of care for advanced HCC. There's an urgent need for reliable biomarkers to predict patient responses and personalize treatment. We collected tumor samples from advanced HCC patients wirth atezolizumab plus bevacizumab therapy and performed comprehensive analyses of the tumor microenvironment using bulk RNA sequencing to identify key features influencing the effectiveness of atezolizumab plus bevacizumab.

overall_design: HCC tumor tissues were obtained from a total of 73 patients who underwent diagnostic liver biopsy and used for RNA isolation and genome-wide transcriptome profiling by bulk RNA sequencing.

first: Takamasa

last: Ishino

first: Sadahisa

last: Ogasawara

first: Yosuke

last: Togashi


title: RNA-seq of oligodendrocyte progenitors immunopanned from postnatal day 6-8 mice treated with high glucose (HG) or low glucose (LG).

city: New York

first: Patrizia

last: Casaccia

address: 85 St Nicholas Terrace

department: Neuroscience

institute: ASRC-CUNY

summary: Myelination is one of the final milestones of post-natal brain development in rodent and man. Oligodendrocytes, the myelinating glia of the CNS, are differentiated from proliferative progenitor cells called OPCs. Local and systemic signals act on OPCs to promote their proliferation and survival in the developing forebrain before growth arrest and differentiation. During this period, altricial mammals, like rodent, experience a dramatic shift in nutrient source (e.g., maternal blood or milk) and composition (e.g., carbohydrate or fatty acid). The influence of metabolism on neural cells is of growing interest, but how metabolic changes in the early postnatal brain impact OPC dynamics remains poorly understood. Here we show that a glucose oscillation in developing forebrain is detectable by MALDI MS imaging and correlates with a temporal and region-specific transition of OPCs from proliferation to differentiation. In dorsal cortex and white matter regions, glucose levels decline in the second postnatal week during a critical window when OPCs slow proliferation and begin differentiation. In ventral regions we observe continually elevated glucose and OPCs persist in a proliferative state, thereby suggesting that glucose availability serves as a local signal promoting progenitor expansion, or cell cycle exit and differentiation, in early brain. When OPCs are cultured in low glucose, we detect glucose-responsive histone acetylation changes and a transcriptional signature of cell cycle exit and differentiation. Mechanistically, we link the activity of the metabolic enzyme ATP citrate lyase, which converts glucose-derived citrate to the central metabolite acetyl-CoA, to acetylation and proliferation dynamics downstream of glucose availability in cultured cells. Pharmacological inhibition or genetic deletion of ACLY in cultured OPCs results in reduced histone acetylation and levels of cell cycle related transcripts, and reduced proliferation, supporting the hypothesis that glucose bioavailability influences OPC dynamics via ACLY. A transgenic animal model of conditional ACLY deletion in OPCs timed to the period of high glucose availability in brain results in decreased histone acetylation and growth-arrest leading to a depletion of the oligodendrocyte pool and hypomyelination. Finally, we link the emergence of ketone bodies in brain to the period of reduced glucose availability and show that alternative sources of acetyl-CoA that bypass glucose rescue Acly-/- OPC viability. Our results support a temporal-metabolic model centered on glucose availability in the timing of OPC growth arrest, and that alternative substrates of acetyl-CoA such as ketone body serve as a metabolic bridge during glucose fluctuations to promote oligodendrocyte survival and differentiation.

overall_design: Transcriptome profiles (bulk RNA-seq assay) of oligodendrocyte progenitors treated with HG (25 mM) or LG (2.5 mM)

first: Ipek

last: Selcen

first: Sami

last: Sauma


title: Adipocyte-derived FABP4 promotes MASLD-induced hepatocellular carcinoma by driving ITGB1-mediated β-catenin activation

overall_design: Chemically induced MASLD-HCC model was generated using male wildtype and Fabp4 knockout C57BL/6N mice. They were treated with N-nitrosodiethylamine at 25mg/kg intraperitoneally at the age of 14 days. Starting at 6 weeks of age, they were fed with high fat diet for 29 weeks. Tumor nodules in the livers were extracted for bulk RNA sequencing.

last: Leung

last: Gurung

last: Chung

last: Lee


title: Mechanisms of maternal antibody interference to rotavirus vaccination

city: Ithaca

first: Tawny

last: Chandler

address: 235 Hungerford Hill Rd

institute: Cornell University

summary: We have employed a single-cell sequencing approach using the 10x Genomics scRNAseq pipeline to study the effect of maternal antibodies on the response to vaccination in the mesenteric lymph node. Given the ability of maternal antibodies to intefere with sero-conversion to rotatvirus vaccination we hypothesized that maternal antibodies would alter the activation and differentiation of lymphocytes. This study presents data on transcriptome dynamics of the mesenteric lymph node following rotavirus vaccination in the absence or presence of maternal antibodies.

overall_design: Following oral rotavirus vaccination at 7 days of age, the mesenteric lymph node chain was isolated at 10 days post-infection from C57Bl/6 mouse pups and a single-cell suspension was analyzed using scRNA-seq. Samples were analyzed from two pups that were vaccinated without maternal antibodies (naive) and samples were analyzed from two pups that were vaccinated with maternal antibodies (MatAb).

first: Sarah

last: Woodyear

first: Faraz

last: Ahmed

last: Caddy


title: Dietary and exercise interventions improve cognition and alter hippocampal transcriptome in a metabolic syndrome mouse model

city: Grand Forks

first: Junguk

last: Hur

state: ND

address: 1301 N. Columbia Rd. Stop 9037

department: Biomedical Sciences

institute: University of North Dakota

summary: The metabolic syndrome (MetS) is a major global health concern that continues to rise in prevalence. Further fueling the burden of disease, MetS predisposes individuals to neural injury, enhancing the risk of developing cognitive impairment (CI). MetS management encourages weight loss and physical activity to ameliorate overall systemic metabolic health with consequent improvement on CI. In this light, diet and exercise (EX) have garnered interest as non-pharmacological interventions for CI, which, besides their salutary benefits on systemic metabolic health, exert multifactorial neuroprotective effects locally within neural tissue. Nevertheless, the detailed molecular and cellular mechanisms of diet- and EX-mediated benefits on CI remain incompletely understood. Moreover, most studies have assessed the impact of either diet or EX on CI, so direct, head-to-head comparisons are lacking, to our knowledge. Herein, we compared high-fat diet (HFD) and ketogenic diet (KD) versus standard-diet (SD) on systemic metabolism, CI, and hippocampus transcriptome. We also assessed the efficacy of dietary reversal (DR, switch from HFD to SD), KD intervention (KDI), EX, and combined KDI-EX for reversing HFD-induced MetS CI. We found HFD, but not KD, impaired systemic metabolism and induced CI relative to SD, and all diets differed in hippocampus transcriptome. All interventions, DR, KDI, EX, and KDI-EX improved the MetS and CI, albeit to differing extents with superior performance from diets with/without EX than EX alone. In tandem, interventions also changed hippocampal gene expression, in metabolic and neuroactive ligand-receptor signaling pathways. Overall, our findings have important health implications and especially advocate diet for improving MetS and associated CI.

overall_design: The 11-week-old male C57BL/6J mice were purchased from Jackson Laboratory. For the study, all mice were singly housed, given access to food and water ad libitum, and maintained on a 12:12 h light/dark cycle. At 12 weeks of age, mice were randomly assigned to seven groups: (i) standard diet (SD; n=16) mice maintained until 26 weeks of age on SD (10 kcal% fat;), (ii) HFD mice maintained until 26 weeks of age on lard-based HFD (60 kcal% fat), (iii) KD mice maintained until 26 weeks of age on cocoa butter-based KD (90% kcal% fat), (iv) DR mice  fed HFD until 18 weeks of age and then switched to SD from 18 to 26 weeks of age, (v) KDI mice fed HFD until 18 weeks of age and then switched to KD from 18 to 26 weeks of age, (vi) EX mice  fed HFD until 26 weeks of age and then provided full access to a voluntary running wheel from 18 to 26 weeks of age, (vii) KDI-EX mice fed HFD until 18 weeks of age and then switched to KD with full access to a running wheel from 18 to 26 weeks of age.At study end, mice were sacrificed and hippocampus tissue were collected for RNA sequencing.

first: Eva

last: Feldman


title: Transcriptome profile of post ovulatory oviduct of pigs

city: Guwahati

first: Jaya

last: Bharati

state: ASSAM

address: ICAR-NRC on Pig, Rani

department: Animal Physiology

country: India

institute: ICAR-National Research Centre on Pig, Guwahati, Assam

summary: The objective of this study was to investigate the global transcriptomic changes in the porcine oviduct after ovulation and to further investigate the differentially expressed genes (DEGs) associated with the transition from estrus to metestrus phase after ovulation. The RNA-Sequencing of the post ovulatory ampulla (POA) and early luteal ampulla (ELA) tissues were conducted using Illumina NextSeq2000.  The R package NOISeq was used to obtain significant differentially expressed genes (DEGs) with probability of differential expression (1-FDR) value ≥ 0.95 and log2 fold change (log2FC) ≥ 1. The DEGs were further explored by bioinformatics analysis for gene ontology, pathway analysis, hub gene analysis and immune system process analysis.

overall_design: The RNA-Sequencing of the post ovulatory ampulla (POA) (n = 3) and early luteal ampulla (ELA) (n = 3) tissues were conducted using Illumina NextSeq2000.

first: Satish

last: Kumar

first: N

middle: H

last: Mohan

first: Vivek

last: Gupta


title: Spatial immune profiling defines a subset of human gliomas with functional tertiary lymphoid structures [GEOMX]

city: Frankfurt am Main

first: Katharina

last: Imkeller

address: Heinrich-Hoffmann-Str. 7

institute: University Hospital Frankfurt

summary: Adult-type diffuse gliomas, the most common primary brain tumors, respond poorly to immune-based therapies and are considered immunologically "cold" tumors. Here, we examined the features and clinical relevance of glioma intratumoral tertiary lymphoid structures (TLSs) using spatial transcriptome and proteome profiling. In a cohort of 642 gliomas, TLSs were present in 15% of tumors and associated with a remodeled perivascular space and spatial redistribution of extracellular matrix components. Three distinct TLS subtypes could be defined based on differing cellular composition and immune activity. While all subtypes lacked classical germinal center architecture, certain TLSs exhibited features of dynamic immune functions, including clonal T and B cell expansion, generation of IgA⁺ and IgG⁺ plasma cells, and dendritic cell-T cell interactions. The presence of TLSs with active immune response features correlated with improved overall survival. Thus, a functional adaptive immune response is detectable in some gliomas, with implications for stratification and treatment.

overall_design:
To explore the molecular and cellular architecture and immunological function of glioma-associated TLS, we analyzed 642 glioma specimens from the Frankfurt University Cancer Center. We found that 15% of gliomas had B cell aggregates (TLS+), while the rest did not (TLS-).We used a multi-modal spatial profiling approach, including spatial transcriptome profiling, whole slide multiplex immunofluorescence staining, and high-plex immunofluorescence staining, on consecutive tissue sections to trace single TLS through different molecular layers.We performed bulk RNA sequencing on 64 gliomas, with and without TLS, matched for IDH status, age, and gender. We examined the transcriptional profiles of 61 TLS from 20 tumors using spatial transcriptome profiling.

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first: Pinar

last: Cakmak

first: Jennifer

last: Lun

first: Aakanksha

last: Singh

first: Jadranka

last: Macas

first: Jonathan

last: Schupp

first: Miriam

last: Köhler

first: Tatjana

last: Starzetz

first: Michael

middle: C

last: Burger

first: Eike

last: Steidl

first: Lucie

last: Hasse

first: Elke

last: Hattingen

first: Karl

last: Plate

first: Yvonne

last: Reiss

first: Jonas

last: Schuck

first: Zeina

last: Mahmoud


title: YAP/TAZ cooperate with AP-1 to drive the mesenchymal cell state in neuroblastoma [ATACseq]

city: Vienna

first: CCRI

last: BiCU

address: Zimmermannpl. 10

department: Bioinformatics Core Unit

country: Austria

institute: St. Anna Children's Cancer Research Institute

summary: Cellular plasticity is a major driver of therapy resistance in cancer. For the pediatric solid tumor neuroblastoma, two distinct tumor cell phenotypes have been identified: adrenergic (ADR) and mesenchymal (MES) cells. Of those, the MES cells pose a rare subtype resistant to common treatment options. Here, we developed an image-based compound screen to interrogate vulnerabilities specific to the MES phenotype at single-cell resolution in heterogeneous neuroblastoma cultures. Among the top hits, we identified inhibition of the transcriptional co-activators YAP/TAZ as a specific target in MES cells. Based on their chromatin binding, we show that YAP/TAZ cooperate with AP-1 transcription factors to regulate MES gene expression by forming a core-regulatory circuitry. We further provide evidence of a subset of tumor cells in patients co-expressing these factors. Collectively, we demonstrate that YAP/TAZ and AP-1 drive neuroblastoma tumor cell plasticity and present a novel therapeutic vulnerability with the potential to overcome treatment resistance.

overall_design: We separated 4 heterogeneous neuroblastoma cell lines into adrenergic (ADR) and mesenchymal (MES) subcultures based on adherence properties. The following cell lines were used: STA-NB-8, STA-NB-10, CLB-Ma, SK-N-SH. From these 8 cultures we isolated cells and performed ATAC-seq.

first: Sören

last: Strohmenger

first: Sabine

last: Taschner-Mandl

first: Kaan

last: Boztug


title: Sequencing data of primary lung tumors and metastatic liver tumors in RP mice with SCLC

first: Yujie

last: Hao

address: 22 Qixiangtai Road

institute: Tianjin Medical University

summary: In RP (Rb1fl/fl;Trp53fl/fl) mice, SCLC phenotype tumors were established eight months after intratracheal injection of an adenovirus carrying Cre recombinase, driven by the CMV promoter. Primary lung tumors and metastatic liver tumors from the same mouse were collected for sequencing, resulting in a dataset.A similarity analysis was conducted between this dataset and the subpopulations with high and low autophagic flux in our RPΔG (Rb1fl/fl;Trp53fl/fl;GFP-LC3-RFP-LC3△G) mice. The analysis revealed that the subpopulation with high autophagic flux exhibited greater similarity to the metastatic data.

overall_design: In RP (Rb1fl/fl;Trp53fl/fl) mice, SCLC phenotype tumors developed within eight months following intratracheal injection of an adenovirus carrying Cre recombinase, driven by the CMV promoter. Primary lung tumors were formed in the lungs, and metastatic tumors were observed in the liver. We collected two lung tumor nodules and one liver metastatic tumor nodule from the same mouse for sequencing analysis.

first: Zhe

last: Liu


title: Gene expression profiling of murine SCLC tumor subpopulations with high and low autophagic flux

summary: Small cell lung cancer (SCLC) is characterized by significant heterogeneity and plasticity, driving its aggressive progression and resistance to therapy. Understanding the underlying mechanisms of these features is crucial for improving treatment outcomes. Autophagy, a conserved cellular process, is involved in many cancers, but its role in SCLC remains unclear. Using a genetically engineered mouse model (Rb1fl/fl;Trp53fl/fl;GFP-LC3-RFP-LC3△G), we tracked autophagic flux in vivo to assess its effects on SCLC biology. Tumor subpopulations with high autophagic flux exhibited increased proliferation, enhanced metastatic potential, and neuroendocrine (NE) characteristics, whereas subpopulations with low autophagic flux exhibited more immune-related signals and non-NE traits.

overall_design: GFP-LC3-RFP-LC3ΔG-knockin mouse model was developed to facilitate in vivo monitoring of autophagic flux. This model was crossed with Rb1fl/fl; Trp53fl/fl (RP) mice to establish an animal model exhibiting molecular and histopathological features similar to human SCLC. Lung tumor tissues from the resulting RPΔG mice were harvested, digested into single cells, and red blood cells were removed. Cellular subpopulations were isolated using Fluorescence-Activated Cell Sorting (FACS). First, cellular debris was excluded, and DAPI-negative live cells were identified. From these live cells, EpCAM-positive and RFP-positive cells were sorted. Subsequently, GFP-positive and GFP-negative cells were separated from the RFP-positive population for downstream RNA sequencing analysis. Notably, the GFP-negative subpopulation represents cells with high autophagic flux, while the GFP-positive subpopulation represents cells with low autophagic flux.


title: Human iPSC-based modeling unveils chromatin remodeling induced by SETBP1 mutation as a potential initiating factor in GATA2 deficiency.

city: Hospitalet de Llobregat

first: Loris

last: Mularoni

state: Barcelona

address: Gran Via de l'Hospitalet, 199

department: P-CMR[C]

institute: IDIBELL

summary: GATA2 deficient patients are prone to develop myelodysplastic syndrome (MDS) that can evolve to acute myeloid leukemia (AML). The MDS progression is usually associated with the acquisition of cytogenetic and/or additional somatic alterations. Mutations in SETBP1 and ASXL1 genes are frequently observed in pediatric GATA2 patients, although how they contribute to the disease progression remains poorly understood. Here we develop a human induced pluripotent stem cells (hiPSCs)-based model to study the impact of germline  GATA2 mutation along with  selected somatic mutations  on GATA2 deficiency progression. We found that, while germline heterozygous GATA2 mutation alone is insufficient to induce an impairment of myeloid development, SETBP1 and ASXL1 mutations lead to a significant decrease of myeloid differentiation potential with a complete monocytopenia. The prominent loss of myeloid progenitor was associated with a down regulation of myeloid-specific genes and an up-regulation of leukemic stem cell markers. Through epigenomic profiling,  we found that mutation in SETBP1 promotes  chromatin remodeling  in genes involved in myeloid neoplasms that preceded the blockage of myeloid differentiation, a state that persisted after the acquisition  of the ASXL1 mutation. Finally, transcription factors motif analysis revealed an enrichment for MEIS1, PU.1, RUNX1 and HOXA9 motifs in more accessible chromatin regions, suggesting their cooperation in disease progression. Beyond establishing a valuable tool for studying the molecular mechanisms underlying GATA2 deficiency, our findings suggest that mutated  SETBP1 primes the onset of hematopoietic impairment at transcriptomic and epigenomic level in GATA2 deficiency, a process exacerbated by the acquisition of the ASXL1 mutation.

overall_design: On day 15 of hematopoietic differentiation, hiPSC-derived myeloid progenitors (CD34⁺CD43⁺CD33⁺CD45⁺) were sorted, yielding at least 50,000 cells from populations P and G, 28,000 from GS, 25,000 from GA, and 8,000 from GSA.

first: Alessandra

last: Giorgetti


title: Differential gene expression in paired DMS114-Tre vs. DMS114

city: Tianjin

summary: Small cell lung cancer (SCLC) is characterized by significant heterogeneity and plasticity, which contribute to its aggressive progression and resistance to therapy. Understanding the underlying mechanisms of these features is essential for improving treatment outcomes. Autophagy, a conserved cellular process, plays a role in many cancers; however, its specific function in SCLC remains unclear. Utilizing a genetically engineered mouse model (Rb1fl/fl; Trp53fl/fl; GFP-LC3-RFP-LC3△G), we tracked autophagic flux in vivo to assess its effects on SCLC biology. Tumor subpopulations with high autophagic flux exhibited increased proliferation, enhanced metastatic potential, and neuroendocrine (NE) characteristics, whereas those with low autophagic flux displayed more immune-related signals and non-NE traits. In vitro modulation of autophagic flux further corroborated these findings: the autophagy activator trehalose induced NE features in non-NE cell lines (DMS114), while the autophagy inhibitor Bafilomycin A1 promoted non-NE characteristics in NE cell lines (H1092). This study provides a model for investigating autophagy in vivo and underscores its role in the heterogeneity and plasticity of SCLC.

overall_design: Sequencing was performed on both the control DMS114 cell line and the DMS114 cell line treated with 200 mM trehalose for 12 hours.


title: Human iPSCs-based modeling unveils a dominant role of SETBP1 mutation in shaping stable chromatin accessibility landscape in GATA2 deficiency

summary: Patients with GATA2 deficiency are predisposed to developing myelodysplastic syndrome (MDS), which can progress to acute myeloid leukemia (AML). This progression is often associated with the acquisition of additional cytogenetic and somatic alterations. Mutations in SETBP1 and ASXL1 genes are recurrently observed in GATA2 patients, but their precise roles in disease progression remain poorly understood. Here we developed a hiPSC-based system to investigate the functional impact of SETBP1 and ASXL1 mutations in the context of germline GATA2 haploinsufficiency. Using precise genome editing, we recreated patient-relevant combinations of these mutations to model distinct premalignant stages of GATA2 deficiency. We demonstrate that heterozygous GATA2 mutation alone has a limited impact on early hematopoietic progenitors, without disrupting myeloid differentiation. In contrast, acquisition of SETBP1 or ASXL1 mutations impairs hematopoietic differentiation in a GATA2 deficient background, leading to a premalignant state marked by reduced myeloid progenitor output. Strikingly, the combination of all three mutations results in a severe depletion of myeloid progenitors, closely recapitulating hematopoietic defects observed in GATA2-related MDS and highlighting a synergistic interplay among the mutations. We provide new insights into the molecular mechanism underlying GATA2 deficiency progression, revealing that SETBP1 mutation plays a dominant role in establishing a stable chromatin accessibility landscape, even when co-occurring with ASXL1. Our study establishes a novel humanized model system for studying GATA2 deficiency. This model provides new insights into the cellular and molecular events underlying the progression of myeloid impairment in GATA2 deficiency and represents a platform for testing future therapeutic strategies.

overall_design: On day 15 of hematopoietic differentiation, 200 hiPSC-derived myeloid progenitors (CD34⁺CD43⁺CD33⁺CD45⁺) derived from parental and mutant hiPSCs were sorted .


title: YAP/TAZ cooperate with AP-1 to drive the mesenchymal cell state in neuroblastoma [RNAseq]

overall_design: We separated 4 heterogeneous neuroblastoma cell lines into adrenergic (ADR) and mesenchymal (MES) subcultures based on adherence properties. The following cell lines were used: STA-NB-8, STA-NB-10, CLB-Ma, SK-N-SH. From these 8 cultures we isolated RNA for RNA-seq. Additionally we generated SK-N-SH and CLB-Ma cell lines stably overexpressing either YAP1, WWTR1, or empty vector (EV) and isolated RNA from these cell lines and performed RNA-seq.


title: Differential gene expression in paired H1092_Baf vs. H1092

overall_design: Sequencing was performed on H1092 cells treated with the autophagy inhibitor Bafilomycin A1 (BafA1;2 μM ) or DMSO (5 μL) for 24 hours.


title: Glial cells missing 1 triggers gliosis and vasculogenesis in the neonatal brain injury

city: Okazaki

first: SHOJI

last: TATSUMOTO

address: Myodaiji

institute: The National Institutes of Natural Sciences NINS

summary: glial cells missing (gcm) in Drosophila plays a crucial role in the fate switch in nervous system and induces glial differentiation. However, function of a mammalian homologue, Gcm1, in the normal neural development and in pathological conditions remains elusive. Here, we report that Gcm1 was upregulated in Nestin+ cells immediately after neonatal brain injury was made, followed by accumulation of GFAP+ and Olig2+ cells in the penumbra region. In addition, Gcm1 strongly induced vasculogenesis in the injury lesion as well as in the developing brain via the action of VEGFA and VEGFC. Lack of Gcm1-mediated vasculogenesis could be one of major causes for dysplasia of placental labyrinths found in Gcm1–/– embryos, which leads to embryonic lethality. Our data suggest that Gcm1 triggers both gliosis and vasculogenesis after brain injury and could be a target for therapeutic intervention.

overall_design: The transcriptome profiles of the GFP-positive tissues from Gcm1 overexpression and control embryonic mouse brains (E16.5) were generated using the Illumina HiSeq platforms. The number of replicates for both Gcm1 overexpression and control samples is five.

first: Yoshitaka

last: Hayashi

first: Seiji

last: Hitoshi

first: Shoji

last: Tatsumoto

first: Yasuhiro

last: Go


title: Oncogenic Kras  cells override homeostatic cell elimination mechanisms in adult pancreas via Wnt signalling and cell dormancy.

city: Cardiff

first: Beatriz

last: Salvador-Barbero

state: Wales

address: Hadyn Ellis Building, Maindy road

department: ECSCRI-BIOSI

country: United Kingdom

institute: Cardiff University

summary: Epithelial tissues use homeostatic defence mechanisms to actively remove aberrant or poorly functioning cells and maintain tissue health. We show that when present in tissues in low numbers, cells expressing KrasG12D or p53R172H  mutations compete with normal cells for survival and are often eliminated. This implies that tumour initiation would require mechanisms whereby mutant cells override tissue homeostasis and remain in a tissue; however, the biology of these initial events is poorly understood. Here, we use an in vivo model of sporadic tumorigenesis in the adult pancreas to show that cell elimination processes are inefficient and a proportion of KrasG12D or p53R172H expressing cells are never eliminated from the epithelium. Using RNA sequencing of non-eliminated mutant populations, we reveal a general activation of the non-canonical  Wnt pathway. We demonstrate that non-eliminated KrasG12D cells express cell dormancy and diapause gene signatures, suggesting non-eliminated KRasG12D cells adopt a dormant cell state in vivo. Using cell competition assays in vitro, we show that active Wnt or cell cycle arrest blocks elimination of RasV12 mutant cells from normal epithelial cell sheets. Importantly, we demonstrate that Wnt signalling is a general mechanism required to promote retention of KrasG12D and p53R172H cells in tissues in vivo . Our results suggest that mutant cells activate Wnt and/or a dormant cell state to avoid homeostatic tissue defence mechanisms and survive in the adult pancreas.

overall_design: To gain an unbiased insight into how non-eliminated mutant cells survive in tissues we performed bulk RNA sequencing. Whole pancreata were harvested from experimental (KC/PC/KPC) and control mice (Control) at 35 days p.i. and digested to cell suspensions. We used anti-leptin antibodies to enrich for acinar/ductal epithelial cells and FACS sorted leptin positive RFP positive cells. We pooled cell suspensions from three mice per genotype to obtain a minimum of 5,000 viable leptin positive RFP positive cells, with n=3 replicates per genotype.

first: Catherine

last: Hogan


title: The E3 ligase RBCK1 reduces the sensitivity of ccRCC to sunitinib through the ANKRD35-MITD1-ANXA1 axis

city: Changsha

first: Huaiyuan

last: Liang

address: 183 Renmin Middle Road

institute: Institute of Urological Cancer, Central South University

summary: Despite the promise of targeted tyrosine kinase inhibitors (TKIs), such as sunitinib, in the extension of survival time in patients with clear cell renal cell carcinoma (ccRCC) progression or metastasis, the patients eventually succumb to inevitable drug resistance. Protein degradation executed by the ubiquitin-dependent proteasome system played an important role in determining the sensitivity of ccRCC to sunitinib. Here, we applied the bioinformatic analysis to identify that E3 ligase RBCK1 was elevated in the sunitinib-resistant renal cancer cell lines or patient specimens. The subsequent in vitro or in vivo studies demonstrated that RBCK1 contributed to decreasing the sensitivity of ccRCC to sunitinib. Then, we showed that inhibition of RBCK1 activated the AKT and MAPK signaling pathways, which might be one of the main reasons why RBCK1 induces sunitinib resistance in ccRCC cells. Mechanistically, our results indicated that RBCK1 promotes the degradation of ANKRD35 and that ANKRD35 destabilizes MITD1 by binding with SUMO2 in ccRCC cells. In addition, we showed that the RBCK1-ANKRD35-MITD1-ANXA1 axis regulates the phosphorylation of AKT and ERK and contributes to the dysregulation of sunitinib in ccRCC cells. Therefore, we identified a novel mechanism for regulating the sensitivity of sunitinib in ccRCC. Therefore, we elucidated a novel mechanism by which RBCK1 regulates sunitinib sensitivity in ccRCC.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for the ccRCC cell after kncokdown of RBCK1, ANKRD35 or MITD1 respectively.

first: Jin

last: Xin


title: VDAC2 primes Myeloma cells for BAK-dependent apoptosis by stabilizing BAK and not BAX and represents a novel therapeutic target

city: Nantes

first: David

last: Chiron

address: 8 quai Moncousu

country: France

institute: CRCI2NA, INSERM_U1307, CNRS_6075, Nantes_Université

summary: We demonstrated that VDAC2 plays a critical role in the apoptotic response by regulating the expression and function of BAK, but not BAX

overall_design: RNA human myeloma cell lines control (CTR) and VDAC2 -/- (STOP)  were extracted with RNeasy Mini Kit (Qiagen) and gene expression profile was performed using RNA-Seq (3'SRP)

first: Ophélie

last: Champion

first: Sophie

last: Maïga

first: Chloé

last: Antier

first: Christelle

last: Dousset

first: Agnès

last: Moreau-Aubry

first: Céline

last: Bellanger

first: Géraldine

last: Descamps

first: François

last: Guillonneau

first: Jose Antonio

last: Moreno

first: Ohyun

last: Kwon

first: Nicoletta

last: Libera Lilli

first: Philippe

last: Moreau

first: Cyrille

last: Touzeau

last: Pellat-Deceunynck

first: Patricia

last: Gomez-Bougie


title: piRNAs dysregulated in calcific aortic valve disease

city: Beijing

first: Dong

last: Han

address: 28 Fuxing street

institute: Chinese PLA general hospital

type: Non-coding RNA profiling by high throughput sequencing

summary: To characterize the piRNA profiles of aortic valves from CAVD and non-CAVD patients, we performed piRNA sequencing using 4 human calcified aortic valves (CAVs) and 4 normal controls

overall_design: Comparative piRNA expression profiling analysis of RNA-seq data for aortic valves from CAVD and non-CAVD patients.

first: Yongjun

last: Wang

first: Nianguo

last: Dong


title: YAP/TAZ cooperate with AP-1 to drive the mesenchymal cell state in neuroblastoma [CnR]

first: CCRI

last: BiCU

overall_design: We separated 2 heterogeneous neuroblastoma cell lines into adrenergic (ADR) and mesenchymal (MES) subcultures based on adherence properties. The following cell lines were used: CLB-Ma and SK-N-SH. From these 4 cultures we isolated nuclei and performed Cut&Run using the following antibodies: YAP1, WWTR1, JUN, H3K27Ac, H3K4me1, IgG

first: A

last: Kutschat

first: M

last: Zaczek

first: S

last: Strohmenger

first: D

last: Seruggia

last: Taschner-Mandl

first: K

last: Boztug


title: Tregs stimulate intestinal repair by integrating epithelial IFNy/IL-10 signaling

city: Regensburg

first: LIT

last: NGS-Core

address: Franz-Josef-Strauß-Allee 11

department: NGS-Core

institute: Leibniz Institute for Immunotherapy

summary: To understand the transcriptional changes on cellular level within the murine intestinal epithelial tissue, we generated small intestinal organoids from wild type mice, co-cultured them with Treg cells +/- rIL10/rIFNg or anti-IFNg/IL10R, dissagregated the samples, sorted into single cells and profiled them by single-cell RNA-seq

overall_design: To understand small intestinal epithelial normal tissue differentiation and growth during the presence of Treg cell and/or IL10/IFNg signaling, small intestinal organoids were generated and co-cultured with indicated wild-type Treg cells +/- anti-IFNg/IL10R or +/- rIFNg/rIL10. Medium was changed after 4 days, stimuli were removed and the organoids were dissagregated, sorted into single cells and profiled by single-cell RNA-seq

first: Sascha

last: Göttert

first: Julius

last: Fischer

first: Paul

last: Heinrich

first: Nicholas

last: Strieder

first: Claudia

last: Gebhard

first: Michael

last: Rehli

first: Hendrik

last: Poeck


title: Analysis of the m6A methylome and downstream targets of piRNA AVCAPIR in human valvular interstitial cells

first: Dong

last: Han

type: Methylation profiling by high throughput sequencing

summary: To further elucidate the molecular mechanism by which piRNA AVCAPIR drives aortic valve calcification, we performed m6A methylated RNA immunoprecipitation sequencing (MeRIP-seq) combined with input RNA sequencing (RNA-seq) in human valvular interstitial cells with or without AVCAPIR overexpression.

overall_design: Human valvular interstitial cells from calcific aortic valve disease patients were transfected with piRNA AVCAPIR mimic or negative control (NC) mimic. Following the confirmation of overexpression, cells were sent for m6A methylated RNA immunoprecipitation sequencing (MeRIP-seq) combined with input RNA sequencing (RNA-seq).

last: Wang

first: Niaoguo

first: Feng

last: Cao


title: MLL2 facilitates long-range gene regulation through LINE1 elements [RNA-Seq]

status: Public on Oct 01 2025

city: Santander

first: Lucio

last: Di Filippo

state: Cantabria

address: PCTCAN - Cl. Albert Einstein, 22

institute: IBBTEC

summary: Transcriptional regulation is tightly linked to chromatin organization, with H3K4me3 commonly marking both active and bivalent promoters. In embryonic stem cells (ESC), MLL2 is essential for H3K4me3 deposition at bivalent promoters, which has been proposed to facilitate the induction of major developmental genes during pluripotent cell differentiation. However, prior studies point to a functional discrepancy between the loss of H3K4me3 at bivalent promoters and the largely unaltered transcription of major developmental genes in Mll2-/- cells. In this study, we investigated MLL2-dependent gene regulation in mouse ESC and during their differentiation. Contrary to the prevailing view, we show that MLL2’s primary role is not to oppose Polycomb-mediated repression at the bivalent promoters of developmental genes. Instead, we identify a previously unrecognized regulatory function for MLL2 at the CG-rich 5' untranslated regions (5'UTR) of evolutionarily young LINE-1 (L1) transposable elements (TE). We found that MLL2 binds to the 5’UTR of L1 elements and is critical for maintaining their active state (H3K4me3 and H3K27ac), while preventing the accumulation of repressive H3K9me3. Using both global genomic approaches (i.e. RNA-seq, ChIP-seq and Micro-C) as well as targeted L1 deletions, we demonstrate that these MLL2-bound L1 elements act as enhancers, modulating the expression of neighboring genes in ESC and, more prominently, during differentiation. Together, our findings illuminate novel aspects of MLL2 regulatory function during early developmental transitions and highlight the emerging role of TE as key components of long-range gene expression control.

overall_design: Transcriptional profiles on WT, Mll1-KO, Mll2-KO and double-KO at day 0 (mESC) and day 4 of a multilineage differentiation protocol.

first: Lara

middle: Z

last: Shahidian

last: di Filippo

first: Sarah

last: Robert

first: Álvaro

last: Rada-Iglesias


title: Broad H3K4me3 domains support oocyte genome silencing and maturation but are dispensable for repression in early embryos

city: Oslo

first: Gareth

last: Greggains

address: Boks 1072 Blindern

country: Norway

institute: University of Oslo (UiO)

summary: To investigate whether demethylation of broad histone H3 lysine 4 trimethyl (H3K4me3) domains is sufficient to trigger premature embryonic genome activation (EGA), we overexpressed the H3K4me3 demethylase KDM5B in mouse zygotes and early 2-cell (2C) embryos via mRNA injection. We performed single-cell RNA sequencing (scRNA-seq) using the SMART-Seq Stranded Kit (Takara Bio) on individual Kdm5b-yfp–injected and water-injected control zygotes and 2C embryos. Differential expression analysis revealed minimal transcriptional changes, and developmental stage, rather than KDM5B overexpression, accounted for most gene expression variance. Our findings demonstrate that wide-scale removal of H3K4me3 in zygotes or early 2C embryos is not sufficient to induce premature EGA, suggesting that genome silencing at these stages does not depend on broad H3K4me3 domains.

overall_design: S-phase zygotes or both blastomeres of G1-phase 2C embryos were microinjected with Kdm5b-yfp mRNA; water-injected zygotes or 2C embryos served as controls. The C-terminal YFP tag enabled live-cell confirmation of KDM5B expression. Samples were collected for scRNA-seq ~5–6 h post-injection (late zygotes: 17 h after ovulation, corresponding to late S/G2 phase; early 2C embryos: 5.5–8 h after division, corresponding to late S phase). During collection, 10 single zygotes from each group (Kdm5b-yfp-injected and control) were transferred into separate tubes. For 2C embryos, we included both single intact embryos and pooled blastomeres from partially lysed embryos to maximise sample use (lysed blastomeres were excluded during zona pellucida removal). In the control 2C group, 9 samples were collected: 6 single embryos with both blastomeres intact, one pool of two embryos with only one blastomere intact, and two pools of three such embryos. In the Kdm5b 2C group, 6 samples were collected: 5 single embryos with both blastomeres intact, and one pool of three embryos with only one blastomere intact.

first: Trine

last: Skuland

first: Madeleine

last: Fosslie

first: Sherif

last: Khodeer

first: Endalkachew

last: Ashenafi Alemu

first: Jens

last: Vilstrup Johansen

first: Yanjiao

last: Li

first: Mads

last: Lerdrup

first: John Arne

last: Dahl


title: Challenge Specific Modulation of Responses to Adjuvant-Induced Innate Immune Memory [RNA-seq]

city: Derio

first: Ana

last: Aransay

address: Parque tecnologico de Bizkaia, Building 801-A

institute: CIC bioGUNE

summary: Understanding the innate immune memory induced by adjuvants provides an opportunity to improve vaccine efficacy by inducing nonspecific secondary responses alongside the intended adaptive defence against the target antigen. To understand the consequences of adjuvant-induced immune training, we treated mice with commercially available Sigma Adjuvant System (SAS) and performed functional assays of bone marrow-derived innate immune cells, assessed its functional consequences in vivo, determined the resulting haematopoietic stem and progenitor cell (HSPC) phenotypes, and extensively analyzed the HSPC transcriptome. SAS induced temporal shifts in HSPC frequencies, alterations in the circulating blood profile, and lowered proinflammatory output by macrophages. SAS-induced training caused disparate outcomes in models of inflammation and acute infection. Further, SAS enhanced antibody responses after primary immunisation, that were profoundly altered upon a secondary dose. Integrated transcriptional analysis revealed shifts in HSPCs defined by altered transcription factor activity and lineage-specific shifts in metabolic, epigenetic, myeloid, and kinase genes, resulting in enhanced antimicrobial neutrophil responsiveness and revealing regulators of central training. Together, these results contribute to the understanding of the plasticity and limitations of innate immune training.

overall_design: Mice were treated with SAS adjuvant or vehicle one month prior to isolating bone marrow and sorting Lin–cKit+ hematopoietic stem and progenitor cells.

first: Samuel

middle: T

last: Pasco

first: Juan

last: Anguita


title: MLL2 facilitates long-range gene regulation through LINE1 elements [ChIP-Seq]

last: Di Filippo

overall_design: Genome-wide binding profiles for COMPASS-like subunits (MLL2, MLL1 and RBBP5), histone modifications (H3K4me1, H3K4me2, H3K4me3, H3K27ac, H3K27me3 and H3K9me3) and RING1B  were investigated by ChIP-seq in WT mouse embryonic stem cells (mESC) as well as in transgenic mESC lines containing different genomic deletions (i.e. Mll1-KO, Mll2-KO and Mll1/Mll2 double-KO). Where indicated the ChIP-seq profiles were generated on differentiated mESC lines following a multilineage protocol.


title: Challenge Specific Modulation of Responses to Adjuvant-Induced Innate Immune Memory [scRNA-seq]


title: DNA-hypermethylated human gastric cancer circumvents apoptosis and premature senescence in the absence of TP53 mutation

city: Chiba

first: Masaki

last: Fukuyo

address: 1-8-1 Inohana, Chuo-ku

department: Department of Molecular Oncology

institute: Chiba University

summary: Comprehensive DNA methylation analysis in various gastric cancer cell lines with different EBV, MSI, and p53 status. Infinium HumanMethylation450 BeadChip was used to obtain DNA methylation profiles across 485,577 CpG sites.

overall_design: Bisulphite converted DNA from the 6 samples were hybridised to the Infinium HumanMethylation450 BeadChip.

first: Yasunobu

last: Mano

first: Keisuke

last: Matsusaka

first: Bahityar

last: Rahmutulla

first: Motoaki

last: Seki

first: Kazuko

last: Kita

first: Genki

last: Usui

first: Masayuki

last: Urabe

first: Hiroyuki

last: Abe

first: Hisahiro

last: Matsubara

first: Tetsuo

last: Ushiku

first: Yasuyuki

last: Seto

first: Masashi

last: Fukayama

first: Atsushi

last: Kaneda


title: Chromatin accessibility landscapes across T-ALL

city: Memphis

first: Daniel

last: Savic

state: Tennessee

address: 262 Danny Thomas Pl

department: Pharmaceutical Sciences

institute: St. Jude Children's Research Hospital

summary: Acute lymphoblastic leukemia (ALL) is the most common malignancy in pediatric patients and represents about a quarter of all pediatric malignancies. While transcriptional and DNA methylation profiling of these subtypes has been extensively examined, the accompanying chromatin landscape and corresponding gene regulatory repertoire is not well characterized for many ALL types. To better understand the ALL epigenome and gene regulatory network we mapped chromatin accessibility for T-ALL patient samples using assay for transposase-accessible chromatin with high-throughput sequencing (ATAC-seq) .

overall_design: Fast-ATAC-seq was performed on purified leukemia cells from human patients. 10,000 cells were used for library preparation.


title: Spatial immune profiling defines a subset of human gliomas with functional tertiary lymphoid structures [bulk RNA seq]

first: Katharina

last: Imkeller

summary: Adult-type diffuse gliomas, the most common primary brain tumors, respond poorly to immune-based therapies and are considered immunologically “cold” tumors. Here, we examined the features and clinical relevance of glioma intratumoral tertiary lymphoid structures (TLSs) using spatial transcriptome and proteome profiling. In a cohort of 642 gliomas, TLSs were present in 15% of tumors and associated with a remodeled perivascular space and spatial redistribution of extracellular matrix components. Three distinct TLS subtypes could be defined based on differing cellular composition and immune activity. While all subtypes lacked classical germinal center architecture, certain TLSs exhibited features of dynamic immune functions, including clonal T and B cell expansion, generation of IgA⁺ and IgG⁺ plasma cells, and dendritic cell-T cell interactions. The presence of TLSs with active immune response features correlated with improved overall survival. Thus, a functional adaptive immune response is detectable in some gliomas, with implications for stratification and treatment.

overall_design:
To explore the molecular and cellular architecture and immunological function of glioma-associated TLS, we analyzed 642 glioma specimens from the Frankfurt University Cancer Center. We found that 15% of gliomas had B cell aggregates (TLS+), while the rest did not (TLS-).We used a multi-modal spatial profiling approach, including spatial transcriptome profiling, whole slide multiplex immunofluorescence staining, and high-plex immunofluorescence staining, on consecutive tissue sections to trace single TLS through different molecular layers.We performed bulk RNA sequencing on 64 gliomas, with and without TLS, matched for IDH status, age, and gender. We examined the transcriptional profiles of 61 TLS from 20 tumors using spatial transcriptome profiling.

>>>Submitter states that raw data are unavailable due to patient privacy concerns.<<<

first: Pinar

last: Cakmak

first: Jennifer

last: Lun

first: Aakanksha

last: Singh

first: Jadranka

last: Macas

first: Jonathan

last: Schupp

first: Miriam

last: Köhler

first: Tatjana

last: Starzetz

first: Michael

last: Burger

first: Eike

last: Steidl

first: Lucie

last: Hasse

first: Elke

last: Hattingen

first: Karl

last: Plate

first: Yvonne

last: Reiss

first: Jonas

last: Schuck

first: Zeina

last: Mahmoud


title: Cytomegalovirus latency exacerbates cardiac inflammation and tissue remodeling after myocardial infarction

city: Rijeka

first: Marko

last: Šustić

address: Jonjić's lab

department: Department of Internal Medicine

country: Croatia

institute: University of Rijeka, Faculty of Medicine

summary: Background: Cardiovascular diseases (CVDs) remain a leading cause of morbidity and mortality worldwide, with immune-mediated processes increasingly recognized as important contributors to CVD onset and progression. Seropositivity rates indicate 60–90% of the population carries latent viral infections, e.g., with cytomegalovirus, that profoundly shape the individual immune phenotype. Epidemiological studies have consistently associated cytomegalovirus (CMV) seropositivity with adverse cardiovascular outcomes, yet the functional consequences of latent CVM cytomegalovirus latency in the context of myocardial infarction (MI) have not been studied, nor has its underlying influence on cardiac tissue. Methods: In this study we employed a murine model of cytomegalovirus (MCMV) infection to investigate the impact of the virus in the cardiac immune environment. We characterized the immune cell populations involved in cardiac immune responses by flow cytometry and performed bulk RNA seq of infected and naive mice to dissect the transcriptional differences that occur after viral exposure. To better understand how viral infections affect the myocardium of infected and naive animals post MI, we conducted a series of experiments involving flow cytometry, single-cell RNA / TCR sequencing, echocardiography, and cMRI 5 days after mice underwent experimental MI. Additionally, we used cMRI to stratify CMV- seropositive patients as “good” or “poor healers” and tested their CMV IgG titers. Using TCR-sequencing, we also identified CMV-responding TCRs and compared blood-derived and heart-derived T cells from post-mortem tissues. Results: Our findings show that exposure to murine CMV induces both long-term changes in the cardiac transcriptional profile and alterations in cardiac immune cell populations. We detected the establishment of virus-specific resident memory T cells that persist in cardiac tissue. Following myocardial infarction (MI), mice previously exposed to MCMV had more abundant cardiac-resident T cells, heightened inflammatory profile, and adverse ventricular remodeling, as revealed by MRI, compared to naive controls. These murine observations were supported by data from CMV-seropositive MI patients, who harbored CMV-responsive T cells and exhibited impaired cardiac healing. Conclusions: Taken together, our findings demonstrate that latent CMV infection leads to long-term immunological changes in cardiac tissue that exert significant effects on post-MI healing outcome.

overall_design: Bulk mRNA sequencing was performed from the cardiac tissue of mice acutely infected with MCMV (day5; mcmv_acute samples), latently infected with MCMV (day56; mcmv_lat samples) or non-infected controls (mock samples). RNA was isolated from 1/3 of the apical portion of a murene left ventricule.


title: Influence of hsa-miR-1265 and hsa-miR-21-5p on meningioma cells

city: Warsaw

first: Szymon

middle: Piotr

last: Baluszek

state: mazowieckie

address: Wilhelma Konrada Roentgena 5

department: Department of Molecular and Translational Oncology

country: Poland

institute: Maria Sklodowska-Curie National Research Institute of Oncology

summary: Meningiomas are common intracranial tumors. Most of thenm benign WHO GI tumors, while approximately 20% are diagnosed as progressively more aggressive GII and GIII meningiomas. The study aimed to identify genes with tumor grade-related expression and to assess their functional relevance. The effect of selected miRNAs including hsa-miR-21-5p and hsa-miR-1265 on the cell phenotypep and genes expression profile was investigated using in vitro culturing of menignigioma cells KT21-MG1 andd Ben-Men-1. The cells were cultured with specific synthetic miRNA (miRNA mimic) or or nonspeciic control miRNA. Genes expression in miRNA-treated anad control cells was determined with RNAseq.

overall_design: KT21-MG1 and Ben-Men-1 meningioma cells were transfected syntetic miRNA mimics using liposomal transfection. The following miRNA micmics were used hsa-miR-1265 (YM00470622-ADB , Qiagen), hsa-miR-21-5p (YM00470856-ADB, Qiagen) and negative control mimic (YM00479902-AGB; Qiagen) that serves as nonspecific negative control. Three independent biological replicates of the transfection experiment with each miRNA was performed and tptal RNA was isolated using High Pure RNA Isolation Kit (Roche). RNA sequencing was performed using poly-A enrichment or library constructing. One μg of RNA from each tissue sample was used for mRNA library preparation with Novogene NGS RNA Library Prep Set (Novogene). The quality of libraries was evaluated with Agilent Bioanalyzer 2100 system (Agilent Technologies). Libraries were sequenced on an Illumina NovaSeq 6000 platform, and 150-bp paired-end reads were generated. A minimum of 30 M read pairs per sample were generated. Sequencing was performed by Eurofins Genomics service.

first: Paulina

last: Kober

first: Mateusz

last: Bujko


title: Potential peptide drug with LCCL core motif differentiating M1 macrophage

city: Seoul

first: Seung Hyun

last: Jang

address: Yonsei-ro 50-1

department: College of Medicine

country: South Korea

institute: Yonsei University

summary: Cochlin, encoded by the COCH gene, mediates innate immunity against bacterial infections by segregating pathogens and recruiting immune cells through its N-terminal LCCL domain. This domain is cleaved and secreted to attract macrophages and neutrophils, but its core motif has remained unclear. Here, we identified a 62–amino acid core LCCL (cLCCL) containing conserved structural elements. RNA-seq in RAW264.7 cells showed that both LCCL and cLCCL peptides induced M1 polarization, with upregulation of TICAM2, CD40, and CD86. Thus, cLCCL drives pro-inflammatory macrophage polarization and represents a promising candidate for antibacterial peptide therapeutics

overall_design: RNA-seq profiling of RAW264.7 cells that were untreated or treated with 1ug or 10ug of LCCL for 6 hours or 24 hours.

first: Hyoyeol

last: Kim

first: Seong hoon

last: Bae

first: Kyeonghwan

first: Soljee

last: Yoon

first: Seung Hyeon

first: Heon Yung

last: Gee

first: YoungSoo

first: Jinsei

last: Jung


title: Zhx2 maintains neural stem/progenitor cell homeostasis via the CELSR1/Wnt/ROCK axis in the mouse brain

city: Jinan

first: Yuan

last: Xia

address: Wenhua road 44#

institute: Qilu hospital of Shandong University

summary: Abnormal proliferation and differentiation of neural stem/progenitor cells (NSPCs) can lead to defects in neural development. However, the key regulators remain undeterminded. Here, we identify the transcription factor zinc fingers and homeoboxes 2 (Zhx2) as a crucial player orchestrating the proliferation and differentiation of NSPCs. Zhx2 conditional deletion in nestin-positive cells (Zhx2Δ/Δ) resulted in a reduction in NSPC number, reduced proliferation, and promoted NSPC differentiation. Zhx2Δ/Δ mice exhibited enlarged lateral ventricles, smaller hippocampi, anxiety, recognition and memory defects, and motor coordination disorders. Transcriptomic analysis revealed CELSR1, a transmembrane calcium adhesive protein, as a direct downstream target of Zhx2 in the Wnt/ROCK pathway. Our findings elucidate Zhx2’s role in brain morphological development and regulation of NSPC proliferation and differentiation, suggesting a promising strategy for neurodevelopmental disorders.

overall_design: RNA-seq profiling of Zhx2+/+ and Zhx2Δ/Δ mice  from the SVZ

first: Ai

last: Peng

first: Xiaojing

last: Wang


title: RNA-Seq analysis of cancer models with altered SLX4/XPF reveals links to migration, DNA damage response, EMT, and drug sensitivity

city: Lyon

first: abdelakamel

last: chettab

address: 8 avenue Rockeffeler

department: centre de recherche en cancérologie de lyon

institute: université claude bernard lyon1

summary: SLX4 and XPF are two proteins involved in DNA repair mechanisms, but for which other properties are possible. After a study on phenotypes of cell models with various expressions of the two proteins, we conducted RNA sequencing analysis on five cell models of different origin (A549, NCI-H1703, COLO-357, HT-29 and HEK-293T). Our results show a much higher transcriptional impact on p53 mutant cell lines than on p53 wild type cells. We also present various signatures or scores based on selected genes, and although interesting differences are observed, no general conclusions can be made for all cell lines. Our study and results add data and knowledge to the roles of SLX4 and XPF in cell biology and represent an important background for new and confirmational studies.

overall_design: RNA-seq profiling of wildtype A549, NCI-H1703, COLO-357, HT-29 and HEK-293T and their knockdown derivatives (SLX4- and/or XPF-deficient cell lines using CRISPR/Cas9 technology)

first: kamel

first: Emeline

last: Cros-Perrial

first: Léa

last: Figuet

first: Michaël

last: Duruisseaux

first: Charles

last: Dumontet

first: Lars Petter

last: Jordheim