title: Integrative analysis reveals synergistic regulation of Sp7 by BRD9 and Wnt/β-catenin signaling during osteogenic differentiation

city: 苏州市

first: lyp

last: l

address: 斜塘街道

institute: 苏州大学

summary: Osteoporosis is a skeletal disorder involving low bone mineral density (BMD) and elevated fracture risk. While epigenetic mechanisms like DNA methylation are well-studied, the role of chromatin remodeling remains less clear. Using integrative genetics and functional studies, we identified BRD9—a non-canonical BAF subunit—as critical for osteoblast differentiation. BRD9 activates Wnt/β-catenin signaling and directly upregulates the key osteogenic factor Sp7. Our findings reveal a novel osteogenic role for BRD9 and suggest its potential as a biomarker and therapeutic target for bone-related diseases.

overall_design: HEK293T and MC3T3-E1 cells were cultured in Dulbecco’s Modified Eagle Medium (DMEM, Gibco) and MEM Alpha Modification (Cytiva) respectively, with addition of 10% fetal bovine serum (FBS, Biological Industries) and 1% penicillin/streptomycin. For in vitro osteogenic differentiation, MC3T3-E1 cell line was maintained in basic medium supplemented with 10 mM M‐glycerol phosphate, 0.25 mM ascorbic acid and 0.1 μM dexamethasone (all from Sigma‐Aldrich, USA). For the BRD9 inhibition assays, cells were treated with either DMSO or I-BRD9 at the final concentrations of 10 μM.


title: Probing DNA damage sites reveals context-dependent and novel DNA damage response factors

status: Public on Oct 16 2025

city: Utrecht

first: Tuncay

last: Baubec

address: Padualaan 8

department: Department of Biology

country: Netherlands

institute: Utrecht University

type: Genome binding/occupancy profiling by high throughput sequencing

summary: DNA damage is a constant threat to genome integrity and function. Diminished capacity for DNA repair is linked to many human diseases, therefore, understanding the molecular pathways responding to DNA damage is key for developing novel therapies. Lack of unbiased probes to report DNA damage dynamics in living cells and animals limits our current efforts to completely understand DNA repair processes. In this study, we overcome these limitations by engineering protein probes containing the tandem-BRCT domain of MCPH1, which we show to have a specific affinity for the DNA-damage-associated histone mark H2AX. We employ these probes to track DNA damage dynamics in living cells exposed to a panel of different genotoxic insults, to visualize DNA damage targeted to heterochromatinised satellite repeats, and to map DNA double strand breaks genome-wide. Finally, we highlight the versatility of our probe to visualize programmed double strand breaks during gametogenesis in C. elegans. Taken together, we present a novel protein probe with broad application potential for DNA damage research.

overall_design: Antibody ChIP sequencing was performed in 4-hydroxytamoxifen- and DMSO-treated U2OS DIvA cells


title: Sap130 ChIP-seq on Mouse E13.5 heart

city: Pittsburgh

first: Hisato

last: Yagi

state: PA

address: 530 45th street, Rangos Res Center 8162

country: USA

institute: University of Pittsburgh

summary: Congenital heart disease (CHD) is a prevalent birth defect affecting up to 1% of live births. While a genetic etiology is indicated by increased recurrence risk and association with chromosomal abnormalities, the genetics of CHD is poorly understood and likely complex. Here we show hypoplastic left heart syndrome (HLHS), a severe CHD with high morbidity/mortality, has a multigenic etiology. Analysis of 8 HLHS mutant mouse lines recovered from a large-scale mutagenesis screen showed no mutations are shared in common. In the *Ohia* mouse line, mutations in 2 genes, *Pcdha9*/*Sap130*, act synergistically to cause HLHS. Cardiomyocyte proliferation and differentiation defects likely act in concert with valve abnormalities to cause HLHS. Network analysis of mutations recovered in HLHS mice and 68 HLHS patients point to Notch signaling disruption, a pathway previously implicated in HLHS. These findings demonstrate large-scale mutagenesis is an effective systems approach for interrogating the complex genetics of human diseases.

overall_design: Examination of Sap130 targets in a mouse heart from E13.5, with 1 Sap130-antibody ChIP and 1 Input control.

first: Cecilia

last: Lo

first: Abha

last: Bais


title: Cold and Lithium Delay Forgetting of Olfactory Memories in C. elegans

city: Tel Aviv

first: Hila

last: Gingold

address: 30 Haim Levanon Street

country: Israel

institute: Tel-Aviv University

type: Expression profiling by high throughput sequencing

summary: The poet W.B Yeats wrote that “All that is personal soon rots, it must be packed in ice or salt”. Here we show that in Caenorhabditis elegans nematodes, memories are preserved on ice and in lithium salt. We discovered that cold delays forgetting of specific olfactory memories by >8-fold. Adaptation to low temperatures cancels delayed forgetting. To study the underlying mechanism we performed RNA-seq, mutant analyses, and pharmacological assays. We found that regulation of membrane properties switches cold-induced delayed forgetting ON and OFF, and, remarkably, that lithium delays forgetting only in cold-sensitive but not cold-tolerant worms. We found that downregulation of the diacylglycerol pathway in AWC sensory neurons is essential for lithium-mediated delayed forgetting, and that long-term suppression occurs in the downstream AIY interneurons, as shown by neuronal activity recordings. We suggest that the worms’ genetic tractability might be harnessed to study how lithium and cold affect the brain, and even more fundamentally, how memory is stored and lost.

overall_design: To investigate the genetic basis of delayed forgetting on ice, C. elegans were trained with the odorant butanone and subsequently placed on ice for 2 hours prior to RNA extraction using Trizol. Gene expression profiles were analyzed through mRNA sequencing under six distinct experimental conditions, with three biological replicates per condition. The experimental groups were defined based on cultivation temperature and training regime: (1) 20°C Cultivation group – Worms cultivated at 20°C, representing cold-sensitive individuals that exhibit delayed forgetting when exposed to ice. (2) 15°C Cultivation group – Worms cultivated overnight at 15°C, representing cold-tolerant individuals that do not exhibit delayed forgetting on ice. (3) 15°C to 20°C Temperature-shift group– Worms cultivated overnight at 15°C, then transferred to 20°C for 2 hours, to reverse the cold tolerance acquired from overnight exposure. cDNA was prepared using either the SMART-Seq HT Kit or SMART-Seq v4 Ultra Kit. For all samples, 10 ng of RNA was used as input and processed according to the manufacturer’s protocol. Double-stranded cDNA was amplified by 10 PCR cycles for SMART-Seq HT samples and 12 cycles for SMART-Seq v4 Ultra samples. cDNA quantity and quality were verified using the TapeStation 2200 (Agilent). Sequencing libraries were prepared from 1 ng of cDNA using the Nextera XT DNA Library Preparation Kit (Illumina), following the manufacturer's instructions. Library quality and concentration were confirmed using the TapeStation 2200, and libraries were pooled according to molarity for sequencing on the Illumina NextSeq 500 platform.

first: Dana

last: Landschaft-Berliner

first: Kesem

last: Goldstein

first: Guy

last: Teichman

first: Sarit

last: Anava

first: Itai

last: Rieger

first: Noam

last: Levi

first: Yehuda

last: Salzberg

first: Vladyslava

last: Pechuk

first: Priti

last: Agarwal

first: Dror

last: Sagi

last: Cohen

first: Evelina

last: Nikel

first: Anat

last: Ben-Zvi

first: Ronen

last: Zaidel-Bar

first: Antonio

last: Miranda Vizuete

first: Meital

last: Oren-Suissa

first: Oded

last: Rechavi


title: FAM114A1 Promotes Immune Evasion of Triple-negative Breast Cancer by Simultaneously Activating PI3K/AKT Signaling and Disrupting E2F4-condensate Formation

city: Shanghai

first: Wenhao

last: Zhang

address: 270 Dongan Road

country: China

institute: Fudan University of Shanghai Cancer Center

summary: Immune checkpoint blockade (ICB) therapy, which revolutionized cancer treatment, has been approved for triple-negative breast cancer (TNBC) treatment. Unfortunately, the majority of TNBC patients are either not eligible for the treatment or exhibit resistance. Understanding the underlying mechanisms and enhancing treatment efficacy are urgently needed. Here, utilizing CRISPR activation screening, we identified FAM114A1 as a key mediator of immune evasion and ICB therapy resistance in TNBC patients. Mechanistically, FAM114A1 binds to p85α to activate PI3K/AKT pathway, and simultaneously, prevents E2F4-condensate formation to promote E2F4-driven MTDH expression. Elevation of these FAM114A1-mediated pathways inhibit tumor antigen presentation and consequently suppress anti-tumor immunity in TNBC. Moreover, FAM114A1-targeting boosts anti-PD-1 treatment in mouse models and the FAM114A1 signature shows strong predictive performance in recognizing TNBC patients who may benefit from ICB therapy. Collectively, our study provides new insights into the mechanisms underlying TNBC immune evasion and a potential avenue to improve ICB treatment effectiveness.

overall_design: To study the role  FAM114A1 in tumorigenesis, Py8119 murine breast cancer cells, either transduced with control shRNA (shCOO2) or engineered with Fam114a1 knocdown (Fam114a1 KD), were orthotopically injected into the mammary fat pads of 4–6-week-old female C57BL/6 OT-I mice. After tumor formation, mice were sacrificed at the defined endpoint, and tumor tissues were collected and processed into formalin-fixed, paraffin-embedded (FFPE) blocks for downstream analyses.


title: Xevinapant plus chemoradiotherapy negatively sculpts the tumour immune microenvironment in head and neck cancer

city: London

first: Anton

last: Patrikeev

state: London

address: Chester Beatty Laboratories, 237 Fulham Rd.

department: Targeted Therapy

country: United Kingdom

institute: The Institute of Cancer Research

summary: Xevinapant is an orally bioavailable antagonist of select members of the inhibitor of apoptosis protein (IAP) family. Despite promising initial data, combining xevinapant with chemoradiation (CRT) failed to improve outcomes in the TrilynX phase III trial for locally-advanced head and neck squamous cell cancer (SCCHN). We investigated the addition of xevinapant to CRT in immunocompetent mouse models of SCCHN and found maintained or improved locoregional control in vivo in a CD8+ T-cell-independent manner. In mEER, numbers of tumour-infiltrating cytotoxic CD8+ T-cells and NK cells were reduced, with remaining CD8+ T-cells characterised by PD-1hi CD38hi expression and Nr4a3 dynamics consistent with non-responsiveness to antigenic re-stimulation. Furthermore, xevinapant plus CRT significantly downregulated gene expression associated with immune-related pathways, increased levels of immunodysregulatory acute phase proteins and decreased levels of necroptosis mediator RIPK3. Overall, xevinapant plus CRT has an immunosuppressive effect on the tumour-immune microenvironment which may explain its lack of clinical benefit.

overall_design: RNA-seq profiling of 8- to 14-week-old females C57BL/6 WT mice, inoculated with head and neck cancer cells from two cell lines and treated with vehicle, radiotherapy and chemoradiotherapy with or without combination with Xevinapant (5 mice per treatment group). Two models of murine immunocompetent HPV-negative and HPV-positive head and neck cancer were used, MOC1 and mEER, respectively.


title: YAP AND TEAD ARE TRANSCRIPTIONAL REGULATORS OF NEUROENDOCRINE DIFFERENTIATION AND GROWTH IN CARCINOID CELLS [ChIP-seq]

city: Kingston

first: Neil

last: Renwick

state: ON

address: 88 Stuart St

department: Pathology and Molecular Medicine

country: Canada

institute: Queen's University

summary: Molecular regulators of variably aggressive carcinoid tumors are unknown. Since carcinoids have low expression of Yes-associated protein (YAP), we hypothesized that low YAP expression provides a molecular advantage to carcinoids by preventing YAP from binding its partner, TEA domain transcription factor (TEAD). To test this hypothesis, we overexpressed constitutively active YAP and a TEAD-binding defective form of YAP in lung (H727) and pancreatic (BON1) carcinoid cells. We found that active YAP overexpression inhibited neuroendocrine markers, morphology, cell proliferation and anchorage-independent cell growth, while TEAD-binding defective YAP recovered these features. Through integrated ChIP-seq and RNA-seq analyses, we found that YAP-TEAD binding downregulated neuroendocrine transcription factor genes and upregulated transforming growth factor (TGFβ) and Notch genes related to cell growth. We conclude that low YAP expression permits neuroendocrine differentiation and growth in carcinoid cells by preventing YAP-TEAD binding and subsequent dysregulation of neuroendocrine transcription factors, TGFβ and Notch gene targets. These results identify unknown molecular mechanisms in carcinoid development that may apply to the broader family of neuroendocrine cancers.

overall_design: ChIP-seq for YAP and TEAD immunoprecipitation in lung (H727) and pancreatic (BON1) human carcinoid cell lines. Experimental conditions included control and active YAP overexpression.

first: Nanayakkara

last: Jina

first: Yang

last: Xiaojing

first: Damiani

last: Simona

first: Imtiaz

last: Tashifa

first: Wang

last: Xiantao

first: Anastasakis

middle: G

last: Dimitrios

first: Shah

middle: M

last: Girish

first: Tyryskin

last: Kathrin

first: Hafner

last: Markus

last: Xiaolong

first: Renwick

last: Neil


title: Moderate chronic treadmill exercise slows dopaminergic neuron loss in a rat model of Parkinson's disease and alters RNA content of circulating plasma exosomes

city: East Orange

first: Bruce

middle: A.

last: Citron

state: NJ

address: 385 Tremont Ave.

department: Pharmacology, Physiology, & Neuroscience, Rutgers- NJMS

institute: VA New Jersey Health Care System

summary: Exercise has been reported to improve outcomes in patients with Parkinson’s disease, but the exact biological mechanisms remain incompletely understood. This study was conducted to determine whether chronic moderate treadmill exercise prevents dopaminergic neuron loss and Lewy body-like inclusion burden in a preclinical model of PD. This study also sought to identify plasma exosome bound “exerkines” with potential to induce neuroprotective brain adaptations. Benefits of exercise are thought to be achieved in part through nucleic acids, lipids, and peptides termed exerkines abundant during exercise. These exerkines can induce cell specific exercise adaptations culminating in neuroprotection. Membrane-free exerkines, are subject to degradation in blood and may not effectively cross the blood brain barrier to induce brain adaptations to exercise limiting their inter-organ signaling potential. This led us to hypothesize that exerkines, bioactive RNAs in particular, may be selectively packaged into exosomes and released into plasma during exercise. Exosomes are small extracellular vesicles, selectively packaged and released by cells, with likely important differences in composition at rest, during injury and disease, and in response to exercise. Exosomes have been demonstrated to play a major role in inter-organ communication. Chronic exercise was found to provide neuroprotection to dopaminergic neurons in the substantia nigra pars compacta, without affecting Lewy body-like inclusion burden in nigra or the striatum. Plasma exosomal RNA was isolated from age matched exercising and sedentary non-PD rats and sequenced. We report 27 unique RNAs upregulated in the exosomes of exercisers, 3 mRNAs with clear neuroprotective potential.

overall_design: RNA-seq analysis of exosomes isolated from plasma of rats that were either sedentary or exercised

middle: A

first: Vedad

last: Delic


title: Multi-layer stratified oncology platform utilizing transcriptomics, prostate cancer organoids, and modeling of drug response

city: Bern

first: Panagiotis

last: Chouvardas

address: Murtenstrasse 24

country: Switzerland

institute: University of Bern

summary: The high intra-patient heterogeneity in multifocal primary prostate cancer (PCa) has curtailed the efficacy of current treatment options. By employing twin biopsies from multiple lesions with matched Patient-derived organoids (PDO) models, the PCa molecular heterogeneity was investigated. We utilized genomics, transcriptomics and machine learning (ML) approaches to elucidate and predict the underlying mechanisms of pharmacological heterogeneity. Our data indicate a vulnerability of primary PCa organoids for small molecule inhibitors targeting receptor tyrosine kinases (MET, ALK, SRC). By exploring gene expression data from matched parental tissue in an unsupervised manner, we identified two distinct clusters of samples. Interestingly, the PDO drug responses were significantly different between the two clusters for 4/11 compounds tested. We developed a transcriptomics-based, cluster prediction model, which can accurately stratify samples into the two clusters. Notably, our prediction model is based on tissue profiles; therefore, it can be utilized to rapidly evaluate new cases and suggest promising drug candidates, even when PDO derivation is not feasible. Taken together, we propose a novel flexible stratified oncology approach that can swiftly and accurately highlight promising drug vulnerabilities of PCa patients.

overall_design: Prostate cancer tissue samples (FFPE) RNA sequencing

first: Juening

last: Kang

first: Andrew

last: Maalouf

first: Daniel

last: Hanhart

first: Laura

last: Fernárdez Cerro

first: Eva

last: Comperat

first: Katja

last: Ovchinnikova

first: Ulrich

last: Schneeberger

first: Beat

last: Roth

first: George

last: N. Thalmann

first: Sofia

last: Karkampouna

first: Marianna

last: Kruithof-de Julio


title: YAP AND TEAD ARE TRANSCRIPTIONAL REGULATORS OF NEUROENDOCRINE DIFFERENTIATION AND GROWTH IN CARCINOID CELLS [RNA-seq]

first: Neil

last: Renwick

overall_design: RNA-seq for lung (H727) and pancreatic (BON1) human carcinoid cell lines. Experimental conditions included control and active YAP overexpression.

first: Nanayakkara

last: Jina

first: Yang

last: Xiaojing

first: Damiani

last: Simona

first: Imtiaz

last: Tashifa

first: Wang

last: Xiantao

first: Anastasakis

last: Dimitrios

first: Shah

last: Girish

first: Tyryskin

last: Kathrin

last: Markus


title: Transcriptome profiling of kidney medulla of Actr3 KO mice

city: Freiburg

first: Manuel

last: Rogg

state: Baden Wuerttemberg

address: Breisacher Straße 115a

department: Institute of Surgical Pathology

country: Germany

institute: University Medical Center Freiburg

summary: Renal tubule-specific Actr3 knockout mice (Actr3-fl/fl*Cdh16-Cre) were generated. Transcriptome profiling (RNA-Seq) and differential gene expression analysis of isolated renal medulla from KO and WT mice at p14 was performed. Actr3 KO mice showed transcriptional changes associated with Actr3 loss and kidney disease.

overall_design: mRNA sequencing analysis of  kidney medulla of WT control and Actr3-fl/fl*Cdh16-Cre mice

first: Christoph

last: Schell


title: Enhancement of melanoma aggressiveness via p38-MAPK, HIF-1α pathways, and metabolic reprogramming induced by Candida albicans

city: Derio

first: Ana

middle: Maria

last: Aransay

state: BIZKAIA

address: Parque tecnologico de Bizkaia, Building 801-A

department: Genome Analysis Platform

country: Spain

institute: CIC bioGUNE

summary:
Recent studies have increasingly focused on the role of fungi, including Candida albicans, in
carcinogenesis. Since C. albicans is a component of the human microbiota, particularly on the skin,
we investigated its effect on the phenotype and signalling pathways of melanoma cells. Assays for
migration, adhesion, angiogenesis, and hepatic metastasis showed that C. albicans promotes a
more malignant phenotype in melanoma cells. At the transcriptomic level, C. albicans increased the
expression of VEGF (Vegfa), and genes associated with MAPK and HIF-1 signalling pathways, and with
aerobic glycolysis. Further in vitro analysis revealed that TLRs and EphA2 receptors are involved in the
recognition of live C. albicans, stimulating VEGF secretion and expression of the AP-1 transcription
factor component c-Fos through p38-MAPK and HIF-1α. These pathways also regulate the expression
of other AP-1 constituents such as Atf3, Jun, and Jund. Moreover, p38-MAPK regulates glycolytic
genes like Hk2, Slc2a1, and Eno2. In conclusion, C. albicans activates the p38-MAPK/c-Fos/AP-1 and
HIF-1/HIF-1α/c-Fos/AP-1 pathways in melanoma cells, promoting a pro-angiogenic environment and
metabolic reprogramming. Therefore, this study clarifies the impact of C. albicans on melanoma cells,
which can lead to the use of antifungal therapies as complementary to traditional treatments for
melanoma.

overall_design: Three independent biological replicates of B16-F10 murine melanoma cell line were co-incubated with Candida albicansor cell growth media (RPMI) and, after six hours, RNA was isolated and RNA sequencing was performed.

first: Leire

last: Aparicio-Fernandez

first: Aitziber

last: Antoran

first: Nuria

last: Macias-Cámara

first: Monika

last: Gonzalez

first: Jose Ezequiel

last: Martin Rodriguez

first: Ana M.

first: Juan

last: Anguita

first: Andoni

last: Ramirez-Garcia


title: Transcriptome profiling of starved Actr3 KO mIMCD3 cells

summary: Actr3 WT (control), Actr3 KO and Actr3-Ift88 double KO mIMCD3 cells were generated using CRISPR/Cas9. Single cells clones (Actr3 Ctrl.-1, Actr3 KO-1, Actr3-Ift88 dKO) were selected and validated by western blotting confirming loss of Actr3 or Ift88 in KO cell lines on protein level. Transcriptome profiling (RNA-Sequencing) and differential gene expression analysis of three independent replicates of starved (ciliated) Actr3 Ctrl.-1, Actr3 KO-1, Actr3-KO Ift88-KO (dKO) and 0.5 µM Ciliobrevin D treated Actr3 KO-1 cells was performed.

overall_design: mRNA sequencing analysis of control, Actr3 KO, Actr3-KO Ift88-KO (dKO) and 0.5 µM Ciliobrevin D treated Actr3 KO-1 mIMCD3 cells


title: Nanopore full length cDNA analysis of Cmtr1 cKO activated CD4 T cells

city: Glasgow

first: Alison

last: Galloway

address: Garscube Estate, Switchback Road

institute: Beatson CRUK

summary: We investigated the role of CMTR1 in T cells using a Cmtr1 conditional knockout mouse model. We demonstrate that CMTR1 has gene-specific impacts in T cells.

overall_design: Nanopore sequencing of oligo-dT selected mRNA from 20 hour activated CD4 T cells from Cmtr1 fl/fl CD4cre (Cmtr1 cKO) and Cmtr1 fl/fl (control) mice.

first: Katarzyna

last: Knop

first: Victoria

middle: H

last: Cowling


title: Targeting calcium signaling with synthetic EB3 inhibitor promotes lung repair through FOXM1 pathway

city: Chicago

first: Mark

last: Maienschein-Cline

state: IL

address: 900 S Ashland Ave, Rm 1058, M/C 937

department: Research Resources Center

institute: University of Illinois at Chicago

summary: Acute respiratory distress syndrome (ARDS) is a severe pulmonary disease characterized by acute, noncardiogenic pulmonary edema and hypoxemia leading to respiratory failure with a diverse array of etiologies, including the recent SARS-CoV-2 infection. The current standard of care for ARDS remains predominantly supportive, underscoring the urgent need for targeted pharmacological interventions. To address this critical gap, we have developed an inhibitor to the microtubule accessory factor end binding protein 3 (EB3), a key mediator in the pathogenesis of ARDS. During injury, EB3 in endothelial cells facilitates the cluster of inositol 1,4,5-trisphosphate receptor 3 (IP3R3) clustering on the endoplasmic reticulum surface activating pathological calcium signaling. Building on our prior research, we have designed and optimized an EB3 inhibitor, termed Vascular Therapeutics (VT)-109, with enhanced physicochemical properties using NMR approaches. Recognizing the diverse etiologies of ARDS, we evaluated the therapeutic potential of VT-109 using a range of preclinical models, including PAR-1 agonist-, endotoxin-, polymicrobial sepsis-, mechanical ventilation-, SARS-CoV-2-induced models of ARDS in mice. Treatment of VT-109 protects the lungs of mice from vascular leakage caused by ARDS by upregulating VE-cadherin at the endothelial junctions. Molecularly, VT-109 reduces the inflammatory NFAT and NFκB pathways while simultaneously activating the endothelial regenerative FOXM1 pathway. Additionally, VT-109 mitigated ARDS-induced lung injury, reduced inflammatory cytokine production, decreased morbidity and mortality, and improved lung functions. Collectively, these data demonstrate that targeting EB3-mediated pathological calcium signaling within pulmonary endothelial cells with VT-109 could provide a promising therapeutic strategy for the treatment of ARDS.

overall_design: CD1 mice were first challenged with LPS and treated with VT-109 . At endpoint, the lung tissues from all mice were obtained and pulmonary endothelial cells were isolated. Bulk RNA-sequencing was performed on the isolated endothelial cells to investigate VT-109's molecular mechanisms.

first: Wan Ching

last: Chan

first: Man Long

last: Kwok

first: Xinyan

last: Qu

first: Hazem

last: Abdelkarim

first: Jonathan

last: Le

first: Deying

last: Yang

first: Benjamin

last: Hitchinson

first: Avik

last: Banerjee

first: Shuangping

last: Zhao

first: Chongxu

last: Zhang

first: Jake

last: Class

first: Marlen

first: Harry

last: Hailemeskel

first: Raman Ghotra

last: Singh

last: Maieschein-Cline

first: Patrick

last: Belvitch

first: Vadim

last: Gaponenko

first: Justin

last: Richner

first: Yulia A

last: Komarova


title: Head-to-head preclinical treatment design prioritizes promising therapies for Neurofibromatosis 1 optic glioma clinical translation

city: St Louis

first: David

last: Gutmann

state: MO

address: 660 S Euclid Ave

department: Neurology

institute: Washington University in St Louis

summary: Authenticated preclinical brain tumor models provide unprecedented opportunities to evaluate next-generation treatments. However, many therapies that exhibit robust anti-tumor activity in mice fail to show efficacy in clinical trials. To prioritize therapeutic candidates for future clinical translation, we implemented a head-to-head preclinical strategy using a well-characterized murine model of NF1-optic pathway glioma (Nf1OPG). Nf1OPG mice were treated with standard of care (carboplatin), clinically evaluated (everolimus, mirdametinib), and investigational (pexidartinib, HBS-101, lamotrigine) drugs during the period of most rapid tumor growth (6-12 weeks of age). Ant-tumoral efficacy was assessed by proliferation (%Ki67+ cells) and optic nerve volume, while vision-related outcomes were measured using retinal nerve fiber layer (RNFL) thickness and retinal ganglion cell (RGC) determinations. Tumor microenvironment (TME) soluble mediator (Ccl2, Ccl3, Ccl4, Ccl5) and tumor cell marker (NeuN, Gpr17) RNA expression was quantitated by qRT-PCR. Outcomes were compared to carboplatin-treated Nf1OPG, untreated Nf1OPG, and Nf1+/- mice. While all agents restored normal tissue architecture, reduced optic nerve proliferation, and decreased TME soluble mediator and tumor cell marker RNA expression, only lamotrigine also reduced optic nerve volume. Everolimus, lamotrigine, and HBS-101 all restored RNFL thickness to wild-type levels, whereas carboplatin showed a trend towards normalization. This referential study design affords direct head-to-head comparisons of investigational therapies relative to standard-of-care-treatment using clinically meaningful outcomes (optic glioma growth and RNFL thickness). Using this strategy, lamotrigine emerged as the most promising therapy for limiting tumor progression and vision loss in Nf1-OPG mice relevant to clinical translation in children with NF1.

overall_design:
Raw sequencing data from Nf1OPG mouse samples were processed using the 10X Genomics Cell Ranger pipeline (version 7.2.0) to generate gene count matrices, which were aligned to the mm10-2020-A mouse reference genome. The aligned data were merged with previously published datasets (GSM7816061 and GSM7816062 from GSE244433), resulting in a total of four samples for analysis. Raw counts were used as input for the Seurat R package (version 5.2.1). For quality control, cells were excluded if they had fewer than 500 or more than 5,000 detected genes, more than 5% mitochondrial gene content, or fewer than 500 or more than 20,000 transcript counts. Normalization and variance stabilization was performed using the SCTransform function and 2,000 highly variable features of each dataset were identified and scaled using the FindVariableFeatures and ScaleData functions. Principal component analysis (PCA) was conducted using RunPCA. The data were integrated using the IntegrateLayers function with CCAIntegration. The integrated data was subjected to dimensional reduction and clustering using RunUMAP, FindNeighbors and FindClusters. Each cell type was identified using cell type-specific markers.

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The table below lists GEO accessions reused/reanalyzed for this study.
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first: Talia

last: Eligator

first: Jit

last: Chatterjee

first: Shintaro

last: Yamada

first: Anthony

last: Kirchner

first: Hareesh B

last: Nair

first: Jason R

last: Fangusaro

first: David H


title: Mitochondrial dicarboxylate carrier SLC25A10 promotes HCC cell resistance to apoptosis by upregulating BCL2A1 expression [RNA-seq]

first: Jun

last: Mi

address: 280 South Chongqing Rd.

department: Biochemistry & Molecular Cell Biology

institute: Shanghai Jiao Tong University

summary: This investigation delved into the role of the mitochondrial dicarboxylate carrier SLC25A10 in hepatocellular carcinoma's (HCC) resistance to chemotherapy. Herein, we disclosed the indispensable role of SLC25A10 in facilitating HCC's resistance to etoposide both in vitro and in mouse models. Hypoxia augmented SLC25A10 expression and instigated a splicing variation in SLC25A10 from isoform 1 to isoform 3. The isoform 3 of SLC25A10 translocated into the nucleus by associating with the nuclear transporter IPO7 and bound to the transcription factor CEBPB to upregulate the BCL2A1 expression, thereby escalating the HCC cell's resistance to Etoposide.

overall_design: To investigate the Effect of hypoxia on SLC25A10 expression, we treated three HCC cell lines with hypoxia and administered RNA-seq together with the control group


title: Mitochondrial dicarboxylate carrier SLC25A10 promotes HCC cell resistance to apoptosis by upregulating BCL2A1 expression [ChIP-seq]

overall_design: Chromatin immunoprecipitation DNA-sequencing (ChlP-seg) for CEBPB as well as SAFB2 in Huh7 cells


title: Lung adenocarcinoma cells respond differently to mechanical stress in 3D versus 2D environments [2D]

city: Toyama

first: Naoya

last: Kitamura

state: Toyama

address: 2630, Sugitani

department: Thoracic Surgery

country: Japan

institute: University of Toyama

summary: Two-dimensional (2D) culture models are commonly used in cancer research, but fail to recapitulate complex mechanical cues of native tissues. In this study, we developed an ex vivo three-dimensional (3D) lung cancer model by seeding human lung adenocarcinoma cells into decellularised rat lungs and culturing them in a pressure chamber and perfusion system mimicking respiratory motion (RM) and blood flow. In 3D culture, RM promoted cell adhesion and proliferation, enhanced the nuclear translocation of β-catenin and YAP, and increased the expression of integrin β1 and E-cadherin. In addition, upregulation of extracellular matrix- and cell adhesion-related genes was particularly notable. In contrast, in 2D culture, RM suppressed cell proliferation and induced apoptosis, with prominent upregulation of tumour suppressor genes. Our findings demonstrate that dimensionality and mechanical stress synergistically influence lung cancer cell dynamics and underscore the need for 3D models in cancer research that closely replicate the native lung tissue microenvironment.

overall_design: A549 human lung adenocarcinoma cells were divided into two groups: one subjected to respiratory motion and the other not. After four days of culture, samples were collected and subjected to RNA sequencing.

first: Mayumi

last: Iwatake

first: Satoshi

last: Mizoguchi

first: Shadil

last: Wani

first: Komei

last: Kobayashi

first: Muhammad

last: Hasnain

first: Dung

middle: V

last: Nguyen

first: Ryo

last: Yokoyama

first: Naru

last: Kitade

first: Toshihiro

last: Ojima

first: Koichiro

last: Shimoyama

last: Koba

first: Hideki

last: Hatta

first: Micha Sam

middle: B

last: Raredon

first: Kenichi

last: Hirabayashi

first: Yoshitomo

last: Morinaga

first: Tomoshi

last: Tsuchiya


title: The 3’-5’ exoribonuclease ISG20L2 contributes to 3’ terminus maturation of 18S and 28S ribosomal RNAs (revision)

city: Strasbourg

first: Dominique

last: Gagliardi

address: 12, rue du General Zimmer

department: IBMP

country: France

institute: CNRS

summary: Ribosome biogenesis is a nodal process in cell growth and proliferation, and its dysfunction is associated to human congenital diseases and tumorigenesis. Despite extensive mechanistic characterization, several processing steps of human pre-ribosomal RNAs remain elusive. The 47S primary transcript contains 3 out of 4 ribosomal RNAs flanked by external (5’ETS, 3’ETS) and internal (ITS1, ITS2) transcribed spacers. The molecular processes leading to the removal of the 3’ETS, one of the earliest maturation steps, is not fully understood. Combining loss-of-function experiments and 3’-RACE high-throughput sequencing, we showed that the vertebrate-specific 3’-5’ exoribonuclease ISG20L2, a DEDDh RNase T superfamily member, is critical for efficient removal of the 3’ETS and formation of large ribosomal subunits. ISG20L2 inactivation led to accumulation of various forms of 3’-extented pre-rRNAs and disorganized PDFC, a sub-nucleolar compartment recently linked to 3’ETS processing. The function of ISG20L2 also extends to the trimming of ITS1 after endonucleolytic cleavage at site 2 and its knockdown reveals the precise location of site 2. Altogether, the present work uncovers the landscape of two pre-rRNA processing steps at nucleotide resolution, and restricts the function of ISG20L2 to the nucleoli where it contributes to the maturation of 18S and 28S 3’ ends.

overall_design: HeLa cells were treated with a control siRNA duplex (siRNA scramble) or siRNA duplexes targeting ISG20L2, DDX51, URB1, RPL3 or RPL26 mRNA.

first: Maxime

last: Aubert

first: Hélène

last: Zuber

first: Marine

last: Mommert-Tripon

first: Sarah

last: Le Page

first: Nathalie

last: Montel-Lehry

first: Vanessa

last: Soldan

first: Stéphanie

last: Bosch

first: Pierre-Emmanuel

last: Gleizes

first: Marie-Françoise

last: O'Donohue


title: Gene expression changes in skin of dihydrotestosterone-induced mice after treatment of a newly-developed traditional Chinese medicine formula, Hanlianxiang.

city: Beijing

first: Zhiyu

last: Ning

address: Room C211, Building of Medical Science, Tsinghua University, Haidian District, Beijing, China.

institute: Tsinghua University

summary: To investigate the effect of Hanlianxiang (HLX) for treatment of androgenetic alopecia, shaved C57BL/6J mice were induced with dihydrotestosterone and treated with extract of HLX every day. The skin samples were collected at 10 and 15 days after treatment.

overall_design: Twenty-four mice were divided randomly into control, model, and treatment groups, and each group contains 8 mice. The control group received daily injections of normal saline and applied only solvent topically. The model group received daily injections of dihydrotestosterone and also applied solvent topically. The treatment group received daily injections of dihydrotestosterone and applied extract of HLX topically. For all the 3 groups, 4 mice were sacrificed at day 10 and the skin samples were collected; the remaining 4 mice were sacrificed at day 15 and the skin samples were collected.

first: Haojie

last: Ma

first: Chengmei

first: Xiaoling

last: Zhang

first: Aixiang

first: Shan

last: Zhao

first: Wenting

last: Huang

first: Hongmei

last: Cao

first: Di

last: Yan

first: Hongyan

last: Guo

first: Zhi

first: Jing

last: Cheng

first: Lan

last: Xie


title: PAD4 promotes macrophage migration to aggravate tubulointerstitial injury in diabetic kidney disease [RNA-seq]

city: Chongqing

first: Yunjie

last: Xiong

address: 1 Youyi Street

institute: The First Affiliated Hospital of Chongqing Medical University

summary: Peptidyl Arginine Deiminase 4 (PAD4) is an enzyme predominantly expressed in myeloid cells, and its role in diabetic kidney disease (DKD) remains unknown. We functionally characterized 48 PAD4 variants identified among 469,779 participants from UK Biobank and examined their associations with renal function. We found that 32 PAD4 variants causes loss of function, which was significantly associated with higher estimated glomerular filtration rate. We observed an enhanced PAD4 expression in renal tubulointerstitium among DKD patients and animal models of DKD. Both PAD4 deficiency in macrophages and PAD4 inhibitor GSK484 significantly alleviated renal tubulointerstitial injury by reducing macrophage infiltration in diabetic mice models. Mechanistically, PAD4 interacted with p65 to promote its binding to Cmklr1 promoter and induce the expression of Cmklr1, which led to an enhanced macrophage migration. These findings demonstrate the crucial role of PAD4-mediated macrophage migration in tubulointerstitial injury of DKD.

overall_design: To investigate the differential genes between PAD4-/- and WT macrophages, we isolated bone marrow derived macrophages  from PAD4-/- and WT mice for RNA-seq, each group contains four independent samples, WT-BMDM were control group


title: PAD4 promotes macrophage migration to aggravate tubulointerstitial injury in diabetic kidney disease [ATAC-seq]

overall_design: To investigate the differential chromatin accessibility between PAD4-/- and WT macrophages, we isolated bone marrow derived macrophages  from PAD4-/- and WT mice for ATAC-seq, each group contains four independent samples, WT-BMDM were control group


title: The effect of time-ordered-expression (TOE) mRNA vaccination on the expression of immune-related genes during the activation and maturation of BMDCs

city: 北京

first: xiangdong

last: zhang

state: 北京市

address: 北京市海淀区清华大学

institute: Tsinghua Univercity

summary: The adjuvant translational control plays a  pivotal role in shaping immune responses,which means that precise kinetic modulation of mRNA vaccines could help to elicit stronger immune responses.Here, we constructed lipid nanoparticles (LNPs) encapsulating the TOE mRNA(OVA-IL-12) encoding OVA (normal expression) and IL-12 (delayed expression), and also constructed LNPs encapsulating a mRNA simultaneously expressing OVA and IL-12 (OVAoIL-12), LNPs encapsulating mRNAs expressing OVA or IL-12 individually, and LNPs encapsulating equimolar mixtures of mRNAs encoding OVA and IL-12 (OVApIL-12) as control groups.we demonstrated that the TOE mRNA kept the activation of the mTORC1 pathway, as characterized by increased expression levels of crucial genes such as Tsc1, Pik3ca, and Eif4ebp1, which potentially contributed to the improved antigen expression in the cells.We also evaluated the overall transcriptome change after LNP transfection via RNA-seq and found that TOE mRNA transfection also markedly upregulated key genes associated with immune activation.Taken together,our study introduces a transformative platform for mRNA vaccine design that could overcome the limitations of conventional mRNA vaccines. By precisely controlling the time course of adjuvant translation, this new platform enhances vaccine efficacy without compromising safety, opening new avenues for the development of advanced therapeutic and prophylactic interventions.

overall_design: To evaluate the potency of TOE mRNA vaccination during the activation and maturation of BMDCs, We transfected different groups of mRNA into BMDC cells and collected transcriptome samples after 24h.

first: Xiangdong

first: Xucong

last: Teng

first: Yicong

last: Dai


title: Long Noncoding RNA LncBAR Enhances BRG1 Protein to Promote Cardiomyocyte Cell Cycle Progression and Cardiac Repair

city: wuhan

first: li

last: jun

state: hubei

address: donghu street

department: wuhan

institute: wuhan university

summary: The mammalian heart retains regenerative capacity during the early postnatal period, but this ability declines as it matures. Enhancing cardiomyocyte proliferation represents a key therapeutic approach to promote heart regeneration and repair, yet the molecular mechanisms remain elusive. Here, we identified LncBAR (BAF complex-associated lncRNA) as a critical regulator of cardiac regeneration. LncBAR expression declines during heart development but is upregulated following cardiac injury. Loss of LncBAR impairs cardiomyocyte growth, suppresses cell cycle gene expression, and diminishes heart regeneration, as evidenced by reduced cytokinesis and cardiac function. Conversely, cardiac specific overexpression of LncBAR restores cardiomyocyte proliferation and enhances cardiac regeneration, especially in adult myocardial infarction model. Mechanistically, LncBAR interacts with Brg1, stabilizing BRG1 protein level and activating cell cycle progression to drive cardiomyocytes proliferation. Collectively, our study identified LncBAR as a crucial regulator for heart regeneration, highlighting the LncBAR-BRG1 axis as a promising therapeutic strategy for cardiac repair.

overall_design:
To investigate the function of LncBAR in regulating the proliferation of mouse cardiomyocytes, we isolated primary neonatal mouse cardiomyocytes to perform loss-of-function or gain-of-function experiments
To explore the effect of LncBAR on cardiac regeneration, we constructed an AR model of LncBAR knockout mice and LncBAR transgenic mice
To explore the effect of LncBAR on adult cardiac regeneration, we constructed an MI model of  LncBAR transgenic mice
To explore the mechanism of LncBAR regulates cardiomyocyte proliferation, we performed RNA seq of LncBAR knockdown in cardiomyocytes

first: Jun

last: Li

first: Huanhuan

last: Cai

first: Yufan

last: Chen

first: Ruiqi

last: Pi


title: Transcriptome profiling of Actr3 KO mIMCD3 cells

first: Manuel

last: Rogg

summary: Actr3 WT (control) and Actr3 KO mIMCD3 cells were generated using CRISPR/Cas9 and independent gRNAs for control and KO cell lines. Single cells clones (Ctrl.-1, Crtl.-2, KO-1, KO-2) were selected and validated by western blotting confirming loss of Actr3 in KO cell lines on protein level. Transcriptome profiling (RNA-Sequencing) and differential gene expression analysis of independent replicates per cell line was performed.

overall_design: mRNA sequencing analysis of control and Actr3 KO mIMCD3 cell lines

first: Christoph

last: Schell


title: Tumor necrosis factor promotes doublecortin-like kinase 1 expression and cellular reprogramming in intestinal epithelial cells leading to neoplastic transformation

city: Nantong

first: Xingmin

last: Wang

state: Jiangsu

address: 399 Century Ave.

department: Institute of Genetics and Reproductive Medicine

institute: Nantong Maternity and Child Healthcare Hospital

summary: Tumor necrosis factor (TNF) plays a crucial role in inflammatory bowel disease and colorectal cancer (CRC). However, its involvement in the regulation of cancer stem cells (CSCs) remains poorly understood. This study aims to elucidate the role of TNF in the origin of colorectal CSCs. Rat intestinal epithelial cells (IEC-6) were treated with TNF, or PBS as control, for 10 treatments and subjected to single-cell RNA sequencing (scRNA-seq). UMAP analysis identified 5 and 3 cell clusters in IEC-6 control (IEC-6Ctrl) cell line and TNF-treated (IEC-6TNF) cell line, respectively. Notably, a substantial number of stem cells emerged in IEC-6TNF cells, while goblet cells and enterocytes diminished, indicating that long-term exposure to TNF induces cellular reprogramming. Furthermore, using Dclk1 as a marker gene, pseudotime trajectory analysis revealed that transient amplifying (TA) cells represented the initial point of the developmental trajectory in both IEC-6Ctrl and IEC-6TNF cell lines. Interestingly, in the IEC-6TNF cell line, the trajectory progressed from TA cells to tuft cells and ultimately to stem cells, indicating that in TNF-treated cells, stem cells arise from Dclk1+ tuft cells. These findings suggest that prolonged TNF treatment depletes differentiated cells, such as goblet cells and enterocytes, while promoting the emergence of stem cells through dedifferentiation and reprogramming.

overall_design: Rat intestinal epithelial cells (IEC-6) were treated with TNF, or PBS as control, for 10 treatments and then subjected to single-cell RNA sequencing (scRNA-seq).

first: Li

last: Huang


title: SF3B1 K700E Mutation Induces Genome-Wide Enhancement of Transcriptional Pause Release in ES Cells

city: Boston

first: Claudia

last: Mimoso

state: MA

address: 45 Shattuck St. LHRRB

institute: Harvard Medical School

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

overall_design: Refer to individual Series


title: Differential gene expression analysis between miR-17 overexpressing and control human chondrocytes

city: Nanchang

first: Jinghong

last: Yuan

state: Jiangxi

address: No.1 Minde Road

institute: The Secondly Affiliated Hospital of Nanchang University

summary: Identify the differentially expressed genes in chondrocytes overexpressing miR-17 compared to controls, and predict the biological functions and potential regulatory signaling pathways of miR-17 through functional enrichment analysis.

overall_design: Total RNA was extracted from three miR-17 overexpressing chondrocyte samples and three normal control chondrocytes, quantified using a NanoDrop ND-2000 (Thermo Scientific), and RNA integrity was assessed using an Agilent Bioanalyzer 2100 (Agilent Technologies). After the RNA passed quality control, labeling, hybridization, and washing of the microarray followed the standard procedure. First, the total RNA was reverse-transcribed into double-stranded cDNA, which was then used to synthesize cRNA labeled with Cyanine-3-CTP (Cy3). The labeled cRNA was hybridized to the microarray, washed, and scanned using an Agilent Scanner G2505C (Agilent Technologies) to obtain the raw images.

first: Yameng

first: Jingyu

last: Jia


title: An alpha-enolase (ENO1) related gene signature predicts prognosis risk and therapeutic response in diffuse large B-cell lymphoma

city: 大连

first: WenliYan

middle: Wenli

last: Yan

state: 辽宁省

address: 甘井子区

department: 附属第二医院

institute: 大连医科大学

summary: High ENO1 expression in Burkitt lymphoma is associated with poor clinical outcomes. ENO1 is an RNA-binding protein, but its function in Burkitt lymphoma is unknown. We made RIP-seq of ENO1 through Illumina HiSeq X Ten sequencing platform, hoping to find RNA that can be bound by ENO1 and further analyze the function of ENO1.

overall_design: RIP-seq of ENO1 was performed in Daudi cells using Illumina HiSeq X Ten sequencing platform to search for RNA that could be bound by ENO1

first: Haina

first: Wenli

first: Xiaoxi

last: Liu

first: Beibei

last: Gao


title: Everolimus and sunitinib induce infantile hemangiomas cell apoptosis through P53 activation

city: Cambridge

first: Jianfeng

last: Ge

state: Cambridgeshire

address: 37, ST THOMAS'S SQUARE

institute: University of Cambridge

summary: Infantile hemangiomas (IH) are common vascular tumors in infants, yet their underlying mechanisms remain poorly understood. In this study, we isolated endothelial cells from IH and utilized hTERT and SV40 to establish an immortalized hemangioma-derived endothelial cell (iHemEC). We employed these iHemEC for in vitro drug screening and investigated the mechanisms of drug-induced inhibition of iHemEC via transcriptome sequencing, western blot analysis, and various cellular assays. We successfully established iHemEC that highly express VEGFR2, CD31, and GLUT-1, markers characteristic of endothelial cells. Screening of 18 putative working drugs were performed on iHemEC. Sunitinib, Elimusertib, HIF-1 inhibitor-4, Rebastinib, and Everolimus can inhibit iHemEC with lower IC50 than Propranolol and Rapamycin. We further performed transcriptome profiling in iHemEC upon Everolimus and Sunitinib intervention. GSEA showed that both drugs can significantly downregulate Hallmark of MYC target V1&V2, E2F Target and G2M Checkpoint which are all cell cycle related Hallmark. PI3K/AKT/mTOR pathway is only downregulated in Everolimus treated cells which is validated by western blot. Chromosome instability was found specifically in Sunitinib treated cells which was reported to cause DNA damage. DHR123 was used to detect DNA damage induced ROS and released extracellular ROS can only be observed in Sunitinib treated cells. Finally, P53 activation was observed in western blot, we found that Sunitinib can trigger P53 activation and BCL2 downregulation from 0.2 µM which is fifty times lower than Everolimus at 10 µM. Our study successfully developed an iHemEC line suitable for in vitro drug screening and mechanistic study. Everolimus and Sunitinib are two of working drugs and both drugs can induce P53 dependent apoptosis on iHemEC might through PI3K/AKT/mTOR inhibition and chromosome instability respectively. These findings provide a valuable basis for further research and potential clinical application in the treatment of IH.

overall_design: comparing gene expression profiling analysis of RNAseq data on Everolimus and sunitinib treated iHemECs

first: RongFang

last: Xie

first: Miaomiao


title: SF3B1 K700E Mutation Induces Genome-Wide Enhancement of Transcriptional Pause Release in ES Cells [PRO-seq]

summary: SF3B1, a critical component of the U2 snRNP splicing factor, is frequently mutated in cancer and plays a crucial role in pre-mRNA splicing. We investigated the effects of the most common SF3B1 mutation, heterozygous substitution of Lysine 700 to Glutamate (K700E), in human embryonic stem (hESC) cells using CRISPR-Cas9 to generate heterozygous SF3B1K700E clones. We observed the upregulation of several key transcription regulators associated with hematopoiesis and a broad range of immune genes in SF3B1K700E hESCs. Despite transcriptional differences between hESC and myelodysplastic syndrome (MDS) cells harboring the SF3B1K700E mutation, several common gene programs were identified in both cell types, independent of splicing alterations. To further elucidate the molecular mechanisms underlying dysregulated gene expression in SF3B1K700E hESCs, we performed Precision Run-On sequencing (PRO-seq) in SF3B1K700E hESCs. These analyses revealed alterations in RNA polymerase II (Pol II) elongation properties induced by the SF3B1K700E mutation. Specifically, a general increase in pause release was noted in SF3B1K700E hESCs. This study identifies several downstream candidate genes that could contribute to the SF3B1 mutated phenotype, shedding light on the impact of the U2 snRNP on transcription by Pol II.

overall_design: Examination of 6 samples by PRO-seq; 3 biological replicate sets of SF3B1 K700E Mutant and SF3B1 WT libraries.

first: Mahtab

last: Dastpak

first: Moein

last: Farshchian

first: Christina

middle: L

last: Paraggio

middle: E

last: Leonard

first: Shanye

last: Yin

first: Binkai

last: Chi

first: Kelsey

middle: W

last: Nassar

first: RGrant

last: Rowe

first: Jiuchun

last: Zhang

first: George

middle: Q

last: Daley

first: Karen

last: Adelman

first: Robin

last: Reed


title: Tissue-specific iron levels modulate lipid peroxidation and the FLASH radiotherapy effect

city: Headington

first: Eui Jung

last: Moon

address: Old Road Campus Research Building, Roosevelt Drive

department: Department of Oncology

institute: University of Oxford

summary: In this study, we investigated how irradiation changes global transcriptomic changes in MDA-MB-231 cells. Cells were treated either at 0Gy or 10Gy and RNA was extracted to perform RNA sequencing.

overall_design: MDA-MB-231 cells were treated with 0Gy or 10 Gy irradiatio using Cs irradiator. 24 hours after the treatment RNA was collected by using Rneasy kit (Qiagen). RNA samples were sent to Novogene (Cambridge, UK) for library preparation and sequencing. Sequencing was performed by Novoseq 6000.

first: Nuria

last: Vilaplana Lopera

first: Jiyoung

last: Kim


title: Irinotecan activates anti-tumor immunity in CT26 subcutaneous tumors

city: Nanjing

first: Xinghua

last: Gao

address: #639 Longmian Dadao

institute: China Pharmaceutical University

summary: Topoisomerase I (Top1) is a classical drug target for anticancer therapy, but its role in immune signaling in cancer cells remain unclear. Here, we aimed to explore the possible role and mechanism of Irinotecan (CPT-11) in anti-tumor immunity.

overall_design: CT26 subcutaneous tumors mRNA profiles of Control and CPT-11 tretment mice were generated by deep sequencing, in duplicate.

first: Yong

last: Yang

first: Yanting

last: Lin


title: DHT alleviates neuroinflammation to reduce PND occurrence in aged mice via mmu_circ_0001442/miR-125a-3p/NUFIP2 axis

city: nan chang

first: chuang

last: suan

address: zhan qian road 163

institute: nan chang university

type: Non-coding RNA profiling by high throughput sequencing

summary: To clarify the role of circRNA in DHT improving cognitive function in mice with perioperative neurocognitive disorder, circRNA sequencing was preformed to analyze the expression of circRNA in hippocampus of mice.

overall_design: The hippocampus tissue of representative mice was extracted for circRNA sequencing in the testosterone group and the control group. Gene abundance was calculated and normalized by the SRPBM (spliced reads per billion mapping) method. The DESeq2 (V1.6.3) of the Bioconductor software package was used to identify differentially expressed circRNA between DHT-treated and control groups. Significantly different genes were those with (FC) ≥ 2 and P value < 0.05.

first: Huai-Gen

first: Li

last: Liu

first: Mei

first: Zhi-Ping

last: Song


title: MDM4-related bone marrow failure

city: Memphis

first: Lance

last: Palmer

state: TN - Tennessee

address: 262 Danny Thomas Pl

department: Hematology

institute: St. Jude Children's Research Hospital

summary: We report 6 unrelated individuals with variable BMF phenotypes and hypocellular MDS. The median age at presentation was 10 years (4 weeks - 53 years). Unbiased genomic analysis revealed germline heterozygous variants in MDM4, including 4 null (frameshift, nonsense, and splice-site resulting in premature truncation confirmed by RNA sequencing) and 2 missense variants. Mechanistically, MDM4 mutations lead to loss-of-function with enhanced p53 activation. We used CRISPR/Cas9 to delete MDM4 in healthy donor hematopoietic stem and progenitor cells (HSPCs). The resulting MDM4-haploinsufficient HSPCs exhibited increased p53 activity, impaired colony-forming capacity, and reduced engraftment potential in immunodeficient mice. Complementation studies revealed the functional necessity of both p53-binding and RING-finger domains in MDM4-mediated hematopoietic regulation. To study variant effect in a genetic background free of potential confounders, we introduced patient-specific MDM4 variants into induced pluripotent stem cells (iPSCs). MDM4-mutant iPSCs yielded significantly reduced erythroid and myeloid cell populations and exhibited increased p53 activity, as evidenced by elevated p21 expression, confirming the role of MDM4 in regulating hematopoiesis through p53 modulation. Transcriptome analysis of iPSC-derived hematopoietic cells revealed upregulation of p53 pathway. Importantly, one patient acquired TP53 mutations, suggesting clonal rescue in the context of MDM4 deficiency. Our findings establish MDM4 deficiency as a new “TP53-opathy” BMF syndrome with variable hematopoietic manifestations. This study also highlights the critical role of the MDM4-p53 axis in maintaining hematopoietic homeostasis.

overall_design: RNA sequencing obtained from iPSC dervied CD43 cells

first: Richa

last: Sharma

first: Senthil

last: Bhoopalan

first: Marcin

last: Wlodarski


title: RNA-Seq shows the changes on transcriptomes after deletion of Nsd2 in KPC1199 cells.

city: shanghai

first: wenxin

last: feng

address: 1954 Huashan Road, Shanghai

institute: shanghai jiaotong university

summary: To explore the possible role of Nsd2 in pancreatic carcinogenesis, the gene expression profile of Nsd2-WT and Nsd2-KO derived from KPC1199 cells was examined by RNA-seq.

overall_design: Nsd2 was depleted with CRISPR/Cas9 in KPC1199 cells. The gene expression profile of Nsd2-WT and Nsd2-KO derived from KPC1199 cells was examined by RNA-seq.

first: Wenxin

last: Feng

first: L

last: i Li


title: Cmtr1 regulates the activated CD4 T cell transcriptome [GEO_Cmtr1_act]

city: Glasgow

first: Alison

last: Galloway

address: Garscube Estate, Switchback Road

institute: Beatson CRUK

summary: We investigated the role of CMTR1 in T cells using a Cmtr1 conditional knockout mouse model. We demonstrate that CMTR1 has gene-specific impacts in T cells.

overall_design: Sequencing of rRNA-depleted RNA from 20 hour activated CD4 T cells from Cmtr1 fl/fl CD4cre (Cmtr1 cKO) and Cmtr1 fl/fl (control) mice.

first: Victoria

last: Cowling


title: Transcriptome analysis of human monocyte-derived myeloid cells

city: Nantes

first: Aurelie

last: Moreau

address: 30 bd Jean Monnet

institute: INSERM U1064

summary: Transcriptome analysis of different populations of human monocyte-derived myeloid cells: Autologous Tolerogenic Dendritic Cells (ATDCs), Monocyte-derived Dendritic Cells (MoDCs) and IL-10 induced dendritic cells (DC-10). GSM 2800573 to GSM 2800584 that were re-analyzed from GSE104438.

overall_design:
CD14+ sorted monocytes from 6 different donors were used to differentiate ATDCs, MoDCs and DC-10 from the same samples. We analyzed transcriptomic profiles from these monocytes-derived cells using Agilent whole genome oligo Microarrays (8x60K).

***************************************************************
The table below lists GEO accessions reused/reanalyzed for this study.
***************************************************************

first: A

first: S

last: Gregori

first: G

last: Amodio


title: CMTR1 regulates the naïve CD4 T cell transcriptome [Cmtr1_naive_rnaseq]

summary: We investigated the role of CMTR1 in T cells using an Cmtr1 conditional knockout mouse model. We report that the cap-specific RNA (nucleoside-2'-O-)-methyltransferase, CMTR1, supports naïve T cell survival and activation-induced proliferation. We demonstrate that CMTR1 has gene-specific impacts in T cells. These RNAseq experiments investigate the effect of Cmtr1 cKO on the naïve CD4 T cell transcriptome.

overall_design: Sequencing of rRNA-depleted RNA from naïve CD4 T cells sorted from the lymph nodes of Cmtr1 fl/fl CD4cre (Cmtr1 cKO) and Cmtr1 fl/fl (control) mice.

first: Aneesa

last: Kaskar

first: Olga

last: Suska


title: CMTR1 regulates the naïve and activated CD4 T cell transcriptome


title: Genome-scale transcriptome augmentation during Arabidopsis thaliana photomorphogenesis

city: Paris

first: Clara

last: Bourbousse

address: 9 quai Saint Bernard

department: UMR 7622 LBD

institute: Sorbonne Université

summary: Plant photomorphogenesis is a light-induced developmental switch combining rapid enrichment in RNA Polymerase II activity and massive gene expression reprogramming. Yet, all former transcriptome analyses of this transition detected no average tendency toward gene upregulation. By applying a spike-in RNA-seq approach, we solved this conundrum and reconciled transcriptome dynamics with epigenomic and cytogenetic data. This further unveiled that Arabidopsis cotyledon photomorphogenesis involves a ~2-fold expansion of the transcriptome, a trend that we reproducibly observed in datasets from independent laboratories upon normalization using a set of stable genes defined ad hoc. This new standpoint enabled us to reinterpret light-mediated gene regulatory paths and unveil a quasi-exclusive positive effect of light-induced transcription factors on target genes. Collectively, this study reveals how environmentally controlled variations of the transcriptional regime can functionally impact plant genome expression. It further establishes a framework for investigating the mechanisms of global genome regulation in these organisms.

overall_design: RNA-seq with drosophila spike-in on dissected cotyledons

first: Geoffrey

last: Schivre

first: Léa

last: Wolff

first: Fredy

last: Barneche


title: Surface mechanics and compressive stress impact mammalian follicle development

status: Public on Oct 15 2025

city: Singapore

first: Chii Jou

last: Chan

address: 5A Engineering Drive 1

department: Mechanobiology Institute

country: Singapore

institute: National University of Singapore

summary: The maturation of functional eggs in ovaries is essential for successful reproduction in mammals. Despite its biological and clinical importance, the underlying mechanisms regulating folliculogenesis remain enigmatic. Here, using murine ovaries, we report that the theca cells surrounding secondary follicles play a critical role in regulating follicle development through mechanical signalling. Using biophysical approaches, we found that the contractile theca cells exert significant compressive stress to the follicular interior through active assembly of fibronectin. Manipulation of compressive stress by targeting theca cell contractility, basement membrane integrity or intrafollicular pressure leads to changes in follicle size and mechanics, granulosa cell YAP signalling and oocyte-granulosa cell communications. Transcriptomics and quantitative immunofluorescence reveal that compressive stress impacts functional follicle growth through regulating the balance between granulosa cell proliferation and death that drives tissue pressure homeostasis. Altogether, our study identifies new mechanical functions of theca cells and provides quantitative evidence of the role of compressive stress in regulating mammalian folliculogenesis.

overall_design: RNA sequencing of granulosa cells and oocytes isolated from encapsulated follicles grown for three days in control, Blebbistatin treatment, and dextran treatment.

first: Arikta

last: Biswas

first: Kosei

last: Tomida


title: Acute Arrhythmias in a Long-chain 3-Hydroxyacyl-CoA Dehydrogenase Deficiency (LCHADD) Mouse Model

city: Portland

first: Gabriela

last: Elizondo

state: OR

address: 3222 SW Research Drive

institute: OHSU

summary: Patients with LCHADD, a mitochondrial fatty acid oxidation (FAO) disorder, frequently present with cardiomyopathy and can suffer life-threatening arrhythmias and heart failure. While these remain the leading causes of death, the pathophysiology remains unknown. We used an LCHADD mouse model to examine the mechanisms of impaired cardiac function. Methods: We previously determined that LCHADD mice (Hadha c.1528G>C homozygotes) recapitulate human disease and develop cardiomyopathy. We performed electrophysiological tests on LCHADD and WT mice, followed by cardiac tissue and molecular expression analysis. Results: LCHADD mice showed significantly increased frequency of atrial premature beats, premature ventricular contractions, atrial flutter, and atrial and ventricular fibrillation after b-agonist stimulation compared to WT mice. Long QRS and long QT intervals were also observed. LCHADD heart sections demonstrated increased cardiomyocyte cross-sectional area, increased lipid and collagen deposition, and decreased glycogen deposits. There was global sympathetic denervation in LCHADD hearts compared to WT. Differentially expressed gene analysis showed increased expression of glycolytic and glutathione synthesis enzymes, decreased gene expression of TCA cycle enzymes, Ca++ signaling, and cardiac muscle contraction proteins. Conclusions: LCHADD cardiomyopathy has a hypertrophic phenotype with diffuse fibrosis, accumulation of lipids, and lower glycogen storage in the absence of obesity. LCHADD cardiomyocyte metabolism suggests a shift from FAO toward glycolysis with chronic oxidative stress. Energy deficiency and lipotoxicity likely influence Ca++ signaling and cardiac contraction. Long QRS and QT intervals with global sympathetic denervation may predispose the heart to repolarization abnormalities susceptible to arrhythmias and increased risk of sudden cardiac arrest and death.

overall_design: RNAseq profiling of mice heart ventricles with LCHADD vs WT in males and females.

first: Arianna

last: Scalco

first: Ayah

last: Asal

first: Hak

last: Chung

first: Garen

last: Gaston

first: Beth

last: Habecker

first: Melanie

last: Gillingham


title: Single-cell gene expression analysis of ulcerated skin in Has2 transgenic and wild-type mice with scratching-induced ulcerative derm

city: Houston

first: Yi

last: Zhu

state: TX

address: 1100 Bates Ave

department: Pediatrics

institute: Baylor College of Medicine

summary: Ulcerative dermatitis (UD) in mice is an idiopathic skin disease characterized by intense pruritus, hair loss, self-inflicted lesions, and progression to ulceration. UD serves as a model for chronic skin inflammation and non-healing wounds in humans, as it shares key pathological features with these conditions. C57BL/6 mice are particularly susceptible to UD, making this strain a valuable model for studying the mechanisms underlying skin injury and inflammation. In previous studies, Has2 transgenic mice exhibited a higher incidence of UD compared with wild-type controls, implicating elevated hyaluronan synthesis in disease susceptibility. To investigate the cellular and molecular mechanisms, we induced scratching-triggered UD in Has2 overexpressing (Has2OE) and wild-type mice (n = 4 per group) and performed single-cell RNA sequencing (scRNA-seq) on lesional skin to compare cell-type composition and gene expression changes.

overall_design: The ulcerated lesional skin from scratching-induced UD wild type or whole-body Has2 overexpression mice were separated and analyzed using single-cell RNA sequencing (scRNA-seq).

first: Jieyi

last: Meng

first: Fan

last: Wu

first: Hong

last: Zhou

first: Malay

last: Shah


title: RNA-seq analysis of differentiated noradrenergic neurons (1C11NE) and microglia (BV2) following exposure to acrylamide (ACR)

city: Noda

first: Gaku

last: Ichihara

address: Yamazaki 2641

department: Faculty of Pharmaceutical Sciences

institute: Tokyo University of Science

summary:
Neurotoxicity of acrylamide (ACR), which is an environmental electrophilic chemical, has been reported in occupational human cases and experimental animal models. Our previous study using murine model demonstrated that exposure to ACR induced dose-dependent degeneration of noradrenergic axons, which has been reported to be extensively related with various cognitive disorders and neurodegenerative diseases. To investigate the mechanism of ACR-induced degeneration of noradrenergic neurons and the role of microglia, in this study, differentiated noradrenergic neuron model (1C11NE), as well as microglia cell line (BV2) were used.
BV2 microglia were exposed to PBS or ACR (1mM) for 24 hrs. 1C11NE neurons were exposed to ACR or to conditioned medium (CM) from ACR-treated BV2 microglial cells (ACR-CM). Transcriptomic RNA-seq were carried out for 1C11NE neurons and BV2 microglia.

overall_design:
For 1C11NE neurons, five groups of samples after different treatments for 24 hrs were analyzed, including:
1) PBS group, 1C11NE cells were exposed to vehicle PBS, (i.e. 0 mM ACR);
2) ACR group, 1C11NE cells were exposed to 1mM ACR;
3) PBS-CM group, 1C11NE cells were exposed to CM of PBS-exposed BV2 microglia;
4) ACR-CM group, 1C11NE cells were exposed to CM of 1mM ACR-exposed BV2 microglia;
5) PBS-CM+ACR group, 1C11NE cells were exposed to PBS-CM with addition of 1mM ACR.

For BV2 microglia, two groups of samples were analyzed, including:
1) BV2_PBS group, BV2 cells were exposed to vehicle PBS, (i.e. 0 mM ACR);
2) BV2_ACR group, BV2 cells were exposed to 1mM ACR.

first: Cai

last: Zong

first: Harue

last: Sato

first: Benoit

last: Schneider

first: Shigeyuki

last: Shichino

first: Satoshi

last: Ueha

first: Bin

first: Kouji

last: Matsushima

first: Makoto

last: Urushitani

first: Sahoko


title: CD2 costimulation strength: A key regulator of T cell function and anti-tumour immunity that is epigenetically regulated.

city: nicosia

first: PHILIPPOS

last: DEMETRIOU

state: nicosia

address: Nicandrou Papamina Avenue, 15, Strovolos

country: Cyprus

institute: THE CENTER FOR THE STUDY OF HEMATOLOGICAL AND OTHER MALIGNANCIES

summary: CD2 is a key costimulatory receptor on human T cells, but its surface abundance regulation and the functional significance of it remained incompletely defined. We found that CD2 expression is markedly reduced in CD4⁺ and CD8⁺ tumor-infiltrating T cells from human brain tumors. To identify factors sustaining CD2 expression, we performed a genome-wide CRISPR-Cas9 screen in Jurkat T cells and discovered BAP1 and SUZ12 as regulators. Loss of BAP1 caused downregulation of CD2, TRAC, and other costimulatory receptors with CD2 and TRAC expression remaining impaired even after activation. Transcriptomic analysis linked BAP1 deficiency to disruption of programs controlling T cell identity and differentiation, while histone deacetylase inhibition partially restored CD2. In primary human T cells, reduced CD2 costimulation impaired the magnitude of proliferation and IFN-γ production. These findings identify BAP1 as a central regulator of receptor expression and highlight CD2 as a tunable modulator of human T cell responses.

overall_design: RNA-seq profiling of wildtype Jurkat T cells and their established BAP1 knockout derivative

first: Philippos

last: Demetriou

first: Maria

last: Iakovou

first: Gregoria

last: Gregoriou

first: Dimitris

last: Vrachnos

first: Jianxiang

last: Chi

first: Athos

last: Antoniades

first: Paul

last: Costeas


title: Sexually Dimorphic Sail Feathers in the Mandarin Duck: A Model for Lifelong Developmental Modulation [ChIP-seq]

city: Los Angeles

first: Ya-Chen

last: Liang

state: CA

address: 2011 Zonal Ave., HMR 304A

department: Department of Pathology

institute: University of Southern California

summary: Developmental processes extend beyond embryogenesis to support lifelong tissue adaptations. Avian feather follicles, with their resident stem cells and capacity for cyclic regeneration, provide a dynamic model for postnatal tissue remodeling. Here, we propose the Mandarin duck (Aix galericulata) as an ideal model to study lifelong developmental modulation, focusing on the sexually dimorphic “sail feather”—a secondary flight feather in males that undergoes seasonal transformation into a strikingly asymmetric, ornamented phenotype during the breeding season. We identified asymmetric morphogen expression in regenerating male sail feathers and used transcriptome and H3K27ac ChIP-seq to uncover male and female signaling pathways and regulatory elements. Comparative epigenomic profiling reveals enriched estrogen receptor binding motifs in females. Hormone profiling shows seasonal variation, with a marked rise in female estrogen levels preceding the mating season. These results imply Mandarin duck sail feathers integrate local morphogenetic programs, epigenetic regulation, and systemic hormonal cues to orchestrate sexually dimorphic and seasonally dynamic feather morphogenesis. This work establishes a framework for further mechanistic study of the interplay between regeneration, regional identity, and hormonal plasticity in a vertebrate integumentary system.

overall_design: We profiled active regulatory elements in Mandarin duck (Aix galericulata) feather follicles using H3K27ac ChIP-seq during early regenerative growth in the breeding season (“in season”). Two body regions were compared: the sexually dimorphic sail feather (remex 12) and the adjacent secondary flight feather (remex 11). For males, we collected regenerating sail feathers that contain lateral blue and medial brown vanes (“blue+brown sail feather”; 2 biological replicates) and regenerating flight feathers with the same vane composition (“blue+brown flight feather”; 2 biological replicates). For females, we collected regenerating sail feathers characterized by dark/black pigmentation (“black sail feather”; 2 biological replicates) and regenerating flight feathers with blue and black pigmentation (“blue+black flight feather”; 2 biological replicates). In total, eight H3K27ac ChIP libraries (2 reps × 4 conditions) were generated; samples were processed in parallel with identical protocols to enable differential analyses by sex and by region (sail vs. flight).

first: Pin-Chi

last: Tang

first: Hsu-Chen

last: Cheng

first: Gee-Way

last: Lin

first: Yung-Chih

last: Lai

first: Ping

last: Wu

first: Tzu-Chiao

first: Chen Siang

last: Ng

first: Isheng

last: Tsai

first: Ang

last: Li

first: Wen Hsiung

first: Chih-Feng

last: Chen

first: Cheng-Ming

last: Chuong

first: Randall

last: Widelitz


title: SF3B1 K700E Mutation Induces Genome-Wide Enhancement of Transcriptional Pause Release in ES Cells [RNA-seq]

city: Boston

first: Claudia

last: Mimoso

address: 45 Shattuck St. LHRRB

institute: Harvard Medical School

overall_design: Examination of 6 biological conditions by RNA-seq; 3 biological replicate sets of SF3B1 K700E Mutant and SF3B1 WT libraries. 3 technical replicates per biological replicate.

first: Mahtab

last: Dastpak

first: Moein

last: Farshchian

first: Christina

last: Paraggio

last: Leonard

first: Shanye

last: Yin

first: Binkai

first: Kelsey

last: Nassar

first: RGrant

last: Rowe

first: Jiuchun

last: Zhang

first: George

last: Daley

first: Karen

last: Adelman

first: Robin

last: Reed


title: RNASeq-based identification of extracellular matrix components impacted by FasL deficiency in osteoblasts

city: Brno

first: Martina

last: Zapletalová

address: Kamenice 5

department: Department of Biochemistry

country: Czech Republic

institute: Masaryk University

summary: Osteoblasts and osteoclasts are two critical cell populations in bone remodelling. FasL is known from osteoblast-induced osteoclast apoptosis. Notably, FasL deficient (gld) mice display increased bone mass pointing to non-apoptotic functions of FasL. Some key extracellular matrix associated molecules, such as osteoprotegerin, osteocalcin, osteopontin and alkaline phosphatase were reported to be affected by FasL deficiency in osteoblasts but a complex insight has been missing. To fill this gap and provide a robust dataset, gld calva-derived cells were differentiated along with controls and subjected to RNASequencing. The analysis revealed statistically significant changes in expression of 1,710 genes. 15 % (263) out of them were associated with the extracellular matrix. This applied for the collagen components,  but also non-collagenous proteoglycans including versican and aggrecan. This report provides enrichment analysis of statistically significant expression changes in calva-derived osteoblastic cells with focus on extracellular matrix components. The dataset further provides a solid background for further functional analyses revealing the exact mechanisms behind and consequences of such dysregulations in pathophysiology.

overall_design: Mice homozygous for the FasL gld mutation (B6Smn.C3-Faslgld/J) were purchased from The Jackson Laboratory (Bar Harbor, ME). C57BL/6 were used as a wild-type control. Mice were kept at the Department of Biomedical Research of the Medical University of Vienna. Calvaria-derived cells (gld and wt) were isolated and expanded as described in Kratochvilova et al. (2022). Differentiation was performed in osteogenic media consisting of MEM alpha (Gibco, Waltham, MA, USA), 10% fetal bovine serum (Sigma-Aldrich, Burlington, MA, USA), 1% penicillin/streptomycin (Sigma-Aldrich), 50 mg/ml ascorbate and 4 mM β-glycerophosphate in 37˚C and 5% CO2. For the stimulatory experiment of gld cells, the osteogenic medium was supplemented with 150 ng/ml recombinant human sFas ligand (Peprotech, 310-03H) at day 14 of differentiation. The cells were then cultured for 72 h, the medium/medium+FasL was changed once during this time, wt cells (wt), gld cells (gld) and gld cells treated by FasL (gld+FasL) were cultured in parallel. Samples for RNA isolation were lysed in 350 μl of RLT lysis buffer (Qiagen) with β-ME (Sigma-Aldrich), total RNA was extracted using RNeasy Mini Kit (Qiagen, Germany) and cDNA was synthesized using the gb Elite Reverse Transcription Kit (Generi Biotech, Czech Republic). Total RNA samples were sent for QuantSeq analysis to Lexogen GmbH, Campus Vienna Biocenter 5, Vienna, where the samples were processed and sequenced according to the company's standard operating procedure. In brief, the library for sequencing was prepared using the QuantSeq 3′mRNA-Seq Library Prep Kit FWD for Illumina (Lexogen) and the Lexogen i5 6 nt Unique Dual Indexing Add-on Kit (Lexogen). Single-read RNA-Seq (1 × 75) was performed using an Illumina NextSeq 500 System (Illumina). Comprehensive analysis of the RNA-Seq data, including demultiplexing, read quality assessment, trimming and filtering, read mapping, and differential expression analysis, was carefully performed by Lexogen GmbH. This analysis was performed according to their standardized pipeline for QuantSeq FWD data. In brief, read quality was assessed using the FastQC , RSeQC  and MultiQC  packages. Samples were trimmed using the Cutadapt  tool and aligned to the reference genome using the STAR  aligner.


title: RNA-sequencing transcriptomic analysis of scrapie-infected ovine mesenchymal stem cells

city: Zaragoza

first: Inmaculada

last: Martín Burriel

state: Zaragoza

address: Miguel Servet, 177

department: Anatomy, Embriology and Animal Genetics

institute: University of Zaragoza

summary: In neurodegenerative diseases, including prion diseases, cellular models arise as useful tools to study the pathogenic mechanisms occurring in these diseases and to assess the efficacy of potential therapeutic compounds. In the present study, a RNA-sequencing analysis of bone marrow-derived ovine mesenchymal stem cells (oBM-MSCs) infected with scrapie was performed to try to unravel genes and pathways potentially involved with prion disease mechanisms and to assess the potential of these cells to act as in vitro models of prion toxicity. oBM-MSCs were cultured in three different conditions: inoculated with brain homogenate of scrapie-infected sheep, with brain homogenate of healthy sheep and in standard growth conditions without inoculum. The cell viability and presence of prions was determined. In the transcriptomic analysis the three conditions were analysed in two infection times: 2 and 4 days’ post-inoculation (dpi). Differentially expressed genes in scrapie-infected oBM-MSCs were found in the two infection times finding the higher number at 2 dpi. These genes were also enriched in multiple pathways and biological functions related with prion replication and toxicity. Moreover, a set of 11 genes was selected for a validation study, having 7 of these genes significant expression changes in scrapie-infected cells and functions related with prion propagation and its associated toxicity. These results indicate that ovine mesenchymal stem cells infected with scrapie could be useful in vitro models to study prion toxicity mechanisms and to test anti-prion compounds.

overall_design: To discover genes and pathways potentially involved with prion disease mechanisms and to evaluate the potential of ovine mesenchymal stem cells as in vitro models of prion toxicity, we performed a RNA-sequencing analysis of oBM-MSCs. Two infection times (2 days and 4 days post-inoculation) and three conditions were studied (cells inoculated with scrapie-infected brain homogenate, cells inoculated with negative brain inoculum and non-inoculated controls) with 3 technical replicates per condition and time.

first: Adelaida

last: Hernaiz

first: Belén

last: Marín

first: Francisco

middle: J

last: Vázquez

first: Juan

last: Badiola

first: Pilar

last: Zaragoza

first: Rosa

last: Bolea

last: Martín-Burriel


title: The 3’-5’ exoribonuclease ISG20L2 contributes to 3’ terminus maturation of 18S and 28S ribosomal RNAs

city: Strasbourg

first: Dominique

last: Gagliardi

address: 12, rue du General Zimmer

institute: CNRS

summary: Ribosome biogenesis is a nodal process in cell growth and proliferation, and its dysfunction is associated to human congenital diseases and tumorigenesis. Despite extensive mechanistic characterization, several processing steps of human pre-ribosomal RNAs remain elusive. The 47S primary transcript contains 3 out of 4 ribosomal RNAs flanked by external (5’ETS, 3’ETS) and internal (ITS1, ITS2) transcribed spacers. The molecular processes leading to the removal of the 3’ETS, one of the earliest maturation steps, is not fully understood. Combining loss-of-function experiments and 3’-RACE high-throughput sequencing, we showed that the vertebrate-specific 3’-5’ exoribonuclease ISG20L2, a DEDDh RNase T superfamily member, is critical for efficient removal of the 3’ETS and formation of large ribosomal subunits. ISG20L2 inactivation led to accumulation of various forms of 3’-extented pre-rRNAs and disorganized PDFC, a sub-nucleolar compartment recently linked to 3’ETS processing. The function of ISG20L2 also extends to the trimming of ITS1 after endonucleolytic cleavage at site 2 and its knockdown reveals the precise location of site 2. Altogether, the present work uncovers the landscape of two pre-rRNA processing steps at nucleotide resolution, and restricts the function of ISG20L2 to the nucleoli where it contributes to the maturation of 18S and 28S 3’ ends.

overall_design: HeLa cells were treated with a control siRNA duplex (siRNA scramble) ou siRNA duplexes targeting ISG20L2 mRNA.

first: Maxime

last: Aubert

first: Hélène

last: Zuber

first: Marine

last: Mommert-Tripon

first: Sarah

last: Le Page

first: Nathalie

last: Montel-Lehry

first: Vanessa

last: Soldan

first: Stéphanie

last: Bosch

first: Pierre-Emmanuel

last: Gleizes

first: Marie-Françoise

last: O'Donohue


title: PCBP1 binding to single-stranded poly-cytosine motifs enhances cGAS sensing and impairs breast cancer development

city: Charleston

first: Cécile

last: Fréreux

state: SC

address: 173 Ashley Avenue

institute: Medical University of South Carolina

summary: The cGAS-STING pathway plays a central role in controlling tumor progression through nucleic acid sensing and type I Interferon production. Here, we identify Poly(rC) Binding Protein 1 (PCBP1) as a tumor suppressor that amplifies cGAS-STING signaling in breast cancer. Using patient datasets and a transgenic mouse model with conditional PCBP1 knockout in mammary epithelial cells, we show that PCBP1 expression correlates with improved survival, reduced tumor burden, increased type I IFN and ISG expression, and elevated cytotoxic T cell infiltration. Mechanistically, PCBP1 binds cytosine-rich single-stranded motifs via its KH domains and increases cGAS affinity to these nucleic acids. Disruption of the conserved GXXG motif impairs PCBP1's nucleic acid binding and cGAS activation. Although cGAS is a double-stranded DNA sensor with no intrinsic sequence specificity, we uncover that the single-stranded nucleic-acid binding protein PCBP1 enhances cGAS sensing by engaging sequence-specific motifs, acting as an important nucleic acid co-sensor that impairs tumorigenesis.

overall_design: We used mammary tumors from a C57BL/6 transgenic mouse model expressing the MMTV-PyMT (polyomavirus middle T antigen) oncogene, which drives mammary tumorigenesis, in addition to a MMTV-Cre PCBP1(fl/fl) system that selectively knocks out PCBP1 in mammary epithelial cells. These mice, abbreviated as PyMT PCBP1–/–, were compared to control animals expressing the MMTV-PyMT and MMTV-Cre constructs along with the non-floxed PCBP1(wt/wt) alleles, referred to as PyMT PCBP1+/+. RNA was prepared from the mammary tumors and RNA-sequencing performed.

first: Joseph

last: Karam

first: Breege

last: Howley

first: Bryan

last: Granger

first: Paramita

last: Chakraborty

first: Annamarie

middle: C

last: Dalton

first: Bidyut

middle: K

last: Mohanty

first: Silvia

last: Vaena

first: Romeo

last: Martin

first: Shikhar

last: Mehrotra

first: Philip

last: Howe


title: PCBP1 binding to single-stranded poly-cytosine motifs enhances cGAS sensing and impairs breast cancer development [snRNA-Seq]

overall_design:
We used sized-matched mammary tumors (~100mg) from a C57BL/6 transgenic mouse model expressing the MMTV-PyMT (polyomavirus middle T antigen) oncogene, which drives mammary tumorigenesis, in addition to a MMTV-Cre PCBP1(fl/fl) system that selectively knocks out PCBP1 in mammary epithelial cells. These mice, abbreviated as PyMT PCBP1–/–, were compared to control animals expressing the MMTV-PyMT and MMTV-Cre constructs along with the non-floxed PCBP1(wt/wt) alleles, referred to as PyMT PCBP1+/+. The mammary tumors were dissociated, the nuclei sorted by flow cytometry and analyzed by single-nuclei RNA-sequencing.
Please note that the same mouse model associated with GSE307616 RNA-seq dataset was used for the current study


first: Clara

last: Bourbousse

overall_design: ChIP-seq of RNA pol II and H2Bub of dissected cotyledons from 5-day-old Arabidopsis thaliana light and dark-grown seedlings. 3 Replicates are available for RNA Pol II, 2 for H2Bub. A spike-in was included (Drosophila S2 cells chromatin).

first: Elodie

last: Armanet

first: Delphine

last: Cuménal

first: Fredy

last: Barneche


title: Molecular mechanisms governing the formation of distinct Upf1-containing complexes in yeast

city: Martinsried

first: Fabien

last: Bonneau

address: Am Klopferspitz 18

department: Structural Cell Biology

institute: Max Planck Institute of Biochemistry

summary: Upf1 is a master regulator of nonsense-mediated mRNA decay (NMD), an mRNA surveillance and degradation pathway conserved from yeast to human. In S. cerevisiae, Upf1 exists in two distinct complexes with factors that mediate NMD activation or 5'-3' mRNA degradation. We combined endogenous purifications and biochemical reconstitutions of yeast Upf1 complexes with structural analyses and biochemical assays to elucidate the molecular mechanisms driving the mutually exclusive organization of the Upf1-5'-3' and Upf1-2-3 complexes. We show that yeast Upf1 is in a constitutive complex whereby its CH, RecA and C-terminal domains interact with the mRNA decapping factor Dcp2, NMD-associated proteins Nmd4 and Ebs1, and the 5'-3' exoribonuclease Xrn1, respectively. Together, the interacting surfaces and closed conformation of Upf1 in the Upf1-5'-3' complex sterically obstruct the binding of Upf2-3. Our work points to a major restructuring upon recruitment of these factors during NMD and provides insights into evolutionary divergence amongst species.

overall_design: RNA-seq of poly(A)-enriched total RNA extracted from wild type yeast or from deletion strains for UPF1, NMD4 or EBS1. Between 3 and 6 replicates for each condition, in 2 sequencing batches.

first: Iuliia

last: Iermak

first: Elena

last: Conti


title: Impaired store-operated Ca2+ entry in mouse epidermis

city: Fukuoka

first: Naoto

last: Haruyama

state: Fukuoka

department: Faculty of Dental Science

institute: Kyushu University

summary: The purpose of this study was to investigate the role of SOCE in the skin epidermis in vivo, using female mice with epithelial tissue-specific Stim1 and Stim2 knockout (Stim1/2 cKO) and control mice (Stim1/2fl/fl).　This study found that SOCE dysfunction led to hyperkeratosis and impaired epidermal barrier function via Klk activation without affecting skin cell proliferation in vivo.

overall_design: RNA samples collected from keratinocytes obtained from epithelial tissue-specific (K14-Cre) Stim1 and Stim2 knockout (Stim1/2 cKO) and control mice (Stim1/2fl/fl).

first: Kaho

last: Mochimatsu

first: Keigo

last: Yoshizaki

first: Ichiro

last: Takahashi


title: Tissue-resident macrophages co-develop with myocardial tissue in human induced pluripotent stem cell-derived organoids

city: Würzburg

first: Anna

middle: Frederike

last: Rockel

address: Koelliker Straße 6

department: Institute of Anatomy and Cell Biology

institute: University of Würzburg

summary: The heart is the first functional organ to develop during embryogenesis, forming in parallel with the vasculature and hematopoietic cell lineages. To advance our understanding of human cardiac development and disease, human induced pluripotent stem cell-derived cardiomyocytes offer a promising in vitro model. However, conventional 2D culture systems lack the complexity required to recapitulate the intricate interactions of different cell types leading to fully functional and mature cardiac tissue. Here, we present a cardiac organoid model that mimics several aspects of cardiogenesis. The organoids develop a functional myocardium consisting of cardiomyocytes and fibroblasts capable of spontaneous rhythmic contractions. The myocard is interspersed with a branched endothelial network. Additionally, macrophages develop within the organoids and integrate into the myocardium. In summary, we describe a complex 3D cell culture platform to study human heart tissue development with all the involved cell types (cardiomyocytes, fibroblasts, endothelial cells, macrophages), paving the way for new insights into the role of macrophages in cardiac development and disease.

overall_design: RNA-seq profiling of human wildtype cardiac organoid at day 35

middle: F

first: Tobias

last: Brunnenbauer

first: Nicole

last: Wagner

first: Brenda

last: Gerull

first: Süleyman

last: Ergün

first: Philipp

last: Wörsdörfer


title: Non-Invasive Detection of Bone Marrow Fibrosis in Myeloproliferative Neoplasms Using Cell-Free RNA

city: Aachen

first: Mohamed

last: Saad

address: Pauwelsstraße 30

department: Institut für Zell- und Tumorbiologie

institute: Uniklinik RWTH Aachen

summary: Myeloproliferative neoplasms (MPNs), particularly with myelofibrosis (MF), involve a disrupted perivascular hematopoietic niche ultimately leading to bone marrow fibrosis. We asked if the transcriptome in cell-free RNA (cf-RNA) from peripheral blood of MPN patients (with JAK2V617F mutation) can detect bone marrow fibrosis. Transcriptomic profiling revealed significant gene expression changes correlating with reticulin fibrosis grades. Advanced reticulin fibrosis grades (2-3) showed upregulation of TGF-β pathways and ECM remodeling markers, with decreased hematopoietic support. Grade 3 fibrosis was associated with increased proliferation signals and elevated inflammatory markers (S100A8/9). RUNX1 was identified as a key transcription factor in fibrosis with its overexpression driving myofibroblast differentiation in mesenchymal stromal cells. IL-18 emerged as a critical inflammatory mediator, with elevated plasma levels correlating with the transformation to high grades fibrosis (reticulin grades 2-3). Functional assays confirmed that IL-18 stimulation of mesenchymal stromal cells induced fibrotic transformation, emphasizing its role as a biomarker and target.

overall_design: Cell-free RNA was obtained from peripheral Platelet-Poor Plasma (PPP) from four cohorts of patients, each diagnosed with different reticulin grades of bone marrow fibrosis: (Grade 0: from patient_1 to patient_5, Grade 1: patient_6 to patient_8, Grade 2: patient_9 to patient_11, Grade 3: patient_12 to patient_16)

first: Stijn

last: Fuchs

first: Carmen

last: Schalla

first: Katrin

last: Götz

first: Jessica

last: Pritchard

first: Niclas

last: Flosdorf

first: Adam

last: Benabid

first: Hélène

last: Gleitz

first: Nils

last: Leimkühler

first: Aurélien

last: Dugourd

first: Rebekka

last: Schneider


title: Impact of somatic XIST deletions on ongoing XIST expression and inactive X silencing and heterochromatin

city: Vancouver

first: Carolyn

last: Brown

address: 2350 Health Sciences Mall

institute: University of British Columbia

summary: The long non-coding RNA XIST is critical during early female development for establishing X-chromosome inactivation. XIST continues to be expressed from the inactive X throughout life, and can establish silenced heterochromatin when ectopically expressed; yet silencing of most genes on the inactive X has been shown to continue in the absence of XIST in somatic cells. As changes in XIST expression are observed in cancers and aging we sought to re-examine the impact of complete or partial XIST loss on gene expression and chromatin structure in the hTERT RPE-1 cell line. Loss of the A repeat region resulted in complete loss of XIST expression. While loss of an adjacent enhancer region spanning the small F repeat region impacted expression and loss of the repeat E region impacted localization, both deletions maintained partial silencing. Upon XIST loss there was reactivation of a subset of X-linked genes, with escape genes showing an average 20% increase in expression; consistent with other studies. Comparison with other studies of XIST loss in human somatic cells revealed some common XIST-dependent escapees, while autosomal genes demonstrated no consistent XIST-dependencies. Loss of XIST in hTERT RPE-1 resulted in loss of H3K27me3 and H2AK119ub; however, inhibition of each of these pathways failed to upregulate candidate escapees on the inactive X. In contrast, reduction of H3K9me3 caused partial reactivation of USP9X but not MED14. XIST regulatory elements lie within the gene, with ongoing expression dependent on the A repeat region, as well as enhancer function from the adjacent F-containing region. Unlike the E region, the F region is not involved in XIST localization. Our work, in agreement with previous studies, reveals that in somatic cells XIST expression and localization suppresses the expression of escape genes, likely through loss of XIST-dependent chromatin modifications. No single chromatin modification was responsible for the XIST-dependency, varying across both genes and studied cell lines, thus implicating combinatorial action of silencing pathways on the inactive X. While disruption of autosomal gene expression is observed, there are no consistent autosomal XIST-dependencies to implicate a direct action of XIST on autosomes across cell types.

overall_design: RNA-seq profiling of wild-type RPE1 cells and RPE1 cells with CRISPR-mediated interal deletion of XIST gene

first: Karanveer

middle: S

last: Bhangu

first: Christine

last: Yang

first: Hannah

last: Illing


title: Structural and functional changes in the gastrointestinal tract of the ACTA2 R179H mouse model of multisystemic smooth muscle dysfunction syndrome

first: Rhian

last: Stavely

address: 185 Cambridge Street, CPZN, 6100

department: Pediatric Surgery

institute: Massachusetts General Hospital

summary: Multisystemic Smooth Muscle Dysfunction Syndrome (MSMDS) is a rare disorder caused by ACTA2 mutations, including the R179H variant, which disrupts actin polymerization and smooth muscle contractility. While cardiovascular complications dominate its clinical presentation, gastrointestinal (GI) dysfunction significantly impacts quality of life. To investigate the structural, functional, and cellular basis of gut dysmotility in MSMDS, we studied the ACTA2 R179H mouse model and reviewed clinical data from 24 MSMDS patients. Patients exhibited severe gut dysmotility, with 75% requiring medication for chronic constipation. ACTA2 mutant mice displayed cecal and colonic dilatation, reduced intestinal length, and disrupted colonic migrating motor complexes (CMMCs). Delayed whole-gut transit and impaired contractile responses to electrical and pharmacological stimulation were observed. Transcriptomic analysis revealed significant actin cytoskeleton-related gene changes in smooth muscle cells, and immune profiling identified increased lymphocytic infiltration. Despite functional abnormalities, enteric neuronal populations remained unchanged. These findings establish ACTA2 mice as a robust model for studying GI pathology in MSMDS, elucidating the role of smooth muscle dysfunction in gut dysmotility. This model provides a foundation for developing targeted therapies aimed at restoring intestinal motility by directly addressing actin cytoskeletal disruptions in smooth muscle cells.

overall_design: Use of 10X Genomics technology to analyze single-nuclei transcriptomics in single nuclei suspensions of muscularis propria from the colon of Myh11-Cre:Acta2R179Hfl/+ mouse model of Multisystemic Smooth Muscle Dysfunction Syndrome (MSMDS)

first: Ahmed

last: Rahman

first: Leah

last: Ott

first: Christopher

middle: Y

last: Han

first: Kensuke

last: Ohishi

first: Ryo

last: Hotta

first: Alan

last: Burns

first: Sabyasachi

last: Das

first: Emily

last: Da Cruz

first: Diana

last: Tambala

first: Mark

last: Lindsay

first: Patricia

last: Musolino

first: Allan

middle: M

last: Goldstein