title: Characterization of Persistency of Lay in Laying Hens

city: Ithaca

first: Laurie

last: Francoeur

state: NY

address: 507 Tower Rd

department: Animal Science

institute: Cornell University

summary: Selective breeding in laying hens has resulted in a laying rate of approximately one egg per day during their first year. Due to variability within a flock, this rate declines after the first year, leading producers to cull hens. The aim of this study was to identify physiological and molecular differences between persistent (PL, egg-laying rate = 100%) and non-persistent layers (NPL, egg-laying rate ≤ 82%) after the first year. Forty laying hens were reared from 16 to 76 weeks of age and a subset was maintained until 96 weeks. Throughout the study, egg-laying data were recorded daily. At 76 weeks, ovarian tissue was collected from PL (n=3) and NPL (n=4) hens for RNA-sequencing. Ovarian RNA-sequencing analysis revealed 279 differentially expressed genes between PL and NPL hens and analysis predicted the estrogen receptor as an upstream regulator. A greater understanding of the physiology and molecular patterns of persistent hens could enhance production efficiency and provide insights into ovarian aging in women.

overall_design: RNA-sequencing of ovarian samples from persistent and non-persistent laying hens.

first: Deena

last: Scoville

first: Jaclyn

middle: G

last: Ahern

first: Patricia

middle: A

last: Johnson


title: Spatially resolved profiling of host and bacteria RNAs in mammalian tissue

status: Public on Apr 01 2026

city: New Haven

first: Yang

last: Liu

state: CT

address: 300 George St., Room 8300C 8th floor

department: Pathology

country: USA

institute: Yale University

summary: The host and microbiome coexist in the natural environment, engaging in constant and dynamic interactions that are fundamental to human health. Understanding these interactions requires unbiased, spatially resolved techniques capable of mapping gene expression in both the host and microbiome within their native microenvironment. In this study, we introduce microDBiT, a spatial sequencing technology that enables simultaneous, high-resolution profiling of both host and bacterial RNAs (mRNA and rRNA). By applying microDBiT, we successfully mapped the spatial distribution of host and bacterial RNAs in the intestines, colon, and tongue of germ-free (GF) mice colonized with bacteria. Furthermore, we utilized this approach in a dextran sulfate sodium (DSS)-induced colitis model, uncovering key mRNA-level changes in both host and microbial cells. This study demonstrates the power of microDBiT in resolving host-microbiome interactions at the transcriptomic level, providing critical insights into host-pathogen dynamics, immune responses, and microbiome-driven disease mechanisms.

overall_design: Here, we present microDBiT (DBiT-seq for microbiome), a technique that can map the gene expression of both bacteria and their host tissue. microDBiT is based on a similar microfluidic system with DBiT-seq, but with tailored protocols that can map bacteria gene expression complementary to host genes. In a typical microDBiT protocol, the bacteria containing tissue will be first fixed with formaldehyde to lock the mRNAs in tissue. We then perform bacterial cell wall removal with lysozyme followed by cell membrane removal with surfactants. Polyadenylation of bacterial RNAs were carried out with E. coli poly(A) polymerase I (PAP), which was reported to preferentially polyadenylates mRNA rather than rRNA in bateria. Revers transcription of both bacterial and host RNAs were completed by reaction in a small reservoir that can cover the region of interest. We used a mixture of polyT based and random hexamer based primers to achieve the best RT efficiency. The 1st microfluidic chip with 50 horizontal channels was placed on the tissue and a set of 50 DNA barcodes annealed with ligation linker were flowed through each channel. After ligation and washing, the 1st chip was removed and a 2nd chip with vertical channels were placed, and a 2nd ligation was completed by flowing another set of 50 ligations barcodes. After two rounds of ligation, the tissue was lysed with proteinase K and the cDNAs were extracted with streptavidin beads. We then performed template switch, PCR and library preparation following protocol described previously.


title: DOT1L enhances BLM-induced pulmonary fibrosis by inducing endothelial-to-mesenchymal transition via H3K79me2 [ChIP-seq]

city: Guangzhou

first: Shu

last: Meng

state: Guangdong

address: No.9, XingDaoHuanBei Road, Guangzhou International Bio-island, Haizhu District

department: Department of Basic Science Research

country: China

institute: Guangzhou National Laboratory

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Endothelial-to-mesenchymal transition (EndoMT) have been reported to contribute to pulmonary fibrosis. Here, we showed that induction of EndoMT activated DOT1L expression and enhanced H3K79me2 level by TGFβ2 in human umbilical vein endothelial cells (HUVECs) in vitro. Using a bleomycin (BLM)-induced idiopathic pulmonary fibrosis (IPF) model, endothelial-lineage tracing reporter mice, and endothelial-specific Dot1L knockout mice, we confirmed that DOT1L mediates EndoMT and drives pulmonary fibrosis in vivo through H3K79 methylation. ChIP-seq revealed direct binding of SMAD2/3 to the DOT1L promoter and increased H3K79me2 deposition at fibrosis-related genes following TGFβ2 stimulation.

overall_design: HUVECs were collected at 24 h with TGFβ2 treatment or not, and histone mark H3K79me2 was profiled using ChIP-seq.

first: Yaofeng

last: Wang

first: Xing

last: Peng


title: Single-cell TCR Profiling in Left Atria Identifies Complement Pathway Involvement in Atrial Fibrillation

city: Kobe

first: Takuo

last: Emoto

state: Hyogo

address: 7-5-1 Kusunoki-cho, Chuo-ku

department: Division of Cardiovascular Medicine, Department of Internal Medicine

country: Japan

institute: Kobe University Graduate School of Medicine

type: Expression profiling by high throughput sequencing

summary: Atrial fibrillation (AF) is the most prevalent arrhythmia and is strongly associated with stroke, heart failure, and increased mortality. However, the role of T cells in AF pathogenesis remains unclear. In this study, we aimed to characterize the detailed landscape and clonal expansion of T cells using single-cell TCR sequencing, and validate our findings via O-link proteomics in plasma. Analysis of left atrial tissues from eight AF patients identified five CD4+ T cells, six CD8+ T cells, and gamma delta T cells based on canonical gene expression markers. Notably, we observed clonal expansion of resident memory and cytotoxic T cells. CellChat analysis highlighted complement signaling–mediated interactions between T cells and fibroblasts. Furthermore, proteomics in plasma using the Olink platform confirmed enriched complement activation in non-paroxysmal AF compared to paroxysmal AF. These findings suggest that activation of complement pathway between T cells and fibroblasts contributes to atrial remodeling and may serve as a potential therapeutic target for AF.

overall_design: CD45 positive cells of human left atium samples were isolated by Fluorescence-activated cell sorting and analyzed using scRNAseq, moreover, all cells of human left atium samples were analyzed using snRNAseq

first: Mitsuhiko

last: Shoda


title: Fibrinogen αC-Domain derived from Group 1 Allergen of Dermatophagoides microceras modulates cell adhesion in human bronchial epithelial Cells

city: Taichung city

first: Yu-Fan

address: No.110. Sec 1, Jianguo N. Rd.

department: Biomedical sciences

country: Taiwan

institute: Chung Shan Medical University

summary: House dust mites (HDMs) allergens are major contributors to allergic asthma, with their protease activity playing a critical role in airway inflammation. Der m 1, a Group 1 HDMs allergen from Dermatophagoides microceras, is a cysteine protease known for its ability to degrade host proteins. In this study, we identified novel fibrinogen cleavage sites targeted by Der m 1, which are distinct from those cleaved by thrombin or plasmin. By employing biochemical and bioinformatic approaches, we identified the fibrinogen αC domain as a key component of Der m 1-derived fibrinogen cleavage products (FCPs). To assess their functional effects, we treated human bronchial epithelial cells with Der m 1-derived FCPs and the fibrinogen αC domain. Both treatments significantly enhanced cell adhesion, with effects peaking at 2–4 hours post-treatment before gradually declining. Transcriptomic analysis, including RNA sequencing (RNA-seq) and gene set enrichment analysis (GSEA), revealed that both Der m 1-derived FCPs and the αC domain induced similar transcriptional responses, particularly in pathways related to cell adhesion, extracellular matrix organization, and integrin signaling. Notably, integrin αV (ITGAV) was identified as a central regulatory hub, suggesting that Der m 1-derived FCPs influence cell adhesion through integrin-mediated mechanisms. To explore this further, integrin-mediated adhesion was evaluated using Cilengitide, a cyclic RGD peptide that antagonizes αVβ3 and αVβ5 integrins. Co-treatment with Cilengitide significantly suppressed the pro-adhesive effects of both FCPs and αC domain, confirming an integrin αV-dependent mechanism. These findings reveal a novel interaction between the protease allergens of HDMs and host proteins. Specifically, they demonstrated that Der m 1 not only cleaves fibrinogen but also generates bioactive fragments that regulate epithelial cell adhesion and signaling. This study sheds new light on the role of HDMs allergen-derived proteases in airway remodeling and allergic asthma pathogenesis, highlighting potential therapeutic opportunities targeting Der m 1 proteolytic activity and its bioactive cleavage products.

overall_design: RNA sequencing was used to profile gene expression in BEAS-2B cells after 4-hour exposure to fibrinogen, Der m 1-derived FCP, or the fibrinogen αC domain to evaluate adhesion-related molecular changes.

first: Chia-Yang

last: Lin

first: Hao-Ruei

last: Hsu

first: Jiunn-Liang

last: Ko


title: Macrophage-Mediated IL1beta/IL23 Signaling Regulates gamma delta (gammadelta) T Cell Immunity Against Non-Tuberculous Mycobacteria

city: Shanghai

first: Xiaoqian

last: Hu

address: No. 130, Dongan Road, Xuhui District, Shanghai

institute: Fudan University

summary: Mechanistic Insights. Our study reveals the crucial role of gammadelta T cells in non-tuberculous mycobacteria (NTM) infection. We observed a significant increase and activation of gammadelta T cells in mice infected with MAB or with MAB infection combined with pulmonary fibrosis. Depletion of gammadelta T cells worsened the infection, while transfer of gammadelta T cells reversed this effect. Mechanistically, we found that MAB infection stimulates macrophages to produce IL-1beta and IL-23, which promotes the expansion of gammadelta T17 cells. MAB can also directly activate gammadelta T cells, leading to the clearance of MAB through an IL-17A-dependent pathway. Our findings suggest that gammadelta T cells represent a potential therapeutic target for NTM infections.

overall_design: For human single-cell sequencing, all patients had a positive etiological diagnosis, clinical symptoms and a clinician's primary diagnosis of NTM infection. Whole blood was drawn from patients with NTM infection. Peripheral blood mononuclear cells were isolated.


title: Transcriptomic Analysis Identifies Urinary CXCL10 as an Early Biomarker for Subclinical Acute Rejection SCAR  in Kidney Transplantation

city: Valenzano-Bari

first: Sharon

middle: Natasha

last: Cox

department: Renal Lab

country: Italy

institute: Schena Foundation

summary: Our study on 4 four main objectives: (i) evaluate the incidence of SCAR in a clinical prospective study of kidney transplant patients who underwent protocol biopsies at established times; (ii) analyze the molecular pattern of SCAR tissue; (iii) identify urinary biomarkers linked to SCAR gene expression; (iv)validate the identified biomarkers in an external independent cohort of kidney transplant patients.

overall_design: Total RNA was extracted from archival FFPE renal tissue samples of 12 patients diagnosed with Subclinical Acute Rejection (SCAR), as assessed independently by two pathologists according to the updated Banff criteria. A control group consisted of 12 patients who showed normal histological findings (NORM) in protocol biopsies performed at 3 and 12 months post-transplantation. Gene expression profiling was performed using the Agilent-072363 SurePrint G3 Human GE v3 8x60K Microarray (Design ID: 039494).

middle: N

first: Samantha

last: Chiurlia

first: Francesco

middle: P

last: Schena


title: Genomic Convergence in Hibernating Mammals Elucidates the Genetics of Metabolic Regulation in the Hypothalamus [bulk RNA-seq]

city: Salt Lake City

first: Chris

last: Gregg

state: UT

address: 20 South 2030 East

department: Neurobiology and Anatomy

institute: University of Utah

summary:
Extreme metabolic adaptations can elucidate genetic programs governing mammalian metabolism. Here we used convergent evolutionary changes in hibernating lineages to define conserved cis-regulatory elements (CREs) and metabolic programs. We characterized mouse hypothalamus gene expression and chromatin dynamics across fed, fasted, and refed states, then used comparative genomics of hibernating versus non-hibernating lineages to identify cis-elements with convergent changes in hibernators. Multi-omics approaches pinpointed CREs, hub genes, regulatory programs, and cell types underlying lineage divergence. Hibernators accumulated loss-of-function effects for CREs regulating hypothalamic responses, and the refeeding period after fasting served as a key phase for molecular processes with convergent evolutionary changes. This work provides a genetic framework for harnessing hibernator adaptations to understand human metabolic control.
Convergent signals define cis-regulatory mechanisms behind food scarcity responses and hibernator-homeotherm divergence.

overall_design: Track gene expression in mouse hypothalamus through a series of diet conditions.

first: Elliott

last: Ferris

first: Christopher

first: Susan

last: Steinwand

first: Cornelia

middle: S

last: Hörndli

first: Pablo

middle: J

last: Maldonado-Catala

first: Josue

middle: D

last: Gonzalez Murcia

first: Riley

last: Spotswood

first: Adriana

middle: C

last: Rodriguez

first: Dimitri

last: Traenkner

first: Alun

last: Thomas

first: Crystal

last: Davey


title: Expression profiling of mouse testes on postnatal day 14 (P14) with conditional knockout of Rif1 in pre-meiotic germ cells.

city: Wuhan

first: ZHIYI

last: CHEN

address: WuHan

institute: WuHan University

summary: To investigate the transcriptomic changes of mouse testes after Rif1 ablation in pre-meiotic germ cells, we collected Rif1 sKO and normal conttrol mouse testes on postnatal day 14 (P14) for RNA sequencing.

overall_design: We collected Rif1 sKO and normal conttrol mouse testes on postnatal day 14 (P14) for RNA sequencing, three replications for every group.

first: Mengcheng

last: Luo

first: Rong

last: Liu

first: Jiemin

last: Chen

first: Weihao

last: Gong

first: Zhiyi


title: Non-redundant roles for ILC2 and TH2 cells during anamnestic lung Type 2 immunity

city: New Orleans

first: Ulrich

last: Femoe Membe

state: Louisiana

address: 1430 Tulane Avenue

department: Microbiology and Immunology

institute: Tulane University School of Medicine

summary: Type 2 immune responses help with wound healing and clearing helminth infections, but the distinct roles of group 2 innate lymphoid cells (ILC2s) and T-helper 2 (TH2) cells are not fully understood. In this study, we examined whether ILC2s and TH2 cells are necessary or sufficient to repair lung injury and prevent re-infection with the parasite Nippostrongylus brasiliensis. Surprisingly, removing TH2 cells before re-infection did not affect lung healing or worm clearance. However, mice lacking ILC2s (LCR1-/-) showed severe IL-17-related lung bleeding and poor parasite clearance. Activated ILC2s expressed high levels of Amphiregulin (Areg) and Tph1, and Areg+ ILC2s were more abundant than TH2 cells in re-infected lungs. Although treatment with recombinant Areg increased TH2 cell numbers and improved worm clearance, it did not reduce lung injury in ILC2-deficient mice. Interestingly, serotonin levels influenced IL-17-driven lung damage regardless of parasite burden. Our findings suggest that while TH2 cells help fight infection, ILC2s play a unique and essential role in repairing lung tissue.

overall_design: Lung ILC2s were sort-purified from wild-type mice as live CD45⁺ CD90.2⁺ CD127⁺ cells using a BD FACS Aria II. Cells with >85% viability were resuspended at 700–1200 cells/μL in PBS with 10% FBS. Single-cell libraries were prepared using the 10x Genomics Chromium Single Cell 3’ Reagent Kit v3 following the manufacturer’s protocol.

last: Membe Femoe

first: De’Broski

middle: R

last: Herbert


title: hnRNPL-orchestrated alternative splicing governs germ cell integrity and primordial follicle pool establishment

city: zhejiang

first: Siyu

address: zhejiang

institute: zhejiang university

summary: The primordial follicle pool established during the perinatal period, serves as the lifelong source of oocytes, with its depletion leading to premature ovarian failure (POF). Germ cell development from primordial germ cells (PGCs) to primordial follicle formation is tightly regulated by transcription and extensive post-transcriptional alternative splicing (AS). However, the dynamics and role of AS during PGC development and follicle formation remains poorly understood. Analysis of single-cell transcriptomes from E14.5 to P5 mouse ovaries revealed dynamic AS changes and key splicing factors involved in primordial follicle formation. Here, we employed a conditional knockout (cKO) model to demonstrate that hnRNPL loss in pre-meiotic germ cells disrupts homologous synapsis, induces extensive DNA damage, and results in abnormal diplotene-stage germ cells. Further analysis revealed that hnRNPL deficiency reduces transcript levels of genes essential for primordial follicle maintenance, causes aberrant splicing and protein expression of synapsis-related genes. These cumulative effects culminate in POF and infertility. Our findings explore AS dynamics and highlight hnRNPL as a key regulator of AS in primordial follicle pool formation and activation.

overall_design: Examination of WT and hnRNPL-null in ocary from E18.5, P1 mice by RNA-seq,

first: Feng-Jie

last: Hu

first: Si-yu


title: Deciphering the STAT3-PXN positive feedback loop in GBM, IDH-wildtype: transcriptional regulation and inhibition of YB-1 ubiquitination

city: Shihezi

first: Xiaodong

last: Li

address: No. 31, Beisi East Road, Shihezi City, Xinjiang

institute: Shihezi University

summary: Y-box binding protein 1 (YB-1) has been implicated in the progression of glioblastoma (GBM), a highly aggressive brain tumor. This study investigated the transcriptional regulatory role of YB-1 in GBM through the deployment of mRNA sequencing (RNA-seq) on U87 and U373 glioblastoma cell lines that underwent stable knockdown of YB-1 utilizing YB-1-targeting short hairpin RNA (shRNA), with vector-delivered scrambled shRNA employed as a control group. High-throughput sequencing elucidated genome-wide transcriptomic alterations resultant from YB-1 depletion, encompassing differentially expressed genes (DEGs) pertinent to critical cellular pathways. Additionally, functional enrichment analysis employing Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) underscored YB-1's probable involvement in tumor progression mechanisms. The findings present a comprehensive resource that enhances our understanding of YB-1-driven molecular mechanisms in glioblastoma.

overall_design: To investigate the transcriptional regulatory role of Y-box binding protein 1 (YB-1) in glioblastoma, we established stable knockdown models using U87 and U373 glioblastoma cell lines, which were transfected with either non-targeting shRNA (NT control) or YB-1-targeting shRNA (shYB-1). For each cell line, one replicate of NT-shRNA (control) and one replicate of shYB-1 (knockdown) were included in the experimental design. During the analysis, the NT control samples (U87-NT and U373-NT; n=2 total) were pooled, as were the shYB-1-treated samples (U87-shYB-1 and U373-shYB-1; n=2 total). Gene expression profiling was performed via RNA sequencing (RNA-seq), comparing the shYB-1 samples against the NT control group. This methodology aimed to identify differentially expressed genes (DEGs) that are specifically regulated by YB-1 expression.


title: Epigenetic gene regulation by type I restriction modification systems in Streptococcus pneumoniae and Escherichia coli

city: Leicester

first: Richard

middle: David

last: Haigh

state: Leicestershire

address: Medical Sciences Building, University Road

department: Department of Respiratory Sciences

country: United Kingdom

institute: University of Leicester

summary: RNA-seq analysis of gene expression in pneumococcus D39 strains with the SpnIII type I restriction modification system locked into one of three available phasotypes.

overall_design: SpnIII-A, -B and -E phasotype locked strains of pneumococcus D39 were grown in TSB medium and total RNA extracted  at mid exponential phase.

first: Yasmeen

last: Althari

first: Marco

last: Oggioni


title: Transcriptional analysis of direct NSD2 target genes in t(4;14) multiple myeloma reveals H3K36me2-dependent regulation and H3K27me3 antagonism [SLAM-seq]

city: Miami

first: sanxiong

last: liu

state: FL

address: 1501 NW 10th Avenue

department: Human Genetics

institute: University of Miami Miller School of Medicine

summary: This study aimed to identify the direct transcriptional targets of the H3K36me2 methyltransferase NSD2 in t(4;14) multiple myeloma (MM), where its aberrant expression drives oncogenesis, and to elucidate the molecular mechanisms underlying its regulatory role. To achieve this with precise temporal control and minimize cellular adaptation artifacts, we established an inducible dTAG-mediated acute NSD2 degradation system in the KMS-11 t(4;14) MM cell line. Using this model, we performed time-resolved SLAM-seq to measure newly synthesized mRNA levels at 7, 14, and 21 days post-NSD2 degradation, enabling the identification of primary transcriptional targets. Further SLAM-seq datasets were generated under conditions of NSD2 depletion followed by reconstitution with either wild-type NSD2 (NSD2WT) or a catalytically inactive mutant (NSD2Y1179A) to evaluate the requirement for SET domain activity. The contribution of H3K27me3 antagonism to NSD2-mediated gene regulation was investigated by performing SLAM-seq on NSD2-depleted cells treated with distinct PRC2 inhibitors (EPZ-6438 and MAK-658). Complementing the transcriptomic data, we performed CUT&Tag to map the genomic distribution of the H3K27me3 histone mark following NSD2 depletion relative to control conditions. Analysis of these datasets revealed 308 primary NSD2 transcriptional targets, predominantly downregulated upon NSD2 loss and enriched for functionally relevant transcription factors. Reconstitution experiments demonstrated that NSD2's transcriptional effects are almost entirely dependent on its SET domain catalytic activity. Furthermore, PRC2 inhibition partially rescued the downregulation of approximately half of the NSD2 target genes, highlighting a significant role for H3K27me3 antagonism. Importantly, CUT&Tag analysis showed that the compensatory increase in H3K27me3 upon NSD2 loss occurred primarily across genome-wide intergenic regions, rather than directly at the promoters or gene bodies of NSD2 target genes. Collectively, these deposited transcriptomic (SLAM-seq) and epigenomic (H3K27me3 CUT&Tag) data support a model where NSD2 regulates target gene transcription via H3K36me2 deposition, which, in part, functions by antagonizing H3K27me3 deposition at distal regulatory elements to foster a permissive chromatin environment, providing a valuable resource for understanding NSD2 function in t(4;14) MM and Wolf-Hirschhorn syndrome.

overall_design: SLAM-seq profiling was performed on two independent clones of human t(4;14) multiple myeloma KMS-11 cells engineered for inducible dTAG-mediated degradation of endogenous NSD2 (NSD2dTAG cells) to assess the impact of acute NSD2 depletion on newly synthesized and total mRNA levels. The experimental variables investigated include: 1) A time course of NSD2 depletion following dTAGV-1 treatment for 0 (control), 7, 14, or 21 days; 2) Reconstitution of NSD2-depleted cells with doxycycline-induced wild-type NSD2 (NSD2WT) or catalytically inactive NSD2 (NSD2Y1179A), compared to NSD2-depleted controls without induction; and 3) Treatment of NSD2-depleted cells with PRC2 inhibitors EPZ-6438 or MAK-658, compared to NSD2-depleted cells treated with a DMSO vehicle control. Each condition and time point includes data from the two biological replicate NSD2dTAG clones.

first: Yubao

last: Wang

first: Sanxiong

first: Gareth

last: Morgan


title: Effect of decitabine on therapeutic response in doxorubicin- and paclitaxel-resistant breast cancer cell lines

city: Brno

first: Core Facility

last: Bioinformatics

address: Kamenice 5

country: Czech Republic

institute: CEITEC - Masaryk University

summary: Breast cancer is the most commonly diagnosed malignancy in women worldwide, yet treatment success is frequently compromised by the development of therapeutic resistance. The complex nature of this resistance necessitates in-depth investigation to identify the mechanisms underlying the resistant phenotype of tumor cells and to develop effective therapeutic strategies. This study details the derivation and comprehensive functional and molecular characterization of doxorubicin- and paclitaxel-resistant breast cancer cell lines representing three distinct subtypes. Additionally, a triple-negative breast cancer (TNBC) cell line was used to explore the potential of the DNA methyltransferase inhibitor decitabine in reversing aberrant DNA methylation patterns associated with chemotherapy resistance. The study also evaluates decitabine's ability to enhance therapeutic efficacy in treatment-resistant TNBC.

overall_design: We established a paclitaxel-resistant breast cancer (BC) cell line from the MDA-MB-231 cell line, which represents the triple-negative BC subtype. Both the paclitaxel-resistant and parental MDA-MB-231 cell lines were used to generate tumor xenografts in SCID-beige immunodeficient mice. These tumors were then used for RNA sequencing (RNA-seq) to investigate whether chemotherapy resistance is linked to DNA methylation-induced transcriptomic changes, and to evaluate the potential of the DNA methyltransferase inhibitor decitabine (DAC) to reverse these alterations, thereby sensitizing resistant cells to chemotherapy. Mice harboring tumors from either the parental or paclitaxel-resistant cell lines were treated for a total of 26 days with vehicle, doxorubicin, decitabine, or a combination of doxorubicin and decitabine. The treatment regimen consisted of two 12-day cycles, separated by 2-day rest period. In each cycle, 4 mice were treated with decitabine on days 1-4 and 10-11, 4 mice were treated with doxorubicin on days 5 and 12, 4 mice received a combination of both agents (decitabine on days 1-4 and 10-11, doxorubicin on days 5 and 12), and 4 mice were treated with vehicle solution at the specified timepoints.

first: Pavel

last: Bouchal

first: Nicolas

last: Blavet


title: Gene Regulatory Network-Driven Drug Repurposing Identifies Anti-Atherosclerotic Properties of Auranofin.

city: New York

first: Michael

last: Gildea

state: New York

address: 550 1st avenue

institute: NYU Langone Health

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

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Refer to individual Series


title: Gene Regulatory Network-Driven Drug Repurposing Identifies Anti-Atherosclerotic Properties of Auranofin [dataset 2]

summary: The identification of new therapies for coronary artery disease (CAD) has been challenging due to its inherent molecular complexity, which involves thousands of genes acting within and across tissues and cells. Gene-regulatory networks (GRNs) address this complexity by providing a mechanistic framework for common disease etiologies. Using system genetics, we previously identified the human arterial wall specific GRN42 as a critical regulator of foam cell formation. In this study, we applied a GRN-driven drug repurposing method by combining transcriptional signatures resulting from the silencing of key drivers of GRN42 to drug-related gene expression profiles from the NIH LINCS Program. This analysis identified candidate compounds predicted to modulate foam cell formation. In vitro screenings of top-selected compounds confirmed the computational predictions and demonstrated the efficacy of auranofin — an FDA-approved gold salt compound for rheumatoid arthritis — in reducing foam cell formation. In vivo, auranofin reduced atherosclerosis progression and inflammation in mice and decreased inflammation and wall thickness in the rabbit atherosclerotic aorta, as measured by 18F-FDG PET/MRI. These findings suggest that a GRN-based drug repurposing approach, combined with in vitro and in vivo validation using translational molecular imaging, can uncover new uses for existing drugs, such as auranofin, for the treatment of CAD.

overall_design: THP-1 macrophages (MPs) were loaded with AcLDL to form foam cells (FCs) and then treated with either vehicle (DMSO, < 0.1% v/v) or auranofin 0.5uM to see auranofin effect on foam cell formation.

first: Letizia

last: Amadori

first: Ravneet

last: Kaur

first: Micheal

first: Chiara

last: Giannarelli


title: RIP-seq analysis of YTHDF2 binding sites in C2C12 myotubes

city: shanghai

first: wang

middle: si

last: qi

address: Lane 485-11, Nan Chen Road, Baoshan District, Shanghai, China

department: School of Life Sciences, Shanghai University

institute: Shanghai University

summary: This dataset contains RIP-seq data investigating the genome-wide binding sites of YTHDF2 in differentiated C2C12 myotubes. RIP was performed using an anti-YTHDF2 antibody, with IgG as a negative control and Input as a reference. The study aims to identify potential target genes and regulatory elements of YTHDF2 in skeletal muscle cells.

overall_design: C2C12 myotubes were used to investigate the genome-wide binding sites of YTHDF2 through RIP-seq. RIP was performed using an anti-YTHDF2 antibody, with IgG as a negative control and Input as a reference. Libraries were prepared and sequenced on the Illumina HiSeq 3000 platform, generating 150 bp paired-end reads. Sequencing reads were aligned to the mouse reference genome (mm10) using Bowtie, and peak calling was performed with MACS.

first: Siqi

first: Jin

first: Junjie

last: Xiao


title: Gene Regulatory Network-Driven Drug Repurposing Identifies Anti-Atherosclerotic Properties of Auranofin [dataset 1]

summary:
The identification of new therapies for coronary artery disease (CAD) has been challenging due to its inherent molecular complexity, which involves thousands of genes acting within and across tissues and cells.
Gene-regulatory networks (GRNs) address this complexity by providing a mechanistic framework for common disease etiologies. Using system genetics, we previously identified the human arterial wall specific GRN42 as a critical regulator of foam cell formation.
In this study, we applied a GRN-driven drug repurposing method by combining transcriptional signatures resulting from the silencing of key drivers of GRN42 to drug-related gene expression profiles from the NIH LINCS Program.
This analysis identified candidate compounds predicted to modulate foam cell formation. In vitro screenings of top-selected compounds confirmed the computational predictions and demonstrated the efficacy of auranofin — an FDA-approved gold salt compound for rheumatoid arthritis — in reducing foam cell formation.
In vivo, auranofin reduced atherosclerosis progression and inflammation in mice and decreased inflammation and wall thickness in the rabbit atherosclerotic aorta, as measured by 18F-FDG PET/MRI.
These findings suggest that a GRN-based drug repurposing approach, combined with in vitro and in vivo validation using translational molecular imaging, can uncover new uses for existing drugs, such as auranofin, for the treatment of CAD.

overall_design:
To investigate the effect of auranofin on atherosclerosis progression, we fed ApoE-/- mice with western diet (WD) -/+ auranofin alone, atorvastatin alone or the combination of the two for 16 weeks
We then performed gene expression profiling analysis using data obtained from RNA-seq of 4 different group of mice at one time point (16 weeks).
Comparative gene expression profiling analysis of RNA-seq data for ApoE-/- mice fed western diet  -/+ auranofin alone, atorvastatin alone or the combination of the two.


title: Effect of miR-369-5p on gene expression in endothelial cells and its possible relation to Sickle Cell Disease complications

city: Chicago

first: CRI

state: IL

address: 5801 S. Ellis Ave.

institute: University of Chicago

summary: Our recent studies demonstrate that circulating small Extracellular Vesicles (EVs) contribute to the abnormal endothelium in Sickle cell disease (SCD). EVs isolated from patients with SCD cause endothelial damage in vitro, in particular when patients experience complications, like Acute Chest Syndrome (ACS). By sequencing the miRNA contents of EVs isolated from patients with SCD, we identified a microRNA (miR-369-5p) that is highly specific to patients with a history of ACS and increases dramatically during an episode of ACS. Treatment of cells with miR-369-5p disrupts intact monolayers of human microvascular endothelial cells in a similar manner to the effect caused by EVs isolated from patients experiencing ACS. We hypothesized that miR-369-5p at least partially contributes to the impact of SCD-derived EVs on endothelium. In the current study, we performed RNA-seq after transfecting endothelial cells with miRNA-369-5p or negative control miRNA to identify pathways that are regulated by miR-369-5p and to understand their impact within the endothelium.

overall_design: RNA-seq profiling of human HMVEC-D cells after tranfection with miR-369-5p

first: Joanna

last: Gemel

first: Eric

last: C. Beyer

first: Gabrielle

last: Lapping-Carr

first: Qiaoshan

last: Lin


title: Transcriptome Analysis Reveals the Regulatory Role of Jianpi Huazhi Wan (JPHZW) in Alleviating DSS-Induced Ulcerative Colitis

city: Nantong

first: Shi

last: Yiyu

address: 19，Qixiu St

institute: Nantong University

summary: In order to investigate the therapeutic efficacy and underlying mechanisms of Jianpi Huazhi Wan (JPHZW), a hospital-formulated Traditional Chinese Medicine (TCM), in treating dextran sodium sulfate (DSS)-induced ulcerative colitis (UC) in mice, this study conducted transcriptome sequencing analysis of colon tissue through DSS induced mouse UC model. Key pathways involved in JPHZW’s therapeutic effects included the PPAR pathway (linked to fat metabolism), NF-κB (associated with inflammation), retinol metabolism, and detoxification processes. JPHZW reduced levels of NF-κB p65, a protein that drives inflammation, while increasing PPARγ, a regulator of metabolic balance. Together, these changes effectively reduced both inflammation and metabolic imbalances in the colon.

overall_design: This study included three groups of samples: a control group (normal group), a UC model group, and a JPHZW treatment group, with 3 biological replicates in each group. The control group consisted of normal mice without any intervention. The UC model group was established by inducing ulcerative colitis in mice. The JPHZW treatment group was treated 200 mg/kg JPHZW for 7 consecutive days. On day 15, colon tissues were collected from all groups. After RNA quality control (RIN value > 7), transcriptome sequencing was performed using the Illumina HiSeq 4000 platform. The goal was to compare gene expression between the control group and the UC model group to identify key genes related to UC pathogenesis. Meanwhile, by comparing the JPHZW treatment group with the UC model group, the study aimed to explore differentially expressed genes and enriched pathways regulated by JPHZW intervention, thereby providing a transcriptomic basis for subsequent validation of mechanisms involving signaling pathways such as PPARγ/NFκB through Western Blot analysis.

first: Yu

last: Wu

first: YiYu

last: Shi

first: CuiPing

last: Yan

first: YingJun

last: Fu


title: MRPGRX2 Antagonist Treatment Prevents Inflammation and Disease in a Mouse Model of Atopic Dermatitis Dataset 1

city: San Diego

first: Joshua

last: Wollam

address: 9761 W. Canyon Ter. Unit 1

institute: Escient Pharmaceuticals

summary: The Mas-Related G-Protein Coupled Receptor X2 (MRGPRX2) is a promiscuous receptor expressed on mast cells that mediates IgE-independent mast cell activation and degranulation in response to a variety of diverse agonists and has been implicated in numerous inflammatory conditions, including atopic dermatitis. We investigated if the small molecule MRGPRX2 antagonist, INCB000262, improves disease phenotype in the house dust mite + Staphylococcus aureus enterotoxin type B (HDM+SEB) mouse model of atopic dermatitis and further characterized mast cell-mediated aspects of disease. MRGPRX2 knock-in mice were sensitized to HDM+SEB and orally dosed once daily with either vehicle or INCB000262 for 4 weeks, and efficacy and skin transcriptional changes evaluated. INCB000262 attenuated HDM+SEB-induced atopic dermatitis in vivo with improvements observed in skin thickness, transepidermal water loss, tissue weight, and overall clinical score. In addition, transcriptome changes induced by HDM+SEB exhibited a mast cell activation signature consistent with human atopic dermatitis lesional skin, which was attenuated by antagonist treatment.  Overall, the MRGPRX2 antagonist, INCB000262, attenuated HDM+SEB-induced atopic dermatitis disease phenotypes and mast cell-associated transcriptional changes, supporting further evaluation of INCB000262 as an oral treatment for atopic dermatitis and other mast cell-mediated diseases.

overall_design: RNAseq profiling of skin from HDM+SEB treated or vehicle-treated MRGPRX2 knock-in mice (without drug treatment)

first: Swetha

last: Srinivasan


title: MRPGRX2 Antagonist Treatment Prevents Inflammation and Disease in a Mouse Model of Atopic Dermatitis Dataset 2

overall_design: RNAseq profiling of skin from HDM+SEB treated or vehicle-treated MRGPRX2 knock-in mice treated with or without the MRGPRX2 antagonist INCB000262


title: H2AK119ub1-MLL2 counteraction underlies heritable H3K27me3 formation in oocytes [CATCH-seq and CUT&RUN]

city: Yokohama

first: Azusa

last: Inoue

state: Kanagawa

address: Suehiro-cho 1-7-22, Tsurumi-ku

department: Center for Integrative Medical Sciences

institute: RIKEN

summary: Polycomb group (PcG) and Trithorax group (TrxG) proteins establish bivalent chromatin marked by H3K27me3, H2AK119ub1, and H3K4me3. However, how bivalent chromatin is formed in vivo in mammals is poorly understood. In mouse oocytes, it arises at thousands of promoters, including noncanonical imprinted loci whose H3K27me3 is intergenerationally inherited by early embryos. Here, we show that H3K27me3 is deposited at H3K4me3-premarked promoters in an H2AK119ub1-dependent manner during oogenesis. We find that H2AK119ub1 deficiency causes transcriptional derepression and loss of H3K27me3 proportional to preexisting H3K4me3 levels in oocytes. Importantly, concomitant deficiency of H2AK119ub1 and MLL2-mediated H3K4me3 substantially restores transcriptional silencing and H3K27me3 deposition, leading to partial restoration of noncanonical imprinting in offspring. Taken together, we propose that H2AK119ub1 antagonizes MLL2 function to repress bivalent genes during oogenesis, thereby conferring heritable H3K27me3. This study reveals how PcG and TrxG counteraction shapes the maternal epigenome for the next generation’s development.

overall_design: CATCH-seq and CUT&RUN of histone modifications in fully grown oocytes. H3K4me3, H3K36me2, and H3K36me3 CATCH-seq were performed in wild type, Pcgf1/6 DKO, and Pcgf1/6 & Mll2 TKO FGO oocytes. H3K27me3 CUT&RUN were performed in wild type, Pcgf1/6 DKO, and Pcgf1/6 & Mll2 TKO FGO oocytes.

first: Hailiang

last: Mei

first: Chisayo

last: Kozuka

first: Mami

last: Kumon

first: Haruhiko

last: Koseki


title: RNA-seq analysis of fat body and brain tissues in wild type and AaegGr34 Aedes aegypti

city: Riverside

first: Anupama

last: Dahanukar

state: CA

address: 900 University Aveenue

department: Molecular, Cell, and Systems Biology

institute: University of California, Riverside

summary: This study examines gene expression changes in the fat body and brain tissues of Aedes aegypti mosquitoes. RNA sequencing was used to identify differentially expressed genes within tissue-type between wild type and mosquitos containing a mutant form of the fructose receptor AaegGr34.

overall_design: RNA sequencing brain: WT (control) vs AaegGr34 mutant fat body: WT (control) vs AaegGr34 mutant for each tissue, diiffreential gene expression was performed for WT vs AaegGr34 3 biological replicates for each sample

first: Emi

last: Maeekawa

first: Vaibhav

last: Menon


title: Whole genome CRISPR drop-out screen in THP-1 cells exposed to mebendazole

city: London

first: Owen

last: Williams

address: 30 Guilford Street

institute: UCL GOS ICH

summary: We previously reported that mebendazole is an effective anti-AML therapeutic and acts via induction of MYB degradation. The present experiemnt was performed in order to uncover pathways of potential resistance in AML cells to mebendazole exposure. A whole genome CRISPR drop-out screen was performed on THP-1 AML cells exposed to 1 micromolar mebendazole or DMSO in order to identify genes that decreased AML sensitivity to this drug.

overall_design: THP-1 cells were transduced with the pooled sgRNA library, 2 ug/ml puromycin added after 48 h. Multiplicity of infection was calculated after 4 days puromycin selection, at which point the culture contained 29%  viable cells by flow cytometry. Cells were selected for 10 days in puromycin after which either 1 uM mebendazole or DMSO was added to the cultures and 10 days later viable cells enriched by density centrifugation and genomic DNA isolated.

first: Alexia

last: Tsakaneli

first: Noelia

last: Che


title: Cadmium-induced gut dysbiosis precedes the onset of hippocampus-dependent learning and memory deficits in mice

city: Seattle

first: Joe

last: Lim

state: WA

address: 4225 Roosevelt Way NE, Suite 100

institute: University of Washington

summary: Background: Cadmium (Cd) is a heavy metal recognized as a neurotoxicant. However, the mechanisms underlying its neurotoxicity remain poorly understood. The gut-brain axis, a bidirectional communication pathway between the central nervous system and the gut microbiome, has been linked to various neurological disorders. Because the gut microbiome is a known target of Cd, it is important to investigate whether the gut-brain axis mechanistically contributes to the Cd-induced neurotoxicity.  Objective: In our initial exploration of the role of the gut-brain axis in modulating Cd neurotoxicity on cognition, we investigated whether Cd exposure induces gut dysbiosis before the onset of cognitive deficits and explored the potential link between gut microbiome alterations and Cd-induced cognitive deficits.  Methods: Adult male mice were exposed to 3 mg/L Cd via drinking water for nine weeks. Behavioral assessments were conducted throughout the exposure period to evaluate cognitive function. Fresh fecal pellets were collected weekly to monitor gut microbiome composition. The effects of Cd on the hippocampus and intestine were analyzed using transcriptomics and mass spectrometry (MS)-based metabolomics.  Results: Cd exposure resulted in hippocampus-dependent learning and memory deficits, first observed at four weeks into exposure. RNA sequencing of the hippocampus at the terminal time point revealed reduced expression of genes involved in cognition and neuroinflammation in Cd exposed mice. Metagenomic shotgun sequencing showed that Cd-induced gut dysbiosis preceded the onset of cognitive impairments, with specific bacterial species associated with Cd-induced cognitive deficits, confirmed by using the cor.test function (Spearman correlation, p < 0.1) in R. Furthermore, Cd exposure compromised intestinal barrier integrity, increased inflammatory cytokines levels, and altered the levels of neuroactive microbial metabolites in mice, which may be linked to Cd-induced gut dysbiosis  Conclusion: Our study is the first to show that Cd exposure triggers gut microbial shifts before the onset of cognitive deficits, accompanied by increased intestinal permeability and elevated proinflammatory biomarkers in both the intestine and brain at the terminal time point. These findings suggest a potential critical role of gut-brain axis in modulating Cd neurotoxicity and underscore the need for future research to elucidate the mechanistic involvement of gut microbiome as a potential target for mitigating Cd-induced cognitive decline.

overall_design: RNA sequencing of C57BL/6 mouse hippocampus exposed to vehicle or Cd for 9 weeks.

first: Hao

last: Wang

first: Cui

middle: Y

last: Julia

first: Xia

last: Zhengui


title: Gene expression profiling of mouse lung tissue in a bleomycin-induced pulmonary fibrosis model

city: Guangzhou

first: Shu

last: Meng

address: No.9, XingDaoHuanBei Road, Guangzhou International Bio-island, Haizhu District

institute: Guangzhou National Laboratory

summary: This study investigates the gene expression changes in mouse lung tissue over time in a bleomycin-induced pulmonary fibrosis model. Lung tissues were collected at day 0 (baseline), day 7, day 14, and day 21 post-bleomycin treatment to analyze the progression of fibrosis. Total RNA of whole lung tissues was extracted, and transcriptomic profiling was performed to identify key genes and pathways involved in the pulmonary fibrosis development. Our study provides insights into the temporal dynamics of gene expression during the fibrotic process.

overall_design: Mouse lung tissues were collected at day 0, day 7, day 14, and day 21 after bleomycin treatment. We got three replicates for each time point. Total RNA were extracted and subjected to RNA-seq profiling.

first: Zhimin

last: Song

first: Yaofeng

first: Xing

last: Peng


title: Mechanistic Insights into the Epigenetic Regulation and Therapeutic Targeting of RET Receptor Tyrosine Kinase in KMT2A-Rearranged Pediatric Acute Myeloid Leukemia

city: Little Rock

first: Samrat

last: Roy Choudhury

state: AR

address: 13 Children's Way, Arkansas Children's Research Institute

institute: University of Arkansas for Medical Sciences

summary: Pediatric acute myeloid leukemia (pAML) driven by KMT2A gene rearrangements (KMT2A-r; 11q23 translocations) is a high-risk leukemia with limited treatment options and a poor prognosis. Previously, we reported (PMID: 38226414) that the RET receptor tyrosine kinase is epigenetically upregulated in major KMT2A-r subgroups. In this study, we utilized a synthetic drug, 8p, which serves as a dual inhibitor of RET and cyclin-dependent kinase 8 (CDK8). We conducted RNA sequencing analysis on 8p-treated KMT2A-MLLT3 fusion-positive MOLM-13 cells to profile genome-wide gene expression changes. This study enhances our understanding of the major pathways affected by the dual inhibition of RET and CDK8 in KMT2A-r AML.

overall_design: This study analyzed mRNA sequencing profiles in the MOLM-13 cell line treated with 8p, a synthetic dual inhibitor of RET and CDK kinases, compared to untreated MOLM-13 cells. Experiments were performed in three independent biological replicates.


title: Distinguishing self from non-self RNA by editing-specific inosine patterns

city: Vienna

first: Alina

middle: F

last: Leuchtenberger

address: Dr. Bohr Gasse 9

department: Max Perutz Labs

country: Austria

institute: Medical University of Vienna and University of Vienna

summary: The cytoplasmic antiviral sensor MDA5 is activated by double-stranded RNAs. Endogenous double-stranded RNAs are modified by the A to I RNA-editing enzymes of the ADAR family to prevent activation of MDA5. In vivo, the cytoplasmic ADAR1p150 version seems critically required to suppress MDA5 activation in vivo, while the editing signature of all ADAR isoforms seems surprisingly overlapping in mice. Further, it is not clear, how A to I modifications in dsRNA prevent MDA5 activation. Here we show that 3' UTRs harboring inverted repeat elements when not edited are able to activate MDA5 in vitro and in cells. Interestingly, in vitro editing by either ADAR isoform leads to editing at overlapping hotspot regions and prevents MDA5 activation in vitro and in cells. Remarkably, only inosines introduced by RNA-editing are capable to suppress MDA5 activation while substitution of guanosines by inosines during in vitro transcription has no impact on MDA5 activation. A comparison of inosines introduced by ADAR1p150 in vitro, in cells, and in vivo, suggests that a small number of A to I conversions may be critically required to suppress MDA5 activation. As those critical editing events are predominantly altering A:U basepairs into I:U wobble basepairs, we suggest that the helical distortion introduced by those wobble pairs may prevent MDA5 polymerization and thus downstream activation of interferon stimulated genes.

overall_design: Liver tissues from 8-9 days old WT and Adar1-/-/Mavs-/- mutant. MDA5-protected, RNase only, Input RNA.

first: Rajagopal

last: Varada

first: Cornelia

last: Vesely

first: Beata

last: Kaczmarek

first: Hamid

last: Mansouri Khosravi

first: Therese

last: Mandl

first: Katarina

last: Milanovic

first: Kasra

last: Honarmand Tamizkar

first: Vinod

last: Rajendra

first: Hannes

last: Senoner

first: Linda

last: Steinbichl

first: Hasan

last: Akyol

first: Marija

last: Borojevic

first: Andy

last: Sombke

first: Katy

last: Schmidt

first: Margret

last: Eckhard

first: Carl

last: Walkley

first: Jacki

last: Heraud-Farlow

first: Ernesto

last: Picardi

first: Carrie

last: Bernecky

first: Michael

last: Jantsch


title: H2AK119ub1-MLL2 counteraction underlies heritable H3K27me3 formation in oocytes

first: Azusa

last: Inoue

overall_design: RNA-seq were performed in wild type (WT) and PRC1 catalytic dead (PRC1-CD) oocytes, in WT, Pcgf1/6 DKO, Pcgf1/6/Mll2 TKO oocytes, and in WT, Pcgf1/6 maternal DKO, Pcgf1/6/Mll2 maternal TKO morula embryos. Then comparative analysis was done between the WT and mutants.

first: Hailiang

last: Mei

first: Chisayo

last: Kozuka

first: Mami

last: Kumon

first: Haruhiko

last: Koseki


title: Regenerative potential of neonatal tendon cells is regulated by intrinsic resistance to inflammation and supportive T cell-secreted factors

first: Alice

middle: H.

last: Huang

department: Orthopedic Surgery

institute: Columbia University

summary: Tendons mediate force transmission from muscle to bone to allow movement. Upon injury, adult tendons heal by scar formation with persistent functional deficits. While the immune response is a key regulator of healing, the roles of specific immune cells and their interactions with resident tendon cells remain understudied. While it is well appreciated that macrophages drive both inflammation and its resolution, other immune cells such as T cells have also been implicated. Here, we apply in vitro culture of CD4+ helper T cell supernatants to determine the role of neonatal vs adult T cells in regulating key tendon cell properties previously associated with neonatal tendon regeneration. While T cells were dominated by inflammatory Th1 cells regardless of source, neonatal T cells were less inflammatory compared to adult. Proliferation and migration potential were also properties intrinsic to neonatal tendon cells. While adult tendon cells were more sensitive to secreted T cell factors, neonatal T cell factors generally supported regenerative properties in adult tendon cells. Using RNA sequencing, we further identified a role for JAK/STAT signaling specific to treatment with adult T cell supernatants; using a small molecule inhibitor of JAK/STAT, we confirmed that suppression of adult tendon cell migration by adult T cell factors can be rescued by JAK/STAT inhibition. Altogether, these data show that regenerative tendon healing in neonates is due to both intrinsic neonatal tendon cell resistance to T cell-mediated inflammation as well as a more favorable immunological environment induced by neonatal CD4+ T cells.

overall_design: 25K thawed tendon cells cultured for 3 days were treated with 1ml of complete DMEM + 1ml of either T cell media alone (+1% P/S) or adult/neonatal stimulated supernatants, before RNAseq processing. Samples adult.1-3 are adult tendon cells treated with T cell media, adult.4-6 are adult tendon cells treated with adult stimulated supernatant, adult.7-9 adult tendon cells treated with neonatal stimulated supernatant. Neo.1-3 are neonatal tendon cells treated with T cell media, neo.4-6 are neonatal tendon cells treated with adult stimulated supernatant and neo.7-9 are neonatal tendon cells treated with neonatal stimulated supernatant.

first: Giulia

last: Crosio

first: Emily

last: King


title: In vitro 3D model of the immune-oncology stromal barrier for evaluating T-cell accumulation and cytotoxicity

city: Sugito-machi

first: Rii

last: Morimura

state: Saitama

address: 4-2-3 Takanodaiminami

institute: TOPPAN Holdings Inc.

summary: To evaluate the efficacy of cancer immunotherapies, infiltration into the tumor and the recognition and attack of cancer cells by T cells ex vivo must be assessed. However, few available in vitro experimental systems can assess T-cell infiltration into tumor tissues in a manner that structurally mimics the tumor tissue due to difficulties in controlling cell position. Here, we developed a stacked three-dimensional (3D) stromal tissue using a cell-assembled viscous tissues method. Stromal tissues, including cancer-associated fibroblasts (CAFs), created a stromal barrier that prevented cytotoxic T cells from attacking cancer cells. Drug screening using the CAF model demonstrated that HDAC inhibitors promote T-cell infiltration and its combined effects and suppress extracellular matrix formation and CAF expression by acting on fibroblasts. Thus, the stromal barrier–inclusive co-culture model that partially reproduces CAF-induced cold tumors could facilitate the development of drugs that promote immune cell infiltration and cell-cell interaction studies.

overall_design: RNA-seq profiling of fi roblast cell with TGFβ or TSA or entinostat


title: NLRP3/CCR2 Blockade by Arglabin and Its Derivative Suppresses Myeloid-Driven Immunosuppression and Potentiates Anti-PD-L1 Immunotherapy in Hepatocellular Carcinoma

city: Nanjing

first: Di

last: Kang

address: 138 Xianlin Ave

department: School of Pharmacy

institute: Nanjing University of Chinese Medicine

summary: Background Hepatocellular carcinoma (HCC) evolves within an NLRP3-enriched immunosuppressive microenvironment where myeloid-derived suppressor cells (MDSCs) orchestrate T cell dysfunction. While the NLRP3 inhibitor arglabin (Arg) shows clinical anti-tumor activity, its immune-specific targets and mechanisms remain undefined. Method NLRP3 and CCR2 expressions were explored in tumor tissues from 14 HCC patients. Overall survival and the correlation between two proteins in HCC patients were analyzed using GEO and TCGA databases. Molecular interactions were validated through CETSA, SPR, and LC-MS/MS. In vivo antitumor efficacy was assessed in syngeneic murine models of H22 (BALB/c) and Hepa1-6 (C57BL/6) liver cancer cells. Functional analyses were conducted using CCK8, MDSC depletion (anti-Gr-1 antibody) and transwell invasion assays. Flow cytometry characterized TME composition, while in vivo bioluminescent imaging monitored tumor burden. Transcriptomic profiling of ChIP-qPCR deciphered CCR2 regulatory mechanisms. Structural optimization yielded compound C2, evaluated through pharmacokinetic studies and mechanism validation. Results NLRP3 overexpression in HCC patients correlated with reduced survival. Arg covalently bound to NLRP3 at Cys280 (KD = 16.32 nM), suppressing CCR2 transcription via non-canonical NLRP3 activity——independent of inflammasome activation. This myeloid-specific mechanism reduced MDSC infiltration (61.20% decrease vs control) while expanding cytotoxic CD8+ T cells (2.4-fold increase), achieving 56.42% tumor growth inhibition (TGI) in immunocompetent models. Synergy with anti-PD-L1 therapy enhanced TGI to 96.99%. Structural optimization generated orally C2, which maintained CCR2 suppression efficacy and MDSC suppression, and achieved 93.86% TGI at 18 mg/kg. Conclusion We redefine NLRP3 as a transcriptional regulator governing CCR2-dependent trafficking of MDSCs and identify Arg as a covalent NLRP3 inhibitor. The NLRP3/CCR2 axis emerges as a druggable target to alleviate immunosuppression in HCC, with Arg-derived C2 demonstrating significant clinical translation potential. This work establishes a framework for developing natural product-derived immunomodulators, which exhibit synergistic efficacy with immune checkpoint inhibitors to overcome resistance in cancer immunotherapy.

overall_design: RNA-seq profiling of MDSCs isolated from murine after treatment with vehicle (negative control) and 10 μM arglabin for 2 hours.

first: Lihong

last: Hu


title: Effect of depletion of FAT4 on gene expression in A673 Ewing sarcoma cells

city: San Antonio

first: Hanzhou

last: Wang

state: TX

address: 8403 Floyd Curl Drive, MSC 7784

department: GCCRI

institute: UT Health at San Antonio

summary: Ewing sarcoma is a cancer of bone and soft tissue in children characterized by a chromosomal translocation that fuses EWS and an ETS family transcription factor, most commonly FLI1. EWS-FLI1 is the driver of this cancer. Using secretome proteomics and molecular cell biology, we found that FAT4, an atypical cadherin inhibiting Hippo signaling, is a transcriptional target of EWS-FLI and is a dependency in Ewing sarcoma. We used RNA-sequencing to determine the gene expression changes caused by FAT4 silencing in Ewing sarcoma cells.

overall_design: A673 cells were transfected with FAT4 siRNA or control siRNA. 24 or 48 hours after transfection, gene expression was profiled by RNA-sequencing.

first: Yuzuru

last: Shiio

first: Zhao

last: Lai

first: Yidong

last: Chen


title: RelA signaling in Scgb1a1+ epithelial progenitors mediates alveolar atypia in RSV-induced post viral lung disease

city: Madison

first: Allan

last: Brasier

state: WI

address: 715 Highland

department: ICTR

institute: university of Wissconsin

summary: Early life respiratory virus infections play an important role in shaping structural and immunological responses of the lung, leading to chronic airway disease   Respiratory syncytial virus (RSV), a member of genus Orthopneumovirus, is an etiological agent in infant lower respiratory tract infections (LRTIs) producing substantial global morbidity.  The mechanisms underlying how transient RSV infection produces long-term structural changes are unexplored.  Although it is known that airway repair is mediated by expansion of parenchymal epithelial progenitors within discrete mesenchymal niches, the nature of these cells and how they are activated by viral infection are unknown.  Herein, we explore the impact of RSV infection on trophic mesenchymal-basal epithelial interactions and the regenerative role of innate NFB/RelA signaling by its conditional knockout (CKO) in secretoglobin (Scgb1a1)-derived progenitors.  We discovered that RSV-induced post viral lung disease (PVLD) induces expansion of parenchymal airspace and replacement of small bronchiolar and alveolar epithelium by tumor protein 63 (Trp63), Aquaporin-3 (Aqp3) and Integrin 4 (Itg4)-expressing cells.  Single-cell RNA sequencing identifies populations of atypical alveolar type (AT)2 cells expressing both AT2 and AT1 markers.  Mechanistically, we find this atypical progenitor expansion is prevented by RelA CKO in the Scgb1a1 lineage.  A probabilistic analysis of the mesenchymal-epithelial cell-cell signaling network shows RSV induces an extensive network of epithelial-mesenchymal signaling through inflammatory platelet activated receptor (PAR), IL1/IL4 and stem-cell signaling by angiopoietin like (ANGPTL)-4 pathway.  Interestingly, ANGPTL4 is normalized after Scgb1a1-directed RelA CKO.  These data indicate RSV-PVLD is mediated, at least in part, by dysregulated mesenchymal-epithelial trophic signaling downstream of RelA activation in Scgb1a1-derived epithelial progenitors.

sample_organism: Human respiratory syncytial virus A strain Long

overall_design: Scgb1a1-Cre X RelAfl/fl mice were Mock (PBS) or RSV-infected 3-5 weeks after birth (107 PFU).  Three days post-infection, when inflammation/viral replication resolved, mice were randomized into corn oil (10% ethanol and 90% corn oil; RelA WT) or tamoxifen (TMX) treatment (20 mg/kg/d i.p.; Sigma Aldrich, St. Louis, MO; T5648; RelA CKO) for 10 doses.  Animals were then rested for an additional week (21d post-RSV infection) before oxygen saturation (MouseOx® Plus, Starr Life Sciences Corp., Oakmont, PA) were measure and then mice were euthanized and tissue and BALF were collected.

first: Brasier

last: Allan R

first: Skibba

last: Melissa


title: Combined Immunotherapy and Particle Therapy for Advanced HCC with Macrovascular Invasion: Phase Ib DEPARTURE Trial

city: Chiba-shi

first: Makoto

last: Fujiya

state: Chiba

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

institute: Chiba university

summary: Hepatocellular carcinoma (HCC) with macrovascular invasion carries a poor prognosis, necessitating novel therapeutic strategies. This phase Ib trial evaluated the safety and preliminary efficacy of combining carbon-ion radiotherapy with immune checkpoint inhibitors in patients with advanced HCC. RNA-seq was conducted to investigate changes in the tumor microenvironment, aiming to identify molecular signatures predictive of response or resistance to the combination therapy. The reduction group showed enrichment of pathways related to inflammation, complement activation, which are often associated with immune activity. In contrast, the progression group exhibited enrichment of pathways linked to mesenchymal characteristics and angiogenesis, processes that may correlate with reduced therapy efficacy.

overall_design: RNA-seq was performed on pre-treatment biopsy specimens from nine patients enrolled in the DEPARTURE trial, with follow-up analysis conducted on non-irradiated lesions from three patients 42 days after treatment initiation.

first: Sadahisa

last: Ogasawara

first: Keisuke

last: Koroki

first: Hiroaki

last: Kanzaki

first: Naoya

last: Kato


title: Faecalibacterium prausnitzii induces an anti-inflammatory response and a metabolic reprogramming in human monocytes [ileum]

city: Saint-Malo

first: Phuong

middle: Hang

last: PHAM

address: 7 allée Métis

department: Data science

country: France

institute: Parean Biotechnologies

summary: We isolated immune cells from human intestinal lamina propria of patients with IBD and non-inflamed controls. We stimulated them with F. prausnitzii EXL01 strain, Cadaverine or lipopolysaccharide (LPS) from Escherichia coli and performed RNA-sequencing analysis. F. prausnitzii EXL01 strain induced the production of IL-10 in CD14+ monocytes from intestinal tissue of IBD patients and non-inflamed controls in a direct and dose-dependent manner, without inducing a pro-inflammatory response as compared to LPS stimulation. RNAseq analysis confirmed these results and revealed that F. prausnitzii EXL01 strain differentially affects cell energy metabolism compared to LPS. The anti-inflammatory response induced by F. prausnitzii in monocytes was dependent on mitochondrial activity. In patients with inflammatory bowel disease (IBD), increased cadaverine levels were associated with higher flare risk.

overall_design: Purified CD14+ monocytes were cultured during 2h or 4h with control medium (n=3), or with cadaverine (1-1000 µM, Sigma Aldrich, n=3) in the presence or absence of standard lipopolysaccharide (LPS) from E. coli K12 strain (100 ng/mL, Invivogen, n=3), or EXL01 strain at 2 doses (MOI 10, n=3 and 100, n=3)

first: Rodrigo

last: de Oliveira Formiga

first: Qing

last: Li

first: Yining

last: Zhao

first: Marcio

last: Campos Ribeiro

first: Laura

last: Creusot

first: Virginie

last: Pisano Puchois

first: Salomé

last: Amouyal

first: Marius

last: Bredon

first: Loïc

last: Chollet

first: Tatiana

last: Ledent

first: Cyril

last: Scandola

first: Jean-Philippe

last: Auger

first: Camille

last: Danne

first: Gerhard

last: Krönke

first: Patrick

last: Emond

first: Guillaume

last: Chevreux

first: Hang-Phuong

last: Pham

first: Rafael

last: Jose Argüello

first: Nathalie

last: Rolhion

first: Marie-Laure

last: Michel

first: Timothy

last: Wai

first: Harry

last: Sokol


title: T, NK, NKT cells in the brain from WT or 15q dup mice [brain]

city: Fukuoka

first: Minako

last: Ito

address: 3-1-1 Maidashi, Higashi-ku

institute: Kyushu University

summary: Autism Spectrum Disorder (ASD) is a neurodevelopmental disorder with no effective treatment, caused by genetic factors such as copy number variations (CNVs) and immunological factors such as maternal infection. The role of immunity in genetic ASD remains unclear. Here, we investigated the immun cells in the brains of a mouse model of ASD (15q11-13 duplication), a common CNV associated with ASD.

overall_design: T cells, NK cells, and NKT cells in the brain were sorted from WT and 15q dup mice at embryonic day 16 and 1, 2, 3, 4, and 6 weeks of age (E16; n = 8 (WT); n = 7 (15q), 1w; n = 11 (WT); n = 8 (15q), 2w; n = 10 (WT); n = 13 (15q), 3w; n = 7 (WT); n = 10 (15q), 4w; n = 9 (WT); n = 9 (15q), 6w; n = 7 (WT); n = 7 (15q)) and performed scRNA-seq.

first: Natsumi

last: Awata


title: ATF3-dependent formation of inclusion bodies in polyQ-expressing human iPSC-derived neurons confers cellular protection [RNAseq]

city: Jerusalem

first: Walaa

middle: Ziad

last: Oweis

state: Israel

country: Israel

institute: Hebrew University of Jerusalem

summary: Huntington’s disease (HD) is an incurable, neurodegenerative disorder. While the causative mutation – CAG expansions within the coding region of the Huntingtin (HTT) gene – has been identified over 30 years ago, the pathological mechanisms underlying HD are still not clear. The abnormal CAG track encodes a polyglutamine (polyQ) expanded protein, which leads to HTT protein misfolding. These polyQ aggregates can form insoluble inclusion bodies (IBs); however, whether IBs are protective or detrimental remains debatable. To ask whether IBs are protective or harmful in human neuronal cells, and to elucidate the pathological pathways involved in polyQ IB formation, we developed an iPSC-based human neuronal models for polyQ-related disorders. We ectopically expressed the first 21 exons of the HTT gene, containing either 18Q or 105Q fused with GFP in HD patient-derived iPSCs containing 180Q or their isogenic corrected cells, respectively, differentiated them into neuronal progenitor cells (NPCs), and enriched for a pure population of polyQ IBs-containing cells (IB+). Comparing gene expression profiles between IB+ and IB- NPCs, growing side-by-side, in both systems, we identified ATF3 as responsible for inducing neuroinflammatory genes specifically in IB+ cells. ChIP-seq for ATF3 confirmed direct binding at their promoters, exclusively in IB+ NPCs. Remarkably, knocking out (KO) ATF3 completely prevented polyQ-IB formation in NPCs and rendered the cells more vulnerable to induced stress. Finally, using time-lapse imaging comparing cell death in IB+ and IB- NPCs, we demonstrate that polyQ IBs have a significant protective effect. Taken together, our results highlight ATF3’s role in polyQ IB formation in human NPCs, acting as an activator of inflammatory genes, and demonstrate that polyQ IBs protect cells from stress-induced death.

overall_design: RNA-seq profiling of differentially expressed genes between cells with and without IBs. RNA-seq analysis was performed on ATF3 wild-type and ATF3 knock-out 105Q-NPCs


title: Human CD14+ monocytes from volunteers before and after a 3 hours, 24 hours and 120 hours-period of methotrexate intake. METOMAC trial

city: Madrid

first: Amaya

middle: Rocío

last: Puig Kröger

state: Madrid

address: Dr. Esquerdo 46

department: Immunology

country: Spain

institute: Hospital General Universitario Gregorio Marañón

summary: Arthritis patients receive a weekly low-dose of Methotrexate (MTX) as a first-line disease modifying anti-rheumatic drug. Following low-dose administration, MTX typically reaches peak plasma concentrations after 1-2 hours, and almost completely disappears from the circulation by 24 hours. However, the kinetics of the anti-inflammatory action of MTX in monocytes after the initial dose is unknown.To address this issue, we carried out a phase I clinical trial (METOMAC) in which peripheral blood from 6 healthy donors receiving a single dose of MTX was analyzed at distinct time points after drug intake (3 hours, 24 hours, 120 hours).  RNA-seq on monocytes isolated at the distinct timepoints was determined.

overall_design: mRNA profiles of human peripheral blood CD14+ monocytes from volunteers at baseline, 3 hours, 24 hours and 120 hours after 20 mg oral methotrexate intake

first: Raquel

last: García Campos

first: Manuel

last: Román Martínez

first: Francisco

last: Abad Santos

first: Isidoro

last: González Álvaro


title: T, NK, NKT cells in the brain from WT or 15q dup mice [multiple tissues]

summary: Autism Spectrum Disorder (ASD) is a neurodevelopmental disorder with no effective treatment, caused by genetic factors such as copy number variations (CNVs) and immunological factors such as maternal infection. The role of immunity in genetic ASD remains unclear. Here, we investigated the immun cells in the several tissues (brain, blood dura, lung, colon, spleen, thymus) of a mouse model of ASD (15q11-13 duplication), a common CNV associated with ASD.

overall_design: TCR-Vγ6+ γδ T cells from the brain, dura, thymus, blood, spleen, lung, and colon at 3 weeks of age (brain; n = 21 (WT); n = 22 (15q), dura; n = 7 (WT); n = 10 (15q), blood; n = 7 (WT); n = 10 (15q), thymus; n = 7 (WT); n = 7 (15q), spleen; n = 7 (WT); n = 7 (15q), lung; n = 7 (WT); n = 5 (15q), colon; n = 7 (WT); n = 5 (15q)) and performed scRNA-seq.


title: PTPMT1-dependent regulatory T cells mediate immunological tolerance to gut pathobionts

city: Cologne

first: Mauro

last: Corrado

address: Joseph-Stelzmann-Str. 26

country: Germany

institute: University of Cologne

summary: Mitochondrial dysfunctions are emerging as key drivers of gut inflammation, colitis, and IBD, yet their role in regulating immune tolerance remains unclear. Meanwhile, pathobiont infections, such as those caused by Helicobacter species, affect nearly half the global population, with symptoms manifesting in only 20%, adding a new layer of complexity. The genetic and environmental factors that disrupt gut tolerogenic mechanisms, tipping the balance toward disease in symptomatic infections, are not fully understood. Here, we show that PTPMT1 impairs tolerance to Helicobacter via Treg cells, independently from T cell-generated Type I or Type II interferons. Without cardiolipin, Treg cells lose metabolic fitness and immunosuppressive potential, unleashing pro-inflammatory myeloid cells in the gut. As a result, PTPMT1 ΔT mice are highly vulnerable to pathobiont infections even without microbiome imbalance. Inflammation and helper T cell imbalance are conserved in Barth syndrome, linked to cardiolipin deficiency from TAFAZZIN mutations. Overall, we propose that T cell-specific PTPMT1 governs the balance between tolerance and inflammation in the gut, dictating outcomes in pathobiont infections.

overall_design: CD45+ cells obtained from 3 pooled wild type and 3 pooled PTPMT1 deficient animals were used in scRNAseq

first: David

middle: E

last: Sanin


title: RNA sequencing of neutrophils treated with microvesicles derived from glucose-deprived hepatocellular carcinoma cells.

city: xiamen

first: feng

last: deyi

state: xiamen

address: Xiamen University

institute: xiamen university

summary: Microvesicles derived from glucose-deprived liver cancer cells can promote tumor initiation and progression through neutrophils. This phenomenon can be rescued by knocking down Ezrin. Comparative analysis revealed that microvesicles from Ezrin-knockdown (Ezrin KD) liver cancer cells exhibit downregulation of VEGFA and PD-L1, along with upregulation of angiogenesis and T-cell regulatory pathways.

overall_design: WT and Ezrin KD Hepa1-6 liver cancer cells were subjected to glucose deprivation, and their microvesicles were collected. Bone marrow-derived neutrophils were then isolated and treated with these two types of microvesicles, followed by RNA sequencing.

first: Yuge

last: Ji

first: Deyi

last: Feng


summary: As tumor progression occurs, liver cancer cells are often in a state of nutrient deprivation, particularly lacking glucose. We found that microvesicles secreted by liver cancer cells under glucose-free conditions can promote tumorigenesis and progression. The specific mechanism involves enhancing neutrophil expression of PD-L1 and VEGFA, thereby suppressing T cell cytotoxicity and promoting angiogenesis.This phenotype is abolished after Ezrin knockout in liver cancer cells.

overall_design: Single-cell RNA-seq of hepatocellular carcinoma after glucose-free microvesicle treatment


title: ATF3-dependent formation of inclusion bodies in polyQ-expressing human iPSC-derived neurons confers cellular protection [ChIPseq]

overall_design: ChIP-seq of ATF3 in 105Q-NPCs with and without IBs, and with and without ATF3.


title: BMAL1 modulates glutamine supply to control hematopoietic stem and progenitor cell expansion

city: Geneva

first: Natacha

last: Civic

address: Rue Michel-Servet 1

department: iGE3 Genomics Platform

country: Switzerland

institute: University of Geneva

summary: Following specification in the dorsal aorta, hematopoietic stem and progenitor cells (HSPCs) proliferate in the HSPC niche, known as the caudal hematopoietic tissue (CHT) in zebrafish. Here we demonstrate that bmal1a, a core component of the circadian clock machinery, is expressed in CHT endothelial cells (ECs) and affects HSPCs in a non-cell autonomous manner. Using endothelial cell-specific dominant-negative Bmal1a zebrafish lines, we demonstrate a striking increase in HSPC numbers in the CHT, resulting from enhanced HSPC proliferation. RNA-sequencing of dominant-negative bmal1a ECs sorted from the CHT shows a downregulation of glud1a, resulting in increased glutamine levels in the CHT. This newly discovered bmal1a-glud1a-glutamine pathway fuels HSPC expansion. We demonstrate that this glutamine synthesis pathway controlling HSPC expansion is likely conserved in the mouse fetal liver (FL) niche, in which hepatocytes are the likely source of glutamine. Together, our data uncover a novel mechanism of HSPC homeostasis, in which EC BMAL1, expressed by the niche, controls the amount of bioavailable glutamine for HSPCs by regulating the expression of genes involved in glutamine synthesis.

overall_design: CHT regions were dissected from transgenic zebrafish embryos (either controls flk1:GFP;UAS:DN-bmal1a or flk1:GFP;flk1:GAL4;UAS:DN-bmal1a) at 36 hours post fertilization, and flk1GFP-positive cells were sorted by flow cytometry (around 5000 cells per sample). Total RNA was extracted and submited to bulk RNA sequencing

first: Tim

last: Petzold

first: Julien

last: Y. Bertrand


title: Faecalibacterium prausnitzii induces an anti-inflammatory response and a metabolic reprogramming in human monocytes

first: Phuong

last: PHAM

summary: We isolated immune cells from human blood of patients with IBD and non-inflamed controls. We stimulated them with F. prausnitzii EXL01 strain, Cadaverin or lipopolysaccharide (LPS) from Escherichia coli and performed Legendplex, ELISA, flow cytometry, RNA-sequencing (RNAseq), and Seahorse analysis. F. prausnitzii EXL01 strain induced the production of IL-10 in CD14+ monocytes from systemic circulation and intestinal tissue of IBD patients and non-inflamed controls in a direct and dose-dependent manner, without inducing a pro-inflammatory response as compared to LPS stimulation. RNAseq analysis confirmed these results and revealed that F. prausnitzii EXL01 strain differentially affects cell energy metabolism compared to LPS. The anti-inflammatory response induced by F. prausnitzii in monocytes was dependent on mitochondrial activity. F. prausnitzii induces an anti-inflammatory response and rewires energy metabolism in human monocytes, which might explain its beneficial impact on intestinal inflammation and human health in general. These results provide new insight into the mechanisms underlying the anti-inflammatory effects of F. prausnitzii and are crucial for a better understanding of its potential use in the treatment of IBD.

overall_design: Fresh PBMCs were isolated from human blood (n=6), CD14+ isolated cells were treated with control medium, Cadaverine, LPS (100 ng/ml) or EXL01 strain at 2 doses (MOI 10, 100) for 2h or 4h

first: Camille

last: Danne

first: Laura

last: Creusot

first: Rodrigo

last: Formiga

first: Florian

last: Marquet

first: Delphine

last: Sedda

last: Hua

first: Pauline

last: Ruffié

first: Hang-Phuong

last: Pham

first: Iria

last: Alonso Salgueiro

first: Loic

last: Brot

first: Marie-Laure

last: Michel

first: Jérémie

middle: H

last: Lefebvre

first: Harry

last: Sokol

first: Nathalie

last: Rolhion


title: Endometrial stromal cell signaling and microRNA exosome content in women with adenomyosis

city: Manchester

first: Angela

last: Simeone

address: 200 Hathersage Rd

institute: Genomic Services QIAGEN

type: Non-coding RNA profiling by high throughput sequencing

summary: Adenomyosis is a chronic, estrogen-driven disorder characterized by the presence of endometrial glands and stroma within the myometrium. Despite its significant impact on reproductive health and quality of life, the pathogenesis of the disease remains unclear. Both the glandular and stromal compartments of eutopic endometrium from women with adenomyosis show alterations compared to healthy subjects. However, the molecular mechanisms driving crosstalk between stromal cells and epithelial glands, along with paracrine signaling underlying lesion development and progression, are still poorly understood. Exosomes, small cell-derived carriers, and microRNAs, non-coding RNA molecules, are crucial to intercellular communication within the endometrium and may elucidate interactions between the two compartments that contribute to adenomyotic lesion formation. To our knowledge, this is the first foundational study to comprehensively isolate and characterize stroma-derived exosomes from women with adenomyosis. Exosome isolation by means of differential ultracentrifugation was validated in 22 samples, including 11 healthy subjects and 11 women with adenomyosis, using nanoparticle tracking analysis, transmission electron microscopy and flow cytometry. MicroRNA profiling in secreted exosomes revealed 10 microRNAs with altered expression in adenomyosis subjects during the menstrual phase compared to controls. Thorough investigations into menstruation-specific molecular mechanisms as well as predicted target genes and enriched pathways of exosomal microRNAs offer promising insights into the pathogenesis of adenomyosis, shedding light on the potential mechanisms underlying stromal cell signaling and adenomyotic lesion establishment. This groundwork study does, however, have certain limitations, including sample size and limited representation due to a lack of readily available endometrial biopsies in the menstrual phase. Future research should seek to validate these findings in larger cohorts and apply functional assays to clarify the role of menstruation-specific stroma-derived microRNA-mediated signaling and its potential impact on adenomyosis development.

overall_design: To investigate the changes in miRNA expression globally, one healthy subject and one subject with adenomyosis have been profiled. Stroma-derived exosomes from the subjects were isolated and used for miRNA profiling.

first: Margherita

last: Zipponi

first: Luciana

last: Cacciottola

first: Alessandra

last: Camboni

first: Christina

middle: A

last: Stratopoulou

first: Hugh

last: Taylor

first: Marie-Madeleine

last: Dolmans


title: Sequencing experiments on poly(U) mutants in C. elegans adults and embryos

city: Bloomington

first: Leanne

last: Kelley

state: IN

address: 1001 E Third St

institute: Indiana University

summary: To investigate mRNAs that are influenced by poly(U) polymerases in C. elegans adults and embryos/

overall_design: We performed Illumina-based mRNA-seq on various poly(U) polymerase deletion mutants at the adult and early embryonic stages.

first: Kelley

last: Leanne

first: Maine

last: Eleanor


title: Expanding the droplet-based microfluidic single-cell toolbox with a cost-effective full-length total RNA sequencing technology

first: Xue

last: Sun

address: Hebrew University, Givat Ram campus

department: Biochemistry department

institute: The Hebrew University of Jerusalem

summary: We developed sc-rDSeq, a high-throughput single-cell full-length total RNA sequencing technology and validated its performance using human cancer cell line, showed benchmarking against traditional scRNAseq method inDrops. sc-rDSeq was further applied in a drug resistance study on NSCLC lines treated with EGFR inhibitors Gefitinib and Osimertinib.

overall_design: We have developed a high-throughput single-cell full-length total RNA sequencing technology, sc-rDSeq. First, we validated its performance with the non-small cell lung cancer (NSCLC) cell line PC9. Both sc-rDSeq and inDrops were applied to PC9 cells for comparison purpose. We then conducted a drug resistance study using PC9 and another NSCLC cell line, HCC827. These cells were treated with 1 μM of two different EGFR inhibitors, Gefitinib and Osimertinib, for 9 days, with the medium containing fresh drugs replaced every three days. Cells that remained adherent were profiled using sc-rDSeq. Control cells treated with an equivalent concentration of DMSO were also analyzed. Raw data were aligned in multiple rounds to exclusively map to total RNA. Reads were first mapped to the whole genome, then counted with different GTF files in each round. Only reads that failed to align proceeded to the next round. The alignment order was short RNA, long RNA exons, long RNA introns, and pseudogenes. Single cell matrix obtained from each round were combined in downstream analysis.

first: Oren

last: Ram


title: Widespread gene-environment interactions shape the immune response to SARS-CoV-2 infection

city: Chicago

first: Luis

middle: B

last: Barreiro

state: Illinois

address: 5841 S Maryland Ave

department: Department of Medicine

institute: University of Chicago

summary: Genome-wide association studies performed in COVID-19 patients have uncovered various loci significantly associated with susceptibility to SARS-CoV-2 infection and disease severity. However, the underlying cis-regulatory genetic factors contributing to heterogeneity in the response to SARS-CoV-2 infection and their impact on clinical phenotypes remain enigmatic. Here, we use single-cell RNA-sequencing to quantify genetic contributions to cis-regulatory variation in 361,119 peripheral blood mononuclear cells of 63 acute COVID-19 patients, 39 convalescent samples, and 106 healthy controls. Expression quantitative trait loci mapping across cell types within each disease state group reveals thousands of cis-associated variants, of which hundreds are detected exclusively in immune cells derived from acute patients. Patient-specific genetic effects dissipate as infection resolves, suggesting that distinct gene regulatory networks are at play in the active infection state. Further, 20.3% of tested loci demonstrate significant cell state interactions with genotype, with pathways related to interferon responses and oxidative phosphorylation showing pronounced cell state-dependent variation, predominantly in CD14+ monocytes. Overall, we estimate that 16.8% of tested genes exhibit gene-environment interaction effects, highlighting the importance of environmental modifiers in the transcriptional regulation of the immune response to SARS-CoV-2. Our findings argue for the existence of extensive gene-environment effects among patients responding to an infection.

overall_design: Multiplexed single-cell RNA expression profiles of peripheral blood mononuclear cells (PBMCs) collected from COVID-19 patients, COVID-19 follow-ups, and healthy controls

first: Haley

last: Randolph

first: Raúl

last: Aguirre-Gamboa

first: Elsa

last: Brunet-Ratnasingham

first: Tomoko

last: Nakanishi

first: Veronica

last: Locher

first: Ellen

last: Ketter

first: Cary

last: Brandolino

first: Catherine

last: Larochelle

first: Alexandre

last: Prat

last: Arbour

first: Anne

last: Dumaine

first: Andrés

last: Finzi

first: Madeleine

last: Durand

first: J Brent

last: Richards

first: Daniel

last: Kaufmann


title: Gene expression data from human amniotic epithelial stem cell (hAESCs) treated with 20 uM Cinnamoylquinc  Acid Derivatives

city: Tsukuba

first: Yu Jia

last: Chen

state: Ibaraki

address: 1 Chome-1-1 Tennodai

institute: University of Tsukuba

summary:
Gene expression profiling reveals structure-activity relationships of cinnamoylquinic acid derivatives in a stem-based tool.
Cinnamoylquinic acids are bioactive polyphenolic compounds with many beneficial effects. Utilizing human amniotic epithelial stem cells (hAESCs), transcriptomic analysis was conducted to study the physiological effects of ten  derivatives. The ten compounds include: Tricaffeoylquinic acid, Tetraferuloylquinic acid, Tricoumaroylquinic acid, Tri(dimethoxycinnamoyl)quinic acid, Tetracaffeoylquinic acid, Triferuloylquinic acid, Methyl Tri(dimethoxycinnamoyl)quinate, Methyl tetracaffeoylquinate, Methyl tetraferuloylquinate, and Methyl tricaffeoylquinate. From gene expression data,  additionalk analysis pinpointed the structure-functionality relationship based on moiety variations while hinting to possible structural improvments for bioactivity and druggability.

overall_design: Human amniotic epithelial cells (hAESCs) spheroids were used.  The control  was maintained in the basal medium, and  the treatment groups had 20 μM of each ten cinnamoylquinic acid derivative compound  administered to the samples for a span of seven days. Duplicates of each condition and triplicate measurements were performed for a total of 33 samples.


title: Human CD14+ monocytes from early inflammatory arthritis patients before and after a 5day-and 30day-period of methotrexate treatment

first: Amaya

last: Puig Kröger

summary: Methotrexate (MTX) continues to be the anchor drug for patients with rheumatoid arthritis and psoriatic arthritis (RA and PsA) both as monotherapy as well as in combination with other drugs because of its efficacy, safety, low relative cost and the possibility of individualizing dose and method of administration. Following low-dose administration, MTX typically reaches peak plasma concentrations after 1-2 h, and almost completely disappears from the circulation by 24 h. Cellular uptake of MTX is mediated by the Reduced Folate Carrier. Once internalize, MTX is converted into MTX-polyglutamates (MTX-PG), a process that is catalyzed by folylpolyglutamate synthase (FPGS), which sequentially adds glutamic acid residues to MTX, and is one of the critical factors for the therapeutic action of MTX. We carried out a clinical observational study to evaluate the influence of MTX-PG levels on the molecular inflammatory state of monocytes from arthritis patients and relate to the clinical efficacy of MTX.

overall_design: mRNA profiles of human peripheral blood CD14+ monocytes from inflammatory arthritis patients at baseline, 5 days (1-dose MTX) and 30 days (4-doses MTX) after methotrexate treatment. The METOMAC-PAC study.

first: Israel

last: Rios

first: María Teresa

last: Schiaffino

first: Baltasar

last: López Navarro

first: Mónica

last: Torres Torresano

first: Ana

last: Triguero Martínez

first: Isidoro

last: González Álvaro

first: Isabel

last: Castrejón


title: Foamy microglia link oxylipins to disease progression in multiple sclerosis

city: Leiden

first: Daan

last: van der Vliet

address: Einsteinweg 55

department: Molecular Physiology

country: Netherlands

institute: Leiden university

summary: Multiple sclerosis (MS) is a neuroinflammatory disease characterized by expanding demyelinating lesions, leading to severe and irreversible disability. The mechanisms driving lesion expansion, however, remain poorly understood. Here, using a multi-omics approach, we identified foamy microglia as primary contributors to the molecular profile of lesions and disease progression in secondary progressive MS. Lesions with foamy microglia are marked by the accumulation of cholesterol esters, bismonoacylglycerolphosphates (BMP), and oxylipins, along with high B-cell infiltration, increased levels of immunoglobulin G1, and elevated expression of Fcγ- and complement receptors. Lesions with foamy GPNMB+-microglia display markers of enhanced phagocytosis, lipid metabolism, lysosomal dysfunction, and antigen presentation, but lack classical pro-inflammatory markers. Our data suggest that sustained phagocytosis of myelin overwhelms microglial endo-lysosomal capacity, leading to lipid droplet and oxylipin formation. This microglial phenotype may induce further recruitment of adaptive immune cells, axonal damage, drive lesion expansion and prevent remyelination. Monoacylglycerol lipase, involved in producing oxylipin precursors, was identified as a potential therapeutic target to disrupt this cycle and prevent chronic lesion expansion.

overall_design: white matter lesions and surrounding tissue were isolated from post-mortem brains from 28 donors diagnosed with MS, and 10 control donors. Specific lesion types were isolated characterized by lesion codes as reported by Luchetti et al Acta Neuropathologica 2018

first: Xinyu

last: Di

first: Tatiana

middle: M

last: Shamorkina

first: Anto

last: Pavlovic

first: Iris

first: Yingyu

last: Zeng

first: Will

last: Macnair

first: Noëlle

last: van Egmond

first: J

middle: Q

first: Aletta

last: van den Bosch

first: Hendrik

last: Engelenburg

first: Matthew

last: Mason

first: Claire

last: Coulon-bainier

first: Berend

last: Gagestein

first: Elise

last: Dusseldorp

first: Marco

last: van Eijk

first: Uwe

last: Grether

first: Netherlands

last: Brain Bank

first: Thomas

last: Hankemeier

first: Amy

last: Harms

first: Ludovic

last: Collin

first: Albert

last: Heck

first: Inge

last: Huitinga

first: Mario

last: van der Stelt


title: Molecular dynamics driving phenotypic divergence among KRAS mutants in pancreatic tumorigenesis [ATAC-Seq]

city: New York

first: Rohit

last: Chandwani

state: NY

address: 413 East 69th St, BRB 1360G

department: Surgery

institute: Weill Cornell Medicine

summary: Inflammation in the context of pancreatic injury drives acinar-to-ductal metaplasia (ADM), a cell state that can be hijacked by mutant Kras to drive the formation of pancreatic cancer. ADM has been described alternatively to bear progenitor features, but the extent to which lineage reversion is a broad feature of the response to injury and early tumorigenesis – particularlyacross the different mutant Kras alleles – remains poorly understood. Herein we implement novel Ptf1a-tdTomato mice to characterize early and late pancreatic progenitors to serve as benchmarks that define cell fate decisions in the context of inflammatory injury and initiation. In so doing, we define ADM as a mixed-lineage transcriptomic and epigenetic state, harboring ductal features but also featuring a lineage reversion to a late progenitor program. By contrast, while inducible mutant Kras alone is able to induce oncogenic gene expression, it does little to alter chromatin in the absence of injury. The most frequent Kras mutant alleles – G12D, G12V, and G12R – display differential cooptation of the injury-induced mixed-lineage state, with mutant KrasG12D able to form ADM and PanIN more robustly than either KrasG12V or KrasG12R. In particular, KrasG12R fails to promote phenotypic transformation on its own or even in concert with inflammatory injury. Whereas KrasG12Dand injury induce enhancer reprogramming at AP-1 chromatin and a lineage reversion to resemble early progenitors, KrasG12Rcan initiate but not sustain the key cell-intrinsic transcriptional and epigenetic programs characteristic of neoplasia. In KrasG12R we identify a decrease in Rac1 signaling, not AKT activation, as the key molecular defect. Together, these data demonstrate that the PDAC-associated Kras variants are not functionally equivalent and distinctly drive lineage reversion and epigenetic reprogramming, such that allele-specific approaches will be essential to therapeutic targeting in pancreatic cancer.

overall_design: Characterization of bulk chromatin accessibility via ATAC-seq of cells from the developing and mature pancreas (including early & late progenitor, adult ductal, adult lineage-traced acinar and acinar-derived cells) exposed to caerulein (or saline as control) and/or mutant Kras (G12D, G12V, G12R).

first: David

last: Falvo

first: Adrien

last: Grimont

first: Paul

last: Zumbo


title: Molecular dynamics driving phenotypic divergence among KRAS mutants in pancreatic tumorigenesis [RNA-Seq]

overall_design: Characterization of bulk RNA via RNA-seq of cells from the developing and mature pancreas (including early & late progenitor, adult ductal, adult lineage-traced acinar and acinar-derived cells) exposed to caerulein (or saline as control) and/or mutant Kras (G12D, G12V, G12R).


title: Compressive Force Induces Differential Gene Expression in Uterine Fibroids

city: Cincinnati

first: Stacey

last: Schutte

state: OH

address: 2901 Woodside Dr.

department: Biomedical Engineering

institute: University of Cincinnati

summary: We investigated how compressive force influences fibroid and myometrial cells. Patient-matched cells were isolated from women undergoing hysterectomy or myomectomy for the treatment of uterine fibroids. Samples from five women with no hormonal modulation within three months of surgery were used for this study. Spheroids fabricated from fibroid or myometrial cells were embedded in agarose hydrogels and exposed to compressive force for seven days. RNA sequencing was performed to identify genes and signaling pathways altered in fibroids in response to compression.

overall_design: Gene expression profiling analysis of RNA-seq data from uterine fibroid and myometrial cell spheroids with and without compression.

first: Carolyn

last: Nietupski

first: Megan

last: Sax

first: Rose

last: Dean

first: Andreja

last: Moset Zupan

first: Emily

middle: G

last: Hurley


title: BV-2 Cells: Control vs.OGD/R

city: harbin

first: Qian

last: Su

address: youzheng

institute: The First Affiliated Hospital of Harbin Medical University

summary: The difference of the m6A modification of tsRNAs of  microglia after OGD/R . Goal was to  reveal the m6A modification of tsRNAs and study the possible role of these RNAs in ischaemic microglia.

overall_design: OGD/R vs NC.


title: Systemic extracellular acidification is a hallmark of ageing

city: London

first: LMS

last: Bioinformatics Core

address: Hammersmith Hospital Campus, Du Cane Road

department: Bioinformatics Core

institute: MRC London Institute of Medical Sciences

summary: Finding the critical pathophysiological processes that promote disease risk with age is needed to uncover effective targets for preventive medicine. Despite being essential for physiology at all levels, the behaviour of protons in bodily fluids is understudied in ageing. Here, we investigate how extracellular pH changes with age and its impact on longevity, using Drosophila melanogaster and rodent models. Extracellular acidification occurs in flies during ageing and correlates with mortality rate, independently of strain, sex and diet. With age, flies also become more susceptible to die from acidotic stress, which can be prevented by alkalotic treatment. Acidification is caused by insufficient acid excretion, linked to downregulation of genes in the fly excretory tract that control pH and ATP production, essential for active secretion initiation. In rodents, we demonstrate that lymph also acidifies with age. Genes whose pathogenic variants cause tubular acidosis in humans are downregulated in the kidneys of ageing mice. Overall, this study sheds light on dysregulated systemic acid-base balance as a conserved pathophysiological mechanism of ageing.

overall_design: To analyse how excretory tract insufficiency occurs with age, we performed RNA-seq on the dissected excretory tracts of young, middle-aged and old male flies.

first: Eliano

last: dos Santos

first: Helena

last: Cocheme