title: The use of three-dimensional primary human myospheres to explore skeletal muscle effects of in vivo krill oil supplementation

city: Oslo

first: Andrea

last: Dalmao-Fernandez

address: Gaustadveien 9

country: Norway

institute: University of Oslo

summary: Purpose: Supplementation with krill oil has shown effects on whole-body lipid and glucose metabolism, as well as on skeletal muscle strength and function. We previously showed that krill oil intervention in vivo promoted fatty acid metabolism and protein synthesis in cultured human myotubes in a two-dimensional (2D) model. The aim of this study was to explore the effects of krill oil supplementation in vivo in a 3D myosphere model and to compare the 3D and 2D models. Methods: Myospheres were formed from myoblasts obtained before and after 7 weeks of in vivo krill oil intervention. Glucose and oleic acid metabolism were assessed, and transcriptomic and proteomic analyses were performed. Results: In vivo intervention with krill oil increased glucose metabolism in myospheres, while no effect was observed on fatty acid metabolism. Transcriptomic analyses of myospheres after krill oil intervention showed increased expression of genes involved in pathways like motor proteins and hypertrophy, as well as in calcium signaling, of which motor proteins and hypertrophy pathways have not been described in 2D myotube cultures. Proteomic analyses after krill oil intervention showed increased expression of proteins in glycolysis/gluconeogenesis and fatty acid degradation. Comparison of proteins expressed in the 3D myosphere model and a 2D myotube model at the basal level showed that in myospheres, mitochondrial gene expression and translation dominated, while in 2D cultures, mitochondrial organization and response to oxidative stress were more important. Conclusion: These findings suggest that in vivo krill oil intervention induces different metabolic effects when comparing 3D and 2D cultures. In contrast to the 2D model, data obtained with the 3D model showed gene expression changes that are more compatible with previously observed results in vivo concerning skeletal muscle motoric function. Hence, the 3D model might better reflect krill oil-induced modifications in skeletal muscle performance in vivo than the 2D model.

overall_design: RNA-seq of primary muscle cells in 3D culture from human donors before (BB) and after (AA) 7 weeks of krill oil in vivo intervention

first: Parmeshwar

middle: B

last: Katare

first: Hege

last: Bakke

first: Håvard

last: Hamarsland

first: Stian

last: Ellefsen

first: Sachin

last: Singh

first: Tula

last: Nyman

first: Eili

last: Kase

first: Arild

last: Rustan

last: Thoresen


title: Natural Microbial exposure populates the maternal fetal interface with diverse T cells.

status: Public on Jul 30 2025

city: Minneapolis

first: Nathan

last: Schuldt

state: MN

address: 2231 6th St. SE

department: Pediatrics

country: USA

institute: University of Minnesota

type: Expression profiling by high throughput sequencing

summary: scRNAseq was used to investigate how maternal microbial burden influences the immunology of the maternal fetal interface (MFI). Female mice werre cohoused with pet store mice for >4 weeks prior to conception and throughout gestation to naturalize maternal immunity. Cohoused dams were compared to specific pathogen free (SPF) control dams. Anti-CD45.2 IV labeling techniques were used to delineate immune cells in tissues from those in contact with circulation. IV labeling also permitted enrichment of placental (IV+) and decidal (IV-) tissue associated immune cells postprocessing. This is the first scRNAseq dataset to compare the immune cell populations from the MFI (combined placental and decidual tissue) of SPF and 'dirty' (pet store cohoused) dams. These data revealed significant changes to the immune cell composition and expansion of populations of T cells that phenocopy those described in the human decidua.

overall_design: Female C57BL/6 mice were cohoused with pet store mice for >4 wks prior to breeding. 14.5 days post conception cohoused and specific pathogen free (SPF) control dams were injected with a bolus of anti-CD45.2 antibody to label circulating immune cells. Dams were then euthanized and the maternal fetal interface (combined placenta and decidua) were harevsted, stained, and IV+ and IV- cells were sorted flow cytometrically and used to make single cell RNA sequencing libraries with the 10X Chromium platform. Onl;y primary syngeneic pregnancies were used in this dataset.

first: Tamara

last: Tilburgs


title: Transcriptomic Profile of Skeletal Muscle Biopsies from Duchenne and Becker Muscular Dystrophy Patients

city: Pavia

first: bartolo

last: rizzo

address: Via Mondino 2

country: Italy

institute: IRCCS Mondino Foundation

summary: The complexity of RNA metabolism has become crucial in neuromuscular diseases, especially for Duchenne Muscular Dystrophy (DMD) and Becker Muscular Dystrophy (BMD). DMD is associated with mutations in Dystrophin gene that disrupt the protein reading frame causing premature stop codons. In contrast, patients with BMD usually have in-frame deletions that maintain the correct reading frame. Our goal is to search for possible pathways that differs between the two diseases, in which DMD develop a severe phenotype compared to BMD. Here we aimed to evaluate the transcriptomic profile in muscle biopsy of DMD and BMD patients. We collected RNA obtained from muscle biopsy of pediatric DMD patients (n=12) and BMD patients (n=6). Through RNA sequencing, the differentially expressed (DE) genes of DMD patients versus BMD patients were analyzed. Through principal component analysis (PCA), we were able to identify a clear difference between the two groups based on gene expression pattern. DMD patients compared to BMD patients showed a particular activation of genes involved in collagen synthesis, extracellular matrix organization, and oncostatin M-dependent pathways, which plays an important role in the fibrosis process. This suggests that a more severe phenotype in DMD than BMD patients may be due to greater deregulation of these pathways, reflecting the clinical picture of patients observed. Furthermore mRNAs expression levels evaluated by RT-qPCR confirmed RNA-seq data. Enrichment pathways analysis revealed the strong alteration in collagen synthesis and extracellular matrix organization, suggesting different severity degree in the establishment of fibrotic processes. All the collagen genes validated by RT-qPCR were strongly upregulated in DMD patients. This study provides preliminary insights into the difference in gene expression between the two groups and lays the basis for the identification of possible mechanism that differentiate between the two diseases.

overall_design: We performed RNA-seq profiling of 12 DMD patients and 6 BMD patients. We used RNA extracted from tissue derived Skeletal muscle

first: Bartolo

last: Rizzo

first: Francesca

last: Dragoni

first: Maria Irene

last: Dainesi

first: Rosalinda

last: Di Gerlando

first: Angela

last: Berardinelli

first: Stella

last: Gagliardi


title: Cardiac-targeted AAV5-S100A1 gene therapy protects against adverse remodeling and contractile dysfunction in post-ischemic herats

city: Heidelberg

first: Patrick

last: Most

address: INF 410

country: Germany

institute: University Hospital Heidelberg

summary: Background: Guided by long-term safety data for AAV5 in humans, our translational study investigated whether AAV5 effectively delivers genes to healthy and achieve therapeutic efficacy in dysfunctional human-sized hearts, using a clinically applicable mode of administration and vector dosages. Methods & Results: In a first biodistribution study, AAV5 (11013 vector genomes; vgs) - carrying the reporter gene luciferase (luc) - achieved broad and homogenous transduction of the left ventricle (LV) of healthy German farm pigs 30 days after percutaneous catheter-based retrograde intravenous delivery (CRID), as measured by vector genome and luc mRNA assessments. Both its myocardial and extra-cardiac distribution patterns were advantageous compared to AAV9-luc and AAV6-luc. Using the cardioprotective human gene S100A1 (hS100A1) in a subsequent therapy study, effective myocardial transduction with AAV5-hS100A1 (11013 vgcs) by CRID prevented LV myocardial infarction (MI) enlargement and improved systolic contractile performance after 3 months in a porcine model with chronic post-MI cardiac dysfunction, as assessed by serial cardiac magnetic resonance imaging. The use of a cardiac-biased promoter ensured cardiac-targeted hS100A1 expression without signs of clinical toxicity, as shown by RT-PCR analysis, clinical chemistry and blood count. A previously unknown anti-inflammatory effect of hS100A1 in damaged myocardium, detected and linked to the therapeutic actions by a cardiac transcriptome weighted gene coexpression network analysis, was confirmed using AAV5-hS100A1 therapy in a post-MI mouse model, as measured by RT-PCR and echocardiography. Conclusion: Providing the clinically relevant proof-of-concept for AAV5 to effectively transduce healthy and dysfunctional human-sized hearts, its clinical long-term safety, scalable producibility as well as low pre-existing immunity in humans may predestine AAV5 as an effective and safe gene carrier for a prevalent disease as chronic heart failure, using therapeutic genetic effectors, such as hS100A1 or others.

overall_design: RNA-seq, WGCNA and enrichment analysis of myocardial tissue (anteromidventricular) of male farm pigs 14 weeks after LCX-myocardial infarction, AAV5-hS100A1 treated vs. AAV5-luc


title: Sequencing of mRNA expressed in cultures and tissues of stugeon integument

city: Davis

first: Robert

last: Rice

state: California

address: 4139 Meyer Hall, One Shields Avenue

department: Environmental Toxicology

institute: UC Davis

summary: Sturgeon species are threatened or endangered worldwide due to habitat loss and increasing pollution. An epithelial cell culture model promises to help investigate hazardous environmental exposures. The stratified squamous integument of green and white sturgeons (Acipenser medirostris and transmontanus, respectively) and cells cultured from their epithelia expressed substantial levels of TGM1-like transglutaminases, types I and II keratins and aryl hydrocarbon receptor (AHR) proteins analogous to those in mammalian integument.

sample_organism:
Acipenser transmontanus
Acipenser medirostris

overall_design: RNA from samples of sturgeon integument (skin, mouth, ampullae of Lorenzini), upper palate, esophagus and confluent epithelial cultures from these tissues were sequened using PacBio methodology to find relative amounts of various transcripts.

first: Sumi

last: Nechat

middle: H


title: Arsenic Toxicity in the Drosophila Brain at Single Cell Resolution

city: Greenwood

first: Anurag

last: Chaturvedi

state: SC

address: 114 Gregor Mendel Cir

department: Center for Human Genetics

institute: Clemson University

summary: Whole brain single nuclei RNA-Seq in Arsenic exposed flies.

overall_design: The dataset is a single nuclie RNA-seq data from Drosophila brains from Canton S (B) flies (CSB) exposed to 250 µM of  NaAsO2 for 6 days


title: Comparative Transcriptomic Analysis of Mouse Macrophages Infected with Live Attenuated Vaccine Strains of Mycobacterium tuberculosis

city: El Paso

first: Enrique

middle: Ivan

last: Ramos

state: Texas

address: 5001 El Paso Dr.

department: Molecular and Translational Medicine

institute: Texas Tech University Health Sciences Center El Paso

summary: The BCG vaccine has been used against tuberculosis (TB) for over hundred years; however, it does not protect adults from pulmonary TB. To develop alternative vaccines against TB, we generated Mycobacterium tuberculosis H37Rv (Mtb)-derived vaccine strains by rationally deleting key virulent genes, resulting in single (SKO; ΔfbpA), double (DKO; ΔfbpA-ΔsapM), triple (TKO-D; ΔfbpA-ΔsapM-ΔdosR and TKO-Z; ΔfbpA-ΔsapM-Δzmp1), and quadruple (QKO; ΔfbpA-ΔsapM-Δzmp1-dosR) strains. To understand how macrophages, the host cells that defend against infection and process antigens for presentation to immune cells, respond to these vaccine strains, we performed transcriptomic analyses of mouse bone marrow-derived macrophages (BMDMs) infected with these strains. The transcriptomic data were compared with similar data obtained from macrophages infected with Mtb H37Rv and BCG. Our analyses revealed that genes associated with various immune and cell signaling pathways, such as NF-kappa B signaling, TNF signaling, cytokine-cytokine receptor interaction, chemokine signaling, hematopoietic cell lineage, Toll-like receptor signaling, IL-17 signaling, Th1 and Th2 cell differentiation, Th17 cell differentiation, and T cell receptor signaling were differentially expressed in BMDMs infected with our vaccine strains. Enhanced expression of cytokines and chemokines, including proinflammatory cytokines such as TNF-α, IL-6, GM-CSF, and IL-1, which are essential for the immune response against Mtb infection, was also observed in BMDMs infected with these strains. In particular, BMDMs infected with all vaccine strains exhibited a significant upregulation of genes associated with the IL-17 pathway. These results may indicate that our vaccine strains could induce a protective immune response against TB.

overall_design: RNA-Seq profiling of mouse BMDMs infected with mycobacterial vacine strains at 24 h and 72 h postinfection

first: Raja

last: Veerapandian

first: Barbara

last: Yang

first: Areanna

last: Carmona

first: Melina

middle: J

last: Sedano

first: Victoria

last: Reid

first: Rodrigo

last: Jimenez

first: Jessica

last: Chacon

first: Chinnaswamy

last: Jagannath

middle: I

first: Shrikanth

middle: S

last: Gadad

first: Subramanian

last: Dhandayuthapani


title: miRNA/mRNA analysis of Chlamydia trachomatis-infected endometrial biopsies indicate increased TGF-β pathways drive epithelial-mesenchymal transition and regulatory T cell differentiation

city: Chapel Hill

first: xiaojing

last: zheng

address: 111 Mason Farm Road

institute: UNC-CH

summary: Chlamydia trachomatis genital tract infection is linked to severe reproductive complications in women, including ectopic pregnancy, infertility, and adverse pregnancy outcomes. Mouse models of infection suggest that chlamydia-induced dysregulation of microRNAs (miRNAs) can drive harmful cytokine responses, pathogenic epithelial-mesenchymal transition (EMT), and fibrosis. To investigate these mechanisms in humans, we profiled miRNA and mRNA expression in endometrial biopsies from women with endometrial infection (Endo+) and compared them to profiles from women with cervix-only infection (Endo-) or no infection. Ingenuity Pathway Analysis (IPA) revealed that Endo+ tissues had upregulated genes associated with innate and adaptive immune response pathways, as well as EMT regulation, while downregulated genes were linked to cell cycle control. An integrative miRNA-mRNA analysis, which combined a review of published miRNA regulation in human infections and immune responses with IPA’s miRNA target filter, identified differentially expressed miRNAs that modulate these pathways in the endometrium of Endo+ women. Functional annotation of these miRNAs showed a predominance of downregulated miRNAs that typically suppress EMT and regulatory T cell (Treg) differentiation, along with miRNAs that usually enhance Th17 responses. Comparisons with previously identified mRNA pathways in blood samples from women with endometrial Chlamydia infection indicated that alterations in TGF-β signaling and EMT were specific to the endometrium. Overall, the miRNA-mRNA interactions inferred from Endo+ tissue suggest increased activity in TGF-β pathways that promote enhanced EMT and Treg differentiation, while reducing Th17 activation. These changes highlight a dual potential for promoting tissue scarring while dampening inflammatory responses that could otherwise limit infection.

overall_design: Endometrial biopsy samples were obtained from cisgender female participants enrolled in two independent cohorts with high exposure to Ct infection. Total RNA was extracted from endometrial biopsies stored at -80°C in tubes containing RNA/DNA Shield (Zymo Research, Irvine, CA). After thawing, samples were weighed, minced, and processed for simultaneous DNA and RNA extraction using the Quick DNA/RNA™ isolation kit according to the manufacturer's protocol (Zymo) with on column DNase I treatment prior to total RNA elution. Libraries were prepared using the Ovation SoLo RNA-Seq kit (NuGen Technologies) and sequenced on an Illumina HiSeq2500 platform in the High Throughput Sequencing Facility (HTSF) at the University of North Carolina.

first: Toni

last: Darville

first: Xuejun

last: Sun

first: Yu

last: Zhang

first: Catherine

middle: M

last: O’Connell

first: Neha

last: Mokashi

first: Weiming

last: Tang

first: Aakash

last: Bhardwaj

first: Bryce

last: Duncan

first: Harold

last: Weisenfeld

first: Xiaojing

last: Zheng


title: Exploration of common pathogenic genes between cerebral amyloid angiopathy and insomnia based on bioinformatics and experimental validation

city: 河南

first: Li

last: Yusheng

state: 河南

address: 八号楼四楼

country: China

institute: 郑州大学第一附属医院

summary: RNA transcriptome analysis results were utilized to assess the shared gene expression between patients with cerebral amyloid angiopathy (CAA) and those with insomnia.

overall_design: Total RNA was obtained from peripheral blood of patients with cerebral amyloid angiopathy (n = 11) and healthy controls (n = 11).

first: Yu-Sheng

last: Li

first: Xin-Yu

first: Yi-Han

last: Wei

first: Wen-Kai

last: Yu


title: miRNA/mRNA analysis of Chlamydial trachomatis-infected endometrial biopsies indicate increased TGF-β pathways drive epithelial-mesenchymal transition and regulatory T cell differentiation

city: CHAPEL HILL

state: NC

address: Booker Creek Apts, 2525 Booker Creek Rd Apt 15F

department: Biostatistics

institute: University of North Carolina Chapel Hill

type: Non-coding RNA profiling by high throughput sequencing

overall_design: Endometrial biopsy samples were obtained from cisgender female participants enrolled in two independent cohorts with high exposure to Ct infection. miRNAs were isolated using HTG EdgeSeq reagents and libraries synthesized in the HTSF at the University of North Carolina. Barcodes samples were pooled, and sequencing was performed on an Illumina NextSeq 500 platform (75 cycles, High Output v2 kit). Data were processed into FASTQ files and analyzed using the EdgeSeq parser software (HTG Molecular Diagnostics, Inc.).

first: Charles

middle: W

last: Andrews Jr


title: Glutamine transporters regulate prostate cancer radiosensitivity through NUPR1-mediated stress response

city: Dresden

first: Vasyl

last: Lukiyanchuk

address: Handelallee 26

institute: OncoRay

summary: Prostate cancer (PCa) presents a significant clinical challenge due to its resistance to conventional therapies such as radiotherapy (RT), which is exacerbated in advanced stages by metabolic and stress response adaptations. Our study investigates the roles of amino acid transporters SLC1A5, SLC7A5, and SLC38A1, in regulating NUPR1-mediated stress response, PCa cell survival, metabolic reprogramming, and response to RT. Depletion of these transporters disrupted glutamine (Gln) uptake, leading to reduced cell viability, altered ROS levels, and enhanced radiosensitivity in DU145 and LNCaP cell lines. Functional assays revealed that targeting these transporters decreases stem cell-like properties, impairs cell cycle progression, and heightens DNA damage under RT. Besides, CB839, a glutaminase inhibitor, combined with RT, demonstrated a synergistic effect in vivo, significantly delaying tumor growth compared to other treatment groups. Our findings indicate that these transporters mediate PCa cells’ adaptation to nutrient stress, while NUPR1 promotes cellular survival under metabolic and genotoxic stress. The results highlight the therapeutic potential of targeting Gln metabolism and stress response pathways to improve treatment efficacy. Our findings indicate that targeting SLC1A5, SLC7A5, SLC38A1, and NUPR1 radiosensitizes PCa by disrupting metabolic adaptations and stress responses. These findings provide a potential therapeutic strategy to enhance the efficacy of RT and improve treatment outcomes for PCa patients.

overall_design: RNAseq profiling after siRNA knockdown of SLC1A5,  SLC7A5 and SLC38A1, compared to scrambled (SCR) siRNA treatment. Experiment was performed in two cell lines (LNCaP and DU145) and inclubes three independent repeats (rep1-rep3)

first: Uğur

last: Kahya


title: Local growth hormone facilitates aging of the colon epithelial microenvironment

city: Los Angeles

first: Richard

last: Ainsworth

address: 8700 Beverly Blvd

institute: Cedars-Sinai Medical Center

summary: We elucidate mechanisms underlying loca non-pituitary GH (npGH) action in the non-tumorous colon tissue microenvironment. We demonstrate autocrine npGH action in normal human colon cells (hNCC) infected with lentivirus-expressing hGH (lentiGH), as well as paracrine npGH action in hNCC co-cultured with lentiGH hNCC and in intact human 3-dimensional intestinal organoids co-cultured with organoids infected with lentiGH. Enriched gene ontology and pathway analysis of intact organoids exposed to paracrine npGH identified distorted extracellular matrix (ECM) and focal adhesion pathways concurrent with altered expression of ECM and cytoskeletal proteins. Significant phosphoprotein changes associated with cytoskeleton and cell migration pathway occurred in GH-exposed hNCC. Paracrine npGH triggers these changes by activating epithelial-mesenchymal transition, as shown by suppression of E-cadherin and induction of Twist2 in cellular models, as well as in the colon of nude mice inoculated with GH-secreting xenografts. These changes are consistent with observed increased migration of hNCC overexpressing lentiGH, or in those co-cultured with GH-secreting hNCC or with GH-secreting normal colon fibroblasts. Furthermore, whole exome sequencing detected increased structural variation in intact organoids co-cultured with lentiGH-infected organoids, likely as a consequence of GH-mediated suppressed DNA damage repair, thereby favoring cell transformation.

overall_design: human colon entestinal organoids were infected with lentivirus expressing GH or lentivirus expressing vector  and cultured for 2 month. Organoid cells growing in a presence of lentiGH or lenti V were selected and compared.

first: Shlomo

last: Melmed

first: Vera

last: Chesnokova

first: Richard I.


title: A temporally resolved BMP4 response in the peri-implantation human embryonic disc is critical for the induction of multipotent TFAP2A + cells and EMT

first: Jonathan

last: DiRusso

address: 615 Charles E. Young Drive

department: Molecular, Cell and Developmental Biology

institute: University of California Los Angeles

summary: The unilaminar embryonic disc, a sheet of epithelized SOX2+ epiblast cells, undergoes complex morphogenesis to create a multi-dimensional human gastrula. This process endows early lineage specification and spatial identities that begin at the posterior end of the disc to create a coordinate system for embryogenesis. Here, we find that simply adding basement membrane extracts (BMEs) to the stem cell media is sufficient to model the early peri-gastrulating embryonic disc. We demonstrate that the emergence of amnion, primordial germ cells (PGCs), and mesoderm arise from BMP4-responsive disc cells that induce transient TFAP2A expression and SOX2 repression. We track the order of embryonic events that take place during disc morphogenesis and show that amnion-like cells (AMLCs) and PGC-like cells (PGCLCs) are specified first from epithelized TFAP2A+ progenitors. Shortly after, gastrulating mesoderm-like cells (MeLCs) arise from transiently expressed TFAP2A+ disc cells that then undergo EMT. We find that BMP4-responsiveness is critical to SOX2 repression, TFAP2A expression, lineage induction and EMT, while the process of EMT itself is not. Thus, we show that the extracellular matrix is necessary to promote disc morphogenesis and EMT.

overall_design: GiMO culture of UCLA hPSCs at d1,2 and 3 were first washed with cold D-PBS 3X in 30sec increments to dissolve Geltrex overlay. Next, samples were treated with 0.25% Trypsin/EDTA for 10 mins at 37 °C and 5% CO2.  After incubation, cells were quenched with cold E8 medium and centrifuged at 1.2 rpm for 3.5 min. Cells were then resuspended with FACS buffer, D-PBS containing 0.5% Bovine Serum Albumin (BSA, Sigma-Aldrich, # A3311), as a wash step and centrifuged at 0.7 rpm for 4 min. Cells were resuspended again with FACS buffer and dissociated to single cells using a Falcon 100 mm Cell Strainer (Corning, # 352360) and manually counted. hPSCs were then further dissociated using EASYstrainer Cell Sieves 40 mm filter and centrifuged at 0.3 rpm for 3 min and resuspended in FACS buffer at a total volume of 1000 cells mL-2. Within 1hr after cell dissociation, cells were loaded into the 10x Genomics Chromium. Alignment was performed by Cellranger v5.0.1 to hg38 2020A.

first: Auriana

last: Arabpour

first: Amander

last: Clark


title: Biomarker genes for model-based prediction of drought-stress perception levels in rice

city: Tsukuba

first: Taiji

last: Kawakatsu

state: Ibaraki

address: 3-1-3 Kan-nondai

country: Japan

institute: National Agriculture and Food Research Organization

summary:
Background
Drought is a global challenge that severely restricts crop yields and threatens food security. Plants respond to drought stress by modulating gene expression before visible phenotypic changes occur. However, most studies of drought resistance have examined phenotypes after drought treatment, with little emphasis on how severely the plants were perceiving drought-stress conditions before the appearance of stress symptoms. We therefore developed drought-stress biomarkers (DSBMs) to detect drought-stress perception levels based on gene expression profiles by performing time-series transcriptome analysis and phenotypic analysis of rice (Oryza sativa) under drought conditions in the growth chamber.

Results
Time-series RNA-seq of the drought-susceptible rice cultivar IR64 revealed drastic changes in the transcriptome after 4–6 days of drought treatment in plants grown in pot culture mimicking drought conditions in the field, particularly for genes related to photosynthesis. Among the differentially expressed genes, we selected 23 DSBM genes that consistently responded to drought stress. Rehydration immediately reset the changes in expression of these DSBM genes, indicating that their expression changes reflect current drought-stress perception levels, but not stress memories. Responses of DSBM genes tended to be conserved among rice accessions, irrespective of the rice subpopulation (such as indica, aus, and japonica). We developed a machine learning model using the expression levels of DSBM genes trained by the time-series RNA-seq data for IR64. This model successfully predicted the drought-stress perception levels of various rice accessions, representing the probability of exposure to drought treatment, with an accuracy of 75%. Extreme root architecture traits, such as the largest root surface area, narrowest crown root diameter, and largest ratio of deep rooting, influenced the predicted drought-stress perception levels.

Conclusion
We identified DSBM genes and developed a machine learning model as a robust tool for assessing drought-stress perception levels in rice. Monitoring and predicting drought-stress perception levels should contribute to more efficient crop management and breeding schemes. Furthermore, our dataset would serve as a resource for further understanding the mechanisms of drought resistance in rice.

overall_design: RNA-seq profiling of IR64 rice leaves subjected to severe drought conditions for 9 days, followed by irrigation for 6 days.

first: Kanami

last: Yoshino


overall_design: RNA-seq profiling of WRC leaves at 5 days after moderate drought conditions


title: The impact of mab_1638 on the M. abscessus transcriptome [ChIP-seq]

city: Worcester

first: Scarlet

last: Shell

state: Massachusetts

address: 60 Prescott St, WPI

department: Biology and Biotechnology

institute: Worcester Polytechnic Institute

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Mycobacterium abscessus is a major human pathogen, mostly infecting people with pre-existing pathological lung conditions such as cystic fibrosis. Only little is known about the ways M. abscessus regulates its virulence factors and pathogenesis phenotypes. The production of glycopeptidolipids (GPL) is a major determinant of virulence of this bacterium, with clinical isolates that lack GPL synthesis and export generally exhibiting more aggressive clinical behavior. The current paradigm is that GPL production is abolished in vivo via irreversible, spontaneous mutations taking place as part of in-host evolution. Little is known about the mechanisms or extent to which GPL production may be regulated. We have found an unusual TetR-like transcription factor of M. abscessus, mab_1638, identified via screening of a comprehensive transposon-mutant library, that appears to be a strong positive regulator of the entire GPL biosynthesis and export gene cluster through a combination of direct and indirect mechanisms. The inactivation of mab_1638 by a transposon led to stable and visually obvious rough colony morphology, as well as increased virulence in infection models, characteristic of rough, non-GPL-producers. Transcriptome analysis found the mab_1638:tn mutant to have 118 differentially expressed genes, including the GPL locus. It appears mab_1638 encodes an unusual TetR transcription factor required for  the production of GPL in M. abscessus and therefore having a profound effect on virulence traits. This finding raises the important possibility that M. abscessus strains appearing smooth in laboratory growth conditions may nonetheless downregulate GPL-cluster genes in other conditions and thus acquire the phenotypic characteristics of rough strains.

overall_design: ChIP-seq was performed with an anti-HA antibody on four strains: (1) WT M. abscessus ATCC19977; (2) M. abscessus ATCC19977 transformed with a construct encoding an HA-tagged M. tuberculosis protein (mmaA2) not expected to bind DNA; (3) M. abscessus ATCC19977 with a transposon disrupting the gene mab_1638 (mab_1638::tn) and transformed with a construct encoding MAB_1638 with an N-terminal HA tag; and (4) mab_1638::tn transformed with a construct encoding MAB_1638 with an C-terminal HA tag.

first: Daniel

last: Barkan

first: Michal

last: Bar-Oz

first: Junpei

last: Xiao

last: Meir

first: Manitosh

last: Pandey

first: Stefan

last: Oehlers


title: The impact of mab_1638 on the M. abscessus transcriptome

overall_design: The mab_1638 gene of M. abscessus strain ATCC19977 was disrupted with a transposon. Triplicate cultures of the parental and mab_1638::tn strains were grown to log phase and RNA harvested and used to contruct RNAseq expression libraries.


overall_design: RNA-seq profiling of IR64 rice leaves subjected to moderate and severe drought conditions for 0-12 days.


title: Transcriptomes of Streptococcus anginosus KH1 in artificial saliva medium and modified serum medium

city: Taoyuan

first: RUEILIN

last: Chiang

address: No.259, Wenhua 1st Rd

country: Taiwan

institute: CGU

summary: The transcriptomes of S. anginosus KH1 under conditions mimicking either the oral cavity or the bloodstream were determined to identify loci that are highly regulated by culture media.

overall_design: Total cellular RNA was isolated from KH1 cultures at OD600 = 0.3. Ribosomal RNA was removed from the RNA preparation using RiboMinus transcriptome isolation kits (Invitrogen). Transcriptome sequencing was performed by a commercial service (Welgene, Taiwan). Briefly, the RNA library was constructed using a SureSelect XT HS2 mRNA library preparation kit (Agilent, USA). The sequences were determined using Illumina's sequencing-by-synthesis (SBS) technology (Illumina, USA). Reads were assessed through a Phred quality score (Q score of 20) and trimmed using Trimmomatic v0.36. The trimmed reads were mapped to the genome sequence of KH1 by using HISAT2. TPM (transcripts per million) was used to calculate the expression level of each gene. The significant difference in the expression level of each locus between the two growth conditions was analyzed using DESeq2 v1.28.1 with genome bias detection/correction and Welgene Biotech’s in-house pipeline. For each condition, duplicate samples were analyzed. Genes exhibiting a fold change >2.0 and a p-value < 0.05 between the two culture conditions were considered significant.

first: Yu-Juan

last: Lin

first: Hsing-Yi

last: Wang

first: Yi-Ywan M.

last: Chen


title: DRG bulk RNAseq: Repeated Injections Of Intra-articular Nerve Growth Factor Into The Naive Murine Knee Joint Cause Synovial Inflammation, Knee Sensitization, And Neuronal Sprouting

city: Chicago

first: Rachel

middle: E

last: Miller

address: 1735 W Harrison St

institute: Rush University Medical Center

summary: We aimed to explore the pain-producing effects of repeated intra-articular (IA) injections of NGF into the knee joints of healthy mice, as well as the effects on joint innervation and structure. In addition DRG bulk RNAseq was performed.

overall_design: WT male mice age 15 weeks were intra-articularly injected with 500 ng NGF or vehicle 2x/week for 1.5 weeks for a total of 3 injections. Twenty-four hours after the last injection, ipsilateral L3-L5 DRGs were collected for bulk RNAseq.

first: Anne-Marie

last: Malfait


title: Hepatocyte reporter cells and integrated metabolomic and transcriptomic analyses reveal insights into hepatocyte changes in offspring of pregnancies with obesity

city: Milwaukee

first: T. Hang

last: Nghiem-Rao

state: WI

address: 999 N. 92 Street, Suite C410

institute: Medical College of Wisconsin

summary: Infants born to mothers with obesity have increased risk for later development of non-alcoholic fatty liver disease (NAFLD); however early hepatic changes that occur in these infants remain unclear. We integrated metabolomic analysis of umbilical cord plasma and transcriptomic analysis of cord plasma-exposed hepatocytes to examine differences in the intrauterine environment of pregnancies with and without maternal obesity. We identified significantly higher abundance of fatty acids, bioactive lipids, and upregulation of glutathione metabolism in cord plasma from pregnancies with obesity compared to normal weight pregnancies. Hepatocytes exposed to cord plasma from pregnancies with obesity exhibited distinct transcriptional changes that favored cellular injury and inflammation, and impaired hepatocyte development compared to hepatocytes exposed to cord plasma of normal weight pregnancies. In integrated analysis, metabolite-gene relationships were distinct between pregnancies with and without obesity, and the abundance of lipids were positively correlated with the expression of KDM4D, DTX3, and NOTCH4 and negatively correlated with the expression of MT_TS1. Our findings provide novel insights into transcriptional changes induced in hepatocytes by circulating factors in the intrauterine environment of pregnancies with obesity. Excess intrauterine lipids may contribute to hepatic injury, inflammation, impaired mitochondrial function, and impaired hepatocyte development in infants of pregnancies with obesity.

overall_design: RNA-seq profiling was done on cultured HepaRG hepatocytes after 24 hours of exposure to media supplemented with cord plasma from pregnancies of mothers with obesity or media supplemented with cord plasma from pregnancies of mothers with normal weight.

first: Tuyet-Hang

first: Svetlana

last: Kozlovich

first: Amy

last: Pan

first: Jennifer

last: McIntosh

first: Anna

last: Palatnik

first: Shuang

last: Jia

first: Martin

last: Hessner


title: Multi-Omics Profiling Reveals Distinct Lipidomic and Transcriptomic Alterations in Gestational Diabetes Mellitus, Preeclampsia, and Coexistence of Both: Implications for Maternal and Neonatal Outcomes

city: Shanghai

first: Chenxiao

last: Zhang

state: Shanghai

address: 227 South Chongqing Road

institute: Shanghai Jiao Tong University

summary: Gestational diabetes mellitus (GDM) and preeclampsia (PE) are major contributors to maternal and perinatal morbidity and mortality, characterized by dysregulated lipid metabolism, chronic inflammation, and immune dysfunction, disrupting maternal-fetal homeostasis. The coexistence of GDM and PE (PG) presents a uniquely complex clinical scenario with molecular mechanisms that remain poorly understood. Peripheral blood samples from 42 pregnant women were categorized into CTL (n=10), GDM (n=12), PE (n=10), and PG (n=10) groups. Lipidomic profiling via LC-MS and transcriptomic analysis through RNA sequencing were performed. Multi-omics integration correlated molecular signatures with clinical and neonatal outcomes, and a predictive model for PE was constructed using differentially expressed lipids. Additionally, UK Biobank data was analyzed to explore associations between pregnancy complications and maternal postpartum depression (PD).PE exhibited the most pronounced lipidomic alterations, correlating with adverse neonatal outcomes, including low birth weight, while GDM showed the most significant transcriptomic changes. PG demonstrated unique transcriptomic signatures associated with neuronal and immune dysfunction, suggesting a potential link to maternal PD. Seven lipid biomarkers were identified, significantly correlating with neonatal outcomes, and a lipid-based predictive model for PE showed robust performance across PE and PG cohorts. GDM and PE were significantly associated with PD, though PG’s association remains inconclusive due to limited data.This study highlights the utility of multi-omics in unraveling shared and disease-specific mechanisms underlying pregnancy complications. The identified biomarkers and PE predictive model offer promising avenues for advancing diagnosis, prognosis, and personalized maternal-fetal care.

overall_design: Peripheral blood (PB) samples were collected in late-stage pregnancy, prior to labor, from 17 pregnant women (5 from the CTL group, 5 from the GDM group, 3 from the PE group, and 4 from the PG group) into a lavender tube containing potassium EDTA (K2EDTA). Peripheral blood mononuclear cells (PBMCs) were isolated from blood in the lavender tube via density gradient centrifugation using Lymphoprep (Serumwerk Bernburg AG, #1858,). Total RNA was extracted using the Takara RNA extraction kit (Takara, TKR-9109). RNA-Seq was done using the DNBSEQ platform (150 bp paired-end).

first: Yanli

last: Huang

first: Xixian

last: Mai

first: Lu

last: Liu

first: Yan

last: Li

first: Fei

last: Zheng

first: Judan

last: Cao

first: Chen

last: Zou

first: Changshan

first: Jinjun

last: Ran

first: Hui

first: Xiaonan


title: Zebrafish sall1a and sall4 contribute to posterior body elongation

city: Minneapolis

first: Micah

last: Gearhart

address: 6-160 Jackson Hall, 321 Church St.

department: Genetics, Cell Biology and Development

institute: University of Minnesota

summary: Vertebrate embryos elongate the body after gastrulation. Unlike in mice, which elongate both the trunk and tail after gastrulation, zebrafish embryos develop the trunk at the end of gastrulation, followed by tail elongation by proliferation of posteriorly located progenitors. Previous studies have shown that the transcription factors SALL1 and SALL4 redundantly regulate tail elongation in mouse embryos. To test whether sall1a and sall4 also regulate tail elongation in zebrafish, we generated zebrafish mutants for these genes. By 24 hours post-fertilization, sall4 mutant embryos developed normally but exhibited changes in gene expression at the posterior end of the body. sall1a mutants also developed normally by 24 hours post-fertilization. However, embryos mutant for both sall1a and sall4 showed a slight but significant reduction in body length compared to wild-type and sall1a mutant embryos. Our results support a role for sall1a and sall4 in tail elongation in zebrafish, though their contribution appears smaller than that observed in mouse embryos.

overall_design: Three replicates of control or sall4 morpholino treated zebrafish.

first: Hiroko

last: Kawakami

first: Abigail

last: Bailey

first: Ella

last: Gavin

middle: D

first: Yasuhiko


title: Large Maf Transcription Factors Reawaken Evolutionarily Dormant Fast-Glycolytic Type IIb Myofibers in Human Skeletal Muscle

first: Shunya

last: Sadaki

address: 1-1-1 Tennodai

department: Anatomy and embryology

institute: University of Tsukuba

summary: Small mammals, such as mice, rely on the rapid contraction of skeletal muscles to achieve swift movements. These capabilities are enabled by type IIb myofibers, which express the fastest myosin IIb in limb muscles, encoded by MYH4. In contrast, larger mammals, including humans, exhibit a marked reduction or complete absence of type IIb myofibers and MYH4 expression, favoring slower-contracting myofiber types. The evolutionary shift away from MYH4 expression in larger mammals and the underlying regulatory mechanisms remain poorly understood. Previously, we identified the large Maf transcription factor family (Mafa, Mafb, Maf) as principal regulators of type IIb myofiber determination in mice. Here, we provide the first evidence that the large MAFs specifically induces MYH4 expression in the skeletal muscles of large mammals, including humans and bovine. Furthermore, induction of MYH4 by large MAFs significantly enhances the glycolytic capacity of human myotubes, as evidenced by flux analyzer data and RNA-seq showing the upregulation of numerous genes associated with glucose metabolism. Lastly, RNA-seq analysis of human muscle biopsies reveals a positive correlation between MAFA, MAF, and MYH4 expression. Our findings propose that the large MAFs promotes the formation of the fastest type IIb myofibers in the skeletal muscles of large mammals. This discovery not only elucidates the mechanisms underlying the loss of type IIb myofibers in larger mammals but also holds potential implications for enhancing athletic performance and counteracting the loss of fast-twitch myofibers associated with aging.

overall_design: RNA-seq profiling of control cells and large MAFs overexpressing cells at Day6 of differentiation.

first: Ryo

last: Fujita


title: tRNA hydroxylation is an epitranscriptomic modulator of metabolic states affecting Pseudomonas aeruginosa pathogenicity

city: Braunschweig

first: Matthias

last: Preusse

address: Inhoffenstr. 7

institute: Helmholtz Centre for Infection Research

summary: Post-transcriptional modification of tRNAs represents an essential layer of translational regulation critical for bacterial adaptation to environmental changes. Increasing evidence links the tRNA epitranscriptome to pivotal roles in the regulation of gene expression and various cellular processes, including stress responses and the establishment of virulence phenotypes. In this study, we used mass-spectrometry and nanopore sequencing to systematically identify and quantify sites of TrhPO-dependent tRNA hydroxylation in total and purified tRNAs in the opportunistic human pathogen Pseudomonas aeruginosa. Furthermore, transcriptomic, ribosome profiling and proteomic data were integrated to demonstrate the post-transcriptional consequences of the absence of xo5U modifications at wobble positions in selected tRNAs. We show that changes in metabolic fluxes drive the impaired ability to infect host cells and strongly attenuated virulence in the Galleria mellonella model. In the absence of TrhPO-mediated tRNA modification, chorismate, the precursor for the biosynthesis of xo5U-modifications, is funneled into alternative pathways including the production of aromatic amino acids and phenazines. Our findings that metabolic rerouting rather than changes in proteome profiles attenuates P. aeruginosa virulence highlights the multifunctional roles of tRNA-modifying enzymes and suggests an underexplored role for these enzymes in monitoring and modulating metabolic fitness. These insights open new avenues for combatting the pathogenicity of this challenging opportunistic pathogen.

overall_design: Pseudomonas aeruginosa UCBPP-PA14 mutant strains were planktonically cultured in LB to an OD600 of 0.4 (ribo seq and RNA seq experiment).

first: Frommeyer

last: Yannick Noah

first: Trinler

last: Nicolas Oswaldo

first: Preusse

last: Matthias

first: Arce Rodriguez

last: Alejandro

first: Neubauer

last: Kerstin

first: Kennepohl

last: Benedikt

first: Witte

last: Julius

first: Bouheraoua

last: Safaa

first: Erdmann

last: Jelena

first: Muesken

last: Mathias

first: Pich

last: Andreas

first: Bähre

last: Heike

first: Depledge

last: Daniel Pearce

first: Haeussler

last: Susanne


title: scRNASeq Data of Tcells in psoriatic skin and healthy skin and TCR analysis of Treg sorted from Psoriatic skin

city: San Francisco

first: Victoire

last: Gouirand

state: CALIFORNIA

address: 513 Parnassus av

department: Dermatology

institute: UCSF

summary: Psoriasis (PSO) is an autoimmune inflammatory skin disease. To better understand alterations within the T cell compartment, we profiled T cells from PSO and healthy control skin via scRNASequencing and analyzed via TCRseq Treg profile expressing or not our target gene.

overall_design: scRNASeq of T cells sort-purified from enzymatically digested skin of biopsied psoriatic or of healthy control skin

first: Margeret

last: Lowe

first: Sean

last: Clancy

first: Michael

last: Rosenblum


title: Single cell RNAseq of FACS isolated embryonic enteroendocrine cells reveals regulators of neuroepithelial circuit formation

first: Kendall

last: Lough

state: North Carolina

address: 160 N Medical Drive

institute: University of North Carolina at Chapel Hill

summary: We have employed a single cell RNA sequencing approach using 10X genomics pipeline to evaluate the transcriptome of embryonic enteroendocrine cells (EECs) isolated from E15, E16, and E17 murine proximal intestine. Terminally differentiated EECs first arise at E15 and form new interactions with neural projectinos in the mucosa at E16 and E17. We evaluated the transcriptome of individual cells to identify regulators of neuronal interactions and communication during circuit formation.

overall_design: We enzymatically dissociated and pooled E15, E16, and E17 proximal intestines from Neurod1-Cre (Jax: 028364);ROSA-mTmG (Jax: 007676) embryos. GFP positive EECs were isolated via FACS and analyzed via scRNAseq.

first: Scott

last: Williams


title: Distinct transcriptomic and epigenomic responses of mature oligodendrocytes during disease progression in a mouse model of multiple sclerosis [RNA-seq]

city: Stockholm

first: Eneritz

last: Agirre

address: Solnavägen 9

department: MBB

country: Sweden

institute: Karolinska Institutet

summary: Multiple sclerosis (MS) is a chronic demyelinating autoimmune disease which targets mature oligodendrocytes (MOLs) and their myelin. MOLs are transcriptionally heterogeneous, and can transition to immune-like states in the context of MS. However, the intricacies of their dynamics throughout disease progression remain poorly understood. Here, we employed simultaneous single-cell multiome ATAC and RNA sequencing targeting oligodendroglia (OLGs) from the experimental autoimmune encephalomyelitis (EAE) MS mouse model, at different stages of the disease course. We found that the transition to immune OLGs states occurs already at early stages of EAE and these persist at late stages of the disease. Interestingly, transcription factor activity suggested immunosuppression activity in MOLs at early stages of EAE and  we also observed a transitory activation of a regenerative programme in MOLs at this stage. Importantly, different MOLs present a differential responsiveness to EAE, with MOL2 exhibiting stronger transcriptional immune response than MOL5/6. Moreover, we observed divergence responses at the epigenetic level of MOL2 and MOL5/6 during disease evolution. Thus, our single-cell multiomic resource highlights dynamic and distinct responses of OLG subpopulations to the evolving environment in EAE, which might modulate their response to regenerative therapeutic interventions in MS.

overall_design: Mice brains from P3-6 pups were dissociated using the Neural Tissue Dissociation Kit (Miltenyi Biotec, 130-092-628) according to the manufacturer’s protocol. OPCs were obtained with MACS with CD140a microbeads following the manufacturer’s protocol (CD140a Microbead kit, Miltenyi Biotec, 130-101-547). Cells were seeded in Poly-L-lysine (Sigma, P4707)-coated dishes and grown on OPC proliferation media comprising DMEM/F-12/GlutaMAX (ThermoFisher, 10565018), N2 media (ThermoFisher, 17502048), penicillin–streptomycin (ThermoFisher, 15140122), NeuroBrew (Miltenyi, 130-097-263), bFGF 40 ng/ml (R&D, 233-FB) and PDGF-AA 20 ng/ml (Peprotech, 315-17).

first: Chao

last: Zheng

first: Bastien

last: Hervé

first: Mandy

last: Meijer

first: Leslie

last: Ann Rubio Rodriguez-Kirby

first: André

last: Ortlieb Guerreiro Cacais

first: Petra

last: Kukanja

first: Mukund

last: Kabbe

first: Tomas

last: Olsson

first: Gonçalo

last: Castelo-Branco


title: Distinct transcriptomic and epigenomic responses of mature oligodendrocytes during disease progression in a mouse model of multiple sclerosis [ATAC-seq]


title: Predicting immune responsiveness in ER-positive breast cancer

city: Gothenburg

first: Axel

last: Stenmark Tullberg

address: Bla Straket

department: Department of Oncology

institute: University of Gothenburg

type: Methylation profiling by genome tiling array

summary: The immune system's role in estrogen receptor (ER)-positive breast cancer is poorly understood. A population-based cohort of 428 breast cancer patients with clinical and molecular data was analyzed to assess how immune biomarkers can inform treatment decisions. Tumor-intrinsic immune responsiveness and local immune infiltration were quantified, and epithelial cell states were derived using EcoTyper. The interaction between ProliferativeIndex and Immunescore predicted risk of local recurrence in ER-positive tumors (HR 0.56, 95% CI 0.36-0.88, p=0.012). EcoTyper identified two epithelial cell states, S04 and S05, with distinct immunomodulatory properties. S04 tumors showed higher proliferation, enrichment for M1 macrophages, CD8 effector T-cells, and plasma cells, alongside hypomethylation of immune-related pathways and hypermethylation of the PI3K signaling pathway. In contrast, S05-enriched tumors were associated with fibroblast activation, immune exclusion, and enrichment for glycosylation-related pathways. These findings suggest that epithelial cell states shape immune responsiveness in ER-positive breast cancer and may inform biomarker-driven treatment strategies.

overall_design: Methylation patterns in ER-positive tumors were analyzed to identify predictors of immune responsiveness

last: Tullberg


title: Targeting osteoblastic Mig6-EGFR signaling ameliorates osteoarthritis progression via inhibiting aberrant subchondral bone remodeling

status: Public on Jul 31 2025

city: Guangzhou

first: Rulong

last: Cai

state: Guangdong

address: No183 West Zhongshan Avenue, Tianhe District

department: Department of Joint Surgery

institute: The Third Affiliated Hospital of Southern Medical University

summary: Aberrant subchondral bone remodeling is a critical factor in osteoarthritis (OA) pathogenesis. We observed significant downregulation of Mitogen-induced gene-6 (Mig6) and upregulation of EGFR phosphorylation in subchondral bone osteoblasts, strongly correlating with OA severity in human and animal models. Mig6 is the most important factor mediating mechanical stress-activated EGFR, which inhibits osteogenic activity and modulates mechano-responsiveness. Osteoblast-specific Mig6 deletion exacerbated OA progression by promoting subchondral bone remodeling, whereas gefitinib-mediated inhibition of EGFR phosphorylation attenuated OA symptoms in mice, rats, and Mig6 knockout rats. Furthermore, loss of osteoblastic Mig6 disrupted the subchondral bone microenvironment, increasing inflammation, angiogenesis, and neuronal activity. Mechanistically, aberrant mechanical loading downregulated Mig6, activating phosphorylation of EGFR and the downstream JAK-STAT3 pathway, thereby promoting subchondral bone remodeling and accelerating OA progression. These findings reveal a novel mechanism by which osteoblastic Mig6 regulates subchondral bone remodeling in OA, highlighting Mig6 as a potential therapeutic target.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for osteoblasts and its OE derivatives (OEMig6)

first: Hang

last: Fang


title: RNAseq data from mouse skin Treg isolated after imiquimod treatment

first: Victoire

last: Gouirand

summary: Regulatory T cells (Tregs) are essential for maintaining immune tolerance in both lymphoid and  non-lymphoid tissues. We discovered that layilin, a C-type lectin receptor, is predominantly expressed on Tregs in skin.

overall_design: Mice were treated for 5 days with tamoxifen to induce Cre recombinase before the start of the treatment. On the last day of tamoxifen treatment, the back skin of the mice were shaved. Two days later,we started the imiquimod 5% cream (Taro) application for 4 consecutive days and harvest on day 5 for sort and bulk RNAseq

last: Rosenblum


title: Spatial transcriptional features of MYCN niche in liver tumorigenesis.

city: Yokohama

first: Xian-Yang

last: Qin

state: Kanagawa

address: 1-7-22 Suehiro, Tsurumi

institute: RIKEN Center for Integrative Medical Sciences

summary: Hepatocellular carcinoma (HCC) is a leading cause of cancer-related death, often diagnosed at advanced stages and characterized by high recurrence rates. While chronic liver inflammation and metabolic dysfunction are recognized contributors to tumorigenesis, the molecular mechanisms linking early microenvironmental stress to malignant transformation remain poorly understood. MYCN, a proto-oncogenic transcription factor, has emerged as a potential biomarker of cancer stemness, yet its functional role in hepatocarcinogenesis is unclear. Here, we elucidate the oncogenic role of MYCN and its dynamic regulation during metabolic liver tumorigenesis. Transcriptomic profiling revealed that MYCN-driven tumors exhibit features of human HCC subtypes enriched in stress-adaptive transcriptional programs. Time-resolved spatial transcriptomics further uncovered a MYCN-enriched niche characterized by epithelial–mesenchymal transition (EMT) and Wnt/β-catenin signaling, which expanded during tumor progression and was spatially proximate to transformed malignant cells.

overall_design: Spatial transcriptomics using the 10× Genomics Visium platform in a metabolic HCC mouse model STAM (STAM16w, STAM20w), which mimics MASH and type I diabetes, and in a fibrotic HCC mouse model DEN+CCL4 (DEN22w, DEN30w), which mimics DNA damage–driven and fibrosis-promoting tumor evolution.


title: Atheroprotective immunity and interleukin-10 linked to reduced plaque stability and recurrent cardiovascular events

first: Anton

last: Gisterå

address: Bioclinicum J8:20, Visionsgatan 4, Karolinska University Hospital, Solna

department: Medicine Solna

summary: Atherosclerotic cardiovascular disease remains a major cause of death worldwide. Autoimmunity to low-density lipoprotein (LDL) has been implicated in the disease process and immunization with LDL components proposed as a preventive strategy. However, mechanisms of atheroprotective immunity remain insufficiently characterized. Two different T cell receptor transgenic mouse strains with T cells reactive against the LDL protein, apoB100 (BT1 and BT3) were crossbred with human APOB100-transgenic Ldlr-/- (HuBL) mice, and atherosclerosis was evaluated. In 52-week-old BT1xHuBL mice, a lower atherosclerotic burden was observed in the aorta, mirrored by reduced plasma cholesterol and elevated anti-apoB100 antibodies. BT3xHuBL mice also exhibited a decrease in aortic atherosclerosis; however, no reduction in plasma cholesterol levels was noted. Instead, type 1 regulatory T cell responses with interleukin (IL)-10 production were mounted. This response was associated with reduced collagen content and a lower stability index of the atherosclerotic lesions. In human carotid artery plaques, IL10 mRNA levels were negatively correlated with collagen expression, and IL-10 was found to inhibit collagen production in vascular smooth muscle cells. We conclude that atheroprotective apoB immunity elicits two distinct pathways: lipid-lowering immune reactions and local anti-inflammatory IL-10 production. Since the latter is associated with decreased plaque stability and cardiovascular events, treatments aimed at increasing IL-10 signaling over extended periods to reduce vascular inflammation need reconsideration.

overall_design: RNA-seq profiling of the aorta and liver from HuBL and BT3xHuBL mice after 52 weeks on a normal laboratory diet.


title: Nucleosome placement and polymer mechanics explain genomic contacts on 100kbp scales

city: Irvine

first: Jiachun

last: Li

state: CA

address: Samueli School of Engineering University of California, Irvine

institute: University of California Irvine

summary: The 3d organization of the genome — in particular, which two regions of DNA are in contact with each other — plays a role in regulating gene expression. Several factors influence genome 3d organization. Nucleosomes (where ∼ 100 basepairs of DNA wrap around histone proteins) also bend, twist and compactify chromosomal DNA, altering its polymer mechanics. How much does the positioning of nucleosomes between gene loci influence contacts between those gene loci? And, to what extent is polymer mechanics responsible for this? To address this question, we combine a stochastic polymer mechanics model of chromosomal DNA including twists and wrapping induced by nucleosomes with two data-driven pipelines. The first estimates nucleosome positioning from ATACseq data in regions of high accessibility. Most of the genome is low-accessibility, so we combine this with a novel image analysis method that estimates the distribution of nucleosome spacing from electron microscopy data. There are no free parameters in the biophysical model. We apply this method to IL6, IL15, CXCL9, and CXCL10, inflammatory marker genes in macrophages, before and after immune stimulation, and compare the predictions with contacts measured by conformation capture experiments (4C-seq). We find that within a 500 kilo-basepairs genomic region, polymer mechanics with nucleosomes can explain 71% of close contacts. These results suggest that, while genome contacts on 100kbp-scales are multifactorial, they may be amenable to mechanistic, physical explanation. Our work also highlights the role of nucleosomes, not just at the loci of interest, but between them, and not just the total number of nucleosomes, but their specific placement. The method generalizes to other genes, and can be used to address whether a contact is under active regulation by the cell (e.g., a macrophage during inflammatory stimulation). Importantly, our findings suggest that gene function may have evolved through selective pressures that co-opted contact-mediated regulatory mechanisms reliant largely on polymer mechanics.

overall_design: 4C-seq of IL6, IL15, CXCL9, and CXCL10 was performed on macrophages before and after immune stimulation

first: John

last: Corrette

first: Hanjuan

last: Shao

first: Praveen

middle: K

last: Veerasubramanian

first: Andrew

last: Spakowitz

first: Timothy

middle: L

last: Downing

first: Jun

last: Allard


title: RNAseq data from expanded human Treg isolated from healthy blood donor and crispr for target candidate or scramble

overall_design: After expansion of human Treg for 12 days, cells have been electroporated using SNP protocol, after 4 days cells were sorted based on layilin expression and put back in culture for 24h before being processed for bulk RNAseq

first: Michael


title: Ferroptosis Mediated by the IDO1/Kyn/AhR Pathway Triggers Acute Thymic Involution in Sepsis

first: Zimei

last: Cheng

state: None Selected

address: 399 Wanyuan Rd, Minhang

institute: Children's Hospital, Fudan University

summary: Sepsis triggers a systemic inflammatory response that leads to immune dysregulation and widespread organ damage. Acute thymic involution (ATI), a hallmark of sepsis, is characterized by decreased T cell production and weakened immune responses. The mechanism of ATI is not fully understood. In this study, we demonstrate that ferroptosis, an iron-dependent form of regulated cell death, plays a pivotal role in ATI during sepsis. Using a polymicrobial sepsis model, we observed significant ferroptosis-associated thymic damage, which was marked by lipid peroxidation, mitochondrial dysfunction, and a reduction in thymic size and cellularity. Treatment with 1-methyltryptophan (1-MT), an inhibitor of indoleamine 2,3-dioxygenase 1 (IDO1), effectively reversed these phenotypes, restoring thymic structure and function, and significantly improved survival outcomes in septic mice. Further mechanistic analysis revealed that IDO1 upregulation led to the accumulation of kynurenine, which activates the aryl hydrocarbon receptor (AhR), thereby driving ferroptosis in thymocytes. Our findings uncover a novel role for the IDO1/Kyn/AhR pathway in ferroptosis and suggest that targeting this pathway could be a promising therapeutic strategy for restoring thymic function and improving outcomes in sepsis.

overall_design: To investigate the role of ferroptosis in sepsis-induced acute thymic involution (ATI), we established a polymicrobial sepsis model using cecal ligation and puncture (CLP). Thymocytes from sham and CLP-treated mice were collected and analyzed to determine ferroptosis markers and related pathways.


city: urumqi

first: tuerjun

last: tuohuti

state: xinjiang

address: People′s Hospital of Xinjiang Uygur Autonomous Region

summary: Transcriptional and post-transcriptional regulation that are mediated by RNA binding proteins (RBPs) have essential influence on the development and progression of colorectal cancer (CRC), while the underlying mechanisms need to be clarified. In this study, we focused on RNA Binding Motif Protein 47 (RBM47) and overexpressed its expression in HCT116 cells to evaluate its influence on cellular phenotypes and performed transcriptome sequencing (RNA-seq) to identify the downstream targets, including the expression and splicing changed genes. After RBM47 overexpression (RBM47-OE), we found the proliferation level was decreased while apoptosis level was increased. Meanwhile, the invasion and migration ability of HCT116 was also significantly inhibited by RBM47-OE. To further decipher the molecular targets of RBM47, we identified 216 up and 97 down differentially expressed genes (DEGs) by RBM47-OE, and found they were significantly enriched in immune response, apoptosis, TNF signaling, and autophagy pathways. At the same time, RBM47-OE can also regulate the splicing pattern of 2541 alternative splicing (AS) events. The regulated AS genes (RASGs) were enriched in cell cycle, DNA damage and repair, mRNA splicing, and cell division associated pathways, indicating that the downstream targets of RBM47 were tightly associated its cellular functions. To validate the regulation on gene expression and AS, we selected several DEGs and AS events to perform RT-qPCR experiment. The results showed that the expression level of CASP3, CCN1, and ATF5, and the splicing pattern of CD44 and MDM2, were significantly regulated by RBM47-OE in HCT116 cells. In summary, our results demonstrated the anti-tumor function and the globally downstream targets of RBM47 in CRC cells. We extend the cellular and molecular cognition of RBM47 in tumor. The identified molecular targets can also be served as potential targets for CRC treatment in future.

overall_design: To investigate the RBM47 functions as an anti-oncogene by regulating expression and alternative splicing of cell proliferation and apoptosis associated genes in colorectal cancer cells, we performed RNA-seq analysis for overexpression of RBM47 in HCT116 cells.

first: Guangshi

last: Liu

first: Peng

last: LI

first: Suyan

last: Wei

first: Kamuran

last: Abulizi

first: Tao


title: Ablation of Hepatic CPT1a Lowers Plasma Cholesterol Levels.

city: Lexington

first: Robert

middle: N

last: Helsley

state: KY

address: 741 S. Limestone St.

department: Intern

institute: University of Kentucky

summary: To investigate the impact of liver-specific deletion of Cpt1a on lipoprotein metabolism in human ApoB100 transgenic mice.

overall_design: We performed bulk RNA-sequencing on livers from WD-fed B100 control and B100 LKO male and female mice who were necropsied in the fed state.

first: Graf

last: Gregory

first: Helsley

last: Robert


title: CAMKK2 promotes prostate cancer progression through an alternative pathway involving CAMKI-CREB-mediated cholesterol metabolism

city: Houston

first: Daniel

last: Frigo

state: TX

address: 1515 HOLCOMBE BLVD

institute: MD Anderson Cancer

summary: Castration-resistant prostate cancer (CRPC) remains an incurable disease driven predominantly by aberrant androgen receptor AR signaling, suggesting that processes downstream of AR represent viable alternative targets for the treatment of CRPC. CAMKK2 (encoding calcium/calmodulin-dependent protein kinase kinase 2) is a direct AR target that is highly expressed during prostate cancer progression, a functional driver of the disease and hence, emerging therapeutic target. To date, CAMKK2’s oncogenic effects in prostate cancer have been attributed to its activation of AMP-activated protein kinase (AMPK), but recent reports suggest that CAMKK2 may also facilitate tumorigenesis through AMPK-independent mechanisms. Here, we demonstrate that AR-mediated CAMKK2 signaling promotes prostate cancer growth through an alternative downstream pathway involving calcium/calmodulin-dependent protein kinase I (CAMKI) and cAMP response element-binding protein (CREB). Unbiased transcriptomics identified CREB-mediated transcription as a CAMKK2-regulated process, findings that were validated using diverse molecular, genetic and pharmacological approaches in vitro and in vivo. CAMKK2 promoted CREB serine-133 phosphorylation and activation through CAMKIa independently of AMPK, CAMKIV or other CAMKI isoforms. Functionally, CREB activity was required for maximal CRPC growth. The CREB family members CREB1 and ATF1 exhibited close redundancy, necessitating co-targeting for optimal anti-tumor efficacy. Pharmacologically, a small molecule inhibitor of CREB1/ATF1, 666-15, blocked CRPC growth with minimal side effects in vitro and in vivo including in patient-derived xenograft models of enzalutamide resistance. Mechanistically, CAMKK2-mediated CREB increased prostate cancer growth through augmenting cholesterol metabolism. Together, these findings identified a novel oncogenic pathway in prostate cancer that could be exploited for the treatment of CRPC.

overall_design: RNA-seq to understand the role of CAMKK2-CREB axis in castration resistant prostate cancer

first: Chenchu

last: Lin


title: Identification of EPLIN as a novel MYCN-independent target in neuroblastoma and medulloblastoma

city: uppsala

first: Xiaonan

last: Zhang

state: Sweden

address: Dag Hammarskjölds väg 20

department: Department of Immunology, Genetics and Pathology

institute: uppsala university

summary: Neuroblastoma and medulloblastoma are the most common solid tumors in children, with MYC(N) proto-oncogene amplification serving as a key marker of aggressive disease and poor treatment outcomes. However, the complex nature of the challenging MYC(N) protein underscores the urgent need for additional targets and therapies to tackle neuroblastoma and medulloblastoma. In this study, we identified FLIX5, a small compound that exhibits broad toxicity against both neuroblastoma and medulloblastoma cells by inducing apoptosis and ferroptosis. Furthermore, FLIX5 enhances the cholesterol dependency of neuroblastoma cells under conditions where mitochondrial function is impaired. FLIX5 as well synergistically enhances the effectiveness of conventional drugs vincristine and vinorelbine against neuroblastoma cells and patient-derived xenograft organoids. Through proteome integral solubility alteration, computational molecular docking predictions, and cellular thermal shift assays for target identification and validation, FLIX5 revealed EPLIN (Epithelial Protein Lost In Neoplasm) as a previously unexplored drug target. EPLIN functions as a tumor suppressor and plays roles in various cellular processes, including cholesterol uptake and mitochondrial activity. The discovery of FLIX5 targeting EPLIN opens new avenues for addressing the significant challenges posed by neuroblastoma and medulloblastoma, and potentially offering broader applications in other types of cancer.

overall_design: Neuroblastoma cell line was obtained from (ATCC, Manassas, VA, USA). Neuroblastoma cell line was maintained in 1:1 ratio of EMEM (ATCC, Cat. #30-2003) and Ham’s F-12 Nutrient Mix (Thermo Fisher Scientific, Waltham, MA, USA, Cat. #11765054) supplemented with 1% penicillin streptomycin (Thermo Fisher Scientific, Cat. # 15140-122) and 10% FBS (Thermo Fisher Scientific, Cat. #10270-106). U87MG and Daoy was maintained in EMEM supplemented with 1% penicillin streptomycin and 10% FBS. HDFa and D283 was maintained in DMEM + Glutmax (Thermo Fisher Scientific, Cat. # 61965026) supplemented with 1% penicillin streptomycin and 10% FBS. GMYC126, GTML-S1, GTML2 and GTML3 were maintained in Neurobasal – A medium (Thermo fisher scientific, Cat. #10888022) supplemented with B27-A (Thermo Fisher Scientific, Cat. #12587010),1% penicillin streptomycin1, 1% L-glutamine (100x) (Thermo fisher Scientific, Cat. #25030081), 20ng/mL bFGF (Thermo Fisher Scientific, Cat. # 100-18B), 20ng/ml EGF (Sigma Aldrich, Cat. #E9644). All cells were maintained at 37°C and 5% CO2. All cell lines were authenticated by STR profiling (ATCC cell authentication service) and the MycoAlert mycoplasma detection kit (Lonza) was used to frequently test for mycoplasma infection. Spheroids was generated by plating 10,000 cells/well in 100µL medium in 96-well ultra-low attachment plates (Corning, NY, USA, Cat. #7007). Cells were settled in the wells for 20min followed by centrifugation at 1000RPM for 5min and cultured in 37°C in 5% CO2. Spheroids were cultured for 4 days before drug exposure and images was taken by Incucyte followed by calculation of the spheroids volume by: V =(4/3*π) *r3

first: Emma

last: Lindell


title: Longitudinal transcriptomic and epigenetic analysis in astronauts reveals dynamic immune response to spaceflight [RNA-seq]

city: Montreal

first: Luda

last: Diatchenko

state: Quebec

address: 3775 Rue University

country: Canada

institute: McGill University

summary: The space industry has made significant strides in recent years, leading to an era of commercial spaceflight. Meanwhile, understanding the molecular responses to spaceflight becomes crucial for astronaut safety in harsh space conditions. To this end, we conducted a study to examine the transcriptomic and epigenetic changes in two astronauts' blood samples at three timepoints: two weeks before spaceflight (T0), 24 hours after spaceflight (T2), and three months after spaceflight (T3). Transcriptomic analysis pinpointed two gene clusters with opposing transient expression trends post-flight (T2) which was normalized at T3: one upregulated and the other downregulated. Pathway analysis of these gene clusters showed enrichment in the protein modification, cell cycle, and regulation of autophagy pathways, suggesting autophagy’s role in monocyte differentiation. Epigenetic analysis identified four methylation patterns that showed transient and persistent changes immediately after the spaceflight, enriched in the nervous system development and cell apoptosis pathways. Methylation changes at specific regions implicated genes associated with bone disorders, including FBLIM1, IHH, and SCAMP2. Further, eQTM analysis suggested a link between RNA transcriptional activity and DNA methylation through a transcriptional regulator ZNF684. In conclusion, our longitudinal study offers a detailed perspective of spaceflight’s physiological effects on human biology, revealing both significant short-term transcriptional and methylation and profound long-term methylation impacts on bodily functions.

overall_design: Samples for this study were collected at three timepoints: T0 = within two weeks before the flight (Pre-Flight), T2= within two weeks after the flight (Post-Landing), and T3= 3 months after the flight (3 months follow up).

first: Xiang

last: Ao

first: Marc

last: Parisien

first: Pablo

last: Ingelmo


title: Longitudinal transcriptomic and epigenetic analysis in astronauts reveals dynamic immune response to spaceflight

type: Methylation profiling by high throughput sequencing


title: Rapamycin-Gliadin Composite Nanoparticles Enhance Hepato-Splenic Dialogue for Gluten Tolerance in Celiac Disease

city: Nanjing

first: Xiaohan

last: Jiang

state: Jiangsu

address: No. 300 guangzhou road, nanjing city, China

institute: Department of digestive endoscopy

summary: Background Celiac disease (CeD) is an autoimmune disorder triggered by gluten, with gliadin as the primary antigen. Therapies targeting gliadin to induce antigen-specific immune tolerance are of significant interest. This study investigates the therapeutic potential of a novel rapamycin-gliadin composite nanoparticle (PLN-GR) in enhancing Kupffer cell-mediated hepato-splenic dialogue to promote gluten tolerance in CeD. Methods Rapamycin-gliadin composite nanoparticles were synthesized using a precipitation self-assembly method and characterized for size, zeta potential, and cellular uptake. A CeD delayed-type hypersensitivity (DTH) mouse model was employed to evaluate the immunomodulatory effects of PLN-GR. Cellular biodistribution, immune phenotyping, and metabolic assessments were conducted to elucidate the nanoparticles' mechanism of action. Results Rapamycin-gliadin composite nanoparticles effectively targeted the liver and were internalized by Kupffer cells, inducing a tolerogenic phenotype. In vivo treatment with PLN-GR ameliorated systemic and intestinal inflammation in the CeD DTH mouse model, evidenced by reduced paw swelling and intestinal histopathology. The nanoparticles induced a metabolic shift from glycolysis to oxidative phosphorylation in macrophages, associated with increased itaconate production. This metabolic reprogramming was linked to an increase in PD-L1+ tolerogenic dendritic cells and a decrease in Th1 cell counts in the spleen. Conclusion The study demonstrates that rapamycin-gliadin nanoparticles can induce antigen-specific tolerance in CeD by modulating hepatic and splenic immune responses. The findings suggest a potential therapeutic strategy for CeD by enhancing immunometabolic reprogramming and inter-organ communication.

overall_design: To elucidate the ameliorative effects of rapamycin-gliadin composite nanoparticles on intestinal inflammation post-treatment in a celiac disease DTH mouse model, RNA sequencing (RNA-seq) was performed on the duodenal tissue of mice from the control group, celiac disease (CeD) group and those treated with PLN-GR. This assessment aimed to evaluate the alterations at the transcription factor level.

first: Ruihan

last: Zou

first: Zhining

last: Fan

first: Lili

last: Zhao


title: Ablation of Hepatic CPT1a Lowers Plasma Cholesterol Levels

summary: To investigate the impact of liver-specific deletion of Cpt1a on lipoprotein metabolism.

overall_design: We performed bulk RNA-sequencing on livers from HFD-fed WT and Cpt1a LKO male mice who were necropsied in the fasted state (16h) or refed state (16h fast/6h refeed).

first: Gregory

last: Graf


title: Non-disruptive 3D Profiling of Combinations of Epigenetic Marks in Single Cells

city: New Haven

first: Myles

last: Alderman III

state: Ct

address: 10 Amistad St

department: Cell Biology

institute: Yale University School of Medicine

summary: Recent advancements in single-cell sequencing and spatial omics technologies have enhanced our understanding of diverse cellular identities, compositions, and functions. However, the single-cell three-dimensional (3D) organization of the epigenome is still not well understood, due to an absence of spatial single-cell methods that allow high-resolution, locus-specific detection of combinations of epigenetic marks while maintaining the 3D organization of the genome. Here, we develop Epigenetic Proximity Hybridization Reaction (Epi-PHR), an image-based single-cell spatial epigenetic profiling technique. Epi-PHR enables high-sensitivity and high-resolution in situ detection of combinations of epigenetic marks at hundreds of single gene targets within the same individual cells, while retaining the 3D organization of the genome, a clear advantage over previous technologies.  Phased Epi-PHR combined with chromatin tracing simultaneously detects allele-specific epigenetic states and chromatin conformations of an imprinting gene cluster in single cells, revealing associations between specific epigenetic mark enrichment and chromatin folding features for the distinct alleles from different parental origins. We expect Epi-PHR to be broadly applicable in research requiring single-cell spatial epigenetic information, and to help understand the combinatorial code of epigenetic marks and its relationship with chromatin folding in diverse biological and medical contexts.

overall_design: To interrogate the epigenetic state of imprinted loci, we cultured F1 Hybrid C57/CAST Trophoblast Stem Cells (TSCs). We then performed RNA-seq in triplicate to quantify allelic frequency of expressed genes. We then investigated whether H3K9me3 was deposited on paternal or maternal strands differentially using CUT&RUN.

first: Yanbo

last: Chen

first: Jonthan

last: Radda

last: Alderman

first: Shengyan

last: Jin

first: Yubao

last: Cheng

first: Miao

last: Liu

first: Andrew

middle: Z

last: Xiao

first: Siyuan

last: Wang


title: Genetic diversity in mouse models unlocks the gut-lung axis in Cystic Fibrosis

city: Milano

first: Luca

last: Massimino

state: MI

address: Via Olgettina, 58

department: Gastroenterology

institute: Ospedale San Raffaele

summary: Despite Cystic Fibrosis Transmembrane conductance Regulator (CFTR) being identified as the gene responsible for cystic fibrosis (CF), there are multiple CF-causing genetic variants affecting phenotypes in people with CF (pwCF). Animal models generated so far have introduced various mutations in the Cftr gene, but none replicate the genetic diversity found in humans. Yet, CF mice exhibit variable degrees of extra-pulmonary phenotypes, lacking the lung dysfunction and susceptibility to infection that are primary manifestations in humans, thus limiting pathogenic studies. We opted for Collaborative Cross (CC) mice, a genetically diverse animal resource population, to identify a suitable genetic background for CF. Here, we show that ΔF508-Cftr homozygosity in CC037 mice produced a fully penetrant lethal phenotype within two months of age. Early in life, in the absence of mucus production, inflammatory and immune responses arise in the lungs and blood. The CF murine lung exhibits an activated immunoinflammatory and defense response to bacterial pathogens, sharing microbiology with the gut. Intestinal mucosal function shows impaired barrier integrity, provides an environmental niche for bacterial accumulation and triggers inflammation. Treating gut pathology protected CF mice from respiratory and systemic inflammation, establishing the groundwork for inter-organ communication, likely via the gut-lung axis. In sum, we report the first mouse model that reproduces human CF and provides a paradigm for mouse modeling relevant to multiple other genetic disorders. The significance of our findings is fundamental for CF, supporting the role of the gut in lung pathology and suggesting new diagnostic and therapeutic interventions beyond lung-related treatments.

overall_design:
4x Colon WT, 4x Colon HO, 5x Lung WT, 3x Lung HO
WT: Collaborative Cross with wt-Cftr
HO: Collaborative Cross with F508-Cftr mutation

first: Alessandra

last: Bragnozi

first: Federica

last: Ungaro


title: The mTORC1-TFE3-NuRD axis mediates pluripotent stem cells fate transition

first: shuhui

last: xu

address: 190 Kaiyuan Avenue, Huangpu District

institute: Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences

summary: Pluripotent stem cells (PSCs), which include embryonic stem cells (ESCs) derived from embryos and induced pluripotent stem cells (iPSCs) reprogrammed from somatic cells, possess significant application potential due to their ability to indefinitely self-renew while maintaining pluripotency. However, many aspects of PSC fate transitions remain poorly understood. Hyperactivation of mechanistic target of rapamycin complex 1 (mTORC1) by deficiency of its upstream repressors TSC1/2 is known to impede both pluripotency re-establishment and exit. Yet, the detailed mechanism by which mTORC1 regulates transcription critical for these transitions, and whether similar mechanisms underlie both processes, remains unclear. In this study, we demonstrate that mTORC1 induces the nuclear translocation of transcription factor TFE3, which binds to the nucleosome remodeling and deacetylation complex NuRD. This interaction leads to the repression of specific target genes crucial for pluripotency re-establishment and exit. Our findings highlight that the mTORC1-TFE3-NuRD axis acts as a transcriptional repressor in PSC fate transitions through regulation of chromatin remodeling modifications. These findings contribute to a better understanding of how mTORC1 governs the intricate regulation of PSC fate transitions, which is relevant to diverse fields including development, metabolic diseases, cancer, and aging.

overall_design: We conducted experiments to identify the binding sites of TFE3 and HDAC2 during the early (Day 5) and late (Day 10) stages of reprogramming from MEFs to iPSCs. Using TFE3 and HDAC2 antibodies, we performed CUT&Tag in Tsc1 WT and Tsc1 KO cell lines at these stages to pinpoint where these factors bind.

first: Peizhi

last: Li

first: Xueting

last: Xu

first: BaoMing

last: Qin

first: Shuhui


title: The gene expression of the zinc finger protein transcription factor  zmzfp69 mutant of the maize inbred line and the control B73 under low-temperature stress at the seedling stage

city: Harbin

first: Sinan

state: Heilongjaing

address: No.368 Xuefu Road

institute: Maize Research Institute, Heilongjiang Academy of Agricultural Sciences

summary: C2H2 type (ZFP type) zinc finger protein can significantly enhance the cold tolerance of plants by directly regulating the downstream cold-related genes of plants. We confirmed through phenotypic and physiological experiments that the zmzfp69 mutant material has a stronger low-temperature resistance compared with the control B73. Therefore, we selected the mutant material (zmzfp69) and the control material (CK), and conducted low-temperature treatment at 4 ° C during the three-leaf stage. The sampling time was 0/24h/48h, and transcriptome sequencing was repeated three times for each sample to provide data for finding the mechanism of low-temperature stress at the maize seedling stage.

overall_design: RNA-seq analysis of the zmzfp69 mutant and control B73 under low-temperature stress at 0h, 24h, and 48h during the seedling stage

first: Minghao

last: Sun

first: Xin

first: Yunlong

first: Yan

first: Jianguo

last: Zhang


title: Humanoid robot upregulates cellular stress pathways in tendon tissue engineering

city: Oxford

first: Jinrong

last: Lin

state: Oxfordshire

address: 22 Windmill Road, 22 Windmill Road, Headington

country: United Kingdom

institute: University of Oxford

summary: Mechanical stimulation is essential in tissue engineering and regenerative medicine for proper tissue maturation. However, conventional dynamic stimulation is typically achieved with uniaxial platforms, which limit functionality due to the oversimplified mechanics compared to the complex mechanical inputs of the human body. In this study, we explore human cell responses to stimulation using a humanoid robot shoulder and a uniaxial platform at equivalent strains. A flexible, biocompatible sensor monitoring in situ strains shows that external maximum forces of 25 N and 50 N during robot abduction-adduction motions lead to strains of approximately 3.5% and 9.5%, respectively. Additionally, we demonstrate in situ cell imaging by utilizing the transparency of the bioreactor membrane. The robot motions significantly enhance cell orientation and induce notable changes in gene and protein expression, particularly within the PI3K-Akt signaling pathway, compared to both static and uniaxial stimulation controls. These findings underscore the need to better match human biomechanics in bioreactor platforms to improve tissue engineering outcomes.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for Green fluorescent protein (GFP)-modified human MSCshTERT) of cell responses to the different stimulation platforms and different loading regime.

first: Pierre-Alexis

last: Mouthuy


title: Allergen induces pulmonary neuroendocrine hyperplasia in asthma

city: La Jolla

address: 9500 Gilman Dr

department: Biological Sciences

institute: University of California, San Diego

summary: Asthma is characterized by exacerbated responses to environmental triggers such as allergen. While pulmonary neuroendocrine cells (PNECs), a rare population of airway epithelial cells, are essential for amplifying allergen-induced asthma response, how they are regulated to achieve this role remains poorly understood. Here we show that in the adult mouse airway, inactivation of achaete-scute like 1 (Ascl1) gene in PNECs led to loss of these cells. Intriguingly, exposure of these mutants to house dust mites (HDM), a common allergen, led to reappearance of PNECs. Similarly, exposure of wild-type mice to HDM led to PNEC hyperplasia, a result of proliferation of existing PNECs and transdifferentiation from club cells. Single cell RNAseq experiments revealed PNEC heterogeneity, including the appearance of an allergen-induced PNEC subtype. Intracellular Notch1 is downregulated in HDM-treated airway, and treatment by Notch agonist prevented PNEC hyperplasia. These findings together suggest that HDM-induced PNEC hyperplasia may contribute to exacerbated asthma response.

overall_design: Single cell RNA-seq from purified adult airway epithelial cells, enriched with Ascl1-lineaged cells, of saline and HDM-challenged lungs

first: Estelle

last: Kim

first: Hannah

last: Indralingam

first: Jamie

last: Verheyden


title: Next generation mRNA and miRNA sequencing data sets from young and adult female and male healthy cats, and female and male adult cats with hypertrophic cardiomyopathy (HCM).

city: Guelph

first: Sonja

last: Fonfara

state: Ontario

address: 36 College Ave W

department: Clinical Studies

institute: University of Guelph

summary: Next generation sequencing for the feline transcriptome (mRNA and microRNA profiles) was carried out using myocardial samples from female and male young healthy cats, adult healthy cats, and cats with hypertrophic cardiomyopathy.

overall_design: The study comprises of myocardial samples from young healthy male cats, adult healthy male cats, young healthy female cats, adult healthy female cats, and female and male cats with hypertrophic cardiomyopathy (HCM). The young healthy cats were control cats from a research cat colony, their hearts were donated for the current study. The healthy adult cats were pet cats that were euthanised for reasons not related to the study. Cats with HCM were pet cats with progressed disease that were euthanased on owners request because of poor prognosis. All cats underwent postmortem examination carried out by a specialist in veterinary pathology to confirm HCM and exclude systemic diseases in cats with HCM, and to exclude cardiac and systemic diseases in cats categorized as healthy. The young healthy cats were 1.5 years old, the adult healthy cats ranged in age between 2 and 12 years, and the cats with HCM range in age between 2 and 15 years. The objective of the study was to investigate the influence of age, sex and HCM on the feline myocardial transcriptome and miRNA profiles. The tissue samples were sequenced using RNA seq technology for mRNA and small RNA seq for miRNA profiling.

first: Verma

last: Ritu

first: Allan

last: Megan

first: Joshua

last: Jessica


title: Investigating the Impact of Genetic MSN Depletion on Gene Expression in MDA-MB-231 Breast Cancer Cells

city: Jongno-gu

first: chenghyun

last: LEE

state: seoul

address: 71, Daehak-ro

country: South Korea

institute: seoul national university

summary: Cellular differentiation is a tightly regulated process, relying on the precise interplay between lineage-specific transcription factors and epigenetic modifications to both initiate and sustain distinct cell fates. Here, we report Moesin as a key regulator of tumor growth and metastasis in the MDA-MB-231 breast cancer cell line. MSN, a linker between the actin cytoskeleton and the plasma membrane, regulates cell morphology and motility. Our results demonstrate that MSN depletion impairs microtubule cytoskeleton organization and microtubule polymerization. Furthermore, we observed elevated MSN levels in Triple-Negative Breast Cancer cells, which exhibit aggressive growth characteristics.  Taken together, our data reveal a crucial role for MSN in mediating tumor growth and metastasis, thereby contributing to the aggressiveness of breast cancer.

overall_design:
To investigate the cooperative function MSN in the regulation of tumor growth and metastasis. We established MDA-MB-231 cell lines in MSN target gene has been knocked down by shRNA.
we then performed gene expression profiling analysis using data obtained from RNA-seq for 2 different cells at three time points.
Comparative gene expression profiling analysis of RNA-seq data obtained for MDA-MB-231 cells and its KD derivatives (shMSN)

first: ChengHyun

last: Lee


title: Investigating the Impact of adriamycin resistance on Gene Expression in MDA-MB-231 Breast Cancer Cells

summary: Cellular mechanisms driving aggressive phenotypes in drug-resistant cancer cells remain to be fully elucidated. This study investigated the differences between MDA-MB-231 adriamycin-resistant cells and their parental counterparts, focusing on cell death, motility, proliferation, and key signaling pathways. Compared to parental cells, the resistant cells exhibited significantly increased cell death resistance, enhanced motility and proliferation, and upregulated NF-κB and STAT3 signaling. These findings suggest that heightened survival mechanisms, increased migratory and proliferative capacity, and dysregulated signaling pathways contribute to the aggressive behavior of adriamycin-resistant MDA-MB-231 cells.

overall_design:
To investigate the cooperative function ADR resistance in the regulation of cell death and pathway. We established MDA-MB-231 cell lines in ADR resistance.
we then performed gene expression profiling analysis using data obtained from RNA-seq for 2 different cells at three time points.
Comparative gene expression profiling analysis of RNA-seq data obtained for MDA-MB-231 cells and its ADR resistance cell line

first: Sooyoung

last: park


title: Cytotoxic CX3CR1+ Vδ1 T cells clonally expand in an interplay of CMV, microbiota, and HIV-1 persistence in people on antiretroviral therapy

city: Toulouse

first: Pierre

last: Delobel

address: CHU Purpan – BP 3028

country: France

institute: Infinity

summary: We performed a comprehensive characterization of Vδ1 T cells in blood of people with HIV-1 on antiretroviral therapy and HIV-seronegative controls, in a substudy of the ANRS EP61 GALT study (NCT02906137). We deciphered the single-cell transcriptome of Vδ1 cells. Vδ1 T cells were mainly terminally differentiated effectors that expanded in the blood with some trafficking with the gut of people with HIV-1. Most expressed CX3CR1 and displayed a highly cytotoxic profile, but low cytokine production, supported by a transcriptomic shift towards enhanced effector lymphocytes. The increase in Vδ1 T cells observed in people with HIV-1 has multiple triggers, particularly CMV and microbiota, and may in turn contribute to the control of the HIV-1 reservoir.

overall_design:
For Vδ1 single-cell RNA sequencing, Vδ1 T cells were sorted after a stainingn step with TotalSeq-B anti-human hashtags (LNH-94; 2M2/BioLegend) directed against CD298 and β2-microglobulin. Sorted Vδ1 T cells were stored on ice and immediately processed for single-cell library generation. Vδ1 cells were sorted from PBMC of 6 PLWH and 6 controls, all CMV seropositive. Single-cell libraries were generated using the Chromium iX Single-Cell Instrument and Chromium Next GEM Single Cell 3′ Kit v3.1, Chip G Single Cell kit, Dual Index kit TT Set A and NT set A, and 3’ Feature Barcode kit (10x Genomics). Sequencing was then performed on a full SP flow cell 100 cycles (2 lanes) on the Illumina NovaSeq 6000 instrument (Illumina, San Diego, USA).

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

last: Collercandy

first: C

last: Vellas

first: M

last: Requena

last: Zahm

first: P


title: A high-temporal-resolution single-cell transcriptomic atlas of pre- to post-implantation transition in mouse embryogenesis

city: Pasadena

first: Magdalena

last: Zernicka Goetz

state: CALIFORNIA

address: CALIFORNIA INSTITUTE OF TECHNOLOGY

institute: California Institute of Technolog

summary: Embryo implantation is a pivotal phase in early mammalian embryonic development. However, the mechanisms guiding the embryos from pre- to post-implantation remain largely elusive. Here, we present a comprehensive transcriptomics atlas of mouse embryo implantation, characterized with high temporal resolution.  We collected mouse embryos at distinct stages— before, during, and after implantation— and performed single-cell RNA sequencing. Our analysis of 22,171 single-cell transcriptomes elucidates the developmental trajectories encompassing the entire implantation process.

overall_design: we collected mouse embryos from pre-to post-implantation stages at E3.5, E4.5, E4.75, E5.0, E5.25, and E5.5 for single-cell RNA sequencing (scRNAseq) with the 10x genomics protocol.

first: Dong-Yuan

last: Chen

first: Wenqi

last: Hu

first: Brian

middle: A

last: A

first: Matt

last: Thompson

first: Barbara

last: Wold

last: Zernicka-Goetz


title: PD1-targeted cis-delivery of an IL-2 variant induces a multifaceted anti-tumoral T cell response in human lung cancer

city: Basel

first: DBM Bioinformatics

last: Core Facility

state: BS

address: Hebelstrasse 20

department: Departement of Biomedicine

country: Switzerland

institute: University of Basel

summary: Antibody-cytokine fusion proteins are being developed as next-generation cancer immunotherapies, aiming to deliver activation signals to targeted immune populations. Among these, PD1-IL2v - an engineered interleukin-2 variant (IL-2v) lacking CD25 binding, fused to a high affinity programmed cell death protein-1 (PD-1) blocking antibody - has shown promising results in murine tumor models. Here, using human model systems, we show that PD1-IL2v elicits a multifaceted anti-tumor T cell response by targeting both CD8⁺ and conventional CD4⁺ T cells (Tconv). Single cell RNA sequencing (scRNAseq) on a lung cancer patient-derived tumor fragment (PDTF) platform revealed that PD1-IL2v drives the expansion of proliferative, cytotoxic CD8⁺ T cells exhibiting features of tumor reactivity. This was accompanied by upregulation of CXCR6, enhancing their migratory capacity. In Tconv cells, PD1-IL2v upregulated CXCL13 expression and promoted a Tfh/Th1-like transcriptional program associated with anti-PD1 responsiveness. Our findings provide mechanistic insights into the effects of IL-2v targeted delivery to PD-1⁺ cells within human tumors, supporting the clinical development of next-generation immunocytokines.

overall_design:
Patient-derived tumor fragments (PDTFs) from three cancer patients with lung tumors were treated with either Isotype control (DP47), anti-PD1 (Pembrolizumab-PGLALA), Isotype-IL2v (DP47-IL2v), or PD1-IL2v for 48 hours. Subsequently, PDTFs were digested into a single cell suspension and CD45⁺CD3⁺ live T cells were sorted. Next, single cell RNA sequencing was performed using the 10x Genomics protocol for 3′ gene expression profiling with feature barcoding (CG000206, Rev A). TotalSeq B (Biolegend) anti-human Hashtag 2, 3, and 4 were used for feature barcoding. Here, we will provide the demultiplexed samples only. The supplementary file contains the whole QC-filtered CD3 Seurat objects as rds file.

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Raw files for human/patient samples are being made available in EGA (https://www.ebi.ac.uk/ega/) for controlled access to the personally identifiable sequence data.
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first: Clara

last: Serger

first: Irene

last: Fusi

first: Marina

last: Natoli

first: Alfred

last: Zippelius


title: Real-time quantitative PCR analysis of extracellular vesicle miRNA from human U2OS cells culture medium [FZD4]

city: Portland

first: Xiao

last: Shi

state: Oregon

address: 3181 SW Sam Jackson PK Rd

department: dept. of psychiatry

institute: Oregon Health and Science University

summary: Human U2OS cells were stimulated with selective agonist Wnt3a of Frizzled class receptor 4(FZD4) for 24 hours. Extracellular vesicles were isolated from U2OS cell culture media. Total RNAs were purified from extracellular vesicle samples. We used TaqMan Low Density Arrays to quantitate miRNA expression in extracellular vesicles secreted by U2OS cells after GPCR activation.

overall_design: qPCR miRNA expression profiling.  Each GPCR stimulation experiment included its own media control, vehicle control, and treated samples.

first: Aaron

last: Janowsky