title: CHI3L1 regulates papillary thyroid tumor progression via TP53 signaling

status: Public on Jan 02 2025

city: BeiJing

first: yanan

last: zhou

address: No.56 Nanlishi Road, Xicheng District

institute: Beijing Children's Hospital, Capital Medical University

summary: RNA-seg profiling of TPC-1 cell line knockdown derivatives(shNC and shCHI3L1)

first: Fen

last: Cai

first: Yanan

last: Zhou

first: Yeran

last: Yang

first: Meng

last: Zhang

first: Xuan

first: Yan

last: Chang

first: Shengcai

last: Wang

first: Yongli

last: Guo

first: Yongbo

last: Yu

first: Jiangqiao

last: Geng

first: Xin

last: Ni


title: Small RNAseq to identify miRNAs in four different morphs of Astyanax mexicanus - Pachón, Tinaja, Molino, and surface fish

status: Public on Jan 03 2025

city: Kansas City

first: Huzaifa

last: Hassan

state: MO

country: USA

institute: Stowers Institute for Medical Research

type: Non-coding RNA profiling by high throughput sequencing

summary: In this pioneering study, we present the first comprehensive catalog of 683 small non-coding miRNAs for Astyanax mexicanus. Focusing on an early developmental stage, miRNAs were extracted and sequenced from 24hpf embryos of surface fish and three distinct cavefish morphs (Pachón, Tinaja, and Molino). We utilized in silico analyses to predict putative 3’UTR targets of these miRNAs, revealing a unique and extensive miRNA landscape in cavefish. Small RNA sequencing identified over 100 differentially expressed miRNAs in each cave morph compared to surface fish at 24hpf, suggesting early activation of miRNA-mediated silencing pathways. Notably, a subset of miRNAs was common across all three cave morphs, constituting cave-specific miRNAs potentially instrumental in cave adaptation. To unravel the functional implications of these cave-specific miRNAs, we analyzed their predicted target genes. Gene Ontology (GO) term analysis unveiled pathways which align with known adaptations in cavefish, primarily affecting development and metabolism. Further, cross-validating with a sample mRNAseq data from Pachón and surface fish also strongly suggested impact of these miRNAs on cave adaptation associated pathways.  This study establishes a foundation for exploring miRNA-mediated gene regulation in cavefish, shedding light on their potential role in regulating early developmental and metabolic adaptations crucial for troglomorphic features. The comprehensive miRNA catalog provided will also guide future investigations into the intricate world of miRNA-mediated evolution in cave-adapted species.

overall_design: We collected small RNA (<200nt) population from 24 hours post fertilization Astyanax mexicanus embryos from all the four morphs - Pachón, Tinaja, Molino, and surface fish.

first: Tathagata

last: Biswas

first: Nicolas

last: Rohner


title: Spatio-temporal X-linked gene reactivation in the mouse germline reveals site-specific retention of epigenetic silencing [WGBS]

status: Public on Jan 06 2025

city: Paris

first: Laurène

last: Syx

address: 11 rue Pierre et Marie Curie

department: Centre de recherche

country: France

institute: Institut Curie

type: Methylation profiling by high throughput sequencing

summary: Random X-chromosome inactivation (XCI) is a hallmark of female mammalian somatic cells. This epigenetic mechanism, mediated by the long non-coding RNA Xist, occurs in the epiblast and is stably maintained to ensure proper dosage compensation of X-linked genes during life. However, this silencing is lost during primordial germ cell (PGC) development. Using a combination of single-cell allele-specific RNA sequencing and low-input chromatin profiling on in vivo developing mouse PGC, we provide unprecedented detailed maps of gene reactivation. We demonstrate that PGC still carry a fully silent X chromosome at embryonic day (E) 9.5, despite the loss of Xist expression. X-linked genes are then gradually reactivated outside the Xist first-bound regions. At E12.5, a significant part of the inactive X chromosome (Xi) still resists reactivation, carrying an epigenetic memory of its silencing. Late-reactivated genes are enriched in repressive chromatin marks, including DNA methylation and H3K27me3 marks. Our results define the timing of reactivation of the silent X chromosome a key event in female PGC reprogramming with direct implications for reproduction.

overall_design:
C57Bl6/J Epiblasts were manually dissected from extra-embryonic tissues of E6.5 embryos, followed by sex determination by PCR on the extra-embryonic tissue
Whole-Genome Bisulfite sequencing libraries from 2 E6.5 female replicates were prepared as described by Smallwood et al 2014 Nature Methods

first: Marius

last: Walter

first: Aurélie

last: Teissandier

first: Déborah

last: Bourc'his

first: Maud

last: Borensztein


title: Interaction and activation of immune cells by CD41a+ extracellular vesicles

city: Créteil

first: Mehdi

last: Khelfa

address: 5 Rue Gustave Eiffel

institute: Institut Mondor de Recherche Biomédicale

type: Expression profiling by high throughput sequencing

summary: The immunological profiles of CD4+ T lymphocytes (TLs) from patients with hematological malignancies differ between patients who have and have not received transfusions. There may be several reasons for these differences, including the presence of extracellular vesicles (EVs) derived from plasma membrane budding and present in the platelet concentrates. Indeed, EVs can modulate the immune system through interactions with many immune cells, but the underlying mechanisms remain incompletely understood.  We therefore investigated how interactions with CD41a+ EVs cause immune cells to change phenotype and function. CD41a+ EVs were cultured with TLs, B lymphocytes, dendritic cells, and monocytes. Given the potential involvement of monocytes in leukemia progression, we performed a new original multi-omics study to confirm the protein changes and gene activation observed following interaction with CD41a+ EVs. The CD41a+ EVs had immunomodulatory effects on all these cell types but this effect depended on the numbers of EVs. CD4+ TLs were activated with large numbers of CD41a+ EVs, whereas monocytes were the most sensitive. With the new multi-omics technique, we confirmed the direct effects of CD41a+ EVs on protein phenotype and gene activation. Transfusion EVs should be considered during the immunological follow-up of patients after transfusion to detect immunological effects on malignant hemopathies and for the development of new immunotherapies.

overall_design: Monocytes were cultured with (or without) EVs for 18 hours at a ratio of 1:10 (cells: EVs). The cells were then harvested and stained with BD AbSeq antibodies. Targeted scRNA-seq analysis was performed with the BD Rhapsody Single-Cell Analysis System.

first: Marie

last: Tamagne

first: Stéphane

last: Kerbrat

first: Benoît

last: Vingert


title: scRNA-seq of EZH2-knockout Memory B cells

city: Atlanta

first: Chris

last: Scharer

state: GA

address: 1510 Clifton Rd, Suite 3086A

department: Microbiology and Immunology

institute: Emory University

summary: To understand the transcriptional circuits controled by the histone methyltransferase EZH2 in memory B cells (MBC) scRNA-seq was performed on influenza-specific MBC that formed at an early day 14 or late day 39 time point.  EZH2-knockout MBC were compared to CRE control MBC isolated from the spleens and mediastinal lymph nodes of mice.

overall_design: scRNA-seq of 4 sample across two time points comparing control and EZH2-deficient memory B cells

first: Christopher

middle: D


title: Inhibition of DEK contributes to the tolerance of replication stress and restores HSC function in Fanconi anemia

city: Chongqing

first: Zhe

last: Chen

address: 1 Yixueyuan Road, Yuzhong District

country: China

institute: Chongqing Medical University

type: Genome binding/occupancy profiling by high throughput sequencing

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

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Refer to individual Series


title: RNA-seq of Mouse Spinal Cord after Lateral Compression Spinal Cord Injury followed by Delayed Atorvastatin or Vehicle Treatment [Bulk RNA-seq of mice spinal cords]

status: Public on Jan 05 2025

city: Rochester

first: Isobel

last: Scarisbrick

state: MN

address: 200 First St SW

institute: Mayo Clinic

summary: This dataset supports a study investigating the effects of delayed atorvastatin treatment on gene expression and functional recovery in a chronic mouse model of spinal cord injury (SCI). Twelve-week-old female C57BL/6 mice were subjected to moderate 0.25 mm lateral compression SCI and after two weeks, were treated with atorvastatin (10 mg/kg) or a vehicle control daily for four weeks. Bulk RNA sequencing of spinal cord tissues at six weeks post-injury revealed broad alterations to gene expression due to SCI (DEGs common to both treatments and unique to each) and a smaller set of alterations due uniquely to atorvastatin treatment. Atorvastatin treatment specifically activated gene programs associated with axon guidance and fatty acid transport, which may contribute to the enhanced sensorimotor recovery. This RNA-seq dataset offers insights into the molecular underpinnings by which atorvastatin enhances sensorimotor recovery and modulates gene expression post-SCI.

overall_design: To investigate the molecular effects of atorvastatin on recovery from spinal cord injury (SCI), twelve-week-old female C57BL/6 mice were divided into two groups: one receiving daily treatments of atorvastatin (10 mg/kg) dissolved in a vehicle composed of 2% dimethyl sulfoxide (DMSO), 35% polyethylene glycol (PEG) 400, 2% Tween 80, and 61% saline—and a control group receiving the vehicle alone. Treatment commenced two weeks after inducing a moderate 0.25 mm lateral compression SCI and continued for four weeks. The efficacy of atorvastatin in enhancing functional recovery was assessed before SCI and at 1, 3, and 7 days post-injury and weekly thereafter to 42 days (6 weeks) post-injury using the Basso Mouse Scale (BMS), BMS subscore, and Inclined Plane Test, with significant improvements noted by the fourth week and continuing through the final six-week post-injury assessment. At this six-week endpoint, spinal cords were harvested and subjected to bulk RNA sequencing to profile changes in gene expression. This RNA-seq run also included samples from the spinal cords of two uninjured 12-week-old female C57BL/6 mice to serve as baseline (pre-SCI, pre-treatment) controls. Analyses described in the accompanying manuscript included using DESeq2 for determining gene expression differences and applying Ingenuity Pathway Analysis and PantherGO for pathway analysis to elucidate the biological processes modulated by atorvastatin. This dataset contains raw counts of gene expression as well as gene length-normalized (transcripts per kilobase million) for each replicate for comprehensive evaluation of the transcriptomic impact of SCI and of atorvastatin on SCI recovery.

first: Samuel

middle: C

last: Buchl

first: Ha

middle: N

last: Kim

first: Benjamin

last: Hur

first: Whitney

middle: L

last: Simon

first: Monica

middle: R

last: Langley

first: Jaeyun

last: Sung

middle: A


title: Systematic functional characterization of the non-coding regulatory SNPs associated with central obesity

city: Xi'an China

first: Renjie

last: Zhu

state: Shaanxi

address: No.28 Xianning West Road, Xi'an, Shaanxi 710049, P.R. China

department: School of Life Science and Technology

institute: Xi'an Jiaotong University

summary: Genome-wide association studies (GWASs) have identified more than 300 susceptibility loci associated with central obesity. However, the functional understanding of these loci is limited by the fact that most loci are in the non-coding region. To address this issue, in this study we firstly selected 2,034  prioritized SNPs based on fine-mapping and epigenomic annotation analysis. Self-transcribing active regulatory region sequencing (STARR-seq) experiment was then performed to systematically assess the enhancer activity of these  prioritized SNPs.

overall_design: Using 2,034 prioritized SNPs, 120-bp DNA sequence centered on each SNP was extracted from the human genomic context, which included reference and alternative alleles. The 15-bp identical adapter sequence was further added on the 5′ and 3′ region for library construction. We synthesized 150-bp long DNA fragments using an oligonucleotides CustomArray(GenScript, USA). Firstly, oligonucleotides were amplified using adapter primers (NEB, USA) and cloned into linearized hSTARR-seq_ORI vector (Addgene, USA) and then we extracted the plasmid library for cell transfection. Secondly, a total of 15μg STARR-seq plasmid library was transfected into 1.0×107 preadipocyte cells. Preadipocytes derived from human subcutaneous adipose tissue was obtained from BLUEFBIO (Shanghai, China). Thirdly, STARR-seq sequencing libraries were prepared and subjected to paired-end sequencing on the Illumina Novaseq 6000 platform. Three biological replicates were performed.

first: Tie-Lin

last: Yang

first: Shan-Shan

last: Dong

first: Yuan-Yuan

last: Duan

first: Ren-Jie


title: Self-reactive B cells traverse a perfect storm of somatic mutagenesis to cause a virus-induced autoimmune disease

city: Darlinghurst

first: Timothy

middle: John

last: Peters

state: NSW

address: 384 Victoria St

department: Immunology

country: Australia

institute: Garvan Institute of Medical Research

summary: The unexplained association between infection and autoimmune disease is strongest for hepatitis C virus-induced cryoglobulinemic vasculitis (HCV-CV). We traced the evolution of the pathogenic rheumatoid factor (RF) autoantibodies in four HCV-CV patients by deep single cell multi-omic analysis, revealing three sources of B cell somatic mutation converged to drive accumulation of a large disease causing clone. A sensitive method for quantifying low affinity binding revealed three recurring heavy/light chain combinations created byV(D)Jrecombination bound self IgG but not viral E2 antigen. Whole genome sequencing revealed accumulation of thousands of somatic mutations, at levels comparable to CLL and normal memory B cells, but with 1-2 corresponding to driver mutations found recurrently in B cell leukemia/lymphoma.V(D)Jhypermutation created autoantibodies with compromised solubility in complex with self-IgG. In this virus-induced autoimmune disease, infection promotes a perfect storm of somatic mutagenesis in the descendants of a single B cell

overall_design: We performed single cell RNA sequencing analysis of CD19+CD20+B cells sorted from the blood of a patient with hepatitis C virus-induced cryoglobulinemic vasculitis (HCV-CV), after HCV clearance with direct acting anti-viral (DAA) therapy. Gene expression (10X 3’) and immunoglobulin receptor sequencing (RAGE-seq) were performed for each individual B cell.

first: Clara

last: Young

first: Mandeep

last: Singh

first: Katherine

middle: J

last: Jackson

first: Matt

last: Field

first: Daniel

last: Suan

last: Goodnow


title: Three-Dimensional Environment Sensitizes Pancreatic Cancer Cells to The Anti-Proliferative Effect of Budesonide by reprogramming energy metabolism (3D)

city: Naples

first: Cristina

last: D'Aniello

address: Via Pietro Castellino, 111

country: Italy

institute: IGB-CNR

summary: Pancreatic ductal adenocarcinoma (PDAC) is the most lethal malignancy with aggressive metastatic phenotype and very poor clinical prognosis. Interestingly, a lower occurrence of PDAC has been described in individuals with severe and long-standing asthma. Here we gained insight into the potential link between the glucocorticoid (GC) budesonide, a first-line therapy to treat asthma, and PDAC development. We found that in classical 2D setting, budesonide, but not classical GCs, used at high micromolar concentrations, modifies the behavior of PDAC cells, reducing their mesenchymal invasive/migrating features, without altering their proliferation or survival. However, a more physiological 3D environment drives PDAC cells towards a general metabolic reprogramming, which involves protein, lipid, and energy metabolism (e.g., increased glycolysis dependency). Remarkably, this metabolic change sensitizes PDAC cells to an unexpected anti-proliferative action of budesonide, which instead induces opposite metabolic changes (e.g., increased OXPHOS). Under these conditions, budesonide, as dexamethasone and hydrocortisone, inhibits PDAC spheroid growth and proliferation at nanomolar concentrations, in a GR-dependent manner, and through the induction of the tumor suppressor CDKN1C. Collectively, our study uncovers how the growth behavior/conditions influence the susceptibility of PDAC cells to glucocorticoids, and the tumor inhibitory action of budesonide in 3D condition (i.e., organotypic cultures, floating spheroids, and in vivo tumors). Validation in other cancer cells will be necessary to broaden the role of 3D setting and OXPHOS-to-glycolytic transition, in the induction of GC susceptibility. The inhibitory effect of budesonide on in vivo tumors suggests its potential suitability for clinical trials as a novel therapeutic approach to fight pancreatic cancer.

overall_design: The effect of budesonide on the morphology, proliferation, motility/invasiveness and tumorigenesis of PDAC cell lines was tested under 2D or 3D culture settings. Analysis of the transcriptome profiles was performed by RNAseq to study the effect of budesonide in 3D spheroids.

first: Gabriella

last: Minchiotti

first: Eduardo

last: Patriarca


title: Three-Dimensional Environment Sensitizes Pancreatic Cancer Cells to The Anti-Proliferative Effect of Budesonide by reprogramming energy metabolism (2D)

overall_design: The effect of budesonide on the morphology, proliferation, motility/invasiveness and tumorigenesis of PDAC cell lines was tested under 2D or 3D culture settings. Analysis of the transcriptome profiles was performed by 3' mRNAseq to study the effect of budesonide in 2D culture condition.


title: CD137 expression in Foxp3+ regulatory T cells is important for controling the progression of type 1 diabetes

city: Milwaukee

first: Yi-Guang

last: Chen

state: WI

address: 8701 Watertown Plank Rd.

department: Pediatrics (Endocrinology) and Microbiology & Immunology

institute: Medical College of Wisconsin

summary: CD137-deficient Foxp3+ regulatory T cells display functional alterations compared to the wildtype counterpart. In this study, we used single-cell RNA sequencing to define the differentiation states of islet-infiltrating Tregs and the impact of CD137 deficiency.

overall_design: This dataset is composed of two mouse strains, NOD.Foxp3-EGFP (wildtype) and NOD.Tnfrsf9-/-.Foxp3-EGFP (CD137 knockout), to determine the effect of CD137 deficiency on regulatory T and CD8 T cells in NOD mouse. Pancreatic islet cells were pooled from 6 mice for each strain and Foxp3+ CD4 T cells (Tregs) and CD8 T cells were isolated for scRNA-seq.

first: Ashley

last: Ciecko


title: Comprehensive single-cell RNA-sequencing study of Tollip deficiency effect in IL-13-stimulated human airway epithelial cells

city: Bronx

first: Grace

middle: Yihua

last: Lee

state: NY

address: 1300 Morris Park Ave, Forchheimer Bldg, Room 726

institute: Singulomics Corporation

summary: We conducted the first single-cell RNA sequencing (scRNA-seq) analysis of Tollip knockdown (TKD) human airway epithelial cells to determine the cell-type-specific role of TKD and its interaction with IL-13.

overall_design: Cultured at an air-liquid interface, TKD cells were treated with or without IL13 (TKDIL13 or TKD), and compared to Tollip-sufficient cells with or without IL-13 (IL-13 or CTR) through an scRNA-seq analysis.

middle: Y

first: Niccolette

last: Schaunaman

first: Hamid

last: Nouri

first: Monica

last: Kraft

first: Hong Wei

last: Chu


title: Revealing role of epigenetic modifers and DNA oxidation in cell‐autonomous regulation of Cancer stem cells

city: Newark

first: Pranela

last: Rameshwar

state: NJ

address: 185 South Orange Avenue

department: Medicine

institute: Rutgers NJ Medical School

summary: Breast cancer cells (BCCs) can remain undetected for decades in dormancy. These quiescent cells are similar to cancer stem cells (CSCs); hence their ability to initiate tertiary metastasis. Dormancy can be regulated by components of the tissue microenvironment such as bone marrow mesenchymal stem cells (MSCs) that release exosomes to dediferentiate BCCs into CSCs. The exosomes cargo includes histone 3, lysine 4 (H3K4) methyltransferases - KMT2B and KMT2D. A less studied mechanism of CSC maintenance is the process of cell-autonomous regulation, leading us to examine the roles for KMT2B and KMT2D in sustaining CSCs, and their potential as drug targets.

overall_design: MDA-MB-231 breast cancer cell line with scramble, KMT2B knockdown, KMT2D knockdown, and DNMT1 knockdown.

first: Alejandra

middle: I

last: Ferrer

first: Yannick

last: Kenfack

first: Lauren

middle: S

last: Sherman


title: Neuroinflammation underlies the development of social stress induced cognitive deficit in sickle cell disease.

city: Cincinnati

first: Hyacinth

middle: Idu

last: Hyacinth

state: Ohi

address: 3230 Eden Avenue

department: Neurology

institute: University of Cincinnati

summary: Cognitive deficit is a debilitating complication of SCD with a multifactorial pathobiology. Here we show that neuroinflammation and dysregulation in lipidomics and transcriptomics profiles are major underlying mechanisms of social stress-induced cognitive deficit in SCD. Townes sickle cell (SS) mice and controls (AA) were exposed to social stress using the repeat social defeat (RSD) paradigm concurrently with or without treatment with minocycline. Mice were tested for cognitive deficit using novel object recognition (NOR) and fear conditioning (FC) tests. SS mice exposed to RSD without treatment had worse performance on cognitive tests compared to SS mice exposed to RSD with treatment or to AA controls, irrespective of their RSD or treatment disposition. Additionally, compared to SS mice exposed to RSD with treatment, SS mice exposed to RSD without treatment had significantly more cellular evidence of neuroinflammation coupled with a significant shift in the differentiation of neural progenitor cells towards astrogliogenesis. Additionally, brain tissue from SS mice exposed to RSD was significantly enriched for genes associated with blood-brain barrier dysfunction, neuron excitotoxicity, inflammation, and significant dysregulation in sphingolipids important to neuronal cell processes. We demonstrate in this study that neuroinflammation and lipid dysregulation are potential underlying mechanisms of social stress-related cognitive deficit in SS mice.

overall_design: To test whether exposure of sickle cell mice to repeated social defeat results intotal transipt tomics changes and whether treatment with minocycline will ameliorate this changes. We performed bulk RNA-sequencing on cortical and hippocampal samples from mice that were exposed to repeated social defeat (RSD), mice treated with minocycline and simultaneously exposed to repeated social disease and animals treated with our exposure to RSD and animals that were neither treated or exposed to RSD.


title: Genome-wide maps of enhancer regulation connect risk variants to disease genes

status: Public on Jan 01 2025

city: Palo Alto

first: Jesse

last: Engreitz

state: CA

address: 240 Pasteur Drive, BMI 3700

institute: Stanford University

overall_design: We generated bulk RNA-seq data in immortalized immune cancer cell lines stimulated with relevant immune ligands

first: Joseph

last: Nasser

first: Tung

last: Nguyen

first: John

last: Ray

first: Charles

last: Epstein

first: Thomas

last: Eisenhaure

first: Nir

last: Hacohen

first: Eric

last: Lander


title: Gene expression profile at the single cell level of tissue derived breast microstructures after lipid exposure

city: Chicago

first: Mariana

last: Bustamante Eduardo

state: il

address: 303 E Superior St.

department: Department of Surgery

institute: Northwestern University

summary: The effects of the medium-chain fatty acid octanoic acid (OA) on breast tissue were investigated using single-cell RNA sequencing.

overall_design: Breast microstructures were exposed to either vehicle (PBS) or octanoic acid (OA) for 24 hours, then dissociated into single cells for analysis using single-cell RNA sequencing.

first: Susan

last: Clare


title: Multi-modal refinement of the human heart atlas during the first gestational trimester

city: Marseille

first: Heather

last: Etchevers

address: 27 boulevard Jean Moulin

department: INSERM U1251

institute: INSERM/Aix-Marseille Univ

summary: Congenital heart defects are collectively frequent and a significant burden for human health. Understanding the developmental origins of such anomalies in the first and longest-lived vital organ is key to improving diagnoses, prognoses and therapies. However, although the atlas of human cardiac cells before birth continues to benefit from increased sampling, equivalencies across different investigators’ datasets or with animal models remain tenuous. We have determined the individual transcriptomes of nearly fifty thousand human heart cells from three fetuses between post-conceptional weeks (pcw) 8-11, and enriched their initial identification with a spatial transcriptomics analysis of six slices from two stage-matched samples. Integrations across modalities, sex and time points both internally and with earlier atlases have revealed the existence of previously unidentified, transient contractile, conductive and stromal cell types and their likely lineage relationships during the first trimester. Further analyses at varying levels of spatiotemporal resolution enabled us to validate charactistics of these cardiac cells in dozens of other samples and across a wide range of cell population sizes and ages. This resource advances knowledge about cell-autonomous states and adds precision to the repertory of contextual influences, including tissular and positional, exerted by and on the diverse lineages of the developing human heart during a critical time window.

overall_design:
First trimester human embryos and fetuses (6-13 pcw) were obtained from induced terminations of pregnancy performed legally in France and sought for reasons other than known fetal abnormality. Tissues were collected after obtaining written consent from donors following procedural initiation, a protocol approved by the national Agency for Biomedical Research (authorization #PFS14-011 to SZ; Agence de la Biomédecine) and declared by the Human Developmental Cell Atlas (HuDeCA; https://hudeca.genouest.org) consortium to the French Ministry of Higher Education and Research under reference DC-2022-5011. Sex was determined by qPCR of the SRY gene and validated in the transcriptomic data.
Three intact hearts from one female [UID HEF_DN_F0000530) at 8.6 post-conceptional weeks (pcw) and two male fetuses (HEF_DN_F0000374, 9.0 pcw and HEF_DN_F0000467, 10.7 pcw) were dissociated for single-nucleus incorporation into the GEMs of the 10X Chromium platform.

first: Christopher

last: De Bono

first: Yichi

last: Xu

first: Samina

last: Kausar

first: Marine

last: Herbane

first: Camille

last: Humbert

first: Sevda

last: Rafatov

first: Chantal

last: Missirian

first: Mathias

last: Moreno

first: Weiyang

last: Shi

first: Yorick

last: Gitton

first: Alberto

last: Lombardini

first: Ivo

last: Vanzetta

first: Séverine

last: Mazaud-Guittot

first: Alain

last: Chédotal

first: Anaïs

last: Baudot

first: Stéphane

last: Zaffran


title: Single-cell parallel analysis of DNA damage and transcriptome reveals selective genome vulnerability

city: New York

first: Dongsheng

last: Bai

address: 101 Avenue of the Americas

institute: New York Genome Center

summary: We used a new technology, named Paired-Damage-seq, to perform simultaneous profiling of DNA damage and mRNA on HeLa cells and mouse cortex at single-cell level.

overall_design: We developed Paired-Damage-seq for joint analysis of oxidative and single-stranded DNA damage with gene expression in single cells. We applied this approach to cultured HeLa cells and the mouse brain as a proof of concept. Our results indicated the associations between damage formation and epigenetic changes. The distribution of oxidative DNA damage hotspots exhibits cell-type-specific patterns; this selective genome vulnerability, in turn, can predict cell types and dysregulated molecular programs that contribute to disease risks.

first: Zhenkun

last: Cao

first: Chenxu

last: Zhu


title: Dual Role of PRC2-EZH1 in Orchestrating Rhythmicity of Circadian Transcriptional Program in Post-mitotic Skeletal Muscle Cells

city: Thuwal

first: Valerio

last: Orlando

country: Saudi Arabia

institute: KAUST

summary: Circadian rhythmicity of gene expression is a conserved feature of cell physiology. This involves the fine tuning between transcriptional and post-transcriptional molecular mechanisms, strongly dependent on the metabolic state of the cell that guarantees intrinsic plasticity of tissue specific genetic programs. To support the plastic properties a key role is played by the dynamics of epigenome structure and its regulators. Here we investigate the role of the Polycomb cell memory complex PRC2-EZH1 in regulating transcriptional rhythmicity in post-mitotic skeletal muscle cells. We show that PRC2-EZH1 core components are under direct regulation of BMAL1, show an oscillatory behavior and control both silencing and activation of target genes. Fully assembled PRC2-EZH1 complex negatively regulates cyclic expression of direct targets through modulation of cyclic H3K27me3 status. Conversely, we show that EZH1 regulates constitutive circadian genes expression, through stabilization of RNA Pol II machinery and maintenance of transcription process fidelity. Collectively, these findings unveil the dual and multi role of PcG in circadian gene regulation in adult skeletal muscle cells, and the plastic nature of PcG cell memory system in somatic cells.

overall_design: The experiment involves sequencing of ChIP-seq samples from skeletal muscle tissue under different conditions and marks (EZH1, H3K27me3, Suz12)

first: Peng

last: Liu


title: DNA methylation epigenome analysis of non-transformed breast cells following lipid exposure.

first: Mariana

last: Bustamante Eduardo

type: Methylation profiling by genome tiling array

summary: The DNA methylation landscape of MCF-10A breast epithelial cells upon octanoic acid (OA) exposure, in the presence or absence of CBR5884, was analyzed using the Illumina Infinium HumanMethylationEPIC microarray.

overall_design: Bisulphite converted DNA from MCF-10A breast epithelial cells were exposed to vehicle (PBS or PBS plus DMSO),  Octanoic Acid or Octanoic Acid plus CBR-5884 for 24 hours were hybridized to the Illumina Infinium HumanMethylationEPIC microarray.

first: Susan

last: Clare


title: Changes in histone modifications measured by CUT&RUN after lipid exposure

summary: The methylation landscape of MCF-10A breast epithelial cells upon octanoic acid (OA) exposure was analyzed using CUT&RUN for the histone marks H3K27me3 and H3K4me3.

overall_design: MCF-10A breast epithelial cells were exposed to vehicle (PBS) or OA for 24 hours. Genomic enrichement of H3K4me3 and H3K27me3 was analyzed by CUT&RUN.


title: Transcriptome Profiling in tissues and blood from NHP-HCT Recipients

city: Boston

first: Kayleigh

last: Ingersoll Omdahl

address: 1 Blackfan st

institute: Boston Children's Hospital

summary: Tissue-specific T cell immune responses play a critical role in maintaining organ health, but can also drive immune pathology during both auto- and alloimmunity. The mechanisms controlling intra-tissue T cell programming remain unclear. Here, we leverage a non-human primate model of acute graft-versus-host disease (aGVHD) after allogeneic hematopoietic stem cell transplantation (HCT) to probe the biological underpinnings of tissue-specific alloimmune disease, using a comprehensive systems immunology approach.Transcriptional profiling revealed substantial biological differences between T cells, infiltrating the lung and liver during aGVHD.

overall_design: Series of HCT performed on n=13 animals with n=37 arrays from the blood and tissue in the post transplant period including arrays from n=42 untransplanted healthy controls

first: Victor

last: Tkachev

first: Leslie

last: Kean


title: Spatial transcriptomics of the aging mouse brain reveals origins of inflammation in the white matter

city: Baltimore

first: Supriyo

last: De

state: Maryland

address: 251 Bayview Blvd

department: Laboratory of Genetics and Genomics

institute: NIA-IRP, NIH

summary: To systematically understand age-induced molecular changes, we performed spatial transcriptomics of young, middle-aged, and old mouse brains and identified seven transcriptionally distinct regions. All regions exhibited age-associated upregulation of inflammatory mRNAs and downregulation of mRNAs related to synaptic function. Notably, aging white matter fiber tracts showed the most prominent changes with pronounced effects in females. The inflammatory signatures indicated major ongoing events: microglia activation, astrogliosis, complement activation, and myeloid cell infiltration. Immunofluorescence and quantitative MRI analyses confirmed physical interaction of activated microglia with fiber tracts and concomitant reduction of myelin in old mice. In silico analyses identified potential transcription factors influencing these changes. Our study provides a resourceful dataset of spatially resolved transcriptomic features in the naturally aging murine brain encompassing three age groups and both sexes. The results link previous disjointed findings and provide a comprehensive overview of brain aging identifying fiber tracts as a focal point of inflammation.

overall_design: We performed spatial transcriptomics on a total of 36 coronal brain sections across 3 age groups (young (Y, ~11 weeks), middle-aged (M, ~57.5 weeks), and old (O, ~126 weeks) and two sexes (male and female) of C57BL/6JN mice. In round 1, each age group contained 4 biological replicates (males (M) n=2 and females (F) n=2) and 2 technical replicates (A or B), i.e., independent, succeeding coronal sections from the same OCT block. In round 2, one technical replicate from each young and old mouse with the added 6 biological replicates (males (M) n=3 and females (F) n=3) for young and old groups were sequenced and analyzed together.

first: Lin

last: Wang

first: Payel

last: Sen


title: Gene expression profile of Fcrls+/CD11b+/Ly6C- microglia from young and old mice after abdominal surgery

first: Zhuoran

last: Yin

state: Massachusetts

address: 60 Fenwood Road

institute: Brigham and Women's Hospital

summary: We used bulk RNA sequencing to investigate the molecular signature of microglia from young (3-5mo) and old (20-22mo). mice exposed to 1.2% isoflurane + abdominal laparotomy. Microglia were isolated from the hippocampus or from the whole hemisphere (without hippocampus).

overall_design: Fcrls+/CD11b+/Ly6C- microglia were isolated by Fluorescence-activated cell sorting (FACS) and analyzed using Smartseq2 RNAseq.

first: Anna

middle: K

last: Leonard

first: Carl

middle: M

last: Porto

first: Zhongcong

last: Xie

first: Sebastian

last: Silveira

first: Deborah

last: Culley

first: Oleg

last: Butovsky

first: Gregory

last: Crosby


title: LIS1 promotes perineural invasion by upregulating the serine metabolism in head and neck squamous carcinoma

city: DaLian

first: YiDing

last: Liu

address: wwde

institute: Dalian Medical University

summary: LIS1 is a critical mediator of neuronal migration during brain development, and  is strongly associated with malignant tumors. We found that LIS1 is highly expressed in HNSCC,which is releated to perineural infiltration(PNI) in HNSCC.To explore the mechanism of PNI, we silenced the LIS1 expression in HNSCC cells and dected the function of PNI.In a word,We sought to validate LIS1 as a key signaling molecule for PNI in HNSCC.

overall_design: We performed high-throughput sequencing on a total of six SCC25 cell samples, with three samples undergoing hairpin knockout of PAFAH1B1, and the other three serving as the control group without knockout.

first: Lu

last: Gao

first: Jing

first: Yiding


title: CUT&RUN of the aging mouse brain reveals origins of inflammation in the white matter

overall_design: CUT&RUN of C/EBPβ and YY1 in microglia isolated from fresh whole brain. Microglia from 2 mice were pooled into one biological replicate.500,000 microglia from one biological replicate were used for each reaction.


title: Comparison of in vitro transcriptomic points of departure with fish acute and chronic toxicity values:  A case study of rainbow trout cells exposed to pesticides

city: Sainte-Anne-de-Bellevue

first: Niladri

last: Basu

state: Quebec

address: 21,1111 Lakeshore Blvd, Apt #2

country: Canada

institute: McGill University

summary: There is growing scientific and regulatory interest in transcriptomic points of departure (tPOD) values from in vitro experiments as an alternative to animal test method. The objective of this study was to calculate tPOD values in rainbow trout gill cells (RTgill-W1 following OECD 249) exposed to 20 pesticides, and to evaluate how these values compare to fish acute and chronic toxicity data from the ECOTOX database.  Cells were exposed to one fungicide (chlorothalonil), ten herbicides (atrazine, glyphosate, imazethapyr, metolachlor, diquat, s-metolachlor, AMPA, dicamba, dimethenamid-P, metribuzin), eight insecticides (chlorpyrifos, diazinon, permethrin, carbaryl, clothianidin, imidacloprid, thiamethoxam, chlorantraniliprole), and OECD 249 positive control 3,4-dichloroaniline. Sequencing libraries were prepared with UPXome, and tPODs calculated with ExpressAnalyst.  The method identified 44,262 unique genes, with 1,115 genes having >5 counts in the 576 samples sequenced.  For all chemicals, tPODs were derived and tPOD mode values ranged from 0.003 to 141µM with an average of 37µM. There were significant correlations between these tPOD mode values (x-value) and in vitro cytotoxicity EC50s from RTgill-W1 cells (y=1.1x+0.89, R2=0.85, p<0.001; n=11), rainbow trout acute toxicity LC50s (y=0.9x+0.59, R2=0.56, p<0.001; n=20), fish chronic sub-lethal effect concentrations (y=0.62x+0.38, R2=0.36, p=0.01; n=16) and fish chronic lethal effect concentrations (y=0.77x-0.28, R2=0.57, p=0.002; n=14).  Bland–Altman plot statistical analyses of these comparisons also showed good agreement. Overall, these data demonstrate that tPOD values can be derived from an experimental platform that links together elements of OECD 249 with a transcriptomic method with high throughput potential.  The findings support the notion that tPODs from short-term in vitro studies may be comparable to effect concentration data from in vivo studies of fish exposed for chronic durations.

overall_design: To dervie transcriptomic points of departure (tPODs) from the in vitro Rainbow trout gill (RTgill-W1) cell line assay following OECD 249 guidelines. RTgill-W1 cells were exposed to 20 pesticides for 24 hours in 96-well plates over 8 concentrations (3-fold serial dilutions). Pesticide concentrations were prepared in DMSO (solvent control) or water. Exposures were repeated 3 times for each chemical over 3 different passages (n=3 biological replicates) for a total of six 96-well plates, and 576 samples. Pesticides were split into two groups (Batch 1; n=10 pesticides, and Batch 2; n=10 pesticides). 3 wells were also designated as unexposed control RTgillW1 cells, referred to as ExpressRef. Following the 24 hour exposure, cells exposed to pesticides and the solvent control DMSO were lysed from the wells and then were prepared for RNA-sequencing using the QIAGEN UPXome protocol. The UPXome protocol individually tags each well in a 96-well plate with a unique code that allows for 24 samples to be pooled, and then tagged with a unique library code. Samples in a library can then be run on a single column for RNA-sequencing. Afterward analysis, R1 and R2 files are paired and demultiplexed according to their unique codes to separate individual samples and allow for subsequent analysis using ExpressAnalyst to derive tPODs.

first: Sophie

last: Emberley-Korkmaz

first: Krittikam

last: Mittal

first: Ke

last: Xu

first: Jessica

last: Head


title: Polyamine metabolism dysregulation contributes to muscle fiber vulnerability in ALS

city: Rome

first: Andrea

last: Bracaglia

address: Via Antonio Scarpa 16

institute: University of Rome La Sapienza

summary: Amyotrophic lateral sclerosis (ALS) is a fatal neurodegenerative disease characterized by progressive paralysis due to primary and secondary degeneration of motor neurons. In spite of extensive biomedical research, no curative therapy has yet been established. One of the primary targets of ALS is skeletal muscle, which undergoes profound functional changes as the disease progresses. To better understand how altered innervation interferes with muscle homeostasis during disease progression, we generated the first spatial transcriptomics dataset of skeletal muscle in the SOD1G93A mouse model of ALS. Using this strategy, we identified polyamine (PA) metabolism as one of the main altered pathways in affected muscle fibers. By establishing a correlation between the vulnerability of muscle fibers and the dysregulation of this metabolic pathway, we show that disrupting polyamine homeostasis causes impairments similar to those seen in ALS muscle. Finally, we show that restoration of polyamine homeostasis rescues the muscle phenotype in SOD1G93A mice, opening new perspectives for the treatment of ALS.

overall_design: Spatial Transcriptomics of Tibialis anterior of transiently denervated mice 3 days and 30 days post-denervation, used as biological replicates for the already published samples od D'Ercole et al., 2022

first: Veronica

last: Ruggieri

first: Silvia

last: Scaricamazza

first: Cristina

last: Parisi

first: Paolo

last: D'Angelo

first: Chiara

last: D'Ercole

first: Daisy

last: Proietti

last: Cappelletti

first: Alberto

last: Macone

first: Lozanoska-Ochser

last: Biliana

first: Marina

last: Bouchè

first: Lucia

last: Latella

first: Cristiana

last: Valle

last: Ferri

first: Lorenzo

last: Giordani

first: Luca

last: Madaro


title: Uterine Organoids Reveal Insights into Epithelial Specification and Plasticity in Development and Disease

city: Columbia

first: Andrew

last: Kelleher

address: 1030 Hitt Street

department: Ob, Gyn Womens Health

institute: University of Missouri

summary: Epithelial differentiation in the female reproductive tract (FRT) is essential for reproductive health, yet the mechanisms that govern epithelial fate specification remain poorly understood. At birth, FRT epithelium exhibits significant developmental plasticity, allowing differentiation into various epithelial subtypes. However, the regulatory pathways driving these early fate decisions, particularly in the uterus, are largely uncharacterized. Here, we employ neonatal mouse endometrial epithelial organoids and assembloid co-culture models to investigate how intrinsic cellular plasticity and mesenchymal signals influence uterine epithelial differentiation. We demonstrate that uterine epithelium undergoes marked age-dependent changes, shifting from a highly plastic state capable of differentiating into both monolayered and multilayered structures to a more restricted fate as development progresses. Interestingly, parallels between the developmental plasticity of neonatal uterine epithelium and pathological conditions such as endometrial cancer emerged, where similar regulatory mechanisms may be reactivated, driving abnormal epithelial differentiation and tumorigenesis. These findings provide new insights into the regulatory networks that guide early development and highlight how disruptions in these processes can contribute to disease, offering a valuable model for studying both normal uterine development and cancer progression.

overall_design: To assess cellular heterogeneity and differentiation dynamics, endometrial epithelial organoids (EEO) were developed from uteri of postnatal day 3 and 15 mice (n=10). EEO were grown for 8 days and then dissociated for downstream analysis

first: Jason

last: Rizo

first: Sarayut

last: Winuthayanon

first: Thomas

middle: E

last: Spencer


title: Long non-coding RNAs expressed in pituitary development and specific cell types

city: Ann Arbor

first: Lev

last: Prasov

state: MI

address: 1241 Catherine Street, 5704 Med Sci II

department: Department of Human Genetics

institute: University of Michigan

summary: Mammalian genomes contain thousands of genes for long non-coding RNA (lncRNAs) that affect expression of other genes through diverse mechanisms. The lncRNA transcripts are longer than 200 nucleotides and are often capped, spliced and polyadenylated, but they are not translated into protein.  Nuclear lncRNAs modify chromatin structure and transcription in trans or cis by interacting with the DNA, forming R-loops, and recruiting regulatory proteins.  Not much is known about the role of lncRNA in pituitary gland differentiation and function.  To develop a research resource for the study of lncRNA, we used cell-type specific cre transgenes to tag individual pituitary cell types in adult mice with fluorescent markers and enriched for thyrotropes, gonadotropes and somatotropes using fluorescence activated cell sorting.  We determined the transcriptome of each cell population using RNA sequencing and mined the data for lncRNA.  We detected hundreds of lncRNA in adult pituitary cells, and some were cell-type specific, and located immediately nearby genes that encode pituitary hormones or lineage-specific transcription factors.  We also mined transcriptome data from mouse pituitary glands collected at embryonic days 12.5 and 14.5 and identified 351 unique lncRNAs, many of which are exclusively expressed during development.   The location of many of these lncRNA suggests a cis-acting regulatory role for them in pituitary development or physiological function.  This research resource sets the foundation examining the actions of lncRNAs on expression of their nearby genes during development and in response to physiological demand.

overall_design: Pituitary glands from Tshbcre x ROSAYFP, Ghcre x ROSAYFP, and Lhbcre x ROSAYFP were harvested at 7 weeks of age or postnatal day 7, like genotypes pooled, and dissociated into single cells.  Cells were FACS sorted and RNA was made from the GFP positive fraction for RNAseq analysis.  An adult nontransgenic as well as a postnatal day 7 nontransgenic were sequenced for comparision.

first: Michelle

last: Brinkmeier

first: Akima

last: George

first: Leonard

last: Cheung

first: Ryan

last: Mills

first: Philippa

last: Melamed

first: Sally

last: Camper


title: Expression data from xenograft HuH7 mice treated with Zinc Acexamate and HuH7 cell line

city: BARCELONA

first: Mónica

last: Higuera

address: Passeig de la vall d'hebron 119-129

country: Spain

institute: Vall d'hebron Institute de Recerca (VHIR)

summary:
the impact of Zn supplementation was evaluated in a xenograft mouse model of HCC, with subsequent analysis of tumor gene expression profiles
The aim was to compare the effects of Zinc supplementation in a in vivo model of HuH7 xenograft mice treated with Zinc Acexamate vs vehicle-treted mice and in HuH7 cell line between different concentrations of Zinc Acexamate

overall_design: RNA from Tumors from mice vehicle and zinc acexamate-treated were processed and hybridizated with Clariom S human microarrays

first: Beatriz

last: Mínguez


title: Chromatin-immunoprecipitation followed by sequencing (ChIPseq) of SOX17 and FOXA2 in yolk-sac tumor cell lines

city: Düsseldorf

first: Daniel

last: Nettersheim

state: NRW

address: Moorenstr. 5

department: Dep. of Urology

country: Germany

institute: Medical Faculty and University Hospital Düsseldorf, Heinrich Heine University

overall_design: ChIPseq of SOX17 and FOXA2 in yolk-sac tumor cell lines GCT72 and 1411H, which highly express both transcription factors. As controls, input samples (each n = 2) were sequenced. SOX17- and FOXA2-ChIP were performed each in technical triplicates.


title: Identification of distinct mesenchymal factors in the developing mouse bladder and urethra (E14.5 and E18.5)

city: Bengaluru

first: Diya

last: Binoy Joseph

state: Karnataka

address: GKVK - Post, Bellary Rd

country: India

institute: Institute for Stem Cell Science and Regenerative Medicine

summary: The lower urinary is derived from the endodermal precursor, the cloaca. Despite common embryological origins, the epithelial linings and surrounding mesenchyme of the bladder and urethra show divergence. The bladder forms from the anterior part of the urogenital sinus, a cloacal derivative formed after septation of the cloaca to give rise to the anorectal and urogenital tracts. The urethra elongates posteriorly and shows sex-specific differences as a result of hormonal action. The bladder is a target for regenerative therapies and tissue reconstruction strategies. A significant shortcoming of these strategies has been the inability to recapitulate all layers of bladder epithelial cells, most importantly the apical uroplakin positive layer that forms a tight, impermeable barrier against components in the urine. The urethral epithelium is contiguous with the bladder epithelium but has distinct cellular architecture and lacks a uroplakin expressing apical layer. We hypothesized that comparison of the developing urethra and bladder epithelium will identify early genes that are responsible for urethra and bladder-specific differentiation. In this study, we compared the epithelial compartments of the developing mouse bladder and urethra to identify genes that are differentially expressed in these two compartments. Our study identified transcription factor genes and other tissue-specific markers that are confined to either the urethra or bladder epithelium. Additionally, we describe sex-specific differences in the lower urinary tract epithelium which are more pronounced between the male and female urethral epithelium and less evident in the bladder epithelium between sexes.

overall_design: The objective of this study was to identify compartment specific gene expression in the developing bladder and urethra. We obtained timed-pregnant CD-1 female mice and collected embryos at embryonic day 14.5 and E18.5. The lower urinary tract, including bladder and pelvic urethra, were dissected from the embryos. The mesenchymal layers of the bladder and urethra were mechanically separated from the epithelial layer after enzymatic digest with trypsin. Tissues from female embryos from a litter were separately pooled. Each litter yielded 4 sample types: Female bladder mesenchyme and female urethral mesenchyme. A total of n=3 biological replicates for each sample were obtained from 3 independent litters at E14.5.  A total of n=3 biological replicates for each sample were obtained from 3 independent litters at E18.5.


title: Identification of distinct epithelial factors in the developing mouse bladder and urethra (E14.5 and E18.5)

overall_design: The objective of this study was to identify compartment specific gene expression in the developing bladder and urethra. We obtained timed-pregnant CD-1 female mice and collected embryos at embryonic day 14.5 and E18.5. The lower urinary tract, including bladder and pelvic urethra, were dissected from the embryos. The epithelial layer of the bladder and urethra were mechanically separated from the mesenchymal layer after enzymatic digest with trypsin. Tissues from female embryos from a litter were separately pooled. Each litter yielded 2 sample types: Female bladder epithelium and female urethral epithelium. A total of n=4 biological replicates for each sample type were obtained from 4 independent litters at E14.5.  A total of n=3 biological replicates for each sample type were obtained from 3 independent litters at E18.5.


title: Chronic intermittent fasting impairs β-cell maturation and function in adolescent mice

city: Neuherberg

first: Peter

last: Weber

address: Ingolstädter Landstraße 1

institute: Helmholtz Zentrum München

summary: Intermittent fasting (IF) is a nutritional lifestyle intervention with broad metabolic benefits, but whether the impact of IF depends on the individual's age is unclear. Here, we investigated the effects of IF on systemic metabolism and pancreatic islet function in old, middle-aged, and young mice. Short-term IF improved glucose homeostasis across all age groups, without altering islet function and morphology. In contrast, while chronic IF was beneficial for adult mice, it resulted in impaired β-cell function in the young. Using scRNAseq, we delineated that the β-cell maturation and function score were reduced in young animals. In human islets, a similar pattern was observed in Type 1 (T1D) and Type 2 diabetes (T2D), suggesting that the impact of chronic IF in adolescence is linked to the development of β-cell dysfunction. Our study suggests considering the duration of IF in younger people, as it may enhance rather than reduce diabetes outcomes.

overall_design: Old (O), middle-aged (M), and young mice (Y) were randomly grouped into ad libitum (AL) and intermittent fasting (IF) groups and were exposed to 9-10 weeks of treatment or 4-5 weeks (short). In the IF group, the food was removed from midnight to the following day (24 hours later), we employed the intermittent fasting protocol 1:2, which consists of 24 hours of food starvation for 48 hours of free access to a chow diet (PMID: 29039412).


title: Effect of APC depletion on gene expression in JEG-3 cells

city: Cambridge

first: Bowen

last: Gu

state: MA

address: 7 Divinity Ave

department: Stem Cell and Regenerative Biology Department

institute: Harvard University

summary: Fetal-maternal immune tolerance guarantees a successful pregnancy throughout gestation. HLA-G, a non-classical human leukocyte antigen (HLA) molecule exclusively expressed in extravillous trophoblasts (EVT), is a crucial factor in establishing fetal-maternal immune tolerance by interacting with inhibitory receptors on various maternal immune cells residing in the uterus. While trophoblast specific Cis-Regulatory Elements (CREs) impacting HLA-G transcription have been described, the identity of trans-acting factors controlling HLA-G expression in EVT remains poorly understood. Utilizing a genome-wide CRISPR-Cas9 knockout screen, we find that the WNT signaling pathway negatively regulates HLA-G expression in EVT. APC is a key component of the destruction complex for cytoplasmic β-catenin, switching off the canonical WNT pathway. This dataset containes the transcriptomics in JEG-3 cells upon APC knockout.

overall_design: To investigate the role of APC in regulating HLA-G expression in JEG-3 cells, we generated APC knockout JEG-3 cell lines. We then performed comparative gene expression analysis of WT and APC knockout cells

first: Jack

last: Strominger

first: Torsten

middle: B

last: Meissner


title: Effect of Amd1 inhibition on C2C12 mouse myotubes in culture after 72h treatment

first: Andrea

last: Bracaglia

summary: Amyotrophic lateral sclerosis (ALS) is a fatal neurodegenerative disease characterized by progressive paralysis due to primary and secondary degeneration of motor neurons. In spite of extensive biomedical research, no curative therapy has yet been established. One of the primary targets of ALS is skeletal muscle, which undergoes profound functional changes as the disease progresses. To better understand how altered innervation interferes with muscle homeostasis during disease progression, we generated the first spatial transcriptomics dataset of skeletal muscle in the SOD1G93A mouse model of ALS. Using this strategy, we identified polyamine (PA) metabolism as one of the main altered pathways in affected muscle fibers. By establishing a correlation between the vulnerability of muscle fibers and the dysregulation of this metabolic pathway, we show that disrupting polyamine homeostasis causes impairments similar to those seen in ALS muscle. Finally, we show that restoration of PA homeostasis rescues the muscle phenotype in SOD1G93A mice, opening new perspectives for the treatment of ALS.

overall_design: We performed gene expression analysis of RNA-Seq of totally differentiated C2C12 mouse myotubes treated with Sardomozide to inhibit Amd1 or DMSO as control.

first: Veronica

last: Ruggieri

first: Silvia

last: Scaricamazza

first: Chiara

last: D'Ercole

first: Daisy

last: Proietti

last: Cappelletti

first: Alberto

last: Macone

first: Biliana

last: Lozanoska-Ochser

first: Marina

last: Bouché

first: Lucia

last: Latella

first: Cristiana

last: Valle

last: Ferri

first: Lorenzo

last: Giordani

first: Luca

last: Madaro

first: Cristina

last: Parisi

first: Paolo

last: D'angelo


title: Polyamine Dysregulation Contributes to Muscle Fibers Vulnerability in ALS

city: Paris

address: 105 bld de l'hôpital

department: Centre de Recherche en Myologie - UMRS974 Sorbonne Université

institute: INSERM

summary: Amyotrophic lateral sclerosis (ALS) is a fatal neurodegenerative disease characterized by progressive paralysis due to primary and secondary degeneration of motor neurons. Despite the incredible effort of biomedical research, no curative therapy for this disease has yet been established. Given the direct interaction with neurons through neuromuscular junction (NMJ) stabilization, skeletal muscle appears to be a primary target of ALS, causing profound alteration in its function. Here we generated the first spatial transcriptomics dataset of SOD1G93A skeletal muscle as a mouse model for ALS. Using this strategy, we identified polyamine (PA) metabolism as one of the main altered pathways in affected muscle fibers. By identifying PA balance as a key factor in fiber vulnerability during disease progression, we show that perturbation of PA balance in muscle resembles disease features observed in ALS-affected muscle. Finally, we show that restoration of PA flux rescues the muscle phenotype of SOD1G93A mice, opening new perspectives in the treatment of ALS.

overall_design: Spatial Transcriptomics analysis of wildtype and SOD1G93A  (B6.Cg-Tg(SOD1 G93A)1Gur/J) murine Tibialis Anterior and Extensor digitorum longus at 75 and 150 days of age


title: Allogeneic HSPC-engineered CD33-targeting CAR-NKT cells synergize with hypomethylating agents for effective and safe treatment of myeloid malignancies

city: Los Angeles

first: Yichen

last: Zhu

state: California

address: 610 Charles E Young Drive S

institute: University of California, Los Angeles

summary: Chimeric antigen receptor (CAR)-engineered T cell therapy holds promise for targeting myeloid malignancies including acute myeloid leukemia (AML) and myelodysplastic syndrome (MDS). However, autologous approaches pose significant challenges in manufacturing and patient selection, emphasizing the need for off-the-shelf cell products. In this study, we systematically characterized primary AML and MDS patient samples, identifying a unique therapeutic opportunity for CAR-engineered invariant natural killer T (CAR-NKT) cell therapy. Utilizing a clinically guided culture method, we generated allogeneic IL-15-enhanced CD33-targeting CAR-NKT (Allo15CAR33-NKT) cells through HSPC engineering and an ex vivo, feeder-free HSPC differentiation culture. These cells demonstrated potent antitumor efficacy against blast cells via multiple tumor-targeting mechanisms. In vivo, Allo15CAR33-NKT cells exhibited effective tumor homing, expansion, and persistence, characterized by high effector function and low exhaustion propensity. Furthermore, these cells synergized with hypomethylating agent (HMA) treatment, which upregulated CD1d and NK ligand expression on tumor cells, enhancing susceptibility to Allo15CAR33-NKT cell-mediated killing. Notably, Allo15CAR33-NKT cells displayed minimal off-tumor effects against hematopoietic precursors, and low risks of graft-versus-host disease and cytokine release syndrome, highlighting their substantial therapeutic potential for myeloid malignancies.

overall_design: Gene expression profiling of therapeutic cells after repeated tumor challenge

first: Yan-Ruide

last: Li

first: Lili

last: Yang

first: Ying

last: Fang

first: Siyue

last: Niu


title: Correcting a pathogenic mouse mitochondrial DNA mutation by base editing

city: Martinsried

first: Danny

last: Nedialkova

address: Am Klopferspitz 18

institute: Max Planck Institute of Biochemistry

summary: Primary mitochondrial disorders are most often caused by deleterious mutations in the mtDNA. Here, we harnessed a mitochondrial base editor, DdCBE, to introduce a compensatory edit (m.5081G￫A) in a mouse model that carries the pathological m.5024C￫T mutation in the mitochondrial tRNAAla gene. For this, the DdCBE gene construct was packaged in recombinant AAV9 and systemically injected into mice. We found that total mt-tRNAAla levels, which are drastically reduced by the mutation, are restored by the m.5081G￫A edit in a dose-dependent manner. However, an excessive expression of DdCBE also induces extensive mtDNA off-target editing, counteracting this positive outcome. To address this, we optimized the dosage to maximize the amount of compensatory edit generated with minimal off-target editing. These results show that mitochondrial base editors are promising candidates for gene therapy for mitochondrial disorders, but their expression need to be carefully controlled.

overall_design: tRNA-Seq datasets were generated from mouse embryonic fibriblasts (MEF) and mouse tissues investigate the impact of correcting a pathogenic mutation in the mitochondrial tRNA-Ala gene by base editing.

middle: D

first: Till

last: Balla

first: Jose

last: Barrera-Paez

first: Carlos

middle: T

last: Moraes


title: miRNA differentially expressed between DU145 sensitive et resistant extracellular vesicles to irradiation

city: Nantes

first: Delphine

last: Fradin

address: 8 quai Moncousu

institute: CRCI2NA, Inserm UMR1307, CNRS UMR6075

summary: Radiotherapy represents a major curative treatment for prostate cancer (PCa), but some patients will develop radioresistance (RR) and relapse. The underlying mechanisms remain poorly understood, and miRNAs might be key players in the acquisition and maintenance of RR. Through their encapsulation in small extracellular vesicles (EVs), they can also be relevant biomarkers of radiation response. Using next-generation sequencing, we found that miR-200c-3p was downregulated in PCa RR cells and in their small EVs due to a gain of methylation on its promoter during RR acquisition. We next showed that its exogenous overexpression restores the radiosensitivity of RR cells by delaying DNA repair through the targeting of HP1α. Interestingly, we also observed downregulation of miR-200c-3p expression by DNA methylation in radiation-resistant lung and breast cancer cell lines. In summary, our study demonstrates that the downregulation of miR-200c-3p expression in PCa cells and in their small EVs could help distinguish radioresistant from sensitive tumor cells. This miRNA targets HP1α to delay DNA repair and promote cell death.

overall_design: Evs were purified from cancer cell lines, miRNAs were extracted and sequenced

first: Maureen

last: Labbé


title: Genome-wide DNA methylation profiling of multiple sclerosis patients in relapse [CD4]

city: Moscow

first: Ivan

last: Kiselev

address: Ostrovitianov st. 1

country: Russia

institute: Pirogov Russian National Research Medical Universitty

summary: Multiple sclerosis (MS) is a chronic autoimmune and degenerative disease of the central nervous system, which develops in genetically predisposed individuals upon exposure to environmental influences. Environmental triggers of MS, such as viral infections or smoking, were demonstrated to affect DNA methylation, and thus to involve this important epigenetic mechanism  in the development of pathological processes. To identify DNA methylation hallmarks, associated with relapse of MS, we performed genome-wide DNA methylation profiling of two cell populations (CD4+ T-lymphocytes and CD14+ monocytes), collected from the same individuals, using Illumina 450K methylation arrays. We revealed changes in DNA methylation for both cell populations of MS patients in relapse when compared wih remission. In CD4+ cells the absolute majority of differentially methylated positions (DMPs) were hypermethylated. In CD4+, but not in CD14+ cells, we found a differentially methylated region within the GNAS complex locus and showed significant differences in the ammount of its transcripts between patients in relapse and remission.

overall_design: We performed a genome-wide DNA methylation analysis in CD4+ T lymphocytes of 8 treatment-naïve patients with multiple sclerosis in relapse.


title: Decoding genome-wide DNA binding sites for AR and ERRα in mouse primary hepatocytes

city: Hangzhou

first: Chen

last: Jie

state: Zhejiang

address: Dunyu Road No.300

department: School of Life Science

institute: Westlake University

summary: Glucagon has recently been found to modulate liver fat content, in addition to its role in regulating gluconeogenesis. However, the precise mechanisms by which glucagon signaling synchronizes glucose and lipid metabolism in the liver remain poorly understood. By employing chemical and genetic approaches, we demonstrate that inhibiting the androgen receptor (AR) impairs the ability of glucagon to stimulate gluconeogenesis and lipid catabolism in primary hepatocytes and female mice. Notably, AR expression in the liver of female mice is up to three times higher than that in their male littermates, accounting for the more pronounced response to glucagon in females. Mechanistically, hepatic AR promotes energy metabolism and enhances lipid breakdown for liver glucose production in response to glucagon treatment through the peroxisome proliferator-activated receptor gamma coactivator 1-alpha (PGC1α)/estrogen-related receptor alpha (ERRα)-mitochondria axis. Overall, our findings highlight the crucial role of hepatic AR in mediating glucagon signaling and the sexual dimorphism in hepatic glucagon sensitivity.

overall_design: Chromatin immunoprecipitation DNA-sequencing(ChIP-seq) for ERRα, AR in WT or AR knockout mouse primary hepatocytes

first: Jie

last: Chen

first: Jia

last: You

first: Lianfeng

last: Wu


title: Genome-wide DNA methylation profiling of multiple sclerosis patients in relapse [CD14]

overall_design: We performed a genome-wide DNA methylation analysis in CD14+ monocytes of 8 treatment-naïve patients with multiple sclerosis in relapse.


title: Expression profiles in pancreatic islets from Wfs1-deficient mice

city: Ube

first: Katsuya

last: Tanabe

state: Yamaguchi

address: 1-1-1 Minamikogushi

country: Japan

institute: Yamaguchi University

summary: Wolfram syndrome is a genetic disorder characterized by insulin-dependent diabetes mellitus due to mutations in the WFS1 gene.  The Wfs1-deficient mice exhibit selective β-cell loss and impaired insulin secretion. This phenotype is believed to be associated with an augmentation of ER stress, although the underlying mechanisms remain unknown. To investigate the molecular basis of β-cell failure resulting from Wfs1 deficiency, we performed gene expression profiling analysis using data obtained from RNA-seq of Wfs1KO and WT islets.

overall_design: Pancreatic islets were isolated from 12-week-old male Wfs1KO and WT mice by ductal collagenase digestion of the pancreas, and then used for RNA-seq (n=4 for each genotype).

first: Kikuko

last: Amo-Shiinoki

first: Meng

last: Zou


title: High-Dimensional Analyses Reveal IL15 Enhances Activation of Sipuleucel-T Lymphocyte Subsets and Reverses Immunoresistance

city: St. Louis

first: Kavita

last: Rwat

state: MO

address: St. Louis

department: Oncology

institute: Washington University in St. Louis

summary: Sipuleucel-T (sip-T) is the only FDA-approved autologous cellular immunotherapy for metastatic castration-resistant prostate cancer (mCRPC). Here, we report the first high-dimensional analyses of sip-T using mass cytometry (CyTOF) and show a lymphoid predominance, with CD3+ T cells constituting the highest proportion (median ~60%) of sip-T, followed by B-cells, and natural killer (NK) and NKT cells. We hypothesized that treatment of sip-T with homeostatic cytokines known to activate/expand effector lymphocytes could augment efficacy against prostate cancer. Of cytokines tested, IL-15 treated sip-T showed the most significant activation/proliferation of effector lymphocytes in an antigen-specific manner, as well as augmentation of tumor cytotoxicity in-vitro. Adoptive transfer of IL-15 treated sip-T into NSG mice resulted in potent prostate tumor growth inhibition compared with control sip-T. Evaluation of tumor-infiltrating lymphocytes revealed a two-to-fourteen-fold higher influx of sip-T and a significant increase in interferon (IFN)-γ producing CD8+ T and NKT cells within the tumor microenvironment (TME) in the IL-15 group.

overall_design: To evaluate the effect of IL-15 treated sip-T on in vivo tumor growth, LNCaP tumor cells  were inoculated subcutaneously in mice. Once average tumor sizes reached 50-100 mm2, mice received four injections of IL-15 treated, or control sip-T (5x10^6/100 µl in PBS, intraperitoneally) with one-week intervals. rhIL-15 (1 µg) was also injected subcutaneously at the time of sip-T injection. All control mice were sham dosed with vehicle (PBS).

first: Russell

last: Pachynski

first: Muhammad

last: Saeed

last: Rawat


overall_design: To evaluate the effect of IL-15 treatment on sip-T


title: Mannose metabolism reshapes T cell differentiation to enhance anti-tumor immunity: scCITE-seq

city: Seattle

first: Daniel

middle: Guorui

state: Washington

address: 1100 Fairview Ave N

department: Immunolog

institute: Fred Hutchinson Cancer Center

summary: Cellular metabolic status profoundly influences T cell differentiation, persistence, and anti-tumor efficacy. By performing single-cell metabolic analyses of T cells from human cancer and mouse chronic infection atlases, we unveiled that diminished mannose metabolism is a prominent feature of T cell dysfunction. Conversely, experimental augmentation/restoration of mannose metabolism in adoptively transferred T cells via D-mannose supplementation enhanced anti-tumor activity and restricted exhaustion differentiation both in vitro and in vivo. Mechanistically, D-mannose treatment induced intracellular metabolic programming and increased the O-GlcNAcylation of β-catenin, which preserved Tcf7 expression and epigenetic stemness, thereby promoting stem- like programs in T cells. Finally, in vitro expansion with mannose supplementation yielded T cell products for adoptive therapy with stemness characteristics, even after extensive long-term expansion, that exhibited enhanced anti-tumor efficacy. Thus, these findings reveal cell-intrinsic mannose metabolism as a physiological regulator of CD8+ T cell fate, decoupling proliferation/expansion from differentiation, and underscored the therapeutic potential of mannose modulation in cancer immunotherapy.

overall_design:
Wild-type female C57BL/6N (B6, CD45.2+) mice were purchased from the Vital River as recipients. Female NCG (NOD/ShiLtJGpt-Prkdcem26Cd52Il2rgem26Cd22/Gpt) mice were purchased from the GemPharmatech. Female C57BL/6-Tg (TcraTcrb) 1100Mjb/J transgenic mice, expressing a TCR specific for chicken egg OVA SIINFEKL epitope in the context of H2Kb, were kindly provided by Dr. Yuting Ma. All male or female mice between 6 and 12 weeks of age were used and the age-matched and sex-matched mice were randomly assigned to all animal experiments. All mice were housed in the specific-pathogen-free facilities at the Institutional Animal Care in the Suzhou Institute of Systems Medicine with a cycle of 12-h/12-h light/dark, a controlled room temperature of 22-24°C, a constant humidity of 60% and with unrestricted food and water availability. All animal studies were approved and performed in accordance with the guidelines and regulations implemented by the Institutional Animal Care and Use Committee (IACUC) of Suzhou Institute of Systems Medicine (ISM-IACUC-0151-R). The maximal tumor burden permitted by IACUC did not exceed 1500mm3 in all animal experiments.

B16 mouse melanoma cells, HepG2 human hepatocellular carcinoma cells, and HEK- 293T cells from the American Type Culture Collection (ATCC) were maintained in DMEM medium (Gibco) supplemented with 10% FBS (Gibco) and 1% penicillin- streptomycin (Gibco). K562 and Jurkat cells from ATCC were cultured in RPMI-1640 medium (Gibco) supplemented with 10% FBS, 0.1M HEPES (Gibco), 1% non- essential amino acids (Gibco), 1mM sodium pyruvate (Gibco), 1% penicillin- streptomycin and 50μM β-mercaptoethanol (Gibco). The B16, HepG2 and K562 cells were transduced with lentivirus to overexpress OVA, human NY-ESO-1 and human CD19 antigen respectively, and were screened with appropriate antibiotics.

Murine CD8+ T cells were isolated from the spleens or lymph nodes of 6-12 weeks male or female OT-I mice and were maintained in RPMI-1640 medium supplemented with 10% FBS, 0.1M non-essential amino acids (Gibco), 1% GlutaMAX (Gibco), 0.1M HEPES (Gibco), 1mM sodium pyruvate (Gibco), 50μM β-mercaptoethanol (Gibco), 1% penicillin-streptomycin (Gibco), 20U/ml mouse IL-2 (Peprotech) in the absence or presence of mannose (20mM). To activate OT-I T cells, the media was further complemented with OVA257-264 peptide (SIINFELK, 1μg/ml, or anti-mouse CD3 (2μg/ml, Biolegend) and anti-mouse CD28 (1μg/ml, Biolegend) monoclonal antibodies, and were cultured in the cell incubator at 37°C, 5% CO2 for 48 h.

To elucidate the effect of mannose on the differentiation of TILs, C57BL/6N mice were injected subcutaneously with B16-OVA cells and adoptive OT-I T cells as described above. For mannose treatment, normal drinking water was exchanged for 200ml of 20% mannose in drinking water (w/v) once every week, and mice received 20% mannose (200μl) by oral gavage three times a week. The tumors were collected after T cell transferring for 14 days, and single-cell suspensions were processed and harvested. Then, the tumor-infiltrating CD8+CD45.1+ T cells were sorted by BD FACS Aria III. Subsequently, sorted T cells were incubated with anti-mouse CD16/32 antibody (Biolegend) to block the Fc receptors and labeled with TotalSeq-B Mouse Universal Cocktail V1.0 (Biolegend) according to the manufacturer’s instructions. Next, the cell suspension was loaded into Chromium microfluidic chips with 30.v3 chemistry and barcoded with a 10×Chromium Controller (10×Genomics). RNA from the barcode was subsequently reverse-transcribed. The scRNA-seq libraries were generated following the manufacturer’s instructions of Chromium Next GEM single Cell 3’Gel Bead kit v.3.1 (10×Genomic) followed by sequencing on a Novaseq6000 at the NGS Core of the Novogene.

middle: G

first: Yapeng

last: Su

first: Guideng

last: Li


title: MicroRNA sequencing data of germ cell tumor cell lines

last: Nettersheim

summary: MicroRNA sequencing of non-seminomatous germ cell tumor cell lines of yolk-sac tumor (YST) and embryonal carcinoma (EC) origin.

overall_design: YST and EC cell lines were cultivated till 80 % confluency. Total RNA has been isolated and subsequently microRNA sequencing has been performed.


title: Fasting-induced miR-7a-5p in AgRP neurons regulates food intake

city: Shanghai

first: Mingyang

last: Yuan

address: No. 573, Xujiahui Road, Huangpu District

institute: Shanghai Institute of Endocrine and Metabolic Diseases

summary: The molecular control of feeding after fasting is essential for maintaining energy homeostasis, and overfeeding usually leads to obesity. RNA interference has been clinically successful in managing diseases, and the identification of a feeding-regulated microRNA (miRNA), which remains a challenge, could be a strategy for combating obesity. By performing a comprehensive genome-wide microRNA screening in the arcuate nucleus of the hypothalamus (ARC) of fasted mice and ad libitum mice, we found a significant increase in miR-7a-5p levels after fasting. miR-7a-5p was highly expressed in the ARC, and inhibition of miR-7a-5p specifically in AgRP neurons reduced food intake and body weight gain. miR-7a-5p inhibited S6K1 gene expression by binding to its 3’-UTR. Furthermore, the reduction of food intake by anti-miR-7a-5p was partially reversed by the downregulated mechanistic target of rapamycin complex 1 (mTOR1)/ribosomal S6 kinase 1 (S6K1) signaling in the AgRP neurons. Importantly, intracerebroventricular administration of the miR-7a-5p inhibitor could reduce food intake and body weight. Collectively, our findings suggest miR-7a-5p as an orexigenic factor in AgRP neurons and a potential novel target for obesity treatment.

overall_design: A comprehensive genome-wide miRNA screening in the arcuate nucleus of the hypothalamus (ARC) of fasted mice and ad libitum mice was performed. Through intracerebral virus injections, intracerebroventricular injections, and miRNA sponge technology, miR-7a-5p was inhibited specifically in AgRP neurons and in the central nervous system, and metabolic phenotypes were monitored. Quantitative Real-time PCR, Western blotting, and luciferase reporter assay were used to investigate the mechanisms underlying miR-7a-5p’s regulation of food intake.


title: Combinatorial in vivo genome editing identifies widespread epistasis and an accessible fitness landscape during lung tumorigenesis

city: Stanford

first: Gabor

last: Boross

address: 450 Serra Mall

institute: Stanford University

summary: Lung adenocarcinoma, the most common subtype of lung cancer, is genomically complex, with tumors containing tens to hundreds of non-synonymous mutations. However, little is understood about how genes interact with each other to enable the evolution of cancer in vivo, largely due to a lack of methods for investigating genetic interactions in a high-throughput and quantitative manner. Here, we employed a novel platform to generate tumors with all pairwise inactivation of ten diverse tumor suppressor genes within an autochthonous mouse model of oncogenic KRAS-driven lung cancer. By quantifying the fitness of tumors with every single and double mutant genotype, we show that most tumor suppressor genetic interactions exhibited negative epistasis, with diminishing returns on tumor fitness. In contrast, Apc inactivation showed positive epistasis with the inactivation of several other genes, including synergistic effects on tumor fitness in combination with Lkb1 or Nf1 inactivation. Sign epistasis was extremely rare, suggesting a surprisingly accessible fitness landscape during lung tumorigenesis. These findings greatly expand our understanding the evolutionary interactions that drive tumorigenesis in vivo.

overall_design: Ultra-deep sequencing of DNA barcode amplicon

first: Jess

last: Hebert

first: Yuning

last: Tang

first: Laura

last: Andrejka

first: Márton

last: Szamecz

first: Steven

last: Lopez

first: Dmitri

last: Petrov

first: Gábor

first: Monte

last: Winslow


title: Mechano-oncogenic cytoskeletal remodeling drives leukemic transformation with mitochondrial vesicle-mediated STING activation

city: wuhan

first: song

last: zemin

address: no.185 the road of eastlake

institute: wuhan university

summary: Mitochondria are integrated within the cytoskeleton for structural integrity and functional regulation, yet the pathological exploitation of these interactions in cell fate decisions remains largely unexplored. Here, we identify a cytoskeleton-mitochondria remodeling mechanism underlying leukemic transformation by the core-binding factor subunit beta and smooth muscle myosin heavy-chain fusion (CBFβ-SMMHC). This chimera reconstructs a cytosolic filamentous cytoskeleton, inducing NMIIA phosphorylation and INF2-dependent filamentous actin (F-actin) assembly, which enhance cellular stiffness and tension, leading to calcium-mediated mitochondrial constriction, termed cytoskeletal co-option of mitochondrial constriction (CCMC). CCMC can also be triggered through diverse approaches independent of CBFβ-SMMHC, reconstructing a similar cytoskeleton and recapitulating acute myeloid leukemia (AML) with consistent immunophenotypes and inflammatory signatures. Notably, CCMC generates TOM20−PDH+mtDNA+ mitochondrial-derived vesicles that activate cGAS-STING signaling, with Sting knockout abrogating CCMC-induced leukemogenesis. Targeted inhibition of CCMC or STING suppresses AML propagation while sparing normal hematopoiesis. These findings establish CCMC as an intrinsic mechano-oncogenic process linking genetic mutations with cytoskeletal remodeling to oncogenic transformation, highlighting its promise as a therapeutic target.

overall_design: Bone marrow cells, extracted from leukemia and wildtype mice, underwent ACK buffer treatment post-extraction. Single-cell RNA sequencing and bulk RNA sequencing were performed to figure out transcriptional profiles of distinct lekemia models.


title: Transcriptomic analysis of BM-MSCs identified EGR1 as a transcription factor to fully exploit their therapeutic potential

city: Milan

first: Stefano

last: Beretta

address: Via Olgettina, 60

institute: San Raffaele Telethon Institute for Gene Therapy

summary: Bone marrow-mesenchymal stromal cells (BM-MSCs) are key components of the BM niche, where they regulate hemato-poietic stem progenitor cells (HSPCs) homeostasis by direct contact and secreting soluble factors. BM-MSCs also protect the BM niche from excessive inflammation by releasing anti-inflammatory factors and modulating immune cell activity. Thanks to these proper-ties, BM-MSCs were successfully employed in pre-clinical HSPC transplantation models, increasing the rate of HSPC engraftment, accelerating the hematological reconstitution, and reducing the risk of graft failure. However, their clinical use requires extensive in vitro expansion, altering their biological and functional properties. In this work, we analyzed the transcriptomic profile of human BM-MSCs sorted as CD45neg, CD105+, CD73+, and CD90+ cells from the BM aspirates of heathy-donors and corresponding ex-vivo expanded BM-MSCs. We found the expression of immune and inflammatory genes downregulated upon cell culture and selected the transcription factor EGR1 to restore the MSC properties. We overexpressed EGR1 in BM-MSCs and performed in vitro tests to study the functional properties of EGR1-overexpressing BM-MSCs. We concluded that EGR1 increased the MSC response to inflam-matory stimuli and immune cell control and potentiated the MSC hematopoietic supportive activity in co-culture assay, suggesting that the EGR1-based reprogramming may improve the BM-MSC clinical use.

overall_design: RNA sequencing of primary BM-MSCs, sorted from the BM aspirates of pediatric healthy donors (n=5) based on the expression of canonical MSC markers, and corresponding ex-vivo cultured MSCs.

first: Ludovica

last: Santi

first: Ivan

last: Merelli

first: Maria

last: Bernardo

first: Stefania

last: Crippa


title: Identification of distinct mesenchymal factors in the developing bladder and urethra

first: Diya

last: Binoy Joseph

summary: The lower urinary is derived from the endodermal precursor, the cloaca. Despite common embryological origins, the epithelial linings and surrounding mesenchyme of the bladder and urethra show divergence. The bladder forms from the anterior part of the urogenital sinus, a cloacal derivative formed after septation of the cloaca to form the anorectal and urogenital tracts. The urethra elongates posteriorly and shows sex-specific differences as a result of hormonal action. The bladder is a target for regenerative therapies and tissue reconstruction strategies. A significant shortcoming of these strategies has been the inability to recapitulate all layers of bladder epithelial cells, most importantly the apical uroplakin expressing cell layer that forms a tight, impermeable barrier against components in the urine. Epithelial-mesenchymal interactions are critical for organogenesis. Several studies have shown the ability of embryonic bladder mesenchyme to reprogram non-bladder epithelium to resemble bladder tissue at the molecular and cellular level. In this study, we performed bulk RNA-sequencing on the mesenchymal layers of the developing mouse bladder and urethra and identified compartmentalized organ-specific gene expression. Our study identified transcription factor genes and secreted protein genes specific to the bladder or urethra mesenchymal compartments. Additionally, we describe sex-specific differences in the lower urinary tract mesenchyme which are more pronounced between the male and female urethral mesenchyme and less evident in the bladder mesenchyme between sexes.

overall_design: The objective of this study was to identify compartment specific gene expression in the developing bladder and urethra. We obtained timed-pregnant CD-1 female mice and collected embryos at embryonic day 16.5. The lower urinary tract, including bladder and pelvic urethra, were dissected from the embryos. The epithelial layer of the bladder and urethra were mechanically separated from the mesenchymal layer after enzymatic digest with trypsin. Male and female samples from a litter were separately pooled. Each litter yielded 4 samples: Female bladder mesenchyme, Female urethral mesenchyme, Male bladder mesenchyme, Male urethral mesenchyme. A total of 4 biological replicates for each sample were obtained from 4 independent litters.

last: Joseph


title: Identification of distinct epithelial factors in the developing bladder and urethra

summary: The lower urinary is derived from the endodermal precursor, the cloaca. Despite common embryological origins, the epithelial linings and surrounding mesenchyme of the bladder and urethra show divergence. The bladder forms from the anterior part of the urogenital sinus, a cloacal derivative formed after septation of the cloaca to give rise to the anorectal and urogenital tracts. The urethra elongates posteriorly and shows sex-specific differences as a result of hormonal action. The bladder is a target for regenerative therapies and tissue reconstruction strategies. A significant shortcoming of these strategies has been the inability to recapitulate all layers of bladder epithelial cells, most importantly the apical uroplakin positive layer that forms a tight, impermeable barrier against components in the urine. The urethral epithelium is contiguous with the bladder epithelium but has distinct cellular architecture and lacks a uroplakin expressing apical layer. We hypothesized that comparison of the developing urethra and bladder epithelium will identify early genes that are responsible for urethra and bladder-specific differentiation. In this study, we compared the epithelial compartments of the developing mouse bladder and urethra to identify genes that are differentially expressed in these two compartments. Our study identified transcription factor genes and other tissue-specific markers that are confined to either the urethra or bladder epithelium. Additionally, we describe sex-specific differences in the lower urinary tract epithelium which are more pronounced between the male and female urethral epithelium and less evident in the bladder epithelium between sexes.

overall_design: The objective of this study was to identify compartment specific gene expression in the developing bladder and urethra. We obtained timed-pregnant CD-1 female mice and collected embryos at embryonic day 16.5. The lower urinary tract, including bladder and pelvic urethra, were dissected from the embryos. The epithelial layer of the bladder and urethra were mechanically separated from the mesenchymal layer after enzymatic digest with trypsin. Male and female samples from a litter were separately pooled. Each litter yielded 4 samples: Female bladder epithelium, Female urethral epithelium, Male bladder epithelium, Male urethral epithelium. A total of 4 biological replicates for each sample were obtained from 4 independent litters.


title: Identification of mechanistic chronic kidney disease biomarkers by comprehensive bulk RNA-seq transcriptomics and SWATH proteomics of the rat sub-total nephrectomy model of kidney fibrosis

city: Slough

first: Andrew

middle: James

last: Skelton

address: 208 Bath Road

department: Translational Bioinformatics

country: United Kingdom

institute: UCB

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

overall_design: Refer to individual Series


title: Identification of mechanistic chronic kidney disease biomarkers by comprehensive bulk RNA-seq transcriptomics and SWATH proteomics of the rat sub-total nephrectomy model of kidney fibrosis [RNA-Seq_2]

summary: The rat sub-total nephrectomy (SNx) is a functional model of chronic kidney disease (CKD), where the main pathological driver is glomerular hypertension. Comprehensive transcriptomics and proteomics analyses on the rat SNx model were performed to identify biomarkers in plasma or urine that correlate with kidney disease and functional kidney loss. Kidneys were subjected to collagen I and III staining for fibrosis scoring, SWATH proteomics and bulk RNA-sequencing transcriptomics (RNA-seq), with SWATH also performed on plasma and urine. Differential expression analysis demonstrated significant dysregulation of genes and proteins involved in fibrosis, metabolism, and immune response in the SNx rats compared to controls. Gene ontology analysis of the intersecting genes and proteins from both studies demonstrated common biology between animal cohorts that reached the predefined kidney disease thresholds (serum creatinine >2-fold or proteinuria >3-fold increase over sham-operated). Thirteen significantly differential molecules were detected with consistent directional changes in both transcriptomics and proteomics datasets. These molecules were detected independently in kidney (both RNA and protein) and urine (protein only), but not in plasma. The bioinformatics analysis enabled the identification of mechanistic CKD biomarkers including lumican and collagen alpha-1(III) chain, whose co-expression has previously been both implicated in fibrosis and detected in urine in CKD patients.

overall_design: Case Control


title: Targeting BCL11B in chimeric antigen receptor-engineered lymphoid progenitors propagates adaptive NK-like cell responses against leukemia

city: Braunschweig

first: Robert

last: Geffers

address: Inhoffenstr. 7

department: Dep. Molecular Bacteriology

institute: HCI - Helmholtz Centre for Infection Research

summary: Chimeric antigen receptor (CAR)-induced suppression of the transcription factor B cell CLL/lymphoma 11B propagates CAR-induced killer (CARiK) cell development. Here, we show that CRISPR-mediated BCL11B knockout (ko) in early lymphoid progenitors distinctively modulates this process depending on its use alone or in combination with a CAR. Upon adoptive transfer into hematopoietic stem cell recipients, Bcl11b-edited progenitors mediated either innate or adaptive anti-leukemic immune responses. With CAR expression being a prerequisite for antigen-specific CARiK responses, additional BCL11B ko was critical for the acquisition of adaptive killer cell functions such as clonal expansion, persistence, and recall responses. These findings have important insights on how BCL11B targeting can be used to tailor anti-leukemia functionality of CAR-engineered lymphoid progenitor cells.

overall_design: Transcriptional profiling of in vivo matured lymphoid progenitor cells transduced with an inducible CD123 CAR and Bcl11b-targeted sgRNA by scRNA sequencing analysis

first: F

last: Baatz

first: M

last: Sauer

first: R


title: Local inflammation precedes respiratory muscle wasting and fibrotic remodeling in a mouse model of PDAC

city: Gainesville

first: Daria

last: Neyroud

state: FL

address: 1275 Center Drive

institute: University of Florida

summary: Cancer cachexia represents a debilitating muscle wasting condition that is highly prevalent in patients with pancreatic ductal adenocarcinoma (PDAC). Cachexia is estimated to contribute to ~30% of cancer-related deaths, with deterioration of respiratory muscles suspected to be a key contributor to cachexia-associated morbidity and mortality. In recent studies, we identified inflammation and fibrotic remodeling of respiratory accessory muscles as a key feature of human PDAC cachexia. To gain insight into mechanisms driving respiratory muscle wasting and fibrotic remodeling in response to PDAC, we conducted temporal histological and transcriptomic analyses on diaphragm muscles harvested from mice bearing orthotopic murine pancreatic (KPC) tumors at time points reflective of pre-cachexia (D8 and D10), mild-moderate cachexia (D12 and D14) and advanced cachexia (endpoint). Compared to Sham, KPC mice showed progressive diaphragm myofiber atrophy beginning on D12 (-16 to -24% , D12toendpointvs.Sham,P< 0.05), which preceded reductions in breathing frequency (-55%,P= 0.0074) and diaphragm excursion (-43%,P= 0.0006) observed at endpoint. During the pre-cachexia phase, diaphragms showed significantleukocyte infiltration (+3 fold to +13-fold; D8–endpointvs.Sham,P< 0.05) and transcriptomic enrichment of inflammatory processes associated with tissue injury that remained increased through endpoint. Diaphragm inflammation was followed by increases in PDGFR+ fibroadipogenic progenitors (+2.5 to +3.8-fold; D10–endpointvs.Sham,P< 0.05), ECM expansion (+1.5 to +1.8-fold; D14–endpointvs.Sham),P<0.05) and collagen accumulation (+3.8-fold; Endpointvs.Sham,P= 0.0013). These processes were supported by changes in the diaphragm transcriptome. Ingenuity pathway analysis predicted factors involved in inflammatory responses to tissue injury, including TGF-B1, Angiotensin, and PDGF BB, as top upstream regulators activated in diaphragms prior to and throughout cachexia progression, while PGC-1α and the insulin receptor were among the top upstream regulators predicted to be suppressed. The transcriptomic dataset further revealed progressive disturbances to networks involved in lipid, glucose and oxidative metabolism, activation of the unfolded protein response and neuromuscular junction remodeling associated with denervation. In summary, our data support leukocyte infiltration and fibroadipogenic progenitor expansion as early events that precede wasting and fibrotic remodeling of respiratory muscles in response to PDAC that may also underlie metabolic disturbances, weakness and respiratory complications.

overall_design: Diaphragm muscles (three biological replicates per time point / phenotype) were harvested from  non-tumor-bearing mice (Sham/Control), and tumor-bearing mice at day 8 (KPC D8), day 10 (KPC D10), day 12 (KPC D12), day 14 (KPC D14) and humane-endpoint (KPC END) after KPC cell orthotopic injection

first: Sarah

last: Judge

middle: R


title: Identification of mechanistic chronic kidney disease biomarkers by comprehensive bulk RNA-seq transcriptomics and SWATH proteomics of the rat sub-total nephrectomy model of kidney fibrosis [RNA-Seq_1]


title: Effects of Subacute Exposure to 4-OH-PCB52 on the Gene Expression of Male Adolescent Rat Cerebellum and Striatum Regions via a Polymeric Implant Exposure System

city: Coralville

first: Hui

last: Wang

state: IA

address: 2501 Crosspark Rd

institute: University of Iowa

summary: Polychlorinated biphenyls (PCBs) are persistent organic pollutants (POPs) that ubiquitously exist in the environment. PCB exposure has been linked to cancer and multi-system toxicity, including neurotoxicity. 2,2',5,5'-Tetrachloro-biphenyl (PCB 52) is one of the most frequently detected congeners in the environment and human blood. The hydroxylated metabolites of PCB 52 may also be neurotoxic, especially for children whose brains are still developing. However, it is challenging to discern the contribution of these metabolites to PCB neurotoxicity because the metabolism of PCB is species-dependent. In this study, we evaluated the subacute neurotoxicity of a human-relevant metabolite, 2,2',5,5'-tetrachlorobiphenyl-4-ol (4-OH-PCB52), on male adolescent Sprague Dawley rats, via a novel polymeric implant drug delivery system grafted subcutaneously, at total loading concentrations ranging from 0%, 1%, 5%, and 10% of the implant (w/w) for 28 days. Y-maze, hole board test, open field test, and elevated plus maze were performed on exposure days 24 to 28 to assess their locomotor activity, and exploratory and anxiety-like behavior. 4-OH-PCB52 and other possible hydroxylated metabolites in serum and vital tissues were quantified using gas chromatography with tandem mass spectrometry (GC-MS/MS). RNA sequencing was performed in striatum and cerebellum. Based on the data including neurobehavior, 4-OH-PCB52 and metabolite levels, gene expression in the striatum and cerebellum; a subacute exposure to 4-OH-PCB52 results in subtle changes in response to exposure.

overall_design: To determine the gene expression alterations following subacute exposure to 4-OH-PCB52 (with levels of 0, 1%, 5% and 10% compound loading in the implants) in male adolescent rats, striatum and cerebellar regions were processed for RNA sequencing. (N = 6 per exposure group)

first: Bullert

last: Amanda

first: Wang

last: Hui

first: Li

last: Xueshu

first: Stevens

last: Hanna

first: Klingelhutz

last: Aloysius

first: Ankrum

last: James

first: Adamcakova-Dodd

last: Andrea

first: Thorne

last: Peter

first: Lehmler

last: Hans-Joachim


title: Txnip deficiency causes a susceptibility to acute cold stress with brown fat dysfunction in mice

first: Katsuya

last: Tanabe