title: Seeing the whole transcriptomics picture: Spatial gene expression analysis reveals photoreceptor stress as modulator of retinal vascular changes

city: Canberra

first: Ulrike

last: Schumann

state: ACT

address: 131 Garran Road

institute: The Australian National University

summary: Photoreceptor cell death is a hallmark feature of many retinal degenerative diseases including age-related macular degeneration. At the molecular level, oxidative stress and inflammation are known central pathogenetic drivers, but the spatial and cellular origins of the underlying molecular mechanisms remain unclear. We used spatial transcriptomics to investigate the spatio-temporal gene expression changes in the mouse retina in response to photo-oxidative damage. In both the healthy and degenerating retina, we uncover regionally distinct transcriptomes, with higher expression of immunity related genes in the superior retina. Exposure to photo-oxidative damage increased the expression of genes involved in inflammatory processes, innate immune responses, and cytokine production in a highly localised manner. This focal region seems a key driver of molecular changes, including upregulation of angiogenic pathways. Consequently, we show substantial alterations in vacular endothelial growth factor, pleiotrophin and midkine signalling between retinal layers, some of which are novel angiogenic signalling pathways within the retina.

overall_design: Parasaggital cross-sections of C57Bl6/J mouse eyes were subjected to Visium spatial gene expression. Tissue from dim-reared (DR) controls was compared to tissue from a 1-day (1PD), 3-day (3PD) and 5-day (5PD) photo-oxidative damage time course, respectively. The experiments were performed in biological duplicates.

first: Lixinyu

last: Liu

first: Riemke

last: Aggio-Bruce

first: Adrian

last: Cioanca

first: Artur

last: Shariev

first: Michele

last: Madigan

first: Krisztina

last: Valter

first: Jiayu

last: Wen

first: Riccardo

last: Natoli


title: Harnessing STING Signaling and Natural Killer Cells to overcome PARP Inhibitor Resistance in Homologous Recombination Repair altered Breast Cancer [RNA-seq]

status: Public on Mar 03 2025

city: Barcelona

first: Lara

last: Nonell

address: C/ NATZARET, 115-117

department: VHIOinformatics

country: Spain

institute: Vall d'Hebron Institute of Oncology (VHIO)

type: Expression profiling by high throughput sequencing

summary: Homologous recombination deficiency (HRD) contributes to genomic instability and leads to sensitivity to poly ADP-ribose polymerase inhibitors (PARPi). HRD also activates the cyclic GMP–AMP synthase (cGAS)-STimulator of INterferon Genes (STING)-Interferon (IFN) pathway, highlighting the need to understand the impact of cGAS-STING-IFN signaling on PARPi efficacy. In this study, we analyzed a cohort of thirty-five breast cancer (BC) patient-derived xenografts (PDX) and mouse-derived allografts (MDA). PARPi sensitivity correlated with HRD, increased genomic instability, and activation of the cGAS-STING-IFN signaling pathway. Single-cell analyses showed that IFN signaling and IFN-based immune interactions were suppressed in preclinical models with acquired resistance to PARPi, lacking concomitant clonal expansion of functional CD8+ T cells. However, the combination of PARPi and a novel STING agonist (STINGa) increased immune infiltration and resulted in superior antitumor activity in these tumors. Notably, the efficacy of PARPi monotherapy and the combination treatment with a STINGa was dependent on Natural Killer (NK) cells. In agreement, BC patients with BRCA1/BRCA2 mutations and good responses to PARPi showed higher abundancy of CD56+ NK cells in the tumor microenvironment and treatment-engaged CD56bright NK cells in the peripheral immune compartment, compared to those with poor responses. Therefore, these findings propose the combination of PARPi and STINGa as a potential novel strategy to enhance the therapeutic response in patients with acquired PARPi resistance and highlight a pivotal role of NK cells in the PARPi antitumor activity.

overall_design: We leveraged bulk RNA sequencing to examine the transcriptomic profiles of PARPi-sensitive (MDA594) and PARPi-resistant (MDA594OR1 and MDA594OR2) tumors untreated and treated with the PARPi olaparib, in order to identify the mechanism of resistance to the PARPi olaparib.

first: Flaminia

last: Pedretti

first: Violeta

last: Serra


title: Injured tubular epithelia-derived CCN1 promotes the mobilization of fibroblasts toward the injury sites in acute kidney injury

city: Kyoto

first: Tetsuro

last: Kusaba

state: Kyoto

address: 465 Kajii-cho, Kamigyo-ku

department: Department of Nephrology

country: Japan

institute: Graduate School of Medical Science, Kyoto Prefectural University of Medicine

summary: Humoral factors that prompt fibroblasts to migrate to an injury site at an appropriate time point are deemed indispensable for repair after kidney injury. We herein demonstrated the pivotal roles for of injured tubule-derived Cellular Communication Network Factor 1 (CCN1) in the mobilization of fibroblasts to the injury site after kidney injury. Based on analyses of ligand-receptor interactions in vitro and tubular epithelial-specific transcriptomics in vivo, we identified the up-regulation of CCN1 during the early phases of kidney injury. CCN1 promotes fibroblast chemotaxis through focal adhesion kinase-ERK signaling. In vivo analyses utilizing tubular-specific CCN1 knockout mice demonstrated the sparse accumulation of fibroblasts around injured sites after injury, resulting that tissue fibrosis was ameliorated in CCN1-KO mice. These results reveal an epithelial - fibroblast CCN1 signaling axis that mobilizes fibroblasts to injured tubule early after acute injury but that promotes interstitial fibrosis at late timepoints.

overall_design:
To examine the paracrine effects of injured tubular epithelial cells on fibroblasts, we initially performed in vitro experiments using rat epithelial cells (NRK52E), fibroblasts (NRK49F), and conditioned medium (CM) from these cell lines (CME and CMF).
We examined differences in the transcriptome between NRK52E treated with 40 μM of cisplatin or vehicle for 24 hours by RNA-seq. We also compared the transcriptome between NRK49F treated with Cis 40-CME and untreated CME for 24 hours.


title: Cross-talks between metabolic and translational controls during beige adipocyte differentiation [RNA-seq]

city: Gwangju

first: Daehwa

last: Youn

address: 123 Cheomdangwagi-ro, Buk-gu

department: Department of Biomedical Science & Engineering

country: South Korea

institute: Gwangju Institute of Science and Technology (GIST)

summary: Whether and how regulatory events at the translation stage shape the cellular and metabolic features of thermogenic adipocytes is hardly understood. In this study, we report two hitherto unidentified cross-talk pathways between metabolic and translation regulation in beige adipocytes. By analysing temporal profiles of translation activity and protein level changes during precursor-to-beige differentiation, we found selective translational down-regulation of OXPHOS component-coding mRNAs. The down-regulation restricted to Complexes I, III, IV, and V, is coordinated with enhanced translation of TCA cycle genes, engendering distinct stoichiometry of OXPHOS and TCA cycle components and altering the related metabolic activities in mitochondria of thermogenic adipocytes. Our high-resolution description of ribosome positioning unveiled potentiated ribosome pausing at glutamate codons. The increased stalling is driven by elevated glutamate consumption that diminishes glutamate-charged tRNA during pan-adipocyte differentiation. The ribosome pauses decrease protein synthesis and mRNA stability of glutamate codon-rich genes, such as actin cytoskeleton-associated genes.

overall_design: RNA-seq of total RNA to measure the RNA levels upon beige adipocyte differentiation. Adipocyte precursor cells were isolated from inguinal white adipose tissue, and induction of beige adipocyte differentiation was performed. Non-induced and differentiated samples for 4 or 8 days were used for library preparation. For each condition, triplicates were constructed.

first: Boseon

last: Kim

first: Dahee

last: Jeong

first: JuYeon

last: Lee

first: Seha

first: Dulguun

last: Sumberzul

first: Rehna

middle: P

last: Ginting

first: Min-Woo

first: Ju Hwan

last: Song

first: Ye Seul

last: Park

first: Yumin

first: Chang-Myung

last: Oh

first: Mihye

first: Jun

last: Cho


title: Bulk RNA sequencing of bovine (cow) lung cells from uninfected, and infected cells (BCG and M. tuberculosis).

city: Hyderabad

first: Bappaditya

last: Dey

state: Telangana

address: Survey No. 37, Extended Q City Road, Gachibowli

country: India

institute: National Institute of Animal Biotechnology

summary: Whole RNA transcriptome were performed on bovine lung cell 3D pulmosphere cultures with or without infection with M. bovis BCG and M. tuberculosis H37Rv strain.

overall_design: Pulmospheres were cultured in U-bottom 96 well plates with or without infection. 24 hours post infection pulmospheres were harvested, total RNA were extracted and subjected to paired-end RNA sequencing.

first: Vinay

middle: G

last: Bhaskar

first: Rishi

last: Kumar

first: Manas

last: Ranjan Praharaj

first: Sripratyusha

last: Gandham

first: Hemanta

last: Kumar Maity

first: Uttam

last: Sarkar


title: Cross-talks between metabolic and translational controls during beige adipocyte differentiation

first: Daehwa

last: Youn

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

overall_design: Refer to individual Series

first: Boseon

first: Dahee

first: JuYeon

first: Seha


title: Modulation of AKAP12 in the liver regulates lipid homeostasis and inflammation

status: Public on Mar 02 2025

city: Los Angeles

first: Komal

last: Ramani

state: CA

address: 8700 Beverly Blvd.

country: USA

institute: Cedars-Sinai Medical Center

summary: Dysregulation of lipid homeostasis is a feature of alcohol-associated liver disease (ALD). A-kinase anchoring protein 12 (AKAP12) is a scaffolding partner of the cAMP-dependent protein kinase, PKA that controls its spatiotemporal localization. Activation of PKA by cAMP inhibits lipogenesis and facilitates fatty acid oxidation (FAO). We examined how AKAP12’ could regulate alcohol-associated steatosis. Alcohol exposure reduced AKAP12’s interaction with PKA and suppressed PKA activation. Forced expression of AKAP12 overcame the suppression of PKA activity in human hepatocytes and in livers of mice exposed to alcohol. This led to a decrease in hepatic steatosis. Disrupting the scaffold of AKAP12 and PKA by CRISPR editing increased steatosis and inflammation. RNA sequencing analysis of hepatocytes from alchol fed mice and normal mice demonstrated key lipogenic and inflammatory pathways regulated by AKAP12 overexpression. RNA sequencing of total liver from mice with AKAP12-PKA binding site CRISPR editing or AKAP12 overexpression confirmed regulation of lipogenic and inflammatory pathways by AKAP12

overall_design: (1) RNA sequencing profiling of hepatocytes from normal, alcohol-fed, normal+AKAP12 overexpression, alcohol+AKAP12 overexpression livers. (2) RNA sequencing profile of total liver from normal, alcohol-fed, normal+AKAP12-PKA CRISPR, alcohol-fed+AKAP12-PKA CRISPR, normal+AKAP12 overexpression, alcohol-fed+ AKAP12 overexpression mice.

first: Chandana

middle: T

last: Gowda


title: Endogenous protein S100A14 stabilizes glutaminase to render hepatocellular carcinoma resistant to sorafenib

city: Shanghai

first: Menghui

last: Wang

address: No. 826, Zhangheng Road, Pudong New District, Shanghai, China.

country: China

institute: Fudan university

summary: Many cases of advanced hepatocellular carcinoma (HCC) are resistant to the widely used drug sorafenib, which worsens prognosis. While many studies have explored how acquired resistance emerges during drug exposure, the mechanism underlying primary resistance before treatment still remain elusive. Here, we performed single-cell lineage tracing and RNA sequencing to identify sorafenib-resistant lineages in HCC, and demonstrated that high expression of S100A14 was positively associated with primary sorafenib resistance. Knocking down S100A14 rendered xenograft tumors in mice significantly more sensitive to sorafenib. Mechanistic studies indicated that S100A14 binds to glutaminase and blocks its phosphorylation at residues Y308 and S314, which in turn inhibits its ubiquitination and subsequent degradation. This stabilization of glutaminase reduces oxidative stress in HCC cells and thereby antagonizes the ability of sorafenib to induce apoptosis. Inhibiting glutaminase with telaglenastat (CB-839) significantly improved sorafenib efficacy against xenograft tumors in vivo. These results suggest that S100A14 can contribute to primary sorafenib resistance in HCC by stabilizing glutaminase. Thus, analyzing the expression of S100A14 may be useful for predicting primary sorafenib resistance, and inhibiting S100A14 or glutaminase may be effective for preventing or overcoming such resistance.

overall_design: We labeled individual cells in drug-naive hepatocellular carcinoma xenografts on mice with randomly unique 14-base pair (bp) DNA sequences called “barcodes”, then exposed the tumors to sorafenib and compared the characteristics of tumor cells before and after drug exposure. The hepatocellular carcinoma cell line Huh7 was transduced with recombinant lentivirus encoding 14 bp barcodes and the fluorescent reporter CopGFP at a sufficiently low multiplicity of infection (MOI) to ensure that most transductants would receive a single barcode.The above cells were injected subcutaneously into NOD/SCID mice and allowed to grow to a volume of approximately 150 mm3, whereupon they were treated for three weeks with sorafenib, which slowed their growth.Two animals were sacrificed before sorafenib treatment and four animals were sacrificed at the end of treatment, their tumors (drug-naive tumors (DN) and drug-treated tumors (DT), respectively) were excised and dissociated, viable CopGFP-positive tumor cells were selected using a flow cytometric sorter,and the DNA barcodes as well as transcriptome in those cells were sequenced.


title: Host responses to S. pneumoniae in wild type and Mertk mutant mice XT

city: Chapel Hill

first: Matthew

last: McPeek

state: NC

address: 125 Mason Farm Rd. CB:7248

institute: University of North Carolina

first: Claire

middle: M

last: Doerschuk


title: The effect of pab2 deletion or clr4-1 mutation on gene expression in the fission yeast Schizosaccharomyces japonicus

status: Public on Mar 05 2025

first: Tomoyasu

last: Sugiyama

address: 393 Middle Huaxia Road

institute: ShanghaiTech University

summary: Pab2/PABPN1 is a nuclear poly(A)-binding protein, but its function is not fully understood yet. To investigate the Pab2 role in shaping transcriptome, we delete the pab2 gene in S. japonicus and characterize it. We found that meiosis-related genes are increased in pab2∆. Surprisingly, we observed the increases in transcripts derived from constitutive heterochromatin. Moreover, the upregulated and downregulated genes in pab2∆ and clr4 (the ortholog of the histone H3 Lys9 methyltransferase SUV39) mutant cells were significantly overlapped. Besides, constitutive heterochromatin is adversely affected in pab2∆. Our analyses demonstrate that Pab2 is required for the assembly of constitutive heterochromatin, and this finding provides a new insight into the Pab2 function(s).

overall_design:
We constructed pab2∆ cells using the standard gene replacement method and clr4-1 mutant cells using the PCR-based random mutagenesis of the clr4 gene.
We then isolated total RNA from vegetative wild-type, pab2∆, and clr4-1 cells twice (two biological replicates) and performed gene expresssion profiling analyses using data obtained from two independent RNA-seq of the three S. japonicus strains.

first: Ziyue

last: LIU

last: SUGIYAMA


title: Impact of aging on pulmonary cellular responses during mechanical ventilation

city: London

first: Sean

last: Gill

state: Ontario

address: 1151 Richmond St

department: Physiology and Pharmacology

country: Canada

institute: Western University

summary: Acute respiratory distress syndrome (ARDS) results in significant morbidity and mortality, especially in the elderly. Mechanical ventilation, a common supportive treatment for ARDS, is necessary for maintaining gas exchange, but can also propagate injury. We hypothesized that aging would exacerbate the pathophysiological responses to mechanical ventilation. Young and aged male mice were mechanically ventilated and changes in surfactant function, inflammation, and vascular permeability were assessed. Additionally, single-cell RNA sequencing was used to delineate cell-specific transcriptional changes. The results showed that surfactant dysfunction was augmented in aged mice, while inflammation was less pronounced in aged animals. Futhermore, vascular permeability was significantly increased with aging. Differential gene expression and pathway analyses revealed that aged endothelial cells exhibited altered cell-cell junction formation and that alveolar macrophages in aged mice showed a blunted inflammatory response. These results highlight the complex interplay between aging and mechanical ventilation, including an age-related predisposition to endothelial barrier dysfunction due to altered cell-cell junction formation and decreased inflammation, potentially due to immune exhaustion.  It is concluded that age-related vascular changes may underlie the increased susceptibility to injury during mechanical ventilation in elderly patients.

overall_design: mRNA profiles of lung tissue cells from young (2-3 month old) and aged (22 month old) mice exposed to mechanical ventilation for 3 hours (3 animals were used per group and were pooled together). mRNA profiles were generated by single cell sequencing using the Illumina NextSeq 500 sequencer

first: Aminmohamed

last: Manji

first: Lefeng

first: Cynthia

last: Pape

first: Lynda

last: McCaig

first: Alexandra

last: Troitskaya

first: Thomas

middle: C

last: Appleton

first: Ruud

middle: W

last: Veldhuizen

middle: E

first: Leah

middle: J

last: McDonald


title: Cross-talks between metabolic and translational controls during beige adipocyte differentiation [Ribo-seq]

first: Daehwa

last: Youn

overall_design: Ribo-seq to measure the translation activity upon beige adipocyte differentiation. Adipocyte precursor cells were isolated from inguinal white adipose tissue, and induction of beige adipocyte differentiation was performed. Non-induced and differentiated samples for 4 or 8 days were used for library preparation. For each condition, triplicates were constructed.

first: Boseon

last: Kim

first: Dahee

last: Jeong

first: JuYeon

last: Lee

first: Seha

first: Dulguun

last: Sumberzul

first: Rehna

last: Ginting

first: Min-Woo

first: Ju Hwan

last: Song

first: Ye Seul

last: Park

first: Yumin

first: Chang-Myung

last: Oh

first: Mihye

first: Jun

last: Cho


title: Characterization of macrophages in healthy and diseased livers in mice

status: Public on Mar 01 2025

city: Rockville

first: Yukun

last: Guan

state: MD

address: 5625 Fishers Lane, Room 2S-30

institute: NIAAA

summary: Healthy livers contain many resident macrophages named Kupffer cells (KCs), which are partially replaced by infiltrating monocyte-derived macrophages (MoMFs) during acute or chronic liver injury. Despite extensive research, understanding macrophage heterogeneity, spatial distribution, and interactions with other cells within the liver remains challenging. We performed single-cell RNA sequencing to investigate liver macrophage gene expression in naïve and Concanavalin A (ConA)-treated mice. MoMF clusters expanded following ConA treatment, while KCs remained stable. Macrophages were divided into distinct subtypes, including C1q+ MoMFs, with differential expression of genes like Trem2, Spp1, Fabp5 and Gpnmb. Newly recruited C1q- MoMFs expressed high levels of Lyz and Ccr2, while Itgax (Cd11c)+ MoMFs expressed endothelin converting enzyme 1 (Ece1), a gene encoding ECE1 enzyme that activates endothelin to promote hepatic stellate cell contraction and necrotic lesion resolution. By immunostaining analysis of the proteins encoded by these signature genes, we identified several populations of MoMFs that were mainly located surrounding the necrotic lesion area and expressed various proteins that are involved dead cell debris clearance.

overall_design: Naïve mice and mice treated with ConA for 72 or 96 hours were anesthetized, and their livers were perfused and digested using a 0.075% collagenase solution (Worthington, Lakewood, NJ). Liver samples were homogenized, filtered through 70 μm cell strainers, and centrifuged at 400g through a Percoll density gradient (40% and 70%).

last: GUAN

first: Dechun

last: FENG

first: Bin

last: GAO


title: Identifying the intergenic ALK fusion LOC388942-ALK as a driver of non-small cell lung cancer

city: Chengdu

first: Donglin

last: Li

address: Sichuan University, 24 South Section 1, 1st Ring Road

institute: Sichuan University

summary: ALK fusions, such as the classic EML4-ALK, are known drivers of lung cancer and effective therapeutic targets. However, variant ALK fusions, including intergenic fusions like LOC388942-ALK (LA), have been detected in increasing numbers of patients, with their roles in tumorigenesis and ALK inhibitor resistance remaining unclear. Using CRISPR/Cas9, we generated the LA fusion in A549 and H441 cells, confirming elevated ALK expression via qRT-PCR and immunohistochemistry (IHC) staining. Functional analyses showed that LA significantly promoted tumor growth in vitro and in vivo while conferring increased resistance to alectinib. RNA-seq revealed upregulation of the FOS pathway in LA tumors, identifying FOS as a potential therapeutic target. Subsequently, we demonstrated that FOS disruption and inhibition sensitized LA tumors to treatment. RNA-seq profiling demonstrated that FOS depletion in LOC388942-ALK tumor significantly downregulated multiple oncogenic pathways related to cell cycle progression, DNA replication fidelity, and extracellular matrix remodeling, suggesting a pivotal role of FOS in maintaining tumor growth. These findings establish LOC388942-ALK as a novel oncogenic driver in lung cancer, highlighting its role in tumor growth and ALK inhibitor resistance. Targeting FOS may provide a promising therapeutic strategy for tumors harboring this intergenic fusion.

overall_design: A549 cells were applied to investigate the functions of LOC388942-ALK (LA) intergenic fusion in NSCLC IPM.

first: Xiaoqian

last: Zhai

first: Manli

last: Wang

first: Qi

last: Zhang

first: Yanmou

last: Wu


title: IPAH signatures in hPASMC and hAdvFB

city: Giessen

first: Jochen

last: Wilhelm

state: Hessen

address: Aulweg 132

department: Institute for Lung Health

country: Germany

institute: Justus-Liebig University Giessen

summary: Microarray analyisis of human pulmonary artery smooth muscle cells (hPASMC) and adventitial fibroblasts (hPF) from donor and IPAH  lungs will give an indication of possible differentially regulated genes. The mRNA was obtained from cells with passage 1 (n=4/group).There was no treatment applied, we investigate the baseline differences.

overall_design: 4 groups with 4 biological replicates each

first: Grazyna

last: Kwapiszewska


title: Gene expression of the mouse ovary treated with tachykinin receptor ligands

city: 相楽郡

first: Tsuyoshi

last: Kawada

address: 精華町精華台8－1－1

institute: Suntory Foundation for Life Sciences

summary: To screen genes regulated by tachykinin in the 2-weeks mouse ovary, we have performed microarray expression profiling. COX-2 gene expression was upregulated in the mouse ovary treated with tachykinin receptor agonist compared to the mouse ovary treated with tachykinin receptor antagonists.

overall_design: Gene expression was examined in the 2-weeks mouse ovary treated with tachykinin receptor ligands for 3 days.

first: Honoo

last: Satake


title: Unveiling the Temporal Dynamics of Mesenchymal Condensations in Tracheal Development through Non-Canonical Wnt Signaling and Notum

status: Public on Feb 28 2025

city: Cincinnati

first: Debora

last: Sinner

state: OH

address: 3333 Burnet Ave

department: Neonatology and Pulmonary Biology

institute: CCHMC

summary: The trachea is essential for proper airflow to the lungs for gas exchange. Frequent congenital tracheal malformations affect the cartilage, causing the collapse of the central airway during the respiratory cycle. We have shown that Notum, a Wnt ligand de-acylase that attenuates the canonical branch of the Wnt signaling pathway, is necessary for cartilaginous mesenchymal condensations. In Notum deficient tracheas, chondrogenesis is delayed, and the trachea is stenotic. It is unknown if Notum attenuates non-canonical Wnt signaling. Notably, after mesenchymal deletion of the non-canonical Wnt5a ligand, we observed premature tracheal chondrogenesis. We hypothesize that Notum and Wnt5a are required to mediate the timely formation of mesenchymal condensations, giving rise to the tracheal cartilage. Ex vivo culture of tracheal tissue shows that chemical inhibition of the Wnt non-canonical pathway promotes earlier condensations, while Notum inhibition presents delayed condensations. Furthermore, non-canonical Wnt induction prevents the formation of cartilaginous mesenchymal condensations. On the other hand, cell-cell interactions among chondroblasts increased in the absence of mesenchymal Wnt5a. By performing an unbiased analysis of the gene expression in Wnt5a and Notum deficient tracheas, we detected that mRNA of genes essential for chondrogenesis and extracellular matrix formation are upregulated by E11.5 in Wnt5a mutants. The expression profile supports the premature and delayed chondrogenesis observed in Wnt5a and Notum deficient tracheas. We conclude that Notum and Wnt5a are necessary for proper tracheal cartilage patterning by coordinating timely chondrogenesis. Thus, these studies shed light on molecular mechanisms underlying congenital anomalies of the trachea.

overall_design: E11.5 tracheas were isolated from Wnt5a f/f and Dermo1Cre;Wnt5a f/f embryos. E13.5, Chondroblasts,Epithelial cells, and Myoblasts  were isolated by FACS  selection from, Notum 300/300; gammaSMAeGFP and Notum 150/150  gammaSMAeGFP mouse trachea using APC-Epcam stain to select epithelial cells and GFP to isolate muscle cells. Double negative cells (Apc-, gfp-) were collected and represented the chondroblast population.RNA was isolated from  tissue or cells and submitted for RNA sequencing.

first: Natalia

last: Bottasso-Arias

first: Yixin

first: Yan

last: Xu


title: The role of CsrA in controls the extracellular electron transfers in Geobacter sulfurreducens

city: Mexico

first: Leticia

last: Vega

state: Mexico

address: Circuito Ext s/n

country: Mexico

institute: Universidad Nacional Autonoma de Mexico

summary: CsrA is a post-transcriptional regulator that controls biofilm formation, virulence, carbon metabolism, and motility, among other phenotypes in bacteria. Although CsrA has been extensively studied in γ-proteobacteria and firmicute, it is unknown which cellular processes are targeted for regulation in δ-proteobacteria. In this work, we constructed and characterized the ΔcsrA mutant strain in Geobacter sulfurreducens to determine the involvement of the CsrA protein in the regulation of biofilm and extracellular electron transfer. The ΔcsrA mutant strain grows on acetate-fumarate and reduces soluble Fe(III) similarly to the wild type strain, but has higher rates of insoluble Fe(III) reduction than the wild type. Quantification and characterization of biofilms by violet staining and confocal laser scanning microscopy showed that the ΔcsrA strain produces up to twice as much biofilm as the wild type strain, containing more than 95% viable cells. Transcriptome analysis by RNA-seq shows that in ΔcsrA biofilms developed on an inert support, 244 (103 upregulated and 141 downregulated) genes changed their expression, including those related to extracellular electron transfer, exopolysaccharide synthesis, c-di-GMP synthesis and degradation. To validate the transcriptome data, RT-qPCR confirmed the differential expression of several selected genes in the ΔcsrA strain. Current production in microbial fuel cells was tested and the ΔcsrA strain was found to produce 45-50% more current than the wild type. To verify the genes that changed expression in the graphite electrodes in the ΔcsrA strain, a transcriptome analysis was performed. 181 genes changed their expression in the ΔcsrA biofilms of which 113 genes showed differentially expression only in MFC and 68 genes changed their expression as well as transcriptome from biofilms grown on inert support. In silico analysis of the 5'-UTR regions revealed that 76 genes that changed expression in the RNA-seq analysis have a consensus sequence for CsrA binding. This is the first report describing the involvement of CsrA in the regulation of extracellular electron transfer and biofilm in a member of the γ-proteobacteria.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for Geobacter sulfurreducens biofilm from wild type and csrA-mutant strains grown on a glass support and graphite electrode. From each sample, experimental duplicates were used.

first: Alberto

last: Hernández-Eligio

last: Vega-Alvarado

first: Xinying

last: Liu

first: Jessica

last: Cholula-Calixto

first: Guillermo

last: Huerta-Miranda

first: Katy

last: Juárez


title: Muscle fiber Myc is dispensable for muscle growth and its forced expression severely perturbs homeostasis [HSA_MycTG]

status: Public on Feb 27 2025

city: Basel

first: Daniel

last: Ham

state: Basel-Stadt

address: Spitalstrasse 41

department: Biozentrum

country: Switzerland

institute: University of Basel

summary: The oncogenic transcription factor Myc stimulates many growth processes including cell cycle progression and ribosome biogenesis. Myc expression is low in adult skeletal muscle, but is upregulated upon growth stimuli. Furthermore, muscle fiber Myc overexpression recapitulates many aspects of growth-related gene expression, leading to the hypothesis that Myc mediates pro-growth responses to anabolic stimuli, such as exercise. Here, we tested this hypothesis by examining mouse models in which Myc was specifically eliminated or overexpressed in skeletal muscle fibers or muscle stem cells (MuSC). While muscle fiber Myc expression increased during muscle growth and Myc expression in MuSCs was required for successful muscle regeneration, muscle fiber Myc expression was dispensable for post-natal, mechanical overload or PKBα/Akt1-induced muscle growth in mice. Similarly, constitutive Myc expression did not promote skeletal muscle hypertrophy, but instead impaired muscle fiber structure and function within days. These data question the role of Myc in skeletal muscle growth.

overall_design: Bulk RNA seq data of mouse skeletal muscles (gastrocnemius) from CON and HSAMerCreMer MycTG (HSA-MycTG) mice

first: Markus

middle: A

last: Rüegg


title: Muscle fiber Myc is dispensable for muscle growth and its forced expression severely perturbs homeostasis [HSA_MycKO]

overall_design: Bulk RNA seq data of mouse skeletal muscles (gastrocnemius) from HSAwt/wt; Mycfl/fl (CON) and HSACre/wt; Mycfl/fl (HSA-MycKO) mice


title: mRNA and miRNA Screening to Identify Treatment Responses in SLE Patients Receiving Belimumab

first: Cristina

last: Sole Marce

address: Pg Vall Hebron 119-129

institute: Vall Hebron Institute Research

type:
Expression profiling by array
Non-coding RNA profiling by array

summary: Systemic lupus erythematosus (SLE) is a complex autoimmune disease driven by autoreactive B cells and the cytokine BAFF (BLyS), which is vital for B-cell function. Despite advances in genomics, no clear profile exists to predict which patients benefit most from BLyS-targeted therapies.    miRNAs, small noncoding RNAs, regulate numerous cellular activities and have emerged as potential biomarkers for autoimmune diseases like SLE. Dysregulated miRNAs in SLE T and B cells contribute to immune hyperactivation, promoting autoantibody production and heightened type 1 interferon levels. While miRNAs are promising diagnostic tools, their role in predicting responses to anti-BLyS therapy remains unexplored.    This study examines miRNA-mRNA interaction networks in T cells, B cells, and myeloid cells from SLE patients before and after BLyS therapy, identifying differentially expressed miRNAs and mRNAs. Integrative analyses reveal novel regulatory networks and pathways associated with clinical improvement, offering new insights into the pharmacological mechanisms of anti-BLyS therapy.

platform_organism:
Homo sapiens
synthetic construct

overall_design: PBMCs were sorted using spectral cytometry to isolate B cells, T cells, and myeloid cell populations. RNA and miRNA were extracted from each subset, followed by a microarray analysis. Gene expression profiling was conducted using the Clariom S assay, and miRNA expression profiling was performed with GeneChip miRNA 4.0 arrays (Thermo Fisher Scientific, Inc.).

first: Cortés-Hernández

last: Josefina

first: Solé

last: Cristina

first: Royo

last: Maria


title: Muscle fiber Myc is dispensable for muscle growth and its forced expression severely perturbs homeostasis [Akt_MycKO]

overall_design: Bulk RNA seq data of mouse skeletal muscles (gastrocnemius) from HSAwt/wt; Mycfl/fl (CON), HSACre/wt; Mycfl/fl (HSA-MycKO), HSAwt/wt; AktTG; Mycfl/fl (Akt-TG) and HSACre/wt; AktTG; Mycfl/fl (Akt-MycKO) mice


title: α-Ketoglutarate promotes trophectoderm induction and maturation from naive human embryonic stem cells [scRNA-Seq 3D]

city: Copenhagen

first: Jan

middle: Jakub

last: Żylicz

address: Blegdamsvej 3B

department: Novo Nordisk Foundation Center for Stem Cell Medicine, reNEW

country: Denmark

institute: University of Copenhagen

summary: Development and lineage choice are driven by interconnected transcriptional, epigenetic and metabolic changes. Specific metabolites, such as α-ketoglutarate (αKG), function as signalling molecules affecting the activity of chromatin-modifying enzymes. However, how metabolism coordinates cell-state changes, especially in human pre-implantation development, remains unclear. Here we uncover that inducing naive human embryonic stem cells towards the trophectoderm lineage results in considerable metabolic rewiring, characterized by αKG accumulation. Elevated αKG levels potentiate the capacity of naive embryonic stem cells to specify towards the trophectoderm lineage. Moreover, increased αKG levels promote blastoid polarization and trophectoderm maturation. αKG supplementation does not affect global histone methylation levels; rather, it decreases acetyl-CoA availability, reduces histone acetyltransferase activity and weakens the pluripotency network. We propose that metabolism functions as a positive feedback loop aiding in trophectoderm fate induction and maturation, highlighting that global metabolic rewiring can promote specificity in cell fate decisions through intricate regulation of signalling and chromatin.

overall_design: scRNA-seq of H9 human embryonic stem cells cultured in Aggrewells in blastoid induction medium for 40h or 120h. Aggregates or blastoids were treated for 40h with 0 or 4mM dimethyl-alphaketoglutarate.

first: Karlien

last: Van Nerum

first: Anne

last: Wenzel

first: Eleni

last: Kafkia

first: Antar

last: Drews

first: Ida

middle: S

last: Brun

first: Viktoria

last: Lavro

first: Annina

last: Roelofsen

first: Nikolaos

last: Stamidis

first: Sandra

middle: B

last: Arnal

last: Zylicz


title: Effect of high fat diet on circadian liver gene expression in wild-type mice and in mice lacking p110alpha in hepatocytes

city: Toulouse

first: Hervé

last: Guillou

address: 180 Chemin de Tournefeuille

department: ToxAlim

country: France

institute: INRAE

summary: Liver gene expression was analyzed by microarrays at different times during 24h. This was done in mice fed a regular diet (Low fat diet: LFD) or a high fat diet (HFD). The experiment was done in wild-type mice (P110aHepWT) and in mice lacking p110alpha in hepatocytes (P110aHepKO).

overall_design: Twelve-week-old p110αhep+/+ (P110aHepWT) and p110αhep-/- (P110aHepKO) mice were fed a control diet (D12450J, Research Diet) or a HFD (D12492, research diet) during 16 weeks. At the end of the experiment, mice were killed at different time points: ZT0, ZT4, ZT8, ZT12, ZT16 and ZT20. All mice had free access to food and water until sacrifice.

first: Tiffany

last: Fougeray

first: Marion

last: Régnier

first: Arnaud

last: Polizzi

first: Claire

last: Naylies

first: Anne-Marie

last: Loustau

first: Yannick

last: Lippi

first: Alexandra

last: Montagner

first: Nicolas

last: Loiseau


title: Liver gene expression profile in wild-type mice (p110aLWT) and in mice lacking p110alpha in hepatocyte (p110aLKO) in response to feeding or fasting

summary: Fed and fasted mouse liver from either wild-type (p110aLWT) and ko (p110aLKO) mice were analyzed by microarrays.

overall_design: Twelve-week-old p110αhep+/+(p110aLWT) and p110αhep-/- (p110aLKO) mice were divided into 2 groups. One group was fed ad libitum until sacrifice. One group was fasted for 24h from ZT16 (n=6 mice/genotype/experimental condition). All mice were killed at ZT16.


title: Effect of High fat diet (HFD) on liver gene expression in wild-type mice (LWT) and in mice lacking p110 alpha in hepatocyte (LKO)

summary: We analyzed the effect of diet-induced obesity on liver gene expression in wild-type mice and in mice lacking p110alpha in hepatocytes. Samples were collected from mice either fed or fasted.

overall_design: Mice lacking p110 alpha in hepatocytes were created by mating the floxed-p110α mouse strain (LWT) with C57BL/6J albumin-Cre transgenic mice to obtain albumin-Cre+/−p110αflox/flox mice, i.e., p110αhep-/- mice (LKO). Twelve-week-old p110αhep+/+ (LWT) and p110αhep-/- (LKO) mice were fed a HFD with 60% calories from fat (D12492, Research Diet) or a control (“CTRL”) diet (D12450J, Research Diet) during 12 weeks. All mice had free access to food and water. At the end of experiment, mice were fasted at Zeitgeber Time (ZT) 16 (with ZT0 being when the light is turned on and ZT12 when light is turned off) for 24h or fed ad libitum prior sacrifice. Mice were killed at ZT16.


title: α-Ketoglutarate promotes trophectoderm induction and maturation from naive human embryonic stem cells [ATAC-Seq]

first: Jan

last: Żylicz

type: Genome binding/occupancy profiling by high throughput sequencing

overall_design: Assay for transposase-accessible chromatin using sequencing (ATAC-seq) of H9 human embryonic stem cells cultured in tt2iLIFGö. Cells were treated for 24hrs with 0 or 4mM dimethyl-alphaketoglutarate.

first: Karlien

last: Van Nerum

first: Anne

last: Wenzel

last: Kafkia

last: Bages Arnal


title: α-Ketoglutarate promotes trophectoderm induction and maturation from naive human embryonic stem cells [RNA-Seq]

overall_design: mRNA-seq experiment of H9 human embryonic stem cells cultured in tt2iLIFGö as well as hiTSC at day 3 of induction. ESC were treated for 24hrs with 0 or 4mM dimethyl-alphaketoglutarate or 1uM A-485. hITSC were induced from such pre-treated ESC.

first: Eleni

last: Lavro

last: Roelofsen

first: Antar

last: Drews


title: Fertilization-induced synergid cell death by RALF12-triggered ROS production and ethylene signaling

city: Wuhan

first: Junyi

last: Chen

state: Hubei

address: Luoyu Road 152

department: Institute of Plant Sciences

institute: Central China Normal University

summary: Plant material from synergid cells before pollination, and persistent synergid cells 12, 18, and 24 hours after pollination (hap) was collected using manual microdissection. Cell- and stage-specific RNA-seq data were generated with these cell samples to (i) investigate molecular mechanisms ensuring timely induction and execution of synergid cell death, and (ii) provide a unique resource to discover novel PCD regulators.

overall_design: Three replicate samples of the cell stages: synergid cell, persistent synergid cell 12 HAP, persistent synergid cell 18 HAP, and persistent synergid cell 24 HAP (25–28 cells for each biological replicate at each stage) were collected.

first: Huan

last: Wang

first: Jinlin

first: Xixi

last: Zheng

first: Wantong

last: Qu

first: Huijian

last: Fang

first: Shuang

first: Le

last: He

last: Hao

first: Thomas

last: Dresselhaus


title: HSV-1 infection induces a downstream-shift of the +1 nucleosome (H2A.Z ChIPmentation)

city: München

first: Caroline

last: Friedel

address: Amalienstr. 17

department: Institut für Informatik

institute: Ludwig-Maximilians-Universität München

summary: HFFF cells were either mock or WT strain 17 HSV-1 infected for 8 h.  Samples were processed according to the original ChIPmentation protocol (Schmidl C et al. ChIPmentation: fast, robust, low-input ChIP-seq for histones and transcription factors. Nat Methods. 2015) with few changes as explained in the Materials and Methods section.

overall_design: We profiled the noncanonical histone H2A.Z  in mock and WT strain 17 HSV-1 infected cells with ChIPmentation.

first: Elena

last: Weiß

last: Hennig

first: Lara

last: Djakovic

first: Adam

last: Whisnant

first: Lars

last: Dölken


title: Lung B cells in ectopic germinal centres undergo affinity maturation

city: Cambridge

first: Sarah

last: Inglesfield

address: Babraham Research Campus

department: Bioinformatics

country: United Kingdom

institute: The Babraham Institute

summary: Chronic exposure to allergens and other airborne antigens can result in the formation of lymphocyte aggregates in the lung, which can harbour ectopic germinal centres (GCs). After allergen exposure, GCs that form in the lung are much smaller and less densely packed with B cells than lymph node GCs. Despite this, ectopic lung GCs can support somatic hypermutation and affinity-based maturation as in lymph node GCs, and can export memory B cells directly into the lung tissue. This demonstrates that the lung itself can locally diversify B cell responses and support the generation of tissue memory B cell populations in situ. Here, we have employed a single cell sequencing approach using 10x Genomics scRNAseq and BCRseq to study germinal centre B cell clonal sharing between the mediastinal lymph node and lungs of mice.

overall_design: C57BL/6 mice were adoptively transfered 50,000 B1-8i cells, followed by four intranasal doses of 4-Hydroxy-3-nitrophenylacetyl (NP) hapten conjugated to keyhole limpet hemocyanin (KLH) in tandem with house dust mite (HDM); NP-KLH/HDM. 21 days post-transfer, the lungs and mediastinal lymph node were collected and and processed to generate single-cell suspensions for fluorescence-activated cell sorting (FACS). Endogenous germinal centre B cells and memory B cells were isolated by FACS for analysis using scRNA-seq and scBCR-seq.

first: Michelle

last: Linterman

first: Stephane

last: Guillaume


title: α-Ketoglutarate promotes trophectoderm induction and maturation from naive human embryonic stem cells

first: Jan

last: Żylicz

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

overall_design: Refer to individual Series


title: HSV-1 infection induces a delay of promoter-proximal pausing linked to a shift of H2A.Z-containing +1 nucleosomes (ATAC-seq)

summary: We investigated transposase accessible chromatin using ATAC-seq in mock and HSV-1 strain 17 infection and infection with several HSV-1 mutants.

overall_design: We used different HSV-1 mutants that lack expression of certain IE genes or VHS and examined the opening of chromatin downstream of transcription termination sites of affected genes. Two biological replicates (four replicates for delta-ICP22) of cells infected with different HSV-1 mutants at MOI 10 were prepared.  ATAC-seq data for mock, WT strain 17 (+/- PAA) and delta-ICP0, delta-ICP22, delta-ICP7 and delta-vhs can also be found under accession GSE185234.


title: HSV-1 infection induces a delay of promoter-proximal pausing linked to a shift of H2A.Z-containing +1 nucleosomes


title: Common Connective Tissue Disorder and Anti-Cytokine Autoantibodies are Enriched in Idiopathic Multicentric Castleman Disease Patients [CTD Array version 3]

status: Public on Feb 26 2025

city: Stanford

first: Allan

last: Feng

address: 269 Campus Dr

department: Imm/Rheum

institute: Stanford School of Medicine

summary: We measued IgG autoantibodies associated with Connective Tissue Diseases (CTDs) and Anti-Cytokine Antibodies (ACA) in idiopathic Multicentric Castleman Disease (iMCD) patients and healthy controls who  received the BNT162b2 vaccine.

overall_design: We constructed protein arrays by coupling recombinant protein antigens to fluorescent carboxylated magnetic beads and then combined the beads into two seperate arrays (i.e., the CTD and ACA arrays). We then used the protein arrays to probe iMCD patient  serum samples, healthy control samples, and Hodgekin lymphoma patients for IgG autoantibodies. A Luminex FLEXMAP 3D® system was used to quantitatively measure autoantibody reactivity in units of mean flourescent intensity (MFI).

first: Michael

middle: V

last: Gonzalez

first: Muge

last: Kalaycioglu

first: Xihui

last: Yin

first: Melanie

last: Mumau

first: Saishravan

last: Shyamsundar

first: Mateo

last: Sarmiento Bustamante

last: Chang

first: Shaurya

last: Dhingra

first: Tea

last: Dodig-Crnkovic

first: Jochen

last: Schwenk

first: Tarun

last: Garg

first: Kazuyuki

last: Yoshizaki

first: Frits

last: van Rhee

first: David

last: Fajgenbaum

first: Paul

last: Utz


title: Common Connective Tissue Disorder and Anti-Cytokine Autoantibodies are Enriched in Idiopathic Multicentric Castleman Disease Patients [CTD array version prototype]

first: Sarah


title: Common Connective Tissue Disorder and Anti-Cytokine Autoantibodies are Enriched in Idiopathic Multicentric Castleman Disease Patients [Protein Fragment Array]


title: Single-cell RNA sequencing of MNU injured mouse retina

city: Daejeon

first: Jin Woo

last: Kim

state: Daejeon

address: 291, Daehak-ro, Yuseong-gu

institute: KAIST

summary: We elucidate the role of prospero-related homeobox 1 (Prox1) in rendering the mammalian retina incompetent for MG(Muller glia cell)-derived regeneration. Prox1 accumulates in MG in the degenerating human and mouse retinas but not in those in the regenerating zebrafish retina. We investigated whether the transition of MG to proliferative MGPCs occurred in MNU-injured Prox1fg/fg;Chx10-CreERT2 mouse retinas through single-cell RNA sequencing analysis.

overall_design: To explore the role of Prox1 in limiting Müller glia (MG)-derived regeneration in the mammalian retina, we performed single-cell RNA sequencing on the entire retina from N-methyl-N-nitrosourea (MNU)-injured Prox1 conditional knockout (Prox1fg/fg;Chx10-CreERT2) mouse models. Comparison with Prox1-intact conditions allowed us to investigate Prox1’s influence on the transition of MG to proliferative Müller glia-derived progenitor cells (MGPCs).

first: Eun Jung

last: Lee

first: Museong

first: Jeong Hwan

first: Seon-Young


title: Common Connective Tissue Disorder and Anti-Cytokine Autoantibodies are Enriched in Idiopathic Multicentric Castleman Disease Patients [ACA Array version prototype]

first: Allan

last: Feng

first: Michael

last: Gonzalez

first: Muge

first: Xihui

first: Melanie


title: Regulation of lung progenitor plasticity and repair by fatty acid oxidation [scRNA-seq]

status: Public on Feb 25 2025

city: Columbus

first: Jhonny

last: Rodriguez Lopez

state: Ohio

address: Holly Ave 1383 203A

department: Internal medicine

institute: The Ohio State University

summary: Idiopathic pulmonary fibrosis (IPF) is an age-related interstitial lung disease, characterized by inadequate alveolar regeneration and ectopic bronchiolization. While some molecular pathways regulating lung progenitor cells have been described, the role of metabolic pathways in alveolar regeneration is poorly understood. We report that expression of fatty acid oxidation (FAO) genes significantly diminishes in alveolar epithelial cells of IPF lungs by single-cell RNA sequencing and tissue staining. Genetic and pharmacological inhibition in AT2 cells of carnitine palmitoyltransferase 1a (CPT1a), the rate-limiting enzyme of FAO, promoted mitochondrial dysfunction and acquisition of aberrant intermediate states expressing basaloid, and airway secretory cell markers SCGB1A1, and SCGB3A2. Further, mice with deficiency of CPT1a in AT2 cells show enhanced susceptibility to developing lung fibrosis with an accumulation of epithelial cells expressing markers of intermediate cells, airway secretory cells, and senescence. We found that deficiency of CPT1a causes a decrease in SMAD7 protein levels and TGF-β signaling pathway activation. These findings suggest that the mitochondrial FAO metabolic pathway contributes to the regulation of lung progenitor cell repair responses and deficiency of FAO contributes to aberrant lung repair and the development of lung fibrosis.

overall_design: To investigate the FAO pathway in AT2 cells, we collected IPF lung explants from patients diagnosed with IPF and undergoing transplantation. In parallel, we collected lung tissue from aged non-IPF individuals. Tissues were formalin-fixed and paraffin-embedded (FFPE) for preservation and used as input material for scRNA-Seq.

first: Quetzalli

middle: D

last: Angeles-López

last: Rodriguez-Lopez

first: Paula

last: Agudelo

first: Jazmin

last: Calyeca

first: Diana

last: Álvarez

first: Marta

last: Bueno

first: Lan

middle: N

last: Tu

first: Myriam

last: Salazar-Terreros

first: Natalia

last: Vanegas-Avendaño

first: Jordan

last: Krull

first: Aigul

last: Moldobaeva

first: Srimathi

last: Bogamuwa

first: Stephanie

last: Scott

first: Victor

last: Peters

first: Brenda

middle: F

last: Reader

first: Sruti

last: Shiva

last: Jurczak

first: Mahboobe

last: Ghaedi

first: Qin

last: Ma

first: Toren

last: Finkel

first: Mauricio

last: Rojas

first: Ana

middle: L

last: Mora


title: Effect of Brief Maternal Exposure to Bisphenol A on the Fetal Female Germline in a Mouse Model

city: Beaverton

first: Lisa

last: Vrooman

state: OR

address: 505 NW 185th Ave.

institute: Oregon Health and Sciences University

summary: Background: Environmental contamination by endocrine disrupting chemicals (EDCs) has created serious public health, ecological, and regulatory concerns. Prenatal exposure can affect a wide range of developing organ systems, adversely affecting behavior, metabolism, fertility, and disease risk in the adult. The most serious and puzzling effect of EDC exposure is the transmission of effects to subsequent unexposed generations (transgenerational effects). This requires the induction of epigenetic changes to the germline that are not subject to the normal processes of erasure and resetting in subsequent generations. Understanding when and how the germline is vulnerable to EDCs is an essential first step in devising strategies to prevent and reverse their effects. Methods: We report here results using a well-established mouse model and the most extensively studied EDC, bisphenol A, to assess effects on the female germline and evaluate the underlying epigenetic changes.  Results: Using a quantitative variable (meiotic recombination), we found germline effects across a wide range of doses with a dose-related increase in severity. We identified a period of dramatic changes in chromatin at the onset of meiotic prophase as the vulnerable window of exposure and found a remarkable effect on chromatin that defies meiotic dogma. Oocyte analysis by mass spectrometry and immunofluorescence suggested H4K20me2, a histone posttranslational modification involved in DNA damage repair, was particularly affected. Subsequent RNA-seq analysis revealed a relatively small number of differentially expressed genes, but in addition to genes involved in chromatin dynamics, several with important roles in DNA repair/recombination and centromere stability also were affected. Discussion: Together, our data suggest BPA exposure induces complex changes to the germline that dysregulate chromatin but also affect several critical and interrelated meiotic pathways.

overall_design: Maternal exposure to placebo or 500 ng/g body weight of bisphenol A from embryonic day 11-13.5. Ovaries were collected from different mouse fetuses. Oocytes were isolated by fluorescent activated cell sorting for DNA content for each experimental group and timepoint. Oocytes were pooled from multiple individuals of the same experimental group and timepoint. RNA-sequencing was performed and analysis for differentially expressed genes comparing placebo and bisphenol A groups was performed for embryonic day E13.5.


title: Common Connective Tissue Disorder and Anti-Cytokine Autoantibodies are Enriched in Idiopathic Multicentric Castleman Disease Patients

first: Allan

last: Feng

first: Michael

last: Gonzalez

first: Muge

last: Kalaycioglu

first: Xihui

last: Yin

first: Melanie

last: Mumau

first: Saishravan

last: Shyamsundar

first: Mateo

last: Sarmiento Bustamante

first: Sarah

last: Chang

first: Shaurya

last: Dhingra

first: Tea

last: Dodig-Crnkovic

first: Jochen

last: Schwenk

first: Tarun

last: Garg

first: Kazuyuki

last: Yoshizaki

first: Frits

last: van Rhee

first: David

last: Fajgenbaum

first: Paul

last: Utz


title: Genome-wide CRISPR/Cas9 screen reveals factors that influence the susceptibility of tumor cells to NK cell-mediated killing

city: Marseille

first: Bertrand

last: Escaliere

address: 163 avenue de Luminy

institute: CIML

summary:
Background Natural killer (NK) cells exhibit potent cytotoxic activity against various cancer cell types. Over the past five decades, numerous methodologies have been employed to elucidate the intricate molecular mechanisms underlying NK cell-mediated tumor control. While significant progress has been made in elucidating the interactions between NK cells and tumor cells, the regulatory factors governing NK cell-mediated tumor cell destruction are not yet fully understood. This includes the diverse array of tumor ligands recognized by NK cells and the mechanisms that NK cells employ to eliminate tumor cells.
Methods In this study, we employed a genome-wide CRISPR-Cas9 screening approach in conjunction with functional cytotoxicity assays to delineate the proteins modulating the susceptibility of colon adenocarcinoma HCT-116 cells to NK cell-mediated cytotoxicity.
Results Analysis of guide RNA (gRNA) distribution in HCT-116 cells that survived co-incubation with NK cells identified ICAM-1 as a pivotal player in the NKp44-mediated immune synapse, with NKp44 serving as an activating receptor crucial for the elimination of HCT-116 tumor cells by NK cells. Furthermore, disruption of genes involved in the apoptosis or IFN-γ signaling pathways conferred resistance to NK cell attack. We further dissected that NK cell-derived IFN-γ promotes mitochondrial apoptosis in vitro and exerts control over B16-F10 lung metastases in vivo.
Conclusion Monitoring ICAM-1 levels on the surface of tumor cells or modulating its expression should be considered in the context of NK cell-based therapy. Additionally, considering the diffusion properties of IFN-γ, our findings highlight the potential of leveraging NK cell-derived IFN-γ to enhance direct tumor cell killing and facilitate bystander effects via cytokine diffusion, warranting further investigation.

overall_design: genome-wide CRISPR-Cas9 screening approach in conjunction with functional cytotoxicity assays to delineate the proteins modulating the susceptibility of colon adenocarcinoma HCT-116 cells to NK cell-mediated cytotoxicity. Sample 1: Collection of mutant cells. Sample 2: Co culture KHYG-1 cells + collection of mutants  round 1. Sample 3: Coculture of KHYG-1 cells + a-NKp44 mAb + collection of mutant cells  round 1. Sample 4: KHYG-1 NKp44 KO + collection of mutant cells round 1.  Sample 5: Co culture KHYG-1 cells + collection of mutants  round 2. Sample 6: Coculture of KHYG-1 cells + a-NKp44 mAb + collection of mutant cells round 2. Sample 7: KHYG-1 NKp44 KO + collection of mutant cells round 2.

first: Sophie

last: Guia

first: Aurore

last: Fenis

first: Justine

last: Galluso

first: Hakim

last: Medjouel

last: Escalière

first: Angelika

last: Modelska

first: Margaux

last: Vienne

first: Noella

last: Lopes

first: Amélie

last: Pouchin

first: Benjamin

last: Rossi

first: Laurent

last: Gauthier

first: Sandrine

last: Roulland

first: Eric

last: Vivier

first: Emilie

last: Narni-Manceinelli


title: α-Ketoglutarate promotes trophectoderm induction and maturation from naive human embryonic stem cells [scRNA-Seq 2D]

first: Jan

last: Żylicz

overall_design:
scRNA-seq of H9 human embryonic stem cells cultured in tt2iLIFGö and hiTSCs. tt2iLIFGö cells were treated for 24hrs with 0 or 4mM dimethyl-alphaketoglutarate. hiTSCs were derived from treated or untreated tt2iLIFGö cells and collected after 72 hours.
HTO barcode sequence hashtagged sample
TotalSeq-A0253 anti-human Hashtag 3 TTCCGCCTCTCTTTG tt2iLIFGo_DMSO
TotalSeq-A0254 anti-human Hashtag 4 AGTAAGTTCAGCGTA tt2iLIFGo_dm-aKG
TotalSeq-A0255 anti-human Hashtag 5 AAGTATCGTTTCGCA hiTSC_DMSO
TotalSeq-A0256 anti-human Hashtag 6 GGTTGCCAGATGTCA hiTSC_dm-aKG

first: Karlien

last: Van Nerum

first: Anne

last: Wenzel

first: Eleni

last: Kafkia

first: Viktoria

last: Lavro

first: Annina

last: Roelofsen

first: Antar

last: Drews

first: Sandra

last: Bages Arnal

last: Zylicz


title: Regulation of lung progenitor plasticity and repair by fatty acid oxidation

first: Jhonny

last: Rodriguez Lopez

first: Quetzalli

last: Angeles-López

last: Rodriguez-Lopez

first: Paula

last: Agudelo

first: Jazmin

last: Calyeca

first: Diana

last: Álvarez

first: Marta

last: Bueno

first: Lan

last: Tu

first: Myriam

last: Salazar-Terreros

first: Natalia

last: Vanegas-Avendaño

first: Jordan

last: Krull

first: Aigul

last: Moldobaeva

first: Srimathi

last: Bogamuwa

first: Stephanie

last: Scott

first: Victor

last: Peters

first: Brenda

last: Reader

first: Sruti

last: Shiva

first: Michael

last: Jurczak

first: Mahboobe

last: Ghaedi

first: Qin

last: Ma

first: Toren

last: Finkel

first: Mauricio

last: Rojas

first: Ana

last: Mora


title: Distinct Vps34-orchestrated signaling processes dictate the transitional heterogeneity and functional adaptation of effector Treg cells [scRNAseq]

city: Memphis

first: Hongbo

last: Chi

state: TN

address: 262 Danny Thomas Place

department: Immunology

institute: St Jude Children's Research Hospital

summary: Emerging evidence highlights regulatory T cell (Treg) heterogeneity in lymphoid and non-lymphoid tissues, but we have limited understanding of context-dependent functions and spatiotemporal regulators of heterogenous Treg states, especially during perinatal life when immune tolerance is established. Using single-cell transcriptomics profiling and experimental validations, we revealed that Vps34 is essential for orchestrating effector Treg (eTreg) transitional heterogeneity during perinatal life. We found that loss of Vps34 reduced terminal eTreg accumulation in lymphoid tissues, associated with decreased generation of Treg cells in non-lymphoid tissues and development of an early-onset autoimmune disease. After perinatal life, Vps34-deficient eTreg accumulation was further impaired due to reduced survival, highlighting temporal regulation of eTreg heterogeneity and maintenance by Vps34. Accordingly, inhibition of Vps34 in mature Treg cells also disrupted immune homeostasis but boosted anti-tumor immunity. Mechanistically, multiomics profiling approaches uncovered that Vps34-orchestrated transcriptional and epigenetic remodeling promotes terminal eTreg programming. Further, via genetic deletion of the Vps34-interacting proteins Atg14 or Uvrag in Treg cells, we established that autophagy (via Atg14) but not endocytosis (via Uvrag) was required for the overall survival, but not transitional heterogeneity, of eTreg cells. Accordingly, mice with Treg-specific deletion of Atg14, but not Uvrag, had moderately disrupted immune homeostasis and reduced tumor growth, with Vps34 and Atg14-dependent gene signatures also being elevated in intratumoral Treg cells from human cancer patients. Collectively, our study reveals distinct Vps34-orchestrated signaling events that temporally regulate eTreg heterogeneity and functional adaptation and the pathophysiological outcomes on autoimmunity versus anti-tumor immunity.

overall_design: We used 3' scRNAseq (10X Genomics) to compare the transcriptome of spleen-derived control (Control; n = 1) and Vps34-deficient (Vps34 KO; n = 1) CD4+Foxp3-YFP+ Treg cells, isolated from 10-day-old perinatal control (Foxp3CrePik3c3+/fl) or Foxp3CrePikc3c3fl/fl mice.

first: Nicole

last: Chapman

first: Hao

last: Shi


title: Distinct Vps34-orchestrated signaling processes dictate the transitional heterogeneity and functional adaptation of effector Treg cells [scMultiomics]

overall_design: We used scMultiomics (snRNA+scATAC; 10X Genomics) to compare the transcriptome of spleen-derived control (Control; n = 1) and Vps34-deficient (Vps34 KO; n = 2)  CD4+Foxp3-YFP+ Treg cells, isolated from 12-day-old control (Foxp3CrePik3c3+/fl) or Foxp3CrePikc3cfl/fl mice.

first: Erienne

last: Norton


title: Distinct Vps34-orchestrated signaling processes dictate the transitional heterogeneity and functional adaptation of effector Treg cells [ATAC-seq1]

overall_design: We used ATAC-seq to compare the chromatin accessibility of splenic-derived control (control; n = 2) and Vps34-deficient (Vps34 KO; n = 4) CD4+Foxp3-YFP+ Treg cells or lung-derived control (control; n = 2) and Vps34-deficient (Vps34 KO; n = 2) CD4+Foxp3-YFP+TCRb+ Treg cells, isolated from 10-day-old perinatal control (Foxp3CrePikc3c3+/fl or Foxp3CrePikc3c+/fl) or Foxp3CrePikc3c3 mice.


title: Distinct Vps34-orchestrated signaling processes dictate the transitional heterogeneity and functional adaptation of effector Treg cells [ATAC-seq2]

overall_design: We used ATAC-seq to compare the chromatin accessibility of spleen-derived control (control; n = 3) and Atg14-deficient (Atg14 KO; n = 4) CD4+Foxp3-YFP+CD44–CD62L+ cTreg cells or spleen-derived control (control; n = 3) and Atg14-deficient (Atg14 KO; n = 4) CD4+Foxp3-YFP+CD44+CD62L– eTreg cells, isolated from control (Foxp3CreAtg14+/fl) or Foxp3CreAtg14fl/fl mixed bone marrow chimeras.


title: Distinct Vps34-orchestrated signaling processes dictate the transitional heterogeneity and functional adaptation of effector Treg cells [microarray 2]

overall_design: We used microarrays to compare the global transcriptomes of lymphoid-tissue (spleen + pLN)-derived CD4+Foxp3-YFP+CD44–CD62L+ cTreg and CD4+Foxp3-YFP+CD44+CD62L– eTreg from control (Atg14 heterozyous; n = 4 for cTreg and 4 for eTreg) and Atg14-deficient (Atg14 KO; n = 3 for cTreg and 3 for eTreg) mixed bone marrow chimeras.


title: Advanced iPSC-CMs maturation by integrating maturation medium, nanopatterning, and electrical stimulation

status: Public on Feb 24 2025

city: Dresden

first: Mario

last: Schubert

address: Fetscherstraße 74

department: Pharmacology

institute: TU Dresden

summary: The immaturity of human induced pluripotent stem cell-derived cardiomyocytes (iPSC-CMs) is a major limitation for their use in drug screening to identify pro-arrhythmogenic or cardiotoxic molecules. Here, we demonstrate an approach that combines lipid-enriched maturation medium with a high concentration of calcium, nanopatterning of culture surfaces and electrostimulation to generate iPSC-CMs with advanced electrophysiological, structural and metabolic phenotypes. Systematic testing reveals that electrostimulation is the key driver of enhanced mitochondrial development and metabolic maturation and improved electrophysiological properties of iPSC-CMs. Increased calcium concentration strongly promotes electrophysiological maturation, while nanopatterning primarily facilitates sarcomere organisation with minor effect on electrophysiological properties. Transcriptome analysis reveals that activation of HMCES and TFAM targets contributes to mitochondrial development, whereas downregulation of MAPK/PI3K and SRF targets is associated with iPSC-CM polyploidy. These findings provide mechanistic insights into iPSC-CM maturation, paving the way for pharmacological responses that more closely resemble those of adult CMs.

overall_design: RNA seq of iPSC-derived cardiomyocytes cultured in lipid-enriched maturation medium (MM), in MM on nanopattern-surfaces (NP) and under the influence of MM, NP and electrical Stimulation (ES, 2Hz, 14 days). 9 Samples from 3 Independent batches/differentiations of cardiomyocytes from 2 different iPSC-lines (iWTD2.1 and isWT7.22).

first: Kaomei

last: Guan

first: Wener

last: Li


title: scRNA and TCR-Seq of peripheral blood mononuclear cells (PBMC)   from r/r classical Hodgkin Lymphoma patients  under anti-PD1 therapy.

city: New York

first: Vanessa

last: Cristaldi

state: NY

address: 522 First Avenue

department: Dermatology

institute: NYU Langone Health

summary: We did scRNA and TCR-seq in order to determine the immunophenotic profile of refractory and relapsed patients under anti-PD1 therapy and evaluate based on their response.

overall_design: PBMC were  isolated from the blood of each patients. All samples wew  sequenced at 3 different time-point: baseline, post cicle 5  and post cycle 9 of therapy.

first: Carmelo

last: CarloStella


title: MIWI2 Regulates Mitochondrial Gene Expression During Influenza and Exacerbates Disease Outcome

city: Boston

first: Matthew

middle: Robert

last: Jones

state: MA

address: 72 East Concord Street

department: Medicine

institute: Boston University School of Medicine

type: Non-coding RNA profiling by high throughput sequencing

summary: The airway epithelium, consisting of diverse cell types, plays a vital role in defending against respiratory viruses. MIWI2 multiciliated (M2MC) cells are a rare subpopulation of multiciliated cells distinguished by the expression of MIWI2, the mouse analogous PIWIL4 argonaute family protein. While recognized for its role in repressing retrotransposons during spermatogenesis and regulating viral RNA in mosquitos, the function of MIWI2 in M2MC cells remains poorly understood. This study explores the transcriptomic changes in retrotransposons, viral RNAs, and host genes in an effort to elucidate MIWI2’s role in the airway. M2MC and nonM2MC cells were sorted from digested lungs of MIWI2 haplosufficient (Miwi2+/tom) and deficient (Miwi2tom/tom) mice intratracheally instilled with saline or mouse adapted A/Puerto Rico/8/1934 (PR8) IAV three days post infection. Our findings indicated that retrotransposon and viral RNA expression is independent of MIWI2 expression. However, MIWI2 deficiency decreased mitochondrial and ribosomal gene expression in M2MC cells during PR8 infection. In addition, a decrease in small RNAs mapped to nuclear mitochondrial (NuMT) DNA was observed in saline treated MIWI2 expressing cells. These findings were then followed up by flow cytometry studies where an increase in intracellular reactive oxygen species (ROS) was observed in PR8 infected multiciliated cells from Miwi2tom/tom mice. In addition, Miwi2tom/tom mice experience decreased viral titer and RNA 7 days post infection and recovered faster in percent body weight compared to wild-type and Miwi2+/tom mice. These studies suggest that MIWI2 exacerbates IAV outcomes by regulating mitochondrial gene expression and function. These results reveal a novel role for MIWI2 in somatic cells and propose MIWI2/PIWIL4 as a potential biomarker for susceptibility to severe respiratory infections. Understanding MIWI2-dependent pathways could lead to new therapeutic targets for respiratory viral infections.

first: Jhonatan

last: Henao Vasquez

middle: R

first: Alan

last: Fine


title: Gene expression analysis of organoid model of human esophageal squamous cell carcinomas (ESCCs)

city: Tokyo

first: Taku

last: Sato

address: 1-5-45 Yushima Bunkyo-ku

department: Department of Biodefense Research

institute: Medical Research Institute, Tokyo Medical and Dental University (TMDU)

summary: Esophageal squamous cell carcinoma (ESCC) is a serious cancer with a poor prognosis and a high recurrence rate after chemotherapy, which is a major clinical challenge. To elucidate the molecular basis of chemotherapy (chemo)-resistance and develop methods to effectively eliminate chemo-resistant tumor clones, we established a cancer organoid model from 24 ESCC patients of various stages, ages, and treatments. These ESCCOs recapitulated most oncogenic mutations of primary ESCC tissues and had tumorigenic properties upon xenografting. Each organoid line differs in its responsiveness to 5-fluorouracil (5-FU) and cisplatin (CDDP), chemotherapeutic agents commonly used to treat ESCC patients, with 7 lines exhibiting potent chemo-resistance. Importantly, these chemo-resistant ESCCOs had enhanced expression of genes involved in antioxidant stress response pathways and increased chromatin accessibility of their genomic loci, compared to chemo-sensitive ESCCOs, and these genes became useful biomarkers that can stratify chemo-resistant ESCC in histopathological specimens.

overall_design: Gene expression of Patient derived ESCCOs were analyzed

first: Shunsaku

last: Nakagawa

first: Toshiaki

last: Ohteki


title: Transcriptomic Profiling of Calcitriol-Mediated Gene Expression Changes in CaSki Human Cervical Cancer Cell Line

city: CDMX

first: Alberto

last: Cedro-Tanda

state: CMDX

address: Periferico sur #4809

institute: INMEGEN

summary: The vitamin D endocrine system, primarily mediated by its principal metabolite calcitriol and the vitamin D receptor (VDR), plays a critical role in numerous physiological processes in humans, ranging from calcium metabolism to the prevention of various tumors, including cervical cancer. To comprehensively understand the genomic regulatory effects of calcitriol in a cervical cancer model, this study investigated the transcriptional changes induced by calcitriol in CaSki cells, a cervical cell line harboring multiple copies of HPV16, the primary causal agent of cervical cancer. Initially, we characterized the presence and functionality of the VDR and its co-receptor retinoid X receptor in CaSki cells via immunofluorescence. Subsequently, we assessed the global transcriptome response to calcitriol treatment compared to its vehicle control using microarray analysis, with validation conducted through qPCR and western blot analysis. Our findings revealed that calcitriol regulated over 1000 protein-coding genes, along with some long non-coding RNAs and microRNAs. Overall, calcitriol exerted a repressive effect on the CaSki cell transcriptome, suppressing twice as many genes as it induced. Functional analysis of the results demonstrated that calcitriol suppressed crucial cellular processes involved in cell progression, particularly inhibiting cell proliferation, a finding validated in this study. These results suggest that in this advanced cervical cancer model, calcitriol exhibits a significant antitumor effect by blocking critical processes for tumor progression, underscoring the importance of maintaining adequate vitamin D nutritional status for cervical cancer prevention.

overall_design:
For this study, three independent experiments were conducted, each comprising three experimental replicates per experimental condition. From each experimental condition, 3 pools of total RNA were prepared, with each pool comprising an equimolar combination
CaSki cells were seeded (150,000 cells) onto 4-well cell culture slides in growth medium. After 24 hours, the medium was aspirated and replaced with either 0.1% ethanol as vehicle or 1x10 -8 M calcitriol in treatment medium.

first: Luis

last: Hernández-Monterde

first: Tomas

last: Lizardi-Aguilera

first: David

last: Barrera

first: Janice

last: García-Quiroz

first: Lorenza

last: Díaz

first: Euclides

last: Avila


title: Inflammatory conditions shape phenotypic and functional characteristics of lung-resident memory T cells

city: Erlangen

first: Mark

last: Dedden

state: Bayern

address: Schwabachanlage 12

department: Department of Medicine 1

institute: Universitätsklinikum Erlangen

summary: The induction and maintenance of pulmonary TRM is potentially affected by the initial inflammatory conditions. We performed scRNA-seq analysis to determine if immunization- and H1N1 infection-induced lung TRM differ in their transcriptional core signatures.

overall_design: Balb/c mice were either intranasally immunized with recombinant adenoviral vectors or intranasally infected with H1N1/PR8. Hashtag-labelled, CD45.2 positive, antigen- (NP-) specific lung CD8+ T cells were sorted by Fluorescence-activated cell sorting and analyzed using scRNA-seq.

first: Anna

last: Schmidt

first: Matthias

last: Tenbusch


title: Tracing functional (epi)genomic imprints and their evolutionary origins in human defense antiviral cellular response (RNA-Seq 2)

city: Athens

first: Marios

last: Agelopoulos

state: Attica

address: 4 Soranou Ephessiou Str

department: Center of Basic Research

country: Greece

institute: Biomedical Research Foundation Academy of Athens

summary: An integral part of human cellular homeostasis substantially relies on defense transcriptional responses tailored to fight microbial pathogens, including Viruses. However, a definitive anatomy of the “virus-responsive” fates of the non-coding genome was largely elusive. Here, we exhaustively assayed the human transcriptome and epigenome under naïve and antiviral cellular states and defined remarkable reprogramming to mark the exchange of cellular fates, involving previously unspecified, unsupervised, or overlooked non-coding entities endowed with thousands of novel virus-responsive enhancers, Super-enhancers (SEs), and Repetitive DNA enhancers. These functional determinants demonstrate superior chromatin architecture, stimulus-specificity, and transcriptional fitness, and neighbor, reside proximal, or entirely coincide with hundreds of the virus-stimulated genes, while a multitude of those is bound by the master antimicrobial TFs, IRF3 or/and NFκB, upon cell infection. A plethora of these DNA elements is traced within the repetitive fate of the human genome including Simple Tandem Repeats (STRs), Dispersed Repeats (DRs) such as retrotransposons and DNA transposons, and chimeras of those, enriched in HCTFBSs recognized by IRF3 or/and NFκB and exhibits pervasive imprints in the genomes of evolutionary recent, old and ancient species, including viruses. These findings emphasize the role of the architectural and functional compartmentalization of the human epigenome in naïve and infected cells on the perplexing natural conflicts and mechanistic dependencies that impose the frontage of defense gene expression in humans.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Marios Agelopoulos

first: Marianna

last: Koutsi

first: Marialena

last: Pouliou

first: Giannis

last: Vatsellas


title: Distinct Vps34-orchestrated signaling processes dictate the transitional heterogeneity and functional adaptation of effector Treg cells [microarray 1]

first: Hongbo

last: Chi

overall_design: We used microarrays to compare the global transcriptomes of lymphoid-tissue (spleen + pLN)-derived CD4+Foxp3-YFP+ Treg cells from control (Wildtype; n = 4) and Vps34-deficient (Vps34 KO; n = 5) mixed bone marrow chimeras.

first: Hao

last: Shi


title: OPA1 mutations associated with dominant optic atrophy affect mitochondrial fusion and cell death in a domain-specific manner

city: Changsha

first: Lin

last: Zhang

state: Hunan

address: No. 87, Xiangya Road, Kaifu District, Changsha City

institute: Xiangya Hospital, Central South University

summary: Our study uncovered the role of OPA1 BSE domain in modulation of mitochondrial dynamics and cell death, and characterized the related signaling pathways, hereby providing the insight into the understanding of the domain-specific effect of OPA1 on mitochondrial morphology and function.

overall_design: RNA-seq profiling of  wild type, OPA1, or OPA1 mutant(V560F,V465F) overexpressed in OPA1 knockdown cells in N2a cells

first: Ke

middle: X

first: Wen

middle: Q

first: Xiao

last: Hou

first: Run

middle: Y

last: Tian

first: Zheng

last: Hu

first: Li

last: Yin

first: Zhong

middle: H


title: DNA methylation profiling of 154 triple negative breast cancers using the Illumina EPIC 850K platform

city: Lund

first: Johan

last: Staaf

address: Medicon Village

country: Sweden

institute: SCIBLU - Swegene Centre for Integrative Biology at Lund University

summary: Genome-wide DNA methylation profiles for 154 triple negative breast cancer (TNBC) samples from the Swedsh Cancerome Analysis Network - Breast (SCAN-B) cohort.

overall_design: Genomic DNA from 154 triple negative breast cancer (TNBC) samples was treated with bisulfite and hybridized to Illumina EPIC 850K arrays using standard protocols. Raw iDat files were processed using the "minfi"-package in R as well as custom R-scripts to produce normalized beta values. Both raw intensity values from minfi and the final normalized data are included for each sample.

first: Mattias

last: Aine


title: Targeting CFTR and FGF2 and TGFβ1 Pathways with MSC-Derived Extracellular Vesicles to Promote Functional Maturation of Preterm Intestinal Epithelium

city: Pohang

first: Jihyun

last: Kim

address: Pohang 37673

institute: Pohang University of Science and Technology

summary: Preterm birth disrupts the critical maturation of the intestinal epithelium, leading to compromised digestive and absorptive functions. This study explores the potential of mesenchymal stem cell (MSC)-derived extracellular vesicles (EVs) to promote the maturation of human preterm intestinal epithelial cells. By establishing human preterm intestinal organoids derived from the ileal tissue of a neonate born at 27 weeks gestational age, we demonstrate that treatment with EVs, particularly the EV39 line, significantly enhances the expression of adult-type enterocyte markers, including genes involved in lipid and nutrient transport, digestive enzymes, and epithelial barrier integrity. These maturation signatures were identified through reanalysis of multiple single-cell RNA sequencing (scRNA-seq) datasets, revealing distinct enterocyte differentiation trajectories and key maturation-specific gene expression profiles. Notably, these maturation effects were dependent on cystic fibrosis transmembrane conductance regulator (CFTR) activity, as CFTR inhibition reversed the observed benefits. Proteomic analysis identified FGF2 and TGFβ1 as key ligands mediating the effects of EV39. Co-treatment with FGF2 and TGFβ1 further enhanced epithelial barrier integrity and fatty acid uptake, highlighting the translational potential of EV39 or its ligands in promoting intestinal functional maturation in preterm infants.

overall_design: To investigate MSCs-derived extracellular vesicles (EVs) on preterm intestinal epithelial maturation, the preterm intestinal organoids (GA27) were treated with EVs derived from two distinct lines of MSCs, designated EV39 and EV42, for 7days and subjected to transcriptomic profiling via RNA-seq.

first: Hyunji

last: Park

first: Na-Young

first: Se In

last: Hwang

first: Dong Kyung

last: Sung

first: Yun Sil

last: Chang

first: Ara

last: Koh


title: Transcriptomic characterisation of Acute Myeloid Leukemia cell lines bearing the same t(9;11) driver mutation reveals different molecular signatures

city: Edinburgh

first: Douglas

last: Vernimmen

address: The University of Edinburgh, Easter Bush Campus, Midlothian

department: Roslin Institute

institute: University of Edinburgh

summary: Background Acute myeloid leukemia (AML) is the most common type of acute leukemia, accounting for 20% of cases in children and adolescents. Genome-wide studies have identified genes that are commonly mutated in AML, including many epigenetic regulators involved in either DNA methylation (DNMT3A, TET2, IDH1/2) or histone post-translational modifications (ASXL1, EZH2, MLL1). Several cell lines derived from AML patients are widely used in cancer research. Whether important differences in these cell lines exist remains poorly characterised. Results Here, we used RNA sequencing (RNA-Seq) to contrast the transcriptome of four commonly used AML-derived cell lines: THP-1, NOMO-1, MOLM13 bearing the common initiating t(9;11) translocation, and MV4-11 bearing the t(4;11) translocation. Gene set and protein-protein interaction enrichment analyses, performed alongside expression profiling of master transcription regulator genes, revealed important differences in the transcriptome distinguishing these different AML models.  Conclusion The present study offers a valuable resource by providing a detailed comparative characterisation of the transcriptome of cell lines within the same AML subtype used as models for leukemia research.

overall_design: To compare these cell lines, we performed RNA-seq using deep sequencing (>120M paired end reads per sample).


title: Tracing functional (epi)genomic imprints and their evolutionary origins in human defense antiviral cellular response (ChIP-Seq)

first: Marios

last: Agelopoulos

summary: An integral part of human cellular homeostasis substantially relies on defense transcriptional responses tailored to fight microbial pathogens, including Viruses. However, a definitive anatomy of the “virus-responsive” fates of the non-coding genome was largely elusive. Here, we exhaustively assayed the human transcriptome and epigenome under naïve and antiviral cellular states and defined remarkable reprogramming to mark the exchange of cellular fates, involving previously unspecified, unsupervised, or overlooked non-coding entities endowed with thousands of novel virus-responsive enhancers, Super-enhancers (SEs), and Repetitive DNA enhancers. These functional determinants demonstrate superior chromatin architecture, stimulus-specificity, and transcriptional fitness, and neighbor, reside proximal, or entirely coincide with hundreds of the virus-stimulated genes, while a multitude of those is bound by the master antimicrobial TFs, IRF3 or/and NFκB, upon cell infection. A plethora of these DNA elements is traced within the repetitive fate of the human genome including Simple Tandem Repeats (STRs), Dispersed Repeats (DRs) such as retrotransposons and DNA transposons, and chimeras of those, enriched in HCTFBSs recognized by IRF3 or/and NFκB  and exhibits pervasive imprints in the genomes of evolutionary recent, old and ancient species, including viruses. These findings emphasize the role of the architectural and functional compartmentalization of the human epigenome in naïve and infected cells on the perplexing natural conflicts and mechanistic dependencies that impose the frontage of defense gene expression in humans.

overall_design: ChIP-Seq

first: Marianna

last: Koutsi

first: Marialena

last: Pouliou

first: Antonis

last: Kokkalis

first: Giannis

last: Vatsellas

first: Konstantinos

last: Zagkas

first: Marili

last: Vasilogianni

first: Lydia

last: Champezou

first: Dimitris

last: Chatzopoulos

first: Alexandra

last: Kouroukli


title: Tracing functional (epi)genomic imprints and their evolutionary origins in human defense antiviral cellular response (RNA-Seq)

overall_design: RNA-seq


title: DNA methylation profiling of human triple negative breast cancer (TNBC) cell lines

status: Public on Feb 23 2025

first: Johan

last: Staaf

type: Methylation profiling by genome tiling array

summary: DNA methylation profiling of TNBC cell lines to target epigenetic regulation of genes as well as global alterations patterns.

overall_design: DNA methylation of tumor DNA was performed using Illumina MethylationEPIC V1 beadchips on 8 cell lines according to manufacturer's instructions. No replicates.


title: Effect of depletion of METTL3 or METTL14 on gene expression in human K562 cell line, a model of chronic myeloid leukemia in the acute myeloid blast phase

status: Public on Feb 22 2025

city: 成都

first: Yuqian

last: Tang

state: 四川

address: 玉林街道

institute: Sichuan university

summary: N6-methyladenosine (m6A) RNA methylation is a significant epigenetic modification in mammalian mRNAs, crucial for tumorigenesis and development. Our study shows that the methyltransferases METTL3 and METTL14 are highly expressed in acute myeloid leukemia (AML) patients, excluding those with acute promyelocytic leukemia (APL). Elevated levels of these enzymes correlate with shorter survival rates, indicating their role as adverse prognostic factors in AML. Through comprehensive analysis of RNA-seq data and subsequent experimental validation, the knockdown of METTL3 and METTL14 was found to significantly perturb the p53 signaling pathway. This alteration resulted in the upregulation of both p53 and CDKN1A (p21), as well as an extended half-life of mdm2 mRNAs. Furthermore, METTL3 influences AML cell survival by regulating the MAPK pathway through PGC-1α, which modulates ROS detoxification and acts as an oncogene. In summary, METTL3 and METTL14 are promising targets for AML treatment.

overall_design:
To investigate the functions of METTL3 and METTL14 in AML cell lines, we constructed K562 cell lines with knockdown of METTL3 or METTL14 using shRNA. We then analyzed the sequencing data to identify changes in signaling pathways following gene knockdown.

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first: Lina

last: Sang

first: Xiaoyan

last: Liu

first: Yuping

last: Gong


title: Tracing functional (epi)genomic imprints and their evolutionary origins in human defense antiviral cellular response (ChIP-seq III)

overall_design: ChIP-seq A549, NIH3T3, THP-1


title: Tracing functional (epi)genomic imprints and their evolutionary origins in human defense antiviral cellular response

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

overall_design: Refer to individual Series


title: Repair-Associated Macrophages Increase after Early-phase Microglia Attenuation to Promote Ischemic Stroke Recovery [scRNA-Seq]

status: Public on Feb 21 2025

city: Hangzhou

first: Xiaotao

last: Zhang

state: Zhejiang

address: 88 Jiefang Road

institute: 2nd Affiliated Hospital,ZJU

summary: Ischemic stroke recovery involves dynamic interactions between the central nervous system and infiltrating immune cells. Peripheral immune cells compete with resident microglia for spatial niches in the brain, but how modulating this balance affects recovery remains unclear. Here, we use PLX5622 to create spatial niches for peripheral immune cells, altering the competition between infiltrating immune cells and resident microglia in male mice following transient middle cerebral artery occlusion (tMCAO). We find that early-phase microglia attenuation promotes long-term functional recovery. This intervention amplifies a subset of monocyte-derived macrophages (RAMf) with reparative properties, characterized by high expression of GPNMB and CD63, enhanced lipid metabolism, and pro-angiogenic activity. Transplantation of RAMf into stroke-affected mice improves white matter integrity and vascular repair. We identify Mafb as the transcription factor regulating the reparative phenotype of RAMf. These findings highlight strategies to optimize immune cell dynamics for post-stroke rehabilitation.

overall_design: Single-cell RNA profiling of blood immune cells,brain CD45high immune cells or whole brain cells in MCAO mice at 5 and 14 dpi.

first: Huaming

last: Li

first: Yichen

last: Gu

first: Jianmin

first: Ligen

last: Shi


title: Distinct Vps34-orchestrated signaling processes dictate the transitional heterogeneity and functional adaptation of effector Treg cells.

first: Hongbo

last: Chi


title: Restraint of inflammasome-driven cytokine responses through the mRNA stability protein TTP

city: Cleveland

first: Meghan

middle: Elizabeth

last: O'Keefe

address: 2103 Cornell Rd

department: Pathology

institute: Case Western Reserve University School of Medicine

summary: Stimulation of the NLRP3 inflammasome causes a massive disruption of cellular homeostasis, with Golgi disruption, mitochondrial dysfunction, and changes in intracellular ion concentration all occurring rapidly upon stimulation. Given this, it would seem near certain that these changes might also globally affect cellular signaling pathways, yet few, if any, studies have explored this possibility. Here, we combine genomics and phosphoproteomics to identify a major disruption in the ERK1/2 MAP kinase signaling cascade upon inflammasome stimulation. This loss of ERK1/2 activity results in rapid inactivation of the mRNA decay-promoting protein tristetraprolin (TTP), with loss of TTP promoting subsequent increased release of cytokines upon pyroptosis. Further, we observe significantly increased levels of TTP expression in patients with inflammatory bowel disease (IBD), a disease for which altered cytokine expression is a key driver of pathogenesis. Inflammasome activation thus rapidly inactivates a pathway designed to suppress cytokine release, exacerbating hyperinflammatory states including those involved in autoinflammatory disease.

overall_design: To investigate changes in gene expression upon NLRP3 inflammasome stimulation, we performed RNA-seq on PMA-differentiated THP-1 cells which were stimulated with nigericin for 0, 2, or 4 hours. Each time point includes three replicates.

first: Derek

middle: W

last: Abbott

first: Hannah

middle: C

last: Kondolf

middle: E


title: Tracing functional (epi)genomic imprints and their evolutionary origins in human defense antiviral cellular response (DNaseI-Seq)

first: Marios

last: Agelopoulos

overall_design: DNaseI-Seq

first: Marianna

middle: A

last: Koutsi

first: Marialena

last: Pouliou

first: Antonis

last: Kokkalis

first: Giannis

last: Vatsellas

first: Konstantinos

last: Zagkas

first: Marili

last: Vasilogianni

first: Lydia


title: The ACTH test fails to diagnose adrenal insufficiency and increases cytokine levels in septic conditions

city: Lexington

first: Xiang-An

address: 741 S Limestone

institute: University of Kentucky

summary: The ACTH test is used to diagnose relative adrenal insufficiency (RAI) or critical illness-related corticosteroid insufficiency (CIRCI). Initially, guidelines recommended corticosteroid/glucocorticoid (GC) therapy for septic patients with RAI, but later trials did not show a survival benefit, leading to updated guidelines that abandon targeting RAI or CIRCI. Recent studies with an RAI mouse model showed a clear survival benefit from GC therapy in mice with RAI, suggesting that the inconclusive GC clinical trials might be due to issues with the ACTH test rather than targeting RAI. To investigate, we performed the ACTH test in septic mice. Interestingly, the ACTH test identified most mice as having adrenal insufficiency in the early and middle stages of sepsis, even those with a normal adrenal stress response. Surprisingly, the ACTH test triggered inflammatory cytokine to lethal levels, moderately increased mortality in septic mice. Mechanistically, RNAseq analysis revealed that these cytokines were generated by the adrenal gland via AP-1 signaling. These findings suggest that the inconclusive results of GC therapy trials may be due to the problematic nature of the ACTH test rather than the ineffectiveness of targeting RAI/CIRCI.

overall_design: C57BL/6J mice treated with cecal ligation and ouncture (CLP) for 3h, followed by ACTH or vehicle treated for 45 min, isolate RNA from adrenal gland for RNA-seq analysis

first: Dan

last: Hao


title: Tracing functional (epi)genomic imprints and their evolutionary origins in human defense antiviral cellular response (ChIP-Seq II)

last: Champezou


title: Repair-Associated Macrophages Increase after Early-phase Microglia Attenuation to Promote Ischemic Stroke Recovery [RNA-Seq]

first: Xiaotao

last: Zhang

overall_design: RNA-seq profiling of mouse bone marrow-derived macrophages treated with Mafb-lentivirus or control-lentivirus, with three biological replicates for each group.

first: Huaming

first: Yichen


title: Cigarette smoke induces angiogenic activation in the cancer field through dysregulation of an endothelial microRNA

city: New Haven

first: Xiting

last: Yan

state: Connecticut

address: 300 Cedar Street, Ste S441D

department: Internal Medicine

institute: Yale School of Medicine

summary: Exposure to cigarette smoke induces the angiogenic activation of the endothelial cells in the cancer field by selective degradation of mature microRNA-1. This change can be detected in the lungs of non-small cell lung cancer patients and correlates with their smoking burden.

overall_design: We collected tumor (T) and lung tissue adjacent to tumor (AT) from NSCLC patients (6 smokers and 3 non-smokers). We first performed a multi-step comparative transcriptome analysis on those tissue samples and compared the expression of genes between the T and AT samples in smokers and non-smokers.

first: Asawari

last: Korde

first: Shervin

middle: S

last: Takyar


title: Targeting Senescent Hepatocytes for Treatment of Metabolic Dysfunction-associated Steatotic Liver Disease and Multi-organ Dysfunction

city: Durham

first: KUO

last: DU

state: NC

address: 905 SOUTH LASALLE STREET, Room 1063

institute: Duke Universty

summary: Senescent hepatocytes accumulate in metabolic dysfunction-associated steatotic liver disease (MASLD) and are linked to worse clinical outcomes. However, their heterogeneity and lack of specific markers have made them difficult to target therapeutically. Here, we define a senescent hepatocyte gene signature (SHGS) using in vitro and in vivo models and show that it tracks with MASLD progression/regression across mouse models and large human cohorts. Single-nucleus RNA-sequencing and functional studies reveal that SHGS+ hepatocytes originate from p21+ cells, lose key liver functions and release factors that drive disease progression. One such factor, GDF15, increases in circulation alongside SHGS+ burden and disease progression. Through chemical screening, we identify senolytics that selectively eliminate SHGS+ hepatocytes and improve MASLD in mice. Notably, SHGS enrichment also correlates with dysfunction in other organs. These findings establish SHGS+ hepatocytes as key drivers of MASLD and highlight a potential therapeutic strategy for targeting senescent cells in liver disease and beyond.

overall_design: To induce hepatocyte senescence, Huh7 cells were treated with the CDK4/6 inhibitor palbociclib (1uM) for 8 days. To test the effects of Dp44mT on senescent Huh7 cells, the cells were treated with Dp44mT or vehicle for 48h. To test the effects of DpC on MASLD, 10-week-old C57BL/6J male mice were fed CDA-HFD for 10 weeks, and DpC (5 mg/kg) or vehicle (10% cavitron™ w7 hp7 pharma cyclodextrin) was given by gavage twice a week for the last 4 weeks (CDAHFD-Veh: n=7; CDAHFD-DpC: n=6). RNA was extracted and subjected to RNA-seq.

first: Kuo

last: Du

first: Liuyang

last: Wang

first: Christopher

last: Pan

first: AnnaMae

last: Diehl


title: Integrative multiomic approaches reveal ZMAT3 and p21 as conserved hubs in the p53 tumor suppression network

city: Stanford

first: Laura

last: Attardi

state: CA

address: 269 Campus Drive

institute: Stanford University

summary: TP53, the most frequently mutated gene in human cancer, encodes a transcriptional activator that induces myriad downstream target genes. Despite the importance of p53 in tumor suppression, the specific p53 target genes important for tumor suppression remain unclear. Recent studies have identified the p53-inducible gene Zmat3 as a critical effector of tumor suppression, but many questions remain regarding its p53-dependence, activity across contexts, and mechanism of tumor suppression alone and in cooperation with other p53-inducible genes. To address these questions, we used Tuba-seqUltra somatic genome editing and tumor barcoding in a mouse lung adenocarcinoma model, combinatorial in vivo CRISPR/Cas9 screens, meta-analyses of gene expression and Cancer Dependency Map data, and integrative RNA-sequencing and shotgun proteomic analyses. We established Zmat3 as a core component of p53-mediated tumor suppression and identified Cdkn1a as the most potent cooperating p53-induced gene in tumor suppression. We discovered that ZMAT3/CDKN1A serve as near-universal effectors of p53-mediated tumor suppression that regulate cell division, migration, and extracellular matrix organization. Accordingly, combined Zmat3-Cdkn1a inactivation dramatically enhanced cell proliferation and migration compared to controls, akin to p53 inactivation. Together, our findings place ZMAT3 and CDKN1A as hubs of a p53-induced gene program that opposes tumorigenesis across various cellular and genetic contexts.

overall_design: RNA-seq profling of E1A/HrasG12V-expressing murine embryonic fibroblasts and their knockout derivations (Zmat3 KO, Cdkn1a KO, Zmat3 + Cdkn1a KO, Trp53 KO, wild-type control)

first: Anthony

middle: M

last: Boutelle

first: Aicha

last: Mabene

first: David

last: Yao

first: Haiqing

last: Xu

first: Mengxiong

first: Yuning

middle: J

last: Tang

first: Steven

last: Lopez

first: Sauradeep

last: Sinha

first: Janos

last: Demeter

first: Ran

last: Chang

first: Brooks

last: Benard

first: Edel

last: McCrea

first: Liz

last: Valente

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