title: Spatial distribution and chromatin accessibility determine the therapeutic capacity of microglial subsets during neurodegeneration [scRNAseq1_LPS_ABX]

summary: Microglial spatial heterogeneity remains a crucial yet poorly studied question in light of potential cell-directed therapies for Alzheimer's disease (AD). Little is known about the dynamics of spatially distinct microglia states, which are either adjacent or non-associated with the plaque site, and their selective contributions to neurodegeneration in vivo. So far, research has essentially focused on pathology-associated microglia. Here, we combined novel multicolour fluorescence fate mapping, single-cell transcriptional analysis, epigenetic profiling, advanced immunohistochemistry and computational modelling to comprehensively characterize the relation of plaque-associated and non-plaque-associated microglia during neurodegeneration in female mice. This approach enabled us to identify and characterize non-plaque-associated microglia as a unique and highly dynamic microglial state in a mouse model of AD. Non-plaque-associated microglia modulate network expansion, quickly adapt to environmental cues and their transition to plaque-associated microglia can be specifically modulated during disease, contrary to their reputation as a passive bystander subpopulation. This description of the dynamics of spatially segregated microglial states and their distinct molecular features may therefore open promising new avenues for state-specific therapeutic interventions during neurodegeneration.

overall_design: Following either lipopolysaccharide (LPS), antibiotics (ABX), or PBS (N) treatment, microglia from early stage (ES) and late stage (LS) 5xfAD positive and negative mice were sorted by fluorescence-activated cell sorting (FACS) and analyzed by single cell RNA seq.


title: p16-expressing microglia and endothelial cells promote tauopathy and neurovascular abnormalities in PS19 mice

status: Public on Apr 30 2025

city: Rochester

first: Darren

last: Baker

state: MN

address: 200 1st ST SW

country: USA

institute: Mayo Clinic

type: Expression profiling by high throughput sequencing

summary: Cellular senescence is characterized by irreversible cell cycle exit, acquisition of a pro-inflammatory secretory phenotype, macromolecular damage, and deregulated metabolism. Senescent cells have been implicated in many age-related diseases, including neurodegenerative disease. We have previously demonstrated that selective elimination of senescent cells, both pharmacologically and genetically, prevents neurodegenerative disease phenotypes in tau (MAPTP301S;PS19) mutant mice. Here, we show that genetically knocking out the senescence mediator p16Ink4a, a cyclin-dependent kinase inhibitor, is sufficient to attenuate senescence signatures in PS19 mice. Neurodegenerative disease phenotypes dependent on senescent cell accumulation, including neuroinflammation, phosphorylated tau burden, neurodegeneration, and cognitive impairment were blunted in the absence of p16Ink4a. Additionally, we found that PS19 mice display altered neurovascular features—including vessel dilation, increased vessel density, deregulated endothelial cell extracellular matrix, and astrocytic endfoot depolarization—which were also attenuated when p16Ink4a was knocked out. Finally, we utilized a cell-type specific knockout of p16Ink4a to show that p16Ink4a deletion in endothelial cells and microglia alone attenuates many of the same tau-dependent phenotypes as whole-body knockout of p16Ink4a. Taken together, these results indicate that onset and progression of neurodegenerative disease in PS19 mice is driven, at least in part, by p16Ink4a expressing endothelial cells and microglia.

overall_design: We isolated hippocampus from 8-month-old female wildtype and PS19 tauopathy mice with and without knockout of p16 and sent extracted total RNA to Azenta Life Sciences for standard bulk RNA-sequencing.

first: Sara

middle: I

last: Graves

middle: J


title: Gas6-Axl signaling drives oral regenerative wound repair [bulk RNA]

city: Stanford

first: Jennifer

middle: Brigitta

last: Parker

state: CA

address: 257 Campus Drive

department: Surgery

institute: Stanford University

summary: Rapid and scarless wound repair is a hallmark of the oral mucosa, yet the cellular and molecular mechanisms that enable this regeneration remain unclear. By comparing populations of oral mucosal fibroblasts (OMFs) and facial skin fibroblasts (FSFs), we have identified the mechanisms that facilitate regeneration over fibrosis. We found that OMFs utilize Growth arrest specific-6 (GAS6)-AXL signaling to suppress fibrosis-related mechanosignaling via Focal adhesion kinase (FAK). Inhibition and knockdown of AXL in the oral mucosa resulted in fibrotic wounds and increased activation of FAK. At the same time, stimulation of AXL in the facial skin yielded wounds that heal regeneratively. Rare human oral scars that resulted from repetitive injury showed decreased expression of GAS6/AXL and increased FAK. Activating AXL in repetitively injured mouse oral tissue resulted in better wound healing outcomes and reduced scarring. Together, our work demonstrates that AXL signaling is necessary for regenerative wound healing in the oral mucosa and sufficient to limit facial skin fibrosis.

overall_design: Mouse wound tissue transcriptomes were profiled using single cell RNA sequencing, Visium spatial transcriptomics, and bulk RNA quencing. Tissue from wounds in oral mucosa and facial skin were compared. Timepoints include unwounded skin and oral mucosa, postoperative (POD) 2, 4, and 7.

first: Michelle

last: Griffin

first: Jessica

last: Cook


title: Gas6-Axl signaling drives oral regenerative wound repair [scRNA-seq]


title: ATAC-seq analyses of developmental EpCAM+ intestinal epithelial cells

status: Public on May 01 2025

city: Portland

first: Guanming

last: Wu

state: OR

address: 3181 S.W. Sam Jackson Park Road

institute: OHSU

type: Genome binding/occupancy profiling by high throughput sequencing

summary: To identify potential cell signaling pathways regulating the proliferative transition of Bmi1+ ISCs from highly proliferative to slow cycling, and also to identify influence for lineage differentiation, we performed bulk ATAC-Seq analyses of FACS-isolated EpCAM+ intestinal cells across developmental time points. Using differential chromatin accessibility analysis we identified enrichment of multiple pathways in the E12.5 population that progressively decreased at E17.5.  We analyzed the dataset using identification of motif discovery within this dataset, we found enhanced utilization of transcription factors in pathways including the Hippo signaling pathway (Tead1, Tead2 and Tead4), a known pathway that regulates organ development and size. When we evaluated enrichment motifs for canonical Wnt-responsive loci, we identified occupancy peaking at E14.5, again consistent with transition of proliferative dependency on Bmi1+ to Lgr5+ ISCs. Global motif enrichment for Wnt-related targets was assessed using ChromVAR, which displayed a similar trend, with the canonical Wnt pathway signature peaking at E14.5 and E15.5 (e.g. Cdx2, Tcf4).

overall_design: Epithelial cells from E12.5, E15.5 and E17.5 were isolated from the intestine and processed for ATAC-seq analyses.

first: Melissa

middle: H

last: Wong

first: Andrew

middle: C

last: Adey


title: MEK inhibition prevents human skin graft rejection by promoting CD8+TCF1+ T cells over CD8 effector differentiated T cells.

city: Nantes

first: Christine

last: Chauveau

address: 30 Boulevard Jean Monnet

country: France

institute: CR2TI UMR 1064

summary: While graft loss remains primarily attributed to rejection, the adverse effects of immunosuppressive therapies significantly contribute to patient morbidity and mortality. Therefore, it is imperative to develop treatments that both prevent alloimmune damage to the transplant and are well tolerated. MEK inhibition has recently been showed to be effective in controlling the alloimmune response in experimental mouse graft-versus-host disease, without abrogating anti-tumor nor anti-viral immunity. Here, we demonstrate that pharmacological MEK inhibition delays human skin graft rejection by human T cells in a preclinical humanized mouse model. Although similar graft infiltration was observed between treated and untreated animals, human epidermal cells were protected by the treatment. Single cell RNAseq analysis of the spleen immune cells revealed that MEK inhibition treatment inhibits CD8 T cell development to an effector phenotype and promotes the accumulation of CD8+TCF1+ stem-like cells. Furthermore, analysis of the CD4 cells showed that MEK inhibition improved CD4 T cell recovery by preserving IL7R expression on CD4 T cells and favored CD4 T cells engagement in the Th1 lineage rather than the Tfh lineage. These findings suggest that MEK inhibition could be an innovative approach to combining allogeneic immune response control and tissue protection after transplantation.

overall_design:
To investigate the role of MEK inhibitors on graft survival we used a humanised mouse model in which human skin is transplanted and then infused with human PBMCs from third donor enabling gradual reconstitution and subsequent graft rejection. Single cell RNAseq experiment was performed on the mouse spleen treated or not with MEK inhibitors.
---------------------
HTO     barcode sequence     hashtagged sample
TotalSeq-C0251 anti-human Hashtag 1      GTCAACTCTTTAGCG     3790-sham
TotalSeq-C0252 anti-human Hashtag 2     TGATGGCCTATTGGG     3798-tra
TotalSeq™-C0253 anti-human Hashtag 3      TTCCGCCTCTCTTTG     3906-sham
TotalSeq™-C0254 anti-human Hashtag 4     AGTAAGTTCAGCGTA     3907-tra

first: Chauveau

last: Christine

first: Nerriere-Daguin

last: Veronique

first: Fourgeux

last: Cynthia

first: Larcher

last: Thibaut

first: Delbos

last: Laurence

first: Braud

last: Martin

first: Rousseau

last: Olivia

first: Haspot

last: Fabienne

first: Blancho

last: Gilles

first: Ville

last: Simon


title: Gas6-Axl signaling drives oral regenerative wound repair

first: Jennifer

last: Parker


title: Comparative analysis of human kidney organoid and tubuloid models

city: Clayton

first: Nitika

last: Kandhari

state: VIC

address: Wellington Road

country: Australia

institute: Monash University

summary: Kidney organoids can be generated from commercially available human induced pluripotent stem cells (iPSC). They are amenable for genetic manipulation and useful for modelling development and early-onset genetic diseases. However, iPSC-derived kidney organoids lack longevity to model chronic stressors associated with chronic kidney disease. Adult epithelial kidney organoids (tubuloids) derived from nephrectomies or from renal cells suspended in urine can be passaged, expanded and cryopreserved, offering avenues to model epithelial injury and repair over longer timeframes. However, patient-derived organoids face regulatory barriers in their utilization. To leverage the benefits of both models, we establish a new protocol to generate tubuloids from iPSC-derived kidney organoids (iTubuloids). Kidney organoids were produced from iPSCs by directed differentiation then dissociated and cultured under adult organoid culture conditions. Epithelial organoids formed in less than 3 days from three distinct iPSC lines, each of which have been passaged > 12 times. Comparative analysis of gene expression profiles with RNA sequencing suggested that adult-derived tubuloids better represented the collecting duct, and iTubuloids showed increased expression of proximal and some distal markers. However, expression of proximal tubule markers was higher in iPSC-derived kidney organoids than any tubuloid model. We then evaluated the capacity of iTubuloids to model repetitive kidney injury and found exacerbation of the response and signs of failed repair as the injured progressed. Our study affirms capacity to extend the lifespan of epithelial cell types from short-lived iPSC-derived kidney organoids and reveal a need to optimise nephron cell identities in the tubuloid culture.

overall_design: Adult tubuloids were generated from three different nephrectomies and compared to the new iTubuloid model. iTubuloids were derived from three different kidney organoids, which in turn were generated from three induced pluripotent stem cell lines. iTubuloids were subjected to a triple hypoxic injury from day 4 to day 6, after three consecutive passages.

first: Ana

middle: B

last: Nunez-Nescolarde

first: Lingyun

last: Kong

first: Elif

last: Ekinci

first: David

last: Nikolic-Paterson

first: Alexander

middle: N

last: Combes


title: Single-cell transcriptomic analysis reveals alterations to cellular dynamics and paracrine signalling in radiation-induced muscle pathology

status: Public on Apr 28 2025

city: Ottawa

first: Nicolas

last: Collao

state: ON

address: 75 Laurier Ave E.

department: Health Science

country: Canada

institute: University of Ottawa

summary: Radiation therapy causes long-term skeletal muscle atrophy and fibrosis in juvenile cancer survivors. The mechanisms responsible for the skeletal muscle late effects of radiation therapy are not well-understood and have prevented the development of effective treatments. Using single-cell RNA sequencing (scRNA-seq), we characterize cellular dynamics and communication in a murine model of therapeutic radiation at 24-hours and 56-days post-irradiation (post-IR). We detected changes in muscle stem (satellite) cells (MuSCs) characterized by an acute preservation of committed MuSCs and long-term relative depletion of deep quiescent MuSCs. A conserved senescence Cdkn1a signature was observed in all muscle-resident cells post-IR. Genes related to fibroblast proliferation were up-regulated and a fibrotic and senescent transcriptome persisted in Fibro-adipogenic progenitors (FAPs) post-IR. Intercellular communication analysis revealed FAPs as the primary contributor of extracellular matrix (ECM) and target of monocyte/macrophage-derived TGF-β signalling post-IR through TGF-βR2 on FAPs. Together, our findings provide insights into the potential mechanisms and intercellular communication responsible for radiation-induced muscle atrophy and fibrosis.

overall_design: A fractionated dose of in vivo irradiation (in vivo-IR) of 8.2 Gy/dose was administered for three days to one hindlimb at age five weeks (IR). The rest of the body was lead-shielded, and the contralateral limb was used as a non-IR control (CON). Three independent samples (IR or CON limb) were pooled together in one batch to avoid batch effects. IR or the CON limb was removed at 24-hours post the final dose of radiation or 56-days post-IR (CON 24-hours, IR 24-hours, CON 56-days, and IR 56-days). A minimum of 10,000 live, mononucleated cells were sorted by Fluorescence-activated cell sorting (FACS) for further scRNA-seq (10X Genomics, Chromium Single Cell 30 Reagent Kits (v3 Chemistry)). The four libraries (CON 24-hours, IR 24-hours, CON 56-days, and IR 56-days) were sequenced on the Illumina NextSeq 500, with a read depth of 10,000 reads per cell.

first: Emma

last: Johannsen

first: Jesper

last: Just

first: Michael

last: De Lisio


title: Single-Molecule Direct RNA Sequencing Reveals the Shaping of Epitranscriptome Across Multiple Species

status: Public on Apr 29 2025

city: Guangzhou

first: Yingyuan

last: Xie

state: GuangDong

address: No. 135, Xingang Xi Road

department: School of Life Sciences

country: China

institute: Sun Yat-sen University

type: Methylation profiling by high throughput sequencing

summary: RNA modifications play a crucial role in gene regulation, yet understanding their transcriptome-wide landscape and biogenesis mechanisms remains challenging. Traditional next-generation sequencing (NGS) methods detect RNA modifications based on the aggregation of short-reads, overlooking the nature of RNA as multiple transcripts from one gene. Third-generation sequencing (TGS) platforms provide direct RNA sequencing at the resolution of individual RNA molecules, offering the promise of detecting RNA modifications and RNA processing events simultaneously. In this study, we introduce SingleMod, a deep learning model tailored for precise m6A modification mapping on individual RNA molecules using nanopore direct RNA sequencing (DRS). We systematically dissect the transcriptome-wide m6A landscape at single-molecule and single-base resolution, refining our understanding of the genomics of m6A and revealing an additive mode through which m6A shapes the epitranscriptome. Through comparative analyses across diverse species, we quantitatively elucidate three distinct m6A distribution patterns that suggest diverse biogenesis mechanisms. This study pioneers single-molecule epitranscriptome exploration across multiple species, deepening our understanding of m6A, including its genomics, biogenesis, mechanisms, and biological implications.

sample_organism:
Chlamydomonas reinhardtii
Arabidopsis thaliana
Oryza sativa
Homo sapiens
Mus musculus

overall_design: Absolute quantification of m6A in mouse embryonic stem cells, Arabidopsis, Rice, and Chamydomonas using GLORI. Single-molecule level m6A profiling of HEK293T, Chamydomonas and Rice using nanopore direct RNA sequencing.

first: Ying-Yuan

first: Zhen-Dong

last: Zhong

first: Hong-Xuan

last: Chen

first: Zhang

last: Zhang

first: Guan-Zheng

last: Luo


title: Dual states of Bmi1-expressing intestinal stem cells drive epithelial development and tissue regeneration

first: Guanming

last: Wu

summary: We demonstrate that Bmi1-expressing cells represent the predominant epithelial ISC in early intestinal development and precede existence of the canonical Wnt-dependent Lgr5+ stem cell population. We reveal that early in development, Bmi1+ ISCs are highly proliferative, then transition to a slow-cycling state with the emergence of the Lgr5+ ISC. Combining single cell RNA-sequencing (scRNA-seq) with bulk population ATAC-seq (Assay for Transposase Accessible Chromatin sequencing) analyses, we identify that a non-canonical Wnt signaling pathway correlates with the temporal presence of the highly proliferative developmental Bmi1+ ISC population

overall_design: Single Bmi1-expressing murine intestinal epithelial cells were FACS-isolated from embryos at E15.5. scRNA-seq was performed using standard protocols.

first: Nicholas

middle: R

last: Smith

first: Sidharth

middle: K

last: Sengupta

first: Melissa

last: Wong


title: Translational application of pharmacogenomics for refractory lung cancer II

city: Goyang-si

first: namhee

last: yu

state: Gyeonggi-do

address: 323, Ilsan-ro, Ilsandong-gu

country: South Korea

institute: National cancer center

summary: Patient-derived cells (PDC) recapitulate the characteristics of lung cancer and its therapeutic response. We collected cancer cells of patients to receive various chemotherapy and performed integrative analysis for pharmachogenomics.

overall_design: To identify the genomics characteristics, RNA-Seq and target-seq dataset was collected from lung cancer PDC of refractory patients. Drug response screening was performed from matched samples, and susceptibilities according to gene expression and variants were tested.

first: Ji-Youn

last: Han

first: Charny

last: Park

first: Sunshin

last: Kim

first: Sung-Ho

last: Gho

first: Namhee

last: Yu

first: Youngjoo

last: Lee

first: Eun

last: Kang


title: CDA HFD mice analysed for hepatic gene expression after treatment with semaglutide

status: Public on Apr 25 2025

city: Maaloev

first: Jenny

last: Norlin

state: Denmark

address: Novo Nordisk Park 1

department: Translational Leads Department

country: Denmark

institute: Novo Nordisk

summary: Metabolic dysfunction-associated steatohepatitis (MASH) is a chronic liver disease strongly associated with cardiometabolic risk factors. Semaglutide, a glucagon-like peptide-1 receptor agonist, improves liver histology in MASH, but the underlying signals and pathways driving semaglutide-induced MASH resolution are not well understood. We show that, in two preclinical MASH models, semaglutide improved histological markers of fibrosis and inflammation, and reduced hepatic expression of fibrosis- and inflammation-related gene pathways.

overall_design: CDA HFD mice were analysed for hepatic gene expression after treatment with semaglutide. Male C57BL/6JRj mice (7–8 weeks old) were obtained from Taconic (Ejby, Denmark) and housed in a controlled environment (12-h light/dark cycle, lights on at 6 AM, 21 ± 1.0°C, humidity 45–65%). Mice had ad libitum access to tap water and either chow or a high-caloric CDA-HFD diet (kcal %; fat 60%, carbohydrates 20%, 5.2 kcal/g, #A06071302, Research Diets, New Brunswick, NJ, USA) for 6 weeks prior to treatment start. CDA-HFD mice were randomly allocated to groups and treated with vehicle or semaglutide 20 µg/kg  for 6 (called 6-12w) or 12 weeks (called 6-18w). A group of CDA-HFD mice were terminated at treatment start to determine baseline levels of NASH ( baseline group). Vehicle-dosed chow-fed mice and mice switched to chow and does with vehicle served as additional controls.  Vehicle-dosed chow-fed mice and mice switched to chow and dosed with vehicle served as additional controls. Dosing was performed subcutaneously once daily in a volume of 5 ml/kg. To reduce initial gastric discomfort, the dose was increased through daily increments until reaching the target dose on treatment day 5.

first: Kasper

last: Almholt

first: Nikos

last: Sidiropoulos


title: DIO-MASH mice analysed for hepatic gene expression after treatment with semaglutide

summary:
Modulation of metabolic, inflammatory, and fibrotic pathways by semaglutide in metabolic dysfunction-associated steatohepatitis
Metabolic dysfunction-associated steatohepatitis (MASH) is a chronic liver disease strongly associated with cardiometabolic risk factors. Semaglutide, a glucagon-like peptide-1 receptor agonist, improves liver histology in MASH, but the underlying signals and pathways driving semaglutide-induced MASH resolution are not well understood. We show that, in two preclinical MASH models, semaglutide improved histological markers of fibrosis and inflammation, and reduced hepatic expression of fibrosis- and inflammation-related gene pathways.

overall_design: DIO-MASH mice were analysed for hepatic gene expression after treatment with semaglutide. C57BL/6JRj mice (5–6 weeks old) were obtained from Janvier Labs (Le Genest Saint Isle, France) and housed in a controlled environment (12-h light/dark cycle, 21 ± 2.0°C, humidity 50 ± 10%). Mice had ad libitum access to tap water and Gubra Amylin NASH diet (4.49 kcal/g, 40 kcal-% fat; of these, 46% saturated fatty acids by weight, 22% fructose, 10% sucrose, 2% cholesterol; D09100310, Research Diets) for 34 weeks for the efficacy trial. A group was maintained on regular mouse chow (2.85 kcal/g, Altromin 1324, Brogaarden, Hoersholm, Denmark) for comparison. A liver biopsy was taken from the mice 4 weeks before treatment start. After the procedure, animals were single-housed and allowed to recover for 4 weeks prior to treatment start. Only mice with steatosis score 3 or mice with fibrosis score >1 and steatosis score >2 were included. Included animals were then randomized into treatment groups based on mean baseline PSR area% one week before dose start. Mice were administered vehicle or semaglutide 123 µg/kg for 8, 16, or 24 weeks. Vehicle-dosed chow-fed mice and mice switched to chow and dosed with vehicle served as additional controls. Dosing was performed subcutaneously once daily in a volume of 5 ml/kg. To reduce initial gastric discomfort, the dose was increased through daily increments until reaching the target dose on treatment day 5.


title: A map of enhancer regions in primary human neural progenitor cells using capture STARR-seq

city: Mount Vernon

first: Sophia

last: Gaynor-Gillett

state: IA

address: 600 1st St. W

department: Biology

institute: Cornell College

summary: Genome-wide association studies (GWAS) and expression analyses implicate noncoding regulatory regions as harboring risk factors for psychiatric disease, but functional characterization of these regions remains limited. We performed capture STARR-sequencing of over 78,000 candidate regions to identify active enhancers in primary human neural progenitor cells (phNPCs). We selected candidate regions by integrating data from NPCs, prefrontal cortex, developmental timepoints, and GWAS. Over 8,000 regions demonstrated enhancer activity in the phNPCs, and we linked these regions to over 2,200 predicted target genes. These genes are involved in neuronal and psychiatric disease-associated pathways, including nervous system development, gliogenesis, and developmental delay. We functionally validated a subset of these enhancers using mutation STARR-sequencing and CRISPR deletions, demonstrating the effects of genetic variation on enhancer activity and enhancer deletion on gene expression. Overall, we identified thousands of highly active enhancers and functionally validated a subset of these enhancers, improving our understanding of regulatory networks underlying brain function and disease.

overall_design: We used primary human neural progenitor cells (phNPCs) isolated from the fetal brain at 15-18 weeks post-conception. Experiments were done on a phNPC line isolated from a female fetus of Mexican decent. We investigated over 78,000 regions for enhancer activity using capture STARR-sequencing. We performed two replicates of STARR-sequencing for each of two separate candidate panels. We further validated a subset of the active enhancer regions using mutation STARR-sequencing and CRISPR deletions. For the validation experiments, we compared phNPC cells with specific mutations to those without (mutation STARR-seq) and with deleted enhancer regions (CRISPR deletions) to those without the deletion.

first: Lijun

last: Cheng

first: Manman

last: Shi

first: Jason

last: Liu

first: Gaoyuan

last: Wang

first: Megan

last: Spector

first: Mary

last: Flaherty

first: Martha

last: Wall

first: Ahyeon

last: Hwang

first: Mengting

last: Gu

first: Zhanlin

last: Chen

first: Yuhang

first: Jennifer

last: Moran

first: Jing

last: Zhang

first: Donghoon

first: Mark

last: Gerstein

first: Daniel

last: Geschwind

first: Kevin

middle: P

last: White

first: Qiuyu

last: Guo

first: Le

last: Qi

first: PsychENCODE

last: Consortium


title: Leukemia-mutated proteins PHF6 and PHIP form a chromatin complex that represses acute myeloid leukemia stemness

status: Public on Apr 26 2025

city: Philadelphia

first: Vikram

last: Paralkar

state: PA

address: 421 Curie Boulevard

department: Division of Hematology and Oncology, Department of Medicine

institute: University of Pennsylvania Perelman School of Medicine

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

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Refer to individual Series


title: Hypothalamic PNOC/NPY neurons constitute mediators of leptin-controlled energy homeostasis

status: Public on Apr 23 2025

city: Cologne

first: Jens

last: Brüning

address: Gleueler Str. 50

country: Germany

institute: Max Planck Institute for Metabolism Research

summary: We show that leptin regulates appetite and body weight via PNOC neurons, and that loss of leptin receptor expression in PNOC-expressing neurons in the arcuate nucleus of the hypothalamus (ARC) causes hyperphagia and obesity.  Lepr inactivation in PNOC neurons increases Npy expression in a subset of hypothalamic PNOC neurons that do not express Agrp and selective chemogenetic activation of PNOC/NPY neurons promotes feeding to the same extent as activating all PNOCARC neurons and overexpression of Npy in PNOCARC neurons promotes hyperphagia and obesity. Thus, we introduce PNOC/NPYARC neurons as an additional critical mediator of leptin action and  a promising target for obesity therapeutics.

overall_design: BacTRAP based RNA sequencing. We crossed control and Pnoc Lepr deletion mice with ROSA-STOP-L10a-bactrap mice, allowing for Cre-dependent expression of the fusion protein of the ribosomal protein L10a tagged with GFP specifically in PNOC neurons. From 12 week old L10a-bactrap animals, we harvested hypothalamic samples and used an anti-GFP antibody to precipitate ribosomes of PNOC neurons (4 pooled animals per sample). Deep mRNA sequencing of RNA associated with immunopurified ribosomes from PNOC neurons yielded a detailed translational profile of hypothalamic PNOC neurons.

first: Marie

last: Solheim

first: Weiyi

first: Paul

last: Klemm

first: Lukas

last: Steuernagel


title: RNA sequencing dataset of spontaneously immortalised pre-adipocyte line from pig

city: Midlothian

first: Xavier

last: Donadeu

address: Easter Bush

country: United Kingdom

institute: Roslin Institute, University of Edinburgh

summary: We have derived a spontaneously immortalised pre-adipocyte line using sequential long-term passaging of porcine mesenchymal stromal cells. Uniquely, this cell line (named FaTTy) gained a high level of adipogenic capacity during immortalisation which was maintained over more than 200 population doublings. Here, we provide transcriptomic data (bulk RNA sequencing) from FaTTy and parental MSCs of origin.

overall_design: To identify transcriptional chages associated with immortalisation and enhanced adipogenesis in FaTTy, we performed comparative bulk RNA sequencing followed by differential gene expression analysis of 4 parental MSC samples and 4 FaTTy cell samples

first: Thomas

last: Thrower

first: Susanna

middle: E

last: Riley


title: CagriSema drives weight loss in rats by reducing energy intake and preserving energy expenditure

city: Måløv

last: Halling

summary: CagriSema is a combination of amylin (cagrilintide) and glucagon-like peptide-1 (semaglutide) analogues being developed for weight management. We quantified CagriSema’s action on energy intake and expenditure in rats. CagriSema caused 12% weight loss and a 39% reduction in food intake. In contrast, pair-feeding caused less weight loss while weight-matching required a 51% decrease in food intake.  Approximately 1/3 of CagriSema’s weight loss efficacy was from an energy expenditure effect, blunting of metabolic adaptation, which is likely a hallmark of successful treatment of obesity.

overall_design: Bulk RNAseq of liver tissue collected from DIO rats after 20 days of CagriSema treatment or weight matched food restriction

first: Jens Frey


title: Gas6-Axl signaling drives oral regenerative wound repair [RNA-Seq]

first: Jennifer

last: Parker

overall_design: Mouse wound tissue transcriptomes were profiled using single cell RNA sequencing, Visium spatial transcriptomics, and bulk RNA sequencing. Tissue from wounds in oral mucosa and facial skin were compared. Timepoints include unwounded skin and oral mucosa, postoperative (POD) 2, 4, and 7.

first: Michelle

last: Griffin

first: Jessica

last: Cook


title: High-Resolution Spatial Map of the Human Facial Sebaceous Gland Reveals Marker Genes and Decodes Sebocyte Differentiation [MERFISH]

city: Hamburg

first: Tolga

last: Düz

address: Beiersdorfstraße 1-9

institute: Beiersdorf AG

summary: The sebaceous gland is essential for skin homeostasis by producing sebum to lubricate and protect the skin. However, its cellular and molecular mechanisms in humans remain poorly understood as most studies have been conducted in mouse models. This study provides a comprehensive molecular analysis of the human sebaceous gland, focusing on cellular interactions, novel gene markers, and sebocyte differentiation. By integrating Stereo-seq spatial transcriptomics, single-cell RNA sequencing, and validation though MERFISH, we identified four distinct stages of sebocyte differentiation, each characterized by unique gene signatures.  These results reveal sebocyte differentiation as a dynamic and complex process. Our findings enhance the understanding of sebaceous gland biology and provide a valuable reference for future research and the development of therapies for sebaceous gland-related disorders, including acne.

overall_design: Tissue section from the temporal region (face) of a healthy Caucasian female.

first: Daniel

last: Torocsik

first: Annika

last: Simmering

first: Peter

last: Wolf

first: Stefan

last: Gallinat

first: Jan

last: Baumbach

first: Nicholas

last: Holzscheck


title: Bone marrow single cell transcriptome profile 3 months after transplantation in blood cancer patients who received hematopoietic stem cell transplantation

city: Daejeon

first: Suyoung

last: Choi

address: 266, Munhwa-ro, Jung-gu

department: Department of Medical Science

institute: Chungnam National University

summary: Relapse after allogeneic hematopoietic stem cell transplantation (allo-HSCT) remains the leading cause of treatment failure in patients with hematologic malignancies. To better understand the mechanisms underlying relapse, we comprehensively explored the expression of inhibitory receptors (IRs) in bone marrow T cell at differentiation stage and examined transcriptional differences. Among the evaluated IRs, TIM3 was significantly upregulated in CD3+ T cells of patients with early relapse (ER) compared to patients with complete remission (CR). Notably, double-negative T (DNT) cells, a unique subset with MHC-independent cytotoxic potential, constituted a high proportion of BM T cells and expressed increased TIM3 expression in ER patients. Moreover, regulatory T cells (Tregs) showed elevated TIM3 levels, contributing to an immunosuppressive microenvironment after allo-HSCT. Transcriptional analysis revealed downregulation of interferon-gamma signaling, oxidative phosphorylation, and T-cell receptor genes in ER patients , indicative of impaired cytotoxic function. Functional assays demonstrated that TIM3 blockade with sabatolimab restored T cell cytotoxicity, leading to enhanced leukemia cell apoptosis in ER patients. These findings highlight TIM3 as a key regulator of immune dysfunction in post-transplant relapse and support its potential as a therapeutic target.

overall_design: Three month samples were collected from bone marrow after chemotherapy and HSCT for leukaemia and subjected to Ficoll gradient isolation.  The dataset includes scRNAseq data from two complete remission (CR), two early relapse (ER) and one late relapse (LR) patients.

first: Ik-Chan

last: Song

first: Thi Thuy Duong

last: Pham


title: High-Resolution Spatial Map of the Human Facial Sebaceous Gland Reveals Marker Genes and Decodes Sebocyte Differentiation

overall_design: We analyzed sections from three tissue samples of healthy female facial skin from different Caucasian donors (49-57 years), focusing on the temporal region, using Stereo-seq. Skin samples were processed to remove subcutaneous fat, cut into 5-7 x 5-7 mm pieces and frozen and stored at -80°C.


title: Targeting inflammation with chimeric antigen receptor macrophages using a signal switch

city: Westmead

first: Jianwei

last: Chen

state: NSW

address: 176 Hawkesbury Rd

department: CTRR

institute: The Westmead Institute for Medical

summary: Chimeric antigen receptor-T (CAR-T) cell immunotherapy has shown great success in clinical cancer, bringing hope that applying CAR strategies to other immune cell lineages may be beneficial in other clinical settings. We developed a CAR-macrophage (CAR-M) that recognizes the major inflammatory molecule TNF-α and activates an intracellular IL-4 signaling pathway, thereby programming engineered macrophages for an anti-inflammatory function. Infused CAR-Ms switched to an anti-inflammatory phenotype in inflamed kidney and attenuated kidney ischemia reperfusion injury (IRI). The anti-inflammatory phenotype of infused CAR-Ms switched off during the recovery phase of kidney IRI, coinciding with the disappearance of TNF-α. In Adriamycin-induced nephropathy, a model of chronic kidney disease, infused CAR-Ms maintained an anti-inflammatory phenotype for several weeks in response to sustained high levels of TNF-α, resulting in an anti-inflammatory milieu that improved kidney function and structure. CAR-Ms also effectively reduced tissue injury in another organ, liver. The CAR-M design, utilizing signal switching, holds promise for the treatment of a broad range of acute and chronic inflammatory diseases.

overall_design: Bone marrow macrophage samples.  S1-4 are samples without any treatment. S5-8 are samples stimulatedbyLPS and IFN-r, S9-12 are samples stimulated by IL4 and IL13, S13-16 are samples transduced with the intact CAR, S17-20 are samples transduced with the intact CAR and stimulated by TNF-a, S21-24 are samples transduced with the truncated CAR, S21-28 are samples transduced with the truncated CAR and stimulated by TNF-a.

first: Qi

last: Cao

first: Yiping

last: Wang

first: Ruifeng

first: Titi

first: Brian

last: Gloss

first: Scott

middle: A

last: Read

first: Vincent

middle: W

last: Lee

first: Guoping

last: Zheng

first: Leighton

last: Clancy

first: Natasha

middle: M

last: Rogers

first: Stephen

last: Alexander

first: Di

last: Yu

first: David

last: Harris


title: A dual histone code specifies the binding of heterochromatin protein Rhino to a subset of piRNA source loci [sRNA-seq]

status: Public on Apr 18 2025

city: Cambridge

first: Susanne

last: Bornelöv

address: Robinson Way

department: Cancer Research UK - Cambridge Institute

institute: University of Cambridge

type: Non-coding RNA profiling by high throughput sequencing

summary: Animal germ cells deploy a specialized small RNA-based silencing system, called the PIWI-interacting RNA (piRNA) pathway, to prevent aberrant expression of transposable elements and maintain genome integrity.  In Drosophila germ cells, the majority of piRNA populations originate from dual-strand piRNA clusters, genomic regions highly enriched in transposon fragments, via an elaborate protein machinery centred on the heterochromatin protein 1 homolog, Rhino.  Although Rhino binds to peptides carrying trimethylated H3K9 in vitro, it is not fully understood why it only occupies a fraction of H3K9me3-decorated heterochromatin in vivo.  Recent work uncovered that Rhino is recruited to a subset of piRNA clusters by the zinc finger protein Kipferl.  Here we identify a Kipferl-independent mode of Rhino targeting that is dependent on the histone H3 lysine 27 methyltransferase Enhancer of Zeste and the presence of H3K9me3 and H3K27me3 marks.  At Kipferl-independent sites, we find that Rhino, through its dimeric chromodomain, specifically binds to loci marked by both H3K9me3 and H3K27me3.  These results expand our understanding of the characteristic binding profile of the heterochromatin protein Rhino and reveal a role for dual histone modifications in defining the specificity of a chromatin binding protein.

overall_design: Small RNA profiling from Drosophila ovaries depleted of E(z), rhi, kipf, or white.

first: Abdou

last: Akkouche

first: Emma

last: Kneuss

first: Yoan

last: Renaud

first: Evelyn

middle: L

last: Eastwood

first: Jasper

last: van Lopik

first: Nathalie

last: Gueguen

first: Mingxuan

last: Jiang

first: Pau

last: Creixell

first: Stéphanie

last: Maupetit-Mehouas

first: Anna

last: Sobieszek

first: Yifan

last: Gui

first: Benjamin

last: Czech Nicholson

first: Emilie

last: Brasset

first: Gregory

last: Hannon


title: A MOUSE ORGANOID PLATFORM FOR MODELING CEREBRAL CORTEX DEVELOPMENT AND CIS-REGULATORY EVOLUTION IN VITRO

status: Public on Apr 20 2025

city: New York

first: Daniel

last: Medina Cano

email: medinacd@mskcc.org, dmcdmc156@gmail.com

state: New York

address: 411E 67th St

department: Developmental Biology

institute: MSKCC

summary: Natural selection has shaped the gene regulatory networks that orchestrate the development of the neocortex, leading to diverse neocortical structure and function across mammals, but the molecular and cellular mechanisms driving phenotypic changes have proven difficult to characterize. Here, we develop a reproducible protocol to generate neocortical organoids from mouse epiblast stem cells (EpiSCs) that gives rise to diverse cortical cell types, including distinct classes of excitatory neurons (pre-plate, deep-layer, and upper-layer) and glia (oligodendrocyte precursor cells, myelinating oligodendrocytes, astrocytes, ependymal cells). Cortical organoids develop with similar kinetics to the mouse cortex in vivo and begin to exhibit features of maturation in glia and neuronal cell types relatively rapidly compared to human brain organoids. Using this new protocol, we generated cortical organoids from F1 hybrid EpiSCs derived from crosses between standard laboratory mice (C57BL/6J) and four wild-derived mouse strains from distinct sub-species spanning ∼1M years of evolutionary divergence. This allowed us to comprehensively map cis-acting transcriptional regulatory variation across developing cortical cell types using scRNA-seq. We identify hundreds of genes that exhibit dynamic allelic imbalances during cortical neurogenesis, providing the first insight into the developmental mechanisms underpinning changes in cortical structure and function between mouse strains. These experimental methods and cellular resources represent a powerful new platform for investigating mechanisms of gene regulation in the developing cerebral cortex.

overall_design: To investigate how natural selection has shaped development across mouse subspecies, we generated F1 hybrid induced pluripotent stem cells (iPSCs) from crosses between standard laboratory mice (C57Bl/6J) and  wild-derived inbred mouse strains from distinct sub-species that span ~1 million years of evolutionary divergence. We performed bulk RNA-seq on 3 clones per backgorund, a total of 12 iPSC samples.

first: Medina-Cano

last: Daniel

first: Islam

last: Mohammed

first: Vierbuchen

last: Thomas

first: Petrova

last: Veronika

first: Wong

last: Emily


title: A dual histone code specifies the binding of heterochromatin protein Rhino to a subset of piRNA source loci [CUT&RUN histone modifications in S2 cells]

first: Susanne

last: Bornelöv

overall_design: CUT&RUN from Drosophila melanogaster S2 cells characterising H2AK119ub, H3K27me3, H3K9me3 or IgG in wildtype cells, or cells depleted for E(z) or Renilla.

first: Abdou

last: Akkouche

first: Emma

last: Kneuss

first: Yoan

last: Renaud

first: Evelyn

last: Eastwood


title: A bioengineered immunocompetent human leukemia chip for preclinical screening of CAR T cell immuno-therapy

city: Brooklyn

first: Weiqiang

last: Chen

address: 6 MetroTech Center

institute: New York University

summary: Single-cell RNA-seq analysis of bioengineered human bone marrow leukemia chip established with human B-ALL cells (REH, ATCC), Human umbilical vein cells (HUVECs, Lonza), Human mesenchymal stem cells (hMSC, Lonza), Human Bone marrow mononuclear cells (STEMCELL Technologies), and Human MSC osteoblasts (Lonza) using the reported Leukemia-on-a-Chip method treated with Healthy donor derived CAR Tcells, Patient derived CAR T cells, Mock T cells, and or left non-treated.

overall_design: Single-cell RNA-sequencing libraries of the retrived cells form the bioengineered human bone marrow leukemia chips. Healthy donor derived CAR Tcells, Patient derived CAR T cells, Mock T cells, and or Human bone marrow mononucelar cellswere also sequenced as controls

first: Chao

last: Ma

first: Huishu

last: Wang

first: Lunan

last: Liu

first: Ruiqi

first: Nandana

last: Mukherjee

first: Jie

last: Tong

first: Shadab

last: Kazmi

first: Xiangyi

last: Fang

first: Matthew

middle: T

last: Witkowski

first: Iannis

last: Aifantis

first: Saba

last: Ghassemi


title: A dual histone code specifies the binding of heterochromatin protein Rhino to a subset of piRNA source loci [CUT&RUN in Drosophila species]

first: Susanne

sample_organism:
Drosophila ananassae
Drosophila erecta
Drosophila melanogaster
Drosophila simulans
Drosophila yakuba

overall_design: CUT&RUN from ovaries in five Drosophila species characterising H3K27me3, H3K9me3 or IgG.

first: Jasper

last: van Lopik

first: Nathalie

last: Gueguen

first: Mingxuan

last: Jiang

first: Pau

last: Creixell

first: Stéphanie

last: Maupetit-Mehouas

first: Anna

last: Sobieszek

first: Yifan

last: Gui

first: Benjamin

last: Czech Nicholson

first: Emilie

last: Brasset

first: Gregory

last: Hannon


title: A dual histone code specifies the binding of heterochromatin protein Rhino to a subset of piRNA source loci [CUT&RUN]

last: Bornelöv

overall_design: CUT&RUN from ovaries in Drosophila melanogaster characterising H3K27me3, H3K9me3 or IgG.

first: Abdou

last: Akkouche

first: Emma

last: Kneuss

first: Yoan

last: Renaud

first: Evelyn

last: Eastwood


title: A programmed decline in ribosome levels governs human early neurodevelopment

city: Dallas

first: Michael

last: Buszczak

state: Texas

address: 5323 Harry Hines Boulevard

department: Molecular Biology

institute: University of Texas Southwestern Medical Center

summary: Many neurodevelopmental defects are linked to genes involved in housekeeping functions, such as those encoding ribosome biogenesis factors. How reductions in ribosome biogenesis can result in tissue- and developmental-specific defects remains unclear. Here we describe variants in the ribosome biogenesis factor AIRIM/C1orf109 that are primarily associated with neurodevelopmental disorders. Using human cerebral organoids in combination with proteomic, single-cell RNA-seq, and single-organoid translation analyses, we identify a previously unappreciated drop in protein production during early brain development. We find ribosome levels decrease during neuroepithelial differentiation, making differentiating cells particularly vulnerable to perturbations in ribosome biogenesis during this time. Reduced ribosome availability more profoundly impacts the translation of specific transcripts, disrupting both survival and cell fate commitment of transitioning neuroepithelia. Enhancing mTOR activity suppresses the growth and developmental defects associated with AIRIM/C1orf109 variants. This work provides evidence for the functional importance of regulated changes in global protein synthesis capacity during cellular differentiation.

overall_design: To characterize how allelic variants in AIRIM and AFG2B disrupt human brain development, we performed scRNA-seq, RNA-seq, and Ribo-seq on human brain organoids derived from iPS cells

first: Chunyang

last: Ni

first: Yudong

last: Wei

first: Cen

last: Cenik

first: Dayea

last: Park

first: Leqian

last: Yu


title: A dual histone code specifies the binding of heterochromatin protein Rhino to a subset of piRNA source loci

first: Susanne

platform_organism:
Drosophila ananassae
Drosophila erecta
Drosophila melanogaster
Drosophila simulans
Drosophila yakuba


title: A dual histone code specifies the binding of heterochromatin protein Rhino to a subset of piRNA source loci [CUT&RUN chromodomains in S2 cells]

summary: Animal germ cells deploy a specialized small RNA-based silencing system, called the PIWI-interacting RNA (piRNA) pathway, to prevent unwanted expression of transposable elements and maintain genome integrity. In Drosophila germ cells, the majority of piRNA populations originate from dual-strand piRNA clusters, genomic regions highly enriched in transposable element (TE) fragments, via an elaborate protein machinery centred on the heterochromatin protein 1 homolog, Rhino. Although Rhino binds to peptides carrying trimethylated H3K9 in vitro, it is not fully understood why in vivo only a fraction of H3K9me3-decorated heterochromatin is occupied by Rhino. Recent work revealed that Rhino is recruited to a subset of piRNA clusters by the zinc finger protein Kipferl. Here we identify a Kipferl-independent mode of Rhino targeting that, in addition to the previously established role of H3K9me3, also depends on the histone H3 lysine 27 methyltransferase Enhancer of Zeste. At Kipferl-independent sites, we find that Rhino, through its chromodomain, specifically binds to loci marked by both H3K9me3 and H3K27me3. Although the exact mechanism of how Rhino binding is influenced by dual histone modifications remains unclear from a structural and biochemical perspective, our work suggests that combinatorial modifications can play a crucial role in influencing the specificity of chromatin-binding protein interactions. These findings provide an enhanced understanding of the multifaceted mechanisms by which Rhino targets piRNA source loci highlighting the sophisticated epigenetic landscape governing TE silencing in Drosophila germ cells. Our work further reveals a role for dual histone modifications defining the binding specificity of a key chromatin protein.

overall_design: CUT&RUN from Drosophila melanogaster S2 cells characterising indicated chromodomain constructs in cells depleted for Kipf, E(z) or control (Renilla luciferase, RL).

first: Jasper

last: van Lopik

first: Nathalie

last: Gueguen

first: Mingxuan

last: Jiang

first: Pau

last: Creixell

first: Stéphanie

last: Maupetit-Mehouas


title: Single-cell RNA seq of ipsilateral L4-L6 DRGs from rats in both Sham and CPIP group

status: Public on Apr 14 2025

city: Hangzhou

first: Boyu

last: Liu

address: Binwen Road

institute: Zhejiang Chinese Medical University

summary: Complex regional pain syndrome type-I (CRPS-I) is chronic neurological disorder accompanied with devastating pain. In this study, we employed single-cell sequencing technology to analyze the ipsilateral L4-L6 dorsal root ganglia in both Sham and CPIP groups, aiming to investigate the mechanisms underlying chronic pain development in the CPIP model.

overall_design: These cells were isolated from WT naïve male SD rats in two different group:Sham, CPIP

first: Huimin

last: Nie

first: Yushuang

last: Pan

first: Boyi


title: Single-nuleus RNA-sequencing of septal cells during postnatal development

status: Public on Apr 13 2025

city: San Francisco

first: Yajun

last: Xie

address: 35 medical center way

institute: UCSF

summary: Purpose: The goal of this study is to use snRNA-seq to identify the diversity of cell types derived from Nkx2.1 lineage and non-Nkx2.1 lineages in the postnatal developing septum, and examine the cell trajectories, especially glial cells in the develping septum; Methods: The septum of P0, P3, P7,P14,P21 Nkx2.1Cre;SunGFP were collected, and nuclei of the septum cells were isolated, then GFP+ and GFP- nuclei were sorted out  and followed by 10X genomics sequencing; Results: we found diversity of astrocytes in the septum based on unique molecular profiles which follows the lineage separation, and we also observed the distinct developmental trajectories of subpopulation of astrocytes.

overall_design: We perform 10X sequencing on Nkx2.1 and non-Nkx2.1-derived cells in the setpum during different postnatal stages.

first: Christopher

last: M. Reid

first: Miguel

last: Turrero Garcia

first: Alejandro

last: A. Granados


title: Bulk RNA-seq of immunopanned astrocytes with the treatment of Shh and Fgf

summary: Purpose: Examine differential gene expression changes in in vitro astrocytes with the administration of Shh agonist and Fgf protein vs control; Methods: Astrocytes were purified using a previously published immunopanning protocol, SAG-Shh agonist and DMSO are added into cell culture medium for 3 days, and Fgf2 and Fgf10 were added to medium respectively for 7 days,  PBS treated astrocytes as controls. RNA-seq were perfomed (Lexongen QuantSeq3'mRNA-SEQ V2 Library prep kit) on all different conditions; Results: We observed differential gene expression changes in SAG treated conditions compared to WT, but did not observe a significant number of genes changes in Fgf treated groups compared to controls.

overall_design: RNA-seq of Shh-agonist and Fgf proteins treated in vitro astrocytes

first: Yi

last: Lu

first: Jiwen

last: Li


title: G-quadruplexes are promoter elements controlling nucleosome exclusion and RNA polymerase II pausing

status: Public on Apr 15 2025

city: Montpellier

first: Amal

last: Makrini

address: 1919 route de mende

institute: IGMM

summary: Despite their central role in transcription, it has been difficult to define universal sequences associated with eukaryotic promoters. Within the chromatin context, recruitment of transcriptional machinery requires promoter opening, but how DNA elements contribute to this process is unclear. Here we show that G-quadruplex (G4) secondary DNA structures are highly enriched at mammalian promoters. G4s are located at the deepest point of nucleosome exclusion at promoters and correlate with maximum promoter activity. We found that experimental G4s exclude nucleosomes in vivo and in vitro while favouring strong positioning. At model promoters, impairing G4s affected both transcriptional activity and chromatin opening. G4 destabilization also resulted in an inactive promoter state and affected the transition to effective RNA production. Finally, G4 stabilization resulted in global reduction of proximal promoter pausing. Altogether, our data introduce G4s as bona fide promoter elements allowing nucleosome exclusion and facilitating pause-release by RNA polymerase II.

overall_design: MNase-seq and ChIP-seq of RNA-Polymerase II (Pol II) were used to address how G-quadruplexes (G4s) influence chromatin organisation and transcription. Functional analyses were performed using pyridostatin, a drug that stabilize G4s and alpha-amanitin that inhibits Pol II.

first: Cyril

last: Esnault

last: Zine El Aabidine

first: Marie-Cécile

last: Robert

first: Anne

last: Cucchiarini

first: Talha

last: Magat

first: Alexia

last: Pigeot

first: Soumya

last: Bouchouika

first: Encar

last: Garcia-Oliver

first: Kevin

last: Gawron

first: Eugénia

last: Basyuk

first: Magdalena

last: Karpinska

first: Rachel

last: Topno

first: Alja

last: Kozulic-Pihrer

first: Yu

last: Luo

first: Daniele

last: Verga

first: Raphael

last: Mourad

first: Ovidiu

last: Radulescu

first: Jean-Louis

last: Mergny

first: Edouard

last: Bertrand

first: Jean-Christophe

last: Andrau


title: Transcriptomic data for: Social context prevents heat hormetic effects againstmutagens during ﬁsh development

city: Hull

first: Lauric

last: Feugere

address: Cottingham Road

department: Biological and Marine Sciences

institute: University of Hull

summary: Climate change increases both the frequency and duration of heat events. Direct negative effects of such heat stress may be exacerbated through heat-induced stress propagation (via stress metabolites) between aquatic animals. Whilst early life stages are vulnerable to stress-induced damage, they also deploy cellular mechanisms to protect cells against their naturally mutagenic environment. Little is known about the fate and performance of fish embryos which have experienced direct or indirect heat stress in a mutagenic environment. Natural environmental mutation rates are typically low which poses an observational challenge. To circumvent this, the present study exposed zebrafish embryos to three treatments consisting of direct heat stress, indirect heat-induced stress metabolites, and combined heat + heat-induced metabolites before undergoing a UVB/UVA damage/repair assay to mimic a mutagenic environment. Indirect heat stress led to expression of keratin and cell structuring-related genes in receivers, associated with longer embryos displaying over-developed pericardial widths and behavioural hypoactivity. Heat stress had a hormetic effect by stimulating the cellular stress response, and presumably facilitating DNA repair, which protected and/or rescued embryos from subsequent UV damage and improved their fitness. However, heat stress combined with stress metabolites emitted by heat-stressed conspecifics overwhelmed embryos, which annihilated the hormetic effect, introduced RNA mutations, and lowered overall fitness indicators. Whilst generated in the laboratory, these findings provide an important baseline for understanding the consequences of thermal stress history in natural environments, where direct and indirect heat stress co-occur.

overall_design: Zebrafish embryos were exposed for 24 hours to thermal stress (TS) and stress metabolites (SM) released by heat-stressed zebrafish embryos, in a two-way factorial design (TSxSM), yielding four experimental treatments: fresh medium at 27°C (control C), fresh medium with thermal stress (TS), medium containing stress metabolites at 27°C (SM), and medium containing stress metabolites with thermal stress (TS+SM). After 24 hours of exposure to C, TS, SM, and TS+SM, embyros were exposed to a DNA damage/repair assay (6 min of DNA damage with UVB and 15 min of UVA-induced photorepair), resulting in four treatments: C+UV, TS+UV, SM+UV, and TS+SM+UV. 1-dpf embryos were processed for RNA-sequencing directly following the DNA damage/repair assay. Each treatment contains n = 3 biological replicates, each representing the pooled gene expression from 20 individual embryos.

first: Claudio

last: Silva De Freitas

first: Adam

last: Bates

first: Kenneth

last: Storey

first: Pedro

last: Beltran-Alvarez

first: Katharina

last: Wollenberg Valero


title: Temporal control of progenitor competence shapes maturation in GABAergic neuron development in mice

status: Public on Apr 09 2025

city: Martinsried

first: Christian

last: Mayer

address: Am Klopferspitz 18

institute: Max Planck Institute for Biological Intelligence

summary: Inhibitory neurons of the telencephalon are generated from progenitors in the ganglionic eminences that mature and differentiate into specialized cell types. Here, we used scRNA-seq and scATAC-seq together with lineage tracing and birthdating techniques to investigate the influence of neurogenesis timing on the development of  GABAergic precursors. We found that the timing of neurogenesis substantially influences the progenitors' maturation competence (the capacity to develop toward a fully functional state), but not their differentiation competence (the ability to evolve into transcriptomically diverse states). The underlying mechanism was chromatin priming, orchestrated by the transcription factor Nfib in collaboration with regulators of inhibitory neuron development. Finally, the heterochronic transplantation of progenitors revealed an interplay between both intrinsic and extrinsic cues acting upon maturation competence. These findings identify a mechanism that coordinates inhibitory neuron development by changing their maturation to achieve maximum adaptability.

overall_design: Transcriptomic,barcode-lineage tracing and Chromatin acessibilty of developping mouse forebrain cell subtypes

first: Ann Rose

last: Bright

first: Yana

last: Kotlyarenko

first: Florian

last: Neuhaus

first: Ilaria

last: Vitali


title: A dual histone code specifies the binding of heterochromatin protein Rhino to a subset of piRNA source loci [RNA-seq]

first: Susanne

last: Bornelöv

overall_design: RNA-seq from Drosophila ovaries depleted of E(z), rhi, or white using shRNA knockdowns.

first: Abdou

last: Akkouche

first: Emma

last: Kneuss

first: Yoan

last: Renaud

first: Evelyn

last: Eastwood

first: Jasper

last: van Lopik

first: Nathalie

last: Gueguen

first: Mingxuan

last: Jiang

first: Pau

last: Creixell

first: Stéphanie

last: Maupetit-Mehouas

first: Anna

last: Sobieszek

first: Yifan

last: Gui

first: Benjamin

last: Czech Nicholson

first: Emilie

last: Brasset

first: Gregory

last: Hannon


title: De novo Assembly and Delivery of Synthetic Megabase-Scale Human DNA into Mouse Early Embryos

status: Public on Apr 16 2025

city: Tianjin

first: Yue

last: Liu

address: 92 Weijin Road, Nankai District

institute: Tianjin University

summary: Epigenetic modifications on natural chromosomes are inherited and maintained in a default state, making it challenging to remove intrinsic marks to study the fundamental principles of their establishment and further influence on transcriptional regulation. Here, we developed SynNICE, a method for precisely assembling and transferring intact, naïve, synthetic Mb-scale human DNA into early mouse embryos, to study de novo epigenetic regulation. By synthesizing and transferring the 1.14 Mb human AZFa (hAZFa) locus, we observed the spontaneous incorporation of murine histones and the establishment of DNA methylation at the 1-cell stage. Notably, DNA methylation from scratch was strongly enriched for repeat sequences without H3K9me3 reinforcement. Furthermore, the transcription of hAZFa initiated at the 4-cell stage was regulated by newly established DNA methylation. This method provides a unique platform for exploring de novo epigenomic regulation mechanisms in higher animals.

sample_organism:
Saccharomyces cerevisiae
Mus musculus

platform_organism:
Saccharomyces cerevisiae
Mus musculus

overall_design: DNA-seq and RNA-seq of hAZFa in yeast, ChIP-seq, ATAC-seq and Hi-C of hAZFa in yeast and yeast nuclei, RNA-seq and WGBS of hAZFa in mouse early embryos.

first: Ying-Jin

last: Yuan


title: snATAC data analysis for Hidradentis Suppurativa patients' epidermis

status: Public on Apr 08 2025

city: Birmingham

first: Yanfeng

last: Zhang

state: AL

address: Kaul Human Genetics Building 720 20th St S

department: Department of Genetics

institute: University of Alabama at Birmingham

summary: In this study, we used single-nucleus ATAC-sequencing (snATAC-seq) to reveal how cellular heterogeneity of Hidradenitis Suppurativa (HS) lesional epidermis was reshaped at the genomic level.

overall_design: The Institutional Review Board of the University of Alabama at Birmingham approved the protocol (IRB-300005214) for obtaining surgically discarded skin tissues from heathy and HS (Hurley II/III stage) subjects. Surgical excisions from 2 patients with HS (axillary and groin lesions) and 2 healthy controls (discarded tissue from breast or abdominoplasty reduction surgery) were collected.

first: Lin

last: Jin


title: Transcriptional effects of co-culture on the spatiotemporal dynamics of T cell motility and cancer-T cell interactions [bulk_seq_invivo]

city: Shenzhen

first: Xuefei

last: Li

address: 1068 Xueyuan Avenue, Shenzhen University Town, Nanshan

institute: Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences

summary: Insufficient infiltration of cytotoxic T cells into solid tumors poses a major challenge in cancer immunotherapy, largely due to the intricate tumor microenvironment. To address this, we co-cultured mouse cancer cell lines (B16-WT or B16-OVA) with cancer-specific cytotoxic T cells (activated OT-1) in vitro to uncover the impact of cancer-T cell interactions on T cell motility, pivotal for effective tumor infiltration. To investigate the potential molecular mechanisms underlying T cell motility patterns in the two coculture contexts, we performed both bulk and single-cell RNA sequencing of cancer and T cells sorted from the co-culture systems at specific time points.

overall_design: To evaluate the antitumor properties of OT-1 CD8+ T cells activated with anti-CD3/anti-CD28 Dynabeads in vivo, melanoma mouse models were established using NOD-SCID mice injected with either B16-F10-OVA (GCaMP6s-transfected) or B16-F10 (GCaMP6s-transfected) cells. To compare T cell gene signatures between in vitro co-culture systems and in vivo tumors, B16-F10-OVA and B16-F10 melanoma-bearing mice were euthanized two days post-T cell administration. Fresh tumor tissues were minced into ~1 mm fragments using sterile scalpels and enzymatically dissociated in digestion medium containing mouse collagenase (1 mg/mL) and hyaluronidase (1000 U/mL) at 37°C for 45 minutes. The resulting cell suspension was filtered through Falcon 100 µm cell strainers to remove undigested tissue, washed repeatedly to eliminate dead cells, and resuspended in culture medium (DMEM supplemented with 10% FBS, 1% penicillin-streptomycin, 1% sodium pyruvate, 1% HEPES, 500 µL insulin, and 10 nM estrogen). OT-1 CD8+ T cells were positively selected from the suspension using CD8+ antibody-conjugated Dynabeads. After magnetic separation, bead-bound cells were incubated with release buffer, and bead-free CD8+ T cells were collected for bulk RNA sequencing. Concurrently, GCaMP6s-expressing B16-F10-OVA and B16-F10 tumor cells were isolated via fluorescence-activated cell sorting (FACS) and processed for bulk RNA sequencing.

first: Xinyue

first: Taoli

first: Lisha

last: Wang

first: Senbin

last: Wu

first: Yerong

first: Ming

first: Weijing

last: Han


title: Recurrent de novo variants in the spliceosomal factor CRNKL1 cause severe microcephaly and pontocerebellar hypoplasia with seizures [HeLa]

city: Dunedin

first: Louise

last: Bicknell

address: 710 Cumberland St

country: New Zealand

institute: University of Otago

summary: Splicing is a complex process, required to create the transcriptomic diversity needed for specialised functions in higher eukaryotes. The spliceosome contains more than 100 proteins and RNA molecules which coordinate this dynamic process, and interestingly, despite the ubiquity of splicing, pathogenic variants in spliceosomal components often cause a tissue-specific phenotype, hinting at further complexities which are not yet fully understood. We have identified a cohort of ten families with de novo missense variants in a spliceosomal component, CRNKL1, where nine individuals harbour one of two missense variants that both affect the same amino acid, p.Arg267. All patients share a common and specific phenotype: profound pre- and post-natal microcephaly, with pontocerebellar hypoplasia, seizures and severe intellectual disability. Microinjection of mutant crnkl1 into a zebrafish model caused significant lack of brain development accompanied by a significant reduction in proliferating cells and widespread cellular stress, as indicated by p53 staining. RNA-seq analysis of injected zebrafish embryos showed widespread transcriptomic changes, with altered expression of neuronal and cell cycle genes. Together, we have identified CRNKL1 as a novel disease gene and demonstrate the requirement for this protein in brain development and functioning. Our findings contribute to a growing disease cluster, where components act at the same spliceosomal stage and cause a brain-specific but severe phenotype, suggesting a more intricate role for these spliceosomal subcomplexes than previously thought.

overall_design: RNA-seq profiling of HeLa cell lines following CRNKL1 siRNA knockdown (including controls)

first: Sankalita

last: Ray Das


title: Recurrent de novo variants in the spliceosomal factor CRNKL1 cause severe microcephaly and pontocerebellar hypoplasia with seizures

overall_design: RNA-seq profiling from zebrafish embryos microinjected with mRNA encoding either Crnkl1 wildtype or Crnkl1-p.Arg105His (3 biological replicates for both)


title: Transcriptional effects of co-culture on the spatiotemporal dynamics of T cell motility and cancer-T cell interactions [bulk_seq_IFN]

overall_design: The goal is to test whether the two tumor cell lines, B16-F10-OVA and B16-F10-WT, respond differently to IFN-gamma treatment. We measured their bulk gene expressions before and after 24 hours of continuous treatment with IFN-gamma at a concentration of 50 ng/ml.


title: Blood DNA methylation data of newborn rhesus macaques

city: Göttingen

first: Roy

last: Lardenoije

address: Robert-Koch-Str. 40

institute: University Medical Center Göttingen

summary: Methylomic profiling of rhesus macaque blood samples. The Illumina Infinium MethylationEPIC kit was used to obtain DNA methylation profiles for over 850,000 CpGs, of which 339,081 were determined to be conserved in rhesus macaques based on the Mmul_10 genome build. A total of 29 samples were included, of which 26 remained after processing.

overall_design: Bisulphite converted DNA from 29 samples was hybridized to the Illumina Infinium MethylationEPIC BeadChip.

first: Mar

last: Sánchez

first: Torsten

last: Klengel


title: High-throughput unbiased RNA-Sequencing (RNA-Seq) to profile gene expression in ipsilateral L4-L6 DRG obtained from rats of Sham+Veh, CPIP+Veh and CPIP+ETA groups

status: Public on Apr 07 2025

first: Boyu

summary: Since TNF-α is a pro-inflammatory cytokine that can promote neuroinflammation to mediate chronic pain, we then explored which signaling molecules or pathways in DRG were affected by TNF-α and contributed to neuroinflammation in CPIP condition.

overall_design: Examination of 3 different groups mRNA profiles in DRG：Sham+Veh, CPIP+Veh and CPIP+ETA

first: Huimin

last: Nie

first: Yushuang

last: Pan

first: Boyi


title: SUMO2 Regulates Histone Pre-mRNA Processing by Stabilizing Histone Locus Body Interactions and Promoting U7 snRNP Assembly

status: Public on Mar 29 2025

city: Baltimore

first: Pin

last: Lyu

address: 400 N Broadway

institute: JHU

summary: Histone mRNAs are the only non-polyadenylated mRNAs in eukaryotic cells and require specialized processing in nuclear organelles known as histone locus bodies (HLBs), where essential processing factors are concentrated, including the U7 snRNP complex. Recent studies have revealed that misregulation of histone pre-mRNA processing can lead to polyadenylation of histone mRNAs and disruption of histone protein homeostasis. Despite the links to human disease, the factors contributing to polyadenylation of histone mRNAs and the mechanisms underlying HLB assembly and U7 snRNP biogenesis remain unclear. Here, we report novel functions of the small ubiquitin-related modifier 2 (SUMO2) in regulating histone pre-mRNA processing. Using a SUMO2 knockout osteosarcoma cell line, we identified a defect in 3’ end cleavage and a global increase in histone mRNA polyadenylation. Subsequent analysis of HLBs revealed increased dynamics and reduced levels of the U7 snRNP complex. By over-expressing U7 snRNP-specific components, Lsm11 and U7 snRNA, we partially rescued U7 snRNP levels and processing defects in SUMO2 knockout cells. Through analysis of Lsm11, we identified a SUMO-interacting motif in its N-terminus required for efficient incorporation into U7 snRNP complexes. Collectively, we demonstrate that SUMO2 promotes histone pre-mRNA 3’ end processing through stabilizing HLB interactions and facilitating U7 snRNP assembly

overall_design: We previously generated U2OS SUMO1 knockout (S1KO) and SUMO2 knockout (S2KO) cell lines with CRISPR/Cas 9, as well as SUMO2 knockout rescue cell lines by stable re-expression of SUMO2 (S2R) (Bouchard, Wang et al. 2021).

first: Shuying

last: He

first: Marnie W.

last: Skinner

first: Anthony

last: Desotell

first: Brendan

last: Foley

first: Wei

last: McCaig

first: Jiang

last: Qian

first: Liang

last: Tong

first: William F.

last: Marzluff

first: Michael J.

last: Matunis


title: Comparative Time-Course RNA-Seq Analysis of Abdominal Muscle cell Remodeling in Drosophila with or without Autophagy

status: Public on Apr 05 2025

city: Sumida-ku

first: Hiroki

last: Taoka

state: Tokyo

address: 2-1-3 Bunka

country: Japan

institute: Kao Corporation

summary: Differentiated muscle cells contain myofibrils and well-organized organelles, enabling powerful contractions. Muscle cell reorganization occurs in response to various physiological stimuli; however, the mechanisms underlying this remodeling remain enigmatic due to the lack of a genetically trackable system. Previously, we reported that a subset of larval muscle cells is remodeled into adult dorsal internal oblique muscle (DIOM) cells through an autophagy-dependent mechanism in Drosophila. To elucidate the underlying mechanisms of this remodeling, we performed a comparative time-course RNA sequencing (RNA-Seq) analysis of isolated DIOM cells with or without autophagy. As a control, we analyzed DIOM cells expressing LacZ. For autophagy-deficient conditions, we analyzed DIOM cells with RNAi-mediated knockdown of Atg18, FIP200, and Stx17. To conduct a time-course analysis, DIOM cells were isolated at distinct developmental time points, including the late third instar larva (3 IL) and four pupal stages; 1 day after puparium formation (1 d APF), 2 d APF, 3 d APF, and 4 d APF. The resulting datasets provide valuable insights into the transcriptional dynamics of muscle remodeling and the role of autophagy in this process.

overall_design: We performed a comparative time-course RNA-seq of DIOM remodeling in Control (UAS-LacZ), Atg18a RNAi, FIP200 RNAi, and Stx17 RNAi DIOMs. Each sample was collected from a single animal. To prepare total RNA, six DIOM cells were isolated at five time points: 3IL  and 1 to 4 days APF.  Each conditon was analyzed with four biological replicates.

first: Tadayoshi

last: Murakawa

first: Naonobu

last: Fujita

first: Yasuyuki

last: Ohkawa

first: Kaori

last: Tanaka

first: Akihito

last: Harada


title: Sustained YAP1 signaling alters the fate of lutein and Müllerian mesenchymal cells in mice

status: Public on Mar 31 2025

city: Saint-Hyacinthe

first: Michael

last: Bérubé

state: QC

address: 3200, Sicotte street

institute: University of Montreal

summary: Recent reports have suggested that the Hippo intracellular signaling pathway is required for homeostasis in a variety of tissues, including the ovary and female reproductive tract.   To further define the role of the Hippo effector YAP1 in the female reproductive system, transgenic mouse models were designed to direct the expression of a dominant stable mutant of YAP1, termed YAP5SA, to the granulosa cells of antral follicles (R26YAP5SA;CYP19-cre) and Müllerian mesenchymal cells (R26YAP5SA;Amhr2cre/+).  Unexpectedly, YAP5SA expression in the ovaries of R26YAP5SA;CYP19-cre mice was not detected in granulosa cells, but rather in a subset of lutein cells.  This caused the lutein cells to transdifferentiate into cells having the morphologic and functional properties of myofibroblasts, including collagen deposition.  These coalesced into roughly spherical lesions that persisted in the ovaries, but did not interfere with ovarian function or fertility.  Seminiferous tubule-like structures also formed in the ovaries of adult R26YAP5SA;CYP19-cre mice, containing SOX9-positive Sertoli-like cells but no germ cells.  Although multi-lineage transdifferentiation had been reported in mice lacking the Hippo kinases Lats1 and -2 in their granulosa cells, comparative RNAseq analyses of granulosa cells expressing YAP5SA vs granulosa cells lacking Lats1/2 showed few similarities in transcriptome alterations.  R26YAP5SA;Amhr2cre/+ mice had severe developmental defects of their uterine horns and ovaries, which were attributed to transdifferentiation of Müllerian mesenchymal cells into myofibroblasts during embryogenesis.  Together, these results indicate that sustained YAP1 signaling induces transdifferentiation in lutein and Müllerian mesenchymal cells, and further underscores the role of Hippo signaling in the maintenance of their fates.

overall_design: Primary culture of mouse preovulatory granulosa cells infected with Adenovirus-Cre (or  Adenovirus-eGFP as control) during 18h.

first: Samuel

last: Gusscott

first: Junhao

last: Mao

first: Gustavo

last: Zamberlam

first: Alexandre

last: Boyer

first: Guillaume

last: St-Jean

first: Julie

last: Brind’Amour

first: Derek

last: Boerboom


title: DNA methylome and transcriptome landscapes of cancer-associated fibroblasts reveal a smoking-associated malignancy index

status: Public on May 01 2025

city: Taipei

first: Chao-Chi

last: Ho

address: 1 Jen Ai Road, Section 1

department: Department of Internal Medicine

country: Taiwan

institute: National Taiwan University Hospital and National Taiwan University College of Medicine

summary: Unlike the better-studied aberrant epigenome in the tumor, the clinicopathologic impact of DNA methylation in the tumor microenvironment (TME), especially the contribution from cancer-associated fibroblasts (CAFs), remains elusive. CAFs exhibit profound patient-to-patient tumorigenic heterogeneity. We asked whether such heterogeneity may be exploited to quantify the level of TME malignancy. We developed a robust and efficient methylome/transcriptome co-analytical system for CAFs and paired normal fibroblasts (NFs) from non-small-cell lung cancer patients. We found 14,781 CpG sites of CAF/NF differential methylation, of which 3,707 sites showed higher methylation changes in ever-smokers than in nonsmokers. Concomitant CAF/NF differential gene expression analysis pointed to a subset of 54 smoking-associated CpG sites with strong methylation-regulated gene expression. A methylation index that summarizes the β values of these CpGs was built for NF/CAF discrimination (MIND) with high sensitivity and specificity. The potential of MIND in detecting premalignancy across individual patients was shown. MIND succeeded in predicting tumor recurrence in multiple lung cancer cohorts without reliance on patient survival data, suggesting that the malignancy level of TME may be effectively graded by this index. Precision TME grading may provide additional pathological information to guide cancer prognosis and open up more options in personalized medicine.

overall_design: Purified RNAs from paired NF/CAF samples as DNAs from 25 NSCLC patients were processed onto Affymetrix GeneChip Human Genome U133 Plus 2.0 Array.

first: Sheng-Fang

last: Su

first: Hao

first: Hsu-Chieh

last: Wang

first: Jia-Hua

last: Li

first: Hsiang-Yuan

last: Yeh

first: Shuenn-Wen

last: Kuo

first: Ker-Chau


title: Spatial transcriptomics of P35 septum

first: Yajun

last: Xie

summary:
Purpose: The goal of this study is to use MERFISH to identify the spatial distribution of septal cells
Methods: P35 CD1 mice were collected.10 µm tissue sections were obtained from along the rostro-caudal axis and adhered to the MERSCOPE Slide. The samples were permeabilized in 70% ethanol overnight, followed by cell boundary staining. A 500-gene panel was generated based on enriched genes in each astrocyte and neuron cluster, with approximately 100 astrocyte genes and 400 neuron genes, The samples were then hybridized using the gene panel mix, followed by gel embedding and clearing steps. Images were processed using the MERSCOPE instrument and analysis computer, along with MERSCOPE visualizer software to streamline the acquisition of high-quality MERFISH data accroding to Vizgen;
Results: Neurons and astrocytespatial clusters were defined in the septum based on unique gene enrichment

overall_design: Defining septal neurons and astrocytes spatial clusters in P35 septum

first: Christopher

last: M Reid

first: Jonathan

last: Liu


title: ATF7IP inhibits Sorafenib-induced ferroptosis in hepatocellular carcinoma cells by inhibiting CYB5R2 transcription and stabilizing PARK7 protein

city: tianjin

first: yijie

last: su

state: tianjin

address: Tianjin Medical University, No.22 Qixiangtai Road, Heping District, Tianjin City.

institute: Tianjin medical university

summary: Ferroptosis, an iron-dependent form of programmed cell death, arises from the accumulation of lipid peroxides at toxic levels. Sorafenib, a first-line treatment for advanced hepatocellular carcinoma (HCC), shows limited clinical efficacy due to drug resistance. However, the mechanisms underlying Sorafenib resistance, especially related to ferroptosis, remain poorly understood. In this study, we extend our previous research by identifying activating transcription factor 7-interacting protein (ATF7IP) as a key inhibitor of ferroptosis. ATF7IP depletion promotes Sorafenib-induced ferroptosis, resulting in decreased cell viability, reduced cellular glutathione level, increased lipid peroxidation, and altered mitochondrial crista structure. Notably, ATF7IP knockdown showed cooperative effects with Sorafenib in inhibiting HCC growth in mice. Mechanistically, ATF7IP interacts with SET domain bifurcated histone lysine methyltransferase 1 (SETDB1) to epigenetically silence the transcription of cytochrome b5 reductase 2 (CYB5R2), thereby reducing cellular Fe2+ levels. Meanwhile, ATF7IP inhibits Sorafenib-induced ferroptosis also by stabilizing the antioxidant sensor Parkinsonism-associated deglycase (PARK7) protein which preserves the transsulfuration pathway to produce glutathione (GSH). In conclusion, our findings identify ATF7IP as a critical ferroptosis inhibitor and represent ATF7IP as a novel therapeutic target for Sorafenib-based combination therapies of HCC.

overall_design: Examination of gene transcription in Control cells, ATF7IP knockdown cells, and SETDB1 knockdown HepG2 cells under Sorafenib treatment


title: Complementary and countervailing actions of Jak2 and Ikk2 in hematopoiesis in mice

city: Saint Louis

first: Stephen

last: Oh

state: MO

address: Room 8834, 320 S. Euclid Ave, CSRB building

institute: Washington University School of Medicine in St. Louis

summary: Hyperactivation of JAK2 kinase is a unifying feature of human Ph- myeloproliferative neoplasms (MPNs), most commonly due to the JAK2 V617F mutation. Mice harboring a homologous mutation in the Jak2 locus exhibit a phenotype resembling polycythemia vera. NFκB pathway hyperactivation is present in myeloid neoplasms, including MPNs, despite scarcity of mutations in NFκB pathway genes. To determine the impact of NFκB pathway hyperactivation in conjunction with Jak2 V617F, we utilized Ikk2 (Ikk2-CA) mice. Pan-hematopoietic Ikk2-CA alone produced depletion of hematopoietic stem cells and B cells. When combined with the Jak2 V617F mutation, Ikk2-CA rescued the polycythemia vera phenotype of Jak2 V617F. Likewise, Jak2 V617F ameliorated defects in hematopoiesis produced by Ikk2-CA. Single-cell RNA sequencing of hematopoietic stem and progenitor cells revealed multiple genes antagonistically regulated by Jak2 and Ikk2, including subsets whose expression was altered by Jak2 V617F and/or Ikk2-CA but partly or fully rectified in the double mutant. We hypothesize that Jak2 promotes hematopoietic stem cell population self-renewal, whereas Ikk2 promotes myeloid lineage differentiation, and biases cell fates at several branch points in hematopoiesis. Jak2 and Ikk2 both regulate multiple genes affecting myeloid maturation and cell death. Therefore, the presence of dual Jak2 and NFκB hyperactivation may present neomorphic therapeutic vulnerabilities in myeloid neoplasms.

overall_design: Floxed mice containing the alleles Ikk2-CA (R26StopFLikk2ca) and Jak2 V617F (Mullally et al., 2010 Cancer Cell) were crossed to Vav1-iCre (B6.Cg-Tg(Vav1-cre)A2Kio/J), and cis-NF-κBEGFP (FVB.Cg-Tg(HIV-EGFP,luc)8Tsb/J) from Jackson Laboratory. This generated hematopoietic specific expression of the Ikk2-CA (Ikk2 S177E, S181E) and Jak2 V617F alleles, together with an NF-κB responsive EGFP reporter. Mice harboring these alleles were crossed to generate double conditional mutant mice, which were then crossed with Vav1-iCre to generate hematopoietic specific double mutant mice. Mice harboring the Vav1-iCre allele but lacking any other mutant alleles were used as controls in this study. LSK (Lin-Sca-1+Kit+) stem and progenitor cells were sorted from pooled bone marrow derived from five mice of each of four genotypes: Vav1-iCre control, Ikk2-CA, Jak2 V617F, and double mutant. Bone marrow cells from 5 mice of each genotype were pooled, and Kit+ cells were purified using Cd117 microbead kit on AutoMACS separator (Miltenyi). Kit+ cells were stained with an antibody panel (Fisher et al, 2023 Experimental Hematology) Bone marrow cells from 5 mice of each genotype were pooled, and Kit+ cells were purified using Cd117 microbead kit on AutoMACS separator (Miltenyi). Kit+ cells were stained with antibody panel and sorted on MoFlo sorter (Beckman Coulter). Sorted cells were resuspended at 1000/μL density in 1x PBS with 0.04% BSA. Cells were subjected to droplet bead capture, followed by cell lysis, reverse transcription, and amplification according to TotalSeqA protocol from 10X Genomics (Pleasanton, CA). Single cell derived cDNA libraries were sequenced on NovaSeq S4 cell sequencer (Illumina, San Diego, CA). CellRanger (10x Genomics, version 3.0.1) was used for transcript alignment, counting, and inter-library normalization of single cell samples. Aggr function was used to merge genotype libraries into a single dataset, and initial visualization utilized LoupeBrowser version 6.0 (10x Genomics). Cluster and gene expression analysis utilized Seurat version 4.0.0. Cells with <500 or >7500 genes captured per cell were removed from analysis, as were cells with 10% or more mitochondrial transcripts. RNA reads were normalized with LogNormalize and data were scaled. Unsupervised cell clustering was performed using an unanchored version of the uniform manifold approximation and projection (UMAP) algorithm in Seurat. Differential gene expression analysis between populations/samples of interest was performed utilizing FindAllMarkers with Wilcoxon rank sum test. Gene set enrichment analysis of DEGs was run using fgsea and the Hallmark gene set from msigdbr. Cell populations were identified from cluster expression of canonical HSC and progenitor population markers and NFκB target genes.

first: Daniel

last: Fisher

first: Angelo

last: Laranjeira

first: Kong

last: Tim

first: Steven

last: Snyder

first: Kevin

last: Shim

first: Mary

last: Fulbright


title: Muc1-C Regulates Neat1 Lncrna Expresmuc1-C Is Essential For Establishing And Recalling Inflammatory Memory Of Osimertinib Resistance In Nsclc Cellssion And Paraspeckle Formation In Cancer Stem Cells

status: Public on Apr 02 2025

city: Brookline

first: Naoki

last: Haratake

state: MA

address: 44 Washington St. #1001,

institute: Dana-Farber Cancer Institute

summary: MUC1-C is necessary for establishing and recalling resistance of NSCLC cells to osimertinib by driving an inflammatory memory responseThe oncogenic MUC1-C protein functions as a master regulator of NSCLC cell resistance to osimertinib by unclear mechanisms. We report that MUC1-C-mediated regulation of STAT1 and the interferon (IFN) type I/II pathways is necessary for establishing osimertinib resistance. Studies of osimertinib-resistant NSCLC cells selected for growth in the absence of drug further demonstrate that revertant cells are dependent on MUC1-C for recalling resistance to osimertinib. We show that establishing and recalling osimertinib resistance is dependent on activation of the MUC1 gene at (i) a proximal enhancer-like signature 1 (pELS-1) by MUC1-C and STAT1 and (ii) a pELS-2 by MUC1-C, JUN/AP-1 and PBAF. The MUC1 pELS regions function as memory domains for activation of MUC1-C and downstream STAT1 and IFN stimulated genes in conferring osimertinib resistance. Of clinical relevance, we report that the MUC1-C-driven inflammatory responses are induced in patient-derived, osimertinib-resistant MGH170 NSCLC cells with MET amplification. Our results further demonstrate that MGH170 cells are dependent on the MUC1-C-induced inflammatory response for resistance to the osimertinib and combination of osimertinib with the MET inhibitor capmatinib. These findings indicate that MUC1-C is necessary for establishing and recalling resistance of NSCLC cells to osimertinib by driving an inflammatory memory response.

overall_design: RNA Seq in EGFR-mutant NSCLC Cell line with MUC1-C shRNA silencing


title: Effects of dexamethasone and KLA on HepG2 gene expression

status: Public on Apr 11 2025

city: Kuopio

first: Einari

last: Niskanen

address: Yliopistonranta 8

department: School of Medicine

country: Finland

institute: University of Eastern Finland

summary: In this study, we exposed HepG2 cells to synthetic glucocorticoid dexamethasone (Dex), Kdo2-Lipid A (KLA), or both (DexKLA) for 24 hours and conducted RNA-seq analysis to investigate the impact of exposures on gene expression. We aimed to elucidate how Dex and KLA disrupt, misregulate, or interfere with inflammatory and metabolic pathways at the transcriptional level. By analyzing the differential gene expression profiles, we sought to identify affected specific pathways and genes, providing insight into the underlying molecular mechanisms.

overall_design: Cultured HepG2 cells were pretreated with growth media containing charcoal-stripped serum for 24 hours. Total RNA was extracted  24 hours after treatments followed by RNA-seq library preparation.

first: Raghavendra

last: Mysore

first: Jorma

last: Palvimo


title: Temporal control of progenitor competence shapes maturation in GABAergic neuron development in mice

first: Christian

last: Mayer

overall_design: Transcriptomic,barcode-lineage tracing and Chromatin acessibilty of developping mouse forebrain cell subtypes

first: Ann Rose

last: Bright

first: Yana

last: Kotlyarenko

first: Florian

last: Neuhaus

first: Ilaria

last: Vitali


title: The epitranscriptome of the MT-4 cell line

status: Public on Mar 28 2025

city: Fuzhou

first: Kunqi

last: Chen

address: Fujian Medical University

institute: Fujian Medical University

summary: Epitranscriptomic modifications appear in MT-4 cell line

overall_design: To investigate whether epitranscriptomic modifications is involved in evolution, we performed RIP-seq on MT-4 cell line


title: CD177+ neutrophils restrict neuroinflammation following CNS injury

status: Public on Mar 27 2025

city: Shanghai

first: Guo

last: Yunlu

address: 160 Pujian Rd

department: Anesthesiology

institute: Renji Hospital, Shanghai Jiao Tong University School of Medicine

summary: Neutrophils are the most abundant circulating leukocyte population that play critical roles in neuroinflammation after ischemic stroke. CD177, a glycoprotein on neutrophils, is emerging as an important immune regulator which fundamentally affects multiple inflammatory diseases. However, the role and regulatory mechanism of CD177 protein of neutrophils in neuroinflammation remains elusive. Using single-cell RNA sequencing (scRNA-Seq), we characterized CD177high neutrophils as a novel anti-inflammatory subset in response to ischemic stroke.

overall_design: Stroke model was induced by middle cerebral artery occlusion (MCAO). scRNA-seq was performed on bone marrow cells from mice after stroke and control conditions.

first: Tingting

last: Huang

first: Wanqing

last: Xie

first: Yunlu

last: Guo

first: Yan

last: Li

first: Jiemin

last: Yin

first: Xia

last: Jin

first: Yezhi

last: Ma

first: Yueman

last: Zhang

first: Dan

first: Caiyang

first: Xin

last: Wang

first: Ziyu

last: Zhu

first: Yu

last: Gan

first: Arthur

last: Liesz

first: Weifeng

last: Yu

first: Junying

last: Yuan

first: Peiying


title: Substance P augments chemokine production by Staphylococcus aureus infected murine osteoclasts

status: Public on Mar 26 2025

city: Charlotte

first: Morgan

middle: Brittany

last: Johnson

state: North Carolina

address: 9201 University City BLVD

department: Biological Sciences

institute: University of North Carolina at Charlotte

summary: Staphylococcal osteomyelitis is a serious infection of the bone and joints characterized by progressive inflammatory tissue damage and leukocyte recruitment leading to net bone loss.  Resident bone cells are capable of recognizing Staphylococcus aureus and initiating an inflammatory immune response that recruits leukocytes and alters bone homeostasis.  Importantly, bone tissue is richly innervated with substance P containing nerve fibers and we have previously shown that this neuropeptide can augment the inflammatory responses of both osteoblasts and osteoclasts to S. aureus infection via neurokinin-1 receptors (NK-1R).  Here, we have extended these studies by demonstrating that pharmacological inhibition of NK-1R ameliorates disease severity in a mouse model of staphylococcal osteomyelitis. This effect was associated with the abolition of infection-induced increases in neutrophil-attracting chemokine production, and reduced local levels of osteoclast and neutrophil activity.  We then assessed the effect of S. aureus infection on bone-marrow derived osteoclast gene expression in the absence or presence of substance P.  We determined that infection upregulates osteoclast expression of mRNAs encoding inflammatory mediators that include the neutrophil-attracting chemokines identified in vivo.  Importantly, we found that, while substance P has no effect on chemokine mRNA expression in infected cells, this neuropeptide significantly increases the release of these chemokines by S. aureus challenged osteoclasts but not osteoblasts.  Together, these data further support the ability of substance P to exacerbate inflammatory damage in staphylococcal osteomyelitis and indicate that this effect may be due, in part, to an augmentation of the leukocyte-recruiting immune functions of osteoclasts.

overall_design: Primary murine osteoclasts were infected with S. aureus at a bacteria-to-osteoclast ratio of 75:1. At 4 hours post-infection, RNA was isolated with TRIzol and purified using a GeneJET RNA Cleanup and Concentration Micro Kit according to the manufacturer’s guidelines (ThermoFisher Scientific). The Genomic Sequencing and Analysis Facility at the University of Texas at Austin prepared Tag-Seq libraries using an established method and they were sequenced using an NovaSeq S1 to generate 100bp single end reads for 3’ end sequencing (35). The adapters of the sequenced reads were adapter cut using cutadapt v. 2.6 (36) and the reads were quality checked using fastqc v0.11.9. The GRCm39 RefSeq transcriptome (GCF_000001635.27) was used as a reference to map the quality controlled reads using Bowtie2 v 2.4.1 (37).  Differential gene expression analysis was performed with the R package DESeq2 version 1.40.2 (38).  Significant changes in gene expression were characterized as a log2 fold change greater than two, and an adjusted p-value of less than 0.05 (Wald Statistic, Benjamini & Hochberg correction).  Gene ontology terms for the transcriptome were annotated using Interproscan 5.60 - 92.0 (39).  Heatmaps were generated using the ComplexHeatmap v2.16.0 package (40).  ShinyGO v0.80 was used to determine pathway enrichment where the top 20 pathways with a False Discovery Rate (FDR) less than 0.05 were sorted by fold enrichment (41). The original datasets are available in the BioProject publicly accessible repository under the identifier PRJNA1168989.

first: Sophie

last: Sipprell

first: Quinton

last: Krueger

first: Erin

last: Mills

first: Ian

last: Marriott


title: RNF25-Mediated NF-κB Activation Drives Anti-Apoptosis and Therapy Resistance in Cancer

status: Public on Mar 25 2025

city: Shaanxi

first: Li

last: Lei

state: Xi 'an

address: 277 Yanta West Road, Xi 'an, Shaanxi

institute: The First Affiliated Hospital of Xi'an Jiaotong University

summary: Dysregulation of the NF-κB pathway is frequently observed in cancers, contributing to therapy resistance by inhibiting apoptosis. In this study, we identify RNF25, an E3 ubiquitin ligase, as a key regulator of signal transduction, inflammation, immune responses, and apoptosis. RNA sequencing (RNA-seq) analysis following RNF25 knockdown revealed significant alterations in key apoptotic regulators and NF-κB signaling components, highlighting the role of RNF25 in apoptotic resistance and therapeutic response. Pathway enrichment analysis further demonstrated disruptions in pro-survival and inflammatory signaling pathways, suggesting that RNF25 knockdown enhances apoptotic sensitivity and may influence treatment efficacy. This dataset provides valuable insights into potential therapeutic targets for overcoming treatment resistance.

overall_design: To investigate the function of RNF25 in the RCC cell lines in which RNF25 has been knocked down by shRNA. We then performed gene expression profiling analysis using data obtained from RNA-seq of control and KD cells with Biological triplicates.

first: Lei

first: Zixi

first: Jian


title: NR4A1 Mediates Offspring Bronchopulmonary Dysplasia-Like Lung Injury Induced by Intrauterine Inflammation in Mice

status: Public on Mar 23 2025

first: Xiya

last: Ding

state: Shanghai

address: 227 Chongqing South Road

department: Departments of Neonatology, International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200030, China.

summary: Background Intrauterine inflammation (IUI) is involved in the development of bronchopulmonary dysplasia (BPD). Previously, we observed BPD-like pathological changes in a mouse model of IUI. Here, we aimed to investigate key molecules involved in IUI-induced neonatal lung injury along with the long-term outcomes. Methods Pregnant C57BL/6 mice were randomly divided into control and IUI groups. Lung injury was evaluated using hematoxylin-eosin and Masson's trichrome staining. An NR4A1 overexpression plasmid was used to explore the downstream molecules acting in vitro. Accordingly, IUI-induced lung injury intervention was verified using Nr4a1 siRNA.  Results The lungs of IUI-induced offspring showed a simple structure from postnatal day 1 to 6 months, with increased pulmonary fibrosis from 3 to 6 months postnatal. Postnatal NR4A1 intervention reversed IUI-induced neonatal lung injury. NR4A1 overexpression decreased cell proliferation and influenced the expression of epithelial-mesenchymal transition (EMT)-related key genes in MLE-12 cells. EREG is a downstream target of NR4A1, and blocking the receptor of EREG would recover the expression of EMT-related genes.  Conclusion IUI induced BPD-like lung injury in neonates and pulmonary fibrosis in adults. The NR4A1-EREG-EGFR signaling pathway in pulmonary epithelial cells plays an important role in IUI-induced lung injury in offspring.

overall_design: The NR4A1 over-expression plasmid, created by cloning the open-reading frame into the pCMV-SPORT6 vector, was purchased from the DNA Library of Shanghai Jiaotong University (https://dnacore.shsmu.edu.cn). The JASPAR database was used to predict the potential transcription factor binding sites on the NR4A1 promoter, and NR4A1 overexpression plasmids were transfected into MLE-12 cells using Lipofectamine 2000 (Invitrogen), with the pCMV-SPORT6 vector set as a control.


title: RNF25-Mediated NF-κB Activation Drives Anti-Apoptosis and Therapy Resistance in Cancer [ChIP-seq]

overall_design: ChIP-Seq of p65 in SW839 cells with  shRNA-induced sciencing of  TRIP4.

last: Li