title: Ectopic endometrial mesenchymal stem cells derived exosomal miR-4466 promotes angiogenesis by targeting RUNX1 in adenomyosis.

city: Nanjing

first: Tao

last: Gui

state: Jiangsu

address: NO.100 Shizi Street, Hongshan Road

institute: Affiliated Hospital of Integrated Traditional Chinese and Western Medicine, Nanjing University of Chinese Medicine

summary: Background Abnormal angiogenesis plays a crucial role in the pathogenesis of adenomyosis (AM). Emerging evidence suggests exosomes derived from endometrial cells can boost AM progression. In this study, we aim to investigate the pro-angiogenic role and potential mechanisms of ectopic endometrial mesenchymal stem cells (eMSCs) derived exosomes (Ec-eMSCs-Exos) in adenomyotic lesions. Methods MicroRNA sequencing (miRNA-Seq) was conducted to identify differentially expressed miRNAs (DE miRNAs) in normal eMSCs derived exosomes (N-eMSCs-Exos) and Ec-eMSCs-Exos. Candidate miRNAs were selected using quantitative real-time polymerase chain reaction (qRT-PCR). The cell internalization assay were performed to confirm the internalization of exosomal miR-4466 into recipient human umbilical vein endothelial cells (HUVECs). The effects of exosomal miR-4466 on HUVEC proliferation, invasion/migration, and tube formation were analyzed in vitro using CCK8, EdU, transwell, wound healing, and μ-slide angiogenesis assays. The target gene of miR-4466 was predicted through bioinformatics analysis and further verified by qRT-PCR, western blot, dual luciferase reporter assay and rescue experiment. Results We identified 81 up-regulated and 92 down-regulated miRNAs between N-eMSCs-Exos and Ec-eMSCs-Exos. Among these DE miRNAs, miRNA-4466 was the most significantly up-regulated. The internalization assay showed that exosomal miR-4466 can be internalized by HUVECs. Overexpression or inhibition of miR-4466 can significantly promote or inhibit the proliferation, invasion/migration, and tube formation of HUVECs in vitro. By using bioinformatics predictions and luciferase reporter assay, we found that runt-related transcription factor 1 (RUNX1) was a direct targrt of miR-4466. Moreover, rescue experiment confirmed that RUNX1 overexpression reversed the pro-angiogenic effect of miR-4466 by inhibiting VEGFA expression. Conclusion Ectopic eMSCs derived exosomal miR-4466 promotes angiogenesis by targeting the RUNX1/VEGFA axis in AM.

overall_design: In this study, we isolated exosomes from the culture supernatant of normal eMSCs (n=3) and ectopic eMSCs (n=3). We performed miRNA Seq to identify miRNA profiles in eMSCs-Exos, and successfully obtained the results.

first: Jindan

last: Wang


title: Separate transcription and splicing gene networks are linked and coordinated by the pRb-E2F pathway

status: Public on Feb 04 2026

city: St. Petersburg

first: Alexander

last: Kanapin

address: 7/9 University Emb.

department: Institute for Translational Biomedicine

country: Russia

institute: St Petersburg Universoty

type: Expression profiling by high throughput sequencing

summary: E2F is a family of master transcription regulators involved in mediating diverse cell fates, and loss of control of the pathway is regarded as a hallmark of cancer. Recent studies have highlighted the pRb-E2F axis as a regulator of a large cellular network, which in addition to its classical target genes includes RNA splicing and non-coding genes. Here, we have addressed the generality of these effects by studying the role of the other key components of the pathway, including pRb, DP and PRMT5. Like E2F1, both pRb and DP1 influence transcription and alternative RNA splicing (AS) which is additionally impacted by PRMT5 activity.  A detailed proteomics analysis of the E2F1 interactome revealed SRSF2 and HNRNPC as partner proteins that assist E2F1 in mediating the effects on RNA splicing.  The ability of E2F1 to influence AS activity was apparent as cells progress through the cell cycle and during the DNA damage response.  Our results highlight the role of the pRb-E2F pathway in mediating cell cycle regulation of gene expression mediated by transcription and RNA splicing, and provide a mechanistic understanding for how this is likely to occur.

overall_design: To investigate the role played by PRMT5 and pRb-E2F pathway components in gene transcription and alternative splicing, we generated CRISPR cell lines in HCT116 and MCF7 cell backgrounds, in which E2F1, DP1, or pRb was knocked out.  These cells were treated with DMSO or a PRMT5 inhibitor as required.  Alternatively, HCT116 WT and E2F1Cr cells were synchronised at the G1/S boundary using a double thymidine block, and then released for 6 hours to allow them to progress into G2/M phase. We then performed gene expression and splicing analysis on RNA-seq data obtained from these various treatments and cell lines.

first: Simon

middle: M

last: Carr

first: Geng

last: Liu

first: Wojciech

last: Barczak

first: Shonagh

last: Munro

first: Hasan

last: Syffudin

first: Mauricio

last: Reyna-Jeldes

first: Iolanda

last: Vendrell

first: Benedikt

last: Kessler

first: Adam

last: Cribbs

first: Anastasia

last: Samsonova

first: Nicholas

middle: B

last: La Thangue


title: Toosendanin Suppresses Acute Myeloid Leukemia by Targeting DDX5/c-Myc Axis to inhibit Protein Synthesis

status: Public on Feb 03 2026

city: Guiyang

first: Xianchao

last: He

state: Guizhou

address: Huaxi

country: China

institute: Guizhou University

summary: The treatment of acute myeloid leukemia (AML) continues to be challenged by relapse and resistance, necessitating the development of novel therapeutic strategies. Toosendanin (TSN), a natural product derived from traditional Chinese medicine, exhibits antitumor activity in solid tumors; however, its mechanism of action and direct molecular targets in AML remain undefined. Here, we demonstrate that TSN potently inhibits AML cell proliferation, induces dual G0/G1 and G2/M phase arrest, and triggers caspase-dependent apoptosis at nanomolar concentrations. Using an integrated approach, including affinity pull-down, cellular thermal shift assay (CETSA), and molecular docking, we identified RNA helicase DDX5 as a direct target of TSN. TSN binding promotes DDX5 degradation via both proteasomal and lysosomal pathways. Transcriptomic and functional analyses revealed that TSN downregulates the c-Myc transcriptional network via DDX5 targeting, leading to the suppression of ribosome biogenesis. Rescue experiments confirmed that DDX5 is the central mediator of this pathway. In an MLL-AF9-driven AML mouse model, TSN treatment significantly prolonged survival, without observable toxicity. Collectively, our study delineates a novel anti-leukemic mechanism wherein TSN targets DDX5 for degradation and consequently inhibits c-Myc signaling, providing a rationale for therapeutic targeting of the DDX5/c-Myc axis and further development of TSN in AML.

overall_design: MOLM-13 cells were treated with 20 nM TSN or DMSO for 48 h (n=3 biological replicates). Total RNA was extracted, and libraries were constructed and sequenced using the NovaSeq™ X Plus platform. Differential gene expression analysis was performed using DESeq2 v1.26.0 (FDR < 0.05, |log₂FC| > 0.584). Gene Set Enrichment Analysis (GSEA) was conducted using the MSigDB Hallmark 2023 gene set (FDR < 0.25), and the analysis was performed on the OmicShare platform v6.2.

first: Jing

last: Luo

first: Hongru

last: Chen

first: Yu

last: Hou

first: Dan

first: Yuanyuan


title: Cochlear tissue from heterzygous or homozygous Myo7a Shaker mutant mice [RNA-seq]

city: Paris

first: Fiorella

last: Grandi

address: 105 Bld d'Hopital

department: Centre de Recherche de Myologie

country: France

institute: Sorbonne Universite

overall_design: Cochlear tissue from heterzygous or homozygous Myo7a Shaker mutant mice were dissected. Coclea from 4-5 mice were pooled per gentoype and RNA was extracted uisng the Qiagen microRNAeasy kit and sequenced .

first: Walter

last: Marcotti


title: Cellular diversity of the developing chick trigeminal ganglion at single-cell resolution

city: San Francisco

first: Erica

middle: J

last: Hutchins

state: CA

address: 513 Parnassus Ave

department: Cell and Tissue Biology

country: USA

institute: University of California San Francisco

summary:
Background: The trigeminal ganglion (TG) is a structure of the peripheral nervous system, composed of neuronal and non-neuronal cell types, that integrates sensory input from the face and jaw. The developing TG is derived from two embryonic cell populations: neural crest and cranial placode. Both populations play critical roles in TG development and must interact to coordinate changes in gene expression that regulate specification, differentiation, and organization. However, the molecular characteristics of the heterogeneous cell populations within the developing TG remain poorly defined.
Results: We performed single-cell RNA-sequencing (scRNA-seq) on TG from developing chick embryos at HH17. Our high-resolution dataset (14 clusters, ~87000 cells) provides insight into cellular diversity within the developing TG. As expected, we identified placode-derived neurons as well as neural crest cells prior to neuronal differentiation. In addition to classic markers, we identified novel transcripts with unknown roles in TG development, including several long non-coding RNAs (lncRNAs).
Conclusions: We generated a single-cell atlas of the developing chick trigeminal ganglion during early axonogenesis and defined the transcriptomic states of its diverse cell populations. Our results provide a useful resource for better understanding the cell populations contributing to TG development and gene expression that drives cell identity and differentiation.

overall_design: Pooled left and right trigeminal ganglia (TG) samples were generated by microdissection of 20 TG from separate embryos (left and right ganglia were never collected from the same embryo). Two duplicate pooled left and right samples of 20 TG were collected in total and enzymatically dissociated to generate single cell suspensions that were then fixed and sequenced to generate single cell RNA seq data using Parse Evercode WT 100K v3 kit.

first: Arvind

last: Arul Nambi Rajan


title: Elicitation of HIV broadly neutralizing antibodies from CRISPR-Cas reprogrammed B cells in non-human primates

city: La Jolla

first: Morgan

last: Bravo

address: 10466 N Torrey Pines Rd

department: Immunology and Microbiology

institute: Scripps Research

summary: HIV broadly neutralizing antibodies (bnAbs) are promising reagents for prevention and therapy of disease; however, their elicitation is constrained by genetic limitations of the human B cell antigen-receptor (BCR) repertoire. Precision genome-editing offers a potential solution by enabling bnAb genes to be programmed into the BCR repertoire as IgH-modified B cells. Such cells can be vaccinated to elicit durable bnAb memory responses in mice; however, extending this success to non-human primates (NHPs) would be a major advance towards clinical translation. Here, we show that ex vivo reprogrammed NHP B cells can survive autologous infusion and respond to immunization, differentiating into antibody-secreting cells (ASCs) that can produce up to 1 µg/ml of a bnAb in serum following vaccination prime. Although durable transgenic memory responses were not generated, vaccination of engineered cells in secondary lymphoid organoid (SLO) cultures recapitulated transient ASC responses in vitro. These findings suggest that NHP-derived SLOs could provide a platform to optimize engineering and vaccination conditions that drive germinal center maturation of IgH-reprogrammed B cells in a clinically relevant NHP model, supporting the development of engineered B-cell vaccines that generate durable bnAb responses as a potential functional cure for HIV.

overall_design: NHP primary B cells were cultured and engineered to express VRC01. For Pilot 1 media cultured cells, VRC01+ cells were enriched by FACS then loaded onto 10x chromium chips. For ImmunoCult cultured cells, cells were directly loaded onto 10x chromium chips. These samples were then sequenced using 10x Genomics Chromium Next GEM Single Cell 5’ Kit (V2 chemistry).

first: Mary

last: Tenuta

first: Jason

last: Weinfurter


title: S100A8/S100A9–toll-like receptor 4 signaling identified using single-cell RNA sequencing in ST36 acupoint mediating acupuncture analgesia

city: Tianjin

first: Ruping

last: Yuan

state: 天津Tianjin

address: 卫津路94号

institute: Nankai University

summary: Pain is a primary indication for acupuncture, with ST36 shown to effectively treat various types and locations of pain. Acupoints serve as pivotal starting points for acupuncture's therapeutic effects. However,  how acupuncture stimulation alters the microenvironment at the ST36 acupoint to treat different pain conditions remains unclear. We investigated the analgesic effects of ST36 acupuncture in mice with adjuvant arthritis, identifying fibroblast and macrophage clusters as the main responsive populations at ST36 through single-cell sequencing analysis. These populations expressed high levels of S100 calcium-binding protein a8 (S100a8), S100a9, and Toll-like receptor 4 (TLR4) on both cells and afferent fibers. Furthermore, acupuncture at ST36 activated A and C afferent nerves. Intriguingly, acupoint injection of an S100a8/S100a9-TLR4 inhibitor reversed the excitation of A and C afferent nerves and diminished the analgesic effect of acupuncture. These findings offer novel insights into the ST36 acupoint microenvironment modulated by acupuncture and underscore the critical role of S100a8/S100a9 in initiating acupuncture-induced analgesia at ST36. The study identifies S100a8/S100a9 as a potential regulatory target for modulating acupuncture effects at acupoints, providing a molecular framework for standardized acupuncture interventions and their clinical applications.

overall_design: After AIA induction, ACU was performed at ST36 on both hindlimbs, each ACU session lasted 30 min, with needles rotated intermittently.  ACU was performed once daily. Mice were anesthetized and tissues from the ST36 acupoint were excised and stored in cold 1640 medium. Then, used single-cell sequencing technology and bioinformatics to reveal the cellular heterogeneity of the ST36 acupoint cell map and microenvironment.

first: Baomin

last: Dou

first: Zezhi

last: Fan

first: Jiangshan

last: Wang

first: Yangyang

last: Liu

first: Shenjun

first: Xiaowei

last: Lin

first: Yanwei

last: Li

first: Kaifang

last: Yao

first: Zhihan

first: Zhifang

last: Xu

first: Gang

last: Hu

first: Yi

last: Guo


title: LncRNA AC098613.1 promotes acute myeloid leukemia cell differentiation through CDC5L/ADAP1/NRD1 axis

city: Yantai

first: qingling

last: jiang

address: No. 346, Guanhai Road, Laishan District

institute: Binzhou Medical University

summary: In this study, ATRA and PMA were employed to induce THP-1 cell differentiation, and whole transcriptome sequencing was used to screen out the significantly differentiated expression of lncRNAs during AML cell differentiation. Further, we found that AC098613.1 was significantly upregulated in differentiated AML cells, while AC098613.1 overexpression significantly promoted the differentiation of THP-1 and HL-60 cells. Therefore, the mechanism of AC098613.1-induced AML cell differentiation and the tumor-suppressive effect of AC098613.1 in vivo were further investigated.

overall_design: ATRA (8.0 µM) and PMA (50 ng/mL) were used to induce THP-1 cells differentiation, and whole transcriptome sequencing was used to screen out the significantly differentiated expression of lncRNAs and mRNA in both ATRA- and PMA-induced cells.

first: xiaoting

last: wang

first: defang

last: li


title: Functional architecture of cardiac TF regulatory landscapes in control of mammalian heart development

city: Bern

first: Ali

last: Hashemi Gheinani

address: Murtenstrasse 35, Department for BioMedical Research, Functional Urology

department: DBMR

country: Switzerland

institute: University of Bern

summary: Congenital heart disease (CHD), the most common human birth defect, often results from disruptions in gene regulatory networks (GRNs) that control cardiac lineage specification and cell type identity during heart development. A conserved core set of cardiac transcription factors (TFs) orchestrates these processes through combinatorial interactions that are cell type-specific and tightly regulated across space and time. However, the genomic enhancer architecture that integrates upstream effectors to establish precise cardiac TF dosage and downstream transcriptional output remains largely unresolved. Here, we assessed the functional necessity of five developmental heart enhancer modules previously linked to the regulation of Gata4 and Hand2, core cardiac TFs exhibiting overlapping roles in myocardial and endocardial development. While individual enhancer deletions in mouse embryonic hearts revealed a surprising degree of transcriptional resilience, a subset of Gata4 enhancers proved indispensable for embryonic progression in a genetically compromised background. To achieve higher precision in cardiac cell type-specific enhancer prediction, we applied single-nucleus multiome profiling, enabling the delineation of cardiac cistromes underlying heart morphogenesis. By integrating this resource with deep learning applications, site-directed transgenesis, and chromatin conformation modeling, we mapped the cardiac enhancer repertoire and regulatory signatures that orchestrate Hand2 dynamics across distinct cardiac compartments and lineages. Genome editing further revealed an essential role for the Hand2-upstream regulatory interval (H2-URI) in transcriptional control of endocardial lineage effectors and, consequently, trabecular network formation and cardiac cushion patterning. Together our findings highlight substantial resilience in the cis-regulatory architectures governing cardiac TF dynamics and demonstrate that combinatorial integration of upstream lineage identities across modular enhancer landscapes establishes the cardiac cell type-specific programs driving heart morphogenesis. These results advance the reconstruction of cardiac GRNs and enhance the functional interpretation of CHD-associated variants.

overall_design: To determine the functinal necessity of the Hand2 upstream regulatory interval (H2-URI), we used CRISPR-Cas9 in mouse embryos to generate a genomic deletion allele lacking 373kb of genomic sequence delimited by a predicted far upsream domain anchor and the Hand2-proximal Uph lncRNA. To determine the role of the H2-URI in regulating Hand2 expression and its impact on downstream GRNs, we performed bulk RNA-seq on hearts from H2-URId/d and wild-type embryos at embryonic day 9.5 (E9.5).Comparative gene expression analysis of RNA-seq data from H2-URId/d and wildtype mouse embryonic hearts at E9.5.

first: Virginia

last: Roland

first: Akshay

last: Akshay

first: Johannes

last: Tüchler

first: Iros

last: Barozzi

first: Marco

last: Osterwalder


title: Hyaluronic acid networks and emergent tissue mechanics orchestrate mammalian limb regeneration

city: Cambridge

first: Ragnhildur

middle: Thora

last: Karadottir

address: Puddicombe Way

country: United Kingdom

institute: Cambridge Stem Cell Institute

summary: In mammals, only distal amputations of the terminal digit regenerate, while more proximal ones result in non-regenerative, fibrotic scarring, underscoring the limits of our regenerative capacity. The mechanisms that direct one wound healing process over the other remain poorly understood. In this study, we investigated the role of cell-extrinsic cues, focusing upon the role of the extracellular matrix (ECM) and the bulk mechanical properties that arise from its composition. Through single-cell RNA sequencing (scRNA-seq), we showed that non-regeneration and regeneration are differentially dominated by a select few mesenchymal cell sub-types that help determine the mechanical properties of their environment by synthesizing collagen remodeling proteins and glycosaminoglycans. In the regenerating blastema, we demonstrated that osteo-lineage cells deposit copious networks of hyaluronic acid (HA) and closely associated proteins, which corresponded with soft tissue mechanical properties. Using synthetic stiffness-tunable scaffolds, we further demonstrated that fibroblast-ECM feedback mechanisms exist, in which soft mechanical cues mimicking the blastema propagate the synthesis pro-regenerative ECM. Knockdown of HA networks critically impairs regeneration, promotes fibrotic viscoelastic mechanical properties, and enhances collagen fibrillogenesis. We further showed that stiffness affects regeneration by modulating the strength of early BMP signaling. Lastly, we stabilized the deposition of HA networks in vivo using Hyaluronic Acid and Proteoglycan Link Protein 1 (HAPLN1) to partially rescue non-regenerative amputations. Altogether, we showed that through feedback mechanisms, the ECM and emergent bulk tissue mechanics mediate mesenchymal cell activity during injury repair. These findings demonstrate that modulating the ECM microenvironment may augment restorative repair and inform future therapeutic strategies to overcome deficiencies in mammalian wound healing.

overall_design: Non-regenerative amputations were performed on adult wild type C57BL/6 mice at the second phalanx, and the single cell transcriptome was compared with datasets of regenerative amputations. To investigate the influence of HA networks in regeneration, mice were fed either control diet or 4-methylumbelliferone-infused diet (50g/kg), which globally depletes the digit of HA and Aggrecan. Regenerative amputations were subsequently conducted, and cells were harvested from the digits at 14DPA for scRNAseq (N=2 per condition). All datasets were generated using the 10X Genomics platform. Raw and processed data are provided.

first: Byron

middle: W

last: Mui

first: Joseph

last: Wong

first: Mekayla

middle: A

last: Storer


title: Characterization of dendritic cells migrated from the tumor site to the thymus [RNA-Seq]

city: Chiba

first: YANGSONG

last: WANG

state: Chiba

address: 1-8-1, Inohana,

department: Experimental Immunology

country: Japan

institute: Chiba University

summary: This study was designed to investigate the specificity of dendritic cells migrated from the tumor site to the thymus.

overall_design:
Mice were inoculated subcutaneously with tumor cells and maintained for 12 days. Subsequently, Yellow-green microspheres (YG) was administered by intratumoral injection. Two days after YG treatment, thymic dendritic cell subsets were isolated for downstream analysis.
Thymic plasmacytoid dendritic cells (pDCs) and Sirpα⁺ conventional dendritic cells (Sirpα⁺ DCs) were sorted using a BD FACSAria™ III cell sorter. pDCs were defined as CD11c^low B220⁺ cells, while Sirpα⁺ DCs were identified as CD11c^high Sirpα⁺ cells.
The following samples were included in this study:
YG+ pDC samples: thymic YG+ pDCs isolated from tumor-bearing mice with YG injection
PBS pDC samples: thymic pDCs isolated from PBS-treated mice
PBS Sirpα+ DC samples: thymic Sirpα+ DCs isolated from PBS-treated mice
Total RNA from sorted cell populations was extracted using TRIzol reagent (Invitrogen) according to the manufacturer’s instructions and used for downstream transcriptomic analysis.

first: Yangsong

last: Wang

first: Ryo

last: Koyama-Nasu

first: Yukihiro

last: Endo

first: Ichita

last: Hasegawa

first: Atsushi

last: Onodera

first: Mingyu

last: Chen

first: Kiyoshi

last: Hirahara

first: Shinichiro

last: Motohashi

first: Toshinori

last: Nakayama

first: Motoko

middle: Y

last: Kimura


title: Role of squalene hopene cyclase in azole-resistance and virulence of Aspergillus fumigatus

city: Beijing

first: Kerui

last: Ye

address: Courtyard 20, East Street

department: Disinfection and Infection Control

institute: Chinese PLA Center for Disease Control and Prevention

summary: As a major fungal pathogen, Aspergillus fumigatus can induce chronic, allergic or severe invasive infections, meanwhile its escalating resistance to azole antifungals has emerged as a global public health menace. Squalene, an essential molecule in the sterol biosynthesis pathway, can be cyclized by squalene hopene cyclase (SHC) to produce hopanoids and affect probably sterol biosynthesis modifying azole resistance; however, the physiological function of SHC in A. fumigatus pathogenesis is poorly understood.

overall_design: Hereby it was found by genetic phylogenetic and protein structural analysis that the three shc genes in A. fumigatus demonstrate structural and functional diversification.  Deletion of none of them substantially hindered fungal growth and development, but intriguingly, loss of shc1 gene increased the azole resistance of A. fumigatus whereas  diminished its pathogenicity. Deletion of one of three shc genes could enhance the adhesion and invasion abilities of A. fumigatus towards lung epithelial cells. More, in A. fumigatus isolated from clinical samples the expression of shc1 gene was obviously higher in azole-resistant strains than in azole-susceptible strains, indicating a possible clinical significance of shc1 in relation to azole resistance. These findings demonstrated that SHC plays an important role in the regulation of azole-resistance and pathogenesis of A. fumigatus.


title: Effect of RXRα agonist bexarotene on gene expression in hepatocytes of hepatic RXRα knockout mice

city: Hangzhou

first: Hang

last: Zeng

state: Zhejiang

address: 79# Qingchun road

institute: Zhejiang university

summary: Retinoid X receptor alpha (RXRα) is a ligand-activated nuclear receptor involved in the regulation of retinoid metabolism. RXRα activation by agonist bexarotene can significantly induce hepatomegaly and promote liver regeneration after 70% partial hepatectomy (PHx) in wild type mice, while these effects were abolished in liver-specific RXRα-knockout mice. However, the underlying mechanisms remain unclear. Our findings reveal that RXRα activation promotes liver proliferation through transactivation of Cyclin D1. These data raise some key questions for understanding the manipulation of liver size and liver regeneration by RXRα agonists.

overall_design: RNA-seq profiling of hepatocytes in male flox and hepatic RXRα knockout mice (C57bl/6) treated with 5 days of RXRα agonist bexaratene (100 mg/kg/d, q.d.)


title: Single myonuclei RNA-seq on control vs AAV-OPDM mouse models

city: ILLKIRCH

first: Nicolas

last: Charlet-Berguerand

address: 1 rue Laurent Fries

institute: IGBMC

summary: We injected in WT BL6 male mice either NaCl (control) or AAV.MYO4A coding either for the GFP (control) of for ATG polyG-GFP, OPDM2 uGIPpolyG-GFP, OPDM3 uN2CpolyG-GFP or OPML LOC6polyG-GFP. These diverse polyGlycine proteins are responsible oculopharyngodistal myopathy (OPDM). Our aim was to determine through single nuclei RNA seq whether expression of these polyGlycine-proteins in muscle leads to a common and specific signature.

overall_design: Single nuclei RNA-seq analysis was performed using 10X Genomics FLEX multiplex technology which uses barcoded probe sets targeting the whole transcriptome and enabling sample multiplexing. Tibialis Anterior (TA), gastrocnemius and quadriceps muscles of 7 months post-AAV injection of two individuals per genotype : NaCl-, GFP-, ATG polyG-GFP-, uGIPpolyG-GFP-, uN2CpolyG-GFP- or LOC6polyG-GFP- injected mice.

first: Manon

last: Boivin


title: TFIIB

city: Berkeley

first: Britt

last: Glaunsinger

state: California

address: RM 565, 1951 Oxford St

department: PMB

institute: University of California, Berkeley

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

overall_design: Refer to individual Series


title: Thymic CD11c+ cells [scRNA-seq]

summary:
This study investigates the dynamics of thymic dendritic cells (DCs) under tumor-bearing conditions and the role of CCR9 in regulating thymic DC homeostasis. CD11c⁺ thymic cells were enriched from wild-type (WT) and CCR9 knockout (CCR9 KO) mice subjected to different experimental treatments.
Four experimental groups were analyzed:
CCR9 WT mice treated with PBS for 2 weeks
CCR9 WT mice bearing MC38 tumors for 2 weeks
CCR9 WT mice bearing MC38 tumors for 3 weeks
CCR9 KO mice bearing MC38 tumors for 3 weeks

overall_design: This dataset contains single-cell RNA sequencing (scRNA-seq) data of thymic CD11c+ cells isolated from CCR9 wild-type (WT) and CCR9 knockout (KO) mice under different experimental conditions. Four samples are included: CCR9 WT mice treated with PBS for 2 weeks, CCR9 WT mice bearing MC38 tumors for 2 weeks, CCR9 WT mice bearing MC38 tumors for 3 weeks, and CCR9 KO mice bearing MC38 tumors for 3 weeks. After subcutaneous MC38 tumor implantation, CD11c+ cells were sorted from the thymus using BD FACS Aria III and subjected to droplet-based single-cell RNA sequencing using the Chromium Next GEM Single-Cell 5’ Reagent Kit v2 (10x Genomics). Libraries were sequenced on a DNBSEQ platform (MGI). Sequencing data were processed using Cell Ranger v7.1.0 (10x Genomics) with the mouse reference (refdata-gex-mm10-2020-A).


title: Dual AAV gene therapy using laminin-linking proteins ameliorates muscle and nerve defects in LAMA2-related muscular dystrophy

city: Basel

first: Eleonora

last: Maino

address: Spitalstrasse 41

department: Biozentrum

institute: University of Basel

summary: Adeno-associated virus (AAV)-mediated gene replacement holds promise for treating genetic diseases but faces challenges due to AAV’s limited packaging capacity and potential immune responses to transgene products, especially in patients lacking endogenous protein. LAMA2-related muscular dystrophy (LAMA2 MD), a severe congenital disorder caused by loss of laminin-α2, presents both hurdles: the LAMA2 gene exceeds AAV capacity, and severely affected patients do not produce the native protein. Here, we developed an AAV-based therapy using two engineered linker proteins derived from endogenously expressed components. These linker proteins restore laminin receptor binding and polymerization, enabling reassembly of a functional basement membrane. Dual AAV delivery of the linkers in a severe LAMA2 MD mouse model resulted in robust expression and significant improvements in muscle histology and function. Employing myotropic capsids enabled therapeutic efficacy at lower vector doses. However, muscle-specific targeting unmasked a LAMA2-related peripheral neuropathy. To address this, we expressed one linker under a muscle-specific promoter and the other under a ubiquitous promoter, delivered via AAV9 or AAV8. This approach achieved near-complete phenotypic restoration when administered neonatally and provided significant benefit when given at progressed disease stages. Our strategy offers a mutation-independent, size-compatible, and potentially immune-tolerable treatment for LAMA2 MD with broad clinical potential.

overall_design: RNA-seq analysis of tibialis anterior (TA) muscle from 8-week-old mice: non-injected wild-type and dyW/dyW mice, and wild-type and dyW/dyW mice injected intravenously at P1 with AAV9-Spc/CBh-DL (1×10¹⁴ vg/kg per construct).

first: Judith

middle: R

last: Reinhard

first: Lin

last: Shuo

first: Maino

last: Eleonora

first: Daniel

last: Ham

first: Markus

last: Rüegg


title: Single cell mRNA sequencing on esophageal cells of WT and Krt5-CreERT2:R26SmoM2/EYFP (K5:Smo) mice 5 days after Tamoxifen administration

city: Anderlecht

first: Louison

last: Descampe

address: Route de Lennik 808

department: IRIBHM

country: Belgium

institute: Université Libre de Bruxelles

summary: In our study, we used single-cell RNA sequencing to investigate the early effects of Hedgehog signaling pathway activation in esophageal progenitors.

overall_design: Esophageal single cell mRNA profiles of WT and Krt5-CreERT2:R26SmoM2/EYFP mice by deep sequencing using 10x genomic.

first: Benjamin

last: Beck


title: Human epicardial organoids from pluripotent stem cells resemble fetal stage with potential cardiomyocyte-transdifferentiation

first: Chengchen

last: Zhao

address: Dunyu Road No.600, Xihu District

institute: Westlake University

summary: Epicardium, the most outer mesothelium, exerts crucial functions in fetal heart development and adult heart regeneration. Here we use a three-step manipulation of WNT signalling entwined with BMP and RA signalling for generating a self-organized epicardial organoid that highly express with epicardium makers WT1 and TCF21 from human embryonic stem cells. After 8-days treatment of TGF-beta following by bFGF, cells enter into epithelium-mesenchymal transition and give rise to smooth muscle cells. Epicardium could also integrate and invade into mouse heart with SNAI1 expression, and give birth to numerous cardiomyocyte-like cells. Single-cell RNA seq unveils the heterogeneity and multipotency exhibited by epicardium-derived-cells and fetal-like epicardium. Meanwhile, extracellular matrix and growth factors secreted by epicardial organoid mimics the ecology of subepicardial space between the epicardium and cardiomyocytes. As such, this epicardial organoid offers a unique ground for investigating and exploring the potential of epicardium in heart development and regeneration

overall_design: H9 samples. All samples were collected for single-cell sequencing on day 7.5, 9.5 and 18.5

first: XINLE

last: ZOU

first: FANWEN

last: WANG

first: HUILING

last: ZHENG

first: TIANCI

last: KONG


title: Differential synaptic signaling responses in human cortical organoids after photon and proton irradiation

city: Groningen

first: Yuting

last: Jiang

state: Groningen

address: Antonius Deusinglaan 1

department: Department of Biomedical Sciences

country: Netherlands

institute: University Medical Center Groningen

summary: Brain tumors are the most common solid cancer in children, with radiotherapy being a primary treatment. Proton therapy, with its precise dose distribution, is increasingly being used in these patients to minimize damage to the developing brain. However, the biological effects of proton irradiation on the human brain remain unclear. To investigate this, human cortical organoids were exposed to conventional photons, plateau and spread-out Bragg peak (SOBP) protons, followed by comparative transcriptomic profiling. While photons and protons induced similar transcriptional profiles characterized by apoptosis and downregulation of DNA replication, SOBP protons uniquely downregulated genes involved in brain development and synaptic signaling. Functional calcium imaging, cell deconvolution analysis and immunostaining indicated that SOBP protons impaired neural network function, due to reduced synaptic density and loss in excitatory neuron progenitors. These findings underscore the distinct biological effects of SOBP protons and their potential adverse impact on the developing brain.

overall_design: Bulk RNA sequencing was performed on human cortical organoids approximately 60 days into differentiation, 48 hours after sham irradiation or exposure to 7 Gy or 14 Gy photon irradiation, proton plateau irradiation, or proton SOBP irradiation. N = 4 pools per group, each pool contains 3-4 organoids.

first: Danieli

last: Guerra

first: Daniëlle

middle: C

last: Voshart

first: Eline

last: Hageman

first: Luiza

last: Reali Nazario

first: Marc-Jan

last: van Goethem

first: Rob

middle: P

last: Coppes

first: Lara

last: Barazzuol


title: Multiscale analysis and functional validation of the cellular and genetic determinants of skeletal disease [Mouse scRNA-seq]

city: SYDNEY

first: Peter

last: Croucher

state: NSW

address: 384 VICTORIA ST, DARLINGHURST NSW 2010

country: Australia

institute: Garvan Institute of Medical Research

summary: Musculoskeletal diseases are a major global health burden. Development of new bone-active therapies is hindered by limited understanding of the complex interactions between the cells and genes that regulate the skeleton. To unravel this complexity, we systematically annotated all cells in bone and defined the genes that control their function at single-cell resolution. Integration with data from human gene-mapping studies of rare skeletal disorders and common skeletal disease traits identified novel disease genes, which we validated by functional analysis in more than one thousand genetic mouse models. This multiscale approach expands the repertoire of cells that regulate bone to include endothelial and vascular smooth muscle cells. This also revealed hundreds of skeletal disease-associated genes in this landscape of cells as potential drug targets. The cellular and genetic mechanisms revealed by this approach overcomes knowledge gaps and helps to accelerate development of next generation therapies to treat skeletal diseases.

overall_design: Single-cell RNA sequencing was performed on bone microenvironment cells isolated from endosteal compartments of the metaphysis and diaphysis, as well as from bone marrow from femurs of adult male C57BL/6J mice. Cells from each of the 3 bone compartments were pooled into 5 replicates (5 mice per replicate) prior to sequencing, resulting in 15 samples total. One sample (Marrow, replicate 2) failed capture.

first: Ryan

last: Chai

first: Mischa

last: Lundberg

first: Bernard

last: Freudenthal

first: James

middle: T

last: Smith

first: Andrew

last: Boughton

first: Yuandan

last: Zhang

first: Kaitlyn

last: Flynn

first: Monika

last: Frysz

first: Alexander

last: Corr

first: Weng

middle: H

last: Khoo

first: Davide

last: Komla-Ebri

first: Michael

last: Dack

first: Siobhan

middle: E

last: Guilfoyle

first: John

middle: G

last: Logan

first: Natalie

last: Butterfield

first: Victoria

middle: D

last: Leitch

first: Andrea

middle: S

last: Pollard

first: Riikka

last: Mäkitie

first: Michelle

last: McDonald

first: Scott

last: Youlten

first: Marcelo

last: Sergio

first: David

last: Evans

first: Joseph

last: Powell

first: Christiaan

last: de Leeuw

first: Adam

last: Ewing

last: Eisman

first: Robert

last: Blank

first: Tri

last: Phan

first: Paul

last: Baldock

first: Emma

middle: L

last: Duncan

first: Graham

last: Williams

first: Duncan

last: Basset

middle: I


title: Arabidopsis mRNA export factor tho5ab: molecular interactions and role in heat stress responses

city: Regensburg

first: Leo

last: Schmutterer

address: Universitätsstraße 31

department: Plant Cell Biology, Biochemistry, and Biotechnology

country: Germany

institute: University of Regensburg

summary: A central function in linking RNA polymerase II transcription and pre-mRNA processing with mRNA export is executed by the transcription and export (TREX) complex. TREX consists of a hexameric core termed THO that associates with various combinations of additional proteins giving rise to alternative versions of TREX. Cell fractionation in combination with transcript profiling demonstrated that THO5 a subunit of the THO complex  is required for export of a subset of mRNAs .

overall_design: To investigate export defects in tho5ab mutants upon heat stress RNA was isolated in nuclear and cytoplasmic fractions at 21° C and 37° C for 3h from wild type Arabidopsis Thaliana (Col-0) and tho5ab mutants

first: Amelie

last: Rödel

first: Valentin

last: Berger

first: Ina

last: Weig-Meckl

first: Uwe

last: Schwartz

first: Klaus

last: Grasser


title: The postcopulatory transcriptional response in different sections of the female reproductive tract

city: Madrid

first: Lena

last: Arévalo

state: Madrid

address: Avda. Puerta de Hierro, 18

department: Animal Reproduction

country: Spain

institute: INIA-CSIC

summary: In internally fertilizing species, the first direct molecular contact between the male and female gene products occurs within the female reproductive tract – a highly complex and rapidly evolving structure in many species. While molecular interactions between sperm and oocyte have received a lot of attention, efforts to gain insight into the crosstalk happening during the sperm cells  journey to the site of fertilization have been limited, especially in mammals. The interactions between sperm cells and the female reproductive tract not only facilitate sperm guiding, storage, and protection against introduced pathogens but also comprise a sophisticated mechanism of female-mediated sperm selection. Molecular interaction partners that are involved directly in sperm assessment and selection, however, are difficult to pinpoint within the massive immunological response happening in the female reproductive tract following copulation. While we have some knowledge of sperm surface proteins interacting with the components of the female reproductive tract, the female counterparts of these interactions are still largely unknown. We characterized the murine female transcriptional response to semen following copulation. We mated males and females from different strains and used strain-specific SNPs to distinguish semen-derived from female reproductive tract-derived transcripts. We specifically focused on the different subdivisions of the female reproductive tract, with the aim to identify female molecules directly involved in sperm assessment. Our results show a large number of differentially expressed genes in uterus, uterotubal junction and oviduct compared to unmated control and significant differences in differential expression between the subsections.

overall_design: RNAseq of the uterus, UTJ and oviduct in three groups of 126SV/S2 female mice in estrous stage of the cycle: unmated control (CTR), females 6-8h after copulation with intact C57/Bl6 males (COP) and females 6-8h after copulation with vasectomized C57/Bl6 males (VAS).

first: Nikola

last: Arsić

first: María

last: de Dios Castresana

first: Eva

last: Pericuesta

first: Beatriz

last: Fernandez-Fuertes

first: Alfonso

last: Gutiérrez-Adán

first: Hubert

last: Schorle


title: Intrinsic mechanisms and microenvironmental cues fine-tune plasticity of esophageal progenitors

first: Louison

last: Descampe

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus


title: Integrative analysis reveals ciliary dysfunction and compartmentalized LCN2 expression as distinct features of COVID-19

city: shenzhen

first: huang

last: peiming

state: Guangdong

address: xinhu

institute: Sun Yat-sen University

summary: The unique pulmonary pathophysiology of COVID-19 compared with other respiratory viral infections remains poorly understood. We performed integrative bulk and single-cell RNA sequencing on bronchoalveolar lavage fluid (BALF) from patients with COVID-19 (n=24) or influenza (n=10) and healthy controls (n=10). While influenza primarily induced conventional inflammatory responses, COVID-19 triggered distinct microenvironmental remodeling characterized by a specific cilium-related gene signature (e.g., DNAH9, FOXJ1) and expansion of ciliated and airway epithelial cells. Cross-tissue comparison with peripheral blood mononuclear cells uncovered a compartmentalized immune response, particularly for Lipocalin-2 (LCN2), which showed opposite expression trends between the lung and systemic circulation. This study identifies ciliary dysfunction and epithelial-immune crosstalk as key features distinguishing COVID-19 from influenza and highlights epithelial-derived LCN2 as a robust, compartmentalized biomarker for disease severity.

overall_design: This study utilized bulk RNA sequencing to characterize the transcriptomic landscape of the lower respiratory tract and systemic circulation during SARS-CoV-2 infection. BALF and PBMC samples were collected from COVID-19 patients, influenza patients (BALF only), and healthy controls. RNA was extracted using TRIzol reagent and sequenced via a commercial platform. Differential expression analysis was performed using the DESeq2 package, and batch effects across datasets were corrected using limma's removeBatchEffect function. The analysis focused on identifying COVID-19-specific signatures by comparing profiles against both healthy controls and influenza-infected samples.

first: Peiming

last: Huang

first: Haiqiong

last: Yu

first: Wenjuan

last: Cao

first: Yixin

last: Zhang

first: Jianteng

last: Zeng

first: Minghua

last: Chen

first: Jingjing

last: Luo

first: Xiaojun

last: Xiao

first: Shuangxin

last: Wu

first: Jianquan

first: Ting

last: Pan


title: Single-cell transcriptomic analysis reveals age-associated alterations in bone marrow niche-related cells

city: Okayama

first: Ikue

last: Tosa

state: Okayama

address: Shikata-cho2-5-1, Kita-ku

institute: Okayama University

summary: Hematopoietic stem cells (HSCs) depend on the bone marrow (BM) niche for self-renewal and differentiation. Within this niche, CXCL12-abundant reticular (CAR) cells are key regulators of hematopoiesis and bone homeostasis. Single-cell RNA sequencing of adult and old mice revealed that old Adipo-CAR cells form a distinct cluster with reduced expression of ossification- and stem cell maintenance–related genes. RNA velocity and pseudotime analyses indicated impaired osteogenic differentiation, which was confirmed by in vitro assays showing diminished osteogenesis and increased adipogenesis. Structural and immunohistochemical analyses further demonstrated sinusoidal and endothelial abnormalities with age. These results suggest that age-related changes in Adipo-CAR cells and the sinusoidal niche underlie defective osteogenesis and hematopoietic decline.

overall_design: Flushed long bone from C57BL6 mice was digested with collagenase IV, dispase, and DNase in HBSS for 30 min at 37 °C. After lysing red blood cells with NH4Cl, cells were filtered through a 70 µm filter.

first: Kei

last: Ishibashi

first: Mitsuaki

last: Ono

first: Ziyi

last: Wang

first: Wakana

last: Kitagawa

first: Anh

last: Dang

first: Kentaro

last: Akiyama

first: Tomoko

last: Yonezawa

first: Toshitaka

last: Oohashi

first: Takuo

last: Kuboki


title: single nucleus RNA sequencing of cells in the whole mouse brain of the rNLS8 model of ALS/FTLD-TDP at 4 weeks post-induction

city: Seattle

first: Nicole

last: Liachko

state: WA

address: 1660 Columbian Way S.

department: GRECC

institute: VA Puget Sound Health Care System

summary: The mouse brain is a complex tissue with many cell types including distinct populations of neurons, astrocytes, and microglia.  We examined cell type specific gene expression in cells across the whole brain of rNLS8 mice that express doxycycline suppressible human TDP-43 (hTDP-43) with a defective nuclear localization signal (hTDP-43ΔNLS) regulated by the NEFH promoter, at a timepoint when they are strongly symptomatic but preceeding robust neurodegeneration.

overall_design: For this study we employed transgenic mice carrying a transgene enabling inducible neuronal expression of human TDP-43 with a deletion of its nuclear localization signal (rNLS8 mice) as a model of ALS  and FTLD-TDP.  The transgene was induced in adult mice, and brains were harvested after 4 weeks, when the mice were strongly symptomatic.  Brains were split down the midline, and whole half-brains were used for single nucleus RNA sequencing (snRNAseq).  Cell-type specific changes in gene expression were observed comparing control and rNLS8 mice.

first: Liachko

last: Nicole


title: Mucus plugs-associated gene expression identifies pathophysiology shared with chronic bronchitis

city: Boston

first: Adam

last: Gower

state: MA

address: 72 East Concord Street, E632

department: Department of Medicine

institute: Boston University School of Medicine

summary: Rationale: Mucus plug formation and chronic bronchitis are manifestations of mucus pathology in chronic obstructive pulmonary disease. Identifying gene expression changes related to mucus pathology could provide insight into its pathogenesis.  Objectives: To investigate gene expression changes in individuals with mucus plugs, identify related biological pathways, and assess whether mucus plug-related gene expression associates with clinical features of other mucus pathologies.  Methods: We studied 290 participants from the Detection of Early Lung Cancer Among Military Personnel 2 study with mainstem bronchial brush bulk RNA-sequencing data (n = 204 discovery, n = 86 validation). We scored mucus plugging based on the number of lung segments with mucus plugs identified on chest computed tomography scans and used correlative analysis to identify differentially expressed genes and examine their association with chronic bronchitis symptoms.  Results: 76 participants (37%) in the discovery set had mucus plugs.  Differentially expressed genes were broadly epithelial- or immune-related. Epithelial-related genes show decreased expression of genes involved in cilia maintenance and microtubule function and increased expression of genes related to mucus production and secretion. Expression patterns of epithelial-related genes are associated with chronic bronchitis symptoms. Immune-related genes are enriched for innate and adaptive pathways. Expression of immune genes varies by lung function and was more weakly associated with mucus plugs than that of epithelial-related genes. Findings were replicated in an independent validation set.  Conclusion: Several distinct gene expression patterns are linked to the presence of mucus plugs, highlighting biological pathways involved in mucus pathophysiology. Variability in gene expression suggests a spectrum of mucus pathophysiology contributes to mucus plugs and chronic bronchitis symptoms.

overall_design:
Bronchial brushings were collected during bronchoscopy from normal-appearing airway epithelium in study participants enrolled in the Detection of Early Lung Cancer Among Military Personnel (DECAMP) 2 study.

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

first: Whitney

last: Souery

first: Marc

last: Lenburg


title: Identification of IL1R2 as a Spermatogonial Stem Cell-specific Sorted Protein in Humans and Mice

first: yu

middle: peng

last: Li

address: Dong Dan San Tiao 5 Beijing , China

institute: Peking Union Medical College

summary: Self-renewal and differentiation of spermatogonial stem cell (SSCs) are critical for sustaining spermatogenesis in adult mammals. SSC populations are highly heterogeneous and dynamic, imposing great challenges in their isolation and functional characterization. The current study aimed to generate Il1r2CreERT2/+; Rosa26mTmG/+ mice to pulse-label Il1r2-expressing cells; through lineage tracing, we discovered that IL1R2+ SSCs, essential for spermiogenesis, possess long-term capacities of self-renewal and differentiation. Under injury-induced regenerative conditions, disruption of spermatogenesis can reactivate IL1R2+ SSCs for proliferation via the PI3K-AKT-mTOR pathway to replenish the SSC pool. We further validated our discovery by systematically characterizing both mouse and human IL1R2+ SSCs isolated. Our findings confirmed the important role of IL1R2+ SSCs in the maintenance of spermatogenesis and regeneration after spermatogenic injury; IL1R2 might serve as a promising marker for enriching human and mouse SSCs.

overall_design: To characterize IL1R2+ SSCs, we isolated IL1R2+, THY1+, and c-KIT+ cells from mouse testes using FACS for RNA-Seq analysis


title: Single cell mRNA sequencing on esophageal cells of human biopsies coming from subtotal esophagectomy

first: Louison

last: Descampe

summary: In our study, we used single-cell RNA sequencing to characterize epithelial cell populations in the human esophagus in control condition compared to Barrett esophagus condition.

overall_design: Oesophageal single cell mRNA profiles of control and Barret biopsies from patient by deep sequencing using 10x genomic.

first: Benjamin

last: Beck


title: Transcriptomes of capsule swapped-strains in Klebsiella (K1, K2, K3, K24)

city: Paris

first: Hugo

last: Varet

address: 28 rue du Docteur Roux

institute: Institut Pasteur

summary: We use the bacterium Klebsiella spp. as a model organism, we are interested in the bacterial capsule and the functional and evolutionnary consequences of capsule exchanges.

overall_design: We have 4 different genetic backgrounds in which we have deleted the capsular locus (∆cap: complete deletion mutant) and then separately inserted 4 different capsular loci (K1, K2, K3, and K24). We want to compare RNA expression upon capsule deletion or swap using the specific reference genome.

first: Julie

last: Le Bris

first: Eduardo

last: Rocha

first: Olaya

last: Rendueles


title: Glucocorticoids suppress early lung inflammation and impair control of SARS-CoV-2 in non-human primates.

city: Bethesda

first: Tom

last: Hill

state: Maryland

address: NIHBC 10 - CLINICAL CENTER BG RM 11N244A, 10 CENTER DR

institute: NIAID

summary: In severe cases of COVID-19, glucocorticoid treatment improves clinical outcomes. However, in non-hospitalized patients, glucocorticoids have limited benefit and may impair viral control. The cell types regulated by glucocorticoids during SARS-CoV-2 infection are currently unknown. Here, we used rhesus macaques to examine the effects of glucocorticoids during the first 14 days of acute SARS-CoV-2 infection. Glucocorticoid treatment decreased local lung inflammation measured with 18FDG-PET/CT imaging. However, glucocorticoid treated animals also had evidence of elevated SARS-CoV-2 viral titers in the lower airways and pulmonary draining lymph nodes. Glucocorticoid treatment blunted plasmacytoid dendritic cell (pDC), eosinophil, innate-like CD8 T cell and early SARS-CoV-2 specific CD8 T cell responses in the airways. These data reveal the cell types that are directly impacted by immunosuppression with glucocorticoids and provide mechanistic insights into the discordant effects of glucocorticoids during SARS-CoV-2 infection.

overall_design: Single cell RNA sequencing using 10x genomics 3' kits v3.1 with sample pooling using hashtag barcodes (Biolegend TotalSeqA #1-10). Samples are a time-course (t0, t1, t2, t3, t4) of bronchoalveolar lavage samples from 10 rhesus macaques infected with SARS-CoV-2, with and without glucocorticoid immunosuppression (n=5 of each). Samples from each treatment group were pooled separately for each of the 5 time points. n=5 control animals (hashtags 1-5) n=5 glucocorticoid animals (hashtags 6-10) Pooling resulted in one control and one glucocorticoid sample at each timepoint. We would like help aligning the data, QC, normalizing, scaling, dimensional reduction and perhaps clustering. We have previously used the Seurat pipeline.

first: Christine E.

last: Nelson

first: Keith D.

last: Kauffman

first: Shunsuke

last: Sakai

first: Taylor

last: Newbolt

first: Jay

last: Bucchnan

first: Taylor W.

last: Foreman

first: April M.

last: Walker

first: Felipe

last: Gomez

first: Joel D.

last: Fleegle

first: Richard

last: Herbet

first: Justin

last: Lack

first: Sevilay

last: Turan

first: Reed

last: Johnson

first: Laura E.

last: Via

first: Daniel L.

last: Barber


title: Transcriptomics of 3D pentaculture models of high grade serous ovarian cancer microenvironment

city: London

first: Eleni

last: Maniati

address: John Vane Science Centre, Charterhouse Square

department: Barts Cancer Institute

institute: Queen Mary University of London

summary: High-grade serous ovarian cancer (HGSOC) is characterized by a complex, immunosuppressive tumor microenvironment (TME) that contributes to poor clinical outcomes and resistance to therapy. To better replicate the human TME in vitro, we developed a 3D pentaculture model incorporating five human cell types: malignant HGSOC cells, primary fibroblasts, mesothelial cells, adipocytes, and monocytes. Bulk RNASequeing was performed to investigate the role of malignant cells in modulating the TME .

overall_design: We constructed three omental microenvironments by incorporating primary adipocytes, fibroblasts, and mesothelial cells isolated from three different donors as biological replicates. Monocytes from a single donor were used in all experiments. Additionally  2D monocultures of fibroblasts (n = 3), mesothelial cells (n = 1), monocytes (n = 1), malignant cells (n = 2 per cell line) and non-diseased omentum free of malignant tissue (n = 3) were included in the analysis.

first: Beatrice

last: Malacrida

first: Samar

last: Elorbany

first: Joash

last: Joy

first: Frances

last: Balkwill


title: T cell-derived TNF drives myocarditis but is dispensable for antitumor efficacy of checkpoint immunotherapy

city: Cincinnati

first: Mengchi

last: Jiao

state: OH

address: 3333 Burnet Ave

institute: Cincinnati Children's Hospital Medical Center

summary: Immune checkpoint inhibition (ICI) has significantly advanced cancer treatment but is associated with immune-related adverse outcomes including lethal myocarditis. T cells against select cardiac antigens have emerged as a cause of myocarditis, yet the mechanisms by which these cells exert pathological effects remain unclear. To investigate the pathogenesis of ICI-induced myocarditis, we developed a mouse model with cardiac-restricted expression of the model antigen ovalbumin (Ova). Immunotherapy with antibodies against cytotoxic T cell antigen-4 (αCTLA-4) and programmed death-1 (αPD-1) uniquely drove the expansion of transferred Ova-specific naïve CD8 T cells and infiltration in the heart. The goal of this study was to identify pathways induced in immune cells interacting with pathogenic T cells. Here, Ova-specific CD8 T cells initiated innate immune activation, resulting in arrhythmias and lethal cardiomyopathy. The innate inflammation and cardiac damage were largely driven by T cell-derived tumor necrosis factor (TNF), as shown by the marked reduction of myocarditis in mice receiving TNF-deficient Ova-specific CD8 T cells or treated with tumor necrosis factor receptor 2 (TNFR2)-blocking antibody. Furthermore, targeting T cell-mediated innate inflammation via the TNF:TNFR2 axis ameliorated myocarditis while preserving the antitumor efficacy of immune checkpoint inhibitor (ICI) therapy. These findings clarify roles for the inhibitory receptors PD-1 and CTLA-4 in regulating self-reactive T cells and offer a clinically actionable path for protection from ICI-induced myocarditis while maintaining antitumor immunity.

overall_design: RNA-seq profiling of CD45+CD90.2- cells from the hearts of cardiac-restricted Ovalbumin (Ova)-expressing transgenic mice following adoptive transfer of Ova-specific CD8 (OTI) T cells

first: Kathrynne

last: Warrick

first: Anne

middle: K

last: Johansen

first: Irene

last: Saha

first: Thomas

last: Hagan

first: Jeffery

last: Molkentin

first: Chandrashekhar

last: Pasare


title: RNA sequeqncing data of Kat6a–/–, Kat6a+/– and Kat6a+/+ E12.5 dorsal telencephalon and of Kat6a+/– and Kat6a+/+ E16.5 cortical neurons

city: Parkville

first: Nishika

last: Ranathunga

state: VIC

address: 1G Royal Parade

institute: Walter and Eliza Hall Institute of Medical Research

summary: Mutation of one allele of the KAT6A gene encoding the histone acetyltransferase KAT6A (MOZ, MYST3) causes Arboleda-Tham-Syndrome (ARTHS), which is characterised by developmental delay, cognitive impairment and autism-like behaviours.  We used mice to examine the effects of  Kat6a mutations on gene expression in the develping cerebral cortex and cortical neurons. We examined the effects of homozygous and heterozygous loss of Kat6a on gene expression in the E12.5 dorsal telecencephalon, the embryonic precursor of the cerebral cortex, and the effects of heterozygous loss of Kat6a on gene expression in foetal cortical neurons.

overall_design: N = 4 Kat6a–/– vs. 4 Kat6a+/+ E12.5 dorsal telencephalon; 4 Kat6a+/– vs. 4 Kat6a+/+ E12.5 dorsal telencephalon; 4 Kat6a+/– vs. 4 Kat6a+/+ E16.5 cortical neurons

first: Alex L

last: Garnham

first: Samatha

last: Eccles

first: Anne K

last: Voss

first: Tim

last: Thomas


title: H3K115 marks fragile nucleosomes at regulatory sites (Sucrose Gradient fractions rep2)

city: Edinburgh

first: Yatendra

last: Kumar

email: yaten2020@gmail.com, ykumar@ed.ac.uk

address: Crewe Road south

department: MRC HGU

institute: MRC Human Genetics Unit, The University Of Edinburgh

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Acetylation of lysine residues in the tail domain of histone H3 at active regulatory elements are well characterised, but the less studied acetylations of histone globular domain lysines also hold regulatory potential based on their potential impact on nucleosome dynamics and stability. Here we have mapped the genome-wide distribution of acetylated H3 lysine 115 (H3K115ac), a residue on the lateral surface of the nucleosomes, in mouse embryonic stem cells. We find that H3K115ac is associated with highly active promoters, especially those associated with CpG islands, and with enhancers. H3K115ac is dynamic, changing in line with gene activation during differentiation and correlated with changes in local chromatin accessibilityas assyed by ATAC-seq. Distinct from other commony studied histone acetylation marks, H3K115ac is enriched on non-canonical “fragile” nucleosomes precisely at the transcription start sites of active gene promoters and within the binding sites of pluripotency transcription factors. Surprisingly we also detect H3K115ac-marked fragile nucleosomes at sites most strongly occupied by CTCF, within the CTCF footprint and oriented relative to the CTCF motif. This unique enrichment and genomic distribution of modified fragile nucleosomes suggests a previously unappreciated role for H3K115ac in gene regulation and chromatin structure. We propose that H3K115ac is a very precise marker for identifying regulatory elements in mammalian genomes.

overall_design: Native Mnase ChIP-seq of H3K115ac on mESC chromatin fractionated on sucrose gradients


title: Dopamine Enhances Surface Glial Glycolysis via Acetylcholine and Insulin/Insulin-Like Growth Factor Signaling in Honeybee

city: Changchun

first: Miaoran

last: Zhang

state: Jilin

address: Xinmin Street

institute: Department of Physiology, College of Basic Medical Sciences, Jilin University

summary: Glycolysis plays a crucial role in maintaining neuronal functional homeostasis and is regulated by neuroendocrine signals, particularly dopamine. However, the underlying regulatory mechanisms remain poorly understood. Here, we investigate dopamine driven neuroendocrine control of glial glycolysis in honeybee through integrated metabolomics and single-cell transcriptomics. Activation of dopamine 2 receptors(D2R) via bromocriptine significantly enhanced glycolytic flux in worker bees, as evidenced by elevated glucose levels, accumulation of glycolytic intermediates, and suppression of pentose phosphate pathway metabolites. Single-cell and single-nucleus RNA sequencing revealed that acetylcholine (ACh) secreted by Kenyon cells (KCs) is a critical node in dopamine-regulated glycolysis. Bromocriptine treatment reduced ACh secretion and directly enhanced surface glial (SG) specific glycolytic gene expression, while also increasing insulin signaling from cortex glial to surface glial. Our findings uncover a dual regulatory mechanism, in which the dopamine-ACh axis coordinates with IIS signaling to orchestrate metabolic plasticity in glial through cell type-specific precision. This study provides insights into how social insects integrate neuroendocrine signals to optimize energy metabolism and highlights the role of ACh in this process.

overall_design: We employed single-nucleus RNA sequencing (snRNA-seq) using the 10x Genomics platform to investigate the effects of bromocriptine, a dopamine agonist, on the neural transcriptome of honeybee (Apis mellifera) forager brains. For this study, foraging bees were divided into two experimental groups: one treated with bromocriptine and the other with water as a control. Brains from 15 foragers per group were dissected and processed for snRNA-seq to resolve cell-type-specific transcriptional responses. This work represents the first application of single-nucleus transcriptomics to explore neuropharmacological modulation in honeybees, offering unprecedented insights into how dopaminergic signaling influences neural plasticity and foraging-related behaviors in a eusocial insect model. By comparing bromocriptine-exposed and control groups, our findings may advance understanding of conserved neuromodulatory pathways and their roles in social insect behavior

first: Peng

last: Chen

first: Xingan

last: Li


title: H3K115 marks fragile nucleosomes at regulatory sites (Sucrose Gradient fractions rep1)


title: Indigenous gut microbes modulate neural cell state and neurodegenerative disease susceptibility [mono-colonized_RNA-seq]

city: Atlanta

first: Timothy

last: Sampson

state: Georgia

address: 615 Michael St

institute: Emory University

summary: The native microbiome influences a plethora of host processes, including neuroimmune function. However, the consequences of individual gut microbes on neuroinflammatory tone remain largely unexplored. In the present dataset, we investigated the consequences of four bacterial type strains representing prevalent genera within the mammalian gut microbiome (Bacteroides thetaiotaomicron (B. theta), Clostridium celatum, Lactobacillus johnsonii, and Escherichia coli) on the transcriptional profile of CD11b+ brain myeloid cells. After 2 weeks of mono-colonization with the bacteria species of interest, it was found that each bacterial type had distinct effects on brain myeloid cell gene expression, highlighting the bacterial dependent consequences of the microbiome for neuroinflammatory outcomes.

overall_design: Germ-free DBA/2NTac were either maintained as germ-free or mono-colonized with Bacteroides thetaiotaomicron, Clostridium celatum, Lactobacillus johnsonii, or Escherichia coli for 2 weeks. Brains were then perfused with PBS and CD11b+ cells were isolated by magnetic activated cell sorting for bulk RNA-seq.

first: Lisa

last: Blackmer-Raynolds

first: Lyndsey

last: Lipson

first: Anna

last: Kozlov

first: Aimee

last: Yang

first: Emily

middle: J

last: Hill

first: Maureen

middle: M

first: Adam

last: Hamilton

first: Isabel

last: Fraccaroli

first: Sean

last: Kelly

first: Pankaj

last: Chopra

first: Jianjun

last: Chang

first: Steven

last: Sloan


title: Indigenous gut microbes modulate neural cell state and neurodegenerative disease susceptibility [snRNA-seq]

summary: The native microbiome influences a plethora of host processes, including neurological function. However, its impacts on diverse brain cell types remains poorly understood. Here, we performed single nucleus RNA sequencing on hippocampi from wildtype, germ-free mice and reveal the microbiome-dependent transcriptional landscape across all major neural cell types. We found conserved impacts on key adaptive immune and neurodegenerative transcriptional pathways, underscoring the microbiome’s contributions to disease-relevant processes. In addition, mono-colonization with Escherichia coli was found to induce a distinct adaptive immune and neurogenerative disease-associated cell state, suggesting increased disease susceptibility.

overall_design: This study consists single nucleus RNA-seq data from the hippocampus of female wildtype mice with a conventional microbiome, germ-free mice without any previous exposure to microbes, and ex-germ-free mice that were mono-colonized with Escherichia coli for either 2 or 4 weeks

middle: A


title: Single cell mRNA sequencing on esophageal cells of Krt5-CreERT2:R26SmoM2/EYFP (K5:Smo) mice untreated and treated with ibuprofen

city: Anderlecht

first: Louison

last: Descampe

address: Route de Lennik 808

institute: Université Libre de Bruxelles

summary: In our study, we used single-cell RNA sequencing to investigate the effect of ibuprofen on cell-mediated communication between esophageal epithelial cells and their microenvironment in K5:Smo mice.

overall_design: Oesophageal single cell mRNA profiles of Krt5-CreERT2:R26SmoM2/EYFP mice by deep sequencing using 10x genomic.

first: Benjamin

last: Beck


title: The tumour suppressor STAG2 cooperates with DREAM  to maintain quiescence in the urothelium [Hi-C]

first: Jaime

last: Martinez de Villarreal

address: Melchor Fernández Almagro, 3

department: Molecular Oncology Programme

institute: CNIO

summary: The maintenance of quiescence is essential for tissue homeostasis. STAG2 is one of the few genes mutated in the normal urothelium of organ donors, with mutant cells undergoing positive selection 1. STAG2 is also a major tumour suppressor gene 2–4 and its inactivation is an early event in bladder carcinogenesis 1,3. However, the mechanisms through which STAG2, a cohesin component, disrupt urothelial homeostasis remain largely unknown. Here, we show that, in normal murine urothelial cells, Stag2 inactivation disrupts differentiation programs, induces a transient cell cycle entry, and primes cells for clonal expansion under stress conditions. In addition, STAG2 loss in urothelial cells expressing mutant FGFR3 —the most important bladder cancer oncogene 5— enhances tumour formation. For the first time, we show that STAG2 co-operates with the transcriptional complex DREAM, a master regulator of quiescence 6,7, binding to common genomic sites, including genes involved in cell cycle control. STAG2 loss results in changes in the expression of DREAM targets, its composition and chromatin distribution, and in the rewiring of chromatin interactions involving DREAM binding motifs in genes critical for cell cycle entry. Our findings provide strong evidence that STAG2 loss leads to changes in 3D genome organization through a novel mechanism involving the DREAM complex, leading to the disruption of homeostatic quiescence and oncogenic sensitivity.

overall_design: To identify the effects of Stag2 inactivation on genome organization in quiescent urothelial cells, we performed Hi-C using Stag2-KO and WT quiescent urothelial organoids derived from Stag2_lox; UBC-CreERT2 mice.

first: Maria

last: Ramal

last: Martínez de Villarreal

first: Francisco X

last: Real


title: DGCR8 controls retrotransposon-derived double-stranded RNA accumulation and interferon activation

city: Castellón de la Plana

first: Guillermo

last: Peris

state: CAstellón

address: Av. Vicent Sos Baynat, s/n

department: Llenguatges i Sistemes Informàtics

institute: Universitat Jaume I

summary: The type I interferon (IFN) response is the main innate immune pathway against viruses in mammals and must be tightly regulated to stop viral spread without excessive immune reaction. Here, we show that inactivation of the double-stranded RNA (dsRNA)-binding protein DGCR8 unleashes the IFN response in human cells. Remarkably, we demonstrate that, independently of its function in miRNA biogenesis, DGCR8 prevents the accumulation of endogenous dsRNA. These dsRNAs derive from protein-coding mRNAs enriched in transposable elements (TEs), mostly Alu elements. We propose that DGCR8 binding to TE-rich mRNAs is key to resolve dsRNA structures. In the absence of DGCR8, these unresolved dsRNAs signal through the RIG-I-like signalling pathway triggering the IFN response. This mechanism may be particularly relevant to conditions such as the 22q11.2 deletion syndrome (22qDS), where DGCR8 expression is reduced. Supporting this, we show that cells derived from 22qDS patients exhibit an exacerbated type I IFN response, highlighting the importance of suppressing endogenous dsRNA accumulation to prevent unwanted immune activation.

overall_design: Data analysis from J2 dsRNA immunoprecipitation for WT PA1 cells and two different DGCR8 heterozygous clones.

first: Ana

last: Gazquez

first: Sara

last: Macias

last: Heras


title: The tumor suppressor STAG2 cooperates with DREAM  to maintain quiescence in the urothelium

overall_design: To dissect the molecular mechanisms underlying transcriptional changes upon Stag2 depletion in quiescent urothelial cells in vivo, we performed ATAC-Seq on peeled urothelium from Stag2 WT and KO mice one week after TMX administration.


title: mRNA sequencing on esophageal organoids derived from K5:Smo mice 5 days after tamoxifen injection.

summary: In our study, we used mRNA sequencing to investigate the effect of 3 days-treatment with a combination of TGFb1 and BMP with or without ibuprofen.

overall_design: mRNA profiles of esophageal organoids derived from K5:Smo mice 5 days after tamoxifen injection, treated for 72h with TGFb inhibitor / TGFb + BMP4 / TGFb + BMP4 + Ibuprofen by deep sequencing using Illumina

last: Dassy

first: Alizée

last: Vercauteren Drubbel


title: Indigenous gut microbes modulate neural cell state and neurodegenerative disease susceptibility [5xFAD_CD11b+_Bulk_RNA-seq]

first: Timothy

last: Sampson

summary: The native microbiome influences a plethora of host processes, including neurological function. We have shown that colonization by Escherichia coli induces a distinct adaptive immune and neurogenerative disease-associated cell state in wildtype mice, suggesting increased disease susceptibility. Further, E. coli exposure in the 5xFAD mouse model results in exacerbated cognitive decline and amyloid pathology, demonstrating its sufficiency to worsen Alzheimer’s disease-relevant outcomes. Here, we performed bulk RNA-seq of CD11b+ brain myeloid cells from E. coli or vehicle treated 5xFAD mice to understand how E. coli modulates neuroimmune responses in the context of amyloid pathology. We demonstrate that E. coli exposed animals have a subtle decrease in genes associated with the disease associated microglia phenotype after 1 month of enrichment, perhaps helping to explain why these animals displayed worsened outcomes.

overall_design: The present dataset consists of bulk RNA-seq samples from CD11b+ brain myeloid cells of 5xFAD mice either treated with 10^8 cfu of E. coli or vehicle control 3x a week for either 2 weeks or one month.

first: Lisa

last: Blackmer-Raynolds

first: Lyndsey

last: Lipson

first: Anna

last: Kozlov

first: Aimee

last: Yang

first: Emily

last: Hill

last: Hamilton


title: The tumour suppressor STAG2 cooperates with DREAM  to maintain quiescence in the urothelium [RNAseq_urothelium]

last: Martinez de Villarreal

summary: The maintenance of quiescence is essential for tissue homeostasis. STAG2 is one of the few genes mutated in the normal urothelium of organ donors, with mutant cells undergoing positive selection 1. STAG2 is also a major tumour suppressor gene 2-4 and its inactivation is an early event in bladder carcinogenesis 1,3. However, the mechanisms through which STAG2, a cohesin component, disrupt urothelial homeostasis remain largely unknown. Here, we show that, in normal murine urothelial cells, Stag2 inactivation disrupts differentiation programs, induces a transient cell cycle entry, and primes cells for clonal expansion under stress conditions. In addition, STAG2 loss in urothelial cells expressing mutant FGFR3 -the most important bladder cancer oncogene 5- enhances tumour formation. For the first time, we show that STAG2 co-operates with the transcriptional complex DREAM, a master regulator of quiescence 6,7, binding to common genomic sites, including genes involved in cell cycle control. STAG2 loss results in changes in the expression of DREAM targets, its composition and chromatin distribution, and in the rewiring of chromatin interactions involving DREAM binding motifs in genes critical for cell cycle entry. Our findings provide strong evidence that STAG2 loss leads to changes in 3D genome organization through a novel mechanism involving the DREAM complex, leading to the disruption of homeostatic quiescence and oncogenic sensitivity.

overall_design: To identify the molecular effects of Stag2 inactivation, we profiled the transcriptome of peeled urothelium from Stag2 WT and KO mice one week and one month after TMX administration.


title: The tumour suppressor STAG2 cooperates with DREAM  to maintain quiescence in the urothelium [ChIP-Seq_NU1]

overall_design: To elucidate the genomic mechanisms involved, we turned to the spontaneously immortalized murine NU1 cells. We  profiled the genome-wide distribution of STAG2, STAG1, and CTCF in proliferative and quiescent NU1 cells using ChIP-Seq.

last: Ramal


title: Purkinje cell intrinsic activity shapes cerebellar development and function

city: Rotterdam

first: Catarina

last: Osorio

address: Westzeedijk 353

department: Neuroscience

institute: Erasmus Medical Center Rotterdam

summary: The emergence of functional cerebellar circuits is heavily influenced by activity-dependent processes. However, the contribution of intrinsic Purkinje cell activity to cerebellar development remains less understood. Here, we demonstrate that before synaptic networks mature, Purkinje cell intrinsic activity is essential for regulating dendritic growth, establishing connections with cerebellar nuclei, and ensuring proper cerebellar function. Disrupting this activity during the postnatal period impairs motor function, with earlier perturbations causing more severe deficits. Importantly, only early developmental disruptions lead to pronounced defects in cellular morphology, highlighting key temporal windows for dendritic growth and maturation. Transcriptomic analyses reveal that early intrinsic activity drives the expression of activity-dependent genes, including Prkcg and Car8, which are essential for dendritic development. Our findings emphasize the importance of temporally regulated intrinsic activity in Purkinje cells in guiding cerebellar circuit development, providing a potential unifying mechanism underlying cerebellum-associated disorders.

overall_design: Purkinje cells were collected from either P7 Pcp2+/+;Kir2.1 (control littermates) or P7  Pcp2cre/+;Kir2.1 experimental mice (both in C57Bl6/J background). Sagittal slices of vermal cerebellar tissue were transferred into a recording chamber and maintained at 34C under continuous perfusion with equilibrated aCSF. For P7 Pcp2cre/+;Kir2.1 mice, Purkinje cells were selected based on their expression of Kir2.1-mCherry. Neurons were extracted into a glass pipette using negative pressure and 50 cells were sampled across the cerebellar cortex. For each genotype, eight biological samples were used for RNA sequencing. Cells were collected in a mild hypotonic lysis buffer composed of 0.2% Triton-X and 2U/µl of RNAse inhibitor. Isolated cells were kept on ice during the collection process or immediately stored at -80°C for RNA extraction. Bulk RNAseq was performed for the eight biological samples.

last: Osório

first: Martijn

last: Schonewille


title: mRNA sequencing on esophageal cells of Krt5-CreERT2:R26SmoM2/EYFP (K5:Smo) mice, untreated and treated with ibuprofen

first: Louison

last: Descampe

summary: In our study, we used mRNA sequencing to investigate the effect of ibuprofen on the transcriptome of esophageal epithelial cells of K5:Smo mice.

overall_design: Oesophageal mRNA profiles of Krt5-CreERT2:R26SmoM2/EYFP mice, 12 weeks after tamoxifen administration, untreated and treated with ibuprofen by deep sequencing using Illumina

last: Beck


title: Cerebellar microglia-derived IL-17A compensates for autism-related deficits [cerebellar crus 1]

city: Nanjing

first: Jun-Yi

last: Chen

state: Jiangsu

address: Xianlin Campus, Nanjing University, No.163 Xianlin Avenue, Qixia District

institute: Nanjing University

summary: Interleukin-17 (IL-17) is a pleiotropic cytokine produced mainly by peripheral Th17 cells. Yet, brain functions of IL-17 derived from central nervous cells remain poorly understood. Here, we find an aberrant IL-17A signaling in the cerebellum of Fmr1-KO mice, a well-established genetic model for autism spectrum disorder (ASD). Cerebellar IL-17A, derived exclusively from microglia, is essential for the regulation of social behaviors by maintaining neuronal excitability and selectively suppressing inhibitory neurotransmission of Purkinje cells (PCs) in the cerebellar Crus I, a brain region critically involved in social cognition. Specific downregulation of IL-17 receptor-mediated signaling in cerebellar PCs recapitulates ASD-like social deficits and repetitive behaviors. Notably, both direct administration of IL-17A and induction of IL-17A release from cerebellar microglia by poly(I:C) effectively restore PC excitability and ameliorate ASD-like symptoms. The findings uncover an indispensable role of microglia-derived IL-17A for cerebellar social processing and suggest potential therapeutic strategies targeting IL-17A signaling for ASD.

overall_design: Comparative gene expression profiling analysis of RNA-seq data in cerebellar crus 1 for the vehicle and poly(I:C) treated Fmr1 knock out mice and FVB background mice.

first: Shu-Tao

last: Xie

first: Jun

last: Yin

first: Xiao-Yang

last: Zhang

first: Jing-Ning

last: Zhu


title: The tumour suppressor STAG2 cooperates with DREAM  to maintain quiescence in the urothelium [CUT&Run]

city: Madrid

first: Jaime

overall_design: We performed Cut&Run for endogenous STAG2, LIN54 and p130 using urothelial cells from WT and Stag2-KO peeled bladders one week post-recombination.

first: Maria

last: Martínez de Villarreal

first: Francisco X

last: Real


title: mRNA sequencing on esophageal organoids derived from wild-type mice

summary: In our study, we used mRNA sequencing to investigate the effect of 3 days-treatment with TGFb1, BMP4 alone or in combination on the squamous and columnar differentiation.

overall_design: mRNA profiles of esophageal organoids derived from wild-type mice treated for 72h with TGFb inhibitor / BMP4 / TGFb / TGFb + BMP4 by deep sequencing using Illumina

first: Benjamin

last: Dassy

first: Alizée

last: Vercauteren Drubbel


title: Cerebellar microglia-derived IL-17A compensates for autism-related deficits [purified cerebellar microglia]

overall_design: Comparative gene expression profiling analysis of RNA-seq data in purified microlias from cerebellum for the vehicle and poly(I:C) treated Fmr1 knock out mice.


title: Transcriptional plasticity of stromal cells amplifies their differentiation efficiency in vitro

city: Odense

first: Alexander

last: Rauch

address: Campusvej 55

department: Department of Clinical Research

country: Denmark

institute: University of Southern Denmark and Odense University Hospital

summary: Human bone marrow-derived stromal cells (also termed mesenchymal stem cells or MSCs) are progenitors capable of differentiating into bone-forming osteoblasts and fat-storing adipocytes. Due to the loss of bone mass being associated with increased marrow fat, the trans-differentiation of osteoblasts into adipocytes has been hypothesized as a contributor to osteoporotic bone loss and fragility. Reprogramming of transcriptional networks is a prerequisite for cellular differentiation, however, to which extent cell-type specific transcriptional networks modulate cellular plasticity within stromal cells remains unknown. In this study, we performed global gene expression analysis at the single cell level in immortalized human stromal cells from bone marrow (hBMSC-TERT4) that were repeatedly exposed to osteogenic and adipogenic inducers in vitro. Surprisingly, cell-type specific gene networks are not suppressive but rather promote the development of an opposing phenotype; for example, osteoblast differentiation of adipogenic pre-stimulated stromal cells is enhanced compared to undifferentiated ones. This is supported by the presence of cells simultaneously showing an osteogenic and adipogenic phenotype highlighting a strong molecular plasticity of transcriptional networks in stromal cells. These observations provide a strong molecular support for the notion of not only progenitor speciation but also the plasticity of differentiated cells contributing to the balance of bone mass and marrow fat content.

overall_design: Single cell and bulk RNA-expression profiles were determined in immortalized human bone marrow-derived stromal cells that were exposed to osteogenic or adipogenic inducers as well as to sequential treatments of both differnetiation cocktails to obtain cells differentiating towards the osteogenic or adipogenic lineage, either directly from undifferentiated cells or from intermediate states that have been previsouly committed to the opposing lineage.

first: Ali

last: Jamil


title: The tumour suppressor STAG2 cooperates with DREAM  to maintain quiescence in the urothelium

last: Martinez de Villarreal

summary: The maintenance of quiescence is essential for tissue homeostasis. STAG2 is one of the few genes mutated in the normal urothelium of organ donors, with mutant cells undergoing positive selection 1. STAG2 is also a major tumour suppressor gene 2-4 and its inactivation is an early event in bladder carcinogenesis 1,3. However, the mechanisms through which STAG2, a cohesin component, disrupt urothelial homeostasis remain largely unknown. Here, we show that, in normal murine urothelial cells, Stag2 inactivation disrupts differentiation programs, induces a transient cell cycle entry, and primes cells for clonal expansion under stress conditions. In addition, STAG2 loss in urothelial cells expressing mutant FGFR3  - the most important bladder cancer oncogene 5 -  enhances tumour formation. For the first time, we show that STAG2 co-operates with the transcriptional complex DREAM, a master regulator of quiescence 6,7, binding to common genomic sites, including genes involved in cell cycle control. STAG2 loss results in changes in the expression of DREAM targets, its composition and chromatin distribution, and in the rewiring of chromatin interactions involving DREAM binding motifs in genes critical for cell cycle entry. Our findings provide strong evidence that STAG2 loss leads to changes in 3D genome organization through a novel mechanism involving the DREAM complex, leading to the disruption of homeostatic quiescence and oncogenic sensitivity.

overall_design: To elucidate the genomic mechanisms involved, we turned to the spontaneously immortalized murine NU1 cells. Stag2 was effectively knocked down (KD) in NU1 cells using lentiviral shRNAs (Fig. 3e), in proliferative or quiescent conditions and the transcriptome was analyzed

last: Ramal


title: Tumor-intrinsic ETV5 Expression Promotes MDSCs-mediated Immune Evasion and Immune Checkpoint Inhibitor Resistance

city: guangzhou

first: mengxing

last: huang

address: huangpu

institute: guangdong

summary: Immunotherapy remains ineffective for a wide variety of solid tumors due to the existence of tumor immune evasion. Patients with tumors expressing high levels of ETV5 respond poorly to immunotherapy, but the understanding of its impact on immune evasion is limited. Here, we reveal that tumor-intrinsic ETV5 drives immune evasion and immune checkpoint inhibitor (ICI) resistance by enhancing the expansion and recruitment of MDSCs. Knockdown of ETV5 in tumor cells reduces the generation of MDSCs from myeloid progenitors and their accumulation in the tumor microenvironment, leading to enhanced anti-tumor response presented by increased T cell infiltration, proliferation and reduced exhaustion. Mechanistically, ETV5 binds to JAK2 protein, facilitates its dimerization and elevates its phosphorylation status. Consequently, this promotes the phosphorylation of STAT3, which activates the transcription of CCL2, augmenting the recruitment of MDSCs. Finally, ETV5 deficiency reduces MDSCs and enriches anticancer T lymphocytes, thereby improving ICI efficacy in mice. Our findings shed light on the crucial role of tumor-intrinsic ETV5 in facilitating immune evasion and its fundamental mechanism. Furthermore, they offer a novel immunotherapy strategy targeting ETV5 for the treatment of solid tumors.

overall_design: RNA-seq of wildtype 4T1 cells lines and their knockdown ETV5(shRNA)

first: Tingting

first: Mengxing

last: Huang


title: Long-term post-ovariectomy mouse model recapitulates hypothalamic transcriptomic changes observed during the menopausal transition in women

first: Victor

last: Navarro

address: 221 Longwood Ave

department: Division of Endocrinology

institute: Brigham and Women's Hospital

summary:
Menopause significantly impacts women's health, yet hypothalamic changes during this transition
remain poorly understood. We analyzed gene expression in human hypothalamic samples across
menopausal transition, revealing significant changes in inflammatory pathways, KNDy neuron
signaling, and thermoregulatory genes. This analysis also identified novel central markers of
menopause, including AKAP5 and CDKN1A (p21). To further investigate these changes, we
developed a novel mouse model based on long-term (4 months) post-ovariectomy (OVX) that
mimics the gonadotropin and temperature fluctuations of menopausal transition. Remarkably, the
posterior hypothalamus of 4-month post-OVX mice closely mirrored the transcriptional changes
observed in women at the late peri-/early post-menopausal age range (ages 51-55). Both species
exhibited increased inflammatory signaling and glial activation, alongside altered KNDy neuron
activity. Our findings provide new insights into the central mechanisms of menopausal symptoms
and offer a valuable preclinical model for testing interventions.

overall_design: RNA-seq of the posterior hypothalamus and the preoptic area of sham, 14 days post-, and 4 months post-ovariectomy (OVX) samples

first: Jordana

last: Bloom


title: single nucleus RNA sequencing of cells from across the whole mouse brain in a mouse model of ALS

city: Seattle

first: Nicole

last: Liachko

address: 1660 Columbian Way S.

institute: VA Puget Sound Health Care System

summary: The mouse brain is a complex tissue with many cell types including distinct populations of neurons, astrocytes, and microglia.  We examined cell type specific gene expression in cells across the whole brain of rNLS8 mice that express doxycycline suppressible human TDP-43 (hTDP-43) with a defective nuclear localization signal (hTDP-43ΔNLS) regulated by the NEFH promoter, at a timepoint when they are strongly symptomatic but preceeding robust neurodegeneration.

overall_design: For this study we employed transgenic mice carrying a transgene enabling inducible neuronal expression of human TDP-43 with a deletion of its nuclear localization signal (rNLS8 mice) as a model of ALS  and FTLD-TDP.  The transgene was induced in adult mice, and brains were harvested after 4 weeks, when the mice were strongly symptomatic.  Brains were split down the midline, and whole half-brains were used for single nucleus RNA sequencing (snRNAseq).  Cell-type specific changes in gene expression were observed comparing control and rNLS8 mice.


title: H3K115 marks fragile nucleosomes at regulatory sites [ChIP-seq]

first: Yatendra

last: Kumar

summary: Acetylation of lysine residues in the tail domain of histone H3 at active regulatory elements are well characterised, but the less studied acetylations of histone globular domain lysines also hold regulatory potential based on their potential impact on nucleosome dynamics and stability. Here we have mapped the genome-wide distribution of acetylated H3 lysine 115 (H3K115ac), a residue on the lateral surface of the nucleosomes, in mouse embryonic stem cells. We find that H3K115ac is associated with highly active promoters, especially those associated with CpG islands, and with enhancers. H3K115ac is dynamic, changing in line with gene activation during differentiation and correlated with changes in local chromatin accessibilityas assyed by ATAC-seq. Distinct from other commony studied histone acetylation marks, H3K115ac is enriched on non-canonical “fragile” nucleosomes precisely at the transcription start sites of active gene promoters and within the binding sites of pluripotency transcription factors. Surprisingly we also detect H3K115ac-marked fragile nucleosomes at sites most strongly occupied by CTCF, within the CTCF footprint and oriented relative to the CTCF motif. This unique enrichment and genomic distribution of modified fragile nucleosomes suggests a previously unappreciated role for H3K115ac in gene regulation and chromatin structure. We propose that H3K115ac is a very precise marker for identifying regulatory elements in mammalian genomes.

overall_design: Native MNase ChIP-seq employed to explore globular and tail-domain acetyl marks in histone H3 in mouse embryonic cells and neural progenitors.


title: Succinate supplementation ameliorates musculoskeletal defects caused by PLOD3 mutations in a BCARD syndrome model

status: Public on Feb 02 2026

city: Nashville

first: Ela

last: Knapik

state: TN

address: 2215 Garland Ave.

department: Medicine

institute: Vanderbilt University Medical Center

summary: Background: BCARD syndrome is a rare complex connective tissue disorder associated with variants in the PLOD3 gene, presenting with musculoskeletal, vascular, and sensory deficits. The role of PLOD3 in post-translational modifications of collagens has been established. However, limited treatment options exist to correct connective tissue deficits linked to PLOD3, largely due to sparse knowledge of cellular and molecular mechanisms driving phenotypic changes. Methods: To explain the mechanisms of PLOD3 genotype-phenotype associations, we have used clinical data, molecular assays in patient-derived fibroblasts, perturbation experiments in zebrafish models, cellular and molecular experiments, and unbiased genome- and transcriptome-wide approaches. Results: We show that wild-type human PLOD3 mRNA partially rescued musculoskeletal, vascular, and brain phenotypes in zebrafish plod3 mutants, while clinically identified variants had only a limited effect, validating the pathogenicity of the variants and the high conservation of PLOD3 function across vertebrates.  We found that, at the molecular level, organ systems selectively upregulated the PERK pathway of the Unfolded Protein Response and subsequently activated autophagy as an adaptive response to an extracellular matrix (ECM) protein backlog; however, autophagy inhibitors did not rescue the plod3 mutant phenotypes. Bulk RNA-seq analysis of plod3 mutants revealed downregulation of genes in metabolic pathways, including the electron transport chain and the tricarboxylic acid (TCA) cycle, consistent with structural defects in electron micrographs of mitochondria. Search of Drug Repurposing Data Portals identified a dietary supplement, succinate, to be associated with PLOD3 and 25 additional genes, involved in the TCA cycle and collagen synthetic pathways. We showed that treatment with succinate ameliorated BCARD features, i.e., musculoskeletal defects, and restored reduced expression of TCA cycle genes in the zebrafish model. Conclusions: Our data indicate that the interaction between ECM synthesis and mitochondrial energy metabolism offers an entry point for novel therapies to prevent complex connective tissue decline in BCARD and, potentially, in other rare and common musculoskeletal disorders and conditions such as aging, cancer, or injury. Moreover, the genetic models developed here, and succinate, should be valuable tools in future studies of the underlying mechanisms of the BCARD extensive medical phenome.

overall_design: Bulk RNA-seq of whole larvae AB zebrafish and plod3 KO mgt zebrafish samples at 4 days post fertilization.

first: Dharmendra

last: Choudhary

first: Gokhan

last: Unlu

first: Taylor

last: Nagai

first: David

middle: B

last: Melville

first: Alexandra

last: Scalici

first: Mais

middle: O

last: Hashem

first: Dylan

last: Ritter

first: Georg

last: Schmidt

first: Cory

last: Guthrie

first: Eric

last: Gamazon

first: Fowzan

last: Alkuraya

first: Nancy

last: Cox

middle: W


title: Adaptive ER stress promotes mitochondrial remodelling and longevity through PERK-dependent MERCS assembly

city: Galway City

first: Jose

middle: Carlos

last: Casas-Martinez

state: Galway County

address: Human Biology Building, University Road

department: Physiology

country: Ireland

institute: University of Galway

summary: The transfer of information and metabolites between the mitochondria and the endoplasmic reticulum (ER) is mediated by mitochondria-ER contact sites (MERCS), allowing adaptations in response to changes in cellular homeostasis. MERCS are dynamic structures essential for maintaining cell homeostasis through the modulation of calcium transfer, redox signalling, lipid transfer, autophagy and mitochondrial dynamics. Under stress conditions such as ER protein misfolding, the Unfolded Protein Response (UPRER) mediates PERK and IRE1 activation, both of which localise at MERCS. Adaptive UPRER signalling enhances mitochondrial function and calcium import, whereas maladaptive responses lead to excessive calcium influx and apoptosis. In this study, induction of mild acute ER stress with tunicamycin (TM) in myoblasts promoted myogenesis that required PERK for increased MERCS assembly, mitochondrial turnover and function. Similarly, treatment of C. elegans embryos with an acute low concentration of TM, promoted an extension in lifespan and health-span. The adaptive ER stress response following a low dose of TM in both myoblasts and C. elegans, increased MERCS assembly and activated autophagy machinery, ultimately promoting an increase in mitochondrial remodelling. However, these beneficial adaptations were dependent on the developmental stage, as treatment of myotubes or adult C. elegans resulted in a maladaptive response. In both models the adaptations to UPRER activation were dependent on PERK signalling and its interaction with the UPRmt. The results demonstrate PERK is required for the increased mitochondrial ER communication in response to adaptive UPR signalling, promoting mitochondrial remodelling and improved physiological function.

overall_design: RNA-seq profiling of wildtype Caenorhabditis elegans Day1 adults that were treated with tunicamycin 1.25 μg/ml at embryonic stage (EMBRYO group) or at L4 stage and their matched controls.

middle: C

first: Qin

last: Xia

first: Penglin

last: Li

first: Maria

last: Borja-Gonzalez

first: Antonio

last: Miranda-Vizuete

first: Emma

last: McDermott

first: Peter

last: Dockery

first: Leo

middle: R

last: Quinlan

first: Katarzyna

last: Goljanek-Whysall

first: Afshin

last: Samali

first: Brian

last: McDonagh