title: Monocytes defined by platelet interactions and oxidative stress signaling underlie HIV-associated atherosclerosis

city: Rochester

first: Ruoqiao

last: Wang

state: NY

address: 601 Elmwood Avenue

department: Biomedical Genetics and Genomics

institute: University of Rochester Medical Center

summary: Background: Monocytes contribute to atherosclerosis (AS) by migrating into inflamed endothelium and differentiating into foam cells. In people living with HIV (PLWH), chronic inflammation increases AS risk, yet the role of specific monocyte clusters remains unclear. We investigated how distinct monocyte populations contribute to vascular pathology in early HIV-associated AS. Methods: We profiled 123,965 circulating monocytes using single-cell RNA-seq and integrated plasma microparticle proteomics in 32 individuals stratified by HIV and AS status. Supervised learning identified cluster- and disease-specific signatures, validated by platelet-monocyte co-cultures, RT-qPCR, bulk RNA-seq, flow cytometry and ELISA. Results: Seven monocyte clusters were identified, including a subset characterized by platelet–monocyte complexes (PMCs). Bulk RNA-seq of platelet–monocyte co-cultures revealed platelet-driven upregulation of genes involved in inflammation, lipid metabolism, oxidative stress, and endothelial adhesion. PMC-derived macrophages secreted higher levels of TGF-β and IL-10, displayed decreased CD14 and increased CD80/CD86 while retaining CD36, and promoted endothelial-to-mesenchymal transition (decreased CDH5, PECAM1; increased S100A4) and vascular inflammation (increased ICAM1, VCAM and IL-6, CCL2 secretion). Additionally, CD14+ monocytes from HIV+AS- and HIV+AS+ groups showed enhanced ROS-NRF2 pathway activities, supported by increased basal and H2O2-induced p90RSK phosphorylation, indicating oxidative stress priming. Conclusions: Two monocyte clusters contribute independently to vascular immune dysregulation in PLWH. PMC-derived macrophages promote endothelial dysfunction while adopting a profibrotic cytokine profile. CD14+ monocytes show heightened oxidative signaling and stress responses, consistent with vascular activation. Together, these mechanisms may accelerate AS development in HIV, even in the absence of traditional cardiovascular risk factors.

overall_design: Fresh blood from an ongoing URMC cohort was used to isolate monocytes and platelets for in vitro coculture experiments. Monocytes were cultured alone or cocultured with collagen-activated platelets at monocyte-to-platelet ratios of 1:100 and harvested at 24 hours (n=7) and 6 days (n=8). After coculture, monocytes were re-isolated and processed for RNA extraction to evaluate platelet-induced transcriptional changes.

first: Zachary

last: Boodoo

first: Karli

last: Sutton

first: Jun-ichi

last: Abe

first: Sanjay

middle: B

last: Maggirwa

first: Giovanni

last: Schifitto

first: Meera

middle: V

last: Singh

first: Juilee

last: Thakar


title: Viral Mimicry may Help Explain Immunogenic Cell Death

status: Public on Feb 17 2026

city: Austin

first: Jonathan

last: Sessler

state: Texas

address: 100 E 24th St, Austin, TX

country: USA

institute: University of Texas Austin

type: Expression profiling by high throughput sequencing

summary: Viral mimicry may be an underappreciated contributor to chemotherapeutic potency in animal models and patients. This hypothesis is based on studies of a bis-Au(I)-NHC complex that was found to generate a strong anti-tumor immune response in vivo in two different challenge studies using an iKAP colorectal cancer mouse model. RNA profiling of treated cells revealed the stimulation of genes that overlap with those upregulated during a viral infection. The bis-Au(I)-NHC complex generates reactive oxygen species (ROS) through the simultaneous redox cycling of the naphthoquinone moiety and inhibition of thioredoxin reductase (TrxR2) with Au(I). This ROS increase causes endoplasmic reticulum stress, activation of the unfolded protein response pathway and upregulation of Ifih1, a gene that encodes for the viral dsRNA sensor MDA5. Activation of MDA5 triggers a strong type I interferon response and expression of chemokine ligand 10 (CXCL10) that can recruit immune cells to the treated tumor in a manner analogous to immune responses during viral infection. This proposed mechanism bridges the gap between cytotoxicity and the innate and adaptive immune responses. We suggest viral mimicry may be a key driver of chemotherapy potency in animals and an important determinant of positive outcomes in cancer patients.

overall_design: RNA seq profiling of iKAP cells treated with either compound 1, oxaliplatin or auranofin vs  untreated.

first: Matthew

middle: S

last: Levine

first: Jiexi

last: Li

first: Lauren I

middle: R

last: Ehrlich

first: Ronald

middle: A

last: DePinho

first: Brent

last: Iverson

middle: L


title: The transcriptional repressor Ssn6 modulates phase separation to regulate fungal gene expression

city: Providence

first: Corey

last: Frazer

state: Rhode Island

address: 171 Meeting Street, Rm573 BioMed GG

department: Molecular Microbiology and Immunology

institute: Brown University

summary: The transcriptional regulation of cell fate plays a central role in eukaryotic cell differentiation. In the human fungal pathogen Candida albicans, the white-to-opaque switch is controlled by a network of eight transcription factors (TFs). These include Ssn6, a negative regulator of the opaque state that can function with its co-repressor Tup1, and together these form a global repressor complex that is conserved from yeast to mammals. Here, we evaluated the roles of four Ssn6 domains (N, TPR, M, and CTD) in white-opaque switching. Loss of the prion-like N or M domains had limited effects on Ssn6 phenotypes. In contrast, the TPR (tetratricopeptide repeat) domain was critical for function, consistent with this domain mediating interactions with Tup1 and DNA-binding TFs. The intrinsically disordered C-terminal domain (CTD) showed complex roles; deletion of this domain increased Ssn6 activity while substitution of acidic residues within this region abolished Ssn6 function. Notably, these phenotypes were linked to the phase separation capacity of Ssn6, as changes to the TPR or CTD altered the properties of Ssn6 condensates in human U2OS cells. Experiments using purified Ssn6 (+/-Tup1) demonstrated that this protein is recruited into condensates formed by other white-opaque-regulating TFs and alters condensate properties in a TPR- and CTD-dependent manner. Together, these observations reveal how individual Ssn6 domains can modulate the phase separation properties of DNA-binding TFs and thereby regulate gene expression and cell fate.

overall_design: Exploration of global gene expression changes in Candida albicans where structured and unstructured domains of SSN6 have been deleted.

first: Maureen

last: Dowell

first: Mae

middle: I

last: Staples

first: Richard

middle: J

last: Bennett


title: RNA-seq of Human nasopharyngeal carcinoma cells in BALF2-LR and BALF2-HR overexpress group

city: Changsha

first: Wei

last: Xiong

state: Hunan

address: 110 Xiangya Road

department: Cancer Research Institute

country: China

institute: Central South University

summary: To investigate the biological function of EBV BALF2-HR in NPC pathogenesis, we constructed overexpression vectors for BALF2-HR and BALF2-LR (used as a control) and transfected them into the EBV-negative NPC cell line HK1 [Fig. S1D]. Differential gene expression analysis, conducted using RNA sequencing (RNA-seq)


title: High-efficiency small-molecule controlled base editing for in vivo cancer functional genomics

city: Philadelphia

first: Diqiu

last: Ren

state: PA

address: 421 Curie Blvd

department: Cancer Biology

institute: University of Pennsylvania

summary: Cancer functional genomics using CRISPR-base editors (BEs) to alter targeted DNA bases within genes of interest holds great promise for molecular characterization and new target discovery. However, traditional BEs, utilizing intact DNA deaminases as mutators, often suffer from limitations given limited control and nonspecific toxicities. These challenges can dampen variant phenotype strength and pose significant barriers to in vivo screening. Here, we developed a small molecule-controllable platform using split-engineered BEs (seBEs) that enables identification of critical residues in cancer targets for in vivo functional genomics screens. By placing deaminase activity under small molecule control, seBE significantly reduced cellular toxicity, and newly enabled robust and controllable functional genomics screens. High-density seBE genetic screens using ~11,000 sgRNAs in vitro and ~ 3700 sgRNAs in vivo, reveal known and previously unknown loss-of-function and dominant negative mutations in cancer therapeutic targets. A deeper tiling seBE screen against ADAR1, a key mediator in cancer immunotherapy, reveals critical residues within functional domains that show no phenotype in vitro, but distinctively elicit non-cell-autonomous cancer dependencies in vivo. Overall, our seBE platform offers a generalizable, controllable, and highly efficient method to systematically identify key residues in cancer functional genomics.

overall_design: To further assess possible mechanisms for BE-related toxicity related to effects on gene expression, RNA-seq analysis was performed on cells lentivirally transduced with either nCas9, intact BE with catalytic mutation of the DNA deaminase, intact BE with or without Rap, or seBE with or without Rap.


title: Unbalanced chromatin binding of Polycomb complexes drives neurodevelopmental disorders [snMultiome]

city: Miami

first: Rodrigo

last: Lucena Borges

state: Florida

address: 1501 NW 10th Avenue

department: Department of Human Genetics

institute: Sylvester Comprehensive Cancer Center

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Heterozygous de novo missense mutations in genes encoding Polycomb-group (PcG) proteins can cause diverse neurodevelopmental disorders (NDDs), but the underlying mechanisms are not yet understood. Here, we identified novel mutations in the two E3-ligases of the Polycomb Repressive complex 1 (PRC1), RING1 and RNF2, in individuals with NDDs and uncover distinct mechanisms by which PRC1 activity can be compromised. Building on this, and as a proof of concept, we generated embryonic stem cells (ESCs) and a novel mouse model carrying a heterozygous Rnf2 allele with a mutation that produces a deleterious Ring1bR70H variant. This variant causes a cell fate change in neuroprecursors (NPCs) towards the non-neuronal lineages glial and microglia. Allele-specific profiling revealed that Ring1bR70H integrates into canonical PRC1, disrupting the balance of PRC1 complexes by displacing variant PRC1 from chromatin, resulting in PcG target genes upregulation. In mutant NPCs, we uncover an aberrant retention of PcG and chromatin compaction at key NPC pioneer factors and Wnt signaling genes. Critically, a heterozygous Rnf2 mutation in mice is sufficient to disrupt neural connectivity and structural organization in key brain regions, including the medial prefrontal cortex and hippocampus. Our findings establish Rnf2 as essential for neurodevelopmental integrity and brain function, shedding light on how PRC1 dysfunction contributes to NDDs.

overall_design: Mutant (R70H) and WT snMultiome(ATAC+RNA)-seq from mus musculus pre-frontal cortex and hippocamus regions of the brain.

first: Gretter

last: Gonzalez

first: Harikumar

last: Arigela

first: Yingyu

last: Huang

first: Lucas

middle: D

last: Caeiro

first: Nikolai

last: Fattakhov

first: Stefano

last: Lepore

first: Liliana

last: Garcia-Martinez

first: Matea

last: Maurice

first: Pushti

last: Mehta

first: Emily

last: Park

first: Kailynn

last: MacGillivray

first: Jevithen

last: Nehru

last: Chau

first: Maria

middle: C

first: Clemer

last: Abad

first: Alicia

last: Bilbao-Martinez

first: Fabiola

last: Monteiro

first: Xi

last: Luo

first: Song

last: Tan

first: Daniel

last: Bilbao

first: Simone

last: Sidoli

first: Bruno

last: Di Stefano

first: Katherina

last: Walz

first: Arneet

last: Saltzman

first: Ramiro

middle: E

last: Verdun

first: Ramin

last: Shiekhattar

first: Lluis

last: Morey


title: Pigs lacking Natural Killer T cells have altered cellular responses to influenza

city: Columbia

first: John

last: Driver

state: MO

address: 1201 Rollins Street

institute: University of Missouri

summary: It is increasingly recognized that innate T cells such as natural killer T (NKT) cells, mucosal associated invariant T (MAIT) cells, and gd T cells play an important role in shaping adaptive immune responses following influenza infection or vaccination. This is largely through the multiple cytokines these cells rapidly release upon activation, which have downstream effects on the scope and magnitude of virus-specific T and B cells, and antibodies which form. Here, we examined the contribution of NKT cells to this process using pigs, which are considered a highly translational model of human influenza infection. CD1D-expressing and CD1D-deficient pigs that respectively possess and lack NKT cells were infected with the swine influenza virus H3N2 A/Swine/Colorado/23619/1999 (CO99) with or without prior mucosal immunization with a recombinant H3N2 A/Swine/Texas/4199-2/1998 (TX98) modified live vaccine encoding a truncated NS1 protein (TX98ΔNS1). Vaccination reduced virus load and lung pathology by similar amounts in both genotypes. However, NKT cell status had a significant impact on the underlying immune response, which manifested in the single cell transcriptomes of lung cells, rate of virus-specific T cell accumulation, distribution of T cells in lung tissue, and ratio of virus-specific IgG subclasses. Additionally, a single cell TCR and BCR sequencing analysis found higher numbers of expanded T and B cell clones in NKT cell-deficient versus -intact pigs, some of which are potential IAV-reactive clones. Collectively, our results indicate that NKT cells play an influential role in coordinating the adaptive immune response to influenza, particularly in restraining cellular immunity during peak infection. Although these changes did not the disease course in the current investigation, they are likely to be of significance in other settings.

overall_design: On day 0, CD1D-/- and CD1D-/+ pigs were intranasally vaccinated with 106 TCID50 of TX98 NS1Δ126 using an atomization device (MAD Nasal™, Teleflex, Morrisville, NC, USA). At 21 DPV [0 days post-challenge (0 DPC)] ,  CD1D-/- and CD1D-/+ pigs were intratracheally challenged with 106 median (50%) of tissue culture infectious dose (TCID50) of CO99 and monitored for 5 days. At 5 DPC (26 DPV), infected pigs were euthanized


title: Activations of transposon elements are associated with onset of Fragile-X disorders

city: Kansas City

first: Huzaifa

last: Hassan

institute: Stowers Institute for Medical Research

summary: We found the modifications of specific transposon elements-derived genes in FXD patients by RNA-sequencing.

overall_design: We analyzed mRNA in 8 kinds of LCLs treated with or without hypoxia.

first: Tamaki

last: Suganuma

first: Madelaine

last: Gogol

first: Jerry

last: Workman


title: The SMARCA4 subunit of SWI/SNF prevents genome instability at G quadruplexes

city: London

first: Jessica

last: Downs

address: 237 Fulham Road

country: United Kingdom

institute: The Institute of Cancer Research

summary: G-quadruplex (G4) structures are secondary structures that can form in guanine-rich single stranded DNA sequences. These play important roles in biological processes such as regulation of gene expression but can also pose challenges to DNA replication and lead to genome instability. The SMARCA4 (BRG1) subunit of the SWI/SNF chromatin remodelling complexes has been identified as a G4 binding protein, and evidence suggests that this interaction can promote SWI/SNF-dependent gene expression. SMARCA4 is frequently misregulated in cancer, where genome instability is common, but whether there is an impact of SMARCA4 on G4 stability was not known. Here, we show that SMARCA4 prevents genome instability at G4s. Mapping unrepaired DNA breaks reveals that these preferentially co-localise with G4 forming structures in SMARCA4-deficient cells. Moreover, using whole genome sequencing approaches, we find that misrepair events in SMARCA4 deficient cells are more likely to map to G4 forming sequences. Consistent with this, SMARCA4 deficient cells show sensitivity to the G4 ligand pyridostatin and defective pyridostatin-induced DNA damage responses. Notably, similar patterns of G4-associated mutations were found in patients with SMARCA4-mutant tumours when compared with control patient groups. These findings suggest that SMARCA4 plays a crucial role in maintaining stability at G4 motifs. This insight provides valuable information about the functional significance of G4 structures and their interaction with SMARCA4, particularly in the context of cancer.

overall_design: Assay for Transposase-Acessible Chromatin by Sequencing (ATAC-seq) in RPE1 cells

first: Lillian

last: Wu

first: Alison

last: Harrod


title: Spatial transcriptomics reveals distinct immune microenvironment characteristics between intestinal-type gastric cancer and paired normal gastric mucosa.

city: Nanjing

first: Qingyuan

last: Wang

state: Jiangsu

address: No. 300 Guangzhou Road

department: The First Clinical Medical College

institute: Nanjing medical university

summary: Gastric adenocarcinoma, particularly the Lauren intestinal-type GAC (IGAC), leads to significant mortality in China due to the limited effectiveness of current treatments. We performed spatial transcriptomics to profile heterogeneous immune cell clusters in IGAC and validated our findings using scRNA-seq. Our study aims to investigate the mechanisms of immune suppression in IGAC to identify potential targets for enhancing immunotherapy outcomes.

overall_design: Gastric cancer and matched normal gastric mucosa tissues (located more than 5 cm from the tumor) from two patients with intestinal-type gastric cancer were collected. For each patient, the gastric cancer sample (upper panel) and the normal gastric mucosa sample (lower panel) were placed on the same slide.

first: Jiajia

last: Shen

first: Sheng

last: Yang

first: Xiaochun

last: Ping

first: Lizong


title: Unbalanced chromatin binding of Polycomb complexes drives neurodevelopmental disorders

first: Rodrigo

last: Lucena Borges

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

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Refer to individual Series


title: N,N Dimethylacetamide attenuates LPS induced neuroinflammation in a murine model

city: Middle Village

first: Teeshavi

last: Acosta

address: 61-53 78th street

institute: St Johns University

summary: Neuroinflammation is a central driver of cognitive decline in many neurodegenerative diseases and is marked by persistent activation of pro-inflammatory pathways. N,N-Dimethylacetamide (DMA), an FDA-approved excipient with emerging anti-inflammatory properties, was evaluated for its therapeutic potential in a murine model of chronic neuroinflammation. Both male and female C57BL/6 mice were administered lipopolysaccharide (LPS; 0.5 mg/kg) to induce neuroinflammation over seven days, followed by treatment with DMA. Behavioral assays—including the Radial Arm Maze and Novel Object Recognition tests—revealed significant cognitive deficits in LPS-treated animals, which were attenuated in DMA-treated mice, indicating preserved spatial memory and object recognition. To elucidate underlying molecular changes, RNA sequencing was performed on brain tissue, and differential gene expression analysis was followed by KEGG pathway enrichment. LPS exposure upregulated pathways related to immune activation, including TNF signaling, NF-κB signaling, MAPK signaling, and cytokine–cytokine receptor interactions. DMA treatment reversed many of these transcriptional changes, downregulating pro-inflammatory signaling and upregulating genes involved in neuroprotection and synaptic signaling. These findings suggest that DMA not only modulates key inflammatory pathways at the transcriptomic level but also improves cognitive function in a neuroinflammatory context. Collectively, this study highlights DMA’s potential as a therapeutic agent for preventing inflammation-associated cognitive decline.

overall_design: RNA sequencing of PBS control, LPS and DMA + LPS treated c57/bl6 brain tissue.

first: Acosta

last: Teeshavi D

first: Wu

last: Jiaqi

first: Khairnar

last: Rhema

first: Reznik

last: Sandra E


title: Müller glial and microglial responses coupled to recovery of cone photoreceptors following limited cone ablation in zebrafish retina

city: Moscow

first: Sarah

last: Hendricks

state: ID

address: 685 S. Line Street, IRIC 210

institute: University of Idaho

summary: We treated gnat2:nfsb-mCherry transgenic adult zebrafish with 24-hour 10 mM Mtz immersion exposure, triggering transient cone stress and subsequent glial and microglial responses.

overall_design: Adult gnat2:nfsb-mCherry transgenic zebrafish were exposed to 0.1% DMSO or 10 mM Mtz in 0.1% DMSO for 24 hours by immersion followed by washout to clean water. For sequencing, whole retinas were isolated, dissociated to single cell suspension, and analyzed using scRNA-seq. Samples were isolated at 96 hours post treatment (DMSO and MTZ 96 HPT) and at 120 hours post treatment (MTZ 120 HPT). Two retinas were pooled per sample for sequencing.

first: Halle

last: Weimar

first: Ashley

last: Farre

first: Jordan

last: Rumford

first: Diana

last: Mitchell


title: RNA functional modulation by Mitoxantrone via RNA structural ensemble repartitioning

city: Groningen

first: Danny

last: Incarnato

state: Netherlands

address: Nijenborgh 7

department: Molecular Genetics

country: Netherlands

institute: University of Groningen

summary: Targeting RNA with small molecules offers a strategy to modulate gene expression at undruggable targets. Traditional screens favor thermodynamically stable, low-entropy RNA motifs with defined conformations, yet these provide limited energetic leverage for functional modulation. Many RNAs instead sample dynamic structural ensembles that small molecules can stabilize or redirect. Using group I self-splicing introns as a model, we identified the antineoplastic drug Mitoxantrone as a competitive inhibitor of RNA self-splicing (IC50 = 4.3 μM) that stabilizes the native conformation of the T4 td intron. Structure-activity analysis showed the anthraquinone scaffold alone is insufficient, and basic amine side chains are required for RNA structural modulation. Transcriptome-wide chemical probing in human cells revealed preferential binding to GC-rich structured regions, although only a subset showed structural change. Furthermore, global analysis of 5′ UTR ensembles showed reduced structural heterogeneity and increased translation, demonstrating functional repartitioning of RNA conformational landscapes.

sample_organism:
Homo sapiens
Escherichia phage T4

platform_organism:
Homo sapiens
Escherichia phage T4

overall_design: RNA structure analysis following treatment with Mitoxantrone

first: C

last: Zhang

first: I

last: Borovská

first: T

last: Iobashvili

first: E

last: Morandi

first: M

last: Lionnez

first: O

last: Olayinka

first: R

last: de Boer

last: Clamer

last: Witte

first: K

last: Pors

first: J

last: Schneekloth

first: D


title: KMT2D-deficiency destabilizes lineage progression in immature neural progenitors

city: Boston

first: Pushpinder

last: Bawa

state: Massachusetts

address: 670 Albany St

department: Boston University Medical Campus

institute: Center for Regenerative Medicine

summary: Neurodevelopment is driven by integrated regulation of chromatin shaping, transcription, and proliferative timing. Although KMT2D is known to catalyze H3K4 methylation at promoters and enhancers to activate lineage genes, its role in regulating fate specification within neural progenitor populations remains poorly defined. We performed single-cell multiome sequencing on human induced pluripotent stem cell (hiPSC)-derived cerebral organoids to simultaneously profile chromatin and transcriptional states in KMT2D-deficient cells. We found that lineage transcription factors such as PAX6, NEUROD4, and OLIG1 showed premature activation accompanied by disrupted temporal coordination between chromatin accessibility and transcription, indicating unstable regulation that fails to sustain the expression of several lineage-specific genes. Live-cell imaging using FUCCI reporters revealed that KMT2D-deficient progenitors accumulate in G1 phase more rapidly within 24-hours of neural induction. Further, KS1 patient-derived neural progenitors showed similar, yet less pronounced, disruptions in lineage mark expression over time. Our findings suggest that loss of KMT2D perturbs the coordination of chromatin accessibility, gene expression, and cell cycle timing in neural progenitors at the onset of lineage acquisition, potentially initiating generational instability that impairs lineage resolution and alters differentiation trajectories over time.

overall_design: Multiome sequencing was performed on cerebral organoids derived from WTC11 (isogenic control) and KMT2D-/- human induced pluripotent stem cells (hiPSCs). Organoids were cultured for two months and sampled at two time points (Day 51 and Day 74), pooled by size, and dissociated to single-cell suspensions. Nuclei isolated from these suspensions underwent simultaneous single-nucleus ATAC-seq and single-cell RNA-seq using the Chromium Next GEM Multiome platform (10X Genomics). The variable investigated was differences between genotypes (WTC11 vs. KMT2D-/-) focused on chromatin accessibility and gene expression to understand neural progenitor cell fate and regulatory dynamics.

first: Carly

last: Golden

first: Feiya

last: Wang

first: Olaf

last: Bodamer

first: Joseph

middle: H

last: Yost

first: Maria

last: Serrano


title: Retinoic Acid-Mediated Signaling Regulates Allantoic and Fetoplacental Vascularization

city: Charlottesville

first: Uma Devi

last: Paila

address: 1335 Lee St

institute: University of Virginia

summary: The placenta is vital for fetal development, and altered placental vascularization underlies prevalent disorders, including fetal growth restriction, prematurity, and pregnancy complications. Impaired placental vascularization is associated with Vitamin A deficiency, but mechanisms are undefined. To investigate this, we used retinoic acid (RA)-deficient Raldh2⁻/⁻ embryos, and found they exhibit placental endothelial hyperproliferation and impaired arterial-venous remodeling, which were rescued by providing all‑trans‑RA (ATRA) via maternal diet. Single cell RNA sequencing of E9.5 Raldh2+/+, Raldh2⁻/⁻,and Raldh2⁻/⁻+ATRA placental cells, and functional assays, revealed that RA regulates endothelial growth and vascular remodeling via Notch signaling.

overall_design: Placentas from  E9.5 embryos that were WT Raldh2, KO Raldh2, WT Raldh2 (from ATRA fed moms), and KO Raldh2 (from ATRA fed moms) were enzymatically digested into a single cell suspension, depleted of CD45+ cells and enriched for CD31+ cells to increase the number of ECs using microbeads. 5% of all other placental cells were spiked back and analyzed using scRNA-seq.

first: Aleksandra

last: Cwiek

first: Umadevi

first: Karen

last: Hirschi


title: TWIST1 mediated transcriptional activation of SPON2 drives colorectal peritoneal metastasis through stromal cell signaling network

city: DALLAS

first: ZHUAN

last: ZHOU

state: TX

address: 7430 W Northwest Hwy APT 1, Dallas, TX 75225, USA

department: Surgery

institute: University if Texas Southwestern Medical Center

summary: Colorectal cancer (CRC) peritoneal metastasis (PM) accounts for 25–35% of stage IV cases. CRC PM carries a median overall survival of 16 months with systemic chemotherapy and an almost 0% five-year survival rate. The molecular mechanisms driving CRC PM remain poorly defined. CRC heterogeneity is classified into four Consensus Molecular Subtypes (CMS1-4), with CRC PM predominantly exhibiting the CMS4 signature—characterized by increased stromal/mesenchymal enrichment and cellular plasticity—features linked to frequent disease progression and therapeutic resistance. Here, we investigated the molecular mechanisms driving CRC PM and CMS4 signature. TWIST1 was identified to be significantly upregulated in CRC PM. We established TWIST1-SPON2 as a novel transcriptional axis contributing to CRC PM tumorigenesis, through mediating tumor-stroma interactions. We identified SPP1, secreted by the tumor stroma, as an upstream regulator of the TWIST1-SPON2 cascade via AKT activation in tumor cells in vitro and in vivo. This defined SPP1-TWIST1-SPON2 signaling circuit is pivotal in shaping the tumor microenvironment and promoting CRC PM progression. The findings establish the SPP1-TWIST1-SPON2 axis as potential biomarkers and therapeutic targets in CRC PM.

overall_design: RNA-seq of TWIST1 knockdown/knockout in MDST8 and LoVo cells; CHIP-seq of TWIST1 in MDST8 and LoVo cells

first: Alex

last: Kim


title: Structural evidence that RNA contributes to polymorphism of tau amyloid fibrils

city: Los Angeles

first: David

middle: S.

last: Eisenberg

state: CA

address: 611 Charles E. Young Dr. East

institute: University of California, Los Angeles

summary: RNA colocalizes with tau deposits in Alzheimer’s disease (AD) and other tauopathies, and drives tau aggregation in vitro. However, molecular details of RNA-tau interactions remain unclear, and in particular whether these interactions contribute to neurodegeneration. Previously, we determined a cryo-EM structure of fibrils of full-length tau bound to unfractionated mammalian RNA, revealing a small tau C-terminal core. Here, we present the cryo-EM structure of fibrils of full-length recombinant tau bound to unfractionated mammalian RNA and seeded by pathological tau fibrils extracted from the postmortem brain of an AD patient. This structure reveals an expanded tau C-terminal core with partial resemblance to AD tau fibrils. RNA sequencing identified 18S ribosomal RNA as the primary fibril-bound species, consistent with the well-documented link between pathological tau and ribosomal dysfunction in neurodegenerative diseases. Next, we determined the cryo-EM structure of fibrils of full-length recombinant tau bound to mammalian 18S ribosomal RNA, revealing a core that consists of the R2 to R4 repeat domains previously seen in several pathological polymorphic tau fibrils. All three of our recombinant RNA-tau fibrils dissolve upon RNase treatment, demonstrating that RNA is the molecular glue of these complexes. In the presence of different RNAs, tau fibrils adopt distinct folds, suggesting that RNA is a cofactor that shapes tau fibril polymorphism.

overall_design: RNA sequencing of RNA bound to full-length 2N4R tau fibrils formed in the presence of unfractionated mouse liver RNA and Alzheimer’s disease brain extracted tau fibrils

first: Romany

last: Abskharon

first: Yi Xiao

last: Jiang

first: Michael

last: Sawaya

first: Peng

last: Ge

first: Jeffrey

last: Zhang

last: Boyer

first: Joshua

last: Dolinsky

first: Justin

last: Pi

first: Duilio

last: Cascio

first: Feng

last: Guo


first: Wei

last: Xiong

overall_design: RNA-seq of Human nasopharyngeal carcinoma cells in BALF2-LR and BALF2-HR overexpress group

first: Xiong

last: Wei


title: MiR-146a-5p and miR-146b-5p limit IL-1beta-mediated inflammation in adipose tissue during polytrauma

city: Ulm

first: Pamela

last: Fischer-Posovszky

address: Eythstr. 24, Haus 16, Forschungslabor KiKli

department: Department of Pediatrics and Adolescent Medicine

country: Germany

institute: Ulm University Medical Center

summary:
MicroRNAs (miRNAs) are small non-coding RNAs and play a crucial role in the regulation of inflammation. White adipose tissue (WAT) covers the body and internal organs in subcutaneous and visceral fat depots, respectively, and represents an important source of circulating miRNAs. The role of WAT and its miRNAs in the context of polytrauma is incompletely understood. However, evidence is accumulating that WAT contributes to the severe inflammatory response observed in polytrauma patients. Therefore, we analyzed the miRNA expression in inguinal WAT depots in a standardized mouse model of polytrauma and hemorrhagic shock (PT+HS). Here, we identified miR-146a-5p and miR-146b-5p to be upregulated upon PT+HS. In an in-vitro model of traumatized human white adipocytes, we found miR-146a-5p to be upregulated by IL-1β-induced NF-B activation. Both, miR-146a-5p and miR-146b-5p, in turn, dampened IL-1β-induced inflammation in human adipocytes. Using target gene prediction tools, we further identified IRAK1 as target of miR-146a-5p, and potentially also miR-146b-5p, confirming the importance of IRAK1 in IL-1β-induced proinflammatory signaling. Thus, miR-146a-5p and miR-146b-5p act as suppressors of IL-1β-induced proinflammatory signaling in human adipocytes during trauma, and blockage of IL-1β or mimics of miR-146a-5p and miR-146b-5p might represent a potential future therapeutic avenue for severe traumatic and inflammatory conditions.
We used Affymetrix microRNA array to determine the expression of different microRNAs in inguinal white adipose tissue (iWAT) from five sham-treated mice and five mice with polytrauma and hemorrhagic shock (PT+HS).

overall_design: The animal experiments were approved by the federal authorities for animal research, Tübingen, Germany. Male C57BL/6 mice aged 10-12 weeks with a mean body weight of 29.5 g were randomly assigned to sham treatment or PT + HS (n=5 animals per group). No specific inclusion/exclusion criteria or outcome measures were deemed relevant for this specific study. In brief, mice were anesthetized with 2.5% sevoflurane (Abbott, Wiesbaden, Germany) in oxygen throughout the experiment before they were subjected to thoracic trauma, closed head injury, and femur fracture including soft tissue injury as described previously (Weckbach S, Hohmann C, Braumueller S, Denk S, Klohs B, Stahel PF, Gebhard F, Huber-Lang MS, Perl M (2013) Inflammatory and apoptotic alterations in serum and injured tissue after experimental polytrauma in mice: distinct early response compared with single trauma or “double-hit” injury. J Trauma Acute Care Surg 74:489–498. doi: 10.1097/TA.0b013e31827d5f1b). Pressure-controlled hemorrhage was induced and monitored by a microcatheter in the femoral artery. A mean arterial pressure of around 30 ± 5 mmHg was maintained for 60 minutes. After resuscitation of the animals with a balanced electrolyte solution, inguinal WAT depots were removed 4 hours after trauma. Euthanasia was performed by thoracic opening under deep narcosis and terminal blood sampling from the right ventricle. Due to the nature of the animal experiment, investigators were not blinded during the animal study protocol.


title: Acute hormonal signaling-induced 3D chromatin loop reorganization controls adipocyte thermogenesis [Micro-C human]

first: Kaifu

last: Chen

state: MA

address: 300 Longwood Ave

department: Cardiology

institute: Boston Children's Hospital

summary: Recent molecular advancements have revolutionized our understanding of the role of three-dimensional (3D) genome organization in gene regulation. Yet, the impact of acute hormonal signaling on reshaping genome structure and its consequences for metabolic processes remain largely unexplored. β3-adrenergic receptor (β3-AR) hormonal signaling is imperative for brown adipose tissue (BAT) thermogenesis. Here, we demonstrate that β3-AR signaling induces rapid reorganization of fine-scale genome architecture in murine and human brown adipocytes within four hours. High-resolution Micro-C profiling reveals dynamic chromatin loop formation associated with activation of thermogenic genes. Mechanistically, β3-AR signaling promotes p18Hamlet/SRCAP complex assembly, catalyzing incorporation of the histone variant H2A.Z into nucleosomes. ATAC-sequencing reveals that H2A.Z enhances chromatin accessibility at loop anchors, supporting loop formation by facilitating the recruitment of looping factors such as the Mediator complex. Disruption of H2A.Z compromises dynamic chromatin looping and transcriptional activation of thermogenic genes in both species. Mice with BAT-specific H2A.Z deficiency exhibit reduced thermogenic activity and impaired glucose tolerance. Revisiting genome-wide association study analysis reveals that H2A.Z-occupied loops are linked to genetic variants associated with obesity and its related metabolic disorders. Together, these findings highlight the rapid adaptability of 3D genome organization to acute β3-AR signaling and its critical role in brown adipocyte thermoregulation.

overall_design: We performed high-resolution Micro-C in vehicle-treated control, forskolin (FSK)-trated control, and FSK-treated H2A.Z knockdowon (KD) primary human brown adipocytes to assess 3D genome reorganization during thermogenesis and the impact of H2A.Z KD on chromatin loop reorganization in humans.

first: Yang

first: Rongbin

last: Zheng

first: Tadataka

last: Tsuji

first: Chih-Hao

last: Wang

first: Xiangyu

last: Liu

first: Yu-Hang

last: Xing

last: Darcy

first: Matthew

last: Lynes

first: Morten

last: Lundh

first: Rini

last: Arianti

first: Rui

last: Dong

first: Brice

last: Emanuelli

first: Miguel

middle: N

last: Rivera

first: Endre

last: Kristóf

first: Ronald

last: Kahn

first: Ferenc

last: Győry

first: Yu-Hua

last: Tseng


title: Regulation of the Balance between Concentric and Eccentric Cardiac Hypertrophy by a CDC14A-KMT5A Signaling Pathway

city: Palo Alto

first: Michael

middle: Seth

last: Kapiloff

state: California

address: 1651 Page Mill Road, Room 2112

institute: Stanford University

summary: RNA-seq analysis was performed to study the effect of cardiomyocyte-specific CDC14a RNA interference on gene expression in the TM54 (Myh6-Tpm1*E54K) mouse dilated cardiomyopathy model.

overall_design: Heart RNA was extracted from wildtype and TM54 mice transduced with AAV9-directed cardiac-specific expression of CDC14a or control shRNA and sequenced for gene expression analysis. 3-6 mice per cohort were analyzed.

first: Xueyi

last: Li

first: Jinliang


title: Setdb1-mediated H3K9 methylation is enriched on the inactive X and plays a role in its epigenetic silencing [MEF_RNAseq]

city: Parkville

first: Andrew

last: Keniry

state: VIC

address: 1G Royal Parade

country: Australia

institute: WEHI

summary: The presence of histone 3 lysine 9 (H3K9) methylation on the mouse inactive X chromosome has been controversial over the last 15 years, and the functional role of H3K9 methylation in X chromosome inactivation in any species has remained largely unexplored. Here we report the first genomic analysis of H3K9 di- and tri-methylation on the inactive X: we find they are enriched at the intergenic, gene poor regions of the inactive X, interspersed between H3K27 tri-methylation domains found in the gene dense regions. Although H3K9 methylation is predominantly non-genic, we find that depletion of H3K9 methylation via depletion of H3K9 methyltransferase Set domain bifurcated 1 (Setdb1) during the establishment of X inactivation, results in failure of silencing for around 150 genes on the inactive X. By contrast, we find a very minor role for Setdb1-mediated H3K9 methylation once X inactivation is fully established. In addition to failed gene silencing, we observed a specific failure to silence X-linked long-terminal repeat class repetitive element. Here we have shown that H3K9 methylation clearly marks the murine inactive X chromosome. The role of this mark is most apparent during the establishment phase of gene silencing, with a more muted effect on maintenance of the silent state. Based on our data, we hypothesise that Setdb1-mediated H3K9 methylation plays a role in epigenetic silencing of the inactive X via silencing of the repeats, which itself facilitates gene silencing through alterations to the conformation of the whole inactive X chromosome.


title: METTL18 Ensures Pancreatic Function by Maintaining Proper Translation and Proteostasis

city: Wako

first: Shintaro

last: Iwasaki

state: Saitama

address: 2-1, Hirosawa

department: Center for Pioneering Research

country: Japan

institute: RIKEN

summary: Methyltransferases fine-tune various biomolecules by site-specific methylation. METTL18, an N3-position-specific histidine methyltransferase, modifies H245 of the ribosomal protein RPL3 (uL3), thereby regulating translation dynamics and proteostasis. However, the physiological role of this enzyme in vivo remains to be elucidated. Here, we show that METTL18 is essential for pancreatic function by regulating translation and suppressing protein aggregation. Mettl18 knockout (KO) mice exhibited partial preweaning lethality, and the surviving mice showed a marked reduction in N3-histidine methylation in the pancreas, diabetic phenotypes, and accumulation of pancreatitis-associated proteins. Ribosome profiling in a pancreatic acinar cell line revealed that loss of METTL18 caused global translational alterations, including accelerated elongation at proline codons. The improper ribosome traverse compromises protein folding, resulting in the aggregation of pancreatitis-associated proteins, including Reg1, and activation of the unfolded protein response. Our findings establish histidine methylation as a physiologically important post-translational modification and highlight METTL18 as a key regulator of pancreatic function through the maintenance of proteostasis.

overall_design: Ribosome profiling of Mettl18 KO pancreatic acinar cell line 266-6

first: Tadahiro

last: Shimazu

first: Megumi

last: Gowa

first: Ayane

last: Kataoka

first: Takehiro

last: Suzuki

first: Kotaro

last: Tomuro

first: Yuichi

last: Shichino

first: Naoshi

last: Dohmae

first: Yoichi

last: Shinkai


title: Acute hormonal signaling-induced 3D chromatin loop reorganization controls adipocyte thermogenesis [ChIP-seq human]

first: Kaifu

last: Chen

overall_design: Chromatin immunoprecipitation-sequencing  (ChIP-seq) for H3K27ac in vehicle-treated control, FSK-treateed-control primary human brown adipocytes. ChIP-seq for H2A.Z in FSK-treateed-control primary human brown adipocytes.

first: Yang

last: Zhang

first: Rongbin

last: Zheng

first: Tadataka

last: Tsuji

first: Chih-Hao

last: Wang

first: Xiangyu

last: Liu

first: Yu-Hang

last: Xing

first: Justin

last: Darcy

first: Matthew

last: Lynes

first: Morten

last: Lundh

first: Rini

last: Arianti

first: Rui

last: Dong

first: Brice

last: Emanuelli

first: Miguel

last: Rivera

first: Endre


title: An immunobiliary single-cell atlas resolves crosstalk between type 2 conventional dendritic cells and γδ T cells in cholangitis

city: Würzburg

first: Stefan

last: Thomann

address: Versbacher Strasse 9

institute: Würzburg Systems Immunology

summary:
The liver biliary niche serves as a reservoir of tissue-resident immune cells and supports tissue fibrosis upon damage, yet the role of peribiliary immune cells during cholangitis remains poorly understood. Here, we induce cholestatic liver injury mirroring human biliary diseases with bile acid retention in mice to establish a spatial and multimodal single-cell RNA sequencing atlas of the liver and liver-draining lymph nodes (LN). We characterized a hepatic disease state trajectory from dendritic cell precursors (preDCs) to a mature subset of pro-inflammatory Mgl2+ type 2 conventional dendritic cells (cDC2B) and observed dynamic crosstalk with γδ  T cells inducing an Il17 response (γδ T17). Dissection of the cDC2B-γδ T cell communication node identified the Icosl-Icos pair as an important cell contact-dependent interaction, which was validated in vitro. In vivo, cDC2B depletion attenuated γδ T17 responses in cholestatic liver injury, and liver fibrosis was reduced in a model of inducible γδ T cell depletion and in an Il17-deficient background.  Our work demonstrates dynamic turnover of cDC2 within the biliary niche during cholestasis, and a profibrogenic function of γδ T cells contingent on the induction by peribiliary cDC2B, highlighting relevant disease determinants within the immunobiliary and liver-draining LN niche.

Spatial Transcriptomics Data (Xenium Platform) of Mouse Liver tissues treated with DDC diet for 5 days.

overall_design: single sample single timepoint

first: Dominic

last: Grün


title: Acute hormonal signaling-induced 3D chromatin loop reorganization controls adipocyte thermogenesis [ChIP-seq mouse, CTCF, SMC1, MED1]

first: Kaifu

overall_design: Chromatin immunoprecipitation-sequencing  (ChIP-seq) for CTCF and SMC1 in vehicle-treated control and β3-AR-stimulated control brown adipocytes. ChIP-seq for MED1  in vehicle-treated control, β3-AR-stimulated control, and β3-AR-stimulated H2A.Z knockdowon (KD) brown adipocyte.

last: Kristóf

first: Ronald

last: Kahn

first: Ferenc

last: Győry

first: Yu-Hua

last: Tseng


title: Acute hormonal signaling-induced 3D chromatin loop reorganization controls adipocyte thermogenesis [CUT&Run mouse]

last: Chen

overall_design: Cleavage Under Targets & Release Using Nuclease (CUT&RUN) for H2A.Z in unstimulated and β3-AR-stimulated primary murine brown adipocytes to profile H2A.Z genome-wide incorporation.

first: Yang

last: Zhang

first: Rongbin

last: Zheng

first: Tadataka

last: Tsuji

first: Chih-Hao


title: Acute hormonal signaling-induced 3D chromatin loop reorganization controls adipocyte thermogenesis [PRO-seq mouse]

overall_design: We performed PRO-seq in mouse.

last: Wang

first: Xiangyu

last: Liu

first: Yu-Hang

last: Xing

first: Justin

last: Darcy

first: Matthew


title: ERRα-KDM5C Restrains STING Enhancer Activity to Modulate Type I Interferon Signaling in Breast Cancer Progression

city: Ganzhou

first: Wenjuan

state: Jiangxi

address: No. 23, Qingnian Road

department: First Affiliated Hospital

institute: Gannan Medical University

summary: Regulation of enhancer activity plays a pivotal role in governing gene expression and cellular behaviors. However, the precise mechanisms underlying dynamic control of active enhancers remain incompletely defined. Here, we demonstrate that the nuclear receptor estrogen-related receptor α (ERRα) forms a functional complex with the H3K4me3-specific demethylase KDM5C to co-occupy a large set of active enhancers, including the locus of STING. In breast cancer cells, ERRα depletion induces STING enhancer hyperactivation, evidenced by H3K4me3 deposition, decreased H3K4me1, and increased enhancer RNA (eRNA) transcription. Accordingly, depletion of ERR leads to further activation of STING gene transcription and TBK1-IRF3 pathway, accompanied by increased type I interferon (IFN) and IFN-stimulated gene (ISG) expression, as confirmed by transcriptomic analysis. Notably, depleting ERRα markedly attenuates breast tumor cell growth in vitro and in vivo, and our in vitro evidence indicates this occurs in part through activating STING signaling. These findings establish that the ERRα-KDM5C serves as a critical checkpoint for STING enhancer activity, revealing a regulatory mechanism of STING enhancer activity in breast tumor progression.

overall_design:
MCF7 cells were transfected with control shRNA (shCTL) or shRNA specifically targeting ERRα(shERRα) or KDM5C (shKDM5C) followed by RNA-seq analysis.
GRO-seq was performed in MCF7 cells transfected with control siRNA (siCTL) , followed by nuclear run-on and BrUTP labeling.
ChIP-seq was performed using an antibody against H3K4me3 in shCTL-, shERRα-, or shKDM5C-transfected MCF7 cells, with corresponding Input DNA as control.

first: Zuhui

last: Xu

first: Xiaonan

last: Wu

first: Wen


title: Transcriptomic Profiling of Ferroptosis in Enteric Neurons: Bulk RNA-Seq of IM-FEN Cells Treated with Palmitate

city: Decatur

first: Shanthi

last: Srinivasan

state: Georgia

address: 5A137-1670 Clairmont Rd,

department: Division of Digestive Diseases

institute: Emory University

summary: Palmitic acid (PA), a major component of Western dietary fats, is known to induce ferroptotic cell death in enteric neurons. In this study, we performed bulk RNA-seq on Immortalized Mouse-Fetal Enteric Neurons (IM-FEN) treated with PA (0.5 mM, 24 h) or vehicle control to characterize transcriptional changes associated with ferroptosis. Sequencing was performed using the Illumina NovaSeq 6000 platform. The dataset provides insight into lipid-induced neuronal stress and ferroptosis-relevant signaling networks.

overall_design: IM-FEN cells were treated with palmitic acid (0.5 mM) or vehicle control (10% BSA) for 24 hours. Each condition included six biological replicates (n = 6). Total RNA was extracted and subjected to paired-end sequencing on the Illumina NovaSeq 6000 platform. The study includes 12 raw FASTQ files (paired-end; R1 and R2) and a normalized gene expression matrix. This dataset enables transcriptomic comparison of ferroptosis-associated gene programs induced by lipid overload in enteric neurons.

first: Arun

last: Balasubramaniam

first: Yunshan

first: Francesca

last: Cingolani

first: Simon

middle: M

last: Mwangi


title: The Conserved Non-Coding Sequence CNS11 Is A Master Control Region for Rorc Transcription in Type 17 Immune Cells [4C-Seq]

city: Beijing

first: Hao

address: Haidian  District

institute: Tsinghua University

summary: As the master transcription factor, RORγt controls the development and function of all type 17 immune cells. Although the trans-regulatory mechanisms governing Rorc expression have been extensively studied, the cis-regulatory mechanisms that differentially regulate Rorc transcription across distinct lymphocytes, particularly in innate lymphocytes, remain largely unknown. Here, we identified CNS11 at the Rorc gene as essential for the development of all type 17 immune cells. Deletion of CNS11 impaired the maintenance but not induction of Th17 cells, abolished the development of RORγt+ Treg cells, RORγt+ γδT cells and RORγt+ antigen-presenting cells, and blocked ILC3 induction from early progenitors, leading to a complete absence of secondary lymphoid organs. Mechanistically, CNS11 mediates the Rorc transcription through a RORγt-dependent feedforward regulatory loop in a cell-type-specific manner. Specifically, the interaction of CNS11 with RORγt and RUNX3 dictated the development of ILC3s, while its interaction with RORγt and/or c-MAF was crucial for RORγt expression in Th17 cells, RORγt+ Treg cells and RORγt+ γδT cells. Our study reveals CNS11 as a key transcription factor binding hub and master control region for Rorc transcription in distinct lymphocytes.

overall_design: 4C experiment of CNS11 in ILC3s isolated from the small intestine lamina propria of Rag1-deficient mice.

first: Ruifeng

last: Li

first: Chen

last: Dong


title: The Conserved Non-Coding Sequence CNS11 Is A Master Control Region for Rorc Transcription in Type 17 Immune Cells [CUT&Tag]

overall_design: CUT&Tag for RUNX3, RORγt and IgG control (rabbit+rat) in ILC3s isolated from the small intestine lamina propria of Rag1-deficient mice.


title: Acute hormonal signaling-induced 3D chromatin loop reorganization controls adipocyte thermogenesis [RNA-seq human]

first: Kaifu

overall_design: We performed RNA-seq in vehicle-treated control, forskolin (FSK)-treated control, and FSK-treated H2A.Z knockdowon primary human brown adipocytes to determine the transcriptional dynamics during thermogenesis and the impact of H2A.Z knockdown on gene activation.

first: Yang

first: Rongbin

first: Tadataka

first: Chih-Hao

last: Lynes

first: Morten

last: Lundh

first: Rini

last: Arianti

first: Rui

first: Brice

last: Emanuelli

first: Miguel

last: Rivera

first: Endre

last: Kristóf

first: C. Ronald

last: Kahn

first: Ferenc

last: Győry

first: Yu-Hua

last: Tseng


title: Regulation of NK cell transcriptome by Hif1a and Ahr under hypoxia

city: Mannheim

first: Carsten

last: Sticht

address: Theodor-Kutzer-Ufer

department: ZMF

institute: University Heidelberg

summary: NK cells responses can be significantly affected by microenvironmental conditions. In pathological conditions, oxygen concentration in tissues can be reduced, lading to hypoxia. Cells adapt to hypoxia by stabilizing transcription factor HIF-1a that mediates its regulatory functions by modifying gene transcription. In many cells, HIF-1a pathway intersect with the activation of the transcription factor AhR due to shared transcriptional co-activator. Here, we investigated how HIF-1a and AhR regulate murine NK cell transcriptome under hypoxia.

overall_design: Trascriptome profiling (RNA-seq) of murine NK cells isolated from spleen of Hif1afl/fl, Ahrfl/fl, Hif1afl/fl Ahrfl/fl or from Ncr1iCreHif1afl/fl, Ncr1iCreAhrfl/fl and Ncr1iCreHif1afl/fl Ahrfl/fl mice, cultured in media supplemented with IL-2 in hypoxia (1% O2) for 7 days

first: Sebastiano

last: Giorgetta

first: Ana

last: Stojanovic

first: Cerwenka

last: Adelheid


title: DNA methylation profiling in Huntington’s disease reveals disease associated changes in the striatum

city: Exeter

first: Gregory

last: Wheildon

address: Stocker Road

department: CBS

institute: University of Exeter

type: Methylation profiling by genome tiling array

summary: Huntington’s disease is caused by a trinucleotide CAG repeat expansion in the HTT gene. Despite displaying autosomal dominance, phenotypic variation exists amongst mutation carriers, in particular relating to the age that symptoms first occur. This variation is predominantly driven by an inverse relationship between CAG expansion size and age of symptom onset. However, the majority of variation in age of onset is thought to be driven by environmental influences, independently of CAG repeat length. Since DNA methylation can be altered by environmental factors, and as methylomic variation is reported in other neurodegenerative diseases, it may offer a potential mechanism underlying disease manifestation. Here, we present the first epigenome-wide association study of Huntington’s disease conducted in the striatum, the primary region of neuropathology, along with the entorhinal cortex and cerebellum in 42 individuals (22 control; 20 Huntington’s disease) on the Illumina EPIC v1 array. We identified seven Bonferroni-significant differentially methylated CpGs within the striatum along with 27 differentially methylated regions. Weighted gene correlation network analysis identified six modules of co-methylated CpGs that were associated with Huntington’s disease, with ontological analyses showing enrichment in disease relevant processes. Furthermore, integration of single-nuclei RNA sequencing data highlighted that genes annotated to these modules are enriched in striatal spiny projection neurons, the primary cell types affected in the disease. These results suggest that DNA methylation is altered at loci associated with Huntington’s disease in disease relevant regions and cell types.

overall_design: We aimed to profile DNA methylation in Huntington's disease (HD) brain tissue in order to identify potential contributors to non-gentic driven phenoypic variation in the disease. DNA methylation was quantifed in DNA samples extracted from post-mortem brain tissue, taken from Huntington's disease patients and compared to samples taken from healthy control individuals, using the Infinium Methylation EPIC array version 1. Following quality control measures, 113 samples (striatum = 37; entorhinal cortex = 38; cerebellum 38) from 42 individuals were used to identify differentially methylated postions associated with HD status.

first: G

first: A R

last: Smith

first: L

last: Weymouth

first: J

last: Harvey

first: M

last: Kouhsar

last: Macbean

first: C

last: Troakes

first: E

last: Pishva

first: R G

first: K

last: Lunnon


title: DEAH-BOX HELICASE 8 IS A REGULATOR OF HEAT SHOCK FACTOR 1

city: London

first: Pradeep

last: Ramagiri

state: Greater London

address: 15 Cotswold Rd

department: Cancer Therapeutics

institute: The Institute of Cancer Research

summary: Heat Shock Factor 1 (HSF1) is a key transcription factor mediating the cellular stress response and promoting cancer cell survival. We identify DEAH-box helicase 8 (DHX8) as a crucial regulator of HSF1 pre-mRNA processing. Silencing DHX8 leads to the accumulation of HSF1 transcripts with retained introns and reduced HSF1 protein. Intron retention is also detected in canonical heat shock and cancer-signature gene sets regulated by HSF1, and in mitosis, G2M checkpoint, cMYC and E2F-associated gene sets. Consistent with intron retention and the role DHX8 in the later stages of splicing, eCLIP analysis finds significant enrichment of DHX8 binding between the lariat branch site and 3’ splice junction. DHX8 silencing induces apoptosis in cancer cells to a greater extent than in non-tumorigenic cells. We show that the ATPase activity of DHX8 is essential for function, and propose DHX8 as a therapeutic target on pathways that protect cancer cells from oncogene-induced stress.

overall_design: H1299 non-small cell lung cancer cells DHX8-dTAG cells were treated for 6 hours with 250 nM dTAG-V1 heterobifunctional small molecule to induce degradation of the DHX8-dTAG fusion protein.  H1299 cells were also treated with 10nM siTOOLs DHX8 or scramble control pooled siRNA for 72 hours.  HCT116 colorectal cancer cells were transduced with a lentiviral construct encoding doxycyline-inducible human DHX8 (DHX8 wild-type, DHX8-K549 ATPase-dead or DHX8-R647G/F648G RNA binding mutant). Cells were treated with DHX8 siRNA to remove endogenous DHX8 or scramble control siRNA or mock transfection conditions. Treatments were run in the absence or presence of doxycycline to assess the impact of inducing the exogenous wild-type or mutant DHX8. Four independent biological repeats were run for each condition

first: Jennifer

last: Tall

first: Alexandra

last: Vasile

first: James

last: Campbell

first: Caitlin

last: Davies

first: Marissa

last: Powers

first: Toby

last: Roe

first: Deivendran

last: Sankaran

first: Hannah

last: Wang

first: Konstantinos

last: Mitsopoulos

first: Bissan

last: Al-Lazikani

first: Robert

last: Montfort

first: Emmanuel

last: Billy

first: Paul

last: Workman

last: Clarke


title: Splenic nerves NE-β2AR axis exacerbate septic acute kidney injury via modulating neutrophilic immunosuppression [scRNA-seq]

city: Shanghai

first: Xiaoqian

last: Hu

address: No. 130, Dongan Road, Xuhui District, Shanghai

institute: Fudan University

summary: Sepsis is characterized by chronic inflammation and immunosuppression, two immune states that hinder effective infection control and significantly contribute to renal pathological damage. Recent studies have underscored the crucial role of splenic neuroimmune interactions in immune response regulation. However, the precise mechanisms and functions of splenic nerve regulation of splenic immune responses in sepsis-associated acute kidney injury (SA-AKI) remain obscure. Our research suggests that preemptive Splenic Denervation in mice can mitigate sepsis-induced renal injury, while local norepinephrine injection into the spleen exacerbates sepsis-induced kidney damage in the cecal ligation and puncture (CLP) mouse model. Targeted blockade of splenic β2-adrenergic receptor signaling leads to increased survival rates and diminished renal damage in the mice treated with CLP. Subsequent experiments involving local splenic administration of Gr-1 antibodies and myeloid cell-specific conditional knockout of Adrb2 in mice validate that during sepsis, NE/β2-AR signaling can impact splenic neutrophils, fostering the progression of acute sepsis. Mechanistic inquiries reveal that splenic Adrb2 signaling boosts neutrophil PGE2 signaling through the cAMP pathway, promoting Th1 activation, diminishing local bacterial infections, and ameliorating SA-AKI. Furthermore, Blocking ADRB2 or PGE2 synthesizing signal significantly modulates the immunosuppression effect of neutrophils, promoting anti-bacterial Th1 immune response. These studies elucidate the role of splenic NE-ADRB2 signaling in regulating neutrophil immunosuppressive functions, thereby influencing the advancement of sepsis and renal tissue damage.

overall_design: For cecal ligation and puncture (CLP)-induced AKI model, mice were anesthetized with 2% isoflurane, then the cecum was ligated at 50% or 30% length and punctured through with a 22-gauge needle. Spleen cells from CLP mice were harvested for single-cell RNA sequencing


title: Splenic nerves NE-β2AR axis exacerbate septic acute kidney injury via modulating neutrophilic immunosuppression [RNA-seq]

overall_design: Bone marrow cells were flushed from the tibia and femurs, neutrophils were sorted from bone marrow cells according to vendor instructions using a neutrophil isolation kit (130-097-658, Miltenyi Biotec). Single-cell suspensions were prepared using RPMI media. Cells were resuspended in MACS buffer and incubated with neutrophil biotin-antibody cocktail and anti-biotin micro-beads respectively. Neutrophils were negative selectively isolated by the magnetic cell separation method. The purity of the isolated neutrophils (>95%) was confirmed by flow cytometer. Neutrophils were prepared from bone of WT mice or Adrb2-/- mice as before. For in vitro experiments, neutrophils were stimulated with or without 20μM norepinephrine bitartrate (A2661, Sigma) for 1 hour, followed by stimulation with 100ng/mL LPS (L2880, Sigma-Aldrich) for 6 hours.


title: Effect of hypoxia on murine splenic NK cells

first: Carsten

last: Sticht

summary: NK cells responses can be significantly affected by microenvironmental conditions. In pathological conditions, oxygen concentration in tissues can be reduced, lading to hypoxia. Here, we investigated how prolonged exposure to hypoxia affects the transcriptome of murine splenic NK cells.

overall_design: Trascriptome profiling (RNA-seq) of murine NK cells isolated from spleen of C57BL/6 mice and cultured media supplemented with IL-2 in normoxia (20% O2) or hypoxia (1% O2) for 7 days

first: Sebastiano

last: Giorgetta

first: Ana

last: Stojanovic

first: Cerwenka

last: Adelheid


title: Unbalanced chromatin binding of Polycomb complexes drives neurodevelopmental disorders [CUT&RUN]

city: Miami

first: Rodrigo

last: Lucena Borges

address: 1501 NW 10th Avenue

institute: Sylvester Comprehensive Cancer Center

summary: Heterozygous de novo missense mutations in genes encoding Polycomb-group (PcG) proteins can cause diverse neurodevelopmental disorders (NDDs), but the underlying mechanisms are not yet understood. Here, we identified novel mutations in the two E3-ligases of the Polycomb Repressive complex 1 (PRC1), RING1 and RNF2, in individuals with NDDs and uncover distinct mechanisms by which PRC1 activity can be compromised. Building on this, and as a proof of concept, we generated embryonic stem cells (ESCs) and a novel mouse model carrying a heterozygous Rnf2 allele with a mutation that produces a deleterious Ring1bR70H variant. This variant causes a cell fate change in neuroprecursors (NPCs) towards the non-neuronal lineages glial and microglia. Allele-specific profiling revealed that Ring1bR70H integrates into canonical PRC1, disrupting the balance of PRC1 complexes by displacing variant PRC1 from chromatin, resulting in PcG target genes upregulation. In mutant NPCs, we uncover an aberrant retention of PcG and chromatin compaction at key NPC pioneer factors and Wnt signaling genes. Critically, a heterozygous Rnf2 mutation in mice is sufficient to disrupt neural connectivity and structural organization in key brain regions, including the medial prefrontal cortex and hippocampus. Our findings establish Rnf2 as essential for neurodevelopmental integrity and brain function, shedding light on how PRC1 dysfunction contributes to NDDs.

overall_design: Cut&Run for RING1B, K27me3, Histone H2B ubiquitination. Rnf2 (RING1B)  libraries are tagged with HA in one allele and with Flag in the other allele (HA for WT, FLAG for WT, HA for M, FLAG for M). MA and MB nomenclatures are to facilitate the the proper use of IgGs.

first: Gretter

last: Gonzalez

first: Harikumar

last: Arigela

first: Yingyu

last: Huang

first: Lucas

last: Caeiro

first: Nikolai

last: Fattakhov

first: Stefano

last: Lepore

first: Liliana

last: Garcia-Martinez

first: Matea

last: Maurice

first: Pushti

last: Mehta

first: Emily

last: Park

first: Kailynn

last: MacGillivray

first: Jevithen

last: Nehru

first: Matthew

last: Chau

first: Maria

first: Clemer

last: Abad

first: Alicia

last: Bilbao-Martinez

first: Fabiola

last: Monteiro

first: Xi

last: Luo

first: Song

last: Tan

first: Daniel

last: Bilbao

first: Simone

last: Sidoli

first: Bruno

last: Di Stefano

first: Katherina

last: Walz

first: Arneet

last: Saltzman

first: Ramiro

last: Verdun

first: Ramin

last: Shiekhattar

first: Lluis

last: Morey


title: Unbalanced chromatin binding of Polycomb complexes drives neurodevelopmental disorders [scRNA-Seq]

first: Rodrigo

last: Lucena Borges

overall_design: Mutant (R70H) and  scRNA-seq for mESCm, mNPCs and Differentiated cells (WT and R70H)

first: Gretter

last: Gonzalez

first: Harikumar

last: Arigela

first: Yingyu

last: Huang

first: Lucas

last: Caeiro

first: Nikolai

last: Fattakhov

first: Stefano

last: Lepore

first: Liliana

last: Garcia-Martinez

first: Matea

last: Maurice

first: Pushti

last: Mehta

first: Emily

last: Park

first: Kailynn


title: In silico reconstruction of primary and metastatic tumor architecture using GIS-augmented spatial transcriptomics

city: Urbana

first: Zeynep

last: Madak-Erdogan

address: 1201 W Gregory Dr

institute: University of Illinois Urbana-Champaign

summary: Tumor microenvironment (TME) consists of different cell populations, whose interactions contribute to tumor heterogeneity and therapy response. Spatial transcriptomics (ST) offers valuable insights into spatial complexity and heterogeneity of TME. We established a Python package, Geographic Information System (GIS)-augmented In-Silico Reconstruction of Tumor Architecture (GIS-ROTA), based on application of GIS methods to ST data to examine/explore spatial heterogeneity of co-regulated gene sets, such as pathways and cell types within the TME.  In our Visium dataset of primary and metastatic estrogen receptor positive breast tumor samples, GIS-ROTA revealed extensive co-localization of estrogen response with metabolic pathway gene sets and mutual exclusivity with metastasis-related and specific immune-related pathway gene sets. Our findings demonstrate the robustness of GIS-ROTA in quantitating tumor heterogeneity and identifying spatially significant regions while minimizing the subjectivity involved in interpreting the clusters from conventional statistical methods. Thus, GIS-ROTA enables the development of therapeutic strategies that target multiple cell populations.

overall_design: Twelve primary and metastatic bone tumor samples from estrogen receptor positive metastatic breast cancer patients were analyzed using spatial transcriptomics. Two additional primary and metastatic bone tumor samples were analyzed using spatial transcriptomics and proteomics.

first: Jin Young

last: Yoo

first: Sabrina

last: Akter

first: Qianying

last: Zuo

first: Amir

last: Kazemi

first: Wenjun

last: Wu

first: Mahima

last: Goel

first: Audrey

last: Lam

first: Debapriya

last: Dutta

first: Betsy

last: Barnick

first: Melike

last: Pekmezci

first: Maria

last: Grosse Perdekamp

first: Aiman

last: Soliman

first: Matthew

last: Rilloraza


title: Unbalanced chromatin binding of Polycomb complexes drives neurodevelopmental disorders  [RNA-Seq]

first: Rodrigo

last: Lucena Borges

overall_design: Mutant (R70H) and WT  RNA-seq for mESCm, mNPCs and Differentiated cells (WT and R70H)

first: Gretter

last: Gonzalez

first: Harikumar

last: Arigela

first: Yingyu

last: Huang

first: Lucas

last: Caeiro

first: Nikolai

last: Fattakhov

first: Stefano

last: Lepore

first: Liliana

last: Garcia-Martinez

first: Matea

last: Maurice

first: Pushti

last: MacGillivray

first: Jevithen

last: Nehru

last: Chau

first: Clemer

last: Abad

first: Alicia

last: Bilbao-Martinez

first: Fabiola

last: Monteiro

first: Xi

last: Luo

first: Song

last: Tan

first: Daniel

last: Bilbao

first: Simone

last: Sidoli

first: Bruno

last: Di Stefano

first: Katherina

last: Walz

first: Arneet

last: Saltzman

first: Ramiro

last: Verdun

first: Ramin

last: Shiekhattar

first: Lluis

last: Morey


title: A single dose of clinically relevant intravenous iron induces cardiac ferroptosis in cardiometabolic heart failure

city: Charlottesville

first: Caitlin

last: Pavelec

state: VA

address: 1340 Jefferson Park Ave

department: Pharmacology

institute: University of Virginia School of Medicine

summary: Heart failure with preserved ejection fraction (HFpEF) is a clinical syndrome in patients with a left ventricular ejection fraction (LVEF) ≥50% and evidence of diastolic dysfunction (abnormal LV filling and elevated filling pressures) causing symptoms including decreased exercise tolerance and dyspnea. Characterization of clinical phenogroups within HFpEF patients using the standards from TOPCAT (Treatment of Preserved Cardiac Function Heart Failure with an Aldosterone Antagonist Trial) identified one of three that predominantly demonstrates cardiometabolic and inflammatory phenotypes (cardiometabolic HFpEF). (1) This patient population accounts for the largest healthcare burden and has the highest mortality of all three phenogroups. While the primary goal of iron infusion is to enhance HF outcomes, it's crucial to acknowledge the potential for unintended acute myocardial injury following IV iron infusion. This realization prompted us to investigate if a single clinically relevant dose of IV iron could induce ferroptosis in the myocardium.  We identified that a single clinically relevant dose of IV iron acutely induced changes consistent with myocardial ferroptosis. This discovery highlights the urgency of determining if repeated doses of IV iron induce repetitive bouts of ferroptosis and if this adversely affects cardiac function. Further studies should evaluate if the co-administration of ferroptosis inhibitors with IV iron mitigates potential harm while providing the benefits of iron supplementation in cardiometabolic HFpEF.

overall_design: Whole heart of mice fed high fta high sucrose diet or standard chow for 18 weeks given a single dose of IV iron dextran. 48 hours after administration hearts were purfused with PBS and harvested for analysis. Hearts were flash frozen and sent for sequencing.

first: Matthew

last: Wolf


title: Unbalanced chromatin binding of Polycomb complexes drives neurodevelopmental disorders [ChIP-Seq]

first: Rodrigo

last: Lucena Borges

overall_design: Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) for H3K27me3, H2A  (Lys119), RING1B, JARID2, POL2 , CBX7 and RYBP in WT and RING1B R70H mESCs.

first: Gretter

last: Gonzalez

first: Harikumar

last: Arigela

first: Yingyu

last: Huang

first: Lucas

last: Caeiro

first: Nikolai

last: Fattakhov

first: Stefano

last: Lepore

first: Liliana

last: Garcia-Martinez

first: Matea

last: Maurice

first: Pushti

last: Mehta

first: Emily

last: Park

first: Kailynn

last: MacGillivray

last: Nehru

first: Maria


title: Effect of interferon gamma on wild type and SORL1 knockout iPSC-derived microglia

city: New York

first: Falak

last: Sher

state: New York

address: 630 W 168th street

institute: Columbia University

summary: This study investigates the transcriptomic response of wild-type (WT) and SORL1 knockout (KO) iPSC-derived microglia following treatment. For microglia differentiation protocol please see PMID: 38600587.  Bulk RNA sequencing was performed to assess gene expression changes induced by a 48-hour treatment with 10 ng/ml of IFN-γ. The study aims to explore the role of SORL1 in microglial function and its potential impact on neuroinflammatory or neurodegenerative pathways. Differential gene expression analysis will help identify pathways regulated by SORL1 deficiency in response to external stimuli.

overall_design: Bulk RNA-Seq was performed on wild-type and SORL1 knockout iPSC-derived microglia following a 48-hour treatment with 10 ng/ml IFN-γ, with appropriate untreated controls

first: Imdadul

last: Haq

first: Jason

last: Ngo

first: Nainika

last: Roy


title: Unbalanced chromatin binding of Polycomb complexes drives neurodevelopmental disorders [ATAC-Seq]

first: Rodrigo

last: Lucena Borges

state: Florida

overall_design: Mutant (R70H) and  WT ATAC-seqs for mESC and mNPCs

first: Jevithen

first: Matthew

last: Chau

first: Clemer

last: Abad

first: Alicia

last: Bilbao-Martinez

first: Fabiola

last: Monteiro

first: Xi

last: Luo

first: Song

last: Tan

first: Daniel

last: Bilbao

first: Simone

last: Sidoli

first: Bruno

last: Di Stefano

first: Katherina

last: Walz

first: Arneet

last: Saltzman

first: Ramiro

last: Verdun

first: Ramin

last: Shiekhattar

first: Lluis

last: Morey


title: Understanding the effect of milk fat containing diet in the gut epithelial homeostasis.

city: New Delhi

first: G Aneeshkumar

last: Arimbasseri

state: Delhi

address: Aruna Asaf Ali Marg

department: Molecular Genetics Laboratory

country: India

institute: National Institute of Immunology

summary: We employed single-cell RNA sequencing using 10X Genomics technology to investigate the effect of  milk fat diet on gut homeostasis. We have observed that mice with dextran sodium sulfate (DSS)-induced colitis, when fed a milk fat diet, exhibit less severe disease compared to those on a regular chow diet. To further explore this, we examined immune cells, including T cells, B cells, and myeloid cells, along with epithelial cells, which play a critical role in the development of gut inflammation. Our study reveals that mice on the milk fat diet have improved barrier function and higher secretion of antimicrobial proteins, which is reflected in their transcriptomes.

overall_design: We used 24-day-old mice, feeding them either  milk fat diet or a regular chow diet until they reached 7 weeks of age. At 7 weeks, the mice were given 1.5% DSS for 7 days. On day 7, the mice were euthanized, and colonic immune and epithelial cells were isolated. These cells were then sorted into epithelial cells (CD45-, EpCAM+), T cells (CD45+, CD3+), B cells (CD45+, CD19+), and myeloid cells (CD45+, CD3-, CD19-). These cells were mixed and analyzed using scRNA-seq.

first: Chen

last: Chongtham

first: Raunak

last: Kar

first: Dr Veena

last: S Patil

first: Dr G Aneeshkumar


title: Lysosomal Downregulation of the Mu Opioid Receptor is Opposed by the Retromer Complex

city: Portland

first: Braden

last: Lobingier

state: Oregon

address: 3181 SW Sam Jackson Park Road, Mail Code L-334

department: Chemical Physiology and Biochemistry

institute: Oregon Health and Sciences University

summary: The mu opioid receptor (MOR) is protected from opioid-induced trafficking to lysosomes and proteolytic downregulation by its ability to access the endosomal recycling pathway through its C-terminal recycling motif, LENL. MOR sorting towards the lysosome results in downregulation of opioid signaling while recycling of MOR to the plasma membrane preserves signaling function. However, the mechanisms by which LENL promotes MOR recycling are unknown, and this sequence does not match any known consensus recycling motif. Here we took a functional genomics approach with a comparative genome-wide screen design to identify genes which control opioid receptor expression and downregulation. We identified 146 hits including all three subunits of the endosomal Retromer complex. We show that the LENL motif in MOR is a novel Retromer recycling motif and that LENL is a necessary, sufficient, and conserved mechanism to give MOR access to the Retromer recycling pathway and protect MOR from agonist-induced downregulation to multiple clinically relevant opioids including fentanyl and methadone.

overall_design: Single guide RNA (sgRNA) enrichment within sorted cell populations based on fluorogenic reaction readout for opioid receptor abundance after receptor agonist stimulation.

first: Aleksandra

last: Dagunts

first: Hayden

last: Adoff

first: Brandon

last: Novy

first: Lamya

last: Ben Ameur

first: Monica

last: De Maria

first: Arpiar

last: Saunders

first: Braden T


title: An immunobiliary single-cell atlas resolves crosstalk between type 2 conventional dendritic cells and γδ T cells in cholangitis [multiplex_and_CITE_seq]

first: Stefan

last: Thomann

summary: The liver biliary niche serves as a reservoir of tissue-resident immune cells and supports tissue fibrosis upon damage, yet the role of peribiliary immune cells during cholangitis remains poorly understood. Here, we induce cholestatic liver injury mirroring human biliary diseases with bile acid retention in mice to establish a spatial and multimodal single-cell RNA sequencing atlas of the liver and liver-draining lymph nodes (LN). We characterized a hepatic disease state trajectory from dendritic cell precursors (preDCs) to a mature subset of pro-inflammatory Mgl2+ type 2 conventional dendritic cells (cDC2B) and observed dynamic crosstalk with γδ  T cells inducing an Il17 response (γδ T17). Dissection of the cDC2B-γδ T cell communication node identified the Icosl-Icos pair as an important cell contact-dependent interaction, which was validated in vitro. In vivo, cDC2B depletion attenuated γδ T17 responses in cholestatic liver injury, and liver fibrosis was reduced in a model of inducible γδ T cell depletion and in an Il17-deficient background.  Our work demonstrates dynamic turnover of cDC2 within the biliary niche during cholestasis, and a profibrogenic function of γδ T cells contingent on the induction by peribiliary cDC2B, highlighting relevant disease determinants within the immunobiliary and liver-draining LN niche.

overall_design:
Multimodal mouse and human scRNA seq data. 6 human liver samples to capture pseudonormal liver cells and identify niche interactions. Furthermore a DDC disease atlas consisting of 12 samples covering a control and 5 disease timepoints to analyse immune cell dynamics in the DDC model. Furthermore, scRNA-seq datasets covering inflammatory resolution after long-term DDC diet and a short term DDC diet in combination with a cDC2B depletion. A CITE-seq dataset from liver draining lymph nodes at a control and two disease timepoints for the analysis of cDC2 dynamics. Two  experiments of liver immune cells capturing transcriptome and genomic accessibility data modalities at steady state and early cholestasis (DDC D5). Finally, multiplexed scRNA seq data of liver and lymph node derived γδ T cells undergoing cholestasis/cholestasis resolution and disease after cDC2B cell depletion.

Please note that the feature_*.csv file (linked to each ADT or CSL sample records) describes what antibody derived tags were detected in the respective .mtx file (containing the ADT data reads), which is linked to the corresponding GEX sample records.

first: Dominic

last: Grün


title: An immunobiliary single-cell atlas resolves crosstalk between type 2 conventional dendritic cells and γδ T cells in cholangitis [Multiome]

overall_design: Multimodal mouse and human scRNA seq data. 6 human liver samples to capture pseudonormal liver cells and identify niche interactions. Furthermore a DDC disease atlas consisting of 12 samples covering a control and 5 disease timepoints to analyse immune cell dynamics in the DDC model. Furthermore, scRNA-seq datasets covering inflammatory resolution after long-term DDC diet and a short term DDC diet in combination with a cDC2B depletion. A CITE-seq dataset from liver draining lymph nodes at a control and two disease timepoints for the analysis of cDC2 dynamics. Two  experiments of liver immune cells capturing transcriptome and genomic accessibility data modalities at steady state and early cholestasis (DDC D5). Finally, multiplexed scRNA seq data of liver and lymph node derived γδ T cells undergoing cholestasis/cholestasis resolution and disease after cDC2B cell depletion.


title: Identifying metabolic mechanisms of metastasis progression

first: Mariia

last: Yuneva

address: 1 Midland Road

institute: The Francis Crick Institute

summary: The lung is one of the most common sites for metastasis, and various cell types within the lung microenvironment have been shown to facilitate and regulate metastatic outgrowth. Here, we aim to identify the metabolic mechanisms driving lung metastasis derived from MYC-driven mammary gland tumors. Using LC-MS, immunofluorescence (IF), and mass spectrometry imaging (DESI, OrbiSIMS), we observed several metabolic changes in metastatic lesions compared to metastasis-infiltrated lungs and normal healthy lungs. First, we detected an accumulation of lipids and fatty acids in the lung tissue surrounding metastatic lesions. IF staining for fatty acid synthase (FASN), a key enzyme in de novo lipogenesis, revealed its upregulation specifically in alveolar type II cells proximal to metastatic lesions. Second, we found increased levels of oxidized glutathione in metastasis-infiltrated lungs compared to normal lungs, along with higher levels of reduced glutathione in metastatic lesions relative to surrounding lung tissue. Finally, scRNA-seq data from normal and metastatic lungs allowed us to identify transcriptional differences (both general and specific to genes encoding metabolic enzymes) between cells in normal lung tissue and those in metastasis-infiltrated lungs.

overall_design: MMTV-MYC mammary gland tumor-derived cells (LM1) were injected into the mammary fat pad (m.f.p.) of FVBN female mice (6–8 weeks old). Within a month, primary tumors (approximately 1.5 cm in diameter) developed, accompanied by the formation of metastatic lesions in the lung. Primary tumours and lung tissues were collected from 6 tumor-bearing mice and normal lungs were collected from 6 wildtype control mice. Tissues were then dissociated using a standard Liberase TM buffer dissociation protocol. The cells were filtered through 40 µm filters to ensure a single-cell suspension, and the samples were submitted for single-cell RNA sequencing. Cells from 3 primary tumours were used for the analysis. Cells from two lungs were pooled together for each out of 3 normal and 3 metastatic lungs. Additionally, original LM1 cells were also submitted for the sequencing.

first: Weigang

last: Cai

first: Yulia

last: Panina

first: Richard

last: Mitter

first: Maria

last: Rodriguez

first: Hubert

last: Slawinski

first: Robert

last: Gunn


title: An immunobiliary single-cell atlas resolves crosstalk between type 2 conventional dendritic cells and γδ T cells in cholangitis [scRNA-seq]


title: DEAH-BOX HELICASE 8 IS A REGULATOR OF HEAT SHOCK FACTOR 1 [DHX8-HSF1 KD]

city: Sutton

middle: te

last: Poele

state: Surrey

address: 15 Cotswold Road

department: Cancer Reserach UK Unit for Cancer Therapeutics

summary: Heat Shock Factor 1 (HSF1) is a key transcription factor mediating the cellular stress response and promoting cancer cell survival. We identified DEAH-box helicase 8 (DHX8) as a crucial regulator of HSF1 pre-mRNA processing. Silencing DHX8 leads to the accumulation of HSF1 transcripts with retained introns and reduced HSF1 protein. Intron retention was also detected in heat-shock and cancer-signature gene sets regulated by HSF1, and in mitosis, G2M checkpoint, cMYC and E2F-associated gene sets. Consistent with the intron retention phenotype and the role DHX8 in the later stages of splicing, eCLIP analysis found significant enrichment of DHX8 binding between the lariat branch site and 3’ splice junction. DHX8 silencing induces apoptosis in cancer cells to a greater extent than in non-tumorigenic cells. We show that the ATPase activity of DHX8 is essential for function, and propose DHX8 as a therapeutic target on pathways that protect cancer cells from oncogene-induced stress.

overall_design: U2-OS cells were transfected with either siRNA for HSF1 or DHX8 or the AllStars Negative Control and treated either with 17-AAG or DMSO vehicle control

last: te Poele

first: Jennifer

last: Smith

first: Emmanuel

last: de Billy


title: High-Complexity Barcoded Rabies Virus for Scalable Circuit Mapping Using Single-Cell and Single-Nucleus Sequencing

city: San Francisco

first: David

last: Shin

address: 1651 4th Street Room 521A

department: Neurosurgery

institute: University of California, San Francisco

summary: Single cell genomics has revolutionized our understanding of the diversity of neuronal cell types. However, scalable technologies for probing single-cell connectivity are lacking, and we are just beginning to understand how molecularly defined cell types are organized into functional circuits. Here, we describe a strategy to generate high-complexity barcoded rabies virus (RV) for scalable circuit mapping that is compatible with both single-cell and single-nucleus RNA sequencing (sc/snRNA-seq) readout. Our barcoded RV libraries contain up to 43 million unique barcodes with a relatively uniform distribution, allowing multiplexed circuit mapping from tens of thousands of individual starter cells. We demonstrate the utility of this approach by mapping the emerging circuits in the developing human cortex using organotypic slice cultures. By leveraging the power and throughput of single cell genomics for mapping synaptic connectivity, we chart a path forward for scalable circuit mapping of molecularly-defined cell types in healthy and disease states.

overall_design: Sequencing of barcoded G-deleted rabies (RVdG) libraries for quantitative analysis

first: Madeline

last: Urbanek


title: Gene expression changes in commensal 3D melanoma skin models induced by skin bacteria

city: Berlin

first: Heike

last: Sprenger

address: Max-Dohrn-Strasse 8-10

department: Food Safety

institute: German Federal Institute for Risk Assessment

summary:
Skin bacteria impact melanoma related pathways

Melanoma represents the most lethal form of skin cancer, with rising numbers of annual incidences worldwide. In an effort to identify new risk factors that promote melanoma development, the contribution of the skin microbiome gained increasing attention. Previous studies already demonstrated an altered composition of the skin microbiome on melanoma sites. Yet, the underlying mechanisms of the interplay between the microbiome and melanoma progression remain elusive. We established a novel co-culture system capable to study host microbiome interactions during melanoma progression in situ. This system consists of a commercial 3D melanoma skin model colonized with skin bacteria obtained from a skin swab of a healthy volunteer. The models showed a stable co-colonization over a period of 12 days, with Streptococcus being the most abundant genus on the last day of cultivation. Transcriptome profiles revealed significant differences in colonized models compared to control. In particular, pathways involved in melanoma progression, like RAF/MAP and PI3K kinase, were upregulated in colonized models. This correlates with the augmented release of the cytokines VEGF, PIGF, and GM-CSF as well as the typical melanoma markers MIA and S100B. Furthermore, the data were supported by an active epithelial-mesenchymal transition in colonized skin models. Taken together, the bacterial community seems to promote the progression of melanoma in our established system, hence we provide an elegant method to elucidate the microbiome’s impact on cancer development in situ.

overall_design: Co-cultures consisting of a commercial 3D melanoma-in-skin model and skin bacteria were analyzed by microarrays. In total the study included 12 samples from 2 conditions and 2 timepoints with 3 biological replicates each: control day 4, colonized day 4, control day 12, colonized day 12.

first: Aline

last: Rosin


title: LARP6 shapes the mRNA translation of fibrogenic genes [RNA-seq]

city: La Jolla

first: Brian

last: Yee

address: 9500 Gilman Dr

department: Health

institute: UCSD

summary: Metabolic syndrome and excessive alcohol consumption result in liver injury and fibrosis, which is characterized by an increased collagen production by activated Hepatic Stellate Cells (HSCs). LARP6, an RNA-binding protein, was shown to facilitate collagen production. However, LARP6 expression and functionality as a regulator of fibrosis development in a disease relevant model remains elusive.  By using snRNA-seq, we show that LARP6 and collagen-associated genes are upregulated mainly in HSCs of hepatic fibrosis patients. Moreover, LARP6 knockdown in isolated HSCs suppressed fibrogenic genes expression. By integrating eCLIP analysis and ribosome profiling in HSCs, we show that LARP6 interacts with mature mRNAs comprising over three hundred genes, including RNA structural elements within COL1A1, COL1A2, and COL3A1 to regulate mRNA expression and translation. Furthermore, LARP6 reduction attenuates fibrosis in human liver spheroids. Altogether, our results suggest that targeting LARP6 in human HSCs may provide new strategies for anti-fibrotic prevention and therapy.

overall_design: eCLIP for LARP6 in TGFb treated HSCs or untreated.

first: Hyun

middle: Y

last: Kim

first: Orel

last: Mizrahi

first: Wonseok

last: Lee

first: Sara

middle: B

last: Rosenthal

first: Cuijuan

last: Han

first: Steven

last: Blue

first: Jesiel

last: Diaz

first: Jyotiprakash

last: Jonnalagadda

first: Kanani

last: Hokutan

first: Haeum

last: Jang

first: Chen-Ting

last: Ma

first: Andrey

last: Bobkov

first: Eduard

last: Sergienko

first: Michael

last: Jackson

first: Branko

last: Stefanovic

first: Tatiana

last: Kisseleva

first: Gene

middle: W

last: Yeo

last: Brenner


title: DEAH-BOX HELICASE 8 IS A REGULATOR OF HEAT SHOCK FACTOR 1 [DHX8-RIP]

first: Robert

last: Poele

overall_design: RNA from exponentially growing U2-OS cells was immunoprecipitated using the EZ-Magna RIP™ RNA-Binding Protein Immunoprecipitation Kit (Millipore) according to manufacturer's instructions. 5 µg of DHX8 antibody (ab54592, Abcam) or mouse IgG was used per immunoprecipitation.

last: te Poele

first: Jennifer

middle: R

last: Smith

first: Emmanuel

last: de Billy


title: LARP6 shapes the mRNA translation of fibrogenic genes [eCLIP]

first: Brian

last: Yee

first: Hyun

last: Kim

first: Wonseok

last: Lee

first: Sara

last: Rosenthal

last: Han

middle: A

last: Blue

first: Orel

last: Mizrahi

first: David


title: Acute hormonal signaling-induced 3D chromatin loop reorganization controls adipocyte thermogenesis [ATAC-Seq mouse]

city: Boston

first: Kaifu

last: Chen

address: 300 Longwood Ave

institute: Boston Children's Hospital

summary: β3-adrenergic receptor (β3-AR) hormonal signaling is imperative for adaptative thermogenesis, facilitating heat generation during cold exposure. This study explores how β3-AR signaling regulates thermogenic gene activation by altering the three-dimensional (3D) genome organization. Our findings reveal a rapid 3D genome reorganization in brown adipocytes following 4 hours of β3-AR stimulation, highlighted by high-resolution Micro-C analysis. This reorganization involves substantial dynamic changes in chromatin loops, coupled with activation of genes involved in thermogenesis. Mechanistically, β3-AR signaling promotes the p18Hamlet/SRCAP complex assembly, catalyzing the chromatin incorporation of the histone variant H2A.Z. H2A.Z incorporation enhances chromatin accessibility at loop anchors, facilitating loop formation. Disruption of H2A.Z impairs loop dynamics and thermogenic function of brown adipocytes, with implications for both mice and humans. Notably, human homologous loop anchors are associated with obesity-related genetic variants. This study underscores the critical role of 3D genome architecture in thermogenic regulation, offering new dimensions into obesity’s molecular underpinnings.

overall_design: We performed ATAC-seq in vehicle-treated control, β3-AR-stimulated control, and  β3-AR-stimulated H2A.Z knockdowon (KD) brown adipocyte to assess chromatin accessibility changes during thermogenesis and the impact of H2A.Z KD on chromatin accessibility.

first: Yang

last: Zhang

first: Rongbin

last: Zheng

first: Tadataka

last: Tsuji

first: Yu-Hang

last: Xing

first: Chih-Hao

last: Wang

first: Justin

last: Darcy

first: Matthew

last: Lynes

first: Rui

last: Dong

first: Miguel

last: Rivera

first: C Ronald

last: Kahn

first: Ferenc

last: Győry

first: Xiangyu

last: Liu

first: Morten

last: Lundh

first: Rini

last: Arianti

first: Brice

last: Emanuelli

first: Endre

last: Kristóf

first: Yu-Hua

last: Tseng


title: Vitamin D binding protein induces skeletal muscle atrophy and contributes to cancer-associated muscle wasting independently of vitamin D status

city: Novara

first: Francesco

last: Favero

state: NO

address: Corso Trieste 15/A

department: Translational Medicine - CAAD (Center for Translational Research on Autoimmune and Allergic Diseases)

country: Italy

institute: University of Eastern Piedmont

summary: We evaluated the modulation of mRNA in gastrocenmii of wild type and Gc-KO C57BL/6 mice upon cachexia induction with LLC.

overall_design: Gastrocnemius mRNA profiles of 3-month-old wild type (WT) and Gc-KO mice were evaluated 23 days after saline (SAL) or Lewis lung carcinoma (LLC) cell injection.

first: Tommaso

last: Raiteri

first: Andrea

last: Scircoli

first: Simone

last: Reano

first: Stefania

last: Faletti

first: Giuliana

last: Pelicci

first: Davide

last: Corà

first: Nicoletta

last: Filigheddu


title: Acute hormonal signaling-induced 3D chromatin loop reorganization controls adipocyte thermogenesis [Micro-C mouse]

first: Kaifu

last: Chen

overall_design: We performed high-resolution Micro-C in vehicle-treated control, β3-AR-stimulated control, and  β3-AR-stimulated H2A.Z knockdowon (KD) brown adipocyte to assess 3D genome reorganization during thermogenesis and the impact of H2A.Z KD on chromatin loop rewiring.

first: Yang

last: Zhang

first: Rongbin

last: Zheng

first: Tadataka

last: Tsuji

first: Yu-Hang

last: Xing

first: Chih-Hao

last: Wang

first: Justin

last: Darcy

first: Matthew

last: Lynes

first: Rui

last: Dong

first: Miguel

last: Rivera

first: C. Ronald


title: Ketone and glycolytic metabolism are key modulators of inflammation during neonatal sepsis

status: Public on Feb 16 2026

city: Frederiksberg

first: Björn

last: Klabunde

address: Dyrlægevej 68

country: Denmark

institute: Copenhagen University

summary: Neonatal sepsis is a life-threatening condition in preterm infants, primarily due to a dysregulated immunometabolic response to infection. Sepsis and infection mortality are associated with excessive glycolysis-induced inflammation, impaired mitochondrial oxidative phosphorylation (OXPHOS) and loss of disease tolerance. Reduced glucose intake can reverse these dysregulations, but it is unclear how the mechanistic control of glycolysis-OXPHOS balance drives defense strategies and infection outcomes. Here, in a preterm piglet model of neonatal sepsis, glycolysis inhibition with 2-deoxyglucose (2-DG) completely prevents acute infection mortality, reduces systemic inflammation and markers of liver injury, accompanied by enhanced mitochondrial metabolism and disease tolerance. Strikingly, this protection by 2-DG is conferred despite elevated blood glucose levels and higher bacterial burdens than the infected controls. Alternatively, partial replacement of glucose intake with the ketone beta-hydroxybutyrate (BHB) abolishes sepsis-related mortality via improving disease tolerance and clinical parameters.

overall_design: Liver samples (2-13 replicates/condition: 10% Glucose (control), 2.5% Glucose + 2.5% BHB (BHB treated), 2.5% Glucose (restricted Glucose), infected and uninfected) were subjected to bulk RNAseq

first: Ole

last: Bæk

first: Duc Ninh

last: Nguyen


title: Acute hormonal signaling-induced 3D chromatin loop reorganization controls adipocyte thermogenesis [RNA-Seq mouse]

overall_design: We performed RNA-seq in vehicle-treated control, β3-AR-stimulated control, and  β3-AR-stimulated H2A.Z knockdowon brown adipocyte to determine the transcriptional dynamics during thermogenesis and the impact of H2A.Z knockdown on gene activation.

last: Kahn

first: Ferenc

last: Győry

first: Xiangyu

last: Liu

first: Morten

last: Lundh

first: Rini

last: Arianti

first: Brice

last: Emanuelli

first: Endre

last: Kristóf

first: Yu-Hua

last: Tseng


title: Vascular mitohormesis couples Mfn2 with improved systemic metabolism and healthspan

city: Genève

first: Jordi

last: Altirriba

address: Rue Michel-Servet 1

department: Dpts de Médecine Interne et de Physiologie cellulaire et Métabolisme

country: Switzerland

institute: Centre Médical Universitaire de Genève

summary: In this study, we hypothesized that mitochondrial dynamics in ECs orchestrates whole-body metabolic status. Here we report that genetic deficiency of endothelial Mfn2 (Mfn2iΔEC) in mice, originated a mitohormetic response that caused favorable vascular adaptations with regards to antioxidant defenses, mitochondrial fitness and lipid oxidation. As a result, Mfn2iΔEC mice exhibited improved metabolism, resistance to diet-induced obesity and delayed age-related decline. Our results reveal vascular mitohormesis as a novel operation mode influencing systemic energy metabolism and healthspan. These findings endorse the endothelium as a genuine metabolic organ and a potential target against metabolic and age-related deterioration.

overall_design: RNAseq profiles of endothelial cells residing in the adipose tissue from Pdgfb-iCreERT2:Rpl22HA (endothelial RiboTag mice "WT" - 4 replicates) andPdgfb-iCreERT2:Mfn2iΔEC:Rpl22HA (Mfn2iΔEC:Rpl22HA) (endothelial RiboTag and endothelial Mfn2 deficient "KO" - 5 replicates) mice.

first: Iñigo

last: Chivite

first: Alicia

middle: G

last: Gómez-Valadés

first: Macarena

last: Pozo

first: Erika

last: Monelli

first: Luis

last: Varela

first: Sara

last: Ramírez

first: Roberta

last: Haddad-Tóvolli

first: Daniel

last: Beiroa

first: Anne

last: Abot

first: Oscar

last: Osorio-Conles

first: José

last: Valer

first: Arnaud

last: Obri

first: Maria

last: Milà-Guasch

first: Pilar

last: Villacampa

first: Elena

last: Eyre

first: Miriam

last: Toledo

first: Xavier

last: Remesar

first: Antonio

last: Zorzano

first: Francesc

last: Ventura

first: Josep

last: Vidal

first: Claude

last: Knauf

first: Rubén

last: Nogueiras

first: Tamas

middle: L

last: Horvath

first: Mariona

last: Graupera

first: Marc

last: Claret