title: IFN-γ-STAT1 Axis Drives MHC-II Antigen Presentation Potentiation in Tumor Associated Macrophages

city: Kunming

first: Yang

last: Naixue

state: Yunnan

address: 727 South Jingming Road, Chenggong District

department: Yunnan Key Laboratory of Primate Biomedical Research & Institute of Primate Translational Medicine

institute: LPBR

summary: While the IFN-γ-STAT1 signaling pathway is well-characterized in promoting MHC class II (MHC-II)-dependent antigen presentation within pro-inflammatory macrophages during acute infections, its functional dynamics in tumor-associated macrophages (TAMs) remain poorly understood. Here, we systematically investigated the immunomodulatory role of IFN-γ-STAT1 axis in TAMs through integrative bioinformatics and experimental validation. Transcriptomic analysis of tumor-infiltrating myeloid cells across multiple cancer cohorts revealed a strong correlation between STAT1 activation and MHC-II pathway enrichment, particularly in IFN-γ-high TAM subsets. To mechanistically dissect this relationship, we employed bone marrow-derived macrophages (BMDMs) polarized under tumor-conditioned media and subjected them to IFN-γ stimulation. Single-cell RNA sequencing demonstrated that IFN-γ triggered STAT1 nuclear translocation, upregulating MHC-II genes.  Our findings establish IFN-γ-STAT1 as a master regulator of TAM immunogenicity, proposing targeted STAT1 activation as a strategy to overcome myeloid-driven immunosuppression in cancer.

overall_design: Collect BMDMs by detaching them from the dish using warm 0.05% trypsin, followed by washing the cells twice with PBS containing 10% FBS. Resuspend these cells with fresh complete medium (DMEM+10%FBS+100 U/ml penicillin 100 mg/ml streptomycin (Coolaber)), and distribute them into 12-well plates (depending on the experimental design). For the M1 activation assay (TH1 cytokines assay), add a final concentration of 100 ng/ml LPS or 100 ng/ml LPS with 50 ng/ml IFNγ. For the M2 activation assay (TH2 cytokines assay), add a final concentration of 10 ng/ml IL-4 and 10 ng/ml IL-13 or 10 ng/ml IL-4 and 10 ng/ml IL-13 with 50 ng/ml IFNγ. Collect the stimulated BMDMs by detaching them from the dish using 5mM EDTA in PBS, followed by washing the cells twice with PBS containing 10% FBS.

first: Naixue

last: Yang

first: Hao

last: Yuan

first: Xun

last: Lan


title: Positive feedback between cDC1s and CD8+ T cells typifies the inflammation of HLA-B27+ arthritis

status: Public on Feb 22 2026

city: Nanjing

first: yang

last: sun

state: Jiangsu

address: Nanjing University Academy of Sciences, No. 163 Xianlin Avenue, Qixia District, Nanjing City, Jiangsu Province

department: Life Sciences

country: China

institute: Nanjing University

type: Expression profiling by high throughput sequencing

summary: Enthesitis-related arthritis (ERA) is a subtype of juvenile idiopathic arthritis (JIA) with enthesitis and sacroiliitis, which differ from other types of JIA in symptoms, pathogenesis, and outcome. Although the association of human leukocyte antigen-B27 (HLA-B27) with ERA has been confirmed for decades, the pathogenesis of ERA is poorly understood. Here, we performed single-cell RNA-seq of 1,73,134 mononuclear cells extricated from patients with oligoarthritis (OligoA) or ERA and integrated 58,725 PBMCs of healthy people to profile the immune characteristic that discriminates ERA from OligoA. We found that conventional type 1 dendritic cells (cDC1s) were enriched in the joints of patients with ERA and exhibited a high level of MHC class I antigen presentation. Central memory CD8+ T cells critically contributed to the elevation of XCL1, recruiting XCR1+ cDC1 in joints of ERA. Flow cytometry and enzyme-linked immunosorbent assay (ELISA) analyses confirmed an increased proportion and interaction of cDC1s and CD8+ T cells. In addition, macrophages occupied the causal position in the pathogenesis of OligoA, along with high expression of MHC class II molecules on macrophages and cDC2s in the joints. This study suggests that the positive feedback between cDC1s and CD8+ T cells is a key mediator of HLA-B27-positive arthritis pathogenesis.

overall_design:
To characterize the specific signature of HLA-B27-positive ERA, we collected peripheral blood and synovial fluid samples of untreated patients with ERA who exhibited evident sacroiliac arthritis or enthesis in intertarsal joints. For a comparison with the ERA samples, the samples of untreated OligoA were chosen according to the International League of Associations for Rheumatology (ILAR) classification criteria. We obtained mononuclear cells from peripheral blood (PBMC) and synovial fluid (SFMC) of patients with OligoA or ERA and analyzed them using single-cell RNA-seq .

>>>Submitter states that raw data are not availble due to patient privacy concerns<<<

first: Fenli

last: Shao

first: Zhigui

last: Wu


title: Early Transcriptional Responses to Human Typhoid Challenge

city: Oxford

first: Amber

last: Barton

state: Oxfordshire

address: Old Road

country: United Kingdom

institute: Oxford Vaccine Group

summary: The whole blood transcriptome 12 and 24 hours after challenge with S. Typhi Quailes Strain. Samples were collected from two studies: a dose finding study aiming to find the challenge dose giving a 60-75% attack rate, published in Waddington et al. 2014 [PMID: 24519873], and the placebo arm of a typhoid oral vaccine trial, published in Darton et al. 2016 [PMID: 27533046]. Participants were treated with antibiotics either following diagnosis or 14 days without diagnosis.

overall_design: Outpatient dose-finding challenge study and placebo arm of a randomised controlled oral vaccine trial. Peripheral blood was collected at baseline, 12 and 24 hours post-challenge in Tempus Blood RNA tubes. RNA was extracted using a Tempus Spin RNA Isolation kit. RNA samples from individuals in the typhoid dose-finding study and typhoid oral vaccine trial were hybridised onto Illumina HT-12v4 bead-arrays, and fluorescent probe intensities captured with GenomeStudio software. Samples were hybridised in three batches: batch 1 (dose-finding study, baseline n = 19, 12 hours post-challenge n = 27); batch 2 (dose-finding study, 12 hours post-challenge n = 41, 24 hours post-challenge n = 41) and batch 3 (typhoid oral vaccine trial, baseline n = 18, 12 hours post-challenge n = 17). Baseline samples from the typhoid oral vaccine trial are a re-analysis of samples in series GSE112958.

first: Christoph

last: Blohmke

first: Andrew

middle: J

last: Pollard


title: Spatially resolving chromatin landscapes in formalin-fixed paraffin-embedded tissues

city: New Haven

first: Haikuo

last: Li

state: CT

address: 55 Prospect St

country: USA

institute: Washington University in St. Louis

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Formalin-fixed paraffin-embedded (FFPE) samples represent an invaluable resource for histopathology research, but chromatin crosslinking in these fixed tissues precludes epigenomic analyses. Here, we present methods for reversing crosslinking in FFPE tissues followed by spatially resolved assay for transposase-accessible chromatin using sequencing (spatial-FFPE-ATAC) or cleavage under targets and tagmentation (spatial-FFPE-CUT&Tag). We applied spatial-FFPE-ATAC on adult mouse brain and revealed region-specific chromatin accessibility profiles with data quality comparable to standard ATAC-seq performed on fresh-frozen samples. Spatial-FFPE-ATAC delineated the epigenetic heterogeneity of clinical archival lymphoma of mucosa-associated lymphoid tissue and follicular lymphoma samples and uncovered tumor-specific karyotypes. Spatial-FFPE-ATAC traced cell proliferation by mitotic age inference and identified cholesterol-mediated cell proliferation in tumor cells. Spatial-FFPE-CUT&Tag in a transformed diffuse large B-cell lymphoma tissue revealed increased H3K27me3 occupancy at a chromosome 2 locus associated with tumor-specific copy number amplification. Therefore, spatial-FFPE-ATAC and spatial-FFPE-CUT&Tag enable genome-wide epigenomic profiling and epigenetic regulation investigations in archival FFPE samples.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Spatial-ATAC-seq or spatial-CUT&Tag on FFPE samples of mouse brain, mouse colon and human lymphoma.

first: Rong

last: Fan


title: Next Generation Sequencing Facilitates Quantitative Analysis of COL,uvr8 mutant treated with ABA or UV-B Transcriptomes

city: Shenzhen

first: Yao

last: Peng

address: 1066 Xueyuan Avenue, Nanshan District

institute: Shenzhen University

summary: To expore whether UV-B induce the expression of ABA-responsive genes, we compared transcriptomes of 10-d-old Col-0 and uvr8 seedlings ± 50 uM ABA treatment and 3-h exposure to 5 mol m–2 s–1 UV-B or white-light control.

overall_design: 10-d-old Col-0 and uvr8 seedlings grown in long-day conditions were treated with or without 50 uM ABA in white light or white light plus UV-B(5 umol m–2 s–1) for 3 h. Total RNA was isolated using the RNAiso Plus (Takara) kit. RNA quality control was performed by gel electrophoresis. Three biological replicates were independently prepared throughout the processes, from the induction of seed germination to the preparation of RNA-seq libraries.

first: Hongtao

last: Liu


title: DNA methylation in episodic migraine and medication overuse headache.

status: Public on Feb 21 2026

city: Bologna

first: Paolo

last: Garagnani

state: BO

address: Via San Giacomo 12

department: Department of Medical and Surgical Sciences (DIMEC)

country: Italy

institute: Univeristy of Bologna

type: Methylation profiling by genome tiling array

summary: These data were generated within the Epimode project - a pilot, longitudinal, prospective, observational study designed to investigate DNA methylation in headache disorders. 20 episodic migraineurs (EM), 25 medication overuse headache patients (MOH) and 13 healthy controls (HC) were enrolled in the study. EM and HC samples were collected at baseline (T0) and ath the follow-up visit 6 months later (T1). MOH samples were collected at baseline (T0), at treatment time point (T1) and at the follow-up visits after 2 (T2) and 6 (T3) months from the therapeutic intervention.   Genome-wide methylation data for overall 142 DNA (WB) samples were generated using Illumina Infinium Methylation EPIC v1.0 BeadChip. Generated dataset allowed us to analyse differential signatures, methylation clocks and stochastic epigenetic mutations related to EM, MOH and response to the treatment.

overall_design: Bisulphite converted DNA from 142 whole blood samples were hybridised to the Illumina Infiniun MethylationEPIC BeadChip following manufacture's protocols.

first: Katarzyna

middle: M

last: Kwiatkowska

first: Sabina

last: Cevoli


title: Parasympathetic nerves in the kidney pelvis contribute to blood pressure regulation

city: Chongqing

first: Xiaofeng

last: Cheng

address: Chongqing City, Shapingba District, Xinqiao Zheng Street

institute: Army Medical University

summary: The existence of parasympathetic innervation in the kidney has long been controversial. Recent anatomical studies have provided evidence supporting such innervation by demonstrating the presence of acetylcholine (ACh) metabolic enzymes and tracing a brain-kidney vagal axis. Although these findings confirm the anatomical pathway, the functional capacity of these nerves to release neurotransmitters remains unverified, and the physiological role of this pathway is still unknown. We delineated the innervation of the renal pelvis by co-labeling sympathetic, parasympathetic, and sensory nerves. ACh receptors expression was assessed through single-cell RNA sequencin, quantitative reverse transcription polymerase chain reaction, and fluorescent in situ hybridization. The ACh release from the renal nerves was monitored via fiber photometry with a genetically encoded ACh sensor. Optogenetic activation was employed to investigate the functional effects of renal parasympathetic efferent and afferent pathways on blood pressure and heart rate. We identified multi-component innervation in the renal pelvis, including sympathetic, parasympathetic, and sensory nerves. Moreover, muscarinic ACh receptors were found to be expressed in this region. Neurogenic ACh release from renal nerves was also detected following transmural stimulation. Furthermore, optogenetic activation of the vagal brain–kidney afferent pathway resulted in a decrease in blood pressure. These results suggest that the renal pelvis receives dual autonomic innervation from both sympathetic and parasympathetic nerves, and the vagal renal afferents are involved in blood pressure regulation.

overall_design: Renal pelvises were dissected from 15 adult (10-week-old) male C57BL/6 mice under a surgical microscope. The tissues were then digested into single-cell suspensions and subsequently analyzed by single-cell RNA sequencing.

first: Jin

last: Zhao

first: Linlin

last: Hu

first: Changwei

last: Guo

first: Ran

last: Ran

first: Mingrui

last: Xu

first: Hui

last: Lu

first: Qi

last: Xie

first: Zhaoyou

last: Meng

first: Sen

last: Lin

first: Chenhao

first: Qingwu


title: Super-enhancers reorganization controls re-sensitization of oxaliplatin-resistant FBXW7-mutated colorectal cancer [ChIP-seq]

city: Udine

first: Nicolò

last: Gualandi

state: Italy

address: P.le Kolbe, 4

department: Department of Medicine

institute: Università degli studi di Udine

summary:
Epigenetic plasticity and large-scale chromatin remodeling characterize tumor evolution and the emergence of subclones resistant to conventional therapies. Catalytically inactive class IIa HDACs (HDAC4, HDAC5, HDAC7, HDAC9) act as acetyl-lysine readers that form the scaffold for the targeted recruitment of chromatin remodeling complexes, making them very attractive therapeutic targets in the field of oncology.
In this study, we found that HDAC4 is proteasomal degraded in cancer cells impaired in DNA repair by homologous recombination. Genetic screening identified FBXW7 as the E3 ligase responsible for this degradation. FBXW7 loss-of-function mutations are frequently found in patients with colorectal cancer (CRC), and FBXW7 mutation status is associated with the development of resistance to oxaliplatin. Deletion of HDAC4 or its forced degradation with a PROTAC-based compound restored oxaliplatin sensitivity in FBXW7-mutated CRC cells, patient-derived organoids (PDOs) and xenografts, with no effect on DNA damage response activation or DNA platination.
Mechanistically, forced removal of HDAC4 in FBXW7-mutant CRC cells and PDOs treated with oxaliplatin resulted in a deep rearrangement of the super-enhancer landscape, with a dramatic loss of super-enhancers found in oxalipaltin-resistant samples and restoration of certain super-enhancers found in oxaliplatin-sensitive cells. The disassembly of HDAC4 complexes achieved with Tasquinimod partially recapitulated the effects obtained with the PROTAC-based HDAC4 compound, demonstrating the importance of the epigenetic function of HDAC4 in supporting drug resistance.
This study supports HDAC4 as a key mediator of oxaliplatin resistance in FBXW7-mutated CRC and highlights the remodeling of a well-defined repertoire of super-enhancers as part of the process of successful re-sensitization.

overall_design: Chromatin was extracted from HCT-116 cells, WT or KO for FBXW7, and transfected for 48h with esiRNAs directed against CT or HDAC4. Cells were treated or not for the last 24h with OxPt (50 µM). After cross-linking, 50µg chromatin was immunoprecipitated from each samples with 3µg antibody against H3K27ac (Abcam, ab4729) or IgG. After de-crosslinking, chromatin was eluted and subjected to library preparation and sequencing.

first: Vanessa

last: Tolotto

first: Ylenia

last: Cortolezzis

first: Eros

last: Di Giorgio


title: The timing of antenatal glucocorticoids determines the receptor sensitivity in preterm infants

city: Leioa

first: Mariana

last: Astiz

state: Bizkaia

address: Barrio Sarriena s/n, Science Park of the UPV/EHU, Sede Building, 3rd floor

country: Spain

institute: Achucarro Basque Center for Neuroscience

summary: Approximately 15 million babies are born too early each year, corresponding to a global preterm birth rate of about 11%. The antenatal glucocorticoid (aGC) therapy is indicated to more than 90% of their mothers when there is a risk of preterm delivery between 24 and 34 weeks of gestation. Synthetic GCs (sGC) accelerate fetal lung maturation and reduce the risk of respiratory distress syndrome (RDS), the leading cause of mortality in preterm infants. However, this treatment has been associated with an increased vulnerability to develop neurobehavioral and immune disorders later in life, effects attributed to permanent changes in the stress axis activity and in the homeostasis of endogenous GCs. In the present study, we assessed the effect of the antenatal administration of aGCs in preterm babies with a special focus on the influence of the time of exposure. We found that preterm infants exposed to aGCs in the late evening (i.e.: out-of-phase relative to the maternal daily cortisol rhythms) exhibited reduced GR sensitivity in peripheral blood mononuclear cells (PBMCs). By comparing the transcriptome of PBMCs we found significant changes in genes involved in antibody production and B cell signaling, leucocyte migration and proliferation, antigen presentation and cellular stress responses. Our data suggests that the aGCs exposure in the morning, in-phase and aligned with the maternal GC rhythms, would be advisable in the clinics to minimize these secondary effects and improve the capacity of preterm infants to fight against pathogens during the first weeks of life.

overall_design: The RNA samples were obtained from peripheral blood mononuclear cells (PBMCs) from 13 term babies (controls) and 34 premature babies exposed to antenatal glucocorticoids (aGCs). We further devided the aGCs exposed babies' samples depending on the time of day in which the mother was exposed. Babies exposed to aGCs in the morning are grouped as in-phase (IP, n=17) (with the maternal circadian rhythms) and babies exposed in the evening are grouped as out-of-phase (OP, n=17).

first: Ingmar

last: Fortmann

first: Jan

middle: H

last: Britsemmer

first: Marianne

last: Lehmann

first: Natalie

last: Taege

first: Henrik

last: Oster

first: Henriette

last: Kirchner

first: Christoph

last: Haertel


title: MeRIPseq of m6A in HL7702 cells with with stable knockdown of TTP

city: Wuhan

first: RUI

last: Zhou

address: Donghu Road 185

institute: Wuhan University

summary: N6-methyladenosine (m6A) modification plays a central role in liver diseases. TTP has been known as a transcriptional co-factor and can interact with some transcription factors to regulate gene expression at the transcriptional level. However, the molecular mechanism underlying the transcriptional regulation of several m6A-associated genes by TTP remains to be defined.

overall_design: m6A IP of total RNA extraction of HL7702 cells with stable knockdown of TTP.

first: Rui

first: Xuejun

last: Zhao

first: Kejun

last: Liu


title: Transcriptomic and Functional Responses of Human Airway Cells to Vaped ∆8-THC and its Oxidation Product ∆8-THCQ

city: Chapel Hill

first: Ilona

last: Jaspers

state: NC

address: 125 Mason Farm Rd

department: Marsico Lung Institute

institute: University of North Carolina at Chapel Hill

summary: Δ8-tetrahydrocannabinol (Δ8-THC) vaping products rapidly expanded following the 2018 Farm Bill, yet remain largely unregulated despite high cannabinoid concentrations, additives and contaminants, and growing links to adverse respiratory outcomes. Here we show that the reactive electrophile Δ8-THC quinone (Δ8-THCQ, HU-336) is present in significant quantities in commercial Δ8-THC distillate and disposable products and increases after vaping. Across high concentration products, Δ8-THCQ rose an average of 3.67-fold, reaching millimolar levels. While Δ8-THC itself produced no measurable transcriptomic response in a bronchial epithelial cell line, Δ8-THCQ markedly altered gene expression, prominently upregulating cilia and stress related programs alongside xenobiotic metabolism and inflammatory pathways. Using primary differentiated human bronchial epithelial cells exposed with the UNC Vaping Product Exposure System (VaPES), we demonstrate that vaped commercial Δ8-THC mixtures induce immediate early stress genes, suppress ribosome and mitochondrial pathways, and trigger fibrosis associated signaling, while juices caused comparatively modest effects, primarily limited to upregulation of cell-cycle and proliferation-associated genes. Computational analysis further mechanistically linked coordinated chemical features of Δ8-THC aerosols to the airway transcriptional programs they induced, identifying clusters of chemicals that drive specific biological responses. Functionally, distillate and disposable aerosols rapidly impaired motile cilia activity. Together, these data identify Δ8-THCQ as a major vaping-generated reactive product in Δ8-THC aerosols and suggest that repeated inhalation may disrupt mucociliary defense and promote chronic airway injury.

overall_design: To characterize the effects of ∆8-THC vaping product mixtures, we performed transcriptomic analysis (RNA-seq) on primary human bronchial epithelial cells or HBECs (n = 4 donors, 2 replicate wells/donor) exposed to the 6 commercially available ∆8-THC products previously used for chemical analysis (10 puffs) using the UNC Vaping Product Exposure System (VaPES). Commercial products were compared to a 40/60 propylene glycol/vegetable glycerin (PG/VG) vaping control. Distillate products were aerosolized with a Silo Battery (Ccell; Phoenix, Arizona; 500 mAh; ~3.7 V; Ceramic Coil) and the juices and control were aerosolized with a CBDFx Tank (part of CBDFx Vape Kit) (CBDFx; Chatsworth, CA; 1000mAh; ceramic coil).

first: Charlotte A

last: Love

first: Hye-Young H.

last: Kim

first: Julia E.

last: Rager

first: Keri A.

last: Tallman

first: Kevin D.

last: Schichlein

first: Ned A.

last: Porter


title: Super-enhancers reorganization controls re-sensitization of oxaliplatin-resistant FBXW7-mutated colorectal cancer

first: Nicolò

last: Gualandi

overall_design: RNA was extracted from HCT-116 cells, WT or KO for FBXW7, and transfected for 48h with esiRNAs directed against CT or HDAC4 or treated with PROTAC compound #11 directed against HDAC4. Cells were treated or not for the last 24h with OxPt (50 µM).

first: Vanessa

last: Tolotto

first: Ylenia

last: Cortolezzis

first: Eros

last: Di Giorgio


title: The impact of Pyruvate dehydrogenase kinase 4 overexpression on the function of vascular smooth muscle cells

city: Guangzhou

first: Li

state: Guangdong

address: 1838 North Guangzhou Avenue,

department: Department of Cardiovascular Surgery

institute: Nanfang Hospital, Southern Medical University

summary: This study investigated the impact of pyruvate dehydrogenase kinase 4 overexpression on the function of vascular smooth muscle cells.

overall_design: Vascular smooth muscle cells were transduced with adenoviral vectors carrying pyruvate dehydrogenase kinase 4 overexpression plasmids or control plasmids. The expression of pyruvate dehydrogenase kinase 4 in vascular smooth muscle cells was detected using RT-qPCR, followed by transcriptomic sequencing to investigate the impact of pyruvate dehydrogenase kinase 4 on the function of vascular smooth muscle cells.

first: Xiu


title: Cholesterol unlinks innate-adaptive immune axis in tuberculosis granulomas [human]

city: beijing

first: lu

last: z

state: - 选择 -

address: beijing

institute: institution of microbology

summary: Chronic lung infection, a long-standing global health issue, associates with compromised protective immunity against pathogens (PMID: 29062070, PMID: 27890913). Lung granulomas, consisting of immune cell aggregates, represent regional immune microenvironments formed in response to chronic infections, such as Mycobacterium tuberculosis (Mtb)-caused tuberculosis (TB) (PMID: 36493751). However, the microenvironmental factors and mechanisms modulating protective immune response in granulomas remain incompletely understood. Here, we employ multiplex immunohistochemistry and spatial transcriptomics of human specimens and mouse models to map the locations, transcriptomes, and interactions of macrophages and T cells in TB granulomas. We identify the immune plasticity of macrophages and T cells shaped by granuloma lesion severity and their proximity to multinucleated giant cells or tertiary lymphoid structures. We further uncover a lipid-related disruption of innate-adaptive immune interplay in necrotic granulomas, with immunopathological features distinct from those of the lung tumor microenvironment. Mechanistically, this immune disruption results from Mtb-induced macrophage lysosomal cholesterol accumulation, which sequesters major histocompatibility complex II in lysosomes, thereby hindering antigen presentation and impairing T cell anti-Mtb response. Pharmacologically restoring cholesterol homeostasis of lung macrophages enhances T cell anti-Mtb protective immunity in mice. Collectively, our study reveals the lysosomal cholesterol overload-impaired innate-adaptive immune axis in granulomas, and indicates a cholesterol-targeting therapeutic strategy against chronic lung infection.

overall_design: For collection of lung tissue specimens, we utilized a retrospective cohort including lung tuberculosis (TB) patients and lung adenocarcinoma (LUAD) patients from the Beijing Chest Hospital (PMID: 33097805). Only archival surgical resection tissues were analyzed, with no active participation of human subjects. For the NanoString GeoMx DSP transcriptional assays, slides containing human TB or LUAD lung tissues (4 μm) were prepared following the manufacturer’s instruction from GeoMx DSP Slide Preparation User Manual (NanoString, MAN-10115-05 for software v2.3), and then scanned with the NanoString DSP instrument with a 20× objective for RNA probes collection.The scanning areas were set to only scan the tissues. The tissue boundaries were determined by adjusting the x and y scanning areas and the sensitivity. Region of interests (ROIs) were placed per tissue based on the selection regions and assessment. For each group of immune cells within a specified tissue region, n = 4 independent ROIs with an area of 0.2–0.5 mm2 each were collected for subsequent analysis. Each ROI contained approximately 300 specific immune cells.

first: Qiyao

last: Chai

first: Zhe

last: Lu

first: Cui


title: Single nucleotide insertion within a remote enhancer causes XX mice to be born as males

city: Ramat Gan

first: Isabelle

last: Stévant

address: Institute of Nanotechnology and Advanced Materials, Building 206

country: Israel

institute: University of Bar Ilan

summary: In this study, we show that mice carrying a 3 bp deletion or 1 bp insertion within the SOX9 BS of Enh13 are born as XX males. At adult stages, mice appear externally and internally as males but their testes are small and devoid of sperm due to the lack of the Y chromosomes. At embryonic stages, XX homozygous gonads appear as ovotestis at various severities with the 1 bp insertion appearing more as a testis. Transcriptomic analysis of E12.5 gonads shows that indeed the XX homozygous gonads are positioned in between the testis and ovary while XY homozygous gonads are indistinguishable of wild type (WT) XY gonads. These findings implicate Enh13 as a dual regulatory element essential for both testicular and ovarian development, placing it at the critical intersection of sexual differentiation pathways.

overall_design: Gonad pairs of E12.5 XX and XY mouse embryos carrying induced mutations in the Enh13 of the Sox9 gene. Control (WT) and heterozygous mutant gonads were collected in triplicates. Homozygous mutant gonads we collected in 5 replicates.

first: Elisheva

last: Abberbock

first: Meshi

last: Ridnik

first: Roni

last: Weiss

first: Carmel

last: Bemberger

first: Shelly

last: Ziv Lherman

first: Maor

last: Lubman

first: Yumi

last: Yao

first: Ariel

last: Afek

first: Francis

last: Poulat

first: Nitzan

last: Gonen


title: Cholesterol unlinks innate-adaptive immune axis in tuberculosis granulomas [mouse]

overall_design: C3HeB/FeJ mice (The Jackson Laboratory, Strain # 000658) were a kind gift of B. Ge (Tongji University School of Medicine, Shanghai, China). All mice were housed in a specific pathogen-free (SPF) facility on the basis of standard humane animal husbandry protocol. In vivo Mycobacterium tuberculosis (Mtb) infection experiments were performed with sex-matched groups of 6–8 weeks mice via the aerosol route using an inhalation exposure system (Glas-Col Inc.) as previously described (PMID: 36227980). The aerosol unit was programmed to deliver ~ 100 colony forming units (CFUs) per animal, as determined by plating whole lung homogenates from five mice on Middlebrook 7H10 agar for CFU counting within 24 hours of infection. For digital spatial profiling (DSP), 7-weeks old female mice were infected with Mtb. At 0, 2, 4, 6, and 8 weeks post-infection, their lungs were excised, and the right lobes were collected for subsequent transcriptional assays. For the NanoString GeoMx DSP transcriptional assays, slides (4 μm) containing a collection of lung tissues from mice infected for 0, 2, 4, 6, and 8 weeks were prepared following the manufacturer’s instruction from GeoMx DSP Slide Preparation User Manual (NanoString, MAN-10115-05 for software v2.3), and then scanned with the NanoString DSP instrument with a 20× objective for RNA probes collection. The scanning areas were set to only scan the tissues. The tissue boundaries were determined by adjusting the x and y scanning areas and the sensitivity. Region of interests (ROIs) were placed per tissue based on the selection regions and assessment. For each group of immune cells within a specified tissue region, n = 3–4 independent ROIs with an area of 0.2–0.5 mm2 each were collected for subsequent analysis. Each ROI contained approximately 300 specific immune cells.

last: Liu


title: A Comprehensive Profile of microRNAs in Human Tear Fluid

city: Augusta

first: Ashok

last: Sharma

state: GA

address: 1120 15th Street

department: Ophthalmology

institute: Augusta University

type: Non-coding RNA profiling by high throughput sequencing

summary: We performed miRNA sequencing on RNA extracted from 32 human tear fluid samples collected using Schirmer strips from healthy individuals. Our goal was to generate a comprehensive profile of miRNA content in human tears and to examine potential demographic-specific differences among healthy samples.

overall_design: miRNA-seq profiling of 32 human tear fluid samples from healthy individuals.

first: Jones

last: Garrett

first: Mayernik

last: Drew

first: Ahmed

last: Saleh

first: Williams

last: Eliza

first: Altman

last: Jeremy

first: Lee

last: Tae Jin

first: Estes

last: Amy

first: Cintia

middle: S

last: de Paiva

first: Pamela

last: Martin

first: Sharma

last: Shruti

last: Ashok


title: Effect of heme on the chromatin accessibility of differentiating mouse B cells

city: Atlanta

first: Chris

last: Scharer

address: 1510 Clifton Rd, Suite 3086A

department: Microbiology and Immunology

institute: Emory University

summary: The effect of heme on the chromatin accessibility of differentiating mouse B cells was assessed by isolating splenic CD43- B cells and culturing with LPS, IL2, and IL5.  After 24 hours heme or vehicle control was added to the cultures.  At 72 hours activated B cells and plasmablasts were FACS isolated and ATAC-seq performed.

overall_design: ATAC-seq was performed on activated B cells and plasmablasts differentiating in the presence or absence of heme in triplicate.

first: Christopher

middle: D


title: scRNA-seq of MHCII-KO and WT B cells during influenza infection

summary: To evaluate the programming of B cells subsets that arise in the absence of CD4 T cell interactions we adoptively transferred wild-type (WT) and majorhistocompatibility class II (MHC-II) knockout B cells into WT hosts and infected the mice with influenza PR8.  All activated responding transferred B cells were profiled at day 14, a time point when T cell independent memory responses arise, and scRNA-seq and BCR-seq performed to understand the transcriptional programming that is dependent on CD4 T cell interactions.  We identified minimal differences between WT and KO B cells, with a diverse number of memory B cell clusters identified that were populated by cells fron both cohorts of mice.  These data indicate that the memory B cells that form early, likely extrafollicularly, do not depend on CD4 T cells for their programming and diversity.

overall_design: 2 biological replicates of MHCII-KO and WT B cells that are responding to influenza infection were isolated at day 14 for scRNA-seq coupled to BCR-seq.


title: FOXA1 loss induces aggressive prostate cancer via unleashing basal/squamous de-differentiation and an immunosuppressive microenvironment

first: Jindan

last: Yu

address: E330, 1760 Haygood Dr NE

department: Urology

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

overall_design: Refer to individual Series


title: FOXA1 loss induces aggressive prostate cancer via unleashing basal/squamous de-differentiation and an immunosuppressive microenvironment [ChIP-seq]

summary: FOXA1 is an epithelial transcription factor that is often found dysregulated in prostate cancer. Previous studies have reported both tumor-promoting and -inhibitory functions of FOXA1. However, a comprehensive analysis of FOXA1 in a physiological, immune-competent setting is still lacking. We here report a novel genetically engineered mouse model with Foxa1 KO in the Pten-null prostate epithelium for the study of FOXA1 loss within an immune-competent prostate tumor context. Here, we report Foxa1 loss induces prostate cancer lineage switch from a  luminal-like to a more aggressive basal/squamous-like phenotype, which is accompanied by  inflammatory and immunosuppressive cytokine signaling.  Mechanistically, in addition to inducing luminal genes, we found FOXA1 directly inhibits several basal/squamous, inflammatory, and cytokine genes, such that its loss unleashes their expression. Moreover, Foxa1 loss induces a striking remodeling of the prostate tumor immune microenvironment, leading to increased immunosuppressive myeloid accumulation and dysfunctional and spatially confined T cells. Altogether, we report critical roles for FOXA1 loss in inducing basal/squamous de-differentiation and an immunosuppressive microenvironment.

overall_design: To investigate the FOXA1 cistrome and H3K27ac changes upon FOXA1 loss, we performed FOXA1 and H3K27ac ChIP-seq  in prostate tissues of intact PbCre4:Ptenf/f (P) and PbCre4:Ptenf/fFoxa1f/f (PF) mice at 18-wk, in triplicate biological samples.

first: Lourdes

last: Brea

first: Qi

last: Chu

first: Jonathan

middle: C

last: Zhao


city: Rehovot

first: Ariel

last: Afek

address: Herzl st 234

institute: Weizmann Institute of Science

summary: Sex determination is mediated by two antagonistic genetic pathways. Sox9 activation or repression governs testis or ovary development, respectively. The remote enhancer Enh13 is critical for testicular Sox9 regulation, with its deletion or mutation causing XY female sex reversal. Here, we demonstrate that specific Enh13 mutations (1 bp insertion or 3 bp deletion) induce complete XX male sex reversal, with embryos exhibiting ovotestes and adults presenting with small testes. Transcriptomic analysis reveals elevated testicular gene expression, including Sox9, and repressed ovarian genes. These mutations disrupt cooperative binding of bipotential transcription factors to Enh13, preventing Sox9 repression in the ovary. Our findings establish Enh13 as a dual regulatory element essential for both testicular and ovarian development, positioning it at a critical intersection of sexual differentiation pathways.

overall_design: Two universal protein binding microarray (PBM) experiments of human transcription factors were performed. Briefly, the PBMs involved binding Flag-tagged transcription factors Sox9 and Runx1 to double-stranded 60K Agilent microarrays containing all 10mer DNA sequences or all 9mer DNA sequences to determine their binding specificity to all possible 8mer DNA sequences or all possible 7mer sequences. In this way, further analysis allowed us to study how the binding of Sox9 and Runx1 changed when there are insertions, deletion and mutations in their canonical binding sites. We report the PBM signal intensity for each spot (raw files) as well as the spatially normalised signal intensity for each spot (normalised data) The PBM protocol is described in Berger et al., Nature Biotechnology 2006 (PMID 16998473).

first: Yumi Minyi

last: Yao


title: FOXA1 loss induces aggressive prostate cancer via unleashing basal/squamous de-differentiation and an immunosuppressive microenvironment [Visium]

overall_design: To understand the spatial organization and distribution of prostate cancer cells and immune populations wihtin the tumor microenvironment, we performed spatial transcirptomics analysis of age-matched PbCre4:Ptenf/f (P) and PbCre4:Ptenf/fFoxa1f/f (PF) mice.

first: Viriya

last: Keo


title: Transcriptional profiling of memory B cells that form during influenza infection of majorhistocompatibility class II (MHC-II) knockout mice.

summary: To evaluate the programming of activated B cells and memory B cell subsets that form in the absence of CD4 T cells we infected wilt-type (WT) and majorhistocompatibility class II (MHC-II) knockout mice with influenza PR8 and profiled the response at day 14, a time point when T cell independent memory responses arise.  We isolated activated, dividing B cells which give rise to memory subsets as well as IgM and class-switched memory B cells from both cohorts of animals.  These studies identify the memory B cell programming that is dependent on CD4 T cells.

overall_design: At day 14 we sorted activated B cells and IgM+ and IgM- class-switched memory B cells from 3 independent biological replicates and performed RNA-seq.


title: Glucocorticoid eceptor dimerization in  tumorigenesis

status: Public on Feb 20 2026

city: Göttingen

first: Sybille

middle: Dorothee

last: Reichardt

address: Humboldtallee 34

department: Institute for Cellular and Molecular Immunology

country: Germany

institute: University Medical Center Göttingen

summary: Glucocorticoids exert prominent effects in the colon, yet the role of glucocorticoid receptor (GR) dimerization remains unclear. AOM/DSS-induced tumorigenesis in GRdim mice harboring a predominantly monomeric GR was investigated. Monomeric GR activities in tumorigenesis followed a biphasic pattern. GRdim mice exhibited a delayed tumor onset and prolonged survival, yet tumors that did develop progressed more rapidly and grew larger. The distinct inflammatory gene signature in GRdim tumors resulted in impaired recruitment and activation of neutrophils and inflammatory macrophages, with Il1b as the central hub gene. GRdim tumor signature overlapped with genes dysregulated in human colorectal cancer and correlated with poor patient survival, thus mimicking the murine tumor model.

overall_design: Colonic tumors were induced via AOM/DSS in wildtype (GRWT) and Glucocorticoid receptor (GR) dimerization deficient (GRDIM) mice. RNA from tumor tissue of both mouse strains was prepared and subsequently analysed by RNAseq profiling.

first: Chiara

last: Muzzi

first: Salinas-Riester

last: Gabriela


title: VISTA Drives Pancreatic Tumor Progression Through Modulation of The Tumor-Associated Macrophage Polarity

city: Seoul

first: Suk-Kyung

last: Shin

address: 103 Daehak-ro, jongno-go

country: South Korea

institute: Seoul National University

summary: Pancreatic ductal adenocarcinoma (PDAC) remains one of the deadliest malignancies due to its highly immunosuppressive tumor microenvironment (TME), which limits effective therapeutic interventions. Here, we demonstrate that V-domain immunoglobulin suppressor of T cell activation (VISTA) plays a crucial role in orchestrating macrophage polarity within the PDAC TME. Using murine PDAC models, we show that VISTA deficiency markedly impairs tumor growth, leading to reduced tumor volumes and prolonged survival. Mechanistically, VISTA loss reprograms tumor-associated macrophages (TAMs) from an immunosuppressive, secreted phosphoprotein 1(SPP1) expressing phenotype to a pro-inflammatory, C-X-C motif chemokine ligand 9 (CXCL9) expressing subtype. This switch enhances the recruitment of C-X-C motif chemokine receptor 3 (CXCR3) positive CD8+ T cells, reducing their exhaustion and sustaining their cytotoxic activity. Additionally, VISTA-deficient TAMs exhibit increased antigen cross-presentation, further amplifying CD8+ T cell response against tumors. These findings are corroborated by human single cell RNA-seq datasets, which suggest a conserved mechanism of VISTA-mediated immune modulation in PDAC TME. By elucidating the upstream role of VISTA in driving Cxcl9:Spp1 macrophage polarity and T cell dynamics, this study highlights VISTA inhibition as a promising therapeutic strategy to reshape the TME, augment CD8+ T cell function, and enhance anti-tumor immunity in PDAC.

overall_design:
To investigate how VISTA deficiency impacts the immune-oncologic landscape of PDAC, we utilized a syngeneic orthothopic model comparing tumor growth between wild-type (WT) and VISTA-deficient mice.
We validated reduction of pancreatic tumor via treatment of anti-VISTA antibody in WT mice.
Using anti-CSF1R model, we identified a population that expresses high VISTA expression.
We then performed gene expression profiling analysis using data obtained from RNA-seq of pancreatic tumors in WT and Vsir-/- mice on day 28 post-inoculation.


title: Preventing trogocytosis by cathepsin B inhibition augments CAR T-cell function

city: Baltimore

first: Carrie

last: McCracken

state: MD

address: 670 W. Baltimore St.

institute: Institute of Genome Sciences

summary: Chimeric antigen receptor (CAR) T-cell therapy has shown remarkable efficacy in cancer treatment. Nevertheless, most patients receiving CAR T cells relapse within 5 years of treatment. CAR-mediated trogocytosis (CMT) is a potential tumor escape mechanism in which cell surface proteins transfer from tumor cells to CAR T cells. CMT results in the emergence of antigen-negative tumor cells, which can evade future CAR detection, and antigen-positive CAR T cells, which have been suggested to cause CAR T-cell fratricide and exhaustion. Whether CMT indeed causes CAR T-cell dysfunction and the molecular mechanisms conferring CMT remain unknown. Using a selective degrader of trogocytosed antigen in CAR T cells, we show that the presence of trogocytosed antigen on the CAR T-cell surface directly causes CAR T-cell fratricide and exhaustion. By performing small molecule screening using a custom high-throughput CMT screening assay, we found that the cysteine protease cathepsin B is essential for CMT and that inhibition of cathepsin B is sufficient to prevent CAR T-cell fratricide and exhaustion, leading to improved long-term in vitro and in vivo CAR T-cell persistence and in vitro antitumor activity. Our data demonstrate that it is feasible to separate CMT from cytotoxic activity, that CAR T-cell persistence, a key factor associated with clinical CAR T-cell efficacy, is directly linked to cathepsin B activity in CAR T cells and that it is possible to improve CAR T-cell function through selective inhibition of CMT.

overall_design: Following production and cryopreservation, CAR and CAR_CSTA T cells from two independent productions were thawed and cultured in T-cell media + 40IU IL-2 for 48 hours. After 48 hours, CAR T cells were washed with FACS buffer, stained with anti-CD3, anti-HA, and DAPI, and sorted for CAR expression. Sorted CAR T cells were then pelleted and flash frozen. RNA was extracted, polyA-enriched, and sequenced using Illumina NovaSeq S4 PE100 sequencing targeting 10 million read pairs per sample.

first: Kenneth

middle: A

last: Dietze

first: Tim

last: Luetkens


title: FOXA1 loss induces aggressive prostate cancer via unleashing basal/squamous de-differentiation and an immunosuppressive microenvironment [scRNA-seq]

overall_design: To investigate how Foxa1 loss regulates the prostate cancer transcriptome, epithelial cell reprogramming, and cellular diversity in prostate tumors, we performed scRNA-seq analysis of whole prostate tissues from age-matched PbCre4:Ptenf/f (P) and PbCre4:Ptenf/fFoxa1f/f (PF) mice. In addition, to phenotype immune populations in further detail, live CD45+ immune cells were sorted from age-matched P and PF mouse prostates for scRNA-seq analysis.


title: FOXA1 loss induces aggressive prostate cancer via unleashing basal/squamous de-differentiation and an immunosuppressive microenvironment [CosMx]

summary: Forkhead box A1 (FOXA1) is a lineage-specifying transcription factor that is often de-regulated prostate cancer (PCa), with previous studies reporting both tumor-promoting and -inhibitory functions. Little is known about FOXA1 function in a physiological setting of PCa progression. Here we report that Foxa1 knockout in the Pten-null prostate epithelium in vivo leads to an aggressive sub-type of PCa marked by basal/squamous de-differentiation, tissue disorganization, and poor survival. Single-cell RNA-seq revealed a major increase of basal/squamous gene expression in the epithelium, which was accompanied by inflammatory and immunosuppressive cytokine signaling. Mechanistically, in addition to its well-known role in inducing luminal genes, FOXA1 directly inhibits many basal/squamous and inflammatory genes, which are unleashed upon Foxa1 knockout. Significantly, there is a striking remodeling of the tumor immune microenvironment in Foxa1-depleted PCa, with increased tumor infiltration by immunosuppressive myeloid populations and dysfunctional and spatially confined T cells. These important findings were further confirmed in human PCa samples via single-cell and spatial transcriptomic analyses. Altogether, we report critical roles for FOXA1 loss in inducing basal/squamous de-differentiation and an immunosuppressive microenvironment.

overall_design: CosMx SMI (CosMx Human Universal Cell Characterization 1000-plex RNA Panel) was applied to an FFPE prostate cancer patient tissue to evaluate the spatial organization of the prostate tumor immune microenvironment.


title: Effect of heme on the gene expression of differentiating mouse B cells [RNA-seq]

summary: The effect of heme on the gene expression of differentiating mouse B cells was assessed by isolating splenic CD43- B cells and culturing with LPS, IL2, and IL5.  After 24 hours heme or vehicle control was added to the cultures.  At 72 hours activated B cells and plasmablasts were FACS isolated and RNA-seq performed.

overall_design: RNA-seq was performed on activated B cells and plasmablasts differentiating in the presence or absence of heme in triplicate.


title: Validation of circulating miRNAs associated with breast cancer subtypes in the MCC-Spain study by RT-qPCR

city: Santander

first: Inés

last: Gómez-Acebo

state: CANTABRIA

address: Avda. Cardenal Herrera Oria S/N

institute: Division of Epidemiology and Computational Biology, School of Medicine, University of Cantabria,  IDIVAL, Santander, Spain

summary: This study represents the validation phase of circulating microRNAs associated with breast cancer detection within the MCC-Spain study. A total of 444 participants (127 cancer-free controls and 317 breast cancer cases) were included. Cases were stratified into molecular subtypes (Luminal A, Luminal B, HER2-positive, and Basal-like) according to St. Gallen criteria. A panel of 46 candidate miRNAs was quantified in serum samples using RT-qPCR (miRCURY LNA technology). Two endogenous miRNAs (let-7d-5p and let-7i-5p) were used for normalization. Differential expression and predictive modeling were performed using normalized and log₂-transformed expression values. This dataset supports subtype-specific and overall breast cancer detection models integrating molecular and epidemiological factors.

overall_design: Case-control study including 317 breast cancer patients and 127 cancer-free controls recruited within the MCC-Spain study. Serum samples were collected prior to any oncological treatment. Expression of 46 selected circulating miRNAs was quantified by RT-qPCR. Analyses were conducted overall and stratified by molecular subtype (Luminal A, Luminal B, HER2-positive, and Basal-like).

first: Sara

last: Valero-Domínguez

first: Javier

last: Llorca

first: Jessica

last: Alonso-Molero

first: Thalía

last: Belmonte

first: Gemma

last: Castaño-Vinyals

first: Víctor

last: Moreno

first: Aina

last: Romaguera

first: Pilar

last: Amiano

first: Juan

last: Alguacil

first: Vicente

last: Martín

first: Beatriz

last: Pérez-Gómez

first: Rosana

last: Burgui

first: Ana

last: Molina-Barceló

first: Paz

last: Rodríguez-Cundín

first: Manolis

last: Kongevinas

first: Marina

last: Pollán

first: Trinidad

last: Dierssen-Sotos


title: ARID1A Deficiency in Diffuse-Type Gastric Cancer Promotes a Pyrimidine Metabolic Vulnerability

city: Chuo-ku

first: Hideaki

last: Ogiwara

state: Tokyo

address: 5-1-1, Tsukiji

department: Division of Cancer Therapeutics

country: Japan

institute: National Cancer Center Research Institute

summary: Loss-of-function mutations in ARID1A define an aggressive subtype of diffuse gastric cancer (DGC) that is often resistant to standard chemotherapy. Here, we uncover a precise metabolic vulnerability in ARID1A-deficient DGC driven by a specific transporter defect. Through integrated metabolomic and transcriptomic analyses, we demonstrate that ARID1A loss transcriptionally represses the high-affinity nucleoside transporter SLC28A3. Our profiling revealed a critical lack of redundancy in the concentrative transporter family (CNT) in DGC, establishing a strict reliance on SLC28A3 for maintaining intracellular deoxycytidine (dC) pools. Consequently, ARID1A deficiency creates a severe "low-dCTP" metabolic bottleneck. We show that the dC analog Gemcitabine exploits this state through a distinct functional dichotomy: it enters via intact equilibrative transporters (ENTs) to target cells that have lost their competitive dC barrier. Mechanistically, Gemcitabine exerts a "dual-hit" effect by outcompeting the scarce dC pool for DNA incorporation while simultaneously inhibiting ribonucleotide reductase, thereby blocking de novo nucleotide synthesis. This synergistic collapse of pyrimidine metabolism was validated in patient-derived ex vivo cultures and in vivo peritoneal dissemination models. Our findings provide a robust mechanistic basis for repurposing Gemcitabine as a precision therapy for ARID1A-deficient DGC, offering a potent strategy for this intractable malignancy.

overall_design:
RNA-seq profiling of the non-treatment condition of DGC cell lines.
ATAC-seq profiling of DGC cell line treated with siRNA for non-targeting or ARID1A for 72 h.


title: Investigating the role of alpha-catenin-cholesterol biosynthesis axis during islet development

city: Duarte

first: Hung-Ping

last: Shih

state: CA

address: 1500 E. Duarte Road

department: Translational Research and Cellular Therapeutics

institute: City of Hope

summary: The major function of alpha-catenin (encoded by Ctnna1) is linking the cadherin-catenin complex to the actin cytoskeleton, thereby regulating cell adhesion, Mechanotransduction, and tissue integrity. Alpha-catenin is a critical component of adherens junctions and plays essential roles in maintaining cellular architecture, transducing mechanical signals, and preserving tissue homeostasis. In this project, we analyze how Ctnna1 regulates islet function and analyze the gene expression profiling related to islet function, structure, and adhesion. We selectively ablate alpha-catenin (Ctnna1) in endocrine cells of murine pancreas. We isolated islets and performed mRNA profiles from 8-week-old wild type (WT) and Ngn3-Cre; Ctnna1 flox/flox (KO) mice (N=6). We mapped about 70 million sequence reads per mouse sample. Our results showed that 115 genes were upregulated and 292 were downregulated by alpha-catenin ablation.

overall_design: Total RNA was extracted from pancreatic islets isolated from 8 weeks old mice of Ngn3-Cre; Ctnna1flox/flox and Wild-type controls. There were six animals for each group.

first: Wilma

last: Tixi


title: Investigating the role of the sterol-responsive element-binding proteins 2 (SREBP2) during islet development

summary: The major function of the sterol-responsive element-binding proteins 2 (SREBP2) is regulating Cholesterol biosynthesis. Cholesterol is important component of the cell membrane, works as signaling molecules and is essential to maintain cellular function. In this project we analyze how SREBP2 regulates islet function and analyze the gene expression profiling related with islet function, structure and adhesion. We selective ablate the sterol-responsive element-binding proteins 2 (SREBP2) in endocrine cells of murine pancreas. Pancreas mRNA profiles of 8-weeks old wild type (WT) and Ngn3-Cre; Srebf2 flox/flox mice. We mapped about 70 million sequence reads per mouse sample. Our results showed that 25 genes were upregulated and 196 were downregulated by SREBP2 ablation.

overall_design: Total RNA was extracted from pancreatic islets isolated from 8 weeks old mice of Ngn3-Cre; Ctnna1flox/flox and Wild-type controls. There were four animals for each group.


title: Single-cell transcriptomics reveals etiology-specific T-cell heterogeneity in hepatocellular carcinoma and implicates regulatory

city: Beijing

first: Fengna

last: Yan

address: No. 8 Jingshun East Street, Chaoyang District

department: Beijing Ditan Hospital

institute: Capital Medical University

summary: Hepatocellular carcinoma (HCC) exhibits remarkable etiological heterogeneity, with hepatitis B virus (HBV) infection and metabolic dysfunction-associated steatohepatitis (MASH) emerging as two leading causes. The tumor microenvironment (TME), particularly T cell subsets, plays a pivotal role in tumor progression and immunotherapy response. However, the etiology-specific T cell landscapes in HBV-HCC and MASH-HCC remain poorly characterized.

overall_design: We performed single-cell RNA sequencing (scRNA-seq) on CD45+ immune cells isolated from peripheral blood mononuclear cells (PBMCs), tumor tissues (T), and peritumor tissues (PT) of HBV-HCC (PBMC: n=4; T: n=3; PT: n=3) and MASH-HCC (PBMC: n=4; T: n=2; PT: n=2) patients. Integrative bioinformatics analyses were conducted to characterize T cell subsets, their functional states, and intercellular crosstalk. Validation induced multiplex immunohistochemistry and Flow cytometry on patients.


title: Context specificity of oxazolidinones-mediated translation inhibition is modulated by antibiotic structure [Ribo-Seq]

city: San Francisco

first: Jordan

middle: I

last: Kleinman

institute: UCSF

summary: The oxazolidinone antibiotic linezolid binds to the peptidyl transferase center of the ribosome, where it inhibits a subset of peptide bond formation events. This context-specificity of translation inhibition is dictated by the nature of the amino acid at the penultimate position of the nascent peptide. It remains unknown whether this is a general feature of oxazolidinones and whether it can be modulated by their structural alterations. Here, we show that the oxazolidinone tedizolid also inhibits translation in a context-specific manner, but with dramatically altered selectivity, favoring Ile, His, and Gln as the penultimate residues. Delpazolid, which shares the C5 hydroxymethyl moiety with tedizolid, shows a similar preference. Structural analysis of the ribosome with tedizolid and a stalled nascent peptide showed a compacted, helical conformation of the nascent chain induced by the drug. Our findings reveal that stalling preferences of oxazolidinones can be modulated by structural modifications within this antibiotic class.

overall_design: Ribosome profiling in E. coli BW25113 ΔacrB with and without antibiotic (tedizolid, delpazolid) treatment; collected in conjunction with RNA-seq samples

first: Danica

last: Galonić Fujimori


title: Context specificity of oxazolidinones-mediated translation inhibition is modulated by antibiotic structure [RNA-Seq]

overall_design: RNA-seq in E. coli BW25113 ΔacrB with and without antibiotic (tedizolid, delpazolid) treatment; collected in conjunction with ribosome profiling samples


title: Responses of Atlantic salmon skin to high water temperature

city: Ås

first: Aleksei

last: Krasnov

state: Viken

address: Øreveien, 47B

country: Norway

institute: Nofima AS

summary: Climate change has resulted in record-breaking sea temperatures, posing significant challenges to the health, growth, and productivity of marine fish species, including farmed Atlantic salmon.  As sea temperatures are projected to continue to rise, the impact of environmental changes requires significant attention. To devise effective climate adaptation strategies, there is a need to understand the response of salmon to sub-optimal temperatures alone and in-combination with other production-related stressors. Gills and skin were analyzed prior to and after temperature peaks, and before and after the varying simulated handling operations. The effects of the different operations upon macro level external injuries were also investigated. Results indicate that fluctuating and constant high temperatures induce macro- and micro-damages to tissues that may challenge salmon health and welfare, by having a negative effect upon scale loss and eye opacity, and reduced skin barrier integrity. This submission contains data of transcriptome analysis in skin.

overall_design: Atlantic salmon post-smolts were exposed to three temperatures: optimal 12°C (T12), high 17°C (H), and fluctuating 12/17°C (F). The temperatures were identified using downscaled climate model projections for salmon farms in the south and north of Norway. Three rounds of fluctuations between 12°C and 17°C were applied to simulate marine heat waves that cycle between near optimal temperature ranges to upper thresholds. Microarray analyses were carried out before the trial (T0) and at two timepoints when temperature in H reached peak (P1 and P2).

first: Elisabeth

last: Ytteborg

first: Krasnov

last: Aleksei


title: Increased Th17 Cell Pathogenicity in Periodontitis: Association of Zap70

first: yu

last: chenhao

state: Haidian District

address: 22 ZhongguancunNandajie, Haidian District, Beijing, China

department: School of  stomatology

institute: Peking University

summary: The progression of periodontitis is closely associated with Th17 cells, yet the functional differences of Th17 cells under periodontitis conditions remain poorly understood. Therefore, we established an experimental periodontitis model using IL-17GFP/+ transgenic mice, isolated Th17 cells via flow cytometry, and performed RNA sequencing. Results showed that periodontitis induced significant changes in Th17 cells, including a marked increase in cell proportion, as well as upregulated expression of Th17-associated immunoinflammatory signaling pathways and inflammatory cytokines (IL-17, IL-23, and GM-CSF). Within Th17 differentiation-related pathways, Zap70 expression was significantly upregulated and exhibited a positive correlation with IL-17. Local silencing of Zap70 via AAV-sh-Zap70 significantly reduced the expression of IL-17, IL-23/IL-23r, and GM-CSF, while alleviating alveolar bone resorption. In conclusion, periodontitis significantly enhances the proinflammatory capacity of Th17 cells, and this change is associated with Zap70, which indicates that Zap70 holds promise as a potential therapeutic target for periodontitis.

overall_design: To investigate the regulatory role of Zap70 in the pathogenicity of Th17 cells in periodontitis and its therapeutic potential, this study used IL-17GFP/+ transgenic mice divided into control and periodontitis groups (established via ligature) and wild-type C57BL/6 mice assigned to six groups (including Zap70-silenced group with AAV-sh-Zap70, vector control group with AAV-luc-GFP, and saline control groups for both healthy and periodontitis conditions); key methods included flow cytometry for Th17 cell sorting, RNA sequencing for gene expression profiling, μCT for alveolar bone resorption assessment, immunofluorescence, and qPCR for detecting related cytokines and gene expression, with results showing that periodontitis significantly enhances the proinflammatory capacity of Th17 cells, Zap70 is highly expressed and positively correlated with IL-17, and local silencing of Zap70 reduces the expression of inflammatory cytokines (IL-17, IL-23/IL-23r, GM-CSF) while alleviating alveolar bone resorption.

first: Chenhao

last: Yu

first: Xudong

last: Xie

first: Xiaotong

first: Peitong

last: Li

first: Jianpeng

last: Zhou

first: Peilei

last: Shi

first: Chunmei

last: Xu

first: Hui

last: Wang

first: Yafei

last: Wu

first: Jun


title: Context specificity of oxazolidinones-mediated translation inhibition is modulated by antibiotic structure

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

overall_design: Refer to individual Series


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

city: Rochester

first: Ruoqiao

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: Monocytes were isolated from cryopreserved PBMCs or whole blood, stained with lineage and monocyte markers, barcoded using TotalSeq-B hashtag antibodies, and viability-gated before sorting. Live singlet monocytes were purified by flow cytometry as lineage-negative CD14⁺ and/or CD16⁺ cells, assessed for viability and concentration, and pooled based on cell counts. Pooled cells were processed using the 10x Genomics Chromium 3′ v3.1 platform, and gene expression and hashtag libraries were sequenced together on an Illumina NovaSeq 6000.

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: Single-cell RNA-seq (SORT-seq) of human heart Treg cells (QMU-SF-s001–QMU-SF-s012)

city: London

first: Federica

last: Marelli-Berg

address: Mile End Road

institute: Queen Mary University of London

summary: Processed scRNA-seq data were generated from primary human heart Treg/T-cell samples across 12 SORT-seq plates (QMU-SF-s001–QMU-SF-s012). Raw reads were mapped to the human reference genome (GRCh38, Ensembl release 98) using STARsolo (v2.7.10b) and cells were retained using STARsolo default filtering plus an additional cutoff of ≥500 UMIs per cell. This submission provides filtered gene-count matrices for downstream analysis; an exploratory Seurat QC/clustering report is provided as supplementary material.

overall_design:
Each SORT-seq plate contains wells from both disease and control subjects; sample/condition assignment is provided via the accompanying barcode-to-well mapping files.

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

first: Alexandros

last: Protonotarios

first: Silvia

last: Fanti

first: Barbara

last: Szomolay


title: Transcriptomic Insights into Aerobic Exercise-Mediated Attenuation of High-Fat Diet–Induced Muscle Wasting

city: Quanzhou

first: Weihao

last: Hong

address: Donghai

institute: Quanzhou Normal University

summary: Chronic consumption of high-fat diet (HFD) induces obesity and metabolic dysfunction and is accompanied by progressive skeletal muscle wasting. Although aerobic exercise is generally considered less effective for maintaining muscle mass, accumulating evidence suggests that it can attenuate HFD-induced muscle wasting. However, the molecular mechanisms underlying this protective effect remain poorly defined. In this study, we investigated the effects of moderate-intensity continuous training (MICT) on HFD-induced muscle wasting and characterized the associated transcriptomic adaptations in the mouse gastrocnemius muscle. Twenty-one weeks of HFD feeding increased body weight and serum glucose levels and induced marked muscle wasting, as evidenced by reduced gastrocnemius muscle index, impaired normalized forelimb grip strength, decreased muscle fiber cross-sectional area, and excessive intramuscular lipid accumulation. These pathological alterations were significantly attenuated by an 8-week MICT intervention. RNA sequencing revealed that HFD predominantly induced a lipid-centered transcriptional program characterized by enhanced fatty acid uptake, trafficking, and β-oxidation. In contrast, MICT predominantly suppressed atrophy-associated genes (Foxo1, Fbxo32, and Trim63), while exerting minimal effects on myogenic genes (Pax7, Myod1, and Myog). Functional enrichment analyses further indicated that MICT modulated signaling pathways related to FoxO, PI3K–Akt, MAPK, and insulin signaling, together with biological processes associated with angiogenesis and calcium signaling. Collectively, these results suggest that MICT mitigates HFD-induced muscle wasting primarily by reprogramming the transcriptome from a lipotoxic, atrophic state toward a more insulin-sensitive, pro-angiogenic profile, with limited myogenic activation.

overall_design: After 1 week of acclimation, 3-week-old male C57BL/6J mice were randomly allocated to four groups: standard chow diet (C), standard chow diet plus MICT (CM), HFD (H), and HFD plus MICT (HM). The dietary intervention was maintained throughout the entire experiment (weeks 1–21). Starting at week 13, mice assigned to the exercise groups completed a 1-week treadmill acclimation phase (10 m/min for 10 min/day, 5 days/week), followed by an 8-week MICT intervention (weeks 14–21). Each session lasted 45 min and was performed 5 days per week, preceded by a 10-min warm-up at 10 m/min. Treadmill speed was progressively increased from 13 m/min (weeks 14–15) to 15 m/min (weeks 16–17), and then to 17 m/min (weeks 18–21). Gastrocnemius muscles were collected for RNA-seq at the endpoint.

first: Jianrong

last: Zheng

first: Yisheng

last: Luan

first: Haibin

last: Yu

first: Yueyun

first: Bing

last: Zhang


title: Cell Atlas and Novel Signal Processing Strategy in Primate Insular Cortex [scRNA-seq]

city: Guangzhou

first: Ruifeng

last: Liu

state: Guangdong province

address: Jinsui Road, 7#

department: Zhongshan Ophthalmic Center

institute: Sun Yat-sen University

summary: The anterior insular cortex (AIC) is a critical hub integrating exteroceptive and interoceptive information into high-order cognition, yet its neural basis remains incompletely understood. Here, by combining whole-cell-based single-cell transcriptomics with Patch-seq recordings, we resolved and characterized 78 detailed cell types in the macaque AIC, revealing the diversity and specialization of this region in cell type, connectivity profile, signal-processing strategy, and metabolic characteristics. Among these, we identified two transcriptomically and morphoelectrically defined von Economo neuron (VEN) subtypes, DSG2-expressing VEN-L and POC5-expressing VEN-S, transcriptomically relating to extratelencephalic and corticothalamic projection neurons, respectively. We also uncovered a previously underappreciated signal-processing strategy in VENs, whereby the geometry of the dendrite-originating axon initial segment (AIS) reshapes action potential dynamics and enhances somatic responsiveness to deep-layer synaptic inputs. Together, this multimodal atlas establishes a molecular and functional framework for investigating the circuit principles underlying deep-layer projection neurons in the primate AIC.

overall_design: Here we employed a massively parallel 10X genomics single cell RNA-sequencing (scRNA-seq) analysis of the AIC to derive a molecular classification and then related each molecularly distinct cell type to well-established AIC cell types via Patch-seq.

first: Sheng


title: Trained immunity of alveolar macrophages promotes injury resolution by enhancing KLF4-MERTK-mediated efferocytosis [ATAC-seq 72h post-LPS]

city: Chicago

first: Jalees

last: Rehman

state: IL

address: 900 S. Ashland Ave. MBRB 2072, Mailcode 669

department: Biochemistry and Molecular Genetics

institute: UIC

summary: Trained immunity of alveolar macrophages promotes injury resolution by enhancing KLF4-MERTK-mediated efferocytosis.

overall_design: Lung macrophages, LPS inhalation, 72h post-LPS.  Two replicates.


title: Transcriptomic Profiling on Intestine of Diabetic and Septic Mice [RNA-seq]

first: Fang

last: Tan

address: Dongfengdong Road 567

institute: Sun Yat-sen University Cancer Center

summary: Sepsis is a severe clinical syndrome related to an exaggerated host immune response to infection as well as systematic inflammation and serious tissue damage. Sepsis-induced intestine injury is one of the most frequent and serious complications of sepsis. This study aimed to identify new mechanisms in sepsis-induced intestine injury through transcriptome profiling (RNA-seq).

overall_design: Mice were randomly divided into 3 groups: wt-CLP group (n=2), db-CLP group (n=2), db-Sham group (n=2).

first: Xinjin

last: Chi

first: Lei


title: Endothelial TLR4 signaling drives tissue inflammation, Claudin-5 internalization, and vascular barrier breakdown in a mouse model of neonatal meningitis

first: Amir

last: Rattner

state: MD - Maryland

address: 725 North Wolfe St.

institute: Johns Hopkins University

summary: Neonatal bacterial meningitis is a leading cause of infant morbidity and mortality, yet the molecular and cellular basis of the leptomeningeal response to infection remains poorly defined. Here, we study a mouse model of neonatal E. coli meningitis, combining celltype specific gene knockouts, leptomeningeal single-nucleus RNA sequencing, and endothelial cell culture to explore the role of Toll-like receptor 4 (TLR4) signaling in the host response to infection. Endothelial-specific deletion of Tlr4 dramatically reduced the inflammatory response in all leptomeningeal cell types and abrogated the infectionassociated increase in vascular permeability. In a brain endothelial cell line (bEnd.3 cells), exposure to E. coli triggered TLR4-dependent NF-κB activation, selective internalization of Claudin-5, and increased monolayer permeability, responses that were eliminated by Tlr4 knockout. RNA-seq showed that endothelial TLR4 controls an NF-κB–driven transcriptional program that orchestrates the leptomeningeal response to infection. These findings reframe the host response in neonatal Gram-negative bacterial meningitis as an endothelial-centric process.

overall_design: Here, we study a mouse neonatal meningitis model and cultured CNS ECs (bEnd.3 cells) to test whether endothelial-intrinsic TLR4 signaling (i) orchestrates the multi-cellular response of the leptomeninges to infection and (ii) regulates Cldn5 trafficking and vascular barrier function. In the present work, we (i) profiled cell-type–specific responses in the leptomeninges from WT, endothelial Tlr4 conditional knockout mice (Tlr4ECKO), and macrophage Tlr4 conditional knockouts (Tlr4MKO) using single nucleus (sn)RNA-seq; (ii) performed wholemount immunostaining to quantify ICAM-1 induction, extravascular tracer leakage, and macrophage activation in vivo; (iii) tracked Cldn5 redistribution and NF-κB nuclear translocation in bEnd.3 cells exposed to E. coli; (iv) generated CRISPR Tlr4KO bEnd.3 lines to assess the TLR4 dependence of NF-κB activation, tight-junction dynamics, and barrier permeability; (v) quantified Cldn5 colocalization with junctional, plasma-membrane, and endosomal/lysosomal markers; (vi) defined TLR4-dependent transcriptional programs in bEnd.3 cells. The results of these experiments establish a framework for understanding the pathophysiology of neonatal meningitis that establishes endothelial TLR4 signaling as a central regulator of both the multicellular leptomeningeal response to infection and Cldn5 trafficking and junctional integrity.

first: Philip

last: Seegren

last: Smallwood

first: Jeremy

last: Nathans


title: Transcriptional profiling of ageing muscle satellite cells treated with recombinant human MG53

city: Columbus

first: Jethro

middle: WANG

last: Zih-Shuo

state: Ohio

address: 460 W 12th Ave.

department: Department of Surgery

institute: Ohio State University

summary: Purpose: Skeletal muscle satellite cells (SCs) are essential for muscle regeneration. MG53 (TRIM72) is a key regulator of membrane repair, but its role in SC fate decisions remains elusive. This study aims to investigate the transcriptional regulatory role of MG53 in satellite cell quiescence maintenance, activation, and proliferation. Methods: Primary satellite cells were isolated from hindlimb muscles of C57BL/6 mice. Cells were cultured and treated with either recombinant human MG53 protein (rhMG53) or BSA (Vehicle Control) for 3 Days. Total RNA was extracted and subjected to high-throughput RNA sequencing (RNA-seq) to identify differentially expressed genes (DEGs). Results: Our analysis reveals that MG53 treatment significantly alters the transcriptomic landscape of satellite cells. Specifically, MG53 treatment upregulated genes associated with activation pathways, while downregulating genes related to inflammation or lineage differentiation. Conclusions: This dataset provides novel insights into the molecular mechanisms by which MG53 promotes satellite cell maintenance and regenerative capacity, highlighting its potential therapeutic value for muscle wasting diseases.

overall_design: Primary satellite cells were isolated from C57BL/6 mice. Cells were cultured in growth medium and treated with either rhMG53 protein or BSA (as vehicle control) for 3 days. Total RNA was harvested from 3 biological replicates per group (Total N=6). Comparative gene expression analysis was performed to identify differentially expressed genes (DEGs) between MG53-treated and Control groups.

middle: W

first: Yanping

last: Xu

first: Hua

last: Zhu


title: FOSL2 binding to enhancer elements regulates endothelial cell state in systemic sclerosis pulmonary vascular disease

city: Pittsburgh

first: Alyxzandria

last: Gaydosik

state: PA

address: 200 Lothrop St

institute: University of Pittsburgh

summary: Systemic Sclerosis (SSc) is characterized by fibrosis and vasculopathy affecting the skin and internal organs, leading to multi-organ dysfunction. Injury of microvascular ECs in SSc impairs blood flow and causes tissue ischemia, leading to vascular complications such as Raynaud’s, digital ulcers, and pulmonary hypertension (PH). PH in SSc presents as group 1 pulmonary arterial hypertension (PAH) or as group 3 PH related to hypoxia and interstitial lung disease (ILD), both major causes of mortality. Analysis of multiome data from SSc ILD-PH lungs inferred transcription factors regulating EC phenotype, including FOSL2. Overexpression of FOSL2 in transgenic mice (Fosl2tg) leads to vascular changes mirroring human SSc-PH, such as intimal thickening and fibrosis. ScRNA-seq analysis of altered EC gene expression in the Fosl2tg mice showed strong overlap with altered EC gene in SSc-ILD-PH. Overlapping as well as discrete EC gene expression in SuGene/hxpoxia- and hypoxia-treated mice suggested that FOSL2 regulates both hypoxia-dependent and independent pathways in Fosl2tg mice and SSc-ILD-PH. The deep learning model, ChromBPNet, inferred increased AP-1 binding at base pair resolution in SSc-ILDPH ECs and binding to the same motifs was found upon FOSL2 overexpression in primary vascular ECs, highlighting FOSL2’s key role in driving the pathological changes seen in SSc-ILDPH.

overall_design: 12 mouse lung samples were run using 10X Genomics FLEX assay. Conditions include 'WT_2', 'FRA2_1','FRA2_2','RAGko','FRA_RAGko1','FRA_RAGko2','WT_3','hypPVP','hypT5224','hypSugenePVP1','hypSugenePVP2', and 'hypSugeneT5224'

first: Rithika

last: Behera

first: Yuechen

last: Zhou

first: Peter

last: Gerges

first: Jingyu

last: Fan

first: Tracy

last: Tabib

first: Mengqi

last: Huang

first: Jishnu

last: Das

first: Elena

last: Pachera

first: Amela

last: Hukara

first: Ying

last: Tang

first: Florian

last: Renoux

first: Yi

middle: Y

last: Tai

first: Oliver

last: Distler

first: Gabriela

last: Kania

first: Stephen Y

last: Chan

first: Harinder

last: Singh

first: Eleanor

last: Valenzi

first: Robert

last: Lafyatis


title: RNA‑seq of midgut from individual female Tabanus nipponicus

city: Obihiro

first: Noboru

last: Inoue

state: Hokkaido

address: 11 Nishi 2-sen, Inada-cho

department: National Research Center for Protozoan Diseases

institute: Obihiro University of Agriculture and Veterinary Medicine

summary: Tabanus nipponicus is a hematophagous insect species with high activity in summer, and its midguts play a critical role in successful blood-feeding, as they are closely associated with blood meal digestion, nutrient absorption, and physiological regulation during hematophagy. In this study, midgut samples from three independent T. nipponicus individuals collected during the peak of summer activity were used for RNA-seq analysis. Prior to sequencing, total RNA was extracted under sterile and low-temperature conditions to ensure RNA integrity. Paired-end sequencing generated 43,569,311 to 46,711,652 raw reads, which were further processed for de novo assembly, yielding 8,039 unigenes. These unigenes were first aligned to the Nr database to obtain functional annotations, and the annotated unigene IDs were subsequently mapped to the GO database, being classified into three main GO categories (biological process, cellular component, and molecular function). Functional annotation revealed enrichment in metabolic processes, membrane-related biological processes, and binding/catalytic molecular activities—all of which are closely related to the physiological functions of the midgut in T. nipponicus, including the digestion and absorption of blood meals, the transport of nutrients and metabolites, and the regulation of physiological processes required for continuous blood-feeding, thereby underpinning the synthesis and secretion of anticoagulant saliva components essential for blood-feeding adaptation and microbial stress resistance. Additionally, the unigenes were aligned to the KEGG database to obtain corresponding KEGG IDs, which were then mapped to unique KOs followed by KEGG enrichment analysis to explore the key metabolic pathways involved. Future studies will focus on the key physiological processes of T. nipponicus midguts, including anticoagulation, blood meal digestion, antioxidant defense, and microbial resistance.

overall_design: RNA‑seq data of midgut tissues from three individual female Tabanus nipponicus (1 sample/individual)

first: Keisuke

last: Suganuma

first: Ercha

last: Hu


title: Development and Application of G4-Flame as a Visual Biosensor for G4-DNA

city: hefei

first: sun

last: xuedan

address: daoxiangcun

institute: ustc

summary: G4-DNA, a non-canonical tetrahelical nucleic acid structure stabilized by stacked G-quartets via Hoogsteen hydrogen bonding, plays critical roles in genomic regulation and disease pathogenesis. Current methodologies for detecting these structures face limitations in specificity, spatiotemporal resolution, and live-cell applicability. To address these challenges, we engineered G4-Flame, a genetically encoded fluorescent biosensor utilizing Circularly Permuted Fluorescent Protein (CPFP) technology. By strategically positioning a G4-specific binding domain proximal to the fluorophore of circularly permuted YFP (cpYFP), G4-Flame achieves real-time, high-resolution visualization of G4-DNA dynamics in living systems, with specificity across diverse G4 conformations. Experimental validation revealed distinct spatiotemporal patterns of G4-DNA during the cell cycle: nuclear G4-DNA levels peaked during the S phase, while mitochondrial G4-DNA was found to suppress the expression of mitochondrial-encoded genes. Clinically, serum analysis revealed significantly elevated G4-DNA levels in cancer patients compared to healthy controls. This work establishes G4-Flame as a transformative tool for investigating G4-DNA spatiotemporal regulation and advances its potential as a biomarker for early cancer detection, bridging fundamental research with clinical translation.

overall_design: The experimental design of this study systematically investigates genome-wide G4-DNA recognition and its cell cycle dynamics by combining genomic mapping and cellular imaging approaches. The core of the methodology employs CUT&Tag to perform a genome-wide consistency analysis, comparing the occupancy profiles obtained using the engineered probe G4-Flame (detected via an anti-HA antibody) with those from the endogenous G4-specific BG4 antibody. To study cell cycle-dependent changes, HEK293T cells expressing an NLS-tagged G4-Flame probe were synchronized at the G1/S boundary using a thymidine double-block protocol. The dynamics of nuclear G4-DNA were then directly visualized and compared between G1 and S phases through fluorescence microscopy imaging, thus integrating genome-wide comparative data with single-cell observational analysis.

first: Xuedan

last: Sun

first: Ruyi

last: Liu


title: The ubiquitin ligase CBL and Fas-associated factor 2 cooperate to regulate the innate immune response to M. tuberculosis

city: Davis

first: Tina

last: Truong

state: California

address: One Shields Ave

institute: UC Davis

summary: As a first line of host defense, macrophages must be able to effectively sense and respond to diverse types of pathogens, and while a particular response may be beneficial in some circumstances, it can be detrimental in others. Upon infection, Mycobacterium tuberculosis (Mtb) induces proinflammatory cytokines and activates antibacterial responses. Surprisingly, Mtb also triggers antiviral responses that actually hinder the ability of macrophages to restrict Mtb growth. In Mtb-infected macrophages, the ubiquitin ligase CBL suppresses antiviral responses and preserves the antibacterial capacity of the macrophage. However, the mechanisms by which CBL regulates immune signaling are unknown. We found that CBL controls responses to multiple immune stimuli and broadly suppresses the expression of antiviral response genes. We used mass-spectrometry to identify potential CBL substrates, and found, in total, over 46,000 ubiquitylated peptides in Mtb-infected macrophages, including roughly 400 peptides with CBL-dependent ubiquitylation. We then performed genetic interaction analysis of CBL and its putative substrates, and identified the Fas associated factor 2 (FAF2) adapter protein as a key signaling molecule downstream of CBL. Together, these analyses reveal thousands of new ubiquitin-mediated signaling events and identify an important new regulator immune signaling.

overall_design: RNA-seq profiling of differentiated WT THP-1 cells and their knockdown derivative (shCBL) mock infected or infected with lpqN Mtb at 6 hours post infection.

first: Abigail

last: Ray

first: Kelsey

last: Martin

first: Nicholas

last: Bates

first: Michelle

last: Salemi

first: Brett

last: Phinney

first: Bennett

last: Penn


title: Early multi-omic signatures and machine learning models predict cardiomyocyte differentiation efficiency and enable robust hPSC differentiation to cardiomyocytes

city: Madison

first: Sean

middle: P.

last: Palecek

state: Wisconsin

address: 1415 Engineering Drive

department: Chemical and Biological Engineering

institute: University of Wisconsin-Madison

summary: Protocols for generating cardiomyocytes (CMs) from human pluripotent stem cells (hPSCs) have existed for nearly two decades, yet manufacturing variability in terminal cell identity continues to limit clinical translation. To uncover the origin of fate divergence during hPSC-CM differentiation, we performed temporal transcriptomics, proteomics, and metabolomics of high and low efficiency differentiations. We identified significant early multi-omic divergence between differentiation batches and key pathways underlying fate divergence at critical differentiation stages included Wnt, MAPK, and glucose metabolism. Machine learning models trained on early candidate gene markers  predicted hPSC-CM purity better than models using canonical cardiac development markers. Lastly, multi-omic insights informed perturbations, including Wnt and MAPK inhibition, which produced higher CM purities and yields. Our results showcase multi-omic analysis coupled with machine learning models as a powerful tool to identify cell fate determinants and enable robust manufacturing of complex cell products such as hPSC-derived cell therapies.

overall_design: We differentiated human pluripotent stem cells (hPSCs) to cardiomyocytes (CMs) and temporally profiled differentiations that resulted in high or low cardiomyocyte purity on Day 16 (cTnT+ cells by flow cytometry). For the multi-omic collection experiment, we used the WTC11 hiPSC line and collected samples on Days 0, 2, 4, 6, 8, 10, 13, and 16. Each replicate is a well replicate of the same differentiation. W52 = high purity CM differentiation and W69 = low CM purity. For the RNAsequencing only collection experiment, we used the WTC11 (W), H9 (H), and IMR90-4 (I) hPSC lines and collected early step-matched differentiation samples from high and low purity CM differentiations. This included sample collection on D0 (+CHIR), D2/D3 (+IWP2), D4/D5 (-IWP2), and D6/7 (+INS). There are no well replicates here with differentiations. Replication is done at the differentiation level across cell lines (n=3 differentiations each for high and low CM purity - one in each cell line). W69 = low purity CM and W81 = high purity CM differentiation. I55 = high purity CM and I75 = low purity CM differentiation. H55 = low purity CM and H58 = high purity CM differentiation.

first: Austin

middle: K

last: Feeney

first: Aaron

last: Simmons

middle: P


title: Study of POLR3A variants in a family trio suggests mutation-specific pathogenetic mechanisms: insights from integrative OMIC approaches

city: Milan

first: Letizia

last: Messa

address: Piazza Leonardo Da Vinci 32

department: Electronics, Informatics and Bioengineering

institute: Politecnico di Milano

summary: Background: Hypomyelinating leukodystrophies (HLDs) are rare genetic neurodevelopmental disorders characterized by defective myelin formation. The genetic cause of these disorders has been ascribed to mutations in genes encoding myelin protein components, such as proteolipid protein 1 (PLP1) and myelin basic protein (MBP), or in genes encoding for transcription and translation-related proteins. Particularly, biallelic pathogenic variants in POLR3A, POLR3B, POLR3K, POLR3D, POLR1C lead to the insurgence of RNA Polymerase III (Pol III)-related HLDs (POLR3-HLDs). The molecular mechanisms linking Pol III dysfunction to hypomyelination remain largely elusive, though the main hypothesis is that impaired Pol III activity likely disrupts gene expression and cellular homeostasis processes critical for myelin development and lipid metabolism. Methods: In this study, we analyzed a family trio consisting of unaffected carrier parents and a proband affected by POLR3A-related HLD, carrying compound heterozygous variants (p.Phe601Tyr and p.Gly1358Arg). We investigated the structural and functional consequences of two POLR3A variants using protein modeling, functional assays and multi-omics profiling in subject-specific primary fibroblasts. Results: Structural analysis revealed alterations in DNA-binding regions and a likely impact on protein stability, whilst functional assays showed an impairment in cellular proliferation. Lipidomic and transcriptomic profiling revealed that p. Gly1358Arg mutation predominantly affects lipidomic metabolism, while p. Phe601Tyr was associated with a widespread transcriptional dysregulation. Both mutations ultimately caused a significant reduction in lipid droplets in the proband’s cells. Conclusions: These results demonstrate mutation-specific pathogenetic mechanisms in POLR3A-HLD and underline the utility of integrative multi-omics approaches in elucidating the molecular basis of rare neurodevelopmental disorders.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for a family trio consisting of unaffected carrier parents and a proband affected by POLR3A-related HLD, carrying compound heterozygous variants (p.Phe601Tyr and p.Gly1358Arg).

first: Federica

last: Rey

first: Alessia

last: Casamassa

first: Samuele

last: Di Cristofano

last: Esposito

first: Amy

last: Amata Soriano

first: Clarissa

last: Berardo

first: Mahsa

last: Hazrati

first: Ilaria

last: Ferrone

first: Maxime

last: Bonnet

first: Fabio

last: Bruschi

first: Ylenia

last: Vaia

first: Massimo

last: Marano

first: Enrico

last: Bertini

first: Francesco

last: Nicita

first: Davide

last: Tonduti

first: Gianvincenzo

last: Zuccotti

first: Angelo Luigi

last: Vescovi

first: Domenico

last: Raimondo

first: Jessica

last: Rosati

first: Stephana

last: Carelli

first: Cristina

last: Cereda


title: IKAROS re-expression modulates transcriptional networks in IKZF1-mutant Ph+ B-ALL [CUT&RUN]

city: Burlington

first: Seth

last: Frietze

state: VT

address: 149 Beaumont Avenue

department: Biomedical and Health Sciences

institute: University of Vermont

summary: With the goal to investigate tumor suppressor mechanisms regulated by IKAROS (IKZF1) in PH chromosome–positive B-cell acute lymphoblastic leukemia (B-ALL) harboring IKZF1 mutations. This dataset includes bulk RNA-seq profiles from human MXP5 and PDX2 cell lines, which were engineered to express doxycycline-inducible wild-type IKAROS (IK1) or an empty vector control. RNA was collected 24 hours post-induction to capture early transcriptional responses to IK1 re-expression. These data are part of a larger multi-omics study integrating RNA-seq, ChIP-seq, CUT&RUN, ATAC-seq, and HiChIP to define IKAROS-regulated transcriptional and chromatin networks in IKZF1-deficient Ph⁺ B-ALL.

overall_design: The experimental design involved the IKZF1-deficient Ph⁺ B-ALL cell line MXP5, which expresses a doxycycline-inducible wild-type IKAROS (IK1) or an empty control vector. Cells were treated with 1 μg/mL doxycycline for 24 hours to induce IK1 expression. Following induction, cells were fixed and subjected to CUT&RUN targeting the histone modifications H3K27me3, H3K9me3 and H3K4me3 with IgG controls. Each condition (IK1-induced and control) was profiled in biological duplicate for each target.

first: Boyd

last: Joseph


title: Tissue-specific clonal selection and differentiation of CD4⁺ T cells during infection.

city: New York

first: Tiago

last: Castro

state: New York

address: 1230 York Avenue

institute: The Rockefeller University

summary: Pathogen-specific CD4⁺ T cells expand and contract during infection, generating memory clones that shape subsequent immune responses. How distinct tissue environments influence differentiation and clonal selection of polyclonal T cells remains unclear. We developed Tracking Recently Activated Cell Kinetics (TRACK) mice, a dual-recombinase fate-mapping system enabling spatial and temporal labeling of recently activated CD4⁺ T cells. Using TRACK mice during influenza infection, we observed organ-specific transcriptional differentiation and clonal selection in lung, mediastinal lymph nodes (medLNs), and spleen. During the effector phase, spleen-derived CD4⁺ T cells adopted a stem-like migratory phenotype, whereas medLN-activated cells differentiated into T follicular helper cells. T cell receptor sequencing showed low clonal overlap between tissues during the effector response, consistent with distinct antigenic landscapes. During memory formation, overlap increased between lung- and medLN-derived cells, while splenic clones retained a distinct repertoire. These findings define tissue-dependent mechanisms that shape CD4⁺ T cell fate and clonal architecture.

overall_design: Single-cell sorted fate-mapped CD4+ T cells from the spleen, mediastinal LN, and lungs of PR8 infected TRACK mice.

first: Roham

last: Parsa

first: Helder

last: Assis

middle: R

last: de Castro

first: Gabriella

last: Lima dos Reis

first: Arpita

last: Sushil

first: Harald

last: Hartweger

first: Angelina

last: Bilate

first: Daniel

last: Mucida


title: IKAROS re-expression modulates transcriptional networks in IKZF1-mutant Ph+ B-ALL [ChIP-Seq]

overall_design: The experimental design involved the IKZF1-deficient Ph⁺ B-ALL cell line MXP5, which expresses a doxycycline-inducible wild-type IKAROS (IK1) or an empty control vector. Cells were treated with 1 μg/mL doxycycline for 24 hours to induce IK1 expression. Following induction, cells were fixed and subjected to ChIP-seq targeting IKAROS, ERG, CTCF, and the histone modifications H3K27ac, H3K36me3 and H3K4me1. Each condition (IK1-induced and control) was profiled in biological duplicate for each target.


title: The gene expression profile of methotrexate-resistant JAR cells

city: Nagoya

first: Kosuke

last: Yoshida

state: Aichi

address: 65 Tsuruma-cho

institute: Nagoya University

summary: Choriocarcinoma is a rare and aggressive malignancy. Although multi-agent chemotherapy is the standard treatment, resistance to anticancer agents remains a significant clinical challenge. In this study, we investigated the gene expression profile of choriocarcinoma cells with acquired resistance to methotrexate (MTX) using mRNA sequencing.

overall_design: MTX-resistant JAR cells were established by continuous stepwise exposure to increasing concentrations of MTX. The cells were initially cultured in 10 nM MTX, and the concentration was gradually increased over several months. Total RNA was then extracted and subjected to mRNA sequencing.

first: Yuki

last: Nishiko

first: Kaoru

last: Niimi

first: Akira

last: Yokoi


title: Dysregulation of the Hippo Pathway in Cancer Associated Fibroblasts is Associated with anti-PD-L1 atezolizumab Resistance

city: South San Francisco

first: Juliette

last: Roels

address: 1 DNA Way

institute: Genentech

summary: The use of immunotherapy in solid tumors has significantly improved the outcomes and quality of life for cancer patients. However, a substantial fraction of patients remain unresponsive, highlighting the urgent need to identify novel mechanisms of resistance to enhance immune-centric, chemo-free treatment regimens. In this study, we investigate associations with immunotherapy resistance by integrating RNAseq data from 2800 bladder cancer patients enrolled in the IMvigor trials, focusing on resistance to the anti-PD-L1 therapy atezolizumab, along with single-cell data from 200 patient samples and healthy donors. To expand the analysis to a massive collection of over 100M cells from hundreds of diverse single cell studies, we present Firmament, a newly developed method to efficiently identify cell populations that show enrichment for expression of gene signatures. Through these analyses, we identify the Hippo pathway as critically associated with immunotherapy resistance in bladder cancer and other solid tumors. Our findings indicate that Hippo dysregulation in stromal cells, rather than cancer cells, drives the high YAP/TAZ signal in these tumors. We specifically identify dysregulated Hippo signaling in cancer-associated fibroblasts compared to healthy donor fibroblasts. These insights will be important for developing novel therapeutic combinations to improve outcomes for patients with solid tumors treated with immune checkpoint inhibitors.

overall_design: RNAseq of human PDAC and NSCLC CAF cell lines treated with or without TEAD inhibitor.

first: Hamid

last: Ghaedi

first: Soren

last: Muller

first: Akshay

middle: T

last: Krishnamurty

first: Ramya

last: Ganesan

first: Priyanka

last: Babu