title: The risk of nephrotic range proteinuria and kidney failure in primary laminopathies is genotype-specific

city: Cambridge

first: Sebastian

last: Sewerin

address: 75 Ames Street

institute: Broad Institute of MIT and Harvard

summary: Background: Primary laminopathies are a heterogeneous group of rare diseases caused by nuclear lamina dysfunction due to pathogenic LMNA variants. However, despite their ubiquitous expression, LMNA variants have rarely been linked to chronic kidney disease (CKD). Here, we systematically investigate clinical implications and functional underpinnings of a distinct LMNA missense variant (lamin A/C p.(Arg349Trp)) that has sporadically been found in patients with a complex phenotype including lipodystrophy, proteinuria, and focal segmental glomerulosclerosis (FSGS). Methods: In clinical and functional terms, we compare lamin A/C Arg349Trp with missense changes at Arg482, the most common hotspot residue for type 2 familial partial lipodystrophy (FPLD2). In particular, we assess renal endpoints in corresponding patient cohorts and investigate disease-associated alterations in vitro. Results: In contrast to FPLD2 patients, individuals with lamin A/C Arg349Trp experience high-grade proteinuria and a rapid decline of glomerular filtration rate with kidney failure at a median age of 43 years. Mechanistically, we demonstrate that Arg349Trp associates with an abrogation of the structural interaction between lamin A/C and nucleoporin 155, nuclear pore complex aggregation, and an alteration of TGF-β1-dependent signaling. Conclusions: While patients with Lamin A/C Arg482 missense changes are at very low risk for progressive CKD, patients harboring Arg349Trp show nephrotic range proteinuria and kidney failure in midlife. Hence, high-grade proteinuric kidney disease is genotype-specific and patients with the Arg349Trp substitution require early renoprotective intervention to potentially halt progression and prevent kidney failure.

overall_design: RNA-seq profiling of primary dermal fibroblasts from two patients with lamin A/C Arg349Trp, three patients with lamin A/C Arg482Trp, two patients with lamin A/C Gly608Gly (i.e., c.1824C>T; activates a cryptic donor splice site and underlies Hutchinson-Gilford progeria syndrome) (all heterozygous), and five non-affected controls.

first: Theodoros

last: Georgomanolis

first: Charlotte

last: Aurnhammer

first: Jan

last: Halbritter


title: Natural compounds magnolol and dicoumarol enhance adipogenesis for food production

status: Public on Jul 07 2026

city: Los Angeles

first: Qingwen

last: Xie

state: California

address: 405 Hilgard Avenue

country: USA

institute: University of California, Los Angeles

type: Expression profiling by high throughput sequencing

summary: Adipogenic enhancers have potential applications in the production of engineered adipose tissue for future foods and in the study of adipocyte biology. To investigate the molecular mechanisms underlying adipogenic enhancement, RNA sequencing was performed on murine 3T3-L1 cells and porcine dedifferentiated fat (DFAT) cells undergoing adipogenic differentiation. Cells were treated with vehicle control, magnolol, dicoumarol, magnolol plus dicoumarol, or rosiglitazone. Transcriptomic profiling was conducted to characterize gene expression changes associated with enhanced lipid accumulation and adipocyte differentiation across species.

sample_organism:
Sus scrofa
Mus musculus

platform_organism:
Sus scrofa
Mus musculus

overall_design: Murine 3T3-L1 preadipocytes and porcine dedifferentiated fat (DFAT) cells were induced to undergo adipogenic differentiation and treated with vehicle control (DMSO), magnolol, dicoumarol, magnolol plus dicoumarol, or rosiglitazone. Cells were harvested on day 5 of differentiation for bulk RNA sequencing

first: Amy

middle: C

last: Rowat

first: Robert

last: Damoiseaux


title: PUS7-Mediated Pseudouridylation of TGFBI Drives Vascular Remodeling in Pulmonary Hypertension II

city: Shenzhen

first: HE

middle: Mu

last: Hua

state: Guangdong

address: 1088 Xueyuan Avenue, Nanshan District

country: China

institute: Southern University of Science and Technology

summary: Background: Pulmonary hypertension (PH) is a life-threatening cardiovascular disorder characterized by irreversible pulmonary vascular remodeling and poor prognosis. RNA pseudouridylation, the most evolutionarily conserved RNA epigenetic modification, and its catalytic enzyme pseudouridine synthase 7 (PUS7) remained uncharacterized in PH, representing a major gap in understanding the epigenetic pathogenesis of the disease. Methods: We generated the first single-base resolution pseudouridine (Ψ) landscape in lung tissues of PH patients using bisulfite-induced deletion sequencing (BID-seq). PUS7 expression was analyzed in hypoxic pulmonary artery endothelial cells (PAECs), the lung tissues of PH patients, and Su5416-hypoxia rodent model. The functional roles of PUS7 were investigated through genetic manipulation (PUS7-deficiency cells, AAV-mediated overexpression, endothelial cell-specific knockdown, and heterozygous knockout mice) and pharmacological inhibition using NSC107512. Results: BID-seq revealed global Ψ dysregulation in the PH patient lung tissues. Among PUS family members, PUS7 was the most markedly upregulated in these tissues and in the hypoxic PAECs. Both gene knockdown and pharmacological inhibition with NSC107512 ameliorated PH, whereas AAV-mediated PUS7 overexpression exacerbated disease progression. RNA immunoprecipitation sequencing and mutagenesis studies demonstrated that PUS7 bound to and catalyzed Ψ at position 688 of Transforming Growth Factor Beta Induced Protein (TGFBI) mRNA, thereby stabilizing TGFBI and activating Phosphatidylinositol 3 Kinase (PI3K)-Protein Kinase B (AKT) signaling pathway. Furthermore, hypoxia-inducible factor 2α (HIF-2α) directly bound the PUS7 promoter, estabilishing a HIF-2α/PUS7/TGFBI/PI3K-AKT positive feedback loop that drives PH pathogenesis. Conclusions: PUS7-mediated pseudouridylation serves as a novel epigenetic driver of PH via the HIF-2α/PUS7/TGFBI/PI3K-AKT axis, positioning PUS7 as a promising therapeutic target for this devastating disease.

overall_design: A total of 6 human lung tissue samples, including 3 healthy control samples (con1-con3) and 3 pulmonary hypertension (PH) patient samples (PH1-PH3), were subjected to single-cell RNA sequencing (scRNA-seq). Single-cell suspensions were prepared from each sample, and libraries were constructed using the 10× Genomics platform. All libraries were sequenced on the Illumina NovaSeq platform in paired-end mode. Raw reads were processed to generate feature-barcode matrices, followed by cell clustering and differential expression analysis to characterize cellular heterogeneity in PH lung tissues.


title: PUS7-Mediated Pseudouridylation of TGFBI Drives Vascular Remodeling in Pulmonary Hypertension

city: Guangdong, Shenzhen

first: Xiaolin

last: Chen

address: No. 1088 Xueyuan Avenue, Nanshan District

summary:
Background: Pulmonary hypertension (PH) is a life-threatening cardiovascular disorder characterized by irreversible pulmonary vascular remodeling and poor prognosis. RNA pseudouridylation, the most evolutionarily conserved RNA epigenetic modification, and its catalytic enzyme pseudouridine synthase 7 (PUS7) remained uncharacterized in PH, representing a major gap in understanding the epigenetic pathogenesis of the disease.
Methods: We generated the first single-base resolution pseudouridine (Ψ) landscape in lung tissues of PH patients using bisulfite-induced deletion sequencing (BID-seq). PUS7 expression was analyzed in hypoxic pulmonary artery endothelial cells (PAECs), the lung tissues of PH patients, and Su5416-hypoxia rodent model. The functional roles of PUS7 were investigated through genetic manipulation (PUS7-deficiency cells, AAV-mediated overexpression, endothelial cell-specific knockdown, and heterozygous knockout mice) and pharmacological inhibition using NSC107512.
Results: BID-seq revealed global Ψ dysregulation in the PH patient lung tissues. Among PUS family members, PUS7 was the most markedly upregulated in these tissues and in the hypoxic PAECs. Both gene knockdown and pharmacological inhibition with NSC107512 ameliorated PH, whereas AAV-mediated PUS7 overexpression exacerbated disease progression. RNA immunoprecipitation sequencing and mutagenesis studies demonstrated that PUS7 bound to and catalyzed Ψ at position 688 of Transforming Growth Factor Beta Induced Protein (TGFBI) mRNA, thereby stabilizing TGFBI and activating Phosphatidylinositol 3 Kinase (PI3K)-Protein Kinase B (AKT) signaling pathway. Furthermore, hypoxia-inducible factor 2α (HIF-2α) directly bound the PUS7 promoter, estabilishing a HIF-2α/PUS7/TGFBI/PI3K-AKT positive feedback loop that drives PH pathogenesis.
Conclusions: PUS7-mediated pseudouridylation serves as a novel epigenetic driver of PH via the HIF-2α/PUS7/TGFBI/PI3K-AKT axis, positioning PUS7 as a promising therapeutic target for this devastating disease.

overall_design: Primary human pulmonary arterial endothelial cells (PAECs) were used for RNA immunoprecipitation sequencing (RIP-seq). Two experimental groups were set: normal rabbit IgG control group (PAECs_IgG) and anti-PUS7 immunoprecipitation group (PAECs_PUS7). RIP experiments were performed following standard protocols. Captured RNA was used to construct strand-specific libraries and sequenced on Illumina NovaSeq 6000 platform with paired-end 150 bp mode. Raw reads were quality controlled, mapped to human reference genome, and subjected to peak calling and downstream bioinformatic analyses.


title: Matrix Stiffness-driven FAK Splicing Tunes Cell Mechanosensing

city: Québec

first: Martial

last: Millet

state: Québec

address: 2250, Boulevard Henri-Bourassa

country: Canada

institute: CHU de Québec - Université Laval

summary: The extracellular matrix (ECM) stiffness influences many physiological and pathological processes. Cells can sense mechanical changes within the ECM through mechanosensors, most notably through the focal adhesion kinase (FAK). Using human-derived data and 2D/3D engineered models, we identified a ubiquitous and uncharacterized FAK isoform lacking exon 4 (FAKΔe4). We demonstrated that FAKΔe4 splicing is regulated by substrate stiffness in a biphasic manner, in which an optimal stiffness is required for a maximal FAKΔe4 expression. We further showed that FAKΔe4 dictates at which stiffness optimal migration speed and invasion occurs, impairs focal adhesion dynamics and maturation, and shifts its autophosphorylation and downstream YAP nuclear translocation toward lower stiffness compared to the canonical FAK isoform. Moreover, the FAKΔe4 expression levels to canonical FAK determine at which stiffness cells will converge during durotaxis. Our results reveal how FAKΔe4 acts as a fine-tuning mechanosensing switch and reframe our understanding of mechanotransduction.

overall_design: We performed long-read RNA sequencing on MDA-MB-231 and MCF10a cells cultured on substrates of different stiffness for 72h and 48 h, respectively, on polyacrylamide substrates of defined stiffness (1 or 10 kPa). Briefly, polyacrylamide substates of different stiffness were prepared by adjusting the ratio of acrylamide (40% w/v) and bis-acrylamide (2% w/v), in Milli-Q water and TEMED solution in 0.25 M HEPES buffer at pH 6. APS was used to initiate gel polymerization. The gels were functionalized using N-6-[(acryloyl)amido]hexanoic acid, succi-nimidyl ester. Then, the polyacrylamide gels were coated with 0.1 mg/ml rat tail type I collagen. After sterilization via UV light, cells were seeded on top of the polyacrylamide gels.

first: Juliette

last: Gouhier

first: Olivier

last: Chancy

first: Elise

last: Tahon

first: William

last: David Zakzuk Vivas

first: Emilie

last: Pic

first: Gabriel

last: Khelifi

first: Solange

last: Landreville

first: Samer

last: Hussein

first: Dwayne

last: Stupack

first: Francois

last: Bordeleau


title: PUS7-Mediated Pseudouridylation of TGFBI Drives Vascular Remodeling in Pulmonary Hypertension [BID-seq]

overall_design: A total of 8 human lung tissue samples, including 4 healthy control samples and 4 pulmonary hypertension (PH) patient samples, were subjected to bisulfite-induced deletion sequencing (BID-seq). For each sample, two libraries were prepared: an untreated "Input" library and a bisulfite-treated "Treat" library. In total, 16 sequencing libraries were generated (8 Input and 8 Treated). All libraries were sequenced on the Illumina platform with 150 bp single-end mode. Raw reads were filtered, aligned to the human HG38 reference genome, and processed to identify pseudouridine (Ψ) modification sites across mRNA and lncRNA. Differential pseudouridine modification analysis and functional enrichment were performed both within each sample (Input vs. Treat) and between groups (PH vs. Control).


overall_design: In this study, primary human pulmonary arterial endothelial cells (PAECs) were transfected with small interfering RNA targeting PUS7 (siPUS7) to generate a PUS7 knockdown model, with a negative control siRNA (NC) group included to control for transfection-related and non-specific effects. Both the siPUS7 and negative control siRNAs were designed and synthesized by Sangon Biotech (Shanghai, China). Transfection was performed using X-tremeGENE siRNA Transfection Reagent according to the manufacturer’s instructions when cells reached 70% confluence, at a final siRNA concentration of 40 nM. Cells were harvested 48 hours post-transfection and subjected to transcriptome sequencing.


title: RNA-seq analysis reveals transcriptional disruption induced by combined Cisplatin and TiO₂ nanoparticles in Drosophila melanogaster

city: Rio de Janeiro

first: Cristiano

middle: Nascimento

last: Costa

state: Rio de Janeiro

address: Rua Senador Furtado, 121/125

department: education department

country: Brazil

institute: Instituto Federal do Rio de Janeiro

summary: Cisplatin, the first metal-based chemotherapeutic drug, remains widely used despite its toxicity and the emergence of drug resistance. Combining Cisplatin with nanoparticles has been proposed to improve its therapeutic profile, although most studies rely on in vitro models. Here, we investigated the in vivo transcriptional effects of Cisplatin (50 μg/ml) and titanium dioxide nanoparticles (TiO₂ NPs; 50 μg/ml), alone and in combination, in Drosophila melanogaster. Using RNA-seq and bioinformatic analyses, we assessed differential gene expression across treatments. Flies exposed to Cisplatin or TiO₂ NPs alone exhibited modulation of genes associated with xenobiotic metabolism and detoxification pathways. In contrast, combined exposure resulted in a markedly reduced number of differentially expressed genes (four DEGs), accompanied by disruption of pathways related to cell division and DNA/RNA metabolism. Mortality rates were not significantly affected in any group. These results suggest that co-exposure to Cisplatin and TiO₂ nanoparticles induces a global transcriptional suppression, potentially impairing essential cellular processes.

overall_design: RNA-seq profile from whole body of the Drosophila melanogaster 3 days treated with cisplatin (50mg/ml); TiO2 nanoparticles (50mg/ml) ; cisplatin (50mg/ml) + TiO2 nanoparticles (50mg/ml); and the control group (non-treated). 3 runs each sample.

first: Luciane

last: Cisapina

first: Ana Cristina

last: Bahia

first: Valdir

last: Braz

first: Fabricio

last: da Silva

first: Francisco

last: Lopes


title: snATAC-seq from T-helper 1 cell (ENCSR251LFB)

status: Public on Jul 24 2026

city: Stanford

first: ENCODE

last: DCC

state: CA

address: 300 Pasteur Dr

institute: ENCODE DCC

type: Genome binding/occupancy profiling by high throughput sequencing

summary: For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: Transcriptomic Profiling of Patients’ Human Brown and White Adipose Tissue Depots

city: Bethesda

first: Aaron

middle: M

last: Cypess

state: Maryland

address: 10 Center Drive, 5N318A

department: NIDDK - DEOB

institute: National Institutes of Health

summary: Human adipose tissues are solid organs distributed throughout the body in specific locations and are thought to have dichotomous functions: white adipose tissue (WAT) stores triglycerides as an energy reservoir, and brown adipose tissue (BAT) uses metabolic fuels to generate heat. To define the transcriptional profile of six principal adipose depots, we analyzed tissue from 11 autopsies (3F/8M, 16-71y) of patients who had different underlying diseases. Despite global similarities in terms of cell type proportions, each depot had a distinct transcriptomic signature and functional profile. Each human’s adipose tissues were more similar to each other than to the anatomically and functionally matching depots in other patients. The transcriptomic pattern of subcutaneous WAT could even be used to predict the human donor. This pattern suggests that individualized factors such as genetics, age, environment, diet, and disease play impactful roles in coordinating the behavior of the whole-body adipose tissue depot.

overall_design: Adipose tissues came from six defined anatomical locations: abdominal subcutaneous (SQ), omental (O), pericardial (PC), periadrenal (AD), paravertebral (PV), and supraclavicular (SCLV). In addition, we procured urinary bladder (U) to serve as a non-AT control

first: Nhuquynh

last: Nguyen

first: Cheryl

last: Cero

first: Ju Hee

last: Kim

first: Kelly

middle: T

last: Long

first: Adrienne

middle: R

last: Guarnieri

first: Jurgen

last: Heymann

first: Sahara

middle: L

last: Ali

first: Emily

middle: V

last: Leary


title: N6-methyladenosine modification of mRNAs in retinal ischemia-reperfusion in mice

city: Guangzhou

first: Jingying

last: Liang

address: Jinsui Rd

institute: Zhongshan Ophthalmic Center

summary: Retinal ischemia-reperfusion injury (RIR) is the main pathogenic mechanisms of acute glaucoma, diabetic retinopathy, central retinal vein occlusion. As a common post-transcriptional modification of eukaryotic RNAs, N6-methyladenosine (m6A) is associated with the pathogenesis of different diseases, including angiogenesis, through the regulation of RNA metabolism and functions. The aim of this study was to identify the potential relevance of m6A RNA methylation in pathogenesis of RIR. A total of 10851 mRNAs and 23270 associated m6A methylation modified peaks were identified in the RIR group. Similarly, 10391 mRNAs and 22935 associated m6A methylation modified peaks were detected in the Sham group. Compared to the Sham group, the RIR group had 3871 hypermethylated and 3624 hypomethylated m6A peaks, with statistically significant  differences (|Fold Change (FC) | ≥2, p < 0.05). Gene ontology (GO) analysis showed that hypermethylated mRNAs were enriched in cellular process, cellular anatomical entity, and binding, while hypomethylated mRNAs were enriched in synaptic signaling, synapse, and gated channel activity. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis indicated that hypermethylated mRNAs were involved in tight junction, hippo signaling pathway, and PI3K-Akt signaling pathway, while hypomethylated mRNAs were involved in Neuroactive ligand-receptor interaction, glutamatergic synapses, cholinergic synapses. Joint analysis identified mRNAs with differential m6A methylation and expression simultaneously. Among them, the expression of Irx4, Kdr, Lyz2 were confirmed upregulated in the RIR group by RT-qPCR. Among them, the expression patterns of Irx4, Kdr, and Lyz2 were confirmed by RT-qPCR to be consistent with the sequencing results. The results revealed an altered m6A epitranscriptome in RIR retinas. These methylated RNAs may act as novel modulators and targets in RIR.

overall_design: Anesthesia was induced by intraperitoneal injection of pentobarbital (60 mg/kg). For surface anesthesia, 0.5% tetracaine hydrochloride was applied topically to the corneas, and 1% tropicamide was to achieve mydriasis. Animals were randomly assigned to each group. Continuous irrigation of the anterior chamber with sterile normal saline was performed using a 23-gauge needle to maintain the intraocular pressure (IOP) at 100 mmHg for 60 minutes. IOP was monitored using the tonometer (Icare TONOLAB tonometer TV02) to ensure consistency. The contralateral eye without IOP elevation functioned as the Sham. After removal of the needle, retinal blood flow was restored. Mice were euthanized at 3 days after the procedure, and retinas were collected for sequencing.


title: Formylpeptide Receptor Activation Attenuates Renovascular Remodeling in Neurogenic Hypertension (Left Ventricle)

city: Singapore

first: Gokce

last: OGUZ

address: 60 Biopolis St, GENOME, #02-01

department: Bioinformatics Consulting and Training Platform

country: Singapore

institute: Genome Institute of Singapore

summary: Inflammation and sympathetic overactivity contribute to end-organ injury associated with hypertension. We previously demonstrated that targeting formylpeptide receptors (FPRs), which regulate and resolve inflammation, prevents cardiovascular damage in preclinical hypertension. Here, we investigated whether the FPR agonist Cmpd17b can reverse renovascular remodeling in established essential hypertension.  Cmpd17b selectively reduced blood pressure in BPH/2J mice and improved aortic distensibility without altering cardiac function. Cmpd17b reduced collagen deposition across organs, most prominently in the kidney. RNA sequencing revealed kidney-specific upregulation of Serpina1e and Igfbp2, normalized by Cmpd17b. These findings identify FPR agonism as a promising therapeutic strategy for lowering blood pressure and reversing renovascular fibrosis.

overall_design: Adult blood-pressure-normal (BPN/3J) and high (BPH/2J) mice received Cmpd17b (50 mg/kg/day, i.p.) for 28 days, with continuous blood-pressure monitoring via radiotelemetry. Cardiac and vascular function were assessed via ultrasonography, and structural remodeling in the left ventricle, kidney, and vasculature was quantified, with RNA sequencing.

first: Jaideep

last: Singh

first: Arun George

last: Devasia

last: Oguz

first: Adaikalavan

last: Ramasamy

first: Helena

last: Qin


title: Formylpeptide Receptor Activation Attenuates Renovascular Remodeling in Neurogenic Hypertension (Kidney)


title: A High-Throughput Screen on Primary Glioblastoma-Associated Macrophages Identifies HDAC Inhibitors as Enhancers of Phagocytosis and Potent Partners for Immunotherapy [CUT&Tag]

first: Mona

last: Khalaj

address: 265 Campus Drive

institute: Stanford University

summary: This study presents the first high-throughput chemical screen on primary tumor-associated macrophages (TAMs) freshly isolated from surgical glioblastoma (GBM) patient samples, testing 1,365 compounds to identify drugs that enhance TAM phagocytosis. HDAC inhibitors, particularly Pracinostat and Resminostat, emerged as potent enhancers of phagocytosis, demonstrating synergy with CD47 blockade across multiple primary human TAM-GBM combinations. In a xenograft GBM model, Pracinostat suppressed tumor growth and extended survival with additive benefit when combined with CD47 antibodies. RNA-seq and H3K27Ac CUT&Tag profiling of Pracinostat-treated TAMs in vivo revealed a two-tier mechanism: transcriptional reprogramming toward a pro-inflammatory state via NF-kB activation, and epigenetic priming of FcgR-mediated phagocytic machinery, providing a mechanistic basis for the observed synergy with CD47 blockade.

overall_design: H3K27Ac CUT&Tag profiling of CD11b+ tumor-associated macrophages (TAMs) sorted from orthotopic T387 GBM xenograft-bearing NSG mice treated with Pracinostat (30 mg/kg, oral, 4x/week for 3 weeks) or DMSO vehicle control. n=3 DMSO, n=4 Pracinostat biological replicates. IgG controls included for background assessment.

first: Andrew

last: Burden

first: Irving

last: Weissman


title: A High-Throughput Screen on Primary Glioblastoma-Associated Macrophages Identifies HDAC Inhibitors as Enhancers of Phagocytosis and Potent Partners for Immunotherapy [RNA-seq]

overall_design: Bulk RNA-seq profiling of CD11b+ tumor-associated macrophages (TAMs) FACS-sorted from orthotopic T387 GBM xenograft-bearing NSG mice treated with Pracinostat (30 mg/kg, oral, 4x/week for 3 weeks) or DMSO vehicle control. n=3 DMSO, n=4 Pracinostat biological replicates.


title: Patch-seq analysis of dorsal striatum cholinergic interneurons in a mouse model of 22q11 deletion syndrome

city: Memphis

first: Stanislav

last: Zakharenko

state: Tennessee

address: 262 Danny Thomas Pl, M2426

department: Developmental Neurobiology

institute: St. Jude Children's Research Hospital

summary: Whole-cell patch-clamp electrophysiology was performed on cholinergic interneurons of the mouse  dorsal striatum. Cells were classified as active or silent based on spontaneous activity at the onset of recordings. Nuclei and surrounding cytoplasm were then collected using the patch pipette, and RNA-seq libraries were prepared using the SMART-Seq mRNA Single Cell LP kit (Takara, 634787). Paired-end 100-cycle sequencing was carried out on a NovaSeq X+ (Illumina) in the St. Jude Hartwell Center Genome Sequencing Core. At least 100 million reads were obtained per cell. Samples were collected and sequenced in two independent batches.

overall_design: Mice expressed fluorescent protein tdTomato in CHIs (ChATCre;Ai14). These mice were then crossed with the Df(16)1/+ mice. All samples were derived from tdTomato-positive CHIs. Mice were heterozygotes or wildtype littermates from the Df(16)1 line and a mixture of males and females. All animals were 2-3 months (82-95 days) old at the time of experiments. Heterozygotes are hemizygous in a region homologous to the human 22q11.2 locus.Cells were classified as active or silent based on spontaneous activity at the onset of patch-clamp recordings.

first: Kristen

last: Thomas

first: Mary

middle: H

last: Patton

first: Brett

last: Teubner

first: Sharon

last: Freshour

first: Christopher

last: Davenport

first: Ildar

last: Bayazitov

first: Alexandra

middle: J

last: Trevisan

first: Cody

middle: A

last: Ramirez

first: Jay

middle: B

last: Bikoff

last: Schild

middle: S


title: Single cell RNA sequencing analysis of stem cells after tenogenic differentiation

city: Rochester

first: Hani

last: Awad

state: NY

address: 601 Elmwood Avenue

department: Biomedical Engineering

institute: University of Rochester

summary: Single cell RNA sequencing was used to compare cells cultured using a tenogenic differentiation protocol. Cells included primary fibroblasts extracted from a tenolysis tissue specimen, mesenchymal progenitor cells (iMPCs) differentiated from induced pluripotent stem cells that were reprogrammed from the primary fibroblasts, as well as primary bone-marrow mesenchymal stromal cells (MSCs) from a different donor. For each cell type, cells were cultured for 21 days using a tenogenic differentiation protocol from STEMCELL Technologies. An undifferentiated negative control of each original cell type was cultured in parallel for 21 days along with a shorter culture of only 7 days. After culture, the gene expression profile of each sample was compared to assess tenogenic differentiation and heterogeneity in the cultures. It was found that tenogenic differentiation of iMPCs resulted in a small population of tenocyte-like cells with positive expression of tenogenic markers TNMD, SCX, and MKX. However, the cultures were heterogenous and had significant populations of non-tenocyte like cells. Furthermore, negative control samples also exhibited low expression of tendon markers in the abscence of tenogenic differentiation media. This study demonstrates that culture of mesenchymal progenitor cells for 21 days at high density alone is enough to promote some tenogenic differentiation. While addition of the tenogenic differentiation media led to more differentiation, the improvement was subtle and there is significant off-target differentiation that can be improved with alteration of the protocol.

overall_design: Primary tenolysis-derived fibroblasts, differentiated mesenchymal progenitor cells, and primary bone-marrow mesenchymal stromal cells were cultured in vitro on tissue culture plastic. For each cell type, cells were either cultured for 21 days using a tenogenic differentiation protocol from STEMCELL Technologies, cultured for 21 days without differentiation, or cultured for 7 days without differentiation. After culture, cells were passaged and analyzed using single-cell RNA sequencing.

first: Victor

middle: Z

last: Zhang

first: Xinying

last: Lu

first: Kyle

last: Jerreld


title: Convection-enhanced delivery of dexamethasone in glioma models suppresses myeloid inflammation while avoiding systemic toxicities

city: New York

first: Dr. Liang

last: Lei

address: 1130 St. Nicholas Ave

department: Pathology and Cell Biology

institute: Columbia University

summary: Dexamethasone is widely used to control cerebral edema and inflammation in glioblastoma, but its benefits are limited by systemic toxicities and adverse prognostic associations.  We evaluated local administration of dexamethasone via convection-enhanced delivery (CED) to maximize intratumoral anti-inflammatory effects by increasing local corticosteroid exposure while minimizing systemic exposure.  In two glioma mouse models, continuous intraparenchymal infusion of dexamethasone was well tolerated with no adverse effects. Pharmacokinetic analyses supported preferential intratumoral distribution and reduced systemic exposure with CED compared with systemic dosing.  Single-nucleus RNA sequencing (snRNA-seq) and immunohistochemistry showed attenuation of glioma-associated inflammation with downregulation of reactive microglial/macrophage programs and reduced tumor-infiltrating myeloid cells with a morphology consistent with a less activated state.  Experiments in human induced pluripotent stem cell (iPSC)–derived microglia confirmed that dexamethasone directly suppresses inflammatory gene expression, indicating a conserved mechanism across species.  This inflammatory suppression was recapitulated in both immortalized microglial (HMC3) and macrophage (THP1) cell lines.  These findings suggest that localized dexamethasone delivered by CED reprograms the glioma immune microenvironment and achieves control of inflammation without the systemic adverse effects associated with standard systemic dexamethasone therapy.  This clinically translatable strategy may improve symptom management and provide a platform for integrating local immunomodulation with future glioblastoma therapies.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design:
Murine glioma model (APCL) was treated with Systemic, Convection Enhanced Delivery (CED) Dexamethasone and Controls. All experimental conditions are in triplicates.
Human iPSC derived microglia were treated with 25 ng/μl of dexamethasone (63 μM) or 1 ng/μl of LPS, either separately or in combination for 24 hours. Vehicle treated cells were controls. All experimental conditions are in triplicates.


title: Single-cell analysis of follicular fluid reveals dysregulation of ovulatory immune function in Polycystic Ovary Syndrome patients undergoing ovarian stimulation

city: Madison

first: Aleksandar

middle: K

last: Stanic

state: WI

address: 202 S Park, PAB1

department: Obstetrics and Gynecology

institute: University of Wisconsin-Madison

summary: Polycystic ovary syndrome is the most common endocrine condition in women and anovulatory cause of female infertility. While a pro-inflammatory cytokines and leukocyte bias in systemic circulation is well-documented in PCOS, it is not known how this inflammation extends to or affects the ovary. Additionally, the relationship between ovulation and inflammation in PCOS is not well-defined. We hypothesize that the ovarian follicular immune environment in PCOS is uniquely dysregulated, and that resolving anovulation through ovulation induction is not sufficient to alleviate this dysregulation. Using single-cell RNA and surface protein analysis of peripheral blood and follicular fluid from patients undergoing in vitro fertilization, we discovered that both control and PCOS follicles were immunologically distinct from circulation. At a systemic level, we find that ovulation induction in PCOS does not alleviate systemic inflammation. In contrast, while healthy control ovaries experienced acute immune-directed ovulatory signaling, PCOS ovarian follicles were deficient in key pro-ovulatory cell to cell communication, and displayed instead a chronic low-grade inflammatory state with fibrotic features. Taken together, a picture emerges where acute ovulation demonstrates a well-ordered series of follicle-specific immune information flows, which are disrupted and replaced by low grade chronic inflammation in the PCOS follicle.

overall_design: 8 pairs of samples – TVOR appointment PBMC and Follicular Cells from each patient— were included in the study design. All patients had both peripheral blood and follicular fluid collected at the time of their transvaginal oocyte retrieval, following either an antagonist or Lupron overlap IVF protocol. Peripheral blood mononuclear cells (PBMC) and follicular fluid mononuclear cells (FFMC) were separated from plasma and follicular fluid respectively by density gradient centrifugation and washed with RPMI + 10% fetal bovine serum. ACK lysis buffer was added to FFMCs to remove red blood cell contamination. Cell suspensions were incubated with appropriate hashing antibodies and FFMCs and PBMCs were pooled. Cells were incubated with CITE-Seq antibodies, and libraries were prepared wtih 10X Genomics platform. Libraries were sequenced on on an Illumina Novaseq X.

first: Andrea

last: Wegrzynowicz

first: Soma

last: Banerjee

first: Emily

last: Grimes

first: Riley

last: Huddleston

first: Fernanda

last: Leyva Jaimes

first: Laura

middle: G

last: Cooney


title: Enhancing the iNKT cell immunotherapy platform by combining optimised CAR endodomains with novel iNKT engagers

city: London

first: Kanagaraju

last: Ponnusamy

address: Du Cane Road

department: Department of Immunology and Inflammation

country: United Kingdom

institute: Imperial College London

summary: iNKT cells are emerging as a highly promising cellular immunotherapy platform for the treatment of cancer. Their distinct biological features including their stereotypical CD1d-restricted TCR and ability to swiftly bridge and activate innate and adoptive T cell immunity underpin their potential for off-the-shelf therapy and pleiotropic anti-tumor effects. Accordingly, chimeric antigen receptor (CAR)-iNKT outperform CAR-T counterparts in preclinical models of blood cancers including myeloma and solid tumors. However, optimal designs of CARs that would maximise the activity of CAR-iNKT against myeloma and their combination with orthogonal therapeutic modalities that would expand their anti-myeloma potency have not been investigated. Here, we find that underpinned by enhanced avidity, amongst five different 2nd and 3rd generation CAR endodomains, BCMA CD28z CAR-iNKT exert the highest anti-myeloma activity in vivo. Increased avidity and anti-myeloma activity of CD28z CAR-iNKT is dependent on a novel cross talk between plexin D1 (PLXND1) on CAR-iNKT and semaphorin 4A (SEMA4A) on myeloma cells in vivo as well as in vitro. PLXND1-dependent avidity also underpins higher anti-myeloma activity of CAR-iNKT over CAR-T counterparts. To expand the anti-myeloma potential of CAR-iNKT, we designed and validated BCMA iNKT-specific engagers and selected a high affinity and efficacy design which exerts significant anti-myeloma activity in vitro and in vivo in conjunction with adoptively transferred iNKT. Finally, combined, dual target therapy with FCRL5 CD28z CAR-iNKT and BCMA iNKT engagers outperforms FCRL5 CAR-iNKT and limits immune escape of FCRL5-negative myeloma. Thus, we provide mechanism-based, proof-of-principle that a novel, optimised iNKT-based, dual-targeting combinatorial therapy has enhanced anti-tumor activity against multiple myeloma and potentially other malignancies.

overall_design: Invariant NKT (iNKT) cells were isolated from peripheral blood of healthy donors and lentivirally transduced to express BCMA CAR with different costimulatory molecules. After expansion of the non-transduced and CAR transduced iNKT cells, total RNA was isolated using Macherey-Nagel™ NucleoSpin™ RNA column and rDNase treatment on the column according to manufacturer’s instructions followed by enrichment for poly-A mRNA for paired-end RNA sequencing in illumina platforms.

first: Aristeidis

last: Chaidos

first: Anastasios

last: Karadimitris


title: Gene expression profile at single cell level of Irinotecan-sensitive and Irinotecan-resistant organoids for colorectal cancer

city: Jinhua

first: Yi

last: Pan

state: Zhejiang Province

address: No. 365, Renmin East Road, Wucheng District

department: Central Laboratory and Precision Medicine Center

institute: Affiliated Jinhua Hospital, Zhejiang University School of Medicine

summary: Organoids derived from both patients contained only epithelial cells.

overall_design: CRC5 consists of organoids derived from patients resistant to irinotecan, while CRC11 comprises organoids derived from irinotecan-sensitive patients.

first: Lin

last: Chen

first: YuQing

last: Hu

first: Jie

last: Chang

first: WenXia

last: Xu

first: XiFeng

first: ShuoChen


title: Peroxisomal ether lipid synthesis regulates cortical neurogenesis and maintains mitochondrial energy homeostasis in radial glial cells

city: Beijing

first: Jianwei

last: Jiao

state: Beijing

address: 1 Beichen West Road

department: State Key Laboratory of Reproductive Biology

institute: Institute of Zoology, Chinese Academy of Sciences

summary: We demonstrate that peroxisomes undergo dynamic remodeling and display functional heterogeneity during neurogenesis. In human brain organoids and mouse models, peroxisome damage leads to mitochondrial dysfunction and inhibits the differentiation of radial glial cells.

overall_design: Total mRNA profiles of E11,E12,E13,E14,E16,E18 cortex or primary stem cells were generated by deep sequencing, in triplicate,  using Illumina HiSeq 2500.

last: Li

first: Wenzheng

last: Zou

first: Yuqing

last: Lv

first: Yingfei

last: Lu

first: Shukui

last: Zhang

first: Jiaqi

last: Liang


title: Long-read proteogenomic atlas of human neuronal differentiation reveals isoform diversity informing neurodevelopmental risk mechanisms.

city: Toronto

first: Shreejoy

last: Tripathy

address: 250 College Street

institute: Centre for Addiction and Mental Health

summary: Reference annotations incompletely capture the transcript diversity of the human brain, obscuring the genetic architecture of neurodevelopmental disorders. Here, we integrated deep long-read RNA sequencing and proteomics in iPSC-derived cortical neurons to generate a high-resolution proteogenomic atlas of human neuron development. We identify 182,371 mRNA isoforms (over half novel) and provide direct peptide evidence for the translation of hundreds of novel protein-coding sequences. Crucially, population genetics demonstrate that novel splice sites are under strong negative selection, comparable to known missense mutations, confirming their functional importance. During neuronal maturation, we observe that ASD risk genes undergo dynamic isoform switching, including microexon usage and intron retention, that remodels key protein domains and regulatory regions. Furthermore, we uncover widespread, long-range coordination between splicing and polyadenylation, revealing complex regulatory logic. Critically, our atlas enables variant reinterpretation in ASD, demonstrating that an isoform-centric view is essential for interpreting pathogenic variation in neurodevelopment.

overall_design:
Illumina short-read RNA-seq from human-derived iPSCs and iPSC-derived intermediate cells at day 4, iPSC-derived neurons at day 30.
NOTE: This is a companion dataset to GSE310131. The two datasets represent data collected on two different sequencing platforms from the same biological samples.


title: Long-read proteogenomic atlas of human neuronal differentiation reveals isoform diversity informing neurodevelopmental risk mechanisms

overall_design: Illumina short-read RNA-seq and PacBio long-read RNA-seq from human-derived iPSCs and iPSC-derived intermediate cells at day 4, iPSC-derived neurons at day 30.


title: ATAC-seq after CRISPR perturbation of CD8⁺ T cells in young vs. aged tumors

city: Boston

first: Alex Chang-Yu

state: MA

address: 149 13th Street, 7th floor, Room 7103

department: Krantz Family Center for Cancer Research

institute: Massachusetts General Hospital

summary: Changes in chromatin accessibility (ATAC-seq) profiling after CRISPR perturbation of CD8⁺ T cells in young vs. aged tumors

overall_design: To perform CRISPR perturbation, we constructed a lentiviral vector containing a single guide RNA (sgRNA) and an ametrine reporter to transduce primary naïve-like splenic CD45.1 Cas9⁺ OT-1 CD8⁺ T cells. Transduced (ametrine⁺) CD45.1 Cas9⁺ OT-1 CD8⁺ T cells were sorted and transferred into young and aged mice one day before B16-OVA tumor inoculation. Fifteen days after tumor inoculation, ametrine⁺ CD45.1 Cas9⁺ OT-1 CD8⁺ T cells were isolated from tumors of young and aged mice using a BD FACSAria™ Fusion sorter. Sorted cells from independent mice were pooled into two or three biological replicates per group, counted, which ranged from 5,000 to 50,000 cells per genotype/subset combination (TProg: Slamf6+Tim-3-, TTran/Eff-like: Slamf6+Tim-3+, TTerm: Slamf6-Tim-3+, and TTAD: Slamf6-Tim-3-). Pelleted cells were incubated in 5–50 μl of reaction mix containing 2×TD, Tn5 enzyme, 2% digitonin in nuclease-free water at 37 °C for 30 min with agitation at 1000 RPM. MinElute Reaction Cleanup kit (Qiagen) was used for DNA purification. Following PCR, bead cleanup was done using AMPure XP beads (Beckman Coulter/Agencourt), library quality was verified using Tapestation analysis, and library quantification was confirmed by KAPA Library Quantification Kit Illumina® Platforms (Roche). Sequencing was performed on NextSeq1000/2000 sequencer using 100-cycle paired-end 50 bp reads each side.

first: Alex

first: Debattama

last: Sen


title: Morphological and Functional Diversity of Spatially Resolved Vestibular Ganglion Neuron Cell Types [scRNA-seq]

city: beijing

first: lucinda

last: liu

state: 北京Beijing

address: 7 Science Park Road ZGC Life Science Park

institute: nibs

summary: Vestibular ganglion neurons (VGNs) are the primary sensory neurons of the vestibular system, a relatively understudied sensory modality that is essential for maintaining visual stability and postural balance. Compared with other sensory systems, our understanding of the molecular heterogeneity of VGNs and its contribution to the diverse functions of the vestibular system remains limited. Using single-cell and spatial transcriptomics, we defined five transcriptionally distinct VGN cell types with discrete spatial distributions across the ganglion. The proper localization of VGN cell types requires intact hair cell mechanotransduction machinery. These VGN cell types demonstrate organ-specific innervation patterns, target defined zones within each organ, and form characteristic synaptic endings. To probe their functional roles, we generated genetic tools that selectively label each VGN cell type. Leveraging these tools, we identified a cell type required for gravity sensing and otolith-dependent vestibulo-ocular reflexes (VORs), revealing a cell-type-specific basis for modality-selective vestibular computations.

overall_design: The cell suspension was processed using the Chromium Single Cell 3' v3 chemistry (10x Genomics). Briefly, cells were loaded onto a Chromium Controller to generate single-cell gel beads-in-emulsion (GEMs), where each cell was co-encapsulated with a uniquely barcoded gel bead in nanoliter-scale droplets. Following cell lysis and barcoding, reverse transcription was performed using the Chromium Single Cell v3 reagent kit (10x Genomics) to generate barcoded cDNA. The cDNA was then amplified by PCR and used to construct sequencing libraries according to the manufacturer's protocol. Sequencing was performed with Illumina (NovaSeq) according to the manufacturer's instructions (Illumina).

first: Ruiqi

last: Liu

first: Jingyue

first: Zhiyu

first: Jingying

first: Zhiyong

first: Shuohao

last: Sun


title: Morphological and Functional Diversity of Spatially Resolved Vestibular Ganglion Neuron Cell Types

overall_design: Tissue sections were hybridized with gene-specific probes (Hybridization Kit, 10x Genomics, PN-1000466/PN-1000667), followed by ligation (Ligase, PN-2000425) to stabilize probe connections. Sections were aligned to the Visium HD slide capture area (6.5X6.5 mm), and probes were transferred using the CytAssist instrument. Released probes were captured by the slide's poly-T oligos and extended to incorporate UMIs, spatial barcodes, and sequencing adapters. The barcoded cDNA was amplified, bead-purified, and ligated with dual-index adapters to construct sequencing libraries. Library concentration was quantified using a Qubit 3.0 fluorometer (Thermo Fisher, Q33216), and fragment size distribution was analyzed with an Agilent 2100 Bioanalyzer (Agilent, G2939AA). Qualified libraries were sequenced on an Illumina platform under PE150 mode to generate high-quality spatial transcriptomic data.


title: scCRISPR screens of CD8⁺ T cells in young vs. aged tumors and tdLNs

summary: Single-cell in vivo CRISPR screens of CD8⁺ T cells across young and aged tumors and tumor-draining lymph nodes (tdLNs)

overall_design: To perform scCRISPR screening, we constructed a lentiviral vector containing a single guide RNA (sgRNA) and an mAmetrine (or known as Vex) reporter to transduce primary naïve-like splenic CD45.1 Cas9⁺ OT-1 CD8⁺ T cells. Transduced (mAmetrine⁺) CD45.1 Cas9⁺ OT-1 CD8⁺ T cells were sorted and transferred into young and aged mice one day before B16-OVA tumor inoculation. Fifteen days after tumor inoculation, ametrine⁺ CD45.1 Cas9⁺ OT-1 CD8⁺ T cells were isolated from tumors and tumor-draining lymph nodes (tdLNs) of young and aged mice using a BD FACSAria™ Fusion sorter. Sorted cells from independent mice were pooled into two biological replicates per group, counted, and loaded onto a Chromium Controller (10x Genomics) for a target recovery of 10,000 single cells per run. Libraries were prepared with the 10x Single Cell 5′ Reagent Kits v2 (Dual Index) and Feature Barcode technology for CRISPR screening, following the manufacturer’s protocol. Sequencing was performed on an Illumina NovaSeq X or NextSeq 1000/2000 system using 100-cycle kits with paired-end reads.


title: Single-cell transcriptomic gene regulatory network analysis uncovers the alteration of colonic stem and immune cell homeostasis in Nr4a1 knockout mice

city: College Station

first: Destiny

last: Mullens

state: Texas

address: 2253 TAMU

department: Nutrition

institute: Texas A&M University

summary: Recent findings suggest that the orphan nuclear receptor 4A (NR4A) can regulate cellular energetics and epithelial defenses, contributing to a resilient disease resistant phenotype. However, its role in regulating intestinal crypt homeostasis remains unclear. To assess the effects of NR4A on intestinal epithelial, stromal and immune cell heterogeneity and functional phenotypes, we utilized single-cell transcriptomics and advanced analytic strategies to generate a high-quality atlas for the colonic epithelium from wild-type and whole body Nr4a1 knockout mice. Here we observed a widespread effect of Nr4a1 deletion on intercellular communication involving intestinal stem cells, macrophages, T and B cells, and fibroblasts, indicating a complex and pervasive remodeling of the colonic epithelial and immune microenvironments and their regulatory networks. This alteration in cell-cell crosstalk was associated with an elevated single-cell entropy, indicative of higher differentiation potential and stem-like properties in epithelial, stromal and immune cell types. Our work provides new evidence of the molecular function of Nr4a1 as a critical regulatory factor in stem cell and immune homeostasis in the colon.

overall_design: From Nr4a1 knockout and C57Bl/6 wild type controls, colons were processed for single cell RNA sequencing.

first: Selim

last: Romero

first: Shreyan

last: Gupta

first: Michael

last: Salinas

first: Jennifer

last: Goldsby

first: Yang Yi

last: Fan

first: Laurie

last: Davidson

first: Jaileen

last: Rivera Rodriguez

first: Gus

last: Wright

first: Steven

last: Safe

first: James

last: Cai

first: Robert

last: Chapkin


title: SKI is critical to counter TGF-β signaling to promote T cell function and autoimmunity

city: Chapel Hill

first: Yisong

last: Wan

state: NC

address: 125 Mason Farm Rd

institute: University of North Carolina at Chapel Hill

summary: TGF-b is an immune regulatory cytokine central to immune homeostasis, tolerance, and autoimmunity. As a major suppressor, how SKI is involved in the fundamental roles of TGF-β in suppressing T cell function in autoimmunity and self-tolerance remains unknown. Here, we found that SKI protein was increased in activated T cells while decreased in response to exogenous and endogenous TGF-β, indicating a counter-balance role for SKI and TGF-β in activated T cells. Indeed, not only SKI deletion in T cells led to ameliorated spontaneous lethal autoimmune disease in mice with T-cell-specific deletion of TGFβRII, but also mitigated experimental autoimmune encephalomyelitis (EAE). Further investigation revealed that SKI deletion caused reduced T cell proliferation and related molecular programs even without TGF-β signaling, associating with enhanced TGF-β-related molecular program. This reveals a previously unappreciated SKI-dependent mechanism of TGF-β signaling in T cells besides current paradigm to explain how TGF-β restricts autoimmunity and bolsters tolerance.

overall_design: RNA-seq profile of wildtype and SKI knockout CD4+ T cells proliferation for 3 days, with or without the treatment of TGF-β inhibitor SB525334

first: Junying

last: Wang

first: Ziyi

last: Chen


title: Therapy-persistent leukemia is selectively vulnerable to SLC23A1 restoration via targeting KHSRP (PDX samples from different disease statuses)

first: Qingyu

last: Luo

address: 450 Brookline Ave

institute: Dana-Farber Cancer Institute

summary: Human PDX cells were enriched from mice treated with vehicle control or venetoclax + azacitidine

first: Andrew

last: Lane


title: Therapy-persistent leukemia is selectively vulnerable to SLC23A1 restoration via targeting KHSRP [eCLIPseq]

summary: eCLIP-seq was performed using CAL-1 cells treated with control (DMSO) or venetoclax+azacitidine (VenAza) for 6 hours to identify KHSRP-interacting RNAs


title: Overexpressed IL1R2 Cooperates with S100P and LEF1 to Mediate Immunosuppression in Preterm Infants

city: Shenzhen

first: Jun

last: Liu

address: No.13 Xinhu road

institute: Shenzhen Hospital of Southern Medical University

summary: Preterm infants exhibit marked heterogeneity in the developmental stages of their immune systems at birth, which vary significantly across gestational ages. The molecular basis of immune incompetence in preterm infants and its association with immunosuppressive mechanisms have not been fully elucidated. To gain a comprehensive understanding of immune heterogeneity pertaining to the early neonatal immune system, we collected peripheral blood samples from preterm infants and full-term infants within 12 h after birth alongside peripheral blood samples from four adults for comparative single-cell transcription analysis. Using single-cell RNA sequencing, we found that myeloid-derived cells from the peripheral blood of preterm infants, especially extremely preterm infants (< 28 weeks), highly expressed IL1R2. IL1R2+ myeloid-derived cells with S100P high expression and IL1R2+ regulatory T cells with LEF1 high expression may play an important role in immunosuppression during early immune development. High expression of IL1R2 in preterm infants may lead to immune suppression, and IL1R2 may affect both myeloid-derived cells and regulatory T cells, promoting immunosuppression with high S100P and LEF1 expression and playing an important role in immune suppression during early immune development in preterm infants.


title: Sustained AMPAR expression in CA3 neurons may mediate neuroprotection following FLASH-RT

city: Genève

first: Marie-Catherine

last: Vozenin

address: Avenue de la Roseraie 53

department: Radio-Oncologie

country: Switzerland

institute: HUG

summary: To elucidate the early mechanisms underlying the long-term neuroprotective effect of FLASH-RT in the normal brain, spatial transcriptomics (Nanostring) were performed after whole-brain irradiation of C57BL/6J mice with either 1 or 3 fractions of 10 Gy at 5.6 × 106 Gy/s (1 pulse-FLASH) or at conventional dose-rate 0.1 Gy/s. FLASH-RT induced a distinct transcriptomic signature in the cornu ammonis region 3 (CA3) and dentate gyrus (DG) neurons, with upregulation of genes encoding glutamate receptors involved in calcium signaling, long-term potentiation, and mitochondrial OXPHOS. Early transcriptional upregulation of Gria genes translated into increased AMPAR protein levels at 48 h in the DG and CA3 region and sustained higher AMPAR expression at 2 and 4 weeks post-FLASH. These findings support a durable activation of AMPAR. We propose a mechanism to explain FLASH-induced neuroprotection initiated by early calcium influx and subsequent sustained expression of glutamate AMPARs in neurons and/or neural progenitors of the CA3, potentially contributing to long-term cognitive sparing.

overall_design: Nine-week-old tumor-free C57BL/6J mice were whole-brain irradiated with 1 or 3 fractions of 10 Gy at 5.6x106 Gy/s delivered in 1 pulse (FLASH ) or at ~0.1-0.2 Gy/s (CONV). Using a digital spatial transcriptomics method (GeoMx Nanostring), neuron specific transcriptomics imprints were generated in the hippocampus and in the cortex with sub-region specificity.

first: Louis

last: Kunz

first: Aymeric

last: Almeida

first: Benoit

last: Petit

first: Charles

last: Limoli


title: RNA Sequencing of the Impact of CXCR3 receptor modulation on activated T cells function

first: Hui

last: Yang

address: 7 Panjiayuan Nanli, Room314

department: Department of Toxicology

institute: China National Center for Food Safety Risk Assessment (CFSA)

summary: First, we used human PBMCs to establish a T - cell activation model, and activated T cells with the polyclonal stimulants PMA and Ionomycin. Before activating the PBMCs, we pretreated them with the CXCR3 antagonist AMG 487 and agonist VUF 11222. Then, through transcriptome sequencing, we explored the effects of these two chemicals on activated T cells, analyzing differentially expressed genes and associated signaling pathway changes to evaluate whether chemical regulation of the CXCR3 receptor impacts T cell function.

overall_design: This study aims to establish an in - vitro activation model of human T cells. It explores the effects of these two chemicals on activated T cells, including differentially expressed genes and related signaling pathway changes, to assess whether chemical modulation of the CXCR3 receptor impacts T cell function.

first: Ying

first: Xu

last: Miao

first: Tian

last: Yaru

first: Zhuang

last: Zhisen

first: Qiannan

last: Zhang

first: Xudong

last: Jia


title: Toxicological assessment of microplastic exposure on Rats

city: Durham

first: Weichun

last: Huang

address: 109 TW Alexander Dr

department: OCSPP

institute: US EPA

summary: Microplastics, derived largely from degraded household and commercial plastics, have become a pervasive environmental concern, and may pose health risks resulting from ingestion and accumulation in living organisms. Polyethylene terephthalate (PET) microplastics, commonly found in consumer products such as plastic bottles and clothing, have been detected in human arteries and brains among other tissues—although their health impacts remain unknown. This study aimed to evaluate sex-based differences in biological effects of a single oral gavage of PET microplastics Sprague-Dawley rats. Adult rats (3 mo) were exposed to PET through oral gavage for approximately 18.5 hr. At the completion of the exposure, rats were evaluated for changes in metabolic rate and blood markers of inflammation, metabolism, stress, and stress. Rats were euthanized and liver, stomach, and duodenal tissue were used to identify exposure dependent changes in gene expression.  Minor sex-dependent differences were observed in metabolic rate, metabolic biomarkers, and blood platelet concentration. Consistent with this, RNA-seq analysis identified few differentially expressed genes in either sex. No overlap among DEGs across all three tissues was observed between males and females. Together these results suggest that even in short term exposures PET alters diverse endpoints across tissues in a sex-dependent manner. Though effects were relatively minor, evaluating the effects of PETs in chronic studies is merited.

overall_design: This is a case-vs-control comparion study across three tissue types with two exposure doses

first: Ashley

last: Lewis

first: Mary Jean

last: See

first: Robert

last: Flick

first: David

last: Bencic

first: Aimen

last: Farraj

first: Adam

last: Biales


title: RNA resequencing of Jurkat T cells activation  model

summary: To gain insights into how different activation methods affect T cells, we established a T cell activation model using human Jurkat T cells. In this model, two activation methods were applied: one with the polyclonal stimulants PMA and Ionomycin, and the other with the monoclonal stimulation antibodies anti - CD3 and anti - CD28. To comprehensively understand the differences caused by these two activation methods at the cellular level and their impact on cell function regulation, we used transcriptome sequencing. This technology aims to analyze the expression of differentially expressed genes and related signaling pathway changes under the two activation methods, offering a molecular basis for revealing their role in cell activation, proliferation, and immune responses.

overall_design: The Jurkat cells were stimulated with PMA/ionomycin (0.16/2.6 mM) for 24 h, followed by RNA sequencing.The Jurkat cells were stimulated with anti-CD3/CD28 mAbs (5/2 μg/mL) for 24 h, followed by RNA sequencing.


title: total RNA-seq from HG03058 (ENCSR227XJB)

city: Stanford

first: ENCODE

last: DCC

address: 300 Pasteur Dr

institute: ENCODE DCC

summary: For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: Cohesin acts as a transcriptional gatekeeper by restraining pause–release to promote processive elongation [mNET-seq]

city: Tokyo

first: Shoin

last: Tei

address: 1-1-1 Yayoi, Bunkyo-ku

department: Institute for Quantitative Biosciences

country: Japan

institute: The University of Tokyo

summary: Cohesin organizes 3D chromatin architecture, including promoter–enhancer loops, yet its loss has surprisingly modest effects on steady-state gene expression. We address this paradox by demonstrating that cohesin acts at different stages of transcription in human cells. First, it promotes Pol II promoter recruitment by facilitating enhancer–promoter communication that maintains active promoter chromatin states. Second, it delays pause release by transiently associating with the transcriptional machinery during the pause–release transition. Kinetic modelling suggests that reduced Pol II recruitment and enhanced pause release have compensatory effects, contributing to minimal changes in steady-state gene expression across genes upon cohesin loss. In contrast, cohesin depletion impairs robust transcriptional induction in response to external stimuli. Moreover, cohesin ensures sufficient pausing duration as a quality-control-like step to promote elongation complex assembly and transcription processivity. Here, we show that cohesin regulates multiple transcriptional steps, offering mechanistic insight into cohesin-related diseases, including cancers and cohesinopathies.

overall_design: Mammalian NET-seq in HCT116 cell line.

first: Toyonori

last: Sakata

first: Atsunori

last: Yoshimura

first: Toyoaki

last: Natsume

first: Masato

last: Kanemaki

first: Takashi

last: Sutani

first: Masashige

last: Bando

first: Katsuhiko

last: Shirahige


title: Cohesin acts as a transcriptional gatekeeper by restraining pause–release to promote processive elongation [RNA-seq]

overall_design: RNA-seq in HCT-116 cell line.


title: Cohesin acts as a transcriptional gatekeeper by restraining pause–release to promote processive elongation [ChIP-seq]

overall_design: Chromatin immunoprecipitation sequencing (ChIP-seq) for RPB1, BRD4, MED1, RAD21, MAU2, NIPBL in HCT116 cell line.


title: Cohesin acts as a transcriptional gatekeeper by restraining pause–release to promote processive elongation [TT-seq]

overall_design: TT-seq in HCT116 cell line.


title: Developmental programming of late-life proteostasis and longevity by NuA4 complex activity in early life [CUT&Tag]

city: Hangzhou

first: Lianfeng

last: Wu

state: Please select a state below

address: 600 Dunyu road

institute: Westlake University

summary: Maintaining proteostasis is essential for healthy aging and preventing neurodegenerative diseases like Alzheimer's disease, yet its collapse in late life leads to irreversible pathologies. It is unknown if there exists an early-life window where proteostasis can be programmed to confer lasting resilience, offering a preventative approach against these conditions. Leveraging short life cycle and the genetical tractability of Caenorhabditis elegans, we discover that inhibition of the TIP60/NuA4 acetyltransferase complex in early life can enhances late-life proteostasis and extends lifespan. We found that reducing early-life NuA4 activity diminishes epigenetic priming of H4K16ac, triggering compensatory activation of the XBP-1-mediated unfolded protein response (UPRER). This early-life-predominant XBP-1 activation remodels ER structure and reprograms lipid metabolism. Crucially, early-life NuA4/H4K16ac suppression boost oleic acid accumulation, which confers late-life health benefits. Overall, our study demonstrates the principle of developmental plasticity in shaping late-life proteostasis and reveals the potential for early interventions to combat neurodegeneration and aging.

overall_design: CUT&Tag-seq of H4K16ac in wild-type C. elegans at embryo 0h (E0), embryo 6h (E6) stage and L1 stage with control and mys-1 RNAi  treatment in parental generation

first: Yihan

last: Wang

first: Xiong

last: Xiong

first: Tianyi

last: Ni

first: Yanxiao

last: Zhang

first: Jie

last: Chen


title: Progesterone receptor isoform PGR-A in female fertility

city: Adelaide

first: Thao

last: Dinh

state: South Australia

address: North Terrace

country: Australia

institute: University of Adelaide

summary: Progesterone is a critical reproductive hormone that acts via progesterone receptor transcriptional regulators. The short PGR-A isoform lacks a 164 amino acid N-terminal region present in PGR-B that markedly enhances its transcriptional activity.  Isoform-specific mutants inactivating either PGR-A (PRAKO) or PGR-B (PRBKO) indicated that PGR-A is specifically essential for female fertility.  This study revises that interpretation by showing that an inadvertent frame-shift mutation in the PRAKO caused ablation of both isoforms, instead of the intended PGR-A isoform-specific null mutation. A true PGR-A specific mutant generated through CRISPR-Cas9 editing with a complete lack of PGR-A, but retained expression of PGR-B showed a phenotype indistinguishable from wild type as previously shown for PRBKO females.  Thus, the distinct function of PGR isoforms is more nuanced than previously appreciated.

overall_design: RNA-seq was performed on 4 replicates of granulosa cells obtained from wildtype and knockout animals from the PGR-A KO strain for comparative analysis

middle: D

first: Rebecca

last: Robker

first: Darryl

last: Russell


title: P2RY2 fuelled by eATP drives cancer immune evasion and therapy resistance

city: Heidelberg

first: Chong

last: Sun

state: Baden-Württemberg

address: Im Neuenheimer Feld 280

department: Immune Regulation in Cancer

country: Germany

institute: German Cancer Research Center

summary: In this study, we identify P2RY2 as a pivotal upstream driver of both PGE2 accumulation and B7-H3 upregulation in the TME. This process is fuelled by extracellular ATP (eATP), a cognate ligand for P2RY2 that is commonly and markedly elevated in the TME and rises further under immunotherapies. Genetic or pharmacological disruption of P2RY2 substantially reduces intratumoural PGE2 and B7-H3, increasing T cell infiltration, effector functions, proliferation, and persistence within the TME. Consequently, targeting P2RY2 substantially improves the efficacy of TCR-engineered T cells, CAR-T cells, and immune checkpoint blockade (ICB) in multiple syngeneic and humanized mouse tumour models, and potentiates patient-derived tumour-infiltrating lymphocytes (TILs) against paired primary tumour cells. By establishing P2RY2 as the crucial link between eATP and tumour-induced immunosuppression, our study reveals how a receptor typically associated with innate “danger” signalling can be hijacked to undermine adaptive immunity, thereby providing a promising therapeutic avenue to overcome a common immune resistance mechanism in cancer and advance T cell–based cancer therapies.

overall_design: mRNA profiles of WT and P2RY2-knockout KBM7, BxPC-3, and SW480 cells were generated through deep sequencing. Prior to harvesting, all cells were treated with 200 μM ATP for 8 hours. Differential gene expression (DGE) analyses were then conducted.

first: Zhaoqing

last: Hu

first: Hitoshi

last: Matsuo


title: Massively parallel reporter assays identify functional enhancer variants at QT interval GWAS loci

first: Jeerthi

last: Kannan

address: 401 Park Dr

department: Nephrology

institute: Boston Children's Hospital

summary: Our goal here is to utilize massively parallel reporter assays (MPRA) to screen for enhancer variants that can explain the observed common variants-based associations with QT interval at GWAS mapped loci. Towards this goal, we selected 1,018 bi-allelic variants that are associated with QT interval variation across 35 GWAS loci and overlap cardiac open chromatin regions, and performed MPRA-based screen in mouse cardiomyocyte HL-1 cells for variant-centered elements that act as enhancers and have significant allelic difference in their activities.

sample_organism:
Escherichia coli
Mus musculus

platform_organism:
Escherichia coli
Mus musculus

overall_design: Amplification and cloning of 101,800 200-mer oligo plasmid libraries designed for MPRA. The vectors house 1018 variants relevant for the QT interval with 50 unique barcode tags assigned to each allele. Then these vectors are transfected into mouse cardiomyocyte HL-1 cells where the transcriptional activity of the variants respective to each allele is measured through barcode counts.

first: Dongwon

last: Lee

first: Lavanya

last: Gunamalai

first: Kyla

last: Vickery

first: Or

last: Yaacov

first: Ana C

last: Onuchic-Whitford

first: Aravinda

last: Chakravarti

first: Ashish

last: Kapoor


title: Lineage master regulator and cancer-selective partner transcription factors rewire 3D genome topology for tumor-specific gene control

first: Namyoung

last: Jung

address: 269 Campus Dr. CCSR Room 2150

department: Medicine

institute: Stanford University

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

overall_design: Refer to individual Series


title: Cohesin acts as a transcriptional gatekeeper by restraining pause–release to promote processive elongation [EU-seq]

first: Shoin

last: Tei

overall_design: 5-ethynyl 2’-deoxyuridine (EU)-labeled nascent RNA sequencing (EU-seq) in HCT-116 cell line.

first: Toyonori

last: Sakata

first: Atsunori

last: Yoshimura

first: Toyoaki

last: Natsume

first: Masato

last: Kanemaki

first: Takashi

last: Sutani

first: Masashige

last: Bando

first: Katsuhiko

last: Shirahige


title: RNA-seq and ATAC-seq of follicular B cells and germinal center B cells with a conditional deletion of Brwd1

city: Chicago

first: Mark

last: Maienschein-Cline

state: IL

address: 900 S Ashland Ave, Rm 1058, M/C 937

department: Research Resources Center

institute: University of Illinois at Chicago

summary: Follicular B cells and germinal center B cell subsets were sorted from Cd23-Cre Brwd1fl/fl and Aicda-Cre Brwd1fl/fl mice, respectively.

overall_design: ATAC-seq of flow-sorted follicular B from Cd23Cre Brwd1fl/fl and wildtype mice, and germinal center B cells from AicdaCre Brwd1fl/fl mice.

first: Nathaniel

middle: E

last: Wright

first: Domenick

last: Kennedy

first: Junting

last: Ai

first: Margaret

last: Veselits

first: Mary

last: Attaway

first: Young

last: Yoon

first: Madeleine

last: Durkee

first: Jacob

first: Malay

last: Mandal

first: Marcus

last: Clark


overall_design: RNA-seq of flow-sorted follicular B and germinal center B cells from Cd23Cre Brwd1fl/fl mice and AicdaCre Brwd1fl/fl mice, respectively.


first: Shoin

last: Tei

overall_design: Chromatin immunoprecipitation sequencing (ChIP-seq) for RPB1, Ser2P, H3K27ac, H3K4me1, H3K4me1, NELFCD, AFF4 and Rad21 in HCT116 cell line.

first: Toyonori

last: Sakata

first: Atsunori


title: Cohesin acts as a transcriptional gatekeeper by restraining pause–release to promote processive elongation [Micro-C]

overall_design: Micro-C in HCT-116 cell line.

last: Yoshimura

first: Toyoaki

last: Natsume

first: Masato

first: Takashi


first: Mark


title: Transcriptional profile of the murine epithelial boundary corresponding to the gastro-esophageal junction

city: Newcastle upon Tyne

first: Heiko

last: Peters

address: Central Parkway

department: Institute of Human Genetics

institute: Newcastle University

summary: Exposure of the gastro-esophageal junction (GEJ) to microenvironmental insults represents a significant risk factor for the induction of metaplastic changes of the esophageal epithelium (Barret’s esophagus) and for initiation of malignant transformation. Little is known about alterations of the genetic programme prior to a pathological manifestation and the use of rodent model systems has been limited due to specific anatomical characteristics. This study was carried out to identify genes that are specifically up-regulated at the mouse squamocolumnar junction (SCJ), the epithelial boundary located at the limiting ridge that separates forestomach and corpus and that is morphologically analogous to the GEJ.

overall_design: Nine normal and healthy C57Bl/6 female mice at 3 months of age were used in this experiment. From each mouse, the stomach was dissected, opened and flushed with sterile PBS. Three directly adjacent stripes of tissues (each approximately 600-800um wide) were dissected from each stomach: a stripe of the non-glandular forestomach (FS), a stripe of corpus (CO) and a stripe representing the squamocolumnar junction (SCJ) between FS and CO. This boundary corresponds to the human gastro-esophageal junction and in rodents is located at the so called limiting ridge. Tissues from three animals were pooled prior to total RNA analysis to create one series of CO, FS and SCJ. RNA was isolated from a total of three series (S1, S2, S3).


title: Transcriptomic Analysis of Drosophila melanogaster With Sirt6 Deletion

status: Public on Jul 06 2026

city: Cleveland

first: Jackson

last: Taylor

state: Ohio

address: 2121 Euclid Avenue

department: Center for Gene Regulation in Health and Disease, Department of Biological, Geological and Environmental Sciences

institute: Cleveland State University

summary: RNA-seq on head, thorax, and eviscerated abdomen tissue from young male control and Sirt6-/- flies

first: Arjun

last: Khanna

first: Roja

last: Sharrma

first: Samira

last: Xhaferi


title: hepatic transcriptional profile of diet-induced obese mice treated with rosuvastatin and GGOH

city: NEW YORK

first: Lale

last: Ozcan

address: 630 West 168th Street, Black Building: 9-905, Molecular Medicine

institute: COLUMBIA UNIVERSITY

summary: Atherosclerotic cardiovascular disease is the leading cause of death worldwide, and statins are the primary therapy for lowering LDL cholesterol and reducing cardiovascular risk. In addition to inhibiting cholesterol synthesis, statins reduce the production of geranylgeranyl isoprenoids, which regulate the activity of small GTPases such as Rap1a. To identify hepatic genes and pathways regulated by geranylgeranyl isoprenoids, we performed RNA sequencing of liver samples from mice treated with vehicle, statin, geranylgeraniol (GGOH), or statin plus GGOH. This dataset was generated to identify transcriptional programs regulated by geranylgeranyl isoprenoids and to discover candidate genes involved in hepatic cholesterol metabolism and PCSK9 regulation.

overall_design: RNA-seq profiling of livers of obese mice treated with vehicle, rosuvastatin or rosuvastatin and GGOH


title: Pioneer transcription factor TAL1 reshapes chromatin architecture to direct erythroid cell fate commitment [ATAC-Seq 2]

city: zhengzhou

first: Hengchao

last: Zhang

state: Henan

address: 河南省郑州市高新技术开发区科学大道100号郑州大学新校区

institute: zzu

summary: Pioneer transcription factors critically regulate chromatin organization and hematopoietic cell lineage commitment. During erythropoiesis, hematopoietic stem cells undergo dynamic transcriptional and chromatin remodeling to differentiate into erythrocytes. Functionally validated pioneer factors capable of orchestrating erythropoiesis through dynamic chromatin remodeling remain limited, leaving their regulatory mechanisms incompletely resolved. Here, we identify T-cell acute lymphocytic leukemia 1(TAL1) as a pioneer factor that remodels chromatin to drive transcriptional reprogramming during erythropoiesis. By recruiting SWI/SNF complex, TAL1 drives erythroid fate specification while suppressing alternative lineages through lineage-restricted chromatin compartment reorganization. As a pioneer factor, TAL1 recruits chromatin remodelers BPTF and KMT2A to establish erythroid-specific genomic architecture. These complexes collectively execute TAL1 directed differentiation programs by transcriptionally activating erythroid regulators while repressing non-erythroid determinants. Our work establishes a generalizable chromatin accessibility-directed pioneer factor screening strategy, we identify TAL1 as a master pioneer factor and resolve its mechanism in driving erythroid commitment through 3D epigenome restructuring.

overall_design: Primary human CD34+ cells from cord blood were isolated from mononuclear cells (MNC) obtained by human peripheral blood lymphocyte isolation fluid and followed by positive selection using CD34+ magnetic selective beads system (Miltenyi Biotechnology, Germany) according to the manufacturer’s protocol. Then we explored the the roles of TAL1 during early stage of erythropoiesis using an in vitro 3 phases erythroid-inducing cell culture system employing CD34+ cells from core blood. Cells were transfected with lentivirus containing shTAL1 at day 2, compared with the scramble control. Next,we performed a TAL1 and BRG1 CUT&Tag sequencing at day 7.

first: Lixiang

last: Chen

first: Ying

last: Cheng

first: Lei

last: Sun

first: Xiuyun

last: Wu


title: Pioneer transcription factor TAL1 reshapes chromatin architecture to direct erythroid cell fate commitment [CUT&Tag]

address: 河南省郑州市高新技术开发区科学大道100号郑州大学新校区


title: Cross-species single cell transcriptomics in fly and beetle reveals the genetic core of brain neuroblast specification

city: Göttingen

first: Noel

last: Cabañas

address: (GZMB) Justus-von-Liebig-Weg 11

department: Evolutionary Developmental Genetics

institute: University of Göttingen

summary: This work defines the conserved core of TFs involved in insect brain NB specification by cross-species comparison of single-cell transcriptomics of NBs from, the red flour beetle, Tribolium castaneum, and the vinegar fly, Drosophila melanogaster. In Tribolium, we established a Gal4 enhancer trap screen system to generate a line that marks NBs. Using the 10x genomics technology, we sequenced 37,137 Tribolium NBs. We also sequenced 32,112 single nuclei of Drosophila NBs. Cross-species comparison followed by in situ hybridization led to the identification brain-specific TFs of insects. This brain NB-specific gene set confirms fundamentally different spatial patterning compared to the well-studied ventral nerve cord.

overall_design: We stablished a Gal4 enhancer trap screen system to generate a line that marks NBs with tGFP in Tribolium. We used this line to produce embryonic cell suspension that were FACS sorted to enrich for neuroblasts. Using the 10x Genomics technology, we then produced single cell sequencing data.

first: Gregor

last: Bucher


title: Candida glabrata YPK2 is a multidrug susceptibility locus

city: Iowa City

first: Scott

last: Moye-Rowley

state: Iowa

address: 6-530 Bowen Science Bldg./Dept. of Mol Physio

department: Molecular Physiology & Biophysics

institute: University of Iowa

summary: The biological conservation between fungi and mammals due to a common ancestor has made development of selective antifungal drugs a difficult challenge. Further complicating this situation is the selection of antifungal drug-resistant organisms during drug treatment. The pathogenic yeast Nakaseomyces glabratus (called here Candida glabrata) presents an especially challenging organism due to its tendency to frequently lose susceptibility to the major antifungal drug class the azoles. Additionally, C. glabrata develops resistance to echinocandin drugs, a second, more recently described antifungal agent at 10 times the rate of other organisms. Previous work has established that the sterol responsive transcriptional regulator Upc2A is a key determinant of azole susceptibility in C. glabrata and plays a role in echinocandin resistance. We used a biochemical approach to identify proteins that co-purified with Upc2A and identified the Ypk2 AGC kinase as an interacting protein. Strains lacking YPK2 exhibited increased susceptibility to fluconazole and the echinocandin caspofungin. A ypk2D strain failed to normally induce transcription of several ERG genes but exhibited normal induction of the CDR1 ATP-binding cassette transporter gene. Isogenic ypk2D strains were also highly susceptible to the three major classes of antifungal drugs, indicating that this kinase behaves as a multidrug susceptibility factor. RNA-seq analyses indicated that the transcriptional response to exposure is different for each drug and each response is differentially altered upon loss of Ypk2. Our data indicate that Ypk2 plays an important role in coordinating gene expression that impacts susceptibility to all major antifungal drug classes.

overall_design: We wanted to determine the transcriptome influenced by Candida glabrata Ypk2 when cells were treated with caspofungin, amphotericin B or fluconazole. Isogenic wild-type and ypk2 null cells were grown in rich medium (YPD) and then treated with these antifungal drugs or left untreated. Total RNA was isolated and subjected to RNA-seq analysis.

first: Thomas

middle: P

last: Conway

first: Lucia

last: Simonicova

first: W


title: Airway microbiome diversity, intra-mucosal bacteria, and spatial immunity in asthmatics and controls.

city: Montreal

first: Tamiko

last: Nishimura

address: 740 ave Dr Penfield

institute: McGill University

summary: Global human gene expression along with a custom panel targeting 29 common respiratory microbes were quantified in epithelial and stromal compartments of 44 asthmatic adults and controls using GeoMx digital spatial profiling (DSP) Whole Transcriptome Assay (WTA) with NGS read-out.

overall_design: In the study presented here, GeoMx Whole Transcriptome Assay was performed on a total of 184 areas-of-illumination (AOI) from 44 lung biopsies. Targets that were detected in at least 1% of the AOIs were retained in the analysis, resulting in inclusion of 12,489 genes.

first: Miriam

last: Moffatt

first: William

last: Cookson


title: long read RNA-seq from renal pelvis (ENCSR229ICS)

first: ENCODE

last: DCC

state: CA


title: Multi-omics identifies promoter methylation and gene expression changes associated with human skeletal muscle atrophy

city: Robina

first: Paul

last: Dunn

state: QLD

address: 14 University Dr

institute: Bond University

type: Methylation profiling by genome tiling array

summary: Skeletal muscle atrophy is a secondary complication in the aetiology of injury and chronic disease. Identifying mechanisms that control muscle mass is necessary to characterise atrophy and develop prevention strategies. We aimed to integrate transcriptomic and epigenomic data to identify key regulatory pathways controlled by promoter DNA methylation during muscle unloading. Twenty-one healthy men (20-40 years) completed a 4-week standardized exercise program prior to a 14-day knee brace immobilisation with dietary control. Skeletal muscle mass and strength were assessed before and after immobilisation and biopsies were collected (m. vastus lateralis) before, at 3-days, and at completion on 14-days. RNA and DNA were isolated and analysed using Illumina RNA sequencing and DNA methylation 850K EPIC BeadChips. The 14-day immobilisation decreased muscle mass (~9%; P<0.0001) and strength (~16%; P<0.0001). At 3 days, most biological processes (BPs) were upregulated/hypomethylated (157 gene-sets); upregulated BPs included cell signalling and protein ubiquitination, downregulated BPs included metabolism. After 14 days, BPs were predominantly downregulated/hypermethylated, including translation and ribosome biogenesis. Across both timepoints, HDAC4, GADD45A, and CHRNA1 emerged as methylation-regulated candidate mediators of atrophy. HDAC4 and GADD45A showed strong correlations primarily at day 3, and CHRNA1 remained significant at both timepoints, extending prior observations in animals to human skeletal muscle. We have characterised changes in gene expression related to hypo- and hyper-methylation during muscle unloading in humans. These data extend our understanding of the regulatory processes that occur during skeletal muscle atrophy that, at the individual gene level, may be useful in developing strategies for reducing muscle wasting.

first: Jamie-Lee

last: Thompson

last: Doering

first: Boris

last: Budiono

first: Kristen

last: Mackenzie-Shalders

first: Kevin

last: Ashton

first: Vernon

last: Coffey


title: Integrated single‑cell transcriptomic profiling of human peripheral blood mononuclear cells across diverse in vitro immune stimuli

city: Oxford

first: Matt

last: Jackson-Wood

address: 9400 Business Park, Garsington Road

institute: Gilead Sciences

summary: Human peripheral blood mononuclear cells (PBMCs) from healthy donors were stimulated in vitro with a panel of commonly used immune stimuli and profiled using single‑cell RNA sequencing. The resulting dataset contains single-cell transcriptomic profiles of PBMCs across multiple donors and stimulation conditions. This resource enables comparative analysis of gene expression across immune cell populations and stimulation conditions and provides a reference for comparison with disease-associated immune signatures.

overall_design: Peripheral blood mononuclear cells isolated from healthy human donors were exposed for 48 hours in vitro to a panel of commonly used immune stimuli, alongside unstimulated controls. Following stimulation, cells were processed for single‑cell RNA sequencing using a combinatorial barcoding strategy. Biological samples were multiplexed during library preparation and sequenced as pooled sub-libraries. Single‑cell transcriptomes were integrated across donors, conditions, and batches to enable comparative analysis of cell type-specific responses to distinct stimuli.

first: Oliver

last: Wood

first: Adam

last: Braithwaite

first: Matthew


title: Dual mechanisms of ADAR1 in regulating radiosensitivity in ESCC via pyroptosis through the cIAP2/NF-κB pathway and C16orf46 RNA editing

city: Jinan

first: Liangchao

last: Sun

address: Jiyan Road No.440, Jinan, 250012, P. R. China.

institute: Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences

summary: Many patients with esophageal squamous cell carcinoma (ESCC) exhibit poor responses to radiotherapy, often due to radioresistance that impairs treatment efficacy. Aberrant adenosine-to-inosine (A-to-I) RNA editing, mediated by ADAR1, plays a crucial regulatory role in the occurrence and development of cancer. To investigate whether ADAR1 contributes to radioresistance in ESCC, we conducted a multi-tiered analysis incorporating clinical data, cellular experiments, and in vivo tumor models. We discovered that ADAR1 was significantly upregulated in ESCC tumor tissues compared to adjacent non-tumorous tissue, and its high expression was associated with a poorer clinical response to neoadjuvant chemoradiotherapy (nCRT). Targeted inactivation of ADAR1 inhibited ESCC cell proliferation and enhanced radiosensitivity both in vitro and in vivo. Mechanistically, ADAR1 depletion promoted GSDME-mediated pyroptosis, thereby sensitizing tumor cells to irradiation. Notably, this effect was mediated through two distinct mechanisms: an RNA editing-independent pathway involving cIAP2 upregulation and activation of nuclear factor-kappa B (NF-κB) signaling, and an RNA editing-dependent mechanism driven by reduced A-to-I editing of C16orf46. Our data supported A-to-I RNA editing as a functional contributor to radioresistance in ESCC, providing new insights and a rationale for targeting ADAR1 as a therapeutic strategy to overcome radioresistance.

overall_design: RNA-seq profiling of wildtype KYSE410 cells and their knockdown derivatives (siADAR1)

first: Ming

last: Zhang


title: total RNA-seq from GM21301 (ENCSR223TPI)

address: 300 Pasteur Dr

institute: ENCODE DCC

summary: For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: Extracellular RNA from leftover pathological specimens that were formalin-fixed are not always of human origin

city: Valhalla

first: Ravi

last: Sachidanandam

state: NY

address: 15 Dana Road

institute: NYMC

type: Non-coding RNA profiling by high throughput sequencing

summary: In healthcare institutions, such as hospitals, pathologists procure specimens used in providing histopathological diagnosis. These tissues when properly stored may be critical resources for researchers. Formalin, which contains ~40% saturated solution of formaldehyde is widely used to fix histochemistry and histopathology preparations, as well as serve as preservatives in embalming solutions used in medical laboratories. The immersion of tissues in a solution of formalin is expected to inactivate biological activities, protect tissues from microbial growth, and thus preserve the tissue.

overall_design: In this study, we have assesed the possibility of obtaining extracellular RNA (exRNA) from leftover FFT for research use.

first: Vyshnavi

last: Tallapaneni

first: Bryson

middle: C

last: Okeoma

first: Chioma

first: Humayun

last: Islam


title: Transcriptome sequencing of MT2A knockdown ovarian cancer cells

city: Charleston

first: Joe

last: Delaney

state: SC

address: 173 Ashley Avenue

department: Biochemistry and Molecular Biology

institute: Medical University of South Carolina

summary: Ovarian cancer cells were knocked down with shRNA targeting MT2A or a scrambled control vector. Whole transcriptome sequencing was performed on actively proliferating cells.

overall_design: Transcriptomes of proliferating ovarian cancer cells with control scrambled or MT2A knockdown lentivirally integrated.

first: Joe R


title: Ptpn2 limits plasma cell fate and antiviral immunity by integrating B cell receptor and IFN-γ signals in B cells

first: Ana Maria

last: Hincapie

address: 1160 Pine avenue West

summary: B cell activation and subsequent plasma cell differentiation are two crucial processes in the establishment of long-term immunity. Understanding the signaling pathways that regulate B cell function and terminal differentiation is crucial to human health. Ptpn2 is a protein tyrosine phosphatase whose role in limiting immune cell activation is well chatacterized. However, it is not known whether Ptpn2 plays a cell-intrinsic role in regulating B cell development and activation. Using a Ptpn2 B-cell-specific knockout mouse model we have discovered a novel role for Ptpn2 in negatively regulating both BCR and IFN-gamma signaling in B cells. As a result, the absence of Ptpn2 leads to the enhanced terminal differentiation of B cells into plasma cells. Consequently, mice lacking Ptpn2 in B cells present improved antibody responses against viral infections, such as Influenza A virus. Overall, our results reveal a novel role for Ptpn2 in B cell activation, highlighting its potential as a therapeutic target to optimize vaccine responses and enhance immunity against infectious diseases.

overall_design: B cells were isolated from the spleens of Ptpn2 fl/fl mb1-cre and control mice. Cells were stimulated ex vivo with anti-IgM or IFN-gamma for 6 hours. RNA was isolated from resting and B cells stimulated with the aforementioned conditions.

first: Hincapie

last: Ana Maria

first: Tremblay

last: Michel L.


title: long read RNA-seq from small intestine (ENCSR212XZB)

city: Stanford

first: ENCODE

last: DCC


title: Transcriptional analysis of transposon mutants disrupted in glutathione or ergothioneine biosynthesis in Burkholderia thailandensis

city: Fresno

first: Mamta

last: Rawat

address: 2555 E. San Ramon Ave. MS S/B 73

department: Biology

institute: California State University, Fresno

summary: In this study we compare logrithmically grown Burkholderia thailadensis wildtype to a transposon mutant that is disrupted in gshA1, or gshA2, which are involved in glutathione biosynthesis or egtB, involved in ergothioneine biosynthesis using RNASeq to identify novel pathways where glutathione or ergothioneine may be involved.

overall_design: RNASeq analysis of wildtype cells, gshA1:Tn, gshA2:Tn, and egtB:Tn grown logarithmically at 37C while shaken.

first: Rawat

last: Mamta

first: Van Laar

last: Tricia

first: Thomas

last: Jason


title: Single-cell transcriptomic profiling of chicken and zebra finch HH28 gonadal cultures and Bulk timecourse mRNA profiling of zebra finch HH28 gonadal cultures

city: New York

first: Matthew

last: Biegler

address: 1230 York Ave

institute: The Rockefeller University

summary: Primordial germ cells (PGCs) are reproductive stem cells that are valuable for avian biobanking and germline transmission. However, their long-term culture remains a challenge beyond a few poultry species. Here, we compare the transcriptomic impact and reproductive viability between short- and long-term chicken and zebra finch gonadal PGC culture protocols. Using single-cell transcriptomics, we identified rapid germline differentiation in zebra finch gonadal cultures compared to stable PGC identity in chicken, highlighting divergent signaling pathway responses to in vitro germline culture between species. These differentiation profiles were similarly found in low-serum zebra finch blood PGC cultures. Nonetheless, injections of these short-term zebra finch gonadal PGC cultures demonstrated sufficient gonadal reconstitution of host embryos to produce zebra finch germline chimeras and donor-derived offspring. This study demonstrates the minimal viability of short-term songbird gonadal cultures, and offers a roadmap to improve the longevity and self-renewal of non-poultry avian PGC cultures.

sample_organism:
Gallus gallus
Taeniopygia guttata

platform_organism:
Gallus gallus
Taeniopygia guttata

overall_design:
single-cell RNA sequence profiling of in vitro gonadal cell cultures in the zebra finch and chicken, collected at day in vitro (DIV) 3, 6, and 150.
Bulk RNA sequence profiling of zebra finch gonadal cell cultures from day in vitro (DIV) 1 to 10.

first: Eli

last: Harter

first: Asha

last: Sidhu

first: Christina

last: Szialta

first: Paul

last: Collier

first: Ji-Dung

last: Luo

first: Wei

last: Wang

first: Anna

last: Keyte

first: Erich

last: Jarvis


title: Transcription co-repressors Panky and Panky-like are essential for retinal cone photoreceptor integrity and survival by modulating ganglioside metabolism

city: Suita

first: Daisuke

last: Motooka

state: Osaka

address: 3-1, Yamadaoka

institute: NGS core facility, Research Institute for Microbial Diseases, Osaka University

summary: To investigate the in vivo functions of mouse Panky and its paralog, Panky-like (Ankrd33b), we generated and analyzed the Panky/Panky-like double knockout (PPL DKO) mice. PPL DKO mice exhibited decreased light-evoked activities, impaired morphology of cone photoreceptors, and disrupted membrane integrity in the cone outer segments and synaptic terminals, followed by cone death at a later stage. RNA-seq analysis revealed that Cerkl gene, whose mutations in human ortholog CERKL cause retinitis pigmentosa (RP26), was upregulated in Panky/Panky-like/Nrl triple KO mouse retinas, in which loss of Nrl converts rods into cones. Our findings suggest that the regulation of Cerkl expression in cone photoreceptors by Panky and Panky-like is essential for cone photoreceptor integrity and survival.

overall_design: We utilized an Nrl-null background to enrich for cone-like cells to investigate downstream molecular mechanisms of Panky and Panky-like. Retinas from 3 littermate pairs of control  (Panky+/-;Panky-like+/-;Nrl-/-) and triple-deficient (Panky-/-;Panky-like-/-;Nrl-/-) mice at postnatal day 12 were used for the analysis.

first: Hung-Ya

last: Tu

first: Daichi

last: Gyoten

first: Takahisa

last: Furukawa


title: Transcriptome profiling of penile tissues in a rat model of hypospadias by RNA sequencing

city: beijing

first: Jingmin

last: Zhang

address: Yabao Road

institute: CMU

summary: Gene expression dysregulation plays an important role in the pathogenesis of congenital malformations, including hypospadias. To characterize transcriptomic alterations associated with hypospadias, RNA sequencing (RNA-seq) was performed on penile tissues collected from normal rats and a rat model of hypospadias. These datasets provide comprehensive gene expression profiles that facilitate the investigation of molecular mechanisms and signaling pathways involved in the development of hypospadias.

overall_design: Timed-pregnant Sprague–Dawley (SD) rats were generated by overnight mating, and the day on which a vaginal plug was detected was designated as gestational day 0 (GD0). Pregnant rats were randomly assigned to either the di-(2-ethylhexyl) phthalate (DEHP)-treated group or the corn oil vehicle control group. DEHP or corn oil was administered by oral gavage daily from GD12 to GD19. On GD19.5, fetuses were collected by cesarean section. Penile tissues from male fetuses with hypospadias and normal male fetuses were isolated for RNA sequencing (RNA-seq).

first: Shan

first: Xianghui

last: Xie


title: Lysyl oxidase inhibition disrupts mitochondrial homeostasis to create vulnerability to ferroptosis in TNBC

first: Ozgur

last: Sahin

address: 86 Jonathan Lucas Street HO703

summary: High metabolic heterogeneity and plasticity of triple-negative breast cancer (TNBC) contribute to therapy resistance, necessitating identification of novel therapeutic vulnerabilities. Here, we identify non-canonical functions of the ECM remodeler, lysyl oxidase (LOX), in regulating glucose metabolism and mitochondrial homeostasis and show that inhibiting LOX generates targetable vulnerability to ferroptosis. Mechanistically, LOX interacts with PARKIN and its upstream kinase PINK1, which we identified as a substrate of LOX. LOX-mediated PINK1 oxidation suppresses PARKIN phosphorylation, stabilizing HIF-1α and increasing glycolysis. Concomitantly, LOX inhibits PARKIN-mediated mitophagy and maintains mitochondria-ER contacts through VDAC1 stabilization while the LOX-HSP90 complex promotes mitochondrial Ca2+ transport and ATP production. Inhibiting LOX suppresses glycolysis, disrupts mitochondrial dynamics, reduces OXPHOS and GPX4/FSP1, and induces compensatory DHODH activity. Our ‘one-two punch’ approach combining LOX inhibition with clinical DHODH inhibitor suppresses tumor growth in vivo in chemo-free setting. Notably, LOX protein correlates with HIF-1α/GLUT1/GPX4 in TNBC patient tumors, supporting its clinical relevance.

overall_design: MDA-MB-436, MDA-MB-231 and HS-578T cells were either untreated or treated with LXG6403 for 24 hrs. There were two replicates for each condition. After treatments, RNA was isolated using Quick-RNA Miniprep Kit (Zymo).

first: Ozge

last: Saatci

first: Burge

last: Ulukan

first: Metin

last: Cetin

first: Hellen

last: Kuasne

first: Constanza

last: Martinez

first: Elif

last: Percin

first: Natalia

last: Oleinik

last: Savoca

first: Ali

last: Nehme

first: Aldo

last: Hernandez-Corchado

first: Evelyn

last: Zavacky

first: Kukkamudi

last: Sreenivas

first: Abdol

last: Rezaeian

first: Jennifer

last: Bethard

first: Jean-Sebastien

last: Anoma

first: Ozlem

first: Adriana

last: Aguilar-Mahecha

first: Marguerite

last: Buchanan

first: Mertkaya

last: Aras

first: Mark

last: Basik

first: Elizabeth

last: Hill

first: Lauren

last: Ball

first: Chintada

last: Rao

first: Campbell

last: McInnes

first: Yasser

last: Riazalhosseini

first: Hamed

last: Najafabadi

first: John

last: Lemasters

first: Besim

last: Ogretmen

first: Morag

last: Park