title: Expression data from Efp-silenced breast cancer cells

city: Hidaka

first: Kazuhiro

last: Ikeda

state: Saitama

address: 1397-1 Yamane

institute: Saitama Medical University

summary: To clarify the  mechanism of Efp/TRIM25 in breast cancer, breast cancer cells (MDA-MB-231 and TNBC-PDC) were transfected with siRNAs targeting Efp (siEfp_1 and siEfp_3) and control siRNA targeting firefly luciferase (siCont). We used microarrays to detail the global programme of Efp-mediated gene expression and identified up- and down-regulated genes.

overall_design: Total RNAs were extracted from human breast cancer cells, MDA-MB-231 and TNBC-PDC, both of which were transfected with siRNAs targeting Efp (siEfp #A and #B) and  control siRNA (siCont). These RNAs were then used for Affymetrix microarrays analysis.

first: Wataru

last: Sato

first: Kuniko

last: Horie

first: Satoshi

last: Inoue


title: Hypoxia-inducible Factor 1α Mediated Lactylation to Enhance Inflammatory Response during Hypoxia induced lung dysfunction

status: Public on Jun 12 2025

city: Beijing

first: Yubing

last: Zeng

address: 9 Dongdan Santiao, Dongcheng District,

country: China

institute: Peking union medical college

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Hypoxia can result in tissue dysfunction, metabolic alterations, and structural damage within the pulmonary tissue, thereby impacting lung ventilation and air exchange. The identification of Hypoxia-inducible factor (Hif) 1α as a pivotal mediator in the inflammatory cascade subsequent to hypoxia induction has been established. However, the mechanism remains elusive. To delve deeper into this phenomenon, we have developed a murine model of sustained hypoxia and utilized nanocarriers for the delivery of lentivirus Hif-1α for knockdown purposes. Our findings suggest that under conditions of sustained hypoxia, knockdown of Hif-1α effectively ameliorated SpO2 levels and attenuated lung injury in our murine model. We observed that Hif-1α-mediated Histone Lactylation was evident in the lungs exposed to sustained hypoxia. Through RNA-seq and ChIP-seq profiling, we determined that upregulation of Hif-1α expression in sustained hypoxic lung tissue is essential for inducing lactylation enrichment of inflammatory response genes. Furthermore, knockdown of Hif-1α returned to normal inflammatory cytokines (e.g. TNF-α, IL-6 and IL-1β). Analysis of plasma metabolites from individuals experiencing restrictive/ obstructive lung disease revealed a significant enrichment of the Warburg effect within the sustained hypoxic group. Thus, our study provides compelling evidence supporting the notion that targeting Hif-1α-mediated histone lactylation may represent a promising therapeutic strategy for managing sustained hypoxia-induced lung injury.

overall_design: Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) for histone modification Kla in mice lung tissues.

first: Youjia

last: Wei

first: Chen

last: Chen

first: Xiaolin

last: Ma

first: Yiqing

last: Miao

first: Chunmei

last: Zhu

first: Shan

last: Wang


title: Genetic variant rs11607019 in SIRT3 regulate gene expression in human cells

status: Public on Jun 11 2025

city: San Diego

first: Chengyu

last: Liu

state: CA

address: 10949 Barbados Way

country: USA

institute: University of California San Diego

type: Expression profiling by high throughput sequencing

summary: SIRT3 is a NAD+-dependent deacetylase located in mitochondria and plays a critical role in various biological processes such as aging and cancer. Recent GWAS analyses have identified an intronic SNP, rs11607019, that significantly influences platelet function. To investigate the genome-wide transcriptional effects of this variant, we performed site-directed mutagenesis experiments. Our results demonstrate that rs11607019 upregulates GABRE, COL12A1, PLEKHG4B, and SERF1B, while downregulating APOBEC3G in human embryonic kidney cells. These findings suggest that rs11607019 is a strong candidate locus for blood cell phenotyping and may warrant further investigation in relation to kidney-related diseases in latent populations.

overall_design: RNA-seq profiling of wild-type HEK293 cells and their rs11607019 variants (T-to-C mutation) under basal culture conditions.

first: Yue

first: Wei

last: Ju

first: Shiqi

first: Ying

last: Hu

first: Yadong


title: Effects of Aging and Exercise Training on Cerebrovascular Vasomotor Reactivity, Depressive Behavior, and the Hippocampal Transcriptome

city: Tallahassee

first: Cynthia

last: Vied

state: Florida

address: 1115 W. Call St

department: Translational Science Laboratory

institute: Florida State University

summary: The aging global population is experiencing an increased prevalence of cerebrovascular diseases, such as stroke and dementia. This highlights a need for understanding the pathophysiological mechanisms of age-related cerebrovascular alterations, alongside benefits of interventions such as physical activity. Therefore, our aims were to 1) examine the impact of aging and exercise training on cerebrovascular function, and 2) to characterize age- and exercise training-related changes in the hippocampus transcriptome. Methods: Young and old male rats were randomized to a sedentary condition or exercise training for 10 weeks. In the first protocol, cerebral arteries were isolated to test vasomotor reactivity, quantify gene/protein expression, and to assess nitric oxide production. In the second protocol, anhedonia was assessed and hippocampal tissue collected for RNA-sequencing. Bioinformatic analyses (i.e., protein-protein interaction mapping) were performed. Results: Aging impaired endothelium-dependent vasoreactivity in the posterior communicating artery (PCoA), with a shift from endothelial NOS- to neuronal NOS-mediated vasorelaxation, and alterations in oxidative stress production. In support, PCoA superoxide-mediated vasoreactivity and nNOS-mediated production of NO increased with age. Exercise enhanced vasodilation in young rats, but results suggested reduced cerebrovascular plasticity in older animals. In the second protocol, exercise training attenuated the age-related increase in anhedonia behavior. Hippocampal RNA-sequencing revealed altered inflammatory and oxidative stress pathways with aging that were mitigated by exercise training. Conclusions: Our findings underscore the complex interplay between vascular/neuronal factors in the aging brain. Furthermore, these findings highlight the therapeutic potential of exercise in mitigating the adverse effects of aging on cerebral health

overall_design: Bulk RNA-sequencing of hippocampal tissue in young/old sedentary/trained rats.

first: Britton

last: Scheuermann

first: Kathryn

last: Nichol

first: Cathy

last: Levenson

first: Kiana

last: Schulze

first: Christopher

last: Woodman

first: Rhonda

last: Prisby

first: Rafael

last: Reyes

first: Kirk

last: Evanson

first: Lih

last: Kuo

first: Carl

last: Ade

first: Judy

last: Muller-Delp


title: Cell Cycle Arrest of a ‘Zippering’ Epithelial Cell Cluster Mediates Face Morphogenesis in Mice and Humans and is Unleashed in Craniofacial Disorders [scRNA-seq]

city: New York

first: Louis

last: Faure

state: NY

address: 321 E 61st Street

institute: Memorial Sloan Kettering Cancer Center

summary: Facial features identify individuals, but the mechanisms shaping the human face remain elusive. Orofacial clefting (OFC), the most common craniofacial abnormality, results from failed fusion of the facial prominences, partly caused by persistence of the cephalic epithelium. Using mouse models to guide our studies, here we uncover the identity, behaviors, and molecular blueprints of a novel craniofacial epithelial population, Zippering Lambda (ZL), similarly characterized by cell cycle arrest in mouse and human embryos. Remarkably, in Pbx1/2 and p63 mutant mice with OFC cell cycle is unleashed in ZL epithelium. Intersecting ZL-enriched genes with human OFC whole-genome sequencing datasets identifies ZFHX3 variants in affected individuals and cephalic epithelial Zfhx3 deletion results in murine OFC. Our findings further demonstrate that ZFHX3 and PBX1 synergistically regulate cell cycle inhibitor genes acting within a complex in embryonic faces. Collectively, we deconstruct new mechanisms that pattern the face, connecting cell cycle arrest to developmental tissue fusion.

overall_design: We performed single cell sequencing of live cells from the pooled lambdoidal junctions from multiple developmental time, using  Chromium Single-Cell 3′ V3 protocol (10X Genomics)

first: T

last: Qu

first: B

last: Chacon

first: L

first: M

last: Losa

first: R

last: Hernandez Martinez

first: K

last: Robinson

first: A

last: Jones

first: J

last: De Anda

last: Risolino

first: G

last: Panagiotakos

first: E

middle: J

last: Leslie-Clarkson

first: I

last: Adameyko

last: Selleri


title: Cancer-Associated Fibroblast-Derived circKLHL24 Drives Perineural Invasion in Pancreatic Cancer via Dual Regulation of the Sec31A-CXCL12 Axis

city: 广州

first: li

last: xiaobai

address: 381 Wushan Road, Tianhe District, Guangzhou

institute: south china university of technology

summary: Background: Cancer-associated fibroblasts (CAFs) are key drivers of neural invasion in pancreatic cancer, yet their regulatory mechanisms remain elusive.This study explores the role of circular RNAs (circRNAs) in CAFs and their involvement in regulating neural invasion in pancreatic cancer. Methods: CAF-derived circRNAs were identified through circRNA high-throughput sequencing and quantitative real-time PCR (qRT-PCR). The impact of CAF-derived circKLHL24 on perineural invasion (PNI) in tumor cells was evaluated both in vitro and in vivo. RNA sequencing, RNA pulldown, RNA immunoprecipitation, and luciferase reporter assays were conducted to identify downstream targets and elucidate the underlying mechanism of circKLHL24 in PNI. Results: CircKLHL24 (hsa_circ_0001369), a CAF-specific circRNA, is associated with PNI and poor survival in advanced PDAC. Silencing or overexpressing circKLHL24 in CAFs altered the ability of CAFs to induce tumor cell invasion and nerve infiltration via chemokine (C-X-C Motif) ligand 12 (CXCL12). Mechanistically, first, circKLHL24 binds to the membrane protein Sec31A, inhibiting its ubiquitination and degradation, thereby enhancing CXCL12 secretion. Second, circKLHL24 acts as a sponge for miR-615-5p, relieving its suppression of CXCL12 mRNA and amplifying CXCL12 expression.Moreover, high circKLHL24 levels were positively correlated with elevated serum CXCL12 levels in PDAC and poor patient survival. Targeting circKLHL24 or neutralizing CXCL12 suppresses PDAC invasion and neuronal recruitment in nude mouse and KPC models. Conclusions: The circKLHL24/Sec31A/miR-615-5p/CXCL12 axis is critical for CAF-induced PNI in PDAC. Therefore, circKLHL24 could serve as a potential therapeutic target for PDAC.

overall_design: To investigate the functional role of circKLHL24 in CAFs, RNA-seq were performed  to compare gene expression profiles following circKLHL24 knockdown in CAFs


title: Gene expression changes in CTCF-knockdown primary human endometrial stromal cells (hESCs) compared to control cells

city: Guangzhou

first: Ji-Long

last: Liu

address: 483 Wushan Rd

institute: South China Agricultural University

summary: To portray the molecular mechanism for CTCF function in hESCs, cell treated with siCTCF and siNC were subjected to RNA-seq analysis.

overall_design: The hESCs treated with siCTCF and siNC were subjected to RNA-seq analysis


title: Clonal CD8 T cells orchestrate arrhythmogenic inflammation in immune checkpoint inhibitor-associated myocarditis

city: Houston

first: Sung Wook

last: Kang

state: TX

address: one plaza

department: Surgery

institute: Baylor college of medicine

summary:
Objective: Immune checkpoint inhibitors (ICIs) have revolutionized cancer therapy but are frequently associated with immune-related adverse events, particularly in combination regimens. ICI-associated myocarditis (ICI-M) is rare but highly lethal, with a mortality rate approaching 50% and a notable risk of fatal ventricular arrhythmias. Prevention and effective management of ICI-M remain significant clinical challenges. This study aims to elucidate the immune landscape and spatial organization of immune cells in ICI-M using single-cell multi-omics in a preclinical mouse model.
Methods: We utilized Ctla4+/–Pdcd1–/– mice, modeling human ICI-induced myocarditis. Single-cell RNA (scRNAseq) and T cell receptor (TCR) sequencing were performed on heart-infiltrating immune cells and peripheral blood mononuclear cells (PBMCs). Spatial transcriptomics was applied to map immune infiltration in cardiac tissue.
Results: Approximately half of Ctla4+/–Pdcd1–/– mice died after 100 days, while Ctla4+/+ mice showed normal survival. ECG monitoring identified ventricular arrhythmias in 15% of Ctla4+/–Pdcd1–/– mice. Histology revealed severe myocardial inflammation and fibrosis. Cardiac scRNAseq data indicated that T cells were the predominant immune population in ICI-M hearts. TCR sequencing demonstrated substantial overlap in TCR clonotypes between cardiac-infiltrating and circulating CD8+ T cells. These TCR-shared CD8+ T cells exhibited an activated phenotype and were enriched in pathways associated with allograft rejection and inflammation. Spatial mapping revealed localization near the AV node and subendocardium, implicating potential CD8+ T cell–mediated conduction disruption.
Conclusion: Clonal, activated CD8+ T cells contribute to arrhythmogenic myocarditis in ICI-M. Targeting specific TCR-peptide-MHC interactions may enable myocarditis prevention without impairing antitumor efficacy.

first: Hyun-sung

last: Lee


overall_design: We utilized Ctla4+/–Pdcd1–/– mice, modeling human ICI-induced myocarditis. Single-cell RNA (scRNAseq) and T cell receptor (TCR) sequencing were performed on heart-infiltrating immune cells and peripheral blood mononuclear cells (PBMCs). Spatial transcriptomics was applied to map immune infiltration in cardiac tissue.


title: Gene expression changes in Ctcf-deleted mouse uterus on gestational day 4 (GD4).

summary: We specifically deleted Ctcf in the female reproductive tract using the Pgr-Cre driver. To portray the molecular mechanism for Ctcf function in uterus, uterine tissues were collected from Ctcf f/f and Ctcf d/d mice on GD4 and subjected to RNA-seq analysis.

overall_design: Uterine tissues were collected from Ctcf f/f and Ctcf d/d mice on GD4 and subjected to RNA-seq analysis.


title: Neuregulin 4 and the Erb-B2 Receptor Promote Hypoxia-Induced Adipose Tissue Browning in Mice

city: Wuhu

first: Huiyun

last: Xu

state: Anhui

address: youyi west road

institute: School of Life Sciences, Northwestern Polytechnical University

summary: Hypoxic conditions in high-altitude environments present unique physiological stressors that drive metabolic adaptations, including adipose tissue browning. In this study, we investigated whether hypoxia (11.6% O₂, simulating 5,300 m altitude) could independently induce browning of adipose tissue in mice, apart from cold-induced mechanisms. Hypoxia significantly promoted the formation of multilocular adipocytes in inguinal white adipose tissue (iWAT) and upregulated thermogenic genes (UCP1, PGC-1α, Cox4i1, VEGF), glucose metabolism-related genes (IRS1/2, PDK2, PPARα), and beige adipocyte markers (Car4, UCP1). In contrast, interscapular brown adipose tissue (iBAT) showed minimal response to hypoxia, with no significant change in UCP1 expression. Notably, hypoxia elevated both Nrg4 and phosphorylated ErbB4 in iWAT. In vitro, Nrg4 overexpression in 3T3-L1 adipocytes increased the expression of PKAcα, PGC-1α, and UCP1, while pharmacological inhibition of ErbB4 phosphorylation using Dacomitinib attenuated Nrg4- and hypoxia-induced browning and lipolysis. In vivo, Dacomitinib treatment impaired hypoxia-mediated improvements in WAT browning and glucose tolerance. To explore the structural basis of this interaction, molecular docking and 100-ns molecular dynamics simulations were conducted, revealing strong and stable binding between Nrg4 and ErbB4, with calculated binding energies of −174.26 kcal/mol (MM/GBSA) and −19.5 kcal/mol (PRODIGY). These findings collectively demonstrate that the Nrg4–ErbB4 axis plays a central role in mediating hypoxia-induced browning and metabolic reprogramming of WAT, providing mechanistic insight into adipose tissue plasticity under low-oxygen conditions.

overall_design: Thirty male C57BL/6J mice, aged 11 weeks, were obtained from Air Force Medical University. Of these, 15 mice were maintained in a normoxic environment (simulated altitude of 399 m, 20.9% O₂) as the control group, while the remaining 15 were acclimatized to a hypoxic environment (simulated altitude of 3,000 m, 15.4% O₂) for 3 days. Following this acclimatization, they were exposed to 11.6% O₂ (simulated altitude of 5,300 m) for a duration of 4 weeks. During the hypoxic treatment, all mice had unrestricted access to food and water, with a light-dark cycle maintained at 12 hours each.after the hypoxia treatment, the mice were anesthetized with sodium pentobarbital (1.5%, 40 mg/kg) and euthanized by cervical dislocation.Subcutaneous inguinal white adipose tissue (iWAT), and interscapular brown adipose tissue (iBAT) were subsequently isolated for analysis.RNA extraction and sequencing of isolated adipose tissue

first: Shiqiang

first: Pengyu

last: Fu

first: Guigui

last: Man

first: Xiangya

last: Dou

first: Shuaiting

first: Jiayue

first: Lizhuo

last: Wang

first: Dongen

first: Jialin

last: Gao


title: Malignant Transformation in Pleomorphic Adenoma:   The impact of DNA methylation profiling and Pathogenic Mutations

city: toulouse ou paris si j'ai une salle

first: Emmanuelle

last: URO-COSTE

state: occitanie

address: 1 avenue Irène Joliot Curie, IUC-T oncopole

country: France

institute: CHU de Toulouse

summary: Salivary gland tumors (SGTs) are a rare and heterogeneous group of lesions with diverse microscopic appearances and variable clinical behavior. The most common SGT subtype, pleomorphic adenoma (PA), can undergo malignant transformation into carcinoma ex pleomorphic adenoma (CXPA). Carcinomatous transformation from PA to CXPA is a highly progressive and multi-step process. Distinguishing a PA with some atypia from a low-grade intracapsular or minimally invasive CXPA is primarily subjective as no mitotic count thresholds exist to help pathologists distinguish between them in difficult cases.  In this prospective study, we collected 140 cases encompassing both PA and CXPA to study their molecular signatures. The primary objective was to investigate the use of DNA methylation profiling as a potential molecular tool for differentiating between these two entities. Methylation analysis was performed on 33 PA cases and 33 CXPA cases. We were able to demonstrate that based on their methylation profiles, PA and CXPA could be classified into three distinct clusters that we called benign, intermediate, and malignant. We also revealed that the presence of TP53, HRAS, PTEN and/or TERT pathogenic mutations were exclusively present in CXPA cases; and that chromosomal alteration on chromosomes 5 and 8 are potentially associated with malignant transformation.   In conclusion, our study provides a comprehensive molecular framework for PA and CXPA.  The presence of a pathogenic mutation in TP53, HRAS, PTEN, or pTERT or HER2 amplification could be integrated into a molecular diagnosis of CXPA for tumors within the PA CXPA spectrum. In the future, we aim to improve our methylomic classification to make it a precision medicine diagnostic tool for the treatment management of tumors within the PA-CXPA spectrum.

overall_design: In this study, we analyzed 66 cases of salivary gland tumors, corresponding to 33 pleomorphic adenomas (PAs) and 33 carcinomas ex pleomorphic adenomas (CXPAs), using DNA methylation profiling. Tumor DNA was analysed using the infinium MethylationEpic array (850k).  Differential methylation analysis according to histological diagnoses was conducted using DMRcate package in R.13 Significantly, deregulated probes (P < .05, Benjamini-Hochberg correction) were ranked by variance, and the top 50 most variable probes were used for hierarchical clustering. Clustering was visualized using the SciPy library (version 1.10.1) in Python (version 3.11.4). The oncoplot was created using Excel 2016.

last: Uro-Coste

first: Yvan

last: Nicaise


title: Structure and repair of replication-coupled DNA breaks

city: Bethesda

first: Ajith

last: Viswanathan Asari Pankajam

address: Building 37

institute: National Institutes of Health

summary: Using CRISPR/Cas9 nicking enzymes, we examine the interaction between the replication machinery and single strand breaks, one of the most common forms of endogenous DNA damage. We show that replication fork collapse at leading strand nicks generates resected single-ended double-strand breaks (seDSBs) that are repaired by homologous recombination (HR). If these seDSBs are not promptly repaired, arrival of adjacent forks creates double ended DSBs (deDSBs), which could drive genomic scarring in HR-deficient cancers. deDSBs can also be generated directly when the replication fork bypasses lagging strand nicks. Unlike deDSBs produced independently of replication, end-resection at nick-induced se/deDSBs is BRCA1-independent. Nevertheless, BRCA1 antagonizes 53BP1 suppression of RAD51 filament formation. These results highlight unique mechanisms that maintain replication fork stability.

overall_design: We used a combinatorial approach of END-seq, ChIP-seq, Amplicon seq, S1-END-seq, TrAEL-seq, and EdU-seq to study replication associated DNA breaks in human cells

first: Raphael

last: Pavani

first: Veenu

last: Tripathi

first: Kyle

middle: B

last: Vrtis

first: Dali

last: Zong

first: Raj

last: Chari

first: Elsa

last: Callen

middle: V

last: Pankajam

first: Gang

last: Zhen

first: Gabriel

last: Matos-Rodrigues

first: Jiajie

last: Yang

first: Shuheng

last: Wu

first: Giordano

last: Reginato

first: Wei

first: Peter

last: Cejka

first: Johannes

middle: C

last: Walter

first: André

last: Nussenzweig


title: Scaffold-free cryopreservable cartilage grafts obtained from hiPSC-derived chondroprogenitor cells for airway reconstruction with growth adaptability

city: Okayama

first: Takeshi

last: Takarada

country: Japan

institute: Okayama University

summary: Pediatric tracheal reconstruction remains a major clinical challenge because of limited graft availability and the need for growth-adaptive materials. Current approaches, such as costal cartilage grafting and use of scaffold-based constructs, often suffer from complications including graft resorption, donor site morbidity, and poor integration. Here, we present scaffold-free cartilage grafts (chondro-plates) derived from expandable limb-bud mesenchymal cells generated from human leukocyte antigen-homozygous human induced pluripotent stem cells. These grafts are cryopreservable and maintain their hyaline cartilage phenotype after a brief pre-culture. In both rat and rabbit tracheal defect models, chondro-plates supported robust cartilage regeneration, epithelial reconstitution, and neovascularization. Importantly, in a pediatric-like growing rat model, chondro-plates preserved luminal patency and structural integrity, outperforming autologous costal cartilage. This study demonstrates a clinically viable, off-the-shelf strategy for tracheal reconstruction using scalable, immunocompatible, and growth-adaptive cartilage grafts.


title: Overcoming intra-tumoral heterogeneity for biomarker discovery in the High-Grade Serous Ovarian Cancer proteome

city: Westmead

first: Brian

middle: S

last: Gloss

state: NSW

address: 176 Hawkesbury Rd

department: Scientific Platforms

country: Australia

institute: Westmead Institute of Medical Research

summary: Improved biomarkers of treatment response are needed for patients with High-Grade Serous Ovarian Cancer (HGSC). A challenge is substantial anatomical site-to-site variation in expression. We completed Data Independent Acquisition – Mass Spectrometry (DIA-MS) analysis of over 404 fresh frozen and 78 formalin fixed, paraffin-embedded HGSC tissue samples from ovary (adnexal) and a common secondary site (omentum) in 11 patients. This was compared with mutation testing, gene expression and whole genome copy number profiling. Proteins with relatively stable intra-, and variable inter-individual expression (n=1,651), included a 52-protein module reflecting interferon mediated tissue inflammation indicative of a cGAS-STING pathway cytosolic double-stranded (ds) DNA response. The dsDNA sensing / inflammation (DSI) score was higher in omentum compared with ovary. Ovarian HGSC samples showed marked inter-individual differences in inflammatory and immune responses to DNA damage. Stable discriminative features of the HGSC proteome, a prerequisite for clinical predictive biomarkers, are detectable in ovary (adnexal) tissue samples.

overall_design: In this multi-omic study of High Grade Serous Ovarian cancer (HGSC), RNA Seq profiles were generated from Fresh Frozen Tissue samples of HGSC from matched primary site (ovary / adexa) and a common secondary site (omentum) in 11 patients.

first: Rosemary

last: Balleine

first: Anna

last: DeFazio


title: Primary head and neck squamous cell carcinoma keratinocyte RNA expression in culture.

city: Philadelphia

first: Andrew

last: South

state: PA

address: 233 S 10th St

department: Cancer Biology

institute: Thomas Jefferson University

summary: 6 cultured primary HNSCC keratinocytes populations derived from HNSCC patients were transcriptionally profiled.

overall_design: sample:6 different primary HNSCC keratinocytes derived from HNSCC patients.

first: Pyung hun

last: Park

middle: P


title: Moesin deficiency leads to microglia-mediated synaptic pruning and social abnormality: a post-GWAS functional genomics study

first: Wanjing

last: Lai

state: Guangdong

address: Jinan University,601 Huangpu Road West

institute: Key Laboratory of CNS Regeneration

summary: Genome-wide association studies (GWAS) implicated a noncoding antisense RNA designated as MSNP1AS in susceptibility to autism spectrum disorders (ASD). MSNP1AS binds to and downregulates the Moesin (MSN) transcript and is highly overexpressed in postmortem cerebral cortex of individuals with ASDs. However, the mechanistic link between Moesin loss in vivo and ASD-related phenotypic traits remains enigmatic. Here, we generated Moesin knockout (Msn KO) mice, on which neurobehavioral tests revealed impaired social novelty and repetitive behaviors. Single-cell transcriptomics and electrophysiology recording indicated activated status of the microglia, leading to aberrant C1q-dependent synaptic pruning followed by synaptic deficits in medial prefrontal cortex in KO mice. Aberrant regulatory pathway from sequencing data guided us to block type I interferon pathway by IFNAR1 blocking antibody via nasal administration, which rescued microglial abnormalities and social deficits in Msn KO mice. Taken together, Moesin mediates interferon signaling and synaptic pruning to affect ASD-like behaviors, providing a functional genetic link between MSN and neurobehavioral abnormalities.

overall_design: Following tissue dissociation and enzymatic digestion, cortical microglia from adult Msn knockout C57BL/6 mice were isolated via Percoll gradient centrifugation and Fluorescence-activated cell sorting (FACS) using CD45 and CD11b antibodies, and subsequently analyzed by single-cell RNA sequencing (scRNA-seq) with alignment to the GRCm39 genome and Seurat-based clustering.

first: Yimei

last: Niu

first: Lingling

last: Shi


title: Modulation of ER Stress in Human Type 1 Diabetic Islets Through Combined Use of Stress Inducer and Inhibitor Treatments

city: Boston

first: Jonathan

middle: M

last: Dreyfuss

state: MA

address: 1 Joslin Pl

department: Bioinformatics & Biostatistics Core

institute: Joslin Diabetes Center

summary: Given the predominance of alpha cells and marked differences in ER stress-related gene expression in Type 1 Diabetes (T1D) islets, we explored the modulation of ER stress pathways using targeted treatments.

overall_design: T1D islets from three separate donors, pre-stained with DTZ, were selectively treated with thapsigargin (TG) and/or taurodeoxycolic acid (TUDCA) for a total of 12 samples. A total of 100 islets for each experimental condition were meticulously selected, excluding any cluster-like structures indicative of acinar cells, and subjected to RNA sequencing. The treatment regimen included inducing ER stress using TG (250 nM) and mitigating it in T1D islets with TUDCA (100 ng/ml), TG, or their combination. These treatments were administered for 24 hours prior to RNA-seq analysis to evaluate the changes in ER stress response.

first: Shibue

last: Kimitaka

first: Kulkarni

last: Rohit


title: Immune Tolerance to HSP60 Attenuates Neurodegeneration in Glaucoma

first: Emil

last: Kriukov

address: 20 Staniford St

institute: Schepens Eye Research Institute

summary:
Our previous study suggests that CD4+ T cells primed by bacterial heat shock proteins (HSP) mediate an autoimmune mechanism contributing to the pathogenesis of glaucoma. The present study showed that the activity of CD4+ T cells from the peripheral blood mononuclear cells (PBMC) of POAG patients was significantly higher than control subjects as revealed by single-cell RNA sequencing. The notion of antigenic mimicry between gut bacteria and mouse HSPs expressed in the eye causes glaucomatous degeneration remains unclear. Here, we report that the induction of immune tolerance by nasal administration of bacterial HSP60 protein led to an increase in regulatory T (Tr1) cells and suppression of HSP-specific Th1 cell frequencies in glaucoma mice. leading to protections against retinal ganglion cell loss and preservation of spatial vision in glaucoma mice. Moreover, this neuroprotective effect on retinal ganglion cells in HSP-immune-tolerant mice was compromised by IL-10 deficiency. Our data suggests that induction of immune tolerance to HSP60 presents a potential therapeutic strategy protecting against retinal degeneration and vision loss in glaucoma by partial restoration of T cell-mediated immune balance.
Detailed information: https://github.com/mcrewcow/PBMC_Glaucoma_human
CellXGene web-browser: https://cellxgene.cziscience.com/collections/de2cde16-c8d3-4a6d-80be-1be9e879aaca

overall_design: Compare the gene expression of PBMC collected from 3 control subjects and 5 patients with primary open angle glaucoma.

first: Petr

last: Baranov

first: Shuhong

last: Jiang

first: Kin-Sang

last: Cho

first: Dong Feng

last: Chen

first: Guangan

last: Hu

first: Jianzhu

first: Lucy

last: Shen


title: Human Cytomegalovirus long non-coding RNA counteracts nuclear cGAS to facilitate immune evasion

city: Seoul

first: Dohoon

last: Lee

address: 1, Gwanak-ro, Gwanak-gu

department: Bioinformatics Institute

country: South Korea

institute: Seoul National University

summary: Viruses have evolved diverse immune evasion strategies including targeting host pattern recognition receptors. The role of viral non-coding RNAs in modulating PRR activity is unclear. Here, we show that human cytomegalovirus (HCMV) produces long non-coding RNA4.9 that counteracts nuclear cyclic GMP-AMP synthase (cGAS)-mediated immune response to facilitate viral infection in primary human foreskin fibroblasts (HFFs). RNA4.9 interacts with host cGAS via its 75-nucleotide (nt) RNA region with predicted hairpin loops. Binding of RNA4.9 to cGAS inhibits cGAS enzymatic activity and downstream interferon response, and facilitates productive viral replication. Sterically blocking the folding of 75-nt region with antisense oligonucleotides during HCMV infection restores cGAS activity and impairs viral replication. We also found that the specific localization of RNA4.9, which concentrates near HCMV DNA, is correlated with its efficient binding to cGAS and subsequent immune suppression. Our findings demonstrate viral non-coding RNAs as critical cGAS regulators and potential therapeutic targets.

overall_design: To investigate the role of RNA4.9 during HCMV lytic replication, HFFs were infected with WT or 1.9-4.9krpsL (The 3kb genomic region from the 3' end of RNA4.9 is replaced by rpsL selection cassette) HCMV and harvested at 6 and 24 hours post infection (hpi).

first: Sungwon

first: Sungchul

last: Kim

first: Hyejun

first: Dongjoon

last: Jeong

first: Hyewon

first: Junhyun

first: Kiwon

first: Sun

first: V

middle: N

first: Kwangseog

last: Ahn


title: Inactivation of histone chaperone HIRA unmasks a link between normal embryonic development of melanoblasts and maintenance of adult melanocyte stem cells (ATAC-Seq)

city: La Jolla

first: Xue

last: Lei

address: 10901 N Torrey Pines Rd

institute: SBP medical discovery institute

summary: Evidence indicates that the integrity of in utero embryonic development can influence late life healthy or unhealthy aging. However, specific links between embryonic development and late life aging are not well defined. Histone chaperone HIRA is thought to play a role in both early development and aging. Here, we explore the relationship between HIRA’s roles in development and aging by comparing lineage-specific constitutive and conditional Hira knock out in the murine pigmentary system, with constitutive knock out initiated during embryogenesis and conditional knock out in young adults. Embryonic Hira knockout leads to reduced melanoblast numbers during embryogenesis but wild type numbers of differentiated melanocytes at birth, normally functioning juvenile and young adult melanocyte stem cells (McSCs), and only a very mildly hypopigmented first hair coat. However, on closer analysis of these mice, Hira knockout melanocytic cells of newborn mice exhibit molecular markers characteristic of cell aging and proliferative deficits. As they age, mice with Hira knock out initiated during embryogenesis display marked defects in McSC maintenance and premature hair graying. Importantly, these defects are only observed when HIRA is inactivated during embryogenesis, but not in young adults. This genetic model shows that HIRA function during early development lays a foundation for subsequent maintenance of adult tissue specific stem cells during aging.

overall_design: ATAC sequencing was used to study the chromatin accessibility changes of HIRA KD on in-vitro melb-a cells. We used two control lenti- shRNAs (shLuciferase, shScramble), as well as two lenti- shRNAs to knock down HIRA (shHIRA I, shHIRA II). Chromatin accessibility analysis was performed using data obtained from bulk-ATAC seq of 4 samples.

first: Rouven

last: Arnold

first: Rabi

last: Murad

first: Farah

last: Jaber-Hijazi

first: Peter

middle: D

last: Adams


title: Inactivation of histone chaperone HIRA unmasks a link between normal embryonic development of melanoblasts and maintenance of adult melanocyte stem cells (RNA-Seq)

overall_design: RNA sequencing was used to study the transcriptomic changes of HIRA KD on in-vitro melb-a cells. We used parental non-transduced cells, two control lenti- shRNAs (shLuciferase, shScramble), as well as two lenti- shRNAs to knock down HIRA (shHIRA I, shHIRA II). Gene expression analysis was performed using data obtained from bulk-RNA seq of 20 samples (4 independent replicates per experimental group).

first: Arnold

last: Rouven

first: Jaber-Hijazi

last: Farah


title: Knockout of the B1 subunit of the GA-binding protein (GABP) [ChIP-seq]

city: Urbana

first: Jun

last: Song

email: songj@illinois.edu, jssong137@gmail.com

state: IL

address: 1110 West Green Street, MC 704

institute: University of Illinois, Urbana-Champaign

summary: We knocked out different exons corresponding to different sections of GABP, a transcription factor known to bind to the telomerase reverse transcriptase (TERT) promoter with the G228 mutation. We investigated the effects of the knockouts in the regulation of TERT expression and other subunits of GABP. GABP genomic binding sites were determined through chromatin immunoprecipitation sequencing (ChIP-seq), and gene expression was determined through total RNA sequencing (RNA-seq). Combining data pertaining to GABP binding sites and gene expression provided insight into the molecular mechanisms of maintaining the length of telomeres in cancers.

overall_design: ChIP-seq for 3 conditions. One condition was a knockout of the exon 2 of the B1 subunit of GABP followed by knock-in of TERT. One condition was a control sample that knocked out ROSA26. One condition was a control sample with no knockouts.

first: Joseph

middle: F

last: Costello


title: CCR1 is a novel target in the treatment of NASH by regulating macrophage activation through mTORC1 signaling

city: Wenzhou

first: Yajiao

last: Wang

address: Chashan Higher Education Zone

institute: Wenzhou Medical College

summary: The number of patients with non-alcoholic steatohepatitis (NASH) is dramatically increasing globally. Recently, specific chemokine receptors have garnered interest as therapeutic targets in NASH. In different murine models with NASH, the level of CCR1 in plasma and the expression of CCR1 in liver increased, suggesting that CCR1 may be involved in the progression of NASH. Recent studies have shown that a variety of chemokines and their receptors play a certain role in the development of NASH. However, the role of CCR1 in pathogenesis of NASH remains obscure. Therefore, this study aims to explore the effect of CCR1 on the development of NASH. The results suggest that the absence of CCR1 prevents hepatic steatosis and abnormal glucose metabolism in the progression of NASH, and these results emphasize the impacts of CCR1 on macrophage recruitment and fibrosis in mice with NASH. Thus, the findings of the current study provide a new strategy for the clinical treatment of NASH.

overall_design: 1. Both 8-week-old male C57BL/6 (wild-type, WT) mice and CCR1 knockout (CCR1- KO) mice were fed with normal chow (NC) and high-fat, high cholesterol and cholate diet (CL) for 12 weeks, respectively. The weight of mice was measured every week. Glucose tolerance test (GTT) and pyruvate tolerance test (PTT) were performed after overnight fasting. After 12 weeks of feeding, the mice were sacrificed and the liver tissues were harvested. The hepatic macrophages were determined by flow cytometry. 2. Plasma triglyceride (TG), total cholesterol (TC), non-esterified free fatty acid (NEFA), insulin (INS), alanine aminotransferase (ALT), aspartate aminotransferase (AST), and hepatic TG, TC, NEFA and hydroxyproline (HYP) were examined using ELISA or spectrophotometer according to the instructions. 3. The mRNA levels of liver lipid metabolism, inflammatory response and fibrosis related genes were detected by real-time fluorescence quantitative PCR (RT-qPCR). 4. Western blotting (WB) was used to detect the expression of proteins related to lipid metabolism, inflammatory signaling pathway and fibrosis in liver. 5. Hematoxylin and eosin (H&E) staining, Sirius Red staining and immunohistochemical staining (IHC) were used to evaluate the histology of liver sections 6. Protein chip and bioinformatic analysis were used to analyze the cluster of inflammatory proteins.

first: Haoran

last: Li

first: Tongtong

last: Pan

first: Lingjia

last: Gao

first: Rongxiu

last: Ding

first: Yongping

first: Chunming


title: Knockout of the B1 subunit of the GA-binding protein (GABP)

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

overall_design: Refer to individual Series


title: Single-cell CRISPRi transcriptome screening focusing on a subset of lncRNAs regulated by hypoxia

city: Valbonne - Sophia-Antipolis

first: Kevin

last: Lebrigand

address: 660 route des lucioles

institute: IPMC/CNRS

summary: In order to gain new insights into the molecular functions of 6 hypoxia-regulated lncRNAs in LUAD cells we performed a single-cell CRISPRi transcriptome screening based on the CROP-Seq approach.

overall_design: We transduced A549 cells expressing double repressor Krab-MeCP2-dCas9 with a mini-library containing 12 validated gRNA targeting CYTOR (also known as LINC00152), LUCAT1, MALAT1, NEAT1, SNHG12 and SNHG21 as well as the two key regulators of the hypoxic response, HIF1A and HIF2/EPAS1. Two additional guides, with no effect on the genome, were used as negative controls. The transduced dCas9-Krab-MeCP2 A549 cells were equally divided in 4 samples, which were then cultured either in normoxia or in hypoxia during 3, 6 or 24 hours. Cells from each sample were labeled with a specific barcoded antibody (HTOs), pooled, and simultaneously sequenced using droplet based scRNA-seq (10X Genomics Chromium).

first: Marin

last: Truchi

first: Caroline

last: Lacoux

first: Julien

last: Fassy

first: Virginie

last: Magnone

first: Rafael

last: Lopez-Goncalvez

first: Cédric

last: Girard-Riboulleau

first: Iris

last: Manosalva-Pena

first: Marine

last: Gautier-Isola

first: Pascal

last: Barbry

first: Salvatore

last: Spicuglia

first: Georges

last: Vassaux

first: Roger

last: Rezzonico

first: Bernard

last: Mari


title: Immune-Metabolic Regulation of Early Osseointegration: Insights from Untargeted RNA Sequencing

status: Public on Jun 10 2025

first: Le Na

last: Lau

address: Daehakro 101, Jongnogu

summary: This study clarified how implant surfaces influence early osseointegration by coupling untargeted RNA sequencing with histomorphometry. Four rabbits each received three tibial implants: turned commercially pure titanium (Ti), sandblasted/large-grit/acid-etched titanium (SLA-Ti), and turned copper (Cu). Surface morphology was characterized by scanning electron microscopy, confocal microscopy, and energy dispersive spectroscopy. After 10 days, bone-to-implant contact (BIC), bone area (BA), and peri-implant transcriptomes were analyzed. Differentially expressed genes and Gene ontology (GO) enrichment were computed. SLA-Ti showed the greatest roughness. Both Ti groups yielded significantly higher BIC and BA than Cu (p < 0.001). GO terms on SLA-Ti were enriched for immune regulation and turned Cu was dominated by mitochondrial-stress pathways. Turned Ti showed minimal enrichment. SLA-Ti simultaneously up-regulated pro-inflammatory cytokines and immunoregulatory genes plus stress-adaptive markers, suggesting a balanced inflammatory milieu conducive to bone formation. Turned Cu markedly elevated mitochondrial genes and oxidative-stress markers, while suppressing antioxidant and innate-defense genes, reflecting immune-metabolic dysregulation. Turned Ti induced only modest transcript changes, consistent with passive biocompatibility. Early osseointegration hinges on a finely tuned immune-metabolic equilibrium rather than surface roughness alone. Optimal integration demands implant surfaces that trigger controlled immunomodulation while limiting oxidative stress, guiding the design of next-generation dental implants.

first: Jun-Ho

last: Cho


title: Single cell RNA Sequencing of murine tdTomato positive skin cells with or without HIRA knockout

first: Xue

last: Lei


title: Single cell RNA Sequencing of murine tdTomato positive skin cells with or without HIRA knockout [dataset 1]

summary:
Skin samples from wild type or HIRA knockout mouse embryos were dissociated to give cellular suspensions, then single cell RNA sequencing was performed using the 10X platform.
Method: Cellular suspensions of skin cells from wild type and HIRA knockout mice were prepared, then sequencing was performed using the Chromium 10X system. Data were then processed using Cellranger version 2.2.0.

overall_design: Isolated single cells from E15.5 skin from wild type and HIRA knockout mice were sequenced using the 10X Genomics platform.

first: Farah

last: Jaber-Hijazi

first: Peter

last: Adams

first: Kathryn

last: Gilroy


title: Systematic characterization of human placenta-derived miRNAs and identification of autophagy-related miRNAs in gestational diabetes mellitus [miRNA-seq]

city: Wuhan

first: yin

middle: di

last: Bao

state: Hubei

address: 238 Jiefang Rd

institute: Renmin Hospital of Wuhan

type: Non-coding RNA profiling by high throughput sequencing

summary: The objective of this study was to identify and investigate the roles of miRNAs in GDM. In the current study, placental miRNA expression profiles of normal controls and GDM patients were analyzed using high-throughput sequencing. Bioinformatics analysis identified  that 4 were upregulated and 6 were downregulated in 10 most differential miRNA in GDM placentas compared with NC placentas. GO and KEGG enrichment analyses demonstrated that metabolic process-associated terms and metabolic pathways that may be related to GDM were significantly enriched. Our study indicates that aberrant expression of miRNAs may play roles in autophagy in GDM placentas, providing new insights into GDM.

overall_design: RNA-seq of placenta  from 3 pregnant women with GDM and 3 healthy pregnant women, and identification of autophagy-related circRNAs in gestational diabetes mellitus

first: Yindi

first: Jing

last: Yang


title: The altered protein profiles in pigmented nodular synovitis revealed the important role of epithelial-to-mesenchymal transition in disease promotion

city: ChengDu

first: Tao

last: Li

address: GuoXueXiang street

institute: West China Hospital

summary:
To investigate the synovium in the PVNS and determine the key role of epithelial–mesenchymal transition (EMT)
we mapped the RNA-seq and identified the core molecular regulatory networks in synovial tissue of PVNS patients by RNA extraction, RNA-Seq library preparation  6 control, 7 OA and 19 PVNS samples.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for epithelial-to-mesenchymal transition.

first: YuBin

last: Luo


title: Shear stress regulates osteogenic differentiation of human dental pulp stem cells via p38 pathway

city: Bangkok

first: Hnin

middle: Yu

last: Lwin

address: Henridunant

country: Thailand

institute: Chulalorngkorn University

summary: This study aimed to investigate the effects of shear stress on osteogenic differentiation of human dental pulp stem cells (hDPSCs). The hDPSCs were subjected to shear stress for 24 hours before osteogenic induction for 21 days. The mRNA expression of osteogenic markers such as RUNX2, OSX, ALP, COL1A1, OCN, and OPN was evaluated by real-time RT-PCR. Alkaline Phosphatase (ALP) activity and Alizarin Red S (ARS) staining were investigated to confirm osteogenic differentiation and mineralization of hDPSCs, respectively. The protein expression of osterix was shown by immunofluorescence staining and western blotting. RNA sequencing was performed to investigate how shear stress affects the osteogenic differentiation of hDPSCs, which was validated through p38 inhibitor (SB203580) treatment. Real-time RT-PCR revealed that shear stress enhanced osteogenic marker gene expression. The increased Osterix protein expression was detected on Day 14 in the shear stress loading group compared to the static group. Shear stress enhanced ALP activity and mineralization, observed on Days 14 and 21. A volcano plot exhibited up- and downregulated genes, while the p38 inhibitor markedly inhibited osteogenic differentiation of hDPSCs triggered by shear stress. In conclusion, shear stress promotes the osteogenic differentiation of hDPSCs through the p38 mitogen-activated protein kinase signaling pathway.

overall_design: RNA-sequence profiling of control (hDPScs) and shear stress applied hPDSCs for 24 hours at day 0 of osteogenic differentiation

middle: Y

first: Watcharaphol

last: Tiskratok

first: Maythwe

last: Kyawsoewin

first: Jeeranan

last: Manokawinchoke

first: Chutimon

last: Termkwanchareon

first: Nuttapol

last: Limjeerajarus

first: Chalida

first: Hiroshi

last: Egusa

first: Thanaphum

last: Osathanon

first: Phoonsuk

last: Limraksasin


title: Proximal Pulmonary Artery Stiffening as a Biomarker of Cardiopulmonary Aging

city: New Haven

first: Ruben

last: De Man

state: CT

address: 333 Cedar St

institute: Yale School of Medicine

summary: To investigate cellular and molecular mechanisms associated with the age-related remodeling observed in the proximal pulmonary artery, we analyzed transcriptomic changes of resident pulmonary arterial cells.

overall_design: Proximal pulmonary arteries were excised from young and aged mice and analyzed using scRNAseq.

first: Zhongyu

last: Cai

first: Aurelien

last: Justet

first: Nebal

last: Abu Hussein

first: Xiting

last: Yan

first: Naftali

last: Kaminski

first: Edward

last: Manning


title: Knockout of the B1 subunit of the GA-binding protein (GABP) [RNA-seq]

first: Jun

last: Song

overall_design:
RNA-seq for 33 conditions. Eight of the conditions were knockouts of the B1 subunit of GABP from exon 2 to exon 9, with four of these conditions being in A-375 cells and four of these conditions being in UM-UC-3 cells. Thirteen of the conditions were knockouts of exon 2 of the B1 subunit, with eight of the conditions being in A-375 cells and five of these conditions being in UM-UC-3 cells. Two of the samples were knockouts of exon 9 of the B1 subunit in A-375 cells. Seven of the samples were control samples that knocked out ROSA26, with four of these conditions being in A-375 cells and three of these conditions being in UM-UC-3 cells. Two of the samples were also control samples with no knockouts.

B1TKO: includes the combination of all samples consisting of knockouts of exons 2-9 in the B1 subunit of GABP (B1KO) and samples consisting of knockouts of exon 2 in the B1 subunit of GABP (B1X2KO).

first: Joseph

last: Costello


title: Organism-wide contributions to systemic skeletal muscle repair in larval zebrafish.

city: St. Louis

first: Aaron

last: Johnson

state: Missouri

address: 660 S. Euclid Ave.

department: Developmental Biology

institute: Washington University in St.Louis

summary: We developed a systemic muscle injury model in zebrafish. Single cell transcriptomic analysis of muscle and non-muscle tissues revealed that systemic and local muscle injuries elicit distinct cellular molecular responses, both quantitatively and qualitatively. These studies suggest that large- and small-scale muscle injuries activate different regenerative programs, resulting in either systemic or local repair.

overall_design: To characterize the regenerative responses and signaling pathways activated after systemic or local muscle injury, we generated Tg(actc1b:NTR-mCherry) transgenic zebrafish lines.At 4 days post fertilization, transgenic larvae were treated with MTZ overnight to systemically injure all myofibers, or were subjected to local mechanical injury (needlestick) of 2-3 somites.Uninjured and systemically injured larvae were collected at 1, 2, and 4 days post injury. Mechanically injured larvae were collected at 2 days post injury. Sequencing results were compared between uninjured, systemically injured, and mechanically injured siblings.

first: Amulya

last: Saini

first: Jennifer

last: McAdow

first: Haley

last: Dean

first: Vishnu

last: Saraswathy


title: Spatial Transcriptomics and Single-Cell RNA-Sequencing Revealed Dendritic Cell-Mediated Inflammation in Keratoconus

city: Beijing

first: Wei

last: Ge

state: State...

address: 5 Dong Dan San Tiao, Dongcheng District

department: Department of Immunology

institute: Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences

summary: Keratoconus (KC) is a corneal disorder characterized by central corneal protrusion and thinning. In this study, spatial transcriptomics was employed to investigate molecular and cellular variations in KC, revealing a distinct pattern of inflammatory responses across the cornea. Upregulation of inflammatory processes was observed in the central cornea, while downregulation was noted in the periphery, indicating complex regional inflammatory changes in the KC cornea. Integration with single-cell RNA sequencing (scRNA-seq) further identified enhanced interactions between dendritic cells (DCs) and stromal cells, particularly mediated via the IL1B pathway, alongside increased matrix metalloproteinase (MMP) production by corneal stromal cells, underscoring the role of inflammation in KC pathogenesis. In vitro and in vivo experiments confirmed that activated DCs promoted the matrix degradation activity of stromal cells, thereby exacerbating KC pathology. Notably, inhibition of the IL-1β pathway effectively mitigated the progression of KC. These findings provide a comprehensive spatial, cellular, and molecular characterization of KC, demonstrating its inflammatory nature. The results also highlight the importance of inflammation in the peripheral cornea for early diagnosis and suggest that anti-inflammatory treatments could serve as potential adjuvant therapy for KC.

overall_design: To elucidate the spatial pathology of KC, transcriptomic sequencing was performed using 10X Visium on corneal samples obtained from five KC patients undergoing penetrating keratoplasty and three control individuals (Ctrl).


title: Single cell RNA Sequencing of murine tdTomato positive skin cells with or without HIRA knockout [dataset 2]

first: Xue

last: Lei

first: Farah

last: Jaber-Hijazi

first: Peter

last: Adams

first: Kathryn

last: Gilroy


title: Synergistic effects of 5-Fluorouracil in combination with Salinomycin promoted ferroptosis via inhibiting SLC7A11/GPX4 in Colorectal Cancer

city: Changchun

first: Can

last: Wang

state: Jilin

address: Ziqiang Street

institute: the second hospital of Jilin university

summary: 5-FU resistance is considered to be a possible reason for the failure of conventional drug treatment of colorectal cancer (CRC). Recently, salinomycin (SAL), as a selective inhibitor of cancer stem cells (CSCs), has been used to sensitize and attenuate a variety of solid tumor chemotherapy drugs. In our study, our goal was to combine SAL with 5-FU to explore whether increase the sensitivity of CRC to 5-FU and the molecular mechanism that involved in enhancing 5-FU sensitivity and promoting tumor cell chemotherapeutic death.

overall_design: SW480 cell lines were treated with 0.1% DMSO, 2.5uM Salinomycin, 5uM 5-Fluorouracil, 2.5uM Sal and 5uM 5-FU for 20h and then RNA-seq was performed.


title: Defining the landscape of chromatin-associated RNAs at human centromeric repeats

city: Stanford

first: Kelsey

last: Fryer

state: California

address: 279 Campus Drive

department: Biochemistry

institute: Stanford University

summary: Centromeres are a specialized chromatin domain that are required for the assembly of the mitotic kinetochore and the accurate segregation of chromosomes. Non-coding RNAs play essential roles in regulating genome organization including at the unique chromatin environment present at human centromeres. To identify RNAs that regulate centromeres we performed Chromatin-Associated RNA sequencing (ChAR-seq) in three different human cell lines to generate a comprehensive list of RNAs associated with centromeric chromatin at a repeat array and chromosome-specific resolution. Centromere enriched RNAs display distinct contact behaviors across repeat arrays and generally belong to three categories: centromere encoded, nucleolar localized, and highly abundant, broad-binding RNAs. Most centromere encoded RNAs remain locally associated with their transcription locus with the exception of a subset of human satellite RNAs. These findings highlight the localized nature of higher order repeat derived RNAs and the diversity of RNA-DNA contact patterns at human centromeres that may reflect or contribute to local chromatin differences.

relation:
Reanalysis of: GSM7697939
Reanalysis of: GSM7697940
Reanalysis of: GSM7697941
Reanalysis of: GSM7697942

overall_design:
We performed chromatin-associated RNA sequencing (ChAR-seq) of human K562 cells to identify and map RNAs assoicated with centromeric chromatin. We generated two replicates split across multiple sequencing runs and combined for analysis.
We also performed the same analysis on previously generated ChAR-seq data in human embryonic stem cells and differentiated definitive endoderm cells (see "Data table" below).

***************************************************************
The table below lists GEO accessions reused/reanalyzed for this study.
***************************************************************

middle: A

first: Charles

last: Limouse

last: Straight


title: Single nuclei transcriptomic and bulk RNA-seq of Populus tremula x alba stem under well-watering and severe drought conditions

city: Pozuelo de Alarcón (Madrid)

first: Daniel

last: Conde

address: Parque Científico y Tecnológico de la U.P.M. Campus de Montegancedo 28223

country: Spain

institute: Centre for Plant Biotechnology and Genomics U.P.M. – I.N.I.A

summary: We have employed snRNA-seq using Singleron technology to dissect the molecular mechanisms controlling secondary xylem plasticity, which allows poplar trees to cope with severe drought. We generated four snRNA-seq libraries using mature stem sections, two per treatment. In this study, we present new molecular drivers of wood plasticity under drought, which allow trees to generate secondary xylem with more and narrower vessels. This trait confers a better adaptation under this abiotic stress. We also performed bulk RNA-seq under the same conditions to evaluate the accuracy of snRNA-seq in our analyses.

overall_design: For the severe drought treatments, in vitro-cultivated hybrid poplars of WT, were transferred to pots containing peat, and grown under LD and 22°C conditions for 6 weeks. Six weeks after potting, the plants were divided into two groups: control and severe drought treatment. Irrigation was carefully controlled during the two weeks of treatment. Control plants were well-watered, keeping the solid moisture around Field Capacity (FC) (0.46 m3/m3) during the treatment. The weight of each pot was calculated at the FC before treatments. Severe drought treatment was achieved by stopping irrigation until the soil reached 15 % of its FC. The wilting threshold was reached when soil moisture decreased to 0.10 m3/m3. Then, a small amount of water was added per pot daily to keep the 15 % of FC by weighing the pots daily during 14 days. Nuclei isolation was performed from the internodes 14 and 15 from one plant, for each library, and snRNA-seq libraries were generated following the Singleron protocol. Bulk RNA-seq was extracted from trees under control and severe drought conditions from the stem. 3 biological replicates were generated per treatment.

first: Daniela

last: Gómez-Soto

first: Wendell

last: Pereira

first: Alejandro

last: Piedrabuena-Díaz

first: Christopher

last: Dervinis

first: Matias

last: Kirst

first: Isabel

last: Allona

first: Mariano

last: Perales


title: Bat organoids reveal antiviral responses at epithelial surfaces

city: Vienna

first: Max

last: Kellner

address: Dr Bohr Gasse 3

country: Austria

institute: IMBA

summary: Bats can host viruses of pandemic concern without developing disease. The mechanisms underlying their exceptional resilience to viral infections are largely unresolved, necessitating the development of physiologically relevant and genetically tractable research models. Here, we developed respiratory and intestinal organoids that recapitulated the cellular diversity of the in vivo epithelium present in Rousettus aegyptiacus, the natural reservoir for the highly pathogenic Marburg virus (MARV). In contrast to human counterparts, bat organoids and mucosal tissue exhibited elevated constitutive expression of innate immune effectors, including type I interferon (IFNε) and IFN-stimulated genes (ISGs). Upon infection with diverse zoonotic viruses, including MARV, bat organoids strongly induced type I and III IFN responses, which conferred robust antiviral protection. Type III IFNλ-3 additionally displayed virus-independent self-amplification, acting as an ISG to enhance antiviral immunity. Our organoid platform reveals key features of bat epithelial antiviral immunity that may inform therapeutic strategies for viral disease resilience.

sample_organism:
Rousettus aegyptiacus
Homo sapiens

platform_organism:
Rousettus aegyptiacus
Homo sapiens

overall_design: 10x genomics single cell RNA-sequencing and pooled 3'-end bulk RNA-sequencing of bat and human organoids as well as bat tissue

first: Jie

last: Jiao

first: Josef

last: Penninger


title: Effect of pattern recognition receptor LE (PGRP-LE) overexpression in Dredd mutant Drosophila enterocytes

city: Cologne

first: Gilles

last: Storelli

address: Joseph Stelzmannstrasse 26

department: CECAD Research Center

country: Germany

institute: University of Cologne

summary: The main goal of this study was to characterize the Dredd-independent functions of PGRP-LE in the adult Drosophila midgut (the midgut is the functional analog of the vertebrate small intestine). We expressed a UAS-PGRP-LE transgene under the control of mex-GAL4, which is specifically active in midgut enterocytes, in a Dredd mutant background. We then collected adult male midguts, extracted total RNA and performed mRNA-seq. Our data show that PGRP-LE overexpression alters fundamental aspects of midgut metabolism in Dredd mutant midguts.

overall_design: Total RNA was extracted from 20 midguts of Dredd mutant adult males (controls - genotype: Dredd D44/Y; mex-GAL4/+), and of Dredd mutant adult males with PGRP-LE overexpression in enterocytes (genotype: Dredd D44/Y; mex-GAL4/UAS-PGRP-LE). mRNA sequencing was performed on 5 biological replicates per genotype. Adult male flies were fed a yeast only diet and dissected 7 days after eclosion.

first: Sofie

last: Burgmer

first: Akos

last: Gyenis


title: 10 Ehlers-Danlos SYndrome (EDS) patients

city: Pozzuoli

first: Rossella

last: De Cegli

address: Via Campi Flegrei 34

country: Italy

institute: Tigem


title: Trap clone accumulation areas (TCAAs) may be involved in maintaining pluripotency in embryonic stem cells

city: Chuo-ku

first: Hitoshi

last: NIWA

state: Kumamoto

address: 2-2-1 Honjo

department: Institute of Molecular Embryology and Genetics

institute: Kumamoto University

summary: Analysis of gene trap clones (TCs) revealed the existence of regions where TCs accumulate in the absence of genes. These regions were designated as trap clone accumulation areas (TCAAs). To ascertain the physiological function of TCAAs, negative control regions devoid of genes and TCs (NC1 and NC11), two randomly selected known gene sets (G1 and G11), and a set of genes presumed to be involved in maintaining pluripotency in embryonic stem (ES) cells (GP) were generated and compared with TCAAs. The assay for transposase-accessible chromatin with sequencing (ATAC-Seq) results indicated that TCAAs exhibited characteristics comparable to G1, G11, and GP, suggesting an open chromatin structure. Oct4-chromatin immunoprecipitation-sequencing (ChIP-seq) demonstrated that TCAAs had markedly elevated signals compared to G1 and 11, and a comparable level to that of GP. With regard to H3K4me1 and H3K27ac, which are associated with enhancer activity, TCAAs were observed to exhibit significantly higher levels than G1 and 11 and a comparable level to that of GP. Furthermore, approximately half of the super-enhancers overlapped with TCAAs in an ES cell-specific manner. These findings suggest that TCAAs are involved in maintaining the pluripotency of mouse ES cells.

overall_design: Chromatin immunoprecipitation DNNA-sequencing (ChIP-seq) for Oct3/4 in mouse Embryonic stem cells.

first: Masatake

last: Araki

first: Runa

last: Ikeda

first: Keika

last: Saitou

first: Takumi

last: Yonemori

first: Kanehiro

last: Kuba

first: Narumi

last: Tsutsumi

first: Kumiko

last: Yoshinobu

last: Ichikawa

first: Mariko

last: Yamane

first: Kimi


title: N6-methyladenosine modification of HCMV IE1 transcript promotes the repressive state of viral genome to achieve latent infection

city: Seoul

first: Daehyun

last: Baek

address: Rm 402, Bldg 504, School of Biological Sciences, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul

department: School of Biological Sciences

institute: Seoul National University

summary: Human cytomegalovirus (HCMV) is a prevalent pathogen that chronically infects the majority of human population. Among the many features that allow such widespread HCMV infection, one is its ability to maintain a transcriptionally dormant immune-evasive state called latency by suppressing its own major immediate early promoter (MIEP) via epigenetic alterations. In this study, we show a novel mechanism of MIEP regulation in which the major immediate early (MIE) gene product, IE1, downregulates its own promoter activity in an m6A modification-dependent manner. We found that the loss of the m6A writer, METTL3, in host cell results in the failure of HCMV to establish latency in these cells. Through transcriptome-wide m6A profiling of latently infected monocytes, we identified that the major immediate early gene product IE1 is m6A-modified during latent infection, with an m6A profile that is distinct from that found during lytic infection. Using an IE1-specific m6A-abolished mutant, we found that latent infection-specific m6A modification of the IE1 transcript was necessary for the efficient repression of MIEP, and this mutant virus failed to establish latency and progressed toward lytic-like infection in THP-1 cells. Our findings demonstrate that HCMV exploits the host m6A machinery to suppress its own lytic program to establish latency and uncover an unexpected role of immediate early gene mRNA in regulating its own expression.

sample_organism:
Homo sapiens
Human betaherpesvirus 5

platform_organism:
Homo sapiens
Human betaherpesvirus 5

overall_design: MeRIP-seq data were generated from HCMV TB40/E-infected THP-1 cells at two time points (1 dpi and 7 dpi) under different treatment conditions (7 dpi + DMSO and 7 dpi + PMA), using two biological replicates. At 5 dpi, a subset of samples was treated with DMSO or PMA and harvested at 7 dpi for MeRIP-seq analysis.

first: Heena

last: Jeong

first: Nagyeong

last: Yeo

first: Hyeonseo

last: Hwang

first: Junhyun

last: Park

first: Kwangseog

last: Ahn


title: MYC couples SWI/SNF and metabolic reprogramming to sustain minimal residual disease in mTORC1-activated cancer cells [WES]

city: Boston

first: Heng

last: Du

address: 45 Francis St

institute: Brigham and Women's Hospital

summary: Therapeutics blocking PI3K-mTORC1 are commonly used for tumor treatment, and at times achieve major responses, yet minimal residual disease (MRD) persists, leading to tumor relapse. We examined the MRD models established both in vitro (Rapamycin persistent, RP) and in vivo after mTORC1 inhibition. All RP/MRD cell lines showed complete growth and signaling insensitivity to rapamycin but variable sensitivity to bi-steric mTORC1 inhibitors. MTORS2035 mutations were identified in 4 of 7 RP cell lines. Multi-omic analysis identified a pronounced shift to oxidative phosphorylation and away from glycolysis in all RP/MRD models, with increased mitochondrial number and function. MYC and SWI/SNF expression were greatly enhanced. Both the SWI/SNF inhibitor AU-15330 and the Complex I inhibitor of oxidative phosphorylation IACS-010759 showed pronounced synergy with bi-steric mTORC1 inhibitors to cause cuproptotic cell death in RP/MRD cells, suggesting these combinations as a potential patient treatment strategy for rapalog resistance.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: To find the MTOR mutations in rapamycin persistent cells. To explore if mutations in other mTORC1 components affect Rapamycin binding.


title: Control of basal-type prostate cancers with a bispecific integrin α5β1/αv antibody

first: Raghav

last: Joshi

address: 800 Washington Street

institute: Tufts Medical Center

summary: Integrin α5β1 and αv crosstalk in chemotaxis and clonogenic survival of prostate cancer cells is abrogated by a bispecific α5β1/αv antibody (BsAbα5β1/αv), which uniquely induces internalization and lysosomal degradation of target integrins. We hypothesized that the BsAbα5β1/αv inactivates pathological mechanosignaling pathways that correlate with integrin expression from patient samples. Mechanistic studies indicate that the BsAbα5β1/αv uniquely reverses YAP, beta-catenin and FAK nuclear localization compared to monospecific integrin α5β1 and αv antibody controls in basal-type androgen-receptor negative prostate cancer cells. Dual integrin αv and α5 knockdown alone phenocopied the BsAbα5β1/αv effect. Following BsAbα5β1/αv treatment, ATAC-seq studies indicated the chromatin accessibility to TEAD and AP-1 family members was markedly reduced. In vitro and in vivo RNA-seq indicated down-regulation of Myc/E2F, TGF-beta and epithelial mesenchymal transition (EMT) and upregulation of Type I and II interferon transcriptomic pathways. The BsAbα5β1/αv induced CXCL10 and CCL5 cytokine secretion, immune-infiltration of tumors, and natural-killer cell-mediated elimination of the basal-type prostate cancer xenografts in nude mice. αv integrin was highly expressed and principally correlated with the Myc signaling pathway in rapid autopsy tissue microarrays, consistent with correlative data from the SU2C metastatic castration-resistant prostate cancer and DKFZ early-onset prostate cancer cohorts. These studies connect integrin signaling with the central biology of basal-type and castration-resistant prostate cancer and define a novel therapeutic strategy that controls critical immunosuppressive pathways.

overall_design: RNA-seq profiling of prostate cancer cell lines and xenografts treated with BsAbα5β1/αv compared to control


title: MYC couples SWI/SNF and metabolic reprogramming to sustain minimal residual disease in mTORC1-activated cancer cells [RNA-seq]

overall_design: To gain a detailed view of how RP/MRD cells differ from their parental countparts, RNA-seq was performed on multiple pairs of cell lines or tumors.


title: MYC couples SWI/SNF and metabolic reprogramming to sustain minimal residual disease in mTORC1-activated cancer cells

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

overall_design: Refer to individual Series


title: Gene expression profiles of healthy mononuclear cells and eosinophils and asthma (moderate and severe) eosinophils

city: Atlanta

first: Edwin

last: Horwitz

state: Georgia

address: 1570 Haygood Drive NE

institute: Emory University

summary: We used scRNAseq to better characterize human eosinophils at resting state in healthy patients (compared to other MNCs). We then compared the healthy eosinophils to eosinophils from asthmatic patients (moderate and severe).

overall_design: Sample preparation was optimized to isolate and process human eosinophils, followed by analysis by scRNAseq.

first: Kyndal

last: Goss

first: Melanie

middle: L

last: Grant

first: Cherish

last: Caldwell

first: Gail

last: Dallalio

first: Susan

middle: T

last: Stephenson

first: Anne

last: Fitzpatrick


title: Transcriptomic analysis of Multicellular spheroids from 10 Ehlers-Danlos SYndrome (EDS) patients.

first: Rossella

last: De Cegli

summary: Multicellular spheroid from 10 Ehlers-Danlos SYndrome (EDS) patients were used to perform transcritomic experiment. These were compared to 4 control healty samples with the aim to identify dysregulated genes and pathways and to use this information to propose potential drugs that could be repurposed for the treatment, based on computational approaches to drug repositioning.In summary, this comprehensive study expands our understanding of the molecular basis of Ehlers-Danlos syndrome, particularly relating to COL3A1 mutations. The integration of transcriptomic analysis, pathway studies, and drug repurposing strategies provides a robust framework for identifying potential therapeutic strategies for EDS.

overall_design: Multicellular spheroids grown 48h were harvested and pooled in 1,5ml tubes. After two PBS washes the spheroids were incubated for 30’ at room temperature with LBE buffer and then frozen over night at -80°C. Total RNA was extracted from Multicellular spheroids of 10 Ehlers-Danlos SYndrome (EDS) patients and 4 controls

first: R


title: SS18::SSX redistributes BAF chromatin remodelers selectively to activate and repress transcription [scRNA-Seq]

city: Salt Lake City

first: Li

last: Li

state: Utah

address: 201 PRESIDENTS CIRCLE

institute: University of Utah

summary: In order to profile the transcriptional changes that accompany SyS development along disparate epithelial, mesenchymal, or poorly differentiated trajectories, we performed single cell transcriptome profiling (scRNA-seq) on mouse SyS tumors similar to those profiled epigenomically. The tumors exhibited a variety of histomorphologies, indicated in hematoxylin and eosin tumor sections of tissue immediately adjacent to that submitted for scRNA-seq.

overall_design: we performed single cell RNA-seq for tumors that arose from SS18::SSX2 expression from the Rosa26 locus by TATCre injection in the limbs of mice (hSS2 allele), which exhibited a variety of histomorphologies

first: Jinxiu

first: Kevin

last: Jones


title: MYC couples SWI/SNF and metabolic reprogramming to sustain minimal residual disease in mTORC1-activated cancer cells [CUT&RUN, ATAC-seq]

overall_design: CUT&RUN of MYC, H3K27ac, H3K4me1, H3K4me3, H3K9Lac and ATAC-seq to gain a comprehensive view of epigenetic chagnes of RP/MRD cells.


title: Transcriptomic analysis of fibroblast from 10 Ehlers-Danlos SYndrome (EDS) patients.

summary: Ehlers-Danlos SYndrome (SEDSY) was performed compared to 4 control healty samples with the aim to identify dysregulated genes and pathways and to use this information to propose potential drugs that could be repurposed for the treatment, based on computational approaches to drug repositioning.In summary, this comprehensive study expands our understanding of the molecular basis of Ehlers-Danlos syndrome, particularly relating to COL3A1 mutations. The integration of transcriptomic analysis, pathway studies, and drug repurposing strategies provides a robust framework for identifying potential therapeutic strategies for EDS.

overall_design: Total RNA was extracted from 10 Ehlers-Danlos SYndrome (EDS) patients and 4 controls


title: Cell type-specific network analysis in Diversity Outbred mice identifies genes potentially responsible for human bone mineral density GWAS associations

city: Charlottesville

first: Luke

last: Dillard

state: VA

institute: UVA

summary: Genome-wide association studies (GWASs) have identified many sources of genetic variation associated with bone mineral density (BMD), a clinical predictor of fracture risk and osteoporosis. Aside from the identification of causal genes, other difficult challenges to informing GWAS include characterizing the roles of predicted causal genes in disease and providing additional functional context, such as the cell type predictions or biological pathways in which causal genes operate. Leveraging single-cell transcriptomics (scRNA-seq) can assist in informing BMD GWAS by linking disease-associated variants to genes and providing a cell type context for which these causal genes drive disease. Here, we use large-scale scRNA-seq data from bone marrow–derived stromal cells cultured under osteogenic conditions (BMSC-OBs) from Diversity Outbred (DO) mice to generate cell type-specific networks and contextualize BMD GWAS-implicated genes. Using trajectories inferred from the scRNA-seq data, we identify networks enriched with genes that exhibit the most dynamic changes in expression across trajectories. We discover 21 network driver genes, which are likely to be causal for human BMD GWAS associations that colocalize with expression/splicing quantitative trait loci (eQTL/sQTL). These driver genes, including Fgfrl1 and Tpx2, along with their associated networks, are predicted to be novel regulators of BMD via their roles in the differentiation of mesenchymal lineage cells. In this work, we showcase the use of single-cell transcriptomics from mouse bone-relevant cells to inform human BMD GWAS and prioritize genetic targets with potential causal roles in the development of osteoporosis.

overall_design: scRNA-seq on bone marrow-derived stromal cells cultured under osteogenic condition (BMSC-OBs) from Diversity Outbred (DO) mice. Each sample pool (e.g., sample pool 1) contains 4 to 5 mice, which are listed in the 'mouse_id' column. Each sample pool (e.g., sample pool 1) was split across two runs (i.e., HGYVNCCX2 or HHFFMCCX2).

first: Gina

last: Calabrese

first: Larry

last: Mesner

first: Charles

middle: R

last: Farber


title: SS18::SSX redistributes BAF chromatin remodelers selectively to activate and repress transcription [RNA-Seq]

summary: Synovial sarcoma (SS) is a rare malignancy, involves a t(X;18) chromosomal translocation that creates a fusion gene SS18-SSX. SS18 is a chromatin remodeling BAF-complexes component, which incorporated in CBAF and GBAF (non-canonical ncBAF). Our previous studies determined that incorporation of the fusion oncoprotein caused degradation of CBAF complexes, emphasizing a critical oncogenic function of GBAF and PBAF in synovial sarcomagenesis.  To determine the SyS dependencies on different subtypes of BAF complexes during tumor development in vivo, we used our SyS mouse model combined with genetic disruption of specific BAF complexes components ARID1A/B or PBRM1. In this study, our fundings suggest that depletion of ARID1A and ARID1B sped tumorigenesis, without significant change in the histomorphology of the developing tumors. Loss of PBRM1 also led to faster tumor growing, but Pbrm1-silenced tumors lacked the full array of SyS histomorphologies observed in wildtype tumors. Overall, Arid1a or Arid1b disruption rendered tumor transcriptomes that clustered within the hSS2 tumor transcriptomes, unlike Pbrm1 disrupted tumors.

overall_design: To explore dependencies of different subtypes of BAF complexes on the synovial sarcomagenesis  in vivo, we used our SyS mouse model cross with conditional knockout mouse targeting either ARID1A, ARID1B or PBRM1. We investigated the tumor development upon disruption of CBAF or PBAF.


title: FOXP3+ Regulatory T Cells Require TBET to Regulate Activated CD8+ T Cells During Recovery from Influenza Infection

city: Chicago

first: Qianli

last: Liu

address: 303 E. Superior St. Simpson Querrey

institute: Northwestern Univesity

summary: Our results demonstrate that TBET+ Treg cells regulate the numbers of activated CD8+ T cells expressing CD69 in the lung following influenza infection. Trm cells accumulated independently of Treg cells but mirrored transcriptional changes observed in activated CD8+ T cells following Treg cell depletion.

overall_design: CD8+ T cells expressing CD69, CD69 and CD103, or neither were flow cytometry sorted from the lungs of Foxp3-DTR mice treated with diphteria toxin or PBS on day 14 to 22 post-inoculation with influenza A/WSN/33 H1N1 virus and subjected to transcriptional profiling with RNA-sequencing.

first: Benjamin

last: Singer


title: Fibrinogen alpha chain promotes the formation of CaOx crystal nuclei by binding to oxalic acid

city: Uchinada

first: Katsuhito

last: Miyazawa

institute: Kanazawa Medical University

summary:
The pathophysiology of Randall's plaque formation has been studied from various perspectives; however, few studies have investigated renal tissue and microenvironmental changes, such as tubular dilation occurring prior to plaque formation. Although previous reports have identified tubular dilation in the renal tissues of patients with kidney stones, the causal relationship between these changes and stone formation remains unclear.  A histological approach is needed to determine which sites in the renal tissue are involved in stone formation. We aimed to identify the site of crystal formation and the early histological changes associated with crystal formation, as well as to identify new factors involved in crystal formation by identifying the genes that are specifically upregulated in the tissue and that participate in stone formation.
To investigate the molecular changes occurring in the proximal tubules and the novel gene target, we divided the kidneys of each group of rats into the cortex and medulla, extracted the total RNA, and performed DNA microarray analysis.

overall_design: Two microarray analyses were performed in the cortex and medulla of kidney, and the genes with a fold-change ≥ 2.0 were selected as variable genes, and the genes that were variable in both analyses were designated as genes with variable expression.

first: Kenshirou

last: Kunii


title: Mitochondria-derived nuclear ATP surge protects against mechanical confinement-induced proliferation defects

city: Barcelona

first: Ritobrata

last: Ghose

address: Carrer del Doctor Aiguader, 88, CRG 5th Floor Reception

institute: Center for Genomic Regulation

summary: The physical microenvironment regulates cell behaviour. Whether physical space constraints reshape the subcellular localisation of organelles and affect metabolism is, however, unknown. Proteomics analysis revealed that cellular confinement induces a strong enrichment of mitochondrial proteins within the nuclear compartment. High-resolution microscopy confirmed that mechanical cell confinement leads to a rapid re-localisation of mitochondria to the nuclear periphery. This nucleus-mitochondria proximity is mediated by an endoplasmic reticulum-based net that entraps the mitochondria in an actin-dependent manner. Functionally, the mitochondrial proximity results in a nuclear ATP surge, which can be reverted by the pharmacological inhibition of mitochondrial ATP production or the reduction of proximity via actin depolymerisation. Inhibition of this nuclear ATP surge reveals long-term effects on cell fitness and proliferation from DNA damage repair delays and cell cycle defects. Together, our data indicate that physical confinement triggers a metabolic rewiring that enables timely nuclear DNA damage repair and cell cycle progression.

overall_design: HeLa cells were treated with or without Oligomycin A (1 µM) for 30 min in glucose-free complete media. Cells were then trypsinized and either left in suspension (controls) or confined using a hybrid confiner. Briefly, cells were confined in glass-bottom 6-well plates (adapted from 4D Cell, CSOW 610) under coverslips with 3µm height microspacers. Both, coverslips and the glass-bottom plate were plasma-cleaned and treated with 0.5 mg/ml PLL(20)-g[3,5]-PEG(2) (Susos) to prevent attachment. Following an acute 15 minute confinement, ATAC seq was perfomed.

first: Fabio

last: Pezzano

first: Ilir

last: Sheraj

first: Verena

last: Ruprecht

first: Sara

last: Sdelci


title: SS18::SSX redistributes BAF chromatin remodelers selectively to activate and repress transcription [ChIP-Seq, Hi-ChIP]

summary: In order to evaluate SS18::SSX distribution across chromatin in synovial sarcoma, we performed ChIP-seq from mouse SyS tumors expressing the human SS18::SSX2 using an antibody specific for the fusion oncoprotein SS18::SS. ChIP-seq was also employed to assess SyS genome profiles of specific chromatin histone marks (H2AK119ub, H3K4me1, H3K4me3, H3K27ac and H3K27me3), and chromatin conformation by HiChIP was evaluated using an antibody against H3K27ac to identify enhancer loops for the purpose of assigning distal regulatory elements to specific genes. Furthermore, we also characterize the distribution of each BAF family subtypes with ChIP-seq ( ARID1A (cBAF), DPF2 (cBAF), PBRM1 (PBAF) and BRD9 (GBAF/non-canonical BAF)). In this study, our fundings suggest that SS18::SSX distributes to proximal and distal regulatory elements bearing ubiquitylated histone 2A and GBAF distributes with the fusion to broad proximal and distal regions; CBAF and PBAF distribute narrowly to active transcriptional start sites.

overall_design: Chromatin immunoprecipitation DNA-sequecning of histone modifications (H2AK119ub, H3K4me1, H3K4me3, H3K27ac and H3K27me3), specific BAF complexes componenants (ARID1A, DPF2, PBRM1, BRD9) and SS18:SSX in mouse SyS tumors expressing the human SS18::SSX2. Chromatin conformation by HiChIP was evaluated using an antibody against H3K27ac to identify enhancer loops for the purpose of assigning distal regulatory elements to specific genes.


title: Aberrant TNF signaling in pancreatic lymph nodes of patients with Type 1 Diabetes

city: Philadelphia

first: Golnaz

last: Vahedi

state: Pennsylvania

address: 421 Curie Boulevard

department: Genetics

institute: University of Pennsylvania

summary: The therapeutic landscape for Type 1 Diabetes (T1D) is rapidly changing as ongoing clinical trials aim to delay beta-cell loss by inhibiting proinflammatory cytokines. However, the precise timing and cellular contexts of cytokine dysregulation remains unknown. We generated the largest existing measurement of gene expression and chromatin accessibility in ~1 million immune cells from the pancreatic lymph nodes and spleens of 34 T1D and non-diabetic organ donors. Our study revealed heightened gene activity of the tumor necrosis factor (TNF) pathway and subsequent chromatin remodeling in central memory CD4+ T cells residing in the pancreatic lymph nodes of T1D and non-diabetic islet-autoantibody positive donors. These findings, validated in mice, offer a mechanism underlying the efficacy of TNF inhibitors, currently undergoing clinical trials to delay T1D onset.

overall_design: The multiome single-cell profiling assay was performed on the pancreatic lymph nodes (PLNs) from 13 non-diabetic controls, 8 non-diabetic but islet autoantibody positive (AAb+),  13 type 1 diabetes (T1D) human organ donors and the spleen tissues from same donors (12 non-diabetic controls, 8 AAb+, and 11 T1D) to identify immune cell signature in T1D.

first: Maryam

last: Abedi

first: Priyadarshini

last: Rai

first: Yeqiao

last: Zhou

first: Chengyang

first: Isabelle

last: Johnson

first: Aditi

last: Chandra

first: Maria

last: Fasolino

first: Susan

last: Rostami

first: Klaus

middle: H

last: Kaestner

first: Ali

last: Naji

first: Robert

last: Faryabi


title: Single-cell transcriptomics of mouse knee joints during embryonic and postnatal stages

city: Pok Fu Lam

first: Peikai

last: Chen

address: Sassoon Road 5

department: Faculty of Medicine

country: Hong Kong

institute: The University of Hong Kong

summary: Synovial joints are structures where two bones meet and essential for mobility. For example, knee joints allow flexion and extension in a single plan for stable walking motions, whereas phalangeal joints together with skeletal muscles facilitate fine motor movements in hands. Joint is enclosed in a capsule and lined by a synovial membrane inside. Articular cartilage covering bone surfaces provide a wear-resistant structure that reduces friction during movement. Meniscus acts like a shock absorber to avoid direct grinding between bone surfaces. Cruciate ligaments reinforce the integrity of a joint by mounting two bones in place and limit the degree of joint movement. All these complex structures with different shapes are fit within the joint capsule for purpose. We established lineage maps of individual joint lineages for human and mouse to understand the progenitors, transcriptional regulators, signaling cues and extracellular matrix (ECM) involved in each differentiation trajectory. We asked whether LGR5+ joint progenitor cells are presence in early stage and decline with maturation as in our findings of mouse, and whether LGR5 and COL22A1 demarcate the chondrogenic and ligamentogenic lineages in human.

overall_design: Knee joints of embryonic and postnatal mice at 5 time-points were harvested for single-cell transcriptomics.

first: Wilson

last: Chan

first: Yan

last: Lam

first: Dany


title: Downregulation of Engulfment and cell motility 1 (Elmo1) induces quiescence and resistance to poly(I:C)-induced apoptosis in endothelial cells

status: Public on Jun 09 2025

city: CHAPEL HILL

first: Yukako

last: Kayashima

state: NC

address: 710 BRINKHOUS-BULLITT BUILDING CB #7525

department: Pathology Lab Med

institute: University of North Carolina at Chapel Hill

summary: Engulfment and Cell Motility 1 (ELMO1) facilitates activation of Ras-related C3 botulinum toxin substrate 1 (RAC1) through interaction with Dedicator of Cytokinesis (DOCK), a family of guanine nucleotide exchange factors (GEF). ELMO1 plays an important role in acute and chronic inflammation by enhancing immune cell migration, phagocytosis of pathogens and dead cells, and production of reactive oxygen species. Endothelial cells, an integral component of inflammatory responses, also express high levels of ELMO1, although the role of ELMO1 in inflammatory endothelial cells is unclear. We demonstrate that knockdown of ELMO1 in EA.hy926 human umbilical vein endothelial cells (HUVECs) leads to cell quiescence, while protects the cells from Toll-like receptor 3 (TLR3)-induced apoptosis and restores inflammatory responses.

overall_design: RNA-seq profiling of EA.hy926 human umbilical vein endothelial cells treated with transfection reagents-only (Mock), cells transfected with non-targeting siRNA (siNT), and those with ELMO1-targeting siRNA (siELMO1), before (0 h) and after (24 h) the stimulation with poly(I:C)

first: Anshulika

last: Ashvinikumar Deshmukh

first: Nobuyo

last: Maeda


title: Commonality of Odorant Receptor Choice Mechanism Revealed by Analysis of a Highly Represented Odorant Receptor Transgene

city: Ar-Rayyan, Doha,

first: Melanie

last: Makhlouf

address: Al Gharrafa Street,

country: Qatar

institute: Sidra Medicine

summary: In the mouse, more than 1,100 odorant receptors (ORs) are expressed in a monogenic and monoallelic fashion, referred to as singular gene expression. Using a 21bp singular-choice enhancer (x21), we radically increase representation of olfactory sensory neurons (OSNs) choosing a 5×21 enhanced OR transgene, but not overexpression of its mRNA on a per cell basis. RNA-sequencing and differential expression analysis identified 425 differentially expressed genes (DEGs). ORs make up 86% of all DEGs, of which 325 have decreased representation and 40 have increased representation. Underrepresented ORs include Class I, Class II and TAAR genes and within each of their respective olfactory bulb domains: DI, DII, and DIII (TAAR) we committedly observe multiple homogeneous glomeruli with an OR1A1-identity. The underrepresentation of endogenous, class-specific ORs across evolutionarily distinct cell types in favor of the expression of the 5×21-OR1A1 transgene argues that a common mechanism of singular gene choice is present for all OR-expressing OSNs

overall_design: mRNA-seq of Mouse Olfactory Epithelium (MOE) from wild-type and Hemizygous 5×21-OR1A1 mice.

first: Mélanie

first: Charlotte

last: D'Hulst

first: Luis

last: Saraiva

first: Paul

last: Feinstein


title: Lipid Droplet Biogenesis by Phase-Separated pORF3 Facilitates HEV Infectivity

city: Hangzhou

first: Li

last: Shen

state: Zhejiang Province

address: 866 Yuhangtang Road

institute: Life Sciences Institute, Zhejiang University

summary: Lipid droplets (LDs) are dynamic organelles mediating lipid metabolism and diverse cellular processes. However, the interplay between hepatocyte LDs and hepatitis E remains poorly understood. Using targeted lipidomics and lipid profiling, we reveal in cellular and rodent models that hepatitis E virus (HEV) infection substantially increases hepatocyte LD biogenesis. Mechanistically, HEV pORF3 is a key LD biogenesis inducer and an essential factor for viral infectivity in vivo. pORF3 formed a unique LD organelle through its liquid-liquid phase-separation (LLPS) property, associating with enhancing cholesterol anabolic pathways, thereby facilitating the synthesis of triglycerides and cholesterol esters. Accordingly, deleting ORF3 or inhibiting LD biogenesis with LD-lowering agent atorvastatin substantially suppressed HEV infection in vivo. These findings position LDs as critical hubs for HEV infection, reveal lipid biogenesis as a crucial function of HEV infectivity, and suggest alternative strategies for HEV intervention.

overall_design: GFP and pORF3 Over-expressed HeLa cells were collected for RNA-seq analysis.

first: Lingdong

last: Xu

first: Yezhang

last: Zhu


title: Identification of glutamate-regulated genes in Arabidopsis seedlings

city: Taipei

first: Yi-Jie

last: Hung

address: 128 Section 2, Academia Road, Nankang

department: IPMB

country: Taiwan

institute: Academia Sinica

summary: To understand the global effect of Glu on gene expression, we performed RNA-seq analysis to compare the gene expression profiles between 12-day-old Arabidopsis seedlings grown on 5 mM NH4NO3 and 5 mM Glu as the sole N source.

overall_design: Total RNA extracted from 12-day-old Arabidopsis seedlings grown on medium containing 1/2 MS-modified basal salt mixture without N (M531, PhytoTechnology Laboratories) plus 0.5% sucrose and supplemented with 5 mM NH4NO3 or 5 mM Glu as the sole N source was used for RNAseq analysis.

first: Jia-Ming

last: Chang

first: Ming-Hsiun

last: Hsieh


title: Chromatin Analysis of Uterine Fibroids/Leiomyomas

city: Grand Rapids

first: Jose

last: Teixeira

state: MI

address: 400 Monroe Ave NW

department: Ob/Gyn

institute: Michigan State University

summary: We performed HiC and ATAC-seq experiments to compare uterine fibroid tissues with matched myometrial tissues.

overall_design: Tissues were collected from consented patients who had hysterectomies because of uterine fibroid symptoms.  The tissues were flash frozen, and nuclei were isolated from the frozen samples.  Standard HiC and ATAC-seq protocols were used with the frozen nuclei and genomic DNA was subsequently analyzed by high throughput sequencing , QCed using MultiQC, and aligned to the human reference genome (hg38) using BWA for HiC and Bowtie2 for ATAC-seq. HiC reads were subsequently analyzed using the HiCExplorer pipeline. ATAC-seq results were analyzed using the pipeline described in doi.org/10.1038/s41467-019-11403-6.

first: Tyler

last: Carpenter

first: Kin

last: Lau


title: Single-cell and spatial transcriptomics reveal the pathogenesis of chronic granulomatous disease under natural conditions [SeekSpace]

city: Tianjin

first: Hanzhi

last: Yu

address: 22 Meteorology Station Road, Heping District, Tianjin

institute: Tianjin Medical University

summary: Chronic granulomatous disease (CGD) is a rare and hereditary immunodeficiency disorder attributed to a malfunction in the NADPH oxidase 2 (NOX2) of phagocytes. Owing to the deficiency of NOX2-derived reactive oxygen species, individuals with CGD exhibit increased susceptibility to pathogens, including bacteria and fungi. This defect also contributes to an excessive inflammatory response, leading to tissue damage. In this study, we established a CGD infection model with Ncf2-/- genetic background through controlled environmental exposure. Within Specific Pathogen-Free (SPF) facilities, Ncf2-/- mice showed no signs of infection. However, under CL grade conditions (CL), these mice spontaneously developed fibro-encapsulated necrotizing lung granulomas. Through single-cell RNA sequencing (scRNA-seq) and flow cytometry, we detected a significant expansion of neutrophils and monocyte-derived macrophages (MDMs) in the lung tissues of CGD mice, identifying a NOS2high neutrophil subset characterized by a proinflammatory transcriptional signature and a specific MDMs subset marked by NOS2 and ARG1. In the spatial transcriptomics data, the NOS2high neutrophils were located in the core area of granulomas, promoting the inflammatory response by highly expressing Mif, Il1b, and Il1a, while the specific macrophage subset was situated at the periphery of granuloma lesions, facilitating extracellular matrix remodeling by expressing Fn1, Mmp9, Mmp12, and Mmp14. Pharmacological inhibition of MIF can significantly diminish neutrophil infiltration and granuloma formation via MIF/NLRP3/IL1β axis. Furthermore, loss of the myeloid-specific pro-survival gene Morrbid resulted in the apoptosis of myeloid cells in CGD and loss of Il1r1 also mitigated diseases, leading to reduction of systemic inflammation in the two compound mutants. In summary, through controlling the environmental factors, we constructed a natural model of CGD infection, elucidated granuloma formation by single-cell and spatial transcriptomics, and developed three interventions.

overall_design: We compared changes in lung tissue in WT and Ncf2-/- mice under different environmental conditions (SPF or CL). We performed Single-cell RNA sequencing (SPF WT, SPF NCF2-/-, CL WT, CL NCF2-/-) and spatial transcriptome sequencing (CL WT, CL NCF2-/-) on mouse lung tissue. In addition, we extracted mouse bone marrow cells for Single-cell RNA sequencing (CL WT, CL NCF2-/-) and sorted bone marrow lin cells for bulk RNA sequencing.

first: Ge

last: Dong

first: Zhigang

last: Cai


title: Single-cell and spatial transcriptomics reveal the pathogenesis of chronic granulomatous disease under natural conditions [RNA-Seq]