title: Murine Dorsal Root Ganglion Single Cell Sequencing of RM1 Intrafemoral Inoculation

summary: We have employed a single cell sequencing approach using 10x Genomics scRNAseq to study murine dorsal root ganglion (DRG) sensory neurons contribution to cancer-induced bone pain. DRG are the hub of sensory neurons and pain signaling. These findings establish a  tumor-bearing reference dataset.

overall_design: Mice were intrafemorally inoculated with 1000 RM1 cells, and after 15 days post-inoculation the lumbar 2-5 ipsilateral DRGs were collected. DRGs were then subjected to enzymatic digestion and density centrifugation to form a single cell suspension. The cells were then processed on a 10X Genomics Chromium controller to generate a cDNA library, which was sequenced on an Illumina NextSeq 500.


title: Accelerated RNA polymerase II elongation drives endothelial transition and plaque vulnerability: pharmacological targeting of the super elongation complex [RNA-seq]

status: Public on Aug 01 2026

city: Leipzig

first: Jes-Niels

last: Boeckel

address: Johannisalle 30

department: Klinik und Poliklinik für Kardiologie

country: Germany

institute: Universitätsklinikum Leipzig

type: Expression profiling by high throughput sequencing

summary: Atherosclerotic plaque rupture is a major cause of myocardial infarction and stroke, yet the mechanisms governing plaque stability remain incompletely understood. Endothelial activation can trigger endothelial-to-mesenchymal transition, a program linked to endothelial dysfunction and lesion vulnerability. Here we investigated whether transcriptional pause release and RNA polymerase II elongation constitute an early regulatory layer that promotes endothelial-to-mesenchymal transition and atherosclerosis. Analysis of human plaque single-nucleus transcriptomics indicated increased expression of super elongation complex components in endothelial cells with a transition signature. In primary human endothelial cell models, pharmacological inhibition of the super elongation complex attenuated induction of mesenchymal markers. AFF4, pCDK9, and pSMAD2/3, showed physical interaction during endothelial transition. Genome-wide profiling of RNA polymerase II occupancy revealed reduced promoter-proximal pausing during early transition, accompanied by a rapid increase in nascent transcriptional elongation rates. Super elongation complex inhibition restored pausing and suppressed fast-responding transition-associated target genes. In a human cardiac organoid model, inhibition of the super elongation complex prevented EndMT-induced fibrillar collagen deposition and reduction in cardiomyocyte beating rate. In a hyperlipidemic Pcsk9 gain-of-function mouse model, super elongation complex inhibition administered both prophylactically and therapeutically after established atherosclerosis reduced plaque burden and improved features associated with vulnerability. Finally, analysis of 1,048 human plaque segments from the Athero-Express biobank showed significant associations between the elongation axis and multiple vulnerability-related plaque traits. Together, these findings identify rapid transcriptional elongation as a mechanistic driver of endothelial plasticity and features of plaque vulnerability and support targeting the elongation machinery as a potential strategy to stabilize atherosclerotic disease.

overall_design: RNA bulk-sequencing was performed on mouse liver from control mice and a hyperlipidemia-induced (high fat diet (HFD)) atherosclerosis mouse model without genetic knockout of metabolic genes (Pcsk9-D377Y-AAV8 with liver specific promoter) with preventive (n=3/4) or therapeutic (n=4/5) treatment with SEC inhibitor KL-2.

first: Karoline E.

last: Kokot

first: Sebastian

last: Reichardt

first: Stephan

last: Erbe


title: Accelerated RNA polymerase II elongation drives endothelial transition and plaque vulnerability: pharmacological targeting of the super elongation complex

type: Genome binding/occupancy profiling by high throughput sequencing

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

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Refer to individual Series


title: Accelerated RNA polymerase II elongation drives endothelial transition and plaque vulnerability: pharmacological targeting of the super elongation complex [4sU-seq]

overall_design: RNA 4sU-DRB sequencing was performed on ECs in control medium, EndMT (DMSO) and EndMT with KL-1 or KL-2 at time points 0 min or 10 min


title: Transcriptomic profiling of the therapeutic effects of Huashibaidu Granules (HBG) on bleomycin-induced pulmonary fibrosis in mice.

city: Beijing

first: jun

last: Huang

address: No.16, Nanxiao Street, Dongzhimen, Dongcheng District, Beijing, China.

country: China

institute: Experimental Research Center, China Academy of Chinese Medical Sciences, Beijing

summary: Pulmonary fibrosis is a chronic and progressive interstitial lung disease characterized by excessive extracellular matrix deposition. Huashibaidu Granules (HBG), a traditional Chinese medicine formula, has demonstrated clinical efficacy in treating inflammatory lung diseases. In this study, we aimed to investigate the molecular mechanisms of HBG in alleviating pulmonary fibrosis. We established a bleomycin-induced pulmonary fibrosis mouse model and administered HBG at different doses. Total RNA was extracted from lung tissues for high-throughput RNA sequencing. Our results provide a comprehensive transcriptomic landscape of HBG’s intervention, highlighting its role in regulating key signaling pathways (such as TGF-β/Smad and PI3K-Akt) and macrophage polarization.

overall_design: Schematic timeline of the in vivo experimental protocol. Mice received early prophylactic intragastric intervention with HBG (7 g/kg) for one week prior to model induction. PF was induced by a single intratracheal instillation of BLM (5 mg/kg), and daily intragastric administration continued until euthanasia on Day 28.


title: Accelerated RNA polymerase II elongation drives endothelial transition and plaque vulnerability: pharmacological targeting of the super elongation complex [ChIP-seq]

overall_design: ChIP-seq was performed on human ECs controls, EndMT, EndMT+KL-1 and EndMT+KL-2.


title: TRI-611, a selective, brain-penetrant molecular glue degrader of ALK

city: Lexington

first: Andrew

last: Conery

state: MA

address: 1050 Waltham St. Suite 301

country: USA

institute: Triana Biomedicines

summary: Tyrosine kinase inhibitors (TKIs) targeting Anaplastic Lymphoma Kinase (ALK) have transformed the treatment landscape of ALK fusion-positive non-small cell lung carcinoma (NSCLC), but limited options for patients who progress on approved TKIs highlight a continued need for an orthogonal therapeutic approach. TRI-611 is a potent, brain-penetrant molecular glue degrader (MGD)   of ALK fusion proteins with the potential to address this need . TRI-611 promotes the proximity of the ALK kinase domain and CRBN via a unique degron interface distal from the kinase active site. The unique binding interface of TRI-611 leads to selectivity across the proteome including known CRBN neo-substrates and other kinases. TRI-611 treatment induces degradation of all forms of oncogenic ALK fusion proteins, including TKI-resistant mutated versions of ALK, leading to regression of cell line and patient-derived subcutaneous and intracranial tumour models of ALK-positive NSCLC. TRI-611 can be combined with orthosteric ALK TKIs, achieving synergistic and durable tumour regressions. TRI-611 represents the first example of a clinical stage MGD targeting an oncogenic gene fusion and has the potential to expand the arsenal of therapeutic options for ALK-positive NSCLC patients.

overall_design: NCI-H3122, NCI-H2228, or SNU2535 cells were treated with DMSO or 3 uM TRI-611 for 3 h.

middle: R


title: Elucidating the mechanism underlying sepsis- induced hemolysis, RNA_seq of Kupffer cells

city: Gent

first: Steven

last: Timmermans

address: Technologiepark 71

country: Belgium

institute: VIB-UGent

summary: An RNA-seq of kupffer cells 2 hours after CLP or sham to investigate differenial gene expression and functional effects.

overall_design: RNA-seq profiling of Kupffer cells 2h after Sham or CLP surgery.

first: Marah

last: Heyerick

first: Louise

last: Nuyttens

first: Robin

last: Van Loke

first: Elise

last: Moens

first: Nikita

last: Gerebtsov

first: Helena

last: Aegeter

first: Bart

last: Lambrecht

first: Domien

last: Vanneste

first: Thomas

last: Marichal

first: Jolien

last: Vandewalle

first: Claude

last: Libert


title: Elucidating the mechanism underlying sepsis- induced hemolysis, RNA_seq of red pulp macrophages

summary: An RNA-seq of red pulp macrophages 2 hours after CLP or sham to investigate differenial gene expression and functional effects.

overall_design: RNA-seq profiling  of Red pulp macrophages 2h after Sham or CLP surgery.


title: LPS stimulation reveals male and female dimorphism in human iPSC-derived macrophages

city: New York

first: Gordana

last: Vunjak-Novakovic

state: NY

institute: Columbia University

summary: Clinical disparities in the inflammatory responses between males and females have been reported for decades, revealing sex-biased disease severity and patient outcomes. However, the underlying mechanisms driving these differences are understudied and poorly understood, despite the growing potential for improved diagnoses and treatment strategies. In this study, we used male and female iPSC-derived macrophages to identify transcriptomic changes in response to the common bacterial antigen lipopolysaccharide (LPS). Bulk RNA sequencing identified 67 genes differentially expressed between male and female macrophages in the absence of inflammation, the majority of which mapped to the sex chromosomes. This sexual dimorphism was amplified by LPS stimulation, with genes predominantly located on autosomes, leading to divergent patterns in secreted protein production that were consistent with clinical findings following LPS exposure. Although future validation with a larger patient cohort is needed, these data collectively suggest that iPSC-derived macrophages can serve as a meaningful tool for understanding and improving treatment of sex-biased pathophysiological conditions.

overall_design: To investigate sexual dimorphism in human macrophages, iPSC lines were obtained from three healthy male donors (WTC11, AA1, FA10), ages 27-36, and three healthy female donors (BS2, CC1, FA11), ages 20-49 years old. iPSCs were differentiated into macrophages (iMacs) and cultured for 48 h in the presence or absence (control) of 100 ng/mL lipopolysaccharide (LPS) to elicit an inflammatory response. Bulk RNA-sequencing was performed on male and female iMacs, with n=2 technical replicates per donor cell line, and gene expression profiling analysis was performed to compare control male and female iMacs, and male and female iMacs during an inflammatory response (LPS).

first: Pamela

middle: L

last: Graney

first: Daniel Naveed

last: Tavakol

first: Roberta

middle: I

last: Lock

first: Connie

last: Chen

first: Maria

last: Samaritano

first: Nicole

last: Hachmann

first: Richard

last: Friedman


title: Early Salivary and Tracheal aspirate miRNAs in Extremely Preterm Infants Predict BPD-related Pulmonary Hypertension

city: Little Rock

first: Roopa

last: Siddaiah

state: AR

address: 1 Children's way

department: Pediatrics

institute: Arkansas Children's Hospital

type: Non-coding RNA profiling by high throughput sequencing

summary: Pulmonary hypertension (BPD-PH) associated with bronchopulmonary dysplasia (BPD) in preterm infants is associated with high morbidity and mortality within the first two years of life. In a previous unbiased study, we identified a panel 16 miRNAs in tracheal aspirates (TA) that were differentially expressed in preterm infants with BPD-PH compared to those with BPD but no PH. To endotype molecular thumbprint of BPD-PH, we used unbiased multiomics approach and identified a panel of miRNAs, mRNAs, and proteins in tracheal aspirates (TA) and found 14 differentially expressed mIRNAs. To explore to predictive potential of these miRNAs, we collected TA and extracted exosomes from extremely low gestational age infants (ELGANs) at 7 days of age and calculated the predictive AUROC of these miRNAs from TA exosomes to diagnose BPD-PH at 36 weeks PMA. AUROC of TA miRNAs was 0.89 with sensitivity and specificity of 77% and 81%, respectively. Due to challenges of obtaining TA in non-invasively ventilated infants, we collected saliva samples (SA) from ELGANs at 7 days of age and calculated the predictive AUROC of the same miRNAs to diagnose BPD-PH at 36 weeks PMA. AUROC of these miRNAs in saliva was = 0.94 with sensitivity and specificity of 93% and 78%, respectively. Of the 14 miRNAs, of particular interest is miR29-a which is highly differentially expressed in BPD-PH and has been studied in animal model for its role in modulating genes responsible for lung growth and development. We studied the effect of miR29-a on the pulmonary artery smooth muscle cells (PASMC) by transfecting them with Ago-miR29a and found low expression PDGFA which is an important key player in angiogenesis and lung development in early growth. Salivary miRNA panel is a potential non-invasive early predictor of BPD-PH in ELGANs with biological plausibility through miR29a pathway.

overall_design: RNA  sequencing profiling for miRNA from  saliva  and tracheal aspirate samples of preterm infant with BPD-PH

first: Claire

last: Miller

first: Vincent

last: Aluquin

first: Tang

last: Li

first: Shaoyi

last: Zhang

first: Ann

last: Donnelly

first: Heather

last: Stephens

first: Shakshi

last: Sharma

first: Roppa


title: DUF4004 protein YhbD (BacR) of Bacillus subtilis is a regulator of bactofilin expression and interacts with bactofilins in a switch-like manner

city: Marburg

first: Peter

last: Graumann

address: Karl-von-Frisch-Str. 14

department: Chemistry

institute: Marburg University

summary: DUF4004-containing proteins are found in a variety of bacteria. The only characterized member was shown to act as transcriptional repressor of genes involved in metabolism in Clostridium acetobutylicum. We have characterized the B. subtilis member of this protein family, encoded by the yhbD gene. The putative transcription factor binds to DNA in vitro, and forms predominantly dimers. The absence of YhbD negatively affects the expression of the yhbDEF operon, and thereby of bactofilin genes, but does not show any other alteration of genome-wide transcript levels. On the other hand, purified bactofilins BacE and BacF bind to YhbD in vitro, and strongly reduce its DNA binding, and the depletion of bactofilins leads to reduced copy numbers of YhbD. In vivo, YhbD localizes in foci at the cell membrane. Depletion of BacE and BacF, leads to a loss of membrane localization of YhbD and induces nucleoid association. These findings suggest that bactofilins can recruit YhbD to the membrane. Treatment of cells with vancomycin also leads to a switch in YhbD localization to the nucleoids, indicating that YhbD may be involved in the response to cell wall stress. Our data suggest that YhbD acts as a regulator of bactofilins, wherefore we propose to rename it BacR, and fine-tunes bactofilin expression involving a switch-like mechanism with BacE and BacF.

overall_design: Bacillus subtilis NCIB 3610 wild-type and ΔyhbD strains were grown under control conditions or treated with 4 μg/mL vancomycin for 30 min. Total RNA was extracted and sequenced using paired-end Illumina sequencing (n = 3 biological replicates per condition). Reads were aligned to the NCIB 3610 reference genome (CP020102.1) using STAR (v2.7.11a) and quantified with featureCounts (v2.1.1). Differential gene expression was analyzed using DESeq2 (v1.44.0) with the design formula ~ cell_type * condition to identify vancomycin-responsive genes and assess whether the ΔyhbD deletion affects the transcriptional stress response.

first: Kristin

last: Velten

first: Patrik

last: Brück

first: Doreen

last: Meier

first: Anke

last: Becker

first: Shahla

last: Alipour

first: Georg

last: Hochberg

first: Paul

last: Klemm

first: Marcus

last: Lechner


title: Edited HSPCs rescue frataxin deficiency and inflammation-driven neurologic, cardiac and pancreatic pathology in Friedreich’s ataxia

city: La Jolla

first: Stephanie

last: Cherqui

state: California

address: 9500 Gilman Drive

department: Department of Pediatrics

institute: University of California San Diego

summary: Friedreich’s ataxia (FRDA) is a multisystemic neurodegenerative disorder caused by GAA repeat expansion in intron 1 of frataxin (FXN), resulting in FXN deficiency and mitochondrial dysfunction. Current therapies do not correct the underlying genetic defect. Here, we demonstrate that ex vivo CRISPR/Cas9 excision of the GAA expansion in hematopoietic stem and progenitor cells (HSPCs) provides a durable, systemic therapy for FRDA. A single infusion of gene-edited Sca1+ HSPCs, mPPL-001, into myeloablated, humanized YG8JR mice resulted in long-term engraftment of donor-derived cells across hematopoietic and FRDA-affected tissues. mPPL-001 increased FXN expression and corrected multiple key pathogenic drivers of FRDA, including mitochondrial stress, microglial and macrophage activation, and inflammatory signaling. These coordinated effects improved motor functions, preserved cerebellar architecture, mitigated cardiac pathology and promoted survival and proliferation of insulin-producing β-cells in the pancreatic islet of Langerhans. Collectively, these findings establish FXN-edited autologous HSPCs as a one-time, disease-modifying therapy for FRDA and support advancement toward a first-in-human trial.

overall_design: To evaluate the neuroprotective impact of mPPL-001 therapy, bulk RNA sequencing was performed on cerebellar tissue at 6-month post-transplant.

first: Anusha

last: Sivakumar

first: Alexis

middle: N

last: Corl

first: Keneth

middle: J

last: Muñoz

first: Subhashini

last: Arumugam

first: Betul

middle: B

last: Gunes

first: Angelyn

last: Solis

first: Rishika

last: Murthy

first: Lilas

last: El-Hachim

first: Donald

middle: P

last: Pizzo

first: Ian

middle: A

last: Blair

first: Teerapat

last: Rojsajjakul

first: Clementina

last: Mesaros

first: Xinlong

last: Wan

first: Josep

last: Rainaldi

first: Rafael

last: Badell Grau

first: Veenita

last: Khare

first: Kevin

middle: E

last: Thai

first: Kavya

last: Beiderman


title: Histone methylation in Gpt2 KO and Gpt2 WT mouse brain tissues

city: Dallas

first: Samuel

last: McBrayer

state: Texas

address: 5901 Forest Park Road

department: Children’s Research Institute

institute: University of Texas Southwestern Medical Center

summary: Alpha-ketoglutarate (αKG) is required for chromatin demethylation but mechanisms controlling αKG abundance in the nucleus are poorly defined. We designed a biosensor to monitor this metabolite pool in human cells using an αKG-responsive cyanobacterial transcription factor, NtcA, and used it to identify genes that regulate αKG in the nucleus. We defined an inter-organelle pathway in which sequential mitochondrial activities of the GPT2 transaminase and SLC25A11 transporter supply nuclear αKG. In a mouse model of GPT2 Deficiency, an inborn error of metabolism, Gpt2 loss caused histone hypermethylation in the brain and dysregulated neurodevelopmental genes. Restoring αKG counteracted these changes and promoted mouse fitness. Our work provides a tool to directly monitor nuclear αKG and reveals nuclear αKG deficiency as a key pathogenic mechanism underlying GPT2 Deficiency.

overall_design: ChIP-seq was performed using mouse brain tissues from Gpt2 WT and Gpt2 KO mice. Histone marks analyzed included H3K27me3, H3K4me3, and H3K9me3, together with input controls. Samples were collected as biological replicates for each genotype and sequenced as paired-end libraries. This design allowed genotype-based comparisons of histone methylation profiles in WT versus Gpt2 KO brain tissues.

first: Alex

middle: C

last: Sternisha

first: Haocheng

last: Li

first: Kumar

last: Gajendra

first: Xin

last: Zhao

first: Morgan

last: Fleishman

first: Qing

last: Ouyang

first: Michael

last: Schmidt

first: Yoon Jung

last: Kim

first: Laura

last: Banaszynski

first: Eric

middle: M

last: Morrow

middle: K


title: Metabolic Dependencies in Medulloblastoma Reflect Underlying Cellular Origins

city: Toronto

first: Alexandria

last: DeCarlo

state: Ontario

address: 686 Bay Street

department: Developmental and Stem Cell Biology

country: Canada

institute: Hospital for Sick Children

summary: Medulloblastoma (MB) is the most common malignant brain tumour of childhood and comprises molecularly and clinically distinct subgroups arising from defined neuronal progenitor populations. Despite extensive genomic characterization, therapeutic strategies have remained largely unchanged for decades, and outcomes for high-risk disease remain poor. Here, we identify a conserved and lineage-encoded metabolic dependency that distinguishes MB from other brain tumours. Using genome-wide CRISPR–Cas9 dropout screens across SHH, TP53-mutant SHH, and MYC-amplified Group 3 MB models, we uncover mitochondrial respiration as a core fitness requirement shared across subgroups. Unbiased metabolomic profiling of primary patient tumours reveals that MB occupies a distinct metabolic state characterized by depletion of glycolytic intermediates relative to ependymoma and glioma, independent of subgroup or MYC status. This metabolic configuration mirrors neuronal bioenergetics and reflects suppressed glycolytic capacity rather than oncogene-driven reprogramming. Consistent with this rigidity, MB cells fail to compensate for mitochondrial inhibition by upregulating glycolysis and are exquisitely sensitive to pharmacologic complex I blockade. In orthotopic patient-derived xenograft models, complex I inhibitors including IACS-010759 and metformin significantly extend survival across high-risk MB subgroups. Together, these findings establish oxidative phosphorylation as a lineage-constrained metabolic vulnerability in MB and provide a strong rationale for therapeutic targeting of mitochondrial respiration in this disease.

overall_design: RNA-seq analysis of three high-risk  human  medulloblastoma models treated in vivo with complex 1 inhibitor IACS 010759 or 0.5% methylcellulose until endpoint

first: Vijay

last: Ramaswamy


title: 1.Effects of L013 treatment on gene expression in KYSE150 and KYSE510 cells. 2. 5 Patient-derived organoids RNA-seq data

first: Xiao

last: Yu

address: No. 17, Panjiayuan Nanli, Chaoyang District, Beijing

institute: Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College

summary: Esophageal squamous cell carcinoma (ESCC) patients with the NRF2 oncogenic activation (NRFA) subtype have poor prognosis and limited response to conventional therapies due to excessive NRF2 accumulation. Here, through high-content screening of 725 CRBN ligand-based PROTACs, we identified L013 as an efficient NRF2 degrader. L013 reduces NRF2 in ESCC cells through dual mechanisms, including ubiquitination-mediated proteasomal degradation and suppression of NRF2 transcription. Functional studies showed that L013 inhibits the proliferation and tumorigenic capacity of NRF2-hyperactivated ESCC cells. In preclinical models, L013 lowered NRF2 levels and suppressed tumor growth in ESCC or lung squamous cell carcinoma (LUSC) patient-derived organoids and xenograft models, while showing acceptable safety. These findings identify L013 as a promising therapeutic candidate for NRFA-subtype ESCC and support a new strategy for targeting NRF2-driven oncogenesis.

overall_design: 1.RNA-seq profiling was performed on KYSE150 and KYSE510 cells after 12 h treatment with DMSO or L013. 2 .5 PDOs mRNA expression profile.

first: Yue

last: Wu

first: Zhihua

last: liu


title: Reduced LACTB expression in myeloid cells is associated with elevated succinyl-carnitine levels and reduced Alzheimer’s disease risk

first: Tulsi

last: Patel

address: Icahn School Of Medicine At Mount Sinai, 1468 Madison Ave

institute: Icahn School of Medicine at Mount Sinai

summary: Lactamase B (LACTB) is a mitochondrial protease previously related with cancer progression, and lipid metabolism. Our mendelian randomization analyses indicate that lower LACTB expression in myeloid cells is protective for Alzheimer’s Disease (AD) and is genetically associated with increased succinyl-carnitine, a poorly characterized metabolite that independently correlates with reduced AD risk. We identify LACTB as a primary enzyme responsible for succinyl-carnitine hydrolysis. Using human LACTB knockdown and knockout macrophage and microglial systems, we show that loss of LACTB enhances oxidative phosphorylation, reduces protein synthesis, and alters lipid profiles. LACTB expression is increased upon IFN/TNF stimulation, and LACTB loss modifies efferocytosis-related pathways following inflammatory activation. In vivo, xenotransplanted human LACTB knockout microglia show enhanced association with amyloid plaques in the mouse brain. Together, these findings define a previously unrecognized metabolic pathway linking LACTB and succinyl-carnitine to myeloid cell function and AD risk. Given its enzymatic druggability and the potential to leverage succinyl-carnitine as a translational biomarker, LACTB represents a promising therapeutic target.

overall_design: Control (scrambled, SCR) and LACTB KO iPSC-derived human microglia-like cells (iMGLs). 1-2 independent differentiations per genotype.

first: Carmen

last: Romero-Molina

first: Edoardo

last: Marcora

first: Alison

last: Goate


title: Gene expression profile for Gpt2 WT and Gpt2 KO mouse brain tissues with vehicle or dm-αKG treatment

first: Samuel

last: McBrayer

overall_design: Mouse brain tissues were collected from Gpt2 wild-type (WT) and Gpt2 knockout (KO) mice treated with either vehicle (Veh) or dm-αKG. RNA-seq was performed on four experimental groups: WT-Veh, WT-dm-αKG, KO-Veh, and KO-dm-αKG. The study included biological replicates for each group (WT-Veh, n=10; WT-dm-αKG, n=8; KO-Veh, n=10; KO-dm-αKG, n=8). The experimental design enabled comparisons between genotypes within each treatment condition and comparisons between treatments within each genotype.

first: Alex

last: Sternisha

first: Haocheng

last: Li

first: Kumar

last: Gajendra

first: Tracey

last: Shipman


title: Knock-down of lncRNA SNHG26 in human embryonic stem cells

city: Quebec City

first: Samer

last: Hussein

state: Quebec

address: 9 rue Mcmahon

department: Departement of medecine

institute: CHU de Québec - Université Laval

summary: The recent development of long-read RNA sequencing (lrRNAseq) technologies has paved the way to the exploration of RNA isoform diversity and its relevance to better understand the gene regulatory network that sustains cell fate and plasticity. However, drawing conclusions regarding the functionality of these newly identified isoforms is still very scarce. Here, we devised a very efficient system to reprogram cells towards an induced pluripotent cell state and leveraged the strengths of lrRNAseq in order to study the isoform diversity of reprogramming. This strategy enabled us to identify differential isoforms throughout the reprogramming process, with a pressure on novel non-coding isoforms to be regulated. More specifically, we highlight a new long non-coding RNA (lncRNA), Snhg26 whose isoform switch during reprogramming enhances the conversion of cells’ identity towards pluripotency. We showes that knocking-down this lncRNA in mouse embryonic stem cells hinders the maintenance of a pluripotent state and primes the cells for differentiation. Additionally, with the data presented here, we show knockdown of the human SNHG26 is associated with loss of naive pluripotency markers in human embryonic stem cells. Together, our study provides a comprehensive resource to study full-length isoform regulation and mechanisms at stake during reprogramming, but more importantly it demonstrates the power of lrRNAseq to identify functionally relevant gene isoforms in the context of pluripotency.

overall_design: We performed Oxford nanopore technologies long-read RNA sequencing H9 human embryonic stem cells (hESCs) in control conditions or with CRISPR-interference (CRISPRi) knockdown of the lncRNA SNHG26. Sequencing was performed with a PCR cDNA sequencing approach using kit SQK-NBD114.24 followed by sequencing on R10.4.1 flowcells, using a P2-Solo Nanopore sequencer.

first: Victoire

last: Fort

first: Gabriel

last: Khelifi

first: He

last: Ruicen

first: Valérie

last: Watters

first: Gertsenstein

last: Marina

first: Yamanaka

last: Nobuko

first: Lelong

last: Emeline

first: Loehr

last: Jérémy

first: Pye

last: Melanie

first: Micha

last: Victoria

first: Lambert

last: Jean-Philippe

last: Yojiro

first: Wranna

last: Jeffrey


title: α2,6-Sialoglycan-regulated anti-tumor immunity of tumor-infiltrating CD8+ T cells in the tumor microenvironment [CD8+T]

first: Qi

last: Tang

address: Chengfu Road #292

institute: Peking University

summary: Cell-surface sialoglycans overexpressed on cancer cells suppress the activation of tumor-infiltrating immune cells (TIICs), and have emerged as a promising target for cancer immunotherapy. However, the functional roles of sialylation in TIICs remain incompletely understood. Here, we develop the single-cell correlative analysis of α2,3- and α2,6-linked sialoglycans and transcriptomes (scCAST_3&6) strategy to correlate cell-surface sialylation in a linkage-specific manner with gene expression of the same cells by single-cell RNA sequencing. Applying scCAST_3&6, we discover that α2,3- and α2,6-sialoglycans are distinctively regulated in specific TIIC subpopulations. Importantly, downregulated α2,6-sialoglycan is demonstrated as a cell-surface marker for labeling and isolating CD8+ T cells with high reactivity to tumor-specific antigens (TSAs) from the tumor. Mechanistically, α2,6-sialyltransferase ST6Gal-I is transcriptionally suppressed upon the activation of intratumoral CD8+ T cells with high-avidity T cell receptors towards tumor antigens, which downregulates α2,6-sialylation and exposes galectin-1 ligands. Functionally, increased galectin-1 binding to TSA-reactive CD8+ T cells promotes T cell apoptosis and cancer immune evasion. This work underscores the functional significance and therapeutic promise of specific sialoglycans on TIICs.

overall_design: To investigate the dynamic regulation of St6gal1 expression in CD8+ T cells upon TCR activation, we performed bulk RNA-seq on splenic CD8+ T cells isolated from OT-I mice. The cells were stimulated in vitro for 24 or 48 hours using a set of antigen peptides, anti-CD3/CD28-coated microbeads, or plate-immobilized anti-CD3 antibodies.

first: Shuyu

last: Liang

first: Xing

last: Chen


title: RNA-seq of a Leigh Syndrome patient blood being treated with Omaveloxolone.

city: Palo Alto

first: Drishti

last: Guin

state: CA

address: 1804 Embarcadero Rd Suite #201

institute: Transcripta Bio

summary: A male patient diagnosed with Leigh Syndrome due to a compound heterizygous mutation in SURF1 (SURF1 c.312_321del10insAT (p.Leu105*); SURF1 c.574C>T (p.Arg192Trp)) was prescribed Omaveloxolone under physican supervision. Pre-treatment patient blood showed deficiency in pathways associated with oxidative phosphorylion and cellular energetics. Omaveloxolone normalized this phenotype via enrichment of these pathways.

overall_design: The patient was prescribed Omaveloxolone by physician and transcriptomic changes were tracked by collecting and profiling patient blood using RNA-seq along with clinical testing. A control sample was collected pre-treatment and 4 post-treatment samples were collected for 4 months post dosing start at monthly intervals.

first: Long

last: Wu

first: Katherine

last: Dyer

first: Nicole

last: Carvajal

last: Rivera Del Toro

first: Michael

last: Blanco

first: Natalie

middle: F

last: Downs

last: Perfito

first: Saima

last: Kayani

first: Ursula

last: Haditsch

first: Christopher

last: Moxham


title: CpG Hypermethylation and WNT/AP-1 cooperativity Define the Epigenetic Landscape and a Clinical Subgroup of High-Risk Pediatric Adrenocortical Carcinoma [Visium HD]

city: Augsburg

first: Victoria

middle: Elisabeth

last: Fincke

address: Stenglinstraße 2

institute: Childens Cancer Center - University hospital Augsburg

summary: To investiagte the cellular heterogenity one sample from each DNA methylation-based subgroup was investiagted using the Visium HD platform by 10x Genomics.

overall_design: One sample per capture area were prepared according to protocol for Visium HD Whole Transcriptome.

first: Mauice

last: Loßner

first: Marina

last: Kunstreich

first: Nic

middle: G

last: Reitsam

first: Irmengard

last: Sax

first: Marlena

last: Mucha

first: Felix

last: Dorn

first: Lorenz

last: Helmschrott

first: Maria

middle: D

last: Hernandez Ramirez

first: Sebastian

last: Dintner

first: Konstantin

last: Okonechnikov

first: Martin

last: Sill

first: Ina

last: Oehme

first: Heike

last: Peterziel

first: Enrique

last: Blanco-Carmona

first: Eva

last: Sipos

first: Stefan

last: Wudy

first: Christoph

last: Slavetinsky

first: Jörg

last: Fuchs

first: Bruno

last: Märkl

last: Jüttner

first: Christian

last: Vokuhl

last: Frühwald

first: Antje

last: Redlich

last: Pfister

first: Matthias

last: Schlesner

first: Rainer

last: Claus

first: Michaela

last: Kuhlen

first: Pascal

last: Johann


title: Human HP1BP3 regulates cortical neurogenesis and drives schizophrenia-like phenotypes

first: Bosong

last: Wang

address: No.19, Xinjiekouwai Street, Haidian District, Beijing, P.R.China

institute: Beijing Normal University

summary: The neurodevelopmental theory of schizophrenia proposes its connection to aberrant early brain development, yet the molecular mechanisms linking genetic risk of schizophrenia to altered neurogenesis remain largely unknown. Here, we used integrative analyses of genome-wide association studies (GWAS) and single-cell transcriptomic datasets to identify HP1BP3, a heterochromatin-associated nuclear protein, as a schizophrenia-associated gene. To investigate its functional role, we generated a Nestin-Cre–driven conditional knock-in mouse model expressing human HP1BP3 (hHP1BP3CKI mice). We performed CUT&Tag profiling of mouse brain tissue. And CUT&Tag profiling revealed that hHP1BP3 binding reshapes chromatin occupancy at transcription start sites and significantly downregulates the centrosomal protein CEP164, a key regulator of ciliogenesis and cell-cycle control.

overall_design: The DNA-binding ability of hHP1BP3 was assessed in the embryonic mouse cerebral cortex via CUT&Tag analysis. Cortical tissues were isolated from six mouse embryos for this assay


title: CIS Modulates Macrophage function

city: Albuquerque

first: Dandan

last: Wu

state: NM

address: 915 CAMINO DE SALUD  NE room 360

department: Molecular Genetics and Microbiology

institute: University of New Mexico

summary: Cytokine-inducible SH2-containing protein (CIS), a member of the SOCS family, negatively regulates cytokine signaling, yet its role in macrophage biology remains incompletely defined. Here, we characterize the function of CIS in controlling macrophage activation, metabolic reprogramming, and inflammatory output. We show that CIS is rapidly upregulated in macrophages in response to cytokines and acts to restrain JAK?STAT signaling, thereby limiting the magnitude and duration of pro-inflammatory gene expression. Loss of CIS results in heightened STAT1/STAT3 activation, and increased production of inflammatory mediators, whereas CIS expression skews macrophages toward an immunoregulatory phenotype. These findings establish CIS as a key regulator of macrophage functional plasticity and reveal its importance in maintaining immune homeostasis.

overall_design: Compared different condition mice, RNA-seq analyzes DEG and related pathways.

first: Xuexian

last: Yang


title: Unraveling Bortezomib Resistance in Multiple Myeloma: Insights from RNA-Seq and PI3K/mTOR Pathway Analysis

city: İzmir

first: Yagmur

last: Kiraz

address: Sakarya st. No:156

department: Genetics and Bioengineering

country: Turkey

institute: İzmir University of Economics

summary: Multiple myeloma (MM) is a cancerous plasma cell condition that is characterized by overproduction of abnormal antibodies by plasma cells. The complete cure for the disease has not been achieved because of development of drug resistance. Bortezomib, the pioneering proteasome inhibitor, is essential in MM treatment; nevertheless, acquired resistance greatly restricts its effectiveness. To clarify the molecular mechanisms behind bortezomib resistance, we performed RNA sequencing (RNA-Seq) on RPMI-8226 MM cells that were bortezomib-sensitive and bortezomib-resistant, as well as healthy B-cells. Analysis of differential expression showed notable changes in immune signaling, proteasome activity, and metabolic pathways. Resistant MM cells showed a significant decrease in the expression of antigen presentation genes, such as HLA-DRA, HLA-DPA1, and CD74, indicating immune evasion. Meanwhile, important metabolic regulators like GLUL (Glutamine Synthetase) and MDK (Midkine) were downregulated, suggesting a transition to glycolytic metabolism. Simultaneously, the enhancement of proteasome-related processes and nucleocytoplasmic transport underscored adaptive mechanisms for preserving protein balance during proteotoxic stress. Notably, PRAME (Preferentially Expressed Antigen in Melanoma), a key oncogene often linked to therapy resistance, was significantly upregulated in resistant MM cells. Pathway analysis further indicated notable enrichment of pathways associated with neurodegenerative diseases, implying a common mechanism linking MM progression to protein misfolding disorders. Significantly, bortezomib-resistant MM cells exhibited cross-resistance to BEZ235, an inhibitor of dual PI3K/mTOR, indicating a four-fold rise in IC50 values, which suggests improved survival signaling and metabolic adaptability in resistance pathways. These results highlight the complex aspects of bortezomib resistance, fueled by metabolic reprogramming, modified immune interactions, and translational regulation. Focusing on these adaptive responses through combination treatments that include proteasome inhibitors, metabolic modulators, and autophagy inhibitors may offer innovative therapeutic approaches to tackle drug resistance in MM.

overall_design: RNA-seq profiling of NCI-BL2171,  RPMI-8226 and its Bortezomib resistant derivative RPMI-8226-R cells

first: Onur

last: Ates


title: Bulk RNA-seq of primary colonic epithelial cells treated with conditioned medium of either young or presenescent primary colonic fibroblasts

city: Suwon

first: Soon Sang

last: Park

address: Worldcup-Ro 206

country: South Korea

institute: Ajou University School of Medicine

overall_design: Primary colonic epithelial cells are treated with conditioned medium of either young or presenescent primary colonic fibroblasts

first: Young-Kyoung

last: Lee

first: Tae Jun


title: Interferon-γ mediated species-specific immune responses in macrophages to Mycobacterium tuberculosis

city: Greifswald - Insel Riems

first: Björn

last: Corleis

state: Mecklenburg-Western Pomerania

address: Südufer 10

department: Institute of immunology

institute: Friedrich-Loeffler-Institut

summary: "IFNγ drives antimicrobial responses in TB, mainly via iNOS induction in mouse macrophages, but its role in humans is unclear. We compared IFNγ responses to Mycobacterium tuberculosis across macrophages from multiple species using RNA-seq, bacterial assays, and functional analyses. Unlike mice, human macrophages lacked iNOS induction and failed to restrict Mtb. Only mouse and cattle monocytes showed iNOS activity. scRNA-seq identified airway epithelial cells as potential iNOS⁺ sources in humans.

overall_design: Transcriptomic analysis of human and murine macrophages stimulated with IFNy and infected with M. tuberculosis, investigating four conditions for each donor: untreated (CTR), only stimulated (IFNy), only infected (Mtb) and stimulated+infected (IFNyMtb).

first: Fabian

last: Stei

last: Zessin

first: Jonathan

last: Pioch

first: Stefan

last: Simm


title: A high-throughput transcriptomic profiling of fibroblasts treated with 0.0005 - 10 µM Omaveloxolone

first: Drishti

last: Guin

summary: Omaveloxolone, an Nrf2 activator, shows enrichment of pathways associated with cellular metabolism and energy production. Dose-dependent up-regulation of Nrf2 marker genes and of genes in the GOBP mitochondrial gene expression pathway was observed compared to vehicle treated wells.

overall_design: High-throughput transcriptomic profiling of wildtype fibroblasts treated with 0.0005-10 µM Omaveloxolone for 24 hours in 384-well plates.

first: Long

first: Katherine

last: Dyer

first: Nicole

last: Carvajal

first: Gabriel

last: Rivera Del Toro

first: Michael

last: Blanco

first: Natalie

last: Downs

last: Perfito

first: Ursula

last: Haditsch

first: Christopher

last: Moxham


title: RNA-seq of a Leigh Syndrome patient blood being treated with Omaveloxolone

summary: A patient diagnosed with Leigh Syndrome due to a compound heterizygous mutation in SURF1 (SURF1 c.312_321delinsAT (p.L105X); c.-13_11del24) was prescribed Omaveloxolone under physican supervision. Pre-treatment patient blood showed deficiency in pathways associated with oxidative phosphorylion and cellular energetics. Omaveloxolone normalized this phenotype via enrichment of these pathways. Enrichment of these pathways could be due to up-regulation of the master transcription factor PPARGC1A.

overall_design: The patient was prescribed Omaveloxolone by physician and transcriptomic changes were tracked by collecting and profiling patient blood using RNA-seq along with clinical testing. A control sample was collected pre-treatment and 7 post-treatment samples were collected for 10 months post dosing start.

last: Wu

first: Saima

last: Kayani


title: Decipherin molecular cues  from nephronopthisis using kidney organoids derived from iPSC

city: Paris

first: Damelys

last: Calderon

address: 24 boulevard du Montparnasse

country: France

institute: Institut Imagine

summary: To dissect the pathological mechanisms underpinning juvenile nephronophthisis, we utilized human induced pluripotent stem cells (hiPSCs) to interrogate tubular and ciliary architecture and to delineate the molecular consequences of NPHP1 deficiency. Kidney organoids lacking NPHP1 demonstrate that gene loss triggers a cascade of deleterious processes, encompassing disrupted primary ciliary signaling, defective autophagy, mitochondrial impairment, and metabolic perturbations. However, the temporal sequence of these events remains unresolved, as does the mechanistic pathway through which these cellular dysfunctions converge to increase inflammatory responses and fibrotic remodeling in NPHP -/- kidney organoids when compared to controls.

overall_design: RNA-seq profiling of wildtype (12G line)  and NPHP1-/- (11H line) kidney organoids at Day 25 and Day 38 of kidney differentiation protocol. Day 36 kidney organoids were treated or nor with IL1b (10ng/ml) for 48 hours.

first: Sophie

last: Saunier


title: Bulk RNA sequencing of quadricep in wildtype and Foxp3-DTR mice in synthetic material implant fibrosis

city: Baltimore

first: Jennifer

last: Elisseeff

state: MD

address: 1800 Orleans St

institute: Johns Hopkins

summary: 6 week VML with PCL implant whole quad bulksequencing of WT and Foxp3-DT. All mice received DT on day -1 and -3 to harvest.

overall_design:
Mice: Wildtype (WT) – C57BL/6J (Jackson Strain 000664) and DTR –Foxp3 DTR (B6.129(Cg)-Foxp3tm3(DTR/GFP)Ayr/J)(Jackson Strain 016958)
Injury: 6-week VML with PCL Implant
DT: 50 ng/g given -1 and -3 days before harvest
Tissue: Whole quadricep plus the PCL fibrosis

first: Joscelyn

last: Mejias

first: Anna

last: Ruta

first: David

last: Maestas

first: Kavita

last: Krishnan


title: Mechanisms of association with amoeba hosts are shared by Paraburkholderia symbionts amid differential responses based on evolutionary history

city: Waterville

first: Suegene

last: Noh

state: ME

address: 5717 Mayflower Hill

department: Biology

institute: Colby College

summary: In order to understand how Dictyostelium discoideum amoebas and Paraburkholderia symbionts establish symbiosis, we exposed amoebas to strains of symbionts from two clades and sequenced both host and symbiont RNA

sample_organism:
Dictyostelium discoideum
Paraburkholderia agricolaris
Paraburkholderia hayleyella
Paraburkholderia bonniea

overall_design: Three strains of Dictyostelium discoideum amoebas were each exposed to a strain of Paraburkholderia agricolaris, P. bonniea, or P. hayleyella. We collected samples at 22 hours post-exposure. Additional samples include hosts grown without symbionts and symbionts grown without hosts, both collected during log-phase growth.

first: Susanne

last: DiSalvo

last: Queller

first: Joan

last: Strassmann


title: RNA-seq of patient-derived glutamatergic neurons carrying Leigh Syndrome causing compound heterozygous mutations in the SURF1 gene treated with Omaveloxolone.

first: Drishti

last: Guin

summary: Leigh Syndrome (LS) is a rare, progressive mitochondrial encephalopathy that manifests in infancy or early childhood and is characterized by neurodevelopmental regression, brainstem and basal ganglia lesions, and premature mortality. At the molecular level, LS is driven by mutations that impair oxidative phosphorylation (OXPHOS), disrupting energy production in metabolically active tissues such as the brain, heart, and muscle. Among these, mutations in SURF1—a nuclear gene essential for cytochrome c oxidase (COX, Complex IV) assembly—are among the most common causes of nuclear-encoded LS. Omaveloxolone, an FDA-approved Nrf2 activator for Friedreich’s Ataxia, has recently gained attention for its neuroprotective properties across a range of preclinical models. Treatment of patient neurons with omaveloxolone promoted neurite outgrowth, and activated PINK1/PRKN-mediated mitophagy. Functionally, omaveloxolone reduced neuronal hyperexcitability and apoptosis, and normalized aberrant synaptic pathway activity via deactivation of the SNARE complex.

overall_design: Patient- and a familial control-derived glutamatergic neurons were treated with a vehicle control (DMSO) and 125, 250 and 500 nM Omaveloxolone.

first: Long

first: Katherine

last: Dyer

first: Nicole

last: Carvajal

last: Rivera Del Toro

last: Blanco

last: Downs


title: RNA Sequencing of Lung Tissue in FTO-Overexpressing Mice Modeling Chronic Obstructive Pulmonary Disease

city: nanning

first: Hai-Guang

last: Xu

address: shuangyong

institute: The First Affiliated Hospital of Guangxi Medical University

summary: Fat mass and obesity-associated protein (FTO) is linked to various diseases; however, its role in COPD remains unclear. We previously found that the expression level of FTO was significantly decreased in COPD models. To explore the downstream target genes and pathways of FTO, we conducted RNA sequencing on lung tissues from wild-type and FTO-overexpressing mice exposed to cigarette smoke. Here, we report that FTO plays a crucial role in regulating inflammation in COPD. We demonstrated that FTO expression can modulate several pathways, including the PI3K-Akt and MAPK signaling pathways, which are associated with inflammation. Transcriptomic analysis further revealed FTO-dependent alterations in genes associated with inflammation. Overall, our study enhances the understanding of the molecular mechanisms by which FTO contributes to the regulation of inflammation in COPD.

overall_design: RNA-seq profiling of lung tissue from wild-type and FTO-overexpressing mice exposed to cigarette smoke

first: Jia-Yuan

last: Liang

first: Chen-Yang

last: Luo

first: Shuang

last: Zhang

first: Qiao-Li

last: He

first: Zhi-Yi


title: Multi-omics unveils GTSE1 promotes esophageal squamous cell carcinoma stemness via Hippo signaling pathway

city: chengdu

first: yujie

last: xie

address: No. 37 Guoxue Lane, Wuhou District, Chengdu City, Sichuan Province

institute: West China Hospital, Sichuan University

summary: Cancer stem cells (CSCs) are pivotal in driving tumorigenesis, metastasis, and resistance to multiple drugs in cancer. In esophageal squamous cell carcinoma (ESCC), CSCs are crucial for disease progression. This investigation sought to pinpoint genes associated with stemness and elucidate the impact and underlying mechanism of GTSE1 on ESCC stemness. The analysis of mRNAsi in bulk RNA-seq and single RNA-seq data reveals elevated expression of GTSE1 in the high mRNAsi subgroup and clusters of highly malignant single cells. Functional studies demonstrate that depletion of GTSE1 hinders self-renewal and tumor progression of ESCC both in vitro and in vivo. Our multi-omics analysis reveals GTSE1 as a novel gene associated with stemness.

overall_design: RNA-seq analysis was performed to identify dysregulated mRNA and lncRNAs in ESCC tissue samples.The RNA-seq analysis cohort consisted of 20 patients, all presenting with T2 stage primary tumors. Within this group, 10 patients exhibited lymph node metastasis (LNM+), while the remaining 10 were free of metastasis (LNM-).

first: Yujie

last: Xie

first: Dongmei

last: Lai

first: Hao

last: Hu

first: Qinghua

last: Zhou

first: Bijun

last: Huang


title: Transcriptome profiling of wild-type C. elegans and strains expressing wild-type or G2019S-mutant human LRRK2

city: luzhou

first: chun

last: li

state: sichuan

address: No. 182 Chunhui Road, Longmatan District

institute: the Affiliated Traditional Chinese Medicine  Hospital of Southwest Medical University

summary: This study presents RNA sequencing data from Caenorhabditis elegans strains expressing human wild-type or G2019S-mutant LRRK2 in a pan-neuronal manner, as well as wild-type control animals. Samples were collected to investigate the transcriptomic effects of LRRK2 expression and mutation on aging-related biological processes. Total RNA was extracted from synchronized animals, and libraries were sequenced using the Illumina NovaSeq 6000 or MGISEQ-T7 platform. Clean reads were aligned to the C. elegans reference genome (WBcel235), and gene expression levels were quantified as FPKM.

overall_design: We performed gene expression profiling analysis using data obtained from RNA-seq of N2 wild-type worms, WLZ1 worms with pan-neuronal expression of human wild-type LRRK2, and WLZ3 worms expressing the G2019S LRRK2 mutant.

first: Chun

last: Li

first: Fuyi

last: Shi

first: Xuanxuan

first: Shiying

last: Xiong

last: Gu

first: Guisheng

last: Wu

first: Chen

first: Huairong


title: Single-Cell RNA-Seq Reveals Effects of Leukemia–Derived Exosomes on Hematopoietic Stem Cells

city: Indiana University

first: Reza

last: Shahbazi

address: 980 W Walnut st

institute: Indiana University

summary: Leukemia-derived exosomes are emerging as key modulators of the bone marrow microenvironment. In this study, we used single-cell RNA sequencing to characterize the impact of leukemia exosomes on hematopoietic stem cells (HSCs). Our results reveal that exosome-treated HSCs exhibit transcriptional signatures associated with impaired self-renewal, altered lineage commitment, and disrupted quiescence. Pathway analysis highlighted activation of inflammatory and stress-response pathways, suggesting that leukemia exosomes reprogram HSC function to favor leukemic progression. These findings provide mechanistic insight into how leukemia-derived extracellular vesicles contribute to hematopoietic dysfunction and disease propagation.

overall_design: CD34⁺ hematopoietic stem and progenitor cells (HSPCs) were isolated from healthy human peripheral blood and cultured under standard conditions. Cells were divided into eight experimental groups: one untreated control group and seven groups treated with exosomes derived from leukemia cell lines; HL-60, MOLM-14, Jurkat, K562, RS4;11, CCRF-CEM, and MOLT-4. Exosomes were isolated using standard ultracentrifugation and purification protocols, and their non-coding RNA (ncRNA) cargo was profiled via high-throughput sequencing to characterize their molecular content. CD34⁺ cells were treated with leukemia-derived exosomes for 48 hours. Following treatment, single-cell Cellular Indexing of Transcriptomes and Epitopes by sequencing (CITE-seq) was performed to assess transcriptomic and surface protein alterations in hematopoietic stem and progenitor cells across all groups.

first: Samaneh

last: Maleknia

first: Sanam

last: Rezaei Benam


title: DNA-PKcs-dependent Non-homologous End Joining Repair Contributes to Ferroptosis Inhibition

city: Hangzhou

first: Min

address: Yuhang

department: School of Public health and Nursing

institute: HangZhouNomal University

summary: Iron-dependent ferroptosis, characterized by the accumulation of lethal lipid peroxidation, plays a critical role in various pathological conditions. Given the limited pharmacological options for inhibiting ferroptosis, there is an urgent need to identify novel ferroptosis inhibitors. Natural plant products, with their structural diversity and complexity, represent a promising source for drug discovery.

overall_design: Through previous systematic screening of natural compounds for anti-ferroptotic activity, we identified Licochalcone A (LA), a flavonoid derived from the root of Glycyrrhiza uralensis, as a potent ferroptosis inhibitor. Our study uncovers a novel mechanism through which LA inhibits ferroptosis: as a downstream target of LA, the transcription factor SP1 is activated and subsequently upregulates its target gene PRKDC, which in turn suppresses ferroptosis by enhancing DNA-PKcs-mediated non-homologous end joining (NHEJ) repair. This mechanism highlights the critical role of LA in mitigating liver ischemia-reperfusion injury by targeting ferroptosis and DNA damage repair pathways. These findings not only deepen our understanding of the interplay between ferroptosis and DNA damage repair but also establish LA as a promising candidate for the prevention and treatment of ferroptosis-related diseases. Taken together, our study provides a strong theoretical foundation for the development of LA-based therapies, offering new insights into its potential clinical applications.

first: Lulu

last: Lu

first: Zhangqi

last: Mao

first: Huanhuan

last: xu

first: Yi

last: Guo

first: Jun

last: Yang

first: Yingying

last: yu


title: Microglial TIA1 in Lateral Septum Facilitates Chronic Inflammatory Pain via Regulating NF-κB Signaling Pathway

first: Furui

last: Liu

address: Yuhangtang

institute: Hangzhou Normal University

summary: Microglia, the resident immune cells of the central nervous system, have emerged as pivotal players in chronic pain pathogenesis, yet their brain region-specific contributions and molecular underpinnings remain poorly defined. Here, we identified microglial T-Cell Intracellular Antigen 1 (TIA1) in the lateral septum (LS) as a critical driver of chronic inflammatory pain via modulation of the NF-κB signaling pathway. Using a Complete Freund’s Adjuvant (CFA)-induced pain mouse model, we found that microglia exhibited most heightened activation in LS compared to other brain regions, and RNA sequencing further found that dysregulation of NF-κB-related genes and RNA metabolic process in the LS in CFA-induced mice. Mechanistical studies showed that TIA1 (an RNA-binding protein) facilitated pain by binding to IκBα mRNA to suppress its translation, subsequently enabled NF-κB activation. Conditional knockout (CKO) of microglial TIA1 (TIA1CX3CR1-CKO) in mice significantly elevated pain threshold, pain thresholds was normalized while restoring IκBα expression in LS microglia of TIA1CX3CR1-CKO mice. Pharmacological inhibition of NF-κB phenocopies the analgesic effects of TIA1CX3CR1-CKO, while IκBα is forcibly degraded degradation in CKO mice restores pain sensitivity and NF-κB activity. Taken together, our findings establish microglial TIA1 in the LS as an RNA-operated switch controlling chronic pain through NF-κB-dependent neuroinflammation and synaptic dysregulation, proposing the TIA1-NF-κB axis as a therapeutic target.

overall_design: The differential genes between saline injection control group and CFA injection experimental group were detected.

first: Hongyan

first: Ziwan

last: He

first: Ruiyi

last: Wang

first: Yue

first: Zhihui

first: Yongjie


title: Small activating RNA AW1-51 (CEBPA-51) elicits targeted DNA demethylation to promote gene activation [EPIC array]

city: Boston

first: Annalisa

last: Di Ruscio

state: Massachusetts

address: 3 Blackfan Circle

institute: Harvard Medical School Initiative for RNA Medicine

type: Methylation profiling by genome tiling array

summary: Small activating RNAs (saRNAs), are short double-stranded RNAs designed to upregulate transcription of target genes. By this virtue, they can be used to restore expression of genes frequently silenced in cancer. AW1-51 (also referred to as CEBPA-51), the first saRNA therapeutic to enter clinical evaluation, has demonstrated biological activity and safety in Phase II trials for hepatocellular carcinoma, both as monotherapy and in combination with sorafenib, and in Phase 1a/1b in combination with pembrolizumab for patients with advanced solid tumors. It targets the master regulator CCAAT enhancer-binding protein alpha (CEBPA), abnormally silenced by DNA methylation in a wide range of hematological and not hematological malignancies. However, the molecular events enabling this mechanism are only partially elucidated. In this study, we uncovered the molecular basis for AW1-51-induced transcriptional reactivation of CEBPA demonstrating that by directly promoting DNA demethylation of CEBPA promoter restores CEBPA expression, protein synthesis, and consequently cell differentiation. These findings unveil AW1-51 as a prototype for RNA-based precision medicine enabling conditional expression of CEBPA in diseases characterized by aberrant gene silencing and extending its potential therapeutic impact beyond cancer.

overall_design: Diagenode EPIC array analysis of K562 and A549 cell lines after AW1-51 saRNA or a non targetting saRNA (NC) 72h after treatment

first: Lucrezia

last: Rinaldi

first: Juan Rodrigo

last: Patiño-Mercau

first: Giulia

last: Gaggi


title: Immunopeptidome-guided personalized peptide vaccines induce potent T cell response in chronic lymphocytic leukemia

city: Freiburg

first: Ariane

last: Lehmann

address: Breisacher Strasse 153

department: IBSM

institute: Medical Center Freiburg

summary: T cell immunity is central for the control of malignant disease. Chronic lymphocytic leukemia (CLL) lacks mutation-derived T cell neoantigens, yet harbours frequent tumor-associated antigens as targets for therapeutic vaccine design. iVAC-XS15-CLL01 is a warehouse-based personalized muli-peptide vaccine of immunopeptidome-defined CLL-associated antigens. We report the results of an open-label phase I trial evaluating the safety, immunogenicity and first efficacy of iVAC-XS15-CLL01 in 20 CLL patients who achieved partial remission under bruton’s tyrosine kinase inhibitor treatment. Vaccination was well tolerated and induced potent T cell response in 95% of patients, targeting multiple vaccine peptides. CLL-specific T cell responses were mediated by polyfunctional T helper 1 CD4+ and CD8+ T cells and persisted until 6 month follow up. Minimal residual disease reduction (median 50%) was observed in 90% of patients and correlated with vaccine-induced T cell response, providing first evidence of iVAC-XS15-CLL01’s clinical efficacy, warranting its further evaluation in an upcoming phase II trial.

overall_design: PBMCs of study participants were isolated on day 1 prior to vaccination (baseline) and at month 3 (EOT) after three doses of iVAC-XS15-CLL vaccine. Cells were either unstimulated or in vitro expaned with the patient-individual vaccine cocktail. T cells were enriched by magnetic cell separation using the Pan T Cell Isolation Kit.

first: Jonas S.

last: Heitmann

first: Yacine

last: Maringer

first: Susanne

last: Jung

first: Marcel

last: Wacker

first: Christopher

last: Hackenbruch

first: Mark

last: Polster

first: Maddalena

last: Marconato

first: Annika

last: Nelde

first: Jens

last: Bauer

first: Melissa

last: Zwick

first: Anna-Sophia

last: Baur

last: Krolla

first: Natalie

last: Köhler

first: Melanie

last: Börries

first: Monika

last: Denk

first: Lisa

last: Zieschang

first: Christine

last: Kammerer

first: Naomi

last: Hoenisch-Gravel

first: Marion

last: Richter

first: Melek Tutku

last: Oezbek

first: Anna

last: Dengler

first: Marissa L.

last: Dubbelaar

first: Marina

last: Pumptow

first: Peter

last: Martus

last: Brüggemann

first: Hans‑Georg

last: Rammensee

first: Helmut R.

last: Salih

first: Juliane S.

last: Walz


title: TRIP13 Promotes the Expansion and Immunosuppression of CD4+Foxp3+ Regulatory T Cells by Sustaining HAT1 Stability

city: Nantong

first: Liwen

last: Zhao

address: 9 Seyuan Road

institute: Nantong University

summary: There is compelling evidence that TNF preferentially activates and expands CD4+Foxp3+ regulatory T cells (Tregs) through TNFR2. However, the precise mechanisms underlying TNF-TNFR2 pathway-mediated Treg proliferation remain to be fully elucidated. In this study, using RNA-seq profiling of TNFR2+ and TNFR2-deficient Treg cells, we identified that Trip13 is required for promoting TNF-TNFR2 pathway-mediated Treg expansion. Mechanistically, TRIP13 inhibited UBE4A-mediated ubiquitination degradation of HAT1 by directly binding to HAT1, thereby competing with UBE4A and promoting Treg expansion. In addition, TRIP13’s ATPase activity was essential for its binding to HAT1, which promoted Treg expansion by increasing Foxp3 expression. In a mouse colitis model, TRIP13 overexpression markedly alleviated colon inflammation by enhancing Treg expansion, an effect that was reversed by HAT1 knockdown. Conversely, genetic ablation of TRIP13 substantially reversed the effects induced by HAT1 overexpression, including enhanced Treg expansion and attenuation of colitis. These findings illustrate the TRIP13/HAT1 axis-mediated mechanism for TNF-TNFR2-induced Treg expansion and indicate that targeting TRIP13 may offer therapeutic potential for autoimmune and inflammatory diseases.

overall_design: we compared differentially expressed genes between TNFR2-deficient Treg cells and TNFR2+ Treg cells based on RNA-seq analysis

first: Tianzhen

last: He

first: Yong-Jing

last: Gao


title: RSK1 reprograms the ubiquitin pathway to promote immune suppression

city: Shanghai

first: LAN

last: FANG

address: 1239 Siping Road

institute: Tongji University

summary: Although immune checkpoint blockade (ICB) is an effective therapeutic strategy, tumor intrinsic resistance to ICB limits its benefits for a majority of cancer patients. Via multiple in vivo screens, we identified RNF19A as an immune-suppressor. RNF19A suppresses ICB efficacy by ubiquitinating cGAS to inhibit the release of type I interferon. Surprisingly, UBE2L6, originally identified as a critical interferon-induced ISG15-conjugating E2 enzyme for ISGylation, functions as the major ubiquitin-conjugating E2 enzyme to enable RNF19A-driven cGAS ubiquitination. Further, RSK1 phosphorylates UBE2L6 to switch its substrate from ISG15 to ubiquitin, thus converting it from an immune response enhancer to a suppressor. In xenograft models, targeting RSK1 or blocking UBE2L6 phosphorylation improves immune response. In patient tissues, the levels of UBE2L6 and its phosphorylation correlate with poor immune infiltration, limited immune and radiation therapy response, and prognosis. Taken together, we demonstrate that RSK1-mediated UBE2L6 phosphorylation and UBE2L6-RNF19A-driven cGAS ubiquitination lead to tumor-intrinsic immune suppression.

overall_design: RNA-seq profiling of sgNC and sgRnf19a B16F10 cells with or without IR treatment


title: Nanoparticles alter the inflammatory landscape of spinal cord injury and attenuate injury severity

city: Ann Arbor

first: Lonnie

last: Shea

address: 1600 Huron Pkwy

institute: University of Michigan- Ann Arbor

summary: Trauma to the spinal cord results in initial damage to the spinal cord and initiates an inflammatory response that causes secondary damage, which collectively can result in loss of function below the level of the injury. The unbalanced risk-benefit-ratio of methylprednisolone led to our development of nanoparticles that associate with circulating monocytes and neutrophils to reduce inflammation and secondary damage. Herein, we investigate the mechanisms by which NPs directly and indirectly modulate the phenotype and trafficking of monocytes and neutrophils, and how altering the inflammatory cascade leads to mechanisms that promote a regenerative environment. Using adoptive transfer of cells to monitor trafficking, NP treatment reduced the extent of myeloid cell recruitment to the injury, yet did not impact the composition of adoptively transferred monocytes or neutrophils. The proportion of inflammatory monocytes was reduced with nanoparticle treatment, and single cell sequencing analysis indicated increased polarization towards an M2-like phenotype. Sequencing analysis also demonstrated that the outgoing signals from the monocytes and neutrophils influenced the phenotype of numerous cell types, including endothelial cells, fibroblasts, oligodendrocyte progenitor cells, and Schwann cells. This signaling between the cell compartments involves a combination of soluble and matrix signals, with NP treatment enhancing expression of genes associated with anti-inflammatory phenotypes, angiogenesis, neuroprotection, and promotion of axon outgrowth or decreasing expression of inhibitors to regeneration. Collectively, NP delivery leads to direct and indirect effects on monocytes and neutrophils, which subsequently influence gene expression and intercellular signaling networks that promote a growth-permissive environment.

overall_design: Female 6–8-week-old C57Bl/6 mice (Jackson) were used for all experiments. A C5 lateral hemisection was performed as previously described (ref). A porous, multichannel PLG was inserted into the injury cavity. Post-operative care consisted of buprenorphine (0.1 mg/kg) twice daily for 3 days, enrofloxacin (2.5 mg/kg, Bayer, Leverkusen, Germany) daily for 14 days, and lactated ringers’ solution (1 mL, MWI Veterinary Supply, Boise, ID) daily for 5 days.

first: Kate

middle: V

last: Griffin

first: Sarah

last: Hocevar

first: Samantha

last: Schwartz

first: Brooke

last: Smiley

first: Brian

last: Ross

first: Kalana

middle: S

last: Athukorala

first: Michael

last: Saunders

first: Aileen

last: Anderson

last: Cummings


title: Analysis of gene expression in SKBR3 cells isolated from xenograft tumors in mice treated with radioinducible TNF producing CAR-T cells

city: Chicago

first: CRI

last: Bioinformatics

state: IL

address: 5801 S. Ellis Ave.

institute: University of Chicago

summary: Adoptive CAR T cell therapies have limited efficacy in solid tumors due to poor infiltration and impaired effector function, while radiotherapy is constrained by tumor radio resistance and  metastatic spread. To overcome these limitations, we developed a strategy that integrates the spatial precision of ionizing radiation with the biological specificity of CAR T cells. We identified radiation-induced genes from irradiated intratumoral T cells and engineered synthetic radio inducible promoters to drive expression of a prototype effector, TNF. Human CAR T cells expressing this construct (riTNF CAR T) secreted high levels of TNF upon irradiation, independently of antigen engagement. In in vivo models of HER2⁺ and FRα⁺ human xenograft tumors, the combination of riTNF CAR T cells with local irradiation resulted in significantly greater tumor regression than either treatment alone or the combination of standard CAR T cells with irradiation. To study the antitumoral mechanisms involved in treatment with riTNF CAR-T cells, we sorted cancer cells from xenograft tumors after treatment and analyzed changes in gene expression caused by riTNF CAR-T therapy vs control treatments.

overall_design: RNAseq profiling in SKBR3 human breast cancer cells sorted ex vivo from xenograft tumors established in NSG mice, after treatment with riTNF Her2 CAR-T cells or control riGFP Her2 CAR-T cells plus/minus radiation, radiation alone or no treatment.

first: Elham

last: Masoumi

first: Paulina

last: Walczak

first: Takemasa

last: Tsuji

first: Edurne

last: Luque

first: Agnes Julia

last: Bilecz

first: Junko

last: Matsuzaki

first: Christian

last: Fernandez

first: Kunle

last: Odunsi

first: Ralph

last: Weichselbaum

first: Ainhoa

last: Arina


title: Runx1+23 enhancer reporter expression in hESC differentiation

city: Kalamazoo

first: Momoko

last: Yoshimoto

state: MI

address: 300 Portage St.

department: Investigative Medicine

institute: WMU Homer Stryker MD School of Medicine

summary: We introduced Runx1+23 enhancer DsRed reporter into human H9 ESC line and examined DsRed expression during ESC differentiation.

overall_design: We differntiated Runx1+23enh H9 ESCs into blood lineage using Laminin511 coated dish. On day 10 of differentiation culture, we collected all cultured cells and sorted CD34+ and/or CD43+ cells, and submitted them for 10X scRNA-seqnencing to examine gene expression profiles of Runx1+23enh+ or - cells.

first: Michihiro

last: Kobayashi


title: Decoding SOS: eIF2B as a Key Driver of Mutant KRAS Signaling and Tumorigenesis [RNA-seq]

city: Montréal

first: Antonis

last: Koromilas

state: QC

address: 3755 Chem. de la Côte-Sainte-Catherine

institute: Lady Davis Institute - McGill University

summary: Beyond its established guanine exchange function (GEF) in regulating mRNA translation initiation, we demonstrate that eIF2B forms a unique complex with mutant, but not wild-type, KRAS and Son of Sevenless (SOS) in tumors, specifically when KRAS is in its active, GTP-bound state. Mechanistically, the catalytic eIF2Bε subunit binds to the allosteric RAS binding domain of SOS in complex with mutant KRAS, thereby enhancing KRAS GTP loading and activation. The eIF2Bε subunit, SOS and mutant KRAS complex localizes to the plasma membrane (PM), where it enhances the mutant KRAS activity and MAPK pathway signaling. In parallel, the translational function of eIF2B plays a key role in the upregulation of the glycosphingolipid (GSL) pathway, thereby promoting the localization and clustering of mutant KRAS at the PM. Genetic inactivation of eIF2Bε subunit significantly reduces the growth of mutant KRAS-driven tumors in both xenograft models and an autochthonous mouse model of lung adenocarcinoma. Notably, increased expression of the catalytic eIF2Bε subunit correlates with poor prognosis in human cancers harboring KRAS mutations. These findings reveal a previously unrecognized link between a core component of mRNA translation machinery and oncogenic KRAS function, offering new mechanistic insight and potential therapeutic avenues in mutant KRAS-driven malignancies.

overall_design: To assess the broader functional impact of eIF2Bε silencing in the context of oncogenic KRAS, we independently performed RNA-Seq in H358, H1703, and the KRAS G12C pancreatic cancer cell line Mia-PaCa-2.

first: Hyungdong

last: Kim

first: Shiqi

last: Diao


title: Longitudinal transcriptomic analysis of SIV-infected rhesus macaques reveals peripheral immune dynamics throughout untreated SIV infection and long-term antiretroviral therapy

city: Cambridge

first: Alex

last: Shalek

state: MA

address: 77 Massachusetts Ave

institute: Massachusetts Institute of Technology

summary: Developing a working knowledge of immune dynamics during prolonged infection and treatment has become critical for both advancing HIV cure strategies and understanding non-AIDS comorbidities, given rises in the age and average time spent on antiretroviral therapy (ART) among people living with HIV. However, at present, we do not fully appreciate the ways in which prolonged suppressive therapy influences immune function. Toward addressing this key knowledge gap comprehensively, we applied single-cell RNA-sequencing (scRNA-seq) to longitudinally profile peripheral blood mononuclear cells from SIV-infected non-human primates longitudinally. Our data reveal significant immune shifts during acute and chronic infection, as well as over five years of subsequent ART. We observe a decline in CD4+ T cells and an increase in aberrant B cells and CD16+ monocytes during untreated chronic infection, as well as widespread dampened transcriptional activity. Further, we uncover transcriptional signatures suggestive of unresolved immune dysregulation during long-term suppressive therapy – most prominently among myeloid cell populations. By examining concurrent measurements of intact proviral DNA, we link peripheral responses to reservoir size via IPDA. We furthermore identify ribosomal-associated pathways as key differentiators of infection stage, treatment status, and time on ART. Finally, we tested whether previously published transcriptional correlates of differential outcomes (e.g. viral rebound, vaccine efficacy) changed over time on ART. Overall, our findings capture dynamic immune remodeling from acute infection through long-term ART, highlighting complexities in achieving complete immune recovery that may influence future therapeutic strategies.

overall_design: PBMCs from a longitudinal cohort of five rhesus macaques during SIV infection and subsequent ART treatment were processed via SeqWell S3 and sequenced. PBMCs from an additional three control rhesus macaques were processed in parallel with the longitudinal cohort.

first: Sarah

middle: L

last: Quinn

first: Micayla

last: George

first: John

last: Ventura

first: Emily

last: Fray

first: Malika

last: Aid

first: Victoria

last: Walker-Sperling

first: Janet

last: Siliciano

first: Robert

first: Son

last: Nguyen

first: Dan

middle: H

last: Barouch


title: Bulk RNA-seq of human IPS-derived MNs treated with peptides

first: Xiaoyang

last: Chen

state: Shanghai

address: No. 393, Huaxia Middle Road, Pudong New Area, Shanghai

department: School of life science and technology

institute: shanghaitech university

summary: In order to figure out the effects of peptides on motor neurons and intervention efficacy in diseases, two human IPS-derived MNs were treated with different concentrations(0nM/250nM/500nM) of peptides for 48h.

overall_design: LJH is obtained from a 67-year-old healthy male, while CMF is obtained from a 17-year-old ALS patient with FUS mutation.The numbers following the characters represent the treatment duration and concentration, and the numbers after the `-` are used to distinguish the replication.For example, `LJH48500-1`means MNs derived from healthy donor and treated with 500nM peptides for 48h, replication 1.


title: Decoding SOS: eIF2B as a Key Driver of Mutant KRAS Signaling and Tumorigenesis [Ribo-seq]

overall_design: To dissect the role of eIF2B in mRNA translation, we performed paired ribosome profiling (Ribo-Seq) and RNA-Seq in the lung adenocarcinoma (LUAD) cancer cell lines H358 (KRAS G12C) and H1703 (KRAS wild-type) following knockdown of the catalytic eIF2Bε subunit using specific shRNAs or non-targeting controls.


title: Single-cell transcriptomic and TCR profiling of peripheral double-positive T cells in healthy human blood [scRNA-seq]

city: Seoul

first: Yunjung

last: Cho

address: 73, Goryeodae-ro, Seoulbuk-gu

department: Department of Laboratory Medicine

institute: Korea University Medicine

summary: CD4+CD8+ double-positive T (DPT) cells are typically associated with thymic development but have also been observed in peripheral blood under physiological and pathological conditions. However, their identity, functional significance, and developmental origin in the periphery remain poorly defined. This project was conducted to comprehensively characterize peripheral DPT cells in healthy human donors using single-cell transcriptomic and T cell receptor (TCR) profiling.  We aimed to define the molecular features that distinguish peripheral DPT cells from conventional single-positive CD4+ and CD8+ T (SPT) cells. Through the integration of single-cell RNA sequencing and paired TCR sequencing, we explored their transcriptional profiles, clonal architecture, and potential developmental trajectories. This allowed us to uncover unique gene expression patterns and TCR usage biases that suggest peripheral DPT cells represent a distinct, stable T cell subset rather than a transient or intermediate population.  In addition, we developed a machine learning-based classifier that can accurately distinguish DPT cells from conventional T cell subsets using transcriptomic features. This approach enabled the identification of key marker genes and molecular pathways underlying the functional specialization of DPT cells.  This dataset provides a valuable resource for the immunology community to further investigate peripheral DPT cells in health and disease. Generated from healthy individuals, it serves as a high-quality reference map of normal peripheral T cell states. In our study, this dataset was further integrated with publicly available single-cell datasets derived from patients with immune-related diseases, enabling comparative analyses to explore how the transcriptional identity and abundance of DPT cells may be altered under pathological conditions. By making this healthy reference dataset publicly available, we aim to support future investigations into T cell heterogeneity, immune dysregulation, and disease-specific perturbations of the T cell compartment.

overall_design: Peripheral blood mononuclear cells (PBMCs) were isolated from healthy human donors by Ficoll-Paque density gradient centrifugation. CD3 memory CD4 and CD8 T cells were enriched using magnetic-activated cell sorting (MACS) to reduce contamination from non-T cells. Approximately 10,000 cells per sample were loaded for single-cell immune profiling using the Chromium Next GEM Single Cell Immune Profiling v2 Kit (10x Genomics). Single-cell RNA sequencing libraries were prepared according to the manufacturers protocols. Libraries were sequenced to generate paired-end reads for gene expression analysis.

first: Eunji

last: Shin

first: Seung Gyu

last: Yun


title: Development of a novel peripherally acting alpha2A- adrenergic receptor antagonist for anti-diabetic

city: Shenzhen

first: 丰

last: 洪

address: Shenzhen Institute of Advanced Technology

summary: Studies have consistently highlighted the role of the alpha2A-adrenergic receptor (α2AAR) in the pathophysiology of type 2 diabetes (T2D), particularly its contribution to impaired insulin release and β-cell dysfunction. Yohimbine, a potent α2AAR antagonist, has shown therapeutic potential for T2D by improving insulin release, but its clinical application has been limited by central nervous system (CNS) side effects. In this study, we developed a novel, peripherally acting α2AAR antagonist (CDS479-2) using molecular docking analysis and a bioisosteric replacement strategy applied to yohimbine`s structure. cryo-EM structures of α2AAR bound to either yohimbine or CDS479-2 confirm the molecular basis of α2AAR antagonism, validate our docking models, and reveal key ligand-receptor interactions for future drug design. Importantly, animal studies demonstrated that acute administration of CDS479-2 effectively lowered blood glucose and improved glucose tolerance in diabetic mice, without central side effects such as anxiety or blood pressure elevation commonly associated with α2AAR antagonism. Remarkably, once-daily administration of CDS479-2 for 2 weeks resulted in sustained normoglycemia and increased pancreatic β-cell density in diet-induced obese (DIO) mice, with upregulation of key genes involved in β-cell maturation and proliferation. These findings suggest that CDS479-2 represents a promising new approach for the treatment of T2D. Furthermore, the strategy we employed here may serve as a model for optimization for other drugs that with both peripheral and central targets.

overall_design: Mice were anesthetized with isoflurane, and collagenase V (10 mg/ml) was injected retrogradely from the pancreatic duct into the pancreas. After digestion for 20 mins at 37 ℃, the pancreatic tissues were collected and placed in pre-cooled Hank's solution to terminate the digestion. The tissues were then transferred to a petri dish, and intact islets were isolated under a stereomicroscope. Single cells were subsequently prepared according to the 10x Genomics Single Cell Protocol.

first: Feng

last: Hong

first: Zuxin


title: ATGL-driven lipolysis defines a targetable metabolic vulnerability in PSMA-high prostate cancer

city: Vienna

first: Gerda

last: Egger

address: Waehringer Guertel 18-20

department: Pathology

country: Austria

institute: Medical University of Vienna

type: Methylation profiling by high throughput sequencing

summary: Prostate-specific membrane antigen (PSMA) is a validated biomarker and therapeutic target in prostate cancer, yet its biological functions remain incompletely understood. Using PSMA-Positron Emission Tomography imaging-guided sampling, we performed integrated proteomic and epigenetic analyses of PSMA-high versus PSMA-low areas within primary prostate tumors, revealing an association between high PSMA expression and lipolytic metabolic reprogramming. This reprogramming was characterized by increased adipose triglyceride lipase (ATGL) protein expression, accompanied by promoter hypomethylation of its encoding gene PNPLA2. We validated the PSMA-ATGL correlation in an independent cohort of 90 treatment-naïve prostate cancer patients (r=0.74, P<0.0001). Metabolic profiling of prostate cancer cell lines revealed that PSMA-high cells exhibit pronounced fatty acid oxidation dependency for mitochondrial respiration. Pharmacological inhibition of ATGL using NG-497 selectively impaired the viability of PSMA-high, metabolically inflexible LNCaP cells while metabolically flexible 22RV1 cells showed relative resistance. Our findings establish ATGL-driven lipolysis as a targetable metabolic vulnerability in PSMA- and ATGL-expressing prostate cancer, providing a biomarker-driven therapeutic strategy for metabolically vulnerable tumors.

overall_design: Reduced representation bisulfite sequencing (RRBS) of primary prostate cancer samples separated into two groups according to PSMA-high and PSMA-low expressing tumor areas.

first: Andreas

last: Tiefenbacher

first: Madeleine

last: Gudenus

first: Raheleh

last: Sheibani-Tezerj

first: Theresa

last: Mendrina

first: Daniel

last: Valcanover

first: Jessica

last: Kalla

first: Laura

last: Pajed

first: Kristina

last: Draganić

first: Andrea

last: Haitel

first: Astrid

last: Haase

first: Barbara

last: Neudert

first: Markus

last: Hartenbach

first: Sasan

last: Razul

first: Walter

last: Berger

first: Rolf

last: Breinbauer

first: Gernot

last: Grabner

first: Martina

last: Schweiger

first: Eva

last: Compérat


title: Multi-omics study of small Intestine adaptation after total colectomy.

first: yi

last: luo

address: 1111XianXia Road

institute: department of surgery,Tongren Hospital,Shanghai Jiao Tong University School of Medicine

summary: Transcriptomic Evidence of Colonic Metaplasia To compare whether total colon resection leads to gene changes in the ileal anastomosis site, we performed transcriptome analysis of the preoperative small intestine, preoperative colon, and 16-week postoperative anastomosis site of the small intestine [32]. Through the analysis, we found significant differences in gene expression between the preoperative small intestine and colon (Figure 3A and B). Furthermore, we observed changes in gene expression at the anastomosis site, where the gene expression profile shifted from typical small intestine genes to colon genes (Figure 3C and D), indicating further evidence of colonic metaplasia at the anastomosis site after TC surgery, which leads to gene expression alterations at the anastomosis site.

overall_design: RNA preparation and RNA-seq analysis Total RNA was isolated from ileum tissue using TRIzol reagent (Invitrogen) following the manufacturer's instructions. The quantity and quality of the total RNA were evaluated using a NanoDrop1000 spectrophotometer (Thermo Scientific, Wilmington, DE, USA) and a Bioanalyzer 2100 (Agilent Technologies, Palo Alto, CA, USA). RNA with an OD260/280 ratio between 1.8-2.2 and an RNA integrity number (RIN) greater than 7 was considered suitable for further analysis. The mRNA in the total RNA was converted into appropriate template libraries using the reagents provided in the Illumina® TruSeq™ RNA Sample Preparation Kit. Specifically, the mRNA was first purified, then fragmented into small pieces. These fragments were reverse transcribed into first-strand cDNA, and then the second strand of cDNA was synthesized to create double-stranded cDNA constructs. The short ds-cDNA fragments were ligated with sequencing adapters, and size selection was performed using agarose gel electrophoresis to obtain fragments with an insert size of 150-180 bp. Subsequently, the TruSeq RNA libraries were amplified by PCR and quantified using real-time quantitative PCR (qPCR) according to the qPCR Quantification Protocol Guide. The quality of the libraries was further validated using the Agilent 2100 Bioanalyzer. The generated RNA libraries were sequenced using the HiSeq™ NextSeq 500 platform (Illumina) with paired-end sequencing, where the read length was 101 bp. For data analysis, the RNA-seq reads were first processed using Trimmomatic (v 0.32) to remove adapters and trim low-quality bases, generating clean reads. These clean reads were then mapped to the Sus scrofa reference genome in the Ensembl database (Sscrofa 11.1) using hisat2 (v 2.1.0). Finally, the unique mapped read counts for 25,880 annotated genes in each sample were predicted based on the Sus scrofa transcript annotation format (GTF) using the featureCounts method in the SUBREAD package (v 1.6.0) [24].

first: Yi

last: Luo

first: Xinyuan

last: Wu

first: Yayun

last: Xie

first: Yingjun

last: Quan


title: CD36-mediated lipid-accumulation in reactive microglia drives retinal degeneration through Nlrp3-IL-1β pathway [Spatial Transcriptomics]

city: Guangzhou

first: xialin

last: liu

address: Jinsui Road

institute: Zhongshan Opythalmic Center, Sun yat-sen University

summary: Lipid accumulation in microglia through CD36 enhances Nlrp3 inflammasome activation, contributing to retinal neurodegeneration.

overall_design: Spatial transcriptomics samples of eyeballs were from  NaIO3 induced retinal degeneration mice and PBS treated control mice, using 10X genomics platform.

first: Tian

last: Zhou

first: Ziqi

last: Yang

first: Biyan

last: Ni

first: Hong

first: Yang

first: Jingpeng

last: Li

first: Minglu

last: Ma

first: Huaicheng

last: Wang

first: Peng

last: An

first: Huiyi

last: Xu

first: Xiaojing

last: Lin

first: Shiya

first: Shida

last: Chen

first: Lixia

first: Wei

last: Yi

first: Xialin

last: Liu

first: Chang

last: He


title: Copy Number Gains of VPS72 Drive De Novo Lipogenesis  and Hepatocarcinogenesis via ATF3/mTORC1/SREBP1 Axis [ChIP-Seq]

city: Hong Kong

first: Qinglin

last: Zhang

address: Room 7N07, Kadoorie Biological Sciences Building, The University of Hong Kong, Sai Ying Pun

institute: The University of Hong Kong

summary: Hepatocellular carcinoma (HCC) is the predominant form of primary liver  cancer and a major contributor to cancer-related mortality globally. Central to  its pathogenesis is the dysregulation of lipid metabolism in hepatocytes,  leading to abnormal lipid accumulation. Our bioinformatics analysis has  identified the histone acetyltransferase complex subunit VPS72 as being  associated with HCC, yet the precise molecular mechanisms through which  VPS72 contributes to hepatocarcinogenesis remain poorly understood. Our  analysis of extensive HCC patient cohorts identifies a significant proportion  with VPS72 copy number gains, which are strongly linked to adverse  prognostic outcomes. By integrating RNA-Seq, ChIP-Seq, ATAC-seq, and  experimental validation, we show that VPS72 overexpression activates  mTORC1signaling, subsequently promoting lipid synthesis and driving HCC  progression. We further uncover that VPS72 modulates the epigenetic  landscape by enhancing DNA methylation at the ATF3 promoter, resulting in  ATF3 repression and subsequent activation of mTORC1. This study elucidates  a novel regulatory axis that links dysregulated lipid metabolism with HCC  progression, highlighting potential epigenetic and metabolic targets for  therapeutic intervention.

overall_design: ChIP-Seq profiling of VPS72 overexpression Huh7 FLAG-tag knock-in cell line versus empty vector lentivirus infected Huh7 FLAG-tag knock-in cell line (negative control) consctructed by lentivirus infection for 24h

first: Yunxing

last: Huang

first: Yin

last: Tong


title: Copy Number Gains of VPS72 Drive De Novo Lipogenesis  and Hepatocarcinogenesis via ATF3/mTORC1/SREBP1 Axis [ATAC-seq]

overall_design: RNA-Seq profiling of VPS72 overexpression Huh7 cell line versus Flag-tagged cell line (negative control) consctructed by lentivirus infection for 24h


title: STC-1 Attenuates Scar Formation via PI3K/AKT Pathway Activation and Immune Modulation

first: Xiaoying

state: Asia

address: 3 East Qingchun Road

institute: Sir Run Run Shaw Hospital, Zhejiang University School of Medicine

summary:
Objective:
To investigate the role of Stanniocalcin-1 (STC-1) in scar formation and elucidate its underlying mechanisms in regulating fibroblast activity, immune microenvironment, oxidative stress, and PI3K/AKT signaling.
Approach:
A combination of clinical sample analysis, in vitro experiments using NIH-3T3 fibroblasts and macrophage co-culture models, RNA sequencing, and in vivo full-thickness wound mouse models were employed. The effects of recombinant human STC-1 and STC-1 overexpression were evaluated on fibroblast function, extracellular matrix remodeling, inflammatory response, and scar formation. The impact on PI3K/AKT signaling was assessed by Western blot analysis.
Results:
STC-1 was specifically overexpressed in keloid tissues, primarily in fibroblasts, and its expression was upregulated by hypoxia in a HIF-1α–dependent manner. In vitro, STC-1 suppressed fibroblast proliferation, migration, and LPS-induced inflammation, while alleviating oxidative stress and mitochondrial dysfunction. STC-1 also promoted angiogenesis and induced M2 macrophage polarization. In vivo, STC-1 reduced scar size, improved collagen organization, modulated immune cell infiltration by activating the PI3K/AKT signaling pathway.
Innovation:
This study identifies STC-1 as a novel immunoregulatory and anti-fibrotic factor in scar pathogenesis. It highlights that STC-1 not only affects fibroblast function but also remodels the immune microenvironment through PI3K/AKT activation.
Conclusion:
STC-1 exerts anti-fibrotic, anti-inflammatory, antioxidant, and immunomodulatory effects during scar formation by activating the PI3K/AKT signaling pathway, highlighting its therapeutic potential in the treatment of pathological scars.

overall_design: Gene expression profiling analysis of RNA-seq data from NIH-3T3 fibroblasts treated with STC-1. Cells were treated with either PBS or 100 ng/mL recombinant STC-1 protein, or TGF-β1-treated (10 ng/mL), and co-treatment with STC-1 and TGF-β1 groups for 24 hours. Each group consisted of three biological replicates.

first: Weiqiang

last: Tan


title: α2,6-Sialoglycan-regulated anti-tumor immunity of tumor-infiltrating CD8+ T cells in the tumor microenvironment

city: Beijing

first: Qi

last: Tang

address: Chengfu Road #292

institute: Peking University

summary: Cell-surface sialoglycans overexpressed on cancer cells suppress the activation of tumor-infiltrating immune cells (TIICs), and have emerged as a promising target for cancer immunotherapy. However, the functional roles of sialylation in TIICs remain incompletely understood. Here, we develop the single-cell correlative analysis of α2,3- and α2,6-linked sialoglycans and transcriptomes (scCAST_3&6) strategy to correlate cell-surface sialylation in a linkage-specific manner with gene expression of the same cells by single-cell RNA sequencing. Applying scCAST_3&6, we discover that α2,3- and α2,6-sialoglycans are distinctively regulated in specific TIIC subpopulations. Importantly, downregulated α2,6-sialoglycan is demonstrated as a cell-surface marker for labeling and isolating CD8+ T cells with high reactivity to tumor-specific antigens (TSAs) from the tumor. Mechanistically, α2,6-sialyltransferase ST6Gal-I is transcriptionally suppressed upon the activation of intratumoral CD8+ T cells with high-avidity T cell receptors towards tumor antigens, which downregulates α2,6-sialylation and exposes galectin-1 ligands. Functionally, increased galectin-1 binding to TSA-reactive CD8+ T cells promotes T cell apoptosis and cancer immune evasion. This work underscores the functional significance and therapeutic promise of specific sialoglycans on TIICs.

overall_design: To verify the functional connections between α2,6-sialylation and CD8+ T cell phenotype observed in the scCAST_Sia6 dataset, we performed bulk RNA-seq on on FACS-isolated B16F10 intratumoral Sia2,6hiPD-1−CD8+, Sia2,6hiPD-1+CD8+, and Sia2,6loPD-1+CD8+ T cells

first: Shuyu

last: Liang

first: Yilan

last: Guo

first: Shaoran

first: Xing


title: Mating-induced DNA replication factor minichromosome maintenance protein 10 promotes oogenesis in Plutella xylostella

city: fuzhou

first: junhao

last: zheng

state: --- Select One ---

address: Cangshan District, Fuzhou City, Fujian Province, China

institute: Fujian Agriculture and Forestry University

summary: During oogenesis, the cell cycle becomes arrested during the DNA replication phase and resumes after mating facilitating crucial processes, including vitellogenesis and chorion formation. However, the molecular mechanisms regulating oogenesis in Plutella xylostella (L.) remain largely unexplored. Here, comparative transcriptomics analysis identified 1,200 differentially expressed genes induced by mating. Among the 769 upregulated genes, minichromosome maintenance protein complex 10 (MCM10) may be a potential target for post-mating DNA replication initiation. The P. xylostella genome encodes 11 MCM genes. Phylogenetic analysis indicated that MCM proteins are relatively conserved across species but form distinct clades. PxMCM10 exhibited expression specificity in adult females and eggs, particularly in the ovaries. Furthermore, PxMCM10 knockdown impaired DNA replication initiation and oocyte development while increasing apoptosis in follicle cells. This downregulated vitellogenin, vitellogenin receptor, and chorion gene transcription, resulted in abnormal ovarian development, defective vitellogenesis, and impaired chorion formation. Hence, PxMCM10 may regulate DNA replication reinitiation post-mating by influencing follicle cell function to control vitellogenesis and chorion formation. We offer insights into the molecular mechanisms governing oogenesis in P. xylostella and other lepidopteran pests. Furthermore, PxMCM10 could be a potential target for innovative genetic strategies in pest management.

overall_design: To explore the role of mating in vitellogenesis of Plutella xylostella, we performed RNA-seq analysis on ovaries tissues of unmated and mated Geneva88 strain.

first: Lu

last: Peng

first: Ruonan

last: Li

first: Junhao

last: Zheng

first: Guofeng

first: Laiwai

last: Tun

first: Yurui

last: Qian

first: Jindong

last: Cui

first: Minhui

last: Cao

first: Mengqi


title: A Proposed Model of Alternative Splicing of Cyclin-Dependent Kinase 8 Underlying Mechanisms of Heart Failure Secondary To Hypertension.

city: Iowa City

first: Chad

last: Grueter

state: IA

address: 169 Newton Rd, 4332 PBDB

department: Internal Medicine

institute: University of Iowa

summary: The regulation of eukaryotic gene expression is a multifacted system in which both gene transcription and post transcriptional modifications play a crucial role in maintaining proper gene expression. The Mediator complex and its associated proteins are integral in the enhancer-driven gene expression with previous literature investigating the potential connections between disrupted Mediator complex function and neurological, cardiovascular, and developmental disease states. Another well-understood mechanism regulating eukaryotic protein expression is alternative splicing of mRNA transcripts, generating protein diversity from a single gene. Alternative splicing is thought to contribute to cellular differentiation and developmental processes and is associated with human disease and cancer. Therefore, the discovery of alternative splicing events in critical genes within essential complexes, like the Mediator complex, may grant better understanding of human disease, and thus lead to better treatments and health outcomes. In this study, we identified alternative splice sites within the mediator complex through RNAseq analysis of murine Sham and Trans-aortic banding ventricular lysates. We also identified alternative splice sites within the mediator complex when comparing human ventricular cardiomyocyte RNA-seq between healthy and decompensated heart failure patients secondary to pulmonary hypertension. Our findings display significant changes in alternative splicing of CDK8 transcripts in models of cardiovascular disease in murine and human samples. This finding implicates the alternative splicing of CDK8 kinase domain as a regulatory mechanism underlying gene expression changes in heart failure.

overall_design: RNAseq profiling of male mice after either Sham or Trans-aortic banding at 12 weeks of age.

first: Duane

last: Hall

first: Kayla

last: Henry

first: Christopher

last: Jun


title: Bulk RNA-seq of pre-senescent, and siDUSP4-treated colonic fibroblasts

city: Suwon

first: Soon Sang

last: Park

address: Worldcup-Ro 206

institute: Ajou University School of Medicine

overall_design: Human primary colonic fibroblasts are treated either with siControl or siDUSP4

first: Young-Kyoung

last: Lee

first: Tae Jun