title: CRISPR -Cas9 Targeting of G-Quadruplex DNA in ADH1 promoter Highlights its role in Transcriptome and Metabolome Regulation

city: Umeå

first: Nasim

last: Sabouri

address: Linnaeus vag

institute: Umeå University

summary: G-quadruplex (G4) structures are crucial regulators of gene expression, yet their roles within native chromatin remain underexplored. Using CRISPR/Cas9, we introduced guanine-to-thymine mutations at a G4-forming motif in the adh1+ (alcohol dehydrogenase 1) promoter of Schizosaccharomyces pombe, generating two mutant strains: one with G4-only mutations (ADH1_G4_MUT) )and another with both G4 and TATA-box mutations (ADH1_G4-TATA_MUT). Bulk-RNAseq analyses revealed that these mutations significantly reduce adh1 transcript levels, with G4 TATA-box mutant causing the strongest transcriptional suppression. This indicates a positive regulatory role for the Adh1 G4 structure in adh1+ gene expression. Furthermore, both mutants displayed altered transcriptomic profiles, particularly impacting the oxidoreductase pathway.  Global transcriptomic shifts further underscored the regulatory influence of the Adh1 G4 structure, with downstream effects on pathways critical for cellular metabolism. These findings demonstrate the pivotal role of a single G4 structure in modulating transcriptomic profiles and offer insights into its potential as a therapeutic target for reprogramming gene expression and metabolic pathways.

overall_design: Bulk RNA-seq profiling on the mRNA isolated from ADH1_G4_WT (wild-type), ADH1_G4-TATA_MUT, and ADH1_G4_MUT strains grown in Yeast extract supplement (YES) media.

first: Ikenna

last: Obi

first: Pallabi

last: Sengupta


title: Investigating in the implications of the γδ T cell receptor in the acquisition of IL-17 producing effector functions

status: Public on Sep 24 2025

city: Hannover

first: Ziqing

last: Wang

address: Carl-Neuberg-Str. 1

country: Germany

institute: Hannover Medical School

type: Expression profiling by high throughput sequencing

summary: One common way to classify functional γδ T cell subsets is based on the expressed variable gene region of the T-cell-receptor (TCR) γ-chain. It is established that the TCRs of murine IL-17 producing γδ T cells are either Vγ6+ or Vγ4+. The majority of IL-17 producers get functionally pre-programmed in the prenatal thymus, and persist thereafter as tissue-resident cells into adulthood. Little is known about the role of the expressed TCR on IL-17 effector fate acquisition, and if also other subsets can produce IL-17 under certain circumstances. To address this question, we took advantage of a mouse model that lack the Vγ4 and Vγ6 γ-chain (Vγ4-/- / Vγ6-/- double knock-out). Initial results indicate that Vγ1+ T cells show increased IL-17 production capability in the absence of Vγ4+ and Vγ6+ γδ T cells, suggesting that the γδTCR does not always instruct the phenotype. This raises the question about the ontogenetic origin, which might be a TCR-independent default mechanism to instruct IL-17 production by γδ T cells, of IL-17+ Vγ1+ T cells. Moreover, it remains elusive if these Vγ1+ T cells (i) adopt highly similar tissue-specific gene expression programs and (ii) functionality in health and disease, than the Vγ4+ and Vγ6+ T cells.

overall_design: To elucidate whether IL-17pos and IL-17neg Vγ1+ T cells show a similar or a different TCR repertoire diversity, an mRNA-based next-generation sequencing analysis of δ-chain sequences (TCR-seq) was performed on FACS-sorted IL-17pos and IL-17neg γδ T cells from pLNs of Vγ4-/- / Vγ6-/- mice.

first: Tao

last: Yang

first: Sarina

last: Ravens

first: Anika

last: Janssen


title: Vascular EC-SOD limits the accumulation, proinflammatory profibrotic reprogramming, and hyaluronan binding of  interstitial macrophages in hypoxia

city: Aurora

first: Caitlin

middle: Vanessa

last: Lewis

state: Colorado

address: University of Colorado Denver AMC, 12700 East 19th Avenue, Mail Stop B131

department: Pediatrics

country: USA

institute: University of Colorado

summary: Dysregulated redox signaling contributes to pulmonary hypertension (PH) and vascular-selective depletion of the redox enzyme EC-SOD (EC-SOD SMC KO) worsens chronic hypoxic PH. Given the important role of macrophages in vascular remodeling and PH, this study aimed to determine if interstitial macrophages (IMs) and their interactions with the extracellular matrix (ECM) component, hyaluronan, are modulated by vascular EC-SOD. Floxed wild-type (WT), EC-SOD SMC KO, and EC-SOD mimetic- or vehicle-treated mice were exposed to hypobaric hypoxia (~10% FiO2), for 4, 14, or 21 days. Using flow cytometry, we demonstrated that the transient increase in IMs at day 4 was exacerbated in EC-SOD SMC KO mice and prevented with EC-SOD mimetic (5 mg/kg, subcutaneous, day 1). Highlighting the importance of targeting vascular oxidative stress in the early response to hypoxia, pretreatment with this single dose of EC-SOD mimetic decreased right ventricular systolic pressure, right ventricular hypertrophy, and small vessel muscularization at day 21. To assess IM phenotypic reprogramming in this model, RNAseq was performed on flow-sorted IMs revealing baseline proinflammatory activation and enhanced activation of vascular and ECM remodeling pathways in response to hypoxia in EC-SOD SMC KO IMs compared to controls. To further investigate the ECM remodeling response, we quantified IMs expressing the hyaluronan receptor Lyve1, and IM-hyaluronan binding. Lyve1+IMs and Lyve1+HA+IMs were increased in response to hypoxia in EC-SOD SMC KO mice and accumulated in the perivascular space. In conclusion, vascular EC-SOD limits IM accumulation and proinflammatory profibrotic IM signaling, including perivascular accumulation of Lyve1+IMs and their binding to hyaluronan.

overall_design:
To investigate the effect of low vascular EC-SOD expression on pulmonary interstitial macrophage (IM) transcriptional responses to hypoxia, we exposed EC-SODloxp/loxp x Tgcre/SMMHC  and EC-SODloxp/loxp control mice to 4 days (peak inflammation) or 14 (resolution) days of hypobaric hypoxia.
IMs were isolated from mouse lungs by FACS and RNAseq performed on each population. 4 male mice were pooled for each sample and n=3-4 samples analyzed per group.

middle: V


title: Investigating in the implications of the γδ T cell receptor in the acquisition of IL-17 producing effector functions.

overall_design: To investigate the molecular programs of lung Vγ1+ T cells in the absence of Vγ4 and Vγ6 T cells, single-cell RNA sequencing (scRNAseq) analysis was performed on flow cytometrically sorted lung Vγ1+ T cells isolated from Vγ4-/- / Vγ6-/- mice (KO). Transcriptional profiles were compared to lung Vγ1- T cells (being most likely Vγ4+ and Vγ6+) of WT mice (WT).


title: Chronic airway inflammation in Drosophila lacking the A20-like protein Trabid

city: Kiel

first: Judith

last: Bossen

address: Am Botanischen Garten 3-9

department: Molecular Physiology

institute: CAU Kiel, Zoological Institute

summary: The long-term alteration of epithelial immune homeostasis is central to the development and persistence of chronic lung disease. Regulators of immune pathways, such as the NF-kB pathway, are critical in this context. A20 (tumor necrosis factor-α induced protein 3 (TNFAIP3)) is one of the inhibitors of the NF-κB pathway associated with chronic lung disease. Using the Drosophila A20 ortholog, called Trabid, we have shown that trabid-deficient animals exhibit chronic immune response activation in the airways. In addition, these animals show a significantly increased sensitivity to airborne stressors such as dehydration, chronic cigarette smoke, and hypoxia. Furthermore, these animals lose the ability to respond to hypoxic stimuli with an otherwise observable plastic adaptation of the terminal cells of the tracheal system. In conclusion, the disease-associated changes in A20/trabid deficiency are not only due to increased immune activity in the epithelia but also to a massive reduction in stress resistance.

overall_design: Dissected larval trachea from Trabid knockout animals and corresponding controls were used for transcriptomic analysis.

first: Mirjam

last: Knop

first: Xiao

last: Niu

first: Marcus

last: Thiedmann

first: Ruben

last: Prange

first: Navid

last: Tahanzadeh

first: Sören

last: Franzenburg

first: Iris

last: Bruchhaus

first: Holger

last: Heine

first: Thomas

last: Roeder


title: POST-TRANSCRIPTIONAL REGULATION OF KRAS GENE: MECHANISM INVOLVING 5’UTR RNA G-QUADRUPLEXES, LONG NONCODING RNA AND NUCLEAR RIBONUCLEOPROTEIN A1

city: Udine

first: Raffaella

last: Picco

address: P.le Kolbe 4

department: Department of Medicine

country: Italy

institute: University of Udine

summary: Previous studies have shown that G-quadruplex (G4) DNA plays a crucial role in the regulation of gene expression. Here we show that the expression of the human KRAS oncogene is not only controlled by promoter G4 DNA, which serves as a platform for transcription factor recruitment, but also by G4 RNA (RG4) structures within the 5’UTR of messanger RNA, which control mRNA stability. The presence of these folded structures in vivo was demonstrated by ChIP-seq and RIP-seq experiments. Genetic abrogation of RG4 structures using CRISPR/Cas9 leads to increased mRNA levels, and point mutations that destabilise RG4s also lead to an increase in transcript levels. Bioinformatic analysis shows that the noncoding RNA HSALNT12722 contains a segment that is fully complementary to the 5’-UTR carrying the RG4 structures. The resulting RNA duplex is recognised and cleaved by RNase III. Furthermore, we could show that hybridisation of HSALNT12722 with the 5’UTR is mediated by hnRNPA1, which binds to the RG4 structures and unfolds them. Overall, our work demonstrates that the human KRAS oncogene is regulated both at the transcriptional level by G4 DNA and at the post-transcriptional level by RG4 structures and noncoding RNA, which determine the stability of KRAS mRNA.

overall_design: Panc-1 cells treated or not for 16h with PDS (1µM). After incubation, cells were harvested and subjected to rG4-IP

first: Ylenia

last: Cortolezzis

first: Francesca

last: Agostini

first: Eros

last: Di Giorgio

first: Luigi

last: Xodo


title: PD-1 expression identifies activated and proliferating chronic lymphocytic leukemia cells and is a potential biomarker that informs response and resistance to BTK inhibitor therapy

city: Blainville

first: Adam-Nicolas

last: Pelletier

state: Quebec

address: 97, Montcalm

country: Canada

institute: RPM Bioinfo Solutions

summary: Multiple signaling pathways have been implicated in promoting malignant B cell proliferation in chronic lymphocytic leukemia (CLL). Here we report that activated and proliferating CLL cells in circulation express the immune checkpoint PD-1. Circulating PD-1+ CLL cells upregulate genes associated with B cell receptor (BCR) and toll like receptor (TLR) signaling, and cell activation and proliferation. We demonstrate that BCR and TLR9 signaling induces PD-1 expression in primary CLL cells ex vivo, an effect that can be blocked by Bruton’s tyrosine kinase inhibition (BTKi). Importantly, profound reductions in circulating PD-1+ CLL cells were observed in patients within 1 month of initiating BTKi therapy and detection of high percentages of circulating PD-1+ CLL cells in patients treated with BTKi preceded the clinical diagnosis of disease progression. These findings suggest that PD-1 expression in circulating CLL cells may predict response and resistance to BTKi therapy.

overall_design: Prospective observational study to investigate the transcriptional profile of PD-1+ and PD-1- CLL cells from patients with CLL who are 1) treatment naïve, 2) on BTK inhibitors, or 3) progressing from BTK inhibitors

first: Andres

last: Chang

first: Donald

last: McGuire

first: Maria

last: Tsagiopoulou

last: Karipidou

first: Amy

last: Ayers

first: Alyssa

last: Leal

first: Michael

last: Churnetski

first: Colin

last: O'Leary

first: Jeffrey

last: Switchenko

first: Carl

last: Davis

first: David

last: Frank

first: Jean

last: Koff

first: Jonathon

last: Cohen

first: Rafick

last: Sekaly

first: Kostas

last: Stamatopoulos

first: Christopher

last: Flowers

first: Rafi

last: Ahmed


title: NETSseq Reveals Inflammatory and Aging Mechanisms in Distinct Cell Types Driving Cerebellar Decline in Ataxia Telangiectasia

city: Cambridge

first: Giuliano

middle: Giuseppe

last: Stirparo

state: Cambridgeshire

address: 418 Cambridge Science Park Milton Rd

country: United Kingdom

institute: Cerevance ltd

summary: The cellular and molecular changes driving the neurological abnormalities associated with the loss or functional deficiency of the ataxia–telangiectasia mutated (ATM) protein are not well understood.   In this study, we applied our proprietary Nuclear Enriched Transcript Sort sequencing (NETSseq) platform to investigate changes in cell type composition and gene expression patterns in human cerebellar post-mortem tissue from ataxia–telangiectasia (A-T) donors and non-neurodegenerative disease control donors.  Compared to single-cell technologies, NETSseq provided a more robust detection of lowly expressed and differentially expressed genes. Our differential gene expression analysis revealed high specificity to individual cell types. For instance, granule neurons exhibited dysregulation in neurotransmitter signaling and apoptotic pathways, potentially underlying the impaired motor coordination observed in A-T. Both astrocytes and microglia in A-T donors exhibited signs of accelerated aging, with astrocytes displaying upregulation of neurotoxic signatures and a downregulation of genes related to synaptic function, while microglia showed activation of pathways involved in the DNA damage response. This comprehensive analysis revealed significant changes in cell type composition and gene expression in the A-T cerebellum, shedding light on the cell type-specific mechanisms underlying neurodegeneration and motor dysfunction in A-T.

overall_design: In this study, the Nuclear Enriched Transcript Sort sequencing (NETSseq) platform was employed to analyze post-mortem human cerebellar tissue from ataxia-telangiectasia (A-T) donors and non-neurodegenerative disease controls


title: TRIM28-Mediated SUMOylation of G3BP1/2 Regulates Stress Granule Dynamics

city: Shanghai

first: Yi

last: Yuan

state: Shanghai

address: Building 13, Room 438, 100 Haike Road, Pudong New Area

department: Interdisciplinary Research Center on Biology and Chemistry

country: China

institute: Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences

summary: Stress granules (SGs) are stress-induced membraneless organelles whose dynamics are tightly regulated by protein interactions and modifications. However, whether SUMOylation directly targets SG core proteins G3BP1/2 and which ligase is involved remains unclear. Capturing these key events while preserving SG integrity is challenging due to their transient and membraneless nature. To address this, we introduce a low-concentration formaldehyde crosslinking (lcFAX) method that stabilizes membraneless organelles, including G3BP1 SGs and TDP-43 nuclear bodies, enabling enhanced proteome identification. Importantly, we identify TRIM28 as a previously undefined SG-associated protein and reveal that TRIM28 SUMOylates G3BP1 at K287 and G3BP2 at K281, establishing a critical mechanism regulating SG dynamics that ultimately impacts cellular ROS and apoptosis. lcFAX-Seq also provides insights into the RNA composition of SGs. Altogether, lcFAX-MS uncovers the critical role of TRIM28-mediated SUMOylation in modulating SG dynamics, establishing lcFAX as a powerful tool for analyzing membraneless organelles and the underlying regulatory mechanisms.

overall_design: RIP-Seq explores the candidate transcriptome of stress granules pulled down under PBS, AS, and AS+FA conditions with G3BP1-GFP.

first: Yaoyang

last: Zhang


title: Injury-Induced Connexin 43 Expression Regulates Endothelial Wound Healing

city: Roanoke

first: Mark

middle: Colin

last: Renton

state: VA

address: 4 Riverside Circle, Room 2208

department: Fralin Biomedical Research Institute

institute: Virginia Tech

summary: Endothelial cell (EC) injury is a major contributing factor to vascular surgical failure. As such, understanding the mechanisms of endothelial healing is essential to the development of vascular therapeutics and procedures. Gap junctions formed by connexin 43 (Cx43) are implicated in regulating skin wound healing, but their role in endothelial healing is unknown. Secondary analysis of RNAseq data from in vivo injured mouse aortas (GEO: GSE115618), identified significant Cx43 upregulation in EC post-injury. We developed a novel in vivo model of EC injury using mouse carotid artery ligation to test the role of Cx43. We identified that EC immediately adjacent to the wound edge upregulate Cx43 protein expression, predominantly at cell-cell junctions. We show significantly delayed EC healing in a mouse model of inducible EC-specific Cx43 deletion (EC-Cx43 KO) at 24 hr post ligation. Single cell RNAseq analysis of 10,829 cells from 18 hr injured EC-WT and EC-Cx43 KO carotids revealed a Cx43-associated reduction in enrichment of EC pathways associated with migration, proliferation, and ERK/MAPK signaling pathways. Finally, the importance of Cx43 phosphorylation on EC healing was tested in mice with single-point alanine mutations (phospho-null) in known phosphorylation sites that alter Cx43 channel assembly and opening. Mice containing alanine mutations at ERK phosphorylated Cx43 serines (Cx43S255/262/279/282A) reduces healing rates similar to EC-Cx43 KO. These data suggest that EC injury-induced Cx43 upregulation, and subsequent Cx43 gap junction-mediated cell-to-cell communication are required for normal EC migration during wound healing after vascular injury.

overall_design: scRNAseq analysis of mouse carotid arteries harvested 18hrs after temporary ligation-induced endothelial injury. One sample is from mice with an inducible endothelial-specific coonexin knockout mouse and the second sample is from a control mouse. Carotids were enzymatically digested to generate a single cell suspension, frozen in 10% DMSO, then submitted for sequencing.

first: Meghan

middle: W

last: Sedovy

middle: C

first: Kailynn

last: Roberts

first: Xinyan

last: Leng

first: Clare

middle: L

last: Dennison

first: Caroline

last: Toler

first: Melissa

middle: R

last: Leaf

first: Paul

middle: D

last: Lampe

first: Angela

middle: K

last: Best

first: Brant

middle: E

last: Isakson

first: Scott

last: Johnstone


title: MnSOD non-acetylation mimic knock-in mice exhibit dilated cardiomyopathy

city: San Antonio

first: Joseph

last: Schell

state: TX

address: 4939 Charles Katz

institute: UT Health San Antonio

summary: Manganese superoxide dismutase (MnSOD/SOD2) is an essential mitochondrial enzyme that detoxifies superoxide radicals generated during oxidative respiration. MnSOD/SOD2 lysine 68 acetylation (K68-Ac) is an important post-translational modification (PTM) that regulates enzymatic activity, responding to nutrient status or oxidative stress, and elevated levels have been associated with human illness. To determine the in vivo role of MnSOD-K68 in the heart, we used a whole-body non-acetylation mimic mutant (MnSODK68R) knock-in mouse. These mice exhibited several cardiovascular phenotypes, including lower blood pressure, decreased ejection fraction, and importantly, dilated cardiomyopathy, as evidenced by echocardiography at four months of age. In addition, both mouse embryo fibroblasts (MEFs) and myocytes from MnSODK68R/K68R mice exhibited an increase in cellular senescence. Finally, MnSODK68R/K68R mouse hearts also showed an increase in lipid peroxidation. We conclude that constitutively active MnSOD detoxification activity, lacking the normal switch between non-acetylated and acetylated forms, dysregulates mitochondrial physiology during development, leading to dilated cardiomyopathy.

overall_design: Mouse embryonic fibroblasts were isolated from WT and mutant SOD2K68R mice with a C57BL/6 background. The SOD2K68R mutation was generated via CRISPR. The MEFs were cultured briefly and then RNA was extracted for sequencing using standard protocols.

first: Sung-Jen

last: Wei

first: Zhao

last: Lai

first: David

last: Gius


title: The Effect of Methyl Donors in a Murine Model of MASLD in a Multidisciplinary Study

city: guadalajara

first: angel

middle: omar

last: vazquez

address: SIERRA MOJADA 950

country: Mexico

institute: IBMMTG

summary: The transcriptional profile of liver samples from male C57BL/6J mice was evaluated using a dual-channel microarray. The mice were divided into two groups: a negative control group fed a high-fat diet, and an experimental group fed a high-fat diet supplemented with methyl donors. This approach allowed for the analysis of gene expression differences associated with methyl donor supplementation in the context of a high-fat diet.

overall_design: Male C57BL/6J mice were used in this study and divided into two groups:  a high-fat and high-sugar diet (HF) for 18 weeks, and a  group receiving a HF diet for 10 weeks followed by 8 weeks of supplementation with methionine, choline, betaine, folate, cobalamin, and ZnSO4 (MET, n=8). At the end of the treatment period, liver samples were collected for RNA extraction and processed for microarray analysis. Gene expression profiles were compared between the HF(Cy5) vs MET(Cy3) groups to identify changes associated with the diet and supplementation.

first: Vazquez-Esqueda

last: Angel

first: Rosas-Campos

last: Rebeca

first: Escutia-Gutiérrez

first: García-Bañuelos

last: Jesus

first: Galicia-Moreno

last: Marina

first: Christian

last: Monroy-Ramirez

first: Jorge

last: Gutiererz-Cuevas

first: José

last: Navarro-Partida

first: Armendáriz-Borunda

last: Juan

first: Sandoval-Rodríguez

last: Ana


title: Development of acquired resistance to sotorasib in NCI-H358 cell line in vitro

city: Boston

first: Alexander

last: Ivliev

state: MA

address: 645 Summer Street, Suite 101

institute: Ikena Oncology, Inc.

summary: NCI-H358 is a KRAS G12C-mutant non-small lung cancer cell line known to be sensitive to KRAS G12C-inhibitor sotorasib. Here, we aimed to develop sotorasib resistance in H358 and interrogate the resulting sotorasib-resistant cell line (H358-R). The H358-R cell line was created by continuous culturing of the H358 cells in sotorasib (250 nM) until cells grew readily under sotorasib pressure (approximately 2 months). We then performed RNA-seq of the resulting sotorasib-resistant cell line (H358-R) with and without sotorasib pressure, compared to the parental sensitive cell line control (H358). KRAS gene expression level was found to be increased in the sotorasib-resistant line compared with the parental cells, likely representing a mechanism of resistance. The increased KRAS expression level in the resistant cell line was maintained under sotorasib pressure.

overall_design: RNA-seq was performed in three sample groups: (1) parental sotorasib-sensitive H358 cell line; (2) sotorasib-resistant H358-R cell line without sotorasib pressure; (3) sotorasib-resistant H358-R cell line under sotorasib pressure (250 nM, profiled 4 days after dosing). Three biological replicates were profiled per sample group.

first: Eric

last: Haines

first: Jeffrey

last: Ecsedy

first: Sabine

last: Ruppel


title: TOLLIP promotes GCRV infection by negatively modulating STING-mediated innate immunity

city: WuHan

first: Wang

middle: Yang

last: Yang

address: IHB

institute: IHB

summary: NOT PROVIDED; REQUESTED

overall_design: CIK CELLS; 2 repeated semples of each experinment

first: Yangyang

last: Wang

first: Mengze

last: Tian


title: Gene expression profiling of wild type and Trim33-deficient AMs after single allergen challenge

city: Beijing

first: Jiaoyan

last: Lv

address: 30 Shuangqing Road, Haidian District

institute: Tsinghua University

summary: Tripartite motif-containing protein 33 (TRIM33) is a multifunctional protein, that participates in multiple physiology and pathology processes. However, whether it plays any roles in regulating the function of AMs, particularly under the condition of allergic asthma remains unexplored. Gene expression profiling of wildtype and Trim33-deficient AMs revealed a crucial role of TRIM33 in regulating the activation status of AMs after single allergen challenge.

overall_design: Gene expression profiling for allergen exposed wildtype and Trim33-deficent AMs with bulk RNA-seq assay

first: Li

last: Wu


title: Endothelial RNF20 Suppresses Endothelial-to-Mesenchymal Transition and Safeguards Physiological Angiocrine Signaling to Prevent Congenital Heart Disease [Bulk_polyA RNA-seq]

city: Mannheim

first: Gergana

last: Dobreva

state: Baden Württemberg

address: Ludolf-Krehl-Str. 7-11

department: Cardiovascular Genomics and Epigenomics

institute: Medical Faculty Mannheim/University of Heidelberg

summary: Heart development and function rely on intricate communication among distinct cardiac cell types. How their co-development and crosstalk are coordinated is largely unexplored. Our study unveils novel functions of the histone H2B ubiquitin (H2Bub1) ligase RNF20 in second heart field development and cardiac endothelial cells, essential for proper cardiac morphogenesis and function. We demonstrate that RNF20-H2Bub1-dependent reduction in Nrg1 expression, coupled with heightened TGF-β signaling due to RNF20's role in inducing RNA polymerase II pausing at TGF-β targets, drives increased endothelial-to-mesenchymal transition (EndMT), abnormal cardiomyocyte proliferation, and irregular contractility upon endothelial RNF20 loss. Importantly, RNF20 expression is significantly reduced in cardiac endothelial cells from congenital heart disease patients showing a positive correlation with oxygen saturation and a negative correlation with key components and downstream effectors of TGF-β signaling. In summary, our work identifies a novel role of RNF20 in controlling signaling inputs that safeguard physiological angiocrine signaling ensuring proper cardiac morphogenesis and function.

overall_design: RNA-seq profiling of Right ventricle of heart tissue from tetralogy of Fallot patients

first: Yonggang

last: Ren

first: Yu-wen

last: Chen

first: Julio

last: Cordero Henriquez


title: RNA-seq of AsPC-1 cell line-derived xenograft mouse tumors treated with a MEK-RAF molecular glue, IK-595

summary: MAPK pathway alterations are the most common oncogenic drivers. Among the approved therapies targeting this pathway are MEK and RAF inhibitors. However, therapeutic resistance and toxicities have limited their clinical success.  To overcome these liabilities, we developed IK595, a potent MEK-RAF molecular glue. IK-595 traps MEK in an inactive complex with all RAF isoforms. In addition, IK-595 precludes CRAF-mediated MEK reactivation and ARAF heterodimerization allowing for prolonged target engagement and durable MAPK pathway inhibition.  This project aimed to explore gene expression modulation by IK-595 in AsPC-1 cell line-derived xenograft mice at different time points following last dose.  Tumor RNA-seq was performed in AsPC-1 tumor-bearing mice treated with three doses of vehicle or IK-595 (at 6 mg/kg QOD). Tumors from the drug-treated mice were collected and profiled at the following time points after the last dose: 2 hours, 4 hours, 8 hours, 24 hours, and 48 hours (four animals per time point group) - to understand longitudinal gene expression changes after dosing.  A significant reduction in most ERK1/2 target genes was observed as early as 2 hours after the last dose, with maximal inhibition observed at 8 hours. Partial recovery of ERK1/2 target gene expression occurred at 24 hours, with most genes returning to baseline levels by 48 hours. While elevated pathway activation following chronic treatment of MAPK pathway inhibitors is known to be associated with resistance in the literature, the expression of ERK1/2 target genes in our study never rebounded above baseline levels upon IK-595 treatment.


title: Spatiotemporal resolving Crohn's disease fibrosis

city: Milano

first: Luca

last: Massimino

state: MI

address: Via Olgettina, 58

department: Gastroenterology

institute: Ospedale San Raffaele

summary: Crohn’s disease is a chronic inflammatory disease of the bowel often complicated by fibrotic strictures that require invasive treatments including surgery. The mechanisms underlying intestinal fibrosis are not defined yet, and specific treatments are missing. Here we employed spatial transcriptomics to track the cellular and molecular evolution from healthy intestine to fibrosis in patients with Crohn’s disease.

overall_design: n=2 10x Visium slides containing tissue composites

first: Massimino

last: Luca

first: Ungaro

last: Federica

first: Parigi

last: Tommaso

first: Riva

last: Matteo


title: Comparative bulk RNAseq between EpH4 WT and Cldn-null cells

city: Kyoto

first: Kazuto

last: Tsukita

state: Kyoto

address: 54 Shogoin-Kawaharacho

country: Japan

institute: Kyoto university

summary: The claudin (CLDN) family, comprising 27 members, includes crucial cell–cell adhesion molecules that form tight junctions (TJs), essential for paracellular barrier and channel functions. The functional diversity among CLDNs may lead to diversity of TJs, contributing to various biological systems and pathological processes. To characterize the functional diversity of CLDNs, we developed a first-ever complete Cldn-null EpH4 epithelial cell line. This cell line was used for the expression of single Cldn family members, uncovering their specific intrinsic properties. Unlike the conventional binary classification of CLDNs as either paracellular barrier or channel forming, we discovered a novel classification axis where CLDNs form TJs autonomously or non-autonomously, exhibiting extensive variation in ion conductivity and selectivity, leading to an innovative classification. This classification offers a fundamental framework for understanding the mechanisms underlying TJ diversity in vivo, and provides a basis for the development of therapies targeting the epithelial barrier.

overall_design: To investigate the overall gene expression profiling, we conducted a comparative bulk RNAseq analysis between EpH4 WT and Cldn-null cells.

first: Hiroka

last: Kashihara

first: Hiroo

last: Tanaka

first: Atsushi

last: Tamura

first: Sachiko


title: Effect of NEK7 hepatocyte knock-out on gene expression in the mice livers.

city: Nanjing

first: Zhenzhen

last: Sun

address: Guangzhou Road#72

institute: Children’s Hospital of Nanjing Medical University

summary: To investigate the genes and pathways affected by depletion of hepatocyte NEK7 in the mice livers.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for liver tissue from the NEK7 hepatocyte knock-out mice (Homo_1, Homo_2, Homo_3) and wild type mice (Ctrl_1, Ctrl_2, Ctrl_3).

first: Zhanjun

last: Jia


title: hPSC-derived sacral neural crest cells restore erectile function in pelvic ganglia injury

city: Suzhou

first: Qiang

last: Shan

address: No. 100, Chongwen Road, Suzhou Industrial Park

institute: Suzhou Institute of Systems Medicine

summary: Pelvic surgeries frequently injure the major pelvic ganglia (MPG), resulting in refractory erectile dysfunction (ED) with limited therapeutic options. Regenerative medicine offers promising avenues for nerve injury-induced ED. Sacral neural crest (NC) cells, the embryonic progenitors of MPG neurons and glia, represent an ideal cell source for targeted neural repair. Here, we establish a robust protocol to differentiate human pluripotent stem cells (hPSCs) into sacral NC cells. Upon transplantation into rats with MPG injury, these cells engraft at the lesion site, differentiate into functional autonomic neurons and glia, and secrete neurotrophic factors. Sacral NC cell therapy reconstructs MPG architecture, promotes axonal regeneration and remyelination, and restores nitrergic innervation. Furthermore, transplantation significantly improves erectile function, evidenced by an increased intracavernous pressure/mean arterial pressure (ICP/MAP) ratio, accompanied by reduced apoptosis and fibrosis and restored smooth muscle and endothelial integrity in the penis. These findings demonstrate that hPSC-derived sacral NC cells offer a novel therapeutic strategy for neurogenic ED by restoring pelvic autonomic nerve structure and function through both neurogenic differentiation and sustained neurotrophic support.

overall_design: The neurogenic erectile dysfunction model was established by bilaterally clamping the major pelvic ganglia (MPG) in rats (injury group). In the Sham group, rats underwent the same surgical procedure without MPG injury. In the sacral NC group, rats received sacral neural crest cell transplantation following MPG injury. Four weeks later, penile tissue from each group was evaluated.

first: Ting

last: Yang

first: Wenwei

last: Liu

first: Yuxin

first: Xiaofeng

last: Wang

first: Tianxiang

last: Lei

first: Qiao

last: Tang

first: Yongxin

last: Zhang

first: Hufei

first: Yebohao

last: Zhou

first: Wu

last: Song


title: Resilience to Endoplasmic Reticulum Stress Mitigates Calcium-Dependent Membrane Hyperexcitability Underlying Late Disease Onset in Spinocerebellar Ataxia Type 6

city: Dallas

first: Genevieve

last: Konopka

state: Texas

address: 5323 Harry Hines Blvd.

department: Neuroscience

institute: University of Texas Southwestern Medical Center

summary: An enduring puzzle in many inherited neurological disorders is the late onset of symptoms despite expression of function-impairing mutant protein early in life. We examined the basis for onset of impairment in Spinocerebellar ataxia type 6 (SCA6), a polyglutamine ataxia with late-onset cerebellar neurodegeneration. In a mouse model of SCA6, we identified a homeostatic response that engages the unfolded protein response early in disease. This protective response provided insight into endoplasmic reticulum (ER) stress-mediated cerebellar Purkinje neuron membrane hyperexcitability as a driver of disease. Age-dependent impairment of chaperone-mediated compensation for ER stress increased calcium-dependent Purkinje neuron membrane excitability. Redundant pathways of the unfolded protein response mediate this resilience to ER stress. ER stress-related decompensation applies also to other late-onset human cerebellar ataxia. These studies elucidate a mechanism of resilience connecting aberrant proteostasis and calcium-dependent intrinsic membrane hyperexcitability to explain delayed disease onset more widely in age-dependent neurodegenerative disease.

overall_design: mRNA sequencing was performed on a NovaSeq instrument (Illumina, Inc.) with ~155 million reads and 150 bp paired-end reads. 5 cerebellum samples from each genotype from each age were used. Samples were prepared individually and pooled together to reduce batch effects. The samples were then demultiplexed into fastq files and statistics were collected using FastQC (Babraham Bioinformatics). The fastq files were trimmed using Trimmomatic (Bolger et al., 2014). 150 bp reads were aligned using STAR (Dobin et al., 2013), and the percent of unique reads were calculated. Raw read counts per gene per sample were calculated using HTSeq (Anders et al., 2015). Outliers were removed based on principal component analysis and hierarchical clustering. Differential gene expression analysis was performed using DESeq2 (Love et al., 2014).

first: Vikram

last: Shakkottai


title: Single cell sequencing of adrenocortical tumor tissue utilizing the scFAST-seq method

city: Moscow

first: Valentin

last: Trofimov

address: Ulyanova str.11

country: Russia

institute: Endocrinology Research Center

summary: Single-cell RNA sequencing (scRNA-seq) is a technology that allows for the analysis of gene expression at the level of individual cells. In many cases, droplet microfluidics are used for preparing DNA libraries. SeekOne DD scFAST-seq from Beijing SeekGene employs semi-random primers, offering advantages in detecting transcripts, particularly non-polyadenylated transcripts and regions that are distant from the polyadenylated RNA tail. The introduction of new strategies in scRNA-seq represents a promising approach for research, such as studying the properties of adrenocortical tumors. This study aims to investigate the biological properties of adrenocortical tumor samples by SeekOne scFAST-seq methodology.

overall_design: Single cells were isolated from tissue samples using ACME HS followed by cryopreservation in 3xSSC*10% DMSO and methanol cell fixation. Key adaptations of the ACME HS method were the supplement of solution composition with 0.1M NAC and the introduction of additional washing steps in cold high salt 3xSSC* buffer. ACME dissociation was conducted in ~ 1 hours on a rotator at room temperature, with periodic pipetting of the solution. Afterward, we removed the ACME solution and washed the pellet with a two-step washing in cold 3xSSC. Single cells were captured, barcoded, and cDNA libraries were generated using the V1.1-SeekOne DD Single Cell Full-length RNA Sequence Transcriptome-seq Kit (SeekGene) according to the manufacturer’s instructions. Final libraries were multiplexed and sequenced on an Illumina Novaseq 6000 platform, using the S4 Reagent Kit v1.5.

first: Marina

last: Utkina

first: Anastasia

last: Shcherbakova


title: Effects of in vitro production on the transcriptomic profile of the embryonic disc and extra-embryonic membranes of day 15 elongated bovine embryo.

city: Utrecht

first: Maria

middle: Belen

last: Rabaglino

address: Yalelaan 7

department: Population Health Science

country: Netherlands

institute: Utrecht University

summary: In vitro-produced (IVP) embryos continue to surpass in vivo-produced (IVV) embryos worldwide. However, there is increased concern about the current drawbacks of IVP embryos, such as a higher pregnancy loss in the early stages of development often associated with impairment in conceptus elongation, which begins from ~day 13 of gestation. The embryonic disc (ED) and the embryonic membranes (EEM) differentiate during this period, and their transcriptomes might be impacted by the in vitro procedures, impairing conceptus development. This study aimed to identify changes in the ED and EEM transcriptome of day 15 IVP conceptuses compared to those conceived in vivo

overall_design: For IVP embryos, oocytes aspirated from slaughterhouse ovaries were matured, fertilized, and cultivated in serum-free medium until transfer at day 7. IVV embryos (n=8) were generated after ovarian super-stimulation and artificial insemination. Eight days after in vitro embryo transfer or 15 days after AI on superovulated cows, the embryos were non-surgically flushed out of the uterine horns using an 18 FR Foley catheter (Minitube) and BoviFlush (Minitube) solution. The recovered day 15 embryos were washed twice with BoviFlush (Minitube) and held in BoviHold medium (Minitube). The embryos were gently checked for the presence of ED and washed twice with 0.1% PVA and PBS medium. Embryos without ED were discarded. The selected embryos were cut into three pieces. The ED and 2 pieces of surrounding EEM were snap-frozen in liquid nitrogen. The final sample size used in the bioinformatic analyses was, for the EEM n=6 and n=8 for IVP and IVV embryos, respectively, while for the ED was n=7 and n=9 for IVP and IVV embryos, respectively.

first: Thomas

last: Behrens

first: Janaki

last: Balasubramanian

first: Marilin

last: Ivask

first: Monika

last: Nõmm

first: Ants

last: Kavak

first: Jan

last: Bojsen-Møller Secher

first: Haja

middle: N

last: Kadarmideen

middle: B


title: KDM1A/LSD1 inhibition enhances chemotherapy response in ovarian cancer

city: SAN ANTONIO

first: YI

last: ZOU

address: 8403 Floyd Curl Drive

institute: UTHSA-GCCRI

summary: We examined global transcriptional changes in SKOV3-control and KDM1A knockdown (KD) cells that are treated with vehicle or cisplatin using RNA-sequencing.

overall_design: SKOV3-control and SKOV3-KDM1A knockdown cells were treated with vehicle or cisplatin (2.5 µM) for 72 hours. Total RNA was isolated using RNeasy mini kit according to the manufacturer's instructions (Qiagen, Valencia, CA).  Illumina TruSeq RNA Sample Preparation was performed following the manufacturer's protocol. Samples were run on an Illumina HiSeq 3000 in duplicate. The combined raw reads were aligned to UCSC hg19 by Tophat2. Genes were annotated and quantified by the HTSeq-DESeq pipeline.

first: Yihong

last: Chen

first: Gangadhara

last: Sareddy


title: BT245 cells with olaparib and/or radiation treatment

city: Ann Arbor

first: Qiang

last: Zhang

state: Michigan

address: 1500 E Medical Center Dr

department: Radiation Oncology

institute: University of Michigan

summary: We aimed to do a bulk RNA sequencing and compare transcriptomes of human diffuse midline glioma cell line BT245 in response to olaparib and/or radiation treatment

overall_design: 12 samples of BT245 cells---untreated (3 samples), olaparib (3 samples), radiation (3 samples), olaparib and radiation (3 samples)

first: Zhuwen

last: Wang

first: Meredith

middle: A

last: Morgan


title: Early life exposure to preterm birth-related conditions induces an aged-like microenvironment that has long-lasting consequences on muscle stem cell function and regenerative capacity

city: Montréal

first: Gael

middle: Louis Max

last: Cagnone

state: QC

address: 3175 Chemin de la Côte-Sainte-Catherine

department: The Montreal single-cell Academy

institute: CHU Sainte Justine

summary: Preterm birth is associated with comorbidities and long-lasting effect on the function of many organs such as skeletal muscle.  Muscle injury resulted in signs of impaired regeneration such as reduced myogenic cell number, lower myonuclear accretion, smaller myofibers, and reduced force. We used Single cell RNA-seq (sc RNA-seq) to understand the mechanisms underlying the alteration of muscle stem cells after exposure to preterm birth related-conditions.

overall_design: Rat pups (Sprague-Dawnley) were exposed to 80% of oxygen from 3 to 10 days of life to mimics preterm birth-related conditions (OI=oxygen induced-injury). Control (CTRL) pups were maintained in room air. Muscle cells were isolated from hind limb muscle (left and right) from 4 males rat at 4 weeks of age (2 CTRL and 2 OI) and cell suspension was sorted using Fluorescence activated cell sorting (FACS). The 4 cell samples were multiplexed using CMO probes and process together in one run (Cell multiplexing) of single-cell RNAseq using 10X Genomics Cellplex 3' GEX v3.1.

first: Alyson

last: Deprez

first: Séverine

last: Leclerc

first: Anne

middle: M

last: Nuyt

first: Severine

last: Landais

last: Molina

first: Nicolas

last: Dumont


title: Mitochondrial Transplantation with Vitamin D Therapy Mitigates Paraspinal Muscle Atrophy and Neuropathic Pain Following Spinal Surgery

city: Gyeonggi-do

first: Seong-Hoon

last: Kim

state: Seongnam

address: Pangyo-ro 335

department: Department of Bioconvergence Science

country: South Korea

institute: CHA university

summary: Chronic pain after spinal surgery (CPSS) is frequently accompanied by paraspinal muscle atrophy (PMA). This study aimed to explore the potential of mitochondrial transplantation and/or vitamin D (VitD) therapy to counteract PMA- and pain-associated mitochondrial dysfunction. Plasma-derived mitochondria (pMT) were collected from human blood samples. The structure, size, and purity of the pMT were verified, and their mitochondrial respiratory enzyme activity was analyzed. A 2-week rat model of CPSS was created at the fifth left lumbar vertebra through denervation and laminectomy. The rats were assigned to 5 groups, namely, pMT/VitD, pMT, VitD, surgery, and control and administered intramuscular pMT ± VitD injections. The effects elicited in each group were investigated after 2 weeks via muscle morphology measurement and comprehensive tissue analysis. Combined pMT and VitD treatments showed potential in alleviating surgery-induced muscle atrophy and modulating pain responses. Thus, pMT and/or VitD treatment restored muscle atrophy by modulating proteostasis, suppressing apoptosis, and increasing PGC1α levels.

overall_design: Male Sprague Dawley rats (age, 12 weeks; weight, 340–370 g) were divided into five groups: pMT/VitD (pMT/VitD injection after surgery), pMT (pMT injection after surgery without VitD), VitD (VitD injection after surgery without pMT), surgery (no treatment after surgery), and control (no injury) groups. Total RNA was extracted from the multifidus muscles using the easy-spin total RNA extraction kit (iNtRON Biotechnology, Seoul, Republic of Korea).The Illumina sequencing NovaSeq platform (Illumina, San Diego, CA, USA) was used for generating paired-end sequencing reads. The reads were prepared for analysis using the Trimmomatic version 0.38 to remove adapter sequences and trim the low-quality bases. Subsequently, the processed reads were aligned to the Rattus norvegicus reference genome (rn6) using HISAT version 2.1.0 by incorporating both HISAT and Bowtie2 for alignment. Reference genome sequences and gene annotation data were sourced from the NCBI Genome Assembly and NCBI RefSeq databases.

first: Ik-hyun

last: Lim

first: Mi-Jin

first: Chang-Koo

last: Yun

first: Kyunghoon

last: Min

first: Yong-Soo

last: Choi


title: A multimodal cross-species comparison of pancreas development [multiome]

city: Neuherberg

first: Heiko

last: Lickert

address: Ingolstaedter Landstraße 1

department: Institute of Diabetes and Regeneration Research

institute: Helmholtz Zentrum München German Research Center for Environmental Health

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Human pancreas development remains incompletely characterized due to restricted sample access. We investigate whether pigs resemble humans in pancreas development, offering a complementary large-animal model. As pig pancreas organogenesis is unexplored, we first annotate developmental hallmarks throughout its 114-day gestation. Building on this, we construct a pig single-cell multiome pancreas atlas across all trimesters. Cross-species comparisons reveal pig closely resembles human in developmental tempo, epigenetic and transcriptional regulation, and gene regulatory networks. This further extends to progenitor dynamics and endocrine fate acquisition. Transcription factors regulated by NEUROG3, the endocrine master regulator, are over 50% conserved between pig and human, many being validated in human stem cell models. Notably, we uncover that during embryonic development, emerging beta-cell heterogeneity coincides with a species-conserved primed endocrine cell (PEC) population alongside NEUROG3-expressing cells. Overall, our work lays the foundation for comparative investigations and offers unprecedented insights into evolutionary-conserved pancreas organogenesis mechanisms across animal models.

overall_design: Pig pancreases from E22, 32, 40, 54, 63 and 85 were analyzed by scRNA-seq

first: Kaiyuan

last: Yang

first: Hannah

last: Spitzer

first: Michael

last: Sterr

first: Karin

last: Hrovatin

first: Sean

last: de la O

first: Xinghao

first: Eunike

middle: S

last: Setyono

first: Minhaz

last: Ud-Dean

first: Thomas

last: Walzthoeni

first: Krzysztof

last: Flisikowski

first: Tatiana

last: Flisikowska

first: Angelika

last: Schnieke

first: Katharina

last: Scheibner

first: James

last: Wells

first: Julie

last: Sneddon

first: Barbara

last: Kessler

first: Eckhard

last: Wolf

first: Elisabeth

last: Kemter

first: Fabian

middle: J

last: Theis


title: A multimodal cross-species comparison of pancreas development

first: Heiko

last: Lickert

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

overall_design: Refer to individual Series


title: A multimodal cross-species comparison of pancreas development [scRNA-seq]

first: Kaiyuan

last: Yang

first: Hannah

last: Spitzer

first: Michael

last: Sterr

first: Karin

last: Zhang


title: MAIT cells drive chronic inflammation in a genetically diverse model of spontenous colitis

city: Aurora

first: Liyen

last: Loh

address: 12800 E 19th Ave, Research 1 North, P18-8401K

institute: University of Colorado

summary: MAIT cells are innate-like T cells conserved across species and bridge innate and adaptive immunity. After T-cell receptor mediated stimulation, they rapidly produce a range of chemokines and inflammatory mediators and thus may contribute important roles in infection, autoimmunity and inflammatory diseases. MAIT cells are rare in many laboratory mice strains. The collaborative cross strain CC011/Unc has high numbers of MAIT cells at steady-state across the peripheral and lymphoid tissues. Strikingly, CC011 mice develop spontaneous colitis after 20 weeks of age. We explored the role of MAIT cells in the CC011 spontaneous colitis model. We used single cell RNA sequencing (scRNA-seq) to analyze the transcriptome of MAIT cells in the spleen and colon of diseased CC011 mice aged (28-30 week old).

overall_design: MAIT cells were enriched by magnetic-bead MR1-5-OP-RU tetramer enrichment from spleen tissue prior to purified by Fluorescence-activated cell sorting (FACS). In the colon, MAIT cells were sort purified directly from enzymatically digested and percoll gradient separated colon tissue. Both tissues were analyzed using scRNAseq.

first: Laurent

last: Gapin


title: Kinetic measurement of gene-specific RNAPII transcription elongation rates

city: Copenhagen

first: Haiyue

last: Liu

address: Blegdamsvej 3B

department: Department of Cellular and Molecular Medicine

country: Denmark

institute: University of Copenhagen

summary: Transcription is regulated at multiple levels, including initiation, elongation, and termination.  Whereas much research has focused on initiation of transcription, regulation of elongation plays an important role not only for transcription dynamics, but also for co-transcriptional RNA processing as the RNAPII elongation rate can influence maturation of the nascent RNA transcript. Despite advances in high-throughput approaches for global identification of RNAPII speed, RNAPII elongation rate studies have been largely limited to a small number of genes. Here, we present DRB/TTchem-seq2, a modified version of DRB/TTchem-seq method, to measure gene-specific elongation rates of more than 3,000 genes. By approximating the distance traveled by RNAPII in certain time intervals using the wave fronts post RNAPII release. Our direct RNAPII elongation rate quantification reveals that elongation rates vary not only among genes but also within genes. Additionally, specific histone modifications and elongation factors are tightly correlated with the elongation rates. Together, we present a robust and powerful method for RNAPII transcription elongation rate measurement.

overall_design: Nascent transcripts following RNA Pol II (RNAPII) stalling and released from promoter-proximal pausing were captured and subsequently sequenced in four different time points (i.e., 5, 10, 15 and 20 minutes) in both U2OS and DLD-1 cells. RNAPII elongation rates were estimated based on the distances traveled by RNAPII in certain time periods for both U2OS and DLD-1 cells.

first: Lea

middle: H

last: Gregersen


title: Visium spatial transcriptomics of the neural complex of Ciona intestinalis type A

city: Suita

first: Daisuke

last: Motooka

state: Osaka

address: 3-1, Yamadaoka

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

summary: To investigate the spatial gene expression in the neural complex of Ciona, we conducted Visium spatial transcriptomics in the tissue sections of the neural complex of Ciona intestinalis type A.

overall_design: Four fresh frozen sagittal sections (10 um thickness) of the neural complex of wild type adult Ciona were used for the analysis. Permeabilization time was set to 15 min.

first: Tomohiro

last: Osugi

first: Akira

last: Shiraishi

first: Honoo

last: Satake


title: Multi-omic analysis of NCOR SMRT function in macrophages

first: Zhiqiang

last: Huang

state: Jiangsu

address: Hankou 22

department: Medical School

institute: Nanjing University

summary: To compare NCOR and SMRT transcriptional repressor complexes in macrophages, we conducted an analysis of protein binding patterns, transcriptomic patterns, and epigenome correlations. Our systematic research revealed both the similarities and functional specificities of NCOR and SMRT, highlighting the synergistic and differential regulation characteristics of these complexes in macrophages. These findings offer a deeper understanding of the distinct manifestations of epigenome differential regulation.

overall_design: We utilized ChIP-seq, RNA-seq, ATAC-seq, and CUT&Tag techniques to investigate the regulatory preferences of the NCOR/SMRT corepressor complex in macrophages. Through these methods, we were able to uncover insights into the regulation patterns and mechanisms of these complexes in macrophages.

first: Astradeni

last: Efthymiadou

first: Eckardt

last: Treuter


title: Induction of CDX2 as a differentiation therapy in colorectal cancers

city: La Jolla, CA 92093

first: Pradipta

last: Ghosh

state: CA

address: 9500 Gilman Drive (MC 0651)

department: Departments of Medicine and Cellular and Molecular Medicine

institute: University of California San Diego


title: Dynamical modeling reveals RNA decay mediates the effect of matrix stiffness on aged muscle stem cell fate

city: Charlestown

first: Fabrisia

last: Ambrosio

institute: Harvard Medical School

summary: Loss of muscle stem cell (MuSC) self-renewal with aging reflects a combination of influences from the intracellular (e.g., post-transcriptional modifications) and extracellular (e.g., matrix stiffness) environment. Whereas conventional single cell analyses have revealed valuable insights into factors contributing to impaired self-renewal with age, most are limited by static measurements that fail to capture nonlinear dynamics. Using bioengineered matrices mimicking the stiffness of young and old muscle, we showed that while young MuSCs were unaffected by aged matrices, old MuSCs were phenotypically rejuvenated by young matrices. Dynamical modeling of RNA velocity vector fields in silico revealed that soft matrices promoted a self-renewing state in old MuSCs by attenuating RNA decay. Vector field perturbations demonstrated that the effects of matrix stiffness on MuSC self-renewal could be circumvented by fine-tuning the expression of RNA decay machinery. These results demonstrate that post-transcriptional dynamics dictate the negative effect of an aged matrix on MuSC self-renewal.

overall_design: Single cell transcriptional profiling of young and old mouse muscle stem cells cultured on either soft (12 kPa) or stiff (29 kPa) polydimethlysiloxane substrates

first: Hettinger

last: Zachary

first: Hu

last: Sophia

first: Mamiya

last: Hikaru

first: Sahu

last: Amrita

first: Iijima

last: Hirotaka

first: Wang

last: Kai

first: Gilmer

last: Gabrielle

first: Miller

last: Amanda

first: Nasello

last: Gabriele

first: D'Amore

last: Antonio

first: Vorp

last: David

first: Rando

last: Thomas

first: Xing

last: Jianhua

first: Ambrosio

last: Fabrisa


title: 5-methylcytosine modifition of mRNA from hippocampi in young and aged mice

city: Xinxiang

first: chengbiao

last: Lu

address: 601 Jinsui Avenue

institute: xinxiang medicial university

type: Methylation profiling by high throughput sequencing

summary:
To investigate the Epigenetics changes during aging, we sequenced hippocampal tissue from young and old mice by methylated RNA immunoprecipitation sequencing (MeRIP-seq)
We then performed 5-methylcytosine profiling analysis using data obtained from mRNA MeRIP-seq of young and aged hippocampus tissues.

overall_design: Comparative 5-methylcytosine profiling analysis of MeRIP-seq data for young and aged hippocampus tissues.

first: Chengbiao

first: Xuan

last: Zhang


title: Distinct top-down control for allodynia and anxiety-like behaviors in chronic pain

city: Guangzhou

first: yao

last: shan

state: Guangdong

address: Xinzao

institute: guangzhou

summary: To further determine the underlying mechanisms mediating the elevated excitatory synaptic activity and anxiety symptoms in the chronic pain model, we collected PrL tissues from SNI and sham mice and subjected them to transcriptome analysis.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for PrL tissues from SNI and sham mice

first: Feng

last: Gao


title: RNA-seq of mosaic Down syndrome hiPSCs derived  cardiac cells (differentiation on 8)

first: Juli

last: Liu

address: Zhongshan 2nd road

department: Medical Research Center

institute: Guangdong provincial people's hospital

summary: To know gene expression patterns affected by 3 copies of chromosome 21 in cardiac cells

overall_design: isogenic pair: Normal hiPSCs- and Trisomy 21 hiPSCs-derived cardiac cells

first: Shaoxian

last: Cheng


title: ANP32B suppresses B-cell acute lymphoblastic leukemia development through activation of PU.1 in mice

city: Shanghai

first: Wei

last: Yusheng

state: New York

address: 227,South Road of Chongqian,Shanghai,China

institute: Shanghai Jiao Tong University of Medicine

summary: The acidic leucine-rich nuclear phosphoprotein 32B (ANP32B) is critical for maintenance of normal and leukemia stem cells. However, no data exist on ANP32B requirement in B-cell acute lymphoblastic leukemia (B-ALL) progression. Here, we observe that ANP32B is lowly expressed in B-ALL patients, which correlates with poor prognosis. Furthermore, we utilize N-myc or BCR-ABLp190-induced B-ALL mouse model to investigate the role of ANP32B in B-ALL development. Intriguingly, conditional deletion of Anp32b in hematopoietic cells significantly promotes leukemogenesis in B-ALL. Mechanistically, ANP32B interacts with PU.1 and enhances the transcriptional activity of PU.1 in B-ALL cells. Overexpression of PU.1 dramatically suppresses B-ALL progression, and highly expressed PU.1 significantly reverses the accelerated leukemogenesis in Anp32b-deficient mice. Collectively, our findings firstly identify ANP32B as a suppressor gene and provide novel insight into B-ALL pathogenesis.

overall_design: RNA-seq data from GFP+ BM cells from recipients receiving N-myc-transduced Anp32b+/+ and Anp32b-/-B220+ BM cells.

first: Qian

last: Yang

first: Yun

last: Yu


title: circRNA expression in human tissue samples

status: Public on Sep 23 2025

city: yinchuan

first: wang

last: linan

state: ningxia

address: ictory Street, Yinchuan, Ningxia

institute: Department of Orthopedics, General Hospital of Ningxia Medical University

summary: Comparative analysis of circRNA expression between experimental and control groups.

overall_design: 3 experimental vs 3 control samples

first: Wang

last: Linan

first: Niu

last: Ningku


title: Precise Gene Editing of Pathogenic Lamin A Mutations Corrects Cardiac Disease

city: Dallas

first: kenian

last: chen

address: 5323 Harry Hines Boulevard

department: Population and Data Science

institute: UTsouthwestern

summary: Mutations in the lamin A (LMNA) gene, which encodes the lamin A and C proteins, cause severe human diseases collectively known as laminopathies. These conditions are often devastating and lack effective therapies. In this study, we developed precise base editing (BE) strategies targeting the human LMNA gene variants L35P and R249Q, which cause Congenital Muscular Dystrophy (CMD) and Dilated Cardiomyopathy with Conduction Defects (DCM-CD), respectively. Induced pluripotent stem cell-derived cardiomyocytes (iPSC-CMs) carrying the R249Q mutation displayed nuclear aberrations, DNA damage, and abnormal Ca2+ transients. Similarly, L35P iPSC-CMs exhibited abnormal contraction, DNA damage, and reduced lamin A/C protein expression. We also generated novel “humanized” mouse models carrying these pathogenic human mutations. R249Q homozygous mice exhibited cardiac conduction abnormalities, cardiac arrhythmias, and premature death. Mice with the homozygous L35P mutation displayed severe muscle-wasting and reduced lifespan, while heterozygous L35P mice displayed dilated cardiomyopathy (DCM). We developed an adenine base editing (ABE) approach for correcting the R249Q mutation and a cytosine base editing (CBE) strategy for the L35P variant. Precise correction of these mutations in iPSC-CMs successfully rescued all of the in vitro abnormalities. Furthermore, delivery of the BE components using adeno-associated virus (AAV) prevented the pathological phenotypes and extended longevity of mice carrying the LMNA L35P and the R249Q mutations. These results demonstrate the efficacy of ABE and CBE in correcting pathogenic LMNA mutations that cause cardiac disease, highlighting BE as a promising therapeutic approach for human laminopathies.

overall_design: Paired-end bulk RNA-sequencing of adult mouse hearts.

first: Xurde

last: Caravia

first: Eric

last: Olson


title: E. coli are poised to grow using 5’-deoxynucleosides via MtnR and CRP regulation of DHAP shunt gene expression

city: Columbus

first: Justin

last: North

address: 484 W 12th Ave

department: Department of Microbiology

institute: Ohio State University

summary: The dihydroxyacetone phosphate (DHAP) shunt is a multifunctional pathway for the metabolism of 5’-deoxynucleosides and 5-deoxypentose sugars, such as 5’-methylthioadenosine (MTA) and 5’-deoxyadenosine (5dAdo), into DHAP and an aldehyde species depending on the substrate. Previous work revealed that E. coli strains with the DHAP shunt can utilize exogenous MTA, 5dAdo, and derivatives thereof as sole carbon and energy sources for growth. However, if and how the DHAP shunt was regulated for 5-deoxynucleoside and 5-deoxypentose sugar metabolism remained unknown. In the present work, the DHAP shunt genes (mtnK, mtnA, ald2) and a putative transporter gene of E. coli ATCC 25922 are observed to form an operon, which can be expressed from two separate transcription start sites (TSSs). The distal, low-activity TSS appears to be constitutive, while the proximal primary TSS is regulated based on the identity of available growth substrates by at least two transcriptional regulators. First YjhU, a DeoR family regulator previously of unknown function that we designate as MtnR, functions as a repressor of the DHAP shunt operon when DHAP shunt substrates are absent. Further, the cyclic AMP receptor protein (CRP) imposes carbon catabolite repression while glucose is available. Based on comparative sequence analysis, the E. coli DHAP shunt promoter region is highly conserved, including strains of the globally disseminated ST131 lineage of Extraintestinal Pathogenic E. coli, indicating a similar regulatory paradigm. Thus the E. coli DHAP shunt is a previously unrecognized pathway for use of 5-deoxynucleosides and 5-deoxypentose sugars as alternative carbon sources when glucose is scarce.

overall_design: RNA-Seq analysis of wild-type E. coli versus DmtnR strains

first: Katherine

last: Huening

first: Caitlin

middle: C

last: Wingerd

first: Joshua

middle: T

last: Groves

first: Katelyn

last: Kapusta

first: Laiba

last: Khan

first: Robert

last: Tabita


title: iNKT Cells Exacerbate Sepsis-Associated Acute Lung Injury through IFN-γ-Mediated Promotion of Macrophage Apoptosis

city: Wuhan

first: Bin

address: jiefang Avenue,Qiaokou District

institute: Tongji Hospital

summary: iNKT cells are a unique subset of T lymphocytes that play important and distinct roles in sepsis due to their specialized characteristics. Unlike conventional T cells, which are restricted by polymorphic major histocompatibility complex (MHC) molecules and recognize peptide antigens, iNKT cells are restricted by the non-polymorphic CD1d molecule and respond to lipid antigens. Upon activation, they rapidly produce large quantities of cytokines such as IFN-γ and IL-4. While the immunoregulatory function of iNKT cells in sepsis has been well established, their dual capacity to exert both pro-inflammatory and anti-inflammatory effects remains incompletely understood. In particular, their specific role during the early stages of sepsis remains elusive. This study aims to elucidate the mechanism by which iNKT cells contribute to immune dysregulation in sepsis through the iNKT-macrophage axis.

overall_design: We elucidated the mechanism by which iNKT cells exacerbate early inflammatory responses and contribute to immune dysregulation in sepsis-associated acute respiratory distress syndrome (ARDS), which involves the modulation of macrophage cell death. Using genetically engineered mouse models in combination with in vitro co-culture experiments (DN32.D3 cells with bone marrow-derived macrophages [BMDMs]), a co-culture system was established between BMDMs and DN32.D3 cells under standardized stimulation conditions. Specifically, DN32.D3 cells were seeded at a macrophage-to-iNKT cell ratio of 3:1 in 6-well plates, with 2 mL of RPMI-1640 complete medium per well. The modeling group was treated with LPS and α-Galactosylceramide. After 6 hours, suspended cells were collected and washed three times with ice-cold PBS.

first: Yiming

last: Tao

first: Xinxin

last: Xu

first: Cheng

last: Li

first: Lijuan

last: Zou

first: Hui

last: Zhao

first: Wenpei

last: Dang


title: miRNA profiles of EVs released from human umbilical cord mesenchymal stem cells (hUCMSC-EVs)

first: JIE

last: LIAN

state: Henan

address: Jinsui Road

department: Henan Joint International Research Laboratory of Stem Cell Medicine

institute: Xinxiang Medical University

summary: To identify specific miRNAs carried by hUCMSC-EVs, and explore their crucial roles in hUCMSC-EV-based improvement of inflammatory diseases.

overall_design: miRNAs expression in hUCMSC-EVs derived from two different donors. EVs were isolated from cell-free conditioned medium after 48 hrs of culture using differential ultracentrifugation. Total RNA was extracted with TRIZOL reagent, quantified spectrophotometrically (NanoDrop ND-2000, Thermo Scientific), and assessed for integrity using an Agilent Bioanalyzer 2100 (Agilent Technologies). Following manufacturer protocols, RNA samples were dephosphorylated, denatured, and labeled with Cyanine-3-CTP. After purification, labeled RNA was hybridized to a miRNA microarray. Slides were washed and scanned using the Agilent Scanner G2505C (Agilent Technologies).

first: Juntang

last: Lin

first: Jie

last: Lian

first: Xinxing

last: Zhu


title: Precisely controlled cell-cell interactions with single-cell transcriptome readout identify a time-demand threshold response of human oncolytic NK cells

city: Vienna

first: Jakob

last: Huemer

state: Vienna

address: Zimmermannpl. 10

country: Austria

institute: Children’s Cancer Research Institute

summary: Cell communication via cell-cell interactions is a fundamental biological process shared by all multicellular organisms and broadly relevant to human health and disease. Activation and function of cells of the im-mune system particularly depends on direct cell-cell interactions, which are fast, transient and hard to study. To characterize NK-cell intrinsic gene expression programs that are activated upon target cell en-counter, we develop a cell interaction profiling system (CIPS) and investigate the genome-wide transcrip-tional responses of individual interacting cells with precise temporal control over the first minutes of inter-action. We utilize di-electrophoretic fields to initiate cell-cell contact of fluorescence microscopy-informed, selected single cells and separate them again with precise control of interaction time followed by single-cell transcriptomics as readout. Applying CIPS to the interaction of NK cells with cancer cells, we find that in-teractions shorter than 15 minutes lead to downregulation of a gene set including the tyrosine kinases TYK2 and LCK, required for NK-cell effector function and tumor surveillance. Dissecting the molecular effects associated with a rare genetic disease that compromises NK cell function, we show that this re-sponse is independent of target cell lysis. Exploiting our method’s ability to orchestrate sequential series of cell-cell interactions, we further demonstrate that the downregulation of the identified gene signature is overcome by repeatedly challenging NK cells with cancer cells. In conclusion, we introduce a method for precise dissection of cell-cell interactions with unprecedented temporal resolution; our observations sug-gest a model where NK cells downregulate genes relevant for engagement of lytic function if the interaction with a potential target cell is too short, but allows responsiveness to further interactions, representing a “time-demand threshold (TDT)”.

overall_design: 447 RNA-seq samples of cells analyzed with the cell interaction profiling system (CIPS) & FACS purified control samples

first: Nikolaus

last: Fortelny

first: Lisa

last: Shaw

first: Dominik

last: Emminger

first: Benjamin

last: Salzer

first: Manfred

last: Lehner

first: Wolfgang

last: Weninger

first: Kaan

last: Boztug

first: Christoph

last: Bock

first: Matthias

last: Farlik


title: Gut Microbiota-Derived Trimethylamine-N-Oxide Protects Pulmonary Vascular Barrier Integrity via VAV3-Mediated Cytoskeletal Remodeling in Acute Lung Injury

city: Guanghzou

first: Xilong

last: Wang

address: 253 Gongye Middle Avenue

institute: Zhujiang Hospital of the Southern Medical University

summary: Acute respiratory distress syndrome (ARDS) and acute lung injury (ALI) are characterized by increased pulmonary capillary permeability, but lack effective pharmacotherapies. Emerging evidence implicates gut-lung axis dysregulation contributes to ARDS pathogenesis through microbiome-host interactions, but the effects of the microbiota-derived metabolite, trimethylamine-N-oxide (TMAO) remains unclear. Here, we demonstrate that plasma TMAO levels are significantly elevated in ARDS patients compared to healthy controls, correlating positively with hypersensitive C-reactive protein (hs-CRP). In a murine lipopolysaccharide (LPS)-induced ALI model, TMAO administration reduced lung vascular leakage and neutrophil infiltration, whereas inhibition of gut-microbiome-derived TMAO synthesis worsened injury. Mechanistically, TMAO enhances endothelial barrier integrity by upregulating VAV3, which drives Rac1-dependent cortical actin reorganization. Knockdown of VAV3 abolished TMAO-mediated endothelial barrier protection, confirming its necessity. Our study identifies TMAO as an adaptive mediator involved in gut-lung axis, that mitigates pulmonary vascular hyperpermeability via VAV3-Rac1-cytoskeletal signaling, highlighting its therapeutic potential for ALI/ARDS.

overall_design: To elucidate the role of TMAO in acute lung injury (ALI), we performed RNA sequencing (RNA-seq) on lung tissue of LPS-ALI mice with or without TMAO treatment

first: Tao

first: Xin

last: Chen


title: Transcriptome analysis of Pseudomonas syringae pv. tomato DAPP-PG 215 in response to silver nanoparticles exposure

city: Perugia

first: Benedetta

last: Orfei

address: Borgo XX Giugno 74

institute: University of Perugia

summary: Silver nanoparticles (AgNPs) are one of the most promising options for the control of bacterial pathogens. The effectiveness of AgNPs has been proven by several recent research studies in which toxicity against a broad range of human and plant pathogenic bacteria was observed, even when used at low doses compared to other conventional bactericides. Nevertheless, the antibacterial mechanism of AgNPs is yet to be completely understood. This study investiagted the first response of Pseudomonas syringae pv. tomato strain DAPP-PG 215, the causative agent of bacterial speck disease of tomato, to AgNPs. Gene expression of P. syringae pv. tomato in response to AgNPs was observed after 10 and 30 minutes of exposure. A total of 78 and 66 genes were identified as differentially expressed, respectively. Gene ontology and KEGG pathway enrichment analysis revealed a high representation of genes related to stress resistance, energy metabolism, and metal ion binding proteins, with different transporters involved. Validation of four selected genes by quantitative RT-PCR analysis, confirmed these observations. These results not only supported initial findings on the antimicrobial action of AgNPs, but also suggested a significant impact of different heavy metal – toxin transporters in the silver detoxification mechanism of bacteria.

overall_design: Transcriptomic response of Pseudomonas syringae pv. tomato strain DAPP-PG 215 to sub-lethal silver nanoparticles (AgNPs) exposure (0.125 ppm) at 10 and 30 minutes

first: Joël

last: Pothier

first: Luca

last: Scotti

first: Antonio

last: Aceto

first: Chiaraluce

last: Moretti

first: Roberto

last: Buonaurio

first: Theo

last: Smits


title: Human peritoneal CCR2LowCRIgHigh macrophage subset exhibits embryonic origin-like phenotypes

city: Kumamoto

first: Naofumi

last: Takahashi

address: 2-2-1 Honjo, Chuo-ku

institute: Kumamoto University

summary: maintained by the differentiation of bone marrow-derived monocytes and the proliferation of macrophages originating from yolk sac or fetal liver. However, to what extent this paradigm shift is the case for human tissues is not fully understood. Here, we detect a human peritoneal macrophage subset which exhibits embryonic origin-like phenotypes. Macrophages in ascites of patients with gastric cancers were divided into CCR2Low and CCR2High subsets, the ratio of which was variable among donors. The gene expression profiles of these subsets were similar to those of macrophage subsets in hearts. CRIg was recently reported as a marker to distinguish two macrophage subsets in ascites of patients with cirrhosis. CCR2Low and CCR2High subsets identified in this study expressed CRIg at high and low levels, respectively. Importantly, the CCR2LowCRIgHigh subset expressed the cell proliferation marker Ki67 and recently-proposed core markers for macrophages with embryonic origin (TIMD4, LYVE1, and FOLR2) at higher levels than those of the CCR2HighCRIgLow subset. Moreover, many other markers shared by TIMD4+LYVE1+FOLR2+ macrophages in heart, lung, kidney and liver exhibited a similar expression pattern in the peritoneal CCR2LowCRIgHigh subset. These results suggest that the CCR2LowCRIgHigh subset in peritoneal cavity contains macrophages with embryonic origin.

overall_design: Total RNA was isolated from sorted peritoneal macrophage subsets in ascitic fluid.

first: Sara

last: Habash

first: Yoshihiro

last: Komohara

first: Shingo

last: Usuki

first: Keiichiro

last: Yasunaga

first: Shinjiro

last: Hino

first: Thorbjorg

last: Einarsdottir

first: Takushi

last: Nomura

first: Takatsugu

last: Ishimoto

first: Shinya

last: Suzu


title: Effects of doxorubicin on miRNA expression in tumor cell small extracellular vesicles

city: Beijing

first: Dong

last: Han

address: 28 Fuxing street

institute: Chinese PLA general hospital

type: Non-coding RNA profiling by high throughput sequencing

summary: To examine the changes of miRNA in the  small extracellular vesicles of breast cancer cells receiving DOX chemotherapy. Human breast cancer cells (MDA-MB-231 cells) were cultured with exorcism-free serum, and treated with DOX. After  24h, cell supernatant was collected and small extracellular vesicles were extracted by ultra-fast centrifugation method, and miRNA content in small extracellular vesicles was obtained for high-throughput miRNA sequencing.

overall_design: miRNA sequencing of 6 samples of small extracellular vesicles from DOX and no drug (control) -treated human breast cancer cells.

first: Han

last: Dong

first: Ma

last: Yan


title: AKK bacteria affects colitis by regulating ferroptosis signaling pathway

city: Fuzhou

first: Yijuan

last: Liu

address: First Affiliated Hospital of Fujian Medical University, Fuzhou 350005, China

summary: To investigate whether Akkermansia muciniphila (AKK) bacteria affects colitis by regulating the ferroptosis signaling pathway, an mouse model of colitis was constructed, and the mice were administered with AKK and the ferroptosis agonist Erastin. HE staining and transmission electron microscopy were used to observe the pathological and microstructural changes of mouse colon tissues. The number of goblet cells was examined using alcian blue staining. The expression levels of oxidative stress-related indicators and ferroptosis-related proteins were detected by ELISA, western blot and immunohistochemisty analyses. Transcriptome and non-targeted metabolome sequencing were carried out to screen for differentially expressed genes and metabolites. Immunofluorescence double staining was used to detect the co-localization of cell adhesion-related indicators.16S microbiota sequencing was performed on mouse feces. Erastin caused damage to colon tissues, decreased the expression of ZO-1 and E-Cadherin, and increased the expression of oxidative stress and ferroptosis-related indicators. The species-abundance was increased after AKK treatment, while it was decreased after treatment with AKK bacteria+Erastin. AKK alleviated inflammatory cell infiltration, reduced organelle damage, and decreased the number of goblet cells in mice with colitis. MDA, ROS, and Fe2+ levels in colitis tissues were increased, but they were decreased after AKK bacteria treatment. The expression of GPX4 and SLC7A11 was decreased, while ACSL4 was  increased. After intervention with AKK bacteria, the trend of changes in the above indicators was reversed, and 19 differential pathways were enriched. In conclusion, AKK bacteria can treat colitis in mice, and its mechanism may be related to regulating the ferroptosis signaling pathway.

overall_design: To investigate whether Akkermansia muciniphila (AKK) bacteria affects colitis by regulating the ferroptosis signaling pathway, an mouse model of colitis was constructed, and the mice were administered with AKK and the ferroptosis agonist Erastin. Transcriptome sequencing were carried out to screen for differentially expressed genes.Sample group "Control" refers to: The SPF grade C57BL/6J mice (male, 6 weeks old) were kept in an environment with a temperature of 20-26℃ and a humidity of 40-70%, and have free access to food and water. Sample group "Model" refers to: To construct the colitis model, the mice were given 3% DSS solution for free drinking for one week, followed by DAI scoring and HE validation. During the intervention period, the model group was administered with equal volumes of PBS by gavage.Sample group "AKK" refers to:During the intervention period, the AKK group was administered with AKK bacteria. The bacterial solution concentration was 1.5 x109 CFU/mL, and the gavage volume was 0.1 mL/animal, once a week for 6 weeks.

first: Lin

last: Zhang

first: Kaiyan

last: Wei


title: Essentiality and dynamic expression of the human tRNA pool during viral infection [CRISPRlib]

city: Rehovot

first: Noa

last: Aharon-Hefetz

address: 234 Herzl Street

country: Israel

institute: Weizmann Institute of Science

summary: Human viruses rely on host translation resources, including the cellular tRNA pool, because they lack tRNA genes. Using tRNA sequencing, we profiled mature tRNAs during infections with human cytomegalovirus (HCMV) and SARS-CoV-2. HCMV-induced alterations in mature tRNA levels were predominantly virus-driven, with minimal influence from the cellular immune response. Certain post-transcriptional modifications correlated with tRNA stability and were actively manipulated by HCMV. By contrast, SARS-CoV-2 caused minimal changes in mature tRNA levels or modifications. Comparing viral codon usage with proliferation- versus differentiation-associated codon-usage signatures in human genes revealed striking divergence. HCMV genes aligned with differentiation codon usage, whereas SARS-CoV-2 genes matched proliferation codon usage. Structural and gene-expression genes in both viruses showed strong adaptation to host tRNA pools. Finally, a systematic CRISPR screen of human tRNA genes and tRNA-modifying enzymes identified specific tRNAs and enzymes that either enhanced or restricted HCMV infectivity and influenced cellular growth. Together, these data define a dynamic interplay between the host tRNA landscape and viral infection and illuminate mechanisms governing host–virus interactions.

overall_design: sgRNA-seq of HFF with tRNA knockout CRISPR library, before and after 3 days of competition and of HCMV-infected HFF with tRNA knockout CRISPR library.Infected cells were FACS-sorted according to HCMV infection progression.

first: Michal

last: Schwartz

first: Noam

last: Stern-Ginossar

first: Orna

last: Dahan

first: Yitzhak

last: Pilpel


title: An inhibitor of UHM splicing factors exerts anti-leukemic activity by altering cell cycle progression and reducing lysosome acidification

city: Memphis

first: Chao-Yie

last: Yang

state: Tennessee

address: 881 Madison Avenue, Rm559

department: Pharmaceutical Sciences

institute: University of Tennessee HSC

summary: Mature mRNAs are generated by spliceosomes that recruit factors to aid RNA splicing in which introns are removed and exons joined. Among the splicing factors, a family of proteins contain a homologous U2 Auxiliary Factor (U2AF) Homology Motif (UHM) to bind with factors containing U2AF ligand motifs (ULM) and recruit them to regulate 3’ splice site selection. Mutations and overexpression of UHM splicing factors are frequently found in cancers. Although a few UHM inhibitors have been reported, their activities in cancer cells were not investigated. Here, we studied our recently discovered UHM inhibitor, SF-153, that targeted RBM39 and SPF45, and found SF-153 exerted anti-tumor activities in three leukemia cell lines. In the cell cycle and apoptosis analysis, SF-153 induces p53 mediated DNA damage response to give protracted S phase in NKM-1 but p53-independent G1 arrest in p53null K562 cells. RNA-seq analysis of NKM-1 treated with SF-153 revealed downregulation of Myc target genes and genes involved in nucleotides and protein synthesis. Western blot analysis confirmed decreased proteins levels of Myc, EEF1A1, and MCM7 suggesting reduced DNA replication activity in NKM-1. Transcript analysis derived from the RNA-seq data indicated six genes changed isoform patterns but downregulation of only one DOCK2 isoform was confirmed in qRT-PCR. RNA-seq analysis additionally uncovered that SF-153 impaired lysosome acidification and inhibited autophagy to enhance the anti-leukemic activities. Taken together, our study characterized the multimodal mechanisms of inhibition by SF-153 in leukemia cells and lay the foundation for studying selective UHM inhibitors in future.

overall_design: RNA-seq experiment of NKM-1 treated with SF-153 (30uM) and DMSO for 48 h

first: Arda

last: Durmaz

first: Valeria

last: Visconte


title: Essentiality and dynamic expression of the human tRNA pool during viral infection [HCMVinfection_tRNAseq]

overall_design: tRNA-seq profiling of HCMV infected HFF in various time points following infection, uninfected samples and two addition treatments- uninfectec with IFNα+β  and HCMV-infected (24hpi) with Ruxolitinib.


title: Essentiality and dynamic expression of the human tRNA pool during viral infection [SARSinfection_tRNAseq]

overall_design: tRNA-seq profiling of SARS-CoV-2 infected Calu3 cells- uninfected and 6hpi.


title: Th1 effector CD4 T cells rely on IFN-g production to induce Alopecia areata

city: Iowa City

first: Ali

last: Jabbari

state: IA

address: 25 South Grand Ave

department: Dermatology

institute: University of Iowa

summary: Alopecia areata (AA) is an autoimmune disease that is characterized by hair loss clinically and peribulbar infiltration of CD8 and CD4 T cells histologically. Prior studies have focused on the role of CD8 T cells in the development of AA; however, the role of CD4 T cells is unclear. Here, we demonstrate that CD4 T cells from the skin draining lymph nodes (SDLN) of AA mice could transfer disease into recipient mice. Further, these cells exhibited a T-helper type 1 (Th1) effector transcriptional and phenotypic profile. Pathogenic activity of these CD4 T cells was dependent upon the presence of endogenous CD8 T cells and host IFN-g signaling. Targeted removal of CD4 T cell-mediated production of IFN-g abrogated the ability of this cell population to transfer disease. Together, our study provides mechanistic insights into pathways that lead to AA development, heightening our understanding of the disease and inviting studies into exploring novel therapeutic strategies for human patients.

overall_design: RNA-seq profiling of live TCRβ+CD4+ T cells that were sorted (Becton Dickinson FACS Aria Fusion) from skin draining lymph nodes (SDLNs) of unaffected (UA) and alopeica areata (AA) affected C3H/HeJ mice.

first: Sam

last: Connell

first: Ryan

last: Reis


title: RNA sequencing analysis of 5- and 7-day old salivary gland organoids

city: Groningen

first: Davide

last: Cinat

address: Hanzeplein 1

institute: University Medical Center Groningen

summary: The specific effects of different radiation types, such as photons and protons, on normal stem cell activity and tissue regeneration remain poorly understood. In our previous work, we characterized salivary gland organoids at 2 days post-irradiation (corresponding to 7-day-old organoids) using single-cell RNA sequencing. To compare the cellular composition of 5-day-old organoids (day of irradiation) with that of 7-day-old organoids, we performed bulk RNA sequencing and applied the deconvolution tool CIBERSORTx, using the 7-day single-cell dataset as a reference. This analysis confirmed that the cell populations in 5- and 7-day-old salivary gland organoids were comparable.

overall_design: Organoids derived from 3 different mice were were collected at day 5 and day 7 and processed for RNA-seq analysis.

first: Rob

middle: P

last: Coppes

first: Lara

last: Barazzuol


title: Cdk8 kinase activity regulates transcriptional responses to pathological cardiac hypertrophy [RNA-seq]

first: Chad

last: Grueter

address: 169 Newton Rd, 4332 PBDB

department: Internal Medicine

summary: Purpose: The objective of this study was to determine the role of CDK8 kinase activity in hypertrophic transcriptional regulation using an in vitro rat neonatal cardiomyocyte hypertrophy model

overall_design: Methods: Neonatal rat cardiomyocytes were treated with phenylephrine in the presence or absence of CDK8 kinase inhibitor, Senexin A

first: Rachel

last: Minerath

first: Kayla

last: Henry


title: ZDHHC13 Modulates Tumor Microenvironment Interactions to Suppress Melanoma Metastasis [scRNA-Seq]

city: Cleveland

first: Shuyang

last: Chen

state: OH

address: 9500 Euclid Ave

institute: Cleveland Clinic

summary: This dataset supports a study investigating the role of ZDHHC13 in melanoma development. Using bulk RNA sequencing and 10x Genomics single-cell RNA sequencing, we analyzed how ZDHHC13 influences tumor progression and the tumor microenvironment. These data provide insights into the transcriptomic changes associated with ZDHHC13 activity in melanoma and serve as a resource for understanding gene expression dynamics in both tumor cells and surrounding immune components.

overall_design: For single-cell RNA sequencing, ZDHHC13-overexpressing or control B16F10 cells were subcutaneously inoculated into immunocompetent C57BL/6 mice. Tumors were harvested at defined time points, dissociated into single-cell suspensions, and processed using the 10x Genomics platform. This design allowed us to examine both tumor-intrinsic and tumor microenvironment responses to ZDHHC13 expression at single-cell resolution.

first: Hongjin

last: Li


title: Extracellular Vesicle miRNAs as Biomarkers of Asthma Severity

city: Kansas City

first: Isaac Kirubakaran

last: Sundar

state: KS

address: University of Kansas Medical Center, Dept. of Internal Medicine/Pulmonary Critical Care and Sleep Medicine

institute: University of Kansas Medical Center

summary: Asthma is a chronic lung disease with various clinical phenotypes, complicating its diagnosis and treatment. The micro-RNA (miRNA) profile of plasma-derived extracellular vesicles (EVs) may serve as potential circulating biomarkers for differentiating asthma phenotypes/endotypes. This study aims to characterize and compare the miRNA profiles in plasma-derived EVs across healthy controls (HC), non-severe asthmatics (NS), and severe asthmatics (SA). EVs were isolated from plasma samples of HC, NS, and SA, followed by physiochemical characterization and RNA isolation. Small RNA sequencing was performed, and differentially expressed (DE) miRNAs were identified through DESeq2 analysis. DE miRNAs and their predicted mRNA targets were identified using Ingenuity Pathway Analysis (IPA), and pathway enrichment was conducted using STRING DB and Enrichr. EVs from all groups were predominantly ~150-200 nm in size, with significantly higher EV counts in SA compared to HC and NS. miRNA expression analysis revealed unique and shared DE miRNAs across the three comparisons (HC vs. NS; HC vs. SA; NS vs. SA). A total of 16 unique DE miRNAs among these comparisons, between which in the NS vs. SA comparison, miR-515-3p positively correlates with lung function, and exacerbation and miR-133a-3p and miR-9-5p with ACT score. Target and pathway analyses from the NS vs. SA comparison indicated the enrichment of key pathways, including IL-4/IL-13, Th1, Th2, and Th17 cell differentiation, MAPK, PI3K-Akt, and receptor tyrosine kinase signaling. This study identified distinct miRNAs in plasma-derived EVs from NS vs. SA which could serve as potential circulating biomarkers for differentiating asthma severity.

first: Sundar

last: Isaac Kirubakaran

first: Pei

last: Dong

first: Griffard

last: Rachel

first: Prasad

last: Chandrashekar


title: Adipocyte- Specific FFA2 Deletion Leads to Increased Adipose Inflammation and Is Associated with Altered Intestinal Lipid Handling

city: Chicago

first: Chioma

last: Nnyamah

state: Illinois

address: 840 South Wood Street, Suite 1020N, MC 787

institute: University of Illinois at Chicago

summary: Obesity and related metabolic disorders are often characterized by chronic adipose tissue inflammation, driving systemic insulin resistance and general metabolic dysfunction. Free Fatty Acid Receptor 2 (FFA2) has emerged as a potential modulator of adipocyte function, inflammation, and metabolism. To investigate the role of FFA2 expressed in the adipose tissue, we generated adipose-specific FFA2 knockout mice (Adipoq-F2-KO) and assessed metabolic outcomes under standard chow and high-fat, high-sugar Western diet conditions, with and without dietary fiber supplementation. We found that adipose-specific FFA2 deletion had minimal metabolic consequences under standard dietary conditions but significantly reduced body weight and adiposity when mice were fed a fiber (fructooligosaccharide)-supplemented Western diet. Subsequent fecal analyses and transcriptomic profiling indicated impaired intestinal lipid absorption as the primary driver of reduced adiposity, suggesting disrupted adipose-intestinal communication. Unexpectedly, the lighter Adipoq-F2-KO mice also exhibited heightened adipose inflammation, characterized by increased macrophage infiltration and pro-inflammatory cytokine expression. Furthermore, in vitro loss-of-function experiments in adipocytes revealed that FFA2 knockdown impaired adipocyte maturation, lipid storage, and anti-inflammatory signaling. Additional studies using intestinal epithelial cells exposed to adipocyte-conditioned media implicated adipose-derived signals in driving intestinal dysfunction. Collectively, our findings highlight adipose-specific FFA2 as critical in regulating adipose tissue inflammation, lipid metabolism, and inter-organ communication. The data uploaded here specifically contains the comparison of mRNA from mature white adipocytes of FFA2 fl/fl mice compared to RNA from Adipoq-F2-KO mice when both are on a normal chow diet.

overall_design: This RNA sequencing dataset was generated to assess baseline transcriptional differences in mature adipocytes resulting from adipocyte-specific deletion of Free Fatty Acid Receptor 2 (FFA2) in mice maintained under standard dietary conditions. Adipoq-F2-KO mice were generated by crossing FFA2 floxed mice (FFA2^fl/fl) with Adiponectin-Cre transgenic mice, enabling adipocyte-specific knockout of FFA2. Male Adipoq-F2-KO mice and their FFA2^fl/fl littermate controls were co-housed and maintained on a standard chow diet (Teklad LM-485) until 20 weeks of age. At this timepoint, mature adipocytes were isolated from perigonadal adipose tissue, and total RNA was extracted for sequencing. RNA integrity was confirmed prior to library preparation and bulk RNA sequencing, which was performed by the UIC sequencing core facility. Differential gene expression analysis was conducted to compare Adipoq-F2-KO and control samples under basal (non-obesogenic) conditions, to identify FFA2-regulated transcriptional programs in adipose tissue independent of dietary challenge.

first: Kai

last: Xu

first: James

last: Boyett

first: Nupur

last: Pandya

first: Layden

last: Brian


title: GCN5-ADA2 Recruits ATP-Citrate Lyase (ACL) and Forms Condensates to Modulate Acetylation at H3K9 for Functional Genes in Rice Meristem

first: Xiaoyuan

last: Guo

state: Hubei

address: No.1 Shizishan Street, Hongshan District

institute: Huazhong Agricultural University

summary: The SAGA complex is a highly conserved histone acetyltransferase (HAT) complex in eukaryotes, playing crucial role in regulating gene transcription throughout organismal development. The complex consists of two core components: GCN5, the HAT subunit, and ADA2, which primarily functions as an adaptor, facilitating interactions between GCN5 and other proteins and enhancing the complex’s accessibility to nucleosomes. Beyond its well-established roles, we discovered that, in rice, ADA2 possesses an evolutionary conserved intrinsically disordered region (IDR) that directs the SAGA complex to form nuclear condensates. Moreover, we identified a physical interaction between ADA2 and ATP-citrate lyase subunit A2 (ACLA2), leading to the formation of a GCN5-ADA2-ACLA2 (GAA) complex. Both GCN5 and ACLA2 exhibit phase separation in vivo, a process that is dependent on ADA2. Within these condensates, ACL contributes to the production and enrichment of acetyl-CoA, thereby promoting histone acetylation. Genetic evidence showed that knock-out or suppression of the three indicated genes collectively resulted in diminished meristem zones at both root tips and inflorescences, accompanied by a significant reduction in genomic H3K9 acetylation and transcriptional attenuation of essential genes for meristem function. In summary, our findings unveiled a novel mechanism for HAT in modulating gene transcription and plant development, in which the GAA complex phase separates and enriches acetyl-CoA metabolites within the nuclear puncta to facilitate the acetylation of histones at target genes.

overall_design: Transcriptome detection by RNA-seq for rice root tips and inflorescence meristems in wild type and the three indicated mutants/RNAi backgrounds. Genomic binding detection for the three components of GAA complex via CUT&Tag. Genomic histone H3 K9 acetylation detection of root tips for wild type and the three indicated mutants/RNAi backgrounds.

first: Tingting

last: Lu

first: Shaoli

last: Zhou


title: Distinct TNF-producing or TNFR2-expressing regulatory T cell subsets cooperate in Treg expansion in cancer and chronic inflammation

city: Rome

first: Valerio

last: Licursi

address: via degli Apuli, 4

department: c/o Dept. Biology and Biotechnologies "C. Darwin", Sapienza University of Rome

institute: Institute of Molecular Biology and Pathology (IBPM), National Research Council (CNR)

summary: TNF is a pleiotropic cytokine that exerts immunomodulatory functions mostly mediated by its interaction with the receptor TNFR2, highly expressed by regulatory T cells. However, Tregs can also produce TNF, and the existence of an autocrine TNF-TNFR2 loop has been proposed. Here, we describe that, indeed, both human and mouse Tregs can produce TNF in physiological conditions, in several mouse organs, and in mouse models of chronic inflammation and cancer. However, TNF production and TNFR2 expression are mutually exclusive in Tregs: indeed, TNFR2+ and TNFR2- Treg subsets are respectively poor and strong TNF producers. In TNFR2+ cells, TNF is both transcriptionally and post-transcriptionally controlled, through the repressing activity of microRNA-146a. The two subsets of TNFR2+ and TNFR2- Tregs partially maintain their different ability to produce TNF, when separately stimulated ex vivo. However, when cocultured, the TNFR2+ cells greatly outnumber the TNFR2- counterpart, and induce in TNFR2- cells the upregulation of Foxp3 and TNFR2, an event that is associated with the transfer of cytoplasmic material from TNFR2+ to TNFR2- cells. Functionally, TNFR2+ Tregs are endowed with superior suppressive activity, in association with a better survival in vitro. This phenotype could be attributed to an improved resistance to oxidative stress, as revealed by gene expression analysis and intracellular ROS staining. Overall, our data indicate that Tregs exist in two states, respectively committed to TNF production or TNF sensing through TNFR2, which cooperate in promoting the suppressive function of the whole Treg pool.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for sorted  TNFR2+ and TNFR2- Tregs from splenocytes of Foxp3CreYFP female mice

first: Gloria

last: Tucci

first: Silvia

last: Piconese