title: Transcriptional and epigenetic programs of in vitro-expanded HSPCs and their T cell progenitors progeny

city: Pasadena

first: Boyoung

last: Shin

state: California

address: 1200 E. California Blvd

institute: Californial Institute of Technology

summary:
Hematopoietic stem and progenitor cells (HSPCs) in the bone marrow are the ultimate sources of all hematopoietic lineage cells, including T cells.  However, gene expression programs and chromatin dynamics that guide the bone marrow progenitor cells to enter the T-development programs are not fully understood due to limited cell numbers and population heterogeneity.  By exploiting the in vitro HSPC expansion approach, which effectively expands HSPCs with high T cell potentials, we monitored the gene expression programs and chromatin accessibility changes underlying the transition from the bone marrow progenitor stages to early T cell development stages.
Notably, expanded HSPCs displayed strikingly similar chromatin accessibility profiles with early-stage T cell progenitors, representing their shared hematopoietic chromatin landscapes.  However, a select set of genomic regions and target genes were specifically regulated as cells first received the strong Notch signaling and engaged with T-development conditions. These events included a robust chromatin opening and transcriptional activation of the T cell receptor (TCR)-C beta locus. In addition, well-known stem and progenitor-associated transcription factors were sharply repressed, often concerted with broad chromatin accessibility losses at those loci.
These gene regulation targets were not an artifact of in vitro expanded HSPC-derived pro-T cells. The progeny of expanded HSPCs and freshly isolated HSPCs share the same T-lineage developmental trajectory at the single-cell transcriptome level, and their gene expression programs were highly similar. However, expanded HSPC-derived pro-T cells showed temporal differences in early T-development speed and progressed through pre-commitment stages slowly.
From cytokine and chemokine screening, we found that a brief Flt3L pre-treatment during the 4-5 days of the expansion period could moderately accelerate the T-development kinetics of expanded HSPCs. Thus, we compared the chromatin accessibility programs, H3K27ac and H3K27me3 histone marks, and gene expression programs upon Flt3L treatment.  Although chromatin state and transcriptional features were mostly not altered by Flt3L treatment at the bulk population levels, scRNA-seq results showed that a set of activation and stress-response genes were upregulated upon Flt3L stimulation. However, Flt3L-primed HSPCs developed through a normal T cell pathway.
Together, these datasets (1) provide comprehensive gene expression and chromatin accessibility profiles of expanded HSPCs and their progeny pro-T cells, (2) reveal molecular events accompanied by bone marrow progenitor cells transition to the T cell program, and (3) suggest a slight modification of the expansion protocol for the use of T cell biology studies by adding acute Flt3L treatment.

overall_design:
In vitro HSPC expansion and early T cell development for bulk RNA-seq, ATAC-seq, and CUT&RUN (C&R):
To expand HSPCs, lineage (CD3e, TCRb, TCRgd, CD19, NK1.1, CD49b, CD11b, CD11c, Ly6G/C)-negative- Kit+ Sca1+ (“LSK”) EPCR+ CD150+ bone-marrow progenitor cells were obtained from 8-10 weeks old C57BL/6J wild-type (WT) animals or Bcl11b-mCitrine reporter mice by FACS sorting. Then, the sorted EPCR+ CD150+ LSK (“ELSK”) cells were expanded in HSPC expansion medium (F12 DMEM, 1 mg/mL of PVA, 1× Insulin–transferrin–selenium–ethanolamine, 10 mM HEPES (pH 7.3-7.5) , 1× Penicillin–streptomycin–glutamine) supplemented with 100 ng/mL of mouse thrombopoietin (TPO) and 10 ng/mL of mouse stem cell factor (SCF) for 2-4 weeks. Expanded HSPCs were enriched for the LSK population by Sca1-positive selection using PE-conjugated anti-Sca1 and anti-PE microbeads (Miltenyi Biotec), or else sorted for ELSK phenotype.  To compare Flt3 ligand (Flt3L)-treatment effects, ELSK-sorted expanded HSPCs were treated with 10 ng/mL of human Flt3L along with 100 ng/mL TPO and 10 ng/mL SCF for 4 days prior to harvest. The unprimed HSPCs were cultured for 4-5 days with 100 ng/mL TPO and 10 ng/mL SCF in the absence of Flt3L.
In vitro early T cell development was achieved by co-culturing Sca1+ expanded HSPCs with OP9-DLL1 stroma cells with human Flt3L and human IL-7 (10 ng/mL each from day 0-day 5, 5 ng/mL each from day 5-day 7, 1 ng/mL each after day 7) in OP9 medium OP9 medium (alphaMEM, 20% FBS, 1×PSQ, and 50 microM beta-mercaptoethanol).  To distinguish DN2 pro-T cells before and after commitment, we used expHSPC from Bcl11b-mCitrine transgenic mice, which activate Bcl11b-mCitrine during commitment. Thus, ETP (Lin-, cKithi, CD25-, Bcl11b-mCitrine-), Bcl11b- DN2a (Lin-, cKithi, CD25+, Bcl11b-mCitrine-), and Bcl11b+DN2a/DN2b (Lin-, cKithi/int, CD25+, Bcl11b-mCitrine+) populations were FACS sorted on day 5 or day 9. The onset of Bcl11b expression is correlated with T-cell lineage commitment (Kueh et al. 2016 Nat Immunol PMID: 27376470).
To measure immediate gene expression changes of expanded HSPCs in response to OP9-DLL1, d10-d14 expanded HSPCs were sorted for LSK. Then, they were subjected to unprimed or Flt3L-primed conditions for 4 days, and re-sorted for LSK phenotype (“d0 expHSPC LSK cells”.  Each input population was co-cultured with OP9-DLL1 for 1 day or for 2 days. After 1 day or 2 days of OP9-DLL1 co-culture, expHSPC progeny cells were sorted for live Lin-negative markers (e.g., “d1 unprimed expanded HSPC progeny” or “d2 unprimed expanded HSPC progeny”) for bulk RNA_seq.
For bulk RNA-seq, total RNA was isolated from 25,000 – 300,000 cells.  ATAC-seq was performed using 50,000 cells. To measure H3K27ac and H3K27me3 marks, 250,000 cells were subjected to C&R.
For bulk RNA-seq, total RNA was isolated from 50,000 – 300,000 cells.  ATAC-seq was performed using 50,000 cells. To measure H3K27ac and H3K27me3 marks, 250,000 cells were subjected to C&R.
Single-cell RNAseq:
ELSK-sorted expanded HSPCs were cultured under “unpriming” or “Flt3L-priming” conditions for 4 days. After 4 days of treatment, unprimed expanded HSPCs were sorted for ELSK (Exp1) or LSK (Exp2). Flt3L-primed expanded HSPCs were sorted for LSK phenotype (Exp1 and Exp2).  Then, these cells were co-cultured with OP9-Dll1 cells for 5 days (Exp1 and Exp2) or 9 days (Exp2).
To compare in vitro T-development pathways that fresh bone marrow progenitor cells utilize, ELSK cells were sorted from freshly isolated bone marrow progenitors and co-cultured with OP9-Dll1 cells for 5 days or 9 days (Exp1 and Exp2).
To measure transcriptional programs of input populations, ELSK cells (Exp1) or LSK cells (Exp2) were sorted from unprimed expanded HSPCs, and LSK cells were sorted from Flt3L-primed expanded HSPCs (Exp1 and Exp2). Similarly, ELSK cells (Exp1 and Exp2) and LSK cells (Exp2) were isolated from fresh bone marrow progenitor cells.  Experiments were designed with staggered starting times for the cultures, in a way that all of these cells within the same experiment could be harvested on the same date. Each population was stained with unique hashtag oligos (HTOs) and loaded to the same 10x Genomics Chromium Controller. Two independent experiments (Exp1 and Exp2) were conducted.

first: Samantha

last: Chang

first: Brendan

last: MacNabb

first: Ellen

middle: V

last: Rothenberg


title: A Polyamine-mediated Posttranslational Modification Required for Macrophage Tissue Residency [scRNA-seq]

status: Public on Jan 15 2026

city: Baltimore

first: Immunometabolism

last: Department

state: Maryland

address: 1650 Orleans Street

department: Immunometabolism

country: USA

institute: Johns Hopkins University

type: Expression profiling by high throughput sequencing

summary: Tissue-resident macrophages (RTMs) form during embryogenesis, self-renew locally, and regulate tissue homeostasis by clearing dead cells and debris. During tissue damage, however, bone marrow-derived monocytes enter tissue sites and differentiate into RTM, repairing the tissue and replenishing macrophages in the niche. Universal cell-intrinsic mechanisms that control the monocyte to RTM transition remain elusive. We investigated mice with myeloid cell deletions in deoxyhypusine synthase (DHPS), an enzyme that mediates the polyamine-dependent hypusine modification of the translation factor eIF5A, and found that DHPS is required for cell adhesion and signaling programs critical for RTMs. Without DHPS expression, immature tissue macrophages form, but RTM and associated homeostatic functions are lost. Thus, the polyamine-hypusine pathway is a global, tissue-agnostic program driving the differentiation trajectory of monocyte-derived macrophages into RTM.

overall_design: Single cells were isolated from the peritoneal cavity of indicated animals with 3-4 biological replicates per genotype (KO and DHPS) and prepared for single cell RNA sequencing using the GemCode Single Cell Platform with GemCode Gel Beads, Chip and Library Kits (v3) and 10X Genomics Chromium Controller following the manufacturer’s protocol.

first: Erika

middle: L

last: Pearce

first: David

middle: E

last: Sanin

first: Gustavo

last: Carrizo


title: Huang Lian Jiedu Decoction ameliorates lipid metabolic disorders in obese mice by modulating gastric inhibitory polypeptide release via intestinal microbiota regulation

city: Nanjing

first: Yue

last: Yang

address: 1 WenYuan Road

country: China

institute: Nanjing Normal University

summary: Obesity is a chronic metabolic disorder that increases the risk of various metabolic diseases, such as type 2 diabetes and metabolic dysfunction-associated steatohepatitis (MASH). While previous studies have shown that Huang Lian Jiedu Decoction (HLJDD) can alters gut microbiota to improve glycolipid metabolism and obesity, the underlying mechanisms still need to be clarified. The present study aimed to explore the potential mechanisms of HLJDD in suppressing obesity more deeply through an integrated research strategy.

overall_design: RNA-seq analysis of the small intestine of mice in the ND, HFD and HLJDD groups (N, H, H2)

first: Kerui

last: Shen

first: Wenjie

last: Zhao

first: Chenxi

last: Guo

first: Yannan

last: Qi

first: Zhigang

last: Hu

first: HongJie

last: Di


title: RNA Polymerase II Transcriptional Pausing and Release Regulates Circadian Transcription

city: Dallas

first: Noheon

last: Park

state: Texas

address: 5323 Harry Hines BLVD, NA4.124

department: Neuroscience

institute: UT Southwestern Medical Center

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Circadian rhythms regulate the harmonized gene expression, metabolism and physiology through transcriptional controls. It is widely accepted that the recruitment of circadian transcriptional factors has a critical role in rhythmic gene expressions. However, the roles of RNA polymerase II pausing and release (RNAP II P/R) on circadian rhythm remain largely unknown. From the massive and precise sequencing experiments, we found the static occupancies of RNAP II complex on the initiation sites and rhythmic elongation controls on Alas1 and Srebf1 genes. The subsequent genome-wide analysis retrieved 54 circadian RNAP II P/R rhythmic genes (91 transcripts) that are closely related to nutritional signals. Those genes kept unique rhythms in clock mutant mice and showed the dynamic responses under the reversed feeding regime. Here, we report a novel circadian transcription mechanism, RNAP II pausing & rhythmic release.

overall_design: The 6 weeks old male mice were housed in the two light chambers with a 2hr shifted light:dark (LD)=12hrs:12hrs condition and fed ad libitum. After 4 weeks of the entrainment, a light/dark chamber was released to constant darkness (DD) condition 24hrs earlier than the other. The liver samples (N=3) were collected after 36 hours of DD condition beginning with the first point (CT00) and subsequent every 4hrs collections for each light chamber till CT44. The harvested liver samples were analyzed by ChIP-seq, PRO-seq and mRNA-seq.

first: Mariko

last: Izumo

first: Byeongha

last: Jeong

first: Carla

middle: B

last: Green

first: Joseph

middle: S

last: Takahashi


title: Comparative Single-Cell Analyses in Infants Revealed RSV-Specific Declines in NK Cell Responses and COVID-19-Specific Increases in Inflammatory Responses [COVID_RSV_snATAC]

city: Farmington

first: Asa

last: Thibodeau

state: CT

address: 10 Discovery Drive

department: Genomic Medicine

institute: The Jackson Laboratory

summary: The clinical phenotype of infants infected with respiratory syncytial virus (RSV) differs from that of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection. RSV is the leading cause of hospitalization for lower respiratory tract infection and carries a significant higher risk of respiratory failure compared to SARS-CoV-2, which has been generally linked to  fever and croup in young infants. The underlying mechanisms these differences remain unclear. We analyzed peripheral blood mononuclear cells (PBMCs) and serum from infants infected with SARS-CoV-2 (n=30), RSV (n=19), and healthy controls (n=17) using single-cell RNA sequencing, single-nucleus ATAC sequencing and cytokine profiling. Both viruses triggered type I interferon responses across PBMC subsets but differed in their NK cell and inflammatory responses. Severe RSV cases were characterized by lower NK cell percentages, lower IFNG expression and diminished chromatin accessibility at T-BET and EOMES binding sites in NK cells. Furthermore, RSV infections were associated with increased frequencies of CD4+ TEMRA and memory Treg cells. In contrast, SARS-CoV-2 infections were marked by more pronounced pro-inflammatory signatures, including increased transcriptional and epigenetic activity at NFKB factors and higher serum TNF concentrations. These findings highlight distinct immune response pathways in RSV and SARS-CoV-2 infections that may inform future therapeutic strategies.

overall_design:
To investigate transcriptional and epigenetic profiles of infant immune responses to SARS-CoV-2 and RSV infections, we obtained blood samples from 30 SARS-CoV-2 infected and 19 RSV infected infants. Peripheral blood mononuclear cells (PBMCs) were isolated to obtain single cell resolution profiles of these cells. Profiles were also obtained for 17 healthy controls for comparison purposes.

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

first: Asunción

last: Mejías

first: Djamel

last: Nehar-Belaid

first: Radu

last: Marches

first: Virginia

last: Pascual

first: Jacques

last: Banchereau

first: Octavio

last: Ramilo

first: Duygu

last: Ucar


title: Metabolic control of innate immune activation in TET2-mutant clonal hematopoiesis

city: Boston

first: Peter

middle: G

last: Kim

state: MA

address: 360 Longwood Ave, LC8202

department: Medical Oncology

institute: Dana Farber Cancer Institute

summary: TET2 mutations drive inflammation in clonal hematopoiesis of indeterminate potential (CHIP), but the mechanism by which TET2 inactivation leads to inflammation is not understood. Here, we used in vivo genome-wide genetic perturbations in primary wildtype (WT) or Tet2 knockout (KO) Cas9+ hematopoietic stem-progenitor cells (HSPCs) in a model of zymosan peritonitis to elucidate the basis of Tet2 KO inflammation. We found that Tet2 restrains O-linked N-acetylglucosamine (O-GlcNAc) glycosyltransferase (Ogt), a Tet2 binding partner and metabolic sensor that integrates nutrient availability. Tet2 loss disrupts this Tet2-Ogt interaction, and dysregulated Ogt facilitates widespread H3K4 trimethylation including lipid-related gene loci and inflammatory lipid droplet formation. We identified ATP citrate lyase (Acly) as a critical node for lipid accumulation, inflammation, and myeloid expansion in Tet2 deficiency. In summary, we reveal that Tet2 serves as a negative regulator of the nutrient sensor Ogt, and that Tet2 inactivation leads to aberrant lipid droplet formation and inflammation.

overall_design: RNAseq profiling from various sources including monocytes via single cell RNAseq and bone marrow derived macrophages exposed to various conditions.

first: Christopher

last: Hergott

first: Aidan

last: Miller

first: Amy

last: Deik

first: Meaghan

last: Boileau

first: Kevin

last: Bullock

first: Kerry

last: Pierce

first: Angeline

last: Choy

first: Wesley

last: Shin

first: Marie

last: McConkey

first: Justin

last: Loke

first: Birgitta

last: Ryback

first: Michael

last: Trinh

first: Hong

last: Yue

first: Hojong

last: Yoon

first: Paul

first: Shourya

last: Burman

first: Matthew

last: Vander Heiden

first: Eric

last: Fisher

first: Scott

last: Armstrong

first: Clary

last: Clish

first: Benjamin

last: Ebert


title: Cellular Quiescence Displays a Transcriptional Inflammatory Phenotype Similar to the One in Cellular Senescence [bulk RNA-seq]

city: Belmont

first: Azucena

last: Rocha

state: Massachusetts

address: 42 Alma Avenue

department: MCB

institute: Brown University

summary: Cellular senescence, traditionally viewed as the irreversible arrest of proliferating cells in response to stress and DNA damage, is a key mechanism underlying cellular aging. Several studies have identified a process called ”quiescence-origin senescence,” where quiescent cells bypass proliferation and transition directly into senescence. In this context, we introduce the concept of the transcriptional Quiescence-Associated Secretory Phenotype (tQASP), a putative inflammatory secretory profile that arises in human quiescent cells and may serve as a precursor to the full senescence-associated secretory phenotype (SASP). We report that quiescent cells express tQASP genes in a cell-type-, induction-dependent manner and that this response is influenced by environmental oxygen levels. tQASP expression is also increased in tissue affected by Idiopathic Pulmonary Fibrosis (IPF) and shows a positive correlation with myofibroblast activation. Together, these data support the concept of a continuum between quiescence and senescence and suggest that the tQASP may be an early marker of cellular aging, with significant implications for tissue homeostasis, aging, cancer, and disease progression.

overall_design: Bulk RNA Sequencing of Proliferating, Quiescent (contact inhibition) and quiescent (serum withdrawal) BJ, IMR90 and LF1 human fibroblasts and human primary preadipocytes

first: Radha

last: Kalekar

first: John

last: Sedivy

first: Nicola

last: Neretti


title: Comparative Single-Cell Analyses in Infants Revealed RSV-Specific Declines in NK Cell Responses and COVID-19-Specific Increases in Inflammatory Responses [COVID_RSV_scRNA]

first: Asa

last: Thibodeau

first: Asunción

last: Mejías

first: Djamel

last: Nehar-Belaid

first: Radu

last: Marches

first: Virginia

last: Pascual

first: Jacques

last: Banchereau

first: Octavio

last: Ramilo

first: Duygu

last: Ucar


title: Sensing steroid hormone 17α-hydroxypregnenolone by GPR56 enables protection from ferroptosis-induced liver injury

city: Jinan

first: Xiao

last: Zhuang

state: Shandong province

address: Shandong University, Wenhuaxi Road 44, Jinan, China

department: Department of Cell Biology

institute: Shandong University

summary: G-protein-coupled receptors (GPCRs) mediate most cellular responses to hormones, neurotransmitters as well as environmental stimulants. However, whether GPCRs participate in modulation of tissue homeostasis through ferroptosis remains unclear. By GPCR cDNA library screening, here we identify that GPR56/ADGRG1 remodels ferroptosis plasticity. Loss of GPR56 sensitizes cells to ferroptosis and deficiency of GPR56 deteriorates ferroptosis-mediated liver injury induced by Doxorubicin (DOX) or ischemia-reperfusion (IR). Mechanistically, GPR56 decreases the abundance of phospholipids containing free polyunsaturated fatty acids (PUFAs) by promoting endocytosis-lysosomal degradation of CD36. By screening a panel of steroid hormones, we identified that 17α-hydroxypregnenolone (17-OH PREG) acts as an agonist of GPR56 to antagonize ferroptosis and efficiently attenuates liver injury before or after insult. Moreover, disease associated GPR56 mutants were unresponsive to 17-OH PREG activation and insufficient to defend against ferroptosis. Together, our findings uncover that 17-OH PREG-GPR56 axis-mediated signal transduction works as a new anti-ferroptotic pathway to maintain liver homeostasis, providing novel insights into the potential therapy for liver injury.

overall_design: To investigate the mRNA levels affected by GPR56 knockdown in HT1080 cells,we utilized CRISPR-Cas9 technology to generate knockout (KO) cell lines.

first: Shuo

last: Liu

first: Dong

first: Bo

last: Chu


title: A scaffold attachment factor PHM-2 regulates synaptic transmission through SLO-2 potassium channel in C. elegans

city: Denton

first: Bojun

last: Chen

state: TX

address: 1511 W Sycamore St

department: Biological Sciences

institute: University of North Texas

summary: Scaffold attachment factor B (SAFB) proteins are evolutionarily conserved DNA/RNA binding proteins that are involved in multiple processes of gene expression. These proteins are broadly expressed with particular high expression observed in the nervous system. However, their physiological roles in neurons are largely unclear. Here we show that PHM-2, the sole SAFB ortholog in C. elegans, regulates synaptic transmission at the neuromuscular junctions through an effect on SLO-2 potassium channel. We found that phm-2 knockout suppresses a sluggish phenotype of worms expressing a hyperactive SLO-2 channel, greatly reduces SLO-2-mediated neuronal whole-cell currents, and enhances neuromuscular synaptic transmission. In addition, we found that PHM-2 genetically interacts with another DNA/RNA binding protein, HRPU-2/hnRNP U, to control SLO-2 expression through a posttranscriptional mechanism. These results reveal a novel function of a SAFB protein in regulating neuronal activity, and may help understand the physiological roles of SAFB proteins in the nervous system of other species.

overall_design: Examination of gene expression in wild type and phm-2 mutant worms in three biological replicates.

first: Niu

last: Longgang

first: Murugasen

last: Karthika

first: Honggodo

last: Shannon

first: Ferdousy

last: Sakia

first: Zhu

last: Lishuang

first: Chen

last: Bojun


title: Alteration of global transcription by the Tormentil and its constituents in Acinetobacter baumannii AB5075

city: London

first: Kavita

last: Gadar

address: Kingston Lane

country: United Kingdom

institute: Brunel University

summary: We perform RNA-seq comparing a treatment with 50 μM agrimoniin, 2.3 μM ellagic acid, 0.05 mg/mL of Wicklow tormentil root extract to a mock treatment (DMSO) in A. baumannii AB5075 in order to describe the alterations in global transcription produced by these treatments. As a result, Agrimoniin elicited a response that led to significant differential expression in 414 genes, with 216 showing upregulation and 198 showing downregulation. Ellagic acid exerted an even more pronounced effect, with 636 genes exhibiting significant differential expression; among these, 455 were upregulated and 181 were downregulated. Similarly, Wicklow tormentil root extract impacted gene expression resulting in significant differential expression in 517 genes, wherein 378 were upregulated and 139 were downregulated.  In highlights, the gene functional groups showing the strongest transcriptional alterations were those related to iron acquisition, storage, siderophore biosynthesis and iron transport genes.

overall_design: A. baumannii AB5075 cultures were grown in LB medium in the presence of with 50 μM agrimoniin, 2.3 μM ellagic acid, 0.05 mg/mL of Wicklow tormentil root extract or a DMSO control (3 biological replicates per condition) until reaching mid-exponential phase. At this point, cells were harvested, treated with RNAlater for preservation of total RNA and stored at -80 C. After that, total RNA was extracted from each sample. Three independent replicates of A. baumannii AB5075 were grown to mid-exponential phase in LB medium supplemented with 50 μM agrimoniin, 2.3 μM ellagic acid or 0.05 mg/mL of Wicklow tormentil root extract and compared to three independent replicates grown in the same conditions but receiving a mock treatment (equivalent volume of DMSO).

first: Maria

last: Pigott

first: Cillian

middle: J

last: Gately

first: Ismael

last: Obaidi

first: Shipra

last: Nagar

first: Helen

last: Sheridan

first: Ronan

middle: R

last: McCarthy


title: Single cell gene expression profile of kdrl+ zebrafish cells at 48 hours post-fertilization in prdx1-morphants

first: Mohamad Ali

last: Najia

address: 1 Blackfan Circle

department: Hematology/Oncology

institute: Boston Children's Hospital

summary: We used single cell gene expression analysis to assess the effect of increased ROS (via Prdx1 knockdown) on vascular and hematopoietic progenitor populations during and after endothelial to hematopoietic transition

overall_design: mCherry fluorescing cells were isolated from Tg(kdrl:mCherry) transgenic reporter zebrafish at 48 hours post-fertilization in both control and prdx1-morpholino injected embryos. The cells were analysed by single cell RNAseq

first: Meader

last: Ellie

first: Najia

last: Mohamad

first: North

last: Trista

first: Morgan

last: Walcheck


title: Transposable Elements Shape Stemness in Normal and Leukemic Hematopoiesis

city: Toronto

first: Mathieu

last: Lupien

state: Ontario

address: 101 College Street

country: Canada

institute: University Health Network

summary: Despite most acute myeloid leukemia (AML) patients achieving complete remission after induction chemotherapy, two thirds of patients will relapse with fatal disease within 5 years. AML is organized as a cellular hierarchy sustained by leukemia stem cells (LSC) at the apex, with LSC properties directly linked to tumor progression, therapy failure and disease relapse. Despite the central role of LSC in poor patient outcomes, little is known of the genetic determinants of their stemness properties. Although much AML research focuses on mutational processes and their impact on gene expression programs, the genetic determinants of cell state properties including stemness expand beyond mutations, relying on the genetic architecture captured in the chromatin of each cell. As LSCs share many functional and molecular properties with normal hematopoietic stem cells (HSC), we identified genetic determinants of primitive populations enriched for LSCs and HSCs in comparison with their downstream mature progeny by investigating their chromatin accessibility. Our work reveals how distinct transposable element families are used in primitive versus mature populations, functioning as docking sites for stem cell-associated regulators of genome topology or lineage-specific transcription factors in primitive and mature populations, respectively. We further show how transposable element families accessible in LSCs define docking sites for several oncogenic drivers in AML, including LYL1. Using chromatin accessibility profiles from a cohort of AML patients, we further show the clinical utility of our transposable element accessibility-based LSCTE121 scoring scheme to identify patients with high rates of relapse. Collectively, our work reveals how different accessible transposable element families serve as genetic determinants of stemness properties in normal and leukemic hematopoietic stem cells.

overall_design:
Assay for Transposase-Accessible Chromatin Sequencing (ATAC-Seq) performed on engrafting (LSC+) and non-egrafting (LSC-) leukemic cells and on bulk AML patients' peripheral blood samples
*** Raw data for these needs controlled access hence are already submitted to EGA (EGAS00001004893, EGAS00001004896 and EGAS00001007191). ***

Assay for Transposase-Accessible Chromatin Sequencing (ATAC-Seq) performed on OCI-AML22 CD34+/CD38- cells expressing CRISPR/dCas9 and scramble or LTR12C gRNA combos

first: Giacomo

last: Grillo

first: Héléna

last: Boutzen

first: Bettina

last: Nadorp

first: Ankita

last: Nand

first: John

last: Dick


title: Cell-free genomics reveals fundamental regulatory principles of the Mycobacterium tuberculosis transcription cycle

city: New York

first: Ruby

last: Froom

address: 1230 York Avenue

institute: Rockefeller University

summary: Tiers of gene regulation govern cellular life. The intrinsic activities of RNA polymerase (RNAP) constitute a primary tier, while direct modulation by accessory transcription factors (TFs) constitutes a secondary tier. Cellular signaling cascades and feedback loops generate tertiary and higher-order tiers. Dissecting gene regulation requires distinguishing direct TF targets at genome-scale from indirect network effects. A major obstacle is the lack of tools to interrogate transcription machineries from difficult-to-culture microbes—such as pathogens, commensals, and environmental species—at genome scale. Here, we introduce cell-free genomics (CFG), an empirical approach that identifies the direct targets of RNAP and TFs and systematizes their transcriptional effects. We demonstrate the efficacy of CFG by characterizing global and essential transcription initiation (CRP and holo-WhiB1) and elongation–termination factors (NusA and NusG) from the deadly pathogen, Mycobacterium tuberculosis. CFG expands our understanding of transcription principles and is broadly extensible to other perturbations and diverse species.

overall_design: RNA samples were prepared by incubating a mixture of purified M. tuberculosis (Mtb) RNA polymerase core enzyme, co-purified Mtb sigma factor A (SigA) and Mtb RbpA, purified Mtb CarD, sonicated Mtb genomic DNA, ribonucleotides, RNase inhibitor, and pyrophosphatase for 1 hour - 5 hours at 37ºC, in the presence or absence of transcription factors of interest (Mtb CRP, Mtb WhiB1, Mtb NusG, Mtb NusA). The aim was to identify TSSs or TTSs where these TFs can individually affect transcription. Similarly-derived in vitro RNA from the E. coli genome was spiked into all reactions at equivalent amounts to control for different amounts of total RNA across samples. 5' or 3' ends of the RNA were then enriched and sequenced. Core RNAP only samples were used to filter out non-SigA-dependent (i.e. non-specific) TSSs from the RNAP-SigA holoenzyme TSS samples. Genomic DNA input samples were used to filter out any TTSs that may be enriched due to non-random fragmentation of the genomic DNA input from the RNAP-SigA holoenzyme TTS samples.

first: Michael

last: Wolfe

first: Kelly

last: Eckartt

first: Rachel

last: Mooney

first: Madeleine

last: Delbeau

first: Alexis Jaramillo

last: Cartagena

first: Jeremy

last: Rock

first: Seth

last: Darst

first: Robert

last: Landick

first: Elizabeth

last: Campbell


title: ACSL4-Associated Lipid Metabolism is a Distinct Therapeutic Vulnerability in KMT2A-Rearranged Acute Myeloid Leukemia

city: Dresden

first: Alexander

middle: Arthur

last: Wurm

address: Fetscherstrasse 74

country: Germany

institute: NCT Dresden

summary: We were interested in transcriptional changes after depletion of the lipid metabolic gene Acyl-CoA Synthetase Long Chain Family Member 4 (ACSL4) in human acute myleoid leukemia (AML) cell lines. We compared global alterations of gene expression upon ACSL4 knockdown in one AML cell line harboring a lysine methyltransferase 2A (KMT2A) gene rearrangement (NOMO1) and one KMT2A WT AML cell line (K562).

overall_design: RNA-Sequencing from NOMO1/K562 cells stably expressing dCas9-KRAB-GFP after transduction with either a sgRNA against a non-targeting control (NTC) or human ACSL4. Experiment was performed in biologically independent triplicates.

middle: A

first: Silvia

last: Schäfer


title: Irisin improves obesity and glucose intolerance through an IL-33-ST2 pathway

first: CBDM

last: Lab

address: 77 Avenue Louis Pasteur

department: Microbiology and Immunobiology

institute: Harvard Medical School

summary: Irisin is secreted by muscle, increased with exercise, and conveys certain physiological benefits. Earlier studies showed that short-term irisin treatment caused browning of subcutaneous white fat in mice, with improved glucose tolerance; the effects of more chronic irisin treatment and mechanisms at play have not been explored. We demonstrate here that chronic irisin application improves obesity and dramatically reduces glucose intolerance. This treatment increases an IL-33+ mesenchymal stromal cell (mSC) population, while genetic ablation of irisin reduces plasma IL-33 levels and decreases thermogenic gene expression in subcutaneous adipose tissue. Importantly, irisin directly induces IL-33 expression in mSCs and stimulates ST2+regulatory T (Treg) cells, inducing their tissue accumulation. Inhibition of IL-33  blunts these irisin-mediated effects on energy expenditure and glucose homeostasis, largely through IL33-mediated regulation of ST2+ Treg cells. These data indicate that irisin improves obesity and glucose intolerance, with no muscle loss, through a key immunomodulatory pathway in obese mice .

overall_design: To verify whether irisin/HSP90α could change mSC fate from adipocyte precursors to immunomodulatory stromal cells, IL-33 (EGFP)- mSCs from eWAT were treated with PBS or 10nM irisin/HSP90α for 3 days.

first: Gang

last: Wang

first: Diane

last: Mathis


title: The CD8 immgenT framework as a universal reference of mouse CD8 T cell differentiation states

status: Public on Jan 14 2026

city: Cambridge

first: Charles

middle: Ara

last: Demurjian

address: 31 Ames Street

institute: BioMicro Center at MIT

summary: Mouse CD8 T cell differentiation has been studied extensively in models of infections and cancer, yet no unified framework spans the full spectrum of immunological contexts. Here, we present the CD8 immgenT framework, integrating >200,000 single-cell transcriptomes and 128-plex surface proteomes from 734 samples across 45 perturbations, 45 tissues, and multiple timepoints. Unbiased analysis resolves 21 robust, recurrent states that capture naive, effector, circulating memory, tissue-resident memory, progenitor-exhausted, and terminally exhausted compartments, among others. These states reproducibly re-emerge with striking molecular convergence across acute and chronic infections, cancer, autoimmunity, aging, and homeostasis, revealing that highly similar transcriptional programs are deployed in dramatically different immunological contexts and can support protective or dysfunctional functions depending on developmental history and microenvironmental cues. Classic archetypes map to discrete clusters yet display previously unappreciated heterogeneity and extensive overlap, cautioning against rigid application of legacy subset nomenclature. We provide validated combinatorial markers, flow cytometry gating strategies, and T cell reference-based integration, a projection tool for reproducible annotation of new datasets. The CD8 immgenT framework thus establishes a universal coordinate system for mouse CD8 T cell biology that harmonizes fragmented literature and clarifies biological relationships across the entire spectrum of immune challenges.

overall_design: Syngeneic MC38-SIY colon carcinoma and B16-SIY melanoma tumors were implanted subcutaneously in C57BL/6 mice. Tumors were harvested 14 days post-implantation, enzymatically digested, and live CD45⁺ immune cells were isolated by flow cytometric sorting. Single-cell 3′ gene expression libraries were generated to profile immune cell transcriptional states within the tumor microenvironment.


title: Functional Dynamic Modulation of Colorectal Cancer Initiation and Metastatic Capacity by a Novel MiR-7974 Regulatory Axis

city: Taoyuan

first: Yi-Tung

last: Chen

address: No.259, Wenhua 1st Rd., Guishan Dist.

country: Taiwan

institute: Chang Gung University

summary: To investgate the funcitonal role of miR-7974 overexpression on transcriptomic regulation

overall_design:
We performed gene expression profiling analysis using data obtained from RNA-seq (2 replicate)
Differentiated gene expression profiling analysis of RNA-seq data for Ctrl and miR-7974 HCT116 cells

first: Yu-Hao

last: Liu


title: Targeting HMGB2 acts as dual immunomodulator by bolstering CD8+ T cell function and inhibiting tumor growth in hepatocellular carcinoma [RNA-Seq]

city: SHANGHAI

first: WEIFENG

last: QU

address: No.180 Fenglin Road

institute: Zhongshan Hospital, Fudan university

summary: Transcriptional features were detected in NC versus HMGB2-knockout CD8+ T cells of C57BL/6J mice.

overall_design: Transcriptional features of NC versus HMGB2-knockout CD8+ T cells in C57BL/6J mice.

first: Weifeng

last: Qu

first: Guiqi

last: Zhu

first: Yinghong

last: Shi


title: Gene expression profile at single cell level of CD45+ immune cells in both peripheral blood mononuclear cells (PBMCs) and allograft biopsy samples obtained from kidney transplant recipients

city: Houston

first: Yulin

last: Dai

address: 7000 fannin, suite 600

department: School of Biomedical Informatics

institute: University of Texas health science center at Houston

summary: Transplant rejection is mediated by immune cells, especially T cells. In this study, we employed single-cell RNA sequencing (scRNA-seq) to analyze the states of these cells in response to kidney transplantation

overall_design: Subjects were retrospectively selected following prospective recruitment and consent at the time of renal biopsy for clinical indications (protocol biopsy for high immune risk, “for cause” such as allograft dysfunction, and post-rejection treatment). Live CD45+ cells were sorted from PBMC or kidney biopsy samples and analyzed by scRNA-seq

first: Stepanie

last: Yi

first: Dawei

last: Zou

first: Wenhao


title: RecQ dysfunction contributes to social and depressive-like behavior and aldolase activity changes in mice

first: Supriyo

last: De

address: 251 Bayview Blvd

department: Laboratory of Genetics and Genomics

institute: NIA-IRP, NIH

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

overall_design: Refer to individual Series


title: Targeting YAP/TEAD signaling disturbs RNA Pol II activity and enhances immunotherapy response via activated cytosolic DNA sensing pathway in gastroesophageal cancer

city: Camden

first: Yanting

last: Zhang

state: NJ

address: 403 Haddon Avenue

institute: Coriell Institute for Medical Research

summary: Gastroesophageal adenocarcinoma (GEAC) accounts for a significant global cancer burden. Our previous studies demonstrated that YAP1/TEAD are highly expressed in GEAC, and play a critical role in tumor progression, therapy resistance and metastasis. Thus, targeting YAP/TEAD signaling presents a promising therapeutic strategy. Here, we developed a novel YAP/TEAD inhibitor VT00278 based on the structure of CA3 and showed that VT00278 strongly downregulated YAP/TEAD transcriptional activity, and potently suppress tumor-promoting phenotypes, including proliferation, invasion, tumor sphere formation; induce apoptosis and inhibit tumor growth in vivo especially in radiation resistant FLO-1 XTR GEAC cells. Mechanistically, in addition to impairing YAP1/TEAD signaling, VT00278 or YAP1 depletion repressed RNA polymerase II transcriptional regulators, reduced RNAPII S2 phosphorylation and decreased anti-apoptosis MCL-1 expression. More interestingly, we revealed that VT00278 strongly induced DNA damage, activated cytosolic DNA sensing pathway, upregulation of innate immune genes (e.g.INFβ) and increased PDL-1 expression. In a syngeneic mouse model, combining VT00278 with anti-PD-1 therapy synergistically inhibited tumor growth and increased CD3+ and CD8+ T cell infiltration and induced the production of INFγ from CD3 and CD8 cells in the combination treatment. These findings support VT00278 as a promising candidate for GEAC treatment, either alone or in combination with immunotherapy.

overall_design: RNA-seq profiling of GA0518 cells without(Untreated_1 and Untreated_2) and with 200nM VT00278 treatment for 24h (VT_200_1 and VT_200_2), and the YAP knockout cells derived from GA0518  (YAP KO_D1 and YAP KO_D2 ) after 48h cell culture. The cell sample collection and RNA extraction were handled together.

first: Yan-ting

middle: Y

first: Ayna

last: Mammedova

first: Dipti

last: Athavale

first: Curt

last: Balch

first: Mikel

last: Ghelfi

first: Xiaodan

last: Yao

first: Gennaro

last: Calendo

first: Songjie

first: David

middle: N

last: Pulipati

first: Yahui

last: Li

first: Xiaoxin

first: Francis

last: Spitz

first: Generosa

last: Grana

first: Vladimir

last: Khazak

first: Shumei

last: Song


title: CUT&Tag profiling of JUND chromatin binding in human mast cell line LAD2 under SCF stimulation and imatinib perturbation

city: Shanghai

first: Tianyu

last: Cao

address: No. 100 Haining Road, Hongkou District

department: Urology

institute: Shanghai General Hospital

summary: Mast cells respond to cytokine cues through rapid transcriptional rewiring. Here we generated CUT&Tag profiles of the transcription factor JUND in the human mast cell line LAD2 under three culture conditions: SCF withdrawal (EM), SCF supplementation (SCF), and SCF withdrawal plus imatinib treatment (IM). Two biological replicates were collected for each condition. Libraries were sequenced as paired-end reads and processed by adapter/quality filtering, alignment to the human reference genome (GRCh38/hg38), peak calling, and generation of normalized genome browser tracks. This dataset provides a resource to examine how SCF signaling and c-KIT pathway inhibition reshape JUND occupancy in mast cells.

overall_design: CUT&Tag (TF binding) profiling in LAD2 cells targeting JUND (Active Motif 61403; RRID:AB_2793621). Three treatment conditions with two biological replicates each: SCF- (EM), SCF+ (SCF), and SCF- + imatinib (IM). Paired-end sequencing; genome: GRCh38/hg38. No IgG/input/no-antibody control library was generated.

first: Yfeng

last: Jing


title: CUL4B functions as a tumor suppressor in KRAS-driven lung tumor by inhibiting recruitment of myeloid-derived suppressor cells

first: xiaochen

last: liu

address: Wenhua West Road No.44

institute: shandong university

summary: Lung cancer is the leading cause of cancer-related death worldwide. KRAS mutations are the most common oncogenic alterations found in lung cancer. Unfortunately, treating KRAS-mutant lung adenocarcinoma (ADC) remains a major challenge in cancer treatment of directly inhibiting the KRAS oncoprotein, indicating the need for understanding the regulatory mechanism with this molecular profile. Here, we used both autochthonous and transplantable KRAS mutant tumor models to investigate the role of tumor-derived CUL4B in KRAS-driven lung cancers. We show that knockout or knockdown of CUL4B promotes lung adenocarcinoma growth and progression in both two models. Mechanistically, CUL4B directly binds to the promoter of Cxcl2 and epigenetically represses its transcription. CUL4B deletion increases the expression of CXCL2, which binds to CXCR2 on myeloid-derived suppressor cells (MDSCs) and promotes their migration to the tumor microenvironment, and in turn, suppresses anti-tumor immunity. Targeting MDSCs with anti-Gr-1 neutralizing antibody or treatment with CXCR2 antagonist SB265610 significantly suppresses MDSCs infiltration and delayed the growth of CUL4B knockdown KRAS mutant lung adenocarcinoma tumors. Moreover, a negative correlation between CUL4B and CXCL2 expression was observed in high-stage KRAS mutant lung ADC patients. Collectively, our study provides mechanistic insights into the novel tumor suppressor-like functions of CUL4B in regulating the KRAS-driven lung tumor development.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for Ad-Cre treated primary lung epithelial cells from KrasG12D; Cul4bflox/Y (KC) mice and KrasG12D mice (K).

first: Xiaochen

last: Liu


title: Resistance Potential of the HLA-A2-restricted Immunodominant SARS-CoV-2 Specific CD8+ T Cell Receptor Repertoire to Antigenic Drift

city: Philadelphia

first: Ning

last: Jiang

state: PA

address: 210 S 33rd St

department: Bioengineering

institute: University of Pennsylvania

summary: A major concern of COVID-19 is immune escape. While T cells are implicated in protection against severe disease, direct evaluation of their capacity to specifically target SARS-CoV-2 variants remains limited. We aim to narrow this gap by profiling the ability of CD8+ T cells to recognize SARS-CoV-2 mutations after vaccination and observe a high degree of phenotype and repertoire diversity. To better understand the breadth of antigen repertoire coverage, we interrogate the ability of SARS-CoV-2 specific TCRs to bind all point mutations of the immunodominant HLA-A2:S269-277 epitope. While mutation space coverage is surprisingly vast, specific substitutions are not recognized by the vaccine-elicited repertoire. Structural analyses reveal a TCR sequence-based antigen recognition limitation intrinsic to vaccination. Further investigation reveals that this repertoire ‘hole’ is not present in the naive repertoire, suggesting future immune escape through these potential escape mutations could be relieved by modifications to vaccines.

overall_design:
To understand the viral mutation coverage of vaccine-elicited T cell receptor repertoires in individuals that have received COVID-19 mRNA vaccines, we multiplexed DNA-barcoded pMHC multimers with single cell T cell receptor and RNA sequencing before and after vaccination.
In vitro expanded antigen specific T cell receptors were also isolated using single cell amplicon VDJ sequencing.

first: Michael

last: Malone

first: Chao

last: Huang

first: Yong

last: Zhang

first: Yi

last: Qi

first: Lea

last: Williams

first: Laura

middle: F

last: Su

first: Jizhong

last: Lou


title: Monocyte-derived IL-10 drives sex differences in pain duration

city: Chapel Hill

first: Sarah

last: Linnstaedt

state: NC

address: 109 Mason Farm Road

institute: University of North Carolina at Chapel Hill

summary: Women frequently experience longer-lasting pain than men, indicating delayed pain resolution. While we understand that pain can be orchestrated by the close interplay between the sensory nervous system and the immune system, it remains unclear whether this interaction contributes to the longer duration of pain in women. Here, we demonstrate that interleukin (IL)-10+ monocytes resolve inflammatory pain by signaling to IL-10R1+ sensory neurons in a mouse model of skin inflammation. A higher number of IL-10+ monocytes in males enables faster resolution of inflammatory pain compared to females. In both sexes, pain resolution was impaired by deleting Il10 from monocytes or Il10ra from sensory neurons. Similarly, in humans, men’s pain resolved faster than women’s after traumatic injury, which was associated with higher levels of circulating monocytes and IL-10 in men. In mice, androgen signaling promotes IL-10 production by monocytes, resulting in sex differences in the number of IL-10+ monocytes. Enhancing IL-10+ monocytes in the inflamed skin through Resolvin D1 treatment accelerated pain resolution in both sexes of mice. Our findings uncover a novel role for peripheral IL-10+ monocytes in driving sex differences in pain resolution. These results reveal a previously underappreciated   contribution of immune cells to resolving pain and preventing the transition to chronic pain.

overall_design:
RNA-seq profiling  of human whole-blood samples collected at enrollment. A supplementary file available at the foot of this record named "GEO_sumission_sample_supplementary_info.xlsx" contains sample metadata and a key to variables.

***************************************************************
Raw files for human/patient samples were not submitted to GEO due to concerns about submitting personally identifiable sequence data for open access.  The raw data files are available under controlled access: DOI:10.15154/e9fp-1e38
***************************************************************

first: Jaewon

last: Sim

first: Elizabeth

last: O’Guin

first: Chiho

last: Sugimoto

first: Sophie

last: Laumet

first: Karli

last: Monahan

first: Matthew

middle: P

last: Bernard

first: Samuel

last: McLean

first: Liz

middle: M

last: Albertorio-Sáez

first: Ying

last: Zhao

first: Hariharan

last: Ramakrishnan

first: Sabrina

last: de Souza

first: Olivia

middle: C

last: Eller

first: Christine

last: Smoyer

first: Kyle

last: Baumbauer

first: Matthias

last: Mack

first: Joseph

middle: K

last: Folger

first: Alfred

last: Robison

middle: D

first: Geoffroy


title: Heliophilum fasciatum regulation in response to available sulfate and thiosulfate concentrations.

city: Columbus

first: Justin

last: North

address: 484 W 12th Ave

department: Department of Microbiology

institute: Ohio State University

summary: Heliophilum fasciatum is an anoxygenic photosynthetic bacteria isolated from rice soil. Previous work outlined the existence of five nitrogen-fixation-like gene clusters potentially involved in sulfur metabolism. In this study, cultures of H. fasciatum were grown with varying sulfate and thiosulfate concentrations, and the transcriptomes were generated using Illumina RNA-sequencing. Differential gene expression analysis was utilized to investigate sulfur-mediated regulation of these nitrogen-fixation-like systems and H. fasciatum genes.

overall_design: Heliophilum fasciatum cultures are grown in the same defined minimal media, but specific sulfur samples of varying concentrations were added separately. The RNA was extracted and prepared with the Illumina stranded total RNA library preparation kit. Differential expression analysis was conducted on the transcriptomes.

first: Calissa

last: Carlisle

first: Kelly

last: Bender


title: KMT2D maintains Treg homeostasis and protects against inflammatory diseases by regulating the purinergic channel P2X7 level

city: Zhengzhou

first: Peng

last: Wang

address: Science Avenue

institute: Zhengzhou University

summary: Regulatory T (Treg) cells are essential for maintaining immune homeostasis and tolerance through the prevention of inflammatory and autoimmune responses. The histone methyltransferase KMT2D is indispensable for induced Treg (iTreg) cell differentiation, its role in the differentiation and function of Treg cells in vivo has remained largely unknown. Here, we demonstrate that KMT2D is critical for the differentiation and function of effector activated Treg (aTreg) cells. We found that KMT2D deficiency in Treg cells impairs aTreg generation and exacerbates inflammatory conditions, such as allergic airway inflammation and colitis. Mechanistically, KMT2D regulates aTreg differentiation through TCR signaling. Furthermore, KMT2D modulates Ca2+ influx by promoting the expression of purinergic receptor P2X7 through H3K4me3 deposition. Collectively, our fundings highlight a pivotal role for KMT2D in Treg cell homeostasis and function, potentially offering a new therapeutic strategy for treating inflammatory diseases.

overall_design: Spleen CD4+FoxP3+ Treg cells from Foxp3YFP-CreKmt2d+/+ and Foxp3YFP-CreKmt2dfl/fl mice were sorted. The sorted Treg cells from three Foxp3YFP-CreKmt2d+/+ mice were pooled into one sample, while Treg cells from three Foxp3YFP-CreKmt2dfl/fl mice were combined into a separate sample for scRNA-seq.


title: Transcriptome profiles of bovine muscle stem cells cultured in serum-containing condition and small molecule–supplemented serum-free media by RNA-seq analysis

city: 江苏省南京市

first: 浩

last: 路

address: 江苏省南京市南京农业大学滨江校区

institute: 南京农业大学郭仁朋课题组

summary: Cultured meat, as an emerging sustainable food production technology, offers multiple advantages. However, its large-scale application still faces critical technical bottlenecks, most notably the strong reliance on fetal bovine serum (FBS). In recent years, serum-free culture systems for bovine muscle stem cells (bMuSCs) have made certain progress, such as the Beefy-9 system and its subsequent optimized versions; nevertheless, existing serum-free formulations remain insufficient to fully replace traditional serum-containing culture conditions in both cost control and functional performance. Meanwhile, the use of small-molecule compounds to precisely regulate cell proliferation and fate determination has gradually emerged as a potentially effective strategy to reduce culture costs, simplify culture systems, and enhance functional stability. In this study, through a functional screening of proliferation activators in bMuSCs, we identified forskolin and a p38 pathway inhibitor SB202190 to robustly promote cell proliferation and maintain myogenic capacity of bMuSCs under serum-free conditions. Based on this, RNA-sequencing analysis was committed to systematically elucidate the molecular differences between serum-free small-molecule regulatory strategies and conventional serum-containing conditions in bMuSCs.

overall_design: BMuSCs with biological replicates were collected simultaneously for RNA extraction and RNA-seq analysis. Specifically, at the fifth passage of proliferation (corresponding to three consecutive passages under different culture conditions), cells cultured in medium containing 15% FBS (the FBS group), in Beefy-9 medium (the Beefy 9 group), and in Beefy-9 medium supplemented with forskolin or/and SB202190 (the Beefy F group, the Beefy S group, and the Beefy FS group) were harvested, with three biological replicates included for RNA-seq analysis.


title: scRNA-seq data of CD8+ T cells isolated from control and DHEA-treated mice

city: haidian district

first: yao

last: feng

state: Beijing

address: No.38 xueyuan road

institute: Peking University

summary: To determine the changes in CD8+ T cells upon DHEA treatment, we performed scRNA-seq to analyze the CD8+T cell  in  C57BL/6 mice subjected to DHEA induced PCOS model.

overall_design: C57BL/6 mice subjected to DHEA induced PCOS model. To obtain CD8+ T cells, spleen tissues were minced and grinded in pre-cold FACS buffer (PBS containing 1% FBS), followed by filtration through a 70 μm cell strainer. After removing red blood cells resuspended with ACK lysis buffer, CD8+ T cells were isolated by magnetic beads and pooled using the 10× Genomics platform and sequenced on an Illumina NextSeq sequencer.

first: Yaruo

last: Qiu

first: Yao

last: Feng

first: Dan

last: Lv


title: A quadrivalent in vivo CAR-macrophage serve as cell vaccine to repress solid tumors and overcome tumor heterogeneity through antigen spreading

city: Hangzhou

first: Shaolong

last: Zhang

address: Wenyixi Road 1369

institute: liangzhu Laboratory

summary: We designed a quadrivalent in vivo CAR-engineered macrophage for treating solid tumors by the LNP-mRNA system. Mechanically, we found that in vivo engineered CAR macrophages can promote the formation of T-cell immune memory against neoantigens through antigen spreading. To further elucidate this phenomenon, we treated orthotopic HCC model mice with PBS, LNP-GPC3 CAR, or LNP-GPC3 CAR-Super IL-2 and subsequently collected splenocytes from these three groups for transcriptomic and TCR sequencing analyses. Based on data from transcriptome and TCR sequencing, we propose a two-signal model for T-cell activation: the GPC3 CAR provides the primary signal by recognizing and presenting tumor antigens, while the secreted Super IL-2 supplies the additional signal necessary for robust T-cell clonal expansion. These findings provide novel mechanistic insights into the anti-tumor activity of in vivo engineered CAR macrophages.

overall_design: Spleens were collected from HCC model mice treated with PBS, LNP-GPC3 CAR, or LNP-GPC3 CAR-Super IL-2 (three mice per group, nine samples in total). Single-cell suspensions were prepared, followed by red blood cell lysis to remove erythrocytes. Subsequent transcriptomic and TCR sequencing were performed on the isolated splenocytes.

first: Hengxing

last: Lu

first: Hailing

first: Qixin

last: Wu

first: Xizhong

last: Ding


title: 9-PAHSA orchestrates TCR-T cell fate to boost anti-tumor immunity

first: xiaozhen

last: zhang

state: province

address: 79 Qingchun Road

institute: The first affiliated hospital, zhejiang university school of medicine

summary: We identify the endogenous lipid 9-PAHSA as a potent enhancer of T cell anti-tumor function and stemness, validated in murine models and a clinical trial. Mechanistically, we identify ICAM2 as a direct surface sensor for 9-PAHSA and delineate a downstream signaling axis whereby the ICAM2-Ezrin-mTORC2 cascade drives FOXO1 O-GlcNAcylation at S318, facilitating its nuclear translocation to enact a stem-like transcriptional program. Translating this discovery, we engineered armored human TCR-T cells with potentiated ICAM2 expression, which achieve superior tumor control through their enhanced intrinsic efficacy and a remarkable ability to ignite a coordinated and durable host anti-tumor immune response. Our work establishes a new paradigm of metabolite-sensing in T cell biology and provides a compelling therapeutic strategy to potentiate cellular immunotherapy for intractable cancers.

overall_design: Single-cell RNA sequencing (scRNA-seq) of the tumor microenvironment from a pancreatic cancer in situ model treated with or without the lipid metabolite 9-PAHSA. Following treatment, cells from dissociated whole tumors were isolated and analyzed using scRNA-seq. Five independent biological replicates (individual tumors) were analyzed per condition (vehicle control and 9-PAHSA treated).

first: Xiaozhen


title: RiboBright reveals cell-type specific differences in ribosome organization and movement

city: Nijmegen

first: Wim

last: Velema

address: Heyendaalseweg 135

country: Netherlands

institute: Radboud University

summary: Ribosomes are responsible for protein synthesis in all living systems. Determining their cellular organization, movement and translational activity is crucial for dissecting ribosomes’ complex functions. In this study, we describe the development of a selective fluorescent probe for eukaryotic ribosomes — RiboBright. Using C-H activation, the natural product cycloheximide was aminated at the C13-position and fluorescently modified to afford RiboBright. We employ RiboBright for quantification of ribosome content in 10 cell lines through microscopy and flow cytometry. RiboBright is applicable in live cells for tracking and quantification of ribosome movement and in fixed cells for visualization of sub-micrometer sized spots, at the single cell level. Strikingly, RiboBright reveals lineage-specific ribosome content, organization, and movement upon differentiation into either extraembryonic endoderm or ectoderm-like lineages. Thus, RiboBright provides a versatile and convenient approach for imaging the cellular dynamics of ribosomes.

overall_design: DMS_MAP_seq of ribobright and cycloheximide treated samples

first: Georgia

last: Poulladofonou

first: Carmen

last: Grandi

first: Xinyu

last: Hu

first: Phillip

last: Yesley

first: Willem

first: Maike

last: Hansen


title: Essential role of NONO-HOXA1-Wnt axis in cardiomyocyte differentiation [scRNA-seq]

first: Feizhen

state: Shanghai

address: Zhangheng Road 825, Pudong

department: Intelligent Medicine Institute

institute: Fudan Univ, Shanghai, China

summary: NONO is recognized as a critical molecular scaffold involved in both transcriptional and posttranscriptional regulation. Mutations in NONO are frequently linked to congenital heart diseases (CHDs) in humans. However, the mechanisms by which NONO regulates cardiac development remain elusive. Here, we identified NONO as a pivotal dual-function regulator of cardiomyocyte differentiation in human induced pluripotent stem cells (hiPSCs). NONO deficiency in hiPSCs results in a distinct defect in early cardiomyocyte differentiation. Mechanistically, NONO interacts with HOXA1 and regulates the dynamic expression of key genes during early cardiomyocyte differentiation. ChIP-seq analysis reveals that NONO loss reduces HOXA1 occupancy at target genes, compromising its transcriptional regulation. Additionally, NONO and HOXA1 cooperatively activate the Wnt signaling. Taken together, these findings establish the NONO-HOXA1-Wnt axis as a key molecular mechanism in cardiomyocyte differentiation and provide new insights into the etiology of CHDs associated with NONO mutations.

overall_design: We performed scRNA-seq in days 2, 5, and 15 differentiated cells derived from WT and NONO-KO hiPSC.

first: Wei

last: Sheng

first: Guoying

last: Huang

first: Zhiyu

first: Yuan

last: Gao


title: Downregulation of MGST3 promotes colorectal cancer progression

city: Qingdao

first: yuchun

last: wu

state: Shandong Province

address: Laoshan District, Ningxia Road

institute: Qingdao University

summary: Colorectal cancer (CRC) is a common malignancy worldwide, and its molecular mechanisms of progression remain incompletely understood. In this study, RNA sequencing was performed on colorectal tissues representing normal tissue, adenomas, early-stage tumors and advanced carcinomas to identify differentially expressed genes associated with tumor progression. Paired-end RNA-seq data were generated on an Illumina NovaSeq 6000 platform. Gene expression levels were quantified and summarized as FPKM values. The resulting dataset provides a transcriptomic resource for investigating molecular changes during colorectal tumorigenesis, including the role of MGST3.

overall_design: A retrospective study was conducted on colorectal tissue samples representing normal tissue, adenomas, early-stage tumors and advanced carcinomas. Fresh-frozen tumor tissues and paired adjacent normal tissues were collected. Total RNA was extracted and subjected to bulk RNA sequencing using paired-end 150-bp reads on an Illumina NovaSeq 6000 platform. Sequencing reads were quality-trimmed, aligned to the hg38 reference genome, and gene expression levels were quantified using Cufflinks.

first: Jianxun

last: Wang

first: Yuqu

last: He

first: Yuchun


title: YWHAZ is Downregulated in the Proliferative Eutopic Endometrium in Endometriosis and Is Required Downstream of Progesterone Receptor and STAT3 Signaling.

city: Columbia

first: Jae-Wook

last: Jeong

state: MO

address: Rutland Drive

department: Obstetrics, Gynecology and Women’s Health

institute: University of Missouri

summary: We performed RNA sequencing on proliferative-phase eutopic endometrium from women with endometriosis (n = 4) and without endometriosis (n = 4). Histological dating of endometrial samples was performed by a certified pathologist. Transcriptomic analysis identified 44 differentially expressed genes, including 13 upregulated and 31 downregulated transcripts in women with endometriosis compared with controls, indicating a distinct transcriptional profile associated with endometriosis. This dataset provides a resource for understanding molecular pertubations associated with the disease.

overall_design: Human eutopic endometrial biopsies were collected from women with and without endometriosis during the proliferative phase, stored in RNA-later until  total RNA was isolated for RNA-seq analysis. Control (n = 4); Endometriosis (n = 4).

first: Tae Hoon

last: Kim

first: Jae Wook


title: Melittin enhances PD-L1 blockade in prostate cancer by inhibiting M2 macrophage polarization and recruitment

first: Rucheng

last: Yan

address: 1800,yuntai road

institute: Shanghai East Hospital

summary: Objective: The immunosuppressive tumor microenvironment (TME) limits the efficacy of immunotherapy in prostate cancer treatment. This study aims to investigate how melittin remodels the TME in prostate cancer and enhances the response mechanism to anti-PD-L1 therapy. Methods: The anti-tumor efficacy of melittin was evaluated in a C57BL/6J mouse prostate cancer model. An in vitro co-culture model of prostate cancer cells (PC-3, 22RV1) and THP-1-derived macrophages was established. RNA sequencing, flow cytometry, qPCR, Western blot, ELISA, Transwell migration assays, and immunohistochemistry were employed to explore the anti-tumor mechanisms of melittin. The synergistic effect of combining melittin with an anti-PD-L1 antibody was assessed in vivo. Results: Melittin significantly inhibited tumor growth in vivo. It remodeled the TME by increasing CD8⁺ T cell infiltration and reducing macrophage numbers. Furthermore, melittin specifically inhibited M2 macrophage polarization, downregulating the expression of CD206, CD163, and TGF-β, an effect potentially mediated through inhibition of the JAK-STAT pathway. Additionally, melittin reduced macrophage recruitment by downregulating tumor-derived CCL2. Combination therapy using melittin and anti-PD-L1 antibody demonstrated synergistic anti-tumor effects, significantly reducing tumor volume and weight, decreasing intratumoral expression of Ki67 and PD-L1, and enhancing CD8⁺ T cell infiltration. Conclusion: Melittin reverses the immunosuppressive TME in prostate cancer by simultaneously inhibiting JAK-STAT-mediated M2 polarization and CCL2-dependent macrophage recruitment. This reprogramming of the TME, combined with PD-L1 blockade, offers a novel combination immunotherapy strategy for prostate cancer.

overall_design: THP-1 cells were differentiated with 100 ng/ml PMA for 48 h in the lower chamber of a Transwell system. Tumor cells were then seeded in the upper chamber and co-cultured with 3 μg/mL melittin for 48 h before.The induced macrophages were usd to RNA-seq.


title: Sequencing of rapamycin-treated yeast strains across genetic backgrounds, with and without U18

city: Santiago

first: Benjamín

last: Szenfeld

state: Las Condes

address: Av Plaza 680

department: Genetics and Genomics

country: Chile

institute: Institute of Science and Innovation in Medicine

summary: This analysis covers the transcriptomes of four yeast strains (NA, WA, WE, and SA) under two rapamycin-based conditions: rapamycin (an autophagy inducer) alone, and rapamycin combined with U18666A (an Ncr1p inhibitor).

overall_design: RNA-seq profiling of four yeast strains (DBVPG6044 [West African, “WA”: Mat alpha ho::NatMX, ura3::KanMXY12], Y12 [Sake, “SA”: Mat alpha ho::NatMX, ura3::KanMX], YPS128 [North American, “NA”: Mat alpha ho::NatMX, ura3::KanMX], and DBVPG6765 [Wine/European, “WE”: Mat alpha ho::NatMX, ura3::KanMX]). Samples were generated under two treatment conditions: rapamycin alone and rapamycin combined with U18666A. Rapamycin was used at 0.25 nM. Yeast cultures were grown in triplicate at 28°C to mid-log phase (OD600 ~0.8) in YNB medium (rapamycin-only condition) or YNB medium supplemented with U18666A (200 µg/mL) (rapamycin + U18666A condition). Cells were centrifuged and treated with zymolyase (2 U) for 30 minutes at 37°C. Total RNA was extracted using the E.Z.N.A. Total RNA Kit I (OMEGA), followed by DNase I treatment (Promega) to remove genomic DNA. RNA integrity was verified using a Fragment Analyzer (Agilent).

first: Macarena

last: Las Heras

first: Valeria

last: Olguín

first: Juan Carlos

last: Rubilar

first: Andrés

last: Klein


title: H3K18 lactylation-mediated ΔNp63α expression promotes self-renewal in limbal stem cells

city: Tsingdao

first: Longfei

last: Li

address: yushan road no.5

institute: Ocean university of China

summary: In the present study, we established MYC-overexpressing limbal epithelial stem cell line (oeMYC-LESC) that exhibits a biomarker expression profile resembling that of limbal progenitor cells (LPCs). The self-renewal capacity of oeMYC-LESCs was markedly enhanced compared to high-passage cells, primarily through lactylation-dependent mechanisms. Specifically, H3K18la upregulates ΔNp63α, a key transcriptional regulator essential for epithelial stem cell function and the maintenance of stratified epithelial integrity [a]. In vivo studies further demonstrated that the H3K18la‑ΔNp63α axis promotes corneal epithelial regeneration.

overall_design: CUT&Tag-seq of H3K18la modification in rLESCs. This expertimental aims at explore how H3K18la affect LESCs proliferation and self-renewal.


title: Cross-species analysis of transcriptomic response to alphaherpesvirus infection in human, bovine and equine cells

city: Freiburg

first: Florian

last: Full

address: Hermann-Herder-Str. 11

institute: Institute of Virology, University Medical Center Freiburg

summary: Comparative transcriptomics offers a powerful approach to elucidate host–virus interactions across related pathogens, yet systematic evaluations across spe-cies-matched cellular systems remain limited. Here, we performed a cross-species RNA-sequencing analysis of respective species’ cells infected with three alphaherpesviruses - herpes simplex virus 1 (HSV-1), bovine al-phaherpesvirus 1 (BHV-1), and equid alphaherpesvirus 1 (EHV-1) - to dissect conserved and virus-specific transcriptional responses. We show that certain orthologous genes and orthologous pathways are differentially regulated upon infection among the three species like pathways related to translation rRNA processing and TNF-alpha signaling. We find that the earliest sampled timepoint of infection, 2 hours post infection (hpi), shows the most commonly enriched pathways among the three species compared to later timepoints. At 6h and 9h post infection, BHV-1- and EHV-1-infections have more in common with each other in terms of enriched pathways than with HSV-1 infections. Moreover, we provide a comprehensive analysis of temporal viral gene expression for all three herpesviruses. Together, these findings provide a comparative framework for understanding alphaherpesvirus–host interactions and reveal both conserved core responses and species-specific transcriptional signatures. This work estab-lishes a foundation for identifying broadly acting antiviral targets as well as vi-rus-specific vulnerabilities that may inform host-directed therapies and cross-species disease management.

sample_organism:
Homo sapiens
Equus caballus
Bos taurus

platform_organism:
Homo sapiens
Equus caballus
Bos taurus

overall_design: RNA-sequencing was performed for MDBK cells infected with BHV-1, EDerm cells infected with EHV-1 and HFF cells infected with HSV-1 in the following conditions: Mock, 2hpi, 6hpi and 9hpi. The HFF cells have the following additional conditions: 6hpi + PAA treatment, 9hpi + PAA treatment and 16hpi.

first: Mirko

last: Schmitz

first: Eva

last: Neugebauer

first: Kristen

last: Conn


title: Bulk RNA-seq of multiple organs in LmnaG609G progeria mice with inducible Δ133p53α

city: Bethesda

first: Huaitian

last: Liu

state: MD

address: Building 37, Room 3050

department: CCR

institute: NCI

summary: Hutchinson–Gilford progeria syndrome (HGPS) is a premature aging disorder caused by LMNA mutations that produce progerin. To investigate whether the senescence-inhibitory human p53 isoform Δ133p53α counteracts progeroid phenotypes in vivo, we generated mice carrying a Cre/loxP-inducible Δ133p53α transgene and crossed them with LmnaG609G mice. Bulk RNA-seq was performed on heart, kidney, liver, and skeletal muscle from wild-type and LmnaG609G/+ mice across five experimental groups. Transcriptomes were analyzed to identify Δ133p53α-associated gene expression programs and pathway-level changes across organs. This dataset provides a multi-organ resource to interrogate transcriptional signatures linked to Δ133p53α induction in a progeria model and support mechanistic interpretation of the associated manuscript.

overall_design: Bulk RNA-seq was performed on heart, kidney, liver, and skeletal muscle collected from 9–10-month-old mice (n = 5 per tissue per group (4 in kidney); total n = 99). The dataset includes five groups: a wild-type group lacking the LmnaG609G allele (Lmna^+/+) and four groups on the heterozygous progeria background (Lmna^G609G/+) defined by a Cre/loxP-inducible human Δ133p53α transgene and tamoxifen exposure as follows: Group-1, CAG-133^Tam/+;Cre^Tg/+;Lmna^G609G/+ injected with tamoxifen at 5–6 weeks of age; Group-2, CAG-133^LSL/+;Cre^Tg/+;Lmna^G609G/+ without tamoxifen injection; Group-3, CAG-133^+/+;Cre^Tg/+;Lmna^G609G/+ injected with tamoxifen at 5–6 weeks of age; and Group-4, CAG-133^+/+;Cre^+/+;Lmna^G609G/+ without tamoxifen injection. Reads were processed to generate gene-level expression matrices for differential expression and pathway analyses.

first: Leo

last: Yamada

first: Natalia von

last: Muhlinen

first: Curtis

last: Harris

first: Izumi

last: Horikawa


title: Prostaglandin I₂ Receptor Activation Promotes Alveolar Regeneration via the JUN/p53 Pathway [Multiome-seq]

city: Tianjin

first: yujun

last: shen

address: 22 Qixiangtai Road, Heping District

institute: Tianjin Medical University

summary: Rationale: Transdifferentiation of alveolar type 2 (AT2) epithelial cells into type 1 (AT1) cells is essential for maintaining lung homeostasis and facilitating repair following injury. However, the molecular mechanisms governing AT2-to-AT1 transdifferentiation remain unclear. Objectives: To investigate the role of the prostaglandin I2 receptor (IP) in regulating AT2-to-AT1 transdifferentiation and elucidate the underlying mechanisms. Methods: Alveolar organoid cultures and bleomycin- or lipopolysaccharide (LPS)-induced murine lung injury models were used to assess the role of IP in AT2-to-AT1 transdifferentiation and lung repair. Single-cell RNA sequencing (scRNA-seq), ATAC-seq, and biochemical assays were performed to explore the regulatory signaling pathways downstream of IP in AT2 cells. Measurements and Main Results: Among all prostaglandin receptors, IP exhibited the strongest association with AT1 gene enrichment in transitional AT2 cells from patients with idiopathic pulmonary fibrosis (IPF). Pharmacological inhibition or genetic deletion of IP significantly impaired the AT2-to-AT1 transition in organoid cultures. Conditional knockout of IP in AT2 cells exacerbated bleomycin- and lipopolysaccharide-induced lung injury by reducing epithelial regeneration and increasing fibrosis. Mechanistically, IP deficiency led to aberrant JUN activation, which suppressed p53-dependent AT1 gene expression. IP activation promoted PKA-mediated inhibition of MAP3K5, thereby suppressing the JNK/JUN axis and enhancing p53-driven AT2-to-AT1 transdifferentiation. Pharmacological activation of IP with selexipag promoted alveolar epithelial regeneration and reduced lung fibrosis in mice. IP agonist also enhanced AT2-to-AT1 transdifferentiation in primary AT2 cells from patients with IPF. Conclusions: IP is a key regulator of alveolar epithelial regeneration. Therapeutic activation of IP may be a promising strategy for promoting lung repair.

overall_design: Multiome-seq, GFP+ AT2 cells were sorted by flow cytometry from bleomycin-treated(8 days post-injury)  SftpcCreERT2; Rosa26mTmG(Control) or SftpcCreERT2; Rosa26mTmG; IPF/F(CKO) mice and analyzed using multiome single-cell  ATAC + Gene expression sequencing(Multiome-seq). Joint snRNA-and scATAC libraries were prepared using the 10x Genomics platform.

first: Tingting

last: Yu

first: Yujun

last: Shen


title: Prostaglandin I₂ Receptor Activation Promotes Alveolar Regeneration via the JUN/p53 Pathway [scRNA-seq]

overall_design: scRNA-seq, EpCAM+CD31-CD34-CD45-CD24-Sca-1- cells were  sorted by flow cytometry from WT or IP-/-(IPKO) mice and analyzed using scRNA-seq.


title: Late-onset sporadic Alzheimer’s disease modeling using patient-derived cells: A review

city: montreal

first: Gilbert

last: Bernier

state: Quebec

address: 5415 Assomption Blvd

institute: Hopital Maisonneuve-Rosemont Research center

summary: Late-onset sporadic Alzheimer’s disease (LOAD) is the most common form of dementia. The disease is characterized by progressive loss of memory and behavioral changes followed by neurodegeneration of all cortical areas. While the contribution of genetic and environmental factors is important, advanced aging remains the most important disease risk factor. Because LOAD does not naturally occur in most know animal species, except humans, studies have traditionally relied on the use of transgenic mice modeling rare, early-onset genetic forms of Alzheimer’s disease. Hence, the development of more representative LOAD models through reprograming of patient-derived cells into neuronal, glial, and immune cells became a necessity to better understand the disease origin and pathophysiology. Herein, and focusing on neurons, we review current work in the field and compare results obtained with two different reprograming methods to generate patient-derived neuronal cells: the induced pluripotent stem cell and induced neuron technologies. We also evaluate if these models can faithfully mimic cellular and molecular pathologies observed in LOAD patient’s brains. Here, we show new ATAC-seq data that support that iPSC can faithfully model LOAD, with an increased number of peaks showing chromatin relaxation in LOAD neurons

overall_design: iPSC reprogrammed from LOAD patient fibroblasts were differentiated into neurons for 60 days followed by an ATAC-seq

first: Katbe

last: Alisar

first: Diagne

last: Ismaila

first: Bernier

last: Gilbert


title: Prostaglandin I₂ Receptor Activation Promotes Alveolar Regeneration via the JUN/p53 Pathway [CUT&Tag]

overall_design: CUT&Tag-seq, GFP+ AT2 cells were sorted by flow cytometry from bleomycin-treated(8 days post-injury)  SftpcCreERT2; Rosa26mTmG(Control) or SftpcCreERT2; Rosa26mTmG; IPF/F(CKO) mice and analyzed using CUT&Tag-seq.


title: Gene expression signatures in the dorsal root ganglion of rats exposed to methylmercury

city: Hachioji

first: Yo

last: Shinoda

state: Tokyo

address: 1432-1 Horinouchi

department: Pharmacy

country: Japan

institute: Tokyo University of Pharmacy and Life Sciences

summary: Methylmercury is known as the causative agent of Minamata disease. To investigate the mechanisms of neurotoxicity in the dorsal root ganglion, male Wistar rats (8 weeks old) were administered methylmercury (6.7 mg/kg/day) for five consecutive days followed by two days without treatment, repeated over a two-week period. Dorsal root ganglia were collected from the control group, as well as on days 7 and 14 after the start of administration. Total RNA was extracted and subjected to DNA microarray analysis.  In the day-7 samples, marked alterations in gene groups involved in inflammatory responses were observed, while in the day-14 samples, in addition to these changes, alterations in approximately 15,000 gene groups were detected.

overall_design: Methylmercury-induced gene expression in the rat dorsal root ganglion was assessed at 7 and 14 days after the initial exposure to 6.7 mg/kg/day. The exposure protocol consisted of five consecutive days of dosing followed by a two-day treatment-free interval, and this cycle was repeated once for day 14 sample. For each time point (day 7 and day 14), four independent experiments were conducted using different animals.

first: Yasuyuki

last: Fujiwara


title: β-Catenin Stabilization Protects Against Alveolar Hemorrhage Through Amphiregulin and BATF-Mediated Regulatory T Cells

city: Syracuse

first: Mobin

last: Karimi

state: NY

address: 766 Irving Ave Suite 2281

department: Microbiology/Immunology

institute: Suny Upstate Medical University

summary: Alveolar hemorrhage (AH) is a life-threatening condition with a high mortality rate, of immune cells in its pathogenesis remains poorly defined. Here, we report of β-catenin stabilization under Lck promoter and its impact on yet the role the protective function AH. Using a novel transgenic mouse model (CAT-Tg) with stabilized β-catenin, we demonstrate that β-catenin stabilization induces a distinct T-cell phenotype characterized by an expansion of central effector memory cells (CD44⁺, CD122⁺, Eomes⁺, T-bet⁺). Mechanistically, this effect was associated with suppression of key proinflammatory pathways, including reduced phosphorylation of STAT1, STAT3, and JAK1. AH was induced using pristane, and CAT-Tg mice were significantly protected from lung damage, showing reduced proteinuria and decreased pulmonary proinflammatory cytokine production compared with wild-type (WT). This protection correlated with a marked increase in FOXP3⁺ regulatory T cells (Tregs) in CAT-Tg mice. We further identified a novel mechanism in which β-catenin stabilization enhances lung expression of Amphiregulin and BATF, two molecules essential for Treg function and tissue repair. Adoptive transfer of Tregs from CAT-Tg mice into WT mice with pristane-induced AH conferred superior protection, as evidenced by reduced lung inflammation and proteinuria. The systemic administration of a β-catenin agonist to mice with AH significantly attenuated disease severity. Our bioinformatic analysis confirmed that β-catenin stabilization upregulates pathways associated with tissue repair and immune homeostasis, including PI3K-Akt, angiogenesis, and STAT5 signaling. Collectively, these findings reveal that β-catenin stabilization protects against alveolar hemorrhage by inducing a specialized T-cell phenotype and establishing a protective Amphiregulin–BATF–Treg axis. This study identifies a novel immunomodulatory pathway with therapeutic potential for AH and other inflammatory lung diseases.

overall_design: Overall design: CAT-Tg, wildtype -and vehcile versus agonist-treated WT mice following pristane challenge.

first: Fiona

last: Mason

first: Hui

last: Xiong

first: Ali

last: Mobeen

first: Md Saddam

last: Hossain

first: Sara

last: Mahmudlu

first: Rosanne

last: Trevail

first: Mikyal

first: Li

last: Chen

first: Sunny

last: Lee

first: Tuncay

last: Delibasi

first: Jyoti

last: Sen


title: Transcriptomic insights into metabolic reprogramming and exo-polysaccharide synthesis in Porphyridium purpureum under gradual nitrogen deprivation

city: AUBIERE

first: Maurean

middle: Tehani

last: Guerreiro

state: Auvergne-Rhône-Alpes

address: 4, Avenue Blaise Pascal

department: Axe GePEB : Génie des Procédés, Énergétique et Biosystèmes

country: France

institute: Institut Pascal, UMR 6602 – Université Clermont Auvergne (UCA)

summary: Porphyridium species are known red microalgae for producing valuable bioactive compounds such as sulfated exopolysaccharides (EPS) with diverse industrial biomed-ical applications due to their functional and rheological properties. Recent studies have investigated how abiotic stresses, particularly nitrogen deprivation, affect Porphyridium’s metabolic regulation and EPS production through transcriptomic analysis. Still, the mechanisms governing EPS biosynthesis and the involvement of carbohydrate-activated enzymes (CAZymes) remain poorly understood. This study investigated the progressive effects of nitrate consumption on unicellular red alga P. purpureum, by integrating physiological, biochemical, and transcriptomic analyses through RNA-Seq, further validated by RT-qPCR. P. purpureum displayed a gradual, phase-dependent metabolic response to progressive nitrogen stress. EPS release coincided with the decline in nitrate uptake, linking nitrogen availability to carbon redirec-tion towards polysaccharide secretion. Transcriptomic data revealed global metabolic downregulation with targeted upregulation of stress-responsive, carbohydrate catabolic, and nucleotide-sugar synthesis pathways, including upregulation of CAZyme families GT4, GT8, and GT77. Our results give insights into the coordinated nitrogen and carbon metabolic regulation underlying polysaccharide biosynthesis, while open-ing future perspectives on enzyme compartmentalization and regulatory flux distribution under nitrogen stress in P. purpureum.

overall_design: RNA-seq profiling of red microalga Porphyridium purpureum cultures exposed to four residual nitrate concentrations (1.5, 0.6, 0.5, 0.3 g·L⁻¹), with technical triplicates to study the onset of nitrate depletion.

first: Coline

last: Emmanuel

first: Céline

last: Dupuits

first: Christine

last: Gardarin

first: Said

last: Mouzeyar

first: João

last: Varela

first: Jane

last: Roche

last: Laroche


title: Primordial cardiomyocytes orchestrate myocardial morphogenesis and vascularization but are dispensable for regeneration

city: ATLANTA

first: Jinhu

last: Wang

state: Georgia

address: 101 WOODRUFF CIRCLE WMB 2304

institute: Emory University

summary: The vertebrate heart is composed of heterogeneous cardiomyocyte (CM) populations, however, the roles of distinct CM subpopulations in heart development and repair remain poorly defined. Here, using single-cell RNA sequencing analysis of adult zebrafish heart, we identified a unique CM subpopulation marked by the expression of phlda2, which is associated with anaerobic metabolism and different from mature CMs which are enriched for oxidative phosphorylation genes. We demonstrated that phlda2+ cells constituted a primordial CM compartment localized between compact and trabecular muscles. Genetic ablation of phlda2+ CMs during development severely disrupted heart morphogenesis, leading to defective myocardial trabeculation and compaction, and impaired coronary vascularization. Surprisingly, despite their essential roles in development, the depletion of phlda2+ CMs didn’t impair myocardial restoration and revascularization following ventricular resection. We found that this was probably due to the limited regenerative capacity of the primordial CMs themselves, as they failed to regenerate after either surgical amputation or genetic ablation. Our findings identify primordial CMs as an organizer for heart morphogenesis but not essential for regeneration, revealing a fundamental difference between developmental and regenerative programs in the vertebrate heart.

overall_design: Single cell RNA sequencing of FACS isolated cardiomycytes (cmlc2:EGFP) from adult hearts

first: Jisheng

last: Sun

first: Lu


title: Arginine deprivation reshapes tumor and immune transcriptional programs and potentiates IFNγ–JAK–STAT signaling in 4T1 murine breast tumors

city: Rehovot

first: Hila

last: Tishler

address: POB 26

department: Molecular Cell Biology

country: Israel

institute: Weizmann Institute of Science

summary: Arginine availability is a key metabolic regulator of tumor and immune cell function. We performed single-cell RNA sequencing of orthotopic 4T1 murine triple-negative breast tumors to define cell type–specific transcriptional adaptations to arginine deprivation. We demonstrate that arginine depletion induces widespread transcriptional reprogramming across both stromal and immune compartments, with particularly pronounced effects in cancer-associated fibroblasts (CAFs) and tumor-associated macrophages (TAMs). In tumor cells, cancer cell–intrinsic (via Ass1 knockdown), systemic (via an arginine-free diet), or combined restriction of arginine availability resulted in elevated inflammatory responses, including activation of interferon-alpha (IFNα) and interferon-gamma (IFNγ) signaling, and, to a lesser extent, IL6–JAK–STAT3 signaling. These changes, mediated by tumor microenvironment (TME)–supportive interactions, sustain tumor cell survival under arginine-deprived conditions.

overall_design: Orthotopic 4T1 mammary tumors were established in female BALB/c mice to assess the effects of tumor-intrinsic and systemic arginine restriction. Mice were divided into four groups: control (Ctrl; shGfp + regular diet), tumor-intrinsic restriction (KD; shAss1 + regular diet), systemic restriction (AFD; shGfp + arginine-free diet), and combined restriction (KD + AFD; shAss1 + arginine-free diet). Tumors were collected on day 16 post-implantation, dissociated into single-cell suspensions, and pooled by treatment group by combining equal numbers of cells from 4–5 tumors per condition.

first: Gil

last: Stelzer

first: Ayelet

last: Erez


title: Analysis of experimental colorectal liver metastases identifies distinct proliferation independent transcriptional programs in micro- versus macrometastases

city: Utrecht

first: Niek

last: Peters

address: Heidelberglaan 100

institute: UMC Utrecht

summary: Human engineered CRC organoids were equiped with the sTomato-p27K- quiescense reporter. Quiescent cells are characterized by distinct transcriptional programs

overall_design: Organoids were grown from single cells for 7-10 days. Then, organoids were dissociated to single cells and sTomato-p27k-high, sTomato-p27k-medium, and sTomato-p27k-low cells were collected by FACS. Samples were then processed for bulk RNA-seq.


title: The liver clock tunes transcriptional rhythms in skeletal muscle to regulate mitochondrial function

city: Barcelona

first: Jacob

last: Smith

state: Barcelona

address: Av. Diagonal, 643

country: Spain

institute: University of Barcelona

summary: Circadian clocks present throughout the brain and body coordinate diverse physiological processes to support daily homeostasis, yet the specific inter-organ signalling axes involved are not well defined. We previously demonstrated that the skeletal muscle clock controls transcript oscillations of genes involved in fatty acid metabolism in the liver, yet the impact of the liver clock on the muscle remains unknown. Here, we use hepatocyte-specific Bmal1 KO mice (Bmal1hep-/-) to reveal that approximately one-third of transcript rhythms in skeletal muscle are influenced by the liver clock in vivo. Treatment of myotubes with serum harvested from Bmal1hep-/- mice inhibits expression of genes involved in metabolic pathways, including oxidative phosphorylation. Only small transcriptional changes were induced by liver clock–driven endocrine communication in vitro, leading us to surmise that the liver clock acts to fine-tune metabolic gene expression in muscle. Consistent with functional tuning, treatment of myotubes with serum collected from Bmal1hep-/- mice during the dark phase lowers mitochondrial ATP production as compared to serum from wild-type mice. Overall, our results reveal communication between the liver clock and skeletal muscle, uncovering a bidirectional endocrine communication pathway that may contribute to the metabolic phenotypes of circadian disruption.

overall_design: RNA-seq profiling of gastrocnemius muscle harvested around the clock at 6 different diurnal time points from wildtype (WT) and mice with liver-specific deletion of Bmal1 (Bmal1hep-/-)

first: Kevin

middle: B

last: Koronowski


title: MicroRNA210 regulated brain pericyte dysfunction exacerbates hypoxic-ischemic brain injury in neonatal mice

city: Loma Linda

first: Qingyi

last: Ma

state: California

address: 11175 Campus St

department: Department of Basic Sciences

institute: Loma Linda University

summary: Background While the role of pericytes in blood-brain barrier (BBB) disruption and neuroinflammation is well-established in adult neurological disorders, their contribution to neonatal brain injury is largely unexplored. Here, we investigated the role of brain pericytes in hypoxic-ischemic (HI) brain injury in the developing brain, with a particular focus on the regulatory role of pericyte-derived microRNA210 (miR210) in pericyte dysfunction.  Methods HI brain injury was induced on postnatal day 9 transgenic mice, including Atp13a5-tdTomato brain pericyte reporter mice, pericyte-specific diphtheria toxin receptor mice, miR210 knockout mice, and wild-type controls. Post-injury assessments include brain infarct, brain edema, BBB permeability, ELISA, western blotting, immunostaining, and neurological function test. BBB-associated cells, including pericytes and endothelial cells, were isolated from mouse brain using an immunomagnetic approach. RNA sequencing analysis was conducted to examine transcriptomic changes in pericytes after HI. To investigate the regulatory role of miR210 in pericyte dysfunction and its underlying mechanisms, primary pericytes were transfected with miR210 mimic or negative control, followed by oxygen-glucose deprivation. Transfected cells were also treated with either interleukin 1 type 1 receptor neutralizing antibody or recombinant interleukin 1 type 2 receptor chimera protein. Post-assays included RT-qPCR, immunostaining and cell viability assay. Student’s t test or one-way ANOVA followed by Bonferroni test was used, as appropriate.  Results HI resulted in a time-dependent loss of pericytes in pericyte reporter mouse pups. Ablation of brain pericytes exacerbated BBB disruption and HI brain injury in neonatal brain. miR210 deletion mitigated brain pericyte loss and BBB leakage post-HI. Transcriptomic analysis revealed that HI-induced pericyte dysfunction was associated with upregulated genes enriched in biological processes such as “cellular response to interleukin 1”. miR210 knockout suppressed the expression of proinflammatory markers such as Il1r1. Mechanistically, miR210 overexpression increased proinflammatory cytokine levels and promoted pericyte cell death under oxygen-glucose deprivation, effects that were reversed by IL1R1 blockade. Importantly, brain pericyte-specific miR210 deletion preserved pericyte viability and BBB integrity, and provided neuroprotection after HI.  Conclusions These findings underscore the critical role of brain pericytes in BBB function in the developing brain and identify miR210 as a central regulator of pericyte dysfunction following neonatal HI brain injury.

overall_design: RNA-seq analysis of isolated PDGFRbeta-positive cells from wildtype and microRNA210 knockout mice 24 hours after neonatal hypoxic-ischemic brain injury

first: Shirley

last: Hu

first: Yanelly

last: Lopez-Robles

first: Elena

last: Liu

first: Wanqiu

last: Chen

first: Chaitra

last: Manjunath

first: Zhen

last: Zhao

first: Lubo

last: Zhang


title: A Senescent Tumor Cell-Derived Nanovesicle Directly Primes Splenic T cells to Potentiate Radiotherapy

city: Shanghai

first: Shun

address: 1665, Kongjiang Road, Yangpu

institute: Xinhua Hospital, School of Medicine, Shanghai Jiao Tong University

summary: Senescent tumor cells (STCs) play a crucial role for radiotherapy-induced immunosuppressive tumor microenvironments (ITM). However, current senolytic strategies lack specificity for STCs and often cause off-target toxicity. Here, we first identified the antigen presenting potential of STCs in patient-derived tumor tissues and demonstrated their capacity for directly priming and inducing STC-specific CD8+ T cells. We thereafter engineered STC-derived nanovesicles for directly priming CD8+ T cells through their upregulated antigen-presenting machinery (termed as nano-APM). Upon systemic administration, nano-APMs specifically accumulated in the spleen and directly primed CD8⁺ T cell, thereby establishing STC-specific T cell pool. Based on these finding, we sequentially combining nano-APM with RT to achieve spatiotemporally-confined activation of anti-senescence immunity via RT-controlled tumor senescence induction. In preclinical mouse models of pancreatic ductal adenocarcinoma and bladder cancer, the sequential combination of the nano-APM with RT effectively eliminated STCs, reprogramed RT-induced ITM (e.g., 21.5-folds higher CD8+ T cell to Tregs ratio than the control group), and induced durable antitumor response. Overall, this study pioneered a STC-derived nanovesicle platform to directly prime splenic T cells and achieve spatiotemporally-confined senolysis for potentiating RT.

overall_design: Senescent or none-senescent tumor cells (MB49 cell, sMB49 cells, KPC cells, and sKPC cells) were treated with 8 Gy-RT and cultured for 48 h.Then the cells were collected for total RNA sequence.

first: Jiaxing

last: Pan


title: RNA-seq of control and  PARylator knockdown TE13 human esophageal squamous carcinoma cells

city: taiyuan

first: Li

last: wenjin

state: Shanxi

address: No. 56, Xinjian South Road, Yingze District

institute: Shanxi medical university

summary: This study generated RNA sequencing (RNA-seq) data to characterize the transcriptomic consequences of PARylator knockdown in human esophageal squamous carcinoma TE13 cells. Control and PARylator-depleted cells were collected, and total RNA was extracted and subjected to high-throughput sequencing on an Illumina platform. The resulting dataset enables differential expression analysis between control and knockdown conditions and provides a transcriptomic resource for investigating PARylation-related gene regulation in esophageal cancer cells.

overall_design: RNA-seq was performed on TE13 human esophageal squamous carcinoma cells with control and PARylator knockdown conditions, each analyzed in 3 biological replicates, to assess transcriptomic changes.

first: Tengfei

last: Qi

first: Xudong


title: Single-cell sequencing technology reveals the characteristics of the tumor microenvironment in gastric cancer and its peritoneal metastases

city: shanghai

first: Jun

address: No.197, Ruijin road

department: Department of Oncology

institute: Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine

summary: To analyze the tumor microenvironment characteristics of gastric cancer and its peritoneal metastases, we collected fresh surgical specimens pathologically confirmed as gastric cancer and peritoneal metastases, and performed single-cell sequencing.

overall_design: Three samples of gastric carcinoma in situ and three samples of gastric cancer peritoneal metastasis were subjected to single-cell sequencing.

first: Qi

last: Wang