title: Transcriptome analysis of TNFα or necroptosis-induced stimulation in the NCI-H441 cell line with RIPK3 knocked down by siRNA.

city: tokyo

first: tomohiro

last: koiwa

state: tokyo

address: 1-3-7 Hongo, Bunkyo-ku,

department: Respiratory medicine

institute: tokyo university

summary: We aimed to elucidate the role of RIPK3 in lung adenocarcinoma by analyzing expression variations through RNA sequencing. To achieve this, we suppressed the expression of RIPK3 in the NCI-H441 lung adenocarcinoma cell line, which highly expresses this gene, using multiple siRNAs. We then subjected the cells with RIPK3 knockdown to TNFα stimulation and necroptosis-inducing stimuli. As a result, we observed changes in the expression of genes involved in chemokine expression and the production of interferons (IFNs)

overall_design: NCI-H441 cells were treated with siRNA for negative control (NC), RIPK3 siRNA #1, and RIPK3 siRNA #2. After the treatment, the cells were incubated for 48 hours and then subjected to stimulation with 10 ng/mL of TNFα, or necroptosis-inducing stimuli consisting of 10 ng/mL of TNFα, 20 µM of zVAD-fmk, and 100 nM of Birinapant.We analyzed the gene expression variations based on data obtained from the treated RNA-seq.

first: Tomohiro

last: Koiwa

first: Hiroshi

last: Takumida

first: Naoya

last: Miyashita

first: Akira

last: Saito


title: Novel therapy for metabolic liver disease by transplantation of human iPS cell-derived 3D-organoids

status: Public on Apr 01 2026

city: Yokohama City

first: Yasuharu

last: Ueno

state: Kanagawa

address: 3-9  Fuku-ura, Kanazawa-ku

department: Graduate School of Medicine

country: Japan

institute: Yokohama City University

summary: Urea cycle dysbiosis—a severe metabolic liver disease caused by ornithine transcarbamylase (OTC) deficiency—is associated with hyperammonemia. Its only curative treatment is liver transplantation; however, severe shortage of organ donors poses a major challenge. Here, we report the generation of clinical-grade liver organoids from human induced pluripotent stem cells (hiPSC), which exhibit in vitro and in vivo ammonia metabolic functions. Quantitative metabolic flux analysis shows that the organoids have sufficient OTC enzyme activity and urea-producing function, implying their ammonia-metabolizing efficacy. The organoids show clear ameliorative effects on hyperammonemia when transplanted into mice with mild/severe OTC deficiency. Isotope-labeled ammonia-loading tests in post-transplant recipients confirm the graft’s efficiency in in vivo urea conversion. Moreover, organoid transplantation improves activity and survival rates in severe OTC-deficient mice. Overall, we demonstrate the therapeutic effects of clinically applicable hiPSC-derived organoids, which highlights their potential application in regenerative therapy.

overall_design: Transcriptome profiling of iPSC derived liver organoids (iPSC-LO) and human liver tissue of various developmental stages.

first: Hideki

last: Taniguchi


title: CITE-seq analysis of Mycobacterium tuberculosis infected wild-type and IL-1R KO mixed bone marrow chimera mouse lungs

city: Berkeley

first: Dmitri

middle: I

last: Kotov

state: CA

address: 415 Weill Hall

department: Molecular and Cell Biology

country: USA

institute: University of California, Berkeley

type: Expression profiling by high throughput sequencing

summary: Mycobacterium tuberculosis (Mtb) causes 1.6 million deaths a year. However, tuberculosis pathogenesis remains poorly understood and is not fully recapitulated in standard mouse models. Here we report that a comparison across three different susceptible mouse models identifies Mtb-induced gene signatures that predict active TB disease in humans significantly better than a signature from the standard C57BL/6 mouse model. Common to signatures from susceptible mice were myeloid cell response and immunosuppressive genes. In line with the signatures, an increase in lung myeloid cells, including neutrophils, was conserved across the susceptible mouse models, mimicking the neutrophilic inflammation observed in humans. Myeloid cells in the susceptible models and non-human primates exhibited high expression of immunosuppressive molecules including IL-1 receptor antagonist, which inhibits IL-1 signaling. Prior reports have suggested that excessive IL-1 signaling impairs Mtb control. By contrast, we found that enhancement of IL-1 signaling via deletion of IL-1 receptor antagonist promoted bacterial control in all three susceptible mouse models. IL-1 signaling enhanced cytokine production by lymphoid and stromal cells, suggesting a mechanism for IL-1 signaling in promoting Mtb control. Thus, we propose that myeloid cell expression of immunosuppressive molecules is a conserved mechanism exacerbating Mtb disease in mice, non-human primates, and humans.

overall_design: Mixed bone marrow chimera mice where generated by transferring a 1 : 1 mixture of CD45.1/2 congenically marked wild-type bone marrow and CD45.2 IL-1R KO bone marrow into lethally irradiated wild-type CD45.1 recipients. Following immune reconstitution, lungs were harvested from Mtb-infected mixed bone marrow chimera mice 25 days post infection (19 mice total with 3 mice left unpooled used for the T cell dataset and the remaining 16 mice pooled into three samples: mouse 1 (5 mice pooled together), mouse 2 (5 mice pooled together), mouse 3 (6 mice pooled together)). The three mice used for the T cell dataset were stained with antibody and Fluorescence-activated cell sorted (FACS) to isolate the T cells. Innate lymphoid cells were magnetically enriched by negatively selecting based on TER119, GR-1, TCR g/d, CD3e, CD11b, and B220. After enrichment, innate lymphoid cells were purified by FACS sorting.

first: Ophelia

middle: V

last: Lee

first: Daisy

middle: X

last: Ji

first: David

middle: L

last: Jaye

first: Sara

last: Suliman

first: Cem

last: Gabay

first: Russell

middle: E

last: Vance


title: Development of uveitis in a mouse model of spontaneous autoimmunity correlates with frequency of autoantigen-specific regulatory T cells

city: SAN FRANCISCO

first: Mianmian

last: Yin

address: 513 Parnassus Avenue

department: Department of Microbiology and Immunology

institute: University of California, San Francisco

summary: B6 AireGW/+Lyn-/-mice are a model of spontaneously autoimmunity in which 50% of mice develop uveitis by 9 weeks of age, and the remaining mice do not develop autoimmunity. Uveitis results from CD4+ T cells responding to the retina protein interphotoreceptor retinoid-binding protein (IRBP). To define cellular mechanisms that determine whether mice developed autoimmunity or not, we did single-cell RNA sequencing (scRNA-seq) of eye-draining lymph node (LN) CD4+T cells that recognize the P2 epitope of IRBP (amino acid 271-290). Uniform manifold approximation and projection (UMAP) analysis showed that these CD4+T cells included distinct subsets that were Teff, Tfh, Il7r_hi, T_prolif, T_trans, Ifit1_hi and Tregs, with the Treg population being overrepresented in mice without disease. In mice without uveitis, depletion of Treg by treatment of AireGW/+Lyn-/- Foxp3DTR+/Y mice with Diphtheria toxin resulted in rapid expansion of P2–specific CD4+T cells in the draining LN, development of inflammation in the retina, and immune activation in other locations leading to lethality. In summary, those results indicated that expansion of P2-specific CD4+Treg cells promote the development of uveitis in AireGW/+Lyn-/-mice.

overall_design: To characterize the diversity of the spontaneous autoimmune P2 response, the single cell mRNA sequencing were performed for the P2+ cells from LN and retina of AireGW/+ Lyn-/- mice with(two dataset) and without uveitis, and LN of AireGW/+ Lyn-/- IRBP-/-mice.

first: Kamir

middle: J

last: Hiam

first: Irina

last: Proekt

first: Jackie

last: Chan

first: Yongmei

last: Hu

first: Clifford

middle: A

last: Lowell

first: Douglas

middle: B

last: Gould

first: Matthew

last: Spitzer

first: Mark

middle: S

last: Anderson

first: Anthony

last: DeFranco


title: IL-1-driven stromal cell response to Mycobacterium tuberculosis in mouse lungs

first: Dmitri

last: Kotov

overall_design: Bone marrow chimera mice were generated by transferring CD45.1 wild-type bone marrow  into lethally irradiated wild-type B6 or IL-1R KO mice. Lungs from the bone marrow chimera mice were harvested from naïve mice (5 animals per genotype) or mice infected with Mycobacterium tuberculosis for 25 days  (5 animals per genotype).  Hematopoietic cells were magnetically depleted based on CD45. After negative selection, non-hematopoietic cells were isolated by Fluorescence-activated cell sorting (FACS).


title: GigaMUGA mouse genotyping array data for Modifiers of Placental Function That Mediate Survival of Sfmbt2 Deficient Embryos

city: Albuquerque

first: Gurdeep

last: Singh

state: New Mexico

address: 915 Camino de Salud NE, Fitz Hall, Rooms 155 (office) & 154 (lab)

institute: UNM School of Medicine

type:
Genome variation profiling by SNP array
Genome variation profiling by array

summary:
To search for potential modifiers of placental function that mediate the survival of Sfmbt2 deficient embryos, we analyzed 44 samples validated to be lacking paternal Sfmbt2 but still born at a low survival rate due to the presence of maternal CD1 genetic content.
The genotyping was performed using Giga Mouse Universal Genotyping Array (GigaMUGA) which provides the status of >143000 SNPs. The GigaMUGA SNP array was performed on DNA extracted from brains of survivors of crosses of (CD1 X B6) F1 females with C57BLB6gt (Sfmbt2 gene trap) males.

overall_design: Heterozygosity of SNPs amongst survivors was analyzed to identify the non-random enrichment and clustering of highly heterozygous SNPs, revealing recombinant regions from the CD1 genome marking genome regions with potential placental modifiers for survival under an Sfmbt2 hypomorphic condition.

first: Susannah

last: Varmuza


title: Acquired resistance in AML cell lines to the bifunctional electrophile busulfan is associated with changes in mitochondrial copy numbers and lipid and cholesterol metabolism

city: Lausanne

first: Vincent

last: Roh

address: Bugnon 25A

country: Switzerland

institute: SIB

summary:
Purpose: Alterations in mitochondrial copy number (mtDNA-CNs) may affect the sensitivity of cells to reactive oxygen species (ROS)-generating compounds, such as busulfan (BU). In this work, we investigated whether the resistance of AML cell lines to ROS-generating compounds, Busulfan (BU), or and the DNA synthesis inhibitor cytarabine (ara-C) was associated with an increase of mtDNA-CNs.
Methods: Myeloid cells (MOLM13) were exposed to five consecutive BU treatments to acquire BU resistance (5TBU). The 5TBU and control cell lines, treated with DMSO, were further exposed to five consecutive ara-C treatments to obtain cells resistant to both BU and ara-C. We estimated the 50% inhibitory concentration (IC50) of BU and ara-C in these cells and quantified mtDNA-CNs by RT-qPCR of MTND1. We also performed gene expression profiling to assess how resistance to BU and treatement with DMSO affect the transcriptional activity of cells.
Results: mtDNA-CNs were associated with cellular sensitivity to BU, but not to ara-C. Cholesterol and fatty acid synthesis pathways appear to be important in cellular adaptation to BU.

overall_design: MOLM13 cells (MOLM13-P, parental) were used to generate a BU-resistant MOLM13 cell line. Cultures of 2.5 × 106 cells were incubated at 37 °C and 5% CO2 for 24 h before treatment. The cells were then exposed for 6 h to gradually increasing concentrations of BU (Sigma-Aldrich, Germany), from 25 to 200 µM, and reconstituted with DMSO (Sigma-Aldrich). After exposure, the cells were washed and maintained in culture until > 80% viability was restored. Recovered cells were cultured at approximately 500,000 cells/mL density and named: 1TBU. For the following treatment courses, the steps mentioned above were repeated four times, followed by 2–3 weeks of recovery in a fresh medium after each treatment course. The maximum number of cell culture passages for MOLM13-P and BU-resistant MOLM13 cells was 20 and 60, respectively. Another compound, the DNA synthesis inhibitor ara-C (Sigma-Aldrich), was used as a non-electrophilic control to compare the BU sensitivity profiles of the cells. Fresh BU-resistant cell model and vehicle (DMSO) control cells were exposed to 400 nM ara-C reconstituted with DMSO for 72 h, followed by 1 week of recovery. The treatment course was repeated four times with 600 nM ara-C. All control cells were prepared in parallel using 1% DMSO.

first: Vid

last: Mlakar

first: Simona

last: Jurkovic Mlakar

first: Yvonne

last: Gloor

first: Yoann

last: Sarmiento

first: Mary

last: Boudal-Khosbheen

first: Denis

last: Marino

first: Chakradhara Rao

last: Satyanarayana Uppugunduri

first: Marc

last: Ansari


title: p27kip1-dependent gene activity within pregranulosa cells implicates pathways relevant for control of primordial follicle activation in mice

city: Edinburgh

first: Güneş

last: Taylor

address: 4-5 Little France Drive

department: Centre of Reproductive Health

country: United Kingdom

institute: University of Edinburgh

summary: The number of primordial follicles within the ovary, and their rate of activation, are critical parameters of the female reproductive lifespan. A finite number of primordial follicles are established during early ovarian development when individual oocytes are surrounded by a layer of somatic supporting pregranulosa cells. Primordial follicles remain quiescent until activated and their selective activation represents the definitive first step towards oocyte maturation and ovulation. Activation is characterised by oocyte and granulosa morphological changes. Activated granulosa cells resume proliferating, downregulating cell cycle inhibitor and transcriptional repressor Cdkn1b/p27kip1. Aside from a single wave of neonatal activation, primordial follicles activate cyclically to enter the pool of growing follicles. Mice lacking p27kip1 are infertile as all their primordial follicles activate during this neonatal wave of activation. Here, we utilise a p27kip1-null (Cdkn1b-/-) mouse line to functionally implicate a gene expression signature within the pregranulosa cells of primordial follicles undergoing activation. Using a combinatorial transcriptomic approach, we find pregranulosa cells undergoing follicle activation are characterised by the expression of several genes previously linked with mature granulosa cells as well several novel candidates: Tnni3, Slc18a2, Fam13a and Klf2. This study implicates pregranulosa cell transition as the key driver of primordial follicle activation and integrates cell-cycle regulator p27kip1 within the molecular mechanism driving pregranulosa cell transition.

overall_design: Ovaries from WT mice and Cdkn1b -/- mice were colelcted at four timepoints (embryonic day 13.5, embryonic day 18.5, postnatal Day 8 and 12 weeks of age) to understand the role of cell cycle regulation in ovarian development. Ovaries were all processed by dissociating using a papain method and then extracting RNA using the Qiagen Micro RNeasy kit.

first: Emily

middle: R

last: Frost

first: Gunes

first: Stefan

last: Boeing

first: Christophe

last: Galichet

last: Baker

first: Jessie

middle: M

last: Sutherland

first: Robin

last: Lovell-Badge


title: DYRK1A enhances antitumor immunity in type 1 conventional dendritic cells via mTORC1 activation

city: Xiamen

first: Hongjiao

last: Wang

address: xiangannanlu

country: China

institute: xiamen university

summary: Type 1 conventional dendritic cells (cDC1s) play an integral role in mediating immune responses and maintaining homeostasis, yet the molecular mechanisms underlying their functions remain poorly understood. In this study, we identify dual-specificity tyrosine phosphorylation-regulated kinase 1A (DYRK1A) as a key kinase that responds to TLR and growth factor stimulation, acting as an essential regulator of cDC1 function. Genetic ablation of Dyrk1a specifically in cDC1s impairs antitumor immunity and accelerates tumor progression in murine models. Mechanistically, DYRK1A mediates the phosphorylation of the mTORC1 inhibitor TSC2 at serine 540, triggering the degradation of TSC2 and promoting the mTORC1 signaling in cDC1s. Notably, Tsc2 deletion in Dyrk1a-deficient cDC1s remarkably restores their antitumor immune functions. Furthermore, DYRK1A-mediated mTORC1 signaling in cDC1s positively correlates with effector T-cell responses across multiple human cancers. Our findings highlight a critical role for the DYRK1A-TSC2-mTORC1 signaling pathway in regulating cDC1 functions in antitumor immunity, offering potential strategies to improve cancer immunotherapy.

overall_design: For tumor-infiltrating DC sequencing, the DCs (CD3-CD19-NK1.1-Ly6C-Ly6G-F4/80-Siglec-CD11c+MHCII+) were purified from tumor tissues of B16-F10 tumor-bearing Dyrk1a+/+-Cd11c-cre mice and Dyrk1a fl/fl-Cd11c-cre mice (day 13 after tumor cell inoculation).


title: Hepatic stellate cell-derived thrombospondin-2 as a novel therapeutic target for liver fibrosis

city: Beijing

first: Wei

last: Chen

state: Beijing

address: No. 95 Yong’an road, Xicheng District

department: Beijing Friendship Hospital

institute: Capital Medical University

summary: The in vivo effects of silencing Thbs2 in hepatic stellate cells (HSCs) were examined using an adeno-associated virus vector (serotype 6, AAV6) containing short hairpin RNAs (shRNAs) targeting Thbs2, under the regulatory control of cytomegalovirus (CMV) or smooth muscle α-actin (αSMA) promoter, in carbon tetrachloride (CCl4) induced liver fibrosis mouse models. Bulk RNA-seq of liver tissues from AAV6-CMV-shThbs2 mice or AAV6-αSMA mice and their controls was performed.

overall_design: Bulk RNA-seq of liver tissues from two AAV6-CMV-shThbs2 mice and two controls was performed on the Illumina HiSeq2500 platform at Biomarker Technologies Co., Ltd (Beijing, China). Bulk RNA-seq of liver tissues from two AAV6-αSMA-shThbs2 mice and two controls was performed on the DNBSEQ-T7 platform at Frasergen Co., Ltd (Wuhan, Hubei, China).

first: Ning

last: Zhang

first: Hong

last: You


title: Gene expression of human macrophages differentially activated in vitro

city: Lyon

first: Benedicte

last: Chazaud

address: 8 Avenue Rockefeller

department: Institut NeuroMyoGène

country: France

institute: Université Claude Bernard Lyon 1

overall_design: Human macrophages were isolated from blood monocytes from healthy donors. After differentiation in macrophages (one week in serum containing medium), they were either i) untreated,ii) treated with IL-4, iii) treated with LPS, iv) treated with IL-10+dexamethasone as described in Saclier et al 2013 (PMID: 23169615). n=3 for each condition.

first: Bénédicte


title: Rebalancing the brain: The therapeutic potential of false neurotransmitters in excitatory-inhibitory imbalance

city: Stanford

first: Eloise

last: Berson

address: 291 Campus Drive

institute: Stanford University

summary: Excitatory-inhibitory (E-I) balance results from a complex interplay between glutamatergic and GABAergic neurons, and E-I imbalance has been proposed to contribute to many neurological diseases. We have created the first excitatory (S-2-methyglutamate or S-2MeGlu) and inhibitory (R-4-aminopentanoate or R-4APA) false neurotransmitters, and using single nucleus RNA sequencing, we have tested their transcriptomic impact in wild-type mice following chronic exposure to the lowest dose

overall_design: To obtain unbiased insight into cell type-specific impact of the false neurotransmitters, we performed snRNA-seq using wild type murine frontal cerebral cortex following chronic low-dose exposure to S-2MeGlu (n=3), R-4APA (n=3), or vehicle (n=2). We selected chronic exposure to the lowest dosing regimen that showed a significant behavior change (10 mg/kg/d IP for eight weeks) and focused on WT mice to avoid potential confounding by coincident effects of toxin exposure or genetic engineering.

first: Amalia

last: Perna


title: PI3K signaling is essential for leukemic transformation of Tet2 mutated pre-leukemic hematopoietic stem cells

city: Indianapolis

first: Reuben

last: Kapur

state: IN

address: 1044 W Walnut St

institute: Indiana University

summary: Inhibition of PI3K rescues Tet2 loss driven leukemia. The signaling pathways by which Tet2 mutations contribute to myeloid transformation are poorly understood. We investigated that loss of Tet2 in HSC/Ps results in myeloproliferation, which is associated with hyperactivation of the PI3Kinase pathway.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for  Tet2 deletion and PI3K-deletion in sorted hematopoietic stem cells (LSKs) from Tet2 knockout or p85alpha knockout or Tet2;P85alpha double knockout mice

first: Palam

last: Lakshmi reddy

first: Kapur

last: Reuben


title: CITE-seq analysis of Mycobacterium tuberculosis infected Irg1- and iNOS-deficient mouse lungs

first: Dmitri

last: Kotov

overall_design: Lungs were harvested from Irg1- and Nos2-deficient naïve mice (2 animals per genotype) or mice infected with Mycobacterium tuberculosis for 25 days  (3 animals per genotype).  Myeloid cells were magnetically enriched based on Ly6G and CD64. After enrichment, infected cells were isolated by Fluorescence-activated cell sorting (FACS)  to separate Mtb infected and bystander myeloid cells based on Wasabi expression. Naive samples where isolated by FACS into macrophages and a monocyte/neutrophil mixture, which were pooled at a 1 to 2 ratio for greater macrophage representation.

first: Ophelia

last: Lee

first: Daisy

last: Ji

first: David

last: Jaye

first: Sara

last: Suliman

first: Cem

last: Gabay

first: Russell

last: Vance


title: TL1A overexpression in Crohn’s Disease patients and mice alters Paneth cell biology and intestinal microbiota in promoting ileal inflammation

city: Los Angeles

first: Kathrin

last: Michelsen

address: 110 George Burns Rd

department: Medicine/GI

institute: Cedars-Sinai Medical Center

summary: Small intestinal Paneth cells regulate host-microbial homeostasis and defects in autophagy and host defense pathways have been associated with inflammatory bowel diseases (IBD). Genetic variants in TL1A (TNFSF15) have been associated with susceptibility to and severity of IBD. TL1A expression is increased in IBD patients, particularly in TL1A risk allele carriers. However, the effects of TL1A on the function of ileal Paneth cells and downstream effect on commensal microbiota and development of ileitis has not been investigated. Here, we demonstrate that TL1A overexpression in mice (Tl1a-tg) induces Paneth cell hyperplasia and morphological abnormalities that precedes the development of spontaneous ileitis. In Crohn’s disease (CD) patients, ileal TL1A expression was associated with abnormal Paneth cell phenotypes. Deficiency of the TL1A receptor DR3 in Paneth cells resulted in Paneth cell abnormalities suggesting a direct effect of TL1A on Paneth cells which we confirmed in human CD patient-derived Paneth cell enriched organoid cultures. Commensal microbiota were required for TL1A-mediated Paneth cell dysfunction, and development of spontaneous ileitis. Overexpression of TL1A results in dysbiosis with an enrichment in short chain fatty acid-producing bacteria Bifidobacterium and Allobaculum and metabolomic analysis revealed an increase of the metabolite acetate. Acetate supplementation in germ-free or SPF housed mice caused ileal inflammation and elevated IFN-g secretion, suggesting that acetate is sufficient to cause ileitis. Our findings provide a mechanistic link between overexpression of TL1A in CD patients with TNFSF15 risk variants, Paneth cell dysfunction, intestinal dysbiosis and enrichment of acetate-producing bacteria that promote ileal inflammation.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for small intestinal crypts isolated from wild-type or Tl1a-transgenic mice

first: Yuefang

last: Ye

first: Yosuke

last: Shimodaira


title: Overlapping and Distinct Transcriptional Functions of an Extended Repertoire of KRAS Mutations

city: Milwaukee

first: Michael

middle: T

last: Zimmermann

state: WI

address: 8701 Watertown Plank Road

department: Mellowes Center

institute: Medical College of Wisconsin

summary: The challenge of interpreting novel genetic variations in genomics is widespread. Previous studies have shown the role of KRAS mutations in heritable and somatic conditions, but more genetic variants have been observed than have been characterized. This study compares a broad genomic landscape of 25 KRAS mutations at three cellular checkpoint levels: ERK and AKT signaling, early cell-intrinsic transcriptional regulation, and secretory inflammatory responses. The results show heterogeneity in KRAS biology, with distinct mutations inducing significantly different levels of phosphorylated ERK, transcriptional profiles, and cytokine protein profiles. This heterogeneity may underlie variation in inter-individual disease patterns and contribute to differences in disease initiation or progression. Transcriptional profiles implicate different extents of feedback from upstream receptor kinases through diverse downstream nuclear targets and immunomodulatory programs. Integrated analysis reveals heterogeneity and potentially actionable outcomes for distinct groups of KRAS mutations in human cells.

overall_design: KRAS variant alleles were genomically integrated into the isogenic, doxycycle inducible Flp-In T-REx HEK 293 cells.  25 different Kras variants and WT inducible Kras cells were established.  The transcriptional changes in HEK293 were then assessed after 24hr treatment with doxycycline and confirmation of KRAS expression.  As a control, all cells were left untreated (no doxycycline) as a comparison for the expression levels and all transcription assessment was compelted on at least biological duplicate samples.

first: Angela

last: Mathison

first: Gwen

last: Lomberk

first: Raul

last: Urrutia


title: Reduced expression of Semaphorin3A derived from osteoclasts cause lymphatic expansion in GSD mouse model

city: Xinxiang

first: dongfang

last: Zhang

state: Henan

address: 46 East Jianshe Rd

institute: Henan Normal University

summary: Gorham-Stout disease (GSD) is a sporadic chronic disease characterized by progressive bone dissolution, absorption, disappearance, and lymphatic vessel infiltration in bone marrow cavities. Although the osteolytic mechanism of GSD has been widely studied, the cause of lymphatic hyperplasia of GSD is rarely touched. In this study, Through comparing RNA expression profile in Osteoclast (OC) with Osteoclast precursors (OCP) by RNA sequencing, we identified a new factor, Semaphorin 3A (Sema3A), as an osteoprotective factor, which is involved in the lymphatic expansion of GSD. Compared to OCP, OC enhanced the growth, migration, and tube formation of lymphatic endothelial cells (LECs), in which the expression of Sema3A is low compared to OCP. In the presence of recombinant Sema3A, the growth, migration, and tube formation of LECs were inhibited, further comfirmed the effect of Sema3A on LECs. Using LEC-induced GSD mouse model, the effect of Sema3A was examined by injecting lentiviral expressing Sema3A into the tibiae. We found that the overexpression of Sema3A in tibiea suppressed the expansion of LECs and alleviated the bone loss, whereas the injection with lentiviral expressing Sema3A shRNA into the tibiae caused GSD-like phenotypes. Histological staining further demonstratsed the Osteoclasts decreased and osteocalcin were increased after the Seme3A treatment with lentiviral of Sema3A compared with the control. Combined with the role of Seme3A on osteoprotection, we propose that reduced Sema3A in OCs is one of pathogenesis of GSD and expressing Sema3A represents a new approach for treatment of GSD.

overall_design: For culturing osteoclasts (OCs) and osteoclast precursors (OCPs), bone marrow cells were flushed and collected from the femora and tibiae of 8 weeks-old WT C57BL/6 mice (purchased from Henan Skbex Biotechnology, China). The collected bone marrow cells were lysed with lysis buffer (Solarbio, China) and cultured in modified eagle medium containing 10% FBS, 100 U /ml penicillin, 100 µg/ml streptomycin sulfate, and 20 ng/ml macrophage colony-stimulating factor (M-CSF, R&D Systems Inc.) at 1 × 104 cells per well in 96-well plates or 5 × 104 cells per well in 24-well plates. Medium which include 20 ng/ml of M-CSF and 10 ng/ml of nuclear factor-κB ligand (RANKL, R&D Systems Inc.) was changed every 2 days. Tartrate-resistant acid phosphatase (TRAP) activity were used to identify OCPs and OCs. OCPs were formed after 3 days of culture. Similarly, all cells became fully mature multinucleated OCs which were the TRAP-positive (TRAP+) cells containing ≥3 nuclei after incubation for 6 d.

first: Wensheng

last: Wang

first: Dongfang

first: Chi

last: Qin

first: Kangming

last: Cai


title: Naoxintong Capsule inhibits endothelial cell injury by regu-lating the generation and function of circulating exosomes

city: Guangzhou 510275

first: Weiyang

last: Fan

address: School of Life Sciences, Sun Yat-sen University, No. 135 Xingang West Road, Guangzhou

department: School of Life Sciences

institute: Sun Yat-sen University

summary: Cardiovascular disease poses a serious threat to the health of middle-aged and elderly people worldwide. It has been shown that the pre-progression of cardiovascular disease is usually ac-companied by endothelial injury, oxidative stress and inflammatory responses, so attention to the protection of injured endothelium is particularly important for the early control and treatment of vascular disease. Circulating exosomes belong to a type of extracellular vesicles with substance transport and signaling roles that act as regulatory mediators and play a great advantage in various diseases treatment. Naoxintong capsule (NXT) is a Chinese medicine with good clinical efficacy in alleviating the progression of cardiovascular diseases. However, the role of circulating exosomes in the treatment of endothelial injury by NXT remains unexplored. Here, we reported the protective effect of NXT on endothelial damage through circulating exosomes. Our results showed that cir-culating exosomes of serum from NXT-treated rats (NXT-EXO) had effects on damaged endothelial cells (ECs) by attenuating apoptosis, inhibiting inflammation and reducing oxidative stress, whereas circulating exosomes of serum from blank-treated rats (Ctl-EXO) had no significant effect. Thus, this study elucidated that circulating exosome played a key role in the efficacy of NXT in protecting against endothelial injury, which may have important implications for the functional studies of circulating exosomes and the clinical diagnosis and treatment of vascular diseases.

overall_design: In order to explore the protective effect of NXT circulating exosomes on endothelial cell injury, we treated LPS induced HUVEC and HMEC-1 cells with NXT-EXO and Ctl EXO, detected inflammation, oxidation and endothelial factor indicators, and sequenced HMEC-1 Transcriptome. QRT-PCR was used to verify the differential genes related to inflammation, autophagy, and apoptosis

first: Ziyan

last: Xu

first: Peibo

last: Li


title: N6-methyladenosine (m6A) sequencing in mouse trophoblast stem cells (mTSCs) with and without knockdown of METTL3

city: Shanghai

first: Junpeng

last: Dong

address: 145 Guangyuan Rd, Xuhui District

department: School of Medicine, Shanghai Jiao Tong University

institute: The International Peace Maternity and Child Health Hospital

type: Methylation profiling by high throughput sequencing

summary: To identify potential mRNA targets of METTL3 whose m6A levels are influenced in mouse trophoblast stem cells (mTSCs), we conducted MeRIP-seq for mRNA isolated from mTSCs with and without knockdown of METTL3.

overall_design: mTSCs transfected with control (i.e., siNC) or Mettl3 siRNA (i.e., siMETTL3) were selected for genome-genome-wide m6A-sequencing (m6A-Seq) assays, in triplicate.

first: J


title: The SWI/SNF complex subunit Smarce1 controls cardiomyocyte proliferation via Jak/Stat3 signaling [ATAC-seq]

city: Ulm

first: Deung-Dae

last: Park

address: Albert-Einstein-Allee 23

department: Internal Medicine II

country: Germany

institute: University Ulm

type: Genome binding/occupancy profiling by high throughput sequencing

summary: To define Smarce1 as an epigenetic key-regulator of pro-proliferative Jak/Stat3 signlaing that controls cell cycle activity in zebrafish embryonic hearts, we performed one time of Assay for Transposase-Accessible Chromatin (ATAC)-sequencing technology using hearts from our identified zebrafish line 'heart of stone (hos)', smarce1-mutated line at 96 hours post fertilization.

overall_design:
Wolfgang, Rottbauer
Steffen, Just

first: Alena

last: Boos


title: The SWI/SNF complex subunit Smarce1 controls cardiomyocyte proliferation via Jak/Stat3 signaling

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

overall_design: Refer to individual Series


title: The SWI/SNF complex subunit Smarce1 controls cardiomyocyte proliferation via Jak/Stat3 signaling [RNA-seq]

summary: To define Smarce1 as an key-regulator of pro-proliferative Jak/Stat3 signlaing that controls cell cycle activity in zebrafish embryonic hearts, we performed RNA-sequencing technology using hearts from our identified zebrafish line 'heart of stone (hos)', smarce1-mutated line, at 96 hours post fertilization.

first: Tillman

last: Dahme


title: mRNA sequencing in mouse trophoblast stem cells (mTSCs) with and without knockdown of METTL3

summary: To determine  the expression of mRNAs after knockdown of METTL3, we performed RNA-Seq in mTSCs with or without knockdown of METTL3.

overall_design: mTSCs transfected with control (i.e., siNC) or Mettl3 siRNA (i.e., siMETTL3) under stem conditions were harvested at 48 h post transfection. The knockdown efficiency was confirmed by qRT-PCR and western blot. mTSCs transfected with control (i.e., siNC) or Mettl3 siRNA (i.e., siMETTL3) were selected for RNA-Seq, in triplicate. Then, RNA extraction was performed using  the mirVana miRNA Isolation Kit (Ambion). And The library preparation was constructed by TruSeq Stranded mRNA LTSample Prep Kit (Illumina).Final libraries were quantified by Agilent 2100 Bioanalyzer then deeply sequenced on the Illumina HiSeq 2500 platform.


title: In vitro expression data from Prdm16 overexpression in Blood Outgrowth Endothelial Cells (BOECs)

city: LEUVEN

first: Aernout

last: Luttun

state: België

address: Herestraat 49 box 911

department: Cardiovascular Sciences; Centre for Molecular and Vascular Biology

country: Belgium

institute: KU Leuven

summary: Previous work of the host lab identified Prdm16 as an arterial-enriched transcription factor (Aranguren et al., Blood 2013). To expand our knowledge on the genes regulated by Prdm16, we performed an Affymetrix microarray on total RNA of BOECs. These BOECs were transduced with Prdm16-overexpressing or Cherry-control lentiviral particles. Three replicate samples were subjected to microarray processing and Prdm16 samples were compared with Cherry control samples for further analysis.

overall_design: BOECs were transduced with Prdm16-overexpressing or Cherry-control lentivirus. Six days after transduction, total BOEC RNA from 6 different samples (3 Cherry samples + 3 Prdm16 samples) was isolated and subjected to microarray processing.

first: Manu

last: Beerens

first: Sander

last: Craps


title: Expression data from budding yeast sec12-4 and sec12-4 ino2Δino4Δ mutant cells

city: Kagamiyama, Higashi-Hiroshima

first: MUNEYOSHI

last: KANAI

institute: National Research Institute of Brewing

summary:
Sec12 is a guanine nucleotide exchange factor (GEF) required for the initiation of COPII vesicle formation in ER to Golgi transport.  The sec12-4 mutant cells show temperature sensitivity in growth and a defect in ER-to-Golgi protein transport. Ino2/Ino4 are components of the heteromeric basic helix-loop-helix transcription activator that binds inositol/choline-responsive elements (ICREs) and are required for derepression of phospholipid biosynthetic genes in response to inositol depletion.
We used microarrays to compare the global gene expression profiles between sec12-4 and sec12-4 ino2Δino4Δmutant cells.

platform_organism:
Schizosaccharomyces pombe
Saccharomyces cerevisiae

overall_design: sec12-4 (FKY4415 MATa sec12-4, his3, leu2, ade2, lys2, trp1, ura3, bar1-1) and sec12-4 ino2Δ ino4Δ (FKY4418 MAT a sec12-4, his3, leu2, lys2, trp1, ura3, bar1-1, ino2Δ::HIS3, ino4Δ::LEU2) cells were grown to log phase at 25°C in YPD medium for RNA extraction and hybridization on Affymetrix microarrays. In order to obtain new insights into the role of Ino2/Ino4, transcription activator in COPII-mediated protein transport, we perfomed the genome-wide expression analysis of sec12-4 and sec12-4 ino2Δino4Δ mutant cells.

first: Mei

last: Kato

first: Atsuko

last: Ikeda

first: Yukari

last: Yabuki

first: Muneyoshi

last: Kanai

first: Kouichi

last: Funato


title: Gene expression profile of human cardiac aging

city: Nantes

first: Marja

last: Steenman

address: 8 quai Moncousu

institute: L'institut du thorax


title: Integrative single cell RNA and spatial profiling identify mechanisms of neonatal brain hemorrhage pathophysiology and repair [scRNA-seq]

status: Public on Mar 31 2026

city: Houston

first: Santiago

middle: Andres

last: Forero

state: TX

address: 6767 Bertner Ave,

department: Neurosurgery

institute: The University of Texas MD Anderson Cancer Center

summary: Here we employed fixed single cell RNA profiling coupled with spatial in situ gene expression profiling to characterize NVU signaling pathways associated with ICH in Itgb8/β8 integrin mutant mice.

overall_design: Fixed single-cell RNA profiling was performed on isolated cerebral cortices of two mutant mice and one wild-type control mouse (used twice) for three ages (P0, P5, and P10).

first: Zhihua

last: Chen

first: Ali

last: Pirani

first: Arpan

last: De

first: Zachary

last: Wise

first: Xiaofeng

last: Zheng

first: John

last: Morales

first: Joseph

middle: H

last: McCarty


title: RNA-seq expression data from parental and SLX4IP-depleted D2.OR cells

city: Cleveland

first: William

last: Schiemann

state: OH

address: 2103 Cornell Rd.

department: Case Comprehensive Cancer Center

institute: Case Western Reserve University

summary:
SLX4IP mediates Hedgehog signaling through isoform-specific SUMOylation of GLI1
We sought to assess genome-wide transcriptomic and signaling changes induced by loss of SLX4IP in D2.OR breast cancer cells, which identified the Hedgehog pathways as being significantly disrupted by SLX4IP depletion

overall_design: We propagated D2.OR cells harboring either non-targeting or SLX4IP-targeting shRNAs in 3D-culture for 7 days (n=3 per genotype), at which point total RNA was isolated and subjected to RNA sequencing using the Illumina HiSeq 2500 system

middle: P

first: Nathaniel

last: Robinson


title: The differentially expressed circular RNA (circRNA) in Collagen-induced arthritis rats compared with normal rats.

city: Changsha

first: Yuqi

last: Wen

address: Xiangya Road

institute: Xiangya Hospital Central South University

summary: To determine te circular expression profile in collagen-induced arthritis (CIA) rats and normal rats, we uesed Arraystar Rat circRNA Array to examine the expression of circRNAs in CIA and normal rats' synovial tissues.

overall_design: Synovial tissues from rats were distributed into two experimental groups: CIA group and normal group, then perform circRNAs chips by Arraystar Rats circRNAs Array (8x15K, Arraystar).

first: Xingui

last: Xiong


title: Aging of the human left atrium

summary: Transcriptional profiling of left atrium samples from human donors with ages varying from 2 months to 65 years

overall_design: 73 human left atrium samples, 1 microarray per sample, two-color microarray


title: Single cell multiomic landscape reveals gene programs driving lipid droplet heterogeneity in hepatic steatosis

city: Rochester

first: Vijay

last: Shah

state: MN

address: 200 First Street SW, Guggenheim Building 10th Floor

institute: Mayo Clinic

summary: Alcohol-associated liver disease (ALD) in its earliest form is evidenced as hepatic steatosis which may progress to liver cirrhosis. Using single-cell multiomics technology, we studied transcriptional mechanisms across the hepatic lobule that could account for liver zonation of lipid droplets in a murine ALD model. Furthermore, chromatin landscape studies demonstrated zonation of regulatory elements and master transcription factors associated with these changes in the transcriptome.

overall_design: Isolated primary cells from mice livers that underwent an 8 week-alcohol or pair-feeding model replicating alcohol-associated liver disease. These were subjected to Single Cell RNA sequencing and Single Nuclear ATAC sequencing.

first: Tejasav

last: Sehrawat

first: Shawna

last: Cooper

first: Sheng

last: Cao


title: Genome-wide DNA methylation profiling in patient-derived airway basal cells and differentiated 3D bronchial organoids

city: Homburg

first: Felix

last: Ritzmann

address: Kirrberger Street

institute: Saarland University

type: Methylation profiling by genome tiling array

summary: Genome-wide DNA methylation profiling was performed in patient-derived airway basal cells and differentiated 3D bronchial organoids to assess smoking- and COPD-associated epigenetic changes.

overall_design: Airway basal cells and matched differentiated 3D bronchial organoids derived from patient samples were subjected to genome-wide DNA methylation analysis.

first: Christoph

last: Beisswenger

first: Gilles

last: Gasparoni


title: RNA-seq profiling of P2 rat neonatal atrial myocytes transfected with non-targetting (control) and Pitx2c (KD) siRNA.

city: Saskatoon

first: Michelle

last: Collins

address: 107 Wiggins Rd

department: Anatomy, Physiology and Pharmacology

country: Canada

institute: University of Saskatchewan

summary: Genome wide association studies have identified numerous cardiac transcription factors in association with atrial fibrillation. Amongst these transcription factors, the paired-like homeodomain transcription factor 2 (PITX2) is the strongest genetic risk variant associated with atrial fibrillation. However, the downstream mechanisms of PITX2 are not completely understood. Here, we explore the role of PITX2 in oxidative metabolism and stress as a unifying mechanism of arrhythmogenesis. To identify PITX2 mechanisms, we performed transcriptomic analysis to identify gene expression changes in Pitx2c-deficient neonatal rat atrial myocytes. We identify oxidative phosphorylation as the top dysregulated pathway and direct transcriptional targets lie in mitochondrial electron transport chain complexes I and IV. Using the Seahorse Extracellular Flux Analyzer, we identified a functional decrease in oxidative metabolism in Pitx2c-deficient cardiomyocytes. As electron transport chain complexes I and IV may generate reactive oxygen species (ROS) under mitochondrial dysfunction, we quantified mitochondrial specific ROS using MitoSOX and observed an increase in mitochondrial specific ROS in Pitx2c-deficient cardiomyocytes. We additionally assessed spontaneous cardiomyocyte calcium cycling using Fluo-8AM and observed an increased frequency of pro-arrhythmogenic mechanisms including early and delayed afterdepolarizations as inferred through calcium traces. Further, we identified sarcomere disassembly including a potential role of PITX2 in regulating Titin, where Pitx2c-deficient cardiomyocytes display Titin mis-localization within the sarcomeres. To assess whether ROS drives these phenotypes, we treated neonatal rat atrial myocytes with N-acetylcysteine, a potent ROS scavenger, and observed decreased early and delayed afterdepolarizations, as well as restoration of Titin localization.

first: Andy

last: Kim

first: Sébastien

last: Gauvrit

first: Frederick

last: Vizeacoumar


title: Uncovering the Heterogeneity and Ontogeny of Mouse Thymic Macrophages Reveals an Unexpected Early Checkpoint Role

city: Toronto

first: Juan Carlos

last: Zuniga-Pflucker

state: Ontario

address: 2075 Bayview Avenue

department: Immunology

institute: University of Toronto

summary: Thymic macrophages (TMs) are critical for maintaining thymus homeostasis, yet their heterogeneity and specific functions in T cell development remain unclear. Through single-cell RNA sequencing and transgenic reporter mice, we revealed two novel TM subsets characterized by distinct surface markers and transcriptional programs. TIMD4⁺ VCAM1⁺ CX3CR1⁻ TMs were enriched for phagocytic and apoptotic-cell–clearance pathways, whereas TIMD4⁻ VCAM1⁺ CX3CR1⁺ TMs exhibited elevated expression of antigen-presentation machinery and interferon‑response genes. Pseudotime trajectory analysis indicated a potential lineage progression from TIMD4⁻ VCAM1⁺ CX3CR1⁺ precursors toward TIMD4⁺ VCAM1⁺ CX3CR1⁻ effectors. Functional interrogation using fetal thymic organ cultures and the MaFIA depletion mouse model demonstrated that acute loss of TMs severely impaired thymocyte development, particularly at the pre‑T cell receptor (TCR) β‑selection checkpoint. TM ablation led to marked reductions in post--selection thymocyte subsets, implicating TMs in both survival and differentiation signals required for early T cell development. Mechanistically, TM depletion disrupted pre‑TCR signaling and hindered transition through β‑selection, likely due to absence of both apoptotic-cell clearance and differentiation cues provided by specialized TM subsets. These findings define two functionally distinct TM populations and establish their role in orchestrating thymocyte maturation. By elucidating TM subset specialization and their dynamic contributions to the β‑selection process, our findings advance our understanding of thymic microenvironment interactions and highlights macrophage heterogeneity as a key regulator of T cell development.

overall_design: CD64+ cells were isolated from the thymus of C57BL/6J adult mice and processed for scRNA-seq

first: Helen

last: Wang

first: Vinothkumar

last: Rajan

first: Anthony

last: Wong

first: Slava

last: Epelman

last: Zúñiga-Pflücker


title: Aging of the human left ventricle

first: Marja

last: Steenman

summary: Transcriptional profiling of left ventricle samples from human donors with ages varying from 2 months to 65 years

overall_design: 57 human left ventricle samples, 1 microarray per sample, two-color microarray


title: Comparative single-cell multiomic analysis reveals evolutionarily conserved and species-specific cellular mechanisms mediating natural retinal aging

city: Baltimore

first: Pin

last: Lyu

address: 400 N Broadway

institute: JHU

sample_organism:
Danio rerio
Mus musculus

platform_organism:
Danio rerio
Mus musculus


title: Single-cell transcriptomics reveals the long-term high-fat diet impairs male reproduction by disrupting spermatogenesis in pubertal mice

city: Qingda

first: yadan

last: Jin

state: 山东Shandong

address: Qingdao

institute: Qingdao Agricultural University

summary: High-fat diet is an important cause of male reproductive dysfunction, but the specific mechanism of its regulation of the molecular expression pattern and cell interaction network of testicular cells is still unclear. This study used a mouse model with high-fat diet as the research subject, and scRNA-seq to systematically analyze the transcriptional dynamic changes of cells in mouse testicular tissue. The results showed that a high-fat diet significantly increased the body weight of mice, induced disordered arrangement and enlarged intercellular spaces of spermatogenic cells in the testes. It also leads to a decreased testicular index and a significant reduction in the number of spermatogenic cells. In addition, the high-fat diet significantly improved the mRNA levels of Espn and Lsm10 genes in testicular tissue, and the apoptosis pathway in testicular tissue was significantly enriched, with weakened intercellular interaction intensity. This study provided experimental evidence for analyzing the molecular mechanism of male reproductive damage mediated by high-fat diet and related intervention strategies.

overall_design: This study utilized five-week-old healthy male C57 BL/6 mice weighing 15-20 g (total n = 20). The mice were fed with standard maintenance feed (SPF-F02-001, SPF, Beijing). During the first week before the experiment, allow them to adapt to the new environment. Keep the animals separately in rooms with controlled temperature and humidity (25 ± 2 ℃ and 55 ± 10 % respectively). After 1 week of adaptive feeding, the mice were randomly divided into a normal diet group (ND, n=10) and a high-fat diet group (HFD, n=10). Mice in the ND group were continuously fed a maintenance feed for 12 weeks, while those in the HFD group received a diet 60 % kcal fat (D12492, Xiaoshuyoutai, Beijing) for 12 weeks.


title: Expression profiling of mouse hippocampus from Apex1 conditional knockout and caloric restriction models across aging

city: Pittsburgh

first: Yejie

last: Shi

state: PA

address: S-510 Biomedical Science Tower, 3500 Terrace Street

department: Neurology

institute: University of Pittsburgh

summary:
Accumulation of oxidative DNA damage is a key contributor to brain aging and cognitive decline. The DNA repair enzyme apurinic/apyrimidinic endonuclease-1 (Apex1) plays a central role in base-excision repair, but its contribution to transcriptional programs associated with brain aging remains incompletely understood. In this study, we performed genome-wide expression profiling of mouse hippocampus to examine the effects of forebrain-specific Apex1 deletion and caloric restriction on age-associated transcriptional changes.
Hippocampal tissues were collected from male mice at young (8-12 weeks) and aged (48 weeks) time points across six experimental groups: young wild-type ad libitum (WT AL), young Apex1 conditional knockout ad libitum (cKO AL), aged WT AL, aged cKO AL, aged WT caloric restriction (WT CR), and aged cKO CR. Apex1 conditional knockout mice carried the genotype Camk2a-Cre+/−;Apex1^flox/flox, while hemizygous CaMKIIα-Cre+/− littermates served as age-matched controls. Microarray analyses were performed to identify transcriptional changes associated with Apex1 deficiency, aging, and dietary intervention. The dataset provides a resource for investigating molecular pathways related to genomic maintenance, metabolism, and neuronal function during brain aging.

overall_design:
Genome-wide transcriptional profiling of mouse hippocampal tissue was performed using Affymetrix Clariom S mouse arrays. Six experimental groups were included: young WT AL, young Apex1 cKO AL, aged WT AL, aged Apex1 cKO AL, aged WT CR, and aged Apex1 cKO CR. Hippocampal tissue from one hemisphere (left or right) of each mouse was collected for RNA extraction. Four biological replicates were generated for each group, yielding a total of 24 samples.
All samples were processed in a single experimental batch. In the associated manuscript, transcriptomic analyses focused on the four aged groups (aged WT AL, aged cKO AL, aged WT CR, aged cKO CR). During downstream statistical analysis, one sample from the aged Apex1 cKO AL group (JC-51) was identified as an outlier and excluded from differential expression analyses; however, the raw microarray data for this sample are included in the deposited dataset.

first: Jun

last: Chen


title: scRNA-seq for LuCaP35CR tumors treated by ENZ, EPZ6438 and combination of ENZ and EPZ.

city: Sacramento

first: Yatian

last: Yang

institute: UC Davis

summary: Tumor tissues were dissociated into single-cell suspensions and processed using the 10x Genomics Chromium platform. The resulting data were analyzed to characterize tumor cell populations and transcriptional programs associated with treatment response and lineage plasticity. This dataset provides single-cell transcriptomic profiles of PDX tumors and serves as a resource for studying tumor heterogeneity and therapy-associated transcriptional changes.


title: Differential methylation of promoters as a tool for histotype stratification in epithelial ovarian cancer

city: Göteborg

first: Hugo

last: Swenson

state: Västra Götaland

address: Medicinaregatan 1G, 6th floor

department: Institute of clinical sciences

country: Sweden

institute: University of Gothenburg

summary: Epithelial ovarian cancer (EOC) is a heterogenous disease with frequent late-stage diagnosis and high mortality rates, for which no reliable screening tests exist. In recent years epigenetic biomarkers in the form of DNA methylation in CpG-rich regions have gained increased attention in the scientific community due to their robust nature and accessibility, allowing for diagnosis without the need for invasive surgery. In this study, we investigated the aberrant methylation of promoter regions in early stage EOC through a novel methodology, with the purpose of finding potential epigenetic biomarkers

overall_design: 86 solid tissue samples from primarive invasive tumors originating from patients diagnosed with early-stage epithelial ovarian cancer were subjected to the Infinium MethylationEPIC BeadChip assay

first: Hanna

last: Engqvist

first: Khalil

last: Helou


title: SIRT7 links H3K36ac epigenetic regulation with genome maintenance in the aging mouse testis [ATAC-Seq]

city: Badalona

first: Irene

last: Fernández Duran

state: State...

address: Josep Carreras Building, Ctra de Can Ruti, Camí de les Escoles, s/n,

country: Spain

institute: Josep Carreras Leukaemia Research Institute

summary: Reproductive aging is an increasing health concern affecting family planning and overall well-being. While extensively studied in females, the mechanisms driving male reproductive aging remain largely unexamined.  Here we found that mammalian Sirtuin 7 (SIRT7) sustains spermatogenesis in an age-dependent manner through the control of histone 3 lysine 36 acetylation (H3K36ac). SIRT7 deficiency in mice resulted in increased levels of H3K36ac in spermatogonia and spermatocytes, a pattern also observed during natural testicular aging.  SIRT7 deficiency altered chromatin accessibility, which was directly linked to H3K36ac activity in a germ cell line, and increased vulnerability to genotoxic stress. Importantly, undifferentiated spermatogonia, which are required for continuous sperm production, decreased prematurely in Sirt7-/- mice and showed enhanced genome damage accumulation during aging or under acute environmental stress. These changes were concurrent with age-dependent defects in double strand break (DBS) repair and partial meiotic arrest. Taken together, our results indicate that SIRT7 connects H3K36ac epigenetic regulation to long-term genome stability in male germ cells, ensuring steady-state spermatogenesis during the lengthy male reproductive lifespan.

overall_design: 50,000 spermatogonia from Pnd 5 mouse testes where isolated and subjected to ATAC-Seq

first: A

last: Guitart-Solanes

first: M

last: Romero

first: I

last: Fernandez-Duran

last: Gamez-Garcia

first: B

last: Niedenberger

first: C

last: Madrid-Sandín

first: N

last: Spears

last: Roig

last: Geyer

last: Vaquero

first: K

last: Schindler

middle: N

last: Vazquez


title: Single cell transcriptomics reveals dendritic cell subsets in bovine afferent lymph and immune cell-resolved responses to BCG vaccination

city: Edinburgh

first: Rachrapee

last: Sukmak

state: Midlothian

address: The University of Edinburgh, Easter Bush Campus

institute: The Roslin Institute

summary: Bovine tuberculosis (bTB), caused by Mycobacterium bovis (M. bovis), remains an ongoing global issue for human and animal health. The Bacille Calmette Guerin (BCG) vaccine offers immunity against bTB, however, the mechanisms underlying the heterogenous protective response, including variations across species and age groups requires further investigation. In this study, we focused on dendritic cells (DCs), which are crucial for adaptive immune stimulation following BCG vaccination. By capturing afferent lymph DCs (ALDCs) migrating from the skin, we investigated shifts in DC profiles and potential subset-specific functions in response to BCG vaccination. Single-cell RNA sequencing (scRNA-seq) was performed on samples from n=3 Bos taurus calves before and after BCG vaccination, capturing the transcriptome of 20,761 individual cells expressing on average 3,036 unique genes, which were clustered into ALDCs, monocytes, T-cells, B-cells and NK cells. The ALDC subsets were further identified as cDC1 and cDC2. In homeostasis, ALDCs expressing potential subset-specific genes for cDC1, including ENSBTAG00000056208 (LINE-1), STX4, NEBL, ADAM23, ART3, and cDC2; FN1, PSPH, FGL2, SHOX2, and WWTR1 were identified. Following BCG vaccination, while both subsets exhibited gene expression signatures indicative of antigen-presenting function, migration, and DC maturation, cDC1 showed upregulation of genes consistent with metabolic alterations and lymphocyte recruitment, whereas cDC2 upregulated genes consistent with inflammatory responses. Overall, this study comprehensively describes the transcriptomic landscape of bovine ALDC subsets, providing evidence for the importance of subset-specific genes to BCG vaccination responses, while advancing knowledge on how ALDCs contribute to protective immunity against bTB.

overall_design: Three calves (n=3) (two male Holstein-Friesian [calves 1 and 2], and one male Norwegian Red [calf 3]), aged 3-6 months and sourced from TB-free farms (Langhill Farm, Roslin, Midlothian, UK), underwent surgery for the cannulation of a pseudo-afferent superficial cervical lymph vessel. Prior to BCG vaccination (‘pre-BCG’), samples were collected at 6-7 days post-cannulation (DPC). The BCG strain Danish (SSI, Denmark) was administered via the subcutaneous route (approximately 1 x 106 bacteria, equivalent to 5x human dose) followed by sample collection at 24 hours after BCG vaccination (‘post-BCG’). All cryopreserved sapmples were sorted and used in scRNA-seq library generation via 10X Genomics Chromium platform.

first: Heather

last: Mathie

first: Richard

last: Taylor

first: Jianxuan

last: Sun

first: Barbara

last: Shih

first: Charlotte

last: Bell

first: Mark

last: Gray

first: Daniel

last: Macqueen

first: Jayne

middle: C

last: Hope


title: SIRT7 links H3K36ac epigenetic regulation with genome maintenance in the aging mouse testis

first: Irene

last: Fernández Duran

overall_design: 50,000 spermatogonia from Pnd 5 mouse testes where isolated and subjected to anti-H3K36ac ChIP-Seq

last: Guitart-Solanes

last: Romero

last: Fernandez-Duran

last: Gamez-Garcia

last: Niedenberger


title: Ascertaining the effect of switching deregulated Myc OFF in KRasG12D/MycER-driven mouse lung tumors

city: London

first: Roderik

last: Kortlever

address: 1 Midland Road

institute: The Francis Crick Institute

summary: The mechanisms by which inhibition of an oncogenic driver induces tumour regression and tissue resolution is unclear. In an autochthonous mouse model of lung adenocarcinoma driven by oncogenic Kras and deregulated Myc cooperation, we initiated acute loss of Myc exclusively in the tumour epithelial cells to identify the sequence of events and crosstalk in a tumour and its attendent microenvironement in the first 24 hours of tumour regression.

overall_design:
Lung cancer growth was induced in Lsl-KrasG12D;LSL-Rosa26MIE/MIE mice by adenoviral Cre recombinase infection. 12 weeks post AdV-CRE infection mice were treated with Tamoxifen (food) for 4 weeks, followed by 2, 4, 8, 12 or 24  hours OFF Tamoxifen treatment (return to regular food). The mice express a Tamoxifen-regulatable Myc (mycER) exclusively in the tumour cells. Mice from 6 groups were isolated:
1. Myc ON: treated for 4 weeks with Tamoxifen – Kras AND Myc lung tumours
2. Myc OFF 2hrs: treated for 4 weeks with Tamoxifen, then OFF tamoxifen for 2 hours - Kras AND Myc lung tumours, then 2 hrs OFF Myc activity
3. Myc OFF 4hrs: treated for 4 weeks with Tamoxifen, then OFF tamoxifen for 4 hours - Kras AND Myc lung tumours, then 4 hrs OFF Myc activity
4. Myc OFF 8hrs: treated for 4 weeks with Tamoxifen, then OFF tamoxifen for 8 hours - Kras AND Myc lung tumours, then 8 hrs OFF Myc activity
5. Myc OFF 12hrs: treated for 4 weeks with Tamoxifen, then OFF tamoxifen for 12 hours - Kras AND Myc lung tumours, then 12 hrs OFF Myc activity
6. Myc OFF 24hrs: treated for 4 weeks with Tamoxifen, then OFF tamoxifen for 24 hours - Kras AND Myc lung tumours, then 24 hrs OFF Myc activity
For singe cell RNA-seq the mouse lung samples were  isolated on the same day in 4 different experiments (CRE68, 75, 82, 98). Whole lungs were isolated, which means both tumour and non-tumour lung tissue. Tumour burden per lung sample on average ~30%.

first: Gerard

middle: I

last: Evan


title: Ascertaining the effect of switching deregulated Myc ON in KRasG12D-driven mouse lung tumours

summary: The mechanisms by which Myc transcriptionally induces tumour progression is unclear. In an autochthonous mouse model of lung adenocarcinoma driven by oncogenic Kras and deregulated Myc cooperation, we initiated acute activation of Myc exclusively in the tumour epithelial cells to identify the sequence of events and crosstalk in a tumour and its attendent microenvironement in the first week of tumour progression, with a focus on the first 24 hours.

overall_design:
Lung cancer growth was induced in Lsl-KrasG12D;LSL-Rosa26MIE/MIE mice by adenoviral Cre recombinase infection. 12 weeks post AdV-CRE infection mice were treated with Tamoxifen (IP) for 8 or 24 hours, or 7 days. The mice express a Tamoxifen-regulatable Myc (mycER) exclusively in the tumour cells. Mice from 4 groups were isolated:
1. Kras Only: no Tamoxifen for 12 weeks after AdvCRE infection
2. Myc ON 8hrs: treated for 8 hours with Tamoxifen,- Kras AND Myc lung tumours
3. Myc ON 24hrs: treated for 24 hours with Tamoxifen,- Kras AND Myc lung tumours
4. Myc ON 7 days: treated for 7 days with Tamoxifen,- Kras AND Myc lung tumours
For singe cell RNA-seq the mouse lung samples were  isolated on the same day in 4 different experiments (CRE78, 79). Whole lungs were isolated, which means both tumour and non-tumour lung tissue. Tumour burden per lung sample on average ~30%.


title: The orally available SIK2/SIK3 inhibitor SK-124 increases bone mass in hypogonadal male mice

city: Boston

first: Roy Byung-Jun

last: Choi

state: MA

address: 50 blossom st

department: Endocrine Unit

institute: MGH

summary: We previously described the synthesis and characterization of SK-124, a pharmacologic SIK2/SIK3 inhibitor that increases trabecular bone formation in eugonadal mice. However, the efficacy of this agent in osteoporosis mouse models remains unknown. In this study, we investigated the therapeutic potential of SK-124 in a male hypogonadal bone loss model (orchiectomy, ORX) in BALB/c male mice.Bone RNA-sequencing analysis demonstrated novel pathways associated with increased bone formation in response to SK-124 treatment.

overall_design: RNA sequencing of marrow flushed in vivo bone of BALB/cJ sham or ORX(orchiectomy) operated vehicle and SK-124 treatd groups. We compared Sham VEH vs ORX Veh and ORX VEH vs ORX SK-124

first: Roy

first: Marc

last: Wein


title: CUT&RUN analysis to investigate the role of FOXF1/2 in senescent cells.

city: Kumamoto

first: Mitsuyoshi

last: Nakao

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

department: Institute of Molecular Embryology and Genetics

institute: Kumamoto University

summary: CUT&RUN analysis revealed the distribution of FOXF1, p-c-JUN, H3K27Ac in senescent cells.

overall_design: Examination of the distribution of FOXF1, p-c-JUN, H3K27Ac in proliferative (Pro) cells, oncogene-induced senescent (SnCs) cells, and FOXF1/2-knockdowned Sen IMR-90 cells.

first: Kan

last: Etoh


title: A tissue-intrinsic mechanism sensitizes HIV-1 particles for TLR-triggered innate immune responses

city: Heidelberg

first: Oliver

middle: Till

last: Fackler

address: Im Neuenheimer Feld 344

department: CIID

institute: Universityhospital Heidelberg

summary: In vivo, HIV-1 replicates within tissues, yet the impact of three-dimensional (3D) environments on viral spread remains poorly understood. We previously showed that collagen-rich 3D extracellular matrix (ECM) imposes an Environmental Restriction to cell-free Virus Infectivity (ERVI). Here, we demonstrate that ERVI is mediated by adhesive ECM components assembled into tissue-like scaffolds. Transient interactions with collagen fibers rapidly diminish virion infectivity across diverse primary strains by impairing virus fusogenicity. Notably, collagen-experienced particles also induce a distinct antiviral transcriptional program and strong pro-inflammatory cytokine secretion in monocyte-derived macrophages. Mechanistically, collagen contact induces conformational changes in the viral glycoprotein Env, enhances its interaction with toll-like receptor 2 (TLR2), and promotes trafficking into TLR8-positive endosomes, thereby amplifying innate immune sensing. Thus, ERVI acts through a dual mechanism: reducing virion fusogenicity while increasing innate immune detection. These findings identify the biophysical properties of the ECM as a tissue-intrinsic arm of antiviral innate immunity.

overall_design: RNAseq profiling of human monocyte derived macrophages (MDMs) from 3 healthy donors after challenge with HIV-1 virions derived from suspension or collagen cultures, for 6 or 24h. Mock and LPS treated MDMs were harvested at t=24h.

first: Samy

last: Sid Ahmed


title: Single cell landscape of MBL/CLL transition [MBL_CLL_GEO_DataSet2]

city: Berlin

first: Livius

last: Penter

address: Augustenburger Platz

institute: Charité - Universitätsmedizin Berlin

summary: The transition of monoclonal B cell lymphocytosis (MBL) to chronic lymphocytic leukemia (CLL) remains ill-defined at the epigenetic and transcriptional level. Here, we performed single cell RNA and ATAC sequencing of low-count (LC) and high-count (HC) MBL and CLL blood samples to track the continuum from physiologic B cells to CLL.

overall_design: Single cell RNA and ATAC sequencing was performed on single cell suspensions after ficoll density centrifugation using 5' RNA and v2 ATAC chemistry (10x Genomics). Total-seq A staining was performed to capture surface marker expression in select cases. BCR sequencing was performed using the V(D)J kit.

first: Catherine

last: Wu


title: Therapeutic targeting of eIF4E cap-binding domain reveals control of lineage fate in prostate cancer [CUT&Run]

city: Seattle

first: Sonali

last: Arora

state: WA

address: 1100 Fairview Ave N,

institute: FHCRC

summary: We demonstrate mRNA translation controls basal to luminal lineage plasticity of prostate epithelium through eIF4E cap-binding domain. Mechanistically, this plasticity is driven by translational repression of basal keratins via cis-regulatory elements in the 5' untranslated regions (UTRs) of their transcripts, alongside promoting androgen receptor (AR) protein stability through the translational upregulation of deubiquitinases BAP1 and OTUD3. This lineage switch is essential for cell survival and represents a druggable vulnerability. In castration-resistant prostate cancer (CRPC), high eIF4E expression is associated with basal phenotype, reduced luminal differentiation and accelerated resistance to AR pathway inhibitors (ARPIs). Notably, tumors resistant to enzalutamide regain sensitivity upon inhibition of the eIF4E cap-binding domain, which reprograms them toward a luminal state. These discoveries uncover a novel oncogenic role of the eIF4E cap-binding domain in lineage plasticity and therapy resistance and suggest that inhibition of this domain offers a promising strategy to overcome treatment resistance in prostate cancer.

overall_design: Cut & Run data  of DMSO, PF, and R1881 samples using AR antibody

first: Rashmi

last: Mishra

first: Andrew

last: Hsieh


title: ATAC-seq analysis to investigate the role of FOXF1/2 in senescent cells.

summary: ATAC-seq analysis revealed that the FOXF1/2 depletion decreased chromatin accessibility at enhancers of pro-inflammatory SASP genes

overall_design: Examination of chromatin accessibility in control, p300/CBP-knockdowned, and FOXF1/2-knockdowned oncogene-induced senescent (Sen) IMR-90 cells.


title: Maternal IntS11 primes embryonic totipotency by organizing early zygotic transcription initiation

city: Kunming

first: Liangliang

last: Wang

state: Yunnan

address: South Section, East Outer Ring Road, Chenggong District

institute: Yunnan University

summary: Zygotic genome activation (ZGA) marks the first transcriptional milestone and establishes embryonic totipotency. Although pioneer factors have been reported to initiate this process, how chromatin is primed for the totipotent state, allowing the binding of pioneer factors for successful ZGA, remains unclear. Here, we identify IntS11, the catalytic subunit of the Integrator complex, as a totipotent determinant of embryonic chromatin governing ZGA in Drosophila. We show that IntS11 functions upstream of pioneer factors in early embryos: maternal IntS11 depletion substantially impairs RNA polymerase II (Pol II) recruitment, thereby preventing pioneer factors Zelda and GAGA factor (GAF) from accessing regulatory elements and initiating genome-wide zygotic transcription. Mechanistically, IntS11 exerts dual roles: its canonical endonuclease activity is required to sustain major-wave zygotic transcription, while a distinct enzyme-independent function drives de novo Pol II loading and pioneer factor engagement. These findings uncover a fundamental maternal-specific mechanism whereby IntS11 establishes transcriptional competence, ensuring totipotent chromatin states and successful ZGA.

overall_design: Refer to individual Series

first: Yiru

first: Yaqi

last: Miao

first: Yuan

last: Song

first: Jialiang

last: Zhou

first: Yuanxiang

last: Zhu

first: Ying

last: Cheng

first: Wenxin

last: Zhang

first: Qinmiao

last: Sun

first: Fan

last: Lai

first: Guoqiang

first: Dahua

last: Chen


title: Single cell landscape of MBL/CLL transition [MBL_CLL_GEO_DataSet3]

first: Livius


title: Ambient temperature regulates CD4⁺ T cell tonic T cell receptor signaling and responsiveness

city: Cincinnati

first: Senad

last: Divanovic

state: Ohio

address: 3333 Burnet Avenue

institute: Cincinnati Children's Hospital Medical Center

summary: Mice (Mus musculus) used in biomedical research are commonly housed at 19-23 °C, below their thermoneutral zone (29-34 °C), where metabolic homeostasis occurs. Although traditional housing exposes mice to chronic cold stress and modulates their immune response, cellular mechanisms by which thermoneutrality shapes immune responses remain underdefined. CD4+ T cells are major contributors to host immunity through T cell receptor (TCR) signaling activated via recognition of peptide-major histocompatibility complex class II (pMHCII). We demonstrate that thermoneutral housing, compared to traditional housing, enhances tonic TCR signaling, upregulates genes associated with endogenous TCR stimulation, and increases TCR-driven TNF expression in CD4⁺ T cells. Mechanistically, these effects are in part dependent on tonic TCR engagement with self-pMHCII. In inflammatory disease models, thermoneutrality-driven increased CD4⁺ T cell TNF production correlates with amplified tissue inflammation. Together, these findings reveal how housing temperature may shape inflammatory responses through self-pMHCII-dependent TCR signaling in CD4⁺ T cells.

overall_design: Bulk RNA-Seq on splenic CD4+ T cells from Nur77-GFP transgenic mice

first: Keisuke

last: Sawada

first: John

last: Eom

first: Bree

last: Mahoney-Sutherland

first: Traci

last: Stankiewicz

first: Jarren

last: Oates

first: Daniel

last: Giles

first: Pablo

last: Alarcon

first: Michelle

last: Damen

first: Angela

last: Cannata

first: Julie

last: Hargis

first: Jaclyn

middle: W

last: McAlees

first: Cassidy

last: Ulanowicz

first: Jennifer

last: Wayland

first: David

last: Hildeman

first: Ian

last: Lewkowich

first: Simon

last: Hogan

first: Nathan

last: Salomonis

first: Maria

last: Moreno-Fernandez


title: Type I interferons induced upon RSV infection change the lung microenvironment and impair seeding of lung metastatic breast cancer cells

first: Ilaria

last: Malanchi

address: 1 Midland Rd,

summary: Invasive breast cancer accounts for 7% of all cancer-related deaths, with the lungs being a common site of metastases. At the same time, lower respiratory tract infections are a common cause of morbidity and mortality worldwide. Acute viral respiratory infections induce transitional changes in the lung; however, the impact of these changes on metastasis initiation and cancer progression remains unclear. Using primary murine MMTV-PyMT breast cancer cells in an experimental lung metastasis model, we show that changes induced by respiratory syncytial virus (RSV) infection impair tumor cell seeding and early establishment in the lung, resulting in lower number of metastatic nodules. Consistent with that notion, intranasal administration of recombinant IFN-a recapitulates the anti-tumor effect of RSV infection. Type I IFNs change the lung cellular composition and induce an Interferon Stimulated Gene (ISG) driven response, creating an alveolar environment that is less supportive of tumor cell growth.

overall_design: Animals were treated intranasally with either IFNa or PBS 18hours prior to intravenous injection with 600k primary MMTV-PyMT cells.  24hrs after the lungs were harvested and digested with liberases to dissociate the cells.  The cells were stained and then fixed.  FACsorting was used to isolate the cancer cells (GFP), immune cells (CD45+), epithelial cells (CD326+) and mesenchymal cells (CD45-, CD31-) and then they were pooled at a ratio of 1:3:3:3 for sequencing.

first: Vicky

last: Bridgeman

first: Ana

last: Farias

first: Cecilia

last: Johansson


title: Preclinical efficacy of combination therapy with allogeneic induced pluripotent stem cell-derived invariant natural killer T and α-galactosylceramide-pulsed antigen-presenting cells

city: Chiba

first: Takahiro

last: Aoki

state: Chiba

address: 1-8-1 Inohana Chuo-ku

institute: Chiba University

summary: Invariant natural killer T (iNKT) cells, upon activation, exhibit antitumor roles by bridging innate and acquired immunity. To overcome the challenges in producing iNKT cells from patients with cancer, we previously developed allogeneic human induced pluripotent stem cell-derived iNKT (iPSC-iNKT) cells. However, the activation of iPSC-iNKT cells by glycolipid ligands remains a critical step for iNKT cell-mediated cancer therapy. To show the effect of iPSC-iNKT cell-mediated antitumor immunity, in this preclinical study, by taking advantage of a human immune cell-transplanted patient-derived xenograft model using human IL-7/15 knock-in NSG mice, we demonstrate that a combination of iPSC-iNKT cells and α-galactosylceramide-pulsed antigen-presenting cells (αGalCer/APC) induces robust antitumor effects. Single-cell analysis of tumor-infiltrating lymphocytes revealed that this combination therapy uniquely expanded tumor-reactive memory-phenotype CD4 and CD8 T cells. Taken together, upon activation by αGalCer/APC, iPSC-iNKT cells are capable of effectively inducing antitumor T cell immunity, making them a promising tool for generating personalized antitumor T cell immunity.

overall_design: scRNA-seq and scVDJ-seq of eight TIL samples from two tumors per treatment group and two samples from pre-transplanted T cells


title: Single cell landscape of MBL/CLL transition [MBL_CLL_GEO_DataSet1]

first: Livius

last: Penter

first: Catherine

last: Wu


title: Functional interaction of Epidermal growth factor and Angiotensin II in female human primary vascular smooth muscle cells

city: Halle (Saale)

first: Virginie

last: Dubourg

address: Magdeburger Str. 6

department: Julius Bernstein Institute for Physiology

institute: Martin Luther University - Halle-Wittenberg

summary: RNAsequencing was performed for human primary aortic (HAoSMC) and cornary artery (HCASMC) smooth muscle cells from female donors after incubation with Epidermal Growth Factor and/or Angiotensin II, in order to investigate the functional interaction of these two pathways

overall_design: HAoSMC and HCASMC were incubated for 48h with 10 µg/L EGF or/and 10 nM Angiotensin II (N=11)

first: Michael

last: Gekle

last: Kopf

first: Sigrid

last: Mildenberger


title: RNA-seq analyses of FOXF1/2- and p300/CBP-depleted senescent IMR-90 cells

first: Mitsuyoshi

last: Nakao

summary: Transcriptome analysis revealed that the FOXF1/2 and p300/CBP depletion supressed the expression of proinflammatory SASP

overall_design: Examination of the role of FOXF1/2 and p300/CBP in oncogene-induced senescent cells

first: Kan

last: Etoh


title: Genome-wide maps of transcriptomic and epigenomic state in melanoma cell lines

first: Wei

last: Wei

address: 401 Terry Ave N

institute: INSTITUTE FOR SYSTEMS BIOLOGY

summary: A mechanistic relationship between tumor epigenetic plasticity and nongenetic adaptive resistance to therapy is described, with MAPK inhibition of BRAF-mutant melanoma cells providing the model system. Upon inhibition, these largely melanocytic cells undergo reversible cell-state changes, ultimately yielding a drug-resistant mesenchymal-like phenotype. Epigenomic and transcriptomic kinetic studies, coupled with information theory and dynamic system modeling, revealed that, after just 3-days of treatment, RelA drives chromatin remodeling to establish an epigenetic program encoding long-term phenotype changes. Specifically, RelA transcriptionally inhibits SOX10 and NFKBIE through recruiting KDM5B and HDAC1 to down-regulate histone marks H3K4me3 and H3K27ac at their promoter regions. Suppression of SOX10 mediates melanoma regression towards drug-refractory phenotypes. These findings were confirmed in melanoma patients under MAPK inhibitor treatment, providing mechanistic insights into resistance-leading epigenetic reprogramming triggered following drug exposure.

overall_design: Examination of 2 different histone modifications ,transcription factor(RelA)and chromatin accessibility and transcriptome in melanoma cell lines

first: Chunmei

last: Liu

first: Xiang

last: Lu

first: Yapeng

last: Su


title: H3K9me3 controls epidermis development by repressing RNA Pol II activity on key promoters and enhancers

city: Ithaca

first: Chris

middle: Ke

last: Bai

state: NY

address: 526 Campus Rd

department: MBG

institute: Cornell University

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


title: Influence of NIPBL Knockdown-Induced Alterations in Cohesin Loop Extrusion on CTCF Loops, Enhancer-Promoter Connectivity, and PRC Domain Contacts During hESC Differentiation into Pancreatic Lineages [Hi-C]

city: XIAMEN

first: XIAOWEN

last: LYU

state: FUJIAN

address: No.4221, Xiang'an South Road, Xiang'an District

institute: XIAMEN UNIVERSITY

summary: Cell differentiation is orchestrated by precise enhancer-promoter interactions that rely on three-dimensional (3D) chromatin organization, influenced by cohesin dynamics and architectural proteins such as CTCF and NIPBL. In this study, we investigated the effects of knocking down NIPBL, a critical cohesin loading factor, in human embryonic stem cells (hESCs) and their differentiated pancreatic lineages. Our results demonstrate that NIPBL depletion leads to a global loss of cohesin occupancy and altered chromatin architecture, particularly affecting enhancer-promoter loops and CTCF loops. Notably, while CTCF anchors maintain cohesin, enhancer-promoter interactions diminish significantly, highlighting the role of cohesive loading in transcriptional regulation. Additionally, we observed disrupted interactions within Polycomb Repressive Complex (PRC) domains and super enhancers, suggesting that NIPBL is crucial for maintaining the structural integrity of these regulatory elements. The study reveals that cohesin loading and loop extrusion processes are vital for establishing and preserving 3D chromatin interactions essential for gene expression during pancreatic differentiation. These findings underscore the intricate relationships between chromatin organization and gene regulation, with implications for understanding developmental processes and diseases associated with chromatin dysregulation.

overall_design: Hi-C derived from H9 human embryonic stem cells (hESCs) treated with si-RNAs targeting NIPBL, CTCF  and WAPL and chemical inbitors including 1,6-HD, UNC3866 and TPA as well as their pancreatic differentiation derivatives.

first: Xiaowen

last: Lyu

first: Longtao

last: Yu


title: Facultative predation expands the ecological repertoire of Streptomyces

city: Turku

first: Mikko

last: Metsä-Ketelä

address: Tykistökatu 6A

department: Department of Life Technologies

country: Finland

institute: University of Turku

summary: Soil is a rich environment for microbes, where they compete for space and resources. Streptomyces bacteria are well-known for their ability to synthesize natural products, particularly antibiotics, that are used in chemical defense against competing microbes. Here we show that Streptomyces are, in fact, predatory bacteria. Upon encountering yeast cells, Streptomyces initiate the production of numerous enzymes that digest the cell wall and cell membrane. In addition, the interaction triggers the production of natural products that destabilize the yeast cell membrane. Collectively these actions lead to the death of yeast cells and release of cellular building blocks that Streptomyces can use as nutrients. The work fundamentally shifts the paradigm of how Streptomyces are perceived within the soil microbiome ecosystem.

sample_organism:
Streptomyces lavendulae
Saccharomyces cerevisiae

overall_design: Comparative gene expression profiling analysis of RNA-seq data for Streptomyces lavendulae cells and Saccharomyces cerevisiae cells between axenic and co-cultures.

first: Keith

last: Yamada

first: Arina

last: Koroleva

first: Heli

last: Tirkkonen

first: Vilja

last: Siitonen

first: Mitchell

last: Laughlin

first: Amanda

last: Moglia

first: Soheila

last: Matroodi

first: Amir

last: Akhgari

first: Guillaume

last: Mazurier

first: Jarmo

last: Niemi


title: The function of α7nAChR in skeletal muscle.

status: Public on Mar 30 2026

city: Nanjing

first: Zhiqiang

last: Huang

state: Jiangsu

address: Hankou 22

department: Medical School

institute: Nanjing University

summary: We found that Chrna7 is involved in regulating cellular mitochondrial metabolism and maintaining the FOXO1 signaling pathway in skeletal muscle, thereby influencing muscle cell atrophy and regeneration.

overall_design: We utilized Chrna7 knockout mice to investigate its mechanistic links with skeletal muscle atrophy, regeneration, and muscle mitochondrial metabolism.

first: Xiaolu

last: Jin

first: Hongwei

last: Wang


title: Intestinal epithelial and immune cell responses to Vibrio cholerae and IL22 therapy at single-cell resolution

first: Yuko

last: Hasegawa

address: 181 Longwood Ave.

institute: Brigham and Women's Hospital

summary: Vibrio cholerae colonizes the small intestine and causes acute severe diarrhea. Knowledge of intestinal cell responses and innate immune defenses to infection with the cholera pathogen is limited. We defined the epithelial and lamina propria immune cell transcriptional responses to experimental cholera using single-cell RNA sequencing using the infant mouse model of V. cholerae infection. Infection increased the abundance of an enterocyte subtype that highly expressed defense-associated functions, as well as the production of Il22 from ILC3 cells. An IL22 Fc-fusion protein markedly limited V. cholerae intestinal colonization and protected mice from diarrhea and death. IL22 treatment induced expression of vibriocidal Reg3b and elevated the abundance of secretory lineage cells that produce Muc2, impairing V. cholerae association with epithelial cells.

overall_design: We performed single-cell RNA-seq using 10X Genomics Chromium Next GEM Single Cell 3' Reagent Kits v3.1 on epithelial and lamina propria immune cells of P5 infant mouse (2.5-3.5 g of body weight) small intestine at 16 hours post-infection. For IL22Fc treated epithelial single-cell RNA-seq, P4 infant mice were administered with 20 mg of IL22Fc intraperitoneally and returned to their dam. After 36 hours, infant mice were euthanized and cells were isolated from SI. We pooled cells in the same group of mice (n=3-4). Live Epcam+ or CD45+ cells were sorted by FACS.

first: Masataka

last: Suzuki

first: Hailong

last: Zhang

first: Matthew

middle: K

last: Waldor


title: ZNF274 constrains lineage plasticity and drives intrinsic resistance to CDK7 inhibitors in pancreatic cancer

first: Sita

last: Kugel

address: 1100 Fairview Ave N

department: Human Biology

institute: Fred Hutch Cancer Center

summary: Pancreatic Ductal Adenocarcinoma (PDAC) is characterized by two distinct transcriptional subtypes: classical and basal, which may interconvert. We show the KRAB-ZNF protein, ZNF274, correlates with PDAC subtype and regulates sensitivity to CDK7 inhibition by facilitating heterochromatin maintenance and gene suppression. We find ZNF274 loss drives a classical to basal transition, induces invasive protrusions and facilitates invasion capacity. We define two mechanistic arms to this regulation.  ZNF274 directly suppresses ZEB1 expression. When ZNF274 is lost, ZEB1 facilitates acquisition of mesenchymal features, keratin gene expression, and susceptibility to CDK7 inhibition. Second, ZNF274 dampens expression of repetitive elements including human endogenous retroviruses (HERVs). HERV expression following ZNF274 loss induces a double stranded RNA response that reinforces the classical to basal subtype transition. Here, we show ZNF274 is an important epigenetic regulator of cellular plasticity and sensitivity to CDK7 inhibition, presenting a therapeutic liability of PDAC subtype transition that is actionable in the clinic.

overall_design: This dataset comprises RNA-seq and CUT&RUN experiments investigating the transcriptional and epigenomic role of ZNF274 in pancreatic cancer cell lines. RNA-seq was performed following transient siRNA-mediated knockdown of ZNF274 in ASPC1 and CFPAC1 cells, alongside 5 µM AZA or DMSO treatment. Additionally, ZNF274 overexpression was performed in Panc3.27 cells, which express low endogenous ZNF274. CUT&RUN profiling of ZNF274 and H3K9me3 was performed in ASPC1 cells following stable shRNA-mediated knockdown of ZNF274, with IgG as a negative control. All conditions were performed in biological triplicate.

first: Jessica

middle: E

last: Gianopulos

first: Aidan

last: Schutter

first: Stephanie

last: Dobersch

first: Adrianne

last: Wallace-Povirk

first: Sophie

last: Kogut

first: Andrea

last: Doak

first: Pritha

last: Chanana

first: Sabrina

last: Ge

first: Luke

last: Mangino

first: Naomi

last: Yamamoto

first: Liberalis

middle: D

last: Boila

first: Monica

last: Padilla-Galvez

first: Justin

last: Hui

first: Nicole

last: Rhoads

first: Robert

middle: J

last: Gifford

first: Kevin

last: Cheung

first: Daniel

last: Blanco Melo

first: Faiyaz

last: Notta


title: α7nAChR activation reduces inflammation and apoptosis, promoting muscle regeneration through the AKT-FOXO1 pathway.

first: Zhiqiang

last: Huang

summary: Inflammatory factors can lead to muscle atrophy. Therefore, this study aims to further explore the role of inflammatory molecules in muscle atrophy and establish an in vitro inflammatory muscle atrophy model.

overall_design: The goal of this study is to examine the role of α7 nicotinic acetylcholine receptors (α7nAChRs) in preserving the functionality of myotubes.

first: Xiaolu

last: Jin

first: Hongwei

last: Wang


title: Autism-like phenotypes and increased NMDAR2D expression in mice with KDM5B histone lysine demethylase deficiency

first: Leticia

last: Perez Sisques

address: Great Maze Pond

department: Centre for Craniofacial and Regenerative Biology

institute: King's College London

summary: Loss-of-function mutations in genes encoding lysine demethylases specific for trimethylated lysine 4 of histone 3 (H3K4me3) are associated with neurodevelopmental conditions, including autism spectrum disorder (ASD) and intellectual disability. To study the role of KDM5B (Lysine DeMethylase-5B)-mediated H3K4me3 demethylation, we investigated neurodevelopmental phenotypes in mice without KDM5B demethylase activity. These mice exhibited autism-like behaviours and increased brain size. H3K4me3 levels and the expression of neurodevelopmental genes were increased in the developing Kdm5b mutant neocortex. Increased H3K4me3 levels at the promoter and associated expression of the Grin2d gene was associated with increased levels of NMDAR2D protein in synaptosomes isolated from the early postnatal Kdm5b-deficient neocortex. Treating mice with the NMDAR antagonist memantine rescued deficits in ultrasonic vocalizations. These findings suggest that increased H3K4me3 levels and associated Grin2d gene upregulation disrupt brain development and function, leading to socio-communication deficits and identify a potential therapeutic target for neurodevelopmental disorders associated with KDM5B deficiency.

overall_design: Total RNA was extracted using Trizol Reagent. RNA was next purified with the Monarch total RNA miniprep kit (New England Biolabs) following manufacturer’s instructions, including the DNAse step. Cortical mRNA profiles of WT and Kdm5b ΔARID/ΔARID mice at postnatal day 5 were generated by sequencing on the Illumina Hiseq 6000.

last: Perez-Sisques

first: Shail

last: Bhatt

first: Angela

last: Caruso

first: Josephine

middle: L

last: Robb

first: Alex

last: A Donovan

first: Rosemary

last: Bamford

first: Alejo

last: Torres-Cano

first: Soshana

last: Spring

first: Eleanor

last: Hendy

first: Talia

last: Gileadi

first: Martyna

last: Panasiuk

first: Jed

last: Trengove

first: Neeru

last: Jindal

first: Mohi

middle: U

last: Ahmed

first: Mara

last: Sabbioni

first: Joyce

last: Taylor-Papadimitriou

first: Diana

last: Cash

first: Nicholas

last: Clifton

first: Jacob

last: Ellegood

first: Laura

last: Andreae

first: Jason

last: Lerch

first: Maria Luisa

last: Scattoni

first: K Peter

last: Giese

first: Cathy

last: Fernandes

first: M Albert

last: Basson


title: Spatial Transcriptomics of  human hepatocellular cancer

city: Birmingham

first: Shishir

last: Shetty

state: West Midlands

address: 5th Floor IBR, Medical School, University of Birmingham

institute: University of Birmingham

summary:
Background: Immune checkpoint inhibition is now standard of care for patients with advanced hepatocellular cancer (HCC) and yet many patients remain resistant to this therapy. The presence of innate immune populations in the tumour microenvironment (TME) have been implicated in regulating the efficacy of these agents. CLEC14A has previously been shown to be upregulated on tumour endothelial cells and we found endothelial upregulation of CLEC14A in a subset of HCC tumours as well as acute liver injuries.  This led us to explore the role of CLEC14A in neutrophil recruitment, critical populations in both liver pathologies.
Methods:Immunohistochemical analysis was undertaken of CLEC14A in human liver tissue across a range of liver diseases and HCC. CLEC14A regulation and function was then explored in primary human liver endothelial cells including responses to shear stress and flow based adhesion assays. Liver injury models were undertaken CLEC14A knockout mice followed by intravital microscopy. Finally, CLEC14A expression was studied in both publically available HCC data sets and through spatial transcriptomics of HCC tissue.
Findings:We found that CLEC14A mediates neutrophil recruitment across liver endothelium in both in vitro and in vivo settings. This process appears to be independent of its interaction with its known ligand Multimerin-2. Additionally, we demonstrated a correlation of CLEC14A expression in human HCC with a neutrophil transcriptional signature.
Interpretation:This study unveils a new link between a tumour angiogenic receptor and neutrophil infiltration to the liver and highlights the potential of combining current immunotherapy in HCC with agents targeting the CLEC14A pathway.

overall_design: A cohort of surgically resected hepatocellular cancers paraffin embedded samples were analyzed for CLEC14A expression by immunohistochemistry,  six cases were selected with strong vascular staining of CLEC14A and six cases were selected with low vascular staining of CLEC14A.  Further sections were taken from these samples and underwent digital spatial profilng by Nanostring GeoMx.

first: Joanne

last: O'Rourke

first: Daniel

middle: A

last: Patten

first: Dean

last: Kavanagh

first: Catherine

last: Willoughby

first: Josep

last: Llovet

first: Helen

last: Reeves

first: Peter

last: Hewett

first: Neena

last: Kalia

first: Tahir

last: Shah

first: Yuk

last: Ma

first: Kelly

last: Hunter

first: Jack

last: McMurray

first: Joe

last: Flint

first: Owen

last: Cain

first: Derek

last: Mann

first: Amy

last: Naylor

first: Victoria

last: Heath

first: Roy

last: Bicknell

first: Fabian

last: Spill

first: Kylie

last: Savoye

first: Kaiyi

last: Yang


title: Circulatory ILC2 convert and persist as part of the long-term tissue-resident pool after infection [Congenic Transfer]

city: Denver

first: Richard

middle: Lee

last: Reinhardt

state: Colorado

address: 1400 Jackson Street, K817A

department: Biomedical Research

institute: National Jewish Health

summary: Circulating ILC2 can serve as a first line of defense against infection prior to the local expansion of lung-resident ILC2. The fate of these circulating ILC2 and their contribution to the long-term lung-resident ILC2 pool is not understood. Using reporter mice in combination with single cell RNA sequencing (scRNA-seq) and novel applications of Cellular Indexing of Transcriptomes and Epitopes sequencing (CITE-seq), we assessed vascular and parenchymal ILC2 populations during helminth infection and the fate of circulatory ILC2. These studies revealed that circulating ILC2 rapidly convert to a tissue-resident phenotype upon arrival in the lung. Once converted, former circulating ILC2 become largely indistinguishable from lung-resident ILC2 over time. Key gene expression retained by converted ILC2 at the peak of the tissue-resident ILC2 response was related to maintained IL-25-responsiveness and unique cytokine potential. These converted ILC2 accumulate, expand, and persist alongside conventional lung-resident populations even after repeated pulmonary infections. These findings reveal an important contribution of circulating ILC2 to the long-term health and maintenance of the lung-resident ILC2 population.

overall_design: B6 CD45.1 recipient mice were infected with the helminth Nippostrongylus brasiliensis. On day 3 of infection, recipient mice received iILC2s by intravenous injection in the tail. These iILC2s had been sorted from the lungs and mesenteric lymph nodes of CD45.2 Arginase1-YFP reporter mice that had been treated with IL-25 (lung and lymph node sorted separately, then pooled for injection). On day 13 of infection, lungs of the recipient mice were harvested and ILC2s sorted for sequencing. Also sorted for sequencing were: ILC2s from lungs of untreated B6 CD45.1 mice (no infection and no cell transfer), sorted iILC2s from lungs of IL-25-treated Arginase1-YFP reporter mice, and sorted iILC2s from mesenteric lymph nodes of IL-25-treated Arginase1-YFP reporter mice. Prior to sort, samples were stained with PE-conjugated anti-CD45.2, followed by secondary stain with anti-PE CITE-seq antibody. This enabled bioinformatic identification of donor cells in the receipient mice. Two biological replicates were hashed and pooled per condition. Experiment was repeated on two consecutive days, for a total of 4 biological replicates per condition. Conditions = lung iILC2s, mesenteric lymph node iILC2s, uninfected lung ILC2s, and recipient lung ILC2s, . "1" and "A" in file names (interchangeably) corresponds to the first experimental day. "2" and "B" in file names (interchangeably) corresponds to the second experimental day.

first: Amita

last: Kashyap


title: Integrative single cell RNA and spatial profiling identify mechanisms of neonatal brain hemorrhage pathophysiology and repair [Xenium]

city: Houston

first: Santiago

middle: Andres

last: Forero

state: TX

address: 6767 Bertner Ave,

institute: The University of Texas MD Anderson Cancer Center

summary: Here we employed fixed single cell RNA profiling coupled with spatial in situ gene expression profiling to characterize NVU signaling pathways associated with ICH in Itgb8/β8 integrin mutant mice.

overall_design: High throuput RNA in situ hybridization performed with Xenium Prime protocols on control and mutant mice brains at different developmental ages.

first: Zhihua

last: Chen

first: Ali

last: Pirani

first: Arpan

last: De

first: Zachary

last: Wise

first: Xiaofeng

last: Zheng

first: John

last: Morales

first: Joseph

last: McCarty


title: Human ChIP-seq of three metastatic Patient-Derived-Organoid (PDO)

status: Public on Mar 27 2026

city: Padova

first: Silvio

last: Bicciato

address: via U. Bassi 59/b

department: Molecular Medicine

country: Italy

institute: University of Padova

summary: A key problem in cancer biology is understanding the phenotypic characteristics of the aggressive cell states present in macrometastases and their molecular underpinnings. Here we report on the cellular constituents of human breast cancer metastases,  revealing that these malignant cells are invariably locked in a chimeric cell state. Human BC metastatic cells indeed display a gene-expression profile associated to embryonic development of tubular organs, while also retaining the transcriptional features of their original adult mammary luminal lineage.

overall_design: Brain metastatic samples were obtained from Istituto Nazionale dei Tumori, Milan, and Istituto Neurologico “Carlo Besta”, Milan, respectively, following ethical approval from their Institutional Review Boards and acquisition of informed consent from all patients. ChIP-seq for five histone modifications was performed on Patient-Derived-Organoid (PDO), derived starting from these samples.

first: Lorenzo

last: Drufuca

first: Michaela

last: Fakiola

first: Massimiliano

last: Pagani

first: Michelangelo

last: Cordenonsi

first: Stefano

last: Piccolo