title: Mapping breakome of multiple cancer cell-lines

city: Jerusalem

first: Rami

last: Aqeilan

address: Ein Kerem

institute: Hebrew University of Jerusalem

summary: Cancer is characterized by uncontrolled proliferation accompanied by the hypertranscription of oncogenes, leading to transcription stress, a key source of DNA double-strand breaks (DSBs) that jeopardize genomic stability. Yet, transcription stress is still underexplored. In this study, we utilized maps of DSBs identified through in-suspension break labeling in situ and sequencing (sBLISS), along with transcription stress markers, revealing that transcription stress regions coincide with the super-enhancer regulatory landscape. Notably, γH2AX mapping indicates its enrichment at transcription stress sites while not all DSB-enriched genes show equal γH2AX marking, but those with DSBs tied to transcription stress are distinctly marked. Intriguingly, genes with high-DSBs marked by γH2AX exhibited significantly higher DSB turnover and repair than those with γH2AX-low genes, manifesting vulnerability to mutagenesis. These findings underscore super-enhancer activity as a determinant of the transcription stress landscape in cancer, posing a threat to the genomic stability of oncogenes in cancer.

overall_design: MCF7 (HTB-22) and T-47D (HTB-133) cells were grown in RPMI supplemented with 10% (vol/vol) fetal bovine serum FBS (GIBCO), glutamine, and penicillin/streptomycin. HEK-293 (CRL-1573), MDA-MB-468 (HTB-132), MDA-MB-231 (HTB-26), and HeLa cells (CCL-2) were grown in DMEM supplemented with 10% (vol/vol) FBS, glutamine, and penicillin/streptomycin. A-4098 cells (HTB-44) were grown in. EMEM supplemented with 10% FBS, glutamine, and penicillin/streptomycin. SH-SY5Y (CRL-2266) were grown in DMEM/F12 supplemented with 10% FBS, glutamine, and penicillin/streptomycin. HMLE cells were grown in Promocell mammary epithelial cell basal media (C-21010) with added supplements (c-93110) whereas MCF10A were grown on DMEM/F12 supplemented with 5% Horse serum, 20 ng/ml EGF, 0.5 mg/ml Hydrocortisone, 100 ng/ml Cholera toxin, 10 mg/ml Insulin and Pen/Strep. MCF-7 cells were synchronized in the G1 cell cycle stage by culturing in serum-free media for 72 hours followed by replacing the media with 5% FBS media for 5 hours. Cells were grown at 37°C under a humidified atmosphere with 5% CO2. Cells were routinely authenticated by STR profiling, and tested for mycoplasma, and cell aliquots from early passages were used. Cells were treated with DMSO (Sigma-Aldrich), dBET6 (Sigma-Aldrich, SML2638), or CDK9i (NVP-2) (MCE, Cat# Y-12214A) 100 nM for 4 hours. Cells were then treated with DMSO or ATMi (20 uM, KU-55933, Sigma) for 5 hours. Transient transfection of siXRCC4 (Dharmacon; SMARTpool siRNA, Catalog ID: L-004494-00-0005) and siSc (Dharmacon; D-00181010) was carried out using Lipofectamine (ThermoFisher). On the day of transfection, cells were seeded to achieve a confluency of 60-70%. The transfection solution was prepared by mixing 1.5 ml of serum and antibiotic-free RPMI with 30 µL of Lipofectamine and incubating for 5 minutes before adding a mixture of 1.5 ml RPMI and 0.6 nmoles of siRNA, followed by a 20-minute incubation at room temperature. This mixture was then added to cells in a 10 cm plate cultured in antibiotic and serum-free media. The media was replaced with fully supplemented media after 5-6 hours, and the cells were incubated in the incubator for 48 hours.

first: Osama

last: Hidmi

first: Sara

last: Oster

first: Diala

last: Shatleh

first: Jonathan

last: Monin


title: Identification of a JAK/STAT/miR155HG positive feedback loop in regulating NK cell proliferation and effector functions

status: Public on Dec 21 2025

city: Beijing

first: Yongjie

last: Liu

address: No. 1 West Beichen Road, Chaoyang District

country: China

institute: Institute of Genetics and Developmental Biology

type: Expression profiling by high throughput sequencing

summary: The Janus kinase (JAK)-signal transducer and activator of transcription (STAT) signaling pathway control NK cell development, expansion and cytotoxic functions. Whether lncRNA regulates the JAK-STAT signaling in NK cells remains unknown. We found that miR155HG was upregulated in activated NK cells and promoted their proliferation and effector functions. Mechanistically, miR155HG bound to miR-6756 and relieved its repression of JAK3 expression, resulting in increased JAK3 level and enhanced NK cells proliferation and function. Further investigations disclosed that upon cytokine stimulation, STAT3 directly interacts with miR155HG promoter and induces miR155HG transcription. Collectively, we identify a miR155HG-mediated positive feedback loop of the JAK-STAT signaling. In brief, STAT3 interacts with miR155HG promoter and induces miR155HG transcription upon cytokine stimulation, and miR155HG may work as a sponge for miR-6756, preventing the miR-6756-mediated repression of JAK3 expression, thereby promoting the JAK-STAT pathway and enhancing NK cell proliferation and function. These findings may provide a promising therapeutic target to improve NK cell therapy.

overall_design: RNA-seq of NK-92-shCtrl/shmiR155HG cells with three replicates


title: NFκB1-deficiency associated with Flt3-myeloid leukemia enhances the self-renewal capacity via dysregulated RelA:p52 and SOD2 expression

city: Los Angeles

first: Stephen

last: Smale

state: Ca

address: 6-730 MRL 675 Charles E. Young Drive South

department: MIMG

country: USA

institute: University of California Los Angeles

type: Genome binding/occupancy profiling by high throughput sequencing

summary: In acute myeloid leukemia (AML), abnormal expression of NFκB and Flt3 are frequently detected, and dual IKK2/Flt3 inhibitor regimes are used for treatment. However, how NFκB is involved in Flt3-driven myelopoiesis remains unknown. We report that AML is associated with reduced expression of NFKB1, and that Nfkb1 deficiency conveys poor survival in a mouse Flt3-ITD-driven myeloid leukemia model. Interpreting myelopoiesis dynamics with mathematical modeling suggests that Nfkb1-/- hematopoietic stem and progenitor cells possess enhanced self-renewal and are skewed towards plasmacytoid dendritic cells. Single-cell RNA-seq confirmed this interpretation via pseudotime analysis and gene signatures indicating stemness and pDC priming. Biochemical analysis and genetic rescues demonstrate how an imbalanced NFκB signaling system elevates basal nuclear NFκB, where RelA:p52 drives Sod2 expression and enables prolonged progenitor proliferation. Our work reveals how the inflammation response NFκB system controls in stress-responsive myelopoiesis, and how system imbalances can contribute to the pathogenesis of myeloid neoplasms.

overall_design: To investigate the interplay between RelA and p50 during BMDC differentiation, we generated RelA ChIP-seq in Flt3 differentiating BMDCs in both wild-type and Nfkb1-/- cells.

first: Allison

middle: E

last: Daly


title: Effects of repetitive hypobaric hypoxia exposure on the transcriptomic profiles of cerebral cortex and hippocampus in rats

city: Taichung

first: Ro-Lin

middle: Ro-Lin

last: Chang

state: --- Select One ---

address: 145 Xingda Road, South District.

department: Department of Life Sciences

country: Taiwan

institute: National Chung Hsing University

summary: Hypobaric hypoxia (HH) exposure poses a significant risk to personnel safety within the realm of military aviation, especially due to its potential damage to brain functionality in physiological and psychological ways. The present study employed a rodent model to investigate the impact of repetitive HH exposure on brain functionality from a transcriptomic perspective. The treatments were conducted by subjecting rats to HH exposure in a hypobaric chamber device for six times, followed by the collection of brain cortex and hippocampus at 24 and 48 h subsequent to the final exposure. Transcriptomic analysis identified a total of 177 differentially expressed genes (DEGs) in the hippocampus, contrasting with 7 DEGs in the cortex post-treatment. Subsequent gene ontology (GO) analysis showed that the majority of hippocampal DEGs are associated with the GO terms related to the functionality of sensory nervous system. Meanwhile, Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis pointed out the enriched mechanisms related to Wnt signaling, melanogenesis, etc. Acute inflammatory responses and cellular apoptosis were almost negligible in rats after repetitive HH exposure. It is significant to note that repetitive HH exposure induces the cerebral expression of elevated concentrations of heat shock protein 90 (HSP90), which may confer neuroprotective benefits to the brain. The findings herein provide valuable information for the health of military aviation personnel engaged in hypobaric hypoxic operations or training.

overall_design: Min-Yu, Tu

first: Chung-Yu

last: Lai

first: Chi-Chan

last: Huang

first: Chao-Chien

last: Cheng

first: I-Chien

last: Chen

first: Chuan-Mu


title: Excess FGFR3 signaling in achondroplasia disrupts turnover of resting zone chondrocytes via CREB signaling

city: Suita

first: Noriyuki

last: Tsumaki

state: Select One

address: 2-2 Yamadaoka

department: Department of Biochemistry and Molecular Biology

country: Japan

institute: Osaka University, Graduate School of Medicine

summary: Achondroplasia, associated with gain-of-function mutations in FGFR3, causes growth plate cartilage dysfunction, resulting in short-limb dwarfism. However, its precise molecular and cellular mechanisms remain unclear. To address this, we aimed to generate knock-in mice (Fgfr3Ach) harboring the achondroplasia mutation (p.Gly380Arg). In addition to previously reported abnormalities, we observed an expansion of the resting zone. EdU labeling and lineage tracing analysis revealed disrupted stem cell properties of resting zone chondrocytes, preventing self-renewal, limiting cell divisions and migration toward the primary ossification center. Single-cell RNA-seq and immunohistochemical analysis identified a cell cluster that corresponded to the expanded resting zone. Pathway analysis and functional experiments revealed that CREB disrupts stem cell properties in resting zone chondrocytes and contributes to dwarfism. Administration of CREB inhibitor 666-15 restored growth plate pathology and bone length. These findings demonstrate that how excess FGFR3 signaling disrupts resting zone chondrocyte properties and suggest potential therapeutic targets for achondroplasia.

overall_design: We harvested growth plate cartilage from wild-type mice and knock-in mice bearing the p.Gly374Arg mutation in Fgfr3 (Fgfr3Ach) at 19- and 22-days old. We subjected these samples to scRNA-seq analysis.

first: Nanao

last: Horike

first: Saeko

last: Koyamatsu

first: Noriko

last: Tanaka


title: Cytoplasmic DIS3 degrades circular RNAs independently of the exosome

city: Regensburg

first: Gerhard

last: Lehmann

address: Universitaetsstrasse 31

department: Biochemistry 1

country: Germany

institute: University of Regensburg

type: Non-coding RNA profiling by high throughput sequencing

summary: Circular RNAs (circRNAs) are frequently generated during splicing. Their physiological roles, however, remain largely elusive. Some specific circRNAs function as microRNA (miRNA) or RNA binding protein (RBP) sponges or encode for proteins and are actively translated. Due to the lack of accessible ends, circRNAs are resistant to exonucleolytic cleavage and thus are more stable than linear RNAs. Nevertheless, circRNAs are most likely turned over by cellular degradation pathways. Here, we used a biochemical purification strategy to find nucleases that could degrade circRNAs. We identified the exosome-associated nuclease DIS3, which contains an endonucleolytic PIN domain and an exonuclease domain. We show that DIS3 can degrade circRNAs independently of the exosome in vitro. Although moderately, RNA-seq reveals that selected circRNAs are stabilized when DIS3 is reduced in vivo. Based on our data, we propose a model, in which cytoplasmic DIS3 contributes to the turnover of circRNAs in human cells.

overall_design: To study the physiological relevance of DIS3 in circRNAs degradation in vivo, we performed knockout experiments using the CRISPR/Cas9 system. First, we stably integrated an inducible tagged DIS3 variant (Flag-HA DIS3) into Flp-In T-REx 293 cell line using the Flp-In system. We then knocked out the endogenous gene DIS3 using CRISPR/Cas9. We refer to these cells as knock down cells since some DIS3 expression is still present in the uninduced state. To identify circRNAs candidates that could be regulated by DIS3, we performed gene expression analysis from two different cell lines (DIS3 KD clone 8 and control, two replicates each).

first: Claudia

last: Latini

first: Si-Nan

last: Zhai

first: Li

last: Yang

first: Gunter

last: Meister


title: Pulmonary B lymphocytes ameliorate Alzheimer's disease-like neuropathology

city: nanjing

first: Weixi

last: Feng

address: hanzhong road

institute: Nanjing Medical University

summary: Increasing evidences reveal that the peripheral immune system is involved in the pathogenesis of Alzheimer's disease (AD). Here, we report that pulmonary B lymphocytes mitigated beta-Amyloid (Aβ) pathology in 5xFAD mice. The proportion of B cells, rather than T cells, increased within the brain, meningeal and lung tissues in 3-month-old 5xFAD mice. Deletion of mature B cells aggravated Aβ load and memory deficits of 5xFAD mice. Furthermore, increasing pulmonary B cells via overexpression of B-cell-activating factor ameliorated brain Aβ load and improved cognitive functions of 10-month-old 5xFAD mice. Together, these results highlighted the lungs as both immune targets and effector organs in Aβ pathogenesis. Pulmonary B cells could serve as a potential target against AD.

overall_design: Pulmonary B cells mRNA profiles of 3-month old wild type (WT) and 5xFAD mice.

first: Yanli

last: Zhang

first: Ming

last: Xiao


title: Hypoxia-inducible factor-1α-deficient adipose-tissue macrophages produce the heat to mediate lipolysis of white adipose tissue through uncoupling protein-1

city: Seoul

first: Tae-Young

last: Roh

address: 52 Ewhayeodae-gil, Seodaemun-gu

department: Life Sciences

country: South Korea

institute: Ewha Womans University

summary:
Background: Uncoupling protein 1 (UCP1) is a proton uncoupler located across the mitochondrial membrane generally involved in thermogenesis of brown adipose tissues. Although UCP1 is known to be strongly expressed in brown adipocytes, recent evidence suggest that white adipocytes can also express UCP1 under certain circumstances such as cold- or β-adrenergic receptor-stimulation, allowing them to acquire brown adipocyte-like features thereby becoming 'beige' adipocytes.

Results: In this study, we report that UCP1 can be expressed in adipose-tissue macrophages (ATM) lacking functional hypoxia-inducible factor-1 (HIF-1) and this does not require cold- nor β-adrenergic receptor activation. By using myeloid-specific Hif-1α knockout (KO) mice, we observed that these mice were protected from diet-induced obesity and exhibited an improved thermogenic tolerance upon cold challenge. ATM isolated from white adipose tissues (WAT) of these mice fed with high fat diet exhibited significantly higher M2-polarization, decreased glycolysis, increased mitochondrial functions and acetyl-CoA levels, along with increased expression of Ucp1, peroxisome proliferator activated receptor-gamma co-activator-1a, and others involved in histone acetylation. Consistent with the increased Ucp1 gene expression, these ATM produced a significant amount of heat mediating lipolysis of co-cultured adipocytes liberating free fatty acid. Treating ATM with acetate, a substrate for acetyl-CoA synthesis was able to boost the heat production in wild-type or Hif-1α-deficient but not UCP1-deficient macrophages, indicating that UCP1 was necessary for the heat production in macrophages. Lastly, we observed a significant inverse correlation between the number of UCP1-expressing ATM in WAT and the body mass index of human individuals.

Conclusions: UCP1-expressing ATM produce the heat to mediate lipolysis of adipocytes, indicating that this can be a novel strategy to treat and prevent diet-induced obesity.

overall_design: The examination of the changes of gene expression in FACS-sorted aerobic tumor cells from LLC tumor-bearing mice with Veh or Clod injection

first: Hoibin

last: Jeong

first: Hyeongrin

last: Jeon

first: G-One

last: Ahn


title: CD276-DM1 Antibody drug conjugate with cmLumiOpto gene therapy to treat triple negative breast cancer.

status: Public on Dec 20 2025

city: COLUMBUS

first: Zhuoxin

last: Zhou

state: OH

address: Gateway Lofts Columbus, 2211 Dublin Rd

institute: Ohio State University

summary: Triple-negative breast cancer (TNBC) is a highly aggressive subtype characterized by resistance to chemotherapy, elevated metastatic potential, and frequent relapse. This study investigated the therapeutic impact of combining an antibody-drug conjugate (ADC) with mitochondria-targeted gene therapy. A CD276-directed monoclonal antibody conjugated to mertansine when paired with cmLumiOpto gene therapy, exhibited potent synergistic activity across three TNBC cell lines, impairing mitochondrial function and amplifying tumor-associated cytokine responses. In vivo experiments further demonstrated that the ADC/cmLumiOpto combination effectively suppressed metastasis in metastatic models and achieved high tumor growth inhibition in patient-derived xenograft mouse models. Mechanistic studies revealed that this dual approach downregulated metastatic signaling pathways, disrupted the tumor microenvironment, and triggered apoptosis. Importantly, histological assessments of normal tissues and body weight monitoring indicated negligible toxicity. Collectively, these findings highlight the therapeutic promise of CD276-targeted ADCs combined with gene therapy as a strategy for treating TNBC.

overall_design: Metastasized 4t1 tumour cells were harvested from the lungs of BALB/cJ mice after three weeks of treatment with CD276-mertansine ADC in combination with cmLumiOpto gene therapy.Total RNA was extracted from the harvested tumour cells using the RNeasy Plus Mini Kit (Qiagen, Germantown, MD, USA). Bulk RNA sequencing with cDNA library construction were performed at Novogene America (Sacramento, CA, USA) using the Illumina HiSeq™ X Ten platform.


title: HPA-Gut Microbiome Axis Dysregulation in Sleep Deprivation: Pharmacological and Microbial Rescue of Lacrimal Gland Homeostasis

city: ZHENGZHOU

first: SHENZHEN

last: HUANG

address: Weiwu Road No. 7

institute: Department of Ophthalmology, Zhengzhou University People's Hospital, Henan Provincial People's Hospital

summary: Sleep deprivation (SD) disrupts systemic homeostasis, yet its impact on lacrimal gland integrity through neuroendocrine–microbial pathways remains unclear. Using a male mice SD model, we show that chronic SD activates the hypothalamic-pituitary-adrenal (HPA) axis, elevates corticosterone, alters gut microbiota, and depletes short-chain fatty acids (SCFAs). These alterations coincide with lacrimal gland atrophy, reduced tear secretion, and increased CD4⁺/CD8⁺ T cell infiltration, accompanied by activation of IL-17-associated inflammatory pathways. Pharmacological inhibition of glucocorticoid synthesis with metyrapone preserves lacrimal gland structure and function while attenuating immune activation. Microbiome-directed interventions, including SCFA supplementation and fecal microbiota transplantation, rebalance gut communities, suppress proinflammatory T cell responses, and maintain lacrimal gland homeostasis. Transcriptomic and immunohistochemical analyses further reveal that all three interventions converge on downregulation of IL-17 signaling. Collectively, these findings establish an HPA-gut microbiome-lacrimal gland axis links neuroendocrine stress to microbial dysbiosis and ocular inflammation, and they suggest therapeutic strategies for SD-associated lacrimal gland dysfunction.

overall_design: Two ELGs from each male mouse were pooled to form a single sample, resulting in six samples from six adult mice for scRNA-seq.

first: Shenzhen

last: Huang

first: Zhijie

last: Li


title: Human tolerogenic dendritic cell subtypes exert divergent effects on induction of cytotoxic CD4+ T cells

city: Newcastle upon Tyne

first: Catharien

middle: MU

last: Hilkens

state: Tyne & Wear

address: Framlington Place

department: Translational and Clinical Research

country: United Kingdom

institute: Newcastle University

summary: Tolerogenic dendritic cells (tolDC) are currently in clinical trials for the treatment of autoimmune diseases such as rheumatoid arthritis and multiple sclerosis. The methods for producing therapeutic tolDC vary widely, with little being known about the commonalities and differences of distinct cell products in terms of their regulatory actions on CD4+ T cells. We compared human monocyte-derived tolDC generated with vitamin D3 alone or in combination with dexamethasone. We found marked differences in the surface expression of HLA-DR and immune regulatory molecules, but also found commonalities, e.g. a strongly reduced capacity to produce interleukin-12 and a concomitant decreased ability to induce interferon- secretion by allogeneic CD4+ T cells. To gain a deeper understanding of how these tolDC types exert their regulatory effects, we co-cultured them with CD4+ T cells from rheumatoid arthritis patients or healthy controls and analysed the gene expression profile and function of the responding T cells. We found that tolDC generated with vitamin D3 alone, but not in combination with dexamethasone, induced potent cytotoxic activity in the responding CD4+ T cells as demonstrated by an enhanced cytotoxic gene signature, increased levels of intracellular granzyme B, and superior cytotoxic activity towards myeloid and B cells. These data identify cytotoxicity as an atypical CD4+ T helper cell effector function induced by some but not all tolDC types, with implications for their individual clinical applications.

overall_design: Periphertal blood mononuclear cells from four RA patients were co-cultured with mature DC or two types of tolerogenic DC (DexVD3DC and VD3DC) for 6 days. Expanded CD4+ T cells were sorted and their gene expression was analysed on the NanoString nCounter® platform using the Immune Exhaustion panel.

first: Gabrielle

last: Barran

first: Najib

last: Naamane

first: Abdul

last: Mannan Baru

first: Amy

last: Anderson

first: Jane

last: Falconer

middle: M


title: RNA-seq analysis of ex vivo microtumor models comprising control or Arpc4 knockout (KO) PDAC cells

city: Heidelberg

first: Yina

last: Qiao

institute: Heidelberg University Hospital

summary: The loss of Arpc4 resulted in reduced expression of other Arp2/3 complex components, rendering the Arp2/3 complex nonfunctional. The ex vivo microtumor(3D) models were composed of either control or Arpc4 knockout (KO) KP 8025 cells, mouse primary pancreatic stellate cells (PSCs), and bone marrow-derived macrophages. To identify genes affected by Arpc4 knockout in this model, RNA-seq analysis was performed on bulk samples. R254 cell line which was derived from primary cells isolated from genetically engineered p48Cre/+; LSL-KrasG12D/+; p53flox/flox (KPC) mice, and 8025 cell line which was derived from primary cells isolated from genetically engineered p48Cre/+; LSL-KrasG12D/+ (KC) mice were also conducted with RNA seq.

overall_design: The 8025 and R254 cell line were established from primary cells isolated from genetically engineered p48Cre/+; LSL-KrasG12D/+ (KC) and p48Cre/+; LSL-KrasG12D/+; p53flox/flox (KPC) mice, and cultured in Dulbecco’s Modified Eagle Medium (DMEM) supplemented with 10% fetal bovine serum (FBS), 100 U/mL penicillin, and 100 µg/mL streptomycin. Cells were maintained at 37°C in a humidified incubator with 5% CO₂. The cell line was transfected with the CRISPR/Cas9 p20-ARC Double Nickase Plasmid (Santa Cruz Biotechnology, USA) to target the Arpc4 gene, alongside a negative control plasmid (Santa Cruz Biotechnology, USA). Transfections were carried out using Lipofectamine 3000 (Thermo Fisher, USA) according to the manufacturer’s protocol. Forty-eight hours post-transfection, green fluorescent cells were sorted via fluorescence-activated cell sorting (FACS) and selected using puromycin (InvivoGen, Toulouse, France) at concentrations of 0.7 mg/mL for 8025 cells and 1.2 mg/mL for R254 cells. After 5–7 days of puromycin selection, cells were seeded into 96-well plates for clonal expansion. Arpc4 knockout (Arpc4ko) clones were validated via Western blot analysis. Total RNA was extracted using the Monarch Total RNA Miniprep Kit in accordance with the manufacturer’s protocol. RNA sequencing was performed at the Core Unit Bioinformatics, Medical Faculty, Ulm University.Ex vivo microtumor models (3D) were constructed using organoids, mouse primary pancreatic stellate cells (PSCs), and bone marrow-derived macrophages embedded in a matrix consisting of 75% Matrigel, 25% Type I collagen, 5 μg/mL fibronectin, and 2.5 μg/mL vitronectin. Total RNA was extracted by adding TRIzol reagent (Thermo Fisher, USA) to the gel after removing the supernatant and dissolving the gel by thorough mixing. Chloroform (Thermo Fisher, USA) was then added, followed by vigorous vortexing for 15 seconds. After incubation at room temperature for 3 minutes, the mixture was centrifuged at 12,000×g for 15 minutes at 4°C. The upper aqueous phase was carefully transferred to a fresh tube, mixed with an equal volume of ≥95% ethanol, and purified using the Monarch Total RNA Miniprep Kit (New England Biolabs, Germany) according to the manufacturer’s protocol. RNA sequencing was performed at the NGS Core Facility, Medical Faculty Mannheim, University of Heidelberg.

first: Xiufen

last: Yang

first: Yifeng

last: Sun

first: Tamer

last: Abdelaal

first: Kathleen

last: Schuck

first: Hend

last: Abdelrasoul

first: Eduard

last: Ryschich

first: Carolina

last: De La Torre

first: Yan

last: Dong

first: Jingxiong

last: Hu

first: Chao

last: Fang

first: Xiaoyan

first: Christoph

last: Kahlert

first: Malte

last: Hermes

first: Ingrid

last: Herr

middle: W

last: Michalski

first: Bo

last: Kong


title: VEGF/ERK activation and PI3K inhibition together drive a vein-to-artery transition in an in vitro model of human angiogenesis

city: stanfofd

first: Zhainib

last: Ugokwe

state: ca

address: 318 campus dr e350

department: biology

institute: stanford university

summary: Artery endothelial cells (ECs) arise through different pathways, including differentiation from mesodermal cells (vasculogenesis) or from already established vein or capillary plexus ECs (angiogenesis), the latter being most common during embryonic development and regeneration. Understanding the vein-to-artery transition could improve revascularization therapies, but progress is limited by a lack of human models. Here, we develop a human pluripotent stem cell (hPSC) differentiation protocol that models the vein-to-artery (v2a) EC conversion. Comparing mesoderm-to-artery (m2a) and v2a transcriptomes with publicly available scRNA-seq data from human embryos showed they reflected vasculogenesis- and angiogenesis-derived artery ECs, respectively. We discovered that full arterial identity could be attained in vein ECs within 48 hours just by activating VEGF signaling while inhibiting PI3K. Overall, we model a critical step in human vascular development and define the minimal signals required for artery differentiation from veins, providing a framework to promote this conversion during revascularization or in therapeutic contexts.

overall_design: bulk RNA-sequencing of hPSC-derived vein and pre-vein ECs treated with arterial media for 24 and 48 hours

last: Amir-Ugokwe

first: Kristy

last: Red-Horse

first: Emily

last: Trimm


title: Investigating epigenetic biomarkers of age, sex, and disease in captive South African cheetahs (Acinonyx jubatus jubatus)

city: 15600 San Pasqual Valley Rd

first: Michelle

last: Ysrael

state: CA

address: 15600 San Pasqual Valley Rd

institute: San Diego Zoo Wildlife Alliance

type: Methylation profiling by genome tiling array

summary: Epigenetic modifications, particularly DNA methylation, are strongly associated with chronological age across mammalian species. This study developed cheetah-specific epigenetic clocks from methylation profiles generated from cheetah blood and liver samples tested on the HorvathMammalMethylChip40 Illumina Array. The resulting age clock used 52 CpG sites and predicted age across blood and liver samples (r = 0.97 and MAE = 0.86). When applied to a test set of blood collected from live cheetahs, the clock provided accurate predictions for adult individuals (age > 3 years) but was less precise at and around age of sexual maturity. A second clock, incorporating cheetah, lion, and tiger profiles, used 46 CpG sites and predicted age across these feline species (r = 0.94 and MAE = 1.16). Additionally, a sex clock using 67 CpG sites accurately predicted sex in all test samples. To explore the potential of methylation as a biomarker beyond age and sex, we conducted a differential methylation analysis to investigate disease-related methylation patterns in cheetahs diagnosed with hepatic sinusoidal obstruction syndrome (SOS). This analysis identified 4,377 CpG sites with significant differences between SOS-positive and SOS-negative cheetahs (adjusted p-value < 0.05). These findings advance the development of epigenetic clocks for precise age and sex prediction in cheetahs and related species and establish a foundation for leveraging methylation biomarkers to investigate diseases in wildlife conservation efforts.

platform_organism:
Homo sapiens
Mus musculus
Rattus norvegicus

overall_design: We aimed to profile the DNA methylome of cheetahs (Acinonyx jubatus) to develop species-specific epigenetic clocks and explore disease-associated methylation patterns. Liver and skin tissues collected opportunistically at necropsy (n = 53) and blood samples collected opportunistically from live animals (n = 6) were analyzed using the Infinium HorvathMammalMethylChip40 array. Methylation profiles were generated and processed through the SeSaMe pipeline, and elastic net regression models were used to construct cheetah-specific clocks for age and sex prediction. In addition, a differential methylation analysis was conducted on liver samples from cheetahs diagnosed with sinusoidal obstruction syndrome (SOS) to identify CpG sites associated with disease status. This study leveraged biobanked materials spanning 30 years and supplemented them with publicly available data from lions and tigers to expand the predictive capacity of the models to other large cat species.

first: Ysrael

last: Michelle

first: Moore

last: Caroline

first: Kubiski

last: Steven


title: Gene expression profiles in injured renal tubules in rat model of colistin-induced nephrotoxicity

city: Tonomachi, Kawasaki-ku, Kawasaki City, Kanagawa, JAPAN

first: Kohei

last: Matsushita

institute: National Institute of Health Sciences

summary: The aim of this study is to investigate the gene expression profiles of injured renal tubules in colistin-induced nephrotoxicity.

overall_design: n = 4/group. 2 groups (Total n = 8). Kidney_Control, Kidney_Colistin


title: bacTRAP profiling of astrocytes in five mouse brain regions in wildtype controls and hippocampus region in a Alzheimer's disease mouse model

city: Chapel Hill

first: Ran

last: Zhang

address: Its Manning, 211 Manning Dr

institute: UNC Chapel Hill

summary: We experimentally generated astrocyte gene expression profiles in five major brain regions in mouse: prefrontal cortex (P), hippocampus (H), amygdala (A), caudate nucleus (C) and ventral striatum (V) (Figure 1A, Methods), with more than three biological replicates in each region. To derive the differences between the regional transcriptional profiles, we utilized TRAP-seq, a method that enables detailed profiling of actively translated mRNA, rather than just transcribed mRNA, thus better capturing the functional state of the cell. This approach enables us to generate ex vivo region-specific astrocyte signatures.

overall_design: Mouse transgenic line Adlh1l1-TRAP (www.gensat.org; gift from Drs. Heintz and Dougherty) and wild type C57Bl/6J mice (JAX strain #000664) were used for this project. Twelve to fourteen-week-old healthy male and female mice were lightly anesthetized with CO2 and the brains were quickly removed and dissected. Sterile and RNase free instruments and buffers were used. Brains were placed in the 0.5mm matrix and following tissue blocks were cut using razor blades: for the prefrontal cortex (Bregma ~3.56 to 1.94mm), with additional removal of the olfactory bulbs using forceps; Bregma ~1.94 to 0.74 mm from which caudate nucleus (dorsal striatum) and ventral striatum, were cut though using forceps, at an ~45% angle in lateral-to-medial plane, avoiding the midline containing basal forebrain; Bregma 0.74 to -0.46 mm tissue block was used to dissect dorsal striatum using forceps, while amygdala was dissected from the ventro-lateral portion of the block Bregma -0.46 to -2.54 mm. The dorsal hippocampus was removed from each block using the hippocampal tool. A block from Bregma -2.54 to -4.90 mm was used to remove the remaining ventral hippocampus using the hippocampal tool. For each brain region, three technical replicates were processed to gather the astrocyte-specific mRNA for sequencing. Technical replicates contained two pooled biological replicates for prefrontal cortex, caudate nucleus, and hippocampus, and six biological replicate samples for ventral striatum and amygdala. Males and female samples were pooled according to the sex. For Alzheimer’s disease mouse model, we utilized two mouse lines, Aldh1l1-TRAP and 5xFAD (B6.Cg-Tg(APPSwFlLon,PSEN1*M146L*L286V)6799Vas/Mmjax; The Jackson Laboratory, strain # 008730). Immunoprecipitation was performed overnight with the mixture of two GFP monoclonal antibodies. mRNAs were purified using Qiagen Rneasy Micro Plus kit, following the manufacturer’s protocol, and quantity and quality were determined with a Nanodrop Spectrophotometer and Agilent Bioanalyser. For each sample, mRNAs were amplified using the Ovation RNA-seq System V2 (NuGEN). Library preparation and amplification were done by the Rockefeller University Genomic Facility, and Illumina HiSeq platform was used.

first: Ana

last: Milosevic


title: Scar-associated endothelial-stellate cellular crosstalk drives fibrosis resolution in MASH [Spatial Transcriptomics]

city: New York

first: Scott

last: Friedman

state: NY

address: 1425 Madison Ave

department: Liver Diseases

institute: Icahn School of Medicine at Mount Sinai

summary: Fibrosis, or scarring, can affect many organs including liver, lung, heart, kidney, intestines etc. and contributes to ~40% of mortality in the industrialized world. Unlike other organs, fibrosis in the liver typically resolves when the source of injury is extinguished. Elucidating the molecular mechanisms that underlie spontaneous fibrosis resolution may lead to novel antifibrotic strategies. In this study we established a robust mouse model of fibrosis regression in MASH (Metabolic dysfunction-Associated Steatohepatitis), a highly prevalent chronic liver disease worldwide, and performed single cell and in situ molecular profiling to define the molecular drivers of fibrosis regression. As fibrosis regressed, inflammatory cell numbers decreased and endothelial cell (EC) numbers increased. Prediction of cell-cell communication using the Calligraphy pipeline identified a Wnt9b-Sfrp2 crosstalk that emerged as fibrosis resolved. To investigate the Wnt9b-Sfrp2 crosstalk as a driver of fibrosis resolution we treated mice with recombinant SFRP2, a WNT inhibitor, which attenuated spontaneous fibrosis regression compared to vehicle-treated mice. Using single nucleus RNA sequencing, we identified a subset of liver ECs termed ‘Endo4’, as the source of Wnt9b. Immunostaining of the Endo4 marker VWF using tissue clearing and 3D imaging identified VWF+ vasculature surrounded by activated hepatic stellate cells (HSCs) that penetrated deep into the fibrotic septa, establishing them as de facto scar-associated ECs. Functionally, using a novel in situ protease activity-based probes, prominent serine protease activity was found to be co-localized with both scar-associated Endo4 ECs and HSCs. In summary, WNT-dependent endo-stellate crosstalk within the fibrotic niche represents a novel regulatory node in murine MASH fibrosis regression and a promising therapeutic target.

overall_design: We treated mice for 6 weeks on either the CCl4 or our previously established FAT-MASH murine model. Tissue from mice were extracted after 6 weeks of disease (‘Peak CCl4 Fibrosis’ and 'Peak MASH Fibrosis'). After cessation of injury, tissue was extracted at 2 weeks ('2wk CCl4 Regression' and '2wk MASH Regression') and 6 weeks of regression ('6wk CCl4 Regression' and ‘6wk MASH Regression').

first: Kenneth

last: Li


title: Microarray data for normal human melanocytes, untreated A375 melanoma cells, and A375 cells treated with Timosaponin AIII

city: Chengdu

first: Bei

last: Zhao

address: No.32, Western 2nd Section, 1st Ring Rd, Qingyang District

institute: University of Electronic Science and Technology Hospital

summary:
Melanoma is an aggressive skin cancer with limited treatment options, particularly in advanced stages. Novel therapeutic agents with defined molecular mechanisms are urgently needed. Timosaponin AIII, a naturally occurring steroidal saponin from Anemarrhena asphodeloides, exhibits broad anticancer activity, but its role in melanoma remains unclear. In this data, we investigated the molecular mechanisms underlying its antimelanoma effects.
Transcriptome profiling was conducted using the Affymetrix PrimeView Human Gene Expression Array (Affymetrix, Santa Clara, CA, USA), which targets over 36,000 transcripts based on the GRCh38/hg38 human reference genome annotation. Raw microarray data (CEL files) were imported into the R statistical environment (v4.2.2) and processed using the affy R package (v1.74.0)

overall_design: Microarray analysis was performed on the following four groups: (1) normal human melanocytes (shown as NC); (2) untreated A375 melanoma cells (shown as A375); and (3) A375 cells treated with 8 μmol/L Timosaponin AIII for 48 hours (shown as A375+T-AIII).


title: Scar-associated endothelial-stellate cellular crosstalk drives fibrosis resolution in MASH [snRNA-Seq]


title: Scar-associated endothelial-stellate cellular crosstalk drives fibrosis resolution in MASH [scRNA-Seq]


title: RNA sequencing transcriptome analysis of lesional to perilesional cortex at 5 days after traumatic brain injury

city: Frankfurt

first: Irmgard

last: Tegeder

state: Hessen

address: Theodor Stern Kai 7

department: Clinical Pharmacology

institute: Goethe University Frankfurt

summary: C57BL6/N male mice (14-week-old) were subjected to a controlled cortical impact (CCI) to induce a unilateral traumatic brain injury (TBI). After surgery, mice were treated and monitored for 5 days after TBI (5 dpi).  There were four treatment groups, each consisting in five male mice (n = 5 per group). Group-1 received the CSF1R antagonist, PLX3397 (pexidartinib) via food pellets (290 mg per kilogram of pellets, feeding at libitum). Group-2 received the interleukin-1 receptor antagonist (IL1RA), anakinra  (100 mg/kg body weight subcutaneously at 5 min, 24h, 48h, and 72h after CCI). Group-3 received both PLX3397 and anakinra (PLX3397+anakinra), and Group-4 got vehicle p.o. and s.c.. A control group was subjected to sham-surgy (n = 4)which included anesthesia, skin incision and suture but no skull penetration. PLX3397 leads to a depletion of microglial cells which was confirmed by immunohistochemistry. Lesional to perilesional cortical tissue was obtained 5 dpi (Brgema: +0.64 mm to -2.86 mm) to assess differential gene and transcript expression, microglia depletion and cortical reorganization. Behavioral scores for well-being and motor functions were obatined repeatedly during the observation time. Histology of brain lesion size, indices of neuronal damage and neuroinflammation were obtained at 5 days after TBI. Neuroinflammatory markers tended to be lower in PLX3397 treated mice, there was almost no effects of anakinra alone but inflammation and lesion volume were strongly reduced in the PLX3397+anakinra group, which was associated with better neurological outcome suggesting synergistic effects of PLX3997 and anakinra after TBI.

overall_design: Total RNA was extracted from lesional-perilesional cortex 5d after TBI in mice treated with PLX3397 (n = 5), anakinra (n = 5), PLX3397+anakinra (n = 5) or vehicle (n = 5) from d1-d5 and from sham treated mice (n = 4). mRNA was analyzed by RNA sequencing in 5 biological replicates per treatment group using an Illumina NovaSeq 6000 system.

first: Michael

middle: K

last: Schäfer

first: Matthias

last: Klein


title: Colorectal Cancer cohort from the Geneva Cancer Registry

city: Geneva

first: MELIVOIA

last: RAPTI

address: Rue du Général-Dufour

department: Medicine

country: Switzerland

institute: University of Geneva

summary: The Geneva Cancer Registry database collected data and tissue for all colorectal cancer patients diagnosed between 1985 and 2013. Samples with available fresh frozen material were selected for gene expression profiling with RNAseq (N=384), these ranged from 2002 until 2011.

overall_design:
The study population has been described in Benhamou S, Fournier E, Puppa G, McKee T, Ris F, Rubbia-Brandt L, et al. Cohort profile: population-based cohorts of patients with colorectal cancer and of their relatives in Geneva, Switzerland. BMJ Open. 2022;12:e063914

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

first: Simone

last: Benhamou

first: Evelyne

last: Fournier

first: Giacomo

last: Puppa

first: Thomas

last: McKee

first: Frederic

last: Ris

first: Laura

last: Rubbia-Brandt

first: Valeria

last: Viassolo

last: Zilli

first: Inti

last: Zlobec

first: Pierre Olivier

last: Chappuis

first: Elisabetta

last: Rapiti

first: Petros

last: Tsantoulis


title: GABPα2β2 tetramer deficiency alters transcriptional profiles in NK cells

city: Beijing

first: Shuyang

last: Yu

address: 2 Yuanmingyuan West Road

department: College of Biological Sciences

institute: China Agricultural University

summary: Natural killer (NK) cells are critical innate lymphocytes with the capacity to elicit the early defense against pathogens and the immune surveillance of tumor cells. The complex transcriptional network involved in NK cells is still many unknowns. By targeting GABPβ isoforms that can form homo- or heterodimers, we found that GABPα2β2 tetramer regulates NK cell development, cytokines secretion and melanoma resistance. To investigate the molecular mechanisms, RNA-seq was performed using NK cells in bone marrow isolated from Ctrl and dKO mice.

overall_design: Bone marrow NK cells (CD3e-NK1.1+CD49b+ cells) were sorted via FACS from GABPα2β2 tetramer-deficient mice and their littermate controls. Total RNA extraction with the miRNeasy Mini Kit according to the manufacturer’s instructions (Qiagen), and then subjected to Annoroad (Beijing, China) for library construction and RNA sequencing. For RNA-seq, 2 biological replicates of NK cells from Ctrl and dKO were used.


title: Examining the effect of oxLDL on CD4+ T cell H3K27ac epigenetic marks

city: Headington

first: Toby

last: Brown

state: Oxfordshire

address: Nuffield Department of Medicine, Roosevelt Dr

institute: Centre for Human Genetics

summary: Elevated circulating low-density lipoprotein cholesterol (LDL-C) is a key risk factor for coronary artery disease (CAD). The pathogenesis of CAD is multifactorial, driven by heritable and lifestyle-related risk factors. Although CD4+ T cells are one of the main cell types in atherosclerotic lesions, their interaction with atherogenic oxidised LDL (ox-LDL) remains poorly understood. Therefore, we sought to characterise the transcriptomic and epigenomic consequences of ox-LDL on CD4+ T cells. We find that ox-LDL causes a shift towards a pro-inflammatory, cytokine-producing CD4+ T cell transcriptomic state. Concurrently, ox-LDL induces genome-wide changes in chromatin accessibility, notably in promoter regions. Multiomic data integration identifies a likely role for NRF1 and SP1 transcription factors in mediating ox-LDL-induced changes in gene expression. In contrast, the influence of AP-1 related factors over CD4+ T cell gene expression decreases following ox-LDL stimulation. We leveraged our multiomic data to investigate the disease-relevance of ox-LDL exposure, by investigating genomic locations where  CAD-associated single nucleotide polymorphisms were found within dynamic ox-LDL-regulated accessible chromatin regions. Together, we demonstrate a disease-relevant role for ox-LDL in atherogenic conditioning of CD4+ T cells. Understanding such cell-type specific interactions with CAD risk factors may facilitate the development of targeted therapies for CAD.

overall_design: Cells were treated for 48 hours with 50 µg/ml ox-LDL or an equivalent volume of control buffer. For ChIP-sequencing the MAGnify Chromatin Immunoprecipitation System (ThermoFisher, Waltham, Massachusetts, USA) was used in accordance with the manufacturer’s instructions with 2µl of antibody [total rabbit IgG or anti-H3K27ac (Abcam (Cambridge, UK) ab472)]. Sonicated but untreated lysates were used as an input control. DNA was purified with a Qiagen (Venlo, Netherlands) MinElute kit prior to TruSeq adaptor ligation.

first: Anil

last: Chalisey

first: Chris

last: O'Callaghan


title: Hereditary Chronic Pancreatitis Induced Plasticity Cooperates with Mutant Kras in Early Pancreatic Carcinogenesis

city: Halle (Saale)

first: Ferdinand

last: Krannich

address: Ernst Grube Street 40

department: Department of Internal Medicine I

institute: Martin Luther University Halle-Wittenberg, University Medicine Halle (Saale)

summary: Hereditary chronic pancreatitis (CP) increases the risk of pancreatic cancer, but the mechanisms by which chronic inflammation influences oncogene-driven pancreatic carcinogenesis remain poorly understood. A recently developed mouse model of CP, carrying the human Carboxypeptidase A1 (CPA1) p.N256K mutation, offers a valuable platform for uncovering the molecular processes linking chronic inflammation to pancreatic carcinogenesis. To investigate the impact of chronic inflammation on pancreatic cancer initiation, we crossed Cpa1N256K mice (Cpa1) with the pancreatic cancer model Ptf1aCre;KrasLSL-G12D (KC). In Cre, Cpa1, KC and KC-Cpa1 mice, we performed phenotypic characterization at different ages using histological, RNA sequencing and single-cell RNA-sequencing analyses.

overall_design: Single cells and total RNA from pancreata of Cre, Cpa1, KC and KC-Cpa1 mice were isolated at different ages.

first: TanviVikrant

last: Inamdar

first: Nico

last: Hesselbarth

first: Helmut

last: Laumen

first: Jonas

last: Rosendahl


title: Nonsense-mediated mRNA decay orchestrates neuronal migration and cortical lamination while modulating reelin and ciliary gene regulatory networks (snRNAseq)

city: Riverside

first: Sika

last: Zheng

address: University Ave 900

department: School of Medicine

institute: University of California, Riverside

summary: Nonsense-mediated mRNA decay (NMD) is associated with various neurodevelopmental disorders. Here, we demonstrate that NMD, mediated by UPF2, previously not linked to cortical organization, is indispensable for neuronal migration and cortical lamination. Conditional deletion of Upf2 in radial glial cells delays neuronal migration and disrupts cortical lamination. Trp53 knockout rescues microcephaly from Upf2 deficiency but cannot rescue lamination defects, showing that UPF2’s role in neuronal migration is uncoupled from its regulation of cell cycle and independent of p53. UPF2 deficiency downregulates key neuronal migration genes in the Reelin signaling pathway and microtubule assembly (e.g., Dab1, Lrp8, Tubb2b, Tuba1a), partly through upregulation of the transcriptional repressor Ino80. Additionally, NMD inhibition causes widespread upregulation of ciliary genes. Ectopic expression of Foxj1, a master regulator of ciliary genes and NMD target, impedes neuronal migration, mimicking the Upf2 knockout phenotype. Therefore, NMD is a central post-transcriptional mechanism that coordinates migration and ciliary gene networks crucial for cortical structure development, providing insight into how NMD dysfunction contributes to neurodevelopmental disorders.

overall_design: Comparative gene expression analysis for E17.5 control and Emx1-Upf2cKO cortices at single-nucleus resolution.

first: Lin

last: Lin

first: Naoto

last: Kubota


title: Stromal MTHFD2 orchestrates a fibrotic–inflammatory niche driving tumor growth and immune evasion

city: Seoul

first: Sangmyung

last: Rhee

state: --None--

address: 84, Heukseok-ro, Dongjak-gu, Seoul, Republic of Korea

institute: Chung-Ang University

summary: Cancer-associated fibroblasts (CAFs) are key drivers of fibrosis and immune suppression; however, the molecular basis linking these processes remains unclear. Here, we identified methylenetetrahydrofolate dehydrogenase 2 (MTHFD2) as a stromal metabolic regulator that integrates fibrotic activation with inflammatory signaling. Fibrotic cues, such as TGF-β and matrix stiffening, induced MTHFD2 expression in fibroblasts, whereas its knockdown reduced α-SMA expression and IL-6/IL-8 secretion. Overexpression enhanced IL-6 production, even without fibrotic stimulation. Single-cell RNA-seq data from non-small-cell lung cancer revealed elevated MTHFD2 levels across CAF subsets, independent of their myofibroblastic or inflammatory states. Mechanistically, MTHFD2 sustained NAD+–ROS signaling and induced mitochondrial stress with DNA release, activating the cGAS–STING–NF-κB pathway and promoting IL-6-dependent PD-L1 expression. Fibroblast-specific deletion of MTHFD2 suppressed tumor growth and reduced PD-L1 expression in vivo. These findings define MTHFD2 as a stromal metabolic–inflammatory switch and highlight stromal metabolism as a potential therapeutic target in desmoplastic cancers.

overall_design: We performed bulk RNA sequencing on human lung fibroblast MRC5 cells following stimulation with TGF-β1. Cells transduced with shRNA targeting MTHFD2 (shMTHFD2) were compared to control shRNA-transduced cells (shMock). This design enabled the assessment of transcriptional changes induced by MTHFD2 knockdown under fibrotic activation conditions.

first: Jung-Woong

last: Kim


title: Glucose metabolism regulates human cortical cell diversification and maturation

city: Tempe

first: Madeline

middle: Gail

last: Andrews

state: AZ

address: 550 E. Orange Street

department: School of Biological and Health Systems Engineering

institute: Arizona State University

summary: Defining metabolic regulation of progenitor expansion and neurogenic differentiation is essential to understand and treat neurodevelopmental disorders driven by metabolic alterations  that have life-long impact on neurological health. In vitro cultures are the only method to temporally study and molecularly manipulate living human brain cells. However, all current cell culture conditions use supraphysiological levels of glucose and oxygen, compared to the developing brain. In our studies, we probed how environmental exposure to endogenous-like concentrations of glucose and oxygen affect metabolic state and developmental progression of human cortical cell types by using pluripotent stem cell (PSC)-derived organoids. In addition to functional assays and immunolabeling, we conducted single cell RNA sequencing of cortical organoids exposed to varying glucose and oxygen conditions using a 10x single cell genomics pipeline.

overall_design: Cortical organoids were exposed to standard culture conditions (18 mM glucose media incubated in 20% oxygen) or experimental culture conditions which consisted of a mix of glucose and oxygen conditions (18 mM glucose at 8% oxygen, 5 mM glucose at 8% oxygen, and 5 mM glucose at 20% oxygen). The 5 mM medias are DMEM/F12 (shortend to DMEM), Plasmax, and RPMI, while the control media is DMEM/F12 (shortened to DMEM) with standard glucose concentrations (18 mM). The DMEM and RPMI with 5 mM media was created by adding 5 mM of glucose to a special ordered basal medium containing no glucose. The Plasmax basal media is manufactured with 5 mM glucose at baseline. Organoids across three PSC lines were exposed to the media and oxygen conditions for 6 or 10 weeks in culture and then captured for single cell RNA analysis, resulting in 36 experimental samples collected.

first: Taylor

middle: R

last: Pennington

first: Alexandria S

last: Morales

first: Ammar

last: Mehdi

first: Sophia

last: Cerna

first: Gradi

last: Bamfonga

first: Alicia

last: Saarinen

first: Fabiha

last: Firoz

first: Tran

last: Ngyuen

first: Sierra

last: Wilferd

first: Christopher

last: Plaisier

first: Benjamin

last: Bartelle

first: Haiwei

last: Gu

first: Clifford

last: Folmes

middle: G


title: The innate thermogenic capacity of brown adipose tissue develops independently of sympathetic signaling

city: Philadelphia

first: Patrick

last: Seale

state: PA

address: 3400 Civic Center Blvd., SCTR 12th Floor

institute: University of Pennsylvania

summary: Brown adipose tissue (BAT) dissipates energy as heat in response to β-adrenergic signaling induced by the sympathetic nervous system (SNS). While this pathway is essential for the cold-induced remodeling and metabolic activity of BAT, its role in developmental programming is unclear. Here, we show that brown adipocytes acquire thermogenic identity during embryogenesis independently of sympathetic innervation and β-adrenergic signaling. Genetic sympathectomy or disrupted β-adrenergic signaling had minimal effects on thermogenic gene expression or tissue morphology during either embryonic or postnatal BAT development in the absence of cold stress. Functional analyses revealed that the SNS is likely required for circulatory support of BAT activity during β-adrenergic stimulation but not for the development of the thermogenic capacity of BAT itself. These findings demonstrate that developmental and cold-responsive BAT remodeling are mechanistically distinct processes. Defining the molecular programs that drive BAT development may reveal new strategies to enhance BAT formation and function without relying on β-adrenergic stimulation.

overall_design: Total RNA of BAT from E15.5-E18.5 embryos and P0.5 neonates was isolated using TRIzol and purified using PureLink RNA Mini columns (Invitrogen #12183025). Library preparation with poly(A) selection and Illumina sequencing were completed by Azenta/GENEWIZ.

first: Ethan

middle: C

last: Fein


title: Zinc Finger and BTB Domain Containing 32 (Zbtb32) transcription factor promotes CD8+ T cell differentiation and function in cancer [ChIP-Seq]

first: Birui

last: Pan

address: Shuang qing road, haidian district

institute: Tsinghua university

summary: In the tumor microenvironment (TME), “exhausted” CD8+ T cells are classified into progenitor (Tpex) and terminally exhausted (Ttex) populations. Tpex cells could be reinvigorated during immune checkpoint blockade (ICB) therapy. However, the mechanisms governing the differentiation of Tpex to Ttex remain not well understood. In this study, we identified that Zinc Finger and BTB Domain Containing 32 (Zbtb32) transcription factor, highly expressed in CD8+ Ttex subset, plays a critical role in regulating CD8+ T cells within tumors. Zbtb32, regulated by CD28 signaling, promotes the differentiation of CD8+ T cells into Ttex subset, enhancing their cytotoxicity, proliferation and anti-tumor capability. Importantly, we found a competitive DNA binding between Zbtb32 and Bcl6, another Zbtb family member promoting the Tpex program, especially in regulation of Id2 expression. Thus, our findings underscore the pivotal role of Zbtb32 in CD8+ T cell anti-tumor function, with implications in cancer immunotherapy.

overall_design: Chromatin immunoprecipitation DNA-sequencing (ChlP-seg) for Zbtb32 of CD8+ T cells transfected with Zbtb32-HA-GFP overexpressing plasmid in vitro. Chromatin immunoprecipitation DNA-sequencing (ChlP-seg) for Zbtb32 of CD8+ T cells transfected with Zbtb32-HA-GFP or Zbtb32-HA-GFP and Bcl6-RFP overexpressing plasmid in vitro.

first: Ruifeng

last: Li

first: Xiaohong

last: Zhao

first: Chen

last: Dong


title: Paracrine stimulation of brown adipose tissue vascularization by adipocyte O-GlcNAc signaling

city: JiNan

first: luwen

last: li

state: Shandong

address: Shandong University Baotuquan Campus, Baotuquan Subdistrict, Lixia District, Jinan City, Shandong Province, China

institute: Shandong University

summary: Brown adipose tissue (BAT) is extensively vascularized, which is essential for its physiological activities. The molecular mechanism that underpins BAT vascularization, however, remains poorly understood. This study presents evidence that acute cold exposure induces an elevation in total protein O-linked β-N-acetylglucosamine modification (O-GlcNAcylation) in BAT. Ablation of O-GlcNAc transferase in brown adipocytes drastically impairs BAT vascularization. Mechanistic studies demonstrate that O-GlcNAcylation of specificity protein 1 (SP1) in brown adipocytes enhances its transcriptional activity towards kielin/chordin-like protein (Kcp). Secreted KCP subsequently promotes BAT angiogenesis by paracrine activation of BMP signaling. Furthermore, boosting O-GlcNAc signaling with glucosamine supplementation effectively augments BAT vascularization and thermogenesis. These findings thus uncover a previously unrecognized role of adipocyte O-GlcNAc signaling in the metabolism-driven regulation of BAT vascularization and function.

overall_design: The samples were derived from brown adipose tissue (BAT) of  wild-type (WT) mice and brown adipocyte-specific OGT knockout mice.

first: Luwen

first: Liwei

first: Yaping

last: Shan

first: Jintang

last: Xie

first: Ting

last: Song

first: Sai

last: Zhang

first: Yun

last: Kong

first: Shiqi

first: Chengwei

first: Die

last: Hu

first: Weijia

last: Wang

first: Yunfan

last: Yang


title: Deoxynivalenol(DON)  and  related compounds target protein processing to induce immunotoxic effects in human T cells and macrophages [M2]

first: Hui

address: 7 Panjiayuan Nanli, Room314

department: Department of Toxicology

institute: China National Center for Food Safety Risk Assessment (CFSA)

summary: Deoxynivalenol (DON) is a fungal toxin mainly produced by Fusarium graminearum and Fusarium graminearum, and is present in cereal crops such as wheat, barley, oats, rye, and corn. It is widely polluted worldwide. DON and its related derivatives have a wide range of toxic effects on humans and animals. This study used zebrafish models and different cell models to verify the toxic effects of DON, and explored the mechanism of DON mediated Jurkat apoptosis and inhibition of M2 macrophage differentiation. The results indicate that the toxic effects of these fungal toxins differ significantly among various cell types. For Jurkat T cells, the IC50 values of DON, NIV, 15 Ac DON, and 3-Ac DON were 488.6 nM, 318.2 nM, 544 nM, and 6516 nM, respectively. There are significant differences in the effects on M2 polarization of macrophages, and DON, NIV, and 15 Ac DON can inhibit M2 differentiation and function of macrophages at lower dose levels. Indicating that immune toxicity is an important toxic effect of DON and its related substances. Research on its mechanism has shown that DON can target protein processing processes, interfere with the normal synthesis and folding of proteins in cells, and trigger cellular stress responses. These findings reveal the toxic effects and potential mechanisms of DON on human immune cells, providing a scientific basis for preventing and controlling DON pollution and its harm to human health.

overall_design: Study the immunotoxicity of DON and its related substances using Jurkat T cells and M2 macrophages. Total RNA was extracted using TRIzol for transcriptome sequencing, and three biological replicates were set for Jurkat T cells and M2 macrophages.

first: Ying

last: yang

last: wang

first: Lijuan

last: You

first: Qiannan

last: zhang

first: Xudong

last: Jia


title: Chronic NK cell activation results in a dysfunctional, tissue resident-like state mediated by KLF2 deficiency

city: Providence

first: Jacob

middle: Andrew

last: Myers

state: RI

address: 171 Meeting St.

institute: Brown University

summary: Adoptive transfer of NK cells can induce complete remissions in 30-50% of patients with refractory acute myeloid leukemia and lymphoma. While blood chimerism occurs, attaining functional homing to the site of tumor without exhaustion has been elusive. During chronic infections and tumorigenesis, exposure to activating stimuli weakens the effector activity of NK cells. Despite this knowledge, there is little known about the mechanisms that govern this dysregulation and whether these disparate activating stimuli use distinct pathways to downregulate effector immunity. In this study, we reveal that chronic NK cell activating receptor (NKAR) stimulation and chronic IL-15 exposure impart distinct modes of dysregulation, with NKAR stimulation inducing a tissue resident-like state that resembles that of tumor-infiltrating NK cells in cancer patients. Using loss- and gain-of-function studies, we identify the transcription factor KLF2 as a master regulator of the NK cell response to chronic activation and provide evidence that KLF2 overexpression promotes NK cell cytotoxicity, cytokine production, and chemotaxis, and inhibits the development of dysfunctional, tissue resident-like features. Using KLF2 reporter mice, we show that in certain tissues, tissue resident NK cells are predominantly KLF2-negative while circulating NK cells in these tissues are overwhelmingly KLF2 + . Lastly, using mixed bone marrow chimeras, we demonstrate that conditional KLF2 deficiency in NK cells leads to altered homing and the acquisition of tissue resident-like features in vivo. Together, these findings highlight the profound changes NK cells undergo during prolonged activation and advance our understanding of how some NK cell therapies fail during malignant relapse.

overall_design: Details of experimental design can be found within the associated publication. There are datasets from two separate figures in this directory. The following is a summary of design for the data in Figure 2: in brief, NK cells from healthy human donor peripheral blood mononuclear cells (PBMCs) were isolated and stimulated with either NK cell activating receptor (NKAR) agonists (i.e. anti-NKp46 and MICA/B) or IL-15 for 4 or 10 days. 10 day stimulations were performed with either continuous IL-15 or with a 2-day (days 5 and 6) reduction in the concentration of IL-15. The following is a summary of design for the data in Figure 4: in brief, human NK cells were isolated as previously described and expanded using K562 leukemia cells expressing membrane-bound IL-21 and 4-1BB-L. Following expansion, NK cells were transduced with AAV vectors carrying either a control insert (mNG) or KLF2-overexpression vector (KLF2-mNG). Following transduction, cells were stimulated for 4 days on control or NKAR-agonist plates as previously described. Cell samples were also collected post-transduction, but prior to plate-bound activation.

middle: A


title: Examining the effect of oxLDL on CD4+ T cell chromatin accessibility

first: Toby

last: Brown

overall_design: Cells were treated for 48 hours with 50 g/ml OxLDL or similar volume of buffer solution. For ATAC-sequencing, samples were repeatedly centrifuged before nuclear pellets were suspended in a transposition reaction mix (25 l 2x TD buffer (from Illumina DNA sample preparation kit), 2.5 l hyperactive Tn5 transposase (from Illumina DNA sample preparation kit), and 22.5 l nuclease-free water) and incubated for 30 minutes at 37C. Transposed DNA was purified with the Qiagen MinElute kit and amplified by PCR.

first: Anil

last: Chalisey

first: Chris

last: O'Callaghan


title: Deoxynivalenol(DON)  and  related compounds target protein processing to induce immunotoxic effects in human T cells and macrophages [Jurkat]

first: Jing

first: Xiaohong


title: Systemically inducing trained immunity overcomes solid tumors’ immunosuppressive microenvironment. [scMULTIome]

city: Amsterdam

first: Lisa

last: Willemsen

address: Meibergdreef 9

country: Netherlands

institute: Amsterdam UMC - locatie AMC

summary: scATACseq on the bone marrow of mice with and without a B16F10 tumor.

overall_design: Bone marrow was isolated from femurs. scATACseq was performed using 10x Genomics scMULTIome.

first: Bram

last: Priem

first: Menno

last: de Winther

first: Willem

last: Mulder


title: Systemically inducing trained immunity overcomes solid tumors’ immunosuppressive microenvironment

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

overall_design: Refer to individual Series


title: Nonsense-mediated mRNA decay orchestrates neuronal migration and cortical lamination while modulating reelin and ciliary gene regulatory networks (RNAseq)

first: Sika

last: Zheng

overall_design: Comparative gene expression analysis for E18.5 control and Emx1-Upf2cKO cortices.

first: Lin

last: Lin

first: Naoto

last: Kubota


title: PLPP1 suppreses breast cancer tumor growth

city: Plainsboro

first: Yong

last: Wei

state: NJ

address: LTL227 Wathington Road

department: Molecular Biology

institute: Princeton University

summary: PLPP1 is kncoked down by shRNA in SUM159, a triple negative breast cancer cell line, and the resulting transcriptome change are investigated.

overall_design: The biological replicates of the pair of samples of SUM159 expressing shRNA targeting PLPP1 and non-targeting control.

first: Li

last: Zhuo

first: Wei

last: Yong


title: Oxidised LDL induces pro-inflammatory transcriptomic and epigenomic responses in human CD4+ T cells

summary: Comprehensive multiomic profiling of the CD4+ T cell response to ox-LDL. Individual experimental design is described in more detail in the subseries.

overall_design: 50ml of peripheral blood was obtained from healthy volunteers by venesection and density centrifugation was used to isolate peripheral blood mononuclear cells (PBMCs). PBMCs were then incubated with CD14 microbeads to isolate and remove the blood monocyte population. Unbound cells were incubated with CD4 microbeads prior to activation with bead-bound anti-CD3 and anti-CD28 at 37⁰C. Ox-LDL was prepared as described previously from fresh human blood. Following activation, cells were treated for 48 hours with 50 µg/ml ox-LDL or an equivalent volume of control buffer. Library preparation was performed as described within the subseries.


title: Examining the effect of oxLDL on CD4+ T cell gene expression

overall_design: Cells were treated for 48 hours with 50 µg/ml ox-LDL or an equivalent volume of control buffer. For RNA-sequencing, RNA was extracted with TRIzol and the PureLink RNA mini kit (Invitrogen, Waltham, Massachusetts, USA) following the manufacturers’ instructions. Illumina (San Diego, CA, USA) reverse-stranded TruSeq library preparation with polyA selection was performed prior to sequencing.


title: Zinc Finger and BTB Domain Containing 32 (Zbtb32) transcription factor promotes CD8+ T cell differentiation and function in cancer [RNA-Seq]

first: Birui

last: Pan

overall_design: Naive Zbtb32-/- and WT OT-I cells were co-transferred into B6 recipient mice one day prior to sub-cutaneous implantation of B16-OVA tumor cells. 30 days later, Zbtb32-/- and WT OT-I cells amongst tumor infiltrating lymphocytes (TILs) were flow sorted. Total RNA was extracted for RNA-seq. Naive Zbtb32-/- and WT OT-I cells were co-transferred into B6 recipient mice one day prior to sub-cutaneous implantation of B16-OVA tumor cells. 30 days later, Tim-3+ Ttex subsets of Zbtb32-/- and WT OT-I cells amongst tumor infiltrating lymphocytes (TILs) were flow sorted. Total RNA was extracted for RNA-seq.

last: Zhao

first: Ruifeng

last: Li

first: Chen

last: Dong


title: Systemically inducing trained immunity overcomes solid tumors’ immunosuppressive microenvironment. [scRNA-Seq]

summary: scRNAseq on B16F10 tumors of mice.

overall_design: Viable CD45+ cells were isolated from B16F10 tumors of mice by flow cytometry. 10X scRNAseq was performed subsequently.


title: Surface marker identification to capture live circulating tumor cells in metastatic triple negative breast cancer

city: Houston

first: Bree

last: Lege

state: TX

address: one baylor plaza

department: Lester and Sue Smith Breast Center

institute: Baylor College of Medicine

summary: Metastatic triple-negative breast cancer (TNBC) is highly aggressive and lacks targeted therapies. Circulating tumor cells (CTCs) are invaluable for monitoring metastatic tumor progression and treatment response but are difficult to capture due to their rarity and heterogeneity. Surface-based staining for live CTCs is essential to preserve RNA quality in single cells, but current markers tend to perform poorly on more mesenchymal tumor cells such as TNBCs. To enhance live TNBC CTC detection, we developed a workflow for live CTC capture and single-cell RNA sequencing (scRNAseq). Using a mouse model of metastatic TNBC, we identified four new CTC surface markers, AHNAK2, CAVIN1, ODR4, and TRIML2, that specifically stain tumor cells. Combining antibodies against these markers improved CTC detection rates in multiple TNBC mouse models and patient samples. Also, combining these new markers with traditional CTC surface markers enhanced detection sensitivity, achieving the highest CTC coverage. This approach identifies diverse CTC populations, while preserving RNA quality for scRNAseq, which is essential for understanding and therapeutically targeting metastatic breast cancer.

overall_design: Single cell sequencing via SMARTseq2 of MDA-MB-231-LM2 cell culture cells and circulating tumor cells (CTCs) isolated from mice implanted with MDA-MB-231-LM2 cells in the mammary fat pad and allowed to spontaneously metastasize.

first: Chonghui

last: Cheng


title: Silencing lipid catabolism determines longevity in response to fasting

status: Public on Dec 19 2025

city: Dallas

first: Peter

last: Douglas

state: Texas

address: 6000 Harry Hines Blvd

department: Department of Molecular Biology

institute: University of Texas Southwestern Medical Center at Dallas

summary: Oscillations between lipid anabolism and catabolism allow for long-term preservation of cellular health amid systemic metabolic fluctuations. As a conserved aging determinant, fasting can improve disease outcomes and extend lifespan. Yet, the relative importance of activating lipid catabolism versus its attenuation in fasting-induced longevity remains unclear. The robust adaptability of the soil-dwelling worms, C. elegans, to variable nutrient availability provides an excellent means to better understand how metabolic transitions alter aging trajectories. Here, we show that, rather than activation, the silencing of lipid catabolism upon nutrient replenishment is essential for lifespan extension through fasting. The fasting-responsive nuclear hormone receptor, NHR-49, is pivotal in activating lipid catabolism through β-oxidation. Unlike traditional ligand-regulated nuclear hormone receptors, NHR-49 employs a unique regulatory mechanism that bypasses ligand binding, instead relying on cofactors to mediate its transcriptional attenuation and turnover during times of nutrient stress. Here, we identify casein kinase 1 alpha 1 (KIN-19) as a central regulator of metabolic plasticity and fasting-induced longevity, which attenuates β-oxidation via primed phosphorylation of NHR-49. Overall, cooperative, ligand-independent silencing of this conserved nuclear hormone receptor promotes longevity associated with fasting.

overall_design: RNAseq profiling of N2 C.elegans were collected at Day 1 under empty vector control RNAi or kin-19 RNAi

first: Lexus

last: Tatge


title: Silencing lipid catabolism determines longevity in response to fasting [fasting RNA-Seq]

overall_design: RNAseq profiling of N2 C.elegans were collected at Day 1 (fed), Day 2 (24 hours fasted), and Day 3 (24 hours refed).


title: Plpp1 protects MaSC (mammary stem cell) from malignant proliferation

summary: Mammary stem cell enriched subpopulations P4 (CD24+CD29hi) and luminal progenitor subpopulation P5 (CD24+CD29lo) were sorted from mammary gland from adult wild type C57BL6 mice and Plpp1 KO mice. The trascriptome profiles are determined and compared. In addition, P4 and P5 cells were sorted from ex vivo cultured mammary gland tissues with and without LPA treatment, the effects of LPA stimulation is investigated.

overall_design:
The 1st set is triplicate of 4 groups MEC subpopulation samples of two variables combination (P4, P5) x Plpp1(+/+, -/-);
The 2nd set is two subpopulations (P4,P5) from 3D ex vivo culture of mammary gland samples with LPA treatment comparing to vehicle control


title: Idelalisib and pneumococcal infection induce distinct transcriptional responses in mouse precision-cut lung slices

city: South San Francisco

first: Jerome

last: Bouquet

address: 121 oyster point blvd

department: integrated Bioanalysis

institute: AstraZeneca

summary: Idelalisib has excellent activity in management of chronic lymphocytic leukemia and follicular lymphoma while inducing serious microbial pneumonia in the clinic. To understand the mechanisms of Idelalisib-induced infection risk, we performed RNAseq analyses on mouse precision-cut lung slices treated with Idelalisib in the absence and presence of human lung pathogen Streptococcus pneumoniae. RNAseq transcriptome profiling identifies distinct response signatures in mouse lung slices in responses to Idelalisib treatment and pneumococcal infection. The expression of genes vital for regulation of transcription, immunity and inflammation, cell proliferation and apoptosis, kinase signaling, metabolism, and extracellular matrix remodeling is significantly modulated by Idelalisib. This study provides a new insight for predicting the immunomodulatory impact of drug candidates on host defense and thereby improving the safety profiling of novel drugs for human respiratory diseases.

overall_design: RNAseq was conducted on mouse lung precision cut lung slices treated with Idelalisib for 2h then infected or not with Streptococcus pneumoniae for 6h.

first: Liu

last: Guanghui

first: Kinga

last: Balogh Sivars

first: Taylor

last: Cohen

first: Catherine

last: Betts

first: Susan

last: Busch

first: Johanna

last: Sagemark


title: Fission yeast Whi5 represses MBF-dependent transcription in quiescent cells II

city: Salamanca

first: Sergio

last: Moreno

email: smo@usal.es, ibfg_smp@usal.es

state: Salamanca

address: Zacarias Gonzalez 2

department: IBFG

country: Spain

institute: Institute of Functional Biology and Genomics (IBFG) (CSIC)

summary: When cells arrest the cell cycle in G1 to enter the non-dividing quiescent state, the transcriptional machinery that promotes G1/S transition must be inactivated. Central to this regulation is Whi5, in budding yeast, and the Retinoblastoma (Rb) protein, in mammalian cells, acting as repressors of the transcription factors SBF, and E2F, respectively. In fission yeast, the MBF complex is the functional homologue of E2F in metazoans. Fission yeast Whi5/Mug54 is an uncharacterized protein predicted to function as a cell cycle transcriptional repressor at the G1/S transition. In this work, we show that after induction of quiescence by nitrogen starvation, fission yeast Whi5 is localised to the nucleus, and it is required for the repression of MBF-dependent genes. Mass spectrometry and bimolecular fluorescence complementation (BiFC) analyses revealed that Whi5 physically interacts with components of both the MBF and the histone deacetylase Clr6-I complexes. Moreover, Whi5 is required for the interaction of the MBF complex with Clr6-I, suggesting a role for Whi5 in maintaining transcriptional repression of MBF-dependent genes in quiescent cells by the recruitment of HDACs to gene promoters.

overall_design: We performed a comparative analysis of gene expression profiles from RNA-seq data between wild-type cells and the mutants whi5∆, nmt41-whi5+, nrm1-3xsAID and nrm1-3xsAID whi5∆ growing in minimal medium (MM) and in minimal medium lacking nitrogen (MM-N) after 24 hours.

first: Celia

last: Gálvez-Merchán

first: Rafael

last: López-San Segundo

first: M. Belén

last: Suárez

first: Daniel

last: González-Ávarez

first: José

last: Ayte

first: Livia

last: Pérez-Hidalgo


title: Aging-dependent dysregulation of EXOSC2 is maintained in cancer as a dependency

city: Los Angeles

first: Kitai

last: Kim

state: California

address: 650 Charles E Young Drive South

institute: UCLA

summary: Reprogramming of aged donor tissue cells into induced pluripotent stem cells (A-iPSC) preserved the epigenetic memory of original aged-donor tissue, defined as genomic instability and poor tissue differentiation in our previous study. The unbalanced expression of RNA exosome subunits affects the RNA degradation complex function and is associated to geriatric diseases including premature aging and cancer progression. Here, we hypothesized that the aging-dependent progressive subtle dysregulation of EXOSC2 (exosome component 2) causes the aging-traits (abnormal cell cycle & division and poor tissue differentiation). We used the embryonic stem cells  as a unique tool to study EXOSC2 function as the aging-trait epigenetic memory determined in A-iPSC because these aging-traits could not be studied in senesced aged cells or immortalized cancer cells. We found that the regulatory subunit of PP2A phosphatase, PPP2R5E, is a key target of the EXOSC2 and controls the microtubule polymerization. We also validated these aging-traits as a dependency in a mouse model of colon carcinogenesis.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for ESC cells and its KD derivatives (shEXOSC2).

first: Maria

last: Skamagki

first: Hu

last: Li

first: Matt

last: Bott


title: Deoxynivalenol(DON)  and  related compounds target protein processing to induce immunotoxic effects in human T cells and macrophages [Zebrafish]

first: Hui

last: Yang

overall_design: Study the immunotoxicity of DON and its related substances using Jurkat T cells and M2 macrophages. Total RNA was extracted using TRIzol for transcriptome sequencing, and three biological replicates were set for Jurkat T cells and M2 macrophages.

first: Ying

first: Xiaohong

last: Wang

first: Lijuan

last: You

first: Qiannan

last: Zhang

first: Xudong

last: Jia


title: Fission yeast Whi5 represses MBF-dependent transcription in quiescent cells

first: Sergio

overall_design: We performed a comparative analysis of gene expression profiles from RNA-seq data between wild-type cells and the mutant whi5∆ growing in minimal medium (MM) and in minimal medium lacking nitrogen (MM-N) after 10 and 24 hours.


title: High-resolution in vivo binding data show that TBP initiates transcription at TATA promoters with and without TFIID [RNA-seq]

city: Kansas City

first: Melanie

last: Weilert

state: MO

institute: Stowers Institute for Medical Research

summary: This study investigates how the general transcription factor TFIID binds to different core promoter types in vivo. We performed high-resolution ChIP-nexus for all 14 subunits of the Drosophila TFIID complex (TBP and TAF1 to TAF13), as well as for NC2α, NC2β, and Mot1, under both DMSO (control) and Triptolide treatments to capture various transcriptional states.The goal of the study was to define TFIID's in vivo architecture and compare its function across promoters. We show that TBP binding is promoter-specific, enabling de novo classification of TATA, DPR, and housekeeping promoters. We provide in vivo evidence for TAF-independent transcription initiation specifically at TATA promoters, which correlates with NC2 binding and offers a mechanistic explanation for their distinct transcriptional bursting properties.

overall_design: Total mRNA from Drosophila melanogaster Kc167 cells.

last: G-M Alcantara

first: Simon

last: Bourdareau

first: Julia

last: Zeitlinger


title: Zinc Finger and BTB Domain Containing 32 (Zbtb32) transcription factor promotes CD8+ T cell differentiation and function in cancer [ATAC-seq]

city: Beijing

first: Birui

last: Pan

overall_design: ATAC-seq of WT and Zbtb32-/- OT-I cells from B16-OVA tumors at day 30 post inoculation

last: Zhao

first: Chen

last: Dong


title: High-resolution in vivo binding data show that TBP initiates transcription at TATA promoters with and without TFIID [ChIP-nexus]

summary: This study investigates how the general transcription factor TFIID binds to different core promoter types in vivo. We performed high-resolution ChIP-nexus for all 14 subunits of the Drosophila TFIID complex (TBP and TAF1 to TAF13), as well as for NC2α, NC2β, and Mot1, under both DMSO (control) and Triptolide treatments to capture various transcriptional states.The goal of the study was to define TFIID's in vivo architecture and compare its function across promoters. We show that TBP binding is promoter-specific, enabling de novo classification of TATA, DPR, and housekeeping promoters. Crucially, we provide in vivo evidence for TAF-independent transcription initiation specifically at TATA promoters, which correlates with NC2 binding and offers a mechanistic explanation for their distinct transcriptional bursting properties.

overall_design: ChIP-nexus of General Transcription Factors in Drosophila melanogaster Kc167 cells. Cells are treated with either DMSO (control) or 10 µM triptolide for 1 hour at room temperature. Non treated samples have not been treated for 1h with DMSO.


title: Skeletal Muscle Methylome-Transcriptome Disruptions During the Onset and Progression of Colorectal Cancer-Induced Cachexia

city: Fayetteville

first: Nicholas

middle: P

last: Greene

state: Arkansas

address: 155 Stadium Dr. HPER Building 321

institute: University of Arkansas

type: Methylation profiling by high throughput sequencing

summary: Cancer cachexia (CC) is experienced by 80% of cancer patients, representing up to 40% of cancer-related deaths. Evidence suggests biological sex dimorphism associated with CC. The initial triggering factors of muscle wasting, biological sex differences, and the epigenetic regulation during the onset and progression of cancer cachexia are not fully understood. The purpose of this study was to define the time course of C26-induced CC in males and females using transcriptomics, compare the transcriptomic changes with a more sever APC+/Min genetic model and identify the impact of epigenetic regulations (methylation) associated to CC.

overall_design: At week-old Balb/c male and female mice (n=6-8/group) receivd 1x10^6 C26 cells injected bilateral, and tumors were developed for 10-, 20-, and 25-days, at endpoints, Tibialis Anterior (TA) muscle were collected.  The control mice received PBS injections  and TAs were colllected 25-days after PBS injections (controls). TA was also collected from 20-weeks-old APC+/Min mice (C57 black mice background) and their wild types (controls). DNA was extracted for RRBS.

first: Nicholas P.

first: Kevin A.

last: Murach

first: Ana Regina

last: Cabrera


title: Optimized multidrug therapy remodels the tumor microenvironment and enhances antitumor immunity in microsatellite-stable colorectal cancer

city: Lausanne

first: Maxim

last: Norkin

address: SV Station 19

institute: EPFL

summary: Four low-dose tyrosine kinase inhibitor (TKI)–based ODCs were evaluated in murine AKP CRC organoids, co-culture systems with tumor-associated endothelial cells and immune cells, and in vivo syngeneic models. Among these, ODCDLD1 (regorafenib, vemurafenib, erlotinib HCl, selumetinib) showed the most potent inhibition of tumor organoid viability (∼90%), promoted leukocyte infiltration in co-cultures, and significantly upregulated endothelial adhesion molecules (ICAM-1, VCAM-1, E-selectin). In vivo, ODCDLD1 reduced tumor growth comparably to oxaliplatin but with a favorable toxicity profile. Immunofluorescence analysis revealed that both ODCDLD1 and oxaliplatin significantly reduced the population of proliferating cancer cells. Furthermore, ODCDLD1-based treatment recapitulated transcriptomic findings by showing a significant reduction in proliferating myofibroblasts, a key stromal component. Bulk RNA sequencing revealed that ODCDLD1, especially when combined with anti-PD-1, induced an immunologically “hot” tumor microenvironment characterized by enhanced immune cell recruitment, reduced fibroblast and stem-like cell signatures, and upregulation of endothelial markers.

overall_design: CRC AKP sc tumors derived from mice treated with different drug combinaitons

first: Pablo

middle: H

last: Lopez

first: Patrycja

last: Nowak-Sliwinska


title: HIV inhibits Warburg metabolism in human macrophages infected with Mycobacterium tuberculosis

city: Dublin

first: Gina

last: Leisching

address: St James's Hospital, Trinity College Dublin

country: Ireland

institute: Trinity Translational Medicine Institute

overall_design: Using the U1 chronically HIV-infected macrophage cell line model coupled with primary human monocyte-derived macrophages (MDMs) exposed to HIV-1 gp120, we systematically characterized transcriptomic and immunometabolic perturbations during Mtb infection.

first: Aaron

last: Walsh


title: Deubiquitinase USP20 promotes breast cancer metastasis by stabilizing SLUG

first: Yong

last: Wei

summary: In the lung metastatic breast cancer MDA-MB231 subline LM2 cells, knockdown of USP20 results in similar changes of a list of migration/invasion-related genes as knockdown of SLUG, and SLUG protein is identified as a target of USP20 for deubiquitination.

overall_design: Breast cancer cell line LM2 cells were transfected with siRNAs targeting USP20, SLUG or non-targeting control, and the transcriptome profiles were determined by microarray. Samples are prepared in duplicates.

first: Li

last: Wenyang

first: Wei

last: Yong


title: RNA Decay via the Nuclear Exosome is Essential for Piwi-Mediated Transposon Silencing

city: Vienna

first: Julius

middle: Fabian

last: Brennecke

address: Dr. Bohr Gasse 3

country: Austria

institute: IMBA-Institute for Molecular Biotechnology

summary: Small RNA pathways in the nucleus safeguard genome integrity by directing transcriptional silencing and heterochromatin formation at transposon loci. Yet, how these pathways achieve effective repression despite requiring transcription for Argonaute targeting has remained unclear. Here, we show that in Drosophila, the Piwi–piRNA pathway enforces transposon silencing through RNA degradation by the nuclear RNA exosome. Using comprehensive proximity proteomics at piRNA target sites combined with genetic analyses, we identify two previously uncharacterized paralogs, TEsup-1 and TEsup-2, which connect Piwi to nuclear exosome adaptor complexes via a distinct binding module for proline-rich peptides. Disruption of this Piwi–TEsup–exosome axis leads to accumulation and nuclear export of transposon RNAs. Strikingly, transposons that evade heterochromatin-based repression, exemplified by the P-element, are repressed primarily through this RNA-decay pathway. These findings reveal a molecular mechanism by which the nuclear piRNA-pathway couples target recognition to RNA degradation, providing a framework that reconciles small RNA-guided heterochromatin formation with ongoing transcription at target loci.

overall_design: Small RNA Sequencing (small-RNA-seq) analyis of small RNA expression changes in fly ovaries after shRNA mediated depletion of CG31510, CG7065, compring to control knockdown.

first: Changwei

last: Yu

first: Toni

last: Manolova

first: Laszlo

last: Tirian

first: Dominik

last: Handler

first: Ulrich

last: Hohmann

first: Filip

last: Nemčko

first: Júlia

last: Portell-Montserrat

first: Guillaume

last: Giraud Collet

first: Jakob

last: Schnabl

first: Ellie

last: Blake

first: Peter

last: Duchek

first: Maria

last: Novatchkova

first: Elisabeth

last: Roitinger

first: Felipe

last: Karam Teixeira

first: Sebastian

last: Falk


title: RNA Decay via the Nuclear Exosome is Essential for Piwi-Mediated Transposon Silencing [TT-seq]

overall_design: Transient transcriptome sequencing (TT-seq) analyis of nascent transrption changes in cultured ovarian somatic cells (OSCs) after siRNA mediated depletion of dZfc3h1, dZcchc7, dZcchc8, or dZfc3h1&dZcchc8, compring to control knockdown.


title: Single-cell mapping of regulatory DNA:Protein interactions IV

city: New York

first: Dan

last: Landau

address: 413 East 69th Street

institute: Weill Cornell Medicine

summary: Gene expression is coordinated by a multitude of transcription factors (TFs), whose binding to the genome is directed through multiple interconnected epigenetic signals, including chromatin accessibility and histone modifications. These complex networks have been shown to be disrupted during aging, disease, and cancer. However, profiling these networks across diverse cell types and states has been limited due to the technical constraints of existing methods for mapping DNA:Protein interactions in single cells. As a result, a critical gap remains in understanding where TFs or other chromatin remodelers bind to DNA and how these interactions are perturbed in pathological contexts. To address this challenge, we developed a transformative single-cell immuno- tethering DNA:Protein mapping technology. By coupling a species-specific antibody-binding nanobody to a cytosine base editing enzyme, this approach enables profiling of even weak or transient factor binding to DNA, a task that was previously unachievable in single cells. Thus, our Docking & Deamination followed by sequencing (D&D-seq) technique induces cytosine-to-uracil edits in genomic regions bound by the target protein, offering a novel means to capture DNA:Protein interactions with unprecedented resolution. Importantly, this technique can be seamlessly incorporated into common single-cell multiomics workflows, enabling multimodal analysis of gene regulation in single cells. We tested the ability of D&D-seq to record TF binding both in bulk and at the single-cell level by profiling CTCF and GATA family members, obtaining high specificity and efficiency, with clear identification of TF footprint and signal retention in the targeted cell subpopulations. Furthermore, the deamination reaction showed minimal off-target activity, with high concordance to bulk ChIP-seq reference data. Applied to primary human peripheral blood mononuclear cells (PBMCs), D&D-seq successfully identified CTCF binding sites and enabled integration with advanced machine-learning algorithms for predicting 3D chromatin structure. Furthermore, we integrated D&D-seq with single-cell genotyping to assess the impact of IDH2 mutations on CTCF binding in a human clonal hematopoiesis sample, uncovering altered binding and chromatin co- accessibility patterns in mutant cells. Altogether, D&D-seq represents an important technological advance enabling the direct mapping of TF or chromatin remodeler binding to the DNA in primary human samples, opening new avenues for understanding chromatin and transcriptional regulation in health and disease.

overall_design: Deamination of cytosine to uracil around DNA binding sites of a target protein using nanobody-tethered deaminase DddA11

first: Wei-Yu

last: Chi

first: Sang-Ho

last: Yoon

first: Evrim

last: Goksel

first: Levan

last: Mekerishvili

first: Joe

last: Pelt

first: Yiyun

last: Lin

first: Saravanan

last: Ganesan

first: Catherine

last: Potenski

first: Franco

last: Izzo

first: Dan A.

first: Ivan

last: Raimondi


title: RNA Decay via the Nuclear Exosome is Essential for Piwi-Mediated Transposon Silencing [RNA-seq]

first: Julius

last: Brennecke

overall_design: RNA-seq analysis of gene and transpable element expression changes in fly ovaries after shRNA mediated depletion of Piwi, CG31510, CG7065, CG31510&CG7065, CG31510 null, CG31510_delta_PRD, CG7065_delta_PRD, dZfc3h1&dZcchc7, dZfc3h1&dZcchc8, compring to corresponding control knockdown.

first: Changwei

last: Yu

first: Toni

last: Manolova

first: Laszlo

last: Tirian

first: Dominik

last: Handler

first: Ulrich

last: Hohmann

first: Filip

last: Nemčko

first: Júlia

last: Portell-Montserrat

first: Guillaume

last: Giraud Collet

first: Jakob

last: Schnabl

first: Ellie

last: Blake

first: Peter


title: RNA Decay via the Nuclear Exosome is Essential for Piwi-Mediated Transposon Silencing [ChIP-seq]

overall_design: Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) for histone modification H3K9me3 or Pol II in OSCs after siRNA mediated depletion of Piwi, CG31510 and/ or CG7065, compring to control knockdown.

last: Duchek

first: Maria

last: Novatchkova

first: Elisabeth

last: Roitinger

first: Felipe

last: Karam Teixeira

first: Sebastian

last: Falk


title: High-resolution in vivo binding data show that TBP initiates transcription at TATA promoters with and without TFIID

first: Melanie

last: Weilert

overall_design: Refer to individual Series


title: Molecular characterisation of circannual interval timing in the preoptic area and anteroventral periventricular nucleus in a rodent.

city: Glasgow

first: Calum

last: Stewart

address: Jarrett Building, University of Glasgow

institute: University of Glasgow

summary: Most temperate animals exhibit seasonal rhythms in reproductive physiology and behaviour. Gonadotropin-releasing hormone (GnRH) cells in the preoptic area (POA) and kisspeptin (Kiss) cells in the anteroventral periventricular (AvPv) nucleus are critical for timing photoperiod-induced changes in seasonal reproduction. In response to prolonged exposure to photoperiod cues, many rodents exhibit endogenously generated programmed changes in physiology that reflect a circannual timing mechanism. Here we used transcriptome sequencing coupled with high tissue sampling across a simulated circannual interval timer to characterise the molecular changes involved in the seasonal control of reproduction and body temperature. Adult male Djungarian hamsters were collected after exposure to short photoperiod on 4-week intervals from 4- to 32-weeks. The POA and AvPv transcriptomes from shot-photoperiod hamsters were compared to a long photoperiod reference group. Our analyses confirmed robust photoperiodic regulation of Kiss1 mRNA expression in the AvPv. Weighted gene co-expression network analyses (WGCNA) identified hundreds (POA: 211, AvPv: 415) of transcript that were associated with testes mass. Gene set enrichment analysis (GSEA) identified ‘gonadotropin secretion’ and ‘glial cell proliferation’ as the primary pathways associated with circannual interval timing. Vimentin had strong negative association with testes mass, indicating AvPv glial morphology increased during gonadal involution. In the POA, pathways associated with ‘regulation at synapse’ and ‘regulation of synaptic plasticity’ were highly enriched and transcripts positively associated with gonadal involution indicated that ribosomal plasticity and intracellular calcium signalling are key mechanisms involved in seasonal reproduction. WGCNA analyses identified 567 in the POA were significantly associated with surface body temperature. GSEA discovered thyrotrophin releasing hormone was significantly negatively associated with surface body temperature. Overall, the POA and AvPv transcriptome datasets provide the foundation to expand our understanding of the molecular representation of seasonal time in the mammalian hypothalamus.

overall_design: To investigate molecular changes occuring in the distinct regions of the hypothalamus. Siberian hamsters were held in long days (LD) or short days (SD) for up to 32-weeks. At 4-week intervals, animals were sacrificed  and hpyothalamic nuclei were dissected. Microdissections were homogenised and RNA was extracted using the RNEasy plus mini kit. following this transcript abundance was assesed using the cDNA-PCR sequencing kit (SQK-PCB109, Oxford Nanopore).

first: Christopher

last: Marshall

first: Tyler

middle: J

last: Stevenson


title: Glycogen synthase 2 knock-out zebrafish exhibit enhanced glucose metabolism in the liver

city: Minami-ku, Sagamihara

first: Fumiya

last: Furukawa

state: Kanagawa

address: 1-15-1, Kitazato

department: Marine Biosciences

institute: Kitasato University

summary: The liver is one of the major organs for glycogen storage and is essential for maintaining glucose homeostasis in the whole body. Glycogen synthesis in liver is regulated by the rate-limiting enzyme, glycogen synthase 2 (Gys2). In fish, however, the detailed roles of glycogen and Gys2 is poorly understood. In this study, we generated, for the first time, gys2 knock-out (gys2 -/-) zebrafish and evaluated the effects of impaired glycogen synthesis on physiological parameters of this fish. No effects on development or maturation were observed in gys2 -/- strain lacking Gys2. PAS staining, immunofluorescence staining with anti-glycogen antibody, and transmission electron microscopy (TEM) observations confirmed that glycogen synthesis does not occur in the gys2 -/- liver. However, glucoamylase treatment released higher amount of glucose from gys2 -/- liver extract than that of the wild-type (WT) counterpart, suggesting the existence of putative compensatory glucose polymer in the gys2 -/- liver. Liquid chromatography-mass spectrometry (LC-MS/MS) metabolite analysis and isotope tracing revealed a marked increase in the activity of glucose metabolism and levels of related metabolites in the livers of adult gys2 -/-. However, RNA-Seq analysis showed no corresponding changes in the expression levels of glucose metabolism–related genes. These results suggest that liver Gys2 is dispensable in zebrafish, and enhanced glucose metabolism and putative backup mechanism to accumulate extra glucose may support the fish lacking Gys2.

overall_design: Eight individuals of wild-type and gys2 mutant strains of the female zebrafish were sacrificed and the livers and muscles were subjected to bulk RNA-Seq analysis

first: Keita

last: Sameshima

first: Aya

last: Yokose

first: Yoshiki

last: Sato

first: Makoto

last: Kashima