title: Morphological innovation without gene co-option: the Drosophila sex comb evolved via changes in developmental tempo and energy metabolism

first: Ben

last: Hopkins

department: Evolution & Ecology

institute: UC Davis

summary: The individualization of serially repeated homologs is one route through which novel traits are thought to evolve. Under this model, a repeated character—like a limb, digit, or sensory bristle—is individualized from its homologs by changes in the regulatory apparatus (‘character identity network’, ChIN) that specifies its development. Individualization then enables downstream gene networks that build the repeated character to diverge from one another in different parts of the body, ultimately allowing new phenotypic endpoints to be reached. Despite this model’s intuitive appeal, the genetic mechanisms through which new ChINs rewire trait-building gene networks remain largely uncharacterized. A promising system in which to study this process is the Drosophila sex comb. Found in a sublineage of Drosophila species, the sex comb is a recently evolved, male-specific innovation that evolved from a more evolutionarily ancient precursor—the mechanosensory (MS) bristle—following the gain of a novel ChIN centered on the sex determination gene dsx and HOX gene Scr. Here, we use time-series single-cell RNA-seq to show that rather than co-opting new genes, this new ChIN orchestrates quantitative and heterochronic changes in the ancestral MS bristle transcriptome. These changes affect gene modules that control energy metabolism, endoreplication, and actin dynamics. The net effect of these changes is an organ-specific shift in developmental rate, leading to accelerated growth in sex comb teeth. Collectively, our work suggests that morphological innovation can proceed without the co-option of new genes into downstream trait-building networks and instead through metabolically driven differences in developmental rate between serial homologs.

overall_design:
First tarsal segment cells from pupal Drosophila melanogaster were isolated separately at different timepoints after puparium formation. Pupae are from a dsx-GAL4 > UAS-mCherry (12h, 20h, 36h), dsx-GAL4 > UAS-GFP (16h), or RAL-517 (24h, 30h) genotype. All samples are from males, except 12hF and 24hF. The raw 24h male and 30h male datasets were published as part of a previous paper and are accessible at NICBI GEO GSE215073. We include here the reprocessed 24h and 30h datasets as part of this submission.

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The table below lists GEO accessions reused/reanalyzed for this study.
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first: Olga

last: Barmina

first: Artyom

last: Kopp


title: Selective CDK7 Inhibition Sensitizes Tumors to Topoisomerase I Inhibitor-Antibody Drug Conjugates by Blocking The Transition of The RNA polymerase II Initiation Complex into Elongation [fastGRO]

status: Public on Feb 12 2026

city: Nam-gu, Pohang-si

first: Hyerim

last: Jung

state: Gyeongsangbuk-do

address: 47, Jigok-ro

department: Dept. of Life Sciences

country: South Korea

institute: Pohang University of Science & Technology (POSTECH)

summary: This study investigates the transcriptional impact of Q901, a highly selective CDK7 inhibitor in clinical development. Q901 primarily disrupted MYC and E2F-dependent transcription program, downregulating cell cycle control and DNA damage repair pathways. CDK7 binding at the promoter-proximal regions was dramatically stabilized by Q901, leading to reduced occupancy of MYC, E2F, and RNA Polymerase II (RNAPII). These findings offered a novel therapeutic strategy to enhance cancer susceptibility to TOP1-DNA protein crosslinks (TOP1-DPCs) induced by TOP1 inhibitors. Resistance to TOP1 inhibitors arises through activation of DNA repair pathway when elongating RNAPII encounters TOP1-DPCs. By suppressing RNAPII transition from initiation to elongation and DNA repair pathways, Q901 stabilizes TOP1-DPCs and sensitizes tumor to TOP1 inhibitors. Preclinical studies demonstrated enhanced tumor suppression when combining Q901 with TOP1 inhibitor-based antibody-drug conjugates (TOP1i-ADCs), highlighting its potential as a therapeutic option for cancers resistant to TOP1i-ADC therapy.

overall_design: fastGRO in MCF-7 cells with Q901 and TPT treatment.

first: Tae-Kyung

last: Kim


title: Genetic deletion of RUNX1 or RUNX2 in adipocytes enhanced beige fat formation [ATAC-seq]

city: Guangzhou

last: He

state: Guangdong

address: No. 9 XingDaoHuanBei Road, Guangzhou International Bio Island, Guangzhou 510005, Guangdong Province, China

department: Department of Basic Research

country: China

institute: Guangzhou National Laboratory

type: Genome binding/occupancy profiling by high throughput sequencing

summary: To uncover novel transcriptional regulatory mechanisms of brown adipogenesis, we performed Assay for Transposase-Accessible Chromatin using sequencing (ATAC-seq) to map genome-wide chromatin accessibility during the early stages of immortalized primary brown preadipocytes differentiation.Intriguingly, we identified a significant enrichment of the RUNX transcription factor binding motif within brown preadipocyte-specific peaks, suggesting a previously unrecognized role of the RUNX family as a potential barrier to brown adipogenesis

overall_design: Differentiation from brown pre-adipocytes toward mature brown adipocyte stage day 0 and day 1

first: Cuihua

last: Wang


title: Selective CDK7 Inhibition Sensitizes Tumors to Topoisomerase I Inhibitor-Antibody Drug Conjugates by Blocking The Transition of The RNA polymerase II Initiation Complex into Elongation [RNA-seq]

type: Expression profiling by high throughput sequencing

overall_design: mRNA-seq in MCF-7 cells with Q901 treatment.

first: Donghoon

last: Yu


title: Genetic deletion of RUNX1 or RUNX2 in adipocytes enhanced beige fat formation [ChIP-Seq; CUT&Tag]

summary: RUNX1 and RUNX2 repress thermogenic gene expression by directly binding to their regulatory genomic regions, thereby acting as key transcriptional repressors of adipocyte thermogenesis. Furthermore, RUNX1 preferentially interacts with HDAC1 to modulate thermogenic gene expression.

overall_design: we performed  ChIP-seq in WT cells and  Cut&Tag Seq in overexpression cells and  iWAT tissue.


title: Engineering prolyl hydroxylase-dependent proteolysis enables the orthogonal control of hypoxia responses in plants

city: Oxford

first: Vinay

last: Shukla

state: United Kingdom

address: South Parks Road Oxford

department: Department of Biology

country: India

institute: University of Oxford

summary: Vascular plants and metazoans use selective proteolysis of transcription factors to control the adaptive responses to hypoxia, although through distinct biochemical mechanisms. The reason for this divergence is puzzling, especially when considering that the molecular components necessary to establish both strategies are conserved across the two kingdoms. To explore an alternative evolutionary scenario where plants sense hypoxia as animals do, we engineered a three-components system aimed to target proteins for degradation in an oxygen dependent manner in Arabidopsis thaliana. Applying the synthetic biology framework, we produced a hypoxia-responsive switch independent of endogenous pathways. When applied to control transcription, the synthetic system partially restored hypoxia responsiveness in oxygen-insensitive mutants. Additionally, we demonstrated its potential to regulate growth under flood-induced hypoxia. Our work highlights the use of synthetic biology to reprogram signalling pathways in plants, providing insights into the evolution of oxygen sensing and ofering tools for crop improvement under stress conditions.

overall_design: One-week-old transgenic Arabidopsis lines expressing HIFODD-ΔRAP2.12-HA in an erfVII background were grown under normoxia and then exposed to hypoxic atmospheres of 1% or 0.1% O₂ for 2 h in controlled chambers. Following treatment, plants and parallel normoxic controls were harvested for downstream molecular analyses to assess hypoxia-responsive changes in gene expression and signaling.

first: Sergio

last: Iacopino

first: Laura

middle: D

last: Carbonare

first: Beatrice

last: Giuntoli

first: Francesco

last: Licausi


title: Epigenetic reactivation of a tumor suppressor program in leukemia

city: Farmington

first: Harshpreet

last: Chandok

state: CT

address: 10 Discovery Dr

country: USA

institute: The Jackson Laboratory

summary: Tumor suppressor genes (TSGs) impart a cellular fitness in human cancers, including acute myeloid leukemia (AML). In contrast to loss-of-function mutations, the siliencing of TSGs without direct mutations further complicates the clinical management of AML. Here, we conducted genome-scale phenotypic CRISPR-Cas9 screens to uncover genes that suppress leukemia differentiation. These screens revealed ZBTB7A as a transcriptional repressor that is downregulated in leukemia stem cells (LSCs) and associated with poor clinical outcome. Mechanistically, we found that the mRNA decay factor ZFP36L2 binds to its 3'-untranslated region (UTR) of ZBTB7A to induct its transcript degradation. Furthermore, the loss of ZBTB7A enhances the transcriptional activation of TNF signaling, resulting in an aberrant inflammatory state that drives leukemia progression. To explore the translational potential, we coupled in situ Flow-FISH readout with CRISPR-based screening, which identified KDM4 as a therapeutic vulnerability to restore ZBTB7A's tumor suppressor fuction. Pharmacologic inhibition of KDM4 elevated ZBTB7A levels, triggered terminal AML differentiation, an dexhibited broad anti-leukemic effects. Finally, targeting of KDM4 in vivo extended survival of leukemic mice while preserving normal hematopoiesis. Together, our work elucidates key regulatory pathways underlying ZBTB7A's tumor suppressor role and highlights an epigenetic therapy as a potential strategy to restore its function in cancer.

overall_design: To determine the exact mechanism underlying ZBTB7A's tumor-suppressive function, THP-1 Cas9 expressing cells were transduced with lentiviral constructs containing guide RNAs targeting ZBTB7A compared to a Rosa non-targeting control gRNA. Three days after infection, mRNA was isolated and polyA mRNAs were enriched and used to generate cDNA libraries sequenced on a Nova-seq X. Conversely, we also transduced THP-1 Cas9 cells with a cDNA construct to overexpress ZBTB7A compared to empty vector control, which were harvested at day 6 and subjected to the same protocol.

first: Han

last: Cuijuan

first: Calderon

last: Alexander

first: Wang

last: Eric


title: Genetic deletion of RUNX1 or RUNX2 in adipocytes enhanced beige fat formation

summary: RUNX1/2 overexpression suppresses critical functions associated with brown adipocyte biology, particularly thermogenesis and cellular respiration. Conversely, deletion of RUNX1 or RUNX2 led to a significant increase in cellular temperature, with DKO cells showing the greatest temperature increase.These findings indicate that RUNX1/2 act as negative regulators of thermogenic adipocyte differentiation and actively suppress the thermogenic gene program and function.

overall_design: we overexpressed RUNX1/2 and Knock out RUNX1/2 in brown preadipocytes and induced them differentiation into mature brown adipocytes for RNA-seq

first: Chuihua


title: The Liver Regulates Tissue Calcification in Pseudoxanthoma Elasticum

city: Los Angeles

first: Yiqian

last: Gu

state: CA

address: 5000D Terasaki Life Sciences Building

institute: University of California Los Angeles

summary: Pseudoxanthoma Elasticum (PXE) is a rare disease caused by loss of function of the gene Abcc6 and characterized by ectopic calcification of multiple tissues including the heart and vasculature. The physiological reasons underlying ectopic calcification in PXE remain unclear. We created a robust model of ectopic cardiac calcification where animals globally deficient in the gene Abcc6 developed extensive mineralization of the heart within 3 days of cardiac injury. To obtain insight into the underlying mechanisms of ectopic cardiac calcification in PXE, we generated animals with cardiomyocyte specific deletion of Abcc6 but did not observe any calcification, suggesting that Abcc6 was acting in a myocyte non-autonomous manner to cause calcification. Inflammation is known to play a key role in ectopic calcification of the cardiovascular system but bone marrow transplantation experiments from wild type animals into Abcc6 deficient animals did not rescue the calcific phenotype. However, tissue specific deletion of Abcc6 in the liver was sufficient to cause post injury cardiac calcification, suggesting a role of the liver in driving ectopic calcification of distant tissues. Metabolomics and gene expression analysis of animals globally deficient or with liver specific deletion of Abcc6 demonstrated deficiencies in nucleotide metabolism and pathways regulating cellular energetics. We show that such metabolic abnormalities are associated with profound abnormalities in cellular respiration in the injured cardiac tissue. Functional abnormalities in cellular respiration in the injured heart were similar in animals globally deficient in Abcc6 or with liver specific deletion demonstrating that abcc6 regulates cellular respiration in the heart in a liver cell autonomous manner. Notably calcification of the heart in Abcc6 deficient states was not secondary to induction of an osteogenic gene expression program in the heart but occurred rapidly secondary to dystrophic calcification with initial mineralization deposits noted with the cardiac muscle. Treatment with clodronate, a clinically approved bisphosphonate that prevents growth of mineralization was sufficient to rescue the phenotype of ectopic cardiac calcification in Abcc6 deficient states. Taken together, these observations highlight the role of the liver in regulating cardiac metabolic and mitochondrial function and causing ectopic calcification in Abcc6 deficient states.

overall_design: Total RNA was used to generate RNA-seq libraries, which were sequenced on an Illumina HiSeq 3000 platform (single-end, 50 bp).

first: Yijie

first: Arjun

last: Deb


title: Evaluating the Suitability of the Rat Footshock Model for Studying Gut-Brain Interactions and IBS-Related Gene Expression in PTSD Research

city: Firenze

first: Matteo

last: Ramazzotti

address: viale Morgagni 50

department: Experimental and Clinical Biomedical Sciences

country: Italy

institute: University of Florence

summary: Post-traumatic stress disorder (PTSD) is a mental health condition that has been associated with changes in gut microbiota and intestinal function. However, the molecular mechanisms driving these changes are not fully understood, and there is a need for an appropriate animal model to study the gut-brain axis in PTSD. The rat PTSD model, induced by footshock stress, is commonly used to simulate PTSD-like behaviors and physiological responses. This study aims to assess whether this model accurately reflects the alterations in gut gene expression and microbiota composition that are observed in PTSD.

overall_design: The total DNA was extracted from colon and faecal samples of rats. The 16S hypervariable region V3-V4 was amplified using the primers 341F and 805R. The amplicon sequencing was performed using the Illumina MiSeq platform.

first: Fazia

last: Ait Zenati

first: Leandro

last: Di Gloria


title: LMO1 expression in neuroblastoma cells reprograms tumor-associated macrophages to promote metastasis.

city: Rochester

first: Cheng

last: Zhang

state: MN

address: 200 1st street SW

institute: Mayo Clinic

summary: Our earlier study has showed that the transcriptional coactivator LMO1 synergizes with the MYCN oncogene to enhance NB tumorigenesis and metastasis. To better understand how these two oncogenes cooperate during NB development, we performed single-cell RNA sequencing analysis on primary tumors from transgenic zebrafish with overexpression of MYCN, either alone or in combination with LMO1. Interestingly, we found significantly enriched signaling pathways involved in biogenesis and metabolism in NB cells with overexpression of LMO1 and MYCN. In addition, the macrophage populations from the two tumor types were distinctly clustered.

overall_design: Primary neuroblastoma tumors from MYCN (n = 2) and MYCN;LMO1 (n = 3) zebrafish lines were isolated, dissociated and submitted individually for a single-cell RNA-sequencing. cDNA libraries from single cells were prepared using the SMART-seq strategy and subjected to Illumina Hi-Seq sequencing at the Harvard Medical School Biopolymers Facility. A total of 16,630 cells were sequenced, and 9,082 high-quality transcriptomes were obtained after quality control and filtering from the 5 tumor samples.

first: Ke-En

last: Tan

first: Zuag

middle: P

last: Her

first: Kok

middle: S

last: Yeo

first: Taylor

last: Weiskittel

first: Cassie

last: Howe

first: Shyang

middle: H

first: Thomas

middle: E

last: Rubino Jr

first: Hu

last: Li

first: Shizhen

last: Zhu


title: Circadian regulator PER1 inhibits osteoclastogenesis by activating inflammatory genes

city: Minneapolis

first: Nobuaki

last: Kikyo

address: University of Minnesota, MTRF, Room 2-216, 2001 6th St SE

institute: University of Minnesota

summary: Disruption of circadian rhythms predisposes shift workers to many chronic conditions, including osteoporosis. However, the effects of disrupted circadian rhythms on bone remodeling remain largely unknown. Here, we show that one of the core circadian regulators PER1 inhibits osteoclastogenesis by upregulating genes involved in inflammation. The conditional knockout of Per1 in osteoclasts and related cells resulted in decreased bone mass in the femurs of mice, along with increased osteoclasts and decreased osteoblasts. Osteoclastogenesis was also promoted by Per1 depletion in vitro with 16 downregulated inflammatory genes. Seven of these genes were known to promote or inhibit osteoclastogenesis depending on the stage of osteoclastogenesis and the presence or absence of infection. Knockdown of Nlrp3, Tlr8, or Tlr9 in the group of genes promoted osteoclastogenesis, mirroring the effects of Per1 knockout and offering a mechanistic explanation for the Per1-mediated inhibition of osteoclastogenesis. These results were not observed following the knockout of a paralog Per2. Per1 knockout mice maintain general circadian rhythms, unlike arrhythmic Per1;Per2 double knockout mice. This gives credence to Per1 as a selective target for therapeutic interventions without disrupting the circadian rhythms. This study uncovered a molecular link between a circadian regulator and osteoclastogenesis in the broader context of inflammatory reactions. Our findings may be mechanistically relevant to inflammatory bone diseases influenced by circadian rhythms, such as rheumatoid arthritis and osteoarthritis, as well as other bone diseases predisposed by chronic circadian disruption.

overall_design: Monocytes were harvested from the bone marrow of 8-12 weeks old mice and induced to differentiate into osteoclasts with M-CSF and RANKL. The cells were harvested 4 days later for RNA-seq.

first: Nobuko

last: Katoku-Kikyo

first: Elizabeth

last: K. Vu

first: Ismael

last: Y. Karkache

first: Samuel

last: Mitchell

middle: W

last: Bradley


title: An oncogenic KRAS-driven secretome involving TNFα promotes niche preparation prior to pancreatic cancer onset [ATAC-Seq]

city: Ulm

first: Alexander

last: Kleger

address: Albert-Einstein-Allee 23, 89071 Ulm

department: Institute of Molecular Oncology and Stem Cell Biology

country: Germany

institute: University Hospital Ulm

summary:
Background: Pancreatic ductal adenocarcinomas (PDACs) are highly lethal and aggressive with oncogenic KRAS being the main oncogenic driver of the disease. PDACs have been extensively profiled at advanced stages, and in advanced disease the tumor microenvironment is a major determinant that critically shapes patient outcomes. Since the molecular events occurring prior to invasive growth remain poorly understood, we aimed to investigate changes in the precancerous epithelium and its surrounding niche.
Methods: We acquired time-resolved, single-cell transcriptomic (scRNAseq), and accessible-chromatin data from human pluripotent stem cell-derived pancreatic duct-like organoids (PDLO) inducibly expressing KRASG12D and from various niche cells.
Results: Analysis of the pure epithelium already revealed key signatures of matrix remodeling and inflammation-related signaling upon few days of KRASG12D expression. Machine learning captured KRASG12D-dependent transcriptomic classifiers with high prediction accuracy and niche preparatory relevance. Various co-culture approaches followed by scRNAseq and functional validation, including T-cell microfluidics, demonstrated that the KRASG12D-induced PDLO-secretome activates pancreatic stellate cells (PaSCs) and protects precancerous organoids from T cell infiltration. Additional, in silico approaches reconstructed a virtual pancreatic (pre)cancerous space to profile cell-cell interactions between PDLOs and niche cells. TNFα emerged as a top-ranked ligand and was functionally validated to mediate T-cell shielding and PaSC activation. Cyst fluid from 80 prospectively sampled Intraductal Papillary Mucinous Neoplasm (IPMNs) –well-known cystic PDAC precursor lesions– showed a stepwise TNFα rise across LGD (low-grade), HGD (high-grade), and IC (invasive cancer).
Conclusion: Our study reveals that oncogenic KRAS orchestrates niche-preparatory programs that precede PDAC formation and highlight a T cell exclusion program governed by epithelial-derived TNFα.

overall_design: ATAC-sequencing of human stem-cell-derived pacnreatic duct-like organoids after 3 days (3d), 5 days (5d), and 7 days (7d) of doxycycline (Dox) treatment to induce KRASG12D expression, including matched untreated controls.

first: Chantal

last: Allgoewer

first: Markus

last: Breunig


title: An oncogenic KRAS-driven secretome involving TNFα promotes niche preparation prior to pancreatic cancer onset [time-series scRNA-Seq]

overall_design: Single-cell RNA-sequencing (scRNA-seq) of human stem-cell derived pacnreatic duct-like organoids after 1 day (d1), 3 days (3d), 5 days (5d), and 7 days (7d) of doxycycline (Dox) treatment to induce KRASG12D expression.


title: Dbf4-Dependent Kinase Finetunes INO80 Function at Chromosome Replication Origins

city: Martinsried

first: Tobias

last: Straub

address: Großhadener Str. 9

department: Biomedical Center, Bioinformatics

institute: LMU Munich

summary: The highly conserved Dbf4-Dependent Kinase (DDK) plays a pivotal role in the nucleus during S phase, where it directly phosphorylates the replicative helicase, the minichromosome maintenance (MCM) complex. This leads to the initiation of chromosome replication. However, aside from the MCM complex, few other targets have been identified to date, leaving DDK an understudied kinase. Here, we describe a two-pronged mass spectrometry-based approach and define the nuclear DDK-dependent phosphoproteome, which consists of approximately 400 phosphorylation events. Within this network, we found that DDK directly phosphorylates the Arp8 subunit of the multi-subunit chromatin remodeler complex INO80. Arp8 phosphorylation stabilises INO80's intramolecular complex integrity, which finetunes its nucleosome spacing activity at replication origins. This adjustment of origin chromatin architecture stimulates replication and is important for the response to replication stress. Our results represent a significant advance in our understanding of the molecular mechanisms underlying the regulation of replication origins.

overall_design: It was tested whether DDK phosphorylation of INO80 might influence the transcriptome genome-wide. Gene expression profiling analysis was performed using RNAseq data obtained from isogenic ARP8 wild-type and arp-8-P (serine 65 to alanine, serine 233 to alanine) strains. Three biological replicates were performed. Another experiment analysed transcription in synchronised cells. Cells were arrested with alpha factor and harvested in G1 and early S phase.

first: Priyanka

last: Bansal

first: Shibojyoti

last: Lahiri

first: Chandni

last: Kumar

first: Lorenzo

last: Galanti

first: Jessica

last: Furtmeier

first: Erika

last: Chacin

first: Lorenz

last: Spechthauser

first: Garp

last: Linder

first: Juan

last: de Dios Barba Tena

first: María

last: Ortíz-Bazán

first: Marisa

last: Müller

first: Petra

last: Vizjak

first: Felix

last: Mueller-Planitz

first: Johannes

last: Stigler

first: Andrés

last: Aguilera

first: Belen

last: Gómez-González

first: Boris

last: Pfander

first: Philipp

last: Korber

first: Axel

last: Imhof

first: Christoph

middle: F

last: Kurat


title: Enhancing Proteasome Activity in T Cells Alleviates Exhaustion and Improves Antitumor Immunity

city: Derio

first: Ana

middle: Maria

last: Aransay

state: BIZKAIA

address: Parque tecnologico de Bizkaia, Building 801-A

department: Genome Analysis Platform

country: Spain

institute: CIC bioGUNE

summary: Chronic T cell receptor (TCR) stimulation combined with adverse conditions in the tumor microenvironment (TME), such as hypoxia and nutrient deprivation, frequently results in T cell exhaustion. Exhausted T cells (TEX) experience oxidative stress, which causes an accumulation of oxidized proteins within the cells. We hypothesized that oxidized protein formation might exceed proteasomal degradation capacity, leading to their accumulation and impairing T cell fitness. Single-cell transcriptomics analysis across 16 tumor types revealed increased expression of proteasome genes in TEX compared to non-exhausted T cells. In a robust in vitro model for the generation of human TEX, the cells exhibited hallmarks of exhaustion, with higher levels of reactive oxygen species (ROS)-induced protein oxidation and increased expression of proteasome genes. Pharmacological and genetic enhancement of proteasome activity delayed the onset of T cell exhaustion, improved T cell fitness, and translated into superior antitumor immunity and tumor control. These findings identify proteasome modulation as a promising strategy to counteract TME-driven T cell dysfunction, potentially overcoming a major obstacle to the efficacy of cell-based immunotherapies in solid tumors.

overall_design: Exhausted human CD8+ T cells were generated by two stimulations with anti-CD3 and anti-CD28 antibodies in the presence of IL-2, followed by two additional stimulations under reduced glucose and normoxia (21% O2) or hypoxia (1% O2). Non-exhausted T cells were generated by a single stimulation cultured with standard glucose levels in normoxia.

first: Ander

last: de Blas

middle: M

first: Endika

last: Prieto-Fernández

first: Asis

last: Palazon


title: Effects of attenuating astrocytic Ca2+ activity in the medial prefrontal cortex with iβARK on transcriptional profiles in 5xFAD mice

first: Yamei

last: Tang

address: 107 Yan Jiang West Road

department: Department of Neurology

institute: Sun Yat-Sen Memorial Hospital

summary: We injected adeno-associated viruses (AAV2/5) carrying an inhibitory peptide derived from β-adrenergic receptor kinase 1 (iβARK), tagged with mCherry for identification, into the medial prefrontal cortex (mPFC) of 5xFAD mice. This strategy aimed to attenuate Gq GPCR-induced Ca2+ activity in astrocytes. In the control group, mice were injected with AAV2/5 expressing only mCherry. Subsequently, RNA sequencing analysis was conducted on the mPFC tissue samples from these mice, enabling a comparative assessment of transcriptomic alterations and an exploration of the potential implications resulting from the modulation of Gq-GPCR signaling.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for WT-mCherry, 5xFAD-mCherry, and 5xFAD-iβARK.

first: Zhan

last: Zhang

first: Sitai

last: Chen

first: Wei-Jye

last: Lin


title: CD38 expression by neonatal human naïve CD4+ T cells shapes their unique metabolic state and high regulatory T cell potential

city: San Francisco

first: Laura

middle: R

last: Dwyer

address: 513 Parnassus Ave

institute: UCSF

summary: Neonatal life is marked by rapid antigen exposure, necessitating establishment of peripheral immune tolerance via conversion of naïve CD4+ T cells into regulatory T cells (Tregs). Here, we demonstrate that increased Treg differentiation by naive CD4+ T cells from human cord blood versus adult blood is integrally linked to their unique metabolic profile and their elevated expression of the NADase, CD38. Early life naïve CD4+ T cells demonstrate a metabolic preference for glycolysis, which directly facilitates their Treg generation. We reveal an age-dependent gradient in CD38 levels on naïve CD4+ T cells and show that high CD38 expression contributes to both the glycolytic state and high Treg potential of neonatal CD4+ T cells, effects that are mediated at least in part via the NAD-dependent deacetylase SIRT1. Thus, the early life window for peripheral tolerance in humans is critically enabled by the immunometabolic state of the naïve CD4+ compartment.

overall_design: Cord blood and adult blood naïve CD4+ T cells were sorted. Cells were then sequenced with bulkRNAseqencing at 0hr (baseline, non-activated) or activated with ImmunoCult soluble anti-CD3/CD28 antibodies and sequenced 3, 24, and 48 hours after activation.

first: Sean

last: Clancy


title: Effect of Nintedanib in a Rat Model of Bleomycin-Induced Lung Fibrosis: A Transcriptome Analysis

city: Parma

first: Ilaria

last: Minato

address: Parco Area delle Scienze 23/a

institute: Università di Parma

summary:
INTRODUCTION: Idiopathic pulmonary fibrosis (IPF) is a progressive lung disease with a poor prognosis, causing irreversible lung parenchymal damage. Pirfenidone and nintedanib exhibit some benefits on IPF, although they cannot cure or reverse its progression. Moreover, the molecular mechanisms responsible for their effects remain not entirely comprehended. Nintedanib, a multi-kinase receptor modulator, suppresses diverse proliferative pathways and displays antifibrotic effects in lung fibrosis models. However, the effects of its administration on the lung transcriptome have not yet been deeply investigated in in vivo models of lung fibrosis. This study aims to assess nintedanib's comprehensive transcriptomic profile in a rat model of bleomycin-induced lung fibrosis.
MATERIALS & METHODS: Lung fibrosis was induced by two intratracheal administrations of bleomycin. Nintedanib “curative” protocol included three weeks of daily oral treatments (100 mg/kg) beginning seven days after the first bleomycin dose. At the end of the experiment, left lungs were processed for histological fibrosis evaluation by using an automated quantification system and the Ashcroft Score assessment. Right lungs were employed for RNA sequencing to undertake Differential Expression Analysis (DEGs) and a correlation network analysis (WGCNA). WGNA modules were thoroughly examined by cell and pathway enrichment analysis. Moreover, lipid peroxidation was assessed through the measurement of malondialdehyde (MDA) amount in right lung lysates.
RESULTS: Bleomycin induced significant fibrotic lesions, as confirmed by the automated quantification and the Ashcroft Score. Nintedanib reduced the size of fibrotic lesions (≃15%) and the incidence of severe Ashcroft scores. The number of differentially expressed genes decreased from over 2000 in fibrotic animals to barely more than 400 in nintedanib-treated rats, when compared to controls. WGCNA identified two gene clusters correlated to histological parameters, both characterized by gene expression patterns where nintedanib-treated animals resemble the profile observed in control animals. One cluster was associated with mesenchymal cells and focused on epithelial to mesenchymal transition and extracellular matrix organization pathways, in line with the exhibited anti-fibrotic effect of nintedanib. The second cluster, involving resident macrophages and inflammatory pathways, was specifically related to lipid homeostasis, potentially uncovering a new mechanistic role of nintedanib in modulating lung fibrosis.
CONCLUSIONS: The mechanisms involving macrophages and lipid metabolism, both of which were influenced by nintedanib treatment in this in vivo study, may open new research directions to better inquire about the role of this cellular type in the regulation of lipid homeostasis and fibrosis, influencing both tissue repair and pathological lung fibrosis.

overall_design: The samples belonged to three experimental groups: BLM, NINT, and SAL. The lung fibrosis model (BLM and NINT groups) consisted of two intratracheal administrations of BLM. The nintedanib curative protocol (NINT group) included three weeks of once-daily oral treatment beginning seven days after the first bleomycin administration. Control animals were given saline solution (SAL group). The right lung mRNA of four animals per group was subjected to trascriptomic analysis.

first: Martina

last: Bonatti

first: Barbara

last: Montanini


title: Transcriptome analysis of mouse bone marrow mesenchymal stem cells treated with ellagic acid

city: JiNan

first: Hui

last: Dong

address: Jiefang Street 105

institute: Shandong University

summary: To investigate the effect of ellagic acid on osteoblast differentiation in mouse bone marrow mesenchymal stem cells, we performed transcriptome analysis，foreseeing a molecular mechanism of ellagic acid-mediated osteoblast differentiation in mouse bone marrow mesenchymal stem cells.

overall_design: EA group received 10 μM Ellagic Acidtreatment and control group received the same dose of DMSO treatment.Total RNA was extracted after 48 hours of treatment, then sequenced on NovaSeq 6000 platform (Illumina) by Shanghai Personal Biotechnology Cp. Ltd.

first: Ke

last: Zou


title: Developmental origins of fibroblasts determine their scarring potential in wound healing

city: Stanford

first: Michael

last: Januszyk

address: 257 Campus Dr

institute: Stanford University

summary: Fibroblasts are the primary cells responsible for depositing extracellular matrix proteins during wound repair and fibrosis. Progress towards the development of treatments aimed at reducing scars has been hampered by our limited understanding of specific fibroblast populations responsible for fibrotic versus regenerative healing. Using a four-site wounding model in mice, we observed that neural crest-derived facial wounds heal with less scarring than cephalic mesoderm-derived scalp wounds, lateral plate mesoderm-derived ventral wounds, and paraxial mesoderm-derived dorsal wounds. Single-cell RNA sequencing identified increased expression of Robo2 and downstream Eid1 in neural-crest derived facial fibroblasts compared to fibroblasts from other sites. Subsequent fibroblast transplantation experiments showed that Robo2 and Eid1 are required for facial fibroblasts’ intrinsic reduced fibrotic potential. This is maintained by the EID1-mediated inhibition of EP300 histone acetyltransferase, leading to a more transcriptionally silent chromatin landscape, including around extracellular matrix genes. Mimicking EID1’s endogenous activity, both small-molecule and transgenic repression of EP300 in dorsal wounds promoted facial-like healing with reduced scarring. Overall, these data highlight the importance of the ROBO2-EID1-EP300 signaling axis in facial wound healing, and demonstrate our ability to modulate the embryologically determined fibrogenic potential of fibroblasts as a therapeutic approach to minimize scar formation.

overall_design: We examined the behaviour of fibroblasts from different regions of the mouse skin including facial, scalp, ventrum and dorsum.

first: Michelle

last: Griffin

first: Li

last: Dayan J


title: Eicosapentaenoic Acid Reprograms Cerebrovascular Metabolism and Impairs Repair after Brain Injury, with Relevance to Chronic Traumatic Encephalopathy [human_brain_OnurE_RNA-seq]

status: Public on Feb 11 2026

city: Jammu

first: Santhilal

last: Subhash

state: Jammu and Kashmir

address: Jagti, NH-44, PO Nagrota

department: Biosciences and Bioengineering

institute: Indian Institite of Technology Jammu

summary: Repetitive mild traumatic brain injury (rmTBI) precedes chronic traumatic encephalopathy (CTE) and involves neurovascular dysfunction. Omega-3 polyunsaturated fatty acids (PUFA) are promoted as neuroprotective, but long-term effects after brain injury remain uncertain. We uncover a metabolic vulnerability associated with cerebral accumulation of eicosapentaenoic acid (EPA), a major PUFA derived from fish oil. In a fish oil diet model, EPA accumulates at baseline yet is selectively depleted after rmTBI, consistent with mobilization during injury-associated metabolic remodeling. This pattern coincides with matrix remodeling, endothelial degeneration, and impaired neurovascular function. Cortical transcriptomics indicates reduced angiogenic programs with increased fatty acid metabolism, and lipidomics links EPA to maladaptive lipid engagement. Mechanistic studies using metabolically adapted endothelial cells show that EPA selectively impairs reparative function. Analysis of postmortem CTE brain tissue reveals parallel vascular and metabolic gene expression changes, strengthening translational relevance. Together, these findings challenge the assumption of uniform omega-3 neuroprotection after brain injury.

overall_design: RNA seq profiling of fresh frozen superior frontal cortex tissue from neuropathologically confirmed CTE cases with documented histories of repetitive TBI and age matched neurologically healthy controls.

first: Onur

last: Eskiocak

first: Burak

last: Berber


title: Eicosapentaenoic Acid Reprograms Cerebrovascular Metabolism and Impairs Repair after Brain Injury, with Relevance to Chronic Traumatic Encephalopathy [mouse_brain_OnurE_RNA-seq]

overall_design: RNA seq profiling of injured cortical tissue from wild type C57BL 6J mice in a 2 by 2 design comparing diet (continuous purified control diet vs cyclic fish oil supplemented high fat diet) and injury (repetitive less than mild closed head injury [rlmTBI], vs sham), collected 6 months after injury following long-term dietary exposure.


title: Control of human mesenchymal stromal cell gene expression levels by sound-guided assembly and stimulation

city: Novara

first: Andrea

last: Cochis

address: Corso Trieste 15/A

department: Department of Health Science

institute: University of Eastern Piedmont

summary: Human bone marrow mesenchymal stromal cells (hBMSCs) play a pivotal role in regenerative medicine due to their multipotent differentiation capacity. Conventional approaches to modulate hBMSC behavior primarily involve mechanical and biochemical cues. However, emerging evidence suggests that acoustic stimulation offers a novel, non-invasive strategy to influence cellular function. Here, we describe and validate a reproducible method to investigate the effects of acoustic assembly and stimulation on hBMSC gene expression, with particular emphasis on the impact of sound-guided cell assembly and subsequent acoustic exposure. This methodological framework provides new insights into the potential of acoustics as standardizable tool for experimentally modulating stem cell behavior at the transcriptional level.

overall_design: Comparison of gene expression across three conditions: (1) Dispersed spheroids ("D"), (2) Sound-guided assembly ("A"), and (3) Sound-guided assembly with additional acoustic stimulation ("A+S"). Samples were analyzed on Day 2. Each group includes n=2 biological replicates.

first: Elena

last: Della Bella

first: Farah

last: Daou

first: Alessandro

last: Cianciosi

first: Junxuan

last: Ma

first: Riccardo

last: Tognato

first: Mauro

last: Alini

first: Lia

last: Rimondini

first: Martin

last: J Stoddart

first: Tiziano

last: Serra


title: LARP6 shapes the mRNA translation of fibrogenic genes

city: La Jolla

first: Brian

last: Yee

address: 9500 Gilman Dr

department: Health

institute: UCSD

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

overall_design: Refer to individual Series


title: A Dominant mutation in Dnmt1 leads epigenetic changes (RIPseq)

city: los angeles

first: Guoping

last: Fan

state: ca

address: 695 Charles E Young Drive South

department: Human Genetics

institute: university of california, los angeles

summary: We report the application of rnaseq on the Dnmt1 A560V mice

overall_design: Examination the epigeneitc changes and gene expression changes due to Dnmt1 mutation

first: Jing

last: Wang


title: Dioxin, an endocrine disruptor, induces long term effects on DNA methylation in men after in-utero exposure.

city: Cusano Milanino

first: Luciano

last: Calzari

state: MI

address: Via Zucchi 18

institute: IRCCS Istituto Auxologico Italiano

type: Methylation profiling by genome tiling array

summary: This study explores how maternal exposure to tetrachlorodibenzodioxin (TCDD) during the Seveso incident in 1976 affected the epigenomes of Italian male descendants in their adulthood. The incident involved the release of a toxic cloud containing dioxin into the atmosphere, resulting in severe health impacts for those exposed. DNA methylation analysis was conducted using EPICv1 Illumina BeadArrays on blood samples from a cohort of 38 individuals.

overall_design: Genome-wide DNA methylation analysis of a cohort of 38 individuals using Illumina Human Methylation EPIC Beadchips.

first: Davide

last: Gentilini

last: Sacco

first: Paolo

last: Brambilla


title: Targeting IGF2BP1 reverses immune evasion in CTL-enriched pancreatic cancer

city: Halle

first: Markus

last: Glaß

address: Kurt-Mothes-Str. 3a

department: Institute of Molecular Medicine

institute: Martin Luther University Halle-Wittenberg

summary: Pancreatic ductal adenocarcinoma (PDAC) remains poorly responsive to immune checkpoint therapy. To investigate tumor-intrinsic immune evasion mechanisms, we performed RNA-sequencing of the basal-like PANC-03.27 PDAC cell line following IGF2BP1 knockdown using pooled siRNAs. Transcriptome profiling revealed induction of interferon-γ signaling and downregulation of curated IGF2BP1 target transcripts, consistent with a conserved immunoregulatory program. Gene set enrichment analysis and STAT reporter assays confirmed activation of JAK/STAT-dependent pathways. These datasets provide a resource for understanding IGF2BP1-mediated transcriptional regulation in PDAC and for identifying potential targets to enhance anti-tumor immune responses.

overall_design: PANC-03.27 cells were transfected with an IGF2BP1-directed siRNA pool (30nM) or control siRNAs 72h before RNA isolation by TRIzol to determined IGF2BP1-dependent changes in gene expression using poly(A) enriched bulk RNA-sequencing.

first: Nadine

last: Bley

first: Alexander

last: Rausch

first: Khursheed

last: Mir


title: Genomic and genetic insights into speciation and pigment pattern diversification in Danio fishes

city: Eugene

first: John

last: Postlethwait

state: OR

address: 1210 University Of Oregon

department: Biology

institute: University of Oregon

summary: The Danioninae subfamily of teleost fishes boasts up to four hundred distinct species that have evolved to display a stunning diversity of morphological forms. Here we use newly assembled genome sequences of four laboratory and wild zebrafish strains as well as eleven species of the Danio and Danionella genera to explore their phylogenetic history and the genetic basis of pigment pattern diversification. Phylogenomic analyses uncover extensive introgression and incomplete lineage sorting that have obscured phylogenetic relationships within Danio and corroborate an ancient hybrid origin of zebrafish. Whereas D. rerio inherited ancestral horizontal stripes, relatives repeatedly evolved spots and vertical bars. Interspecific complementation tests reveal functional divergence of the adhesion molecule gene igsf11 and the gap junction gene gja5b between the striped zebrafish and Danio species with divergent patterns. Comparative genomic and transcriptomic analyses suggest that protein and regulatory evolution have accompanied pigment pattern diversification. Our analyses elucidate complex genetic changes underlying the phylogenetic history and morphological diversification in the Danio genus. Resolved phylogenetic relationships, available genome assemblies, transcriptomes, and genetic tractability establish Danio fish species as excellent models for biomedical research in vertebrates.

sample_organism:
Danio rerio x Danio aesculapii
Danio rerio x Danio albolineatus
Danio rerio x Danio kyathit
Danio rerio x Danio nigrofasciatus

overall_design: Bulk RNA-seq of FACS-sorted pigment cells and whole skin from adult interspecies Danio hybrids carrying cell-type specific fluorescent reporters for melanophores (tyrp1b:mem-mCherry), xanthophores (aox5:mem-EGFP)49 or iridophores (pnp4a:mem-mCherry). D. aesculapii, D. kyathit, D. albolineatus, and D. nigrofasciatus to female D. rerio. We dissociated and FACS sorted adult hybrid skin to enrich for iridophores, melanophores, or xanthophores based on reporter expression, yielding 36 cell-enriched biological samples (3 cell types x 3 replicates x 4 paternal species) and 12 whole skin control samples (3 replicates x 4 paternal species).

first: Jianguo

last: Lu

first: Marco

last: Podobnik

first: Junrou

last: Huang

first: Braedan

last: McCluskey

first: Shane

middle: A

last: McCarthy

first: Jonathan

last: Wood

first: Joanna

last: Collins

first: James

last: Torrance

first: Ying

last: Sims

first: Dong

last: Gao

first: Jia

last: Liu

first: Wenyu

last: Fang

first: Peilin

first: Chunlei

last: Ma

first: David

last: Parichy

first: Uwe

last: Irion

first: Jian

first: Kerstin

last: Howe


title: Antiviral and anti-inflammatory effects of Tabamide A derivative, TA25, against human rhinovirus and multiple zoonotic viruses in vitro and in silico

city: Chuncheon

first: Bohyeon

last: Kim

state: Gangwon-do

address: Department of Microbiology, College of Medicine Hallym  University 1, Hallimdaehak-gil, Chuncheon-si 24252, Gangwon-  do, Republic of Korea

department: Department of Microbiology

institute: College of Medicine, Hallym University

summary: Human rhinovirus (HRV), first isolated in 1956, belongs to the family Picornaviridae. HRV causes mild cold and severe respiratory disease. To date, no FDA-approved antiviral or anti-inflammatory drugs are available. TA25 is a phenolic amide derivative extracted from Nicotiana tabacum. To investigate the potential candidate for antiviral therapeutics, we evaluated the antiviral potency of TA25 for HRV and multiple zoonotic viruses. The antiviral and anti-inflammatory effects were evaluated using RT-qPCR and RNA-seq. Strand-specific RT-qPCR was performed to measure genomic and anti-genomic RNA expression after TA25 treatment. In addition, an AI-based docking test was conducted to investigate the binding affinity of TA25 with viral proteins. TA25 induced significant reduction in viral replication and suppressed the expression of pro-inflammatory genes. Inhibition of viral replication by TA25 treatment was confirmed by strand-specific RT-qPCR. TA25 showed broad-spectrum antiviral activity against multiple viruses, including HRV-1A, ZIKV, DENV, VACV, and IBV. Using AI-driven structure-based docking analysis, TA25 showed strongest binding affinity with HRV 2B protein. This study demonstrates that TA25 confers the broad antiviral and anti-inflammatory activity against HRV and multiple zoonotic viruses. These findings provide valuable insights into antiviral strategies of TA25 for a promising therapeutic candidate in response to emerging RNA and DNA viruses.

overall_design: Innate immune and pro-inflammatory genes expression profiling analysis of total RNA-seq data from HeLa, HRV-infected HeLa or HRV-infected and 30 μM of TA25-treated HeLa cells. Samples were colleted at 48 hpi.

first: Altanzul

last: Bat Ulzii

first: Taehun

last: Lim

first: Jin Woo

first: Wonkyun Ronny

last: Im

first: Shivani

last: Rajoriya

first: Augustine

last: Natasha

first: Divya

last: Misra

first: Hennisa

last: Hennisa

first: Na Young

last: Kwag

first: Daewoon

last: Yoon

first: Gyunghee

last: Jo

first: Young Bin

last: Park

first: Jinkyu

first: Jeong Tae

last: Lee

first: Sung Ho

last: Jeon

first: Won-Keun


title: RNAsequencing comparing WT S. aureus and an evolved mutant EVOL-A and EVOL-A ∆sarA

first: Caitlin

last: Kowalski

address: 1585 E 13th Ave

institute: Univeristy of Oregon

summary: The goals of this experiment were to understand the basal changes in transcription between the EVOL-A strain that is an evolved strain in the NRS193 background with a mutation in Rel (Q672*) that has unknown impacts on transcription. The EVOL-A delSarA mutant was used to understand which changes in EVOL-A comapred to WT (NRS193) are dependent on the DNA-binding protein SarA.

overall_design: S. aurues strains WT NRS193 (WT), EVOL-A (EV), and EVOL-A ∆sarA (delsarA) were grown overnight in TSB at 37C shaking and then back diluted 1:10 in fresh TSB for 1 hour. From this subculture RNA was prepared for sequencing. Performed in three biological replicates.

first: Kowalski

last: Caitlin H

first: Barber

last: Matthrew F


title: Quantification of the effects of single nucleotide variants in NKX2.1 transcription factor binding sites

city: Berlin

first: Markus

last: Schuelke

state: Berlin

address: Augustenburger Platz 1

department: Neuropediatrics

institute: Charite

summary: Transcription factors recognise and bind specific DNA sequence patterns in promoters and enhancers thereby regulating gene expression. Variations in the DNA sequence of transcription factor binding sites (TFBSs) can alter gene regulation and may disrupt development. The transcription factor NKX2.1 is a crucial regulator of thyroid, lung, and neural development. Mutations in its coding gene NKX2-1 may cause choreoathetosis and congenital hypothyroidism with or without pulmonary dysfunction (CAHTP, OMIM #610978). Most genetically solved patients carry mutations in the coding regions of NKX2-1 that affect DNA binding, while the majority of patients with CAHTP-like symptoms do not carry mutations in the NKX2-1 coding sequence. We hypothesise that variations in NKX2.1 DNA-binding at promoter and enhancer sites could cause disease as well. We employ EMSA-seq to quantify the effects of genetic variation on NKX2.1 binding strength. We used this data to train neural network models to forecast the influence of DNA variation on NKX2.1 binding and validated our models using microscale thermophoresis, X-ray crystallography, and publicly available ChIP-seq data. The neural networks were able to detect TFBSs in ChIP-seq data and can thus be used to evaluate whole genome sequencing data of CAHTP-patients in order to prioritise potential disease-causing variants in regulatory elements.

overall_design: We created mutant libraries that contain single nucleotide variants or combinations thereof in the NKX2.1 binding site. To design the libraries, we took a 24 bp sequence of the NKX2.1 binding site (see below: middle sequence) in the rat thyroglobulin promoter and added constant primer regions to either end (see below: italics) for library preparation. We performed EMSA-seq to determine the effect of these variants on protein binding. In this experiment we incubated the NKX2.1 DNA binding domain with the mutant libraries and separated the bound sequences using electromobility shift assays (EMSAs). The bound DNA was purified from the gel and used in high-throughput sequencing. EMSA-seq was performed with three different mutant libraries [CORE: the 4 "CAAG" core nucleotides  are randomised, FLANK: 5 nucleotides on each side of the core motif are randomised, ALL: all 14 flanking and core nucleotides are randomised]. The binding reactions either contained no protein (control for sequence bias) or with protein at different DNA:protein molar ratios (e.g. 1:0.1 is 10 times more DNA than protein). All experiments were performed in three technical replicates. Binding site sequence: 5'-TCGTCGGCAGCGTCAGATGTGTAT CACTGCCCAGTCAAGTGTTCTTGA TCACCGCTCCGACTGCAGAAAA-3'. CORE: 5'-TCGTCGGCAGCGTCAGATGTGTAT CACTGCCCAGTNNNNTGTTCTTGA TCACCGCTCCGACTGCAGAAAA-3'. FLANK: 5'-TCGTCGGCAGCGTCAGATGTGTAT CACTGCNNNNNCAAGNNNNNTTGA TCACCGCTCCGACTGCAGAAAA-3'. ALL: 5'-TCGTCGGCAGCGTCAGATGTGTAT CACTGCNNNNNNNNNNNNNNTTGA TCACCGCTCCGACTGCAGAAAA-3'

first: Freyda

last: Lenihan-Geels


title: P21+TREM2+-Senescent Macrophages Fuel Inflammaging and Metabolic Dysfunction-Associated Steatotic Liver Disease. [Blood]

city: Los Angeles

first: Ivan

middle: Alexander

last: Salladay-Perez

address: 615 Charles E Young Dr S

department: Department of Microbiology Immunology and Molecular Genetics

institute: University of California, Los Angeles

summary: Cellular senescence drives chronic sterile inflammation during aging via the senescence-associated secretory phenotype (SASP); however, the cell types responsible for this pathology remain poorly defined. Here, we identify p21⁺Trem2⁺ senescent macrophages as a major source of inflammaging. Using primary mouse and human macrophages, we developed a model of DNA damage and cholesterol-induced senescence and applied multi-omic profiling to fully characterize senescent macrophages. We found that senescent macrophages exhibit a distinctive p21-TREM2 expression profile and SASP, driven in part by type-I interferon signaling via secreted mitochondrial DNA. We also found that senescent macrophage accumulation occurs in aged and MASLD mouse livers and is enriched in human cirrhotic liver tissue. Finally, senolytic treatment targeting senescent macrophages reduced liver inflammation and steatosis in both aged and MASLD mice. Together, these findings establish macrophage senescence as a central driver of chronic inflammation in aging and metabolic liver disease, highlighting a promising, tractable therapeutic target.

overall_design:
Blood from biological male or female human donors were collected and PBMCs were isolated at UCLA's Virology Core. 100 x 106  blood cells were collected from 3-5 donors with no clinical information. PBMCs were centrifuged at 100 g for 5 minutes then 25 x 107 single cells were seeded onto 10 cm polystyrene treated culture plates (VWR) with 10% adherence and allowed to differentiate into macrophages in the presence of 50 ng*ml-1 Human M-CSF recombinant protein (PeproTech, 300-25-100) in the same RPMI composition above. Cells were provided an additional 5 mL of M-CSF containing media 5 days into differentiation. 7 days after seeding, confluent macrophage cultures were placed under similar senescence inducing conditions using irradiation and doxorubicin (Thermo).

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human data generated by UCLAhealth
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first: Anthony

middle: J

last: Covarrubias

first: Anika

last: Dhingri


title: A Critical Role for α7 Nicotinic Acetylcholine Receptor Signaling in Myeloid Lineage Cells in Chronic Neuropathic and Inflammatory Pain Responses

city: Richmond

first: Imad

last: Damaj

state: Virginia

address: 1201 E Marshall St

department: Department of Pharmacology and Toxicology

institute: Virginia Commonwealth University

summary: Neuroinflammation influences the development of chronic pain, an increasingly prevalent condition impacting the lives of many worldwide. Given the challenges of managing chronic pain, it is essential to explore new neuroimmune targets for the development of safe and effective analgesics. Alpha 7 nicotinic acetylcholine receptors (α7 nAChRs) have been explored for their role in pain and inflammation. We hypothesize that α7 nAChR expression within myeloid cells mediates an anti-inflammatory response that mitigates pain states. We engineered mice with deletion of the α7 gene (Chrna7) from myeloid lineage cells conditionally using LysM-Cre. We characterized these mice in chemotherapy-induced peripheral neuropathy (CIPN) using paclitaxel. RNA-sequencing and pathway enrichment analysis of spinal cord tissues from mice treated with paclitaxel were performed. Our study suggests α7 nAChR expression in myeloid cells mediates an endogenous cholinergic anti-inflammatory pathway, which plays a critical role in chronic neuropathic and inflammatory pain.

overall_design: RNA-sequencing was performed on spinal cord tissue from 24 adult mice using a 2x2x2 factorial design: genotype (wild-type vs myeloid-specific Chrna7 knockout), treatment (vehicle vs paclitaxel), and sex (male vs female), with 3 biological replicates per condition.

first: Alexis

last: Swift

first: Martial

last: Caillaud

first: Alexandru

last: Graur

first: Bryan

last: Mckiver

first: Wisam

last: Toma

first: Eda

last: Koseli

first: Jared

last: Mann

first: William

middle: B

last: Lynch

first: Jacob

last: Beierle

first: Emily

last: Yao

first: Jolene

last: Windle

first: Harvens

last: Beauzile

first: Unsong

last: Oh

first: Ganesh

last: Thakur

first: Michael

last: Burton

first: Camron

last: Bryant

first: Nadine

last: Kabbani

first: M. Imad


title: Epigenomic Roadmap of Ovarian Reserve Development: Polycomb-Mediated Programming and Reprogramming [CUT&Tag]

city: Davis

first: Satoshi

last: Namekawa

address: One Shields Avenue

institute: UC Davis

summary: Ovarian reserve defines the female reproductive lifespan, which in humans spans decades due to the robust maintenance of meiotic arrest in non-growing oocytes residing in primordial follicles. Dynamic epigenomic reprogramming and programming occur during mammalian germline and early embryonic development. However, the chromatin-based mechanisms that underlie the establishment and maintenance of ovarian reserves are poorly defined. Here, we report a comprehensive epigenomic landscape of mouse perinatal oocytes and unravel Polycomb-based mechanisms underlying ovarian reserve development. By quantitatively profiling key histone modifications, including the Polycomb-mediated repressive marks H2AK119ub and H3K27me3, and the active marks H3K4me3 and H3K27ac, we identified two major epigenomic transitions: one for ovarian reserve formation from meiotic prophase I to dictyate-arrested non-growing oocytes, and another for ovarian reserve activation from non-growing to growing oocytes. Combining conditional loss-of-function mouse models for Polycomb Repressive Complex 1 or 2 (PRC1/2), we show that PRC1-H2AK119ub and PRC2-H3K27me3 undergo differential dynamics during perinatal oogenesis and have distinct biological functions in ovarian reserve formation and maintenance. Notably, PRC1-H2AK119ub presets the epigenetic states in non-growing oocytes and provides a blueprint for the PRC2-H3K27me3 profile, which is globally reprogrammed as oocytes exit the ovarian reserve and grow. We also demonstrated how coordinated changes of key histone modifications at promoters drive the two major transcriptome transitions during ovarian reserve formation and activation. Importantly, Polycomb complexes play crucial roles in shaping both promoter bivalency and enhancer landscape in the ovarian reserve. Our study determines a comprehensive epigenomic roadmap of perinatal oogenesis, shedding light on how the ovarian reserve is formed, maintained, and activated, emphasizing a critical window of epigenetic programming during female germline development.

overall_design: Chromatin profiling analysis of quantitative CUT&Tag data for (1) WT perinatal oocytes; (2) PRC1ctrl and PRC1cKO non-growing oocytes and early growing oocytes; (3) PRC2ctrl and PRC2cKO non-growing oocytes.

first: Mengwen

last: Hu


title: P21+TREM2+-Senescent Macrophages Fuel Inflammaging and Metabolic Dysfunction-Associated Steatotic Liver Disease. [Trem2ko]

first: Ivan

last: Salladay-Perez

overall_design: Primary bone marrow derived macrophages both C57BL/6J WT and TREM2 KO (Jackson Strain #:027197) . Data represents .csv and .fastq.gz files of 2x100 bp mRNA sequencing.

first: Anthony

last: Covarrubias

first: Ronal

last: Hedge


title: P21+TREM2+-Senescent Macrophages Fuel Inflammaging and Metabolic Dysfunction-Associated Steatotic Liver Disease. [macro_senescence]

overall_design: BMDMs used in experiments were derived from bone marrow extracted from the femurs of euthanized mice (6-12 weeks old male C57BL/6J) by mortar and pestle. Femurs were placed in the mortar and were washed with 70% ethanol to sterilize followed by two washes with complete RPMI (cRPMI; standard RPMI (Corning) supplemented with 10% fetal calf serum, penicillin-streptomycin solution (Corning), 1mM sodium pyruvate solution (Corning), 2 mM L-Glutamine solution (Corning), 10nM HEPES buffer (Corning), and 50μM 2-mercaptoethanol). After washing, 10 ml of cRPMI was added to the mortar and the femur bones were gently crushed. The resulting media was collected and filtered through a 70μm filter and placed in a conical tube. The filtered supernatant was centrifuged at 100 g (150 RCF) for 5 minutes. Cells were resuspended, counted and plated at a density of 3E6 cells/10 cm dish in 10 ml of macrophage growth media (cRPMI containing 25% M-CSF containing L929 conditioned media (made in house)). Cells were left to grow for 7 days to differentiate and were supplemented with 5 ml of macrophage growth media on day 5. On day 7, BMDMs (yielding 10-12x106 cells/10cm dish) were lifted off the plate using cold PBS containing 5mM EDTA. BMDMs were counted and replated in macrophage growth media overnight prior to experiments. On the day of experiments, macrophage growth media was replaced with cRPMI 6 hours prior to stimulation to remove M-CSF. M2 polarization was performed by stimulating macrophages with 10 ng/ml recombinant mouse IL-4 (Peprotech). For M1 polarization macrophages were stimulated with 100 ng/ml LPS (LPS EK-Ultrapure, Invivogen). To induce senescence, day 7 BMDMs were either irradiated (10 Gy) or treated with doxorubicin (Fisher) for 24 hours at 250 nM in 60% cRPMI: 40 MGM. DNA damaged cells were left in culture for 10 days and media components were replaced every 2-3 days. As a negative control, a mock irradiated or drug treated condition was cultured in parallel and required passing every 2-3 days. All senescent macrophage experiments were performed 10-13 days post DNA damage

first: Lizeth

last: Estrada


title: Ex vivo long-term expansion of human hematopoietic stem and progenitor cells as a tool for modeling vector integration sites and clonality

city: Hannover

first: Jenni

last: Fleischauer

address: Carl-Neuberg-Strasse 1

department: Institute of Experimental Hematology

institute: Hannover Medical School

summary: The small molecules A83-01, pomalidomide, and UM171 (APU) were used for the ex vivo expansion, lentiviral transduction, and long-term cultivation of umbilical cord blood-derived HSPCs. We determined the influence of APU on the stemness of HSPCs and their differentiation capacity via single-cell RNA sequencing (scRNA seq). APU supported the expansion of CD34+CD38-CD45RA-CD90+EPCR+ HSPCs. scRNAseq confirmed the enrichment of HSC signature genes in 24-h, 7-day, and 14-day APU-expanded HSPCs compared to the clinically used medium SFT3 (SCF, FLT3-L, TPO, IL-3).

overall_design: The setup comprised HSPCs expanded for 7 days in single (A_7d, P_7d, U_7d), minus-one (AP_7d, AU_7d, PU_7d), and complete APU medium (APU_7d) in comparison to the basal medium (SFT3_7d) and uncultivated CD34+CD38−CD45RA− cells (uncultivated) (Fig. 2B). Additionally, we aimed to verify the HSC expansion capability of 0.2 µM Poma in the APU combination (APU_0.2_7d) compared to the standard concentration of 2 µM Poma described by Ebina. We also compared the short-term APU cultivation without IL-3 to detect initial intracellular signaling cascades after 24h (APU_24h, SFT_24h). Later, we included HSPCs that had been expanded for 14 days to assess long-term cultivation effects. The dataset also includes two samples that were not part of the manuscript. Here, the HSPCs were cultivated for 24h with conditioned medium from native mesenchymal stromal cells (MSCs) and TGFβ-selected MSCs.

first: Philipp

last: John-Neek

first: Maike

last: Kosanke

first: Oliver

last: Dittrich-Breiholz

last: Rothe


title: Single-cell profiling of tumor lineage plasticity and the immune microenvironment in transformed small cell lung cancer

city: Guangzhou

first: Guodi

last: Cai

state: Guangdong Province

address: 132, Waihuandonglu, Daxue Cheng

department: School Of Pharmaceutical Sciences

institute: Sun Yat-Sen university

summary: Background The transformation of non-small cell lung cancer (NSCLC) into small cell lung cancer (SCLC) is a recognized treatment resistance mechanism, most often arising from EGFR-mutant lung adenocarcinoma (LUAD). However, the underlying mechanisms of transformation remain poorly understood. Methods Single-cell RNA sequencing was employed to analyze the tumor cell heterogeneity and to map the intratumoral immune cell landscape of 73,195 cells from five LUAD, three transformed small cell lung cancer (T-SCLC) and four SCLC patients. Multiplex immunofluorescence (mIF) staining and in vitro studies were further conducted to validate the stem-like feature of a malignant cell cluster and the enrichment and the function of interferon-stimulated gene-positive (ISG+) lymphocytes in transformation. Results Although increased intratumoral heterogeneity was observed upon SCLC transformation, a stem-like malignant cell subpopulation was identified to recur across subtypes and groups as the pioneering force of lineage plasticity for SCLC transformation. Further mIF staining and transcription factor analysis validated the stem-like feature. Additionally, tumor immune microenvironment (TIME) analysis revealed that ISG+ T cells and B cells were enriched in T-SCLC. Further cell co-culture analyses disclosed that ISG+ lymphocytes promoted neuroendocrine differentiation in LUAD cells via type I interferons (IFN-Is). Deciphering cell-cell interactions revealed that the stem-like malignant cells might activate and attract ISG+ T cells. Finally, we developed an ISG-associated gene signature that significantly correlates with poor prognosis in LUAD. Conclusion Our findings provide a comprehensive understanding of the lineage plasticity and the immune landscape in T-SCLC, highlighting the crucial role of the stem-like cell cluster and ISG+ lymphocytes in LUAD-to-SCLC transformation.

overall_design: Four samples were from treatment-naïve SCLC patients, and three were from T-SCLC patients who had transformed from EGFR-mutant NSCLC following treatments. After resection and biopsy, tumor-tissue samples were immediately transferred for tissue preparation and subjected to single-cell isolation.

first: Jie

last: Huang

first: Zhenhua

last: Zhang

first: Junjian

last: Wang


title: mtDNA leakage promotes neuron-glia crosstalk to induce epilepsy by cGAS-STING-driven neuroinflammation and serine metabolic reprogramming

city: Wuhan

last: Jiang

address: 13 Hangkong Road, Qiaokou District

department: insititue of pathology

institute: Institute of pathology, Tongji Hospital，Tongji Medical College, Huazhong University of Science and Technology

summary: Epilepsy is increasingly recognized as a disorder involving metabolic dysregulation beyond neural hyperexcitability, yet the underlying metabolic mechanisms remain poorly defined. Here, we identify a mitochondrion-immunity-metabolism axis that drives spontaneous chronic epilepsy. Brain-specific deletion of Mic19 impairs mitochondrial cristae structure and mitochondrial integrity in neurons, leading to activation of the Z-mtDNA–ZBP1–RIPK3-MLKL axis and p-MLKL-mediated pore formation on the mitochondrial membrane. This process results in cytosolic and extracellular leakage of mitochondrial DNA (mtDNA), which is subsequently taken up by microglia and triggers cGAS-STING-dependent inflammatory signaling. The resulting neuroinflammation promotes sustained activation of astrocytes. Critically, reactive astrocytes undergo profound metabolic reprogramming, marked by upregulated glycolysis and enhanced L-serine biosynthesis. Astrocyte-derived L-serine is subsequently transferred to neurons and converted into D-serine, a key NMDA receptor co-agonist that enhances neuronal excitability. This metabolic shift in astrocytes exacerbates excitotoxicity and sustains epileptic activity. Importantly, pharmacologic inhibition of STING with H-151 treatment markedly suppresses seizures, reinforcing the therapeutic potential of targeting immunometabolic crosstalk in epilepsy. Our findings reveal that mtDNA-mediated cGAS-STING activation and D-serine act as important drivers of epilepsy initiation, offering new mechanistic insights into neuron-microglia-astrocyte crosstalk and highlighting immunometabolic modulation as a promising therapeutic strategy for epilepsy.

overall_design: RNA-seq profiling of 6-month-old ctrl and BKO mice cortex and analyze inflammation related genes expression.

first: Meiling

last: Zuo

first: Kehan

last: Zhao

first: Zhihao

last: Ling

first: Zhida

last: Wu

first: Dongfang

last: Xue

first: Shouyong

last: Mo

first: Yuanhui

last: Liu

first: Yongjun

last: Chen

first: Bin

last: Lu

first: Chuanzhou

last: Li

first: Yaqi

last: Duan

first: He

last: He

first: Zhiyin

last: Song


title: A Dominant mutation in Dnmt1 leads epigenetic changes (RNA-BS-seq)

first: Guoping

last: Fan

type: Methylation profiling by high throughput sequencing

first: Jing


title: HPV-related DNA methylation alterations shape head and neck tumor microenvironment in space and time

city: Campinas

first: Felipe

last: Silva

address: R. Márcia Mendes, 506

country: Brazil

institute: Boldrini

summary: This study explores DNA methylation profile and their impact on tumor microenvironment (TME) of head and neck cancer (HNC). By integrating advanced high-throughput platforms, including Human Methylation 450K BeadChip microarrays and single-cell imaging mass cytometry (IMC), we identified distinct methylation signatures and immune landscapes in HNC associated with HPV-positive vs. HPV-negative tumors. Differentially methylated sites between HPV-positive and HPV-negative tumors showed enrichment for immune system regulatory pathways, with marked signatures of T lymphocyte regulation. To better understand the relationship between DNA methylation and tumor microenvironment regulation, we sought to evaluate the immunological components from a spatial perspective and observed that in HPV-positive tumors, T lymphocytes appear to activate a self-regulatory mechanism, while in HPV-negative tumors this mechanism is blocked by the action of fibroblasts, which are the cells that interact most with T lymphocytes. The spatial dynamics within the TME regulated by epigenetic mechanisms pave the way for more precise clinical decision-making and personalized therapies for HNC patients.

overall_design: DNA methylation alterations in 21 HNC patients were evaluated using bisulfite-converted DNA hybridized on Infinium HumanMethylation450 BeadChip, following characterization of differentially methylated sites.

first: Sabrina

last: Wurzba

first: Mariana

last: Maschietto


title: The chromatin remodeling factor Arp9 modulates the drug-resistance of Aspergillus flavus

city: 福建省

first: mei

middle: dong

last: Ma

address: Shangxiadian Road, Jianxin Town, Cangshan District, Fuzhou City

institute: Fujian Agriculture and Forestry University

summary: Transcriptome analysis, combined with RT-qPCR validation and high-performance liquid chromatography (HPLC) assay, determined that the absence of Arp9 down-regulated the expression levels of genes Erg3 and Erg6 in the ergosterol synthesis pathway, resulted in reducing the amount of ergosterol synthesized, which rendered A. flavus more sensitive to AMB. This study further revealed that ΔArp9 strain resistance to VOR was modulated by up-regulating VOR's drug target Erg11A and the drug efflux pumps Mdr1 and AtrF.

overall_design: In order to study the gene expression differences between Arp9 and WT, we constructed an Arp9 gene deletion strain

first: Dongmei

first: Zhenhong

last: Zhuang


title: Phenylalanine Reprograms TLS Maturation and Plasma cell differentiation in MASH-HCC [scRNA-seq]

city: Indianapolis

first: Yamei

state: Indiana

address: 975 W. Walnut St., IB552

institute: Indiana University

summary: Metabolic dysfunction–associated steatohepatitis (MASH) is a rapidly growing cause of hepatocellular carcinoma (HCC) and is associated with poor clinical outcomes and limited responsiveness to immune checkpoint inhibitors. Emerging evidence suggests that immune dysregulation within the tumor microenvironment contributes to disease progression; however, the transcriptional programs distinguishing MASH-associated HCC from non-MASH HCC remain incompletely characterized. To address this gap, we performed bulk RNA sequencing on total RNA isolated from MASH and non-MASH tumor tissues. This dataset was generated to enable comparative transcriptomic analysis of tumor-intrinsic and immune-related pathways associated with MASH-driven hepatocarcinogenesis, with particular relevance to immune organization, metabolic stress responses, and tumor–immune interactions.The resulting RNA-seq data provide a resource for investigating alterations in immune cell–associated gene signatures, metabolic pathways, and microenvironmental features that may underlie immune dysfunction in MASH-HCC.

overall_design: C3H mice were fed a 60% kcal high-fat diet (HFD; Research Diets, Inc.) for 8 weeks. To induce nonalcoholic steatohepatitis (NASH), mice were then switched to a modified methionine- and choline-deficient (MCD) diet formulated to contain 60% kcal from fat (Research Diets, Inc.). Age- and sex-matched control mice were maintained on a non-NASH control diet. The establishment of the NASH phenotype was confirmed after dietary intervention using standard histological and metabolic assessments prior to tumor inoculation. Following confirmation of NASH, mice in both NASH and control groups were subcutaneously inoculated with the HCA-1 murine hepatocellular carcinoma cell line. Tumor growth was monitored and measured for 4 weeks. At the experimental endpoint, tumors were harvested, snap-frozen in liquid nitrogen, and stored at −80 °C until processing. For RNA extraction, frozen tumor tissues were pulverized using a mortar and pestle under liquid nitrogen. TRIzol reagent was added directly to the homogenized tissue, and total RNA was extracted according to the manufacturer’s protocol. RNA purity was assessed by spectrophotometry (260/280 ratio), and high-quality RNA samples were submitted to Novogene for bulk RNA sequencing.

first: Chunru

last: Lin

first: Liuqing

last: Yang

first: Lisa

last: Huang


title: P21+TREM2+-Senescent Macrophages Fuel Inflammaging and Metabolic Dysfunction-Associated Steatotic Liver Disease.

first: Ivan

last: Salladay-Perez

overall_design: BMDMs used in experiments were derived from bone marrow extracted from the femurs of euthanized mice (6-12 weeks old male C57BL/6J) by mortar and pestle. Femurs were placed in the mortar and were washed with 70% ethanol to sterilize followed by two washes with complete RPMI (cRPMI; standard RPMI (Corning) supplemented with 10% fetal calf serum, penicillin-streptomycin solution (Corning), 1mM sodium pyruvate solution (Corning), 2 mM L-Glutamine solution (Corning), 10nM HEPES buffer (Corning), and 50μM 2-mercaptoethanol). After washing, 10 ml of cRPMI was added to the mortar and the femur bones were gently crushed. The resulting media was collected and filtered through a 70μm filter and placed in a conical tube. The filtered supernatant was centrifuged at 100 g (150 RCF) for 5 minutes. Cells were resuspended, counted and plated at a density of 3E6 cells/10 cm dish in 10 ml of macrophage growth media (cRPMI containing 25% M-CSF containing L929 conditioned media (made in house)). Cells were left to grow for 7 days to differentiate and were supplemented with 5 ml of macrophage growth media on day 5. On day 7, BMDMs (yielding 10-12x106 cells/10cm dish) were lifted off the plate using cold PBS containing 5mM EDTA. BMDMs were counted and replated in macrophage growth media overnight prior to experiments. On the day of experiments, macrophage growth media was replaced with cRPMI 6 hours prior to stimulation to remove M-CSF. M2 polarization was performed by stimulating macrophages with 10 ng/ml recombinant mouse IL-4 (Peprotech). For M1 polarization macrophages were stimulated with 100 ng/ml LPS (LPS EK-Ultrapure, Invivogen). To induce senescence, day 7 BMDMs were either irradiated (10 Gy) or treated with doxorubicin (Fisher) for 24 hours at 250 nM in 60% cRPMI: 40 MGM. DNA damaged cells were left in culture for 10 days and media components were replaced every 2-3 days. As a negative control, a mock irradiated or drug treated condition was cultured in parallel and required passing every 2-3 days. All senescent macrophage experiments were performed 10-13 days post DNA damage.

first: Anthony

last: Covarrubias


title: SRSF1 regulates the formation of the Brd4/P-TEFb complex.

city: Xiamen

first: Min

last: Liu

address: Xiamen University-Xiang'an Campus, Xiang'an District

department: School of Life Sciences

institute: Xiamen University

summary: Positive transcription elongation factor P-TEFb, which consists of CDK9 and CycT1, modulates transcriptional elongation by alternating between an inactive and an active complex state. This state transition is strictly controlled by several closely interconnected steps that begin with the release of P-TEFb from the inactive 7SK snRNP complex in the nucleoplasm, followed by reassembly of active P-TEFb and functional restart of paused transcriptional elongation on chromatin. Our previous work has elucidated the mechanisms underlying HMBA-induced P-TEFb release and subsequent functional restart of transcriptional elongation. Here, we identify that HMBA-stimulated SRSF1 regulates the assembly of the active Brd4/P-TEFb complex to enable productive transcriptional elongation.

overall_design: HeLa cells were transfected with shGFP (control) or shSRSF1, and pretreated with or without HMBA. ChIP-seq was performed to assess the genomic occupancy of RNA polymerase II.

first: Huixin

last: Wen

first: Songkuan


title: Phenylalanine Reprograms TLS Maturation and Plasma cell differentiation in MASH-HCC [Spatial Transcriptomics]

last: Chen


title: Single-cell transcriptomic profiling of Siniperca chuatsi spleen in response to ISKNV infection

city: Zhuhai

first: Mincong

last: Liang

address: No. 2 Daxue Road

department: School of Marine Sciences

institute: Sun Yat-sen University

summary: Single-cell RNA sequencing was employed to investigate the host-virus interaction between Mandarin fish (Siniperca chuatsi) and Infectious spleen and kidney necrosis virus (ISKNV). Comparative analysis was performed on spleen samples obtained from ISKNV-infected individuals and healthy controls.

overall_design: Comparative single-cell RNA sequencing was performed to investigate the splenic immune response of Siniperca chuatsi to ISKNV infection. The study design consists of two experimental groups: an ISKNV-infected group (sampled at 7 days post-infection) and a matched mock-infected control group (PBS-injected). To minimize individual heterogeneity and ensure biological representativeness, each sequenced sample represents a pool of spleen tissues collected from six distinct biological individuals. The experiment aims to characterize cell-type-specific transcriptional changes and immune dynamics induced by the virus compared to the healthy control.

first: Weiqiang

last: Pan

first: Shaoping

last: Weng

first: Jianguo

first: Changjun

last: Guo


title: Endothelial DNA damage orchestrates cardio-kidney-metabolic dysfunction through ET-1/ETAR signaling.

city: tokyo

first: akihito

last: hishikawa

address: Shinanomachi35, shinjyukuku

country: Zimbabwe

institute: keio university

summary: DNA damage, a hallmark of aging, is a major trigger of inflammation and age-related pathologies. Here, we show that vascular endothelial cells (ECs) exhibit a distinct response to DNA damage, characterized by dysregulation of endocrine signaling via ET-1. EC-specific DNA double strand breaks under high-fat diet conditions led to a rapid elevation of blood pressure, dyslipidemia, hepatic steatosis, visceral fat accumulation and kidney aging. Elevated EC-derived endothelin-1 (ET-1) triggered liver hypoxia and ET-A receptor (ETAR) activation, promoting lipid metabolic reprogramming via increased acetyl-CoA synthetase 2 (ACSS2), and ETAR inhibition mitigated these phenotypes. In humans, kidney EC DNA damage correlated with reduced eGFR and HDL-C, and increased hepatic steatosis indices. Collectively, EC DNA damage is a possible driver of cardio-kidney-metabolic dysfunction via ET-1-ACSS2 signaling, which is targetable by ETAR blockade. These findings highlight the organ-specific impact of endothelial cell DNA damage in driving cardio-kidney-metabolic dysfunction.

overall_design: RNA-sequencing was performed on endothelial cells isolated from kidneys of endothelial-specific I-PpoI-expressing mice and control littermates (n=3 per group) after 4 weeks of high-fat diet feeding.

first: Wataru

last: Ito

first: Ran

last: Nakamichi

first: Akihito

last: Hishikawa

first: Kaori

last: Hayashi


title: The Role and Therapeutic Potential of Splicing Factor SF3B6 in Hepatocellular Carcinoma

city: Yangsan

first: young-In

last: Hwang

address: 49, Busandaehak-ro, Mulgeum-eup, Yangsan-si, Gyeongsangnam-do, Republic of Korea

department: Department of Anbatomy

institute: Pusan National University

summary: Hepatocellular carcinoma (HCC) is a major global health burden, and effective systemic therapies remain limited. Dysregulated RNA splicing, driven by aberrant activity of core spliceosome components, has emerged as a key hallmark of cancer. SF3B6, a structural subunit of the SF3B complex within the U2 small nuclear ribonucleoprotein (snRNP), is required for branch-point recognition during spliceosome assembly, but its mechanistic role in HCC is poorly understood. Pan-cancer bioinformatic analyses further highlight spliceosome components as recurrently altered, essential for tumor cell survival, and associated with poor prognosis, suggesting that spliceosome subunits may represent shared oncogenic vulnerabilities.

overall_design:
In this study, I integrated public database analyses with in vitro and in vivo functional assays and transcriptomic profiling to define the role of SF3B6 in HCC. SF3B6 was significantly upregulated in HCC, and higher SF3B6 expression was associated with poor prognosis. SF3B6 depletion suppressed HCC cell proliferation, clonogenic growth, migration, invasion, and tumor formation in vivo. RNA sequencing (RNA-seq) revealed broad transcriptomic remodeling following SF3B6 knockdown, including attenuation of KRAS/RTK–MAPK oncogenic signaling and splicing alterations in KRAS-pathway genes (e.g., PIK3CB and ERBB4).
Together, these findings indicate that SF3B6 coordinately regulates oncogenic signaling pathways and alternative splicing programs in HCC and highlight SF3B6 as a potential therapeutic vulnerability in hepatocellular carcinoma.

first: Susmita

last: Sen

first: Van-Thanh

last: Duong

first: Uijin

last: Lee

first: Dongjun

first: Sik

last: Yoon

first: Sae-Ock

last: Oh


title: TRIM28 orchestrates SUMO-ubiquitin crosstalk to stabilize PPARG and drive bladder cancer progression

city: hefei

first: Dexin

last: Shen

address: lujiang road

institute: university of science and technology of china

summary: Bladder cancer (BLCA) is a growing health burden with rising incidence and limited therapeutic options. To define the role of the Tripartite Motif (TRIM) family in BLCA, we integrated multi-cohort transcriptomic analyses with functional and mechanistic validation. TRIM28 was identified as the most consistently upregulated TRIM member in BLCA and correlated with poor prognosis. TRIM28 depletion suppressed, whereas its overexpression enhanced, BLCA cell proliferation. Mechanistically, TRIM28 directly bound to PPARG and acted as a SUMO E3 ligase to catalyze SUMOylation of PPARG at Lys94 within a noncanonical YKYD motif. This modification impaired PPARG recognition by the E3 ubiquitin ligase STUB1, reduced ubiquitin–proteasome degradation, and stabilized PPARG protein. Stabilized PPARG transcriptionally activated cholesterol biosynthetic genes, including DHCR7 and DHCR24, reprogramming cholesterol metabolism to promote BLCA progression. In summary, we identify a TRIM28-PPARG SUMO-ubiquitin crosstalk axis that drives metabolic remodeling and tumor growth in BLCA, highlighting TRIM28-mediated PPARG SUMOylation as a potential therapeutic target for metabolic intervention.

overall_design: Bladder cancer cells were transfected with TRIM28-targeting siRNA (siTRIM28) or a non-targeting negative control siRNA (siNC). Total RNA was extracted after knockdown and subjected to RNA-seq to profile transcriptome-wide changes induced by TRIM28 depletion. Differential gene expression analysis was performed by comparing siTRIM28 versus siNC samples, followed by pathway/gene set enrichment analyses to identify TRIM28-regulated biological processes (with emphasis on metabolic pathways such as cholesterol biosynthesis).

first: Jun

last: Xiao


title: Screening of histone modulators small molecule library reveals Kdm5b as a major epigenetic modulator of cell cycle gene expression in Cardiomyocyte

city: Houston

first: Riham

middle: Raafat Elgharib

last: Abouleisa

state: Texas

address: 6519 Fannin Street

department: surgery

institute: Baylor College of Medicine

summary: In this study, through a small molecule screening, we defined the histone lysine demethylase, Kdm5b, as a major epigenetic driver that controls the CM cell cycle gene expression in neonatal stage and can be reintroduced in adult CMs to induce cell cycle. Mechanistically, RNAseq and CUT&RUN analyses of Kdm5b KD in NMCM P1 revealed that Kdm5b modulates the expression and the enrichment of H3K4me3 methylation around the regulatory regions of the genes involved in cell cycle.

overall_design: RNA sequencing profiling in postnatal P1 control Kdm5b FF mice heart and Kdm5b cardiac specific KO mice heart

first: Tamer

last: Mohamed


title: RNA-seq profiling of zinc sulfate-stimulated MFF-1 cells from Siniperca chuatsi

first: Mincong

last: Liang

summary: Bulk RNA sequencing (RNA-seq) data were generated to characterize transcriptomic responses to zinc stimulation in MFF-1 cells. Cells were assigned to two experimental conditions: a control group (Mock) and a zinc-treated group (Zinc; 200 µM zinc sulfate). Three biological replicates were established for each condition, and samples were collected following 72 hours of treatment.

overall_design: A controlled, two-condition in vitro RNA-seq experiment was performed to assess the effect of zinc sulfate on gene expression in MFF-1 cells. The experimental variable was zinc treatment (Zinc) versus control (Mock). Three independent replicates were included for each condition (total n = 6 libraries). Comparative transcriptome analysis between the Zinc and Mock groups was designed to define the gene expression programs associated with zinc stimulation.

first: Yanlin

last: You

first: Shaoping

last: Weng

first: Jianguo

last: He

first: Changjun


title: Targeting PKMYT1 enhances antitumor immune responses in castration-resistant prostate cancer.

city: Jinan

first: Lin

last: Gao

address: No.44, Wenhua Xi Road

institute: shandong university

summary: Although immunotherapy has been successful in various tumors, its efficacy in castration resistant prostate cancer (CRPC) is minimal, due to reduced presence of intratumoral immune effector cells in CRPC. How CRPC cells escape immune surveillance is not fully defined. Here we demonstrate that PKMYT1 expression is elevated in CRPC cases, which related to low immune infiltration in these patients. Patients with high PKMYT1 expression exhibit low CD8+ T cells signature and resistance to ICB therapy. Targeting PKMYT1 can suppress CRPC progression, accompanied with increased intratumoral CD8+ T cells. Selective PKMYT1 inhibitor, RP-6306, augmented ICB in a manner dependent on CD8+ T cells. PKMYT1 inhibitors alone or in combination with PD-L1 blockade causes CD8+ T cell infiltration and remarkable tumor suppression, which suggests a promising immunotherapeutic approach in CRPC. Mechanically, targeting PKMYT1 activated the cGAS-STING pathway, which increases expression of type I and II interferon response genes and led to upregulation of key immune regulators. These findings highlight a key role of PKMYT1 in CRPC progression and rationalize PKMYT1 as a potential therapeutic target.

overall_design: In this research, RM-1 cells were injected subcutaneously into C57BL/6 mice.Tumor tissues were collected from two RM-1 tumor-grafted mice on 10d post-treatment with either vehicle control or RP-6306. scRNA-seq profiling of RM-1 tumors treated with vehicle or RP-6306 (CD45⁺ cells were isolated from tumors by flow cytometry. CD45⁺ cells were then mixed with tumor cells at a ratio of 3:1).

first: Bo

last: Han


title: A Single-Cell Bioprinting Approach with Subcellular Resolution to Reconstruct Native Cellular Microenvironments and Interrogate Spatial Biology

city: Portland

first: Luiz

last: Bertassoni

address: 2720 S Moody Ave

department: Knight Cancer Institute

institute: Oregon Health and Science University

summary: Tissue development, function, and disease are largely driven by the spatial organization of individual cells and their interactions within a complex and heterogeneous cellular microenvironment. Engineered tissue models provide a controllable platform to dissect these spatially driven processes. However, strategies to fabricate tissues that replicate near-exact spatial organization and cellular composition of native microenvironments, necessary to faithfully recapitulate in vivo spatial relationships, have remained elusive to date. Here we present a precision bioprinting approach capable of generating high-fidelity replicas of patient biopsies that preserve complex cellular organization and heterogeneity with subcellular resolution. We demonstrate spatial placement of individual cells with down to ~3 µm spatial precision and up to eight cell types per bioprint. Using this approach, we demonstrate for the first time that altering the microscale spatial organization of tumor microenvironments of similar cellular composition can significantly alter transcriptomic programs of cell response. The ability to engineer and manipulate native cellular microenvironments with single-cell resolution marks a significant advancement toward understanding the critical influence of spatial biology on complex biological systems, such as the tumor microenvironment and organogenesis.

overall_design: A combination of MCF10A, MCF7, and primary human fibroblasts cells were single-cell bioprinted onto a collagen coated glass microscope slide either in a patterened or randomly deposited arrangement. The cells were cultured in M87 media for 24 hours before being fixed with 4% PFA and permeabilized with 100% methanol. The Visium HD spatial transcriptomics protocol was then followed to generate the data deposited here. Complete protocol for sample preparation through library preparation can be found at: Helms HR and Bertassoni LE. Single-cell spatial transcriptomic profiling of cultured cells and engineered tissues without embedding or sectioning. STAR Protocols. 2025. DOI: 10.1016/j.xpro.2025.104074

first: Haylie

last: Helms


title: RNA-Seq quantitative analysis of the regulation of imatinib-resistant cell-derived exosomes on CML cell transcriptomes

first: Fei

last: Li

address: 135 Xingang West Road, Haizhu District

summary: Drug resistance frequently results in treatment failure for leukemia and leads to the progression of chronic myeloid leukemia (CML) into an accelerated or blast phase. Although new tyrosine kinase inhibitors (TKIs) and combined TKI therapies have been developed to address BCR-ABL1 mutation-induced drug resistance in CML patients, an increasing number of primitive CML cases exhibit reduced responsiveness or are unresponsive to TKIs. Herein, we discovered that drug-resistant CML cell-derived exosomes (R-Exo) promote resistance to imatinib (IM) in CML compared to drug-sensitive CML cell-derived exosomes (S-Exo). To shed light on the mechanism underlying R-Exo-induced CML drug resistance, we performed high throughput RNA-Seq analyses to reveal the differentially expressed genes in CML cells treated with or without R-Exo. We observed that there was a significant overlap in the expression of drug resistance-related genes that were altered in K562 upon R-Exo treatment. Of these, ATP-binding cassette subfamily B member 1 (ABCB1) exhibited the most obvious upregulation.

overall_design: RNA-seq profiling of IM-sensitive and IM-resistant CML cells, R-Exo-treated K562 cells, and the S-Exo-treated K562 control group

first: Qing

last: Zhang


title: Extracellular vesicle-miR-93-5p cargo regulates glomerular endothelial cell damage in Alport syndrome

city: Los Angeles

first: Charmi

last: Dedhia

address: 4661 W Sunset Blvd, MS#35,

institute: Children's Hospital Los Angeles

summary: Modulation of miRNA expression in glomerular cells is associated with renal disease. Here, we investigated the role of miR-93-5p in mitigating glomerular damage in Alport syndrome and whether the disease-modifying activity of extracellular vesicles from human amniotic fluid stem cells (hAFSC-EVs) is mediated by their miR-93-5p-specific cargo.  We identified downregulation of miR-93-5p specifically in glomerular endothelial cells in Alport syndrome along disease progression. Silencing of miR-93-5p in hAFSC-EVs changed the transcriptomic and proteomic profile, regulating EV disease-modifying activity. Compared to naive hAFSC-EVs, silenced hAFSC-EVs did not rescue glomerular endothelial function in vitro and did not restore kidney function in vivo. We established that hAFSC-EVs regulate VEGFR1 and VEGFR2 signaling by miR-93-5p cargo transfer, highlighting that miR-93-5p can restore glomerular endothelial cell biology. Spatial Transcriptomics analysis of hAFSC-EVs injected kidneys showed that EVs can reverse pathways altered during disease progression by stimulating pro-regenerative processes, specifically in the glomerulus, by regulating miR-93-5p targets. Alteration of glomerular endothelial cell transcriptomics and miR-93-5p targets was also confirmed in biopsies of human Alport patients using Spatial Molecular Imaging. We demonstrated the critical role of miR-93-5p in glomerular endothelial cells and the capability of hAFSC-EVs to regulate miR-93-5p and its targets in Alport syndrome.

overall_design: RNA-seq was performed to characterize transcriptomic changes in glomeruli from wild-type (WT) mice, Alport syndrome (AS) mice, male and females. Biological replicates were included for each group.

first: Laura

last: Perin


title: Corilagin Induces Pyroptosis in AML Cells by Activating the TXNIP-Caspase-3-GSDME Pathway

first: hui

last: zeng

address: 106 Zhongshan 2nd Rd

institute: Guangdong Provincial People's Hospital

summary: Acute myeloid leukemia (AML) is a challenging hematological malignancy characterized by high relapse rates and limited treatment options. Compound corilagin, an ellagitannin derived from ethnopharmacological plants, shows promise as an anti-cancer agent, although its anti-leukemic effects remain poorly understood. This study aims to investigate whether corilagin induces cell death in AML cells and explore the underlying mechanisms. In AML cells, corilagin induces pyroptosis, as characterized by the formation of pyroptotic bubbles, increased lactate dehydrogenase (LDH) release and a higher proportion of propidium iodide (PI)-positive cells. Corilagin activates caspase-3, which in turn cleaves gasdermin E (GSDME) to generate GSDME-NT, promoting pyroptosis. Additionally, corilagin activates thioredoxin-interacting protein (TXNIP), and the knockdown of TXNIP rescues cells from corilagin-induced pyroptosis. Corilagin reduces cell viability and induces pyroptosis in primary AML cells, and in an AML cell-derived xenograft (CDX) mouse model, it inhibits leukemia progression and prolongs survival. These findings imply that corilagin induces pyroptosis in AML through the TXNIP/caspase-3/GSDME pathway, presenting a prospective novel therapeutic strategy for AML treatment.

overall_design: RNA-Seq analysis was performed on MV411 cells treated with DMSO and Corilagin for 48 hours.

first: Ganlu

last: Feng

first: Hui

last: Zeng

first: Juan

last: Du

first: Ying

last: Wang


title: Expression data from Knockdown of SKA2 in SNU638 cell line

city: Shenzhen

first: Hong

middle: Lei

last: Chen

address: Room 3025, Shen Nan Middle Road, Futian District

department: Gastrointestinal Endoscopy Center

institute: The Eighth Affiliated Hospital of Sun Yat-sen University

summary: Gastric cancer (GC) has a rapid metastatic rate and is associated with high mortality worldwide. During tumorigenesis, the oncogenic genes mutation or expression, following specific sets of genes are up-regulated or down-regulated. Some of them, for example, control metabolism reprogramming to promote tumor growth and malignant progression. We used microarrays to detail the global programme of gene expression regulated by SKA2, which is overexpressed in gastric cancer.

overall_design: RNA-seq was carried out on the BGISEQ-500 platform. We sought to obtain gene expression profiles regulated by SKA2 in gastric cancer cell. SNU638 was infected with packaged lentivirus supernatant and selected resistant clones in stably expressing cell lines by puromycin.

first: peng

last: zhang

first: Jianfeng

last: Zhong

first: Depei

last: Jiang

first: Lekun

last: Fang

first: Huizhen

last: Xiong

first: Honglei