title: Histotripsy-initiated immune response in a neuroblastoma murine model

city: Chicago

first: Yuqing

last: Xue

state: IL

address: 900 E 57th St

institute: University of Chicago

summary: High-risk neuroblastoma (NB) is a pediatric malignancy associated with metastases and an immunosuppressive tumor microenvironment. Standard-of-care treatments like chemotherapy are often ineffective, which motivates the investigation of adjuvant approaches. Histotripsy is a noninvasive focused ultrasound therapy that ablates tissue through the mechanical action of bubble clouds. In addition to disruption of the targeted tumor, non-targeted lesions exhibit growth delay after the histotripsy procedure. The primary hypothesis of this study was histotripsy-induced shifts in the tumor microenvironment will improve the response of metastatic NB to chemotherapy.

overall_design: The goal of this data set is to evaluation of local and systemic immunological effects of histotripsy. For the immune response experiments, randomization within blocks was used to assign tumors to one of three groups: 1) untreated, 2) histotripsy, or 3) contralateral (the untreated tumor within a treated mouse). Within each group, a subgroup of mice was monitored for tumor growth until terminal endpoint criteria were met. For the other subgroup, animals were sacrificed 5-7 days post-treatment and tumor samples analyzed with flow cytometry, immunohistochemistry, single-cell RNA sequencing (scRNA-seq).

first: Natalia

last: Antonides-Jensen

first: Muskan

last: Singh

first: Fernando

last: Flores-Guzman

first: Lydia

last: Wu

first: Samantha

last: Yee

first: Jacky

last: Gomez-Villa

first: Timothy

last: Hall

first: Mark

last: Applebaum

first: Kenneth

last: Bader

first: Sonia

last: Hernandez


title: An ancient monoaminergic signaling system coordinates contractility in a nerveless sponge

status: Public on Feb 18 2026

city: New Haven

first: Jacob

middle: M.

last: Musser

state: CT

address: 260 Whitney Avenue YSB 223D

department: MCDB

country: USA

institute: Yale University

type: Expression profiling by high throughput sequencing

summary: Chemical neurotransmission was a key animal innovation, enabling multicellular coordination of physiology and locomotion. Sponges are early-diverging animals that lack neurons and muscles, yet still coordinate contraction and relaxation of their filter-feeding water canals. Here, we show that Spongilla lacustris synthesizes the monoamines tryptamine, phenethylamine, and tyramine to elicit distinct canal behaviors. We identify previously uncharacterized decarboxylases and vesicular transporters coexpressed in secretory neuroid and metabolic cells. Using phosphoproteomics and label-free 3D imaging, we show that tryptamine activates GPCR signaling and Rho GTPases, remodeling adhesion and actomyosin networks in contractile canal epithelia to drive localized constrictions and whole-body deflations. Together, these findings define an ancestral monoaminergic system linking secretory and contractile cell types that predate neurons and was later elaborated for neuromodulation of synaptic transmission.

overall_design: RNA-seq profiling of juvenile freshwater sponge (Spongilla lacustris) treated with 37.5 µM tryptamine for 1 h, 4 h, or  4h with washout and 24 h recovery.

first: Rong Xuan

last: Zang

first: Jamie

middle: D

last: Maziarz

middle: M


title: The alarmone pGpp inhibits translation through GTP depletion II

city: Ithaca

first: Heather

last: Feaga

state: NY

address: 123 Wing Dr

institute: Cornell University

summary: Bacteria produce the alarmone nucleotides ppGpp and pppGpp during stress to affect replication, transcription, and metabolism. ppGpp and pppGpp also attenuate translation by competitively binding translational GTPases to conserve resources during stress. Recently, pGpp was identified as a third alarmone, and important pathogens like Clostridioides difficile exclusively produce pGpp in response to stress. Despite its abundance as an alarmone, the precise role of pGpp in mediating stress responses is poorly understood. Here, we show that, while pGpp is a weaker inhibitor of protein synthesis than ppGpp and pppGpp in vitro, pGpp production in the model Gram-positive bacterium Bacillus subtilis leads to faster translation inhibition in vivo. pGpp production leads to fewer ribosomes engaged in translation and more hibernating ribosome dimers than (p)ppGpp production, suggesting that translation initiation is strongly inhibited. Additionally, pGpp production depletes cellular GTP more rapidly than (p)ppGpp production, which we show is sufficient for translation inhibition. Faster GTP depletion during pGpp production is also accompanied by more robust transcriptome remodeling. This work expands the model by which alarmones inhibit translation to include GTP depletion and demonstrates how production of different alarmone species exert varying effects on physiology.

sample_organism: Bacillus subtilis subsp. subtilis str. 168

overall_design: RNA-seq comparing Bacillus subtilis (p)ppGpp0 mutant (KAE55) vs. (p)ppGpp0 nahA(E49Q, E53Q) mutant (KAE213). Total RNA was collected from log-phase cells for differential expression analysis (t = 0 minutes), and repeatedly sampled 2 and 5 minutes post-rifampicin treatment (150 µg/mL) to calculate mRNA stability. 2 biological replicates for each strain.


title: The alarmone pGpp inhibits translation through GTP depletion I

platform_organism: Bacillus subtilis subsp. subtilis str. 168

overall_design: RNA-seq comparing Bacillus subtilis pGpp inducible mutants (168 trpC2 dsasBdsasA amyE::Pxyl-sasA drel::kan, KAE60) and (p)ppGpp inducible mutants (168 trpC2 dsasBdsasAdnahA amyE::Pxyl-sasA drel::kan, KAE74). Two biological replicates of each strain were grown with repeated sampling pre-alarmone induction, 10 minutes post-, and 20 minutes post-induction.


title: Netrin-1 blockade alleviates resistance to first line chemotherapy in locally advanced pancreatic cancer

city: Bron

first: Hector

last: Hernandez-Vargas

state: Rhone

address: 36 bis Rue de la Batterie

country: France

institute: Genomics Consulting

summary: Netrin-1, a developmental cue, is a master regulator of tumor Epithelial-to-mesenchymal transition (EMT). Pancreatic cancer is a challenging indication where netrin-1 and its receptor neogenin have been shown to promote tumor progression and metastasis in animal models. Here we report the results of a single arm phase 1b study assessing the combination of an anti-netrin-1 antibody (NP137) with standard chemotherapy (mFOLFIRINOX) in first-line patients with locally advanced pancreatic cancer. Fourty-three patients were included in this trial and received mFOLFIRINOX plus NP137 once every two weeks for up to 12 cycles (6 months). NP137 was well tolerated. Median PFS was 10.85 months (95% CI, 10.03 – 15.61) and median OS was 16.43 months (95% CI, 12.75 – NR) with 21 patients still alive at time of the data cut-off. Laser capture microdissection followed by microbulk RNA sequencing was  performed on 22 pre-therapeutic and 6 surgery samples and revealed that the main pathway downregulated with the combination mFOLFIRINOX+NP137 is EMT, strengthening the mechanism of action of NP137. Moreover, analysis of pre-therapeutic samples revealed extended survival outcomes of patients with tumor cells expressing high levels of the netrin-1 receptor Neogenin, an observation validated by Neogenin immunostaining. Our results support netrin-1 blockade alleviates resistance to standard of care chemotherapy by inducing tumor re-epithelialization, particularly in neogenin-high pancreatic cancer.

overall_design:
Single arm phase 1b study assessing the combination of an anti-netrin-1 antibody (NP137) with standard chemotherapy (mFOLFIRINOX) in first-line patients with locally advanced pancreatic cancer.
---------
Phenotype variables:
# ID_paired= subject ID
# timepoint
Pre = sample obtained before therapy
Post = sample obtained after therapy
# response (RECIST)
PR= Partial Response
SD= Stable Disease
# survival
PFS_time= Progression free survival (days)
PFS_status: 0= no progressed, 1= progressed
OS_time= Overall survival (days)
OS_status: 0=alive, 1=dead


title: Early-Life Odor Exposure Rewrites Innate Aversion through a Frizzled1-Regulated Critical Period

city: Cleveland

first: Davin

middle: J

last: Marro

state: Ohio

address: 2210 Circle Dr

department: Neurosciences

institute: Case Western Reserve University

summary: Animals are born with innate mechanisms to detect environmental danger, yet they must also learn to recognize their nest and caregivers through early-life experience. When an innately aversive stimulus becomes associated with the maternal environment, a fundamental conflict arises between hardwired predispositions and experience-dependent learning. How the brain resolves this conflict remains unknown. Here we show that in mice, exposure to aversive odors during the first postnatal week not only abolishes innate aversion but also converts these cues into safety signals. Remarkably, this altered response bears the hallmarks of innate perception and cannot be reversed by associative learning in adults, constituting a form of olfactory imprinting with lifelong consequences for social behavior. Mechanistically, early odor exposure reshapes axonal projections of neurons expressing the corresponding odorant receptors, thereby altering odor identity as encoded by olfactory glomerular activity patterns. This plasticity is restricted to a defined developmental critical period, after which the circuit changes become permanent. We find that this critical period coincides with a transient surge in activity of specific genetic regulatory networks in mature olfactory sensory neurons (mOSNs). Although these regulons are first engaged in neuronal progenitors, their activation in mOSNs does not alter neuronal identity. We identify the Wnt receptor Frizzled1 (Fzd1) as a key regulator of this critical period. Loss of Fzd1 selectively perturbs gene expression at the peak and termination of the critical period, prevents its closure, and abolishes odor imprinting. Genetic evidence indicates that Fzd1 expression at the onset of the critical period provides feedback to dampen regulon activity, thereby triggering a molecular cascade that irreversibly reduces plasticity. Together, these findings reveal a genetically controlled mechanism that stabilizes early-formed olfactory circuits, enabling innate aversive perception while permitting early-life experience to permanently redefine its valence.

overall_design: WT and Fzd1cKO cells derived from olfactory epithelial tissue across different developmentally relevant timepoints is compared. scRNA-seq analysis was performed on samples to compare the effects of conditional Fzd1 knockout in mature olfactory sensory neurons, on broader neurodevelopment, and the maintenence of plasticity throughout an established olfactory critical period. (First postnatal week)

first: Yunming

first: Limei

last: Ma

first: Qiang

last: Qi

first: Ai

last: Fang

first: Wenjing

last: Xu

first: Aviral

last: Misra

first: Jillian

last: Blanck

first: Allison

last: Scott

first: Shiyuan

last: Chen

first: Huzaifa

last: Hassan

last: Corbin

first: Andrea

last: Moran

first: Kate

first: Hua

last: Li

first: Anoja

last: Perera

first: C

middle: R

last: Yu


title: CD4+ T-cell gene expression following 980 nm stimulation

city: xiamen

first: Qingxiang

last: Gao

address: Xiang'an south way

country: China

institute: Xiamen University

summary: Photobiomodulation (PBM) employs red and near-infrared light to modulate biological processes and shows promise in treating inflammatory conditions. Autoimmune colitis involves dysregulated CD4+ T cell responses, with an imbalance between pro-inflammatory effector cells and regulatory T cells (Tregs). Here we applied pulsed 980 nm near-infrared PBM in a murine adoptive transfer model of CD4+ T cell-mediated colitis. PBM treatment reduced disease severity, preserved intestinal barrier function, and reshaped the CD4+ T cell compartment by promoting Treg differentiation and suppressing pro-inflammatory Th1 and Th17 subsets.. Mechanistically, PBM promoted the differentiation of naïve CD4+ T cells into regulatory T cells (Tregs), leading to increased production of the anti-inflammatory cytokine interleukin-10 (IL-10), while concomitantly suppressing pro-inflammatory CD4+ T cell subsets, including TNFα+, IFNγ+ and IL-17A+ CD4+ T cells. Collectively, these findings indicate that PBM exerts potent immunomodulatory effects by restoring the balance between effector and regulatory CD4+ T cell responses, suggesting its potential as a safe, non-pharmacological therapeutic approach for inflammatory bowel disease.

overall_design: the CD4 T-cell from the PBM treating autoimmune colitis and lymph node sorted by cytoflex and using the 3‘ race sequencing library to identify the gene expression pattern.

first: linyin

first: yantong

last: Wan

first: qingxiang

first: Shih-Chin

last: Cheng


title: Mechanical Gating of Tendon Fibrogenic Transcription in Systemic Sclerosis

city: Zurich

first: Jess

middle: G.

last: Snedeker

address: Lengghalde 5

department: Department of Health Science and Technology

country: Switzerland

institute: ETH Zurich

summary: Fosl-2(Tg) mice develop spontaneous multiorgan fibrosis. RNA-seq was performed with tendon tissue from young animals before they develop tissue fibrosis (Early phenotype) and old animals with advanced fibrosis (Established phenotype), to explore gene expression changes that may contribute to the phenotype in tendons.

overall_design: Comparative RNA-seq transcriptome profiling analysis of Fosl-2(Tg) vs. non-transgenic wild-type controls at the early vs. established phases of tendon fibrosis.

first: Amro

middle: A

last: Hussien

middle: G


title: Single-Cell Profiling of HDAC Inhibitor-Induced EBV Lytic Heterogeneity Defines Abortive and Refractory States in B Lymphoblasts

city: Durham

first: Micah

last: Luftig

state: NC

address: 213 Research Dr

institute: Duke University

summary: Epstein-Barr virus (EBV) is associated with multiple malignancies including Burkitt lymphoma (BL), Hodgkin’s lymphomas, nasopharyngeal carcinomas (NPC), and gastric cancers. Canonically, EBV positive tumors display latent gene expression programs that are difficult to target pharmacologically. To overcome this hurdle, lytic reactivation therapies have been developed based on HDAC inhibition with limited mechanistic studies. We therefore characterized the impact of pan-HDAC inhibitor, panobinostat, and class I HDAC inhibitor, nanatinostat, on the growth, survival, and lytic reactivation of four EBV-positive cell lines: P3HR1-ZHT BL, Jijoye BL, IBL-1 immunoblastic lymphoma, and de novo infection derived lymphoblastoid cell lines (LCL). All lines were sensitive, enabling us to define ranges of sensitivity within which to use single cell approaches to assess early EBV lytic gene expression, cell cycle state, and apoptosis. We observed that each EBV-positive model of malignancy responded uniquely to the same HDAC inhibitors and that lytic reactivation was successful in only a small percentage of the cell population. To elucidate the potential role of host factors in preventing successful lytic reactivation, we performed single-cell RNA sequencing on the P3HR1-ZHT BL line treated with the HDAC inhibitor panobinostat. We observed that abortive lytic cells, or cells that do not successfully progress through the lytic cycle, upregulated genes downstream of NF-kB activity. Additionally, genes involved in immune signaling including the CD137/CD137L signaling axis, were upregulated in abortive lytic cells. These data have important implications for how we approach oncolytic therapies for EBV-associated malignancies.

overall_design: Induction of EBV lytic reactivation was examined in an EBV-positive Burkitt Lymphoma line P3HR1-ZHT. Sequence libraries were prepared from untreated cells (P3HR1-ZHT_UT) and cells treated with 50 nM panobinostat for 48h (P3HR1-ZHT_Pan).

first: Lauren

middle: E

last: Haynes

first: Ashley

middle: P

last: Barry


title: Transcriptomics of whole brain tissue in heterogeneous stock rats

city: La Jolla

first: Daniel

last: Munro

state: CA

address: 9500 Gilman Drive

department: Psychiatry

institute: UC San Diego

summary: Transcriptome-wide association studies (TWAS) integrate genome-wide association studies (GWAS) and gene expression datasets to prioritize causal genes at GWAS loci. The NIDA center for genetic studies of drug abuse in outbred rats (P50DA037844) has collected genetic data from thousands of HS rats to perform GWAS on numerous behavioral traits that are relevant to substance use disorders. However, GWAS loci remain difficult to interpret. In this scenario, TWAS offer an orthogonal approach to prioritize causal variants. TWAS rely on a reference gene panel in which both gene expression in relevant tissues and genetic variation has been measured from the same individuals to learn per-gene predictive models of expression variation. This dataset will be used to generate transcriptomic phenotypes from brain tissues of naïve heterogeneous stock rats for use in molecular QTL mapping, TWAS reference panels, expression prediction, and other transcriptomic applications.

overall_design: RNA-seq profiling of whole brain tissue from a cohort of naive outbred rats for use in statistical genetic analyses

first: Francesca

last: Telese

first: Hao

first: Abraham

last: Palmer

first: Patricia

last: Montilla-Perez

first: Pejman

last: Mohammadi


title: Comparative Analysis of Defensin Expression in Hyalomma asiaticum Ticks Exposed to Staphylococcus aureus and Escherichia coli

city: Xinjiang

first: 马祯

last: 祯

state: Xinjiang Uygur  Autonomous Region

address: nongda east road 311

department: College of Veterinary Medicine

institute: Xinjiang Agricultural University

summary: Background: Hyalomma asiaticum, which acts as a vector of zoonotic pathogens, relies on its innate immune system for defense. Methods: This study employed comparative transcriptomics to investigate defensin expression and immune pathway activation in ticks exposed to Staphylococcus aureus and Escherichia coli bacteria. Unfed adult female ticks were injected with bacteria, followed by RNA-Seq analysis after 24 h. Results: De novo assembly generated 195,132 unigenes. A total of 15 defensin genes were identified. Functional enrichment demonstrated pathogen-specific immune responses: E. coli challenge led to significant enrichment of the IMD pathway, while S. aureus stimulation resulted in enrichment of the Toll pathway. A shared response to both E. coli and S. aureus infection was the significant up-regulation of the MAPK signaling pathway (P < 0.01). Key defensin isoforms showed significant differential up-regulation, up to 8-12-fold, suggesting functional diversification. Beyond direct antimicrobial activity, defensin-associated genes were enriched in apoptosis and oxidative stress responses. Conclusions: These findings reveal distinct signaling mechanisms underlying H. asiaticum antibacterial defense and highlight defensins as multifunctional effector molecules. This study offers a preliminary reference for comprehending immune mechanisms of H. asiaticum.

overall_design: Unfed female ticks of similar body weight, from the same artificially reared batch at two weeks post-molting, were selected as the target samples for bacterial stress experiments. To minimize the impact of environmental microorganisms on the tick samples, their body surfaces were cleaned thoroughly. Briefly, Each tick was immersed in sterilized PBS and subjected to shaking for 15 seconds, followed by transfer to a 75% ethanol solution for an additional 15 seconds with agitation. Subsequently, the ticks were rinsed three times with ddH2O with agitation applied during each rinse. Finally, the cleaned ticks were placed on sterilized absorbent paper for surface drying. Injections of S. aureus and E. coli into unfed female ticks of Amblyomma americanum are described previously . Briefly, unfed female ticks were injected using a precision microsyringe (Hamilton Bonaduz, Switzerland) with a 10⁷ CFU/ml dilution of S. aureus or E. coli on the right side, between the fourth coxal segments, at a volume of 0.5 µl per tick. Immediately after completing the injection procedure, the injection site was sealed with a minimal amount of sterile Vaseline to prevent hemolymph leakage. After 24 h post-injection, ten individuals were randomly selected from each group to be pooled. The PBS-injected group was designated as the negative control to establish baseline gene expression profiles for comparative analysis. Each treatment group, including the negative control group, comprised 10 unfed female adult ticks. Three biological replicates were included for each group. Ticks were immediately transferred to freezing tubes and immersed in liquid nitrogen for snap-freezing to preserve RNA integrity prior to RNA-Seq.

first: Zhen

last: Ma

first: Depeng

last: Yang

first: Tingxiang

last: Luo

first: Sen

first: Wenxiu

last: Hu

first: Qiya

last: Wu

first: Zhengxiang

first: Yongchang

first: Yang

last: Zhang

first: Wei

first: Bayinchahan

last: Gailike

first: Qingyong

last: Guo

first: Ercha

first: Caishan


title: Effect of HIF-1alpha and HIF-2alpha on hypoxic response in Panc1 cells

city: Farmington

first: Yasir

last: Suhail

state: Connecticut

address: 263 Farmington Avenue

department: BME

institute: UCHC

summary: The hypoxic response is influence by both the tissue of origin and local environmental influences, and mediated in large part by the hypoxia-inducible transcription factors HIF-1 and HIF-2. We looked at Panc1 cells, a pancreatic adenocarcinoma cell line, and compared the response to hypoxia in both regular tissue culture media and in pancreatic TIFM (tumor interstitial fluid media), and assessed the degree to which HIF-1 and HIF-2 knockout mediates  changes in the hypoxia response.

overall_design: RNA-sequencing of Panc1 control cells, HIF-1a knockout cells, and two independently derived clones of HIF-2a knockout cells, generated by CRISPR-Cas 9 technology. Samples are exposed to normoxia (20% O2)/regular media (DMEM + 10% FBS + 1% P/S), hypoxia (1% O2)/regular media, or hypoxia/pancreatic TIFM (described by Muir A et al., eLife 2023), for 48 hours.

first: Maimon

last: Hubbi

first: Chi

middle: V

last: Dang


title: Whole-Genome Bisulfite Sequencing Reveals Formaldehyde-Induced DNA Methylation Alterations in Chicken Embryo Liver and Skeletal Muscle

city: Kayseri

first: Saffet

last: Teber

address: Erciyes University Faculty of Agriculture, Köşk Mahallesi, Fuat Sezgin Caddesi No:12, Melikgazi/KAYSERİ

country: Turkey

institute: Erciyes University

type: Methylation profiling by high throughput sequencing

summary: Pre-incubation formaldehyde (FA) fumigation of hatching eggs is widely implemented for microbial control, yet its epigenetic consequences in embryonic tissues remain unclear. Here, we profiled the methylome of chicken embryo liver and skeletal muscle following commercial-dose FA fumigation using whole-genome bisulfite sequencing (WGBS). We generated 16 WGBS libraries (per tissue: control n=4; FA n=4), producing ~1.80 billion clean reads with mapping rates of 88.1–89.9% and bisulfite conversion efficiencies of ~99.4–99.7%. Although global methylation patterns were largely maintained, FA exposure induced widespread locus-specific remodeling dominated by CpG hypomethylation in both tissues. We identified 10,496 DMRs in liver and 10,487 DMRs in muscle, with hypomethylated DMRs comprising 83.4% and 91.2%, respectively. Functional enrichment analyses revealed a tissue-specific adaptive logic. In liver, CG-DMR–associated genes were significantly enriched in Focal adhesion, Tight junction, and core signaling pathways (MAPK, Wnt, Insulin signaling). Notably, hypermethylated genes were enriched for Glycine, serine and threonine metabolism, whereas hypomethylated genes were enriched for Protein processing in endoplasmic reticulum and Autophagy. In the CHG context, hypomethylation preferentially involved ether lipid metabolism, glycerolipid metabolism, and cell–cell adhesion pathways (Adherens junction, Focal adhesion), while CHH-context hypermethylation enriched MAPK and tight junctions. In muscle, CG-DMRs were enriched for “housekeeping” stress-response pathways (Autophagy, Ubiquitin-mediated proteolysis), while a distinct metabolic signature emerged: hypermethylated genes were enriched for PPAR signaling and Biosynthesis of amino acids, whereas hypomethylated genes enriched for Fatty acid metabolism. A decisive metabolic switch was evident in the CHH context, where promoters of Biosynthesis of amino acids were hypermethylated, while catabolic energy pathways (Fatty acid degradation, Valine, leucine and isoleucine degradation, TCA cycle) were hypomethylated. Collectively, these data demonstrate that commercial-dose FA fumigation leaves tissue- and context-specific epigenetic imprints in embryonic liver and skeletal muscle, characterized by CpG-dominant hypomethylation coupled with pathway-level reprogramming of adhesion/signaling and lipid homeostasis in liver, and energy-flux rewiring in muscle.

overall_design: Genome-wide DNA methylation profiling of liver and muscle tissues between FA-treated and control samples

first: Mustafa

last: Özdemir

first: Ghulam Asghar

last: Sajid

first: Selma

last: Büyükkılıç Beyzi

first: Yunus

last: Arzık

first: Mehmet

last: Kızılaslan

first: Servet

last: Yalçın

first: Mehmet Ulas

last: Cinar


title: Inactivation of CDKN2A-ARF Promotes p53-Independent Remodeling of the PDAC Tumor Microenvironment [RNA-Seq]

city: Stanford

first: Sofia

last: Ferreira

address: 269 Campus Drive

department: Radiation Oncology

institute: Stanford University School of Medicine

summary: The CDKN2A locus, which is frequently deleted in pancreatic ductal adenocarcinoma (PDAC), encodes two tumor suppressors, ARF and INK4A, that may influence tumorigenesis through distinct mechanisms. Distinguishing their individual contributions to cancer could help improve the understanding of PDAC pathogenesis and potentially uncover targetable vulnerabilities. Moreover, while ARF is known to enhance p53 function, defining its p53-independent activities could elucidate new processes that drive PDAC development. Here, we sought to understand ARF function in PDAC suppression. Analysis of gene expression and mutational patterns in human PDAC TCGA data indicated that CDKN2AARF and CDKN2AINK4A are commonly both affected by point mutations and/or deletions, suggesting that their combined inactivation contributes to PDAC development. In genetically engineered mouse models (GEMMs), Arf inactivation accelerated KRASG12D-driven PDAC development, both in the presence and absence of Trp53, demonstrating that ARF is a PDAC suppressor and can act in a p53-independent manner. Transcriptomic analyses of PDACs supported a p53-independent role for ARF, with ARF deficiency promoting extracellular matrix, collagen synthesis/assembly, and epithelial-mesenchymal transition gene expression programs. Accordingly, ARF-deficient PDACs displayed extensive remodeling of the tumor microenvironment (TME), associated with collagen deposition, increased tissue stiffness, and higher fibroblast content – hallmarks of aggressive and treatment-resistant PDAC stroma. Together, this study shows how ARF deficiency associated with CDKN2A inactivation sculpts the PDAC TME in a p53-independent fashion. Given the central role of the TME in PDAC progression and therapeutic resistance, these findings may provide insight critical for improving therapeutic interventions for PDAC.

overall_design: RNA-Seq was performed on pancreatic ductal adenocarcinoma (PDAC) tumors originating from mouse models of acinar cell-derived (Ptf1aCreER) of the following genotypes KT;KPT; KAT; KPAT. K = KrasLSL-G12D/+; T = R26LSL-tdTom/LSL-tdTom; P = Trp53fl/fl; A = Cdkn2A-Arf fl/fl

first: Brittany

last: Flowers

first: Laura

last: Attardi


title: Xeno-Free Biomimetic-Scaffold Supports hiPSC-Derived Dental Organoid Formation and Tooth Regeneration

city: Seattle

first: YANG

last: Zhou

state: WA

address: 1410 NE Campus Pkwy

institute: university of washington

summary: Tooth regeneration remains an unmet clinical challenge due to the structural complexity of dental tissues and the requirement for precise epithelial–mesenchymal interactions during development. Here, we present a xeno-free, biomimetic strategy for dental organoid engineering by integrating human induced pluripotent stem cell (hiPSC)–derived oral epithelial cells (OECs) and neural crest cells (NCCs) within a biodegradable chitosan–alginate (CA) scaffold. The CA scaffold provides a mechanically compliant and highly porous 3D microenvironment that supports hiPSC maintenance, lineage-specific differentiation, and spatial organization. Recombined OECs and NCCs self-organized into dental organoids that recapitulated key features of early odontogenesis, including coordinated epithelial–mesenchymal interactions, progressive expression of odontogenic markers (DSPP and AMBN), and time-dependent mineral deposition. Transcriptomic profiling revealed activation of gene programs associated with odontogenesis, amelogenesis, and craniofacial morphogenesis. Upon orthotopic implantation into a rat maxillary molar extraction site, cell-laden scaffolds supported cell survival, early tooth-like tissue organization, and localized mineralized matrix formation in vivo. Together, these results establish a xeno-free, scaffold-based platform for dental organoid formation and early tooth regeneration, providing a translational framework for stem cell–based dental tissue engineering and regenerative therapies.

overall_design: Bulk RNA-seq analysis of hiPSC and the hiPSC-derived dental organoid at week 5

first: Yang


title: Inactivation of CDKN2A-ARF Promotes p53-Independent Remodeling of the PDAC Tumor Microenvironment [WES]

type: Genome variation profiling by high throughput sequencing

overall_design: WES was performed on pancreatic ductal adenocarcinoma (PDAC) tumors originating from mouse models of acinar cell-derived (Ptf1aCreER) of the following genotypes KT;KPT; KAT; KPAT. K = KrasLSL-G12D/+; T = R26LSL-tdTom/LSL-tdTom; P = Trp53fl/fl; A = Cdkn2A-Arf fl/fl


title: A significant change in the 5-hmCSeal signal is observed between UT-7 WT cells and cells carrying single or dual phospho-site substitution cells around the BCL11A gene enhancer region

first: Yong

last: Peng

address: 929 E 57th Street

department: Department of Chemistry

summary: An allogeneic blood stem cell transplantation is the only durable cure for sickle cell disease. Non-cell therapy approaches that target suppressor proteins of fetal hemoglobin gene (HBG) expression will provide the basis for novel therapies. Here we identify TET2 dioxygenase as a unifying regulator of both HBG suppressor BCL11A, and HBG activators HBBP1 and BGLT3 lncRNAs. Down regulation of TET2 functions by replacement of a single c-terminus phospho tyrosine residue is sufficient for activation of HBG by a mechanism that involves loss of TET2 binding with transcription factor GATA1 and redistribution of DNA hydroxymethylation in BCL11A enhancer and HBBP1/BGLT3 genes. By creating a transgenic sickle cell mouse in a Tet2 phospho tyrosine null background we demonstrate reactivation of fetal hemoglobin with resulting improvement in anemia and loss in sickle cell morphology and normalization of blood counts thereby identifying a mechanism for HBG activation without the need for gene editing approach.

overall_design: 5-hmCSeal profiling of wildtype UT7 cells and their Crispr derivatives (Y1939A, Y1964A, and DM)  around the BCL11A gene enhancer region (+55, +58, and +62).

first: Jong

last: Jeong

first: Trinath

last: Das

first: Shannon

last: Delaney

first: John

last: Froehlich

first: Xiu

last: Chen

first: Linda

last: Degenstein

first: Ahri

last: Choe

first: Prasanth

middle: K

last: PunathilKannan

first: Hyun

last: Lee

first: Kith

last: Pradhan

first: Srinivas

last: Aluri

first: Alana

last: Beadell

first: Charith

last: Wickrema

first: Jagadeesh

last: Ramasamy

first: Sriram

last: Sundaravel

first: Chuan

last: He

first: Amit

last: Verma

first: Amittha


title: Enrichment of neural crest cells by antibody labelling and flow cytometry for single-cell transcriptomics in a lizard

city: Plön

first: Robin

last: Pranter

address: August-Thienemann-Straße 2

country: Germany

institute: Max Plank Institute for Evolutionary Biology

summary: Single-cell transcriptomic data were generated from embryos of the common wall lizard (Podarcis muralis). Neural crest cells (NCCs) were enriched by fluorescence-activated cell sorting based on HNK-1 antibody staining. The dataset includes two unsorted samples representing all embryonic cells, one leniently sorted sample containing the top 15% of HNK-1–positive cells, and two strictly sorted samples containing the top 5% of HNK-1–positive cells. Unsorted and leniently sorted samples were generated from pools of three embryos each and sequenced using the 10x Genomics Chromium platform. Strictly sorted samples were generated from a single embryo, split across two plates, and sequenced using the Smart-seq3 protocol. These data enable characterization of NCC transcriptional profiles in a non-model vertebrate species and provide a resource for studying neural crest biology in systems lacking transgenic tools.

overall_design: Eggs were collected within 24 h of oviposition and incubated at 24C. Eggs were dissected in cold PBS and embryos were dissociated, fixed by methanol, stored at -80C, stained with HNK-1 and sorted using FACS. The unsorted samples were not stained or sorted. The Leniently sorted sample consist of cells above the 85th percentile of HNK-1 staining. The Strictly sorted samples consist of cells above the 95th percentile of HNK-1 staining.

first: Cedric

last: Patthey

first: Nathalie

last: Feiner


title: A virus-free nanoparticle–3D scaffold platform for efficient human iPSC reprogramming and differentiation

first: YANG

last: Zhou

summary: Human induced pluripotent stem cells (hiPSCs) hold substantial promise for regenerative medicine and cell manufacturing, yet their widespread adoption remains limited by reprogramming strategies that are inefficient, costly, unsafe, and difficult to scale, driven by reliance on viral vectors, limited virus-free gene delivery technologies, and two-dimensional (2D) culture systems lacking microenvironmental control.  Here, we present a virus-free, materials-guided reprogramming platform that integrates engineered polymeric nanoparticles with a biomimetic three-dimensional (3D) scaffold to jointly regulate gene delivery and cell-state transitions during fate conversion. A rationally designed fluorocarbon- and heparin-modified polymer nanoparticle enables efficient, low-toxicity episomal delivery of reprogramming factors, while a porous chitosan scaffold provides a permissive 3D microenvironment that accelerates reprogramming kinetics and suppresses somatic cell overgrowth. This integrated strategy concurrently improves reprogramming efficiency, kinetics, and workflow simplicity without the use of viral vectors or manual colony isolation. Scaffold-supported reprogramming yields an approximately eightfold increase in SSEA-4⁺/TRA-1-60⁺ cells by day 25 compared with non-viral 2D conditions, with pluripotent populations emerging as early as day 7, enabling hiPSC generation within weeks rather than the months typically required by conventional workflows. Transcriptomic analyses reveal that the 3D scaffold functions as an active regulatory element, suppressing inflammatory and extracellular matrix–associated programs that stabilize somatic identity while promoting chromatin-remodeling and stem-cell-associated pathways. Importantly, the platform supports a continuous, selection-free workflow, enabling direct differentiation of hiPSCs within the scaffold and further reducing processing time. By coupling delivery chemistry with microenvironmental control, this nanoparticle–scaffold platform provides a safe, efficient, and scalable route for hiPSC generation with direct relevance to regenerative medicine and patient-specific cell manufacturing.

overall_design: Bulk RNA-seq analysis of hiPSC reprogrammed under 2D culture condition and 3D scaffold culture conditions

first: Yang


title: KDM5B-mediated regulation of microglial reactivity as revealed by comprehensive multi-omic analysis

status: Public on Feb 19 2026

city: Tampa

first: Jessica

last: Wohlfahrt

state: FL

address: 4202 E Fowler Ave

institute: University of South Florida

summary: The biological significance of microglia are highlighted by their critical role as the resident immune cells of the central nervous system. In this capacity, microglia maintain homeostasis through various pathways that include cell migration, phagocytosis as well as secretion of immune-related and signaling factors into the extracellular environment. Microglial reactivity is associated with a variety of functional outcomes that are highly context-dependent and therefore microglia can exhibit a wide range of phenotypes. Epigenetic regulation through DNA methylation and histone modifications has recently been implicated in this complex control of microglial reactivity. Specifically, in relation to histone methylation status, the histone demethylase KDM5B has been implicated in many pathophysiological states including alcohol use disorder (AUD), cancer, and inflammatory disorders; however, the cell type-specific role of KDM5B in microglial reactivity has yet to be fully investigated. In this study, transcriptomic and proteomic analyses were used to characterize the effects of KDM5B knockdown on microglial pathways using CRISPR editing of adult-derived murine microglial cells to generate a Kdm5b knockout pool. From this multi-omic analysis, over 34,000 genes and 9,000 proteins  were identified across all replicates of wild-type (WT) and KDM5B-depleted microglia. Additionally, various stimuli including LPS, IL4, and alcohol were used to study the effects of KDM5B knockdown on immune reactivity in microglia using deep proteomic analysis. Through this deep characterization, an overall decrease in inflammatory and immune reactivity pathways was observed in KDM5B-depleted microglia, which was then functionally validated through measurement of secreted factors including TNFα, IL6, IL4, IL10, IL16, and SPP1. The results from this study has provided critical insight into KDM5B-mediated effects on microglial function as well as a molecular framework for future studies aimed to understand epigenetic regulation of microglia and implications in neurodegenerative disease pathogenesis and progression.

overall_design: To determine the function of KDM5B, a CRISPR knockout pool of Kdm5b was generated in an immortalized mouse microglia cell line (IMG). RNA-seq analysis was performed in triplicate of wildtype control and Kdm5b knockout pool IMG cells.

first: Tiara

last: Wolf

first: Alexis

last: Coiner

first: Brant

last: Burkhardt

first: Bin

last: Liu

first: Jennifer

last: Guergues

first: Stanley

last: Stevens Jr


title: A single-atom-based Rubik's cube as an energy generator via boosted NAD+ production

city: Suzhou

first: Xiaowei

last: Xia

state: Jiangsu

address: 899 Pinghai Road

institute: orthopedics department

summary: Chondrocyte senescence has been recognized as a pivotal pathogenic mechanism in osteoarthritis (OA) progression. Elevating nicotinamide adenine dinucleotide (NAD+) levels constitutes a promising strategy for promoting energy metabolism. In this study, single-atom copper (Cu-SAC) supported on nitrogen (N)-doped carbon exhibits N-configuration-dependent NADH-oxidase mimicking activity, with pyridinic N contributing more prominently to catalytic activity than pyrrolic N. A cubic-structured Cu-SAC enriched with pyridinic N achieves superior efficacy in augmenting intracellular NAD+ levels relative to NAD+ precursor supplementation. Furthermore, Cu-SAC enhances chondrocyte energy production by upregulating glycolytic and tricarboxylic acid cycle flux, facilitating cartilage extracellular matrix synthesis. Cu-SAC administration attenuates chondrocyte senescence by enhancing the NAD+-dependent deacetylase activity of sirtuin 3, reduces knee joint degeneration, and slows the progression of post-traumatic OA. These findings highlight a promising strategy for enhancing mitochondrial energy metabolism, offering potential therapeutic value for aging and age-related disorders.

overall_design: RNA-seq of Mus musculus Chondrocyte in blank control group, Inflammation group and Inflammation induced Cu SAC group


title: Targeted delivery of TGF-β inhibitor via LHRH-NanoTi reverses the NAT10/ac4C-mediated cisplatin-induced immunosuppressive tumor microenvironment in ovarian cancer [Ribo-Seq]

city: Hangzhou

first: Lv

last: Fei

address: The First People's Hospital of Hangzhou, Zhejiang Province

institute: Zhejiang Chinese Medical University

summary: Background: Platinum-based chemotherapy for ovarian cancer is frequently compromised by the development of resistance, a process often accompanied by an immunosuppressive tumor microenvironment. The molecular mechanisms linking cisplatin resistance to immune evasion remain poorly understood, hindering the development of effective combination therapies. Results: This study reveals that cisplatin-induced immunosuppression and resistance are driven by a reduction in N-acetyltransferase 10 (NAT10)-mediated N4-acetylcytidine (ac4C) modification, which produces two parts of unfavorable effects: 1) activating the DNA damage repair pathway, thereby confers resistance to cisplatin; 2) enhancing the expression of TGF-β via NAT10's interaction with ribosomal proteins RPS3 and RPS6. The elevated TGF-β increases the infiltration of myeloid-derived suppressor cells (MDSCs), M2 macrophages, exhausted CD8+ T cells, and regulatory T cells (Tregs) within the tumor microenvironment. To target this pathway, we developed a LHRH receptor-targeted nanodelivery system for a TGF-β inhibitor, which synergized with cisplatin to achieve superior antitumor efficacy by effectively reversing the immunosuppressive microenvironment. Conclusions: Our study defines the NAT10/ac4C–TGF-β axis as a pivotal mechanism coordinating cisplatin resistance and immunosuppression in ovarian cancer. These findings propose targeted inhibition of TGF-β signaling as a promising therapeutic strategy to overcome platinum resistance by revitalizing the antitumor immune response.

overall_design: Based on the hypothesis that NAT10 may regulate the translational process in ovarian cancer cells, we performed ribosome profiling (Ribo-seq) in sgNC (control) and sgNat10 (NAT10-depleted) ID8 cells.

first: Fei

last: Lv


title: H4K20me1 and gene expression in adult myocyte hypertrophy

city: San Diego

first: Yuliang

last: Tan

address: 9500 Gilman Dr.

institute: UCSD

type: Genome binding/occupancy profiling by high throughput sequencing

summary: The lysine methyltransferase KMT5A is shown to mediate the effects of CDC14A in the adult cardiomyocyte by regulating H4K20 mono-methylation, such that reduced KMT5A expression promotes a phenotype resembling Dilated Cardiomyopathy.

overall_design: Adult rat ventricular myocytes were transfected with control or KMT5A siRNA as indicated for 2 days and then treated with phenylephrine (20 μmol/L) or vehicle control for 1 hour before harvest.

first: Xueyi

last: Li

first: Jinliang

first: Michael

last: Kapiloff


title: Inhibition of Astrocytic MAGL Reprograms Glial Reactivity and Prevents Seizure Sequelae

city: San Antonio

first: Chu

last: Chen

state: TX

address: 7703 Floyd Dr

department: Department of Cellular and Integrative Physiology

institute: The University of Texas Health Science Center at San Antonio

summary:
Background Temporal lobe epilepsy (TLE) is the most common form of focal epilepsy and is characterized by a pathological cascade of excitotoxicity that leads to neuroinflammation, progressive neuronal loss, and subsequent cognitive decline. Despite its prevalence, effective disease-modifying therapies remain lacking. Previous studies have demonstrated that the endocannabinoid system contributes to epileptic activity. In particular, inactivation of monoacylglycerol lipase (MAGL), the key rate-limiting enzyme responsible for the degradation of the endocannabinoid 2-arachidonoylglycerol (2-AG), an endogenous lipid mediator with anti-inflammatory and neuroprotective properties, suppresses seizures and reduces neuroinflammation. However, the cellular and molecular mechanisms underlying these protective effects remain unclear.
Methods To dissect the cellular mechanisms underlying MAGL-mediated neuroprotection, we employed a kainic acid (KA)-induced status epilepticus model in mice with global, astrocyte-specific (aKO), and neuron-specific (nKO) deletion of mgll. We combined single-nucleus RNA sequencing (snRNA-seq) to map the transcriptomic landscape of glial responses with pharmacological interventions to validate key signaling pathways, as well as behavioral assays to assess functional recovery.
Results We demonstrated that astrocyte-specific, but not neuron-specific, mgll deletion was sufficient to attenuate seizure susceptibility and hippocampal neurodegeneration, thereby recapitulating the protective phenotype observed in global knockouts. Transcriptomic profiling revealed that astrocytic MAGL deficiency fundamentally reshaped the glial response to injury by preventing the transition to pro-inflammatory reactive astrocyte states and suppressing the activation of disease-associated microglia (DAM). Mechanistically, we identified a signaling pathway in which the neuroprotective effects of MAGL inhibition depend on cannabinoid receptor 1 (CB1) activation and are mediated by downstream peroxisome proliferator-activated receptor γ (PPAR-γ) signaling. Either genetic deletion of CB1 or pharmacological blockade of PPAR-γ abolished the protective effects. Furthermore, aKO mice exhibited reduced neuronal loss, preserved synaptic structural integrity and protection against post-seizure cognitive deficits.
Conclusion These findings reveal astrocytic MAGL as a crucial regulatory node in the epileptic brain and demonstrated that enhancing 2-AG signaling in astrocytes orchestrates neuroprotection via CB1-PPAR-γ signaling pathways, thereby reducing neuroinflammation, preserving synaptic function, and preventing the cognitive comorbidities associated with epilepsy.

overall_design: Following kainic acid (or saline) i.p. injection, the bilateral hippocampal tissue of WT and Mgll astrocytic knockout (aKO) mice were collected at Day 4. Each sample was pooled from 5 mice per group (WT-Veh, WT-KA, aKO-Veh, aKO-KA).

first: Chudai

last: Zeng

last: Gao

first: Jian

last: Zhang

first: Dexiao

last: Zhu

first: Mei

last: Hu

first: Li

last: Sun

first: Jianlu

last: Lyu

first: Mingzhe

last: Pan


title: Targeted delivery of TGF-β inhibitor via LHRH-NanoTi reverses the NAT10/ac4C-mediated cisplatin-induced immunosuppressive tumor microenvironment in ovarian cancer [RNA-Seq]

overall_design: To investigate the potential molecular mechanisms underlying the reduction of DNA damage associated with decreased NAT10/ac4C levels, this study performed RNA-seq analysis on ID8 cells stably transfected with sgNC (control group) and sgNat10 (NAT10 knockdown group). By comparing the whole-genome expression profiles between the two groups, we aim to systematically reveal the transcriptome changes triggered by NAT10 depletion and the consequent reduction in ac4C modification, thereby identifying key differentially expressed genes and signaling networks related to the DNA damage response pathway. This analysis will provide transcript-level evidence to elucidate the role of NAT10/ac4C in maintaining genome stability.


title: 3-Hydroxystearic acid promotes cholesterol efflux and attenuates atherosclerosis via the ALKBH5/PAX-8/ABCA1 pathway

city: Hengyang

first: Qin-Yi

last: Zhou

state: Hunan

address: Institute of Cardiovascular Disease, Affiliated Nanhua Hospital, 336 S Dongfeng Road, Hengyang, Hunan 421002, China

institute: University of South china

summary:
Introduction: Atherosclerosis can trigger various cardiovascular and cerebrovascular diseases with complex pathogenesis. Macrophage proliferation, inflammatory responses, and lipid phagocytosis, which induce foam cell formation and accumulation, are critical in the development of early atherosclerotic lesions. The role of 3-Hydroxystearic acid (C18-3OH), a recently identified gut microbiota-derived metabolite, in atherosclerosis has not yet been clarified. This study aimed to investigate the role of the ALKBH5/PAX-8/ABCA1 pathway in C18-3OH-mediated regulation of macrophage cholesterol efflux and atherosclerosis and explore novel mechanisms of ABCA1 regulation from the perspective of m6A modification.
Methods: RT-qPCR and Western blotting were used to detect gene and protein expression, respectively. ChIP-Seq was used to screen PAX-8 target genes, and ChIP-qPCR was used to validate PAX-8 binding to ABCA1. The SRAMP platform was used to predict m6A modification sites in PAX-8 mRNA sequences. Methylated RNA immunoprecipitation-qPCR (MeRIP-qPCR) was used to measure m6A modification levels of PAX-8 mRNA in foam cells. UHPLC-OEMS untargeted metabolomics were used to analyze differential fatty acid metabolites in an atherosclerotic mouse model. Specific kits were used to detect serum liver function markers (aspartate transaminase, AST; alanine aminotransferase, ALT), renal function markers (serum creatinine, Scr; blood urea nitrogen, BUN), and lipid profiles (HDL-C, TG, LDL-C, TC). Aortic sinus sections were prepared, and H&E, Oil Red O, and Masson staining were used to evaluate atherosclerotic plaques.
Results: The results demonstrated that C18-3OH promoted cholesterol efflux in foam cells and alleviated lipid accumulation by upregulating ABCA1 expression. C18-3OH inhibited ALKBH5, increased PAX-8 mRNA m6A modification and PAX-8 expression, and upregulated ABCA1 to enhance cholesterol efflux. Serum metabolomics revealed reduced C18-3OH levels in high-fat diet-fed apoE-/- atherosclerotic mice. C18-3OH suppressed aortic ALKBH5 expression, elevated m6A modification of PAX-8 mRNA, and increased PAX-8 and ABCA1 expression. Furthermore, C18-3OH improved lipid metabolism and reduced the atherosclerotic plaque area in apoE-/- mice.
Discussion: This study clarifies the impact and mechanisms of gut microbiota-derived C18-3OH on atherosclerosis progression, providing novel strategies for the precise prevention and treatment of atherosclerosis.

overall_design: ChIP-Seq was used to screen PAX-8 target genes in THP-1 cells

first: Wang

last: Liu

first: Zhen-Wang

last: Zhao

first: Duo

last: Gong

first: Xiao-Feng

last: Ma

first: Chao-Ke

last: Tang


title: Identification of early glutamate-responsive genes in Arabidopsis

city: Taipei

first: Yi-Jie

last: Hung

address: 128 Section 2, Academia Road, Nankang

department: IPMB

country: Taiwan

institute: Academia Sinica

summary: To understand the global effect of Glu on gene expression, we performed RNA-seq analysis to compare the gene expression profiles between Arabidopsis seedlings treated with Glu for 0hr and 0.5hr.

overall_design: Total RNA extracted from 14-day-old Arabidopsis seedlings grown on liquid medium containing 1/2 MS-modified basal salt mixture without N (M531, PhytoTechnology Laboratories) and then treated with Glu for 0hr and 0.5hr was used for RNAseq analysis.

first: Hong-Sheng

last: Liao

first: Ming-Hsiun

last: Hsieh


title: Single-nucleus and Spatial Transcriptomics Reveal Intestinal Cellular Heterogeneity, Differentiation, and Cell Communication Mechanisms in SAP-induced Intestinal Injury [Spatial Transcriptomics]

city: Jinan

first: Shulei

state: China

address: Department of Gastroenterology, Shandong Provincial Hospital Affiliated to Shandong First Medical University, 324 Jingwu Weiqi Rd, Jinan 250021, China.

department: Gastroenterology

summary: Background Acute pancreatitis (AP) is a severe inflammatory disease that frequently causes multi-organ damage, with intestinal injury being a major complication. The mechanisms underlying SAP-induced intestinal injury remain unclear, particularly regarding spatial cellular reorganization and functional interactions. Methods This study constructed a severe acute pancreatitis (SAP) rat model and employed single-nucleus RNA sequencing (snRNA-seq) and spatial transcriptome sequencing (stRNA-seq) technologies to systematically analyze the dynamic changes in intestinal cellular composition, spatial distribution, and function during SAP-induced intestinal injury. Results snRNA-seq identified 18 major ileal cell populations spanning epithelial, immune, stem/TA, and stromal compartments. SAP was associated with compositional remodeling characterized by downward trends in Lgr5⁺/Olfm4⁺ stem cells, TA1, goblet cells, and Paneth cells, with a reciprocal increase in enterocytes, although most proportion changes did not reach statistical significance at the animal level. Spatial transcriptomics independently captured SAP-associated tissue remodeling, including a significant reduction in Paneth cells accompanied by increases in fat cells, macrophages, goblet cells, and TA2 cells. Across epithelial lineages, SAP induced a transcriptional shift toward immune interaction with up-regulation of antigen presentation–related genes (e.g., Cd74, Apoa1) and down-regulation of antimicrobial/barrier effectors (e.g., Defa24, Pla2g2a, Dmbt1), which was corroborated by spatial expression patterns and spatially variable gene programs enriched for host defense responses. Pseudotime analysis suggested a redistribution of epithelial states along the stem/TA-to-enterocyte continuum, with relative depletion of early states and expansion of enterocyte-dominant states in SAP. CellChat analysis revealed globally intensified intercellular communication and nominated FN1 as the pathway with the highest differential information flow, with Lgr5⁺ stem cells predicted as prominent FN1 senders targeting enterocytes and smooth muscle cells. SCENIC identified reduced activity and expression of Hmga2/Myb regulons in stem compartments, and immunofluorescence showed decreasing trends in Hmga2/Myb-positive Olfm4⁺ and Lgr5⁺ stem cells in SAP. Conclusions Integrated single-nucleus and spatial transcriptomics reveal that SAP is accompanied by spatially organized ileal remodeling, epithelial immune-interacting rewiring, and altered neighborhood architecture, together with an ECM-centered FN1 signaling axis and attenuated Hmga2/Myb-associated regulatory programs in stem compartments. These findings provide a spatially informed cellular framework and generate testable hypotheses for mechanisms underlying impaired epithelial regeneration during SAP-associated intestinal injury.

overall_design: Severe acute pancreatitis (SAP) was induced in Sprague–Dawley rats and compared with control (CON) rats. Ileal tissues were collected and profiled using single-nucleus RNA sequencing (snRNA-seq; CON n=3, SAP n=3) and Stereo-seq spatial transcriptomics (CON n=2, SAP n=2) to characterize SAP-associated changes in cellular composition, differentiation trajectories, spatial organization, and cell–cell communication.

first: Lechang

first: Changqin

last: Xu

first: Tong

last: Su

last: Xiao

first: Xu

last: Yi

first: Yuemin

last: Feng

first: Jing

last: Wang


title: Human iPSC cardiomyocyte patch transplantation modifies extracellular matrix and fibroblast behavior after myocardial infarction

city: Suita

first: Kosuke

last: Torigata

state: Osaka

address: 2-2 Yamadaoka

department: Graduate School of Medicine, Department of Cardiovascular Surgery

country: Japan

institute: The University of Osaka

summary: Myocardial infarction (MI) followed by chronic heart failure is the main cause of mortality of heart diseases. Although reparative cell transplantation therapies with pluripotent stem cell-derived cardiomyocytes (CMs) represent a promising therapeutic strategy, molecular mechanisms of the therapy remain elusive. Here, we show that transplantation of the hiPSC-derived CM patch onto the damaged heart after MI, increases the ratio of collagen type I against collagen type III to modulate alignment of the collagen fibers at the infarcted zone. As a result, tissue elasticity of the heart is improved and fibrosis at the remote zone is reduced. Mechanistically, we find that hiPSC-derived CM patches secrete TGF-β1, directly inducing collagen type I production in fibroblasts but not collagen type III. Our results suggest the direct effect of the transplanted CM patch on the cardiac fibroblasts to improve elasticity of the damaged heart, resulting in functional recovery after MI.

overall_design: Bulk RNA-seq profiling of rat left ventricular tissues (ischemic lesion, border zone, and uninjured remote myocardium) in a myocardial infarction model. One week after LAD ligation, human iPSC-derived cardiomyocyte patches were transplanted onto the ischemic area of the left ventricle. Hearts were collected at Day 3, 1 week, and 4 weeks after transplantation. To avoid cross-species contamination, reads were aligned to a combined rat (Rnor_6.0) and human (GRCh38) reference, and only rat-derived uniquely mapped reads were retained and reported in this dataset.

first: Ryohei

last: Matsuura

first: Masanori

last: Nakayama


title: CRISPR screens identify PRMT7 as a therapeutic target to enhance T cell-mediated killing in breast cancer

city: Brisbane

first: Jonathan

last: Beesley

state: QLD

address: 300 Herston Rd Herston

country: Australia

institute: QIMR Berghofer

summary: Genome-wide association studies (GWAS) have identified more than 220 loci associated with breast cancer susceptibility, yet identifying effector genes, their modes of action and prioritising therapeutic targets remains a significant challenge. To address this, we performed pooled CRISPR knockout and inhibition screens to identify genes at risk loci that influence cytotoxic T lymphocyte (CTL) killing of MCF7 breast cancer cells in co-culture. These screens uncovered 33 candidate modulating genes, of which we validated six by single gene editing in two cell lines. Deletion of IRF1, ATF7IP, and CASP8 conferred resistance to CTL killing, while disruption of CFLAR, CREBBP and PRMT7 enhanced sensitivity. Analysis of clinical data showed that PRMT7 expression is negatively correlated with CD8+ infiltration and survival in breast cancer patient cohorts. Pharmacological inhibition of PRMT7 sensitized breast cells to CTL killing in vitro, and Prmt7-deficient tumors exhibited reduced growth and increased CD8+ T cell infiltration in immunocompetent mice. Enhanced Prmt7-dependent tumor growth was not observed in immunodeficient mice, implicating Prmt7 in immune evasion. This study underscores the utility of CRISPR screens for high-throughput functional follow-up of GWAS findings and identifies PRMT7 inhibition as a promising therapeutic strategy.

overall_design: CRISRP deletion and inhibition screens to identify predicted breast cancer risk genes which influence evasion from cytotoxic T cells. Target genes were predicted from GWAS and TWAS studies and perturbed in MCF7 breast cancer cells. Target cells were co-cultured with HLA matched primary human T cells and surviving cell sequenced.


title: Single-nucleus and Spatial Transcriptomics Reveal Intestinal Cellular Heterogeneity, Differentiation, and Cell Communication Mechanisms in SAP-induced Intestinal Injury [snRNA-seq]

last: Zhao

institute: Shandong Provincial Hospital Affiliated to Shandong First Medical University

last: Zhang


title: Scaffolding of the H4K5ac chromatin remodeling complex by lncRNA MAHAC mediates epithelial-mesenchymal transition

city: Taoyuang

first: Kou-Juey

last: Wu

state: Taiwan

address: No.15, Wenhua 1st Road, Gueishan Dist

department: Cancer Genome Research Center

institute: Chang Gung Memorial Hospital at Linkou

summary: Anchoring of a chromatin remodeler complex by long non-coding RNAs (lncRNAs) is a frequently utilized mechanism for lncRNAs to regulate gene expression. Hypoxia is a microenvironemntal condition that plays a crucial role in promoting tumor progression. We previously identified a hypoxia-inducible lncRNA, RP11-390F4.3, that regulates epithelial–mesenchymal transition (EMT) without a delineated mechanism. Here we show that the lncRNA RP11-390F4.3 (renamed MAHAC: MAintenance of Histone ACetylation) specifically induces histone H4 lysine 5 acetylation (H4K5ac) mark and promotes the enrichment of H4K5ac mark on the promoters of EMT transcription factors. MAHAC scaffolds the ILF3/NF90–ILF2–CBP complex, which is co-localized with the members of the complex inside nucleus under hypoxia. The minimal MAHAC region (nt 686–741) required for scaffolding the complex was mapped and it induces allosteric activation of H4K5ac in in vitro histone acetyltransferase assay. This minimal MAHAC region is essential for hypoxia-induced EMT, migration, invasion, and H4K5ac activation. These findings demonstrate that hypoxia-induced MAHAC represents an unexplored allosteric regulator of H4K5ac that activates EMT and induces tumor progression.

overall_design: ChIP was conducted following previously established methods (Hsu K.W et al., 2022), using the antibodies H3K4Ac. Each ChIP was carried out with 1 × 10^7 cells and 2 μg of antibody.

first: Kai-Wen

last: Hsu


title: Dissecting Context-Specific Effects of ERK5 Signaling in Triple-Negative Breast Cancer

city: New Orleans

first: Van

last: Barnes

state: LA

address: 1430 Tulane Ave SL-78

institute: Tulane SOM

summary: Triple negative breast cancer (TNBC) is an aggressive subtype of cancer with poor clinical outcomes. There is a critical need to identify novel, druggable targets for TNBC to improve therapy response and patient outcomes. Kinases are attractive therapeutic targets due to their roles in cell fate, and irregular kinase activity drives tumor progression. The role of extracellular signal-regulated kinase 5 (ERK5) in mediating TNBC extracellular matrix (ECM) has previously been described in 2D culture and in vivo. Here, we characterized the impact of ERK5 on breast cancer biology in 2D culture, 3D spheroids, and our 3D breast adipose-macrophysiological system (BA-MaPS). Methods. We assessed migration changes in MDA-MB-231 parental and ERK5-knockout (ERK5-ko) cells cultured in the three in vitro models using transwell, scratch, and spheroid pseudo-migration assays. Differential gene expression among these cell lines in the three platforms was evaluated by RNA sequencing and pathway analysis. Stromal remodeling of adipocytes and matrix was evaluated by H&E and Masson’s Trichrome. Results Across the in vitro models, ERK5 deletion impaired TNBC cell migration. ERK5-mediated transcriptomic changes included genes associated with epithelial-to-mesenchymal transition (EMT) and migration, with further analysis showing significant alterations in core and associated matrisome. Histological staining corroborated downregulation of collagen with ERK5 depletion in the BA-MaPS. The NFκB pathway was significantly upregulated only in the ERK5-ko 2D-cultured cells, not in 3D spheroids nor the BA-MaPS model. Conclusions. These results indicate a link between ERK5 and TNBC progression through regulation of TME remodeling, EMT, and cell motility. Differences in 2D culture, 3D spheroid, and BA-MaPS underscore the importance of using physiologically relevant models in breast cancer research.

overall_design: TNBC cell line MDA-MB-231 was acquired from American Type Culture Collection (ATCC). ERK5-ko cells were previously generated using a pU6-driven guide strand with dual expression cassettes for Cas9/EGFP approach (Hori-zon, Cambridge, UK). For all studes MDA-MB-231 cells and MDA-MB-231-ERK5-KO cells were used. For 2D culture, all cell lines were grown to 80% confluency in a T25 flask with Dulbecco’s Modified Eagle Medium (Invitrogen, Carlsbad, California, USA, DMEM; pH 7.4) supplemented with 10% Fetal Bovine Serum (Thermo Scientific, Waltham, Massachusetts, USA, FBS), 1% nonessential amino acids, minimal amino acids, sodium pyruvate, antibiotic/anti-myotic, and insulin (complete media) under mycoplasma-free conditions at 37°C in humidified 5% CO2  (n=3). At 80% confluence, cells pelleted for RNA extraction. For 3D studies, two million MDA-M-231 cells of each cell line were seeded in an AggreWell 400 24 well plate (Stem Cell Technologies, Vancouver, BC, Canada) that was prepped with Anti-Adherence solution (Stem Cell Technologies, Vancouver, BC, Canada) in accordance with the manufacturer’s protocol and grown overnight in the same media used in 2D experiments to form 1200 3D spheroids containing about 1700 cells/spheroid (n=3). 24 h later, spheroids were pelleted for RNA extraction. To assemble the BA-MaPS, 500,000 cells were seeded into 250μL of minced breast tissue (n=4 different donor breast tissues) and assembled using a plunger method to sandwich the breast tissue between two confluent brASC cell sheets (n=4). BA-MaPS was collected after 5 days of cultured in MEM Alpha (Thermo Scientific, Waltham, Massachusetts, USA, #12571063) supplemented with 10% Fetal Bovine Serum Premium Select (R&D Systems, Minneap-olis, Minnesota, #S11550) and 1% antibiotic/anti-myotic (ASC media) at 37°C in hu-midified 5% CO2. BrASCs were used between passages 1-5. At end point, whole construct was collected and RNA was extracted.

first: Elizabeth

middle: C

last: Martin

middle: T

last: Hoang

first: Matthew

last: Burow

first: Katherine

middle: L

last: Hebert


title: Single-nucleus and Spatial Transcriptomics Reveal Intestinal Cellular Heterogeneity, Differentiation, and Cell Communication Mechanisms in SAP-induced Intestinal Injury

first: Shulei

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

overall_design: Refer to individual Series


title: The impact of maternal diet exposure on postnatal mouse beta cells

city: Nashville

first: Guoqiang

last: Gu

state: TN

address: 2213 Garland Avenue, MRB4, Rm 9415

department: Cell and Developmental Biology

institute: Vanderbilt University

summary: The goal of this study is to examine how maternal diet exposure (nornal control diet vs. high-fat-deitor low-protein diet) impact adult beta-cell function and gene expression. Mice were used as models.

overall_design: Female wild-type mice (CD1) (~7 wks after birth)  were fed with control diet, high-fat-diet or low-protein diet for two weeks. They were then crossed with Ins1Apple males. After birth, all mice were switched to control diet until tissue collection. Islets were  isolated ~ 7 wks after birth, dissociated, and FACS-sorted for Total RNA exaction. Totl RNA were prepared using a DNA-free RNA kit from Zymo, quality-checked with Agilent Pico RNA analyzer, and suqenced using the Illumina platforms (NovaSeq 6000) in the Vanderbilt Technologies for Advanced Genomics (VANTAGE). VANTAGE also provided quality control data and primary data processing for alignment and feature (gene) identification. Only RNA preps with RIN>=9.4 were used for these experiments.

first: Simone

last: Nevills

first: Ruiying

last: Hu

first: Qi

last: Liu

first: Yu


title: Smad4-p65 interactions drive BMP-mediated protection against inflammatory cell death [ChIP-Seq]

city: Okayama

first: Shigeki

last: Suzuki

state: Okayama

address: 2-5-1 Shikata-cho, Kita-ku

department: Department of Operative Dentistry

institute: Okayama University

summary: Inflammation-induced osteoblast death undermines bone homeostasis and can aggravate bone-destructive diseases, yet how pro-survival BMP signaling intersects with inflammatory TNF–NF-κB signaling remains poorly defined. Here we show that BMP4 protects mouse osteoblasts from TNF-α–triggered apoptosis and cytotoxic death and that this cytoprotection requires both Smad4 and NF-κB p65. Integrative epigenomic profiling (ChIP-seq/ATAC-seq/RNA-seq) reveals extensive Smad4–p65 co-occupancy and identifies Samd9l as a prominent TNF-α–inducible gene that is selectively repressed by BMP4. Two Smad4/p65-bound distal elements physically contact the Samd9l promoter, exhibit TNF-responsive enhancer activity, and are required for Samd9l induction, as demonstrated by 4C-seq and CRISPR/dCas9-based chromatin closing/opening. Functionally, Samd9l depletion attenuates TNF-α–driven caspase activation and cytotoxicity in osteoblasts and enhances BMP2-driven ectopic bone formation in vivo. Cross-species mapping suggests that the two mouse regulatory elements converge into a single promoter-proximal composite element at the human SAMD9L locus, supporting a conserved inflammatory control node. Together, these findings define a BMP4–Smad4 mechanism that reshapes NF-κB enhancer outputs to limit osteoblast death and nominate the SAMD9L regulatory circuit as a therapeutic entry point for inflammatory bone loss.

overall_design: Stimulus-dependent ChIP-seq profiling of p65 and Smad4 occupancy in murine osteoblastic cells

first: Shizu

last: Hirata-Tsuchiya


title: RNA-Seq profiling of blood and jejunal samples from subclinical Holstein cattle naturally infected with Mycobacterium avium subsp. paratuberculosis revealed host transcriptional adaptations to a latent MAP infection

city: Derio

first: Marta

last: Alonso-Hearn

state: Bizkaia

address: Berreaga 1

department: Animal Health

country: Spain

institute: NEIKER

summary: Bovine paratuberculosis (PTB), caused by Mycobacterium avium subsp. paratuberculosis (MAP), is a chronic granulomatous intestinal disease that leads to substantial economic losses in the global dairy industry. Current diagnostic tests have limited sensitivity, as they can reliably detect only animals that have advanced stages of disease characterized by diffuse lesions and with the presence of clinical signs, but fail to identify those in earlier or subclinical stages, with focal or multifocal lesions in gut tissues. Previous studies have suggested that multifocal granulomas prevent lesions progression, but the molecular mechanisms involved in the establishment and maintenance of a chronic MAP infection are not fully understood. This study aimed to compare the whole transcriptomic profiles of peripheral blood (PB), jejunum (JE), and jejunal lymph node (JELN) samples from Holstein cattle with multifocal lesions and those without lesions in gut tissues. Total RNA was extracted from samples from 11 cows with multifocal lesions and 4 control cows without lesions. RNA libraries were prepared using 250 ng of RNA with the Illumina NEBNext Ultra Directional RNA library preparation kit and sequenced on an Illumina NovaSeq sequencer. On average, 34.08, 33.85, and 36.92 million raw reads were sequenced from the PB, JE and JELN samples, respectively. In cows with multifocal lesions compared to controls, 1,272 differentially expressed (DE) genes were identified in PB, mainly linked to translation, RNA splicing, and mRNA processing. In JE, 7 genes were DE and related to metabolic processes, oxidative stress response, and granulocyte migration. In JELN, 18 genes were DE and associated with the mTOR signaling, response to reactive oxygen species and hypoxia, and regulation of autophagy. The protein-to-protein interaction (PPI) analysis revealed that several differentially expressed genes are highly interconnected and associated with pathways related to splicing and translation inhibition, as well as activation of a robust innate immune response in peripheral blood. Overall, this study demonstrates that MAP persistence with multifocal granulomas results from a complex interplay of host innate immune activation and regulation, autophagy suppression, translational reprogramming, and metabolic adaptation, providing new insights into MAP pathogenesis and identifying potential biomarkers or therapeutic targets.

overall_design: RNA-Seq libraries prepared from peripheral blood (PB), jejunum (Ty), and jejunal lymph node (Tg) samples from Holstein cattle with multifocal lesions (N = 11) and without lesions in gut tissues (N = 4).

first: Gerard

last: Badia-Bringué

first: Arrate

last: Prado-López


title: Activated Interferon Signaling Suppresses Age-Dependent Liver Cancer [RNAseq_Hepatocytes]

city: La Jolla

first: Kathryn

last: Lande

address: 10010 N Torrey Pines Rd

department: IGC

institute: Salk Institute

summary: Age is a major risk factor for liver cancer, as is the case for most adult human cancers. However, the underlying mechanisms are not well defined. A better understanding of the role of aging in liver and other cancers can facilitate approaches for risk assessment, early detection and prevention. We hypothesize that age-driven changes render aged liver more sensitive to oncogenic stress and hence tumorigenesis. To investigate how the liver changes with age, we documented the immune profile, transcriptome and epigenome of healthy livers from both young and aged mice, revealing pronounced alterations with aging. Notably, in aged hepatocytes, we identified heightened interferon (IFN) signaling, as well as simultaneous tumor suppressor and oncogene signaling at both bulk and single cell level, suggestive of an aged liver that is poised for neoplasia. To challenge this seemingly poised state, we employed adeno-associated virus (AAV)-mediated expression of a c-Myc oncogene in young and aged mouse liver hepatocytes in vivo. Analysis of aged hepatocytes expressing c-Myc revealed further elevated expression of IFN Stimulated Genes (ISGs). This ISG upregulation was evident in multiple models of oncogenic stress and transformation in older mice and also observed in aged humans with Metabolic dysfunction-Associated Steatohepatitis (MASH). We determined that Stat1 is both necessary and sufficient for the age specific elevated ISG expression in old wild type mice. Remarkably, inhibiting Jak/Stat signaling alongside ectopic c-Myc expression led to high-grade hepatocyte dysplasia and tumor formation, selectively in aged mice. Together, these results suggest that an aged liver is in a state of “precarious balance”, due to concurrent activation of oncogenic and tumor suppressor pathways, but protected against neoplastic progression by IFN-signaling. Age-dependent activation of IFN signaling has been observed in many tissues and recent studies have demonstrated its detrimental consequences on aging, raising the question as to why IFN-signaling is activated during aging. We propose that aged tissues are intrinsically at higher risk of cancer and age-dependent activation of IFN-signaling is an adaptive process to protect from tumorigenesis, but one that also has maladaptive consequences.

overall_design: RNAseq profiling of hepatocytes isolated from young and old mice using 2-step perfusion, Black6J single line.

first: Aaron

last: Havas

first: Peter

last: Adams


title: Modeling early human heart development using an iPSC-based 3D bioprinted model of embryonic heart tube

city: Atlanta

first: Linqi

last: Jin

state: Georgia

address: 1750 Haygood Dr HSRB II, Floor 4 Room S435

department: Biomedical Engineering

institute: Emory University

summary: Human heart development is a precisely coordinated process involving dynamic transcriptional and morphological changes. Due to limited access to the developing human heart in utero and lack of accurate experimental models, the cell-microenvironmental interactions underlying human heart development remain elusive. Advances in 3D bioprinting and stem cell technologies have enabled the fabrication of in vitro analogues of cardiac tissues with complex structures, while incorporating cell intrinsic (genetic) and microenvironment factors. Here we present a perfusable 3D bioprinted model of human embryonic heart tube (eHT), composed of distinct layers of myocardium, cardiac jelly, and endocardium. Human induced pluripotent stem cell-derived cardiomyocytes and endothelial cells were cocultured in the engineered eHTs under dynamic flow. This system demonstrated robust cell viability and cardiac function, including full lumen endothelialization, progressive myocardial compaction, and global tissue contraction. A promoting effect of dynamic flow on cardiac maturation and cell lineage commitment was revealed by single-cell RNA sequencing. The established eHT model offers a novel research-enabling platform to study human heart development, various (congenital) heart disease, and therapeutic interventions.

overall_design: scRNA-seq: hiPSC-CMs and HUVECs cocultured in 3D bioprinted heart tube models were harvested after (1) 7 days of 3D static coculture and (2) 7 days of 3D static coculture + 5 days perfusion coculture. Cell subpopulations and phenotypical gene expression related to 3D coculture and flow-regulated cardiac development were analyzed in this study.

first: Vahid

last: Serpooshan


title: Molecular Indicators of Isometric Exercises Efficacy in Early Rehabilitation of Older Adults after Total Hip Arthroplasty

city: Puschino

first: Kirill

middle: S

last: Krasnov

state: Moscow region

address: institutskay 3

country: Russia

institute: ITEB RAS

summary: Developing molecular methods for assessing the effectiveness of physical rehabilitation remains a pressing task. Our study aimed to assess the utility of transcriptome analysis of muscle biopsies in evaluating the efficacy of the isometric exercises (IE) added to the standard protocol in early rehabilitation of older patients during the initial two weeks post total hip arthroplasty (THA). Blood concentrations of total leukocytes, neutrophils, IL6, IL8, IL1β, myoglobin, etc. were measured, and transcriptome analysis of rectus femoris biopsies from the operated leg was performed before and after (1 and 12 days) THA in women aged 73–77 years. The additional IE in the experimental rehabilitation group led to a significant acceleration in the recovery of IL6, IL8 and IL1β blood levels to the normal ranges compared to the control group, as confirmed by Fisher’s exact test for this cytokine combination. The results of Gene Set Enrichment Analysis and Differen-tially Expressed Gene Analyses for the muscle biopsies point to accelerated resolution of inflammation, along with enhanced activation of genes associated with angiogenesis, lymphangiogenesis, vasodilation, and vasoconstriction in the experimental rehabilita-tion group compared to the control group. Thus, IL6, IL8 and IL1β blood levels can serve being in combination as molecular indicators of the efficacy of early rehabilitation after THA, and transcriptome analysis of the rectus femoris biopsies of the operated leg allows revealing molecular indicators of regenerative processes in muscle tissue near the surgery area after THA.

overall_design: Eight female patients aged 73–77 years underwent THA. Exclusion criteria included the presence of acute or decompensated somatic conditions, as well as those with any severe comorbidities that, in the physician’s judgement, could hinder study participation, were excluded. Patient exclusion criteria due to failure to comply with protocol requirements were anticipated but not implemented, and all patients fully completed the rehabilitation programs. Patients were allocated to two groups sequentially (without formal randomization) as they were enrolled according to the dates of their hospitalization. Control group (n=4) followed standard IE protocols in accordance with the Russian Ministry of Health’s national clinical guidelines “Coxarthrosis”. Patients of the experimental group (n=4) performed a novel rehabilitation regimen incorporating additional IE, as described in our patent. Rehabilitation was initiated on the first postoperative day following THA and continued for 12 consecutive days. Each patient underwent two daily sessions, with session duration ranging from 15 minutes to 1 hour depending on the assigned rehabilitation protocol. The clinical parameters of blood, ESR, CRP, and the concentrations of some pro-inflammatory interleukins (IL6, IL8, IL1β) in the blood were evaluated before the THR, as well as 1 day and 12 days after the THR for each patient. At these times, rectus femoris biopsies of the operated leg were performed from each patient for transcriptomic analysis.

first: Elena

last: Maksimova

first: Anatoly

last: Senotov

first: Victor

middle: I

last: Shevchenko

first: Vladimir

last: Akatov

first: Artem

last: Ermakov

first: Elizaveta

last: Zhdanova


title: Smad4-p65 interactions drive BMP-mediated protection against inflammatory cell death [RNA-Seq]

first: Shigeki

last: Suzuki

overall_design: Examination of the effects of TNFa and/or BMP4 on gene expression in murine osteoblastic cells


title: Smad4-p65 interactions drive BMP-mediated protection against inflammatory cell death [4C-Seq]

overall_design: Examination of the effects of TNFa and BMP4 effects on genome-wide chromatin interaction from the fixed viewpoints in murine osteoblastic cells.

first: Shizu

last: Hirata-Tsuchiya


title: 6K-plex RNA CosMx data fra human FFPE samples from patients with psoriasis.

city: Aarhus N

first: Thomas

last: Emmanuel

state: Midtjylland

address: Palle Juul Jensens Boulevard 99

department: Dermatology

country: Denmark

institute: Aarhus University

summary: IκBζ, encoded by NFKBIZ, is a key transcriptional regulator in psoriasis, with a well-known role in keratinocytes but an unclear function in dermal fibroblasts. This study investigates cytokine-driven regulation of IκBζ in primary human dermal fibroblasts and integrates spatial transcriptomics to map NFKBIZ expression in psoriatic skin. Spatial transcriptomics (CosMx™) revealed expected expression of NFKBIZ in keratinocytes and additionally demonstrated elevated expression in dermal fibroblasts in lesional compared with non-lesional skin. Together, these findings identify IκBζ as an important regulator of inflammatory responses in dermal fibroblasts, broadening its established role in psoriasis pathogenesis.

overall_design: To determine whether cytokine-induced NFKBIZ upregulation in fibroblasts also occurs in vivo, we performed single-cell spatial transcriptomics on paired lesional and non-lesional psoriatic skin tissue microarray cores (n=7) using the CosMx™ platform with 6k-plex + 20 custom genes. The psoriasis samples were subset from a larger cohort of TMA skin biopsies placed on the slide.

first: Svraka

last: Lejla

first: Andersen

last: Anna Skarnvad

first: Touborg

last: Toke

first: Emmanuel

last: Thomas

first: Udayaraja

first: Kadarmideen

last: Haja N.

first: Bertelsen

last: Trine

first: Vestergaard

last: Christian

first: Johansen

last: Claus


title: Comparison of the kidney transcriptome of 45 days old principal cell-specific Tsc1 knockout (Tsc1f/f/Aqp2 Cre) vs Wild-type (WT) mice.

city: Albuquerque

first: Marybeth

last: Brooks

state: New Mexico

address: 915 Camino de Salud

department: DOIM - Nephrology

institute: University of New Mexico

summary: Tuberous sclerosis complex is a genetic disorder that affects multiple organs. In the kidney, it presents as hamartomas and cysts. The epithelium of TSC renal cysts is primarily composed of A-intercalated cells. In these studies, we compared the renal transcriptomes of 45 days old principal cell-specific Tsc1 knockout (Tsc1f/f/Aqp2 Cre; Tsc1 KO) and WT mice.

overall_design: The kidney transcriptome of principal cell-specific C57BL/ 6 Tsc1 knockout mice (Tsc1f/f/Aqp2 Cre) vs WT C57BL/ 6 at 45 days of age were compared.

first: Manoocher

last: Soleimani

first: Kamyar

last: Zahedi

first: Sharon

last: Barone


title: Smad4-p65 interactions drive BMP-mediated protection against inflammatory cell death [ATAC-Seq]

overall_design: Examination of the effects of TNFa and/or BMP4 on chromatin accessiblity in murine osteoblastic cells


title: Mechanisms linking cytoplasmic decay of translation-defective mRNA to transcriptional adaptation	 [TT-seq]

city: Cambridge

first: Mohamed

middle: A.

last: El-Brolosy

state: MA

address: 455 Main Street

institute: Whitehead Institute for Biomedical Research

summary: Transcriptional adaptation (TA) is a genetic robustness mechanism through which mutant mRNA decay induces sequence-dependent upregulation of so-called adapting genes. How cytoplasmically generated mRNA fragments impact nuclear transcription remains poorly understood. Using genome-wide CRISPR screens, we uncover ILF3 as an RNA-binding protein connecting cytoplasmic mRNA decay and transcription during TA, and show it is required for a range of TA substrates. ILF3 is enriched at adapting genes’ RNAs, and its artificial recruitment via dCas13 promotes gene expression. Using tiling oligonucleotide screens, we identify trigger RNA fragments that activate adapting genes when introduced into cells. Further functional dissection reveals critical role for homology between trigger and target sequences. These findings enhance our molecular understanding of TA and inform design of programmable oligonucleotides for gene expression augmentation.

overall_design: TT-seq For each replicate, 10 million cells were seeded into two 15-cm dishes one day prior to the experiment. Two replicates were performed per genotype, resulting in a total of four plates per genotype. On the day of the experiment, one plate per genotype was processed at a time to avoid handling more than four plates simultaneously. The media was aspirated and replaced with fresh media containing 500 µM 4-thiouridine (4sU) for 20 minutes. Following incubation, the media was aspirated again, and cells were rapidly washed with PBS. Two milliliters of TRIzol were then added per plate, and the cells were scraped and collected into tubes, which were flash-frozen in liquid nitrogen. TRIzol samples were then handled to the Nascent Transcriptomics Core at Harvard Medical school which performed the TT-seq library preparation and sequencing as described before (Vlaming et al., NSMB, 2022 & Stein et al., Mol Cell, 2022).

first: Jonathan

last: Weissman


title: Comparison of the kidney transcriptome of 45 days old principal cell-specific Tsc1 knockout (Tsc1f/f/Aqp2 Cre), 45 days old principal cell-specific Tsc1 knockout/Foxi1 knockout (Tsc1/Foxi1 dKO), and 45 days old WT mice

summary: Tuberous sclerosis complex is a genetic disorder that affects multiple organs. In the kidney, it presents as hamartomas and cysts. The epithelium of TSC renal cysts is primarily composed of A-intercalated cells. The transcription factor FOXI1 is indispensable in the development of intercalated cells. The expression of Foxi1 mRNA is significantly upregulated in the kidneys of various mouse models of TSC. The simultaneous ablation of Tsc1 and Foxi1 prevents the formation of cysts in the kidneys of Tsc1 KO mice. In these studies, we compared the renal transcriptomes of 45 days old principal cell-specific Tsc1 knockout, Tsc1/Foxi1 double knockout, and WT mice.

overall_design: The kidney transcriptome of principal cell-specific C57BL/6 Tsc1 knockout mice (Tsc1f/f/Aqp2 Cre), principal cell-specific C57BL/ 6 Tsc1 and Foxi1 double knockout mice and WT C57BL/6 at 45 days of age were compared.

last: Zahdei


title: Dynamin 1 promotes colorectal cancer progression by activating the PI3K/Akt signaling pathway

city: Shanghai

first: Rui

last: Chen

address: No. 128 Ruili Road, Minhang District

institute: The Fifth People's Hospital of Shanghai, Fudan University

summary: Background: Uncontrolled proliferation, local invasion, and distant metastasis are hallmarks of malignancies, and they play crucial roles in tumor progression. Dynamin 1 (DNM1) is a member of the dynamin guanosine-5′-triphosphatease (GTPase) subfamily that regulates membrane fission, cytokinesis, and vesicle secretion. However, its function in colorectal-cancer (CRC) progression remains unclear. Methods: We used public datasets and a tissue microarray (TMA) cohort to analyze differential expression of DNM1 between CRC tissues and adjacent nontumor tissues (NTs). The role of DNM1 in CRC cells was determined by in vitro experiments, including colony formation, Cell Counting Kit-8 (CCK-8), and Transwell assays. Ribonucleic acid sequencing (RNA-seq) and bioinformatics analysis were performed to investigate mechanisms that DNM1 may be involved in. Xenograft and metastatic models were established to investigate the effects of DNM1 on tumor growth and metastasis. Results: We found that DNM1 expression was upregulated in CRC tissues, which significantly correlated with poor patient prognoses. DNM1 overexpression (OE) enhanced the proliferation, migration, and invasion capabilities of CRC cells both in vitro and in vivo, whereas DNM1 knockdown (KD) yielded the opposite results. Mechanistic studies revealed that DNM1 mediated the activation of epithelial–mesenchymal transition (EMT) and the phosphoinositide 3-kinase (PI3K)/protein kinase B (Akt) signaling pathway. Conclusion: Our findings demonstrated that DNM1 promoted cell proliferation, migration, and invasion as well as EMT through the PI3K/Akt signaling pathway in CRC, making it a potential prognostic marker and therapeutic target in this disease.

overall_design: To identify genes differentially expressed upon DNM1 knockdown, we performed RNA-seq analysis comparing SW620 cells transduced with a control vector to those with stable DNM1 knockdown.

first: Runqi

last: Hong

first: Qichang

last: Liu

first: Zhipeng

last: Cao

first: Liang

first: Huipeng

last: Wang

first: Shanliang

last: Han

first: Chongwei

last: Ke


title: COP9 Signalosome is Required for Adipose Tissue Maintenance and Metabolic Health

city: Augusta

first: Weiqin

state: GA

address: 1462 Laney Walker Blvd

department: Physiology

institute: Augusta University

summary: COP9 (constitutive photomorphogenesis mutant 9) signalosome (CSN) is composed of eight subunits (CSN1 through CSN8). It acts as an essential regulator of Cullin-RING-ubiquitin ligases (CRLs), which target critical cellular regulators for degradation via the ubiquitin (Ub) proteasome pathway. The role of CSN in adipose tissue development and function has not yet been studied. We sought to determine the role of CSN8, the smallest subunit of the CSN complex, in adipogenesis, adipose tissue maintenance, and metabolic balance. In this study, we generated mice with adipocyte-specific deletion of CSN8 (Csn8AKO) and confirmed the deletion of CSN8 and the disruption of CSN holo-complex formation and Cullin deneddylation in white and brown adiposes. We performed bulk RNA-Seq and identified significant remodeling of white and brown adipose tissues, characterized by adipocyte cell death and inflammation. Specifically, white and brown adipose tissues lacking CSN8 exhibited marked upregulation of apoptotic and pyroptotic cell death, which was associated with alterations in ubiquitination and proteasome activity. Taken together, our data highlight that CSN8/CSN is crucial for maintaining protein homeostasis in adipose tissue, promoting adipocyte survival, supporting adipose tissue maintenance, and overall metabolic health.

overall_design: We performed bulk RNA-Seq in subcutaneous adipose tissues from 12-week-old male wildtype (WT) and Csn8AKO (KO) mice (n=4/group), and brown adipose tissues from 4-week-old male WT and KO mice (n=5/group).

first: Hongyi

last: Zhou


title: Social Processing in the Amygdala: Single-Nucleus RNA-Sequencing Reveals Distinct Neuronal Responses to Dominant and Subordinate Cues

city: Austin

first: Madeleine

last: Dwortz

address: 2506 Speedway, NMS BLDG

department: Center for Biomedical Research Support

institute: University of Texas at Austin

summary: Single-nucleus RNA-sequencing (snRNA-seq) was performed on mouse amygdala tissue to examine transcriptional responses to social olfactory cues associated with dominant and subordinate individuals. nuclei were isolated from the amygdala and processed using the 10x Genomics 3’ platform. The resulting dataset includes cell-type annotations and differential expression profiles across conditions. These data support investigation of neuronal population structure and gene expression changes underlying social cue processing.

overall_design: Following presentations with urinary olfactory cues from dominant or subordinate hierarchy members, fresh frozen brains were collected.  Bilateral amygdala samples from three subjects were pooled for each sample.

middle: F

first: James

last: Curley

first: Hans

last: Hofmann


title: Transcriptional programs dictating tumor cell fate decisions in neuroblastoma lymph node metastasis [spatial transcriptomics]

city: Cincinnati

first: Richard

last: Lu

state: Ohio

institute: CINCINNATI CHILDREN'S HOSPITAL MEDICAL CENTER

summary: Neuroblastoma, a deadly pediatric cancer from the sympathetic ganglia of the peripheral nervous system, frequently metastasizes, driving poor outcomes in high-risk cases. While primary tumors are well-characterized, the cellular and molecular dynamics of metastasis  remain poorly understood. Here, we employed  single-cell multi-omics and spatial transcriptomics to profile lymph node metastases in high-risk neuroblastoma compared to primary adrenal masses. We found that lymph node metastases displayed unique cellular heterogeneity and plasticity marked by a shift toward mesenchymal-like and cancer stem cell states, with enriched epithelial-to-mesenchymal transition (EMT) programs. Lymph node metastatic niche exhibited altered tumor microenvironment dynamics, characterized by increased immunosuppressive myeloid subsets, heightened immune checkpoint signaling and lymphocyte exhaustion, indicative of immune evasion and dysfunction. Our multi-omics studies reveal distinct features of high-risk neuroblastoma that contribute to metastasis and therapy resistance, pointing to potential therapeutic vulnerabilities of the aggressive metastatic disease.

overall_design: One high-risk neuroblastoma from primary adrenal mass and one high-risk neuroblastoma from reticuloendothelial cervical lymph nodes were analyzed using spatial transcriptomics.

first: Natalie

last: Wu


title: AMPKα1 Deficiency in Macrophages Impairs Tendon Regeneration and Tendon Stem Cell Function via TNF-α–FBP2 Signaling

city: shanghai

first: lisha

last: zhu

address: yanchangzhonglu street

institute: tongji university

summary: Tendon healing is limited by the minimal intrinsic regenerative capacity of the tissue, resulting in the formation of fibrovascular scar tissue rather than functional regeneration. Macrophage immunometabolism governs the balance between inflammation and repair; however, its effects on tendon regeneration are poorly understood. In this study, we investigated the differential activation of macrophage AMP-activated protein kinase (AMPK) and its phenotypic alterations in neonatal and adult tendon injury models. Using myeloid-specific AMPKα1 knockout (LysM-Cre; Ampkα1fl/fl) mice, we found that macrophage AMPKα1 deficiency impairs tendon regeneration and repair capacity, leading to compromised proliferation, migration, and differentiation functions of tendon stem/progenitor cells (TSPCs). Mechanistically, AMPKα1-deficient macrophages exhibited increased TNF-α production, which promoted the expression of Fructose-bisphosphatase 2 (FBP2) in a PI3K/AKT-dependent manner. In addition, knockdown of Fbp2 rescued mitochondrial dysfunction in TSPCs and facilitated tissue repair and regeneration. Collectively, these findings underscore the immunometabolism mechanism linking macrophage AMPKα1 activity to stem cell injury responses via a TNF-α–FBP2 axis and provide potential therapeutic targets for regulating stem cells.

overall_design: tendon tissues from control and Lysm-Cre; Ampkα1fl/fl mice (3 mice per condition, neonatal mice) were snap frozen in liquid nitrogen for further analyses.

first: Lisha

last: Zhu

first: Yu

first: Xinmeng

last: Shi

last: Jiang

first: Yan


title: Cytosolic DNA structures produced by mismatch-repair deficiency coordinate anti-tumor immunity in colorectal cancer

city: Edmonton

first: Kristi

last: Baker

state: AB

address: 11560 University Ave NW, Room 2308

country: Canada

institute: University of Alberta

summary: Patients with the microsatellite instable (MSI) subtype of colorectal cancer (CRC) have better prognosis and immunotherapy response than patients with the chromosomally instable (CIN) subtype due to improved cytotoxic T cell responses. This is in part due to high production of the chemokines CXCL10 and CCL5 from constitutive activation of the cytosolic DNA (cyDNA) sensor cGAS/STING by specific features of MSI cyDNA that lead to more effective cGAS/STING pathway activation. Here, we investigate MSI and CIN cyDNA structure and show that MSI cyDNA is enriched in G-quadruplexes which improve cGAS/STING and CD8+ T cell activation. We also show that micronuclei are less effective at inducing anti-tumor immunity and instead increase Treg activation and IL10 production. Overall, these data highlight the role of specific cyDNA structures in anti-tumor immunity and provide knowledge for improved design of therapeutic DNA-based cGAS/STING agonists to improve the prognosis of poorly immunogenic tumors like CIN CRCs.

overall_design: On day 1, C57BL/6 mice were injected orthotopically into the descending colon wall with 5x10E5 MSI or CIN MC38 cells as performed previously using a flexible needle (Hamilton) inserted through the working channel of a Wolfe endoscope and visualized using the ColoView Imaging System. Fresh bone marrow derived dendritic cells (BMDCs) were resuspended in RPMI at 2x10E6 cells/mL for stimulation using 2ug MSI or CIN free cyDNA or micronuclei and 0.125uL/mL Lipofectamine 2000 per 2x10E6 cells for 30 minutes at 37°C as per manufacturer instructions. Following 2 PBS washes, 2x10E6 BMDCs were injected intraperitoneally into the tumor bearing mice on days 1, 6, and 12. On day 15, tumors were collected and pulverized using glass beads (Sigma Aldrich) and a Mini Beadbeater before RNA isolation using TRIzol (Invitrogen). Equal RNA quantities from each of the 3 biological replicates were then combined for bulk RNA sequencing.

first: Shayla

last: Mosley