title: A transcriptomic map of ligand-receptor interactions within bovine antral follicles reveals commonality and redundant strategies for intercellular communications and predicts intrafollicular factors for improving oocyte quality

city: 北京市

first: Zhaochen

last: Wang

address: 2 Yuanmingyuan West Road, Haidian District, Beijing

institute: China Agricultural University

summary: Background: Ovarian follicle is an enclosed microenvironment that ensures oocyte growth and maturation, making it essential for female fertility. Normal folliculogenesis development and oocyte maturation strictly rely on orchestrated intercelluar interactions among the mural granulosa cells (MGCs), cumulus cells (CCs), and the oocyte within antral follicles. Despite the importance, how these cell populations communicate remains largely unknown. Due to this knowledge gap, current oocyte in vitro maturation (IVM) systems fail to fully replicate the physiological follicular microenvironment due to the lack of MGC regulation, leading to poor oocyte quality and lower success rate of assisted reproductive technologies. Results: RNA-seq was performed on MGCs, CCs, and oocytes isolated from single bovine antral follicles at different developmental stages (3–5 mm, 6–8 mm and 9–12 mm). Using a ligand-receptor interaction scoring strategy, we constructed a dynamic intrafollicular interaction map. We revealed that MGCs are the most active cell type, acting as either secretors or receivers. Intriguingly, intrafollicular crosstalk utilizes a spatiotemporally degenerate strategy, characterized by extensive ligand-receptor redundancy across cell types and stages. Notably, the intrafollicular communication map enables the prediction of MGC-secreted factors that can improve the oocyte quality after IVM. Based on the predicted candidate factors, we have confirmed that supplementation with PTN significantly improved in vitro matured oocyte quality and subsequent embryonic development. In addition, we also revealed significant heterogeneity at single-follicle resolution, unhealthy follicles showed aberrant activation or loss of partial core interaction signaling, suggesting the critical role of interactions in determining follicular fate. Conclusions: By reconstructing a map of intrafollicular interaction map, our study provides novel insights and important clues for understanding cellular and molecular mechanisms that fine-tune antral folliculogenesis. We also offer a roadmap for predicting candidate factors that can be used for optimizing mammalian in vitro embryo production system.

overall_design: RNA-seq was performed on matched mural granulosa cells (MGCs), cumulus cells (CCs), and oocytes isolated from single bovine antral follicles at three different developmental stages: small (3-5 mm), medium (6-8 mm), and large (9-12 mm).

first: Zhenni

last: Zhang

first: Jianhui

last: Tian

first: Yinjuan

first: Lei

last: An


title: AIP Mutation Leads to Significant Alterations in Gene Expression, Altered Sensitivity to AHR Ligands, and Early Lethality in Zebrafish

status: Public on Jul 22 2026

city: Corvallis

first: Dante

last: Perone

state: Oregon

country: USA

institute: Oregon State University

type: Expression profiling by high throughput sequencing

summary: Humans and other organisms are regularly exposed to chemical compounds that elicit toxicity through the aryl hydrocarbon receptor (AHR) signaling pathway. AHR agonists include polycyclic aromatic hydrocarbons, polychlorinated biphenyls, as well as some natural products, pharmaceuticals, and endogenous compounds. Interindividual sensitivity to AHR agonists exists. Several populations of Atlantic Killifish (Fundulus heteroclitus) have independently evolved resistance to high levels of pollution. Genome-wide association demonstrated that variation in the AHR interacting protein (AIP) was associated with resistance to AHR ligands. AIP binds to the AHR in the cytosol where it plays a role in stability and nuclear localization, however its exact function is poorly understood. Aip mutant zebrafish (Danio rerio) lines were generated using CRISPR-Cas9 technology. Deletions were generated in exon 2 (aipwh86) or exon 5 (aipwh239), both resulting in an early stop codon. Zebrafish homozygous for either mutation died at 7–10-days post-fertilization (dpf). No such effect was observed in ahr mutant lines. Larvae from the aipwh239 line were exposed to four toxic AHR ligands from diverse chemical classes. Homozygous mutant larvae exposed to PCB126, 5-nitroacenaphthene, and benzo(k)fluoranthene showed reduced sensitivity compared to both heterozygous and wildtype larvae. However, changes in sensitivity were ligand-dependent. In contrast, homozygous larvae demonstrated increased sensitivity to leflunomide. mRNA sequencing was performed at 5 dpf in unexposed larvae from both aip lines. Around one thousand DEGs and alternative splicing products were observed in homozygous mutants from both lines. Gene sets and binding motifs involved in cellular stress, apoptosis, innate immune response, proteolysis, replication, and metabolism were enriched. Our findings highlight the context-dependent nature of Aip in Ahr modulation and the critical roles that Aip plays in regulating cellular homeostasis.

overall_design: Single 5 day post fertilization (dpf) zebrafish larvae were homogenized in a 96-well format. RNA was extracted from the single larvae. Following genotyping or extracts single larval extracts were combined into pools of five larvae. Four replicates of each genotype and line (aip(+/+), aip(+/-), and aip(-/-) for both aipwh86 and aipwh239 lines) were submitted to Lexogen for CORALL mRNA-Seq V2 whole transcriptome sequencing.

middle: M

first: Jane

middle: K

last: La Du

first: Sibel

middle: I

last: Karchner

first: Neelakanteswar

last: Aluru

first: Spencer

middle: R

last: Stinson

first: Lisa

last: Truong

first: Mark

middle: E

last: Hahn

first: Robyn

middle: L

last: Tanguay


title: Arid3b suppresses CD8+ T cell infiltration and function in Microsatellite-stable colorectal cancer via Runx3

city: Beijing

first: Zhidong

last: Gao

address: No.11 Xizhimen South Street

country: China

institute: Peking University People’s Hospital

summary: Microsatellite stable/proficient mismatch repair (MSS/pMMR) colorectal cancer (CRC) is characterized by a cold tumor microenvironment, marked by sparse CD8⁺ T cell infiltration and resistance to immune checkpoint inhibitors (ICIs). To uncover regulators that limit CD8⁺ T cell infiltration in MSS CRC, we conducted an in vivo CRISPR/Cas9 screen targeting genes in CD8⁺ T cells using a CMT93 cell-derived tumor model. This screen identified Arid3b as a key negative regulator of CD8⁺ T cell tumor infiltration and antitumor activity. Genetic ablation of Arid3b in CD8⁺ T cells significantly enhanced their intratumoral accumulation and mediated robust tumor control. Mechanistically, Arid3b deficiency upregulated Runx3, promoting a tissue-resident memory phenotype and effector function. Notably, the benefits conferred by Arid3b knockout were abrogated by Runx3 deletion, indicating a Runx3-dependent mechanism. In summary, targeting ARID3B could offer a promising strategy to reshape the tumor microenvironment and sensitize MSS CRC to immunotherapy.

overall_design: RNA-seq profiling of Arid3b/Runx3 double knockout (Arid3b/Runx3-dKO), Runx3 knockout (Runx3-KO), Arid3b knockout (Arid3b-KO) or intergenic sequence knockout (Control) OT1 CD8+ T cells co-cultured with or without CMT93-OVA cells for 4 hours

first: Shuo

first: Sen

last: Hou

first: Ce

last: Luo

first: Yingjiang

last: Ye

first: Zexian

last: Zeng


title: DNA methylation profiles of typeA spermatogonia of the control group and arsenic group [pro]

city: Tsukuba

first: Takehiro

last: Suzuki

state: Ibaraki

address: 16-2 Onogawa

country: Japan

institute: National Institute for Environmental Studies

type: Methylation profiling by high throughput sequencing

summary: Pregnant C3H mice were given tap water (control group) and tap water containing 85 ppm sodium arsenite from gestational day 8 to 18 (arsenic group), respectively. The DNA methylomes of prospermatogonia of F1 mice were investigated by RRBS method.

overall_design: Comparative DNA methylation analysis of RRBS data for control group and arsenic group

first: Keiko

last: Nohara


title: RNA sequencing of adult mouse brain microvascular fragments

city: Uppsala

first: L.

last: He

address: Dag Hammarskjölds Väg 20

country: Sweden

institute: Uppsala University

summary: In this study, brain microvascular fragments were isolated and subjected to bulk RNA sequencing.

overall_design: Bulk RNA sequencing was performed on isolated brain microvascular fragments from three wild‑type mice.

first: Maarja

last: Andaloussi Mäe

first: Elisa

last: Vazquez-Liebanas

first: Khayrun

last: Nahar

first: Michael

last: Vanlandewijck

first: Liqun

first: Christer

last: Betsholtz


title: Multiome-based identification of HSC subtype markers shows that ageing, but not inflammatory stress, increases HSC platelet bias

city: Oxford

first: Claus

last: Nerlov

address: John Radcliffe Hospital, University of Oxford

department: MRC Molecular Haematology Unit

country: United Kingdom

institute: Weatheral Institute of Molecular Medicine

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Individual haematopoietic stem cells (HSCs) display heterogeneous capacities to reconstitute the major blood lineages, including platelets, erythrocytes, myeloid cells, B cells, and T cells. Single-cell transplantation assays have revealed that the HSC compartment contains lineage-restricted subtypes capable of reconstituting only specific lineages, such as platelets, alongside true multi-lineage HSCs. The proportion of these lineage-restricted HSCs increases with age, contributing to declined immunity and potentially to clonal haematopoiesis. To date, their identification and isolation have primarily relied on transgenic reporters, such as the Vwf-EGFP mouse line, which offer only moderate accuracy. In this study, we profiled highly purified adult mouse long-term HSCs (LT-HSCs; LSK CD48⁻ CD150⁺ CD34⁻) using the DOGMAseq platform, which enables simultaneous measurement of transcriptome (RNA-seq), chromatin accessibility (ATAC-seq), and surface protein expression (CITE-seq). We subsequently identified candidate clusters corresponding to platelet-biased and multi-lineage HSCs, and developed a fluorescence-activated cell sorting (FACS) strategy to enrich these populations. This strategy employs four surface markers detectable with commercially available antibodies and achieves higher enrichment specificity than the Vwf-EGFP reporter.

overall_design: Fresh bone marrow cells were harvested from 24-month-old female C57BL/6 mice. Cells were stained with a combination of fluorescence-conjugated antibodies for FACS and oligo-tagged antibodies for CITE-seq. Long-term haematopoietic stem cells (LT-HSCs) were then isolated by flow cytometry and processed using the DOGMA-seq workflow.

first: Bowen

last: Zhang

first: Yiran

last: Meng

first: Xiying

last: Ren


title: DNA methylation profiles of typeA spermatogonia of the control group and arsenic group [typeA]

summary: Pregnant C3H mice were given tap water (control group) and tap water containing 85 ppm sodium arsenite from gestational day 8 to 18 (arsenic group), respectively. The DNA methylomes of type A spermatogonia of F1 mice were investigated by RRBS method.


title: Increased mRNA translation delays tumor initiation and exposes a therapeutic vulnerability in lung cancer

city: Glasgow

first: Joseph

middle: Alexander

last: Waldron

address: Switchback road

institute: Beatson Institute for Cancer Research

summary: Although protein synthesis inhibitors are being evaluated as anti-cancer agents, the dynamics of mRNA translation in early tumorigenesis are still poorly understood. We report that deletion of the mRNA-translation repressor, eIF4A2 in early KRAS-driven lung adenocarcinoma leads to a dysregulated protein synthesis landscape characterised by a strongly upregulated secretome, enlarged secretory compartments, increased oxidative metabolism and acquisition of senescence-like characteristics. Paradoxically, this overdriven protein synthesis landscape delays tumorigenesis and leads to appearance of clusters of non-proliferative, p21-positive KRAS-expressing cells in the lung. Administration of rapamycin to reduce mRNA translation, suppresses senescence and restores tumorigenesis following eIF4A2 deletion. Importantly, some eIF4A2 deleted cells overcome senescence to form tumors that growth aggressively. Analysis of these eIF4A2-deleted tumors through a combination of multiplex imaging and spatial transcriptomics pointed to a rewiring of KRAS downstream pathways through enhanced MAP-kinase and reduced PI3K signalling. Consequently, these tumors may be eradicated by administration of a MEK inhibitor, in contrast to eIF4A2 positive lesions. Thus, dysregulated mRNA translation exposes a potential therapeutic vulnerability in KRAS-driven lung adenocarcinoma by forcing cancer cells to rely on MEK signalling.

overall_design: Ribosome protected RNA fragments or total cytoplasmic RNA samples were harvested from cell line. Totals represent the paired cytoplasmic control, which was extracted with TRIzol from the cytoplasmic lysate prior to RNase1 digestion. Each sample represents a biological replicate (independent experiments where cells are plated and harvested on different days). All samples were taken from KMNTC, and KM4A2cr cells, plated in 10cm plates and allow to reach 90% confluency prior to processing

middle: A

first: June

last: Munro

first: Luis

last: Pardo-Fernandez

first: Martin

last: Bushell

first: Jim

last: Norman


title: Targeting microglial phosphatidylethanolamine synthesis pathway promotes GABARAP-associated phagocytosis and A clearance in Alzheimer's disease

city: Gwangju

first: Eunkyung

last: Lee

address: 123 Cheomdan-gwagiro, Buk-gu

country: South Korea

institute: Gwangju Institute of Science and Technology

summary: Alzheimer’s disease (AD) is a major cause of dementia and a prevalent age-related neurodegenerative disorder, characterized by progressive cognitive impairment and memory loss. Although metabolic activation or dysfunction of microglia is implicated in AD pathogenesis, the phospholipid metabolism–associated signaling mechanisms within microglia remain poorly defined. In this study, we demonstrate that quinolinic acid (QA), a byproduct of tryptophan catabolism via the kynurenine pathway, activates the microglial Kennedy pathway—responsible for de novo phosphatidylethanolamine (PE) biosynthesis—by upregulating the enzymes EPT1 and ETNK1. This activation markedly enhances the synthesis of PE species enriched in polyunsaturated fatty acids. Concurrently, QA significantly increases the expression of gamma-aminobutyric acid receptor–associated protein (GABARAP), promotes its lipidation, and facilitates GABARAP-associated phagocytosis (GAP) of Aβ oligomers by microglia. Knockdown of EPT1 and ETNK1 attenuated QA-induced PE synthesis and impaired GAP of Aβ oligomers, while inhibition of GABARAP lipidation via STBD1-deconjugase substantially reduced QA-mediated GAP. QA administration upregulated microglial Gabarap expression and decreased Aβ plaque burden in the hippocampus of AD (5xFAD) mice, whereas Gabarap knockdown abrogated QA-induced microglial clearance of Aβ. Collectively, these findings reveal a paradoxically beneficial role of QA in activating a microglia-specific signaling cascade that promotes PE biosynthesis and GAP, thereby enhancing Aβ clearance and mitigating AD pathology. Targeting the microglial PE synthesis pathway and GAP may represent a promising therapeutic strategy to ameliorate Aβ accumulation and slow AD progression

overall_design: Bulk RNA-seq was performed on hippocampal tissues from three experimental groups: quinolinic acid (QA)-injected 5xFAD mice, vehicle-injected 5xFAD mice, and vehicle-injected wild-type (WT) mice, with three biological replicates per group, to investigate transcriptomic changes associated with QA treatment in an Alzheimer's disease mouse model.


title: Endothelial cytochrome P450 -derived cholesterol limits angiogenesis [ext632_RNA-seq]

city: bad nauheim

first: Stefan

last: Günther

address: ludwigtr. 43

country: Germany

institute: MPI for heart and lung research

summary: The cytochrome P450 reductase (POR) monooxygenase system is essential for endogenous cholesterol biosynthesis. Elevated circulating cholesterol is a well-established risk factor for cardiovascular disease, however, the role of intracellular cholesterol synthesis in normal endothelial function remains unclear. To investigate this, we generated CRISPR/Cas9 knockouts of POR in primary human endothelial cells (EC) and studied a previously developed endothelial-specific, tamoxifen-inducible POR knockout mouse (ecPOR-/-). Deletion of POR led to the accumulation of lanosterol, the substrate of POR/CYP51A1, and a reduction in desmosterol. Functionally, POR deficiency promoted basal and VEGF-induced angiogenesis in spheroids and mouse aortic segments. Moreover, retinal angiogenesis was increased in ecPOR-/- mice in vivo. Mechanistically, POR deletion activated the Sterol Regulatory Element Binding Transcription Factor (SREBP2) regulatory pathway, as shown by increased nuclear translocation of cleaved SREBP2 in EC and in en face-stained mouse aortae. Overexpression of nuclear SREBP2 in endothelial cells mimicked the angiogenic phenotype observed upon POR deletion. Conversely, double deletion of POR and SREBP2 normalized angiogenesis to levels of control cells. RNAseq of POR-deficient EC revealed an upregulation of PI3K-related signaling pathways and genes involved in cholesterol homeostasis, including enhanced expression of pro-angiogenic factors. In line with these findings, knockout of POR increased cellular PIP3 levels, AKT phosphorylation, and activation of downstream targets such as p70 S6 kinase. These findings demonstrate that inhibition of the endothelial POR/CYP51A1 axis impairs endogenous cholesterol synthesis, activates SREBP2, and enhances angiogenesis via PI3K/AKT/mTOR signaling, highlighting a critical and novel link between intracellular cholesterol metabolism and vascular growth.

overall_design: RNA seq of human aortic endothelial cells (HAEC) after CRISPR/Cas9 deletion of the cytochrome P450 reductase (POR) compared to NTC (non-target control). Cells were cultured in EGM.

first: Pedro

middle: F

last: Malacarne

first: Melina

last: Lopez

first: Flavia

last: Rezende

first: Ralf

middle: P

last: Brandes


title: Endothelial cytochrome P450 -derived cholesterol limits angiogenesis [ext631_RNA-seq]

overall_design: Previously generated HUVEC reporter cell lines expressing cyan fluorescent protein (CFP) or yellow fluorescent protein (YFP) were also used for CRISPR/Cas9-mediated knockout of POR and NTC, followed by a puromycin selection. Initially, mixed cultures were prepared containing non-target control (NTC) and POR-/- cells expressing CFP or YFP, including reciprocal labelling conditions (NTC-CFP/POR-/--YFP and NTC-YFP/POR-/--CFP) mixed at a 1:1 ratio. Cells were detached, collected, and resuspended in FACS buffer to obtain a single-cell suspension prior to sorting.They were subjected to fluorescence-activated cell sorting using the Sony SH800S Cell Sorter (Sony Biotechnology). Cells were first gated based on forward scatter (FSC-A) and side scatter (SSC-A) parameters to select the main cell population and exclude debris according to size and granularity. Doublets were excluded by gating FSC-A versus FSC-H to obtain single-cell events. Within the singlet population, CFP and YFP fluorescence signals were used to distinguish CFP-positive and YFP-positive cells. Fluorescence thresholds were defined based on the distribution of CFP and YFP intensities, and the respective populations were sorted into separate collection tubes using the Sony Cell Sorter Software (Version 2.1.6, Sony Biotechnology).

first: Lisa

last: Weiss


title: Transcriptome Sequencing of BAPN-Induced Aortic Dissection in Male and Female Mice

city: Zhengzhou

first: Shuai

last: Cheng

address: No.1, East Jian She Road

institute: The First Affiliated Hospital of Zhengzhou University

summary: Transcriptional profiling of thoracic aortic tissue from male and female C57BL/6J mice after aortic dissection (AD) induction via continuous β-aminopropionitrile (BAPN) administration, compared with sex-matched control mice. This study aims to investigate the sex-based differences in AD susceptibility and elucidate the molecular mechanisms underlying female resistance to AD.

overall_design: Multi-condition experiment based on sex, treatment, and disease outcome. Male and female mice were divided into Control (Con) and BAPN-treated groups. The BAPN-treated mice were further stratified based on the macroscopic disease outcome at day 28: mice that developed  AD/aneurysm (AAD) and those that did not (NonAD). Transcriptomic comparisons were performed among these groups. Total 48 samples: 10 Male Control, 10 Female Control, 4 Male NonAD, 7 Male AAD, 8 Female NonAD, and 9 Female AAD.

first: Xinyu

last: Hao

first: Shirui

last: Liu

first: Linfeng

first: Yutian

last: Chen

first: Lei

last: Wang

first: Shijie

last: Xin

first: Zhen

last: Li

first: Zhaohui

last: Hua

first: Hui

last: Cao


title: Paired Transcriptomic Profiling of Airspace and Peripheral Blood Mononuclear Cells in Severe ARDS

city: Denver

first: Elizabeth

last: Wynn

state: CO

address: 1400 Jackson St.

institute: National Jewish Health

summary: The main objective of our study was to determine whether central biologic processes inferred from transcriptomic profiling of distal airspace mononuclear cells are reflected among circulating peripheral blood mononuclear cells (PBMCs) during the acute phase of ARDS. To compare mononuclear cells from the airspaces and bloodstream we collected paired peripheral blood and non-bronchoscopic BAL (NBBAL) samples from mechanically ventilated patients with severe ARDS and enriched for mononuclear cells using density centrifugation and cryopreservation.  We then performed bulk RNA sequencing and evaluated gene expression profiles and gene expression networks between compartments.

overall_design: Adults with ARDS requiring mechanical ventilation were enrolled within 72 hours of intubation. Paired non‑bronchoscopic bronchoalveolar lavage (NBBAL) and peripheral blood samples were collected early in the ICU course. Gene expression profiling was performed using targeted AmpliSeq RNA sequencing for BAL cells and bulk RNA‑seq for peripheral blood mononuclear cells (PBMCs) to compare compartment‑specific and shared transcriptional programs and assess co‑expression network preservation across tissues.

first: William

last: Janssen

first: Neil

last: Aggarwal

first: Camille

last: Moore

first: Scott

last: Alper


title: Endothelial cytochrome P450 -derived cholesterol limits angiogenesis

first: Stefan

last: Günther

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

overall_design: Refer to individual Series


title: A multi-subunit capture complex facilitates degradation of ER stalled MHC-I in pancreatic cancer

city: Stanford

first: Anthony

last: Venida

state: CA

address: 240 Pasteur Drive

institute: Stanford University

summary: Pancreatic ductal adenocarcinoma (PDAC) evades immune surveillance partly through autophagic capture and lysosomal degradation of major histocompatibility complex class I (MHC-I). However, the basis for this susceptibility remains unclear. Using synchronized ER exit assays, we show that PDAC cells retain MHC-I in the endoplasmic reticulum and inefficiently traffic it to the plasma membrane. An autophagic capture complex composed of the ER-phagy receptor TEX264 and the cargo receptor NBR1 mediates targeting of MHC-I for lysosomal degradation. Suppression of either receptor restores MHC-I levels and increases surface presentation. Binding of MHC-I to the capture complex is linked to antigen presentation efficiency as inhibition of antigen loading enhances MHC-I binding to the TEX264–NBR1 complex, whereas expression of high-affinity ER-targeted peptides reduces binding and promotes surface localization. A genome-wide CRISPRi screen identified the ER-resident E3 ligase NFXL1 as a mediator of MHC-I ubiquitylation and autophagic capture. Elevated NFXL1 correlates with reduced MHC-I expression and poor patient prognosis, highlighting a targetable pathway regulating PDAC immunogenicity.

overall_design: A whole genome CRISPRi screen was performed in PaTu8902 cells stably expressing dCas9 fused to the KRAB domain of Kox1a transcriptional repressor. Cells were immunostained for cell surface MHC-I and the top and bottom 30% of cells that were MHC-I high and low were isolated by fluorescence-activated cell sorting (FACS).

middle: C

first: Thomas

last: O'Loughlin

first: Luke

last: Gilbert

first: Rushika

last: Perera


title: A positive feedback loop between BACH1 and IL-1β promotes the progression of HPV-negative head and neck squamous cell carcinoma

first: Zishanbai

last: Zhang

address: No.1 Dongjiaominxiang, Dongcheng District

institute: Beijing Tongren Hospital

summary: Human papillomavirus (HPV)-negative head and neck squamous cell carcinoma (HNSCC) is associated with a poorer prognosis compared to its HPV-positive counterpart; however, the underlying regulatory molecular mechanisms driving its progression remain poorly understood. In this study, we identify BTB Domain and CNC Homolog 1 (BACH1) as a critical oncogenic regulator that is upregulated in HPV-negative HNSCC. We demonstrate that BACH1 promotes tumor progression by enhancing the proliferation and inhibiting apoptosis of cancer cells. Mechanistically, BACH1 is associated with the SWI/SNF chromatin remodeling complex and transcriptionally activates downstream target genes, including IL1B, thereby inducing a transcriptional reprogramming that promotes proliferation and resists apoptosis. Notably, BACH1-driven upregulation of interleukin-1β (IL-1β) establishes a positive feedback loop that sustains oncogenic signaling. Pharmacological disruption of this axis using the IL-1 receptor antagonist Anakinra significantly attenuates tumor growth in vitro and in vivo. Clinically, co-upregulation of BACH1, BRG1, and IL-1β is correlated with reduced overall survival in patients with HPV-negative HNSCC. Collectively, our findings characterize the BACH1–IL-1β signaling axis as a prognostic biomarker and highlight IL-1R blockade as a promising therapeutic strategy for the treatment of HPV-negative HNSCC.

overall_design: Control FaDu cells and FaDu cells  transfected with BACH1 and IL-1β siRNA were analyzed through RNA-seq.

first: Miao

first: Wenjuan

first: Minghui

last: Zhao

first: Yiming

last: Ding

first: Tingyao

last: Ma

first: Zhaohan

first: Xilin

first: Yuchen

last: Xiang

first: Yaning

first: Wenying

last: Zhong

first: Zicheng

last: Wu

first: Xiaohong

first: Lin

last: Shan


title: Elovanoid neuroprotection targets cell transcriptomics and proteomics to sustain synaptic integrity ater brain injury

city: New Orleans

first: Surjyadipta

last: Bhattacharjee

state: Louisiana

address: 2020 Gravier Street, Suite D, 8th floor

department: Neuroscience Center of Excellence

institute: LSU Health, New Orleans

summary: Traumatic brain injury (TBI), a leading cause of death and disability, is the largest non-genetic, non-aging-related contributor to cognitive impairments. Currently, there are limited effective therapies to protect neurons after acute brain injury. Our results suggest that intranasal-delivered (IN) elovanoid (ELV) shortly after TBI elicits neuroprotection that involves synaptic and mitochondrial pathways that mediate neuroprotection. Using a single-cell multiome approach, we found an upregulation of genes involved in synaptic integrity. Furthermore, we discovered that ELVs improve synaptosomal mitochondrial function, reduce lipid peroxidation, and increase the activity of antioxidant transcriptional programs, including the NRF2 pathway, in neurons. We suggest that these changes, together with the induction of cell-type-specific gene regulation in glutamatergic neurons and other cells, underlie ELV-elicited neuroprotection.

overall_design: Multiome sequencing (scRNA and scATAC) of rat cortex following controlled cortical impact model of traumatic brain injury. Groups include a sham condition, a TBI condition with saline treatment, and a TBI condition with ELV treatment.

first: Brian

last: Giles

first: Jeff

middle: X

last: Ji

first: Pranab

last: Mukherjee

first: Ludmila

last: Belayev

first: Carlos

last: Vieira

first: Nicolas

middle: G

last: Bazan


title: A positive feedback loop between BACH1 and IL-1β promotes the progression of HPV-negative head and neck squamous cell carcinoma [CUT&Tag]

first: Zishanbai

overall_design: Genome binding/occupancy profiling of BRG1 and BACH1 by high throughput sequencing.

first: Miao

last: Wang

first: Wenjuan

first: Minghui

first: Yiming

last: Chen


title: Caffeine in the context of sorafenib chemotherapy: Insights from experimental hepatocarcinogenesis

city: Botucatu

first: Guilherme

middle: Ribeiro

last: Romualdo

state: SP

address: Rua Dr José Barbosa de Barros, 1486

country: Brazil

institute: UNESP

summary: Background: Hepatocellular carcinoma (HCC) features a high mortality burden worldwide, highlighting the need for improved therapeutic strategies. Caffeine (CAF), a widely consumed bioactive compound, has been reported to exert chemopreventive effects in HCC, but its interaction with standard therapies remains poorly explored. Purpose: We investigated whether CAF promotes the antitumoral effects of sorafenib (SOR) chemotherapy in HCC preclinical platforms. Study design: C3H/HeJ mice were submitted to diethylnitrosamine (DEN)-induced hepatocarcinogenesis and treated with CAF (50 mg/kg), SOR (30 mg/kg) or their combination for three weeks. C3A/LX2 spheroids and transwell co-cultures were also exposed to CAF, SOR or their combination at 1/5 or 1/10 of half maximal effective concentration. Results: The combination of CAF and SOR produced a synergistic reduction in tumor spheroid viability and inhibited HCC cell colony formation. Nonetheless, treatments exerted comparable effects on reducing liver tumor volume and Afp expression in vivo. Although only CAF+SOR reduced serum ALT levels and uniquely downregulated HCC-related Ccl3, treatments showed differential and subtle transcriptomic impacts during hepatocarcinogenesis - not showing promoting or additive effects when combined. Conclusion: In summary, while CAF potentiated SOR antitumoral activity in vitro, their combination did not lead to major effects in vivo, eliciting the need for further investigation.

first: Letícia

last: Valente

first: Luana

last: Riechelmann-Casarin


title: Chromatin rewiring of β-globin and MYC enhancers by TGF-β1 drives defective erythropoiesis [RNA-seq]

city: Bronx

first: Kith

last: Pradhan

state: ny

address: 1300 Morris Park Ave

institute: Einstein College of Medicine

summary: Erythropoiesis is a tightly regulated process involving rapid cell proliferation with orderly differentiation to ensure production of millions of RBCs. TGF-β1 is a key regulator of erythropoiesis, however, the mechanisms via which it regulates erythropoiesis are not well elucidated. Using myelodysplastic syndromes patient samples, we show that elevated TGF-β1 and SMAD2 signaling correlates with the degree of anemia. Functional studies in primary human HSPCs demonstrate that TGF-β1 exerts a bifurcated effect — suppressing proliferation and inducing premature erythroid differentiation — both of which are rescued by clinical-stage TGFBR1 inhibitors. Through integrative RNA-seq, ChIP-seq, and Micro-C analyses, we found TGF-β1 activates the β-globin LCR, driving early differentiation, while concurrently disrupting the MYC enhancer–promoter interaction to block proliferation. We validated our erythropoiesis defect in vivo by performing single-cell RNA-seq in a TGF-β1 transgenic mouse. Our findings show that TGF-β1/SMAD2 signaling re-wire chromatin to regulate erythropoiesis by affecting β-LCR and MYC super enhancer regions.

overall_design: Bulk RNA sequencing was performed on primary human CD34⁺ day 6 (d6) erythroid progenitors treated with vehicle control or recombinant TGF-β1. Two independent biological replicates were analyzed per condition (vehicle replicate 1 and 2; TGF-β1 replicate 1 and 2), resulting in four total samples.

first: Aluri

last: Srinivas

first: Verma

last: Amit


title: Chromatin rewiring of β-globin and MYC enhancers by TGF-β1 drives defective erythropoiesis [scRNA-seq]

overall_design: Single-cell RNA sequencing was performed on bone marrow cells isolated from control (wild-type) mice and Alb/TGF transgenic mice. Two independent biological replicates were analyzed per genotype (Control replicate 1 and 2; Alb/TGF replicate 1 and 2), resulting in four total samples. Samples were processed independently and sequenced using the 10x Genomics Chromium Single Cell 3′ workflow.


title: Charting Postnatal Heart Development Using In Vivo Single-Cell Functional Genomic

city: Chapel Hill

first: LI

last: QIAN

address: 111 Mason Farm Road, MBRB

department: Department of pathology

institute: UNC

summary: The transition at birth, marked by increased circulatory demands and rapid growth, necessitates extensive remodeling of the heart’s structure, function, and metabolism. This transformation requires precise spatial and temporal coordination among diverse cardiac cell types; central to this process is cardiomyocyte maturation, yet the regulatory mechanisms driving these changes remain poorly understood. Here, we present a temporal and spatial atlas of postnatal hearts by integrating single-nucleus transcriptomics with image-based spatial transcriptomics, which uncovers the dynamic regulatory networks of cardiomyocyte maturation. To functionally interrogate candidate regulators in vivo, we developed Probe-based Indel-detectable Perturb-seq, a high- throughput platform that uses probe-based chemistry to directly capture sgRNA expression, perturbation status, and transcriptomic profiles at single-nucleus resolution. Applying PIP-seq to postnatal cardiac development identified 21 novel regulators of cardiomyocyte maturation, highlighting critical nodal points in this process. Our study establishes a high-resolution framework for dissecting postnatal heart development, underscoring the integrative and highly ordered roles of microenvironment and intercellular communication in cardiomyocyte maturation. Importantly, PIP-seq enables systematic, high-throughput exploration of gene function and networks underlying complex biological processes in their native in vivo context.

overall_design: RNA-seq: AAV9-sgRreb1 and AAV9-sgNT were injected into neonatal mice at postnatal day 0. 3 hearts per group were harvested on postnatal day 35. Total RNA was extracted form isolated nuclei using RNeasy Micro Kit (Qiagen) with genome DNA removed through on-column DNase I digestion. RNA-seq libraries were constructed using kapa mRNA Stranded library Kit and were on a Nextseq 2000 (Illumina) with 100 base-pair pair-end reads.

first: HAOFEI

last: WANG

first: YANHAN

last: DONG

first: YIRAN

last: SONG

first: JIANDONG

last: LIU


title: TET1 non-catalytic activity shapes the chromatin landscape that directs de novo methylation establishment in the male germline [methylation array]

city: Philadelphia

first: Rexxi

middle: Diptya

last: Prasasya

state: PA

address: 3400 Civic Center Blvd

department: Cell and Developmental Biology

institute: University of Pennsylvania

type: Methylation profiling by genome tiling array

summary: In the germline, DNA methylation is globally erased in primordial germ cells (PGCs), enabling establishment of sex-specific methylomes in prospermatogonia or oocytes. The catalytic activity of TET1 is required for complete demethylation in PGCs, yet sperm from Tet1-/- mice display methylation defects not explained by incomplete erasure. Instead, these defects arise from abnormal de novo methylation during development, coinciding with erosion of H3K4me3, a chromatin modification that blocks DNMT3A/3L. Using a catalytically inactive Tet1HxD mouse line, we demonstrate a non-catalytic role of TET1 in promoting H3K4me3 deposition and protecting a subset of sperm hypomethylated regions from aberrant methylation in prospermatogonia.

overall_design: Bisulfite converted DNA from FACS sorted PGCs were subjected to 2 rounds of Klenow amplification (primed with random hexamer 6) were hybridized to the Illumina Mouse Methylation285 12v1-0 BeadChip Array

middle: D

first: Jean

middle: J

last: Kim

first: Zhengfeng

last: Liu

first: Rahul

last: Kohli

first: Marisa

middle: S

last: Bartolomei


title: Far-red perception by vegetative organs and not fruits drives fruit growth responses in tomato plants

city: Wageningen

first: Elena

last: Vincenzi

address: Droevendaalsesteeg 1

department: Horticulture and Product Physiology

country: Netherlands

institute: Wageningen University and Research (Netherlands)

summary: Responses to far-red are mediated by phytochromes, specialised photoreceptors present in all organs of a tomato plant. Although fruit-localised phytochromes can influence starch and sugar metabolism, their involvement in modulating fruit growth responses to far-red is unknown. We explored whether fruit growth responses to far-red are driven by local far-red perception within the fruits, or by a systemic response initiated in the vegetative organs. We applied far-red exclusively to the fruiting trusses, from anthesis to ripening, to the vegetative organs, to both, or to neither. We quantified plant development and fruit growth responses to far-red and carried out a transcriptomic analysis to establish the temporal dynamics of far-red perception and signalling in leaves and fruits. Supplementing far-red to the vegetative organs led to a significant increase in ripe fruit weight and sugar concentration, regardless of the light conditions experienced by the trusses, whereas far-red supplementation to the generative organs alone had no measurable effect. This study establishes that far-red perception by vegetative organs drives fruit growth responses in tomato. Local responses to far-red included a transient increase in auxin concentration and upregulation of the auxin-signalling pathway in leaves, a conserved response to decreasing R:FR ratios. In fruits, early transcriptomic responses carried signatures of auxin, cytokinin, and gibberellin biosynthesis and signalling, suggesting a role for hormones as mediators of far-red-induced fruit responses. Finally, this work reveals how responses to far-red perception by vegetative organs promote sink strength and starch biosynthesis in early developing fruits, contributing to higher fruit weight and sugar concentration in ripe fruits.

overall_design: RNA-seq profiling of samples from fruit and leaf tissues of the commercial greenhouse tomato cultivar Foundation. Samples were collected from plants exposed to two different light treatments: NFR and FR. Plants under NFR treatment were exposed to Red and White light only. Plants under FR treatment had their vegetative organs (leaves, stem and apex) exposed to Red and White light plus Far-Red. Fruits of FR treatment were not exposed to any Far-Red. Samples of fruit and leaves, under both treatments, were collected at six time points from the start of the FR treatment to 96 hours later. The six time points included: 0 h (pre-FR exposure), 6h, 12h, 24h, 48h and 96h. Four biological replicates were taken per light treatment, per tissue, per time point.

first: Lisa

last: Oskam

first: Mohan

last: Lu

first: Ronald

last: Pierik

first: Esther

last: de Beer

first: Frank

last: Millenaar

first: Leo

last: Marcelis

first: Ep

last: Heuvelink


title: Non-canonical function of transferrin receptor-1 promotes breast cancer metastasis by activating HCK-STAT3-MMP9 signaling

city: Shanghai

first: Qing

last: Zhao

state: None Selected

address: 555 Zuchongzhi Rd., Zhangjiang Hi-Tech Park, Shanghai, 201203, China

institute: shanghai institute of materia medica

summary: Transferrin receptor 1 (TfR-1), a key mediator of cellular iron uptake, is significantly upregulated across a broad spectrum of malignancies, and its overexpression highly correlated with poor clinical outcomes, such as in breast cancer. However, its precise role in breast cancer progression remains unclear. In this study, analysis of clinical samples from breast cancer patients and public databases demonstrated that high level of TfR-1 in breast cancer samples is strongly associated with metastasis. We further verified that elevated TfR-1 enhances the proliferative and metastatic potential of breast cancer cells both in vitro and in vivo. Mechanistically, we uncovered an unexpected protein kinase activity of TfR-1, which directly phosphorylates hematopoietic cell kinase (HCK). Concurrently, TfR-1 activates ubiquitin-specific protease 32 (USP32), thereby stabilizing HCK protein. Subsequently, phosphorylated HCK facilitates the activation of the transcription factor STAT3, resulting in increased expression and secretion of matrix metalloproteinase 9 (MMP9). Moreover, HCK exerts reciprocal phosphorylation on TfR-1, forming a positive feedback loop. Collectively, our findings unravel a novel molecular mechanism underlying TfR-1-mediated metastasis in breast cancer, highlighting the importance of TfR-1’s non-canonical phosphorylation activity beyond its established role in iron transport, and identifying potential therapeutic targets for cancer intervention.

overall_design: MDA-MB-231/4175 cells were stably transfected with a TfR-1 overexpression plasmid. Empty vector–transfected cells were used as controls. Bulk RNA-seq was performed to profile transcriptomic changes associated with TfR-1 overexpression. Each condition included biological replicates.


title: RNA sequencing of Follicular Cytotoxic CD8+ T Cells from Trypanosoma cruzi-infected mice

city: Córdoba

first: Yamila

middle: Natali

last: Gazzoni

state: Córdoba

address: Avenida Haya de La Torre y Medina Allende

country: Argentina

institute: CIBICI-Facultad de Ciencias Químicas-UNC

summary: Follicular cytotoxic CD8? T (Tfc) cells are a specialized subset of CD8? T lymphocytes that combine helper and cytotoxic functions. While their phenotypic and functional properties have been described in several infectious and inflammatory settings, little is known whether Tfc cells exhibit distinct characteristics across secondary lymphoid organs. Using acute Trypanosoma cruzi infection as a model of systemic immune activation, we performed a comparative phenotypic, transcriptomic, metabolic, and functional characterization of Tfc cells arising in the spleen and inguinal lymph nodes. Tfc cells emerged transiently in both organs with similar kinetics and antigen specificity, yet segregated primarily according to tissue of analysis at the transcriptional level. Splenic Tfc cells exhibited enhanced glycolytic and mTORC1-associated signatures, increased mitochondrial mass, and stronger cytotoxic and B cell helper functions, promoting immunoglobulin production and plasmablast death. In contrast, Tfc cells from lymph node preferentially displayed memory-associated features, including higher CD127 and CD122 expression, increased IL-2 production, and preferential persistence during chronic infection. Together, these findings indicate that Tfc populations from spleen and lymph nodes are characterized by distinct transcriptional, metabolic, and functional states.

overall_design: This dataset comprises RNA sequencing data from follicular (Tfc) CD8+ T cells isolated from the spleens and inguinal lymph nodes of mice at 18 days post-Trypanosoma cruzi infection. The study aims to characterize the transcriptional profiles of these immune cell subsets during the acute phase of infection, offering insights into their functional roles in the immune response.

first: Laura

last: Almada

first: Adriana

last: Gruppi


title: TET1 non-catalytic activity shapes the chromatin-landscape that directs de novo methylation establishment in the male germline

first: Rexxi

last: Prasasya


title: TET1 non-catalytic activity shapes the chromatin-landscape that directs de novo methylation establishment in the male germline [5hmCSeal]

overall_design: Genomic DNA was isolated from 30000 snap frozen E17.5 germ cells pooled from multiple embryos using Phenol:Chloroform:Isoamyl Alcohol (25:24:1; Sigma-Aldrich) and ethanol precipitated, followed by resuspension in 10 mM Tris-HCl pH 8.0. 50 ng of genomic DNA was sheared using NEBNext UltraShear (NEB) and was used as input for enrichment of 5-hydroxymethylcytosine using 5hmC-Seal following manufacturer protocol (5hmC Profiling Kit; Active Motif). Sequencing libraries were prepared from both input and enriched fractions using NEBNext UltraII DNA Library Prep Kit for Illumina (NEB)

first: Jean

last: Kim

middle: M


title: TET1 non-catalytic activity shapes the chromatin-landscape that directs de novo methylation establishment in the male germline [RNAseq]

overall_design: RNA-seq in E17.5 Prospermatogonia Tet1-/- and Tet1+/+

first: Zhengfeng

last: Liu


title: ESRG maintains human pluripotent stem cell self-renewal by binding NPM1 to regulate BMP4 protein and TGF-β signaling pathway

city: Changsha

first: caiping

last: ren

address: 110 Xiangya Road,

institute: Central South University

summary: Human pluripotent stem cells (hPSCs) present considerable potential for regenerative medicine; however, their clinical application is hindered by an incomplete understanding of the molecular mechanisms governing self-renewal. The long non-coding RNA ESRG is integral to maintaining hPSC self-renewal, with its depletion leading to reduced levels of nucleophosmin 1 (NPM1) protein, thereby compromising the self-renewal capacity of hPSCs. Mechanistically, ESRG physically interacts with NPM1, and a reduction in ESRG/NPM1 expression results in elevated bone morphogenetic protein 4 (BMP4) levels and decreased polypyrimidine tract-binding protein 1 (PTBP1) levels, which subsequently suppress TGF-β signaling by destabilizing TGF-β1 mRNA. Notably, treatment with the TGF-β activator SRI-011381 partially mitigates the self-renewal defects induced by ESRG or NPM1 downregulation. Collectively, our findings elucidate that the ESRG/NPM1/BMP4/PTBP1/TGF-β axis precisely regulates hPSC self-renewal. This study enhances the understanding of the molecular regulatory network underlying hPSC self-renewal maintenance and identifies ESRG as a potential target for optimizing hPSC in vitro expansion, thereby advancing the field of regenerative medicine.

overall_design: NPM1 expression was knocked down in human pluripotent stem cells (hPSCs), followed by transcriptomic profiling and comparative analysis between NPM1-knockdown and control groups, with three biological replicates included per group.

first: Ziling

last: Liao

first: Cong

first: Xingjun

last: Jiang

first: Caiping

last: Ren


title: TET1 non-catalytic activity shapes the chromatin-landscape that directs de novo methylation establishment in the male germline [CUTandRUN]

overall_design: Nuclei were extracted from 4000 cryopreserved E17.5 Oct4-GFP+ prospermatogonia cells that were stored  in PGC media (DMEM supplemented with 15% FBS, 100 U/mL leukemia inhibitory factor, 5 µM forskolin, 1 ng/mL stem cell factor with 10% DMSO). 4000 nuclei were used for each epitope (H3K4me3 or IgG). Three biological replicates were ran for each genotypes and each epitopes.

first: Rahul

last: Kohli

first: Marisa

last: Bartolomei


title: Intercellular communication between the lung and adipose tissue

city: Poznań

first: Wojciech

last: Langwiński

address: Fredry

country: Poland

institute: Poznan University of Medical Sciences

summary: We used microarray gene expression analysis to profile mRNA levels in the lungs and adipose tissue of a rat model of asthma.

overall_design: Brown Norway rats were used in these experiments and the animals were exposed to house dust mite (HDM) to induce allergic inflammation. After sacrifice, tissues were rinsed in PBS and RNA was isolated. The study group included five HDM-exposed animals, and three animals served as controls.

last: Langwinski


title: The Combination of Remdesivir and Ivermectin Exerts Highly Potent and Synergistic Antiviral Activity Against Murine Coronavirus and SARS-CoV-2 Infections

city: Singapore

first: Solomonraj

last: Wilson

address: 8A Biomedical Grove

country: Singapore

institute: SIgN

summary: The COVID-19 pandemic highlighted the urgent need to develop effective and broad-spectrum antiviral therapies against coronaviruses. One strategy to address this concern is combination therapy using repurposed drugs against zoonotic viruses with pandemic potential. We previously demonstrated that the combination of remdesivir and ivermectin is highly potent and synergistic in inhibiting the replication of murine hepatitis virus, a surrogate model for SARS-CoV-2. Time-of-addition and time-of-removal assays were performed to determine the viral replication processes affected. The interactions between the drug combination, virus and host were investigated by proteomics and bulk RNA sequencing of MHV-infected H2.35 mouse liver epithelial cells. The combination (at their respective IC50 concentrations) drastically diminished the coronavirus titer by ~4log10 greater than the respective monotherapies. Based on proteomic and transcriptomic analyses, viral protein and RNA levels were significantly depressed upon combination treatment. While remdesivir exhibited considerable negative effects upon host RNA processes, ivermectin resulted in the upregulation of host protein processes (e.g. response to unfolded protein; protein insertion into ER membrane). Molecular pathways affected by the combination treatment were markedly distinct from the monotherapies, and indicated that ivermectin enhances remdesivir by modulating critical host processes to synergistically exert its inhibitory effect on the coronavirus replication cycle.

overall_design: RNA-seq of H2.35 cells infected with MHV treated with varying concentrations of Remdesivir and Ivermectin in concert or in isolation.

first: Ryan

last: Lew

first: Douglas

last: Tay

first: Jocelyn

last: Ong

first: Jing Hui

last: Low

first: Jing

first: De Yun

last: Wang

first: Justin

last: Chu

first: Anand

last: Andiappan

first: Kai Sen

last: Tan

first: Vincent

last: Chow


title: Phenotype-dependent epithelial–mesenchymal plasticity in pancreatic ductal adenocarcinoma and redox modulation by sodium selenite in vitro and ex vivo

city: Huddinge

first: Tímea

last: Szekerczés

address: Alfred Nobels allé 8

department: LabMed

institute: Karolinska Institutet

summary: Pancreatic ductal adenocarcinoma (PDAC) is lethal and exhibits epithelial–mesenchymal transition (EMT) plasticity linked to invasion and therapy resistance. Selenite is a redox-active compound with tumor-selective cytotoxicity, but its impact on EMT-related phenotypes in PDAC is unclear. We integrated cell-line profiling and patient-derived tissue-slice cultures to quantify selenite-driven EMT modulation using a multiplex protein panel (EpCAM, CK, E-cad, AHNAK2, ITGAV, Vimentin), histologic regression scoring, and paired RNA sequencing. Across three PDAC cell lines (PANC-1, HPAF-II, Capan-2), selenite effects were phenotype-contingent. HPAF-II and Capan-2 showed epithelial reinforcement and increased EM ratio, whereas mesenchymal-like PANC-1 showed limited epithelial restoration and blunted EM-ratio changes. Selenite most consistently suppressed mesenchymal markers, particularly ITGAV and Vimentin. After TGF-β priming, HPAF-II retained an epithelial-promoting response; in Capan-2, this was evident mainly at the higher selenite dose. In ex vivo PDAC tissue slices (n=10), effects were largely confined to tumor region. Tumors showed dose-dependent EpCAM induction and non-linear E-cad and AHNAK2 responses, while acinar compartments remained stable. Tumor EM ratio was higher at 15 µM than at 5 µM, with improved regression by Evans/CAP criteria. In paired RNA-seq, 5 µM produced no significant EMT-gene differential expression, whereas 15 µM upregulated immediate-early/stress-responsive genes and downregulated genes that build and connect the basement membrane and extracellular matrix, the adhesive scaffold supporting EMT, rather than a canonical MET program. Together, these data indicate that selenite is a dose- and context-dependent modulator of complex, phenotype-dependent EMT-related changes in PDAC and support the translational potential of selenite as a therapeutic strategy.

overall_design: RNA-seq was performed on four patient-derived PDAC tissue cultures (OT127, OT138, OT142, OT146). For each patient, four conditions were profiled: 0 h baseline; 48 h treatment control; and 48 h cultures treated with sodium selenite during the second 24 h at 5 µM or 15 µM.

first: Ozan

last: Aricak

first: Wenyang

last: Shi

first: Carlos

last: Fernandez Moro

first: Mehran

last: Ghaderi

first: Joakim

last: Dillner

first: Jonas

last: Fuxe

first: Mikael

last: Bjornstedt

first: Timea

last: Szekerczes


title: Single cell RNA-seq of mouse brain microvascular fragments with Smart-seq2 method

city: Uppsala

first: L.

last: He

address: Dag Hammarskjölds Väg 20

institute: Uppsala University

summary: In this single cell RNAseq analysis, we analyzed brain microvascular fragments  from adult mice with the Smart-seq2 platform.

overall_design: The cells in the microvascular fragments from the adult mouse brain were isolated, sorted into 384-well plates. The cells were sequenced following the SMART-Seq2 protocol

first: Maarja

last: Andaloussi Mäe

first: Elisa

last: Vazquez-Liebanas

first: Khayrun

last: Nahar

first: Michael

last: Vanlandewijck

first: Liqun

first: Christer

last: Betsholtz


title: Enhanced Endocytosis, Mitochondrial Stress and NK/NKT Cells Mediated Immune Response Underlie Severe Retinitis Pigmentosa with RHO P347L Mutants

first: Chenyue

last: Hang

address: 100 Haining Road, Shanghai 200080, China

institute: Shanghai general hospital

summary: Abstract Purpose: Rhodopsin (RHO) is the initiator of phototransduction and the most frequent cause of autosomal dominant retinitis pigmentosa (adRP). While Class 1 RHO mutations cause a more severe phenotype than Class 2, the underlying pathogenesis remains poorly defined. This study investigates the mechanistic basis for this disparity using cell models and humanized mouse models of Class 1 (P347L) and Class 2 (L125R) mutations. Methods: We first analyzed the localization, degradation and downstream pathway of wild-type (WT) and mutant rhodopsin in 293T cells overexpressing the corresponding plasmids. Then we used humanized mouse models to conduct a side-by-side comparison of mitochondrial dysfunction, photoreceptor death, and neuroinflammation in vivo. Results: Unlike WT rhodopsin, the P347L mutant exhibited plasma membrane localization in a non-polarized manner, whereas the L125R mutant showed partial trafficking to the membrane. Correspondingly, the degradation of P347L was primarily mediated by the lysosomal pathway, while L125R was processed through both proteasomal and lysosomal pathways. The P347L mutant demonstrated a propensity to bind visual arrestin, potentially explaining its observed higher rate of endocytosis. In vivo, the P347L model displayed more severe mitochondrial dysfunction. However, both mutants induced a comparable level of neuroinflammation, characterized by the activation of microglia, natural killer (NK) cells, and natural killer T (NKT) cells. Conclusions: We propose a pathogenic model in which elevated endocytosis and mitochondrial impairment directly underlie the severe RP in P347L mutants, with neuroinflammation serving to amplify the initial insult.

overall_design: RNAseq profiling of retinas of 3-week-old C57BL/6J, hRHOL125R/L125R and hRHOP347L/P347L mice

first: Xinchao

first: Tianyuan

last: Zhao

first: Jianqing

last: Li

first: Ting

last: Zhang

first: Zhixuan

last: Chen

first: Yidong

last: Wu

first: Yuhui

last: Zhou

first: Shuang

first: Yutian

last: Jiao

first: Yazhi

last: Wang

first: Junran

last: Sun

first: Tong

first: Jian

first: Huixun

last: Jia

first: Xiaoling

last: Wan

first: Jieqiong

first: Bo

last: Yu

first: Xiaodong


title: Estrogenic Endocrine Disrupting Compounds Increase Cell Proliferation and Cancer Stemness in Estrogen Receptor Positive Breast Cancer Cells

city: Piscataway

first: Cassandra

last: Winz

state: NJ

address: 160 Frelinghuysen Rd

institute: Rutgers University

summary: Estrogenic endocrine disrupting compounds (EDCs) found in plastics, drinking water, and food are able to bind to the estrogen receptor (ER). Excessive estrogen signaling drives proliferation, progression, and the formation of breast cancer stem cells (CSCs) in ER-positive breast cancer. Thus, we hypothesized that estrogenic EDCs mimic estrogen (E2) in breast cancer cell lines. Three estrogenic EDCs routinely found in human biosamples were selected for analysis: bisphenol-A (BPA), diethyl-hexyl phthalate (DEHP), and alpha-zeranol (αZAL). We assessed proliferation, transcriptional reprogramming, and CSC formation in several breast cancer cell lines. E2, BPA, and αZAL significantly increased cell proliferation in ER-positive, but not in ER-negative cell lines. This was reversed with the administration of an ER-antagonist, ICI 182,780. BPA and αZAL upregulated estrogen target genes (PGR, TFF1) and increased levels of cell cycle protein. Whole-transcriptome RNA sequencing analysis revealed that BPA and αZAL altered the expression of genes in pathways related to cell division, DNA repair, and estrogen signaling, with a substantial transcriptional overlap between EDC and estrogen treatments. Additionally, in the ER-positive cell line MCF-7, BPA and αZAL increased the proportion of CSCs, defined as the CD24low/CD44high expressing subpopulation. Overall, these data indicate that BPA and αZAL act as functional estrogen mimics in breast cancer cells, activating canonical estrogen signaling pathways and promoting stem-like characteristics. Exposure to EDCs is nearly unavoidable; therefore, understanding their estrogenic activities is crucial for assessing environmental contributions to breast cancer risk.  This work provides mechanistic insight into how environmental EDCs may influence ER-positive breast cancer biology.

overall_design: MCF-7 cells were treated with compound and RNA was harvested at various timepoints after treatment. Sample groups include: control (DMSO 0.01%), estrogen (100 pM), BPA (1 uM), aZAL (1 uM). Timepoints include: 12 hours and 72 hours. 3 independent replicates were performed and sent for sequencing.


title: CD73 inhibition overcomes adaptive immune resistance to PARP inhibition in models of prostate cancer

city: Chicago

first: ping

last: xie

state: IL

address: 300 E Superior St, Tarry 4-726

institute: Northwestern University Feinberg School of Medicine, Chicago , Illinois, US

summary: Metastatic castration-resistant prostate cancer (mCRPC) remains a major cause of cancer-related mortality in the male population. While poly(ADP-ribose) polymeraseinhibitors (PARPi) are approved for selected mCRPC patients with homologous recombination repair (HRR) deficiencies, combinations with PD-1/PD-L1 inhibitors immunotherapy have demonstrated limited efficacy in unselected populations. To investigate the immunomodulatory effects of PARPi in an unbiased manner, we performed bulk RNA sequencing on HRR-proficient MyC-CaP cells treated with PARPi Olaparib or control vehicle. Pathway enrichment analysis revealed a marked upregulation of CD73 (NT5E), an emerging immune checkpoint ectoenzyme that generates extracellular adenosine, suggesting an adaptive mechanism that undermines PARPi efficacy and enables unwanted immunosuppression. CD73 induction by PARPi was confirmed in both human and mouse prostate cancer cell lines, with more pronounced effects in the HRR-compromised PTEN knock-out (KO) cells. Mechanistically, Olaparib-driven CD73 expression was mediated through the DNA damage-activated ATR-CHEK1-IRF1 and TGF-β1-ΑΚΤ signaling pathways. Concurrently, PARPi enhanced tumor cell immunogenicity by activating the type I interferon pathway and antigen presentation machinery. In vivo, combining Olaparib with CD73 blockade therapy delayed tumor growth, improved T-cell infiltration, and augmented antigen-specific CD8⁺ T-cell effector function across HRR-proficient and PTEN KO prostate cancer models. These findings highlight PARPi-induced CD73 upregulation as a novel resistance mechanism and support PARPi plus CD73 blockade as a promising therapeutic strategy for mCRPC, irrespective of HRR status.

overall_design: Prostate Cacer cells were treated with Olaparib for 24 hours, harvested for bulk RNA seqence.

first: Ping

last: Xie

first: Renqiang

last: Ma

first: Minghui

first: Jie

last: Fan

first: Hui

last: Tang

first: longzhen

last: Song

first: Bin


title: Single cell RNA-seq of mouse brain vascular cells with Smart-seq2 method

first: L.

last: He

summary: In this single cell RNAseq analysis, we analyzed brain vascular cells from adult mice with the Smart-seq2 platform.

overall_design: Vascular single cells from the adult mouse brain were isolated, sorted into 384-well plates, and sequenced using the Smart-seq2 protocol.

first: Jianping

last: Liu

first: Lars

last: Muhl

first: Michael

last: Vanlandewijck

first: Liqun

first: Christer

last: Betsholtz


title: Analysis of host gene differential expression after PAM cells were infected with ΔD250R ASFV

city: Harbin, Heilongjiang Province

first: Linfei

address: 678 Haping Road, Xiangfang District

institute: Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences

summary: PAMs infected with either WT or ΔD250R ASFV revealed widespread transcriptional upregulation in ΔD250R-infected cells compared with WT-infected cells.The upregulated genes showed significant enrichment of innate immune signaling pathways, with four of the top five pathways corresponding to innate immune activation, including the cytosolic DNA-sensing, NOD-like receptor, RIG-I-like receptor, and Toll-like receptor signaling pathways.

overall_design: RNA seguencing analysis was performed in PAM cells infected with WT or ΔD250R ASFV after 12 hours.

first: Jiwen

last: Zhang

first: Menglong

last: Cao

first: Xiangpeng

last: Sheng

first: Dongming

last: Zhao


title: Lactiplantibacillus plantarum DS1073 protects the gastric mucosa under infection and alcohol stress

city: Daejeon

first: Mi-Young

last: Son

address: 111 Gwahangno, Yuseong-gu

institute: Korea Research Institute of Bioscience and Biotechnology (KRIBB)

summary: Helicobacter pylori (H. pylori) infection and alcohol consumption are major drivers of gastric injury, highlighting the need for non-antibiotic strategies that prevent colonization and preserve mucosal integrity. We screened 340 probiotic-derived cell-free supernatants (CFSs) under microaerophilic conditions, assessed anti-adhesion activity using human antral gastric organoids and organoid-derived epithelial monolayers, and evaluated efficacy in mouse models of acute gastric injury induced by ethanol and hydrochloric acid. Lactiplantibacillus plantarum DS1073 reduced H. pylori viability, inhibited epithelial adhesion, and downregulated key virulence and adhesion genes, including cagA, vacA, ureA, amiE, dupA, hpaA, babA, and ureB. In vivo, both DS1073 CFS and live bacteria decreased gastric colonization and inflammation, improved macroscopic lesion scores, preserved epithelial architecture, restored mucus production, and suppressed expression of acid secretion genes in a mouse model of acute gastric injury. Transcriptome profiling of ethanol-injured human gastric epithelial cells revealed attenuation of cytokine–cytokine receptor interactions, reduced mitogen-activated protein kinase signaling, and normalization of calcium signaling pathways. These findings support DS1073 as a promising non-antibiotic strategy to promote and maintain gastric health, particularly by preventing mucosal damage from chronic infection and acute chemical injury. Clinical evaluation is warranted to assess its preventive and adjunctive potential.

overall_design: RNA-seq profiling of the human gastric epithelial cell line (GES-1) exposed to ethanol (EtOH) and EtOH combined with bacterial cell-free supernatant (CFS), compared to untreated controls.


title: miR-155 Regulates AML Tumor-Specific mRNA Vaccine Responses

city: Salt Lake City

first: Ryan

last: O'Connell

state: UT

address: Emma Eccles Jones, Medical Research Building, 15 North Medical Drive East

department: Pathology, Microbiology & Immunology

institute: University of Utah

summary: Acute myeloid leukemia (AML) is a malignant clonal expansion of myeloid stem and progenitor cells, impeding normal hematopoiesis and culminating in bone marrow failure and mortality. Treatment with cytotoxic chemotherapy is often initially successful, but the development of chemo-resistant disease is common, indicating that new treatments are still needed. Recently, messenger RNA (mRNA) vaccines have emerged as potent inducers of antitumor immunity against solid tumors, yet their utility in the setting of AML, and the molecular mechanisms that govern their activity, are poorly defined. In our study, we demonstrate that microRNA-155 (miR-155) function in T cells is vital both for anti-tumor immunity against AML and mRNA vaccine efficacy against AML. Loss of miR-155 in both CD4+ and CD8+ T cells in conditional knockout mice (miR-155 fl/fl CD4+Cre) resulted in deficient antitumor immunity against syngeneic ovalbumin-expressing C1498 murine AML (C1498-OVA). Further, sterilizing immunity was provided by a tumor antigen-specific mRNA vaccine against C1498-OVA AML, but only if T cell-expressed miR-155 was present, in a process that included the differentiation of KLRG1+ CD8+ T cells. Single-cell RNA sequencing revealed distinct, miR-155-dependent transcriptome regulation of mRNA vaccine-responsive CD8+ T cells, which included a subset of genes that are regulated by miR-155 only during the mRNA vaccine response, indicating a novel context specific role for miR-155. These data indicate that T cell expressed miR-155 governs responses to tumor-specific mRNA vaccines by facilitating activation and differentiation cascades in CD8+ T cells and expanding memory CD8+ T cell reservoirs.

overall_design: CD45+ positive immune cells were purified from bone marrow from miR-155 TCKO and WT littermates, each of which had receiving mRNA-OVA LNP or vehicle control post-challenge with C1498-OVA.

first: Benjamin

last: Battistone

first: Arevik

last: Ghazaryan

first: William

middle: W

first: Jacob

last: Thompson

first: Kaylyn

last: Bauer

first: Cindy

last: Barba

first: Soh-Hyun

last: Lee

first: Morgan

last: Nelson

first: Van

last: Tran

first: Liam

last: O’Malley

first: Quynh

last: Ngo

first: Colton

last: Hernandez

first: Amber

last: Thibeaux

first: Zekiye Busra

last: Agir

first: Atakan

last: Ekiz

first: Warren

last: Voth

first: Dinesh

last: Rao

last: O’Connell


title: The transcription factor SREBP2 supports the activation and homeostasis of CD4+ Foxp3+ regulatory T cells

city: Miami

first: Thomas

middle: R

last: Malek

state: FL

address: 1600 NW 10th Avenue

department: Microbiology/Immunology

institute: University of Miami

summary: Periodic activation of regulatory T cells (Treg) is necessary to restrict autoreactive T cells and maintain immune homeostasis. IL-2-STAT5 signaling instructs several metabolic processes underlying Treg activation, including the mevalonate pathway, which is crucial for optimal Treg responses. However, direct links between IL-2-STAT5, mevalonate and Treg function have yet to be established. To explore this relationship, we deleted sterol regulatory binding element protein 2 (Srebp2), a critical mediator of mevalonate metabolism, selectively in Tregs. Here we show that when Srepb2-deficient Tregs are placed under physiological stress by competing with wild-type Tregs, the former exhibit impaired proliferation, survival, and activation. RNA-seq of Tregs in this competitive setting demonstrate that Srebp2 contributes to pathways controlling IL2R signaling, cholesterol homeostasis, activities associated with the mevalonate pathway, and expression of genes associated with activated Tregs. These findings link Srebp2, the IL-2R, and the mevalonate pathways for efficient Treg homeostasis and activation. These effects, however, require a competitive setting as mice with only Srebp2-deficient Tregs were outwardly normal with respect to their development, homeostasis, metabolic activity, and function. Thus, Srebp2 is necessary to optimally tune Treg homeostasis and activation, but sufficient redundancy exists to compensate for the lack of Srebp2 to maintain Treg development and function in the absence of physiological stress.

overall_design: To explore downstream consequences of Srebp2 deficiency, we compared transcriptomes in Srebp2-deficient Tregs with those of WT Tregs. Purified Tregs were collected from mouse spleens and LNs from either Srebp2cKO or Srebp2WT mice. RNA was purified from these Tregs and processed for sequencing.

first: Acacia

middle: N

last: Shouse

first: Alejandro

middle: V

last: Villarino


title: Mucosal inflammation and pre-existing antibodies define protection and disease outcomes in human Bordetella pertussis challenge

city: Amsterdam

first: Lisa

last: Willemsen

address: Meibergdreef 9

institute: Amsterdam UMC - locatie AMC

summary: Whooping cough, caused by Bordetella pertussis (BP), persists despite widespread vaccination with acellular pertussis (aP) vaccines, which protect against disease but provide incomplete and short-lived immunity against infection and transmission. To define correlates of protection and mechanisms underlying symptom development, we characterized systemic and mucosal immune responses in a North American BP-controlled human infection model (CHIM). Healthy adults, primed in infancy with either whole-cell or aP vaccines, were intranasally challenged with escalating BP doses and classified as symptomatic, asymptomatic, or non-infected. Longitudinal paired blood and nasal samples were analyzed to measure antibody titers, cell subset frequencies, cytokine concentrations, gene expression, and T cell polarization and activation. Non-infected participants exhibited significantly higher pre-challenge serum antigen-specific IgG titers, identifying these antibodies as potential correlates of protection. Only symptomatic individuals developed robust antigen-specific IgG responses post-challenge and displayed pronounced nasal transcriptional inflammation peaking on day 7, characterized by induction of interferon and NF-κB signaling and the presence of HLA-DR⁺ myeloid cells. Systemic responses were modest: plasma cytokine concentrations decreased following challenge regardless of outcome, peripheral blood mononuclear cell transcriptomes remained largely unchanged, and antigen-specific T cell activation and polarization were unaffected. Together, these findings reveal that protection from BP colonization associates with pre-existing serum antibodies, whereas symptom development is driven by localized mucosal inflammation dominated by myeloid cells. The predominance of nasal over systemic immune activation highlights the importance of mucosal immunity in controlling BP and provides critical insights to guide the design of next-generation vaccines aimed at preventing both disease and transmission.

overall_design: bulkRNAseq data was performed on peripheral blood mononuclear cells (PBMC) and nasopharyngeal swabs (NPS) of participants challenged with Bordetella pertussis. Samples were taken before and after challenge at multiple time points. Study outcomes were categorized as symptomatic infection, asymptomatic infection, or non-infected based on diagnostic testing and symptom manifestation.

first: Ziyuan

last: Ren

first: Pramod

last: Shinde

first: Nicola

last: Thrupp

first: Jiyeun

first: Aanya

last: Gupta

first: Aaron

last: Sutherland

first: Shelby

last: Orfield

first: Mari

last: Kojima

first: Ahmed

last: Azhan

first: Jian

last: Sun

first: April

last: Frazier

first: Scott

last: Halperin

first: May

last: Elsherif

first: Bjoern

last: Peters


title: Identification and validation of central amygdala FGFR1 as a therapeutic target for alcohol use disorder using single nucleus sequencing in rat

city: Austin

first: Elizabeth

last: Osterndorff-Kahanek

state: TX

address: 2500 Speedway

institute: University of Texas at Austin

summary: Understanding why some individuals are more vulnerable to alcohol addiction is key to developing effective treatments. We used cell-specific transcriptomics to dissect the central amygdala (CeA) of rats that continued drinking alcohol despite punishment—a hallmark of compulsive-like behavior. We found profound transcriptional changes in PKCδ+ neurons, with FGFR1 emerging as a central upstream regulator. Silencing FgfR1 in these neurons significantly reduced compulsive-like alcohol self-administration, positioning FGFR1 signaling as a promising therapeutic target—especially given the availability of FDA-approved inhibitors. We also uncovered major transcriptional shifts in Calcrl+/Drd2+ neurons, suggesting a broader CeA network reorganization that may contribute to compulsive-like self-administration. Together, these findings identify distinct CeA circuits driving addiction vulnerability, and open new avenues for targeted intervention.

overall_design: Single-nucleus RNA sequencing (snRNA-seq) was performed on the central amygdala of adult male Wistar rats trained to self-administer 20% ethanol under a fixed ratio 2 (FR2) schedule and exposed to foot-shock punishment. Based on their behavior, animals were classified as either punishment-resistant or punishment-sensitive. Yoked controls were included for comparison.

first: Estelle

last: Barbier

first: Leon

last: Höglund

first: Li

last: Xu

first: Nihal

last: Salem

first: Riccardo

last: Barchiesi

first: Antonio

last: Lacorte

first: Lief

last: Fenno

first: Robert

last: Messing

first: Dayne

last: Mayfield

first: Markus

last: Heilig


title: Loss of CSDE1 Function Enhances mRNA Stability of Interleukin-6 and Promotes Malignant Transformation in Endometrial Cancer Cells.

last: Cheng

state: Shanghai

address: 500 Quxi Road, Shanghai 200011

department: Department of Rehabilitation Medicine

institute: The Ninth People's Hospital Affiliated to Shanghai Jiaotong University School of Medicine

summary: CSDE1 (cold shock domain-containing protein E1) is an RNA-binding protein that plays a critical role in regulating mRNA stability and translation. Previous studies suggest that CSDE1 is downregulated or mutated in various cancers, including endometrial cancer (EC), but its exact role in tumor progression remains unclear. In this study, we demonstrate that the loss of CSDE1 function promotes malignant transformation in EC cells by enhancing the stability of interleukin-6 (IL-6) mRNA. Using data from The Cancer Genome Atlas (TCGA), we show that CSDE1 is frequently mutated and significantly reduced in EC tissues. CSDE1 depletion in EC cell lines using CRISPR-Cas9-mediated knockout (KO) significantly increases cell proliferation, migration, and invasion, and induced epithelial-to-mesenchymal transition (EMT). Transcriptomic analysis reveals robust mRNA upregulation of IL-6, a cytokine known to drive inflammation and tumor progression. We show that CSDE1 directly interacts with IL-6 mRNA and CSDE1 loss stabilizes IL-6 mRNA. Functionally, silencing IL-6 or inhibiting its signaling with siltuximab reverse the malignant phenotypes induced by CSDE1 knockout. These findings identify CSDE1 as a tumor suppressor in EC and uncover a novel CSDE1–IL-6 regulatory axis that drives tumor progression, positioning IL-6 as a potential therapeutic target in CSDE1-deficient EC.

overall_design: The TCGA database was analyzed to evaluate CSDE1 mutations in endometrial cancer (EC) and their clinical significance. Immunohistochemistry was performed to assess CSDE1 expression in EC tissues and normal endometrium, while Western blotting was used to determine CSDE1 protein levels in EC cell lines. A CSDE1-knockout EC cell model was established using CRISPR-Cas9, and RNA-seq was conducted to profile transcriptome-wide changes and identify differentially expressed genes. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses were applied to uncover the most significantly altered pathways. Cell proliferation and migration were evaluated using CCK-8, colony formation, EdU incorporation, and Transwell assays. Immunofluorescence staining was performed to examine changes in EMT-related markers following CSDE1 loss. RNA immunoprecipitation (RIP) assays were carried out to validate the interaction between CSDE1 and IL-6, and actinomycin D chase experiments were used to assess the effect of CSDE1 on IL-6 mRNA stability.

first: Yuanlin

last: Liu


title: Addressing the multiple facets of ligand-receptor network inference

city: Montpellier Cedex 5

first: Jacques

last: Colinge

address: 208 avenue des Apothicaires

country: France

institute: IRCM

summary: Part of a broader study about ligand-receptor interaction inference and a new framework expanding our SingleSignalR tool, we show how particular experimental designs, incuding bulk analyses, can be handled by this single-cell-orientate tool. Among these, the case of PDX is illustrated with a collection of PDAC PDX whose bulk RNA-sequencing data are made available here.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Paired-end bulk RNA-seq profiling of PDAC PDX in nude mice

first: Christel

last: Larbouret


title: Interkingdom Endodontic Biofilm Supernatant Induces Biphasic Inflammatory and Metabolic Reprogramming in Dental Pulp Stem Cells

city: Sakaka

first: Saeed

last: Alqahtani

country: Saudi Arabia

institute: Jouf University-College of Dentistry

summary: This study investigate how soluble by-products derived from a four-species endodontic biofilm model impacts upon the viability, transcriptomic profile, and inflammatory response of human dental pulp stem cells (DPSCs). The sterile-filtered supernatant was extracted from an established interkingdom endodontic biofilm model comprising Streptococcus gordonii, Fusobacterium nucleatum, Porphyromonas gingivalis, and Candida albicans. DPSCs were exposed to the microbial biofilm supernatant (BSN) for 4 and 24 hours. Cellular responses were evaluated via MTT, CCK-8, LDH assays, and Annexin V/PI staining. Whole transcriptomic sequencing was performed to assess gene expression dynamics, with GO and KEGG pathway enrichment analyses. IL6 and IL8 expression was validated by qPCR and ELISA.It was found that BSN significantly suppressed DPSC metabolic activity without inducing apoptosis or necrosis. RNA-seq revealed 723 significantly differentially expressed genes at 4 h and 1667 at 24 h. Early responses were dominated by upregulation of inflammatory mediators (e.g., CXCL8, IL6, TNFAIP2), with enrichment of TNF, NF-κB, and JAK-STAT signalling pathways. At 24 h, the expression profile shifted toward redox regulation and metabolic suppression, including downregulation of glycolytic and purine metabolism pathways. IL6 and IL8 expression was markedly increased at both transcript and protein levels. Indeed, soluble factors produced by a biofilm model representative of deep caries and carious pulp exposures are capable of reprogramming DPSC function in a time-dependent manner. The soluble factors initiate a biphasic response characterized by early immune activation and later metabolic adaptation. The findings underscore the potential role of biofilm-derived products associated with deep caries and carious pulp exposures in compromising DPSC function. In addition, they emphasise the need for the development of vital pulp therapy strategies that not only neutralise microorganisms but also their secreted products.

overall_design: DPSCs were exposed to 1:1 sterile-filtered supernatant from a four-species interkingdom endodontic biofilm for 4 and 24 hours, followed by RNA-seq, differential gene expression analysis, GO and KEGG pathway enrichment, and validation of IL6/IL8 expression by qPCR and ELISA.

first: Christopher

last: Nile


title: A novel pharmacological inhibitor of MAP4K4 activity protect against preclinical model of metabolic dysfunction-associated steatohepatitis

city: College Station

first: Aditya

last: Joshi

state: Texas

address: 560 Raymond Stotzer Pkwy

institute: Texas A&M University

summary: Metabolic dysfunction-associated steatohepatitis (MASH) is characterized by accumulation of fats in liver, chronic inflammation, hepatocytic ballooning, and fibrosis. In this study, glucosyl pyrrolo-pyrimidinone (GPPD), a newly synthesized pharmacological inhibitor of mitogen activated protein kinase kinase kinase kinase 4 (MAP4K4) was utilized to investigate significance of MAP4K4 signaling in MASH. To elucidate the effect of GPPD, wild-type (WT,C57BL6) mice were subjected to control diet (CD), high-fat high-fructose high-cholesterol diet (MASH diet, MD), and fed with MASH diet and treated with GPPD thrice a week for 30-week period. MAP4K4 immunoblotting and activity assay showed downregulation of MAP4K4 kinase activity without altering its expression. GPPD was able to mitigate hallmarks of MASH including steatosis, inflammation, fibrosis, and liver injury. Single-nuclei RNA sequencing revealed significant downregulation of calcium/calmodulin-dependent protein kinase II (CamKII). Subsequent immunoblotting confirmed that GPPD decreased expression and phosphorylation of CamKII in hepatocytes potentially conferring protection against steatohepatitis.

overall_design: Eight-week-old male wild-type (WT, C57BL6) mice were subjected to control diet, CD (10 kcal% fat and matching sucrose), high-fat, high-fructose, high-cholesterol diet termed MASH diet, MD (40 kcal% fat, 20 kcal% fructose, and 2% cholesterol), and MD + glucosyl pyrrolo-pyrimidinone (MD+GPPD) for 30 weeks, ad libitum. Mice in the MD + GPPD cohort received 10 mg/kg (body weight) GPPD three times a week on Mondays, Wednesdays, and Fridays via intraperitoneal (i.p.) injection. Mice in the CD and MD groups were treated with vehicle (0.2% DMSO + 99.8% saline) via i.p. three days a week (Mondays, Wednesdays, and Fridays) for 30 weeks. For single-nuclei RNA sequencing, at end of the 30-weeks, 20 mg livers were collected from each mice within a group, pooled, frozen in liquid nitrogen, and stored at -80°C.

first: Felix

last: Ampadu

first: Nikhil

middle: Y

last: Patil

first: Venkateshwara

last: Eeda

first: Iulia

last: Rus

first: Woncheol

last: Jung

first: Hassan

last: Abu shukair

first: Tae Gyu

last: Oh

first: Vibhudutta

last: Awasthi


title: Circadian rhythms in microglia mediate early life synaptic development in a sex-specific manner.

first: Laura

middle: K

last: Fonken

address: 107 W Dean Keeton St

department: Pharmacy

institute: The University of Texas at Austin

summary: Children today experience widespread circadian disruption from nighttime screen use and irregular sleep, yet how internal clocks shape brain development is unclear. Adolescence is a critical window when synaptic connectivity is refined, in part by microglia that engulf synaptic elements. Here, in adolescent mice, we show that hippocampal microglia exhibit diurnal transcriptional rhythms, with synaptic pruning gene expression peaking during the rest phase. Inducible deletion of the core clock gene Bmal1 in microglia abolishes these rhythms and alters developing hippocampal synapses in a sex-dependent manner. In males, clock disruption increases synapse engulfment, reduces dendritic spine density, and decreases synaptic connectivity; females show similar reductions in synaptic connectivity without overt postsynaptic structural changes. Microglial clock disruption also induces broad, sex-specific changes in synapse-related gene expression that overlap with neurodevelopmental disorder pathways and lead to impaired memory and sociability, indicating microglial clocks as key regulators of developmental synapse refinement.

overall_design: One experiment with RNA 3'-Tag sequencing of microglia isolated at zeitgeber time 6 or 18 on postnatal day 28 from wildtype mice and microglia-specific Bmal1 knockout (Bmal1 cKOMG) littermates. One experiment with RNA 3'-tag sequencing of hippocampal CA1 micropunches taken at zeitgeber time 6 on postnatal day 28 from wildtype and Bmal1 cKOMG mice.

first: Routh

last: Brandy

first: Fonken

last: Laura

first: Gibson

last: Cecily

first: Yang

last: Celina

first: Doan

last: Leanna

first: Gaudet

last: Andrew

first: Hofmann

last: Hans

first: Mangieri

last: Regina


title: Unveiling Transcriptional Heterogeneity and Discovering Footprints in Pediatric Medulloblastoma via Spatial RNA-Seq and Machine Learning

city: Mexico city

first: Aarón

last: Vázquez-Jiménez

state: Mexico city

address: Periferico Sur 4809

country: Mexico

institute: INMEGEN

summary: Medulloblastoma is the most common malignant pediatric brain tumor and is classified into four molecular subgroups: WNT, SHH, Group 3, and Group 4. Accurate characterization and classification of these subtypes are critical for prognosis and personalized treatment. In this study, we integrate spatial transcriptomics, machine learning, and explainable artificial intelligence to comprehensively analyze the spatial and transcriptional heterogeneity of the most prevalent and aggressive medulloblastoma subtypes (SHH, Group 3, and Group 4) in Mexican pediatric patients. By implementing a multiscale framework, we uncover extensive intra- and intertumoral variability that challenges traditional molecular classification. Our approach reveals subtype-specific gene expression signatures, identifies a core set of robust biomarkers and highlights distinct spatial patterns of tumor organization, including invasive and metabolically active niches. Notably, we demonstrate that Group 3 tumors, despite being the most aggressive, exhibit the lowest transcriptional heterogeneity, suggesting a streamlined malignant program centered on invasion and plasticity. These findings underscore the scope of bulk molecular profiling and support the implementation of spatially informed diagnostic tools and personalized therapeutic strategies that account for the complex architecture and functional diversity within MB tumors.

overall_design: We performed a comprehensive analysis of the transcriptional landscape of medulloblastoma (MB) using spatial transcriptomics (stRNA-seq) from five pediatric MB patients (3 MB-SHH, 1 MB-Group 4, and 1 MB-Group 3), including one biological replicate for two patients—one classified as MB-SHH and the other as MB-Group 4. Tissues were paraffin-embedded and sequenced using the 10x Genomics Visium V1 platform and the Illumina HiSeq 2000 system.

first: Edgar

last: Krötzsch

first: Vilma

last: Maldonado-Lagunas

first: Magali

last: Espinosa

first: Sergio

last: Juárez-Mendez

first: Jorge

last: Melendez-Zajgla

first: Osbaldo

last: Resendis-Antonio


title: Transcriptomic profiling of cardiac tissue in control and HFpEF model mice induced by ISO + L-NAME

city: Kumamoto

first: Michio

last: Sato

address: 1-1-1 Honjyo Cyu-ou-ku

department: Molecular Genetics

institute: Kumamoto University

summary: This project encompasses RNA-seq analysis of left ventricular tissue from 12week-old C57BL/6N male mice. Three mice received no treatment (control), and three mice were subjected to continuous administration of isoproterenol (ISO) and L-NAME for 6 weeks to induce a non-obese heart failure with preserved ejection fraction (HFpEF) phenotype. The study aims to identify transcriptomic alterations associated with non-obese HFpEF development and cardiac remodeling.

overall_design: RNA-seq profiling was performed on heart tissues from 12-week-old C57BL/6N male mice. After 6 weeks of treatment, samples were collected from control mice (n = 3) and ISO + L-NAME–treated mice (n = 3).

first: Yuya

last: Kinoshita


title: Multiome-based identification of HSC subtype markers

city: Oxford

first: Claus

last: Nerlov

address: John Radcliffe Hospital, University of Oxford

institute: Weatheral Institute of Molecular Medicine

summary:
Individual haematopoietic stem cells (HSCs) display heterogeneous capacities to reconstitute the major blood lineages, including platelets, erythrocytes, myeloid cells, B cells, and T cells. Single-cell transplantation assays have revealed that the HSC compartment contains lineage-restricted subtypes capable of reconstituting only specific lineages, such as platelets, alongside true multi-lineage HSCs. The proportion of these lineage-restricted HSCs increases with age, contributing to declined immunity and potentially to clonal haematopoiesis. To date, their identification and isolation have primarily relied on transgenic reporters, such as the Vwf-EGFP mouse line, which offer only moderate accuracy.
In this study, we profiled highly purified adult mouse long-term HSCs (LT-HSCs; LSK CD48⁻ CD150⁺ CD34⁻) using the DOGMAseq platform, which enables simultaneous measurement of transcriptome (RNA-seq), chromatin accessibility (ATAC-seq), and surface protein expression (CITE-seq). We subsequently identified candidate clusters corresponding to platelet-biased and multi-lineage HSCs, and developed a fluorescence-activated cell sorting (FACS) strategy to enrich these populations. This strategy employs four surface markers detectable with commercially available antibodies and achieves higher enrichment specificity than the Vwf-EGFP reporter.

overall_design: Fresh bone marrow cells were harvested from 8-week-old female C57BL/6 mice. Cells were stained with a combination of fluorescence-conjugated antibodies for FACS and oligo-tagged antibodies for CITE-seq. Long-term haematopoietic stem cells (LT-HSCs) were then isolated by flow cytometry and processed using the DOGMA-seq workflow.

first: Bowen

last: Zhang

first: Yiran

last: Meng

first: Xiying

last: Ren


title: Ex vivo drug sensitivity testing predicts treatment outcomes in advanced ovarian cancer

city: Basel

first: Francis

last: Jacob

address: Hebelstrasse 20

department: Department of Biomedicine (DBM)

country: Switzerland

institute: University Hospital Basel and University of Basel

summary: Effective clinical management of advanced epithelial ovarian cancer (EOC) remains a major challenge, with most patients relapsing despite standard therapies, emphasizing the need for individualized treatment strategies and predictive approaches. Here, functional ex vivo drug testing may provide a translational approach to match patients with effective, personalized therapies based on drug sensitivity. We present DRUGSENS, a scalable and clinically adaptable ex vivo drug response screening platform that enables quantitative assessment of single-cell, on-target effects in both cultured cell lines and patient-derived samples. DRUGSENS supports high-resolution analysis of cellular responses to individual therapeutic agents and clinically relevant drug combinations, with the potential to inform personalized treatment strategies across diverse tumor types and tissue contexts. This semi-automated ex vivo assay integrates immunofluorescence-based confocal imaging with computational analysis using QuPath, Fiji, and a developed DRUGSENS R package. We successfully generated individualized drug sensitivity profiles for 21 samples derived from 17 patients across both chemotherapy-naive and relapsed disease states, achieving a 100% success rate of culture efficiency and generating individualized drug profiles within a 10-day turnaround time. Notably, most resistant samples showed poor response to multiple agents, suggesting a multidrug-resistant phenotype. Ex vivo drug responses significantly correlated with clinical outcomes, including progression-free and overall survival. In conclusion, DRUGSENS platform enables rapid, clinically relevant functional profiling of therapeutic responses in EOC and represents a valuable tool to guide treatment recommendations and suggest drug prioritization for clinical application.

overall_design:
Single-cell RNAseq from fixed material obtained from human ascites samples of 3 patients with diagnosed with advanced stage ovarian cancer. Sequenced with the 10x Flex . Human data raw files wil be available upon request >>Submitter states: Raw data couldn't be included due patient privacy concerns. Requests can be made to the PI for access to the raw data.<<<

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

last: Lombardo

first: Ricardo

last: Coelho


title: KNUCKLES promotes meiotic cell-cycle progression by directly repressing the expression of KRP1 and KRP3 to ensure male fertility

city: Shanghai

first: Chenjiang

last: You

address: 2005 Songhu Rd

institute: Fudan University

summary: Meiosis is an essential process for sexual reproduction in most eukaryotes. Unlike mitosis, the specific cell cycle regulation for meiotic progression control is elusive. As the terminator for floral meristem activity and carpel development, loss function of the transcriptional repressor KNUCKLES (KNU) leads to male sterility in Arabidopsis, but the detailed regulatory mechanism remains unknown. Here, we find that during anther development, KNU specifically localizes in meiocytes and mutating KNU disrupts the meiotic progression with relatively more cells in meiotic prophase I, thus undergoing apoptosis. Transcriptome analysis shows that the numerous genes related to meiosis were down-regulated in knu-2 meiocytes. Further, we demonstrate that KNU can directly repress two cell cycle inhibitors of INTERACTOR/INHIBITOR OF CDK 1/KIP-RELATED PROTEIN 1 (ICK1/KRP1) and KRP3. Knockout of either KRP1 or KRP3 in knu-2 background largely rescues the knu-2 defects in male meiosis and fertility, suggesting that KNU modulates male meiotic progression and fertility via likely repressing KRP1 and KRP3 in cell cycle dependent manner. Taken together, our findings uncover that KNU is a “stabilizer” of cell-cycle progression for male meiotic progression and could be potentially applied as a candidate gene for genetic improvement for crops.

overall_design: Extraction of meiocytes from Arabidopsis ler and knu-2 with three replicates in this research.

first: Yingxiang

last: Wang

first: Bo

last: Sun

first: Cong

first: Zhiyu

last: Chen


title: Temporal inhibition of ADAM17 in fibroblasts reduces stiffness and promotes vascularization following myocardial infarction

city: Edmonton

first: Zamaneh

last: Kassiri

state: Alberta

address: 474 HMRC

department: Physiology

country: Canada

institute: University of Alberta

summary: Myocardial infarction (MI) triggers a complex remodelling process that leads to heat failure if uncontrolled. A Disintegrin and metalloproteinase-17 (ADAM17), a transmembrane sheddase, is upregulated in patients with ischemic cardiomyopathy, colocalized to myofibroblasts (myoFB) in the infarct tissues. Fibroblasts are key players in post-MI scar formation and exist in different states with diverse functions. Using mice with inducible Adam17 deletion in homeostatic FBs (Adam17 FB-KD ), or activated FBs (Adam17 myoFB-KD ), we found that ADAM17 loss in homeostatic FBs impaired infarct formation post-MI and increased mortality due to left ventricular (LV) rupture. Conversely, ADAM17 loss in myoFBs limited infarct expansion, LV dilation and dysfunction up to 4 weeks post-MI. Ex vivo and in vitro experiments revealed that the beneficial effects in Adam17 myoFB-KD mice are due to reduced stiffness of the infarct tissue through suppressing activation of EGFR-YAP-pathway, which promoted vascularization and thereby limited infarct expansion. Pharmacological inhibition of ADAM17 prior to MI was ineffective, but short-term ADAM17 inhibition after MI by targeting myoFBs significantly alleviated the adverse LV remodeling and dysfunction with beneficial effects up to 4wks post-MI. Our study identifies a short-term therapeutic window for ADAM17 inhibition to prevent long-term adverse remodeling, dysfunction and heart failure post-MI.

overall_design: Li, Yingxi

first: Al Rimon

last: Razoan

first: Wong

last: Faqi

first: Li

last: Haoyang

first: Epelman

last: Slava

first: Tallquist

last: Michelle D

first: Westover

last: Lindsey

first: Oudit

last: Gavin Y

last: Kassiri (Corresponding author)