title: Type I and II interferons drive inflammation through STAT1 in murine macrophage activation syndrome.

city: Zwijnaarde

first: VIB

last: Single Cell Core

address: Technologiepark-Zwijnaarde 71

department: VIB Single cell core

country: Belgium

institute: VIB

summary: Macrophage activation syndrome (MAS) exemplifies a cytokine storm syndrome by liver inflammation whereby interferon (IFN)-γ, which activates the JAK1/2-STAT1 pathway, is being a key driver cytokine. Ruxolitinib, a JAK1/2 inhibitor, has shown promising results in treating MAS patients, however the exact mechanism responsible for disease remission is unclear. One of the mediators inhibited by Ruxolitinib is STAT1, but its role in MAS pathogenesis remains unexplored. In this study, we explored the hepatic immune landscape of MAS and the role of STAT1 herein, using a Toll-like receptor (TLR)9-induced murine model of MAS. Cellular indexing of transcriptomes and epitopes-single cell RNA sequencing (CITE-seq) was performed on the immune compartment of the livers from wild-type (WT) and STAT1 knockout (KO) mice in naive conditions and upon induction of MAS.

overall_design: We performed CITE-seq on the immune compartment of the liver from PBS-injected and CpG-injected C57BL/6 WT and C57BL/6 STAT1 KO. Of each condition, a pool of cells (n = 4-8 mice, 1:1 female:male) was stained with fluoresence-activated cell sorting (FACS) antibodies and CITE-seq antibodies. Sorted CD45+ liver cells (69,000) were enriched with CD3-CD19-CD45+F4/80+ cells (1,000 cells) and subjected to sequencing (10x Genomics).

first: Amber

last: De Visscher

first: Jarne

last: Beliën

first: Eline

last: Bernaerts

first: Marte

last: Vandeput

first: Bert

last: Malengier-Devlies

first: Fran

last: Prenen

first: Hanne

last: Meers

first: Liliana

last: Sokol

first: Tania

last: Mitera

first: Nele

last: Berghmans

first: Philippe

last: Van den Steen

first: Jochen

last: Lamote

first: Niels

last: Vandamme

first: Anna

last: Bujko

first: Charlotte

last: Scott

first: Carine

last: Wouters

first: Patrick

last: Matthys


title: Transcriptional profiling of DLBCL-like murine pBIC10 tumors (p53F/F; Blimp1F/F; IKK2castopF/stopF; Cg1Cre/+; IL-10F/F)

status: Public on Jan 28 2026

city: Pamplona

first: Francisco

middle: J

last: Novo

address: Irunlarrea 1

department: Biochemistry and Genetics

country: Spain

institute: University of Navarra

type: Expression profiling by high throughput sequencing

summary: Germinal center (GC) B cells have been presented as the cell-of-origin of diffuse large B-cell lymphoma (DLBCL), and these cells can be functionally targeted with the use of Cgamma1-cre mice (Cg1cre) in which the expression of Cre recombinase is induced by transcription of the Ig gamma1 constant region gene segment. Here, we aimed to develop and characterize novel immunocompetent multi-lesion mouse models of DLBCL that, by triggering genetic alterations specifically in GC B cells, recapitulate relatively fast the molecular, cellular and tumor microenvironment of aggressive human DLBCL.

overall_design: RNAseq profiling of FACS-sorted reporter positive splenic B cells (B220+GFP+ lymphoma cells) were compared between IL-10-proficient and -deficient DLBCL murine models and to normal controls (B220+YFP+ GC B cells) during secondary immune response to sheep-red blood cells (SRBC) immunization (i.e. 10 days after second intraperitoneal immunization with SRBC, following a first immunization 20 days before).

first: Sergio

last: Roa


title: Charting the DNA methylation landscape of the Killifish across age and tissues

city: Berlin

first: Helene

last: Kretzmer

address: Ihnestraße 63

department: Genome Regulation

country: Germany

institute: Max Planck Institute for Molecular Genetics

type: Methylation profiling by high throughput sequencing

summary: Killifish are among the shortest-lived vertebrates and are considered a promising model organism for aging. However, so far virtually nothing is known about its DNA methylome, which is frequently used for age and health status predictions in mammals. Here, we provide a comprehensive whole-genome killifish methylation map covering different tissues, age groups, and species. We show that the methylome of all individuals follows the typical, bimodal distribution of either high or low methylation rates. Furthermore, we find the major methylation variance within a species is driven by cell type-specific methylation and small but detectable aging related dynamics separating the age groups.

sample_organism:
Nothobranchius furzeri
Nothobranchius orthonotus

overall_design: Analysis of the DNA methylome of different tissues and age goups from the turquoise (Nothobranchius furzeri) and spotted killifish (Nothobranchius orthonotus).

first: Dario

middle: R

last: Valenzano

first: Alexander

last: Meissner

first: Mara

last: Steiger


title: Mechanisms of augmented tumor immunogenicity via ATR inhibition in Merkel cell carcinoma

status: Public on Jan 27 2026

city: Seattle

first: Daniel

last: Jones

state: WA

country: USA

institute: Fred Hutchinson Cancer Center

summary: There is an urgent unmet need to develop novel therapeutic strategies for tumors that do not respond to immune checkpoint inhibition (ICI) via PD-1 pathway blockade. The ATR-mediated DNA replication checkpoint has been reported to have immune-augmenting properties; however, the mechanisms underlying these properties are not well characterized. Here we explore the potential immunogenic effects of ATR inhibition in Merkel cell carcinoma (MCC), a cancer that is particularly relevant due to its high proliferative index and frequent response to anti-PD-(L)1 therapy. ATR inhibition induced tumor cell cytotoxicity in both Merkel cell polyomavirus-positive and UV-induced MCC cell lines in the absence of exogenous DNA damage. ATR inhibition alone or in combination with low-dose radiation induced numerous proinflammatory TNF-NF-κB signals as assessed via bulk transcriptomic profiling. These included increased expression of MHC class-I alleles, antigen processing machinery, interleukins, chemokines and interferon genes associated with anti-tumor immune responses in diverse tumor types. In parallel, we observed enhanced surface exposure of the “eat-me” signal calreticulin on MCC cells and subsequent phagocytosis by human monocyte-derived macrophages. Given that MCC tumors are often cGAS-STING-deficient (including two cell lines examined here), these ATRi-induced mechanisms are significant as they were activated regardless of cGAS-STING functional status. These data provide a mechanistic basis for the clinical evaluation of ATRi in advanced ICI-refractory MCC (NCT05947500), and suggest biomarkers that may be associated with response in human MCC tumors treated with ATRi.

overall_design: Early passaged WaGa, MKL2, MCC26 and MCC13-HL cell lines were used (sub-cultured less than 25 times). 72 hours of ATRN-119 (100 nM for MCPyV-positive and 250 nM for MCPyV-negative) ± 4 Gy radiation treatment was initiated in triplicate for cells seeded in 10 cm tissue-culture dishes. Untreated cells were used as negative control. Harvested cells were submitted for RNA extraction, library preparation and sequencing (DNBseq platform, BGI Genomics, Cambridge, MA, USA). Raw paired-end reads (~ 30 million per sample; 100 base pair read length) were quality-checked, adapter-trimmed, and aligned to GRCh38 with Bowtie236. Genes with counts less than 10 across all samples were filtered out. The subsequent raw RNA-Seq count data were normalized using FPKM (fragments per exonic kilobase per million) with effective library sizes estimated using TPM (transcripts per million),  followed by log2 transformation with a pseudocount of 2, as implemented in the edgeR R/Bioconductor package37 and used for further analyses. Differential analysis at the gene level was performed using the Limma package38, with false discovery rate method used to adjust the p-values for multiple testing. Genes with an absolute log2 fold change of at least 0.5, normalized against mock-treated cells, were considered either up or downregulated and used for relative quantification across different treatment groups. Statistical significance was defined by a Q value of ≤ 0.05. Dot plots were generated using the R ggplot2 package39. Transformed expression data matrices were uploaded to an integrative cloud-based multi-omics RNA-seq data mining browser from BGI Genomics (“Dr. Tom”) and then used as input for computation of treatment-induced transcriptomic enrichment via the Molecular Signatures Database (MSigDB) hallmark gene set analysis. Hallmark interpretations were queried using a minimum of 15 and a maximum of 500 genes per set for statistically significant signatures. Distribution of normalized enrichment scores (NES) and gene set enrichment analysis (GSEA)-defined false discovery rate (FDR) significance threshold  0.05, along with leading edge (LE) gene set sizes for a characteristic biological phenotype, can be found in Supplemental Figure 3. Variable clustering of gene expression data across all samples was performed and visualized through principal component analysis.

first: Rashmi

last: Bhakuni

first: Junghyun

last: Lee

first: Peter

last: Goff

first: Long

last: Nguyen

first: Rongxiang

last: Lin

first: Evan

last: Newell

last: Hall

first: Oren

last: Gilad

first: Eric

last: Brown

first: Paul

last: Nghiem


title: Respiratory viral infections prime accelerated lung cancer growth [scATAC-Seq]

city: Charlottesville

first: Xiaoqin

last: Wei

state: Virginia

address: 2512 Fontaine Ave

institute: University of Virginia

type: Genome binding/occupancy profiling by high throughput sequencing

summary: The COVID-19 pandemic has highlighted long-term health consequences of viral pneumonia, yet its potential impact on cancer development and growth remains poorly understood. Here, we show that prior SARS-CoV-2 or influenza infection accelerates lung tumor progression by reprogramming the local immune landscape. To test whether heightened cytokine responses after tumor initiation reflect durable epigenetic priming, we performed scATAC-seq on total lung cells from SARS-CoV-2–infected mice (28 d.p.i.) and PBS controls. Across macrophages, epithelial cells, fibroblasts, and endothelial cells, infection induced mild-to-moderate increases in chromatin accessibility at the Csf3 promoter and putative enhancers, with similar accessibility gains at Il6, Il1b, Cxcl1, and Cxcl5 loci in multiple compartments. Motif enrichment and regulon analyses further indicated increased accessibility/activity of NF-κB and AP-1, along with elevated STAT3/STAT4 activity. Collectively, these data demonstrate that prior respiratory viral infection drives long-lasting epigenetic remodeling of cytokine loci in lung immune and structural cells.

overall_design: Lung single-cell suspensions freshly isolated from PBS- or SCV2-infected mice at 28 d.p.i. were processed for ATAC library construction using the Chromium Next GEM Single Cell ATAC Kit v2 (10x Genomics), following the manufacturer’s protocol.

first: Wei

last: Qian

first: Xiangyu

last: Ye

first: Jie

last: Sun


title: RNAseq anaylsis of three Islet-1+ Cardiac Stem Cell Clones derived from Neonatal Cardiac Tissue

city: Loma Linda

first: Lorelei

last: Hughes

state: CA

address: 11021 Campus

department: Pathology and Human Anatomy

institute: Loma Linda University

summary: Islet-1+ Cardiac Stem Cells (CSCs) derived from neonatal cardiac tissue are promising candidates for cardiac repair due to their ability to differentiate into all cells of the cardiovascular lineage and the innate ability of the neonatal heart to regenerate after injury. In this study we analyzed the transcriptome and differentiation capability of Islet-1+ cardiac progenitor cell clones isolated from neonatal human patient-derived tissue and demonstrated that matched ovine CSCs restore function when administered for cell-based repair in an allogeneic ovine model of myocardial infarction.

overall_design: Neonatal Islet-1+ CSCs were derived from discarded patient cardiovascular tissue. This tissue was used to generate uniform clonal populations for transcriptomic anaylsis.

first: Mary

middle: K

last: Kearns-Jonker

first: Nahidh

last: Hasaniya

first: Leonard

middle: L

last: Bailey

first: Jonathan

last: Baio

first: Victor

last: Camberos


title: KDM4A promotes NEPC progression through regulation of MYC expression [ChIP-seq]

city: Houston

first: Guocan

last: Wang

state: TX

address: 1515 Holcombe Blvd, T7.3900

institute: MD Anderson Cancer Center

summary: Neuroendocrine prostate cancer (NEPC) represents one of the most lethal forms of prostate cancer (PCa) and lacks life-prolonging treatment. Incidence NEPC is increased due to the widespread use of AR pathway inhibitors (ARPIs) in the treatment of non-metastatic CRPC and hormone-sensitive metastatic tumors. Here we identified histone lysine demethylase KDM4A as a key player in NEPC progression and an effective therapeutic target. We performed ChIP-seq to identify KDM4A target genes in human NEPC cell line 144-13.

overall_design: Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) for KDM4A in 144-13 cells.

first: Feng

first: Abhinav

last: Jain


title: Promoter Capture Hi-C performed on human Type 3 Innate Lymphoid Cells (ILC3s)

city: London

first: Mikhail

last: Spivakov

address: Du Cane Road

country: United Kingdom

institute: MRC London Institute of Medical Sciences

summary: This promoter capture Hi-C data in tonsil-derived ILC3 cells accompanies the manuscript: "High-resolution promoter interaction analysis implicates genes involved in the activation of Type 3 Innate Lymphoid Cells in autoimmune disease risk"

overall_design: Human ILC3s were isolated from tonsillectomies of three children and promoter capture Hi-C was performed. Libraries were sequenced using paired-end NGS and chromatin interactions were called using CHiCAGO.

first: Valeriya

last: Malysheva

first: Helen

last: Ray-Jones

first: David

last: Ohayon

middle: F

last: Smith

first: Stephen

last: Waggoner


title: snFLARE-seq and mrFRIGID for the transcriptomic and metabolomic landscape of prostate cancer with different anatomical origins

city: Shanghai

first: xiao

last: kai

address: YueYang Road 420

country: China

institute: SIBCB

summary: snFLARE-seq for the transcriptomic landscape of prostate cancer with different anatomical origins. Prostate cancer cells of different anatomical locations display remarkable heterogeneity. This poses a challenge to the clinical relevance of pre-clinical models and the efficacy of contemporary therapeutic approaches. Here we developed the snFLARE-seq methodologies to directly investigate the transcriptomic landscape of prostate cancer patients utilizing formalin-fixed paraffin-embedded (FFPE) specimens. A retrospective analysis revealed the clinical disparities of prostate cancer from peripheral zone (PZ), transition zone (TZ), and across PZ and TZ. The snFLARE-seq, refined for enhanced single-nucleus sequencing, unveiled distinct cell type distributions and signaling pathways between PZ and TZ samples. Hormone therapy substantially affected cancer cells and microenvironment, leading to a polarized feature of epithelial cells and a subverted immune microenvironment. With improvements on metabolite extraction, mrFRIGID revealed unique metabolic features of prostate cancer from different origins. The metabolomic results indicate that PZ cancer cells were in a metabolic-dormant status, which were probably awaken by hormone therapy. Integrative analysis of results from snFLARE-seq, mrFRIGID, and TCGA database uncovered four metabolic pathways and related genes associated with disease aggressiveness. Our work would accelerate investigations on disease heterogeneity and evolution in real-world clinical settings, stimulating patient-specific precision healthcare solutions.

overall_design:
Single‑nucleus RNA‑seq profiling of prostate cancer tissues from different anatomical zones (peripheral zone, transition zone, and mixed PZ/TZ) using the snFLARE‑seq method optimized for FFPE specimens. Nuclei were isolated from FFPE samples of prostate cancer patients and subjected to in‑nucleus reverse transcription and library preparation with mixed random and oligo‑dT primers. Sequencing libraries were generated using the SeekOne® DD single‑cell 3′ Transcriptome Kit and sequenced on Illumina NovaSeq 6000.

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first: Zhenfei

last: Li

first: Kai

last: Xiao

first: Dongyin

last: He


title: Meningeal Lymphatic Vessel Dysfunction Exacerbates Brain Injury in CVST Mice via Endoplasmic Reticulum and Oxidative Stress Pathways.

city: fuzhou

first: jianbin

last: ying

address: No. 156, North Section of West Second Ring Road, Gulou District

institute: Fuzong Clinical Medical College of Fujian Medical University

summary: Meningeal lymphatic vessels (mLVs) play a crucial role in maintaining neurological homeostasis and disease development. However, their function in brain injury following cerebral venous sinus thrombosis (CVST) remains unclear. This study investigates how dysfunction of meningeal lymphatic vessels influences the pathological progression of CVST by regulating the endoplasmic reticulum (ER) and oxidative stress (OS) pathways.

overall_design: Through RNA sequencing (RNA-seq) analysis, we induced cerebral venous sinus thrombosis (CVST) models and divided them into three groups: one CVST group, one CVST group with bilateral cervical lymph node ligation, and one CVST+ group receiving 4-PBA intervention after lymph node ligation. On day 2 post-modeling, differentially expressed genes (DEGs) were identified among cortical tissues across the three groups.

first: jin

last: li

first: junjie

last: jing

first: shousen

last: wang


title: Systematic Identification of Germ Granule Proteins Reveals Specialized Roles in RNAi and Small RNA Inheritance

city: Los Angeles

first: Carolyn

middle: Marie

last: Phillips

address: 1050 Childs Way, RRI 201

department: Biological Sciences

institute: University of Southern California

summary: Biomolecular condensates, such as germ granules, organize RNA pathways critical for fertility and genome regulation. Yet, the protein composition and functional specialization of these condensates remain poorly defined. Here, we applied TurboID proximity labeling to the Caenorhabditis elegans germ granule protein SIMR-1, integrating mass spectrometry with genetic screening, CRISPR-based tagging, and small RNA sequencing. This systematic approach identified several previously uncharacterized germ granule proteins that are required for fertility, germline immortality, exogenous RNAi, and transgenerational inheritance. Small RNA sequencing of 21 mutants revealed broad and class-specific defects in siRNA and miRNA biogenesis, with distinct factors required for amplification of WAGO-class 22G-RNAs, CSR-class 22G-RNAs, or histone-directed small RNAs. Among these, we identified PINT-1, a highly disordered protein that directly interacts with and is recruited to germ granules by the PIWI Argonaute PRG-1. PINT-1 is required for piRNA-dependent and -independent secondary siRNA biogenesis and germline development. Comparative genomics revealed that PINT-1 has co-evolved with PRG-1 across nematodes, with a conserved structured N-terminus and a rapidly diverging repeat-rich intrinsically disordered region. Together, our findings expand the germ granule proteome and reveal how distinct condensate components contribute to specialized functions within the small RNA pathways, while highlighting an evolutionarily co-adapted PIWI interactor critical for siRNA biogenesis.

overall_design: Total small RNA sequencing of wild-type and RNAi pathway mutants in day-1-adult animals.

first: Shihui

last: Chen

first: Lucas

middle: H

last: Prescott

first: Craig

middle: C

last: Mello

middle: M


title: Respiratory viral infections prime accelerated lung cancer growth [scRNA-Seq]

first: Xiaoqin

last: Wei

summary: The COVID-19 pandemic has highlighted long-term health consequences of viral pneumonia, yet its impact on cancer development and progression remains poorly understood. Here, we show that prior SARS-CoV-2 or influenza infection accelerates lung tumor progression by reprogramming the local immune landscape. To define mechanisms underlying infection-induced tumor promotion, we performed single-cell RNA-seq on whole-lung cells from KP mice at 6 weeks (PBS_T6, IAV_T6) and 12 weeks (PBS_T12, IAV_T12) after tumor induction, along with tumor-free PBS and IAV controls (time matched to T6). Across conditions, scRNA-seq revealed that prior viral pneumonia programs a pro-tumor lung microenvironment marked by increased pro-tumor myeloid programs and diminished anti-tumor CD8+ T cell immunity. Notably, we identified a dominant SiglecF^hi tumor-associated neutrophil subset enriched in infected tumors that exhibits hypoxia/glycolysis- and immunosuppression-associated transcriptional programs and shows the strongest predicted interactions with progenitor and tumor epithelial populations.

overall_design: KP mice infected with IAV for 3 weeks were i.t. administered Ad5-SPC-Cre virus to initiate lung tumorigenesis. Lung single-cell suspensions were generated at weeks 6 (early-stage) and 12 (late-stage) after tumor induction for scRNA-Seq analysis. Tumor free PBS- and IAV-treated mice served as controls. Each group was representing pooled samples from 3-5 mice. Single-cell libraries were prepared using the Chromium Single Cell 3′ Reagent Kit (10x Genomics) following the manufacturer’s protocol.

first: Wei

last: Qian

first: Jie

last: Sun


title: circPCMTD1: A protein-coding circular RNA that regulates DNA damage response in BCR/ABL1-positive leukemias

city: Salt Lake City

first: Ramiro

last: Garzon

state: UT

address: 2000 Circle of Hope

department: Division of Hematology and Hematologic Malignancies

institute: Huntsman Cancer Institute

summary: Circular RNAs are a novel class of RNA transcripts, which regulate important cellular functions in health and disease. Herein, we report on the functional relevance of circPCMTD1 in BCR/ABL1- positive myeloid leukemias. In screening experiments, we found that circPCMTD1 depletion strongly inhibited the proliferative capacity of leukemic cells with BCR/ABL1 translocations. RNA sequencing and mass cytometry experiments identified aberrant activation of the DNA damage response (DDR) pathway as a downstream effect of circPCMTD1 depletion. DNA fiber assays, Comet assays and profiling of DDR markers (phospho-H2AX, phospho-CHK1, etc.) further underscored the pronounced effect of circPCMTD1 depletion in increasing genotoxic stress and inhibiting leukemic cell growth. circPCMTD1 targeting also led to aberrant DDR activation in leukemia patient blasts with BCR/ABL1 translocations. In in vivo experiments, circPCMTD1 knock-down prolonged the survival of mice engrafted with BCR/ABL1-positive leukemia cells. Mechanistically, we found that circPCMTD1 is enriched in the cytoplasm and associates with the ribosomes of leukemic blasts. We detected a cryptic open reading frame within the circPCMTD1 sequence and found that circPCMTD1 generates a 127 amino-acid peptide product (cPCMTD1-127aa). Using a custom-produced antibody, we found that the cPCMTD1-127aa interacts with the BCR/ABL1 oncoprotein, as well as with the BLM, TOP3A and RMI1 proteins, which form the BTR complex and regulate DNA repair and genome stability. cPCMTD1-127aa enhanced BTR complex formation, thereby increasing cellular tolerance to genotoxic stress. In summary, we identify and characterize circPCMTD1 as a molecular vulnerability and potential therapeutic target in BCR/ABL1-positive leukemias.

overall_design: circPCMTD1 was knocked down in K562 cells by antisense gapmers targeting the backsplice junction and whole transcriptome was analyzed by RNA-seq. Controls samples were transfected with scrambled antisense gapmers. Each group has 3 biological replicates and each biological replicate has 3 technical replicates.

first: Garzon

last: Ramiro

first: Urs

last: P Amog

first: Papaioannou

last: Dimitrios

first: Goda

last: Chinmayee


title: Synergistic Targeting of eIF4A - Mediated Translation Initiation and Apoptosis in Acute Myeloid Leukemia

city: Boston

first: Peter

last: van Galen

state: Massachusetts

address: 4 Blackfan Circle

department: Hematology

institute: Brigham and Women's Hospital / Broad Institute of MIT and Harvard

summary: Targeted therapies like the BCL-2 inhibitor Venetoclax have expanded treatment options for acute myeloid leukemia (AML) patients, but survival remains poor due to drug resistance and disease relapse. We found that the translation initiation factor EIF4A1, which unwinds complex mRNA structures in the 5’ UTR of oncogenic transcripts, is highly expressed in AML stem- and progenitor-like cells relative to healthy hematopoietic stem and progenitor cells (HSPCs). Inhibition of eIF4A with the first-in-class small molecule Zotatifin reduces translation efficiency of transcripts related to the cell cycle and oncogenic signaling via PI3K/AKT/mTOR pathway, as shown by ribosome profiling and gene set enrichment analysis. Western blot analysis corroborated these findings, demonstrating downregulation of AKT, STAT-5, and MCL-1, factors implicated in resistance to Venetoclax-based regimens. The combination of Zotatifin and Venetoclax synergistically kills AML cells in vitro and induces apoptosis across AML genotypes, with selectivity toward progenitor-like cells in primary AML bone marrow (BM), whereas its effect in primary healthy BM is limited. Using three in vivo relapsed and refractory AML patient-derived xenograft models, the combination significantly suppressed tumor burden and prolonged survival. These results support eIF4A-mediated protein translation as a therapeutic target in AML and highlight the potential of Zotatifin and Venetoclax in relapsed/refractory disease.

overall_design: MOLM-13 cells were treated with DMSO (control) or the eIF4A inhibitor Zotatifin for four hours. Then cells were harvested for RNA-seq and Ribo-sequencing.

first: Yoke Seng

last: Lee

first: Noha

last: Awais

first: Jingting

last: Lin


title: Neofusicoccum laricinum disrupts larch defenses through coordinated cell wall degradation and antioxidant suppression

city: Shenyang

first: Yongfeng

last: Yang

address: No. 120, Dongling Road, Shenhe District

institute: Shenyang Agricultural University

summary: Larch (Larix spp.), a key species in China's reforestation efforts, faces increasing threats from shoot blight caused by Neofusicoccum laricinum. This study characterized the biological traits, virulence mechanisms, and host interactions of this pathogen to inform disease management. Twenty-five N. laricinum strains were isolated from six regions in Northeast China and identified through morphological and molecular analysis. Comprehensive growth assessments revealed optimal development at 18°C and pH 9-11, with significant strain-specific variation in virulence (lesions 18.4-38.8 mm). Pathogenicity assays revealed that the hypervirulent TM02 strain exhibited early and robust production of cell wall-degrading enzymes，such as pectin methylgalacturonase (PMG, 208.9 U/mg) and polygalacturonase (PG, 54.9 U/mg), correlated with its aggressive infection phenotype. Biochemical analyses revealed that the pathogen actively disrupted host oxidative defenses, with superoxide dismutase (SOD) activity peaking at 3 dpi (456.7 U/g·min-1) before decreasing to 0.8× control levels by 7 dpi, whereas peroxidase (POD) activity exhibited a transient 4.6-fold increase followed by rapid suppression. Transcriptome analysis revealed generally downregulation of defense genes, mainly cellulose synthase (21/25 genes) and peroxidase (38/45 genes), with –10.5-fold inhibition of Ces-g8671 and an –11.4-fold reduction in Pod-g18614 expression, indicating that pathogens can simultaneously damage larch cell wall synthesis and the ROS scavenging defense system. These findings establish N. laricinum’s sophisticated two-phase infection strategy: initial physical breach of cell walls facilitated by CWDEs, followed by systematic suppression of host antioxidant defenses. This study identifies specific molecular targets for developing intervention strategies and provides critical insights into host‒pathogen dynamics in larch plantations under climate change scenarios.

overall_design: Neofusicoccum laricinum was inoculated on healthy L.kaempferi seedlings (treatment group). Three parts of L.kaempferi seedlings at the disease site were taken, and three parts of healthy L.kaempferi seedlings were taken as controls, and then transcriptome analysis was performed.


title: Cellular and molecular landscapes of human tendons across the lifespan revealed by spatial and single-cell transcriptomics

city: Oxford

first: Sarah

last: Snelling

address: Windmill Road

department: NDORMS

institute: UNIVERSITY OF OXFORD

summary: Tendon injuries are common and often heal poorly. While developing tendons heal without scarring, this capacity declines with age, yet the underlying cellular transitions remain poorly defined. Here, we integrate histological, single-nucleus, single-cell, and spatial transcriptomic profiling of human Achilles and quadriceps tendons across embryonic, foetal, and adult stages, including ruptured adult tendons. We identify seven embryonic progenitor states that give rise to three distinct tendon-associated fibrillar, connective tissue, and chondrogenic lineages. These populations diversify during development and occupy distinct spatial niches, adopting specialised roles in matrix synthesis, tissue remodelling, and mechanical adaptation. While non-fibroblast populations remain transcriptionally stable with age, fibroblasts undergo marked reprogramming, shifting to homeostatic or injury-responsive states. In ruptured adult tendons, a subset of fibroblasts partially reactivates developmental programs but remains transcriptionally distinct from their regenerative counterparts. These findings define the cellular architecture of human tendon development and ageing and reveal lineage-specific targets for therapeutic repair.

overall_design: Human fetal Achilles and quadriceps tendons (including muscle and bone attachment sites) were dissected from lower limbs of fetuses aged 9-20 post-conception weeks (pcw). The tissues were then snap-frozen in liquid nitrogen and stored at -70°C to -80°C before being used for single-nuclei RNA-sequencing. Only midbodies were used from 20 pcw tendons, while 12 and 17 pcw tendons were processed whole.

first: Alina

last: Kurjan

first: Jolet

middle: Y

last: Mimpen

first: Lorenzo

last: Ramos-Mucci

first: Ali

last: Aksu

first: Carla

last: Cohen

first: Mate

last: Naszai

first: Christopher

middle: D

last: Buckley

first: Adam

middle: P

last: Cribbs

first: Mathew

last: Baldwin


title: Gαi1 and Gαi3 Mediate IL-11-Induced Signal Transduction and are Potential Therapeutic Targets for LUAD

city: suzhou

first: Gaomeng

last: Luo

address: 199 Renai Road, Industrial Park

institute: soochow university

summary: Lung adenocarcinoma (LUAD) is the main histologic subtype of lung cancer, and its incidence is on the rise. However, since the vast majority of patients are already in advanced stages at the time of diagnosis, their 5-year survival rate is only 15%, so it is urgent to explore the mechanism of the development of LUAD and improve the survival time of patients. Interleukin-11 (IL-11), a member of the IL-6 cytokine family, has an influential role in the development and progression of a variety of tumors, but the specific molecular mechanisms that promote the malignant progression of LUAD are unknown. Here, we found that the IL-11-induced activation of Akt, Erk, and STAT3 could be inhibited by knocking out the expression of Gαi1/3. In contrast, overexpression of Gαi1/3 could enhance IL-11-induced signaling. The binding of Gαi1/3 to GP130 mediates IL-11-induced downstream activation of Akt-mTOR, Erk, and STAT3, which requires recruitment of Grb2-associated binding protein 1 (Gab1). In LUAD cells, shGαi1/3 inhibited cell growth, proliferation, and migration as well as blocked the tumor-promoting ability of IL-11. However, overexpression of Gαi1/3 enhanced the IL-11-induced cell growth, proliferation, and migration. ShGαi1/3 also inhibited the proliferation of LUAD cells in vivo. Overall, the findings of this study demonstrate the Gαi1 and Gαi3 are critical for IL-11 signal transduction. Moreover, we reveal that Gαi1 and Gαi3 are highly expressed and associated with poor overall survival in lung adenocarcinoma and may thus act as potential therapeutic targets in LUAD. These results provide a novel therapeutic strategy for LUAD patients with upregulated IL-11 expression.

overall_design: To investigate the role of IL11 in lung adenocarcinoma, we constructed A549 cell lines transfected with lentiviruses expressing scr-shRNA and sh-IL11, respectively.

first: Wenxuan

last: Hu

first: Jian

first: Zheng

last: Lu

first: Yuan

last: Cui

first: Weibiao

last: Zeng

first: Hao

last: Ding

first: Qifan

last: Li

first: Zhike

last: Chen

first: Xin

last: Tong

first: Cheng

first: Chun

last: Xu

first: Jun

last: Zhao


title: Mitochondrial Genome Comparison and Functional Analysis of atp8 Underlying Cytoplasmic Male Sterility in Medicago sativa L.

city: Changchun

first: Bo

address: 5268 Renmin Street

department: College of Forestry and Grassland Science

institute: Jilin Agricultural University

summary: Cytoplasmic male sterility (CMS) represents a crucial biological tool for the effective utilization of heterosis in plant breeding. Despite its importance, the molecular mechanisms underlying cytoplasmic male sterility in M. sativa have not yet been fully elucidated. In this study, the mitochondrial genomes of the cytoplasmic male-sterile line MS-JN1A and the maintainer line MS-JN1B of M. sativa were assembled and sequenced. Comparative analysis of the mitochondrial genomes revealed that the mitochondrial genome of the sterile line has undergone pronounced structural rearrangements. Moreover, the differentially expressed mitochondrial gene atp8, together with its associated open reading frames (ORFs), was identified as a key candidate underlying CMS. In the anthers of MS-JN1A, ATP levels and reactive oxygen species (ROS) accumulation were concomitantly elevated, indicating a disruption of mitochondrial energy-redox homeostasis. Further functional analyses demonstrated that anther-specific overexpression of atp8 directly induced premature programmed cell death (PCD) in the tapetum, accompanied by extensive transcriptional reprogramming of pathways associated with energy metabolism and ROS responses.. Collectively, our findings propose that atp8-mediated disruption of mitochondrial energy-ROS homeostasis represents a central molecular mechanism driving cytoplasmic male sterility in M. sativa, and they provide new insights into mitochondrial regulation of male fertility in plants.

overall_design: RNA-seq of Medicago sativa L. in Wild plant and Overexpression atp8 group


title: Chronic TCR signaling-driven suppression of FOXO1-KLHL6 axis promotes T cell exhaustion

city: Suzhou

first: Xiaoli

last: Pan

state: Jiangsu

address: No. 100, Chongwen Road.

institute: Suzhou institude of systems medicine

summary: This study was published as a “Brief Report” and therefore does not include an abstract.

overall_design: Naive CD8⁺ T cells were isolated from the spleens of OT-I mice and activated with anti CD3 (2ug/ml) and anti-CD28 (1ug/ml) antibodies in the presence of IL-2 (10ng/ml) for 48 h. The cells were then removed from the activation plates and cultured under normal conditions. CD8⁺ T cells were collected at the naive state and at 24 h, 48 h, and 72 h after activation for RNA-seq analysis, with three biological replicates per group.

first: Guideng

first: Hongcheng

last: Cheng

first: Yujia


title: Screen differentially expressed genes regulated by hnRNPF

city: Xi’an

first: Jianlin

last: Wang

state: shaanxi

address: 127 West Changle Street

institute: Fourth Military Medical University

summary: To explore how hnRNPF regulates the migration and invasion of iCCA cells,RNA sequencing was perfomed by using parental iCCA cells and those subjected to hnRNPF knockout to screen differentially expressed genes (DEGs) between these cells.

overall_design: Construct the hnRNPF knockedout cell, then total RNA was extracted and analyzed to screen differentially expressed genes in hnRNPF-KO cell and the parental cell.

first: Weiwei

last: Shen


title: Increased stiffness mimicking ovarian aging induces a fibroinflammatory response in follicles and impairs oocyte quality

city: St Louis

first: Sara

last: Pietroforte

state: Missouri

address: 425 S. Euclid Avenue

department: Ob&Gyn

institute: Washington University in St Louis

summary: Reproductive aging in females is characterized by decreased ovarian reserve and oocyte quality. With aging, both mouse and human ovaries become pro-fibrotic and stiff. However, whether follicles sense and respond to microenvironmental stiffness and affect folliculogenesis and oocyte quality independent of other aging-related factors is unknown. To address this question, we cultured mouse secondary follicles in alginate hydrogels that reproduce the stiffness of young and reproductively old mice. RNA-sequencing revealed that follicles respond rapidly to increased stiffness and exhibit enrichment in genes related to inflammation and extracellular matrix remodeling. Long-term culture in stiff hydrogels resulted in reduced follicle survival, granulosa cell viability, estradiol synthesis, and oocyte quality. To begin to determine how stiffness is transmitted within the follicle, we examined transzonal projections, which mediate granulosa cell–oocyte communication and nutrient exchange. In stiff conditions, the number of transzonal projections decreased. Our findings demonstrate that follicles are highly mechanosensitive and that stiffness alone can trigger hallmarks of ovarian aging, including reduced follicle growth, reduced oocyte quality, and a fibroinflammatory phenotype potentially integrated to the oocyte via TZPs.

overall_design: RNA-seq profiling of ovarian secondary follicles isolated from pre-pubertal  (12-13days) CB6F1 mice and cultured in 0.5% and 2% alginate beads in groups of 5 follicles per bead. Follicles were than isolated and processed for sequencing at 3h, 6h, 12h and 24h of in vitro culture.

first: Farners

last: Amargant


title: Wnt Activation and Dual SMAD Inhibition For Induction and Maintenance of Hindbrain-like Neural Stem Cell from hiPSCs [scRNA-seq]

city: Kyoto

first: Makoto

last: Ikeya

address: 53 kawahara-cho, shogoin

department: Center for iPS Cell Research and Application(CiRA)

country: Japan

institute: Kyoto University

summary: Neurons exhibit region-specific identities corresponding to functional distinctions across different brain areas. Region-restricted neural stem cells (NSCs) have previously been generated from pluripotent stem cells; however, maintaining their regional identity over extended passages remains challenging. Here, we report the generation of hindbrain-like induced NSCs (Hb-LiNSCs) with upregulated hindbrain-specific markers and downregulated forebrain, midbrain, and spinal cord markers under xeno- and basic fibroblast growth factor-free conditions using three chemicals—CHIR99021 (at a high concentration), a potent activator of the Wnt pathway, A-83-01, a potent inhibitor of the TGF-β/Activin/Nodal pathway, and LDN193189, a potent inhibitor of the bone morphogenetic protein pathway. Hb-LiNSCs maintained their chromosomal integrity, multipotency, and differentiation capacity even after long-term culture for more than 60 weeks. This innovative approach enhances our understanding of neurodevelopmental and neurodegenerative processes in the hindbrain region and paves the way for developing targeted cell-based therapy as well as disease modeling for drug discovery.

overall_design: Human iPSCs were induced into hindbrain like neural stem cells using small molecules then maintained for 60 weeks in culture and sequenced at different timepoints

first: Ziadoon

last: Al-Akashi

first: Denise

last: Zujur

first: Nicholas

last: Boyd-Gibbins

first: Nathalie

middle: E

last: Wiguna

first: Masato

last: Nakagawa

first: Tetsuhiro

last: Kikuchi

first: Asuka

last: Morizane

last: Takahashi


title: Effect of SAND variant in Aire, R249C, on thymus epithelial gene expression.

city: Aurora

first: Jordan

middle: Keith

last: Abbott

state: CO

department: Allergy and Immunology

institute: University of Colorado School of Medicine

summary: The novel human AIRE variant, R247C, profoundly impairs transcription of AIRE-target genes, including tissue restricted antigens whose expression is essential for forming T cell central tolerance. The equivalent amino acid was similarly mutated in mice, resulting in Aire R249C mice.

overall_design: RNA-seq profiling of thymus epithelial cells (epCAM+, CD45-) from 4 to 8 week old NOD.AireWT/WT, NOD.AireWT/R249C, NOD.AireR249C/R249C.

first: Jack

last: Roser

first: Sudip

last: Acharya

first: Angelica

last: Ehler


title: SAGA/ATAC complexes sustain aberrant chromatin regulation and promote tumorigenesis in diffuse midline glioma

first: Jamie

middle: N.

last: Anastas

address: 1 Baylor Plaza

department: Neurosurgery

institute: Baylor College of Medicine

summary: Diffuse midline gliomas (DMG) are aggressive pediatric brain tumors characterized by chromatin and transcriptional dysregulation induced by H3K27M mutations. Strategies for overcoming epigenetic dysfunction to reduce DMG tumorigenesis remain limited. We identified multiple components of the SAGA and ATAC chromatin regulatory complexes as DMG genetic dependencies and found that genetic or pharmacological inhibition of the SAGA/ATAC-associated chromatin reader, SGF29, reduces DMG proliferation. Small molecules targeting SAGA/ATAC-associated histone acetylation, ubiquitination, and methylation similarly suppressed DMG growth. Further chromatin profiling and RNAseq analyses reveal that SGF29 controls H3K9ac and H3K4me3 dynamics at both H3K27M-bound and H3K27M-independent target genes linked to proliferation, differentiation, and metabolism. Finally, we find that SAGA/ATAC inhibition may reduce DMG viability by repressing cholesterol metabolism gene expression and show that combinations of cholesterol- and SAGA/ATAC-targeting drugs synergistically reduce DMG growth. These findings reveal a functional link between SAGA/ATAC-dependent chromatin regulation and both transcriptional and metabolic dysregulation underlying DMG malignancy.

overall_design: In one experiment, BT245+Cas9 cells were transduced with control or SGF29-targeting sgRNAs and selected with 250 ug/mL hygromycin for 7 days 48 hours later. Equal live cell numbers were collected for RNAseq analysis at day 14 following the start of hygromycin selection and processed for bulk RNAseq of polyA transcripts.

first: Adam

last: Kebede


title: Transcriptomic profiling of intestinal tissue in a rat model of radiation-induced enteritis treated with Changbing Formula

city: Nanning

first: Lingzhang

last: Meng

state: Guangxi

address: Qingxiu District

institute: Guangxi Academy of Medical Sciences

summary: Radiation-induced enteritis is a common and severe complication of abdominal radiotherapy, yet effective therapeutic strategies remain limited. In this study, a Sprague–Dawley rat model of radiation-induced intestinal injury was established using a single dose of 10 Gy X-ray irradiation. Rats were divided into control, radiation model, and treatment groups, with the treatment group receiving Changbing Formula intervention following irradiation. Intestinal tissues were collected for transcriptome sequencing to investigate gene expression changes associated with radiation injury and therapeutic intervention. High-throughput RNA sequencing was performed using the Illumina NovaSeq platform, and gene-level expression profiles were generated to elucidate molecular mechanisms underlying radiation-induced enteritis and the protective effects of Changbing Formula.

overall_design: Sprague–Dawley rats were randomly assigned to three groups: control, radiation-induced enteritis model, and treatment. The model and treatment groups were exposed to a single dose of 10 Gy X-ray irradiation to induce intestinal injury. The treatment group received Changbing Formula intervention after irradiation. Intestinal tissues were harvested for bulk RNA sequencing to compare transcriptomic alterations among the three groups.

first: Donglin

last: Zheng


title: Gene expression of microdissected prostate stroma

city: Chicago

first: Larisa

last: Nonn

state: IL

address: 840 S. Wood St, MC847

department: Pathology

institute: University of Illinois at Chicago

summary: African American men experience a higher incidence and severity of prostate cancer relative to European American men, and there is a range of risk factors that may contribute to this disparity. Prostate adenocarcinoma originates from the epithelium, which is significantly influenced by signaling from the surrounding fibromuscular stroma. To identify ancestry-associated differences in the stroma, gene expression profiling was compared between laser-capture microdissected prostate cancer stroma from patients of African descent and those of European descent. Estrogen receptor signaling was the top differential pathway between the groups, with the steroid hormone dehydrogenase HSD17B7 identified as the most differentially expressed gene. In a separate cohort of patients, protein expression of HSD17B7 was higher in African American patients relative to European American patients in a radical prostatectomy tissue microarray, validating the transcriptional findings. African American patients also exhibited significantly increased levels of HSD17B7 protein in the stroma surrounding benign areas compared to the stroma near tumors. These studies provide important evidence of ancestry-associated differences in stromal estrogen signaling.

overall_design: RNA was isoloated from laser-capture micordissected stroma surrounding benign or cancer epithelium


title: Sensory innervation induced by osteoblast-derived netrin-4 attenuates bone loss in aged mice

first: Ming

last: Cai

address: Yanchang road

institute: Shanghai Tenth People’s Hospital

summary: The sensory denervation has a causal role in bone loss. The mechanism of bone cells regulation of sensory nerve wiring and sprouting for maintaining bone homeostasis remains unclear. Here we found that netrin-4, secreted by osteoblasts, facilitates the sprouting of sensory nerves through the DCC receptor and plays a regulatory role in bone formation. Decreased bone formation is coupled with reduced sensory innervation in aged mice and ablation of sensory nerves recapitulates this phenotype. Both mice and human data reveal that netrin-4 is positively correlated with bone volume, which expression was not affected by ablation of sensory nerves in mice. The sensory sprouting and bone formation are inhibited by siDCC, a netrin-4 receptor antagonist, in vivo and in vitro. Specifically, knockout of the netrin4 gene in the osteoblastic cells significantly reduces both sensory innervation and bone volume in adult mice. Thus, we show that sensory innervation induced by osteoblast-derived netrin-4 preserve bone homeostasis and attenuates bone loss in aged mice.

overall_design: RNA-seq profiling of bone marrow from young (3-month-old) and aged (20-month-old) female C57BL/6 mice to identify differentially expressed genes associated with sensory innervation during aging.

first: Qi

last: Sun

first: Kaihang

last: Song

first: Benwei

last: Lu

first: Lingxuan

last: Deng

first: Qiyun

last: Chen

first: Yiwei

last: Liu

first: Yusheng

last: Li


title: Single cell RNA sequence data from peripheral blood mononuclear cells of CHB(chronic hepatitis B) patients

city: Suita

first: Takahiro

last: Kodama

state: Osaka

address: 2-2 Yamadaoka

department: Department of Gastroenterology and Hepatology

institute: Osaka university, Graduate School of Medicine

summary: Our study provides novel insights into the role of monocyte-derived IL-1β in the decline of serum HBsAg during nucleotide analogs (NAs) therapy for CHB(chronic hepatitis B). IL-1β not only emerges as a mechanistically relevant biomarker but may also represent a future therapeutic target for strategies aimed at achieving a functional cure.

overall_design: Peripheral blood mononuclear cells of CHB(chronic hepatitis B) patients were analysed by scRNA-seq under nucleotide analogs (NAs) therapies.


title: A transport-independent role for SLC25A12 in mitochondrial stress signaling

city: Beijing

first: Guan

last: Jialiang

state: Beijing

address: China, Beijing, Haidian district, Peking University, 1000871

institute: Peking University

summary: Mitochondria are central hubs for energy production and cellular adaptation to stress. When mitochondria are damaged, cells activate protective signaling pathways to restore homeostasis and ensure survival. One such pathway, known as the integrated stress response (ISR), reduces overall protein synthesis while enhancing the production of stress-responsive proteins. The mitochondrial carriers SLC25A12 and SLC25A13 transport similar metabolites but are expressed in different tissues and linked to distinct genetic diseases. Mutations in SLC25A13 cause a metabolic disorder, while mutations in SLC25A12 are associated with a severe neurodevelopmental condition. Here we show that SLC25A12 plays a previously unrecognized role in stress signaling that is independent of its transport activity. SLC25A12 interacts with the mitochondrial protease OMA1, enabling activation of ISR during mitochondrial damage. This signaling function is disrupted by a disease-linked mutation but preserved in transport-deficient variants. Our findings reveal SLC25A12 as a dual-function mitochondrial protein, acting as both a metabolite transporter and a regulator of stress signaling, and suggest that defective ISR activation may contribute to certain SLC25A12-associated pathologies.

overall_design: To provide a broader view of the expressions for different ISR-target genes in five types of HEK293T cells with different genotypes or transfected by different cDNAs, we performed bulk RNA sequencing on these five types of cells (n=4). This allowed for the identification for regulators in ISR and relationship between ISR and mitochondrial respiration.

first: Liu

last: Jiang

first: Li

last: Lan

first: Jialiang

last: Guan

first: Ying


title: AMPK mutant dauer transcriptome [RNA-seq daf2_aak_alg34]

city: Montreal

first: Sabih

last: Rashid

state: Quebec

address: 3611 Rue Sainte Famille, Unit 11

department: Biology

country: Canada

institute: McGill University

summary: C. elegans lacking AMPK do not exhibit reproductive defects during normal growth, but when passaged through dauer, exhibit germline hyperplasia and premature spermatogenesis, followed by complete sterility post-dauer (Narbonne and Roy, Development, 2006). Loss of RNAi pathway  components suppresses several of these phenotypes (Kadekar and Roy, PLoS Biol, 2019). We sought to carry out a transcriptomic analysis of control and AMPK mutant animals in the dauer and post-dauer stage to understand what gene expression changes occur due to the absence of AMPK, and how RNAi pathway components may be affected. The daf-2 mutation was used to induce dauer by a temperature shift to 25 °C.

overall_design: RNA-Seq of dauer (96 hours post-hatching at restricted temperature) and post-dauer (96 hours after shift to permissive temperature) in the daf-2 and daf-2; aak-1; aak-2 (aak(0)), and daf-2; aak(0); alg-3; alg-4 (alg-3/4) genetic backgrounds. Standard Trizol RNA extraction of collected samples.

first: Rashid

last: Sabih

first: Roy

last: Richard


title: Schisantherin B Alleviates Cisplatin-Induced Hearing Loss via CNPY2 Coordination

city: Shanghai

first: Ziwen

last: Gao

address: Fenyang Road

department: ENT Institute and Department of Otorhinolaryngology

institute: Eye & ENT Hospital, Fudan University

summary: Cisplatin-induced hearing loss (CIHL), is characterized by irreversible hearing impairment and no effective interventions, is a major chemotherapy side effect. Schisantherin B (STB), a natural compound isolated from Schisandra chinensis, have been shown to possess neuroprotective and hepatoprotective properties, whereas research in the auditory field is limited. This study alleviates cisplatin-mediated auditory toxicity in vitro and successfully rescued auditory brainstem response (ABR) thresholds in a CIHL model of adult albino guinea pigs by protecting hair cells, synaptic ribbons and spiral ganglion neurons. The drug affinity responsive target stability (DARTS) assay, the cellular thermal shift assay (CETSA), and the surface plasmon resonance (SPR) assay have determined that the canopy FGF signaling regulator 2 (CNPY2) protein, a key initiator of ER stress, is an important partner of STB, inhibiting downstream signals PERK/CHOP signals and endoplasmic reticulum (ER) stress-induced apoptosis. The collective findings of this study demonstrate that STB is a promising candidate drug for protecting against CIHL. Moreover, the results indicate that CNPY2 primed ER stress is a critical biological process for STB-mediated oto-protection.

overall_design: RNA-seq profiling of cochlears from guinea pigs following treatment with cisplatin, cisplatin plus STB and wildtype.

first: Ping

last: Yang

first: Hui

last: Huang

first: Weida

last: Zhang

first: Yilai

last: Shu


title: 3’tRNAAsp(GTC)-derived fragment links inflammation to post-transcriptional reprogramming in chondrocytes during osteoarthritis. [Cartilage small RNA-seq]

city: La Jolla

first: Aishwarya

last: Sundaresan

address: 10550 N Torrey Pines Rd

institute: The Scripps Research Institue

type: Non-coding RNA profiling by high throughput sequencing

summary: Background/Aim: Transfer RNA-derived fragments (tRFs) are an emerging class of small non-coding RNAs that dynamically respond to metabolic stressors and drive different pathological processes, yet their role in osteoarthritis (OA) remains poorly explored. We aimed to define the tRF landscape in OA and investigate the function of 3′tRFAsp(GTC) in chondrocyte stress adaptation and translational control. Methods: Ex vivo, cartilage specimens from OA patients and healthy donors were analyzed by small RNA sequencing to define disease-associated tRF signatures. In vitro, primary chondrocytes derived from OA patients were treated with lipopolysaccharide (LPS) to mimic the pro-inflammatory environment of OA. Functional studies included antisense oligonucleotide (ASO)-mediated 3′tRFAsp(GTC) inhibition, AGO2-RNA immunopreicipitation (RIP), polysome profiling, stress granule (SG) immunofluorescence, and differential protein analysis. Computational target prediction and pathway enrichment were used to explore tRF-mediated regulatory networks. Results: Both ex vivo OA cartilage and LPS-treated OA chondrocytes displayed upregulation of 3′tRFAsp(GTC) and 5′tRFGlu(CTC), indicating a shared inflammatory tRF signature. Silencing 3′tRFAsp(GTC) attenuated LPS-induced COX2 and MMP13 expression, prevented ER stress, and blocked SG assembly. RIP confirmed selective recruitment of 3′tRFAsp(GTC) into AGO2 complexes. Polysome profiling revealed association with 40S ribosomal subunits, mediating translational arrest and influencing selective mRNA expression. Predicted targets of upregulated tRFs were enriched in stress-adaptive, proteostasis, and translational control pathways, whereas downregulated tRFs modulated mitochondrial processes. Conclusions: 3′tRFAsp(GTC) emerges as crucial regulator linking inflammatory stress to translational control and SG dynamics in OA. tRFs thus could represent a novel therapeutic targets to counteract chronic inflammatory stress in degenerative joint disease.

overall_design: Small RNA-sequencing of human articular cartilage samples from osteoarthritis patients and non-osteoarthritic donors.

first: Francesco

last: Alabiso

first: Aleksandra

last: Seragnoli C

first: Cristina

last: Cosentino

first: Irene

last: Bissoli

first: Veronique

last: Menoud

first: Ilaria

last: Bedei

first: Merissa

last: Olmer

first: Veronica

last: Panichi

first: Isabella

last: Rusciano

first: Paolo

last: Dolzani

first: Fabrizio

last: Ferré

first: Stefano

last: Ratti

first: Martin K.

last: Lotz

first: Rosa Maria

last: Borzì

first: Romano

last: Regazzi

first: Flavio

last: Flamigni

first: Silvia

last: Cetrullo

first: Stefania

last: D'Adamo


title: 3’tRNAAsp(GTC)-derived fragment links inflammation to post-transcriptional reprogramming in chondrocytes during osteoarthritis. [Primary Chondrocytes small RNA-seq]

city: Bologna

state: BO

address: Via Irnerio 48

department: DIBINEM

country: Italy

institute: University of Bologna

overall_design: Small RNA-sequencing of primary human articular chondrocytes isolated from osteoarthritic cartilage, comparing lipopolysaccharide (LPS)-treated and untreated cells in a patient-paired experimental design.

first: Francesco

last: Alabiso

first: Aleksandra

last: Seragnoli Chystyakova

first: Carla Renata

last: Arciola


title: IAP retrotransposons contribute to the transcriptional diversity of the murine placenta

city: London

first: Miguel

last: Branco

address: 4 Newark Street

institute: Blizard Institute

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

sample_organism:
Mus musculus
Mus pahari

platform_organism:
Mus musculus
Mus pahari

overall_design: Refer to individual Series


title: Regulation of transcriptomic profile by ZL0580 and JQ1

city: Galveston

first: Haiping

last: Hao

state: Texas

address: 301 University Blvd

institute: UTMB NGS Core

summary: Epigenetic suppression and durable silencing of HIV represent a promising strategy to achieve ART-free remission, consistent with the “block and lock” HIV cure paradigm. BRD4 is a host epigenetic reader and plays a critical role in HIV transcriptional regulation. We previously identified ZL0580, a first-in-class BRD4-selective small molecule that epigenetically suppresses HIV, whereas the pan-BET/BRD4 inhibitor JQ1 activates HIV transcription. The present study utilizes RNA-Sequencing (RNA-Seq) to examine the impact of ZL0580 and JQ1 on transcriptomic profile in the latently HIV-infected J-Lat cells (Clone 10.6). In summary, ZL0580 induces a transcriptomic profile opposing to that induced by JQ1, which is highly consistent the opposing effects of the two compounds on HIV transcription and latency.

overall_design: J-Lat cells (10.6) were treated with DMSO (as negative control), ZL0580 (5 uM), or JQ1 (5 uM). 24 hours after treatment, cells were subjected to bulk RNA-Seq analysis.

first: Haitao

last: Hu

first: Naveen

last: Kumar


title: Comparative transcriptomics reveals differences mainly in magnitude, not pattern, of orchid protocorms responses to field and in vitro growth conditions in Dactylorhiza majalis (Orchidaceae)

city: Gdańsk

first: Marcin

last: Jakalski

address: Wita Stwosza 59

department: Center for Applied Genomics and Bioinformatics

country: Poland

institute: University of Gdansk

summary: In vitro techniques have become key to studying orchid symbiosis, particularly mycoheterotrophic germination. Physiological responses at this early stage have traditionally been assessed by comparing symbiotic and asymbiotic protocorms grown in vitro, though this simplified model does not fully capture environmental complexity. Here, we compared, for the first time, the transcriptomic (RNA-seq) profiles of in vitro-grown symbiotic and asymbiotic protocorms of the autotrophic orchid Dactylorhiza majalis with those grown in the field, enabling analysis of responses to both symbiosis and environmental factors. We showed that environmental conditions modulate protocorm physiology to some extent, subtly influencing the transcriptomic landscape but without undermining the general validity of the in vitro model. Field response (FS/IVA) showed stronger upregulation in nutrient and ion transporters (sugars, amino acids, phosphorus) than in vitro symbiotic response (IVS/IVA). Moreover, they both appear to maintain compatibility with mycorrhizal fungi and cope with environmental stressors, but through distinct regulatory strategies shaped by environmental context. FS prioritized transcriptional regulation and immune repression (via TIFY/JAZ/NINJA/ERF), whereas IVS prioritizes oxidative buffering (OPDA-skewed oxylipins + antioxidant metabolism) to cope with culture/light-driven stress. The presented research provides a more comprehensive picture of physiology of mycoheterotrophic germination of orchids seeds.

overall_design: The seeds were disinfected in syringes according to the method by (Ponert et al., 2012). Subsequently they were incubated for five minutes in 70% ethanol, washed with deionised water, incubated for five minutes in a Ca(OCl)2 solution (10 g of chlorinated lime in 50 mL of deionised water), washed with sterile deionised water, and then injected on the surface of a solid medium as a suspension in 9 cm plastic Petri dishes. For symbiotic experiments, we have used simple medium OMA as described in (Figura et al., 2021). This medium contained 1 % agar (w/v, Sigma-Aldrich) and 0,3% oatmeal powder (Himedia). For asymbiotic germination, the sugar-amended complex ¼-2 medium was used (Figura et al., 2018). In this case, the pH was adjusted to 5.8 using KOH and HCl. Media of both types were autoclaved at 144 kPa, 121 °C (Tuttnauer 2540 EK-N) for 20 min and poured into 9 cm plastic Petri dishes.

first: Julita

last: Minasiewicz

last: Jąkalski

first: Marie-Laure

last: Martin

first: Tomas

last: Figura

first: Piotr

last: Mleczko

first: Monika

last: Lipińska

first: Konrad

last: Ślusarz

first: Marc-André

last: Selosse

first: Etienne

last: Delannoy


title: The noncanonical function of S1PR1 in mediating CD8 + T cell dysfunction in tumor [RNASeq]

city: KOLKATA

first: Puspendu

last: Ghosh

state: WEST BENGAL

address: CNO6,SECTOR V, BIDHANNAGAR

department: CBID

country: India

institute: CSIR-IICB

summary: Sphingosine-1-phosphate receptor 1 (S1PR1) signaling has been linked to the regulation of immunosuppressive cell populations within the tumor microenvironment (TME); however, its role in shaping anti-tumor CD8⁺ T cell responses remains poorly defined. Herein, we demonstrate that intratumoral CD8⁺ T cells express S1PR1, with expression predominantly enriched in the terminally exhausted subset. Transcriptomic profiling, combined with pharmacological inhibition and genetic knockdown, reveals that S1PR1-S1P signaling activates the PERK (protein kinase R (PKR)-like endoplasmic reticulum kinase)-CHOP (C/EBP homologous protein) axis of the endoplasmic reticulum stress response. CHOP, in turn, upregulates transcription of Map3k13 and Map3k15, triggering downstream MAPK signaling and culminating in activation of p38MAPK. Activation of this pathway impairs CD8⁺ T cell metabolism and effector function while increasing apoptotic susceptibility. This ultimately limits the persistence and accumulation of functional CD8⁺ T cells within the TME, thereby compromising their responsiveness to anti-PD-1 therapy. Targeting the S1PR1-S1P axis or its downstream effectors offers a promising strategy to improve cancer immunotherapy outcomes.

overall_design: RNA-seq profiling of murine CD8+ T cells activated for three days in presence or absence of S1P.

first: Debashree

last: Basak

first: Shilpak

last: Chatterjee


title: Hippocampal estrogen levels, receptor types and epigenetics contribute to sex-specific memory-vulnerabilities to concurrent acute stresses [Cut & Run]

city: Philadelphia

first: Shuo

last: Zhang

state: PA

address: 3400 Civic Center Blvd

institute: University of Pennsylvania

summary: It is increasingly recognized that acute traumatic events (e.g., mass shootings, natural disasters) can provoke enduring episodic memory deficits and generalization of trauma cues, and these are more common in women. We investigated mechanisms and sex differences of memory vulnerability to multiple acute concurrent stresses (MACS) in mice, focusing on the sex hormone 17β-estradiol and its receptors in hippocampus. Surprisingly, high physiological hippocampal estradiol levels, observed in proestrus females and males, were required for MACS-induced episodic memory disruption and sensitization and generalization of stress cues. High estradiol levels  were associated with permissive chromatin states in stress-vulnerable mice, while chromatin permissiveness and hippocampal estradiol were low in stress-resilient estrus females. Estrogen receptor (ER)β activation in resilient estrus females increased chromatin permissiveness and  enduring vulnerability to MACS, while ERα mediated milder stress-induced memory disruptions in males. Thus, hippocampal estradiol levels and sex modify chromatin states to enable long-lasting memory vulnerabilities to MACS.

overall_design: Cut&Run-seq profiling of H3K27me3 and H3K4me3 in the hippocampus of naive males, females in estrus or females in proestrus. Cut&Run-seq profiling of H3K27me3 and H3K4me3 of females in estrus with MACS, control vehicle or MACS and an ERβ agonist, Diarylpropionitrile (DPN).

first: Rachael

last: Hokenson

first: Kiara

last: Rodríguez-Acevedo

first: Yuncai

last: Chen

first: Annabel

last: Short

first: Sarah

middle: A

last: Samrari

first: Brinda

last: Devireddy

first: Brittany

last: Jensen

first: Julia

last: Winter

first: Christine

last: Gall

first: Kiran

last: Soma

first: Elizabeth

last: Heller

first: Tallie

middle: Z

last: Baram


title: Single-cell RNA sequencing analysis of HUVEC in monolayer alone or exposed to (bacterially-infected) macrophage-like U937 cells for 8 h.

city: Tübingen

first: Effie

last: Bastounis

state: Baden-Württemberg

address: Auf der Morgenstelle 28/E7

department: Interfaculty Institute of Microbiology and Infection Medicine

institute: University of Tübingen

summary: We sought to identify changes in gene expression that occur when endothelial cells (HUVEC) in monolayer interact with either uninfected or Listeria monocytogenes-infected macrophages. To that end we seeded HUVEC in monolayer and either exposed them to nothing, or to uninfected PMA-differentiated macrophage-like U937, or to Listeria monocytogenes-infected PMA-differenitated U937. At 8 hours post U937 exposure (hpe), cells were detached from the wells and cryopreserved for scRNA-seq. scRNa-seq analysis allowed us to distinguish endothelial cells from macrophage like cells and create appropirate clusters. By then analyzing the differentially expressed genes between all conditions for HUVEC and U937 separately, we identified a significant number of differentially regulated genes related to innate immune signaling in both infected U937 exposed HUVEC and to a lesser degree uninfected U937 exposed HUVEC, as compared to control unexposed HUVEC. By perofming pathway enrichment analysis, we also discovered that HUVEC exposed to uninfected U937 showed a higher upregulation in pathways related to mechanotransdcution, like "focal adhesions" and "regulation of the actin cytoskeleton", compared to those exposed to infected U937. This is consistent with the reinforsement of traction and monolayer stresses of HUVEC with uninfected U937 which we observe, a feature that is attenuated significanlty during infection. Finally, when we compare uninfected versus infected U937 cells from co-cultures, we find that the later upregulate cell adhesion molecules, the PI3K signaling pathway and focal adhesions, suggestive of increased cell contractility and adhesion as compared to uninfected U937.

overall_design: Primary endothelial cells HUVEC were seeded in monolayer and exposed to: (1) nothing, (2) uninfected PMA-differentiated U937 macrophage-like cells, or (3) Listeria monocytogenes-infected U937 macrophage-like cells. After 8 hours post-exposure (hpe) to U937, samples were gently washed and detached,  and then cryopreserved for scRNA-seq . For each condition three samples were analysed using 10x Genomics scRNAseq technology. Equipment: 10X Chromium platform with Chromium Next GEM Single Cell 3ʹ Kit v3.1 following the manufacturer’s protocol for library construction. Library sequencing was done with llumina NovaSeq X platform, at 20000 reads per cell per sample. Sequencing read mode applied was: Read 1 28bp; Read 2 90bp; Index Reads 1 and 2 10 bp each.

first: Effie E.

first: Marie

last: Muenkel

first: Julio C.

last: Sanchez-Rendon


title: Hippocampal estrogen levels, receptor types and epigenetics contribute to sex-specific memory-vulnerabilities to concurrent acute stresses [RNA-Seq]

first: Shuo

overall_design: RNA-seq profiling of the mouse whole hippocampus of males, females in estrus or females in proestrus.

middle: J


title: Sinus Mast Cell Density Suggests a Unique Phenotype in Toxin Exposure-Associated Chronic Rhinosinusitis

first: Yung-An

last: Huang

address: 9500 Gilman Dr

department: Medicine

institute: University of California, San Diego

summary: Chronic rhinosinusitis (CRS) is more prevalent and severe in military Veterans with deployment-related environmental toxin exposures. The mechanisms driving this aggressive phenotype are poorly understood, and the role of mast cells remains understudied. We sought to characterize the immunophenotype of toxin-associated CRS and develop a preclinical model to investigate disease persistence. We identified a significant and selective expansion of sinus mast cells in Veterans with deployment-related exposures compared to unexposed controls, an effect most prominent in patients without nasal polyps. RNA sequencing of sinus tissue from exposed patients confirmed the upregulation of mast cell activation pathways. We also developed a murine model in which co-exposure to burn pit constituents (BPC) and an aeroallergen synergistically exacerbated sinonasal inflammation. Strikingly, mast cell accumulation persisted and continued to increase for weeks after toxin exposure ceased, a phenomenon not observed in mice challenged with allergen alone. Our findings reveal a novel mast cell-driven phenotype in toxin exposure-associated CRS. The persistent accumulation of mast cells in our preclinical model provides a potential mechanism for the chronicity of sinonasal symptoms following xenobiotic exposures, identifying mast cells as a potential therapeutic target for this emerging CRS phenotype.

overall_design:
Ethmoid sinus tissue was obtained from Veterans with and without deployment-related exposures undergoing endoscopic sinus surgery for CRS.
CRSsNP: Chronic Rhinosinusitis without Nasal Polyps.
CRSwNP: Chronic Rhinosinusitis with Nasal Polyps.

first: Xinyu

last: Wang

first: Anshika

last: Sethi

first: Christopher

last: Yue

first: Sydney

last: Brack

first: Aiswarya

last: Chattuparrambil-binoy

first: Lauren

last: Crowther

first: Carol

last: Yan

first: Adam

last: Deconde

first: Anton

last: Kushnaryov

first: Andrew

last: Vahabzadeh-Hagh

first: Jacob

last: Husseman

first: Maia

last: Little

first: Allyssa

last: Strohm

first: Lily

last: Jih

first: Jonathan

last: Lyons

first: David

last: Broide

first: Taylor

last: Doherty


title: Attenuating AAV-Triggered Innate Immunity in the Adult Mouse Nervous System via cGAS-STING Pathway Inhibition

city: Guangzhou

first: Zheng

last: Wu

state: Guangdong

address: 601 West Huangpu Road

institute: Jinan University

summary: While adeno-associated virus (AAV)-mediated gene delivery has emerged as a promising therapeutic modality for neurological disorders, dose-dependent immune responses remain a critical barrier to clinical translation. Here we identify the cyclic GMP-AMP synthase-stimulator of interferon genes (cGAS-STING) pathway as a key mediator of innate immune activation following intracranial AAV administration. Through comparative analyses in genetic and pharmacological intervention models, we demonstrate that STING signaling mediates key neuroinflammatory sequelae including glia reactivation, cytotoxic T cell infiltration, and neuronal injury. Mechanistically, microglia serve as the predominant sentinels detecting AAV immunogenicity via cGAS-STING activation. Therapeutic inhibition of this pathway by either microglia depletion or antagonism of STING by small molecules significantly mitigates high-dose AAV9-induced neurotoxicity while enhancing transgene delivery efficacy. Our work delineates a unified mechanistic framework linking AAV-triggered DNA sensing to neuroinflammatory pathology, and provides two clinically actionable approaches to decouple therapeutic gene delivery from detrimental immune activation in nervous system targeted gene therapy.

overall_design: step1:In this study, we first used bulk-RNA sequencing technology to investigate the early changes in gene expression profiles of AAV-injected brain tissue with different dose（contributor：Yaowei Guo). Bulk RNA sequencing analysis showed that in the brains administered with 1010 GC AAV9, classical innate immune responses were significantly upregulated, including TLRs and NOD-like receptors (NLRs). In addition, high dose AAV administration robustly upregulates gene expression that involved in the cGAS-STING pathway. Using Sting knockout transgenic mice, we further confirmed that the cGAS-STING signaling pathway plays a crucial role in mediating inflammation, immune responses, and neuronal injury in the adult mouse brain following high-dose AAV9 intracranial injection. Further studies have found that both reactive microglia and astrocytes are involved in the activation of the cGAS-STING pathway. step2:Microglia depletion significantly inhibited cGAS-STING pathway activation and subsequent inflammation and T cell infiltration. H-151 is a novel STING inhibitor that effectively suppressed inflammation, reactive glial cells, T cell infiltration and neuronal damage, while also significantly increasing the expression of transgene in AAV vectors. Altogether, our findings suggest that inhibiting the cGAS-STING pathway may improve the safety and efficacy of AAV gene therapy in the nervous system.(contributor：Yaowei Guo)

first: Yaowei

last: Guo

first: Yuqi

last: Zhang

first: Jiehao

last: Huang

first: Zeru

last: Li

first: Gong

last: Chen


title: Single-cell RNA-seq analysis reveals distinct tumor and immunosuppressive T-cell phenotypes in CLL patients treated with ibrutinib

city: Columbus

first: Bradley

middle: Wayne

last: Blaser

state: OH

address: 400 W 12th Ave

department: Comprehensive Cancer Center

institute: Ohio State University

summary: The development of Bruton tyrosine kinase inhibitors (BTKi) and their introduction into clinical practice represents a major advance in the treatment of chronic lymphocytic leukemia (CLL). However, monotherapy with ibrutinib or other BTKis generally does not induce complete remissions or undetectable minimal residual disease (MRD) even with extended therapy. Therefore, there is a need to understand the differences between ibrutinib sensitive and resistant CLL cells along with the immune microenvironment to identify novel therapeutic approaches for controlling residual disease during BTKi treatment. Here, we investigated the cellular heterogeneity of peripheral blood mononuclear cells from patients with CLL treated with ibrutinib using single-cell RNA sequencing. We identified unique transcriptional heterogeneity within the B cell cluster in the ibrutinib-sensitive and resistant patients. Ibrutinib sensitive cells showed enrichment of B cell populations with upregulation of MHC I molecules and TNF family members.  Additionally, we observed that inflammatory response and metabolism related pathways were decreased, whereas cellular response to stress and DNA repair programs were increased in the ibrutinib resistance samples.  T cells in ibrutinib-resistant patients showed expansion of Tregs and an exhausted CD8 effector T cell compartment.  Furthermore, CD14+ and CD16+ monocytes from ibrutinib resistant patients preferentially expressed a gene expression program of antiviral immunity. At the single-cell level, our findings demonstrate a picture of transcriptional heterogeneity in the tumor compartment and immune milieu. Overall, these findings suggest that T cell exhaustion and monocyte functional polarization may have a crucial role in BTKi resistance.

overall_design: Peripheral blood was collected from patients with CLL patients with and without BTK resistance mutations.  Samples were collected at diagnosis, time of detection of the BTK C481S mutation and at relapse.  For those without mutations, samples were collected 3 and 5 years after diagnosis.  Single cell immune profiling was performed using the 10X Genomics 5' capture technology with BCR and TCR sequencing.

first: Shanmugapriya

last: Thangavadivel

first: Jami

last: Shaffer

first: Shrilekha

last: Misra

first: Samon

last: Benrashid

first: Britten

last: Gordon

first: Alexander

last: He

first: Wantong

first: Konur

last: Oyman

first: Annika

last: Chura

first: Shelby

last: Cabrera

first: Altan

last: Turkoglu

first: Tzung-Huei

last: Lai

first: Kerry

last: Rogers

first: Seema

last: Bhat

first: John

last: Byrd

first: James

middle: S

last: Blachly

first: Jennifer

last: Woyach

middle: W


title: Tachykinin signaling defines distinct populations of glia in the enteric nervous system [scRNA-seq]

city: Boston

first: Meenakshi

last: Rao

state: MA

address: 300 Longwood Ave

department: Pediatrics-Division of Gastroenterology

institute: Boston Children's Hospital

summary: One of the largest populations of glia outside the brain is in the gut. These enteric glia are involved in many functions from intestinal peristalsis to immunity, yet it is unclear if there are defined types with distinct roles in homeostasis. Comparing glia from divergent microenvironments in the mouse intestine, we found that mucosal glia resembled microglia and macrophages, while muscularis glia resembled satellite glia. Tacr3, encoding the receptor for neuropeptide Neurokinin B (NKB), was enriched within muscularis glia associated with neuronal soma and was undetectable in extraintestinal glia. Genetic or pharmacological manipulation of NKB-TACR3 signaling disrupted establishment of enteric glial populations during postnatal development, and dynamically modulated intestinal motor behaviors in adult mice. Collectively, we delineate spatially, transcriptionally and functionally distinct populations of enteric glia, identify one as an unanticipated target of TACR3 antagonists in clinical use, and establish this pathway as necessary for enteric glial diversification and function.

overall_design: To determine the transcriptomes of intraganglionic, connectives, and intramuscular glia, we performed single cell sequencing on FACS sorted glia from the ileal muscularis in Plp1eGFPTacr3IRESCre Rosa26tdTomato/+

first: Anoohya

middle: N

last: Muppirala

first: Perry

last: Mitchell

first: Neha

last: Mani

first: Maryam

last: Dadabhoy

first: Sushmita

last: Debnath

first: Maria

last: Paraskevopoulou

first: Thomas

last: Gould


title: Context-dependent translation inhibition as a novel oncology therapeutic modality [RNA-seq]

city: SOUTH SAN FRANCISCO

first: Paige

last: Diamond

state: California

address: 201 HASKINS WAY

institute: Interdict Bio

summary: Inhibitors of protein synthesis, including anisomycin, homoharringtonine, and other natural products bind in the peptidyl-transferase center (PTC) of the eukaryotic ribosome to inhibit translation. Recent work has demonstrated that some PTC-binding antibiotics act in a sequence-selective manner, inhibiting translation elongation at specific amino acids while the polypeptide is engaged in the PTC. However, this phenomenon has yet to be documented for compounds that inhibit translation by the human ribosome. Here we use structure-based design to guide synthesis of molecules called interdictors that bind to the human ribosome PTC and act in a context-selective manner to inhibit translation elongation. Using ribosome profiling, in combination with in vitro biochemistry and cryo-electron microscopy, we characterize the context selectivity of unique analogues and observe their preferred interactions with nascent chain residues with complementary properties. Furthermore, we present a structure for an interdictor bound to a portion of the MYC protein at ~ 1.9 Å resolution and identify resulting structural rearrangements in both the nascent chain and ribosomal RNA. Finally, we document how these compounds differentially impact the ribotoxic stress response pathway which monitors ribosome collisions and can lead to apoptosis. Together, our data establish sequence-selective inhibition of translation as a novel small-molecule therapeutic modality for historically difficult to address cancers by targeting translation of oncogenic dependency factors in the human ribosome PTC.

overall_design: To determine the impact and context selectivity of Interdictors on translation, we treated HCC1143 TNBC cells with compound for 1 hour and performed ribosome profiling. DMSO treated samples were used as a control.

first: Paul

middle: V

last: Sauer

first: Mikael

last: Holm

first: Canessa

last: Swanson-Swett

first: Lucas

last: Ferguson

first: Natalie

last: Bratset

first: Grant

last: Wienker

first: Justin

last: Sim

first: Hailey

middle: K

last: Adams

first: Lillian

last: Kenner

first: Margot

last: Meyers

first: David

last: Gygi

first: Zef

last: Könst

first: Sogole

last: Bahmanyar

first: Lawrence

middle: G

last: Hamann

first: Anthony

last: Schuller


title: CD4+ T-Cells Mediate CART Immune-Related Adverse Events (CirAE) Following BCMA CART Therapy

first: Julia Han

last: Noll

state: Pennsylvania

address: 3400 Civic Center Blvd.

summary: We employed single-cell RNA sequencing (scRNA-seq) using the 10x Genomics platform to study the immune landscape of CAR T cells in the peripheral blood (PBMC) and cerebrospinal fluid (CSF) of patients treated with Cilta-cel who developed CAR T-cell immune-related adverse events (CiRAE). CAR T cells were captured and profiled across both compartments. This study offers insights into how CAR T cell phenotypes and functional states diverge between the periphery and central nervous system during inflammatory neurotoxicity.

overall_design: Paired PBMC and CSF samples (n = 4 each) were collected from 4 patients treated with Cilta-cel who developed CiRAE

first: Matthew

last: Ho

first: Luca

last: Parruzzo

first: Alfred

middle: L

last: Garfall

first: Marco

last: Ruella

first: Adam

last: Cohen

first: Joseph

last: Fraietta


title: Identification of altered salivary microRNAs in Cavalier King Charles Spaniels affected by mitral valve disease at different ACVIM stages

city: Torino

first: Raffaele

last: Calogero

state: To

address: Via Nizza 52

department: Molecular Biotechnology Center

institute: University of Torino

summary: Myxomatous mitral valve disease (MMVD) in Cavalier King Charles Spaniels (CKCSs) can be diagnosed at a young age. Early and sensitive biomarkers related to the disease are currently lacking. MicroRNAs (miRNAs) are involved in the onset and progression of canine MMVD. This study aimed to profile the salivary miRNAs associated with MMVD severity in CKCSs and to identify their target genes. This was a pilot prospective, cross-sectional study. Saliva was collected from twenty-five CKCSs belonging to the American College of Veterinary Internal Medicine (ACVIM) stages A (n. 6), B1 (n. 13), and B2 (n. 6), and salivary miRNAs’ expression was profiled by Next Generation Sequencing. MiRNAs’ target genes were identified using bioinformatic tools. Results showed that 25 miRNAs were differentially expressed (DE) in the ACVIM A versus B1 group; 35 DE-miRNAs were identified in the ACVIM B2 versus B1 group; 4 miRNAs were up-regulated in ACVIM stage B1 patients compared to both ACVIM stages A and B2. The identified miRNAs impacted genes related to cell survival and functions. Results demonstrated that miRNAs can be extracted and quantified from canine saliva, and that their profile changes following disease progression. Validation studies are necessary to investigate their diagnostic value.

first: Sara

last: Ghilardi

first: Gaspare

last: Salvi

first: Mara

last: Bagardi

first: Ombretta

last: Balbi

first: Asia

last: Balgera

first: Yasmine

last: Dadi

first: Giovanni

last: Romito

first: Michele

last: Polli

first: Maddalena

last: Arigoni

first: Paola

last: Brambilla

first: Cristina

last: Lecchi


title: Epigenetic programs shaping lung-specific metastasis in triple-negative breast cancer

city: Palma

first: Diego

middle: M.

last: Marzese

state: Balearic Islands

address: Carretera de Valldemossa 79

department: Department of Cancer Epigenetics

institute: IdISBa

type: Methylation profiling by genome tiling array

summary: Triple-negative breast cancer (TNBC) is a major cause of cancer mortality, with distant metastases, particularly to the lung, presenting a significant clinical challenge. While epigenetic mechanisms like DNA methylation (DNAm) are known to influence TNBC progression, their specific role in driving metastasis remains underexplored. To address this gap, we present a comprehensive multi-omics analysis, integrating epigenomic and transcriptomic profiles from TNBC xenograft models and patient cohorts. Genome-wide DNAm profiling of primary tumors, lymph nodes, and lung metastases revealed pronounced global hypomethylation in lung lesions, consistent with clinical samples. Promoter-methylation changes were enriched in pathways linked to invasion and proliferation, and transcriptomic integration identified 22 epigenetically regulated genes. Among these, elevated AK1, SLC2A5, TPI1, and ZBTB17 expression correlated with a higher risk of lung dissemination. These findings highlight aberrant methylation as a driver of TNBC lung colonization and identify candidate prognostic markers, emphasizing the importance of epigenetic reprogramming in organ-specific metastasis.

overall_design: Human TNBC cells (MDA-MB-231; 1 × 10^⁶) were injected into the right flank of nude female mice, generating cancer cell line-derived xenografts. We generated genome-wide DNAm profiles from these XEN mouse models, analyzing primary tumors, lymph nodes, and lung distant metastases. DNAm patterns were assessed using the Infinium Methylation EPIC v2.0 array.

middle: M

first: Pere

last: Llinàs-Arias

first: Andrés

middle: F

last: Bedoya-López


title: RNA sequencing of HSkM myotubes deficient in DMD, full-length dystrophin (DP427) and utrophin reveals common transcriptomic alterations

city: Poznań

first: Paulina

last: Kościelniak-Wawro

address: Uniwersytetu Poznańskiego 6

department: Faculty of Biology, Institute of Human Biology and Evolution

institute: Adam Mickiewicz University

summary: iRNA approaches were used to knock down the expression of dystrophin (DMD), including its full-length isoform DP427, and utrophin (UTRN) genes. Specifically, iRNA-mediated knockdown of both DMD (full-length dystrophin DP427) and UTRN was performed in HSkM myotubes. It is known that the shorter dystrophin isoform DP71 compensates for full-length dystrophin DP427 in the early stages of myofiber differentiation in cell models of Duchenne muscular dystrophy. Accordingly, DP427-deficient and DP71/DP427-deficient HSkM myotubes exhibit distinct changes in the expression of genes involved in membrane integrity and cytoskeletal functions. RNA-sequencing analyses revealed overlapping transcriptomic alterations in these HSkM cell lines, which corresponded to observed phenotypic abnormalities such as increased membrane permeability and intracellular calcium levels, mitochondrial aggregation, elevated reactive oxygen species (ROS), enhanced cyto- and genotoxicity, and induction of apoptosis.

overall_design: RNA-seq profiling of HSkM myotubes after siCtrl delivery and wild-type HSkM myotubes after siDMD, siDP427 and UTRN delivery. Myotubes were obtained after 12 days of differentiation.

first: Patryk

last: Konieczny

first: Sylwia

last: Szwec


title: Halofuginone exerts broad-spectrum cytotoxic effects by regulating p-eIF2α-S100A8/A9-calcium signaling, inhibiting global protein synthesis, and reversing the resistance of idarubicin in acute myeloid leukemia [RNA-Seq]

city: wenzhou

first: bin

last: zhou

address: Nanbaixiang, Ouhai District, Wenzhou, Zhejiang Province

institute: Affiliated Hospital of Weifang Medical University

overall_design: Ethnopharmacological relevance: Alkaloid febrifugine., an herbal medicine in China, is prescribed routinely for malaria treatment. Halofuginone (HF), a natural product isolated from alkaloid febrifugine, exhibits anti-tumor and anti-inflammatory ability. Aim of the study: Acute myeloid leukemia (AML) is a heterogeneous hematological malignancy with low overall survival (OS). Resistance to chemotherapeutic drugs such as idarubicin (IDA) results in treatment failure. This study investigated the role of HF in anti-AML ability and in overcoming IDA resistance in AML cells. Materials and methods: Apoptosis, proliferation, cell cycle, and colony were assessed in AML cells treated with HF. RNA sequencing (RNA-seq) was performed to identify the potential targets of HF. Human relapsed and refractory (R/R) AML samples were xenografted into mice to assess the anti-leukemic effects of HF in vivo.

first: Liuzhi

last: Shi

first: Yigang

last: Yuan

first: Bin

last: Zhou

first: Shenmeng

last: Gao

first: Liu

first: Min

last: Zhao

first: Yue

last: Cai


title: Halofuginone exerts broad-spectrum cytotoxic effects by regulating p-eIF2α-S100A8/A9-calcium signaling, inhibiting global protein synthesis, and reversing the resistance of idarubicin in acute myeloid leukemia

summary: NOP2/Sun RNA methyltransferase family member 2 (NSUN2) catalyzes 5-methylcytosine (m5C) modifications in tRNA, rRNA, and mRNA, playing critical roles in various malignancies. However, its expression and functional relevance in B-acute lymphoblastic leukemia (B-ALL) remain largely undefined. Lineage-negative progenitor cells from Nsun2 knockout (Δ/Δ) and wild-type (fl/fl) mice were used to generate BCR-ABL (P190)-driven murine B-ALL model. Furthermore, RNA sequencing (RNA-seq) was performed to identify NSUN2 targets. Here, we found that NSUN2 expression was significantly higher in bone marrow (BM) cells from B-ALL patients than normal controls (NCs). Knockdown of NSUN2 reduced m5C amounts, induced apoptosis and ferroptosis in B-ALL cells. Moreover, Nsun2 knockout significantly suppressed the leukemic burden and extended the OS in murine B-ALL model in vivo. RNA-seq and subsequent studies identified ferritin heavy chain 1 (FTH1) as a downstream target of NSUN2. Mechanistically, NSUN2 knockdown reduced m5C modifications on 3'UTR of FTH1 mRNA, impairing its stability and reducing FTH1 expression. Overexpression of wild-type (WT) NSUN2, but not its mutants, blocked NSUN2 knockdown-induced cytotoxic effects, indicating that NSUN2 enhances leukemogenesis in an m5C-dependent manner. In addition, NSUN2 facilitated global protein synthesis and ribosome biogenesis by enhancing fibrillarin (FBL) translation efficiency. In contrast, Nsun2 depletion was dispensable for hematopoiesis and exerted minimal impact on ferroptosis and protein synthesis in murine pre-B (B220+) cells, suggesting selective leukemic dependency. Our results demonstrate that NSUN2 facilitates leukemogenesis by increasing FTH1 expression and enhancing FBL-mediated ribosome biogenesis in an m5C-dependent manner. Targeting NSUN2 might provide a promising therapeutic strategy for B-ALL.


title: Detection of mitochondrial DNA mutations in T cells following 5-FU or cisplatin exposure

city: Little Rock

first: Yong-Chen

middle: William

last: Lu

address: 4301 W Markham St

institute: University of Arkansas for Medical Sciences

summary: T cells are pivotal to cancer immunotherapy, yet chemotherapy may erode their fitness. Using a single-cell technique, we show that exposure to two widely used chemotherapeutic agents, 5-FU (5-fluorouracil) and cisplatin, induces non-synonymous mitochondrial DNA mutations (mtDNA) in T cells. Notably, nearly all detected mtDNA mutations are transition mutations. Like the effects observed in genomic DNA mutations, the impacts of mtDNA mutations in T cells appear to be random. Some T cells with mtDNA mutations concentrate in clusters associated with gene markers, while others do not. Additionally, several mtDNA mutations are found in the fraction of treated T cells with low mitochondrial activity, suggesting their potential effect on mitochondrial function. Importantly, mtDNA mutations are detected in tumor-infiltrating T cells from patients with colorectal cancer who received chemotherapy. Our findings uncover an unappreciated consequence of chemotherapy on T cell mitochondria, and these results raise concerns about administering immunotherapy and chemotherapy concurrently.

overall_design: 5-FU-treated and untreated (N) T cells from peripheral blood lymphocytes (PBL) from 3 donors (D1007, D2008, D6053) were studied using scRNAseq/scTCRseq. Single-cell RNA and TCR-seq libraries were prepared using the 10X Genomics 5' immune profing kit (including single-cell 5' mRNA and TCR sequencing). The scRNAseq gene expression (GEX) libraries and scTCRseq libraries were sequenced by an Illumina Novaseq 6000 sequencer. The sequencing data was processed by a Cell Ranger-multi pipeline (v7.1.0; 10X Genomics). The gene expression (GEX) sequencing data was mapped to the standard reference genome database (GRCh38-2020-A, 10X Genomics), and the TCR sequencing data was also mapped to the standard reference genome database (GRCh38-alts-ensembl-7.1.0, 10X Genomics).  For single-cell ATAC-seq, the following samples were studied (1) 5-FU-treated and untreated (N) T cells from 4 donors (2) Cisplatin-treated and untreated (N) T cells from 3 donors, (3) Cisplatin-treated T cells from 3 samples were labeled with mitochondria dyes TMRM or MitoTracker-Green (labeled as MASS). Single-cell sequencing was performed on TMRM or MASS high (Hi) and low T cells. (4) Tumor infiltrating lymphocytes (TILs) and PBL from 3 patients with metastatic colorectal cancer (P1, P2, P3) were subjected to single-cell ATAC-seq sequencing (10X Genomics). The prepared samples were sequenced by an Illumina Novaseq 6000 sequencer. The sequencing data was processed a Cell Ranger-ATAC pipeline (v2.1.0; 10X Genomics) and mapped to reference genome database (GRCh38-r107).

first: Catherine

last: Kirkpatrick

first: Charles

last: Quick

first: Steven

middle: R

last: Post

first: Yuet-Kin

last: Leung

first: Ruud

last: Dings

first: Chrystal

last: Paulos

first: Lyle

last: Burdine


title: Estrous cycle influences cell-type-specific translatomic signatures of repeated ketamine exposure in the rat nucleus accumbens

city: Tallahassee

first: Mohamed

last: Kabbaj

state: Florida

address: 1115 W Call St

department: Biomedical Sciences

institute: Florida State University

summary: The growing therapeutic promise of repeated, low-dose ketamine treatment across various psychopathologies-including depression and drug addiction-warrants clarity on its potential addictive properties and their associated mechanisms in both sexes. Accordingly, the present work examined the effects of repeated low-doses ketamine in male and female rats on behavioral sensitization to the locomotor activating effects of ketamine, as well as the associated molecular profiles in dopamine D1- and D2-receptor-expressing medium spiny neurons (D1- and D2-MSNs) of the nucleus accumbens (NAc). Following intra-NAc infusion of a Cre-inducible RiboTag virus, locomotor activity was measured in adult Drd1a-iCre and Drd2-iCre male and female rats in either diestrus or proestrus following repeated administration of ketamine (0, 10, or 20 mg/kg, i.p.) to evaluate the development of locomotor sensitization. Female-but not male-rats developed sensitization to the locomotor-activating effects of ketamine, occurring more rapidly in proestrus than in diestrus females at the lower dose tested. To examine enduring context- and cell-type-specific changes in translating mRNAs associated with sensitization to ketamine, RNA sequencing   was performed on polyribosome-bound mRNA of D1- and D2-MSNs isolated from the NAc of sensitized females in a drug-free state. A greater number of differentially expressed genes were observed selectively in D1-MSNs of ketamine-treated proestrus compared to diestrus females, which were broadly related to regulation of transcription and epitranscriptional modification. These findings provide novel evidence of cell-type-specific and estrous-cycle-dependent molecular profiles responsive to intermittent ketamine treatment in female rats and identify post-transcriptional mechanisms with relevance to ketamine's effects on behavioral plasticity.

overall_design: RNA-seq profiling of total RNA extracted from RiboTag-immunoprecipitated (IP) polyribosomes in nucleus accumbens tissue punches collected from female Drd1a-iCre and Drd2-iCre Long Evans rats receiving intermittent ketamine (10 mg/kg, i.p., 6 injections 4-5 days apart) or saline (i.p., 6 injections 4-5 days apart) in the proestrus or diestrus phase of the estrous cycle.

first: Samantha

last: Saland

first: Florian

last: Duclot

first: Mary Kay

last: Lobo