title: Specific cPRC1 complexes are co-opted to mediate oncogenic gene repression in diffuse midline glioma

city: Edinburgh

first: Gerry

last: Brien

address: Western General Hospital  Crewe Road South

department: Institute of Genetics and Cancer

institute: University  of Edinburgh

summary: Diffuse midline glioma (DMG) is a fatal childhood brain tumour characterised primarily by mutant histone H3 (H3K27M). H3K27M causes a global reduction in Polycomb Repressive Complex 2 (PRC2)-mediated H3K27me3 by inhibiting PRC2 enzymatic activity. Paradoxically, PRC2 is essential in DMG tumour cells where residual complex activity is required for oncogenic gene repression, although the molecular mechanisms acting downstream of PRC2 in this context are poorly understood. Here, we’ve discovered this oncogenic gene repression is mediated by specific canonical PRC1 (cPRC1) formations. By combining CRISPR screening, biochemical and chromatin mapping approaches with functional perturbations we show that cPRC1 complexes containing CBX4 and PCGF4 drive oncogenic gene repression downstream of H3K27me3 in DMG cells. Remarkably, the altered H3K27me3 modification landscape characteristic of these tumours rewires the distribution of cPRC1 complexes on chromatin. CBX4 and PCGF4 containing cPRC1 accumulate at sites of H3K27me3 while other cPRC1 formations are displaced. Despite accounting for <5% of cPRC1 complexes in DMG, CBX4/PCGF4-containing complexes predominate as gene repressors. Our findings link the altered distribution of H3K27me3 with imbalanced cPRC1 function, promoting oncogenic gene repression in DMG cells, revealing new disease mechanisms and highlighting potential therapeutic opportunities in this incurable childhood brain tumour.

overall_design: Submission contains gene expression (Quantseq) data and CUT&RUN-Rx data for PRC1 and PRC2 related antibodies in SU-DIPGXIII H3K27M and DIPGXIII H3K27M-KO cells.

first: Eimear

last: Lagan

first: Adrian

last: Bracken

first: Gerard

middle: L


title: METTL3-dependent m6A RNA methylation regulates activation of the NLRP3 inflammasome [RNA-Seq]

status: Public on May 28 2025

city: Camperdown

first: RENHUA

last: SONG

state: NSW

address: Charles Perkins Centre - D17, Level 4 West. The University of Sydney Johns Hopkins Drive

country: Australia

institute: Centenary Institute

type: Expression profiling by high throughput sequencing

summary:
Inflammasomes are signalling complexes that are activated in response to infection, cellular stress and other cues to initiate an inflammatory response. The NLRP3 (NOD-, LRR- and pyrin domain-containing protein 3) inflammasome is a cytosolic sensor that mediates caspase-1-dependent maturation and release of the pro-inflammatory cytokines IL-1β and IL-18, and Gasdermin D-induced pyroptotic cell death. While a broad range of pathogens can activate the NLRP3 inflammasome, in most cases, it appears to be dispensable to fight infection.
In recent work, m6A has emerged as a key regulator of the immune response. However, the specific role played by METTL3 and RNA m6A methylation during inflammasome activation is still unknown. Using genetic manipulation and pharmacological inhibition, we demonstrate that METTL3 is essential for activation of the NLRP3 inflammasome in vitro and in vivo. We show that pharmacological inhibition of METTL3 attenuates NLRP3 hyperactivation in PBMCs isolated from patients affected by Cryopyrin Associated Periodic Syndrome (CAPS).

overall_design: Comparative gene expression profiling analysis of  mRNA-Seq in THP-1-derived macrophages treated with LPS , Nigericin, Mettl3-deletion and untreated cells as control.

first: Natalia

last: Pinello

first: Quintin

last: Lee

first: Dan

last: Ye

first: Justin

middle: J

last: Wong


title: Single-cell sequencing of CD45+ cells isolated from nasal mucosa of mice

status: Public on May 27 2025

city: Shanghai

first: Jin

last: Hou

address: 800 Xiangyin Road

country: China

institute: Second Military Medical University

summary: To explore the impact of nasal commensal viruses on the onset and progression of allergic rhinitis, We used single cell RNA sequencing (scRNA-seq) to analyze the diversity of CD45+ cells in the nasal mucosa of control and AR mice treated with Vehicle or Ribavirin.

overall_design: CD45+ cells were isolated from nasal mucosa of mice using magnetic beads .Using 10X Genomics Chromium Controller Instrument and Chromium Single Cell 3’V3.1 Reagent Kits (10X Genomics, Pleasanton, CA) to measure single-cell RNA sequence (3' scRNA-seq) to comprehensively characterize the lung immune mincroenvironment.

first: Ye

last: Zhou

first: Zhixuan

last: Li


title: Large B-cell lymphoma microenvironment archetype profiles (LymphoMAPs). [macrophage]

city: Houston

first: Michael

last: Green

state: Texas

address: 7455 Fannin Street

department: Department of Lymphoma/Myeloma

country: USA

institute: The University of Texas MD Anderson Cancer Center

summary: Large B-cell lymphomas (LBCL) are clinically and biologically heterogeneous lymphoid malignancies with complex microenvironments that are central to disease etiology. Here we have employed single-nucleus multiome profiling of 232 tumor and control biopsies to characterize diverse cell types and subsets that are present in LBCL tumors, effectively capturing the lymphoid, myeloid, and non-hematopoietic cell compartments. Cell subsets co-occurred in stereotypical Lymphoma Microenvironment Archetype Profiles (LymphoMAPs) defined by; (i) a sparsity of T-cells and high frequencies of cancer-associated fibroblasts and tumor-associated macrophages [FMAC]; (ii) lymph node architectural cell types with naïve and memory T-cells [LN]; or (iii) activated macrophages and exhausted CD8 T-cells [TEX]. Divergent patterns of cell-cell communication underpinned the transcriptional phenotypes of archetype-defining cell subsets resulting in exclusion, support or suppression of T-cells, respectively. Consistent with this, LymphoMAPs were associated with significantly different clinical outcomes following CD19 CAR T-cell therapy.

overall_design: Peripheral blood-derived monocytes were isolated from cryopreserved peripheral blood mononuclear cells obtained from 3 different healthy donors (Stemcell) using pan-monocyte isolation kit (Miltenyi) with autoMACS Neo cell separator (Miltenyi) according to the manufacturer’s instructions. Cells were cultured in ImmunoCult SF Macrophage medium (Stemcell) containing 50 ng/mL of recombinant human M-CSF (Stemcell) in temperature-responsive polymer-treated UpCell plates (Thermo Fisher) for 4 days, followed by either supplementation with 50 ng/mL of recombinant human IFN-gamma (Stemcell) or replacement with supernatant of exhausted T-cells (Tex sup) for an additional 2 days. For Tex sup production, a serial killing assay was conducted using healthy donor-derived CAR T cells and HT cell line, starting at a 1:1 ratio in IMDM (Gibco) supplemented with 10% FBS (Gibco). HT cells were added every 2 days along with medium exchange. The supernatant was collected on day 10 and then cryopreserved until use. Tex sup and ImmunoCult SF macrophage medium were mixed at a 1:1 ratio and supplemented with 50 ng/mL rhM-CSF. RNA was extracted using RNeasy micro kit (QIAGEN) according to the manufacturer’s protocol after washing the cells with PBS, followed by library preparation for RNAseq.


title: Epigenetic reprogramming of cell identity in the rat primary neuron-glia cultures involves histone serotonylation

city: Moscow

first: Alexander

last: Beletsky

address: Butlerova street, building 5a

country: Russia

institute: IHNA

summary: Epigenetic rearrangements can create a favorable environment for the intrinsic plasticity of brain cells, leading to cellular reprogramming into virtually any cell type through the induction of cell-specific transcriptional programs. In this study, we assessed how chromatin remodeling induced by broad-spectrum HDAC inhibitors affects cellular differentiation trajectories in rat primary neuron-glia cultures using a combination of transcriptomics, qPCR and cytochemistry. We described epigenetic regulation of transcriptional programs controlled by master transcription factors and neurotrophins in the context of neuronal and glial differentiation and evaluated the expression of representative cell-specific markers. The results obtained suggest that HDAC inhibitors reduce proliferative potential of cultured cells and induce transcriptomic changes associated with cell differentiation and specialization. Particularly, we revealed a significant upregulation of genes typically expressed in neuromodulatory neurons, and downregulation of genes expressed in glia and inhibitory neurons. Transcriptional changes were accompanied by continuous elevation of histone serotonylation levels in both neurons and glia. We assume that early appearance of the enhanced histone serotonylation marks, and the persistence of these changes over many hours in distinct brain cells may indicate that chromatin remodeling induced by histone serotonylation contributes to the maintainance of a new transcriptional programs associated with cellular reprogramming.

overall_design: Samples were obtained from individual rat primary neuron cultures treated with the broad-spectrum histone deacetylase inhibitor trichostatin A (TSA, 100 nM) for 19 h or sodium butyrate (NaB, 5 µМ) for 24 h. The dataset includes samples from control (n=3) and TSA-treated cultures (n=3), as well as samples from control (n=2) and NaB-treated cultures (n=2), processed in parallel. There are 3 biological replicates for the Control/TSA and 2 biological replicates for the Control/NaB groups.

first: Anastasia

middle: A

last: Borodinova

first: Yulia

last: Leontovich

middle: P

last: Beletskiy

middle: V

last: Revishchin

first: Galina

last: Pavlova

first: Pavel

middle: M

last: Balaban


title: Large B-cell lymphoma microenvironment archetype profiles (LymphoMAPs). [tonsil frc]

overall_design: Tonsillar fibroblastic reticular cells (tFRCs) were isolated from fresh tonsils. The cells were passaged for six generations in Insulin-Transferrin-Selenium (Thermo Fisher) containing Dulbecco's Modified Eagle Medium (DMEM, Corning) supplemented with 10% fetal Bovine serum (FBS) and Penicillin (100 units/mL)-streptomycin (100 µg/mL). The tFRCs were stimulated with 10 ng/mL and 50 ng/mL TGFB (Peprotech). The cells were harvested after 48 hours post treatment and subjected to bulk RNA sequencing.


title: Preferential Release of microRNAs via Extracellular Vesicles is Associated with Ductal Carcinoma In Situ to Invasive Breast Cancer Progression [miRNA-Seq]

city: Oklahoma city

first: Bethany

last: Hannafon

state: OK

address: 975 NE 10th Street

department: Obstetrics and Gynecology

institute: University of Oklahoma Health Sciences Center

type: Non-coding RNA profiling by high throughput sequencing

summary: Ductal carcinoma in situ (DCIS) is a precancerous condition that increases the risk of invasive breast cancer (IBC), but not all DCIS cases progress to IBC. The molecular factors driving this transition remain unclear. Small extracellular vesicles (sEVs), or exosomes, play a role in advanced cancer progression, though their function in DCIS is poorly understood. This study explores the role of sEVs and their RNA content in DCIS progression. We found that Rab27A, a key regulator of exosome release, is upregulated in DCIS and IBC tissues compared to normal breast tissue. Inhibiting sEV release by knocking down Rab27A disrupted pro-invasive signaling and reduced invasion in a DCIS mouse model. Using the MCF10 breast cancer progression series, we observed increased microRNA (miRNA) content in sEVs as cells transitioned from normal to malignant, with the most significant differential miRNA expression seen in IBC-derived sEVs. In vivo, DCIS progression raised circulating sEV miRNA levels, which were reduced by Rab27A knockdown. Reintroducing miR-205, enriched in IBC-derived sEVs, suppressed DCIS cell proliferation, invasion, and epithelial-mesenchymal transition (EMT) markers. Co-expression of miR-205 with Rab27A knockdown also suppressed TGF-β signaling, activated MAPK p38, and induced cell cycle arrest and apoptosis. These findings show that the RNA cargo of sEVs changes during malignancy, with specific miRNAs driving DCIS progression. Re-expression of miR-205 offers a promising therapeutic approach to prevent DCIS from becoming invasive.

overall_design: To understand how the content of small extracellular vesicles (sEVs) changes from benign to IBC and contributes to invasive programs, we isolated sEVs from each cell line in the MCF10 isogenic series comprising MCF10A (normal mammary epithelial cells), MCF10AT1 (benign proliferative cells), MCF10DCIS (spontaneous malignant progression), and MCF10CA1 (malignant cells with metastatic capabilities), and profiled their small RNA by small RNA sequencing.

first: Elayapillai

last: Sugantha Priya

first: Hannafon

last: Bethany


title: Preferential Release of microRNAs via Extracellular Vesicles is Associated with Ductal Carcinoma In Situ to Invasive Breast Cancer Progression [RNA-Seq]

overall_design: RNA sequencing was conducted to evaluate the gene expression programs modulated by miR-205 and Rab27A knockdown in DCIS cells.


title: Effect of MAOI on antitumor immunity in a B16-OVA melanoma tumor model

city: Los Angeles

first: Lili

last: Yang

state: California

address: 610 Charles E. Young Dr. East

department: Microbiology Immunology & Molecular Genetics

institute: University of California, Los Angeles

summary: MAOIs, a class of antidepressant drugs that inhibit the degradation of monoamine neurotransmitters including serotonin, have been shown to significantly enhance antitumor immunity. Employig a single cell sequencing approch using 10xGemonics scRNAseq, we investigated how MAOI alters tumor-infiltrating CD8 T cell compartment and signaling pathways. This study provides new insights into the mechanistic differences in how MAOIs and SSRIs regulate CD8 T cell antitumor immunity.

overall_design: C57BL/6J mice were challenged with B16-OVA melanoma and then daily treated with a MAOI (phenelzine) starting from day 3. CD45+ tumor-infiltrating immune cells (TIIs) were sorted from day 10 B16-OVA tumors and then subjected to scRNA-seq analysis.

first: Bo

first: James

last: Elsten-Brown

first: Yuning

last: Chen

first: Elliot

last: Kang


title: Integrative multi-omics identifies AP-1 transcription factor as a targetable mediator of acquired osimertinib resistance in non-small cell lung cancer

city: Izmir

first: Serif

last: Senturk

address: Dokuz Eylul University - iBG

department: Functional Cancer Genomics Lab

country: Turkey

institute: Izmir Biomedicine and Genome Center

type: Genome binding/occupancy profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: Integrative multi-omics identifies AP-1 transcription factor as a targetable mediator of acquired osimertinib resistance in non-small cell lung cancer [RNA_SEQ_FOSL1 and JUN KO]

summary: Osimertinib, a third-generation EGFR tyrosine kinase inhibitor (EGFR-TKI), has dramatically transformed the treatment landscape for patients with EGFR-mutant NSCLC. However, the long-term success of this therapy is often compromised by the onset of acquired resistance, with non-genetic mechanisms increasingly recognized as pivotal contributors. Here, we exploit a multi-omics approach to profile genome-wide chromatin accessibility and transcriptional landscapes between drug sensitive and resistant EGFR-mutant cells. Our findings reveal a robust concordance between epigenetic regulome and transcriptomic changes that characterize the osimertinib resistant state. Using CRISPR-based functional genomics screen targeting epigenetic regulators and transcription factors, we uncover a critical regulatory network featuring key members of the NuRD and PRC2 complexes that mediate resistance. Most critically, our screen identifies FOSL1 and JUN, two subunits of the AP-1 transcription factor within this network, as the most significant hits. Mechanistically, we demonstrate that cis-regulatory elements exhibiting altered chromatin accessibility in the resistant state are enriched for cognate AP-1 binding motifs, enabling AP-1 to orchestrate a gene expression program that underpins the druggable MEK/ERK signaling axis, potentially enhancing cell viability and fitness of resistant cells. Importantly, genetic depletion or pharmacological inhibition of AP-1 reinstates cellular and molecular sensitivity and reverts resistance-associated phenotypes, such as epithelial-to-mesenchymal transition, upon anti-EGFR rechallenge by repressing AKT and ERK signaling. The findings provide novel insights into the epigenetic and transcriptional control of osimertinib resistance in EGFR-mutant NSCLC, highlighting AP-1 as a targetable vulnerability of resistance-related hallmarks and offering a promising avenue for developing resistance reversal strategies.

overall_design: To investigate the role of FOSL1 and JUN in osimertinib resistance in non-small cell lung cancer (NSCLC), we developed FOSL1 and JUN knockout HCC827-OsiR cell lines.

first: Senturk

last: Serif

first: Karakulah

last: Gokhan


title: Modulation of infiltrating CD206-positive macrophages restricts progression of pulmonary lymphangioleiomyomatosis (LAM)

city: Haining

first: Heng-Jia

last: Liu

state: Zhejiang

address: 718 East Haizhou Road

department: International Campus

institute: Zhejiang University - University of Edinburgh

summary: Lymphangioleiomyomatosis (LAM) is a progressive neoplastic interstitial lung disease that primarily affects women of reproductive age. It is characterized by the infiltration of the lungs by atypical "LAM" cells, which leads to the cystic destruction of lung tissue. In our study, we employed spatial transcriptomics to analyze cell populations within LAM in order to understand the significance of the spatial organization of LAM cells and macrophages. Each Visium spot covers from one to ten cells. We discovered that some spots have highly expressed macrophage-associated genes (defined as Macro:only) and some highly expressed LAM-associated genes (defined as LAM:only). There are also some spots that have highly expressed both macrophage and LAM markers; we defined these as the LAM_Macro interaction spots. To further understand the spatial organization of LAM and macrophages, we extracted all spots expressing LAM and macrophage-associated genes in our data and examined the molecular profile. In our analysis of PMEL-positive LAM samples, we observed that genes associated with macrophage homing (specifically CCL2, CSF1, CSF2, CXCL12, and IL7) are highly expressed in the LAM:Macro interaction spots. Immunofluorescence analyses showed that CD206+ macrophages are in close proximity to LAM cells in LAM patient lungs. Targeting M2 macrophages via treatment with the CD206 modulator RP-182 impaired the growth of TSC2-deficient tumors in vivo. In conclusion, M2-like CD206high macrophages may represent a potential therapeutic target in LAM.

overall_design: Eight human pulmonary lymphangioleiomyomatosis (LAM) areas from four LAM patients were analyzed using 10x Visium spatial transcriptomics.

first: Remi

last: Diesler

first: Joelle

last: Chami

first: Boxiang

last: Wu

first: Heng

last: Du

first: Yue

last: Jin

first: Melissa

last: Daou

first: Nicola

last: Alesi

first: Damir

last: Khabibullin

first: Caroline

last: Leroux

first: Vincent

last: Cottin

first: Lloyd

middle: G

last: Cantley

first: Udo

last: Rudloff

first: Elizabeth

last: Henske


title: Integrative multi-omics identifies AP-1 transcription factor as a targetable mediator of acquired osimertinib resistance in non-small cell lung cancer [RNA_SEQ_HCC827 OsiR]

first: Serif

last: Senturk

overall_design: To investigate osimertinib resistance in non-small cell lung cancer (NSCLC), we developed the HCC827-OsiR cell line.


title: NF1-depleted ER+ breast cancers are differentially sensitive to CDK4/6 inhibitors

first: Jonathan

middle: Thomas

last: Lei

state: TX

address: 1 Baylor Plaza

department: Medicine - Lester and Sue Smith Breast Center

institute: Baylor College of Medicine

summary: Neurofibromin/NF1-depletion (NF1low) is associated with endocrine therapy resistance in approximately 20% of ER+/HER2– early-stage breast cancer but specific treatments for NF1low tumors are not established.  Proteogenomic analyses on ER+/HER2– breast cancer demonstrated that NF1low tumors exhibit elevated CDK4/6 activity.  NF1-silencing in cell lines promoted ER recruitment to CCND1, thus increasing cyclin-D1 levels.  Additionally, RAF is demonstrated to directly phosphorylate the CDK4 activation-loop (pT172) thus providing a direct connection between NF1 loss and an increase in CDK4 activity.  Consequently, NF1low cancer cells are differentially sensitive to a fulvestrant plus CDK4/6 inhibitor (CDK4/6i) combination, with cell-death induction in vitro, and durable tumor regressions in ER+ NF1low PDX models in vivo. Furthermore, NF1low ER+/HER2– tumors treated neoadjuvantly with 4 weeks of anastrozole exhibited a minimal reduction of a multigene mRNA proliferation score vs NF1high tumors but exhibited marked sensitivity to the subsequent addition of palbociclib. In conclusion, dual ER and downstream RAF activation following NF1-loss drives endocrine therapy resistance and CDK4/6i sensitivity in NF1low ER+ breast cancer.  NF1 status should therefore be prioritized for biomarker investigations in adjuvant CDK4/6i trials to determine whether the NF1low status identifies a particularly sensitive subset where CDK4/6i therapy is critical.

overall_design: ER-ChIP-seq of doxycycline inducible knockdown of NF1 in hormone-deprived MCF7 breast cancer cell lines  -/+ E2.

first: Eric

middle: C

last: Chang

first: Ze-Yi

last: Zheng

middle: T

first: Meenakshi

last: Anurag


title: endometrium:control vs intrauterine adhesion (IUA)

city: Nanjing

first: Xing

last: Chen

state: Jiangsu

address: 368 Jiangdong North Road

department: Gynecology

institute: The First Affiliated Hospital with Nanjing Medical University

summary: To screen differentially expression circRNAs between tissues of normal endometrium (control) and intrauterine adhesion (IUA) in human.

overall_design: Biological replicates: 3 control replicates, 3 IUA replicates.


title: SERT inhibits CD8 T cell antitumor immunity through regulating the intratumoral serotonin axis

first: Lili

last: Yang

summary: Identifying new immune checkpoint molecules hindering antitumor T cell responses and devising new therapeutic blockades are key to the development of next-generation cancer immunotherapies. Here, we report the induction of the serotonin transporter (SERT) in solid tumor-infiltrating cytotoxic CD8 T cells, a molecule best known for its role in regulating serotonin neurotransmission in the brain. In solid tumors, CD8 T cells secrete serotonin, which stimulates their antitumor reactivities, while SERT functions as a negative regulator by depleting intratumoral serotonin. Inhibition of SERT using clinically approved selective serotonin reuptake inhibitors (SSRIs), a popular class of antidepressants, significantly suppressed tumor growth and enhanced CD8 T cell-mediated antitumor responses in various preclinical mouse syngeneic and human xenograft tumor models. Importantly, SSRI treatment exhibited significant therapeutic synergy with anti-PD-1 therapy, and clinical data correlation studies negatively associated intratumoral SERT expression with patient survival in a range of cancers. These findings highlight the significance of the intratumoral serotonin axis and identify SERT as a novel immune checkpoint, positioning SSRIs as promising candidates for next-generation combination cancer therapies.

overall_design: Gene expression profiling of tumor infiltrating immune cells in an in vivo study using a B16-OVA syngeneic mouse melanoma model treated with fluoxetine or anti-PD-1

first: Bo

last: Li

first: Miao

first: Yuning

first: Feiyang

last: Ma

first: James

last: Elsten-Brown


title: Multiomic and clinical analysis of multiply recurrent meningiomas reveals risk factors, underlying biology, and insights into evolution

city: St. Louis

first: Sangami

last: Pugazenthi

address: 4949 W Pine Blvd

institute: Washington University School of Medicine

summary: Although meningiomas, the most common primary brain tumor, are often effectively treated with surgery and radiation, an important subset of meningiomas behave aggressively and are characterized by treatment resistance and multiple recurrences. In this dual institution study, we identify clinical, genetic, and epigenetic predictors of multiply recurrent meningiomas (MRMs) and also evaluate the evolution of these meningiomas in matched samples. On multivariable binomial logistic regression, MRMs were significantly associated with male sex (p=0.012), subtotal resection (p=0.001), higher number of meningiomas on presentation (p=0.017), and histopathological sheeting (p=0.002). Multiomic analysis of primary meningiomas revealed that MRMs exhibit greater global copy number alternations (CNA) (p=0.0113) and increased DNA methylation (p=0.0236). Integrated methylation profiling and RNA-sequencing identified candidate driver genes of MRMs. Among these genes, we demonstrated in meningioma cells that knockdown of EDNRB, a locus with greater promoter methylation and decreased gene expression in MRMs, leads to increased meningioma cell proliferation. CNA, subclonal evolution, and methylation profiles of MRMs did not significantly change from primary tumor to recurrences, even after radiation treatment, suggesting MRMs are molecularly aggressive from initial diagnosis. This first clinical and multiomic investigation of MRMs harbors implications for the future development of biomarkers and therapeutic agents for these challenging tumors.

overall_design: We samples 43 total tumors from institution A (n=15) which were EPIC Bead Chip Version 1 and Institution B (n=28) which were EPIC Beach Chip Version 2. 31 were primary tumors, 10 were recurrence 1 and 2 were recurrence 2. Of the 31 primary tumors, 13 were multiply recurrence and 18 were non-recurrent.

first: Bhuvic

last: Patel

first: Akash

first: Albert

middle: H

last: Kim


title: Effect of maternal obesogenic diet exposure on murine Neurofibromatosis Type 1 optic pathway glioma

first: Nicole

last: Brossier

state: United States

address: 660 S. Euclid Ave Campus Box 8208

department: Pediatrics

institute: Washington University in St. Louis

summary: Pediatric low-grade glioma incidence has been rising in the U.S., mirroring the rising rates of pediatric and maternal obesity. Recently, children of obese mothers were demonstrated to develop brain tumors at higher rates. Importantly, obesity in the U.S. is largely driven by diet, given the abudnance of high fat and high sugar food choices. We identified that combined maternal and postnatal obesogenic (Ob) diet exposure accelerated glioma formation in murine Neurofibromatosis type 1 (Nf1) optic pathway glioma (OPG)-forming mice, a model of pediatric glioma formation. Postnatal dietary exposure alone could not fully recaptiulate these effects, indicating maternal exposure was critical for this phenotype. To determine how Ob exposure affected gene expression in the optic nerve, we isolated Ob-exposed versus CD-exposed optic nerves and performed RNASeq. Enriched pathways included nervous system development, neuronal signaling and appetite regulation.

overall_design: To determine how obesogenic diet exposure affected gene expression in the optic nerve of Nf1-OPG forming animals, we collected optic nerves from control diet versus obesogenic diet exposed GFAP-Cre; Nf1-R681X/Flox mice at 6 weeks of age. Bulk RNASeq was performed. Three replicates were analyzed per group.

first: Ambrose

last: Chan

first: Kailong

last: Zhang

first: Gemma

last: Martin

first: Sabiha

last: Bano

first: Jit

last: Chatterjee

first: Sarvika

last: Mahto

first: Avery

last: Wang

first: David

last: Gutmann


title: Transcriptome sequencing of alveolar macrophages from RACK1 myeloid knockout mice and control mice

city: 重庆

first: 蒋

last: 慧

address: 中国重庆

institute: 南华大学

summary: To investigate the effects of RACK1 myeloid deletion on the growth and development of alveolar macrophages in mice, we sorted alveolar macrophages from RACK1 myeloid deletion mice and control mice for transcriptome sequencing

overall_design: Comparative analysis of gene expression profiles of RNA-seq data from alveolar macrophages of RACK1 myeloid knockout mice and control mice

first: Jiyan

first: Hui

last: Jiang


title: Deep mutational scanning of the human insulin receptor ectodomain to inform precision therapy for insulin resistance

first: Vahid

last: Aslanzadeh

address: Crewe Road

department: Human Genetics Unit

country: United Kingdom

institute: The University of Edinburgh

summary: The insulin receptor (INSR) entrains tissue growth and metabolism to nutritional conditions. Complete loss of function in humans leads to extreme insulin resistance and infantile mortality, while loss of 80-90% function permits longevity of decades. Even low-level activation of severely compromised receptors, for example by anti-receptor monoclonal antibodies, thus offers the potential for decisive clinical benefit. A barrier to genetic diagnosis and translational research is the increasing identification of INSR variants of uncertain significance. We employed saturation mutagenesis coupled to multidimensional flow-based assays to stratify approximately 14,000 INSR extracellular domain missense variants by cell surface expression, insulin binding, and insulin- or monoclonal antibody-stimulated signaling. The resulting function scores correlate strongly with clinical syndromes, offer insights into dynamics of insulin binding, and reveal novel potential gain-of-function variants. This INSR sequence-function map has high biochemical, diagnostic and translational utility, aiding rapid identification of variants amenable to activation by non-canonical INSR agonists.

sample_organism:
Escherichia coli
Mus musculus

platform_organism:
Escherichia coli
Mus musculus

overall_design: This study aimed to assess the impact of INSR variants on human insulin receptor surface expression, insulin binding, and insulin signalling. Additionally, it explored whether certain damaging variants could be activated by antibodies.  To achieve this, saturation mutagenesis was performed on the INSR gene, generating a library of variants, each linked to a unique barcode sequence via PacBio sequencing. This variant library was then transfected into MEF cells and screened using FACS sorting into four bins based on their effects on receptor expression, insulin binding, and signalling. Cells from each bin were collected and subjected to Illumina sequencing to determine the frequency of each barcode in each bin. These frequencies, combined with the PacBio data, were used to calculate a functional score for each variant.

last: Brierley

first: Rupa

last: Kumar

first: Hasan

last: Çubuk

first: Corinne

last: Vigouroux

first: Kenneth

last: Matreyek

first: Grzegorz

last: Kudla

first: Robert

middle: K

last: Semple


title: CHIP-seq analysis of H3K27ac in papillary thyroid carcinoma patient's tissues and paired normal tissues

city: Tianjin

first: Xiukun

last: Hou

address: Huanhu Road

institute: Tianjin Cancer Institute and Hospital

summary: To identify the super enhancers, we performed Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) for H3K27ac in in papillary thyroid carcinoma patient's tissues

overall_design: H3K27ac ChIP-seq on normal and tumor tissue

first: Wei

last: Zhang


title: A microbiota-derived bile acid modulates biofilm formation by the probiotic strain Escherichia coli Nissle 1917

status: Public on May 26 2025

city: South San Francisco

first: Barath

last: Udayasuryan

state: CA

address: 1 DNA Way

department: Department of Infectious Diseases and Host-Microbe Interactions

institute: Genentech Inc.

summary: Bacteria that colonize the human gut must withstand a variety of stressors, including detergent-like compounds known as bile acids. Here, we investigated how bile acids found in the human cecum and colon impact the behavior of the probiotic strain Escherichia coli Nissle 1917 (EcN). We found that lithocholic acid (LCA), which is a microbiota-derived secondary bile acid, promotes the formation of a distinctive surface-coating biofilm by EcN, including on an organoid-derived model of the human colonic epithelium. Mechanistic investigations, including RNA-sequencing, revealed that LCA upregulates the production of several components of flagella, which are essential for LCA-induced biofilm formation and form part of the biofilm extracellular matrix.

overall_design: Wildtype (plasmid-cured) E. coli Nissle was grown to log phase anaerobically in YCFA media at 37C, then treated with 1% DMSO (solvent control), 100 µM lithocholic acid, or 100 µM chenodeoxycholic acid for different periods of time (15, 30, 90, 180 minutes) prior to RNA extraction.

first: Elena

last: Perry

first: Elias

last: Zegeye

first: Christopher

last: Rose

first: Mike

last: Reichelt

first: Man-Wah

last: Tan


title: Influence of three-dimensional culture in an interwoven hollow fiber bioreactor on the gene expression profile of hepatic HepG2 cells

first: Brandon

middle: Justin

last: Blau

address: 2011 Zonal Avenue

department: Department of Surgery, Keck School of Medicine

institute: University of Southern California

summary:
Purpose: In this study, we aimed to elucidate the specific molecular mechanisms that are activated when hepatic cells are cultured in the 3D environment of an interwoven hollow fiber bioreactor device.
Methods: HepG2 human hepatocellular carcinoma cells were either cultured in an interwoven hollow fiber bioreactor or on a conventional two-dimensional (2D) surface. The cells were harvested and RNA sequencing was performed to identify the differentially expressed genes between the two culture conditions. Ingenuity Pathway Analysis (IPA) software was utilized to algorithmically generate gene networks and canonical pathways that were either activated or repressed as a result of the experimental conditions.
Results: RNA sequencing analysis identified 5,711 genes that were differentially expressed (FDR < 0.05). Of these, 1,248 genes were biologically upregulated (FC > 2) and 629 genes were biologically downregulated (FC < -2). Several of these upregulated genes have known associations with metabolic activity, cellular proliferation, and apico-basal cell organization. IPA analysis confirmed the likely activation of metabolic pathways in 3D culture and suggest a strong relationship between hepatic metabolism, cell-cell interactions, and polarity markers
Conclusions: Our results demonstrate the likely activation of metabolic pathways in 3D culture and suggest a strong relationship between hepatic metabolism, cell-cell interactions, and polarity markers. Further experimentation must be performed to further elucidate the connections between these pathways.

overall_design: cDNA libraries were generated from mRNAs extracted from HepG2 cells cultured in a conventional 2D culture and in a 3D bioreactor; these libraries were applied to deep sequencing followed by transcriptome analysis

first: Ryoichi

last: Sakiyama

first: Meng

last: Li

first: Toshio

last: Miki


title: RNA-seq of papillary thyroid carcinoma (PTC)  patient's tissues and paired normal tissues

summary: To describe the transcriptome of PTC, we performed RNAseq analysis of PTC  patient's tissues and paired normal tissues

overall_design: RNA-seq

first: Xianhui

last: Ruan


title: Transcriptome Response of Leaves from Young Cannabis sativa L. under Heat Stress

city: Chuncheon-si

first: Byeong-Ryeol

last: Ryu

state: Gangwon-state

address: 1, Kangwondaehak-gil

department: Department of Bio-Health Convergence

country: South Korea

institute: Kangwon National Univsersity

summary: Cannabis sativa L. is a dioecious, annual herbaceous crop (2n = 20) known for its diverse applications across textile, food, cosmetic, and medicinal industries. Recent increases in global temperatures have raised concerns about the impact of heat stress on hemp physiology. Although previous studies have demonstrated reductions in photosynthetic efficiency and cannabinoid levels under heat stress, transcriptome-wide insights into molecular responses remain limited. In this study, we performed a genome-wide transcriptomic analysis to investigate the molecular mechanisms of heat stress response in C. sativa cv. Pink Pepper. This dataset provides a high-resolution transcriptomic resource to explore thermotolerance in C. sativa and contributes to a better understanding of its molecular adaptation to heat stress. The findings can aid future breeding and biotechnology efforts aimed at enhancing stress resilience in hemp.

overall_design: Plants were exposed to high temperature conditions (45 ± 2 °C) for seven days in a controlled growth chamber, and leaf tissues were harvested for mRNA sequencing.

first: Min-Jun

last: Kim

first: Min-Ji

last: Kang

first: Sang-Hyuck

last: Park

first: Jung-Dae

last: Lim


title: Restriction of innate Tgd17 cell plasticity by an AP-1 regulatory axis [CUT&Run]

city: Durham

first: Maria

last: Ciofani

state: NC

address: 207 Research Drive, 128 Jones Building

department: Integrative Immunobiology

institute: Duke University School of Medicine

summary: IL-17-producing gd T (Tgd17) cells are innate-like mediators of intestinal barrier immunity. While Th17 cell and ILC3 plasticity have been extensively studied, the mechanisms governing Tgd17 cell effector flexibility remain undefined. Here, we combined type 3 fate-mapping with single cell ATAC/RNA-seq multiome profiling to define the cellular features and regulatory networks underlying Tgd17 cell plasticity. During homeostasis, Tgd17 cell effector identity was stable across tissues, including for intestinal T-bet+ Tgd17 cells that restrained IFNg production. However, S. typhimurium infection induced intestinal Vg6+ Tgd17 cell conversion into type 1 effectors, with loss of IL-17A production and partial RORgt downregulation. Multiome analysis revealed a trajectory along Vg6+ Tgd17 effector conversion, with TIM-3 marking ex-Tgd17 cells with enhanced type 1 functionality. Lastly, we characterized and validated a critical AP-1 regulatory axis centered around JunB and Fosl2 that controls Vg6+ Tgd17 cell plasticity by stabilizing type 3 identity and restricting type 1 effector conversion.

overall_design: CUT&RUN occupancy for JunB and Fosl2 was performed on sort purified Vg6+ ZS+ gd T cells from day 5 mesenteric lymph node Tgd17 cell expansion cultures.

first: Morgan

middle: E

last: Parker

first: Tzu-Chieh

last: Liao


title: Effect of constant inflammation on in vitro expanded adipose-derived mesenchymal stromal cells

city: Copenhagen

first: Tu

last: Hu

address: 5 Artillerivej

department: Infectious Disease Immunology

country: Denmark

institute: Statens Serum Institut

summary: Human adipose-derived mesenchymal stromal cells (AD-MSCs) are known for their immunomodulatory responses to inflammation, a key trait for their therapeutic use in tissue injury and chronic inflammatory diseases. However, the effects of constant inflammation on their transcriptomic profile, proliferative capacity, and immunosuppressive potential remain largely unexplored. To investigate this, we evaluated the in vitro response of human AD-MSCs from three donors expanded across seven passages under, non-inflamed (DMEM), acute (IFNγ-24h) and constant (IFNγ-C) inflammatory conditions. Bulk RNA-sequencing results demonstrated that AD-MSCs respond significantly to inflammatory stimuli. Both acute and constant inflammation induced extensive transcriptomic alterations, with differentially expressed genes related to cell cycle regulation, DNA replication, metabolism, and immunomodulation. Notably, constant inflammation was associated with a transcriptomic shift toward oxidative phosphorylation (OXPHOS). Moreover, microscopy analysis revealed a significant reduction in AD-MSCs proliferative capacity under constant inflammation, as evidenced by lower cumulative population doubling and the appearance of senescence‐like morphological changes in early passages when compared to non-inflamed (DMEM) and acute inflammatory (IFNγ‐24h) conditions. Despite proliferation was impaired, co‐culture assays with PBMCs demonstrated that under constant inflammation AD-MSCs immunosuppressive potential was maintained in early and late passages. Therefore, our results provide novel insights into the dual effects of constant inflammation on AD-MSCs, impairing cell proliferation while maintaining their immunosuppressive capacity. Understanding AD-MSCs’ behaviour in chronically inflamed microenvironments is essential for optimizing AD-MSCs' clinical applications.

overall_design: Adipose-derived mesenchymal stromal cells (AD-MSCs) were isolated from human subcutaneous adipose tissue of three independent donors and expanded from passage 0 to passage 7 under three conditions: non-inflamed medium (DMEM), 24-hour interferon-gamma (IFNγ) exposure, or continuous IFNγ treatment. At each passage, cells were grown to approximately 80% confluency, harvested by trypsinization, and pelleted for RNA extraction using the RNeasy Mini Kit (Qiagen). RNA purity and concentration were assessed by NanoDrop, and RNA integrity was confirmed by TapeStation (RIN ≥7). High-quality RNA was used for cDNA library preparations, which were sequenced at BGI using a paired-end protocol (100-bp reads). Raw FASTQ files were produced for downstream differential expression and pathway analyses, and pertinent metadata, including donor identity, passage number, and treatment condition, were recorded for each sample.

first: Marina

middle: R

last: Galera

first: Lisa

last: Harth

first: Mariana

last: Bronze

first: Lea

last: Munthe-Fog

first: Jesper

last: Svalgaard

first: Anders

last: Woetmann


title: Restriction of innate Tgd17 cell plasticity by an AP-1 regulatory axis

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

overall_design: Refer to individual Series


title: Searching for the influencers among placental immune cells in preeclampsia.

city: Daejeon

first: Tae Lyun

last: Ko

address: 245, Daehak-ro, Yuseong-gu

institute: Korea Institute of Science and Technology Information

summary: It has been posited that cells of the maternal and fetal immune systems communicate to lead to immune tolerance during pregnancy however been inconclusive. Here, we profiled single-cell transcriptional signatures by placental layers consisting of maternal-fetal interface (MF) and deep-placenta (Pla) regions, then searched influencer gene for preeclampsia (PE). As underpin principle of the failure of immune tolerance, we start by clarifying the systemic framework, which consists of immune interactions frequency (IIF) and specific trigger (i.e., influencer) tolerance (IT) models. We elaborate single-cell transcriptional profiles of normal term (Norm) and preeclampsia preterm parturitions (PePT). Fetal and maternal cells admixed across placenta, in both of Norms and PePTs, rejecting IIF model of immune failure of pregnancy posed by exceed interactions of fetomaternal cells. Whereases placental layers are well mixed with maternal cells, we identified conserved gradual immune transition of fetal T cells in both of PePT and Norm, disapproving IIF model. To search the influencer of PePT in IT model, we established and validated a classification model for PePT and Norm immune cells including T cells, then prioritized major contributors for classifier model. Interestingly, those prioritized genes are highly enriched with ligands and receptors (p-value 5.98e-05). Out of prioritized ligand-receptors, SPP1 and CD44 suggested as influencer of inflammation signatures and experimentally validated by exclusive colocalization of SPP1 and CD44 expressed cells in placentas of PePT. Different IL4 and IFN-g levels in the serum and urine of PePTs further support contribution of SPP1 in associated pathways, including allograft rjection pathway. Collectively, our finding provide insight into the influence of specific immune interactions between cells in human placenta and these influencer-derived impact the immune harmonization of PePT.

overall_design: Following elective cesarean delivery, placental tissues were collected from the maternal-fetal interface and deep-placenta of women with term birth (Norm, ≥37 weeks) or preeclampsia-associated preterm birth (PePT, ≤34 weeks). These tissues were freshly isolated, dissociated into single-cell suspensions, and subjected to scRNA-seq analysis.

first: Hyojung

last: Paik

first: Tae-Lyun

first: Sung-Ki

last: Lee


title: A cost-effective and flexible workflow for high-resolution spatial transcriptomics in fixed tissue

city: qingdao

first: Xue

last: Dong

address: 238 songling road

institute: Ocean University of China

summary: The spatial heterogeneity of gene expression has driven the development of diverse spatial transcriptomics technologies. Here, we introduce photocleavage and ligation sequencing (PCL-seq), a spatial indexing method based on a light-controlled DNA labeling strategy applied to tissue sections. PCL-seq employs photocleavable oligonucleotides and sequence adapters to construct transcriptional profiles of specific regions of interest (ROIs), designated via microscopically controlled photo-illumination. In frozen mouse embryos, PCL-seq generates spatially aligned gene expression matrices and achieves high-quality data outputs, detecting approximately 170,000 unique molecular identifiers (UMIs) and 8,600 genes (irradiation diameter=100 µm). Moreover, PCL-seq is compatible with formalin-fixed and paraffin-embedded (FFPE) tissues, successfully identifying thousands of differentially enriched transcripts in the digits and vertebrae of FFPE mouse embryo sections. Additionally, PCL-seq achieves subcellular resolution, as demonstrated by differential expression profiling between nuclear and cytoplasmic compartments. These features establish PCL-seq as an accessible and versatile workflow for spatial transcriptomic analyses in both frozen and FFPE tissues at subcellular resolution.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: We designed a series of experiments to evaluate the performance of our newly developed sequencing method, PCL-seq. This method utilizes a photocleavable (PC) linker as a photosensitive compound, enabling precise photolytic cleavage and ligation of target regions within tissue sections. To verify the ability of PCL-seq to specifically amplify cDNA molecules from illuminated regions, we performed an experiment using co-cultured cells. In this setup, one cell type served as a non-illuminated background, while a small portion of the other cell type was selectively illuminated at varying ratios. The specificity of PCL-seq was assessed by comparing the differential genic reads between the two cell types through sequencing.Furthermore, we evaluated the data quality of PCL-seq on both cryo-preserved and FFPE (formalin-fixed paraffin-embedded) tissue sections, examining its ability to maintain spatial localization of gene expression. To test whether PCL-seq can achieve subcellular resolution, we irradiated the nuclear and cytoplasmic regions of HeLa cells separately and analyzed the resulting data. These experiments allowed us to systematically characterize the precision, spatial resolution, and versatility of PCL-seq under diverse experimental conditions.

first: Mengzhu

first: Xiaonan

last: Cui

first: Wenjian

last: Zhou


title: Integrative multi-omics identifies AP-1 transcription factor as a targetable mediator of acquired osimertinib resistance in non-small cell lung cancer [ATAC-SEQ]

first: Serif

last: Senturk

summary: Osimertinib, a third-generation EGFR tyrosine kinase inhibitor (EGFR-TKI), has dramatically transformed the treatment landscape for patients with EGFR-mutant NSCLC. However, the long-term success of this therapy is often compromised by the onset of acquired resistance, with non-genetic mechanisms increasingly recognized as pivotal contributors. Here, we exploit a multi-omics approach to profile genome-wide chromatin accessibility and transcriptional landscapes between drug sensitive and resistant EGFR-mutant cells. Our findings reveal a robust concordance between epigenetic regulome and transcriptomic changes that characterize the osimertinib resistant state. Using CRISPR-based functional genomics screen targeting epigenetic regulators and transcription factors, we uncover a critical regulatory network featuring key members of the NuRD and PRC2 complexes that mediate resistance. Most critically, our screen identifies FOSL1 and JUN, two subunits of the AP-1 transcription factor within this network, as the most significant hits. Mechanistically, we demonstrate that cis-regulatory elements exhibiting altered chromatin accessibility in the resistant state are enriched for cognate AP-1 binding motifs, enabling AP-1 to orchestrate a gene expression program that underpins the druggable MEK/ERK signaling axis, potentially enhancing cell viability and fitness of resistant cells. Importantly, genetic depletion or pharmacological inhibition of AP-1 reinstates cellular and molecular sensitivity and reverts resistance-associated phenotypes, such as epithelial-to-mesenchymal transition, upon anti-EGFR rechallenge by repressing AKT and ERK signaling. The findings provide novel insights into the epigenetic and transcriptional control of osimertinib resistance in EGFR-mutant NSCLC, highlighting AP-1 as a targetable vulnerability of resistance-related hallmarks and offering a promising avenue for developing resistance reversal strategies.

overall_design: To investigate osimertinib resistance in non-small cell lung cancer (NSCLC), we developed the HCC827-OsiR cell line.

first: Senturk

last: Serif

first: Karakulah

last: Gokhan


title: Spatiotemporal regulation of target mRNA cleavage by 21-nt phasiRNAs in maize anthers [degradome-seq]

city: Beiing

first: Yijun

last: Qi

address: NO.1 Qinghuayuan

department: School of Life Sciences

institute: Tsinghua University

summary: In grasses, 21- and 24-nt phasiRNAs are abundantly expressed in anthers and play crucial roles in anther development and male reproduction. 21-nt phasiRNAs can act in cis to direct the cleavage of their own precursor transcripts and is thought to lack trans cleavage targets in maize. Here we show that 21-nt phasiRNAs direct the cleavage of hundreds of target mRNAs in maize, with the cleavage activity being enriched in male germ cells. Interestingly, whereas 21-nt phasiRNAs in anthers (somatic anther wall cells) do not have obvious preference for a particular nucleotide at the 5’ end and target genes implicated in stress response and cellular homeostasis, 21-nt phasiRNAs in male germ cells preferentially initiate with 5’ C and associate with ZmAGO5c/MAGO2/MS28 to target genes related to meiotic processes. Our results indicate that mRNA cleavage is a conserved mechanism used by 21-nt phasiRNAs for gene regulation. However, the sequences of 21-nt phasiRNAs and their targets show low conservation in maize and rice, suggesting that 21PHAS loci and 21-nt phasiRNA targets have undergone fast divergence in monocots.

overall_design: To explore potential targets of 21-nt phasiRNA  and their regulatory roles in their targets in  maize，we collected maize anthers,male germ cells across various these developmental stages. and embryos from seeds  .We then using these samples performed low-input sRNA-seq, RNA-seq and high sensitive degradome-seq

first: Bi

last: Lian

first: Tianxiao

last: Huang

first: Wei

first: Pengfei

last: Jiang

first: Weiwei

last: Jin


title: Spatiotemporal regulation of target mRNA cleavage by 21-nt phasiRNAs in maize anthers [sRNA-seq]


title: mtTF1: A Novel Factor Involved in Mitochondrial Gene Expression in Trypanosoma brucei

city: Bern

first: Torsten

last: Ochsenreiter

state: Bern

address: Blatzerstrasse 4

department: Biology

country: Switzerland

institute: Institute of Cell Biology

summary: Mitochondrial DNA replication and gene expression are essential for cell survival. In Trypanosoma brucei, a protozoan animal and human parasite, the mitochondrial RNA polymerase (mtRNAP) plays roles in both transcription and DNA replication. This study identifies and characterizes the first mitochondrial transcription factor (mtTF1) in the Kinetoplastea. mtRNAP and mtTF1 form a high-molecular-weight complex that localizes to the kinetoplast DNA (kDNA) and is essential for parasite survival in both life cycle stages. Their localization is interdependent, and both proteins influence maxicircle replication, but not minicircle replication. Knockdown of either protein result in altered gene expression, particularly affecting the minor strand of the mitochondrial genome. Since mtTF1 is unique to the Kinetoplastea, it might prove to be a promising drug target.

overall_design: Study: AEKC-20231011 + AEKC-20250213; Libraries: AEKC-1-2 + AEKC-3-4; Run type: 2x150; Reference MK584625.1. fasta (T. brucei maxicircle sequence) and Tbrucei_EATRO1125.fasta (T. brucei minicircle sequence). Library ID and sample names: AEKC-1: mtRNAP_0d; AEKC-2: mtRNAP_2d; AEKC-3: mtTF1_0d and AEKC4: mtTF1_2d.

first: Bianca Manuela

last: Berger

first: Himaja

last: Manjunatha

first: Markus

last: Gerber


title: Presentation of immunoregulatory sialoglycans on T cells is divergent between mice and humans

city: Toronto

first: Haissi

address: 80 St George St

department: Chemistry

country: Canada

institute: University of Toronto

summary: Glycans are emerging as important regulators of T cell function but remain poorly characterized across the functionally distinct populations that exist in vivo. Here, we couple single-cell analysis technologies with soluble lectins and chemical probes to interrogate glycosylation patterns on major T cell populations across multiple mouse and human tissues. Our analysis focused on terminal glycan epitopes with immunomodulatory functions, including sialoglycan ligands for Siglecs. We demonstrate that glycosylation patterns are diverse across the resting murine T cell repertoire and dynamically remodelled in response to antigen-specific stimulation. Surprisingly, we find that human T cell populations do not share the same glycoprofiles or glycan remodelling dynamics as their murine counterparts. We show that these differences can be explained by divergent regulation of glycan biosynthesis pathways between the species. These results highlight fundamental glycophysiological differences between mouse and human T cells and reveal features that are critical to consider for glycan-targeted therapies.

overall_design: Low input total RNAseq, murine T cells sorted by SNA signal, CD4+ and CD8+ cells

first: Landon

last: Edgar

first: Fauzia

middle: N

last: Izzati

first: Hani

last: Choksi


title: Single-cell transcriptomic profile of innate cell populations in mesenteric lymph nodes of inflammatory bowel disease patients

city: Montreal

first: Laurence

last: Chapuy

state: QC

address: 3175 chemin de la Cote Sainte-Catherine

institute: Université de Montréal

summary: Innate immune cells, including dendritic cells (DCs), monocytes (Mono), macrophages (Mac), natural killer (NK) and innate lymphoid cells (ILC), contribute to chronic inflammation in lymphoid tissues. Here, we characterized the innate immune cell landscape in inflamed mesenteric lymph nodes (MLNs) of patients with inflammatory bowel diseases (IBD) at the single-cell level. CITE-seq analysis unveiled the molecular signature of 11 Mono/Mac/DC (MMDC) and 7 NK/ILC enriched clusters in human MLNs. DC clusters included 3 newly characterized DC clusters: CD1c/CD163/VCAN/CD64-expressing DC3; AXL-expressing DCs; and a CD103+ DC subset, expressing LTB, S100B, and IL22RA2 (encoding IL22BP). Mono/Mac clusters comprised inflammatory monocytes, which accumulated in IBD compared to non-IBD MLNs.  Among NK/ILC clusters, we identified a cytotoxic ILC subset (IL7R, KLRD1, GNLY), previously not reported in MLNs, reminiscent of cytotoxic ILC1-like cells found in inflamed gut mucosa.

overall_design: Surgically resected colonic MLNs were obtained from patients with Crohn’s disease (CD; n=3), ulcerative colitis (UC; n=3), non-inflamed UC (n=1) and non-IBD (n=2).  CD45+CD3-CD19- non-T/non-B cells were FACS-sorted to capture rare innate immune cells. Cellular Indexing of Transcriptomes and Epitopes by Sequencing (CITE-seq) was performed on the BD RhapsodyTM platform alongside multiparameter flow-cytometry staining.

first: Wils

last: Pauline

first: Habibi-Kavashkohie

last: Mohammad Reza

first: Sélos Guerra

last: Fabiana

first: Landais

last: Séverine

first: Rubio

last: Manuel

first: Mehta

last: Heena

first: Sarfati

last: Marika

first: Chapuy

last: Laurence


title: Spatiotemporal regulation of target mRNA cleavage by 21-nt phasiRNAs in maize anthers [RNA-seq]

first: Yijun

last: Qi

first: Bi

last: Lian

first: Tianxiao

last: Huang

first: Wei

first: Pengfei

last: Jiang

first: Weiwei

last: Jin


title: Endogenous hormonal dynamics and transcriptional regulations in internodal growth in Cunninghamia lanceolata: based on comparative analysis of two clones with different internode growing patterns

status: Public on May 25 2025

city: Fuzhou

first: Yu

last: Chen

state: Fujian

address: NO.15 Shangxiadian Road

institute: Fujian Agriculture and Forestry University

summary: Background Internodal characteristics are critical for cultivating knot-free Cunninghamia lanceolata, but limited knowledge of internode growing mechanisms has hindered breeding efforts for longer-internode types of C. lanceolata. In this study, we selected two clones with distinct internodal traits (C1 clone exhibited a 25.03% longer internodal length than C11) as materials. Enzyme-linked immunosorbent assay (ELISA) method and RNA-seq were used to investigate the changes in endogenous hormones and their associated transcriptional regulation during internodal growth and lateral bud formation. Result Our findings suggest that the differences in the dynamic rhythm of Indole-3-Acetic Acid (IAA) in apical buds are a key factor in C1's longer internodal growth. Specifically, IAA levels in C1 showed a significant decline at the S4 stage, which occurred later than in C11. Higher levels of IAA and cytokinins in the apical buds of C1 clone likely supported sustained internodal growth. The greater number of upregulated IAA-related genes in the upper phloem, including PIN1 and SAURs, which involved in polar transport and signal response, indicates a stronger capacity to establish apical dominance. The higher strigolactones (SLs) content, combined with IAA-driven apical dominance, delayed lateral bud emergence. Meanwhile, the lower brassinosteroids content and the high expression of brassinosteroid-activity-regulating genes such as UGT85A1 and BAS1 suggest that brassinosteroids (BRs) may serve as significant secondary hormonal signals promoting internodal growth. Weighted Gene Co-expression Network Analysis (WGCNA) further indicated that hormones transport may regulated by very-long-chain fatty acids (VLCFAs), coordinating both lateral bud emergence and internodal growth. Conclusion This study offers a preliminary understanding of the mechanisms behind internodal growth in C. lanceolata, providing insights for genetic control and germplasm selection in breeding, and serves as a guide for using exogenous hormone interventions to regulater internodal growth for cultivate of knot-free timber.

overall_design: RNA-seq profiling of the Apical Bud (AB), Upper Phloem (UP) and Lateral Bud (LB) tissues of two Chinese fir clones (C1 and C11) with obvious differences in growth and branching characteristics.

first: Chao

last: Wu

first: Fang-fang

last: Wang

last: Ma

first: Ling-peng

last: Ye

first: Shi-yan

last: Mu

first: Ya-ting

last: Yang

first: Xiao-yu

last: Qu

first: Ya-ling

last: Zhang

first: Shu-bin

last: Li

first: Shan-shan

last: Xu

first: Xiang-qing

first: Zong-ming

last: He

first: Si-zu

last: Lin

first: Guang-qiu

last: Cao


title: The multiple roles of PehC during Ralstonia solanacerum  infection

city: Wuhan

first: ying

last: yuan

address: No.1 Lion Mountain Street, Hongshan District

department: Molecular Building

institute: Huazhong Agricultural University

summary: Here, we identified PehC, a Ralstonia protein belonging to the glycoside hydrolase family 28 (GH28), triggers typical immune responses in tomato and related Solanaceae plants as a novel microbe-associated molecular pattern (MAMP).

overall_design: Two-weeks old tomato seedling roots treated with or without 10 μg/ml GST-PehC for 1 h and 6 h with four biological replicates were harvested.

first: Jingjing

last: Ke

first: Wanting

last: Zhu

first: Ying

last: Yuan

first: Bo


title: Hypergravity promotes osteoclast differentiation via UPR signaling pathway

city: Xi'an

first: Yazhen

address: 169 West Changle Road

institute: The Fourth Military Medical University

summary: To investigate the effect of hypergravity stress on osteogenesis and osteoclast, we put the BMDM and BMSCs of mice treated with hypergravity  perform transcriptome analysis.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for hypergravity mice and the control mice.

first: Yuan

last: Jiang

first: Kang

last: Tang

first: Yue

last: Fu


title: RNA-seq analysis of the abdomens from fat body-specific BuGZ-overexpressing and control flies following 24 hours of starvation

city: Chengdu

first: Tingting

last: Jia

state: None Selected

address: No. 37, Guoxue Street, Chengdu, Sichuan, China

institute: West China Hospital of Sichuan University

summary: To investigate the role of BuGZ in metabolic regulation under nutrient stress, RNA-seq analysis was performed on the abdomens of fat body-specific BuGZ-overexpressing and control Drosophila after 24 hours of starvation. This approach aimed to identify differentially expressed genes and pathways potentially regulated by BuGZ in response to energy deprivation, providing insights into its function in lipid metabolism and stress adaptation.

overall_design: Fat body-specific BuGZ-overexpressing and control Drosophila were generated using the UAS-Gal4 system. Adult female flies were starved for 24 hours on water-soaked filter paper. Abdomens were dissected post-starvation, and total RNA was extracted for RNA-seq to assess transcriptional changes associated with BuGZ overexpression under nutrient stress.

first: Tingtinng

first: Shengyu

first: Shengye

first: Lu

first: Qian

first: Haiyang

last: Chen

first: Hao


title: The transcription factor HOXA9 induces expression of the chromatin modifier SMYD3 to drive leukemogenesis

city: Guangzhou

first: Liping

address: 54 S. Xianlie Road

institute: Sun Yat-sen University Zhongshan Ophthalmic Center

summary: Fusion oncogene MLL-AF9 initiates AML via downstream targets such as HOXA9. Drivers in the complicated settings of advanced AML, however, remain to be incompletely elucidated. Any factors to incur upregulation of the effector HOXA9 predictably aggravate the effect of DOT1L-mediated H3K79 methylation on HOXA9 expression in MLL-AF9-driven AML. In the present study, we identified that SET and MYND domain-containing protein 3 (SMYD3) was overexpressed in AML and predicted a poor prognosis for AML patients. Given that H3K4me3 typically activates the transcription of oncogenes, we hypothesized that SMYD3-catalyzed H3K4me3 may directly increase HOXA9 transcription, offering an additional regulation layer to HOXA9 gene transcription activation in MLL-AF9 AML. We tested this hypothesis and unveiled that SMYD3 is responsible for mediating H3K4me3 enrichment and for independently activating HOXA9 transcription. Transcription factor HOXA9 in turn bound to the promoter region of SMYD3 and enhanced its transcription. The resultant vicious circle of SMYD3-H3K4me3-HOXA9 exacerbated proliferation and blocked differentiation in both AML cell lines and primary cells fractionated from patients with AML. Combinational disruption of this loop and DOT1L inhibition led to enhanced anti-leukemia activity against MLL-AF9 AML in vitro and in vivo. In conclusion, our findings may advocate the current understanding regarding the underlying mechanism and offer SMYD3 as a promising intervention target to override the complicated settings in advanced AML.

overall_design: RNA-seq profiling of MOLM-13 cells stably expressing lentiviral Scramble or shRNA targeting two different fragments of SMYD3


title: Luteolin Modulates miRNA–mRNA Regulatory Networks to Attenuate TGF-β1-Induced Fibrogenesis: Insights from Next-Generation Sequencing

status: Public on May 24 2025

city: Kaohsiung

first: Yu-Hsin

last: Tseng

address: No.100, Tzyou 1st Rd., Sanmin Dist.

department: Department of Pediatrics

country: Taiwan

institute: Kaohsiung Medical University Hospital

summary: Luteolin has demonstrated therapeutic potential against pulmonary fibrosis, yet the underlying miRNA-mediated regulatory mechanisms remain poorly defined. In this study, we employed next-generation sequencing to explore the effects of luteolin on TGF-β1-induced fibrogenesis in MRC5 cells, with a focus on miRNA–mRNA interactions. Real-time PCR analysis confirmed that luteolin pretreatment significantly suppressed TGF-β1-induced expression of key fibrotic markers, including TGFB1, ACTA2, COL1A1, and FN1, indicating a potent anti-fibrotic effect. Transcriptomic profiling revealed that luteolin reversed the expression of 692 genes dysregulated by TGF-β1, with functional enrichment analyses highlighting significant pathways related to cellular movement and localization. Furthermore, integrated miRNA–mRNA network analysis identified eight negatively correlated pairs potentially involved in these processes. These findings provide new insights into the anti-fibrotic mechanisms of luteolin and underscore the role of miRNA–mRNA regulatory networks in pulmonary fibrosis. This study enhances our molecular understanding of fibrogenesis and supports the potential of luteolin as a modulator of post-transcriptional gene regulation in fibrosis.

overall_design: RNA-seq and small RNA-seq of control, TGF-β1 treatment, and luteolin plus TGF-β1 treatment in MRC5 cell line.


title: DNA methylation profiling in thyroid cancer in Chinese population

city: Tianjin

first: xiangqian

last: zheng

address: Huan-hu-xi Road, He-xi District

department: Department of Thyroid and Neck Tumor

institute: Tianjin Medical University Cancer Institute and Hospital

type: Methylation profiling by high throughput sequencing

summary: Around 20-30% of Thyroid cancers are difficult to accurately diagnose with fine needle aspiration (FNA) due to their shared features with benign nodules. Although there are molecular tools to assist the diagnosis, such as the Afirma Gene Expression Classifier and ThyroSeqv3, which are the most widely used in the United States, however, these tests all show low positive predictive value and would lead to unnecessary removal of the thyroid in non-cancer patients. In addition, the prediction model of these tests is trained mainly based on the American population. Therefore, it is required to develop a highly accurate test for thyroid nodule diagnostic which could not only increase the PPV, and reduce the unnecessary surgeries, but also is based on Chinese population datasets. To overcome the potential overfitting issues of the prediction model, here we provide a function-guided DNA methylation biomarker selection method through multi-omics datasets. To develop a novel DNA methylation based diagnostic test for thyroid cancer, we characterized the genome-wide DNA methylation pattern in 49 malignant and benign fresh thyroid tissues by using Reduced Representation Bisulfite Sequencing (RRBS) analysis on a single nucleotide level. And we found a group of differentiated DNA methylation sites that could be used to distinguish thyroid cancer and benign tissues.

overall_design: We characterized the genome-wide DNA methylation pattern in 49 malignant and benign fresh thyroid tissues by using Reduced Representation Bisulfite Sequencing (RRBS) analysis on a single nucleotide level.

first: Xianhui

last: Ruan

first: Feng

last: Yang

first: Weijing

last: Hao

first: Xinwei

last: Yun

first: Dapeng

first: Jingzhu

last: Zhao

first: Xuan

last: Qin

first: Lei

last: Wang

first: Yi

last: Pan

first: Ming

last: Gao

first: Xiangqian

last: Zheng


title: Transcriptomic analyses reveal the potential regulators of the storage root skin color in sweetpotato

city: Xuzhou

first: Cen

middle: Ai

last: Zhang

address: No.2 Kunpeng

institute: Xuzhou Institute of Agricultural Sciences in Jiangsu Xuhuai District

summary: Sweetpotato (Ipomoea batatas (L.) Lam.) is an important storage root crop exhibiting diverse storage root skin and flesh colors across varieties. The storage root skin color (SRSC) is a vital commercial trait which significantly influences the marketability and consumer preference of sweetpotato. To clarify the regulatory mechanism of SRSC, the storage root of sweetpotato line M1-125 and its natural mutant were sampled and transcriptomic sequenced in this study.

overall_design: The wild type line M1-125  and its natural mutant MT were planted in the modern agricultural experimental farm of the Xuzhou sweetpotato research. The flesh and skin of their storge root were sampled with three biological replicates at 120 DAP (days after planting), then washed and cut into small pieces. All samples were immediately frozen in liquid nitrogen and subsequently stored at −80 °C for RNA extraction and library construction.Total RNA was prepared from flesh and root skin samples using TRIzol reagent kit (Invitrogen, Carlsbad, CA, USA). The concentration and integrity of RNA were measured by an Agilent 2100 bioanalyzer (Agilent Technologies, Palo Alto, CA, USA) and RNase-free agarose gel electrophoresis, respectively. Following the removal of rRNA using the Ribo-ZeroTM Magnetic Kit (Epicentre, Madison, WI, USA), the mRNA was enriched by Oligo (dT) beads. The completed mRNA was then used for library construction following the manufacturer’s protocol of NEBNext Ultra RNA Library Prep Kit for Illumina (NEB #7530, New England Biolabs, Ipswich, MA, USA).  All mRNA-seq libraries were sequenced on Illumina NovaSeq 6000 platform in Gene Denovo Biotechnology Company, Guangzhou, China.

first: Zhang

last: Aicen

first: Li

last: Qiang


title: A brain-to-lung signal controls pulmonary inflammatory responses

city: Hangzhou

first: Xiangming

last: Fang

address: 866 Yuhangtang Road, Xihu District, Hangzhou, Zhejiang Province, China

institute: Zhejiang University

summary: Immune cells in the lungs are considered a heterogeneous population in the context of pneumonia. We used single-cell RNA sequencing (scRNA-seq) to analyze the diversity of immune cells in the lungs under different severities of pneumonia. Additionally, we employed bulk RNA sequencing (bulk RNA-seq) to study the transcriptional changes of sorted macrophage subsets in the lungs after NE(Norepinephrine), LPS, and NE+LPS stimulation.

overall_design:
In this study, the samples were categorized into 'sham', 'mild', and 'severe' groups to reflect different severities of pneumonia in the mouse model. Specifically, 'sham' refers to the control group with no pneumonia, 'mild' represents mice with mild pneumonia symptoms, and 'severe' indicates mice with severe pneumonia symptoms. Pulmonary immune cells from these different severity groups were isolated using Fluorescence-activated cell sorting (FACS), based on the presence or absence of CD45, and analyzed using single-cell RNA sequencing (scRNA-seq).
For bulk RNA-seq, the sorted macrophages were divided into four groups: the control group, which received no treatment; the LPS-only group, which was treated with LPS for 3 hours; the Norepinephrine (NE)-only group, which was treated with Norepinephrine for 3 hours; and the final group, which was pretreated with Norepinephrine for 3 hours and subsequently treated with LPS for 3 hours.


title: 6K-plex RNA  CosMx data from DLBCL sections.

city: Houston

first: Michael

last: Green

address: 7455 Fannin St

institute: MD Anderson Cancer Center

summary: Diffuse large B-cell lymphomas (DLBCLs) are a common and heterogeneous group of mature B-cell malignancies that typically arise in lymph nodes; sites in which stromal and endothelial cells, antigen-presenting cells and other myeloid cells facilitate adaptive immune responses by T-cells and B-cells against pathogens. In this study, we have leveraged the spatial transcriptomic platform of CosMx together with CODEX imaging technology to investigate the spatial immunology and pathobiology of DLBCL.

overall_design: CosMxTM technology [CosMxTM Human Universal Cell Characterization RNA Panel (1000-plex) + 20 custom genes; Bruker Spatial, USA] was applied to  6 tissue microarrays (TMAs i.e, TMA DLBCL 1, TMA DLBCL 2, TMA DLBCL 3, TMA DLBCL 4, TMA DLBCL 5, TMA DLBCL 6  ) from excisional biopsies of 78 large B-cell lymphomas and 5 controls (4 tonsil, 1 lymph node). Large B-cell lymphomas included 66 DLBCL not otherwise specified (DLBCL NOS); 5 EBV+ DLBCL NOS; 4 T-cell/histiocyte-rich large B-cell lymphoma (TCHRBCL); 2 primary mediastinal large B-cell lymphoma (PMBCL); and 1 post-transplant lymphoproliferative disease (PTLD). Note: The raw data is common for all the samples in the corresponding TMA and the corresponding FOV for each sample has been described in the Supplementary File or can be requested from the contributor.

first: Atish

last: Kizhakeyil

first: Dai

last: Yibo


title: Histone H1 Variants Regulate Neurodevelopmental Transcriptional Programs in Autism and Schizophrenia with 16p11.2 CNV

city: Tel Aviv

first: Gil

last: Ast

state: Israel

address: Haim Levanon 55

country: Israel

institute: Tel Aviv University

summary: Neurodevelopmental disorders, including autism spectrum disorder (ASD) and schizophrenia (SCZ), involve widespread transcriptional dysregulation. Copy number variations (CNVs) at 16p11.2 are among the strongest genetic risk factors for ASD and SCZ, yet the molecular mechanisms by which these CNV contribute to neurodevelopmental pathology remain unclear. Here, we identify significant genetic associations between ASD susceptibility and the HIST1 histone gene cluster through genome-wide analysis. Transcriptomic profiling across multiple experimental systems—including postmortem human brain tissue, patient-derived neural progenitor cells (NPCs), neurons, and cerebral organoids—reveals consistently elevated expression of histone variants H1.2 and H1.5 in idiopathic ASD and in 16p11.2 CNV carriers with ASD or SCZ, but not in idiopathic SCZ or bipolar disorder. Functional assays demonstrate that dysregulated H1 expression disrupts networks involved in synaptic signalling, chromatin remodelling, and neural differentiation. Using a deep learning framework incorporating Variational Autoencoder (VAE) and SHAP-based feature importance, we uncover distinct regulatory pathways driven by H1 overexpression. Notably, this overexpression induces bidirectional transcriptional changes within the 16p11.2 locus, mirroring expression signatures of both deletions and duplications. Our findings establish H1.2 and H1.5 as key regulators of transcriptional programs in neurodevelopmental disorders, highlighting chromatin-mediated mechanisms underlying ASD and SCZ and their potential as biomarkers.

overall_design: Comparative gene expression analysis of RNA-seq data for WT SH-SY5Y and its KD and OE

first: Roni

last: Brudno

first: Dan

last: Askayo

first: Ronna

last: Shayevitch

first: Ifat

last: Keydar

first: Michal

last: Zmudjal-Olevson

first: Galit

last: Lev-Maor


title: H3K27ac ChIP-seq and RNA-seq of papillary thyroid carcinoma patient's tissues and paired normal tissues

first: Xiukun

last: Hou

address: Huanhu Road

institute: Tianjin Cancer Institute and Hospital

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

overall_design: Refer to individual Series


title: H3 Acetylation and H2A.Z Levels Interplay to Regulate Gene Expression and Plant Development [RNA-seq]

city: Yangling

first: Su

middle: Ying

last: Pei

state: Shaanxi

address: No. 3 Taicheng Road

department: College of Life Sciences and Institute of Future Agriculture

institute: Northwest A&F University

summary: H2A.Z is a conserved histone variant that plays essential roles in various DNA-templated processes across eukaryotes. H2A.Z and histone post-translational modifications (PTMs) exert a bidirectional and context-dependent influence on each other. Nevertheless, the functions of the interplay between PTMs and H2A.Z level and the underlying molecular mechanism remain poorly understood. Here, we found that the loss of the histone acetyltransferase GCN5 impedes the overexpression of BSU1 typically observed in nrp1-1 nrp2-2, accompanied by changes in H3 acetylation and H2A.Z levels. Interestingly, the increment in H2A.Z levels typical of nrp1-1 nrp2-2 mutant alleviates the morphological and molecular phenotypes of gcn5. Conversely, H2A.Z-depleted mutants aggravate the phenotype of gcn5. In the gcn5 mutant, the H2A.Z level is globally reduced in the gene bodies, and this reduction is dependent on the histone chaperones NRP1 and NRP2. Additionally, the reduction of H3 acetylation levels caused by GCN5 depletion can be recovered in the nrp1-1 nrp2-2 mutant background, likely due to the over-accumulation of H2A.Z. In conclusion, our genetic, molecular, and genomic findings demonstrate that GCN5-mediated H3 acetylation promotes H2A.Z deposition, H2A.Z over-accumulation recovers the loss of GCN5-mediated H3 acetylation, and this interplay is crucial for regulating gene expression and plant development.

overall_design: RNA-Seq profiling of wildtype Columbia-0, along with gcn5-7, nrp1-1 nrp2-2 and gcn5-7 nrp1-1 nrp2-2 mutants at 12 days after germination (12DAG) seedlings.

first: Israel

last: Ausin

first: Yafei

last: Wang

first: Yingpei

last: Su

first: Qin

last: Hu

first: Weiye

last: Qian

first: Min

last: Liu

first: Chao

last: Xu

first: Junjie


title: Gene regulatory programs of NK cells show that NCAM1 (CD56) and KIRs are controlled by genetically polymorphic distal regulatory elements [scATAC-seq]

city: Columbus

first: Patrick

last: Collins

state: Ohio

address: 460 West 12th Avenue, Biomedical Research Tower 770

department: Microbial Infection and Immunity

institute: The Ohio State University

summary: Owing to their immunoprotective properties, natural killer (NK) cells are critical for the innate response to pathogens, as well as a new wave of cancer immunotherapy that harnesses natural cytotoxicity. We sought to understand the genetic and epigenetic drivers behind human specific NK cell receptors, so that we can better understand the underlying cellular function. Here, we present a transcriptomic, proteomic (CITE-seq), and chromatin (single nuclei ATAC-seq and Hi-C) analysis of human peripheral NK cell subsets, uncovering key regulatory programs governing NK cell differentiation. Through integrative multi-omics, we demonstrate that CD56bright versus CD56dim NK cell subsets have differential distal regulatory element (DRE) landscapes, with fewer accessible DREs in the CD56dim NK cells. We combine epigenetic, chromatin looping, and human genetic data to show mechanisms governing the NCAM1 (encoding CD56) and KIR loci. For example, we identify NCAM1 DREs that bind STAT in most NK cells, while identifying a genetic cohort that has motifs for binding repressive BLIMP1 at the DRE and resulting in less CD56 expression.  Together, our findings reveal novel epigenetic and transcriptomic systems for regulation of NK cells cytotoxicity and diversity, deepening our understanding of their function and how transcription factor networks govern CD56bright versus CD56dim phenotypes.

overall_design: Natural killer (NK) cells were isolated from peripheral blood mononuclear cells (PBMCs) using the RosetteSep™ Human NK Cell Enrichment Cocktail (STEMCELL Technologies). ). Following the addition of the cocktail, density gradient centrifugation was performed using Ficoll-Paque to separate enriched NK cells from the remaining blood components. This was performed on three different blood samples. Nuclei were isolated from NK cells and 10x Genomics snATAC-seq protocol was performed

first: Mariam

last: Salem

first: Aditi

last: Varkey

first: Matthew

middle: D

last: Estrada

first: Caprice

last: Eisele

first: Aharon

last: Freud

first: Bethany

middle: L

last: Mundy-Bosse


title: Endothelial KLF15/VASN axis inhibits angiogenesis via activation of Notch1 signaling [ATAC-Seq]

city: Shanghai

first: jia

last: zhang

address: Ruijin 2nd Road 197

institute: Shanghai Jiao Tong University School of Medicine Department of Hypertension

summary: Kruppel like factors (KLFs) are a subfamily of zinc finger proteins. As one of the family members, KLF15 can specifically bind to GC rich sequences on the promoter, thereby exerting transcriptional regulatory effects. Here we found that KLF15 negatively regulates angiogenesis in endothelial cells. KLF15 induces an increase in vasorin (VASN) expression, thereby activating the Notch signaling pathway and leading to a decrease in angiogenesis. These findings point to an KLF15/VASN axis as critical determinants of Notch signaling activation.

overall_design: ATAC-seq of endothelial cells transfected with control adenovirus or adenovirus carrying KLF15 gene

first: Xiao-Dong

last: Li

first: Ping-Jin

last: Gao

first: Ji-Guang

first: Jia

last: Zhang

first: Jia-Jia

last: Zhao


title: RNA-seq of control and TIA1-knockdown HMC3 cells

first: hong

last: yu

address: 2318 Yuhangtang Road

department: School of Pharmacy

institute: Hangzhou Normal University

summary: The study aims to utilize RNA-seq to characterize the transcriptomic alterations in TIA1-knockdown HMC3 cells compared to control cells, with the goal of identifying differentially expressed genes and elucidating the molecular pathways and biological processes regulated by TIA1, a key RNA-binding protein. By profiling gene expression changes following TIA1 depletion, the research seeks to uncover how this protein influences cellular functions in HMC3 cells, a model of human microglia critical for central nervous system immunity and homeostasis. Given the established role of TIA1 in mRNA metabolism and its links to neurodegenerative disorders like amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD), this study holds relevance for understanding microglial gene regulatory mechanisms disrupted in disease contexts. Identifying TIA1-dependent transcriptomic signatures in HMC3 cells can provide insights into the functional consequences of TIA1 dysfunction in microglia, potentially revealing novel therapeutic targets or biomarkers for neurological diseases while advancing our understanding of RNA-mediated regulatory networks in immune cells of the brain.

overall_design: RNA - seq analysis was performed on wild - type HMC3 cells and their knockdown - derived cells (shTIA1). Samples were collected 4 hours after oxygen - glucose deprivation (OGD).

first: Yiming

first: Hong

last: Yu

first: Jianhong

last: Dong

first: Ying

last: Wang

first: Zhihui

last: Huang

first: Lipei


title: Screening lncRNAs that binding with catenin.

first: Hongyan

state: --- Select One ---

address: 253 Industrial Avenue middle, Haizhu District, Guangzhou

institute: Southern Medical University, Zhujiang hospital

summary: Because of its insensitivity to existing radiotherapy, namely chemotherapy and targeted treatments, triple-negative breast cancer (TNBC) remains a great challenge to overcome. Increasing evidence has indicated abnormal Wnt/β-catenin pathway activation in TNBC but not luminal or HER2+ breast cancer, and lncRNAs play a key role in a variety of cancers. Through lncRNA microarray profiling between activated and inactivated wnt/β-catenin pathway of TNBC tissues, lnc-WAL (wnt/β-catenin associated lncRNA; WAL) was selected as the top upregulated lncRNA in wnt/β-catenin pathway activation compared with the inactivation group. RIP-seq was used to compare the β-catenin and IgG groups, where lnc-WAL could interact with β-catenin. Clinically, increased lnc-WAL in TNBC tumor tissue was associated with shorter survival. lnc-WAL promoted EMT, the proliferation, migration and invasion of breast cancer stem cells (BCSCs), and TNBC cells. Mechanistically, lnc-WAL inhibited β-catenin protein degradation via Axin-mediated phosphorylation at serine 45. Subsequently, β-catenin accumulated in the nucleus and activated the target genes. Importantly, wnt/β-catenin pathway activation stimulated the transcription of lnc-WAL. These results pointed to a master regulatory role of lnc-WAL/Axin/β-catenin in the malignant progression of TNBC. Our findings provide important clinical translational evidence that lnc-WAL may be a potential therapeutic target against TNBC.

overall_design: RNA of catenin IP was extracted from the MDA-MB-231 using phenol-alcohol, sheared to approximately 300-500 bp using a Covaris S220 instrument.


title: NR4A1 Expression Aberrations Contribute to Radiotherapy Resistance in Gastric Cancer

first: Peidong

last: Ni

address: 199 Jiefang South Road

department: General Surgery

institute: xuzhou central hospital

summary: The expression of NR4A1 was significantly reduced in radioresistant cells, namely MKN45-R and AGS-R, as opposed to their parental counterparts. Overexpressing NR4A1 in MKN45-R and AGS-R cells resulted in heightened sensitivity to radiation. Additionally, NR4A1 overexpression exerted inhibitory effects on the growth and metastasis of GC tissues in animal models following irradiation (IR). Our observations indicate that NR4A1 plays a crucial role in enhancing the radiation sensitivity of gastric cancer cells, underscoring the therapeutic potential of NR4A1 in GC treatment.

overall_design: RNA-seq profiling of radioresistant cells MKN45-R and their parental MKN45 cells.

first: Chuming

last: Zhu


title: Low-intensity pulsed ultrasound regulates Th17/Treg balance through the IL-1β/IL1R1/MyD88 signaling pathway to alleviate pelvic pain in a rat prostatitis model

city: Hefei

first: Wang

last: Zhou

address: Mozitan Road

institute: Anhui

summary: In this study, we looked examined how CP/CPPS rats responded to pain when treated with LIPUS of varying intensities and durations.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for prostate tissues from CP/CPPS rat model treated with varying intensities of low-intensity pulsed ultrasound (LIPUS) to explore the molecular mechanisms affecting Th17/Treg balance and inflammatory signaling pathways.

first: Hexi

last: Du

first: Zicheng

first: Xiachuan

last: Qin

first: Bao

last: Tang

first: Xinan

last: Lv

first: Chaozhao

last: Liang

first: Chaoxue


title: Single cell RNA sequencing of control and cecal ligation-and puncture mouse kidneys

status: Public on May 23 2025

city: Durham

first: Jamie

last: Privratsky

address: 303 Research Dr., Sands 101

department: Anesthesiology

institute: Duke University

summary: Differences in gene expression in kidney cell clusters before and after sepsis

overall_design: Cecal ligation (1.5cm), puncture with 21g needle, and extrusion of ~1mm of fecal contents into peritoneum. Mice received imipenem/cilastatin at 6 and 18 hours along with fluid resuscitation. Mice harvested at 24 hours. Sham (control) mice received surgery and treatments but without ligation of cecum or extrusion of contents.

first: Steven

last: Crowley

first: Shintaro

last: Ide

first: Yanting

last: Chen

first: Hiroki

last: Kitai

first: Jiafa

last: Ren

first: Helene

last: Fradin

first: Xiaohan

last: Lu

first: Tomokazu

last: Souma


title: Targeting LRBA triggers CTLA4 degradation and antitumor immunity for cancer immunotherapy

first: Xiaolu

last: Ge

state: Shanghai

address: 650 Xinsongjiang Road

institute: Shanghai General Hospital

summary: The lipopolysaccharide-responsive beige-like anchor protein (LRBA) deficiency causes severe autoimmune diseases and cytotoxic T-lymphocyte-associated protein 4 (CTLA4) loss in humans. However, the impact of LRBA on antitumor immunity remains understudied. Here, we identified the role of LRBA in antitumor immunity and developed a novel immunotherapy  for cancers. Interestingly, LRBA was negatively associated with antitumor immunity in human patients. Using high-throughput screening and subsequent structure-based hit optimization, we discovered a small molecule LC427 that bound directly to LRBA, and selectively interfered with the LRBA-CTLA4 interaction. This mechanistically unique LC427 facilitated the lysosomal degradation of CTLA4, and bolstered survival and functions of activated T cells. Importantly, orally administrated LC427 increased tumor-infiltrating CD8+ T cells and displayed effective antitumor activity in tumorbearing mouse models. Notably, LC427 did not induce typical irAEs observed with immune checkpoint inhibitors in colitis models. Our study demonstrates that targeting LRBA offers a novel and effective strategy with a favorable safety profile, highlighting the potential of LRBA-based immunomodulatory therapies in the treatment of cancers.

overall_design: MC38 cells (2×105) were implanted in C57BL/6 female mice. Mice were treated with LC427 or not. On day 14, tumors from mice treated with LC427 or not were harvested. Then, tumor tissues were cut into pieces, followed by enzymatic digestion using 0.5 mg/mL collagenase type IV (Roche) and 100U/mL DNase I (Aladdin, China) solution, and were incubated on a shaker (300 rpm) for 30 minutes at 37℃. The digested tissues were homogenized by passage through a 70 μm filter and centrifuged for 15 minutes at 4℃ and 400g. The dead cells were removed from single-cell pellets using  the dead cell removal microbeads (Miltenyi, Germany) and CD45 positive cells were collected with CD45 MicroBeads (Miltenyi, Germany). The CD45 positive cells were  analyzed using scRNA-seq.

first: Liang

last: Yu

first: Lei

last: Zhang

first: Liqing

last: Jia

first: Mingjing

last: Meng

first: Jingquan

last: He

first: Fan

last: Bu

first: Yue

last: Song

first: Gaorui

last: Sun

first: Shiming

first: Desheng

last: Mei

first: Yutao

last: Yang

first: Dakang

last: Xu

first: Jingfa

first: Shengping

first: Chuangui

last: Wang

first: Deshui

last: Gao

first: Xiangliang

last: Yuan

first: Baokun


title: Brg1 defect causes aberrent nucleosome landscape and affects totipotency & pluripotency transcriptional factors binding during embryogenesis [MNase-Seq]

first: Xinyu

address: Siping Road 1239

institute: Tongji University

summary: Mammalian embryogenesis involves intricate epigenetic reprogramming and chromatin remodeling. In this study, we investigated the role of Brg1, a catalytic ATPase subunit of the SWI/SNF complex, in early embryonic development and mouse embryonic stem cell (mESC) pluripotency. By generating Smarca4 flox/flox Gdf9-Cre female mice to knockout Brg1 in MII oocytes and using CRISPR-Cas9 to knockout Brg1 in mESCs, we found that Brg1 deficiency led to multiple defects. In mouse embryos, maternal knockout of Brg1 caused reduced blastocyst formation, delayed development, elevated nucleosome occupancy at gene promoters, and dysregulation of zygotic genome activation (ZGA) genes, potentially due to disrupted binding of totipotency-related transcription factors (TFs). In mESCs, Brg1 knockout resulted in abnormal clone morphology, decreased pluripotency marker expression, and reduced cell proliferation. Brg1 affected pluripotency mainly by influencing the binding of pluripotency-related TFs such as Oct4 through enhancer accessibility. We identified those TFs as totipotency/pluripotency Brg1-dependent TFs. Overall, this study demonstrates the crucial role of Brg1 in ZGA and mESC identity maintenance in affecting specific TF binding on proximal and distal regulatory elements.

overall_design: RNA-seq, ULI-MNase-seq and ATAC-seq of mouse embryo and ESC. To get MII oocytes for ICSI, B6D2F1 or Smarca4flox/flox Gdf9 Cre C57BL/6 female mice (8–12-weeks old) were superovulated by injection with 7 IU each of pregnant mare serum gonadotropin (PMSG), followed by injection of 5 IU of human chorionic gonadotropin (hCG) (San-Sheng Pharmaceutical) 48 h later. Brg1 knockout R1 ES cell lines are generated by CRISPR-Cas9 technology targeting the exon 4 & 5 of Smarca4.

first: Qi

last: Shi

first: Chong

last: Li

first: Shaorong

first: Xiaoyu

last: Liu


title: Epigenetic remodeling via HDAC6 inhibition amplifies anti-tumoral immune responses in pediatric AML [ATAC-seq]

city: Düsseldorf

first: Julian

last: Schliehe-Diecks

address: Moorenstr. 5

country: Germany

institute: Uniklinik Düsseldorf

summary: Histone deacetylase 6 (HDAC6) has emerged as a promising therapeutic target in cancer due to its immunomodulatory effects. While its prognostic significance remains debated, we demonstrate that HDAC6 loss significantly impairs myeloid leukemia progression in vivo, despite having no functional impact on leukemia cell proliferation in vitro. Proteome and secretome profiling of HDAC6-knockout (KO) cells revealed upregulation of several immune-related modulators, including RNase T2, a tumor suppressor known to modulate the tumor microenvironment. RNase T2 upregulation upon HDAC6 loss was restricted to myeloid but not B-ALL cells. Pharmacological inhibition of HDAC6 recapitulated this phenotype, leading to RNase T2 upregulation in myeloid leukemia cells. ATAC-seq revealed increased chromatin accessibility of RNase T2 following HDAC6 loss, highlighting a functionally epigenetic regulatory contribution. Further functional assays conducted in an immunocompetent setting both ex vivo and in vivo demonstrated that HDAC6 inhibition sensitized murine AML cells to broad CD8+ T cell activation as evidenced by increased TNFα and CD107a expression. Consistently, in a syngeneic AML model, HDAC6 inhibition restricted AML cell growth. Moreover, an extended drug screening analysis identified Cytarabine and Clofarabine as significantly synergizing with HDAC6 inhibitor Ricolinostat in AML cell lines or pediatric patient derived PDX-AML cells, while showing limited synergy in ALL cell lines, PDX-ALL cells or healthy controls. These findings establish HDAC6 inhibition as a dual-modality therapeutic strategy in myeloid leukemia, enhancing both immune activation and chemosensitivity.

overall_design: ATAC-seq duplicates of K562 HDAC6 knock outs were compared to an empty vector control

first: Jia-Wey

last: Tu

first: Sanil

last: Bhatia


title: Clonal lineage tracing and parallel multiomics profiling reveal transcriptional diversification induced by ARID1A deficiency

city: Tokyo

first: Kenichi

last: Miyata

country: Japan

institute: JFCR

summary: Phenotypic heterogeneity among genetically identical cancer cells underpins tumor progression and therapy resistance. However, how epigenetic dysregulation drives such divergence remains unclear. Here, we introduce IMPACH, a scalable platform that integrates lineage tracing, genetic perturbation, and multimodal single-cell analysis. Applying IMPACH, we demonstrate that loss of epigenetic regulators—particularly ARID1A—enhances transcriptomic and epigenetic heterogeneity under controlled conditions. ARID1A deficiency promotes stochastic chromatin opening and induces an atypical gene expression program associated with poor clinical outcomes. Despite increased epigenetic randomness, chromatin changes remain localized to biologically meaningful regulatory elements, partially linked to SMARCA4 binding sites. These findings reveal that chromatin remodeling defects promote clonal diversification through both stochastic and constrained mechanisms. Given its scalability and versatility, IMPACH provides a powerful framework for dissecting how epigenetic perturbations shape cellular heterogeneity in cancer.

overall_design: shPseuMO-Tag constructs targeting ARID1A (two independent shRNAs: ARI3# and ARI4#) or a nontargeting control (SCR#) were introduced into BxPC3 cells. Following single-cell cloning and approximately 20 cell divisions, 28 clonal subpopulations were established (eight controls and 20 ARID1A knockdowns). Subsequently, all 28 clones were pooled into a single cellular mixture, and scRNA-seq and scATAC-seq were performed to minimize the batch effect while evaluating transcriptional variations within and across clones.

first: Reo

last: Maruyama


title: Epigenetic remodeling via HDAC6 inhibition amplifies anti-tumoral immune responses in pediatric AML [RNA-seq]

overall_design:
RNA-seq Triplicates of K562 HDAC6 knock outs were compared to a previously published empty vector controll (GSE208005;  GSM6329899, GSM6329900, GSM6329901). The data was processed simultaneously & analogue to the previous submission.

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