title: Spatial transcriptomic analysis of Yersinia pseudotuberculosis infected ileum reveals novel enterocyte transcriptional state and bacterial localization

city: Philadlephia

first: Daniel

last: Beiting

address: 380 S. University Avenue

institute: University of Pennsylvania

summary: The distal small intestine plays vital roles in host physiology by regulating nutrient and fluid homeostasis.  Despite being  impacted in Crohn’s disease and a major target for a range of infections, we know relatively little about the complexity of cellular responses and cell-cell communication in the ileum during infection.  Single cell and spatial transcriptomics have emerged as powerful technologies to study tissue complexity in the gut, but these tools have focused on the large intestine, in part due to the accessibility of this tissue for biopsies and its importance in cancer.  Here we present GutPath, an atlas of over 500,000 single cells that captures RNA and protein expression profiles for 91 cell states in the ileum across a range of model infectionsdiverse infectious archetypes.  We show that GutPath accurately captures established immune responses to infection while revealing pathogen-specific responses in enterocytes.  To highlight the discovery potential of this atlas, we identify a novel enterocyte cell state present during Yersinia pseudotuberculosis infection that is spatially linked to bacterial load and tissue pathology.  GutPath establishes a much-needed resource for the immunology community that will accelerate the study of the transcriptional diversity of cellular landscapes in the small intestine.          As part of the mouse ileum infection single cell and spatial transcriptomic atlas, GutPath (GutPath.org), these data provide Complete Genomics - Stereo-seq spatially resolved transcriptional information about the intestine during infection. Yersinia pseudotuberculosis is a natural enteric pathogen that can become systemic in mice and people. In this study, we evaluate the finding that enterocytes are uniquely altered by Yersinia pseudotuberculosis infection and investigate the role of pyogranuloma strcutures in the spatial distribution of enterocyte transcriptional states. These data using the species agnostic Omni platform of Complete Genomics profile host and bacterial RNA.

overall_design: A Yersinia pseudotuberculosis infected mice (5 days post infection) was used. 5 cm sections of the ileum from each mouse were Swiss rolled and fixed in 10% NB formalin before paraffin embedding andspatial transcriptomics. This FFPE block was sectioned and all protocols for OMNI STereoSeq by Complete Genomics were performed. Data were sequenced and analyzed.

first: Andrew

last: Hart

first: Suhas

last: Bobba

first: Bethan

last: Wallbank

first: Igor

last: Brodsky


title: IL-26-driven epigenetic remodelling promotes immune evasion in colorectal cancer

status: Public on Jun 19 2026

city: Bunkyo-ku

first: Yuta

last: Hasegawa

state: Tokyo

address: Hongo 2-1-1

department: Graduate School of Medicine

country: Japan

institute: Juntendo University

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Cancer cells acquire malignant traits through epigenetic remodeling driven by exposure to inflammatory secretomes within the tumor microenvironment. However, how immune-derived inflammatory factors regulate cancer cell epigenetics remains poorly understood. Here, we show that IL-26 produced by tumor-specific type 17 T cells acts as a key mediator that induces epigenetic reprogramming associated with cancer malignancy. We identify a selective accumulation of IL-26–expressing T cells in tumors resistant to immune checkpoint blockade therapy in colorectal cancer. Notably, IL-26 functioned as a noncanonical cytokine by translocating into the nucleus of tumor cells, where it directly bound the transcription factor STAT1 and formed transcriptional complexes with NF-κB and AP-1. Nuclear IL-26 further induced a transcriptionally active chromatin state characterized by enrichment of BRD4 and H3K27ac, resulting in robust upregulation of CXCL chemokines. This process promoted excessive neutrophil infiltration and enhanced immune evasion and tumor progression through suppression of CD8+ T cell responses. Together, these findings support a conceptual model in which tumor-specific type 17 T cells directly reprogram cancer cell epigenetics through IL-26, thereby reshaping the tumor immune microenvironment to promote immune evasion.

overall_design: COLO205 colorectal cancer cells were left unstimulated or stimulated with IL-26, TNF-α, and IL-1β, with or without JQ1 treatment, to investigate IL-26-dependent chromatin remodeling. ChIP-seq was performed for H3K27ac and BRD4 across the indicated treatment conditions. Libraries were sequenced as paired-end reads using an Illumina NovaSeq X Plus platform.

first: Takumi

last: Itoh

first: Nao

last: Hosokawa


title: Genomic H3K36me2 enrichment profile for Vehicle or dimethyl fumarate-treated mouse bone marrow-derived neutrophil

city: Suzhou

first: Xiaoqin

last: Yang

state: Jiangsu

address: NO. 199 Renai Road

country: China

institute: Soochow University

summary: This study focuses on the epigenomics and transcriptomic changes driven by the GSK3B gene in colon cancer, offering valuable insights into tumor biology and its progression. Gaining a deeper understanding of these processes may contribute to developing more effective therapeutic strategies and enhance prognostic outcomes.

overall_design: Vehicle or dimethyl fumarate (DMF)-treated mouse bone marrow-derived neutrophil (BMDN) for 15 hours, then the ChIP-Seq was  performed to map the distribution of H3K36me2. The ChIP-Seq experiment was performed by Annoroad Gene Technology (Beijing) Co., Ltd.

first: Hua

last: Wu


title: The effect of Intestinal epithelial GSK3B loss on chromatin accessibility in the AOM/DSS-induced colon cancer model

overall_design: We generated conditional GSK3B knockout mice by specifically deleting GSK3B in the intestinal epithelium (Gsk3b IEC-/- mice). ATAC-Seq was performed on colon tumors of AOM/DSS-induced Gsk3b (IEC+/+) and Gsk3b (IEC-/-) mice by Seqhealth Technology Co., Ltd. (Wuhan, China).


title: Impact of GSK3B on genome-wide H3K27ac in colon cancer RKO cells

overall_design: To assess the effect of the GSK3B gene on genome-wide H3K27ac enrichment in colon cancer cells, H3K27ac ChIP-Seq was performed on the GSK3B-knockout (GSK3B/KO) and wild-type (GSK3B/WT) RKO cells by Shanghai Jiayin Biotech Co., Ltd. (Shanghai, China).


title: Impact of GSK3B on accessible chromatin regions in colon cancer RKO cells

overall_design: To assess the effect of the GSK3B gene on accessible chromatin regions in colon cancer, ATAC-Seq was performed on the GSK3B-knockout (GSK3B/KO) and wild-type (GSK3B/WT) RKO cells by CloudSeq Biotech Co., Ltd. (Shanghai, China).


title: Transcriptome change led by GSK3B knockout (KO) in colon cancer RKO cells

type: Expression profiling by high throughput sequencing

overall_design: To assess the transcriptome change driven by GSK3B level, RNA-Seq was performed on the GSK3B-knockout (GSK3B/KO) and wild-type (GSK3B/WT) RKO cells by Shanghai OE Biotech Co., Ltd. (Shanghai, China).


title: The scRNA-Seq analysis for the effect of Intestinal epithelial GSK3B loss in the AOM/DSS-induced colon cancer model

overall_design: scRNA-Seq was performed on colon cancer tissues of AOM/DSS-induced Gsk3b (IEC+/+) and Gsk3b (IEC-/-) mice by OE Biotech Co., Ltd. (Shanghai, China).


title: Autophagic flux blockade under hypocapnia reveals CO₂-sensitive regulation of autophagy-lysosome homeostasis

city: Houston

first: Jeanine

middle: L

last: Van Nostrand

state: TX

address: One Baylor Plaza M502C Van Nostrand

department: Molecular and Cellular Biology

country: USA

institute: Baylor College of Medicine, Houston

summary: Hypocapnia, a reduction in partial pressure of carbon dioxide (CO₂), commonly occurs in clinical contexts such as mechanical ventilation, panic disorder, and brain injury. However, its impact on cellular homeostasis remains poorly understood. Given the central role of autophagy in stress adaptation, we investigated how low CO₂ influences autophagic flux and lysosomal function. We found that hypocapnia induces autophagosome accumulation while impairing cargo degradation, indicating a blockade in autophagic flux. This response was accompanied by increased lysosome biogenesis yet, paradoxically, reduced lysosomal fusion and proteolytic activity. Mechanistically, hypocapnia promoted TFE3 dephosphorylation and nuclear translocation, driving transcriptional activation of the lysosomal program. Concurrently, suppressed AMPK activity and sustained mTOR signaling revealed a unique metabolic state, uncoupling energy stress from canonical autophagy signaling. As such, mTORC1/2 inhibition was capable of rescuing the impaired autophagy. Notably, increased pH was not sufficient to drive this program. These findings identify hypocapnia as a previously unrecognized modulator of autophagy that disrupts autophagosome-lysosome fusion and terminal degradation, positioning CO₂ tension as a critical regulator of cellular stress responses.

overall_design: Immortalized Mouse embryonic fibroblast cells were cultured in full media at 2% or 10% CO2 for 24 hours prior to collection

first: Naghmana

last: Ashraf

first: Zhen

last: Sun


title: DOT1L shapes ncPRC1-target gene repression to maintain cell identity of DLBCL [RNA-Seq]

city: Amsterdam

first: Rachele

last: Niccolai

address: Plesmanlaan 121

department: Tumor Biology and Immunology

country: Netherlands

institute: The Netherlands Cancer Institute

summary: Germinal center (GC) B cell-like diffuse large B cell lymphoma (GCB-DLBCL) depends on the cooperative activity of the histone methyltransferases DOT1L and EZH2 to maintain its pro-proliferative GCB cell identity while repressing plasma cell (PC) differentiation. To explore the mechanisms underlying the co-dependency between DOT1L and EZH2 in GCB-DLBCL, we performed an EZH2 inhibition (EZH2i)-anchored genome-wide CRISPR interference screen and identified multiple candidate genes encoding components of non-canonical (nc) PRC1 complexes, including USP7, KDM2B, RING1, and PCGF1. We identified USP7 as potential direct target of DOT1L, whose downregulation was associated with increased EZH2i sensitivity in multiple GCB-DLBCL cell lines. Furthermore, we observed that DOT1L influences the composition of chromatin-bound ncPRC1 complexes and regulates, in part, the deposition of H2AK119 monoubiquitination (H2AK119ub1) at gene promoters co-occupied by H3K27me3, here defined as PRC1/2 target genes. These PRC1/2 targets were specifically enriched in PC signature genes, whose derepression was associated with DOT1L inhibition (DOT1Li)-mediated loss of H2AK119ub1. This study reveals novel insights into the role of DOT1L and its functional co-dependence with EZH2 in maintaining GCB identity in DLBCL, supporting a model in which concurrent reduction of H2AK119ub1 and H3K27me3 promotes differentiation toward an anti-proliferative, plasma cell–like state.

overall_design: To investigate the effect of DOT1L and EZH2 inhibition on transcriptional changes, we treated four GCB-DLBCL cell lines for 6 days with DOT1L inhibitor (EPZ-5676) and EZH2 inhibitor (GSK343) as a single agent or in combination. The concentrations of both inhibitors were based on the maximal global loss of either H3K79me2 or H3K27me3, as determined by DOI: 10.1182/blood.2024025500

first: Camiel

last: Gobel

first: Sebastian

last: Gregoricchio


title: A long-read RNA sequencing and polysome profiling framework reveals transposable element–driven transcript diversity and translational rewiring in glioblastoma [polysome]

city: Providence

first: Mattia

last: Pizzagalli

state: RI

address: 593 Eddy St

department: Neurosurgery Department

institute: Rhode Island Hospital

summary: Transposable elements (TEs) account for over half of the human genome and are often derepressed in cancer. TEs can add cryptic splice sites, undergo exonization, and generate gene–TE fusion transcripts, but the combined effects of TEs on RNA processing and translation in glioblastoma stem cells (GSCs) remains incompletely elucidated. We combined long-read RNA sequencing with polysome profiling in four patient-derived GSCs and two neural stem cell (NSC) controls to resolve TE-associated transcript diversity and its relationship to ribosomal engagement. Across GSCs, we identified 13,421 alternative splicing (AS) events, 3,077 of which contained TEs within 150 bp of splice junctions. AS sites proximal to TEs were associated with increased isoform switching compared to non–TE-associated AS sites (odds ratio 2.9 - 4.3). Moreover, AS isoforms generated from TE-proximal sites were more likely to exhibit altered ribosomal association (odds ratio 2.54). Directional shifts were observed, with shorter isoforms associating with monosome fractions and longer isoforms with polysome fractions. To enable systematic detection of gene - TE chimeric transcripts, we developed FuTER (Fusion TE Reporter), a long-read–based framework for identifying TE-associated fusions. Application to GSC datasets identified 78 GSC enriched fusion transcripts, several supported by breakpoint-spanning reads in polysome fractions, consistent with ribosome association. Our data suggest that TEs correlate with abnormal splicing activity and altered ribosome engagement in glioblastoma stem cells. By integrating long-read sequencing with polysome profiling and fusion detection, we establish a framework for analysis of TE-induced transcript diversity and its effects on cancer evolution and plasticity.

overall_design: Polysome sequencing was performed on patient derived glioblastoma stem cells

first: Shiven

last: Sasipalli

first: Nikos

last: Tapinos


title: A long-read RNA sequencing and polysome profiling framework reveals transposable element–driven transcript diversity and translational rewiring in glioblastoma [LR]

overall_design: Oxford Nanopore long read RNA sequencing was performed on patient derived glioblastoma stem cells and neural stem cells grown as spheres for two days


title: Langerhans cells regulate immunity in adulthood by regulating dermal lymphatic development in early life

city: New york

first: Yurii

last: Chinenov

state: New York

address: 535 E 71 str, Hospital for Special Surgery

department: Research Division

institute: Hospital for special surgery

summary: The communication between skin and draining lymph nodes is crucial for immune responses to skin insults. Lymphatic vessels play critical roles in this communication by transporting antigens from skin to lymph nodes, and mechanisms that compromise dermal lymphatic function can disrupt immunity. Here, we show that Langerhans cells (LCs), epidermis-derived antigen-presenting cells, have a lymphatic-regulating role in promoting dermal lymphatic expansion and phenotype acquisition during early life. This function is mediated by PlGF and VEGF-C, and LCs have a large impact uniquely on the transcriptomic profile of lymphatic endothelial cells compared to other skin cells. Compromise of this early life LC-mediated lymphatic expansion results in reduced soluble antigen flow to draining lymph nodes and T cell responses in adulthood. Our data provide a tissue-based mechanism by which LCs regulate T cells remotely across time and space and raise the possibility that immune diseases in adulthood could reflect compromise of the LC-lymphatic axis in childhood.

overall_design: LECs, BECs, CD45+ cells, and CD45negCD31neg cells were sorted from of young WT, adult WT, and adult Lang-DTA skin and then combined the populations together at equal proportions.

first: Ji Hyun

last: Sim

first: Richard

last: Bell

first: Theresa

last: Lu


title: TRRAP enables MMB-dependent mitotic transcription and determines sensitivity to CHK1 inhibition

city: Wuerzburg

first: Stefan

last: Gaubatz

address: Am Hubland

department: Biochemistry and Cell Biology

country: Germany

institute: University of Wuerzburg

summary: The B-MYB-MuvB (MMB) complex is a key regulator of mitotic gene expression and is activated upon inhibition of the ATR-CHK1 pathway, resulting in premature mitotic entry, replication catastrophe, and cell death. Here we identify the transcriptional co-factor TRRAP as a critical regulator of MMB-dependent mitotic transcription. TRRAP physically interacts with B-MYB and is required for the expression of MMB target genes during both normal G2/M progression and CHK1-inhibitor-induced premature mitosis. These results identify TRRAP as a critical chromatin co-factor for MMB-driven mitotic transcription, linking chromatin regulation to checkpoint sensitivity and highlighting a potential vulnerability in cancer cells.

overall_design:
RNA-sequencing of S-phase synchronized A459 cells with degron-tagged TRRAP (mAID-TRRAP). Cells were control-trated, treated with the CHK1 inhibitor prexasertib, treated with 5-Ph-IAA to induce degradation of TRRAP or treated with 5-Ph-IAA and prexasertib.
CUT&RUN of A459 cells with degron-tagged TRRAP (mAID-TRRAP) for HA-tagged TRRAP and B-MYB (pT487). Cells were control-treated, treated with the CHK1 inhibitor prexasertib, treated with 5-Ph-IAA to induce degradation of TRRAP or treated with 5-Ph-IAA and prexasertib.

first: Franziska

last: Liss

first: Devi

last: Bala Murugan

first: Carsten

middle: P

last: Ade


title: RXR agonist increases newly characterized GM-CSF-producing B220+CD8αα interepithelial T cells

city: Wakayama

first: Yutaka

last: Nakamura

state: Wakayama

address: Shichi-bancho 25-1

department: Pharmaceutical Science

institute: Wakayama-Medical University

summary: Context-dependent cytokine granulocyte-macrophage colony-stimulating factor (GM-CSF) plays a crucial role in maintaining intestinal immune homeostasis and exacerbating inflammation. Although multiple cell types produce GM-CSF in the gut, whether intraepithelial lymphocytes (IELs) contribute to GM-CSF production during the steady state remains unclear. In the small intestinal epithelial layer, we identified B220-expressing CD8αα T cells that selectively produced GM-CSF but not interleukin-17A or interferon-gamma. Transcriptional analysis combined with weighted parametric gene set analysis revealed the upregulation of retinoid X receptor (RXR)-related genes in this population. Consistently, the RXR agonist bexarotene increased GM-CSF-producing B220+CD8αα T cells without affecting other cytokines or CD8αβ T cells. These findings identify B220+CD8αα IELs as a spatially distinct source of GM-CSF in the epithelial layer and indicate that the RXR pathway specifically facilitates GM-CSF-producing program, potentially contributing to maintaining immune homeostasis in the small intestine.

overall_design: RNA-sequencing profiles of B220+CD3ε+CD45+ and B220－CD3ε+CD45+ live cells sorted from epithelial area in the small intestine of C57BL/6J mice.

first: Shintaro

last: Sato


title: MPO/HOCl upregulates gene expression of mitophagy in murine macrophages

city: Nanjing

first: Chaorui

last: Guo

state: Jiang Su

address: Longmian Avenue No.639

institute: China Pharmaceutical University

summary: HOCl, the main product of myeloperoxidase in vivo, could induce extensive cell damage, however, how HOCl regulates gene transcription remains unclear. In this study, we treated murine macrophage cell line with different concentrations of HOCl to clarify the regulatory role of MPO on inflammatory environment. Results showed that HOCl could induce the upregulation of autophagy-related genes and extensive changes on mitochondria-related gene expression. These results were validated by other experiments, like RT-qPCR and WB. And we also observed that HOCl could induce colocalization of autophagosomes and mitochondria in confocal images, showing mitophagy. These results were consistent with in vivo experiments showing that macrophage mitophagy was MPO-dependent. One interesting result in our study was that the vehicle of HOCl treatment, HBSS, and the sublethal HOCl could also regulate macrophage function, which was mostly ignored by HOCl-related studies.

overall_design: RNA-seq profiling of murine macrophage J774A.1 cells treated with cell media and different concentrations of HOCl. Considering that HOCl could react with moleculs in cell media, HBSS was used as the vehicle control (0 µM HOCl). Both sublethal and lethal concentrations of HOCl were used.


title: Mycobacterium tuberculosis Co-opts Monocytic Niches to Evade Immunity in Lymph Nodes

city: Seattle

first: Urdahl

last: Lab

state: WA

address: 307 Westlake Ave North, Suite 500

institute: Seattle Childrens Research Institute

summary: Mycobacterium tuberculosis (Mtb) not only establishes lung infection but also disseminates to lung-draining lymph nodes (LNs), where it can persist long-term. Paradoxically, these same LNs are critical for initiating protective T cell responses that help control infection. To understand how these divergent outcomes coexist within the same tissue, we examined the spatiotemporal dynamics of myeloid and CD4 T cell responses in the mediastinal LN (medLN) of mice after aerosol Mtb infection and BCG vaccination. During early infection (2-3 weeks), Mtb disseminated to the medLN via conventional dendritic cells (cDC) and monocytes, which localized to the T cell zone and typically harbored single bacilli. This phase was marked by robust Th1 priming, driven by IL-12-producing cDC1 and type I IFN-induced inflammatory cDC2s. By 3-4 weeks, however, cDC migration declined and medLNs became dominated by large monocyte-derived aggregates containing multiple bacilli. These aggregates exhibited alternative activation profiles and coincided with reduced T cell priming and Th1 differentiation. Strikingly, Mtb-specific T cells appeared unable to engage these infected aggregates, suggesting immunological ‘blindness’ to this niche. BCG vaccination curtailed Mtb burden and limited monocyte aggregate formation in the medLN without significantly altering myeloid trafficking or T cell priming, suggesting that vaccination impairs the formation of the monocytic niche rather than initial dissemination. Together, these findings reveal a narrow temporal window for effective T cell priming in LNs and identify a later-arising monocytic niche that supports Mtb persistence while evading immune recognition, highlighting how spatially organized host-pathogen interactions govern both protection and persistence during tuberculosis.

overall_design: We performed single-cell RNA sequencing (scRNA-seq) on innate immune cells isolated from the mouse blood, lung, and medLN at early (day 15) and later (day 28) stages of standard dose (50-100 CFU) Mtb (H37Rv.mCherry) infection—two timepoints associated with distinct cellular and structural changes in the medLN. To establish tissue-specific baselines, we also included uninfected samples (day 0). To focus our analysis on infected versus bystander populations, we sorted both Mtb-infected (mCherry⁺) and uninfected (mCherry⁻) innate cells (CD11b⁺ or CD11c⁺, CD3⁻ B220⁻) from parenchymal (IV⁻) compartments of each organ. Blood samples were included given the monocytic predominance among infected cells. Following quality control filtering, 93,145 cells were retained for downstream analysis.

first: Elya

last: Shamskhou

first: Fergal

last: Duffy

first: Lauren

last: Cross

first: Vitaly

last: Ganusov

first: Courtney

last: Plumlee

first: Benjamin

last: Gern

first: Alan

last: Dierks

first: Sara

last: Cohen

first: Kevin

last: Urdahl

first: Michael

last: Gerner


title: GLP-1R agonist semaglutide protects developing human forebrain organoids from cholesterol-induced neurotoxicity—scRNA sequence

status: Public on Jun 20 2026

city: shenzhen

first: Yibo

last: Hou

state: State...

address: Guangdong province

institute: TsingHua university

summary: Neurological disorders are increasingly linked to disrupted lipid metabolism. The GLP-1R agonist semaglutide is well-established for improving systemic lipid profiles and is gaining attention for its clinical neuroprotective potential; however, the mechanisms underlying its direct action on neural cells remain poorly understood. Using hiPSC-derived forebrain organoids, we modeled cholesterol-induced metabolic stress to investigate direct drug-cell interactions. We show that semaglutide protects neural cells from lipotoxic injury. Intracellularly, GLP-1R activation engages the cAMP-PKA and PI3K-AKT-mTOR signaling, contributing to the reduction of lipid droplet and ROS levels. Intercellularly, single-cell transcriptomics indicates that semaglutide partially reestablishes disrupted cellular communication, including the Midkine signaling network associated with progenitor support. Functionally, semaglutide mitigates excitotoxicity and stabilizes calcium dynamics. In summary, these findings highlight the importance of cholesterol homeostasis during early brain development and suggest that GLP-1R signaling may represent a candidate neuroprotective axis in the central nervous system, offering insights into therapeutic strategies for neurological disorders.

overall_design: RNA-seq profile of human forebrain organoids with or without treatment of cholesterol or semaglutide

first: Shaohua

last: Ma

first: Feifei

last: Yu

first: Jiani

last: Xu

first: Honghui

last: Zheng


title: Effect of overexpression of LY6D on gene expression in L02 hepatocytes

city: Chongqing

first: Xiaohe

last: Luo

state: Chongqing

address: No. 165, Xincheng Road, Wanzhou District, Chongqing

department: Central lab

institute: Chongqing University Three Gorges Hospital

summary: To investigate the regulatory function of LY6D in NAFLD, we established a LY6D-overexpressing L02 cell line treated with FFAs.

overall_design: We then performed gene expression profiling using RNA-seq data from 2 different cells treated with the same concentration of FFAs.Comparative gene expression profiling analysis of RNA-seq data for L02 cells (LY6D-OE) treated with FFAs.

first: Qiurong

last: Zhao

first: Linxin

last: Chen


title: Small interfering RNA-mediated silencing of mutant NPM1 suppresses acute myeloid leukemia via reversing KAT7 and p300-mediated histone acetylation [CUT&Tag]

city: XIAMEN

first: Lanfen

state: Fujian Province

address: No.4221, Xiang'an South Roa

department: School of Life Sciences

institute: XIAMEN UNIVERSITY

summary: NPM1 mutation (NPM1c)-driven acute myeloid leukemia (AML) is characterized by the sequestration of nuclear proteins and chromatin hijacking. Current treatment strategies targeting NPM1c AML are often indirect, which might lead to toxicity and resistance. In this study, we developed an allele-specific siRNA that selectively silences NPM1c while preserving the function of wild-type NPM1. This approach inhibited proliferation and promoted myeloid differentiation in NPM1-mutated AML cells in vitro. Notably, the systemic delivery of chemically optimized siNPM1c via lipid nanoparticles (LNPs) significantly reduced leukemogenesis, and enhanced the therapeutic efficacy of the menin inhibitor revumenib and overcame its resistance in vivo. Mechanistically, NPM1c recruits KAT7 and p300, driving leukemogenic transcription and establishing a pathogenic acetylome and open chromatin state. KAT7 recruitment is crucial for the retention of this complex on chromatin. Targeting NPM1c with siRNA disrupts this interaction, reverses the oncogenic epigenetic landscape, and suppresses transcription. Our findings demonstrate that silencing NPM1c effectively suppresses AML by dismantling a pathogenic KAT7/p300-dependent acetylome, highlighting the potential of LNP‑delivered siNPM1c as a promising therapeutic strategy, either as a monotherapy or in combination with menin inhibition.

overall_design: NPM1c, H3K14Ac, H3K27Ac, KAT7 and p300 CUT&Tag profiles of OCI-AML3 cells after 3-day treatment with NPM1c siRNA or control.

first: Yongqiang

first: Yunzhi

last: Xing

first: Dawang

last: Zhou


title: Single-Nuclei RNA Sequencing Reveals Obesity-Driven Reprogramming of Estrogen Signaling in Endometrioid Adenocarcinoma

city: Detroit

first: Katherine

last: Gurdziel

state: MI

address: 275 E. Hancock

institute: Wayne State University

summary: Obesity is a major risk factor for endometrioid adenocarcinoma, but how it alters estrogen-driven signaling and tumor–immune dynamics remains unclear. To address this, we performed single-nuclei RNA sequencing on thirteen primary tumors from postmenopausal patients with normal and obese body mass indices. Tumors from obese patients exhibited widespread transcriptional remodeling across tumor and immune compartments. Notably, weighted gene correlation network analysis revealed that estrogen receptor–associated gene modules in tumors from obese patients were compositionally distinct from those in normal-weight patients, suggesting that estrogen may signal through alternative regulatory networks in the obese tumor microenvironment. Additional obesity-associated features included epithelial-to-mesenchymal transition, metabolic stress, immune suppression, and altered cell–cell communication. These findings demonstrate that obesity not only amplifies estrogenic signaling but may rewire its molecular context in tumor epithelial cells. Our work identifies mechanistic differences in hormone signaling linked to obesity and highlights pathways that may inform future strategies for therapeutic targeting in obesity-associated endometrial cancer.

overall_design: Fifteen endometrioid adenocarcinoma patient samples were obtained from the Karmanos Biobanking Core, including eight from obese patients and seven from patients with normal BMI. One sample from each group was excluded following quality control assessment, resulting in a final cohort of 13 samples.

first: Jessica

last: Long

first: Sophia

last: Agrusa

first: Sworna

last: Pukhrambam

first: Sanjeev

last: Ganesh

first: Mark

last: Gregory

first: Areebah

last: Qazi

first: Myegenet

last: Faris

first: Anna

last: Gottschlich

first: Ayesha

last: Alvero

first: Charlie

last: Fehl

first: Robert

middle: T

last: Morris

first: John

middle: J

last: Wallbillich

first: Heather

middle: M

last: Gibson

first: Julie

last: Boerner

first: Mike

middle: R

last: Wilson


title: An Optimized Methods for Reconstruction of Transcriptional Regulatory Networks in Bacteria Using ChIP-exo and RNA-seq Datasets [RNA-seq]

city: Ulsan

first: Donghyuk

last: Kim

address: 50 UNIST-gil, Eonyang-eup, Ulju-gun

department: Department of Chemical Engineering

country: South Korea

institute: UNIST

summary: We propose an optimized protocol to reconstruct bacterial transcriptional regulatory networks (TRNs) using ChIP-exo and RNA-seq datasets. For the reconstruction of TRNs, the omics datasets were targeted to RpoS and generated in Escherichia coli K-12 MG1655 cultured at mid-exponential phase in M9 glucose media.

overall_design: [RNA-seq] E. coli K-12 MG1655 cells and it derivates were grown to mid-exponential phage, cultured in M9 minimal 0.2% glucose with a biological replicate under 37°C with constant agitation.

first: Minchang

last: Jang

first: Joon

middle: Y

last: Park


title: The transcriptional regulatory landscape of LMO2 in tumor angiogenesis and breast cancer metastasis

city: Beijing

first: Yushu

last: Zou

address: 38 Xueyuan Rd

institute: Peking University

summary: To study the role of LMO2 in in human umbilical vein endothelial cells(Huvecs) and analyze the genes regualted by LMO2, we performed siRNA (3 replicates) of LMO2 and negative siRNA as control in Huvecs for deep sequencing.  Further more, to research the regualatory mechanism of LMO2. We use Chromatin Immunoprecipitation sequencing (ChIP) to find the genes bound with LMO2. In this way, we confirm LMO2 activates genes through binding genes and promotes cancer related functions.

overall_design: To investigate the role of LMO2 in tumor angiogenesis, we performed and analyzed ChIP-Seq in human umbilical vein endothelial cells (HUVECs), and preformed RNA-Seq in LMO2 knockdown and CT knockdown HUVECs to explore its mechanism and interaction.

first: Tinghong

last: Zhang

first: Dongyu

last: Zhao

first: Shu

last: Meng


title: An Integrated Transcriptomics Atlas of Healthy Human Skin Focusing on the Pilosebaceous Unit

city: Hamburg

first: Tolga

last: Düz

address: Beiersdorfstraße 1-9

institute: Beiersdorf AG

summary: Single-cell and spatial transcriptomics have transformed our ability to chart human tissue organization at unprecedented resolution. These technologies enable the construction of high-quality reference atlases, essential for mapping healthy tissue architecture and identifying robust gene markers. We developed a healthy Human Skin Cell Atlas (HSCA), systematically integrating 34 public datasets and totaling 819,068 cells, with curated metadata and harmonized cell type nomenclature to ensure consistency. We place particular emphasis on the pilosebaceous unit, a key epithelial structure critical for both homeostasis and pathology. While prior studies captured the interfollicular epidermis and immune landscape in detail, deeper hair follicle regions remained under-characterized. By leveraging high-resolution spatial transcriptomics (Visium HD), we spatially resolved and transcriptionally defined the lower hair follicle compartments and pinpointed important signalling hubs. Furthermore, the HSCA enables the detection of cell types not detectable in standalone datasets, such as Merkel cells. Our results illustrate the value of the integrated single-cell atlas and spatial data in refining tissue organization and highlight the PSU as a complex and diverse epithelial niche.

overall_design: Full-thickness human facial skin specimens from the temporal region were obtained from a healthy, 48-year-old White female undergoing facelift surgery, with written informed consent. The donor had a BMI of 22.2, low sun exposure, was a non-smoker, non-menopausal, used no hormonal contraception, and had no signs of baldness. Subcutaneous fat was removed, and the skin was cut into 6 × 8 mm pieces, embedded in OCT mounting medium, and frozen at –80 °C for seven months before sectioning two samples (designated D1 and D2) for Visium HD analysis.

first: Daniel

last: Torocsik

first: Sonia

last: Momnougui

first: Mhaned

last: Oubounyt

first: Benjamin

last: Al

first: Stefan

last: Gallinat

first: Jan

last: Baumbach

first: Nicholas

last: Holzscheck


title: Small interfering RNA-mediated silencing of mutant NPM1 suppresses acute myeloid leukemia via reversing KAT7 and p300-mediated histone acetylation [ATAC-seq]

first: Lanfen

last: Chen

overall_design: ATAC-seq of OCI-AML3 cells after 3-day treatment with NPM1c siRNA or control

first: Yongqiang

last: Hou

first: Yunzhi

last: Xing

first: Dawang

last: Zhou


title: Small interfering RNA-mediated silencing of mutant NPM1 suppresses acute myeloid leukemia via reversing KAT7 and p300-mediated histone acetylation [RNA-Seq]

overall_design: Transcriptional profiles of OCI-AML3 cells after 3-day treatment with NPM1c siRNA or control


title: Mammalian Methylation Array analysis of blood samples from Korean domestic dogs for epigenetic aging studies

city: Jinju-si

first: Jaemin

last: Kim

state: Gyeongsangnam-do

address: 501, Jinji-daero

institute: Gyeongsang National University

type: Methylation profiling by genome tiling array

summary: Genome-wide DNA methylation profiles were generated from whole blood of Korean companion dogs (n = 84) using the Illumina HorvathMammalMethylChip40 array. Samples cover a broad age range (0.58–14 years), both sexes, and multiple breeds. The dataset provides a resource for investigating age-associated CpG variation and epigenetic aging markers in domestic dogs.

platform_organism:
Homo sapiens
Mus musculus
Rattus norvegicus

overall_design: Peripheral whole blood samples were collected from Korean companion dogs (n = 84) covering a broad age range (0.58–14 years), both sexes, and multiple breeds. No technical replicates or external controls were included. Samples were analyzed to evaluate age-associated variation in DNA methylation and to derive epigenetic aging markers in the Korean dog population.

first: Subin

last: Jang

first: Seong Jun


title: ABCA4 Deletion and its effect on Photoreceptor Function

city: Oklahoma City

first: Rahul

last: Rajala

state: Oklahoma

address: 825 NE 13th Street

department: Cardiovascular Biology

institute: Oklahoma Medical Research Foundation

summary: ABCA4 is an ATP-binding cassette transporter expressed in photoreceptor cells, where it plays a critical role in the visual cycle by facilitating the clearance of all-trans-retinal derivatives from photoreceptor outer segment discs. Mutations in ABCA4 are implicated in inherited retinal degenerative diseases such as Stargardt disease, leading to the accumulation of toxic bisretinoids and progressive photoreceptor and retinal pigment epithelium (RPE) dysfunction. Although the role of ABCA4 in the visual cycle is well established, emerging studies have begun to explore broader implications of ABCA4 dysfunction on retinal homeostasis and disease mechanisms.  In the present study, we utilized Abca4⁻/⁻ mice to investigate the consequences of ABCA4 loss in photoreceptors and its impact on retinal structure and function using translating ribosome affinity purification (TRAP) followed by next-generation sequencing of photoreceptors RNA.

overall_design: Total tissue lysate and Rod-TRAP RNASeq data were collected from the retinas of 2-month-old littermate control mice (RiboTag;i75-Rod-Cre) and experimental ABCA4  knockout mice (RiboTag; Abca4-/-;i75-Rod-Cre).

first: Ammaji

first: Raju

middle: V


title: PRMT5 regulates splicing of detained introns from DNA damage repair genes to protect against replication stress.

city: Cambridge

first: Camille

last: Cushman

state: MA

address: 700 Main St

institute: Viska Bio

summary: Protein arginine methyltransferase 5 (PRMT5) catalyzes the formation of symmetric dimethyl arginine on a broad range of cellular targets, and PRMT5 inhibitors (PRMT5i) show drastic anti-proliferative effects in preclinical studies. Several models have been proposed to explain and predict sensitivity to PRMT5 inhibition including through p53 activation and DNA damage response regulation. Here, we interrogate the underlying mechanisms of PRMT5i sensitivity in Merkel cell carcinoma, a high-grade neuroendocrine carcinoma of the skin that is that is highly sensitive to p53 activation. We observed that although PRMT5 inhibition activated p53, p53 loss did not impact PRMT5i sensitivity. To identify critical pathways altered by PRMT5i, we conducted a genome-wide CRISPR/Cas9 screen and found that PRMT5i-treated cells have an increased dependency on splicing factors. Furthermore, proteomic analysis found that levels of mRNA splicing factors increased after PRMT5i treatment. Characterization of the transcriptome revealed a disruption in mRNA splicing of detained introns in both PRMT5i sensitive and resistant lines. We observed that basal levels of detained introns correlated with PRMT5 inhibitor sensitivity, and that PRMT5 was required to maintain genome integrity through ATR/CHK1 signaling. Our findings support a threshold model of genome stability, in which cells can tolerate an increase in detained introns until a point where DNA damage pathways are triggered, and cells undergo apoptosis.

overall_design: RNA-seq of MCC cell lines (WaGa, MKL-1, and MS-1) treated with PRMT5 inhibitor (JNJ-64619178) or DMSO (control) for 4 days in triplicate.

middle: H

first: Colin

middle: E

last: Fowler

first: Jacqueline

middle: A

last: Lees

first: James

last: DeCaprio

first: Jingwei

last: Cheng


title: Nicotinamide Riboside Enhances Adoptive T Cell Therapy by Promoting Memory Differentiation and Metabolic Fitness

city: Guangzhou

first: Lili

last: Yang

address: No. 135, Xingang West Road

institute: Sun Yat-sen University

summary: Enhancing the efficacy of adoptively transferred T cells is essential for successful immunotherapy. The cytotoxic activity of these T cells is closely related to their mitochondrial function, which plays a critical role in T cell differentiation. This study explored the potential of nicotinamide riboside (NR), known to enhance mitochondrial function, to improve the efficacy of adoptively transferred CD8+ T cells against hepatocellular carcinoma (HCC). In subcutaneous and metastatic HCC tumor models, NR treatment significantly improved the effectiveness of adoptive T-cell therapy (ACT). NR promoted the differentiation of CD44hiCD62Lhi central memory T cells (TCM) and upregulated memory-associated genes (Tcf7, Ccr7, and Foxo1). Upon restimulation, NR-treated CD8+ T cells exhibited strong recall responses, as evidenced by metabolic reprogramming and increased cytokine production. Furthermore, RNA sequencing revealed an increased expression of Foxo1 and its target genes. Inhibition of Foxo1 partially reversed the beneficial effects of NR on mitochondrial fitness and cytotoxic function, suggesting a role for Foxo1-associated pathways in mediating these effects.   In summary, NR improved mitochondrial fitness and promoted TCM differentiation, in part through a transcriptional program associated with Foxo1, thereby improving the efficacy of adoptive T-cell therapy. These findings identify NR as a promising and translatable metabolic adjuvant for HCC immunotherapy.

overall_design: Mouse OT-I CD8+ T cells were treated with nicotinamide riboside (NR, 500 μM) or vehicle control for 7 days, followed by transcriptome sequencing to identify differentially expressed genes and enriched signaling pathways.

first: Zhenfeng

last: Zhang

first: Nengzhi

last: Pang


title: Multi-modal single-cell sequencing reveals network transition in circulating monocytes that aligns with faster recovery in trauma patients and favors a response to M-CSF

city: Pittsburgh

first: Timothy

last: Billiar

state: PA

address: 200 Lothrop Street

department: Surgery

institute: University of Pittsburgh

summary: Previous transcriptomic studies to characterize the changes in circulating immune cells after major trauma in humans have demonstrated a dramatic early upregulation of inflammatory features and simultaneous downregulation of MHCII and IFN signaling pathways in monocytes; changes that gradually return to baseline. The magnitude and duration of these changes is associated with post-injury complications. To determine if unique immune cell subsets or features emerging in the subacute time frame associated with patient outcomes after severe injury, we applied DOGMA-seq (single-cell RNA + ATAC + ADT sequencing) on peripheral blood mononuclear cells isolated at day 3 after injury. Patients were segregated into slow or fast recovery from critical illness (8 patients/ group) and compared to age and sex matched healthy controls. An analysis that integrated all three single cell modes identified a subset of CD172a hi/MHCII hi, CD14+ monocytes overrepresented in patients that recovered faster and distinct from baseline monocytes.  This monocyte subset appeared prior to recovery and increased over time and was associated with changes in several key gene co-expression networks (referred to as a red-to-green network transition). A green-shifted pattern (associated with chemotaxis and cell adhesion) was overrepresented in fast recovery patients, continuously deviated from baseline, and specifically associated with increased accessibility of AP1 family motifs. In contrast, the red-shifted pattern (mainly pro-inflammatory genes) was associated with slow recovery, increased accessibility of CEBPB, less accessibility of IRF motifs, and gradually returned to baseline. Subsequent in vitro cell culture demonstrated that, compared to red-shifted cells, green shifted cells favored higher response to M-CSF-stimulated macrophage differentiation that included the upregulation of the genes involved in cell motility, while not obviously influenced the response to GM-CSF stimulation. Our findings add a new information layer to the current human paradigm for the immune response to injury, that includes the trauma-inducible features augmented along recovery leading to post-traumatic monocytes continuously different from baseline. The changes in circulating monocytes may have a wide influence on peripheral tissues via differentiated macrophages.

overall_design: We applied DOGMA-seq (single-cell RNA + ATAC + ADT sequencing) on peripheral blood mononuclear cells isolated at day 3 after injury. Patients were segregated into slow or fast recovery from critical illness (8 patients/ group) and compared to age and sex matched healthy controls.

first: Tianmeng

first: Julia

last: Hughes

last: Cornoy


title: Multi-modal single-cell sequencing reveals network transition in circulating monocytes that aligns with faster recovery in trauma patients and favors a response to M-CSF [scRNA-Seq]

overall_design: We enriched for monocytes from PBMC from the same four patients using flow sorting by deleting T and B lymphocytes (CD3+, CD19+) and subjected these cells to scRNA-seq (named D3D7 dataset). PBMCs from D3 and D7 from two trauma patients (MM5027 and MM5040) were cultured under three different conditions, including medium alone and medium with M-CSF or GM-CSF. The scRNA-seq dataset generated from this experiment is referred as Ma-Trauma.  Cells from two HC were cultured with or without GM-CSF or M-CSF, and subjected to scRNA-seq (Ma-healthy dataset).

first: Chen

last: Tianmeng

first: Hughes

last: Julia

first: Cornoy

first: Billiar

last: Timothy


title: SNP array for ABE- and Cas9-treated human zygotes as well as ABE treated embryos at fertilization

city: North Brunswick Township

first: Jia

last: Xu

state: NJ

address: 675 US Highway One

institute: Genomic Prediction, Inc.

summary: Donated human MII oocytes and zygotes were injected with ABE mRNA or RNP, or Cas9 RNP targeting indicated genes. The purpose of the experiment is to study DNA repair after base editing in preimplantation human embryos. Key findings are a lack of chromosomal aneuploidies in base editing samples, contrasting with the outcomes after Cas9 cleavage at the same sites. Off target base editing is highly gRNA dependent. Base editing is efficient, and lacks the genotoxicity of Cas9.

overall_design: SNP array for Cas9 treated human embryos

first: Dieter

last: Egli

first: Nathan

last: Treff

first: Diego

last: Marin


title: The m6A methylome is remodeled in Alkbh5 knockout spermatocytes from P18 males

city: Hangzhou

first: Long

last: Bai

state: Zhejiang

address: No. 268, Kaixuan Road

institute: Zhejiang University

type: Methylation profiling by high throughput sequencing

summary: The MeRIP-seq results showed that m6A was mainly detected in the 3’ untranslated regions (3’UTR) and near the exon stop codon. Meanwhile, m6A was confined to the consensus motif “RRACH” (R = G or A; H = A, C, or U). There were 3374 m6A peaks exhibit differentially changes in Alkbh5-null spermatocytes, including 1911 increased and 1463 decreased enrichments.

overall_design: To decipher the m6A methylome dynamics landscape in Alkbh5-null spermatocytes, the m6A-methylated RNA immunoprecipitation sequencing (MeRIP-seq) on P18 testis from WT and Alkbh5-/- males were performed.

first: Qingqing

last: Chen

first: Yu

last: Xiang

first: Yimin

last: Zhu


title: ALKBH5 regulates transcriptomic changes from leptene/zygotene to pachytene/diplotene stages in spermatocytes

summary: ALKBH5-mediated m6A modification plays a determinant role in posttranscriptional RNA fate decision, including RNA degradation, splicing, and transport et.al. As expected, the transcriptome in Alkbh5-/- spermatocytes were completely altered compared with these in WT spermatocytes in both P12 and P18 males.

overall_design: To explore the function of ALKBH5 in spermatogenesis, we subjected testis from the P12 (mainly leptene/zygotene stages spermatocytes) and P18 (mainly pachytene/diplotene stages spermatocytes) WT and Alkbh5-null males to RNA sequencing (RNA-seq)


title: Co-translational profiling in the cardiac endothelium in response to LPS-induced inflammation in female mice in vivo: a proof-of-concept approach

city: Chicago

first: Paul

middle: H.

last: Goldspink

state: IL

address: 909 S. Wolcott Ave

institute: University of Illinois Chicago

summary: Producing functional proteins involves multiple steps during mRNA translation on the ribosomes. However, co-translational regulatory mechanisms remain poorly characterized in intact mammalian systems. As a proof-of-concept, we developed a multi-omics approach to investigate endothelial-specific, co-translational regulation by modifying the translating ribosome affinity purification (TRAP) in vivo. We simultaneously co-immunoprecipitated (IP) polysome-associated mRNAs and proteins from the hearts of hemagglutinin-tagged ribosomal protein L22 mice (RiboTag) crossed with inducible endothelial-specific Cdh5CreERT2 mice (RiboTagEC). To perturb endothelial function, female mice were injected with E. coli lipopolysaccharide (LPS) (6 mg/Kg, i.p., 12 h). Hearts were homogenized, with ~ 10% used for input RNA-Seq and proteomics controls, and the remainder for IP of ribosome-bound polyadenylated mRNA and proteins. Endothelial cell transcripts (pecam1, cdh5) were enriched > 5-fold, while markers characteristic of other cell types were significantly depleted (< 0.05 q-value). We aligned transcriptomic and proteomic datasets (> 1250 overlapping terms) to identify pathways associated with concordant and discordant co-translational regulation. LPS was identified as the upstream regulator of the co-translational dataset that was concordantly regulated. Upregulated mRNAs but not proteins related to glycolysis were discordantly regulated. These findings validate our proof-of-concept multi-omics approach as a predictive platform for identifying disease-relevant pathways regulated at the co-translational level in vivo.

overall_design: A RiboTagEC mouse line (Rpl22HA/+/ Cdh5CreERT2) was used to investigate in-situ endothelial cell-specific and whole tissue changes using lipopolysaccharide (LPS) to model sepsis in mouse hearts. To study the effects of LPS, 8 female RiboTagEC mice were equally split into two groups, 4 receiving 6 mg/kg E. coli O111:B4 bacterial LPS (E, Experimental) and the other 4 receiving Saline (C, Control) treatment at a single time point (12 hours). Mouse hearts were immunoprecipitated (IP) to enrich endothelial-specific cells (EC), while a portion of the whole heart homogenate was not immunoprecipitated and served as an input or Pre-IP EC control. Gene expression analysis of RNA-seq data where in all we had 4 groups, each consisting of 4 biological replicates. The four binary comparisons were IP LPS vs. IP Sal, IN LPS vs. IN Sal, IP Sal vs. IN Sal, and IP LPS vs. IN LPS.

first: Chad

last: Warren

first: Bhairavi

last: Swaminathan

first: Paulina

last: Langa

first: Stephanie

last: Villa

first: Walter

middle: C

last: Thompson

first: Magdalena

last: Chrzanowska

first: Jan

middle: K

last: Kitajewski

first: R. John

last: Solaro

first: Beata

last: Wolska


title: ATAC-seq analysis of RKO cells with combinatorial genetic perturbations of H1FX and GSK3B.

city: Suzhou

first: Xiaoqin

last: Yang

state: Jiangsu

address: NO. 199 Renai Road

institute: Soochow University

summary: This study focuses on the epigenomics and transcriptomic changes driven by the GSK3B gene in colon cancer, offering valuable insights into tumor biology and its progression. Gaining a deeper understanding of these processes may contribute to developing more effective therapeutic strategies and enhance prognostic outcomes.

overall_design: Endogenous H1FX was depleted in RKO cells, followed by reconstitution with either wild-type H1FX (H1FX/WT) or the mutant H1FX/S31A. These cells were then transfected with or without GSK3B, and ATAC-seq was performed to assess chromatin accessibility.

first: Hua

last: Wu


title: Transcriptome sequencing of palmitic acid-treated HepG2 cells upon intervention of curcumin or curcumin-copper complex

first: si

last: qin

institute: The Third Affiliated Hospital of Chongqing Medical University

summary: Globally, non-alcoholic fatty liver disease (NAFLD) poses a major risk to human health. The natural polyphenol curcumin (Cur) can act as a copper (Cu) transporter in a Cur-Cu complex for enhanced Cu cell loading, but the effects of such a complex on NAFLD remain unclear. HepG2 liver cancer cells were treated with palmitic acid (PA) to create an in-vitro NAFLD model. And the purpose of this study was to investigate the impacts of a Cur- Cu complex on this model, and its potential mechanisms and targets in the reduction of fatty-acid accumulation in HepG2 cells.

overall_design: We performed RNA expression profiling analysis using data obtained from RNA sequencing (RNA-seq) of PA-treated HepG2 cells with Cur alone or co-treated with Cur and CuCl2 for 12 h. For PA group, The HepG2 cells pre-treated with 750 μM for 24h. For PA-Cur group, the cells pre-treated with 750 μM for 24h, were then incubated with 20 μM Cur for 12 h. For PA-Cur-Cu group, the PA-treated HepG2 cells were co-treated with Cur (20 µM) and CuCl2 (5 µM) for 12 h. RNA-seq was performed on three replicates per condition.PA: PA-stimulated HepG2 cells, PA-Cur: Cur treated PA-stimulated HepG2 cells.PA–Cur-Cu: Cur-Cu treated PA-stimulated HepG2 cells

first: Si

last: Qin

first: Xiang

last: Li


title: Pyruvate Kinase M2 Regulates Photoreceptor Neuroprotection

first: Rahul

last: Rajala

summary: Pyruvate kinase M2 (PKM2) is a glycolytic enzyme and transcription co-activator that is expressed in cancer cells. Its role in tumor metabolism is not definitively established, but investigators have suggested that regulation of PKM2 activity can cause accumulation of glycolytic intermediates and increase flux through the pentose phosphate pathway. Recent evidence suggests that PKM2 also may have non-metabolic functions, including as a transcriptional co-activator in gene regulation. We reported previously that PKM2 is abundant in photoreceptor cells in mouse retinas. In the present study, we conditionally deleted PKM2 (rod-cre PKM2-KO) in rod photoreceptors and studied how PKM2 gene expression in rods.

overall_design: Total tissue lysate and Rod-TRAP RNASeq data were collected from the retinas of 2-week-old littermate control mice (RiboTag;Pkm2fl/+;i75-Rod-Cre) and experimental rod photoreceptor PKM2 knockout mice (RiboTag;Pkm2fl/fl;i75-Rod-Cre).

first: Ammaji

first: Raju


title: Impact of Conditional Knockout of Complement C3 and Sphingosine-1-Phosphate Receptor 1 (S1PR1) on Lung Metastasis in MMTV-PyMT Mice

city: Charleston

first: Alhaji

middle: Harune

last: Janneh

state: SC

address: 86 Jonathan Lucas Street

department: Biochemistry and Molecular Biology

institute: Medical University of South Carolina

summary: Recent evidence suggests that sphingosine-1-phosphate receptor 1 (S1PR1) modulates the intracellular complement system or the complosome to induce NLRP3 inflammasome formation and the release of IL-1β through caspase-1, thereby promoting tumor metastasis. Here, we examined the transcriptomic effects of S1PR1 and complement C3 conditional knockouts on lung metastasis in MMTV-PyMT Mice, a widely used model for studying mammary tumor progression and metastasis.

overall_design: Three different strains of mice were generated by breeding MMTV-PyMT mice with MMTV-Cre, MMTV-Cre;S1pr1fl/fl, and MMTV-Cre;C3Tdt strains. These three strains were named: 1) Wild-type= MMTV-Cre; MMTV-PyMT, 2) S1pr1 knockout= MMTV-Cre;S1pr1fl/fl; MMTV-PyMT, and 3) C3 knockout= MMTV-Cre;C3Tdt:MMTV-PyMT. After 4.5 months, the mice were sacrificed, and the lung tissue samples were collected from all three strains and stored immediately in an RNAlater stabilization solution. The total isolated RNA from these samples was sent to Novogene Corporation Inc. for RNA sequencing.


title: PEG3 function in trophoblast stem cells

city: Calgary

first: Myriam

last: Hemberger

state: Alberta

address: 3330 Hospital Drive NW

country: Canada

institute: University of Calgary

summary: Investigating the impact of Peg3 deletion on trophoblast stem cells.

overall_design:
Comparative gene expression profiling by RNA-seq analysis and DNA methylation profiling by meDIP-seq data in wild-type (WT) and Peg3 KO trophoblast stem cells.
Please note that the meDIP-seq data has no processed data files as the study's conclusion is based on BAM files (included as raw data).

first: C

last: Kokorudz

first: N

middle: N

last: Ballasy

first: B

last: Radford

first: W

last: Dean

first: M


title: RNA-seq and TrAEL-seq of Osimertinib-treated PC9 cells in specific cell cycle stages

status: Public on Jun 18 2026

first: Laura

last: Biggins

address: Babraham Research Campus

department: Bioinformatics

country: United Kingdom

institute: The Babraham Institute

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

overall_design: Refer to individual Series


title: Transcriptional regulation of disease-relevant microglial activation programs

city: San Francisco

first: Martin

last: Kampmann

state: CA

address: 675 Nelson Rising Lane

institute: University of California, San Francisco

summary: Microglia, the brain’s innate immune cells, can adopt a wide variety of activation states relevant to health and disease. Dysregulation of microglial activation occurs in numerous brain disorders, and driving or inhibiting specific states could be therapeutic. To discover regulators of microglia activation states, we conducted CRISPR interference screens in iPSC-derived microglia for inhibitors and activators of six microglial states. We characterized 31 regulators at the single-cell transcriptomic and cell-surface proteome level in two distinct iPSC-derived microglia models, uncovering new protein markers of relevant states. We functionally characterized several multi- state regulators. ZNF532 and PRDM1 knockdown drive disease-associated, lipid-rich signatures and enhance phagocytosis while showing opposing effects on antigen-presentation signatures. DNMT1 knockdown results in widespread loss of methylation, activating negative regulators of interferon signaling. These findings provide a framework to direct microglial activation to selectively enrich microglial activation states, define their functional outputs, and inform future therapies.

overall_design: A pool of sgRNAs in the CROP-seq vector pMK1334 targeting 31 genes was transduced into CRISPRi iPSCs. These cells were differentiated into microglia by doxycycline-induced expression of six microglia transcription factors (iTF-MG; Drager et al. Nat Neuro 2022) or by cytokine-directed differentiation (iMG, McQuade et al. Mol Neurodegen. 2018). Before generation of GEMs, microglia were stained with a custom CITE-seq library targeting ~180 surface proteins. Transcriptomes of ~20,000 Day 12 Microglia were obtained by 10X Chromium (v2). CITE-seq libraries were also amplified from the same cells. sgRNA-containing transcripts were additionally amplified to facilitate sgRNA assignment.

first: Amanda

last: McQuade

first: Reet

last: Mishra

first: Venus

last: Hagan

first: Weiwei

last: Liang

first: Peter

last: Colias

first: Vincent

last: Castillo

first: Bianca

last: Gonzalez

first: Justin

last: Lubin

first: Verena

last: Haage

first: Victoria

last: Marshe

first: Masashi

last: Fujita

first: Thomas

last: Ta

first: Layla

last: Gomes

first: Olivia

last: Teter

first: Xia

last: Han

first: Nathaniel

last: Robichaud

first: Sarah

last: Chasins

first: Jessica

last: Rexach

first: Philip

last: DeJager

first: James

last: Nuñez


title: Maternal Vitamin C Deficiency and Genetic Risk Factors Contribute to Congenital Malformations through Dysregulation of DNA Methylation. [CUT&Tag E8.5]

city: Leuven

first: Bernard

middle: Klaas

last: van der Veer

state: Vlaams-Brabant

address: Herestraat 49 - box 651

department: Deparment of Human Genetics

country: Belgium

institute: KU Leuven

summary: Maternal dietary insufficiencies can reshape the offspring epigenome during gestation, contributing to birth defects and developmental disorders. Vitamin C (VitC) is a critical co-factor for Ten-Eleven-Translocation (TET) DNA demethylases, but the impact of its deficiency on embryonic development remains unclear. Here, we show that insufficient maternal VitC combined with genetic susceptibility can give rise to congenital malformations, including neural tube defects (NTDs), through dysregulation of DNA methylation. We previously reported NTDs in Tet1 knockout (KO) mice at low penetrance in C57BL/6J (B6) congenic inbred strains, but at two- to three-fold higher rates when outbred or highly backcrossed (incipient congenic) on a 129S6.B6 background. Similarly, maternal VitC deficiency in L-gulonolactone oxidase (Gulo) KO mice, which like humans are unable to synthesize VitC, resulted in highly penetrant congenital malformations in non-inbred mice, during a vulnerable window coinciding with gastrulation. DNA hypermethylation is a signature of VitC-deprived 129S6.B6-Gulo-/- embryonic headfold tissues, being absent in B6 embryos which are grossly normal. In outbred Gulo-/- embryonic brains, genomic regions harboring hypermethylation – hallmarks of TET dysfunction - increased with the severity of embryonic pathologies. A moderate reduction in VitC status is sufficient to induce hypermethylated regions and cause NTDs. Severe embryonic defects in VitC-deprived embryos can be rescued by timely re-supplementation of VitC at the onset of gastrulation, which normalized DNA methylation at most loci. Our results suggest that promoting timely VitC supplementation by at-risk pregnant mothers may prevent many birth defects currently refractory to folic acid supplementation and enhance the “health-span” of future generations.

overall_design: WGBS in E8.5 headfolds, collected from B6 and 129S6.B6-Gulo<-/-> embryos, with or without VitC supplementation.

first: Kian

last: Koh


title: Hypoxia-preconditioned tendon stem cell-derived extracellular vesicles promote tendon regeneration by modulating macrophage heterogeneity

city: Hefei

first: Mingzhao

last: Zhang

state: Anhui

address: Jixi Rd

institute: The First Affiliated Hospital of Anhui Medical University

summary: Tendon injuries result in poor healing outcomes and functional impairment. Extracellular vesicles (EVs) derived from tendon stem cells (TSCs) have shown therapeutic potential for tendon regeneration. Because tendon tissues exist in a relatively hypoxic microenvironment under both physiological and injured conditions, we investigated whether hypoxic preconditioning could enhance the biological activity of TSC-derived EVs.  In this study, EVs were isolated from rat tendon stem cells cultured under normoxic (21% O₂) or hypoxic (1% O₂) conditions, referred to as EVs and Hypo-EVs, respectively. To explore the molecular mechanisms underlying macrophage regulation by Hypo-EVs, RAW264.7 macrophages were stimulated with lipopolysaccharide (LPS) to induce an M1 inflammatory phenotype and subsequently treated with Hypo-EVs or normoxic EVs. Total RNA was extracted and subjected to high-throughput RNA sequencing (RNA-seq).  The transcriptomic profiles generated in this study provide insights into the regulatory effects of hypoxia-preconditioned TSC-derived EVs on macrophage polarization and inflammatory signaling pathways during tendon repair.

overall_design: RAW264.7 macrophages were stimulated with lipopolysaccharide (LPS) to induce an inflammatory M1 phenotype and subsequently treated with normoxic tendon stem cell-derived extracellular vesicles (EVs) or hypoxia-preconditioned extracellular vesicles (Hypo-EVs). Total RNA was extracted from each group and subjected to RNA sequencing. Differential gene expression and pathway enrichment analyses were performed to identify molecular mechanisms associated with the enhanced immunomodulatory effects of Hypo-EVs.

first: Chenfeng

last: He


title: Microaerobic Copper Stress Redirects Pyruvate Metabolism and Reveals a CopL-linked Nitrogen Response in Staphylococcus aureus.

city: Leicester

first: Sean

middle: Cathal

last: Brennan

address: Univeristy Road

department: Division of Microbiology and Infection

institute: University of LEicester

summary: Copper is both an essential enzyme cofactor and an antimicrobial agent deployed by the host immune system to eradicate micro-organisms. The epidemic community-acquired methicillin-resistant Staphylococcus aureus (CA-MRSA) lineage USA300 carries mobile genetic elements that encode copX/B and copL, conferring hyper-resistance to copper, but the role of CopL beyond extracellular copper sequestration remains unclear. We have combined RNA sequencing with targeted metabolite assays under microaerobic conditions, more reflective of host environments, to define key copper induced responses in WT and copL mutant strains. Subinhibitory copper exposure in microaerobic conditions triggered a distinctive transcriptional response across multiple biological functions. Unlike previous studies, copper exposure did not induce an oxidative stress response. Instead, classical copper resistance, teichoic acid modification, immune-evasion factors and core metabolic genes were induced, while genes for stress responses, metal homeostasis and virulence were repressed. Gene set enrichment analysis (GSEA) identified regulation by multiple global regulators, e.g. SigB, CodY, CcpA, Agr and Sae. Copper exposure affected metabolism, redirecting pyruvate flux toward acetoin and lactate production rather than acetate, accompanied by coordinated shifts in TCA cycle and amino acid pathways, including glutamate accumulation. Inactivation of copL revealed a distinct adaptive response, with strong induction of nitrogen metabolism genes and nitrite reduction. Together, these data show that copper functions as a regulatory signal, triggering coordinated transcriptional and metabolic remodelling that potentiates S. aureus fitness in the host.

overall_design: RNAseq profiling of S. aureus USA300 JE2 wild-type and copL copper resistance lipoprotein mutant. Overnight cultures of S. aureus WT and copL strains were grown in RPMI-A for 16 hours at 37 °C in 5 % CO2. To collect and extract RNA, the bacteria were subcultured into fresh pre-warmed RPMI-A and grown to mid-exponential phase in the presence or absence of 100μM CuCl2. RNA was stabilised using RNAprotect Bacteria Reagent (Qiagen; 76104) according to the manufacturer’s instructions and were stored at -80°C.

first: Inderpreet

last: Kaur

first: Daniella

last: Spencer

first: Jo

last: Purves

first: Hannah

last: Sampson

first: Julian

last: Ketley

first: Joan

last: Geoghegan

first: Peter

middle: W

last: Andrew

first: Kevin

last: Waldron

first: Julie

last: Morrissey


title: Impact of Peg3 deletion in mouse trophoblast stem cells on H3K9me3 profiles

first: Ankita

last: Ankita

state: AB

address: 3330 Hospital Dr NW

department: Alberta Children’s Hospital Research Institute

summary: Peg3 is an imprinted gene that in itself is a KRAB zinc finger protein. We established knockout trophoblast stem cell lines (TSCs) in which we ablated the majority of the zinc finger motifs of the PEG3 coding region using CRISPR-Cas9-mediated deletion. We then profiled wild-type (WT) and knockout (KO) TSC lines for the genome-wide distribution of the epigenetic repressive mark H3K9me3 by ChIP-seq.

overall_design: Mouse trophoblast stem cells were grown in self-renewal conditions untile 80-90% confluent, then trypsinized and the pellet resuspended in Nuclei EZ Lysis Buffer. The subsequent ChIP procedure was performed as previously described (https://doi.org/10.1038/s41467-023-36019-9) using an antibody against H3K9me3 on Peg3 WT and KO mouse TSCs. Three independently derived WT and KO clones were used, and are grouped into WT rep1, WT rep2, WT rep3 and KO rep1, KO rep2, KO rep3.

first: Caroline

last: Kokorudz

first: Noura

last: Ballasy

first: Bethany

last: Radford

first: Anshul

middle: S

last: Jadli

first: Alexa

last: Krala

last: Narang

first: Wendy

last: Dean

first: Myriam

last: Hemberger


title: The effect of Intestinal epithelial GSK3B loss on transcriptomic profiles in the AOM/DSS-induced colon cancer model

first: Xiaoqin

last: Yang

overall_design: RNA-Seq was performed on colon cancer tissues of AOM/DSS-induced Gsk3b (IEC+/+) and Gsk3b (IEC-/-) mice by Jiayin Biotech Co., Ltd. (Shanghai, China).

first: Hua

last: Wu


title: The FGF4–integrin β1 axis restores directed collective migration to accelerate diabetic wound regeneration.

city: Wenzhou

first: Zhiming

last: Zhang

address: Chashan Campus of Wenzhou Medical University

institute: Department of Cardiology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, China

summary: This dataset was generated to investigate the mechanisms underlying the pro-healing effects of Fibroblast Growth Factor 4 (FGF4) on diabetic wounds. We performed RNA sequencing on wound tissues from streptozotocin (STZ)-induced diabetic mice. The mice received daily topical applications of either recombinant FGF4 (rFGF4) or PBS vehicle control. Wound tissues were harvested on day 7 post-wounding for transcriptomic analysis.

overall_design:
To investigate the effects of high glucose and FGF4 treatment, this study employed ChIP-seq to analyze the binding of C-FOS to the ITGB1 promoter in HacaT cells under low glucose, high glucose, and high glucose combined with FGF4 treatment conditions.
Please be advised that this batch of samples is different from the GSE318682 samples. These are newly prepared samples that we have re-submitted for sequencing, and they are not from the same batch as before.

first: Jian

last: Sun

first: Zhifeng

last: Huang

first: Jie

last: Zhou

first: Shuodan

last: Ding


title: Imeglimin Attenuates Skeletal Muscle Atrophy in Mouse Models of Obesity and Aging

city: Tokyo

first: Motoharu

last: Awazawa

state: - Select State/Region -

address: 1-21-1, Toyama, Shinjuku-ku

institute: Research Institutte, National Center for Global Health and Medicine (NCGM)

summary: Abstract Background Sarcopenia is a major contributor to frailty and mortality in aging and obesity and is tightly linked to metabolic dysfunction. Imeglimin is a first-in-class oral hypoglycemic agent targeting mitochondrial function; however, despite the central role of mitochondria in skeletal muscle homeostasis, its effects on skeletal muscle under sarcopenia-relevant conditions remain unclear. Methods Imeglimin was administered to male C57BL/6 mice with high-fat diet (HFD)–induced obesity for six weeks and to naturally aged (18-month-old) male mice for 12 weeks. Skeletal muscle fiber morphology and transcriptomic profiles were analyzed in fast- and slow-twitch muscles. In parallel, C2C12 myotubes were exposed to palmitate with or without imeglimin, and inflammatory gene expression and reactive oxygen species (ROS) generation were assessed. Results Imeglimin significantly increased the cross-sectional area (CSA) of Type II fibers in the extensor digitorum longus (EDL) muscle of HFD-fed mice (+66%, P < 0.01 vs. controls). Transcriptomic analyses revealed suppression of conserved molecular signatures of muscle atrophy, including activation of immediate-early genes and inflammatory pathways (-62 to -79%, P < 0.05 vs. HFD-fed mice). In palmitate-treated C2C12 myotubes, imeglimin attenuated lipotoxicity-induced inflammatory gene expression (-28 to -72%, P < 0.05 vs. controls) with reduced ROS generation, consistent with its cell-autonomous effect on myocytes. Notably, in naturally aged mice, 12-week imeglimin treatment preserved EDL muscle fiber size (+14%, P < 0.05 vs. controls) without altering systemic glucose tolerance, accompanied by transcriptomic changes overlapping with those observed in the HFD model (-27 to -82%, P < 0.05 vs. aged controls). Conclusions Imeglimin attenuates skeletal muscle atrophy in obesity and aging, accompanied by coordinated suppression of stress- and inflammation-associated transcriptional programs. These findings indicate that pharmacological regulation of mitochondrial stress responses influences skeletal muscle vulnerability under chronic metabolic stress and identify skeletal muscle as a previously underappreciated target of imeglimin action.

overall_design: RNAseq of EDL muscle from 24 week old lean control mice, high-fat-diet (HFD) fed obese mice and HFD-fed obese mice administered with imeglimin for 6 weeks.

first: Yangli

last: Ye

first: Diandian

last: Qian

first: Kohjiro

last: Ueki


title: Respiratory syncytial virus inhibits Type I Interferon signaling to maintain HLA-DM expression in CD1c + Dendritic cells

first: EnJun

state: California

address: 1 Letterman Drive, Suite D3500

institute: Parker Institute for Cancer Immunotherapy

summary: Respiratory Syncytial Virus (RSV) infection often elicits ineffective long-term immune responses due to inefficient immune priming, complicating disease management and vaccine development. Dendritic cells (DCs) play a pivotal role as initiators of immune responses and viral clearance. However, the direct impact of RSV on antigen presentation mechanisms remains poorly understood. In this study, we characterized the impact of RSV on blood DCs, revealing high HLA-DM expression- a unique phenotype closely associated with wider DC peptide repertoire but compromised T cell engagement during antigen presentation. We found inhibition of TBK1, a key kinase in Type I Interferon responses, restored antigen presenting capacities in RSV-infected DCs. This underscores the critical role of TBK1-mediated mechanisms in initiating adaptive immunity and downstream T cell responses during RSV infection. Our findings fill a significant knowledge gap in RSV pathogenesis, suggesting TBK1 as a potential molecular target for enhancing DC responses and immune protection against RSV.

overall_design: scRNAseq + Abseq on Dendritic Cells purified from PBMCs taken from 3 donors, stimulated with either RSV, heat killed RSV, or Flu Virus for 0h, 4h, 8h or 18h. Mock infected cells from the same were used as negative controls for each timepoint.

first: Weiyee

last: Ong

first: Richard

last: Hopkins

first: Novita

last: Novita

first: Najwa

last: Talib

first: Bijin

last: Au

first: John

last: Connolly


title: Integration of Transcriptional Signatures from Brain Tissue and Plasma Extracellular Vesicles of a Preclinical Tauopathy Mouse Model [EV ncRNA-Seq]

first: Iliya

last: Lefterov

address: 130 De Soto St

department: Environmental and Occupational Health

type: Non-coding RNA profiling by high throughput sequencing

summary: Tauopathies, including Alzheimer’s disease, involve progressive neurodegeneration and sustained neuroinflammation. We present a multi-compartment transcriptomic atlas of 9.6-month-old PS19 tauopathy mice compared with wild-type (WT) controls (n=8/group), profiling cortical mRNA, cortical non-coding RNA (ncRNA), and plasma small extra-cellular vesicle (pEV) ncRNA. In the PS19 cortex, mRNA sequencing identified 917 dif-ferentially expressed genes (DEGs), with microglial deconvolution revealing a robust transition toward disease-associated microglia (DAM) gene signature and downregulation of genes involved in oxidative phosphorylation and cholesterol biosynthesis relative to WT. Cortical ncRNA profiling identified 466 differentially expressed ncRNAs, primarily circular RNAs (circRNAs; n=331). In pEVs, 822 ncRNAs were differentially abundant, of which 657 circRNAs were identified in PS19 compared to WT mice. Cross-compartment integration demonstrated that pEV miRNA gene targets functionally mirrored genes involved in the brain’s inflammatory and metabolic failure. We identified a core shared signature of 33 ncRNAs, including miR-5114 (up in brain, down in pEV), circ_0008242 and circ_0002153 (up in brain and pEV), and circ_0007688 (down in brain and pEV) differ-entially enriched across both brain and periphery in PS19 compared to WT mice. These results demonstrate that the pEV non-coding landscape effectively tracks central tau-mediated changes in the brain transcriptional response. This study identifies circRNAs as the most numerically perturbed ncRNA class and provides a foundation for non-invasive biomarker development in tauopathy.

overall_design: We used preclinical tauopathy mouse model and by integrating transcriptomic data across central and peripheral compartments, we aimed to identify a convergent molecular signature with high fidelity for tracking the progression of tau-mediated neurodegeneration


title: Integration of Transcriptional Signatures from Brain Tissue and Plasma Extracellular Vesicles of a Preclinical Tauopathy Mouse Model [brain ncRNA-Seq]


title: DOT1L shapes ncPRC1-target gene repression to maintain cell identity of DLBCL [CUT&Tag]

city: Amsterdam

first: Rachele

last: Niccolai

address: Plesmanlaan 121

institute: The Netherlands Cancer Institute

summary: DOT1L inhibition leads to a loss of H2AK119ub1 in different GC B-DLBCL cell lines. To determine whether this loss is global or gene specific, performed H2AK119ub1 and H3K27me3 CUT&Tag in the Oci-Ly7 cell line following six days of treatment with DMSO or DOT1Li. As reference, we used a doxycycline-inducible knockdown of USP7 due to its role in ncPRC1-mediated deposition of H2AK119ub1 in Oci-Ly7 cells.

overall_design: CUT&Tag sequencing for the histone modification H3K27me3 and H2AK119ub1 in Oci-Ly7 cell line

first: Camiel

last: Gobel

first: Sebatian

last: Gregoricchio


title: Integration of Transcriptional Signatures from Brain Tissue and Plasma Extracellular Vesicles of a Preclinical Tauopathy Mouse Model

institute: University of Pittsburgh


title: Disease-associated RNA and protein signatures in iPSC-derived microglia model of Alzheimer’s disease

city: Galveston

first: Xiaoyong

last: Bao

state: TX

address: 301 University Boulevard

department: Pediatrics

institute: University of Texas Medical Branch

summary: Microglia, the primary immune cells of the brain, are essential for maintaining neural homeostasis. Dysfunction of microglia is strongly associated with neurodegenerative diseases, including Alzheimer’s disease (AD), yet the underlying molecular mechanisms remain incompletely understood. In this study, we compared microglia derived from induced pluripotent stem cells (iPSCs) of sporadic AD patients and healthy donors, identifying AD-associated alterations in mRNAs, proteins, and small non-coding RNAs (sncRNAs). Gene Ontology analysis of total RNA sequencing and proteomic data suggested significant dysregulation of pathways involved in extracellular communication, intracellular transport, cytoskeletal dynamics, and protein–protein interactions. Using a modified T4 PNK–sncRNA sequencing approach, we further identified disease-associated sncRNAs, including several previously uncharacterized species. Together, these findings highlight the utility of iPSC-derived microglia for modeling AD and uncover molecular alterations that may inform future therapeutic strategies.

overall_design: RNA sequencing (RNA-seq) and small noncoding RNA sequencing (sncRNA-seq) profiling of human microglia cells derived from induced pluripotent stem cells (iPSCs) obtained from sporadic Alzheimer's disease patients and healthy controls.

first: Wenzhe

last: Wu

first: Eun Seok

last: Choi

first: Luke

last: Liu

first: Veena

last: Thamilselvan

first: Le

last: Li

first: Meagan

middle: D

last: Rippee-Brooks

first: Kashish

last: Khatkar

first: Dar-Yin

first: Denise

last: McGrath

first: Aidan

last: Manning

first: Sergio

last: Barberan-Soler

first: Inhan

last: Lee

first: Yingxin

last: Zhao

first: Xiang

last: Fang


title: Signaling through RXRβ and its agonist, bexarotene, promotes neuron formation in Xenopus laevis embryos

city: Portsmouth

first: Colin

middle: Richard

last: Sharpe

state: Hampshire

address: King Henry Building, King Henry I Street

department: School of Environment and Life Sciences

institute: University of Portsmouth

summary: Retinoic acid, acting through RAR/RXR nuclear receptors, is required for neuronal differentiation in Xenopus laevis. Bexarotene, characterised as a pan-RXR agonist, reduces the symptoms of Alzheimer’s disease (AD) in mouse models by clearing amyloid plaque and by promoting neurogenesis. In this paper, we show that RXR-initiated bexarotene signaling generates additional neurons both during normal Xenopus laevis development and in ectodermal explants in which BMP- signaling is inhibited. Differential gene expression between ectodermal explants taken from uninjected and embryos co-injected with mRNA that expresses Noggin, a BMP antagonist, and RXRβ identifies genes mediating change from an epidermal to a neural fate. The explants express genes associated with an anterior neural, but not neuronal fate. The addition of bexarotene to equivalent co-injected explants activates genes that promote neuronal differentiation and posterior character, including genes of the canonical Wnt signaling pathway. Xenopus ectodermal explants therefore provide a simple and efficient tool to identify novel retinoid agonists that promote neuronal differentiation. The genes expressed in response to bexarotene are consistent with a pathway to neuronal differentiation allied to standard retinoid signalling.

overall_design: RNA-seq profiling of Xenopus laevis animal caps at the gastrula stage: 1 - untreated, 2 - co-injected with Noggin and RXRβ mRNA, and 3 - co-injected with Noggin, RXRβ mRNA treated with Bexarotene, to generate neurons.

first: Daniela

last: Lopes Cardoso

first: Marilena

last: Loizou

first: Danai

last: Fourla

first: Charles

last: Woodman

first: Matthew

middle: J

last: Guille


title: Loss of Rab44 Attenuates Ovalbumin-Induced Allergic Airway Inflammation by Modulating Immune Responses and Eosinophil Function

city: Nagasaki

first: Takayuki

last: Tsukuba

state: Nagasaki

address: 1-7-1 Sakamoto

department: Dental Pharmacology

institute: Nagasaki University

summary: Introduction: Asthma is a chronic inflammatory disease of the airways accompanied by mucus hypersecretion, airway remodeling, and bronchial hyperresponsiveness. However, the mechanisms by which membrane trafficking molecules contribute to the development of asthma remain unclear. In the present study, we investigated the role of Rab44 in a murine model of allergic airway inflammation mimicking human asthma, as we previously identified Rab44 and are exploring its function. Methods: Experimental allergic airway inflammation was induced in Rab44-knockout (KO) and wild type (WT) mice sensitized to ovalbumin (OVA). Histopathological analysis, RNA sequencing (RNA-seq) analysis, degranulation assays, adhesion and migration assays, and flow cytometric analysis of adhesion and chemokine receptors were performed. Results: Compared with WT mice, Rab44-KO mice exhibited impaired OVA-induced allergic airway inflammation. RNA-seq analysis revealed that Rab44 deficiency affected several signaling pathways involved in immune and inflammatory responses in the lungs of OVA-induced mice. Moreover, the mRNA levels of cytokines and the numbers of lymphocytes, monocytes, and eosinophils infiltrating the bronchoalveolar lavage fluid were decreased in KO mice compared with WT mice. In cultures of eosinophils derived from bone marrow cells, Rab44-KO eosinophils exhibited aberrant differentiation and impaired release of eosinophil peroxidase but not major basic protein. Rab44-KO eosinophils exhibited reduced cell adhesion and chemotaxis. Consistent with these findings, Rab44-KO eosinophils showed impaired surface expression of adhesion and chemokine receptors. Conclusion: These results indicate that Rab44 deficiency attenuates OVA-induced allergic airway inflammation by modulating immune responses and eosinophil function.

overall_design: RNA-seq analysis of altered genes in the lungs of normal and OVA-induced Wild type (WT) and Rab44-knockout (KO) mice

first: Haruka

last: Mawatari

first: Yu

last: Yamaguchi

first: Takao

last: Ayuse

first: Takuro

last: Sanuk

first: Tomoko

last: Kadowaki


title: Dietary Supplementation with Methionine and Lysine Enhances Antioxidant Function and Muscle Quality of Hefang Crucian Carp (Carassius auratus)

city: Changsha

first: Chen

last: Xiao

address: Lushan Road, Juzizhou Street, Yuelu District

institute: Hunan Normal University

summary: Methionine (Met) and lysine (Lys), as primary limiting amino acids, play important roles in regulating muscle quality in aquatic animals. This study investigated the effects of dietary Met and Lys supplementation on the growth performance, antioxidant function, and muscle quality of Hefang crucian carp (HCC) using physiological and transcriptome analysis. Fish were fed three diets for 8 weeks: a basal diet (LA) and two diets supplemented with DL-methionine at 1.7% (MA) and 3.4% (HA), respectively, with L-lysine supplementation fixed at 3.4%. The results indicated that dietary Met and Lys supplementation had no significant effect on the growth performance of HCC (P > 0.05), but significantly reduced serum triglyceride (TG) and cholesterol levels (T-CHO) (P < 0.05). Additionally, serum total protein (TP) content was significantly increased in the MA group (P < 0.05). Analysis of serum antioxidant enzyme activities indicated that appropriate Met and Lys supplementation improved antioxidant capacity and upregulated the expression of antioxidant-related genes (Nrf2, GPX1a, GSTO1, GSTP1) in the muscle. Moreover, the MA group exhibited superior muscle hardness and gumminess, while the HA group had higher springiness and chewiness (P <0.05). Muscle fiber density was significantly increased, whereas diameter and area showed the opposite trend in fish fed 1.7% Met and 3.4% Lys (P < 0.05). Furthermore, appropriate Met and Lys supplementation significantly affected muscle fiber development genes (MyoD, MyoG, and MRF4), with MyoG highest in the HA group and MyoD and MRF4 highest in the MA group (P < 0.05). Comparative transcriptomic analysis of muscle tissue showed DEGs functional enrichment primarily correlated with muscle quality, involving cardiac muscle contraction, actin cytoskeleton regulation, PPAR signaling pathway and ECM-receptor interaction. Taken together, our findings enhance the understanding of the molecular mechanisms underlying the effects of dietary Met and Lys on muscle quality in HCC, providing valuable insights for the development of nutritional strategies in the aquaculture industry.

overall_design: To further investigate the regulatory effects of dietary Met and Lys on the muscle gene network of Hefang Crucian Carp.Experimental diets were prepared by further supplementing the basal diet with different levels of Met (1.7% for MA and 3.4% for HA), while keeping the additional Lys supplementation constant at 3.4% for both MA and HA groups.After RNA extraction and purification, libraries were constructed from three bio-logical replicates per group (n = 3) and sequenced


title: The p.Ser143Pro lamin A/C mutation leads to dilated cardiomyopathy and activates the unfolded protein response pathway in a knock-in mouse model

city: Turku

first: Pekka

last: Taimen

address: Kiinanmyllynkatu 10D

department: Institute of Biomedicine

country: Finland

institute: University of Turku

summary: Dilated cardiomyopathy (DCM) is characterized by progressive ventricular dilation, systolic dysfunction, and an increased risk of arrythmias and sudden cardiac arrest. Variants in the LMNA gene, which encodesing for the nuclear lamins A and C, have been linked to familial form of the disease and the founder variant p.Ser143Pro is particularly common among Finnish DCM patients. To clarify elucidate the complex and poorly understood pathogenic mechanisms behind LMNA-related DCM, we generated a mouse model carrying the p.Ser143Pro mutation in the Lmna gene. All genetically modified mice appeared normal at birth. However, based on echocardiographyic, necropsy, B-type natriuretic peptide (Nppb) expression levels, and histopathological data, homozygous males developed progressive left ventricular dilatation, myocardial fibrosis, and cardiac failure after six months of age, with all succumbing before ten months. A reduced disease penetrance was observed in heterozygous male and homozygous female mice, with one-year survival rates of 40% and 60%, respectively. No signs of skeletal myopathy were observed in mice carrying the mutation. Whole-transcriptome RNA sequencing analysis of left ventricular cardiac tissue from asymptomatic two-month-old homozygous male mice revealed an upregulation of classical heart failure markers, such as atrial natriuretic peptide (Nppa ) and myosin heavy chain β (Myh7), and an elevated unfolded protein response signaling, as shown by elevated DNA damage-inducible transcript 3 (Ddit), Bcl-2-associated athanogene 3 (Bag3) and CCAAT/enhancer-binding protein beta (Cebpb) levels especially in the homozygous males compared to wild-type mice. In conclusion, p.Ser143Pro-Lmna mice closely mimic the clinical phenotype observed in patients with the p.Ser143Pro LMNA variant and offerserve as a valuablepotential in vivo model for investigatingstudying the underlying pathogenic mechanisms of LMNA-related DCM in greater detail.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: mRNA  sequencing of left ventricular cardiac tissue from 8-week-old homozygous and heterozygous p.S143P-Lmna male mice and wild-type littermates.

first: Fanny

last: Lindholm

first: Gun

last: West

first: Laura

last: Virtanen

last: Kähäri

first: Mia

last: Ståhle

first: Wail

last: Elnammas

first: Carl-Gustaf

last: Stenvall

first: Maria

last: Liivrand

first: Fu-Ping

last: Zhang

first: Petra

last: Sipilä

last: Gardberg

first: Diana

last: Toivola

first: Marko

last: Salmi

first: Antti

last: Saraste

first: Petteri

last: Rinne


title: Multi-site Assessment of Methods for Cell Preservation Upstream of Single Cell RNA Sequencing

city: Lebanon

first: Fred

middle: W.

last: Kolling IV

state: NH

address: 1 Medical Center Dr

department: Dartmouth Cancer Center

institute: Dartmouth College

summary: Single cell RNA sequencing (scRNA-seq) is a revolutionary technique to identify cell types and their molecular phenotype in heterogeneous biological specimens. ScRNA-seq typically requires fresh, high quality single cell suspensions that are processed immediately to preserve their molecular profiles. This presents a challenge for samples with long preparation times and prevents collection at remote sites lacking the required instrumentation for sample processing. Recently, several commercial assays have been released that enable sample preservation at the time of collection either via fixation or cryopreservation, allowing for sample processing to occur months after the initial collection. The Association of Biomolecular Research Facilities’ (ABRF) DNA Sequencing (DSRG) and Genomics Bioinformatics (GBiRG) Research Groups have undertaken a cross-platform, multi-site study to assess the performance and reproducibility of three platforms: a) 10x Genomics FLEX, b) Parse Bioscience Evercode WT v2 and c) Honeycomb Bio HIVE. Total leukocytes were isolated from a single healthy individual using the EasySep RBC depletion reagent. Cells were then characterized by collecting a 21-color flow cytometry dataset for reference and the remaining material was used for scRNA-seq procedures where different sites then processed either the fixed or cryopreserved cells for each method.  We evaluated performance of each method across traditional scRNA-seq quality control metrics and analysis applications, including gene/transcript detection sensitivity, cell type discovery and annotation, and differential expression. We demonstrate that data from the methods tested can be effectively integrated and produce concordant results with regard to cell type annotation and relative abundance, though we observe platform-specific differences in the expression of a subset of genes. Preservation-based methods also show better retention of fragile granulocyte populations compared with fresh samples processed using the 10x 3’ workflow. The improvements to preservation methods are changing the way research is conducted and our thorough investigation into the performance of each method provides a valuable resource to help scientists determine the most appropriate single cell preservation workflow given their sample collection logistics and laboratory infrastructure constraints.

overall_design: RBC-depleted total leukocytes or PBMCs isolated from a single human donor were either run fresh on 10x Genomics Chromium 3p, or preserved for 10x FELX, Parse or Honeycomb according to manufacturer's instructions. Samples were stored for up to 1mo and shipped to 4 separate sites for library preparation, and libraries shipped to a single site for sequencing.

first: Fred W.

last: Kolling

first: Jessica W.

last: Podnar

first: Owen

last: Wilkins

first: Claire J.

last: Fraser

first: Madolyn L.

last: MacDonald

first: Shawn W.

last: Polson

first: Zachary T.

last: Herbert

first: Sridar V.

last: Chittur

first: Andrew

last: Hayden

first: Marcy

last: Kuentzel

first: Michael

last: Heinz

first: Gabriella M.

last: Huerta

first: Holly S.

last: Stevenson

first: Aditi

last: Karmakar

first: Catrina

last: Fronick

first: Lisa

last: Cook

first: Sean

last: Vargas

first: Xiaoling

last: Xuei

first: Patrick

last: McGuire

first: Molly

last: Zeller

first: Yanping

first: Ru

last: Dai

first: Xinkun

last: Wang

first: Ching Man

last: Wai

first: Jyothi

last: Thimmapuram

first: Devender

last: Arora

first: Tania

last: Mesa

first: Jun

last: Fan

first: Yuriy O.

last: Alekseyev

first: Francis

last: Cervone

first: Christopher

last: Williams

first: Nickolas

last: Gorham

first: Alexander

last: Lemenze

first: Sara

last: Goodwin

first: Jonathan

last: Preall

first: Charles A.

last: Whittaker


title: Conserved anterior/posterior tissue asymmetry encodes proximal/distal positional information during axolotl limb regeneration

city: Dallas

last: Trostle

address: 6000 Harry Hines Blvd

institute: UT Southwestern

summary: The ability of mammals to regenerate missing limb structures is limited to the distal fingertip. In contrast, axolotls can regenerate entire limbs, offering a powerful model to uncover conserved patterning mechanisms. Axolotl limb regeneration requires the active deployment of molecular signaling pathways that re-create the anterior-posterior (A/P) axis. However, how A/P patterning is modulated across limb segments, and whether similar mechanisms operate in mammals, remains unclear. To address this, we performed spatial transcriptomic analyses on regenerating axolotl limbs using a newly developed SpatialFlux package. Interestingly, we found that A/P genes were expressed in an asymmetric fashion along the limbs proximal/distal (Pr/Di) axis in uninjured and regenerating axolotl limb tissues. This asymmetric A/P boundary aligns with the expression of AP-1 complex components and ERK signaling activation previously shown to be distally enriched in developing embryonic limb buds. Treatment of blastemas in different limb positions with an ERK inhibitor shows that ERK signaling is an upstream modulator of both distal and posterior limb patterning genes, linking the asymmetric A/P  boundary with the Pr/Di positioning of the blastema along the limb axis. These findings challenge the long-standing model of a symmetrical A/P midline boundary in limbs, offering clarity to findings that previously were incongruent with the midline boundary model. Here, we propose a revised asymmetric boundary model, in which shifting A/P ratios regulates Pr/Di patterning. Remarkably, this same pattern is observed in fetal human limbs, revealing a new, evolutionarily conserved paradigm for developmental and regenerative limb patterning.

overall_design: Axolotl limb regenerates are generated from uninjured contro tissue, pure anterior tissue, pure posterior tissue, and pure posterior tissue treated with ERK inhibitor (U0126)

first: Matthew

last: Cherubino

first: Robert

last: Tower

first: Catherine

last: McCusker


title: Pax9 governs anterior identity and deployment of sclerotome to the median fins

city: Cincinnati

first: Lindsey

last: Barske

state: OH

address: 3333 Burnet Ave MLC 7016

department: Human Genetics

institute: Cincinnati Children's Hospital Medical Center

summary: The caudal fin is an anomaly among vertebrate locomotory appendages: its internal skeleton is as asymmetric as the human hand, but it lacks the Shh-secreting Zone of Polarizing Activity (ZPA) and the Gli3/HoxD/Hand2 programs that govern anterior-posterior patterning in other appendages. As the caudal fin was also the first appendage to evolve, deciphering its alternative patterning program may provide clues to the ancestral state. Pax9 is one of few conserved appendage patterning factors reported to also be active in the caudal fin, specifically in the anterior domain. We report that loss of pax9 function in zebrafish not only disrupts anterior-specific caudal fin anatomy, but also results in a spectacular fusion of the caudal and anal fins along the ventral midline. The dorsal fin is also expanded to a lesser degree, the paired fins not at all. The mutant caudal fin initially forms as an irregularly patterned structure lacking anterior molecular identity, with supernumerary elements spilling out beyond the normal anterior boundary. Unexpectedly, this phenotype is subsequently compounded by neighboring trunk somites erroneously deploying skeletal mesenchyme in the normally finless caudal peduncle region, completing the ectopic skeleton. scRNAseq analysis at caudal fin bud stage indicates that pax9 mutants gain skeletal mesenchyme at the expense of a specialized type of fibroblast involved in the formation of fin fold actinotrichia. Median fin skeletal mesenchyme and fin fold fibroblasts both arise from the sclerotome, a somite compartment that also robustly expresses pax9. We propose that, within the sclerotome, Pax9 pushes progenitors towards fin fold fibroblast fate, limiting how many cells will later be available to make median fin skeleton. Within the fin bud, it drives anterior identity, with the strongest impact on the ZPA-free caudal fin bud. These dual sites of action make Pax9 a uniquely powerful governor of median fin development.

overall_design: Tails were microdissected from wild-type and closely related pax9^el622 mutant zebrafish larvae at 3 or 8 days post-fertilization (n = 75 per genotype/time point), dissociated, and submitted for scRNAseq on the 10x Genomics platform.

first: Sarah

last: McLeod

first: Melissa

last: Scott-Preusse

first: Sandhya

last: Paudel