title: Comparative single-cell multiomic analysis reveals evolutionarily conserved and species-specific cellular mechanisms mediating natural retinal aging

city: Baltimore

first: Pin

last: Lyu

address: 400 N Broadway

institute: JHU

summary: We performed integrated single-cell RNA- and ATAC-Seq analyses of the retina and retinal pigment epithelium (RPE) across the natural lifespan in zebrafish, mice, and humans. By profiling gene expression and chromatin accessibility, we identified extensive cell type- and species-specific aging-dependent changes, with a much smaller number of broadly expressed and conserved genes that include regulators of inflammation and autophagy. We constructed predictive aging clocks for retinal cell types and observed dynamic, reversible shifts in cellular age following acute injury. Spatial transcriptomic analysis revealed region-specific aging signatures and proximity effects, with Müller glia exhibiting pro-rejuvenative influences on neighboring neurons. Targeted Müller glia-specific induction of Yamanaka factors reduced molecular age in rod photoreceptors and bipolar cells without altering glial age. Our findings define conserved and divergent regulatory and signaling pathways mediating retinal aging, highlighting Müller glia as potential therapeutic targets for combating age-associated retinal degeneration.

overall_design: we generated mouse datasets by the Xenium 5k platform to analyze aging-dependent gene expression changes in the mouse retina in situ. This retina dataset consists of 4 ages of retina samples, at 5, 12, 55, and 112 weeks, and each age contains two sections (center and peripheral) from one male and one female. We directly tested whether constitutive, low level, Muller glia-specific expression of these factors resulted in rejuvenation of any retinal cell types, using the Muller glia-specific inducible Cre line GlastCreER 65 in conjunction with Cre-inducible rtTA and doxycycline-inducible Oct4, Sox2, Klf4, and mCherry. Doxycycline-treated retinas were analyzed using Xenium 5K spatial transcriptomics.

first: Isabella

last: Palazzo

first: Yang

last: Jin

first: Leah

last: Campbell

first: Clayton

middle: P

last: Santiago

first: Rogger

last: Carmen-Orozco

first: Thanh

last: Hoang

first: Jared

last: Tangemen

first: Alexander

middle: D

last: Park

first: Shawn

middle: H

last: Yang

first: Jianming

last: Shao

first: Rui

last: Chen

first: David

last: Hyde

first: Jiang

last: Qian

first: Seth

last: Blackshaw


title: SARS-CoV-2 NSP14 inhibitor exhibits potent antiviral activity and reverses NSP14-driven host modulation

status: Public on Sep 06 2025

city: Hangzhou

first: Wei

last: Xie

address: No. 866 Yuhangtang Road, West Lake District

country: China

institute: Zhejiang University

type: Expression profiling by high throughput sequencing

summary: The emergence of SARS-CoV-2 variants and drug-resistant mutants underscores the urgent need for novel antiviral therapeutics. SARS-CoV-2 NSP14, an N7-guanosine methyltransferase, plays a critical role in viral RNA capping, enabling viral replication and immune evasion. While NSP14 has emerged as a promising drug target, its role in host-virus crosstalk and the cellular consequences of NSP14 inhibition remain poorly understood. Here, we present the identification and characterization of C10, a highly potent and selective first-in-class non-nucleoside inhibitor of the NSP14 S-adenosylmethionine (SAM)-binding pocket. C10 demonstrates robust antiviral activity against SARS-CoV-2, including its variants, with EC50 values ranging from 64.03 to 301.9 nM, comparable to the FDA-approved drug remdesivir in our cell-based assays. C10 also exhibits broad-spectrum activity against other betacoronaviruses and directly suppresses SARS-CoV-2 genomic replication. C10 specifically reversed NSP14-mediated alterations in host transcriptome and restored host cell cycle progression disrupted by NSP14. The antiviral efficacy of C10 was further validated in a transgenic mouse model of SARS-CoV-2 infection. Our findings highlight C10 as a promising candidate for the development of effective treatments against SARS-CoV-2 and its emerging variants. This study also uncovers a novel mechanism of NSP14 in SARS-CoV-2 pathogenesis and its therapeutic potential, providing insights that may extend to other viral capping methyltransferases.

overall_design: NGS seqence of NSP14 in SARS-COV-2 resistance mutants

first: Mengxin

last: Luo


title: Bulk RNA sequencing for various tissues using SENCR-BAC transgenic mice

status: Public on Sep 05 2025

city: Chongqing

first: Qing

middle: Rex

last: Lyu

state: Chongqing

address: #118 Xingguang Avenue

department: Affiliated Chongqing General Hospital

institute: Chongqing University

summary: SENCR is a vascular-restricted long noncoding RNA specifically expressed in humans. To investigate its biological role in vivo, we generated a transgenic mouse line by introducing a ~220 kb genomic locus encompassing SENCR and its antisense neighbor FLI1, using a bacterial artificial chromosome (BAC clone: RP11-744N12) in combination with PiggyBAC technology. To assess whether SENCR-BAC mice recapitulate the human tissue-specific expression pattern, we collected multiple tissues, including the aorta, heart, brain, kidney, liver, lung, spleen, and stomach, and performed bulk RNA sequencing to evaluate SENCR expression levels across different tissues. The clean reads were mapped to genome using human genome database, but not mouse genome database, due to the objective of this experiment is focused on comparing the level of SENCR, which is human specific.

overall_design: The aorta, brain, heart, kidney, liver, lung, spleen, and stomach were collected in biological triplicates for bulk RNA-seq.

first: Yuyan

first: Songmao

last: Wang


title: Adipose-Specific GHR Knockout Confers Multidimensional Anti-Aging Advantages via Adipose Tissue Remodeling and Enhanced Metabolic Elasticity

city: Liaoning

last: Ma

address: No. 9, West Section of Lushun South Road, Dalian City, Liaoning Province

institute: Dalian Medical University

summary: The global growth hormone receptor knockout (GHR-/-) extends lifespan but causes adverse effects. Adipose tissue serves as a critical target organ for growth hormone (GH). Recent studies have suggested that GH signaling in adipose tissue influences aging progression, but the underlying regulatory mechanisms remain poorly understood. We generated adipose-specific GHR knockout mice (Ad-GHRKO; hereafter termed AKO) using 5-month-old and 20-month-old C57BL/6J males. The crucial function of adipose tissue GHR was examined by assessing age-related changes in mice during advanced aging. Adipose-specific GHR knockout extended healthspan through multifaceted geroprotection, manifested as significantly improved cognitive function, enhanced muscular/skeletal integrity, and a trend toward increased longevity. Mechanistically, adipose remodeling alleviated age-related lipid redistribution and restored glucose homeostasis, establishing a low-inflammation, high-plasticity depot that enhanced inter-tissue communication. Notably, we discovered that AKO mice exhibited significantly improved metabolic elasticity in adipose tissue. This enhancement is mechanistically linked to activation of the AMPK-SIRT1-Ac-PPARγ signaling axis. In vitro, pharmacological inhibition of AMPK abolished the beneficial effects of GHR ablation, confirming the central regulatory role of this pathway in maintaining adipose elasticity. These findings establish adipose GH signaling antagonism as a novel "metabolic elasticity switch" during aging, orchestrating adipose tissue to initiate reprogramming cascades that enhance metabolic elasticity and modulate healthspan through dynamic regulatory capacity rather than absolute activity levels, circumventing the adverse effects of systemic GH deficiency. These results resolve a critical knowledge gap in understanding how localized hormonal signaling in adipose tissue influences systemic aging trajectories. Our findings lay the foundation for developing targeted therapeutic strategies to mitigate age-related metabolic decline.

overall_design: RNA-seq analysis was performed on subcutaneous adipose tissue from 20-month-old Flox mice and 20-month-old Ad-GHRKO mice.

first: Li-yuan

last: Ran

first: Jin-yang

last: Geng

first: Jie

last: Liu

first: Bin

last: Liang

first: Li

last: Qiang

first: Ying-jie

last: Wu


title: Mechanistic dissection of GRHL2 and PR transcriptional co-regulation in breast cells

city: Amsterdam

first: Renee

last: van Amerongen

address: Science Park 904

department: Swammerdam Institute for Life Sciences

country: Netherlands

institute: University of Amsterdam

type: Genome binding/occupancy profiling by high throughput sequencing

summary: This dataset belongs to a study in which we functionally dissect the transcriptional co-regulation by grainyhead-like 2 (GRHL2) and progesterone receptor (PR, also referred to as PGR) in human breast cancer cells. As part of these efforts, we performed CUT&RUN in T47DS for endogenous GRHL2 and PR.  Gene expression is controlled by complex transcriptional networks in which transcription factors and their cognate enhancer elements integrate developmental and environmental cues. The progesterone receptor (PR), a hormone-activated transcription factor, is essential for breast development and physiology, yet how it engages with the chromatin and lineage-specific cofactors remains unclear. Using an unbiased approach, we identify the epithelial transcription factor grainyhead-like 2 (GRHL2) as a key co-regulator of PR activity in hormone responsive breast cancer cells. We show that GRHL2 interacts with PR in a progesterone-independent manner. Upon progesterone stimulation, GRHL2 and PR are both recruited to distal enhancer elements. Furthermore, GRHL2- and PR-bound elements connect spatially through chromatin looping to regulate shared targets. These findings uncover a previously unrecognized mechanism by which GRHL2 and PR coordinate gene regulation through both chromatin binding and 3D genome architecture modification, positioning GRHL2 as a crucial modulator of steroid hormone receptor function.

overall_design: CUT&RUN for PR, GRHL2 and IgG in T47DS cells either non-treated or 1nM R5020 treated for 4 hours.

first: Marleen

middle: T

last: Aarts

first: Anna

last: Nordin

first: Claudio

last: Cantù

first: Antonius

middle: L

last: van Boxtel

first: Renée


title: Atf3 Deficiency Promotes Mesodermal Commitment and Enhances Endothelial Differentiation in Embryonic Stem Cells

city: 厦门

first: DC

last: JZY

address: 福建省厦门市厦门大学翔安校区

institute: 无

summary: Ischemic disease has become a major threat to global health, and endothelial cells (ECs) damage is closely associated with its occurrence and development. Cell therapies to repair the endothelium has thus become a treatment approach of great interest, but obtaining clinically approved ECs for such therapies has not been fully established. One possible approach for obtaining ECs from stem cells may be by modulating activating transcription factor three (Atf3) expression; however, its precise involvement in ECs development and differentiation from stem cells remains unclear. In this study, we aimed to elucidate the potential role of Atf3 in embryonic stem cells (ESCs)-to-ECs differentiation.

overall_design: RNA was extracted from mESCs, on days 0, 3, 6, and 9 of differentiation, using TriZol, collected into 5 mL centrifuge tubes, and high-throughput RNA-seq was carried out by HaploX Biotechnology Co to establish a RNA-seq library. The original image files obtained were subjected to base identification and error filtering to obtain sequencing data. Filtered clean reads were compared to the mouse reference genome with HISAT2 software, thereby identifying unique mapped reads.

first: Zongyue

last: Jiang

first: Lide

last: Su

first: Cuiting

last: Chen

first: Ronghai

last: He

first: Lili

first: Yanyan

last: Shu

first: Dandan

last: Dai

first: Man

first: Ailing

last: Guo

first: Jianlei

first: Suhuan

first: Zonghong


title: IL-1β priming triggers an adaptive stress response that enhances pancreatic β-cell resilience to subsequent cytotoxic inflammatory insult

city: Pilar

first: Marcelo

middle: Javier

last: Perone

state: Buenos Aires

address: Av. Juan Domingo Perón 1500

country: Argentina

institute: Instituto de Investigaciones en Medicina Traslacional (IIMT), CONICET-Universidad Austral

summary: In this study, we explored the role of IL-1β-mediated hormesis in defending β-cells against dysfunction and death induced by pro-inflammatory cytokines (CYT). Preconditioning β-cells with physiological circulating levels of IL-1β (IL-1βlow) induced a resilient state, protecting them from CYT-induced cell death while preserving glucose-stimulated insulin secretion through hormesis. IL-1βlow-treated INS-1E cells reduced CYT-induced NO secretion by suppressing NF-κB signaling and decreasing iNOS expression, correlating with reduced β-cell death. IL-1βlow conditioning reduced ER stress and upregulated p-eIF2a in response to CYT, thereby enhancing the expression of ER chaperones and biomarkers linked to improved β-cell identity/functionality.

overall_design: RNA-seq profiling of INS-1E cells conditioned with IL-1β 10 pg/ml for 72h (IL-1βlow), with fresh cytokine added every 24h without replacing the culture media. Then, the culture media was renewed, and cells were challenged with a proinflammatory cytokine mixture (CYT: IL-1β 100 pg/ml + IFN-γ 5 ng/ml) for 16h. Experimental conditons: untreated, IL-1βlow, CYT, IL-1βlow + CYT. Three biological replicates were included for each condition.

first: Carolina

last: Sétula

first: Ingrid

last: Pensado Evans

first: Andrea

last: Scelza Figueredo

first: Miranda

middle: S

last: Orellano

first: Ignacio

last: Rodríguez-Valero

first: Eduardo

last: Spinedi

first: Raghavendra

middle: G

last: Mirmira

first: Luz

last: Andreone

middle: J


title: Antecedent enhancer activity predicts future susceptibility to seizures in mice

city: St. Louis

first: Joseph

last: Dougherty

state: MO

address: 4370 Duncan Ave

department: Genetics

country: USA

institute: Washington University in St. Louis

summary: Wide variation of responses to identical stimuli presented to genetically inbred mice suggests the hypothesis that stochastic non-genetic variation, such as in chromatin state or enhancer activity during neurodevelopment, can mediate such phenotypic differences. However, this hypothesis is largely untested since capturing pre-existing molecular states requires non-destructive, longitudinal recording. Therefore, we tested the potential of Calling Cards (CC) to record transient neuronal enhancer activity during postnatal development, and thereby associate such non-genetic variation with a subsequent phenotypic presentation – degree of seizure response to the pro-convulsant pentylenetetrazol. We show that recorded differences in enhancer activity at 243 loci predict a severe vs. mild response, and that these are enriched near genes associated with human epilepsy. We also validated pharmacologically a seizure-modifying role for two novel genes, Htr1f and Let7c. This proof-of-principle supports using CC broadly to discover predisposition loci for other neuropsychiatric traits and behaviors.  Finally, as human disease is also influenced by non-genetic factors, similar epigenetic predispositions are possible in humans.

overall_design: Calling Cards viral reagents were injected transcranially into neonatal mouse brains. At one month of age, acute seizures were induced with PTZ and brains were collected. Cortical tissue was split into up to six pieces, from which bulk Calling Cards libraries were prepared independently. Sample names contain animal ID as the first two integers, followed by tissue piece number. e.g. CT14-5_piece_2 indicates animal CT14-5, tissue piece 2.

first: Benjamin

last: Boros

first: Mariam

middle: A

last: Gachechiladze

first: Juanru

first: Dylan

last: Galloway

first: Shayna

middle: M

last: Mueller

first: Mark

last: Shabsovich

first: Allen

last: Yen

first: Xuhua

first: Alexander

last: Cammack

first: Tao

last: Shen

first: Robi

last: Mitra

first: Timothy

last: Miller


title: ALKBH5 Demethylates the m6A Modification of SOCS3 in Microglia/Macrophages and Alleviates Neuroinflammation after Brain Injury [scRNA-seq]

city: Shanghai

first: Xiaoyu

last: Li

address: Dongan Road

institute: Fudan University

summary: Microglia/macrophage-induced neuroinflammation plays a crucial role in the progression of traumatic brain injury (TBI). However, the involvement of N6-methyladenosine (m6A) RNA modifications in this process remains elusive. Single-cell RNA sequencing (scRNA-seq) and m6A RNA immunoprecipitation sequencing (MeRIP-seq) across multiple time points post-injury revealed a strong correlation between m6A modifications and genes enriched in microglia/macrophage. Furthermore, the m6A demethylase ALKBH5 was identified as a key regulator of dynamic m6A patterns at the injury site. ALKBH5 suppression in microglia/macrophage exacerbated neuroinflammation in vitro and worsened neurological deficits in controlled cortical impact (CCI) models. MeRIP-qPCR and RNA pull-down assays revealed SOCS3 was a downstream target of ALKBH5-mediated m6A demethylation. This demethylation stabilized Socs3 mRNA and enhanced its protein expression, which in turn suppressed neuroinflammation via inhibiting the JAK2-STAT3 pathway. Conversely, SOCS3 depletion impaired functional recovery after injury. These findings unveiled a critical ALKBH5-m6A-SOCS3 regulatory axis that mitigated microglia/macrophage-driven neuroinflammation after TBI, underscoring its potential as a therapeutic intervention target for TBI progression.

overall_design: Cortical tissues from mouse brains in the sham group and at 1, 3, 7, and 14 days following traumatic brain injury were minced and enzymatically dissociated for single-cell RNA sequencing.

first: Lin

last: Cai

first: Yuqing

last: Liang

first: Yanxia

last: Rao

first: Bo

last: Peng

first: Hengli

last: Tian


title: Universal Enrichment and Sequencing of DNA Modifications Using a Click-Coupled IgG-Protein G System

city: Shenzhen

first: yuanfang

last: Liu

state: Guangdong

address: Zhenyuan Road

institute: The Seventh Affiliated Hospital of Sun Yat-sen University (Shenzhen)

summary: Efficient nucleic acid enrichment is pivotal for deciphering epigenetic modifications and disease biomarkers, yet current methods are constrained by insufficient specificity, poor versatility, and high costs. We developed a universal strategy named ‘Click-IP-Seq’ by leveraging the high-affinity binding between Protein G and Fc region of DBCO-modified IgG. This enabled the directional conjugation of DBCO-IgG with azide-modified nucleic acids via copper-free strain-promoted azide-alkyne cycloaddition (SPAAC) click chemistry, achieving specific capture and enrichment of modified nucleic acids. Firstly, this method efficiently enriched two major DNA modifications, 8-oxo-7,8-dihydroguanine (8-oxo-dG) and 5-hydroxymethylcytosine (5hmC) in model DNA systems. Then, genome-wide distribution of 8-oxodG from human cells and tissues align with previously reports. Finally, employing ‘Click-IP-Seq’, we performed the first comprehensive analysis of 8-oxo-dG spatial distribution and associated biological functions in human colorectal carcinoma tissues. This technology provides a high-specificity and versatile enrichment platform for nucleic acid modifications, which is expected to promote the application of cancer molecular diagnosis.

sample_organism:
Homo sapiens
mixed organisms

platform_organism:
Homo sapiens
mixed organisms

overall_design: We performed sequencing analysis using normal intestinal epithelial cells (NCM460), colorectal cancer cells (HCT116), along with healthy tissues, paracancerous tissues, and cancerous tissues from colorectal cancer patients. Enrichment-based library construction was employed for 8-oxo-dG analysis (experimental group), while non-enriched direct library construction served as the control group, to characterize the genomic distribution of 8-oxo-dG in biological systems.


title: Single-cell glycome and transcriptome profiling uncovers the glycan signature of each cell subpopulation of human iPSC-derived neurons

city: Tsukuba

first: Haruki

last: Odaka

state: Ibaraki

address: Tsukuba Central 6, 1-1-1 Higashi

country: Japan

institute: National Institute of Advanced Industrial Science and Technology

summary: Human induced pluripotent stem cells (iPSC)-derived cells are often heterogeneous, posing challenges for disease modeling and cell therapy. We previously developed single-cell glycan and RNA sequencing (scGR-seq) to analyze the glycome and transcriptome simultaneously. Here, we applied scGR-seq to examine heterogeneous populations of human iPSC-derived neurons. We identified four subpopulations: mature neurons, immature neurons, undifferentiated neural progenitor cells (undiffNPCs), and mesenchymal cells (MCs). Lectin binding patterns indicated high α1,3-fucose expression in undiffNPCs. MCs exhibited strong binding of a poly-LacNAc-recognizing lectin (rLSLN) and high expression of B3GNT2, a poly-LacNAc synthetic enzyme. Pseudotime analysis revealed that a subpopulation of NPCs acquired mesenchymal features and differentiated into MCs. Immunocytochemistry confirmed the specific detection of undiffNPCs and MCs using anti-Lewis X (α1,3-fucosylated glycan) antibodies and rLSLN. Beyond identifying cell heterogeneity, scGR-seq enables the discovery of glycan markers and detection probes for iPSC-derived cells, aiding in their further cell processing and manipulation.

overall_design: Differentiation of human iPS cells into neural progenitor cells (NPCs) and neurons was performed. Human iPS cells (n=96), NPCs (n=96), and neurons (n=80) were collected, and sequencing analysis was conducted using Ramda-seq protocol.

first: Hiroaki

last: Tateno


title: ALKBH5 Demethylates the m6A Modification of SOCS3 in Microglia/Macrophages and Alleviates Neuroinflammation after Brain Injury

summary: Microglia/macrophage_induced neuroinflammation plays a crucial role in the progression of traumatic brain injury (TBI). However, the involvement of N6_methyladenosine (m6A) RNA modifications in this process remains elusive. Single_cell RNA sequencing (scRNA_seq) and m6A RNA immunoprecipitation sequencing (MeRIP_seq) across multiple time points post_injury revealed a strong correlation between m6A modifications and genes enriched in microglia/macrophage. Furthermore, the m6A demethylase ALKBH5 was identified as a key regulator of dynamic m6A patterns at the injury site. ALKBH5 suppression in microglia/macrophage exacerbated neuroinflammation in vitro and worsened neurological deficits in controlled cortical impact (CCI) models. MeRIP_qPCR and RNA pull_down assays revealed SOCS3 was a downstream target of ALKBH5_mediated m6A demethylation. This demethylation stabilized Socs3 mRNA and enhanced its protein expression, which in turn suppressed neuroinflammation via inhibiting the JAK2_STAT3 pathway. Conversely, SOCS3 depletion impaired functional recovery after injury. These findings unveiled a critical ALKBH5_m6A_SOCS3 regulatory axis that mitigated microglia/macrophage_driven neuroinflammation after TBI, underscoring its potential as a therapeutic intervention target for TBI progression.

overall_design: Cortical tissues from mouse brains in the sham group and at 1, 3, 5 and 7 days following traumatic brain injury were minced and enzymatically dissociated for m6A sequencing.


title: Modeling arrhythmogenic cardiomyopathy fattyfibro pathology through the use of PKP2-deficient human iPSC-derived epicardial cells

city: Tucson

first: Jared

last: Churko

state: Arizona

address: 1501 N CAMPBELL AVE LSN 461

department: CMM

institute: University of Arizona

summary: Arrhythmogenic cardiomyopathy (ACM) is an inherited cardiac disease characterized by progressive fatty-fibro replacement of the ventricular myocardium leading to arrhythmias and an increased risk of sudden cardiac death. To date, the cell types and signaling mechanisms involved in fatty-fibro infiltration of the myocardium have yet to be fully resolved. However, given that fatty-fibro replacement is initiated within the subepicardial layer, epicardial cells are predicted to contribute to the development of this pathology. To investigate the epicardial contributions to the development of ACM, we generated human induced pluripotent stem cell (hiPSC) lines from ACM patients harboring either a PKP2 1849C>T or a PKP2 2013delC mutation alongside CRISPR/Cas9 gene-edited isogenic control lines and a PKP2 knockout line. Epicardial cells derived from patient and knockout conditions displayed enhanced epithelial-to-mesenchymal transition characteristics, dysregulated Wnt and interferon signaling, increased lipid accumulation, and an enhanced fibrotic phenotype when converted to epicardial-derived fibroblasts. Transcriptomic analysis revealed upregulation of insulin growth factor 2 (IGF2) in ACM hiPSC-EPCs as well as in human ACM heart tissue. Subsequent treatment with exogenous IGF2 enhanced expression of the adipogenic transcription factors CEBPA and PPARG in hiPSC-EPCs, suggesting insulin growth factor signaling contributes to ACM fatty-fibro remodeling.

overall_design: We generated hiPSC lines from two ACM families carrying either a PKP2 1849C>T or PKP2 2013delC mutation, corrected each by CRISPR/Cas9 to create isogenic controls, and produced a PKP2 knockout line. All lines were differentiated into epicardial cells, then assayed for EMT markers, cell migration, lipid accumulation (Nile Red), and fibrotic marker expression. Epicardial-derived fibroblasts versus non-epicardial fibroblasts were compared under adipogenic induction. RNA-seq profiled global transcriptional changes; key findings were functionally validated by IGF2 treatment and IGF-1R inhibition.


title: Immunocompetent murine models recapitulate the heterogeneous tumor immune microenvironment of human liposarcoma [human]

city: Ann Arbor

first: Christina

middle: Vadala

last: Angeles

state: MI

address: 1500 E Medical Center Drive

department: Surgery

institute: University of Michigan

summary: Here we sought to transcriptomically characterize human liposarcoma tumors and normal fat from patient samples

overall_design: Patients with soft tissue tumors and a pathological diagnosis of liposarcoma provided written consent to obtain fresh tumor and normal fat tissue from surgical specimens as part of the Sarcoma Research Working Group Biobank at the U-M Rogel Cancer Center.

first: Amanda

last: Shafer

first: Emma

last: Kenna

first: Lexi-Ann

middle: F

last: Golden

middle: V


title: Dynamic alterations of dural and bone marrow B cells in an animal model of progressive MS

city: Toronto

first: Michelle

last: Zuo

state: ON

address: 1 King's College Circle

department: Immunology

country: Canada

institute: University of Toronto

summary: In multiple sclerosis (MS), the leptomeninges (LM) are populated with immune cell aggregates that correlate with disease progression. The impact of LM inflammation on the adjacent dura is largely unknown. Using a mouse model of MS that induces brain LM inflammation and age-dependent disease progression, we found that encephalitogenic T cells and B220high B cells accumulate substantially in the brain LM and parenchyma of both young and aged mice, while the adjacent dura remains relatively inert. We also observed a population of anti-CD20-resistant B220low B cells in the dura and bone marrow that virtually disappear at disease onset and accumulate in the brain of young mice concomitant with disease remission. In contrast, aged mice show a paucity of brain-resident B220low B cells at the expense of class-switched B220high B cells accompanied by severe, chronic disease. In summary, dynamic changes in the brain, LM, and dural B cells are associated with age-dependent disease severity in an animal model of progressive MS.

overall_design: Dural cells were collected from young and aged SJL/J mice at homeostasis, acute EAE (D11), and post-acute EAE (D25). Cells were sorted for live (Calcein violet+) and then resuspended in BSA + PBS and submitted for sequencing at Princess Margaret Genomics Centre

first: Alexandra

last: Florescu

first: Angela

last: Wang

first: Kevin

last: Champagne-Jorgensen

first: Mohammed

last: Noor

first: Lesley

last: Ward

first: Erwin

last: van Puijenbroek

first: Christian

last: Klein

first: Jennifer

last: Gommerman


title: Base-resolution profiling of 5-glyceryl-methylcytosine in Chlamydomonas reinhardtii via deaminase-assisted sequencing [Bisulfite-Seq]

first: Fanchen

state: Shanghai

address: 1239 Siping Road

institute: Tongji University

type: Methylation profiling by high throughput sequencing

summary: 5gmC (5-glyceryl-methylcytosine), a vitamin C-derived hypermodified base, has been identified in the genome of Chlamydomonas reinhardtii. However, the global distribution of 5gmC and its role as an epigenetic mark remain poorly understood. In this study, we employed a DNA deaminase to distinguish 5gmC from 5mC (5-methylcytosine) and cytosines, enabling precise profiling of 5gmC across the genome. This deaminase-assisted sequencing (DEA-seq) demonstrates superior performance compared to the previously proposed TET-coupled bisulfite sequencing. Using both methods, we identified numerous confident 5gmC sites. Unlike 5mC, which predominantly occurs at CpG sites, 5gmC is preferentially located in CHH contexts. Remarkably, over half of 5gmC sites are mutually exclusive from 5mC, suggesting a role in active DNA demethylation. Additionally, 5gmC is enriched within introns, contrasting with the more extensive localization of 5mC in intergenic and promoter regions. Importantly, 5gmC levels are positively correlated with transcription, while 5mC typically exhibits an inverse relationship with gene expression, consistent with the enrichment of 5mC but loss of 5gmC at repressive H3K9me1 sites. Collectively, these findings suggest that 5gmC is not only an intermediate for active DNA demethylation but also functions as a stable epigenetic mark, potentially influencing transcriptional regulation independently of 5mC.

overall_design: WGBS of 5mC (BS) and 5gmC (DEA/TET-BS) in the C. reinhardtii strains (CC125, CC5325 and CC5325KO).

first: Baodan

last: He

first: Zixin

first: Xuan

last: Deng

first: Tong

last: Ge

first: Hui

last: Chen

first: Weiying

last: Meng

first: Yutao

last: Fu

first: Wanyue

last: Zou

first: Shuxia

last: Sun

first: Keyao

last: Zhao

first: Haoming

last: Jiang

first: Zhiyan

first: Guoliang

last: Xu

first: Kaiyao

last: Huang

first: Jianhuang

last: Xue


title: Immunocompetent murine models recapitulate the heterogeneous tumor immune microenvironment of human liposarcoma

first: Christina

last: Angeles

summary: Here we sought to transcriptomically characterize autochthonous tumors from our novel ACPP GEMM of Liposarcoma

overall_design: We harvested autochthonous tumors generated after injection of our AAV8-Cre virus into the flank fat pad of Trp53f/fPtenf/f C57BL/6J mice or non-injected normal flank fat pads for bulk RNA sequencing

first: Amanda

last: Shafer

first: Emma

last: Kenna

first: Lexi-Ann

last: Golden


title: Single cell RNA profiling of blood CD4+ T cells identifies distinct helper and dysfunctional regulatory clusters in children with SLE (5' PBMC validation dataset)

city: New York

first: Simone

last: Caielli

state: NY

address: 413 E 69th Street

department: Department of Pediatrics

institute: Weill Cornell Medicine

summary: Expansion of different CD4+ CXCR5+ and CXCR5- memory T helper cells has been reported in human systemic lupus erythematosus (SLE) blood. To understand their complexity, we profiled blood CD4+ T cells from heathy donors (HD) and pediatric SLE patients at the single cell level and identified naïve, memory, regulatory (Treg) and proliferative clusters, as well as a cluster defined by high expression of interferon-stimulated genes (ISGs). Within the memory compartment, we mapped follicular (Tfh) and peripheral (Tph and Th10) helper cells and confirmed their expansion in patients with lupus nephritis (LN) and/or high disease activity. Cytotoxic programs mapped  to effector memory T cells re-expressing CD45RA (TEMRA), as well as to two memory subclusters, one of which overlapped with Th10 cells. Importantly, we identified an expansion of dysfunctional Tregs in patients with LN, and an upregulation of TLR5 and FCRL3 in naïve SLE Tregs, potentially linking their dysfunction with mucosal microbial dysbiosis. Our studies shed light into CD4+ T cell subsets that may contribute to dysfunctional B cell help and T cell suppression in SLE.

overall_design: 10X 5' scRNA-Seq of PBMCs from SLE children and HD. This dataset is used to validate memory T cell and Treg subclusters.

first: Preetha

last: Balasubramanian

first: Uthra

last: Balaji

first: Jeanine

last: Baisch

first: Cynthia

last: Smitherman

first: Lynnette

last: Walters

first: Paola

last: Sparagana

first: Lorien

last: Nassi

first: Katie

last: Stewart

first: Julie

last: Fuller

first: Terry

last: Means

first: Virginia

last: Savova

first: Jacques

last: Banchereau

first: Tracey

last: Wright

last: Pascual

first: Jinghua

last: Gu


title: Endothelins influences the proliferation-migration balance of IDH1-mutant glioma cells and promotes proneural to mesenchymal transition [RNAseq-275HCMEC]

city: Montpellier

first: Donovan

last: PINEAU

address: 141 Rue de la Cardonille

country: France

institute: IGF

summary: Adult diffuse gliomas are the deadliest brain tumours including IDH-wildtype glioblastomas of worst prognosis and diffuse low grade IDH-mutant astrocytomas and oligodendrogliomas. These glial tumours display distinct tumoral cell population defeating current therapies. Our group has unveiled the role of NOTCH signalling in glioblastoma cell plasticity and in the conversion of oligodendrocytic-like to astrocytic-like tumoral cells in IDH-mutant low-grade gliomas which escalate inevitably to higher grade malignant gliomas. To gain insight into signalling pathways regulating glioma cell plasticity and malignancy, we focused our work on endothelin signalling including endothelin peptide ligands (ET-1, ET-2, ET-3) binding to G-protein coupled endothelin receptors A and B (EDNRA, EDNRB).  Here, using glioma patient samples and glioma patient-derived cell lines, we showed that endothelin reduces glioma cell proliferation while increasing migration initiating a proneural to mesenchymal transition. Mechanistically, EDNRB activation led to IP3-dependent calcium mobilization, apamin-sensitive KCNN2/KCNN3 potassium currents and phosphorylation of ERK1/2 and STAT3 in glioma cells. Finally, we studied endothelin receptor regulation by tumoral microenvironment stimuli highlighting a role for EDNRA induced by NOTCH and hypoxia in perivascular hypoxic area in glioblastoma. Altogether, this study demonstrates endothelin signalling as a key player in mesenchymal transformation of diffuse IDH-mutant gliomas and glioblastomas.

overall_design: RNAseq analyses of a diffuse low-grade glioma LGG275 cells upon cocultures with hCMEC/D3 endothelial cells (human blood brain barrier capillary microvascular endothelial cell line)

first: Jean-Philippe

last: HUGNOT


title: Endothelins influences the proliferation-migration balance of IDH1-mutant glioma cells and promotes proneural to mesenchymal transition [RNAseq-Gb7-HUVEC]

overall_design: RNAseq analyses of Gb7 glioblastoma stem cell line cells upon coculture with HUVEC endothelial cells (Human Umbilical Vein Endothelial Cells)

first: Hugo

last: ARNOLD


title: RNAseq analysis of LGG275, a diffuse IDH-mutant low-grade astrocytoma cell line treated with different molecules (cytokines, compounds and coatings) plus Gb4, IDH-wildtype glioblastoma stem cell line treated with ET1

summary: The goal of the present study was to identify regulators of diffuse low-grade glioma cell behaviour (proliferation, differentiation and cell death) based on candidates anti- and pro-proliferative molecules identified by an in vitro custom drug screening assay using absolute cell number as a readout

overall_design: RNA-seq profiling of LGG275, a diffuse IDH-mutant low-grade glioma cell line upon different compounds and RNA-seq profiling of Gb4, a diffuse IDH-wildtype glioblastoma stem cell line upon ET1 after 5 days of treatment once a day before proceeding to RNA extraction 8 hours after the last treatment.

last: Pineau

first: Stefan

last: Nicolescu

last: Hugnot


title: Endothelins influence the proliferation-migration balance of IDH1-mutant glioma cells and promote proneural to mesenchymal transition

summary: Adult diffuse gliomas are the deadliest brain tumours including IDH-wildtype glioblastomas of worst prognosis and diffuse low grade IDH-mutant astrocytomas and oligodendrogliomas. These glial tumours display distinct tumoral cell population defeating current therapies. Our group has unveiled the role of NOTCH signalling in glioblastoma cell plasticity and in the conversion of oligodendrocytic-like to astrocytic-like tumoral cells in IDH-mutant low-grade gliomas which escalate inevitably to higher grade malignant gliomas. To gain insight into signalling pathways regulating glioma cell plasticity and malignancy, we focused our work on endothelin signalling including endothelin peptide ligands (ET-1, ET-2, ET-3) binding to G-protein coupled endothelin receptors A and B (EDNRA, EDNRB). Here, using glioma patient samples and glioma patient-derived cell lines, we showed that endothelin reduces glioma cell proliferation while increasing migration initiating a proneural to mesenchymal transition. Mechanistically, EDNRB activation led to IP3-dependent calcium mobilization, apamin-sensitive KCNN2/KCNN3 potassium currents and phosphorylation of ERK1/2 and STAT3 in glioma cells. Finally, we studied endothelin receptor regulation by tumoral microenvironment stimuli highlighting a role for EDNRA induced by NOTCH and hypoxia in perivascular hypoxic area in glioblastoma. Altogether, this study demonstrates endothelin signalling as a key player in mesenchymal transformation of diffuse IDH-mutant gliomas and glioblastomas.

overall_design: For RNA sequencing experiments upon endothelin, LGG275, LGG336, BT237, Gb4, Gb7, Gb21 were seeded at 260,000 cells/wells in 3.5 mL of +GFs medium in 6-well plates (#140685, ThermoFisher Nunclon). Cells were treated either with endothelin dilution buffer (PBS with BSA 0.1%) for control condition or with ET-1 at 10 nM final once a day for 5 days before proceeding to RNA extraction 8 hours after the last treatment.


title: Endothelins positively influences the proliferation vs migration balance of IDH1-mutant glioma cells and promotes proneural to mesenchymal transition [RNAseq-275HUVEC]

overall_design: RNAseq analyses of a diffuse low-grade glioma LGG275 cells upon endothelial cells cocultures with HUVEC cells (Human Umbilical Vein Endothelial Cells)


title: Topoisomerase IIIb protects from immune dysregulation and tumorigenesis

city: Bethesda

first: Anjali

last: Dhall

state: MD

address: 37 Convent Drive

department: DTB

institute: NCI

summary: Topoisomerase III-beta (Top3b) reduces nucleic acid torsional stress and intertwining generated during RNA and DNA metabolism while protecting the genome from pathological R-loops, which otherwise result in DNA breakage and genome instability. By studying Top3b knockout mice (Top3b-KO), we find that the loss of Top3b accelerates the development of spontaneous atypical lymphoid hyperplasia and lymphomas arising in spleens and lymph nodes, the organs with prominent Top3b expression. Aging Top3b-KO mice also display splenomegaly and systemic immune alterations including neutrophilia and lymphopenia consistent with chronic inflammation. At the molecular level, Top3b deficiency causes genome-wide R-loop accumulation in splenocytes as measured by CUT&Tag sequencing. Increased R-loops are associated with genomic breaks and activation of immune signaling pathways including innate and adaptive immune cell signaling, IL-4 signaling, FAK signaling and cGAS-STING. Additionally, knocking-out Top3b promotes the rapid development of syngeneic EL4 T-cell lymphomas. In conclusion, our work suggests that Top3b protects from lymphoma, tumorigenesis and immune dysregulations.

overall_design: To investigate the roles of topoisomerase III-beta (Top3b) in preventing tumorigenesis and immune dysregulation we performed R-loop CUT&Tag sequencing using S9.6 antibody (R-loop CUT&Tag) to map genomic locations of R-loops and genome-wide transcriptomics in WT vs Top3b-KO splenocytes. We isolated RNA from three replicates of WT and three replicates of Top3b-KO splenocytes followed by ribo-depleted total RNA-seq.

first: Md Rasel Al

last: Mahmud

first: Simone

last: Andrea Baechler

first: Sourav

last: Saha

first: Hongliang

last: Zhang

first: Laura

last: Bassel

first: Shuling

first: Min-Jung

last: Lee

first: Nahoko

last: Sato

first: Shraddha

last: Rastogi

first: Suresh

last: Kumar

first: Muhammad

last: S. Alam

first: Liton

first: Beverly

last: Mock

first: Valentina

last: M Factor

first: Yves

last: Pommier


title: Base-resolution profiling of 5-glyceryl-methylcytosine in Chlamydomonas reinhardtii via deaminase-assisted sequencing [RNA-Seq]

first: Fanchen

last: Wang

overall_design: RNA-seq of C. reinhardtii strains (CC125, CC5325 and CC5325KO).

first: Baodan

last: He

first: Zixin

first: Xuan

last: Deng

first: Tong

last: Ge

first: Hui

last: Chen

first: Weiying

last: Meng

first: Yutao

last: Fu

first: Wanyue

last: Zou

first: Shuxia

last: Sun

first: Keyao

last: Zhao

first: Haoming

last: Jiang

first: Zhiyan

first: Guoliang

last: Xu

first: Kaiyao

last: Huang

first: Jianhuang

last: Xue


title: Single cell RNA profiling of blood CD4+ T cells identifies distinct helper and dysfunctional regulatory clusters in children with SLE [CD4+ T cells]

first: Simone

last: Caielli

overall_design: 10X scRNA-Seq of sorted CD4+ T cells from SLE children and matched healthy donors.

first: Preetha

last: Balasubramanian

first: Uthra

last: Balaji

first: Jeanine

last: Baisch

first: Cynthia

last: Smitherman

first: Lynnette

last: Walters

first: Paola

last: Sparagana

first: Lorien

last: Nassi

first: Katie

last: Stewart

first: Julie

last: Fuller

first: Terry

last: Means

first: Virginia

last: Savova

first: Jacques

last: Banchereau

first: Tracey

last: Wright

last: Pascual

first: Jinghua

last: Gu


title: DeepWheat: Predicting the Effects of Genomic Variants on Gene Expression and Regulatory Activities Across Tissues and Varieties in Wheat Using Deep Learning [ChIP-Seq]

city: Beijing

first: Zefu

last: Lu

state: Haidian

address: No.12 Zhongguancun South St.,Haidian District, Beijing, P.R.China

institute: Institute of Crop Sciences

summary: Accurate prediction of genomic variant effects and gene expression is essential for identifying functional variations and enabling precise genome editing of cis-regulatory elements (CREs). Spatiotemporal gene expression patterns are fundamental to the formation of key traits, yet tissue-specific predictions remain inaccurate, particularly in large-genome crops like wheat. In this study, we developed DeepWheat, a suite of two models for predicting epigenomic features and gene expression in wheat. DeepEXP, a deep learning model, integrates epigenomic and transcriptomic data across various wheat tissues, achieving Pearson correlation coefficients (PCC) over 0.8 and outperforming sequence-only models, especially for tissue-specific genes. DeepEPI predicts epigenomic features from DNA sequences, helping identify regulatory sequences and facilitating model transfer across wheat varieties. Using chromatin accessibility and transcriptomic data from 9 additional wheat varieties, we validated the model’s accuracy and transfer efficiency. Our analysis further revealed that indels have a greater impact on gene expression than SNPs, and that, compared to promoter regions, the 5’UTR, 3’UTR, and introns exert even stronger regulatory effects on gene expression. These models also identified mutations that alter gene expression, supporting precise CRE editing. They provide valuable tools for tissue-specific predictions, regulatory sequence identification, and saturation mutagenesis to pinpoint high-effect sites.

overall_design: RNA-seq, ATAC-seq and Chip-seq in multiple wheat different tissues

first: Zhigang

last: Ma

first: Jiazi

last: Zhang

first: Hongcui

last: Pei

first: Yanhong

last: Lui

first: Lei

last: Wang


title: Gene expression profile at single cell level of endothelial cells (ECs) from the WT and Apoa1bp-/- mice adductors with femoral artery ligation (FAL) injury

city: Changsha

first: Lingping

last: Zhu

address: Xiangya Road

institute: Xiangya hospital

summary: Establishment of collateral circulation (CC) is crucial for the treatment of ischemic disease, such as peripheral artery disease (PAD). We performed single-cell transcriptomic analysis to explore the cellular mechanism underlying CC.

overall_design: Adductors from WT or Apoa1bp-/- mice were collected for scRNA-seq on the day7 of FAL injury.

first: Yong

last: Bai

first: Long

last: Fang


title: Single cell RNA profiling of blood CD4+ T cells identifies distinct helper and dysfunctional regulatory clusters in children with SLE [PBMCs]

first: Simone

last: Caielli

overall_design: 10X scRNA-Seq of PBMCs from SLE children. This dataset is used to validate naïve CD4+ T cell subclusters.

first: Preetha

last: Balasubramanian

first: Uthra

last: Balaji

first: Jeanine

last: Baisch

first: Cynthia

last: Smitherman

first: Lynnette

last: Walters

first: Paola

last: Sparagana

first: Lorien

last: Nassi

last: Stewart


first: Anjali

last: Dhall

overall_design: To investigate the roles of topoisomerase III-beta (Top3b) in preventing tumorigenesis and immune dysregulation we performed R-loop CUT&Tag sequencing using S9.6 antibody (R-loop CUT&Tag) to map genomic locations of R-loops in replicates of WT vs Top3b-KO splenocytes.

first: Md Rasel Al

last: Mahmud

last: Andrea Baechler

first: Sourav

last: Saha

first: Hongliang

first: Laura

last: Bassel

first: Shuling

first: Min-Jung

last: Lee

first: Nahoko

last: Sato

first: Shraddha

last: Rastogi

first: Suresh

last: Kumar

first: Muhammad

last: S. Alam

first: Liton

first: Beverly

last: Mock

first: Valentina

last: M Factor

first: Yves

last: Pommier


title: Genome-wide whole blood methylation profiles of patients after aneurysmal subarachnoid haemorrhage (aSAH) with and without symptomatic cerebral vasospasm

city: Szczecin

first: Tomasz

last: Klepinowski

state: West Pomerania

address: Ul. Unii Lubelskiej 1

department: Department of Neurosurgery

country: Poland

institute: Pomeranian Medical University Hospital No.1

type: Methylation profiling by genome tiling array

summary: Genome-wide DNA methylation patterns were quantified in peripheral blood samples collected from 61 individuals (with determined cerebral vasospasm status) using the Illumina Infinium HumanMethylationEPIC v2.0 BeadChip

overall_design: In this study, we prospectively recruited 32 patients after aSAH with symptomatic cerebral vasospasm and 29 patients after aSAH without cerebral vasospasm. From each participant we collected peripheral blood sample for DNA extraction and performed DNA methylation analyses using Illumina Infinium HumanMethylationEPIC v2.0 BeadChip. Symptomatic cerebral vasospasm was determined by a combination of clinical symptoms (decreased consciousness or/and new neurologic deficit not attributable to other cause) and radiographic (transcranial Doppler ultrasonography, computed tomography angiogram, or digital subtraction angiogram) vasospasm. This research was funded by the National Science Centre, Poland (grant number 2021/41/N/NZ2/00844).

first: Patrycja

middle: K

last: Przybyłowicz

first: Olga

last: Taryma-Leśniak

last: Wojdacz

first: Andrzej

last: Ossowski

first: Dagmara

last: Lisman

first: Leszek

last: Sagan


title: DeepWheat: Predicting the Effects of Genomic Variants on Gene Expression and Regulatory Activities Across Tissues and Varieties in Wheat Using Deep Learning [ATAC-seq]

first: Zefu

last: Lu

overall_design: ATAC-seq  in multiple wheat different tissues

first: Zhigang

last: Ma

first: Jiazi

last: Zhang

first: Hongcui

last: Pei

first: Yanhong

last: Lui

first: Lei

last: Wang


title: MTA-cooperative PRMT5 inhibitors enhance T cell-mediated antitumor activity in MTAP-loss tumors

city: Houston

first: Shuyue

address: 1901 East Rd

institute: MD Anderson

summary: Background: Hyperactivated protein arginine methyltransferases (PRMTs) are implicated in human cancers. Inhibiting tumor intrinsic PRMT5 was reported to potentiate antitumor immune responses, highlighting the possibility of combining PRMT5 inhibitors (PRMT5i) with cancer immunotherapy. However, global suppression of PRMT5 activity impairs the effector functions of immune cells. Here, we sought to identify strategies to specifically inhibit PRMT5 activity in tumor tissues and develop effective PRMT5i-based immuno-oncology (IO) combinations for cancer treatment, particularly for methylthioadenosine phosphorylase (MTAP)-loss cancer.  Methods: Isogeneic tumor lines with and without MTAP loss were generated by CRISPR/Cas9 knockout. The effects of two PRMT5 inhibitors (GSK3326595 and MRTX1719) were evaluated in these isogenic tumor lines and T cells in vitro and in vivo. Transcriptomic and proteomic changes in tumors and T cells were characterized in response to PRMT5i treatment.  Results: transcriptomic and proteomic profiling analysis reveals that MRTX1719 successfully reduces activation of the PI3K pathway, a well-documented immune-resistant pathway. It highlights the potential of MRTX1719 to overcome immune resistance in MTAP-loss tumors.  Conclusion: Collectively, our results provide a strong rationale and mechanistic insights for the clinical development of MRTX1719-based IO combinations in MTAP-loss tumors.

overall_design: To explore the molecular mechanisms through how PRMT5-dependent tumorigenesis effect on anti-tumor immune response, we generated the following genetically modified MC38/gp100 cell lines and pmel-1 T cells. Samples were in vitro treated by PRMT5is for mechanistic studies.  A1, MC38/gp100 cells control; A2, MC38/gp100 cells treated by 0.5 μM GSK3326595; A4, MC38/gp100 cells treated by 0.5 μM MRTX1719; B1, MC38/gp100 Mtap-KO cells control; B2, MC38/gp100 Mtap-KO cells treated by 0.5 μM GSK3326595; B4, MC38/gp100 Mtap-KO cells treated by 0.5 μM MRTX1719; C1, pmel-1 T cells isolated from transgetic mice, control; C2, pmel-1 T cells isolated from transgetic mice, treated by 0.5 μM GSK3326595; C4, pmel-1 T cells isolated from transgetic mice, treated by 0.5 μM MRTX1719.

first: Si

last: Chen

first: Rongjie

last: Fu

first: Han

last: Xu

first: Weiyi

last: Peng

first: Yue


title: SLC6A8-mediated creatine uptake suppresses ERK2-FSP1 signaling and induces ferroptosis in colorectal cancer

city: Zhengzhou

first: Xiaojun

last: Zhou

state: Henan

address: 100 Lianhua Street

department: College of Bioengineering

institute: Henan University of Technology

summary: We discovered, through untargeted metabolomics, that creatine promotes ferroptosis in colorectal cancer. Our study identifies ERK2 as a creatine sensor that mediates active FSP1 and ferroptosis resistance, and highlights the potential of targeting tumor SLC6A8 for cancer treatment.

overall_design: To explore the role of creatine in regulating the ferroptosis of colorectal cancer, we performed the RNA-Seq assay after creatine treatment.

first: Youjun

last: Li


title: Glycerol metabolism modulates antibiotic tolerance in Pseudomonas aeruginosa

city: Birmingham

first: Jessica

last: Scoffield

state: Alabama

address: 1720 2nd Ave S

department: Microbiology

institute: The University of Alabama at Birmingham

summary: Chronic infections with Pseudomonas aeruginosa are a leading cause of morbidity and mortality in persons with cystic fibrosis (pwCF). P. aeruginosa persists in the CF lung by utilizing adaptation strategies to cause infection, including altering the expression of metabolic genes to acquire nutrients that are abundant in the CF airway. Glycerol in the airway is imported and metabolized by the glp regulon, which is under the control of the GlpR repressor. It has been shown that the loss of GlpR results in increased biofilm development in P. aeruginosa CF isolate compared to a wound isolate. Based on the increased biofilm phenotype observed and because biofilms are associated with increased antibiotic tolerance, we questioned whether GlpR plays a role in mediating antibiotic resistance of P. aeruginosa. We measured tobramycin tolerance in wild-type and glpR-defective P. aeruginosa isolates from the CF airway (FRD1) and a wound (PAO1). Cultures were grown in lysogeny broth or synthetic cystic fibrosis sputum consisting of the base formula of primarily amino acids (SCFM1) or supplemented with mucins and DNA (SCFM2), with dose-dependent concentrations of tobramycin. We tested the impact of a glpR mutation on P. aeruginosa adherence on bronchial epithelial cells from pwCF (CFBE) in the presence of tobramycin. CFBE cells were inoculated at an MOI of ~1:20 for 1 hour, given fresh apical media for 5 more hours, then apical and basal media was replaced with media containing 20 µg/ml tobramycin. We measured colony forming units (CFUs) and lactate dehydrogenase (LDH) release for cytotoxicity. Loss of glpR increased tolerance to tobramycin in both the PAO1 and FRD1 backgrounds in vitro at a concentration of 0.625 µg/mL in lysogeny broth and SCFM1. On both CFBE’s and 16HBE’s, the antibiotic resistance phenotype was more prominent in FRD1 glpR with a 2-log increase in viable bacteria when grown on cells and treated with 20 ug/ml tobramycin. However, changes in cytotoxicity where not observed between wildtype and GlpR mutants as LDH measurements were not significantly different. Our results indicate that GlpR may regulate antibiotic tolerance, in addition to biofilm development and glycerol metabolism. Additional studies are necessary to determine the mechanism of how GlpR modulates biofilm development and antibiotic tolerance.

overall_design: Transcriptome comparison of Pseudomonas aeruginosa strains PA01 and FRD1, with and without GlpR, the glycerol repressor, with and without treatment with 5 μg/mL tobramycin. All samples were grown in SCFM2 until mid-exponential phase, ~8 hours for untreated PA01 and ~20 hours for the FRD1 and treated cultures, then harvested for RNA-seq.

first: Nicholas

last: Evans


title: Altered Cell Clusters and Upregulated Aqp1 in Connexin 50 Knockout Lens Epithemium

city: Berkeley

first: Xiaohua

last: Gong

state: CA

address: 695 Minor Hall

department: School of Optometry

institute: University of California, Berkeley

summary: To characterize the heterogeneity and cell clusters of postnatal lens epithelial cellsLens epithelial cells exhibit an intrinsic heterogeneity of different cell clusters in regulating lens homeostasis and lens growth. Upregulated Aqp1 in Cx50KO lens epithelial cells suggests that both connexin 50 and AQP1 likely play important roles in regulating water homeostasis in lens epithelial cells. (LECs) and to investigate the downstream targets of connexin 50 (Cx50) in the regulation of lens homeostasis and lens growth. To determine differentially expressed genes (DEGs) in the connexin 50 knockout (Cx50KO) lens epithelial cells that shed light on novel mechanism underlying the cataract and small size of the Cx50KO lenses.

overall_design:
Single-cell RNA sequencing (scRNA-seq) of lens epithelial cells isolated from one-month-old Cx50KO and wild-type (WT) mice were performed.
Please note that R2 mate file of the 'lens epithelium,cx50ko,biorep1' sample (paired-end) raw data files is corrupted and thus only R1 file is provided as raw data.

first: Chun-Hong

last: Xia

first: William

last: Lin

first: Rachel

first: Xinfang

last: Xing

first: Guangdu

last: Shang

first: Haiwei


title: Single-cell RNA-seq data of large-scale bone calluses from skeletally immature and mature mice

first: Olivier

last: Duverger

address: 30 Convent Drive - Bldg 30 - Room 202

institute: National Institute of Dental and Craniofacial Research

summary: Age and skeletal maturity impacts the capacity for bone regeneration. Using a mouse model of large-scale rib resection, we demonstrated that skeletally immature mice regenerate the rib around 14 days post resection, whereas skeletally mature mice never fully regenerate the rib. Here, we performed single-cell RNA sequencing analysis of rib calluses from skeletally immature and mature mice at 5 and 14 days post-resection to characterize the age-related changes in cell population frequencies and their gene expression profiles during the early and late stages repair of bone repair.

overall_design:
Rib calluses from 4 young skeletally immature and 4 old mature mice at 5 and 14 days post lage-scale rib resection were used in these studies. Repair rib calluses were enzymatically dissociated and analyzed by scRNAseq using 10x Genomics platform.
NIDCD/NIDCR Genomics and Computational Biology Core

first: Luciana

middle: Y

last: de Almeida

first: Daniel

last: Martin

first: Janice

last: Lee


title: Large-scale bone calluses from skeletally immature and mature mice

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

overall_design: Refer to individual Series


title: Bulk RNA-seq data of large-scale bone calluses from skeletally immature and mature mice

summary: Age and skeletal maturity impacts the capacity for bone regeneration. Using a mouse model of large-scale rib resection, we demonstrated that skeletally immature mice regenerate the rib around 14 days post resection, whereas skeletally mature mice never fully regenerate the rib. Here, we performed bulk RNA sequencing analysis of rib calluses from skeletally immature and mature mice at baseline, 0, 2, 5, and 14 days post-resection to characterize the age-related changes in gene expression profiles during the early and late stages repair of bone repair.

overall_design:
Rib calluses were dissected from the rib cages of young skeletally immature and old skeletally mature mice at different stages of rib regeneration (baseline, 0, 2, 5, and 14 days post-resection) and snap frozen. Frozen tissue was ground using a mortar and pestle kept in liquid nitrogen. Powdered frozen tissue was immediately transferred to a clear tube and total RNA was extracted using TriPure Isolation Reagent (Sigma-Aldrich) followed by PureLink™ RNA Mini Kit (Thermo Fisher Scientific).
NIDCD/NIDCR Genomics and Computational Biology Core

first: Natasha

last: Curry

first: Xin

last: Gao


title: On the way to elucidate the effects of cannabidiol (CBD) on living organisms - assessment of changes in the global transcription profile of the hippocampus in a mouse model

city: Kraków

first: Artur

last: Gurgul

address: Rędzina 1C

department: Center for Experimental and Innovative Medicine

institute: University of Agriculture in Krakow

summary: Cannabidiol (CBD) is a phytocannabinoid that has anti-inflammatory, immunomodulatory, antioxidant, anxiolytic, antipsychotic, and anticonvulsant effects. This study aims to examine the effects of CBD on behavior, immune system activity, and stress levels, and to determine its impact on transcriptomic alterations in selected mouse organs.

overall_design: Male mice of the standard C57BL/6J strain were used. The animals were classified into two groups - (I) short-term CBD administration (2 days) and (II) long-term CBD administration (28 days). In each of the main groups, there were three subgroups receiving different doses of CBD - from low, commonly used in supplementation (0.2 mg/kg bw), through medium (10 mg/kg bw), to high, used in some clinical trials (20 mg/kg bw). Additionally, a control group (placebo/vehicle) was maintained in each of the main groups. Chemically pure Cannabidiol (CBD) was administered intraperitoneally (in the research group) to ensure that the substances reached the blood vessels of the digestive system. CBD was administered in a single daily dose. The mice were housed under standard conditions and with standard feeding and watering ad libitum. They were also tested daily (group I) or every third day (group II) to determine well-being and health. After the period of CBD administration, the mice were immediately euthanized and organs such as the brain (various brain structures including hippocampus), spleen, and liver were collected. In this part of the experiment, hippocampus samples were used to isolate total RNA. The recovered RNA was quality assessed and used to prepare directional libraries for high throughput transcriptome sequencing using CORALL mRNA-Seq V2 kit (Lexogen).  The libraries were sequenced commercially in a 2x150bp paired-end run. The obtained sequence data were used to analyze the differential expression between the different CBD dosages and the control group. Differentially expressed genes were classified into particular processes or functions and were subjected to statistical testing for overrepresentation. The synthesis of the obtained data will allow the proposal of potential mechanisms of CBD action and create an atlas of changes taking place in the transcriptome of the main target organs.

first: Jakub

last: Żurowski

first: Sebastian

last: Sawicki

first: Ewa

last: Ocłoń

first: Tomasz

last: Szmatoła

first: Igor

last: Jasielczuk

first: Karolina

last: Mizera-Szpilka


title: Expression data of transmigrated hMSCs from 3D collagen barriers

city: Hong Kong

first: Pui

last: Chan

state: Hong Kong

address: Room 711, Haking Wong Building, The University of Hong Kong, Pokfulam Road

department: Department of Mechanical Engineering

institute: The University of Hong Kong

summary: Identification of molecular pathways induced by 3D collagen encapsulation and transmigration of hMSCs via collagen barriers

overall_design: Human MSCs isolated from two subjects were encapsulated in 3D collagen (3DM) followed by a total of 9-day cultivation and  transmigration via collagen barriers in comparison to seeding 2D monolayer MSCs for the same period. Total RNA was extracted from cells by the RNeasy Mini Kit (Qiagen), and gene expression profiling was performed using an Affymetrix Human Gene 2.0 ST microarray platform.

first: B

middle: P

first: H

last: Wong

first: M

first: Y

first: K

last: Lam

last: Li

last: Tong

first: D

last: Hua

first: S

last: Han

first: Z

last: Yang

first: G

middle: C


title: Functional and mechanistic study of the inhibitory role of the antisense long non-coding RNA (IRF1-AS1) in regulating the transcriptional activity of IRF1 and M1 polarization of macrophages in ARDS.

city: Jinan

first: zhang

last: shi

address: handong First Medical University

institute: handong First Medical University

summary: Through high-throughput sequencing and further cell and animal experiments, we found that the antisense long non-coding RNA of IRF1 (IRF1-AS1) binds to the intronic region of IRF1, inhibiting its transcriptional activity and thereby regulating macrophage activation and inflammation-induced lung injury in ARDS.

overall_design: CD14 cells were obtained from our hospital's biobank. After 48 hours of in vitro colony-stimulating factor induction, total RNA and DNA were extracted from cells treated with LPS and IFNγ for 24 hours. ChIP-seq/ATAC-seq and RNA-seq were performed using specific antibodies and assay kits.

first: Shi

last: Zhang


title: scRNAseq of mouse proliferative vitreoretinopathy

city: Tianjin

first: ye

last: zhisheng

address: qixiangtai road no.22

institute: tianjin medical university general hospital

summary: We performed single cell transcriptional profiling of mouse proliferative vitreoretinopathy (PVR), to decipher the molecular mechanisms underlying mouse PVR fibrogenesis. In this study, through combination of the single-cell transcriptional profiling and genetic tracing, we provided comprehensive discrimination for the sources of PVR-associated fibroblasts during ocular wound healing.

overall_design: Single-cell RNA-seq (10X) data from disperesed proliferative vitreoretinopathy of dispase induced mice. Dispase (Sigma) was intravitreal injected in 8-week-old C57BLJ/6 mice and sacrificed in 7 days.

first: Mengyu

last: Liao

first: Zhisheng

last: Ye

first: Xiaohong

last: Wang

first: Hua

last: Yan


title: Differential gene expression in BCap37 cell xenografts in nude mice with different treatments.

city: Wuxi

first: Junjie

address: No. 20 Qianrong Road

institute: Jiangsu Institute of Nuclear Medicine

summary: The mechanism of LM treatments remains unknown. Therefore, RNA-seq was employed to investigate the function of each drugs.

overall_design: We treated xenografts with saline, Ga, TM, LM after reaching proper tumor size, respectively. Then we performed tissue homogenization of xenografts and extracted RNA by Trizol reagent kit.


title: Deciphering histone mark-specific fine-scale chromatin organization at high resolution with Micro-C-ChIP

city: Copenhagen

first: Mariia

last: Metelova

address: Blegdamsvej 3b

department: Novo Nordisk Foundation Center for Protein Research

country: Denmark

institute: Copenhagen University

summary: The regulation of cell-type-specific transcription programs is a highly controlled and complex process that needs to be fully understood. The gene regulation is often influenced by distal regulatory elements and their interactions with promoters in three-dimensional space. Although proximity ligation techniques like Hi-C have revolutionized our understanding of genome organization, the genomic resolution for many of these methods is limited by both experimental and financial constraints. Here, we introduce Micro-C-ChIP to provide extremely high-resolution views of chromosome architecture at genomic loci marked by specific covalent histone modifications. This is achieved by affinity isolation of specific chromatin states in order to target chromosome folding libraries to focus on chromatin domains (regulatory elements, heterochromatin, etc.) of interest, yielding extremely high sequencing depth at these loci. We applied Micro-C-ChIP to mouse embryonic stem cells (mESC) and hTERT-immortalized human retinal epithelial cells (hTERT-RPE1), revealing architectural features of genome organization with comparable or higher resolution than Micro-C datasets sequenced to 10X higher depth. In particular, we discovered extensive promoter-promoter networks in both cell types and characterized the specific architecture of bivalently bookmarked promoters in mESC. Together, these data highlight Micro-C-ChIP as a cost-effective approach to exploring the landscape of genome folding at extraordinarily high resolution.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Micro-C-ChIP was performed against H3K4me3 and H3K27me3 in two cell types, mESC and hTERT-RPE1. Each condition (histone marks and cell types) has two biological replicates.The replicates for each condition were merged and converted to mcool format.

first: Nils

last: Krietenstein


title: Analysis of differential expression of circular RNAs between psoriatic lesional tissues and healthy skin tissues

status: Public on Sep 04 2025

city: Harbin

first: jiangtian

last: Tian

state: Heilongjiang

address: 246 Xuefu Road

institute: The  Second Affiliated Hospital of Harbin Medical University

type: Non-coding RNA profiling by high throughput sequencing

summary: Psoriasis is a chronic inflammatory skin disorder characterized by abnormal keratinocyte proliferation and immune dysregulation. Circular RNAs (circRNAs) have emerged as important regulators of gene expression in various diseases, but their expression patterns and potential roles in psoriasis remain incompletely understood.In this study, we performed circular RNA sequencing on lesional skin tissues from 3 psoriasis patients and normal skin tissues from 2 healthy individuals. The identified DEcircRNAs, particularly circLDLR, may serve as promising diagnostic biomarkers or therapeutic targets for psoriasis.

overall_design: Circular RNA sequencing analysis of lesional tissues from 3 psoriasis patients and skin tissues from 2 healthy individuals

first: Jiangtian

first: Xuanqi

last: Deng

first: Siyu

last: Hao


title: Nuclear accumulation of ADAMTS1 zymogen: A novel mechanism promoting chemoresistance and metastasis in breast cancer [RNA-Seq]

city: beijing

first: wang

middle: xi

last: lin

address: 10 You’anmen Outer West 1st Street

institute: capital medical univercity

summary: Chemoresistance and metastasis are the primary causes of mortality in patients with breast cancer. Here, we demonstrated that the metalloproteinase ADAMTS1 is upregulated in chemotherapy-treated and metastatic breast cancer samples. Mechanistically, the zymogen form of ADAMTS1 undergoes nuclear translocation via importin-dependent transport, where it cooperates with the SWI/SNF complex to activate a set of genes, including TBK1, STING, TRAF6, and MARCHF2, leading to STING ubiquitination and the non-classical cGAS-STING-NF-kB signaling activation, which in turn promotes chemoresistance and metastasis. Notably, long-term chemotherapy establishes a self-reinforcing loop by: (i) NF-kB/p65-mediated transcriptional induction of ADAMTS1, and (ii) MARCHF2-dependent ubiquitin-proteasomal degradation of FURIN, the protease responsible for ADAMTS1 maturation. This dual regulation results in nuclear accumulation of catalytically inactive ADAMTS1 zymogen. Clinical analyses have shown that high ADAMTS1 expression combined with low FURIN expression is strongly associated with poor patient prognosis. These results reveal a key role for the zymogen ADAMTS1 in inducing tumor chemoresistance and metastasis in response to long-term chemotherapy stimulation, supporting the use of its inhibitor melatonin as a therapeutic strategy in combination with chemotherapy for patients with breast cancer.

overall_design: we overexpressed ADAMTS1 in MDA-MB-231 cells and performed RNA sequencing (RNA-seq) .

first: Zhaohan

first: Yu

first: Xilin

first: Yaning

first: Zicheng

last: Wu

first: Minghui

last: Zhao

first: Yuchen

last: Xiang

first: Wenying

last: Zhong

first: Tingting

first: Yingqi

last: Lv

first: Wenjuan

first: Lulu

first: Jia

first: Hao

last: Zhuang

first: Lin

last: Shan


title: Alpha hemolysin enhances the immune response by modulating dendritic cell differentiation via ADAM10-Notch signaling

city: Chongqing

first: Ke

address: No. 30, Gaotan Yanzheng Street, Shapingba District, Chongqing

institute: Army Medical University

summary: In this study, we used PA0833 a novel protective antigen from Pseudomonas aeruginosa (P. aeruginosa) as the target antigen to evaluate the immune protective effect of the carrier antigen HlaH35A. The transcriptional profiling of bone marrow derived dendritic cells (BMDCs)  from mice indicated that HlaH35A predominantly modulates DC maturation, cytokine production, and subsequent T-cell activation. Structural prediction (AlphaFold-Multimer) and fluorescence confocal microscopy confirmed that the specific binding of HlaH35A to ADAM10 enhanced its antigen uptake capacity in dendritic cells. Meanwhile, this interaction between HlaH35A and ADAM10 further activated the downstream Notch signaling transduction in dendritic cells. The HlaH35A-ADM10–Notch axis in cDCs drives their differentiation into type2 cDCs (cDC2s)—particularly the Notch2-dependent cDC2—rather than involving monocyte-derived dendritic cells. This process promotes Th17 and T follicular helper (Tfh) cell responses in draining lymph nodes, leading to elevated antigen-specific IgG1 titers and robust protection against acute Pseudomonas aeruginosa lung infection. Thus, HlaH35A enhances immune response against acute lung infection by modulating cDC differentiation to amplify Th17 and T follicular helper responses, providing a promising Th17/Tfh-oriented vaccine design strategy.

overall_design: We collected bone marrow cells from the femurs and tibias of BALB/c mice. The cells were then cultured in RPMI-1640 medium supplemented with 10% FBS, penicillin and streptomycin and human recombinant Flt3L. The cells were harvested on day 8 and stimulated for 7.5 h. The cells were then subjected to bulk RNA-seq sequenced on the DNBSEQ platform (BGI).


title: Murine kidneys： WT Models vs  METTL3-cKO Models

city: Hefei

first: Bingbing

last: Hou

state: China

address: No. 218 Jixi Road, Hefei 230032, China

institute: Department of Urology, First Affiliated Hospital of Anhui Medical University

summary: MeRIP and RNA Epitranscriptomic Microarray analysis in kidneys of conditional knockout (cKO) METTL3 mice and wild type mice following glyoxylate-induced CaOx nephrocalcinosis.In METTL3-cKO mice, METTL3 subjected the specific absence from renal tubular epithelial cells. Goal was to determine the effects of METTL3 gene knockout on the expression and N6-methyladenosine (m6A) modifications of global  gene.

overall_design:
Two-condition experiment, WT Models vs  METTL3-cKO Models. Biological replicates: 3 WT Models replicates, 3 METTL3-cKO Models replicates.
These two-channel arrays were analyzed with a single-channel method so that each sample and dye is represented by a separate sample(GSM) in this series.

first: Zongyao


title: Cpeb4 regulates cardiomyocyte apoptosis/proliferation imbalance in heart failure via modulating Eif4a2 splicing

city: Urumqi

first: Zhang

middle: Qing

last: hua

state: Xinjiang

address: Liudao Bay Street

institute: The Second Affiliated Hospital of Xinjiang Medical University

summary: Heart failure (HF) involves pathological cardiac remodeling, including cardiomyocyte loss and dysfunction. While the RNA-binding protein CPEB4 has been linked to cardiomyocyte activation, its role in HF remains unclear. We established in vivo and in vitro models of cardiac injury using isoproterenol (ISO). An HF mouse model was induced by chronic ISO administration (10 mg/kg/day, 3 weeks), while cellular injury was modeled by treating HL-1 cardiomyocytes with ISO (10 μM, 48 h). To investigate the molecular mechanisms, we employed transcriptome sequencing, qRT-PCR, and functional assays following siRNA-mediated knockdown of Cpeb4. Key endpoints included cell viability (CCK-8), apoptosis (Annexin V/7-AAD flow cytometry), and the alternative splicing of Eif4a2. In the HF mouse model, we observed significant cardiac hypertrophy and inflammatory infiltration, which correlated with a marked upregulation of Cpeb4 expression in cardiomyocytes. Notably, in vitro, siRNA-mediated knockdown of Cpeb4 significantly attenuated ISO-induced apoptosis and enhanced cell viability in HL-1 cells. Mechanistically, Cpeb4 depletion corrected the ISO-induced dysregulation of Eif4a2 alternative splicing, restoring the expression of its major isoforms and thereby ameliorating cellular injury. Our study identifies the Cpeb4-Eif4a2 axis as a key regulator in heart failure, with Cpeb4 driving cardiomyocyte apoptosis via aberrant Eif4a2 splicing, suggesting a promising therapeutic target.

overall_design: Male SPF-grade C57BL/6 mice were injected subcutaneously with ISO (10 mg/kg/d) for 3 weeks to establish a heart failure model. The control group mice were injected with the same volume of normal saline.

first: Changsheng

last: Xu

first: Qinghua

last: Zhang

first: Jinglong


title: Foxn3 is part of a transcriptional network that regulates primary cilia in the developing mouse retina [RNA-Seq]

city: Ann Arbor

first: David

last: Turner

address: 109 Zina Pitcher Place

department: Michigan Neuroscience Institute

institute: University of Michigan

summary: Analysis of retinas from mice with a targeted disruption of the Foxn3 gene revealed additional displaced amacrine interneurons and additional retinal astrocytes in the inner plexiform layer and in the ganglion cell layer. The forkhead transcription factor Foxn3 is a transcriptional repressor. Numerous genes linked to cilia structure or assembly were upregulated in embryonic retinas without Foxn3, including Foxj1, a forkhead transcription factor required for motile cilia. Ectopic primary cilia were observed on bipolar and amacrine interneurons in postnatal retinas without Foxn3. CUT&RUN analysis revealed that many upregulated retinal genes were bound by the Foxn3 and Rfx3 proteins. A short hydrophobic motif shared by Foxj1, Foxn4, and Foxn3 proteins was found to be required for association with the Rfx3 protein and for transcriptional repression by Foxn3, as well as for full transcriptional activation by Foxn4 with Rfx3. AlphaFold 3 predicts an interaction between the hydrophobic motif and the Rfx3 dimerization domain. Mutations in Rfx3 at the predicted interaction site disrupted association of Rfx3 with Foxn3 or Foxn4. These results reveal a new layer of transcriptional regulation of genes required for cilia, with Foxn3 functioning as a repressor of cilia genes and limiting primary cilia formation in the developing retina.

overall_design: RNA-seq analysis of gene expression in E19 retinas from wild-type and Foxn3 knockout (C57BL/6NJ-Foxn3em1(IMPC)Bay/Mmnc) embryos.

first: Fan

last: Meng

first: Huanqing


title: Foxn3 is part of a transcriptional network that regulates primary cilia in the developing mouse retina [CUT & RUN]

overall_design: CUT&RUN analysis of genomic binding sites for the Foxn3, Foxn4, and Rfx3 transcription factors in E16 CD-1 mouse retinas.


title: Adoptive Macrophages Suppress Glioblastoma Growth by Reversing Immunosuppressive Microenvironment through Programmed Phenotype Repolarization

city: Shanghai

first: Yang

last: Fan

address: Zhangheng Road 826

institute: Fudan University

summary: Glioblastoma (GBM) is a highly lethal brain tumor resistant to immunotherapy due to poor drug brain delivery and an immunosuppressive microenvironment. This study introduces a macrophage-based adoptive cell therapy that reprograms the tumor immune landscape to suppress GBM growth. We reveal that  macrophage homing to GBM is phenotype-dependent, with anti-inflammatory macrophages more efficiently navigating brain vasculature and targeting tumors. Based on this observatioin, we developed engineered M2-like macrophages (eM2-Mφs) capable of programmable polarization. These adoptive cells maintain an anti-inflammatory phenotype during early circulation, allowing deep tumor infiltration, and subsequently switch to a proinflammatory state within the tumor to trigger immune activation. Treatment with eM2-Mφs alone, or combined with low-dose irradiation and/or checkpoint inhibitor, remarkably suppressed tumor growth and extended survival in mouse models. This approach offers a promising strategy to overcome GBM’s immunosuppressive barriers and enhance immunotherapy efficacy

overall_design: After treatment,the single-cell suspension from glioma specimens was stained with Fixable Viability Dye eFluor™ 780 and antibodies of anti-mouse CD45.2 and anti-mouse CD45.1  for fluorescence activated cell sorting (FACS). Single living endogenous immune cells (eFluor™ 780-CD45.2+CD45.1-) were sorted and collected after FACS, following analyzed with single cell RNA-seq.

first: Hang

last: Yin

first: Jing

first: Bolin

last: Yao

first: Guangli

last: Cheng

first: Yaqi

last: Yang

first: Minghao

first: Luo

last: Chen

first: Jian

first: Ji

last: Zhou

first: Ren

last: Li

first: Botao

first: Xiao-Yong

first: Cong

last: Wang

first: Xihui

last: Gao


title: Transcriptomic profiile of B16F10 melanoma cell treated with Olive oil and Ozoanted olive oil

city: Sapporo-shi

first: Seong-jin

last: An

state: Hokkaido

address: Kita 12 nishi 6, kita-ku

department: Graduate School of Pharmaceutical Sciences

institute: Hokkaido university

summary: To investigate the transcriptional effects of ozonated olive oil, we performed a comprehensive gene expression analysis of B16F10 murine melanoma cells treated with either ozonated olive oil or olive oil as a control.

overall_design: B16F10 cells were treated with olive oil or ozonated olive oil for 6 h and gene expression profile was analyzed by NGS.

first: Jun-ichi

last: Kashiwakura

first: Sumihito

last: Togi

first: Tadashi

last: Matsuda


title: Transcriptomic profiile of A375 melanoma cell treated with Olive oil and Ozoanted olive oil

summary: To investigate the transcriptional effects of ozonated olive oil, we performed a comprehensive gene expression analysis of A375 human melanoma cells treated with either ozonated olive oil or olive oil as a control.

overall_design: A375 cells were treated with olive oil or ozonated olive oil for 6 h and gene expression profile was analyzed by NGS.


title: Developmental regulation of long-range neuroblast migration by Eph/ephrin signaling

city: Storrs

first: Daria

last: Yeroshenko

state: Connecticut

address: 75 North Eagleville Road

department: PNB

institute: University of Connecticut

summary: In the developing mouse anterior forebrain, the rostral migratory stream (RMS) supports continued proliferation and efficient transportation of large quantities of neuroblasts from the ventricular-subventricular (V-SVZ) stem cell niche to the olfactory bulb (OB). Astrocytes aid this migration by providing a glial network through which chains of fasciculated neuroblasts move. The largest receptor tyrosine kinase family, Eph receptors, and their ephrin ligands have been implicated in controlling neuroblast migration and astrocyte organization within this pathway. However, a clear understanding of the regulatory mechanisms underlying Eph/ephrin signaling remains elusive, in part due to the complexity of heterogeneous expression patterns in both neuroblasts and astrocytes, as well as the cytoarchitectural changes that occur during postnatal development. Our studies provide a framework to deconvolute and characterize Eph and ephrin signaling as the RMS changes from a diffuse stream of migratory neuroblasts to a highly constricted pathway of neuroblast chains within astrocytic networks. Specifically, we identify temporally regulated, cell type-specific receptor-ligand interactions, revealing the prevalence and dynamic shifts of neuroblast-neuroblast, neuroblast-astrocyte, astrocyte-astrocyte interactions.

overall_design: Mice were harvested at P6, P12, or P60 ages. Their brains were harvested, and the rostral migratory stream was microdissected. Live cells were sorted by FACS from dead cells and debris and analyzed using scRNA seq.

first: Chamalka

last: De Silva

first: Anika

last: Burli

first: Sarah

last: Bellizzi

first: Vijender

last: Singh

first: Joanne

last: Conover


title: Diminished osteogenic capacity in mature periodontal ligament stem cells via RELB downregulation

city: Xi’an

first: Xin

last: Shao

address: 98 Xiwu Road

institute: Xi’an Jiaotong University

summary: Although periodontal ligament stem cells (PDLSCs) are pivotal for periodontal tissue regeneration, their regenerative capacity diminishes with the PDL maturity. This study aims to elucidate the mechanisms underlying this phenomenon.Single-cell RNA sequencing (scRNA-seq) was conducted on immature and mature human PDL tissues to characterize the heterogeneity and predict critical regulators affecting osteogenic capacity of PDLSCs. Subsequently, the predicted role of RELB was experimentally validated both in vitro and in vivo using small interfering RNA.Our scRNA-seq analysis revealed significant heterogeneity within the PDLSC population. Notably, PDLSC-5 subtype, which exhibited osteogenic potential and positioned at the terminus of the pseudotime trajectory, was markedly reduced in mature PDL tissues. RELB was specifically overexpressed in PDLSC_5 and identified as a key transcription factor (TF) for this subcluster. Knockdown of RELB significantly inhibited the osteogenic differentiation capacity of PDLSCs in vitro and bone formation potential in vivo at both developmental stages. This inhibitory effect appears to be mediated, at least in part, through the downregulation of its target gene, superoxide dismutase 2 (SOD2).This study demonstrates that the proportion of PDLSCs with osteogenic ability significantly declines with maturity, accounting for the diminished regeneration capacity of mature periodontal tissue. Furthermore, RELB was identified as a crucial TF for maintaining the osteogenic potential of PDLSCs. These findings provide a theoretical basis for strategies aimed at optimizing the bone regeneration capacity of PDLSCs.

overall_design: For orthodontic reasons, human premolars without endodontic or periodontal disease were extracted at the Stomatology Hospital of Xi’an Jiaotong University and used for PDL isolation. All donors signed informed consent forms. According to the root developmental stage and donor age, the obtained teeth were divided into 2 groups, one group with 1/2-2/3 root development was called immature group, and the other group with complete root development was named mature group. PDL tissues from the root surface were collected for PDLSCs culture and scRNA-seq.After enzymatic digestion and lysis of red blood cells, the cell suspension of PDL tissues were filtered and counted. Libraries were constructed using Single-Cell 3′ Reagent Kit v3.1 (10× Genomics) according to the manufacturer’s protocol. Indexed libraries were pooled and sequenced on an Illumina sequencer using paired-end 26×98 bp read length.After non-linear dimensional reduction using uniform manifold approximation and projection (UMAP), clustering was run using the FindNeighbors and FindClusters functions with the SLM algorithm and 27 interactions. Clustering was performed at varying resolution values with a value of 1.5 used as the initial stage. Clusters were assigned preliminary identities based on the expression of combinations of known marker genes for major cell classes and types. Subclustering was performed on each major cell type data subset to resolve additional cell types and subtypes.

first: Fan

last: Wu

first: Yang

last: Song

first: Peng

first: Kun

last: Qi

first: Liying


title: RNA-seq of primary cardiomyocytes under ischemia-reperfusion injury reveals altered expression in DNA damage repair genes including Xrcc6

city: Xiamen

first: Hongwen

last: Xiao

state: Fujian

address: No. 1999, Guankou Middle Road, Jimei District

department: Department of Basic Medicine

institute: Xiamen Medical College

summary: To investigate the molecular response of cardiomyocytes to ischemia-reperfusion (I/R) injury, we established an in vitro I/R model using primary neonatal mouse cardiomyocytes. Oxidative stress was simulated by treating the cells with 100 μM hydrogen peroxide (H₂O₂) for 24 hours, followed by a 24-hour recovery period in complete medium to mimic the ischemia and reperfusion phases, respectively. Bulk RNA sequencing was performed on both control (n = 3) and I/R-treated (n = 4) cardiomyocytes. Transcriptomic profiling identified differentially expressed genes and enriched pathways associated with oxidative stress response, DNA damage repair, and regulation of cell death. This dataset provides valuable insights into the molecular mechanisms underlying myocardial I/R injury and may help identify potential therapeutic targets.

overall_design: Primary cardiomyocytes were isolated from 1–3-day-old C57BL/6 neonatal mice and cultured under standard conditions. The ischemia-reperfusion (I/R) injury model was induced in vitro using 100 μM H₂O₂ in serum-free medium for 24 hours to simulate ischemia, followed by replacement with normal culture medium for another 24 hours to mimic reperfusion. RNA was extracted from untreated control (n=3) and I/R-injured(n=4) cells, and RNA-seq libraries were constructed using the VAHTS Universal V5 RNA-seq Library Prep Kit. Sequencing was performed on the Illumina NovaSeq 6000 platform. Differential expression and pathway analyses were conducted to identify genes associated with oxidative stress, DNA damage, and potential drug targets.

first: Yijie

last: He

first: Jin

last: Li

first: Linlong

last: Guo

first: Mu

last: Chen

first: Haiqing

last: Pan

first: Zhanqing

first: Hua

last: Tian

first: Huan

last: Yu

first: Yuhong

last: Zhou


title: AS03-adjuvanted chimeric HA-based influenza vaccine induces long-lived stalk-specific plasma cells in bone marrow and lymph nodes of non-human primates

city: Atlanta

first: Gregory

last: Tharp

state: GA

address: 954 Gatewood Dr

department: Developmental and Cognitive Neuroscience

institute: Yerkes National Primate Research Center

summary: Current influenza vaccines face challenges due to antigenic evolution of the circulating virus and waning immunity in humans. Here, we investigated the durability of humoral immunity induced by an AS03-adjuvanted chimeric hemagglutinin (cHA) based influenza vaccine in non-human primates (NHPs). Two groups of NHPs (n=7 or 8) received two doses of a seasonal quadrivalent influenza vaccine (QIV) on weeks 0 and 4, followed by sequential immunization with split virus cHA vaccines cH8/1N1 (week 21), and cH5/1N1 (weeks 33 and 94). One group received cHA immunizations with AS03 adjuvant. We monitored serum antibodies and long-lived plasma cells in bone marrow for nearly 2 years after the final vaccination. The seasonal QIV vaccine induced poor HA stalk-specific antibodies and failed to give rise to detectable long-lived plasma cells in bone marrow. In contrast, cHA vaccines significantly induced stalk-specific antibody responses. Importantly, the addition of AS03 enhanced both the magnitude and durability of humoral immunity by establishing the persistence of long-lived plasma cells in the bone marrow and lymph nodes for nearly 2 years. Passive transfer of NHP serum provided protection against challenge with heterologous influenza A virus strains in mice. This study highlights the potential of the AS03-adjuvanted chimeric HA vaccine strategy to provide durable and broadly protective humoral immunity.

overall_design: Ten male Rhesus macaques were innoculated with cH5/1N1, five in an un-adjuvanted group and 5 adjuvanted with AS03, following a common immunization with QIV. Blood samples were collected at Days 0, 1, 2, 4 and 7 post-innoculation for RNA-Seq analysis.

first: Akil

last: Akhtar

first: Tiffany

last: Styles

first: Chunyang

last: Gu

first: André

middle: N

last: León

first: Kasey

last: Stokdyk

first: Anass

last: Abbad

first: Cora

last: Hirst

first: Shirin

last: Strohmeier

first: Gabriele

last: Neumann

first: Sara

middle: T

last: Richey

first: James

last: Ferguson

first: Hasan

last: Ahmed

first: Julianna

last: Han

first: Juan

last: Carreño

first: Carl

middle: W

last: Davis

first: Rustom

last: Antia

first: Peter

last: Palese

first: Andrew

middle: B

last: Ward

first: Yoshihiro

last: Kawaoka

first: Florian

last: Krammer

first: Rafi

first: Rama

middle: R

last: Amara


title: Precision Medicine Study of Post-Exertional Malaise epigenetic changes in Myalgic Encephalomyelitis/Chronic Fatigue patients during Exercise

city: Dunedin

first: Aniruddha

last: Chatterjee

state: Otago

address: 270 Great king Street

department: Pathology

country: New Zealand

institute: University of Otago

summary: We generated reduced representation bisulfite sequencing (RRBS) data of 21 samples (5 ME/CFS patients and 2 Healthy Controls at 3 time points, 0h, 24h, 48h each) from PBMCs to understand the epigenetics behind Post-exertional Malaise in ME/CFS patients.

first: Sayan

last: Sharma

first: Lynette

last: D. Hodges

first: Katie

last: Peppercorn

first: Jemma

first: Christina

last: D. Edgar

first: Euan

last: J. Rodger

first: Warren

last: P. Tate


title: Anti-Leukemic Effects of Velcrin in SLFN12-Expressing Acute Myeloid Leukemia

city: Chicago

first: Priyam

last: Patel

state: IL

address: 750 North Lake Shore Drive, Rubloff 11-146

department: Quantitative Data Science Core

institute: Northwestern University

summary: Schlafen 12 (SLFN12) is a member of the Schlafen (SLFN) family of proteins, a group of interferon-stimulated genes with diverse roles in cellular regulation with implications for human malignancies. Accumulating evidence indicates that SLFN family proteins may serve as prognostic markers across various cancer types. In acute myeloid leukemia (AML), SLFN12 is notably overexpressed, which prompted us to investigate its potential as a therapeutic target. Employing a panel of leukemia cell lines, we explored the effects of velcrins, a class of small molecules able to modulate SLFN12 biological activity. Mechanistic studies showed that velcrin treatment increases expression of SLFN12 and promotes SLFN12 complex formation with PDE3A or PDE3B. Functionally, these effects were associated with growth inhibition and induction of apoptosis. Further, velcrin treatment induced potent suppressive effects on the clonogenic capability of primary human AML progenitors and suppressed tumor growth and significantly extended survival in a mouse AML xenograft model. Taken together, these findings highlight the potential of using velcrins as a promising therapeutic strategy for the treatment of AML patients.

overall_design: Animal experiment protocols were approved by the Northwestern University Institutional Animal Care and Use Committee and performed accordingly. 5–6-week-old NU/NU nude female mice were acquired from Charles River laboratories (Strain Code 088). To induce flank tumors, 5x106 early passage HEL cells in the logarithmic growth phase were collected, washed, and resuspended in a final volume of 100 µL in PBS and loaded into a U-100 insulin syringe with an attached 27-gauge needle and injected into the right flank.  Approximately 13 days after injection, once tumors were palpable, tumor measurements were collected and mice were randomized into two treatment groups: vehicle control or treatment with a velcrin (BAY 2666605), with 5 mice per group. Mice were treated with vehicle control or BAY 2666605 (5 mg/kg), which was administered orally, twice daily for 2 weeks, with two days off. Tumor size was measured three times per week by caliper and the formula was calculated as follows (D × d2)* π/6, where D is the longest diameter and d is the shorter diameter.  Body weights and clinical observations were recorded 3 times per week.  For survival, mice were observed daily and all animals were compassionately euthanized 30 minutes following the last treatment dose. Tumor sections (n=4 per experimental group) were subsequently processed for SDS page or RNA-seq analysis.

first: Jamie N

last: Guillen Magaña

first: Markella

last: Zannikou

first: Aneta

middle: H

last: Baran

first: Elspeth

last: Beauchamp

first: Matthew

last: Schipma

first: Elizabeth

last: Bartom

first: Leonidas

last: Platanias


title: Modulation of immune response and tissue repair mechanisms in the gill filaments of Atlantic salmon (Salmo salar) affected by complex gill disease (CGD) in a marine open sea-cage environment

city: Santiago

first: Felipe

middle: E.

last: Reyes-López

state: Santiago

address: Av. Libertador Bernado O'Higgins 3363

country: Chile

institute: Universidad de Santiago de Chile

summary: Complex gill disease (CGD) presents significant challenges in Atlantic salmon aquaculture, resulting in reduced growth, higher production costs, and mortality rates of up to 80%. CGD is influenced by a multifactorial interaction of environmental factors and pathogens. Given the impact of CGD and the lack of molecular studies aimed at its characterization and modulation, the objective of this work was to analyze changes in the modulation of genes and biological processes that take place in the CGD-affected gill filaments in Atlantic salmon. Gill samples were taken from CGD-affected fish at an open sea-cage marine farm in the Patagonian fjords of Chile (Aysen Region). Gills were portioned into damaged (CGDdt) and undamaged (CGDndt) tissue for total RNA extraction and subsequent transcriptomic analysis by RNA-Seq, to identify differentially expressed genes and the biological functions they belong to. As a control, gill filaments from healthy fish were also sampled. The results demonstrated a clear distinction in gene expression profiles between CGDdt and CGDndt, with 364 upregulated differentially expressed genes (DEGs) and 332 downregulated, identified with key genes such as mmp9, ccl19, and il8, indicating a promotion of a pro-inflammatory environment. In contrast, underexpression of processes associated with cellular homeostasis, cell communication, and structural development suggests altered tissue homeostasis and regeneration. The comparison between CGDndt and control showed changes in the expression of 5ntla and ca12 that suggest the activation of response mechanisms due to the proximity with the branchial filament affected by CGD. In sum, this study provides valuable insights into the transcriptomic responses of Atlantic salmon to CGD and improves the understanding of tissue repair mechanisms in the mucosal tissues of aquatic organisms.

overall_design: RNA-seq profiling of Atlantic salmon gill filament tissue samples from healthy (control) and complex gill disease (CGD) fish, differentiating between damaged tissue (CGDdt) and undamaged tissue (CGDndt).

first: Mabel

last: Vidal

first: María Jesús

last: Santillán-Araneda

first: Alexis

last: Rivera

first: Merari

last: Goldstein

first: Sebastian

last: Reyes-Cerpa

first: Marcos

last: Mancilla

first: Patricio

last: Bustos

first: Eva

last: Vallejos-Vidal

middle: E


title: Sulfatide deficiency-induced astrogliosis and myelin lipid dyshomeostasis are independent of Trem2-mediated microglial activation_Male cerebrum study

city: SAN ANTONIO

first: Sijia

last: He

state: Texas

address: 7703 Floyd Curl Dr.

institute: uthealth sa

summary: This study investigates the impact of central nervous system sulfatide (ST) deficiency on gene expression in the male mouse cerebrum tissues, both in the presence and absence of Trem2, using the NanoString Neuroinflammation panel.

overall_design: The measurement set contains 12 samples, composed of 4 genotypes (Cre-/Trem2 WT, Cre-/Trem2 KO, Cre+/Trem2 WT, and Cre+/Trem2 KO) in triplicates. Note that Cre- indicate mice with ST, Cre+ indicate mice of adult-onset ST-deficiency.

first: Namrata

last: Mittra

first: Xianlin

last: Han