title: Identification of Diagnostic Exosomal miRNAs and Pathogenic Regulatory Networks in Hepatocellular Carcinoma via mRNA Sequencing

city: GuiLin

first: jingwen

last: Xiao

address: No.109, Huancheng Beier Road

institute: GuiLin Meidical University

summary: Background/Objectives: Hepatocellular carcinoma (HCC) is the sixth most common malignancy worldwide and the third leading cause of cancer-related mortality. Prognosis is stage-dependent, but most patients are diagnosed at advanced stages when curative treatment is not feasible. Alpha-fetoprotein (AFP), the most widely used biomarker, has limited sensitivity and specificity for early detection. Serum-derived exosomal mi-croRNAs (miRNAs) are stable in circulation, tumor-specific, and actively involved in cancer biology, making them promising non-invasive biomarkers. This study aimed to identify, validate, and functionally characterize serum-derived exosomal miRNAs with diagnostic potential in HCC.   Methods: Serum exosomes were isolated from 50 HCC pa-tients and 50 matched healthy controls, characterized by transmission electron micros-copy, nanoparticle tracking analysis, and CD9/CD63/CD81 flow cytometry. High-throughput small RNA sequencing of 3 HCC and 3 control samples identified dif-ferentially expressed miRNAs (DEMs). Target genes were predicted via multiple data-bases, integrated into STRING protein–protein interaction networks, and analyzed with cytoHubba. Gene Ontology (GO) and KEGG enrichment analyses were performed. Hub gene expression and survival relevance were evaluated using GEPIA2. Candidate miRNAs were validated by RT-qPCR, and diagnostic performance was assessed with receiver operating characteristic (ROC) analysis. Results: Seven DEMs were identified; FOXO1 and SRSF11 emerged as hub genes. hsa-miR-27a-3p targeted FOXO1, and hsa-miR-493-3p targeted SRSF11. RT-qPCR confirmed hsa-miR-27a-3p upregulation (P = 0.003) and hsa-miR-493-3p downregulation (P = 0.014) in HCC exosomes. ROC analysis showed high diagnostic accuracy for hsa-miR-493-3p (AUC = 0.840) and hsa-miR-27a-3p (AUC = 0.827), comparable to AFP (AUC = 0.828), with improved performance when combined. Conclusions: Serum-derived exosomal hsa-miR-27a-3p and hsa-miR-493-3p are promising non-invasive biomarkers for HCC, with diagnostic value comparable to AFP and mechanistic links to FOXO1 and SRSF11. Their integration into miRNA-based panels may improve early detection.

overall_design: miRNA-seq profiling of human serum that were collect from 3 patients withHepatocellular Carcinoma and 3 healthy control.

first: Xiao

last: Jingwen

first: Ma

last: Shiyue

first: Tan

last: Qiupei

last: Jianlong

first: Liu

last: Shanshan

first: Shi

last: Qingfeng

first: Yang

last: Jun


title: Basal level of ATF4 promotes T cell readiness for activation-induced proliferation [ATAC-seq]

status: Public on Jan 21 2026

city: Beijing

first: Yushan

last: YI

address: No.38 Xueyuan Road, Haidian District, Beijing

department: Department of Immunology

country: China

institute: Peking University

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Stress responding elements such as eIF2α phosphorylation are either upregulated or required during late-phase T cell activation and differentiation. However, it is not well understood whether these elements are essential within the first 12-24 hours post-stimulation, a period when mitochondrial activation and metabolic reprogramming are critical. Here, we demonstrate that T cell activation-induced mTOR and GCN2 phosphorylation leads to the upregulation of ATF4 protein as early as 12 hours after stimulation. This early induction of ATF4 has transcriptional activities that positively or negatively regulate stress response, signaling, and metabolism. Loss of Atf4 in T cells alters transcriptome dynamics, impairs amino acid transport and biosynthesis, and disrupts cellular adaptive responses to ER stress and oxidative stress. It also hinders cell growth, resulting in defective effector cell differentiation in vitro or in vivo in a chronic LCMV infection model. Our findings suggest that a basal level of ATF4 during the early phase of T cell activation enhances the preparedness of cells to cope with integrated nutritional, protein folding, and oxidative stresses during the activation course. This, in turn, protects cells from stress-related cell death or senescence.

overall_design: Naïve CD8+ T cells were isolated from the lymph nodes of 8-week-old female WT (Atf4fl/fl) and KO (Atf4fl/flCD4Cre) mice , stimulated with anti-CD3 (1 μg/ml) and anti-CD28 (1μg/ml) for 12 hours. Profiling of chromatin was performed by ATAC-seq, 1000000 cells were washed with PBS and resuspended in cold lysis buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% IGEPAL CA-630).

last: Yi

first: Ce

last: luo

first: Xiuyuan

last: Sun

first: Qing

last: Ge


title: microRNA profiles of melanoma samples from patients responsive or resistant to BRAF inhibitor

city: Milan

first: Loris

last: De Cecco

address: via Venezian 1

country: Italy

institute: IRCSS Istituto Nazionale Tumori

summary:
microRNA profiles of formalin-fixed-paraffin-embedded melanoma samples including pre-treatment (PRE) and post-treatment (POST) specimens from 35 patients treated with BRAF inhibitor
90 samples including 66 melanoma metastases and 24 peritumoral normal tissues from 35 patients showing a long-term response (LR) or a short-term response (SR) to treatment

overall_design: Loris, De Cecco


title: Elevated Dnah11 Expression in Hippocampal CaMKII Neurons Impairs Memory via Disrupted Synaptic Plasticity in a Mouse Model of Noise-induced Hidden Hearing Loss

city: Xi'an

last: Fu

address: No.169, Changle West Road

department: School of Aerospace Medicine

institute: Air Force Medical university

type: Expression profiling by high throughput sequencing

summary: Although traditional noise-induced hearing loss (NIHL) has been widely investigated, the cognitive effects of noise-induced hidden hearing loss (NIHHL), particularly its impact on memory, remain poorly understood. The Dnah11 gene, which encodes a dynein motor protein involved in synaptic development, may play a role in NIHHL-related cognitive impairment. We aimed to investigate whether NIHHL induces memory impairment and explore the role of Dnah11 expression in this process. Behavioral experiments identified the peak of memory impairment at 1 month following noise exposure. To elucidate molecular changes, hippocampal gene expression was analyzed using transcriptomic sequencing, reverse transcription quantitative polymerase chain reaction (RT-qPCR), and immunofluorescence. RNA sequencing revealed significant Dnah11 upregulation, with immunofluorescence confirming DNAH11 overexpression in hyperactivated CaMKII-positive excitatory neurons. Stereotaxic injection of recombinant adeno-associated virus (rAAV) vectors to knock down hippocampal Dnah11 expression improved memory performance in NIHHL mice without improving hearing loss. This cognitive improvement was accompanied by partial restoration of synaptic plasticity-related proteins, including SYN and PSD95. These findings indicate that Dnah11 upregulation in hippocampal excitatory neurons contributes to NIHHL-induced cognitive dysfunction, and targeting Dnah11 may offer a therapeutic strategy for memory impairment associated with hidden hearing loss.

overall_design: To identify genes associated with NIHHL-induced memory impairment, we performed transcriptomic sequencing of hippocampal tissues from NIHHL and CON mice 1 month post-induction.Subsequently, RNA-seq data from the CON and NIHHL groups were analyzed to identify genes associated with learning or memory using GO enrichment analysis. Additionally,KEGG pathway enrichment analysis was conducted to identify genes linked to neurodegeneration diseases. The intersection of GO and KEGG analyses facilitated the identification of differential genes.

first: Tong

last: Chang


title: Identification of molecular target of Vindeburnol and its derivatives

city: Moscow

first: Artem

last: Grigorov

address: Ulitsa Miklukho-Maklaya, 16/10

department: Genomics and Postgenomic Technologies

country: Russia

institute: Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry

summary: Natural products (NPs) often act as sources of CNS-active agents and provide inspiration for the development of synthetic molecules that incorporate their best features. Vindeburnol (VIND; (±)-(3α,14β)-20,21-dinoreburnamenin-14-ol; developmental codes RU24722 or BC19), based on the core structure of eburnamine-vincamine alkaloids, has been extensively investigated for its biological activities. This molecule has demonstrated potential therapeutic properties in various in vivo models of CNS disorders such as multiple sclerosis, Alzheimer’s disease, and depressive-like behavior. Many biochemical experiments which characterize vindeburnol influence on neuromediaters have been studied and published but molecular target in CNS is still unknown. Our research is new attempt to discover it.

overall_design: Randomized controlled study comparing vindeburnol (n=5) and VB-127 derivative (n=6) versus untreated controls (n=6) in male C57BL/6 mice. Both compounds administered at 20 mg/kg/day oral gavage for 5 days. Locus coeruleus tissue collected 24h post-treatment for RNA-seq analysis.

first: Yana

last: Zorkina

first: Evgeni

last: Zubkov

first: Olga

last: Riabova

first: Luidmila

last: Borets

first: Tatyana

last: Azhikina

first: Vadim

last: Makarov


title: Leo1 deletion reveals Set1-dependent transcription activation

city: Chuncheon-si

first: Shinae

last: Park

address: Kangwondaehak-gil

country: South Korea

institute: Kangwon National University

summary: Histone H3 lysine 4 methylation is closely associated with gene expression, yet the instructive roles remain incompletely understood. In Saccharomyces cerevisiae, deletion of the Paf1C subunit Leo1 alters transcription without disrupting global H3K4 methylation levels or genome-wide distribution. Under these conditions, a subset of genes involved in sterol transport becomes highly induced and acquires de novo H3K4me3 at promoter-proximal regions. This transcriptional activation is abolished in leo1Δ set1Δ cells and restored by reintroduction of SET1, indicating that Set1-mediated H3K4me3 is required for their expression. The induced genes also exhibit enhanced sterol uptake, indicating physiological relevance. Importantly, these effects are specific to Leo1 deficiency and are not observed in mutants lacking other Paf1C components. Our findings define a native chromatin context in which H3K4me3 directly promotes gene activation, providing in vivo evidence for the instructive role of this histone modification.

overall_design: Sample number (1-8): We performed RNA-seq with WT(1,2), leo1Δ(3,4), leo1Δset1Δ(5.6), and paf1Δ(7,8) strains. Experiments were performed in duplicates.

first: Jung-Shin

last: LEE

last: PARK


title: The effect of modified pharyngeal electrical stimulation on the gene expression profile of the brainstem in rats after brainstem ischemia.

city: Guangzhou

first: Yueqin

last: Tian

state: Guangdong

address: No. 600, Tianhe Road

institute: The Third Affiliated Hospital, SYSU

summary: The therapeutic mechanism of modified pharyngeal electrical stimulation (mPES) for swallowing disorders in rats after cerebral ischemia remains unclear. Here, we validated the therapeutic efficacy of mPES for swallowing disorders in rats after brainstem ischemia and analyzed changes in gene expression profiles at the brainstem single-cell level using single-cell RNA sequencing (scRNA-seq).

overall_design: To investigate the mechanism by which mPES improves swallowing function in rats with swallowing disorders following brainstem ischemia, scRNA-seq analysis was performed on brainstem ischemic dysphagia model rats, either treated or untreated with mPES. The rats were divided into two groups, the Brainstem ischemia group and the mPES group, with two rats in each group. Comparative gene expression profiling analysis was conducted on the single-cell sequencing data from both groups.

first: Qianqian

last: Wang

first: Jiahui

last: Hu

first: Jia

last: Qiao

first: Chao

last: Li

first: Xiangxiang

last: Zhang

first: Tingting

last: Jiang

first: Nenggui

last: Xu

first: Hongmei

last: Wen

first: Zulin

last: Dou

first: Qiuping

last: Ye


title: DKK3 initially preserves acinar integrity through MEK-Fos signalling but later switches to an oncogenic role in PDAC

city: Ulm

first: Alexander

last: Kleger

address: Albert einstein allee 23

department: Institute for Molecular Oncology and Stem Cell biology

country: Germany

institute: Universitaetsklinikum Ulm

summary: Pancreatic ductal adenocarcinoma (PDAC) is characterized by its intricate tumor biology complicated by the spatiotemporal dynamics in the expression and function of specific proteins driving such biology. Here, we employ a mouse model with homozygous and heterozygous DKK3 knockout together with pancreas-specific expression of KRASG12D (DDKC,DKC,KC) to investigate the compartment- and time-dependent roles of DKK3. Our findings demonstrate that DKK3 functions to inhibit oncogenesis during the early stages of cancer while paradoxically promoting tumor progression in the later stages. DDKC and DKC mice exhibited significantly shorter lifespans compared to KC mice, with a higher incidence of high-grade, desmoplastic, “cold” and metastatic cancers. Accordingly, DKK3-deficient acinar cells exhibited a marked increase in acinar-to-ductal-metaplasia, accompanied by increased MAPK-signaling with enhanced expression of the immediate-early genes cfos and Jun. Treatment with the MEK-inhibitor trametinib preserved acinar integrity in DKK3-null pancreata. Additionally, FOS-inhibition restricted the migratory capabilities of DDKC cancer cells. Throughout the progression of mouse and human PDAC, DKK3 expression shifted from epithelial cells to the stromal compartment by the endpoint. DKK3-null tumor cells displayed enhanced migratory abilities when exposed to recombinant DKK3.  In line, DKK3-expressing cancer-associated fibroblasts (CAFs) emerged as crucial contributors to this tumor aggressiveness. Orthotopic transplantation studies revealed that DKK3 expression within CAFs promotes tumor growth and fibrosis, particularly in aggressive DDKC tumors. Collectively, these findings highlight the complex and context-dependent role of DKK3 in PDAC, suggesting that it may serve as a promising therapeutic target for the management of this challenging malignancy.

overall_design: RNA sequencing of pancreatic tumor cells isolated from KC and KC Dkk3 null pancreata

first: Dharini

last: Srinivasan

first: Eleni

last: Zimmer


title: Leo1 deletion reveals Set1-dependent transcription activation [ChIP-Seq]

last: Park

overall_design: Sample number (1-13): We performed anti-H3K4me1, H3K4me2, and H3K4me3 ChIPseq with WT, Δleo1, and Δset1 strains. H3K4me3 ChIP-seq was performed in WT(1,2), Δleo1(3,4), and Δset1(5). H3K4me2 ChIP-seq was performed in WT(6,7) and Δleo1(8,9). H3K4me1 ChIP-seq was performed in WT(10,11) and Δleo1(12,13).


title: HIV-1 Tat protein exposure alters the morphological characteristics and gene expression in the primary mouse cortex endothelial cells and human brain microvascular endothelial cells

city: Chiba

first: Ichiro

last: Manabe

address: 1-8-1 Inohana, Chuo

country: Japan

institute: Chiba University

summary: HIV-1-associated neurocognitive disorders (HAND) are highly prevalent in the era of combination of antiretroviral therapies. Recent studies suggest that damage of blood-brain barrier (BBB) may serve as an early biomarker of cognitive dysfunction in people living with HIV. In this study, we focused on endothelial cells, the core component of the BBB, to investigate the effects of HIV-1 transactivator of transcription (Tat) protein on their morphological alterations and gene expression profiles of human brain microvascular endothelial cells (HBMVECs). Our results demonstrated that Tat-exposed HBMVECs showed reduced CD31 expression, increased phalloidin staining intensity, and activation of inflammatory response pathways as revealed by RNA-seq analysis.

overall_design: HBMVECs grew to 80-90% confluence on 24-well plates which then were seeded at a density of 10,000 cells/well in 96-well plates. The cells were exposed to control medium containing 0.1% protease inhibitor cocktail for preventing Tat protein degradation or the same medium containing recombinant Tat1-86 or heated Tat (95°C for 5 min) at a 12.5 nM final concentration and incubated at 37°C, 5% CO2 incubator. Eight hours after Tat treatment, cells were harvested for RNA isolation.

first: Lili

last: Quan

first: Rieko

last: Muramatsu

first: Jun

last: Zhu


title: Basal level of ATF4 promotes T cell readiness for activation-induced proliferation

first: Yushan

last: YI

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

overall_design: Refer to individual Series


title: PUMA-induced apoptosis in telomere biology disorders

city: Freiburg

first: Geoffroy

last: Andrieux

address: Breisacherstr 153

institute: University clinics Freiburg

summary: Serial transplantations using WT, Puma-/- , G3 mTerc-/-Puma+/+ and G3 mTerc-/-Puma-/- donors were used to analyze the effects of PUMA deficiency on the hematological phenotype of telomerase-deficient mice. RNAseq was performed to assess how downstream signaling was affected.

overall_design: Generation breeding and serial LSK cell transplantation

first: Melanie

last: Boerries

first: Sheila

last: Bohler

first: Miriam

last: Erlacher


title: Regulatory Role for Tumor Suppressor REST on Estrogen Receptor (ESR1) Expression and Leiomyoma Pathophysiology

city: Kansas City

first: Sumedha

middle: S

last: Gunewardena

state: Kansas

address: 2146 West 39th Avenue

department: Dept. of Molecular and Integrative Physiology

country: USA

institute: University of kansas medical center

summary: Uterine fibroids, benign tumors of the smooth muscle layer of the uterus, plague approximately 80% of the female population by age 50. While there have been efforts to understand the mechanism behind this pathophysiology, it largely remains unclear. Lack of preclinical animal models that recapitulate aberrant steroid hormone pathways in UL has significantly hampered the development of long-term hormonal therapies for uterine fibroids. In addition, cultured myometrial as well as leiomyoma smooth muscle cells rapidly silence both estrogen receptor alpha (ESR1) and progesterone receptor (PGR) expression through unknown mechanisms, further limiting in vitro mechanistic studies of UL. Previous work by our lab has determined the loss of REST, a master regulator of epigenetic gene silencing, in leiomyoma results in the upregulation of ESR1 targets and therefore estrogen signaling. Using ChIP-PCR, we find REST is directly associated with ESR1 genomic locus, playing a role in its epigenetic regulation. ChIP-seq analysis of Rest cKO mouse uterus samples reveal a global role for REST in the regulation of progesterone receptor target genes and highlights alterations in PGR binding within the Esr1 locus. Additionally, we find REST inhibition of ESR1 expression is regulated through upstream WNT planar cell polarity molecule, PRICKLE1. Based on REST’s role in silencing ESR1 expression in cultured myometrial cells, our results support the development of a potential cell culture method to maintain ESR1 expression through REST modulation. Finally, we establish a broad role for REST in epigenetic regulation relevant to leiomyoma pathophysiology.

overall_design: ChIP-Seq for REST and PR in mouse uterus of wildtype mouse, Restf/f, and REST conditional knockout mouse, Restf/f PR+/Cre

first: Skylar

middle: G

last: Bird

first: Ashley

last: Cloud

first: Sornakala

last: Ganeshkumar

first: Vargheese

middle: M

last: Chennathukuzhi


title: N-acetyl-L-cysteine ethyl ester (NACET) induces the transcription factor NRF2 in the retina and prevents its aging and diabetic retinopathy. [II]

city: Kiel

first: Seyed Mohammd Mahdi

last: Rasa

state: Schleswig-Holstein

address: Michaelisstrasse 5

department: Institut for Immunology

institute: Universitätsklinikum Schleswig-Holstein

summary: Age-related macular degeneration (AMD) and diabetic retinopathy (DR) are leading causes of visual impairment in older people, with oxidative stress playing a central role in the development of these diseases. In fact, the cells of the retina are particularly susceptible to oxidative damage due to high metabolic activity and exposure to light. Glutathione (GSH), a key intracellular antioxidant, is essential for retinal protection but it becomes limited during aging and in diabetes patients. Cysteine (Cys), the rate-limiting precursor for GSH synthesis, can be supplemented by derivatives such as N-acetylcysteine ethyl ester (NACET), which has better bioavailability and cellular uptake compared to the widely used N-acetylcysteine (NAC). NACET effectively increases intracellular Cys and GSH levels, improves the viability of retinal pigment epithelium (RPE) cells under oxidative stress and increases in vivo GSH levels after oral administration. In this study, we show that NACET strongly stimulates NRF2 expression and activity in RPE cells, with a distinctive transcriptomic response. Using RNA interference, mass spectrometry and KEAP1 mutagenesis, we identify direct cysteinylation of sensor residues Cys226 and Cys613 on KEAP1 as the molecular mechanism underlying NRF2 activation after NACET treatment. Furthermore, in vivo administration of NACET induces NRF2 activity and increases GSH content in the retina, mitigating oxidative damage in aging and diabetic mouse models. These results position NACET as a promising therapeutic candidate for oxidative stress-related retinal diseases such as AMD and DR by targeting the KEAP1–NRF2–GSH axis.

overall_design: Gene expression analysis of ARPE-19 expressing a defective NRF2, treated with H2O2 or N-acetilcysteine ethyl ester (NACET) in 1% FCS. ARPE-19 knockout for NRF2 were obtaned by transducing cells with lentiviral particles for the expression of the endonuclease Cas9 and a guide RNA (gRNA), the latter specific for the exon 5 of NFE2L2 (NM_006164.5). As negative control, other cells were transduced with similar particles, but missing the gRNA sequence in the viral genome. The two NRF2 edited alleles had a stop codon introduced in position 503 and 505, respectively. 20x10^3  cells/cm^2 were cultured in DMEM/F12 10% FCS for 40 hours and then treated with 1 mM NACET or 0.2 mM H2O2 for 8 hours..

first: Giuliam

last: Realini

first: Rosario

last: Amato

first: Mahdi

first: Roberto

last: Ceccatelli

first: Laura

last: Bottoni

first: Federico

last: Marchini

first: Alberto

last: Minetti

first: Daniela

last: Giustarini

first: Anna

last: Krepelova

first: Francesco

last: Annunziata

first: Maurizio

last: Cammalleri

last: Orlandini

first: Mario

last: Chiariello

last: Neri

first: Massimo

last: Dal Monte

last: Galvagni


title: Elucidating the mechanisms underlying KRT19 contributes to NSCLC progression [PC-9 cells_RNA-Seq]

city: Zhengzhou

first: Yue

last: Du

address: No. 1, Jianshe East Road, Erqi District, Zhengzhou City, Henan Province

department: Department of Clinical Laboratory

institute: The First Affiliated Hospital of Zhengzhou University

summary: As a member of the acidic type I cytokeratin family, keratin 19 (KRT19) is originally known to form the intermediate filament cytoskeleton and responsible for structural rigidity and multipurpose scaffolds.KRT19 is abnormally expressed in various cancers including hepatocellular carcinoma, breast cancer,serous ovarian cystadenocarcinoma and et.al. KRT19 has been revealed to mediate cell cycle arrest, cancer stem cell reprogramming by interacting with cellular molecules including receptors, adaptors, effectors and kinases.  Increasing evidence illustrates the clinical significance of KRT19 in lung cancer, extensive studies are urged to elucidate the role and underlying mechanism of KRT19 in NSCLC progression, we performed RNA-Seq to identify its target genes in PC-9 cell lines.

overall_design: RNA-Seq profiles of  KRT19 knockdown and non-targeting shRNA groups (control group) in PC-9 cells


title: Targeting C1q signaling in fibro-adipogenic progenitors prevents regenerative fibrosis of aged muscle

city: Los Angeles

first: Thomas

last: Rando

state: California

address: 615 Charles E Young Drive

institute: University of California, Los Angeles

summary: Skeletal muscle fibrosis, as occurs with age, in response to injury, or in the setting of degenerative diseases, results in impairments of muscle regeneration and function. Fibroadipogenic progenitors (FAPs), a distinct population of muscle-resident mesenchymal progenitor cells that reside in muscle interstitium, play a crucial role in normal muscle regeneration by supporting muscle stem cell proliferation. However, in pathological conditions such as severe or recurrent muscle injury, FAPs can aberrantly differentiate into fibrogenic cells, resulting in excessive deposition of extracellular matrix and fibrosis. In this study, we explore the molecular regulation of FAP differentiation along the fibrogenic lineage to gain insights into the mechanisms of fibrosis in aged muscle in response to injury. Our findings reveal that aging is associated with an increased expression of the complement Component 1q (C1q) in muscle-resident macrophages and elevated expression of the complement proteins C1r and C1s in FAPs. Exposure of proliferating FAPs to C1q results in the activation of the Wnt signaling pathway, elevated expression of collagen genes, and FAP fibrogenic differentiation, leading to increased tissue fibrosis. We demonstrate that either pharmacological inhibition of the complement pathway or genetic ablation of C1s in FAPs in aged mice reduces fibrogenic differentiation of FAPs by suppressing Wnt signaling. This reduction in FAP differentiation attenuates the fibrotic response to injury in aged animals as well as in a mouse model of muscular dystrophy. Our study supports the inhibition of complement signaling as a potential therapeutic strategy for mitigating fibrosis in skeletal muscle injury or degeneration.

overall_design: Fibroadipogenic progenitors from mouse skeletal muscles were treated with control or C1q and subjected to bulk-RNA seq analysis.

first: Abhijnya

last: Kanugovi

first: Paola

last: Aguiari

first: Rachel

last: Choi

first: Soochi

last: Kim

first: Di

last: Wu

first: Antoine

last: De Morree

first: Summer

last: Bui

first: Richard

last: Lam

first: Stefano

last: Biressi

first: Ling

last: Liu

middle: A


title: Kidney transcriptomic profiling of immune-related genes in ANCA-associated vasculitis

city: Angers

first: Benoit

last: BRILLAND

address: 4 rue Larrey

country: France

institute: Angers University Hospital

summary: Introduction. ANCA-associated vasculitis with glomerulonephritis (AAV-GN) frequently progresses to kidney failure. However, tools for risk stratification of renal outcomes remain limited. Existing approaches inadequately capture the molecular complexity underlying kidney injury, despite its potential value to tailor therapeutic management. We explored whether kidney transcriptomics could identify molecular signatures linked to renal outcomes.    Methods. We included 199 patients with AAV-GN from two multicenter biobanks, and 23 controls. Kidney biopsies were profiled using NanoString nCounter to assess the expression of 750 immune-related genes. We conducted differential gene expression analysis, pathway enrichment analysis, and immune cell infiltration estimation to explore associations with kidney function and survival. A 12-gene prognostic signature was developed via LASSO-penalized Cox regression and compared to established histological classifications (Berden classification, Renal Risk Score, and ANCA Kidney Risk Score) with robust internal validation.    Results. AAV-GN demonstrated extensive immune dysregulation with 150 differentially expressed genes versus controls, highlighting complement activation, immune cell recruitment and activation, TGFβ signaling, and immunometabolism pathways. Immune cell infiltration was marked by increased macrophages, dendritic cells, neutrophils, and T cell subsets, reflecting broad immune activation. Initial eGFR correlated with the expression of 319 genes. A 12-gene signature (CLU, C3, LTF, FLT1, PLCG2, FES, PRKCD, TXNIP, SLC7A5, PTEN, NRBF2, NFATC1) was significantly more strongly associated with kidney survival than were established histological classifications (adjusted p-value < 0.0001). Both high and low expression of several immune pathways (especially lymphocyte trafficking) were associated with better outcomes compared to intermediate expression.    Conclusion. Transcriptomic analysis of kidney biopsies in AAV-GN identified 150 differentially expressed immune-related genes and led to the development of a 12-gene signature that correlated strongly with kidney survival, outperforming established histological classifications.

overall_design: Targeted (750 immune-related genes) transcriptomic profiling was performed in kidney biopsies from 199 AAV-GN patients (including 2 duplicates for batch calibration) and 23 non-proliferative non inflammatory kidney samples, included as disease control.

last: Brilland

first: Jean

middle: F

last: Augusto


title: Circulating MicroRNAs Do Not Provide a Diagnostic Benefit Over Tissue Biopsy in Patients With Brain Metastases

city: Brno

first: Robin

last: Jugas

address: Kamenice 5

country: Czech Republic

institute: CEITEC MU

type: Non-coding RNA profiling by high throughput sequencing

summary: Brain metastases (BMs) are frequent and devastating complications of systemic malignancies, necessitating accurate diagnosis and origin identification for effective treatment strategies. Invasive biopsies are currently required for definitive diagnosis, highlighting the need for less invasive diagnostic approaches and robust biomarkers. Circulating microRNAs (miRNAs) have demonstrated potential as sensitive and specific diagnostic biomarkers in various cancers. Thus, our objective was to identify and compare miRNA profiles in BM tissue, cerebrospinal fluid (CSF), and plasma, with a specific focus on liquid biopsies for diagnostic purposes. Total RNA enriched for miRNAs was isolated from histopathologically confirmed BM tissues (n=30), corresponding plasma samples (n=30), and CSF samples (n=27) obtained from patients with diverse BM types. Small RNA sequencing was employed for miRNA expression profiling. Significantly differentially expressed miRNAs were observed in BM tissues, enabling the differentiation of primary origins, particularly breast, colorectal, renal cell carcinoma, and melanoma metastases. The heterogeneity observed in lung carcinomas also manifested in the corresponding BMs, posing challenges in accurate discrimination from other BMs. While tissue-specific miRNA signatures exhibited the highest precision, our findings suggest low diagnostic potential of circulating miRNAs in CSF and blood plasma for BM patients. Our study represents the first analysis of miRNA expression/levels in a unique set of three biological materials (tissue, blood plasma, CSF) obtained from the same BM patients using small RNA sequencing. The presented results underscore the importance of investigating aberrant miRNA expression/levels in BMs and highlight the low diagnostic utility of circulating miRNAs in patients with Bms.

overall_design: microRNAs profiling of 5 various diagnosis across tissue, blood plasma and cerebro-spinal fluid. We aimed on detecting biomarkers present in blood plasma and CSF.

first: Michaela

last: Ruckova

first: Dagmar

last: Al Tukmachi

first: Marek

last: Vecera

first: Tereza

last: Deissova

first: Ondrej

last: Slaby

first: Jiri

last: Sana


title: Nano MiRNA-Functionating Tetrahedral Framework Nucleic Acid for Cartilage-targeted Ferritinophagy Modulation to Attenuate Temporomandibular Joint Osteoarthritis

city: fuzhou

first: Wenxiu

last: Yuan

state: Fujian Province

address: No. 246 Yangqiao Middle Road, Gulou District

institute: Fujian Medical University

summary: Background and objectives: Current clinical interventions lack effective strategies to arrest temporomandibular joint osteoarthritis (TMJOA) progression. Emerging evidence highlights the therapeutic potential of microRNAs (miRNAs) in osteoarthritis (OA) management, though critical challenges persist regarding delivery efficiency, including unsatisfactory cellular uptake, immunogenicity, and structural instability of miRNA-based therapeutics. Methods and results: Considering the powerful editability of tetrahedral framework nucleic acids (tFNAs) for gene delivery, we engineered a novel nanoscale gene delivery system using tetrahedral framework nucleic acids functionalized with miR-143-3p (tFNAs-143). Through comprehensive in vivo modeling of TMJOA destabilization and in vitro simulation of IL-1β-induced inflammatory microenvironments, we systematically investigated the therapeutic efficacy and molecular mechanisms underlying OA pathophysiology of tFNAs-143. Our results demonstrated that tFNAs-143 exhibited excellent cellular internalization in chondrocytes and effectively mitigated TMJOA progression by impeding ferritinophagy-mediated ferroptosis. Conclusions: This study advanced miRNA delivery technology for TMJOA therapy, deepened the insights into TMJOA pathogenesis, and proposed a promising nano therapeutic strategy for developing targeted TMJOA therapies.

overall_design: RNA-seq profiling of chondrocytes with or without treatment of IL-1β, tFNAs-143  for 24 hours.

first: Maotuan

last: Huang

first: Linxin

last: Chen

first: Sihang


title: Basal level of ATF4 promotes T cell readiness for activation-induced proliferation [CUT&Run]

first: Yushan

last: YI

summary: Stress responding elements such as eIF2α phosphorylation are either upregulated or required during late-phase T cell activation and differentiation. However, it is not well understood whether these elements are essential within the first 12-24 hours post-stimulation, a period when mitochondrial activation and metabolic reprogramming are critical. Here, we demonstrate that T cell activation-induced mTOR and GCN2 phosphorylation leads to the upregulation of ATF4 protein as early as 12 hours after stimulation. This early induction of ATF4 has transcriptional activities that positively or negatively regulate stress response, signaling, and metabolism. Loss of Atf4 in T cells alters transcriptome dynamics, impairs amino acid transport and biosynthesis, and disrupts cellular adaptive responses to ER stress and oxidative stress. It also hinders cell growth, resulting in defective effector cell differentiation in vitro or in vivo in a chronic LCMV infection model. Our findings suggest that a basal level of ATF4 during the early phase of T cell activation enhances the preparedness of cells to cope with integrated nutritional, protein folding, and oxidative stresses during the activation course. This, in turn, protects cells from stress-related cell death or senescence.

overall_design: Naïve CD8+ T cells were isolated from the lymph nodes of three 8-week-old female C57BL/6J mice, stimulated with anti-CD3 (1 μg/ml) and anti-CD28 (1μg/ml) for 12(A4-A6;IgG1-4) or 48 (A7-A9;IgG5)hours. The cells from 3 mice were pooled to generate biological duplicates with approximately 500,000 cells per replicate for CUT&RUN.

last: Yi

first: Ce

last: luo

first: Xiuyuan

last: Sun

first: Qing

last: Ge


title: N-acetyl-L-cysteine ethyl ester (NACET) induces the transcription factor NRF2 in the retina and prevents its aging and diabetic retinopathy. [I]

first: Seyed Mohammd Mahdi

last: Rasa

overall_design: Gene expression analysis of confluent retinal pigment epithelial cell line (ARPE-19) treated with N-acetilcysteine (NAC) or N-acetilcysteine ethyl ester (NACET) in 1% or 10% FCS. Confluent ARPE-19 cells were cultured for 44 hours in DMEM/F12 with 1% or 10% FBS and treated chronically with NAC, NACET or H2O (as a negative control). 0.4 mM NAC or NACET were added at 0, 24, and 40 hours after medium change with DMEM/F12 with 1% or 10% FBS.

first: Giuliam

last: Realini

first: Rosario

last: Amato

first: Mahdi

first: Roberto

last: Ceccatelli

first: Laura

last: Bottoni

first: Federico

last: Marchini

first: Alberto

last: Minetti

first: Daniela

last: Giustarini

first: Anna

last: Krepelova

first: Francesco

last: Annunziata

first: Maurizio

last: Cammalleri

last: Orlandini

first: Mario

last: Chiariello

last: Neri

first: Massimo

last: Dal Monte

last: Galvagni


title: Development of transcriptome profiling for MSC-exo treated HUVECs

city: Shanghai

first: Lingjie

last: Kong

address: 83 Fen Yang Road

institute: Fudan University

summary: To determine the key mediators responsible for the anti-angiogenic activity of MSC-exos, we performed transcriptome profiling using the Agilent Human ceRNA Microarray for HUVECs stimulated by H2O2 and cocultured with MSC-exos or not.

overall_design: MSC-exo induced gene expression in HUVECs was measured while HUVECs were stimulated by H2O2 for 24 h, and then cocultured with MSC-exos for another 24 h or not.

first: Xiaoyan

last: Han


title: N-acetyl-L-cysteine ethyl ester (NACET) induces the transcription factor NRF2 in the retina and prevents its aging and diabetic retinopathy. [III]

last: Rasa

overall_design: Chronic oxidative stress is widely recognized as a key factor in retinal cell damage and death in retinal degenerative diseases. With the aim of proposing NACET as a therapeutic and preventive agent against AMD, we investigated the effects of NACET in vivo on the aging retina of mice. To this end, we treated young (8-20 weeks) and old (80-110 weeks) C57BL/6J mice with or N-acetilcysteine ethyl ester (NACET) added to drinking water (daily oral intake of 50 mg/Kg). After 5 days mice have been sacrificed by CO2 euthanasia, then we proceed with the dissection of the eyes to collect the retinas as described in Simmons and Fuerst, 2018 (Simmons AB, Fuerst PG. Analysis of Retinal Vascular Plexuses and Interplexus Connections. Methods Mol Biol. 2018;1753:317-330). One retina of each mouse was used for RNA-seq analysis.

last: Realini


title: N-acetyl-L-cysteine ethyl ester (NACET) induces the transcription factor NRF2 in the retina and prevents its aging and diabetic retinopathy. [IV]

overall_design: Akita mice were used to test the effect of NACET administration as compared with that obtained in C57BL/6J mice (WT), used as normoglycemic control. Only male mice were involved in the study as female Akita mice are reported to develop a milder and less consistent diabetic phenotype (Al-Awar et al., 2016). All the procedures were performed in compliance with the ARVO Statement for the Use of Animals in Ophthalmic and Vision Research, the EU Directive (2010/63/EU), and the Italian guidelines for animal care (DL 26/14; Italian Ministry of Health, decree number 606/2024-PR). Akita mice were obtained from The Jackson Laboratories (Bar Harbor, ME, USA). At 4 weeks of age, WT and Akita mice were randomly assigned to either vehicle- or NACET-treatment group. NACET was dissolved in drinking water at the concentration of 0.33 mg/mL to obtain a daily oral intake of 50 mg/Kg. Mice received the oral administration of vehicle (water) or NACET everyday up to the 24th week of age. During the treatment period, mice underwent a longitudinal assessment of blood glucose level using a OneTouch Ultra glucometer (LifeScan Inc., Milpitas, CA, USA).

last: Amato

last: Ceccatelli


title: Differential microglial responses to structurally distinct alpha-synuclein polymorphs

first: Jina

last: Kim

state: CA

address: 8700 Beverly Blvd

institute: cedars-sinai medical center

summary: Synucleinopathies are age-related neurological disorders which include dementia with Lewy bodies (DLB), Parkinson’s disease (PD), and multiple system atrophy (MSA). The diseases are characterized by the abnormal deposition and aggregation of a-synuclein and neuroinflammation. Recent studies have demonstrated the existence of structurally distinct a-synuclein aggregates in this group of the diseases. While the correlation between specific forms of a-synuclein and distinct pathological characteristics has been extensively studied, their relationship to neuroinflammation remains elusive. Here, we examined the effects of structurally distinct a-synuclein polymorphs on microglial neuroinflammation. Human induced pluripotent stem cells (iPSCs)-derived microglia (iMicroglia) were treated with a-synuclein polymorphs including EGCG stabilized a-synuclein oligomers (EO), kinetically stable a-synuclein oligomers (KSO), dopamine stabilized a-synuclein oligomers (DO), a-synuclein preformed fibrils (PFF), sonicated a-synuclein preformed fibrils (sPFF), and matured a-synuclein fibrils (Fib). Microglial gene expressions were accessed by transcriptome analysis and Toll-like receptor agonist activities were determined by HEK-Blue TLR reporter assay. Exposures to kinetically stable a-synuclein oligomers and matured a-synuclein fibrils induced the expression of microglial cytokines and chemokines, while other species did not. Microglial transcriptome analysis yielded that all polymorphs commonly induce toll-like receptor (TLR) signaling cascade despite differential transcriptomic phenotypes. Among structurally distinct a-synuclein polymorphs, live cell TLR reporter assay showed that kinetically stable a-synuclein oligomers induce the activities of TLR2 and 4, and sonicated a-synuclein preformed fibril TLR4, relative to the control. These results suggest that structurally distinct a-synuclein polymorphs have likewise distinct neuroinflammatory properties.

overall_design: Structurally distinct α-synuclein polymorphs were applied to human iPSC-derived microglia, and their neuroinflammatory effects were evaluated by transcriptome profiling and TLR reporter assays.

first: Katherine

last: Chang

first: Changyoun


title: TCR-seq of each iNKT subset isolated from the thymus of BALB/c and B6 mice

first: Ryo

last: Nasu

state: Chiba

address: 1-8-1 Inohana, Chuo-ku

summary: iNKT cells show significant lineage diversity among mouse strains. We used TCR-seq to analyze the mechanism underlying the increased number of iNKT2 cells in BALB/c mice.

overall_design: Each iNKT subset (i.e. iNKT1, iNKT2, iNKT17 cells), CD4T cells and CD8T cells  were sorted and subjected to TCR-seq.

first: Yukihiro

last: Endo

first: Ichita

last: Hasegawa

first: Akemi

last: Igi

first: Atsushi

last: Onodera

first: Satomi

last: Mita

first: Koichi

last: Higashi

first: Ken

last: Kurokawa

last: Toyoda

first: Masahiro

last: Kiuchi

first: Miho

last: Shinzawa

first: Yangsong

last: Wang

last: Koyama-Nasu

first: Kiyoshi

last: Hirahara

first: Shinichiro

last: Motohashi

first: Toshinori

last: Nakayama

first: Motoko

last: Y. Kimura


title: NSMF Mitigates Excessive Replication Stress to Facilitate Colorectal Cancer Progression

city: Ulsan

first: YOU

last: SEONGJUN

institute: Ulsan National Institute of Science and Technology

summary: Replication stress is a fundamental driver of genomic instability and tumorigenesis, but excessive levels result in irreparable DNA damage, requiring precise regulation to support cancer cell proliferation and survival. Here, we identify NSMF as a critical regulator of replication stress in colorectal cancer (CRC), enabling cancer cells to prevent catastrophic DNA damage while sustaining proliferation. NSMF expression is elevated in CRC and correlates with replication stress level. In ApcMin/+ mice, NSMF knockout selectively induced replication-dependent DNA damage in tumors, suppressing tumor growth and prolonging survival without harming normal tissues. Mechanistically, NSMF deficiency impairs replication fork progression under stress, triggering DNA damage, growth arrest, and senescence. Moreover, NSMF overexpression conferred tolerance to oncogene-induced replication stress, allowing normal cells to evade senescence. These findings establish NSMF as a crucial safeguard against lethal replication stress, highlighting its potential as a therapeutic target for CRC suppression.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: RNA sequencing was performed on paired tumor and adjacent normal tissues from 5 colorectal cancer (CRC) patients. Histologically confirmed non-tumor colonic mucosa adjacent to the tumor was collected during surgical resection at Asan Medical Center (Seoul, Korea)_Human. We performed RNA sequencing of colon tissues from 16-week-old Nsmf+/+;ApcMin/+ and Nsmf-/-;ApcMin/+ mice. Tumor and adjacent normal regions were microdissected from the same colon and processed for transcriptome analysis to evaluate genotype-dependent transcriptional changes during early colorectal tumorigenesis._Mouse

first: Kyeong Jin

last: Shin

first: Yu Jin

last: Lee

first: Gyuri

last: Kim

first: Seongjun

last: You

first: Kyoung Lock

first: Sabin

last: Park

first: KyoungJun

first: Eun A

first: Sung Min

last: Jung

first: Jang Hyun

last: Choi

first: Hyung-Sik

first: Kyungjae

last: Myung

first: Semin

first: Seung-Jae

first: Young Chan

last: Chae


title: ATAC-seq of DP thymocytes

first: Ryo

last: Nasu

summary: iNKT cells show significant lineage diversity among mouse strains, which correlate with the SLAMF6 expression on immature thymocytes. We used ATAC-seq to analyze the genetical locus that affects Slamf6 gene expression.

overall_design: DP thymocytes from B6, BALB/c and F2 mice were sorted and subjected to ATAC-seq.

first: Yukihiro

last: Endo

first: Ichita

last: Hasegawa

first: Akemi

last: Igi

first: Atsushi

last: Onodera

first: Satomi

last: Mita

first: Koichi

last: Higashi

first: Ken

last: Kurokawa

last: Toyoda

first: Masahiro

last: Kiuchi

first: Miho

last: Shinzawa

first: Yangsong

first: Kiyoshi

first: Shinichiro

first: Toshinori

first: Motoko


title: The m6A methyltransferase METTL14 promotes oncogenic Kras induced juvenile myelomonocytic leukemia through dysregulating autophagy [RNA-seq]

first: Peihua

middle: Second Affiliated Hospital of Xi'an Jiaotong

last: Zhang

state: shannxi

address: NO.157 Xiwu Rd

department: National and Local Joint Engineering Research Center of Biodiagnosis and Biotherapy

institute: Xi'an Jiaotong University Second Affiliated Hospital

summary: The M6A modification plays an important role in the pathogenesis of various myeloid malignancies. However, its specific role in RAS mutant-induced myeloid malignancy is incompletely understood. In this study, we found that m6A methyltransferase METTL14 was highly expressed and associated with a shorter survival in a RAS-mutant myeloid malignancy, juvenile myelomonocytic leukemia (JMML). The knockout of METTL14 was revealed to significantly promote hematopoietic stem/progenitor cells (HSPCs) expansion and suppresses disease progression in a KrasG12D/+ mutant-induced mouse model of JMML. Moreover, knockout of METTL14 reduces hyperproliferation of KrasG12D/+ HSPCs and suppresses oncogenic KrasG12D/+-induced myeloid disease in a cell-autonomous manner. Mechanistically, we revealed that the knockout of METTL14 reduced the autophagy levels of HSPCs by suppressing the transcription and translation of autophagy-related genes, such as Atg5 and Atg9a, through m6A modification. Furthermore, we found that the autophagy inhibition through knockout of ATG5 in Kras mutant mice promoted the expansion of HSPCs and inhibited the progression of leukemia disease, consistent with the phenotypes of knockout of METTL14. Finally, we observed that combined treatment with an m6A inhibitor and a MEK inhibitor synergistically suppressed JMML growth. Collectively, these findings highlight the critical role of METTL14 in JMML tumorigenesis and suggest that m6A RNA modification represents a promising therapeutic target for this disease.

overall_design: The RNA-seq analysis was performed on Mettl14 fl/fl;Mx1-Cre; KrasLSL G12D/+ Lin-ckit+ cells and the results were analyzed together with our previous sequencing results of Mx1-Cre; KrasLSL G12D/+ mice and wild type mice Lin-ckit+ cells.

first: Guangyao

last: Kong


title: RNA-seq of whole thymocytes and purified CD4+CD8+TCRlow DP thymocytes

first: Ryo

summary: iNKT cells show significant lineage diversity among mouse strains. We used RNA-seq to analyze the molecules differentially expressed between BALB/c and B6 thymocytes.

overall_design: Whole thymocytes or DP thymocytes (CD4+CD8+CD69–H57lo/med) were sorted and subjected to RNA-seq.

last: Wang

last: Koyama-Nasu

last: Hirahara

last: Motohashi

last: Nakayama

last: Y. Kimura


title: Elucidating the mechanisms underlying KRT19 contributes to NSCLC progression

first: Yue

last: Du

summary: As a member of the acidic type I cytokeratin family, keratin 19 (KRT19) is originally known to form the intermediate filament cytoskeleton and responsible for structural rigidity and multipurpose scaffolds.KRT19 is abnormally expressed in various cancers including hepatocellular carcinoma, breast cancer,serous ovarian cystadenocarcinoma and et.al. KRT19 has been revealed to mediate cell cycle, cancer stem cell reprogramming by interacting with cellular molecules including receptors, adaptors, effectors and kinases.  Increasing evidence illustrates the clinical significance of KRT19 in lung cancer, extensive studies are urged to elucidate the role and underlying mechanism of KRT19 in NSCLC progression, we performed RNA-Seq to identify its target genes in A549 cell lines.

overall_design: RNA-Seq profiles of KRT19-overexpressing and empty vector in A549 cells.


title: CSF immune cell alterations in women with neuropsychiatric Long COVID

city: New Haven

first: Shelli

last: Farhadian

state: CT

address: 135 College St, PO BOX 208022

institute: Yale School of Medicine

summary:
Background: Women are disproportionately affected by neuropsychiatric symptoms following recovery from acute COVID-19, commonly termed neuropsychiatric long COVID (NP-long COVID). However, whether there are central nervous system-specific changes in gene expression in women with NP-long COVID remains unknown.
Methods: Twenty-two women with and ten women without NP-long COVID were enrolled from New Haven, CT, and the surrounding region and consented to a blood draw and large volume lumbar puncture. Total RNA was extracted from cerebrospinal fluid (CSF) cells and peripheral blood mononuclear cells (PBMC). Polyadenylated RNA was then sequenced, and differential expression analyses were performed using DESeq2.
Results: Both CSF and PBMC samples showed differential gene expression associated with long COVID status. While some pathways were dysregulated in both the CSF and PBMC of long COVID compared to controls, including those related to androgen response, MTORC1 signaling, and lipid metabolism, these are likely driven by different suites of genes. Moreover, there were also CSF-specific differentially expressed genes in people with long COVID, indicating compartment-specific immune responses. Notably, oxidative stress, reactive oxygen species, and P53 response were all enriched in the CSF of women with long COVID but not PBMC.
Conclusions: Women with NP-long COVID show distinct, compartment-specific, transcriptional profiles in the CSF.

overall_design: Bulk RNA-seq of cerebrospinal fluid cells and peripheral blood mononuclear cells from women with and without self-reported neuropsychiatric Long COVID

first: Benjamin

last: Orlinick

first: Sameet

last: Mehta

first: Lindsay

last: McAlpine

first: Saba

last: Khoshbakht

first: Sofia

last: Fertuzinhos

first: Allison

last: Nelson

first: Jennifer

last: Chiarella

first: Bibhuprasad

last: Das

first: Vansh

last: Patel

first: Paraskevas

last: Filippidis

first: Michael

middle: J

last: Corley

first: Serena

last: Spudich


title: scRNA-seq of thymic iNKT cells

last: Nasu

summary: iNKT cells show significant lineage diversity among mouse strains. We used scRNA-seq to analyze the diversity of thymic iNKT cells between BALB/c and B6 mice.

overall_design: Thymic CD3+ CD1d.PBS57+ cells were sorted and subjected to scRNA-seq.

first: Yukihiro

last: Endo

first: Ichita

last: Hasegawa

first: Akemi

last: Igi

first: Atsushi

last: Onodera

first: Satomi

last: Mita

first: Koichi

last: Higashi

first: Ken

last: Kurokawa

last: Toyoda

first: Masahiro

last: Kiuchi

first: Miho

last: Shinzawa

first: Yangsong

last: Wang

last: Koyama-Nasu

first: Kiyoshi

last: Hirahara

first: Shinichiro

last: Motohashi

first: Toshinori

first: Motoko


title: Histone 3 lysine 56 acetylation (H3K56ac) regulates extrachromosomal DNA (ecDNA) hub biogenesis

city: Taoyuang

first: Kou-Juey

last: Wu

state: Taiwan

address: No.15, Wenhua 1st Road, Gueishan Dist

department: Cancer Genome Research Center

country: Taiwan

institute: Chang Gung Memorial Hospital at Linkou

summary: Extrachromosomal DNAs (ecDNAs) play an important role in tumor progression. ecDNA hubs have been shown to be anchored by BRD4, a chromatin reader. However, the epigenetic regulation of ecDNA hub biogenesis remains unknown. Here we show that histone 3 lysine 56 acetylation (H3K56ac) mark binds to BRD4 specifically. Analysis of ChIP-seq datasets showed that both H3K56ac and H3K27ac co-occupied with BRD4 binding at the ecDNA-chromosome interaction sites and ecDNA itself.

overall_design: ChIP-seq of BRD4 and Histone Modification H3K56ac in two cancer cell lines with ecDNA, PC3 DM and COLO320 DM.

first: Chang-Jiun

first: Li-Zhu

last: Liao

first: Yu-An

last: Chen

first: Tzu-Chin

last: Lin

first: Po-Hung

first: Chia-Lin

middle: L

last: Wei


title: Highly effective combination of BRG1/BRM inhibitor with BET inhibitor or decitabine for high-risk MECOM-rearranged AML [RNA-seq]

city: Houston

first: Xiaoping

last: Su

state: Texas

address: 7300 Brompton St, Apt 5633

institute: MD Anderson Cancer Center

summary: In AML with 3q26.2 rearrangements (r) the distal GATA2 hematopoietic enhancer becomes aberrantly relocated leading to activation of EVI1 expression EVI1 is a transcriptional regulator that plays a role in proliferation and maintenance of a stem cell-like phenotype in AML. BRG1 (SMARCA4) and BRM (SMARCA2) are the mutually exclusive ATPases of the BAF (BRG1/BRM-associated factor) chromatin remodeling complexes. They regulate access to enhancers/promoters and gene-expressions orchestrating AML stem/progenitor cell proliferation and differentiation. AML with 3q26.2 rearrangements are clinically challenging and prognosis remains very poor. FHD-286 is an orally bioavailable, selective inhibitor of BRG1/BRM under clinical development in AML. Present studies show that FHD-286 induced differentiation and lethality in AML cells with MECOM-r, perturbed chromatin accessibility and depleted expression of EVI1, c-Myc, CD44 and CDK4. Co-treatment with FHD-286 and decitabine, BET inhibitor (BETi) or HAT inhibitor synergistically induced in vitro lethality in patient-derived AML cells with MECOM-r. In patient-derived xenograft (PDX) models of AML with MECOM-r, compared to each drug, co-treatment with FHD-286 and BETi OTX015 significantly reduced AML burden and improved survival, without inducing significant toxicity. These findings highlight the FHD-286-based combinations as promising therapy of AML with chromosome 3q26.2 rearrangement and EVI1 overexpression.

overall_design: Paired end RNA Seq of MECOM rearranged AML242, AML191, AML194, and UCSD-AML1 cells treated with 100 nM of FHD-286 for 16 hours.

first: Warren

last: Fiskus

first: Kapil

last: Bhalla


title: The impact of U2AF2 deficiency on gene expression in ovarian cancer cells

city: Hefei

first: Yifan

last: Feng

state: Anhui

address: Jixi Road 218

institute: The Anhui Medical University

summary: U2AF2 is an RNA processing-related factor that has a substantial impact on various cellular processes and is also closely associated with cancer development.Here, functional experiments demonstrated that U2AF2 significantly promotes ovarian cancer progression.RNA-seq analysis revealed that differentially expressed genes downstream of U2AF2 are significantly enriched in the Wnt signaling pathway, which was validated by Western blot.In summary, our data provide new molecular insights into ovarian cancer.

overall_design: The U2AF2 SINC and U2AF2 SI OVCA433 ovarian cancer cell lines were used for 3v3 RNA-seq.

first: Min

last: Li


title: Highly effective combination of BRG1/BRM inhibitor with BET inhibitor or decitabine for high-risk MECOM-rearranged AML [ATAC-seq]

overall_design: Paired end ATAC-Seq of EVI1-expressing AML samples treated with FHD-286 for 16 hours.


title: Highly effective combination of BRG1/BRM inhibitor with BET inhibitor or decitabine for high-risk MECOM-rearranged AML [ChIP-Seq]

overall_design: Chromatin immunoprecipitation DNA-sequencing (ChIP-seq)  for the histone modification H3K27Ac and BRG1 binding in AML242 cells treated with FHD-286 for 16 hours.


title: scTCR-seq of thymic iNKT cells

first: Ryo

last: Nasu

institute: Chiba University

summary: iNKT cells show significant lineage diversity among mouse strains. We used scTCR-seq to analyze the diversity of thymic iNKT cells between BALB/c and B6 mice.

first: Yukihiro

last: Endo

first: Ichita

last: Hasegawa

first: Akemi

last: Igi

first: Atsushi

last: Onodera

first: Satomi

last: Mita

first: Koichi

last: Higashi

first: Ken

last: Kurokawa

last: Toyoda

first: Masahiro

first: Miho

first: Yangsong

last: Nakayama

last: Y. Kimura


title: RNA-seq data of Methylorubrum extorquens AM1 wild-type and methanol-adapted strains [RNA-seq]

first: Donghyuk

last: Kim

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

department: Department of Chemical Engineering

institute: UNIST

summary: Transcriptomic analysis of wild-type and methanol-adapted Methylorubrum extorquens AM1 strains under methanol stress.

overall_design: RNA-seq was performed for six strains (WT, Am01–Am05) under two methanol concentrations (0.5% and 2.5%), each in duplicate, resulting in 24 samples.

first: Gyu Min

last: Lee

first: Ina

last: Bang


title: Coexpression of MYCN and ALK Induces Neuroblastoma-Like Tumors From Human iPS Cell-Derived Cranial Neural Crest Cells [RNA-seq]

city: Saitama

first: Kyosuke

last: Mukae

state: Kitaadachi-gun

address: 818, Komuro, Ina-machi

department: Research Institute for Clinical Oncology

institute: Saitama Cancer Center

summary: Neuroblastoma (NB) is a pediatric solid tumor originating from neural crest cells (NCCs), which are precursors of the sympathetic nervous system. MYCN amplification is a key factor contributing to poor prognosis of NB. Additionally, anaplastic lymphoma kinase (ALK) mutation or amplification drives oncogenic signaling pathways, such as MAPK signaling, which together with MYCN amplification exacerbate NB malignancy. NCCs are mainly classified into cranial NCCs (cNCCs) and trunk NCCs (tNCCs), and recent studies have reported NB development from tNCCs. However, the potential for NB development from cNCCs remains unexplored. In this study, we sought to mimic the tumorigenic process of NB by overexpressing MYCN and ALK in cNCCs derived from human induced pluripotent stem cells. These modified cells when subcutaneously transplanted into immunodeficient mice induced NB -like tumors, and could thus be used an in vitro model to study this tumor. Through extensive gene expression profiling and whole exome sequencing of MYCN/ALK-induced clones, we identified key features of NB, including activation of the MAPK pathway and gain of 17q chromosome, which is critical for malignant tumor development. This model provides a valuable platform for studying the biological mechanisms driving ALK and MYCN amplification in NB derived from cNCCs.

overall_design: Total RNA was prepared using ISOGENII (NIPPON GENE). High-throughput sequencing were performed by the Takara Bio INC. Quality-checked mRNA was captured using the SMART-Seq mRNA kit (Takara Bio INC) and sequenced using a NovaSeq 6000 (Illumina, California, USA). RNA sequencing paired-end reads were mapped to the reference genome GRCh38 and the downstream processes were performed by the sequencing service provider.

first: Tianyuan

last: Shi

first: Takehiko

last: Kamijo


title: High p16⁺ senescence load confers increased responsiveness to senolytic therapy in aged female mice

city: GRONINGEN

first: Marco

last: Demaria

state: Groningen

address: Antonius Deusinglaan, 1

country: Netherlands

institute: umcg

summary: Aging is accompanied by the accumulation of senescent cells, which contributes to tissue dysfunction and chronic inflammation. However, the burden of senescent cells and the efficacy of their clearance may differ between sexes, which is a critical yet understudied aspect of geroscience. Here, we combined transcriptomic, proteomic, and functional analyses to investigate sex-specific accumulation and removal of p16⁺ senescent cells during aging. Using single-nucleus and bulk RNA-seq, senescence-specific GLF16 staining, and bioluminescence imaging, we showed that aged female mice accumulated a higher burden of p16⁺ cells across multiple tissues, particularly the liver. Targeted elimination of p16⁺ cells via ganciclovir (GCV) in the p16-3MR mouse model resulted in significant improvements in physical performance, liver function, and skin regeneration in females but not in males. Multi-omics profiling revealed that p16⁺ cell clearance in females reprograms liver tissue toward a more youthful state, characterized by the upregulation of mitochondrial pathways and downregulation of immune and inflammatory signatures. These molecular changes closely mirror those induced by established longevity interventions such as calorie restriction, rapamycin, and acarbose. Moreover, integrative analysis across independent senescence-targeting studies identified a core set of conserved transcriptional regulators and gene targets, including Srm, Cd36, and Lrrfip1, which are involved in mitochondrial health and immune modulation. Together, our findings highlight the sex-specific benefit of senescent cell clearance in aging and provide mechanistic insight into the rejuvenating effects of targeting p16⁺ cells, supporting their potential as therapeutic targets in age-related diseases.

overall_design: RNA-Seq profiling of liver samples from p16-3MR and wild type female and male mice treated with ganciclovir (GCV) or vehicle. 3 biological replicates per group.

first: Lin

last: Yao

first: Wang

last: Boshi

first: Demaria

last: Marco


title: The m6A methyltransferase METTL14 promotes oncogenic Kras induced juvenile myelomonocytic leukemia through dysregulating autophagy

city: Xi'an

first: Peihua

last: Zhang

first: Guangyao

last: Kong


title: Metabolic beneficial effects of targeting a long non-coding RNA, lnc-Megacluster, in obesity

city: Duarte

first: Rama

last: Natarajan

address: 1500 E Duarte Rd

department: Department of Diabetes Complications and Metabolism

institute: Beckman Research Institute, City of Hope

summary: The long noncoding RNA (lncRNA) lnc-Megacluster (lncMGC) is implicated in diabetic kidney disease and pancreatic islet dysfunction. However, its role in obesity and insulin resistance (IR) is unknown.  Herein, we investigated the regulatory role of lncMGC in obesity and adipose dysfunction using lncMGC knockout (KO) mice, and further determined the translational potential of lncMGC-based therapeutics for obesity using GapmeR antisense oligonucleotides in wild-type and partially humanized-lncMGC mice. We found lncMGC is upregulated in perigonadal white adipose (gWAT) and brown adipose tissues (BAT) from high-fat diet (HFD)-induced obese mice along with increased endoplasmic reticulum stress signaling. Inhibition of lncMGC in mice via genetic ablation or GapmeRs targeting mouse or human lncMGC displayed protective effects against HFD-induced IR, weight gain, and associated adipose dysfunction. In parallel, key lncMGC targets involved in gWAT and BAT functions were altered. The metabolic beneficial effects in gWAT were accompanied by improved angiogenesis, reduced adipocyte hypertrophy, and inflammation.  Notably, lowering lncMGC levels in HFD-fed lncMGC KO or via GapmeR treatment enhanced BAT functional markers, mitochondrial thermogenic program/structure, and mitophagy markers. Collectively, these new findings underscore the pathogenic role of lncMGC in adipose dysfunction and the therapeutic potential of targeting key lncRNAs for obesity and associated metabolic dysfunction.

overall_design: Eight-week-old male and female C57BL/6J WT, lncMGC KO and partially humanized lncMGC female mice were randomly divided into groups and fed a control chow or HFD [(60% kcal from fat) for 10 or 20 weeks. Body weight and blood glucose levels were measured during the experiments. At the end of the studies, mice were fasted overnight, then, after euthanasia, plasma was collected to measure insulin levels. Perigonadal white adipose tissue (gWAT), interscapular brown adipose tissue (BAT) and pancreas were harvested for molecular and histological analysis.

first: Maryam

last: Abdollahi

first: Vinay

last: Tanwar


title: Induction of a renal developmental cell state is associated with chemotherapy resistance in favorable-histology Wilms tumor

city: Memphis

first: Hongjian

last: Jin

state: TN

address: 262 Danny Thomas Place

department: Center for Applied Bioinformatics

institute: St Jude Children's Research Hospital

type: Methylation profiling by genome tiling array

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

overall_design: Refer to individual Series


title: PROtection MEdiated by Antioxidant NanoTEchnOlogy Against Neuronal Damage in Space (PROMETEO, Antioxidant Protection)

city: Pontedera

first: Giada Graziana

last: Genchi

address: Viale Rinaldo Piaggio 34

institute: Istituto Italiano di Tecnologia

summary: Oxidative stress (OS) is the mechanism at the base of many deleterious effects of spaceflight, involving exposure to microgravity (MG, also termed µg) and cosmic radiation (CR), and it is inherent to the genesis of several pathological conditions on Earth (among which Crohn’s and Parkinson’s diseases). Arising from the unbalanced production and elimination of pro-oxidant chemical species, OS implies short- and long-term alterations of targets from the molecular up to the whole organism level. The central nervous system (CNS) is the most critical target of OS, requiring special antioxidant protection with the increasing duration of spaceflights and in view of interplanetary travels. MG- and CR-induced cognitive and motor alterations, which are well known to progressively deteriorate human performance in space and can have life-threatening consequences on astronauts, can indeed be ascribed to dopamine dysregulation following OS generated during spaceflight This project proposes the use of polydopamine-based nanoparticles (NPs) to provide 1) antioxidant protection and 2) catecholaminergic support to neurons undergoing exposure to altered gravity and radiation. The focus is on neuronal cells involved in cognitive and motor functions both in space, where any behavioural impairments pose significant risks to manned expeditions, and on Earth, where dopaminergic neuron loss underlying Parkinson’s disease (PD) progression still requires effective contrast. This project in particular aims at exploring the connection between spaceflight and OS, by discriminating the effects of MG from those of CR, and at providing nanotechnology countermeasures to short- and potentially long-term alterations of the CNS due to spaceflight-induced reduction/oxidation (redox) reaction imbalance. This project also aspires at providing relevant evidence and therapeutic tools for the treatment of neurodegenerative conditions like PD on Earth.

overall_design:
To assess potentially protective effects of antioxidant nanoparticles on neuron-like cells during spaceflight, cell cultures were prepared on ground in triplicate for each experimental class, and they were then integrated in fluidic bioreactors qualified for spaceflight. Cell culture medium was either added or not with nanoparticles.
Cell cultures were uploaded to the International Space Station (ISS) and integrated in both static and dynamic slots of Kubik incubator. Static slots determined exposure of cell cultures to real microgravity with cosmic radiation. Dynamic slots instead determined exposure of cell cultures to simulated Earth gravity with cosmic radiation. The experiment was conducted on board the ISS for four days. Then, the cell cultures were rinsed, fixed and cold stowed until return to the home laboratory.
Spaceflight cell cultures were de-integrated from fluidic bioreactors and prepared for analysis by total RNA extraction/purification. Control cell cultures were set on ground in triplicate for each experimental class, and they were exposed to the thermal profile of spaceflight samples. Cells were kept under static or dynamic culture conditions. Static conditions determined exposure to real Earth gravity without cosmic radiation. Dynamic conditions were obtained by rotation on random positioning machine, and they determined exposure to simulated microgravity without cosmic radiation. Cell cultures were prepared for analysis, and RNA sequencing was conducted on all samples.

first: Gianni

last: Ciofani

first: Alessio

last: Carmignani

first: Melike

last: Belenli Gümüş

first: Zeidler

last: Maximilian

first: Neumann

last: Alexander


title: The role of Fibulin-2 during cardiac regeneration in zebrafish

city: Montreal

first: Rubén

last: Marín-Juez

address: 3175 Chem. de la Côte-Sainte-Catherine

country: Canada

institute: CHU Sainte-Justine

summary: We used a 10X Genomics single-cell RNA sequencing approach to compare the single-cell transcriptome of heart ventricles from fbln2sjr3-/- and wild-type siblings, at uninjured state and at 4 days post-cryoinjury.

overall_design: Uninjured WT heart ventricles (pool of 4), cryoinjured WT heart ventricles at 4 days post-cryoinjury (pool of 4), uninjured fbln2sjr3-/- heart ventricles (pool of 4), cryoinjured fbln2sjr3-/- heart ventricles at 4 days post-cryoinjury (pool of 4) and cryoinjured fbln2sjr7-/- heart ventricles at 4 days post-cryoinjury (pool of 4) were extracted for single-cell dissociation and library preparation.

last: Marin Juez

first: Gülsüm

last: Kayman-Kürekçi

first: Gursimran

last: Kaur Bajwa

first: Gregor

last: Andelfinger

first: Séverine

last: Leclerc

first: Emilie

last: de Chantal

first: Darrell

last: Belke

first: Justin

last: Deniset

first: Shaoqiu


title: rRNA-modifications connect mesenchymal fate selection in neural crest and prognosis in neuroblastoma

city: Kansas City

first: Shiyuan

middle: (Cynthia)

last: Chen

state: MO

department: Computational Biology

institute: Stowers Institute for Medical Research

summary: transcriptomic analysis of ribosome biogenesis in mutant mice during embryonic development

overall_design: scRNA-seq from 4 control and 4 mutant mice at E12.5

first: Lorena

last: Maili

first: Paul

last: Trainor


title: IOP-induced blood-retinal barrier compromise contributes to RGC death in glaucoma

city: New York

first: Simon

last: John

state: NY

address: 630 West 168th Street

institute: Columbia University

summary: The integrity of the blood-retinal barrier (BRB) has been largely unexplored in glaucoma. We reveal that elevated intraocular pressure (IOP) partially compromises the BRB in two human-relevant inherited mouse models of glaucoma (DBA/2J and Lmx1bV265D). Experimentally increasing IOP in mouse eyes further confirms this. Notably, the compromise induces subtle leakage, happening without bleeding or detected endothelial cell junction disruption, and it precedes neurodegeneration. Leakage occurs from peripheral veins in the retinal ganglion cell layer with a concomitant loss of the transcytosis inhibitor MFSD2A. Supporting this, bulk RNA sequencing of retinal veins revealed upregulated vesicular transport and downregulated Wnt signaling in hypertensive versus control veins. Transmission electron microscopy confirmed intact tight junctions in D2 glaucoma mice, while increased vesicles suggest enhanced transcytosis. In human glaucoma eyes, albumin immunostaining showed BRB leakage in retinal veins, mirroring our mouse findings. Importantly, stabilizing β-catenin in retinal endothelial cells prevents both vascular leakage and neurodegeneration in the DBA/2J model. The occurrence of leakage in all 3 high IOP models and in human glaucoma indicates that BRB compromise may be a common, yet overlooked, mechanism in glaucoma. These findings suggest that IOP-induced BRB compromise plays a critical role in glaucoma, offering a new therapeutic target.

overall_design: 9 months old DBA/2J and DBA/2J-Gpnmb+/SjJ were intraperitoneally injected with 0.33 mg/g body weight sodium fluorescein (AK-FLUOR, Akorn). 5 minutes after injection, mice were euthanized by cervical dislocation, eyes enucleated and retinal veins were dissected using super fine forceps (Dumont, NC9497215) under the fluorescent dissection scope. 4 major veins from the same mouse, including main branches were combined as one sample. Total RNA was extracted using RNeasy Micro kit (Qiagen, 74004). RNA concentration and quality (RIN) was measured by Bioanalyzer. About 100 pg total RNA (RIN>9) were reverse transcribed to cDNA using SMART-Seq v4 Ultra Low Input RNA Kit for Sequencing (Takara). The library was prepared using Nextera XT (Illumina) and sequenced by Aviti Element. Bulk RNA-seq data was aligned to GRCm38 and gencode M23 and quantified by Kallisto. Transcript quantifications were imported into R framework for downstream analysis.

first: Chi

last: Zhang


title: Aldosterone stimulation of fibroblasts affects gene expression and function relevant to muscle injury and disease

city: Columbus

first: Jill

last: Rafael-Fortney

state: OH

address: 460 W. 12th Ave

department: Physiology & Cell Biology

institute: The Ohio State University

summary: Here, we report the RNA sequencing of fibroblasts isolated from wild-type (C57BL/10) neonatal hindlimb skeletal muscle. The fibroblasts were directly treated with the MR agonist aldosterone, the MR antagonist spironolactone, or vehicle control (DMSO). We find that aldosterone treatment increased expression of genes involved in fibrosis, muscle function, and metabolism, and that aldosterone treatment decreased expression of genes involved in cell migration and cytokine receptor binding. This data suggests that MR signaling can directly affect fibroblasts and contribute to pathology in skeletal muscle.

overall_design: RNA-seq profiling of wild-type (C57/BL 10) neonatal mouse hindlimb skeletal muscle fibroblasts, treated for 48h with either 1 uM aldosterone, 1 uM spironolactone, or vehicle control (DMSO).

first: Chetan

middle: K

last: Gomatam

first: Swathy

last: Krishna

first: Jeovanna

last: Lowe

first: Esther

last: Silver

first: Christoph

last: Lepper


title: Androgen Signaling in Type 2 Innate Lymphoid Cells Drives Sex Differences in Helicobacter-Induced Gastric Inflammation and Atrophy

city: Morgantown

first: Lei

last: Wang

state: West Virginia

address: 64 Medical Center Drive

department: Department of Microbiology, Immunology and Cell Biology

institute: west virginia university

summary: Gastric cancer is the fifth most common cancer worldwide. Men are disproportionately affected by gastric cancer, which ranks as the fourth most common cancer in men compared to eighth in women worldwide. Chronic inflammation driven by Helicobacter pylori infection remains the leading gastric cancer risk factor. Emerging evidence suggests that sex hormones modulate immune responses, contributing to sex differences in infection outcomes and cancer susceptibility. This study investigates how androgens influence the gastric inflammatory response to Helicobacter infection and contribute to sex disparities in disease progression.

overall_design: Male and female C57BL/6 mice were colonized with Helicobacter felis to investigate sex differences in gastric inflammation. Tissue from the gastric corpus was collected two months post-infection.

first: Benjamin

middle: C

last: Duncan

first: Maeve

middle: T

last: Morris

first: Jordan

last: Pascoe

first: Jonathan

last: Busada

first: Gangqing

last: Hu

first: Stuti

last: Khadka


title: Pkm1 is required for embryonic cardiomyocyte proliferation through energetic regulation of NFYa stability

city: Shanghai

first: zhang

last: dandan

address: 1239 Siping Road, Shanghai, P.R. China

department: School of  Life Sciences and Technology

institute: Tongji University

summary: Pyruvate Kinase M1 (PKM1) is a critical enzyme in energy metabolism, particularly in high-energy-demand tissues like the heart. However, previous knockout strategies for PKM1 were confounded by compensatory upregulation of its low-activity splice variant, PKM2. Here, we generated a Pkm1 mutant mouse model using a point mutation that deletes Pkm1 without elevating PKM2. Homozygous Pkm1 mutants exhibited perinatal lethality associated with cardiac dysfunction, characterized by thin myocardium and reduced cardiomyocyte proliferation during mid-to-late gestation. We found that PKM1 sustains ATP levels to inhibit AMPK, which otherwise promotes NFYa phosphorylation and destabilization. NFYa, a transcription factor essential for cardiomyocyte proliferation, is identified as a key mediator linking metabolic status to cell cycle activity. These findings identify the PKM1-AMPK-NFYa axis in energetic regulation of cardiomyocyte proliferation in embryonic heart, offering new insights into the function of PKM1 and the broader impact of energy metabolism on cardiac development, while also shedding light on the potential metabolic underpinnings of congenital heart diseases.

overall_design: RNA-seq profiling of wildtype and pkm1-knockout mouse hearts at embryonic days 18.5.

first: Dandan

first: Yansong

last: Tang

first: Wen

last: Ye

first: Lan

last: Kang

first: Ke

last: Wei

first: Shaorong

last: Gao


title: Beyond BRCA deficiency: Clinical and molecular predictors of survival in patients with BRCA-deficient tubo-ovarian high-grade serous carcinoma [Methylation]

status: Public on Jan 26 2026

city: Melbourne

first: Dale

last: Garsed

state: Victoria

address: 305 Grattan St

department: Cancer Research

country: Australia

institute: Peter MacCallum Cancer Centre

summary: Homologous recombination DNA repair deficient (HRD) tumors account for about 50% of tubo-ovarian high-grade serous carcinomas (HGSC) and are associated with a high response to platinum-based chemotherapy. However, a subset of patients with HRD tumors have unexpected resistance to chemotherapy and experience short survival. Our study compared BRCA-deficient and proficient HGSC among patients with short (<3 years, the lowest quartile of overall survival (OS)) versus longer-term (>3 year OS) to identify prognostic markers and potential therapeutic opportunities.  Primary tumors from a cohort of patients with advanced-stage HGSC (n=154) enriched for those with HRD tumors and short survival (n=42) were analyzed using whole-genome sequencing, bulk RNA-sequencing, and DNA methylation profiling. A subset of HRD tumors (n=143) were characterized for immune cell densities by multiplex immunofluorescence. Clinicopathological features were assessed in 1,389 patients with HGSC, including 282 with pathogenic germline BRCA variants (gBRCApv). Findings were validated in two international HGSC cohorts: the Ovarian Tumor Tissue Analysis consortium (n=5,875) and Multisciplinary Ovarian Cancer Outcome Group (n=895).  In gBRCApv-carriers, residual disease following surgical cytoreduction was not associated with shorter OS unlike in non-carriers where it was strongly associated. While most patients with gBRCApv had a more favorable OS compared to non-carriers, a survival advantage was not apparent in those with variants located outside of BRCA1 exon 10/23 and BRCA2 exon 11/27. Patient survival correlated with HRD score, such that those with a score ≥63 had significantly longer OS compared to those with HRD scores of 42-63 and <42. While higher HRD scores were associated with better survival outcomes, most gBRCApv carriers with a short survival had tumor HRD scores that exceeded the threshold typically considered predictive of a good response to carboplatin or PARP inhibitors. BRCA2-deficient HGSC with loss of the tumor suppressor NF1 was associated with exceptionally favorable outcome (median OS 17 years), whereas amplification of both PIK3CA and RAD21, was associated with poor outcome in BRCA2-deficient HGSC (median OS 2.9 years). The density of tumor-infiltrating CD8+ PD-1+ T cells was prognostic for OS in gBRCApv-carriers.   In summary, rather than simply the presence or absence of a germline BRCA pathological variant influencing patient survival, the co-occurrence of specific somatic gene alterations, the extent of immune cell infiltration, the level of homologous recombination deficiency, and BRCA-variant location may modify clinical outcomes in patients with BRCA-deficient HGSC. Analysis of exceptional outcome patients, in this case gBRCApv-carriers with an atypically short survival, may identify determinants of outcome applicable to the wider HGSC patient population.

overall_design: Genome wide DNA methylation profiling of 24 primary tumours of long-term survivors of high grade serous ovarian cancer. The Illumina Infinium MethylationEPIC BeadChip was used to obtain DNA methylation profiles across approximately 850,000 CpGs. 77 primary tumors from GSE65820 and 53 primary tumors from GSE211686 were also used in the project.

first: Tibor

last: Zwimpfer

first: Ahwan

last: Pandey

first: David

last: Bowtell


title: High-throughput 3D glioblastoma model for rapid personalized therapeutic screening

first: Caghan

last: Kizil

institute: Columbia University Irving Medical Center

summary: Glioblastoma (GBM) is a devastating brain tumor with limited therapeutic success, largely due to the inability to pre-test patient-specific responses to treatment in a reliable and timely manner with diagnostic and analytical methods as current tests fail to provide actionable insights within the critical timeframes necessary for clinical decision-making. To address this gap, we developed a high-throughput 3D culture system utilizing matrix metalloproteinase-responsive starPEG-sulfated glycosaminoglycan hydrogels. This platform enables encapsulation of patient-derived GBM cells, recreating physiologically relevant microenvironments in 384-well plates for rapid, automated drug testing on primary tumor cells from patients. Transcriptomic analyses revealed that 3D cultures significantly resemble primary and recurrent GBM transcriptomic profiles, particularly in pathways critical for tumor growth, invasion, and therapeutic resistance, such as hypoxia, immune modulation, and extracellular matrix regulation. The platform’s versatility extends to drug screening, where single and combinatorial chemotherapeutic treatments elicited robust and reproducible cytoskeletal and transcriptomic responses. Notably, the system effectively characterized synergistic interactions between 5-fluorouracil and carmustine, highlighting its potential for optimizing combinatorial therapies. Our 3D model surpasses traditional 2D cultures in representing tumor-specific molecular programs, offering an invaluable tool for translational research. By delivering reliable, individualized data on therapeutic efficacy within a clinically relevant timeframe, this model holds transformative potential for personalized medicine, enabling optimized, patient-specific treatment strategies for GBM. Its scalability and compatibility with high-throughput workflows position this system as a critical innovation in GBM research, advancing the paradigm of personalized medicine in neuro-oncology.

overall_design: Total RNA was extracted from the 3D encapsulated cells using the Norgen`s Total RNA purification kit, [Norgen Biotek Corporation], following the manufacturer’s protocol. For each drug condition- 5-FU/U, Carmustine and their combination, RNA was isolated from 12 wells (biological replicates) of 3D cell cultures, including untreated controls to enhance data reliability. The RNA samples from each condition and controls were pooled and sequenced together. Briefly, cells were lysed in Buffer RL and homogenized to ensure complete cell disruption. RNA was isolated via column-based purification, and on-column DNase treatment was performed to remove any genomic DNA contamination. The RNA quality and concentration were assessed using a NanoDrop spectrophotometer (Thermo Fisher Scientific, US). Additionally, RNA integrity was first assessed using the Agilent 2100 Bioanalyzer (Agilent Technologies, US) with the Eukaryote Total RNA Pico Kit, providing RNA Integrity Numbers (RIN) to ensure high-quality RNA (RIN ≥ 8.0) for sequencing. Also, 300 ng of total RNA per sample was analyzed using the Fragment Analyzer NGS LAB3877 (Agilent Technologies) to confirm the size distribution and integrity of the RNA, further ensuring suitability for downstream library preparation and sequencing.

first: Rajvinder

last: Kaur Trautman


title: Basal level of ATF4 promotes T cell readiness for activation-induced proliferation [RNA-seq]

city: Beijing

first: Yushan

last: YI

address: No.38 Xueyuan Road, Haidian District, Beijing

department: Department of Immunology

institute: Peking University

summary: Stress responding elements such as eIF2α phosphorylation are either upregulated or required during late-phase T cell activation and differentiation. However, it is not well understood whether these elements are essential within the first 12-24 hours post-stimulation, a period when mitochondrial activation and metabolic reprogramming are critical. Here, we demonstrate that T cell activation-induced mTOR and GCN2 phosphorylation leads to the upregulation of ATF4 protein as early as 12 hours after stimulation. This early induction of ATF4 has transcriptional activities that positively or negatively regulate stress response, signaling, and metabolism. Loss of Atf4 in T cells alters transcriptome dynamics, impairs amino acid transport and biosynthesis, and disrupts cellular adaptive responses to ER stress and oxidative stress. It also hinders cell growth, resulting in defective effector cell differentiation in vitro or in vivo in a chronic LCMV infection model. Our findings suggest that a basal level of ATF4 during the early phase of T cell activation enhances the preparedness of cells to cope with integrated nutritional, protein folding, and oxidative stresses during the activation course. This, in turn, protects cells from stress-related cell death or senescence.

overall_design: To globally analyze the genes regulated by ATF4 during T cell active, we performed Bulk RNA-seq analysis of (Atf4fl/flCd4cre, Atf4 cKO) vs( ATF4fl/fl，WT) murine naïve CD8+ T cells activated in vitro by anti-CD3(1μg/ml) and anti-CD28(1μg/ml) at 0h,12h,24h and 48h.

last: Yi

first: Ce

last: Luo

first: Jingyi

last: Wang

first: Yujia

first: Guoping

last: Deng

first: Rong

last: Jin

first: Qing

last: Ge


title: Gene expression analysis and proximity labeling reveal posttranscriptional functions of the yeast RNA Polymerase II regulator Def1

city: University Park

first: Oluwasegun

middle: Tosin

last: Akinniyi

state: PA

address: 463 North Frear

department: Biochemistry and Molecular Biology

institute: Pennsylvania State University

summary: Def1 is a yeast protein that promotes transcription elongation and regulates the degradation of RNA polymerase II during transcription stress. Although Def1 is localized in the cytoplasm, its functions in this cellular compartment are not yet understood. Despite its well-established roles in transcription, a comprehensive genome-wide analysis of its impact on gene expression has not been conducted. Here, we performed RNA sequencing (RNA-seq) analysis on cells lacking DEF1 and surprisingly found that only a few hundred genes exhibited altered expression, both upregulated and downregulated. To evaluate mRNA synthesis and decay rates in these DEF1-deficient cells, we used a nascent transcription metabolic labeling technique called RATE-seq. As expected, we observed reduced synthesis rates across the genome in these cells. Additionally, a global decrease in mRNA decay rates was observed, suggesting that Def1 plays a role in the post-transcriptional regulation of mRNAs. The changes in synthesis and decay rates showed a strong correlation, indicating that this compensation helps buffer steady-state mRNA levels. To gain further insight into Def1's functions, we conducted proximity labeling experiments to identify its protein binding partners within the cells. Our findings revealed that Def1 primarily interacts with cytoplasmic regulators involved in post-transcriptional processes, including proteins responsible for deadenylation, decapping, and translation regulation. Using an mRNA decay reporter assay, we demonstrated that recruiting Def1 to mRNA reduces its expression and accelerates its turnover. In summary, we have identified a novel cytoplasmic function for Def1, establishing it as a key regulator of gene expression in both transcription and mRNA decay.

overall_design:
The role of Def1 in translation and in the regulation of RNA was studied by using RNA-seq, RNA metabolic labeling, and Ribo-seq
Wild type (W303) and def1△ strains were grown to log phase (OD~0.8-1) and then treated with 5mM 4-thiouracil
For metabolic labeling, cells were labeled for different times, then harvested, followed by RNA isolation and pull-down.
For Ribo-seq, RNA was isolated from monosomes
For steady-state RNA-seq, RNA was isolated at log phase
Libraries were prepared and sequenced. Analysis was carried out.

first: Aswathy

last: Sebastian

first: Joseph

last: Reese


title: Gene Expression Changes Induced by Met-Enkephalin and β-Endorphin (1–9) in Rat Keratinocytes

city: Nagakute-shi

first: Hiroyuki

last: Yamamoto

state: Aichi

address: 2-9 Katahira

institute: Aichi Shukutoku University

summary: To investigate the biological effects of β-END(1–9), DNA microarray analysis was performed using FRSK cells treated with β-END(1–9).  Differential gene expression analysis revealed that Met-enkephalin and β-END(1–9) modulate a similar set of genes, suggesting that they may regulate cellular functions through a shared receptor.

overall_design: Samples of rat fetal keratinocytes stimulated with either Met-enkephalin or β-END(1–9) were analyzed. Unstimulated cells were used as the control. Each sample was analyzed with n = 1.


title: Distinct SOX9 single-molecule dynamics characterize adult differentiation and fetal-like reprogrammed states in intestinal organoids

city: Berkeley

first: Robert

last: Tjian

state: CA

address: University of California, Berkeley 450 Li Ka Shing #3370

department: MCB

institute: UC Berkeley

summary:
Transcription factors (TFs) mediate gene expression changes during differentiation and development. However, how TF biophysical properties and abundance dynamically regulate specific cell state transitions remains poorly understood.

Using automated live-cell single-molecule tracking (SMT) in intestinal organoid models, we revealed an expression level-independent decrease in the fraction of immobile SOX9 molecules during differentiation from ~48% to ~38%, largely dependent on DNA binding. Strikingly, long-term SOX9 overexpression caused organoids to transition from budding to spheroid morphology accompanied by increased proliferation and a loss in gene expression signatures for intestinal identity and function. In this fetal-like reprogrammed state, a larger fraction of partially self-interacting SOX9 molecules (~61%) binds to DNA.

Our results suggest context-dependent SOX9 single-molecule dynamics during adult intestinal differentiation and fetal-like reversion in consequence to long-term SOX9 overexpression. Our work underpins the power of our automated live-cell SMT framework to generate testable hypotheses towards unraveling molecular mechanisms underlying tissue-level phenotypes.

Contact: nikewalther.science@gmail.com

overall_design: Please check the following: Poly-A RNA-seq profiling of mouse small intestinal organoids stably expressing Halo-NLS (control organoids, 3 biological replicates) or Halo- or mEGFP-tagged Sox9 (organoids and "spheroids", 3 biological replicates each)

first: Nike

last: Walther

first: Claudia

last: Cattoglio


title: ARTS confers chemoresistance of breast cancer by inducing apoptosis-dependent autophagy via Livin-MDM2-p53 pathway

city: Hefei

first: Zheng-sheng

last: Wu

address: 81 Meishan Road

institute: Anhui Medical University

summary: Apoptosis and autophagy are two fundamental pathophysiological processes of cell fate regulation under stress conditions, especially in anti-cancer therapy. However, the interplay between apoptosis and autophagy in the cancer chemoresistance is not fully elucidated. Herein, we identified apoptosis-related protein in TGF-β signaling pathway (ARTS) as a key link between apoptosis and autophagy, facilitating cell survival and chemoresistance. ARTS was highly expressed in chemoresistant breast cancer tissues and was associated with patient poor prognosis. Expression of ARTS conferred the resistance of doxorubicin (DOX) and docetaxel (DTX) by inducing autophagy in breast cancer cells in vivo and in vitro. As regards the mechanism of action, ARTS translocated from the mitochondrial intermembrane space to the cytoplasm after pro-apoptotic signals from chemotherapeutic drugs, subsequently inducing autophagy through the SIAH1-mediated Livin degradation and further activation of the MDM2/p53 pathway, thus resulting in the survival of breast cancer cells. The inhibition of apoptosis or autophagy effectively suppressed the chemoresistance mediated by ARTS. Generally, this study identified a new pathway of ARTS/Livin/MDM2/p53 conferred chemoresistance of breast cancer through inducing autophagy in an apoptosis-dependent manner.

overall_design: For pre- and post-chemotherapy breast cancer HE-stained sections, histological responses were evaluated by two pathologists according to the Miller-Payne Grading (MPG) system. Among the pre-chemotherapy samples submitted, five were classified as Grade 1 (G1) and five as Grade 5 (G5). These samples were utilized to assess genes associated with chemotherapy resistance.

first: Zhengsheng

first: Hao


title: MYRF Controls Mesothelium Specification, Signaling, and Plasticity [scRNA-Seq]

city: La Jolla

first: Gidsela

last: Luna

state: California

address: 9500 Gilman Dr

institute: UC San Diego

summary: The mesothelium is a squamous monolayer that ensheathes internal organs and lines the body cavities. Aside from facilitating tissue sliding, its additional functions remain poorly understood. Here, we study the mesothelium through investigating myelin regulatory factor (Myrf), a transcription factor expressed in the mesothelium and a top mutated gene in congenital diaphragmatic hernia (CDH), a developmental disorder that affects the lung and diaphragm. In mice, inactivation of Myrf early in embryogenesis resulted in CDH and defective mesothelium specification, compromising its role as a signaling center for lung growth. Inactivation after mesothelium specification led to additional defects, including enhanced differentiation into various mesenchymal cell types, causing a striking accumulation of elastin-expressing smooth muscle/myofibroblasts encasing the lung, mimicking pleuroparenchymal fibroelastosis (PPFE), a rare adult lung condition. Compound mutants demonstrate that MYRF functions synergistically with YAP/TAZ in mesothelium differentiation. Together, these findings highlight the complex role of the mesothelium in development and disease.

overall_design: Myrf mutant and control mesothelial cells were isolated by fluorescent activated cell sorting (FACS) and analyzed using scRNA-Seq

first: Jamie

last: Verheyden

first: Chunting

last: Tan

first: Estelle

last: Kim

first: Ziai

last: Zhu

first: Michelle

last: Hwa

first: Jugraj

last: Sahi

first: Yufeng

last: Shen

first: Wendy

last: Chung

first: David

last: McCulley

first: Xin

last: Sun