title: Anti-inflammatory and phosphorylation effects of CFTR modulator triple therapy in cystic fibrosis

city: Westmead

first: Nader

last: Aryamanesh

state: NSW

address: 214 Hawkesbury Rd

department: Bioinformatics

institute: CMRI

summary: Cystic Fibrosis is an autosomal recessive disorder caused by mutations in the CFTR gene, which encodes a key chloride channel, leading to impaired ion transport and severe progressive respiratory failure. CFTR modulators, such as Trikafta© has improved morbidity in CF, but its systemic effects remain unclear. This study evaluated the clinical outcomes, safety, and cellular mechanisms of Trikafta© in young children (< 11 years) with CF using a multi-omic approach. Seventeen children with CF (median age 8.7 years, 26% female) and 12 healthy controls (median age 9.6 years, 42% female) were included for multi-omic analysis. The analysis included RNA sequencing, proteomics and phosphoproteomics. Baseline pathway enrichment analysis (FDR < 0.05) revealed systemic inflammation, transmembrane transporter deficiencies, reduced protein kinase, and reduced GTPase activity. Three months post-Trikafta© treatment, anti-inflammatory effects, epigenetic modulation, and increased protein kinase activity were observed, indicating partial reversal of cellular abnormalities. Trikafta© improves clinical outcomes and reduces inflammation, epigenetic changes and key phosphorylation pathways in young children with CF, offering insights into CF pathology and potential biomarkers for monitoring treatment.

overall_design: Bulk RNA sequencing

first: Hiran

last: Selvadurai

first: Velda

last: Han

first: Brooke

last: Keating

first: Mark

last: Graham

first: Lee

last: Marshall

first: Suat

last: Dervish

first: Xianzhong

last: Lau

first: Ruwani

last: Dissanayake

first: Stephen

last: Alexander

first: Shrujna

last: Patel

first: Russell

last: Dale


title: Deep learning identifies Pbx1 as a network hub of hematopoietic stem cell aging [scRNA-seq]

status: Public on Aug 03 2026

city: Sendai

first: Keiyo

last: Takubo

address: 2-1 Seiryo-machi Aoba-ku

department: Graduate School of Medicine

country: Japan

institute: Tohoku University

type: Expression profiling by high throughput sequencing

summary: Hematopoietic stem cells (HSCs) constitute a well-structured hematopoietic system that undergoes an age-related bias toward myeloid/platelet differentiation. The mechanism by which this aging hallmark is deeply embedded in intrinsic HSC programs is unknown. Using single-cell RNA-seq data, old HSCs harbor two distinct transcriptional programs: one shared with megakaryocytes and the other associated with the most primitive HSCs. By employing a transformer-based model that captures higher-order differences between young and aging HSCs and integrating time-series transcriptomic analyses, epigenetic studies, and comprehensive transcription factor screens, we identified Pbx1 as a central gene controlling both age-related transcriptional programs and differentiation defects in old HSCs. Pbx1 suppresses erythroid differentiation by repressing Gata1 expression. In addition, we found that the histone methyltransferase G9a/GLP acts as an epigenetic regulator that specifically inhibits Gata1 expression and erythroid differentiation. These findings provide insight into the differentiation defects associated with stem cell aging and potential strategies for rejuvenation.

overall_design: Fresh CD150+CD48-CD41-CD34- LSK cells (HSCs) or CD150+CD48-CD41+ LSK cells from 10-week-old mice or CD150+CD48-CD41-CD34- LSK cells from 7 month-old, 12 month-old, 18 month-old or 2-year old were sorted into 500 µL SF-O3. Either GFP+ or GFP- CD150+CD48-CD34- LSK cells from Scl-tTA:H2B-GFP mice treated with doxycycline from 1 year old for 2.5 months were sorted as well and were subjected to single cell RNA-sequencing by the Fludigm C1 system.

first: Hiroshi

last: Kobayashi

first: Yusuke

last: Shiozawa

first: Seishi

last: Ogawa


title: Transcriptomic analysis of Jurkat T cells upon transient expression of HTLV-1a, -1b, -1c and STLV-1mac Tax proteins

city: Lyon

first: Thomas

last: Duchateau

state: Rhône

address: 46 allée d'Italie

country: France

institute: ENS de Lyon

summary: Molecular analyses of Human T-cell Leukemia Virus type 1 (HTLV-1) have historically focused on the Japanese strain HTLV-1aB-ATK. However, with the identification of endemic genotypes such as the transcontinental HTLV-1aTC, the major African subtype HTLV-1b, and the Australo-Melanesian subtype HTLV-1c, emerging clinical evidence have suggested that these genotypes may be associated with distinct risks of developing HTLV-1-associated diseases. Tax1a, one of the major viral oncoprotein encoded by HTLV-1a, displays pleiotropic functions, including the manipulation of signalling pathways and the transcriptomic reprogramming of infected cells. We hypothesize that Tax proteins from distinct viral genotypes might share some common transcriptional properties, but might also induce some specific transcriptional landscapes in host cells. In this study, we conducted a comparative transcriptomic analysis of Jurkat T cells expressing HTLV-1a, -1b, -1c and STLV-1mac Tax proteins and highlighted commonalities and specificities in Tax-induced transcriptomic reprogramming.

overall_design: Jurkat T cells were co-microporated using pEF-myc-cyto vectors containing the sequences of Tax1aB-ATK, Tax1b-SF26, Tax1c-EM5, Tax1c-AusCSK or TaxMac-Mra18C9 (or without coding sequence for Empty control), together with a pMACS-LNGFR plasmid encoding a membrane LNGFR-peptide.  After 20 hours, LNGFR-positive cells were sorted using MicroBeads anti-LGNFR and separated using autoMACS (Miltenyi) to enrich for Tax-positive cells.  RNA-Seq analysis was conducted on 5 replicates of the microporation series.

first: Chloé

last: Journo

first: Philippe

last: Afonso


title: Human CCNB1IP1 regulating the increase of cortical folding during human evolution

city: Kunming

first: lei

last: shi

state: Yunnan

address: No.17 Longxin Road

country: China

institute: Kunming Institute of Zoology

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

sample_organism:
Homo sapiens
Tupaia belangeri chinensis

platform_organism:
Homo sapiens
Tupaia belangeri chinensis

overall_design: Refer to individual Series

first: Lei

last: Shi


title: Transcriptional profiling of 3 dpf and 5 dpf WT zebrafish intestinal epithelial cells

status: Public on Aug 02 2026

city: Durham

first: Daniel

last: Levic

state: NC

address: 307 Research Drive

department: Cell Biology

country: USA

institute: Duke University

summary: For this experiment, we analyzed gene expression changes and intron splicing events in the WT zebrafish intestine at two developmental stages (3 dpf and 5 dpf). To perform this analysis, we collected  > 125 M paired end reads from total RNA isolated from purified cldn15la+ intestinal epithelial cells at each time point.

overall_design: For RNAseq of isolated IECs, TgKI(cldn15la:tdTomato)pd1249 embryos (3 and 5 dpf; n > 500; 3 replicates each) and non-transgenic controls (n = 60) were anesthetized with 1X tricaine, decapitated, and the remaining larval bodies were pooled (≤ 70 per 1.5 mL tube). Embryos were washed in Ca²⁺-free Ringer’s solution (116 mM NaCl, 2.9 mM KCl, 5 mM HEPES, pH 7.2) and incubated in 0.25% Trypsin/EDTA (Life Technologies, 25200-056) supplemented with collagenase (2 µL, 100 mg/mL) at 28 °C under agitation for approximately 1.5 h, with periodic gentle pipetting. The cell suspension was then washed with 2% FBS in 1× PBS twice (3,000 rpm, 5 min), resuspended in 2% FBS, and passed through 30 µm CellTris filters (Partec, 04-004-2326) into FACS tubes kept on ice. Cells were stained with 7AAD (5 µL/mL; Sigma, A9400) and sorted on a MoFlo Astrios EQ cell sorter (Beckman Coulter) into 300 µL Monarch DNA/RNA Protection Reagent 1× (NEB, T2010S). RNA was isolated using the Monarch Total RNA Miniprep Kit (NEB, T2010S) according to the manufacturer’s instructions. Library preparation and sequencing were performed by the Duke Cancer Institute Sequencing and Genomic Technologies Core using KAPA HyperPrep (Roche) and Illumina NovaSeq X Plus to collect > 125 M paired-end reads per sample.

first: Michel

last: Bagnat

first: Carina

last: Block


title: The absence of Trim28 in nephron progenitors results in impaired kidney development and function

city: Wuerzburg

first: Matthias

last: Becker

state: Bavaria

address: Am Hubland

department: Biochemistry and RNA-Biology

country: Germany

institute: University Wuerzburg

summary: The TRIM28 gene encodes a transcriptional regulator involved in a variety of molecular processes. Inactivation of TRIM28 has been linked to the epithelial subtype of Wilms tumor, the most common paediatric renal malignancy.  Therefore, TRIM28 may also impact early kidney morphogenesis. To investigate its role in nephrogenesis, we analyzed Trim28 conditional knockout (Trim28Δ/Δ) mice. We found that deleting Trim28 in nephron progenitors resulted in early postnatal lethality and reduced kidney weight. While all renal structures were present, the proximal tubules (PTs) were disorganized. Transcriptome analyses revealed cell-type-specific deregulation of retroelement expression following Trim28 deletion. Further analysis of scRNA-seq data revealed a decreased frequency of nephron progenitor cells (NPCs), an increase in PT cells, and a clear shift towards inflammatory gene expression patterns. While there was no evidence of tumor formation in Trim28Δ/Δ kidneys, the differentially expressed genes in Trim28Δ/Δ progenitors reflected reduced translation, similar to patterns observed in TRIM28 mutant tumor-derived NPCs. Thus, our data demonstrate that TRIM28 primarily influences the maintenance and differentiation of NPCs and PT cells, as well as their subsequent function.

overall_design: Bulk RNA-seq analyses of P0 Trim28Δ/Δ and Trim28f/f or Trim29w/f control kidneys. Single cell RNA-seq of E17.5 Trim28Δ/Δ and Trim28f/f control kidneys.

first: Balazs

last: Palhazi

first: Alireza

last: Paikari

first: Silke

last: Appenzeller

first: Fabian

last: Imdahl

first: Manfred

last: Gessler


title: Targeting polyamine metabolism and eIF5A hypusination in pediatric acute myeloid leukemia

city: Cincinnati

first: Courtney

last: Jones

state: OH

address: 3333 Burnet Ave MLC 7013

institute: Cincinnati Children's Hospital Medical Center

summary: Pediatric acute myeloid leukemia (AML) is a devasting disease with 5-year survival outcomes of approximately 60%. Therefore, there is an urgent need to develop novel therapies for pediatric AML patients. Numerous studies have demonstrated that cellular metabolism is a key vulnerability in adult AML; however, we understand very little about metabolism in pediatric AML. Using pediatric AML patient derived xenograft models, we demonstrate that polyamine metabolism is a pharmacologically targetable vulnerability of pediatric AML cells. Further, depletion of polyamines sensitizes pediatric AML cells to chemotherapy in vitro and in vivo. Mechanistically, polyamine depletion causes reduced protein synthesis through decreased hypusination of translational elongation factor eIF5A. Pharmacologic polyamine depletion and inhibition of eIF5A hypusination result in reduced protein synthesis and decreased expression of cell cycle regulatory proteins resulting in a G1 cell cycle arrest and eventual cell death through apoptosis. In summary, this study reveals polyamine metabolism and hypusination of eIF5A as a vulnerability in pediatric AML that can be targeted using clinically trackable approaches.

overall_design: An AML PDX specimen was treated in technical triplicates for 24 hours with vehicle, DENSpm, or GC7. Cells were collected and subjected to ribosome-seqencing or RNA-sequecning. Each sample is paired (the RNA and ribosome sequencing was performed on the same treatment replicate).

first: Nathan

last: Salomonis


title: Short read direct RNA-sequencing of mammalian bone marrow derived macrophages for chimeric RNA discovery

city: Boston

first: Ruaidhrí

last: Jackson

state: MA

address: New Research Building, 77 Avenue Louis Pasteur

department: Immunology

institute: Harvard Medical School

summary: Eukaryotic mRNA is classically expected to be monocistronic, linear, and encoded by a single defined genetic locus. Conversely, emerging evidence has identified bicistronic translation and circularized mRNA as pervasive unconventional features of mammalian transcriptomes. During oncogenic translocation in humans, DNA from distinct genes can fuse together and encode chimeric mRNAs that directly contribute to tumorigenesis. However, it remains widely unknown whether or not chimeric mRNAs exist in the absence of chromosomal rearrangements, and if they contribute to normal physiological processes. To assay for chimeric mRNA (chRNA) expression in mammalian innate immune cells while circumventing chRNA detection limitations associated with conventional RNA-sequencing (RNA-seq) technology, including read fragmentation and artifact generation by template switching, we performed long read direct RNA sequencing (LR-DRS) of differentially polarized bone marrow-derived macrophages (BMDMs) using the Oxford Nanopore platform, and complemented this with conventional short-read RNA-sequencing.

overall_design: We performed short-read RNA-sequencing of bone marrow derived macrophages (BMDMs) to complement detection of chimeric RNAs (chRNAs) using long-read direct RNA-sequencing (LR-DRS). While conventional RNA-sequencing technologies are prone to several caveats that impede detection of chRNAs, including read fragmentation and the generation of artificial chRNAs via template switching of reverse tranascriptase enzymes used for cDNA synthesis, LRDRS does not possess these disadvantages. Therefore, LRDRS was selected as an appropriate modality for chRNA discovery, and short-read RNA-sequencing was carried out to complement long-read data. To allow for the detection of potential changes in chRNA expression in response to immunological stimuli and alterations in cell state, BMDMs were differentially polarized to either a steady state (no additional treatment), inflammatory (LPS + IFNγ treatment) or tissue reparative (IL-4 + IL-13 treatment) phenotype.

first: Harry

last: Kane

first: Olivia

last: Venezia


title: Hi-C data from murine bone marrow derived macrophages to study chimeric RNAs

city: Parkville

first: Hannah

middle: D

last: Coughlan

state: Victoria

address: 1G Royal Parade

country: Australia

institute: WEHI

summary: Individual mammalian mRNA and proteins are typically believed to originate from single genomic loci, with isoform diversity arising through cis-splicing of pre-mRNA. However, whether mRNA from distant genes can undergo trans-splicing to generate functionally relevant chimeric transcripts has remained unclear. Here, we developed a pipeline combining long-read direct RNA sequencing with unbiased and targeted validation to systematically identify chimeric transcripts in macrophages. Chromatin conformation capture studies revealed that inflammation induces interchromosomal DNA interactions, positioning parent genes proximally to facilitate chimeric RNA formation. Notably, we identified a protein-coding chimeric mRNA representing a fusion between the pore forming protein gasdermin D (GSDMD) and a C-terminal domain translated out-of-frame from Tmem106a (GSDMD:TMEM106A). We show that inflammasome priming signals upregulate GSDMD:TMEM106A, with the protein localizing to the plasma membrane, where it remains inactive. Upon inflammasome activation and cleavage of canonical GSDMD, GSDMD:TMEM106A synergizes with the liberated GSDMD N-terminal effector domain to accelerate and enhance pore formation, IL-1β release, and pyroptosis. Finally, we demonstrate that GSDMD:TMEM106A is necessary and sufficient to coordinate bacterial defense in vivo. This discovery reveals a new class of protein-coding mRNA formed by regulated transcript fusion events during inflammation, unveiling diverse new therapeutic targets for the treatment of human disease.

overall_design: Genome-wide Hi-C data from murine bone marrow derived macrophages at steady state or after LPS stimulation treated with an siRNA targeting CTCF for knockdown or a control scrambled siRNA. Triplicates for each of the four groups: CTCF siRNA steady state, CTCF siRNA LPS stimulation, scramble siRNA steady state and scramble siRNA LPS stimulation. Samples were sequenced with an Illumina Nextseq2000 paired-end 66-bp reads.

first: Timothy

middle: M

last: Johanson

first: Rhys

middle: S

last: Allan


title: Collagen-heparan sulfate microcarriers support mesenchymal stem cell culture in microgravity and streamline post-flight recovery

city: Mayaguez

first: Maribella

last: Domenech

state: PR

address: PO Box 9000

country: Puerto Rico

institute: Universidad de Puerto Rico

type: Non-coding RNA profiling by high throughput sequencing

summary: The objective of this study was to validate a scalable, integrated workflow for Mesenchymal Stem Cell (MSC) culture in Low Earth Orbit (LEO) using pre-seeded, surface-engineered microcarriers (uCs).  Cell thaw and expansion were conducted at ambient temperature (22 °C) in serum-free and DMSO-free media. Consequently, the primary objective of the miRNA sequencing was to verify the presence and stability of bioactive cargo within the extracellular vesicle (EV)-enriched fraction. This genomic analysis serves as a critical quality metric to ensure that the "pre-seed-freeze-thaw-and-expand" logistical framework preserves the integrity of the MSC secretome during orbital transit and post-flight. Small RNA sequencing was performed on EV-enriched fractions isolated from frozen conditioned media processed post-flight to assess the stability of bioactive miRNA signatures across different surface chemistries (engineered HS/COL vs. commercial COL uCs) and gravitational environments. MSCs in suspension (lacking microcarriers) served as the matrix-attachment control.

overall_design: The study utilized 47 samples consisting of extracellular vesicle (EV)-enriched fractions isolated from frozen conditioned media via sequential centrifugation and ultracentrifugation. Three biological replicates were pooled per donor for each specific time point and experimental condition. The experimental design assessed three donors in a factorial design with three culture substrates (engineered HS/COL uCs, commercial COL uCs, and a suspension control) and two gravitational environments (microgravity vs. Ground Control). rHS29 has a high sulfate density, and rHS01 has a low sulfate density. Samples were collected from Day 6 and Day 9 of culture at an ambient temperature of 22°C.

last: Domenech-Garcia

first: Camilo

last: Mora

first: Leonel

last: Velez-Roman


title: Transcriptomic analysis of colchicine effects in adenine-induced chronic kidney disease

city: Seodaemun-gu,

first: Ga YOung

last: Heo

state: seoul

address: 50-1 Yonsei-ro, Sinchon-dong,

country: South Korea

institute: yonsei university

summary: Colchicine is an anti-inflammatory drug that has emerged as a therapeutic option in various inflammatory diseases, but its role in chronic kidney disease (CKD) remains unclear. This study investigates the reno-protective effects of colchicine in an experimental CKD model and its potential role in modulating the NOD-like receptor, pyrin domain containing protein 3 (NLRP3) inflammasome pathway. A CKD animal model was established in C57BL/6 mice by feeding a 2% adenine-containing diet for 4 weeks. Mice received either colchicine (0.3 mg/kg/day) or saline intraperitoneally. RNA sequencing of kidney tissue was performed by E-Biogen Inc. (Seoul, Korea) to capture molecular signatures associated with the therapeutic mechanism of colchicine in CKD, with a focus on inflammatory pathways including nuclear factor-κB and NLRP3 pathways.

overall_design: RNA sequencing was performed on kidney tissues from three experimental groups with 4 biological replicates each: (1) Control group (CON, n=4), (2) Adenine-induced CKD group (CKD, n=4), and (3) Adenine-induced CKD with colchicine treatment group (CKD+COL, n=4). Total of 12 samples were sequenced.

first: Gyuri

last: Kim

first: Ga Young

first: Seung Hyeok

last: Han


title: Polystyrene microplastics disrupt ovarian development via cytoskeletal remodeling and epigenetic reprogramming particularly in granulosa cells [scRNA-seq]

city: Shanghai

first: Ji

last: Wu

address: No.800, Dongchuan Road, Minhang District

institute: Shanghai Jiao Tong University

summary: The emerging environmental health issue posed by micro (nano) plastics (MNPs) has raised significant concerns. Accumulating evidence suggested that MNPs can bioaccumulate in gonads and impair fertility in animals, yet the underlying cellular mechanisms and tissue-specific responses remain poorly understood. In this study, we employed in vivo and in vitro models to systematically investigate the impact of polystyrene microplastics (PS-MPs; 100 nm and 5 µm) on ovarian development and function in pubertal female mice. Following 35 days of exposure, we observed size-dependent reproductive toxicity, with 100 nm PS-MPs causing reduced body weight gain and ovarian size, and compromised ovarian structures and functions, including altered follicle and corpora lutea counts, alongside disrupted hormone levels. Leveraging single-cell RNA-sequencing (scRNA-seq), we uncovered profound alterations in intracellular communication networks and signaling flow patterns across seven identified ovarian cell types. Granulosa cells (GCs) were identified as the primary target PS-MPs, exhibiting marked transcriptional changes, including dysregulation of FSCN1, a critical actin cytoskeleton regulator. In vitro experiments confirmed that only 100 nm PS-MPs were internalized by GCs, leading to cell cycle arrest, necroptosis and hormonal dysfunction. Mechanistically, PS-MPs triggered F-actin cytoskeleton remodeling, increasing cell stiffness and reducing histone marks (H3K4me3, H3K27ac) associated with chromatin accessibility. Integrated ATAC-seq and RNA-seq analyses implicated STAT1 as a key transcriptional regulator driving PS-MP-induced epigenetic and transcriptional changes. Overall, this study first revealed PS-MP-mediated reproductive toxicity from a single-cell perspective, identifying granulosa cells as particularly vulnerable targets. It uncovered novel mechanisms involving cytoskeletal disruption and epigenetic reprogramming, while demonstrating size-dependent internalization patterns that directly correlate with reproductive impairment. These findings provide unprecedented insights into the molecular and epigenetic consequences of MNPs in mammalian reproduction, emphasizing the potential health risks of environmental MNPs exposure.

overall_design: Post-weaning (three-week-old) female ICR mice were randomly assigned to 5 groups (n >15 per group): Control (ddH2O), 0.1 µm PS-MPs low-dose (0.1-L; 0.1 mg per 100 µL per mouse), and 0.1 µm PS-MPs high-dose (0.1-H, 1 mg per 100 µL per mouse), 5 µm PS-MPs low-dose (5-L, 0.1 mg per 100 µL per mouse), and 5 µm PS-MPs high-dose (5-H, 1 mg per 100 µL per mouse). Mice received daily oral gavage administrations for 35 days, with body weight monitored weekly in the morning. Terminal sacrifices were performed 24 h post-final administration, with subsequent collection of organs for downstream analyses.

first: Mengyao

last: Liu


title: Polystyrene microplastics disrupt ovarian development via cytoskeletal remodeling and epigenetic reprogramming particularly in granulosa cells [ATAC-seq]

type: Genome binding/occupancy profiling by high throughput sequencing

overall_design: GCs were isolated from ovaries of 21-day-old female post-weaning ICR mice by two-step enzyme digestion.GCs (2 × 104 cells/ 0.15 mL/well) were seeded in 96-well plates, adhered for 12 h, then treated with sonicated PS-MPs (100 nm ; 0,  750 μg/mL) for 24 h. GCs treated with 0 and 750 µg/mL PS-MPs for 24 h were collected and counted at room temperature before nuclear extraction via 5-min lysis. Nuclei resuspended in a Tn5 transposase-containing reaction mixture for tagmentation. Following enzymatic digestion and DNA purification, the resulting products were amplified by polymerase chain reaction (PCR) with introduction of specific indexes. The PCR amplification conditions were as follows: incubation at 72°C for 3 min, pre-denaturation at 98°C for 1 min, denaturation at 9 °C for 10 s, annealing at 60°C for 25 s, extension at 72°C for 25 s, for a total of 13 to 15 cycles, with a final extension at 72°C for 5 min. Library fragments (200-700 bp) were obtained through bead selection and subjected to paired-end sequencing (PE150) on a Illumina NovaSeq XP platform. Raw sequencing reads were preprocessed to obtain clean data through adapter trimming and removal of low-quality reads and short fragments. Genome alignment is performed using Bowtie2 (v2.5.0) to map short reads to the reference genome and determine the exact positions of each read. Next, peak calling is done using MACS2 (v2.2.9.1) to identify open chromatin regions. The IDR (v2.0.3) method is used to extract highly consistent peak regions from multiple biological replicates. For differential peak analysis, DiffBind (v3.8.4) is employed to detect differential binding regions between control and PS-MPs treatment. Motif analysis is performed using HOMER (v4.11) to scan the sequences of the peak regions and identify shared motif regions. Footprint analysis of transcription factor binding sites is carried out using TOBIAS (v0.16.1), which helps reveal the binding states of transcription factors.


title: Lecithin-cholesterol acyltransferase Lcat promotes hepatic steatosis through fatty acid metabolism reprogramming in zebrafish larvae

city: Jinan

first: Yuanyuan

last: Fu

address: No. 44, West Wenhua Road

institute: Shandong University

summary: Lecithin-cholesterol acyltransferase (Lcat), the key enzyme in reverse cholesterol transport (RCT), has been traditionally recognized for its role in high-density lipoprotein (HDL) maturation and systemic cholesterol homeostasis. However, its hepatocyte-autonomous function in fatty acid metabolism remains elusive. Here, we established a hepatocyte-specific lcat-overexpressing zebrafish model (Tg(fabp10a:lcat-T2A-mCherry)) and integrated transcriptomic with metabolic phenotyping to reveal that lcat overexpression in zebrafish hepatocytes directly drives early-stage hepatic steatosis. lcat overexpression induces triglyceride (TG)-specific accumulation and cytoplasmic lipid droplet deposition. Surprisingly, transcriptomic profiling revealed unexpected upregulation of fatty acid elongation pathway. Crucially, genetic knockdown of hsd17b12a or pharmacological inhibition of Elovl1 partially rescued Lcat-induced hepatic steatosis. These findings decouple Lcat from classical RCT function, thereby providing a molecular rationale for targeted metabolic interventions in metabolic dysfunction-associated steatotic liver disease (MASLD).

overall_design: In this study, hepatocytes were FAC-sorted from Tg(fabp10a:eGFP) or (Tg(fabp10a:lcat-T2A-mCherry; fabp10a:eGFP) at 6 dpf zebrafish larvae, respectively (n = 3, 2000 hepatocytes each). We analyzed transcriptomic changes involved into lcat-overexpression induced early-stage hepatic steatosis using high-throughput RNA-sequencing.

first: Junjie

last: Xu

first: Lei

last: Li


title: Polystyrene microplastics disrupt ovarian development via cytoskeletal remodeling and epigenetic reprogramming particularly in granulosa cells

overall_design: GCs were isolated from ovaries of 21-day-old female post-weaning ICR mice by two-step enzyme digestion.GCs (2 × 104 cells/ 0.15 mL/well) were seeded in 96-well plates, adhered for 12 h, then treated with sonicated PS-MPs (100 nm ; 0,  750 μg/mL) for 24 h. Total RNA was extracted from GCs using TRIzol reagent (Thermo Fisher Scientific, 15596018) and then subjected to cDNA library construction and RNA sequencing (LC-Bio Technology CO., Ltd., Hangzhou, China). Raw reads were aligned to GRCm39 reference genome using HISAT2 package. Transcript quantification was performed using StringTie and ballgown with FPKM (fragment per kilobase of transcript per million mapped reads) value. Differential gene expression analysis was conducted using DESeq2, applying a false discovery rate (FDR) cutoff of 0.05 and minimum 1.5-fold change threshold. Significant DEGs were subsequently analyzed for enrichment analysis of Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways.


title: A unified network systems approach uncovers a core program underlying T follicular helper cell differentiation [CUT&RUN]

city: Cambridge

first: Vinay

last: Mahajan

address: 65 Landsdowne Street

institute: Brigham and Women's Hospital

summary: We investigated Tfh cell differentiation across multiple levels of biological organization by integrating diverse data types through interpretable network-based approaches. Our multi-scale network framework successfully combines transcriptomic and epigenetic datasets, capturing known regulators of Tfh differentiation identified in numerous prior studies. Through this approach, we identify a core set of Tfh-associated genes that is conserved across various tissues and disease conditions. Although individual components of this core set have been reported previously, a central contribution of our study is the unbiased discovery and in-depth characterization of this conserved gene signature.

overall_design: CUT&RUN analysis of H3K4me1, H3K4me3 and H3K27Ac marks from distinct stages of human Tfh differentiation

first: Grace

middle: J

last: Yuen


title: A unified network systems approach uncovers a core program underlying T follicular helper cell differentiation [RNA-Seq]

overall_design: Bulk RNAseq analysis of cells from distinct stages of human Tfh differentiation

first: Hamid

last: Mattoo

first: Viswanadham

last: Vinayak


title: A unified network systems approach uncovers a core program underlying T follicular helper cell differentiation [ATAC-seq]

overall_design: ATACseq analysis of cells from distinct stages of human Tfh differentiation


title: Effect of adenoviral COVID-19 vaccines on human umbilical vein endothelial cells

city: Kuopio

first: Nihay

last: Laham Karam

address: Neulaniementie 2

department: A.I. Virtanen Institute

country: Finland

institute: University of Eastern Finland

summary: Coronavirus disease 2019 (COVID-19) continues to cause outbreaks around the world despite the vast vaccination programs against it. Thus, it is important to keep developing better vaccines and other strategies to protect vulnerable populations. Here, we studied the safety of an adenovirus-based COVID-19 vaccine on human umbilical vein endothelial cells by total RNA sequencing and found, that the adenoviral vector vaccines had minimal effects on the gene expression profile of these cells.

overall_design: To investigate the effects of the adenoviral COVID-19 vaccines expressing the spike protein (Ad5-S-3M) or the spike receptor binding domain (Ad5-RBD-3M), each containing three common RBD mutations (K417N, E484K, and N501Y; referred to as 3M), we transduced human umbilical vein endothelial cells (HUVECs) with these vectors in triplicates. As controls, HUVECs were transduced with Ad5-CMV in triplicates. Cells were lysed and RNA extracted 72 h after the transduction.

first: Aino

last: Sormonen

last: Laham-Karam

first: Einari

last: Niskanen

first: Seppo

last: Ylä-Herttuala


title: The effect of UV irradiation on the distribution of RNAPII NTD and DIS3

city: Stockholm

first: Neus

last: Visa

address: Svante Arrhenius väg 20c

country: Sweden

institute: Stockholm University

summary: It is well established that exposure to UV light alters the distribution of RNA polymerase II (RNAPII), but the impact of UV irradiation on the genomic distribution of DIS3 has not been investigated. We generated ChIP-seq profiles of DIS3 in U2OS cells that express a HA-tagged DIS3 protein (DIS3FLAGHA). We analyzed the total occupancy of RNAPII using an antibody against the N-terminal domain of RPB1 (NTD). Average RNAPII occupancy at transcription start sites (TSSs) was significantly decrease 3 hours after UV irradiation, consistent with previous reports, and was notably recovered 8 hours  after irradiation. Upon UV irradiation, DIS3 exhibited a redistribution that closely aligned with the changes observed in RNAPII. This similarity, was particularly pronounced in highly expressed genes. Our results suggests that DIS3 is associated with the transcription machinery and can act locally at the transcription site during elongation.

overall_design: ChIP-seq in U2OS Flp-In/T-REx human cell line expressing an exogenous DIS3-HA variant under tetracycline-regulated promoter. Cells were collected pre UV or 3h or 8h exposure to 20J/m2 UV-C irradiation.  ChIP-Seq was performed targeting Rpb1 NTD or DIS3-HA.

first: Elin

last: Enervald

first: Indranil

last: Sinha


title: Long read direct RNA-sequencing of human monocyte derived macrophages for chimeric RNA discovery

first: Ruaidhrí

last: Jackson

summary: Classically, mammalian mRNA and protein are thought to be encoded from a single genetic locus known as a gene. Whether mRNA can contain exons from geographically distinct genes to form chimeric mRNA in the absence of malignancy is widely unknown. Pervasive and naturally occurring chimeric mRNA could greatly expand the functional diversity of mammalian transcriptomes and potentially generate novel hybrid proteins that underpin diverse biological processes. Here we demonstrate that long-read direct RNA-seq, paired with targeted mRNA splice-isoform analysis, enables the identification of a plethora of dynamically regulated chimeric mRNA in innate immune cells.

overall_design: We performed long read direct RNA-sequencing (LRDRS) of human monocyte derived macrophages (MDMs) using the Oxford Nanopore platform to facilitate the detection of chimeric RNAs (chRNAs). While conventional RNA-sequencing technologies are prone to several caveats that impede detection of chRNAs, including read fragmentation and the generation of artificial chRNAs via template switching of reverse tranascriptase enzymes used for cDNA synthesis, LRDRS does not possess these disadvantages. Therefore, LRDRS was selected as an appropriate modality for chRNA discovery. To allow for the detection of potential changes in chRNA expression in response to immunological stimuli and alterations in cell state, MDMs were differentially polarized to either a steady state (no additional treatment) or an inflammatory (LPS + IFNγ treatment) phenotype.

first: Harry

last: Kane

first: Olivia

last: Venezia

first: Hongshen

last: Wang

first: Liang

last: Shan


title: Long read direct RNA-sequencing of mammalian bone marrow derived macrophages for chimeric RNA discovery

summary: Eukaryotic mRNA is classically expected to be monocistronic, linear, and encoded by a single defined genetic locus. Conversely, emerging evidence has identified bicistronic translation and circularized mRNA as pervasive unconventional features of mammalian transcriptomes. During oncogenic translocation in humans, DNA from distinct genes can fuse together and encode chimeric mRNAs that directly contribute to tumorigenesis. However, it remains widely unknown whether or not chimeric mRNAs exist in the absence of chromosomal rearrangements, and if they contribute to normal physiological processes. To assay for chimeric mRNA (chRNA) expression in mammalian innate immune cells while circumventing chRNA detection limitations associated with conventional RNA-sequencing (RNA-seq) technology, including read fragmentation and artifact generation by template switching, we performed long read direct RNA sequencing (LR-DRS) of differentially polarized bone marrow-derived macrophages (BMDMs) using the Oxford Nanopore platform.

overall_design: We performed long read direct RNA-sequencing (LRDRS) of bone marrow derived macrophages (BMDMs) using the Oxford Nanopore platform to facilitate the detection of chimeric RNAs (chRNAs). While conventional RNA-sequencing technologies are prone to several caveats that impede detection of chRNAs, including read fragmentation and the generation of artificial chRNAs via template switching of reverse tranascriptase enzymes used for cDNA synthesis, LRDRS does not possess these disadvantages. Therefore, LRDRS was selected as an appropriate modality for chRNA discovery. To allow for the detection of potential changes in chRNA expression in response to immunological stimuli and alterations in cell state, BMDMs were differentially polarized to either a steady state (no additional treatment), inflammatory (LPS + IFNγ treatment) or tissue reparative (IL-4 + IL-13 treatment) phenotype.

first: Pathricia

last: Tilstam


title: An EZH2—SREBP2 axis promotes cholesterol biosynthesis and represents a noncanonical vulnerability in tumorigenesis

first: Arum

last: Kim

address: Medical Sciences Research Building III  3 Genome Ct

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Refer to individual Series


title: The 3D architecture of gene regulation in the distal convoluted tubule (RNA-Seq)

city: Nijmegen

first: Lotte

last: Tholen

state: Gelderland

address: Geert Grooteplein Zuid 28

department: Physiology

country: Netherlands

institute: Radboudumc

summary: Cell-type specific gene expression patterns are essential for kidney function. This is governed by binding of polymerases and transcription (co)-factors to regulatory DNA elements that can either be located close to their target genes or at great genomic distances from their target genes. Therefore, the 3D structure of the genome is an essential factor in cell-type specific gene transcription. Here, we generated a chromosome conformation capture (Hi-C) map in a distal convoluted tubule (DCT) cell line with a 5kb resolution. To study the role of the 3D genome in transcriptional regulation in the DCT the Hi-C data was integrated with chromatin accessibility (ATAC-seq), gene expression (RNA-seq) and histone mark ChIP-seq data of the same cell line.   Our analysis uncovered the basis of 3D genome characteristics in the DCT. Similar to other studies, promoter connectivity correlated with gene expression levels of the participating genes. As proof of principle, we studied the importance of long-range chromatin interactions in transcriptional regulation mediated by transcription factor HNF1β. Our analysis revealed that HNF1β controls the expression of housekeeping genes primarily by binding to promoters in close proximity of the transcription start site (TSS) of the gene, while the expression of developmental genes is regulated by both promoters and distal enhancers. Moreover, by employing a CRISPR/Cas9 enhancer mutant, we demonstrated that Caveolin-1 expression is regulated by an HNF1β-bound enhancer ~95kb from the TSS of the gene.  In conclusion, we describe the first Hi-C map in a DCT cell line and demonstrate that the 3D architecture of the genome controls specificity of HNF1β-mediated gene transcription.

overall_design: Gene expression profiling analysis of RNA-seq data in WT mpkDCT4a cells.

first: Eveline

last: Kahlman

first: Peter

last: Krijger

first: Branco

last: Heuts

first: Amin

last: Allahyar

first: Joost

last: Martens

first: Wouter

last: de Laat

last: Hoenderop

first: Jeroen

last: de Baaij


title: The 3D architecture of the genome determines specificity of HNF1β-mediated gene regulation (ChIP-Seq)

overall_design: Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) for histone variants H3K27ac in mpkDCT4a cells.


title: The 3D architecture of gene regulation in the distal convoluted tubule


title: The 3D architecture of the genome determines specificity of HNF1β-mediated gene regulation (ATAC-Seq)

overall_design: Assay for transposase-accessible chromatin (ATAC)-sequencing in mpkDCT4a cell line


title: Electronic nicotine delivery system use and expectorated sputum microbiota in Lebanese adults: A Pilot Study

status: Public on Aug 01 2026

city: Beirut

first: AUB

last: Submission

address: Bliss street

country: Lebanon

institute: American University of Beirut

summary: Electronic nicotine delivery systems (ENDS) are increasingly used worldwide, but their effects on respiratory microbial communities remain understudied. This pilot cross-sectional study compared the expectorated sputum microbiota of Lebanese adult ENDS users and non-ENDS users. Sputum samples were collected from 15 ENDS users and 15 non-ENDS users without chronic respiratory illness or recent antibiotic exposure. Samples were analyzed using 16S rRNA V3-V4 amplicon sequencing. Overall microbial richness, diversity, and evenness did not differ significantly between groups. In addition, presence/absence-based community composition showed no significant group-level separation. Both groups shared broadly similar dominant bacterial profiles with Bacillota, Pseudomonadota, and Bacteroidota among the most abundant phyla. Moreover, there was substantial overlap at the genus level. Despite these broad similarities, selective taxonomic differences were observed at finer resolutions including increased relative abundance of Nanosynbacter and decreased abundance of a putative Rothia species-level taxon among ENDS users after FDR correction. Actinomyces showed a nominal increase in ENDS users, but this did not remain significant after FDR correction. These findings suggest that ENDS use was not associated with broad sputum microbiota disruption in this cohort but may be associated with selective shifts in specific bacterial taxa.

overall_design: Cross-sectional, observational, case-control pilot study using 16S rRNA gene sequencing.

first: Ali

last: El Tawil

first: Joelle

last: Korban

first: Hassan

last: Abbas

first: Fayez

last: Yassine

first: Abdallah

last: Kurdi

first: Ghassan

last: Matar

first: Nisrine

last: Makarem

first: Melhem

last: Bilen


title: Effects of CRP1 Overexpression on Transcriptional Levels of Genes in Tomato Roots and Leaves

city: nanjing

first: hai

last: zhu

address: xiaolingwei Street 50th

institute: nanjing agricultural university

summary: The perception of pathogen-associated molecular patterns (PAMPs) by plant pattern recognition receptors triggers frontline immunity. The Fusarium oxysporum effector CRP1 acts as a dual-function protein, serving as both a virulence factor and a potent apoplastic elicitor that triggers robust immunity and a pronounced growth-defense trade-off in plants. To elucidate the molecular basis of CRP1-mediated enhanced disease resistance, we performed transcriptomic profiling of Solanum lycopersicum (tomato) plants overexpressing CRP1 (OE-CRP1-2) compared to wild-type (WT) plants. This study investigates the extensive, tissue-specific transcriptional reprogramming induced by CRP1-triggered immunity. By comparing the leaves and roots of 5-week-old WT and OE-CRP1-2 plants, we identified differentially expressed genes (DEGs) associated with defense-related pathways, including secondary metabolite biosynthesis (e.g., flavonoid biosynthesis in leaves) and physical barrier formation (e.g., cutin, suberin, and wax biosynthesis in roots). These transcriptomic data provide crucial molecular insights into the spatially distinct systemic defense strategies orchestrated by a fungal effector, offering valuable genomic resources for engineering broad-spectrum disease resistance in crops.

overall_design: Sample Source: Leaves and roots of 5-week-old Solanum lycopersicum (tomato, cv. Ailsa Craig) plants. Genotypes: Wild-type (WT) and CRP1 overexpression line (OE-CRP1-2). Tissues: Leaves and Roots. Experimental Groups & Replicates: The experiment consisted of four groups, with three biological replicates per group (12 samples in total): WT leaves (3 biological replicates) OE-CRP1-2 leaves (3 biological replicates) WT roots (3 biological replicates) OE-CRP1-2 roots (3 biological replicates)

first: Hai

last: Zhu


title: Gene duplication of SNAPC1 generates transcription factors for snRNAs and sex-specific piRNAs

city: Baltimore

first: John

last: Kim

state: MD

address: 3400 Charles Street

department: Department of Biology

institute: Johns Hopkins University

summary: Piwi-interacting RNAs (piRNAs) are small non-coding RNAs essential for transposon silencing and germline integrity across metazoans. In many species, piRNA expression is sexually dimorphic, yet the molecular mechanisms underlying this sex specificity remain poorly understood. In Caenorhabditis elegans, sexually dimorphic piRNA expression is regulated at the transcriptional level. We previously identified SNPC-1.3, a paralog of the small nuclear RNA (snRNA) activating protein complex (SNAPc/SNPC) subunit SNAPC1, as a male-specific piRNA transcription factor. However, the factors governing female piRNA expression remained elusive. Here, we identify SNPC-1.2, a second SNPC-1 paralog, as a female-specific piRNA transcription factor. SNPC-1.2 interacts with the core piRNA transcriptional machinery, binds female piRNA loci, is required for female piRNA expression, and promotes hermaphrodite fertility. In contrast, a third paralog, SNPC-1.1, retains the ancestral SNAPc function in snRNA transcription and is dispensable for piRNA biogenesis. Together, these findings reveal how gene duplication and functional specialization within the snpc-1 gene family generate specificity factors that direct the core SNAP complex to distinct genomic targets, providing a molecular mechanism for sexually dimorphic piRNA expression while maintaining canonical snRNA transcription.

overall_design: small RNA-seq of wild-type C. elegans and small RNA pathway mutants at the 48-hour L4 and 72-hour gravid adult stages.

first: Lars

middle: K

last: Benner

first: Margaret

middle: R

last: Starostik

first: Rebecca

last: Tay

first: Ayaka

last: Inoki

first: Mindy

last: Clark

first: Suhua

last: Feng

first: Michael

middle: C

last: Schatz

first: Steven

middle: E

last: Jacobsen


title: iMSC-Derived Extracellular Vesicles Attenuate Cisplatin-Induced Renal Tubulointerstitial Fibrosis

city: Pyeongchang-gun

first: Ran

state: Gangwon-do

address: 1447 Pyeongchang-daero, Daehwa-myeon

institute: Seoul National University

summary: Background: Cisplatin is a widely used chemotherapeutic agent for various solid tumors. However, its use is often limited by nephrotoxicity, which can lead to acute kidney injury and, with repeated exposure, cumulative tubular damage and chronic renal dysfunction. Induced mesenchymal stem cell-derived extracellular vesicles (iMSC-EVs) have emerged as a promising cell-free therapeutic approach because of their anti-inflammatory, anti-apoptotic, and regenerative properties. The therapeutic efficacy of  iMSC-EVs in cumulative cisplatin nephrotoxicity remains unclear. Methods: Male C57BL/6 mice were subjected to renal injury by intraperitoneal cisplatin administration at 9 mg/kg once weekly for five cycles. After the final cisplatin injection, mice received intravenous PBS or iMSC-EVs at doses of 200 or 400 μg every 3 days for five doses. Renal injury, fibrosis, inflammation, cell-death signaling, oxidative stress, and peritubular capillary loss were evaluated by histology, immunoblotting, immunostaining, and quantitative polymerase chain reaction. RNA sequencing of renal tissue was performed to identify pathways regulated by iMSC-EV treatment. Results: iMSC-EVs ameliorated repeated cisplatin-induced renal injury in a dose-associated manner, with the 400 μg group showing more pronounced therapeutic effects. iMSC-EV treatment reduced collagen deposition, tubular damage, immune-cell infiltration, and peritubular capillary loss. Fibrosis-related markers and inflammatory mediators were suppressed by iMSC-EV. RNA-sequencing of renal tissues revealed that iMSC-EV treatment modulated and partially reversed RLDC-induced transcriptional alterations, particularly those associated with inflammatory, immune, and extracellular matrix-related pathways. Conclusion: iMSC-EVs mitigated key pathological features of repeated cisplatin-induced kidney injury, with the most consistent effects observed at the 400 μg dose. These findings support iMSC-EVs as a promising cell-free therapeutic strategy for tubulointerstitial fibrosis induced by cumulative cisplatin nephrotoxicity.

overall_design: Male C57BL/6 mice were divided into four experimental groups: normal control, cisplatin plus PBS, cisplatin plus 200 μg iMSC-EVs, and cisplatin plus 400 μg iMSC-EVs. Cumulative kidney injury was induced by intraperitoneal administration of cisplatin at 9 mg/kg once weekly for five cycles. After the final cisplatin administration, mice received intravenous PBS or iMSC-EVs every 3 days for a total of five doses. Kidney tissues were collected after treatment, and total RNA was subjected to bulk RNA sequencing. Biological replicates were included for each experimental group.

first: Hongduk

first: Sungok

last: Hong

first: KangYeon

first: Minjae

first: Yudam

last: Ha

first: Jimin

first: Seul Ki

last: Lee

first: Soo

first: Tae Min


title: Atractylenolide III Alleviates Cisplatin-Induced Acute Liver Injury by Regulating Gut-Liver Axis Through Inhibiting ACT1/TRAF6/NF-κB-Mediated IL-17 Pathway

city: Hangzhou

first: Guoyin

last: Kai

address: No. 548 Binwen Road, Binjiang District

institute: Zhejiang Chinese Medical University

summary: Introduction: Cisplatin (DDP) is a highly effective and broad-spectrum chemotherapeutic agent. However, its clinical application is limited by severe hepatotoxicity. Currently available hepatoprotective agents are often associated with insufficient efficacy or side effects. Therefore, developing new hepatoprotective agents that are highly efficient and low in toxicity is urgent. Objectives: Atractylodes macrocephala Koidz. is a well-known traditional Chinese medicine for strengthening the spleen function. According to the theory of traditional Chinese medicine, “When liver disease occurred, the spleen should be strengthened first” suggests that A. macrocephala Koidz. might possess hepatoprotective properties. Therefore, this study focuses on the molecular mechanism by which the active factors of A. macrocephala Koidz. exert their liver-protective effects. Methods: Animal experiments were adopted to screen the active factors of A. macrocephala Koidz. Multi-omics integrated analysis, including gut microbial diversity, transcriptomics, and metabolomics, combined with fecal microbiota transplantation (FMT) experiments were performed to clarify the mechanism of liver-protective effects of atractylenolide III (AT-III). Results: We found that AT-III-derived from A. macrocephala Koidz. significant decreased ALT, AST levels and hepatic pathological symptoms in DDP-induced acute liver injury (ALI). AT-III alleviated DDP-induced ALI via the “gut-liver axis” by inhibiting the ACT1/TRAF6/NF-κB-mediated IL-17 signaling pathway. Eight distinct microbial species, including Parabacteroides and Alloprevotella, were identified with significant differences. Besides, metabolite N6-(1,2-dicarboxyethyl)-AMP was identified as a novel biomarker for hepatotoxicity. Meanwhile, the FMT results indicated that the intestinal microbiota has a better alleviating effect on ALI than the metabolites of the intestinal microbiota.

overall_design: Male BALB/c mice were injected with DDP solution


title: Transcriptomic analysis of FTO knockdown in MG63 osteosarcoma cells

city: Xi'an

first: Zhaoliang

last: Shen

state: Shaanxi

address: NO.157 Xiwu Rd

department: Department of Orthopedics

institute: the Second Affiliated Hospital of Xi’an Jiaotong University

summary: Fat mass and obesity-associated protein (FTO), a key N6-methyladenosine (m6A) demethylase, plays critical roles in tumor progression and chemotherapy resistance. However, the downstream transcriptional networks regulated by FTO in osteosarcoma remain incompletely understood. To investigate the molecular mechanisms underlying FTO-mediated osteosarcoma progression and cisplatin sensitivity, we performed transcriptome sequencing (RNA-seq) on MG63 osteosarcoma cells following FTO knockdown. This dataset provides a comprehensive view of the gene expression changes induced by FTO depletion, which may help identify key downstream targets and pathways involved in osteosarcoma pathogenesis and chemoresistance.

overall_design: Transcriptome profiling of MG63 human osteosarcoma cells with stable FTO knockdown (shFTO) compared to control cells (shNC). Total RNA was extracted from three independent biological replicates per group and subjected to strand-specific RNA-sequencing (RNA-seq) on the Illumina NovaSeq 6000 platform. This dataset serves to identify FTO-regulated downstream targets and signaling pathways in osteosarcoma.


title: Transcriptomic responses of HAP1 cells to Bu-DIF-3 and CP-DIF-3

city: Tokorozawa-shi

first: Taichi

last: Hara

state: Saitama

address: 2-579-15 Mikajima

department: Faculty of Human Science

institute: Waseda university

summary: Dictyostelium differentiation-inducing factors (DIFs) and their derivatives regulate diverse cellular functions in mammalian cells, but the molecular responses elicited by individual derivatives remain incompletely understood. We performed RNA sequencing of HAP1 cells treated for 24 h with vehicle, 5 µM Bu-DIF-3, or 5 µM CP-DIF-3. This dataset enables comparison of the transcriptomic responses to the two DIF-3 derivatives, including stress-response, redox, metabolic, and autophagy-related pathways.

overall_design: Bulk RNA-seq was performed using HAP1 WT cells under three conditions: vehicle control, 5 µM Bu-DIF-3, and 5 µM CP-DIF-3. Each condition included three independent biological replicates (nine libraries in total). Cells were exposed for 24 h before total RNA extraction. Libraries were sequenced as paired-end 150-bp reads on an Illumina NovaSeq 6000.

first: Yue

last: Cai

first: Ryu

last: Yamada


title: Effect of levofloxacin on apoptosis pathways in SW48 colorectal cancer cells

city: Wuhan

first: Jiangyang

last: Chi

address: Youyi street

institute: Hubei University

summary: We profiled transcriptomic changes in SW48 cells after 5-day 100μM levofloxacin treatment. Levofloxacin induces DNA damage and moderate p53 activation biased toward DNA repair over pro-apoptotic programs, while remodeling mitochondrial metabolism via enhanced OXPHOS and ROS accumulation. Though levofloxacin alone does not trigger robust apoptosis, it primes cells for apoptotic sensitivity via metabolic stress and redox imbalance, defining a novel anti-tumor mechanism of this clinical antimicrobial.

overall_design: 6 RNA-seq samples from SW48 cells with/without 100μM levofloxacin treatment for 5 days (3 biological replicates per group).

first: Yongli

last: Fan

first: Chenmeng

last: Huang


title: Cholesterol-Dependent Metabolism Promotes Bedaquiline Tolerance in Mycobacterium tuberculosis by Limiting Energetic Disruption

first: Chuan

last: Wang

address: 131 # Dong An Road

institute: Fudan University

summary: Bedaquiline (BDQ) is a diarylquinoline antibiotic that targets mycobacterial ATP synthase and is used in the treatment of drug-resistant tuberculosis. Cholesterol is an important carbon source for Mycobacterium tuberculosis during infection and has been shown to influence antibiotic susceptibility. To investigate how the growth environment shapes the transcriptomic response to BDQ, we performed RNA-seq on M. tuberculosis H37Rv cultures grown in standard medium or cholesterol-supplemented medium (0.2 mM) and treated with low-dose (0.625 μg/mL) or high-dose (2.5 μg/mL) BDQ, or DMSO as vehicle control, for 4 hours.

overall_design: RNA-seq profiling of Mycobacterium tuberculosis H37Rv grown in standard medium or cholesterol-supplemented medium (0.2 mM) and treated with DMSO (vehicle control), 0.625 μg/mL BDQ (low dose), or 2.5 μg/mL BDQ (high dose) for 4 hours. Three biological replicates per condition (18 libraries total).

first: Qian

last: Gao

first: Cheng

last: Bei

first: Shimin

last: Tan

last: Zhang

first: Peng

last: Xu


title: Vitamin B2 Sensing by the Nuclear Receptor AhR Reprograms Hepatic Metabolism [RNA-Seq]

city: Palo Alto

first: Yohei

last: Abe

state: California

address: 3181 Porter Dr

institute: Arc Institute

summary: Nuclear receptors such as RAR/RXR and VDR directly sense vitamins A and D, but analogous sensing mechanisms for most other vitamins remain unknown. Here we identify a metabolite sensing pathway linking vitamin B2 (riboflavin) availability to an adaptive gene expression program. Riboflavin deficiency limits the FAD-dependent enzyme kynurenine 3-monooxygenase, leading to accumulation of kynurenine, an endogenous ligand of the aryl hydrocarbon receptor (AhR). Kynurenine-induced AhR nuclear translocation selectively activates poised hepatic enhancers in cooperation with AP-1 and C/EBPα, inducing glucuronidation genes and the FAD synthase gene FLAD1. This response is required to maintain intracellular FAD levels and support cell fitness under riboflavin-limiting conditions. In vivo, dietary riboflavin deficiency enhances hepatic drug clearance and reduces irinotecan toxicity. Together, these findings reveal a vitamin-sensing mechanism in which a cofactor-dependent enzyme acts as the sensor and AhR functions as the transcriptional effector that enables both flavin homeostasis and hepatic clearance capacity.

overall_design: RNA-seq for comparative gene expression profiling

first: Augustinus

middle: G

last: Haribowo

first: Ankur

last: Garg

first: Rebekah

last: Nicholson

first: Enchen

last: Zhou

first: Christopher

last: Glass

first: Isha

middle: H

last: Jain


title: Vitamin B2 Sensing by the Nuclear Receptor AhR Reprograms Hepatic Metabolism [ATAC-Seq]

overall_design: ATAC-seq for chromatin accessibility


title: Vitamin B2 Sensing by the Nuclear Receptor AhR Reprograms Hepatic Metabolism [ChIP-Seq]

overall_design: Transcription factors and H3K27ac ChIP-seq for transcription factor binding and enhancer activity.


title: Single-cell transcriptomes of subcutaneous and orthotopic RM-1 mouse prostate tumors collected 7 days after sham or irreversible electroporation

city: wuhan

first: Qi-Dong

last: Xia

address: No. 1095 Jiefang Avenue

department: Urology

institute: Tongji Hospital

summary: This submission describes a single-cell RNA-sequencing resource generated from two mouse prostate cancer models. The dataset contains six subcutaneous RM-1 tumors and four orthotopic RM-1 prostate tumors collected 7 days after sham intervention or irreversible electroporation (IRE). Each excised tumor represents one biological replicate and was processed as an independent whole-cell suspension before library construction. Raw sequencing reads were previously submitted to SRA under BioProject PRJNA1497318 and are linked here through the corresponding SRA accessions. The GEO submission provides the processed filtered gene-barcode matrices used for downstream quality control, integration, clustering, and cell-type annotation.

overall_design: RM-1 tumors were established in male C57BL/6 mice either subcutaneously or orthotopically in the prostate. Samples comprise three sham-treated and three IRE-treated subcutaneous tumors, together with two sham-treated and two IRE-treated orthotopic tumors. Tumors were collected 7 days after intervention, dissociated into whole-cell suspensions, and sequenced as single-cell 3' RNA-seq libraries.

first: Zhi-Yu

first: Jia-Cheng

last: Xiang

first: Jian-Xuan

last: Sun

first: Jin-Zhou

first: Shao-Gang


title: Single-cell transcriptomes of paired peripheral blood mononuclear cells collected before and 7 days after irreversible electroporation in patients with localized prostate cancer

summary: This submission describes paired single-cell RNA-sequencing profiles of peripheral blood mononuclear cells (PBMCs) from five patients with clinically localized prostate cancer undergoing irreversible electroporation (IRE). For each participant, one PBMC sample was collected immediately before IRE and one PBMC sample was collected 7 days after IRE, generating ten independent single-cell libraries. Raw sequencing reads were previously submitted to SRA under BioProject PRJNA1497318 and are linked here through the corresponding SRA accessions. The GEO submission provides the processed filtered gene-barcode matrices used for downstream quality control, integration, clustering, and annotation.

overall_design: Five patients with clinically localized prostate cancer contributed paired PBMC samples collected before IRE and 7 days after IRE. Each sample was processed independently without pooling before library construction. Libraries were generated from whole-cell PBMC suspensions and sequenced as single-cell 3' gene-expression libraries.


title: Distinct phenotype and effector function of CD4 coreceptor disparate iNKT cell subsets

city: Bethesda

first: Jung-Hyun

last: Park

address: 10 Center Drive

department: NCI/CCR/EIB

institute: National Institutes of Health

summary: Invariant natural killer T (iNKT) cells are thymus-derived innate-like T cells that lack CD8 and express either CD4 (CD4SP) or no coreceptors (DN). The role of coreceptors in iNKT cell development and effector functions, however, remains unclear. Here, we show that CD4 expression correlates with the subset identity of iNKT cells, specifically unveiling a dichotomy of CD4 coreceptors among IFNγ-producing iNKT cells that we refer to as NKT1.4+ and NKT1.4– cells, based on CD4 expression. These CD4 disparate NKT1 cells markedly differed in their gene transcription profiles, surface phenotypes, and effector functions, revealing a CD4 coreceptor-associated divergence in iNKT cells. Moreover, CD4 expression was associated with enhanced TCR signaling in iNKT cells, such that CD4-deficiency heavily disturbed their generation and differentiation in the thymus. Collectively, these results reveal a previously unappreciated association between CD4 coreceptor expression and iNKT effector function, establishing CD4 as a functional marker in iNKT cell biology.

overall_design: RNA sequencing of BALB/c mouse thymic NKT1.4+ and NKT1.4− invariant natural killer T cells isolated by flow cytometric sorting.

first: Yongmei

last: Zhao

first: Can

last: Li


title: Mast Cell Arachidonate 5-lipoxygenase Deficiency Attenuates Ischemia/Reperfusion-induced Cardiac Fibrotic Remodeling in Mice by Limiting Mast Cell Leukotrienes

city: Chengdu

first: lingyu

last: li

address: Sichuan University West China Hospital

institute: Sichuan University

summary: Following myocardial ischemia/reperfusion (I/R), mast cells play a key regulatory role in fibrotic remodeling through their arachidonic acid 5-lipoxygenase (ALOX5)–leukotriene (LT) signaling axis. We found that specific knockout of ALOX5 in mast cells in mice reduces mast cell aggregation, lowers local LT levels, alleviates myocardial fibrosis, and improves cardiac function. Mechanistically, TNF-α drives the colocalization of ALOX5 and FLAP at the mast cell nuclear membrane, promoting the synthesis and release of LTB4 and cysteinyl leukotrienes, which in turn activate leukotriene receptors on cardiac fibroblasts and promote fibroblast proliferation, migration, and myofibroblast differentiation via the NF-κB, AKT, and STAT3 pathways. Genetic or pharmacological inhibition of ALOX5 in mast cells blocks LT production and suppresses fibroblast activation, suggesting that targeting ALOX5 in mast cells is a potential therapeutic strategy for reducing fibrotic remodeling following I/R.

overall_design: To define the downstream signaling programs through which LTs derived from activated mast cells promote fibroblast pro-fibrotic responses, we performed RNA-seq on NRCFs cultured with conditioned medium from TNF-α-stimulated BMMCs.

first: Lingyu

first: Lan

last: Lin

first: Fan

last: Wang

first: Sisi

last: Wu

first: Linling

last: Liu

first: Xuemei

first: Wenjing

last: Huang


title: Dexmedetomidine Mitigates Pulmonary Ischemia-Reperfusion Injury by Targeting Ferroptosis through β-catenin/TCF4 Pathway Activation

city: Wuxi

first: Youyi

state: Jiangsu

address: No. 1800, Lihu Avenue

department: Wuxi School of Medicine

institute: Jiangnan University

summary: RNA sequencing was performed to characterize transcriptomic changes associated with dexmedetomidine treatment in MLE-12 mouse lung epithelial cells subjected to hypoxia/reoxygenation. Differential expression and functional enrichment analyses were used to identify genes and pathways potentially involved in the protective and anti-ferroptotic effects of dexmedetomidine.

overall_design: MLE-12 cells were assigned to two experimental groups: hypoxia/reoxygenation (I/R) and dexmedetomidine-pretreated hypoxia/reoxygenation (I/R + Dex). Three independent biological replicates were analyzed per group, for a total of six RNA-seq libraries. Cells in the I/R group were exposed to 1% O2 for 12 h followed by reoxygenation for 4 h. Cells in the I/R + Dex group were pretreated with 10 µM dexmedetomidine for 12 h before hypoxia and were then subjected to the same hypoxia/reoxygenation protocol. Paired-end 150-bp sequencing was performed on an Illumina NovaSeq 6000 platform.

first: Sha

first: Hao

last: Hang

first: Xinyu

first: Xian

last: Ding

first: Liangliang

last: Cao

first: Xiao

last: Chen


title: α7 integrin is a critical co-regulator of chromatin accessibility and gene expression in HPV-negative head and neck cancer

city: Dresden

first: Nils

last: Cordes

state: saxony

address: Fetscherstrasse 74 / PF 41

department: Dept. of Radiation Oncology

institute: OncoRay - National Center for Radiation Research in Oncology

summary: Epigenetic regulation and gene transcription are dynamically modulated by extracellular signals, including focal adhesions; however, the role of integrins in these processes remains poorly understood. In this study in HPV-negative head and neck squamous cell carcinoma, we combined investigations in physiological 3-dimensional matrix cell models with multi-omics analyses, bioinformatics and artificial intelligence, to unmask the integrin effector signaling network that reshapes chromatin to drive cancer. Among the 12 α/β1 integrin receptors, α7 integrin emerged as the most potent modulator of histone post-translational modifications, associated with significant changes in gene transcription and chromatin accessibility. Mechanistically, phosphoproteomics revealed significant inhibition of MAPK- and PI3K/AKT-dependent signaling with concomitant functional impairment of cell cycling and cell survival upon ITGA7 depletion. In summary, these findings establish α7 integrin as a key co-regulator of chromatin accessibility and gene transcription in HPV-negative HNSCC, acting through an AURKA-centered axis that couples adhesion signaling to cell cycle control and patient survival, and nominate AURKA as an actionable therapeutic node downstream of the currently non-druggable ITGA7.

overall_design: RNA sequencing was performed on the HPV-negative HNSCC cell lines Cal-33 and SAS cultured in three-dimensional (3D) laminin-rich extracellular matrix (lrECM). ITGA7 was silenced using siRNA, and transcriptomic profiles of siITGA7 and siControl cells were generated and compared.

first: Borodins

last: Olegs

first: Vehlow

last: Anne

first: Sameith

last: Katrin

first: Dahl

last: Andreas

first: Cordes

last: Nils


title: α7 integrin is a critical co-regulator of chromatin accessibility and gene expression in HPV-negative head and neck cancer [ATAC-seq]

overall_design: ATAC-seq was performed in Cal33 and SAS HPV-negative head and neck squamous cell carcinoma cell lines cultured in three-dimensional laminin-rich extracellular matrix (3D lrECM). Cells were transfected with non-targeting siControl or siRNA targeting ITGA7. Twenty-four hours after transfection, cells were embedded in 3D lrECM, and nuclei were isolated 48 hours after transfection. Four independent biological replicates were analyzed for each cell line and condition, yielding 16 ATAC-seq libraries. Libraries were sequenced in 2 × 100 bp paired-end mode on an Illumina NovaSeq 6000. Chromatin accessibility was compared between siControl and siITGA7 within each cell line.


title: Clinical and Single-Cell Sequencing Characteristics of Adult-Onset Intestinal Hypoganglionosis

city: Longmata District, Luzhou City, Sichuan Province.

first: zheng

last: ran

address: No. 1, Xianglin Road, Section 1

institute: Southwest Medical University

summary: Hypoganglionosisis a rare motility disorder characterized by a significant reduction in enteric ganglion cells.scRNA-seq indicated immune microenvironment remodeling in the lesioned bowel segment, characterized by an increased proportion of plasma cells. These plasma cells exhibited features of endoplasmic reticulum stress, activation of the unfolded protein response pathway, and enrichment in immune regulatory functions. B cells and T cells also showed enrichment in immune-related pathways.

overall_design: Single-cell RNA sequencing data were collected from multiple batches of colorectal samples. The data pre-processing was performed using the BD Rhapsody Pipeline(v2.0) to generate gene expression matrices. Samples were categorized into three groups: Lesion, Patient Control (pControl), and Normal Control (nControl).

first: Ran

last: Zhen

first: Zhang

last: Yuanchuan

first: Chen

last: Quanyu

first: Wang

last: Xinping

first: Feng

last: Siyuan


title: Macrophage VISTA Restrains Inflammatory and Antigen-Presenting Programs During Alloimmune Tissue Injury [Cut&Tag]

city: Shanghai

first: Lifei

last: Liang

address: 180 Fenglin Road

institute: Zhongshan Hospital, Fudan University

summary: Macrophage inflammatory plasticity is a central determinant of immune-mediated tissue injury, yet the intrinsic checkpoint mechanisms that restrain inflammatory macrophage programming remain incompletely defined. Here, using acute cardiac allograft rejection as an alloimmune tissue-injury model, we found that Vsir, encoding V-domain Ig suppressor of T-cell activation (VISTA), was preferentially expressed in graft macrophages but declined as macrophages acquired inflammatory and antigen-presenting states. Single-cell RNA sequencing and pseudotime analysis revealed that VISTA downregulation accompanied macrophage progression from reparative/resident-like states toward inflammatory programs. In vitro, VISTA overexpression intrinsically restrained pro-inflammatory macrophage polarization, reduced inflammatory cytokine expression, and limited the induction of antigen-presenting molecules including MHC-II and CD80, thereby attenuating macrophage-driven CD4⁺ T-cell proliferation. Integrative CUT&Tag and RNA-seq analyses further showed that VISTA overexpression was associated with reduced H3K4me3 enrichment at inflammatory regulatory loci, including TRAF5 and CHDH, together with transcriptional repression of NF-κB-, TNF-, MAPK-, and IL-17-associated inflammatory programs. In vivo F4/80 promoter-directed Vsir restoration shifted intragraft macrophages away from inflammatory polarization, reduced T-cell accumulation, and attenuated early rejection-associated tissue injury. Together, these findings identify VISTA as an intrinsic regulator of macrophage inflammatory programming and point to H3K4me3-associated chromatin remodeling as a regulatory layer linked to VISTA-mediated inflammatory restraint.

overall_design: At day 5 after transplantation, syngeneic and allogeneic grafts were enzymatically digested to generate single-cell suspensions. Cell viability and cell number were assessed before library preparation. Single-cell RNA-seq libraries were generated using the 10x Genomics Chromium platform according to the manufacturer’s instructions, and sequencing was performed on an Illumina platform.

first: Rui

last: Shi

first: Cuidi

last: Xu

first: Xiaohan

last: Yu

first: Maoxin

last: Liao

first: Tongyu

last: Zhu

first: Ruiming

last: Rong

first: Jiangang

last: Hou

first: Dong

first: Cheng

last: Yang


title: Macrophage VISTA Restrains Inflammatory and Antigen-Presenting Programs During Alloimmune Tissue Injury [RNA-Seq]


title: Immune architecture of the colon in ICI-mediated colitis compared with ulcerative colitis

city: Nijmegen

first: Harm

last: Westdorp

address: Geert Grooteplein Zuid

department: Medical Oncology

institute: Radboudumc

summary: Despite clinical success of immune checkpoint inhibitors (ICI), many cancer patients experience immune-related adverse events (irAEs). Among these, ICI-mediated colitis (IC) is prevalent and is associated with a significant burden on patients and healthcare. Despite resemblance to ulcerative colitis (UC) with respect to clinical symptoms and treatment approaches, IC’s specific causes and cellular mechanisms are incompletely understood.

overall_design: We performed bulk RNAseq  analyses on colon biopsies. In addition to IC and UC patients, two groups served as controls: patients who received ICI but did not develop IC, and patients with diarrhea but without inflammation on histology.


title: Macrophage VISTA Restrains Inflammatory and Antigen-Presenting Programs During Alloimmune Tissue Injury


title: DNA methylation hotspots reveal a critical window of susceptibility for growth and disease resilience in preweaning dairy calves

city: Québec

first: Aldcejam

last: Martins da Fonseca Junior

state: QC

address: Services Pavilion, 2440 Bd Hochelaga Suite 1710

department: Animal Sciences

country: Canada

institute: Laval University

type: Methylation profiling by high throughput sequencing

summary:
Background: The preweaning period in dairy calves represents a critical window of susceptibility during which physiological stressors can induce lasting phenotypic shifts in growth and disease resilience. To investigate the epigenetic basis of this environmental programming, enzymatic methyl-sequencing (EM-seq) was performed on whole-blood DNA from 48 Holstein calves at approximately 40 days of age, stratified into resilient controls or groups exhibiting low body mass index (BMI), respiratory disease (RESP), or diarrhea (DIAR).
Results: A genome-wide epigenetic reconfiguration distinguishing resilient from susceptible animals was identified, comprising a 58-gene multi-phenotype core of convergent methylation signals. Deconvolution analysis confirmed that these signatures were independent of leukocyte composition, reflecting intrinsic cellular reprogramming rather than cell-type shifts. The methylomic landscape was dominated by hypermethylation of genes regulating neuronal and immune excitability (DPP6, CNTNAP2) and cytoskeletal dynamics (DIAPH3), suggesting a state of leukocyte activation and impaired migration. Furthermore, metabolic sensors (PRKAG2) and barrier integrity genes (FRMD4A) emerged as dense methylation hotspots, linking growth impairment to a thrifty metabolic phenotype and compromised mucosal repair.
Conclusions: These findings suggest that the preweaning window of susceptibility can act as an immune filter, leaving a stable epigenetic memory that constrains immune plasticity and metabolic allocation, thereby offering new targets for biomarkers in livestock health.

overall_design:
To investigate the epigenetic basis of this environmental programming, enzymatic methyl-sequencing (EM-seq) was performed on whole-blood DNA from 48 Holstein calves at approximately 40 days of age, stratified into resilient controls or groups exhibiting low body mass index (BMI), respiratory disease (RESP), or diarrhea (DIAR).
The study strictly monitors 48 individual calves stratified into Resilient Controls, Low BMI, RESP, and DIAR groups.
Submitters' note: The physical enzymatic methyl-sequencing (EM-seq) setup generated exactly 12 multi-contrast library lanes. Each single physical library sample records encompasses distinct down-stream single-nucleotide resolution processed report files (*.CX_report.txt) corresponding to our matched analytical comparisons.

last: Fonseca Junior

first: Mohamed

last: Oudihat

first: Sébastien

last: Buczinski

first: Jean

last: Silva Ramos

first: Camila

middle: B

last: de Lima

first: Marc-André

last: Sirard


title: Drosophila melanogaster lactate dehydrogenase deficiency recapitulates the exercise intolerance of human glycogen storage disease type XI

city: Bloomington

first: Jason

last: Tennessen

email: tennessenlab@gmail.com, tennlab@iu.edu, jtenness@iu.edu, tourigny@iu.edu

state: IN

address: 1001 E 3rd St

department: Biology

institute: Indiana University

summary: Lactate dehydrogenase A (LDHA) is a key glycolytic enzyme that commonly exhibits altered expression in human diseases such as cancers and neurodegeneration, making it a valuable disease biomarker and putative therapeutic target. However, any treatment targeting LDHA will also disrupt normal metabolism, underscoring the need to investigate physiological consequences of inhibiting this enzyme. We previously established the fruit fly Drosophila melanogaster as a genetic model for studying LDH function in the context of growth, metabolism, and development. Here we expand upon those studies by investigating a serendipitous observation that Ldh mutant larvae exhibit diet-dependent lethality. Using a multiomic approach, we discovered this diet-dependent phenotype is independent of nutritional composition or hypoxic microenvironments. Instead, Ldh mutant larvae are exercise intolerant and display reduced mobility, rendering mutant larvae sensitive to food consistency. Moreover, tissue-specific analysis reveals that LDH activity within muscle and peripheral glia are essential for larval viability raised on solid food. Intriguingly, these phenotypes recapitulate the pathophysiology of LDHA deficiency (Glycogen Storage Disease Type XI; GSD Type XI) in humans, where mild symptoms are exacerbated by physical exertion and environmental stress. Together, our findings further highlight the value of using Drosophila to explore the developmental and physiological consequences of human LDHA inhibition.  Included here are the transcriptomic data of LDH mutant and control flies fed Bloomington food vs. molasses + yeast.

overall_design: RNA-seq profiling of heterozygous control (Impl3 17/+) versus Ldh mutant (Impl3 17/16) larvae, comparing those raised on BDSC food to those raised on Molasses + Yeast food.

first: Madhulika

last: Rai

middle: P

last: Tourigny


title: Transcriptomic profiling of Piezo1-deficient osteoclast precursors

city: Boston

first: Yizhong

last: Hu

address: 190 Longwood Ave.

institute: Harvard School of Dental Medicine

summary: Mechanical stimulation regulates bone remodeling, but the molecular mechanisms by which mechanosensing controls osteoclast differentiation remain incompletely understood. To identify transcriptional pathways downstream of the mechanosensitive ion channel Piezo1, bulk RNA sequencing was performed on osteoclast precursors derived from bone marrow monocytes of female control and monocyte-specific Piezo1 conditional knockout mice. Differential gene expression analysis was used to identify signaling pathways regulated by Piezo1 during osteoclastogenesis.

overall_design: Bone marrow-derived monocytes were isolated from female wild-type (Piezo1fl/fl) and monocyte-specific Piezo1 conditional knockout (Csf1r-iCre;Piezo1fl/fl) mice for RNA-seq profiling. Cells were cultured in the presence of M-CSF and RANKL to induce osteoclast differentiation. Total RNA was collected after 3 days of differentiation, corresponding to an early stage of osteoclastogenesis. Poly(A)-selected RNA libraries were prepared using the xGen RNA Library Prep Kit (Integrated DNA Technologies) and sequenced on an Illumina NextSeq platform using paired-end 2 × 45 bp reads. Two biological replicates were analyzed for each genotype.

first: Fuhua

last: Wang

first: Yizhong Jenny

first: Yu

last: Jin

first: Yuchen

last: Liu

first: Yingzi


title: Menopause transition timing reflects systemic biological aging

city: Reus

first: Dorota

last: Komar

address: avenida univeritat 1

country: Spain

institute: center for omic sciences, Eurecat

type: Methylation profiling by genome tiling array

summary: Natural menopause marks the end of female reproductive capacity, yet its relationship with biological aging remains unclear. Earlier menopause has been associated with reduced lifespan and increased disease risk, but whether menopause itself accelerates aging or reflects an underlying faster biological aging trajectory remains unresolved. Here, we combined animal models of menopausal transition with epigenetic analyses in postmenopausal women, to investigate this relationship. In rats, neither surgically induced menopause nor natural reproductive senescence resulted in increased epigenetic age acceleration. In women, accelerated epigenetic aging was observed only in individuals who reached postmenopause earlier than the cohort median, independent of metabolic health status. Differential methylation analysis suggested an association between age at menopause and pathways involved in longevity, chromatin regulation, and neurodegeneration. Together, these findings support a model in which the timing of reproductive aging reflects systemic biological aging rather than directly driving it, positioning age at menopause as a potential biomarker of the rate of biological aging

overall_design: we aimed to calculate epigenetic age using EPICv2 DNA methylation microarray in postmenopausal women and compare epigenetic age acceleration/pace of aging depending on the metabolic group: healthy, hepatic, lipid, cardiovascular; and separately depending on the age at menopause


title: Expression data from Arabidopsis, with methyl jasmonate (MeJA) and far-red light treatment.

city: Chiayi City

first: Meng-Chun

last: Lin

address: No.300 Syuefu Rd.

department: Department of Agronomy

country: Taiwan

institute: National Chiayi University

summary: Arabidopsis seedlings treated with or without far-red light in the presence or absence of MeJA.

overall_design: our-day-old Ler and hy5-1 mutant seedlings grown on GM plates with or without 50 micro molar of MeJA under cFR light (1.5 umol m-2 s-1)treatment for total RNA extraction. Isolated total RNAs were checked for quality and used for library analysis. The library was used for Affymetrix ATH1 genome array analysis. The raw data was normalized using the GeneSpring GX software.

first: Hsu-Liang

last: Hsieh


title: Mast cell St8sia1-GD3 axis as a glyco-epigenetic checkpoint driving maladaptive cardiac remodeling [RNA-seq]

city: shanghai

first: Lisheng

last: Fu

address: No. 650, Xin Songjiang Road, Songjiang District, Shanghai

institute: shanghaijiaotong

summary: Pathogenical immune-cardiac crosstalk underlies maladaptive remodeling in chronic heart failure, yet therapies directly targeting this axis are lacking. Glycoconjugates, which are crucial for signal transduction and extracellular matrix integrity, represent an underexploited therapeutic avenue. This study sought to define the role of glycoconjugate-metabolizing enzymes at the immune-cardiac interface and evaluate their translational potential. We performed integrative analyses of bulk and single-cell RNA sequencing data from failing human and mouse hearts. Employing mouse models of pressure overload (transverse aortic constriction, TAC) and ischemia-reperfusion (IR), we utilized global and mast cell (MC)-specific gene deletion, bone-marrow chimeras, and pharmacologic neutralization. Mechanistic insights were gained through multi-omics profiling, including RNA-seq, ATAC-seq, and CUT&Tag.

overall_design: This study includes three independent transcriptomic/epigenomic profiling components: (1) RNA-seq of primary neonatal rat cardiomyocytes (NRCMs) and cardiac fibroblasts (CFs) co‑cultured with WT or St8sia1-KO bone marrow-derived mast cells (BMMCs) to assess the paracrine effects of mast cells on cardiac parenchymal cells (3 biological replicates per condition); (2) ATAC-seq of WT and St8sia1-KO BMMCs to assess global chromatin accessibility changes (2 biological replicates per genotype); and (3) CUT&Tag for H2A.Z histone variant in WT and St8sia1-KO BMMCs to map H2A.Z occupancy changes (2 biological replicates per genotype, plus IgG control). All mouse samples were from male C57BL/6J mice.

first: Changzuan

last: Zhou

first: Tianyou

last: Yuan

first: Fangfang

last: Li

first: Fanhuan

last: Tang

first: Songwen

last: Chen

first: Jun


title: Gene expression profile at the single cell level of mammary cells

city: Chicago

first: Mariana

last: Bustamante Eduardo

state: IL

address: 303 E. Superior St. Lurie 4-220

department: Department of Surgery

institute: Northwestern University

summary: Migratory breast epithelial cells exposed to vehicle or octanoic acid were collected after 48 hours and analyzed by single-cell RNA sequencing to identify and characterize condition-specific migratory populations.

overall_design: Primary breast cells from premenopausal donors were cultured under selective conditions to enrich for cells that migrate in response to octanoic acid (OA). Breast microstructures were plated in Corning Primaria plates and exposed to either vehicle media or OA-containing media (5 mM). Cells were allowed to migrate from the microstructures onto the culture dish surface over 48 hours. Migrated cells were then resuspended at a concentration of 3,400 viable cells/μL in Cell Suspension Buffer and processed for library preparation using the Illumina Single Cell 3′ RNA Prep, T10 kit and subsequently sequenced on the Illumina NovaSeq X Plus platform.

first: Brian

last: Wray

first: Susan

last: Clare


title: Androgens mediate sexual dimorphism in Pilarowski-Bjornsson Syndrome

city: Reykjavik

first: Kimberley

last: Anderson

address: Sturlugata 8

country: Iceland

institute: University of Iceland

summary: Sex-specific penetrance in autosomal dominant Mendelian conditions is largely understudied. The neurodevelopmental disorder Pilarowski-Bjornsson syndrome (PILBOS) was initially described in females. Here, we describe the clinical and genetic characteristics of the largest PILBOS cohort to date, showing that both sexes can exhibit PILBOS features, although males are overrepresented. A mouse model carrying a human-derived Chd1 missense variant (Chd1R616Q/+) displays female-restricted phenotypes, including growth deficiency, anxiety and hypotonia. Orchiectomy unmasks a growth deficiency phenotype in male Chd1R616Q/+ mice, while testosterone rescues the phenotype in females, implicating androgens in phenotype modulation. In the gnomAD and UK Biobank databases, rare missense variants in CHD1 are overrepresented in males, supporting a male protective effect. We identify 33 additional highly constrained autosomal genes with missense variant overrepresentation in males. Our results support androgen-regulated sexual dimorphism in PILBOS and open novel avenues to understand the mechanistic basis of sexual dimorphism in other autosomal Mendelian disorders.

overall_design: RNA-seq: E18.5 murine cortical NPCs were transduced with pLenti-CRISPR-v2-contol or  pLenti-CRISPR-v2-CHD1 gRNA. After 48h of puromycin selection, cells were expanded then treated with either 10nM DHT, 10nM DHT+ 10µM Enzalutamide, or DMSO vehicle control for 24h.

first: Hans

middle: T

last: Björnsson


title: RNA-Independent Cis-Autoregulatory Circuits within Bidirectional Gene Pairs Control Metabolism

first: Xiang-Yu

address: 3 Blackfan St

institute: Harvard University

summary: Many genes share promoters with another gene on the opposite DNA strand, forming bidirectional pairs. During metabolic transitions, most pairs are coordinately regulated in liver, in part through chromatin topology. In pairs composed of a long non-coding RNA (lncRNA) and a protein-coding gene (PCG), lncRNA transcription cis-activates PCG transcription by establishing an active chromatin environment at the promoter-proximal enhancer of PCG. Reciprocally, PCG transcription cis-inhibits lncRNA transcription, forming internal cis-autoregulatory circuits. Interestingly, both directions of regulation are independent of the RNA products, but dependent on the transcription process itself. Similar promoter-proximal enhancer signatures and cis-autoregulatory circuits are present in many lncRNA/PCG and PCG/PCG pairs, underscoring the generalizability of these circuits. Using the conserved lncRNA/PCG pair Gm15663/Tmtc2 as a model, we show that blocking lncRNA transcription in liver in vivo disrupts this coordinated regulation, decreasing Tmtc2 expression and inducing hepatic steatosis. These data demonstrate the physiological importance of transcription-dependent cis-autoregulatory circuits in metabolic homeostasis and their potential for dysregulation in disease.

overall_design: RNA-seq profiling of Gm15663 overexpression. RNA-seq profiling of Tmtc2 knockdown.

last: Kahn


title: Distinct transcriptional programs define cranial motor neuron subtypes during vertebrate development

city: Seattle

first: Austin

last: Seroka

state: WA

address: 1100 Fairview Ave. North

department: Basic Sciences

institute: Fred Hutchinson Cancer Center

summary: Closely related neurons that share core differentiation programs can be difficult to distinguish by gene expression, even when they differ in connectivity and function. Cranial motor neurons (cMNs) exemplify this challenge, forming discrete nuclei that control behaviors as diverse as eye movement, feeding, facial expression, and regulation of visceral organ function. However, the developmental programs that drive cMN target choices and functional specialization have not been comprehensively studied in any vertebrate. Here, we present an integrated single-cell RNA-sequencing atlas of zebrafish cMN development from 18 to 144 hours post-fertilization, combining FACS-purified cMNs with cMNs computationally extracted from published whole-embryo datasets and perform extensive validation by HCR in situ hybridization.

overall_design: This dataset contains single-cell RNA sequencing data of zebrafish embryos at four developmental timepoints. Hindbrains were dissected manually, and isl1:kaede+ cranial motor neurons were isolated by FACS purification. The goal is to create a developmental atlas of cranial motor neuron developmental gene expression programs.

first: Adam

last: Isabella

first: Cecilia

last: Moens


title: Hypoxic preconditioning attenuates renal ischemia–reperfusion injury by suppressing the IL-17A/IL-17RA/TRAF6 inflammatory axis

city: Xining

first: Drolma

last: Gomchok

address: No. 16 Kunlun Road

institute: Qinghai university

summary: To explore the molecular mechanisms responsible for the renoprotective effect of Hypoxic preconditioning, we performed proteomic profiling of kidney tissues

overall_design: To explore the molecular mechanisms responsible for the renoprotective effect of HPC, we performed integrated transcriptomic and proteomic profiling of kidney tissues from NS, NR, HS and HR groups at one timsepoint.NS: normoxic sham (no RIRI, no HPC); NR: normoxic RIRI (RIRI without HPC); HS: HPC sham (HPC alone without RIRI); HR: HPC‑pretreated RIRI (HPC followed by RIRI). RIRI was induced by transabdominal clamping of bilateral renal pedicles for 45 min, followed by 12 h of reperfusion, after which the kidneys were harvested.HPC was performed in a normobaric hypoxic chamber with 8% O₂ (reduced from room air over 20 min) for 2 h on day 1, 4 h on day 2, and 8 h on day 3. Three mice were included in each group (n = 3 per group).

first: Tana

last: Wuren

first: Pengli

last: Luo


title: RNA-seq profiling of FBXO8 knockdown in HONE-1 nasopharyngeal carcinoma cells

city: guangzhou

first: ran

last: ding

state: guangdong

address: School of Biomedical Sciences and Engineering, South China University of Technology, Guangzhou International Campus, Guangzhou 511442, China.

institute: South china university of technology

summary: This dataset contains bulk RNA-seq profiles of HONE-1 nasopharyngeal carcinoma cells transfected with negative control siRNA or siRNA targeting FBXO8. Three biological replicates were included in each group. Total RNA was extracted for paired-end RNA sequencing to investigate transcriptional changes associated with FBXO8 knockdown in nasopharyngeal carcinoma cells.

overall_design: HONE-1 cells were divided into two groups: negative control siRNA (NC1, NC2, NC3) and FBXO8 knockdown by siRNA (si1_1, si1_2, si1_3). RNA-seq libraries were constructed from total RNA and sequenced using a paired-end strategy.

first: Ding

last: Ran

first: Long

last: Zhiqing


title: Cellular senescence dysregulates antiviral interferon responses in idiopathic pulmonary fibrosis

city: Novato

first: Jun-Wei

middle: Brendan

last: Hughes

state: CA

address: 8001 Redwood Blvd

institute: Buck Institute for Research on Aging

summary: Patients with idiopathic pulmonary fibrosis (IPF) are highly vulnerable to respiratory virus infections, but the cellular mechanisms linking fibrotic remodeling to impaired local antiviral defense remain unclear. Here, we investigated how cellular senescence shapes the response of patient-derived healthy and IPF primary lung fibroblasts to influenza A virus (IAV) infection. Transcriptomic profiling identified infection as the driver of gene expression in both DNA damage-induced senescent healthy and IPF fibroblasts and revealed induction of canonical antiviral pathways in both cell states. However, senescent IPF fibroblasts adopted a distinct antiviral response state characterized by a broader set of uniquely induced genes and differential coordination of antiviral transcriptional networks. Functionally, senescence increased viral titers in healthy and IPF fibroblasts, while senescent IPF fibroblasts displayed an altered inflammatory response. Network analysis linked viral response- and cell cycle-associated modules specifically to the senescent healthy infected state, whereas these programs were weaker in senescent IPF fibroblasts. Transcription factor inference identified IRF3 and STAT1 as candidate regulators of this altered antiviral state in both senescent healthy and IPF fibroblasts. Consistent with the network and transcription factor analyses, siRNA-mediated depletion of IRF3 or STAT1 significantly reduced IFN-β secretion in senescent healthy fibroblasts, whereas IPF fibroblasts showed only milder effects, indicating a disease-specific dependence on these pathways for antiviral control. Together, these findings show that the combination of cellular senescence and fibrotic fibroblast identity creates a dysfunctional antiviral state that may help explain the high susceptibility of IPF patients to virus-associated acute exacerbations and disease worsening.

overall_design: RNA-seq profiling of primary, human lung fibroblasts 10 days after senescence induction with influenza infection for 24 hours

first: Yasmina

last: Reisser

first: Franziska

last: Hornung

first: Pierre-Yves

last: Desprez

first: Stefanie

last: Deinhardt-Emmer


title: Insights into the impact of archaeal proteasome activity on cell division: CCTF1 plays a decisive role in regulating cellular proteasome activity [aCcrK OE]

city: Qingdao

first: yunfeng

last: yang

address: State Key Laboratory of Microbial Technology, Shandong University, No. 72 Binhai Road, Qingdao 266237, P.R. China

institute: shandong university

summary: The cell cycle is a precisely coordinated series of events of cell growth, DNA replication and cell division, all of which are imperative for the proliferation of organisms. Archaea of the order Sulfolobales exhibit a cell cycle similar to that of eukaryotes. It has been suggested that the proteasome degradation of the cell division protein CdvB controls the progression of cell division. This raises a question regarding the regulation of proteosome activity in these archaea. In this paper, we report that an ArsR family cyclically-transcribed cell cycle transcription factor, CCTF1 (cell cycle transcription factor 1), plays a decisive role in regulation of the proteasome activity. We revealed that transcription of the proteasome regulatory subunit PAN (proteasome-activating nucleotidase) is specifically regulated by CCTF1 through binding to an AT-rich palindromic sequence. We show that CCTF1, rather than aCcrK (ePK2), is the key factor controlling the proteasome activity. Our study provides important insights into the proteosome-mediated cell cycle regulation mechanism in archaea.

overall_design: The control group consists of empty plasmid strains, while the experimental group comprises strains overexpressing aCcrK, induced by arabinose.

first: Yunfeng

last: Yang

first: Zixin

last: Geng

first: Shikuan

last: Liang

first: Haodun

last: Li

first: Fan

last: Zhou

first: Junfeng

last: Liu

first: Mart

last: Krupovic

first: Yulong

last: Shen


title: Insights into the impact of archaeal proteasome activity on cell division: CCTF1 plays a decisive role in regulating cellular proteasome activity [CCTF1 OE]

overall_design: The control group consists of empty plasmid strains, while the experimental group comprises strains overexpressing transcription factors CCTF1, induced by arabinose.


title: Murine Bone Marrow Single Cell Sequencing of RM1 Intrafemoral Inoculation

city: WINSTON SALEM

first: Yang

last: Yu

state: NC

address: 1 Medical Center Blvd

department: Cancer Biology

institute: Wake Forest University

summary: We have employed a single cell sequencing approach using 10x Genomics scRNAseq to study murine bone marrow contribution to cancer-induced bone pain. bone marrow are the mediator of sensory neurons and pain signaling. These findings establish a  tumor-bearing reference dataset.

overall_design: Mice were intrafemorally inoculated with RM1, and after 15 days post-inoculation bone marrow cells from ipsilateral femurs were collected. Cells were then subjected to enzymatic digestion and density centrifugation to form a single cell suspension. The cells were then processed on a 10X Genomics Chromium controller to generate a cDNA library, which was sequenced on an Illumina NextSeq 500.

first: Yusuke

last: Shiozawa

first: Lance

last: Miller


title: Murine Bone Marrow Single Cell Sequencing of Sham Intrafemoral Inoculation

summary: We have employed a single cell sequencing approach using 10x Genomics scRNAseq to study murine bone marrow contribution to cancer-induced bone pain. bone marrow are the mediator of sensory neurons and pain signaling. These findings establish a  non-tumor-bearing reference dataset.

overall_design: Mice were intrafemorally inoculated with saline, and after 15 days post-inoculation bone marrow cells from ipsilateral femurs were collected. Cells were then subjected to enzymatic digestion and density centrifugation to form a single cell suspension. The cells were then processed on a 10X Genomics Chromium controller to generate a cDNA library, which was sequenced on an Illumina NextSeq 500.