title: Cytoplasmic competition between separate parental pronuclei in zygotes

summary: Embryogenesis begins with a zygote, a single cell with two pronuclei that separately enclose maternal and paternal chromosomes. The functional significance of the separation of parental chromosomes into distinct pronuclei remains unexplored, despite the fact that one-pronuclear biparental zygotes are used clinically. Here, using a combination of mouse zygote manipulation, quantitative imaging and theoretical approaches, we show a cytoplasm-mediated competition mechanism between separate parental pronuclei. This mechanism limits pronuclear volume and prevents the loss of epigenetic marks, including maternally inherited trimethylated histones. One-pronuclear biparental zygotes lack this mechanism, resulting in a reduced rate of development to term. This low developmental potential can be rescued by competition-based or drug-based restoration of epigenetic marks. In human zygotes, epigenetic loss correlates with pronuclear volume. This study provides insight into strategies to improve the clinical use of one-pronuclear biparental zygotes.

overall_design: Single two-cell embryos derived from 1PN, 2PN and parthenote were analyzed by RNA-seq.

first: Akihito

last: Harada

first: Yasuyuki

last: Ohkawa


title: MafB is a conserved transcriptional regulator of macrophage development and identity across tissues and species [RNA-seq]

status: Public on Feb 25 2026

city: Liège

first: Thomas

last: Marichal

address: Avenue de l'Hopital 11

department: GIGA Institute

country: Belgium

institute: University of Liege

type: Expression profiling by high throughput sequencing

summary: Resident tissue macrophages (RTM) are characterized by a remarkable diversity but also share common features that are thought to be driven by conserved transcriptional programs. While the transcription factor MafB is highly expressed in the macrophage lineage, little is known about its role in establishing RTM identities. Here, we show that the absence of MafB results in a profound imbalance across many RTM populations and in a disruption of global and tissue-specific RTM signatures in mice. Furthermore, we found that MafB was required for the differentiation of bone-marrow-derived macrophages (BMDMs) ex vivo and of RTM populations from monocytes in vivo. Mechanistically, epigenetic profiling of MafB binding sites in BMDMs revealed that MafB directly regulated expression of key RTM differentiation and identity genes, including Csf1r and Fcgr1. Finally, in silico analyses showed that MafB binding sites were highly conserved across vertebrates. Our findings demonstrate the crucial and evolutionarily conserved role of MafB as regulator of RTM development and identity, connecting MafB-dependent transcriptional programs with unique defining features of RTM.

overall_design: We sought to identify transcriptional programs affected by MafB deficiency and performed bulk RNA-seq on BMDM from Lyz2CreMafbfl/fl and Mafbfl/fl littermate control mice.

first: Domien

last: Vanneste

first: Joan

last: Abinet


title: Selective targeting of a histone-like silencer Sfx to the R6K conjugal transfer operon [ChIP-Seq]

status: Public on Feb 24 2026

city: Columbus

first: Irina

last: Artsimovitch

state: Ohio

address: 318 W 12th Ave

department: Microbiology

country: USA

institute: The Ohio State University

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Conjugative plasmids drive bacterial evolution and the spread of antibiotic resistance, yet their gene expression must be silenced to protect the host. A histone-like protein H-NS represses many mobile and sedentary xenogenes but fails to silence the conjugal transfer vir operon of R6K, a prototype IncX plasmid. Instead, R6K encodes its own H-NS homolog, Sfx, to repress the vir operon. Here, we show that, unlike other plasmid silencers that target promoters, Sfx cooperates with Rho factor to arrest transcription elongation. ChIP-seq reveals that despite sharing similar DNA motifs and a preference for negative supercoiling, Sfx and H-NS occupy distinct niches: Sfx binds weakly to the chromosome but is enriched on the R6K vir operon while H-NS is excluded. We hypothesize that this selective targeting is mediated by Sfx-vir DNA interactions and phase separation. We show that Sfx binding to vir DNA critically depends on DNA topology but not on the target location. Our results suggest that Sfx forms stable nucleoprotein filaments that are impermeable to competitors and phase separates with R6K DNA to exclude H-NS. Our results suggest how functionally distinct histone-like proteins may achieve target specificity despite broad recognition motifs.

overall_design:
ChIP-seq assays for comparing the binding sites of H-NS and its homolog Sfx encoded on R6K plasmid in Escherichia coli. The sequences of all plasmids used in this study can be found in the accompanying manuscript.
ChIP-seq of RNA polymerase in E. coli carrying the Sfx deletion R6K plasmid to identify potential promoters in R6K.
RNA ChIP-seq assay to identify RNAs ChIPed by FLAG-tagged Sfx.

first: Bing

last: Wang


title: MafB is a conserved transcriptional regulator of macrophage development and identity across tissues and species

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

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Refer to individual Series


title: Inflammation-enhanced synapse-specific phagocytosis by adult APP microglia in a microfluidic neuron–microglia co-culture model

city: LILLE

first: Florence

last: MAURIER

address: 1 rue du Professeur Calmette BP 245

department: Plateformes Lilloises en Biologie & Santé

country: France

institute: Institut Pasteur de Lille

summary: Microglia play a critical role in synapse remodeling and neuroinflammation, both of which are dysregulated in Alzheimer’s disease (AD). However, most in vitro models rely on neonatal or immortalized microglia, limiting their relevance to adult pathophysiological context. Here, we present a compartmentalized microfluidic co-culture platform that enables spatially controlled interactions between primary cortical neurons and adult microglia from wild-type (WT) and APP-transgenic mice. This system allows precise functional analysis of microglia–synapse interactions under defined inflammatory conditions. Upon lipopolysaccharide (LPS) stimulation, APP microglia exhibited exaggerated morphological activation, elevated IL-1β secretion, and selectively increased engulfment of synaptic material. In contrast, phagocytosis of non-specific substrates such as pHrodo™ Zymosan remained unchanged, suggesting a substrate-specific enhancement of microglial phagocytic activity. Blocking the complement receptor CD11b abolished the LPS-induced increase in synaptic uptake, confirming the role of complement-dependent pathways. Transcriptomic profiling revealed robust inflammatory responses in both genotypes, with selectively heightened expression of proinflammatory genes in APP microglia, consistent with a primed immune phenotype. Importantly, increased synaptic uptake occurred without measurable loss of global synaptic connectivity, highlighting the specificity and sensitivity of the system to detect microglial functional changes. This model captures genotype-dependent microglial reactivity (revealing phenotypes not fully captured by transcriptomic rofiling) and provides a physiologically relevant, tractable in vitro platform for dissecting microglial contributions to synaptic pathology in neurodegenerative disease.

overall_design: Adult cortical microglia were isolated from 10–11-month-old wild-type and APP-transgenic mice, maintained in vitro for four weeks, and treated with vehicle or lipopolysaccharide (100 ng/mL, 6 h). After a 16 h recovery, total RNA was extracted, libraries prepared using Lexogen QuantSeq 3′ mRNA-Seq FWD (with UMIs and ERCC spike-ins), and sequenced on an Illumina NovaSeq 6000 (single-end 100 bp). Nineteen samples were collected across four conditions: WT+Vehicle (n=4), WT+LPS (n=5), APP+Vehicle (n=5), APP+LPS (n=5).

first: Dolores

last: Siedlecki-Wullich

first: Devrim

last: Kilinc

first: Jean-Charles

last: Lambert

first: Lukas

last: Iohan

first: Delphine

last: Beury

first: Myriam

last: Delacre

first: David

last: Hot


title: MafB is a conserved transcriptional regulator of macrophage development and identity across tissues and species [scRNA-Seq]

overall_design: We sought to investigate whether MafB deficiency could alter the transcriptional identity of RTM. Live peritoneal lavage CD45+Lin−Ly6C−CD11b+CD115+ cells, liver CD45+Lin−Ly6C−CD11bint/+F4/80+CD64+ cells, colon CD45+Lin−CD11b+F4/80+CD64+ cells and brain CD45+Lin−Ly6C−CD11b+F4/80+CD64+ cells were FACS-sorted from Lyz2CreMafbfl/fl and Mafbfl/fl littermate controls, were hashtag-barcoded and subjected to scRNA-seq.


title: MafB is a conserved transcriptional regulator of macrophage development and identity across tissues and species [CUT&Run]

overall_design: To identify MafB binding sites we performed CUT&RUN for MafB on wild-type BMDM.


title: Single cell and Spatial RNA-seq in Oral Squamous Cell Carcinoma with Different Stage

status: Public on Feb 26 2026

city: Luzhou

first: Fengtian

last: Li

address: Zhongshan Road

country: China

institute: Southwest Medical University

summary: To investigate the dynamic changes in the tumor microenvironment during the progression of oral squamous cell carcinoma (OSCC), we collected 16 treatment-naïve OSCC samples for single-cell RNA sequencing (scRNA-seq). Among these, 6 cases were additionally subjected to spatial transcriptomic profiling to capture the tissue architecture and spatial organization of the tumor microenvironment.

overall_design: 16 oral squamous cell carcinoma (OSCC) samples from 16 individuals with different stage were used to single cell RNA-seq by Mobinova-100 system. 6 samples from the 16 samples were also used to perform 10X visium spatial RNA-seq.

first: Hu

last: Chen


title: Impact of vitamin D deficiency on defective endometrial decidualization and the repressive role of VDR in the epigenomic network

city: Durham

first: MyeongJin

last: Yi

state: NC

address: 111 TW Alexander Dr

institute: NIEHS

summary: The identification of the factors regulating female reproduction is critical to understanding how the environment and nutrition impact female fertility and reproductive health. Vitamin D and its cognate receptor, VDR, are recognized for their role in calcium homeostasis; however, their broader impact on female reproduction remains underexplored. Here, we demonstrate that vitamin D and VDR are involved in the hormonal induction of uterine stromal cell differentiation, known as decidualization. Mice fed a vitamin D-deficient diet displayed an impaired hormonally induced decidual response. In a human endometrial stromal cell line, T-HESC, VDR decreases during decidualization. siRNA knockdown of VDR in T-HESC enhanced decidualization, while overexpression of VDR inhibited decidualization. Chromatin accessibility and histone modification analyses revealed that VDR functions as a chromatin regulator, restricting accessibility and maintaining transcriptional repression in specific genomic regions. Transcriptomic analyses confirmed that VDR broadly modulates gene expression, with most ligand-mediated effects dependent on its presence. These findings identify VDR as a key regulator of transcriptional and chromatin landscapes in endometrial stromal cells, offering novel insights into vitamin D signaling in reproduction. This study highlights the potential of targeting vitamin D pathways to treat uterine disorders associated with impaired decidualization.

overall_design: Experimental Design: There are 2 groups, and 6 samples in total. All ATACseq libraries were prepared from the human endometrial stromal cell line (T-HESC). 1) Non-targeting siRNA transfection (control) n=3 2) VDR siRNA transfection (VDR knockdown) n=3  Data Analysis Strategy: Dr. Tianyuan Wang and Dr. Austin Bell-Hensley from the informatics group supported Dr. MyeongJin Yi with the analysis. 1) Remove adaptor 2) QC with trim-galore 3) Map the pair-end reads 4) Count reads mapped to chrM 5) Remove duplicated reads 6) Remove unmapped reads 7) Remove reads mapped to chrM 8) Prepare SAM file based on trimmed 9bp reads 9) Random sampling to the same depth 10) Compare between different groups (siNT vs siVDR)

first: Tianyuan

first: Austin

last: Bell-Hensley

first: Francesco

last: DeMayo


title: Impact of vitamin D deficiency on defective endometrial decidualization and the repressive role of VDR in the epigenomic network [CUT&Run]

overall_design:
Experimental Design: 2 Different Experiments
Experiment 1. Identification of cistromic changes in human endometrial stromal cells by the receptor (VDR) and the ligand (1,25(OH)2D3).
There are 8 groups, and 24 samples in total. All libraries were prepared from the human endometrial stromal cell line (T-HESC).
1) Control lentiviral GFP vector transduced T-HESCs treated with vehicle and precipitated with VDR antibody, n=3
2) Control lentiviral GFP vector transduced T-HESCs treated with vehicle and precipitated with IgG, n=3
3) Control lentiviral GFP vector transduced T-HESCs treated with 1,25(OH)2D3 and precipitated with VDR antibody, n=3
4) Lentiviral VDR plasmid transduced T-HESCs treated with 1,25(OH)2D3 and precipitated with IgG, n=3
5) Lentiviral VDR plasmid transduced T-HESCs treated with vehicle and precipitated with VDR antibody, n=3
6) Lentiviral VDR plasmid transduced T-HESCs treated with vehicle and precipitated with IgG, n=3
7) Lentiviral VDR plasmid transduced T-HESCs treated with 1,25(OH)2D3 and precipitated with VDR antibody, n=3
8) Lentiviral VDR plasmid transduced T-HESCs treated with 1,25(OH)2D3 and precipitated with IgG, n=3
Experiment 2.  Impact of VDR and 1,25(OH)2D3 on histone modifications
There are 8 groups, and 24 samples in total. All libraries were prepared from the human endometrial stromal cell line (T-HESC).
1) Non-targeting pooled siRNA-transfected T-HESCs and precipitated with H3K4me3, n=3
2) Non-targeting pooled siRNA-transfected T-HESCs and precipitated with H3K27me3, n=3
3) Non-targeting pooled siRNA-transfected T-HESCs and precipitated with H3K27ac, n=3
4) Non-targeting pooled siRNA-transfected T-HESCs and precipitated with IgG, n=3
5) VDR siRNA-transfected T-HESCs and precipitated with H3K4me3, n=3
6) VDR siRNA-transfected T-HESCs and precipitated with H3K27me3, n=3
7) VDR siRNA-transfected T-HESCs and precipitated with H3K27ac, n=3
8) VDR siRNA-transfected T-HESCs and precipitated with IgG, n=3
Data Analysis Strategy: Dr. Austin Bell-Hensley, Dr. Tianyuan Wang, and Dr. Abdull Massri from the informatics group supported Dr. MyeongJin Yi with the analysis.
1) Remove adaptor 2) QC with trim-galore 3) Map the pair-end reads 4) Count reads mapped to chrM 5) Remove duplicated reads 6) Remove unmapped reads 7) Remove reads mapped to chrM 8) Prepare SAM file based on trimmed 9bp reads 9) Random sampling to the same depth 10) Compare between different groups

first: Skylar

last: Montague Redecke

first: Abdull

last: Massri


title: A viral transcriptional regulator from a dsRNA virus antagonizes the innate immune response by manipulating the host co-transcription factor DHX9

city: Tianjin

first: Xueyang

last: Pang

state: Tianjin

address: 22 Meteorological Observatory Road, Heping District, Tianjin

institute: TMU

summary: Viral transcriptional regulators (vTRs) have emerged as potent factors that shape the host anti-viral gene expression programs. Delineating the molecular mechanisms by which vTRs inhibit or promote transcription would provide fundamental insights for developing anti-viral strategies. Using Mammalian orthoreovirus (REOV) as a model system, we identified a new viral mechanism by which viruses antagonize the host innate immune response. We found that the REOV outer capsid protein σ3 functions as a vTR to suppress NF-κB gene expression via its direct interaction with the host helicase DHX9. Mechanistically, σ3 impairs the initial recruitment of Pol II by disrupting the interaction between DHX9 and Pol II. More interestingly, σ3 suppresses DHX9 helicase activity, resulting in the aberrant accumulation of R-loops at promoter-proximal regions, thereby affecting Pol II pause-release and ultimately suppressing NF-κB gene expression. Together, our findings reveal an unprecedented strategy employed by a viral protein that regulates anti-viral gene expression by directly modulating the host transcription factor DHX9.

overall_design: R-Loop occupancy on chromatin upon TNFa, IFNβ or REOV treatment in 293T cells were assessed by Cut&Tag assay.

first: Shiyu

last: Liu

first: Yixiao

last: Zhu

first: Meleana

last: Hinchman

last: Qiao

first: Xuejun

first: Weiqian

last: Dai

first: Yingying

last: Tong

first: Man

last: Xing

first: Jiling

last: Ren

first: John

last: Parker

last: Guo

first: Dongming

last: Zhou


title: Selective targeting of a histone-like silencer Sfx to the R6K conjugal transfer operon [RNA-Seq]

first: Irina

last: Artsimovitch

summary: Conjugative DNA transfer is mediated by large membrane-spanning type IV secretion system (T4SS) complexes encoded by long plasmid operons (commonly called tra or vir). Conjugative IncX plasmids encode histone-like protein H-NS homolog as core gene. R6K, a prototype IncX plasmid, encodes its own H-NS homolog, Sfx, to repress the vir operon. Here, we show that, unlike other plasmid silencers that target promoters, Sfx cooperates with Rho factor to arrest transcription elongation. Our results show that Sfx mainly targets the R6K vir operon.

overall_design: RNA-seq profiling of E. coli harboring plasmid R6K derivatives to detect the targets of histone-like silencer Sfx.

first: Bing

last: Wang


title: A viral transcriptional regulator from a dsRNA virus antagonizes the innate immune response by manipulating the host co-transcription factor DHX9 [RNA-Seq]

summary: Viral transcriptional regulators (vTRs) have emerged as potent factors that shape the host anti-viral gene expression programs. Delineating the molecular mechanisms by which vTRs inhibit or promote transcription would provide fundamental insights for developing anti-viral strategies. Using Mammalian orthoreovirus (REOV) as a model system, we identified a new viral mechanism by which viruses antagonize the host innate immune response. We found that the REOV outer capsid protein σ3 functions as a vTR that limits RNA polymerase II (Pol II) recruitment to the promoter regions of NF-κB-dependent genes via its direct interaction with the host helicase DHX9. σ3 competes with DHX9 for its interaction with Pol II, which led to marked attenuation of Pol II loading onto chromatin. More interestingly, σ3 also suppresses DHX9 helicase activity, leading to aberrant accumulation of R-loops at promoter-proximal regions and a decrease in NF-κB-dependent gene expression. Together, our findings uncover an unprecedented strategy of a viral protein that regulates anti-viral gene expression by directly manipulating host transcription factor DHX9.

overall_design: Plasmids expressing σ3 were transfected into HEK293 cells using PEI. At 48 h post-transfection, cells were treated with 10 ng/ml TNF-α for 3 h. Total RNA was extracted with TriZOL for library construction and subsequent sequencing.

last: Li


title: CATCH-seq analysis of 1PN and 2PN zygotes.

city: Kobe

first: Hirohisa

last: Kyogoku

state: Hyogo

address: 1-1, Rokkodai-chou

department: Agricultural Science

country: Japan

institute: Kobe university

summary: Embryogenesis begins with a zygote, a single cell with two pronuclei that separately enclose maternal and paternal chromosomes. The functional significance of the separation of parental chromosomes into distinct pronuclei remains unexplored, despite the fact that one-pronuclear biparental zygotes are used clinically. Here, using a combination of mouse zygote manipulation, quantitative imaging and theoretical approaches, we show a cytoplasm-mediated competition mechanism between separate parental pronuclei that ensures developmental potential. This mechanism limits pronuclear volume and prevents epigenetic mark dysregulation, including loss of maternal trimethylated histones. One-pronuclear biparental zygotes lack this mechanism, resulting in a reduced rate of development to term. This low developmental potential can be rescued by competition-based or drug-based restoration of epigenetic marks. This study provides a spatial mechanism linking fertilization to the establishment of the full developmental potential for the next generation, highlighting caveats in clinical use of one-pronuclear biparental zygotes.

overall_design: 1PN and 2PN zygotes were analyzed by CATCH-seq for H3K4me3 and H3K27me3.

first: Tappei

last: Mishina

first: Tomoya

middle: S

last: Kitajima

first: Masahiro

last: Matsuwaka

first: Mami

last: Kumon

first: Azusa

last: Inoue


title: Combination of single-cell and bulk RNA-seq reveals changes in the immune landscape in osteomyelitis

city: Changchun

first: zhenhua

last: zhu

address: Xinmin  Street 71#

institute: The First Hospital of Jilin University

summary: Objective: This study profiled the osteomyelitis immune micro-environment in depth, pinpointed driver genes and cell populations that fuel disease progression, and mined the data for actionable drug targets. Methods: We analyzed time-series transcriptomic sequencing data from mouse tibial osteomyelitis samples in dataset GSE168896. Fuzzy c-means clustering was applied to reveal gene sets linked to disease progression. Immune cell infiltration analysis was conducted through online tool ImmuCellAI-mouse. Furthermore, by leveraging single-cell sequencing data, we characterized immune cell subpopulations and pinpointed the key cell subtypes that exhibited in osteomyelitis mouse. Results: We identified six gene clusters exhibiting distinct temporal expression patterns and functional roles in osteomyelitis processes, such as leukocyte and lymphocyte activation, ossification. Single-cell sequencing analysis further revealed 7 distinct cellular subpopulations. Among these, M2-like macrophages demonstrated a significant increase following osteomyelitis. Arg+Sdc4+ Mac and Cxcl1+Ccl4+ Mac were new subpopulations of macrophages that emerged after osteomyelitis, the infiltration of Mif+Cd63+ Mac significantly increased. Besides, Cxcl2-Cxcr2 ligand-receptors contributed mostly in immune cells.

overall_design: Single cell RNA-seq profilling of bone marrow flox mouse, osteomylities flox mouse and Trim59-cKO mouse (flox_ctrl,flox_om,cko_om) two weeks after modeling.

first: Zhenhua

last: Zhu

first: Xiaopeng

last: Jing

first: Jun

last: Chen

first: Jie

last: Tan

first: Ji

last: Zeng

first: Zheng

last: Jin


title: Canonical transcription termination mechanisms explain a minority of operons in cyanobacteria

status: Public on Feb 23 2026

city: Cambridge

first: Jennifer

last: Cascino

state: MA

address: 31 Ames Street

department: Biology

institute: Massachusetts Institute of Technology

summary: Cyanobacteria are the most abundant phototrophs and hold potential as a carbon-negative platform for bioengineering applications. However, these efforts have been hampered by limited mechanistic understanding of their gene expression, including transcription termination. Unlike most bacteria, cyanobacteria lack the transcription termination factor Rho, raising the speculation that all transcription ends with intrinsic terminators. Here we show that most transcription units (TUs) in Synechococcus elongatus PCC 7942 are not terminated by known termination pathways. Although many TUs (52%) have unique, well-defined 3' ends, only a small fraction have features that resemble canonical intrinsic terminators (30%). The noncanonical 3' ends (22%) broadly lacked strong secondary structure, leaving it unclear how these ends are protected against 3'-5' exonucleolytic decay, but a dinucleotide motif was observed. Furthermore, many TUs (46%) have diverse positions of mRNA 3' ends, suggesting a potentially diffuse termination signal. Finally, we provide evidence that the transcription-repair coupling factor Mfd reduces transcriptional readthrough at the well-defined 3' ends, suggesting that Mfd-dependent termination may be prevalent in this species. Together, our work reveals unique end architectures of the cyanobacterial transcriptome and suggests that undescribed transcription termination mechanisms are active in the phylum.

sample_organism: Synechococcus elongatus PCC 7942 = FACHB-805

overall_design: Rend-seq mapping of transcription unit architectures including RNA 3' ends at single-nucleotide resolution in the wild-type (WT) freshwater cyanobacterium Synechococcus elongatus PCC 7942 and a mutant deleted for the transcription-repair coupling factor Mfd (Mfd_KO). Rend-seq libraries for two technical replicates of WT (cells collected from the same flask) and two biological replicates of Mfd_KO (separate flasks) were prepared.

first: K. Julia

last: Dierksheide

first: Gene-Wei


title: Cytoplasmic competition between separate parental pronuclei in zygotes.


title: Hypoxia Promotes an Adrenergic to Mesenchymal Transcriptional Program Transition in Neuroblastoma

city: Chicago

first: Mark

last: Applebaum

state: IL

address: 900 E 57th St

department: Pediatrics, Section of Hematology/Oncology

institute: University of Chicago

summary: Purpose: Neuroblastoma is the most common extracranial solid tumor in childhood. We previously showed that circulating cell-free DNA (cfDNA) and tumor biopsy derived 5-hydroxymethylcytosime (5-hmC) profiles identified patients with neuroblastoma who experienced subsequent relapse. Here, we hypothesized that 5-hmC modifications selectively enriched in cfDNA compared with tumor biopsy samples would identify epigenetic changes associated with aggressive tumor behavior and identify novel biomarkers of outcome in patients with high- risk neuroblastoma.  Methods: 5-hmC profiles from cfDNA (n = 64) and tumor biopsies (n = 48) were compared. Two neuroblastoma cell lines underwent chromatin immunopre- cipitation followed by sequencing (ChIP-Seq) for H3K27me3, H3K4me3, and H3K27ac; kethoxal-associated single-stranded DNA sequencing; hmC-Seal for 5-hmC; and RNA-sequencing (RNA-Seq). Genes enriched for both H3K27me3 and H3K4me3 in the included cell lines were defined as bivalent. Using bivalent genes defined in vitro, a bivalent signature was established in three publicly available cohorts of patients with neuroblastoma through gene set variation analysis. Differences between tumors with high or low bivalent signatures were assessed by the Kaplan-Meier method and Cox proportional hazards models.  Results: In cfDNA compared with tumor biopsy derived 5-hmC profiles, we found in- creased 5-hmC deposition on Polycomb Repressive Complex 2 target genes, a finding previously described in the context of bivalent genes. We identified 313 genes that bore bivalent chromatin marks, were enriched for mediators of neuronal differentiation, and were transcriptionally repressed across a panel of heterogeneous neuroblastoma cell lines. In three distinct clinical cohorts, low bivalent signature was significantly and independently associated with worse clinical outcome in patients with high-risk neuroblastoma.  Conclusion: Low expression of bivalent genes is a biomarker of worse outcome in patients with high-risk neuroblastoma.

overall_design: RNA-Seq performed in 8 neuroblastoma cell lines that were incubated in hypoxic conditions for 48 hours.

first: Mohansrinivas

last: Chennakesavalu

first: Kelley

last: Moore

first: Gepoliano

last: Chaves

first: Sahil

last: Veeravalli

first: Rachel

last: TerHaar

first: Tong

last: Wu

first: Ruitu

last: Lyu

first: Alexandre

last: Chlenski

first: Chuan

last: He

first: Andrea

last: Piunti


title: HIF-1α+ CD4 T cells coordinate a tissue resident immune cell network in the lung [scRNA-seq]

city: Basel

first: Carolyn

last: King

address: Hebelstrasse 28

department: Department of Biomedicine

country: Switzerland

institute: University of Basel

summary: Pulmonary infection leads to the development of CD4+ T resident helper (TRH) cells in the lung. TRH cells generated after influenza infection support local humoral responses and exhibit differentiation plasticity following infectious challenge. A subset of TRH cells is enriched for expression of the transcription factor HIF-1α which has unknown function in the lung. Here we find that inducible deletion of HIF-1α in CD4 T cells leads to decreased numbers of CXCR6+ tissue resident T cells with minimal impact on peripheral lymphoid responses. At the same time, HIF-1α deletion impairs the replenishment of tissue resident macrophages and NK cells, as well as influenza specific IgA titers. These seemingly disparate responses converge upon a requirement for IL-21 produced by HIF-1α+ CD4 T cells. A similar HIF-1α dependent network is engaged in a lung adenocarcinoma model, highlighting novel roles for HIF-1α+ CD4 T cells in coordinating protective immunity during infection and cancer.

overall_design: Following influenza infection control (Hif1a wt/wt CD4 ert2 ki wt ROSA ki wt) and Hif1a KO mice (Hif1a fl/fl CD4 ert2 ki wt ROSA ki wt) were treated with tamoxifen to delete Hif1a in CD4 T cells.  Individual mice were hashtagged, and CD45+ cells were sorted from lungs at d45 p.i. and submitted for library preparation.


title: RIP-seq analysis of HUVEC cells overexpressed wild-type or mutanted DDX24

status: Public on Feb 20 2026

city: Zhuhai

first: Simeng

address: 52 Meihuadong Road, Xiangzhou

institute: Sun Yat-sen University

summary: To investigate the impact of DDX24 mutation on the RNA binding activity in HUVEC cells, we conducted RIP-seq analysis.

overall_design: For RIP-seq, RNA interacting with DDX24-WT or DDX24-ΔRBD was isolated following the RIP protocol. The immunoprecipitated RNA was then subjected to mRNA selection using Oligo dT-based Poly(A) mRNA Magnetic Isolation Module (NEB) and prepared for sequencing libraries using Ultra II Directional RNA Library Prep Kit for Illumina (NEB). Libraries were pooled and sequenced on an Illumina Hiseq 3000 PE150 platform.

first: Bin

last: Li


title: Extracellular vesicles and their RNA cargo facilitate bidirectional cross-kingdom communication between human and bacterial cells [smallRNA-Seq]

city: Saarbrücken

first: Shusruto

last: Rishik

state: Saarland

address: Informatik Campus E2.1

department: Zentrum für Bioinformatics

country: Germany

institute: Universität des Saarlandes

type: Non-coding RNA profiling by high throughput sequencing

summary: Extracellular vesicles (EVs), released by both eukaryotic and prokaryotic cells, have emerged as key mediators of cell-to-cell communication. Recent advances highlight their crucial role in cross-kingdom communication, bridging the microbial world with human biology. Here, we investigated the molecular mechanisms underlying EV-mediated bidirectional communication within the gastrointestinal ecosystem. Using a model that includes human colon cells and both Gram-positive and Gram-negative gut bacteria, we reveal an intricate exchange of information between these kingdoms. Our analysis uncovered highly specific responses of host cells to bacterial EVs (BEVs) and BEV-RNA cargo, including uptake rates by human cells, impact on human cell viability, and alterations in their transcriptomic landscape. In parallel, we discovered that host-derived EVs and miR-192-5p are internalized by gut bacteria, leading to changes in their growth pattern. These findings highlight the precision with which EVs and their RNA cargo mediate interkingdom communication. Our results underscore the importance of tailored, context-specific analyses for understanding the scope of EV-mediated interactions in complex biological systems.

overall_design: Sequencing of smallRNAs isolated from EVs purified from Caco-2 cell culture supernatant (conditioned medium) and fresh cell culture medium (unconditioned medium). EVs were isolated via ultracentrifugation and purified using size-exclusion chromatography. RNA was isolated from EVs and used for smallRNA-seq.

first: Laura

last: Gröger

first: Nicole

last: Ludwig

first: Amila

last: Beganovic

first: Marcus

last: Koch

first: Stefanie

last: Rheinheimer

first: Martin

last: Hart

first: Petra

last: König

first: Tabea

last: Trampert

first: Pascal

last: Paul

first: Annette

last: Boese

first: Claus-Michael

last: Lehr

first: Sören L.

last: Becker

first: Gregor

last: Fuhrmann

first: Andreas

last: Keller

first: Eckart

last: Meese


title: Ribo-seq analysis of HUVECs upon DDX24 knockdown

first: Simeng

last: He

summary: To investigate the impact of DDX24 silencing on the translation landscape in HUVEC cells, we conducted Ribo-seq analysis.

overall_design: To investigate changes in translation in response to DDX24 knockdown, we performed ribosome profiling (Ribo-seq) and matched RNA-seq in HUVEC cells subjected to DDX24 knockdown for 48 h using siRNAs. Both Ribo-seq and the matched RNA-seq experiments performed in 3 replicates.

first: Bin

last: Li


title: Minimizing far-extending chromatin perturbation in genome editing preserves stem cell identity

city: Haidian District

first: Jiawei

last: Yu

state: Beijing

address: Tsinghua  University

department: School of Pharmaceutical Sciences

institute: Tsinghua University

summary:
Advancing CRISPR/Cas9 genome editing demands a thorough understanding of its associated risks.Yet, most of risk assessments have focused on the mutagenic effects stemming from off-target cleavage in gene-coding regions, largely neglecting the implications of cleavage within the extensive non-coding genome. We observed that CRISPR/Cas9-induced DNA cleavage, even at sites several kilobases away from the nearest regulatory elements, can trigger premature differentiation of somatic neural stem cell in vivo.Leveraging a refined multi-omics technology, we delved into the consequences of CRISPR/Cas9-induced DNA cleavage in these non-coding regions. Our findings reveal an impact, especially pronounced in cells with high stemness, where cleavage-induced disruptions can span long ranges, potentially culminating in the loss of stemness. These effects are tied to extensive chromatin perturbations. Building on this understanding, we used chromatin perturbation as a key marker to refine gene editing technologies that could minimize such disruptions.This key finding illuminates the path towards the development of safer and more broadly applicable genome editing technologies.

This SuperSeries is composed of the SubSeries listed below.

overall_design: Refer to individual Series

first: Ming

last: Zhu

first: Junsong

last: Yuan

first: Qiuchen

last: Meng


title: A bifunctional, moonlighting RNA coordinates pathways to regulate human embryonic development [snRNA-seq]

city: Redwood City

first: Jin

last: Chen

state: CA

address: 2800 Bridge Parkway

institute: Altos Labs

summary: Early embryogenesis and cellular differentiation require complex choreography between nuclear and cytoplasmic pathways. Through integrative analysis and a short open reading frame functional screen, sORF-seq, we identified lncPRESS1, a bifunctional long-non-coding RNA that also encodes a microprotein. In the nucleus, lncPRESS1 binds BRG1 to regulate chromatin remodeling and modulate the expression of pluripotency and differentiation genes. In the cytoplasm, lncPRESS1 is translated into a microprotein that binds to IFT57, regulating ciliogenesis and SHH signaling pathways to control lineage commitment. Together, these results reveal a novel mechanism where the dual functions of lncPRESS1 simultaneously coordinate chromatin remodeling and signaling pathways. This coordination co-regulates the initial developmental decisions specifying neuroectoderm and mesoderm fates during human embryonic development, underscoring the underappreciated complexity of multifunctional RNAs.

overall_design: The lncPRESS1 WT, KO, and ΔATG hESCs with matrigel (medium:matrigel=1:1) were injected into the flank of NSG™ immunodeficient mice for teratoma development. The teratoma were flash frozen and sent for scRNA-seq analysis.

first: Kaiyuan

first: Wan-Chen

first: Jamin

last: Liu

first: Benjamin

last: Yang

first: Elmer

last: Guzman

first: Morgane

first: Rene

last: Sit

first: Rose

last: Yan

first: Shi-An

first: Udit

last: Parekh

first: Mia

last: Pulos-Homes

first: Yeyun

last: Ouyang

first: Ana

last: Granat

first: Maya

last: Yamazaki

first: Carla

last: Mulas

first: Renato

last: Minopoli

first: Stefka

last: Tyanova

first: Daniel

last: Itzhak

first: Diego

last: Acosta-Alvear


title: A bifunctional, moonlighting RNA coordinates pathways to regulate human embryonic development [scRNA-seq]

first: Jin

overall_design: The lncPRESS1 WT, KO, and ΔATG hESCs were pretreated with 3.25 uM of CHIR99021 for 24 hours and then 0.5 uM of CHIR99021 for 72 hours to develop 3D gastruloids. These gastruloids were dissociated into single cells using ACCUTASE and then sent for scRNA-seq analysis.

first: Kaiyuan

last: Zhu

first: Wan-Chen

last: Li

first: Jamin


title: Extracellular vesicles and their RNA cargo facilitate bidirectional cross-kingdom communication between human and bacterial cells [RNA-Seq]

first: Shusruto

last: Rishik

overall_design: RNA-seq profiling of Caco-2 cells after incubation with BEVs from Lacticaseibacillus casei, Enterococcus faecalis, and Proteus mirabilis, or transfection with RNA isolated from the respective BEVs for 10 h, 24 h or 48 h. Controls used included PBS, AllStars Negative Control siRNA (ANC), and LPS from Proteus mirabilis. RNA was isolated from cells and used for RNA-seq.

first: Laura

last: Gröger

first: Nicole

last: Ludwig

first: Amila

last: Beganovic

first: Marcus

last: Koch

first: Stefanie

last: Rheinheimer

first: Martin

last: Hart

first: Petra

last: König

first: Tabea

last: Trampert

first: Pascal

last: Paul

first: Annette

last: Boese

first: Claus-Michael

last: Lehr

first: Sören L.

last: Becker

first: Gregor

last: Fuhrmann

first: Andreas

last: Keller

first: Eckart

last: Meese


title: A viral transcriptional regulator from a dsRNA virus antagonizes the innate immune response by manipulating the host co-transcription factor DHX9 [ChIP-Seq]

first: Xueyang

last: Pang

summary: Viral transcriptional regulators (vTRs) have emerged as potent factors that shape the host anti-viral gene expression programs. Delineating the molecular mechanisms by which vTRs inhibit or promote transcription would provide fundamental insights for developing anti-viral strategies. Using Mammalian orthoreovirus (REOV) as a model system, we identified a new viral mechanism by which viruses antagonize the host innate immune response. We found that the REOV outer capsid protein sigma3 functions as a vTR that limits RNA polymerase II (Pol II) recruitment to the promoter regions of NF-κB-dependent genes via its direct interaction with the host helicase DHX9. sigma3 competes with DHX9 for its interaction with Pol II, which led to marked attenuation of Pol II loading onto chromatin. More interestingly, sigma3 also suppresses DHX9 helicase activity, leading to aberrant accumulation of R-loops at promoter-proximal regions and a decrease in NF-κB-dependent gene expression. Together, our findings uncover an unprecedented strategy of a viral protein that regulates anti-viral gene expression by directly manipulating host transcription factor DHX9.

overall_design: RNA Pol II/R-Loop/H3K4me3 occupancy on chromatin upon TNFa treatment in sigma3 overexpressing cells were assessed by Cut&Tag assay.

first: Shiyu

last: Liu

first: Yixiao

last: Zhu

first: Meleana

last: Hinchman

last: Qiao

first: Xuejun

last: Li

first: Weiqian

last: Dai

first: Yingying

last: Tong

first: Man

last: Xing

first: Jiling

last: Ren

first: John

last: Parker

last: Guo

first: Dongming

last: Zhou


title: RNA half-life seq in HUVECs upon DDX24 knockdown

first: Simeng

last: He

summary: DEAD-box (DDX) RNA helicases play crucial roles in gene regulation by interacting with RNAs and influencing RNA fate and function. Previously, we have associated DDX24 with vascular development, but its precise role in RNA metabolism remains unclear. In this study, we demonstrate that DDX24 facilitates the decay of the target mRNAs, in a CCR4-NOT deadenylase complex dependent manner. These results establish a link between DDX24-dependent regulation of mRNA stability and endothelial cell function, providing novel therapeutic targets for angiogenesis.

overall_design: To investigate the role of DDX24 in mRNA stability, RNA half-life-seq of HUVEC with DDX24 knockdown by siRNA was performed. We performed gene expression profiling analysis using data obtained from RNA-seq of 2 different processed cells at 3 time points. Comparative gene expression profiling analysis of RNA-seq data for HUVECs(siNC) and its derivative (siDDX24).

first: Bin


title: A bifunctional, moonlighting RNA coordinates pathways to regulate human embryonic development [RNA-seq]

first: Jin

last: Chen

overall_design: The hESCs, including the WT, KO, and ΔATG, were differentiated into the three germ layers (neuroectoderm: treated with SMADi; mesoderm: treated with BMP4; definitive endoderm: treated with STEMdiff™ Definitive Endoderm Kit). Daily samples were collected for 5 days for bulk RNA-seq. The gain-of-function variants of lncPRESS1 hESCs were collected at early, intermediate, and late stages for RNA-seq.

first: Kaiyuan

first: Wan-Chen

first: Jamin

first: Benjamin

last: Yang

first: Elmer

last: Guzman

first: Morgane

first: Rene

last: Sit

first: Rose

last: Yan

first: Shi-An

first: Udit

last: Parekh

first: Mia

last: Pulos-Homes

first: Yeyun

last: Ouyang

first: Ana

last: Granat

first: Maya

last: Yamazaki

first: Carla

last: Mulas

first: Renato

last: Minopoli

first: Stefka

last: Tyanova

first: Daniel

last: Itzhak

first: Diego

last: Acosta-Alvear


title: Maternal Inflammation Alters Nuclear and Mitochondrial DNA Methylation Patterns in the Neonatal Brain

status: Public on Feb 19 2026

city: Wilmington

first: Elizabeth

last: Wright-Jin

state: Delaware

address: 200 Powder Mill Road

department: Neurology

institute: Nemours Children's Health

summary: Neonatal hypoxic ischemic encephalopathy (HIE) is a common birth complication that can cause death or lifelong disabling conditions like cerebral palsy, epilepsy, and autism. It is well established that maternal infection and inflammation are significant risk factors for HIE but reasons for this increase in neurological risk to the offspring remain unknown. Inflammation or infection are associated with epigenetic changes and may contribute to the increased risk of neurodevelopmental disability in exposed offspring. Here, we analyzed and compared DNA methylation patterns in brain monocytes isolated from control, maternal immune activation (MIA), and an inflammation sensitized HIE (IS-HIE) mouse model at postnatal day 7. We found that maternal inflammation induced significant methylation differences in neonates relative to control samples in both MIA and IS-HIE samples with no significant differences identified between the MIA and IS-HIE groups. MIA samples showed hypermethylation at loci involving craniofacial development and transcription factors important for regulating neurodevelopment and immune function. MIA samples also demonstrated significant hypermethylation at multiple mitochondrial genome CpGs. These findings suggest that maternal inflammation induces epigenetic alterations in fetal brain immune cells that are detectable in neonates. These changes may contribute to heightened neurodevelopmental risk in offspring following hypoxic injury, highlighting potential molecular pathways for future therapeutic targeting.

overall_design: Illumina Infinium Mouse Methylation BeadChip of monocyte cells from 4 samples each of P7-aged  C57bl/6 mice brains treatment groups of Maternal Immune Activation, Hypoxic Ischemic Encephalopathy, and Controls. Bisulfite Conversion by QIAGEN, EPItect Bisulfite Kit. Bead Arrary name and version: Infinium MouseMethylation-12 v1.0.

first: Andrew

middle: T

last: Ebenezer

first: Jonathan

last: Hicks

first: Brooke

last: Hollander

first: Alexander

last: Hone

first: Mona

last: Batish

first: Robert

last: Akins

first: Adam

middle: G

last: Marsh


title: A bifunctional, moonlighting RNA coordinates pathways to regulate human embryonic development [ATAC-seq]

first: Jin

last: Chen

overall_design: The hESCs, including the WT, KO, and ΔATG, were differentiated into the two germ layers (neuroectoderm: treated with SMADi; mesoderm: treated with BMP4). Daily samples were collected for 5 days for ATAC-seq.

first: Kaiyuan

last: Zhu

first: Wan-Chen

last: Li

first: Jamin

last: Liu

first: Benjamin

last: Yang

first: Elmer

last: Guzman

first: Morgane

first: Rene

last: Sit

first: Rose

last: Yan

first: Shi-An

first: Udit

last: Parekh

first: Mia

last: Pulos-Homes


title: Enrichment of neural crest cells by antibody labelling and flow cytometry for single-cell transcriptomics in a lizard

status: Public on Feb 18 2026

city: Plön

first: Robin

last: Pranter

address: August-Thienemann-Straße 2

institute: Max Plank Institute for Evolutionary Biology

summary: Single-cell transcriptomic data were generated from embryos of the common wall lizard (Podarcis muralis). Neural crest cells (NCCs) were enriched by fluorescence-activated cell sorting based on HNK-1 antibody staining. The dataset includes two unsorted samples representing all embryonic cells, one leniently sorted sample containing the top 15% of HNK-1–positive cells, and two strictly sorted samples containing the top 5% of HNK-1–positive cells. Unsorted and leniently sorted samples were generated from pools of three embryos each and sequenced using the 10x Genomics Chromium platform. Strictly sorted samples were generated from a single embryo, split across two plates, and sequenced using the Smart-seq3 protocol. These data enable characterization of NCC transcriptional profiles in a non-model vertebrate species and provide a resource for studying neural crest biology in systems lacking transgenic tools.

overall_design: Eggs were collected within 24 h of oviposition and incubated at 24C. Eggs were dissected in cold PBS and embryos were dissociated, fixed by methanol, stored at -80C, stained with HNK-1 and sorted using FACS. The unsorted samples were not stained or sorted. The Leniently sorted sample consist of cells above the 85th percentile of HNK-1 staining. The Strictly sorted samples consist of cells above the 95th percentile of HNK-1 staining.

first: Cedric

last: Patthey

first: Nathalie

last: Feiner


title: irCLIP-seq of DDX24 in HUVECs

first: Simeng

last: He

summary: DEAD-box (DDX) RNA helicases play crucial roles in gene regulation by interacting with RNAs and influencing RNA fate and function. Previously, we have associated DDX24 with vascular development, but its precise role in RNA metabolism remains unclear. In this study, we demonstrate that DDX24 modulated endothelial cell functions by binding to and regulating mRNAs crucial for vascular morphogenesis and angiogenesis. We further identify DDX24-bound mRNAs in endothelial cells using crosslinking immunoprecipitation (CLIP) sequencing. Mechanistically, DDX24 facilitates the decay of the target mRNAs, such as CLEC14A and ERG, by recruiting the deadenylase complex CCR4-NOT. These results establish a link between DDX24-dependent regulation of mRNA stability and endothelial cell function, providing novel therapeutic targets for angiogenesis.

overall_design: To investigate the role of DDX24 in vascular endothelial cells, CLIP-seq of HUVEC with DDX24-FLAG transfected followed by FLAG pull-down. We then identify DDX24-binding targets using data obtained from CLIP-seq of HUVECs.

first: Bin


title: Monocytes acquire a tumor-associated IL1B program upon encountering patient-derived colon cancer organoids

city: Mannheim

first: Volker

last: Ast

address: Theodor-Kutzer-Ufer 1-3

department: NGS Core Facility

institute: University Hospital Mannheim

summary: Tumor-associated monocytes and macrophages (TAM) accumulate in colorectal cancer (CRC) and play an active role in shaping the tumor microenvironment (TME). While they have been linked to both pro- and anti-tumor functions, understanding the cues that instruct the phenotype of individual subsets as well as their functional impact on the TME remains challenging. In this study, we established co-cultures comprising primary human monocytes and patient-derived organoids (PDOs) from CRC tumors to emulate myeloid cell/carcinoma interactions in vitro that drive tumor-associated monocyte  programming. Upon encountering PDOs, monocytes acquired a complex phenotype not reflected by classical TAM markers or polarization protocols. Single-cell RNA sequencing revealed that PDO-exposed monocyte transcriptionally resembled IL1B-programmed monocytes previously identified in CRC patients. This phenotype emerged independently of the tumors’ mutational profiles or CMS type. Mechanistically, soluble PDO-derived mediators induced the production of chemotactic CXCL2, CXCL5 and CXCL7, while phagocytic uptake of tumor debry limited the MHC class II-mediated antigen presentation capabilities of monocytes in co-culture. Additionally, our in vitro system allowed the functional assessment of PDO-exposed monocytes demonstrating a compromised capacity to mount an inflammatory response upon TLR stimulation. Together, our PDO–monocyte co-cultures offer a tractable, human-specific model system to study the interplay between epithelial cancer cells and monocytes, and advance our understanding of myeloid plasticity and function in cancer patients.

overall_design: Single-cell RNA sequencing of CD45+ sorted monocytes after four days of monoculture or co-culture with PDO19 or PDO30

first: Bianca

middle: M

last: Balzasch

first: Adelheid

last: Cerwenka


title: RNA-seq in HUVECs upon DDX24 knockdown

summary: DEAD-box (DDX) RNA helicases play crucial roles in gene regulation by interacting with RNAs and influencing RNA fate and function. Previously, we have associated DDX24 with vascular development, but its precise role in RNA metabolism remains unclear. In this study, we demonstrate that DDX24 modulated endothelial cell functions by binding to and regulating mRNAs crucial for vascular morphogenesis and angiogenesis. These results establish a link between DDX24-dependent regulation of mRNA stability and endothelial cell function, providing novel therapeutic targets for angiogenesis.

overall_design: To investigate the role of DDX24 in vascular endothelial cells, RNA-seq of HUVEC with DDX24 knockdown by siRNA was performed. We then performed gene expression profiling analysis using data obtained from RNA-seq of 2 different processed cells.Comparative gene expression profiling analysis of RNA-seq data for HUVECs(siNC) and its derivative (siDDX24).


first: Carsten

last: Sticht

address: Theodor-Kutzer-Ufer

department: ZMF

institute: University Heidelberg

overall_design: Bulk RNA sequencing of EpCAM+ sorted PDOcells from patient 30 (PDO30) after four days of monoculture or co-culture with primary human monocytes


title: Comparative Analysis of Defensin Expression in Hyalomma asiaticum Ticks Exposed to Staphylococcus aureus and Escherichia coli

city: Xinjiang

first: 马祯

last: 祯

state: Xinjiang Uygur  Autonomous Region

address: nongda east road 311

department: College of Veterinary Medicine

institute: Xinjiang Agricultural University

summary: Background: Hyalomma asiaticum, which acts as a vector of zoonotic pathogens, relies on its innate immune system for defense. Methods: This study employed comparative transcriptomics to investigate defensin expression and immune pathway activation in ticks exposed to Staphylococcus aureus and Escherichia coli bacteria. Unfed adult female ticks were injected with bacteria, followed by RNA-Seq analysis after 24 h. Results: De novo assembly generated 195,132 unigenes. A total of 15 defensin genes were identified. Functional enrichment demonstrated pathogen-specific immune responses: E. coli challenge led to significant enrichment of the IMD pathway, while S. aureus stimulation resulted in enrichment of the Toll pathway. A shared response to both E. coli and S. aureus infection was the significant up-regulation of the MAPK signaling pathway (P < 0.01). Key defensin isoforms showed significant differential up-regulation, up to 8-12-fold, suggesting functional diversification. Beyond direct antimicrobial activity, defensin-associated genes were enriched in apoptosis and oxidative stress responses. Conclusions: These findings reveal distinct signaling mechanisms underlying H. asiaticum antibacterial defense and highlight defensins as multifunctional effector molecules. This study offers a preliminary reference for comprehending immune mechanisms of H. asiaticum.

overall_design: Unfed female ticks of similar body weight, from the same artificially reared batch at two weeks post-molting, were selected as the target samples for bacterial stress experiments. To minimize the impact of environmental microorganisms on the tick samples, their body surfaces were cleaned thoroughly. Briefly, Each tick was immersed in sterilized PBS and subjected to shaking for 15 seconds, followed by transfer to a 75% ethanol solution for an additional 15 seconds with agitation. Subsequently, the ticks were rinsed three times with ddH2O with agitation applied during each rinse. Finally, the cleaned ticks were placed on sterilized absorbent paper for surface drying. Injections of S. aureus and E. coli into unfed female ticks of Amblyomma americanum are described previously . Briefly, unfed female ticks were injected using a precision microsyringe (Hamilton Bonaduz, Switzerland) with a 10⁷ CFU/ml dilution of S. aureus or E. coli on the right side, between the fourth coxal segments, at a volume of 0.5 µl per tick. Immediately after completing the injection procedure, the injection site was sealed with a minimal amount of sterile Vaseline to prevent hemolymph leakage. After 24 h post-injection, ten individuals were randomly selected from each group to be pooled. The PBS-injected group was designated as the negative control to establish baseline gene expression profiles for comparative analysis. Each treatment group, including the negative control group, comprised 10 unfed female adult ticks. Three biological replicates were included for each group. Ticks were immediately transferred to freezing tubes and immersed in liquid nitrogen for snap-freezing to preserve RNA integrity prior to RNA-Seq.

first: Zhen

last: Ma

first: Depeng

first: Tingxiang

last: Luo

first: Sen

first: Wenxiu

last: Hu

first: Qiya

last: Wu

first: Zhengxiang

first: Yongchang

first: Yang

last: Zhang

first: Wei

first: Bayinchahan

last: Gailike

first: Qingyong

last: Guo

first: Ercha

first: Caishan


title: RNA functional modulation by Mitoxantrone via RNA structural ensemble repartitioning

status: Public on Feb 17 2026

city: Groningen

first: Danny

last: Incarnato

state: Netherlands

address: Nijenborgh 7

department: Molecular Genetics

country: Netherlands

institute: University of Groningen

summary: Targeting RNA with small molecules offers a strategy to modulate gene expression at undruggable targets. Traditional screens favor thermodynamically stable, low-entropy RNA motifs with defined conformations, yet these provide limited energetic leverage for functional modulation. Many RNAs instead sample dynamic structural ensembles that small molecules can stabilize or redirect. Using group I self-splicing introns as a model, we identified the antineoplastic drug Mitoxantrone as a competitive inhibitor of RNA self-splicing (IC50 = 4.3 μM) that stabilizes the native conformation of the T4 td intron. Structure-activity analysis showed the anthraquinone scaffold alone is insufficient, and basic amine side chains are required for RNA structural modulation. Transcriptome-wide chemical probing in human cells revealed preferential binding to GC-rich structured regions, although only a subset showed structural change. Furthermore, global analysis of 5′ UTR ensembles showed reduced structural heterogeneity and increased translation, demonstrating functional repartitioning of RNA conformational landscapes.

sample_organism:
Homo sapiens
Escherichia phage T4

platform_organism:
Homo sapiens
Escherichia phage T4

overall_design: RNA structure analysis following treatment with Mitoxantrone

first: C

first: I

last: Borovská

first: T

last: Iobashvili

first: E

last: Morandi

first: M

last: Lionnez

first: O

last: Olayinka

first: R

last: de Boer

last: Clamer

middle: D

last: Witte

first: K

last: Pors

first: J

last: Schneekloth

first: D


title: ERRα-KDM5C Restrains STING Enhancer Activity to Modulate Type I Interferon Signaling in Breast Cancer Progression

city: Ganzhou

first: Wenjuan

state: Jiangxi

address: No. 23, Qingnian Road

department: First Affiliated Hospital

institute: Gannan Medical University

summary: Regulation of enhancer activity plays a pivotal role in governing gene expression and cellular behaviors. However, the precise mechanisms underlying dynamic control of active enhancers remain incompletely defined. Here, we demonstrate that the nuclear receptor estrogen-related receptor α (ERRα) forms a functional complex with the H3K4me3-specific demethylase KDM5C to co-occupy a large set of active enhancers, including the locus of STING. In breast cancer cells, ERRα depletion induces STING enhancer hyperactivation, evidenced by H3K4me3 deposition, decreased H3K4me1, and increased enhancer RNA (eRNA) transcription. Accordingly, depletion of ERR leads to further activation of STING gene transcription and TBK1-IRF3 pathway, accompanied by increased type I interferon (IFN) and IFN-stimulated gene (ISG) expression, as confirmed by transcriptomic analysis. Notably, depleting ERRα markedly attenuates breast tumor cell growth in vitro and in vivo, and our in vitro evidence indicates this occurs in part through activating STING signaling. These findings establish that the ERRα-KDM5C serves as a critical checkpoint for STING enhancer activity, revealing a regulatory mechanism of STING enhancer activity in breast tumor progression.

overall_design:
MCF7 cells were transfected with control shRNA (shCTL) or shRNA specifically targeting ERRα(shERRα) or KDM5C (shKDM5C) followed by RNA-seq analysis.
GRO-seq was performed in MCF7 cells transfected with control siRNA (siCTL) , followed by nuclear run-on and BrUTP labeling.
ChIP-seq was performed using an antibody against H3K4me3 in shCTL-, shERRα-, or shKDM5C-transfected MCF7 cells, with corresponding Input DNA as control.

first: Zuhui

last: Xu

first: Xiaonan

first: Wen

last: Liu


title: High-Complexity Barcoded Rabies Virus for Scalable Circuit Mapping Using Single-Cell and Single-Nucleus Sequencing

city: San Francisco

first: David

last: Shin

address: 1651 4th Street Room 521A

department: Neurosurgery

institute: University of California, San Francisco

summary: Single cell genomics has revolutionized our understanding of the diversity of neuronal cell types. However, scalable technologies for probing single-cell connectivity are lacking, and we are just beginning to understand how molecularly defined cell types are organized into functional circuits. Here, we describe a strategy to generate high-complexity barcoded rabies virus (RV) for scalable circuit mapping that is compatible with both single-cell and single-nucleus RNA sequencing (sc/snRNA-seq) readout. Our barcoded RV libraries contain up to 43 million unique barcodes with a relatively uniform distribution, allowing multiplexed circuit mapping from tens of thousands of individual starter cells. We demonstrate the utility of this approach by mapping the emerging circuits in the developing human cortex using organotypic slice cultures. By leveraging the power and throughput of single cell genomics for mapping synaptic connectivity, we chart a path forward for scalable circuit mapping of molecularly-defined cell types in healthy and disease states.

overall_design: Sequencing of barcoded G-deleted rabies (RVdG) libraries for quantitative analysis

first: Madeline

last: Urbanek


title: Age-associated chromatin reorganization drives overexpression of a novel Btaf1 variant regulating HSC self-renewal and MkP differentiation in male mice

city: Baltimore

first: Bongsoo

last: Park

state: Maryland

address: 251 Bayview Blvd

department: Translational Gerontology Branch

institute: National Institute on Aging

summary: Age-associated hematopoietic stem cell (HSC) dysfunction is accompanied by dramatic transcription changes, but it remains unclear whether specific transcripts could orchestrate these HSC aging phenotypes. Here, we performed epigenetic profiling in male mice to investigate the regulatory mechanisms underlying the HSC aging transcriptome and screen for potential aging driver genes. We show dysregulated 3D chromatin organization, altered histone modifications and changed chromatin accessibility shape the HSC aging transcriptome. From the compilation of these data, we identified a new looping structure formed between part of the Btaf1 gene and the whole Ide gene in old HSCs (OHSCs) which is accompanied by overexpression of a novel, shorter variant of Btaf1 (nBtaf1). Mechanistically, elevated expression of nBtaf1 drives the aging-associated overexpression of HSC- and megakaryocyte progenitor (MkP)-related genes by regulating TBP binding at their promoters which contributes to HSC expansion and elevated MkP production in aged mice. ShRNA mediated knockdown of nBtaf1 restores a younger HSC transcriptome and specifically represses aging-associated HSC expansion and elevated MkP production. In summary, our data provide high resolution analysis of a dysregulated HSC aging epigenome and reveal a novel Btaf1 variant that drives HSC aging phenotypes in mice.

overall_design: ChIP-sequencing, RNA-sequencing, and Hi-C were performed to compare the transcriptome between Young and Old mice samples.

first: Le

last: Zong

first: Yaqiang

last: Cao

first: Fei

last: Ma

first: Ferda

last: Tekin-Turhan

first: Wakako

last: Kuribayashi

first: Keji

last: Zhao

first: Isabel

last: Beerman


title: MiR-146a-5p and miR-146b-5p limit IL-1beta-mediated inflammation in adipose tissue during polytrauma

city: Ulm

first: Pamela

last: Fischer-Posovszky

address: Eythstr. 24, Haus 16, Forschungslabor KiKli

department: Department of Pediatrics and Adolescent Medicine

institute: Ulm University Medical Center

summary:
MicroRNAs (miRNAs) are small non-coding RNAs and play a crucial role in the regulation of inflammation. White adipose tissue (WAT) covers the body and internal organs in subcutaneous and visceral fat depots, respectively, and represents an important source of circulating miRNAs. The role of WAT and its miRNAs in the context of polytrauma is incompletely understood. However, evidence is accumulating that WAT contributes to the severe inflammatory response observed in polytrauma patients. Therefore, we analyzed the miRNA expression in inguinal WAT depots in a standardized mouse model of polytrauma and hemorrhagic shock (PT+HS). Here, we identified miR-146a-5p and miR-146b-5p to be upregulated upon PT+HS. In an in-vitro model of traumatized human white adipocytes, we found miR-146a-5p to be upregulated by IL-1β-induced NF-B activation. Both, miR-146a-5p and miR-146b-5p, in turn, dampened IL-1β-induced inflammation in human adipocytes. Using target gene prediction tools, we further identified IRAK1 as target of miR-146a-5p, and potentially also miR-146b-5p, confirming the importance of IRAK1 in IL-1β-induced proinflammatory signaling. Thus, miR-146a-5p and miR-146b-5p act as suppressors of IL-1β-induced proinflammatory signaling in human adipocytes during trauma, and blockage of IL-1β or mimics of miR-146a-5p and miR-146b-5p might represent a potential future therapeutic avenue for severe traumatic and inflammatory conditions.
We used Affymetrix microRNA array to determine the expression of different microRNAs in inguinal white adipose tissue (iWAT) from five sham-treated mice and five mice with polytrauma and hemorrhagic shock (PT+HS).

overall_design: The animal experiments were approved by the federal authorities for animal research, Tübingen, Germany. Male C57BL/6 mice aged 10-12 weeks with a mean body weight of 29.5 g were randomly assigned to sham treatment or PT + HS (n=5 animals per group). No specific inclusion/exclusion criteria or outcome measures were deemed relevant for this specific study. In brief, mice were anesthetized with 2.5% sevoflurane (Abbott, Wiesbaden, Germany) in oxygen throughout the experiment before they were subjected to thoracic trauma, closed head injury, and femur fracture including soft tissue injury as described previously (Weckbach S, Hohmann C, Braumueller S, Denk S, Klohs B, Stahel PF, Gebhard F, Huber-Lang MS, Perl M (2013) Inflammatory and apoptotic alterations in serum and injured tissue after experimental polytrauma in mice: distinct early response compared with single trauma or “double-hit” injury. J Trauma Acute Care Surg 74:489–498. doi: 10.1097/TA.0b013e31827d5f1b). Pressure-controlled hemorrhage was induced and monitored by a microcatheter in the femoral artery. A mean arterial pressure of around 30 ± 5 mmHg was maintained for 60 minutes. After resuscitation of the animals with a balanced electrolyte solution, inguinal WAT depots were removed 4 hours after trauma. Euthanasia was performed by thoracic opening under deep narcosis and terminal blood sampling from the right ventricle. Due to the nature of the animal experiment, investigators were not blinded during the animal study protocol.


title: Vascular STING activation facilitates NK cell anti-tumor immunity in small cell lung cancer

status: Public on Feb 15 2026

city: Boston

first: Zhaorong

last: Li

address: 60 Fenwood Road

institute: Dana Farber Cancer Institute

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

overall_design: Refer to individual Series


title: Time‑resolved multi-omic analysis of paclitaxel exposure in human iPSC‑derived sensory neurons unveils mechanisms of chemotherapy‑induced peripheral neuropathy

city: Berlin

first: Christian

last: Schinke

address: Charitéplatz 1

institute: Charité Universitätsmedizin Berlin

summary: The microtubule-stabilizing drug paclitaxel remains standard of care for various solid malignancies but frequently leads to chemotherapy-induced peripheral neuropathy (CIPN). CIPN is a leading cause for premature treatment termination and a significantly reduced quality of life in long-term cancer survivors. The molecular mechanisms of neuro-axonal degeneration, neuroinflammation and pain in patients treated with paclitaxel remain incompletely understood, and there are currently no predictive biomarkers or preventive treatments. We used human iPSC-derived sensory neurons exposed to paclitaxel to comprehensively model the pathophysiology of CIPN. Neurotoxicity was assessed over time using viability assays and sequential RNA sequencing as well as deep proteome and lipidomic analyses. We observed a time and dose-dependent decline of cell viability at clinically relevant paclitaxel doses. Sequential RNA sequencing defined JUN as an early immediate gene, followed by the overexpression of genes of the neuronal stress response (e.g., ARID5A, WEE1, DUSP16, GADD45A), neuronal injury and apoptotic pathways (e.g., ATF3, HRK, BBC3 [PUMA], BCL2L11 [BIM], CASP3), neuroinflammation and nociception (CALCB, MMP10, IL31RA, CYSLTR2, C3AR1, TNFRSF12A) and neuronal transduction (e.g., CAMK2A, STOML3, PIRT), while key enzymes of lipid biosynthesis were markedly downregulated (e.g., LSS, HMGCS1, HMGCR, DHCR24). Deep proteome analyses following 48 hours of exposure to 100nM paclitaxel revealed a strong correlation of differentially expressed RNA with proteins, and a marked degradation of essential axonal transport proteins such as kinesins, stathmins and scaffold proteins. Consistent with the downregulation of rate-limiting enzymes of lipid biosynthesis, lipidome analysis confirmed deregulation of neuronal lipid homeostasis. In summary, paclitaxel induces transcriptomic and proteomic signatures of the neuronal stress response, neuroinflammation, nociception and disturbed metabolism. These may explain, in part, the clinical phenotype of sensory loss, hypersensitivity and neuropathic pain frequently observed in patients suffering from CIPN, but constitute pharmacologically addressable targets.

overall_design: 72 samples were included in RNA sequencing analyses from 12 different experimental units (plates): Seven time points from BIHi264-A (7 × 6-well plates) and 48-h samples from five cell lines (5 × 6-well plates). iPSC-DSN were maintained in geltrex coated 6-well plates at 10^6 cells/well, as described in the CDDis manuscript entitled above. After maturation for >60d, three wells were either treated with DMSO at 1/60.000 or paclitaxel at 100 nM, respectively. Investigated time points were 48h of paclitaxel incubation for all five cell lines (30 samples), and for BIHi264-A, the additional time points of 2h, 6h, 12h, 24h and 24h or 120h following removal of the drug after 48h incubation (s.c. 72h and 168h timepoints; in total, 42 samples). RNA was harvested with the Aurum™ Total RNA Mini Kit according to manufacturers’ instructions. RNA sequencing was performed by Brooks Life Sciences Genewiz® with PolyA selection for RNA removal, 2x150 bp sequencing configuration and 20-30 million reads per sample. RNA Library Preparation and NovaSeq Sequencing by AzentaLifeSciences Genewiz: RNA samples were quantified using Qubit 4.0 Fluorometer (Life Technologies) and RNA integrity was checked with an RNA Kit on Agilent 5300 Fragment Analyzer (Agilent Technologies). RNA sequencing libraries were prepared using the NEBNext Ultra RNA Library Prep Kit for Illumina following the manufacturer’s instructions (NEB, Ipswich). Briefly, mRNAs were first enriched with Oligo(dT) beads. Enriched mRNAs were fragmented for 15 minutes at 94 °C. First-strand and second strand cDNAs were subsequently synthesized. cDNA fragments were end repaired and adenylated at 3’ends, and universal adapters were ligated to cDNA fragments, followed by index addition and library enrichment by limited-cycle PCR. Sequencing libraries were validated using NGS Kit on the Agilent 5300 Fragment Analyzer (Agilent Technologies), and quantified by using Qubit 4.0 Fluorometer (Invitrogen). The sequencing libraries were multiplexed and loaded on the flowcell on the Illumina NovaSeq 6000 instrument according to manufacturer’s instructions. The samples were sequenced using a 2x150 Pair-End (PE) configuration v1.5. Image analysis and basecalling were conducted by the NovaSeq Control Software v1.7 on the NovaSeq instrument. Raw sequence data (.bcl files) generated from Illumina NovaSeq was converted into fastq files and de-multiplexed using Illumina bcl2fastq program version 2.20. One mismatch was tolerated for index sequence identification. Computational Methods. RNA Seq reads were mapped to human genome (GRCh38.p7) with STAR-version 2.7.3a [100] using the default parameters. Reads were assigned to genes with featureCounts version 2.0.0 [101] with the following parameters: -t exon -g gene_id -s 0 -p, gene annotation - Gencode GRCh38/v25. The differential expression analysis was carried out with DESeq2-version 1.32.0 [102] using the default parameters. We kept genes that have at least 5 reads in at least 3 samples. Gene set enrichment analysis was carried out with R/tmod package version 0.50.07 using MSigDB gene sets [103]. For Reference Numbers: Please refer to CDDis manuscript CDDis-25-4526.

first: Smilla

last: Maierhof

first: Lois

last: Hew

first: Valeria

last: Fernandez Vallone

first: Silke

last: Frahm

first: Narasimha

last: Swamy Telugu

first: Sebastian

last: Diecke

first: Andranik

last: Ivanov

first: Richard

last: Kovács

first: Dieter

last: Beule

first: Marieluise

last: Kirchner

first: Philipp

last: Mertins

first: Ulrike

last: Brüning

first: Jennifer

last: Kirwan

first: Harald

last: Stachelscheid

first: Matthias

last: Endres

first: Petra

last: Huehnchen

first: Wolfgang

last: Boehmerle


title: Loss of meningeal lymphatic endothelial cells results in formation of a novel vascular network with scavenging function.

status: Public on Feb 16 2026

city: Huddinge

first: Lars

last: Muhl

address: Blickagången 6

department: MedH

country: Sweden

institute: Karolinska Institutet

summary: For an extended period of time, the meninges were believed to be devoid of lymphatic vessels. The recent discovery of lymphatic vessels in the dura mater of humans, mice, and zebrafish, and the identification and characterization of scavenging lymphatic endothelial cells in zebrafish leptomeninges have contributed to a better understanding of waste removal routes from the brain. Zebrafish brain lymphatic endothelial cells (BLECs), in particular, have a high propensity for particulate waste removal from the cerebrospinal fluid. To further understand the function of BLECs, we have established a protocol for specifically ablating this cell type during embryonic stages. We show that BLECs do not recover upon complete depletion, even at adult stages. The absence of BLECs results in detrimental effects on the meningeal blood vasculature and on arachnoid mater structure. We further report that, upon BLEC ablation, a novel vessel network forms, which shares characteristics with lymphatic vessels and is able to take up substances injected into the brain parenchyma, thus possibly providing compensatory functions in the absence of BLECs.

overall_design: Single-cell transcriptomes were generated from individual FACS-sorted cells captured from the meninges of adult zebrafish for single-cell RNA-sequencing (Smart-seq3).

first: Katharina

last: Uphoff

first: Andreas

last: van Impel

first: Martin

last: Stehling

first: Christer

last: Betsholtz

first: Stefan

last: Schulte-Merker


title: Bulk RNA-seq analysis of WT C57BL/6 mise treated with Control, Choleste-help normal lot, toxic lot, and Puberulic acid

city: Bunkyoku

first: Yuta

last: Sekiguchi

state: Tokyo

address: 1-5-45, Yushima

institute: Institute of Science Tokyo

summary: Puberulic acid has been suggested as the causative agent in the toxic lot of Choleste-Help, but no detailed toxicological data have been published to date. In this study, we demonstrated a striking similarity in the renal transcriptomic profiles induced by puberulic acid and the toxic lot of Choleste-Help, supporting the conclusion that puberulic acid is the likely causative compound. Furthermore, both treatments led to a significant downregulation of mitochondria-related transcripts, suggesting that the kidney injury involves mitochondrial dysfunction.

overall_design: Male C57BL/6 mice were orally administered one of the following for 6 consecutive days: vehicle control, a normal lot of Choleste-Help, a toxic lot of Choleste-Help, or puberulic acid. On day 7 (after one drug-free day), whole kidney tissues were harvested for transcriptome analysis.

first: Makiko

last: Mori

first: Hiroaki

last: Kikuchi

first: Yutaro


title: Vascular STING activation facilitates NK cell anti-tumor immunity in small cell lung cancer [Spatial_Transcriptome]

first: Zhaorong

last: Li

summary: Small cell lung cancer (SCLC) typically displays a "cold" tumor microenvironment with a paucity of immune infiltrate. Neuroendocrine SCLC cells also profoundly repress MHC-I expression, rendering them vulnerable to NK cell-mediated cytotoxicity. Here, we confirm that neuroendocrine SCLC cells are sensitive to NK cell mediated attack, yet quantitative spatial profiling of the SCLC immune microenvironment in patient samples reveals that effector immune cells, including NK cells, are excluded from MHC-Ilow/neg SCLC regions. To study this biology, we develop dynamic single cell RNA sequencing of microphysiological immune tumor environments (DynaMITE-seq) and integrate findings with spatial transcriptomics in patient tissue, unveiling the microvasculature as a major checkpoint restricting NK cell extravasation/recruitment. We demonstrate that activation of vascular Stimulator of Interferon Genes (STING) signaling restores NK cell infiltration and killing of neuroendocrine SCLC, suggesting a strategy to overcome this key SCLC immunologic barrier and prime therapeutic response to DLL3-targeted CAR-NK cell therapy.

overall_design: Spatial transcriptomics of SCLC patient samples  from FFPE tissues (Visium platform)

first: Marco

last: Campisi

first: Ian

last: Dryg

first: Jason

last: Weirather

first: David

middle: A

last: Barbie

first: Navin

middle: R

last: Mahadevan


title: Gene expression profiles in pancreatic cancer cells with high or low baseline autophagy flux levels [Low-Auto_High-Auto_RNASeq]

city: Manhattan

first: Mohamad

last: Assi

state: NY

address: 550 1st Ave

department: Radiation Oncology

institute: NYU Medical Center

summary: In this study, we characterize the transcriptional signature of pancreatic cancer cells with different autophagy flux levels.

overall_design: PATU8902 cells were cultured in 3D-Matrigel to form spheroids. Cells with high (High-Auto) or low (Low-Auto) autophagy levels were flow-sorted, prior to RNA extraction and sequencing.

first: Alec

last: Kimmelman


title: Identify positive and negative regulators of autophagy in pancreatic cancer spheroids.

summary: In this study, we reveal the regulators of autophagy in 3D culture and 2D starvation conditions in pancreatic cancer.

overall_design: PATU8902 cells were transduced with the whole-genome Brunello library and cultured under various conditions, prior to flow sorting, DNA extraction and sequencing.


title: Effects of constitutive YAP1 activation on gene expression in pancreatic cancer spheroids [EV_YS6A_RNASeq]

summary: In this study, we investigate the role of YAP1 in regulating autophagy flux in pancreatic cancer spheroids.

overall_design: YAP1S6A constitutively active phosphomutant was expressed in PATU8902 cells, which were then cultured in 3D-Matrigel as spheroids, prior to RNA extraction and sequencing. Empty Vector (EV) is used as a control.


title: Effects of Integrin-alpha3 (ITGA3) knockdown on gene expression in pancreatic cancer cells [Scr_siITGA3_RNASeq]

summary: In this study, we investigate the role of ITGA3 in regulating autophagy flux in pancreatic cancer.

overall_design: ITGA3 was knocked-down using siRNA in PANC2.03 cells prior to RNA extraction and sequencing. Scramble (Scr) is used as a control.


title: Define the pattern of YAP1-bound genes in pancreatic cancer spheroids.

summary: In this study, we investigate the genes that are preferentially bound by YAP1 in pancreatic cancer spheroids.

overall_design: Endogenous YAP1 was pulled-down from PATU8902 spheroids, prior to DNA elution and sequencing. IgG is used as an isotype control.


title: Transcriptome-wide analysis of Sense and Natural Antisense Transcripts (NATs) in Plasmodium vivax clinical isolates from uncomplicated or complicated diseases manifestation.

status: Public on Feb 12 2026

city: Bangalore

first: Genotypic

last: technology

state: Karnataka

address: 259, Apoorva 4th cross,80 feet Road,RMV 2ND STAGE

country: India

institute: Genotypic Technology

summary: We developed a custom-designed 8×60K Plasmodium vivax microarray to enable genome-wide expression profiling of both nuclear and mitochondrial transcripts from field isolates. Probe selection was guided by a combination of bioinformatic prediction and experimental validation to ensure optimal detection of parasite transcripts in clinical samples. The array features 60-mer oligonucleotide probes in situ synthesized on glass slides using Agilent technology. It includes validated probes representing 5,565 nuclear genes and 19 mitochondrial genes in sense orientation, along with 5,566 and 19 genes, respectively, in antisense orientation capturing dual-stranded expression. In most cases, multiple probes were designed in both orientations against each transcript. Validation using 14 clinical samples (including both uncomplicated and severe (Hepatic Dysfunction) cases, demonstrated a high sensitivity, with ≥ 90% transcript detection. Multiple probes targeting the same gene showed consistent expression profiles across samples. Hybridization results were further validated against previous transcriptomic data and qRT-PCR assays, confirming the array's reliability. Uniquely designed for P. vivax, this sensitive and reproducible microarray provides a powerful functional genomics platform to generate high-confidence expression data and identify differentially regulated genes for both sense and Natural Antisense transcripts (NATs) from field isolates, including both the nuclear and mitochondrial transcriptomes.

overall_design: Total RNA from 14 clinical isolates of Plasmodium vivax was isolated from malaria patients with Hepatic Dysfunction manifestations (n=14). Each of these samples was hybridized individually on custom-designed 8*60K arrays printed on the Agilent platform for their sense and antisense transcriptional profiling

first: Priyanka

last: Roy

first: Ashis

last: Das


title: Transcriptomes of endothelial cells from mesenteric adipose tissue from wildtype and Myct1ecKO mice

city: Lausanne

first: Tania

last: Wyss

address: Rue du Bugnon 25A

institute: SIB Swiss Institute of Bioinformatics

summary: Single cell RNA sequencing of mesenteric adipose endothelial cells from adult willdtype and Myct1ecKO mice

overall_design: Wildtype and Myct1ecKO (Myct1 fl/fl; Pdgfb-CreERT2) mice (C57BL6) were induced with tamoxifen at 3 weeks old. When they reached 14 weeks old, mesenteric adipose tissue was collected and endothelial cells (CD45-CD31+) were sorted by FACS. Sorted cells from 2 replicates per genotype were subjected to 10x Genomics single-cell RNA seq analysis.

first: Anna

last: Köck

first: Amélie

last: Sabine

first: Tatiana

middle: V

last: Petrova


title: Erastin-Induced Ferroptosis Enhances Natural Killer Cell Anti-Tumor Activity  and Offers Therapeutic Potential in Neuroblastoma

city: Göteborg

first: Ganesh

last: Umapathy

address: Medicinaregatan 9 a-b

department: Sahlgrenska University Hospital

institute: University of Gothenburg

summary: High-risk neuroblastoma (NB) often relapses and becomes refractory to treatment, making it a significant contributor to childhood cancer mortality despite its relative rarity. Addressing the challenges posed by NB’s resistance to conventional apoptosis-inducing therapies (e.g., chemotherapy and radiation) has become a pressing concern in pediatric oncology research. In recent years, the growing comprehension of  alternative cell death modalities distinct from apoptosis has revealed a promising avenue in the endeavor to combat treatment-resistant cancers. One such mechanism, ferroptosis, has attracted increasing attention for its potential role in combating therapy-resistant cancer cells. High-risk NB typically exhibits an immune-excluded phenotype, characterized by minimal immune cell infiltration. Despite this characteristic, the mechanisms underlying immune exclusion and impaired immune activation in NB remain unclear. Here, we demonstrate that the induction of ferroptosis  using Erastin, a cysteine-glutamate antiporter inhibitor, reduces NB cell proliferation and foci formation. Furthermore, our transcriptomics analysis revealed that treatment  with Erastin in NB cells led to increased expression of ULBP1, a ligand to the activating natural killer (NK) cell receptor, NKG2D. Upon ferroptosis induction, the transcription factor ATF4 was found to drive ULBP1 expression in NB cells. Consistent with this, pre-treatment with Erastin sensitized NB cells to NK cell cytotoxicity in co-culture experiments. These results suggest the NK cell’s cytotoxic function can be enhanced with Erastin-mediated ferroptosis, which may be beneficial for NB patients.

overall_design: Human neuroblastoma cell lines KELLY (Kelly) and SK-N-AS (AS) were treated with Erastin (Era) for 24 hours or vehicle control. Each condition was performed in biological triplicate. Bulk RNA-seq was performed to characterize transcriptional changes associated with ferroptosis induction.

first: Umapathy

last: Ganesh

first: Anthonydhason

last: Vimala


title: Species-Specific Roles of SP1 in Bovine and Human Embryonic Genome Activation and Early embryonic Development

city: hangzhou

first: Hao

last: Jin

address: Nongshenghuan Building E, Zhejiang University, Hangzhou, Zhejiang

institute: Zhejiang University

summary: Embryonic genome activation (EGA) marks the onset of embryonic program and enables the transition toward the first lineage specification. However, the molecular features of EGA and the transcription factors (TFs) orchestrating this process remain unclear. Here, by performing single-cell RNA-seq on bovine embryos, we reveal that major EGA is asynchronously initiated among blastomeres at the 8-cell stage. Integrative analyses reveal distinctive protein accumulation compared to transcription and translation activation during bovine EGA. Furthermore, we investigate the role of SP1, a TF activated at the minor EGA stage, with motifs enriched in accessible chromatin during major EGA stage in bovine and human embryos. SP1 deficiency leads to morula arrest in bovine and impairs EGA in human embryos. Multi-omics analysis demonstrates that SP1 promotes early lineage gene expression by modulating nearby chromatin states in bovine and directly targets key EGA genes in human embryos. Together, our study delineates the dynamics of bovine EGA and uncovers the conserved and species-specific roles of SP1 in regulating EGA and early development in mammals.

sample_organism:
Homo sapiens
Bos taurus

platform_organism:
Homo sapiens
Bos taurus

overall_design:
To investigate the dynamic expression during bovine embryonic genome activation, we performed scRNA-seq of bovine embryos at GV, MII, zygote, 2-cell (2C), 4-cell (4C), early/late 8-cell (E/L8C), and 16-cell (16C) stages.
To investigate the role of SP1 during bovine early embryo development, we performed RNA-seq, SP1 CUT-Tag, H3K27ac ChIP-seq, and ATAC-seq in control, SP1 KD and SP1 KO embryos at 8C, 16C and morula stage,
To investigate the role of SP1 during human early embryo development, we performed RNA-seq, SP1 CUT-Tag in control, SP1 KD embryos at 8C stage,

first: Lieying

last: Xiao

first: Kun

last: Zhang


title: Protein-interaction network reveals a role of Prp19 splicing factor in transcription of both intron-containing and intron-less genes

status: Public on Feb 11 2026

city: Warren

first: Katherine

last: Dwyer

state: MI

address: 29529 Cunningham Drive

institute: Wayne State University

summary: We have previously demonstrated that the transcription-dependent interaction of the promoter and terminator ends of a gene, which results in the formation of a gene loop, is facilitated by the interaction of the general transcription factor TFIIB with the CF1, CPF and Rat1 termination complexes. To further elucidate the protein-protein interactions that stabilize gene loop, we performed mass spectrometry of affinity purified termination complexes from chromatin fraction. Quantitative proteomic analysis revealed additional interactions of termination factors with TFIID and SAGA complex. Since gene looping of intron-containing genes involves additional contacts of the promoter and terminator with the intron, we examined if termination factors interact with the splicing factors as well. All three termination complexes displayed statistically significant interactions with Prp19, Prp43, Sub2, Snu114, Brr2 and Smb1 splicing factors. Since Prp43 and Prp19 consistently emerged as the interactor of both initiation and termination factors, we affinity-purified both and performed mass spectrometry. Prp19 exhibited interactions with subunits of TFIID, CPF complex, and the RSC chromatin remodeling complex. These interactions were observed exclusively in the chromatin context, thereby implicating the factor in transcription of protein coding genes. Since fewer than 4% of yeast genes contain introns, we hypothesized that Prp19 might have a broader role in RNAPII transcription cycle. Auxin-mediated depletion of Prp19 resulted in about two-fold decrease in transcription of a subset of both intron-containing and intron-less genes. Specifically, the promoter recruitment of TBP registered a significant decline in the absence of Prp19. Chromatin immunoprecipitation (ChIP) analysis revealed crosslinking of Prp19 to the promoter proximal as well as downstream regions of both intronic and non-intronic genes. These findings demonstrate that Prp19 has a novel role in the initiation step of transcription in budding yeast.

overall_design: Global run-on (GRO)-seq profiling of wildtype W303 cells that have Prp19 tagged with the auxin-inducible degron (AID) treated with DMSO (control) and auxin (Prp19-depletion). The cells were treated with DMSO or auxin (500 uM) for 90 minutes.

first: Mary-Ann

last: Essak

first: Ahlam

last: Awada

first: Zuzer

last: Dhoondia

first: Athar

last: Ansari


title: A genome-wide DNA methylation survey reveals salicylic acid-induced distinct hypomethylation linked to defense responses against biotrophic pathogens

city: Kifissia

first: Theoni

last: Margaritopoulou

state: Attiki

address: Stefanou Delta 8

department: Phytopathology

country: Greece

institute: Benaki Phytopathological Institute

type: Methylation profiling by high throughput sequencing

summary: DNA methylation is a conserved regulatory mechanism of gene expression, genome stability, and development, and highly associated with effective induction of defense responses for plant priming. In the Green Deal era, the use of plant defense inducers (PDIs), compounds that activate defense and prime plants against imminent pathogen attacks, is a safe and environmentally sustainable approach to support plants against pathogens. Even though efforts have deciphered part of PDIs mode of action, more information is needed to understand the underlying pathways of their effectiveness. Here, salicylic acid (SA) loaded in chitosan nanoparticles, increased hypomethylation more than 25% on 56 genomic regions that corresponded to defense-related genes, such as pectin lyases, defensins and leucine-rich repeat transmembrane protein kinases against the biotrophic fungal pathogen Podosphaera xanthii. A genomic region of the promoter of SKP1A, a core member of the SCF E3 ubiquitin ligase complex, was found to be a Differentially Methylated region (DMR) with 60% hypomethylation, both after PDI application and pathogen inoculation, possibly indicating a similar activation mechanism. Examination of this DMR revealed the presence of SA-, auxin-, and defense-related cis-elements. Investigation of proteins associated with the above cis-elements showed significant upregulation in expression after PDI. Moreover, association of the identified DMR with transcriptomics showed enrichment of the SA pathway. Overall, these findings shed light on the epigenetic mechanisms that underlie SA- related defense priming in plants

overall_design: All sequencing experiments were performed at Biomedical Research Foundation Academy of Athens on an Illumina NovaSeq 6000 sequencing system. Libraries were sequenced with 2 × 150 bp paired end reads at 30× coverage. According to NIH Roadmap Epigenomics Project the use of two biological replicates with a combined total coverage of 30× in sufficient for unbiased genome-wide DNA methylation profiling.

first: Spyros

last: Foutadakis

first: Giannis

last: Vatsellas

first: Martina

last: Samiotaki

first: Emilia

last: Markellou


title: Age-stratified transcriptomic profiling reveals biologically distinct molecular phenotypes across pediatric, adolescent, and adult osteosarcoma

city: Beijing

first: Jichuan

last: Wang

address: No. 11 Xizhimen South St.

institute: Peking University People's Hospital

summary: Osteosarcoma exhibits a bimodal age distribution with distinct clinical behaviors between pediatric and adult patients. In this study, bulk RNA sequencing was performed on tumor specimens from 70 osteosarcoma patients stratified into pediatric (14 years and younger), adolescent (15 to 18 years), and adult (19 years and older) groups. Differential expression, functional enrichment, and immune infiltration analyses were conducted to characterize age-associated transcriptional differences. Pediatric tumors exhibited a hyperproliferative phenotype, adolescent tumors showed enhanced immune-related signatures, and adult tumors displayed activation of osteogenic differentiation programs. A characteristic pediatric-specific gene signature was further identified, providing insights into age-related molecular heterogeneity in osteosarcoma.

overall_design:
Tumor specimens from 70 osteosarcoma patients were analyzed by bulk RNA sequencing to investigate age-associated transcriptional differences among pediatric, adolescent, and adult groups.

***************************************************************
Due to limitations in data archiving and long-term storage, the raw sequencing data are currently unavailable.
***************************************************************

first: Li

last: Hu

first: Feiyang

last: Qi

first: Huimin

last: Liu


title: Corilagin Induces Pyroptosis in AML Cells by Activating the TXNIP-Caspase-3-GSDME Pathway

city: Guangzhou

first: hui

last: zeng

address: 106 Zhongshan 2nd Rd

institute: Guangdong Provincial People's Hospital

summary: Acute myeloid leukemia (AML) is a challenging hematological malignancy characterized by high relapse rates and limited treatment options. Compound corilagin, an ellagitannin derived from ethnopharmacological plants, shows promise as an anti-cancer agent, although its anti-leukemic effects remain poorly understood. This study aims to investigate whether corilagin induces cell death in AML cells and explore the underlying mechanisms. In AML cells, corilagin induces pyroptosis, as characterized by the formation of pyroptotic bubbles, increased lactate dehydrogenase (LDH) release and a higher proportion of propidium iodide (PI)-positive cells. Corilagin activates caspase-3, which in turn cleaves gasdermin E (GSDME) to generate GSDME-NT, promoting pyroptosis. Additionally, corilagin activates thioredoxin-interacting protein (TXNIP), and the knockdown of TXNIP rescues cells from corilagin-induced pyroptosis. Corilagin reduces cell viability and induces pyroptosis in primary AML cells, and in an AML cell-derived xenograft (CDX) mouse model, it inhibits leukemia progression and prolongs survival. These findings imply that corilagin induces pyroptosis in AML through the TXNIP/caspase-3/GSDME pathway, presenting a prospective novel therapeutic strategy for AML treatment.

overall_design: RNA-Seq analysis was performed on MV411 cells treated with DMSO and Corilagin for 48 hours.

first: Ganlu

last: Feng

first: Hui

last: Zeng

first: Juan

last: Du

first: Ying


title: Effects of NF2 deletion on gene expression in pancreatic cancer spheroids [sgLUC_sgNF2_RNASeq]

first: Mohamad

last: Assi

summary: In this study, we investigate the role of NF2 in regulating autophagy flux in pancreatic cancer spheroids.

overall_design: NF2 gene was deleted using CRISPR/Cas9 in PATU8902 cells, which were then cultured in 3D-Matrigel as spheroids, prior to RNA extraction and sequencing. A sgRNA against Luciferase (sgLUC) is used as a control condition.

first: Alec

last: Kimmelman


title: R-loop-induced DNA replication defects drive neuropathy in Koolen-de Vries syndrome

status: Public on Feb 10 2026

city: Utrecht

first: Jeroen

last: van den Berg

state: Utrecht

address: Uppsalalaan 8

institute: Hubrecht Institute

summary: Koolen-de Vries syndrome (KdVS) is a neurodevelopmental disorder caused by KANSL1 haploinsufficiency. KANSL1 encodes a scaffold protein of the non-specific lethal (NSL) complex, which regulates transcription of constitutively expressed genes via acetylation of H4K5 and H4K8 around transcription start sites (TSS). How loss of KANSL1/NSL contributes to the neurodevelopmental defects in KdVS is unknown. Here, we find that KANSL1/NSL prevents the accumulation of R-loops (three-stranded DNA-RNA hybrid structures) at transcription start sites (TSSs) with low basal transcription and H4K5/H4K8 acetylation, where R-loops are typically not detected. If not suppressed, these R-loops delay DNA replication in early S-phase by stalling of the replisome. KdVS neural organoids also suffered from perturbed DNA replication concomitantly with neurodevelopmental defects, while KdVS neuronal cells showed reduced synaptic activity in a manner-dependent on R-loop accumulation. Our study offers insights into how KANSL1/NSL controls R-loop homeostasis to ensure faithful DNA replication during neuronal development, preventing neuropathy in KdVS patients.

overall_design: U2OS WT cells treated with siLuciferase, siKANSL1 and siKANSL3 to a double pulse of EdU (10uM for 15 min, 60 minutes washout  and 10uM for 15 min,). Next, cells were sorted in 384 well plates and subjected to scEdU-seq (van den Berg et al., 2024) . SOX2+ WT or KANSL+/- organoids were subjected to a single pulse of EdU (10uM for 20 min).  Next, cells were sorted in 384 well plates and subjected to scEdU-seq (van den Berg et al., 2024) .

first: Jolanthe

last: Lingeman

first: Haico

last: van Attikum