title: Largazole targets Musashi protein expression via miR-125b-5p and sensitizes triple-negative breast cancer cells to irradiation

city: Münster

first: Lasse

last: Reichstein

state: NRW

address: Robert-Koch-Straße 31

department: Department of Radiation Oncology

institute: Münster University Hospital

summary: Background: Recent findings implicate the histone deacetylase (HDAC) inhibitor largazole as an inhibitor of Musashi RNA-binding protein function. Here, we assess this interplay and evaluate the relevance of largazole for triple-negative breast cancer (TNBC) progression and resistance to radiotherapy. Methods: Primary patient-derived TNBC cells and cell lines were treated with largazole and cell vitality, proliferation, motility, cell cycle, DNA synthesis as well as repair, and stemness were analyzed via MTT assay, digital holographic microscopy, and flow cytometry. To unravel the connection between largazole treatment and Musashi expression, miR-125b-5p was assessed after largazole treatment and overexpressed in wildtype cells to determine influence on Musashi levels. Targeted mRNA and protein expression analyses were complemented with RNA sequencing data after largazole treatment. Finally, DNA double strand breaks and post-radiogenic survival were quantified using γ-H2AX and clonogenic assays. Results: Largazole showed cytotoxic effects in TNBC, but not in non-malignant cultures. Largazole treatment strongly abrogated proliferation, DNA synthesis, cell motility, and induced a cell cycle arrest. Levels of the Musashi proteins were downregulated after largazole treatment via upregulation of the miR-125b-5p. Protein expression and RNA sequencing analysis indicated a loss of cancer stemness-, cell cycle progression-, and DNA repair-associated signaling. Consequently, radiotherapy-induced DNA double strand breaks were increased while post-radiogenic cell survival was decreased in largazole-treated samples. Conclusions: The HDAC inhibitor largazole compromises tumor growth and motility and downregulates the Musashi proteins via the miR-125b-5p in TNBC. Additionally, largazole acts as a radiosensitizer by attenuating DNA repair, therefore supporting therapeutic efficacy.

overall_design: RNA-seq profiling of the primary human breast cancer cell culture UIVC-IDC-4 cells after treatment with 20nM Largazole or DMSO for 24 hours

first: Kathrin

last: Brücksken

first: Lea

last: Lappe

first: Qi-Yin

last: Chen

first: Hendrik

last: Luesch

first: Eberhard

last: Korsching

first: Anne

last: Marzi

first: Nancy

last: Espinoza-Sánchez

first: Timo

last: Habig

first: Ezequiel

last: Fuentes-Pananá

first: Björn

last: Kemper

first: Joke

last: Tio

first: Martin

last: Götte

first: Hans Theodor

last: Eich

first: Burkhard

last: Greve

first: Fabian

last: Troschel


title: The McbR transcription factor links intracellular folate pool to virulence in enteric pathogens

status: Public on May 26 2026

city: Madison

first: Quentin

last: Perraud

state: Wisconsin

address: 1550 Linden Drive

department: Medical microbiology and immunology

country: USA

institute: University of Wisconsin-Madison

type: Expression profiling by high throughput sequencing

summary: Bacterial pathogens must coordinate the expression of metabolically expensive virulence programs during host colonization. While the impact of environmental cues on virulence has been extensively studied, direct sensing of metabolic intermediates to inform virulence expressions is less understood. Sudden competition with the resident microbiota in the case of an infection is guaranteed to have a massive impact on the bacteria’s central metabolism, which may be used as a cue for the expression of virulence factors. Here, we identify how fluctuations in the intracellular folate pool can affect expression of virulence factor in enterohemorrhagic E. coli (EHEC). Using transcriptomics, mutagenesis, and ligand-binding assays, we demonstrate that EHEC’s type III secretion system is repressed when the bacteria’s folate biosynthetic pathway is pharmacologically disrupted, and that this effect is mediated by two regulatory proteins: PurR and McbR. Additionally, we identify dihydrofolate as a ligand of the previously orphaned McbR transcription regulator.

overall_design: RNAseq profiling of enterohemorrhagic Escherichia coli treated with DMSO (vehicle), sulfapyridine, sulfapyridine+5-aminosalicylique acid or sulfasalazine (5µM)

first: Vanessa

last: Sperandio


title: Integration of Alzheimer’s GWAS, 3D genomics, and single-cell CRISPRi non-coding screen implicates causal variants in a microglial enhancer regulating TSPAN14. [RNA-Seq]

city: Philadelphia

first: Alessandra

last: Chesi

address: 422 Curie Blvd

institute: University of Pennsylvania

summary: While GWAS have been successful in providing variant-to-trait associations for human complex diseases, functional dissection of the discovered loci has lagged behind. Here, we describe a variant-to-gene (V2G) mapping effort for Alzheimer’s disease (AD) to implicate causal variants and effector genes from the most recent AD GWAS meta-analyses (101 loci). We leveraged our genomics datasets comprising high-resolution promoter Capture C, ATAC-seq, and RNA-seq from brain-relevant cell types to fine-map AD GWAS variants, identifying 89 candidate causal SNPs and 69 effector genes. We then designed a single-cell CRISPRi screen to perturb candidate regulatory regions (n=74) and assess the transcriptional response in the human microglial cell line, HMC3. Our screen across ~97,000 cells identified 19 regulatory regions and 19 effector genes. We then elected to functionally dissect our top hit, the TSPAN14 locus, and we show that an intronic region containing AD-associated SNPs rs7080009, rs1870138, and rs1870137 is a microglia-specific enhancer, with the AD risk haplotype increasing its activity. CRISPR precise genomic deletion of this region decreases TSPAN14 expression, alters specific cellular pathways including cell adhesion, and decreases secreted levels of pro-inflammatory cytokines IL-6 and IL-8, which are known biomarkers of aging and AD. Our work provides a systematic framework to map GWAS signals to their effector genes for AD and other brain-related disorders, and provides robust leads to follow up with in-depth functional investigations.

overall_design: Lentiviral CRISPR-Cas9 with one sgRNA targeting the 5' end and one sgRNA targeting the 3' end was utilized to induce a ~800bp deletion containing the candidate AD risk SNPs rs7080009, rs1870138, and rs1870137 in HMC3 cells, and single cell clones were isolated by FACS. Two clones harboring homozygous deletions (Clone1 and Clone2), three control clones harboring non-targeting sgRNAs (NTC1, NTC2, NTC3) and one clone harboring the empty vector (EV) were subjected to bulk transcritomic analysis (RNA-seq). HMC3 cells were cultured using standard culture conditions.

first: Natalia

last: Tulina


title: Integration of Alzheimer’s GWAS, 3D genomics, and single-cell CRISPRi non-coding screen implicates causal variants in a microglial enhancer regulating TSPAN14. [scRNA-Seq]

overall_design: A human microglial cell line (HMC3) constitutively expressing CRISPRi (KRAB-dCas9) was transduced at low MOI with a pooled library of 269 sgRNAs. This library included guides targeting 76 non-coding candidate regulatory regions, the transcription start sites of 7 genes as positive controls, and 23 non-targeting guides as negative controls. Following transduction, successfully transduced cells were selected for by puromycin treatment and subsequently sorted for BFP expression via FACS. Twelve days post-transduction, cells were submitted for sequencing.

first: Shannon

last: Laub


title: MSC-dependent intercellular communication: an interactome for skeletal muscle homeostasis and regeneration

city: Manhattan

first: Xingyu

last: Liu

address: 433 first avenue

institute: NYU Langone Health

summary: Mesenchymal stromal cells (MSCs) support tissue homeostasis and regeneration, yet their molecular signals remain largely enigmatic. In skeletal muscle (SkM), MSCs, known as fibroadipogenic progenitors (FAPs), are essential for maintenance and repair, orchestrating these processes through intricate cellular communication networks. Given the critical role of SkM in lifelong health and longevity, FAP signaling has drawn significant interest as a potential therapeutic target and a model for MSC interactions. However, deciphering FAP-derived regulatory signals remains challenging due to their pleiotropic complexity. Here, we employ a systems-level approach to construct a comprehensive FAP interactome in both homeostatic and regenerating SkM. By integrating unique single-cell RNA sequencing atlases with advanced computational analyses, we identify putative FAP-mediated signaling pathways and validate their biological relevance through FAP depletion experiments, assessing disruptions in key pathways. This approach reveals novel signaling networks across diverse SkM cell populations, corroborates key FAP interactions from recent studies, and provides a valuable dataset for modeling MSC interactions and their roles in SkM homeostasis and regeneration.

overall_design: Transgenic mice - referred to as depleted were PDGFRɑCreER/+; R26DTA/NG or R26DTA/+ and controls were littermates that did not carry both the CreER and DTA. - were administered tamoxifen. Following tamoxifen dosing and a subsequent chase period, hindlimb skeletal muscle was collected from uninjured samples, or lower hindlimb muscle was injected with a 1.2% BaCl₂ solution and isolated 3 days post injury (dpi) for injured samples. Cells were isolated by FACS with propidium iodide for live cell selection and these cell suspensions were delivered to our genomics core (Stanford) and processed for 10X Chromium libraries and sequenced on an Illumina HiSeq 4000 sequencer.

first: Edgar

middle: E

last: Perez Carbajal

first: Benjamin

middle: W

last: Gilman

first: Yih-Chii

last: Hwang

first: Christapher

middle: S

last: Morrissey

first: Michael

middle: N

last: Wosczyna


title: Integrative Molecular Analyses of Inflammatory and Autoimmune Signals in Cardiac Sarcoidosis [Xenium]

status: Public on May 25 2026

city: Boston

first: Meraj

last: Neyazi

address: 77 Avenue Louis Pasteur

department: Genetics

institute: Harvard University

summary: Background: Cardiac sarcoidosis (CS) is an enigmatic disorder characterized by unexplained patchy, sterile granulomas intermixed with preserved myocardium, and fibrotic regions without granuloma, that causes arrhythmias, sudden cardiac death, and heart failure. The mechanisms producing this remarkable histopathology and disease progression remains unexplained.     Methods:  Using comprehensive single cell and spatial transcriptomic analyses, we characterized the cellular composition and gene expression in preserved, granulomatous, and fibrotic regions of human CS hearts. From the identification of clonally expanded cardiac B cells with rearranged immunoglobulin sequences, we reconstructed antibodies and screened libraries containing the human peptidome or microbial and allergen peptides to define reactive epitopes in CS heart.     Results: Ventricular regions with preserved, granulomatous, or fibrotic histopathology exhibited marked differences in cell composition and gene expression. Cardiomyocytes upregulated arrhythmogenic and inflammasome transcripts that would drive pyroptosis, and along with fibroblasts, activated chemoattractant cytokines that sustained myeloid and lymphoid infiltration. Within granulomas, abundant macrophages expressed modulators of cell-cell fusion and with Th17-skewed T cells upregulated B cell activating factor. Fibrotic regions, without active granulomas, exhibited tertiary lymphoid structures, with clonal expansion of mature B and plasma cells. Reconstructed antibodies derived from expanded B cell clones were inert to microbial and allergen peptides, but strongly reacted to periplakin, a desmosome protein, defining a target autoantigen.     Conclusions: CS is an inflammatory, autoimmune disorder that activates proarrhythmic and chemoattractant genes in cardiomyocytes within preserved myocardium, cell-cell fusion modulators in macrophages within granulomatous regions, and tertiary lymphoid structures in fibrotic regions that produce autoimmune antibodies. The identification of a target desmosome epitope, periplakin, links CS to arrhythmic desmosome cardiomyopathies, disorders with shared clinical manifestations. The centrality of humoral autoimmunity in perpetuating CS provides specific therapeutic opportunities to limit granuloma formation and B-cell activation. Parallel analytic strategies have potential to define autoantigens in other enigmatic cardiac immune disorders.

overall_design: Spatial transcriptomics on human cardiac tissues using the 10x genomics xenium platform.

first: Gabriela

last: Venturini

first: Kemar

middle: J

last: Brown

first: Youjung

last: Choi

first: Joshua

middle: M

last: Gorham

first: Olivia

middle: G

last: Layton

first: Arjun

last: Verma

first: Adam

last: Wang

first: Ryan

middle: T

last: Gross

first: Barbara

middle: A

last: McDonough

first: Michelle

last: Mendiola Pla

first: Anissa

last: Viveiros

first: Daniel

last: DeLaughter

first: Steven

middle: R

last: DePalma

first: Yuri

last: Kim

last: Reichart

first: Hiroko

last: Wakimoto

first: Stephen

last: Elledge

first: Sanjay

last: Divakaran

first: Richard

last: Mitchell

first: Jiwon

last: Koh

first: Jun-Bean

last: Park

first: Dawn

last: Bowles

first: Carolyn

last: Glass

first: Gavin

middle: Y

last: Oudit

first: Jonathan

last: Seidman

first: Christine


title: Paired transcriptomics reveals similarities between cytokine-stimulated organoids and ulcerative colitis epithelial responses

city: Trondheim

first: Arun

last: Sridhar

address: Prinsesse Kristinas gate 3

department: IKOM

country: Norway

institute: Norwegian University of Science and Technology

summary: The intestinal epithelium mediates critical crosstalk between microbiota and immune cells in inflammatory bowel disease. While patient-derived intestinal organoids offer potential for modeling ulcerative colitis, their ability to replicate in vivo inflammation and utility for precision medicine remain unclear. By comparing transcriptomic profiles from microdissected colonic epithelium of ulcerative colitis patients with paired patient-derived organoids under various inflammatory conditions, we demonstrated that organoids established from uninflamed biopsies can effectively model epithelial inflammation. Combined IFNγ and TNF stimulation or a cocktail of pro- and anti-inflammatory signals induced inflammatory signatures matching in vivo ulcerative colitis patterns, including upregulation of interferon signaling, antigen presentation, and unfolded protein response pathways. Strong correlations between in vivo and in vitro expression of over 200 disease-relevant genes validate intestinal organoids as a suitable preclinical model. These findings substantiate intestinal epithelial organoids’ value for investigating ulcerative colitis pathogenesis and developing personalized medicine approaches.

overall_design:
Paired laser capture microdissected uninflamed (n=10) and inflamed (n=12) colonic epithelial compartments from UC patients with active disease

***************************************************************
Raw files for human/patient samples were not submitted to GEO due to concerns about submitting personally identifiable sequence data for open access.
***************************************************************

first: Gunnar

last: Walaas

first: Lusie

middle: F

last: Kuraas

first: Siri

last: Sæterstad

first: Atle

middle: v

last: Granlund

first: Arne

middle: K

last: Sandvik

first: Ann

last: Østvik

first: Ingunn

last: Bakke

first: Torunn

last: Bruland


title: Mechanisms of Zika Virus Lineage-Dependent Pathogenesis Defined in Cerebral Organoids Derived from Human Embryonic Stem Cells

city: Cambridge

first: Yann

last: Vanrobaeys

state: MA

address: 500 Main Street, Building 76

institute: Massachusetts Institute of Technology

summary: Zika viruses (ZIKV) have pandemic potential, with infections that cause serious human diseases, including microcephaly and Guillain-Barre syndrome. The pathogenesis properties of ZIKV lineages vary widely, and defining the underlying mechanisms has been complicated by the use of different cell-based and animal models to test ZIKV infections.  The goal of this work was to define differential pathogenesis mechanisms among mild and severe ZIKV infections through comparative infections, using a relevant human stem cell-derived cerebral organoid experimental model system. ZIKV RNA does not persist in organoid ventricle cells during mild Asian/American lineage ZIKV infections; however, viral RNA persisted in ventricle cells during severe African lineage infections. The data suggest that mild and severe ZIKV lineages are differentiated in pathogenesis by host antiviral, interferon, and stress responses that cause apoptosis and oxidative stress. Stress-related hydroxyl radical damage to the organoids was partially blocked by Trolox, a hydroxyl radical scavenger drug, suggesting potential therapeutic benefit.

overall_design: We performed bulk RNA sequencing obtained from cerebral organoid derived from human embryonic stem cells 7 days after infection from three Zika virus lineages: African (Uganda), Asian (Malaysia) and American (Puerto Rico). We performed single-cell RNA sequencing obtained from from from cerebral organoid derived from human embryonic stem cells 7 days after infection from three Zika virus lineages: African (Uganda), Asian (Malaysia) and American (Puerto Rico).

first: Alfred

last: Harding

first: Yichen

last: Zhang

first: Jane-Jane

last: Chen

first: Jenna

last: Antonucci

first: Alexsia

last: Richards

first: Valerie

last: Leger

first: Charlie

last: Whittaker

first: Divyansh

last: Agarwal

first: Tenzin

last: Lungjangwa

first: Rudolf

last: Jaenisch

first: Lee

last: Gehrke


title: Integrative Molecular Analyses of Inflammatory and Autoimmune Signals in Cardiac Sarcoidosis [snRNA-Seq]

status: Public on May 24 2026

first: Meraj

last: Neyazi

summary:
BACKGROUND:Cardiac sarcoidosis (CS) is an enigmatic disorder characterized by unexplained patchy, sterile granulomas intermixed with preserved myocardium and fibrotic regions without granuloma. CS causes arrhythmias, sudden cardiac death, and heart failure. The mechanisms producing this remarkable histopathology and disease progression remain unexplained.
METHODS:Using comprehensive single-cell and spatial transcriptomic analyses, we characterized the cellular composition and gene expression in preserved, granulomatous, and fibrotic regions of human CS hearts. From unexpectedly identified clonally expanded cardiac B cells with rearranged immunoglobulin sequences, we reconstructed antibodies and screened libraries comprising the human peptidome or microbial and allergen peptides to define reactive epitopes in CS hearts.
RESULTS:Cellular composition and gene expression differed substantially in CS tissues with preserved, granulomatous, or fibrotic histopathology. Cardiomyocytes upregulated arrhythmogenic and inflammasome transcripts associated with pyroptosis. Cardiomyocytes and fibroblasts activated chemoattractant cytokines that sustained myeloid and lymphoid infiltration. Granulomas contained abundant macrophages expressing modulators of cell–cell fusion, along with Th17-skewed T cells that upregulated B-cell–activating factor, thereby promoting antibody production. Fibrotic regions, without active granulomas, exhibited tertiary lymphoid structures, with clonal expansion of mature B and plasma cells. Reconstructed antibodies derived from expanded B-cell clones were inert to microbial and allergen peptides, but reacted to PPL (periplakin), a desmosome protein, and other peptides expressed on cardiac cells.
CONCLUSIONS:Progressive inflammatory signals in CS are mediated by chemoattractant genes in cardiomyocytes and fibroblasts within preserved myocardium, cell–cell fusion modulators in activated macrophages within granulomatous regions, and tertiary lymphoid structures in fibrotic regions that produce patient-specific autoimmune antibodies. Identification of PPL as a CS autoantigen may account for shared clinical manifestations in CS and arrhythmic desmosomal cardiomyopathies. CS autoantigens may underlie enigmatic histopathologic findings, perpetuate disease, and contribute to adverse outcomes. Uncovering an intracardiac humoral autoimmune axis in CS provides specific therapeutic opportunities to limit granuloma formation and B-cell activation, which may reduce arrhythmogenicity and progressive dysfunction. Parallel analytic strategies have potential to define autoantigens in other enigmatic cardiac immune disorders.

overall_design:
Nuclei were extracted from human cardiac tissues of CS patients and snRNA-seq libraries were prepared using the 10x Genomics platform.
Human cardiac tissue samples were fixed, paraffin-embedded, and processed using the Xenium platform from 10x Genomics.

first: Gabriela

last: Venturini

first: Kemar

last: Brown

first: Youjung

last: Choi

first: Joshua

last: Gorham

first: Olivia

last: Layton

first: Arjun

last: Verma

first: Adam

last: Wang

first: Ryan

last: Gross

first: Barbara

last: McDonough

first: Michelle

last: Mendiola Pla

first: Anissa

last: Viveiros

first: Daniel

last: DeLaughter

first: Steven

last: DePalma

first: Yuri

last: Kim

last: Reichart

first: Hiroko

last: Wakimoto

first: Stephen

last: Elledge

first: Sanjay

last: Divakaran

first: Richard

last: Mitchell

first: Jiwon

last: Koh

first: Jun-Bean

last: Park

first: Dawn

last: Bowles

first: Carolyn

last: Glass

first: Gavin

last: Oudit

first: Jonathan

last: Seidman

first: Christine


title: Nr2f1a and Isl1 repress acquisition of epicardial identity in venous atrial cardiomyocytes

status: Public on May 22 2026

city: Cincinnati

first: Joshua

last: Waxman

state: OH

address: 240 Albert Sabin Way

department: Molecular Cardiovascular Biology Division

institute: Cincinnati Children's Hospital Medical Center

summary: Regulatory networks that maintain cardiomyocyte identity are not completely understood. Here, we examined the relationship of the transcription factors (TFs) Nr2f1a and Isl1, which respectively repress and promote pacemaker cardiomyocyte (PC) differentiation within the venous pole of zebrafish atria. Using zebrafish nr2f1a;isl1 mutants, we found that loss of Isl1 exacerbates the inability to maintain atrial cardiomyocyte (AC) identity found in nr2f1a mutant hearts. Subsequently, while nr2f1a;isl1 mutants have a failure of PC differentiation and inability of ACs to transdifferentiate into PC identity, ACs in nr2f1a;isl1 mutant hearts lose myocardial marker expression, gain epicardial cell (EC) gene expression, and exit the myocardial layer. Single cell RNA-seq analysis of hearts supports that the ACs and ECs of nr2f1a;isl1 mutant embryos share common myocardial and EC transcriptomic signatures. Depletion of tcf21 and tbx18 in nr2f1a;isl1 mutants was sufficient to prevent the acquisition of EC identity within putatively transdifferentiating ACs. Thus, our results reveal reiterative requirements for Nr2f and Isl1 TFs in binary fate decisions within the genetic hierarchy that maintains distinct AC, PC, and EC identities at the venous pole of vertebrate hearts.

overall_design: Isolated hearts from wildtype, nr2f1a mutant, isl1 mutant, and nr2f1a;isl1 mutant zebrafish embryos at 96 hours were analyzed using scRNA-seq.

first: Kendall

last: Martin

first: Andrew

last: Fernandes

first: Mohammed

last: Sayed

first: Margaret

last: Hanlon

first: Samuel

last: Fallon

first: Hee-Woong

last: Lim


title: RNA-seq profiling of osteosarcoma and healthy bone samples from a Central Mexican cohort

status: Public on Aug 05 2026

city: México city

first: Rogelio Frank

last: Jiménez-Ortega

state: Alcaldía Tlalpan

address: Calzada México-Xochimilco No. 289

department: Subdirección de investigación Biomédica

country: Mexico

institute: Instituto Nacional de Rehabilitación

summary: This bulk RNA-seq dataset contains transcriptomic profiles from osteosarcoma tumor samples and healthy bone reference samples from a Central Mexican cohort. Gene-level raw count and TPM-normalized expression matrices were generated from paired-end RNA-seq reads processed through a standardized quality-control, alignment, and quantification workflow. The dataset supports analyses of differential gene expression and molecular pathways involved in osteosarcoma biology, bone remodeling, extracellular matrix organization, immune regulation, and osteo-immune programs.

overall_design: Fourteen bulk RNA-seq libraries were analyzed: seven osteosarcoma tumor samples and seven healthy bone reference samples. Paired-end FASTQ files were quality-controlled, trimmed, aligned to the human GRCh38 reference genome, quantified at gene level, normalized, and analyzed for differential gene expression. The processed matrices submitted with this dataset are a gene-level raw count matrix and a gene-level TPM-normalized matrix.

first: Rogelio

last: Jimenez-Ortega

first: Alberto

last: Hidalgo-Bravo


title: Characterization of 3′UTRCES-mediated alternative polyadenylation (APA) engineering in prostate cancer and 293FT cells

city: Durham

first: Qianben

last: Wang

address: 905 S. Lasalle Street

institute: Duke University

summary: To determine SPSB1 3′UTR alternative polyadenylation (APA) usage following 3′UTRCES-mediated editing in prostate cancer cells, and to evaluate global gene expression changes and potential off-target effects of the 3′UTRCES system in 293FT cells.

overall_design: Total RNA was extracted from LNCaP-abl cells following transfection with 3′UTRCES-SPSB1-g5 or g6 or a non-targeting control gRNA for 12h. QuantSeq 3′mRNA-Seq libraries were prepared using the Lexogen QuantSeq 3′mRNA-Seq kit REV V2 according to the manufacturer’s instructions. To assess potential off-target effects of 3'UTRCES system, 293FT cells were co-transfected with dCas13b plasmid together with gCtrl, SPSB1-g5, or SPSB1-g6 plasmids at a 2:1 ratio. After 24 h, cells were further transfected with the SPSB1-pSTUB plasmid harboring the proximal polyadenylation site (pPAS) of the SPSB1 gene for an additional 24 h. RNA-seq was then performed to characterize differential gene expression and polyadenylation site (PAS) usage between gCtrl and SPSB1-g5 or SPSB1-g6 transfected groups.

first: Furong

last: Huang

first: Kexin

last: Li

first: Fuwen

last: Yuan

first: Ya

last: Cui

first: Wenbin

last: Ye


title: Matched  sampling reveals uncoupled phenotypic plasticity during metastasis formation in uveal melanoma

city: Essen

first: Karim

last: Al-Ghazzawi

address: Hufelandstraße 55

department: Ophthalmology

country: Germany

institute: University-Clinic Duisburg-Essen

summary: Uveal melanoma (UM) is a genetically well-defined yet phenotypically diverse malignancy with a strong predilection for liver metastasis. While genetic and epigenetic evolution has been studied using primary or metastatic tumors, the transcriptomic relationship between matched pairs remains poorly understood. We performed comprehensive gene expression profiling of paired primary (pUM) and metastatic (mUM) samples to define phenotypic divergence during progression. Two principal molecular subtypes were identified in both entities; however, matched pUM–mUM pairs showed little transcriptional concordance, indicating extensive reprogramming during metastasis. Approximately half of pUM samples exhibited a proliferative, MAPK/PI3K-driven phenotype, suggesting heterogeneous dependency on PKC signaling. Immune subtypes also diverged between sites, with pUM dominated by adaptive immune responses, whereas mUM displayed innate immune signaling and macrophage-driven immunosuppression. The inflammatory pUM-A subtype was associated with poor survival, consistent with TCGA data linking chromosomal aberrations such as monosomy 3 to progression.

overall_design: RNA seq of FFPE tissue tumor area from 23 Tumor samples. Primary tumors included 13 enucleated uveal melanomas without any prior therapy, as well as 10 samples from metastatic sites from patients with matched evaluable primary tumors.

first: K

first: F

last: Mairinger

first: H

last: Kalkavan


title: Transcriptional regulation of APE1-redox Axis in Esophageal adenocarcinoma

city: Miami

first: Wael

last: El-Rifai

state: FL

address: Griffin Cancer Research Building,1425 NW 10th Ave

department: Department of Surgery and Sylvester Comprehensive Cancer Center

institute: University of Miami Miller School of Medicine

summary: Apurinic/apyrimidinic endonuclease 1 (APE1/Ref-1) plays an essential role in ROS-sensitive transcriptional regulation in esophageal adenocarcinoma (EAC). While the redox function of APE1 is known to modulate the activity of multiple transcription factors, its global downstream targets in EAC remain to be fully characterized. This study investigates APE1-redox-dependent transcriptional regulation by targeting OE33 cells with the APE1-redox-specific inhibitor, APX2009, to map the underlying gene expression networks.

overall_design: This study investigates the downstream transcriptional network and homeostatic mechanisms regulated by the redox signaling function of APE1. Human EAC cells (OE33) were treated APE1 redox-specific small-molecule inhibitor APX2009 (15 µM) for 24 hours. Untreated cells work as control. To determine how APE1-mediated redox function modulates transcript stability and downstream effector expression, total RNA was extracted from three independent biological replicates for each experimental group.

first: Heng

last: Lu


title: Genome-wide DNA methylation profiling of DNMT3A-knockout SW620 colorectal cancer cells.

city: Wuhan

first: jianhong

last: zhao

state: Hubei

address: Donghu Road, No. 115

country: China

institute: Wuhan University

type: Methylation profiling by genome tiling array

summary: DNA methyltransferase 3A (DNMT3A) contributes to tumor immune evasion by regulating TNF signaling and cholesterol biosynthesis in colorectal cancer cells. To characterize DNMT3A-dependent changes in the DNA methylation landscape, genome-wide DNA methylation profiling was performed in control and DNMT3A-knockdown SW620 colorectal cancer cells using the Infinium MethylationEPIC BeadChip array. Comparative analysis identified 14,390 differentially methylated regions, of which 12,059 were annotated to known genes. These methylation alterations were predominantly localized to promoter-associated regions, including TSS1500, TSS200, and 5′ untranslated regions. DNMT3A loss reduced promoter methylation at genes involved in TNFα- and IFNγ-related signaling pathways, including TNFRSF1A and TNFRSF1B. These data define the DNMT3A-dependent DNA methylation landscape in SW620 cells and support a role for DNMT3A-mediated promoter methylation in the transcriptional regulation of tumor immune signaling pathways.

overall_design: Genome-wide DNA methylation profiles were compared between control shCtrl and shDNMT3A SW620 colorectal cancer cells. Two independent biological replicates were analyzed per group using the Infinium MethylationEPIC BeadChip array. DNA methylation levels were quantified as β-values, and differentially methylated probes or regions were identified using an adjusted P value < 0.05 and an absolute methylation difference |Δβ| > 0.10.

first: Jianhong

last: Zhao

first: Yanrong

last: Deng

first: Haonan

last: Chen

first: Xiaojun

last: Zhou

first: Siyuan

last: Yin

first: Qun

last: Qian

first: Xiaoyu

last: Xie

first: Quanjiao

first: Jinfang

last: Zhang

first: Lifang

last: Fan

first: Xianghai

last: Ren

first: Baoxiang

first: Congqing

last: Jiang


title: Covalent inhibitors of human papillomavirus type 16 E6 protein restore p53 function and suppress growth of HPV-driven tumors in vivo

city: Indianapolis

first: Anne

last: Rietz

address: 980 W Walnut St RM C636

institute: Indiana University

summary: High-risk human papillomavirus (HPV) infections are the etiology of approximately 5% of all cancers worldwide, including cervical, anal, and oropharyngeal malignancies. HPV E6 is a multifunctional oncoprotein that drives tumorigenesis and is best known for bridging the ubiquitin ligase E6AP (UBE3A) and p53 into a complex that leads to proteasome mediated destruction of p53. We developed small molecule inhibitors that covalently bind to cysteine-51 (Cys-51) in HPV16 E6. In HPV16-positive cancer cells, these compounds increase p53 protein levels and activate p53-dependent transcriptional programs associated with apoptosis and senescence, resulting in reduced tumor cell viability. In vivo, E6 inhibition suppresses the growth of human HPV16 expressing cervical and oropharyngeal tumor cell lines in mice. The strategy of targeting a viral oncoprotein with a covalent inhibitor demonstrates a genotype-specific therapeutic strategy for HPV-associated cancers and premalignant infections, addressing a significant unmet need in current treatment options.

overall_design: SiHa, SiHa C51S, and RPE-1 cells were cultured in 5 µM KTI-240 or DMSO for 16 hours. Total RNA from each of the 18 samples was isolated from cultures harvested from three independent experiments.

first: Lokesh

last: Kumari

first: Ankeeta

last: Koirala

first: Stephane

last: Pelletier

first: Zhijian

first: Elliot

last: Androphy


title: A pan-cancer immune and genomic feature-based classification of tumor microenvironment and resistance to immunotherapy

city: GUANGZHOU

first: Han

last: ZhiRen

state: GUANGDONG

address: 107 Yan Jiang West Road

institute: Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University

summary: The tumor microenvironment (TME) profoundly influences responses to immune  checkpoint blockade (ICB) therapies, however characterizing its complexity has been  challenging. While the immune-inflamed, immune-excluded, and immune-desert T  cell immunophenotypes are commonly used to classify the TME, their association  with clinical outcomes to ICBs remains inconsistent. Here we demonstrated that  integrating T cell immunophenotypes and tumor mutational burden (TMB) enables a  more precise stratification of tumors into five distinct subtypes: immune-inflamed  phenotype with high TMB (TMB-H), immune-inflamed phenotype with low TMB  (TMB-L), TMB-H excluded phenotype, TMB-L excluded phenotype, and desert  phenotype. Subsequently, we revealed the underlying mechanisms of tumor resistance  to ICBs of each phenotype within the novel classification and elucidate several  combination treatment approaches aiming at overcoming these inherent resistance  mechanisms. Our study suggested that tailored combination therapy regimens  addressing distinct patterns of immune resistance in different TME subtypes hold  promise for enhancing immunotherapy efficacy

overall_design: The RNA-seq data included in this submission were generated from tumor tissue samples obtained from hospital patients undergoing surgical resection. The samples were collected immediately after surgery and processed into formalin-fixed paraffin-embedded (FFPE) pathological slides. RNA was subsequently extracted from these slides and subjected to RNA sequencing (RNA-seq) to investigate gene expression profiles. The study aims to explore the transcriptomic landscape of tumor tissues, with a focus on identifying differentially expressed genes and potential biomarkers associated with the disease.

first: Yiming

first: Pei

last: Wang

first: Zhiren

last: Han

first: Zixuan

last: Qiu

first: Hai

last: Hu

first: Man-Li

last: Luo


title: Mevalonate pathway activation in Ewing sarcoma reveals a 3D-specific synergy between statins and BCL-xL inhibition

status: Public on May 21 2026

city: Vienna

first: Florian

last: Halbritter

address: Zimmermannplatz 10

country: Austria

institute: St. Anna Children's Cancer Research Institute (CCRI)

summary: Bone sarcomas are rare and aggressive pediatric cancers with limited progress in targeted therapy development, partly due to the poor physiological relevance of conventional two-dimensional (2D) culture systems used for preclinical testing. To address this gap, we developed a standardized three-dimensional (3D) culture and drug-testing platform for Ewing sarcoma (ES) and osteosarcoma (OS) that more accurately recapitulates in vivo tumor biology. Notably, gene-expression analyses demonstrated that ES and OS spheroids transcriptionally converge toward patient tumor cell states, underscoring their physiological relevance for preclinical testing. Across 3D spheroids, bioprinted constructs, and patient-derived xenograft (PDX) cultures, we observed a consistent activation and dependency on the mevalonate pathway in ES. Leveraging this platform, we identified a selective therapeutic synergy between statins, which inhibit mevalonate pathway flux, and BCL-xL inhibitors—a vulnerability not detectable in 2D cultures. Importantly, this synergistic interaction was tumor-specific and absent in non-malignant fibroblasts, indicating a favorable therapeutic window. Together, these findings highlight the mevalonate pathway as a targetable metabolic dependency in ES and demonstrate how physiologically grounded 3D models can uncover clinically actionable treatment strategies that remain hidden in traditional 2D systems.

overall_design: Two sets of RNA-seq experiments comparing Ewing sarcoma and osteosarcoma cell lines in different 2D and 3D culture

first: Branka

last: Radic-Sarikas

first: Marica

last: Markovic

first: Martha

last: Zylka

first: Caterina

last: Sturtzel

first: Mathias

last: Ilg

first: Didier

last: Surdez

first: Martin

last: Metzelder

last: Distel

first: Aleksandr

last: Ovsianikov

first: Heinrich

last: Kovar


title: Rifampicin time-series of Nostoc sp. PCC 7120 under different nitrogen conditions

city: Freiburg im Breisgau

first: Manuel

last: Brenes-Álvarez

address: Schänzlestraße 1

department: Genetics and Experimental Bioinformatics

institute: University of Freiburg

summary: The ability of microbes to adapt to highly dynamic environments depends on subtle post-transcriptional regulatory mechanisms. The interaction between antisense RNAs or small non-coding RNAs and their mRNA targets can alter their half-life, thereby playing a role in the adaptation to different physiological conditions. Here, we have used rifampicin, an antibiotic that inhibits transcription initiation, to estimate the half-life of all transcripts in Nostoc sp. PCC 7120, a heterocyst-forming cyanobacterium. The analysis of the rifampicin time-series under two different growth conditions has revealed new layers of post-transcriptional regulation that may include transcriptional interference events (collisions between two elongating RNA polymerases).

overall_design: RNA-seq rifampicin time-series analysis for Nostoc sp. PCC 7120 cells in the presence of ammonia or subjected to nitrogen deficiency for 9 hours.

first: Isidro

last: Álvarez-Escribano

first: Jens

last: Georg

first: Agustín

last: Vioque

first: Alicia M.

last: Muro-Pastor


title: Transcriptome analysis of estrogen-related receptor (ERR) knockout in adult Drosophila females

city: Bloomington

first: Lesley

middle: Nicole

last: Weaver

state: IN

address: 1001 E. 3rd Street

department: Biology

summary: ERR is a conserved metabolic nuclear receptor required for energy metabolism. Here, we took an RNA sequencing approach to identify candidate ERR targets in adult Drosophila females. We found that loss of ERR downregulates enzymes associated with glycolysis and the pentose phosphate pathway, similar to what is observed in larvae and adult males.

overall_design: To determine differentially expressed expression of transcripts dependent on ERR, we conditionally knocked out ERR specifically in adult females and performed RNA sequencing 7 days after conditional knockout. We processed whole Drosophila females for RNA extraction and sequencing.


title: Cellular and Molecular Characterization of T cells in Malignant Pleural Effusions

city: New Haven

first: Benjamin

last: Lu

state: CT

address: 300 George Street

institute: Yale School of Medicine

summary: We are performing a comprehensive cellular and molecular characterization of malignant pleural effusions. This work includes single-cell RNA and T cell receptor (TCR) sequencing of T cells isolated from the blood, tumor, and malignant pleural effusion of patients with advanced cancer. Whole exome sequencing on tumor and normal tissue was also performed.

overall_design:
FACS sorted live, CD3+ T cells were sorted from synchronously collected a lung metastasis, malignant pleural effusion, and blood from a patient with metastatic cutaneous melanoma and analyzed by single-cell RNA and TCR sequencing.
Raw sequencing files correspond with dbGaP phs004859.v1.p1

***************************************************************
Raw files for human/patient samples are being made available in dbGaP (https://www.ncbi.nlm.nih.gov/gap/) for controlled access to the personally identifiable sequence data.
***************************************************************


title: Hyperbaric oxygen therapy protects against CTX‑induced ovarian injury by preserving the follicle pool and improving oocyte quality

city: Xi'an

first: Song

last: Yan

state: Shaanxi Province

address: Xinsi Road, Baqiao District, Xi’an City

department: Department of Gynecology and Obstetrics, Tangdu Hospital

institute: Air Force Medical University

summary: Background The ovaries hold a limited supply of primordial follicles that form the ovarian reserve. Chemotherapy with cyclophosphamide (CTX) quickly depletes this reserve, causing premature ovarian insufficiency (POI), infertility, and lasting hormonal problems. Current options for preserving fertility—such as freezing eggs, embryos, or ovarian tissue—must be done before chemotherapy starts, so they avoid damage rather than protecting the ovaries during treatment. These approaches have major drawbacks, and drugs like GnRH agonists have not shown consistent protective effects. Hyperbaric oxygen therapy (HBOT) is beneficial in many medical areas, but whether it can protect against chemotherapy induced ovarian injury and how it might work are still unknown. Methods We used female ICR mice exposed to CTX either chronically (150 mg/kg per week for 4 weeks) or acutely (a single 200 mg/kg injection). Some mice also received HBOT (100% oxygen at 2.5 atmospheres absolute). We measured ovarian reserve (follicle counts and anti Müllerian hormone), oocyte quality, granulosa cell apoptosis (TUNEL and cleaved caspase 3), ovarian fibrosis (Masson’s trichrome and α SMA), and transcriptomic profiles. Results HBOT prevented CTX from depleting primordial follicles by stopping them from entering the growing pool too quickly, bringing follicle numbers back to nearly normal levels. It also improved oocyte quality in both models: in the chronic model, abnormal oocytes fell by 15%, and in the acute model, HBOT partly restored the number of oocytes and fully normalized their shape. HBOT reduced granulosa cell apoptosis as early as 24 hours after CTX and lessened the fibrosis caused by chronic CTX. Transcriptome analysis found 67 genes whose expression changed with HBOT, and pathway analysis pointed to the Hippo signaling pathway. We confirmed that HBOT restored the expression of YAP, a key protein in that pathway, using Western blot and immunofluorescence. Conclusions HBOT exerts multi‑target protective effects against CTX‑induced ovarian injury by preserving the primordial follicle pool, improving oocyte quality, suppressing granulosa cell apoptosis, and mitigating fibrosis. Mechanistically, transcriptomic and validation analyses implicate YAP signaling as a candidate mediator of HBOT’s protective actions. Given its established safety profile in clinical practice, HBOT represents a promising adjunctive strategy for fertility preservation in young cancer patients receiving gonadotoxic chemotherapy.

overall_design: Ovarian tissues from NC, CTX, and CTX+HBOT groups were used for RNA-seq profiling. Total RNA was extracted, and libraries were constructed following standard protocols. Paired-end sequencing was performed on the Illumina platform. All sequencing services were completed by Tsingke Biotechnology Co., Ltd.

first: Shuqiang

last: Chen

first: Yefei

last: Ma

first: Cong

last: Li

first: Ying

last: Su

first: Hui

last: Lei

first: Xiaohong

last: Wang

last: Ju


title: Regulation of the histone H3K36 methyltransferase Set2 by the histone chaperone Spt6 [RNA-seq]

status: Public on May 20 2026

first: James

middle: L

last: Warner

address: 77 Avenue Louis Pasteur, Room 358

institute: Harvard Medical School

summary: Histone H3 lysine 36 methylation is a conserved histone modification that is critical for maintaining eukaryotic transcriptional fidelity and genomic stability. In Saccharomyces cerevisiae, this modification is catalyzed by Set2, an ortholog of the mammalian H3K36 methyltransferase SETD2. Previous genetic, biochemical, and structural studies showed that Set2 activity is repressed by a Set2 autoinhibitory domain (AID) and that activation requires the direct binding of the histone chaperone Spt6. To study the role of Spt6 and Set2 autoinhibition in vivo, we have isolated and analyzed multiple classes of Spt6 and Set2 mutants. Our results suggest an autoinhibited form of Set2 in which the catalytic domain is bound by the AID. In strong agreement with our genetic results, biophysical experiments demonstrate that the catalytic domain and AID physically interact, and that the autoinhibition mutants disrupt this interaction. Finally, RNA-seq and ChIP-seq studies show the importance of the Set2-Spt6 interaction for transcription and H3K36 methylation genome-wide. Taken together, our results support a model in which Set2 exists in an inactive, autoinhibited state in vivo through direct catalytic domain-AID interactions, with binding by Spt6 required to relieve this autoinhibited state.

overall_design: RNA-sequencing (RNA-seq) analysis to measure the level of antisense transcripts in spt6 and set2 mutants. Total RNA was extracted from cells. An oligo-dT primer was used to enrich poly-A RNA for sequencing. Experiments were performed in biological triplicate (rep1, rep2, and rep3).

first: Alexandra

last: Elchert

first: Vanda

last: Lux

first: Tereza

last: Nešporová

first: Václav

last: Veverka

first: Fred

last: Winston


title: Resolving METTL5 Specificity: Direct RNA Sequencing Reveals No Evidence for METTL5 mediated mRNA m6A Methylation in mESCs

status: Public on May 19 2026

city: Neuherberg

first: Robert

last: Schneider

address: Ingolstädter landstr. 1

department: IFE

institute: Helmholtz Munich

summary: The methyltransferase-like 5 (METTL5) has been shown to catalyze m6A deposition on 18S ribosomal RNA. However, whether it also methylates mRNAs remains unclear. To address this, we employed direct RNA sequencing (ONT) for m6A detection on native mRNA molecules. We first validated the quantitative detection of m6A by ONT by treating mESCs with a METTL3 inhibitor. We then compared methylation levels of m6A sites between Mettl5-KO and WT mESCs. Our analysis provides no compelling evidence for METTL5 mediated mRNA methylation in vivo, indicating that its activity is restricted to rRNA.

overall_design: Nanopore direct RNA sequencing of mESCs treated with either STM2457 or DMSO (control dataset) and of WT mESCs and their Mettl5 knockout derivatives.

first: Samuel

last: Le Cam

first: Magdalena

last: Valenta


title: Regulation of the histone H3K36 methyltransferase Set2 by the histone chaperone Spt6 [ChIP-Seq]

city: Boston

type: Genome binding/occupancy profiling by high throughput sequencing

overall_design: Chromatin immunoprecipitation sequencing (ChIP-seq) analysis to determine how spt6 and set2 mutants affect H3K36 di- and tri-methylation (H3K36me2/3) levels on chromatin. We performed ChIP to determine levels of H3, H3K36me2, H3K36me3, Rpb1, and Set2 (using an HA epitope tag). Experiments were performed in biological triplicate.


title: Maternal microRNAs Linked To Birth Deficits Due To Prenatal Alcohol Exposure Are Dominant Modifiers of Gene Expression in Invasive Trophoblast Cells

city: Bryan

first: Rajesh

middle: C.

last: Miranda

state: Texas

address: 8447 John Sharp Parkway

department: Neuroscience and Experimental Therapeutics

institute: Texas A&M University

summary: Prenatal alcohol exposure (PAE) can impair placental development and result in fetal growth restriction. However, the underlying molecular mechanisms are unclear. We previously found that PAE in some, but not all pregnancies, resulted in significantly elevated circulating levels of 11 microRNAs (HEamiRNAs) in the 2nd trimester. This subgroup of PAE women experienced adverse infant birth outcomes due to PAE, Subsequently, these HEamiRNAs collectively but not individually, were found to inhibit a defined set of placental epithelial-mesenchymal transition (EMT) genes and, inhibited invasiveness of placental trophoblast cells. Here we extend these findings by performing whole-transcriptome analysis to dissect the contribution of ethanol compared to HEamiRNAs in HTR-8/SVneo cells, a model for invasive, human extravillous trophoblasts. We observed a large, distinct and statistically dominant effect of HEamiRNAs mimics on trophoblast transcript profiles irrespective of ethanol exposure, specifically on EMT, extracellular matrix, angiogenesis and immune signaling pathways among others. Weighted gene co-expression network analysis (WGCNA) identified additional placental growth networks related to epithelial cell proliferation and differentiation and MAPK/PI3K, Hippo and Rap1 signaling. This study provides a mechanistic framework to explain that the effects of PAE vary across pregnancies, because they are contingent in part, on the elevation key maternal circulating miRNAs.

overall_design: RNA-seq profiling of HTR-8 cells, a model for invasive, human extravillous trophoblast cells (EVTs) to assess the collective effects of the 11 identified human HEamiRNAs (miRNAs, hsa-miR-222-5p, hsa-miR-187-5p, hsa-miR-299-3p, hsa-miR-491-3p, hsa-miR-885-3p, hsa-miR-518f-3p, hsa-miR-760, hsa-miR-671-5p, hsa-miR-449a, hsa-miR-204-5p, and hsa-miR-519a-3p) as well as the effects of sequential exposure to ethanol and HEamiRNAs.

first: Deepa

last: Upreti

first: Christina

last: Chambers

middle: C


title: Leukemia risk factor ARID5B Coordinates HDAC-Mediated Transcriptional Repression

first: Ana

middle: Patricia

last: Kutschat

department: Pediatric Leukemia Biology

institute: St. Anna Children's Cancer Research Institute - CCRI

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

overall_design: Refer to individual Series


title: Leukemia risk factor ARID5B Coordinates HDAC-Mediated Transcriptional Repression [CUT&Run]

summary: We employed a combination of proteomics, genomics and transcriptomics to describe the molecular mechanisms of ARID5B. We identify that ARID5B interacts with MIER1, C16ORF87, HDAC1 and HDAC2 forming a repressor complex. The former localizes to active regions of the genome, tethering HDAC1 and HDAC2 to enhancers and promoters. Genes actively repressed by the ARID5B repressor complex are involved in B cell-specific signaling.

overall_design: We performed CUT&Run in Cas9-expressing NALM6 WT and ARID5B KO cells as well as in Cas9-expressing NALM6 WT cells treated with vehicle (DMSO) or 500nM Entinostat for 24h. CUT&Run for active and repressive histone marks, as well as for ARID5B and its intreactors was performed in WT and ARID5B KO cells, while only H3K27ac CUT&Run was perfomed in vehicle or Entinostat treated WT cells.

middle: P

first: Davide

last: Seruggia


title: Leukemia risk factor ARID5B Coordinates HDAC-Mediated Transcriptional Repression [RNA-Seq]

overall_design: We performed mRNAseq in Cas9-expressing NALM6 WT and ARID5B KO cells as well as in Cas9-expressing NALM6 WT cells treated with vehicle (DMSO) or 500nM Entinostat for 24h.

first: Sophie

last: Müller


title: In the Drosophila germline H2Av and Arp6 suppress germline transposons indirectly by driving piRNA pathway expression

status: Public on May 18 2026

city: Ithaca

first: Katalin

last: Fejes-Tóth

state: NY

address: Biotechnology Building Room 358, 526 Campus Rd

department: MBG

institute: Cornell University

type: Non-coding RNA profiling by high throughput sequencing


title: CGRP reception potentiates anxiety in an influenza A derived immune engram

first: Benjamin

last: Devlin

state: North Carolina

address: 210 Research Drive

department: Psychology and Neuroscience

summary: An “immune engram” is a recently described phenomenon in which neuronal populations encode functional aspects of an immune challenge. Here we investigate an immune engram arising from respiratory infection with influenza A virus, demonstrating a molecular mechanism with differential influence over behavioral and immunological aspects of the engram. We first define a cellular response to acute non-neurotropic influenza A/Puerto Rico/8/1934 (PR8) infection by mapping cFos+ cells and microglia morphology across brain regions. In the posterior insula, this response has an early peak at 3 days post infection. Using a cre-dependent excitatory chemogenetic system in TRAP2 mice, we capture an engram at this same region and infection timepoint. Activation of this PR8 engram results in anxiety behavior and increased transcriptional expression of cytokines in lung tissue but not spleen tissue. We further explore how pulmonary signals contribute to this PR8 engram. Using tissue-specific, cre-dependent expression of diphtheria toxin fragment in Calcacre mice, we ablate calca-expressing cells including pulmonary neuroendocrine cells in respiratory tissue. Loss of calca-expressing cells prevents changes in synaptic engulfment by microglia in the insula during PR8 infection without altering the cellular response to infection in pulmonary tissue. Signaling of calcitonin gene related peptide (CGRP), a peptide encoded by calca, can be blocked with the small molecule CGRP receptor antagonist rimegepant. Using rimegepant during acute PR8 infection we again demonstrate that loss of calca signaling prevents the cellular response to PR8 infection in the insula. Finally, applying rimegepant alongside the chemogenetic system in TRAP2 mice we show that CGRP receptor antagonism during engram formation prevents anxiety behavior but not peripheral gene expression changes resulting from PR8 engram activation.

overall_design: B6.Cg-Calcatm1.1(cre/EGFP)Rpa/J mice bred in -/- (wt) or +/- (cre+) given an intratracheal delivery of pAAV6-mCherry-flex-dtA were administered an infection of influenza A/Puerto Rico/8/1934 (FLU) or saline vehicle (CON) to create four treatment groups. Bulk sequencing data is collected from whole lung homogenate.

first: Sarah

last: Monroe

first: Staci

last: Bilbo


title: In the Drosophila germline H2Av and Arp6 suppress germline transposons indirectly by driving piRNA pathway expression [ChIP_H3K9me3]

summary: The spatiotemporal control of transcription and the maintenance of germline genome integrity depend on dynamic chromatin architecture. In Drosophila, the actin-related protein Arp6—a core subunit of the SWR1-like Domino chromatin remodeling complex—mediates the deposition of the histone variant H2Av. Previous studies have established H2Av as a key transcriptional regulator that modulates the +1 nucleosome barrier to promote RNA Polymerase II (Pol II) pause release and productive elongation. Conversely, H2Av is also integral to heterochromatin assembly and gene silencing. Here we demonstrate that Arp6 and H2Av are essential for female fertility and the global repression of transposable elements (TEs) in the Drosophila ovary. Rather than repressing TEs directly, we show that Arp6 and H2Av maintain genomic stability indirectly by driving the transcription of core PIWI-interacting RNA (piRNA) pathway genes. Depletion of either chromatin factor leads to a significant loss of piRNAs and reduced non-canonical transcription of dual-strand piRNA clusters. This defect stems from a failure to express the Rhino-Deadlock-Cutoff (RDC) complex, alongside the downregulation of multiple other piRNA biogenesis factors. Genomic profiling confirms that H2Av acts predominantly as an activating signal at host gene promoters. Upon H2Av or Arp6 depletion, genes that rely on H2Av for their expression exhibit a distinct upstream shift and more precise spatial localization of the Pol II peak at the TSS, indicating an impaired transition from transcription initiation into productive elongation. Together, our findings build upon the known transcriptional activation functions of the Arp6-H2Av axis, revealing that this established chromatin mechanism is critical for licensing piRNA-mediated genome defense and ensuring germline maintenance.

overall_design: Profiling of H3K9me3 ChIP-seq to characterize enrichment across the genome and specifically at piRNA clusters in Drosophila melanogaster in H2Av and Arp6 knockdown ovaries.

first: Norbert

last: Andrasi

first: Hannah

last: Ryon

first: Yicheng

last: Luo


title: In the Drosophila germline H2Av and Arp6 suppress germline transposons indirectly by driving piRNA pathway expression [ChIP_Pol2_pSer5]

overall_design: Profiling of Pol2 Ser5 ChIP-seq  in  Drosophila melanogasterupon knockdown of Arp6 or H2Av.


title: A global molecular code for birth order and neuronal identity in Drosophila

city: Cambridge

first: Sebastian

last: Cachero

address: Francis Crick Avenue

country: United Kingdom

institute: MRC-LMB

summary: The assembly of functional neural circuits relies on the generation of diverse neural types with precise molecular identity and connectivity. Unlocking general principles of neuronal specification and wiring across the nervous system requires a systematic and high-resolution characterization of its diversity, recently enabled by advances in single-cell transcriptomics and connectomics. However, linking the molecular identity of neurons to circuit architecture remains a key challenge. Here we present a high-resolution developmental transcriptional atlas for the Drosophila melanogaster nerve cord, the central hub for sensory–motor circuits. With an considerable 38× aggregate coverage relative to its reference connectome, our atlas captures extensive molecular diversity and enables robust alignment to the adult connectome. We identified three developmental principles underlying neuronal diversity in the nerve cord. First, the timing of neurogenesis shapes diversification of molecular identity: embryonic-born neurons diverge faster than larval-born neurons, as also observed in the adult connectome. Second, 17 transcription factors common to neurons from all lineages provide a global molecular identity code for birth order. Lastly, by mapping sex-specific transcriptional profiles to the connectome, we identified female-specific apoptosis and transcriptional divergence as key global drivers of sex specification. By revealing key organizational axes of molecular identity, this atlas opens avenues to dissect the molecular mechanisms underpinning the development and evolution of neural circuits.

overall_design: Using single cell RNA sequencing we built an atlas containing 459,091 cells for the ventral nerve cord of Drosophila melanogaster. We dissected and dissociated sample at developmental stages 6, 24, 36 and 48h after puparium formation. The atlas includes a balanced number of male and female cells. We mixed samples containing chromosomes from different DGRP lines which were later used for demultiplexing the reads.

first: Myrto

last: Mitletton

first: Isabella

last: Beckett

first: Elizabeth

last: Marin

first: Laia

last: Serratosa Capdevila

first: Marina

last: Gkantia

first: Jelly

middle: H

last: Soffers

first: Haluk

last: Lacin

first: Gregory

middle: S

last: Jefferis

first: Erika

last: Donà


title: Bone marrow immunosuppressive states associate with survival after guadecitabine and atezolizumab therapy in HMA-R/R MDS

city: Grand Rapids

first: Hyo Sik

last: Jang

state: Michigan

address: 333 Bostwick Ave. NE

institute: Van Andel Institute

summary: Approximately half of patients with myelodysplastic syndromes (MDS) relapse or are refractory to hypomethylating agents (HMAs) and experience poor clinical outcomes. We previously reported improved survival in a Phase I/II clinical trial combining the HMA guadecitabine with PD-L1 blockade (atezolizumab) in HMA-relapsed or -refractory MDS, yet the biological features associated with durable responses to this combined epigenetic and immunotherapy approach remain unclear. Here, we performed integrated bulk and single-cell transcriptomic profiling of bone marrow samples from patients treated on this trial to identify molecular and cellular features associated with survival. Long-term survival was associated with the presence of immunosuppressive myeloid cells and primed dendritic cells at baseline, together with therapy-induced immune reinvigoration characterized by interferon pathway activation and expansion of effector lymphocytes. In contrast, short-term survival was associated with persistent senescence-associated inflammatory programs in CD34⁺ bone marrow cells and elevated expression of immunosuppressive immune checkpoint molecules. These findings suggest that chronic inflammatory and senescent microenvironmental states constrain effective immune activation despite combined epigenetic and immune checkpoint therapy. Here, we reveal distinct bone marrow microenvironments associated with patient survival after combined epigenetic and immune checkpoint therapy and suggest candidate biomarkers to guide patient stratification in high-risk MDS.

overall_design: Bulk total RNA-seq profiling of CD34+ cells from patient bone marrow aspirates across from screening, post-cycle 2, and post-cycle 4 treatment timepoints. CITE-seq profiling of bone marrow mononuclear cells and peripheral blood cells from patient samples collected during screening and post-cycle 2 treatment timepoints.

first: H. Josh

first: Peter

last: Jones


title: Maternal Hyperhomocysteinemia Compromises Female Offspring Fertility Through Over-Activation of Primordial Follicles

city: Yinchuan

first: Jinmei

last: Gao

state: Ningxia

address: Shengli

institute: General Hospital of Ningxia Medical University

summary: Hyperhomocysteinemia (HHcy), characterized by elevated plasma homocysteine levels exceeding 15 µmol/L, has been associated with various issues impacting personal health and offspring's well-being. This study examines the impact of maternal HHcy, induced by a high-methionine diet, on the fertility of female offspring mice. The results showed that maternal HHcy caused the over-activation of primordial follicles in female offspring mice by promoting the phosphorylation of key factors, including RPS6, MTOR, FOXO3A, and AKT. Meanwhile, the number of mitochondria in mature oocytes decreases, and mitochondrial function declines, further leading to an increase in reactive oxygen species (ROS) levels, an increase in the proportion of DNA damage, and spindle abnormalities, ultimately impairing the quality of oocytes. These findings demonstrate that maternal HHcy decreases offspring fertility by inducing primordial follicle over-activation and impairing oocyte quality. This provides new insights into the pathological mechanisms of HHcy affecting offspring's reproductive potential.

overall_design: Female C57BL/6J mice were randomly assigned to either a control group or a hyperhomocysteinemia (HHcy) group. HHcy was induced by feeding a high-methionine diet starting 4 weeks prior to mating and continuing throughout gestation and lactation. Control mice received a normal diet. All females were mated with normal diet-fed males to generate F1 offspring. Ovaries were collected from female F1 offspring at postnatal days 3, 7, and 21 (Pd3, Pd7, Pd21). Total RNA was extracted from each ovary and subjected to RNA sequencing (RNA-seq). The goal was to compare the transcriptomic profiles of ovarian tissues between the F1 HHcy group and the F1 control group at each developmental time point, aiming to elucidate the molecular mechanisms by which maternal HHcy affects primordial follicle activation and subsequent ovarian development in female offspring.

first: Lu

last: Wang

first: Jie

last: Ma

first: Jialing

last: Li

first: Yajie

first: Jinfang

first: Rong

last: Hu


title: Effects of histone acetyltransferase dead mutation of KAT6A and KAT6B on gene expression in E9.5 mouse embryos and E14.5 mouse foetal liver hematopoietic cells

status: Public on May 17 2026

city: Parkville

first: Nishika

last: Ranathunga

state: VIC

address: 1G Royal Parade

country: Australia

institute: Walter and Eliza Hall Institute of Medical Research

summary: The paralogous histone acetyltransferases KAT6A and KAT6B are large 200 kDa proteins of identical protein domain structure with high sequence similarity within the functional protein domains. Kat6a and Kat6b null mutation have severe effects on mouse embryonic and foetal development as well as on adult stem cell populations. Apart from the well-defined MYST family histone acetyltransferase domain, the proteins have N-terminal winged-helix domains followed by tandem plant homeodomain fingers preceding the histone acetyltransferase domain, as well as a long unstructured acidic region and serine and methionine rich regions following the histone acetyltransferase domain. In this study we examined the effects of point mutations that reduce the histone acetyltransferase function to background levels on gene expression in E9.5 mouse embryos and E14.5 mouse foetal liver haematopoietic cells and compared these to the effects of the null mutations of the Kat6a and Kat6b gene.

overall_design: RNA-sequencing of E9.5 mouse embryos of the following six genotypes Kat6a+/+;Kat6b+/+, Kat6a–/–;Kat6b+/+,  Kat6a+/+;Kat6b–/–, Kat6aG656E/G656E;Kat6b+/+,  Kat6a+/+;Kat6bG577E/G577E. Kat6aG656E/G656E;Kat6bG577E/G577E and E14.5 mouse foetal liver haematopoietic cells of the following four genotypes  Kat6a+/+;Kat6b+/+, Kat6aG656E/G656E;Kat6b+/+,  Kat6a+/+;Kat6bG577E/G577E. Kat6aG656E/G656E;Kat6bG577E/G577E. N = 4 embryos or foetuses per genotype.

first: Alexandra

last: Garnham

first: Anne

last: Voss

first: Tim

last: Thomas

first: Ranathunga

last: Nishika


title: In the Drosophila germline H2Av and Arp6 suppress germline transposons indirectly by driving piRNA pathway expression [ChIP_GFP-Rhino]

first: Katalin

last: Fejes-Tóth

overall_design: Profiling of GFP-Rhino ChIP-seq to characterize enrichment across the genome and specifically at piRNA clusters in Drosophila melanogaster in H2Av and Arp6 knockdown ovaries.

first: Norbert

last: Andrasi

first: Hannah

last: Ryon

first: Yicheng

last: Luo


title: In the Drosophila germline H2Av and Arp6 suppress germline transposons indirectly by driving piRNA pathway expression [ChIP_H2Av]

overall_design: Profiling of H2Av ChIP-seq to characterize H2Av enrichment  in  Drosophila melanogaster in wildtype and Arp6 knockdown lines.

first: Andrasi

last: Norbert

first: Ryon

last: Hannah

first: Luo

last: Yicheng

first: Fejes-Tóth

last: Katalin


title: GABAergic neurons exhibit subtype-specific changes in the developing somatosensory cortex of a rat model of Fragile X Syndrome

status: Public on May 16 2026

city: Edinburgh

first: Anna

last: Sumera

address: Hugh Robson Building, 15 George Square

institute: University of Edinburgh

summary: GABAergic interneurons (IN) are critical for the precise timing and flow of information in cortical circuits. Loss of GABAergic IN function has been suggested as a potential translationally relevant mechanism of neuropathology in Fragile X Syndrome (FXS). Indeed, in rodent models of FXS, some IN populations may display reduced number, while genes associated with other IN type upregulated. However, it remains unknown how these cell populations, and their cell-type specific gene expression patterns are regulated in early development across other mammalian models fo FXS. Here we utilise an outbred rat model of FXS, in which we performed single-nucleus RNA sequencing analysis in neonatal development of the somatosensory cortex. We then use immunohistochemistry to measure the number and distribution of neurochemically identified GABAergic IN subtypes from early development until adolescence in the somatosensory cortex. We find that GABAergic INs in a rat model of FXS display clear evidence of transcriptomic alteration compared to wild-type littermates in early brain development. These effects are most profound in putative parvalbumin INs, but with modest changes in other cell types. From immunohistochemistry, we find that parvalbumin INs appear largely unaffected in density in distribution, but we observe a large upregulation in the number of somatostatin-expressing INs. GABAergic INs may display cell-type specific transcriptomic regulation in response to the loss of FMRP. Our data suggests minimal alteration of parvalbumin IN density or distribution, but upregulated somatostatin cell numbers. These data partially agree with previous observations in mouse models of FXS.

overall_design: We dissected S1 cortex from 3 WT and 3 Fmr1-/y rats at P9, dissociated single nuclei and performed 10X snRNA-seq.

first: Abbi

last: Crichton

first: Peter

last: Kind

first: Christopher

last: Sibley

first: Sam

last: Booker


title: Macrophages control regenerative neurogenesis directly and indirectly via Sema4ab after spinal cord injury in zebrafish

city: Dresden

first: Mehmet Ilyas

last: Cosacak

state: Saxony

address: Fetscherstr. 105

institute: Center for Regenerative Therapies, TU Dresden

summary: After spinal cord injury, interactions of multiple tissues inhibit neuronal regeneration in mammals, but not in anamniotes, such as zebrafish. These pivotal interactions are poorly understood. Here we analyse the role of the cell signalling molecule sema4ab in the cell communication network leading to regenerative neurogenesis after spinal injury in larval zebrafish. Sema4ab is expressed by macrophages and gene ablation doubles the rate of regenerative neurogenesis. Disruption of the receptor plxnb1a/b, expressed by spinal progenitor cells, also moderately increases regenerative neurogenesis. In addition, single cell transcriptomics reveals altered interactions between macrophages and multiple additional cell types after sema4ab disruption. Pro-inflammatory cytokines are down-regulated and fibroblasts upregulate expression of the anti-inflammatory cytokine tgfb3. Inhibition of tgfb3 abolishes effects of sema4ab disruption on regenerative neurogenesis. This highlights sema4ab as a direct and indirect inhibitor of regenerative neurogenesis and as a potential therapeutic target in non-regenerating mammals.

overall_design: Single-cell sequencing of 4 days old zebrafish larvae. In brief, embryos were injected with control guide RNA (gCOntrol) or haCR guide for sema4ab gene (gSema4ab) at single-cell stages. The spinal cord injury performed at 3dpf and 1 dpl, the injury sites were cut and tissue was dissociated. GFP positive cells and viable cells were sorted by FACS and cells were encapsualted using 10X genomices. gControl has 1 replicate, gSema4ab has 2 technical replicates.

first: Alberto

last: Docampo-Seara

first: Mehmet

middle: I

first: Catherina

last: G. Becker

first: Thomas

last: Becker


title: A core transcriptional regulatory circuitry controls super-enhancer-driven activation of LGR5 in colorectal cancer: RNA-seq

city: Shenzhen

first: Xing-sheng

last: Shu

state: Guangdong

address: No 3688, Nanhai Avenue

department: Medical School

institute: Shenzhen University

summary: The core transcriptional regulatory program governed by a small set of master transcription factors is pivotal for establishing context-specific cellular features, as has been elegantly illustrated in embryonic stem cells. Here, we reported an uncharted role of master transcription factor MYC in actively regulating cancer-type specific super-enhancer (SE) activity, and identified a core transcriptional regulatory circuitry consisting of MYC, ETS2, and FOXP1 in colorectal cancer (CRC). MYC/ETS2/FOXP1 bound to their own SEs and the SEs of other circuitry factors, thereby rapidly amplifying transcriptional effects upon activation. The majority of SEs were co-occupied by all three circuitry factors, and acute perturbation of the circuitry factors severely and selectively repressed a series of SE-controlled genes. Furthermore, there was functional inter-dependency between the circuitry and BRD4 in regulating SE-driven transcription, and targeting the circuitry factors sensitized CRC cells to BET inhibition. Notably, the key stemness gene LGR5 was activated by a circuitry-controlled distal SE in CRC, which was one of the most significantly gained tumor-specific SEs and was required for establishing CRC liver metastases. Lgr5 transcription in intestinal stem cells (ISCs) was likewise sustained by a Myc-regulated SE. Depletion of Myc in murine ISCs led to shrink of Lgr5-positive cell population, and impaired the renewal capacity of ISCs and intestinal epithelium integrity. Collectively, our study unveiled a core transcriptional regulatory module in CRC, advanced current understanding of MYC in transcription regulation, and provided mechanistic explanation for LGR5 overexpression in cancer. These findings may pave the way for precisely targeting detrimental transcription events in CRC therapy.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design:
The MYC gene was taggged by a auxin-inducible degron (AID) in colon cancer cells stably expressing E3 ligase AtAFB2. MYC-AID cells were pre-treated with 500 μM IAA (auxin) for 30 min followed by 100 μM s4U treatment for 150 min. Total RNA was extracted through the Trizol method and was dissolved in RNase-free water with 1 mM DTT followed by incubation at 55°C for 10 min. 5 μg of the RNA was used for thiol modification with 100 mM iodoacetamide at 50°C for 15 min in a dark place. The thiol-modified RNA was then precipitated by anhydrous ethanol, and used for library preparation with the QuantSeq 3’ mRNA-Seq Library Prep Kit (Lexogen) according to the manufacturer's instructions.
The MYC gene was taggged by a auxin-inducible degron (AID) in colon cancer cells stably expressing E3 ligase AtAFB2. Acute degradation of MYC was induced by auxin (IAA) treatment, cells were then harvested for transcriptome analysis. For conditional knock-out of Myc in intestinal stem cells, Mycf/f ; Lgr5-CreERT2 mice were intraperitoneally injected with Tamoxifen (TAM) dissolved in corn oil (80mg/kg) daily for there consecutive days, three days post last injection mice were sacrificed and intestinal crypt was harvested for transcriptome analysis.


title: RTT109 regulates Polycomb-repressed genes independently from H3K56 acetylation status

city: Athens

first: Zachary

last: Lewis

state: GA

address: 120 E. Green St.

department: Microbiology

institute: University of Georiga

summary: In animals, plants, and some fungi, Polycomb Repressive Complex 2 (PRC2) catalyzes trimethylation of histone H3 lysine 27 (H3K27me3) to establish transcriptionally repressed chromatin. Here, we identify the histone acetyltransferase RTT109 as a key regulator of PRC2-repressed domains in the model fungus Neurospora crassa. Although RTT109 interacts with the VPS75 homolog Nucleosome Assembly Factor 2 (NAF-2), we show that proper structure and function of PRC2-methylated chromatin require RTT109 catalytic activity but are independent of NAF-2 and H3K56 acetylation. We further demonstrate that H3K27me3 can be stably propagated over multiple rounds of mitosis in the absence of sequence-specific PRC2 targeting, and that RTT109 is essential for maintenance of the repressed state. These findings uncover a replication-linked mechanism for epigenetic memory and establish RTT109 as a key regulator of Polycomb-mediated chromatin inheritance.

overall_design:
ChIP-seq in wild type and mutants was performed with two or three replicates for each genotype. Samples were grown in Vogel's minimal medium plus 1.5% Glucose. TetR-PRC2 strains were exposed to tetracyclince for 0 or 24 hours

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The table below lists GEO accessions reused/reanalyzed for this study.
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first: Rochelle

middle: E

last: Yap

first: Felicia

last: Ebot-Ojong

first: Abigail

middle: J

last: Ameri-Solanki


title: A humanized monoclonal antibody targeting human ENPP1, an ectonucleotidase expressed in the diseased human kidney, enhances tubular proliferation and kidney repair and is safe in non-human primates [scRNA-seq]

city: Los Angeles

first: Lianjiu

last: Su

address: 500 Landfair Ave.

institute: University of California, Los Angeles

summary: The human kidney possesses a poor ability to robustly regenerate after acute injury and chronic kidney disease affects millions of individuals worldwide. There are no drugs that enhance tissue repair after acute kidney injury. Here, we demonstrate, in a cohort of individuals with kidney disease, that the ectonucleotidase ENPP1 (ectonucleotide pyrophosphatase/phosphodiesterase-1) is robustly expressed in diseased human kidneys and strongly correlates with clinical indices of renal dysfunction. Genetic targeting of ENPP1 in mouse models of kidney disease enhanced renal repair, decreased fibrosis and was associated with significant rescue of post injury kidney function. A humanized monoclonal antibody, targeting the catalytic domain of human ENPP1 when administered to humanized mouse models led to proliferation of tubular cells, enhanced renal glomerular filtration rate, decreased fibrosis and rescued kidney function in multiple pre-clinical models of kidney injury. In animals that express human ENPP1 and exhibit clearance kinetics of immunoglobulins similar to those in humans, a single dose of the monoclonal was sufficient to rescue kidney function after an acute insult. Metabolic profiling demonstrated that antibody mediated ENPP1 inhibition led to beneficial effects on nucleotide metabolism and cellular energetics enabling proliferation and rescuing cell cycle arrest. Single cell transcriptomics and pulse chase labeling demonstrated that hENPP1mAb promotes tubular repair by expanding regenerative tubular cell subsets and reducing populations associated with failed repair. In a multi dose GLP (good laboratory practice) compliant study, the humanized monoclonal antibody was found to be non-toxic and highly tolerated when administered to non-human primates at high doses. Taken together, our findings identify ENPP1 as a central regulator of epithelial injury and metabolic control after acute kidney injury and provide proof of concept of an engineered humanized monoclonal antibody targeting human ENPP1, as a potential therapeutic agent for enhancing human kidney repair.

overall_design: Mice were assigned to three experimental groups: (1) a CHOW diet control group, (2) an adenine diet group treated with control IgG, and (3) an adenine diet group treated with hENPP1 monoclonal antibody (mAb). Each group consisted of four biological replicates. The adenine-induced kidney injury model was established by feeding mice an adenine-containing diet for 14 days. Control IgG or hENPP1 mAb was administered by intraperitoneal injection at a dose of 50 mg/kg, twice per week. At day 14, kidneys were harvested and processed for single-cell RNA sequencing analysis.


title: A humanized monoclonal antibody targeting human ENPP1, an ectonucleotidase expressed in the diseased human kidney, enhances tubular proliferation and kidney repair and is safe in non-human primates

overall_design: 1）Generation of ENPP1 knockout mice and bulk RNA sequencing ENPP1 conditional knockout mice were generated by crossing ENPP1^fl/fl^ mice with CAG-ERCre transgenic mice. Tamoxifen administration was used to induce Cre-mediated recombination and generate homozygous ENPP1 knockout mice. Mice were assigned to three groups: a CHOW diet control group (n = 4), a wild-type group (CAG-ERCre⁻) fed an adenine diet (n = 6), and an ENPP1 knockout group (CAG-ERCre⁺) fed an adenine diet (n = 6). The adenine-induced kidney injury model was maintained for 14 days, after which kidney tissues were harvested for bulk RNA sequencing analysis. 2）Antibody treatment in the adenine-induced kidney injury model The adenine-induced kidney injury model was established by feeding mice an adenine-containing diet（n=4）for 14 days. Mice received either control IgG or hENPP1 monoclonal antibody (mAb) via intraperitoneal injection at a dose of 50 mg/kg, administered twice per week. At day 14, kidneys were collected and processed for bulk RNA sequencing analysis.


title: Exogenous 24nt siRNAs induce AGO4A-dependent silencing via promoter DNA methylation and H3K9me2 deposition

status: Public on May 15 2026

city: Neustadt an der Weinstraße

first: Veli

middle: Vural

last: Uslu

address: Epigenetics, Breitenweg 71

department: Epigenetics

institute: AgroScience GmbH AlPlanta-Institute for Plant Research

summary: Transcriptional Gene Silencing (TGS) is an essential process in plants for development, gene regulation, defense against viruses, and genome integrity. TGS is predominantly established by RNA-directed DNA methylation (RdDM), a self-reinforcing mechanism in which sRNAs guide transcriptional suppressors to target genomic loci by sequence complementarity, and methylated DNA in turn facilitates sRNA genesis. Recently, exogenous application of promoter targeting long dsRNAs was associated with promoter methylation without any detectable gene silencing. A plethora of sRNAs of different sizes and types form as cleavage products of precursor double-stranded RNAs such as pre-miRNAs, inverted-repeats, viral replication intermediates, or exogenous dsRNAs. Due to the complexity of sRNA products, the features of the sRNAs, which trigger de novo RdDM, remain enigmatic. Here, we demonstrated that in planta delivery of chemically synthesized 24-nucleotide(nt) small interfering RNAs (siRNAs), targeting 35S promoter of GFP-expressing Nicotiana benthamiana (Nb) 16c line, was sufficient to induce RdDM, H3K9me2 deposition, and also TGS. Using CRISPR/Cas-mediated gene editing, we showed that exogenous 24nt siRNA-triggered TGS is dependent on ARGONAUTE 4A (NbAGO4A) but not on NbAGO4B. Exogenously administered 24nt siRNAs could provide the means to investigate such initiation events, while allowing functional dissection of siRNA classes and their modifications in planta.

overall_design: siRNAs are exogenously applied on Nicotiana benthamiana 16C via High Pressure Spraying Protocol and the silencing phenotype is evaluated by sRNA-seq

first: A

last: Hanke

first: L

last: Schütz

first: M

last: Walz

first: N

last: Wunsch

last: Kreis

last: Hohenwarter

last: Baßler

last: Wassenegger

last: Dalakouras

first: G

last: Krczal

last: Koch

first: VV


title: A proteomics screen uncovers CTCF as a key G-quadruplex binding protein

city: Chicago

first: Vipul

last: Shukla

state: Illinois

address: 303 E. Superior Street

department: Department of Cell and Developmental Biology

institute: Northwestern University

overall_design: Refer to individual Series


title: Expression data from mice kidneys with urinary tract infection treated with NlpD or LytM

city: Lund

first: Ines

last: Ambite

address: Klinikgatan 28

department: Laboratory Medicine

country: Sweden

institute: Lund University

summary: Finding new ways of treating bacterial infections is essential. The NlpD protein, which inhibits RNA Polymerase II (Pol II), has shown therapeutic efficacy against urinary tract infection. This study investigated the mechanism of Pol II inhibition and protection by NlpD and its LytM peptide. Recombinant NlpD and LytM were screened for interactions with constituents of the RNA Polymerase II complex, using AlphaFold predictions and protein interaction technology. Treatment effects were quantified in infected tissues and regulated host response pathways identified by genome-wide transcriptomics analysis in models of acute pyelonephritis and acute cystitis in Irf3-/- and Asc-/- mice, respectively. LytM was shown to interact with constituents of the Pol II multiprotein complex, inhibiting the CDK12 kinase from phosphorylating the Pol II subunit RPB1 and disrupting Pol II complex formation by interfering with the interaction between PAF1C and RPB1. The protection by LytM against acute pyelonephritis was accompanied by a reduction in gene expression in infected kidneys from >1,900 significantly regulated genes (FC>6) in the placebo group to about 150 in LytM treated mice. The inhibition of gene expression in infected kidneys particularly targeted the excessive innate immune response. A similar effect was observed in acute cystitis. Bacterial clearance was accelerated in both model by LytM treatment, with effects against antibiotic sensitive and resistant Escherichia coli strains. The results suggest that inhibiting the disease response of the host, using NlpD or LytM, may offer an efficient alternative to antibiotics in these models.

overall_design: Urinary tract infection was induced in female Irf3−/− mice by intravesical infection with E. coli strain CFT073. The treatment groups received rNlpD protein or LytM (27.13 μM) by intraperitoneal injection daily, for 7 days. Placebo control mice received the same volume of buffer (50 mM Tris-HCl, 150 mM NaCl, 10% Glycerol) in PBS. Kidneys samples were collected after 7 days. Isolated RNA was subjected to Affymetrix whole genome transcriptomic analysis.

first: Hien

last: Tran

first: Catharina

last: Svanborg


title: A proteomics screen uncovers CTCF as a key G-quadruplex binding protein [Hi-C]

summary: DNA G-quadruplexes (G4s) are non-B form secondary DNA structures that are highly conserved across evolution. G4 structures occupy key regulatory sites in the mammalian genomes and are implicated in several cellular processes. However, the mechanisms by which G4s contribute to distinct facets of genome function are not well understood. Here, we conduct an unbiased proteomics screen with G4s of diverse topologies to uncover novel G4 binding activities in key genomic regulators involved in regulation of nucleosome remodeling, paraspeckle assembly, RNA splicing, transcriptional elongation, and 3D genome organization. Among the most prominent hits, we identify the genomic architectural protein, CTCF as one of the strongest G4 binders. Building on this discovery, we perform extensive biochemical validation of CTCF-G4 interaction and identify CTCF mutants, with pronounced affinity for G4s over its consensus DNA motif. By implementing well-established approaches and newly developed G4 mapping tools, we define a comprehensive catalog of genomic  G4s and study their association with CTCF binding. Furthermore, using genetic reconstitution studies with specific CTCF mutants, we ascribe genomic functions to CTCF-G4 interactions in regulation of CTCF occupancy, chromatin looping and gene expression. Our work establishes the G4 binding activity of CTCF and provides new insights into the functional significance of G4 structures.

overall_design: Hi-C for CTCF and G-quadruplexes of mESCs treated without auxin (control) or with auxin to promote CTCF deletion (EV+AUX) and cells that had reintroduction of FL CTCF or mutant CTCF (H373R) after auxin treatment

first: Daniela

last: Samaniego-Castruita

first: Isabella

last: Han

first: Roxroy

last: Morgan

first: Samantha

last: Carpenter

first: Bryce

last: Williams

first: Ishwar

last: Radhakrishnan

first: Abhijit

last: Chakraborty

first: Samuel

last: Myers

first: Ferhat

last: Ay

first: Anjana

last: Rao


title: Bulk RNA-seq of dorsal root ganglion (DRG) neuron with 3 conditions

city: Cold Spring Harbor

first: Yue

last: Wu

address: One Bungtown Rd, Demerec RM 120

department: Cancer and Neuroscience

institute: Cold Spring Harbor Laboratory

summary: Bulk RNA sequencing was performed to compare mRNA expression profiles across six experimental conditions: monoculture of primary dorsal root ganglion (DRG) neurons isolated from C57BL/6J mice; conditioned medium from EO771 cells applied to DRG neurons; and direct co-culture of EO771 and DRG neurons followed by fluorescence-activated cell sorting (FACS) to DRG neuron population. The aim was to identify transcriptional programs regulated by tumor–neuron interactions, including acute gene expression changes, intercellular signaling pathways, and broader pathway-level alterations. The dataset is intended for differential expression analysis, pathway enrichment, and hypothesis generation for downstream functional studies.

overall_design: Biological replicates: n = 3 independent samples per condition. RNA was extracted from each sample and processed for library preparation using standardized protocols. Differential expression of mRNAs were compared between three groups: mono-culture; conditioned medium and co-culture in DRG population. Where feasible, sample processing was performed with the operator blinded to experimental groups.

first: Elena

last: Ghiban

first: Jeremy

last: Borniger


title: ChIP-seq analysis of MYRF-1 transcription factor in C. elegans

city: New York City

first: Sevinc

last: Ercan

address: Brown Building 31 Washington Place Room 852

institute: New York University

summary: ChIP–seq on staged animals expressing an endogenously tagged GFP::MYRF-1 fusion at peak nuclear abundance during the L1 stage.

overall_design: Endogenously GFP-tagged MYRF-1 animals were synchronized at the L1 stage by hypochlorite treatment of gravid adults followed by overnight hatching in M9 buffer. Synchronized L1 larvae were plated on 150-mm NGM plates seeded with E. coli OP50 and grown for ∼11 h, when GFP::MYRF-1 is predominantly localized to the nucleus. Approximately 100 µL of packed worms were collected by washing in M9 buffer, crosslinked in 2% formaldehyde, and quenched with 125 mM glycine. Two biological replicates were collected for each ChIP experiment.

first: Ercan

last: Sevinc

first: Ritter

last: David


title: Transcriptome profiling of two novel Mycobacterium species, Mycobacterium camsae and Mycobacterium pumcae

city: NanJing

first: Tian

last: Gan

address: Jiang-wang-miao street 12

institute: Chinese Acdemy of Medical Science

summary: This study performed transcriptome sequencing of two newly identified Mycobacterium species, Mycobacterium camsae and Mycobacterium pumcae, under standard culture conditions to establish baseline gene expression profiles. RNA was extracted from cells grown to mid-log phase in standard medium and sequenced using Illumina paired-end technology. The data provide a foundational resource for future functional studies of these novel strains.

sample_organism:
Mycobacterium pumcae
Mycobacterium camsae

overall_design: RNA-seq was performed on Mycobacterium camsae and Mycobacterium pumcae under standard culture, with three biological replicates per condition. Cells were grown to mid-log phase, total RNA was extracted, rRNA-depleted, and sequenced using Illumina paired-end technology. Raw reads were processed, aligned to the respective reference genomes, and gene-level expression profiles were generated.

first: Youming

last: Mei

first: Haiqin

last: Jiang

first: Wenyue

last: Zhang

first: Yin

last: Shi

first: Hongsheng

last: Wang


title: Understanding impact of aging on intestinal epithelial cells by comparing transcriptional profiles at single cell resolution.

city: Bronx

first: Jiahn

last: Choi

address: 1300 Morris Park Ave

institute: Albert Einstein College of Medicine

summary: Aging is a risk factor that initiates pathogenesis in the intestinal mucosa. We used single cell RNA sequencing to dissect the aging process and how the alterations are associated with aging phenotypes.

overall_design: Intestinal epithelial cells from C57B/6 mice were isolated by FACS (Epcam+, CD45 neg) at either 3-month-old (young), or 24-month-old (old).

first: Leonard

last: Augenlicht

first: Derek

middle: M

last: Huffman


title: Recurrent ZC3H18 mutations stabilize oncogenic endogenous retroviral RNA [SW480_pA]

city: Boston

first: Tanzina

last: Tanu

state: MA

address: 450 Brookline

department: Medical Oncology

institute: DFCI

summary: Endogenous retroviral (ERV) RNA is highly expressed in cancer, although the molecular causes and consequences remain unknown. In multiple cancer types, we identified recurrent truncating mutations in ZC3H18 (Z18), a nuclear RNA surveillance component. We show that Z18 truncating (Z18trunc) mutations are oncogenic and that Z18 plays an evolutionarily conserved role in nuclear RNA surveillance of oncogenic ERV RNA. In zebrafish, Z18trunc accelerated melanoma onset and selectively increased ERV RNA. Z18 mutant human cell lines from the Cancer Cell Line Encyclopedia, TCGA melanoma, and TCGA uterine cancer patient samples also expressed higher levels of ERV RNA. In engineered human melanoma cells, Z18trunc enhanced ERV RNA accumulation more than loss of one Z18 allele, indicating dominant negative activity. In human melanoma cells, Z18trunc directly bound to and stabilized ERV RNA in the cytoplasm. Expression of zebrafish and human Z18-regulated ERV RNA was sufficient to accelerate melanoma in zebrafish. Z18-regulated ERV RNA was required for Z18trunc melanocyte development in zebrafish and for human melanoma cell growth. Our work suggests that ERV RNA, the most highly expressed transposable element RNA in cancer, promotes melanoma and potentially other cancers. This work illuminates a mechanism for elevated ERV transcripts in cancer and supports that aberrant RNA accumulation is broadly oncogenic.

overall_design:
pLENTI CMV Clover (fluorescent control) and pLENTI CMV Z18trunc-expressing human SW480 colon adenocarcinoma cell lines were generated via lentiviral transduction. polyA-selected RNA-sequencing was done.
Lentivirus transduction and antibiotic selection was used to generate Clover-expressing (n=3) and ZC3H18 trunc-expressing (n=3) cell lines.

first: Anna

last: Cox

first: Jennifer

last: Karlow

first: Priyanka

last: Sharma

first: Kaiwen

last: Sun

first: Xueyang

last: He

first: Swathy

last: Babu

first: Madeline

last: Roelofs

first: Ethan

last: Jeon

first: Jiajia

last: Chen

first: Constance

first: Jared

last: Brown

first: Nelson

middle: B

last: Barrientos

first: Andrew

last: McCallion

first: Kevin

first: Stephen

last: Chanock

first: David

last: Liu

first: Tongwu

first: Kathleen

last: Burns

first: Paul

last: Boutz

first: Megan

last: Insco


title: Recurrent ZC3H18 mutations stabilize oncogenic endogenous retroviral RNA [A375_ribominus]

first: Tanzina

last: Tanu

overall_design:
pLENTI CMV Clover (fluorescent control) and pLENTI CMV Z18trunc-expressing human melanoma A375 cell lines were generated via lentiviral transduction. Bulk ribominus RNA-sequencing was done.
Lentivirus transduction and antibiotic selection was used to generate Clover-expressing (n=3) and ZC3H18 trunc-expressing (n=3) cell lines.

first: Anna

last: Cox

first: Jennifer

first: Priyanka

first: Kaiwen

last: Wu

last: Zhang


title: Three immunoregulatory signatures define non-productive HIV infection in stem cell memory CD4+ T cells

city: New York

first: Viviana

last: Simon

address: 1 Gustave L. Levy Pl

institute: Icahn School of Medicine at Mount Sinai

summary: The persistent HIV reservoir constitutes the main obstacle to curing HIV/AIDS disease. Our understanding of how non-productive HIV infections are established in primary human CD4+ T cells during the first round of infection is, however, still incomplete. In this study, we leverage the HIV reporter virus pMorpheus-V5 to delineate cellular expression patterns that are upregulated in non-productively infected primary stem cell memory (TSCM) CD4+ T cells.  We find that CD4+ TSCM harboring non-productive proviruses display a distinct transcriptomic signature comprising 118 upregulated genes. This non-productive expression profile is distinct from that of productively infected cells as well as from negative-exposed and mock-infected cells. Among the cellular genes most upregulated in CD4+ T cells harboring non-productive proviruses are CCR4-binding migratory chemokines (CCL22, CCL17), tryptophan catabolic enzymes (IDO1, KYNU), and genes encoding cytoskeletal rearrangement proteins (BASP1, TNFAIP2). Intracellular flow cytometry-based analyses confirm that non-productively infected CD4+ TSCM cells are enriched for CCL22 and IDO1 co-expression compared to the other CD4+ T memory subsets, underscoring a clear CD4+ T cell subset specificity for the upregulation of these two immune gene sets associated with non-productive infections. These findings suggest that primary human CD4+ TSCM harboring non-productive proviruses display a distinct immunoregulatory phenotype, which may facilitate immune evasion and contribute to the persistence of the HIV reservoir.

overall_design: RNA seq profiling of flow cytometry sorted CD4+ Tscm infected with HIV reporter (pMorpheus-V5). Sorted for productive infection, nonproductive infection, negative exposed, and mock unexposed.

first: Giacomo M.

last: Butta

first: Bremy

last: Alburquerque

first: Charlotte

last: Kearns

first: Yoav

last: Hadas

first: Max

middle: W

last: VanDyck

first: Susanna

last: Scaglioni

first: Noah

last: Peña

first: Hoi Tong

last: Wong

first: Elizabeth

last: Levendosky

first: Charles

last: Gleason

first: Xiao

last: Lin

first: Lara

last: Manganaro

first: Dalila

last: Pinto

first: Lubbertus C.F.

last: Mulder


title: Molecular evidence for early deuterostome origins of ovarian cell types and neuroendocrine control of reproduction

city: Woods Hole

first: Zak

last: Swartz

address: 7 MBL Street

department: Eugene Bell Center for Regenerative Biology & Tissue Engineering

institute: Marine Biological Laboratory

summary: We performed scRNA-seq combined with high-resolution 3D-imaging to reveal the ovarian cell types and their spatial organization.

overall_design: Generation and analysis of Patiria miniata ovary scRNA-seq data to use along with imaging techniques to generate identify P. miniata ovarian cell types.

first: Periklis

last: Paganos

first: Beverly

last: Naigles

first: Carsten

last: Wolff

first: Danila

last: Voronov

first: S. Zachary