title: Collagen-disrupting attIL12 TIL therapy boosts deep T-cell infiltration via dual signaling activation and CCKAR reduction in sarcomas

city: Houston

first: Jiemiao

last: Hu

address: 1515 Holcombe Blvd

institute: University of Texas MD Anderson Cancer Center

summary: Tumor-targeted T-cell therapies of various types have been booming, but T-cell therapy is limited by its inability to penetrate the collagen barrier surrounding tumors. The destruction of tumor collagen is significant because collagen both suppresses T cells and contributes to the formation of the extracellular matrix. Our previously reported cell surface vimentin (CSV)–targeted and membrane-anchored IL12-armed (attIL12) T cells can reduce collagen production by killing cancer-associated fibroblasts, but fail to reduce collagen expression by tumor cells, resulting in resistance to attIL12-T cell treatment. In this study, we discovered that CCKAR directly boosts collagen production by tumor cells in vitro and in vivo. attIL12-modified tumor-infiltrating lymphocytes (TILs) disabled collagen production by CCKAR-high autologous tumor cells in vitro and sarcoma patient-derived xenografts (PDXs) in vivo. This disruption of collagen production by tumor cells by attIL12-TILs overcomes resistance to attIL12-T cell treatment and required a simultaneous interaction between the CSV on autologous tumor cells, which is targeted by attIL12, and HLA-TCR on attIL12-TILs; when either interaction was abrogated, collagen production and CCKAR expression were not shut down. Mechanistically, the interaction between attIL12-TILs and autologous tumor cells induced IFNγ production synergistically, which in combination with CCKAR downregulation reduced collagen expression through suppression of both TGFβ-stimulated SMAD activation and CCKAR-AKT signaling. Diminishing collagen expression from tumor cells significantly increased T-cell infiltration and improved tumor growth inhibition in PDX sarcomas. Thus, this attIL12-TIL therapy holds great clinical potential for boosting T-cell infiltration in high-grade, collagen-rich tumors.

overall_design: Transcriptome profile comparison between attIL12-T cell responders vs. non-responders


title: RNAseq analyses of Esophageal biopsies from proton pump inhibitor (PPI)-responsive and PPI-unresponsive Pediatric patients with Eosinophilic Esophagitis.

status: Public on Jul 24 2025

city: Ann Arbor

first: Simon

last: Hogan

state: Michigan

address: 109 Zina Pitcher Place

department: Pathology

country: USA

institute: University of Michigan

type: Expression profiling by high throughput sequencing

summary: Clinical trials have identified two distinct eosinophilic esophagitis (EoE) treatment phenotypes, proton pump inhibitor (PPI)-responsive (PPI-R) and PPI-unresponsive (PPI-UR). Herein, we performed clinical, endoscopic, and histologic evaluation of esophageal biopsies from pediatric PPI-R and PPI-UR EoE individuals prior to PPI therapy (diagnosis) and following PPI trial.  RNAseq analyses of esophageal biopsy samples revealed common immune and inflammatory transcriptional signatures in both PPI-R EoE and PPI-UR EoE at diagnosis and distinct signatures enriched for processes related to neuropeptide signaling and cell cycle and division. PPI therapy induced histologic, endoscopic, and transcriptional remission in PPI-R EoE, but not in PPI-UR EoE. Persistent disease in PPI-UR EoE was associated with the presence of Th2 inflammatory and dedifferentiated esophageal epithelial transcriptomic signatures, while PPI-R EoE revealed genes enriched in cellular responses to LPS, host defense to viruses and type-I interferon signaling. In silico analyses identified common and unique EoE disease gene drivers in PPI-R and PPI-UR EoE. These studies indicate that the two EoE phenotypes have unique transcriptomic elements that underlie the molecular nature of PPI-R and PPI-UR EoE disease.

overall_design: Experimental Design Description: This study employed RNA sequencing to investigate transcriptomic differences in esophageal tissue from pediatric patients with eosinophilic esophagitis (EoE) and their response to proton pump inhibitor (PPI) therapy. Esophageal biopsies were collected from pediatric patients presenting with EoE symptoms who underwent esophagogastroduodenoscopy (EGD) with biopsies at the Mount Sinai Center for Eosinophilic Disorders. Study Groups: PPI-Responsive (PPI-R): EoE patients with symptom resolution and eosinophil counts reduced to <15/HPF following high-dose PPI treatment (n=5). PPI-Unresponsive (PPI-UR): EoE patients who did not meet response criteria after PPI treatment (n=5) Controls: Patients with 0 esophageal eosinophils/HPF, normal endoscopy, and no esophageal or gastrointestinal pathology (n=5). Sample Size: The study included 15 pediatric patients across three groups, with 5 biological replicates per condition to ensure adequate statistical power for differential gene expression analysis. Inclusion/Exclusion Criteria: EoE diagnosis required symptoms of esophageal dysfunction and ≥15 eosinophils per high-power field (HPF) per consensus guidelines. All EoE patients received standardized high-dose omeprazole or lansoprazole treatment (1-2 mg/kg/day up to adult dose twice daily) according to current pediatric and adult guidelines. Patients with concurrent gastrointestinal diseases, additional therapies, or dietary changes during the study period were excluded. Sample Collection and Processing: Esophageal biopsies were immediately preserved in RNALater solution for transcriptomic analysis. RNA sequencing was performed using Illumina platform with stringent quality control measures (RNA Integrity Number >8). Bioinformatics Pipeline: Raw sequencing reads underwent quality assessment using FASTQC and were processed with Trimmomatic for adapter removal and quality trimming. Processed reads were aligned to the human reference genome (GRCh38) using HiSAT2 aligner, followed by gene quantification using feature-counts. Duplicate sample validation confirmed >99% genome alignment identity and >98% sequencing depth consistency across replicates. Statistical Analysis: Differential gene expression analysis was conducted using DESeq2 with statistical significance defined as adjusted p-value ≤0.05 and absolute log2 fold change >1. Study Population: The cohort included both male and female pediatric patients. Reflecting the known male predominance in EoE, males comprised 60% of the study population.

first: Somdutta

last: Chakraborty

first: Ankit

last: Sharma

first: Sahiti

last: Marella

first: Christian

last: Rizza

first: Patrick

middle: A

last: O’Brien

first: Varsha

last: Ganesan

first: Gila

last: Idelman

first: Susie

last: Min

first: Mayee

last: Chen

first: Talaya

last: McCright-Gill

first: Nancy

last: Gonzalez

first: Alexandros

middle: D

last: Polydorides

first: Paul

middle: S

last: Foster

middle: P

first: Mirna

last: Chehade


title: Effect of JAM3 knockdown on glioma cell transcriptome

city: Nantes

first: Julie

last: Gavard

address: 8 quai Moncousu

country: France

institute: INSERM

summary: The JamC adhesion molecule plays a potential role in glioblastoma stem cell adhesion and interaction with the vascular niche. To study this, we performed JamC knock-out (KO) in GSC1 and GSC4 cells and analyzed transcriptomic changes using 3’ end RNA-seq (3’SRP).

overall_design: 3’ RNA sequencing of 20 samples from GSC1 and GSC4 glioblastoma stem cells: 8 wild-type (WT) and 12 JamC knock-out (KO), analyzed for differential gene expression.

first: Sara

last: Rosinska


title: Sox11 genes affect neuronal differentiation in the developing zebrafish enteric nervous system

status: Public on Jul 23 2025

city: Pasadena

first: Yuanyun

last: Huang

state: CA

address: 1200 E.California Blvd MC156-29, Caltech

department: Biology and Biological Engineering

institute: California Institute of Technology

type: Genome binding/occupancy profiling by high throughput sequencing

summary: The vertebrate enteric nervous system (ENS) is derived from vagal neural crest cells, which enter the foregut as progenitors that migrate from rostral to caudal to populate the entire length of the gut. Here, we show that transcription factors sox11a and sox11b, zebrafish orthologs of the human sox11 gene, are highly expressed in neural crest cells transitioning from progenitors to differentiating neuronal subtypes. Accordingly, CRISPR-Cas9 depletion shows that loss of sox11 paralogs reduces the number of neurons that express the inhibitory motor neuron marker adcyap1b without affecting cell proliferation or death. Transcription factor footprinting analysis of open chromatin regions identified by ATAC-seq reveals sox11 binding sites in the adcyap1b enhancer. Furthermore, mutational analysis shows these binding sites are required for mediating enhancer-driven reporter expression. Taken together, our results demonstrate an important and previously unrecognized role for sox11a and sox11b in neuronal subtype specification in the developing zebrafish ENS.

overall_design: bulk ATAC-seq of trunk region (head removed) of Tg(phox2bb:Kaede) zebrafish line at 3dpf, including bulk ATAC-seq of phox2bb+ and phox2bb- cells, respectively.

first: Can

last: Li

first: Ayyappa Raja

last: Desingu Rajan

first: Marianne

middle: E

last: Bronner


title: Fusion oncoproteins and cooperating mutations define disease phenotypes in NUP98-rearranged leukemia [RNA-seq]

city: Memphis

first: Jeffery

last: Klco

state: TN

address: 262 Danny Thomas Place

institute: St Jude Children's Research Hospital

summary: This series of expression data aims to investigate transcriptional profiling of cell lines or cord blood CD34+ cells transduced with various NUP98 fusion oncoproteins with or without cooperating alterations of RB1 loss or WT1 frameshift alterationss and menin inhibition with revumenib treatment.

overall_design: Differentially expressed genes between conditions were assessed by Limma using triplicated samples at least. Functional annotation of DEGs were performed by DAVID. GSEA was used to assess changes related to signals or pathways as well. Expression data from cell lines or cord blood CD34+ cells transduced with NUP98 fusion oncoproteins were also analyzed with patient sample RNA-sequencing data from patient samples separately deposited to EGA. Detailes of analytic pipelines are found in the Method section of the manuscript.

first: Masayuki

last: Umeda


title: Fusion oncoproteins and cooperating mutations define disease phenotypes in NUP98-rearranged leukemia

summary: This series of single cell RNA sequencing data aims to investigate the heterogeneity of cellular hieararchies among pediatric acute myeloid leukemia and acute lymphoblastic leukemia with NUP98-rearrangement.

overall_design:
In total, 9 samples from 8 patiets of pediatric leukemia with NUP98-rearrangements (NUP98::NSD1, NUP98::KDM5A, NUP98::RAP1GDS1) were subjected for single cell RNA sequencing. Publicly available diagnosis and relapse-paired samples from a patient with NUP98::NSD1 AML is included from GSE235063 (GSM7494309, GSM7494310). Data processing, embedding, and projection of data onto normal hematopoietic cell reference (PMID: 39587259) were performed using Seurat (v4.1.0, RRID: SCR_007322).

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human primary patient data
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title: A novel mutant allele of Mta3 in the mouse: genetic analysis of roles in immunity and androgen biology

city: Research Triangle Park

last: Wade

state: NC

address: 111 TW Alexander Drive

department: Laboratory of Molecular Carcinogenesis

institute: NIEHS

summary: The metastasis associated (MTA) proteins, encoded in mammals by three highly similar gene paralogs, Mta1, Mta2, and Mta3, are integral components of the nucleosome remodeling deacetylase (NuRD) complex. While biochemical and molecular studies have probed the functions of the Mta gene family, genetic data in animals is less complete. Here we report the creation of a novel allele of Mta3 in which the first two coding exons, which encode the bromo-adjacent homology (BAH) domain of Mta3, are deleted. Animals homozygous for this Mta3DBAH allele are viable, fertile, and have no obvious deleterious phenotype. Exploration of the Mta3DBAH allele revealed that the Mta3 locus has an unannotated promoter located between Mta3 exons 3 and 4, which is unperturbed in the Mta3DBAH allele, which appears to drive expression of an MTA3 protein variant lacking the BAH domain. To explore the genetic relationship of this allele to the paralog Mta1, the Mta3DBAH animals were crossed to animals bearing the Mta1tm1a(EUCOMM)Wtsi allele, no double homozygous mutant animals were recovered, indicating synthetic lethality between these two Mta alleles. To understand the impact of the Mta3DBAH allele on functions previously described ex vivo, studies were performed to examine roles of Mta3 in the immune response and in androgen biology. Mta3DBAH homozygous animals have modest defects in B lymphocyte activation and antibody production, which could result in a selective disadvantage in a natural environment. Conditional mutation in B lymphocytes revealed selection for cells escaping deletion in post germinal center stages of antigen-dependent activation. No genetic requirements for Mta3 in androgen biology in adults were documented, but mutant animals display behavior defects consistent with altered androgen levels during early postnatal life. These studies clarify the genetic requirements for MTA proteins in mammalian development and identify specific functions for MTA3.

overall_design: Bulk RNAseq profiling of mouse testis from wild type or Mta3 mutant (lacking BAH domain) genotypes.

first: Kathryn

last: Headley


title: Orchestration of pluripotent stem cell genome reactivation during mitotic exit [ATAC-seq]

city: Lausanne

first: David

middle: Michael

last: Suter

address: Station 19

department: SV-IBI

country: Switzerland

institute: EPFL

summary: The maintenance of cell identity faces many challenges during mitosis, as most DNA-binding proteins are evicted from DNA and transcription is virtually abolished. How cells maintain their identity through cell division and faithfully re-initiate gene expression during mitotic exit is unclear. Here, we developed a novel reporter system enabling cell cycle synchronization-free separation of pluripotent stem cells in temporal bins of < 30 minutes during mitotic exit. This allowed us to quantify genome-wide reactivation of transcription, sequential changes in chromatin accessibility, and re-binding of the pluripotency transcription factors OCT4, SOX2, and NANOG (OSN). We found that transcriptional activity progressively ramped up after mitosis and that OSN rapidly reoccupied the genome during the anaphase-telophase transition. We also demonstrate transcription factor-specific, dynamic relocation patterns and a hierarchical reorganization of the OSN binding landscape governed by OCT4 and SOX2. Our study sheds light on the dynamic orchestration of transcriptional reactivation after mitosis.

overall_design: ATAC-seq on OCT4, SOX2, and NANOG in CGR8 Cdt1-MD mESCs under physiological conditions or of 44iN in the presence or absence of doxycycline

first: Silja

last: Placzek

first: Ludovica

last: Vanzan

first: Cédric

last: Deluz

middle: M


title: High levels of endogenous Omega-3 Fatty Acids prolong the lifespan, promote antigen presentation, and improve DC-based cancer vaccine efficacy in mice

status: Public on Jul 29 2025

city: Bethesda

first: Katherine

last: Goldfarbmuren

state: MD

address: 41 Center Dr

department: Advanced Biomedical Computational Science

institute: NCI, Frederick National Laboratory for Cancer Research

summary: Antigen presentation by dendritic cells (DCs) is crucial in activating T-cells. DCs capture, process, and present antigens to T-cells, making them attractive vaccine vehicles. However, most DC cancer vaccines have had limited clinical efficacy, suggesting a need to increase their potency. We report that high omega-3 fatty acids in mice can significantly prolong lifespan and reduce tumor growth and body weight loss. This effect is mediated in part by more effective DC antigen presentation.  DCs derived from Tg(CAG-fat-1)JxkJ (FAT-1) transgenic mice expressing high omega-3 lipid levels are better vaccine vehicles than wild-type (WT) DCs in treating cancers in WT mice and in stimulating CD8 T cell responses in vitro and in vivo. While no effect on costimulatory molecules was detected, we discovered a marked enhancement of T-cell dwell time on DCs. Differentiating DCs from bone marrow in the presence of omega-3 lipids can increase DC vaccine efficacy.

overall_design: For the bulk RNAseq part of this study, we compared bone marrow, immature and mature BMDCs from FAT1 or WT mice (3 independent biological replicates per group).

first: Shweta

last: Tiwary

middle: C

first: Kevin

last: Hsu

first: Zhen

last: Xia

first: Jay

last: Berzofsky


title: Orchestration of pluripotent stem cell genome reactivation during mitotic exit [ChIP-seq]

overall_design: Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) on OCT4, SOX2, and NANOG in different mESC lines under physiological conditions or in the precence or absence of doxycycline


title: Orchestration of pluripotent stem cell genome reactivation during mitotic exit [RNA-Seq]

overall_design: RNA-seq on CGR8 Cdt1-MD mESCs under physiological conditions


title: Orchestration of pluripotent stem cell genome reactivation during mitotic exit

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

overall_design: Refer to individual Series


title: Orchestration of pluripotent stem cell genome reactivation during mitotic exit [ChIP-Seq]


title: Orchestration of pluripotent stem cell genome reactivation during mitotic exit [RNA-seq]


title: endometriosis stromal cell with estrogen

status: Public on Jul 22 2025

city: bunnkyo Tokyo

first: Gentaro

last: Izumi

address: 7-3-1 hongo

country: Japan

institute: The university of Tokyo

summary: Objective : To compare transcriptomes induced by the estrogen components of combined oral contraceptives, estetrol (E4), and ethynylestradiol (EE), and estradiol (E2) in human primary endometriotic stromal cells (ESCs). Design: ESCs were cultured in the presence of E4 (10-6 mol/L), E2 (10-8 mol/L) or EE (10-9 mol/L) for 24 hours. The transcriptomes induced by E4 were compared with those by E2 and EE. Subjects: ESCs were obtained from patients with ovarian endometriomas. Main Outcome Measures: Comprehensive transcriptomes were examined using RNA sequencing analysis. mRNA levels were measured using reverse transcription and quantitative polymerase chain reaction (RT-qPCR) analysis. Results: E4 treatment resulted in 114 differentially expressed genes compared to the control (|log2fold change| >0.2). Within these genes, 79% (90 genes) changed in the same manner as with EE and E2. Of these genes, the expression levels of GREB1, PGR and BMP6 were validated using RT-qPCR analysis. In contrast, 21% (24 genes) changed in E4-preferential manner. Of these genes, FAM72A and ENSG00000280800 were validated using RT-qPCR analysis. Conclusion: Our results showed that the effect of E4 on ESC gene expression generally similar to those caused by EE and E2 but differed for some genes. This study will advance our understanding of combined oral contraceptives that have practical importance for the treatment of endometriosis.

overall_design: compare RNA-experession of endometriosis stromal cell with E2,E4 or EE.

first: Marie

last: Nakajima

first: Kaori

last: Koga

first: Vita

last: Silvana

first: Mohammed

last: Elsherbini

first: Atsushi

last: Okumura

first: Michihito

last: Wada

first: Satoru

last: Yamanaka

first: Yasushi

last: Hirota

first: Yutaka

last: Oosuga


title: Sequencing-free whole genome spatial transcriptomics at molecular resolution in intact tissue

city: New Haven

first: Yubao

last: Cheng

state: Connecticut

address: 333 Cedar Street, 387A: Nathan Smith Bldg

institute: Yale University

summary: Recent breakthroughs in spatial transcriptomics technologies have enhanced our understanding of diverse cellular identities, spatial organizations, and functions. Yet existing spatial transcriptomics tools are still limited in either transcriptomic coverage or spatial resolution, hindering unbiased, hypothesis-free transcriptomic analyses at high spatial resolution. Here we develop Reverse-padlock Amplicon Encoding FISH (RAEFISH), an image-based spatial transcriptomics method with whole-genome coverage and single-molecule resolution in intact tissues. We demonstrate spatial profiling of 23,000 human or 22,000 mouse transcripts in single cells and tissue sections. Our analyses reveal transcript-specific subcellular localization, cell-type-specific and cell-type-invariant zonation-dependent transcriptomes, and gene programs underlying preferential cell-cell interactions. Finally, we further develop our technology for direct spatial readout of gRNAs in an image-based high-content CRISPR screen. Overall, these developments provide the research community with a broadly applicable technology that enables high-coverage, high-resolution spatial profiling of both long and short, native and engineered RNA species in many biomedical contexts.

overall_design: Gene expression profiling (RNA-seq) of A549-Cas9 cell line.

first: Shengyuan

last: Dang

first: Siyuan

last: Wang


title: A pan-immunotherapy signature to predict intratumoral CD8+ T cell expansions [bulkTCRseq_Trilateral]

city: Noda-shi

first: Mikiya

last: Tsunoda

state: Chiba

department: Molecular Preventive Medicine

institute: The University of Tokyo

summary: Effective cancer immunotherapy relies on the clonal proliferation and expansion of CD8+ T cells in the tumor.  However, our insights into clonal expansions are limited, owing to an inability to track the same clones in tumors over time. Here, we developed a multi-site tumor mouse model system to track hundreds of expanding and contracting CD8+ T cell clones over multiple timepoints in tumors of the same individual. Through coupling of clonal expansion dynamics and single-cell RNA/TCR-seq data, we identified a transcriptomic signature in PD-1+Ly108+ precursor exhausted cells that strongly predicts rates of intratumoral clone expansion. The signature correlates with expansion in mice, both with and without immunotherapies, and in patients undergoing PD-1 blockade therapy. Expression of the signature during treatment corresponds with positive clinical outcomes. Downregulation of the signature precedes clone contraction – a phase in which clones contract but maintain revivable precursor exhausted cells in the tumor. LAG-3 blockade re-activates the expansion signature, re-expanding pre-existing clones, including previously contracted clones. These findings reveal how the study of clonal expansion dynamics provide a powerful ‘pan-immunotherapy’ signature for monitoring immunotherapies with implications for their future development.

overall_design: Lewis lung carcinoma (LLC) cells (5 × 10^5 cells /mouse) were inoculated subcutaneously (s.c.) into the left flank, right flank and the left hip of C57BL/6 mice (untreated : n=5, aLAG3 : n=6).  tumors were excised sequentially in the order of left flank tumor, right flank tumor and left hip on days 14, 21 and 28. CD8+ T cells obtained from each tumor were analyzed by bulk TCR-sequencing.

first: Munetomo

last: Takahashi

first: Hiroyasu

last: Aoki

first: Masaki

last: Kurosu

first: Haru

last: Ogiwara

first: Shigeyuki

last: Shichino

first: David

last: Bending

first: Shumpei

last: Ishikawa

first: James

last: Thaventhiran

first: Kouji

last: Matsushima

first: Satoshi

last: Ueha


title: Gene expression profile of Cd45 positive cells in single cell level from KRASLSL.G12D/+P53LSL.R172H/+Pdx-Cre mice (KPC tumor mouse) model treated with stimulator of interferon genes  (STING) and lymphotoxin-beta receptor (LTbR) agonist [2024_v2]

first: Fumiaki

last: Kanamori

state: FL

address: 600 5th Street S

department: Department of Orthopaedic Surgery

institute: Johns Hopkins All Children’s Hospital.

summary: The combination treatment using STING and LTbR agonists improves the immune landscape in KPC tumor model. We used single-cell RNA sequence (scRNAseq) analysis to investigate the characteristics of Cd45 positive cells after treating the tumor.

overall_design:
Subcutaneous syngeneic KPC tumor of C57BL/6 mice was harvested. The tumor was dissociated into single cells, and Cd45-positive cells were sorted by fluorescence-activated cell sorting (FACS). We analyzed the immune landscape using scRNAseq.
Please note that two independent sRNAseq experiements were carried out (in 2023 and 2024, accessioned as GSE275840 and current record). Although treatment strategy is same, the mice cohort and 10X kit version is different (v2 or v3).

first: Yasuhiro

last: Kikuchi

first: Masanobu

last: Komatsu


title: Gene expression profile of Cd45 positive cells in single cell level from KRASLSL.G12D/+P53LSL.R172H/+Pdx-Cre mice (KPC tumor mouse) model treated with stimulator of interferon genes  (STING) and lymphotoxin-beta receptor (LTbR) agonist

overall_design: Subcutaneous syngeneic KPC tumor of C57BL/6 mice was harvested. The tumor was dissociated into single cells, and Cd45-positive cells were sorted by fluorescence-activated cell sorting (FACS). We analyzed the immune landscape using scRNAseq.

first: Junko

last: Sawada


title: Analysis of gene expression profiling in HCC treated with secreted lumican

city: Hong Kong

first: Chi Ho

last: Lin

address: 6th Floor, The Hong Kong Jockey Club Building for Interdisciplinary Research, 5 Sassoon Road, Pokfulam

department: Centre for PanorOmic Sciences

country: Hong Kong

institute: The University of Hong Kong

summary: RNA extracted from MHCC97L xenograft treated with or without recombinant human lumican (rhLUM) was subjected to RNA sequencing profiling. Expression profiling of RNA between the control and rhLUM-treated group was compared.

first: Regina

last: Lo


title: Orchestration of pluripotent stem cell genome reactivation during mitotic exit [ATAC-Seq]

last: Suter

first: Silja

last: Placzek

first: Ludovica

last: Vanzan


title: Ablation of Linker Histone H1.4 Reveals Focal Regulation of AP-1 Directed Enhancers and Chromatin Accessibility [ATAC-seq]

status: Public on Jul 21 2025

first: Nolan

middle: Garrity

last: Gokey

state: North Carolina

address: 111 TW Alexander Dr, Building 101 Room C432

department: DIR

summary: Linker histone H1 and the four nucleosomal histone proteins form the greater chromatosome superstructure of chromatin. While a critical component of the epigenetic landscape, the specific role of H1 has remained elusive due in part to compensation by other H1 family members, a lack of genome-wide analyses, and suitable model systems. Ablation of H1.4 in a human osteosarcoma line with high H1-4 expression resulted in broad changes in DNA accessibility as well as gene expression. Genes in critical signaling pathways are upregulated with H1.4 loss (RAR, acetylcholine/glutaminergic receptors) while extracellular matrix and collagen biosynthesis genes are repressed. The gene loci of the same critical pathways were enriched in differentially accessible chromatin after loss of H1.4, and many of this differential chromatin overlaps regions of known enhancer regions. The AP-1 binding motif was highly enriched at sites with reduced accessibility while sites with gained chromatin accessibility were enriched in more basal factor motifs (TBP, SRF). At sites of altered chromatin accessibility following H1.4-loss, concomitant changes to core histone proteins were observed (H3K27ac and H3K4me1), and the changes in PTMs was concordant with the change in accessibility. Alterations to chromatin accessibility and epigenetic activity were enriched at regions with known enhancer-like chromatin, and the size of the altered chromatin footprints were consistent with enhancer regions. Sites which gain chromatin accessibility localize to polycomb, heterochromatin and quiescent/low chromatin states, but were found to gain RNA transcription in cells lacking H1.4. Broad changes in chromatin accessibility and activity, as well as robust changes in gene transcription when H1.4 is abolished, place linker H1.4 as a hitherto underappreciated regulator of transcription response patterns as well as a dynamic member of regulatory chromatin.

overall_design: Establishment of two Linker histone H1.4-deficient human osteosarcoma cell lines and interrogation of changes to chromatin accessibilty (ATAC-seq) and chromatin activity (H3K27ac and H3K4me1 ChIP-seq). Further analysis of changes to both gene expression (RNA-seq) and nascent transcription (4sU-seq) were also performed.

middle: G

middle: W

last: Ward

first: Trevor

middle: K

last: Archer


title: Ablation of Linker Histone H1.4 Reveals Focal Regulation of AP-1 Directed Enhancers and Chromatin Accessibility [ChIP-seq]


title: Ablation of Linker Histone H1.4 Reveals Focal Regulation of AP-1 Directed Enhancers and Chromatin Accessibility [RNA-seq]


title: Ablation of Linker Histone H1.4 Reveals Focal Regulation of AP-1 Directed Enhancers and Chromatin Accessibility [4sU]


title: Pathogenic DICER1 RNase IIIb Hotspot Mutation Induces 3p-miRNA Gain-of-Function via Argonaute Strand Switch [RNA-seq]

status: Public on Jul 18 2025

city: Frederick

first: Sharan

last: Malagobadan

address: 1050 Boyles Street, Building 560, Room 11-2

institute: National Institutes of Health

summary: Dicer is an essential enzyme in microRNA biogenesis. Mutations in the DICER1 gene are linked to various cancers, notably through the DICER1 syndrome. To investigate the impact of the pathogenic hotspot mutations in DICER1-associated tumors, we introduced a hotspot mutation into the endogenous Dicer1 locus of a mouse embryonic carcinoma cell line using CRISPR. Our findings not only confirm the loss of 5p-miRNAs, as previously reported, but also uncover an unexpected upregulation of specific 3p-miRNAs. These upregulated 3p-miRNAs, usually considered as passenger strands in the wild-type cells, are selectively loaded into the Argonaute protein in mutant cells based on their 5' end characteristics, resulting in a "strand-switch" phenomenon. Functional assays and transcriptome analyses demonstrate the passenger 3p-miRNAs’ activity. This study suggests that the Dicer hotspot mutation is not merely a loss-of-function mutation for 5p-miRNAs but also a gain-of-function mutation for passenger 3p-miRNA, potentially contributing to DICER1-associated tumorigenesis.

overall_design: To generate cell line isogenic to the DICER1 syndrome (P19 HM), P19 mouse embryonic carcinoma cell line was endogenously modified with CRISPR to harbor the biallelic loss-of-function mutation RNase IIIb hotspot mutation (mouse E1797G) on the Dicer1 gene. P19 HetKO (with only loss-of-function mutation on one allele) is included as a control. Library for mRNA-seq was generated using Illumina® Stranded mRNA Prep (Illumina, 20040532) and sequenced on NovaSeq 6000 SP using paired-end sequencing by the NCI CCR Sequencing Facility.

first: Shuo

last: Gu


title: Pathogenic DICER1 RNase IIIb Hotspot Mutation Induces 3p-miRNA Gain-of-Function via Argonaute Strand Switch [CLASH]

overall_design: To generate cell line isogenic to the DICER1 syndrome (P19 HM), P19 mouse embryonic carcinoma cell line was endogenously modified with CRISPR to harbor the biallelic loss-of-function mutation RNase IIIb hotspot mutation (mouse E1797G) on the Dicer1 gene. Cross-linking, ligation, and sequencing of hybrids (CLASH) was used to identify miRNA-target RNA interaction sites.


title: ALS-associated RNA binding proteins converge on UNC13A transcription through regulation of REST

city: Sendai city

first: Yasuaki

last: Watanabe

state: Miyagi

address: 2-1, Seiryo-machi

department: Neurology

institute: Tohoku University

summary: Amyotrophic lateral sclerosis (ALS) is characterized by motor neuron degeneration. We demonstrate that ALS-associated RNA-binding proteins (RBPs)—MATR3, FUS, and hnRNPA1—regulate UNC13A transcription via REST mRNA stabilization. Loss of these RBPs increases REST levels, repressing UNC13A transcription and implicating synaptic dysfunction in ALS pathogenesis.

overall_design: We performed RNA-seq using wild-type and CRISPR/Cas9-generated MATR3-, FUS-, hnRNPA1-, and TDP-43-KO SH-SY5Y cell lines. Libraries were prepared using Illumina TruSeq Standard mRNA LT Sample Prep Kit and sequenced using Illumina HiSeq 2500 with paired-end 151 nt reads. Data were processed to identify gene expression changes associated with loss of ALS-related RBPs.

first: Keiko

last: Nakayama


title: YAP1/TAZ knockdown in melanoma

city: Philadelphia

first: Andrew

last: Aplin

state: PA

address: 233 South 10th St.

institute: Thomas Jefferson University

summary: Targeted therapies in cancer are limited by cells exhibiting drug tolerance. We aimed to target drug tolerance in order to delay the development of acquired resistance. In melanoma, tolerance to MAPK pathway inhibitors is associated with loss of SOX10 and an enhanced TEAD transcriptional program.  We show that loss of SOX10 is sufficient to up-regulate TEAD targets with dependence on the co-activator, TAZ. Active TAZ was sufficient to mediate tolerance to BRAF inhibitors and MEK inhibitors.  We developed novel covalent inhibitors, OPN-9643 and OPN-9652, designed to target the central palmitate binding pocket of TEADs.  In SOX10-deficient cells, OPN-9643 and OPN-9652 reduced TEAD-dependent reporter activity and expression of TEAD targets, CTGF and CYR61. OPN-9643 and OPN-9652 treatment enhanced the inhibitory effects of MAPK-targeted therapies in 2D and 3D growth assays and reversed tolerance mediated by active TAZ. In vivo, OPN-9652 delayed the onset of acquired resistance to BRAF inhibitors and MEK inhibitors from minimal residual disease. Thus, TAZ-TEAD activity plays an important role in melanoma drug tolerance and the development of acquired resistance.

overall_design: A375, 2.18 SOX10 KO, and 4.21 SOX10 KO cells were treated with reagent alone (-), non-targeting control siRNA, siYAP1, or siTAZ for 72 hrs and analyzed in triplicates. 54 total samples.

first: Connor

last: Ott

first: Timothy

middle: J

last: Purwin


title: Genetic Effects in Response to Exercise and Diet-induced Weight-loss in Human Skeletal Muscle Tissues

city: Singapore

first: Wenjing

last: Wang

address: Tahir Foundation Building, MD1 12 Science Drive 2; #13-05; Singapore 117549

country: Singapore

institute: National University of Singapore

summary: Bulk RNA sequencing on paired skeletal muscle biopsies collected from participants before and after a 16-week weight loss intervention.

overall_design: Paired-end RNA sequencing was performed with four technical replicates per sample. The experimental design implemented a paired-sample strategy where matched Pre and Post skeletal muscle biopsies from each participant (n = 54 pairs) were processed and sequenced in the same batch to control for technical variation.


title: Fusion oncoproteins and cooperating mutations define disease phenotypes in NUP98-rearranged leukemia [CUT&RUN]

first: Jeffery

last: Klco

summary: This series CUT&RUN data aims to investigate epigenetic profiling of primary leukemia samples, cell lines, or cord blood CD34+ cells transduced with various NUP98 fusion oncoproteins.

overall_design:
NUP98 fusion oncoproteins binding was assessed by CUT&RUN using HA antibodies in cord blood CD34+ cell models with HA-tagged NUP98 fusion oncoproteins or N-terminus NUP98 antibody in primary samples and cell lines. Epigenetic status and binding of epigenetic regulators (KMT2A, menin) were also assessed. Peaks are called using MACS2 for narrow peaks and SICER for broad peaks. Differential epigenetic status was assessed using PBS (probability-being signals).

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

first: Masayuki

last: Umeda


title: Pathogenic DICER1 RNase IIIb Hotspot Mutation Induces 3p-miRNA Gain-of-Function via Argonaute Strand Switch [miR-seq]

type: Non-coding RNA profiling by high throughput sequencing

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: To generate cell line isogenic to the DICER1 syndrome (P19 HM), P19 mouse embryonic carcinoma cell line was endogenously modified with CRISPR to harbor the biallelic loss-of-function mutation RNase IIIb hotspot mutation (mouse E1797G) on the Dicer1 gene. P19 HetKO (with only loss-of-function mutation on one allele) is included as a control. For Dicer overexpression experiments, wild-type of human E1813G Dicer was transfected in HEK293T Dicer KO cells. Sequencing was done with total RNA and AGO2-IP samples for each group with replicates. miR-seq was performed using the QIAseq miRNA Library Kit for all samples.

first: Malagobadan

last: Sharan

first: Gu

last: Shuo


title: Single-cell and bulk RNA sequencing of mouse atherosclerosis disease stage course [TRAP-seq]

city: Kuopio

first: Tiit

last: Örd

address: Neulaniementie 2

country: Finland

institute: A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland

summary: Atherosclerotic coronary artery disease (CAD) development encompasses changes in immune cell activation across different tissues, including vascular and metabolic tissues. However, the specific disease-associated transcriptional changes occurring within each of the tissue cell types remain incompletely characterized. Here, we combine an atherosclerosis mouse model with a mouse strain designed for translating ribosome affinity purification followed by RNA sequencing (TRAP-Seq). The mice express a fusion protein of EGFP and ribosomal protein L10a (EGFP-L10a) under the control of the macrophage-specific Csf1r (Cfms) promoter. Using EGFP as an affinity tag, this enables the enrichment of macrophage-specific ribosome-associated RNA from whole tissue lysates. Here, we profile the macrophage-enriched RNA fraction from aorta, liver and adipose tissue.

overall_design: A disease stage course of atherosclerosis in mouse was established by varying genotype (wild type and proatherogenic LDLR-/- ApoB100/100) and diet (0, 1 or 3 months of high-fat diet) in mice expressing EGFP-tagged ribosomal protein L10a (EGFP-L10a) under the control of a macrophage-specific promoter. Using the EGFP-L10a transgene, TRAP-Seq was performed from aorta, liver and perigonadal adipose tissue (epididymal in male and periovarial in female) to sequence macrophage-enriched RNA.

first: Henri

last: Niskanen

first: Aarthi

last: Ravindran

first: Retu

last: Haikonen

first: Minna

middle: U

last: Kaikkonen


title: TEADi treatment in melanoma cells

overall_design: 2µM treatment for 48 hours of either OPN-9652 or OPN-9643, or DMSO in A375 Parental, 2.18 or 4.21 SOX10 KO analyzed in triplicates. 27 total samples.


title: Daphnane diterpenoids for cancer therapy by suppressing ATR-mediated DNA damage response pathway

status: Public on Jul 15 2025

city: Guangzhou

first: 雷名

last: 吴

address: sun-yat san university

country: China

institute: 中山大学药学院

summary: In this study, 26 structurally diverse daphnane diterpenoids (1-26) including six undescribed ones (1-6) were isolated from the whole plants of Daphne odora.  Compounds 1 and 2 were the most active with IC50 values of 3.57 ± 0.32 and 4.35 ± 0.14 μM, respectively. Mechanistic study indicated that 1 and 2 could significantly induce cell cycle arrest at the G2/M phase and cause cell apoptosis. Further examination by transcriptome sequencing analysis revealed that 1 and 2 significantly suppressed ATR-mediated DNA damage response and cell cycle checkpoint.

overall_design: HCC827 non-small cell lung cancer cells mRNA profiles of treatment with compounds 1 and 2 (5 μM, 24h)

first: Sheng

last: Yin

first: Shuqi

last: Wu

first: Leiming


title: Unveiling the Molecular Legacy of Transient Insulin Resistance: Implications for Hepatic Metabolic Adaptability [RNA-Seq]

status: Public on Jul 17 2025

city: Lille

first: Alexandre

last: Berthier

address: U1011, Bâtiment J&K, Bd du Pr Leclerc

institute: Inserm

summary: Metabolic flexibility (MetF) refers to an organism's capacity to adapt to changes in metabolic supplies and energy demands. MetF involves various organs, such as skeletal muscle, white adipose tissues, and the liver, and plays a critical role in altering fuel selection. Insulin acts as a central coordinator of MetF, regulated at the molecular level through various mechanisms, including signaling cascades, transcriptional responses, and circadian regulation. Insulin resistance (IR) can hinder MetF, leading to the development of type 2 diabetes and obesity. These conditions are primarily linked to long-term, chronic exposure to sedentary lifestyles, unbalanced diets, and disruptions in circadian rhythms. However, transient episodes of IR significantly elevate the risk of later-in-life development of type 2 diabetes, as seen in cases like gestational diabetes and stress-induced hyperglycemia. Despite their significance to human health, the molecular processes underlying metabolic dysregulation after these transient episodes remain poorly understood. In our study, we demonstrate that a temporary and fully reversible insulin receptor blockade in young mice results in later-in-life hepatic abnormalities that impair the PPARα-mediated response to a high-fat diet. This impairment is associated with increased histone repressive marks at PPARα-centered loci and decreased hepatic content of PPARα endogenous ligands. Transient insulin receptor blockade temporarily disrupts the liver's circadian rhythm, and this disruption specifically propagates to high-fat diet-fed animals. Our findings reveal that PPARα ligand responsiveness is critically influenced by the circadian clock, adding another layer of (dys)regulation to hepatic homeostasis due to early transient events.  In summary, our data suggest that seemingly reversible and unnoticed metabolic challenges in early adulthood may predispose the liver to exacerbated metabolic dysfunctions when confronted with chronic challenges later in life.

overall_design: Pemafibrate-dependent transcriptome modulation of ("circadianly")synchronized AML12 cells by RNA sequencing. Each condition has been conducted in triplicate. We conduced this experiment in a classical way as reference (24h exposition) or in a short term exposition (6h) a two diffrent circadian periods mimicing day (t14) or night (t24) expositions

first: Loïc

last: Guille

first: Philippe

last: Lefebvre


title: Remote-control of AMPK via extracellular adenosine controls tissue growth

status: Public on Jul 16 2025

city: Heidelberg

first: Yao

last: Zhang

address: Im Neuenheimer Feld 580

country: Germany

institute: Deutsches Krebsforschungszentrum (DKFZ)

summary: AMPK is a regulator of cellular catabolism that is activated by AMP. Since AMP accumulates in cells with low ATP, AMPK is considered a stress activated kinase. Here, while studying organ growth during Drosophila development, we find that AMPK is activated by a signaling metabolite not related to stress. We find that the two main physiological inputs that regulate organ growth rates during development - the hormone ecdysone and dietary protein - both regulate expression in the intestine of an enzyme, adenosine deaminase. This leads to changes in the levels of adenosine in circulation. Circulating adenosine acts as a signaling molecule by entering into cells, becoming phosphorylated to adenosine mono-phosphate (AMP) and activating AMPK to inhibit organ growth. Thus AMPK activity is regulated developmentally, and AMPK in one tissue such as the wing can be remote-controlled by another tissue such as the intestine via circulating adenosine. Interestingly, this mechanism accounts for half of the effect of dietary protein on tissue growth rates in Drosophila.

overall_design: RNA-seq profiling of intestine from spoki larvae with con and EcRi in enterocytes

first: Katrin

last: Strassburger

first: Aurelio

last: Teleman


title: Single-cell RNA-seq of human kidney organoids [5_250K cells]

city: Pamplona

first: Asier

last: Ullate-Agote

state: Navarra

address: Av. de Pío XII, 55

department: Hemato-Oncology

country: Spain

institute: CIMA

summary: Human pluripotent stem cells (hPSCs) derived organoids hold great promise for transplantation purposes however technological advances to overcome their massive production while ensuring differentiation fidelity are still missing. Here we develop a new procedure sustaining the derivation of hPSC-kidney organoids to identify a new scalable, uniform, and affordable approach empowering differentiation and cellular diversity. Using single-cell RNA sequencing, confocal image analysis and metabolic assays we show that hPSC-kidney organoids exhibit transcriptional variety and cellular composition which is boosted forcing cell-to-cell contact. To demonstrate the applicability of these findings we infused CRIPSR/Cas9 engineered WT1 GFP kidney organoids during normothermic machine perfusion (NMP) using porcine kidneys. NMP flow patterns showed stable rates among biological experiments. Samples were analyzed by in situ hybridization, confocal microscopy, and flow cytometry identifying cells of human origin after infusion. This work paves the way to the utilization of hPSC-kidney organoids for ex vivo cell-based therapies to improve graft function before transplantation.

first: Nuria

last: Montserrat

first: Elena

last: Garreta


title: Metabolic control of adaptive b-cell proliferation by the protein deacetylase SIRT2

city: La Jolla

first: Maike

last: Sander

address: 2880 Torrey Pines Scenic Dr.

institute: UC San Diego

summary: Selective and controlled expansion of endogenous b-cells has been pursued as a potential therapy for diabetes. Ideally, such therapies would preserve feedback control of b-cell proliferation to avoid excessive b-cell expansion and an increased risk of hypoglycemia. Here, we identified a regulator of b-cell proliferation whose inactivation results in controlled b-cell expansion: the protein deacetylase Sirtuin 2 (SIRT2). Sirt2 deletion in b-cells of mice increased b-cell proliferation during hyperglycemia with little effect in homeostatic conditions, indicating preservation of feedback control of b-cell mass. SIRT2 restrains proliferation of human islet b-cells cultured in glucose concentrations above the glycemic set point, demonstrating conserved SIRT2 function. Analysis of acetylated proteins in islets treated with a SIRT2 inhibitor revealed that SIRT2 deacetylates enzymes involved in oxidative phosphorylation, dampening the adaptive increase in oxygen consumption during hyperglycemia. At the transcriptomic level, Sirt2 inactivation has context-dependent effects on b-cells, with Sirt2 controlling how b-cells interpret hyperglycemia as a stress. Finally, we provide proof-of-principle that systemic administration of a GLP1-coupled Sirt2-targeting antisense oligonucleotide achieves b-cell selective Sirt2 inactivation and stimulates b-cell proliferation under hyperglycemic conditions. Overall, these studies identify a therapeutic strategy for increasing b-cell mass in diabetes without circumventing feedback control of b-cell proliferation.

overall_design: The response of pancreatic beta cells to systemic insulin resistance caused by the insulin receptor antagonist S961 in control islets and in islets of beta cell-specific Sirt2 KO mice was assessed by scRNAseq.

first: Matthew

last: Wortham


title: The Tip60 acetylome is a hallmark of the proliferative state in Drosophila

city: Planegg-Martinsried

first: Zivkos

last: Apostolou

address: Großhaderner Strasse 9

institute: Biomedical Center Munich, LMU

summary: The acetyltransferase KAT5/Tip60 is an epigenetic regulator of transcription and the DNA damage response. In Drosophila, Tip60 acetylates histones as part of the Dom-A complex, but it is unclear whether it has other substrates. In this work, we comprehensively studied the functions of Tip60 in a Drosophila proliferative cell model. Depletion of Tip60 arrests the cell cycle, but remaining viable cells resist mutagenic irradiation. The impaired proliferation is explained by reduced expression of critical cell cycle genes. Tip60 binds their transcription start sites and Tip60-dependent acetylation of the histone variant H2A.V correlates with transcription activity. A potentially synergistic pathway for cell cycle regulation involves the acetylation of proteins other than histones. The Tip60-dependent nuclear acetylome contains hundreds of proteins, many of which are involved in diverse aspects of cell growth and division, including replication, mitosis, gene expression, chromatin organization and ribosome biogenesis. We hypothesize that Tip60 coordinates the proliferative state through histone and non-histone effectors. Reversible acetylation of diverse effector proteins bears potential for fine-tuning energy-intensive processes in response to stresses or nutritional shortcomings. Our study portrays the DOM-A/TIP60 complex as a general promoter of cell proliferation.

overall_design: CUT&RUN profiling was performed for Tip60, H2A.V, H2A.Vac, and H4K12ac in Drosophila Kc167 cells following RNAi-mediated depletion of Tip60. Three biological replicates were generated for all conditions, except for H4K12ac, which included one replicate. Additionally, ChIP-seq was conducted for H4K12ac in S2 cells with one biological replicate.

first: Anuroop

middle: V

last: Venkatasubramani

first: Lara

last: Kopp

first: Gizem

last: Kars

first: Alessandro

last: Scacchetti

first: Aline

last: Campos-Sparr

first: Tamas

last: Schauer

first: Axel

last: Imhof

first: Peter

middle: B

last: Becker


title: Effect of diurnal oxygen variation on gene expression in Pacific white shrimp reared in green water system tanks

city: Auburn

first: Jason

last: Abernathy

state: AL

address: 990 Wire Road

institute: USDA-ARS

summary: World aquaculture production of the Pacific white shrimp (Litopenaeus vannamei) is estimated to account for 80% of the total shrimp produce worldwide. The global demand for shrimp has driven the industry to utilize and rely on semi-intensive and intensive shrimp systems. In the United States, Pacific white shrimp production can take place in semi-intensive earthen ponds, recirculating aquaculture systems (RAS), biofloc technology and green water. In this study, the effects of lowering dissolved oxygen conditions in outdoor green water tanks on global gene expression is examined. Tissue samples from the gill and intestine were collected for gene expression analysis via RNA sequencing. Among all comparisons, RNA sequencing revealed the up-regulation of a single gene: hydroxyacid oxidase 1 gene. The HOA1 gene was found to be 7-fold higher in the intestine sample at the medium aeration level compare to that of the high (control) level. The HAO1 gene, also known as glycolate oxidase 1 (GOX1) is a gene related to the 2-hydroxyacid oxidase enzyme that is part of the oxidoreductase family and plays a role in glyoxylate and dicarboxylate metabolism. The identification of a single differentially expressed gene across all analyzed samples suggests that Pacific white shrimp exposed to lowering dissolved oxygen set points does not induce global changes in gene expression at these levels.

overall_design: Twelve (800 L) round tanks were stocked each with 35 shrimp (1.99 ± 0.06g) and reared in 15 ppt green water system tanks for 6 weeks. Four of the tanks were aerated at 0.25 cubic feet per second (cfs; low), four at 0.35 cfs (medium) and four at 0.7 cfs (high). The experiment was terminated 42 days after stocking, when two shrimp per tank were randomly collected, and gill (fourth gill filament from one side) and intestine were extracted and preserved in DNA/RNA shield (ZYMO Research, Irvine, CA, USA) for RNA sequencing.

first: Cristhian

last: San Andres

first: Julio

last: García

first: Nithin

last: Sankappa

first: Adela

last: Araujo

first: Trenton

last: Corby

first: Khanh

last: Nguyen

first: Melanie

last: Rhodes

first: Luke

last: Roy

first: Donald

last: Davis


title: Single-cell and bulk RNA sequencing of mouse atherosclerosis disease stage course [adipose_liver_bulkRNA]

first: Tiit

last: Örd

summary: In addition to the pathological processes in the vascular wall, atherosclerotic coronary artery disease (CAD) development is affected other tissues, including metabolic tissues such as liver and white adipose tissue (WAT). However, the transcriptional events occurring in metabolic tissues in response to pro-atherosclerotic conditions (hypercholesterolemia and obesogenic diet), remain incompletely understood. Here, we profile liver and WAT gene expression in mouse at increasing exposure levels of atherogenic factors.

overall_design: A disease stage course of atherosclerosis in mouse was established by varying genotype (wild type and proatherogenic LDLR-/- ApoB100/100) and diet (0, 1 or 3 months of high-fat diet), followed by bulk RNA-Seq of liver and perigonadal adipose tissue (epididymal in male and periovarial in female).

first: Henri

last: Niskanen

first: Aarthi

last: Ravindran

first: Retu

last: Haikonen

first: Minna

last: Kaikkonen


title: Repurposing Zafirlukast Confers Renal Protection in Ischemia-Reperfusion Injury via Suppressing Macrophage METosis [RNA-Seq]

status: Public on Jul 14 2025

city: wenzhou

first: Longwei

last: Zhao

address: University-Town, Wenzhou, Zhejiang, P.R.China

institute: Wenzhou Medical university

summary: Tacrolimus is widely used to prevent post-transplant acute kidney injury (AKI) but causes severe toxicities (e.g., nephrotoxicity, hyperglycemia). We repurposed zafirlukast (ZFK), an FDA-approved asthma drug, to address this limitation. In a murine kidney ischemia-reperfusion injury (KIRI) model, ZFK significantly attenuated renal dysfunction, reducing serum creatinine and blood urea nitrogen (BUN) to levels comparable to tacrolimus, without inducing metabolic adverse effects. RNA sequencing revealed that ZFK recapitulated tacrolimus’ anti-inflammatory gene signatures while uniquely suppressing macrophage extracellular trap formation (METosis). Mechanistically, ZFK inhibited METosis by downregulating PAD4 and CitH3 expression, confirmed by immunofluorescence and flow cytometry. Single-cell transcriptomics (Tabula Muris and GEO database) identified macrophages as the primary target via CysLT1R antagonism. This study provides the first evidence that ZFK protects against KIRI by targeting METosis, a key driver of sterile inflammation. Given its established safety profile, ZFK could bypass Phase I trials, accelerating clinical translation as a safer alternative to calcineurin inhibitors. Our findings also highlight the broader potential of ZFK in METosis-related diseases (e.g., sepsis, atherosclerosis) and underscore drug repurposing as a strategic approach for rapid therapeutic development.

overall_design: Male C57BL/6J mice were randomly divided into two experimental groups (n=6 per group) as follows: (i) I/R group: Received daily oral administration of 0.9% saline for 1 consecutive day, followed by partial bilateral renal ischemia for 30 minutes and subsequent 24-hour reperfusion;(ii) Tacrolimus + I/R group: Received daily oral administration of tacrolimus (1 mg/kg/day) for 1 consecutive day, followed by laparotomy with bilateral renal artery occlusion for 30 minutes and subsequent 24-hour reperfusion. All animals were anesthetized by intraperitoneal injection of pentobarbital sodium (0.5%, 0.01 mL/g). At the conclusion of the experimental period, the animals were humanely sacrificed by decapitation. Blood was collected via cardiac puncture and centrifuged at 4,000 × g for 10 minutes. The resulting sera were isolated and stored at -80°C for biochemical assessments. The kidneys were excised and divided into three portions. The first portion was homogenized in phosphate-buffered saline, then centrifuged, and the supernatant was stored at -80°C for RNA sequencing assays. The second portion was rapidly frozen in liquid nitrogen and stored at -80°C for Western blot analysis and quantitative PCR. The third portion was immersed in 4% paraformaldehyde for histopathological and immunohistochemical investigations.

first: Xiaochun

last: Ye

first: Meiyun

last: Wen

first: Yumei

last: Huang

first: Ruofang

last: Zheng

first: Ping

last: Wang

first: Ran

last: Chen


title: Paired-Tag single-cell joint profiling of H3K27me3-H3K4me1 and transcriptome revealed prenatal e-cigarette induced abnormal neuronal lineage development in rat neonatal prefrontal cortex

city: Loma Linda

first: Charles

address: 11021 Campus Street

department: Department of Basic Sciences

institute: Loma Linda University

summary: We performed single-nucleus joint profiling of transcriptome and histone modifications, namely H3K27me3 and H3K4me1, in prenatal electronic cigarette exposed neonatal rat prefrontal cortex. We found that e-cig not only induced unique histone mark patterns for H3K27me3-H3K4me1 within the gene body in many cell type-specific marker genes, e.g., Fibcd1, Slc1a3, Apq4, and Rfx4, but also caused a differential gene expression for these genes. We demonstrated that H3K27me3-H3K4me1 bivalency regulated the neuronal lineage differentiation by controlling the accessibility of promoter regions in genes  responsible for cell specifications. Prenatal e-cig exposure also caused differential gene expressions in both excitatory and inhibitory neurons in many genes involved in specific neuronal functions, which was orchestrated by different H3K27me3-H3K4me1 methylations. Furthermore, prenatal e-cig smoking altered the gene expression of circadian genes involved in circadian entrainment and circadian rhythm including calcium signaling genes Cacna1c, Camk2b, and Ryr2; cAMP and protein kinase signaling transduction gene Adcy1 and Prkcb; as well as synaptic transmitter receptor Gria4. These results suggested that nicotine addiction could be epigenetically imprinted at a very early stage of brain development. Our study showed a profound effect of epigenomic regulation of histone marks by prenatal e-cig exposure on neuronal lineage development and highlighted a new underlying epigenetic mechanism of nicotine addiction, which could potentially lead to the identification of therapeutical targets for nicotine abuse disorders.

overall_design: Pregnant rats were exposed to e-cigarette vapor during E4 to E20. Paired-Tag single-cell joint profilling were performed on transciptome and H3K27me3-H3K4me3 in postnatal day 7 ( P7) brain prefront cortex to study the epigenetic influence of maternal vaping on rat neonates' brain development.


title: The CpxR response regulator mediates the virulence of Klebsiella pneumoniae by regulating the expression of virulence associated genes

status: Public on Jul 10 2025

city: Shanghai

first: Runze

address: School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, No.800, Dongchuan Road, Minhang District, Shanghai, People's Republic of China

institute: State Key Laboratory of Microbial Metabolism, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University

summary: Klebsiella pneumoniae is a prominent human pathogen that has developed resistance to multiple antibiotics. While the roles of capsules and siderophores are well established, the identification of additional virulence determinants remains limited. In this study, we hypothesize that the two-component system response regulator CpxR is integral to the regulation of K. pneumoniae virulence via control of specific virulence-associated genes. Deletion of the cpxR gene resulted in reduced serum resistance and attenuated virulence in both Galleria mellonella larvae and murine infection models compared to the wild-type strain. To elucidate the repertoire of virulence-associated genes regulated by CpxR, a multidisciplinary workflow was employed, integrating RNA sequencing, Real-Time quantitative PCR, gene knockout strategies, serum resistance assays, and infection experiments utilizing Galleria mellonella. Among the genes identified with significantly diminished expression following cpxR deletion, KPHS_28080 emerged as a novel candidate virulence-associated gene. Deletion of KPHS_28080 impaired serum survival in both the carbapenem-resistant CRKp HS11286 and the hypervirulent hvKp ATCC43816 strains. Furthermore, deletion of KPHS_28080 in hvKp ATCC43816 led to significantly decreased colonization and impaired dissemination to multiple organs in murine models, corresponding with an overall reduction in virulence. The promoter region of KPHS_28080 harbors a conserved CpxR binding motif, which enhances promoter activity and gene transcription upon CpxR binding. Sequence alignment revealed that KPHS_28080 encodes a member of the short-chain dehydrogenase family, and this gene is highly conserved among K. pneumoniae strains. These results elucidate the pivotal role of CpxR in mediating virulence in K. pneumoniae and clarify its regulatory impact on virulence-associated gene expression.

overall_design: RNA-seq profiling of wild-type and cpxR deletion mutant of Klebsiella pneumoniae HS11286

first: Zhiyuan

last: Liu

first: Jiahao

last: Guan

first: Hong-Yu

last: Ou


title: Analysis of chromatin accessibility relative to epigenetic features of azacitidine response in high-risk myelodysplastic syndrome

city: Ulsan

first: Dayoung

last: Kim

address: 50 Unist-gil

country: South Korea

institute: UNIST

summary: Azacitidine is used to treat patients with myelodysplastic syndrome, which alters epigenetic regulatory program that changes global gene expression by inhibiting DNA methylation. However, epigenomic factors affecting azacitidine response have not been studied in the context of chromatin.  The efficacy of the hypomethylating agent differs by patient, leaving approximately 40% of patients fail to respond. Here, we demonstrate that chromatin accessibility features in patient-derived bone marrow cells can distinguish azacitidine responders from non-responders before treatment. Profiling chromatin accessibility from 23 high-risk myelodysplastic syndrome patients discovered that treatment response is strongly associated with distinct hematopoietic cell states. While non-responders showed enrichment of myeloid progenitor signatures, responders were characterized by elevated T cell populations. Notably, CD8+ T cells from non-responders exhibited selective loss of chromatin accessibility at TBX/EOMES binding sites, revealing a previously unrecognized link between T cell differentiation state and azacitidine response. These findings suggest the importance of immune cell differentiation and their activity in hypomethylating agent response for myelodysplastic syndromes, providing insights for patient stratification and treatment optimization based on the chromatin accessibility in high-risk myelodysplastic syndrome patients.

overall_design:
Bulk ATAC-seq profiling of bone marrow collected from high-risk myelodysplastic syndrome patients, acute myeloid leukemia patients, healthy donors. when they are diagnosed, before treatment using azacitidine. The patients can be grouped into azacitidine responders and non-responders.
ATAC-seq profiling of CD4+ T cells and CD8+ T cells from high-risk myelodysplastic syndrome patients. The patients can be grouped into azacitidine responders and non-responders.

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

first: Silvia

last: Park

first: Hee-Je

first: Yoo-Jin

first: Seung Woo

last: Cho


title: Profiling the spatial architecture of multiple myeloma in human bone marrow trephines with spatial transcriptomics [human]

city: Parkville

first: Yunshun

state: VIC

address: 1G Royal Parade

department: ACRF Cancer Biology and Stem Cells

country: Australia

institute: Walter and Eliza Hall Institute of Medical Research

summary: Here, we used subcellular spatial transcriptomics to profile the expression of 5,001 genes in human bone marrow in the context of monoclonal gammopathy of undetermined significance, smouldering myeloma and multiple myeloma. Using this approach, we explored the plasma cell and stroma ecosystem in bone marrow trephines from 21 individuals including 7 with pre-malignant disease and 10 with active multiple myeloma.

overall_design: Xenium profiling on bone marrow trephines.

first: Raymond

last: Yip

first: Jeremy

last: Er

first: Edwin

last: Hawkins


title: TAF1,the largest subunit of TFIID, is dispensable for adult hematopoiesis [Pro-seq]

status: Public on Jul 09 2025

city: Miami

first: Stephen

middle: D.

last: Nimer

address: 1120 NW 14th Street

department: Sylvester Comprehensive Cancer Center

institute: University of Miami

summary: While many sequence-specific transcription factors (TFs) have been identified as key regulators of hematopoietic stem cell (HSC) lineage determination, the function of general TFs in HSC behavior is poorly understood. To evaluate the function of the TFIID subunit TAF1 in normal hematopoiesis, we generated Taf1 conditional knockout mice and identified an essential role of TAF1 in fetal erythropoiesis. Surprisingly, TAF1 deletion in adult mice was not lethal to hematopoiesis; rather, we observed a marked expansion of the hematopoietic stem and progenitor cell (HSPC) compartment, with increased self-renewal and impaired differentiation capacity in these cells. TAF1-null HSPCs failed to produce mature blood cells in chimeric mice; these cells also failed to up-regulate key differentiation genes when induced to differentiate in vitro. TAF1 loss not only disrupted TFIID assembly and chromatin recruitment, but also reduced RNAPII promoter-proximal pausing. Thus, HSPCs utilize distinct transcriptional regulatory mechanisms to undergo differentiation versus maintaining self-renewal.

overall_design: To determine how Taf1 loss affects RNAPII activity in mouse HSPCs , we generated Taf1 conditional KO mouse models, and isolated HSPCs from 3 control and 2 KO mice 2 weeks post poly (I:C) induced Taf1 deletion.  Nuclear run-on assays (Pro-seq) were performed with one million purified nuclei.

first: Fan

first: Pradeepkumar

middle: R

last: Cingaram

first: Felipe

last: Beckedorff


title: TAF1, the largest subunit of TFIID, is dispensable for adult hematopoiesis [scRNA-Seq]

overall_design:
To determine how Taf1 loss affects HSPC gene expression profile, we generated Taf1 conditional KO mouse models.  We isolated HSPCs from control and KO mice (n=3), and sent 1x10^4 cells for single cell RNA-sequencing using Illumina 10x Genomics Chromium Single Cell Controller at Onco-genomics Shared Resources (OGSR) in Sylvester Comprehensive Cancer Center (SCCC). We then performed analyses, including cell clustering and annotation, DEG, and   differentiation trajectory.
We then performed analyses, including cell clustering and annotation, DEG, and   differentiation trajectory.

first: Francesco

last: Tamiro


title: TAF1, the largest subunit of TFIID, is dispensable for adult hematopoiesis [ATAC-Seq]

overall_design:
To determine how Taf1 loss affects HSPC chromatin structure, we generated Taf1 conditional KO mouse models, and isolated HSPCs from control and KO mice 2 weeks post poly (I:C) induced Taf1 deletion.  ATAC-seq were performed with 1x10^5 cells from 3 control and 2 KO mice using the Tagment DNA Enzyme and Buffer Small Kit (Illumina, 20034197).
ATAC-seq libraries were generated with with 5 to 7 cycles of amplification using NEBNext 2x Master Mix (NEB, M0541S) and uniquely indexed i7/i5 primer pairs.


title: TAF1, the largest subunit of TFIID, is dispensable for adult hematopoiesis [RNA-Seq]

overall_design: To determine how Taf1 loss affects HSPC differentiation, we generated Taf1 conditional KO mouse model. We isolated HSPCs from control and KO mice, cultured cells in vitro with cytokines forcing cells to differetiate toward either macrophages or granulocytes for a total of 7 days, and collect cells at day0, day3, day5 and day7 for RNA-sequencing. All samples are in triplicates. We then performed a time-series analysis to determine how Taf1 loss affects the activation of differentiation associated genes.


title: TAF1, the largest subunit of TFIID, is dispensable for adult hematopoiesis [ChIP-Seq]

overall_design: To determine how TAF1 loss affects RNAPII genomic distribution, we isolated Lin- cells from Taf1 control and KO mice 2 weeks post poly(I:C) induced Taf1 deletion and performed ChIP-seq using antiboies against mouse TAF1 and RPB1 (the largest subunit of RNAPII). In order to obtain enough cells for ChIP, we combined cells from several mice with the same genotype.

first: Jun

last: Sun


title: Lpar5 Regulates CD8 T Cell Survival and NK Receptor Expression During the Early Response to LCMV Clone 13

status: Public on Jul 06 2025

city: Aurora

first: Raul

last: Torres

state: CO

address: 12800 East 19th Avenue,

department: Immunology and Microbiology

institute: The University of Colorado Anschutz Medical Campus

summary: Persistent antigen exposure during chronic viral infection and tumor development drives CD8 T cells into an exhausted, hypofunctional state. Understanding the molecular pathways that enforce T cell exhaustion is critical for improving current immunotherapies. Work from our lab described how the bioactive lipid lysophosphatidic acid (LPA) regulates CD8 T cell function through LPA receptor 5 (LPAR5) signaling. Lpar5–/– CD8 T cells also exhibit enhanced tumor clearance in murine models of melanoma. Importantly, significantly elevated levels of LPA have been identified in individuals with different cancers and persistent viral infections such as HIV, HCV, and HBV. To investigate the role of Lpar5 in the differentiation and maintenance of exhausted CD8 T cells, we utilized the LCMV infection model. In response to infection with LCMV Clone 13, but not Armstrong, one quarter of Lpar5–/– animals succumbed to infection, and this was accompanied by an increased frequency of LCMV-specific Lpar5–/– CD8 T cells maintained in a less terminally exhausted state. Using P14 transgenic mice, we demonstrate that Lpar5 acts in a cell-intrinsic and temporal manner to regulate CD8 T cell accumulation and exhaustion programming during Clone 13 infection. The enhanced accumulation of Lpar5–/– P14 cells during the acute phase of Clone 13 infection appears to be regulated by Lpar5-mediated changes in T cell survival and not through trafficking or proliferation. RNA sequencing analyses and surface phenotyping show that Lpar5 likely regulates CD8 T cell exhaustion through modulation of the CD94/NKG2A inhibitory axis.

overall_design: At day 6 post-LCMV-Clone 13 infection, CD8 T cells were isolated and sorted for unique CD45 isoform expression to identify wild-type [WT] and Lpar5-deficient P14 transgenic CD8 T cells. RNA was isolated for bulk RNA sequencing analysis

first: Marc

middle: A

last: D'Antonio

first: Brian

last: Ware

first: James

last: DiLisio

first: Mary

last: Michaels

first: Jacqueline

last: Turner

first: Lauren

last: Habenicht

first: Bennett

last: Davenport

first: Thomas

last: Morrison

first: Roberta

last: Pelanda

first: Laurent

last: Gapin


title: Profiling the spatial architecture of multiple myeloma in human bone marrow trephines with spatial transcriptomics [mouse]

first: Yunshun

last: Chen

first: Raymond

last: Yip

first: Jeremy

last: Er

first: Edwin

last: Hawkins


title: Xenium Spatial Transcriptomics of Cisplatin-Resistant Head and Neck Tumors in Humanized Mice Treated with PI3K Inhibitor Gedatolisib

city: Houston

first: Kelli

last: McCord

state: TX

address: 1 Baylor Plz

institute: Baylor College of Medicine

summary: The therapeutic potential of the PI3K inhibitor gedatolisib on head and neck tumor progression, the tumor microenvironment, and immune cell infiltration was investigated using a humanized orthotopic mouse model implanted with cisplatin-resistant HN30R8 cells.

overall_design: HN30R8 human head and neck cancer cells were orthotopically implanted into the oral tongue of eight NOD humanized mice (HLA-A matched to the human cell line). Once tumors were established, mice were randomly assigned to two treatment groups: four received gedatolisib and four received saline as a control. Clinical-grade gedatolisib (Celcuity Inc., Minneapolis, MN, USA) was administered via tail vein injection at a dose of 16 mg/kg every three days. At the study endpoint, mice were humanely euthanized, and tumors were excised for analysis. Tumors were embedded in OCT compound and flash-frozen in an isopentane bath. Cryosections (10 µm) were mounted onto Xenium slides for spatial transcriptomic analysis using the 10x Genomics Xenium platform. The Xenium Prime 5K Human Pan-Tissue and Pathways Panel was used in combination with a custom 45-gene panel. This custom panel included select mouse genes (denoted in title case) and additional human genes of interest (denoted in uppercase).

first: William

middle: H

last: Hudson


title: A distinct subset of the Arabidopsis group S1 basic leucine zipper transcription factors controls plant resource management during starvation and recovery

status: Public on Jul 03 2025

city: Berlin

first: Cezary

last: Smaczniak

address: Philippstr. 13

department: Institute for Biology

institute: Humboldt-Universität zu Berlin

summary: Plants possess an enormous plasticity to adapt their metabolism to the fluctuating energy supply in a natural environment. Using dark-induced senescence (DIS) as an experimental system, a mutant study combining phenotypical, transcriptomic and Chromatin Immunoprecipitation Sequencing (ChIPseq) approaches identifies distinct members of the Arabidopsis group S1 basic leucine zipper transcription factors that orchestrate the starvation response. While excluding bZIP2, bZIP11 and bZIP44 to function in DIS, the in part redundantly acting bZIP1 and bZIP53 control a co-expression network governing amino acid catabolism and transport, gluconeogenesis and energy homeostasis. Moreover, they regulate genes involved in asparagine – glutamine balance, which are critical for C/N homeostasis. This transcriptional reprogramming in resource management is required for survival during starvation and regaining meristematic activity during recovery from stress. Thus, we provide insights into the transcriptional control of plant resource and energy management during starvation. Finally, this work sheds light on the discrepancy between in vitro DNA-binding and overexpression studies versus mutant analyses and in vivo DNA-binding, providing a critical view on how to define specific transcription factor functions within large families.

overall_design: We performed ChIP-seq experiments on the leaf tissue of the two Col-0 wild type replicates and three pbZIP1:bZIP1-GFP bzip1 replicates with the input samples as controls. We used GFP antibodies (ab290, Abcam) for the immunoprecipitation.

first: Kerstin

last: Kaufmann

first: Christoph

last: Weiste

first: Wolfgang

last: Dröge-Laser


title: Activated T cells secrete extracellular vesicles in the allergic airway that enhance eosinophil viability

city: Nashville

first: Heather

middle: H.

last: Pua

state: Tennessee

address: 1161 21st Avenue South

department: Pathology, Microbiology, and Immunology

institute: Vanderbilt University Medical Center

summary: T cells are not only central orchestrators of immune responses, but they drive tissue pathology in many inflammatory diseases. In allergic asthma, the activation of CD4+ T helper cells in response to allergens drives chronic type 2 lung inflammation characterized by the recruitment of eosinophils. Given the emerging roles of extracellular vesicles (EVs) as mediators of cell-to-cell communication, we hypothesized that T cells would secrete EVs in the lung to regulate the local inflammatory response. Using T cell specific membrane tagging and single vesicle flow cytometry, we found that T cell EVs are secreted into lung lining fluid during allergic inflammation in a mouse model of asthma. Functionally, EVs secreted by polarized T helper type 2 (Th2) cells promote eosinophil survival in vitro. This effect is only seen with EVs collected from Th2 cells activated through the T cell receptor. Activated Th2 cell EVs promote eosinophil survival by a surface-cargo dependent anti-apoptotic mechanism, inducing pro-survival and activation gene expression programs in these target cells. In vivo, activated Th2 cell EVs prolong eosinophilia in the lung after administration into the airways during allergic inflammation. Together, this study adds to emerging literature linking cellular activation state to EV function and supports a role for T cell EVs in enhancing tissue inflammation.

overall_design: To investigate the effects of Th2 cell extracellular vesicles (EVs) on eosinophils, we differentinated eosinophils from bone marrow and treated the eosinophils with EVs purified from Th2 cell culture media by size exclusion chromatography and ultrafiltration or parallelly processed non-conditioned media as a control. We performed RNA-sequencing on 3 eosinophil biological replicates treated with 5e9 EVs/ml or an equal volume of media control for 24 hours. We then analyzed differential gene expression between Th2 cell EV-treated and media-treated eosinophils.

first: Kaitlyn

last: Bunn


status: Public on Jul 08 2025

city: Seattle

first: Brian

last: Hanratty

state: WA

address: 1100 Fairview Avenue

department: Division of Human Biology

institute: Fred Hutchinson Cancer Cancer

summary: ATAC-Seq of LuCaP PDX models in human prostate cancer.

overall_design: ATAC-Seq of Patient-Derived Xenografts in Metastatic Castration Resistant Prostate Cancer (LuCaP Series).

first: Paloma

last: Cejas

first: Yingtian

last: Xie

first: Miguel

last: Munoz Gomez

first: Henry

last: Long

first: Michael

last: Haffner

first: Peter

middle: S

last: Nelson


title: Pharmacological Targeting of IL17/neutrophil axis to Treat Calciphylaxis

city: Los Angeles

first: Bo

last: Tao

state: CA

address: 675 Charles E Young Drive

department: Cardiology

institute: University of California Los Angeles

summary: Calciphylaxis is a rare but life-threatening disorder characterized by ectopic calcification affecting the subcutaneous tissues and blood vessels of the skin. Calciphylaxis affects individuals with end stage renal disease but increasingly recognized to occur in individuals with normal kidney function. Once diagnosed, survival rates are less than a year and yet despite the severity of the condition, the pathobiology of calciphylaxis is ill understood. Here, we create animal models of calciphylaxis that recapitulate many characteristics of the human phenotype. We demonstrate that calcific deposits in the skin are preceded by recruitment of inflammatory cells. We show that increased local inflammation of the skin, regardless of the inciting cause, in the presence of hypercalcemia and hyperphosphatemia contributes to cutaneous ectopic calcification. Using multiple models of genetically modified rodents that have deficits in immune activation of T and B cells or NK cells, we demonstrate that such immunocompromised rodents are resistant to developing cutaneous calcification. Consistent with this observation, administration of the immunosuppressive cyclophosphamide rescued calcific deposits as did T cell suppression with cyclosporine. We demonstrate IL17 is upregulated in calcific skin and neutrophils are the predominant cell types expressing IL 17 and tissue alkaline phosphatase that is necessary for ectopic calcification.  Targeting IL17 with a monoclonal antibody or use of a myeloperoxidase inhibitor to blunt neutrophil activation significantly attenuated calcific deposits in vivo. Taken together, these observations provide fresh insight into the role of the immune system and the IL17/neutrophil axis in mediating ectopic calcification in rodent models of calciphylaxis.

overall_design: RNA-seq was performed on skin tissues collected from wildtype Sprague-Dawley rats and immunodeficient SRG rats subjected to different treatment conditions to investigate gene expression changes related to inflammation and skin calcification. Additional groups were treated with immunosuppressive agents or antibodies. Selected samples were also used for single-cell RNA sequencing.

first: Edward

last: Cao

first: Feiyang

last: Ma

first: Arjun

last: Deb


title: Unveiling the Molecular Mechanisms of ligustilide in Enhancing Endometrial Receptivity

city: Zhengzhou

first: Aiwu

last: Wei

address: No. 19, Renmin Road, Jinshui District

institute: The First Affiliated Hospital of Henan University of Chinese Medicine

summary: Endometrial receptivity (ER) refers to the ability of the endometrium to accept embryos in the window of implantation during which the endometrial tissue allows embryo implantation and pregnancy initiation. In women with certain gynecological diseases, including polycystic ovary syndrome, tubal disease and endometriosis, ER appears to be impaired, leading to infertility and pregnancy failure. Ligustilide (LIG) treatment can restore endometrial receptivity and promote implantation in pregnant rats with low endometrial receptivity (LER). However, the mechanism by which LIG affects LER is unknown. In the current study,we conducted a bioinformatic analysis of endometrial tissues of rats with NER, LER, and LIG-treated LER.

overall_design: mRNA profiles of endometrial tissue obtained from NER, LER, and LIG-treated LER rats were analyzed.

first: Dongjie

last: He

first: Xingxing

last: Ren

first: Jing

last: Mao

first: Shaoqi

last: Shi

first: Yanli

last: Song

first: Huidongzi

last: Xiao


title: A longitudinal single cell analysis of GLP-2 treatment in the patients with short bowel syndrome

city: Yokohama

first: Jonathan

last: Moody

address: 1-7-22 Suehiro-cho

institute: RIKEN Center for Integrative Medical Sciences

summary: A glucagon-like peptide-2 (GLP-2) analog is clinically used to enhance nutrient absorption in patients with short bowel syndrome (SBS); however, its precise mechanism remains unclear. To address this, we conducted longitudinal single-cell RNA sequencing (scRNA-seq) of intestinal tissue from patients with SBS over a year, integrating microbiome composition analysis. Post-treatment, the beta diversity of the gut microbiome increased, indicating a more varied microbial environment. scRNA-seq analysis revealed a decrease in TCRγδ cells and an increase in regulatory T (Treg) cells, suggesting a shift towards an immunoregulatory intestinal environment. Additionally, nutrient-absorbing enterocyte-top2 and middle clusters expanded, enhancing the absorption capacity, whereas MHC class I/II-expressing enterocyte-top1 cells declined, potentially modulating immune responses. Our study employed a cutting-edge longitudinal single-cell approach to track cellular dynamics in response to GLP-2 analog treatment. These findings indicate that GLP-2 analogs reshape intestinal immunity and microbiota, fostering a less inflammatory environment, while promoting nutrient uptake efficiency. These insights offer a deeper understanding of GLP-2’s role in gut adaptation and provide a foundation for refining the clinical strategies for SBS treatment.

overall_design: Longitudinal single-cell RNA sequencing (scRNA-seq) and 16S rRNA sequencing to analyze intestinal cell and microbiome changes over time in patients with short bowel syndrome

first: Yumi

last: Kudo

first: Kentaro

last: Miyamoto

first: Akihiko

last: Chida

first: Anna

last: Tojo

first: Ikuko

last: Koya

first: Yoshinari

last: Ando

first: Shohei

last: Suzuki

first: Masayasu

last: Sato

first: Aya

last: Kondo

first: Tomoko

last: Kumagai

first: Harunori

last: Deguchi

first: Yoshiki

last: Sugiyama

first: Koji

last: Shirosaki

first: Satoko

last: Yamagishi

first: Yutaro

last: Maeda

first: Hiroki

last: Kanamori

first: Motohiro

last: Kano

first: Mototoshi

last: Kato

first: Hanako

last: Tsujikawa

first: Yusuke

last: Yoshimatsu

first: Kaoru

last: Takabayashi

last: Okabayashi

first: Takanori

last: Kanai

first: Naoki

last: Hosoe

first: Motohiko

first: Chung-Chau

last: Hon

first: Tatsuo

last: Kuroda

first: Yohei

last: Yamada

first: Akihiro

last: Fujino

first: Tomohisa

last: Sujino


title: Gut microbiome-derived LPS aggravated cognitive impairment by promoting systemic inflammation via the TLR4/MyD88/NF-κB signaling pathway in hypoxic-ischemic neonatal rats

status: Public on Jul 01 2025

city: Fuzhou

first: Jianjie

last: Wei

state: Please Select

address: No. 134, East Street, Gulou District

institute: Fujian Province Hospital

summary: Hypoxic ischemic brain damage (HIBD) is the primary cause of neurological deficits in neonates, leading to long-term cognitive impairment. Recent studies have demonstrated that gut microbiota plays a crucial role in the development of cognitive impairment after brain injury, known as the microbiota-gut-brain axis.

overall_design: RNA sequencing analysis of colon and hippocampus tissues was also conducted.

first: Andi

last: Chen


title: Super-enhancer profiling reveals ThPOK/ZBTB7B, a CD4+ cell lineage commitment factor, as a breast cancer master regulator that restricts cells to a luminal non-migratory phenotype

city: San Francisco

first: Denise

middle: Paula

last: Muñoz

state: California

address: 2340 Sutter St.

department: Hematology/Oncology

institute: University of California, San Francisco

summary: Despite considerable efforts to understand the biology of breast cancer, metastatic disease remains a clinical challenge. Identifying suppressors of breast cancer progression and mechanisms of transition to more invasive phenotypes could provide game changing therapeutic opportunities. Transcriptional deregulation is central to all malignancies, highlighted by the extensive reprogramming of regulatory elements that underlay oncogenic programs. Among these, super-enhancers (SEs) stand out due to their enrichment in genes controlling cancer hallmarks. To reveal novel breast cancer dependencies, we integrated the analysis of the SE landscape with master regulator activity inference for a series of breast cancer cell lines. As a result, we identified T-helper-inducing Poxviruses and Zinc-finger (POZ)/Krüppel-like factor (ThPOK, ZBTB7B), a CD4+ cell lineage commitment factor, as a breast cancer master regulator that is recurrently associated with a SE. ThPOK expression is highest in luminal breast cancer, but is significantly reduced in the basal subtype. Manipulation of ThPOK levels in cell lines shows that its repressive function restricts breast cancer cells to the luminal subtype by suppressing the expression of genes involved in the epithelial-mesenchymal transition (EMT), WNT/b-catenin pathway, and the pro-metastatic TGFb. Our study reveals ThPOK as a breast cancer master transcription factor with opposing forces to the acquisition of metastatic features.

overall_design: Chromatin immunoprecipitation against Histone 3 acetylated in lysine 27 was performed for a panel of breast cancer cell lines

middle: P

first: Ignacio

middle: E

last: Schor


title: Gene expression profile at single cell level of Mycn-nGEMM mouse neuroblastoma tumors and their tumor microenvironment

status: Public on Jun 30 2025

first: Hiroyuki

last: Yoda

address: 1450 3rd street

institute: UCSF

summary: Neuroblastomas are highly heterogeneous tumors originating from neural crest-derived cells destined to form the sympathetic nervous system. We used single cell RNA sequencing (scRNA-seq) to analyze the tumor microenvironment of Mycn-nGEMM mouse neuroblastoma.

overall_design: Mycn-nGEMM tumors were enzymatically digested and single-cell FACS sorted for scRNA-seq.

first: Liron

middle: D

last: Grossmann

first: William

last: Weiss


title: Proliferative stem cell-like population of blasts in KMT2A-rearranged infant ALL [scRNA-seq]

status: Public on Jun 26 2025

city: oxford

first: Thomas

last: Jackson

address: weatherall institute of molecular medicine

department: paediatrics

country: United Kingdom

institute: University of Oxford

summary: Among pediatric acute lymphoblastic leukemias (ALL), KMT2A-rearranged infant ALL (KMT2Ar iALL) carries a uniquely poor prognosis due to high rates of treatment-refractory or relapsing disease. It is important to understand how KMT2A mutations drive such aggressive disease in order to develop more effective and less toxic therapies. The PROM1 gene, encoding the pentaspan glycoprotein prominin-1/CD133, is activated by the direct action of the most common KMT2A fusion protein; KMT2A::AFF1 (MLL-AF4). CD133 expression is essential for proliferation of KMT2A::AFF1+ cell lines but its role in primary disease remains unclear with heterogenous expression seen in iALL patient samples. To clarify the role of CD133 in KMT2Ar iALL we have used a highly physiological primary human fetal liver derived model (CRISPRKMT2A::AFF1 ALL) which recapitulates CD133 heterogeneity. We show that CD133 expression marks a highly proliferative subset of CRISPRKMT2A::AFF1 blasts with a stem-cell gene expression profile capable of causing more aggressive disease in vivo. CRISPR inactivation of PROM1 limits leukemic proliferation, suggesting a functional role in our model and providing a strong rationale for targeting therapies against CD133.

overall_design: RNA-seq of fetal derived MLL-AF4 iALL model (patient samples).

first: Joe

last: W Cross

first: Lucy

last: Field

last: Hamer

first: Alastair

last: Smith

first: Nicholas

last: T Crump

first: Siobhan

last: Rice

last: Harman

first: Rebecca

last: Ling

first: Natalina

last: Elliott

first: Qinqing

middle: Q

last: Wu

first: Nouhad

last: El Ouazzani

last: Thomas

first: Sarah

last: Inglott

first: Jack

last: Bartram

first: Irene

last: Roberts

last: Milne

first: Anindita

last: Roy


title: Perinatal Fentanyl Exposure Leads to Lasting Behavioral Vulnerabilities and Altered in the Central Amygdala in Rats

status: Public on Jun 27 2025

city: La Jolla

first: Ye Ji

last: Shin

address: 9500 Gilman Dr

institute: University of California, San Diego

summary: Opioid use during pregnancy is a growing public health concern, with in utero exposure to synthetic opioids like fentanyl linked to Neonatal Opioid Withdrawal Syndrome (NOWS) and long-term neurobehavioral impairments. However, the long-term neurodevelopmental consequences of in utero opioid exposure remain poorly understood. We developed a translationally relevant rat model of perinatal fentanyl exposure to investigate the behavioral and molecular outcomes of prenatal opioid exposure. Offspring born to fentanyl-exposed dams showed reduced survival rates, lower body weight, and spontaneous withdrawal symptoms. In adolescence, they displayed mechanical hypersensitivity and behaviors consistent with negative affect. In adulthood, these rats exhibited enhanced fentanyl self-administration, increased reinstatement behavior, and elevated plasma corticosterone levels during withdrawal. Furthermore, they showed increased risk-taking behavior in the Elevated Plus Maze, suggesting altered anxiety or impulsivity regulation. To investigate molecular correlates of these phenotypes, we performed transcriptomic profiling of the central amygdala of adult rats. Differential gene expression and gene set enrichment analyses revealed that perinatal fentanyl exposure led to dysregulation of pathways involved in synaptic signaling, neurodevelopment, GPCR signaling, and immune responses. These transcriptional changes provide a molecular framework for understanding how early fentanyl exposure leads to long-lasting vulnerability to stress and addiction-related behaviors. These findings underscore the lasting impact of perinatal opioid exposure on brain function and behavior and support the utility of this model for translational research on NOWS and opioid-related neuropsychiatric risk.

overall_design:
RNA-seq from the Central Amygdala of Rats was performed after perinatal exposure to fentanyl or saline.
Brain tissues were collected in adulthood, 1 day after the last IVSA session.
Each condition included 8 offspring (6 males and 2 females) from the perinatal treatment groups.

first: Courtney

last: Wood

first: Francesca

last: Telese

first: Giordano

last: de Guglielmo


title: Targeting histone H2B acetylated enhanceosomes via p300/CBP degradation in prostate cancer (ChIP-Seq)

city: Ann Arbor

first: Arul

last: Chinnaiyan

state: MI

address: 1500 East Medical Center Dr

department: MCTP

institute: University of Michigan

summary: Prostate cancer (PCa) is driven by oncogenic transcription factor enhanceosomes comprising chromatin and epigenetic regulators. The lysine acetyltransferases p300 and CBP are key cofactors that activate enhancers through histone acetylation. Here, we identify p300/CBP-mediated multisite acetylation of the histone H2B N-terminus (H2BNTac) as a defining feature of oncogenic enhanceosomes in androgen receptor (AR)-positive prostate cancerPCa. p300/CBP are essential for AR and ERG transcriptional activity, and their dual degradation eliminates H2BNTac and H3K27ac marks at hyperactive enhancers, leading to stronger suppression of oncogenic transcription more effectively than targeting either paralog or bromodomains alone. Cytotoxicity profiling across >900 cell lines revealed that tumors with high H2BNTac, including AR-positive prostate cancerPCa, are selectively dependent on p300/CBP. In preclinical models, systemic p300/CBP degradation inhibited tumor growth, synergized with AR antagonists, and showed no evident toxicity. These findings position H2BNTac as an  key epigenetic marker of enhancer addiction and establish support dual p300/CBP degradation as a promising therapeutic strategypy for enhancer-driven cancers.

overall_design: Chromatin landscape of p300/CBP degrader treated VCaP cells

first: Jie

last: Luo

first: Eleanor

last: Young

first: Yuping

last: Zhang

first: Abhijit

last: Parolia


title: Effect of hFWE KO on gene expression in mature epidermal organoids

city: Omaha

first: Laura

middle: A.

last: Hansen

state: NE

address: 2500 California Plaza

institute: Creighton University

summary: Specialized secretory cells, including keratinocytes in the last viable layers of mammalian epidermis, utilize lysosome-related organelles (LROs) to exocytose distinct cargoes vital for tissue function. Here, we demonstrate that the Flower isoform, hFWE4, a putative Ca2+ channel that permits endocytic retrieval of presynaptic vesicles and lytic granules, also resides on epidermal lamellar bodies (LBs), an LRO that extrudes a proteinaceous lipid-rich matrix to finalize the epidermal barrier. We show that hFWE4-positive LBs associate with a distinct ensemble of LRO trafficking mediators and that, in a process required for maturation of the epidermal barrier, hFWE4 elevates cytosolic Ca2+ to facilitate the apically polarized exocytosis of LBs. Finally, supporting a critical role for hFWE4-dependent trafficking in establishing the epidermal barrier, we demonstrate that this process is dysregulated in genetic diseases of cornification that are driven by impairments in keratinocyte Ca2+ handling. Our results provide new insight into the biogenesis and trafficking of epidermal LBs and more broadly suggest that hFWE4 is a core component of LRO trafficking machinery that endows Ca2+ dependency to distinct stages of the transport process depending on the cell of origin.

overall_design: To investigate the effects of hFWE expression on epidermal differentiation and barrier function, we used CRISPR-Cas9 to knockout endogenous hFWE in N/TERT-2G keratinocytes. Wild-type N/TERT-2G, polyclonal KO pool and three distinct monoclonal KO cell lines were grown at air-liquid interface for 10d prior to isolation of total RNA from resulting cornified epidermal organoids.


title: Targeting histone H2B acetylated enhanceosomes via p300/CBP degradation in prostate cancer (RNA-Seq)

overall_design: Distinct prostate cancer cells were treated in vitro with the 100nM p300/CBP degrader CBPD-409 (abbreviated as CBPD), 1uM p300/CBP inhibitor,  CCS1477 (abbreviated as CCS), 1uM  p300/CBP inhibitor,  GNE-049 (abbreviated as GNE)  for indicated durations, and processed for multi-omic characterization.

middle: M


title: Unraveling the miRNA Landscape in the Salivary glands and Saliva of the Tsetse Fly, Vector of African Trypanosomes

status: Public on Jun 24 2025

city: Antwerp

first: Pieter

last: Monsieurs

address: Nationalestraat 155

country: Belgium

institute: Institute of Tropical Medicine

summary: MicroRNAs (miRNAs) are emerging as potential mediators of cross-species gene regulation in vector-borne diseases. In this study, we investigate miRNA presence in the tsetse fly (Glossina morsitans)-trypanosome system, focusing on salivary glands and saliva during Trypanosoma brucei infections. Using small RNA sequencing and a consensus approach combining two bioinformatics tools, miRDeep2 and sRNAtoolbox, we identified 54 unique miRNAs in tsetse saliva and salivary glands, with none originating from T. brucei. To ensure the accuracy of miRNA annotations, a robust pipeline was implemented, including de novo prediction, comparative analyses across tools, and manual curation to minimize false positives. Among the identified miRNAs, 12 were novel to tsetse flies, and 5 represented putative novel miRNAs. Salivary gland samples contained the majority of detected miRNAs, with a subset also present in saliva, with some of those saliva miRNAs exhibiting notably high relative abundance. This study demonstrates the power of integrated bioinformatics pipelines to investigate miRNAs in non-model organisms and unconventional matrices like insect saliva. Our findings contribute to the growing understanding of miRNA roles in host-vector-pathogen interactions and lay the groundwork for future functional validation studies to elucidate their biological significance.

overall_design: miRNA-seq profiling of Glossina morsitans salivary glands and saliva, either infected or non-infected with Trypanosoma brucei

first: Klaas

last: Dewaele

first: Peter

last: Otieno Odhiambo

first: Lieve

last: Vermeiren

first: Jan

last: Van Den Abbeele