title: Paired-end RNA Sequencing on primary human umbilical endothelial cells (HUVEC) exposed to uninfected or bacterially-infected PMA-differentiated macrophage-like U937 for 8 or 24 h

first: Effie

last: Bastounis

summary: We sought to identify changes in gene expression that occur when endothelial cells in monolayer interact with either uninfected or Listeria monocytogenes-infected macrophages. To that end we seeded HUVEC in monolayer and either exposed them to nothing, or to uninfected PMA-differentiated macrophage-like U937, or to Listeria monocytogenes-infected PMA-differenitated U937. At 8 or 24 hours post U937 exposure (hpe), we washed the samples thoroughly to remove U937 and then collected the mRNA to to perform RNA-Sequencing and gene expression profiling for the six conidtions described. By analyzing the differentially expressed genes between all conditions we find a significant number of up- or down-regulated genes related to innate immune signaling in both (un)infected U937 exposed HUVEC as compared to control unexposed HUVEC, irrespective of the time post-exposure. For example we found significant upregulation of genes related IL-17, NF-kB and TNF related signaling pathways, though to a lesser degree for HUVEC exposed to uninfected U937 as compared to bacterially infected. Interestingly, we found that only HUVEC exposed to uninfected but not infected U937 and only at 8hpe showed significant upregulation of genes related to focal adhesions and regulation of the actin cytoskeleton. We found that consistent with alterations in the dynamics of HUVEC under this condition, which show a significant rise in the traction on monolayer stresses they exert. At later times post-exposure (i.e., 24 hpe) were these changes in gene expression are not present anymore, HUVEC dynamics are also identical irrespective of whether they were exposed or not to (un)infected U937. Thus the RNA sequnecing results at 8 hpe that reveal upregulation of genes related to focal adhesions and the actin cytoskeleton for uninfected U937 exposed HUVEC match with the results of traction force and monolyaer stress microscopy that reveal strong enhancement of these forces over the first 10 hpe and which are absent in the other two conditions or at the later time point of 24 hpe.

overall_design: Primary endothelial cells HUVEC were seeded in monolayer and exposed to: (1) nothing (unexposed HUVEC, UE), (2) uninfected PMA-differentiated U937 macrophage-like cells (uninfected macrophage exposed HUVEC, UI), or (3) Listeria monocytogenes-infected U937 macrophage-like cells (infected macrophage exposed HUVEC, I). After 8 or 24 hours post-exposure (hpe) to U937, the samples were washed to remove U937, and mRNA was collected for RNA sequencing and gene expression profiling across these six conditions. For each condition four samples were analysed, using Illumina NovaSeq 6000 using the NovaSeq 6000 S4 Reagent Kit (300 cycles). Equipment: Illumina with 2x150 read length and 40 million reads per sample.

first: Marie

last: Muenkel


title: snFLARE-seq and mrFRIGID for the transcriptomic and metabolomic landscape of prostate cancer with different anatomical origins

status: Public on Jan 27 2026

city: Shanghai

first: xiao

last: kai

address: YueYang Road 420

country: China

institute: SIBCB

type: Expression profiling by high throughput sequencing

summary: snFLARE-seq for the transcriptomic landscape of prostate cancer with different anatomical origins. Prostate cancer cells of different anatomical locations display remarkable heterogeneity. This poses a challenge to the clinical relevance of pre-clinical models and the efficacy of contemporary therapeutic approaches. Here we developed the snFLARE-seq methodologies to directly investigate the transcriptomic landscape of prostate cancer patients utilizing formalin-fixed paraffin-embedded (FFPE) specimens. A retrospective analysis revealed the clinical disparities of prostate cancer from peripheral zone (PZ), transition zone (TZ), and across PZ and TZ. The snFLARE-seq, refined for enhanced single-nucleus sequencing, unveiled distinct cell type distributions and signaling pathways between PZ and TZ samples. Hormone therapy substantially affected cancer cells and microenvironment, leading to a polarized feature of epithelial cells and a subverted immune microenvironment. With improvements on metabolite extraction, mrFRIGID revealed unique metabolic features of prostate cancer from different origins. The metabolomic results indicate that PZ cancer cells were in a metabolic-dormant status, which were probably awaken by hormone therapy. Integrative analysis of results from snFLARE-seq, mrFRIGID, and TCGA database uncovered four metabolic pathways and related genes associated with disease aggressiveness. Our work would accelerate investigations on disease heterogeneity and evolution in real-world clinical settings, stimulating patient-specific precision healthcare solutions.

overall_design:
Single‑nucleus RNA‑seq profiling of prostate cancer tissues from different anatomical zones (peripheral zone, transition zone, and mixed PZ/TZ) using the snFLARE‑seq method optimized for FFPE specimens. Nuclei were isolated from FFPE samples of prostate cancer patients and subjected to in‑nucleus reverse transcription and library preparation with mixed random and oligo‑dT primers. Sequencing libraries were generated using the SeekOne® DD single‑cell 3′ Transcriptome Kit and sequenced on Illumina NovaSeq 6000.

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first: Zhenfei

last: Li

first: Kai

last: Xiao

first: Dongyin

last: He


title: Mechanisms of augmented tumor immunogenicity via ATR inhibition in Merkel cell carcinoma

city: Seattle

first: Daniel

last: Jones

state: WA

country: USA

institute: Fred Hutchinson Cancer Center

summary: There is an urgent unmet need to develop novel therapeutic strategies for tumors that do not respond to immune checkpoint inhibition (ICI) via PD-1 pathway blockade. The ATR-mediated DNA replication checkpoint has been reported to have immune-augmenting properties; however, the mechanisms underlying these properties are not well characterized. Here we explore the potential immunogenic effects of ATR inhibition in Merkel cell carcinoma (MCC), a cancer that is particularly relevant due to its high proliferative index and frequent response to anti-PD-(L)1 therapy. ATR inhibition induced tumor cell cytotoxicity in both Merkel cell polyomavirus-positive and UV-induced MCC cell lines in the absence of exogenous DNA damage. ATR inhibition alone or in combination with low-dose radiation induced numerous proinflammatory TNF-NF-κB signals as assessed via bulk transcriptomic profiling. These included increased expression of MHC class-I alleles, antigen processing machinery, interleukins, chemokines and interferon genes associated with anti-tumor immune responses in diverse tumor types. In parallel, we observed enhanced surface exposure of the “eat-me” signal calreticulin on MCC cells and subsequent phagocytosis by human monocyte-derived macrophages. Given that MCC tumors are often cGAS-STING-deficient (including two cell lines examined here), these ATRi-induced mechanisms are significant as they were activated regardless of cGAS-STING functional status. These data provide a mechanistic basis for the clinical evaluation of ATRi in advanced ICI-refractory MCC (NCT05947500), and suggest biomarkers that may be associated with response in human MCC tumors treated with ATRi.

overall_design: Early passaged WaGa, MKL2, MCC26 and MCC13-HL cell lines were used (sub-cultured less than 25 times). 72 hours of ATRN-119 (100 nM for MCPyV-positive and 250 nM for MCPyV-negative) ± 4 Gy radiation treatment was initiated in triplicate for cells seeded in 10 cm tissue-culture dishes. Untreated cells were used as negative control. Harvested cells were submitted for RNA extraction, library preparation and sequencing (DNBseq platform, BGI Genomics, Cambridge, MA, USA). Raw paired-end reads (~ 30 million per sample; 100 base pair read length) were quality-checked, adapter-trimmed, and aligned to GRCh38 with Bowtie236. Genes with counts less than 10 across all samples were filtered out. The subsequent raw RNA-Seq count data were normalized using FPKM (fragments per exonic kilobase per million) with effective library sizes estimated using TPM (transcripts per million),  followed by log2 transformation with a pseudocount of 2, as implemented in the edgeR R/Bioconductor package37 and used for further analyses. Differential analysis at the gene level was performed using the Limma package38, with false discovery rate method used to adjust the p-values for multiple testing. Genes with an absolute log2 fold change of at least 0.5, normalized against mock-treated cells, were considered either up or downregulated and used for relative quantification across different treatment groups. Statistical significance was defined by a Q value of ≤ 0.05. Dot plots were generated using the R ggplot2 package39. Transformed expression data matrices were uploaded to an integrative cloud-based multi-omics RNA-seq data mining browser from BGI Genomics (“Dr. Tom”) and then used as input for computation of treatment-induced transcriptomic enrichment via the Molecular Signatures Database (MSigDB) hallmark gene set analysis. Hallmark interpretations were queried using a minimum of 15 and a maximum of 500 genes per set for statistically significant signatures. Distribution of normalized enrichment scores (NES) and gene set enrichment analysis (GSEA)-defined false discovery rate (FDR) significance threshold  0.05, along with leading edge (LE) gene set sizes for a characteristic biological phenotype, can be found in Supplemental Figure 3. Variable clustering of gene expression data across all samples was performed and visualized through principal component analysis.

first: Rashmi

last: Bhakuni

first: Jung

middle: H

last: Lee

first: Peter

last: Goff

middle: C

first: Long

last: Nguyen

first: Rongxiang

last: Lin

first: Evan

middle: W

last: Newell

first: Khalid

last: Garman

last: Hall

first: Oren

last: Gilad

first: Isaac

last: Brownell

first: Eric

middle: J

last: Brown

first: Paul

last: Nghiem


title: A role for condensin-mediator interaction in mitotic chromosomal organization [ChIP-Seq]

city: Sapporo

first: Hideki

last: Tanizawa

state: Hokkaido

address: Kita 15, Nishi 7, Kita-ku

department: Institute for Genetic Medicine

country: Japan

institute: Hokkaido University

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Eukaryotic genomes are organized into layers of chromatin domains, such as topologically associating domains (TADs) and A/B compartments.  TADs (i.e., cohesin-mediated chromatin domains) are restricted by CCCTC-binding factor (CTCF) and convergent genes in higher eukaryotes and fission yeast, respectively.  However, molecular mechanisms underlying the formation of condensin-mediated chromatin domains remain largely unclear.  Here, we investigate the role of newly identified interaction between the Cnd1 condensin and Pmc4 mediator subunits.  We develop a condensin mutation, cnd1-K658E, that impairs the condensin-mediator interaction and find that this mutation diminishes condensin-mediated domains and causes defects in chromosomal segregation.  The condensin-mediator interaction is involved in recruiting condensin to highly transcribed genes and mitotically activated genes, the latter of which demarcate condensin-mediated domains.  Our study also predicted that the condensin-mediator interaction and its function in chromosomal segregation are potentially conserved in human cells.  This study provides a novel insight into how genome-wide gene expression is connected to the mitotic chromosomal architecture via the condensin-mediator interaction.

overall_design: (1) Genome-wide distributions of condensin were determined by ChIP-seq using mitotic cells with wild-type Cnd1 expression (Cnd1 WT-Pk) and with Cnd1-K658E expression (Cnd1-K658E-Pk) from the plasmids.  The endogenous Cnd1 was repressed by culturing cells in EMM medium containing auxin.  Mitotic cells were prepared by the cdc25-22 G2/M block-release and harvested at a 60-minute time point after the release.   (2) In addition, genome-wide distributions of Cnd1-Pk in cells with wild-type and Pmc4 depletion are prepared.  (3) Genome-wide distributions of the Cnd2-Flag (WT and C703R) expressed from the plasmids were determined using cells depleting the endogenous Cnd2. (4) Genome-wide distributions of Cnd1-WT-Myc and Cnd1-K658-Myc expressed from the endogenous locus. Mitotic cells were prepared in YEA using the cdc25-22 G2/M block-release and harvested at a 40-minute time point after the release. (5) Genome-wide distributions of Cnd1, Pmc4, Pol II in mitotic cells with or without 5% HD treatment for 5min. Mitotic cells were prepared in YEA using the cdc25-22 G2/M block-release and harvested at a 40-minute time point after the release.

first: Osamu

last: Iwasaki

first: Tomomi

last: Hayashi

first: Claire

last: Yik-Lok Chung

first: Sanki

last: Tashiro

first: Gabrielle

last: Tabor

first: Shinya

last: Ohta

first: Xuebing

last: Wang

first: Mikihiro

last: Kawagoe

first: Ken-ichi

last: Noma


title: Allosteric effectors of PRC2 synergise to restrict Polycomb domains spread

city: Clayton

last: Healy

state: VIC

address: 23 Innovation Way, Building 77,, Monash University

country: Australia

institute: Monash University

summary: Broad chromatin marks are often spread through read-write loops, where chromatin modifiers bind to their products. Polycomb domains are broad repressive chromatin regions in metazoan species, defined by the repressive chromatin mark H3 lysine 27 tri-methyl (H3K27me3) of the Polycomb repressive complex 2 (PRC2). PRC2 is an allosteric enzyme: it switches into a stimulated state by its own H3K27me3 product in a positive feedback loop that maintains Polycomb domains. Yet, it is unknown what prevents this PRC2-H3K27me3 positive feedback loop from spreading H3K27me3 indefinitely. Here we show that mutant mouse embryos, defective in the allosteric activation of PRC2 by its accessory subunits, exhibit a homeotic transformation characteristic of a Polycomb gain-of-function. The same mutations in mouse embryonic stem cells lead to a global gain of H3K27me3 and its spread beyond Polycomb domains. Collectively, we show that the allosteric effector activity of PRC2 accessory subunits restricts H3K27me3 deposition and prevents its spread beyond Polycomb domains.

overall_design: Quantitative ChIP sequecning for H3K27me3, H3K4me3, RING1B & H2AK119ub1 performed in wild type and SOF (JARID K116R, PALI1 K1241R + JARID2 K116R) mutant mouse embryonic stem cells. Independent replicates included. RNA sequencing of total RNA in wild type and JARID2 K116R mutant mouse embryonic tailbud tissue.

first: Samuel

last: Agius

first: Marion

last: Boudes

first: Yoona

last: Kim

first: Yi-Cheng

last: Chang

first: Melanie

last: Murray

first: Jan

last: Manent

first: Jeanette

last: Rientjes

first: Zhihao

last: Lai

first: Sophie

last: Nixon

first: Jihane

last: Homman-Ludiye

first: Vitalina

last: Levina

first: Edwina

last: McGlinn

first: Chen

last: Davidovich


title: Nanoluciferase-CD63 labeling reveals extracellular vesicle kinetics in a mouse intraductal model of ductal carcinoma in situ

status: Public on Jan 26 2026

city: Oklahoma city

first: Bethany

last: Hannafon

state: OK

address: 975 NE 10th Street

department: Obstetrics and Gynecology

institute: University of Oklahoma Health Sciences Center

summary: Background. Ductal carcinoma in situ (DCIS) is a non-invasive precursor to breast cancer that increases lifetime risk for invasive disease and, in rare cases, causes distant metastases without local recurrence. Tumor-derived small extracellular vesicles (sEVs), or exosomes, mediate tumor progression, systemic signaling, and metastasis; however, the timing of release and biodistribution of sEVs from early preinvasive lesions remains unclear. Methods. Here, we investigated the release kinetics and systemic dissemination of sEVs secreted by DCIS cells confined to the mammary ducts using an orthotopic mouse mammary intraductal xenograft model with MCF10DCIS cells engineered to express NanoLuc (NLuc)-tagged CD63, an sEV marker. Tumor growth was monitored using bioluminescent imaging (BLI) in vivo and ex vivo; DCIS outgrowth and focal invasion were confirmed by fluorescent immunohistochemistry; and NLuc activity was assayed in tissue lysates. Next-generation RNA sequencing of brain tissue was used to evaluate gene expression changes at 28 days post-implantation (dpi). Results. Longitudinal BLI revealed CD63-NLuc signals in mammary glands (P < 0.05), and distant organs, including spleen (P < 0.05), liver (P < 0.05), lungs (P < 0.01) and brain (P < 0.01) by day 14 followed by detection in heart tissue (P < 0.001) and in the circulation by day 21, preceding histological evidence of invasion. Further, CD63-NLuc activity was significantly and positively correlated with BLI levels in mammary glands and plasma (P < 0.05). Immune, metabolic, and stress response pathways were downregulated in brain tissue at 28 dpi compared to 3 dpi. Conclusions. These findings demonstrate systemic dissemination of tumor-derived sEVs during DCIS progression, suggesting roles in early microenvironmental conditioning and metastatic preconditioning prior to overt invasion.

overall_design: RNA sequencing was performed to evaluate gene expression changes in brain tissue collected at days 3 and 28 from mice implanted with MCF10DCIS CD63-NLuc cells.

first: Hladik

last: Cole

first: Hannafon

last: Bethany


title: Sex-Based Differences in Cell Types and Gene Expression within the Anterior Cruciate Ligament

city: San Francisco

first: Brian

middle: T

last: Feeley

state: CA

address: 1700 Owens St

department: Orthopedic Surgery

institute: University of California, San Francisco

summary: ACL tear rates in females is significantly higher compared to their male counterpart. We utilized 9 patient samples to explore the biological and transcriptomic differences that exist in male and female ACL.

overall_design:
Human anterior cruciate ligament was mechanically and enzymatically digested. Live cells were sorted by FACS and then sequenced. All cells were analyzed by 10x Genomics 3' single cell RNA sequencing.

Please note that the processed data files for GSM8656015 sample have been replaced with individual files for each patient on Feb 25, 2026.

first: Justin

last: Lau

first: Steven

middle: M

last: Garcia

first: Xuhui

last: Liu

first: Stephanie

last: Wong


title: Transcriptomic profile of B cells in response to IL-2 signal in vitro

city: Rennes

first: Simon

last: Leonard

address: 2 avenue du Prof Léon Bernard

country: France

institute: Université Rennes

summary: IL-2 is one of the first cytokine discovered but its complex roles in T cell effector functions has shadowed its function in B cell responses. B cells transiently expressed IL-2 receptor upon activation but it is unclear whether all mature B cell subsets have an equal dependence upon IL-2 and how IL-2 dictates B cell fate. Using our newly generated B-cell-specific Il2rb conditional knockout (KO) model of mice lacking IL2RB signaling in mature B cells, our objectives were to characterize the transcriptomic profile of B cells in response to IL-2 signal. We found that IL-2 acts intrinsically on IL2RB expressing B cells to promote Il10 expression and plasma cell reprogramming in context dependent manner in vitro. In contrast, an inflammatory response was observed in KO B cells.

overall_design:
To investigate the role of IL-2 on B cell fate we developed a new mice model invalidated for IL2 signaling in B cells only (Il2rb KO)
We recovered spleen from Ctrl and Il2rb KO mice, isolated B cells and cultured them 3 days with aBCR + IL+5 +/- IL-2 (n=4)
We then extracted RNA and performed RNA-sequencing on these sixteen samples with illumina technology
We performed comparative gene expression profiling analysis of RNA-seq data

first: Juliette

last: Gauthier

first: Celine

last: Delaloy


title: The Rpd3 histone deacetylase is critical for temperature-mediated morphogenesis and virulence in the human fungal pathogen Histoplasma – HDAC mutant histone acetyl ChIP-seq

first: Mark

last: Voorhies

address: 513 Parnassus, S472

department: Microbiology and Immunology

institute: University of California

summary: Adaptive responses to environmental stimuli are integral to the survival and virulence of microbial pathogens. The thermally dimorphic human fungal pathogen Histoplasma senses temperature to transition between a mold form in soil and a pathogenic yeast in mammalian hosts. The contributions of chromatin-modifying enzymes to the ability of Histoplasma to appropriately respond to temperature have never been explored. Through chemical inhibition and genetics, we determined that the class I histone deacetylase (HDAC) RPD3 is required for normal Histoplasma yeast morphology at 37 ºC. Rpd3 regulated the expression of key morphology-specific genes, including critical virulence factors and transcription factors (TFs), was required for normal DNA-binding activity of yeast-promoting TFs, and influenced histone acetylation levels at the loci of putative pro-filamentation TFs. Furthermore, Rpd3 was required for virulence in a macrophage model of infection. Taken together, Rpd3 is a critical regulatory component that both activates the pathogenesis program and represses the filamentation program to enable thermal dimorphism in Histoplasma. This work uncovers the crucial role that chromatin regulation plays in temperature response of this ubiquitous pathogen.

overall_design: ChIP-seq with antibodies to the histone modifications H4K16Ac or H3K9Ac for WT or rpd3 mutant Hisoplasma cells with three bioreps per treatment.

first: Nebat

last: Ali

first: Anita

last: Sil


title: MitoPerturb-Seq identifies gene-specific single-cell responses to mitochondrial DNA depletion and heteroplasmy [multiome]

city: Cambridge

first: Stephen

middle: Peter

last: Burr

address: Mitochondrial Biology Unit, Keith Peters Building, Cambridge Biomedical Campus, Hills Road

department: Clinical Neurosciences

country: United Kingdom

institute: University of Cambridge

summary: Mitochondria contain their own genome, the mitochondrial DNA (mtDNA), which is under strict control of the cell nucleus. mtDNA occurs in many copies in each cell, and mutations often only affect a proportion of them, giving rise to heteroplasmy. mtDNA copy number and heteroplasmy level together shape the cell- and tissue-specific impact of mtDNA mutations, ultimately giving rise to rare mitochondrial and common neurodegenerative diseases. However, little is known about how copy number and heteroplasmy interact within single cells, and how this is regulated by the nuclear genes and pathways that sense and control them. Here we describe MitoPerturb-Seq for CRISPR/Cas9-based high-throughput single-cell interrogation of the impact of nuclear gene perturbation on mtDNA copy number and heteroplasmy. We screened a panel of nuclear mtDNA maintenance genes in cells with heteroplasmic mtDNA mutations. This revealed both common and perturbation-specific aspects of the integrated stress-response to mtDNA depletion, that were only partially mediated by Atf4, and caused cell-cycle stage-independent slowing of cell proliferation. MitoPerturb-Seq thus provides novel experimental insight into disease-relevant mito-nuclear interactions, ultimately informing development of novel therapies targeting cell- and tissue-specific vulnerabilities to mitochondrial dysfunction.

overall_design: Mouse Embryonic Fibroblasts (MEFs) carrying a heteroplasmic mitochondrial (mt)DNA mutation in mt-Ta (m.5024C>T) and stably expressing Cas9 were transduced with a pooled lentiviral CRISPR library targeting 19 genes (three guides per gene) plus three non-targeting control gRNAs using the CROPseq method. 10 days post-transduction cells were flow sorted to select transduced cells based on expression of mRFP, and sorted cells were fixed and permeabilized before being submitted for 10X Genomics single-cell MultiOme ATAC and gene expression (GEX) sequencing. Following library preparation, CROPseq guide mRNA sequences were enriched from the GEX cDNA library using the TAP-seq protocol, and mtDNA sequences were enriched from the final ATACseq library by hybridization capture using a bespoke probeset from IDT

middle: P

first: Kathryn

last: Auckland

first: Angelos

last: Glynos

first: Abhilesh

last: Dhawanjewar

first: Wei

last: Wei

first: Cameron

last: Ryall

first: Antony

last: Hynes-Allen

first: Malwina

last: Prater

first: Matylda

last: Sczaniecka-Clift

first: Julien

last: Prudent

first: Patrick

middle: F

last: Chinnery

first: Jelle

last: van den Ameele


title: A role for condensin-mediator interaction in mitotic chromosomal organization [Hi-C]

first: Hideki

last: Tanizawa

overall_design: (1) Hi-C experiment in mitotic cells with wild-type Cnd1 expression from the plasmid , without exogenous Cnd1 expression , and with exogenous Cnd1-K658E expression.  The endogenous Cnd1 was repressed by culturing cells in EMM medium containing  auxin.  Mitotic cells were prepared by the cdc25-22 G2/M block-release and harvested at the 60-minute time point after the release. (2) Hi-C experiment in mitotic cells with wild-type Pmc4 expression from the plasmid  and without exogenous Pmc4 expression.  The endogenous Pmc4 was degraded by the AID system.  The mitotic cells were prepared using the cdc25-22 block-release. (3) Hi-C experiment in asynchronous culture cells of various mediator deletions. (4) Hi-C experiment in asynchronous culture cells with Cnd2 depletion.  Cells were cultured in EMM liquid medium containing thiamine and auxin to induce transcriptional inhibition of cnd2 gene and post-translational degradation of endogenous Cnd2 proteins  The Cnd2 WT or C703R mutant was expressed from the plasmid. (5) Hi-C experimets in motitic cells with Cnd1 WT or Cnd1 K658E expression from the endogenous locus. Mitotic cells were prepared in YEA using the cdc25-22 G2/M block-release and harvested at the 40-minute time point after the release. (6) Hi-C experiments in mitotic cells with Cnd1, Pmc4 or Cnd1/Pmc4 double depletion. Mitotic cells were prepared in YEA using the cdc25-22 G2/M block-release and harvested at the 40-minute time point after the release. (7) Hi-C experiments in mitotic cells with 5 or 10 % HD treatment for 5min before fixation. Mitotic cells were prepared in YEA using cdc25-22 G2/M block-release and harvested at the 40-minute time point after the release.

first: Osamu

last: Iwasaki

first: Tomomi

last: Hayashi

first: Claire

last: Yik-Lok Chung

first: Sanki

last: Tashiro

first: Gabrielle

last: Tabor

first: Shinya

last: Ohta

first: Xuebing

last: Wang

first: Mikihiro

last: Kawagoe

first: Ken-ichi

last: Noma


title: The Rpd3 histone deacetylase is critical for temperature-mediated morphogenesis and virulence in the human fungal pathogen Histoplasma – HDAC mutant RNA-seq

first: Mark

last: Voorhies

overall_design: Expression profiling by RNA-seq of WT, rpd3, and hos2 mutant Histoplasma yeast cells at 37C or room temperature with three bioreps per treatment.

first: Ali

last: Nebat

first: Voorhies

last: Mark

first: Sil

last: Anita


title: A role for condensin-mediator interaction in mitotic chromosomal organization [PRO-Seq]

overall_design: Nascent RNA profiles in the following conditions were determined by PRO-seq.  The endogenous Cnd1 expression was repressed by culturing cells in EMM medium containing thiamine and auxin, and the exogenous Cnd1 proteins (WT and K658E) were provided from the plasmids.  For Pmc4 depletion, the endogenous Pmc4 was degraded by the AID system, and the exogenous Pmc4 protein was provided from the plasmid (Pmc4 WT).


title: Defining transcriptome signature consistent between cell types in blood and brain and related to the severity of Prader-Willi syndrome.

city: Parkville

first: Shokouh

last: Shahrokhi Sabzevar

address: Royal Children's Hospital, 50 Flemington Rd

institute: MCRI

summary: This study defined genetic subtype and cell type-specific gene expression changes and dysregulated pathways in the prefrontal cortex (PFC) of individuals with Prader-Willi syndrome (PWS). Genes identified to be differentially expressed consistently between all cell types of the PFC, were examined in blood with their mRNA levels related to the severity of PWS including intellectual functioning and behavioral problems. It was hypothesised that genes identified to be consistently differentially expressed across all cell types in the brain tissues examined from individuals with Prader-Willi syndrome (PWS) would be also affected in blood and with their mRNA levels related to the severity of PWS.

overall_design: single-nucleus RNA-sequencing was performed on the PFC tissue from 8 donors with PWS (4 15q11-q13 deletion and 4 non-deletion subtypes) and 4 age and sex-matched neurotypical controls. The shortlisted differentially expressed genes (DEGs) that were shared across all cell types of the brain, were examined using droplet digital PCR (ddPCR) in peripheral blood mononuclear cells (PBMCs) from an independent cohort of 36 individuals with PWS (16 deletion and 20 non-deletion).

first: David

middle: E

last: Godler

last: Shahrokhi

first: Michael

last: See

first: Fernando

last: Rossello


title: The Rpd3 histone deacetylase is critical for temperature-mediated morphogenesis and virulence in the human fungal pathogen Histoplasma -- HDACi RNA-seq

overall_design: Expression profiling by RNA-seq of Hisoplasma yeast cells treated with two concentrations of Entinostat or control or room temperature with three bioreps per treatment and sampled after 1 or 2 days.

first: Nebat

last: Ali

first: Anita

last: Sil


title: Single cell transcriptomic profile of splenic B and T cells from  B-cell specific Il2rb deficient mice

first: Simon

last: Leonard

summary: IL-2 is one of the first cytokine discovered but its complex roles in T cell effector functions has shadowed its function in B cell responses. B cells transiently expressed IL-2 receptor upon activation but it is unclear whether all mature B cell subsets have an equal dependence upon IL-2 and how IL-2 dictates B cell fate. Using our newly generated B-cell-specific Il2rb conditional knockout (KO) model of mice lacking IL2RB signaling in mature B cells, our objectives were to characterize the heterogeneity of splenic B cell early response to in vivo immunization (SRBC) comparing scRNAseq data from control and KO mice. In parallel, we analyzed T cell subsets.

overall_design:
Il2rb KO and Ctrl mice were immuninized intraperitoneally with sheep red blood cells (SRBC).
Spleen of unimmunized mice (KO and Ctrl) and day 4 SRBC-immunized mice (KO and Ctrl) were recovered. Splenic B and CD4+ T cells were magnetically isolated.
We then extracted RNA and performed scRNA-sequencing.
ADT/HTO: barcode sequence: hashtagged sample
TotalSeq-C0301 anti-mouse Hashtag1: ACCCACCAGTAAGAC: KO D4
TotalSeq-C0302 anti-mouse Hashtag2: GGTCGAGAGCATTCA: Cre D4
TotalSeq-C0303 anti-mouse Hashtag3: CTTGCCGCATGTCAT: KO D0
TotalSeq-C0304 anti-mouse Hashtag4: AAAGCATTCTTCACG: Cre D0

first: Juliette

last: Gauthier

first: Celine

last: Delaloy


title: The Rpd3 histone deacetylase is critical for temperature-mediated morphogenesis and virulence in the human fungal pathogen Histoplasma – HDAC mutant TF ChIP-seq

overall_design: Ryp1, Ryp2, and Ryp3 ChIP-seq of WT or rpd3 mutant Histoplasma yeast cells with three bioreps per genotype.


title: The Rpd3 histone deacetylase is critical for temperature-mediated morphogenesis and virulence in the human fungal pathogen Histoplasma – HDACi histone acetyl ChIP-seq (PE)

overall_design: ChIP-seq with antibodies to the histone modifications H4K16Ac or H3K9Ac for Hisoplasma cells treated with Entinostat or DMSO control at 37C or RT with three bioreps per treatment.


title: ACBP: a poor-prognosis biomarker in sepsis and a target for disease mitigation [Lung]

city: PARIS

first: Guido

last: Kroemer

address: 15 rue de L'école de médecine

institute: Centre de Recherche des Cordeliers

summary: Sepsis remains a major clinical challenge, with high mortality and long-term disability despite current interventions. Here, we identify the tissue hormone acyl-CoA–binding protein (ACBP), also known as diazepam-binding inhibitor (DBI), as a biomarker and driver of poor outcome in sepsis. ACBP/DBI was elevated in the plasma of septic patients and associated with organ dysfunction and increased mortality. In murine models of endotoxemia, Escherichia coli infection, and polymicrobial sepsis, genetic deletion or antibody-mediated neutralization of ACBP/DBI conferred robust protection by enhancing pathogen clearance, dampening cytokine storm, and preserving organ function. Notably, ACBP/DBI inhibition could be favorably combined with glucocorticoids, enhancing survival and reversing histopathological, transcriptional, or metabolic signatures of septic shock across heart, kidney, liver, lung, spleen, and plasma. These findings position ACBP/DBI as a mechanistic amplifier of sepsis pathophysiology and propose its neutralization, alone or in combination with corticosteroids, as a promising therapeutic strategy to interrupt the fatal trajectory of septic shock.

overall_design: Eight-week-old male C57Bl/6J mice were randomly assigned to treatment groups and administered either a monoclonal antibody against ACBP/DBI (aDBI; 4h and 1h prior to surgery) or its isotype control (IgG), administered 1h before surgery. Sepsis was induced by cecal ligation and puncture (CLP) under isoflurane anesthesia. Briefly, the cecum was exteriorized, ligated at 75% of its length using non-absorbable 4-0 silk suture, and punctured once through-and-through with a 21-gauge needle. A small amount of fecal content was gently extruded, and the cecum was returned to the abdominal cavity. Sham-operated mice underwent the same procedure, including treatment injections, but without ligation or puncture. Mice that died within the first 24h post-surgery were considered to have succumbed to perioperative complications and were excluded from further analysis. For molecular analyses, organs were collected on the day of euthanasia (6h and 24h post-CLP) and immediately snap-frozen in liquid nitrogen. For RNA-sequencing library preparation, RNA was extracted from mouse lungs using RNA Plus Mini Kit (Qiagen) according to manufacturer’s instructions. The concentration and integrity of total RNA was analysed using electrophoretic separation on microfabricated chips in Agilent 2100 Bioanalyzer System (Agilent, CA, USA). After, mRNA-sequencing library preparation (1.5 µg total RNA per sample) was carried out on NovaSeq 6000 PE150 instrument (2 x 150 bp, 40 million reads per sample). For RNA-sequencing data analysis, Fastq files were align on mm10, Mus musculus genome, by Hisat2, BAM files were count by HTSeq-count. The obtained raw count files were analyse with R package (R Foundation for Statistical Computing; https://www.R-project.org/) DESeq2. Our genes of interest were selected based on the thresholds abs (Fold Change) ≥ 1.5 and a pvalue ≤ 0.05. Heatmaps were performed with the R package ComplexHeatmap, Venn diagrams with ggVennDiagram, all other plots are realized with ggplot2. Gene ontology was realized with gprofilr, clusterProfiler and enrichplot.

first: Flavia

last: Lambertucci

first: Omar

last: Motiño

first: Uxía

last: Nogueira-Recalde

first: Yan

last: Rong

first: Léa

last: Montégut

first: María

last: Pérez-Lanzón

first: Vincent

last: Carbonnier

first: Sijing

last: Li

first: Sylvère

last: Durand

first: Fanny

last: Aprahamian

first: Hui

last: Chen

first: Yanbing

last: Dong

first: Allan

last: Sauvat

first: Silvia

last: Mingoia

first: Sylvie

last: Lachkar

first: Ester Gloria

last: Saavedra Díaz

first: Jonathan

last: Pol

first: Federico

last: Pietrocola

first: Estela

last: Rocha-Oliveira

first: Roberto

last: Roncon-Albuquerque Jr

first: Francisco

last: Vasques-Nóvoa

last: Lozano-Rodríguez

first: José

last: Avendaño-Ortiz

first: Eduardo

last: López-Collazo

first: Mahmoud

last: Abdellatif

first: Isabelle

last: Martins


title: Coviretinopathy: COVID-19-induced VEGF-dependent retinopathy

city: Wuxi

first: Xiaolu

last: Wang

state: China

address: 299 Qingyang Road

institute: The Affiliated Wuxi People's Hospital of Nanjing Medical University

summary: COVID-19 has been associated with high prevalences of retinal diseases in humans. However, cellular and molecular mechanisms that underly the COVID-19-associated retinopathy remains unknown. Here, we deployed a mouse COVID-19 model to investigate the causative link between SARS-CoV-2 infection and retinopathy development. Our data showed that COVID-19-induced pulmonary hypoxia triggered systemic hypoxia and markedly augmented VEGF expression levels in the retina and plasma. High VEGF levels altered vascular structures and functions in the retina, resulting in neovascularization, vascular disorganization and increased leakiness. We deployed a new terminology of coviretinopathy to accurately describe these COVID-19-induced pathological changes in the retina. Consequently, blocking VEGF by a specific neutralizing antibody (VEGF blockade) completely ablated the COVID-19-associated vascular changes in the retina. Together, these findings provide new mechanistic insights into the COVID-19-associated retinopathy and propose a new therapeutic paradigm for effective treatment of coviretinopathy.

overall_design: Mouse lung and retinal tissues were dissociated into single-cell suspensions and processed by CapitalBio Technology (Beijing, China) using the 10x Genomics Chromium platform with the Single Cell 3′ Library Kit v2. Libraries were sequenced on an Illumina NovaSeq 6000 (paired-end 150 bp, >100,000 reads/cell). The data were processed with Cell Ranger, and downstream analysis, including clustering (Seurat), pseudotime trajectory (Monocle 2), and functional enrichment (DAVID), was performed using standard pipelines.

first: Yihai

last: Cao


title: Hypercholesterolemia impairs the expression of angiogenic microRNAs in extracellular vesicles within ischemic skeletal muscles

city: Montreal

first: Alain

last: Rivard

state: Qc

address: 900 rue St-Denis

country: Canada

institute: CRCHUM

type: Non-coding RNA profiling by high throughput sequencing

summary: Background/Objectives: In severe peripheral artery disease (PAD) with limb ischemia, hypercholesterolemia (HC) is associated with impaired neovascularization. Extracellular vesicles (EVs) are present within ischemic muscles, and they contain microRNAs (miRs) involved in several biological functions, including angiogenesis and neovascularization. Methods: We used a mouse model of PAD and compared the response to hindlimb ischemia in hypercholesterolemic ApoE−/− vs. normocholesterolemic mice. Next generation sequencing (NGS) was used to perform a complete profiling of miR expression in ischemic skeletal muscles, and in EVs of varying sizes — large EVs (lEVs) and small EVs (sEVs) — within these muscles. Results: We identified several miRs with potential pro-angiogenic effects (angiomiRs) that are reduced by HC in lEVs (Let-7b-5p, miR-151-3p, Let-7c-5p) or sEVs (miR-21a-5p, miR-196b-5p, miR-340-5p). As proof of principle, we show that overexpression of Let-7b-5p in lEVs, or miR-21a-5p in sEVs, can significantly increase the angiogenic capacity of these EVs in vitro. HC also impaired the enrichment of specific angiomiRs in lEVs (miR-100-5p), sEVs (miR-142a-3p), or in both lEVs and sEVs (miR-146b-5p). In silico approaches including prediction of functional miR targets, pathway unions and gene unions, identified predictive resulting effects of HC-modulated miRs in EVs on processes having key roles in the modulation of angiogenesis and neovascularization, such as the regulation of actin cytoskeleton and focal adhesion, and HIF-1, MAPK, AMPK and PI3K-Akt signaling pathways. Conclusions: Our results constitute an important first step towards the identification of miRs that could be targeted to improve the angiogenic function of EVs in atherosclerotic conditions and reduce tissue damage in patients with severe PAD.

overall_design: small RNAseq profiling of ischemic muscles and of sEVs and lEVs from ischemic muscles from ApoE ko mice on western diet chow for 4 weeks prior to ischemia induction and from control C57Bl/6 on regular chow.

first: Nozha

last: Raguema

last: Dussault

first: Kevin

last: Sawaya

first: Michel

last: Desjarlais

first: Eric

last: Boilard

first: Sylvain

last: Chemtob


title: The Rpd3 histone deacetylase is critical for temperature-mediated morphogenesis and virulence in the human fungal pathogen Histoplasma – HDACi TF ChIP-seq

first: Mark

last: Voorhies

overall_design: Ryp1, Ryp2, and Ryp3 ChIP-seq of WT Histoplasma yeast cells treated with DMSO or 50uL Entinostat with three bioreps per treatment.

first: Nebat

last: Ali

first: Anita

last: Sil


title: The Rpd3 histone deacetylase is critical for temperature-mediated morphogenesis and virulence in the human fungal pathogen Histoplasma – HDACi histone acetyl ChIP-seq (SE)

overall_design: ChIP-seq with antibodies to the histone modifications H4K16Ac or H3K9Ac for Hisoplasma yeast cells treated with Entinostat or DMSO control with three bioreps per treatment.


title: RORγt⁺ Dendritic Cells Are a Distinct Lymphoid-Derived Lineage [CITE-seq]

city: St. Louis

first: Marco

last: Colonna

state: MO

address: 660 S. Euclid Ave.

department: Pathology and Immunology

institute: Washington University School of Medicine in St. Louis

summary: How tolerogenic dendritic cell (DC) lineages are established to prevent inappropriate immune responses to commensals and food antigens remains unclear. We identify RORγt⁺ DCs in mice as a distinct lymphoid-derived lineage to safeguard intestinal tolerance. Using lineage tracing and single-cell transcriptomics, we unveiled bone marrow–resident Rorc(t)⁺ progenitors, which include a RORγt⁺ innate lymphoid progenitor (RILP) that generates both ILC3s and RORγt⁺ DCs, and a pre-RORγt⁺ DC precursor committed exclusively to the RORγt⁺ DC lineage. RORγt⁺ DC development required the Rorc +7 kb enhancer, whose accessibility was ensured by the repressors REV-ERBα and REV-ERBβ, and depended on the transcription factors PRDM16 and PU.1 for lineage commitment. Loss of any of these regulators abrogated RORγt⁺ DC differentiation, reduced peripheral regulatory T (Treg) cell induction, and skewed toward T helper 2 responses. Together, these findings define murine RORγt⁺ DCs as a lymphoid-derived lineage whose enhancer- and transcription factor–driven development is essential for peripheral Treg cell-mediated immune homeostasis.

overall_design: We performed scRNA-seq on B220– CD3– Ly6C– tdTomato+ hCD2+ (Sample 1) and tdTomato+ hCD2- (Sample 2) cells from BM, spleen, cLN, mLN, and sLN of 15-day-old and adult Gm38411 iCre-hCD2 R26tdTomato mice.

first: Patrick

last: Rodrigues


title: X-ray activated platinum complex induces DNA damage and enhances cancer immunotherapy through abscopal effect

city: Hefei

first: Chen

last: Guiyuan

address: Jinzhai Road

institute: University of Science and Technology of China

summary: Radiotherapy is used in more than half of cancer patients, yet most radiosensitisers increase reactive oxygen species (ROS) to enhance cytotoxicity in treated cells. This approach is limited in hypoxic tumours and may cause oxidative injury to healthy tissues. We developed a platinum(II) azido complex (Complex 1) that releases platinonitrene upon X-ray exposure. Platinonitrene reacts with nucleophilic sites on DNA bases, forming covalent adducts that disrupt DNA integrity and cause double-strand breaks, leading to tumour cell death through a mechanism distinct from classical platinum coordination. Computational modelling elucidated this pathway and supported its role in radiosensitisation. Complex 1 was synthesised by sequential ligand exchange of potassium tetrachloroplatinate with cyclohexanediamine, silver nitrate, and sodium azide. In murine models, Complex 1 showed negligible toxicity to major organs and normal immune cells while selectively reducing regulatory T-cell infiltration in tumours. Combined with low-dose radiotherapy and programmed cell death protein 1 blockade, it achieved complete regression of bilateral tumours in forty per cent of mice, demonstrating a strong abscopal effect. This work establishes metallonitrene-based, ROS-independent radiosensitisation for precision radiotherapy.

overall_design: RNA-seq of CT26 tumor tissues from different groups of mice treated with Complex 1 and radiation therapy

first: Guiyuan

last: Chen

first: Xiangxia

last: Li

first: Yu

last: Huang

first: Cheng

last: Zheng

first: Yuanzeng

last: Min


title: RORγt⁺ Dendritic Cells Are a Distinct Lymphoid-Derived Lineage

overall_design: We performed single-cell RNA sequencing on B220– CD3– Ly6C– tdTomato+ hCD2+ cells (ILC3s and RORγt+ DCs) isolated from bone marrow cultures of 15-day-old Gm38411 iCre-hCD2 R26-tdTomato mice after 8 days of culture.


title: Smyd5 mediates IL-4 epigenetic control of macrophage antigen presentation to drive cooperative T cell-mediated tumor suppression [RNA-Seq]

city: Xiamen

first: dang

last: buyun

state: Fujian

address: Xiang 'an District Xiang Annan Road

institute: xiamen university

summary: IL-4 is classically associated with “M2” macrophages considered tumor-immunosuppressive, yet marker-based labels poorly reflect macrophage function in tumors. Reports of a non-canonical, IL-4–imprinted macrophage state (M2inf) with trained-immunity features prompted us to test whether such imprinting contributes to antitumor immunity in vivo. Here we show that, in B16F10 melanoma, IL-4 programs macrophages through the lysine methyltransferase Smyd5 to deposit promoter-proximal H3K36me3, increase MHC class II, and potentiate T cell activation. Myeloid Il4ra deletion increased tumor burden and reduced MHC class II and intratumoral T cell activation, whereas co-transfer of IL-4–primed macrophages suppressed tumors and expanded activated CD4 and CD8 T cells. Antitumor benefit required adaptive lymphocytes and macrophage-intrinsic MHC class II, as Rag1 deficiency or macrophage Rfx5 deletion abrogated tumor suppression. These findings identify a non-canonical, IL-4–imprinted macrophage program that enables antigen presentation and cooperative T cell immunity in this tumor context.

overall_design:
The BMDM macrophages of WT or Smyd5 KO were treated with IL-4 for 24 hours and then ATAC library construction was performed

UPDATE: [Apr-28-2026] The GSM9426189_Mix_pool_library_RNA-seq.counts.txt file was updated.

first: Buyun

last: Dang

first: Yuling

last: Hong

first: Qingxiang

last: Gao

first: Shih-Chin

last: Cheng


title: The site-mutated Ehd3 failed to rescue the aberrant H3K36me2/me3 distribution patterns in the ehd3-1 mutant background.

first: Jiachen

last: Wang

state: Shanghai

address: No. 2005, Songhu Road

department: Institute of Plant Biology

institute: Fudan University

summary: We examined the genome-wide occupancy of H3K36me2/H3K36me3 in the transgenic plants HA-Ehd3/ehd3-1-1 and HA-Ehd3mu/ehd3-1-1.

first: Jiabing

last: Wu

first: Kangxi

last: Du

first: Wenhao

last: Xie

first: Xiang

first: Xiaolong

first: Aiwu

last: Dong


title: MYC modulates TOP2A diffusion to promote substrate detection and activity [SLAM-seq]

city: Solna

first: Vladislav

last: Kuzin

state: Stockholm

address: Solnavägen 9

department: Cell and Molecular Biology

country: Sweden

institute: Karolinska Institute

summary: Topoisomerases are essential enzymes that alleviate DNA supercoiling by cleaving and resealing DNA strands. Regulation of their abundance and activity is crucial for maintaining genomic stability and supporting nuclear functions. Previously, we showed that the oncoprotein MYC recruits and stimulates topoisomerases to remove DNA entanglements generated by oncogenic transcription. Understanding this mechanism may suggest methods to inhibit MYC-driven topoisomerase activation, thereby selectively targeting tumor-specific transcription. Here, we demonstrate that the essential topoisomerase TOP2A in human cells exists in a dynamic equilibrium between sequestration in the nucleolus, substrate searching in transcription hubs, and active engagement on chromatin. This equilibrium is highly responsive to changes in DNA topology, allowing cells to regulate TOP2A levels in the nucleoplasm. Using single molecule tracking, we show that MYC accelerates TOP2A diffusion in cells. In vitro, we demonstrate that MYC decreases the size of TOP2A condensates, likely by limiting non-specific self interactions. By increasing TOP2A diffusion, MYC promotes substrate binding and increases TOP2A engagement on the chromatin genome-wide, revealing the mechanism underlying MYC stimulation of TOP2A activity.

overall_design: SLAM-seq in HCT116 MYC-mAID cells in triplicates.

first: Donald

last: Cameron

first: Kathryn

last: Jackson

first: Evanthia

last: Iliopoulou

first: Laura

last: Baranello


title: A hierarchical Rorc(γt) cis-regulatory cascade orchestrates differentiation of RORγt⁺ innate immune cells [ChIL-seq]

city: Fukuoka

first: Shinichiro

last: Sawa

address: 3-1-1 Maidashi, Higashiku

institute: Kyushu University

summary: Beyond its well-established role in type 3 immunity, RORγt+ innate immune cells are also essential for secondary lymphoid organ (SLO) formation and gut homeostasis. However, the transcriptional regulatory mechanisms governing RORγt expression in these cells, including ILC3s, LTi cells, and antigen-presenting cells (APCs), remain largely unknown. Here, we identify two key cis-regulatory elements within conserved non-coding sequences (CNS) 9 and 11 in the Rorc locus, which are sequentially utilized during their differentiation. Initially, Runx-binding sites in CNS11 establish chromatin accessibility as early as the HSC stage. Notably, disruption of this chromatin priming prevents subsequent transcriptional activation, thereby abolishing the initial induction of RORγt in these cells. At later stages, CNS9 plays a critical role, particularly in the development of RORγt⁺ APCs, contributing to colonic pTreg induction. This hierarchical transcriptional regulation is essential for SLO formation, postnatal type 3 immunity, and restraining excessive intestinal type 2 immune responses through pTreg induction.

overall_design: ChIL-seq targeting CBFβ was performed in MNK3 cells cultured with IL-7, IL-2, and IL-15 in the presence of ATRA. A total of 5,000 cells were used per sample for the analysis.

first: Takuma

last: Fukui

first: Akihito

last: Harada

first: Kaori

last: Tanaka


title: A hierarchical Rorc(γt) cis-regulatory cascade orchestrates differentiation of RORγt⁺ innate immune cells [ATAC-seq]

overall_design: ATAC-seq of HSC,MPP,aLP-ILCP,ILC2 and DP thymocyte collected from bone marrow, E14.5 fetal liver, small intestine and thymus of either Control, CNS11mut/mut, CNS114th/4th or VavCre Cbfb flox/flox mice.

first: Miyuki

last: Watanabe

first: Satoshi

last: Kojo

first: Eriko

last: Sumiya


title: A hierarchical Rorc(γt) cis-regulatory cascade orchestrates differentiation of RORγt⁺ innate immune cells [ChIP-seq]

overall_design: Using a CBFβ antibody, we performed ChIP-seq analysis on Lin⁻ cells isolated from the E12.5 fetal livers of WT and CNS11mut/mut mice.


title: A human iPSC model of Tauopathies engineered for 4R Tau isoform expression endogenously develops late-stage neuronal Tau pathology

city: Munich

first: Dominik

last: Paquet

state: Bavaria

address: Feodor-Lynen-Str. 17

department: Institute for Stroke and Dementia Research

country: Germany

institute: University Hospital LMU Munich

summary: Tauopathies, such as Alzheimer’s disease and Frontotemporal Dementia, are common neurodegenerative diseases characterized by misfolding, hyperphosphorylation, and aggregation of Tau. Molecular mechanisms underlying Tauopathies are still poorly understood, which is in part due to a lack of human models autonomously developing major disease hallmarks. Formation of late-stage disease phenotypes may require adult Tau isoform expression, which contributes to Tau pathogenesis but is challenging to replicate in human stem-cell-derived systems, thus impeding research on underlying mechanisms and drug development. Here we show that induction of adult human brain-like 4R Tau isoform expression enables cell-intrinsic formation of late-stage Tauopathy hallmarks in iPSC-derived neurons engineered to contain synergistic Tau mutations, without exogenous sources of Tau pathology. Neurons accumulated seeding-competent, hyper-phosphorylated, fibrillar Tau in tangle-like structures. Furthermore, exclusive expression of mutant 4R in the absence of the 3R Tau isoform disproportionately intensified pathology, resulting in highly abundant Tau misfolding and aggregation. Finally, we provide proof-of-principle that our model can be translationally applied both to test chemical disease modulators and evaluate human Tau PET tracers. Collectively, our model corroborates the central role of 4R Tau isoform expression for pathogenesis in human neurons and enables novel investigations to elucidate mechanisms underlying human Tauopathy formation. Moreover, it may also serve as a platform supporting urgently needed development of disease-modifying drugs.

overall_design: Bulk RNA sequencing was performed on human induced pluriptent stem cell derived cells during dual-SMAD-inhibition directed cortical neuron differentiation to investigate changes occuring as a result of gene editing. Samples include wild type and 4 different lines with edits of the endogenous MAPT locus, as well as wild-type cells treated with Nocodazole as a control. Three biological replicates (i.e. independent differentiations) were analyzed for each sample at  day in vitro (DIV) 15 and 35.

first: Angelika

last: Dannert

first: Caterina

last: Carraro


title: Trans-acting long non-coding RNA modulates long-range chromatin interactions associated with oncogenic MYC signaling [VCaP_HiChIP]

city: Chicago

first: Rendong

last: Yang

state: IL

address: 420 E Superior St

department: Urology

institute: Northwestern University

summary: To investigate the functional role of the novel lncRNA IGF1R-AS1 in prostate cancer, we generated VCaP cells with siRNA-mediated knockdown and performed CTCF HiChIP to profile associated changes in 3D chromatin architecture.

overall_design: CTCF HiChIP-seq in VCaP cells with IGF1R-AS1 knockdown versus control.

first: Tingyou

last: Wang

first: Yongyong

first: Josh

last: Fry


title: ACBP: a poor-prognosis biomarker in sepsis and a target for disease mitigation

first: Guido

last: Kroemer

summary: Septic shock remains a major clinical challenge, with high mortality and long-term disability despite current interventions. Here, we identify the tissue hormone acyl-CoA–binding protein (ACBP), also known as diazepam-binding inhibitor (DBI), as a biomarker and driver of poor outcomes in sepsis. ACBP/DBI was elevated in the plasma of septic patients, correlating with organ dysfunction and mortality. In murine models of endotoxemia, Escherichia coli infection, and polymicrobial sepsis, genetic deletion or antibody-mediated neutralization of ACBP/DBI conferred robust protection by enhancing pathogen clearance, dampening cytokine storms, and preserving organ function. Notably, ACBP/DBI inhibition could be favorably combined with glucocorticoids, enhancing survival and reversing transcriptional and metabolic signatures of septic shock across spleen, liver, heart, and kidney. These findings position ACBP/DBI as a mechanistic amplifier of sepsis pathophysiology and propose its neutralization—alone or combined with corticosteroids—as a promising therapeutic strategy to interrupt the fatal trajectory of septic shock.

overall_design: Eight-week-old male C57Bl/6J mice were randomly assigned to treatment groups and administered either a monoclonal antibody against ACBP/DBI (aDBI; 4h and 1h prior to surgery) or its isotype control (IgG), administered 1h before surgery. Sepsis was induced by cecal ligation and puncture (CLP) under isoflurane anesthesia. Briefly, the cecum was exteriorized, ligated at 75% of its length using non-absorbable 4-0 silk suture, and punctured once through-and-through with a 21-gauge needle. A small amount of fecal content was gently extruded, and the cecum was returned to the abdominal cavity. Sham-operated mice underwent the same procedure, including treatment injections, but without ligation or puncture. Mice that died within the first 24h post-surgery were considered to have succumbed to perioperative complications and were excluded from further analysis. For molecular analyses, organs were collected on the day of euthanasia (24h post-CLP) and immediately snap-frozen in liquid nitrogen. For RNA-sequencing library preparation, RNA was extracted from mouse livers using RNA Plus Mini Kit (Qiagen) according to manufacturer’s instructions. The concentration and integrity of total RNA was analysed using electrophoretic separation on microfabricated chips in Agilent 2100 Bioanalyzer System (Agilent, CA, USA). After, mRNA-sequencing library preparation (1.5 µg total RNA per sample) was carried out on NovaSeq 6000 PE150 instrument (2 x 150 bp, 40 million reads per sample). For RNA-sequencing data analysis, Fastq files were align on mm10, Mus musculus genome, by Hisat2, BAM files were count by HTSeq-count. The obtained raw count files were analyse with R package (R Foundation for Statistical Computing; https://www.R-project.org/) DESeq2. Our genes of interest were selected based on the thresholds abs (Fold Change) ≥ 1.5 and a pvalue ≤ 0.05. Heatmaps were performed with the R package ComplexHeatmap, Venn diagrams with ggVennDiagram, all other plots are realized with ggplot2. Gene ontology was realized with gprofilr, clusterProfiler and enrichplot.

first: Flavia

last: Lambertucci

first: Omar

last: Motiño

first: Uxía

last: Nogueira-Recalde

first: Yan

last: Rong

first: Léa

last: Montégut

first: María

last: Pérez-Lanzón

first: Vincent

last: Carbonnier

first: Sylvère

last: Durand

first: Fanny

last: Aprahamian

first: Hui

last: Chen

first: Yanbing

last: Dong

first: Allan

last: Sauvat

first: Silvia

last: Mingoia

first: Sijing

last: Li

first: Sylvie

last: Lachkar

first: Ester Gloria

last: Saavedra Díaz

first: Jonathan

last: Pol

first: Federico

last: Pietrocola

first: Estela

last: Rocha-Oliveira

first: Roberto

last: Roncon-Albuquerque Jr

first: Francisco

last: Vasques-Nóvoa

last: Lozano-Rodríguez

first: José

last: Avendaño-Ortiz

first: Eduardo

last: López-Collazo

first: Mahmoud

last: Abdellatif

first: Isabelle

last: Martins


title: Ehd3 plays an essential role in recruiting SDG724 to H3K4me1-enriched chromatin regions (CUT&Tag).

city: Shanghai

first: Jiachen

last: Wang

summary: We performed CUT&Tag assays to examine SDG724 enrichment in the sdg724 and ehd3 sdg724 mutant backgrounds.

first: Jiabing

last: Wu

first: Kangxi

last: Du

first: Wenhao

last: Xie

first: Xiang

first: Xiaolong

first: Aiwu


title: Mitochondrial metabolism and signaling direct dendritic cell function in antitumor immunity [ATAC-seq2]

city: Memphis

first: Hongbo

last: Chi

state: TN

address: 262 Danny Thomas Place

department: Immunology

institute: St Jude Children's Research Hospital

summary: ATAC-seq profiling of intratumoral cDC1s

overall_design: Intratumoral cDC1s were sorted from B16-OVA tumor-bearing mice at day 7 or day 21 after tumor inoculation, followed by ATAC-seq analysis

first: Hao

last: Shi

first: Zhiyuan

last: You


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

first: Hongjian

last: Jin

department: Center for Applied Bioinformatics

summary: Children with favorable histology Wilms tumor (FHWT) who experience disease relapse or whose tumors exhibit blastemal predominance after chemotherapy often have poor outcomes. We established a FHWT patient-derived xenograft model, KT-47, that exhibited blastemal predominance after chemotherapy treatment with vincristine, actinomycin, and doxorubicin (VAD) and ultimately developed complete resistance to VAD after serial exposures to this combination. Histologic analyses and comprehensive multi-omics approaches were used to evaluate changes associated with resistance. CUT&TAG identified increased transcriptionally active H3K4me3 at stem cell and nephrogenesis gene promoters among the most different regions in KT-47 resistant compared to the KT-47 pretreatment model including the HOXB cluster, HOXC cluster, MYCN, SIX2, IGF2, CITED1, and OSR1. In contrast, decreased H3K27me3 was identified at HOX gene cluster and nephrogenesis gene promoter regions. The most significantly upregulated transcript and protein that associated with resistance in KT-47 was the let7 microRNA processor LIN28B. LIN28B upregulation was associated with copy number gain at MYCN and plasticity of cancer cells marked by open chromatin at the LIN28B locus rather than expansion of a minor subclone expressing LIN28B present in the original primary tumor material. The stem cell-associated multidrug resistance protein ABCB1 was upregulated in epithelial cells in association with an inter-chromosomal interaction between chromosomes 1 and 7. The impact of these findings at MYCN, LIN28B, and ABCB1 were validated in additional WT models and samples. Overall, these results support de-differentiation of FHWT cancer cells to a stem-like state which is associated with chemotherapy resistance. Targeting epigenetic modifiers that modulate differentiation of cancer cells with a stem-like phenotype could be a future treatment strategy in chemotherapy resistant FHWT.

overall_design: CUT&TAG analysis of KT-47 pretreatment (KT-47PT) and KT-47 resistance (KT-47R1) samples. KT-47 pretreatment received no chemotherapy in the xenograft model.  KT-47R1exhibited complete resistance to vincristine, actinomycin-D, and doxorubicin.

first: Andrew

last: Murphy

first: Beisi

last: Xu

first: Carolyn

last: Jablonowski

first: Surbhi

last: Sona


title: Mitochondrial metabolism and signaling direct dendritic cell function in antitumor immunity [microarray3]

summary: Transcriptional dissection of intratumoral cDC1s

overall_design: Intratumoral cDC1s were sorted from B16-OVA tumor-bearing mice at day 7 or day 21 after tumor inoculation, followed by microarray analysis


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

overall_design: RNA-seq profiling of KT-47 pretreatment (KT-47PT), KT-47 pre-resistance, and KT-47 resistance (KT-47R1 and KT-47R2) samples. KT-47 pretreatment received no chemotherapy in the xenograft model. KT-47 pre-resistance received vincristine, actinomycin-D, and doxorubicin in the xenograft model but did not yet demonstrate resistance. KT-47R1 and KT-47R2 exhibited complete resistance to vincristine, actinomycin-D, and doxorubicin.


title: Targeting Notch signaling to restore neural development and behavior in mouse models of ASD [RNAseq_htr]

city: Wako

first: Yoko

last: Hanno

state: Saitama

address: 2-1 Hirosawa

institute: RIKEN Center for Brain Science

summary: Autism spectrum disorder (ASD) is a neurodevelopmental disorder with diverse genetic and environmental origins, yet whether these factors converge on common molecular pathways remains unclear. This study identifies dysregulation of the Notch signaling pathway as a shared mechanism in both hereditary and nonhereditary ASD models. Aberrant histone deacetylase 3-mediated epigenetic regulation of Notch signaling during embryonic forebrain development disrupts the specification of caudal ganglionic eminence (CGE) progenitors into vasoactive intestinal peptide (VIP+) GABAergic interneuron subtypes (VIP-INs). CGE-specific ablation of Notch1/2 genes in ASD models restores the loss of VIP-INs, normalizes maladaptive excitatory and inhibitory balance, and selectively improves social behaviors. Remarkably, a single antenatal dose of a γ-secretase inhibitor ameliorates multiple ASD-associated neuronal, behavioral, and transcriptomic changes in adult models. The study indicates a strong convergence of ASD-related factors on Notch signaling dysregulation and establishes this pathway as a promising therapeutic target for developmental and behavioral deficits in ASD.

overall_design: RNA-seq profiling of adult forebrain from wildtype and Notch conditional knockout mice, with or without prenatal valproic acid exposure.


title: Targeting the ferritinophagy-lysosome axis as a therapeutic vulnerability in gastroenteropancreatic neuroendocrine tumors [CRISPR]

city: Ann Arbor

first: Arul

last: Chinnaiyan

state: MI

address: 1500 East Medical Center Dr

department: MCTP

institute: University of Michigan

summary: This study aims to elucidate the transcriptomic changes and metabolic reprogramming in gastroenteropancreatic neuroendocrine tumor (GEP-NET) cells following PIKfyve inhibition, using both genetic (CRISPR-mediated knockdown) and pharmacological (Apilimod treatment) approaches. The research focuses on the impact of PIKfyve inhibition on lipid metabolism, cholesterol homeostasis, and mTOR signaling in QGP-1, BON-1, and GOT-1 cell lines. By analyzing RNA sequencing data from these experimental conditions, we seek to identify differentially expressed genes and enriched pathways associated with PIKfyve inhibition. This investigation is part of a broader effort to develop novel combination therapies that could potentially overcome resistance to mTOR inhibitors, the current standard of care for advanced GEP-NETs. The study's findings may provide insights into the therapeutic potential of targeting PIKfyve-driven lipid metabolism in combination with mTOR inhibition, potentially offering new strategies to improve treatment efficacy and patient outcomes in GEP-NETs and other mTOR-driven cancers.

overall_design: Genes were screened for essentiality in GEP-NET cancer cells after 14-days of growth using the human kinome CRISPR knockout pooled libraries (Brunello), Addgene #1000000083. Days 0 and 14 were screened using each half-pool  separately, yielding 4 total screens. The half-pools containing sgRNA sets 1-4 and sets 5-8 are here labeled "A" and "B", respectively.

first: Yizhi

last: Cao

first: Yuanyuan

last: Qiao

first: Caleb

last: Cheng

first: Brian

last: Magnuson

first: Xuhong

first: Andrej

last: Coleski

first: Eleanor

last: Young


title: Nucleoli-localized KANSL2 as an epigenetic regulator of ribosome biogenesis in glioblastoma cells.

city: Capital federal

first: Carolina

last: Perez-Castro

state: Argentina

address: Godoy Cruz 2090

department: Cell plasticity

country: Argentina

institute: IBioBA (Instituto de investigacion en Biomedicina de Buenos Aires - Instituto partner de la sociedad Max Planck)

summary: KANSL2 is a subunit of the non-specific lethal (NSL) chromatin-modifying complex involved in epigenetic reprogramming and plays a critical role in tumorigenesis of glioblastoma (GBM), by enriching the GBM stem-like cell population. Analysis of KANSL2 expression in TCGA-GBM tumor samples and GTEx normal brain tissue confirmed that KANSL2 is highly expressed in GBM and positively correlates with both the stemness index score and ribosomal protein mRNA expression. KANSL2 localized to nucleoli, depending on the cell cycle phase, suggesting its dynamic shifting during the cell cycle. Ectopic overexpression of KANSL2-RFP upregulated 45S pre-rRNA and 28S rRNA expression, concomitant with higher cell proliferation. In contrast, KANSL2 downregulation decreased proliferation, 45S pre-RNA and 28S rRNA expression levels, and acetylated levels of H4 at lysine 5 and 8 in the rDNA promoter region, suggesting KANSL2 is necessary for proper rRNA gene expression potentially via histone acetylation. In support, RNA-seq analysis of patient-derived GBM spheroids silenced for KANSL2 showed significant downregulation of ribosomal biogenesis-related genes. Collectively, these findings revealed an unprecedented role of KANSL2 as a positive regulator of rRNA expression in GBM, suggesting it to be a critical mediator of cell stemness and proliferation, making it an attractive target for potential therapy.

overall_design: F18-1 and F2-4 cells used for the RNA-seq assay were obtained from the University of Colorado, Colorado, USA, through the Neurosurgery Nervous System Biorepository (protocol COMIRB #13–3007), with no expiration date. According to the WHO CNS5 (2021) classification, F18-1 is a grade 4 glioblastoma (GBM), IDH-wildtype, with O(6)-methylguanine-DNA methyltransferase (MGMT) promoter methylation. F2-4 is a grade 4 IDH-mutant astrocytoma (positive for the IDH1 mutation by immunohistochemistry), negative for epidermal growth factor receptor (EGFR) amplification, but positive for the loss of phosphatase and tensin homolog (PTEN) sequences relative to chromosome 10 centromere sequences. F18-1 was derived from a primary tumor, whereas F2-4 was obtained from a resection of a recurrent tumor.  Briefly, stable cells expressing small hairpin RNA of a non-targeting control and two KANSL2-targeting sequences were cultured in serum-free medium supplemented with B27, N2, 20 ng/ml bFGF, 20 ng/ml EGF, 2 mM L-glutamine, 2 mM non-essential amino acids, 50 U/ml penicillin/streptomycin, and 75 µg/ml low-endotoxin bovine serum albumin (Sigma, USA). Cells were plated onto Geltrex (A1413202)-coated plates for three days before being harvested for sequencing.

first: Nicolás

last: Budnik


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

overall_design: Chromosome-chromosome interactions were profiled using Hi-C of KT-47 pretreatment (KT-47PT) and KT-47 resistance (KT-47R1) samples. KT-47 pretreatment received no chemotherapy in the xenograft model. KT-47R1 exhibited complete resistance to vincristine, actinomycin-D, and doxorubicin.


title: MYC modulates TOP2A diffusion to promote substrate detection and activity [CAD-seq]

first: Vladislav

last: Kuzin

overall_design: Covalent Adduct Detection of topoisomerase and sequencing (TOP CAD-seq) in HCT116 MYC-mAID cells for TOP2A in triplicates.

first: Donald

last: Cameron

first: Kathryn

last: Jackson

first: Evanthia

last: Iliopoulou

first: Laura

last: Baranello


title: Targeting Notch signaling to restore neural development and behavior in mouse models of ASD [RNAseq_embryo_hanno]

overall_design: RNA-seq profiling of embryonic whole brain from wildtype mice and valproic acid or poly(I:C) exposed mice.


title: ACBP: a poor-prognosis biomarker in sepsis and a target for disease mitigation II

first: Guido

last: Kroemer

overall_design: Eight-week-old male C57Bl/6J mice were randomly assigned to treatment groups and administered either a monoclonal antibody against ACBP/DBI (aDBI; 4h and1 h prior to surgery) or its isotype control (IgG), in combination with dexamethasone (DEX) or PBS 1X, administered 1h before CLP. Sepsis was induced by cecal ligation and puncture (CLP) under isoflurane anesthesia. Briefly, the cecum was exteriorized, ligated at 75% of its length using non-absorbable 4-0 silk suture, and punctured once through-and-through with a 21-gauge needle. A small amount of fecal content was gently extruded, and the cecum was returned to the abdominal cavity. Sham-operated mice underwent the same procedure, including treatment injections, but without ligation or puncture. Mice that died within the first 24h post-surgery were considered to have succumbed to perioperative complications and were excluded from further analysis. For molecular analyses, organs were collected on the day of euthanasia (24h post-CLP) and immediately snap-frozen in liquid nitrogen. For RNA-sequencing library preparation, RNA was extracted from mouse spleens using RNA Plus Mini Kit (Qiagen) according to manufacturer’s instructions. The concentration and integrity of total RNA was analysed using electrophoretic separation on microfabricated chips in Agilent 2100 Bioanalyzer System (Agilent, CA, USA). After, mRNA-sequencing library preparation (1.5 µg total RNA per sample) was carried out on NovaSeq 6000 PE150 instrument (2 x 150 bp, 40 million reads per sample). For RNA-sequencing data analysis, Fastq files were align on mm10, Mus musculus genome, by Hisat2, BAM files were count by HTSeq-count. The obtained raw count files were analyse with R package (R Foundation for Statistical Computing; https://www.R-project.org/) DESeq2. Our genes of interest were selected based on the thresholds abs (Fold Change) ≥ 1.5 and a pvalue ≤ 0.05. Heatmaps were performed with the R package ComplexHeatmap, Venn diagrams with ggVennDiagram, all other plots are realized with ggplot2. Gene ontology was realized with gprofilr, clusterProfiler and enrichplot.

first: Flavia

last: Lambertucci

first: Omar

last: Motiño

first: Uxía

last: Nogueira-Recalde

first: Yan

last: Rong

first: Léa

last: Montégut

first: María

last: Pérez-Lanzón

first: Vincent

last: Carbonnier

first: Sylvère

last: Durand

first: Fanny

last: Aprahamian

first: Hui

last: Chen

first: Yanbing

last: Dong

first: Allan

last: Sauvat

first: Silvia

last: Mingoia

first: Sijing

last: Li

first: Sylvie

last: Lachkar

first: Ester Gloria

last: Saavedra Díaz

first: Jonathan

last: Pol

first: Federico

last: Pietrocola

first: Estela

last: Rocha-Oliveira

first: Roberto

last: Roncon-Albuquerque Jr

first: Francisco

last: Vasques-Nóvoa

last: Lozano-Rodríguez

first: José

last: Avendaño-Ortiz

first: Eduardo

last: López-Collazo

first: Mahmoud

last: Abdellatif

first: Isabelle

last: Martins


title: Mitochondrial metabolism and signaling direct dendritic cell function in antitumor immunity [microarray1]

first: Hongbo

last: Chi

summary: Transcriptional dissection of cDC1s with polarized mitochondria or cDC1s with depolarized mitochondria

overall_design: Splenic [TMRM/MG]hi or [TMRM/MG]lo cDC1s were sorted from WT mice, followed by microarray analysis

first: Hao

last: Shi

first: Zhiyuan

last: You


title: Targeting the ferritinophagy-lysosome axis as a therapeutic vulnerability in gastroenteropancreatic neuroendocrine tumors [RNA-Seq]

first: Arul

last: Chinnaiyan

overall_design: RNA-seq profiling of QGP1 cells with or without PIKFYVE knockdown; or QGP1 cells transcriptome changes after Apilimod or Torin1 treatment.

first: Yizhi

last: Cao

first: Yuanyuan

last: Qiao

first: Caleb

last: Cheng

first: Xuhong

first: Andrej

last: Coleski

first: Eleanor

last: Young


first: Jiachen

last: Wang

summary: To investigate the distribution patterns of histone modifications across the genome in osldl3 mutants, we analyzed the data derived from ChIP-seq.

overall_design: ChIP-seq of histone modifications in rice NiP and osldl3 using H3, H3K4me1, H3K4me2, H3K4me3 antibodies.

first: Jiabing

last: Wu

first: Kangxi

last: Du

first: Wenhao

last: Xie

first: Xiang

last: Li

first: Xiaolong

first: Aiwu

last: Dong


title: Mitochondrial metabolism and signaling direct dendritic cell function in antitumor immunity [microarray2]

first: Hongbo

summary: Transcriptional dissection of splenic WT and OPA1-deficient cDC1s

overall_design: Splenic cDC1s were sorted from WT or CD11c-Cre; OPA1 flox mice, followed by microarray analysis


title: VAMP7-dependent late endosomal secretion of ER and mitochondrial proteins impacts the tumor microenvironment and macrophage engagement

city: Paris

first: Thierry

last: Galli

address: 102 Rue de la Sante

institute: Institute of Psychiatry and Neuroscience of Paris

summary: Late endosomal secretion is an unconventional secretion mechanism that depends on the SNARE protein VAMP7. We previously showed that VAMP7 mediates the secretion of the ER protein Reticulon3.  However, the functional relevance and molecular mechanism of this secretory pathway remain unclear. Here, we show that VAMP7 knockout cells  exhibit impaired secretion of ER- and mitochondrial-derived proteins and signs of ER and mitochondrial stress. In addition, pharmacological induction of organellar stress enhances the VAMP7-dependent secretion. We assess the pathophysiological significance of this mechanism using a preclinical glioblastoma model. VAMP7 knockout glioblastoma cells implanted in male rat brain develop into larger, more necrotic tumors with reduced macrophage infiltration compared to controls, suggesting that VAMP7-dependent late endosomal secretion contributes to the tumor microenvironment and affects macrophage infiltration. Together, our results support a model in which late endosomal secretion functions as an organelle quality-control and stress-communication mechanism, with particular relevance to cancer.

overall_design: Quadriplicate samples of WT, VAMP7KO and ATG5KO NRK cells grown in basal condition in Growth Medium


title: Trans-acting long non-coding RNA modulates long-range chromatin interactions associated with oncogenic MYC signaling [RNA-seq]

first: Rendong

last: Yang

summary: To investigate the function and affected pathways of novel lncRNA IGF1R-AS1 in the prostate cancer, we established VCaP cell lines in which SMARCA1/SMARCA4 has been knocked down by siRNA.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for controls and its SMARCA1/SMARCA4 KD derivatives in VCaP cell lines.

first: Tingyou

first: Yongyong

first: Yanan

last: Ren


title: Trans-acting long non-coding RNA modulates long-range chromatin interactions associated with oncogenic MYC signaling [SMARCA1_ATAC-Seq]

summary: To investigate the functional role of the novel lncRNA IGF1R-AS1 in prostate cancer, we generated VCaP cells with siRNA-mediated knockdown and performed ATAC-seq to profile the corresponding changes in chromatin accessibility

overall_design: Analysis of ATAC-seq data for controls and its SMARCA1 KD derivatives in VCaP cell lines.

first: Qingshu

last: Meng


title: Transcriptome data (mRNA-seq) for Physcomitrella patens (Physcomitrium patens) wild type.

summary: Gene expression profiling analysis of RNA-seq data for Physcomitrella patens (Physcomitrium patens).


title: Trans-acting long non-coding RNA modulates long-range chromatin interactions associated with oncogenic MYC signaling [ATAC-seq]

summary: To investigate the function and affected pathways of novel lncRNA IGF1R-AS1 in the prostate cancer, we established VCaP cell lines in which IGF1R-AS1 has been knocked down by siRNA.

overall_design: Analysis of ATAC-seq data for controls and its IGF1R-AS1 KD derivatives in VCaP cell lines.


title: Transcriptome data (mRNA-seq) for NiP, ehd3-1, sdg724-1, and ehd3 sdg724.

summary: To explore how Ehd3 and SDG724 regulate gene transcription at the genome-wide level, we conducted RNA-seq analyses of NiP, ehd3-1, sdg724-1, and ehd3 sdg724.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for WT and mutants.


title: High throughput sequencing data for Oryza sativa, Chlamydomonas reinhardtii, and Physcomitrella patens

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

sample_organism:
Chlamydomonas reinhardtii
Physcomitrium patens
Oryza sativa

overall_design: Refer to individual Series


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

first: Hongjian

last: Jin

type: Methylation profiling by genome tiling array

overall_design: Illumina methylation beachip array profiling of KT-47 pretreatment (KT-47PT), KT-47 pre-resistance, and KT-47 resistance (KT-47R1 and KT-47R2) samples. KT-47 pretreatment received no chemotherapy in the xenograft model. KT-47 pre-resistance received vincristine, actinomycin-D, and doxorubicin in the xenograft model but did not yet demonstrate resistance. KT-47R1 and KT-47R2 exhibited complete resistance to vincristine, actinomycin-D, and doxorubicin.

first: Andrew

last: Murphy


title: Transcriptome data (mRNA-seq) for Chlamydomonas reinhardtii wild type.

summary: Gene expression profiling analysis of RNA-seq data for Chlamydomonas reinhardtii.


title: ChIP-seq of H3K4me1, H3K4me2, H3K4me3, H3K36me1, H3K36me2, and H3K36me3 for Physcomitrella patens (Physcomitrium patens).

summary: We performed H3K4 and H3K36 methylation occupancy analysis (ChIP-seq) for Physcomitrella patens.

overall_design: H3K4 and H3K36 methylation levels on wild-type Physcomitrella patens genes.


title: ChIP-seq for Ehd3 and SDG724 using HA or GFP antibodies.

summary: To investigate the distribution patterns of Ehd3 and SDG724 across the rice genome, we analyzed the data derived from ChIP-seq.


title: ChIP-seq of H3K4me1, H3K4me2, H3K4me3,H3K36me1, H3K36me2, and H3K36me3  for Chlamydomonas reinhardtii.

summary: We performed H3K4 and H3K36 methylation occupancy analysis (ChIP-seq) for Chlamydomonas reinhardtii.

overall_design: H3K4 and H3K36 methylation levels on wild-type Chlamydomonas reinhardtii genes.


overall_design: Comparative gene expression profiling analysis of RNA-seq data for controls and its IGF1R-AS1 KD derivatives in VCaP cell lines.


title: Kidney Transcriptome Sequencing of Mice with Diabetic Nephropathy

status: Public on Jan 25 2026

city: Shenzhen

first: Shu

address: 1017 Dongmen North Road, Luohu District, Shenzhen

institute: shenzhen people's hospital

summary: Aging is a major risk factor for diabetic kidney disease (DKD), with both conditions exhibiting similar renal pathology. We identify the energy-sensing molecule Retinoic acid-related orphan receptor γ (RORγ) as significantly downregulated in diabetic and aged kidneys. Tubule-specific RORγ deficiency exacerbates kidney injury, whereas its overexpression protects. Mechanistically, RORγ stabilizes insulin-induced gene 1 (INSIG1) by upregulating the deubiquitinase YOD1 and enhancing AMPK activity via CAB39, which together promote INSIG1 phosphorylation and subsequent stabilization. Stabilized INSIG1 potently blocks the ER-to-Golgi transport and activation of SREBP2 (cholesterol synthesis) and STING (inflammatory signaling). In diabetes, RORγ itself is suppressed transcriptionally by CTCF and functionally by impaired AMPK/SIRT1 signaling, which hinders its activation. Importantly, administration of a RORγ agonist or RORγ-enriched exosomes effectively alleviates diabetic kidney injury. Thus, RORγ emerges as a key regulatory node that mitigates DKD and renal aging by co-regulating AMPK-mediated metabolic and STING-driven innate immune pathways through INSIG1 stabilization.

overall_design: db/db mice were used as the diabetic model and db/m mice as the control, followed by renal transcriptome sequencing.


first: Jiachen

summary: To investigate the distribution patterns of histone modifications across the genome in different mutants, we analyzed the data derived from ChIP-seq.

overall_design: ChIP-seq of histone modifications in rice NiP, ehd3-1, sdg724-1, and ehd3sdg724 using H3, H3K4me1, H3K4me2, H3K4me3, H3K36me1, H3K36me2, and H3K36me3 antibodies.


title: Global regulation of mediated by the histidine-responsive local transcription factor HutC in Pseudomonas aeruginosa

city: Auckland

first: Xue-Xian

last: Zhang

address: 3a Symonds Street

country: New Zealand

institute: University of Auckland

summary: Pseudomonas aeruginosa is a metabolically versatile environmental pathogen whose virulence relies on coordinated expression of catabolic genes, particularly the histidine utilization (hut) operon. Disruption of the hut operon reduces virulence, but the underlying mechanism remains rudimentary. Here, we genetically characterized the histidine-responsive transcriptional factor HutC in P. aeruginosa PAO1, alongside HutC in the non-pathogenic strain P. fluorescens SBW25. Two important features emerged. First, HutC recognizes two distinct DNA-binding motifs with little sequence similarity; notably, a noncanonical binding site was identified in the hutF promoter of SBW25 but was absent in PAO1. Second, HutC exhibits low-affinity binding to genes beyond histidine catabolism and contributes to the expression of multiple virulence traits. These findings identify HutC as a local regulator linking histidine catabolism with virulence and as a unique prokaryotic model for studying how noncanonical transcriptional factor-DNA interactions achieve binding specificity, a phenomenon so far investigated only in eukaryotes.

overall_design: Compare trasncriptomes between wild-type PAO1 with each of three derived mutants with hutC expressed at different levels. Bacteria were gorwn on minimal medium supplemented with histidine (10 mM) as the sole source of carbon and nitrogen.

first: Xinyi

last: Liu


title: Single-Cell RNA Sequencing Reveals that Bach2 with Inactive Heme-Binding Sites Sustains the Stemness of CD8+ T Cells

city: Tianjin

first: Yingxi

last: Xu

address: 288 Nanjing Road

department: State Key Laboratory of Experimental Hematology

institute: Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College

summary: Bach2 is vital for the formation of progenitor exhausted T cells and for maintaining their stem-like properties. In B cells, Bach2 undergoes conformational changes that reduce its transcriptional repression activity due to decreased DNA-binding affinity and increased degradation, subsequently triggering Blimp1 expression. Therefore, we aimed to use scRNA-seq to determine whether mutation of the heme-binding site in Bach2 (Bach2MUT) could more efficiently preserve stem-like properties in tumor-infiltrating lymphocytes (TILs) compared to wild-type Bach2 (Bach2WT).

overall_design: P14 cells were isolated from P14 mice and then overexpressed with either Bach2WT (CD45.1) or Bach2MUT (CD45.1/.2). The cells were co-transferred into Yumm1.7-gp33 tumor-bearing mice. Nine days later, CD3+CD8+CD44+CD45.1 or CD3+CD8+CD44+CD45.1/.2 cells were sorted and subjected to CMO multiplexing followed by scRNA-seq.

first: Josep

last: Garnica

first: Ping-Chih

last: Ho


title: RNA-seq Unveils that Exogenous Hemin Treatment Accelerates CD8+ T Cell Exhaustion

summary: Regulatory heme is known to control cellular behavior by regulating the activities of hemoproteins. We hypothesized that increased levels of regulatory heme may drive T cell exhaustion. To test this, we first confirmed that treatment with hemin, a heme analog, effectively increased intracellular regulatory heme levels in T cells. To evaluate the transcriptional changes in CD8+ T cells treated with hemin, we conducted RNA sequencing on CD8+ T cells with and without exogenous hemin treatment. The RNA-seq data revealed that hemin treatment strongly modulated gene expression patterns associated with terminally exhausted T cells. Pathway enrichment analysis further revealed that hemin suppressed pathways involved in proliferation and cytokine production while altering metabolic processes, such as cholesterol efflux and fatty acid biosynthesis, which are known to regulate T cell function. These results suggest that increased levels of regulatory heme drive T cell exhaustion differentiation.

overall_design: Primary normal CD8 T cell treated with 25uM Hemin or veicle for bulk RNA-seq analysis, 5 replicates are included in each group.

first: Yu-Ming

last: Chuang


title: Trans-acting long non-coding RNA modulates long-range chromatin interactions associated with oncogenic MYC signaling [Iso-Seq]

overall_design: Total RNA  was extracted using Promega ReliaPrep RNA Cell system(Z6011). 3' Race was done using 5'/3' RACE Kit, 2nd Generation (Roche). One microgram of total RNA was used for reverse transcription step with olig-anchor primer 5’-GACCACGCGTATCGATGTCGACTTTTTTTTTTTTTTTTV-3’ according to the manufacturer's instructions. One microliter  of the RT product was used for the subsequent PCR reaction using IGF1-AS1 exon1 specific forward primer (5'-ACTATGTTTCAGCGGCTGGT-3') and the PCR anchor reverse primer in the kit(5’-GACCACGCGTATCGATGTCGAC-3’). The PCR product was cleaned using a PCR cleaning kit(Qiagen) and submitted for PacBio sequencing.

last: Wang


title: An SP110-SP100 axis is a critical regulator of PML body dynamics and mitotic fidelity

city: Zurich

first: Eric

last: Aird

address: Otto-Stern-Weg 7

country: Switzerland

institute: ETH Zurich

summary: Stimulation of the innate immune system by foreign RNA elicits a potent interferon response and can trigger cell death. The mechanisms by which cells balance a robust response with cell-intrinsic lethality are still being uncovered. Employing genome-wide CRISPR-Cas9 genetic screens with triphosphorylated RNA stimulation, we discovered that the promyelocytic leukemia (PML) nuclear body-localized speckled protein 110 (SP110) is a potent inhibitor of type 1 interferon-driven cell death. Death suppression by SP110 counteracts a toxic activity of SP100, a major constituent of PML bodies. Loss of SP110 leads to mitotic retention of SP100 and PML bodies which associate with and perturb segregating chromosomes leading to micronucleus formation, DNA damage, and genotoxic cell death. A combination of cryo-electron microscopy, AlphaFold modeling, and cellular biochemistry reveals that SP110 dissolves toxic SP100 oligomers via necessary and sufficient direct interactions between their caspase activation and recruitment domains (CARDs). These data reveal critical roles of SP100 and SP110 in governing disassembly of PML bodies during mitosis and the repercussions if this process is mis-regulated.

overall_design: Endogenous anti-SP100 ChIP-sequencing of interferon stimulated WT and SP110 KO cells treated with interferon beta for 6 h.


title: ATAC-seq Reveals that Heme Regulates the Transcriptional Activity of Transcription Factors Driving CD8⁺ T Cell Exhaustion

summary: Regulatory heme is known to influence cellular behavior by modulating the activity of hemoproteins. We hypothesized that elevated levels of regulatory heme might drive T cell exhaustion through the modulation of transcription factor activity. To test this hypothesis, we first confirmed that treatment with hemin, a heme analog, effectively increased intracellular regulatory heme levels in T cells. To assess the transcriptional and chromatin changes induced by hemin, we performed ATAC-seq on CD8⁺ T cells treated with or without exogenous hemin. The ATAC-seq analysis revealed that hemin-treated T cells displayed a distinct chromatin accessibility landscape compared to vehicle-treated controls. Integration of ATAC-seq and transcriptomic data using the Taiji analytical algorithm revealed that hemin modulates the activity of transcription factors involved in T cell exhaustion, including BACH2, MYB, MAF, BATF, RUNX3, and PRDM1.

overall_design: Primary normal CD8 T cell treated with 25uM Hemin or veicle for bulk ATAC-seq analysis, 4 replicates are included in each group.


title: Single-nucleus RNA sequencing dataset of diverse tissues from wild-type monkey and Tau-P301L transgenic monkey

status: Public on Jan 24 2026

city: Guangzhou

first: BoFeng

last: Han

state: Guangdong

address: No. 601, West Huangpu Avenue, Tianhe District, Guangzhou, Guangdong Province, China

institute: Jinan University

summary: Utilizing non-human primates to study the role of human Tau and its related pathologies is logical and important due to their closer similarity to human brain structure and function. In our earlier research, we generated a transgenic cynomolgus monkey model expressing Tau (P301L) through lentiviral infection of monkey embryos. These monkeys exhibited age-dependent neurodegeneration and motor dysfunction. Single-cell RNA sequencing (scRNA-seq) is a powerful and promising technique for elucidating the cellular complexity and pathology across different tissues. However, single-cell data from non-human primate models of Tau pathology are currently nonexistent. In this study, we performed single-nuclei RNA sequencing (snRNA-seq) on the hippocampus, striatum, and spinal cord of Tau (P301L) monkey, providing the first single-cell atlas of multiple tissue regions in a non-human primate model that simulates human tauopathies. This will offer crucial data references for cross-species single-cell level studies of tau and its related pathologies.

overall_design: We performed single-nuclei RNA sequencing (snRNA-seq) on the hippocampus, striatum, and spinal cord of Tau (P301L) monkey and wilde type control

first: Zhuchi

last: Tu

first: Bofeng

first: Weijie

last: Ouyang

first: Yan

last: Chen

first: Danyi

first: Weien

last: Liang


title: snRNAseq molecular characterization of pig dorsal root ganglion neurons [snRNAseq]

city: Toronto

first: Shreejoy

last: Tripathy

state: Ontario

address: 250 College st.

institute: CAMH

summary: This dataset offers snRNAseq data from dorsal root ganglia (DRG) of pigs, targeting molecular markers of sleeping nociceptors. It combines high-throughput sequencing with detailed tissue processing, advancing our knowledge of nociceptor diversity and providing insights for sensory and pain research.

overall_design: Samples obtained from male Landrace pigs, DRGs were preserved post-euthanasia, processed for nuclei isolation through methods like tissue lysis and density gradient centrifugation, and enriched for neuronal nuclei analysis.The aim is to characterize sensory neuron transcriptomic profiles in DRGs, enhancing understanding of nociceptor diversity for pain study applications. This dataset aids comparative sensory neuron research, offering a detailed molecular resource for integration with other transcriptomic datasets.

first: Hans

last: Jürgen Solinski

first: Jannis

last: Körner

first: Derek

last: Howard

first: Angelika

last: Lampert

first: Martin

last: Schmelz


title: Gene expression profiles from multimodal patch-seq neuron samples of the pig dorsal root ganglion

summary: This dataset comprises single-cell transcriptomic profiles derived from the dorsal root ganglia (DRG) of pigs, aimed at elucidating the molecular identity of mechano-insensitive C-fibres (CMis) implicated in neuropathic pain. Using an innovative approach that combines electrophysiological characterization with Patch-seq, we have successfully captured and analyzed the transcriptomes of primary sensory neurons. These neurons were characterized based on their electrophysiological properties, mirroring those of human CMis, which play a pivotal role in the persistence of neuropathic pain. The presented dataset enriches our understanding of the cellular and molecular landscape of neuropathic pain but also opens new avenues for the development of targeted therapeutic interventions. This dataset is expected to serve as a valuable resource for researchers in the fields of sensory biology and pain neuroscience.

overall_design: DRGs from cervical, thoracic, and lumbar segments were processed through mincing, enzymatic digestion, mechanical trituration, and centrifugation for neuron isolation. Cultured neurons were assessed electrophysiologically and analyzed via Patch-seq for molecular profiling. The experimental design concentrated on assaying the diverse array of neuron types in the DRG by examining their electrophysiological characteristics and gene expression.The study aimed to identify molecular markers of mechano-insensitive C-fibres (CMis) to advance understanding of neuropathic pain mechanisms. Objectives included electrophysiological characterization of pig sensory neurons and integration with larger RNA-seq reference atlas data.

last: Korner


title: Pig dorsal root ganglion neurons


title: ERCC6L2 ensures repair fidelity for staggered-end DNA double-strand breaks

summary: DNA double-strand breaks (DSBs) both pose threats to genome integrity and are commonly used for genome editing applications. Structural features of DSB ends play key roles in determining DNA repair pathway usage and outcomes during genome editing, but the cellular factors involved in these processes are only partially known. Through genome-wide CRISPRi screening, we identified ERCC6L2 as critical for repairing Cas12a-induced staggered DSBs but irrelevant for Cas9-induced blunt DSBs. We show that ERCC6L2 acts as a protection factor for staggered DSBs with either 5’ or 3’ polarity, preventing large deletions and translocations stemming from DNA damage induced by Cas12a, TALENs, or dual Cas9 nicks. ERCC6L2 loss furthermore hyper-sensitizes cells to multiple staggered DSBs induced by promiscuous Cas12a activity or etoposide-induced TOP2 trapping. By combining genetics and biochemical reconstitution, we find that ERCC6L2 counteracts ATM-driven resection by binding and melting staggered DNA ends, thereby promoting accurate end joining. Our data reveal a protective role of ERCC6L2 in staggered DSB repair, which suggests the molecular underpinnings of pathology in patients with ERCC6L2 mutations and cautions against using overhang-inducing genome editing tools for their treatment.

overall_design: Endogenous anti-MRE11 ChIP-sequencing of RPE1 TP53 null WT and ERCC6L2 KO cells edited with Cas12a gMulti and collected 12 h later.

first: Almu

last: Serrano-Benitez

first: Sebastian

last: Siegner