title: Multimodal integration of transcriptomics, proteomics and radiomics improves prediction of recurrence in patients with IDH-mutant Glioma

city: Pessac

first: Andreas

last: Bikfalvi

address: Allée Geoffroy St-Hilaire

country: France

institute: University of Bordeaux

summary:
Isocitrate dehydrogenase mutant gliomas remain lethal brain cancers which impair quality of life in young adults. These tumors are molecularly and cellularly heterogeneous and have a wide range of survival prognoses. Consequently, the identification of pa
Here, we analyzed imaging, transcriptomic, and proteomic profiles using machine learning to 1) describe the biological characterization of subtypes of IDH-mutant gliomas categorized by PET and histology, 2) reinforce the integration of PET metrics in the

overall_design: Patient samples were collected during tumor resection and snap-frozen. RNAs were isolated from 59 patients with IDH-mutant gliomas and subjected to RNA sequencing.

first: Tiffanie

last: Chouleur

first: Christèle

last: Etchegaray

first: Laura

last: Villain

first: Antoine

last: Lesur

first: Thomas

last: Ferté

first: Marco

last: Rossi

first: Laetitia

last: Andrique

first: Costanza

last: Simoncini

first: Anne-Sophie

last: Giacobbi

first: Matteo

last: Gambaretti

first: Egesta

last: Lopci

first: Bethania

last: Fernades

first: Gunnar

last: Dittmar Olivier

first: Rolf

last: Bjerkvig

first: Boris

last: Hejblum

first: Rodolphe

last: Thiébaut

first: Olivier

last: Saut

first: Lorenzo

last: Bello


title: Asymmetric Histone Inheritance Regulates Differential Transcription Re-initiation and Cell Fate Decisions in Mouse Olfactory Horizontal Basal Cells

status: Public on Mar 26 2025

city: Baltimore

first: Guanghui

last: Yang

state: MD

address: 3400 North Charles Street

department: Biology

country: USA

institute: Howard Hughes Medical Institute/The Johns Hopkins University

type: Expression profiling by high throughput sequencing

summary: Histones, major carriers of epigenetic information, play critical roles in regulating gene expression patterns and cell fate decisions. While asymmetric histone inheritance has been shown to regulate distinct cell fates in Drosophila adult stem cells, its relevance in mammals remains unclear. In this study, we investigated cell division modes and histone inheritance patterns in horizontal basal cells (HBCs) of the mouse olfactory epithelium following injury. We found that approximately 40% of telophase HBCs show asymmetric division, with a corresponding asymmetric segregation of histone H4. In primary cultured HBCs, we observed asymmetric cell division accompanied by asymmetric distribution of histones, including H4, H3, and H3.3, but not H2A-H2B. Asymmetric histone segregation leads to asymmetric association of a key ‘stemness’ transcription factor p63 and asynchronous transcription re-initiation during mitotic exit. Single-cell RNA sequencing of paired daughter cells further revealed asymmetric cell fate priming in cultured HBCs. Disruption of asymmetric cell division abolished asymmetric transcription re-initiation, asymmetric histone inheritance in culture HBCs and further caused regeneration defects in OE. These findings reveal the conservation of asymmetric histone inheritance in mammalian adult stem cells and highlight its biological significance in tissue regeneration.

overall_design: Single daughter cells were individually picked using mouth pipette soon after division of ex vivo cultured mouse horizontal basal cells (HBCs). The pairing information were noted and RNA profiles in each cell were examined using the Smart-seq2 method.

first: Binbin

last: Ma

first: Haiqing

last: Zhao

first: Xin

last: Chen


title: Inherent Specificity and Mutational Sensitivity as Quantitative Metrics for RBP Binding

status: Public on Mar 28 2025

city: Cleveland

first: Soon Yeul

last: Yi

state: OH

address: CWRU Wood Research Building W127A, 2109 Adelbert Rd,

department: Biochemistry

institute: Case Western Reserve University

summary: Interactions between RNAs and RNA binding proteins (RBPs) regulate gene expression in eukaryotic cells. RNA-RBP affinities measured in vitro reveal diverse binding specificities, yet approaches to directly compare specificities across RBPs are lacking. Here, we introduce two quantitative metrics: inherent specificity, which measures how selectively an RBP distinguishes its strongest binding motif from all possible motifs, and mutational sensitivity, which assesses tolerance to single nucleotide variations within preferred motifs. Analyzing high-throughput sequencing datasets, we compared these metrics across 100 RBPs in vitro and 27 RBPs in cells, finding strong correlation between in vitro and cellular measurements for RBPs that bind RNA independently of a local structural context. Through CLIP experiments with swapped RNA recognition motifs between a low-specificity RBP (RBM25) and a high-specificity RBP (HNRNPC), we demonstrated that sequence specificity can be transferred between protein contexts. Using these insights, we developed mathematical models showing how RBPs with different specificity profiles compete for binding sites, revealing how variations in inherent specificity and mutational sensitivity influence target selection. Together, our results provide a quantitative framework for modeling RNA-RBP interactions and designing RBPs with targeted specificity.

overall_design: To investigate the effect of RRM swap in the biological specificity of an RBP, four different cell lines expressing the wildtype hnRNPC and RBM25 and the mutant RBPs with their RRMs swapped were expressed in HEK293 cells. These exogenously expressed RBPs were tagged with V5 tag at the N-terminus for efficient immunoprecipitation. Then, UV crosslinking and immunoprecipitation using V5 antibody followed by hight-throughput sequencing (CLIP-Seq) was performed in the four cell lines.

first: Joseph

middle: M

last: Luna

first: Soon

first: Shashi

last: Singh


title: FBXO44 Regulates Rac1 Spatiotemporal Dynamics: An Exploitable Therapeutic Vulnerability for Actin Cytoskeleton-Targeted Treatment in Gastric Cancer

status: Public on Mar 22 2025

city: Hangzhou

first: Guangzhao

last: Pan

address: Dongfang street

department: Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences

country: China

summary: The dynamic homeostasis of the cytoskeleton represents a critical vulnerability in tumor cells, yet the molecular mechanisms governing this equilibrium remain elusive. In the present study, we identify FBXO44 as a crucial regulator of Rac1 nucleocytoplasmic shuttling through its interaction with MTSS1. In gastric cancer (GC), FBXO44 orchestrates dual ubiquitination programs on MTSS1: K63-linked polyubiquitination promotes Rac1 nuclear translocation to drive cytoskeletal remodeling, whereas K11-linked modification triggers MTSS1 proteasomal degradation to restrict Rac1 nuclear trafficking. Structural analysis reveals that FBXO44 engages MTSS1 through distinct domains, dynamically balancing these opposing ubiquitination events through precise control MTSS1 protein levels, thereby calibrating actin cytoskeletal dynamics. Clinically, this regulatory axis maintains an oncogenic equilibrium-FBXO44 overexpression correlates with Rac1 signaling activation in progressive GC patients. Therapeutically, pharmacological disruption of this balance using the novel inhibitor DQ2405 achieves dual anti-tumor effects: suppressing tumor growth and metastatic capacity. Our findings establish FBXO44-mediated Rac1 spatiotemporal control as a druggable strategy for actin-cytoskeleton targeted therapy, providing both mechanistic insights into cytoskeletal homeostasis and a translational framework for GC treatment.

overall_design: RNA-sequencing (RNA-seq) of MKN74 cells expressing MTSS1 to reveal its molecular effects on host cells.

first: Qianqian

last: Xu


title: RNAseq of the peripheral cornea and limboscleral tissues of rats treated with systemic spironolactone in a model of corneal neovascularization

status: Public on Mar 17 2025

city: Paris

first: Daniela

last: Rodrigues-Braz

address: 15 rue de l'Ecole de Médecine

institute: Inserm

summary: The aim of this study was to analyse the transcriptional regulation in the corneal and limbal tissues of rats treated with spironolactone in a model of limbal stem cell deficiency (LSCD). CNV was induced by total corneal de-epithelialization and limbal resection. Rats were injected subcutaneously with spironolactone (25mg/kg/day) diluted in 90% olive oil and 10% DMSO  or vehicle (90% olive oil and 10% DMSO) for 14 days. On day 3 (early inflammatory stage) and day 7 (angiogenic stage), rats were euthanized and the peripheral cornea and the limboscleral tissues were exised for RNA-sequencing. Total RNA samples were sequenced at the iGenSeq transcriptomic platform of the Brain and Spine Institute (ICM, Paris, France). RNA quality was checked by capillary electrophoresis (Agilent 2100 Bioanalyzer system) and RNA with integrity numbers (RIN) ranging from 7.8 to 8.2 was accepted for library generation. Quality of raw data has been evaluated with FastQC. Illumina DRAGEN bio-IT Platform (v3,8,4) was used to align reads on reference genome rd6 and quantification with genecode vM25 annotation gtf. Library orientation, library composition and coverage along transcripts were checked with Picard tools. differential analysis has been also conducted with edgeR. Multiple hypothesis adjusted p-values were calculated with the Benjamini-Hochberg procedure to control FDR. We identified genes differentially regulated by spironolactone vs. vehicle on day 3 and day 7.

overall_design: Corneal and limboscleral mRNA profiles of rats treated with systemic spironolactone in a rat model of limbal stem cell deficiency

first: Min

first: Francine

last: Behar-Cohen

first: Justin

last: Guegan


title: Tonic ISG expression promotes efficient induction of IFNL in response to influenza infection

status: Public on Mar 14 2025

city: urbana

first: christopher

last: brooke

state: IL

address: B103 CLSL, MC-110, 601 South Goodwin Avenue

institute: University of Illinois at Urbana-Champaign

summary: The innate immune response, especially the interferon (IFN) response, plays a critical role in limiting initial dissemination of viruses from the site of infection. While the pathogen-associated molecular patterns (PAMPs) and pattern recognition receptors (PRRs) involved in sensing and inducing the innate immune response during influenza A virus (IAV) infections are well-characterized, the factors that regulate IFNL production in infected cells remain poorly understood. Previous studies have highlighted that most infected cells fail to express either type I or III IFNs in response to stimulus, suggesting a regulatory mechanism that controls the activation of IFNs during infection. To investigate the factors influencing IFNL induction during IAV infection, we performed single-cell RNA sequencing (scRNA-seq) of A549 cells infected with A/Perth/16/2009 and sampled at multiple time points post-infection. Using a novel pseudotime analysis approach tailored for temporal scRNA-seq data, we aim to identify host genes whose tonic expression modulates IFNL production in response to IAV infection.

overall_design: Comparison of host gene expression in Perth09 (H3N2) infected human alveolar epithelial cells at different times post-infection

first: Joel

last: Rivera-Cardona

first: Tarun

last: Mahajan

first: Qi Wen

last: Teo

last: Lederer

first: Elizabeth

middle: F

last: Rowland

middle: A

last: Thayer

first: Neeha

last: Kakuturu

first: Kyle

last: Heimburger

first: Nicholas

middle: C

last: Wu

first: Sergei

last: Maslov

first: Christopher

middle: B

last: Brooke


title: Single-cell transcriptomics of infant and adult T cells across human tissues

status: Public on Mar 11 2025

city: New York

first: Peter

last: Sims

state: NY

address: 3960 Broadway, Lasker 203AC

institute: Columbia University

summary: We performed bulk and single-cell RNA-seq on resting and stimulated T cells from tissues and blood of infant and adult organ donors.

first: Thomas

last: Connors

last: Szabo

first: Hanna

last: Levitin

first: Donna

middle: L

last: Farber


title: A human-specific enhancer fine-tunes radial glia potency and corticogenesis

status: Public on Mar 06 2025

city: Durham

first: Jing

last: Liu

state: NC

address: 218 CARL buildling

department: Molecular Genetics and Microbiology

institute: Duke University

summary: Humans evolved an extraordinarily expanded and complex cerebral cortex, associated with developmental and gene regulatory modifications1-3. Human accelerated regions (HARs) are highly conserved DNA sequences with human-specific nucleotide substitutions. Although there are thousands of annotated HARs, their functional contribution to species-specific cortical development is largely unknown4,5. HARE5 is a HAR transcriptional enhancer of the WNT signaling receptor Frizzled8 (FZD8) active during brain development6. Here, using genome-edited mouse and primate models, we demonstrate that human (Hs) HARE5 fine-tunes cortical development and connectivity by controlling the proliferative and neurogenic capacity of neural progenitor cells (NPCs). Hs-HARE5 knock-in mice have significantly enlarged neocortices, which contain more excitatory neurons. By measuring neural dynamics in vivo we show these anatomical features result in increased functional independence between cortical regions. To understand the underlying developmental mechanisms, we assess progenitor fate using fixed and live imaging, lineage analysis, and single-cell RNA sequencing. We discover Hs-HARE5 modifies radial glial progenitor behavior, with increased self-renewal at early developmental stages followed by expanded neurogenic potential later.  We use genome-edited human and chimpanzee (Pt) NPCs and cortical organoids to assess the relative enhancer activity and function of Hs-HARE5 and Pt-HARE5. Using these orthogonal strategies we show four human-specific variants in HARE5 drive increased enhancer activity which promotes progenitor proliferation. Finally, we show that Hs-HARE5 promotes progenitor proliferation by increasing canonical WNT signaling. These findings illustrate how small changes in regulatory DNA can directly impact critical signaling pathways to modulate brain development. Our study uncovers new functions for HARs as key regulatory elements crucial for the expansion and complexity of the human cerebral cortex.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for wildtype and HARE5Hs/Hs knock-in mice cortices at two timepoint, E12.5 and E14.5.  Three biological replicates have been collected for each condition. Conditions:  E12.5 WT, E12.5 HARE5Hs/Hs,  E14.5 WT, E14.5 HARE5Hs/Hs.

first: Debra

last: Silver


title: sc-RNA-seq for study: A human-specific enhancer fine-tunes radial glia potency and corticogenesis

overall_design: sc-RNA seq of E14.5 cortices from wildtype littermates and HARE5 knock-in mice. Two replicates each genotype.Conditions:  E14.5 WT, E14.5 HARE5Hs/Hs.


title: Methylation pseudotime analysis for label-free profiling of the temporal chromatin landscape with long-read sequencing

status: Public on Mar 05 2025

city: Irvine

first: Annie

last: Trinh

state: CA

address: 419 S. Circle View Drive

department: Microbiology & Molecular Genetics

institute: University of California, Irvine

summary: Faithful epigenetic inheritance across cell divisions is essential to maintaining cell identity and involves numerous epigenetic modifications, whose roles in coordinating chromatin architecture are less understood. Technological approaches to temporally order epigenetic modifications throughout the cell cycle often face limitations in sequence resolution and rely on potentially damaging mitotic labeling or conversion steps. Herein, we present Methylation Pseudotime Analysis Through read-level Heterogeneity (MPATH), a label- and conversion-free method to infer post-replication DNA strand maturity from methylation patterns across single molecules. We showed that MPATH is generally applicable across human embryonic stem cell (hESC) lines in which CpG methylation heterogeneity is coupled to replication, but not applicable to breast cancer cells, in which CpG methylation heterogeneity may also be associated with other factors. We also analyzed differentiated human cell lines and human and mouse mesenchymal stem cells and found that while MPATH showed reduced ability to infer DNA strand maturity within these contexts, it still captured general trends in DNA methylation that were associated with chromatin maturation. When applied to long reads generated by NOMe-seq, MPATH revealed that nucleosome compaction and CpG methylation uniformity are coupled across replication-associated timescales. Finally, extension of MPATH to phased reads reveals allele-specific trends in pseudotime distribution associated with X chromosome inactivation. Our findings suggest that when coupled with multimodal sequencing strategies, MPATH could provide valuable insights into chromatin restoration dynamics.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design:
HUES64 hESCs, H9 hESCs, HUES8 TKO hESCs, MDA-MB-231 breast cancer cells, BJ human fibroblasts, THP-1 human monocytes, human primary bone marrow-derived mesenchymal stem cells (hBMMSCs), and mBMMSC mouse bone marrow-derived mesenchymal stem cells (mBMMSCs) were subjected to several different experimental conditions prior to DNA extraction for long-read sequencing. In the first experiment, HUES64 hESCs were treated with 1µg/ml nocodazole for 16h. BrdU pulse-chase experiments were conducted on all cell lines to investigate DNA methylation patterns during chromatin maturation. For the pulse optimization, cells were subjected to 50 µM BrdU for durations of 10 minutes, 20 minutes, 30 minutes, and 1 hour, followed by genomic DNA collection at 0h (nascent chromatin) and 16h (mature chromatin). Mock controls were included for both 0h and 16h timepoints. Optimized labeling conditions included a 500 µM BrdU pulse (10 minute duration) with 0h and 16h chase points (an additional 8h chase point collected for mBMMSC mBMMSCs). Unlabeled HUES64 samples were also generated (sequenced to a total of 62x coverage across 2 technical replicates). All long-read data was acquired using ONT sequencing platforms. In a separate sequencing experiment, hESCs were subjected to Repli-ATAC sequencing in order to temporally profile chromatin accessibility across replication-associated timescales.  >>>Raw data in POD5 or FAST5 will be available upon request by the submitter.<<<
>>>Raw data in POD5 or FAST5 will be available upon request by the submitter.<<<

first: Kehan

last: Ren

first: Nandor

last: Laszik

first: Navied

last: Akhtar

first: Kwadwo

last: Bonsu

first: Tanye

last: Wen

first: Asia

last: Mendelevich

first: Yoshiko

last: Takahashi

first: Julien

last: P Morival

first: Katelyn

middle: E

last: Diune

first: Mitchell

last: Frazeur

first: Justin

last: Vega

first: Edouard

last: Aleman

first: Minji

last: Byun

first: Alexander

last: Gimelbrant

last: Read

first: Timothy

last: Downing


title: Inference of secreted protein signaling activities in intercellular communication

status: Public on Mar 04 2025

city: Bethesda

first: Peng

last: Jiang

state: Maryland

address: 41 Center Drive

department: Center for Cancer Research

institute: National Cancer Institute

summary: The human genome encodes ~1,900 secreted proteins, many of which mediate intercellular communication. Secreted proteins do not act cell-autonomously, limiting systematic approaches to characterize their functions. Here we introduce SecAct (Secreted Activity, https://secact.ccr.cancer.gov ), a computational framework that infers the signaling activities of 1,170 human secreted proteins from spatial, single-cell and bulk transcriptomic data. The inference model harnesses precomputed intercellular signaling signatures trained on 1,258 spatial transcriptomics samples spanning 37 cancer types. Transcriptomics data from antisecreted protein therapies validate SecAct's accuracy in predicting the repression of secreted protein activity following treatment. For spatial and single-cell transcriptomics data, SecAct provides interactive modules for analyzing secreted protein-mediated cell-cell communication. Applying SecAct to 54 cancer immunotherapy cohorts comprising 5,174 patients, we identified secreted proteins associated with tumor immunity. In vivo experiments validated lymphocyte antigen 86 (LY86), whose function in cancer was previously unknown, as an antitumor regulator.

overall_design: B16F10-Ly86 and B16F10-Vector tumors from mice that received 4 rounds of anti-PD-1 + anti-CTLA4 treatment were harvested and immediately snap-frozen in liquid nitrogen.

first: Beibei

last: Ru

first: Lanqi

last: Gong


title: VEGFR2 blockade overcomes acquired KRAS G12D inhibitor resistance driven by PI3Kγ activation [scRNA-Seq]

status: Public on Mar 03 2025

city: Seongnam

first: Ji-Won

last: Kim

state: Gyeonggi-do

address: 82 Gumi-ro-173-beon-gil

department: Internal Medicine

country: South Korea

institute: Seoul National University Bundang Hospital

summary: KRAS G12D mutation is a key oncogenic driver in many solid tumors, including pancreatic, gastric, and colorectal cancers. While recent studies have characterized features associated with primary and acquired resistance to KRAS inhibitors, strategies to overcome such resistance, particularly in the context of gastrointestinal cancers, remain underexplored. Here, we have generated nine human gastrointestinal cancer models, including three patient-derived organoids (PDOs), with acquired resistance to the KRAS G12D-selective inhibitor MRTX1133. Using single-cell RNA sequencing analysis, we identified the enrichment of angiogenesis, hypoxia, and epithelial-to-mesenchymal transition (EMT) signatures in the resistant PDO relative to the parental counterpart. Across all resistant models, VEGFA expression and VEGFR2 phosphorylation were uniformly elevated, which were driven by AKT activation and SP1 nuclear translocation. Mechanistic investigations uncovered increased PI3Kγ activity in MRTX1133-resistant models via KRAS/HRAS overexpression and complex formation of KRAS-p110γ with p101. This leads to the formation of an autocrine VEGFA-VEGFR2 signaling loop and EMT induction. Therapeutically, the disruption of VEGFA-VEGFR2 signaling restored MRTX1133 sensitivity and inhibited EMT. Furthermore, cancer-endothelial paracrine signaling amplified angiogenesis, hypoxia, and EMT signatures in cancer cells and simultaneously promoted endothelial cell proliferation, reinforcing an adaptive feedback mechanism. In MRTX1133-resistant tumor xenograft mouse models, a combination of anti-VEGFR2 therapy and MRTX1133 more effectively reduced tumor growth, angiogenesis, and proliferation markers than monotherapy without significant body weight change. These findings establish VEGFA-VEGFR2 signaling by PI3Kγ activation as a key driver of acquired resistance to KRAS G12D inhibition and provide a rationale for combining VEGFA-VEGFR2 inhibition with KRAS blockade in KRAS-mutant cancers.

overall_design: scRNA-seq of normal, patental, and resistant organoids

first: Sung-Hyun

last: Hwang

first: Mingyun

last: Bae


title: VEGFR2 blockade overcomes acquired KRAS G12D inhibitor resistance driven by PI3Kγ activation

status: Public on Mar 02 2025

overall_design: RNA-seq profiling the interactions between patient derived organoids and endothelial cells


title: Alpha-ketoglutarate -mediated carnitine synthesis promotes homologous recombination via histone acetylation

status: Public on Feb 26 2025

city: Pittsburgh

first: Katherine

last: Aird

state: PA

address: 5051 Centre Ave.

institute: University of Pittsburgh School of Medicine

summary: Homologous recombination (HR) deficiency enhances sensitivity to DNA damaging agents commonly used to treat cancer. In HR-proficient cancers, metabolic mechanisms driving response or resistance to DNA damaging agents remain unclear. Here we identified that depletion of alpha-ketoglutarate (αKG) sensitizes HR-proficient cells to DNA damaging agents by metabolic regulation of histone acetylation. αKG is required for the activity of αKG-dependent dioxygenases (αKGDDs), and prior work has shown that changes in αKGDD affect demethylases. Using a targeted CRISPR knockout library consisting of 64 αKGDDs, we discovered that Trimethyllysine Hydroxylase Epsilon (TMLHE), the first and rate-limiting enzyme in de novo carnitine synthesis, is necessary for proliferation of HR-proficient cells in the presence of DNA damaging agents. Unexpectedly, αKG-mediated TMLHE-dependent carnitine synthesis was required for histone acetylation, while histone methylation was affected but dispensable. The increase in histone acetylation via αKG-dependent carnitine synthesis promoted HR-mediated DNA repair through site- and substrate-specific histone acetylation. These data demonstrate for the first time that HR-proficiency is mediated through αKG directly influencing histone acetylation via carnitine synthesis and provide a metabolic avenue to induce HR-deficiency and sensitivity to DNA damaging agents.

overall_design: We used Ovcar8 high grade serous cancer cells with CCNE1 overexpression and knocked down TMLHE using 2 independent shRNAs. All samples were done in triplicate. Comparative gene expression profiling analysis for CCNE1 overexpression vs. control and shTMLHE vs. CCNE1 overexpression.


title: Genome stability disrupted by the circRBM39-RPA2 axis represses breast tumorigenesis

status: Public on Feb 22 2025

city: Hefei City

first: Dun

last: Liu

state: Anhui Province

address: Division of Life Sciences and Medicine, 443 Huangshan Road

institute: University of Science and Technology of China

type: Non-coding RNA profiling by high throughput sequencing

summary: Genome instability (GI) is a hallmark of cancer. GI is associated with accumulative DNA damage and tumor-specific defects in DNA repair. Multiple anti-tumor drugs have been developed to promote persistent GI and to drive DNA damage beyond a threshold that tumor cells can survive. However, regulatory roles of circRNAs in GI and DNA damage remain elusive. Through circRNA profiling and an siRNA-mediated screen, we have identified a circRNA termed circRBM39, which is significantly decreased in breast cancer (BC) and disrupts DNA damage response. CircRBM39 inhibits breast tumorigenesis through increasing DNA damage and promoting sensitivity to the anti-tumor drug PARP inhibitor (PARPi). Mechanistically, cytoplasmic circRBM39 interacts with replication protein A2 (RPA2), an essential DNA repair factor, through a 7-nt AG-rich motif and destabilizes RPA2 protein by facilitating HERC2-mediated ubiquitination, thus repressing homologous recombination repair. Importantly, administration of in vitro synthesized circRBM39 substantially inhibits breast tumorigenesis, sensitizes BC cells to PARPi, and renders them susceptible to synthetic lethality (SL) in distinct breast tumorigenesis mouse models. Our findings highlight the interplay between circRNA and GI in cancers, and the SL of circRBM39 to PARPi provides new strategies for RNA-based BC therapeutics.

overall_design: In an effort to investigate functional roles of circRNAs in breast cancer, we performed RNA sequencing (RNA-seq) of three-paired breast cancer specimen and adjacent non-tumor (NT) tissues to identify promising circRNA candidates. We also conducted RPA2 RIP-seq with the cytoplasmic fraction of MDA-231 cells. To further explore the functional mechanism of circRBM39 in breast cancer, we also performed polyadenylated RNA-seq in control and circRBM39 OE MDA-231 cells.

first: Xing

last: Bian

first: Xiaolin

last: Wang


title: Transcriptomic changes after orexin receptor antagonism in P301S/E4 mouse model of tauopathy

status: Public on Feb 25 2025

city: St. Louis

first: Eric

last: Tycksen

state: Missouri

address: 4444 Forest Park Avenue

department: McDonnell Genome Institute

institute: Washington University in St. Louis School of Medicine

summary: Our aim was to investigate whether increasing sleep via orexin receptor antagonism can modify tau-mediated neurodegeneration and neuroinflammation.

overall_design: Cortex mRNA profiles of 41 weeks old P301S/E4 mice were generated by deep sequencing, in triplicate, using Illumina NovaSeq 6000.

first: Samira

last: Parhizkar

first: David M

last: Holtzman

first: Xin

last: Bao

first: Wei

last: Chen

first: Nicholas

last: Rensing

first: Yun

first: Michael

last: Kipnis

first: Sihui

last: Song

first: Grace

last: Gent

first: Melissa

last: Manis

first: Choonghee

last: Lee

first: Javier Remolina

last: Serrano

first: Megan E

last: Bosch

first: Emily

last: Franke

first: Carla M

last: Yuede

last: Landsness

last: Wong


title: Gene expression profiling of HIV and EBV-associated classic Hodgkin lymphomas from Malawi

status: Public on Feb 19 2025

city: Chapel Hill

first: Yuri

last: Fedoriw

address: 160 Medical Dr

institute: University of North Carolina - Chapel Hill

summary: To investigate the biological differences between EBV-/HIV-, EBV+/HIV- and EBV+/HIV+ classic Hodgkin lymphoma, we performed RNA sequencing of 19 pre-treatment formalin-fixed paraffin-embedded (FFPE) whole lymph node biopsies of cHL.

overall_design:
We performed RNA sequencing of 19 pre-treatment formalin-fixed paraffin-embedded (FFPE) whole lymph node biopsies of cHL, inclusive of EBV-association and HIV status.

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

first: Samantha

last: Beck

first: Sophia

last: Roush

first: Tamiwe

last: Tomoka

first: Matthew

middle: S

last: Painschab

first: Kate

last: Westmoreland


title: Single-nucleus and spatial transcriptomics of human ovary: Molecular insights into signaling pathways underlying primary ovarian insufficiency in classic galactosemia

first: Raghuveer

last: Kavarthapu

address: 10 Center Dr, Bldg 10, Room 1E3340

department: NICHD

institute: National Institutes of Health (NIH)

summary: Classic galactosemia (CG) is a rare inborn error of galactose metabolism caused by mutations in GALT gene. Primary ovarian insufficiency (POI) is a later complication that affects 80% of women with CG due to significant decline in ovarian follicle reserve. The definite mechanisms underlying the early onset of POI in CG patients is not fully understood. We utilized single-nucleus RNA sequencing (snRNA-seq) to generate a single-nucleus transcriptomic atlas of human ovaries from pre-pubertal girls with CG to investigate dynamic gene expression profiles in ovarian follicles and stromal cells. Our snRNA-seq analysis revealed activation of several key genes involved in endoplasmic reticulum-stress and oxidative stress pathways which can promote apoptosis and autophagy of follicles. PTEN/PI3K/AKT signaling pathway crucial for primordial follicle activation and survival was dysregulated as evident by upregulated PTEN transcripts, marked reduction in phospho-AKT and increased CASP9 immunostaining intensity in the ovarian follicles of CG group.

overall_design: Nuclei were isolated from flash-frozen ovarian tissues from five classic galactosemia and four control patients using a 10X genomics chromium nuclei isolation kit. Nuclei suspension samples were loaded onto chromium microfluidic chip used to generate single-cell gel bead emulsions using the 10x Genomics Chromium controller. Later cDNA amplification was performed, and libraries were prepared as per the manufacturer’s protocol. Libraries were pooled and sequenced on S2 flow cell (paired-end 100 bp) using an Illumina NovaSeq 6000 platform.

first: Hong

last: Lou

first: Thang

last: Pham

first: Han

last: Do

first: Taylor

last: Badger

first: Jacqueline

last: Yano

first: Ramya

last: Balasubramanian

first: Maria

last: De La Luz Sierra

first: Veronica

last: Gomez-Lobo


title: MSKCC Study 1- Mapping the Temporal Impact of Perturbations on Lineage Plasticity and Gene Regulation

status: Public on Feb 03 2025

city: Hinxton

first: MorPhiC

last: Consortium

address: Wellcome Genome Campus

country: United Kingdom

institute: EMBL-EBI

summary: This study characterizes gene and enhancer knockout phenotypes of 30 genes in a human pluripotent stem cell (hPSC)-directed islet differentiation system. Samples were collected at five differentiation stages from hPSCs to SC-islet cells for scRNA-seq to examine transcriptional impact of the knockouts over time.

overall_design:
30 genes were edited using CRISPR-Cas9, including HHEX, GATA6, PDX1, GATA4, FOXA1, FOXA2, MNX1, NEUROD1, NKX2-2, RFX6, GSC, HNF4A, PAX6, PBX1, GLIS3, NEUROG3, ARX, OTUD5, BMPR1A, TLE3, BCOR, QSER1 , TET1, TET2, TET3, TADA2B, KDM2B, PROSER1 gene knockouts, and HHEX, ONECUT1 and NANOG enhancer deletions. The CRISPR-Cas9 edited lines were generated in two hPSC backgrounds (HUES8 and H1 human embryonic stem cells), with each genotype represented by multiple clones. The clonal lines were individually barcoded (using the expressed LARRY barcodes) and pooled for differentiation. Samples were collected at five differentiation stages as follows, ESC, definitive endoderm (DE, Day 3), Posterior foregut (PFG or PP1, Day 7), pancreatic progenitor (PP, Day 11), islet-like (SC-islet, Day 18) for scRNA-seq. In addition, WT cells in H1 and HUES8 backgrounds were differentiated and sequenced in parallel at 17 time points: day -1 (ESC), 3, 5, 7, 9, 10, 11, 12, 13, 14, 15, 16, 18, 21, 25, 26, 35.
Please note that processed .h5ad data was generated from both *transcriptome and *larry samples, and is linked to the corresponding *transcriptome records.

first: Danwei

last: Huangfu

first: Dingyu

last: Liu

first: Dapeng

last: Yang

first: Renhe

last: Luo


title: UCSF Study 1- Bulk RNAseq of differentiation timecourse of embryoid bodies

summary: Bulk RNAseq of differentiation timecourse of embryoid bodies from KOLF2.2J AAVS1 inducible CRISPRi lines

overall_design: Aggregates were generated using StemCell Tech aggrewell media on day 0 and then aggregates were moved into suspension dishes on day 1 using DMEM+20% KSR media. EBs remained in DMEM+20% KSR throughout experiment.

first: Aaron

last: Huebner

first: Ashir

last: Borah

first: Luke

last: Gilbert


title: TL1A(TNFSF15)-ENO1 axis promotes osteoarthritis by disrupting redox homeostasis via the PI3K/AKT pathway[II]

status: Public on Feb 01 2025

city: shenyang

first: juntan

last: Li

address: huaxiang street

institute: Shengjing hospital of China Medical University

summary: Osteoarthritis (OA) is a prevalent degenerative joint disease characterized by progressive cartilage degradation, chronic inflammation, and chondrocyte senescence. Tumor necrosis factor-like cytokine 1A (TL1A), a member of the TNF superfamily, has recently been implicated in regulating inflammatory processes and tissue remodeling. However, its precise role in OA pathogenesis remains incompletely understood. In this study, we investigated the impact of TL1A deficiency on OA progression and its underlying mechanism with a focus on oxidative stress-induced chondrocyte senescence.

overall_design: Clinical sample collection in this study was reviewed and approved by the Institutional Review Board (IRB) of the First Hospital of China Medical University (EC-2021-HS-004). All patients involved in this study gave informed consent. Paired smooth and damaged cartilage was obtained from the same OA patients undergoing total knee arthroplasty (n = 8). The difference between the smooth (relatively healthy area) and damaged (severely damaged area) articular surfaces was distinguished using the Mankin scoring system[33]. Detailed patients’ information is listed in Table S2.

first: Xiang

last: Gao

first: Juntan

first: Xu

first: Xun

last: Sun


title: TL1A deficiency attenuates osteoarthritis by regulating oxidative stress-induced senescence in articular chondrocytes [I]

overall_design: To investigate the transcriptional changes in human primary chondrocytes upon silencing of the TL1A gene, human primary chondrocytes were divided into two groups: the control group (siNC), transfected with non-targeting siRNA, and the experimental group (siTL1A), transfected with siRNA targeting TL1A, each with three biological replicates (siNC1, siNC2, siNC3; siTL1A1, siTL1A2, siTL1A3). After 48-72 hours of transfection, total RNA was extracted, and its quality assessed before preparing RNA-Seq libraries. Transcriptome sequencing was performed on the Illumina NovaSeq 6000 platform to identify differentially expressed genes (DEGs) between the siNC and siTL1A groups.


title: Paternal histone H2A variant incorporation and function before and after fertilization in C. elegans [RNA-seq]

city: San Francsisco

first: Diana

last: Chu

address: 1600 Holloway Ave

institute: San Francisco State University

summary: During spermatogenesis, chromatin repackaging transforms germ cells into sperm and transmits paternal epigenetic information to embryos. We have found distinct functions in these processes for two C. elegans H2A variants, HTAS-1, a sperm-specific paralog, and HTZ-1, a conserved H2A.Z homolog. HTAS-1 activates and represses gene expression less than two-fold, indicating HTAS-1 does not globally silence genes. In contrast, during spermatogenesis HTZ-1 regulates different germline genes compared to HTAS-1. During oogenesis, HTZ-1 strongly represses sperm gene expression over six-fold and activates oocyte and sex-independent genes, revealing tissue-specific modes of HTZ-1 regulation. ChIP-seq analysis of sperm chromatin shows HTZ-1 is present in 75% of HTAS-1 targets. HTZ-1 is incorporated at promoters of targets not occupied by HTAS-1 but is depleted in promoters of genes also occupied by HTAS-1. Instead HTAS-1 and HTZ-1 incorporate within gene bodies of shared targets. Post- fertilization, paternally-contributed HTAS-1 regulates the expression of a large number of genes in mixed-staged embryos. Correspondingly, loss of HTAS-1 causes decreased fertility and delayed development. Our studies indicate H2A variants have distinct incorporation mechanisms during sperm formation and tissue-specific functions in gene expression and fertility.

overall_design: We performed short-read RNA-sequencing on HTZ-1 and HTAS-1 knockouts and wildtype controls. For HTAS-1, we examined knockouts vs wildtype expression in male gonads and mixed embryos. For HTZ-1, we compared expression between wildtypes and knockouts in male and hermaphrodite germlines.

first: Swadha

last: Singh

first: Keiko

last: Hokeness

first: Tomoko

last: Tabuchi

first: Jesus

last: Hinojosa Paiz

first: Eric

last: Tang

first: Emma

last: Harms


title: Paternal histone H2A variant incorporation and function before and after fertilization in C. elegans [ChIP-seq]

type: Genome binding/occupancy profiling by high throughput sequencing

overall_design: Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) for histone variants HTZ-1 and HTAS-1 was performed in C. elegans sperm.

first: Susan

last: Strome


title: Next Generation Sequencing of OVA-treated MutuDC Transcriptome

status: Public on Jan 28 2025

city: Beijing

first: Zhongfei

last: Ma

address: DongDanSanTiao, DongCheng district

institute: Chinese Academy of Medical Sciences

summary: The goal of this study is to get the profile of the OVA-treated MutuDC transcriptome. Based on the dada of transcriptome, we processed our sgRNA sequencing data of genome-wide CRISPR/Cas9 screening. Briefly, after we have obtained the enriched gene list from our sgRNA sequencing, we excluded the  genes undetected in OVA-treated MutuDC transcriptome to further refine our screening gene list.

overall_design: To get the profile of the OVA-treated MutuDC transcriptome, we did the next generation sequencing of MutuDC at 9 h after treated with 3 mg/ml OVA.

first: Yaxin

last: Liu

first: Xuetao

last: Cao


title: Maternal cause of early-onset preeclampsia: excessive endometrial gland-derived apolipoprotein D induces placental ferroptosis and developmental abnormalities

status: Public on Jan 27 2025

city: Hong Kong

first: Jianlin

address: L 7-08, Department of Obstetrics and Gynecology  Laboratory block, 21th Sassoon Road, Hong Kong

country: Hong Kong

institute: The University of Hong Kong

summary: Early-onset pre-eclampsia (ePE) is a severe pregnancy complication affecting millions of pregnancies worldwide, resulting in significant maternal and fetal morbidity. The etiology of ePE is associated with defective trophoblast functions, leading to abnormal placental development. Regulatory factors released by endometrial glands are crucial for proper placental development. While circumstantial evidence indicates that defective endometrial gland development or function may lead to defective placental development and ePE in humans, direct evidence has been lacking. This study explored the role of endometrial gland-derived factors both in vitro and in vivo and correlated the findings with the clinical phenotypes of ePE. Our findings revealed that the secretome of organoids derived from the endometrial tissues of ePE patients impeded spiral artery remodeling and thus disrupted proper placental perfusion. Transcriptomic and proteomic analyses identified an increased apolipoprotein D (APOD) production in ePE organoids and decidual tissues compared to their normotensive (NT) counterparts. Overexpression of endometrial APOD impaired the vascular remodeling functions of extravillous trophoblasts (EVT) and endothelial cells in vitro. These findings were corroborated using an endometrial-specific APOD knock-in mouse model. APOD-induced ferroptosis through the PI3K/Akt pathway in both human ePE placentas and the mouse model. Moreover, elevated APOD levels were detected in the first-trimester serum of pregnant women who subsequently developed ePE. These results provide the first direct evidence that dysregulated endometrial gland secretome is a maternal cause of defective placental development and ePE. Clinically, APOD could serve as a biomarker for early detection of ePE, enabling early intervention with  the potential to improve outcomes for both mothers and their babies.

overall_design: Study the effect of pre-eclampsia  endometrial organoid secretion on the functions on EVTs in vivo and in vitro.

first: Yang

last: Dong

first: Cheuk-Lun

last: Lee

first: Philip C.N.

last: Chiu


title: IL-2 Mutein Promotes Antigen-Specific Acceptance of Transplanted Organs by Activating ST2+ Tissue-Resident Regulatory T Cells

city: Boston

first: Leonardo

middle: V.

last: Riella

state: MA

address: 149 13th Street

department: Medicine

institute: Massachusetts General Hospital

summary: Transplantation is the preferred treatment for most patients with end-stage organ disease, but long-term outcomes are hindered by immunosuppressive drug toxicity and immune-mediated injury. Developing therapies that promote immune tolerance while minimizing systemic immunosuppression is essential to improve graft health and survival. Regulatory T cell (Treg)-based therapies offer promise for inducing antigen-specific transplant tolerance, with recombinant IL-2 analogs emerging as potentially effective tools to selectively expand Tregs while minimizing adverse effects. mIL-2 therapy combined with co-stimulation blockade significantly prolonged allograft survival in an antigen-specific manner without adverse events. The immunomodulatory effects of mIL-2 persisted even after treatment cessation at 60 days after transplantation, with sustained graft function and preservation of histopathological integrity. Treatment with mIL-2 increased graft-infiltrating Tregs and decreased effector T cell activation. Donor-specific antibody production was reduced in mIL-2-treated recipients, which correlated with an enhanced follicular regulatory T-cell proportion. These findings were consistent across fully mismatched kidney and haplo-mismatched heart transplant models. Transcriptional profiling revealed the expansion of an ST2-positive, tissue-resident Treg population critical for long-term graft survival. Accordingly, the mIL-2-induced Treg suppression was abrogated in Treg-specific ST2 knockout graft recipients.

overall_design: We investigated the effects of a novel IL-2 mutein molecule (mIL-2) with enhanced receptor specificity and extended half-life in experimental models of solid organ transplantation. Following fully mismatched heart or kidney transplantation (BALB/c to C57BL/6), mIL-2 was administered biweekly with a single dose of CTLA-4 Ig co-stimulation blockade. Graft survival, immune cell phenotyping of graft-infiltrating cells and splenocytes, and donor-specific antibody production were assessed. Mechanistic insights into Treg function were obtained through functional suppression assays and RNA sequencing, while the role of ST2+ Tregs was studied using Treg-specific ST2 knockout mice.

first: Yoshikazu

last: Ganchiku

first: Guilherme

last: T. Ribas

first: Thiago

last: J. Borges

last: V. Riella


title: Single-cell multiomics study of cell-type-specific neuron activation unravels context-dependent gene regulation of brain disorders

status: Public on Jan 17 2025

city: Evanston

first: Jubao

last: Duan

address: 1001 University Place

department: Center for Psychiatric Genetics

institute: NorthShore University HealthSystem

summary: Genome-wide association studies (GWAS) have identified many risk genes for neuropsychiatric disorders (NPD) such as schizophrenia (SCZ). However, functional interpretation of these GWAS findings remains challenging; a major hurdle is that polygenic risk may manifest its effect conditionally upon neural activation, i.e., context-dependent. Human induced pluripotent stem cell (hiPSC)-derived neurons are a tractable cellular model for ascertaining context-dependent polygenic effects, e.g., neural activation that may mimic the physiological effects of environmental stimuli. Here, we modelled neural activation by depolarisation using high potassium chloride (KCl) in co-cultured excitatory/inhibitory neurons of 100 hiPSC lines (28 from SCZ donors), followed by assaying single-cell multiomes (scRNA/ATAC-seq) of over 700,000 nuclei from neurons at 0 hr (unstimulated), 1 hr (early response), and 6 hr (later response) of high KCI exposure. We linked genes with open chromatin peaks for each main neural subtype (GABAergic inhibitory, NEFM+ or NEFM-excitatory neurons) and confirmed a significant correlation between peak accessibility and target gene expression. Compared to static genes/peaks, dynamic ones, specifically those activity-upregulated, were more enriched for NPD GWAS risk, with the most robust enrichment for SCZ. Based on the dynamic gene expression pattern across the three time points, we found NPD risk genes tend to be continuously upregulated (i.e., with up-up dynamics). We further analysed context-specific SCZ-associated differentially expressed genes (DEGs) using MAST for single neurons of 28 SCZ cases and 72 controls. We found that 3-5%, 4-6%, and 15-23% of genes were SCZ-associated DEGs in NEFM+ excitatory, NEFM- excitatory, and GABAergic neurons, respectively, most of which were cell activity-specific. Notably, we found that SCZ-associated DEGs in high-activity neurons were more enriched for synapse-related GO terms and NPD risk genes. Interestingly, upstream regulatory sequences of the stimulation-specific SCZ-associated DEGs were enriched for binding sites of TCF4, which is a strong GWAS risk gene and was considered the master regulator of other SCZ-related genes. Moreover, the upregulated genes in SCZ cases in the stimulated (only at 6hr) NEFM+ excitatory neurons showed strong enrichment for GO terms related to cholesterol synthesis. Single-neuron DEG analysis for 28 SCZ cases and 28 matched controls gave similar results. Our study suggests that many NPD genes may only elicit disease-relevant effects upon neuronal activation, providing novel insights into how polygenic risk factors interact with environmental stimuli for NPD.

overall_design: Raw FASTQ files complies 10x Genomics multiome scARC (scRNA-seq + scATAC-seq) standard. Library generated using cultured glutamatergic and GABAergic neurons derived from iPS cells with Chromium Next GEM Single Cell Multiome ATAC + Gene Expression Reagent Kit. The output folders, including all matrices files, of Cell Ranger 2.0.2 were packaged and compressed sample-wise in according to their BioSample and SRA metadata

first: Siwei

last: Zhang


title: Nuclear and Cytoplasmic HEK293 Cell 3' end mRNA-seq

status: Public on Jan 16 2025

city: Cambridge

first: Harry

last: Fischl

address: Babraham Research Campus

institute: Storm Therapeutics

summary: Alternative polyadenylation analysis on mRNA from nuclear and cytoplasmic fractions of HEK293 cells

overall_design: RNA was extracted from nuclear and cytoplasmic subcellular fractions of HEK293 cells. The 3’ ends of extracted RNA were generated into libraries using the QuantSeq 3’mRNA-Seq library kit for Ion Torrent (Lexogen). Libraries were loaded onto the Ion Chef System (ThermoFisher) for template preparation and chip loading and the resulting chips were sequenced on the Ion Proton Sequencing System (ThermoFisher). Sequences were aligned using the Ion Torrent Server TMAP aligner to genome build hg19.

first: Andre

last: Furger

first: Jane

last: Mellor


title: The SinR•SlrR heteromer internally attenuates a long transcript of flagellar genes in B. subtilis [RNA-seq]

status: Public on Jan 04 2025

city: Bloomington

first: Ayushi

last: Mishra

state: Indiana

address: Biology Building, BB432, 1001 E 3rd St

institute: Indiana University

summary: Bacillus subtilis differentiates into two cell types during growth, dictated by the activity of the alternative sigma factor SigD. The frequency of SigD-ON motile cells is increased when the heteromeric transcription factor SwrA•DegU activates the promoter of the long fla/che operon that encodes SigD. Conversely, the frequency of SigD-ON cells is decreased by the heteromeric transcription factor SinR•SlrR but the mechanism and location of inhibition is poorly understood. Using ChIP-Seq analysis, we determine the binding sites of the SinR•SlrR heteromer, including five sites within the fla/che operon. The first two sites were found to be both necessary and sufficient to attenuate transcript abundance within the operon upstream of the gene that encodes SigD. We conclude that the SinR•SlrR heteromer inhibits SigD accumulation by binding within the operon by causing RNA polymerase to pause and prematurely terminate. Thus, the development of motile cells, and the motility-to-biofilm transition, depends on the expression of a long operon governed by two opposing heteromeric transcription factors that operate at two different stages of the transcription cycle.

sample_organism: Bacillus subtilis subsp. subtilis NCIB 3610 = ATCC 6051 = DSM 10

overall_design: RNA extraction and sequencing was performed on wild type and mutant cells of Bacillus subtilis 3610 grown in LB at 37C. Before sequencing, ribosomal RNA was depleted.


title: SIRPa ablation overcomes exhaustion and enhances the antibody- and CAR-mediated antitumor activities of iPSC-derived CAR Macrophages

status: Public on Jan 03 2025

city: Madison

first: Igor

last: Slukvin

state: Wisconsin

address: 1220 Capital Ct

department: Wisconsin National Primate Research Center

institute: University of Wisconsin-Madison

summary: SIRPa-CD47 “don’t eat me” checkpoint axis plays a critical role in defining anti-tumor activities of macrophages within the tumor microenvironment. However, targeting this axis with anti-CD47 antibodies to improve anti-tumor responses in clinical trials has proven challenging. Here, we demonstrated that iPSC-derived macrophages (iMacs) with ablated SIRPa yield a superior antitumor effect in conjunction with cancer-targeted antibodies (Ab) or chimeric antigen receptor (CAR) against a variety of CD47-expressing tumors in vitro. Moreover, SIRPA-KO protected macrophages from Ab- or CAR-driven exhaustion, allowing for efficient phagocytosis of tumors after multiple rounds of cancer re-challenges.  Ablation of SIRPa in iMacs improved survival of mice grafted ovarian carcinoma and treated with anti-HER2 Abs, while anti-GD2 CAR iMacs with KO SIRPA demonstrated reduction of initial tumor burden in mice with metastatic neuroblastoma xenograft. Overall, our studies support the feasibility of using the iPSC platform to generate SIRPα-ablated iMacs that are resistant to CD47-mediated inhibition for therapeutic applications.

overall_design: RNA-seq data of SIRPA-KO, SIRPA-ITAM, and WT iMacs either cultured alone, with SKOV-3 ovarian cancer and anti-HER2 for 24 hours, or for 96 hours. All co-culture samples were sorted for CD45-bead selection prior to total RNA isolation.

first: Portia

last: Smith

first: Mark

last: Berres


title: NWU Study 1- Bulk RNA seq timecourse of KOLF2.2J hiPSC after Auxin-induced protein degradation of specific gene products

first: MorPhiC

last: Consortium

summary: This study investigates the impact of 2 gene products (RBBP4, CHD1) on transcriptional programming in growing hiPSC at 0, 6 & 24 hours after acute protein depletion. Crispr editing was used to add an auxin-dependent degron to the C-termini of gene products expressed from the endogeneous loci and to insert an auxin-responsive degradation E3 ligase to the AAVS locus. Rapid (<30 min), specific target protein degradation in KOLF2.2J hiPSCs was induced by a synthetic auxin derivative (5-Ad-IAA) and bulk RNA-seq was performed at timepoints to define early (6 hr) and later (24 hr) downstream transcriptional dependencies.

overall_design: Crispr editing was used to introduce an auxin dependent E3 ligase (atOsTir1) into the AAVS locus of the parental KOLF2.2J hiPSC line.    Cells were subsequently Crispr-edited to create independent clones with an auxin-specific degron added to the C-terminus of individual target gene products expressed from endogenous loci. Rapid degradation of target proteins was induced by treatment with the synthetic auxin derivative, 5-Ad-IAA, and protein loss was confirmed by Western blotting. Control cells were treated with DMSO. Bulk RNA-seq was performed in duplicate at 0 hr, 6hr, and 24 hr to evaluate transcriptional responses.

first: Mazhar

last: Adli

first: Tao

last: Bai

first: De

last: Xing

first: Ozlem

last: Neyisci

first: Hengqiang

last: Zhao

first: Xintong

last: Chen


title: CD137 expression in Foxp3+ regulatory T cells is important for controling the progression of type 1 diabetes

city: Milwaukee

first: Yi-Guang

state: WI

address: 8701 Watertown Plank Rd.

department: Pediatrics (Endocrinology) and Microbiology & Immunology

institute: Medical College of Wisconsin

summary: CD137-deficient Foxp3+ regulatory T cells display functional alterations compared to the wildtype counterpart. In this study, we used single-cell RNA sequencing to define the differentiation states of islet-infiltrating Tregs and the impact of CD137 deficiency.

overall_design: This dataset is composed of two mouse strains, NOD.Foxp3-EGFP (wildtype) and NOD.Tnfrsf9-/-.Foxp3-EGFP (CD137 knockout), to determine the effect of CD137 deficiency on regulatory T and CD8 T cells in NOD mouse. Pancreatic islet cells were pooled from 6 mice for each strain and Foxp3+ CD4 T cells (Tregs) and CD8 T cells were isolated for scRNA-seq.

first: Ashley

last: Ciecko


title: Bacillus strains act independently of immune system activation and compensate for its absence

status: Public on Jan 01 2025

city: Jerusalem

first: Moshe

last: Alon

state: Israel

address: Gelber

country: Israel

institute: Hebrew University of Jerusalem

summary: The microbiota plays a crucial role in protecting plants from pests and pathogens. The protection provided by the microbiota constitutes not just the plant’s first line of defense, but possibly its most potent one, as experimental disruptions to the microbiota cause plants to succumb to otherwise asymptomatic infections. To understand how microbial plant defense is deployed, we applied a complex and tractable plant-soil-microbiome microcosm. This system, consisting of Arabidopsis plants and a 150-member bacterial synthetic community, provides a platform for the discovery of novel bacterial plant-beneficial traits, under a realistically complex microbial community context. To identify which components of the plant microbiota are critical for plant defense, we deconstructed this microcosm top-down, removing different microbial groups from the community to examine their protective effect on the plant when challenged with the leaf pathogen Pseudomonas syringae. This process of community deconstruction revealed a critical role for the genus Bacillus in protecting the plant from infection. Using plant RNA-seq and bacterial co-culturing experiments, we demonstrated that Bacillus-provided plant protection is independent of plant immune system activation. We also show that the level of plant protection is strongly dependent on the diversity of the protective inoculum. We show that deconstructing the microbiome top-down is a powerful tool for identifying and prioritizing microbial taxa with specific functions within it.

overall_design: To validate our hypothesis that Bacillus protects the plant via direct inhibition of pathogen growth and not via activation of plant immunity, we investigated how the presence of Bacillus in the soil affects the expression of immune system genes in plants. We performed RNA-seq on the leaves of plants treated with different SynCom configurations, specifically comparing the full SynCom, Bacillota dropout, and Bacillus dropout groups in both uninfected and Pto-infected plants.

first: Amal

last: Ghosheh


title: Genome-wide maps of enhancer regulation connect risk variants to disease genes

city: Palo Alto

first: Jesse

last: Engreitz

address: 240 Pasteur Drive, BMI 3700

institute: Stanford University

overall_design: We generated bulk RNA-seq data in immortalized immune cancer cell lines stimulated with relevant immune ligands

first: Joseph

last: Nasser

first: Tung

last: Nguyen

first: John

last: Ray

first: Charles

last: Epstein

first: Thomas

last: Eisenhaure

first: Nir

last: Hacohen

first: Eric

last: Lander


title: Transcriptomic profiling of 30 serum EV Sample

city: Kalyani

first: Kartiki

last: Desai

state: West Bengal

address: N.S.S kalyani

country: India

institute: National Institute of Biomedical Genomics

summary: 26 breast cancer patient serum EV derived RNA and 4 control serum EV derived RNA was sequenced to explore the diagnostic potential of EVs. EV RNA was isolated by EXOQUICK® Exosome isolation and RNA purification kit for serum/plasma (System Biosciences,CA) and was reverse transcribed to make amplified cDNA by SMART seq v4 ultra-low input RNA kit (Takara Bio Inc, USA). A sequencing library was made using 1 ng of sheared cDNA using The Low Input Library Prep Kit v2 (Takara Bio Inc, USA). DNA unique Dual index kit was used to combine libraries for sequencing (Takara Bio Inc, USA).  NOVASEQ 6000 was used for sequencing to generate 25 million paired end reads per sample.

overall_design:
Comparison of gene expression profiles of serum EVs between Healthy control and breast cancer patients using RNA-seq data .

August 13, 2026: Processed data file Normalised_EV_count_file.tabular.txt (incomplete) was replaced by Normalised_countsGSErevision.tabular which represents all samples.

middle: V

first: Aritra

last: Gupta


title: Single-Cell RNA Sequencing of Trav4 Gene-Edited Mouse Lung Tissue

city: Guilin

first: Honghao

last: Yu

state: Guangxi

address: Guilin Medical College, Lingui District, Guilin City, Guangxi

institute: Guilin Medical University

summary: This dataset contains single-cell RNA sequencing data from lung tissues of Trav4 gene-edited mice .  The samples were collected for the investigation of molecular changes induced by Trav4 gene mutations, specifically focusing on lung injury.  The dataset includes gene expression profiles of individual cells and enables the study of cell-type-specific responses, immune cell changes, and alterations in key cellular pathways.  This dataset is useful for further understanding the pathophysiology of lung injury associated with Trav4 gene mutations.

overall_design: Lung tissues from Trav4 gene-edited mice were collected, and single cells were isolated for RNA sequencing. The single-cell suspension was processed using the SeekOne® Digital Droplet Single Cell Library Kit, followed by sequencing on the Illumina NovaSeq 6000 platform.

first: Pengpeng

last: Yue

first: Haobo

last: Wang

first: Zhihao

last: Li

first: Yong

first: Lantao

last: Gu

first: Can

last: Fu


title: Single-cell RNA-sequencing data of microfluidic spinal cord-like structures

status: Public on Jun 30 2025

city: Ann Arbor

first: Jeyoon

last: Bok

state: MI

address: 2350 Hayward Street

department: Mechanical Engineering Department

institute: University of Michigan

summary: We analysed scRNA-seq data in human pluripotent stem cell-derived embryonic spinal cord model. This in vitro system recapitulates some key aspects of spinal cord DV patterning as well as neural crest migration.

overall_design: scRNA-seq was performed on dissociated cells from microfluidic spinal cord-like structures at day 12.

first: Jianping


title: Single-Cell Profiling of DNA Methylation in Autism Spectrum Disorder Prefrontal Cortex Reveals Distinct Regulatory and Aging Signatures

status: Public on Jun 17 2025

city: Los Angeles

first: Nasser

last: Elhajjaoui

address: 695 Charles E Young Dr S

department: Human Genetics

institute: University of California, Los Angeles

type: Methylation profiling by high throughput sequencing

summary: Autism spectrum disorder (ASD) is a prevalent and heterogeneous condition that profoundly impacts health and behavior. Analysis of gene expression in the cortex broadly implicates decreased synaptic functioning in excitatory neurons and increased reactivity in glia in ASD; however, whether these phenotypes are reflected in epigenetic signatures is unknown. Here, we report on the first single-cell analysis of DNA methylation (DNAm) in ASD. We profile DNAm from over 60,000 nuclei derived from 49 donors and interpret our findings with gene expression from the same nuclei using snmCT-seq.

overall_design:
Single-nucleus joint profiling of postmortem cortical brain samples isolated from the prefrontal cortex (PFC; Brodmann area 9, BA9) of 26 autistic male donors and 23 non-autistic male  controls. 1 low RIN donor (5302) was excluded from RNA analysis.

CpG-level DSS outputs are available in Zenodo at:
https://zenodo.org/records/15298839

***************************************************************
Raw files for human/patient samples were not submitted to GEO due to concerns about submitting personally identifiable sequence data for open access. The raw data (controlled-access fastq files) is available through the NeMO Archives: https://assets.nemoarchive.org/collection/nemo:dat-htywcnb
***************************************************************

first: Katherine

middle: W

last: Eyring

first: Cuining

last: Liu

first: Kevin

middle: D

last: Abuhanna

first: Yi

last: Zhang

first: Zachary

last: von Behren

first: Eleazar

middle: H

last: Eskin

first: Daniel

last: Geschwind

first: Chongyuan

last: Luo

first: Min

middle: J

last: Tsai


title: Smad3 deficiency attenuates disease severity in a zebrafish model for Smad6-related aortic disease

status: Public on Jan 13 2025

city: Ghent

first: Michiel

last: Vanhooydonck

address: Corneel Heymanslaan  10

department: Biomolecular medicine

country: Belgium

institute: Ghent University

summary: Thoracic aortic dissection (TAD) associates with a high mortality rate. Treatment options are limited and mainly consist of surgical repair at critical aortic diameters as current pharmacological interventions are unable to stop disease progression. Despite the existence of different mouse models for thoracic aortic aneurysm (TAA) and TAD, the underlying disease mechanisms remain elusive. In humans, loss-of-function of SMAD3 or SMAD6 increases the risk for TAA. We therefore targeted both ohnologs of smad3 and smad6 in zebrafish in order to further investigate their contribution to aortic homeostasis. We found an increased diameter of the ventral aorta in smad3a−/−;smad3b−/− double knockout (smad3a/b DKO) zebrafish larvae, while smad6a−/−;smad6b−/− (smad6a/b DKO) zebrafish larvae have a reduced aortic diameter. Smad3a/b DKO survive normally to adulthood, but smad6a/b DKO die before the age of 8 months due to dissections and ruptures in the ventral aorta. Smad6a/b DKO zebrafish also show hypoplasia of the aortic arches and the distal part of the ventral aorta. Surprisingly, the smad3a−/−;smad3b−/−;smad6a−/−;smad6b−/− quadruple knockout (qKO) zebrafish model has normal survival and a milder vascular phenotype compared to the smad6a/b DKO. RNA sequencing of zebrafish larvae indicates upregulation of pathways related to melanogenesis, ribosome, blood vessel development and carboxylic acid transport, and downregulation of negative regulation of endopeptidase activity and immune system. Transcriptomic data of damaged aorta compared with healthy control aorta identifies significant differences in oxidative phosphorylation, mitochondrial function, extracellular matrix and the citrate cycle. In conclusion, data from our novel zebrafish models of thoracic aortic dissection and rupture indicate that SMAD3 function has an important modifying effect on the severe aortic manifestations induced by loss of SMAD6.

overall_design: For RNA extraction, the Rneasy® minikit (Qiagen; Hilden, Germany) was used following manufacturers guidelines. One experiment was performed using TruSeq. RNA sequencing was performed on five pools, each containing five smad3a-/-;smad3b-/-;smad6a-/-;smad6b-/- quadruple knockout (qKO) zebrafish or wt control cousins.  Only samples with RNA integrity number (RIN) values higher than 9 were considered. All other experiments were performed using Quantseq. For quantseq sample 1-10, RNA sequencing was performed on five pools, each containing three smad3a-/-;smad3b-/-;smad6a-/-;smad6b-/- quadruple knockout (qKO)  adult aortas  and five pools of three wt control cousins aortas. For quantseq sample 11-20, RNA sequencing was performed on five pools, each containing three smad3a-/-;smad3b-/- double knockout (DKO) zebrafish or wt control cousins.  For quantseq sample 21-30, RNA sequencing was performed on five pools, each containing three smad6a-/-;smad6b-/- double knockout (DKO) zebrafish or wt control cousins.

first: Maxim

last: Verlee

first: Marta

last: Santana Silva

first: Lore

last: Pottie

first: Annekatrien

last: Boel

first: Matthias

last: Van Impe

first: Hanna

last: De Saffel

first: Lisa

last: Caboor

first: Piyanoot

last: Tapaneeyaphan

first: Adelbert

last: De Clerq

first: Andy

last: Willaert

first: Delfien

last: Syx

first: Patrick

last: Sips

first: Bert

last: Callewaert


title: SIRT7 regulates NUCKS1 chromatin binding to elicit metabolic and inflammatory gene expression in senescence and liver aging.

status: Public on Jun 01 2025

city: Philadelphia

first: Khoa

last: Tran

address: 3400 Civic Blvd

institute: University of Pennsylvania

summary: Sirtuins, a class of highly conserved histone/protein deacetylases, are heavily implicated in senescence and aging. The regulation of sirtuin proteins is tightly controlled both transcriptionally, translationally and via localization within the cell. While Sirtuin proteins are associated with aging, how their levels are regulated during aging across cell types and how they elicit tissue-specific age-related cellular changes are unclear. Here, we demonstrate that SIRT7 is targeted for degradation during senescence and liver aging. To uncover the significance and regulation of SIRT7 loss, we performed proteomics analysis and found that the E3 Ligase TRIP12 reduces SIRT7 levels during senescence. We identified the HMG box transcription factor NUCKS1 as a new SIRT7 interactor. We found that NUCKS1 is recruited onto chromatin during senescence, mediated by SIRT7 loss and accompanied by increased NUCKS1 acetylation. Depletion of NUCKS1 delayed senescence upon DNA damage leading to reduced inflammatory gene expression. Examination of transcriptional regulation by NUCKS1 during senescence revealed target genes of transcription factors NFKB1, RELA, and CEBP—all previously associated with senescence. Consistently, in Sirt7 KO mouse liver and in naturally aged livers, NUCKS1 was recruited to chromatin, bound at promoters and enhancers of age-related genes, including transcription factor Rela, and these bound sites had increased accessibility during aging. Overall, our results uncover NUCKS1 as a novel interactor of SIRT7, showing that proteosomal loss of SIRT7 during senescence and liver aging promotes chromatin binding of acetylated NUCKS1 to induce metabolic and inflammatory genes.

overall_design: Investigate the function of SIRT7 mediated regulation of NUCKS1 in senescence and liver aging. To assess SIRT7 function during liver aging, RNA-sequencing of WT or SIRT7 KO livers was performed on young and aged livers. To determine NUCKS1 role in eliciting senescence associatd gene expression, RNA-sequencing of shRNA targeting control or NUCKS1 was done in proliferating and senescent IMR90 lung fibroblasts.

first: Khoa A

first: Shelley

last: Berger


title: Uterine Organoids Reveal Insights into Epithelial Specification and Plasticity in Development and Disease

city: Columbia

first: Andrew

last: Kelleher

state: MO

address: 1030 Hitt Street

department: Ob, Gyn Womens Health

institute: University of Missouri

summary: Epithelial differentiation in the female reproductive tract (FRT) is essential for reproductive health, yet the mechanisms that govern epithelial fate specification remain poorly understood. At birth, FRT epithelium exhibits significant developmental plasticity, allowing differentiation into various epithelial subtypes. However, the regulatory pathways driving these early fate decisions, particularly in the uterus, are largely uncharacterized. Here, we employ neonatal mouse endometrial epithelial organoids and assembloid co-culture models to investigate how intrinsic cellular plasticity and mesenchymal signals influence uterine epithelial differentiation. We demonstrate that uterine epithelium undergoes marked age-dependent changes, shifting from a highly plastic state capable of differentiating into both monolayered and multilayered structures to a more restricted fate as development progresses. Interestingly, parallels between the developmental plasticity of neonatal uterine epithelium and pathological conditions such as endometrial cancer emerged, where similar regulatory mechanisms may be reactivated, driving abnormal epithelial differentiation and tumorigenesis. These findings provide new insights into the regulatory networks that guide early development and highlight how disruptions in these processes can contribute to disease, offering a valuable model for studying both normal uterine development and cancer progression.

overall_design: To assess cellular heterogeneity and differentiation dynamics, endometrial epithelial organoids (EEO) were developed from uteri of postnatal day 3 and 15 mice (n=10). EEO were grown for 8 days and then dissociated for downstream analysis

first: Jason

last: Rizo

first: Sarayut

last: Winuthayanon

first: Thomas

last: Spencer


title: Smooth Muscle Cell Populations of Differing Embryonic Origins in the Ascending Aorta Exhibit Minor Differences in Angiotensin II-driven Transcriptional Alterations in Mice

city: Lexington

first: Hisashi

last: Sawada

state: KY

address: 741 South Limestone BBSRB B251

institute: University of Kentucky

summary: Ascending thoracic aortopathy is a life-threatening disease significantly influenced by angiotensin II (AngII). Thoracic aortopathy exhibits regional heterogeneity with the ascending region being susceptible. Smooth muscle cells (SMCs), a major component of the aortic wall, originate from two embryonic origins in the ascending aorta: second heart field (SHF) and cardiac neural crest (CNC). However, functional differences between the origins in AngII-induced thoracic aortopathy formation remain unknown. The present study determined transcriptomic differences between origins in response to AngII by single-cell RNA sequencing using the lineage tracing approach. Mef2c-Cre +/0 mT/mG mice were infused with AngII (1,000 ng/kg/day). To investigate causative mechanisms, ascending aortas were harvested after 3 days of AngII infusion, representing the prepathological phase of thoracic aortopathy. Aortic samples were also harvested from Mef2c-Cre +/0 mT/mG mice without AngII infusion as a control. Following single-cell suspension, cells were sorted based on their origin using mTotamto and mGFP signals. mGFP proteins were present on Mef2c-Cre-driven cells indicating the cells were derived from the SHF, while cells with mTomato signal were not derived from the SHF (nSHF). After sorting cells by origin, single-cell RNA sequencing was performed. Two-way ANOVA analysis identified 1718 differentially expressed genes (DEGs) in the interaction between origin and infusion. Among these DEGs, 1207 genes significantly differed between origins in response to AngII infusion. However, the magnitude of difference in most of these DEGs was modest, ranging between −0.05 and 0.05 Log2FC. Commonly studied molecules, such as TGF-β, SMC contraction, and extracellular matrix molecules, were undetectable or modestly different. In conclusion, transcriptomic differences in SMCs between origins in response to AngII were modest in the pre-pathological phase of AngII-induced thoracic aortopathy.

overall_design: Comparative gene expression analysis of scRNAseq data to determine transcriptomic differences in response to AngII infusion between cells derived from the second heart field and other origins in the ascending aorta of mice.


title: Drosophila non-gonadal PIWI protein Aubergine regulates regenerative stem cell proliferation and tumourigenesis in the adult intestine

status: Public on Dec 29 2024

city: Acton

first: Rippei

last: Hayashi

state: Australian Capital Territory

address: 131 Garran Road

department: John Curtin School of Medical Research

country: Australia

institute: The Australian National University

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

overall_design: Refer to individual Series


title: Unexpected combination of increased protein translation and decreased endoplasmic reticulum stress during pancreatic cancer initiation

status: Public on May 14 2025

city: Gosselies

first: Denis

middle: LJ

last: Lafontaine

state: Hainaut

address: Av Profs Jeneer & Brachet, 12

institute: Universite libre de Bruxelles

summary: Background & Aims: Tumorigenesis is usually associated with increased protein synthesis rates coupled with increased endoplasmic reticulum (ER) stress. In the pancreas, acinar cells already exhibit a very high protein synthesis rate in normal condition, which raises the question as to how this cell type adapts during pancreatic tumor formation. Here, we characterize how acinar cells modulate their protein synthesis rate in metaplastic lesions, which are precursor lesions of pancreatic ductal adenocarcinoma (PDAC). Methods: We evaluated protein synthesis by puromycin incorporation assays and investigated the control of translation and ER stress by transcriptomic analyses and phenotyping of a mouse model of PDAC. We also assessed the level of ribosomal RNA (rRNA) methylation systematically using a deep-sequencing-based technique, RiboMethSeq. Results: During pancreatic tumorigenesis, protein synthesis levels in acinar-to-ductal metaplasia exhibited a significant increase as compared to normal acinar cells. This was associated with enhanced expression and activity of translation initiation factors, and with increased production of ribosomal components and ribosome assembly factors. We detected differential rRNA methylation at conserved ribosomal positions near the peptidyl-transferase center and the exit tunnel, suggesting a possible role in modulating translation and/or initial protein folding. Despite increased protein synthesis, ER stress was reduced, which was associated with an overall reduction in N-glycosylation and increased expression of proteasome components. Conclusions: Our work provides evidence for a pancreas-specific adaptation of the translation program during tumorigenesis, characterized by the production of differentially modified ribosomes and a rather unexpected combination of increased protein synthesis rate and decreased ER stress. This highlights the diversity of adaptive protein translation in transforming tissues.

overall_design: RiboMethSeq sequencing data from "Ela-K" and "Ela-K+cerulein" samples that refer to Fig.4 A and B

first: Maxime

last: Libert

first: Sophie

last: Quiquempoix

first: Leyre

last: Lopez

first: Christiane

last: Zorbas

first: Ludivine

last: Wacheul

first: Sabine

last: Cordi

last: Jacquemin


title: GCN5-mediated histone H3 Acetylation Orchestrates Gene Expression and Plant Development via H2A.Z [RNA-seq]

status: Public on May 24 2025

city: Yangling

first: Su

middle: Ying

last: Pei

state: Shaanxi

address: No. 3 Taicheng Road

department: College of Life Sciences and Institute of Future Agriculture

institute: Northwest A&F University

summary: H2A.Z is a conserved histone variant that plays essential roles in various DNA-templated processes across eukaryotes. H2A.Z and histone post-translational modifications (PTMs) exert a bidirectional and context-dependent influence on each other. Nevertheless, the functions of the interplay between PTMs and H2A.Z level and the underlying molecular mechanism remain poorly understood. Here, we found that the loss of the histone acetyltransferase GCN5 impedes the overexpression of BSU1 typically observed in nrp1-1 nrp2-2, accompanied by changes in H3 acetylation and H2A.Z levels. Interestingly, the increment in H2A.Z levels typical of nrp1-1 nrp2-2 mutant alleviates the morphological and molecular phenotypes of gcn5. Conversely, H2A.Z-depleted mutants aggravate the phenotype of gcn5. In the gcn5 mutant, the H2A.Z level is globally reduced in the gene bodies, and this reduction is dependent on the histone chaperones NRP1 and NRP2. Additionally, the reduction of H3 acetylation levels caused by GCN5 depletion can be recovered in the nrp1-1 nrp2-2 mutant background, likely due to the over-accumulation of H2A.Z. In conclusion, our genetic, molecular, and genomic findings demonstrate that GCN5-mediated H3 acetylation promotes H2A.Z deposition, H2A.Z over-accumulation recovers the loss of GCN5-mediated H3 acetylation, and this interplay is crucial for regulating gene expression and plant development.

overall_design: RNA-Seq profiling of wildtype Columbia-0, along with gcn5-7, nrp1-1 nrp2-2 and gcn5-7 nrp1-1 nrp2-2 mutants at 12 days after germination (12DAG) seedlings.

first: Israel

last: Ausin

first: Yafei

last: Wang

first: Yingpei

last: Su

first: Qin

last: Hu

first: Weiye

last: Qian

first: Min

last: Liu

first: Chao

last: Xu

first: Junjie


title: Drosophila non-gonadal PIWI protein Aubergine regulates regenerative stem cell proliferation and tumourigenesis in the adult intestine [RNA-seq]

first: Rippei

last: Hayashi

summary: Somatic stem cells are executors of physiological and pathological proliferation of adult self-renewing tissues, such as the intestine. The actions of intestinal stem cells (ISCs) rely on the integration of cell intrinsic and niche-derived signals, which are necessary to achieve a balanced response to the multiple stimuli that constantly challenge tissue homeostasis and organismal health. Disruption of such balance is causative of age-associated tissue dysfunction and hyperproliferative conditions, including inflammation and cancer.  The highly conserved PIWI-interacting RNAs (piRNAs) biosynthesis pathway, also known as the PIWI pathway, has been classically studied in the Drosophila germline for its role in the repression of transposable elements (TEs) and the regulation of germline stem cell homeostasis. Recent reports have emerged on a role of Piwi, the founding member of the pathway, in the maintenance of ISC homeostasis in the adult Drosophila midgut. The implications of these findings regarding a general role of the PIWI pathway and piRNAs in the intestine remain to be addressed. Here, we characterise a cell autonomous role of the PIWI family protein Aubergine (Aub) in ISCs. We show that, while dispensable for homeostatic self-renewal of the midgut, inducible Aub is essential to regulate ISC proliferation following acute damage of the intestinal epithelium and in oncogenic settings. Our work suggests that the role of Aub in ISCs is independent of its piRNAs regulatory function. Instead, Aub drives ISC proliferation through the induction of regenerative stem cell factors Myc and Sox21a, and through the initiation of protein translation by the eukaryotic initiation factor 3 complex (eIF3). In summary, our results discover a role of Aub in damage induced proliferation of the adult Drosophila intestine involving the regulation of major regenerative signalling pathways and the protein translation machinery. Furthermore, we present genetically distinct hyperplastic settings fostering a role of Aub as an intestinal tumour promoter or suppressor.

overall_design: The study aims at understanding the role of the PIWI family protein Aubergine in the proliferation of intestinal stem cells (ISCs) upon damage in Drosophila melanogaster. We generated oxidised small RNA sequencing libraries from freshly dissected midguts, sorted ISCs/Enteroblasts (marked by escargot-Gal4) and ovaries. We also generated RNA sequencing libraries from poly-A plus RNA to determine the abundance of transposon mRNAs expressed in the ISCs/Enteroblasts.

first: Karen

last: Bellec


title: Drosophila non-gonadal PIWI protein Aubergine regulates regenerative stem cell proliferation and tumourigenesis in the adult intestine [ncRNA-seq]


title: The SinR•SlrR heteromer internally attenuates a long transcript of flagellar genes in B. subtilis [ChIP-seq]

first: Ayushi

last: Mishra

department: Biology

summary: Bacillus subtilis differentiates into two cell types during growth, dictated by the activity of the alternative sigma factor SigD. The frequency of SigD-ON motile cells is increased when the heteromeric transcription factor SwrA•DegU activates the promoter of the long fla/che operon that encodes SigD. Conversely, the frequency of SigD-ON cells is decreased by the heteromeric transcription factor SinR•SlrR but the mechanism and location of inhibition is poorly understood. Using ChIP-Seq analysis, we determine the binding sites of the SinR•SlrR heteromer, including five sites within the fla/che operon. The first two sites were found to be both necessary and sufficient to attenuate transcript abundance within the operon upstream of the gene that encodes SigD. We conclude that the SinR•SlrR heteromer inhibits SigD accumulation by binding within the operon by causing RNA polymerase to pause and prematurely terminate. Thus, the development of motile cells, and the motility-to-biofilm transition, depends on the expression of a long operon governed by two opposing heteromeric transcription factors that operate at two different stages of the transcription cycle.

platform_organism: Bacillus subtilis subsp. subtilis NCIB 3610 = ATCC 6051 = DSM 10

overall_design: ChIP-Seq experiments were performed on wildtype and other mutants using anti-SinR antibody. All strains were grown in LB and crosslinked with 3% formaldehyde.


title: Analysing environmentally induced genome-wide frameshift in S. cerevisiae and bacteria  using 5PSeq

city: stockholm

first: yujie

last: zhang

address: Tomtebodavägen 23

country: Sweden

institute: Karolinska institutet

summary: In this study, we examine the impact of poor nutrient conditions on -1 ribosome frameshifting and its effect on mRNA degradation.To explore this process, we utilized HT-5PSeq (Zhang & Pelechano, 2021, PMID:35474692) to measure the ribosome footprint of co-translationally degraded mRNAs in S.cerevisiae under different stresses in YPD and CSM (poor nutrients).  To show the mechanism is conserved in bacteria, we performed HT-5PSeq in  B.subtilis upon starvation .Our goal with HT-5PSeq is to identify gene- and codon-specific features that contribute to genome-wide frameshifting events.

sample_organism:
Bacillus subtilis
Saccharomyces cerevisiae

overall_design:
HT5P-seq was carried out on S. cerevisiae and B. subtilis 168 (trpC2) under various environmental conditions (3 replicates). Stress-induced S. cerevisiae cells were subjected to heat shock , oxidative stress, and amino acid deprivation. S. cerevisiae cells grown with amino acid addition were individually supplemented with arginine, proline, and serine as single amino acids to achieve a comparable concentration to that of SC medium.  For B. subtilis,  cells were grown in both LB and minimal media.

Funded by "ERC Synergy grant" (Grant ID 101118521, European Research Council).

first: Yujie

last: Zhang

first: Vicent

last: Pelechano


title: Longitudinal gene expression profiling in Nodal-induced and control zebrafish embryonic explants

status: Public on Dec 16 2024

city: Houston

first: Amrit

last: Koirala

state: TX

address: 1 Baylor Plaza

institute: Baylor College of Medicine

summary: We report RNA-sequencing from zebrafish explants generated from embryos injected with mRNA encoding the Nodal ligand ndr2 (N), constitutively active Nodal receptor CA-acvr1b* (T), and uninjected (U) controls. Explants of all 3 conditions were compared at each of 7 developmental stages: sphere (SR), 30% epiboly (30), 50% epiboly (50), shield (SH), 75% epiboly (75), 90% epiboly (90), and 2-somite (2S) (corresponding to 4, 4.7, 5.3, 6, 8, 9, and 11 hours post fertilization, respectively).

overall_design: Sequencing of polyadenylated mRNAs from ndr2 (N), CA-acvr1b*(T), and uninjected (U) explants with 3 biological replicates (A-C) per condition per stage (SR - 2S).

first: Margot

last: Kossmann Williams

first: Cristian

last: Coarfa


title: Differential effects of p95HER2 and FL-HER2 on gene expression in PB2 mouse breast tumor xenografts at early and late stages.

status: Public on Dec 14 2024

city: Pittsburgh

first: Dong

address: 530 45th Street

institute: University of Pittsburgh

summary: To explore how p95HER2 regulates gene expression to promote tumor growth in immunocompetent mice, we engineered PB2 mouse breast cancer cells to express either p95HER2 or control FL-HER2 under the control of doxycycline. Both FL-HER2 and p95HER2 cells were implanted to the mammary fat pads of immunocompetent C57BL/6 mice that were placed under a DOX625 doxycycline diet. Tumor xenografts were harvested 10 and 22 days after inoculation. We then performed transcriptomic analysis using RNA-seq data from PB2-FL-HER2 and PB2-p95HER2 tumors.

overall_design: Comparative gene expression profiling analysis of RNA-seq data from PB2-FL-HER2 and PB2-p95HER2 tumors collected 10 and 22 days after implantation.

first: Linda

last: McAllister-Lucas

first: Peter

last: Lucas


title: CD137 agonism enhances anti-PD1 induced activation of clonally expanded CD8+ T cells in a neoadjuvant pancreatic cancer clinical trial

city: Baltimore

first: Elana

middle: Judith

last: Fertig

state: MD

address: 670 W. Baltimore Street, 3rd floor

department: Institute for Genome Sciences

institute: University of Maryland, Baltimore

summary: Successful pancreatic ductal adenocarcinoma (PDAC) immunotherapy requires therapeutic combinations that induce quality T cells. Tumor microenvironment (TME) analysis following therapeutic interventions can identify response mechanisms to guide design of more effective combinations. We provide a reference single-cell dataset from PDAC-infiltrating T cell and monocyte subsets from a human neoadjuvant clinical trial comparing the granulocyte-macrophage colony-stimulating factor (GM-CSF)-secreting allogeneic PDAC vaccine GVAX alone, in combination with anti-PD1, or with both anti-PD1 and a CD137 agonist. Tumor infiltrating leukocytes analyzed two weeks post neoadjuvant therapy revealed shifts in CD8+ T cell activation as well as cytoskeletal and extracellular matrix (ECM)-interacting components with Cy/GVAX and anti-PD1. Addition of a CD137 agonist was associated with increased abundance of activated and clonally expanded CD8+ T cells with distinct perturbations in cytoskeletal and ECM components. Furthermore, a new computational method to compare ligand-receptor networks between patients from different treatment arms found that CD137 agonism is associated with immunosuppressive TREM2 signaling in tumor associated macrophages (TAMs) that corresponds to changes in cell metabolism, function, and ECM interactions. Altogether these findings associate therapy with GVAX, anti-PD1, and CD137 agonist with enhanced CD8+ T cell function while inducing alternative immunosuppressive pathways in patients with PDAC.

overall_design:
Single-cell RNA-seq and single-cell TCR-seq data were collected from tumor-infiltrating leukocytes in primary human pancreatic cancer tumors following neoadjuvant immunotherapy. Treatments included  seven patients receiving cyclophosphamide (Cy)/GVAX alone (Arm A), four patients receiving the combination of Cy/GVAX and anti-PD1 (nivolumab, Arm B), and four patients receiving Cy/GVAX, anti-PD1, and CD137 agonist (urelumab, a human IgG4 agonistic monoclonal antibody, Arm C).

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Raw files for human/patient samples are being made available in dbGaP (https://www.ncbi.nlm.nih.gov/gap/) for controlled access to the personally identifiable sequence data.
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dbGaP (phs003002.v2.p1)

first: Janelle

last: Montagne

first: Jacob

middle: T

last: Mitchell

first: Joseph

last: Tandurella

first: Eric

last: Christenson

first: Ludmila

last: Danilova

first: Atul

last: Deshpande

first: Melanie

last: Loth

first: Dimitrios

middle: N

last: Sidiropoulos

first: Emily

last: Davis-Marcisak

first: Daniel

middle: R

last: Bergman

first: Qingfeng

last: Zhu

first: Hao

last: Wang

first: Luciane

last: Kagohara

first: Logan

last: Engle

first: Benjamin

last: Green

first: Alexander

last: Favorov

first: Won Jin

last: Ho

first: Su Jin

last: Lim

first: Rui

first: Pan

last: Li

first: Jessica

last: Gai

first: Guanglan

last: Mo

first: Sarah

first: Rulin

first: Ajay

last: Vaghasia

first: Wenpin

last: Hou

first: Yao

first: Jacquelyn

last: Zimmerman

first: Jennifer

last: Elisseeff

first: Srinivasan

last: Yegnasubramanian

first: Robert

last: Anders

first: Elizabeth

last: Jaffee

first: Lei

last: Zheng


title: Effect of p95HER2 overexpression on gene expression in PB2 mouse breast tumor xenografts.

first: Dong

last: Hu

summary: To explore how p95HER2 regulates gene expression to promote tumor growth in immunocompetent mice, we engineered PB2 mouse breast cancer cells to express p95HER2 under the control of doxycycline. Both empty vector (EV) and p95HER2 cells were implanted to the mammary fat pads of immunocompetent C57BL/6 mice, which were placed under a DOX625 doxycycline diet. Tumor xenografts were harvested 3 weeks after inoculation. We then performed transcriptomic analysis using the RNA-seq data from PB2-EV and PB2-p95HER2 tumors.

overall_design: Comparative gene expression profiling analysis of RNA-seq data from PB2-EV and PB2-p95HER2 tumors.

first: Linda

middle: M

last: McAllister-Lucas

first: Peter

middle: C

last: Lucas


title: Single-cell mass cytometry and transcriptomic profiling of circulating immune cells identifies an expansion of CD25hi switched memory B cells in Osteoarthritis

status: Public on May 01 2025

first: Nidhi

last: Bhutani

state: California

address: 240 Pasteur Drive

department: Orthopaedic Surgery

institute: Stanford

summary: Osteoarthritis (OA) is a chronic, debilitating disease with no available disease-modifying drugs with end-stage surgery being the only treatment option. Biomarker identification in blood specimens of OA patients has hitherto been limited to serum proteins and bulk transcriptomics and epigenomic feature identification. We sought to capitalize on high resolution, single-cell techniques of mass cytometry by time-of-flight (cyTOF) and sc-RNA-seq to identify OA-associated features in the immune cells of the patients’ peripheral blood. Comparison of healthy donors and OA patients’ peripheral blood mononuclear cells (PBMC) revealed that frequencies of specific subpopulations of B cells, monocytes, CD4+ and CD8+T cells were distinctly perturbed in OA. While many immune subtypes were depleted, a CD25hiCD27+IgD- switched memory B cell population was identified to be significantly expanded in OA blood. Sc-RNA seq revealed a dysfunction of IL2/Stat3 and Notch signaling in the switched memory B cells expanded in OA. Upon profiling peripheral blood of patients with degenerative meniscal tears (DMT), a population known to be at enhanced risk for OA, we observed a similar expansion of CD25hiCD27+IgD- switched memory B cells suggesting that it can be a biomarker of early and late OA. Unsupervised clustering utilizing immune cell correlates stratified the profiled OA patients into three distinct subsets. Development of such single cell platforms can be a powerful clinical tool for OA prognosis as well as precision therapeutics.

overall_design: PBMC samples from OA patients and healthy donors (3 samples pooled as 1 replicate, n = 2/group) were enriched for B-cells and profiled using scRNAseq. 3 samples each were pooled to obtain 2 single cell cDNA libraries per group.

first: Yudhishtar

last: Bedi

first: Neety

last: Sahu


title: m6A related mRNAs in ovarian-endometriosis control vs normal endometrial tissue

status: Public on Nov 22 2024

city: Harbin

first: Chengcheng

last: Ren

address: Youzheng 23

institute: The first affiliated hospital of Harbin Medical University

type:
Expression profiling by array
Non-coding RNA profiling by array

summary: aberrant m6A- related mRNAs in EI and NE tissues were uncovered

overall_design: By arraystar m6A-mRNA epitranscriptomic microarray, biological information analysis technologies, and validation of other databases and clinical tissues, aberrant m6A- related mRNAs were uncovered

first: Yanan

last: He