title: A dual role of EZH2 in regulating A-to-I RNA editing and mRNA stability through ADAR1

status: Public on Nov 15 2025

city: Boston

first: Yanqiang

last: Li

state: MA

address: 300 Longwood Ave.

department: Cardiology Department

institute: Boston Children's Hospital

summary: Adenosine-to-inosine (A-to-I) RNA editing, catalyzed by adenosine deaminases acting on RNA (ADARs), is a widespread modification in mammals. Cumulative evidence has suggested the altered A-to-I editing profile in prostate cancer (PCa), but the underlying mechanism remains unclear. Here, we discover enhancer of zeste homologue 2 (EZH2) as a novel ADAR interactor and editing regulator in PCa. Through competing with Interleukin Enhancer Binding Factor 2 (ILF2) for ADAR1 binding, EZH2 reshapes the substrate selectivity of ADAR1 and thus exhibits a bidirectional role in editing regulation. Moreover, EZH2 depletion induces the translational repression of Transportin-1 (TRN1), which further results in the accumulation of cytoplasmic ADAR1 to protect many oncogenic transcripts from degradation. Consistently, depletion of ADAR1 dramatically enhances the sensitivity of PCa cells and tumors to EZH2 selective degraders. Collectively, our study highlights the significance of EZH2-ADAR1 cascade in governing RNA editing and mRNA stability, which may provide novel perspectives for the advancement of EZH2-targeting cancer therapies.

overall_design: RNA-seq (n=4 for siCTRL, n=4 for siEZH2, n=6 for siADAR1 and n=5 for siADAR2) was isolated from C4-2 cells were used to detect RNA editing(0h). To analyze the impact of EZH2 or ADAR1 suppression on mRNA decay rate, control, EZH2- or ADAR1-deficient C4-2 cells were incubated with 5 μg/ml ActD (Sigma). Cell samples were collected at 0, 3, 6, 12 and 24 h post-treatment. Human true PCR-free 30x coverage WGS of C4-2 cells was considered as cell line reference genome. eCLIP-seq of EZH2, ADAR and ILF2 were profomed to detect their RNA binding target in C4-2.

first: Yang

last: Yi

first: Qi

last: Cao

first: Kaifu

last: Chen


title: TOP2B cooperates with ATRX to resolve G-quadruplexes and maintain replication fork stability in glioma

status: Public on Nov 13 2025

city: Shanghai

first: Chunlong

last: Zhong

state: Shanghai

address: 150 Jimo Road

department: Department of Neurosurgery

country: China

institute: Shanghai East Hospital, School of Medicine, Tongji University

type: Expression profiling by high throughput sequencing

type: Genome binding/occupancy profiling by high throughput sequencing

summary: G-quadruplexes (G4s) are noncanonical DNA structures that promote genomic instability, particularly in α-thalassemia/mental retardation X-linked (ATRX)-deficient gliomas. Although TOP2B has been implicated in chromatin remodeling, its role in G4 resolution remains poorly understood. Here, we identify TOP2B as a previously unrecognized regulator of G4 homeostasis and show that it functionally cooperates with ATRX to facilitate G4 resolution during DNA replication. Disruption of this pathway by CX-5461, a small molecule originally developed as an RNA polymerase I inhibitor, leads to G4 accumulation, replication stress, and DNA damage. Mechanistically, CX-5461 acts as a TOP2B poison that selectively impairs TOP2B binding at G4 sites, alters replication fork dynamics, and induces MRE11-dependent degradation of stalled forks. These effects are strongly enhanced in ATRX-deficient glioma cells, where TOP2B plays a dominant role in G4 regulation. While etoposide similarly induces G4-related DNA damage, it does not affect the ATRX-TOP2B interaction, highlighting CX-5461's unique mechanism. Our findings establish TOP2B as a critical player in G4 resolution, reveal CX-5461's dual function as a TOP2B poison and G4 stabilizer, and propose G4-associated replication stress as a potential therapeutic target in ATRX-deficient gliomas.

overall_design: To investigate the cooperative role of the ATRX/TOP2B complex in DNA replication, DNA damage response, and G-quadruplex (G4) regulation in glioma cells, we performed both RNA sequencing (RNA-seq) and CUT&Tag analyses. For RNA-seq, U87MG glioma cells were subjected to siRNA-mediated knockdown of ATRX, TOP2B, or both ATRX and TOP2B to characterize transcriptional changes associated with loss of the ATRX/TOP2B complex. In parallel, U87MG cells were treated with CX-5461 to evaluate the transcriptional effects of pharmacological TOP2B perturbation and disruption of ATRX/TOP2B-associated functions. For CUT&Tag, patient-derived glioma cells (PDCs) were used to profile the genome-wide distributions of ATRX, TOP2B, and G4 structures. CUT&Tag was performed under control and CX-5461-treated conditions to determine how CX-5461 affects ATRX and TOP2B chromatin occupancy and their association with G4 regions. These datasets were integrated to assess the cooperative roles of ATRX and TOP2B in G4 regulation, replication-associated stress, and DNA damage responses in glioma cells.

first: Ying

last: Pang

first: Meng

last: Cheng

first: Rui

last: Wang

first: Xu

first: Jingzhe


title: scRNAseq to understand hormonal control on pubertal transcription in the medial preoptic area

city: Seattle

first: Koichi

last: Hashikawa

state: WA

address: 1959 NE Pacific St. HSB J135

country: USA

institute: University of Washington

summary: Pubertal maturation aids developments in emotion, cognition and reproduction. The conserved roles of elevated circulating gonadal sex steroids for the continued maturation of the nervous system via steroid hormone receptor mediated gene regulation is well documented. However, critical transcriptional dynamics mediated by steroids throughout puberty in molecularly defined circuitry remains elusive. We investigated pubertal transcriptional dynamics in the medial preoptic area (MPOA), a hypothalamic center for reproductive behaviors, in male and female mice at single cell resolution (scRNAseq).

overall_design: scRNAseq on the MPOA tissues from pre-, mid and post puberty mice of both sex


title: Sequential transcriptional gates in the thalamo-cortical circuit coordinate memory stabilization

city: New York

first: Andrea

last: Terceros

address: 1230 York ave

institute: The Rockefeller University

summary: The molecular mechanisms that enable memories to persist over long time-scales from days to weeks and months are still poorly understood. To develop insights we created a behavioral task where, by varying the frequency of learned associations, mice formed multiple memories but only consolidated some, while forgetting others, over the span of weeks. We then monitored circuit-specific molecular programs that diverge between consolidated and forgotten memories. We identified multiple distinct waves of transcription, i.e., cellular macrostates, specifically in the thalamo-cortical circuit, that defined memory persistence. Notably, a small set of transcriptional regulators orchestrated broad molecular programs that enabled entry into these macrostates. Targeted CRISPR-knockout studies revealed that while these transcriptional regulators had no effects on memory formation, they had prominent, causal, and strikingly time-dependent roles in memory stabilization. In particular, the calmodulin-dependent transcription factor Camta1 was required for initial memory maintenance over days, while Tcf4 and the histone methyl-transferase Ash1l were required later to maintain memory over weeks. These results identify a critical Camta1-Tcf4-Ash1l thalamo-cortical transcriptional cascade required for memory stabilization, and puts forth a model where the sequential, multi-step, recruitment of circuit-specific transcriptional programs enable memory maintenance over progressively longer time-scales.

overall_design: Cells from rodent brain were isolated and processed using scRNA-seq, at different time points during training and retrieval, for both HR and LR conditions. At least 3 replicates were included per time point and condition.

first: Celine

first: Yujin

last: Harada

first: Tim

last: Eilers

first: Millennium

last: Gebremedhin

first: Richard

last: Koche

first: Pierre-Jacques

last: Hamard

first: Roshan

last: Sharma

first: Priya

last: Rajasethupathy


title: Cannabis Use and Cannabidiol Modulate HIV-Induced Alterations in TREM2 Expression: Implications for Age-Related Neuropathogenesis

status: Public on Nov 07 2025

city: La Jolla

first: Jerel

middle: Adam

last: Fields

state: CA

address: 5320 La Jolla Hermosa Ave

department: Psychiatry

institute: University of California, San Diego

summary: The study investigates the modulation of TREM2 and related gene expression in HIV- and HIV+ individuals with varying cannabis use patterns. RNA-seq data were obtained from monocyte-derived macrophages exposed to CBD, IL1B, and CBD+IL1B. This study aims to identify mechanisms by which CBD may alter neuroinflammatory processes relevant to TREM2, aging, and neuropathogenesis in people living with HIV.

overall_design: Peripheral blood mononuclear cell (PBMC) isolation was performed on blood collected from HIV+ and HIV- individuals with different cannabis use patterns. Monocytes were cultured in human-serum-supplemented media and differentiated into monocyte-derived macrophages (MDMs) over 7 days. Treatments with vehicle, IL1B, cannabidiol (CBD), and CBD+IL1B (C+I) occurred for 6 hours before RNA isolation. This experiment includes gene expression profiling analysis of RNA-seq data from treated MDMs isolated from HIV- Naïve, HIV+ Naïve, HIV+ Moderate, and HIV+ Daily cannabis users.

middle: A

first: Bryant

last: Avalos


title: Senescence of tumor-specific Non-Classic Monocytes Facilitates Immune Suppression and Prostate Cancer Progression through Tumor and Host Immune Interactions

status: Public on Oct 31 2025

city: Birmingham

first: Runhua

last: Liu

state: AL

address: 1720 2nd Avenue South

institute: University of Alabama at Birmingham

summary: Prostate cancer remains a leading cause of cancer-related mortality in men, with metastatic cases presenting significant therapeutic challenges due to genetic alterations that drive disease progression and immune evasion. While localized prostate cancer generally has favorable outcomes, metastatic disease is associated with much poorer survival rates. This study investigates the role of specific tumor-associated senescent non-classical monocytes (NC-Mo) in MYC amplification and PTEN deletion-mediated lethal prostate cancer progression, focusing on tumor-host immune interactions. Key genetic alterations, such as MYC amplification and PTEN deletion, lead to tumor cell apoptosis via mitochondrial Complex I dysfunction, driven by metabolic reprogramming characterized by increased glycolysis and arginine biosynthesis. A specific subtype of Ly6cLowCD43LowCXCR2+ NC-Mo is activated by the phagocytosis of apoptotic tumor cells and damage-associated molecular patterns (DAMPs) through TLR4 activation, promoting their differentiation into a senescent phenotype.TLR4 activation further induces NC-Mo to secrete TNF-α, which stimulates intra-tumor endothelial cells to produce G-CSF, circulating to the bone marrow and promoting the transition of classical monocytes into NC-Mo. Once senescent, NC-Mo secrete more TGF-β1, which enhances CXCL5 secretion from tumor cells, mainly via the AKT/PI3K pathway, creating a feedback loop that recruits more peripheral NC-Mo into the tumor microenvironment (TME). Additionally, IL-18 secreted by senescent NC-Mo suppresses T cells and NK cells, weakening both adaptive and innate immune responses in the TME. Targeting NC-Mo and key pathways, such as TLR4, CXCL5-CXCR2, and IL-18-IL18R, reduce immune suppression and inhibit tumor progression. These findings provide insights into how MYC/PTEN dysfunction accelerates prostate cancer progression through specific tumor-associated senescent NC-Mo, offering novel therapeutic opportunities.

overall_design: Based on Hi-Myc and Pten cKO mice model, we explore the mechanisms promoting prostate cancer progression and metastasis.

first: Chao

last: Zhang

first: Haiyan

last: Yu

first: Chen

last: Huang

first: YanFeng

first: Lizhong

first: Jianmei

last: Leavenworth


title: Moderate levels of folic acid benefit outcomes for cilia based neural tube defects

status: Public on Oct 15 2025

city: Boulder

first: David

last: Engelhardt

state: CO

address: 347 UCB

department: MCDB

institute: CU Boulder

summary: Neural tube defects (NTDs) are a common and devastating birth defect. The current NTD rate in the U.S. reflects an approximately 30% decrease following folic acid (FA) supplementation in the 1990’s as a public health measure. Yet, questions remain including which gene mutations are sensitive to folic acid levels and how folic acid acts to alter NTD risk. We studied the relationship between FA dosage and NTD rates in NTD mouse models and propose that genes involved in cilia formation and function represent an FA sensitive ontology and a possible avenue for further reducing NTD rates. We demonstrate that in cilia mutant mice, a more moderate level of FA is beneficial in reducing NTD rates and promoting primary and motile cilia formation and function. We present a mechanism through which fortified FA levels reduce basal levels of reactive oxygen species (ROS) which in turn reduces ROS-sensitive GTPase activity required for ciliogenesis.

overall_design: This dataset represents an investigation into differential gene expression between wild type and Rsg1L3P/L3P mouse embryonic fibroblasts isolated from F3 moderate and fortified folic acid diet mice.

first: Cara

last: Martyr

first: Lee

last: Niswander


title: Arabidopsis DXO1 is an evolutionarily diverged homolog that impacts translation and translation-dependent mRNA decay

status: Public on Oct 28 2025

city: Canberra

first: Diep

middle: R

last: Ganguly

state: ACT

address: 46 Sullivans Creek Rd

department: Research School of Biology

country: Australia

institute: The Australian National University

summary: The Rai1/Dxo1/DXO protein family function in eukaryotic 5′-end RNA quality control by hydrolyzing non-canonical mRNA cap structures, such as the NAD+ 5′-cap. The plant ortholog, DXO1, shows distinct biochemical properties compared to its fungal and mammalian counterparts, but only minor phenotypic differences are attributed to its NAD+-decapping (deNADding) activity. On the other hand, abnormalities in chloroplast development and growth in dxo1 mutant plants appear linked to the serine-rich N-terminal extension (NTE) of DXO1. Here, we report that plant DXO1 is a distinct ortholog that likely diverged earlier than its fungal and mammalian counterparts. We attribute this to the presence of a serine-rich N-terminal extension, which is found almost exclusively in plants and likely arose during the emergence of angiosperms. Degradome analysis revealed that Arabidopsis DXO1 contributes to translation-dependent mRNA decay, including mRNA surveillance and co-translation RNA decay, in a manner that is reliant on its serine-rich NTE. Furthermore, polysome profiling revealed that plants lacking DXO1 exhibit globally reduced translation, which may explain the loss of translation-dependent mRNA decay and changes in pre-rRNA processing. From our data, we propose that 5′-end RNA quality control by Arabidopsis DXO1 is important for translation and translation-dependent mRNA decay.

overall_design: GMUCT was performed in biological duplicate on 12-day old Arabidopsis seedlings expressing DXO1 variants fused to GFP under the control of the 35S promoter from the cauliflower mosaic virus (Kawsnik et al 2019 Nucleic Acids Research). Polyomse-sequencing was performed in biological triplicate on 12-day old WT and dxo1 seedlings.

first: Xiang

first: Marten

last: Moore

first: Pravin

last: Khambalkar

first: Brian

middle: D

last: Gregory


title: DNA-Diffusion  STARR-Seq Validation

status: Public on Oct 07 2025

first: Gue-ho

last: Hwang

address: 300 Longwood Ave

institute: Boston Children's hospital

summary: To test how DNA-Diffusion sequences can induce transcription, we select 2150 sequences, including DNA-Diffusion synthetic and natural occurring DHS sites for each cell type (K562, HepG2, and GM12878) and insert them into STARR-Seq plasmids  (N= 6450 sequences). all synthetic and naturally occurring sequences were combined  into a single library, and this same library was experimentally tested using STARR-Seq in different cell lines (K562, HepG2, GM12878).

overall_design: A STARR-Seq plasmid library containing 6,000 enhancer candidates was synthesized and constructed following methods described previously (Neumayr et al., Gordon et al.). Each candidate was uniquely barcoded with five random nucleotides during synthesis, PCR amplified using specific primers (forward: TAGAGCATGCACCGG, reverse: TCGACGAATTCGGCC), and cloned into the STARR-Seq plasmid vector (hSTARR-seq_ORI, Addgene #99296) via NEBuilder HiFi assembly. Recombinant plasmids were electroporated into NEB® 10-beta electrocompetent E. coli and amplified plasmid libraries were purified using PureLink HiPure plasmid midiprep kits. Library complexity was assessed by sequencing PCR-amplified inserts prepared with NEBNext Ultra II DNA kits. Subsequently, plasmids of sufficient complexity were electroporated into three cell lines (K562, HepG2, GM12878), and post-transfection RNA and DNA were isolated after 6 hours. Following DNase treatment and reverse transcription of isolated RNA, both RNA-derived cDNA and genomic DNA underwent targeted amplification with specific primer pairs and were sequenced using Illumina-compatible NEBNext library preparations. Counts of enhancer sequences were quantified using Kallisto, aligning reads to a constructed index with k-mer size 23, filtering for the presence of specific homology arms. The final enhancer activity (mRNA/DNA ratio) was computed with the R "mpra" package (version 1.14.0), employing voom normalization and limma analysis to generate log2 fold changes (log2FC) and associated error ranges across all cell line replicates, considering only sequences with non-zero DNA counts.

first: Lithin

middle: K

last: Louis

first: DaSilva

middle: L

last: Ferreira

first: Senan

last: Simon

first: Hwang

last: Gue-Ho

first: Emily

middle: S

last: Wong

first: Pinello

last: Luca


title: MLL2 facilitates long-range gene regulation through LINE1 elements [ChIP-Seq]

status: Public on Oct 01 2025

city: Santander

first: Lucio

last: Di Filippo

address: PCTCAN - Cl. Albert Einstein, 22

country: Spain

institute: IBBTEC

summary: Transcriptional regulation is tightly linked to chromatin organization, with H3K4me3 commonly marking both active and bivalent promoters. In embryonic stem cells (ESC), MLL2 is essential for H3K4me3 deposition at bivalent promoters, which has been proposed to facilitate the induction of major developmental genes during pluripotent cell differentiation. However, prior studies point to a functional discrepancy between the loss of H3K4me3 at bivalent promoters and the largely unaltered transcription of major developmental genes in Mll2-/- cells. In this study, we investigated MLL2-dependent gene regulation in mouse ESC and during their differentiation. Contrary to the prevailing view, we show that MLL2’s primary role is not to oppose Polycomb-mediated repression at the bivalent promoters of developmental genes. Instead, we identify a previously unrecognized regulatory function for MLL2 at the CG-rich 5' untranslated regions (5'UTR) of evolutionarily young LINE-1 (L1) transposable elements (TE). We found that MLL2 binds to the 5’UTR of L1 elements and is critical for maintaining their active state (H3K4me3 and H3K27ac), while preventing the accumulation of repressive H3K9me3. Using both global genomic approaches (i.e. RNA-seq, ChIP-seq and Micro-C) as well as targeted L1 deletions, we demonstrate that these MLL2-bound L1 elements act as enhancers, modulating the expression of neighboring genes in ESC and, more prominently, during differentiation. Together, our findings illuminate novel aspects of MLL2 regulatory function during early developmental transitions and highlight the emerging role of TE as key components of long-range gene expression control.

overall_design: Genome-wide binding profiles for COMPASS-like subunits (MLL2, MLL1 and RBBP5), histone modifications (H3K4me1, H3K4me2, H3K4me3, H3K27ac, H3K27me3, H3K9me3 and H4K16ac) and RING1B  were investigated by ChIP-seq in WT mouse embryonic stem cells (mESC) as well as in transgenic mESC lines containing different genomic deletions (i.e. Mll1-KO, Mll2-KO and Mll1/Mll2 double-KO). Where indicated the ChIP-seq profiles were generated on differentiated mESC lines following a multilineage protocol.

first: Lara

middle: Z

last: Shahidian

last: di Filippo

first: Sarah

middle: M

last: Robert

first: Álvaro

last: Rada-Iglesias


title: Sequential transcriptional gates in the thalamo-cortical circuit support memory stabilization [ChIP-seq]

status: Public on Sep 28 2025

first: Richard

last: Koche

state: New York

institute: Memorial Sloan Kettering Cancer Center

summary: The molecular mechanisms that enable memories to persist over long time-scales from days to weeks and months are still poorly understood. To develop insights, we created a behavioral task where by varying the frequency of learned associations, mice formed multiple memories, but only consolidated some while forgetting others, over the span of weeks. We then monitored circuit-specific molecular programs that diverge between consolidated and forgotten memories. We identified multiple distinct waves of transcription, i.e., cellular macrostates, specifically in the thalamo-cortical circuit, that defined memory persistence. Notably, a small set of transcriptional regulators appeared sufficient to orchestrate broad molecular programs that enabled entry into these macrostates. Targeted CRISPR-manipulations of these transcriptional regulators revealed that while they had no effects on memory formation, they had prominent, causal, and strikingly time-dependent roles in memory stabilization. In particular, the calmodulin-dependent transcription factor Camta1 was required for initial memory maintenance over days, while Tcf4 and the histone methyl-transferase Ash1L were required later to maintain memory over weeks. These results identify a critical Camta1-Tcf4-Ash1L thalamo-cortical transcriptional cascade required for memory stabilization, and puts forth a model where the sequential, multi-step, recruitment of circuit-specific transcriptional programs enable memory maintenance over progressively longer time-scales.

overall_design: ChIP sequencing of sorted neurons (NeuN-Ax488 antibody; Millipore, #MAB377X) from mouse brains after experiencing control or behavioral training conditions.

first: Andrea

last: Terceros

first: Celine

last: Chen

first: Priya

last: Rajasethupathy


title: Sequential transcriptional gates in the thalamo-cortical circuit support memory stabilization [ATAC]

overall_design: ATAC sequencing of sorted neurons (NeuN-Ax488 antibody; Millipore, #MAB377X) from mouse brains after experiencing control or behavioral training conditions.


title: Fatty acid-activated proton transporter SR4 prevents hepatic steatosis and metabolic alterations in diabetic mice by improving mitochondria function, energy balance and oxidative stress

status: Public on Sep 25 2025

city: Duarte

first: Yate-Ching

last: Yuan

address: 1500 East Duarte

institute: City of Hope

summary: Type 2 diabetes (T2D) is a growing global health crisis, largely driven by rising obesity rates. Untreated T2D leads to severe complications such as cardiovascular disease, nephropathy, retinopathy, neuropathy, and hepatic dysfunction. Current therapies primarily manage hyperglycemia but often fail to address core pathophysiological drivers like insulin resistance and obesity. This highlights an urgent need for novel therapeutics with distinct mechanisms, particularly those targeting energy metabolism and insulin sensitivity, to improve long-term T2D outcomes. Modulating mitochondrial respiration through mild uncoupling has emerged as a promising strategy to promote negative energy balance. SR4, a small-molecule mitochondrial uncoupler, represents a novel class of fatty acid-activated proton transporters. In this study, we investigated the metabolic effects of oral SR4 administration in male db/db mice model of T2D. SR4 significantly reduced body weight gain and improved body composition by selectively decreasing fat mass without affecting lean mass. Indirect calorimetry confirmed that SR4 treatment increased oxygen consumption and total energy expenditure, independent of food intake. Importantly, SR4 substantially improved glycemic control, reduced insulin resistance, and prevented dyslipidemia, hepatic steatosis, and liver injury. Mechanistically, SR4 activated hepatic AMP-activated protein kinase (AMPK), enhanced mitochondrial respiration, and mitigated oxidative stress. Liver transcriptomic profiling further demonstrated broad metabolic reprogramming, including downregulation of lipogenesis and peroxisome proliferator-activated receptor γ (PPARγ) signaling, concurrently with upregulation of genes involved in energy metabolism and antioxidant defense. Collectively, these findings demonstrate that SR4 ameliorates multiple aspects of metabolic dysfunction in an obese T2D mouse model by targeting key pathways in energy regulation and lipid metabolism. Our results provide additional mechanistic insights into the effects of mitochondrial uncouplers in the liver and support further investigation of SR4 and related fatty acid anion transporters as a novel therapeutic class for metabolic diseases.

overall_design: RNA sequence profiling of livers from  db/db mouse after 5 weeks treatment via  vehicle control versus after 5 weeks of SR4 treatment

first: James

last: Figarola

first: Jyotsana

last: Singhal

first: Sharad


title: Microplastic exposure promotes atherosclerotic lesion formation through endothelial dysfunction in LDL receptor-deficient mice

city: Riverside

first: Changcheng

last: Zhou

state: California

address: 900 University Avenue

department: School of Medicine

institute: University of California, Riverside

summary: Microplastics (MPs) have emerged as ubiquitous environmental contaminants due to widespread plastic use. However, whether MP exposure promotes atherosclerosis remains unclear. In this study, we investigated the atherogenic effects of MPs in low-density lipoprotein receptor-deficient (LDLR⁻/⁻) mice. We found that nine weeks of MP treatment significantly increased atherosclerotic lesion size in the aortic root of male LDLR⁻/⁻ mice. Single-cell RNA sequencing revealed that MP exposure promoted the formation of macrophage-like endothelial cells in the aorta. These findings highlight the potential cardiovascular risks of MP exposure and underscore its implications for both human and environmental health.

overall_design: We treated C57BL/6J LDLR⁻/⁻ mice fed a low-cholesterol diet (LCD) with 1 µm microplastics (10 mg/kg) for nine weeks and assessed atherosclerotic lesion size, macrophage content, and expression of inflammation-related genes. In addition, we performed single-cell RNA sequencing of the aorta to identify cell types and gene expression changes to elucidate the underlying mechanisms.

first: Ting-An

last: Lin

first: Jianfei

last: Pan

first: Sijie

last: Tang

first: Qianyi

last: Ma

first: Matthew

last: Campen

first: Hong


title: Transcriptional responses to protoplasting in the early leaf developmental zone of Brachypodium distachyon

status: Public on Sep 23 2025

city: BERN

first: Michael

middle: T

last: Raissig

address: Altenbergrain 21

department: Institute of Plant Sciences

country: Switzerland

institute: University of Bern

summary: We employed bulk RNA-seq to find protoplasting-induced genes in the wild model grass Brachypodium distachyon.

overall_design: Samples were collected from leaf developmental zones of 3 weeks old Brachypodium distachyon Bd21-3. 10 leaf developmental zones were digested to release single cells (protoplasted) and 5 leaf developmental zones were used for the non-protoplasted samples. Three replicates were produced per treatment. Total RNA extraction, poly-A-based library preparation and bulk-RNA sequencing of these samples allowed to check for genes that are affected by protoplasting.

first: Lea

last: Berg

first: Inés

last: Hidalgo Prados

first: Ambuj

last: Gore


title: Platelet-rich fibrin induces an inflammatory phenotype of U937 macrophages

status: Public on Sep 21 2025

city: Vienna

first: Reinhard

last: Gruber

address: Sensengasse 2a

country: Austria

institute: Medical University Vienna

summary: Platelet-rich fibrin (PRF) is widely used to support local healing, a process that requires the transient polarization of macrophages towards an inflammatory phenotype. PRF and blood clot components, in general, can potentially incite this macrophage response. To test this hypothesis, we performed a screening assay to identify the overall response of macrophages to PRF. To this aim, U937, a histiocytic lymphoma cell line, and THP1, a leukemia cell line, both commonly used bioassays to study macrophage responses, were exposed to PRF lysates. Transcriptomic changes were identified by bulk RNA sequencing. Analysis was based on significantly regulated genes with an adjusted p-value of p<0.05. In U937 macrophages, consistent with our hypothesis, the clustering of increased genes revealed chemokine activity (CCL2, CCL3, CCL4, CCL5, CCL7, CCL8, CCL20, CCL23, CCL26, CXCL5, CXCL6, CXCL8, CXCL16, and PPBP), RAGE receptor binding (FPR1, S100A8, S100A9, and S100A12), IgG binding (FCGR1A, FCGR2A, FCGR2B, FCGR3A), prostaglandin biosynthetic process (CBR1, CD74, EDN1, FABP5, IL1B, MIF, PTGES, PTGS1) and collagen catabolic process (CTSL, FAP, MMP3, MMP7, MMP9, MMP12, MMP14, MMP19 and MRC2). In THP1 cells, clustering highlighted only steroid biosynthesis. These findings emphasize U937 as an appropriate bioassay to study inflammatory macrophage polarization upon PRF exposure, being consistent with clinical macrophage signatures during early wound healing and holding the potential to recover inflammatory macrophages in chronic wounds.

overall_design: We proposed using THP-1 and U937, as THP-1 is a leukemia cell line, and U937 originates from the pleural effusion of a patient with histiocytic lymphoma, both widely established monocytic cell lines, exposed to PRF lysates, to identify the overall response of macrophages to PRF. Transcriptomic changes were determined by bulk RNA sequencing. In the indicated experiments, RT-PCR was conducted to verify some gene expression changes relevant to the RNA-seq.

first: Panahipour

last: Layla

first: Xiaoyu

last: Huang


title: cGAS-STING Pathway Mediation in Osteoclast Function and Bone Fracture Healing

status: Public on Sep 19 2025

city: shanghai

first: miaomiao

last: zheng

address: No. 168 Changhai Road, Yangpu District

institute: Changhai Hospital

summary: Inflammation, as a crucial initial phase of bone healing, typically commences in the early stages of fracture repair. The cGAS-STING pathway serves as a key mediator of inflammation. The aim of this study is to explore the biological role and molecular mechanisms of the cGAS-STING pathway in the fracture healing process, with a particular focus on its function during the early inflammatory phase.

overall_design: A murine femoral fracture model was utilized to investigate the activation of the cGAS-STING pathway during the early and late stages of bone healing. The methodologies encompassed transcriptome sequencing and immunohistochemistry. Pathway modulation was accomplished through the application of the STING inhibitor H-151 and the activator SR-717, with the effects being assessed via in vivo experiments (transcriptome sequencing, microCT, safranin O-fast green staining, and TRAP staining) and in vitro assays (TRAP staining, F-actin ring formation, bone resorption tests, qPCR, and Western blot analysis).

first: Miaomiao

last: Zheng


title: Maternal administration of probiotics augments IL17-committed γδ T cells  in the newborn lung

status: Public on Sep 16 2025

city: Brussels

first: David

last: Vermijlen

state: non-US Resident

address: Boulevard de Triomphe, accès 2 (CP205/3)

department: Pharmacotherapy and Pharmaceutics

country: Belgium

institute: Université Libre de Bruxelles

summary: The early-life period is increasingly being recognized as a window of opportunity to shape immunity where microbiota and related probiotics have an important impact. Innate γδ T cells are the first T cells generated in utero populating epithelial tissues such as the lung contributing to tissue protection through, for example, IL17 production. Here, we studied the influence of maternal microbiota and probiotic supplementation during pregnancy on innate γδ T cells in the lung and thymus of newborn mice. Detailed time-kinetic experiments showed that at birth the murine lung T cell population was specifically dominated by IL17-committed γδ T cells expressing an invariant Vγ6Vδ1 TCR. Single-cell-RNA-sequencing showed that the biased IL17-commitment of perinatal lung γδT cells is highly conserved between mice and humans. While maternal microbiota depletion with antibiotics tended to decrease the frequency of the lung Vγ6 T cells of the offspring at birth, the maternal administration of Lacticaseibacillus rhamnosus(L.rhm.), but not of Bifidobacterium animalis subsp.lactis(B.lac.), increased significantly their frequency resulting in the augmentation of the IL17-commitment of the mouse lung T cell compartment. Altogether, our data indicate that the maternal microbiota contributes to the shaping of IL17-committed γδT cells in the lungs of newborns and that maternal administration of specific probiotic strains can enhance this process.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: ϒδT cells were sorted from fetal lung samples, followed by 5'-RNA single cell transcriptome and TCR sequening (10x genomics).

first: Yohannes

last: Tafesse

first: Arnaud

last: Köhler

first: Guillem

last: Sanchez Sanchez

first: Patricia

last: Brito Rodrigues

first: Marko

last: Verce

first: Panagiotis

last: Vitsos

first: Isoline

last: Verdebout

first: Moosa

last: Rezwani

first: Maria

last: Papadopoulou

first: Amandine

last: Everard

first: Véronique

last: Flamand


title: Bone Marrow Failure (BMF) Model Mimics Aplastic Anemia (AA) Patients: Single-Cell Landscape of Immune Response Reveals Novel Mechanisms of Immune Imbalance in AA

city: Beijing

first: yumeng

last: Li

address: Changchun street.

department: Xuanwu hospital

institute: Capital Medical University

summary: Background: the pathogenesis of HSPCs impairment in aplastic anemia (AA) remains unclear.We focused on CD8+ T cells, and investigated platelets, CD4+ T cells, macrophages, and mitochondrial energy metabolism, aiming to elucidate the cellular atlas changes associated with bone marrow failure (BMF). Methods: We have successfully established a mouse model of bone marrow failure and analyzed the immune response at the single-cell level. Results: platelets regulate CD4+/CD8+ T cells, and macrophages by releasing PF4. CXCR3/CXCR5 bind to PF4, activating mitochondrial signaling pathways. The decrease of Treg, weakening immunosuppression. Additionally, there is a significant increase in CD8+ effector T cells. Increased energy metabolism was observed in CD8+ stress T cells. It should be noted that, platelet reduction itself in AA weakens energy metabolism, subsequently impairing the hemostatic and thrombotic functions. However, platelets' regulatory function in immune cells remains significant. An imbalance in M1 and M2 macrophage polarization is observed. While a phenotype macrophage and CD8+ naive T cells are important cell phenotypes in marrow aging, not contribute to pathology failure. Conclusion: the possible mechanisms of BMF in AA: based on PF4, platelet-T cell/macrophage crosstalk leads to immune overactivation and the release of cytokines such as IFN-γ and TNF-α, which attack the marrow. Therefore, transforming imbalanced CD8+ effector T cells, stress T cells, Treg cells, and M1/M2 macrophages into CD8+ naive T cells and a phenotype of macrophages via inhibiting platelet immune regulatory function, may provide a promising strategy to reverse BMF.

overall_design: The mice were divided into four groups: The BMF group (experimental group), the total-body irradiation (TBI) group (control group), the normal young mouse group (wild type, WT), and the normal aged mouse group (Aged). Bone marrow samples were collected from all four groups, with one sample from each group, for a Single Cell RNA-seq Workflow (WTA for whole-transcriptome amplification and ABseq for antibody sequencing) (Fig 1A). The study was approved by the Experimental Animal Welfare Ethics Committee of Xuanwu Hospital, Capital Medical University (approval number: XW-20210531-1). The more details were in "Supplementary materials-METHODS", and the Fig 1A for the experimental design.

first: Shuai

last: Tan

first: Fang

last: Fang

first: Jing

last: Sun

first: Yumeng

first: Yaochi

last: Chen

first: Wanling

last: Sun*


title: The SPN-4 Rbfox RNA-binding protein selects maternal mRNAs for CCR4-NOT-dependent clearance in C. elegans embryos

status: Public on Sep 10 2025

city: Minneapolis

first: Micah

last: Gearhart

state: MN

address: 6-160 Jackson Hall, 321 Church St.

department: Genetics, Cell Biology and Development

institute: University of Minnesota

summary: The elimination of many maternal mRNAs is an essential feature of the maternal-to-zygotic transition. We report an essential pathway that clears many maternal transcripts from early C. elegans embryos using the RbFox-related SPN-4 RNA-binding protein as a specificity factor and the CCR4-NOT deadenylase complex as an effector. We biochemically identified SPN-4-associated mRNAs from late-stage oocytes and found that the set of SPN-4-associated transcripts is enriched for maternal mRNAs that undergo early decay. Single-molecule fluorescence in situ hybridization experiments established that many SPN-4-associated mRNAs fail to be eliminated in the absence of SPN-4. In the 3’UTRs of two target mRNAs, we identified RbFox motifs that bind SPN-4 in vitro and are required for SPN-4-dependent clearance in vivo. In a genetic screen to identify factors that work with SPN-4, we isolated alleles of CCR4-NOT components. Auxin-induced degradation of the LET-711/NOT1 scaffold and the CCF-1 deadenylase disrupted clearance of two SPN-4-associated transcripts. Our results support a model in which SPN-4 initiates expression in late-stage oocytes, associates with maternal mRNA targets through RNA sequences in their 3’UTRs and promotes CCR4-NOT-mediated decay during early embryogenesis.

overall_design: Transcripts present in cell lysates and immunoprecipitates from SPN-4, LIN-41, and OMA-1 ribonuclear protein complexes were profiled by RNA sequencing. An amplification method was utilized for low input RNA because of the restricted distribution of SPN-4 in the adult C. elegans gonad.

first: Tsukamoto

last: Tatsuya

first: Gearhart

last: Micah

first: Greenstein

last: David

first: Osborne Nishimura

last: Erin


title: Integrated epigenetic and genetic programming of primary human T cells [RNA-seq]

status: Public on Sep 08 2025

city: San Francisco

first: Laine

last: Goudy

address: 400 Parnassus Ave

institute: University of California, San Francisco

summary: Targeted epigenetic engineering of gene expression in cell therapies would allow programming of desirable phenotypes without many of the challenges and safety risks associated with double strand break-based genetic editing approaches. Here, we develop an all-RNA platform for efficient, durable, and multiplexed epigenetic programming in primary human T cells, stably turning endogenous genes off or on using CRISPRoff and CRISPRon epigenetic editors. We achieve epigenetic programming of diverse targeted genomic elements without the need for sustained expression of CRISPR systems. CRISPRoff-mediated gene silencing is maintained through numerous cell divisions, T cell stimulations, and in vivo adoptive transfer, avoiding cytotoxicity or chromosomal abnormalities inherent to multiplexed Cas9-mediated genome editing. Finally, we successfully combined genetic and epigenetic-engineering using orthogonal CRISPR Cas12a/dCas9 systems for targeted CAR knockin and CRISPRoff silencing of therapeutically relevant genes to improve preclinical CAR T cell-mediated in vivo tumor control and survival.

overall_design: RNA-sequencing of human primary T cells that have been treated with CRISPRoff mRNA and sgRNAs targeting genes of interest or a NTC. Samples also include primary human T cells that have been treated with nuclease active Cas9 mRNA and sgRNAs targeting genes of interest or a NTC.

first: Alvin

last: Ha

first: Ashir

last: Borah

first: Jennifer

last: Umhoefer

first: Lauren

last: Chow

first: Carinna

last: Tran

first: Aidan

last: Winters

first: Alexis

last: Talbot

first: Rosmely

last: Hernandez

first: Zhongmei

first: Sanjana

last: Subramanya

first: Abolfazl

last: Arab

first: Nupura

last: Kale

first: Jae Hyun

middle: J

last: Lee

first: Joseph

last: Muldoon

first: Chang

last: Liu

first: Ralf

last: Schmidt

first: Philip

last: Santangelo

first: Julia

last: Carnavale

first: Justin

last: Eyquem

first: Brian

last: Shy

first: Alex

last: Marson

first: Luke

last: Gilbert


title: m6A RNA modification controls reproductive development and metabolic adaptation in the human parasite Schistosoma japonicum [m6a-seq]

status: Public on Sep 02 2025

city: Shanghai

first: Guofeng

last: Cheng

address: #500, Zhennan Road, Shanghai

institute: Tongji University

summary: N6-Methyladenosine (m6A) is an abundant eukaryotic post-transcriptional mRNA modification, which plays pivotal role in regulating RNA metabolism. m6A is crucial for dynamic processes in many parasites, however, its presence, roles, and contribution to Schistosoma japonicum, a parasitic flatworm with a complex lifecycle involving dynamic transcriptional reprogramming, remain entirely unexplored. Here, we report the first evidence that m6A is abundant on S. japonicum RNA, and demonstrate its critical contribution to parasite biology. We identify the m6A writer as a crucial regulator of female reproductive development, including ovary morphogenesis and egg production, and in orchestrating metabolic reprogramming essential for survival and parasitism in male worms. Given the central role of eggs in host pathology and transmission, our findings uncover a key regulatory layer in schistosome biology and pinpoint m6A deposition as a potential target for anti-schistosomiasis interventions.

overall_design: identification of m6A modifcation in Schistosoma japonicum and differential expression genes after mettl3 KD, in three biological replicates

first: BIKASH

last: GIRI

first: ZIHAO

last: ZHANG


title: m6A RNA modification controls reproductive development and metabolic adaptation in the human parasite Schistosoma japonicum [RNA-seq]

overall_design: identification of differential expression genes after mettl3 KD, in two biological replicates


title: tRNA binding and modification by the Escherichia coli dihydrouridine synthase DusA

status: Public on Sep 01 2025

city: Winnipeg

first: Sarah

last: Schultz

state: Manitoba

address: 144 Dysart Rd

department: Chemistry

country: Canada

institute: University of Manitoba

summary: Dihydrouridine (D) is one of the most highly conserved tRNA modifications throughout all domains of life. D20 is particularly conserved and is formed by DusA in E. coli, but its mechanisms and functions remain uncovered. Here, we characterized the molecular mechanisms of DusA in tRNA binding, cofactor oxidation, and tRNA modification, in addition to the cellular functions of DusA in tRNA maturation and mRNA translation. Thereby, we reveal DusA binds tRNA using a two-step mechanism involving local tRNA conformational changes. Although DusA can modify an unmodified tRNA substrate, it binds to previously modified tRNA with a higher affinity. In contrast to the well-studied T arm modifying enzymes TrmA and TruB, DusA does not globally increase tRNA aminoacylation levels, but does improve aminoacylation for specific tRNA species. Despite only few changes in tRNA charging, DusA improves the translation for several specific codons, suggesting a direct role for dihydrouridine in tRNA function on the ribosome. Thus, we propose DusA functions non-redundantly with TrmA and TruB to fine-tune protein synthesis.

overall_design: Total RNA samples were extracted from early log phase WT (n=3) and ΔdusA (n=3) E. coli strain BW25113 under acidic conditions (pH <5) using TRIzol. Samples were sent to MesoRNA on dry ice where they were underwent periodate oxidation/beta elimination, library preparation, and sequencing as described previously (PMID: 35513407).

first: Nadia

last: Hossain

first: Lauren

last: Barnes

first: Kristin

last: Koutmou

first: Ute

last: Kothe


title: CRISPR library screening analysis on DMSO and Erlotinib 10µM treated samples

city: Melbourne

first: Goknur

last: Giner

state: VIC

address: 1G Royal Parade

institute: The Walter and Eliza Hall Institute of Medical Research

summary: Triple-negative breast cancers (TNBCs) are the most aggressive subtype of breast cancer that have poor prognosis and very few treatment options. Although approximately 40-70% of TNBC patients have EGFR overexpression, anti-EGFR therapies exerted little to no clinical benefit. This could be due to (i) the presence of an inherent resistance mechanism, (ii) the presence of EGFR protein in its inactive form, or (iii) lack of EGFR on the surface of plasma membrane. Several studies have shown that EGFR is present in the intracellular compartments, instead of the plasma membrane surface, in TNBC patients. Previous studies have demonstrated that intracellular EGFR renders TNBC tumors resistant to anti-EGFR therapies. Here, we used genome wide CRISPR library screening to identify the markers of resistance to EGFR inhibitors. Our CRISPR screening identified a redox protein, thioredoxin reductase 3 (TXNRD3), to be depleted in erlotinib-treated MDA-MB-231 cells suggesting that loss of TXNRD3 may sensitize TNBC cells to EGFR inhibitors. siRNA-induced knockdown and pharmacological inhibition of TXNRD3 using an FDA-approved drug auranofin significantly sensitized EGFR-high TNBC cells to EGFR inhibitors. Mechanistically, TXNRD3 knockdown or inhibition increased oxidative stress resulting in increased EGFR phosphorylation at Y1068 (active EGFR protein). Moreover, auranofin also increased surface accumulation of EGFR and sensitized SUM159PT cells to cetuximab-induced ADCC. Auranofin and erlotinib combination therapy exerted a significant anti-cancer activity in vivo in MDA-MB-231 cell line-derived xenograft and in murine syngeneic 4T1.2 TNBC model. Collectively, these data suggests that TXNRD3 inhibition using auranofin activates EGFR and increases its surface localization, which then sensitizes TNBC cells to anti-EGFR therapies. Hence, auranofin combined with anti-EGFR therapies may be a viable approach for the treatment of TNBC patients.

overall_design: To to identify the markers of resistance to EGFR inhibitors, we performed CRISPR library screening analysis and compared DMSO samples with the samples treated with Erlotinib  10µM. Sequencing experiments were run for three replicates on 4 lanes for each sample in vivo in MDA-MB-231 cell line-derived xenograft and in murine syngeneic 4T1.2 TNBC model cell lines.

first: Giner

last: Goknur


title: A transcriptomic cell atlas of the developing Brachypodium leaf at single-cell resolution

first: Michael

last: Raissig

summary: We employed scRNA-seq to generate a cell atlas of the early leaf development in the wild model grass Brachypodium distachyon.

overall_design: Samples were collected from 15 leaf developmental zones (per dataset) (2021, 2022 and 2024 datasets) and 8 or 10 vegetative shoot apices with young leaf primordia (2023 datasets) of 3 weeks old soil-grown plants. Two genotypes were harvested: Wild type Bd21-3 (WT) and the sid/bdmute-1 (sid) mutant. The tissue was digested to release single cells (protoplasts) which were then sent for 10X Genomics single-cell sequencing. The 2022 libraries were sequenced twice (indicated by -1 and -2).

first: Lea

last: Berg

first: Inés

last: Hidalgo Prados


title: Establishing a Canine Urothelial Carcinoma Organoid Repository: A Platform for Comparative and Translational Studies [snRNA-Seq]

status: Public on Aug 30 2025

city: Ames

first: Christopher

last: Zdyrski

state: Iowa

address: 1800 Christensen Dr, Bms 1072 Vet Med, Bms 1072 Vet Med

institute: Iowa State University

summary: Despite the increasing number of treatment options for patients with muscle-Invasive Bladder Cancer (MIBC), many of these patients ultimately have a poor prognosis. Drug responses vary considerably among patients and in many who respond initially, drug resistance may ultimately develop leading to tumor progression. Scope for improvement has been limited by the phenotypic and molecular diversity of MIBC, which impact the selection pressures of therapy. To address this translational gap, we describe the largest known canine urothelial carcinoma organoid bioarchive, with in-depth phenotypical and molecular characterization. Immunohistochemistry confirmed the expression of key biomarkers including UPKIII, E-cadherin, Vimentin, and Ki-67 in organoids. Single-nucleus RNA sequencing revealed cellular heterogeneity, while bulk RNA sequencing showed canine patient-to-patient variability in transcriptomic profiling. Bulk RNA sequencing also displayed highly similar expression profiles between tissue- and urine-derived organoids, as well as similarity to human MIBC transcriptome data. Whole genome sequencing in a subset of patients further supported the overall genomic fidelity of organoids with their tissue of origin. Finally, for proof-of concept of functional usefulness, organoid cytotoxicity to vinblastine was tested in several organoid lines. These canine bladder cancer organoid lines can be thawed, expanded, and screened for response to potential novel therapeutics to expand personalized medicine approaches. In addition, the organoid lines can serve as a valuable resource for comparative bladder cancer research, and as a pre-clinical screening tool to identify efficacious drugs before taking them into canine clinical trials to support future human clinical trials.

overall_design: RNA-seq profiling of a canine bladder cancer patient tissue and organoid line.

first: Karin

last: Allenspach

first: Jonathan

middle: P

last: Mochel


title: Patient-Specific Pharmacogenomics demonstrates xCT as Predictive Therapeutic Target in Colon Cancer with Possible Implications in Tumor Connectivity

city: Jerusalem

first: Keren

last: Zohar

address: Safra Campus, Givat Ram

country: Israel

institute: Hebrew University of Jerusalem

summary: Colorectal cancer (CRC) represents the third-leading cause of cancer-related deaths. Knowledge covering diverse cellular and molecular data from individual patients has become valuable for diagnosis, prognosis, and treatment selection. Here, we present an in-depth comparative mRNA-seq analysis of tissue samples from 32 CRC patients, pairing tumors with adjacent healthy tissues. The differential expression gene (DEG) analysis revealed apparently dysregulated metabolic programs,in what we focused on the impact of overexpressed SLC7A11 (xCT) and SLC3A2 genes which compose the cystine/glutamate transporter (Xc-) system. To assess the oncogenic potency of the Xc- system in a cellular setting, we applied a knowledge-based approach for analyzing gene perturbations from CRISPR screens across various cell types as well as using a variety of functional assays in five primary patient-derived organoid cell models to functionally verify our hypothesis. We identified a previously undescribed cell surface protein signature predicting chemotherapy resistance and further highlighted the causality and potential of pharmacological blockage of ferroptosis as promising avenue for cancer therapy. Biological processes such as redox homeostasis, ion/amino acid transporters and regulators of neuronal survival and differentiation were associated with these co-dependent genes in patient specimens. This study highlights a number of potential clinical targets for CRC and promotes patient-individual in vitro model systems as functionally validate in silico predictions.

overall_design: The mRNA expression levels of all genes (coding and non-coding) were determined by pairwise analysis of cancerous and healthy tissues obtained from the same patient. Healthy tissue samples were harvested from the aboral margin of the colectomy specimen, at least 5–7 cm distal to the primary tumor, in accordance with national and international guidelines for oncologic resection safety. These normal adjacent tissue samples were macroscopically examined, approved by the pathologist and underwent extensive washing procedures prior to sequencing to ensure the absence of tumor cell contamination. Total of 32 patients were analyzed with 73 deep sequencing results. Altogether, there were 36 samples marked as tumor (T) and 37 samples marked as healthy (H). Each participant provided at least one sample for T and H. For four participants the number of samples was higher. Each sample was studied by partition total RNA by size to support mRNA and miRNA transcriptomics.

first: Ethical approval to conduct this study was granted by the ethics committee of the medical faculty of Magdeburg (33/01

last: amendment 43/14). Transcriptomic data from Magdeburg patients can be shared upon sending reasonable a request to the corresponding author UDK.

first: Marco

last: Strecker

first: Martin

last: Böttcher

first: Thomas

last: Wartmann

first: Henry

last: Freudenstein

first: Maximilian

last: Doelling

first: Mihailo

last: Andric

first: Wenjie

last: Shi

first: Or

last: Kakhlon

first: Katrin

last: Hippe

first: Beatrix

last: Jahnke

first: Dimitrios

last: Mougiakakos

first: Franziska

last: Baenke

first: Daniel

last: Stange

first: Roland

last: Croner

first: Michal

last: Linial

first: Ulf

last: Kahlert


title: Establishing a Canine Urothelial Carcinoma Organoid Repository: A Platform for Comparative and Translational Studies [RNA-Seq]

first: Christopher

last: Zdyrski

overall_design: RNA-seq profiling of canine bladder cancer tissues and organoids which were either urine or tissue derived.

first: Karin

last: Allenspach

first: Jonathan

last: Mochel


title: RNA sequencing of murine ovarian follicles +/- NTY

city: Aarhus N

first: Morten

last: Veno

state: DK

address: Aabogade 15

country: Denmark

institute: Omiics ApS

summary: NOT PROVIDED; REQUESTED

overall_design: Differential gene expression comparison

first: Mahboobeh

last: Amoushahi

last: Lykke-Hartmann


title: Single-cell RNA-seq of neutrophils from germ-free and specific-pathogen-free mice reveals gut-microbiota-driven heterogeneity and NETosis in acute pancreatitis

status: Public on Aug 20 2025

city: Nanchang

first: Yaoyu

last: Zou

state: Jiangxi

address: 17 Yong Waizheng Street, Donghu District

institute: The First Affiliated Hospital of Nanchang University

summary: We performed single-cell RNA sequencing (scRNA-seq) using the 10x Genomics platform to characterize pancreatic immune cell populations in germ-free (GF) and specific-pathogen-free (SPF) mice with cerulein-induced acute pancreatitis (AP). scRNA-seq analysis identified distinct neutrophil subpopulations influenced by gut microbiota presence. SPF mice showed enrichment of pro-inflammatory neutrophil clusters associated with increased neutrophil extracellular trap (NET) formation, whereas GF mice exhibited neutrophil subsets expressing reparative and protective signatures. Our data highlight the role of gut microbiota in shaping immune responses during AP.

overall_design: Following induction of AP by repeated intraperitoneal injection of cerulein (100 µg/kg hourly for 10 doses), pancreatic tissues were harvested from GF and SPF male C57BL/6 mice (7–8 weeks old). Single-cell suspensions of pancreatic immune cells were obtained by enzymatic digestion, and libraries were prepared using the 10x Genomics Chromium Single Cell 3′ v3.1 protocol. Sequencing was performed on an Illumina NovaSeq 6000 (paired-end, 2×150 bp). Raw FASTQ files and processed data (gene-cell count matrices) were deposited in GEO

first: Yin

last: Zhu

first: Jianping

last: Liu

first: Cong

last: He

first: Nianshuang

last: Li


title: Projecting development of TB-IRIS using RNA velocity of whole blood

status: Public on Aug 26 2025

city: London

first: Rachel

last: Lai

address: Du Cane Road

department: Infectious Disease

country: United Kingdom

institute: Imperial College London

summary: TB-associated immune reconstitution inflammatory syndrome (TB-IRIS) is characterised by severe inflammation and immunopathology directed to TB pathogen shortly after commencing antiretroviral therapy (ART) in HIV-TB coinfected patients. This study aims to investigate if RNA Velocity strategy can be used to predict development of TB-IRIS

overall_design: Whole blood was collected from 95 patients with HIV-associated TB at 2 weeks following antiretroviral initiation. Among the 95 patients, 36 developed TB-IRIS by week 2, with another 8 that would eventually develop TB-IRIS. All patients were from the placebo arm of the PredART clinical trial

first: Graeme

last: Meintjes

first: Claire

last: Dunican


title: Exploring mechanisms of scar-free skin wound healing in adult zebrafish

status: Public on Sep 12 2025

city: Zürich

first: Ismail

last: Kücükaylak

address: Otto-Stern-Weg 7

institute: ETH Zurich

summary: We performed single-cell RNA sequencing to better characterize the dynamics and heterogeneity of involved cell types during different stages of zebrafish cutaneous wound healing.

overall_design: Full-thickness wounds of adult zebrafish with a diameter of 2 mm were introduced with a clinical dermatology laser. For single cell RNA sequencing, single cell suspensions were prepared. For this task, unwounded skin tissue from three adult zebrafish was collected. In addition, the wound tissues for 2 dpw, 4 dpw and 6 dpw were collected using a biopsy punch with a diameter of 4 mm from three adult zebrafish each.

first: Matthias

last: Hammerschmidt


title: Maternal care during early development is necessary for the acquisition of a calming response to back stroking

status: Public on Aug 19 2025

city: Ota-ku

first: Sachine

last: Yoshida

address: 5-21-16 Omori-Nishi

department: Faculty of Medicine

country: Japan

institute: Toho University

summary: In many mammals, early postnatal interactions between caregivers and offspring involve rich physical contact, including stroking, holding, and grooming. Offspring typically remain calm and close to the caregiver during such stimulation. Although these behaviors are widely believed to support emotional regulation and bonding during infancy, the underlying biological mechanisms and the role of prior experience in eliciting the calming response remain poorly understood. Here, we demonstrate that back stroking induces a conserved calming response in both human infants and mouse pups, characterized by reductions in spontaneous movement and heart rate. In mouse pups, stroking further facilitated sleep onset, increased EEG delta power, and attenuated stress-induced corticosterone elevations. These sleep-promoting and stress-buffering effects were absent in artificially reared pups deprived of postnatal maternal contact, underscoring the importance of early tactile experience. Transcriptomic analysis revealed downregulation of the voltage-gated calcium channel subunit gene Cacna1b in the hypothalamus of artificially reared pups. Moreover, targeted knockdown of hypothalamic Cacna1b in maternally reared pups abolished stroking-induced reductions in movement and heart rate, as well as the increase in delta power. This study identifies a conserved, experience-dependent calming response to affiliative tactile input, biologically embedded through plasticity, that supports physiological regulation and stress resilience during early development. While the developmental plasticity of discriminative tactile sensation has long been recognized, our results highlight that affiliative tactile sensation similarly depends on early experience to organize neural mechanisms regulating internal states.

overall_design: Total RNA was extracted from the hypothalamus of postnatal day 13 mouse pups that were either maternally reared or artificially reared. Bulk RNA sequencing was performed to obtain comprehensive transcriptomic profiles, and differential gene expression analysis was conducted to identify genes with altered expression between the two rearing conditions.

first: Akiko

last: Harauma

first: Toru

last: Moriguchi

first: Yousuke

last: Tsuneoka

first: Kimiya

last: Narikiyo

first: Kazuya

last: Miyanishi

first: Makoto

last: Kashima

first: Hiromasa

last: Funato


title: Dads matter, too: The behavioural and neurogenomic effects of receiving paternal care [ATAC-Seq]

status: Public on Aug 18 2025

city: University Park

first: Jason

last: Keagy

state: PA

address: 410 Forest Resources Bldg

department: Ecosystem Science and Management

institute: Penn State University

summary: Offspring are often influenced by the care they receive from their parents. However, we know little about the underlying neurogenomic mechanisms. Using a half-sib design, threespine stickleback fish were either raised by their fathers or hand-reared (“orphaned”). As offspring developed, they were tested in one of three behavioural assays: an open field assay with a simulated predator attack, a social behaviour assay with a simulated predator attack, and a scototaxis assay. Offspring that received parental care were bolder, more social, and less anxious. Fish in the open field assay had their brains sampled one hour following the simulated attack; brains were sampled at the same time from full-sib controls. These brains were processed for gene expression (via Tag-seq) and chromatin accessibility (via ATAC-seq). Experiencing paternal care affected brain gene expression, but sex was also a major factor, despite the fish being reproductively immature. The predator attack in the open field assay affected expression of fewer genes. Sex, and to lesser extent, paternal care, also influenced chromatin accessibility at a whole genome scale. Our findings further our understanding of the mechanistic basis for offspring response to variation in the care they receive from their parents.

overall_design: Using a half-sib design, threespine stickleback fish were either raised by their wild-caught fathers (from Putah Creek, CA = Day 10) or hand-reared (“orphaned” = Day 0). Prior to sexual maturity, when these offspring were 6-8 months old, a subset were individually introduced to an open field assay and allowed to explore for 10 minutes. At 10 minutes, a model sculpin was moved through the pool in one complete circuit simulating a predatory attack. The subsequent behaviour of the juvenile fish was observed for an additional 10 minutes. Following this observation, the fish was left in the open field assay without any more disturbance. Sixty minutes after the attack, the juvenile fish was gently captured, euthanized via decapitation and its brain quickly dissected. Half of the brain was placed in RNAlater for subsequent RNA extraction for 3'TagSeq and the other half was placed in cold PBS and Roche cOmplete Mini Protease Inhibitor Cocktail (PIC) for processing for ATAC-seq. Fish were sexed with a DNA marker.

first: Alison

last: Bell


title: DNA damage burden causes selective CUX2 neuron loss in neuroinflammation

status: Public on Feb 02 2026

city: Los Angeles

first: Riki

last: Kawaguchi

address: 760 Westwood Plaza, Room 37-420

department: Department of Psychiatry and Neurology Department of Psychiatry

institute: University of California, Los Angeles

summary: Neurodegeneration shows regional and cell-type-specific patterns in ageing and disease1, but the underlying mechanisms for cell type-specific neuronal losses remain poorly understood. Previous studies have shown upper cortical layer thinning in progressive human multiple sclerosis (MS) and that cortical layer 2/3 excitatory neurons (L2/3 ENs) that express CUT like homeobox 2 (CUX2) are selectively vulnerable to degeneration2. Here, we report that L2/3 ENs within MS cortical lesions have elevated DNA damage. DNA damage and selective loss of L2/3 ENs was recapitulated in diverse mouse models of demyelination and pan-cortical inflammation, confirming their intrinsic vulnerability. Functions of Cux2 and Activating transcription factor 4 (Atf4) were essential for resilience of L2/3 ENs during postnatal neuroinflammation, acting in neurons to enhance DNA double strand break repair. Interferon-γ, a cytokine implicated in MS pathogenesis3,4, was sufficient to elevate reactive oxygen species leading to DNA damage-mediated neuronal death in vitro and caused selective depletion of L2/3 neurons in mice. These findings indicate that DNA damage burden and inadequate repair in CUX2+ L2/3 ENs contributes to selective vulnerability in neuroinflammatory injury.

overall_design: We collected E18.5 Wildtype, Cux2-Cre/Cre, Cux2-Cre/Wt;Atf4 fl/fl, Cux2-Cre/Cre;Atf4 fl/fl whole cortex to do the snRNA sequencing to compare the gene expression changes in between the different genotypes


title: Characterization of WDR5 WIN-site Inhibition in Two Glioblastoma Cancer Stem Cell Models using Bulk RNAseq

status: Public on Aug 15 2025

city: Cleveland

first: Jesse

middle: Aaron

last: Coker

state: OH

department: Center for Experimental Therapeutics

institute: Cleveland Clinic Research

summary: WDR5 inhibitors have been implicated as a therapeutic vulnerability in glioblastoma cancer stem cells (CSCs). We tested the transcriptional effects of two different WDR5 WIN-site inhibitors, the dihydroisoquinoline C16 and the triazole C3TD078, in two CSC models (L0 and DI318) by bulk RNAseq.These data are associated with Coker et al., "Development and Characterization of Triazole-Based WDR5 Inhibitors for the Treatment of Glioblastoma," bioRxiv, 2025, https://doi.org/10.1101/2025.07.29.667410.

overall_design: L0 and DI318 CSCs were treated for 72 hours with DMSO (0.1% v/v), 200 nM C16, or 200 nM C3TD078 (triplicate for all treatments). Total RNA was purified using a Qiagen RNeasy Plus kit and quality controlled for integrity and concentration on a Qubit® (Invitrogen). Bulk RNAseq was performed at MedGenome Inc. using the Illumina® Stranded mRNA Library Prep Kit and sequencing at 20M paired-end read-depth on a NovaSeq 6000 (PE100).

first: Amit

last: Gupta

first: Shaun

last: Stauffer

first: Justin

last: Lathia

first: Feixiong

last: Cheng


title: SUMO E3 ligase SIZ1 sustains nuclear condensate-mediated immune activation in plants

city: Berkeley

first: ENRICO

last: CALVANESE

address: Koshland Hall 371

department: Plant & Microbial Biology

institute: University of California, Berkeley

summary: SIZ1, a major plant SUMO E3 ligase, has diverse roles in development and immunity. Although loss-of-function studies have positioned SIZ1 as a negative immune regulator, the pleiotropic effects of its broad substrate repertoire may obscure its core function. Here we report that SIZ1 overaccumulation unexpectedly triggers robust pro-immune responses and cell death, dependent on its E3 ligase activity. We demonstrate that SIZ1 functionally converges on the MOS4-Associated Complex (MAC), a key immune signaling module, with both SIZ1 and the immune receptor SNC1 recruited to MAC-dependent nuclear condensates (MDNCs) upon pathogen challenge. These condensates serve as essential platforms for potentiating immune activation and cell death. Within the MDNC, SIZ1 promotes SUMOylation and stabilizes MAC components, thereby sustaining MDNC integrity during immune responses. Our findings reveal a previously unrecognized pro-immune role for SIZ1 and establish a mechanistic link between SUMOylation, MAC stability, and condensate-mediated immune signaling in plants.

overall_design:
RNA-Seq profiling of 4-week-old soil grown Col-0, siz1-2 loss-of-function mutant and SIZ1 overexpression mutant.

For RNA-Seq, four-week-old WT and siz1-2 pSIZ1:SIZ1g-GFP seedlings were collected, and total RNA was extracted using the Direct-zol RNA Miniprep kit. Library construction, quality control, and RNA sequencing were performed by Novogene (https://en.novogene.com/) on an Illumina NovaSeq X Plus Series (PE150) platform. The raw RNA-seq reads generated were filtered using trim-galore v0.6.6 with the default parameters to remove low-quality reads. Cleaned data were then mapped to the Arabidopsis thaliana genome TAIR10 using HISAT2 v2.2.051 with default parameters. BAMs were sorted by Samtools v1.9.52.

first: Yangnan

last: Gu

first: Min

last: Jia

first: Enrico

last: Calvanese


title: Integrated epigenetic and genetic programming of primary human T cells [WGBS]

first: Laine

last: Goudy

type: Methylation profiling by high throughput sequencing

overall_design: Whole genome bisulfite sequences of human primary T cells that have been treated with CRISPRoff mRNA and sgRNAs targeting genes of interest or a NTC. Cells were collected from 2 independent donors and technical replicates were performed for each donor.

first: Alvin

last: Ha

first: Ashir

last: Borah

first: Jennifer

last: Umhoefer

first: Lauren

last: Chow

first: Carinna

last: Tran

first: Aidan

last: Winters

first: Alexis

last: Talbot

first: Rosmely

last: Hernandez

first: Zhongmei

last: Li

first: Sanjana

last: Subramanya

first: Abolfazl

last: Arab

first: Nupura

last: Kale

first: Jae Hyun

last: Lee

first: Joseph

last: Muldoon

first: Chang

last: Liu

first: Ralf

last: Schmidt

first: Philip

last: Santangelo

first: Julia

last: Carnavale

last: Eyquem

first: Brian

last: Shy

first: Alex

last: Marson

first: Luke

last: Gilbert


title: Dads matter, too: The behavioural and neurogenomic effects of receiving paternal care

status: Public on Aug 13 2025

first: Jason

last: Keagy

overall_design: Using a half-sib design, threespine stickleback fish were either raised by their wild-caught fathers (from Putah Creek, CA = Day 10) or hand-reared (“orphaned” = Day 0). Prior to sexual maturity, when these offspring were 6-8 months old, a subset were individually introduced to an open field assay (= open-field) and allowed to explore for 10 minutes. At 10 minutes, a model sculpin was moved through the pool in one complete circuit simulating a predatory attack. The subsequent behaviour of the juvenile fish was observed for an additional 10 minutes. Following this observation, the fish was left in the open field assay without any more disturbance. Sixty minutes after the attack, the juvenile fish was gently captured, euthanized via decapitation and its brain quickly dissected. Half of the brain was placed in RNAlater for subsequent RNA extraction for 3'TagSeq and the other half was placed in cold PBS and Roche cOmplete Mini Protease Inhibitor Cocktail (PIC) for processing for ATAC-seq. Each fish that went through the open field assay was paired with a full-sibling who was gently removed from its home tank and acted as a ‘baseline control’ (= baseline). This fish did not go into the pool, but had its brain dissected within 30 minutes of the fish with which it was paired. Fish were sexed with a DNA marker.

first: Alison

last: Bell


title: Acclimation of the Escherichia coli transcriptome after 10 hours of incubation in the presence of silver nitrate at sublethal levels.

city: Calgary

first: Daniel Armando

last: Salazar-Alemán

state: Alberta

address: 2500 University Drive NW

department: Department of Biological Sciences

institute: University of Calgary

summary:
Silver nitrate has been explored as an FDA-approved alternative to treat antibiotic-resistant bacterial strains. Questions remain as it relates to the full-systems response elicited to counteract its toxic effects, especially in the context of a non-lethal exposure.
We explored the transcriptomic response profile of Escherichia coli K12 BW25113 when challenged to grow planktonically for 10 hours in M9-glucose minimal media spiked with a sublethal concentration of silver nitrate (7 µM, 1.18 µg/mL).
Our results yielded significant changes in gene expresson levels: 131 genes were up-regulated, while 558 were down-regulated in our silver nitrate treatment. Some biological processes became dysregulated to cope with the presence of this metal stressor, including iron metabolism and protein folding at the inner membrane and periplasm.
Altogether, this work provides a valuable snapshot of how our indicator strain adapts to metal-induced stress. This is a significant step in understanding how bacteria can adjust their physiology to coexist with sublethal concentrations of metal-based antimicrobials.

overall_design: Two treatment groups were set up: a non-metal control with M9-glucose minimal media, and a metal challenge using the same culture media but spiked with a sublethal concentration of silver nitrate (7 µM, 1.18 µg/mL). Both treatments were inoculated with Escherichia coli K12 BW25113, with three biological trials each. RNA extraction took place after an incubation time of 10 hours at 37 ºC 150 rpm. Differential gene expression was identified by contrasting both treatments, using p-adj value < 0.05 and absolute fold-change (FC) of at least 2 (|log2 FC| > 1) as significance thresholds.

first: Daniel

first: Raymond

last: Turner


title: An unbiased survey of distal element-gene regulatory interactions with direct-capture targeted Perturb-seq

city: Stanford

first: Jesse

last: Engreitz

address: 450 Serra Mall

department: Genetics

institute: Stanford University

summary: We developed Direct-Capture Targeted Perturb-seq (DC-TAP-seq), a cost-effective and sensitive approach that integrates U6-driven guide RNA capture with TAP-seq, enabling high-throughput screening of thousands of E–G connections at lower read depth. We applied this method to perform unbiased enhancer screens in two human cell types, K562 and WTC11. Our dataset revealed novel classes of non-canonical cis-regulatory elements (CREs) that were under-sampled in previous CRISPRi screens

overall_design:
We generated pilot datasets from K562 and WTC11 cells to develop and optimize DC-TAP-seq, a targeted single-cell RNA-seq method for capturing both gene expression and guide RNAs. To benchmark assay performance, we also generated conventional scRNA-seq and TAP-seq datasets from K562. We use the pilot datasets for comparisons of capture efficiency, guide detection, and knockdown assessment.
To validate the significant DE-G pairs, we repeated the DC-TAP-seq experiment for a subset of 24 significant and 6 not significant DE-G pairs (30 DE-G pairs total) in WTC11 at a range of MOIs: low MOI (1.1, 1.5) and high MOI (12.6, 14.4) in 2 replicates. WTC11 cells were infected with 582 guides (482 targeting 30 elements + 100 non-targeting) in sgOpti-CS vector. We measured gene expression changes by DC-TAP-seq for 203 genes. We ran 16 lanes of 10x Genomics lanes with DC-TAP-seq.

[UPDATE] The records have been updated with additional samples (GSM9932448-GSM9932479) on Aug 5, 2026.

first: Judhajeet

last: Ray

first: Eugenio

last: Mattei

first: Glen

last: Munson

first: Jacob

last: Huang


title: Overcoming ADC resistance in advanced colorectal cancer by dual targeting of TROP2 and PERK to suppress Wnt/β-catenin signaling [TROP2+GSK RNA-Seq]

status: Public on Dec 18 2025

city: Ganzhou

first: zhou

last: dongdong

address: hexie avenue

institute: Gannan Medical University

summary: Targeted therapy for advanced colorectal cancer (CRC) remains a significant clinical challenge. In this study, we systematically examined the anti-tumor efficacy and underlying mechanisms of IMMU132, an FDA-approved anti-TROP2 antibody conjugate linked to the topoisomerase I inhibitor SN-38, both as a standalone treatment and in combination with the PERK inhibitor GSK2606414 in TROP2-positive advanced CRC. We first established that TROP2 expression was markedly elevated in CRC cohorts and correlated with poor patient prognosis. In vitro experiments demonstrated that IMMU132 inhibited CRC cell proliferation and viability in a dose-dependent manner. In patient-derived xenograft (PDX) models, IMMU132 monotherapy significantly inhibited tumor growth. Mechanistically, transcriptomic analysis indicated that PERK, a key factor in endoplasmic reticulum stress (ERS), may serve as a critical synergistic target for IMMU132’s anti-tumour activity. Subsequent screening of various ERS inhibitors revealed that the specific PERK inhibitor GSK2606414 significantly enhanced the effects of IMMU132. In diverse experimental models, including cell lines, organoids, and PDX models, combination therapy exhibited superior anti-tumor effects compared to monotherapy, highlighting a pronounced synergistic effect. Furthermore, transcriptomic analysis showed that combination therapy notably inhibited the Wnt/β-catenin signaling pathway. Gene set enrichment analysis confirmed significant upregulation of Wnt pathway-related genes, while Western blot analysis showed downregulation of key molecules in the Wnt pathway, including β-catenin, GSK3B, JUN, and WNT2B, following combination therapy. These findings suggest that the synergistic anti-tumour effects of IMMU132 and GSK2606414 may arise from their dual modulation of ERS and Wnt signalling pathways, offering novel insights for targeted therapy in advanced CRC and informing strategies for combining antibody-drug conjugates (ADCs).

overall_design: This study systematically characterized TROP2 expression in colorectal cancer through integrated bioinformatics and tissue microarray analysis, with validation across multiple preclinical models. The TROP2-targeting antibody-drug conjugate IMMU132 demonstrated potent monotherapeutic efficacy across diverse molecular subtypes in cell lines, patient-derived organoids and xenografts. Transcriptomic analysis identified PERK, a key endoplasmic reticulum stress regulator, as crucial to IMMU132's mechanism. The specific PERK inhibitor GSK2606414 significantly enhanced IMMU132's anti-tumor effects through synergistic modulation of both endoplasmic reticulum stress and Wnt/β-catenin signaling pathways. These findings elucidate IMMU132's mechanism of action and propose a novel combination strategy with strong translational potential for advanced colorectal cancer therapy.

first: Jie

last: Liu

first: Mei

last: Li

first: Jianming


title: Acclimation of the Escherichia coli transcriptome after 10 hours of incubation in the presence of tetrachloroauric acid at sublethal levels.

summary:
Tetrachloroauric acid has been explored as an FDA-approved alternative to treat antibiotic-resistant bacterial strains. Questions remain as it relates to the full-systems response elicited to counteract its toxic effects, especially in the context of a non-lethal exposure.
We explored the transcriptomic response profile of Escherichia coli K12 BW25113 when challenged to grow planktonically for 10 hours in M9-glucose minimal media spiked with a sublethal concentration of tetrachloroauric acid (10 µM, 3.39 µg/mL).
Our results yielded significant changes in gene expresson levels: 1028 genes were up-regulated, while 1025 were down-regulated in our tetrachloroauric acid treatment. Several biological processes became dysregulated to cope with the presence of this metal stressor, including iron metabolism, ribosome assembly, sulfur metabolism, cysteine biosynthesis, zinc uptake, and the copper homeostasis system Cue.
Altogether, this work provides a valuable snapshot of how our indicator strain adapts to metal-induced stress. This is a significant step in understanding how bacteria can adjust their physiology to coexist with sublethal concentrations of metal-based antimicrobials.

overall_design: Two treatment groups were set up: a non-metal control with M9-glucose minimal media, and a metal challenge using the same culture media but spiked with a sublethal concentration of tetrachloroauric acid (10 µM, 3.39 µg/mL). Both treatments were inoculated with Escherichia coli K12 BW25113, with three biological trials each. RNA extraction took place after an incubation time of 10 hours at 37 ºC 150 rpm. Differential gene expression was identified by contrasting both treatments, using p-adj value < 0.05 and absolute fold-change (FC) of at least 2 (|log2 FC| > 1) as significance thresholds.

first: Ashley

last: McGibbon


title: Acclimation of the Escherichia coli transcriptome after 10 hours of incubation in the presence of copper sulfate at sublethal levels.

summary:
Copper sulfate has been explored as an FDA-approved alternative to treat antibiotic-resistant bacterial strains. Questions remain as it relates to the full-systems response elicited to counteract its toxic effects, especially in the context of a non-lethal exposure.
We explored the transcriptomic response profile of Escherichia coli K12 BW25113 when challenged to grow planktonically for 10 hours in M9-glucose minimal media spiked with a sublethal concentration of copper sulfate (39 µM, 6.22 µg/mL).
Our results yielded changes in gene expresson levels: 80 genes were up-regulated, while 76 were down-regulated in our copper sulfate treatment. Some biological processes became dysregulated to cope with the presence of this metal stressor, including iron metabolism, sulfur metabolism, cysteine biosynthesis, and the copper homeostasis systems Cue and Cus.
Altogether, this work provides a valuable snapshot of how our indicator strain adapts to metal-induced stress. This is a significant step in understanding how bacteria can adjust their physiology to coexist with sublethal concentrations of metal-based antimicrobials.

overall_design: Two treatment groups were set up: a non-metal control with M9-glucose minimal media, and a metal challenge using the same culture media but spiked with a sublethal concentration of copper sulfate (39 µM, 6.22 µg/mL). Both treatments were inoculated with Escherichia coli K12 BW25113, with three biological trials each. RNA extraction took place after an incubation time of 10 hours at 37 ºC 150 rpm. Differential gene expression was identified by contrasting both treatments, using p-adj value < 0.05 and absolute fold-change (FC) of at least 2 (|log2 FC| > 1) as significance thresholds.


title: Effect of Myosin 10 or Jagged 1 knockout on gene expression in H1299 Non-small cell lung cancer leader cells.

status: Public on Aug 10 2025

city: Atlanta

first: Raaven

last: Goffe

state: GA

address: 100 Woodruff Circle

institute: Emory University School of Medicine

summary: While minimizing lung cancer metastasis can improve overall survival, few models exist where subpopulations with stable high and low metastatic potential can be easily and reliably isolated. Our previous work characterized two stable subpopulations, termed Leaders and Followers, from the H1299 Non-Small Cell Lung Cancer model. H1299 Leaders and Followers have different transcriptional profiles, biomarkers, genomic methylation patterns, metabolic states, and morphologies.Of note, H1299 Leaders express high levels of Jagged1 (JAG1) and Myosin 10 (MYO10) and drive collective invasion and metastasis. To determine how JAG1 and MYO10 contribute to Leader cell biology and lung cancer metastasis, we utilized CRISPR-Cas9 to generate edited pools of H1299 cells targeting either JAG1 or MYO10. Fluorescence-activated cell sorting using a Leader-Follower biomarker, IL13R2, was used to generate single cell derived candidate clones. Candidate clones were screened using western blot for Leader and Follower cell biomarkers (JAG1, MYO10, HTATIP2 and IL13R2) followed by Sanger sequencing of candidate clones was also conducted to confirm target gene status. Using this method, 2 JAG1 knockout, 2 MYO10 knockout, 1 MYO10 knockdown and, 2 wildtype MYO10 JAG1 H1299 single-cell derived clones were generated.

overall_design: RNA-seq profiling of  2 JAG1 knockout, 2 MYO10 knockout, 1 MYO10 knockdown and, 2 wildtype MYO10 JAG1 clonal cell lines along with H1299 parental, leader and follower cell lines.

first: Henry

last: Claussen

first: Robert

last: Aurther

first: Adam

middle: I

last: Marcus


title: Investigation of LARP1 regulated cellular pathways in acute myeloid leukemia

status: Public on Aug 06 2025

city: Chicago

first: Elspeth

last: Beauchamp

state: IL

address: 303 E Superior St

department: Medicine

institute: Northwestern University-Feinberg School of Medicine

summary: We demonstrate that LARP1, an RNA-binding protein regulated by mTOR and CDK9, promotes leukemic cell fitness and drug resistance in acute myeloid leukemia (AML). Using CRISPR/Cas9-mediated knockout models and multi-omics profiling, we show that LARP1 uniquely regulates the translation of transcripts involved in metabolism, cell cycle, and immune signalling, independent of mTOR or CDK9 inhibition. LARP1 loss reprograms mitochondrial and amino acid metabolism, downregulates cytidine deaminase, and enhances sensitivity to azacitidine and cytarabine. These findings establish LARP1 as a critical integrator of translational and metabolic control in AML and a potential therapeutic target.

overall_design: This study investigates the role of LARP1 in acute myeloid leukemia (AML) using CRISPR/Cas9-mediated knockout in human U937 cells. Total and polysome-associated RNA-seq was performed on LARP1 knockout cells (carrying single guide (sg) RNA targeting LARP1) and control cells (carrying non-targeting sgRNA), as well as cells treated with pharmacological inhibitors of mTOR (Vistusertib), CDK9 (Enitociclib), or their combination. Control U937 cells expressing non-targeting sgRNA were treated with 500 nM of each inhibitor or DMSO as vehicle.

first: Dominik

last: Nahotko

first: Brian

last: Lee

first: Leonidas

middle: C

last: Platanias


title: Beta-Adrenergic Stimulation and MYH7 G256E Mutant Gene Dosage Drive Hypertrophic Cardiomyopathy Phenotype Penetrance

status: Public on Aug 01 2025

city: STANFORD

first: Paul

last: Heinrich

address: 265 CAMPUS DRIVE

department: Cardiovascular Insititute

summary: We characterized the baseline transcriptomic phenotype of day30 iPSC-Cardiomyocytes carrying hypertrophic cardiomyopathy associated heterozygous mutations MYH7 G256E and H251N using scRNAseq. We additionally analzyed trancriptomic signatures of HOM MYH7 G256E iPSC-CMs, and of HET MYH7 G256E iPSC-CMs after isopreterenol treatment.

overall_design: Our study includes the data of 7 independent scRNAsequencing runs using 10X Genomics characterizing the trancriptomic signature of the H251N and G256E mutation in iPSC-CMs. Individual conditions for each run is specified below. 10X CellPlex Feature barcoding technology was used to multiplex samples 2-7 for scRNAseq. Antibody-based labeling of CD29 and B2M and single indexing was used to multiplex sample 1. Please refer to each scRNAseq batch information for de-multiplexing settings used for this study. In the raw data, the FB files contain feature barcode sequencing information for sample multiplexing, while the GE files contain gene expression sequencing information.

first: Soah

first: Sean

last: Wu


title: Astroglial TNFR2 signaling regulates hippocampal synaptic function and plasticity in a sex dependent manner

city: Miami

first: Roberta

last: Brambilla

state: FL

department: Neurological Surgery

institute: University of Miami Miller School of Medicine

summary: Astrocytes participate in synaptic transmission and plasticity through tightly regulated, bidirectional communication with neurons, both pre- and post-synaptic elements, as well as microglia and oligodendrocytes. A key component of astrocyte-mediated synaptic regulation is the cytokine tumor necrosis factor (TNF). TNF signals via two cognate receptors, TNFR1 and TNFR2, both expressed in astrocytes. While TNFR1 signaling in astrocytes has been long demonstrated to be necessary for physiological synaptic function, the role of astroglial TNFR2 has never been explored. Here, we demonstrate that astroglial TNFR2 is essential for maintaining hippocampal synaptic function and plasticity in physiological conditions. Indeed, GfapcreERT2:Tnfrsf1bfl/fl mice with selective ablation of TNFR2 in astrocytes exhibited dysregulated expression of neuronal and glial proteins (e.g. SNARE complex molecules, glutamate receptor subunits, glutamate transporters) essential for hippocampal synaptic transmission and plasticity. Hippocampal astrocytes sorted from GfapcreERT2:Tnfrsf1bfl/fl mice displayed downregulation of genes and pathways implicated in synaptic plasticity, astrocyte-neuron and astrocyte-oligodendrocyte communication. These alterations were accompanied by increased glial reactivity and impaired astrocyte calcium dynamics, and ultimately translated into functional deficits, specifically impaired long-term potentiation (LTP) and cognitive functions. Notably, male GfapcreERT2:Tnfrsf1bfl/fl mice exhibited more pronounced hippocampal synaptic and cellular alterations, suggesting sex-dependent differences in astroglial TNFR2 regulation of synaptic function. Together, these findings indicate that TNFR2 signaling in astrocytes is essential for proper astrocyte-neuron communication at the basis of synaptic function, and that this is regulated in a sex-dependent manner.

overall_design: RNA-seq profiling of sorted hippocampal astrocytes from adult naive male mice with ablation of astroglial TNFR2 (GfapcreERT2:Tnfrsf1bfl/fl ) and corresponding controls (Tnfrsf1bfl/fl )

first: Brianna

middle: N

last: Carney

first: Placido

last: Illiano

first: Taylor

last: Pohl

first: Haritha

last: Desu

first: Shwetha

last: Mudalegundi


title: The evolution and heterogeneity of lethal metastatic bladder cancer subtypes

city: Seattle

first: Sonali

last: Arora

state: WA

address: 1100 Fairview Ave N,

institute: FHCRC

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

overall_design: Refer to individual Series


title: YAP1 and QSER1 are Key Modulators of Embryonic Signaling Pathways in the Mammalian Epiblast [ChIP-seq]

status: Public on Jul 31 2025

city: Philadelphia

first: Naiara

last: Akizu

address: 3501 Civic Center Blvd

department: Pathology And Lab Medicine

institute: Children's Hospital of Philadelphia

summary: The Hippo:YAP1 signaling pathway was long considered a master regulator of organ growth. However, recent evidence has challenged this view, showing that the loss of YAP1 does not prevent several organs from reaching their normal size. Hence, resolving the functions of YAP1 in the embryo has become a central question in the field. To shed light into this, we analyzed YAP1’s role in regulating pluripotency of the mammalian epiblast, using scRNAseq approaches. Conditional deletion of Yap1 in the mouse epiblast (Sox2-Cre) altered the expression of signaling and differentiation genes, including Nodal, Wnt3, Fgf8, and Nanog, without impairing cell proliferation. Instead, Yap1 loss led to hyperactivation of Nodal signaling and enhanced differentiation of the epiblast toward mesodermal fate.  Furthermore, an unbiased screening in human pluripotent stem cells revealed that YAP1 transcriptionally cooperates with QSER1 protein, to regulate multiple WNT and NODAL signaling genes. Mechanistically, QSER1 represses lineage enhancers of signaling genes by counteracting RNA Polymerase II recruitment on YAP1-targets.  Accordingly, QSER1 depletion, similar to YAP1, leads to hyperactive Nodal signaling in human 2D-gastruloids. Overall, our findings not only advance our understanding of YAP1’s role in early development but also open new avenues for exploring how the interplay with QSER1 could influence additional developmental processes.

overall_design: Single-cell RNA sequencing (scRNAseq) data were obtained from E7 mouse embryos, including cYAP KO (Sox2cre:Yapflox/flox) and control (Sox2cre:Yapflox/+).

first: Elizabeth

last: Abraham

first: Thomas

last: Roule

first: Aidan

last: Douglas

first: Emily

last: Megil

first: Alex

last: Morris

first: Mikel

last: Zubillaga

first: Conchi

last: Estaras


title: TAK1 is a key regulator of oncogenic signaling and differentiation blockade in rhabdomyosarcoma

status: Public on Dec 16 2025

city: Houston

first: Ashok

last: Kumar

state: Texas

address: 4349 Martin Luther King Blvd.

department: Pharmacological and Pharmaceutical Sciences

institute: University of Houston

summary: Rhabdomyosarcoma (RMS) is a malignant soft tissue sarcoma with a skeletal muscle phenotype, accounting for approximately 50% of all pediatric soft tissue sarcomas and 8% of all childhood cancers. Although RMS cells express myogenic regulatory factors, they fail to undergo terminal differentiation into mature muscle cells. Transforming growth factor β-activated kinase 1 (TAK1) is a major signaling protein that activates multiple intracellular pathways in response to growth factors, cytokines, and microbial products. Emerging evidence suggests that TAK1 is also an important regulator of self-renewal, proliferation, and differentiation of muscle progenitor cells. However, the role and mechanisms of action of TAK1 in RMS remain completely unknown. In this study, we demonstrate that TAK1 expression and activity are markedly elevated in a panel of RMS cell lines and in patient tumor specimens. Reverse phase protein array (RPPA) analyses revealed that TAK1 regulates the expression and activity of many molecules involved in cell cycle control, cell proliferation, and oncogenic signaling. Genetic knockdown or pharmacological inhibition of TAK1 suppresses RMS cell proliferation, migration, and invasiveness, while also promoting terminal myogenic differentiation. TAK1 inhibits differentiation in RMS, at least in part, through up-regulating YAP1 signaling. Our results also demonstrate that inducible knockdown of TAK1 in human RMS xenografts retards tumor growth and enhances myogenic differentiation in vivo. Collectively, these findings uncover a previously unrecognized role for TAK1 in RMS growth and differentiation, and suggest that TAK1 can be a potential therapeutic target for the treatment of RMS.

overall_design:
Bulk RNA-seq profiling of RD cells expressing Scrambled or TAK1 shRNA (n=3 each).

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The raw data are no longer available since the sequencing was performed 4 years ago. In addition,  NOVOGENE, the company who performed the sequencing,  does not have the data archived.
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first: Anh

last: Vuong

first: Aniket

last: Joshi

first: Anirban

last: Roy

first: Kavya

last: Mathukumalli

first: Phuong

last: Ho

first: Raksha

last: Bhat

first: Meiricris

last: Tomaz da Silva

first: Meghana

last: Trivedi

first: Bin

last: Guo

first: Benny

last: Kaipparettu


title: YAP1 and QSER1 are Key Modulators of Embryonic Signaling Pathways in the Mammalian Epiblast [scRNA-seq]

first: Naiara

last: Akizu

first: Elizabeth

last: Abraham

first: Thomas

last: Roule


title: Gut resident T-bet expressing Tr1 cells driven by dietary signals dominate the small intestinal immune landscape III

city: San Diego

first: Eduardo

last: Ansaldo

address: 15550 Torrey Pines Rd

department: IMM

institute: Scripps Research

summary: Intestinal immunity provides defense against enteric pathogens, mediates symbiotic relationships with the resident microbiota, and provides tolerance to food antigens, safeguarding critical nutrient absorption and barrier functions of this mucosal tissue. Despite the large abundance of tissue resident activated T cells, how T cell immunity contributes to these various roles remains poorly understood. Here we describe a previously uncharacterized dominant T-bet expressing Tr1 T cell population in the small intestine lamina propria present at homeostasis. Importantly, this IL-10 secreting CD4^+^T-bet^+^ T cell population appears in the small intestine at the time of weaning independently of the resident microbiota, presenting similar accumulation, functional capacity, and TCR repertoire in germ free conditions. Instead, small intestinal T-bet^+^ Tr1 T cells respond to dietary signals driving their accumulation, suppressive program, and clonal selection; and depend on cDC1s, IL-27 signaling, and T-bet, but not IL-12. Altogether, this work uncovers a previously unappreciated dominant player in homeostatic small intestinal immunity with the potential to play critical suppressive roles in oral tolerance to dietary antigens, raising important implications for the understanding of food allergy and celiac disease.

overall_design: SILP CD4^+^T-bet^+^ T cells (Live, CD45+CD90.2+, TCRb+, CD4+, T-bet-ZsGreen+) from GF T-bet-ZsGreen mice raised on casein, amino acid, or regular chow diet were sorted from samples labeled with TotalSeqC hashtags antibodies (Biolegend) using a Sony MA900 sorter. Sorted cells were pooled during sorting and 40000 cells per lane (total of 4 lanes) were loaded on a Chromium Single Cell Controller (10X Genomics) to encapsulate the cells into droplets. The gene expression (GEX), hashtag oligonucleotide (HTO) and VDJ (TCR) sequencing libraries were prepared using Chromium Single Cell 5’ v2 reagent kits following the manufacturer’s instructions, and sequenced on an Illumina Nextseq1000 platform (NextSeq 1000/2000 P2 reagents)

first: Eduard

first: Daniel

last: Yong

first: Nathan

last: Carrillo

first: Taryn

last: McFadden

first: Mahnoor

last: Abid

first: Dan

last: Corral

first: Claudia

last: Rivera

first: Taylor

last: Farley

first: Nicolas

last: Bouladoux

first: Inta

last: Gribonika

first: Yasmine

last: Belkaid


title: ChAHP Displaces Transcriptional Regulators Through Active Chromatin Remodeling

status: Public on Jul 21 2025

city: Basel

first: Fabio

last: Mohn

address: Maulbeerstrasse 66

institute: Friedrich Miescher Institute for Biomedical Research