title: Threonine Phosphorylation of STAT1 Safeguards Gut Epithelial Integrity and Restricts Interferon-mediated Cytotoxicity [RNA-seq]

city: Kanagawa

first: Kazuki

last: Okuyama

address: 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama

department: IMS

institute: RIKEN Yokohama

summary: Uncontrolled inflammation drives tissue damage, highlighting the need for tightly regulated immune responses and tissue integrity, particularly in barrier tissues like the intestine. To maintain this exquisite balance, intestinal epithelial cells (IECs) employ molecular circuits that preserve tissue integrity following inflammation. STAT1 is traditionally viewed as a pro-inflammatory driver in the intestine, acting as a central signaling mediator downstream of interferons (IFN). Here, we identify threonine 748 (Thr748) phosphorylation of Stat1 as an evolutionarily conserved adaptation that reciprocally regulates IEC integrity and IFN responsiveness. Mice expressing a phospho-deficient T748A Stat1 mutant exhibit severe pathology similar to Stat1 deficient littermates, underscoring Thr748’s critical role in Stat1-driven protection following intestinal inflammation. Bone marrow transfer experiments further demonstrate that this protective effect is non-hematopoietic. Integrated genomic and transcriptomic analyses reveal that Thr748 phosphorylation modulates Stat1 DNA binding, directly activating the Itgb4 promoter and enhancing integrin β4 expression in IECs following inflamamtion. In vitro intestinal organoid models, combined with gain- and loss-of-function experiments, show that Stat1 promotes integrin β4 expression via Thr748 phosphorylation following damage, boosting epithelial resilience independently of IFN-induced Tyrosine 701 (Tyr701) phosphorylation. In contrast, IFN stimulation triggers Tyr701 phosphorylation of Stat1, upregulating Zbp1—a sensor of cytotoxic damage-associated nucleic acids—while suppressing integrin β4, leading to epithelial cytotoxicity, which is mitigated by Thr748 phosphorylation. Our findings uncover a modular architecture of Stat1 signaling that enables epithelial adaptation to damage, with Thr748 phosphorylation acting as a rheostat to preserve tissue integrity while restricting IFN-mediated cytotoxicity.

overall_design: To elucidate the protective epithelial transcriptional programs driven by the Thr748 phosphorylation of Stat1 following colitis-induced damage, we performed RNA sequencing (RNA-seq) on IECs isolated from Wt and Stat1T748A mice under both basal and DSS-treated conditions. A total of 2–5 × 10⁵ cells per condition were lysed in 0.5 mL of TRIzol Reagent (Thermo Fisher) following the indicated treatments. RNA-seq analysis was performed by the Genome Information Research Center (GIRC) at Osaka University. Briefly, total RNA was extracted, and cDNA libraries were prepared using the TruSeq Stranded mRNA Sample Prep Kit (Illumina, Cat. No. 20020594) according to the manufacturer’s instructions. Sequencing was conducted on an Illumina HiSeq 2500 platform using 75-base single-end reads. Base calling was performed with Illumina Casava v1.8.2 software. Sequenced reads were aligned to the mouse reference genome (mm10/GRCm38) using TopHat v2.0.13 with Bowtie2 v2.2.3 and SAMtools v0.1.19. Gene expression levels were quantified as fragments per kilobase of exon per million mapped reads (FPKM) using Cuffnorm v2.2.1. Further data processing and analysis were conducted on the Galaxy platform (https://usegalaxy.org/). Read quality was assessed using FastQC (v0.73), and adaptor sequences were trimmed prior to alignment with HISAT2 (v2.2.1) using default parameters. Gene counts were generated with featureCounts (v2.0.3), and differential expression analysis was performed using DESeq2 (v2.11.40.7). Visualization of results, including volcano plots and heatmaps, was performed using Volcano Plot (v0.0.5) and heatmap2 (v3.1.3), respectively. Gene ontology enrichment and pathway analysis were conducted using the PANTHER GO-Slim Biological Process database (v17.0, released 2022/02/22).

first: Hozaifa

last: Metwally

first: Tadamitsu

last: Kishimoto


title: Spatial transcriptomics data of EMP2-progressive symmetric erythrokeratoderma

status: Public on Jul 09 2025

city: New Haven

first: Ryland

last: Mortlock

state: Connecticut

address: 15 York Street, HRT 618C

country: USA

institute: Yale University

summary: Genetic investigation in Mendelian skin disorders featuring generalized or localized skin scaling and redness, known as the ichthyoses, has revealed novel pathways relevant to epidermal integrity, barrier function, and desquamation. Here we show that a recurrent de novo missense variant in EMP2 (epithelial membrane protein 2), which encodes a cell surface tetraspan protein in the growth-arrest specific 3 (GAS3)/peripheral myelin protein 22 (PMP22) family, is associated with a previously undescribed Mendelian disorder in the progressive symmetric erythrokeratoderma spectrum. The disorder features severely thickened, red and scaly skin at sites of wound healing or repetitive movement including on the face, genitals, flexural areas, and the palms and soles. EMP2 has previously been shown to directly associate with focal adhesion kinase (FAK), which links cell junction forces to signaling pathways relevant to proliferation, migration, and wound healing. Using single-cell spatial transcriptomics in affected tissue, we discovered ectopic suprabasal activation of signaling pathways downstream of receptor tyrosine kinases including epidermal growth factor receptor (EGFR), which we confirmed with Western blotting in affected cells, supporting a gain-of-function mechanism for mutant EMP2. Remarkably, treatment with erlotinib, an EGFR inhibitor, led to marked clinical improvement underscoring the key role of EMP2 in epidermal differentiation and proliferation.

overall_design: Spatial transcriptomic data from an affected individual with EMP2-PSEK and healthy control skin were sequenced on the same capture area of a Visium HD slide.

first: Xingyuan

last: Jiang

first: Keith

last: Choate


title: Multigenerational Proteolytic Inactivation of Restriction Upon Subtle Genomic Hypomethylation in Pseudomonas aeruginosa

city: Ramat-Gan

first: Ilana

last: Lebenthal-Loinger

address: Bar-Ilan University

department: The Mina & Everard Goodman Faculty of Life Sciences

country: Israel

institute: Bar-Ilan University

type: Expression profiling by high throughput sequencing

summary: Restriction-modification (R-M) systems protect against phage infection by detecting and degrading invading foreign DNA. However, like many prokaryotic anti-phage defenses, R-M systems pose a significant risk of auto-immunity, exacerbated by the presence of hundreds to thousands of potential cleavage sites in the bacterial genome. Pseudomonas aeruginosa strains experience the temporary inactivation of restriction endonucleases (tiREN) upon growth at high temperatures, but the mechanisms and implications of this are unknown. Here, we report that P. aeruginosa Type I restriction endonuclease (HsdR) is degraded, and the methyltransferase (HsdMS) is partially degraded, by two Lon-like proteases when replicating above 41 °C. This post-translational regulation prevents self-DNA targeting and leads to partial genomic hypomethylation, as demonstrated by SMRT sequencing and eTAM-seq. Interestingly, upon return to 37 ºC, restriction activity and full genomic methylation do not fully recover for up to 60 bacterial generations. Our findings demonstrate that Type I R-M is tightly regulated post-translationally with a long memory effect that ensures genomic stability and mitigates auto-toxicity.

overall_design: Samples were collected from cultures grown overnight at either 43°C or 37°C, as well as after recovery at 37°C for 18 and 54 hours following incubation at 43 °C

first: Ehud

last: Banin

first: Esther

last: Shmidov


title: Threonine Phosphorylation of STAT1 Safeguards Gut Epithelial Integrity and Restricts Interferon-mediated Cytotoxicity [ChIP-seq]

country: Japan

type: Genome binding/occupancy profiling by high throughput sequencing

overall_design: To  assess the impact of Thr748 phosphorylation on Stat1’s transcriptional activity in intestinal epithelial cells (IECs), we performed chromatin immunoprecipitation sequencing (ChIP-seq) on IECs isolated from Wt and Stat1T748A mice following DSS treatment. ChIP assays were performed using the Pierce Magnetic ChIP Kit (Thermo Fisher) following the manufacturer’s protocol. Briefly, IECs were isolated from DSS-treated Wt and Stat1T748A littermate mice and cross-linked with 3.7% formaldehyde for 10 minutes at room temperature. Cross-linking was quenched with 1.375 M glycine for 5 minutes at room temperature. Nuclei were isolated, and chromatin was enzymatically sheared using micrococcal nuclease for 17 minutes at 37 °C. Five percent of the sheared chromatin was reserved as input, and the remainder was subjected to immunoprecipitation using anti–STAT1 antibody (1:50 dilution). Immunocomplexes were reverse cross-linked overnight at 65 °C with Proteinase K, and DNA was purified using phenol/chloroform extraction. ChIP DNA libraries were prepared using the KAPA Hyper Prep Kit (KAPA Biosystems) according to the manufacturer’s instructions. Paired-end sequencing (2 × 101 bp) was performed on an Illumina NovaSeq 6000 platform (Illumina Inc., San Diego, CA, USA). Adapter trimming was conducted with Cutadapt (v4.8), using the following adapter sequences: Read 1: 5′-AGATCGGAAGAGCACACGTCTGAACTCCAGTCA-3′; Read 2: 5′-AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT-3′. Read quality was assessed using FastQC (default settings). Trimmed reads were aligned to the mouse reference genome (mm10) using Bowtie2 (v2.5.3) with the “very sensitive end-to-end” preset. BAM files were further processed using the Galaxy platform. Low-quality reads (MAPQ < 30), improperly paired reads, mitochondrial reads, and PCR duplicates were removed using ‘Filter’ (v2.4.2) and ‘MarkDuplicates’ (v3.1.1.0). Peak calling was performed using MACS2 callpeak (v2.2.9.1).


title: Protocol for single-cell spatial transcriptomic profiling of cultured cells and engineered tissues without embedding or sectioning

city: Portland

first: Luiz

middle: E

last: Bertassoni

state: OR

address: 2720 S Moody Ave

department: Knight Cancer Institute

institute: Oregon Health and Science University

summary:
The deposited data corresponds to the development of a protocol for spatial transcriptomic profiling of 2D engineered tissues and cell cultures that are not compatible with standard embedding and sectioning. By fixing and permeabilizing cells grown directly on a microscope glass slide, we demonstrate how Visium HD spatial gene expression kit can be used to investigate the function of these cells.

Manuscript link: https://star-protocols.cell.com/protocols/4456
Github repository: https://github.com/HaylieHelms/vhd-scbioprint1

overall_design: A combination of primary human cells (mammary eptithelial cells, mammary myoepithelial cells, mammary fibroblasts, umbilical vein endothelial cells, and macrophages) and human cell lines (MDA-MB-231 and MCF10A) were patterned onto a collagen coated glass microscope slide using a single-cell bioprinter (Biopixlar, Fluicell). The cells were cultured in M87 media for 24 hours before being fixed with 4% PFA and permeabilized with 100% methanol. The Visium HD spatial transcriptomics protocol was then followed to generate the data deposited here.

first: Haylie

middle: R

last: Helms


title: Transcriptional responses to nitric oxide are widescale and source-dependent

city: Cleveland

first: Joseph

middle: C.

last: Schindler

state: OH

address: 10900 Euclid Ave.

department: Biochemistry

institute: Case Western Reserve University

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

overall_design: Refer to individual Series


summary: The transcriptomic effects of nitric oxide (NO) have been widely studied across phylogeny. However, while gene expression is canonically altered by NO, general principles have not emerged. Here, we characterize genetic regulation within a single cell type after exposure to NO derived from endogenous or synthetic donor compounds or produced by three different NO synthase (NOS) isoforms under basal and activated conditions. Using RNAseq, we uncover distinct, source-dependent effects of NO on as many as ~10,000 genes mediated largely by S-nitrosylation. NOS enzymes and NO donors each generated unique transcriptional responses. Our data reveal non-overlapping transcriptional responses to NO that are likely mediated by distinct effectors and enzymes and highlight that NO-treated cell systems may undergo a dramatic and widespread transcriptional response.

overall_design: RNA-seq analysis of HEK293 cells exposed to different concentrations of NO donor compounds or overexpressing each NOS isoform (without calcium activation)

middle: C

first: Puneet

last: Seth

first: Richard

middle: T

last: Premont

first: Jonathan

middle: S

last: Stamler


title: Transcriptomic profiling of thymocytes in CDC42-deficient and wild-type mice using single-cell RNA-seq

city: Gwangju

first: Changduk

last: Jun

state: Not US or Canada

address: Bukgu oryongdong GIST

department: life science

country: South Korea

institute: Gwangju institute of science and technology(GIST)

summary: We performed single-cell RNA sequencing (scRNA-seq) on thymocytes isolated from wild-type (WT) and CDC42 knockout (CDC42 KO) mice to investigate the role of CDC42 in thymocyte development. This dataset includes raw UMI counts, normalized expression data, and metadata for thousands of thymocytes across different developmental stages. Comparative analysis revealed transcriptional differences between WT and CDC42 KO thymocytes, highlighting CDC42’s role in T cell differentiation.

overall_design: Thymocytes were isolated from five wild-type (WT) and five CD4-specific CDC42 knockout (CDC42 KO) littermate mice at 6 weeks of age. Single-cell suspensions from each group were pooled to capture a comprehensive transcriptomic profile.

first: Sangmoo

last: Park

first: Hatice

last: Karabulut

first: Wonchang

last: Soh


title: PTH Counteracts Hippo Signaling via Src-dependent YAP Stabilization to Enhance Bone Marrow Stromal Cell Differentiation

city: Boston

first: Roland

last: Baron

state: MA

address: 188 Longwood Ave

department: Division of Bone and Mineral Research Oral Medicine, Infection & Immunity

institute: Harvard University

summary: Parathyroid hormone (PTH) regulates serum calcium and phosphate through its actions in bone and the kidney and is used to increase bone in osteoporosis treatment. In bone, PTH targets osteoblasts and osteocytes to regulate bone remodeling but also bone marrow stromal cells (BMSCs), regulating their differentiation in the osteoblast and/or the adipocyte lineages. PTH exerts its action through the PTH/PTH-related peptide (PTHrP) receptor (PTH1R), a G protein-coupled receptor (GPCR), activating adenylyl cyclase and phospholipase C (PLC). Although the effects of cAMP and PKA are well characterized, little is known about the effects of PLC activation or on the cross-talk between PTH signaling and other pathways. Here, bulk RNA-seq of PTH-treated murine BMSC line (W-20) revealed significant changes in the Hippo pathway. PTH stabilized YAP, a key target of Hippo, by decreasing YAP/LATS1 interaction, YAPS127 phosphorylation and YAP ubiquitination, leading to YAP nuclear translocation and expression of YAP target genes. Similar events occurred in osteocyte cell lines. This occurred via an increase in Src kinase activity: we identified YAPY428 as a key tyrosine residue phosphorylated by Src in response to PTH. Preventing Y428 phosphorylation led to YAP instability, blocking both osteogenic and adipogenic differentiation of W-20 cells. These results demonstrate active crosstalk between the PTH/PTHrP and the Hippo signaling pathways and reveal that PTH signaling utilizes the PLC-Ca2+-Src tyrosine kinase signaling cascade to influence YAP stability, antagonizing Hippo signaling and favoring stromal cell differentiation. Thus, PTH signaling counteracts the effects of Hippo signaling in BMSCs to favor their differentiation.

overall_design: To gain insight the cross-talk between parathyroid hormone (PTH) signaling and Hippo signaling pathways in bone marrow stromal cells (BMSCs) and bone cells, with a focus on understanding the role of PTH in regulating YAP (Yes-associated protein) stability and activity. The murine bone marrow stromal cell line W-20 was used as the primary model to study PTH-induced signaling and differentiation. Cells were treated with PTH to evaluate its effects on signaling pathways and cellular outcomes. The role of Src kinase in PTH-mediated YAP regulation was investigated, with a focus on YAP-Y428 phosphorylation.

first: Sara

last: Monaci

first: Mengrui

last: Wu

first: Hiroyuki

last: Okada

first: Kedkanya

last: Mesil

first: Byeong-Rak

last: Keum

first: Maisa Monseff

last: Rodrigues da Silva

first: Clifford

middle: J

last: Rosen

first: Francesca

last: Gori


title: Spatial Coding Dysfunction & Network Instability in the Aging Medial Entorhinal Cortex

city: San Francisco

first: Jeremy

middle: Michael

last: Shea

state: CA

address: 513 Parnassus Avenue

department: Anatomy

institute: University of California, San Francisco

summary: Across species, spatial memory declines with age, possibly reflecting altered hippocampal and medial entorhinal cortex (MEC) function. However, the integrity of cellular and network-level spatial coding in aged MEC is unknown. Here, we leveraged electrophysiology to assess MEC function in young, middle-aged, and aged mice navigating virtual environments. In aged grid cells, we observed impaired stabilization of context-specific spatial firing, correlated with spatial memory deficits. Additionally, aged grid networks shifted firing patterns often but with poor  alignment to context changes. Aged spatial firing was also unstable in an unchanging environment. In these same mice, we identified 462 genes differentially expressed with age in MEC, 61 of which had expression correlated with spatial firing stability. These genes were interneuron-specific and related to synaptic transmission. Together, these findings identify coordinated transcriptomic, cellular, and network changes in MEC implicated in impaired spatial memory in aging.

overall_design: Neuronal nuclei were isolated from subdissected MECs to compare transcriptomes of young, mature, and aged mice with electrophysiological recordings.

middle: M


title: The transcription factor BATF pioneers the differentiation program of cytolytic effector CD8+ T cells through the direct interaction with IRF4 (CUT&RUN)

city: Kanazawa

first: Sotaro

last: Fujisawa

state: Ishikawa

address: 13-1 Takara-machi

institute: Kanazawa University

summary: The transcription factor BATF plays critical roles in the differentiation of various immune cells, including CD8+ T cells. Here, we demonstrated that BATF controls epigenomic and transcriptomic reprogramming of CD8+ T cells at an early phase of acute viral infection, thereby promoting the differentiation of cytolytic effector CD8+ T cells. Loss of BATF drastically perturbed gene expression, chromatin accessibility, and the bindings of key transcription factors including Jun, T-bet, and IRF4. The direct interaction with IRF4 was essential for BATF-mediated effector differentiation, as the BATF mutant lacking this interaction failed to induce proper chromatin remodeling and proliferation of antigen-specific CD8+ T cells. Notably, IRF4 binding was exhaustively dependent on BATF, whereas BATF retained binding capacity even in IRF4-deficient CD8+ T cells. Furthermore, BATF initiated chromatin remodeling in the absence of IRF4, whereas subsequent dynamic epigenomic reorganization required IRF4. Our data proposed that BATF serves as a “pioneer transcription factor” spearheading the reorganization of chromatin architecture upon antigen encounter, followed by further rearrangement of epigenomic and transcriptomic landscapes through the cooperation with IRF4.

overall_design: This submission contains the CUT&RUN portion of the data. There are three datasets described below. (1) Wild-type and Batf-deficient P14 cells were FACS-sorted at days 0 and 3 post-infection with LCMV Armstrong. The bindings of BATF, IRF4, T-bet, JunB, JunD, and FoxO1 were analyzed. (2) CD4cre and IRF4-conditional knockout P14 cells were FACS-sorted at day 3 post-infection with LCMV Armstrong. The bindings of BATF were analyzed. (3) Batf-deficient P14 cells retrovirally transduced with Batf or Batf mutants were cultured in vitro. RV+ cells were FACS-sorted 3 days after RV transduction and the bindings of BATF and IRF4 were examined.

first: Yamato

last: Tanabe

first: Makoto

last: Kurachi


title: Transcriptional responses to nitric oxide are widescale and source-dependent (calcium)

first: Joseph

last: Schindler

overall_design: RNA-seq analysis of HEK293 cells overexpressing NOS isoforms activated by calcium

first: Puneet

last: Seth

first: Richard

last: Premont

first: Jonathan

last: Stamler


title: The transcription factor BATF pioneers the differentiation program of cytolytic effector CD8+ T cells through the direct interaction with IRF4 (ATAC-seq)

overall_design: This submission contains the ATAC-seq portion of the data. There are three datasets described below. (1) Wild-type and Batf-deficient P14 cells were FACS-sorted at days 0 and 3 post-infection with LCMV Armstrong. (2) CD4cre and IRF4-conditional knockout P14 cells were FACS-sorted at day 3 post-infection with LCMV Armstrong. (3) Chromatin accessibilities of Batf-deficient P14 cells retrovirally transduced with Batf or Batf H55Q mutant at day 4 post-infection with LCMV Armstrong.


title: The transcription factor BATF pioneers the differentiation program of cytolytic effector CD8+ T cells through the direct interaction with IRF4 (RNA-seq)

overall_design: Wild-type and Batf-deficient P14 cells were FACS-sorted at days 0 and 3 post-infection with LCMV Armstrong and subsequently analyzed by RNA-seq.


title: Regulation of airway fumarate by S. aureus promotes pneumonia

status: Public on Jul 10 2025

city: Newark

first: Tania

last: Wong Fok Lung

state: New Jersey

address: 205 South Orange Avenue

department: Department of Microbiology, Biochemistry & Molecular Genetics

institute: Center for Immunity and Inflammation, Rutgers NJ Medical School

summary: Staphylococcus aureus is a leading cause of healthcare-associated pneumonia, contributing significantly to morbidity and mortality worldwide. As a ubiquitous colonizer of the upper respiratory tract, S. aureus must undergo substantial metabolic adaptation to achieve persistent infection in the distinctive microenvironment of the lung. We observed that fumC, which encodes the enzyme that converts fumarate to malate, is highly conserved with low mutation rates in S. aureus isolates from chronic lung infections. Fumarate, a pro-inflammatory metabolite produced by macrophages during infection, is regulated by the host fumarate hydratase (FH) to limit inflammation. Here, we demonstrate that fumarate, which accumulates in the chronically infected lung, is detrimental to S. aureus, blocking primary metabolic pathways such as glycolysis and oxidative phosphorylation (OXPHOS). This creates a metabolic bottleneck that drives bacterial FH (FumC) activity for airway adaptation. FumC not only degrades fumarate but also directs its utilization into critical pathways including the tricarboxylic acid (TCA) cycle, gluconeogenesis and hexosamine synthesis to maintain metabolic fitness and form a protective biofilm. Itaconate, another abundant immunometabolite in the infected airway enhances FumC activity, in synergy with fumarate. In a mouse model of pneumonia, a DfumC mutant displays significant attenuation compared to its parent and complemented strains, particularly in fumarate- and itaconate-replete conditions. Our findings underscore the pivotal role of immunometabolites in promoting S. aureus pulmonary adaptation.

overall_design: WT S. aureus USA300 LAC was grown in LB with or without 100 mM fumarate to late exponential phase. Bacterial pellets were lysed and RNA isolated. A ribosomal RNA-depleted cDNA library was prepared and sequenced with Illumina HiSeq.

last: Lung

first: Shwetha Hara

last: Sridhar


title: Myeloid cell coagulation factor Xa-protease activated receptor 2 signaling inhibition expands progenitor exhausted T-cells in the tumor microenvironment

city: Mainz

first: Federico

last: Marini

address: Obere Zahlbacher Strasse 69

department: Institute of Medical Biostatistics, Epidemiology and Informatics (IMBEI)

country: Germany

institute: University Medical Center - Mainz

summary: Coagulation protease signaling within the tumor-microenvironment (TME) causes cancer immune evasion and impairs immune checkpoint-inhibitor therapy. Tumor-associated macrophages produce factor X and drive immune-evasive protease activated receptor-2 (PAR2) signaling. Myeloid FXa-PAR2 signaling promotes the enrichment of resident-like macrophages displaying an immunosuppressive repair phenotype within the TME of mice with genetically induced spontaneous breast cancer development. Conversely, loss of FXa-PAR2 signaling favors the expansion of monocyte-derived macrophage subsets relevant for DNA-sensing, autophagy and cGAS-STING-IFNβ mediated stimulation of anti-tumor immunity. Thereby FXa suppresses the function of CD103+ dendritic cells relevant for priming, reactivation, and expansion of CD8+ T-cells, including antigen-experienced progenitor exhausted T-cells. Our findings thus emphasize the translational potential of FXa inhibition to synergize with immunotherapy.ompacted abstract

overall_design: CD11c+ cells or T cells from the TME of wild-type vs Fxa-PAR2 signaling deficient (PAR2 G37I) mice were processed for single-cell sequencing on the 10x Genomics platform

first: Claudine

last: Graf

first: Hartmut

last: Weiler

first: Wolfram

last: Ruf


title: SMAD3 and p300 complex scaffolding by long non-coding RNA LIMD1-AS1 promotes TGF-β-induced breast cancer cell plasticity [CRISPR screen, inhibition]

status: Public on Jul 08 2025

city: Solna

first: Bernhard

last: Schmierer

state: (optional)

address: Biomedicum 9B, Solnavagen 9

department: Medical Biochemistry and Biophysics

country: Sweden

institute: Karolinska Institutet

summary: Transforming growth factor (TGF)-β signaling enhances cancer cell plasticity by inducing epithelial-to-mesenchymal transition (EMT). Here, we identified a TGF-β-induced long non-coding RNA, LIMD1 Antisense RNA 1 (LIMD1-AS1) that strengthens the SMAD-mediated transcriptional response to TGF-β. LIMD1-AS1 expression is upregulated in breast cancer tissues compared to normal breast tissues, and high LIMD1-AS1 expression is associated with poor prognosis in breast cancer patients. Depletion of LIMD1-AS1 hinders TGF-β-induced EMT, migration, and extravasation of breast cancer cells. Mechanistically, LIMD1-AS1 promotes the interaction between SMAD3 and its transcriptional coactivator p300, thereby enhancing SMAD3 transcriptional activity and TGF-β/SMAD signaling. We demonstrated that LIMD1-AS1 binds to the MAD homology 2 (MH2) domain of SMAD3 and the interferon-binding domain (IBiD) of p300. Displacing LIMD1-AS1 from p300 by its competitor interferon regulatory factor 3 (IRF3) suppressed the effects of LIMD1-AS1 on potentiating TGF-β/SMAD signaling. Furthermore, blockage of p300 acetyltransferase activity with a pharmacological inhibitor A-485 reduced the ability of LIMD1-AS1 to enhance SMAD3 transcriptional activity, TGF-β-induced EMT, and migration. This study identifies LIMD1-AS1 as a novel stimulator of TGF-β signaling by establishing a positive feedback loop and highlights its potential as a therapeutic target for breast cancer.

overall_design: CRISPR-inhibition screen for a custom set of lncRNAs. MDA-MB231 expressing a TGF-β inducible GFP reporter and dCas9-KRAB(ZIM3) were transduced with a guide library. An early time point (ETP) control sample was taken at day 5 post-transduction. At day 7 post transduction, cells were treated with TGF-β for 24 hours. An unsorted control sample was taken, and the 15% highest and lowest GFP expressors were sorted. The screen was performed in two replicates.

first: Chuannan

last: Fan

first: Davy

last: Cats

first: Miriam

last: Selle

first: Olga

last: Khorosjutina

first: Soniya

last: Dhanjal

first: Hailiang

last: Mei

first: Peter

last: ten Dijke

first: Qian

last: Wang


title: Reproducibility of PD patient-specific midbrain organoid data for in vitro disease modelling (passages)

city: Belval

first: Matthieu

last: Gobin

address: 6, avenue du Swing

country: Luxembourg

institute: LCSB

summary: Midbrain organoids are advanced in vitro cellular models for disease modelling. They have been used successfully over the past decade for Parkinson’s disease (PD) research and drug development. The three-dimensional structure and multicellular composition allow disease research under more physiological conditions than is possible with conventional 2D cellular models. However, there are concerns in the field regarding the organoid batch-to-batch variability and thus the reproducibility of the results. In this manuscript, we generate multiple independent midbrain organoid batches derived from healthy individuals or GBA-N370S mutation-carrying PD patients to evaluate the reproducibility of the GBA-N370S mutation-associated PD transcriptomic and metabolic signature as well as selected protein abundance. Our analysis shows that GBA-PD-associated phenotypes are reproducible across organoid generation batches and time points. This proves that midbrain organoids are not only suitable for PD in vitro modelling, but also represent robust and highly reproducible cellular models.

overall_design: Comparative gene expression analysis of Parkinson's disease patients carrying genetic variant in the GBA1 genes and healthy individuals. RNAseq was performed on midbrain organoids from cell lines (WT or GBA PD) at difference passages and coming from distinct individual organoid generation batches (early passage = batches 1-4; late passage = batches 5-8).

first: Elisa

last: Zuccoli

first: Haya

last: Al Sawaf

first: Mona

last: Tuzza

first: Sarah

last: Nickels

first: Alise

last: Zagare

first: Jens C.

last: Schwamborn


title: Targeting neuronal FTL1 rescues cognitive impairments in aging

city: Stanford

first: Julien

last: Couthouis

address: 279 Campus Dr

department: Genetics

institute: Stanford University

summary: Understanding cellular and molecular drivers of age-related cognitive decline is necessary to identify targets to restore cognition at old age. Here we report that ferritin light chain 1 (FTL1) is a pro-aging neuronal factor that impairs cognition. Targeting neuronal FTL1 in the hippocampi of aged mice elicits synaptic and metabolic-related molecular changes and rescues cognitive impairments. Our data identify neuronal FTL1 as a key molecular mediator of cognitive rejuvenation.

overall_design:
To assess the effect of mimicking an age-related increase in neuronal FTL1, young mice were given bilateral stereotaxic injections of high titer lentivirus encoding Ftl1 or GFP under the control of the neuron-specific Syanpsin-1 promoter into their hippocampi. We then performed expression profiling analysis using data obtained from neuronal nuclei RNA-seq of young mice overexpressing Ftl1 or GFP (controls).

To explore the potential benefit of targeting the age-related increase in hippocampal FTL1, aged mice were given bilateral stereotaxic injections of high-titer lentivirus encoding shRNA sequences targeting either Ftl1 or luciferase control into their hippocampus . We then performed expression profiling analysis using data obtained from neuronal nuclei RNA-seq of controls and Ftl1 KD aged mice.

To assess the molecular changes in neurons that occur during aging in the hippocampus. NeuN-positive neuronal nuclei were isolated by fluorescence activated cell sorting (FACS) from hippocampi of young (3 months) and aged (18 months) wt mice. We then performed expression profiling analysis using data obtained from neuronal nuclei RNA-seq of young and old wt mice.

first: Laura

last: Remesal

first: Karishma

middle: B

last: Pratt

first: Juliana

last: Sucharov-Costa

first: Saul

middle: A

last: Villeda


title: Clonal Expansion and Diversification of Germinal Center and Memory B Cell Responses to Booster Immunization in Primates

status: Public on Jul 07 2025

city: New York

first: Gabriela

last: Silva Santos

state: NY

address: 1230 York Avenue

institute: The Rockefeller University

summary: Effective vaccines elicit B cell clonal expansion in germinal centers (GCs) that produce memory B cells and antibody secreting plasma cells. Studies in mice indicate that, whereas the plasma cell compartment is enriched for cells producing high affinity antibodies, the memory pool is more diverse and contains only a relatively small proportion of higher affinity cells. Upon boosting, murine memory B cells producing high affinity antibodies tend to develop into plasma cells but few if any re-enter GCs. However, mice live for only a few weeks in nature, and in keeping with the rather limited requirement for immune memory, this compartment comprises only 1–2% of all B cells. In contrast, memory accounts for nearly 50% of all B cells in primates. Here we examine memory and GC B cell responses in rhesus macaques immunized and boosted ipsilaterally or contralaterally with an mRNA vaccine encoding severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Spike protein. The neutralizing activity of antibodies cloned from the memory compartment, and the size of the compartment, was independent of the site of boosting. Moreover, in primates, memory B cells enter and undergo iterative expansion in newly developing GCs when boosting is at a site distal to the site of priming. Thus, in primates, high affinity memory B cells constitute a reservoir that actively participates in further development of immunity irrespective of the anatomical site of vaccine boosting.

overall_design: Single-cell RNA-seq libraries were performed to document the gross circulating memory B cell repertiore of the Rhesus macaues used in our investigation. Data are from 6 male ~7-year-old Rhesus macaques.

first: Lachlan

middle: P

last: Deimel

first: Yoshiaki

last: Nishimura

first: Viren

last: Baharani

first: Brianna

last: Hernandez

first: Thiago

middle: Y

last: Oliveira

first: Andrew

last: MacLean

first: Marie

last: Canis

first: Sadman

last: Shawraz

first: Anna

last: Gazumyan

first: Harald

last: Hartweger

first: Paul

middle: D

last: Bieniasz

first: Theodora

last: Hatziioannou

first: Malcolm

last: Martin

first: Michel

last: Nussenzweig


title: NR2F1 underlies persistence of residual disease in BRAF-mutant melanoma

city: Philadelphia

last: Aplin

state: PA

address: 233 South 10th St.

institute: Thomas Jefferson University

summary: Despite the clinical success of targeted therapy inhibitors, tumor responses are transient, and a subpopulation of residual drug-tolerant cells may seed resistance. Understanding minimal residual disease (MRD) mechanisms and the connection with dormancy-like traits may guide strategies to target drug-tolerant persister cells and optimize target therapies. Here, we studied the relationship between persister cell tolerance to BRAF and MEK inhibitors (BRAFi + MEKi) and expression of nuclear receptor subfamily 2 group F member 1 (NR2F1), which has been linked to tumor dormancy in the context of cutaneous melanoma. In previously published RNA-seq datasets, NR2F1 expression was enriched in melanoma samples following BRAF inhibitor and MEK inhibitor (BRAFi + MEKi) treatment compared to pre-treatment patient-matched samples. We also found that NR2F1 is highly expressed in the residual drug-tolerant cell state following BRAFi + MEKi treatment in patient-derived and cell line-derived melanoma xenografts. Additionally, xenografts overexpressing NR2F1 displayed higher tumor growth and poorer animal survival following BRAFi + MEKi treatment compared to control xenografts expressing basal levels of NR2F1. In vitro, NR2F1-overexpressing cells showed increased tumor proliferation and higher expression of cell cycle and survival-related proteins on targeted therapy, such as phosphorylation of both RB and S6K proteins. In addition, NR2F1, highly expressed in invasive melanoma cells, was sufficient to promote invasiveness following BRAFi + MEKi in 3D tumor spheroid assays. Furthermore, when compared to young mice, NR2F1 was overexpressed in tumor xenografts in an old microenvironment. The use of shRNA NR2F1 in older mice led to slower tumor growth and the highest survival in animals on BRAFi + MEKi treatment. We also tested a pharmacological approach to target drug-tolerant persister cells that overexpress NR2F1 on BRAFi + MEKi treatment. The inhibition of mTORC1 delayed NR2F1-overexpressing cell proliferation compared to non-NR2F1-overexpressing cells on targeted therapy. Altogether, our findings suggest that NR2F1 plays a role in the persistence of MRD in melanoma, indicating that targeting NR2F1 expression could improve targeted therapy outcomes in melanoma patients.

overall_design: RNA was obtained from 1205LuTR-NR2F1, WM793TR-NR2F1, and A375TR-NR2F1 cell lines treated with DMSO (control) -/+ BRAF plus MEK inhibitors (Combo), -/+ doxycycline (DOX). Comparison of doxycycline(DOX)-inducible NR2F1 overexpression melanoma cells lines treated with BRAF and MEK inhibitors (Combo) with or without DOX for 72 hours.

first: Manoela

last: Tiago

first: Timothy

last: Purwin


title: Peptide Driven Identification of TCRs (PDI-TCR) reveals dynamics and phenotypes of CD4 T cells in tuberculosis [TCR-Seq]

city: La Jolla

first: Bjoern

last: Peters

address: 9420 Athena Cir

institute: La Jolla Institute for Immunology

summary: We developed the Peptide-Driven Identification of TCRs (PDI-TCR), an approach that leverages antigen-specific peptide pools, bulk TCR sequencing, and statistical analyses to pinpoint antigen-specific TCRs. We discerned antigen-specific TCRs within a group of active tuberculosis (ATB) patients and individuals with a positive Interferon-γ release assay (IGRA+). We found Mtb-specific effectors to have an HLA-DR+ Th1* phenotype, and to be exclusive to active disease. Conversely, HLA-DR- Mtb-specific T cells appeared in Th1 cells in both ATB and IGRA+ cohorts. We also identified Cross-reactive T cells, that were abundant ex vivo regardless of disease state having a cytotoxic phenotype.

overall_design:
PBMCs were stimulated with a Mtb-specific (MTB300) or a PT-specific (PT132) peptide pool and cultured for 14 days. Cells were harvested and their DNA was extracted for bulk survey TCR sequencing using the immunoseq platform. Simultaneously Ex vivo PBMCs from 4 ATB donors were subjected to CD4 isolation and deep TCR sequencing.

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


title: Pentoxifylline and Norcantharidin Synergistically Suppress Melanoma Growth in Mice: A Multi-Modal In Vivo and In Silico Study

city: , Nueva Industrial Vallejo, Gustavo A. Madero

first: Israel

last: Lara-Vega

state: Ciudad de México, CDMX

address: v. Wilfrido Massieu 399

country: Mexico

institute: IPN

summary: Background: Melanoma is a highly aggressive skin cancer with limited therapeutic re-sponse. Targeting intracellular signaling pathways and promoting tumor cell differen-tiation are promising therapeutic strategies. Pentoxifylline (PTX) and norcantharidin (NCTD) have demonstrated antitumor properties, but their combined mechanisms of action in melanoma remain poorly understood. Methods: The effects of PTX (30 and 60 mg/kg) and NCTD (0.75 and 3 mg/kg), administered alone or in combination, in a DBA/2J murine B16-F1 melanoma model via intraperitoneal and intratumoral (IT) routes were evaluated. Tumor growth was monitored, and molecular analyses included RNA se-quencing, immunofluorescence quantification of PI3K, AKT1, mTOR, ERBB2, BRAF, and MITF protein levels, and molecular docking simulations were performed. Results: Combination therapy significantly reduced tumor volume compared to monotherapies, with relative tumor volume decreasing from 18.1 in the IT control group to 0.6 in the IT combination-treated group. RNA-seq revealed over 3,000 differentially expressed genes in intratumoral treatments, with enrichment in pathways related to oxidative stress, immune response, and translation regulation (KEGG and Reactome analyses). Minimal transcript-level changes were observed for BRAF and PI3K/AKT/mTOR genes; however, immunofluorescence showed reduced total and phosphorylated levels of PI3K, AKT1, mTOR, BRAF, and ERBB2. MITF protein levels and pigmentation increased, especially in PTX-treated groups, indicating enhanced melanocytic differentiation. Docking analyses predicted direct binding of both drugs to PI3K, AKT1, mTOR, and BRAF, with affinities ranging from -5.7 to -7.4 kcal/mol. Conclusions: The combination of PTX and NCTD suppresses melanoma progression through dual mechanisms: inhibition of PI3K/AKT/mTOR signaling and promotion of tumor cell differentiation.

overall_design: Inbred DBA/2J mice (6–8 weeks old) were obtained. The animals were housed in polycarbonate cages with sawdust bedding under controlled conditions (23°C, 40–60% humidity) and maintained on a 12-hour light:12-hour dark cycle. Food and water were provided ad libitum, with rodents receiving NUTRICUBOS Rodent Chow Cargill® (SAGARPA Authorization A-0207-246) and potable water.  The study included two main experimental groups: (1) an intraperitoneal (IP) treatment group, in which 7 × 10⁵ cells (melanoma B16-F1 cells (ATCC® CRL-6323™) ) were subcutaneously implanted on the right flank of the mouse, and therapeutic agents were administered intraperitoneally; (2) an intratumoral (IT) treatment group, in which 7 × 10⁵ cells ( melanoma B16-F1 cells (ATCC® CRL-6323™) ) were subcutaneously implanted on the right flank of the mouse, and drugs were administered directly into the tumor. On Day 0, cells were implanted, and once a visible and palpable tumor developed, treatment groups were sex-matched and randomly assigned, and pharmacological treatment was initiated. For the IP treatment group, animals were randomly assigned to the following subgroups: Subgroup 1 (control), receiving sterile saline solution; Subgroup 2, receiving PTX at 60 mg/kg; Subgroup 3, PTX at 30 mg/kg; Subgroup 4, NCTD at 3 mg/kg; Subgroup 5, a combination of PTX at 60 mg/kg and NCTD at 3 mg/kg; Subgroup 6, PTX at 60 mg/kg combined with NCTD at 0.75 mg/kg; and Subgroup 7, NCTD at 0.75 mg/kg. For the IT treatment group, animals were divided into four subgroups as follows: Subgroup 1 (control), receiving DMSO; Subgroup 2, PTX at 60 mg/kg; Subgroup 3, NCTD at 3 mg/kg; and Subgroup 4, PTX at 60 mg/kg combined with NCTD at 3 mg/kg.

first: Minerva

last: Najera-Martinez

first: Armando

last: Vega-Lopez


title: Ethanol increases diffuse amyloid plaque load and impairs memory in the 5xFAD mouse model of Alzheimer’s disease

city: Rochester

first: Ania

middle: K.

last: Majewska

address: 601 Elmwood Ave

department: Department of Neuroscience

institute: University of Rochester Medical Center

summary: Alzheimer’s disease (AD) is the most common age-related dementia. Lifestyle factors, including alcohol use, can increase the risk of AD. While human studies demonstrate that alcohol use can negatively impact AD risk and disease progression, the underlying alcohol-dependent mechanisms that increase Aβ burden and impair cognition remain elusive. We have recently shown that alcohol (ethanol)  can acutely affect microglial dynamics, which are critical to microglial function, and many other studies have reported inflammatory activation of microglia after long-term alcohol exposure in both humans and animal models. Here, we administered 4 weeks of ethanol at dosages that mimic human binge drinking to 2.5-month-old male 5xFAD mice, a common mouse model of AD. After a two-week abstinence period, we performed behavior assays and analyzed amyloid pathology and microglial transcriptome in the hippocampus and morphology in the subiculum  where amyloid pathology develops earlier than in other brain regions. We found that ethanol exposure facilitated amyloid pathology and worsened cognitive function in 5xFAD mice, while microglial transcriptomic landscape, arborization and phagocytosis appeared unchanged. Overall, our results suggest that pronounced ethanol exposure, when started early in the disease before amyloid pathology is established, can worsen AD progression in an amyloidosis model.

overall_design: To investigate whether long-term exposure to alcohol affected microglial transcriptome, microglia from young adult male 5xFAD mice treated with either ethanol or saline were isolated by Fluorescence activated cell sorting (FACS), their total RNA were sequenced and subsequently analyzed.

first: Linh

middle: H

last: Le

first: Nisha

last: Arya

first: Florence

last: Varodayan

first: M

middle: K

last: O’Banion


title: A Human-Mouse Atlas of Intrarenal Myeloid Cells in Lupus Nephritis Identifies Conserved Disease-Associated Macrophages

city: Cambridge

first: Nir

last: Hacohen

address: 415 Main St

institute: Broad Institute of MIT and Harvard

summary: Monocytes and macrophages in patients with lupus nephritis exhibit altered behavior compared to healthy kidneys. How to optimally use mouse models to develop treatments targeting these cells is poorly understood. This study compared intrarenal myeloid cells in four mouse models and 155 lupus nephritis patients using single-cell profiling, spatial transcriptomics, and functional studies. Across mouse models, monocyte and macrophage subsets consistently expanded or contracted in disease. A subset of murine classical monocytes expanded in disease; these cells, expressed Cd9, Spp1, Ctsd, Cd63, Apoe, and Trem2, genes associated with tissue injury in other organs and that play roles in inflammation, lipid metabolism, and tissue repair. Resident macrophages expressed similar genes in clinical disease. In humans, we identified analogous disease-associated monocytes and macrophages that were associated with kidney histological subtypes and disease progression, sharing gene expression and localizing to similar kidney microenvironments as in mice. This cross-species analysis supports the use of mouse functional studies for understanding human lupus nephritis.

overall_design:
This experimental study investigated lupus nephritis using two types of mouse models: male mice with Tlr7-overexpression (B6.Sle1.Yaa and NZW/BXSB strains) and female mice with lymphoid-expansion (NZB/W and MRL/lpr strains) before and after the onset of clinical nephritis. To monitor disease, urine samples were collected biweekly for proteinuria assessment and blood samples taken for BUN levels. Clinical nephritis was defined as fixed proteinuria >300mg/dl for two weeks, while mice with BUN >30 mg/dl were excluded for terminal renal failure. For kidney analysis, mice were perfused with PBS, their kidneys harvested and dissociated into single-cell suspensions, and myeloid or CD45+ cells isolated using magnetic beads for flow cytometry or FACS sorting.
(contributor) The Kidney Precision Medicine Project
(contributor) The Accelerating Medicines Partnership RA-SLE network

last: Hoover

first: Chirag

last: Raparia

first: David

last: Lieb

first: Yochay

last: Tzur

first: Joyce

last: Kang

first: Arnon

last: Arazi

first: Rollin

last: Leavitt

first: Sujal

middle: I

last: Shah

first: Daimon

last: Simmons

first: Stephen

last: Li

first: Michael

first: Thomas

last: Eisenhaure

last: Few-Cooper

first: Saisram

last: Gurajala

first: Abraham

last: Sonny

first: Jeffrey

last: Hodgin

first: Joel

last: Guthridge

first: Andrea

last: Fava

first: Robert

last: Clancy

first: Chaim

last: Putterman

first: Peter

last: Izmirly

first: H

last: Belmont

first: Kenneth

last: Kalunian

first: Diane

last: Kamen

last: Wofsy

first: Jill

last: Buyon

first: Judith

last: James

first: Michelle

last: Petri

first: Betty

last: Diamond

first: Soumya

last: Raychaudhuri

first: Shai

last: Shen-Orr

first: Anne

last: Davidson


title: The autophagy-targeting compound V46 enhances antimicrobial responses to Mycobacteroides abscessus by activating transcription factor EB

city: Daejeon

first: Taylor

last: Roh

address: 266, Munhwa-ro

department: Microbiology

institute: Chungnam National University

summary: Mycobacteroides abscessus (Mabc) is a rapidly growing nontuberculous mycobacterium that poses a considerable challenge as a multidrug-resistant pathogen causing chronic human infection. Effective therapeutics that enhance protective immune responses to Mabc are urgently needed. This study introduces trans-3,5,4′-trimethoxystilbene (V46), a novel resveratrol analogue with autophagy-activating properties and antimicrobial activity against Mabc infection, including multidrug-resistant strains. Among the resveratrol analogues tested, V46 markedly inhibited the growth of both rough and smooth Mabc strains in murine bone marrow-derived macrophages and in the lungs of infected mice. Additionally, V46 significantly reduced Mabc-induced increases in chemokine and pro inflammatory cytokine levels in macrophages and in vivo during infection. Mechanistic analysis showed that V46 suppressed the activation of the AKT-mammalian target of rapamycin signaling pathway and enhanced AMP-activated protein kinase signaling in Mabc-infected cells. Notably, V46 activated autophagy and nuclear translocation of transcription factor EB, which is crucial for antimicrobial host defenses against Mabc. Furthermore, V46 upregulated genes associated with autophagy and lysosomal biogenesis in Mabc-infected bone marrow-derived macrophages. The combination of V46 and rifabutin exerted a synergistic antimicrobial effect. These findings identify V46 as a candidate host-directed therapeutic for Mabc infection that activates autophagy and lysosomal function via transcription factor EB.

overall_design: To investigate the function of V46 in the Mycobacteroides abscessus-infected mice, we treated V46 to Mabc-infected bone marrow-derived macrophages.


title: Spatiotemporal profiling reveals the impact of caloric restriction in the aging mammalian brain

first: Zehao

last: Zhang

address: 1230 York Ave, The Rockefeller University

summary: Aging induces functional declines in the mammalian brain, increasing its vulnerability to cognitive impairments and neurodegenerative disorders. Among various interventions to slow aging and delay age-related diseases, caloric restriction (CR) consistently extends lifespan across species. However, the specific molecular and cellular mechanisms through which CR benefits the aging brain remain unclear. In this study, we performed spatiotemporal profiling of mouse brains to uncover detailed mechanisms underlying the anti-aging effects of CR. We analyzed the transcriptional states of over half million single cells from mouse brain samples across various ages and in response to CR treatment. Monitoring the dynamics of over 300 transcriptionally distinct cellular states, we captured the temporal dynamics of cellular states particularly vulnerable to aging and those rescued by CR (e.g., CR delays the expansion of inflammatory glia and preserves neurogenesis cells). Further spatial transcriptome analysis revealed gene expression and cellular dynamics across brain regions in aged mice upon CR treatment, uncovering region-specific anti-aging effects. In summary, our spatiotemporal mouse brain profiling delineated highly cell-type-specific molecular pathways in response to aging and CR, shedding light on the nuanced regulatory roles of CR across different cell types and brain regions.

overall_design:
Single nucleus RNA-seq profiling for caloric restricted and ad libitum C57BL/6 mouse brain cells at 12,18,24 months.
Spatial transcriptomic profiling for caloric restricted and ad libitum C57BL/6 mouse brain cells at 24 months.

first: Alexander

last: Epstein

first: Chloe

last: Schaefer

first: Abdulraouf

last: Abdulraouf

first: Weirong

last: Jiang

first: Wei

last: Zhou

first: Junyue

last: Cao


title: Entospletinib modulates spatial gene expression in kidney immune microenvironments during injury and repair

city: Calgary

first: Esteban

middle: Enrique

last: Elias

state: Alberta

address: 3300 Hospital Dr

department: Medicine

country: Canada

institute: University of Calgary

summary: Spatial transcriptomic profiling was performed on mouse kidney sections using the NanoString GeoMx Digital Spatial Profiler with the Whole Transcriptome Atlas. Mice were subjected to ischemia-reperfusion injury (IRI) and treated with the SYK inhibitor Entospletinib or vehicle control. Regions of interest were selected from the renal cortex and medulla in two mice per condition at days 1, 7, and 14 post-injury. The dataset captures spatial gene expression dynamics during kidney injury and repair, and the effects of SYK inhibitio

overall_design: C57BL/6 male mice were subjected to unilateral renal ischemia-reperfusion injury (IRI) and pretreated with Entospletinib or vehicle control. Kidneys were collected at days 1, 7, and 14 post-injury (n=2 mice per condition per timepoint). FFPE sections were processed using the NanoString GeoMx Whole Transcriptome Atlas. For each mouse and condition, 2–3 regions of interest (ROIs) were selected from both the cortex and medulla. Tubular segments were identified based on CD10 and/or PanCK positivity, and macrophage segments were selected based on IBA1 staining.

first: Esteban E

first: Daniel A

last: Muruve


title: Effect of the SYK Inhibitor Entospletinib on Renal Inflammation and the Transition from Acute Kidney Injury to Chronic Kidney Disease Induced by Ischemia-Reperfusion Injury

summary: We used single-cell RNA sequencing with the Evercode™ WT kit (Parse Biosciences) to profile kidney immune cells in a mouse model of ischemia-reperfusion injury (IRI), with or without treatment with the SYK inhibitor Entospletinib. The dataset captures immune dynamics at early and late stages of injury and was used to identify leukocyte populations associated with inflammation and its resolution, as well as the immunomodulatory effects of SYK inhibition in vivo.

overall_design: Kidneys were collected from C57BL/6 mice at days 1, 7, and 14 after ischemia-reperfusion injury (IRI), with or without Entospletinib treatment. Single-cell suspensions were pooled from 3 mice per condition. Live immune cells were enriched by FACS, fixed, and processed using the Evercode™ WT kit (Parse Biosciences) for single-cell RNA sequencing.

middle: E

first: Daniel


title: Human Papillomavirus Genomes Associate with Active Host Chromatin during Viral Genome Maintenance [ATAC-seq]

city: Bethesda

first: Alison

middle: Anne

last: McBride

state: MD

address: 33 North Drive

department: DIR

institute: NIAID

summary: Human papillomaviruses (HPVs) maintain their genomes as minichromosomes in the nuclei of infected keratinocytes. This study investigates the association of HPV31 genomes with host chromatin using both HiC and 4C-seq chromosome conformation capture techniques. We show that HPV31 genomes preferentially associate with transcriptionally active A compartments of host chromatin, regions of open chromatin defined by ATAC-seq, and super-enhancers defined by Brd4 and H3K27ac ChIP-seq. The viral genome association sites were also highly correlated with genomic loci previously identified as common HPV integration sites in cervical cancers. Recent studies have shown that transcriptionally active sites are prone to dsDNA breaks, and we find a strong correlation among dsBREAK datasets with transcriptionally active and open regions of host chromatin and the HPV31 genome association sites defined in our study. These findings suggest that HPV genomes associate with cellular transcriptional epicenters to maintain active viral gene expression during persistent infection, but also indicate that the susceptibility of these regions to dsDNA breaks could explain their propensity for viral DNA integration in HPV-associated cancers.

overall_design: ATAC-seq analysis of growing and calcium-induced differentiated CIN612-9E cervical keratinocytes that were untreated or treated for 48 hours with 0.5 µM keratinocyte differentiation inducer (KDi) for the differentiated condition only.

first: Alix

last: Warburton

first: Tovah

last: Markowitz

first: JJ

last: Miranda

first: Kinjal

last: Majumder


title: Single-cell level gene expression profiles of enteroendocrine cell lineages, control guts and guts with Xrp1 overexpressed in EEs

city: Tsukuba

first: Ryusuke

last: Niwa

state: Ibaraki

address: 1 Chome-1-1 Tennodai

institute: University of Tsukuba

summary: Differentiated cells exhibit cell plasticity, where they dedifferentiate to stem cells or trans-differentiate into cells of another lineage, when necessary. We studied the cell plasticity of secretory enternendocrine cells (EEs) in the fruit fly Drosophila melanogaster. We resolved single-cell transcriptomics of EEs and cells derived from EEs. Our scRNA-seq data of EE lineages have characterized intermediate cell types derived from EEs. We also specifically focused on a gene called Xrp1 and examined potential changes of all epithelial cell types by EE-specific Xrp1 overexpression (O/E). Our scRNA-seq data of Xrp1 O/E EEs have provided evidence on changes in gene expression profiles of each cell type by Xrp1 O/E in EEs.

overall_design: Flies had EEs lineage traced from adulthood to 7 days of age. Cells from their midguts were collected and isolated by Fluorescence Activated Cell Sorting. Flies with Xrp1 overexpressed in EEs had their midgut cells collected. Cells were proceeded to 10X Genomics scRNA-seq.

first: Qingyin

last: Qian

first: Hayashi

last: Makoto

first: Ken-ichi

last: Kimura

first: Yuya

last: Sanaki


title: Human Papillomavirus Genomes Associate with Active Host Chromatin during Viral Genome Maintenance [4C-seq]

overall_design: 4C-seq in CIN612 cells containing extrachromosomal (9E cells) or integrated (6E cells) HPV31 DNA using the viral genome as bait.


title: Human Papillomavirus Genomes Associate with Active Host Chromatin during Viral Genome Maintenance [Hi-C]

overall_design: Hi-C in CIN612-9E cells containing extrachromosomal HPV31 DNA


title: EBV induces CNS homing of B cells attracting inflammatory T cells

city: Zurich

first: Eanna

last: Fennell

address: Winterthurerstrasse 190

department: Institute of Experimental Immunology

country: Switzerland

institute: University of Zurich

summary: Epidemiological data have identified Epstein-Barr virus (EBV) infection as the main environmental risk factor for the central nervous system (CNS) autoimmune disease multiple sclerosis (MS). However, how EBV infection initiates MS pathogenesis remains unclear. We now demonstrate that EBV differentiates oligoclonal B cells into MS-associated T-bet+CXCR3+ B cells that home to the CNS in humanized mice. Effector memory CD8+ T cells and CD4+ TH17 cells co-migrate to the brain of EBV infected humanized mice. T-bet+CXCR3+ B cells are capable of colonizing submeningeal brain regions in the absence of other lymphocytes and attract T cells. Depletion of this T-bet+CXCR3+ B cell subset with Rituximab significantly decreases lymphocyte infiltration into the CNS. Thus, we suggest that symptomatic primary EBV infection generates B cell subsets that gain access to the CNS, attract T cells and thereby initiate MS.

overall_design: Humanised BRGS-A2DR2 mice were infected with EBV and monitored for 6 weeks. After 6 weeks, spleens (n=3) were dissociated and CD19+ B cells were fluorescence-activated cell sorted (FACS). Joint scRNAseq and scBCRseq libraries were prepared from CD19+ B cells using the 10x Genomics platform.

first: Fabienne

last: Läderach

first: Paul

last: Gueguen

first: Christian

last: Münz


title: ICOS limits memory-like properties and function of exhausted PD-1+ CD8 T cells [ATAC-seq]

first: Dan

last: Filipescu

state: New York

address: 1470 Madison Ave

department: Oncological Sciences

institute: Icahn School of Medicine at Mount Sinai

summary: During persistent antigen stimulation, PD-1+CD8 T cells are maintained by progenitor exhausted PD-1+TCF-1+CD8 T cells (Tpex). Tpex respond to PD-1 blockade, and regulation of Tpex differentiation into more functional Tex is of major interest for cancer immunotherapies. Tpex express high levels of Inducible Costimulator (ICOS), but the role of ICOS for PD-1+CD8 T cell responses has not been addressed. In chronic infection, ICOS-deficiency increased both number and quality of virus-specific CD8 T cells, with accumulation of effector-like Tex due to enhanced survival. Mechanistically, loss of ICOS signaling potentiated FoxO1 activity and memory features of Tpex. ICOS-deficient Tex displayed enhanced survival and improved cytokine production. In chronically-infected mice, ICOS-Ligand blockade expanded effector-like Tex, reduced viral load and potentiated anti-PD-L1 therapy. In a mouse model of hepatocellular carcinoma, ICOS inhibition improved cytokine production by tumor-specific PD-1+CD8 T cells and sensitized tumors to PD-1 targeted therapy. Overall, we show that sustained ICOS costimulation limits CD8 T cell responses during chronic antigen exposure.

overall_design: P14 (LCMV-specific CD8 T cell) electroporated with Cas9/gRNA control or targeting Icos were transfered into mice prior to LCMV c13 infection. Once mice are chronically infected (>42DPI), 2 to 3 mice were pooled per experimental replicate for CD8 T cell isolation from spleen. Progenitor Tpex (CD39neg PD1+)  and differentiated Tex (CD39+ PD1+) P14 control or sgICos were sorted for ATACseq profiling.

first: Etienne

last: Humblin

first: Alice

last: Kamphorst


title: ICOS limits memory-like properties and function of exhausted PD-1+ CD8 T cells [RNA-seq]

summary: During persistent antigen stimulation, PD-1+CD8 T cells are maintained by progenitor exhausted PD-1+TCF-1+CD8 T cells (Tpex). Tpex respond to PD-1 blockade, and regulation of Tpex differentiation into more functional Tex is of major interest for cancer immunotherapies. Tpex express high levels of Inducible Costimulator (ICOS), but the role of ICOS for PD-1+CD8 T cell responses has not been addressed. In chronic infection, ICOS-deficiency increased both number and quality of virus-specific CD8 T cells, with accumulation of effector-like Tex due to enhanced survival. Mechanistically, loss of ICOS signaling potentiated FoxO1 activity and memory features of Tpex. In mice with established chronic infection, ICOS-Ligand blockade resulted in expansion of effector-like Tex and reduction in viral load. In a mouse model of hepatocellular carcinoma, ICOS inhibition improved cytokine production by tumor-specific PD-1+CD8 T cells and delayed tumor growth. Overall, we show that ICOS constrains CD8 T cell responses during chronic antigen exposure.

overall_design: P14 (LCMV-specific CD8 T cell) electroporated with Cas9/gRNA control or targeting Icos were transfered into mice prior to LCMV c13 infection. Once mice are chronically infected (>42DPI), Tpex (CD39neg PD1+), effector-like Tex (CD39+ CX3CR1+ PD1+) and terminal Tex (CD39+ CX3CR1neg PD1+) P14 control or sgICos were sorted for gene expression analysis of bulk  RNAsequencing to understand the molecular impact of ICOS on differentiation of PD-1+ virus-specific CD8 T cells.


title: ICOS limits memory-like properties and function of exhausted PD-1+ CD8 T cells

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

overall_design: Refer to individual Series


title: Antagonistic stem cell fates under stress govern decisions between hair greying and melanoma [scRNA-Seq]

city: Tokyo

first: Yasuaki

last: Mohri

address: 4-6-1 Shirokanedai, Minato-ku

institute: The Institute of Medical Science, The University of Tokyo

summary: The exposome, an individual’s lifelong environmental exposure, profoundly impacts health. Somatic tissues undergo functional decline with age, exhibiting characteristic ageing phenotypes including hair graying and cancer. However, the specific genotoxins, signals and cellular mechanisms underlying each phenotype remain largely unknown. Here, we report that melanocyte stem cells (McSCs) and their niche coordinately determine individual stem cell fate through antagonistic, stress-responsive pathways, depending on the type of genotoxic damage incurred. McSC fate-tracking in mice revealed that McSCs undergo cellular senescence-associated differentiation (seno-differentiation) in response to DNA double-strand breaks (DSBs), resulting in their selective depletion and hair graying, and effectively protecting against melanoma. Conversely, carcinogens can suppress McSC seno-differentiation, even in DSB-harboring cells, by activating arachidonic acid metabolism and the niche-derived KIT ligand, thereby promoting McSC self-renewal. Collectively, the fate of individual stem cell clones - expansion versus exhaustion - cumulatively and antagonistically governs ageing phenotypes through interaction with the niche.

overall_design: Gene expression profiling of the skin epithelium of  young (2 months) and old (24 months) mice (n=4) using single-cell RNA sequencing.

first: Emi

last: Nishimura


title: Deconstructing the Intercellular Interactome in Vascular Dementia with Focal Ischemia for Therapeutic Applications

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: Vascular dementia (VaD), the second-leading cause of dementia, is primarily a white matter ischemic disease with no direct therapies. Cell-cell interactions within lesion sites dictate disease progression or repair. To elucidate key intercellular pathways, we employed a VaD mouse model with focal ischemia replicating many elements of the complex pathophysiology of human VaD, combined with transcriptomic and functional analyses. Integrating cell-type-specific mouse VaD transcriptomes and human VaD snRNA-Seq data, plus a custom ligand-receptor database (4,053 human and 2,032 mouse pairs), conserved dysregulated intercellular pathways in both species were identified. We demonstrate that two intercellular signaling systems, Serpine2-Lrp1 and CD39-A3AR, are disrupted in VaD. Reduced Serpine2 expression enhances oligodendrocyte progenitor cell (OPC) differentiation, promoting repair, while an A3AR-specific agonist—currently in clinical trials for psoriasis—restores tissue integrity and behavioral function in the VaD model. This study reveals intercellular signaling targets and provides a foundation for developing innovative therapies for VaD.

overall_design: Cell-type specific RNA-Seq

first: Min

last: Tian

first: Yang

last: Shen

first: Michal

last: Machnicki

first: Nikole

middle: G

last: Villegas

first: Delaney

middle: R

last: Cooper

first: Natalia

last: Montgomery

first: Ying

last: Cai

first: Jacqueline

last: Haring

first: Ruirui

last: Lan

first: Angelina

last: Yuan

first: Christopher

last: Williams

first: Shino

last: Magaki

first: Harry

middle: V

last: Vinters

first: Ye

last: Zhang

first: Lindsay

last: De Biase

first: Alcino

last: Silva

first: Thomas

last: Carmichael


title: Antagonistic stem cell fates under stress govern decisions between hair greying and melanoma [RNA-Seq]

first: Yasuaki

last: Mohri

overall_design: Gene expression profiling of FACS-purified melanocyte stem cells from mice that were treated with vehicle (three replicates), 5Gy (three replicates), or DMBA (three replicates).

first: Emi

last: Nishimura


title: Single cell analysis of splenic control and ICOS deficient P14 cells from LCMV chronically infected mice

first: Alice

last: Kamphorst

address: 1425 Madison Avenue

department: Immunology and immunotherapy

institute: Icahn school of medicine at Mount Sinai

summary: During persistent antigen stimulation, PD-1+CD8 T cells are maintained by progenitor exhausted PD-1+TCF-1+CD8 T cells (Tpex). Tpex respond to PD-1 blockade, and regulation of Tpex differentiation into more functional Tex is of major interest for cancer immunotherapies. Tpex express high levels of Inducible T-cell Costimulator (ICOS), but the role of ICOS for PD-1+CD8 T cell responses has not been addressed. In chronic infection, ICOS-deficiency increased both number and quality of virus-specific CD8 T cells, with accumulation of effector-like Tex due to enhanced survival. Mechanistically, loss of ICOS signaling potentiated FoxO1 activity and memory features of Tpex. In mice with established chronic infection, ICOS-Ligand blockade resulted in expansion of effector-like Tex and reduction in viral load. In a mouse model of hepatocellular carcinoma, ICOS inhibition improved cytokine production by tumor-specific PD-1+CD8 T cells and delayed tumor growth. Overall, we show that ICOS constrains CD8 T cell responses during chronic antigen exposure.

overall_design: P14 (LCMV-specific CD8 T cell) electroporated with Cas9/gRNA control or targeting Icos were transfered into mice prior to LCMV c13 infection. Once mice are chronically infected (>42DPI), P14 control and sgICos were sorted for scRNA-sequencing (10x)  to understand the molecular impact of ICOS on differentiation of virus-specific PD-1+ CD8 T cells.

first: Etienne

last: Humblin

first: Nataliya

last: Prokhnevska


title: Antagonistic stem cell fates under stress govern decisions between hair greying and melanoma [RNA-seq]

summary: The incidence of diseases, including cancer, increases with age. While age-associated diseases with stem cell exhaustion are potentially antagonistic to cancer development1, the relationship between those is still largely unknown. Here, we report that melanocyte stem cells (McSCs) and their niche coordinately govern the antagonism between poliosis (hair graying) and melanoma. We found that McSCs undergo senescence-associated differentiation (seno-differentiation) in response to DNA double strand breaks (DSBs) such as by ionizing radiation (IR) and ageing upon their activation for self-renewal, leading to their depletion and resultant hair graying at the cost of cancer protection. RNA-seq and functional analysis of the skin exposed to different types of genotoxic stress revealed that activation of the p53-p21 axis and TBK1 pathway by DSBs within McSCs causes their depletion. Comparative analysis of the young vs. aged stem cell niche identified the KIT ligand (KITL/SCF) as a master niche factor for McSC self-renewal. Strikingly, co-exposure of the irradiated skin to carcinogens rescued hair graying by augmenting the secretory phenotype of niche cells to repress McSC seno-differentiation through the dual activation of KIT signaling and arachidonic acid pathway in McSCs. Collectively, our data provide concrete evidence for the phenotypic trade-off between ageing and cancer based on the niche.

overall_design: Gene expression profiling of FACS-purified hair follicle stem cells/hair germ from young and old mice in telogen and early anagen (n=3).


title: Antagonistic stem cell fates under stress govern decisions between hair greying and melanoma


title: Antagonistic stem cell fates under stress govern decisions between hair greying and melanoma [array]

overall_design: Gene expression profiling of FACS-purified melanocyte stem cells from WT and K14-SCF Tg mice.


title: TAF1 is required for fetal but not adult hematopoiesis in mice

city: Miami

first: Stephen

middle: D.

last: Nimer

state: FL

address: 1120 NW 14th Street

department: Sylvester Comprehensive Cancer Center

institute: University of Miami


title: Comparative CRISPRi screens reveal a human stem cell dependence on mRNA translation-coupled quality control

city: Martinsried

first: Danny

last: Nedialkova

address: Am Klopferspitz 18

institute: Max Planck Institute of Biochemistry

summary: The translation of mRNA into proteins in multicellular organisms needs to be carefully tuned to changing proteome demands in development and differentiation, and defects in translation often have a disproportionate impact in distinct cell types. Here we used inducible CRISPR interference screens to compare the essentiality of genes with functions in mRNA translation in human induced pluripotent stem cells (hiPSC) and hiPSC-derived neural and cardiac cells. We find that core components of the mRNA translation machinery are broadly essential, but the consequences of perturbing translation-coupled quality control factors are highly cell type dependent. Human stem cells critically depend on pathways that detect and rescue slow or stalled ribosomes, and on the E3 ligase ZNF598 to resolve a novel type of ribosome collisions at translation start sites on endogenous mRNAs with highly efficient initiation. Our findings underscore the importance of cell identity for deciphering the molecular mechanisms of translational control in metazoans.

overall_design: CRISPRi screen, RNA-Seq and ribosome profiling data.

first: Geraldine

last: Rodschinka

first: Sergio

last: Forcelloni

first: Andrew

last: Behrens

first: Sascha

last: Wani


title: Comparative CRISPRi screens reveal a human stem cell dependence on mRNA translation-coupled quality control [sgRNA]

overall_design: CIRPSRi cell lines were transduced with sgRNA libraries, selected with puromycin and cultured in +/- doxycycline (Dox) for the same timeframe. sgRNA depletion/ enrichment was calculated for +Dox vs matched - Dox control samples.


overall_design: Gene expression in hair follicle stem cells/hair germ was measured at three days after exposure to either the vehicle (acetone) or DMBA. Three independent samples were collected from different mice under each condition (vehicle or DMBA).


summary: The synthesis of proteins in multicellular organisms needs to be carefully tuned to changing proteome demands during development, and defects in this process often have a disproportionate impact in specific cell types and tissues. Here, we compared the essentiality of 262 genes from the mRNA translation machinery by inducible CRISPRi screens in HEK293 cells, human induced pluripotent stem cells (hiPSC) and hiPSC-derived neuronal progenitor cells, neurons, and cardiomyocytes. While ribosomal proteins and core translation factors were broadly essential, the cellular responses and phenotypic consequences of perturbing translation-dependent quality control pathways were highly dependent on the cellular context. By profiling ribosome occupancy in cells that are particularly sensitive to ZNF598 loss, we discovered a previously unappreciated role of this protein in detecting ribosome collisions during translation initiation. Our findings illuminate the importance of cell identity for deciphering the molecular mechanisms of translational control in metazoans.

overall_design: Ribosome profiling libraries  generated from human induced pluripotent stem cells depleted for ZNF598 by CRISPRi or expressing a ZNF598 RING domain mutant.


title: Astrocyte priming enhances microglial Aβ clearance and is compromised by APOE4

status: Public on Jul 06 2025

city: Seoul

first: Jinsoo

last: Seo

address: 50 Yonsei-ro

department: Department of Systems Biology

institute: Yonsei University

summary: The innate immune system can develop a form of memory called priming, where prior exposure to a stimulus enhances subsequent responses. While well-characterized in peripheral immunity, its function in brain-resident cells such as astrocytes under non-disease conditions remains unclear. Here we show that human astrocytes derived from the induced pluripotent stem cells of healthy female donors, but not microglia, acquire a primed state following transient immune stimulations. Upon subsequent exposure to amyloid-β (Aβ), these astrocytes secrete elevated levels of cytokines and promote microglial Aβ uptake. In contrast, astrocytes carrying the Alzheimer’s disease (AD) risk allele APOE4 exhibit reduced priming and fail to support microglial phagocytosis. These findings are validated in astrocyte-microglial co-cultures, cerebral organoids, and male mice, where astrocyte priming enhances Aβ clearance in an APOE4-sensitive manner. Our findings identify astrocytic immune memory as a modulator of microglial function and Aβ pathology, providing insights into how early protective responses in AD may be disrupted by genetic risk factors.

overall_design: To investigate alterations in chromosome accessibility between primed astrocytes with or without Aβ treatment

first: Se-In

last: Lee

first: Fan

last: Gao


title: Epigenetic Reactivation of CNS Endothelial Developmental Programs Triggers Adult Brain Angiogenesis, Promotes Post-Stroke Revascularization and Neuroregeneration [RNAseq-Stroke]

city: Houston

first: Peeyush Kumar

last: Thankamani Pandit

state: TEXAS

address: 6431 Fannin St,

department: Neurosurgery

institute: University of Texas Health Science Center Houston

summary: We identified the role of brain endothelial cell Hdac2 and Ezh2 mediated epigenetic mechanism in maintaining blood brain barrier in adult mice. Also, we we studied the impact of reactivation of brain endothelial cell Wnt/β-catenin signaling in adult mice. .We evaluated derepression of Hdac2 mediated epigenetic mechanism in imice model of schemic stroke.

overall_design: Ultra-low mRNA sequencing of FACS sorted CD31+ve/CD41-ve/CD45-ve adult mice brain cortical endothelial cells isolated from ipsilateral and contralateral sides of sham, MCAO, MCAO-Hdac2 ECKO and MCAO-Ezh2 ECKO mice. For inducing stroke, middle cerebrai artery occclusion model of stroke was used. For endothelial specific deletion of Hdac2 or Ezh2, Hdac2lox/lox:Cdh5CreERT2 or Ezh2lox/lox:Cdh5CreERT2 mice were  treated with Tamoxifen (75mg/Kg body weight), starting day 0 to day4 (total 5 doses) and brains were harvested on 7th day of stroke induction.

first: Peeyush

last: Kumar

first: Sithara

last: Thomas


overall_design: To investigate transcriptomic profiles in human microglia cell lines treated with ACM from Aβ-treated or non-treated primed astrocytes


title: A novel regulatory role for RPS4Y1 in inflammatory and fibrotic processes

status: Public on Jul 05 2025

city: Ultimo

first: Karosham

middle: Diren

last: Reddy

state: NSW

address: 15 Broadway

department: Life Sciences

country: Australia

institute: University of Technology Sydney

summary: Asthma is a chronic inflammatory respiratory disease well-known to demonstrate sexual dimorphism in incidence and severity, although the mechanisms causing these differ-ences remains incompletely understood. RPS4X and RPS4Y1 are X and Y-chromosome-linked genes coding ribosomal subunits previously associated with in-flammation, airway remodelling and asthma medication efficacy. Particularly, RPS4Y1 has been under-investigated within the context of disease, with little examination of molecular mechanisms and pathways regulated by this gene. The ribosome, a vital cellular machinery, facilitates the translation of mRNA into peptides and then proteins. Imbalance or dysfunction in ribosomal components may lead to malfunctioning proteins. Using CRISPR-Cas9 knockout cellular models for RPS4Y1 and RPS4X, we characterised the function of RPS4Y1 in the context of the asthma-relevant processes, inflammation and fibrosis. No viable RPS4X knockouts could be generated. We highlight novel molecular mechanisms such as specific translation of IL6 and tenascin-C mRNA by RPS4Y1 con-taining ribosomes. Furthermore, an RPS4Y1-centric gene signature correlates with clinical lung function measurements specifically in adult male asthma patients. These findings inform the current understanding of sex differences in asthma, as females do not produce the RPS4Y1 protein. Therefore, the pathologically relevant functions of RPS4Y1 may contribute to the complex sexually dimorphic pattern of asthma susceptibility and pro-gression.

overall_design: Gene expression profiling analysis was completed for each genotype (wild type and RPS4Y1  KO). Each genotype was analysed in triplicate. The wild type cell line functioned as a reference for normal gene expression.

first: Senani

middle: N

last: Rathnayake

first: Sobia

last: Idrees

first: Fia

last: Boedijono

first: Dikaia

last: Xenaki

first: Matthew

last: Padula

first: Maarten

last: van den Berge

first: Alen

last: Faiz

first: Brian

last: Oliver


title: The small nucleolar RNA NONCODING RNA 1 negatively regulates drought tolerance in Arabidopsis thaliana

city: Changchun

first: Liangliang

last: Li

address: 4888 Shengbei Street, Kuancheng District

department: Northeast Institute of Geography and Agroecology

country: China

institute: Chinese Academy of Sciences

summary: To understand the role of NCR1 in regulating drought tolerance, we performed the comparative transcriptome profiling WT and ncr1 mutant seedlings.

overall_design: 12-day-old WT and ncr1 mutant seedlings were transferred from 1/2 Murashige and Skoog (MS) plates to soil and grown for 12 additional day. The rosette leaves of this 24-day-old seedlings were harvested after dehydration for 0, 2, and 4 h, and then frozen in liquid nitrogen immediately. Total RNA was extracted using Trizol reagent kit (Invitrogen, Carlsbad, CA,USA) according to the manufacturer’s protocol. RNA quality was assessed on an Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA, USA) and checked using RNase free agarose gel electrophoresis. After total RNA was extracted, eukaryotic mRNA was enriched by Oligo (dT) beads. Then the enriched mRNA was fragmented into short fragments using fragmentation buffer and reversly transcribed into cDNA by using NEBNext Ultra RNA Library Prep Kit for Illumina (NEB#7530,New England Biolabs, Ipswich, MA, USA). The purified double-stranded cDNA fragments were end repaired. A base added, and ligated to Illumina sequencing adapters. The ligation reaction was purified with the AMPure XP Beads (1.0X).And polymerase chain reaction (PCR) amplified. The resulting cDNA library was sequenced using Illumina Novaseq6000.

first: Xianpeng

last: Yang

first: Haodong

last: Huang

first: Chenbo

last: Zhu

first: Minghui

last: Xing

first: Kaixin

first: Xiaofan

last: Nie

first: Jiahe

last: Fu

first: Mingming

last: Wang

first: Zhengwei

last: Liang

first: Shiyou

last: Lü

first: Weiqiang

last: Qian

first: Lam-Son

last: Tran

first: Xiaojian

last: Yin


first: Jinsoo

last: Seo

overall_design: To investigate transcriptomic profiles in primed astrocytes with or without immune or Aβ challenge, we utilized hiPSC-derived astrocytes

first: Se-In

last: Lee

first: Fan

last: Gao


title: Identification and characterization of two distinct Natural Killer cell subpopulations in RAG1 knockout chicken model

first: JAE

middle: YONG

last: HAN

address: 1 Gwanak-ro, Gwanak-gu

department: Department of Agricultural Biotechnology

institute: Seoul National University

summary: Natural Killer (NK) cells are cytotoxic lymphocytes without expression of CD3 and T cell receptor. However, NK cells in chicken are not fully understood. We used single cell RNA sequencing (scRNA-seq) to analyze the diversity of lymphocytes in RAG1 disrupted chicken spleen.

overall_design: The RAG1 disrupted chicken and wild-type chicken spleen were dissociated into single cells and analyzed using scRNA-seq.

first: Jae

last: Han

first: Seung

middle: J

last: Woo


title: Single-cell analysis of immune cell characteristics induced by Aoah over-expression in MYC-Luc spontaneous hepatocellular carcinoma tumors

status: Public on Jul 04 2025

first: Peng

last: Jiang

state: Maryland

address: 41 Center Drive

department: Center for Cancer Research

institute: National Cancer Institute

summary: Secreted proteins are central mediators of intercellular communications and can serve as therapeutic targets in diverse diseases. The ~1903 human genes encoding secreted proteins are difficult to study through common genetic approaches. To address this hurdle and, more generally, to discover cancer therapeutics, we developed the Cancer Immunology Data Engine (CIDE, https://cide.ccr.cancer.gov), which incorporates 90 omics datasets spanning 8575 tumor profiles with immunotherapy outcomes from 17 solid tumor types. CIDE systematically identifies all genes associated with immunotherapy outcomes. Then, we focused on secreted proteins prioritized by CIDE without known cancer roles and validated regulatory effects on immune checkpoint blockade for AOAH, CR1L, COLQ, and ADAMTS7 in mouse models. The top hit, AOAH (Acyloxyacyl Hydrolase), potentiates immunotherapies in multiple tumor models by sensitizing T-cell receptors to weak antigens and protecting dendritic cells through depleting immunosuppressive arachidonoyl phosphatidylcholines and oxidized derivatives.

overall_design: We used two murine hepatocellular carcinoma models driven by MYC overexpression with (LucOS) or without (Luc) highly immunogenic OVA+SIN+SIY (OS) antigens and beta-catenin (encoded by CTNNB1) activation. Both models show resistance to anti-PD1 immunotherapy. A sterile 0.9% NaCl solution/plasmid mixture was prepared as follows: We prepared 10 μg of pT3-EF1a-MYC-IRES-luciferase (MYC-Luc), 10 μg of pT3-EF1a-MYC-IRES-luciferase-OS (MYC-LucOS), 10 μg of pT3-N90-CTNNB1 (CTNNB1), 10 μg of PKT2/CLP-Vec, 10 μg of PKT2/CLP-Aoah, and a 3:1 ratio of transposon to SB100 transposase–encoding plasmid dissolved in 2 mL of 0.9% NaCl solution and tail-vein injected 10% of the weight of each C57BL/6 mouse in volume in 5-7 seconds. To specifically study the effects of Aoah overexpression (OE) on immune cells, we performed single-cell RNA-seq on CD45+ cells isolated from MYC-Luc spontaneous hepatocellular carcinoma (HCC) tumors induced with and without OS antigens.

first: Lanqi

last: Gong

first: Jie

last: Luo

first: Beibei

last: Ru

first: Xinyuan

last: Guan


title: Mouse CD8 T cells treated with human recombinant AOAH protein or phosphatidylcholine with C16:0 on the sn-1 and C20:4 on the sn-2 positions

overall_design: To compare the genetic differences between AOAH-treated and vehicle-treated activated mouse CD8+ T cells: The mouse CD8+ T cells were first isolated from splenocytes of C57BL/6 mice using EasySep™ Mouse CD8+ T Cell Isolation Kit (Stem cell technologies), and pre-treated in T-cell medium (Miltenyi) with either 10 µg/mL rhAOAH-His (Wuxi Biologics) + ethanol control, or an equal volume of 10% glycerol PBS + ethanol control, or  10% glycerol PBS + 60 µM PC16:0-20:4 (Avanti Lipids) for 22 hours. Next, the pre-treated CD8+ T cells were activated by 1 µg/mL plate-bound anti-mouse CD3 antibody (Cytek Biosciences) and 0.5 µg/mL anti-mouse CD28 antibody (Cytek Biosciences) for 24 hours.


title: Co-cultures between hgp100-pulsed splenocytes with Pmel mouse CD8 T cells treated with human recombinant AOAH protein or vehicle (10% glycerol PBS)

overall_design: The CD8 T cells were first isolated from the splenocytes of pmel mice and pre-treated in the T-cell medium (Miltenyi) with either rhAOAH-His (Wuxi Biologics, 10 µg/mL or 5 µg/mL) or Buffer (PBS + 10% glycerol) for 22 hours. Next, the splenocytes from C57BL/6 mice were pulsed with 100 nM hgp100 antigens (GeneScript) in RPMI-1640 at 37 °C for 2 hours and mixed with the pre-treated pmel CD8 T cells at 3:1 or 2:1 ratios in T-cell medium (Miltenyi) + 100 IU/mL recombinant human IL-2 (R&D Systems) with either 10 µg/mL rhAOAH-His (Wuxi Biologics) or buffer control (PBS + 10% glycerol) for 24 hours.


title: Xist upstream deletion leads to dysregulation of Xist and autosomal gene expression

city: Bangalore

first: SRIMONTA

last: GAYEN

state: Karnataka

address: GE14, new biological science building, Indian institute of Science

department: Department of Developmental biology and Genetics

country: India

institute: Indian Institute of Science, Bangalore, India

overall_design: Refer to individual Series

first: Sudeshna

last: Majumdar

first: Lakshmi

middle: S

last: Bammidi

first: Hemant

middle: C

last: Naik

first: Avinchal

last: Manhas

first: Runumi

last: Baro

first: Akash

last: Kalita

first: Amlan

last: Naskar

first: Nidharshan

last: Sundarraj

first: Girija

last: Bariha

first: Dimple

last: Notani

first: Srimonta

last: Gayen


title: Bulk RNA-seq analysis of molecular characteristics induced by Aoah over-expression in MYC-Luc spontaneous hepatocellular carcinoma tumors

first: Peng

last: Jiang

overall_design: We used two murine hepatocellular carcinoma models driven by MYC overexpression with (LucOS) or without (Luc) highly immunogenic OVA+SIN+SIY (OS) antigens and beta-catenin (encoded by CTNNB1) activation. Both models show resistance to anti-PD1 immunotherapy. A sterile 0.9% NaCl solution/plasmid mixture was prepared as follows: We prepared 10 μg of pT3-EF1a-MYC-IRES-luciferase (MYC-Luc), 10 μg of pT3-EF1a-MYC-IRES-luciferase-OS (MYC-LucOS), 10 μg of pT3-N90-CTNNB1 (CTNNB1), 10 μg of PKT2/CLP-Vec, 10 μg of PKT2/CLP-Aoah, and a 3:1 ratio of transposon to SB100 transposase–encoding plasmid dissolved in 2 mL of 0.9% NaCl solution and tail-vein injected 10% of the weight of each C57BL/6 mouse in volume in 5-7 seconds. To study the effects of Aoah overexpression (OE) in tumors, we performed bulk RNA-seq on the MYC-Luc spontaneous hepatocellular (HCC) tumors induced with and without OS antigens.


title: Bulk RNA-seq analysis of molecular characteristics induced by Aoah over-expression in B16 subcutaneous implanted tumors

overall_design: To compare genetic differences between B16-mhgp100-Vec and B16-mhgp100-Aoah (and B16F10-Vec vs. B16F10-Aoah) subcutaneous tumors grown on C57BL/6 mice in response to anti-PD1 treatment (and anti-PD1+ anti-CTLA4 treatments for B16F10 models): 10 days (6 days for B16F10 cells) after the inoculation of tumor cells, anti-PD1 (BioXCell, #BE0146, 200 μg/dose) or  anti-PD1+ anti-CTLA4 (BioXCell, #BE0131, 200 μg/dose) was given to the tumor-bearing mice twice per week for a total of 4 doses. One day after the last dose, tumor samples were harvested from the mice and used for RNA extraction.

first: Lanqi

last: Gong


title: Bulk RNA-seq analysis of molecular characteristics induced by Colq over-expression in B16mhgp100 subcutaneous implanted tumors

overall_design: To compare differences between B16-mhgp100-Vec and B16-mhgp100-Colq subcutaneous tumors grown on C57BL/6 mice in response to anti-PD1 treatment: 10 days after the inoculation of tumor cells, anti-PD1 (BioXCell, #BE0146, 200 μg/dose) was given to the tumor-bearing mice twice per week for a total of 4 doses. One day after the last dose, tumor samples were harvested from the mice and used for RNA extraction.

first: Ziyang

last: Qi


title: Coupling CRISPR scanning with targeted chromatin accessibility profiling using a double-stranded DNA deaminase [Nanopore]

first: Heejin

last: Roh

state: MA

address: 12 Oxford St

institute: Harvard

summary: Genome editing enables sequence-function profiling of endogenous cis-regulatory elements, driving understanding of their mechanisms. However, these approaches lack direct, scalable readouts of chromatin accessibility across long single-molecule chromatin fibers. Here we leverage double-stranded DNA cytidine deaminases to profile chromatin accessibility at endogenous loci of interest through targeted PCR and long-read sequencing, a method we term targeted deaminase-accessible chromatin sequencing (TDAC-seq). With high sequence coverage at targeted loci, TDAC-seq can be integrated with CRISPR perturbations to link genetic edits and their effects on chromatin accessibility on the same single chromatin fiber at single-nucleotide resolution. We employed TDAC-seq to parse CRISPR edits that activate fetal hemoglobin in human CD34+ hematopoietic stem and progenitor cells (HSPCs) during erythroid differentiation as well as in pooled CRISPR and base-editing screens tiling an enhancer controlling the globin locus. We further scaled the method to interrogate 947 variants in a GFI1B-linked enhancer associated with myeloproliferative neoplasm risk in a single pooled CRISPR experiment in CD34+ HSPCs. Together, TDAC-seq enables high-resolution sequence-function mapping of single-molecule chromatin fibers by genome editing.

overall_design: Nanopore sequencing was performed on TDAC-seq libraries or DddA11-WGS library on K562 cells or CD34+ HSPCs

first: Simon

last: Shen

first: Yan

last: Hu

first: Hui Si

last: Kwok


title: Bulk RNA-seq analysis of molecular characteristics induced by Cr1l over-expression in B16mhgp100 subcutaneous implanted tumors

overall_design: To compare differences between B16-mhgp100-Vec and B16-mhgp100-Cr1l subcutaneous tumors grown on C57BL/6 mice in response to anti-PD1 treatment: 10 days after the inoculation of tumor cells, anti-PD1 (BioXCell, #BE0146, 200 μg/dose) was given to the tumor-bearing mice twice per week for a total of 4 doses. One day after the last dose, tumor samples were harvested from the mice and used for RNA extraction.


title: ChIP-seq of histone modifications in Arabidopsis thaliana Col-0, clf-29, elf6-126,ino80-5 and elf6-126/ino80-5 using H2AZ, H3, H3K4me3 and H3K27me3 antibodies as well as input DNA control

city: Shanghai

first: Xiaolong

last: Wu

state: Shanghai

address: 2005 Songhu Road, Shanghai

institute: Fudan University

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

first: Fan

last: Wang

first: Linghao

last: Zhang

first: Wenhao

last: Xie

first: Xixi

last: Cai

first: Jiachen

first: Youchao

first: Aiwu

last: Dong

first: Wei

last: Su


title: Transcriptome data (mRNA-seq) for Col-0, clf-29, elf6-126,ino80-5 and elf6-126/ino80-5.

summary: Gene expression profiling analysis of RNA-seq data for Arabidopsis thaliana.


title: Transient splicing inhibition causes persistent DNA damage and enhances chemotherapy vulnerability in homologous recombination proficient triple-negative breast cancer

city: Rome

first: Marco

last: Pieraccioli

address: Largo Francesco Vito 1

country: Italy

institute: Catholic University of the Sacred Heart rome

summary: Triple negative breast cancer (TNBC) is an aggressive subtype of breast cancer. Most TNBCs are initially sensitive to DNA damaging chemotherapy, a substantial fraction acquire resistance to treatments and progress to advanced stages associated with poor prognosis. We identify the spliceosome U2 small nuclear ribonucleoprotein (snRNP) complex as a modulator of chemotherapy efficacy in TNBC. Transient treatment with U2snRNP inhibitors induced a persistent DNA damage in TNBC cells and patient-derived organoids (PDOs), regardless of their homologous recombination proficiency. Transcriptome analyses revealed that U2snRNP inhibition causes a pervasive deregulation of genes involved in the DNA damage response (DDR), which relied on their genomic structure characterized by a high number of small exons. Importantly, a pulse of splicing inhibition was sufficient to elicit long-lasting repression of DDR proteins and to enhance the cytotoxic effect of platinum-based drugs and poly ADP-ribose polymerase inhibitors (PARPi) in multiple TNBC models. These findings identify the U2snRNP as an actionable target that can be exploited to enhance chemotherapy efficacy in TNBCs.

overall_design: RNA-seq study of MDA-MB-231 TNBC cells  treated for 16 hours with 10 nM Pladienolide B (PdB) to reveal DEGs upon Pladienolide B treatment and after 24 hours of recovery from drug treatment.

first: Cinzia

last: Caggiano

first: Valerio

last: Petrera

first: Miriana

last: Ferri

first: Eleonora

last: Cesari

first: Alba

last: Di Leone

first: Martin

middle: A

last: Sanchez

first: Alessandra

last: Fabi

first: Riccardo

last: Masetti

first: Chiara

last: Naro

first: Claudio

last: Sette


title: Bulk RNA-seq analysis of gene expression characteristics induced by Adamts7 over-expression in B2905-M4 subcutaneous implanted tumors

first: Peng

last: Jiang

overall_design: For subcutaneous tumor models, 3E6 B2905-M4 cells were injected subcutaneously into 7-8-week-old female C57BL/6J. Tumor volume was measured based on the formula: (Length×Width^2)/2. Mice were euthanized according to a pre-determined survival endpoint defined as tumor volume ≥ 2000 mm^3 or the tumor length (longer diameter) ≥ 20 mm. We aim to harvest tumors on the same day for RNA-seq analysis. However, as tumors with Adamts7 over-expression (OE) grew much faster than tumors with vector OE, vector-OE tumors were too small for analysis when Adamts7-OE tumors reached endpoints. Thus, first, we harvested two Adamts7-OE tumors at day 35 post-tumor inoculation when they reached endpoints. Three tumors from the Adamts7 and vector OE groups were collected together at day 45 post-tumor inoculation. Finally, two vector tumors reached a reasonable size (shortest edge > 5mm) at day 50 post-tumor inoculation and were harvested for analysis.

first: Lanqi

last: Gong

first: Anshu

last: Rani

first: Emily

last: Yang


title: Coupling CRISPR scanning with targeted chromatin accessibility profiling using a double-stranded DNA deaminase [ATAC-seq]

city: Cambridge

first: Heejin

last: Roh

overall_design: ATAC-seq was performed on K562 cells or CD34+ HSPCs transduced with a single sgRNA and electroporated with Cas9 protein to profile how CRISPR deletions alter chromatin accessibility.

first: Simon

last: Shen

first: Yan

last: Hu

first: Hui Si

last: Kwok