title: Novel Crosstalk Between Mechanosensitive TRPV4 and NF-κB Inhibits Pulmonary Inflammation

city: Cleveland

first: Rachel

last: Scheraga

state: Ohio

address: 2111 E. 96th Street NE4-254a

department: Inflammation and immunity

institute: Cleveland Clinic Foundation

summary: The NF-κB signaling pathway plays a critical role in activating macrophages in the pathogenesis of many pro-inflammatory diseases. Mounting evidence has pointed to the importance of tissue mechanical properties in modulating key cellular pro-inflammatory responses. Previous studies have highlighted the role of the mechanosensitive membrane cation channel transient receptor potential vanilloid 4 (TRPV4) in limiting macrophage pro-inflammatory responses and attenuating lung injury in bacterial pneumonia. Our current study demonstrates that alveolar macrophage TRPV4 suppresses pro-inflammatory gene expression following activation of multiple Toll-like receptors (e.g., TLR 1, 2, 4, and 9) in response to P. aeruginosa pneumonia in vivo and TLR agonists in vitro, highlighting the broad regulatory role of TRPV4 in modulating the inflammatory response. TRPV4 suppresses pro-inflammatory cytokines by dampening p65-dependent cytokine transcriptional activity, thereby implicating TRPV4 as a negative regulator of the NF-κB pathway. Upon stimulation with lipopolysaccharide (LPS), TRPV4 translocates to the plasma membrane, in part releasing p65 for nuclear translocation. In addition, TRPV4 was found to have sequence homology with IκBα largely within the TRPV4 ankyrin repeat domain (ANKRD), suggesting that TRPV4 may be acting as a mechanosensitive inhibitor of NF-κB. Further, TRPV4 ANKRD was proven to be critical for TRPV4 binding to the NF-κB pathway subunit, p65, in live cells. Given the diverse roles of TRPV4 and NF-κB/p65 in different cell types, we provide a specific example of novel mechanosensitive crosstalk in macrophages that have general consequences to a broad array of NF-κB dependent inflammatory and malignant diseases.

overall_design: BMDMs from 3 individual WT and 3 individual Trpv4 KO mice ± LPS (n=12 total samples)  were analyzed via 10X Genomic Sequencing.

first: Adam

last: Boulton

first: Megan

last: Grund

first: Erica

last: Orsini

first: Susamma

last: Abraham

first: Ryan

last: Musich

first: Caitlin

last: Snyder


title: Transcriptional regulation of temporal dynamics in human neurogenesis and neuronal maturation [RNA-seq]

status: Public on Dec 30 2025

city: Hefei

first: lingling

last: zhu

address: JinZhai Road

country: China

institute: University of Science and Technology of China

type: Expression profiling by high throughput sequencing

summary: Human pluripotent stem cells (hPSCs) provide a valuable platform for studies of human neuronal differentiation, but the mechanisms regulating the timing of this process remain poorly understood. This study compares two differentiation systems with distinct timing of differentiation, transcription factor (TF)-induced forward programming and stepwise cellular differentiation. Our analyses reveal that divergent cellular trajectories drive distinct neurogenesis timing. Multi-omic analysis identifies crucial gene regulatory networks (GRNs) that govern cell fate determination and timing control. Modulation of these GRNs modulates neurogenesis and timing of neuronal maturation. Specifically, OLIG family TFs, enriched in the TF-induced system, promoted cell cycle exit through NOTCH signaling regulation; conversely, ablation of these TFs delayed neurogenesis. In contrast, NEUROD2 overexpression accelerated neuronal maturation through precocious activation of maturation gene modules. Collectively, these findings illuminate characteristics of the cell-intrinsic mechanisms that govern timing of differentiation; the studies also offer a framework for investigation into, and the rational design of, timing-controlled in vitro differentiation strategies.

overall_design: We performed scRNA-seq on cells over the time course of TF-induced forward programming (hPSCs female and male cell lines, with mRNA or dox inducbile NEUROG1, NEUROG2, NEUROD1 overexpression induced neurogenesis) and stepwise cellular differentiation (dual-SMAD inhibition).Taken together, these data indicate that TF-induced forward programming represents a distinct differentiation shortcut from hPSCs to neuronal fate. In order to further decipher the regulatory landscape underlying the drastic cell fate changes, several experiments were performed including high-resolution time-course RNA expression profiling, chromatin accessibility analysis, and TF binding profiling by CUT-TAG (NEUROG1, NEUROG2, and NEUROD1). We next aimed to infer GRNs that may play a crucial role in facilitating rapid neurogenesis (OLIG1, OLIG2, OLIG3) and subsequent neuronal maturation (NEUROD2, MSC). To gain mechanistic insights, scRNA seq of cells induced from OLIG KO cell line, TF binding profiling by ChIP (OLIG2) and CUT-TAG (NEUROD2, MSC) were performed.


title: Transcriptomic Profiling of Kinase Inhibitor Treated Cancer Cell Lines Reveals Insights into Drug Response Mechanisms

city: Seattle

first: Mehlam

middle: M

last: Saifudeen

state: WA

address: 1100 Fairview Ave North

department: Human Biology

country: USA

institute: Fred Hutchinson Cancer Center

summary: Protein kinases regulate essential cellular processes, including growth, differentiation, and apoptosis, and their dysregulation is implicated in cancer progression. Kinase inhibitors have emerged as critical therapeutic agents; however, challenges such as drug resistance and selectivity gaps necessitate further investigation. To address these challenges, we performed RNA sequencing-based transcriptomic profiling to assess the impact of targeted kinase inhibitors on cancer cells. Specifically, we analyzed the gene expression changes induced by Tepotinib (1 μM) in GSC923 glioblastoma cells, Gilteritinib (1 μM) in MDA-MB-231 triple-negative breast cancer cells, and Brigatinib (1 μM) in PANC-1 pancreatic cancer cells. Wild-type (WT) untreated controls were included for comparative analysis. RNA sequencing was conducted using a paired-end strategy, and differential gene expression analysis was performed to uncover treatment-induced transcriptional alterations. This dataset provides insights into the molecular mechanisms of kinase inhibitor response, highlighting potential repurposing opportunities and informing future therapeutic strategies in glioblastoma, breast cancer, and pancreatic cancer.

overall_design: 1. GSC923 Cells - Tepotinib Treatment: RNA-seq profiling of human glioblastoma GSC923 cells cultured in Neurobasal-A medium supplemented with N2 and B27 supplements, recombinant human basic fibroblast growth factor (bFGF) and epidermal growth factor (EGF), L-glutamine, penicillin, and streptomycin. Cells were treated with 1 μM Tepotinib for 1 day, and total RNA was extracted for sequencing. DMSO controls were included for comparison.  2. MDA-MB-231 Cells - Gilteritinib Treatment: RNA-seq profiling of human triple-negative breast cancer MDA-MB-231 cells (ATCC) cultured in DMEM medium supplemented with 10% fetal bovine serum (FBS), penicillin, and streptomycin. Cells were treated with 1 μM Gilteritinib for 3 days, and total RNA was extracted for sequencing. DMSO controls were included for comparison.  3. PANC-1 Cells - Brigatinib Treatment: RNA-seq profiling of human pancreatic cancer PANC-1 cells (ATCC) cultured in DMEM medium supplemented with 10% FBS, penicillin, and streptomycin. Cells were treated with 1 μM Brigatinib for 1 day, and total RNA was extracted for sequencing.DMSO control controls were included for comparison.

first: [contributor]  Gujral Lab


title: Transcriptional regulation of temporal dynamics in human neurogenesis and neuronal maturation [CUT&Tag]

type: Genome binding/occupancy profiling by high throughput sequencing


title: RNA-seq analysis reveals dysregulated pathways in CAFs following NPs treatment.

status: Public on Dec 24 2025

city: Beijing

first: wang

last: zaozao

state: Beijing

address: No. 52 Fucheng Rd., Haidian District

department: Key Laboratory of Carcinogenesis and Translational Research

institute: Peking University Cancer Hospital & Institute

summary: Cancer-associated fibroblasts (CAFs) contribute to immunotherapy resistance in colorectal cancer (CRC) by creating physical barriers and fostering an immunosuppressive microenvironment, critically influencing tumor development and metastasis.Nowadays, nanotherapy has been extensively explored in oncology for its dual capabilities in cancer targeted treatment.However, the mechanisms by which nanoparticles (NPs) exert their antitumor effects through targeting and eliminating CAFs remain incompletely understood.In this study,NPs modulated intrinsic signaling pathways in CAFs, leading to altered chemokine secretion profiles. This modification enhanced dendritic cell maturation and promoted CD8+ T cell activation and functionality, ultimately amplifying the anti-tumor immune response to suppress CRC progression.

overall_design: To elucidate the underlying mechanism by which NPs influnence CAFs, RNA sequencing analysis was performed to explore regulated pathways in CAFs after NPs treatment compared to control cells.  Each experimental group includes three biological replicates

first: Shuren

last: Wang

first: Zaozao


title: NKG2A+ NK Cell Cytotoxicity of Epstein-Barr Virus Infected B Cells is Mediated Through the NKG2D and NKp30 Activating Receptors

status: Public on Dec 22 2025

city: Stanford

first: Josselyn

middle: K

last: Pena

state: CA

address: 1201 Welch Rd

department: Surgery

institute: Stanford University

summary: Epstein–Barr virus (EBV) is a ubiquitous gamma-herpesvirus that persists as a chronic, asymptomatic infection in over 90% of the adult human population. EBV infections are mainly asymptomatic and subside due to a vigorous host T cell response with the virus transitioning to latency in a subset of memory B cells. Failure to control latent EBV infection can result in a variety of EBV-associated malignancies, including lymphoproliferative diseases in immunocompromised people. Studies in both experimental models and humans suggest that NK cells are critical in the host defense against EBV. In this study we utulized scRNA-seq to better understand the phenotype of NK cells that respond to EBV-infected B cells. We generated a panel of EBV+ lymphoblastoid cell lines (EBV+ LCL) and performed coculture experiments with primary NK cells and their autologous EBV+ LCL  using 10x Genomics scRNA-seq. Subsequent analyses following alignment and data processing were completed in Python.

overall_design: Following coculture with an autologous EBV+ LCL, cells were sorted for CD107a+ (responsive) and CD107a- (nonresponsive) NK cells using scRNA-seq.

first: Joshua

middle: S

last: Badshah

first: Sheri

last: Krams


title: Recruitment of BRD4 to the ASXL1 genomic targets depends on the extra-terminal domain of BRD4

city: Chicago

first: Lu

state: Illinois

address: 303 E. Superior Street Simpson Querrey 7-414

department: Biochemistry and Molecular Genetics

institute: Northwestern University

summary: Additional sex combs like 1 (ASXL1) is a well-established driver of a wide range of cancers. Here, we identified a high level of genetic correlation between ASXL1 and the major transcriptional activator BRD4 in cancer cells and characterized the molecular mechanism underlying this correlation. Structural and biochemical data show the formation of a tight complex between the extraterminal domain of BRD4 (BRD4ET) and the ET-binding motif of ASXL1 (ASXL1EBM). ChIP-seq analysis of ASXL1 impaired in binding to BRD4ET demonstrates that the recruitment of BRD4 to the ASXL1 genomic targets is ASXL1EBM-dependent. We find that the cancer-related truncated variants comprising residues 1-645 and 1-591 of ASXL1 (ASXL11-645 and ASXL11-591) retain BRD4 binding function, with ASXL11-645 showing an enhanced ability to recruit BRD4 to promoters of ASXL1 target genes. Genomic data from six cancer types reveals a strong positive ASXL1-BRD4 relationship, with BRD4 occupying the ASXL1 promoter and thus further suggesting a possible feed-forward mechanism. Our findings shed light on the mechanistic details by which ASXL1 associates with BRD4 and may provide potential therapeutic avenues for developing cancer treatments through targeting the ASXL1-BRD4 axis.

overall_design: HEK293T cells were transduced with lentivirus expressing either GFP, GFP-tagged ASXL1-1-645-WT, or GFP-ASXL1-1-645-I574D. The ChIP-seq experiments were conducted with GFP monoclonal antibody and BRD4 antibody to determine the impact of ASXL1 cancer-specific mutation on BRD4 occupancy at the genome wide level

first: Zibo

last: Zhao


title: Identification of Macrophage-Dependent Fcer1g+ Mesenchymal Cells as Key Regulators of Scar Formation in Wound Healing

city: Madison

first: Jianhong

last: Ou

state: Wisconsin

address: 330 N Orchard Street

institute: Morgridge Institute For Research

summary: Scarring is a common outcome of wound healing in adult skin, often leading to fibrotic tissue that lacks the functional and aesthetic properties of normal, uninjured skin. To effectively reduce and prevent scar formation, understanding the cellular players involved in fibrosis is crucial. Among these, macrophages and mesenchymal cells have received significant attention due to their vital roles in both tissue regeneration and fibrosis. Research has shown that depleting macrophages during the early stages of wound healing reduces the number of myofibroblasts in the wound bed and delays wound closure, but results in reduced scar formation, suggesting that macrophages contribute to fibrosis by regulating mesenchymal cells. However, there remains a need for unbiased, high-throughput approaches to precisely investigate the mechanisms through which macrophages regulate and induce mesenchymal subtypes in scar formation. In this study, we performed single-cell RNA sequencing to investigate changes in mesenchymal cell subpopulations during adult skin wound healing in a conditional macrophage depletion mouse model, macrophage Fas-induced apoptosis (MaFIA).

overall_design: To identify mesenchymal cell subtypes regulated by acute-phase macrophages during wound healing, we performed single-cell RNA sequencing (scRNA-seq) on 3 day-post-injury skin cells isolated from the wounds of MaFIA mice, with or without macrophage depletion.

first: Xinyi

last: Ma

first: Ergang

first: Vijitha

last: Puviindran


title: Global stabilization of the transcriptome in mitotic cells [PALseq]

status: Public on Dec 23 2025

city: Cambridge

first: Ekaterina

last: Khalizeva

state: MA

address: 455 Main St

department: Biology

institute: Whitehead Institute

summary: In the presence of cell division errors, mammalian cells can pause in mitosis for tens of hours with little to no transcription, while still requiring continued translation for viability. These unique aspects of mitosis require substantial adaptations to the core gene expression programs. During interphase, the homeostatic control of mRNA levels involves a constant balance of transcription and degradation, with a median mRNA half-life of ~2–4 hours. If such short mRNA half-lives persisted in mitosis, cells would be expected to rapidly deplete their transcriptome in the absence of new transcription. Here, we report that the transcriptome is globally stabilized during prolonged mitotic delays. Median mRNA half-lives are increased >4-fold in mitosis compared to interphase, thereby buffering mRNA levels in the absence of new synthesis. Moreover, the poly(A)-tail-length profile of mRNAs changes in mitosis, strongly suggesting a partial mitotic repression of deadenylation. In contrast, the machinery required for siRNA-mediated mRNA degradation remains active. We further show that mitotic mRNA stabilization is dependent on cytoplasmic poly(A)-binding proteins PABPC1&4. Depletion of PABPC1&4 and consequently reduced mRNA stability disrupts the maintenance of mitotic arrest, highlighting the critical physiological role of mitotic transcriptome buffering.

overall_design: RNA-seq data from transcription inhibition timecourses in HeLa cells arrested in mitosis, G2, or G1 using double thymidine block followed by STLC, RO3306, or STLC release respectively. One timecourse experiment only contained STLC-arrested cells without additional transcriptional inhibition. Also included are PAL-seq data from the STLC timecourse and the G2-vs-M timecourse in the presence of actinomycin D. RNA-seq data from HCT116 PABPC1&4-AID cells arrested in mitosis, with or without IAA-induced PABPC1&4 depletion (0 h and 4 h post-IAA addition)

first: Arash

last: Latifkar

first: Kehui

last: Xiang

first: Jimmy

last: Ly

first: Iain

last: Cheeseman

first: David

middle: P

last: Bartel


title: Generation of Drug Perturbational Profiles in SF8628 and DIPG6 DMG Cell Lines

city: New York

first: Lorenzo

last: Tomassoni

address: 1130 St Nicholas Avenue

institute: Columbia University

summary: 372 clinically relevant drugs, including FDA-approved and late-stage experimental oncology drugs were tested in both SF8628 and DIPG6 DMG Cell Lines

overall_design: RNA-seq profiles were then generated at 24 hours following treatment of each cell line with the 372 drugs—titrated at the lowest of their highest sublethal concentration (48h EC20) or max tolerated serum concentration from the literature—as well as DMSO as vehicle control, using the PLATE-Seq microfluidic automation platform

first: Ester

middle: C

last: Fernandez

first: Xu

last: Zhang

first: Junqiang

first: Aleksandar

last: Obradovic

first: Pasquale

last: Laise

first: Aaron

middle: T

last: Griffin

first: Lukas

last: Vlahos

first: Hanna

middle: E

last: Minns

first: Diana

middle: V

last: Morales

first: Christian

last: Simmons

first: Matthew

last: Gallitto

first: Hong-Jian

last: Wei

first: Timothy

middle: J

last: Martins

first: Pamela

last: Becker

first: John

middle: R

last: Crawford

first: Theophilos

last: Tzaridis

first: Robert

last: Wechsler-Reya

first: James

last: Garvin

first: Robyn

middle: D

last: Gartrell

first: Luca

last: Szalontay

first: Stergios

last: Zacharoulis

first: Cheng-Chia

last: Wu

first: Zhiguo

first: Andrea

last: Califano

first: Jovana

last: Pavisic


title: Elucidating and Pharmacologic Targeting of Coexisting Diffuse Midline Subpopulation Dependencies

first: Lorenzo

last: Tomassoni

summary: Diffuse Midline Glioma (DMG) are universally fatal, primarily pediatric malignancies affecting the midline structures of the central nervous system. Despite decades of clinical trials, their treatment remains limited to palliative radiation therapy. A major challenge is the coexistence of molecularly distinct malignant cell states with potential orthogonal drug sensitivities. To address it, we leveraged established network-based methodologies to elucidate Master Regulator (MR) proteins representing mechanistic dependencies of seven coexisting subpopulations identified from tumor biopsies. We then leveraged perturbational profiles of 372 clinically relevant drugs to identify those capable of inverting the activity of subpopulation specific MRs and validated their specificity in vivo. While individual drugs predicted by the analysis to target individual subpopulations—such as avapritinib, larotrectinib, and ruxolitinib—produced only modest tumor growth reduction in orthotopic allograft models, they systemic co-administration induced highly significant survival extension.

overall_design: Single cells were isolated and sequenced from NOD.Cg Prkdcscid/J (NSG) subcutaneously injected with 500,000 patient-derived DMG cells (SU-DIPG-XVII) at five days following treatment with Etoposide, Dinaciclib, Avapritnib, Trametinib, Mocetinostat, Larotrectinib, Ruxolitnib, Napabucasin and Venetoclax

first: Ester

last: Fernandez

first: Xu

last: Zhang

first: Junqiang

last: Wang

first: Aleksandar

last: Obradovic

first: Pasquale

last: Laise

first: Aaron

last: Griffin

first: Lukas

last: Vlahos

first: Hanna

last: Minns

first: Diana


title: Bulk RNA Sequencing of 3 DIPG Cases

summary: Tumors of 3 DIPG Patients have been subjected to Bulk RNA Sequencing as part of a program at Rady Children's Hospital

overall_design: Tissue from 3 untreated DIPG Tumors was isolated and prepared for Bulk RNA-Sequencing

last: Morales

first: Christian

last: Simmons

first: Matthew

last: Gallitto

first: Hong-Jian

last: Wei

first: Timothy

last: Martins

first: Pamela

last: Becker

first: John

last: Crawford

first: Theophilos

last: Tzaridis

first: Robert

last: Wechsler-Reya

first: James

first: Robyn


title: Generation of Syngeneic Orthotopic DMG Murine Models

first: Lorenzo

last: Tomassoni

summary: Diffuse Midline Glioma (DMG) syngeneic orthotopic murine mouse models were used as high fidelity model of human DMG tumors as they recapitulate the heterogeneity, cell states and OncoTarget/OncoTreat drug predictions of human DMG tumors.

overall_design: Single-cells were isolated and sequenced from B6(Cg)-Tyrc-2J/J (B6) mice. An intracranial injection with 100,000 DIPG4423 cells was performed and tumor was isolated 3 weeks post-injection for single cell. Additionally, single cells were also isolated from normal brainstem (no tumor) of the same model

first: Ester

last: Fernandez

first: Xu

first: Junqiang

last: Galitto

last: Garvin

last: Gartrell

first: Luca

last: Szalontay

first: Stergios

last: Zacharoulis

first: Cheng-Chia

last: Wu

first: Zhiguo

first: Andrea

last: Califano

first: Jovana

last: Pavisic


title: CRISPR/Cas9-mediated validation of candidate Master Regulators Proteins in DMG/GBM Cell Lines

summary: Three GBM and three DMG cell lines were selected to be used in a function validation CRISPR screening to elucidate essentiality of canidate Master Regulator proteins

overall_design: A pooled CRISPR/Cas9-mediated KO screen was performed in three human DMG cell lines (SF8628, DIPG4 and DIPG17) and three human GBM cell lines (GBM22, KNS42 and GBM43)—using guide RNAs (sgRNAs) targeting 1,433 genes

last: Zhang

last: Wang

first: Aleksandar

last: Obradovic

first: Pasquale

last: Laise

first: Aaron

last: Griffin

first: Lukas

last: Vlahos

first: Hanna

last: Minns

first: Diana

last: Morales

first: Christian

last: Simmons

first: Matthew

last: Gallitto

first: Hong-Jian

first: Timothy


title: RNA sequencing of ex vivo microtumor models embedded in different matrices and constructed from either control or Arpc4-knockout cells.

status: Public on Dec 21 2025

city: Heidelberg

first: Yina

last: Qiao

country: Germany

institute: Heidelberg University Hospital

summary: The loss of Arpc4 resulted in reduced expression of other Arp2/3 complex components, rendering the Arp2/3 complex nonfunctional. The ex vivo microtumor(3D) models were composed of either control or Arpc4 knockout (KO) KC 8025 cells embedded in different matrices containing three condition:25% collagen I, 25% collagen I + 75% Matrigel, and 75% Matrigel for 5 days. To identify genes affected by Arpc4 knockout in this model, RNA-seq analysis was performed on bulk samples. 8025 cell line was derived from primary cells isolated from genetically engineered p48Cre/+; LSL-KrasG12D/+ (KC).

overall_design: The 8025 cell line were established from primary cells isolated from genetically engineered p48Cre/+; LSL-KrasG12D/+ (KC) mice and cultured in Dulbecco’s Modified Eagle Medium (DMEM) supplemented with 10% fetal bovine serum (FBS), 100 U/mL penicillin, and 100 µg/mL streptomycin. Cells were maintained at 37°C in a humidified incubator with 5% CO₂. The cell line was transfected with the CRISPR/Cas9 p20-ARC Double Nickase Plasmid (Santa Cruz Biotechnology, USA) to target the Arpc4 gene, alongside a negative control plasmid (Santa Cruz Biotechnology, USA). Transfections were carried out using Lipofectamine 3000 (Thermo Fisher, USA) according to the manufacturer’s protocol. Forty-eight hours post-transfection, green fluorescent cells were sorted via fluorescence-activated cell sorting (FACS) and selected using puromycin (InvivoGen, Toulouse, France) at concentrations of 0.7 mg/mL. After 5–7 days of puromycin selection, cells were seeded into 96-well plates for clonal expansion. Arpc4 knockout (Arpc4ko) clones were validated via Western blot analysis. Ex vivo microtumor models (3D) were constructed using organoids derived fron 8025 control or Arpc4ko cells embedded in different matrices containing three condition:25% collagen I, 25% collagen I + 75% Matrigel, and 75% Matrigel for 5 days. Total RNA was extracted by adding TRIzol reagent (Thermo Fisher, USA) to the gel after removing the supernatant and dissolving the gel by thorough mixing. Chloroform (Thermo Fisher, USA) was then added, followed by vigorous vortexing for 15 seconds. After incubation at room temperature for 3 minutes, the mixture was centrifuged at 12,000×g for 15 minutes at 4°C. The upper aqueous phase was carefully transferred to a fresh tube, mixed with an equal volume of ≥95% ethanol, and purified using the Monarch Total RNA Miniprep Kit (New England Biolabs, Germany) according to the manufacturer’s protocol. RNA sequencing was performed by Biomarker Technologies(BMKGENE), Münster, Germany.

first: Xiufen

last: Yang

first: Yifeng

last: Sun

first: Christoph

middle: W

last: Michalski

first: Bo

last: Kong


title: RNA-seq analysis of ex vivo microtumor models comprising control or Arpc4 knockout (KO) PDAC cells

summary: The loss of Arpc4 resulted in reduced expression of other Arp2/3 complex components, rendering the Arp2/3 complex nonfunctional. The ex vivo microtumor(3D) models were composed of either control or Arpc4 knockout (KO) KP 8025 cells, mouse primary pancreatic stellate cells (PSCs), and bone marrow-derived macrophages. To identify genes affected by Arpc4 knockout in this model, RNA-seq analysis was performed on bulk samples. R254 cell line which was derived from primary cells isolated from genetically engineered p48Cre/+; LSL-KrasG12D/+; p53flox/flox (KPC) mice, and 8025 cell line which was derived from primary cells isolated from genetically engineered p48Cre/+; LSL-KrasG12D/+ (KC) mice were also conducted with RNA seq.

overall_design: The 8025 and R254 cell line were established from primary cells isolated from genetically engineered p48Cre/+; LSL-KrasG12D/+ (KC) and p48Cre/+; LSL-KrasG12D/+; p53flox/flox (KPC) mice, and cultured in Dulbecco’s Modified Eagle Medium (DMEM) supplemented with 10% fetal bovine serum (FBS), 100 U/mL penicillin, and 100 µg/mL streptomycin. Cells were maintained at 37°C in a humidified incubator with 5% CO₂. The cell line was transfected with the CRISPR/Cas9 p20-ARC Double Nickase Plasmid (Santa Cruz Biotechnology, USA) to target the Arpc4 gene, alongside a negative control plasmid (Santa Cruz Biotechnology, USA). Transfections were carried out using Lipofectamine 3000 (Thermo Fisher, USA) according to the manufacturer’s protocol. Forty-eight hours post-transfection, green fluorescent cells were sorted via fluorescence-activated cell sorting (FACS) and selected using puromycin (InvivoGen, Toulouse, France) at concentrations of 0.7 mg/mL for 8025 cells and 1.2 mg/mL for R254 cells. After 5–7 days of puromycin selection, cells were seeded into 96-well plates for clonal expansion. Arpc4 knockout (Arpc4ko) clones were validated via Western blot analysis. Total RNA was extracted using the Monarch Total RNA Miniprep Kit in accordance with the manufacturer’s protocol. RNA sequencing was performed at the Core Unit Bioinformatics, Medical Faculty, Ulm University.Ex vivo microtumor models (3D) were constructed using organoids, mouse primary pancreatic stellate cells (PSCs), and bone marrow-derived macrophages embedded in a matrix consisting of 75% Matrigel, 25% Type I collagen, 5 μg/mL fibronectin, and 2.5 μg/mL vitronectin. Total RNA was extracted by adding TRIzol reagent (Thermo Fisher, USA) to the gel after removing the supernatant and dissolving the gel by thorough mixing. Chloroform (Thermo Fisher, USA) was then added, followed by vigorous vortexing for 15 seconds. After incubation at room temperature for 3 minutes, the mixture was centrifuged at 12,000×g for 15 minutes at 4°C. The upper aqueous phase was carefully transferred to a fresh tube, mixed with an equal volume of ≥95% ethanol, and purified using the Monarch Total RNA Miniprep Kit (New England Biolabs, Germany) according to the manufacturer’s protocol. RNA sequencing was performed at the NGS Core Facility, Medical Faculty Mannheim, University of Heidelberg.

first: Tamer

last: Abdelaal

first: Kathleen

last: Schuck

first: Hend

last: Abdelrasoul

first: Eduard

last: Ryschich

first: Carolina

last: De La Torre

first: Yan

last: Dong

first: Jingxiong

last: Hu

first: Chao

last: Fang

first: Xiaoyan

last: Huang

last: Kahlert

first: Malte

last: Hermes

first: Ingrid

last: Herr


title: Hydrogel with cell-cell adhesion cues enhances neural regeneration

status: Public on Dec 19 2025

city: Nantong

first: Xiaoxuan

last: Tang

address: 19 Qixiu road

institute: Nantong university

summary: Cell-cell adhesion is crucial for maintaining cell functions and the integrity of tissue structure in organisms. However, cell-cell adhesion cue has not been effectively replicated in biomaterials and cell-cell adhesion associated mechanisms that enhance neural regeneration remained largely unexplored. Here, we present a diffusive N-cadherin functionalized hydrogel system, which provided cell-cell adhesion cue to modulate intercellular communications to significantly promote the formation of active neural network. The dynamic assembly of N-cadherin at cell membrane-hydrogel interface driven by adhered cells occurred at a timescale of minutes, facilitating the reshaping of membrane protrusions to initiate intercellular adherens junctions and modulate long-term cell-cell communications. Focusing on the mechanisms, it is associated with Thrombospondin-1 (THBS-1) mediated neural communication and activation of TGF-β/Smad pathway. Further, this hydrogel system promisingly promoted neurological function recovery in rats following traumatic brain injury. Our study provided the principles of replicating diffusive cell adhesion molecules to mediate cell-cell adhesion in hydrogels, which may have broad applications in the development of engineered biomaterials aimed at modulating cell fates in regeneration of various tissues.

overall_design: To reveal the molecular mechanism of cell-cell adhesion cue in hydrogel promoting neural growth, primary cells from cerebral cortex were cultured on hydrogels for 24 hours, respectively. The differentally expressed genes were screened by RNA sequencing. The transcriptome sequencing studies were performed by deep sequencing, using Illumina NovaSeq 6000.

first: Yumin

first: Jue

last: Ling

first: Yifan

last: Ge

first: Shuxuan

last: Zhang

first: Mengke

last: Liu

first: Yuxin

last: Liang

first: Yulan

last: Fan

first: Xinyue

first: Chang

last: He

first: Xuewa

first: Rong

last: Zhu

first: Xiaoling

last: Jin

first: Qianxing

last: Zhuang


title: DeCAF redefines fibroblast states uncovering multidimensional tumor-stroma relationships driving clinical tumor progression and immunotherapy response [Spatial Transcriptomics]

status: Public on Dec 18 2025

city: Chapel Hill

first: Jen Jen

last: Yeh

state: North Carolina

address: 450 West drive

institute: The University of North Carolina at Chapel Hill

summary: Cancer-associated fibroblast (CAF) heterogeneity within pancreatic ductal adenocarcinoma (PDAC) has been previously assessed through single-cell RNA sequencing (scRNAseq) to discover distinct CAF populations such as myCAFs and iCAFs. While useful as a biological framework, no studies have conclusively and robustly demonstrated a correlation of CAF subpopulations with clinical prognosis or therapy response. We define restraining (rest) and promoting (pro) CAFs in patient samples that are both prognostic and predictive of therapy response in disparate tumor types. Using a single sample classifier, DeCAF, we uncover distinct clinical and spatial interactions between pro- and restCAF subtypes and basal-like and classical tumor subtypes that support tumor stroma crosstalk where basal-like tumors are enriched in proCAFs and classical tumors are enriched in restCAFs. Finally, we find striking differences in the immune contexture of pro- and restCAF tumors where restCAF dominant tumors are enriched in patients who respond to immune checkpoint inhibition (ICI) in two large clinical trials, and proCAF dominant tumors are enriched in patients who respond to myeloid inhibition. This work is the first to define CAF subtypes that are clinically robust, prognostic, predictive of immunotherapy response, and associate with tumor molecular subtype.

overall_design:
129 de-identified primary PDAC patient samples were collected from the IRB-approved University of North Carolina Lineberger Comprehensive Cancer Center Tissue Procurement Core Facility and were flash frozen in liquid nitrogen.  FFPE samples were prepared, hematoxylin and eosin stained.

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

first: Xianlu

middle: L

last: Peng

first: Ian

last: McCabe


title: Delayed transcriptional response of Daphnia pulex to thermal stress

city: West Lafayette

first: Nathan

last: Backenstose

state: Indiana

address: 915 Mitch Daniels Blvd

institute: Purdue University

summary: Changing global climates present threats to aquatic ecosystems with events such as heatwaves and prolonged increased temperatures altering habitats and affecting species survival. Aquatic organisms are particularly vulnerable to these elevated temperatures often due to a lack of suitable migration routes. A decrease in population abundance and survival in species occupying lower trophic levels may have cascading effects on the health of an ecosystem. In this study, we investigated the fitness (fecundity) and transcriptional response of Daphnia pulex, a common grazer in lentic freshwater systems, to sublethal temperature stress. D. pulex were exposed to control (20℃) and elevated sublethal (25℃) temperature to simulate an increased water temperature from a mild heat wave for 168 hours. Our findings indicate a dynamic transcriptional response to elevated temperatures. Notably, differential gene expression between the control and temperature-elevated treatment increased throughout the experiment with a three-fold increase in counts of DEGs at 168 hours as compared to 96 hours. D. pulex within the experimental treatment had higher mean cumulative offspring produced compared to the control treatment. Given D. pulex’s role as a foundational species in aquatic food webs, the observed transcriptional response provides insight into the potential for both plastic and adaptive responses in the face of environmental change.

overall_design: RNA-Seq profiling of Daphnia pulex reared at 20 and 25C at day 4 and day 7.

first: Backenstose

last: Nathan

first: Christie

last: Mark


title: Immune Gene Diversity and STING1 Variants in Shaping Cancer Immunity Across Different Genetic Ancestry Populations

status: Public on Dec 17 2025

city: Philadelphia

first: Lin

state: PA

address: 421 Curie Blvd

institute: Univerisity of Pennsylvania

summary: As human populations migrated to diverse geographical regions, they encountered varying pathogens, leading to pronounced natural selection pressures on the immune system. Analysis of nonsynonymous single nucleotide polymorphisms (nsSNPs) across major geographically structured populations showed greater variation in immune-related genes than in non-immune genes, consistent with pathogen-driven selection, whereas cancer-related genes exhibited lower variation, reflecting evolutionary conservation of critical cellular functions. We prioritized nsSNPs in pattern recognition receptor genes based on population diversity and their association with type I interferon activity. Among the top-ranked variants were rs11554776, rs78233829, and rs7380824 in STING1, which demonstrated functional impacts on intrinsic cGAS-STING1-IFN signaling in cancer cells and potential influences on tumor immunity. We further conducted a genome-wide characterization of nsSNPs in immune-related genes across genetic ancestry populations and established a publicly accessible database. Our study suggests that genetic ancestry-related germline variations may influence cancer immunity and treatment, supporting their consideration in personalized medicine.

overall_design: The SK-OV-3 parent cells and clones obtained from the dual CRISPR/Cas9 experiment were treated with 2’3’-cGAMP for 30 minutes and then allowed to rest for 4 hours. Subsequently, cells were harvested immediately and extracted using TRIzol Reagent. Illumina mRNA TruSeq library preparation was employed, followed by sequencing on an Illumina NovaSeq platform with paired-end 150 bp reads.

first: Xiaowen

last: Hu

first: Jie

last: Huang

first: Zhongyi


title: Epigenetic Regulation of Serine Biosynthesis by PHF8 During Neurogenesis

city: Barcelona

first: Marta

middle: Artés

last: Hernández

address: Baldiri Reixac 15

country: Spain

institute: IBMB-CSIC

summary: During neurodevelopment, progenitor proliferation is a highly orchestrated process, involving precise epigenetic modifications and immense metabolic demands. Yet, the intricate interplay between epigenetics and metabolism remains largely unexplored. To investigate this, we utilized neural stem cells to examine the role of PHF8, a histone demethylase whose mutations are linked to Siderius-Hamel syndrome, a rare neurodevelopmental disorder. Through an integrated multi- omics approach—combining transcriptomics, epigenomics, and metabolomics—we identify PHF8 as a key driver of the serine biosynthesis pathway, safeguarding the intracellular serine pool essential for neural progenitor proliferation. PHF8 fine- tunes chromatin accessibility at promoters of metabolic genes, ensuring their activation during development. Notably, loss of PHF8 not only disrupts amino acid metabolism and mTORC1 signaling, but also blocks autophagic flux, and impairs vesicle formation—ultimately stalling proliferation and triggering replicative defects and DNA damage. In vivo, PHF8 deficiency in mouse embryos halts neurogenesis, affecting progenitor expansion and neuron generation in the developing brain. Altogether, our work positions PHF8 as a pivotal molecular node linking chromatin dynamics, metabolic regulation, and neural development. These findings not only deepen our understanding of brain development but also open new avenues for exploring the epigenetic basis of metabolic and neurodevelopmental disorders.

overall_design: Cells were infected with lentiviral shRNA either scramble (control) or against PHF8 (shPHF8), and then used for RNA extraction,  ChIP-seq or ATAC-seq

last: Artés

first: Simona

last: Iacobucci

first: María

last: Balladore

first: Paula

last: Caballeria

last: García

first: Alex

last: Pérez

first: Natalia

last: Padilla

first: Silvina

last: Natch

first: Guillermo

last: Vicent

last: Vaquero

first: Mariona

last: Arbonés

first: Xavier

last: de la Cruz

last: Nieto

first: Neus

last: Agell

first: Caroline

last: Mauvezin

first: Marian

last: Martínez


title: Spaceflight induces systemic effects on extracellular matrix and immune system in different age-stages

city: Saarbrücken

first: Friederike

last: Grandke

address: Saarbrücken Campus

institute: Saarland University

summary: Spaceflights significantly impacts astronaut health, causing muscle atrophy, bone loss, cardiovascular deconditioning and immune system dysregulation, especially during long missions. To explore molecular changes, we generated a single-cell RNA sequencing dataset, of 216 samples from 28 mouse organs and tissues under spaceflight and control conditions. Since spaceflight effects closely resemble aspects of aging, we included two age groups (3 and 8 months) to assess age-related influences. Our data revealed that spaceflight drives age-independent systemic changes, primarily affecting tissue remodeling and alterations in cytoskeleton, membrane and extracellular matrix (ECM), particularly in endothelial cells. In contrast, aging has a weaker impact, mainly altering immune regulation in an age-dependent manner. These findings suggest that cytoskeletal and ECM changes may contribute to immune Dysregulation.

overall_design:
We performed single-cell RNA-sequencing (scRNA-seq) on organ samples from four female Balb/C mice exposed to 40 days of spaceflight on the ISS, alongside four age-matched controls housed under identical conditions on earth (Figure 1A, 1B). Our study design incorporated two age groups, 3-months-old (young adult) and 8-months-old (mature adults), capturing the typical age range of astronauts. Three days after splashdown, the mice were taken down, and the tissues were immediately processed for single-cell RNA sequencing.

UPDATE: [Apr-22-2026] Due to a sample annotation error identified post-submission, the original tissue, age, and treatment labels for a subset of samples are unreliable. These have been reassigned to "unknown". The raw data and processed data remain unchanged.

first: Nicholas

last: Schaum

first: Fabian

last: Kern

first: Jérémy

last: Amand

first: Thomas

middle: H

last: Ambrosi

first: Teni

last: Anbarchian

first: Karl

last: Annusver

first: Reza

last: Ashrafi

first: Kruti

last: Calcuttawala

first: Shubhangi

last: Das Barman

first: Antoine

last: de Morree

first: Angela

last: Detweiler

first: Hala

last: Dhowre

first: Annika

last: Engel

first: Tobias

last: Fehlmann

first: Virginia

last: Ferguson

first: Matthias

last: Flotho

first: Astrid

last: Gillich

first: Michael

last: Haney

first: Yan

last: Hang

first: Pascal

last: Hirsch

first: Taichi

last: Isobe

first: Joanna

last: Kalucka

first: Maria

last: Kasper

first: Seung

last: Kim

middle: A

last: Kluiver

first: Davis

last: Lee

first: Song

first: Olivia

last: Leventhal

first: Ling

last: Liu

first: Catriona

middle: Y

last: Logan

middle: F

last: Lugo-Fagundo

first: Luca

last: Mannino

first: Maxim

last: Markovic

first: Maurizio

last: Morri

first: Shravani

last: Mukherjee

first: Norma

last: Neff

first: Patricia

last: Nguyen

first: Róbert

last: Pálovics

first: Weng

last: Peng

first: Maksim

last: Plikus

first: Ermelinda

last: Porpiglia


title: Transient Sprr1a expression defines a population of border zone cardiomyocytes that survive ischemic injury

status: Public on Dec 16 2025

city: Rochester

first: Cameron

last: Baker

state: NY

address: 601 Elmwood Ave

institute: University of Rochester

summary: Cardiomyocytes in the border zone (BZ) of a myocardial infarction (MI) reside directly adjacent to the ischemic core, a niche characterized by tissue necrosis, immune cell infiltration, and altered mechanical properties. Very few tools exist to study the BZ, limiting the development of strategies to prevent cardiomyocyte death and infarct expansion or promote heart regeneration. Here, we describe two novel mouse lines to visualize, track, and isolate BZ cardiomyocytes, which has revealed their transcriptional signature and surprising longevity.

overall_design: We subjected Sprr1a-GFP mice to MI at 12 weeks of age.  5 days after MI, we isolated cardiomyocytes by langendorff digestion. We separated GFP+ border zone myocytes from GFP- remote zone myocytes by flow cytometry using  a 130um nozzle and slow flow rate. RNA was isolated from the cell pellets and subjected to RNA-sequencing. n= 5 mice.

first: Eric

middle: M

last: Small

first: Emily

last: Marshall

first: Daniel

last: Zuppo

first: Kimberly

middle: N

last: Burgos Villar


title: The mechano-biological microenvironment of pancreatic ductal adenocarcinoma

city: London

first: Eleni

last: Maniati

address: John Vane Science Centre, Charterhouse Square

department: Barts Cancer Institute

country: United Kingdom

institute: Queen Mary University of London

summary: GelMA hydrogels of different stiffness (5% and 7.5%) provide a microenvironment capable of directing not only pancreatic cancer cell growth but also stiffness- and matrisome-related gene programs. BxPC-3 and PANC-1 cells were chosen for this analysis as representative epithelial and mesenchymal-like cell lines respectively. Transcriptomic signatures of GelMA-embedded cells were compared against those of cells cultured in commonly-used collagen hydrogels (Col).

overall_design: RNA sequencing was performed on the pancreatic cancer cell lines BXPC3 and PANC1 embedded in GelMA or in collagen hydrogels. Two replicates per condition were analysed per cell line.

first: Eleonora

last: Peerani

first: Juliana

last: Candido

first: Daniela

last: Loessner


title: HPA-Gut Microbiome Axis Dysregulation in Sleep Deprivation: Pharmacological and Microbial Rescue of Lacrimal Gland Homeostasis

city: ZHENGZHOU

first: SHENZHEN

last: HUANG

address: Weiwu Road No. 7

institute: Department of Ophthalmology, Zhengzhou University People's Hospital, Henan Provincial People's Hospital

summary: Sleep deprivation (SD) disrupts systemic homeostasis, yet its impact on lacrimal gland integrity through neuroendocrine–microbial pathways remains unclear. Using a male mice SD model, we show that chronic SD activates the hypothalamic-pituitary-adrenal (HPA) axis, elevates corticosterone, alters gut microbiota, and depletes short-chain fatty acids (SCFAs). These alterations coincide with lacrimal gland atrophy, reduced tear secretion, and increased CD4⁺/CD8⁺ T cell infiltration, accompanied by activation of IL-17-associated inflammatory pathways. Pharmacological inhibition of glucocorticoid synthesis with metyrapone preserves lacrimal gland structure and function while attenuating immune activation. Microbiome-directed interventions, including SCFA supplementation and fecal microbiota transplantation, rebalance gut communities, suppress proinflammatory T cell responses, and maintain lacrimal gland homeostasis. Transcriptomic and immunohistochemical analyses further reveal that all three interventions converge on downregulation of IL-17 signaling. Collectively, these findings establish an HPA-gut microbiome-lacrimal gland axis links neuroendocrine stress to microbial dysbiosis and ocular inflammation, and they suggest therapeutic strategies for SD-associated lacrimal gland dysfunction.

overall_design: Two ELGs from each male mouse were pooled to form a single sample, resulting in six samples from six adult mice for scRNA-seq.

first: Shenzhen

last: Huang

first: Zhijie

last: Li


title: A dual role for GLI3 signaling in neural crest development

status: Public on Dec 25 2025

city: Cincinnati

first: Simon

middle: J. Y.

last: Han

state: OH

address: 3333 Burnet Ave

institute: Cincinnati Children's Hospital Medical Center

summary: Neural crest cells (NCCs) are a multipotent cell population that undergo specification, epithelial-to-mesenchymal transition, migration, and differentiation into a plethora of cell types. A wealth of studies across various embryonic model systems have established dogma as to the molecular mechanisms and signaling cascades that contribute to NCC development. While Wnt, FGF, and BMP signaling pathways have well-established and essential roles in several aspects of NCC development, the Hedgehog (HH) signaling pathway has received limited attention for any specific role in this process. Herein, we propose two distinct, temporal roles for the transcription factor GLI3 in NCC development. Gli3, and other members of the HH pathway, were robustly co-expressed with established NCC induction and specification markers in chick, mouse, and human embryonic stem cell derived NCCs. Early knock-down of GLI3 reduced expression of key markers of NCC specification and conditional knock-out of Gli3 post-specification specifically impaired the ability of cranial NCCs to differentiate into ectomesenchymal derivatives. Together, these results demonstrate dual, novel roles for GLI3 in early NCC specification and later in cranial NCC differentiation.

overall_design: scRNA-seq of E13.5 Gli2f/f;Gli3f/f; Wnt1-Cre mandibular prominences

first: Kelsey

last: Elliott

first: Samantha

last: Brugmann


title: Time-course analysis of gene expression of HT29 human colon cancer cells incubated with Methotrexate

status: Public on Dec 15 2025

first: Carlos

last: Ciudad

state: Barcelona

address: Av. Juan XXIII-27

department: Biochemistry and Molecular Biology

institute: University of Barcelona

summary:
We had previously analyzed the gene expression changes observed in HT29 colon cancer cells resistant to Methotrexate (MTX). Now, we explored the expression changes produced by short term incubation with MTX
HT29 cells were incubated with 70 nM Methotrexate for 0, 8, 24 and 48 h, RNA extracted and Affymetrix Exon microarrays performed to determine gene expression

overall_design: The HT29 human colon cancer cell line sensitive to methotrexate was used in the study. 12 samples are provided, which correspond to triplicates of 4 experimental conditions. The conditions were cells incubated with 70 nM MTX for 0,8,24 and 48 h. The platform used was:  Affymetrix.ExonExprChip.HuGene-1_0-st-v1 (na31_hg19_2010-09-03)

first: Veronica

last: Noe

first: Nuria

last: Mencia


title: KRAS-Dependent Metabolic Reprogramming of Endothelial Cells as a Therapeutic Vulnerability in Brain Arteriovenous Malformations

city: Toronto

first: Ruilin

last: Wu

state: Ontario

address: 101 College Street

country: Canada

institute: University of Toronto

summary: Brain arteriovenous malformation (bAVM) is a disease characterized by the formation of tangled blood vessels with direct connections between arteries and veins. There is currently limited understanding of the underlying molecular mechanisms that are responsible for the development of bAVM. Our previous work identified the presence of somatic activating KRAS mutations in endothelial cells (ECs) isolated from clinical bAVM tissue. Given the association between mutant KRAS, metabolic reprogramming and EC angiogenesis, we aimed to investigate if altered endothelial metabolism is involved in the pathogenesis of bAVM to drive abnormal vascular remodeling. As such, we engineered a human EC model with inducible expression of mutant KRAS G12V. We observed a significant increase in glucose metabolism upon mutant KRAS expression. This elevation in EC glycolysis contributes to the angiogenic behaviours that are observed in our mutant KRAS EC models. To further explore the transcriptional alterations underlying these changes, we performed this RNA-sequencing study with various glycolysis inhibitors and a MEK inhibitor (the major signaling pathway altered in mutant KRAS ECs) to profile the impact of glucose metabolism changes on endothelial biology.

overall_design: Bulk mRNA sequencing of telomerase-immortalized human umbilical vein endothelial cells (Telo-HUVECs) with stable expression of KRAS G12V proteins. The mutant KRAS cells were treated with various glycolysis inhibitors and a MEK inhibitor to examine the effects of glycolytic and MAPK/ERK pathway suppression on the transcriptional landscape of mutant KRAS endothelial cells.

first: Negar

last: Khosraviani

first: Ann

last: Mansur

first: Emilie

last: Boudreau

first: Dakota

last: Gustafson

first: Sneha

last: Raju

first: Crizza

last: Ching

first: Amira

last: Klip

first: Thomas

last: Wälchli

first: Kathryn

last: Howe

first: Ivan

last: Radovanovic

first: Joshua

last: Wythe

first: Jason

last: Fish


title: Fat mass and obesity-associated (FTO)/SOCS6-m⁶A axis epigenetic modification links obesity to atopic dermatitis by regulating keratinocyte function

status: Public on Dec 14 2025

city: Changsha

first: Zeng

last: Jinrong

address: No.138 Tongzipo Rd, Yuelu District, Changsha, Hunan, China, 410013

institute: the Third Xiangya Hospital, Central South University

summary: Atopic dermatitis is one of the severe skin diseases. Keratinocytes, as the epidermal barrier cells, are an important component for maintaining the skin barrier function. In this dataset, we have included the m⁶A methylation RNA data obtained from normal human keratinocytes (N group) and keratinocytes from patients with atopic dermatitis (AD group).

overall_design: We generated the following comparisons using Fold-change (FC) ≥ 1.5 or ≤ 0.5, and p < 0.05 were used to identify the differentially m6A methylated RNAs.The total RNAs were immunoprecipitated with anti-N6-methyadenosine (m6A) antibody. The modified RNAs were eluted from the immunoprecipitated magnetic beads as the “IP”. The unmodified RNAs were recovered from the supernatant as “Sup”.  Two channel arrays were used for these samples but the data were analyzed as single-channel so that each sample  represents either IP or supernatent and the sample table includes the normalized signal values.

first: Fugang

last: Xiao

first: Jinrong

last: Zeng


title: Epigenetic Regulation of Serine Biosynthesis by PHF8 During Neurogenesis [ChIP-Seq H3K9me3]

first: Marta

last: Hernández

overall_design: 1x 10^6 shCTR and shPHF8 NSCs were cross-linked with Cross-link Gold 0.4% (Diagenode, C01019027) in PBS 30 minutes, and then fixed with methanol-free formaldehyde 1% for 10 min and stopped with 0.125 mM glycine for 10 minutes. Sonication was performed using a Bioruptor sonicator. The libraries were prepared and amplified to make DNA NanoBall (DNB) Libraries were loaded into a nanoarray and single end 50 base pairs reads were generated by combinatorial Probe-Anchor synthesis (cPAS)

last: Artés

first: Simona

last: Iacobucci

first: María

last: Balladore

first: Paula

last: Caballeria

last: García

first: Alex

last: Pérez

first: Natalia

last: Padilla

first: Bárbara

last: Viegas

first: Aitana

last: Díaz

first: Silvina

last: Natch

first: Guillermo

last: Vicent

last: Vaquero

first: Mariona

last: Arbonés

first: Xavier

last: de la Cruz

last: Nieto

first: Neus

last: Agell

first: Caroline

last: Mauvezin

first: Marian

last: Martínez


title: EGR proteins mediate interferon-independent anti-HSV-1 responses through viral and host targets

status: Public on Dec 13 2025

city: Hangzhou

first: Shuaishuai

last: Wang

address: 866 Yuhangtang Road

institute: Zhejiang University

summary: Herpes simplex virus type I (HSV-1) establishes a latent infection that evades the host's defense system, and the latent virus can be reactivated by some stimulation. At present,a key problem in the latent studies of HSV-1 has not been clarified, that is, HSV-1 mainly selectively latent in neurons. Therefore, we have found the host transcription factor EGR in Neuro-2a cells by RNA-seq. EGR1 regulates HSV-1 replication and latency by binding to the viral genome or recruiting co-factors. Our data intend to find the role and mechanism of EGR family repressing HSV-1 replication and promoting HSV-1 latency. This study will provide a theoretical basis for the development of drugs to treat of HSV-1 infection.

overall_design: Neuro-2a cells( knockout EGR1) were cultured in 100-mm plates for 24 h and then infected with KOS virus strain for 5 h  before being harvested for chip-seq. Library preparation and sequencing were performed by Novogene.

first: Dongli

last: Pan

first: Yuhang

last: Xiang


title: DeCAF redefines fibroblast states uncovering multidimensional tumor-stroma relationships driving clinical tumor progression and immunotherapy response

first: Jen Jen

last: Yeh

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

overall_design: Refer to individual Series


overall_design:
Neuro-2a cells( knockout EGR1) were transfected with pEGR1 or pcDNA plasmid for 24 h and then infected with KOS virus strain for 10 h (MOI = 0.5) before being harvested for RNA extraction using a LS1040 Eastep Super total RNA extraction kit (Promega). Library preparation and sequencing were performed by BGI.

pcDNA is mock group, that transfected pcDNA plasmid;EGR1human is experiment group, that transfected EGR1 plasmid. And they all infected HSV-1 10h.
pc is mock group, that transfected pcDNA plasmid; e1human is experiment group, that transfected EGR1 plasmid. And they all infected HSV-1 3h.


title: Oxidative Stress Signaling and Regenerative Responses in a Larval Zebrafish Model of Retinal Light Damage

city: Messina

first: Luigi

last: Donato

state: Italy

address: via Consolare Valeria, 1

department: BIOMORF

country: Italy

institute: University of Messina

summary: The zebrafish (Danio rerio) is widely used to investigate the cellular and molecular mechanisms that support retinal regeneration. Although several adult injury paradigms have been established, models that capture the earliest stages of degeneration and Müller glia-mediated repair in larvae remain comparatively underexplored. Here, we validate a light-induced retinal degeneration (LIRD) paradigm at the larval stage as a tractable system to study acute phototoxic injury and early regenerative responses. This approach enables high-throughput RNA sequencing and provides a comprehensive transcriptomic view of retinal responses 48 hours after injury. At this timepoint, larvae display photoreceptor loss and robust Müller glia activation and proliferation, mirroring key features described in adult LIRD models. Transcriptomic analyses further highlight both canonical and previously undercharacterised pathways engaged during the early injury response. Together, this work establishes larval LIRD as a practical and informative model and provides a resource for hypothesis-driven studies aimed at dissecting the molecular events that initiate retinal regeneration.

overall_design: Two experimental groups were analyzed: control and light damage (LIRD) (n = 10–11 animals per group). Retinal RNA-seq was performed on Danio rerio (paired-end 150 bp, Illumina NovaSeq 6000). Differential expression and pathway analyses were conducted to assess the impact of LIRD.

first: Ignacio

last: Babiloni-Chust

first: S.

last: Sartori

first: Darin

last: Zerti

first: Matthias

last: Carl

first: Rosalia

last: D’Angelo

first: Rita

last: Maccarone

first: Lucia

last: Poggi


title: Single‑cell RNA sequencing unveils fibroblast heterogeneity in proliferative vitreoretinopathy membranes

city: Shanghai

first: Xin

last: Huang

address: No.83, Fenyang Rd.

institute: Fudan University

summary: Proliferative vitreoretinopathy (PVR) is a vision-threatening fibrotic disorder characterized by pathological membrane formation, yet its cellular and molecular mechanisms remain incompletely understood. Here, we employed single-cell RNA sequencing (scRNA-seq) to profile 18,213 cells from 5 human PVR membranes (PVRMs), uncovering cellular heterogeneity and novel pathogenic pathways.

overall_design: BD Rhapsody system was used to capture the transcriptomic information of the single cells. Single-cell capture was achieved by random distribution of a single-cell suspension across >200,000 microwells through a limited dilution approach.

first: Fengjuan

last: Gao

first: Gezhi

last: Xu


title: study on the role and mechanism of SOCS6 in keratinocytes

first: Zeng

last: Jinrong

summary: Atopic dermatitis is a severe skin disorder. Keratinocytes, as the epidermal barrier cells, are an important component in maintaining the skin barrier function. The role of SOCS6 in keratinocytes is still unclear. In this dataset, we extracted keratinocytes from the foreskin tissue of healthy individuals and conducted mRNA sequencing data for SOCS6 knockdown (KD) and overexpression (OE).

overall_design: Knockdown and overexpression of SOCS6 were respectively compared with the control group to explore the effect of SOCS6 on keratinocytes.

first: Fugang

last: Xiao

first: Jinrong

last: Zeng


title: Mycobacterial Metallophosphatase MmpE Functions as a Nucleomodulin to Regulate Host Gene Expression and Promote Intracellular Survival

status: Public on Dec 12 2025

city: Wuhan

first: Liu

last: Chen

address: No.1 Shizishan Street, Hongshan District

department: College of Animal Science & Technology

institute: Huazhong Agricultural University

summary: Nucleomodulins are bacterial effectors that target host cell nuclei and play crucial roles as virulence factors in mycobacterial pathogenesis. Mycobacterium tuberculosis, the causative agent of tuberculosis, presents a significant global health challenge; however, the mechanisms of nucleomodulins in Mtb remain unclear. In this study, we characterize the hypothetical protein Rv2577 (designated MmpE) as a critical nucleomodulin involved in immune evasion and intracellular persistence. We performed ChIP-seq in HEK293T cells transfected with EGFP-MmpE, identifying 2,903 potential MmpE-binding sites: 537 in intergenic regions and 1,144 in intragenic regions. Remarkably, 99.7% (2,894) of these sites were associated with protein-coding regions. Among them, 1,013 sites were located within 3 kb of transcription start sites (TSS), primarily targeting promoter regions (<1 kb: 63.18%; 1–2 kb: 22.9%; 2–3 kb: 13.92%), indicating MmpE’s role in transcription regulation. Further analysis of the 1,013 potential target genes revealed significant enrichment in protein kinase-related genes, such as PRKCB, PLCG2, and PIK3CB, involved in immune activation and inflammatory responses via the PI3K–Akt and mTOR signaling pathways. Additionally, we identified four transcription factors (CREBBP, VDR, GREB1, and FOXP4) that MmpE directly targets in their promoters. This finding points to the critical role of MmpE in shaping host immune responses and highlights its potential as a therapeutic target in combating Mycobacterium tuberculosis infections.

overall_design: This study used CUT&Tag to identify genome-wide binding sites of the MmpE protein in HEK293T cells. Cells were transfected with either MmpE-pEGFP or empty pEGFP-N1 vector as a control. After 36 hours, cells were harvested and subjected to CUT&Tag using an anti-GFP antibody to target MmpE-bound chromatin regions. Libraries were sequenced on the Illumina NovaSeq 6000 platform. Peaks were identified using MACS2, and downstream analyses including genomic annotation, GO enrichment, and motif discovery were performed using HOMER and TOMTOM.

first: Chen

last: Liu

first: Baojie

last: Duan

first: Qiang

last: Jiang

first: Yifan

last: Wang

first: Yingyu

first: Lei

last: Zhang

first: Aizhen

last: Guo


title: Functional chromatin signatures premark future lineage-specific enhancers [ChIP-Seq 2]

city: New York

first: Julian

last: Pulecio

department: Developmental Biology

institute: Memorial Sloan Kettering Cancer Center

summary: It remains unknown whether early embryonic cells harbor a blueprint for future enhancers that regulate the expression of lineage-specific genes in adult tissues. Here, we demonstrate that embryonic stem cells (ESCs) have transcriptionally competent chromatin regions (CCRs) prepared to induce the expression of lineage genes prior to differentiation. CCRs represent activatable pre-enhancers within the topological chromatin domains of lineage genes, marked by chromatin signatures distinguishable from primed/poised enhancers, enabling their genome-wide identification. The pioneer transcription factor (TF) FOXA2 preferentially binds CCRs during early lineage specification, promoting their conversion into active enhancers. CCRs can be harnessed to boost the expression of master TFs and promote the direct reprogramming of ESCs into differentiated cells, showcasing their potential for practical applications. Our findings identify a mechanism by which ESCs rapidly establish enhancer activity during early lineage differentiation and expand our understanding of the epigenetic features supporting transcriptional regulation and cellular plasticity.

overall_design: 2 biological replicates for each condition (ESC and DE timepoints) and WT and TET1/QSER1 double-KO (DKO) cells.

first: Danwei

last: Huangfu

first: Denis

last: Torre


title: Glycaemic variability underlies myocyte dysfunction and myocardial injury risk in diabetes

city: Brisbane

first: Yuanzhao

last: Cao

state: QLD

address: 306 Carmody Road

department: Institute for Molecular Bioscience

country: Australia

institute: The University Of Queensland

summary: This study evaluates mechanisms of glycaemic stress underpinning cardiovascular risk in diabetes. Using in vitro and in vivo models, we demonstrate that glycaemic variability rather than hyperglycaemia alone is a dominant risk factor for heart muscle dysfunction and myocardial injury sensitivity in diabetes. These findings provide new preclinical models for mechanistic and drug discovery studies and inform strategies for managing cardiovascular outcomes in patients with diabetes.

overall_design: hiPSC-CMs cultured in backbone media conditions or underwent constant and variable glycaemic stress disease modelling, and cells were harvested for RNA preparation and genome-wide RNA sequencing.

first: Woo Jun

last: Shim

first: Nathan

last: Palpant


title: Reversible Fibroblast Trajectories Regulated by MR Underlie Diastolic Dysfunction

status: Public on Dec 09 2025

city: Freiburg

first: Achim

last: Lother

state: --- Select One ---

address: Albertstr. 25

department: Institute of experimental and clinical Pharmacology and Toxicology,

institute: University of Freiburg

summary: Heart failure with preserved ejection fraction (HFpEF) is driven by co-morbidities. While specific treatments to enable recovery of HFpEF are lacking, recent clinical trials indicate beneficial effects of mineralocorticoid receptor (MR) antagonists. Here, we performed single nucleus RNA sequencing in an aldosterone/salt-induced model of cardiorenal HFpEF in mice and compared it to the high fat diet/L-NAME model of cardiometabolic HFpEF. We found a fibroblast subtype induced that is distinct from the classical myofibroblast observed in heart failure with reduced ejection fraction. Notably, after aldosterone withdrawal the HFpEF-like phenotype fully recovered. This was linked to a restored expression of MR target genes and an upregulation of collagen III, VI, and XV in fibroblasts during recovery. MR deletion from fibroblasts prevented cardiac remodeling and diastolic dysfunction, confirming the central role of fibroblast MR in cardiorenal HFpEF. In summary, our study reveals fibroblast gene expression signatures in heart failure from different causes that may determine the response to pharmacological treatment and potential for recovery.

overall_design: single nucleus RNAseq of mouse left ventricular free-wall tissue after aldosterone infusion with and without recovery and untreated control

first: David

last: Meral

first: Argen

last: Mamazhakypov

first: Duygu

last: Koca

first: Ramona

last: Emig

first: Rémi

last: Peyronnet

first: Sebastian

last: Preissl


title: Integrated  stress response and Drug-Induced Acute Kidney Injury: Involvement of ATF4-STAT1-GBP2 Signaling

status: Public on Dec 11 2025

city: Ningbo

first: Xiaoyan

last: Sun

address: 247 Renmin Road, Jiangbei District, Ningbo City, Zhejiang Province, China

institute: Fudan University,The First Affiliated Hospital of Ningbo University,

summary: Background: Pyroptosis plays a critical role in eliminating pathogens and facilitating tissue repair; however, sustained pyroptosis-driven inflammation accelerates kidney injury and disease progression. Thus, elucidating the mechanisms governing pyroptosis is essential for developing effective therapies for inflammatory kidney diseases such as acute kidney injury (AKI), which currently lacks specific treatment options. Methods: Changes in tubular epithelial cells following drug-induced AKI were assessed using single-cell RNA sequencing, immunohistochemistry, and immunofluorescence. Mechanistic insights were obtained through RNA sequencing, genomic manipulation, transcriptomic profiling, luciferase reporter assays, co-immunoprecipitation, and Western blotting. Tubular epithelial cell fate was further evaluated using transgenic mouse models and pharmacological interventions. Results: We identified activating transcription factor 4 (ATF4) as a key regulator of inflammation in drug-induced AKI. As the master regulator of the integrated stress response, ATF4 was markedly upregulated in renal tubules and positively correlated with kidney dysfunction in both human and murine AKI models. The specific deletion of ATF4 in tubular epithelial cells significantly ameliorated kidney dysfunction, inflammation, and mitochondrial apoptosis, whereas ATF4 activation exacerbated these pathological features. Mechanistically, ATF4 suppression inhibited STAT1 phosphorylation and disrupted its interaction with GBP2, thereby attenuating NLRP3 inflammasome activation, preventing tubular epithelial cells' pyroptosis, and improving kidney function. Notably, inhibition of ATF4—either pharmacologically using our prioritized integrated stress response antagonist ERMT1 or through engineered nanobiologics-mediated silencing of tubular epithelial cells—significantly reduced renal inflammation and injury. Conclusions: ATF4 promoted pyroptosis in drug-induced AKI through STAT1–GBP2 signaling.

overall_design: Transcriptional profiling was performed via high-throughput RNA sequencing (RNA-seq) on murine renal tissues. The study cohort comprised a total of nine samples, stratified into three distinct experimental groups with three biological replicates per group (n=3):Vehicle-treated  controls (ATF4_flox/flox + Vehicle);Cisplatin-treated mice (ATF4_flox/flox + Cisplatin);Cisplatin-treated Atf4 knockout mice (Atf4-/- + Cisplatin).

first: Hongli

first: Wei

last: Chen


title: Delineating the role of co-stimulatory signals on human virus-specific memory CD8+ T cell activation and expansion using highly selective T cell receptor-targeted biologics

status: Public on Dec 08 2025

city: Bronx

first: Harris

last: Goldstein

address: 1300 Morris Park Avenue

department: Pediatrics

institute: Albert Einstein College of Medicine

summary: To delineate the minimum signals required to activate and expand antigen-specific memory CD8+ T cells, we recapitulated the discrete activation signals delivered by antigen-presenting cells using antigen-specific T-cell receptor-specific biologics termed Immuno-STAT (IST), which can specifically deliver a T cell receptor (TCR) signal alone or paired with a defined co-stimulatory signal to antigen-specific CD8+ T cells. Using a reductionist approach that provides defined TCR and co-stimulatory signaling, we demonstrated that different IST could engage TCR alone or in combination with either CD28 or 4-1BB to initiate distinct transcriptional programs in memory CMV-specific CD8+ T cells. As compared to activation by TCR signaling alone, the combination of TCR and CD28 or 4-1BB co-stimulatory signals significantly altered the transcriptome and drove expression of genes related to growth and survival. Nevertheless, TCR signaling in the presence of IL-2 (5 U/ml) was sufficient for robust recall activation and expansion of functional cytomegalovirus CMV(NLV)-specific and HIV(SL9)-specific memory CD8+ T cells. This response contrasts with naïve CD8+ T cells, which required CD28 co-stimulation in addition to TCR stimulation for antigen-specific activation and expansion even in the presence of high levels of IL-2 (100 U/ml). These results have important implications for antigen-specific immunotherapy by indicating that biologics that deliver TCR signals alone in the presence of IL-2 may be sufficient for immunotherapeutic strategies designed to expand memory CD8+ T cells to eliminate cancerous or infected cells. In contrast, strategies that aim to stimulate naïve T cell responses may benefit from the codelivery of TCR and CD28 signals.

overall_design: To understand the transcriptional response of CMV-specific memory CD8 T cells to TCR-stimulation with or without CD28 or 4-1BB co-stimulation, human PBMC were stimulated with a pMHC-based TCR agonist linked to either a CD28 or 4-1BB agonist. After stimulation, CMV-specific CD8 T cells were collected using FACS and RNA was isolated. Replicates were samples of PBMC from the same donor that underwent treatment, cell sorting, RNA isolation, and sequencing independently. Samples that received no treatment or retreatment were used as controls.

first: Christopher

last: Hiner

first: Hong

last: Hur

first: April

last: Mueller

first: Manoj

last: Kandpal


title: The single-cell transcriptional landscape of the pediatric cystic fibrosis airway from minimally invasive respiratory specimens

status: Public on Dec 10 2025

first: Yifei

address: 1468 Madison Ave

institute: Icahn School of Medicine at Mount Sinai

summary: Cystic fibrosis (CF) is a multisystemic, autosomal recessive disorder caused by mutations in the cystic fibrosis transmembrane conductance regulator (CFTR) gene with the majority of morbidity and mortality extending from lung disease. In this study, we leveraged single-cell transcriptional analyses to characterize the immune and airway epithelial cell populations in minimally invasive respiratory specimens obtained from pediatric patients with CF and pediatric non-CF controls at the time of clinically indicated flexible bronchoscopy. We focused on the pediatric population in an effort to better understand the early pathophysiology of CF lung disease. Through our approach, we provide insights into the composition of and functional changes within the immune and airway epithelial cell populations in the pediatric CF lung. Understanding the early pathophysiology of CF lung disease, including the changes present in the early cycles of airway infection, inflammation, and tissue damage, may reveal new potential therapeutic targets for CF lung disease.

overall_design: Bronchoalveolar Lavage (BAL), bronchial brush  and tracheal brush samples were collected from CF and non-CF patients. Samples were cleaned and made into  single-cell suspensions, then immediately processed according to manufacturer’s instructions.

first: Alfin

middle: G

last: Vicencio

first: Mary

middle: B

last: Beasley

first: Martin

last: Walsh

first: Megan

last: Januska


title: Differential transcriptional effects of mycobacterial nucleomodulins MgdE and MmpE in THP-1 macrophages

status: Public on Dec 05 2025

first: Liu

summary: This study uses RNA-seq to quantitatively compare the gene expression profiles of THP-1 macrophages infected with the wild-type (WT), mgdE-deleted (ΔmgdE), and mmpE-deleted (ΔmmpE) strains of Mycobacterium bovis BCG, in order to investigate the roles of two conserved nucleomodulins, MgdE (Rv1075c) and MmpE (Rv2577), in host-pathogen interactions.

overall_design: RNA-seq profiling was performed on THP-1 macrophages infected for 24 h with wild-type (WT), ΔmgdE, and ΔmmpE strains of M. bovis BCG. Each condition included three biological replicates, with the WT group serving as a shared control for both mutants

first: Chen

last: Liu

first: Baojie

last: Duan

first: Qiang

last: Jiang

first: Yifan

last: Wang

first: Yingyu

first: Changmin

last: Hu

first: Lei

last: Zhang

first: Aizhen

last: Guo


title: Germ cell motility clock

city: Münster

first: Katsiaryna

last: Tarbashevich

state: NRW

address: Von-Esmarch-Str. 56

department: Institute of Cell Biology

institute: University Münster

summary: Organ development relies on interactions among different cell types that form three-dimensional structures to carry out specific tasks. This process often involves active migration of progenitor cells toward specific positions within the embryo, where the cells then become immotile and form stable connections among each other and with neighboring cell types. Yet, surprisingly little is known about processes of motility loss and the emerging organization of the cells at the site where the organ forms. In this work, we study these the process of motility loss processes using zebrafish primordial germ cells as an in vivo model. We show that changes in embryonic tissues as well as cell-autonomous events regulate germ cells’ behavior as they arrive at their target region. Importantly, we find that reduction in germ cell motility is correlated with the decay of RNA encoding for Dead end 1 (Dnd1), a conserved vertebrate RNA-binding protein that is essential for PGC migration. Indeed, decreasing or increasing the level of Dnd1 results in a premature or delayed stop to motility, respectively. These findings represent a novel RNA decay-based mechanism for timing the duration of cell migration in vivo.

overall_design: RNA-seq profiling of the zebrafish primordial germ cells (PGCs) positioned at the gonad region (wild-type condition) and at ectopic sites (ody mutant condition) at 2 developmental stages (24 and 36 hpf)

first: Zahra

last: Labbaf

first: Jan

last: Schick

first: Lucas

last: Kühl

first: Sargon

last: Gross-Thebing

first: Moritz

last: Ophaus

first: Michal

last: Reichman-Fried

first: Dennis

last: Hoffmann

last: Stehling

first: Jochen

last: Seggewiss

first: Jan Philipp

last: Junker

first: Erez

last: Raz


title: A Serum-free Culture Medium for Long-term Expansion of Human Airway Basal Stem Cells

city: Guangzhou

first: Mingyue

last: Jiang

address: No. 74, Zhongshan Second Road, Yuexiu District, Zhongshan University North Campus

institute: Sun Yat-sen University

summary: Background: Human basal stem cells, with their self-renewal and multilineage differentiation capacity, are essential tools for modeling airway diseases and advancing regenerative medicine. However, existing culture systems often rely on undefined components like serum, bovine pituitary extract, or feeder cells, limiting reproducibility and clinical translation. To address this limitation, we developed a well-defined culture medium that enables the long-term expansion of human airway basal stem cells while preserving their proliferative and differentiation potential. Methods: We formulated a novel medium (sfBSC) comprising 14 defined components, including basal media, supplements, growth factors (EGF, FGF10), and signaling inhibitors (Y-27632, A-83-01, DAPT, DMH1). Human bronchial and small airway epithelial cells were cultured over multiple passages in sfBSC and assessed for morphology, population doublings, marker expression, and differentiation capacity via air-liquid interface and organoid cultures. RNA-seq was performed to explore molecular changes across passages. Results: Bronchial and small airway epithelial cells were expanded up to 17 and 24 passages, respectively, with stable morphology and consistent cell size (10-15 μm). Cells maintained expression of canonical BSC markers (TP63, KRT5, NGFR) throughout long-term culture. Differentiation assays confirmed the ability to generate ciliated, goblet, and club cells. Optimized concentrations of EGF (1 ng/mL) and FGF10 (0.4 ng/mL) were critical for sustained proliferation. RNA-seq revealed stable marker expression and metabolic changes over time.Conclusions: sfBSC medium offers a defined, reproducible, and scalable platform for basal stem cell culture, enabling applications in disease modeling, regenerative medicine, and clinical-grade cell production.

overall_design: RNA-seq pofiling of HBECs (P3, P6, P9, and P13) and HSAECs (P2, P7, P14, and P21) cultured in a novel medium (sfBSC)


title: IL-22 induces Paneth cell metaplasia in the colonic epithelium of ulcerative colitis, promoting wound healing via REG3A [mouse RNA-seq]

status: Public on Dec 03 2025

city: Kiel

first: Joana

middle: P.

last: Bernardes

state: SH

address: Am Botanischen Garten 11

department: Systems Immunology

institute: IKMB

summary: Paneth cell metaplasia (PCM) is a phenomenon in which Paneth cells, typically found in the small intestine, appear in the colonic epithelium of patients with ulcerative colitis (UC). Our study demonstrates that the PCM occurrence correlates with disease duration and active inflammation. Furthermore, we reveal that the inflammation-induced cytokine IL-22 suppresses Notch signaling, thereby promoting PCM formation in the colonic epithelium while simultaneously inducing REG3A expression in metaplastic niches. In vitro, we show that Reg3a directly enhances cell proliferation and promotes wound healing using mouse colonic organoids. In vivo, Reg3aΔIEC mice in both acute and chronic DSS-induced colitis models exhibit delayed wound healing. Additionally, studies conducted with patient-derived human colonic organoids revealed that REG3A administration stimulates cell proliferation and accelerates wound healing. These findings underscore a novel protective role of PCM-mediated REG3A in the colonic epithelium of patients with UC.

overall_design: RNA-seq analysis comparing Reg3afl/fl and Reg3aΔIEC mouse colonic organoids.

first: Muto

last: Tomohiro

first: Go

last: Ito

first: Hiromune

last: Katsuda

first: Yui

last: Hiraguri

first: Satoru

last: Fujii

first: Kurara

last: Yamamoto

middle: P

first: Finn

last: Hinrichsen

first: Uchida

last: Hitoshi

first: Yasuhiro

last: Nemoto

first: Mayumi

last: Kinoshita

first: Eri

last: Ooshina

first: Kouhei

first: Shuji

last: Hibiya

first: Sayaka

last: Nagata

first: Fenja

last: Schuran

first: Shiro

last: Yui

first: Penelope

last: Pelczar

first: Samuel

last: Huber

first: Stefan

last: Schreiber

first: Philip

last: Rosenstiel

first: Mamoru

last: Watanabe

first: Ryuichi

last: Okamoto


title: Severe preeclampsia is not associated with significant DNA methylation difference but cell proportion in cord blood

city: Ann Arbor

first: Lana

last: Garmire

state: Michigan

address: 1600 Huron Parkway

institute: University of Michigan

type: Genome binding/occupancy profiling by genome tiling array

summary: Preeclampsia (PE) is a severe pregnancy complication that threatens maternal and neonatal health and well-being. Previous studies on epigenome-wide association analysis (EWAS) of preeclampsia produced inconsistent results, and one possible explanation is their failure to rigorously adjust for confounders. Here, we calculated the DNA methylation change in cord blood from newborns affected by preeclampsia, using a multi-ethnic cohort from Hawaii populations. We comprehensively adjusted confounders from clinical variables such as maternal age, BMI, parity and estimated the cell proportions, in hope of resolving the conflicting results of preeclampsia’s impact on babies epigenetic-wide profile.We showed that after adjusting cell type proportions and patient clinical characteristics, most of the so-called significant CpG methylation changes associated with severe PE disappear. Rather, the major effect of severe PE on cord blood is through the proportion changes in CD8T and natural killer (NK) cell types. We validated such a lack of CpG methylation changes, using multiple previously published cord blood DNA methylation datasets. Moreover, we found that in additional to severe PE,  gestation progression is accompanied by significant proportion changes in several cell types, such as granulocyte, nRBC, CD8T, and B cells. In summary, our study shows that the previously reported significantly differentially methylated patterns are actually artifacts due to confounding of cell type heterogeneity and clinical factors such as gestational age. Severe preeclampsia is not associated with significant DNA methylation changes but cell proportion changes. This finding alerting the scientific rigor needed in EWAS.

overall_design: The umbilical cord whole blood DNA samples were obtained from Hawaii Biorepository (HiBR).  The HiBR collected placenta, maternal, and cord blood samples from deliveries at Kapiolani Women and Children’s Hospital from 2006 to 2013. Severe PE was characterized by OBGYNs at Kapiolani Medical Center as sustained pregnancy-induced hypertension(systolic/diastolic blood pressure >= 140/90) with urine protein and/or organ dysfunction. We originally collected 63 samples. The demographic and clinical information of the patients was collected and analyzed to identify any potential confounding effects.  Data usage was approved by IRB #CHS23976.

first: Xiaotong

last: Yang

first: Wenting

last: Liu

first: Zhixin

last: Mao

first: Yuheng

last: Du

first: Cameron

last: Lassiter

first: Fadhl

last: AlAkwaa

first: Paula

last: Benny

middle: X


title: Protective Effects of Recombinant Depolymerase Dep44 Against K64-CRKP-Induced Pulmonary Infection in a Murine Infection Model

status: Public on Dec 02 2025

city: hefei

first: Chengcheng

last: Ma

address: jixi road

institute: anhui chest hospital

summary: Carbapenem-resistant Klebsiella pneumoniae (CRKP), particularly the K64 serotype, poses a severe clinical threat due to its high virulence and multidrug resistance. In this study, we investigated the gene expression profiles of host lung tissues to understand the pathogenesis of K64-CRKP infection and the therapeutic mechanism of Dep44, a capsule-degrading depolymerase. An acute pneumonia mouse model was established via intranasal infection with K64-CRKP. We performed high-throughput RNA sequencing (RNA-seq) on lung tissues from four experimental groups: the negative control group (healthy mice), the positive control group (K64-CRKP infected model), the treatment group (infected mice treated with Dep44), and the drug control group (healthy mice treated with Dep44). The analysis aims to elucidate the host immune response to K64-CRKP infection and evaluate how Dep44 treatment modulates these transcriptomic changes to exert its therapeutic effect.

overall_design: Lung tissue samples were collected from BALB/c mice to analyze gene expression changes. The study design included four groups: (1) Negative Control Group: Mice were mock-infected with PBS to serve as a healthy baseline. (2) Positive Control Group (Model): Mice were intranasally infected with K64-CRKP to induce acute pneumonia, serving as the disease model for comparison. (3) Treatment Group: Mice were intranasally infected with K64-CRKP and subsequently treated with Dep44. (4) Drug Control Group: Healthy mice were administered Dep44 alone to evaluate the potential off-target effects of the drug itself. Total RNA was extracted from the lung tissues of each group. Libraries were constructed and subjected to high-throughput sequencing on the Illumina platform to compare the transcriptomic differences among these groups.

first: Tao

last: Yan


title: Effect of oscillating and non-oscillating Ca2+ signal on gene expression in RBL-2H3 cells

city: Durham

first: Anant

last: Parekh

state: NORTH CAROLINA

address: 111 TW Alexander Drive

institute: NIH

summary: Oscillations of Ca2+ signal are generated in all cell types, seen throughout the life of a cell, and are indispensable for diverse biological processes ranging from fertilization to cell death.  Here we report that Ca2+ nanodomains near Ca2+ channels at the cell surface and not cytosolic Ca2+ oscillations are central to gene expression.  Ca2+ nanodomains activate Ca2+-dependent transcription factors to the same extent as Ca2+ oscillations, at the same average cytosolic Ca2+, leading to equivalent activation of a range of intracellular pathways.  Our results establish that the fundamental unit of excitation-transcription coupling is the Ca2+ channel nanodomain at the cell surface.

overall_design: RNAseq transcriptomic profiling of RBL-2H3 cells after treatment with IgE, 2uM thapsigargin, or 20nM thapsigargin.

first: Yu-Ping

last: Lin


title: IL-22 induces Paneth cell metaplasia in the colonic epithelium of ulcerative colitis, promoting wound healing via REG3A

first: Joana

last: Bernardes

overall_design: RNA-seq analysis comparing Reg3afl/fl and Reg3aΔIEC colonic organoids. Treated or not with IL22.

first: Muto

last: Tomohiro

first: Go

last: Ito

first: Hiromune

last: Katsuda

first: Yui

last: Hiraguri

first: Satoru

last: Fujii

first: Kurara

last: Yamamoto

first: Finn

last: Hinrichsen

first: Uchida

last: Hitoshi

first: Yasuhiro

last: Nemoto

first: Mayumi

last: Kinoshita

first: Eri

last: Ooshina

first: Kouhei

first: Shuji

last: Hibiya

first: Sayaka

last: Nagata

first: Fenja

last: Schuran

first: Shiro

last: Yui

first: Penelope

last: Pelczar

first: Samuel

last: Huber


title: Tuneable hydrogel-based micropillar arrays for myelination studies.

city: London

first: Emad

last: Moeendarbary

state: -- Please select --

address: Torrington Place, Roberts Engineering Building,

institute: University College London

summary: Oligodendrocytes (OLs) play a critical role in central nervous system (CNS) function by myelinating axons and enabling rapid signal conduction. To model the key biomechanical parameters that regulate myelination, we developed a tuneable hydrogel-based micropillar array system that mimics the three-dimensional (3D) architecture and mechanical softness of axons. This platform supports a long-term culture of OLs and permits the formation of multilayered compact myelin by both rodent and human iPSC-derived OLs. Using fluorescence confocal imaging and transmission electron microscopy (TEM), we observed a strong linear correlation between immunostained myelin thickness and the number of myelin wraps, enabling fast, high-content quantification of myelination. By systematically varying pillar stiffness, diameter, and surface coatings, we show that both the mechanical and geometric properties of axon-like substrates critically regulate OL differentiation and myelin wrapping. Importantly, we demonstrate that pharmacological agents exhibit stiffness-dependent effects on myelination, suggesting that overly rigid in vitro models may yield false-positive drug hits. This cost-effective and scalable platform offers a physiologically relevant, high-throughput assay to dissect OL biology and accelerate the discovery of remyelinating therapies for demyelinating diseases such as multiple sclerosis.

overall_design: RNA-seq profiling of oligodendrocytes isolated from P7 Sprague Dawley rats, cultured and differentiated on flat or micropillar hydrogels.

first: Soufian

last: Lasli

first: Claire

last: Vinel


title: Eos maintains Treg homeostasis and plays a critical role in the function of recirculating thymic Tregs [ChIP-Seq]

city: Bethesda

first: Tovah

middle: E

last: Markowitz

state: MD

address: 10 Center Dr, Building 29B

department: Integrated Data Sciences Section (IDSS)

institute: NIAID

summary: Eos, a member of the Ikaros family of transcription factors, is expressed by T regulatory cells (Tregs) and has been postulated to play a role in Treg suppression and maintenance of Treg stability. We demonstrate that expression of Eos was limited to a subpopulation of thymus-derived, activated Tregs and is undetectable in resting or activated T conventional cells (Tconvs). Eos associates with Helios, Foxp3 and Hdac1 and binds directly to the CD25 locus at a site identical to the Foxp3 binding site resulting in enhancement of CD25 expression. Studies in heterozygous female mice demonstrate that Eos is critical for Treg survival and activation. Eos+ Tregs also represent the major population of recirculating thymic Tregs, in which Eos plays a critical role in regulating their migration and suppression of Treg precursors in the thymus by competing for IL-2 and depleting MHC II from thymic dendritic cells (DCs).

overall_design: Single replicate ChIP-seq of anti-Helios or anti-Eos in WT and EosKO conditions

first: Xuan

last: Xie

first: Ethan

last: Shevach


title: Crucial roles of mesenchymal Gata2 in murine epididymal development

city: Madison

first: Fei

last: Zhao

state: Wisconsin

address: 2015 Linden Dr

department: Comparative Biosciences

institute: University of Wisconsin-Madison

summary: Androgens drive the morphogenesis and differentiation of the Wolffian duct (WD) into the epididymis, an essential organ for male reproduction, by binding to the androgen receptor (AR). However, it remains unclear whether other transcriptional programs operate beyond the central androgen/AR signaling in promoting WD development. We discovered that mesenchyme-specific deletion of the transcription factor Gata2 resulted in defective epididymal coiling in the corpus and caudal regions. The defective coiling in the absence of mesenchymal Gata2 did not result from androgen production deficiency, as there were no abnormalities in androgen production or AR/Ar expression, and dihydrotestosterone supplementation did not restore epididymal coiling in cultured WDs. Instead, Gata2 deletion might disrupt mesenchymal identity, as indicated by the significant downregulation of Itga4, an mesenchymal epididymal marker. This loss of mesenchymal identity was accompanied by reduced expression of the mesenchyme-derived morphogen Inhba and decreased epithelial proliferation, both of which are critical for proper epididymal coiling. The developmental defects persisted into adulthood, with the uncoiled corpus and caudal epididymis exhibiting abnormal epithelial morphology and luminal environments, ultimately creating conditions unsuitable for sperm storage and leading to infertility. Notably, in adult knockouts, the epididymal epithelium aberrantly expressed αSMA, further indicating a failure to properly establish epithelial differentiation. Our findings reveal an androgen-independent role for mesenchymal GATA2 in maintaining mesenchymal identity during epididymal development, highlighting the importance of proper fetal mesenchymal specification for male reproductive function.

overall_design: To explore the functional role of mesenchymal Gata2 in Wolffian duct development, we generated a tissue-specific conditional knockout model by crossing Gata2-flox mice with Osr2-Cre. We prepared 3 Gata2cKO and 3 control mesonephroi from mouse embryos at embryonic day (E) 16.5. The mesonephroi used in this study included mesonephric tubule region. Embryonic day (E16.5) mesonephroi were snap frozen and then extracted for RNA.

first: Allyssa

last: Fogarty


title: Small non-coding RNAs encapsulating mammalian cells fuels innate immunity

city: shanghai

first: Xu

last: Chu

address: Dong'an Road

institute: Fudan University Shanghai Cancer Center

summary: Our study addresses the void in understanding surface RNAs, notably glycan-RNAs, abundant on the cell exterior yet lacking precise mapping, particularly in rare cell populations. We present AMOUR, a technique uniting RNA capture with T7-based linear amplification, facilitating accurate profiling of surface RNAs while maintaining plasma membrane integrity. Validation via surface fluorescence in-situ hybridization and RNA aptamer imaging confirms their presence on the outer membrane, autonomously associating in vitro, independent of protein scaffolding. Our work reveals non-coding RNAs as integral components of diverse human and murine hematopoietic cell surface RNAs. Single-cell sequencing of human umbilical cord blood mononuclear cells identifies prevalent Y RNAs on monocyte surfaces. Notably, these Y RNAs interact with histones, critically regulating interleukin-6 (IL-6) gene expression and subsequent protein secretion upon histone stimulation. Highlighting the pivotal role of Y RNAs, our findings clarify their involvement in innate immune activation by capturing and presenting extracellular histones.

overall_design: Gene expression profiling analysis of RNA-seq data  after Histone treatment

first: Jiang

last: Xiao


title: LSD1 Performs Demethylase-Independent and Context-Specific Roles in Ewing Sarcoma

city: Columbus

first: Rachel

middle: D

last: Dreher

address: 575 Children's Crossroad

institute: Nationwide Children's Hospital

summary: Lysine specific demethylase 1 (LSD1), encoded by the gene KDM1A, is overexpressed and correlates with poor patient prognosis in Ewing sarcoma. LSD1 colocalizes with the FET-fusion (EWSR::FLI1, EWS::ERG, etc) throughout the genome and has therefore been considered a critical co-regulator driving the progression of Ewing sarcoma. However therapeutic targeting of LSD1 by irreversible and noncompetitive inhibitors has yielded mixed results. Irreversible, enzymatic inhibition seems ineffective, but reversible noncompetitive inhibition has predominant off target mechanisms, leaving open the question of LSD1 function in Ewing sarcoma. Here we take a robust approach through multiple methods of depletion in multiple cell lines to define LSD1 function, both enzymatic and nonenzymatic, in Ewing sarcoma cell lines. We define a core set of 22 genes that are commonly repressed by LSD1 in all cell lines and that repression of these genes downregulates synapse functioning and e-cadherin target genes. De-repression of these genes with LSD1 loss is an early and sustained genotype in all cell lines tested. Furthermore, we define distinct gene sets in each cell line that are regulated by the enzymatic and nonenzymatic functions of LSD1 and find repression of e-cadherin target genes to be nonenzymatically regulated. This finding supports the growing body of evidence that in addition to their canonical catalytic activity, enzymes serve essential noncanonical roles as well. Lastly, we uncovered evidence through use of the irreversible inhibitor OG-L002 that 2D cytotoxicity and proliferation assays may be insufficient to determine how Ewing sarcoma responds to LSD1 inhibition.

overall_design: To evaluate the transcriptomic changes resulting from loss of LSD1 by CRISPR KO, UM171 degredation at 6hrs, 24hrs, and 96hrs, and OG-L002 inhibition in 3 Ewing sarcoma cell lines. In addition, we rescued LSD1 KO cell lines in A673 with empty vector, HA and twinstrep tagged full wild type LSD1 and HA and twinstrep tagged K661Q/A539 enzymatically dead mutant LSD1.

first: Cenny

middle: C

last: Taslim

first: Ira

last: Miller

first: John

last: Sherman

first: Emily

middle: R

last: Theisen