title: Gelated Apoptotic Extracellular Vesicles via Enzyme-Instructed Self-Assembly with Multifunctional Microcapsule for Targeted Atherosclerosis Therapy

city: Guangzhou

first: Xian

address: No. 381 Wushan Road, Tianhe District

institute: South China University of Technology

summary: While current atherosclerosis therapies control lipid levels, they poorly regulate macrophages, key drivers of plaque progression. Apoptotic extracellular vesicles (apoEVs) offer a cell-free approach to modulate macrophage-driven inflammation, but their applications are limited by cargo leakage, structural instability, and off-target effects. Herein, we developed engineered apoEVs by combining enzyme-instructed self-assembly (EISA) and surface modification techniques. The hydrogel core formed within apoEVs via EISA enabled efficient encapsulation of atorvastatin while also improving vesicle stability. Concurrently, ROS/pH-responsive degradable microcapsules decorated on the apoEV surface enhanced plaque accumulation through hitchhiking and active targeting via the hyaluronic acid-CD44 interaction. Our engineered apoEVs demonstrated potent anti-atherosclerosis effects both in vitro and in vivo by inhibiting foam cell formation, inducing macrophage repolarization, restoring mitochondrial functions, and improving fibrous cap stability. These therapeutic outcomes were further validated using single-cell transcriptomics and multiplex imaging. This study presents a universal and nondestructive strategy for apoEV engineering and highlights its potential for atherosclerosis therapy.

overall_design: All animal experiments were carefully performed in accordance with the international Guide for the Care and Use of Laboratory Animals and approved by the Laboratory Animal Research Center of South China University of Technology (#2024038). ApoE KO mice (6-8 weeks old) were raised in specific pathogen-free conditions. The mice were fed with a high-fat diet (HFD) for 14 weeks, and the control group was fed with a low-fat diet. After 8 weeks of the HFD diet, atherosclerotic mice were randomly divided into 4 groups, receiving saline and AVT@apoEVs@Cap (5 mg total protein / kg body weight) through intravenous injection once every 3 days.

first: Tianzi

last: Chen

first: Shichun

first: Xiaoling

last: Fu

first: Yingjun


title: MSKCC Study 3- A dual barcoding system for pooled analysis of gene knockouts in polyclonal populations (30KO_GEM-X)

status: Public on Aug 12 2026

city: Hinxton

first: MorPhiC

last: Consortium

address: Wellcome Genome Campus

country: United Kingdom

institute: EMBL-EBI

type: Expression profiling by high throughput sequencing

summary: This study characterizes gene knockout phenotypes of 30 genes in a human pluripotent stem cell (hPSC)-directed islet differentiation system. Samples were collected at stage definitive endoderm (DE, Day 3).

overall_design: 30 genes were edited using CRISPR-Cas9 knockin and knockouts, including EOMES, PAX6, MEIS1, SIX3, HES1, HNF1A, NEUROG3, ONECUT1, INSM1, MAFB, ISL1, FEV, SIM1, PBX2, HNF4A,NOTCH2, MEN1, GCM1, CARM1, CBX4, DPY30 , JMJD6, NCOA5, NKX6-1, NOTCH1, PDX1, RFX3, RFX7, RREB1 and SIX2 gene knockouts. The CRISPR-Cas9 edited lines were generated in H1 pooled larry barcoded human embryonic stem cell. The each ko gene were individually barcoded (using the poly3 gene barcode ) and pooled for differentiation. Samples were collected at stage definitive endoderm (DE, Day 3).In addition, we mixed 6% WT cells togethet with 94% 30 KOs for this round of experiment.

first: Huangfu

last: Danwei

first: Xianming

last: Wang

last: Hu


title: MSKCC Study 2- A dual barcoding system for pooled analysis of gene knockouts in polyclonal populations (30KO)

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

overall_design: 30 genes were edited using CRISPR-Cas9 knockin and knockouts, including EOMES, PAX6, MEIS1, SIX3, HES1, HNF1A, NEUROG3, ONECUT1, INSM1, MAFB, ISL1, FEV, SIM1, PBX2, HNF4A,NOTCH2, MEN1, GCM1, CARM1, CBX4, DPY30 , JMJD6, NCOA5, NKX6-1, NOTCH1, PDX1, RFX3, RFX7, RREB1 and SIX2 gene knockouts. The CRISPR-Cas9 edited lines were generated in H1 pooled larry barcoded human embryonic stem cell. The each ko gene were individually barcoded (using the poly3 gene barcode ) and pooled for differentiation. Samples were collected at 6 differentiation stages as follows, ESC, definitive endoderm (DE, Day 3), early Pancreatic progenitor ( PP1, Day 7), late pancreatic progenitor (PP2, Day 11), endocrine stage at s5 ( Day 18) , beta cell stage at S6 ( Day 32) for scRNA-seq. In addition, we mixed 6% WT cells togethet with 94% 30 KOs for this round of experiment.


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

type: Genome binding/occupancy profiling by high throughput sequencing

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

first: Adli

last: Mazhar

first: Bai

last: Tao

first: Xing

last: De

first: Neyisci

last: Ozlem

first: Zhao

last: Hengqiang

first: Hemis

last: Bervis

first: Yu

last: Shaojun

first: Polat

last: Fidan


title: JAX scRNAseq Study01- Single-cell RNA sequencing of male KOLF2.2J hiPSC-derived cortical brain organoids homozygous null for PAX6

summary: This study characterizes the transcriptional dynamics underlying cortical brain organoid development in the absence of the transcription factor PAX6. A PAX6 null allele was engineered by introducing a premature termination codon causing a frameshift mutation (PTC+1). Single-cell RNA sequencing (scRNA-seq) was performed on samples collected at days 7, 8, and 9 following the initiation of differentiation from human induced pluripotent stem cells (hiPSCs), enabling a detailed temporal analysis of gene expression changes.

overall_design: Cortical brain organoids derived from PAX6-null and wildtype hiPSCs were subjected to scRNA-seq across a three-day time course. The Chromium Fixed RNA Profiling Reagent Kit (10x Genomics) was employed for multiplexed single-cell transcriptomic profiling, allowing for high-resolution comparison of transcriptional programs during early neurodevelopment in the presence and absence of PAX6.

first: Juliana

middle: A

last: Diniz

first: Bill

last: Skarnes

first: Paul

last: Robson


title: MSKCC Study 4-  LARRY-barcoded pooled Knock out scRNA-seq (40KO)

summary: This study characterizes gene knockout phenotypes of 40 genes in a human pluripotent stem cell (hPSC)-directed islet differentiation system. Samples were collected at six differentiation stages from hPSCs to SC-islet cells for scRNA-seq to examine transcriptional impact of the knockouts over time.

overall_design: 40 genes were edited using CRISPR-Cas9 knockin and knockouts, including ARID1A, PRR12, TCF4, TCF7L2, CDKN1C, SOX11, PAX6, MEIS1, SIX3, HES1, ISL1, KLF11, PBX1, NOTCH2, CBX4, JMJD6, MORC3, NOTCH1, SMARCC2, SMARCD3, MEF2C, NR2F1, NR2F2, POU3F2, TET1, SETD1B, FOXP2, MEN1, HNF1B, PAX4, PTF1A, SYT4, ZNF800, CTNNBIP1, HEY1, VEZF1, ZNF608, RB1, RCOR2, and SOX17 gene knockouts. The CRISPR-Cas9 edited lines were generated in H1 pooled larry barcoded human embryonic stem cell. The each ko gene were individually barcoded (using the poly3 gene barcode ) and pooled for differentiation. Samples were collected at 6 differentiation stages as follows, ESC, definitive endoderm (DE, Day 3), early Pancreatic progenitor ( PP1, Day 7), late pancreatic progenitor (PP2, Day 11), endocrine stage at s5 ( Day 18) , beta cell stage at S6 ( Day 32) for scRNA-seq. In addition, we mixed 10% WT cells togethet with 90% 40 KOs for this round of experiment.


title: MSKCC Study 5- RNA-seq of ISL1 overexpression across different knockout genotypes during islet differentiation

summary: This study aims to investigate the impact of ISL1 overexpression on hPSC-derived islet differentiation. hPSCs from four genotypes (WT, ISL1-/-, PDX1-/-, and PAX6-/-) were differentiated to pancreatic progenitors (day 11), transduced with ISL1-IRES2-BFP or BFP control lentivirus, and further differentiated to SC-islet (day 18). The BFP+ cells were isolated by flow cytometry sorting and subjected to RNA-seq to assess transcriptional responses to ISL1 overexpression across different genetic backgrounds.

overall_design: This study generated RNA-seq on 21 samples. Cells were transduced with either ISL1-IRES2-BFP or BFP control on day 11 of islet differentiation and harvested on day 18. Most conditions were represented by three biological replicates. Three conditions, ISL1 overexpression in WT, BFP control in WT, and ISL1 overexpression in PDX1-/-, were represented by two biological replicates.

first: Danwei

last: Huangfu

first: Dingyu

last: Liu

first: Jiahui

last: Zhao


title: Self-assembled jawbone periosteal cell spheroids drive rapid osteogenic commitment through F-actin/NF-κB-mediated mechanotransduction

city: Wuhan

first: Ying

address: Luojia Hill, Wuchang District

country: China

institute: Wuhan university

summary: Three-dimensional (3D) organoid has emerged as a revolutionary approach for studying ossification and bone regeneration. However, it remains unclear whether a 3D organoid system can trigger rapid osteogenic commitment in a physiologically relevant, induction-free condition. In this study, we established a scaffold-free, induction-free self-assembling spheroid model using mouse jawbone periosteum-derived cells (jb-PDCs). Remarkably, spheroid formation triggered a significant upregulation of osteogenic commitment markers Col1 at 12 hours, Sp7 at 24 hours, and Spp1 at 48 hours progenitor cells without exogenous inductive factors. Transcriptomic profiling revealed prominent enrichment of the NF-κB signaling pathway, and increased phosphorylation of the p65 subunit confirmed pathway activation. Pharmacological inhibition of NF-κB pathway abolished the upregulation of Col1, Sp7 and Spp1. In contrast, direct activation in conventional monolayer cultures recapitulated the same gene expression program. Furthermore, spheroid formation induced significant disassembly of filamentous actin, and pharmacological stabilization of actin filaments downregulated both p65 phosphorylation and osteogenic gene expression. These findings establish a mechanotransduction axis whereby three-dimensional self-assembly triggers actin cytoskeletal remodeling, leading to NF-κB activation and subsequent osteogenic commitment. Our work reveals that the physical event of cellular condensation intrinsically couples to an osteogenic priming program, providing new insights into how biophysical cues govern the early phases of bone formation, The jb-PDCs spheroid system established here also offers a unique platform for dissecting the mechanobiology of osteogenic initiation and may inform biomimetic strategies for craniofacial bone regeneration.

overall_design: RNA-seq profiling of mouse jawbone periosteum‑derived cells after 48 h of culture under monolayer and spheroid conditions.

first: Jingxian

last: Zhu


title: Circulating tRNA-Derived Fragments in Women with Endometriosis: A Pilot Study

city: New Haven

first: Ramanaiah

last: Mamillapalli

state: CT

address: 310 Cedar Street

department: OBGYN

country: USA

institute: Yale University

summary:
Objective: To investigate whether circulating transfer RNA–derived fragments (tRFs) are differentially expressed in women with surgically confirmed endometriosis compared with healthy controls, and to assess the robustness and translational relevance of identified tRF signatures.
Design: This exploratory case-control study analyzed circulating small RNA profiles in serum samples obtained from women with and without endometriosis. Following RNA extraction and small RNA sequencing, tRF abundance was quantified and assessed for differential expression using established statistical frameworks. Robustness of findings was evaluated through complementary analytical methods and internal validation, and cross-species relevance was examined by comparison with previously published primate endometriosis data.
Results: A total of 82 circulating tRFs were significantly differentially expressed between endometriosis and control groups (adjusted p < 0.05), including 19 upregulated and 63 downregulated fragments. The top 10 candidate tRFs exhibited large effect sizes (absolute log2 fold change range: −3.81 to +4.49). Effect size estimates were highly concordant across statistical methods (DESeq2 vs edgeR; Pearson r ≈ 0.99). Leave-one-out analysis demonstrated stability of effect direction across samples. Seven tRFs with significant differential expression in humans demonstrated fully concordant regulation in a non-human primate endometriosis model, supporting biological relevance.
Conclusion: Circulating tRF profiles differ between women with endometriosis and healthy controls and demonstrate robust statistical support and cross-species concordance. These results suggest that systemic tRF dysregulation could be a source of minimally invasive biomarkers.

overall_design:
Patient population
This study was approved by the Institutional Review Board of the Yale University School of Medicine (New Haven, CT, USA). Written informed consent was obtained from all participants aged 18 years or older. For participants younger than 18 years, written informed assent was obtained together with consent from a legal guardian. Participants were recruited at Yale-New Haven Hospital between March 2018 and December 2021. Women who were undergoing laparoscopic surgery for suspected benign gynecologic conditions or evaluation of chronic pelvic pain were eligible for inclusion. Exclusion criteria included pregnancy, inability to provide informed consent or assent in English, cognitive or physical limitations precluding participation, or refusal to participate. All surgical procedures were performed using a laparoscopic approach. Serum samples were collected predominantly on the day of surgery. Laboratory personnel performing. For the present pilot analysis, participants were assigned to the endometriosis group if endometriosis was confirmed by intraoperative findings and/or histopathology. Control participants had no surgical evidence of endometriosis. The presence of other benign gynecologic findings in the control group (e.g., paratubal cysts) was permitted. In participants diagnosed with endometriosis, disease severity was staged according to the revised American Society for Reproductive Medicine (rASRM) classification system. Clinical and surgical characteristics of the study cohort are summarized in Table 1.
Sample collection and processing
Peripheral blood samples were obtained from participants prior to surgical intervention. A total volume of approximately 5-10 mL of blood was collected into sterile collection tubes (BD, Franklin Lakes, NJ, USA). Following collection, samples were processed promptly to obtain serum. Blood samples were centrifuged at 2,500 rpm for 10 minutes at 4 °C, and the resulting serum fraction was carefully separated. Serum aliquots were stored at -80 °C until RNA extraction and downstream analyses.
***Please note that only 11 patients are the scientifically relevant samples which have tRF counts above the baseline (75,000 reads) and are included in the processed data files.

first: Alla

last: Vash-Margita

first: Hanna

last: Surmann

first: Hugh

middle: S

last: Taylor


title: Transcriptomic profiling of representative anti-sigma factor deletion mutants in Pseudomonas aeruginosa PAO1

city: shandong qingdao

first: Can

middle: can

last: wu

state: shandong province

address: State Key Laboratory of Microbial Technology, Shandong University, 72 Binhai Road

institute: shandong university

summary: Sigma and anti-sigma factor systems enable bacteria to rapidly remodel transcriptional programs in response to environmental changes. Pseudomonas aeruginosa relies on these regulatory modules to coordinate diverse physiological states, including motility, biofilm formation, secondary metabolism and virulence-associated behaviors. In this study, RNA sequencing was performed to characterize transcriptional changes caused by representative anti-sigma factor deletions in Pseudomonas aeruginosa PAO1. Transcriptomic analysis of ΔPA1774, ΔflgM (PA3351) and ΔfiuR (PA0471) mutants revealed distinct regulatory states associated with SigX, FliA and FiuI pathway activation. These data provide insights into how anti-sigma factor perturbation reshapes sigma-dependent transcriptional programs and contributes to adaptive-state transitions in P. aeruginosa.

overall_design: RNA-seq was performed to investigate transcriptional consequences of anti-sigma factor deletion in Pseudomonas aeruginosa PAO1. Wild-type PAO1 and representative anti-sigma factor deletion mutants, including PAO1 deletePA1774, PAO1 deletePA3351 (flgM) and PAO1 deletefiuR (PA0471), were analyzed under matched growth conditions. Each strain was analyzed using two biological replicates. Differential gene expression analysis was performed to identify regulatory changes associated with sigma pathway de-repression and to characterize module-specific transcriptional states.

first: Wu

last: Cancan

last: Shubao


title: TLR7 Agonist Nanomedicine Suppresses Lung Metastasis of Osteosarcoma by Remodeling the Immune Microenvironment

city: Chengdu

first: Zhnag

last: Xinyue

address: No. 17, Block 3, Southern Renmin Road, Chengdu, Sichuan 610041, PR China.

institute: Sichuan University

summary: This study aimed to evaluate a TLR7 agonist liposome (1V209-Cho-Lip) for its anti-metastatic effects and mechanisms in osteosarcoma. Single-cell transcriptomics analysis demonstrated that treatment with 1V209-Cho-Lip alleviates myeloid-mediated immunosuppression, promotes CD8+ T cell activation and clonal expansion, and improves intercellular communication between tumor cells and immune cells.

overall_design: Female Balb/C mice bearing orthotopic K7M2 osteosarcoma xenografts were randomly assigned to control (PBS) and treatment (1V209-Cho-Lip) groups. Lung tissues from three mice per group were pooled for each sample, and total RNA was extracted and subjected to RNA-seq library preparation using the 10× Genomics platform. Sequencing was performed on an Illumina NovaSeq 6000 platform. Raw sequencing reads were processed using Cell Ranger and aligned to the mm10 reference genome. Differential gene expression analysis and pathway enrichment analysis were performed to evaluate transcriptomic changes associated with 1V209-Cho-Lip treatment.

first: Xinyue

last: Zhang

first: Hao

last: Zeng

first: Dandan

last: Wan

first: Furong

last: Qin


title: Hypoxia-induced FTO nuclear export promotes m6A-dependent NMNAT3 mRNA stabilization and intracellular NAD+ accumulation in porcine granulosa cells

city: Nanjing

first: Chengyu

last: Li

state: Jiangsu

address: No. 1 Weigang

department: College of Animal Science and Technology

institute: nanjing agriculture university

summary: Hypoxia is a central feature of the follicular microenvironment and influences granulosa-cell metabolism. This study profiled transcriptome-wide m6A enrichment and RNA abundance in primary porcine granulosa cells cultured under normoxia or hypoxia. Integrative MeRIP-seq and input RNA-seq identified NMNAT3 as a hypoxia-responsive transcript with increased m6A enrichment and expression, supporting a hypoxia-responsive FTO-m6A-NMNAT3 regulatory axis linked to intracellular NAD+ accumulation.

overall_design: Primary porcine follicular granulosa cells were cultured for 12 h under normoxia (21% O2, 5% CO2, 74% N2) or hypoxia (1% O2, 5% CO2, 94% N2). Three independent biological replicates were analyzed per condition. Poly(A)+ RNA from each replicate was used to generate a matched input library and an m6A-immunoprecipitated library, yielding 12 paired-end libraries in total (6 input and 6 m6A-IP). The input libraries served both as background controls for MeRIP-seq peak calling and as RNA-seq libraries for gene-expression analysis.

first: Linjie

first: Tong

last: He

first: Benlong

last: Hua

first: Hongmin

first: Honglin


title: Dual Regulation of Transcription Factor Binding by Tup11/12-Mediated Destabilization and DNA Loop-Mediated Stabilization Ensures Stress-Specific Gene Activation in Fission Yeast

city: Hachioji-shi

first: Yusuke

last: Tsuruta

state: Tokyo

address: Minamiosawa 1-1

department: Department of Chemistry, Graduate School of Science,

country: Japan

institute: Tokyo Metropolitan University

summary: An appropriate transcriptional response to external stresses is crucial for all organisms. Gene expression is regulated by transcription factors (TFs) binding to specific DNA cis-elements. However, how individual TFs achieve stress-specific binding remains elusive. Here we examine the molecular basis of the stress-specific transcriptional response of the Schizosaccharomyces pombe fbp1 gene. The fbp1 gene is activated upon glucose starvation, with transcriptional co-repressors Tup11 and Tup12 playing pivotal roles in maintaining stress-specificity. In the absence of Tup11 and Tup12, nonspecific activation of fbp1 transcription occurs, which requires the TFs Atf1 and Rst2—both essential for fbp1 induction. Moreover, this aberrant fbp1 activation is diminished by the loss of Php5, a factor indispensable for DNA-loop formation between Atf1- and Rst2-binding sites. The defective nonspecific transcription in the tup11∆/tup12∆/php5∆ mutant is restored when Atf1- and Rst2-binding sites are artificially positioned in proximity to each other, indicating that reciprocal stabilization between these TFs facilitates their binding. These findings demonstrate that fbp1 achieves stress-specific transcriptional activation through the counteractive regulation of TF-binding: Tup11/12-mediated destabilization and DNA loop-mediated stabilization. The synergistic reduction in stress tolerance observed in the tup11∆/tup12∆/php5∆ mutant further suggests that this dual regulatory mechanism is crucial for cellular adaptation to environmental stresses.

overall_design: RNA-seq profiling of S. pombe strains (wild-type, tup11∆/tup12∆, and tup11∆/tup12∆/php5∆ cells) in glucose rich, glucose starvation, or nitrogen starvation conditions for 2 hours.

first: Hirotaka

last: Inoue

first: Kenta

last: Hagiwara

first: Charles

last: Hoffman

first: Kouji

last: Hirota


title: Investigating the potential of an α7 nicotinic acetylcholine receptor agonist in adult mammalian retinal neurogenesis through Müller glia reprogramming and progenitor cell formation

city: Kalamazoo

first: Cindy

last: Linn

state: MI

address: 1903 W Michigan Ave

institute: Western Michigan University

summary: Purpose: Adult mammalian Müller glia (MG) typically undergo a gliotic response after injury that inhibits neuronal regeneration. Here, we tested whether the α7 nicotinic acetylcholine receptor agonist PNU-282987 can promote MG proliferation and progenitor formation. Methods: Primary retinal pigment epithelium (RPE) cells were treated with 100 nM PNU-282987 or 0.1% DMSO, then co-cultured with primary MG cells. RNA was extracted, sequenced on the Illumina NovaSeq platform, and mapped to the Mus musculus (GRCm38) genome. Differential expression was assessed (|log2FC| ≥ 1, padj ≤ 0.05). Results: Significantly differentially expressed genes (sDEGs) were identified, including genes associated with progenitor formation, retinal development, and regeneration. Selected targets were validated by RT-qPCR. Conclusion:PNU-282987 treatment induced transcriptomic changes in MG cells consistent with progenitor formation and regenerative/developmental signaling, with more robust effects than those observed in immortalized MG lines.

overall_design: RNA was extracted from primary Müller glia (MG) cultures co-cultured with RPE cells in transwell plates under both experimental and control conditions using the Direct-zol RNA Miniprep kit (Zymo Research) according to the manufacturer’s instructions. Eluted RNA was stored in RNase- and DNase-free water on dry ice and shipped to Genewiz for RNA sequencing on the Illumina® NovaSeq™ platform. RPE cells treated with PNU-282987 for 2 and 6 hours were compared to RPE cells exposed to 0.1% DMSO for the same durations, allowing point-by-point assessment of drug effects. Both experimental and control groups underwent 4 passages. N=3 for each condition and timepoint.

first: Hope

middle: K

last: Hedblad

first: Giovanna

middle: V

last: Nolasco de Carvalho

first: Sarah

middle: E

last: Webster

first: Mark

first: Jake

middle: B

last: Spitsbergen

first: Dave

middle: M

middle: L


title: Macrophage NPM1 drives anti-tumor immunity via the STAT3-CCRL2 axis

city: Suzhou

first: Rongchuan

last: Zhao

address: Keling road 88

institute: Suzhou Institute of Biomedical Engineering and Technology

summary: Although nucleophosmin (NPM1) is a well-characterized oncogene in acute myeloid leukemia, much less is known about its role in solid tumor immunity. Here, we examined the function of NPM1 in regulating anti-tumor immunity within the tumor microenvironment.

overall_design: The proportion and functional changes of macrophages and T cells were detected by flow cytometry, the downstream regulatory genes of NPM1 were detected by RNA-seq, the binding ability of NPM1 and STAT3 was analyzed by Chip and luciferase assay.


title: TGFB2-mediated Regeneration of Pelvic Ligament Equivalents Using a Stem Cell-Fibroblast-Decellularized Membrane Composite

city: Shanghai

first: Zhijun

last: Xia

address: No. 506, Fangxielu, Huangpu District

institute: Obstetrics and Gynecology Hospital of Fudan University

summary: Pelvic organ prolapse (POP) is a prevalent condition characterized by weakened pelvic floor tissues, significantly impacting women's quality of life. Current treatments, including synthetic meshes and native tissue repair, face challenges of high recurrence rates and complications. This study developed a novel tissue-engineered strategy utilizing a decellularized human amniotic membrane (HAAM) scaffold seeded with autologous adipose-derived mesenchymal stem cells (ADSCs) and vaginal wall fibroblasts (HVFs) to construct a bioactive pelvic ligament equivalent. We first validated the successful preparation of HAAM with preserved extracellular matrix integrity and characterized the phenotypic markers of ADSCs and HVFs. In a rat abdominal wall defect model, the HAAM+ADSCs+HVFs composite demonstrated superior tissue regeneration and integration, reduced fibrosis, and effective modulation of the host immune microenvironment—evidenced by enhanced repair and decreased infiltration of pro-inflammatory cells—compared to all control groups (including HAAM alone and single-cell groups). Transcriptomic analysis revealed that the composite treatment promoted extracellular matrix organization and collagen synthesis while suppressing matrix degradation (MMP2/MMP9) and inflammatory pathways. Most importantly, mechanistic studies identified TGFB2 as the key paracrine mediator through which ADSCs exert their effects: TGFB2 inhibition abolished ADSCs-induced improvements in HVFs proliferation, migration, and anti-apoptosis, while its overexpression replicated these benefits. Western blot confirmed that TGFB2 coordinately upregulates COL1A1/COL3A1 and downregulates MMP2/MMP9 to restore ECM homeostasis. These comprehensive findings demonstrate that the HAAM-based ADSCs-HVFs composite promotes functional tissue regeneration via TGFB2-mediated mechanisms, offering a safe, effective, and regenerative therapeutic strategy with strong translational potential for POP.

overall_design: An expression profiling study utilizing high-throughput transcriptomic analysis to evaluate abdominal wall defect repair using biohybrid cell-scaffold constructs in an immunocompetent Sprague Dawley (SD) rat model. The overall design compares two distinct functional cohorts at a predefined endpoint of Day 14 post-modeling : an untreated MODEL Group and the ADSCs+HVFs Experimental Group. Total RNA was extracted from harvested tissue constructs on Day 14. A total of 10 biological sample replicates were analyzed, consisting of n = 5 independent biological replicates for the Control/Model cohort and n = 5 independent biological replicates for the Experimental (ADSCs+HVFs) cohort.


title: Lipid-based mRNA chimeric antigen receptor T cells for enhanced in vitro antitumor activity

first: Haixia

last: Gao

address: No. 1585 Yuanguo Road, Building 1A, Anting Town, Jiading District

institute: Shanghai University

summary: Chimeric antigen receptor (CAR) T cell therapy provides substantial clinical benefits in hematologic malignancies. However, cell engineering using conventional viral vectors is costly, labor-intensive, and prone to safety risks, while electroporation-induced cellular damage limits manufacturing scalability. This study reports a safe, high-efficiency, nonviral platform for generating mRNA-engineered CAR-T cells. Herein, eight ionizable lipids are synthesized and formulated into lipid nanoparticles. Systematic screening and structural optimization identified Lipid 6 as the lead candidate. Transfection efficiency is validated by delivering eGFP mRNA into DC2.4, peripheral blood mononuclear, dendritic, and natural killer cells. Murine models confirm robust in vivo expression and a favorable safety profile. Lipid 6–mediated delivery of MUC1 mRNA generates MUC1–CAR-T cells characterized by high surface receptor expression and potent cytotoxicity against MUC1-positive tumor cells. These findings establish Lipid 6 as a feasible strategy for primary human T-cell engineering, facilitating functional CAR expression with minimal toxicity.

overall_design: Total 6 samples, consisting of two experimental groups with n=3 independent biological replicates:  1. Treatment group: activated primary human T cells transfected with Lipid 6-MUC1 mRNA LNPs, harvested 24 h post-transfection; 2. Control group: untreated activated primary human T cells, cultured in identical medium without LNP treatment. All samples underwent total RNA extraction, Illumina paired-end RNA sequencing, read mapping to the human GRCh38 reference genome, differential expression analysis via DESeq2, and GO/KEGG functional enrichment to characterize transcriptional alterations induced by LNP-mediated MUC1 mRNA delivery.

first: Yuan

last: Fang

first: Zhidan

last: Tian

first: Chuanxin

last: Guo

first: Pei

last: Wang

first: Tao

last: Liu

first: Yan

last: Sun


title: GENE EXPRESSION DURING SEA LAMPREY EMBRYOGENESIS

city: Lexington

first: Kaan Ihsan

last: Eskut

state: Kentucky

address: 195 Huguelet Dr.

department: Biology

institute: University of Kentucky

summary: During early embryogenesis, the sea lamprey Petromyzon marinus undergoes a dynamic form of genome rearrangement whereby several specific chromosomes are selectively eliminated from somatic progenitor cells. These elimination events effectively silence all genes on these chromosomes in all somatic cells., and Pprevious studies in lamprey and other eliminating species have provided strong evidence that other epigenetic silencing marks (DNA and histone posttranslational modifications) are enriched in the germline-restricted chromosomes and contribute to micronucleus packaging during elimination. These silencing marks include the histone marks H3K9me3 and H4K20me3, which are respectively deposited by KMT1A/SUV39 and KMT5/SUV420 methyltransferases in . To test whether lamprey homologs of methyltransferases contribute to deposition of these marks on elimination micronuclei and whether these marks contribute to the highly coordinated process of DNA elimination in sea lamprey, we leveraged CRISPR/Cas9 gene editing and lightsheet imaging to investigate their potential roles during early development and during the progression of DNA elimination. Analysis of knockout embryos for four methyltransferases show that these KMT genes contribute to the deposition of repressive histone marks on micronuclei, but are not essential for programmed DNA elimination per se. Analyses of later embryogenic stages suggests that these marks may contribute to interim silencing of germline-specific chromosomes, and reveals major impacts on post-blastula survival and developmental patterning.

overall_design: A temporal RNA-seq profiling of sea lamprey early development starting from unfertilized eggs to 72 hours post fertilization.

first: Claire

last: Scott

first: Cody

last: Saraceno

first: Vladimir

last: Timoshevskiy

first: Zachary

middle: D

last: Root

first: Jeramiah

middle: J

last: Smith


title: Atlas of gene expression in the Murciano-Granadina goat

city: Cerdanyola del Vallès

first: Diego

middle: Alonso

last: Vargas Donayre

state: Barcelona

address: Carrer de la Vall Moronta

department: Plant and Animal Genomics

country: Spain

institute: Centre for Research in Agricultural Genomics (CRAG)

summary: We generated a tissue-wide gene expression atlas for adult domestic goats (Capra hircus) using total RNA sequencing. RNA was extracted from 33 tissues obtained from six adult Murciano-Granadina female goats and sequenced to characterize transcript abundance across tissues. This dataset provides a reference resource for studies of gene function, tissue-specific expression, and comparative genomics in livestock species.

overall_design: RNA-seq profiling of 33 tissues dissected from six adult Murciano-Granadina female goats (Capra hircus). Total RNA libraries were sequenced on an Illumina NovaSeq 6000 platform to generate a comprehensive adult goat gene expression atlas.

first: Minjing

first: Diego Alonso

last: Vargas-Donayre

first: Antonia

last: Noce

first: María

last: Luigi-Sierra

first: Emilio

last: Mármol-Sánchez

first: Ke

first: Elena

last: Petretto

first: Sergi

last: Olvera-Maneu

first: Paula

last: Serrés-Corral

first: Jaume

last: Gardela

first: Manel

last: López-Béjar

first: Marcel

last: Amills


title: CpG Hypermethylation and WNT/AP-1 cooperativity Define the Epigenetic Landscape and a Clinical Subgroup of High-Risk Pediatric Adrenocortical Carcinoma [Methylation array]

city: Augsburg

first: Victoria

middle: Elisabeth

last: Fincke

address: Stenglinstraße 2

country: Germany

institute: Childens Cancer Center - University hospital Augsburg

type: Methylation profiling by genome tiling array

summary: Treatment of three adult ACC cell lines (H295R and ACC1, ACC2) with entinostat and decitbaine led to consistent dose-dependent changes in DNA methylation patterns. These findings support entinostat's potential to reverse high-risk epigenetic programs in pACT and highlight HDAC inhibition as a promising therapeutic avenue, particularly when combined with established treatments.

overall_design: DNA methylation analysis of ACC cell lines untreated and treated with entinostat or dectiabine at 0.5µM and 1µM for 72h or 168h.

first: Mauice

last: Loßner

first: Marina

last: Kunstreich

first: Nic

middle: G

last: Reitsam

first: Irmengard

last: Sax

first: Marlena

last: Mucha

first: Felix

last: Dorn

first: Lorenz

middle: C

last: Helmschrott

first: Maria

last: Hernandez Ramirez

first: Sebastian

last: Dintner

first: Konstantin

last: Okonechnikov

first: Martin

last: Sill

first: Ina

last: Oehme

first: Heike

last: Peterziel

first: Enrique

last: Blanco-Carmona

first: Eva

last: Sipos

first: Stefan

last: Wudy

first: Christoph

last: Slavetinsky

first: Jörg

last: Fuchs

first: Bruno

last: Märkl

last: Jüttner

first: Christian

last: Vokuhl

first: Michael

last: Frühwald

first: Antje

last: Redlich

last: Pfister

first: Matthias

last: Schlesner

first: Rainer

last: Claus

first: Michaela

last: Kuhlen

first: Pascal

last: Johann


title: CpG Hypermethylation and WNT/AP-1 cooperativity Define the Epigenetic Landscape and a Clinical Subgroup of High-Risk Pediatric Adrenocortical Carcinoma [cell line]

first: Victoria

last: Fincke

summary: Treatment of two adult ACC cell lines (H295R and CU-ACC1) with the HDAC inhibitor entinostat led to consistent dose-dependent reductions in viability, outperforming the DNA demethylating agent decitabine. scRNA-seq analyses revealed global transcriptional reprogramming. This included downregulation of AP-1 transcription factors (FOS, JUND, JUNB), suppression of oxidative phosphorylation and steroidogenic pathways, and increased expression of pro-apoptotic genes. These findings support entinostat's potential to reverse high-risk epigenetic programs in pACT and highlight HDAC inhibition as a promising therapeutic avenue, particularly when combined with established treatments.

overall_design: scRNA-seq (10x Genomics) of 2 ACC cell lines untreated and treated with entinostat at 0.5µM and 1µM for 72h

first: Mauice

last: Loßner

first: Marina

last: Kunstreich

first: Nic

last: Reitsam

first: Irmengard

last: Sax

first: Marlena

last: Mucha

first: Felix

last: Dorn

first: Lorenz

last: Helmschrott

first: Maria

last: Hernandez Ramirez

first: Sebastian

last: Dintner

first: Konstantin

last: Okonechnikov

last: Sill

last: Oehme


title: Dual Lineage Tracing Identifies Cellular Mechanisms Underlying Radiation-Associated Changes in Atherosclerotic Lesion Composition

city: Charlottesville

first: Anita

last: Salamon

state: VA

address: 415 Lane Road

department: Robert M. Berne Cardiovascular Research Center

institute: University of Virginia

summary: Background: Phenotypic plasticity of smooth muscle cells (SMCs) and endothelial cells (ECs) contributes to atherosclerotic plaque composition and stability, yet how shifts in one population influence the contribution and function of the other under conditions of vascular stress, such as irradiation, is poorly understood. A major limitation has been the inability to simultaneously fate map both cell types within the same lesion, with most studies mapping one lineage while inferring the other using unreliable dynamically changing marker genes, risking false-positive and false negative assignment. Methods: We generated dual lineage-tracing Apoe-deficient mice, enabling simultaneous fate mapping of SMCs and ECs. This model was used to extend prior findings from single lineage tracing models demonstrating irradiation-induced loss of SMC lesion investment and expansion of EC-derived cells. Dual lineage-tracing mice were subjected to irradiation followed by Western diet feeding to induce atherosclerosis. Lineage tracing, immunostaining and scRNA-seq analysis were used to define coordinated SMC and EC responses and identify changes relevant to plaque instability. Results: Dual lineage tracing simultaneously labeled SMC- and EC-derived cells in healthy and atherosclerotic vessels. Irradiation induced divergent responses: SMC-derived cells failed to invest in lesions and upregulated stress-activated inflammatory genes, whereas EC-derived cells expanded and upregulated SMC-associated genes. However, EC-derived cells within lesions failed to induce extracellular matrix genes, and lesions from irradiated mice exhibited reduced collagen content and fewer ACTA2+ cells within the fibrous cap, consistent with reduced plaque stability. Conclusions: Dual lineage-tracing of SMCs and ECs demonstrated that irradiation-induced loss of lesional SMC and expansion of EC-derived ACTA2+ cells are not artifacts of false lineage assignment. By resolving SMC and EC fate within the same lesion, we identify irradiation-induced cell dynamics including inflammatory reprogramming of SMCs, EC phenotypic modulation, impaired extracellular matrix organization, and reduced ACTA2⁺ fibrous cap cellularity that may contribute to radiotherapy-associated increased atherosclerotic cardiovascular disease risk. Key Words: Atherosclerosis; smooth muscle cells; endothelial cells; lineage tracing; radiation; extracellular matrix; cellular plasticity

overall_design: Single-cell RNA sequencing (scRNA-seq) of pooled brachiocephalic artery (BCA) regions from female dual lineage-tracing Apoe-deficient mice (n=4 for control; n=3 for irradiated). SMC-EC dual Apoe-/- mice were subjected to irradiation (two 600 cGy doses, 3 hours apart), bone marrow (BM) transplantation, and antibiotic treatment, followed by Western diet feeding for 18-20 weeks to induce advanced atherosclerosis. Control mice received no irradiation, sterile saline in lieu of donor BM and antibiotic drinking water for 6 weeks to parallel irradiated mice.

first: Tajbir

last: Raihan

first: Rebecca

last: Deaton

first: Gary

last: Owens


title: Cellular adaptations of fission yeast to inositol starvation

city: New York

first: Ana

last: Sanchez

state: NY

address: 430 E 67th Street, RRL-865

department: Molecular Biology

institute: Memorial Sloan Kettering Cancer Center

summary: RNA-seq analysis compares the gene expression profiles of fission yeast wild-type cells at various times after inositol (INO) starvation (4, 8, 12 and 24h) with that of wild-type cells grown in inositol-replete conditions (0h, prior to inositol starvation).

overall_design: 4 test samples and 1 control sampe were processed (each sample has 3 replicate experiments).

first: Jill

last: Babor

first: Michelle

last: Saoi

first: Isabel

last: Prucker

first: Henning

last: Jessen

first: Beate

last: Schwer

first: Stewart

last: Shuman


title: Systemic single-cell analysis of GPP reveals treatment-responsive and persistent immune signatures

city: Jongno-gu, Seoul

first: Soyoung

last: Jeong

address: 103 Daehak-ro

country: South Korea

institute: Seoul National University

summary: Generalized pustular psoriasis (GPP) is a rare autoinflammatory skin disease characterized by recurrent episodes of widespread sterile pustulation and systemic inflammation. Although biologic therapies targeting the IL-23/Th17 axis have demonstrated clinical efficacy, the systemic immune alterations associated with disease activity and treatment response remain incompletely understood, particularly in pediatric familial GPP associated with IL36RN mutations. In this study, we performed single-cell RNA sequencing of peripheral blood mononuclear cells (PBMCs) from two pediatric siblings with familial GPP before and after biologic treatment, together with two unaffected mutation-negative sibling controls. Single-cell transcriptomic profiling was used to characterize immune-cell-specific alterations associated with disease and treatment response.

overall_design: Peripheral blood mononuclear cells (PBMCs) were collected from two pediatric patients with familial generalized pustular psoriasis (GPP) associated with IL36RN mutations before and after biologic therapy and from two unaffected mutation-negative sibling controls. Single-cell RNA sequencing was performed using the 10x Genomics Chromium platform.

first: Seungbok

last: Lee

first: Christine

last: Joh

first: James

last: Krueger

first: Hyun Je

last: Kim

first: Seong Jin

last: Jo

first: Jong-Hee

last: Chae


title: Exposure to Perfluorooctanoic acid accelerates Drosophila melanogaster juvenile development and disrupts mitochondrial metabolism

city: Bloomington

first: Jason

last: Tennessen

email: tennessenlab@gmail.com, tennlab@iu.edu, jtenness@iu.edu, tourigny@iu.edu

state: IN

address: 1001 E 3rd St

institute: Indiana University

summary: Per- and polyfluoroalkyl substances (PFAS) are persistent environmental contaminants with poorly understood sublethal effects on insects. Perfluorooctanoic acid (PFOA), one of the most widely distributed legacy PFAS, bioaccumulates globally and is increasingly recognized for altering organismal physiology beyond traditional toxicity endpoints. Here, we use the fruit fly Drosophila melanogaster as a model to examine how PFOA exposure during growth reshapes insect life-history progression and metabolic homeostasis. We show that PFOA exposure induces a tradeoff between developmental rate and physiological robustness, providing a framework for understanding its context-dependent effects on insect fitness. At environmentally relevant concentrations (tens of ppb to low µM), PFOA induces precocious expression of stage-regulated genes and leads to lasting changes in adult metabolic state. At higher concentrations used to probe mechanism, PFOA accelerates larval development, disrupts mitochondrial membrane potential, and increases whole-organism metabolic heat production, indicative of altered mitochondrial energetic efficiency. Consistent with this tradeoff, larvae that develop faster under permissive conditions exhibit heightened sensitivity to environmental stressors, including elevated temperature and reduced food hydration. Together, these findings demonstrate that PFOA disrupts conserved metabolic and developmental processes in a dose- and context-dependent manner, highlighting sublethal effects that may influence insect resilience under environmental stress.

overall_design: We used Dorosophila melanogaster to investigate the effects of the forever chemical Perfluorooctanoic acid on development and metabolism. We took age syncronized populations of first instar larvae and exposed them to 0, 15 or 1500 ppb (0, 0.03623 or 3.623 µM) PFOA. At mid third instar (84 hours after egg laying) we collected larvae, extracted RNA and performed pair-end sequencing on them.

first: Eric

last: Kilbourn

first: Matthew

middle: R

last: Lowe

first: Kaniskha

last: Panda

first: Akshay

last: Bhaskaran

first: Guomao

last: Zheng

first: Adam

last: Malave

first: Sophia

last: White

first: Anna

last: Graber

first: Nika

last: Zulkowski

first: Robert

last: Pepin

first: Travis

last: Nemkov

first: Angelo

last: D'Alessandro

first: Pramod

last: Reddy

first: Edgar

last: Meyhofer

first: Swathi

last: Yadlapalli

first: Amina

last: Salamova


title: Comparative transcriptomic profiling of human aortic smooth muscle cells exposed to cyclic stretch and normotensive or hypertensive hydrostatic pressure

city: Shinjyuku

first: Takahiro

last: Kusume

address: 6-1-1, Shinjyuku

institute: Tokyo medical university

summary: Mechanical stress plays important roles in vascular physiology and pathophysiology. Although vascular smooth muscle cells are continuously exposed to cyclic stretch and hydrostatic pressure, the individual effects of these mechanical stimuli on global molecular profiles remain poorly understood. Using a custom-made cyclic hydrostatic pressure culture system developed in our laboratory, we performed transcriptome analyses of human aortic smooth muscle cells exposed to cyclic stretch or hydrostatic pressure to characterize the molecular profiles induced by these stimuli.

overall_design: Human aortic smooth muscle cells were cultured under control (no mechanical loading) conditions, cyclic stretch (10%), normotensive hydrostatic pressure (120/60 mmHg), or hypertensive hydrostatic pressure (180/120 mmHg). Total RNA was isolated after 24 h of mechanical stimulation and subjected to RNA sequencing.

first: Hana

last: Inoue

first: Utako

last: Yokoyama


title: TNFR1 expression on cancer cells is critical for immune escape shaping an immunosuppressive tumor microenvironment

city: Pamplona

first: David

last: Ruiz Guillamón

state: Navarra

address: Av. de Pío XII, 55

department: Programa de Inmunología e Inmunoterapia

institute: Centro de Investigación de Medicina Aplicada (CIMA) - Clínica Universidad de Navarra

summary: TNFα is an proinflammatory cytokine that can mediate immunosuppressive effects in cancer. Tumors in which we silenced TNFR1 by CRISPR/Cas9 showed disability of the TNFR1 KO variants to engraft in immunocompetent hosts, whilst engraftment in immunodeficient or CD8 T lymphocyte-depleted mice was preserved. The mechanism was mediated by secondary chemotactic inflammatory mediators elicited by TNFα in the malignant cells themselves. As a result, TNFR1 KO variants recruited drastically fewer myeloid-derived suppressor cells into the tumor microenvironment, thus explaining the immune escape of the WT variants. Interestingly, small amounts of TNFR1-sufficient tumor cells co-engrafted with the TNFR1 KO variants rescued tumorigenicity in the same tumor lesion but not in a distantly implanted TNFR1 KO tumor. Secondary mediators chiefly include CXCR1/2-acting chemokines, prostaglandin-E2 and TNFα itself. Knocking-down TNFR1 in a human tumor cell line rendered comparable results when xenografted. Analyses of scRNA-seq and spatial transcriptomics datasets from human solid tumors corroborate the role of TNFR1 on tumor cells in the induction of secondary pro-tumor inflammatory mediators.

overall_design: RNA-seq profiling of CD11b positive cells from TNFR1 KO tumors and TNFR1 WT tumors.

first: Elixabet

last: Bolaños

first: Lorena

last: Cañas-Zabala

first: Irene

last: Olivera

last: Ruiz-Guillamón

first: Enric

last: Vercher

first: Pedro

last: Berraondo

first: Ignacio

last: Melero


title: Transcriptomic response of human corneal epithelial cells to extracellular vesicles derived from Pseudomonas aeruginosa and Staphylococcus epidermidis

city: Oviedo

first: Noelia

last: Blanco-Agudín

state: Asturias

address: Facultad de Medicina

institute: University of Oviedo

summary:
Extracellular vesicles released by bacteria are important mediators of host-microbe communication. In this study, human corneal epithelial cells (HCE) were exposed to extracellular vesicles derived from Pseudomonas aeruginosa or Staphylococcus epidermidis. RNA sequencing was performed to characterize transcriptional changes induced by bacterial vesicles compared with untreated control cells. This dataset contains transcriptomic profiles from control cells and cells exposed to bacterial extracellular vesicles.
Article available: https://doi.org/10.3389/fcimb.2026.1899147

overall_design: Human corneal epithelial cells were cultured under standard conditions and exposed to bacterial extracellular vesicles derived from Pseudomonas aeruginosa or Staphylococcus epidermidis. Untreated cells served as controls. Total RNA was extracted after 15 h of exposure and subjected to paired-end RNA sequencing using the Illumina NovaSeq X Plus platform. Three biological replicates were analyzed per condition.

first: Suhui

last: Ye

first: Sara

last: González-Fernández

first: Iván

last: Fernández-Vega

first: Jesús

last: Merayo-Lloves

first: Luis

last: Quirós


title: Integrative transcriptomic profiling of pediatric bone marrow failure syndromes: shared coding and long non-coding RNA signatures

city: Incheon

first: Jaeeun

last: Yoo

address: Bupyoung-gu

institute: Incheon St. Mary Hospital

summary: Pediatric bone marrow failure (BMF) comprises inherited and immune-mediated disorders, many of which remain genetically unclassified. We performed total RNA sequencing of bone-marrow aspirates from pediatric BMF patients and controls to identify shared coding and long non-coding RNA (lncRNA) transcriptional signatures across genetically-defined (g-BMF) and genetically-undefined (u-BMF) disease. This record provides processed gene-level quantification (raw counts and CPM) for all 14 samples; raw sequencing reads are in SRA under BioProject PRJNA1406476.

overall_design: 14 bone-marrow total-RNA samples: 4 g-BMF (3 Fanconi anemia, 1 dyskeratosis congenita), 8 u-BMF, and 2 controls with morphologically normal marrow. Paired-end, reverse-stranded (TruSeq Stranded Total RNA, Ribo-Zero). Raw reads previously deposited in SRA (PRJNA1406476); this submission adds the processed gene-level quantification.

first: Jae Wook

last: Lee

first: Nack-Gyun

last: Chung

first: Jae Won

first: Yonggoo

last: Kim

first: Myungshin

first: Hyunjoo

last: Bae

first: Jong-Mi


title: Single Cell Transcriptional Signatures of Microglia and Monocytes after ICH

city: New Haven

first: Yuki

last: Kawamura

address: 333 Cedar Street

institute: Yale School of Medicine

summary: CNS-resident microglia and recruited myeloid cells populate the haematoma in intracerebral haemorrhage (ICH), but the contribution of these cell populations to injury and repair has been controversial. To better characterise myeloid cell changes over time, we employed single-cell RNA sequencing to generate a unique paired dataset of live haematoma and peripheral blood samples from 10 ICH patients. This work presents a temporal atlas of ICH myeloid populations and identifies population-specific in-situ transcriptional drivers. In addition to distinct populations of activated microglia and TNF-low microglia, we found a unique and highly activated population of CD14+ monocytes in the haematoma. Perturbation analysis comparing haematoma-associated monocytes to shared populations in blood and haematomas identified TNF signalling as the primary driver of their activation. Employing a custom temporal trajectory analysis based on the embeddings of a single-cell foundation model, we found that this TNF response in monocytes was transient, peaking early after haemorrhage and decreasing over the ensuing 48 hours. Our analysis further identified a transient population of highly activated microglia as the likely source of TNF during the acute stage of ICH. Acute TNF signalling in CD14+ monocytes associated with better adjusted outcomes both in our and external cohorts. Overall, our results suggest that acute TNF signalling between transient populations of activated microglia and unique haematoma-associated monocytes could potentially be beneficial in recovery after ICH.

overall_design: 10 human samples of CSF + Blood

first: Conor

middle: W

last: Johnson

first: Jonathan

last: DeLong

first: Lucas Paulo

last: de Lima Camillo

first: Sofia E

last: Velazquez

first: Munetomo

last: Takahashi

first: Hannah

last: Beatty

first: Ryan

last: Herbert

first: Branden

last: Cord

first: Charles

last: Matouk

first: Michael

last: Askenase

first: Lauren

last: Sansing


title: CBASS limits bacteriophage production while maintaining cell viability in Pseudomonas aeruginosa

city: Princeton

first: Bruce

last: Wang

address: Carl Icahn Lab

institute: Princeton University

summary: Single-cell data for phage infected Pa011 cells, with phage gene expression

overall_design: Cells were grown to OD=0.3, then infected with PaMx41 Deltaacb2 for 160 mintues and then processed for bacterial scRNA-Seq using M3-Seq.

first: Erin

last: Huiting

first: Esther

last: Shmidov

first: Sriharshita

last: Musunuri

first: Zemer

last: Gitai

first: Joseph

last: Bondy-Denomy


title: Mouse liver bulk RNA-seq profiling of acute ethanol-induced liver injury

city: guangzhou

first: ran

last: ding

state: guangdong

address: School of Biomedical Sciences and Engineering, South China University of Technology, Guangzhou International Campus, Guangzhou 511442, China.

institute: South china university of technology

summary: This dataset contains bulk RNA-seq profiles of mouse liver tissues from control mice and acute ethanol-exposed mice. Male C57BL/6J mice were fasted for 12 h and administered a single oral dose of 50% ethanol at 6 g/kg. Liver tissues were collected 24 h after ethanol administration for RNA extraction and sequencing.

overall_design: Liver tissues were collected from male C57BL/6J mice in two experimental groups: control (H1, H2, H3) and ethanol-exposed (A1, A2, A3). RNA-seq libraries were constructed and sequenced using Illumina NovaSeq 6000 PE150.

first: Ran

last: Ding

first: Fan

last: Qi

first: Qianqian

last: Dai

first: Kangfan

last: Li

first: Yuan

last: Zhang


title: Succinic acid inhibits hepatocyte proliferation by targeting the STAT3 SH2 domain

city: Hangzhou

first: Yiyuan

last: Chen

state: Zhejiang

address: Jiefang Road No.88

institute: The Second Affiliated Hospital, College of Medicine, Zhejiang University

summary: We collected liver tissues from 20 split liver transplantation donors and performed RNA-seq analyse to identify regeneration-associated genes.

overall_design: To investigate the difference between liver regeneration, we conducted a retrospective study of 20 patients who underwent split liver transplantation. Patients with severe underlying diseases were excluded from the study. We used 3D Slicer to rebuild the patients' livers from their CT slides. The standard liver volume (SLV) was calculated based on the liver weight, patients' body weight, and height. We divided these 20 patients into two groups (LR+ and LR-) based on their liver regeneration rate. To investigate the metabolite landscape of the liver in response to liver resection, we used a quasi-targeted metabolomics and transcriptomics approach in this study to identify the key factors that regulate liver regeneration.


title: Neutrophil nucleolar stress rapidly releases nucleoli-stored IFNα during infection

city: St Louis

first: Shuying

last: Xu

state: MO

address: 425 South Euclid Ave

institute: Washington University in St. Louis

summary: Type I interferons (IFN-I) are critical for antiviral defense but can drive severe pathology when dysregulated. Excess IFN-I is associated with prominent neutrophil accumulation, however, the contribution of neutrophils to IFN-I overproduction remains underexplored. In all cell types previously studied, IFN-I is synthesized de novo upon pathogen sensing. Contrary to this paradigm, we find that neutrophils express IFNα during development and store it in the nucleolus, an intranuclear condensate classically functioning in ribosome biogenesis. TLR-mediated bacterial sensing induces nucleolar stress and rapid secretion of nucleoli-stored IFNα from neutrophils independent of de novo protein synthesis. These findings reveal roles for the neutrophil nucleolus in IFN-I storage and secretion, identify the first naturally occurring regulatory function of nucleolar stress, and provide insight into the relationship between detrimental IFN-I levels and neutrophil accumulation.

overall_design: Primary mouse neutrophils were extracted from bone marrow of mice of two genotypes (C57BL/6J and C57BL/6J Infar-/-) and 1×106 neutrophils from each genotype were incubated with Mtb at a multiplicity of infection (MOI) of 5 at 5% CO2 at 37°C for indicated time points. RNA was extracted, and used in bulkRNAseq. Each genotype was collected in biological triplicate.

first: Asya

last: Smirnov

first: Rachel

last: Kinsella

first: Ananda

last: Rankin

first: Ashley

last: Wise-Mitchell

first: Jessica

last: Alexander

first: Sophie

last: Mikhail

last: Bello

first: Darren

last: Kraemalmeyer

first: Sebastian

last: Boluarte

first: Aamir

last: Khan

first: Ben

last: Allsup

first: Sheikh

last: Mahmud

first: Bryan

last: Bryson

first: Josh

middle: T

last: Mattila

first: Eric

last: Greer

first: Siyuan

first: Regina

middle: A

last: Clemens

first: Andrew

last: Monteith

first: Eliezer

last: Calo

first: Christina

last: Stallings


title: Structural mechanism governing the directionality of IS110 bridge recombination

city: Bunkyo-ku

first: Hiroshi

last: Nishimasu

address: 7-3-1 Hongo

institute: University of Tokyo

summary: Bridge recombinases from the IS110 family of transposons, such as IS621, associate with a bridge RNA (bRNA) to mediate programmable recombination between donor and target DNAs. While insertion is mediated by the recombinase–bRNA complex, it remains unknown how these elements are excised from genomes to form circular intermediates. Here, we show that bRNA is weakly expressed from IS621 loci in the Escherichia coli genome and that the IS621 recombinase–bRNA complex mediates excision less efficiently than insertion. Furthermore, we determine the cryo-electron microscopy structures of the IS621 recombinase–bRNA complex bound to excision DNA substrates, providing mechanistic insights into the excision reaction. Similar to the previously reported donor- and target-bound insertion complex, the excision complex comprises two recombinase dimers, each accommodating target- and donor-binding loops of the bRNA. However, DNA recognition differs notably between the two complexes. While the donor and target DNA form a bent U-shape during insertion, the excision substrates adopt linear conformations and bind across both bRNA loops, forming an X-shaped structure, which reduces the efficiency of top-strand exchange and contributes to the naturally observed bias in reaction direction against excision. Despite such differences, the efficiencies of both reactions are similarly modulated by base pairing between the bRNA handshake guides and the top strands of DNA. Overall, this study provides mechanistic insights into the complete IS110 transposition cycle, and facilitates the optimal design of programmable bridge editing applications.

overall_design: RNA-seq profiling of bridge RNA expression from various types of bridge recombinase systems, including systems within plasmids and those integrated into E. coli genomes.

first: Januka

middle: S

last: Athukoralage

first: Lauren

last: Lee

first: Gwanggyu

last: Sun


title: Tubular epithelial cells promote macrophage pyroptosis through PANX1-extracellular ATP-P2X7 signaling in aldosterone-dependent renal injury

city: Shanghai

first: Chongjian

last: Wang

address: Ruijin 2nd Road

institute: Ruijin Hospital, School of Medicine, Shanghai Jiao Tong University

summary: Macrophage-mediated inflammation is among the most important characteristics of hypertension-induced CKD, but the molecular events that drive these processes are poorly understood. Here, we conducted single cell RNA sequencing (scRNA-seq) of deoxycorticosterone acetate (DOCA)-salt-induced hypertensive mouse model to characterize the change of cell signaling in macrophages of mouse kidneys. Our scRNA-seq data confirmed that the proportion of macrophages was the most significantly altered cell type among all clusters in response to DOCA-salt treatment. In addition, P2X7 was specifically enriched in macrophages, and NLRP3 signaling was significantly enriched in macrophage DEGs. Our scRNA-seq data showed that P2X7/NLRP3-related pyroptosis pathway was activated in macrophages of DOCA-salt treated mice.

overall_design: Male C57BL/6 mice aged 8–10 weeks were used for establishing DOCA-salt model. The mice were anesthetized with isoflurane (induction: 5%, maintenance: 2%), and the left kidney was removed. One week after nephrectomy, the mice were implanted with 50 mg of DOCA pellets (Innovative Research of America, Sarasota, FL) subcutaneously and received drinking water containing 1% NaCl for 21 days. The mice in the sham group received a sham surgery and normal drinking water and were not implanted with the DOCA pellets. Three weeks after DOCA pellet implantation, the sham mice and the DOCA-salt mice were sacrificed, and their kidneys were used for scRNA-seq. Three samples were included in each group and no repeated samples were used.

first: Zhiyu

first: Wen

last: Zhang


title: Genomic characterization of a novel victorivirus detected in a sample derived from a human-biting tick in Japan

city: Okayama City

first: MAN

last: LIU

address: 2-5-1 Shikata-cho, Kita-ku

institute: Okayama University

summary: Surveillance of tick-associated viruses may contribute to our understanding of viral diversity and evolution. We identified a novel viral sequence from a sample derived from a human-biting tick, Amblyomma testudinarium, in Japan. The viral sequence that we found was 4621 bp in length with 54% GC content. Two major open reading frames were predicted to encode a putative coat protein (CP) and an RNA-dependent RNA polymerase (RdRp), respectively. Two ORFs overlapped at the tetranucleotides, AUGA. The C-terminal region of putative CP was enriched in alanine, glycine, and proline residues. All these features are similar to those commonly observed in victoriviruses. Phylogenetic analyses based on the amino acid sequences of the putative CP and RdRp showed that the virus belongs to the genus Victorivirus of the family Pseudototiviridae. Based on these, we designated this putative virus as Amblyomma testudinarium-associated victorivirus 1 (ATaVV1). These findings expand current knowledge of hidden diversity of virome associated with tick-related samples.

overall_design: Vero cells were treated with PBS (mock control) or tick homogenate (infection group), followed by RNA-seq profiling.

first: Man

last: Liu

first: Da

last: Teng

first: Jiajia

last: Wu

first: Sayumi

last: Gouchi

first: Shinnosuke

last: Fukushima

first: Tomoyuki

last: Honda


title: Enterotoxigenic Bacteroides fragilis induces host genotype-specific colonic epithelial and immune responses in mice, sample set #2: leukocyte-enriched colon prep

city: Baltimore

first: Jessica

last: Queen

state: Maryland

address: 600 N. Wolfe St.

institute: Johns Hopkins

summary: Colorectal cancer pathogenesis involves complex interactions between multiple risk factors including somatic mutations and microbial dysbiosis. A number of individual microbiota members have been implicated in colorectal cancer, including enterotoxigenic strains of Bacteroides fragilis (ETBF). ETBF promotes inflammation in mouse models, which has been mechanistically linked to colon tumorigenesis. We hypothesized that ETBF would promote distinct patterns of colonic damage and inflammation in mice expressing different oncogenic mutations.  Mice expressing mutations in the Apc tumor suppressor gene or the BRAF or Kras oncogenes were colonized with ETBF to induce acute colitis. Seven days after colonization, tissues and stools were collected to assess for colonization, epithelial damage, and local and systemic immune responses. RNA sequencing analysis revealed varied transcriptional profiles based on mouse genotype and colon region.

overall_design: We performed bulk RNA sequencing on RNA extracted from leukocyte-enriched (CD45+) cell preparations from distal and midproximal colons of mice 7 days after orogastric gavage with Enterotoxigenic Bacteroides fragilis (ETBF). The mouse strains in the study included:  1. BL (Loxp flanked BRAFV600E crossed with leucine rich repeat containing G protein-coupled receptor 5 (Lgr5) CreERT2) 2. KL (Loxp-flanked KrasG12D crossed with leucine rich repeat containing G protein-coupled receptor 5  (Lgr5) CreERT2)

first: Taylor

last: Southward

first: Yongbao

last: Zhuang

first: Ada

last: Tam

first: Hana

last: Minsky

first: Jacqueline

last: Ferri

first: John

last: Michel

first: Shaoguang

first: Xinqun

first: Tatianna

last: Larman

first: Franck

last: Housseau

first: James

last: White

first: Cynthia

last: Sears


title: Systemic degradation of repressive transcription factors gates gene expression and cell fate specification [CUT&RUN]

city: Berkeley

first: Michael

last: Rape

state: CA

address: 330F Li Ka Shing Center

department: MCB

institute: University of California Berkeley

summary: While proteasomes are best known for eliminating defective proteins or turning off signaling path-ways, they also enable many cellular activities. Critical among these, proteasomes allow cells to initiate gene expression, but underlying targets and regulatory mechanisms remain poorly under-stood. Here, we report that proteasomes drive systemic degradation of repressive transcription factors to constantly eject co-repressors of the TLE family from chromatin and thus broadly free transcription start sites for activator binding. Systemic transcription factor degradation depends on the E3 ligase SCFFBXL14, which gains substrate access through constitutive complex formation with TLE co-repressors. While energetically costly, cycling co-repressors on and off chromatin is essential for stem cells to translate developmental cues into lineage-specific gene expression, a regulation that is disrupted by cancer mutations in TLE1 that impair SCFFBXL14 recognition. We conclude that proteasomes enable gene expression and cell differentiation by driving systemic transcription factor degradation and thereby establishing dynamic co-repressor function.

overall_design: Endogenous 3xHATLE1 CUT&RUN experiments from either WT or FBXL14ΔCTE iPSCs undergoing neural conversion for 4 days were performed in biological triplicates using CUTANA™ ChIC/CUT&RUN Kit (EpiCypher, 14-1048) according to the manufacturer’s protocol (User Manual Version 6.0). Cells at 4 days of neural conversion were dissociated in Accutase, washed in PBS and 6x105 cells was used per condition. Cells were permeabilized using a final working concentration of 0.015% digitonin. Endogenous 3xHATLE1 was bound using 1 μg anti-HA tag antibody (Abcam, ab9110) and 1 µl of manufacturer supplied IgG antibodies were used as negative control and incubated at 4 °C overnight. Samples were washed with cell permeabilization buffer and pAG-MNase was added to each sample and incubated at room temperature for 15 min. Targeted chromatin digestion was initiated by adding calcium chloride to each sample and samples were digested at 4 °C for 1 h. Reactions were quenched with stop buffer followed by incubation at 37 °C for 10 min to release digested chromatin fragments. DNA was purified using SPRIselect beads, washed with 85% ethanol and eluted in 0.1X TE Buffer. DNA concentration was determined using the Qubit dsDNA High Sensitivity assay kit (Thermo Fisher, Q33230). Libraries were prepared using the CUTANA™ CUT&RUN Library Prep Kit (EpiCypher, 14-1001). Library DNA size distribution was assessed using a Fragment Analyzer (Agilent). Final libraries were pooled and sequenced by QB3 Genomics, UC Berkeley, Berkeley, CA (RRID:SCR_022170) on an NextSeq P1 150PE (Illumina). Pair-end reads were quality-checked with FastQC (version 0.12.1), trimmed with cutadapt (version 2.6) and aligned onto the human genome (hg38 assembly) using Bowtie2 (version 2.5.4). Peaks were called with MACS3 (version 3.0.3)

first: Predrag

last: Jevtić

first: Samuel

last: Witus

first: Devlon

last: McCloud

first: Zhi

last: Yang

first: Ana

last: Milunović-Jevtić

first: Heegwang

last: Roh

last: Rapé


title: Transcriptome of TEX cell line following two CDK8 inhibitors treatment

status: Public on Aug 13 2026

city: Warsaw

first: Michal

last: Mikula

address: Roentgena 5

department: Experimental Oncology

country: Poland

institute: Maria Skłodowska-Curie National Research Institute of Oncology

summary: TEX cells maintaining functional and phenotypic hierarchy of AML, with leukemia stem cells (LSC) characteristics (PMID: 16094415) was treated with two CDK8 inhibitors (CDK8i) RVU120 (Ryvu) and CCT251921 (Merck), to delineate molecular changes upon CDK8i time course (3h, 24h and 72 hours). There were 984, 4357 and 4257 common differentially expressed genes (FDR <0.05) for both inhibitors with correlation coefficients of 0.82, 0.95 and 0.95, respectively, for 3h, 24h and 72h time points. The dataset generation was supported by the National Science Center grant (2018/30/E/NZ2/00801).

overall_design: TEX cells were treated with RVU120 (0.5mM), CCT251921 (0.5mM), or DMSO (5%) for 3h, 24h, and 72h in three biological replicates.

first: Izabela

last: Rumienczyk

first: Malgorzata

last: Statkiewicz

first: Maria

last: Kulecka

first: Urszula

last: Pakulska

first: Tomasz

last: Rzymski

first: Milena

last: Mazan


title: Enterotoxigenic Bacteroides fragilis induces host genotype-specific colonic epithelial and immune responses in mice, sample set #1

first: Jessica

last: Queen

overall_design: We performed bulk RNA sequencing on RNA extracted from midproximal or distal colon tissue of 7 days after orogastric gavage with PBS (sham) or Enterotoxigenic Bacteroides fragilis (ETBF). The mouse strains in the study included:  1. WT (Wildtype C57BL/6J) 2. BL (Loxp flanked BRAFV600E crossed with leucine rich repeat containing G protein-coupled receptor 5 (Lgr5) CreERT2) 3. KL (Loxp-flanked KrasG12D crossed with leucine rich repeat containing G protein-coupled receptor 5  (Lgr5) CreERT2) 4. Min (ApcMinD716-)

first: Taylor

last: Southward

first: Yongbao

last: Zhuang

first: Ada

last: Tam

first: Hana

last: Minsky

first: Jacqueline

last: Ferri

first: John

last: Michel

first: Shaoguang

last: Wu

first: Xinqun

first: Tatianna

last: Larman

first: Franck

last: Housseau

last: White


title: Transcriptomic profiling of human corneal epithelial cells following direct contact with Pseudomonas aeruginosa or Staphylococcus epidermidis

first: Noelia

last: Blanco-Agudín

summary:
Direct interactions between microorganisms and host epithelial cells play a critical role in ocular surface homeostasis and disease. In this study, human corneal epithelial cells (HCE-2) were directly exposed to either Pseudomonas aeruginosa or Staphylococcus epidermidis. RNA sequencing was performed to characterize transcriptional changes induced by direct bacterial contact compared with untreated control cells.
Article available: https://doi.org/10.3389/fcimb.2026.1899147

overall_design: Human corneal epithelial cells (HCE-2) were cultured directly exposed to Pseudomonas aeruginosa or Staphylococcus epidermidis in antibiotic-free culture medium supplemented with species-specific antibiotics at MIC concentrations. Untreated cells served as controls. Total RNA was extracted after 15 h of co-culture and subjected to paired-end RNA sequencing. Three biological replicates were analyzed per condition.

first: Suhui

last: Ye

first: Sara

last: González-Fernández

first: Iván

last: Fernández-Vega

first: Jesús

last: Merayo-Lloves

first: Luis

last: Quirós


title: Systemic degradation of repressive transcription factors gates gene expression and cell fate specification [delWD40TLE1 RNAseq]

first: Michael

last: Rape

overall_design: RNAseq from differentiating WT iPSCs and TLE1ΔWD40 iPSCs at 5 days of neural induction. Stem cells were dissociated with Accutase and 2x106 cells were seeded on matrigel-coated 6-well plates and subjected to neural conversion using the STEMdiff™ Neural Differentiation medium with neural crest supplement (STEMCELL Technologies, 08610) which gives equal proportion of neural progenitors and neural crest cells.

first: Predrag

last: Jevtić

first: Samuel

last: Witus

first: Devlon

last: McCloud

first: Zhi

last: Yang

first: Ana

last: Milunović-Jevtić

first: Heegwang

last: Roh

last: Rapé


title: Systemic degradation of repressive transcription factors gates gene expression and cell fate specification [RNAseq R610S-TLE1]

overall_design: RNAseq from differentiating WT iPSCs and TLE1R610S iPSCs at 5 days of neural induction. Stem cells were dissociated with Accutase and 2x106 cells were seeded on matrigel-coated 6-well plates and subjected to neural conversion using the STEMdiff™ Neural Differentiation medium with neural crest supplement (STEMCELL Technologies, 08610) which gives equal proportion of neural progenitors and neural crest cells.


title: Systemic degradation of repressive transcription factors gates gene expression and cell fate specification [WT_vs_delCTEFBXL14_RNAseq]

overall_design: RNAseq from differentiating WT iPSCs and delCTE-FBXL14 iPSCs at 5 days of neural induction. Stem cells were dissociated with Accutase and 2x106 cells were seeded on matrigel-coated 6-well plates and subjected to neural conversion using the STEMdiff™ Neural Differentiation medium with neural crest supplement (STEMCELL Technologies, 08610) which gives equal proportion of neural progenitors and neural crest cells.


title: Differential impact of cancer- and chemotherapy-induced cachexia: a comparative analysis in a pre-clinical model of colorectal cancer by biological sex

city: Fayetteville

middle: Regina

last: Cabrera

state: AR

address: 155 Stadium Dr

institute: University of Arkansas

summary: Cancer cachexia is a wasting condition characterized by muscle loss and reduced quality of life in cancer patients. Although biological sex differences in the progression of cancer cachexia have been increasingly recognized, their role during chemotherapy-induced cachexia remains largely unexplored. Here, we aimed to evaluate those differences using male and female mice implanted subcutaneously with Colon-26 (C26) allografts. We employed a novel approach to disentangle the effects of chemotherapy by administering two cycles of 75% of the maximum tolerated dose of 5-fluorouracil, cisplatin, or paclitaxel, in the presence (C26) and absence of cancer (PBS). Gastrocnemius muscle were collected 25 days following tumor implant, and gene expression through RNA sequencing was evaluated.

overall_design: At week-old Balb/c male and female mice (n=6-8/group) receivd 1x10^6 C26 cells injected bilateral, and tumors were developed for 25-days or PBS injection for control mice. At day 12 of tumor/PBS injections, mice received 75% of the MTD of 5-fluorouracil, Paclitaxil, or Cisplatin in 2 cycles of chemotherapy distributed in 2 injections per week. Cancer and PBS control mice received saline as vehicle control. Gastrocnemius muscle was collected after 25 of cancer/PBS injections and RNA sequencing was performed.

first: Nicholas P.

last: Greene

first: Ana Regina


title: Epigenomic changes in chromatin accessibility following 1,25-dihydroxyvitamin D3 treatment in human endometrial stromal cells

city: Durham

first: MyeongJin

last: Yi

state: NC

address: 111 TW Alexander Dr

institute: NIEHS

summary: Chromatin accessibility is a key determinant of gene regulation and cellular responsiveness to hormonal signaling. Although vitamin D has been implicated in diverse biological processes, its effects on chromatin accessibility in human endometrial stromal cells remain incompletely characterized. In this study, the impact of 1,25-dihydroxyvitamin D₃ on chromatin accessibility was examined using ATAC-seq. Overall, these findings indicate that 1,25-dihydroxyvitamin D₃ is associated with changes in chromatin accessibility in human endometrial stromal cells and suggest a potential epigenomic basis for vitamin D–mediated cellular responses.

overall_design: Experimental Design: There are 2 groups, and 6 samples in total. All ATACseq libraries were prepared from the human endometrial stromal cell line (T-HESC). 1) Vehicle treatment (control) n=3 2) 2 nM of 1,25(OH)2D3 treatment n=3 Data Analysis Strategy: Dr. Hamed Bostan from the informatics group supported Dr. MyeongJin Yi with the analysis. 1) Remove adaptor 2) QC with trim-galore 3) Map the pair-end reads 4) Count reads mapped to chrM 5) Remove duplicated reads 6) Remove unmapped reads 7) Remove reads mapped to chrM 8) Prepare SAM file based on trimmed 9bp reads 9) Random sampling to the same depth 10) Compare between different groups (vehicle vs 1,25(OH)2D3)

first: Hamed

last: Bostan

first: Francesco

last: DeMayo


title: RNA sequencing of meningeal lymphatic vessels in dural metastasis models

first: Rui

last: Zeng

address: Dong An Road

institute: Fudan University

summary: Dural metastasis (DM) is a rarely researched disease with limited therapeutic options, largely due to our circumscribed understanding of dura mater. However, recently emerging studies suggest the dura mater is an immune hub and implements immunosurveillance of the central nervous system. These evidences imply potential immunotherapies of DM. Here, we established a preclinical murine model of DM. We have employed a RNA sequencing approach using SMART-seq to study the meningeal lymphatic vessels of DM model. Briefly, on day 12, the dorsal dura maters were isolated from the head of 4T1-DM mice treated with PBS, ZOL or ZOL+Ang2, and were enzymatically digested to single cells with collagenase VIII and DNase I. The meningeal lymphatic endothelial cells (LECs) were harvested using fluorescent activated cell sorting, CD45-CD31+PDPN+ dural cells were sorted for sequencing.

overall_design: 4T1-DM mice were treated with PBS, ZOL or ZOL+Ang2. 12 days after 4T1-DM cell inoculation, the dorsal dura maters were isolated from the head of 4T1-DM mouse model, and were enzymatically digested to single cells with collagenase VIII and DNase I. Mixture of samples from 6 mice per group were subjected to subsequent sequencing.

first: Jiaxu

last: Zhao

first: Haibao

last: Peng

first: Yudan

last: Chi


title: PTPN13 Contributes to Ebola Virus Induced Immune Dysregulation via dephosphorylation of IRF3 and PI3K-p85

city: Cincinnati

first: Matthew

last: Weirauch

state: Ohio

address: 3333 Burnet Avenue

department: Center for Autoimmune Genomics and Etiology (CAGE)

institute: Cincinnati Children's Hospital Medical Center

summary: Ebola virus disease (EVD) is characterized by immune dysregulation and damaging hyperinflammation. We aimed to characterize the signaling pathways and regulatory mechanisms dysregulated during EVD. To avoid hyperinflammation, innate immune signaling is regulated by posttranslational modifications, including the process of protein phosphorylation. Here, we show that the Protein tyrosine kinase nonreceptor type 13 (PTPN13) negatively regulates IFNβ while also positively regulating the neutrophil chemoattractant CXCL1. Using vectors encoding mutations on IRF3 phosphorylation sites we identified Y292 on IRF3 as PTPN13 target of dephosphorylation. Knockout of PTPN13 increased IRF3 phosphorylation and expression of IFNβ and IFN-stimulated genes, following poly(I:C) stimulation, suggesting that PTPN13 negatively regulated IFNβ and ISG production via IRF3. Intriguingly, depletion of PTPN13 during Ebola virus (EBOV) infection resulted in decreased IFNβ and ISG induction at later timepoints post-infection, which correlated with increased viral titers, suggesting that increased levels of EBOV can efficiently inhibit the IFN response in the absence of PTPN13. Additionally, PTPN13 knockout cells showed a decrease in the induction of inflammatory chemokines, including CXCL1, late during EBOV infection. These effects could be explained by increased phosphorylation on the regulatory p85 subunit of PI3K. Phosphorylation on p85 promotes its degradation, subsequently enhancing PI3K kinase activity and downstream signaling via AKT. Together our study suggests that PTPN13 is involved in immune regulation and efficient antiviral responses by dephosphorylation of IRF3 and PI3K-p85.

overall_design: We performed RNA-seq on A549 and A549-PTPN13-KO cells infected with EBOV or Mock infection at two time points( 24 and 48 hpi).

first: Ricardo

last: Rajsbaum

first: Alexander

last: Bukreyev

last: Freiberg

first: Jefferey

last: Johnson

first: William

last: Russell


title: MiaA-mediated tRNA modifications couple tryptophan attenuation and changes in tRNA abundance to complex phenotypes in Pseudomonas aeruginosa [RNA-seq]

city: Braunschweig

first: Matthias

last: Preusse

address: Inhoffenstr. 7

department: Molecular Bacteriology

institute: Helmholtz Center for Infection Research

summary: tRNA-modifying enzymes are emerging as key regulators of bacterial physiology. MiaA, a tRNA isopentenyltransferase, is well studied in model organisms, but its role in the opportunistic pathogen Pseudomonas aeruginosa remains unclear. Using LC–MS, nanopore tRNA sequencing, as well as transcriptional, translational, and proteomic profiling, we mapped MiaA-dependent tRNA modifications and revealed unexpected effects of MiaA loss. Impaired translation of MiaA-sensitive codons reduced quorum-sensing-controlled virulence gene expression and attenuated pathogenicity in Galleria mellonella. Ribosome stalling at trp codons in miaA mutants overrides the attenuation-controlled repression of tryptophan biosynthesis, causing overproduction of tryptophan, along with upregulation of cognate tRNAs, thereby linking translation to global metabolic adaptation. MiaA is tightly regulated and is so central to bacterial physiology that its expression level correlates directly to virulence in clinical isolates, highlighting its role as a hub connecting translation, transcription, metabolism, and pathogenicity. These findings position MiaA as a key integrator of cellular processes critical for pathogen fitness and host interactions.

overall_design: Pseudomonas aeruginosa UCBPP-PA14 wild type and delta miaA mutant strains were cultured in LB medium at 37°C.

first: Yannick

middle: N

last: Frommeyer

first: Janne

last: Thöming

first: Nicolas

middle: O

last: Gomez

first: Svenja

last: Grobe

first: Alejandro

last: Arce-Rodríguez

first: Kerstin

last: Neubauer

first: Benedikt

last: Kennepohl

first: Tim

last: Kirk

first: Raimo

last: Franke

first: Mark

last: Brönstrup

first: Meina

last: Neumann-Schaal

first: Mathias

last: Müsken

first: Daniel

middle: P

last: Depledge

first: Heike

last: Bähre

first: Andreas

last: Pich

first: Susanne

last: Häussler


title: Influenza-activated alveolar macrophages protect against death by malaria-associated acute lung injury (MA-ALI) during coinfection

city: Salt Lake City

first: Tracey

last: Lamb

address: 15 N Medical Drive

department: Pathology

institute: University of Utah

summary: Lower respiratory tract infections can be exacerbated in children living in malaria endemic areas, but there is little data on the interaction between malaria and influenza. Here we show that malaria-influenza coinfection does not yield worse prognosis in mice. Rather, coinfection with Influenza/A/X31 protects mice from severe malaria-associated acute lung injury (MA-ALI). This effect arises from differences in CD8-mediated pathology, rather than a failure by Plasmodium parasites to establish infection, and it depends on an active influenza infection in the lung. Surprisingly, recruitment of Plasmodium-reactive CD8 T cells to the lung was unaffected by influenza coinfection. Rather, an influenza-induced expansion of Arginase 1 (Arg1)-expressing alveolar macrophages suppressed the cytotoxic capabilities of pathogenic CD8 T cells once they had been recruited to the lung, rendering them harmless. Ablating this Arg1+ alveolar macrophage population in coinfected animals reverted the protective phenotype of influenza infection and reestablished death by malaria-associated pulmonary leak. Given that respiratory complications have been reported following infection by all five human-infecting Plasmodium species and the high mortality rate of MA-ALI, this study highlights suppressive alveolar macrophages as a potential therapeutic target to dampen pulmonary vascular inflammation during Plasmodium infection.

overall_design: Mice were infected with Plasmodium berghei NK65-Edinburgh (PbE) and/or Influenza/A/X31 (X31) at 0 days post-infection. PbE infections were performed via intraperitoneal injection of 5x10^5 parasitized red blood cells of Plasmodium berghei NK65-E with injection of Krebs-Ringer saline solution in control mice. X31 infections were performed by intranasal inoculation of 3x10^4 plaque forming units under anesthesia, with 1X PBS administered in control mice. At 6 days post-infection, mice were euthanized and the lungs were harvested and processed into single-cell suspensions. T cells were isolated by magnetic-activated cell separation (negative selection) using the Pan T Cell Isolation Kit II, mouse (Miltenyi Biotec, 130-095-130) and analyzed by single-cell RNA sequencing and T Cell receptor sequencing.

first: Reed

last: Jenna

first: Nayan

last: Ritika

first: Deckers

last: Margot

first: Cornwall

middle: H

last: Douglas

first: Ostrand-Rosenburg

last: Suzanne

first: Evavold

last: Brian

first: Lamb

last: Tracey


title: Fibrotic Differentiation Proile of Skeletal and Cardiac Muscle Fibroadipogenic Progenitors in D2-mdx Mouse

city: San Francisco

first: Brian

last: Feeley

address: 1700 Owens St

department: Orthopedic Surgery

institute: University of California, San Francisco

summary: Muscle fibrosis is a key pathological feature of Duchenne muscular dystrophy (DMD) and is closely associated with disease progression. Fibroadipogenic progenitors (FAPs) are major contributors to fibrosis, yet the precise mechanisms remain unclear. To investigate FAP dynamics and lineage specification, we generated dual-reporter mice (PRURD2) by crossing D2.B10-Dmdmdx/J (D2-mdx) mice with FAP and brown/beige adipose tissue (BAT) reporter lines. Corresponding control mice (PRURDBA) were established on the DBA/2J background. At 12 months, heart, diaphragm, and tibialis anterior (TA) muscles were collected for histological analysis. FAPs were isolated via FACS and subjected to single-cell RNA sequencing. PRURD2 mice exhibited increased fibrosis across all muscles compared to controls (p < 0.01) and a significant rise in PDGFRα-GFP+ FAPs (p < 0.05). UMAP clustering identified 11 distinct FAP subpopulations, with the fibrosis-associated CD55 cluster enriched in PRURD2 mice. Pseudotime analysis showed lineage progression from progenitor clusters toward the fibrogenic CD55 cluster. CellChat analysis indicated increased interactions in PRURD2 mice involving fibrosis-related pathways like COLLAGEN, TGF-β, WNT, NOTCH, and ANGPTL. Additionally, fibrosis-related signaling pathways such as THY1, TWEAK, EPHA, EPHB, and SEMA6 showed increased interactions among FAP clusters in PRURD2 mice. Differential gene expression analysis revealed top upregulated genes including Cxcl13, Cxcl3, Ly6d, Klk1, Fgf23, Serpinb2, Mmp13, Ccl17, Postn, and Adam12. PRURD2 mice develop severe fibrosis in skeletal and cardiac muscle, driven by FAP-induced signaling pathways and genes. This model is valuable for understanding muscle fibrosis in DMD and developing anti-fibrotic therapies.

overall_design: Heart, diaphragm, and bilateral TA muscle were harvested from the PRURDBA mice (n=3) and PRURD2 mice (n=3). Using sterile micro-dissecting scissors, excess adipose tissue, tendons, and connective tissue were removed. Tissues were finely minced and subjected to enzymatic digestion in a sterile biosafety cabinet. The digestion media consisted of Collagenase Type III (Worthington Biochemical Corporation, Cat# NC0021929) at a concentration of 15 mg per gram of tissue, prepared in Dulbecco’s Modified Eagle Medium (DMEM) (Gibco, Cat# 11965084) supplemented with 10% fetal bovine serum (FBS) (Gibco, Cat# 10437028) and 1% penicillin/streptomycin (P/S) (Gibco, Cat# 15140122). Tissue samples were incubated in this digestion media at 37 ˚C for 70 min, with mechanical trituration using an 18-gauge needle performed midway through the incubation to facilitate dissociation. Samples were washed with PBS and subjected to a second enzymatic digestion using 0.25% trypsin-EDTA (Gibco, Cat# 25200056) at 37 ˚C for 12 min. Digestion was quenched with FBS, and the resulting cell suspension was passed through a 40 μm nylon mesh filter. Cells were then washed in PBS containing 2% FBS, and erythrocytes were lysed using ammonium-chloride-potassium (ACK) lysing buffer (Quality Biological, Cat# 188-156-101) for 5-7 min on ice. Samples were then washed with 2% FBS in PBS and resuspended in 100 µL flow cytometry buffer, composed of PBS with 2% FBS, 5 mM EDTA (Corning, #MT-46034CI), and 2 mM HEPES (Quality Biological, #118-089-721) per 1 g of starting tissue weight. FAPs were isolated by fluorescence-activated cell sorting (FACS) based on PDGFRα-GFP reporter expression, enabling enrichment of the FAP population. Single-cell RNA sequencing (scRNAseq) was performed on FACS-isolated FAPs from the diaphragm, heart, and TA of PRURDBA mice (n=3) and PRURD2 mice (n=3). For each tissue, FAPs from three mice of the same genotype were pooled and loaded into a single lane of a 10x Genomics Chromium controller, resulting in six separate scRNAseq libraries (one per tissue per genotype). Libraries were prepared using the 10x Genomics Chromium Single Cell 3’ Reagent kit (10x Genomics, NEXT Gel Beads-in-emulsion (GEM) Single Cell 3’ version 3.1, dual index PN-1000268), according to the manufacturer’s protocol for GEM generation, cDNA production, and library construction. Sequencing of constructed libraries was carried out on Illumina NovaSeq. Raw sequencing reads were processed using CellRanger (version 9.0.1) to demultiplex, align reads to the mm10 mouse reference genome (provided by 10x Genomics), and quantify unique molecular identifiers (UMIs). Doublets were removed using DoubletFinder based on input cell concentrations and expected multiplet rate estimates as recommended by 10x Genomics. Downstream analysis was performed using Seurat (v5.0). For each tissue, dataset was filtered, clustered, and visualized using uniform manifold approximation and projection (UMAP). Datasets were then integrated using canonical correlation analysis (CCA) integration, following the Seurat integration tutorial. Raw, unintegrated gene counts were pseudo-bulked by experimental group, and differential expression analysis was performed using NOISEQ. Pseudotime trajectory analysis was carried out using Monocle3 and cell-cell communication between each FAP subpopulation was performed using CellChat (version 1.1.3).

first: Hiroyori

last: Fusagawa

first: Justin

last: Lau

first: Sankalp

last: Sharma

first: Mengyao

last: Liu

first: Yusef

last: Samimi

first: Gabriel

last: Franchet Schaer

first: Ashley

last: Fang

first: Hubert

last: Kim

first: Xuhui


title: MiaA-mediated tRNA modifications couple tryptophan attenuation and changes in tRNA abundance to complex phenotypes in Pseudomonas aeruginosa

first: Matthias

last: Preusse

first: Yannick

last: Frommeyer

first: Janne

last: Thöming

first: Nicolas

last: Gomez

first: Svenja

last: Grobe

first: Alejandro

last: Arce-Rodríguez

first: Kerstin

last: Neubauer

first: Benedikt

last: Kennepohl

first: Tim

last: Kirk

first: Raimo

last: Franke

first: Mark

last: Brönstrup

first: Meina

last: Neumann-Schaal

first: Mathias

last: Müsken

first: Daniel

last: Depledge

first: Heike

last: Bähre

first: Andreas

last: Pich

first: Susanne

last: Häussler


title: Gene expression profiling of vulnerable spinal motor neurons in the SMNΔ7 mouse model of SMA upon modulation of p53 signaling

city: New York

first: Maria

middle: Jose

last: Carlini

department: Neurology

institute: Columbia University

summary: Selective motor neuron degeneration in spinal muscular atrophy (SMA) is driven by converging mechanisms that promote stabilization and phosphorylation of p53 in vulnerable motor neurons. However, the downstream transcriptional programs that execute motor neuron death remain incompletely defined.To characterize p53-associated transcriptional changes in vulnerable motor neurons, we performed RNA sequencing of cholera toxin subunit B (CTB)-labeled lumbar (L1–L3) motor neurons isolated by laser-capture microdissection from postnatal day 6 SMNΔ7 (SMNΔ7;SMN2;Smn−/−) SMA mice and wild-type littermate controls. Disease-associated gene expression changes were defined by comparison of SMA and wild-type motor neurons. To assess pathway-specific contributions, untreated SMA mice were compared to SMA mice treated with Pifithrin-α (inhibitor of p53 transcriptional activity), MW150 (p38 MAPK inhibitor that prevents p53 phosphorylation), or SMN-C3 (SMN splicing modifier). Differential gene expression analysis was performed using kallisto-based transcript quantification and DESeq2.

overall_design: RNA-seq profiling of cholera toxin subunit B (CTB)-labeled lumbar (L1–L3) motor neurons isolated by laser-capture microdissection from postnatal day 6 mice. Five groups were analyzed: wild-type (WT), SMNΔ7 (SMNΔ7;SMN2;Smn−/−) SMA, SMA+Pifithrin-α, SMA+MW150, and SMA+SMN-C3, with 3 biological replicates per group.

first: Xuemei

last: Xu

first: Leonie

last: Sowoidnich

first: Archana

last: Yadav

last: Savin

first: Jason

middle: Q

last: Garcia

first: Charlotte

last: Sumner

first: Vilas

last: Menon

first: Christian

middle: M

last: Simon

first: Livio

last: Pellizzoni


title: rFSTL1 Treatment of Macrophages

city: xi'an

first: Lin

last: Sun

address: xincheng street,169

department: Department of Hepatobiliary Surgery, Xijing Hospital, Fourth Military Medical University

institute: Fourth Military Medical University

summary: RAW264.7 cells were  treated with   rFSTL1 for 24 hours before being harvested for subsequent analysis.

overall_design: RAW264.7 cells were seeded in 6 or 12 well plates at 70-80% confluence. The cells were  treated with 100 ng/mL  rFSTL1 for  24 hours before being harvested for subsequent analysis.


title: T Cell Antigenic Recognition Sequencing (TAR-seq) enables precise characterization of vaccine-elicited cellular immunity ex vivo and in vivo

city: Beaverton

first: Benjamin

last: Bimber

state: OR

address: 505 NW 185th Ave

summary: This project contains T cell single-cell RNA/TCR-seq data from rhesus macaques, including antigen-stimulated T cells. These data were used to generate a probalistic model for detection of TCR-stimulation.

overall_design: These data include CD8 and CD4 T cells from rhesus macaque PBMC and tissues. Conditions vary by sample, as indicated in the sample-level metadata. The project includes: 1) cell sorted using MHC-I tetramers, 2) CD4 or CD8 T cells stimulated ex vivo with peptide-pulsed antigen presenting cells, 3) CD4 T cell stimulated with superantigen, 4) CD8 T cells stimulated with autologous SIV-infected CD4 T cells, and 5) cells from multiple rhesus macaque tissues without sorting.


title: CpG island density predicts CBP/p300 dependency across 3D chromatin clusters

city: Cleveland

first: Matthew

last: Chang

address: 2109 Adelbert Rd

institute: Case Western Reserve University School of Medicine

summary: RNA Polymerase II (Pol2) organizes transcription through higher-ordered chromatin clusters that integrate promoter and enhancer interactions to coordinate gene expression. Nevertheless, the features that distinguish unique classes of Pol2-mediated clusters remain to be defined. Here, we identify two distinct classes of Pol2-mediated clusters: one enriched for CpG islands, promoter-promoter interactions, and housekeeping gene expression, and another characterized by high CBP/p300 occupancy, enhancer-promoter looping, and lineage-defining (LD) transcriptional programs. Acute inhibition of CBP/p300 catalytic activity leads to rapid loss of acetylation at enhancers and preferential downregulation of LD genes, resulting in impaired cellular proliferation and activation of apoptotic programs. Integrative machine learning modeling reveals that cluster strength, RNA half-life, and CpG island content as strong predictors of CBP/p300 inhibition. Together, these findings identify H2B acetylation as a biomarker for enhancer-addiction and vulnerability to CBP/p300 inhibition.

overall_design: RNA-seq, ChIP-seq, and ChRO-seq profiling of RH4 cells treated with CBP/p300 inhibitors or degraders.

first: Berkley

middle: E

last: Gryder