title: PIWI-interacting RNAs (piRNAs) expression profiles of exosomes derived from stem cells from apical papilla (SCAP-Exo)

city: Shenyang

first: AoChen

last: Wang

state: Liaoning

address: School of Stomatology

institute: China Medical University,

summary: SCAP were collected from intact, caries-free impacted third molars with immature roots extracted from three healthy human patients (12–15 years of age). The cells were cultured to the 5th passage. Then, the supernatant was collected after 48 h of continuous culture in exosome-free serum medium (SBI, USA) and centrifuged successively at increasing speeds: 3,000 × g for 20 min, 20,000 × g for 30 min, and 120,000 × g for 2 h (Beckman Optima L-100XP, USA) to obtain SCAP-Exo.

overall_design: To investigate the expression differences of piRNAs of SCAP-Exo.

first: Aochen

first: Xu

last: Chen

first: Shuman


title: Single-cell level decoding anabolic effect of peptides-induced bone regeneration in pigs

status: Public on Apr 08 2026

city: Chengdu

first: Fanyuan

last: Yu

state: Sichuan

address: No.14, 3rd Section, Ren Min Nan Rd

department: Endodontics

country: China

institute: State Key Laboratory of Oral Diseases, West China Hospital of Stomatology

type: Expression profiling by high throughput sequencing

summary: In this study, single-cell transcriptome was used to profile the single-cell heterogeneity of regenerated bone tissue

overall_design: 1797 peptide group (2 samples) and control peptide group (10 samples) regenerated bone cells were isolated for single-cell transcriptome analysis

first: Feifei

last: Li


title: Gene expression profile at single cell level of different phenotypic tumors derived from human non-muscle invasive bladder carcinoma cell lines

status: Public on Apr 07 2026

city: Shenzhen

first: Zeqin

last: Yan

address: No. 1, Fuxin Road, Pinghu Street, Longgang District, Shenzhen, Guangdong Province, China

institute: Shenzhen University

summary: The cellular states of bladder carcinoma change dynamically as tumor recurrence evolves under Gemcitabine treatment, facilitating phenotypic transitions. Thus, we employed single-cell RNA sequencing (scRNA-seq) to gain a high-resolution view of the cellular landscape in bladder carcinoma.

overall_design:
In this study, we performed single-cell RNA sequencing on four phenotypically distinct tumors derived from the human non-muscle invasive bladder carcinoma cell line, MGH-U3 (i.e., urothelial carcinoma (UC), urothelial carcinoma with squamous differentiation (UCSD), mixed phenotype (MP), and metastasis (Mets). We also sequenced two phenotypically distinct tumors derived from another cell line, RT4.
The phenotypes derived from RT4 are UC and UCSD. All samples are processed immediately after collection, dissociated into high-viability single-cell suspensions using a standardized enzymatic protocol, and subjected to single-cell capture and library preparation on the 10x Genomics platform.

first: Yan

last: Zeqin


title: Mesenchymal stem cell–derived extracellular vesicles alleviate immunoparalysis in sepsis-associated ARDS via reprogramming the lactate–H3K18 lactylation–PSMD14 axis

city: jinan

first: yuanyuan

last: Zhang

address: jinan

institute: Shandong Second Medical University

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Sepsis-associated acute respiratory distress syndrome (S-ARDS) is characterized by immune dysfunction and high mortality. Here, we show that elevated lactate induces P300-dependent H3K18 lactylation, which enhances PSMD14 transcription. Increased PSMD14 activates the AKT/mTOR pathway, leading to macrophage immunosuppression, including reduced inflammatory cytokine production, impaired phagocytosis, increased M2 polarization, and T cell dysfunction.Integrated analyses of public datasets, RNA-seq, and ChIP-seq identified PSMD14 as a key immune-related gene associated with poor outcomes and reduced HLA-DR expression in patients. Extracellular vesicles derived from P300 inhibitor (C646)-preconditioned mesenchymal stem cells suppress the H3K18la–PSMD14 axis, restore immune function, and improve survival.

overall_design: This study combined bioinformatics analysis, in vitro experiments, and in vivo models to investigate lactate-driven epigenetic regulation in S-ARDS. Public transcriptomic datasets were analyzed to identify immune-related prognostic genes. CD14⁺ macrophages were treated with lactate and/or genetic and pharmacological interventions, followed by assays for gene/protein expression, phagocytosis, and polarization. ChIP-seq and ChIP-qPCR were used to assess H3K18 lactylation at the PSMD14 promoter. RNA-seq and multi-omics integration identified key targets. In vivo, a CLP-induced sepsis model was used to evaluate immune function, bacterial burden, lung pathology, and survival following treatment with MSC-derived extracellular vesicles.

first: Shi

first: Yuanyuan


title: Neuronal MCT2 for activity-induced blood vessel formation by increasing lactate to promote astrocytic HIF1α-VEGFa signaling

city: Cleveland

first: Daehoon

last: Lee

state: OH

address: 10900 Euclid Ave.

country: USA

institute: Case Western Reserve University

summary:
To investigate the mechanisms of neural activity regulation of blood vessel (BV) formation in the brain, we subjected mice to whisker stimulation (WS).
We then performed gene expression profiling analysis using data obtained from RNA-seq from the primary somatosensory (S1) cortex without or with whisker stimulation.

overall_design: Comparative gene expression profiling analysis of RNA-seq data without or with whisker stimulation from (S1) cortex.


title: Control of Cellular Differentiation Trajectories for Cancer Reversion

city: Yuseong-gu

first: Jeong-Ryeol

last: Gong

state: Daejeon

address: 291, Daehak-ro

country: South Korea

institute: KAIST

summary: Cellular differentiation is controlled by intricate layers of gene regulation, involving the modulation of gene expression by various transcriptional regulators. Due to the complexity of gene regulation, identifying master regulators across the differentiation trajectory has been a longstanding challenge. To tackle this problem, a computational framework, single-cell Boolean network inference and control (BENEIN), is presented. Applying BENEIN to human large intestinal single-cell transcriptome data, MYB, HDAC2, and FOXA2 are identified as the master regulators whose inhibition induces enterocyte differentiation. It is found that simultaneous knockdown of these master regulators can revert colorectal cancer cells into normal-like enterocytes by synergistically inducing differentiation and suppressing malignancy, which is validated by in vitro and in vivo experiments.

overall_design: RNA-seq profiling of three colorectal cancer cell lines (HCT116, CACO2, and HT29) with scramble shRNA control (NC) and simultaneous shRNA-mediated knockdown of MYB, HDAC2, and FOXA2 (MHF), with two biological replicates per condition.

first: Chun-Kyung

first: Hoon-Min

last: Kim

first: Juhee

first: Jaeog

last: Jeon

first: Sunmin

last: Park

first: Kwang-Hyun

last: Cho


title: Bulk RNA-seq profiling of pleural mesothelioma and comparator pleural specimens

city: Durham

first: David

last: Severson

state: North Carolina

address: 2301 Erwin Road

department: Department of Surgery

institute: Duke University Health System

summary: This GEO submission contains processed bulk RNA sequencing data generated from pleural mesothelioma tumors and comparator pleural specimens. Raw sequencing data are available through controlled access in dbGaP under accession phs004285. Processed gene expression matrices and sample-level metadata for the bulk RNA-seq libraries are provided in this submission.

overall_design:
Bulk RNA sequencing was performed on 89 surgical specimens with either confirmed pleural mesothelioma diagnosis or normal pleura obtained from non-mesothelioma resections. Sample identifiers in this GEO submission are matched exactly to dbGaP SAMPLE_ID values for cross-reference with controlled-access raw data and associated subject/sample metadata.  Raw counts are found in "bulkRNA_rawcounts_matrix.tsv.gz". Raw counts were converted to transcripts per million (TPM) adjusting for gene length and normalized library size using TMM normalization in edgeR. Normalized counts are found in "bulkRNA_TPMcounts_matrix.tsv.gz". Sample metadata is found in "bulkRNA_sample_metadata.tsv.gz".
dbGAP,  accession phs004285

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

middle: T

first: Sam

last: Freyaldenhoven

first: Ben

last: Wadowski

first: William

middle: G

last: Richards

first: Raphael

last: Bueno


title: Spatial transcriptomic profiling of human pancreatic ductal adenocarcinoma  using 10x Genomics Visium platform

city: Beijing

first: xin

last: zhao

address: 8#， Gong Ti South Road

institute: Beijing Chaoyang Hospital

summary: In this study, we performed spatial transcriptomics (ST) to investigate the gene expression features across one normal pancreatic tissue, PC tissue, adjacent tumor tissue, and tumor stroma using 10x Genomics Visium spatial gene expression platform. We generated high-quality spatial gene expression profiles combined with histomorphological information, aiming to reveal the spatial heterogeneity of pancreatic cancer microenvironment and identify spatially restricted gene signatures associated with tumor progression. Sequencing was performed on Illumina NovaSeq 6000 platform, and data processing was conducted using SpaceRanger software with hg38 reference genome. The results revealed that KRT13+FABP5+ malignant cell subpopulation had keratinization characteristics in the tumor tissue. Fibroblasts from adjacent tumor tissue exhibited a tumor-inhibiting role such as “B-cell activation” and “positive regulation of leukocyte activation.” The FGG+CRP+ inflammatory cancer-associated fibroblasts replaced the islets in tumor stroma. During PC progression, the damage to pancreatic structure and function was heavier in the pancreatic exocrine (AMYA2+PRSS1+) than in the endocrine (INS+GCG+). Our results revealed the spatial heterogeneity of dynamic changes and highlighted the significance of impaired exocrine function in PC.

overall_design: the study employed the 10x Genomics Visium platform for spatial transcriptomics analysis of normal pancreatic tissue, pancreatic cancer tissue, adjacent tumor tissue, and tumor stroma.

first: Zhangyong

last: Ren

first: Bing

last: Pan

first: Fangfei

last: Wang

first: Shaocheng

last: Lyu

first: Jialei

last: Zhai

first: Xiumei

last: Hu

first: Zhe

last: Liu

first: Lixin

first: Ren

last: Lang

first: Qiang

last: He

first: Xin

last: Zhao


title: Phylogenetic information of different phenotypic tumors derived from human non-muscle invasive bladder carcinoma cell lines

first: Zeqin

last: Yan

summary: Evolutionary principles govern cancer relapse. This process involves defined phylogenetic signatures at each step and is initiated by the acquisition of therapeutic resistance to form relapsed tumours. Exploring this process, particularly by real-time monitoring, has been challenging because recurrence is a complex and dynamic process involving multiple steps in residual cancer cells. Thus, we leveraged an evolving lineage tracing approach to map cell genealogies and investigate the evolutionary principles underlying cancer recurrence.

overall_design: In this study, we performed sequencing on four phenotypically distinct tumors derived from the human non-muscle invasive bladder carcinoma cell line, MGH-U3 (i.e., urothelial carcinoma (UC), urothelial carcinoma with squamous differentiation (UCSD), mixed phenotype (MP), and metastasis (Mets). We also sequenced two phenotypically distinct tumors derived from another cell line, RT4. The phenotypes derived from RT4 are UC and UCSD. All samples are processed immediately after collection, dissociated into high-viability single-cell suspensions using a standardized enzymatic protocol, and subjected to single-cell capture and library preparation on the 10x Genomics platform. Gene expression libraries were prepared according to the Chromium Single Cell 3’ Kit User Guide (v3.1 Chemistry). To collect the indels information, the cDNA libraries were further amplified with target site-specific primers containing Illumina-compatible adapters and sample indices. Approximately 7 fmol of template cDNA was used per PCR reaction. The PCR products from four identical reactions for each sample were pooled and then purified and size-selected. RNA expression libraries and amplicon libraries of target sites from each sample were pooled. Two types of libraries were further pooled with approximately 10% PhiX genomic DNA library added in each lane for quality control. A custom sequencing strategy (R1: 28 cycles and R2: 290 cycles) was applied in the pooled libraries on the NovaSeq S4 platform (Illumina) to acquire the full-length sequence of target sites and gene expression readouts simultaneously.

first: Yan

last: Zeqin


title: CDK4/6 Inhibition Enhances CAR-T Cell Therapy in Solid Tumors

city: Melbourne

first: Shom

last: Goel

state: Victoria

address: 305 Grattan St

country: Australia

institute: Peter MacCallum Cancer Centre

summary: CDK4/6 inhibitors promote anti-tumor immunity through diverse mechanisms, positioning them as promising adjuvants to cancer immunotherapies. While CDK4/6 inhibitors have demonstrated strong synergy with immune checkpoint inhibitors across numerous preclinical cancer models, their combination with CAR-T cell therapy remains unexplored. In this study, we examined the efficacy of combined CDK4/6 inhibition (trilaciclib) and CAR-T therapy across a range of pre-clinical blood and solid cancer models. In vitro, trilaciclib enhanced human CAR-T cell cytotoxicity and metabolic fitness while reducing expansion. In vivo, the combination outperformed single agents against RB-proficient, trilaciclib-sensitive CD19+ leukaemia. However, in an equivalent RB-deficient model, the combination therapy was no more effective than CAR-T cells alone, suggesting that enhanced CAR-T cell function may be offset by reduced expansion. In contrast, in solid cancer models the combination was consistently more efficacious than either monotherapy. Notably, combination effects were most pronounced in immunocompetent mouse models, including a model with poor sensitivity to trilaciclib as a monotherapy. Mechanistically, CDK4/6 inhibition reduced tumor-infiltrating T-regulatory cells while enhancing CD8+ CAR-T cell persistence, tumor trafficking and cytotoxic function within the tumor. Together, these findings suggest that trilaciclib and CAR-T cell therapy may be an effective combinatorial treatment for solid cancers.

overall_design: HER2-directed mouse CAR-T cells were transferred into immunocompetent C57BL/5 mice 5 days post mammary fat pad inoculation with the mouse breast cancer cell line E0771-hHER2. Mice were treated with continuous 3 days on/4 days off trilaciclib regimen starting the day of CAR-T cell transfer. After 2 cycles of treatment (approximately 14 days after CART cell transfer), CD8+ CAR-T cells isolated from tumors of vehicle- or trilaciclib-treated mice subjected to RNA-sequencing. Differential gene expression analysis was conducted with DESeq2 (v1.36.0) with comparison of Trilaciclib (n=3) versus Citrate (n=3) buffer groups excluding one replicate from the trilaciclib group due to technical issues resulting in an outlier. The package msigdbr (v7.5.1) was used to load genesets from Hallmarks, Kegg and Immunesig. The fgsea bioconductor package (v1.2.0) was used to conduct Gene set enrichment analysis (GSEA) and generate barcode plots.

first: Emily

last: Lelliott

first: Jonathan

last: Naddaf

first: Kun-Hui

last: Lu

first: Katherine

last: Cummins

first: Kelly

last: Ramsbottom

first: David

last: Reynolds

first: Michael

last: Taylor

first: Krutika

last: Ambani

first: Isabelle

last: Munoz

first: Susan

last: Jackson

first: Jessica

last: Li

first: Cheok Weng

last: Chan

first: Kara

last: Britt

first: Paul

last: Beavis

first: Jane

last: Oliaro


title: Population Heterogeneity of Lactobacillus delbrueckii subsp. bulgaricus in Microbial Liquid, Freeze Dried, and Freeze Dried Storage by Single Cell Sequencing

city: qingdao

first: Liang

last: Liu

institute: Ocean University of China

summary: we employed high-throughput scRNA-seq to systematically profile bacterial populations throughout the freeze-drying and storage processes. Through unsupervised clustering, we delineated functional clusters with distinct physiological characteristics and fitness advantages.

overall_design: L. bulgaricus sp1.1 was cultured twice in MRS medium at 37 ℃ for 24 h with a 2% (v/v) inoculation volume, and then cultured for 12 h in MRS medium at 37 ℃ with a 2% (v/v) inoculation volume as the normal state bacterial suspension (CT). After the above cultivation, bacterial cells were washed twice with 1 × PBS at 6000 × g for 10 min, mixed with the same volume of 30% (w/w) maltodextrin, and pre-cooled at -80 ℃ for 24 h. Then, it was freeze-dried at -60 ℃ for 48 h (FD) using a freeze dryer (BIOCOOL, FD-1A-50+). The dried bacterial powder was vacuum packed and stored at 4 ℃ for 2 weeks (FD2w).


title: Multimodal profiling reveals a Notch-responsive regenerative subpopulation of cochlear supporting cells

city: Omaha

first: Litao

last: Tao

state: NE

address: 2500 California Plaza

department: Biomedical Sciences

institute: Creighton University

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

overall_design: Refer to individual Series


title: Targeting one-carbon metabolism in stem cell-like T cells to prevent chronic graft rejection [RNA-seq]

city: wuhan

first: wang

last: yi

address: no.1095 Jiefang Avenue

institute: Institute of Organ Transplantation, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology

summary: Transcription factor phosphorylation is required for lymphocyte proliferation after activation. We here report an important role for MAPK13 in TCF-1 phosphorylation. Inhibition of MAPK13 results in decreased transcription of TCF-1 downstream genes and suppresses CD4+ lymphocyte proliferation and function.

overall_design: Splenic CD4+ T cells were sorted and stimulated with anti-CD3/CD28 antibodies in the presence of MAPK13 inhibitors or DMSO for 72h. And then cells were collected for RNA-seq.


title: De novo transcriptome assembly of the Korean minipig (Sus scrofa) [I]

city: Seoul

first: Suyeon

last: Wy

address: 20, Neungdong-ro, Gwangjin-gu

department: Department of Biomedical Science and Engineering

institute: Konkuk University

summary: Minipigs are animal models widely used in biomedical studies due to their physiological and anatomical similarities to humans. However, a comprehensive resource for the Korean minipig (Sus scrofa) transcriptome remains unavailable. In this study, we constructed a de novo transcriptome of the Korean minipig using RNA-seq data obtained from ten tissues across ten samples. The final assembly comprised 57,085 coding transcripts with an average length of 3,075 nucleotides and an N50 of 4,258 nucleotides. In total, 65.4% of the transcripts were annotated, and biological functions were assigned. Transcript expression profiling and principal component analysis showed that samples clustered by tissue type, reflecting transcriptomic features shared across tissues. Comparative analysis demonstrated that the novel transcriptome assembly had contiguity and completeness comparable to those available for pig and minipig breeds. Overall, this study provides a comprehensive transcriptomic resource for the Korean minipig, facilitating further functional analyses.

overall_design: Analyzing transcriptomic features of two different types of Korean minipigs, ET- and L-type minipigs, using RNA-seq data for ten tissues.

first: Woncheoul

last: Park

first: Jaebum

last: Kim


title: Ocy454 cell gene expression changes with PTH, FAK inhibitor and PDE8A deletion

city: Boston

first: Garyfallia

last: Papaioannou

state: Massachusetts

address: 55 Fruit St

department: Medicine, Endocrine

institute: Massachusetts General Hospital

summary: Cells from the osteocyte cell line Ocy454 were treated with vehicle (DMSO), +/- PTH (100nM), +/- FAK inhibitor (PF431396 10uM) or underwent PDE8A deletion via CRISPR/Cas9. The goal of this study is to determine the similarity between the genes that are differentially expressed with PTH treatment, FAK inhibition and PDE8A deletion and identify common molecular pathways.

overall_design: Ocy454 RNA samples were measured with High Sensitivity RNA ScreenTape analysis (Agilent). High quality RNA samples with RIN > 7 (n = 6) were processed for RNA library construction and sequencing using the Novoseq6000 platform (Novogene). Quality of raw sequencing data was confirmed with quality control using FastQC/0.11.5. Transcripts were quantified using Salmon 100. Salmon index for mouse was generated based on the Ensembl fasta file for GRCm38. Differential expression analysis was performed using DESeq2 101 package based on the criteria of p adjusted value (padj) < 0.05 and log2|FC | ≥ 1.

first: Courney M

last: Mazur


title: TLR9 Agonists Potentiate Adoptive T Cell Therapy in Cancer through a B Cell–CD2 Costimulatory Axis

city: Atlanta

first: Ayana

last: Ruffin

state: Georgia

address: 1365 Clifton Rd NE,

department: Surgery

institute: Emory University

summary: Adoptive T cell transfer (ACT) therapy offers curative potential for some patients with cancer. Toll-like receptor (TLR) agonists improve the efficacy of ACT therapy, but the underlying mechanism of potency remains poorly understood. Here, we identify a previously unrecognized innate-adaptive circuit in which TLR9-activated B cells augment CD8 T cell fitness and antitumor activity through CD2-dependent costimulation. Among multiple TLR agonist tested, class B CpG uniquely programmed murine and human CD8⁺ T cells for superior effector differentiation, metabolic fitness and antitumor control. Disruption of CD2 signaling blunts the benefits of TLR9 agonism, including glycolytic capacity and tumor control. Independently, blocking CD86/CD80/CD28 or ICOS did not impair CpG conditioned CD8 T cell anti-tumor activity. Gain of function experiments revealed that CD2 stimulation recapitulated the effect of TLR9 agonism, bolstering the effector function of TIL and CAR T cells. Clinically, consistent with these findings, elevated CD2 expression in human tumors correlated with improved overall survival across multiple cancer cohorts, underscoring the importance of this signaling cue. Together, these data uncover a non-canonical B cell-CD2 costimulation axis through which TLR9 agonists potentiate ACT, revealing a targetable pathway to overcome resistance to cell therapy in solid tumors.

overall_design: RNA seq profiling of Day 7 activated pmel-1 CD8 T cells with and without anti-CD2 blockade

first: Chrystal

last: Paulos


title: Deciphering Metabolic Resistance to Multiple Herbicides in Palmer amaranth (Amaranthus palmeri S. Watson) via Transcriptome Analysis

city: Urbana

first: Rishabh

last: Singh

state: Iillinois

address: 1604 Melrose VAlley Ct

department: Agronomy

institute: Kansas State University

summary: Multiple herbicide resistance in Palmer amaranth (Amaranthus palmeri S. Watson) poses a serious threat to US crop production. A Palmer amaranth population (KCTR) from Kansas was found resistant to herbicides across six sites of action, including ALS-, PS II-, EPSPS-, PPO-, HPPD-inhibitors and synthetic auxins. Moreover, a predominance of metabolic resistance, possibly mediated by P450s or GSTs enzyme activity was reported in this population. This study aims to identify the specific genes involved in multiple herbicide metabolism in this Palmer amaranth population via transcriptome analysis. Vegetative clones were developed from three biological replicates of both resistant (KCTR/KCTR-G2) and susceptible (KSS) Palmer amaranth populations. Ten to 12 cm tall clones from each biological replicate were treated with labelled doses of chlorsulfuron, 2,4-D, atrazine, lactofen and mesotrione. Leaf samples were collected for RNA isolation at 6 hours after treatment with respective herbicides along with non-treated plants. Upon RNA sequencing, paired end reads generated were mapped to the Palmer amaranth transcriptome using HISAT2. Differential gene expression analysis revealed 414, 129, 529, 688 and 152  genes expressed differentially in resistant plants following chlorsulfuron, 2,4-D, atrazine, lactofen and mesotrione treatments, respectively. Isoforms of CYP72A219 or CYP704B1 and GST C-terminal were alternatively up-regulated expression across treatments. Transcripts for CYP72A219 and CYP704B1 show up-regulated expression of 3.4- to 6.6-fold and 5.9- to 12.4-fold in resistant plants as validated by qRT-PCR. Identification of genes involved in multiple herbicide metabolism in Palmer amaranth is crucial to predict the evolutionary course of herbicide resistance in weed species.

overall_design: RNA-seq profiling of resistant and susceptible Palmer amaranth plants under treated with five different herbicides along with control at 6 hours after treatment

first: Yaiphabi

last: Kumam

first: Mohit

last: Mahey

first: Eric

last: Patterson

first: Sanzhen

first: Sarah

last: Lancaster

first: Mithila

last: Jugulam


title: PEPITEM regulates the synovial microenvironment during immune-mediated inflammatory arthritis to limit disease

city: Birmingham

first: Adam

last: Croft

state: Please Select

address: Birmingham

country: United Kingdom

institute: University of Birmingham

summary: Objective: Here we investigate the status of the adiponectin-PEPITEM pathway in early, treatment naïve, rheumatoid arthritis (RA) and psoriatic arthritis (PsA) and the therapeutic efficacy of PEPITEM administration in preclinical models. Methods: Peripheral blood was isolated from patients with clinical suspect arthralgia and suspected inflammatory arthritis and analysed by flow cytometry or western blot. Effect of PEPITEM treatment on inflammatory arthritis were assessed in mice by histology; scRNAseq, flow cytometry or multiplex analysis. Results: Newly diagnosed RA and PsA patients had significantly reduced expression of adiponectin receptor 2 and its downstream signalling adaptor protein APPL-1 on their peripheral blood mononuclear cells, resulting in diminished response to adiponectin and local synovial concentrations of PEPITEM. Building on these observations, treatment with PEPITEM in three distinct inflammatory arthritis animal models significantly reduced arthritis severity, joint swelling, leukocyte infiltration and expression of several pro-inflammatory mediators (e.g., JE (CCL2), RANTES, IL-16) in the synovium. Mechanistically, PEPITEM treatment suppressed the COX2 and NF-B signalling pathways. Moreover, PEPITEM altered the composition of leukocyte subsets recruited into the joint. Conclusion: Collectively, these findings underscore the importance of understanding the dysregulation of the adiponectin-PEPITEM pathway in different immune-mediated inflammatory diseases (IMIDs), such as RA and PsA. The observed differences in expression and downstream signalling through ADIPOR suggest potential targets for therapeutic intervention to restore the balance of this regulatory pathway to mitigate chronic inflammation and disease progression in these patients, paving the way for its clinical use as an alternative and/or combination therapy for early IMIDs.

overall_design: C57BL/6 mice were immunized by subcutaneous (s.c.) injection with methylated bovine serum albumin (mBSA, 10μg, Sigma-Aldrich) in complete Freund’s adjuvant (CFA, Fisher Scientific)31. On day 21, monoarthritis was induced by intraarticular (i.a.) injection of mBSA (100μg) into the knee. Mice were treated sub-clinically from day 21 by intraperitoneal (i.p.) injection with either vehicle control phosphate buffered saline (PBS) or PEPITEM (300μg, SVTEQGAELSNEER- PEG (352)-Amide; Cambridge Research Biochemicals Limited; Cambridge, UK). Joint thickness (mm) was measured by callipers daily for up to 7 days. Mice were culled by cervical dislocation and lower limbs dissected. Isolated joints were enzymatically digested for 45 min at 37°C in collagenase D (0.1g/ml, Roche) and DNase I (0.01g/ml, Sigma-Aldrich) diluted in RPMI1640 containing 2% fetal calf serum (Biosera) (step 1), prior to filtering using 100m cell strainer (vicedeal). Subsequently joints were subjected to a further incubation with an enzyme mixture containing 0.1g/ml Collagenase Dispase (Roche) and 0.01g/ml DNase diluted in RPMI1640 (Sigma-Aldrich) containing 2% FBS at 37°C for 30 min (step 2). Cells from step 2 were filtered as described and combined with those from step 1 and centrifuged at 400g for 5 min. Samples were incubated in the RBC lysis buffer (Sigma-Aldrich: R7757) for 10 minutes, followed by centrifugation at 400g in PBS and then re-suspension in MACS buffer (0.1mM EDTA (Sigma-Aldrich) and 0.6% BSA (Gibco) in PBS) prior to analysis.  cDNA libraries from FACS sorted CD45+ synovial digested cells were prepared using Chromium Next GEM Single Cell 3’ Kit v3.1 (4 rxns PN-1000269) according to manufacturer’s instructions, with the aim to capture about 10,000 cells/10µl for each biological replicate.

first: Chris

middle: B

last: Mahony

first: Musserat

last: Wahid

first: Helen

last: McGettrick


title: ChREBPα: A Central Metabolic Sensor Driving Lipid Droplet Renewal in Preimplantation Mouse Embryos

city: Teramo

first: Domenico

last: Iuso

address: Via Balzarini 1

country: Italy

institute: Universisty of Teramo

summary: Background: Lipid droplets (LDs) are abundant during early embryogenesis; however, yet, the mechanisms that govern their synthesis, maintenance, and functional relevance remain poorly defined. This study aimed to investigate how early mouse embryos sense lipid depletion and activate adaptive metabolic responses to sustain developmental progression. Methods: Mouse zygotes were mechanically delipidated and cultured under fatty acid free conditions, and LD recovery was quantified by BODIPY staining across development. RNA sequencing was performed at the 2-cell stage embryos to identify transcriptional responses to delipidation. Furthermore, immunofluorescence microscopy, quantitative assays, and functional studies were conducted by the use of inhibitors to investigate molecular actors of LDs de novo synthesis and their role in embryonic survival. Results: Delipidated embryos rapidly regenerated LDs and progressed to the blastocyst stage at rates comparable to controls. Transcriptomic profiling identified ChREBP (Mlxipl) as the principal gene upregulated in response to lipid depletion, with both mRNA and protein levels markedly increased in delipidated embryos. ChREBP displayed dynamic subcellular localization, including nuclear accumulation associated with LD biogenesis and the formation of cytoplasmic foci preferentially localized at the cell cortex and in proximity to endoplasmic reticulum–enriched regions. Partial co-localization of ChREBP with LDs was observed across stages of de novo LD synthesis following delipidation. Furthermore, an association with lipid LDs was observed during active LD regeneration following delipidation. Notably, the inhibition of ChREBP impaired lipid droplet regeneration and resulted in developmental arrest, identifying the morula-to-blastocyst transition as a critical window of sensitivity and the trophectoderm formation as a vulnerable bottleneck Discussion: These findings identify ChREBP as a key metabolic sensor that coordinates LD synthesis and supports normal developmental progression during early embryogenesis, highlighting LDs as critical regulators of early embryonic competence.

overall_design: Rna-seq profiling of 2 cells embryos derived from delipidated and control mouse zygotes.

first: Abdul Majid

last: Khan

first: Dawid

last: Winiarczyk

first: Francesca

last: Boffa

first: Domenica

last: Zbikowska

first: Luca

last: Palazzese

first: Silvestre

last: Sampino


title: Single-cell RNA-seq profiling of pleural mesothelioma and comparator pleural specimens

first: David

last: Severson

summary: This GEO submission contains processed single-cell RNA sequencing data generated using the Seq-Well platform from pleural mesothelioma tumors and comparator pleural specimens. Raw sequencing data are available through controlled access in dbGaP under accession phs004285. Processed expression matrices and cell-level metadata for the single-cell libraries are provided in this submission.

overall_design:
Single-cell suspensions were generated from surgical specimens and profiled by Seq-Well. Sample identifiers in this GEO submission are matched exactly to dbGaP SAMPLE_ID values for cross-reference with controlled-access raw data and associated subject/sample metadata.  Cells were isolated from 93 multi-site resected specimens (113 libraries when separating technical an biologic replicates) and 40 patients. Most specimens were anatomically mapped to six pleural tumor sites, where samples without mapping are denoted with ND. Most sites were also associated with immediately adjacent tissue slides that underwent histopathologic analysis and bulk RNA-sequencing. Patient, sample, site, and associated metadata including tissue type, clinical diagnosis, and features of adjacent tissue or bulk RNA-sequencing are found in "PM_cell_metadata.tsv.gz". Initial QC filtering on technical parameters yielded 266,262 cells. Raw counts from this initial QC analysis are available in 'initial_scRNA_counts_matrix.mtx.gz' (sparse matrix), 'initial_scRNA_geneIDs.tsv.gz' (row gene IDs), and 'initial_scRNA_cellIDs.tsv.gz' (column cell IDs).  To facilitate deeper analysis including identifying malignant cells by inferring CNVs, more stringent filtering was applied including strict cluster-based exclusion of ambient-contaminated and ambiguous cell types described in the methods of the related manuscript, "Multiomic, Histologic, and scRNA-seq Profiling of Pleural Mesothelioma Reveals Negative Prognosis Associated With a Novel Uncommitted Molecular Phenotype" (PMID: 41319863). Strict filtering yielded 93,351 cells. Counts from this highly filtered analysis are available in stringent_scRNA_counts_matrix.mtx.gz (sparse matrix), stringent_scRNA_geneIDs.tsv.gz (row gene IDs), and stringent_scRNA_cellIDs.tsv.gz (column cell IDs). These cells are denoted by the "stringent_filtering" field in cell metadata.
dbGAP, accession phs004285

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

first: Sam

last: Freyaldenhoven

first: Ben

last: Wadowski

first: William

last: Richards

first: Raphael

last: Bueno


title: Identification of potential treatment strategies to overcome acquired bortezomib-resistance due to clonal evolution

city: Hyderabad

first: Rama Krishna

last: Kancha

state: Telangana

address: Centre for Plant Molecular Biology, Osmania University Campus

department: CPMB

country: India

institute: Osmania University

summary: The clinical efficacy of bortezomib in multiple myeloma (MM) is limited due to secondary drug resistance driven by clonal evolution and currently available pre-clinical models are inadequate for comprehensive understanding of mechanisms underlying drug resistance. In the present study, we have established and characterized bortezomib-resistant cell lines BR1 and BR2, and identified upregulation of proteasome pathway as the potential mechanism underlying bortezomib resistance. Furthermore, both the cell lines retained sensitivity towards imatinib suggesting the lack of general resistance towards broad classes of inhibitors. Notably, BR1 and BR2 showed increased sensitivity than the parental cell line towards the next-generation proteasome inhibitor carfilzomib, suggesting its utility in treating patients who relapse upon bortezomib treatment. When compared to the wild type cell line, BR1 and BR2 displayed similar sensitivity towards sorafenib and vorinostat, but enhanced sensitivity towards geldanamycin treatment. Taken together, our study identified carfilzomib and HSP90 inhibition as promising therapeutic strategies to overcome bortezomib resistance.

overall_design: Transcriptome sequencing analysis of K562 wildtype (WT) cells, K562 bortezomib resistant cell lines (BR1 and BR2), geldanamycin treated WT, BR1 and BR2 cells. Biological duplicates were included for each cell type and technical replicates were generated for every sample to ensure reproducibility.

first: Shravanthi

last: Ravula

first: Vinod

last: PK


title: Loss of p130Cas impairs palatal mesenchymal expansion and causes cleft palate

city: Fukuoka-shi

first: TAO

last: HAN

address: Maidashi 3-1-1

country: Japan

institute: Faculty of Dental Science, Kyushu University

summary: Palatogenesis is a complex developmental process requiring coordinated growth, elevation, and fusion of the palatal shelves. Disruption of these events results in cleft palate, one of the most common congenital craniofacial anomalies. p130Crk-associated substrate (p130Cas) is an adaptor protein involved in integrin-mediated signaling and cytoskeletal regulation; however, its roles in late embryonic development remain poorly understood because global p130Cas-deficiency leads to early embryonic lethality. In this study, we used tamoxifen-inducible conditional knockout mice to investigate the function of p130Cas during palatal development. Conditional deletion of p130Cas resulted in cleft palate characterized by impaired horizontal growth of the palatal shelves. Reduced mesenchymal cell proliferation within the palatal shelves was confirmed by Ki-67 immunostaining and EdU incorporation. Consistently, primary mouse embryonic palatal mesenchymal (MEPM) cells derived from p130Cas-deficient embryos exhibited impaired proliferation and migration in vitro. In contrast, epithelial-specific deletion of p130Cas did not result in cleft palate, indicating that p130Cas function in the palatal mesenchyme is critical for normal palatal development. Together, these findings identify p130Cas as an important regulator of palatal mesenchymal expansion during secondary palatogenesis. Impaired proliferative growth of palatal mesenchyme likely underlies the developmental basis of cleft palate in this model.

overall_design: Bulk RNA-seq was performed on E14.5 mouse palatal shelf tissues from control and p130CascKO embryos (n=3 per group) to identify transcriptional changes.

first: Tao

last: Han

first: Jing

last: Gao

first: Wei

last: Wu

first: Mitsushiro

last: Nakatomi

first: Ichiro

last: Nakamura

first: Hiroaki

last: Honda

first: Sho

last: Tsukamoto

first: Takenobu

last: Katagiri

first: Eijiro

last: Jimi


title: Transcriptome analysis of treated and control samples from bladder carcinoma

city: Shenzhen

first: Zeqin

last: Yan

address: No. 1, Fuxin Road, Pinghu Street, Longgang District, Shenzhen, Guangdong Province, China

institute: Shenzhen University

summary: We provide bulk RNA-seq data for the following: (1) Relapsed tumors after Gemcitabine treatment and their corresponding control tumors, derived from a genetically engineered mouse model (GEMM) of bladder carcinoma. (2) IGFBP5 knockout (KO) MP-MGH-U3-LT and CUUC-G cell lines and their corresponding control cell lines.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: In this study, we collected relapsed tumors and their corresponding controls, extracted total RNA, and prepared RNA-seq libraries for high-throughput deep sequencing. Additionally, we constructed IGFBP5 knockout (KO) MP-MGH-U3-LT and CUUC-G cell lines along with their corresponding controls and similarly extracted total RNA and prepared libraries for high-throughput deep sequencing.


title: Necroptosis triggers inflammatory interferon signatures in patient-derived metastatic breast cancer organoids

city: Frankfurt a.M.

first: Francesco

last: Pampaloni

address: Max-von-Laue-Str. 15

country: Germany

institute: Goethe University Frankfurt a.M.

summary: Breast cancer (BC) is the most common type of cancer among women worldwide and underlies relapse, disease progression and metastasis. Resistance to chemotherapy and programmed cell death (PCD), including apoptosis, strongly affects BC therapy success and remains a major challenge. Although necroptosis, a lytic, and via damage-associated molecular patterns (DAMP) release, highly immunogenic mode of PCD, might overcome apoptosis resistance, there is an urgent need for physiological and translational human models to model necroptosis and PCD resistance in BC. Here, we apply 3D patient-derived, metastatic human mammary organoids (hMOs) to model apoptosis resistance, necroptosis and inflammatory signaling using single-cell CITE-sequencing, time-lapse live cell brightfield and immunofluorescent confocal microscopy as well as biochemical approaches. Smac mimetic-triggered apoptosis triggered could be confirmed in a panel of BC hMOs. Upon inducing apoptosis resistance with caspase inhibition, BC hMOs rapidly undergo necroptosis with profound MLKL phosphorylation. Necroptotic cell death was preceded by prominent transcriptional upregulation of inflammatory cyto- and chemokines, including interferons, that activate natural killer cells. Finally, necroptosis and the expression and release of inflammatory messengers in metastatic BC hMOs could be attenuated upon the inhibition of linear ubiquitination. We describe a novel experimental platform to model PCD, inflammation and necroptosis that allows therapeutic screening to overcome chemotherapy resistance in patient-derived metastatic BC hMOs. With this platform, we identified necroptosis-induced interferon signaling, suggesting Smac mimetics and necroptosis as potential immunotherapy strategy against metastatic BC.

overall_design: scCITEseq: Following treatment, metastatic breast cancer organoids from three donors were harvested and processed to single cells individually and stained with sample tags (HTOs). Viable cells were sorted using fluorescence-activated cell sorting (FACS) and stained with CITEseq antibodies (ADTs) and analyzed using scCITEseq.

first: Kaja Nicole

last: Wächtershäuser

first: Jana

middle: V

last: Schneider

first: Alec

last: Gessner

first: Geoffroy

last: Andrieux

first: Ivan-Maximiliano

last: Kur

first: Nadine

last: Duschek

first: Andreas

last: Weigert

first: Melanie

last: Boerries

first: Michael

middle: A

last: Rieger

first: Ernst HK

last: Stelzer

first: Sjoerd JL

last: van Wijk


title: Single-cell, clonal and spatial atlases of neural plate border and neurogenic placodes illuminate their specification and evolution.

city: Solna

first: Felix

middle: Robert Nicodemus

last: Waern

state: Uppland

address: Solnavägen 9

department: Physiology and Pharmacology

country: Sweden

institute: Karolinska Institutet

summary: Neurogenic placodes are specialized ectodermal thickenings that generate key sensory structures of the vertebrate head. This dataset provides a clonal atlas of mouse neural plate border and neurogenic placodes, integrating single-cell RNA-sequencing, spatial transcriptomics, and high-resolution clonal tracing. These data define the lineage architecture of placodal and cranial ectodermal progenitors and provide a resource for understanding the emergence and diversification of vertebrate sensory structures.

overall_design: Embryonic day (E) 7.5 and 8.5 embryos were injected with a lentiviral construct into the amniotic cavity under ultrasound guidance to label neural plate derivatives. Embryos were collected at E11.5, and tdTomato-positive embryos were dissected into defined cranial and sensory ganglia–containing regions. Tissues were enzymatically dissociated into single-cell suspensions, filtered, and tdTomato-positive cells were sorted and used for 10x Genomics.

first: Aliia

last: Murtazina

first: Julia

last: Fatieieva

first: Helen R.

last: Maunsell

first: Ankita

last: Thawani

first: Bettina

last: Semsch

first: Johan

last: Bostroem

first: Caleb

last: Reagor

first: Polina

last: Kameneva

first: Karina

last: Araslanova

first: Sergei

last: Isaev

first: Franziska

last: Schelb

first: Kaj

last: Fried

first: Alek

last: Erickson

first: Alexander

last: Klimovich

first: Andrea

last: Streit

first: Lena

last: Kutscher

first: Iryna

last: Kozmikova

first: Zbynek

last: Kozmik

first: Emma R.

last: Andersson

first: Gerhard

last: Schlosser

first: Andrew K.

last: Groves

first: Igor

last: Adameyko


title: Stem cell-derived exosomes inhibit the inflammatory response of microglia in neuropathic pain through m6A modification mechanisms

city: Qingdao

first: Shuixian

last: Du

state: Shandong

address: No. 5, Donghai Middle Road

institute: Qingdao Municipal Hospital

summary: Activated microglia-induced neuroinflammation is a critical pathological basis for the exacerbation of neuropathic pain. In our in vitro experiments, we found that exosomes derived from human umbilical cord mesenchymal stem cells exhibit a potent inhibitory effect on microglial inflammation, significantly downregulating the expression of lipopolysaccharide (LPS)-induced inflammatory factors such as interleukin-6 and interleukin-1, and suppressing microglial activation. However, the underlying molecular mechanism requires further investigation. m6A modification is considered one of the key molecular mechanisms regulating neuropathic pain, but whether stem cell-derived exosomes inhibit microglial inflammation through modulating m6A methylation remains to be further elucidated. Therefore, this study aims to investigate changes in m6A modification following exosome treatment, identify key m6A-modified genes and the regulatory enzymes involved, and use them as research targets to explore the molecular mechanism by which stem cell-derived exosomes alleviate neuropathic pain.

overall_design: BV-2 cells were pre-incubated with hUC-MSC-EXO (10 μl, 1 μg/mL) in six-well plates for 24 hours, then washed twice with PBS, and subsequently exposed to LPS (1 μg/mL) for 6 hours to establish a microglial activation model. Cells were divided into three groups: Control, LPS, and LPS+EXO. Changes in m6A modification in each group were detected by m6A methylation sequencing.

first: Gao

last: Xu

first: Jia

last: Shu

first: Meng

last: Chunyang


title: Fate mapping reveals a prenatal-to-neonatal wave of ILC2s with a history of Cd3g expression

city: Oklahoma City

first: Aneta

last: Pankow

state: Oklahoma

address: 825 NE 13th St

department: Arthritis and Clinical Immunology

institute: Oklahoma Medical Research Foundation

summary: Group 2 innate lymphoid cells (ILC2s) are thought to develop in the bone marrow and fetal liver. However, increasing evidence supports the presence of thymic ILC2s in mice and humans. In this study, we introduce a novel fate-mapping mouse model designed to track thymic ILC2s in peripheral tissues. Thymic ILC2s are labeled by ZsGreen whose expression is induced by Cd3giCre. While they are present in the thymus and peripheral tissues, they are not found in the bone marrow. These cells are predominantly abundant during the neonatal stage, when the intense alveolarization and tissue remodeling occur. RNA sequencing revealed elevated expression of cytokine genes, Il13 and Il4, as well as Klrg1 in these cells. They also harbor TCR gene rearrangements suggesting common developmental pathways with T cells. Furthermore, we demonstrate that neonatal ILC2s play a critical role in macrophage polarization in a naphthalene-induced injury lung model. These findings help explore the differences between pediatric and adult immunity and future therapeutic strategies.

overall_design: Thymic DN3 and lung ZsGreen- and ZsGreen+ ILC2s were sorted from 14 days old Cd3giCreRosa26stopZsGreen mice to compare their gene expression profile by bulk RNA sequencing.

first: Xiao-Hong

last: Sun


title: Pulsed photobiomodulation reprograms the tumor immune microenvironment to restore local T cell–mediated antitumor immunity

city: Xiamen

first: chuanfang

middle: C

last: Chen

state: Fujian

address: No.4221, Xiang'an South Road, Xiang'an District

department: College of Life Science

institute: XIAMEN university

summary: We have employed a single cell sequencing approach using 10X Genomics scRNA-seq to study MC38 tumor infiltrated immune cell under Photobiomodulation(PBM) treatment. PBM, also termed low-level laser therapy (LLLT), is a non-invasive, drug-free physical modality that uses defined light wavelengths to modulate cellular functions.  This study represents the first transcriptomic analysis of how PBM reshapes the tumor microenvironment and inhibits MC38 tumor growth.

overall_design: MC38 tumor cells were subcutaneously implanted into C57BL/6 mice. PBM treatment started at day 7 daily, while tumors were harvest at day 14. Tumor infiltrated CD45+ immune cell were sorted  for scRNA-seq.

first: Xiunan

last: Wang

first: Chuanfang

first: Yuling

last: Hong

last: Zhang

first: Shih-Chin

last: Cheng


title: Single-cell transcriptomic profiling of SPAST exon 17 deletion–induced neurodegeneration in human cortical organoids

city: Daejeon

first: Youngsun

last: Lee

address: 125, Gwahak-ro, Yuseong-gu

institute: Korea Research Institute of Bioscience and Biotechnology

summary: Alu-mediated structural variants are enriched in the human genome but their contribution to neurodegeneration remains poorly defined. We generated CRISPR/Cas9-edited human pluripotent stem cells harboring a patient-relevant deletion of exon 17 in the SPAST gene (SPASTΔe17), a recurrent mutation associated with hereditary spastic paraplegia (SPG4) with dementia. Wild-type (WT) and SPASTΔe17 hPSCs were differentiated into cortical organoids and subjected to single-cell RNA sequencing at day 100 of differentiation.

overall_design: Human H9 hPSCs were genome-edited using CRISPR/Cas9 to generate homozygous SPAST exon 17 deletion (SPASTΔe17) clones. WT and SPASTΔe17 hPSCs were differentiated into cortical organoids following a standardized protocol and cultured up to 100 days.  Organoids were dissociated into single-cell suspensions using Accutase. Single-cell libraries were prepared using the 10x Genomics Chromium Single Cell 3′ Reagent Kit v3.1 and sequenced on an Illumina NovaSeq 6000 platform. Raw sequencing data were processed using Cell Ranger (GRCh38 reference genome) to generate gene–barcode matrices.


title: Intravitreal AAV delivery induces integrin-dependent ocular inflammation and activation of complement, antiviral and DNA damage responses

city: Philadelphia

first: Jon

middle: E

last: Chatterton

state: PA

address: 3025 Market St

institute: Roche Therapeutics

summary: Intravitreal (IVT) AAV administration is a promising, non-invasive strategy for retinal transduction. However, IVT AAV delivery is often associated with dose-limiting inflammation, and corticosteroid treatment used to manage ocular uveitis is contra-indicated in some patients. Therefore, novel immunomodulatory strategies are needed, requiring further understanding of AAV-triggered immunity mechanisms. Here we characterized immune responses to AAV2.7m8 in mice and pigs. IVT AAV delivery in mice revealed a key role for peripheral leukocytes in mediating ocular inflammation, while the response in pigs was predominantly driven by microglia activation and monocyte infiltration.  Analysis of ocular humors identified MCP-1 and IP-10 as common AAV-induced inflammation markers in both species, with subsequent identification of MIP-1α, IL-6, and complement factor C3a as additional markers in pigs. We also detected DNA damage foci in treated retinas, including in regions exhibiting low or absent transgene expression, but with significant presence of vector genomes. Finally, snRNAseq detected significant transduction of retinal ganglion cells, identified astrocytes and microglia as the main sources of MCP-1 and IP-10, and revealed marked induction of interferon and pro-inflammatory signaling across all retinal cell populations. Thus, our work identified new markers of ocular inflammation and potential targets to modulate AAV-induced uveitis.

overall_design: Female Yucatan minipigs received bilateral intravitreal injections of AAV2.7m8/CAG-GFP or vehicle control, followed by sacrifice at 2, 3, or 4 weeks post-injection. Retinal nuclei were isolated from flash-frozen whole globes, purified by FACS based on DAPI fluorescence, and analyzed using single-nuclei RNA sequencing on the 10x Chromium platform.

first: Helena

last: Costa Verdera

first: Deepa

last: Jamwal

first: Emily

last: Fabyanic

first: Ariel

last: Hippen

first: Madeleine

last: Salvatore

first: Aiping

first: Anna

last: Majowicz

first: David

last: Markusic

first: Virginia

last: Haurigot

first: Klaudia

last: Kuranda


title: tRF and tiRNA Sequencing

city: Chengdu

first: Xue

last: Zhao

state: SiChuan

address: Sichuan Agricultural University, Chendu, Sichuan province

institute: Sichuan Agricultural University

summary: 3-NP,ES-Cu treated mouse Follicle

overall_design: Twenty-four 6-week-old female C57BL/6 mice were randomly divided into three groups (n=8): (I) control (Con), (II) copper chloride (CuCl2) PBS solution gavage (Cu), and (III) 3-NP injected copper solution gavage (3-NP/Cu).


title: Effects of Sphk1 deletion in smooth muscle cells on murine arterial transcriptome in hypertension

city: Kraków

first: Mateusz

last: Siedliński

address: Skarbowa 1

country: Poland

institute: Jagiellonian University Medical College

summary: The function of the cardiovascular system is regulated by sphingosine-1-phosphate (S1P) signalling. Vascular sphingosine kinase 1 (Sphk1), an S1P-producing enzyme, is upregulated in hypertension (HTN), and mice lacking Sphk1 globally exhibit alleviated angiotensin II (AngII)-induced HTN. Identifying the cellular mechanisms that provide this protection remains challenging due to the pleiotropic action of S1P. To obtain mice lacking Sphk1 in smooth muscle cells (SMCs), Sphk1 f/f (flox/flox) mice were crossed with transgenic mice harboring Cre recombinase gene under control of the mouse smooth muscle protein 22-alpha/transgelin (SM22α/Tagln) promoter. Subsequently, resulting Sphk1f/-Tagln-cre+ offsprings were mated to Sphk1f/f mice to generate mice lacking Sphk1 specifically in SMCs (Sphk1f/fTagln-cre+, later referred to as SMC KO-Sphk1) and control mice (Sphk1f/fTagln-cre-, hereafter referred to as wild type (WTf/f) mice).

overall_design: RNASeq analyses encompassed aorta and mesenteric arteries derived from wild-type (C57BL6J Sphk1 flox/flox) and knockout (Sphk1f/fTagln-cre+) male mice under normotensive or hypertensive (2-weeks angiotensin II infusion at 490 ng/kg/min rate) conditions.

last: Siedlinski


title: Pleuromutilins alleviate psoriasis via inhibition of hnRNP-U/TNF-α [HaCaT]

city: Nanjing

first: Shuya

last: Sun

state: Jiangsu

address: No.12 Jiangwangmiao Street, Xuanwu District, Nanjing, Jiangsu Province, China

institute: Hospital for Skin Diseases, Institute of Dermatology, PUMC

summary: Retapamulin and lefamulin block TNF-α pathway and alleviate psoriasis-related inflammation in vitro.

overall_design: Ccmparetive gene expression profing anelysis of RNA-seq data of M5-induced HaCaT cells, including WT (n=3), M5 (n=3), M5+Retapamulin (n=3) and M5+Lefamulin (n=3).

first: Ruiyu

last: Xiang

first: Weijian

last: He

first: Hao

last: Shen

first: Yong

last: Yang


title: Zone-specific hepatocytes orchestrate the early onset of host defence mechanisms during Staphylococcus aureus bloodstream infection

city: Würzburg

first: Alexander

middle: M.

last: Leipold

address: Josef-Schneider-Str. 2

institute: Helmholtz Institute for RNA-based Infection Research

summary: Bloodstream infections (BSI) cause substantial morbidity and mortality, with Staphylococcus aureus among the most lethal pathogens. The liver plays a central role in host defence against blood-borne microbes, yet how its zonal organization shapes this response remains unclear. In a murine model of S. aureus bacteraemia, the liver sequestered ~90% of bacteria within 4 h and markedly reduced bacterial loads by 24 h, indicating rapid activation of local immune defences. Single-cell RNA sequencing identified periportal and midzonal hepatocytes, and to a lesser extent pericentral hepatocytes, as the principal responders. Besides acute-phase proteins, periportal and midzonal hepatocytes strongly upregulated Bmper, a regulator of bone morphogenetic protein signalling and a likely new mediator of the hepatic acute-phase response. Expansion of Kupffer cells, essential for bacterial clearance, was also observed and was primarily driven by local proliferation. These findings demonstrate that hepatocyte zonation orchestrates early hepatic immune responses during S. aureus BSI.

overall_design: Single-cell RNA sequencing (scRNA-seq) of livers from C57BL/6 mice after intravenous infection with S. aureus at 4 and 24 hours post-infection.

first: Obiageli Vivian

last: Nwofor

first: Qian

last: Chen

first: Robert

last: Geffers

first: Antoine-Emmanuel

last: Saliba

first: Oliver

last: Goldmann

first: Eva

last: Medina


title: scRNA-seq of mouse cochlea organoid cells

city: Galveston

first: Marie

last: Kubota

state: TX

address: 301 University Blvd

department: Otolaryngology

institute: University of Texas Medical Branch

summary: Neonatal mouse cochlear epithelium retains regenerative capacity, attributed to the greater epithelial ridge (GER) cells. GER cells proliferate to form organoids and give rise to nascent hair cells and supporting cells. To investigate the growth-promoting pathways in GER cells, we generated organoids from highly enriched mouse GER cells and performed single-cell RNA sequencing. Data analysis revealed changes in gene expression in GER-derived cells during the early growth phase of organoid development. Integrating single-cell RNA sequencing data with in vitro and in vivo functional assays, we identified galectins and Myc activity as essential regulators of GER cell proliferation.

overall_design: We used postnatal day 2 Sox2-GFP/Fgfr3-CreERT2/Ai14-tdTonato transgenic mice to isolate GER cells with flow cytometry. The cells were seeded for organoid formation. Grown organoids were harvested and dissociated at culture days 1, 3, and 7, and analyzed with single-cell RNA sequencing.

first: Julia

middle: M

last: Abitbol

first: Paul

middle: K

last: Lee

first: Maggie

middle: S

last: Matern

first: Sonia

last: Bustos Barocio

first: Taha

last: Jan

first: Alan

last: Cheng

first: Stefan

last: Heller


title: Membrane Fusion Inhibition, Immune Modulation, and Cholesterol Synthesis Dysregulation During Dengue Virus Inhibition by 25-Hydroxycholesterol

city: Bengaluru

first: Debayani

last: Chakraborty

address: CV Raman road

department: Chemical Engineering

institute: Indian Institute of Science

summary: Physicochemical properties and composition of cellular membranes are crucial for regulating broad cellular responses including signaling and defense against pathogens. Dengue virus (DENV) exploits cholesterol-rich membranes and host lipid pathways, such as cholesterol biosynthesis, lipid raft organization, and lipid droplet formation, for entry, replication, and assembly. Additionally, lipid-based plasma membrane signaling can trigger innate immune responses that attenuate viral growth, underscoring the dual role of lipids in facilitating and restricting DENV infection. Here, we demonstrate that 25-hydroxycholesterol (25-HC), an oxidized cholesterol metabolite, inhibits DENV infection through a multifaceted mechanism. 25-HC disrupts viral membrane fusion by altering cholesterol distribution and lipid raft organization, impairing the binding and fusion of the DENV envelope (E) protein with host membranes. Additionally, 25-HC modulates host cholesterol metabolism by suppressing biosynthesis pathways essential for viral replication while enhancing lipid droplet formation and stress-response pathways. Transcriptomic analyses reveal that 25-HC primes innate immune responses, activating pro-inflammatory pathways such as the NLRP3 inflammasome and MAPK signaling, while selectively modulating interferon-stimulated gene expression. Notably, 25-HC exhibits synergistic antiviral effects when combined with direct-acting antivirals like Remdesivir, underscoring its potential in combination therapies. These findings establish 25-HC as a promising candidate for host-directed antiviral strategies against DENV and other enveloped viruses.

overall_design: RNAseq profiling of RAW 264.7 cells treated with 1 µM 25-HC for eight hours, followed by wash and DENV infection for 24 hours.

first: Achinta

last: Sannigrahi

first: Mahammed

last: Kaif

first: Arijit

last: Patra

first: Deep

last: Thakkar

first: Debarati

first: Rahul

last: Roy


title: Whole-genome sequencing and DigiPico of fallopian tube, tumor, and PBMC samples from high-grade serous ovarian cancer (HGSOC) patients [WGS/DigiPico]

city: Oxford

first: Breeshey

middle: Jane

last: Roskams-Hieter

address: John Radcliffe Hospital/Headley Way

institute: MRC Weatherall Institute of Molecular Medicine

summary:
The fallopian tube (FT) has been proposed as a potential site of origin for high-grade serous ovarian cancer (HGSOC), supporting investigation of genomic alterations across matched tissues.
This dataset includes whole-genome sequencing (WGS) and DigiPico data from matched samples, including peripheral blood mononuclear cells (PBMCs), fallopian tube tissue, and tumor tissue from HGSOC patients.
The data support analysis of germline and somatic variants, copy number alterations (CNAs), and neoantigen prediction across matched sample types. This submission contains the WGS data DigiPico data associated with this study.

overall_design:
This submission contains whole-genome sequencing data from patients 11642 and 11658, including PBMC, fallopian tube, and tumor samples. PBMC samples were used to define germline DNA variants, and somatic mutations were identified in fallopian tube and tumor samples.
Tumor samples were prepared using DigiPico to reduce false positives. Bulk RNA sequencing data from tumor samples were also included to support integrative analyses, including driver mutations and CNAs profiling and neoantigen prediction.

first: Luyao

last: Wang

first: Nancy

last: Zaarour

first: Ahmed

last: Ahmed


title: Simultaneous orthogonal cell engineering by a single CRISPR-Cas9 polyfunctional editor [CAST-seq]

city: Milano

first: Sara

last: Valsoni

state: MI

address: via Olgettina 60

department: TIGET

institute: SR-TIGET

summary: The parallel disruption of multiple genes coupled with targeted transgene insertion offers a powerful strategy for more effective and precise cell engineering. However, such orthogonal editing involves the induction of multiple DNA breaks, raising safety concerns related to the risks of chromosomal translocations. Here, we present a polyfunctional CRISPR-Cas9-based strategy that enables both transgene insertion and epigenetic silencing at distinct genomic loci in a single treatment without inducing reciprocal chromosomal translocations. This is accomplished through an optimized all-in-one epigenome editor equipped with a catalytically active Cas9, whose endonuclease activity is selectively disabled at epigenetically silenced loci by the use truncated gRNAs. As a proof of concept, we demonstrated that this platform enables efficient multi-locus editing, including functional replacement of the endogenous TCR with a selectable retargeting cassette, targeting a prototypic CAR and an immunomodulatory receptor into a ubiquitously expressed gene, and durable, multiplexed epigenetic silencing of clinically relevant genes in primary human T cells. Polyfunctional editing establishes a versatile framework for orthogonal editing with an enhanced safety profile, broadening the scope of genome and epigenome engineering in cancer immunotherapy and beyond.

overall_design: CAST-Seq analysis of poly-edited vs. triple-KO gene-edited T cells targeting either TRAC, B2M and TET2, or B2M, CD3D and TGFBR2

first: Deborah

last: Cipria

first: Tania

last: Baccega

first: Miriana

last: Rizzo

first: Piergiuseppe

last: Quarato

first: Alice

last: Reschigna

first: Rita

last: El Khoury

first: Martino

last: Cappelluti

first: Sandra

last: Ammann

first: Valeria

last: Mollica Poeta

first: Matteo

last: Conti

first: Pietro

last: Spinelli

first: Ivan

last: Merelli

first: Toni

last: Cathomen

first: Monica

last: Casucci

first: Angelo

middle: L

last: Lombardo


title: Physiologic recovery of Mycobacterium tuberculosis from drug injury: A molecular study of post antibiotic effect in vitro

city: Aurora

first: Jo

last: Hendrix

state: CO

department: Pulmonology

institute: University of Colorado

summary: Post-antibiotic effect (PAE) describes the delay in bacterial growth that continues after antibiotics are cleared. Here, we evaluated the long-standing hypothesis that PAE reflects the time required for bacteria to recover from drug-induced physiologic damage by comparing Mtb after varying durations of treatment with the HRZE in vitro. Our results revealed that longer drug exposure was associated with greater injury and adaptation during treatment, as well as slower recovery after treatment, i.e., longer PAE. Our observation that PAE in Mtb depends on the duration of drug exposure and correlates with the degree of bacterial injury support the hypothesis that nonlethal physiologic damage contributes to PAE. Molecular evaluation of bacterial physiology provides a new basis for probing recovery from drug exposure and understanding PAE.

sample_organism: Mycobacterium tuberculosis str. Erdman = ATCC 35801

overall_design: Mtb in aerobic axenic culture were treated with HRZE for 0, 6, or 48 hours. After treatment stopped, RNA-seq profiling with SEARCH-TB was performed at various timepoints of the PAE phase.

first: Reem

last: Al Mubarak

first: Matthew

middle: J

last: Reichlen

first: Samuel

last: Tabor

first: Adeline

last: Bateman

first: Lisa

last: Massoudi

first: Karen

last: Rossmassler

first: Firat

last: Kaya

middle: D

last: Zimmerman

first: Holly

last: Nielsen

first: Elizabeth

last: Wynn

first: Martin

middle: I

last: Voskuil

first: Gregory

last: Robertson

first: Camille

last: Moore

first: Nicholas

last: Walter


title: Effect of CSDE1 knockout in RAW264.7 cells on gene expression following SARS CoV-2 RNA stimulation

city: Jinan

first: zheng

last: yi

address: 07 Wenhua xi road, Jinan, Shandong

institute: Shandong  University

summary: RIG-I-like receptors (RLRs)-mediated antiviral innate immunity is critical for restricting RNA viral infection. The liquid-liquid phase separation (LLPS) is crucial for fine-tuning cellular signaling transduction, but whether RLR signaling is under the regulation of LLPS remains largely enigmatic. In this study, we identify the RNA-binding protein cold shock domain containing E1 (CSDE1) as a novel negative regulator of RLR signaling to promote viral immune evasion. The deficiency of CSDE1 in macrophages results in increased expression of type I interferon and ISGs following RNA viral infection. Mice with macrophage conditional knockout of CSDE1 are less susceptible to RNA viral infection. CSDE1, with multivalent CSD motifs, forms bio-molecular condensates with long single stranded RNA (ssRNA). The LLPS of CSDE1 sequesters viral RNA from recognition by RLRs to inhibit RLR signaling. Notably, virus-activated TBK1 kinase mediates the phosphorylation of CSDE1 to disturb its LLPS. Consequently, phosphorylation of CSDE1 relieves its suppression of RLR signaling. Intriguingly, LLPS of CSDE1 promotes the condensation of the SARS-CoV-2 nucleocapsid (N) protein and is critical for the anti-interferon activity of the N protein. Repression of CSDE1 condensation with screened compound abrogates the CSDE1 LLPS and subsequent replication of SARS-CoV-2. Overall, our study delineates a novel regulatory mechanism of RLR signaling transduction by phosphorylation-modulated LLPS of CSDE1, indicating that targeting the LLPS of CSDE1 is a promising strategy for RNA viral infection treatment.

overall_design: gene expression in RAW264.7 cells with or without CSDE1 following SARS CoV-2 viral RNA (S RNA) stimulation

first: Yi

last: Zheng

first: Xuejing

last: Zhang

first: Chengjiang

last: Gao


title: Bulk RNA sequencing of ovarian tumor samples from high-grade serous ovarian cancer patients [RNA-Seq]

first: Breeshey

last: Roskams-Hieter

summary:
High-grade serous ovarian cancer (HGSOC) is thought to originate from the fallopian tube (FT), highlighting the importance of studying molecular features across tumor samples.
This dataset contains bulk RNA sequencing data from tumor samples of HGSOC patients. The data can be used for driver mutations and  copy number alterations (CNAs) profiling  and analysis of gene expression patterns, including regions relevant to HLA typing.
This submission contains bulk RNA sequencing data associated with this study.

overall_design: This submission contains bulk RNA sequencing data from tumor samples for patients 11642 and 11658. The data were used for transcriptomic analysis, including reads mapping to the HLA region for HLA typing.

first: Luyao

last: Wang

first: Nancy

last: Zaarour

first: Ahmed

last: Ahmed


title: Early-life RNA sequencing of colon stromal cells and iNKT cells

city: Boston

first: Xi

last: Lin

state: MA

address: 77 Avenue Louis Pasteur, Rm641

institute: Brigham and Women's Hospital

summary: The early-life intestinal microenvironment plays a pivotal role in shaping immune cell development, yet the mechanisms regulating colonic invariant natural killer T (iNKT) cells remain incompletely understood. To investigate how embryonic macrophages regulate iNKT cells during early life, we collected Day 9 whole-colon lamina propria cells after embryonic macrophage depletion and performed both bulk RNA sequencing and single-cell RNA sequencing. We also performed bulk RNA sequencing on distinct colonic stromal cell populations, conventional αβT cells, and iNKT cells under homeostatic early-life conditions to identify factors that directly imprint iNKT cells during this developmental period.

overall_design: For scRNA-seq, Day 9 whole colon LP cells were isolated from three CT and three MMDTR mice (DT injection Day 6-8) and pooled by group. Live cells were FACS-sorted for single-cell RNA sequencing. For whole tissue RNA-seq, total RNA from Day 9 whole colon tissue of three CT and three MMDTR mice (DT injection Day 6-8) was extracted used as input material for library preparation and sequencing. For bulk RNA sequencing of FACS-sorted cells, two hundred P1 and P2 stromal cells from four Day 9 or four Day 15 wild-type (WT) mice, two hundred conventional αβT cells and 50 iNKT cells from four Day 9 WT mice, as well as 50 iNKT cells from four Day 9 CT and four MMDTR mice (DT injection Day 6-8), were sorted using BD FACSAria II.

first: Thomas

last: Gensollen


title: Sirtuin 7 regulates dosage compensation and safeguards the female X-chromosome [RNA-seq_male_female_MEF]

city: Piscataway

first: Joshua

last: Thackray

state: NEW JERSEY

address: 145 Bevier Road

department: Human Genetics Institute of New Jersey

institute: Rutgers University

summary: Sirtuins are deacetylases implicated in stress responses and longevity in mammals. Although their differential impact on the two sexes has been noted, underlying causes for sex biases in aging and cancer are not known. Here, using Sirtuin 7 (SIRT7) as a model in mice, we probe mechanisms leading to sex differences. We find that Sirt7-/- females have decreased fitness during embryogenesis and throughout life. Intriguingly, SIRT7 preferentially localizes to the X-chromosome, suggesting a potential defect in X-inactivation — the arm of dosage compensation that equalizes X-chromosome expression between XX females and XY males. Indeed, SIRT7 ablation causes increased Xist RNA levels, H3K27me3 enrichment, and gene repression on the inactive X (Xi) chromosome. Surprisingly, however, loss of SIRT7 exerts greatest effects on the active X (Xa). In Sirt7-/- females, the Xa demonstrates 3D structural disorganization, increased chromatin mixing, and acute propensity to break and form chromosome fusions in an Xa-specific manner. Disproportional to autosomes and Xi, the Xa becomes super-acetylated on H3K36 and super-activated in gene expression, resulting in an imbalance in the 2nd arm of dosage compensation — known as “Xa-hyperactivation” — which evolved to balance X-linked gene expression against the genome. These data reveal a crosstalk between sirtuins and dosage compensation and identify a novel regulator of Xa-hyperactivation.

overall_design: RNA-seq profiling of  WT and SIRT7-KO, male or female, primary mouse MEF cells.

first: Nicolas

last: Simonet

first: Barry

last: Kesner

first: François

last: Serra

first: Maria

last: Espinosa-Alcantud

first: Anna

last: Lappala

last: Guitart

first: Laia

last: Marin

first: Uri

last: Weissbein

first: Danni

first: Josema

last: Castelló

first: Llorenç

last: Rovirosa

first: Jay

last: Tischfield

first: Lourdes

last: Serrano

first: Berta

middle: N

last: Vazquez

first: Aurora

last: Ruiz-Herrera

first: Bernhard

last: Payer

first: Biola

last: Javierre

first: Alejandro

last: Vaquero

first: Jeannie

middle: T

last: Lee


title: Sirtuin 7 regulates dosage compensation and safeguards the female X-chromosome [ChIP_SIRT7_primary_TTF]

first: Joshua

last: Thackray

overall_design: ChIP-seq profiling of SIRT7 enrichment in WT and SIRT7-KO primary mus/cas hybrid TTF cells.

first: Nicolas

middle: G

last: Simonet

first: Barry

last: Kesner

last: Wang


title: Uncoupling Neocortical Neuron Fate and Migration via a Let-7–RBX2 Axis

city: Davis

first: Sergi

last: Simo

state: CA

address: One Shields Avenue, 3402 Tupper Hall

department: Cell Biology and Human Anatomy

institute: University of California Davis

summary: Throughout the central nervous system, the fate and migration of projection neurons are tightly coordinated to ensure that specific neuronal fates settle in precise spatial locations. This is particularly evident in the mammalian neocortex, where early-born projection neurons predominantly remain in the deeper layers of the cortical plate, whereas later-born neurons localize more superficially. However, it remains unclear whether neuronal fate acquisition directly primes the molecular mechanisms driving pyramidal neuron migration and positioning, or on the contrary fate and positioning are regulated independently. MicroRNAs have emerged as key regulators of cell fate determination in the neocortex. Among them, let-7 is known to influence neural progenitor competence and promote the neurogenesis of late-born projection neurons. Here, we show that let-7 also regulates projection neuron migration and positioning by targeting RBX2, a core component of the E3 ubiquitin ligase CRL5, which has been previously shown to inhibit neuron migration by terminating the Reelin/DAB1 signaling pathway. Let-7 directly binds to a conserved motif in the 3′ UTR of RBX2, reducing its translation and thereby diminishing CRL5 activity. Importantly, restoring RBX2 levels in the context of let-7 overexpression rescues the positioning of pyramidal neurons without altering let-7-induced effects on neuronal fate. Furthermore, we demonstrate that let-7 enhances pyramidal neuron migration by increasing locomotion speed and prolonging migratory activity. Together, these findings reveal that let-7 coordinates neuronal fate specification and migration via distinct molecular pathways, ensuring the proper laminar positioning of late-born pyramidal neurons in the neocortex.

overall_design: RNA seq profiling of HER10 cells transfected with a let-7a mimic (n=5) or let-7 antagomiR (n=5)

first: Steven

last: Decker

first: Keiko

last: Hino

first: Anna

last: La Torre

last: Simó


title: RNA-seq of mononuclear immune cells isolated from breast cancer wound fluid after IORT or surgery alone

city: Neuherberg

first: Benedek

last: Dankó

address: Ingolstädter Landstraße 1

institute: Helmholtz Munich

summary: This dataset comprises RNA-seq profiles from mononuclear immune cells purified from wound fluid of breast cancer patients who received intraoperative radiotherapy (IORT) or surgery only (control). Samples were collected on postoperative day 2 and processed for total RNA extraction and 3′-end mRNA sequencing. The study aims to characterize the transcriptional immune landscape in the early wound-healing phase following IORT.

overall_design: Wound fluid samples were collected on postoperative day 2 from patients undergoing breast-conserving surgery with or without IORT. Mononuclear cells were isolated by Ficoll-like density gradient centrifugation (Biocoll), cryopreserved in 90% FCS + 10% DMSO, and later processed for RNA extraction. RNA-seq libraries were generated using a 3′-end mRNA-seq protocol. Comparative transcriptomic analysis was performed between the IORT and control groups (n = 17 and 20, respectively).

first: Nikko

last: Brix

first: Martin

last: Selmansberger


title: Sirtuin 7 regulates dosage compensation and safeguards the female X-chromosome [ChIP_H2AX_gH2AX_TTF]

overall_design: ChIP-seq profiling of H2AX and gammaH2AX enrichment in WT and SIRT7-KO mus/cas hybrid TTF cells.

first: François

last: Serra

first: Maria

last: Espinosa-Alcantud

last: Lappala

last: Guitart

first: Laia

last: Marin

first: Uri

last: Weissbein

first: Danni

first: Josema

last: Castelló

first: Llorenç

last: Rovirosa

first: Jay

last: Tischfield

first: Lourdes

last: Serrano

last: Vazquez

last: Ruiz-Herrera


title: scRNAseq of whole lung homogenates from WT and Scnn1b-Tg mice.

city: Chapel Hill

first: Hong

last: Dang

state: North Carolina

address: 125 Mason Farm Rd, Cb#7248

institute: University of North Carolina at Chapel Hill

summary: We use 10x genomics scRNAseq to study whole lung homogenates of WT and Scnn1b-Tg mice.  Scnn1b-Tg mice are a model of mucoobstructive lung disease. This is the first study to perform scRNAseq in this model.

overall_design: Lungs were harvested from naive, 10-12 week olf female mice. The single cell populations were enriched for epithelial cells using cell sorting with flow cytometry. scRNAsequencing was perfomed using the10x genomics platform.

first: Padraig

last: Hawkins

first: Sarah

middle: R

last: Leist

first: Minako

last: Saito

first: Lisa

last: Morton

first: Rodney

last: Gilmore

first: Stephen

last: Schworer

first: Ella

middle: F

last: Burns

first: Jason

last: Rock

first: Robert

last: Hagan

first: James

last: Pestka

first: Alexandra

last: Schäfer

first: Kenichi

last: Okuda

first: Lauren

last: Heine

first: Jack

last: Harkema

first: Wanda

last: O'Neal

first: Alessandra

last: Livraghi-Butrico

first: Raymond

last: Pickles

first: Ralph

last: Baric

first: Richard

last: Boucher


title: EPIMETRIC (EPIgenetic MEthylation-based Algorithm for Respiratory Illness Classification - COPD)

city: Granada

first: Cristobal

last: Fresno

state: Andalucia

address: Avda. de la Ilustración 114

department: Centre for Genomics and Oncological Research

country: Spain

institute: Pfizer/University of Granada/Andalusian Regional Government (GENyO)

summary: EPIMETRIC is an innovative algorithm based on the analysis of epigenetic methylation profiles for diagnosing and accurately stratifying Chronic Obstructive Pulmonary Disease (COPD). This approach combines advanced molecular biology techniques with computational tools, enabling the identification of specific DNA methylation patterns associated with the progression and severity of COPD.

overall_design: The methylation profiles of cell-free DNA (cfDNA) extracted from the blood of COPD patients and healthy controls were studied. The group variables (COPD or healthy) and the Global Initiative for Chronic Obstructive Lung Disease (GOLD) were investigated. A support vector machine (SVM) classifier was constructed from the differential methylation analysis, which we call EPIMETRIC.

first: Cristóbal

first: Abel

last: Garcia-Diaz

first: María

last: Serrano

first: Valeria

last: Denninghoff

first: Marta

last: Alarcon


title: Combinatorial delivery of low-dose irradiation and immunotherapy to patients with immune-excluded tumors effectively enhances CD8+ T cell functionality in tumors with homologous recombination repair deficiency [bulk RNA-seq]

city: Lausanne

first: Nicolas

last: Rayroux

address: Rue du Bugnon 25A

department: Oncology

country: Switzerland

institute: Centre Hospitalier Universitaire Vaudois

summary: Immune-checkpoint blockade (ICB) has shown significant efficacy across various tumor types. However, tumors with low intraepithelial T-cell infiltration, often referred to as "cold" tumors, are expected to yield poor responsiveness to ICB. We investigated the potential of LDRT to enhance immune-checkpoint blockade (ICB) responses in 25 patients with multimetastatic immune-excluded solid tumors through a multi-cohort phase I clinical trial (RACIN).  Primary endpoint was to determine the safety and tolerability of the combination of a backbone treatment, comprising nivolumab, ipilimumab, aspirin/celecoxib, and low-dose cyclophosphamide in association with escalated LDRT. Secondary endpoints included among others disease control rate (DCR) and overall survival (OS). Exploratory endpoints included biomarkers and molecular correlates of response. The combination treatment showed a manageable safety profile, with Grade 3 or higher adverse events in 12% to 21% of patients across cohorts. The overall disease control rate (CR + PR + SD) was 41.6%. Progression free survival across all cohorts was 2.1 months (95% C.I.: 1.8 – 4.2 months), with the highest PFS observed in cohort 1 which received 0.5 Gy (5.7 months, (95% C.I.: 1.9 - 11.3 months). Median overall survival was 14.0 months (95% CI: 8.5–24.6 months), with one patient with ovarian cancer still maintaining a complete response at three years follow-up. Site-paired tumour biopsies collected for each patient at baseline and after LDRT +/- Cy enabled the comprehensive characterization of the dynamics of their excluded/desert tumour microenvironments (TME) at the single cell level. Response to LDRT and ICB was associated with DNA damage and repair responsiveness and the presence of detectable intratumoral PD1+CD8+ tumour infiltrating lymphocytes (TILs) at baseline. Our data revealed that LDRT amplified CD8+ TIL functionality in responding patients offering mechanistic insights on how LDRT improves ICB effectiveness. In contrast, we observed a radiosensitivity of TILs in tumours of non-responders. Detailed single cell immune profiling before LDRT also highlighted a lack of key immune stimulatory myeloid cells that can therefore limit ICB efficacy in excluded tumors. Collectively, this study represents the most comprehensive profiling of longitudinal samples of cancer patients treated with LDRT. Our findings highlight several genetic, transcriptomic and TME parameters associated with response to combinatorial LDRT and ICB in advanced immune-excluded solid cancers, generating rationale for their validation in larger cohorts.

overall_design:
Transcriptomic data from bulkRNA sequencing of human tumors from 24 patients undergoing combinatorial delivery of low dose radiotherapy and immunotherapy with matched pre- and post-treatment biopsies for 21 patients.

***************************************************************
The table below lists GEO accessions reused/reanalyzed for this study.
***************************************************************

first: Maria

last: Ochoa-de-Olza

first: Fernanda

last: Herrera

first: Denarda

last: Laniti


title: Anti-HIV Immunotoxin and Antibody-Drug Conjugate Targeted by the Same Anti-gp41 Antibody Display Distinct Modes of Cellular Killing

city: Bozeman

first: SETH

middle: H.

last: PINCUS

state: Montana

address: 103 Chemistry and Biochemistry Building

department: Chemistry

institute: Montana State University

summary: Background:  We are developing cytotoxic immunoconjugates (CICs) to eradicate the persistent reservoir of HIV infection, the barrier to a cure. Having identified the most effective monoclonal antibodies (mAbs) for targeting CICs to HIV-infected cells, we investigated the efficacy and mode of killing of different forms of CICs targeted by the same mAb, an immunotoxin (IT) and antibody drug conjugate (ADC). Methods: We compared the in vitro effects of CICs made by conjugating anti-gp41 mAb 7B2 to either deglycosylated ricin A chain (7B2-dgA) or the anthracycline derivative PNU-159682 (7B2-PNU). Cytotoxicity was tested on cell lines stably expressing the HIV envelope. Metabolic and transcriptional analyses of treatment effects were performed on cells persistently infected with HIV.  Results: 7B2-dgA was more potent and acted more rapidly to kill cells. 7B2-PNU induced bystander-cell killing but stimulated cell growth upon low dose or brief exposure. Six hr post treatment, 7B2-dgA elicited both metabolic and transcriptional alterations, whereas 7B2-PNU treated cells did not differ from untreated cells. At 24 hr, the profiles following both treatments differed from untreated cells and from each other. 7B2-dgA treated cells exhibited elevated intracellular levels of many AAs, and early activation of gene pathways for apoptosis and transcriptional control; later transcriptional changes included decreases in expression of enzymes involved in AA synthesis and carbon metabolism.  Conclusions: An IT and ADC, each delivered by the same antibody and tested in the same cell lines showed substantial differences in their mode of killing, of potential clinical significance. The results of this side-by-side comparison of an ADC and IT have implications for the development of CICs to treat other conditions, including cancer.

overall_design: RNA-Seq was performed on H9 CD4+ lymphoma cells that were persistently infected with the  HIV isolate H9/NL4-3. Cells were either untreated or exposed to an anti-HIV immunotoxin (7B2-dgA) or antibody-drug conjugate (7B2-PNU159682). RNA was extracted 6 and 24 hr post treatment.

first: Seth

middle: H

last: Pincus


title: Effect of Rnf111 S254D mutant on gene expression at intestine tissues

city: Beijing

first: Zhiqiang

last: Peng

address: 38 Life Science Park Road

institute: State Key Laboratory of Medical Proteomics, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics

summary: Transcriptome analysis of RNAs extracted from intestine tissues of wild type or Rnf111 S254D heterozygous mice

overall_design: RNA-seq profiling of WT or Rnf111 S254D HET at intestine tissues

first: Lingqiang

last: Zhang

first: Cuihua

last: Liu


title: Pulmonary fibroblast activation during Aspergillus fumigatus infection enhances lung defense via immunomodulation and tissue remodeling [scRNA-seq]

city: Columbus

first: Jose

middle: P

last: Guirao-Abad

state: OH

address: 2255 Kenny Rd

department: Emergency Medicine

institute: Ohio State University

summary: Aspergillus fumigatus is the etiologic agent of invasive aspergillosis, a life-threatening fungal pneumonia that is initiated by the inhalation of conidia (spores) into the lung. If the conidia are not cleared, they secrete large quantities of hydrolytic enzymes and toxins as they grow, resulting in extensive damage to pulmonary tissue. Stromal fibroblasts are central responders to tissue damage in many organs, but their functional response to pulmonary injury caused by A. fumigatus has not been explored. In this study, we employed cell lineage tracing, targeted cell ablation, and single-cell RNA sequencing to monitor the dynamics of fibroblast behavior upon exposure to A. fumigatus in both immunocompetent and immunosuppressed hosts. The results demonstrate that a subset of pulmonary fibroblasts becomes activated in an immunocompetent host in response to a challenge with A. fumigatus conidia, acquiring a gene expression program reflecting the acquisition of new immunomodulatory properties as well as enhanced extracellular matrix (ECM)-secreting ability. Remarkably, through targeted ablation of fibroblasts that express the profibrotic activation marker periostin, we demonstrate that the progression of an invasive A. fumigatus infection in an immunosuppressed host is accelerated by the absence of periostin lineage cells and is accompanied by severe alveolar hemorrhage and angioinvasion. These findings uncover a novel protective role for fibroblasts in limiting the severity of A. fumigatus-induced pulmonary injury and emphasize the importance of the pulmonary stroma in host defense against this invasive fungal infection.

overall_design: Immunocompetent mice were exposed to either a single inoculum of conidia or a mock inoculation with saline. The stromal cell population was then isolated from total lung cells on days 1 and 7 post-inoculation by flow cytometry, excluding the non-stromal population based on expression of CD31, CD45 and EpCAM. The resulting stromal cell population was then subjected to a single-cell transcriptome analysis.

first: Shannon

last: Shearer

first: Jon

last: Bowden

first: Daniel

middle: A

last: Kasprovic

first: Christina

last: Grisham

first: Mustafa

last: Ozdemir

first: Elliot

last: Lowe

first: Michael

last: Tranter

first: Yunguan

last: Wang

first: David

last: Askew

first: Onur

last: Kanisicak


title: Sirtuin 7 regulates dosage compensation and safeguards the female X-chromosome [ChIP_H2AX_gH2AX_MEF]

first: Joshua

last: Thackray

overall_design: ChIP-seq profiling of H2AX and gammaH2AX enrichment in WT and SIRT7-KO primary mouse MEF cells.

first: Nicolas

last: Simonet

first: Barry

last: Kesner

first: François

last: Serra

first: Maria

last: Espinosa-Alcantud

first: Anna

last: Lappala

last: Guitart

first: Laia

last: Marin

first: Uri

last: Weissbein

first: Danni

first: Josema

last: Castelló

first: Llorenç

last: Rovirosa

first: Jay

last: Tischfield

first: Lourdes

last: Serrano

first: Berta

last: Vazquez

first: Aurora

last: Ruiz-Herrera

first: Bernhard

last: Payer

first: Biola

middle: M

last: Javierre

first: Alejandro

last: Vaquero

first: Jeannie

last: Lee


title: Sirtuin 7 regulates dosage compensation and safeguards the female X-chromosome [ChIP_SIRT7_MEF]

first: Joshua

middle: K

last: Thackray

overall_design: ChIP-seq profiling of SIRT7 enrichment in WT and SIRT7-KO, male or female, primary mouse MEF cells.

first: Nicolas

last: Simonet

first: Barry

last: Kesner

last: Wang


title: Combinatorial delivery of low-dose irradiation and immunotherapy to patients with immune-excluded tumors effectively enhances CD8+ T cell functionality in tumors with homologous recombination repair deficiency [scRNA-seq]

last: Rayroux

overall_design: Transcriptomic data from single-cell sequencing of human tumors from 11 patients undergoing combinatorial delivery of low dose radiotherapy and immunotherapy with matched pre- and post-treatment biopsies for 7 patients.

first: Maria

last: Ochoa-de-Olza

first: Fernanda

last: Herrera

first: Denarda

last: Dangaj-Laniti


title: Nuclear myosin 1 regulates platelet activation and immune response in mice

city: Abu Dhabi

first: Piergiorgio

last: Percipalle

state: abu dhabi

address: NYUAD Saadiyat Island

country: United Arab Emirates

institute: Biology

summary: Cellular differentiation involves a complex series of events associated with changes in cellular shape, function, and proliferative capacity. This process is mostly regulated by specific expression of multiple genes which guide the cell through the differentiation process but also ensure proper function of terminal cell types. Over the last decade, the role of cellular metabolism in maintaining the pluripotency of stem cells and subsequent differentiation is getting more attention as there is a direct link between the metabolic status of cells and their differentiation potential. We have recently shown that deletion of Nuclear Myosin 1 (NM1) leads to a molecular switch from oxidative phosphorylation to glycolysis and subsequent tumorigenesis in mice. Here we performed an in vitro analysis of metabolomic profiles associated with NM1 loss and measured the cytokine and chemokine levels in cells to provide evidence for a possible role of NM1 during hematopoiesis. Moreover, we explored the role of NM1 during the differentiation of hematopoietic progenitor stem cells to terminal blood cells by transcriptomic analysis of bone marrow, spleen, and peripheral blood. We found that in bone marrow, NM1 deletion leads to overexpression of genes associated with glycolysis-dependent platelet activation and suppression of the innate immune system genes. Remarkably, these expression patterns are preserved and become more complex in the spleen and peripheral blood. The study therefore provides novel insights into the underlying mechanisms of hematopoietic differentiation and activation of specific blood cell types and suggests NM1 as a potential therapeutic target for blood-related disorders.

overall_design: RNA seq of blood and spleen tissues isolated from NM1 WT and KO mice

first: Tomas

last: Venit

first: Nizar

last: Drou


title: Spatially resolved profiling and Footprint Analysis of the Steroid Nuclear Receptors Reveals a Role for the Disordered N-Terminal Domains in Genome Targeting and AP-1 Interaction

city: Rehovot

first: Naama

last: Barkai

state: HaMerkaz

address: Herzl 234

department: Molecular Genetics

country: Israel

institute: Weizmann Institute of Science

summary: Transcription factors (TFs) regulate gene expression by binding to cis-regulatory regions within vast genomes. In budding yeast, intrinsically disordered regions (IDRs) emerged as key effectors of genome preferences, but whether this holds in the complex mammalian genomes remains unclear. Mammalian TFs are enriched with long IDRs, exemplified by the disordered N-terminal domains (NTDs) of the nuclear steroid receptors (SRs). Here, by comparing genomic locations of three SRs and their truncation mutants, we show that the NTDs direct the selection of SR target sites. Footprint analysis revealed that SR mutants lacking the NTD become dependent on the AP-1 motif and further suggest that the NTD can direct genome recognition independent of co-binding TFs, which we confirmed by testing SR binding across the budding yeast genome. Our results suggest that IDRs assist in defining the TF binding targets, opening new avenues for modulating activities of therapeutically relevant TFs.

sample_organism:
Saccharomyces cerevisiae
Homo sapiens
Mus musculus

overall_design: Binding of Nuclear steroid receptors and their mutants was profiled using ChEC-seq in 2 different systems. Mammalian cell-lines - NMuMG (mouse) and HepG2 (human), and yeast (S.Cerevisiae)

first: Zigdon

last: Inbal

first: Shoham

last: Achinoam

first: Mindel

last: Vladimir

first: Manadre

last: Wajd

first: Yahav Har-Shai

last: Dekel

first: Antebi

last: Yaron

first: Barkai

last: Naama


title: Sirtuin 7 regulates dosage compensation and safeguards the female X-chromosome [Hi-C]

first: Joshua

last: Thackray

overall_design: CHART-seq profiling of Xist transcript binding in WT and SIRT7-KO hybrid (mus/cas) mouse Tail Tip Fibroblasts (TTF).

last: Simonet

last: Kesner

first: François

last: Serra

last: Espinosa-Alcantud

first: Anna

last: Lappala

last: Guitart

first: Laia

last: Marin

first: Uri

last: Weissbein

first: Danni

first: Josema

last: Castelló

first: Llorenç

last: Rovirosa

first: Jay

last: Tischfield

first: Lourdes

last: Serrano

first: Berta

last: Vazquez

first: Aurora

last: Ruiz-Herrera

first: Bernhard

last: Payer

first: Biola

last: Javierre

first: Alejandro

last: Vaquero

first: Jeannie

last: Lee


title: Elucidating early intestinal stem cell response to bacterial infection

city: Jerusalem

first: Matan

last: Hofree

address: The Edmond J. Safra, Givat Ram Campus

department: School of Computer Science and Engineering | The Lautenberg Center for Immunology and Cancer Research

institute: The Hebrew University of Jerusalem

summary: Intestinal stem cells (ISCs) are the regenerative force of the gut epithelium. Lgr5+-ISC have been shown to respond to changes in their microenvironment by coping with different metabolites, adapting to caloric changes, and recovering from injury and inflammation. However, how pathogenic bacteria affect adult stem cell regeneration and, as a consequence, the overall tissue adaption to infection has yet to be explored in depth. Here, we interrogated early Lgr5+ ISC responses to an enteric intracellular pathogen by profiling individual IECs from the mouse small intestine. Utilizing GFP-labeled Salmonella enterica, we isolated intracellular invaded cells to elucidate invasion programs of epithelial cell subsets. In particular, we identified a Salmonella-specific infection signature comprised of antimicrobial peptide (AMP) genes, including the Defensin gene family. Our findings demonstrate that Salmonella enterica targets differentiated Paneth, enterocytes, and stem/progenitor cells at these early stages of infection. In response, a rapid Lg5+ ISC-driven cellular remodeling to enterocyte and Paneth lineages expressing AMP genes is initiated to combat the intruders. Importantly, we uncovered an ISC differentiation program via inflammasome activation to protect the crypt environment, while eliminating infected stem cells from the overall stem cell pool. This novel Lgr5+ stem cell defense mechanism not only protects the gut epithelium from persistent bacterial infection but also promotes tissue regeneration. We propose epithelial remodeling to AMP-secreting cells as a novel innate immune response to handle different gut stresses mediated by Lgr5+ ISCs to maintain organizational principles of gut homeostasis and physiology.

overall_design: The data here is from a single-cell RNAseq experiment by 10x (v3), comparing small intestine epithelium under normal, 12, 24 hours post-infection by Salmonella enterica, 24 hours post-infection by Listeria.

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