title: Biomimetic model of human small airways reveals functional impacts of the cystic fibrosis microenvironment on monocytes and macrophages

first: Rabindra

last: Tirouvanziam

state: GA

address: 2015 Uppergate Dr

institute: Emory University

summary: Several muco-obstructive lung diseases in humans, including cystic fibrosis (CF), feature the chronic recruitment of blood leukocytes and their reprogramming within the lumen of small airways to drive pathological adaptations such as altered immune mediator secretion and defective killing of bacteria. To investigate these mechanisms, we engineered a biomimetic model in which primary human blood monocytes migrate through a human small airway epithelium, andepithelium and differentiate into macrophages upon 4-day exposure to macrophage colony-stimulating factor. We observed that airway-recruited monocytes (ArMos) obtained with the control chemoattractant C-C motif ligand 2 (CCL2) altered their transcriptome and secretome upon transmigration, and further upon differentiation into airway-recruited macrophages (ArMas), as compared to circulating monocytes. We observed specific additional alterations in transcriptomic and secretomic properties of ArMos and ArMas when they were conditioned in CF airway supernatant (derived from cell- and bacteria-free sputum) [CFASN], compared CCL2 conditions. Critically, CF ArMas (but not CF ArMos), showed a much reduced ability to kill P. aeruginosa, a common CF pathogen. These findings extend prior studies on small airway-recruited neutrophils, and identify immune tolerance by macrophages as one underlying cause  of bacterial colonization in CF. This biomimetic model support further mechanistic and preclinical investigations of small airway-recruited monocytes and macrophages  in CF and other diseases featuring chronic inflammation and infection, like non-CF  bronchiectasis, and chronic obstructive pulmonary disease.

overall_design: RNA-seq profiling of monocytes and macrophages under different transmigration, culutre, and drug treatment differences

first: Justin

last: Hosten

first: Diego

last: Moncada Giraldo

first: Rabin


title: Trithorax balances ISC fate decisions via Ptx1-mediated repression of EE specification [RNA-seq]

status: Public on Dec 01 2025

city: Heraklion

first: Zoe

last: Veneti

address: Nikolaou Plastira 100

country: Greece

institute: Institute of Molecular Biology & Biotechnology Foundation for Research & Technology - Hellas

type: Expression profiling by high throughput sequencing

summary: Adult stem cells must coordinate transcriptional programs with external cues to maintain tissue homeostasis. In the Drosophila midgut, intestinal stem cells (ISCs) generate enterocytes (ECs) or enteroendocrine (EE) cells through Notch-dependent fate decisions, but how chromatin regulators influence this balance remains unclear. In this study we identified the Trithorax gene (trx) as a key factor that safeguards ISC lineage fidelity. Trx depletion biases ISCs toward EE differentiation without affecting proliferation, a phenotype exacerbated during aging or DSS-induced damage. Transcriptomic and chromatin profiling revealed the homeobox transcription factor Ptx1 as a Trx-dependent target. Ptx1 knockdown phenocopies Trx loss, whereas Ptx1 overexpression reverts trx-RNAi-induced EE overproduction, establishing Ptx1 as a critical mediator of Trx function. These findings support a model in which Trx constrains the scute–prospero axis through Ptx1-mediated repression, thereby limiting inappropriate EE specification and maintaining ISC plasticity.

overall_design: To identify genes regulated by Trx, we performed RNA-seq on FACS-sorted adult GFP⁺ progenitor cells from control (esgtsGFP x w1118) and trx RNAi (esgtsGFP x UAS-trxRNAi BDSC#33703)  female midguts under homeostatic (sucrose-fed) and regenerative (DSS-treated) conditions. We then performed gene expression profiling analysis using RNA extracted with miRNeasy Micro Kit and libraries were prepared with the QuantSeq 3′ mRNA-Seq Library Prep Kit (Lexogen).

first: Virginia

last: Fasoulaki

first: Aristides

middle: G

last: Eliopoulos

first: Alexandros

last: Galaras

first: Pantelis

last: Hatzis

first: Christos

last: Delidakis


title: Trithorax balances ISC fate decisions via Ptx1-mediated repression of EE specification [ATAC-seq]

type: Genome binding/occupancy profiling by high throughput sequencing

overall_design: To identify genes regulated by Trx, we performed Assay for Transposase-Accessible Chromatin using sequencing (ATAC-seq) on FACS-sorted adult GFP⁺ progenitor cells from control (esgtsGFP x w1118)  and trxRNAi (esgtsGFP x UAS-trxRNAi BDSC#33703) female midguts under homeostatic (sucrose-fed) and regenerative (DSS-treated) conditions.


title: Lamin A/C regulates lipid metabolism and inflammation: insights from models of familial partial lipodystrophy 2 sub1

city: Ann Arbor

first: Ormond

middle: A.

last: MacDougald

state: MI

address: 2800 Plymouth Rd

department: Molecular & Integrative Physiology

country: USA

institute: University of Michigan

summary: Familial partial lipodystrophy 2 (FPLD2) is a rare disease characterized by adipose tissue loss and redistribution, and metabolic dysfunction. FPLD2 is caused by pathogenic variants in the LMNA gene, encoding nuclear lamins A/C, structural proteins that control nuclear function and gene expression. However, the mechanisms driving adipocyte loss in FPLD2 remain poorly defined. In this study, we recruited eight families with developing or established FPLD2 and performed clinical, histological, and transcriptomic analyses of subcutaneous adipose tissue biopsies. Bulk and single-nuclei RNA-sequencing revealed suppression of lipid metabolism and mitochondrial pathways, alongside increased inflammation. These signatures were mirrored in tamoxifen-inducible adipocyte-specific Lmna knockout mice, in which lamin A/C-deficient adipocytes shrank and disappeared. Lmna-deficient fibroblasts shared similar gene expression changes, linked to altered chromatin accessibility, underscoring lamin A/C’s potential regulatory role in lipid metabolism and inflammatory programs. By directly comparing atrophic and hypertrophic adipose depots in FPLD2, and integrating human, mouse, and in vitro models, this study provides new insights into disease progression and potential therapeutic targets.

overall_design: Bulk RNA-seq from human subcutaneous white adipose tissue, either from the upper neck or the abdominal depot. These samples are from control patients (Group C), patients with developing FPLD2 (Group A), or developed FPLD2 (Group B).

first: Jessica

middle: N

last: Maung

first: Akira

last: Nishii

middle: A


title: Transcriptome and proteome response is uncoupled under glutamine limitation

city: Nijmegen

first: Cyriel

last: Huijer

address: Houtlaan 4

department: Molecular Developmental Biology

country: Netherlands

institute: Radboud University Nijmegen

summary: Understanding the quantitative relationship between transcript and protein concentrations remains a key challenge in biology. Absolute measurements of both transcript and protein concentration is critical but has not been done in human cells yet. Additionally, within-gene correlations were determined across different tissues, allowing environmental and genetic variability. Here, we address these limitations by analyzing within-gene correlations across the human cell line MCF10A with decreasing concentrations of glutamine in tissue culture as the sole independent variable. We find that the transcriptome and proteome response is uncoupled: the transcriptome primarily reallocates its resources, while the proteome changes in total protein. Furthermore, high within-gene correlations are observed in specific functional groups. Furthermore, genes with high within-gene correlation share common gene features, with the 3’ UTR length shows the largest effect. These results will provide valuable insights that could improve the prediction of protein concentrations from transcripts in biomedical research and biotechnology.

overall_design: MCF10A human breast epithelial cells were cultured in glutamine-free DMEM/F12 supplemented with four different concentrations of glutamine (0.04, 0.12, 0.20, and 0.28 mM) as well as normal glutamine concentration in DMEM/F12 (2.5 mM). Each glutamine condition included three biological replicates.

first: Rosemary

last: Yu


title: Lamin A/C regulates lipid metabolism and inflammation: insights from models of familial partial lipodystrophy 2 sub 2

overall_design: Bulk RNA-seq from mouse parametrial white adipose tissue, from control (Lmna fl/fl) or inducible Lmna adipocyte-specific KO (Lmna iADKO) mice. Mice were injected with tamoxifen at 12-14 weeks of age, and adipose tissue was analyzed two weeks post-tamoxifen administration.


title: Effect of CAMK2D inhibition in RBM20 loss of function mouse models

city: Heidelberg

first: Maarten

last: van den Hoogenhof

state: (select)

address: In Neuenheimer Feld 669

country: Germany

institute: Institute of Experimental Cardiology

summary: Mutations in RBM20, a splicing factor that targets multiple pivotal cardiac genes including TTN and CAMK2D, cause a clinically aggressive form of dilated cardiomyopathy (DCM) with a high risk of malignant ventricular arrhythmias. We hypothesized that the RBM20 target CAMK2D contributes critically to RBM20 cardiomyopathy. Here, we sequenced the hearts of Rbm20/Camk2d double knockout mice, as well as the hearts of Rbm20-R636Q knock-in mice treated with the CAMK2 inhibitor Hesperadin.

overall_design: RNAseq of RBM20/CAMK2D double knockout mice and RBM20-R636Q knock-in mice with CAMK2 inhibition using Hesperadin


title: Investigating conjunctival immune pathways in Sjögren and non-Sjögren disease associated dry eye

city: Houston

first: Cintia

middle: Sade

last: de Paiva

state: Texas

address: One Baylor Plaza

department: Ophthalmology

institute: Baylor College of Medicine

summary: This study aimed to investigate changes in immune related genes on the ocular surface of patients with different diagnoses. We compared DEGs from 21 healthy controls, 12 aqueous tear deficient (ATD), and 12 Sjögren disease dry eye using the nanostring immunology v2 panel. We identified DEGs in immune pathways relating to viral response and adaptive immunity. We did not identify DEGs in comparison of ATD vs SjD, suggesting there are no differences in the immune response on the ocular surface, despite different diagnoses.

overall_design: 42 patient samples were submitted for Nanostring analysis. 25 healthy controls, 12 aqueous tear deficient dry eye, and 13 Sjögren disease dry eye. All samples were age and sex matched.

first: Kaitlin

middle: K

last: Scholand

first: Laura

last: Schaefer

first: Zhiyuan

first: Stephen

middle: C

last: Pflugfelder

first: Robert

last: Britton


title: T cells in B16 tumor model with ACT and checkpoint blockade - scRNA-seq, CITE-seq and TCRab [i35]

city: Boston

first: Liang

last: Yang

state: MA

address: 77 Avenue Louis Pasteur

department: Pathology

institute: Harvard Medical School

summary: This study is part of the immgenT Open Source Project, specifically from IGT35, which focuses on characterizing T cells in the B16.gp33 melanoma model following adoptive cell therapy (ACT) and immune checkpoint blockade. T cells were isolated from tumors and  draining inguinal lymph nodes of C57BL/6J male mice (7–8 weeks old) subjected to subcutaneous implantation of B16.gp33 melanoma cells, followed by adoptive cell transfer treatment with intravenous transfer of P14 and pmel T cells, and treatment with either isotype control antibodies or a combination of anti-PD-1 and anti-4-1BB antibodies. Samples were collected at day 14 post post-tumor implantation (1 day post-final antibody treatment). The study targeted all CD3+ T cell populations, including transgenic P14 and pmel T cells

overall_design: T cells were isolated from tumors and draining inguinal lymph node samples using mechanical dissociation or collagenase I digestion.  Sorted CD3+ T cell populations, including transgenic P14 and pmel T cells were profiled using single-cell RNA sequencing (10x Genomics), combined with CITE-seq (TotalSeq C) and paired TCR α/β sequencing. Samples from multiple mice were pooled using hashtag oligonucleotides for multiplexing.

first: David

last: Zemmour

first: Christophe

last: Benoist

first: Nicole

last: Scharping


title: The complex transcriptomics of RNA classes for biomonitoring and mechanistic studies

city: Santa Cruz

first: Aidan

middle: Christian

last: Manning

state: CA

address: 2125 Delaware Ave. Suite B

institute: RealSeq Biosciences

type: Non-coding RNA profiling by high throughput sequencing

summary: The effects of exposure to chemical compounds and/or particulate matter on genetic material, including the risks of disease, are frequently evaluated by analyses of biomarkers. Among them, RNA markers play an important role in understanding the changes in the dynamics of transcriptomic processes. Currently, most transcriptome analyses are based on an assessment of individual RNA molecules using qPCR techniques, the application of array approaches, or RNA sequencing techniques with the potential to detect novel transcripts. Despite methodological progress, limitations linked with RNA fragmentation remain and thus many important results can be lost. In this pilot study we tested a new methodological approach of RNA libraries preparation using the RiboMarker® platform in combination with Illumina sequencing to analyze the complex transcriptome, including fragmented RNAs. Four sets of samples collected from firefighters at three time points according to their exposure (before, after – immediately, after – a day later) were analyzed. A wide range of RNA types [non-coding RNAs (rRNA, tRNA, miRNA, snRNA, snoRNA, lncRNA, piRNA) and protein coding mRNAs] were detected which allowed us to track the dynamics of their expression in different time periods. The application of this comprehensive RNA profiling in a large future biomonitoring study is promising: (i) for identification of the novel biomarkers of specific exposures; and (ii) to study the complex mechanisms of transcription including protective adaptation changes, as well as potentially harmful deregulations increasing the risk of diseases, including cancer.

overall_design: Small RNA sequencing of cell-free RNA in circulating blood from a time series of four firefighters after fire intervention.

first: Andrea

last: Rossnerova

first: Zuzana

last: Simova

first: Denise

last: McGarth

first: Sergio

last: Barberan-Soler

first: Pavlina

last: Klusackova

first: Daniela

last: Pelclova

first: Pavel

last: Rossner

first: Michal

last: Sima


title: Recapitulating Patient-to-Patient Colorectal Cancer Tumor Heterogeneity  Using Patient-Derived Xenograft Cells in an Engineered Tissue Model

city: Auburn

first: Michael

middle: W

last: Greene

state: AL

address: 260 Lem Morrison Dr

institute: Auburn University

summary: Establishing in vitro cancer models that more closely recapitulate patient tumor microenvironmental heterogeneity, including variations in stromal cells and mechanical properties that influence colorectal cancer (CRC) progression, is crucial for advancing  CRC research. This study evaluated the ability of 3D engineered CRC-PDX (3D-eCRC-PDX) tissues to recapitulate the heterogeneity found between patient-derived xenograft (PDX) tumors from three CRC patients (stage II, III-B, and IV). To form the 3D-eCRC-PDX tissues, CRC-PDX tumor cells were encapsulated in PEG-fibrinogen hydrogels and maintained for 29 days in vitro. 3D-eCRC-PDX tissues recapitulated key patient-specific tumor characteristics. During long-term culture, 3D-eCRC-PDX tissues mimicked the patient-specific growth rates of the originating CRC-PDX tumors. Importantly, tumor cellular subpopulations, including the ratio of human cancer cells to mouse stromal cells and the ratios of proliferative human cancer cells and CK20+ cells were maintained in 3D-eCRC-PDX tissues, unlike in 2D cell culture.  Differences in mechanical stiffness between the originating CRC-PDX tumors were also recapitulated by the 3D-eCRC-PDX tissues. Principle component analysis of transcriptomic data clustered 3D-eCRC-PDX tissues and CRC-PDX tumors together by patient, indicating similar gene expression profiles.  These findings highlight the potential of 3D-eCRC-PDX tissues as a promising tool for CRC research, capable of maintaining patient-specific tumor microenvironment heterogeneity.

overall_design: mRNA profiles of 3D engineered CRC tissues cultured for 15 days and the corresponding in vivo PDX subcutaneous tumor grown in NOD.Cg-Prkdcscid Il2rgtm1Wjl/SzJ (NOD-SCID) mice.

first: Elizabeth

last: Lipke


title: CD200+ CD8 T Cell Generated through Arginine Deprivation to Activate Macrophage Cross-presentation and Improve Anti-Tumor Immunity [RNA-Seq 2]

city: Chengdu

first: Long

middle: Qian

last: Kang

state: Sichuan Province

address: 新川路2222号

department: Biotherapeutics

country: China

institute: Sichuan University

summary: Arginine is indispensable for both tumor progression and the function of immune cells, yet how arginine deprivation within the tumor microenvironment shapes anti-tumor immunity has remained unclear. In this study, we established an in vivo arginine-restriction model using a diet lacking arginine, which significantly suppressed tumor growth and activated global anti-tumor immune responses. Mechanistically, arginine deprivation triggered the integrated stress response in CD8+ T cells via the GCN2–cREL signaling axis, leading to elevated CD200 expression. These CD200+ CD8+ T cells in turn enhanced the antigen cross-presentation capacity of tumor-associated macrophages through CD200–CD200R interactions, forming a cooperative immune network that reinforced anti-tumor activity. Moreover, this arginine deprivation–induced cellular synergy improved the therapeutic efficacy of immunotherapy in colorectal cancer models. We further conducted a single-arm phase I clinical trial (NCT07038044), which demonstrated that an arginine-free diet is both feasible and safe for modulating systemic immunity in patients. Together, our findings provide a new conceptual framework for understanding the role of arginine in reshaping the tumor immune microenvironment and highlight arginine restriction as a promising and clinically translatable anti-tumor strategy.

overall_design: We used 5-week-old BALB/c mice and randomly assigned them into a normal diet group and an arginine-deficient diet group based on body weight. The arginine-deficient diet was formulated to remove arginine while maintaining the same total caloric intake as the control diet. After one week of dietary pre-intervention, CT26 cells were subcutaneously inoculated to establish a colorectal cancer xenograft model. On day 20 after tumor implantation, mice were euthanized and tumor tissues were collected for RNA sequencing.

first: Qianlong

first: Zedong

last: Jiang

first: Keqin

last: Tan

first: Xuelei

last: Ma


title: Stable inheritance of the Streptomyces linear plasmid SCP1 by dual ParABS partition systems [SCP1_PCN]

city: Norwich

first: Leah

last: McPhillips

address: Colney Lane

department: Molecular microbiology

country: United Kingdom

institute: John Innes Centre

summary: Low copy number plasmids must encode maintenance mechanisms, such as partitioning systems, to ensure that the plasmid is sustained through host generations. Plasmid partition systems segregate sister plasmid copies and are subdivided into different types based on the NTPase they encode. The characterisation and distribution of partition system types is well understood in Enterobacteriaceae plasmids. However, how these systems maintain plasmids and are distributed across wider bacterial diversity is poorly understood. We searched a large and diverse plasmid database to identify the distribution of partition system types and found that plasmids encoding multiple partition systems are more widespread than previously realised, composing ~19% of all plasmids predicted to encode partition systems. Many of these plasmids were predicted to encode multiple partition systems of the same type, which had never been studied previously. We used the Streptomyces coelicolor A3(2) plasmid SCP1, which encodes two type Ia partition systems, as a model to investigate this. Sequence analysis of the SCP1 partition systems revealed that both ParB proteins contain less conserved CTP-binding pockets, suggesting one or both proteins may not behave like canonical ParB proteins. However, using a combination of chromatin immunoprecipitation with deep sequencing (ChIP-seq), biochemistry and mutagenesis we show that both ParB proteins behave like bone fide ParB proteins: they bound to distinct parS sites on SCP1, both proteins bound and hydrolysed CTP and both proteins required CTP and their cognate parS site to accumulate, or spread, on DNA. Intriguingly, however, only ParB1 was critical for SCP1 stability. Together, our findings further our understanding of Streptomyces plasmid maintenance by providing the first functional characterisation of two type Ia partition systems coexisting on a single plasmid and offer new insights into the diversity and distribution of plasmid partition systems.

overall_design: To determine the plasmid copy number per chromosome of the two plasmids of Streptomyces coelicolor A3(2), the wild type strain was grown on solid soya flour mannitol (SFM) agar until visably sporeulated. Spores were harvested and the genomic DNA was extracted from these spores and sequenced in order to determine what the plasmid copy number was compared to the chromosome. Spores were chosen over vegetative mycelium as they are metabolically inactive and therefore should represent the true ratio of the plasmid copy number per spore, as during vegetative growth differences in the replication rate of these genetic elements could artifically inflate/deflate the true plasmid copy number ratio to the chromosome.

first: Tung

last: Le


title: CD200+ CD8 T Cell Generated through Arginine Deprivation to Activate Macrophage Cross-presentation and Improve Anti-Tumor Immunity [RNA-Seq]

overall_design: We established an in vitro culture system mimicking arginine deprivation. CD8+ T cells isolated from postnatal day 14 mice were first activated in nutrient-replete medium and subsequently transferred to arginine-containing or arginine-free medium for four days.


title: CD200+ CD8 T Cell Generated through Arginine Deprivation to Activate Macrophage Cross-presentation and Improve Anti-Tumor Immunity [scRNA-Seq]

overall_design: We used 5-week-old BALB/c mice and randomly assigned them into a normal diet group and an arginine-deficient diet group based on body weight. The arginine-deficient diet was formulated to remove arginine while maintaining the same total caloric intake as the control diet. After one week of dietary pre-intervention, CT26 cells were subcutaneously inoculated to establish a colorectal cancer xenograft model. On day 20 after tumor implantation, mice were euthanized and tumor tissues were collected for single-cell RNA sequencing.


title: CD200+ CD8 T Cell Generated through Arginine Deprivation to Activate Macrophage Cross-presentation and Improve Anti-Tumor Immunity [ATAC-Seq]


title: Transcriptome analysis of 4T1 cells treated with CM-PEG-PLGA@DOX/R848 nanoparticles vs PBS control

city: xiamen

first: Zhiyuan

last: Chen

address: Xiamen, Fujian Province, China, 361000

institute: Xiamen University

summary: RNA-seq analysis of 4T1 murine breast cancer cells treated for 24 hours with CM-PEG-PLGA@DOX/R848 nanoparticles (equivalent DOX 2μg/ml) compared to PBS-treated controls. The study aims to identify transcriptomic changes induced by the nanomaterial treatment to to investigate the mechanism of anti-tumor action of CM-PEG-PLGA@DOX/R848 nanoparticles.

overall_design: 4T1 cells were divided into two groups: experimental group treated with CM-PEG-PLGA@DOX/R848 nanoparticles and control group treated with PBS. After 24 hours of treatment, cells were harvested for RNA extraction and sequencing.

first: Hongpeng

last: Duan

first: Xinyue

last: Wang

first: Shengmin

last: Zhang


title: Transcriptome analysis of RAW264.7 cells treated with CM-PEG-PLGA@DOX/R848 nanoparticles vs PBS control

summary: RNA-seq analysis of RAW264.7  cells treated for 24 hours with CM-PEG-PLGA@DOX/R848 nanoparticles (equivalent DOX 2μg/ml) compared to PBS-treated controls. The study aims to identify transcriptomic changes induced by the nanomaterial treatment to to investigate the mechanism of immunomodulatory activity of CM-PEG-PLGA@DOX/R848 nanoparticles.

overall_design: RAW264.7 cells were divided into two groups: experimental group treated with CM-PEG-PLGA@DOX/R848 nanoparticles and control group treated with PBS. After 24 hours of treatment, cells were harvested for RNA extraction and sequencing.


title: Multi-omics integrative approach of senescent endothelial cells and derived extracellular vesicles in a replicative senescence model [miRNA-seq]

city: Madrid

first: Fátima

middle: Milhano

last: Santos

address: Av. de los Reyes Católicos, 2 4 planta izquierda, Moncloa - Aravaca

country: Spain

institute: IIS-FJD

summary: Aging is a major unmodifiable risk factor for cardiovascular disease (CVD). Replicative endothelial senescence (RES), characterized by permanent cell-cycle arrest and a senescence-associated secretory phenotype (SASP), is a hallmark of vascular aging and contributes to endothelial dysfunction. However, RES molecular mechanisms, particularly the role of extracellular vesicles (EVs), remain poorly understood. To elucidate these mechanisms, an integrated multi-omics approach (proteomics, transcriptomics, and miRNA profiling) was used to characterize senescent endothelial cells (ECs) and their secreted EVs compared with early-passage counterparts. Senescent ECs and EVs displayed canonical senescence signatures, exhibiting enrichment of cell cycle, DNA damage response, p53 and NF-κB signaling, and SASP components, which are strongly linked to CVD.  Senescent EVs also showed a marked suppression of RNA metabolism, chromatin organization, and repair machinery, while carrying pro-inflammatory, adipogenic, and angiogenic mediators, reinforcing their role as vectors of secondary cellular senescence. Multi-omics integration revealed a coordinated regulatory network involving transcription factors (e.g., REST) and miRNAs. Angiogenic regulators miR-22-3p and miR-126-5p also emerged as RES mediators in both ECs and EVs, with miR-22-3p exhibiting compartment-specific regulation. Downregulation of key miRNAs (miR-335-3p, miR-590-3p, miR-29, and miR-17 families) promoted the derepression of downstream targets, driving endothelial phenotypic drift and dysfunction, primarily characterized by impaired PI3K–Akt signaling, maladaptive angiogenesis, and extracellular matrix remodeling. Our study provides a comprehensive map of RES-driven molecular alterations, identifying potential candidate biomarkers and therapeutic targets for age-related CVD. These findings also emphasize the role of EVs in propagating senescence and CVD risk, opening perspectives for EV-based interventions to counteract vascular aging.

overall_design: miRNA profiling of senescent and early-passage HUVECs and their respective secreted extracellular vesicles. Cells studied within passages 2–8 (early passage; PD <20) were regarded as early-passage endothelial cells (ECs), whereas those passaged 28–38 times (PD >96) were regarded as senescent ECs.

last: Milhano Santos

first: Rafael

last: Ramírez-Carracedo

first: Sergio

last: Ciordia

first: Laura

last: Clavaín

first: Juan

last: Pablo Hernández-Fonseca

first: Beatriz

last: Martín-Jouve

first: Guillermo

last: Bodega

last: Ramírez

first: Caridad

last: López-Granero

first: Marta

last: Ruiz-Ortega

first: Matilde

last: Alique


title: Multi-omics integrative approach of senescent endothelial cells and derived extracellular vesicles in a replicative senescence model [RNA-seq]

overall_design: RNA-seq (3'mRNA) profiling of senescent and early-passage HUVECs and their respective secreted extracellular vesicles. Cells studied within passages 2–8 (early passage; PD <20) were regarded as early-passage endothelial cells (ECs), whereas those passaged 28–38 times (PD >96) were regarded as senescent ECs.


title: Multi-omics integrative approach of senescent endothelial cells and derived extracellular vesicles in a replicative senescence model

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

overall_design: Refer to individual Series


title: Stable inheritance of the Streptomyces linear plasmid SCP1 by dual ParABS partition systems [ChIP-Seq]

last: McPhillips

summary: Low copy number plasmids must encode maintenance mechanisms, such as partitioning systems, to ensure that the plasmid is sustained through host generations. Plasmid partition systems segregate sister plasmid copies and are subdivided into different types based on the NTPase they encode. The characterisation and distribution of partition system types is well understood in Enterobacteriaceae plasmids. However, how these systems maintain plasmids and are distributed across wider bacterial diversity is poorly understood. We used the Streptomyces coelicolor A3(2) plasmid SCP1, which encodes two type Ia partition systems, as a model to investigate this. Sequence analysis of the SCP1 partition systems revealed that both ParB proteins contain less conserved CTP-binding pockets, suggesting one or both proteins may not behave like canonical ParB proteins. However, using a combination of chromatin immunoprecipitation with deep sequencing (ChIP-seq) we demonstrate that both the SCP1 ParB proteins, ParB1 and ParB2, bound to distinct parS sites on SCP1, and accumulate, or spread, on DNA approximately 20 kb away from their initial parS loading site. Together, our findings further our understanding of Streptomyces plasmid maintenance by providing the first functional characterisation of two type Ia partition systems coexisting on a single plasmid and offer new insights into the diversity and distribution of plasmid partition systems.

overall_design: ChIP-seq experiment to determine the DNA-binding sites of the ParB1 and ParB2 proteins of the linear plasmid SCP1 in its host, Streptomyces coelicolor A3(2). ParB1-3xFLAG and ParB2-3xFLAG were constructed by inserting 3x-FLAG tags at the 3' ends of the parB1 and parB2 genes at their native loci on the SCP1 plasmid, allowing for detection of the FLAG-tagged proteins under the production of their native promoters using the ReDirect gene editing method which inserts the tag and an apramycin resistance casette.Non-tagged alleles were included as negative controls. Two biological replicates were carried out per strain. Anti-FLAG agarose beads were used for the ChIP experiment.

last: Le


title: Signaling and mechanistic insights into folate binding protein induced cytotoxicity in KB cancer cells

city: Clayton

last: Perlaza-Jimenez

state: Victoria

address: 15 Innovation Walk

country: Australia

institute: Monash University

summary: To investigate the mechanism(s) underlying FBP-induced cytotoxicity and apoptosis in FR-overexpressing KB cancer cells, using next-generation sequencing (NGS), followed by bioinformatics analysis.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for KB cells treated with 50 µM FBP for 0, 6, 12, and 24 hours.

first: Hajar

last: Samadian

first: Mark

middle: M

last: Banaszak Holl

first: Jennifer

last: Dyson

first: Manuel

last: Rosa-Garrido

first: Rujula

last: Pradeep


title: Intestinal Stem and Progenitor Cells Exhibit Distinct Adaptive Responses to Inflammatory Stress in IBD

city: Nottingham

first: Brinda

last: Balasubramanian

address: University Park

institute: University of Nottingham

summary: Intestinal epithelial stem cells (SCs) and their transit-amplifying (TA) progeny are critical for mucosal repair and regeneration. However, their behaviour under chronic inflammatory conditions, such as those observed in Inflammatory Bowel Disease (IBD), remains incompletely understood. We investigated the impact of chronic inflammation on intestinal stem/progenitor cells by integrating bulk RNA sequencing from the largest IBD biopsy cohort to date with single-cell transcriptomic analysis and experimental assays using patient-derived intestinal organoids. Active inflammation was associated with a reduction in canonical LGR5⁺ intestinal stem cells and a concurrent expansion of OLFM4⁺ populations, consistent with an inflammation-induced epithelial repair program. Notably, SC/TA cells from both inflamed and non-inflamed IBD tissues exhibited persistent transcriptional changes that were distinct from those in healthy controls. Single-cell analysis identified transcriptionally heterogeneous SC/TA subpopulations, including a previously uncharacterized inflammation-associated cluster enriched in immune signalling pathways. Pseudotime trajectory analysis demonstrated a shift in differentiation toward deep crypt secretory (Paneth-like) cell lineages under inflammatory conditions. Chronic intestinal inflammation reshapes the epithelial stem/progenitor cell compartment, promoting altered differentiation and the emergence of immune-responsive epithelial states. These findings highlight the plasticity of the human intestinal epithelium in IBD and point to new avenues for therapeutic strategies aimed at maintaining epithelial integrity during chronic inflammation.

overall_design: RNA-seq profiling of patient derived organoids from healthy donors and IBD patients.

first: Balasubramanian

last: Brinda

first: Patel

last: Shivam

first: Ordonez-Moran

last: Paloma


title: YBX1 regulates cellular homeostasis to prevent inflammation

city: Galveston

first: Tania

middle: I

last: Strilets

address: 301 University Blvd

department: BMB

institute: University of Texas Medical Branch

summary: Tolerance of endogenous nucleic acids is crucial for cellular homeostasis and when perturbed can lead to immune dysregulation. RNA-binding proteins (RBPs) bind, modify and compartmentalize endogenous RNAs to prevent their recognition by the innate immune system. We discovered that loss of a highly abundant RBP, the cold shock domain containing Y-box binding protein 1 (YBX1), results in the spontaneous induction of an IL6/STAT3 inflammatory response and the upregulation of interferon-stimulated genes (ISGs).

overall_design: CRISPR Cas9 technology was used to generate hepatocellular carcinoma cell lines (Huh7) depleted of YBX1 protein. Partental (wildtype WT) Huh7 cells and two independently generated YBX1 KO clonal cell lines (YBX1 KO1, YBX1 KO3) were grown for two days in 10cm dishes before harvesting for RNA isolation and sequencing.

first: Sarah

middle: E

last: Dremel

first: Mariano

last: Garcia-Blanco


title: Gene expression profiling of human fibroblast MRC5 cells in response to RAF oncogene activation

city: Lyon

first: jean-michel

last: flaman

address: 28 rue Laennec

department: CRCL

country: France

institute: Inserm 1052

summary: Oncogene-induced senescence (OIS) is a well-known tumor-suppressive mechanism where normal cells undergo a permanent cell-cycle arrest in response to oncogene activation. Here we studied the early transcriptomic response to oncogene RAF activation in human normal fibroblasts (MRC5).

overall_design: MRC5 human fibroblasts were transduced with a RAF–estrogen receptor (RAF-ER) fusion construct, enabling conditional activation of RAF signaling upon treatment with 4-hydroxytamoxifen (4-OHT). Gene expression profiling was performed using Agilent microarray technology on RNA isolated from MRC5 RAF-ER cells one day after treatment with 4-OHT or control vehicle.

first: Jean-Michel Flaman

last: David Bernard


title: Directed Functional Reinnervation to Curb Nociception and Enable Sensation

first: Lillian

last: Zhu

state: Massachusetts

address: 150 Western Avenue

department: Bioengineering

institute: Harvard University

summary: Peripheral nerve injuries lead to diminished function and pain via nociplastic phenomena. We propose a new strategy called Directed Functional Reinnervation, in which nerves are reassigned to new peripheral targets with the goal of altering circuit function. Here, we redirect pure sensory nerves into skeletal muscle grafts to curb nociplasticity and provide benign or useful inputs for prosthetic applications. Electrophysiological characterization of the functional signaling capabilities demonstrated robust afferent responses to mechanical stimuli. Immunofluorescence staining of the saphenous nerve graft indicated widespread innervation of various synapses within the muscle. With immediate graft placement, the injured nerves’ dorsal root ganglia revealed comparable levels of nociceptive markers to uninjured nerves, suggesting a molecular basis for the prevention of pain sensitization. These findings support the use of skeletal muscle grafts for the alleviation of neuropathic pain and use as a sensory transmitter in conjunction with neural interfaces.

overall_design: RNA seq profiling of dorsal root ganglia, comparing expression levels in unoperated controls with those upstream of saphenous nerve and skeletal muscle grafts

first: Benjamin

last: Johnston

first: Vlad

last: Tereshenko

first: Joshua

last: Bernstock

first: Sabrina

last: Liu

first: Alexander

last: Madinger

first: Patrick

last: Pariseau

first: Arriyan

last: Dowlatshahi

first: Kyle

last: Eberlin

first: Shriya

last: Srinivasan


title: TCF3::HLF orchestrates an enhancer-promoter network with activation of MEF2C to promote an immature HSC gene expression program in leukemia.

city: Zürich

first: Valdemar

middle: Jacob Sven-Åke

last: Priebe

address: Lengghalde 5

country: Switzerland

institute: Kindersptal Zürich/University of Zurich

summary: Oncogenic fusion transcription factors (TFs) frequently drive hematopoietic malignancies by altering gene expression in key developmental programs. TCF3::HLF is a fusion TF that characterizes a rare, treatment-resistant subtype of B-cell acute lymphoblastic leukemia (t(17;19) TCF3::HLF-positive B-ALL). Despite its clinical significance, the mechanisms by which TCF3::HLF induces leukemia are unclear. We used HiChIP mapping and genetic interference to analyze TCF3::HLF at the 3D-genome level, revealing enhancer-promoter interactions that control gene activation or repression. Notably, TCF3::HLF directly regulates MEF2C expression through its enhancer, as interference disrupted MEF2C transcription and inhibited leukemia propagation. This disruption also diminished embryonal hematopoietic stem cell (HSC) gene signatures and restored mature HSC and B-lymphoid markers. These findings highlight MEF2C as a critical component of the transcriptional network reprogrammed by TCF3::HLF. Our study provides insight into how TCF3::HLF rewires the 3D genome to drive leukemia and serves as a resource for further exploration of the TCF3::HLF regulome.

overall_design:
To delineate the 3D-genomic interactions orchestrated by the fusion protein TCF3::HLF in t(17;19) ALL cells, we knocked out the  TCF3 wild-type allele, thereby enabling selective immunoprecipitation of the fusion protein when using antibodies against TCF3.  We compare the RNAseq expression profile for wild-type TCF3 knockout  HAL-01 with parental HAL-01 control samples to verify that no major changes occure. We included 697 with shSCR as an additional control representing the TCF3::PBX1 fusion protein.
Expression datasets for parental HAL-01 cells, TCF3-KO HAL-01 cells (TCF3_KO) and 697 cells with shSCR (X697) were used to generate PCA plots visualizing the variability among the cell lines.

first: Bartimée

last: Galvan


title: TCF3::HLF orchestrates an enhancer-promoter network with activation of MEF2C to promote an immature HSC gene expression program in leukemia

overall_design:
To delineate the 3D-genomic interactions orchestrated by the fusion protein TCF3::HLF in t(17;19) ALL cells, we knocked out the  TCF3 wild-type allele, thereby enabling selective immunoprecipitation of the fusion protein when using antibodies against TCF3. We compare the TCF3/TCF3::HLF DNA occupancy profiles of parental HAL-01 and wild-type TCF3 KO HAL-01.
Chromatin prepared from parental HAL-01 cells (TCF3_IP_Parental) and TCF3-KO HAL-01 cells (TCF3_IP_Knockout) was prepared for ChIP assay using E2A (CST #12258) antibody for pull-down.
ChIP-seq outputs were processed to generate bigwig files using bamCoverage from deepTools and call peaks using MACS2 to visualize the enrichment landscapes with the deepTools software.

first: Kaivalya

last: Walavalka


title: Hutchinson Gilford Progeria Syndrome alters the endothelial genetic response to laminar shear stress

city: Durham

first: Crystal

last: Kennedy

state: North Carolina

address: 101 Science Drive

department: Genetics and Genomics

institute: Duke University

summary: Hutchinson-Gilford Progeria Syndrome (HGPS) is a fatal, accelerated-aging disease caused by a mutation in the nuclear envelope protein Lamin A. The resulting mutant protein, progerin, accumulates on the nuclear envelope, causing nuclear blebbing, altered gene expression, and other cellular defects. The primary pathology of HGPS is atherosclerosis, leading to stroke or heart attack. Given that atherosclerosis begins with endothelial dysfunction in non-HGPS individuals, we examined whether the HGPS endothelium has an altered genetic response to shear stress, contributing to atherogenesis. We examined morphology and gene expression of HGPS and healthy iPSC-derived endothelial cells (viECs) after exposure to steady laminar shear stress (12 dynes/cm^2 for 24 hours) in a parallel-plate flow channel. We found that elongation in response to flow is impaired in HGPS viECs compared with healthy viECs. Differential expression (DE) analysis showed fewer significant differentially expressed genes and a lower magnitude of gene expression change after flow in HGPS compared with healthy viECs. Gene Set Enrichment Analysis identified differences in the gene sets altered by flow-induced DE, including Cholesterol Homeostasis, which was overrepresented in HGPS viECs. LGALS3, encoding the atherosclerosis marker galectin-3, was a main driver of this overrepresentation. RT-PCR confirmed LGALS3 as a shear-sensitive gene robustly upregulated in HGPS viECs compared with healthy viECs after flow. Treatment with an adenine base editor correcting the HGPS mutation restored LGALS3 expression to healthy levels. These observations indicate that HGPS ECs have an aberrant molecular response to atheroprotective shear stress, contributing to atherogenesis in HGPS patients.

overall_design: RNA sequencing of iPSC-derived endothelial cells after 24h shear stress at 12dynes/cm^2 and accompanying static controls. ECs are healthy or diseased (HGPS).

first: Jon

middle: L

last: Carter

first: George

last: Truskey


title: Dinutuximab beta effectively treats Ewing sarcoma when combined with chemotherapy

city: Rome

first: Probiomics

state: RM

address: via Montpellier 1

country: Italy

institute: Probiomics s.r.l

summary: Ewing sarcoma is a rare and aggressive cancer of the bone and soft tissues that mainly affects children and young adults. Despite intensive multimodal therapy, the prognosis of patients with metastatic or recurrent disease remains poor. Therefore, novel therapeutic approaches are needed to improve the outcomes of patients with Ewing sarcoma. The disialoganglioside GD2 is highly expressed on Ewing sarcoma cells, making this tumor eligible for treatment with Dinutuximab beta, a monoclonal antibody targeting this antigen.  Through in vitro and in vivo approaches, this study demonstrated that Dinutuximab beta effectively suppressed tumor growth by 60% (p=0.0135 vs vehicle) and improved survival rate by 68% (p=0.0006 vs vehicle) in a mouse model xenograft. The combination therapy with doxorubicin demonstrated superior efficacy compared to monotherapy, with enhanced tumor suppression (86%; p=0.0009 vs vehicle) and an extension of survival rate (146%; p=0.000025 vs vehicle). Overall, this study showed that Dinutuximab beta is effective against Ewing sarcoma, especially in combination with the standard induction chemotherapy regimen for this tumor. Integrating Dinutuximab beta into the standard chemotherapy regimen for Ewing sarcoma offers a promising new therapeutic approach that can potentially improve the prognosis for patients with high-risk disease, offering a more effective alternative to existing treatments.

overall_design: Human Ewing Sarcoma derived cells were subcutaneously injected into athymic nude mice. Animals were treated with either vehicle or Dinutuximab beta for 5 conscutive days. At day 5 (T1) and 11 (T2) tumor were collected and analysed. 4 tumors for each experimental group were analysed.

first: Roberta

last: Frapolli

first: Marina

last: Meroni

first: Ezia

last: Bello

first: Valentina

last: Kebede

first: Matteo

last: Malinverno


title: Dual-antigen Doggybone DNA vaccine induces potent anti-tumour immunity against immunosuppressive oral cancer

city: Liverpool

first: Grace

last: Tan

address: 6 West Derby Street

department: MCCM

institute: University of Liverpool

summary: Immunotherapy has demonstrated durable responses in a subset of patients with head and neck cancer, offering potential survival benefits to those with poor prognoses and resistance to first-line treatments. Despite this, only a modest 15-20% are shown to respond. Cancer vaccines have recently demonstrated efficacy in some solid tumours including melanoma, as well as immune-cold pancreatic and liver cancer, inducing a cytotoxic T cell response and eradicating cancer cells. Our previous research identified cancer testis antigens MAGED4B and FJX1 as highly immunogenic and overexpressed in the majority of HPV-independent head-and-neck squamous cell carcinoma (HPVnegHNSCC) patients. In this study, we developed a novel DNA vaccine utilising the non-plasmid doggyboneTM (dbDNATM) platform to deliver these antigens for targeting head and neck cancer. A series of doggyboneTM vaccine prototypes targeting MAGED4B and FJX1 were generated both to optimise the backbone and to present antigens in an immunogenic form. Vaccine immunogenicity and cytotoxicity were accessed using interferon-gamma. Enzyme-Linked Immunospot (ELISpot) assay. Vaccine efficacy was evaluated in the MOC-2 oral cancer model through tumour monitoring, assessing the infiltration of CD4+, CD8+ and regulatory T cells by immunohistochemistry as well as RNAseq analysis. The optimised dual antigen dbDNA DNA vaccine significantly reduced tumour size. Furthermore, combining the vaccine with anti-PD1 therapy significantly delayed tumour growth and metastasis, thereby enhancing survival in tumour-bearing mice. Vaccination resulted in significant recruitment of CD4+ and CD8+ T cells but not regulatory T cells. IHC analysis also confirmed the ability of dbDNA™ vaccine TGL-100 OPT in shifting M2 to M1 polarisation, highlighting their therapeutic promise. Transcriptomic analysis of immune cells in the tumour indicates that vaccination promotes long term anti-tumour responses by upregulating memory T cell genes T cell factor-7 (Tcf7) and lymphoid enhancer binding factor 1 (Lef1) while suppressing PDL-1 and inhibiting anti-inflammatory cytokines such as IL-10 and IL-27. These findings suggest that our cancer vaccine effectively recruits cytotoxic T cells to immune cold tumours, minimising the host’s immune inhibitory mechanisms within the tumour and resulting in long-term protection against head and neck cancer.

overall_design: RNAseq data of CD45+TILs isolated from MOC-2 tumours. Treatment group included control mice and vaccinated mice, isolated day 15 and day 30 post vaccination

first: Natalia

last: Savelyeva

first: Chuan

last: Wang

first: Martina

last: Meschis

first: Christian

last: Ottensmeier


title: The transcription factor OsWRKY36 regulates lamina joint development and the leaf angle in rice by modulating brassinosteroid signalling [DAP-seq]

city: Kunming

first: Lirong

last: Zhao

state: Yunnan

address: No.88 Xuefu Road

department: Xishuangbanna Tropical Botanical Garden

institute: Chinese Academy of Sciences

summary: WRKY transcription factors constitute a crucial protein superfamily that plays a vital role in orchestrating diverse responses to environmental stimuli in plants. Although considerable research has been conducted on the stress resistance mechanisms associated with WRKYs, little is known about the roles of WRKYs in regulating plant growth and development. Here, we identified a key regulator of the rice leaf angle and plant architecture, OsWRKY36, from a rice oswrky mutant library. OsWRKY36 is highly expressed in the leaf lamina joint and promotes cell growth and expansion in adaxial parenchyma cells, leading to a greater leaf angle. A mechanistic investigation revealed that OsPUB24, an E3 ubiquitin ligase that is inhibited by brassinosteroid (BR), interacts with and facilitates the ubiquitination and degradation of OsWRKY36. Genetic evidence indicated that OsWRKY36 acts downstream of OsPUB24 to regulate the BR-induced increase in the leaf angle. Furthermore, OsWRKY36 physically interacts with DLT, a positive regulator of BR, and cooperatively activates the expression of the BR response gene OsBZR4. Thus, BR facilitates the degradation of OsPUB24, leading to enhanced stability of the OsWRKY36 protein. Consequently, a substantial quantity of OsWRKY36 interacts with DLT, thereby inducing the expression of OsBZR4 and ultimately exerting a positive regulatory effect on BR-induced leaf inclination. Collectively, our findings reveal the mechanism underlying the regulation of leaf inclination and plant architecture by the BR-OsPUB24-OsWRKY36 and DLT-OsWRKY36-OsBZR4 modules and thus provide an innovative strategy for optimizing crop production by manipulating the BR signalling pathway.

overall_design: To identify the downstream target genes bound by the transcription factor OsWRKY36 in rice, we conducted a DNA affinity purification sequencing (DAP-seq) assay. The MBP-OsWRKY36 protein was synthesized in vitro, and a genomic DNA library (200~800 bp) derived from Nipponbare (Oryza sativa japonica variety) was used for the DNA affinity purification assay. MBP  was used as a negative control.

first: Shidie

last: Chen

first: Houping

first: Diqiu

last: Yu


title: Splicing variants in MYRF cause partial loss of function in the retinal pigment epithelium

city: Ann Arbor

first: Lev

last: Prasov

address: 1241 Catherine Street, 5704 Med Sci II

department: Department of Human Genetics

institute: University of Michigan

summary: Improper light focus on the retina, refractive error, is primarily caused by eye size differences and is the leading cause of vision loss worldwide. C-terminal variants in the Myelin Regulatory Factor (MYRF) gene, a retinal pigment epithelium (RPE)-derived transcription factor, lead to isolated nanophthalmos characterized by a small, though structurally sound eye. However, other MYRF loss-of-function variants cause syndromic disease. To address this discrepancy, in vitro and animal studies were performed on a pathogenic C-terminal variant dG-MYRF (p.Gly1126fs30*, c.3376-1G>A ). Human RPE-cells or primary RPE transduced with dG-MYRF showed reduced target gene expression, with decreased steady-state levels of the C-terminal cleavage product, but normal cleavage and localization. A homozygous humanized MYRF C-terminal mouse model (MyrfhumdG/humdG) was embryonic lethal by embryonic day (E) 18.5, while wildtype (MyrfhumWT/humWT) mice were viable. Single-cell RNA-seq from E17.5 MyrfhumdG/humdG and knockout RxCre;Myrffl/fl (E15.5 and P0) mice revealed shared differentially expressed genes, with decreased effect size in the MyrfhumdG/humdG  eyes. These findings support dG-MYRF as a hypomorphic allele. Additionally, two novel MYRF splicing variants creating nonfunctional isoforms were found in families with isolated nanophthalmos. Overall, hypomorphic MYRF alleles underlie isolated nanophthalmos, supporting a tissue-specific threshold effect and highlighting unique roles for the MYRF C-terminus in the RPE.

overall_design: Eyes were collected from e17.5 litters, the cornea, lens, and optic nerve were removed. Three MyrfhumWT/humWT and three MyrfhumdG/humdG samples were pooled for each time point, dissociated, and scRNAseq was performed.

first: Gabrielle

last: Rozumek

first: Michelle

last: Brinkmeier

first: SuQing

first: Ford

last: Hannum


title: The transcription factor OsWRKY36 regulates lamina joint development and the leaf angle in rice by modulating brassinosteroid signalling [ChIP-Seq]

overall_design: To identify the downstream target genes bound by the transcription factor OsWRKY36 in rice, we conducted a chromatin immunoprecipitation sequencing (ChIP-seq) assay. The shoot tissues obtained from 10-day 35S:OsWRKY36-Myc seedlings were subjected to ChIP. The samples were harvested, cross-linked with 1% (v/v) formaldehyde under vacuum for 30 minutes and subsequently treated with 0.125 M glycine to terminate the crosslinking process. The tissues were ground into fine powder using liquid nitrogen, and the chromatin was subsequently isolated and sheared into 200–1000-bp fragments by sonication. The ChIP assay was performed using the EpiQuik™ Plant ChIP Kit (EpigenTek) according to the manufacturer’s recommended protocol. The chromatin complex was immunoprecipitated using an anti-Myc antibody.

first: Yunwei

last: Liu


title: Combining Spironolactone to Antiretroviral Therapy Accelerates HIV Decay in Humanized Mice

city: Jupiter

first: Susana

middle: T

last: Valente

state: FL

address: 130 Scripps Way

department: Immunology and Microbiology

institute: The Herbert Wertheim UF Scripps Institute for Biomedical Innovation & Technology

summary: Spironolactone (SP), a clinically used aldosterone antagonist, has been explored as an anti-HIV agent in models of HIV-1 latency for inducing transcriptional silencing of the viral reservoir. SP promotes the degradation of xeroderma pigmentosum group B (XPB) protein, a crucial component of transcription factor II H (TFIIH) required  for RNA polymerase II transcriptional initiation. This study evaluated the impact of a long-acting formulation of SP on HIV replication within the context of antiretroviral therapy (ART) in the humanized mice model of HIV infection. The findings demonstrate that adding SP to ART accelerates viral decline and reduces expression of inflammation-related genes in human immune cells - genes often upregulated in chronic viral infections. Although SP treatment did not alter levels of cell-associated viral DNA, it led to a significant 4.4-fold decrease in systemic cell-associated viral RNA. This supports the role of XPB in HIV transcriptional regulation and advocates for incorporating transcriptional inhibitors like SP into primary HIV therapy. Additionally, SP treatment diminished markers of immune activation and inflammation, critical factors contributing to morbidity and mortality in individuals with chronic HIV infection. These results highlight SP’s potential to enhance HIV treatment by mitigating key aspects of viral persistence and associated immune challenges.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: A comparative RNA-seq analysis of mononuclear cells (MNCs) isolated from the liver, lung, spleen and lymph nodes of BLT humanized mice that were infected with HIV and then treated with ART or ART + Spironolactone (200 mg long-acting subcutaneous pellets) for 35 days. We compared gene expression of samples treated with ART alone or with the combination of ART + SP.

first: Lijun

last: Ling

first: Luisa

middle: P

last: Mori

first: Victor

last: Garcia-Martinez


title: Sulforaphane Inhibits Colorectal Cancer Progression via PI3K/AKT/mTOR and HIF-1α Suppression with Enhanced Efficacy under Hypoxia

city: Jinan

first: Jinshen

state: Shandong Province

address: Jingwu Weiqi Road, Huaiyin District, Jinan 250021, Shandong, China.

department: Department of Gastrointestinal Surgery

institute: Shandong Provincial Hospital Affiliated to Shandong First Medical University

summary: Sulforaphane (SFN) exhibits anticancer activity across diverse tumor models, yet its role under hypoxia—a hallmark of the colorectal cancer microenvironment—remains incompletely defined. In this study, colorectal cancer cells were cultured under hypoxic conditions and treated with SFN or a combination of SFN and 5-fluorouracil (5-FU). RNA-seq profiling was performed to characterize transcriptional alterations associated with SFN activity and SFN-mediated reversal of hypoxia-induced 5-FU resistance. The dataset includes paired-end raw FASTQ files, supporting further investigation into hypoxia-related signaling networks, including PI3K/AKT/mTOR and HIF-1α pathways.

overall_design: This study includes three groups of colorectal cancer cells cultured under hypoxia: (1) hypoxia control, (2) hypoxia + sulforaphane (SFN), and (3) hypoxia + SFN + 5-fluorouracil (5-FU). Each group contains three biological replicates. Total RNA was extracted after 48 h of treatment and sequenced using Illumina paired-end RNA-seq. Raw FASTQ files and corresponding md5 checksum files are provided.

first: Yuxuan

last: Yan

first: Haining

last: Hao

first: Zexin

first: Litao

last: Tian

first: Pingxiang

first: Yutao


title: Transcriptomic profiling of human saphenous veins during ex vivo culture–induced neointima proliferation

city: Augusta

first: David

middle: S

last: Kim

department: Vascular Biology Center

institute: Augusta University

summary: Vein graft failure is a major limitation of coronary and peripheral bypass surgery, driven by neointima proliferation and smooth muscle cell (SMC) phenotypic modulation. To investigate the early molecular events underlying this process, we cultured segments of human saphenous veins ex vivo for seven days. Bulk RNA sequencing and 10x Visium spatial transcriptomics  were performed on paired fresh (Day 0) and cultured (Day 7) samples. Differential gene expression analysis revealed significant downregulation of contractile SMC markers and cytoskeletal genes, and upregulation of extracellular matrix (ECM), inflammatory, and stress-response pathways. Integration of both datasets highlighted coordinated suppression of SMC contractile phenotype and activation of matrix remodeling programs, consistent with early neointima development. These results provide a multi-omics resource defining molecular transitions that drive human vein graft remodeling.

overall_design: Bulk RNA-seq profiling was performed on paired segments of human saphenous veins cultured ex vivo under serum-enriched conditions for 7 days (Day 7) compared with freshly isolated segments (Day 0).

first: Vy

last: Ong

first: Jiang

last: Zhou

first: Yang

last: Shi

first: Austin

last: Chang

first: Neal

last: Weintraub


title: Ecdysone Receptor autonomously controls germ cell differentiation in the Drosophila ovary

city: Greenville

first: Weihua

last: Huang

address: 600 Moye Blvd, Brody 7S-24

institute: East Carolina University

summary: In the Drosophila ovary, the steroid hormone ecdysone controls germline stem cell (GSC) maintenance and germ cell differentiation. Prior studies demonstrated that ecdysone regulates germ cell differentiation non-autonomously via the nuclear receptor Ecdysone Receptor (EcR) in ovarian somatic cells. Although EcR is also expressed in GSCs and their differentiating daughters, potential direct roles for EcR in GSCs independent of the soma have not been examined. Here, we demonstrate that EcR functions autonomously in GSCs and cystoblasts to control germline differentiation. While depletion of EcR from GSCs mildly reduces GSC self-renewal, over-expression of EcR specifically in GSCs and cystoblasts impedes germ cell differentiation, phenotypically resembling bag of marbles loss-of-function and Bone Morphogenetic Protein signaling constitutive activation. We propose that while low levels of EcR are essential to maintain GSC self-renewal and permit initial differentiation, higher levels of EcR accumulate in differentiated germ cells to promote transcription of maternal genes, providing temporal control over germline differentiation. These data support the model that stem cells harbor unique mechanisms to integrate signals from multiple cell sources that safeguard their self-renewal in response to local and physiological cues.

overall_design: Adult female ovaries (100 pairs) of each genotype were dissected and dissociated by the protocol of Slaidina et al Lehmann (2021). Libraries were constructed using 10X Genomics Chromium single cell 3' V3 kit according to manufacturer's protocol. Sequencing of pooled libraries performed on Illumina NextSeq 2000.

first: Elizabeth

last: Ables


title: Cisplatin and osimertinib treatment of M0-polarized THP-1 cells

city: Gangnam-gu

first: Yoon Soo

state: Seoul

address: #413 63-gil 20 Eonju-ro

department: Internal Medicine

country: South Korea

institute: Yonsei University College of Medicine

summary:
This series examines gene expression changes induced by cisplatin and osimertinib in M0-polarized THP-1 monocytic cells. M0 THP-1 cells were treated with vehicle, 0.5 μM cisplatin, or 100 nM osimertinib for 16 hours, and total RNA from three independent biological replicates per condition was profiled using the GeneChip Human Gene 2.0 ST Array.
The goal of the study is to identify differentially expressed genes and pathways regulated by cisplatin and osimertinib in innate immune cells and to explore how these agents modulate inflammatory and immunoregulatory responses.

overall_design: Human THP-1 monocytic cells were differentiated to an M0 macrophage-like state and divided into three treatment groups: vehicle control, cisplatin (0.5 μM), and osimertinib (100 nM). Each condition was represented by three independent biological replicates (total n = 9 arrays). Total RNA from each replicate was isolated and hybridized individually to Affymetrix GeneChip Human Gene 2.0 ST Arrays (platform GPL16686). Raw CEL files were processed by the service provider using standard Affymetrix pipelines, and gene-level summarized expression values were used for downstream differential expression analysis.


title: Effect of Recombinant ApoE on Gene Expression During Osteoblast Differentiation of Mouse Bone Marrow Stromal Cells (BMSCs)

first: Gurpreet

last: Baht

address: 300 North Duke Street

department: Orthopaedic

summary: Advanced age impairs bone fracture healing; however, the underlying mechanisms remain unclear. We found that circulating levels of apolipoprotein E (ApoE) increase with age and contribute to impaired fracture healing. In vitro, ApoE treatment of aged bone marrow stromal cells (BMSCs) inhibited osteoblast differentiation. To investigate the mechanism by which ApoE inhibits osteoblast differentiation, we treated primary BMSCs isolated from the femurs and tibiae of 24-month-old C57BL6/J mice with recombinant ApoE.  For osteoblast differentiation, BMSCs were cultured in osteogenic medium. Recombinant ApoE (rApoE) was added at a concentration of 100 ng/mL starting two days after induction of differentiation and continued throughout the 10-day differentiation period. BMSCs treated with vehicle or rApoE were harvested on day 10. Total RNA was extracted using TRIzol Reagent (Invitrogen) according to the manufacturer’s protocol for downstream transcriptomic analysis.

overall_design: RNA-seq profiling of bone marrow stromal cells (BMSCs) derived from 24-month-old wild-type (C57BL/6) mice during osteoblast differentiation. After 2 days of differentiation, cells were treated with either vehicle (n = 3) or recombinant ApoE (n = 3) for 8 additional days (total 10 days of differentiation) before RNA extraction and sequencing.

first: Mingjian

first: Abhinav

middle: R

last: Balu

first: Kristin

middle: H

last: Molitoris

first: Akshay

last: Bareja


title: Precision nanotherapy remodels the tumor-associated macrophage to reverse immunnosuppressive in pancreatic cancer.

city: Hsinchu

first: Hsin mei

last: Lee

address: Guangfu Rd.

country: Taiwan

institute: National Tsing Hua University

summary: Pancreatic ductal adenocarcinoma (PDAC) is characterized by an immunosuppressive stroma rich in tumor-associated macrophages (TAMs) that limit the therapeutic efficacy. We introduce a TAM-targeted nanotherapy platform that selectively delivers either a CSF1R inhibitor or the STING agonist cGAMP to immunosuppressive TAMs. While CSF1R inhibitor–loaded nanoparticles efficiently depleted TAMs and produced moderate antitumor effects, TAM-targeted cGAMP nanoparticles reprogrammed TAMs into immune-stimulating effectors. This reprogramming normalized aberrant vasculature, alleviated desmoplasia, and enhanced infiltration and activation of cytotoxic immune cells. In combination with gemcitabine, PD-1 checkpoint blockade, or CAR-NK cell therapy, TAM-targeted STING activation provided an in situ immunostimulatory signal that markedly improved antitumor efficacy in preclinical PDAC models. Ex vivo efficacy in human PDAC tissues and a favorable safety profile show the translational potential of this TAM-targeted nanotherapy to overcome the immune desert of PDAC.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for murine PDAC tumors with or without treatment of TAM-cGAMPnp

first: Yunching

last: Chen

first: Hsin-Mei


title: Transcript-wide m6A methylation affects the cap-independent translation initiation [Ribo-seq]

city: Pushchino

first: Ivan

middle: V

last: Kulakovskiy

address: Institutskaya 4

country: Russia

institute: Institute of Protein Research

summary: In this study, we generated transcriptome (RNA-Seq) and translatome (Ribo-Seq) profiles from the wild-type HEK293T cells and HEK293T cells with knockdown of METTL3 and METTL14 (HEK293T KD), cultivated in normal conditions or under Torin1 treatment. The data were produced to explore the effect of m6A methylation on cap-dependent translation.

overall_design: We established HEK293T with a double METTL3/14 knockdown (HEK293T KD) using the siRNA approach. RNA-Seq and Ribo-Seq data were collected from HEK293T and HEK293T KD cells, treated with either DMSO (control) or Torin1 (250 nM) for 2 hours.

first: Dmitry

middle: N

last: Lyabin

first: Irina

middle: A

last: Eliseeva

first: Andrey

last: Buyan

first: Egor

last: Smolin


title: Transcript-wide m6A methylation affects the cap-independent translation initiation [RNA-seq]


title: The Histone Methyltransferase KMT2D is a Critical Mediator of Lineage Plasticity and Therapeutic Response in Castration Resistant Prostate Cancer [H3K4me1 CUT&RUN]

city: Baltimore

first: Yangzhenyu

last: Gao

state: MD

address: 2917 Saint Paul

department: Oncology

institute: johns hopkins university

summary: Castration-resistant prostate cancer (CRPC) is largely dependent on the androgen receptor (AR) for growth and often exhibits hyperactive PI3K signaling, most frequently due to PTEN loss. Therapeutic pressure from anti-AR therapies can induce trans-differentiation toward an AR-independent phenotype. Recently, different subtypes of AR-independent CRPC have been redefined, with the stem cell-like (SCL) subtype emerging as one of the most prevalent. Elucidation of the epigenetic mechanisms controlling the maintenance of these distinct CRPC cell states could pave the way for effective combinatorial therapies for CRPC. In this study, we identified a key role for the histone methyltransferase KMT2D in establishing the chromatin competence necessary for the recruitment of AR and FOXA1 transcription factors (TFs) that are essential for the AR transcriptional output in AR-dependent CRPC cell lines, patient derived organoids, and patient samples. Unexpectedly, KMT2D maintained the identity of the AR-low CRPC-SCL subtype and controlled activity of AP-1 TFs such as FOSL1, which acts as a master regulator of this subtype. Single cell transcriptomics and chromatin assays underscored the role of KMT2D in sustaining a mixed lineage cell state via AP-1 and FOXA1. The combined suppression of PI3K/AKT and KMT2D reduced cell proliferation in prostate cancer cells and patient-derived organoids in both CRPC-AR and CRPC-SCL subtypes. Altogether, these results unveil KMT2D as a major mediator of the epigenetic landscape in subtype-specific CRPC, contributing to tumor growth and therapeutic response.

overall_design: H3K4me1 CUT&RUN was performed in LNCaP AR-high cells with doxycycline-inducible knockdown of KMT2D

first: Eneda

last: Toska

first: Wouter

last: Karthaus

first: Srushti

last: Kittane

first: Erik

last: Ladewig

first: Taibo

last: Li


title: The ErbB3 receptor tyrosine kinase regulates small intestinal barrier function and expression of the tight junctional protein Pmp22

city: Los Angeles

first: Jonathan

middle: Jay

last: Hsieh

address: 4650 Sunset Blvd

institute: Children's Hospital Los Angeles

summary: We tested the role of ErbB3 in small intestinal permeability. Loss of ErbB3 in the intestinal epithelium results in increased intestinal permeability and reduced expression of Pmp22. Permeability induced by LPS can be reduced by administration of the ErbB3 ligand Nrg1.

overall_design: Bulk RNA sequencing of ileal mucosal scrapings from ErbB3-FF and ErbB3-dIE mice at baseline.

middle: J

first: Mark

last: Frey


title: The Histone Methyltransferase KMT2D is a Critical Mediator of Lineage Plasticity and Therapeutic Response in Castration Resistant Prostate Cancer [FOSL1 ChIP-Seq]

overall_design: FOSL1 ChIP-Seq was performed in DU145 AR-neg prostate cancer cells with doxycycline-inducible knockdown of KMT2D


title: Global Transcriptomic Shifts in Mitochondrial DNA-Depleted Neuronal Cells Reveal Alzheimer's Disease-Related Pathway Changes

city: Fairway

first: Russell

last: Swerdlow

state: KS

address: 4350 Shawnee Mission Parkway

institute: University of Kansas Alzheimer's Disease Center

summary: Background: Mitochondrial dysfunction, a prominent feature of Alzheimer’s disease (AD), could represent a cause or consequence of the disease. Objective: We determined the extent to which mitochondrial dysfunction due to mitochondrial DNA (mtDNA) depletion induces transcription changes that link to AD phenomena. Methods: We performed a transcriptomic survey of human neuronal SH SY5Y and NTERA 2/NT2 mtDNA-depleted (ρ0) and intact (ρ+) cell lines. Differentially expressed genes (DEGs) between SH-SY5Y or NT2 ρ0 and ρ+ cells were identified using edgeR, and we used the Equivalent Change Index (ECI) approach to quantify concordant DEG behavior across the cell lines. Gene set enrichment and over representation analysis (GSEA; ORA) were used to determine impact on the KEGG Alzheimer’s and other neurodegenerative disease pathways, ascertain pathway and term enrichment in the Reactome and Gene Ontology databases, and generate activation z-scores in the Ingenuity Pathway Analysis (IPA) database. Results: Relative to their ρ+ comparators, ρ0 lines differentially expressed >75% of their genes, and >20% more than doubled or halved expression. The KEGG Alzheimer’s pathway was significantly enriched, and ECI-identified genes ranked the Alzheimer’s, Parkinson’s, ALS, and Huntington’s KEGG pathways among the most enriched gene sets. There was broad enrichment of pathways and terms relating to AD phenomena, which reflected lipid, insulin signaling, inflammation/immune response, synapse, endosome/endocytosis, RNA, and proteostasis biology. Conclusion: In neuronal cell lines, mitochondrial dysfunction due to mtDNA depletion alters gene expression in ways that recapitulate or predictably promote AD molecular phenomena.

overall_design: RNA-seq profiling of SY5Y and NT2 cell lines with and without mitochondrial depletion

first: Blaise

middle: W

last: Menta

first: Emily

last: Schueddig

first: Amol

last: Ranjan

first: Yanming

first: Heather

last: Wilkins

first: Dong

last: Pei


title: Multimodal integration of epigenetics, spatial transcriptomics and immune microenvironment in sacral chordoma

city: Philadelphia

first: Yee Hoon

last: Foong

state: PA

address: 3400 Civic Center Blvd

institute: University of Pennsylvania

type: Methylation profiling by genome tiling array

summary: Multimodal study elucidated the complex epigenetic and immunological landscape in sacral chordomas

overall_design: Bisulfite converted DNAs from 29 sacral chordoma tissues  were analyzed on Illumina EPIC platforms (21 on EPICv1 and 8 on EPICv2)

first: Yee

first: George

last: Jour

first: Garima

last: Sinha

first: Jamal

last: Benhamida

first: Nathan

last: Aleynick

first: Yanyun

first: Travis

last: Hollmann

first: Mrinal

last: Gounder

first: Rohan

last: Sardana

first: Carla

last: Saoud

first: Max

last: Vaynrub

first: Patrick

last: Boland

first: Rami

last: Vanguri

first: Meera

last: Hameed


title: Transcriptomic profiling of ARMCX3 knockdown reveals activation of p53–IFIH1 axis and immune pathways in breast cancer cellsbreast cancer.

city: 成都

first: jiandong

last: wang

state: 四川

address: 新都大道

department: 生命科学学院

institute: 成都医学院

summary: ARMCX3 has been implicated in the regulation of mitochondrial dynamics and cancer progression. To investigate its role in breast cancer, we performed RNA-seq following lentiviral-mediated ARMCX3 knockdown in MCF-7 and MDA-MB-231 cell lines, compared to negative controls. The resulting transcriptomic profiles revealed changes in p53 signaling and immune-related pathways, providing insights into the molecular functions of ARMCX3 in breast cancer.

overall_design: Breast cancer cell lines MCF-7 and MDA-MB-231 were transduced with lentiviral vectors carrying either ARMCX3-specific shRNA (shARMCX3) or non-targeting control (NC). RNA was extracted from three biological replicates per group (total of 12 samples) and subjected to paired-end 150 bp RNA-seq on an Illumina NovaSeq 6000 platform. Differential expression analysis was conducted to identify ARMCX3-regulated pathways.

first: Jiandong

last: Wang

first: Haixiang

last: Ma

first: Hong

last: Zhang

first: Xinyan

last: Deng


title: Synthetic oleanane triterpenoids reduce tumor growth and promote an anti-tumor immune response independent of cancer KEAP1-mutational status

city: Indianapolis

first: Ana

last: Leal

state: IN

address: 980 W Walnut St

department: Department of Medicine

institute: Indiana University

summary: KEAP1 negatively regulates the cytoprotective factor NRF2 and is commonly inactivated in lung cancer cells. Loss of function KEAP1 mutations in cancer cells contribute to NRF2 activation and tumor immune evasion through immunosuppression and drug resistance. Counterintuitively, treatment with synthetic oleanane triterpenoids, potent NRF2 activa-tors, reduces preclinical tumor burden. This suggests the functional target of these drugs in cancer models is not the cancer cells but another tumor immune microenvironment (TIME) cell population. The anti-tumor potential of cells within the TIME, particularly macrophages, is potentiated by triterpenoid treatment in cancers with wild-type KEAP1 status. As KEAP1-mutant cancers show reduced tumor immune responses, triterpenoid-mediated immune stimulation may particularly benefit these cases, but this has not been investigated. To characterize the immunomodulatory effects of triterpenoids in KEAP1-mutant lung cancer, we studied tumor-educated bone marrow-derived macrophages (TE-BMDMs) and lung cancer models treated with the triterpenoids CDDO-Me or omaveloxolone. RNA-sequencing of TE-BMDMs cultured in KEAP1 KO compared to WT cancer-conditioned media had enhanced tumor-promoting phenotypes which reversed with CDDO-Me treatment. Similarly, subcutaneous KEAP1 KO tumors were larger and more immune-suppressed compared to WT tumors. Both CDDO-Me and omaveloxolone reduced tumor burden and improved immune cell phenotypes within the TIME, independent of KEAP1 mutational status.

overall_design: RNA sequencing of bone marrow-derived macrophages treated for 24 hours with cancer conditioned media and 100nM CDDO-Me or vehicle control. Conditioned media was generated from LL2 cancer cells possessing different KEAP1 pathway mutations (WT, KEAP1 KO, and NRF2 KO).

first: Christopher

last: Occhiuto

first: Jessica

last: Moerland

first: Karen

last: Liby


title: Gene expression of Foxp3+CD8+ Tregs induced with or without laminin α5

first: yang

last: song

address: HSF-3, 3rd Floor; 670 W Baltimore St.

department: Department: Institute for Genome Sciences

institute: University of Maryland in Baltimore

summary: Foxp3+CD8+ regulatory T cells (CD8 Tregs) help to establish immune tolerance in models of chronic inflammation and antigen stimulation, such as graft versus host disease and chronic infections. However, the elements contributing to CD8 Treg induction remain obscure. In this study, we found that laminin α5 enhanced CD8 Treg inducation from mouse naive T cells stimulated with a combination of anit-CD3/anti-CD28/IL-2/TGFβ. While, the suppressive ability of CD8 Tregs induced with laminin α5 was reduced by 23.8% compared to these induced without laminin α5; the cytotoxic ability of CD8 Tregs induced with laminin α5 was significant reduced (more than 64%) compared to these induced without laminin α5. Mechanistically, laminin α5 was invovled in modulating both TCR signaling and cytokine responses during induction of CD8 Tregs. Laminin α5 inihbited IFNg and TNFa expression by CD8 T cells, which further enhanced Foxp3+CD8+ Treg induction. Laminin α5-Itga6 enhanced TCR signaling by promoting activation of the LAT/Zap70/PLCγ1 pathways.

overall_design: sorted Foxp3-eGFP CD8+, Foxp3-eGFP CD4+ cells induced with or without laminin α5 in vitro at day 3.

first: Shunqun

last: Luo

first: Jonathan

last: Bromberg


title: Conditional Fibroblast BCL-2 Expression Promotes Persistent Pulmonary Fibrosis, which is Reversible by Therapeutic BCL-2 Inhibition

city: Denver

first: Elizabeth

last: Redente

state: CO

address: 1400 Jackson Street

department: Pediatrics

institute: National Jewish Health

summary: Idiopathic pulmonary fibrosis (IPF) is a progressive, fatal lung disease that develops in response to chronic epithelial injury. Unlike homeostatic lung repair and regeneration following injury, the lungs of IPF patients accumulate apoptosis-resistant, pro-fibrotic, extracellular matrix producing fibroblasts. It has been 10 years since the introduction of two FDA-approved, though relatively ineffective, therapies. Thus, there is a dire need for mechanistic investigations to enable new therapeutics to enter clinical trails. Here, using the normally resolving model of bleomycin-induced lung injury and newly engineered mice that express human BCL-2 in PDGFRa+ alveolar fibroblasts along with studies in IPF lung tissues, we show that BCL-2 blocks fibroblast apoptosis, which is crucial for lung regeneration. This inhibition leads to the emergence of senescent, pro-fibrotic fibroblasts along with persistent, pathologic, fibrotic lung remodeling. Conversely, selective BCL-2 inhibition with ABT-199 (VenetoclaxTM) in fibrotic mice re-engaged the apoptotic pathway, reduced senescence, caused fibroblast elimination, and promoted fibrosis resolution and lung regeneration. Our findings suggest that sustained BCL-2 expression in fibroblasts prevents homeostatic lung repair, drives persistent fibrosis and is a therapeutically relevant target to reverse persistent pulmonary fibrosis.

overall_design: Naive, 3wk bleomycin hBcl2, 3wk bleomycin Wild Type/CO, 6wk bleomycin hBcl2, 6wk bleomtcin Wild Type/CO

middle: F

first: Tengyao

last: Song

first: Nomin

last: Javkhlan

first: Benjamin

last: Edelman

first: Daniel

middle: G

last: Foster

first: Jasmine

last: Wilson

first: Sangita

last: Chakraborty

first: Joseph

middle: C

last: Cooley

first: Rohit

last: Gaurav

first: Satria

last: Saguthi

first: Max A

last: Seibold

first: Rachel

middle: Z

last: Blumhagen

first: David

last: Schwartz

first: Ivana

last: Yang

first: Jennifer

last: Matsuda

first: James

last: Bridges

last: Zemans

first: Rubin

last: Tuder

last: Riches


title: Somatic deficiency of human CBL in leukocytes impairs B cell but not T cell development and function

city: New York

first: Yelena

last: Nemirovskaya

address: 1230 York Avenue

institute: Rockefeller University

summary: The casitas B lineage lymphoma (CBL) proto-oncogene promotes positive selection and antigen responses in murine T lymphocytes by ubiquitinating ZAP70. However, CBL and CBL-B are redundant for ubiquitination of SYK and regulation of B cell receptor (BCR) signaling in murine B cells. We studied lymphocyte development, maturation and function in patients with somatic homozygosity for CBL loss-of-function variants in leukocytes. Surprisingly, human CBL is largely redundant for the development and function of human T cells. Conversely, CBL is critical for B cell development and function. Patients with somatic, hematopoietic CBL deficiency have a 10-fold increase in transitional B cells during childhood and are susceptible to bacterial infections. CBL deficiency impairs B cell maturation in a cell-intrinsic manner through reduced apoptosis and dysregulated BCR signaling, thereby reducing the proportions and numbers of memory B cells. Overall, our findings demonstrate that CBL deficiency has two major effects on human B cells. First, B-cell development in the bone marrow is altered at the immature stage, resulting in enhanced survival and differentiation of autoreactive B cell clones and impaired B cell tolerance, manifested as the production of autoantibodies. Second, the generation of antigen-specific B cells is impaired, thereby disrupting the establishment of adaptive immune memory. Thus, our study reveals the critical role of human CBL in B cells and its redundancy in T cells.

overall_design: Bulk RNASeq on healthy donor and CBL LOH naïve B cells RNA was extracted with the RNeasy Plus Micro Kit (Qiagen) from sorted naïve B cells (2 × 104 cells) sorted from the PBMCs of CBL LOH patients, and age-matched healthy children. Full-length cDNA was generated from 1 ng total RNA with the SMART-Seq v4 Ultra Low Input RNA Kit (Clontech, 634888), and 1 ng cDNA was then used to prepare libraries with the Nextera XT DNA Library Preparation Kit (Illumina, FC-131-1024). Libraries with unique barcodes were pooled at equal molar ratios and sequenced on an Illumina NovaSeq 6000 sequencer with V1.5 reagents and NovaSeq Control Software V1.7.0 to generate 100 bp paired-end reads, according to the manufacturer’s protocol. The FASTQ files generated were first inspected by fastqc to check sequencing quality. Sequences were aligned with the GENCODE reference genome (GRCh37.p13 and GRCm38.p6 for human and mouse, respectively) with STAR aligner v2.6. Gene-level features were quantified with featureCounts v1.6.0. Geneset enrichment analysis (GSEA) was conducted with the fgsea package by projecting genes ranked by their fold-changes in expression with effect-size shrinkage onto the Hallmark genesets retrieved from the MSigDB database (https://www.gsea-msigdb.org/gsea/msigdb/). Several of the healthy pediatric donor datasets are already published (68) and accessible on the NCBI Sequence Read Archive (accession no. PRJNA1141130).

first: Jonathan

last: Bohlen

first: Taja

last: Vatovec

first: Masato

last: Ogishi

first: Anna-Lena

last: Neehus


title: The inhibitory receptor CD200R educates ILC1s for optimal cytotoxicity

city: 合肥市

first: yawen

last: chen

state: 蜀山区

address: 稻香村街道

institute: USTC

summary: Conventional natural killer (cNK) cells are educated through inhibitory receptor engagement with MHC-Ⅰ ligands, ensuring functional competence and self-tolerance. However, as a population likewise exhibiting cytotoxicity, whether type 1 innate lymphoid cells (ILC1s) undergo education and the underlying mechanisms remain unclear. Our study reveals that, CD200R, an inhibitory receptor specifically expressed by ILC1s, selectively suppresses ILC1 cytotoxicity upon CD200 engagement. Surprisingly, CD200R deficiency impairs ILC1 degranulation and cytotoxic activity without affecting inflammatory cytokine production. This defect is accompanied by compromised metabolic fitness in ILC1s. Analogous to cNK cell education, we demonstrate that CD200R educates ILC1 cytotoxicity primarily through the WNT/β-catenin pathway. Importantly, the impaired effector functions of uneducated ILC1s could be restored by exposure to certain cytokines. Collectively, our study defines a critical role for the inhibitory receptor CD200R in educating ILC1s to achieve cytotoxic maturity, revealing a parallel yet distinct mechanism from cNK cell education.

overall_design: RNA-seq profiling of liver ILC1s from WT and Cd200r−/− adult mice

first: Yawen

last: Chen

first: Hui

last: Peng

first: Zhigang

last: Tian


title: In vitro overexpression of Nhp2, Emg1 and Tsr3 genes in iPSC-derived neural crest cells

city: Vienna

first: Irina

last: Poverennaya

address: Spitalgasse 4

country: Austria

institute: Medical University of Vienna

summary: During embryonic development, the neural crest contributes to craniofacial formation by differentiating into skeletogenic mesenchyme and neuro-glial lineages. Previous single-cell transcriptomic analysis revealed that mesenchymal fate commitment correlates with expression of rRNA-modifying and ribosome assembly factors, including EMG1 and NHP2, which introduce post-transcriptional modifications into 18S rRNA (notably m¹acp³Ψ at U1248) with final maturation requiring TSR3. To explore the functional importance of m¹acp³ψ modification in the embryonic neural crest, we utilized lentiviral vectors to overexpress of Nhp2, Emg1, and Tsr3 in iPSC-derived neural crest cells.

overall_design: Human iPSCs were infected with lentiviral vectors carriyng the exogeneous Nhp2, Emg1 or Tsr3, and then were differentiated into neural crest cells, with doxycycline-induced overexpression of NHP2, EMG1, or TSR3 during differentiation; cells were collected at day 6 and analyzed by 10x Genomics Chromium Single Cell 3′ RNA-seq.

first: Rozalina

last: Galimullina

first: Ornella

last: Clara

first: Tobias

last: Steinschaden

first: Igor

last: Adameyko


title: Age-associated G-quadruplex accumulation and DDX5 loss shape chromatin landscapes in human astrocytes [ATAC-seq]

city: San Diego

first: Christopher

last: Hartl

address: Pacific Heights Blvd

department: Cell Biology

institute: Epigenome Technologies

summary: Aging disrupts genome organization and transcriptional fidelity, but the role of non-canonical DNA structures in the aging process remains unclear. G-quadruplexes (G4s), stable guanine-rich DNA and RNA structures are established regulators of gene expression and genome integrity, yet their contribution to physiological aging is unknown. Using primary human astrocytes derived from individuals spanning early to late adulthood (22–73 years) and fluorescent imaging, we observed increased G4 accumulation and reduced nuclear expression of the G4-resolving helicase DDX5 in older cells. To investigate how these changes relate to genome architecture, we performed ATAC-seq and G4 CUT&Tag across all astrocyte cultures. Older cells exhibited global chromatin compaction and focal G4 enrichment, with gains occurring in both accessible and closed chromatin regions, indicating locus-specific and context-dependent regulation. To determine whether DDX5 modulates these features, we overexpressed DDX5 in young astrocytes and identified transcriptional targets involved in chromatin organization and genome maintenance. Acute DDX5 knockout caused focal G4 accumulation without widespread chromatin changes, indicating that DDX5 maintains and modulates G4 dynamics at defined genomic regions. Together, these findings reveal G4s as dynamic, age-sensitive features of the genome with potential roles in epigenetic regulation and establish DDX5 as a modulator of G4 dynamics and genome integrity during human brain aging.

overall_design: RNA-seq, ATAC-seq, G4 Quadruplex CUT&Tag in resection-derived human astrocytes across the human age span, and with DDX5 over-expression and knockout

first: Vijay

middle: M

last: Kumar

first: Rocio

middle: D

last: Escarcega

first: Ellery

last: Wheeler

first: Nitin

last: Tandon

first: David

last: Monchaud

first: Andrey

last: Tvetkov


title: Transcriptomic Analysis of Zebrafish Immune Response Induced by Green Synthesis Zinc Oxide Nanoparticles using Propolis Extract

city: Bandung

first: Alia

middle: Putri

last: Syahbaniati

state: West Java

address: Jl. Ganesa No.10

department: Biology and Biotechnology

country: Indonesia

institute: School Of Life Sciences and Technology, Institut Teknologi Bandung

summary: The present study aims to synthesize zinc oxide nanoparticles using propolis extract and evaluate its effect on zebrafish immune response following caudal fin amputation model on zebrafish (Danio rerio). The phytochemical composition of extract was identified using Gas Chromatography Mass Spectrometry (GC-MS). The synthesized Pro-ZnO NPs were characterized using UV-Vis spectrophotometer, Fourier transform infrared (FTIR) and transmission electron microscopy (TEM) analysis. The toxicity of Pro-ZnO NPs was evaluated in zebrafish larvae, with the LC50 values of 4 mg/L which classified as toxic. Male zebrafish (n = 5 per group, triplicate) underwent caudal fin amputation and were divided into two groups to assess their immunological response: a control group and a Pro-ZnO 2 mg/L treatment group for a duration of four days. Total RNA was extracted from the caudal fin blastema four days post-amputation (dpa), and subsequently subjected to strand-specific mRNA sequencing using Illumina Platform. The principal component analysis (PCA) yielded a clear delineation between the ZnO-treated group and the control group, thereby indicating a distinct grouping pattern.

overall_design: RNAseq profile of the zebrafish immune response induced by zinc oxide nanoparticles for four days post caudal fin amputation

first: Indra

last: Wibowo

first: Roya Suffah

last: Zain

first: Alia Putri

first: Juan Dennis

last: Bahrian

first: Popi

last: Septiani

first: Antonius

last: Indarto


title: Age-associated G-quadruplex accumulation and DDX5 loss shape chromatin landscapes in human astrocytes [RNA-seq]

middle: L


title: Developmental trajectory of the mouse transcriptome following placental allopregnanolone insufficiency in the somatosensosry cortex, hippocampus and cerebellum

first: Jacquelyn

last: Salzbank

state: NY

institute: Columbia University Irving Medical Center

summary: This study investigates the developmental impact of placental allopregnanolone (ALLO) insufficiency on the mouse brain transcriptome in an age-, sex-, and region-specific manner. We generated mice with reduced ALLO levels by specifically deleting the gene encoding the synthetic enzyme for ALLO (Akr1c14) in trophoblasts using an Akr1c14-floxed mouse with a Cyp19a-Cre mouse. The somatosensory cortex, hippocampus, and cerebellum of both WT and plKO mice were collected from males and females at postnatal days 0, 7, 15, and 30. Libraries were prepared using the Illumina TruSeq Stranded mRNA Library prep kit and sequenced on an Illumina NovaSeq sequencer with 2 x 100 bp paired-end cycles. The analysis reveals sex- and region-specific transcriptomic changes following reduced placental ALLO, with differentially expressed genes associated with inflammatory signaling.

overall_design: mRNA profiles for WT and plKO mice at postnatal day 0, 7, 15, and 30, were generated by paired-end sequencing for the somatosensory cortex, hippocampus and cerebellum using and Illumina NovaSeq sequencer.

first: Helene

last: Lacaille

first: Jiaqi

last: O'Reilly


title: SPP1+ Macrophages Contribute to Hair Growth in Contact Hypersensitivity

city: Taipei

first: Kai-Rong

last: Huang

address: No. 1, Sec. 4, Roosevelt Rd., Taipei 10617, Taiwan

department: Biomedical Engineering

institute: National Taiwan University

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

overall_design: Refer to individual Series


title: SPP1+ Macrophages Contribute to Hair Growth in Contact Hypersensitivity [bulk RNA-Seq]

summary: Transcriptomic analysis of sorted HFSCs revealed dynamic transcriptional reprogramming during inflammation, including activation of stress response and immune-modulatory genes. Pathway enrichment highlighted metabolic adaptation and signaling networks linked to stem cell activation. These findings demonstrate that HFSCs undergo intrinsic molecular changes that parallel their regenerative response.

overall_design: We sorted hair follicle stem cells (HFSCs) from day2 DPCP-treated skin and day0 control skin using flow cytometry based on established surface markers. Cell populations were sorted directly into TRIzol LS Reagent (Invitrogen). RNA was isolated using Direct-zol RNA Miniprep Kits. Purified RNA were subjected to transcriptomic profiling to uncover molecular signatures and regulatory pathways underlying stem cell activation during skin inflammation.

first: Sabrina Mai-Yi

last: Fan

first: Sung-Jan

last: Lin


title: SPP1+ Macrophages Contribute to Hair Growth in Contact Hypersensitivity [scRNA-Seq]

summary: Skin inflammation involves complex interactions between immune cells. To address this gap, we applied single-cell RNA sequencing to dissect cellular states and regulatory programs in DPCP-induced dermatitis. This approach enables high-resolution mapping of immune crosstalk and identification of novel macrophage subsets. Our study establishes a framework for understanding how immune and metabolic signals orchestrate skin inflammation and regeneration.

overall_design: We isolated CD45+ single cells from DPCP-challenged skin on day 2 and control skin to capture dynamic immune responses. Comparative scRNA-seq profiling across control and inflamed groups was performed to dissect temporal changes in cell states and interactions.


title: EBNA1 SUMOylation by PIAS1 Suppresses EBV Lytic Replication and Enhances Episome Maintenance

city: Pittsburgh

first: Febri

last: Sugiokto

state: Pennsylvania

address: 5117 Centre Avenue

institute: University of Pittsburgh

summary: Epstein-Barr virus nuclear antigen 1 (EBNA1) is essential for the replication and stable maintenance of the viral episome in infected cells. Here, we identify the SUMO E3 ligase PIAS1 as a key regulator of EBNA1 through site-specific SUMOylation. Our Chromatin-Immunoprecipitation Sequencing (ChIP-seq) analysis revealed that PIAS1 is enriched at the viral origin of plasmid replication (oriP), where it physically associates with EBNA1 and catalyzes its SUMOylation. Using mutational analysis, we identified three lysine residues on EBNA1 (K17, K75, and K241) as major SUMOylation sites. Disruption of these sites compromises EBNA1’s ability to restrict EBV lytic replication. In addition, both PIAS1 depletion and the disruption of EBNA1 SUMOylation lead to reduced retention of EBNA1-OriP-based EBV mini-replicon, indicating the importance of EBNA1 SUMOylation in viral episome maintenance. Together, these results uncover a conserved post-translational mechanism by which PIAS1-mediated SUMOylation modulates EBNA1 function and EBV episome maintenance and suggests a broader role for SUMOylation in viral latency, lytic replication and persistence.

overall_design: ChIP seq of PIAS1 in Akata (EBV+) Burkitt lymphoma

first: Kun

last: Zhang

first: Yunash

last: Maharjan

first: Renfeng

last: Li


title: SPP1+ Macrophages Contribute to Hair Growth in Contact Hypersensitivity [spatial transcriptomics]

summary: Using Visium HD spatial transcriptomics and immunostaining, we mapped skin compartment dynamics during DPCP-induced allergic contact dermatitis. Dermal white adipose tissue transitioned from metabolic homeostasis to immune activation and inflammatory remodeling, accompanied by sustained lipolysis. Concurrently, CD45⁺ immune cells accumulated in the lower dermis and dWAT. These findings identify dWAT as an immune-metabolic hub orchestrating inflammatory progression and highlight spatial transcriptomics as a powerful tool for dissecting skin niche regulation.

overall_design: Spatial transcriptomics was conducted using the Visium HD (10X Genomics) system. Skin tissue was collected on days 1, 2, and 3 after DPCP challenge and from the control group on day 0. All samples were embedded in one paraffin block.


title: gyf mutants

city: Weifang

first: Yingtang

last: Ma

address: No. 699 Binhu Road, Xiashan Ecological Economic Development Zone

institute: Peking University Institute of Advanced Agricultural Sciences

summary: Purpose: To elucidate the molecular mechanism underlying GYF-mediated flowering regulation, we conducted whole-genome RNA-seq analysis using 1-week-old seedlings of WT, gyf1, gyf2, gyf1 gyf2-1, gyf1 gyf2-2. Conclusions: GYF proteins appear to regulate flowering time through direct modulation of FLC transcript levels

overall_design: mRNA profiles of 1-week-old seedlings of WT (Col-0), gyf1, gyf2, gyf1 gyf2-1, gyf1 gyf2-2 mutants were generated by deep sequencing, in duplicate, using Illumina HiSeq PE-150.

first: Yu

last: Tang

first: Sen

last: Wang