title: Single-cell transcriptomic analysis of PBMCs from IgAN patients

city: Seoul

first: Hang-Rae

address: 81, Irowon-ro, Gangnam-gu

department: Samsung Precision Genome Mediciine Institute

institute: Samsung Medical Center

summary: IgA nephropathy (IgAN), the most common primary glomerulonephritis, is a significant cause of chronic kidney disease. While previous studies have highlighted the role of immune cells in IgAN development, the disease’s heterogeneous clinical presentation and prognosis have hindered a comprehensive understanding of its specific pathogenesis. This study aimed to identify circulating immune cell subsets linked to the progression of IgAN. Peripheral blood samples were obtained from 9 healthy controls and 17 biopsy-proven IgAN patients, and stratified into early- and late-stage groups based on their estimated glomerular filtration rate (eGFR) at the time of blood sampling. To characterize IgAN-specific immune cell profiles and underlying regulatory mechanisms, single-cell RNA sequencing was conducted to observe distinct immune cell profiles and transcriptomic differences between the IgAN groups. Notably, CD8+ T cells, particularly IL-7Rαlow effector memory, exhibited a significant correlation with the disease progression. Trajectory analysis highlighted distinct CD8+ T-cell developmental patterns, with the early-stage group showing unique enrichment of memory CD8+ T cells. Gene expression profiling of CD8+ T-cell clusters indicated differences in activation and differentiation, emphasizing the critical role of CD8+ T cells in IgAN progression. In contrast, CD4+ T cells and B cells exhibited limited correlation with disease progression. The present transcriptome profiling underscores the prognostic significance of CD8+ T-cell subpopulations in IgAN progression. The findings highlight their potential as therapeutic targets and offers novel insights into the role of circulating immune cells in the progression of IgAN.

overall_design: Blood samples were collected from a cohort of 26 donors consisting of 17 IgAN patients and 9 volunteer healthy donors and peripheral blood mononuclear cells (PBMCs) were purified using a Ficoll–Histopaque gradient (1.077 g/mL; GE Healthcare Life Sciences, Piscataway, NJ, USA). The samples were stored in liquid nitrogen until analysis, preserved in a freezing medium containing 50% fetal bovine serum. Live PBMCs were subsequently isolated using BD FACSAria™ III (BD Biosciences, Franklin Lakes, NJ, USA). Among the 26 subjects, 8 scRNA-Seq libraries were prepared using Chromium Next GEM Single Cell 5' Reagent Kits v1.1 (10x Genomics, Pleasanton, CA, USA) (refer to first batch), while the remaining 18 were processed using Chromium Next GEM Single Cell 5’ Reagent Kits v2.0 (10x Genomics, Pleasanton, CA, USA) (refer to second batch). Libraries were sequenced on Novaseq 6000 platform (Illumina, San Diego, CA, USA). All cell barcodes and gene expression levels were compiled in a table format using Cell Ranger (10x Genomics, Pleasanton, CA, USA).

first: Gwanghun

first: Soojin

last: Lee

first: Ik Soo

first: Hyun Mu

last: Shin

first: Dong Ki


title: LOXL2 deletion in post-traumatic injury dysregulates knee joint homeostasis and promotes pain sensitivity, inflammation, and osteoarthritis

status: Public on Jan 21 2026

city: Boston

first: Manish

middle: V.

last: Bais

state: MA

address: W216, 700 Albany street

department: Translational Dental Medicine

country: USA

institute: Boston University

type: Expression profiling by high throughput sequencing

summary: Traumatic knee injuries lead to cartilage degeneration and osteoarthritis (OA). Cartilage has limited potential for self-regeneration, and any damage can lead to structural, molecular, and functional aberrations in the knee joint. Early changes in extracellular matrix (ECM) affecting cartilage are primarily asymptomatic and progress towards knee joint dysfunction, pre-OA, and finally OA. This study aimed to elucidate the mechanism of lysyl oxidase-like 2 (LOXL2) in maintaining healthy knee joint articular cartilage, its regeneration, and potential therapeutic applications. LOXL2 loss-of-function was evaluated using Acan promoter-specific inducible Loxl2 knockout, followed by immunohistochemistry, RNA-seq, transcriptional analysis,  and knee joint functional and pain analysis. Our results showed that LOXL2 deletion increases the severity of destabilized medial meniscus (DMM) -induced cartilage damage. LOXL2-overexpressing mice were protected against degenerative cartilage changes in the knee joint compared with their wild-type littermates. Interestingly, Intra-articular injection of adenovirus-delivered LOXL2 protected knee joint function, alleviated cartilage degeneration, restored treadmill running capability, and reduced allodynia. Overall, LOXL2 loss initiates cartilage damage, inflammation, and pain, leading to OA. The gain of LOXL2 protects against progressive cartilage damage and relieves pain and inflammation. Thus, we identified a novel function for LOXL2 in OA-related local pain.

overall_design: A total of 8 mice knee joint samples from Acan-Cre;Loxl2^fl/fl mice (Jax #019148) were subjected to RNA sequencing using the Illumina NovaSeq 6000 platform. Among these, 4 samples were vehicle-treated controls, and 4 were LOXL2 conditional knockouts. Raw fastq files were processed by aligning the reads to the Mus musculus mm10 genome assembly. Gene expression levels were quantified using featureCounts to generate a count matrix. Differential gene expression analysis was performed using the DESeq2 package in R, where standard normalization and filtering were applied to identify significant changes in gene expression between the control and knockout groups.

middle: V

first: Rajnikant

middle: D

last: Raut

first: Faiza

last: Ali


title: Pancreas homeostasis maintenance in health and disfunction

city: Padua

first: Marco

last: Fantuz

state: Veneto

address: Via Orus, 2

country: Italy

institute: Veneto Institute of Molecular Medicine

type: Genome binding/occupancy profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: Interplays between gene therapy vector and host cell genome [Capture Hi-C]

city: Memphis

first: Yong

last: Cheng

state: TN

address: 262 Danny Thomas Place

department: Hematology

institute: St. Jude Children's Reserach Hospital

summary: Lentiviral vectors are commonly used to deliver ectopic genetic material into host cells, but our knowledge of how integrated DNA sequences—such as cis-regulatory elements (CREs)—interact with the host genome remains limited. In this study, we analyzed chromatin accessibility, three-dimensional chromatin organization, and transcriptome profiles at 254 precisely mapped integration sites of a clinically used lentiviral vector. We found that the expression of integrated transgenes is influenced by the chromatin environment of the host cell. Moreover, integrated lentiviral vectors can form chromatin loops with the host genome, increase chromatin accessibility in adjacent regions, and alter splicing patterns of host gene transcripts. Notably, adding insulator elements reduced fluctuations in transgene expression levels and minimized changes in chromatin accessibility near integration sites. While insulator elements decreased local chromatin interactions, they did not affect the structure of topologically associating domains (TADs) or global chromatin organization. By assessing various genomic factors influencing the risk of integrated lentiviral vectors, we found that insulators consistently reduced genotoxicity.

overall_design: Capture-HiC using biotinylated baits targeting cassette DNA sequences on CTCF-LV and dCTCF-LV cells

first: Qian

last: Qi

first: Yichao

last: Li

first: Tiffany

last: Yee


title: Mitochondrial metabolism and signaling direct dendritic cell function in antitumor immunity

first: Hongbo

last: Chi

department: Immunology

institute: St Jude Children's Research Hospital


title: DNA methylation predicts lung function and pulmonary exacerbation in sputum samples from patients with cystic fibrosis

city: Montpellier

first: Albertina

last: DE SARIO

address: 641, av du doyen Gaston Giraud

department: PhyMedExp

country: France

institute: INSERM 1046-CNRS 9214-Univ Montpellier

type: Methylation profiling by genome tiling array

summary: To better understand the molecular determinants of lung disease variability among patients with cystic fibrosis (CF), we carried out an epigenome-wide association study (EWAS) in sputum samples from patients with CF. Sputum samples were collected from 50 patients with CF at four time points (visit 1, 2, 3 and 4) over an 18-month follow-up period. We profiled 64 sputum samples collected at visit 1 and 2, using human methylation BeadChips (EPIC). Selected CpG sites were reassessed in independent sputum samples collected at visit 3 and 4, by pyrosequencing. Overall, we provide the first longitudinal assessment of genome-wide DNA methylation in a cohort of patients with CF and identify CpG sites that predict clinical traits of key importance for lung disease. Specifically, we identified (i) differentially methylated CpG sites that correlate with lung function (FEV1pp), (ii) a DNA methylation signature that predicts patients with a pulmonary exacerbation and (iii)  CpG sites that split patients with declining lung function from those whose lung function either improved or remained stable.

overall_design: Sputum samples were collected from 50 patients with cystic fibrosis. Bisulphite converted DNA from 64 sputum samples were hybridised to the human methylation BeadChips (EPIC Illumina).

first: Jorg

last: Tost

last: De Sario


title: Interplays between gene therapy vector and host cell genome [ATAC-Seq]

overall_design: Assay for transposase-accessible chromatin with sequencing  (ATAC-seq) on Jurkat, CTCF-LV, dCTCF-LV cell lines


title: MYRF Controls Mesothelium Specification, Signaling, and Plasticity [CUT&Run]

city: La Jolla

first: Gidsela

last: Luna

state: California

address: 9500 Gilman Dr

institute: UC San Diego

summary: The mesothelium is a squamous monolayer that ensheathes internal organs and lines the body cavities. Aside from facilitating tissue sliding, its additional functions remain poorly understood. Here, we study the mesothelium through investigating myelin regulatory factor (Myrf), a transcription factor expressed in the mesothelium and a top mutated gene in congenital diaphragmatic hernia (CDH), a developmental disorder that affects the lung and diaphragm. In mice, inactivation of Myrf early in embryogenesis resulted in CDH and defective mesothelium specification, compromising its role as a signaling center for lung growth. Inactivation after mesothelium specification led to additional defects, including enhanced differentiation into various mesenchymal cell types, causing a striking accumulation of elastin-expressing smooth muscle/myofibroblasts encasing the lung, mimicking pleuroparenchymal fibroelastosis (PPFE), a rare adult lung condition. Compound mutants demonstrate that MYRF functions synergistically with YAP/TAZ in mesothelium differentiation. Together, these findings highlight the complex role of the mesothelium in development and disease.

overall_design: E16.5 wildtype mesothelial cells were stained with surface markers and sorted by flow cytometry for H3K27ac CUT&RUN.

first: Jamie

middle: M

last: Verheyden

first: Chunting

last: Tan

first: Estelle

last: Kim

first: Ziai

last: Zhu

first: Michelle

last: Hwa

first: Jugraj

last: Sahi

first: Yufeng

last: Shen

first: Wendy

middle: K

last: Chung

first: David

middle: J

last: McCulley

first: Xin

last: Sun


title: An EGR1-dependent cascade modulates genome architecture at the CSF1R locus [Hi-C]

city: PHILADELPHIA

first: Sandra

last: Deliard

state: PA

address: 3601 Spruce St

institute: The Wistar Institute

summary: The organization and dynamics of chromatin are key to regulating gene expression during myeloid cell differentiation. Sequence-specific transcription factors initiate and maintain a complex network of enhancer-promoter contacts, which is supported by insulating elements and genome folding organizers such as CTCF and Cohesin.  The spatial arrangement of enhancers and promoters, as well as their epigenetic state, drives cell and tissue-specific transcriptomes. Here we dissect the spatial, transcriptional, and epigenetic landscape of the CSF1R locus in monocytes and macrophages. CSF1R is a receptor tyrosine kinase that triggers the signaling cascade required for macrophage differentiation.  Previous work showed that CSF1R expression is regulated by multiple enhancers, including the fms-intronic regulatory element (FIRE). Here, we find that a single EGR-1 binding motif dictates activation of CSF1R. We also discover that the CSF1R entire locus folds into a hub of gene regulation, affecting an extended network of myeloid and inflammatory genes. Globally, EGR1 may have an expanded role as a macrophage-specific boundary element, supporting enhancer-promoter looping at several genes. In sum, we describe a novel 3D chromatin network that is critical for macrophage development and function.

overall_design: HiC in primary human monocytes and  macrophages from healthy donors. HiC also in HL-60 wildtype and CRISPR/Cas9 mutant cell line targeting the EGR1 binding site in FIRE enhancer of the CSF1R gene. HL-60 wildtype and mutant cells were either untreated or treated with phorbol 12-myristate 13-acetate (PMA)  to induce monocytic differentiation.

first: Elisa

last: Barbieri

first: Marco

last: Trizzino

first: Avery

last: Zucco

first: Francis

last: Picone

first: Alessandro

last: Gardini


title: MYRF Controls Mesothelium Specification, Signaling, and Plasticity [RNA-Seq]

first: Gidsela

last: Luna

overall_design: RNA-Seq profiling of the E13.5 Tbx4tetOcre;MyrfE6 mutant lung and cre control


title: Pancreas homeostasis maintenance in health and disfunction [snRNA-seq]

last: Fantuz

summary: Local inflammation in the pancreas is transient but imprints a durable epigenetic memory on epithelial cells, making them more amenable to oncogenic transformation. However, it is unclear whether epithelial cell heterogeneity is impacted by acute pancreatitis (AP) or whether population dynamics during regeneration contributes to the establishment of inflammation memory.  To tackle those questions, we deployed experimental pancreatitis in mice and performed paired sequencing of transcriptomic and chromatin accessibility profiles at single nucleus resolution. We documented cell type abundance but also applied integrative analyses to infer phenotypically-distinct clusters of mesenchymal and exocrine cells. We found that AP perturbs a subset of “idling” acinar cells, which separate from more canonical “secretory” acini based on a more diversified proteome, which include elevated expression of signal transduction receptors. We linked acinar cell heterogeneity to epigenetic differences that also endow idling cells with superior plasticity. These constitute about 40% of acinar cells but can proliferate and skew their phenotype in response to AP. This leads to a remarkable recovery of pancreas histology and function, but also to the dissemination of idling-like features across the exocrine parenchyma. Mechanistically, idling acinar cells are characterized by enhanced transcriptional activity and protein synthesis. After recovery from pancreatitis, acini show elevation of both and establishment of chronic Unfolded Protein Response (UPR). We finally demonstrated that AP-primed pancreata show signs of elevated UPR and that ER stress promotes acinar cell metaplasia.  Our data interrogate phenotypical dynamics during tissue regeneration to identify cell states amenable to epigenetic imprinting. They also suggest that UPR-alleviating strategies might curtail the risk of developing pancreatic cancer for individuals who experiences AP.

overall_design: Mice were subjected to 8 hourly injection/die over two subsequent days. Control mice were injected with saline solution, and sacrificed after 28 days. Cerulein-treated mice were injected with 50mg/kg of cerulein dissolved in saline solution at every injection, and sacrificed either at 7 days post injection (7days samples) or at 28 days post injection (28days samples).

first: Johannes

last: Liebig

first: Giovanni

last: Fontana

first: Sören

last: Lukassen

first: Christian

last: Conrad

last: Carrer


title: An EGR1-dependent cascade modulates genome architecture at the CSF1R locus [ChIP-seq]

overall_design: ChIP-seq of chormatin marks and transcriptional regulators in HL-60 wildtype and CRISPR/Cas9 mutant cell lines targeting the EGR1 binding site in FIRE enhancer of the CSF1R gene. HL-60 wildtype and mutant cells were either untreated or treated with phorbol 12-myristate 13-acetate (PMA)  to induce monocytic differentiation.


title: Pancreas homeostasis maintenance in health and disfunction [snATAC-seq]

summary: Local inflammation in the pancreas is transient but imprints a durable epigenetic memory on epithelial cells, making them more amenable to oncogenic transformation. However, it is unclear whether epithelial cell heterogeneity is impacted by acute pancreatitis (AP) or whether population dynamics during regeneration contributes to the establishment of inflammation memory. To tackle those questions, we deployed experimental pancreatitis in mice and performed paired sequencing of transcriptomic and chromatin accessibility profiles at single nucleus resolution. We documented cell type abundance but also applied integrative analyses to infer phenotypically-distinct clusters of mesenchymal and exocrine cells. We found that AP perturbs a subset of “idling” acinar cells, which separate from more canonical “secretory” acini based on a more diversified proteome, which include elevated expression of signal transduction receptors. We linked acinar cell heterogeneity to epigenetic differences that also endow idling cells with superior plasticity. These constitute about 40% of acinar cells but can proliferate and skew their phenotype in response to AP. This leads to a remarkable recovery of pancreas histology and function, but also to the dissemination of idling-like features across the exocrine parenchyma. Mechanistically, idling acinar cells are characterized by enhanced transcriptional activity and protein synthesis. After recovery from pancreatitis, acini show elevation of both and establishment of chronic Unfolded Protein Response (UPR). We finally demonstrated that AP-primed pancreata show signs of elevated UPR and that ER stress promotes acinar cell metaplasia. Our data interrogate phenotypical dynamics during tissue regeneration to identify cell states amenable to epigenetic imprinting. They also suggest that UPR-alleviating strategies might curtail the risk of developing pancreatic cancer for individuals who experiences AP.


title: Coexpression of MYCN and ALK Induces Neuroblastoma-Like Tumors From Human iPS Cell-Derived Cranial Neural Crest Cells [Microarray]

city: Saitama

first: Kyosuke

last: Mukae

state: Kitaadachi-gun

address: 818, Komuro, Ina-machi

department: Research Institute for Clinical Oncology

country: Japan

institute: Saitama Cancer Center

summary: Neuroblastoma is a pediatric solid tumor originating from neural crest cells, which are precursors of the sympathetic nervous system. Amplification of MYCN proto-oncogene is a key factor contributing to poor prognosis of neuroblastoma and is strongly associated with aggressive disease progression. Additionally, the anaplastic lymphoma kinase plays an important role in the pathogenesis of neuroblastoma. Mutation or amplification of anaplastic lymphoma kinase drives oncogenic signaling pathways, such as the MAPK and Ras pathways, which together with MYCN amplification exacerbate tumor malignancy. The use of human induced pluripotent stem cell-derived cranial neural crest cells to establish a neuroblastoma model is expected to be of great significance in studying the pathogenesis of this disease. In this study, we sought to mimic the tumorigenic process of neuroblastoma by overexpressing MYCN and anaplastic lymphoma kinase in cranial neural crest cells derived from human induced pluripotent stem cells. These modified cells when subcutaneously transplanted into immunodeficient mice induced neuroblastoma-like tumors, and could thus be used an in vitro model to study this cancer. Through extensive gene expression profiling and whole exome sequencing of MYCN/anaplastic lymphoma kinase-induced clones, we identified key features of neuroblastoma, including activation of the MAPK signaling pathway and gain of 17q chromosome, which is critical for malignant tumor development. This model provides a valuable platform for studying the biological mechanisms driving anaplastic lymphoma kinase mutations and MYCN amplification in neuroblastoma derived from cranial neural crest cells as well as for exploring potential therapeutic approaches against these targets to improve patient prognosis.

overall_design: Total RNA was extracted, and a microarray analysis was performed using the Agilent platform of 8x60 K design ID G4851B (Agilent Single Color. 39494, Agilent Technologies). Two hundred nanograms of total RNA was labeled with Cyanine3 using a Low Input Quick-Amp Labeling Kit (one color, Agilent Technologies) according to the manufacturer’s instructions. Purified labeled total RNA was hybridized to the expression microarray. Hybridization, the scanning of microarrays, and data extraction from scanned images were conducted according to Agilent protocol version 6.9.

first: Takehiko

last: Kamijo

first: Miki

last: Ohira

first: Tianyuan

last: Shi


title: Macrophage Lyn kinase is a Sex-Specific Regulator of Post-SAH Neuroinflammation

city: Camden

first: Khalid

last: Hanafy

state: NJ

address: 401 Broadway,

department: Biomedical Sciences

institute: Cooper Medical School of Rowan Univ

summary: Lyn kinase is a member of the Src family of tyrosine kinases, primarily known for its role in regulating immune cell signaling. It can phosphorylate and modulate the activity of various proteins involved in immune responses, including TLR4. In our study, we investigated the sex-specific involvement of Lyn kinase in regulating TLR4 signaling to understand the TLR4 mediated inflammatory response after SAH. Our results highlight sex-specific modulation of Lyn kinase activity in TLR4 signaling after hemorrhagic stroke and indicate that successful treatment of neuroinflammation may require sex-specific treatments.

overall_design:
WT, MG-cKO and BMM-cKO three animal groups of both sexes (male and female) were used for spatial transcriptomics experiment. Each brain slices were assayed with Tmem119 (microglia) and Iba-1 (macrophage) markers using 4 ROIs each.
Please note that while four groups (Sham, WT-SAH, MG-cKO, and BMM-cKO of both sexes with 4ROIs each) are included in the records (i.e. total 32 data samples), the analysis was performed between the 3 groups: WT-SAH, MG-cKO and BMM-cKO, which in total 24 data samples.

first: Rezwanul

last: Islam


title: Epigenetic biomarker discovery in IgA nephropathy: chromatin openness analysis of circulating CD8+ T cells using ATAC-Seq

first: Hang-Rae

last: Kim

country: South Korea

summary: Chromatin openess plays a critical role in understanding epigenetic regulation in disease states. Using ATAC-seq, we profiled circulating CD8+ T cells from IgA nephropathy (IgAN) patients to identify biomarkers distinguishing early and late disease stages. A total of 279 differential ATAC peaks were identified, with 122 selected as biomarkers based on fold change (>2) and statistical significance (P < 0.05). These biomarkers exhibited distinct chromatin accessibility patterns, highlighting differential regulatory mechanisms. Combining multiple biomarkers through weighted scoring enhanced predictive accuracy, with ROC analysis confirming their diagnostic potential. Our findings demonstrate that chromatin openness in circulating CD8+ T cells provides valuable insights into disease progression and serves as a robust platform for biomarker discovery in IgAN.

overall_design: Peripheral blood mononuclear cell (PBMC) samples were collected from a cohort of 17 IgAN patients. The patients were stratified into early- and late-stage groups based on their estimated glomerular filtration rate (eGFR) at the time of blood collection.

first: Gwanghun

first: Soojin

last: Lee

first: Ik Soo

first: Hyun Mu

last: Shin

first: Dong Ki


title: The effects of TGFBR3 on adipogenesis of FAPs

city: Chengdu City

first: Huizhen

last: Zou

address: No. 270, Tianhui Road, Rongdu Avenue, Jinniu District

country: China

institute: The General Hospital of Western Theater Command PLA

summary: Platelet-rich plasma (PRP) is used to treat musculoskeletal diseases, such as rotator cuff tears, and has been proven to attenuate fatty infiltration in muscle injury; however, the effective components are still unclear. Furthermore, PRP is currently strictly used by donors in themselves, and it is unknown whether and how the heterogeneity of donors, especially aging, would change the composition of PRP and impact the therapeutic effects. In this study, we found that young donor-derived exosomes, but not those from old people, were critical components in PRP that regulate fatty infiltration in muscle injury by directly inhibiting adipogenesis of muscle-resident FAPs. The characteristics of young donor-derived PRP exosomes were quite different from those of old donor-derived PRP exosomes. Mechanistically, we demonstrated that two components of miRNA cargo, hsa-let-7f-5p and hsa-miR-16-5p, played an essential role in regulating adipogenesis of FAPs and fatty infiltration by targeting TGFBR3.

overall_design: RNA-seq profiling of FAPs were transfected with TGFBR3 overexpressing plasmids or vectors and then were cultured in adipogenic induction medium.


title: Interplays between gene therapy vector and host cell genome

first: Yong

last: Cheng


title: An EGR1-dependent cascade modulates genome architecture at the CSF1R locus [CUT&Run]

first: Sandra

last: Deliard

overall_design: CUT&RUN perfomed in primary human monocytes and  macrophages from healthy donors.

first: Elisa

last: Barbieri

first: Marco

last: Trizzino

first: Avery

last: Zucco

first: Francis

last: Picone

first: Alessandro

last: Gardini


title: Hepatic gene expression profiling of Eisai hyperbilirubinemic rats

city: Kusatsu

first: Chieri

last: Fujino

state: Shiga

address: 1-1-1 Noji-higashi

institute: Ritsumeikan University

summary: Eisai hyperbilirubinemic rats (EHBR) are a mutant strain of Sprague-Dawley (SD) rats known for their naturally occurring hyperbilirubinemia, which was later found to result from a deficiency of an efflux transporter, multidrug resistance-associated protein (MRP) 2. This strain was developed by the Japanese pharmaceutical company Eisai Co., Ltd. and is widely used as an animal model for studying hyperbilirubinemia and the transport mechanisms of various compounds. In our study, the effects of decreased MRP2 expression on the gene expression of drug-metabolizing enzymes and transporters were investigated using the EHBR liver. In addition, activation of transcription factors and nuclear receptors was evaluated based on changes in target gene expression from RNA-seq data.

overall_design: RNA-seq profiling of the liver of male 5-week-old EHBR and SD rats


title: FLYNC: A Machine Learning-Driven Framework for Discovering Long Non-Coding RNAs in Drosophila melanogaster

city: Portugal

first: Catarina

middle: CF

last: Homem

address: Rua Campo Mártires da Pátria, 130

country: Portugal

institute: CEDOC - NMS

summary: Non-coding RNAs have increasingly recognized roles in critical molecular mechanisms of disease. However, the non-coding genome of Drosophila melanogaster, one of the most powerful disease model organisms, has been understudied. Here, we present FLYNC – FLY Non-Coding RNA discovery and classification – a novel machine learning model that predicts the probability of a newly identified RNA transcript being a long non-coding RNA (lncRNA). Integrated into an end-to-end bioinformatics pipeline capable of processing single-cell or bulk RNA sequencing data, FLYNC outputs potential new non-coding RNA genes. FLYNC leverages large-scale genomic and transcriptomic datasets to identify patterns and features that distinguish non-coding genes from protein-coding genes, thereby facilitating lncRNA prediction. We demonstrate the application of FLYNC to publicly available Drosophila adult head bulk transcriptome and single-cell transcriptomic data from Drosophila neural stem cell lineages and identify several novel tissue- and cell-specific lncRNAs. We have further experimentally validated the existence of a set of FLYNC predicted lncRNAs by RT-PCR and RNA PolII binding. Overall, our findings demonstrate that FLYNC serves as a robust tool for identifying lncRNAs in Drosophila melanogaster, transcending current limitations in ncRNA identification and harnessing the potential of machine learning.

overall_design: We performed targeted DamID experiments to determine RNA Polymerase II-subunit DNA association in neural stem cells in the Drosophila melanogaster developing brain.

first: Tiago

last: Baptista


title: An EGR1-dependent cascade modulates genome architecture at the CSF1R locus [RNA-Seq]

overall_design: Total RNA-seq perfomed in primary human monocytes and  macrophages from healthy donors and  3'mRNA-seq on HL-60 wildtype and CRISPR/Cas9 mutant cell lines targeting the EGR1 binding site in FIRE enhancer of the CSF1R gene. HL-60 wildtype and mutant cells were either untreated or treated with phorbol 12-myristate 13-acetate (PMA)  to induce monocytic differentiation prior to RNA isolation.


title: DKK3 initially preserves acinar integrity through MEK-Fos signalling but later switches to an oncogenic role in PDAC.

city: Ulm

first: Alexander

last: Kleger

address: Albert einstein allee 23

department: Institute for Molecular Oncology and Stem Cell biology

country: Germany

institute: Universitaetsklinikum Ulm

summary: Pancreatic ductal adenocarcinoma (PDAC) is characterized by its intricate tumor biology complicated by the spatiotemporal dynamics in the expression and function of specific proteins driving such biology. Here, we employ a mouse model with homozygous and heterozygous DKK3 knockout together with pancreas-specific expression of KRASG12D (DDKC,DKC,KC) to investigate the compartment- and time-dependent roles of DKK3. Our findings demonstrate that DKK3 functions to inhibit oncogenesis during the early stages of cancer while paradoxically promoting tumor progression in the later stages. DDKC and DKC mice exhibited significantly shorter lifespans compared to KC mice, with a higher incidence of high-grade, desmoplastic, “cold” and metastatic cancers. Accordingly, DKK3-deficient acinar cells exhibited a marked increase in acinar-to-ductal-metaplasia, accompanied by increased MAPK-signaling with enhanced expression of the immediate-early genes cfos and Jun. Treatment with the MEK-inhibitor trametinib preserved acinar integrity in DKK3-null pancreata. Additionally, FOS-inhibition restricted the migratory capabilities of DDKC cancer cells. Throughout the progression of mouse and human PDAC, DKK3 expression shifted from epithelial cells to the stromal compartment by the endpoint. DKK3-null tumor cells displayed enhanced migratory abilities when exposed to recombinant DKK3.  In line, DKK3-expressing cancer-associated fibroblasts (CAFs) emerged as crucial contributors to this tumor aggressiveness. Orthotopic transplantation studies revealed that DKK3 expression within CAFs promotes tumor growth and fibrosis, particularly in aggressive DDKC tumors. Collectively, these findings highlight the complex and context-dependent role of DKK3 in PDAC, suggesting that it may serve as a promising therapeutic target for the management of this challenging malignancy.

overall_design: RNA sequencing of acinar cells isolated from Wildtype and Dkk3 null pancreata, and ex vivo ADM assay was performed for 3 days and samples were harvested at day 3 for RNA sequencing

first: Dharini

last: Srinivasan

first: Eleni

last: Zimmer


title: SASP Suppression by hTSCs Secretome

city: Bathesda

first: Kotb

last: Abdelmohsen

state: MD

address: 9000 Rockville Pike

institute: NIH

summary: Cellular senescence, a state of irreversible cell cycle arrest, contributes to aging and age-related diseases through the accumulation of senescent cells and their secretion of a pro-inflammatory senescence-associated secretory phenotype (SASP).Recent studies indicated that extracellular vesicles (EVs) as key SASP components mediating intercellular communication. Here, we investigated the effects of human trophoblast stem cell secretome and EVs (hTSC-S, hTSC-EVs) on cellular senescence. Our results show that hTSC-S and hTSC-EVs reduce SASP-associated mRNAs and cytokines, including CXCL1 and GDF15, and suppress NF-κB activation in senescent WI-38 cells. Proteomic analysis revealed an enrichment of ECM-remodeling proteins in hTSC-EVs, suggesting restorative properties. In vivo, hTSC-S decreased GDF15, CXCL1, and markers of DNA damage in aged mice, underscoring its therapeutic potential to modulate SASP and promote healthier aging.

overall_design: On Day 1, WI-38 cells were treated with ionizing radiation (IR) and 20% hTSC secretome or control media. On Day 3, the media was refreshed with new media containing 20% hTSC secretome or control. On Day 5, the cells were harvested, and RNA was isolated for RNA-seq analysis.

first: Martina

last: Rossi


title: Effects of ENO1 knockdown and LPS+Lactate stimulation on EA.HY926 cells

city: Shanghai

first: Xie

middle: xue

last: ru

address: wanyuan road 399

department: Institutes of Biomedical Sciences

institute: Fudan university

summary: Elevated lactate was associated with vascular endothelial cells (ECs) dysfunction in sepsis. However, the underlying mechanisms remain to be defined. In this study, we found that elevated lactate in sepsis promotes lactylation of enolase 1 (ENO1) at K71 site through the action of lactyltransferase P300. The lactylation at ENO1 K71 site reduces the binding of TRIM21(an E3 ubiquitin ligase) mRNA to ENO1 (an RNA-binding protein), resulting in enhanced TRIM21 mRNA stability and expression. Elevated TRIM21 can bind to VE-Cadherin and exert its E3 ubiquitin ligase function, causing the ubiquitination and degradation of VE-Cadherin, which disrupts endothelial adhesions junctions (AJs) and increases endothelial permeability. Targeting lactylation of ENO1 K71 via a specific peptide alleviated endothelial injury and enhanced survival rates among septic mice. These findings suggest that lactyaltion of ENO1 plays a pivotal role in vascular endothelial dysfuncyion during sepsis, while inhibiting lactylation may offer a novel strategy for sepsis treatment.

overall_design: To investigate the function of ENO1 lactylation in endothelial cells after LPS and lactate stimulation, we conduct four groups: 1.Negtive control(NC), without stimulation; 2.LPS+lactate stimulation (NC-L-L); 3.ENO1 knockdown with siRNA (siENO1); 4.LPS+lactate stimulation after ENO1 knockdown with siRNA (siENO1-L-L).

first: Xueru

last: Xie

first: Caiyan

last: Zhang

first: Guoping

last: Lu

first: Yufeng

last: Zhou


title: Lineage tracing reveals the origins and dynamics of macrophages in lung injury and repair

first: Yan

last: Li

state: Shanghai

address: 555 Zuchongzhi Rd

institute: Shanghai Institute of Materia Medica, Chinese Academy of Sciences,

summary: Macrophages play a vital role in tissue repair and regeneration following injury. However, the cell fate, dynamic change, and functional roles of macrophages from different origins during lung injury and repair are not fully understood. Here we used genetic lineage tracing and scRNA-seq approaches to explore the temporal and spatial roles of tissue-resident and recruited macrophages during pulmonary fibrosis. We observed a sharp reduction in tissue-resident macrophages during the early inflammatory phase, with their number stabilizing during recovery. Monocytes contributed substantially to the macrophage population during the fibrotic phase, initially differentiating into interstitial macrophages and later transitioning into alveolar macrophages through a transient state. Genetic ablation of monocytes led to a reduction in recruited macrophages and alleviated pulmonary fibrosis. Mechanistically, Notch signaling was found to negatively correlate with Wnt/β-catenin signaling in regulating monocyte recruitment and pulmonary fibrosis. Our study revealed the dynamic contributions and functions of macrophages from various sources in lung injury and regeneration.

overall_design: To comprehensively understand the macrophage dynamics bleomycin-injured lungs, we performed a time series of single-cell RNA sequencing (scRNA-seq) analysis. Immune cells were isolated from PBS-treated and bleomycin-injured lungs at days 3, 7, 14, and 28 post-treatment.

first: Hengwei

last: Jin

first: Huan

last: Zhu

first: Bin


title: High Resolution Spatial Mapping of Microbiome-Host Interactions via in situ Polyadenylation and Spatial RNA Sequencing [Ileum, with in situ Polyadenylation]

city: Ithaca

first: Iwijn

last: De Vlaminck

state: New York

address: 237 Tower Road

department: Biomedical Engineering

institute: Cornell University

summary: Inter-microbial and host–microbial interactions are thought to be critical for the functioning of the gut microbiome, but few substantive tools are available to measure these interactions. Here, we report a method for unbiased spatial sampling of microbiome-host interactions in the gut at high spatial resolution. This method combines enzymatic in situ polyadenylation of both bacterial and host transcripts with spatial RNA-sequencing. Application of this method revealed the biogeography of the mouse gut microbiome as function of location in the intestine, short-range intermicrobial interaction, local shaping of the microbiome by the host, and tumor-associated changes in the architecture of the host-microbiome interface. This method is compatible with broadly available commercial platforms for spatial RNA-sequencing, and can therefore be readily adopted to broadly study the role of short-range, bidirectional host-microbe interactions in microbiome health and disease.

overall_design: Spatial transcriptomics: Ileum, with in situ Polyadenylation

first: Ioannis

last: Ntekas

first: David

middle: W

last: McKellar

first: Lena

last: Takayasu


title: Innate tissue immunosurveillance by γδ T cells has real-time dependence on the T cell receptor [RNA-seq]

city: London

first: Probir

last: Chakravarty

address: 1 Midland Road

country: United Kingdom

institute: Francis Crick Institute

summary: With clonotypic potential to engage different ligands, T cell receptor (TCR) γδ fulfils a key tenet of adaptive immunity. Nonetheless, many γδ repertoires are non-circulating, display limited diversity, and are commonly classified as innate-like, questioning any requirement for the TCR beyond the cells’ development. Addressing this long-standing issue, we now show that the steady-state phenotypes of different tissue-intrinsic γδ T cell compartments share a dependence on constitutive TCR expression.  Deprived of this, cells rapidly become dysregulated, losing their capacity to respond to wide-ranging tissue insults, including imiquimod, an innate inducer of psoriasis-like pathology, u.v. irradiation, and melanoma. Thus, beyond any developmental requirements, the TCR is required in real time to regulate the cells’ innate-like tissue immunosurveillance. Biologically, this clearly distinguishes intrinsic γδ T cells from NK and other innate lymphoid cells, while clinically it stresses the importance of the TCR in delivering gd T cell-based immunotherapies.

overall_design:
Genetic deletion of TCRγδ specifically in tissue-resident γδ T cells was achieved in Cγ1fl/fl mice in vivo by tamoxifen-inducible TCRδ-CreERT2 for skin or Rosa26-CreERT2 for gut.
TCRγδ-deficient (KO) tissue-resident γδ T cells were purified from mouse epidermis, dermis and small intestine. TCR competent (WT) tissue-resident γδ T cells were identically purified as controls. Between 3 to 5 mice per genotype were analyzed per tissue. Each sample came from a individual mouse and corresponds to a biological replicate.
Transcriptomic analysis of TCRγδ KO cells was performed with RNA-seq data to determine gene expression signatures for each set of tissue-specific cells.

first: Miguel

last: Munoz-Ruiz

first: Nicolas

last: Veland

first: Adrian

last: Hayday


title: An EGR1-dependent cascade modulates genome architecture at the CSF1R locus [Capture-C]

first: Sandra

last: Deliard

overall_design: Capture HiC targeting CSF1R gene locus in primary human monocytes and macrophages and HL-60 wildtype and CRISPR/Cas9 mutant cell lines targeting the EGR1 binding site in FIRE enhancer of the CSF1R gene. HL-60 wildtype and mutant cells were either untreated or treated with phorbol 12-myristate 13-acetate (PMA)  to induce monocytic differentiation.

first: Elisa

last: Barbieri

first: Marco

last: Trizzino

first: Avery

last: Zucco

first: Francis

last: Picone

first: Alessandro

last: Gardini


title: Innate tissue immunosurveillance by γδ T cells has real-time dependence on the T cell receptor [ATAC-seq]

overall_design:
Genetic deletion of TCRγδ specifically in tissue-resident γδ T cells was achieved in Cγ1fl/fl mice in vivo by tamoxifen-inducible TCRδ-CreERT2 for skin or Rosa26-CreERT2 for gut.
TCRγδ-deficient (KO) tissue-resident γδ T cells were purified from mouse epidermis, dermis and small intestine. TCR competent (WT) tissue-resident γδ T cells were identically purified as controls. Between 3 to 5 mice per genotype were analyzed per tissue. Each sample came from a individual mouse and corresponds to a biological replicate.
Chromatin accesibility analysis of TCRγδ KO cells was performed with ATAC-seq data to determine differences in chromatin landscape for each set of tissue-specific cells.


title: High Resolution Spatial Mapping of Microbiome-Host Interactions via in situ Polyadenylation and Spatial RNA Sequencing [Ileum, without in situ Polyadenylation]

overall_design: Spatial transcriptomics: Ileum, without in situ Polyadenylation


title: CD40L-targeting engineered regulatory T cells as a novel cell therapy approach for T cell mediated inflammatory diseases

city: Regensburg

first: LIT

last: NGS-Core

address: Franz-Josef-Strauß-Allee 11

department: NGS-Core

institute: Leibniz Institute for Immunotherapy

summary: Restoring immune tolerance by engineered regulatory T cell (Treg) cell therapy is a promising strategy to treat patients suffering from autoimmune and inflammatory diseases. However, in many of these conditions, relevant disease-driving antigens are unknown. Therefore, suitable target (auto-)antigens for antigen-specific Treg cell therapy are rarely available. Here, we present a novel artificial immune biosensor for Treg cells that circumvents this limitation by targeting the immune costimulatory protein CD40-ligand (CD40L), transiently expressed by activated T cells. The artificial immune receptor (AIR) comprises a CD40-derived extracellular binding domain, an intracellular costimulatory signaling domain and a T cell receptor signaling domain of the CD3-ζ chain. After interaction with its membrane-bound ligand, this synthetic receptor triggers a TCR-like activation program in Treg cells including induction of Treg effector molecules and cell proliferation. In a mouse model of graft-versus-host disease, transfer of Treg cells expressing the CD40-AIR significantly improved survival and demonstrated immune control of the alloantigen-reactive T cell compartment. The expression and signaling of the corresponding human CD40-AIR in human Treg cells illustrate the potential for translating this concept. Engineering Treg cells with a CD40L-sensing AIR, that detects activated T cells and, thereby, induces Treg cell activation, presents a promising therapeutic approach for a broad range of T cell mediated inflammatory diseases.

overall_design: Experiment 1: anti-HLA-A2 CAR or CD40 AIR-expressing Treg cells were rested and then co-cultured with HEK cells that expressed endogenous HLA-A2 and +/- CD40L or left unstimulated. After 18 hours activated CD137 and Nr4a1 positive Treg cells were FACS-sorted and sequenced. Three biological experiments (A,B, C) were perfomed. Experiment 2: Irradiated BALBc mice that recieved bone marrow cells (2.500.000 )and spleen cells (500.000) (GvHD group), or mice that recieved250.000 Treg cells (control: truncated AIR construct or full lenght CD40 AIR construct)as treatment were sacrificed 7 days after transplantation. CD4+ T cells from spleens of these mice were FACS-sorted (10.000) and RNA-Seq was performed. n=5 mice (per group)

first: Sebastian

last: Bittner

first: Brigitte

last: Ruhland

first: Nicholas

last: Strieder

first: Markus

last: Feuerer


title: The effects of Platelet-rich plasma on adipogenesis of FAPs

first: Huizhen

last: Zou

summary: Platelet-rich plasma (PRP) is used to treat musculoskeletal diseases, such as rotator cuff tears, and has been proven to attenuate fatty infiltration in muscle injury; however, the effective components are still unclear. In this study, we found that young donor-derived exosomes were critical components in PRP that regulate fatty infiltration in muscle injury by directly inhibiting adipogenesis of muscle-resident FAPs.

overall_design: RNA-seq profiling of FAPs were treated by PRP or vehicle and then were cultured in adipogenic induction medium.


title: A novel association of EZH2 and E2F1 promotes breast cancer cell proliferation through chromatin remodeling [ATAC-Seq]

city: Seoul

first: Tae-Young

last: Roh

state: --- Select One ---

address: 52 Ewhayeodae-gil, Seodaemun-gu

department: Life Sciences

institute: Ewha Womans University

summary: This study provides transcription, histone modifications, chromatin accessibility in MDA-MB-231. We identified the non-canonical role of EZH2 by analyzing mutli-omics data.

overall_design: ATAC-Seq were performed to survey chromatin accessibility in MDA-MB-231 with EZH2 or E2F1 presences. For knockdown experiment, cells at approximately 70-80% confluency were transduced with the lentivirus for 24 h and selected with puromycin (2 μg/ml) for 72 h.

first: Mijoung

last: Yoo

first: Hyeonji

last: Lee


title: A comprehensive atlas of testicular interstitium reveals Cd34+/Sox4+ mesenchymal cells as potential Leydig cell progenitors [CUT&Tag]

city: Guangzhou

first: Jia

middle: Xiao

last: Huang

state: Guangdong

address: Zhongshan 2rd

institute: GDPH

summary: Decreasing fertility rates has emerged as a significant social and medical concern, with male infertility accounting for at least half of the cases. Conventional semen analysis offers restricted prognostic utility for male fertility, largely because a considerable number of male infertility incidents are attributed to dysfunctions in the testicular interstitium. Here we have not only characterized transcriptome data and reveals Cd34+/Sox4+ mesenchymal cells as potential Leydig cell progenitor, but also examined super enhancers information in both young, adult and aged mice Leydig cell progenitors. Our findings reveal A comprehensive atlas of testicular interstitium during aging in both H3K27ac modifications and gene expression alterations. Specifically, the transcriptional activities of key genes involved in progenitor stemness appear to be regulated by super-enhancers. These discoveries offer pivotal insights for developing novel cell-based therapies to ameliorate testicular dysfunction in older individuals.

overall_design: To investigate the gene expression and histone modifications changes , we utilized scRNA-seq to delve into the molecular diversity patterns of Leydig cells within the testicular interstitium across postnatal development and aging.


title: A comprehensive atlas of testicular interstitium reveals Cd34+/Sox4+ mesenchymal cells as potential Leydig cell progenitors [scRNA-Seq]


title: Multiple molecular links between the circadian clock and memory centers in honey bees

city: Bangalore

first: Axel

last: Brockmann

state: Karnataka

address: Bellary Road

department: Neurobiology

country: India

institute: National Centre for Biological Sciences, Tata Institute of Fundamental Research (NCBS-TIFR)

summary: Time and memory are intimately linked: the capability to learn and recall varies over the day and humans and many animals can associate important events with the time of day. However, how the circadian clock and memory centers are connected is not well understood. We time-trained honey bee foragers, collected them at several different time-points for a complete circadian day and performed time-series RNA-sequencing (RNA-seq) to analyze gene expression changes in focal populations of mushroom body (MB) neurons. Thus, we identified synchronized peak-level expression of memory-related genes during training time, receptor for pigment dispersing factor, the major neuropeptide exclusively produced by some central pacemaker neurons, and expression of major clock genes that might represent local clocks.

overall_design:
To identify candidate molecular interactions between the clock and memory centers we used laser capture microdissection (LCM) to collect small Kenyon cell (sKC)-enriched tissue samples, the major multimodal neuronal population of the MBs and an identified locus involved in time-memory processes.
We performed time-series RNA-seq with sKC-enriched samples from time-trained honey bee foragers collected at 7 different time-points over a complete circadian day.
For each of the 7 different time-points, we collected two replicates each from two different colonies. The two colonies were independent and the behavioral experiments were performed separately.

first: Tiyasa

last: Roy

first: Rikesh

last: Jain


title: High Resolution Spatial Mapping of Microbiome-Host Interactions via in situ Polyadenylation and Spatial RNA Sequencing

first: Iwijn

last: De Vlaminck

overall_design: Spatial transcriptomics

first: Ioannis

last: Ntekas

first: David

last: McKellar

first: Lena

last: Takayasu


title: A novel association of EZH2 and E2F1 promotes breast cancer cell proliferation through chromatin remodeling [CHIP-Seq]

overall_design: ChIP-seq for E2F1 or H3K27me3 were conducted in MDA-MB-231 cell lines. For knockdown experiment, cells at approximately 70-80% confluency were transduced with the lentivirus for 24 h and selected with puromycin (2 μg/ml) for 72 h. For the drug treatment, cells were exposed to DMSO or GSK126 (Tocris Bioscience) for 72 h.


title: Maternal indole supplementation protects offspring from NAFLD through altered microbiota- and AHR-mediated ceramide metabolism

city: Oklahoma City

first: Karen

last: Jonscher

address: 975 NE 10th St. BRC North rm 358

department: HHDC

institute: University of Oklahoma Health Sciences Center

summary: MaternalWestern-style diet (WD) disrupts early life gut microbiota in the offspring and is associated with pediatric nonalcoholic fatty liver disease (NAFLD). Here, we report that oral supplementation with gut-derived tryptophan metabolites indole (Ind) or indole-3-acetate (I3A) during pregnancy and lactation in WD-fed dams had persistent effects in offspring liver, acting on key upstream regulators in WD-challenged offspring that suppress pathways for steatosis, fibrosis, and oxidative stress. Maternal Ind or I3A activated aryl hydrocarbon receptor (AHR) signaling, leading to increases in long-chain and very long-chain (VLC) ceramides in offspring liver and small intestine. These effects were evident as early as postnatal day 14. The tryptophan metabolite 5-hydroxyindoleacetate (5-HIAA), an AHR ligand, was depleted in offspring by maternal WD and restored by maternal I3A treatment. Fecal transplantation studies demonstrated that VLC ceramides and liver fibrosis remodeling were mediated by maternal indoles altering the gut microbiota, with strong associations with Lactobacillaceae. Collectively, these findings define a novel and persistent protective effect of maternal Ind and I3A to prevent NAFLD, acting both directly on the liver and through the microbiota. These tryptophan metabolites may serve as therapeutic targets for future interventional studies aimed at prevention of pediatric NAFLD.

overall_design: A mouse model of maternal WD was used to investigate the effect in offspring of indole (Ind) or indole-3-acetate (I3A)  exposure during gestation and lactation.  Offspring were weaned to a chow (CH) diet for 9 weeks, followed by a 4-week WD challenge until 16 weeks of age. Bulk RNA-seq was run on liver tissue from these four groups of offspring.

middle: R

first: Jacob

middle: E

last: Friedman

first: Ashok

last: Mandala

first: Benjamin

middle: N

last: Nelson


title: A novel association of EZH2 and E2F1 promotes breast cancer cell proliferation through chromatin remodeling [RNA-Seq]

overall_design: RNA-Seq were performed to survey transcriptomics in MDA-MB-231. For knockdown experiment, cells at approximately 70-80% confluency were transduced with the lentivirus for 24 h and selected with puromycin (2 μg/ml) for 72 h. For the drug treatment, cells were exposed to DMSO or GSK126 (Tocris Bioscience) for 72 h.


title: Increased CPT1a expression is a critical cardioprotective response to pathological stress that suppresses gene programs for remodeling and enables rescue by gene transfer

city: Columbus

first: Maciej

last: Pietrzak

state: OH

address: 1800 Cannon Drive, 340C Lincoln Tower

department: Department of Biomedical Informatics College of Medicine

institute: Ohio State University

summary: Carnitine palmitoyl transferase 1 (CPT1) is a rate-limiting enzyme for long chain fatty acid oxidation (FAO) in cardiac mitochondria. In adult hearts, CPT1b predominates, while CPT1a is co-expressed at lower levels. Pathological stress on the heart is known to induce CPT1a expression, but it’s role in pathological remodeling is unknown. CPT1 isoform expression was assayed in myocardium of human heart failure (HF) patients with nonischemic cardiomyopathy (NICM). To explore the role of CPT1a upregulation in response to pathological stress, mice were subjected to cardiac pressure overload via transverse aortic constriction (TAC) or sham surgery (sham) with cardiac-specific CPT1a knockdown or cardiac-specific, AAV9 mediated overexpression of CPT1a (AAV9.cTNTN.Cpt1a).  MiR370, known to suppress hepatic CPT1a, was also overexpressed to determine if miR370 regulates cardiac CPT1a expression. CPT1a protein was elevated and miR370 reduced in myocardium of male and female NICM patients (204% vs. non-failing unused donor hearts), as well as in failing mouse hearts. AAV mediated miR370 overexpression in mouse hearts suppressed CPT1a expression and attenuated the response of CPT1a to TAC. Preventing CPT1a upregulation in response to TAC in cardiac specific CPT1a knockout mice (csCPT1a ko) exacerbated adverse remodeling during TAC, causing severe dysfunction and increased mortality. In contrast, CPT1a overexpression (2.8 fold), attenuated impaired ejection fraction (EF, by 54%), fractional shortening (FS, 65%) and +/-dp/dt, and reduced ANP expression and heart mass/tibia length vs. PBS-infused TAC hearts (p<0.05). Delivery of AAV9.cTnT.Cpt1a 4 wks after TAC surgery during cardiac dysfunction, led to significant rescue of EF and FS vs. animals receiving empty virus and mitigated the exacerbated dysfunction of csCPT1a ko hearts at 4 wks TAC. RNA-seq and reverse transcription-quantitative PCR revealed a novel function of CPT1a in suppressing hypertrophic, profibrotic and cell death gene programs in both sham and TAC hearts, irrespective of changes in FAO. The effects of CPT1a in the heart extend beyond FAO and include a non-canonical regulation of cardiac gene programs. In addition to an animal model of HF, CPT1a upregulation occurs in failing human hearts, and is a critical and cardioprotective adaptation to pathological stress that attenuates adverse cardiac remodeling.

first: Andrew

last: Carley

first: Santosh

last: Maurya

first: Chandan

first: Yang

last: Wang

first: Azariyas

middle: A

last: Challa

first: Zhentao

last: Zhang

first: Hua

last: Zhu

first: Ahlke

last: Heydemann

first: Kenneth

middle: C

last: Bedi Jr

first: Christos

middle: P

last: Kyriakopoulos

first: Craig

middle: H

last: Selzman

first: Stavros

middle: G

last: Drakos

middle: B

last: Margulies

first: E

last: Lewandowski


title: Expression data from NC/Nga mice with HDM-induced dermatitis

city: Cambridge

first: Xin

last: Chen

state: Massachusetts

address: 200 Sidney St

institute: AbbVie

summary:
Six applications (twice per week) of HDM cream (Biostir AD) to the back skin and ears of NC/Nga mice resulted in robust phenotype of dermatitis (skin inflammation, itch and barrier function impairement). Expression of an array of genes are altered. IPA and upstream regulator analysis showed similarities to human atopic dermatitis.
We used microarray to detail the gene expression to understand the relevant pathways and upstream regulators activated in HDM-induced dermatitis in NC/Nga mice

overall_design: We collected inflammed ear and back skin tissue at the end of the study. Tissues were stored in 1 mL of RNAlater. RNA was extracted with standard method. Gene array was conducted using Mouse Clariom D assay.

first: Zhi

last: Su

first: Elizabeth

last: Asque

first: Kathleen

last: Smith

first: Jacqueline

last: Loud


title: The melatonin delivery system based on nano-SiO2 optimizes photosynthetic carbon metabolism and yield formation of soybeans in saline-alkali land

status: Public on Jan 20 2026

city: Daqing

first: Qiang

middle: zihan zhao

last: Zhao

state: Heilongjiang

address: 5 Xinfeng Road

institute: Heilongjiang Bayi Agricultural University

summary: Nanomaterials show a great potential in regulating plant growth and improving stress resistance due to their unique physical and chemical characteristics. In this study, nano-silicon dioxide (nano-SiO2) was prepared by the sol-gel method and used to construct a highly efficient melatonin delivery system. Soybean cultivars Hefeng 50 and Henong 95 were field-grown in saline-alkali soil and foliar-sprayed with 200 mg/L nano-SiO2, 300 μM melatonin (MT), or their combination at the V3 stage. In the MT-nano-SiO2system, the encapsulation efficiency and drug-loading capacity of melatonin by nano-SiO2were 35% and 53%, respectively. The system can significantly enhanced melatonin photostability. Scanning electron microscopy results showed that the MT-nano-SiO2 composite can be directly adsorbed on the leaf surface. The MT-nano-SiO2 treatment significantly reduced salt-alkali stress induced reactive oxygen species (ROS) accumulation by activated the enzymatic and non-enzymatic antioxidant system expressed as enhancing the activities of SOD, CAT, and APX and regulating glutathione (GSH/GSSG) levels. The results of physiology, RNA-seq and qRT-PCR indicated that MT-nano-SiO2 treatment can repair photosynthetic carbon metabolism damage induced by salt-alkali stress. Specifically, it increased leaf area, photosynthetic pigment content, photosystem II (PSⅡ) efficiency (Fv/Fm, Qy), net photosynthetic rate (Pn), stomatal conductance (Gs), and intercellular CO2concentration (Ci). It also promoted the activities of sucrose phosphate synthase (SPS), sucrose synthase (SuSy), but inhibited the activities of α-amylase, β-amylase to enhance soluble sugar, sucrose, and starch accumulation. Ultimately, MT-nano-SiO2 treatment significantly improved pod number per plant, seed number per plant, 100-seed weight, and yield of soybean plants.

overall_design: RNA-seq analysis was performed on the functional leaves of soybean cultivar HN95 at 7 days after MT,  nano-SiO2 and nano-SiO2+MT foliar application

first: Jianing

last: Cui

first: Suyu

first: Yanli

last: Du

first: Chunyuan

last: Ren

first: Liang

last: Cao

first: Yuxian


title: Next generation sequencing from primary glioblastoma patient tissues (Total RNA-seq)

city: Seongnam-si

first: Jaejoon

last: Lim

address: 59 Yatap-ro, Bundang-gu

department: College of Medicine

institute: CHA University

summary: To investigate transcriptome landscape in primary GBM, we performed total RNA-seq using 72 tumor tissues from 52 patients with primary GBM.

overall_design: Whole transcriptome, total RNA seq profiles of 52 primary GBM patient (sample n=72).

first: JeongMin

last: Sim

first: JeongMan

last: Park

first: Yu

last: Kim

first: DongKil

first: Kyunggi

last: Cho


title: Genetic and Pharmacological Targeting of the EphA4/Tie2 Axis Results in Improved Pial Collateral Response following Ischemic Stroke

city: Blacksburg

first: Michelle

last: Theus

state: VA

address: 234 Craig Drive

institute: Virginia Polytechnic Institute and State University

summary: Background: Pial collaterals are a major determinant of patient outcome following ischemic stroke, however, targeted treatments for enhancing these blood vessels remain elusive. EphA4, a receptor tyrosine kinase, has been found to restrict the growth of these vessels, potentially through modulation of the Tie2 signaling pathway. The present study assessed the endothelial cell (EC)-specific role of EphA4 in arteriogenesis and the therapeutic potential of Vasculotide, a Tie2 agonist, after ischemic stroke. Methods: EC-specific EphA4 knockout mice and wildtype controls, as well as wildtype mice treated with vehicle or Vasculotide, were subjected to a permanent middle cerebral artery model of stroke. Infarct volume and functional recovery were assessed. Vessel painting coupled with immunohistochemistry was employed to assess collateral size and cellular changes. Bulk RNA sequencing of the pial surface was performed to identify unique transcriptional changes.  Results: Deletion of EphA4 in ECs resulted in increased collateral size and accelerated cellular remodeling, which correlated with reduced infarct volume, enhanced CBF recovery, and improved performance on behavioral assessments. These effects could be replicated in wildtype mice through the administration of 3g/kg Vasculotide immediately following stroke. Treatment with 150g/kg Vasculotide provided neuroprotection and increased collateral size but lacked the robust improvements in CBF recovery and motor recovery seen in the 3g/kg treated group. Additionally, pial surfaces from 3g/kg Vasculotide and EphA4 KO mice showed significant changes in mRNA transcripts associated with the Krt5/Krt14 pathway compared to WT controls.  Conclusion: The EphA4/Tie2 signaling axis mediates collateral growth and can be successfully therapeutically targeted by Vasculotide.

overall_design: Stroke was induced in CD1 WT and EphA4 EC-Ko mice, then after 24hours, the contralateral and ipsilateral meningeal brain layer was dissected and RNA isolated for bulk sequencing.

first: Alexandra

middle: M

last: Kaloss

last: Lin

first: Hehuang

last: Xie


title: Loss of cisPTase function in the liver promotes a highly penetrant form of fatty liver disease that rapidly transitions to hepatocellular carcinoma

city: New Haven

first: Abhishek

middle: K

last: Singh

state: CT

address: 10 Amistad Street

department: Pharmacology and VBT

institute: Yale University

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

overall_design: Refer to individual Series

first: Balkrishna

last: Chaube

first: Kathryn

last: Citrin

first: Joseph

last: Fowler

first: William

last: Sessa

first: Sonal

last: Shree


title: Loss of cisPTase function in the liver promotes a highly penetrant form of fatty liver disease that rapidly transitions to hepatocellular carcinoma [RNA-seq]

summary: In developed countries, obesity-linked fatty liver is a significant risk factor for hepatocellular carcinoma (HCC); however, the molecular mechanisms underlying the transition from non-alcoholic fatty liver disease (NAFLD) to HCC remains unclear. The present study explores the role of the endoplasmic reticulum (ER)-associated protein NgBR, an essential component of the cis-prenyltransferases (cis-PTase) enzyme, in chronic liver disease. Here we show that genetic depletion of NgBR in hepatocytes ofmice (N-LKO) intensifies triacylglycerol (TAG) accumulation, inflammatory responses, ER/oxidative stress, and liver fibrosis, ultimately resulting in HCC development with 100% penetrance after four months on a high-fat diet. Comprehensive genomic and single cell transcriptomic atlas from affected livers provides a detailed molecular analysis of the transition from liver pathophysiology to HCC development. Importantly, pharmacological inhibition of diacylglycerol acyltransferase-2 (DGAT2), a key enzyme in hepatic TAG synthesis, abrogates diet-induced liver damage and HCC burden in N-LKO mice. Overall, our findings establish NgBR/cisPTase as a critical suppressor of NAFLD- HCC conversion and suggests that DGAT2 inhibition may serve as a promising therapeutic approach to delay HCC formation in patients with advanced non-alcoholic steatohepatitis (NASH).

overall_design: Comparative gene expression in Wild type (WT) and Liver specific NgBR KO mice fed with either High Fat Diet (HFD) or Western type of diet (WD) for 16 weeks.


title: Effect of Kdm4a knockdown (KD) on gene expression in mosue PTR NEPC cells derived from Pb-Cre+,Pten f/f, Trp53 f/f, Rb1 f/f NEPC mouse model

city: Houston

first: Guocan

last: Wang

state: TX

address: 1515 Holcombe Blvd, T7.3900

institute: MD Anderson Cancer Center

summary:
To investigate the role of KDM4A in the regulation of gene expression in NEPC cells, we established Kdm4a KD cell lines in which Kdm4a gene has been knocked down by shRNA.
We then performed gene expression profiling analysis using data obtained from RNA-seq of 4 different cells at two time points.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for PTR cells infected with non-targeting shRNA control and its KD derivatives (shKDM4A-#4).

first: Celia

middle: S

last: Mak


title: Loss of cisPTase function in the liver promotes a highly penetrant form of fatty liver disease that rapidly transitions to hepatocellular carcinoma [scRNA-seq]

overall_design: Comparative gene expression in Wild type (WT) and Liver specific NgBR KO mice fed with  Western type of diet (WD) for 16 weeks.


title: Endothelial Cell-specific Activation of NOX1 Drives Obesity and Metabolic Syndrome via Skeletal Muscle Mitochondrial Dysfunction with Novel Genetic Signatures

city: Los Angeles

first: hua

last: cai

state: California

address: 450 Hilgard Ave

institute: University of California, Los Angel

summary: Presently, we investigated hypothesized roles and mechanisms of cell type-specific, selective activation of different vascular NADPH oxidase (NOX) isoforms in obesity and metabolic syndrome.  Expression of NOX1 was significantly upregulated in WT mice fed high-fat diet.  Global knockout of NOX1 (NOX1-/y), rather than of NOX2/NOX4, markedly abrogated high-fat feeding induced body weight/fat mass gain, preadipocyte differentiation, fatty liver, glucose intolerance, and insulin/leptin resistance.  Intriguingly, endothelial-specific NOX1 knockout (Cdh5cre-NOX1CKO), rather than vascular smooth muscle-specific NOX1 knockout (Myh11cre-NOX1CKO), substantially alleviated these features of obesity and metabolic syndrome.  Consistently, endothelial-specific NOX1 knockin mice (Cdh5cre-NOX1CKI) fed high-fat diet displayed exaggerated metabolic disorders.  Endothelial cell (EC)-specific knockout/knockin of NOX1 was confirmed using EC washout experiments.  Food/water intakes were not different from corresponding controls in high-fat fed NOX1-/y, Cdh5cre-NOX1CKO or Cdh5cre-NOX1CKI mice, indicating no difference in energy intake.  Instead, spontaneous activity, exercise capacity, mitochondrial oxygen consumption/ATP production, skeletal muscle mitochondrial function (ROS production and swelling activity), and mitochondrial cristae structure were all substantially improved in NOX1-/y or Cdh5cre-NOX1CKO mice, indicating augmented energy expenditure attributed to preserved skeletal muscle mitochondrial function.  Supportively, Cdh5cre-NOX1CKI mice displayed deteriorated exercise capacity and skeletal muscle mitochondrial dysfunction.  Endothelium-dependent vasorelaxation was restored in high-fat fed NOX1-/y or Cdh5cre-NOX1CKO mice, confirming improved endothelial function.  RNA-seq identified 4 genes (Cntnap4, Sgsm1, Tll2 and Syt9) and 7 genes (Odf3l2, Col9a1, Cldn23, Atp5g2, Nkx6-3, Ntsr2 and Zfp69) significantly down/upregulated in high-fat fed Cdh5cre-NOX1CKO mice, among which Cntnap4 and COL9A1 linked to muscular disorders.  Importantly, we observed marked upregulation of NOX1 in isolated coronary arteries from human obese patients.  Taken together, our data for the first time establish a novel and paradigm-shifting concept that endothelial NOX1 drives systematic metabolic phenotypes, via impairment in skeletal muscle mitochondrial dysfunction with novel genetic signatures.  Tissue-specific targeting of endothelial NOX1 and novel candidate genes may prove to be robustly effective in treating obesity and metabolic syndrome.

overall_design: RNAs isolated from soleus muscles of experimental mice (3 each group from 4 experimental groups of Cdh5cre-WT mice under 8 weeks regular diet, Cdh5cre-WT mice under 8 weeks  high-fat diet, Cdh5cre-NOX1CKO mice under 8 weeks regular diet, and Cdh5cre-NOX1CKO mice under 8 weeks high-fat diet)

first: Kai

last: Huang

first: Yuanli

first: Yuhan

last: Zhang

first: Yixuan

first: Nicholas

last: W. Hatch

first: Julie

last: K. Freed

first: Hua

last: Cai


title: microRNAs in congenital diaphragmatic hernia: insights into prenatal and perinatal biomarkers and altered molecular pathways

city: Aurora

first: JAMES

last: BARDILL

state: CO

department: Surgery

institute: UNIVERSITY OF COLORADO-ANSCHUTZ MED

type: Non-coding RNA profiling by high throughput sequencing

summary: BACKGROUND: Congenital diaphragmatic hernia (CDH) is characterized by a diaphragmatic defect, leading to herniation of abdominal organs into the chest, lung compression, and impaired lung development, often resulting in pulmonary hypertension and lung hypoplasia. Prenatal imaging techniques like ultrasound and MRI provide anatomical predictors of outcomes, but their limitations necessitate novel biomarkers for better prognostic accuracy. OBJECTIVE: This study aims to identify unique circulating maternal, fetal, and neonatal microRNAs (miRNAs) that can distinguish CDH pregnancies from healthy controls and assess their potential as markers of disease severity. STUDY DESIGN: We conducted a prospective study involving third-trimester maternal blood, amniotic fluid, cord blood, and neonatal blood samples from pregnancies complicated by CDH and healthy controls. miRNA expression was analyzed using RNA-sequencing, and random forest analysis identified miRNAs distinguishing CDH survivors from nonsurvivors. Pathway enrichment analyses were performed to explore the biological relevance of differentially expressed miRNAs. RESULTS: Significant miRNA expression differences were observed between CDH and control samples across all sample types. In infant blood, 148 miRNAs were up-regulated, and 36 were down-regulated in CDH cases. Pathway analysis revealed that dysregulated miRNAs in CDH targeted pathways related to protein binding, transcription regulation, and signaling pathways implicated in pulmonary hypertension and lung hypoplasia. Random forest analysis identified miRNAs in maternal blood (miR-7850-5p_L-1R+2, miR-942-3p, and miR-197-3p) that distinguished CDH survivors from nonsurvivors, with an receiver operating characteristic area under the curve of 1.0. CONCLUSION: Circulating miRNAs in maternal blood offer promising biomarkers for predicting CDH outcomes. miRNAs from infant blood provide mechanistic insights and potential targets for therapeutic intervention in critical pathways of pulmonary hypertension and lung hypoplasia. Further studies with larger cohorts are needed to validate these findings and explore the clinical application of miRNA biomarkers in CDH management.

overall_design: microRNA sequencing of amniotic fluid, cord blood, fetal blood, and 3rd trimester maternal serum from control and CDH pregnancies.

first: James

last: Bardill

first: Chris

last: Derderian


title: Directed Evolution of Enzymes for Bioorthogonal Chemistry Using Acid Chloride Proximity Labeling

city: Chicago

first: Bryan

last: Dickinson

state: il

address: 929 E 57th St

institute: UChicago

summary: MDA-MB-231 cells expressing BS2-TRFLE in different compartments (cytosol, mitochondria, nucleus) were labeled with pAC-2. Subsequent enrichment of labeled RNAs, PolyA capture and RNA-seq reveals RNA populations in those compartments.

overall_design: Differentially Expressed Gene (DEG) analysis of transcripts enriched in different compartments

first: Shubhashree

last: Pani

first: Ashley

last: Ogorek

first: Bryan C.

first: Jeffrey

last: Martell


title: Tumor-specific lncRNA IGF1R-AS1 trans-regulates chromatin interactions associated with oncogenic MYC signaling

first: Rendong

last: Yang

state: IL

address: 420 E Superior St

department: Urology

institute: Northwestern University


title: Lactate-mediated cholesterol uptake promotes liver cancer progression through the SCARB1-autophagy axis

city: GUANGZHOU

first: jiamin

last: chen

address: WAIHUAN EAST ROAD

institute: SOUTH CHINA UNIVERSITY OF TECHNOLOGY

summary: Metabolic reprogramming supports the proliferation of cancer cells under hypoxic stress, including enhanced glycolysis and altered fatty acid metabolism. However, the mechanism underlying its regulation of cholesterol metabolism remains incompletely understood. Here, we show that lactate-induced cholesterol accumulation activates mammalian target of rapamycin complex 1 (mTORC1) signaling under hypoxic conditions, thereby promoting hepatocellular carcinoma (HCC) progression. Mechanistically, lactate upregulates scavenger receptor class B type 1 (SCARB1) expression by enhancing histone H3 lysine 18 lactylation (H3K18la), leading to increased cholesterol levels. We furthermore demonstrate that SCARB1-mediated cholesterol uptake is essential for the activation of mTORC1, which promotes tumor growth by preventing HCC cells from excessive autophagy. Importantly, analysis of clinical HCC samples showed a positive correlation between H3K18la and SCARB1 expression. Taken together, these findings provide novel insights into hypoxia-driven metabolic reprogramming and reveal a previously unrecognized connection between lactate and cholesterol metabolism, suggesting a potential innovative cancer therapy for HCC.

overall_design: RNA-Seq profiling of Hep3B cells cultured under normoxia, hypoxia, hypoxia treated with oxamate sodium for 48 hours

first: Jiamin

last: Chen

first: Mingyue

last: Zhao

first: Kengcheng

last: Liu

first: Shengqi

last: Shen

first: Shi-Ting

last: Li

first: Jin

first: Guanxu

last: Ji

first: Linchong

last: Sun

first: Ping

last: Gao

first: Tong


title: BDNF engages pituitary stem cells for establishment of the adult gland and for homeostasis of the corticotrope lineage

city: Montreal

first: Kevin

last: Sochodolsky

state: QC

address: 110 Av des Pins O

department: Molecular Genetic

country: Canada

institute: Institut de recherche clinique de Montreal

summary: The development and maintenance of complex organs rely on the balanced expansion of cells of different lineages to establish a functional tissue. In the pituitary gland, maintenance of the adult corticotrope lineage relies heavily on replication of differentiated cells. In contrast in pathological conditions, such as adrenalectomy that depletes circulating glucocorticoids (Gc), pituitary stem cells (PSC) are activated to increase the number of corticotropes. In the present work, we used the proopiomelanocortin (POMC) knockout mouse model of Gc deficiency to characterize pre-corticotrope precursors that are normally rare and short lived but accumulate in this model. Differentiation of PSCs into pre-corticotropes is repressed by Gc and requires the lineage-specific transcription factor Tpit. Pre-corticotrope maintenance is dependent on a brain-derived neurotropic factor (BDNF) autocrine loop that is sensitive to Gc. In normal development, BDNF is critical for engagement of PSCs into proliferation and differentiation during the postnatal expansion of the gland.

overall_design: RNA was extracted from pituitaries from 2 WT male mice and 2 POMC-KO male mice.

first: Konstantin

last: Khetchoumian

first: Jacques

last: Drouin


title: Novel Mesoporous Silica Nanoparticles Enhances Soybean Salt-Alkali Stress Resistance and Yield by Regulating Photosynthetic Carbon Metabolism

first: Qiang

summary: Soil salinization-alkalization is a widespread abiotic stress globally, severely impairing crop growth and environmental ecology. Nanomaterials hold significant potential for application in regulating plant stress tolerance due to their unique physical and chemical properties. In this study, the sol-gel method was optimized to synthesize a type of spherical, monodisperse, amorphous mesoporous silica nanoparticles (MSNs) with an average particle size of 40-50 nm and a positive surface charge of 35 mV. A 20 mg/L MSN solution was foliarly applied to two soybean cultivars, Hefeng 50 (HF50) and Henong 95 (HN95), in a pot experiment at the R1 stage to investigate its effects on plant growth and yield-related traits under saline-alkali stress (pH 9.2). MSNs treatment significantly alleviated the growth inhibition induced by saline-alkali stress. Specifically, MSNs significantly increased the plant height, leaf area, root volume, and root surface area of soybean plants under saline-alkali stress. MSNs also increased the dry matter accumulation of plant shoots and roots, improved root activity, and increased the number of pods and seeds per plant. MSNs enhanced cell mechanical strength by activating the synthesis of cuticle and epidermal wax, and maintained intracellular metabolic homeostasis by activating the antioxidant defense system and suppressing the excessive activation of pathways such as the mitogen-activated protein kinase (MAPK) pathway. Additionally, MSNs increased the content of photosynthetic pigments in soybean leaves, thereby enhancing light energy absorption and utilization efficiency, and elevating carbohydrate levels. MSNs promoted the directed translocation of photosynthates to sink organs such as seeds and roots by regulating the activity of carbon metabolism enzymes and source-sink allocation. Taken together, these cumulative effects improved soybean saline-alkali stress tolerance, and ultimately increasing the number of pods per plant, seeds per plant, 100-seed weight, and total yield per plant. The study provides theoretical basis and technical support for the development of nanomaterial-based cultivation practices to improve crop saline-alkali tolerance.

overall_design: RNA-seq analysis was performed on the functional leaves of soybean cultivar HN95 at 7 days after MSNs foliar application

first: Yuxuan

last: Huang

first: Yanli

last: Du

first: Suyu

first: Qifeng

last: Pan

first: Yuxian

last: Zhang


title: Perioperative administration of fucoidan induced immune-suppressive changes that resulted in no beneficiary outcomes in postoperative neurocognitive recovery

first: Linpeng

address: Tianhe District

institute: Jinan University

summary: For many of the versatile functions of polysaccharides as natural ingredients in human foods, the immunomodulatory and anti-inflammatory activities of fucoidan, partly owing to its high sulfate content, attracted extensive attention in its potential application in cancer therapy as well as in prevention of neurodegeneration. In this study, we characterized the impact of long-term supplementation of Undaria pinnatifida-derived fucoidan on the gene expression and immune cell abundance in mouse PBMCs. Despite the significantly increased Th17 cells and activated NK cells, naïve B cells were substantially reduced in the PBMCs in fucoidan mice.  Fucoidan supplementation induced prominent expression changes in genes associated with Th1/Th2 cell differentiation. Although fucoidan displayed a remarkable anti-inflammatory capacity in our mouse models, perioperative administration of fucoidan failed to show any noticeable beneficiary effect in relieving synaptic and cognitive dysfunction at the acute phase after surgery, which was believed to cause neurocognitive impairment by inducing neuroinflammation. Comparing with that of the mice with control diet, mitigated microglia activities including neuronal surveillance and phagocytosis were also observed in mice with perioperative administration of fucoidan. In addition, no influence on either basal level or surgery-induced oxidative stress was observed in mice with fucoidan supplementation. Given the complex features of inflammation as the first response to various detrimental situations, we proposed that the anti-inflammation potential of fucoidan was likely to induce an immune-suppressive change in the postoperative mouse brain and conferred unfavorable environment for the neurocognitive recovery at least at the acute phase after surgery.

overall_design: This study employed a controlled animal experiment to investigate the impact of dietary fucoidan supplementation on peripheral immune transcriptomes and immune cell composition in mice. Peripheral blood mononuclear cells (PBMCs) were used as the biological material for transcriptomic profiling. Male C57BL/6J mice were assigned to experimental groups based on dietary intervention. Adult mice (8 weeks old) received either fucoidan supplementation or saline by daily oral gavage for one month while maintained on a standard basal diet. Fucoidan was derived from Undaria pinnatifida and administered at a dose of 200 mg/kg/day. Control animals received an equivalent volume of saline under identical conditions. At the end of the supplementation period, peripheral blood was collected by cardiac puncture, and PBMCs were isolated using density-gradient centrifugation. Total RNA extracted from PBMCs was subjected to high-throughput mRNA sequencing to characterize global gene expression profiles. The primary experimental variable was dietary supplementation with fucoidan versus saline control. The experimental design enabled comparison of PBMC transcriptomes between treatment groups to assess fucoidan-associated alterations in immune-related gene expression and inferred immune cell composition. All samples were processed in parallel using the same RNA extraction, library preparation, sequencing platform, and bioinformatics pipeline to minimize technical variability.

first: Cundong

first: Yuan

last: Zhou

first: Xiaosheng

last: Liang

first: Chao

last: Song

first: Shan

last: Xiao

first: Shufang

first: Yi

last: Zou


title: Prolonged Loss of Oxidative Phosphorylation and Mitochondrial Mass Characterize CD66b+ Leukocytes from Patients with Sepsis

city: Gainesville

first: Philip

last: Efron

state: FL

address: 1600 SW ARCHER RD

department: MD-SURGERY-CRITICAL CARE

institute: University of Florida

summary: Introduction: Sepsis leads to expansion of myeloid-derived suppressor cells (MDSC) and their subtypes. These normally transitory MDSC suppress T cell activation and alter T cell cytokine production while simultaneously promulgating systemic low-grade inflammation. Immune metabolism has been demonstrated to shape cell responses and regulate immune suppression or enhance effector activity. While the metabolism of MDSC has been extensively studied in cancer, the metabolic phenotype of this heterogeneous population in sepsis remains unclear. Our goal was to assess metabolic flux in MDSC during and after sepsis and stratify these patients by characteristics and outcome to determine differences that may guide treatment decisions. Methods: Peripheral blood mononuclear cells (PBMC) from healthy subjects and sepsis patients at four days, 2-3 weeks, and 6 months underwent CD66b+ or CD3+ isolation, followed by assessment of metabolic flux, flow cytometry, mRNA sequencing, and epigenetic analysis. Results: Mitochondrial basal oxygen consumption rates (OCR) and maximal oxygen consumption rates (SRC) were decreased in MDSC from septic patients at four days after infection and persisted for up to six months after sepsis onset. Glycolysis was not impacted by sepsis. In contrast, oxidative metabolism in CD3+ T cells was similar between sepsis patients and healthy subjects. Reduced MDSC oxidative metabolism was linked to adverse clinical outcomes. The decline in oxygen consumption from MDSC in septic patients was also linked to significant reductions in MDSC mitochondrial content. Transcriptomic analysis of CD66b+ cells isolated from PBMC healthy participants and patients with sepsis at four days, 2-3 weeks, and 6 months revealed 19 differentially expressed genes and two long non-coding RNAs as potentially responsible for this decline in mitochondrial mass. Specifically, NR4A3, NR4A2, and TAMLIN/NR4A1 (all critical for mitochondrial biogenesis) expression were persistently decreased with reduced chromatin accessibility indicative of gene silencing. Discussion: After sepsis, PBMC CD66b+ cells present with a unique metabolic signature that is not shared with CD3+ T-cell subsets in these patients or other disease cohorts. These changes in mitochondrial function result from a reduced content of these organelles. We have identified gene silencing, reduced gene expression of key transcription factors that regulate mitochondrial biogenesis, as well as increased long non-coding RNA as potential drivers of this unique metabolic phenotype. These results highlight a need to target metabolism in sepsis to promote immune homeostasis and recovery.

overall_design: A total of 383 samples were collected from septic patients: 9 samples at day four, 6 at 2-3 weeks, and 6 samples at six months, as well as individual samples from 12 healthy participants. CD66b+ cells were isolated as described above and total RNA isolated using RNeasy Mini kit (Qiagen 74104) following manufacturers’ recommendations.  RNA was quantified using Qubit RNA Broad Range Assay Kit (Ref# Q10210; Invitrogen, MA) and RNA integrity was assessed using RNA ScreenTape kit (Ref# 5067-5576) on TapeStation 4200 (Agilent). Illumina Stranded mRNA Prep and Ligation kit (Ref# 20040534; Illumina, CA) were used to prepare sample libraries following the manufacturer’s recommendations. Very briefly, 300 ng/uL high quality RNA was captured and purified, followed by reverse transcription to convert the captured mRNA into first and second strands of cDNA. The resulting double stranded cDNA molecules were then enzymatically fragmented in preparation for unique dual indexing using IDT for Illumina RNA UD Set Ligation Indexes (Ref# 20091655; Illumina, CA). The ligated samples were subsequently enriched through PCR amplification on Bio-Rad Thermal cycler (T100; Bio-Rad, CA) and purified using AMPure XP magnetic beads (Ref# A63881; Beckman Coulter, CA). The average fragment length of the library insert was measured to be ~300–400 bp using the dsDNA 1000 kit (Ref# 5067-5582) on Agilent TapeStation. Optimized libraries were pooled to a final concentration of 150pM. The libraries were sequenced on NovaSeq X Plus Platform (Illumina, CA) at UF’s Interdisciplinary Center for Biotechnology Research (ICBR).

first: Christine

last: Rodhouse

first: Evan

middle: L

last: Barrios

first: Leilani

last: Zeumer-Spataro

first: Leandro

last: Balzano-Nogueira

first: Ruoxuan

last: Wu

first: Xuanxuan

last: Yu

first: Guimei

last: Tian

first: Jason

middle: O

last: Brant

first: Miguel

last: Hernandez-Rios

first: Valerie

last: Polcz

first: Whitman

last: Wiggins

first: Angel

last: Charles

first: Marvin

last: Dirain

first: Ricardo

last: Ungaro

first: Jaimar

last: Rincon

first: Tyler

last: Loftus

first: Feifei

first: Guoshuai

last: Cai

first: Lyle

last: Moldawer

first: Robert

last: Maile

first: Michael

last: Kladde

first: Clayton

last: Mathews


title: Hepatocyte-specific knockout of YAP protects against atherosclerosis via inhibition of ANGPTL3 in mice

city: Xi'an

first: Yulong

last: Chen

state: Shaanxi

address: No 1. Xinwang Road

institute: Xi'an Medical University

summary: Background and Aims Lipid-lowering therapy is a cornerstone in the treatment of atherosclerotic cardiovascular disease (ASCVD). Although some lipid-lowering drugs have demonstrated positive effects in patients with ASCVD, their effects are limited in those with homozygous familial hypercholesterolemia (HoFH). It is essential to seek new lipid-lowering targets. Yes-associated protein (YAP) may be involved in lipid metabolism in liver; therefore, we investigated the function of hepatocyte YAP in hyperlipidemia and atherosclerosis. Methods Hyperlipidemia models were generated in apoE-/- mice or mice injected with AAV8-D377Y-mPCSK9, which degrades and deletes low density lipoprotein receptor (LDLR), by being fed a high cholesterol diet (HCD) for 12 weeks. We measured the expression level of hepatic YAP in these apoE-/- mice. Next, we created YAPΔHep apoE-/- mice to further determine the role of YAP in hyperlipidemia and atherosclerosis. AML12 cells and mice injected with AAV8-D377Y-mPCSK9 or YAPΔHepapoE-/- mice were used to elucidate its mechanism. Finally, apoE-/- or LDLR-/- mice were used to observe the therapeutic efficacy of AAV8-Alb-shYAP for hyperlipidemia and atherosclerosis. Results HCD-fed apoE-/- mice showed increased levels of YAP in the liver. Further investigation indicated that YAPΔHepapoE-/- mice exhibited lighter hyperlipidemia and atherosclerosis than YAPflox/floxapoE-/- mice fed with HCD. Conversely, hepatocyte-specific overexpression of YAP (5S) deteriorated hyperlipidemia and atherosclerosis in HCD-fed apoE-/- mice. Furthermore, the lipid-lowering effect of YAP deficiency in hepatocytes was independent of LDLR. Hepatocyte-specific overexpression of angiopoietin-like-3 (ANGPTL3) aggravated hyperlipidemia and atherosclerosis in YAPΔHepapoE-/- mice, indicating that ANGPTL3 is responsible for the function of YAP in hyperlipidemia. Mechanistically, YAP upregulated ANGPTL3 via TEAD4 in hepatocytes independent of LDLR. Notably, AAV8-Alb-shYAP lowered lipid levels in apoE-/- or LDLR-/- mice. Conclusion Taken together, our findings revealed a novel role for the YAP-TEAD4-ANGPTL3 axis in lipid metabolism independent of LDLR. Inhibition of hepatocyte YAP may be an effective lipid-lowering strategy for HoFH.

overall_design: RNA-sequencing analysis of liver tissues from the YAPΔHepapoE-/-mice and the YAPflox/floxapoE-/-mice fed with HCD for 12 weeks

first: Ying

last: Hou

first: Xin

last: Zhang

first: Xia

last: Sun

first: Qiaohong

last: Qin

first: Min

last: Jia

first: Xingli

last: Su


title: Inositol hexakisphosphate Functions as a Cofactor and Modulator of ADAR1 Activity

city: Marburg

first: Francisco

last: Venegas Solis

address: Hans-Meerwein-Straße

institute: Institute of Immunology, Philipps University of Marburg

summary: Adenosine-to-inosine (A-to-I) RNA editing, catalyzed by adenosine deaminases acting on RNA (ADARs), is a key post-transcriptional modification that regulates RNA splicing, stability, and translation. Dysregulation of ADAR activity caused by mutations in ADAR1 leads to Aicardi-Goutières syndrome (AGS), an autoimmune disorder characterized by aberrant activation of Melanoma differentiation-associated protein 5 (MDA5) by self RNA and excessive type I interferon production. Despite its biological and clinical relevance, the regulation of ADAR1 activity remains incompletely understood. Here, we show that ADAR1 protein levels and RNA editing activity in mammalian cells critically depend on the cofactor inositol hexakisphosphate (IP6). Using Inositol-pentakisphosphate 2-kinase (IPPK)-knockout cells, next-generation sequencing (NGS), and a cell-permeable IP6 prodrug (Pro-IP6), we demonstrate that IP6 depletion drastically reduces global RNA editing, while supplementation with Pro-IP6 restores and even enhances editing levels. In vitro ADAR1 translation and RNA editing assays revealed that IP6 contributes to the folding and full catalytic activity of ADAR1, and that inositol pentakisphosphate (1,3,4,5,6-IP5) can partially substitute IP6 as a cofactor. Molecular dynamics simulations and biochemical analyses identified the C6-phosphate of IP6 as a critical determinant of ADAR1 catalytic efficiency, functioning within a hydrogen-bonding network that indirectly governs Zn²⁺-ion positioning through interactions with key residues, including K1039 and N907. Notably, the AGS-associated N907S mutation impairs RNA editing, by altering IP6 coordination and introducing more dynamic situation in the hydrogen-bonding network of IP6 and Zn²⁺-ion. Together, these findings identify IP6 as an essential cofactor and regulator of ADAR1 activity. Through a network of interactions and the availability of IP6, this may represent a new strategy for therapeutically controlling RNA editing in the disease.

overall_design: RNAseq of HeLa WT and HeLa KO IPPK cells  treated or untreated with Pro-IP6 for 24 h. Three independent experiments.

last: Venegas-Solis

first: Mengsi

last: Lu

first: Roni

last: Cohen-Fultheim

first: Felix

last: Bender

first: Valeria

last: Fedeli

first: Takuya

last: Masunaga

first: Mikako

last: Fujita

first: Thomas

last: Zillinger

first: Sabine

last: Schneider

first: Andreas

last: Kaufmann

first: Adolfo

last: Saiardi

first: Erez Y.

last: Levanon

first: Henning

last: Jessen

first: Stefan

last: Bauer


title: Total RNA-seq of C2C12 myotubes treated with agrin or MuSK antibodies

city: Leiden

first: Hailiang

last: Mei

address: Einthovenweg 20

department: Sequencing Analysis Support Core

country: Netherlands

institute: Leiden University Medical Center

summary: Total RNA-seq was performed to investigate if MuSK antibody binding directly affects (NMJ) gene expression in muscle cells. C2C12 differentiated myotubes were treated for 16 hours with bivalent MuSK antibodies (activating MuSK signaling) or functionally monovalent MuSK antibodies (inhibiting agrin-induced MuSK signaling) derived from B-cell receptor sequences from a MuSK myasthenia gravis patient. The total RNA transcriptome was compared to treatment with agrin (the natural activator of MuSK) or a negative control antibody targeting a protein not present in myotubes.

overall_design: RNA-seq profiling of C2C12 differentiated myotubes treated with bivalent MuSK antibodies (13-3B5) or agrin + monovalent MuSK antibodies (13-3B5xb12 or 11-3F6xb12). For each condition 4 biological replicates were generated and used for statistical analysis.

first: Dana

last: Vergoossen

first: Maartje

last: Huijbers


title: Novel repressors of cambium activity in Arabidopsis

city: Durham

first: Wenbin

last: Wei

address: Stockton Road

department: Biosciences

institute: Durham University

summary: Higher order mutants between PXY and ER families are characterised by profound secondary growth defects. It is likely that genes involved in regulating cambium homeostasis are differentially expressed in these backgrounds and consequently they could be used as a tool for gene discovery. The secondary growth region of 3-week-old hypocotyls and roots from wild type, pxy pxl1 pxl2 (pxf), er erl2, and pxf er erl2 lines were analysed for tissue composition and subjected to RNA-seq.

overall_design: RNA-seq profiling of 3-week-old Arabidopsis wild type (Col-0), pxf (pxy-3 pxl1-1 pxl2-1 triple mutant, Etchells et al., 2013), er erl2 (er-105 erl2-1 double mutant), and pxf er erl2 (quintuple mutant, Wang et al., 2019) lines. Hypocotyls and the upper 5mm of root were excised prior to RNA extraction. Comparisons allow the identification of differentially expressed genes in radial growth. Each genotype has three biological replicates.

first: Emma

last: Turley

first: Peter

middle: J

last: Etchells