title: Effect of fiin2 on gene expression of Hep3B cells

city: Changsha

first: Maoyu

last: Li

state: Hunan

address: 87 xiangya road

institute: Xiangya Hospital

summary: Fibroblast growth factor receptor (FGFR) inhibitors have emerged as an important class of targeted therapies in oncology, targeting key pathways associated with tumor growth, angiogenesis, and resistance to conventional treatments. FIIN-2, the first irreversible covalent pan-FGFR inhibitor, has shown promise in overcoming resistance due to gatekeeper mutations; however, its selectivity and molecular mechanisms in tumors remain poorly understood. In this study, an FIIN-2 chemical probe was designed and synthesized to identify both established and novel targets in hepatocellular carcinoma (HCC) via chemoproteomic profiling. An integrative multi-omics approach, including chemoproteomic, phosphoproteomic, transcriptomic, and proteomic analyses, is utilized to elucidate the full spectrum of target proteins, signaling pathways, and downstream effectors regulated by FIIN-2 in HCC. This study greatly advances the understanding of FIIN-2’s on- and off-target effects, offering a comprehensive view of its molecular mechanisms in cancer cells. The integrative multi-omics approach provides a valuable framework for the development and optimization of covalent kinase inhibitors.

overall_design: RNA-seq profiling of Hep3B cells treated with 1um fiin2 or dmso

last: Fu

first: Dandan

last: Zhu

first: Xiaojuan

last: Chen

first: Lingzhi

last: Qu

first: Ming

last: Guo

first: Shuhong

first: Guangyu

last: Xu

first: Zhuchu

first: Yongheng


title: Lamin A/C restrains replication domain activity through higher-order chromatin structures and PCNA interaction [BRU-Seq]

status: Public on Feb 22 2025

city: Beijing

first: Wenxue

last: Zhao

address: Yiheyuan Road

country: China

institute: Peking University

summary: Lamin A/C, a critical nuclear lamina protein, is essential for maintaining nuclear architecture, organizing chromatin and preserving genomic stability. However, its role in directly regulating DNA replication remains unclear. This study investigates how Lamin A/C orchestrates replication initiation by modulating chromatin structure and interacting with proliferating cell nuclear antigen (PCNA). Utilizing high-resolution imaging, chromatin accessibility assays, and sequencing, we demonstrate that Lamin A/C stabilizes replication domains (RDs) by restricting chromatin mobility, preserving spatial organization, and maintaining accessibility. Furthermore, Lamin A/C interacts with PCNA via its Ig-fold domain, regulating PCNA availability by sequestering a pool of PCNA and modulating its expression, and thereby controlling its recruitment to replication machinery. The loss of Lamin A/C results in chromatin architecture reorganization and elevated PCNA availability at RDs, which coordinately trigger excessive activation of replication origins, leading to replication stress and DNA damage. These disruptions prolong the S phase and compromise genome stability, highlighting Lamin A/C as a critical gatekeeper of balanced replication initiation. Our findings reveal Lamin A/C’s dual role in chromatin organization and replication machinery regulation, offering valuable insights into its involvement in replication-associated diseases such as cancer and viral infections and highlighting potential therapeutic opportunities through targeting replication dynamics.

overall_design: BrdU-seq of PCNA in wild-type (WT) and Lamin A/C knockout Hela cells during G1/S phase.


title: Ectopic endometrial stromal cell-derived extracellular vesicles encapsulating PKM2 inhibit autophagy inducing endometrial collagen I deposition in endometriosis

city: China

first: Yuan

address: Hankou Road 22, Nanjing 210008

institute: Nanjing University medical school

type: Expression profiling by high throughput sequencing

summary: Endometriosis (EMs) is a common infertility-related disease in women of reproductive age. Impaired endometrial decidualization is one of the most important factors contributing to the embryo implantation failure EMs patients. However, the exact mechanism remains unclear. Previous studies have shown collagen I deposition in the eutopic endometrium of EMs patients, which may lead to impaired endometrial decidualization. The level of collagen I in eutopic endometrium of EMs was analyzed. We performed a proteomic analysis of ectopic endometrial stromal cell-derived extracellular vesicles (EMs-EVs) and extracellular vesicles derived from endometrial stromal cells in the endometrium of control patients (CTL-EVs). An endometrial transcriptional profiles of EMs patients and normal controls in the mid-secretory phase of menstrual cycle was compared. Endometrial stromal cells (ESCs) were stimulated with chloroquine or rapamycin to evaluate the association between autophagy and collagen I. The expression of PKM2 in EMs-EVs and serum extracellular vesicles from EMs patients were examined by western blotting. PKM2 was overexpressed or knockdown in ESCs to investigate the level of autophagy and collagen I. ESCs were treated with ectopic ESC-derived extracellular vesicles with highly expressed PKM2 protein, and the potential molecular mechanisms were further confirmed through western blotting and immunohistochemical analysis. We found that endometrial collagen I expression during the mid-secretory phase was increased in the EMs group. We demonstrated that autophagy is defective in eutopic endometrial stromal cells (ESCs) of EMs patients. In ESCs, pharmacological inhibition of autophagy by chloroquine (CQ) promoted collagen I deposition. Ectopic endometrial stromal cell-derived extracellular vesicles (EMs-EVs) inhibited autophagy of ESCs and promoted collagen I deposition in vivo and in vitro. Mechanistically, EMs-EVs encapsulating PKM2 impair eutopic endometrial autophagy via Akt/mTOR signaling pathway. Together, we demonstrated that EMs-EVs encapsulating PKM2 impaired endometrial autophagy inducing collagen I deposition in EMs, which provided a potential target for therapeutic implications.

first: Jianjun

last: Zhou


title: Targeting PILRα, an immune checkpoint mediating T cell suppression, for cancer immunotherapy

city: Xiamen

first: Guosheng

last: Hu

state: Fujian

address: Xiang'an South Road, Xiang'an District

department: School of Pharmaceutical Sciences

institute: xiamen University

summary: One of the most successful therapies in cancer treatment involves immune checkpoint blockade using the anti-programmed death-1 (anti-PD-1)/programmed death-ligand 1 (PD-L1) antibody, which targets the interaction between tumors and T cells. However, the overall response rate is < 30% in patients with cancer. Therefore, there is an urgent need to identify additional immune checkpoints that can modulate T-cell function. In this study, we identified the tumor cell-expressed paired Ig-like type 2 receptor α (PILRα) as an immune suppressor that targets T cells, using a high-throughput screening approach. PILRα suppresses T-cell activation, proliferation, and effector function in both cultured cells and mouse xenograft and allograft models. It specifically targets CD99, a T cell surface antigen, to suppress the ZAP70/NFAT/IL2/JAK/STAT signaling in T cells. The cluster of O-glycosylated serine (Ser)/threonine (Thr) residues within the stalk region plays a critical role in PILRα–CD99 interactions, thereby influencing the immunosuppressive function of PILRα. Blocking interactions between PILRα and CD99 using an anti-PILRα antibody that targets the stalk region potently enhances T cell antitumor immunity and suppresses tumor growth. Additionally, when combined anti-PILRα with anti-PD-1 antibodies, synergistic effects on tumor suppression were observed. Notably, PILRα is highly expressed in various human cancers, and its expression levels serve as a predictive marker for poor prognosis in patients with cancer. Taken together, our results unveil PILRα as an immune checkpoint and highlight the promising therapeutic potential of targeting PILRα in clinical cancer immunotherapy.

overall_design: RNA-seq performed in this study was designed to reveal the T cell gene expression regulated by PILRα

first: Wen

last: Liu

first: Lin

last: Xia

first: Jun-yi

first: Guo-sheng


title: RNA sequencing of RBP4 or control treated cells

city: Guangzhou

first: Lei

last: Su

address: Zhongshan Second Road

institute: Sun Yat-sen University

summary:
Purpose: The purpose of this study was to find the differentially expressed genes in RBP4 and control treated cells by transcriptome analysis (RNA-seq) for subsequent mechanism study.
Methods: Illumina Novaseq™ 6000 was used to sequencing RBP4 and control-treated human umbilical vein endothelial cells.Genes differential expression analysis was performed by DESeq2 software between two different groups (and by edgeR between two samples). The genes with the parameter of false discovery rate (FDR) below 0.05 and absolute fold change ≥ 2 were considered differentially expressed genes. Differentially expressed genes were then subjected to enrichment analysis of GO functions and KEGG pathways.GO enrichment analysis provides all GO terms that significantly enriched in DEGs comparing to the genome background. Firstly all DEGs were mapped to GO terms in the Gene Ontology database (http://www.geneontology.org/), gene numbers were calculated for every term, significantly enriched GO terms in DEGs comparing to the genome background were defined by hypergeometric test.
Results:The RNA-seq results showed that compared to the untreated HUVECs, RBP4 treatment resulted in significant changes in the gene expression, including 180 up-regulated and 53 down-regulated genes among a total number of 233 DEGs. GO enrichment were analyzed for relationships among all DEGs.
Conclusions:  Our study analyzed the mechanism of RBP4 on human umbilical vein endothelial cells and its possible pathway in detail by RNA-seq technique, and provided a basis for elucidating the damage of RBP4 on endothelial cells through large-scale gene screening.

overall_design: RNA sequencing of RBP4 or control treated human umbilical vein endothelial cells

first: Lina


title: Upregulation of N6-methyladenosine Transcript Landscape in Diabetic Cataract

city: Shang Hai

first: Xiaoyan

last: Han

address: 83 Fenyang Road, Shanghai 200031, People’s Republic of China.

institute: Eye Institute and Department of Ophthalmology, Eye & ENT Hospital, Fudan University

summary: Epitranscriptomic profiling of human LECs of DC patients comparing normal control LECs. Goal was todetermine the potential functions and mechanism of N6-methyladenosine (m6A) abnormality of RNAs in human lens epithelium cell (HLEC) lesions in diabetic cataract (DC).

overall_design: Two-condition experimen,  LECs of DC vs  LECs of NC. Biological replicates: 3 control replicates, 3 DC replicates.

last: Cai

first: Dan

first: Yi

last: Lu

first: Jin

last: Yang


title: MiRNA Expression Profiling and Clinical Implications in Prostate Cancer Across Various Stages

status: Public on Feb 21 2025

city: Nanchang

first: Zhengjie

last: XIANG

address: 1 Minde Road, Donghu District, Nanchang City, Jiangxi Province, China

institute: The Second Affiliated Hospital of Nanchang University

summary: This study aims to screen and identify microRNA (miRNA) expression profiles across different stages of prostate cancer (PCa) and benign prostatic hyperplasia (BPH) using high-throughput sequencing. The study seeks to determine whether specific miRNAs show consistent differential expression across various stages of PCa, with the goal of identifying potential biomarkers relevant to disease progression.

overall_design: A total of 12 specimens from PCa and BPH were collected from September 2021 to June 2022 at the Second Affiliated Hospital of Nanchang University, China (including 3 specimens from early localized tumors, local invasion, and distant metastasis tumors, and 3 specimens from BPH). miRNA expression profiles were screened using high-throughput sequencing, and differentially expressed miRNAs were identified using bioinformatics analysis. Further analysis, including target miRNA site analysis, GO enrichment analysis, and KEGG enrichment analysis of miRNA-derived genes, was performed. The expression of hsa-miR-6715b-3p in PCa tissues was verified using qRT-PCR.


title: CEBPB-high dormant tumor cells drive immune evasion [ChIP-Seq]

city: Shanghai

first: Yang

last: Dong

state: 上海

address: Shanghai

institute: Tongji University

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Triple negative breast cancer (TNBC) poorly responds to immune checkpoint blockade (ICB) therapy. Dormant tumor cells are recognized as immunotherapy-resistant reservoirs, potential leading to tumor relapse, highlighting the importance to elucidate the mechanisms underlying immunotherapy resistance. Herein, we demonstrated that dormant tumor cells were resistant to ICB therapy and occupied an immunosuppressive niche with enhanced tumor-associated macrophages (TAMs) and decreased CD8+T cells infiltration in mouse TNBC allografts via a label-retention system. CEBPB was highly expressed in dormant tumor cells and maintained tumor dormancy by transcriptionally activating cell cycle negative regulators like CCNG2 and p27.

overall_design: ChIP-seq of CEBPB in 4T07 cells.

last: Bai

first: Yong

last: Gao


title: CEBPB-high dormant tumor cells drive immune evasion [RNA-Seq]

overall_design: To investigate which genes were regulated by CEBPB in triple negative breast cancer, we transfected 4T07 cell lines with either pLenti-CMV-MCS or pLenti-CMV-Cebpb by lentivirus. Stable tracfected cells were selected by puromycin.We extracted RNA from each group with three biological replicates. We performed gene expression profiling assay using data obtained from RNA-seq of 6 samples (two groups with three biological replicates per group). Comparative gene expression profiling analysis of RNA-seq data for OE-Control and OE-Cebpb


title: Transcriptomic profiling of signet ring cell precursors of diffuse-type gastric cancer informs latent phenotype

city: BETHESDA

first: Cihan

last: Oguz

state: MD

address: NIHBC 29B BG RM 1NN20, 9000 ROCKVILLE PIKE

country: USA

institute: NIH

summary: Germline CDH1 loss-of-function mutations are causally linked to an increased lifetime risk of diffuse gastric cancer (DGC). Early, multifocal signet ring cell (SRC) lesions are ubiquitous among CDH1 variant carriers, yet only a subset of patients will develop advanced DGC. Transcriptomic profiling was performed to establish the molecular phenotype of early SRC lesions.

overall_design: We performed single cell RNA sequencing (scRNA-Seq) of normal-appearing gastric mucosa that contained SRC lesions from three patients that contributed a total of 20 replicates (eight replicates each from patients 1 and 2, and four replicates from patient 3).

first: Amber

middle: F

last: Gallanis

first: Lauren

middle: A

last: Gamble

first: Sarah

middle: G

last: Samaranayake

first: Noemi

last: Kedei

first: Maria

middle: O

last: Hernandez

first: Madeline

last: Wong

first: Desiree

last: Tillo

first: Benjamin

middle: L

last: Green

first: Paul

last: McClelland

first: Cassidy

last: Bowden

first: Irene

last: Gullo

first: Mark

last: Raffeld

first: Liqiang

last: Xi

first: Michael

last: Kelly

first: Markku

last: Miettinen

first: Martha

last: Quezado

first: Sun

last: Kim

first: Andrew

middle: M

last: Blakely

first: Justin

last: Lack

first: Theo

last: Heller

first: Jonathan

first: Jeremy

last: Davis


title: Spatial transcriptomic profiling of signet ring cell precursors of diffuse-type gastric cancer

first: Cihan

last: Oguz

overall_design: We performed NanoString GeoMx digital spatial profiling (DSP) using the whole transcriptome atlas (WTA) panel to characterize gastric tissue regions of interest (ROIs). Early tumor stage (T1a) gastric epithelial (T1a_NEP) and SRC lesion (T1a_SRC) ROIs were captured from total gastrectomy samples of four patients with germline CDH1 P/LP variants. In four patients with advanced DGC found on gastrectomy explants, ROIs were selected from gastric epithelial (GC_NEP), superficial lamina propria (GC_sup), as well as from submucosa and deeper (GC_deep).

first: Amber

last: Gallanis

first: Lauren

last: Gamble

first: Sarah

last: Samaranayake

first: Noemi

last: Kedei

first: Maria

last: Hernandez

first: Madeline


title: In-Depth Functional Analysis of BRD9 in Fetal Hematopoiesis Reveals Context-Dependent Roles [ATAC-seq_2]

city: Suita

first: Masaki

last: Nomura

state: Osaka

address: 2-2, Yamadaoka

department: Department of Cancer Pathology

country: Japan

institute: Graduate School of Medicine, The University of Osaka

summary: The hierarchical organization of hematopoietic stem cells (HSCs) governing adult hematopoiesis has been extensively investigated. However, the dynamic epigenomic transition from fetal to adult hematopoiesis remains incompletely understood, particularly regarding the involvement of epigenetic factors. In this study, we investigate the roles of BRD9, an essential component of the non-canonical BAF (ncBAF) complex known to govern the fate of adult HSCs, in fetal hematopoiesis. Consistent with observations in adult hematopoiesis, BRD9 loss impairs fetal HSC stemness and disturbs erythroid maturation. Intriguingly, the impact on myeloid lineage was discrepant: BRD9 loss inhibited and promoted myeloid differentiation in fetal and adult models, respectively. Through comprehensive transcriptomic and epigenomic analyses, we elucidate the differential roles of BRD9 in a context- and lineage-dependent manner. Our data uncover how BRD9/ncBAF complex modulates transcription in a stage-specific manner, providing deeper insights into the epigenetic regulation underlying the transition from fetal to adult hematopoiesis.

overall_design: To obtain fetal livers (FL), mating pairs were setup between Brd9fl/fl male mice and Vav1-iCre; Brd9fl/fl female mice. The day when mouse pregnancy was confirmed was counted as E0.5. On E14.5, the mice were sacrificed for sample preparation.

first: Yifan

last: Zhang

first: Koutarou

last: Nishimura

first: Weijia

last: Zang

first: Daichi

last: Inoue


title: Chimeric Antigen Receptor-Macrophage Extracellular Vesicles Reprogram Immune Microenvironment for Cancer Therapy

city: Wuhan

first: Minghe

state: Hubei

address: Donghu Road

institute: WuHan University

summary: Immunotherapy has become a new milestone in cancer treatment, with chimeric antigen receptor (CAR)-T cell therapy proven to be an effective method for treating hematologic malignancies. However, its efficacy in solid tumors remains limited. Macrophages, the most infiltrative innate immune cells in the tumor microenvironment, are being genetically engineered to express CARs, rapidly emerging as a promising new therapy for non-hematologic malignancies. Yet, CAR- Macrophages therapy is associated with unique acute toxicities and is susceptible to immunosuppressive mechanisms. Here, we propose using CAR macrophages-derived extracellular vesicles (CAR-MEVs) as an optimization of CAR-Ms therapy. Compared to CAR-Ms cells, CAR-MEVs exhibit lower toxicity and enhanced drug delivery capabilities. In an in vivo liver cancer model, CAR-MEVs administration proved safer than CAR-Ms therapy, reducing tumor burden and prolonging overall survival. In a humanized mouse model, CAR-MEVs further demonstrated the ability to induce a pro-inflammatory tumor microenvironment and enhance anti-tumor T cell activity. Mechanistically, CAR-MEVs target tumor cells, inducing immunogenic cell death (ICD) and subsequently leading to neutrophil infiltration in tumor tissues. We demonstrated that the anti-tumor effects of CAR-MEVs depend on neutrophils and are partially reliant on inducible nitric oxide synthase (iNOS). This study supports the potential of macrophage extracellular vesicles as a novel therapeutic approach for solid tumors.

overall_design: Orthotopic mouse models of hepatocellular carcinoma were established using HepA1-6 cells. The mice were then treated with either CAR-MEVs or PBS, and tumor tissues were subsequently harvested for RNA-sequencing transcriptome analysis.

first: Peng

last: Xia

first: Yufeng

last: Yuan


title: Acetaldehyde Induced Cell Damage and Genotoxic Effects by Modulating PI3K/AKT and MAPK/ERK Pathways in Human Lung Epithelial Cells

city: Hefei

first: Jingni

address: No. 350 Shushanhu Road

institute: Anhui Institute of Optics and Fine Mechanics, Hefei Institutes of Physical Science, Chinese Academy of Sciences

summary: Long-term acetaldehyde exposure is associated with cell death, oxidative stress, and DNA damage in lung injury such as chronic obstructive pulmonary disease and respiratory distress syndrome, but the signal transduction mechanism linking key processes remains largely unknown. This study aims to reveal molecular mechanisms of cytotoxicity and genotoxicity induced by acetaldehyde based on human bronchial epithelial cells. Firstly, RNA-seq analysis indicated that differentially expressed genes are most enriched in MAPK/ERK and PI3K/AKT pathways. Secondly, significant up-regulation of four key signaling proteins was confirmed. Subsequently, we found that inhibitors of these pathways could significantly reduce cytotoxicity, oxidative stress, and genotoxicity induced by acetaldehyde. Finally, gene silencing was employed to further validate the importance of these pathways, and toxic effects were more effectively alleviated. Our research suggests that acetaldehyde-induced cell damage and genotoxic effects through PI3K/AKT and MAPK/ERK pathways, provide new insights into toxic mechanisms of acetaldehyde-induced lung injury.

overall_design: RNA-seq profiling of wild-type BEAS-2B cells exposed to acetaldehyde (0, 10, and 16 mM) for 24 hours.

first: Hongjuan

last: Wang

first: Jun

last: Li

first: Huan

last: Chen

first: Yong

last: Liu

first: An

first: Hongwei

last: Hou

first: Qingyuan

last: Hu


title: In-Depth Functional Analysis of BRD9 in Fetal Hematopoiesis Reveals Context-Dependent Roles [RNA-seq]


title: RNA sequencing identifies MAP1A and PTTG1 as predictive genes of aging CD264+ human mesenchymal stem cells at early passage

city: New Orleans

first: Kim

last: OConnor

state: LA

address: 6823 St. Charles Ave

institute: Tulane University

summary: Molecular profiles of mesenchymal stem cells (MSCs) are critically needed to standardize the composition and effectiveness of MSC therapeutics. This study employs RNA sequencing to identify genes to be used in concert with CD264 as a molecular profile of aging MSCs at a clinically relevant culture passage. CD264- and CD264+ populations were isolated by fluorescence-activated cell sorting from passage 4 MSC cultures. Donor-matched CD264-/+ mRNA samples from 5 donors were subjected to pair-ended, next-generation sequencing. An independent set of 5 donor MSCs was used to validate differential expression of select genes with quantitative reverse transcription PCR. CD264+ cells accounted for 15% to 60% of the cells in MSC cultures and exhibited an aging phenotype. Pairwise differential expression analysis identified 2,322 downregulated genes and 2,695 upregulated genes in CD264+ MSCs relative to donor-matched CD264- MSCs with a Benjamini-Hochberg adjusted p-value (BH padj) < 0.1. Nearly 25% of these genes were unique to CD264-/+MSCs and not differentially expressed at a significance level of BH padj < 0.1 in previous RNA sequencing studies of early- vs. late-passage MSCs. Kyoto Encylopedia of Genes and Genomes pathways for DNA replication, cell cycle, spliceosome, RNA transport and ribosome biogenesis were downregulated in CD264+ MSCs and extracellular matrix-receptor interactions was upregulated (BH padj < 0.1). Pathway results were confirmed by Database for Annotation, Visualization, and Integrated Discovery gene set enrichment analysis. Least Absolute Shrinkage and Selection Operator regression was performed on the most significant genes and pathways and identified microtubule-associated protein 1A (MAP1A) and pituitary tumor-transforming gene 1 (PTTG1) as signature genes of CD264+ MSCs. For both the sequencing and validation sets, the combination of MAP1A and PTTG1 expression clustered MSC samples into distinct groups that had the correct CD264 classification with an accuracy of 100% (p ≤ 0.01). This study provides the first linkage of MAP1A upregulation to aging, CD264, and stem cells, and confirms previous reports of PTTG1 downregulation in aging MSCs. Our findings have application as quality metrics to standardize the composition of MSC therapies and as molecular targets to slow/reverse cellular aging.

overall_design:
The molecular profile of aging mesenchymal stem cells (MSCs) was investigated using subconfluent cultures of human bone marrow MSCs at passage 4 from 5 donors.
Fluorescence-activated cell sorting was used to isolate passage 4 MSCs based on their expression of CD264, a cell surface marker of aging.
PolyA RNA samples were isolated from donor-matched CD264- and CD264+ MSCs from 5 donors.
Pair-ended RNA sequencing and pairwise differential expression analysis of the donor-matched CD264-/+ MSCs samples identified predictive genes of the aging CD264+ phenotype.
Predictive genes were validated with donor-matched CD264-/+ MSCs samples from an independent set of 5 donors.


title: In-Depth Functional Analysis of BRD9 in Fetal Hematopoiesis Reveals Context-Dependent Roles [ATAC-seq]

first: Masaki


title: Dysregulation of BCL3 expression in epithelial cells from normal, asthmatic and adenocarcinoma lung cells inform it’s role in regulation of hallmarks of cancer.

city: Sharjah

first: Rifat

last: Hamoudi

state: Sharjah

address: M32 Sharjah Institute for Medical Research, College of Medicine, University of Sharjah, , Sharjah

department: Clinical Sciences

country: United Arab Emirates

institute: University of Sharjah

summary: The study shows the dysregulation of BCL3 in asthma and lung cancer cell lines can induce apoptosis and proliferation, the hall marks of cancer.

overall_design: Epithelial cells from normal bronchium and asthmatic lung were studied for overexpression of BCL3 gene. In addition, silencing BCL3 in lung adenocarcionam cell lines was conducted using siRNA specific for BCL3. RNA from all these cells before the trabsfection  and after the ransfection was isolated. RNA from the cell lines thus obtained was subjected for whole transcriptomic analysis uisng Ampliseq transcriptome panel on Ion S5 XL sequencer.

first: Poorna

last: Manasa Bhamidimarri

first: Laila

last: Salameh

first: Dua

last: Hammash

first: Alaa

last: Mohammed

first: Bassam

last: Mahboub


title: In-Depth Functional Analysis of BRD9 in Fetal Hematopoiesis Reveals Context-Dependent Roles [scRNA-seq]

last: Nomura

first: Yifan

last: Zhang

first: Koutarou

last: Nishimura

first: Weijia

last: Zang

first: Daichi


title: Transcriptomic profiling analysis between RPCs treated with Ad-NC and Ad-hTCF7L2

first: Keling

last: Wu

address: #7 Jin-Sui Road, Zhujiang New Town

institute: zhongshan ophthalmic center

summary: Ad-hTCF7L2 was utilized to overexpress TCF7L2 in RPCs. We identified 1622 differentially expressed genes, including 1134 upregulated genes and 488 downregulated genes. We found that overexpressed TCF7L2 in RPCs significantly downregulate genes involving in cell cycle and DNA replication

overall_design: Retinal progentior cells (RPCs) were dividied into two groups, including Ad-hTCF7L2 (n=3) and its control Ad-NC (n=3). Sequencing of the library preparations were performed on an Illumina NovaSeq platform and 150-bp paired-end reads were generated.

first: Tingfang

last: Mei

first: Minglei

last: Zhao

first: Ling


title: Gene expression profiling of the olm (Proteus anguinus)

city: Bochum

first: Arne

last: Sahm

address: Universitätsstr. 150

country: Germany

institute: Ruhr-Universität Bochum

summary: The study comprises a hybrid transcriptome assembly of the olm (Proteus anguinus) that was created from Illumina short-reads and ONT long-reads. The transcriptome assembly is based on samples from six organs animals: brain, gut, heart, liver, lung and skin. In addition, we used the assembled transcripts and Illumina short-reads from two to three animals per organ to profile the gene expression in the olm.

overall_design: RNA-seq profiling of 14 samples from three olm individuals covering six organs.

first: Susanne

last: Holtze


title: Exploration for blood biomarkers of human long non-coding RNAs predicting oxaliplatin-induced chronic neuropathy through iPS cell-derived sensory neuron analysis

status: Public on Feb 20 2025

city: Tokyo

first: Atsushi

last: Sakai

address: 1-1-5 Sendagi, Bunkyo-ku

institute: Nippon Medical School

summary: We explored extracellular long non-coding RNAs (lncRNAs) released from primary sensory neurons as biomarker candidates for oxaliplatin-induced peripheral neuropathy. Because many human-specific lncRNA genes exist, we induced peripheral sensory neurons from human induced pluripotent stem cells. Oxaliplatin treatment changed the levels of many lncRNAs in extracellular vesicles (EVs) released from cultured primary sensory neurons.

overall_design: EV and cellular total RNA obtained from oxaliplatin-treated primary sensory neurons induced from human iPS cells

first: Motoyo

last: Marauyama

first: Hidenori

last: Suzuki


title: The neuronal architecture of autonomic dysreflexia

city: Geneve

first: Alan Yue Yang

last: Teo

address: Chem. des Mines 9, Campus Biotech

department: SV

country: Switzerland

institute: EPFL

summary: This submission is a dataset of single-nucleus transcriptomics in the spinal cords of mice. The single-nuclei transcriptomics data is harvested and profiled using 10x Genomics Chromium Single Cell Kit Version.

overall_design: We used single-nucleus RNA-sequencing to profile the lower-thoracic and the lumbosacral spinal cord in SCI mice, SCI mice subjected to repeated autonomic dysreflexia episodes and SCI mice that underwent repeated EES at the lower-thoracic spinal cord.

first: Jan

middle: E

last: Soriano

first: Remi

last: Hudelle

first: Lois

last: Mahe

first: Matthieu

last: Gautier

first: Alan

middle: Y

first: Michael

last: Skinnider

first: Achilleas

last: Laskaratos

first: Steven

last: Ceto

first: Claudia

last: Kathe

first: Thomas

last: Hutson

first: Rebecca

last: Charbonneau

first: Samer

middle: D

last: Shamout

first: Marcus

last: Tso

first: Anthony

last: Incognito

first: Kelly

last: Larkin-Kaiser

first: Nicolas

last: Hankov

first: Aasta

last: Gandhi

first: Yashwanth

last: Vyza

first: Eduardo

last: Martin-Moraud

first: Stephanie

last: Lacour

first: Robin

last: Demesmaeker

first: Leonie

last: Asboth

first: Quentin

last: Barraud

first: Mark

last: Anderson

first: Jocelyne

last: Bloch

first: Jordan

middle: W

last: Squair

first: Aaron

last: Phillips

first: Gregoire

last: Courtine


title: Metabolic reprogramming in astrocytes prevents neuronal death through a UCHL1/PFKFB3/H4K8la positive feedback loop

city: Nanjing

first: junjun

last: xiong

address: No. 300 Guangzhou Road, Nanjing

department: Department of Orthopedics

institute: The First Affiliated Hospital of Nanjing Medical University

summary: Astrocytic metabolic reprogramming is an adaptation of metabolic patterns to meet increased energy demands, although the role after spinal cord injury (SCI) remains unclear. Analysis of single-cell RNA sequencing (scRNA-seq) data identified an increase in astrocytic glycolysis, while PFKFB3, a key regulator of glycolytic flux, was significantly upregulated following SCI. Loss of PFKFB3 in astrocytes prohibited neuronal energy supply and enhanced neuronal ferroptosis in vitro and inhibited astrogliosis, expanded neuroinflammation, exacerbated neuronal loss, and hindered functional recovery in vivo after SCI. Mechanistically, deubiquitinase UCHL1 plays a crucial role in stabilizing and enhancing PFKFB3 expression by cleaving K48-linked ubiquitin chains. Genetic deletion of Uchl1 inhibited locomotor recovery after SCI by suppression of PFKFB3-induced glycolytic reprogramming in astrocytes. Furthermore, the UCHL1/PFKFB3 axis increased lactate production, leading to enhanced histone lactylation and subsequent transcription of Uchl1 and several genes related to glycolysis, suggesting a glycolysis/H4K8la/UCHL1 positive feedback loop. These findings help to clarify the role of the UCHL1/PFKFB3/H4K8la loop in modulation of astrocytic metabolic reprogramming and reveal a potential target for treatment of SCI.

overall_design: Detection of transcriptional targets of H4K8la in sham and SCI mouse spinal cord astrocytes.

first: Junjun

last: Xiong

first: Xuhui

last: Ge

first: Dishui

last: Pan

first: Yufeng

last: Zhu


title: Single-cell multiomics study of cell-type-specific neuron activation unravels context-dependent gene regulation of brain disorders [022]

city: Evanston

first: Jubao

last: Duan

state: IL

address: 1001 University Place

department: Center for Psychiatric Genetics

institute: NorthShore University HealthSystem

summary: Genome-wide association studies (GWAS) have identified many risk genes for neuropsychiatric disorders (NPD) such as schizophrenia (SCZ). However, functional interpretation of these GWAS findings remains challenging; a major hurdle is that polygenic risk may manifest its effect conditionally upon neural activation, i.e., context-dependent. Human induced pluripotent stem cell (hiPSC)-derived neurons are a tractable cellular model for ascertaining context-dependent polygenic effects, e.g., neural activation that may mimic the physiological effects of environmental stimuli. Here, we modelled neural activation by depolarisation using high potassium chloride (KCl) in co-cultured excitatory/inhibitory neurons of 100 hiPSC lines (28 from SCZ donors), followed by assaying single-cell multiomes (scRNA/ATAC-seq) of over 700,000 nuclei from neurons at 0 hr (unstimulated), 1 hr (early response), and 6 hr (later response) of high KCI exposure. We linked genes with open chromatin peaks for each main neural subtype (GABAergic inhibitory, NEFM+ or NEFM-excitatory neurons) and confirmed a significant correlation between peak accessibility and target gene expression. Compared to static genes/peaks, dynamic ones, specifically those activity-upregulated, were more enriched for NPD GWAS risk, with the most robust enrichment for SCZ. Based on the dynamic gene expression pattern across the three time points, we found NPD risk genes tend to be continuously upregulated (i.e., with up-up dynamics). We further analysed context-specific SCZ-associated differentially expressed genes (DEGs) using MAST for single neurons of 28 SCZ cases and 72 controls. We found that 3-5%, 4-6%, and 15-23% of genes were SCZ-associated DEGs in NEFM+ excitatory, NEFM- excitatory, and GABAergic neurons, respectively, most of which were cell activity-specific. Notably, we found that SCZ-associated DEGs in high-activity neurons were more enriched for synapse-related GO terms and NPD risk genes. Interestingly, upstream regulatory sequences of the stimulation-specific SCZ-associated DEGs were enriched for binding sites of TCF4, which is a strong GWAS risk gene and was considered the master regulator of other SCZ-related genes. Moreover, the upregulated genes in SCZ cases in the stimulated (only at 6hr) NEFM+ excitatory neurons showed strong enrichment for GO terms related to cholesterol synthesis. Single-neuron DEG analysis for 28 SCZ cases and 28 matched controls gave similar results. Our study suggests that many NPD genes may only elicit disease-relevant effects upon neuronal activation, providing novel insights into how polygenic risk factors interact with environmental stimuli for NPD.

overall_design: Raw FASTQ files complies 10x Genomics multiome scARC (scRNA-seq + scATAC-seq) standard. Library generated using cultured glutamatergic and GABAergic neurons derived from iPS cells with Chromium Next GEM Single Cell Multiome ATAC + Gene Expression Reagent Kit. The output folders, including all matrices files, of Cell Ranger 2.0.2 were packaged and compressed sample-wise in according to their BioSample and SRA metadata

first: Siwei

last: Zhang


title: FADD Functions as an Oncogene in Chr11q13.3 Amplified Head and Neck Squamous Cell Carcinoma

first: Yang

last: Zheng

state: --- Select One ---

address: No.115, Jinzun Road, Pudong District

institute: Department of Oral and Maxillofacial-Head Neck Oncology, Shanghai Ninth People's Hospital

summary: Chromosomal 11q13.3 amplification is the most common gene copy number variation event in head and neck squamous cell carcinoma (HNSCC) that corresponds with poor prognosis. Although cyclin D1, a G1/S phase cell cycle regulatory protein at this locus, is considered as a key driver of malignant progression, further exploration is needed to develop more effective targets for cases with this amplification. Using CRISPR-based gene knockout screening of genes located in chr11q13.3, we found that loss of the gene encoding the Fas-associated death domain (FADD) protein, a well-recognized adaptor to caspase-8 that induces cell apoptosis, significantly reduced cancer cell proliferation. FADD expression was elevated in chr11q13.3 amplified tumors and correlated with poor prognosis. RNA-sequencing, mass spectrometry, and proteomics analyses revealed a direct relationship between FADD and the DNA helicase MCM5 in the S phase. FADD and cyclin D1 acted at different stages of the cell cycle to synergistically induce proliferation, and caspase-8 deficiency was required for the oncogenic activity of FADD. In a patient-derived xenograft model with chr11q13.3 amplification, combined administration of DNA helicase complex inhibitor and CDK4/6 inhibitor effectively curtailed tumor growth. Overall, this study identified a non-classical oncogenic role for FADD in mediating tumor progression in HNSCC and provided a feasible treatment option for patients with chr11q13.3 amplification.

overall_design: RNA-seq profiling in HN4 cell stably transfected with full-length FADD or control.

first: Zhiyuan

first: Hanlin

last: Zeng

first: Yue

last: He


title: Long-term in vivo monitoring of transplanted mesenchymal stromal cells in colitis mice with magnetic particle imaging

city: soochow

first: yuzhu

last: Liu

state: Jiangsu

address: renai road 199

institute: soochow university

summary: Background: The successful development of mesenchymal stromal cells (MSC)-based therapeutic strategies in inflammatory bowel disease (IBD) hinges on the ability to assess the influence of the administration route, while also tracking the cells’ in vivo location, distribution, and long-term viability. Moreover, understanding the biological fate of these cells—particularly their activation, differentiation, and interaction within the host environment—is crucial to optimizing their therapeutic potential. Methods: This study explores the use of magnetic particle imaging (MPI) with superparamagnetic iron oxide nanoparticles (SPIONs) to track MSCs in colitis mice. SPION-labeled MSCs were administered through intravenous (IV), intraperitoneal (IP), and intrarectal (IR) routes. MPI was employed to track MSCs. Findings: MPI provided real-time tracking of MSC distribution, viability, and homing, revealing that IP injections led to more targeted and sustained delivery to inflamed colon tissues, with higher cell survival and efficacy in modulating inflammation. Other administration routes also demonstrated specific distribution patterns, but with shorter retention times. The prolonged survival of MSCs following IP injection may be attributed to the immune environment in the peritoneal cavity, which significantly impacts MSCs, influencing their survival and migration. Further analyses showed that MSCs exposed to inflammatory peritoneal fluid exhibited enhanced homing capabilities, and IFN-γ pretreatment significantly improved MSC retention in the inflamed colon, as detected by MPI/CT imaging. Interpretation: Our findings, observed through MPI, highlight the potential of IP injection as a preferred method for MSC-based therapies, offering strategies to improve treatment outcomes specifically in IBD and potentially in other inflammatory conditions.

overall_design: Peritoneal interstitial fluid (PF) was collected from control mice, IBD mice (treated with TNBS for 3 days).Mesenchymal stromal cells (MSCs) were co-cultured separately with PF from control mice, PF from TNBS-induced mice, and phosphate-buffered saline (PBS).Three replicates of each MSC sample were collected for gene expression profiling analysis of RNA-seq.

first: Tuo

last: Shao

first: Zelin

last: Gu

first: Yuzhu

first: Xiaoyi

last: Wang

first: Chao

last: Tang

first: Nannan

last: Chen

first: Mengqi


title: Effect of edodine in gene expression of Erwinia amylovora

city: Daejeon

first: Yeong Seok

last: Kim

state: Yuseong

address: 141, Gajeong-ro

country: South Korea

institute: Korea Research Institute of Chemical Technology

summary: To investigate the metabolism by edodine treatment in Erwinia amylovora, E. amylovora grown with edodine. Total RNA from the cell pellets of E. amylovora TS3128 that cultured in MGY at 28 ºC with the control group and edodine treated group (IC50) was extracted. Our data provide differentially expression genes, including flagella biosynthesis, nutrient metabolisms, and protein folding, and RNA degradation, in presence of edodine.

overall_design:
RNA-seq profiling of edodine treatment and non-treatment in E. amylovora at 0.6 of optical density.
Edodine is a novel compound derived from microbe strain 761.

first: Hun


title: Transcriptomic Profiling of Efflux Pump Genes in Mycobacterium tuberculosis Under Linezolid Stress

city: Delhi

first: Mandira

last: Varma Basil

address: University of Delhi

department: Department of Microbiology

country: India

institute: Vallabhbhai Patel Chest Institute

summary: In this study, we investigated the role of efflux pump genes in linezolid resistance. M. tuberculosis H37Rv cultures were exposed to sub-inhibitory concentrations of linezolid (¼ MIC) for 24 hours, and transcriptomic analysis was performed to identify upregulated genes. Of the 120 genes involved in cell wall processes, 9/120 (7.5%) were efflux pump genes, primarily belonging to the ATP-binding cassette (ABC), major facilitator superfamily (MFS), resistance nodulation division (RND), and small multidrug resistance (SMR) families. qRT-PCR, performed at 1/2, 1/4 and 1/8 MIC of linezolid, confirmed the RNA-seq results, showing that 8/9 (88.88%) of the efflux pump genes were upregulated at 1/8 MIC of linezolid, indicating that this concentration is optimal for studying efflux pump activity. These findings not only identify 1/8  MIC as optimum concentration for efflux pump studies after linezolid exposure, they also highlight the significant role of efflux pumps in linezolid resistance, providing potential targets for further research on efflux pumps in clinical isolates of M. tuberculosis.

overall_design: This study aimed to identify efflux pump genes influenced by linezolid exposure through transcriptomic analysis. Cultures of M. tuberculosis H37Rv were exposed to delamanid at a sub-inhibitory concentration of 1/4 MIC for 24 hours and transcriptomic sequencing was performed on exposed and unexposed cultures.

first: Anupriya

last: Singh

first: Varsha

last: Chauhan

first: Chanchal

last: Kumar

first: Deepali

last: Vashisth

first: Nishant

last: Gautam

first: Kamal

last: Shrivastava

first: Anupam

last: Prakash

last: Varma-Basil


title: Effect of intrananasally administered deferoxamine in the intracerebroventricular streptozotocin rat model of Alzheimer's disease

city: Saint Paul

first: Jared

last: Fine

state: MN

address: 295 Phalen Blvd

institute: HealthPartners

summary: Intranasal (IN) deferoxamine (DFO) has emerged over the past decade as a promising therapeutic in preclinical experiments across neurodegenerative and neurovascular diseases. As an antioxidant iron chelator, its mechanisms are multimodal, involving the binding of brain iron and the consequent engagement of several pathways to counter pathogenesis across multiple diseases. We and other research groups have shown that IN DFO rescues cognitive impairment in several rodent models of Alzheimer Disease (AD). This study was designed to probe dosing regimens to inform future clinical trials, while exploring mechanisms within the intracerebroventricular (ICV) streptozotocin (STZ) model.  Using RNA-sequencing and pathway analysis, STZ was shown to induce several pathways of cell death and neuroinflammation, and IN DFO engaged multiple transcriptomic pathways involved in hippocampal neuronal survival. To our knowledge this study is the first to assess the transcriptomic pathways and mechanisms associated with either the ICV STZ model or DFO treatment, and the first to demonstrate efficacy at this low dose.

overall_design: To determine effects of both IN DFO and ICV STZ on RNA-sequencing pathways in rat brain tissue, rats were first sibjected to either a sham surgery or ICV-STZ injection to induce the model.  They were then treated intranasally with either saline or a 1% solution of DFO.  Their brains were collected and analyses with RNA-sequencing.

first: Juan

last: Abrahante


title: Identifying modifiers of seed-induced TDP-43 loss of function

city: Zurich

first: Davide

last: Caredio

state: Switzerland

department: Institute of Neuropathology

institute: University Hospital of Zurich

summary: Both gain of toxicity and loss of normal function of the RNA-binding protein TDP-43 contribute to neurodegeneration in ALS and FTD, but their mechanistic connection remains unclear. Increasing evidence suggests that TDP-43 aggregates act as self-templating seeds, propagating pathology through the central nervous system via a prion-like cascade. We developed a robust TDP-43 seeding platform for quantitative, high-throughput assessment of TDP-43 aggregate uptake, cell-to-cell spreading and direct quantification of TDP-43 nuclear function within living cells, while they progress towards pathology. We show that both patient-derived and recombinant TDP-43 pathological aggregates are abundantly internalized in human neuron-like cells, efficiently recruit endogenous TDP-43 and form cytoplasmic inclusions reminiscent of ALS/FTD pathology. These neoaggregates progressively drive the nuclear egress of TDP-43 leading to its loss of function. The scope of this project is to identify the signatures involved in the progressive egress of TDP-43 from the nucleus to the cytoplasm.

overall_design: We generated a cell line which incorporates a sensor (TDP-REG) capable of reporting for TDP-43 loss of function in living cells. Specifically, TDP-REG encodes for the fluorescent protein mScarlett, but contains a TDP-43-inhibited cryptic exon essential for the complete mScarlett transcript. In cells with functional TDP- 43, this cryptic exon is repressed and the presence of a downstream premature termination codon results in nonsense mediated decay of the transcript, and therefore, no mScarlett protein. Conversely, in the absence of functional TDP-43, the cryptic exon is derepressed and included in the mature mRNA, leading to the translation of mScarlett fluorescent protein. We observed that after treatment with fluorescently labeled (Atto-488) TDP-43 aggregates, a small percentage of cells (0.1-0.2% of the total) shows the activation of the reporter.

first: Carlo

last: Scialo

first: Magdalini

last: Polymenidou


title: Peromyscus leucopus, Mus musculus, and humans have distinct transcriptomic responses to larval Ixodes scapularis bites.

city: Boston

first: Linden

last: Hu

state: MA

address: 136 Harrison Avenue

department: Microbiology

institute: Tufts University School of Medicine

summary: Ixodes scapularis are an important vector for at least six tick-borne human pathogens, including the predominant North American Lyme disease spirochete Borrelia burgdorferi. The ability for these ticks to survive in nature is credited, in part, to their ability to feed on a variety of hosts without excessive activation of the vertebrate immune system. While the ability for nymphal ticks to feed on a variety of hosts has been well-documented, the host-parasite interactions between larval I. scapularis and different vertebrate hosts is relatively unexplored. Here we report on the changes in the vertebrate transcriptome present at the larval tick bite site using the natural I. scapularis host Peromyscus leucopus, a non-natural rodent host Mus musculus (BALB/c), and humans. We note substantially less evidence of inflammation in P. leucopus compared to BALB/c mice and pronounced evidence of inflammation in humans. These data suggest that larval I. scapularis may have a reduced ability to suppress host immunity in non-natural hosts and expand our overall understanding of I. scapularis feeding.

sample_organism:
Peromyscus leucopus
Mus musculus

platform_organism:
Peromyscus leucopus
Mus musculus

overall_design: A heated 1:4 mixture of melted beeswax to rosin gum mixture was used to attach a modified microcentrifuge tube lined with mesh between the shaved shoulder blades of each rodent. Ten I. scapularis larvae (National Tick Research and Education Resource, Oklahoma State University) were placed inside the mesh cap. Mice were singly housed in cages surrounded by a water moat for 48 hours. The tick containment chamber was carefully removed, and a 2-mm punch biopsy was taken surrounding a single feeding tick and transferred immediately RNAlater, stored overnight at room temperature, and then frozen at –80oC until use. Biopsies were intentionally restricted to regions away from the edge of the tick containment chamber where damage from removal could skew results. A second biopsy was taken on the outside of the tick containment chamber as a matched control.

first: Julie

last: McCarthy

first: Jeffrey

middle: S

last: Bourgeois

middle: T


title: Divergent gene expression and kinetics of circulating tumor-infiltrating lymphocytes with highly homologous T-cell receptor sequences during immunotherapy

city: Buffalo

first: Mark

last: Long

state: NY

address: Elm & Carlton Streets

department: Bioinformatics & Biostatistics

institute: Roswell Park Comprehensive Cancer Center

summary: single-cell RNA/TCR sequencing (scRNA/TCR-seq) of circulating T cells from longitudinally obtained blood samples from the same a patient with NSCLC who had a response and a subsequent progression to anti-PD-1/CTLA-4 blockade therapy.

overall_design: Single live CD45+ CD3+ cells were enriched from cryopreserved PBMC samples obtained pre-treatment and on-treatment at 4, 8, 12, 24, and 32 weeks by flow cytometry sorting using a BD FACSAria II (BD Biosciences).

first: Ryutaro

last: Kajihara

first: Fumito

last: Ito


title: In-Depth Functional Analysis of BRD9 in Fetal Hematopoiesis Reveals Context-Dependent Roles.

city: Suita

first: Masaki

last: Nomura

address: 2-2, Yamadaoka

institute: Graduate School of Medicine, The University of Osaka

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

overall_design: Refer to individual Series


title: Real-time quantitative PCR analysis of human metastasis-related genes in cell pairs with different ROS stress conditions.

city: Guangzhou

first: Liu

last: Rui

state: Guangdong

address: 651 Dongfeng East Road

institute: Sun Yat-sen University Cancer Center

summary: HEK293 T-Rex/K-ras cells were induced by doxycycline (20 ng/mL) for 6 h, K-ras/Off cells were treated with 15 mU GOx for 6 h, whereas K-ras/On cells were treated with 2 mM NAC for 6 h. Expression of metastasis-related genes was analyzed using the Human Tumor Metastasis RT² Profiler PCR Array.

overall_design: Human Tumor Metastasis RT² Profiler PCR Array profiling.  HEK293 T-Rex/K-ras cells  were used and treated with 15 mM GOX or 2 mM NAC separately as indicated in the summary. RNA was extracted from the cells using Trizol (T9424, Sigma), and cDNA was synthesized with the PrimeScript™ RT-PCR Kit (RR014B, Takara). Equal amount of total RNA extracted from cells with different pre-treatment was quantified prior to RT-PCR assay. Gene expression was analyzed by qPCR using TB Green® Fast qPCR Mix (RR430S, Takara) on a CFX384 Real-Time System (Biorad). Microarray analyses were performed according to the protocol for human tumor metastasis RT² Profiler PCR Arrays (PAHS-028Z, QIAGEN).

first: Rui

last: Liu

first: Peng

last: Huang


title: Microbiome analysis of chronic suppurative otitis media and middle ear cholesteatoma in China

city: KUNMING

first: Ruiqing

last: LONG

state: YUN NAN PROVINCE

address: XICHANG ROAD

institute: the first affiliated hospital of Kunming medical university

summary: Chronic suppurative otitis media (CSOM) and middle ear cholesteatoma (MEC) are two different types of chronic otitis media (COM), and there may be differences in bacterial diversity. Fully exploring the bacterial differences between these two diseases plays an important role in the treatment of the disease and in the study of pathogenic mechanisms. Twelve and twenty-nine patients with CSOM and MEC, respectively, were recruited. Middle-ear lesion tissue was collected intraoperatively after opening the tympanic sinus and mastoid cavity under general anaesthesia and sterile conditions. The full-length 16S rRNA genome sequenced using third-generation sequencing (TGS) was then used to profile the bacterial community of each patient. Principal coordinate analysis (PCoA) showed that PC1 and PC2 could explain more than 50% of the between-group differences. Similarity analysis (ANOSIM) using the Binary Jaccard distance matrix indicated that between-group differences were greater than within-group differences (P < 0.05). Staphylococcus aureus was the most common strain in both groups. At the species level, the abundance of Anaerococcus_octavius was significantly different between both groups (P < 0.05). According to the linear discriminant effect size (LefSe) analysis, at the class and genus levels, Alphaproteobacteria and Bacillus were abundant in the CSOM group, respectively. Peptoniphilus_grossensis and Peptostreptococcaceae_bacterium_oral_taxon_929 were abundant at the species level in the MEC group (P < 0.05). Four COG (Clusters of Orthologous Groups) functions at level 2 were significantly different between the two groups (P < 0.05). The CSOM and MEC groups were inhabited by more diverse microbial communities, and the bacterial diversity of the two diseases differed markedly. This could guide the regular use of antibiotics and decrease the likelihood of multidrug-resistant bacteria formation. Further research on the pathogenic diseases of CSOM and MEC will focus on the functional differences between flora.

overall_design: Twenty-nine patients diagnosed with MEC (B1–B29) and twelve with CSOM (A1-A12) that underwent surgical treatment in the Otolaryngology Department of the First Affiliated Hospital of Kunming Medical University were enrolled in this study.Middle-ear lesion tissues from the MEC and CSOM were collected intraoperatively after opening the tympanic sinus and mastoid cavity. Pathological tissues were immediately stored in liquid nitrogen until batch processing.DNA was isolated from the specimens and processed for microbiome analysis by 16S rRNA gene sequencing, and we evaluate the microbiomes of CSOM and MEC using the full-length 16S rRNA genome sequenced by third-generation sequencing (TGS).


title: Time-course analysis to characterize the molecular mechanisms for 5637 gemcitabine-resistant cancer (5637GRC) cell line [GRC1]

city: Yuseong-gu

first: Seung Woo

last: Baek

state: Daejeon

address: Gwahak-ro 125

institute: Korea Research Institute Biology & Biotechnology

summary: transcriptomic data for 5637 were generated to observe the process of acquiring gemcitabine resistance in time-course.

overall_design: Chemotherapy resistance is the biggest obstacle in many cancer patients, and this is closely related to the survival rate due to treatment failure or recurrence. In general, the mechanism of drug-specific resistance was studied by simple comparison with cancer cells that obtained resistance. In this study, we focused on the molecular mechanisms that cancer cells acquire through gemcitabine exposure in the 5637 bladder cancer cell line. By defining one phase as confirming the survival of the cell line, we sequentially constructed a total of 15 phases with 5637 gemcitabine-resistance cancer (5637GRC) cell lines. In addition, two different types (5637GRC1 and 5637GRC2) and four time-points (phase 0, phase 3, phase 7, and phase 15) were defined by the method schematized.

first: Seung-Woo

first: Sun-Hee

last: Leem


title: Tbx1 haploinsufficiency causes brain metabolic and behavioral anomalies in adult mice which are corrected by vitamin B12 treatment

city: Naples

first: Gabriella

last: Lania

address: Via Pietro Castellino

country: Italy

institute: IGB-CNR

summary: Introduction  The brain-related phenotypes observed in 22q11.2 deletion syndrome (22q11.2DS) are highly variable and their origin is poorly understood. Changes in brain metabolism may cause or contribute to the phenotypes, given that many of the deleted genes (approx. 10%) are implicated in metabolic processes, but this is currently unknown. It is clearly important to address this knowledge gap, but in humans, the primary material required for studying brain metabolism is inaccessible. For this reason, we sought to address the issue using two mouse models of 22q11.2DS.  Methods  We used three independent approaches to investigate brain metabolism in young adult mice, namely, mass spectrometry, nuclear magnetic resonance spectroscopy and transcriptomics. We selected to study primarily Tbx1 single gene mutants because it is the primary candidate disease gene. We then confirmed key findings in the multi-gene deletion mutant Df1/+.  Results   We found that Tbx1 mutants have alterations of specific brain metabolites, including methylmalonic acid, which is highly brain-toxic, as well as a more general metabolomic imbalance. We provide transcriptomic evidence of an interaction genotype-vB12 treatment, and behavioural evidence of a response to vB12 treatment, which rescued some of the behavioural anomaly observed in Tbx1 mutants. We conclude that Tbx1 haploinsufficiency causes extensive brain metabolic anomalies, which are partially responsive to vB12 treatment. We suggest that alterations of glutamine-glutamate metabolism and fatty acid metabolism are key components of the metabolic phenotype in these mutants.

overall_design: Tbx1+/- and WT mice were injected intraperitoneally with vB12 dissolved in PBS 20 mg/kg (stored away from light) or with PBS, twice a week for 4 weeks starting at 4 weeks of age.Tthe brains were surgically removed after cervical dislocation and Total RNA was isolated from whole brains with Qiazol (QIAGEN) according to the manufacturers protocol with an additional precipitation step.

first: Antonio

last: Baldini

first: Elizabeth

last: Illingworth

first: Claudia

last: Angelini


title: Time-course analysis to characterize the molecular mechanisms for 5637 gemcitabine-resistant cancer (5637GRC) cell line [GRC2]


title: Genome-wide research of epigenetic regulation in arabidopsis

city: Beijing

first: Yao

last: Yao

state: China

address: Tsinghua university Biotechnology building Haidian  District, Beijing, 100084, China

department: school of life sciences

institute: Tsinghua university

summary: In Arabidopsis, there are still many areas of epigenetic modification functions that remain to be explored. In this study, we used multiple high-throughput sequencing technologies to investigate the regulation of histone modifications in the model organism Arabidopsis.

sample_organism:
Arabidopsis thaliana
Oryza sativa

platform_organism:
Arabidopsis thaliana
Oryza sativa

overall_design:
Chromatin immunoprecipitation DNA-sequencing (ChlP-seq) for histone modifications in arabidopsis
Comparative gene expression profiling analysis of RNA-seq data for two genotypes including WT(Col-0) and sdg8 mutant.

first: JingCong

last: Zhou


title: Time-course analysis to characterize the molecular mechanisms for 5637 gemcitabine-resistant cancer (5637GRC) cell line


title: A preclinical model of irritable bowel syndrome driven by CHRM3 activation

status: Public on Feb 19 2025

city: Nanchang

first: Xueyang

last: Li

address: yongwai street

institute: the first affliated hospital of nanchang university

summary: Irritable bowel syndrome (IBS) is a prevalent functional gastrointestinal disorder that significantly reduces patients' quality of life. However, current animal models have limitations in replicating the complex pathophysiology of IBS. In this study, we successfully developed a mouse model by mating intestinal epithelium-specific Cre tool mice with chemically modified human muscarinic acetylcholine receptor 3 (hCHRM3) mice, resulting in specific expression of the hCHRM3 in the intestinal epithelial cells. Activation of the hCHRM3 with clozapine-N-oxide (CNO) mimicked IBS attacks. The model mice exhibited typical IBS symptoms such as diarrhea, pain, and visceral hypersensitivity, along with pathological changes like intestinal edema and inflammatory cell infiltration, and disruption of the intestinal mucosal barrier. RNA sequencing revealed significant differentially expressed genes between the model and control groups, with KEGG and GO enrichment analyses indicating significant enrichment of immune and inflammation-related pathways. Additionally, the model mice showed increased levels of short-chain fatty acids and imbalances in the diversity and composition of the gut microbiota. This new IBS mouse model effectively simulates the symptoms and pathological processes of human IBS, providing a powerful tool for in-depth research into the pathogenesis of IBS and the development of therapeutic strategies.

overall_design: RNA sequencing analysis of control mice and IBS model mice at 0.5 hours after modeling.

first: Junmin

last: Yang

first: Chong

last: Wang

first: Xiaoyu

first: Pan

last: Zheng

first: Jie

last: Liang

first: Li

last: Zhang

first: Liang

last: Xia

first: Jianhua

last: Wan


title: Determining how bacterial presence can impact gene regulation for lung adenocarcinoma cells

city: Louisville

first: Eric

middle: Christian

last: Rouchka

state: Kentucky

address: 522 East Gray Street

department: Biochemistry and Molecular Genetics

institute: University of Louisville

summary: ntroduction: Recent studies have discovered lung cancer subtypes to have their own profile of microbiome within the tumor microenvironment. Additionally, the tumor associated microbiome exhibited altered bacterial pathways, suggesting that certain bacterial families are more fit to facilitate tumor progression than others. We believe that there exists a crosstalk between lung adenocarcinoma cells (LUAD) and bacterial cells. Methods and Materials: RNA-seq was performed on LUAD cell lines to understand the paracrine signaling effects that bacterial biomolecules have. From our RNA-seq data, we chose to investigate glycolysis by measuring glucose uptake and lactate production, investigate invasive potential through invasion assays, and measure EMT markers. As lipopolysaccharides (LPS) are found abundantly on the cell wall of gram-negative bacteria and can activate toll like receptor 4 (TLR4), we inhibited TLR4 with C34 to determine the relationship between TLR4 and the phenotypic changes. Finally, to gain a better understanding of the bacterial biomolecules leading to the changes observed, we treated our media with either RNAse, charcoal, or dialyzed molecules > 3kDa. Results and Discussion: From our RNA-seq data, we observed a total of 948 genes upregulated in the presence of E. coli biomolecules. Of the 948 upregulated genes observed in LUAD cell lines incubated in E. coli biomolecules, we witnessed increased expression of Hexokinase II, JUN proto-oncogene, and Snail Family Transcriptional Repressor 1. We verified the elevation of glycolytic enzymes through western blot and saw elevation of 2-deoxyglucose uptake and lactate production in LUAD cell lines incubated in E. coli biomolecules using scintillation counter and lactate luminescence assay, respectively. In addition to E. coli elevating glycolysis in LUAD cell lines, we also saw increase in invasive potential by Boyden chamber. Inhibition of TLR4 did not lead to decreasing the impact of E. coli biomolecules on glycolysis or invasive potential of LUAD. Modulating our E. coli supplemented media with either RNAse, dextran-coated charcoal, or using a spin column to remove biomolecules < 3kDa resulted in changes in HKII and Claudin protein expression. Overall, these findings indicate a direct relationship between E. coli and LUAD, wherein several well-known hallmarks of cancer are upregulated. Future studies would do well in investigating these molecules further and fully understanding the impact of a microbial shift in the tumor microenvironment.

overall_design: Lung adenocarcinoma cell lines (A549 and H2009) grown in either vehicle control (1:1 RPMI: PBS) or bacterially supplemented media (1:1 RPMI: bacterially supplemented media) with three replicates for each of the four groups: (1) A549 vehicle; (2) A549 bacteria; (3) H2009 vehicle; and (4) H2009 bacteria.

first: Alexis

last: Vega

first: Parag

middle: P

last: Shah

middle: C

first: Brian

last: Clem

first: Calista

middle: R

last: Dean

first: Natassja

last: Woodrum

first: Preeti

last: Tanwani

first: Leah

middle: J

last: Siskind

first: Levi

last: Beverly


title: Fabp4 is Essential for the Maintenance of Leukemia Stem Cells while Sparing Hematopoietic Stem Cells [bulkRNA-seq]

city: changsha

first: Cheng

last: Xing

state: Hunan Province

address: Department of Hematology, the Second Xiangya Hospital, Central South University,

department: Department of Hematology

summary: Fatty acid-binding protein 4 (FABP4) plays a crucial role in the uptake, transport, and metabolic regulation of fatty acids. Previous research has found that the abnormal expression of FABP4 is associated with certain cancers, and it may become a new target for tumor therapy. We discovered that a haploinsufficient or absent dosage of Fabp4 does not affect the function of hematopoietic stem cells in mice, but significantly impacts the maintenance of leukemia stem cells (LSC). Our findings indicate that while Fabp4 does not influence the  initiation of acute myeloid leukemia (AML) transformed by MLL-AF9 (MA9) in mice, it markedly promotes the progression of AML. A haploinsufficient or absent dosage of Fabp4 significantly extends the survival time of MA9 mice. Our research reveals the key role and mechanism of Fabp4 in MA9-LSC, suggesting that Fabp4 is a potential target for selectively eliminating MLL-rearranged leukemia.

overall_design: Nine murine bone marrow samples,bone marrow cells from 3 wild-type, 3 heterozygous knockout, and 3 homozygous knockout mice for Fabp4.Nine vitro bone marrow samples,bone marrow cells from 3 wild-type, 3 heterozygous knockout, and 3 homozygous knockout mice for Fabp4


title: The Histone Demethylase LSD1/ZNF217/CoREST Complex is a Major Restriction Factor of Epstein-Barr Virus Lytic Reactivation

first: Yifei

last: Liao

state: Massachusetts

address: 181 Longwood Ave, 8th Floor

institute: Brigham and Women's hospital

summary: Epstein-Barr virus (EBV) contributes to ~1.5% of human cancers, including lymphomas, gastric and nasopharyngeal carcinomas. In most of these, nearly 80 viral lytic genes are silenced by incompletely understood epigenetic mechanisms, precluding use of antiviral agents such as ganciclovir to treat the 200,000 EBV-associated cancers/year. To identify host factors critical for EBV latency, we performed a human genome-wide CRISPR-Cas9 screen in Burkitt B-cells. Top hits included the lysine-specific histone demethylase LSD1 and its co-repressors ZNF217 and CoREST. LSD1 removes histone 3 lysine 4 (H3K4) and histone 3 lysine 9 (H3K9) methylation marks to downmodulate chromatin activation. LSD1, ZNF217 or CoREST knockout triggered EBV reactivation, as did a LSD1 small molecule antagonist, whose effects were additive with histone deacetylase inhibition. LSD1 blockade reactivated EBV in Burkitt lymphoma, gastric carcinoma and nasopharyngeal carcinoma models, sensitized cells to ganciclovir cytotoxicity and induced EBV reactivation in murine xenografts. ZNF217 and LSD1 co-occupied the EBV immediate early gene BZLF1 promoter, which drives B-cell lytic cycle, as well as to the oriLyt enhancer regions recently implicated in EBV reactivation. LSD1 depletion increased levels of activating histone 3 lysine 4 (H3K4) methylation but not repressive histone lysine 9 methylation marks at BZLF1 and oriLyt and induced their interaction by long-range DNA looping. An orthogonal CRISPR screen highlighted a key H3K4 methyltransferase KMT2D role in driving EBV reactivation. Our results highlight H3K4 methylation as a major EBV lytic switch regulator and suggest novel therapeutic approaches.

overall_design: EBV+ Akata cells collected for chromatin immunoprecipitation, library preparation and sequencing.

first: Jinjie

last: Yan

first: Isabella

last: Kong

first: Zhixuan

last: Li

first: Weiyue

last: Ding

first: Sarah

last: Clark

first: Lisa

last: Giulino-Roth

first: Benjamin

last: Gewurz


title: In vitro expansion affects the response of human bone marrow stromal cells to irradiation

city: Wuhan

first: Dong

last: Chen

state: Hubei

address: 388 GaoXin 2nd Road, East Lake Hi-Tech Development Zone

department: Center for Genome Analysis

institute: ABLife, Inc.

summary: Cell passage in vitro affected the irradiation response of BMSCs via molecular mechanisms that mediated differences in apoptosis, the cell cycle, senescence and the cytokines secretion.

overall_design: BMSCs were passaged in vitro and irradiated at passage 6 (P6) and passage 10 (P10).  The gene expression profile were analysed for the P6, P10, and non-irradiated (0h) BMSCs at different post-irradiation time points (2h and 8h).

first: Xiang

last: Yang


title: A triple independent inducible expression system for human pluripotent stem cells

city: Denver

first: Pluto

last: Bio

state: CO

address: 3575 Ringsby Ct Suite 414

institute: Pluto Bio

summary: Human pluripotent stem cells (hPSC) and their differentiated derivatives represent valuable tools for studying development, modeling diseases, and advancing cell therapy. Recent improvements in genome engineering allow precise modifications of hPSC, further enhancing their utility in basic and translational research. Here we describe a Recombinase-Mediated Cassette Exchange (RMCE) platform in hPSC that allows highly efficient, rapid, and specific integration of transgenes. The subsequent RCME process to integrate any desired DNA sequence is nearly 100% efficient, without negatively affecting pluripotency or karyotypic stability of hPSC. Taking advantage of this convenient system, we first established a dual inducible expression system based on Tet-On and Cumate-On systems, allowing inducible expression of two transgenes independently. Secondly, we incorporate a Tet-on inducible system driving expression of three genes simultaneously. However, two genes also contain degron sequencing allowing precise control over expression of each gene individually. We demonstrated the utility of these systems in hPSC as well as their functionality after differentiation into cells representative of the three germ layers. Lastly, we used this system to interrogate lineage commitment induced by transcription factor expression. We found that controlled dual expression but not individual expression of the pancreatic transcription factors NKX6.1 and PDX1 biases hPSC embryoid body differentiation towards the pancreatic lineage by inducing expression of the NeuroD program. In sum, we describe a novel genetic engineering platform that allows for the efficient and fast integration of any desired transgene(s) in hPSC using RMCE. We anticipate that the ability to modulate expression of three transgenes simultaneously will further accelerate discovery using stem cell technology.

overall_design: hPSC were genetically modified to contain a triple gene inducible system to guide unbias differentiation into pancreatic tissue. We induce expression of transcription factor PDX1 and NKX6.1 in modified hPSC and started unbiased differentiation. 7-8 days later we collected cells for RNA-seq analysis.

first: Roberto

last: Castro-Gutierrez

first: Ankita

last: Arora

first: Katherin

last: Veith

first: Matt

last: Taliaferro

first: Holger A.

last: Russ


title: Two unrelated distal genes activated by a shared enhancer benefit from localizing inside the same small topological domain [CRISPRi RNA-seq]

city: Utrecht

first: Peter

last: Krijger

address: Uppsalalaan 8

country: Netherlands

institute: Hubrecht Institute

summary: Enhancers are tissue-specific regulatory DNA elements that can activate transcription of genes over distance. Their target genes most often locate in the same topologically associating domain (TAD). TADs are structural entities within chromosomes in which cohesin DNA loop extrusion supports intra-domain DNA contacts and CTCF-bound boundaries serve to halt and concentrate paralogous genes. Enhancers shared by multiple unrelated genes may be more common than those acting on paralogous gene clusters, but are underexplored. Here, we analyzed the interplay between an enhancer and two distal, functionally unrelated, genes residing at opposite domain boundaries. The enhancer stimulated boundary and gene-gene contacts and required cohesin as well as two intact domain boundaries to support gene activation. The two genes preferentially transcribed when spatially together, but did not rely on each other’s transcription, nor showed gene competition. Placing them and the enhancer in smaller domains caused their upregulation. Domain boundaries, therefore, can support long-range enhancer-promoter communication inside domains. Boundary proximity thereby matters as the distal enhancer functions more effectively inside smaller domains. We propose that smaller domains have more concentrated cohesin loop extrusion activity to facilitate enhancer action over distance.

overall_design: RNA-seq in K562 cells depleted for SMC1A using CRISPRi.

first: Yike

last: Huang

first: Marjon

last: Verstegen

first: Sjoerd

last: Tjalsma

first: Kavvya

last: Gupta

first: Minhee

last: Park

first: Alistair

last: Boettiger

first: Wouter

last: de Laat


title: Flagellin nebulization enhances respiratory immune responses in the porcine model

city: LILLE

first: Florence

last: MAURIER

address: 1 rue du Professeur Calmette BP 245

department: Plateformes Lilloises en Biologie & Santé

country: France

institute: Institut Pasteur de Lille

summary: Respiratory delivery of the Toll-like receptor 5 agonist FLAMOD, a recombinant flagellin, offers a promising approach for treating bacterial pneumonia. FLAMOD stimulates the airway epithelium, mobilizing and activating immune cells and effectors to combat infections. While previous evidences were obtained in mouse models, this study represents the first comprehensive assessment of FLAMOD delivered by nebulization in pigs. Our results demonstrate that a single nebulization of FLAMOD did not cause any adverse effects on clinical parameters. Histological analysis supported that FLAMOD treatment led to immune cell infiltration in the lung tissue, indicative of an active immune response. Flow cytometry confirmed granulocyte recruitment in conducting airways. RNA sequencing established immune activation across the respiratory tract, from the nose, trachea, bronchi to the lungs, highlighting innate immunity, bacterial defense, cytokine and chemokine signaling, and granulocyte chemotaxis as key biological pathways. These findings demonstrated FLAMOD’s capacity to induce a robust and common immune response throughout the porcine respiratory system as well as specific compartmentalized immune signature. This study establishes FLAMOD as a potent activator of innate immunity, providing a proof-of-concept for inhalation-based therapeutic strategies to combat bacterial pneumonia in clinical setting.

overall_design: Twelve male six-week-old pigs (Sus scrofa domestica, line LRxLW TOPIGS 20, Lelystad) were nebulized with diluent buffer for 24h, flagellin for 4h and flagellin for 24h (n=4 per group).  Nose, trachea, bronchus, and lung tissue as well as blood were sampled and processed for RNA isolation and sequencing.

first: Jean-Claude

last: Sirard

first: David

last: Hot

first: Mara

last: Baldry

first: Arndt

last: Benecke


title: Clec12a controls colitis by tempering inflammation and restricting expansion of specific commensals

city: Salt Lake City

first: W. Zac

last: Stephens

state: UT

address: 15 N. Medical Drive, EEJMRB 4208, EEJMRB 4208

department: Pathology

institute: University of Utah

summary: Microbiota composition regulates colitis severity, yet mechanisms employed by the innate immune system to regulate this remain unclear. We show that severity of colitis in Clec12a deficient animals is dependent on microbiota composition. Microbiota from a Clec12a-/- animal has expanded Faecalibaculum rodentium and transplantation of the Clec12a-/- microbiota or treatment with F. rodentium is sufficient to worsen colitis in wild-type mice. However, Clec12a-/- animals are resistant to colitis developmemt when rederived into an 11-member community, while addition of F. rodentium worsens disease.  Colitis in Clec12a-/- mice is dependent on monocytes and cytokine and sequencing analysis in Clec12a-/- macrophages and serum shows enhanced inflammation with a reduction in phagocytic genes. We demonstrate that F. rodentium specifically binds to Clec12a and Clec12a-/- deficient macrophages are specifically impaired in their ability to phagocytose F. rodentium. Thus, Clec12a is an innate-immune surveillance mechanism to control the expansion of potentially harmful commensals while limiting inflammation

overall_design: RNAseq profiling of BMDMs from WT or Clec12a-/- mice in the presence of Faecalibaculum rodentium for 24 hours.

first: Tyson

last: Chiaro

first: W

last: Zac Stephens

first: Morgan

last: Greenewood

first: June

last: Round


title: Inflammatory responses revealed through HIV infection of microglia-containing cerebral organoids

city: Chicago

first: Ramon

last: Lorenzo-Redondo

state: IL

address: 303 E Superior St.

institute: Northwestern University

summary: Cerebral organoids (COs) are valuable tools for studying the intricate interplay between glial cells and neurons in brain development and disease, including HIV-associated neuroinflammation. We developed a novel approach to generate microglia containing COs (CO-iMs) by coculturing hematopoietic progenitors and inducing pluripotent stem cells from the same line. This approach allowed for the differentiation of microglia within the organoids concomitantly with the neuronal progenitors. Compared with conventional COs, CO-iMs were more efficient at generating CD45+/CD11b+/Iba-1+ microglia and presented a physiologically relevant proportion of microglia (~7%). CO-iMs presented substantially increased expression of microglial homeostatic and sensome markers as well as markers for the complement cascade. CO-iMs are susceptible to HIV infection, resulting in a significant increase in several pro-inflammatory cytokines/chemokines and compromised neuronal functions, which are abrogated by the addition of antiretrovirals. Thus, CO-iM is a robust model for deciphering neuropathogenesis, neurological disorders, and viral infections of brain cells in a 3D culture system.

overall_design: Develop a new approach to model the interaction of human microglia with their neuronal environment in order to unmask the role of microglia and their specific genes in HIV-related inflammation, their role in viral persistence under cART, and the biological consequences of infection for CNS inflammation and neuronal health. We generated a novel 3D culture cerebral organoid model offering a platform where physiological proportions of microglia with or without HIV-1 infection can crosstalk with other glial and neuronal cell types in a human-brain-like environment.  Assessed the differences between COs and CO-iMs with respect to microglia phenotype and genotype and  the response of microglia to HIV-1 infection. Further,   and to assessed the effectiveness of antiretrovirals in infected CO-iMs. We compared and characterized the global transcriptome profile bwetween COs and CO-iMs, and between  uninfected CO-iMs, infected CO-iMs and infected+cART treated CO-iMs via bulk RNA-seq analysis.Performed RNA-seq analysis for 12  iPSC-Ru line derived organoids (~65 day old) divided into 4 groups: COs uninfected (CO 8, CO 9, and CO 10; n=3), CO-iMs uninfected (CO-iM 4, CO-iM 5, and CO-iM 6; n=3), CO-iM HIV-1 BAL infected  (n = 3; CO-iM 12, CO-iM 19, and CO-iM 21), and CO-iM HIV-1 BAL infected + cART treated  (CO-iM 15, CO-iM 24, and CO-iM 25; n = 3).

first: Srinivas

last: Narasipura

first: Janet

last: Zayas

first: Michelle

middle: K

last: Ash

first: Anjelica

last: Reyes

first: Tanner

last: Shull

first: Stephanie

last: Gambut

first: Jeffrey

last: Schneider

first: Lena

last: Al-Harthi

first: João

middle: I

last: Mamede


title: Gene expression profile at single cell level of peripheral blood mononuclear cells from Cx3cr1-/-  mice and wt mice under C57BL/6J background

city: Jinan

first: Weijie

last: Wu

address: Wenhuaxilu No.107

institute: Qilu Hospital of Shandong University

summary: CX3CR1 is a receptor for chemokines, primarily expressed in peripheral blood mononuclear cells, particularly in monocytes and macrophages. It influences the chemotaxis, adhesion, and migration of immune cells to vascular endothelial cells. We used peripheral blood from Cx3cr1 monocyte/macrophage-specific knockout mice for single-cell sequencing to analyze the changes in monocytes, macrophages, and other cells in the circulating blood after knockout.

overall_design: Peripheral blood was collected from Cx3cr1 monocyte/macrophage-specific knockout mice and wild-type C57BL/6J mice for the extraction of peripheral blood mononuclear cells, with the latter being used for single-cell sequencing analysis.

first: Sizhe

last: Chen


title: ChREBP-mediated control of Them1 expression coordinates thermogenesis with glycolysis and lipogenesis

city: Boston

first: Xu

last: Xu

address: 330 Brookline Ave

department: Surgery

institute: Beth Israel Deaconess Medical Center

summary: Activation of thermogenic brown adipose tissue (BAT) and inducible beige adipose tissue (BeAT) is triggered by environmental or metabolic stimuli, including cold ambient temperatures and nutrient stress. Thioesterase superfamily member 1 (Them1), a long chain fatty acyl-CoA thioesterase that is enriched in BAT, suppresses acute cold-induced thermogenesis. Here, we demonstrate that Them1 expression was induced in BAT and BeAT by the carbohydrate response element binding protein (ChREBP) in response to chronic cold exposure or to the activation of the integrated stress response (ISR). Under either condition, Them1 suppressed energy expenditure. Consequently, mice lacking Them1 in BAT and BeAT exhibited resistance to obesity and glucose intolerance induced by feeding with a high-fat diet. During chronic cold exposure or ISR activation, Them1 accumulated in the nucleus, where it interacted with ChREBP and reduced the expression of its target genes, including those encoding enzymes that mediate glycolysis and de novo lipogenesis. These findings demonstrate that in response to chronic cold- or nutrient-induced stress, the induction of Them1 by ChREBP limits thermogenesis while coordinately reducing glucose utilization and lipid biosynthesis through its distinct activities in the cytoplasm and nucleus. Targeted inhibition of Them1 may represent a potential therapeutic approach to increase the activity of BAT and BeAT to enhance energy expenditure in the management of obesity-associated metabolic disorders.

overall_design: To characterize transcriptomic changes in BAT and BeAT in response to acute or chronic cold exposure, we analyzed mRNAs of both BAT and iWAT of WT mice acclimated to 30 °C before or after exposure to 4 °C for 3 days or 3 weeks.

first: David

last: Cohen


title: Hi-C results of single ICM of E3.5 blastocyst

first: Zhenhai

last: Du

address: Qinghua Yuan, Haidian District

institute: Tsinghua University

overall_design: Small scale in situ high throughput chromatin conformation capture (sisHi-C) for inner cell mass from single embryos

first: Wei

last: Xie


title: Single-cell multiome and enhancer mapping of human retinal pigment epithelium and choroid nominate pathogenic variants in age-related macular degeneration

first: Jiaying

last: Li

state: Beijing

address: Dongjiaomin Road

institute: Beijing Tongren Hospital

summary: Age-related macular degeneration (AMD) is a leading cause of vision loss, with genetic variants contributing to disease susceptibility. To identify functional regulatory variants, we performed allelic-specific STARR-seq under both normal conditions and complement-stimulated environments, mimicking inflammatory stress relevant to AMD pathogenesis. Using a high-throughput screening approach, we systematically assessed the impact of AMD-associated single nucleotide polymorphisms (SNPs) on enhancer activity. Our analysis revealed a subset of SNPs exhibiting differential regulatory effects between normal and stimulated conditions, highlighting context-dependent enhancer modulation. These findings provide insights into the genetic regulation of AMD and potential targets for therapeutic intervention.

overall_design: Age-related macular degeneration (AMD) is a leading cause of vision loss worldwide. Genome-wide association studies (GWAS) of AMD have identified dozens of risk loci that may house disease targets. However, variants in these loci are largely noncoding, making it difficult to assess their function and whether they are causal. Here, we present a single-cell gene expression and chromatin accessibility atlas of human retinal pigment epithelium (RPE) and choroid to systematically analyze both coding and noncoding variants implicated in AMD. We employ HiChIP and Activity-by-Contact modeling to map enhancers in these tissues and predict cell and gene targets for risk variants. We further perform allele-specific self-transcribing active regulatory region sequencing (STARR-seq) to functionally test variant activity in RPE cells, including in the context of complement activation. Our work nominates new pathogenic variants and mechanisms in AMD and offers a rich and accessible resource for studying diseases of the RPE and choroid.

first: Sean

last: Wang


title: The macrophage response to LPS is marked by dynamic nucleosome positioning and increases in nucleosome sensitivity corresponding with immune regulatory factor footprints

city: Tallahassee

first: Jonathan

middle: H

last: Dennis

state: FL

address: 319 Stadium Drive

department: Biological Science

institute: Florida State University

summary: Macrophages detect lipopolysaccharide (LPS) through toll-like receptor 4 (TLR-4) on the cell surface which initiates a signaling cascades resulting in the recruitment of regulatory factors to chromatin and subsequent expression of chemokine and cytokine genes. Primary response genes, which are marked by poised promoters and enhancers, are rapidly expressed after LPS stimulation and activate secondary response genes via paracrine and autocrine signaling pathways. While immune signaling following macrophage activation is well understood, the dynamics of nucleosome architecture and regulatory factor binding in promoter regions during early and late LPS responses remain unclear. Here, we stimulated THP-1 derived macrophages with LPS and assessed nucleosome distribution, MNase sensitivity, and small factor footprints across promoters at eight time points. We found that while nucleosome distribution was static over most promoters, LPS stimulation resulted in transient remodeling of immune and DNA repair gene promoters. We also observed distinct MNase sensitivity alterations in two phases which aligned with early/late gene expression patterns. Notably, while most Pol II promoters showed altered chromatin sensitivity, only a subset exhibited transcriptional changes, suggesting widespread chromatin remodeling uncoupled from gene expression. Small factor footprints suggested regulatory factor binding increased at promoters with altered nucleosome distributions or sensitivity, implying that nucleosome sensitivity may  result from  a combination of histone modifications, genome accessibility, and protein-DNA interactions. These findings provide new temporal insight into the transient and long term effects of immune stimulation on promoter architecture. This also provides a methodological framework for additional time-resolved studies of chromatin remodeling in other systems.

overall_design: Nucleosome mapping by micrococcal nuclease (MNase) digestion and DNA sequencing of promoter captured mononucleosomes from THP-1 macrophages after LPS stimualtion

first: Jane

last: Benoit

first: Brandon

last: Buck

first: Hank

last: Bass


title: Single-cell transcriptome analysis reveals distinct cell populations in the celiac ganglia

city: Kobe

first: Hirosato

last: Kanda

state: Hyogo

address: 1-3-6 Minatojima, Chuo-Ku

institute: Hyogo Medical University

summary: In the peripheral nervous system, the prevertebral ganglion (PVG) serves as an important relay station, transmitting centrifugal signals to visceral organs; the PVG is also known to innervate enteroanal afferent neurons (IFANs) and spinal sensory neurons innervating the intestinal tract. It has been suggested that there are neural circuits within the PVG consisting of sensory and sympathetic neurons. Here, we used a single nuclei RNA sequencing method to characterize the gene expression profiles of individual cells constituting the ventral ganglion in normal rats. These data provide valuable material for examining the neural circuits within the PVG.

overall_design: We performed a single-nuclei RNA-seq experiment on the celiac ganglion from 10 normal male Sprague-Dawley rats.


title: Gasdermin D deficiency attenuates development of ascending aortic dissections in a novel mouse model

city: Gainesville

first: Zhihua

last: Jiang

address: 1600 SW Archer Rd

institute: University of Florida

summary: This study established a novel mouse model for TAD. Bulk RNA sequencing was performed to investigate the mechanisms underlying TAD pathogenesis in this model. The data revealed acute inflammation activation in both TAD and control aortas. However, while inflammation in control aortas resolved within two weeks, TADs exhibited a sustained inflammatory response throughout the observation period. Ingenuity Pathway Analysis and functional annotation of differentially expressed genes indicated that a distinct inflammatory microenvironment, rather than generalized inflammation, drives TAD onset by specifically recruiting neutrophils to the aortic wall. At later stages, T-cell-mediated immune injury became the predominant driver of pathology

overall_design: TADs and control aortas were collected on days 7 and 14, with ascending aortas from age-matched naïve mice serving as baseline references (n=6 per group). Comparisons were conducted to assess temporal differences (d0 vs d7 vs. d14) and pathology-specific differences (TAD vs. control aorta) in gene expression during TAD development.

first: Jiang

last: Zhihua

first: Cai

last: Guoshuai

first: Dirain

last: Marvin Louie Servanez


title: NIH3T3 serum stimulation and cordycepin treatment (Agilent mouse 60K microarray)

city: Nottingham

first: Keith

last: Spriggs

state: Notts

address: University Park

department: Pharmacy

country: United Kingdom

institute: University of Nottingham

summary: 3’deoxyadenosine, also known as cordycepin, has been widely researched as a potential treatment for cancer, yielding promising results in tissue culture as well as in pre-clinical models. A wide variety of mechanisms of action have been proposed, with little agreement between different studies. Here, we confirm that cordycepin triphosphate is likely to be the active metabolite of cordycepin. Data from single and high throughput experiments showed that cordycepin represses growth factor induced gene expression. Bioinformatic analysis, quantitative PCR and western blotting confirmed that cordycepin blocks the PI3K/AKT/mTOR and/or MEK/ERK pathways in 6 cell lines. Effects of cordycepin on translation through mTOR pathway repression were detectable within 30 minutes, indicating a rapid process. Our data show that cordycepin has a broadly similar mechanism of action in all cell lines studied and indicate that its therapeutic target is a cordycepin triphosphate sensitive molecule that is required for growth factor signal transduction.

overall_design: NIH3T3 cells were serum starved for 24 hours, treated with vehicle (DMSO) or vehicle plus 20 μM cordycepin for 1.5 hour and stimulated with serum for 30 minutes, in independent triplicate. Total RNA was isolated and used for microarray analysis.

first: Cornelia

last: de Moor

first: Steven

last: Lawrence

first: Richa

last: Singhania

first: Graeme

last: Thorn

middle: A


title: Carboplatin-resistance-related DNA damage repair prognostic gene signature and its association with immune infiltration in breast cancer

city: Shanghai

first: Shuwen

last: Dong

address: Huangpu District

institute: Shanghai Jiao Tong University

summary: Breast cancer is among the most prevalent malignant tumors globally, with carboplatin serving as a standard treatment option. However, resistance often compromises its efficacy. DNA damage repair (DDR) pathways are crucial in determining responses to treatment and are also associated with immune infiltration. This study aimed to identify the DDR genes involved in carboplatin resistance and to elucidate their effects on prognosis, immune infiltration, and drug sensitivity in breast cancer patients. We constructed the 3D-culture model of the MDA-MB-231 cell line, both resistant and sensitive to carboplatin, and identified a set of DDR genes. By integrating data from a public database, we established a prognostic signature comprising thirteen DDR genes. Our analysis indicated that this model is associated with immune infiltration patterns in breast cancer patients, particularly concerning CD8+ T cells and NK cells. Additionally, it demonstrated a significant correlation with sensitivity to other DDR-related drugs, suggesting its potential as a biomarker for treatment efficacy. Compared to the control group, TONSL-knockdown cell lines exhibited a diminished response to DNA-damaging agents, marked by a notable increase in DNA damage levels and enhanced drug sensitivity. Furthermore, single-cell analysis revealed elevated TONSL expression in dendritic and epithelial cells, particularly in triple-negative breast cancers.


title: Interleukin-1 Signaling and CD4+ T Cells Control B Cell Recruitment to the Lungs in Chronic Beryllium Disease

city: Aurora

first: Shaikh

last: Atif

address: Research Complex II (RC2): P15-10005 Department of Medicine, Division of Allergy and Clinical Immunology, University of Colorado Anschutz Medical Campus, 12700 E 19th Ave

department: Medicine

institute: University of Colorado

summary: Chronic beryllium disease (CBD) is a debilitating pulmonary disorder that occurs due to persistent exposure to beryllium (Be) particles in the workplace. Be-exposure causes activation of the innate immune system, resulting in the secretion of interleukins and chemokines that drive the accumulation of B and T cells in the lungs. However, the mechanisms by which innate molecules influence the recruitment of B cells and B cell-mediated protection in CBD are poorly understood. In this study, we employed multiple approaches to examine the role of innate immune signaling and CD4+ T cells in B cell recruitment and function in the lungs. We show that the absence or blocking of IL-1 receptor prevents the recruitment of B cells to the lungs of BeO-exposed mice.  Additionally, we show that B cell recruitment to the lungs depends on the chemokine receptor, CXCR5, and CD4+ T cells. Further, RNA sequencing of pulmonary tissue-resident B cells in CBD revealed distinct gene signatures compared to splenic B cells, with increased expression of pathways involved in antigen presentation, tight junction interactions, and interferon signaling. Overall, our study shows that B cell recruitment and aggregate formation during CBD are dependent on sequential activation of both innate and adaptive immune responses.

overall_design: RNA sequencing of beads and FACS sorted B cells from the lungs of BeO-exposed mice and CD23+ follicular B cells from the spleens of PBS-treated mice. The transcriptional changes were compared between the lung B cells and splenic follicular B cells.

first: Joseph

last: Gaballa


title: Multiomics analysis decodes biosynthesis of specialized metabolites constituting the therapeutic terrains of Magnolia obovata

city: Chiba

first: Mami

last: Yamazaki

state: Chiba

address: 1-8-1 Inohana, Chuo-ku, Chiba City Pharmaceutical Research Building II

department: Department of Molecular Biology and Biotechnology

institute: Chiba University

summary: In this study, we performed LC-QTOF-MS-based metabolomics and RNA-seq based transcriptome analysis using seven tissues of Magnolia obovata

overall_design: Examination of 7 tissues of Magnolia obovata

first: Kazuki

last: Saito

first: Hideyuki

last: Suzuki

first: Michimi

last: Nakamura

first: Ryo

last: Nakabayashi

first: Tetsuya

last: Mori

first: Towa

last: Yokosaka

first: Amit

last: Rai

first: Megha


title: Gene expression profile at single cell level of leg muscles from E18.5-day WT and SYISL KO fetal mice from the same litter

city: wuhan

first: wei

last: jiang

address: No.1, Shizishan Street, Hongshan District, Wuhan, China

institute: Huazhong Agricultural University

summary: To further explore the mechanism of SYISL knockout on muscle fiber development, we performed 10X Genomics single-cell RNA sequencing of leg muscles from E18.5-day WT and KO fetal mice from the same litter.

overall_design: Samples were collected from the leg muscles of E18.5 embryos from both genotypes, with each condition including two biological replicates. Analysis was conducted using single-cell RNA sequencing (scRNA-seq).

first: Hao

last: Zuo

first: Wei

last: Jiang

first: Rong

last: Zheng

first: Bo