title: Constitutive expression of cardiomyocyte Klf9 precipitates metabolic dysfunction and spontaneous heart failure.

city: Newark

first: Danish

last: Sayed

state: NJ

address: 185 south orange avenue

department: CBMM

institute: Rutgers-NJMS

summary: Metabolic adaptations and flexibility during development and disease play an essential in cardiomyocyte function and survival. We recently reported Glucocorticoid receptor (GR)-Krüppel-like factor 9 (Klf9) axis in mediating metabolic adaptations in cardiomyocytes stimulated with Dexamethasone. Klf9 expression decreases in hypertrophic and failing hearts, suggesting its importance in cardiac homeostasis and its potential contribution to dysfunction under pressure overload. Genome wide Klf9 occupancy in adult hearts revealed 2,242 genes directly associated with Klf9, with enrichment in metabolic pathways, autophagy, ubiquitin-mediated proteolysis, and cellular senescence. We generated and characterized a conditional cardiac specific Klf9 knock-In (Klf9KI) mice, which developed progressive cardiac hypertrophy, cardiac dysfunction and cardiac failure by 8wks of age, with mortality by 12-14wks. RNA-seq analysis at 1wk, 4wks, and 8wks showed stage-specific transcriptional changes. At 1 week, 64.81% of differentially expressed genes were downregulated, aligning with Klf9’s predicted role as a transcriptional repressor. At 4wks and 8wks, more genes were upregulated, suggesting more of secondary targets in response to cardiac phenotype. KEGG pathway analysis showed dysregulation in lipid, carbohydrate and glutathione metabolism, transcriptional regulation, apoptosis, and innate immunity. Untargeted Metabolomics at 4wks identified significant alterations in tissue metabolite levels, particularly in pathways involving fatty acid metabolism, amino acids, and glucose, correlating with transcriptome data. Mitochondrial function assays revealed progressive dysregulation. At 2 weeks, complex I activity was significantly reduced, while complex II and IV activities were partially preserved. By 4 weeks, all measured respiratory complexes showed significant declines, consistent with decline in mitochondrial function. These mitochondrial deficits preceded overt cardiac dysfunction and likely contributed to the development of hypertrophy and failure. In conclusion, constitutive Klf9 overexpression disrupts transcriptional and metabolic homeostasis, driving progressive hypertrophy, cardiac dysfunction, and failure.

overall_design: Klf9-ChIP-Seq data from adult (Sham) hearts, RNAseq data from Klf9 knockIn mice at 1week, 4weeks and 8weeks of age.

first: Chandni

last: Thakkar


title: Unravelling the tumorigenesis mechanisms of oncocytic cell tumors: discoveries from a comparative omics studies

status: Public on Dec 31 2025

city: Vizela

first: Marta

middle: Patrícia

last: Ferreira

state: Braga

address: Rua da junuqeira, Santo Adrião

country: Portugal

type: Expression profiling by high throughput sequencing

summary: Transcriptome analysis of  thyroid tumors from frozen tissue sections.

overall_design: We performed an extensive comparative analysis of transcriptomic between oncocytic cell tumors (5 oncocytic adenoma-OA and 7 oncocytic carcinoma -OCA) and mitochondrion-rich neoplasms (2 oncocytic subtype of papillary thyroid carcinoma-O-PTC and 4 low-risk neoplasms with oncocytic morphology), irrespective of their biological behavior. Our focus was to explore molecular distinctions within these two tumor categories characterized by oncocytic morphology.

first: Sule

last: Canberk

first: Luisa

last: Pereira

first: Carla

last: Oliveira

first: Paula

last: Soares

first: Valdemar

last: Máximo


title: Potent Suppression of Heme-Induced Ferroptosis in Cardiomyocytes Enhances Cardiac Function Following Myocardial Infarction/Reperfusion Injury

city: Shanghai

first: hui

last: chen

address: 639 Zhizaoju Road, Shanghai 200011, People’s Republic of China

country: China

institute: Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine

summary: Myocardial ischemia-reperfusion injury (MIRI) significantly worsens outcomes following myocardial infarction, primarily due to microvascular obstruction-induced myocardial hemorrhage in deeper regions. This hemorrhage leads to heme accumulation and triggers ferroptosis, a crucial pathological mechanism recently identified. Existing pharmacological treatments are ineffective and fail to reach the infarct core. To address this issue, we developed DecAS-PC@NM, a novel heme-responsive biomimetic vesicle loaded with decursin, an anti-ferroptosis herbal monomer. The vesicle is composed of synthetic phosphatidylcholines derived from artemisinin and thioether, engineered to disassemble and release decursin in response to heme-triggered reactive oxygen species that oxidize the thioether within the phospholipid bilayer. Incorporation of neutrophil membranes enhances targeting to the lesion. In vitro and in vivo studies demonstrated that DecAS-PC@NM effectively accumulates in the infarct core, counteracts ferroptosis and inflammatory responses, and significantly improves cardiac function. This targeted approach offers a promising therapeutic strategy for MIRI by specifically addressing heme accumulation and ferroptosis.

overall_design: In this study, C57BL/6 mice were used to investigate the protective effects of Decursin on myocardial ischemia-reperfusion injury. A total of 18 mice were randomly divided into three groups, with 6 mice in each group:SHAM Group, IR (Ischemia-Reperfusion) Group,  IR + Decursin Group. All mice were sacrificed at 7 days post-surgery, and heart tissues were collected for RNA sequencing (RNA-seq) analysis. This design aims to elucidate the molecular mechanisms by which Decursin may confer cardioprotective effects in the context of ischemia-reperfusion injury, with a focus on gene expression changes associated with the treatment.

first: Hui

last: Chen

first: Yan

last: Liu

first: Ke

last: Yang


title: Hypoxia-induced circPRELID2 promotes gastric cancer metastasis by facilitating ZEB2 translation via PCBP1 O-GlcNAcylation

first: Pengshan

last: Zhang

state: Shanghai

address: No. 650, Xinsongjiang Road

institute: Shanghai General Hospital

type:
Expression profiling by array
Non-coding RNA profiling by array

summary: To identify crucial hypoxia-associated circRNAs in gastric cancer, we conducted microarray analysis to examine the circRNA expression profiles in two different gastric cell lines under normoxia or hypoxia

overall_design: Two different gastric cancer cell lines were cultured in a hypoxia chamber with 1% O2, 94% N2 and normoxia at 37°C for 24h, then microarray were performed to examine the circRNA expression profiles.

first: Zai

last: Luo

first: Yitian

last: Xu

first: Yuan


title: Narrow-band ultraviolet B induces peripheral regulatory T cells to exert antigen-specific immune suppression [scRNA-seq]

city: Taipei

first: Yungling

middle: Leo

last: Lee

address: Sec. 2, Academia Rd.

department: Institute of Biomedical Sciences

country: Taiwan

institute: Academia Sinica

summary: Narrow-band ultraviolet B (UVB) is a commonly used therapy for autoimmune diseases. While alloantigen immunization combined with NB-UVB has been shown to induce antigen-specific regulatory T cells (Tregs), the underlying mechanism remains elusive. Single-cell RNA sequencing analysis of patient PBMCs showed that UVB suppressed negative regulators of Treg development, thereby promoting CD4+ T differentiation into Tregs.

overall_design: We collected blood samples from psoriasis patients before and after UVB treatmet. Cells were isolated from whole blood to preform single-cell RNA sequencing (scRNA-seq).

first: Chun-Hao

last: Lu


title: Narrow-band ultraviolet B induces peripheral regulatory T cells to exert antigen-specific immune suppression [RNA-seq]

summary: Narrow-band ultraviolet B (UVB) is a commonly used therapy for autoimmune diseases. While alloantigen immunization combined with NB-UVB has been shown to induce antigen-specific regulatory T cells (Tregs), the underlying mechanism remains elusive. We used Treg RNA-seq from psoriasis-like mice model to investigate differentially expressed genes under UVB treatemnt.

overall_design: The backs of mice were shaved before initiation of psoriasiform dermatitis. Aldara treatment was performed by daily applying 60 mg Aldara cream containing 5% imiquimod (IMQ) on the backs of mice. The mice were exposed to NB-UVB every other day for 3 times. The dorsal skin of mice presented erythema and scaling and the psoriasis-like dermatitis was in remission when mice receiving NB-UVB irradiation. Treg cells were isolated from mice skin with or without UVB treatment for RNA-seq.


title: Finding Sorafenib-Responding Signature in Hepatocellular Carcinoma (HCC)

city: Houston

first: Han

last: Liang

address: 1515 Holcombe Blvd

country: USA

institute: The University of Texas MD Anderson Cancer Center

summary: Sorafenib has been a cornerstone in hepatocellular carcinoma (HCC) therapy; however, its efficacy is limited, and identifying patients that will respond to sorafenib is challenging.  Gene expression data from 33 HCC tumors treated with sorafenib were analyzed to construct a prediction model aimed at identifying patients with greater benefit from sorafenib treatment. The analysis of transcriptome data revealed a 50-gene signature, KUSS50 (Korea University Sorafenib Signature with 50 genes), that exhibited high predictive power in identifying patients responded to sorafenib treatment in a training cohort. Extensive validation across 2 independent cohorts (IMbrave150 and BIOSTORM) given sorafenib demonstrated KUSS50's high specificity in predicting sorafenib response. Genomic analyses identified distinct molecular characteristics linked with KUSS50 subtypes, including an increased mutation rate and activation of ferroptosis, suggesting increased baseline ferroptotic activity in HCCs, which may sensitize them to sorafenib. The benefit subtype also overlapped with those in previously defined genomic HCC subtypes associated with stemness and aggressiveness. Conversely, the non-benefit subtype correlated with -catenin mutations and increased tumor purity, underscoring the biological significance of the signature. In conclusion,  KUSS50 is a clinically actionable biomarker for optimizing HCC patient selection for treatment with sorafenib, providing an opportunity to improve outcomes. Further exploration of KUSS50's underlying biology, particularly the involvement of ferroptosis in sorafenib sensitivity, could provide additional therapeutic insights.

overall_design: All patients underwent liver biopsy analysis prior to sorafenib use, and total RNA was obtained from their formalin-fixed, paraffin-embedded tissue blocks. Total RNA was extracted from slides containing tissue sections from these blocks using a Purigen Biosystems Ionic Purification System, and the DV200 values (representing the percentage of fragments >200 nucleotides) exceeded 15%. mRNA expression data for HCCs in the study patients were subsequently generated on the Illumina NovaSeq 6000 platform, employing S4-xp-200 lanes with a sequencing depth of 50 million reads per sample. The quality of the raw reads was checked using FastQC (v0.11.5) and summarized using MultiQC (v1.7). FASTQ files were mapped to the human reference genome (GRCh38) using STAR (v2.7.10a), and gene expression level was quantified using RSEM (v1.3.3) with default parameter settings.

first: Sun Young

last: Yim

first: Yitao

last: Tang

first: Ji Hoon

last: Kim

first: Ju-Seog


title: RNA-seq data analysis of TgNF7 on Toxoplasma gondii tachyzoite development

city: shenyang

first: Gao

middle: jun

last: ying

address: 120 Dongling Road

department: College of Animal Science and Veterinary Medicine

institute: Shenyang Agricultural University

summary: To investigate transcriptional role of TgNF7 on Toxoplasma gondii type I  RH by generate knockout TgNF7 strain.

overall_design: Generate knockout TgNF7 parasites and then total RNA of RH wide type and knockout-TgNF7 were extracted for deep sequencing

first: Qijun

first: Junying

last: Gao

first: Hongbo

last: Yu

first: Ang

last: Li

first: Ran

first: Ying

last: Feng

first: Xiaoyu

last: Sang


title: Characterization of the global bovine microRNAome of peripheral blood mononuclear cells isolated from Mycobacterium bovis exposed cattle

city: Edinburgh

first: Elisabeth

middle: Margaretha Diana Louise

last: van der Heijden

state: Midlothian

address: Easter Bush Campus

department: Division of Immunology

country: United Kingdom

institute: The Roslin Institute, The University of Edinburgh

type: Non-coding RNA profiling by high throughput sequencing

summary: Accurate diagnostics are urgently needed for bovine TB in cattle – an economically devastating disease posing a re-emerging threat to veterinary and public health worldwide. MicroRNAs, post-transcriptional regulators of gene expression, are involved in a wide range of biological processes and immunological pathways, and have emerged as promising diagnostic biomarkers for numerous diseases. In human TB, microRNAs have been widely studied, but not much is currently known about their role in bovine TB. The aim of this study was to investigate the diagnostic potential of microRNAs in bTB through comprehensive analysis of their expression profiles in disparate states of M. bovis (BCG) exposure. We used a state-of-the-art RNA sequencing approach to characterize the global microRNAome of peripheral blood mononuclear cells isolated from cattle that were either unvaccinated, BCG-vaccinated, unprotected or protected. A total of 468 microRNAs were detected across all samples, none of which were uniquely expressed in any group. Significant differential expression between groups was observed for 3 microRNAs (bta-miR-6122-3p, bta-miR-3533 and bta-miR29b) in various comparisons. Subsequent target analysis of bta-miR-29b, a candidate biomarker of disease in human tuberculosis, revealed that several genes (ACVR2A, PIK3R1, TBX21, TGFBR1 and TGFBR2) involved in a number of relevant T-cell and immune signaling pathways, were amongst the predicted targets. Overall, this study provides evidence that microRNAs could be a promising novel biomarker for bovine TB diagnostics.

overall_design: PBMC were isolated from whole blood of cattle in previous study (doi: 10.3389/fimmu.2020.588180). The present study compared two groups of animals: unvaccinated controls and vaccinated with live M. bovis BCG (Danish SSI 1331; 0.5 mL 4.6 x 10^6). Animals were vaccinated at T=0 and challenged endobronchially with virulent M. bovis (AF2122/97; 10^4 CFU) after 9 weeks. Samples used in this study were taken 8 weeks after vaccination (week 8) and 8 weeks after challenge (week 17). Samples were selected on the basis of presence (VL) or absence (NVL) of lesions at PM. Animals were subsequently grouped according to their immunological and infection status (“status”): controls (unvaccinated, prior to challenge), vaccinated (BCG-vaccinated, prior to challenge), unprotected (unvaccinated, post-challenge, VL) and protected (BCG-vaccinated, post-challenge, NVL).

first: Anna

last: Karagianni

first: Lindert

last: Benedictus

first: Sabine

last: Steinbach

first: Tom

last: Holder

first: Femke

last: Broere


title: TNF-α Driven m6A Modification Disrupts MSCs Immune Regulatory Function by Regulating HDAC5-dependent Super Enhancer [RNA-seq]

city: shenzhen

first: weihao

last: zhang

address: futian

department: Department of Orthopedics, The Eighth Affiliated Hospital

institute: Sun Yat-sen university

summary: Mesenchymal stem cells (MSCs) are widely used to treat inflammatory diseases due to their strong immunosuppressive functions. However, these functions were greatly affected by inflammatory microenvironment in vivo and therefore limited the therapeutic effect of MSCs. The present study demonstrates that TNF-α impairs immunosuppression capability of MSCs on T cells proliferation. Mechanistically, TNF-α treatment decreased the expression of H3 deacetylation eazyme HDAC5, therefore leading to the enhanced super enhancer (SE) signals and upregulated expression of leukemia inhibitory factor (LIF) in MSCs. Moreover, TNF-α downregulated HDAC5 expression through promoting WTAP-mediated m6A modification of HDAC5 mRNA, which was subsequently regulated by YTHDF2 to reduce the mRNA stability. Notably, intravenous infusion of MSCs overexpressing HDAC5 showed improved therapeutic efficacy in SKG mice with inflammatory arthritis. Our results elucidate a synergistic epigenetic regulatory mechanism between super-enhancer and m6A modification of the MSCs immunosuppressive functions, and provide a novel strategy to enhance the clinical therapeutic potential of MSC infusion in inflammatory diseases.

overall_design: RNA-seq in MSCs with/without TNF-α treatment at Day 2, of which 3 biological replicates collected from 3 healthy donors.


title: Histone H1 non-autonomously promotes lipolysis in depressive Drosophila

city: Beijing

first: jianquan

last: Ni

address: Shuangqing Road 30

institute: Tsinghua University

summary: Depression, a prevalent mental disorder, is influenced by genetic materials and environmental factors and is often associated with weight loss, though the underlying molecular mechanisms remain unclear. Here, we performed RNA-seq on Drosophila models of depression induced by drug treatment. We found that reduced histone acetylation correlates with the specific upregulation of linker histone H1 in the brain. Remarkably, conditional overexpression of H1 in the brain, simulating drug-induced H1 elevation, led to similar gene downregulation patterns and resulted in a depressive phenotype. Moreover, both drug-treated and H1-overexpressing Drosophila displayed weight loss. Interestingly, we observed that H1 is non-autonomously required for lipid droplet homeostasis in the fat body of adult flies. Furthermore, depressive Drosophila exhibited elevated AKH signaling, promoting lipolysis, while H1 did not directly affect AKH signaling. Finally, we found that H1 preferentially binds and suppresses the transcription of rk, encoding an upstream regulator of AKH signaling. Together, these findings reveal a molecular mechanism linking depression with weight loss in animal models.

overall_design: We observed the decrease of acetylation and increased of histone H1 protein in depressed flies triggered by the Levodopa, then we performed the RNA-seq to detect the transcription profiles in the depressed flies triggered by Levo, as well as the conditional H1 overexpression to see wethere the histone H1 is required and sufficient for the depression

first: Qinyun

last: Che

first: Yijia

last: Xie

first: Bo

last: Peng


title: The effect of CLEC16A in Dendritic Cells (Single Cells)

city: Boston

first: Zhaorong

address: 60 Fenwood Road

institute: Dana Farber Cancer Institute

summary: CLEC16A were conditionally knocked out in Dendritic Cells, and the dendritic cells were sorted out using FACS and 10X single cell RNA-Seq protocol was used to profiled the transcriptome of individual cells.

overall_design: For single cell RNA-sequencing, Spleen Dendritic cells from n=3 Control EAE and n=3 CLEC16AGFAP EAE (Day 23) were hashed before FACS sorting using multiplex 3’ Cell Plex Set Kit A (#100261, 10x Genomics).  After sorting and washing,  astrocytes from 6 samples were pooled and loaded into one well of a 10X Chromium Next GEM Chip G (10X Genomics). Single-cell libraries were further generated using the Single Cell 3’ Reagent Kit v3.1 chemistry (10x Genomics) using Chromium Next GEM Single Cell 3’ GEM, Library & Gel Bead Kit v3.1 (PN-1000128) according to the manufacturer’s protocol. The generated scRNA-seq libraries were sequenced by NOVA-Seq S1 at the Broad Institute.

first: Atsushi

last: Kadowaki

first: Michael

last: Wheeler

first: Brian

last: Andersen

first: Hong-Gyun

last: Lee

first: Tomer

last: Illuz

first: Francisco

last: Quintana


title: Transcriptional profiling of calcifying human primary coronary artery smooth muscle cells

city: Dresden

first: Claudia

last: Goettsch

state: SA

address: Fetsherstr. 74

country: Germany

institute: TU Dresden Faculty of Medicine Carl Gustav Carus

summary:
Transcriptomics analysis of human coronary artery smooth muscle cells cultured in osteogenic medium and PIKfyve inhibition.
To study the underlying molecular mechanisms of PIKfyve-mediated vascular calcification, we analyzed the transcriptome of osteogenic medium (OM)-calcified human coronary artery smooth muscle cells that were treated with PIKfyve inhibitors (Apilimod, YM201636) or DMSO control on day  7.

overall_design: Human primary coronary artery smooth muscle cells from three independent donors were cultured in osteogenic medium (OM) and treated with Apilimod, YM201636 or DMSO control.

first: Nicolas

last: Hense

first: Bilal

last: Mir

first: Andrea

last: Gorgels

first: Emiel

last: van der Vorst

first: Guillaume

last: Falgayrac

first: Mara

last: Terlieser

first: Isabel

last: Goncalves

first: Andreas

last: Edsfeldt

first: Jiangming

last: Sun

first: Martina

last: Rauner

first: Alexander

last: Gombert

first: Christian

last: Preisinger

first: Nikolaus

last: Marx


title: Analysis of organoid-derived microglia implicates microglial dysfunction in C9ORF72 ALS/FTD

city: Utrecht

first: Roland Jeroen

last: Pasterkamp

state: Utrecht

address: Universiteitsweg 100

department: Translational Neuroscience

country: Netherlands

institute: UMC Utrecht

summary: Amyotrophic lateral sclerosis (ALS) is an adult-onset neurodegenerative disease characterized by loss of upper and lower motor neurons and progressive muscle wasting. Accumulating evidence indicates a role for non-neuronal cells in ALS pathogenesis, but their exact role and mechanism-of-action remain incompletely understood. A hexanucleotide (GGGGCC) repeat expansion (HRE) in C9ORF72 is the most common genetic cause of ALS (C9-ALS) and a frequent cause of frontotemporal dementia (FTD). Several lines of experimental evidence support a role for the immune system and microglia in C9-ALS/FTD, and, dependent on experimental settings and species used, both reduced and increased microglial activity have been reported. To further study microglia in C9-ALS/FTD in the context of a complex, three-dimensional disease environment, we developed cerebral organoids that innately develop microglia derived from induced pluripotent stem cells (iPSCs) of C9ORF72 patients and controls. To define changes in C9-organoid derived microglia (oMG) activational state due to C9-HRE, we performed RNA sequencing from four C9 iPSC lines and four healthy controls (HC).

overall_design: iPSC derived cerebral organoids were generated as previously described (Ormel et al., 2018). Organoid derived microglia cells were isolated from day 64 cerebral organoids using CD11b-coated beads. Around 10-12 organoids were used per line. Sequencing was performed on C9-oMGs (n=4) and HC-oMGs (n=4).

first: Tijana

last: Ljubikj

first: Mayte

last: Mars

first: Astrid

middle: T

last: van der Geest

first: Nils

last: Bessler

first: Channa

middle: E

last: Jakobs

first: Xynthia

middle: P

last: van den Oetelaar

first: Marina

last: de Wit

first: R

middle: J


title: Cholesterol Homeostasis Disruption and Monocyte Recruitment Drive Atrial Fibrillation in Hypertension

first: Qianwan

last: Deng

address: Ruijin 2nd Road 197

institute: Shanghai Institute of Hypertension

summary: ABSTRACT BACKGROUND: Atrial fibrillation (AF) is the most common cardiac arrhythmia, with hypertension as its primary risk factor. While immune dysfunction is known to play a crucial role in hypertension, its specific impact on AF in the hypertensive setting remains underexplored. This study aims to elucidate the immune landscape of AF in the context of hypertension and explore the potential mechanisms. METHODS: Single-cell RNA transcriptomic analysis was employed to profile peripheral blood mononuclear cells (PBMCs) in hypertensive patients with AF, using hypertensive patients without AF as controls. Flow cytometry, serum cytokine analysis, and cohort studies were used for validation. RESULTS: Monocytes were identified as the most significantly affected cell type in hypertensive patients with AF, showing heightened disruption of cholesterol homeostasis and immune-inflammatory responses. Interestingly, a unique cluster of CD14+ megakaryocytes were identified to exhibit the most active intercellular interactions. Flow cytometry confirmed elevated proportions of CD14+ monocytes and CD14+ megakaryocytes in hypertensive patients with AF. Serum analysis of a larger cohort revealed significantly higher levels of monocyte chemoattractant protein-1 (MCP-1) and interleukin-6 (IL-6). Integration of single-cell data from blood and cardiac tissue confirmed enhanced monocyte recruitment and differentiation in hypertensive patients with AF. Cohort studies further supported that the increased number of circulating monocytes was associated with a higher incidence of AF in hypertensive patients. CONCLUSIONS: Our study demonstrated that the interplay between cholesterol homeostasis disruption and inflammatory cell recruitment may play an important role in the pathogenesis of AF in hypertension. These findings offer new insights into potential therapeutic targets for managing AF in hypertensive patients.

overall_design: Single-cell RNA sequencing was performed on human peripheral blood samples from four experimental groups (hypertension + atrial fibrillation, hypertension) and two control groups (hypertension) to investigate cellular gene expression patterns associated with these conditions.

first: Jinqiu

last: Wei

first: Ziqi

last: Xu

first: Wei

last: Zhang

first: Xiaodong

last: Li

first: Jiguang

last: Wang


title: Development and Validation of a Standardized Adipogenesis Assay Using Human Bone Marrow Mesenchymal Stem Cells

city: Irvine

first: Brittanie Yukimtiao

middle: Arcenal

last: Yukimtiao

state: CA

address: Ring Rd

department: Department of Dev & Cell

institute: University of California, Irvine

summary: Obesity is a global health concern linked to various diseases. Recently, chemicals known as "obesogens" have been identified as significant contributors to obesity, which highlighting the need for reliable methods to screen chemicals for their obesity-promoting potential. This study aimed to develop a standardized adipogenesis assay using human bone marrow-derived mesenchymal stem cells (hBM-MSCs) to evaluate the adipogenic potential of chemicals. Lipid accumulation in hBM-MSCs was measured after chemical exposure. The assay conditions of cell confluency and detection methods were optimized. Results showed that initiating differentiation at complete confluency was crucial for reliable outcomes. Reliable data was ensured by detecting at least nine points per well, and fluorescence signals remained stable for up to ten days post-staining. Using the established method, we evaluated the effects of six selected chemicals on adipogenesis. Testing adipogenic responses of hBM-MSCs from different donors identified specific cell lots suitable for studies. Comparisons with the 3T3-L1 adipogenesis assay validated the hBM-MSCs model. Additionally, we immortalized an hBM-MSC cell line which displayed similar gene expression profiles to primary cells showed greater sensitivity to adipogenesis-inducing chemicals. These findings confirm the robustness and reliability of the hBM-MSC adipogenesis assay for studying the adipogenesis effects of chemicals.

overall_design: Primary human mesenchymal stem cells were immortalized using Lenti-hTERT method and RNA-seqencing was performed to examine transcriptomal similiarity between original cells verse immortalized cells after 14-day adipogenesis

first: Brittanie

first: Cheng-An Richard

last: Chang

first: Bruce

last: Blumberg


title: Effects of chemotherapy on the elimination of various viruses and viroids from grapevine

city: Godollo

first: Eva

last: Varallyay

address: 4 Szent-Györgyi Albert Street

department: Institute of Plant Protection

country: Hungary

institute: Hungarian University of Agriculture and Life Sciences

summary: Our experiments investigated the effects of various known chemotherapeutic agents (2-thiouracil, ribavirin and zidovudine) on grapevine for the elimination of several different viruses and viroids. Viruses and viroids were identified by small RNA HTS in the mother plants of different grapevine cultivars, and RT-PCR verified the results. Among  the tested agents, ribavirin had the broadest elimination effect on most viruses. It proved to be particularly effective against GFkV, GLRaV-4, GPGV and GRSPaV, however, as a single treatment it was not able to eliminate GFLV. In our experiments, ribavirin also showed very low efficacy against GLRaV-1 and GVA viruses. The application of 2-TU caused high phytotoxicity, with only 25% efficacy against GLRaV-4 among the viruses tested. Zidovudine failed to eliminate any of the viruses we tested. However, the combination of ribavirin and zidovudine was able to eliminate GFLV, though with low efficacy (12.5%). In contrast, the combination of ribavirin and 2-TU has been shown to be very effective against GRSPaV and GPGV. Compared to ribavirin, zidovudine and 2-thiouracil did not demonstrate significant virus elimination efficacy in the case of tested viruses. In our experiments ribavirin could not remove HSVd and GYSVd-1 viroids. To the best of our knowledge, no prior studies have been published the successful use of ribavirin or other chemotherapeutic agents against GLRaV-4, and this is the first publication of a successful application of 2-TU and zidovudine against grape viruses .

overall_design: virome was determined by sRNA HTSfor each grapevine plants

first: Mihaly

last: Turcsan

first: Robert

last: Olah

first: Nikoletta

last: Jaksa-Czotter

first: Zsuzsanna

middle: N

last: Galbacs

first: Krisztina

first: Diana

last: Sardy


title: S100A9 Overexpression Drives Chemoresistance and Poor Prognosis in AML with Adavivint as a Targeted Therapeutic

city: Guiyang

first: Dan

last: Ma

state: Guizhou

address: No. 9 Beijing Road, Guiyang City, Guizhou Province

department: Guizhou Provincial Engineering Technology Research Center for Chemical Drug R&D

institute: Guizhou Medical University

summary: Drug resistance and poor prognosis in acute myeloid leukemia (AML) are major challenges, underscoring the need for effective biomarkers and targeted therapies. In this study, we identified S100A9 as a critical biomarker for drug resistance and poor prognosis in AML through integrative bioinformatics analysis and experimental validation. Using transcriptomic datasets, single-cell sequencing, and proteomics, we demonstrated that S100A9 overexpression is enriched in drug-resistant AML cells, particularly in the M5 subtype. High S100A9 expression correlates with shorter survival and higher risk scores, establishing its role as a prognostic marker. Functional studies revealed that S100A9 promotes AML cell proliferation and chemoresistance by enhancing mitochondrial oxidative phosphorylation and maintaining redox homeostasis through interaction with thioredoxin (TXN). This axis prevents excessive reactive oxygen species (ROS) accumulation, supports cell survival, and activates the WNT/β-catenin pathway to drive tumor growth. To explore therapeutic options, we identified Adavivint (Ada) through computational screening as a selective cytotoxic agent for S100A9-overexpressing AML cells. Ada demonstrated superior efficacy compared to standard drugs such as venetoclax and cytarabine, while showing reduced toxicity to normal bone marrow cells. In vivo, Ada significantly suppressed tumor progression and prolonged survival in murine models of S100A9-overexpressing AML. These findings highlight S100A9 as a promising therapeutic target and establish Adavivint as a potential agent to overcome chemoresistance in S100A9-positive AML, offering new avenues for improving outcomes in this challenging disease.

overall_design: RNA-seq was performed on U937 and THP-1 cells following S100A9 knockdown and overexpression. Additionally, THP-1 cells transduced with either an empty vector or S100A9 overexpression lentivirus were treated with Adavivint (1 μM) for 36 hours, and gene expression profiling was conducted on these samples. These analyses aimed to investigate the gene expression profiles in response to S100A9 manipulation and Adavivint treatment.

first: Chujiao

last: Hu

first: Junzhao

last: Wan

first: Qian

last: Kang

first: Yan

first: Ping

last: Liu


title: Inflammatory proteomics of uterine fluid is potentially a non-invasive predictor for endometrial receptivity: a pilot study

city: Guangzhou

first: Hong

last: Zeng

state: Hunan

address: 87 Xiangya Street

department: Reproductive medicine center

institute: Xiangya Hospital Central South University

summary: Objective: To evaluate if the inflammatory proteomics of uterine fluid could define the endometrial receptivity phase. Methods: Inflammatory proteomics of uterine fluid were measured using the OLINK Target-96 Inflammation panel. Endometrial receptivity testing (ERT) combined with endometrial dating was a gold standard for defining the endometrial receptivity phase. A predictive model based on proteomics of uterine fluid was established to predict the endometrial receptivity phase. Results: The inflammatory factors in uterine fluid were differentially expressed between window of implantation (WOI) and displaced WOI groups, and the displaced WOI group was characterized by the increased expression of a variety of inflammatory factors. The predictive model established based on the top 5 differential proteins could accurately classify the endometrial receptive phase. Transcriptomic data from endometrial tissues showed that the differential gene sets between different receptive phases were mostly enriched in immune-related processes, and the expression of immune-related genes in the WOI group was significantly lower than that in the displaced WOI group. Conclusions: Detection of inflammatory proteins from the uterine fluid using the OLINK inflammation panel could be a novel non-invasive method to define the endometrial receptive phase. The inflammatory immune response during the embryo implantation window was inhibited to adapt to the implantation of the semi-alloimmune embryos.

overall_design: Observational study

first: Shuyi


title: Connectome-seq: High-throughput Mapping of Neuronal Connectivity at Single-Synapse Resolution via Barcode Sequencing

city: Urbana

first: Boxuan

last: Zhao

state: IL

address: 505 S Goodwin Ave

institute: UIUC

summary: Understanding neuronal connectivity at single-cell resolution remains a fundamental challenge in neuroscience, with current methods constrained by an inherent trade-off between throughput and synaptic precision. Here we present Connectome-seq, a high-throughput method that combines engineered synaptic proteins, RNA barcoding, and single-compartment sequencing to map neuronal connectivity at single-synapse resolution. We validate this approach in the mouse pontocerebellar circuit, successfully identifying thousands of connections including the predominant excitatory projections from pontine neurons to cerebellar granule cells, while also revealing potentially novel synaptic partnerships. By enabling systematic mapping of neuronal connectivity across brain regions with single-cell precision, Connectome-seq provides a scalable platform for comprehensive circuit analysis across different experimental conditions and biological states. This advance in connectivity mapping methodology opens new possibilities for understanding circuit organization in complex mammalian brains.

overall_design: Pons and cerebellum tissue was obtained from Sun1-sfGFP-Myc mice, and nuclei and synaptosomes were subsequently isolated via fluorescence-activated cell sorting, selecting based on GFP, HA, or V5 signals, before undergoing single-nucleus and single-synaptosome RNA sequencing (snRNA-seq, ssRNA-seq) analysis.


title: ExRNAcarrier_comp_small

city: San Francisco

last: Raffai

state: California

address: 4150 Clement St

department: Surgery

institute: University of California San Francisco

summary: Profiling small RNA cargo in exRNA carriers

overall_design: 84 samples, human plasma exRNA fractionated via DGUC, Izon SEC, exoEasy, exoRNeasy, and lipoprotein flotation, and DiFi (Izon SEC) or THP-1 (DGUC) conditioned media exRNA

middle: L

first: Martin

last: Ng


title: The GABA-modulated energy metabolism reconfiguration positively regulates cotton (Gossypium hirsutum L.) responses during post-waterlogging recovery

city: 安阳

first: 新彦

last: 刘

address: 文峰区黄河大道38号

institute: 中国农业科学院棉花研究所

summary: Plant response to waterlogging is well studied, but the understanding of plant responses during post-waterlogging recovery remains limited. In this study, we show that the waterlogging-sensitive (Z4847) and waterlogging-tolerant (ZM9001) cotton varieties have different rates of post-waterlogging recovery that correlate with waterlogging tolerance. The performance of a comparative transcriptome and metabolome analysis of the roots from two cotton varieties during recovery processes indicated the significant inhibition of the abundance of genes and metabolites related to energy metabolism in both varieties during post-waterlogging. The results also showed that the waterlogging tolerant ZM9001 plants maintained the higher carbon flows from glycolysis to the first reaction of the TCA cycle, leading to more energy production and restoring root activity during recovery processes. The interaction analysis of KEGG pathways in ZM9001 vs. Z4847 comparison during post-waterlogging displayed an extremely significant correlation between GABA metabolism and the glycolysis-citrate cycle. Therefore, we combined both multi-omics and physiological approaches and showed that the induced elevation of the GABA levels in the ZM9001 plants during recovery processes is essential in restoring its root function by generating more energy through the activation of the GABA shunt pathway. Consistent with this, the loss of GABA synthesis showed increased sensitivity to post-waterlogging, which was partially rescued by the exogenous application of GABA. Subsequently, elevated GABA levels could also provide better redox homeostasis by enhancing the antioxidant enzyme system during post-waterlogging recovery. Therefore, these findings indicate that the energy metabolism reconfiguration via re-activating GABA shunt participates in seedling survival after waterlogging stress, shedding light

overall_design: The waterlogging tolerant cotton variety ZM9001 and the flood-sensitive cotton variety Z4847 at the four-leaf stage were treated Do not take 96 h of darkness for 0 h (control group in the flooding stage, DN-0), and 96 h of dark flooding for 0 h (flooding). The stage treatment group, DW-0), the dark 96 h re-light for 24 h (the recovery phase control group, DN-24), and the dark flooding for 96 h Transcriptome sequencing analysis was performed on the roots of cotton seedlings after 24 h of dehydration and re-light (recovery stage treatment group, DW-24).


title: Epigenome-wide association study of differential DNA-methylation in background mucosa among adults with colorectal adenoma

city: Taiyuan

first: Yue

last: Sui

state: --- Select One ---

address: No.85 of South Jiefang Road, Yingze District, Taiyuan, Shanxi, China

institute: First Hospital of Shanxi Medical University

type: Methylation profiling by genome tiling array

summary: Background: Colorectal adenoma is the primary precursor in colorectal cancer development, partially driven by epigenetic alteration occurring at a very early stage. While aberrant DNA-methylations have been observed in mucosa adjacent to primary tumors, this study aimed to investigate whether such alterations exist in distant background mucosa as global defect rather than local transition, and identify adenoma-related CpG sites which may serve as potential targets for early intervention. Methods: DNA methylation in normal rectal mucosal biopsies from 24 individuals with colorectal adenoma and 20 normal controls were profiled utilizing the Illumina Infinium MethylationEPIC v2.0 BeadChip (935K). Linear regression model was employed to investigate the relationship between adenoma incidence and DNA methylation at each CpG site, adjusted for demographic characteristics. GO and KEGG enrichment analysis were conducted using genes containing CpG sites significantly associated with adenoma. A sensitivity analysis was conducted with individuals who had one or more known risk factors for colorectal adenoma. Results: Twenty-seven CpG sites with aberrant DNA-methylation were significantly correlated with the incidence of adenoma (P<1×10-5, |Δβ|≧0.2). Through GO and KEGG enrichment analysis and lookups in EWAS atlas, a group of CpG sites and genes were identified as potential intervention targets. Conclusions: A group of adenoma-related CpG sites and genes with aberrant DNA-methylation was identified in normal-appearing rectal mucosa. Further extensive validation of the adenoma-related loci as targets for molecular intervention could pave the way for colorectal cancer prevention.

overall_design: Individuals aged 40–74 years undergoing initial screening colonoscopy and diagnosed with adenomas were eligible for enrollment, as well as healthy controls (without abnormalities on full colonoscopy).Two pinches of biopsies of normal mucosa in the lower rectum (DNA>1ug) (between the middle Houston valve and the dentate line) were obtained using biopsy forceps, and were promptly frozen in a -80℃ freezer. The biospecimens were shipped to Novogene Company Limited on dry ice for DNA extraction and bisulfite treatment.DNA-methylation was progiled with Illumina Infinium MethylationEPIC v2.0 BeadChip.The correlation between DNA-methylation and adenoma incidence was assessed using linear regression models, adjusted for sex, age, obesity, diabetes, current smoking, and regular alcohol consumption.


title: Elevated 1-deoxysphingolipids in adipose tissue promote inflammation

city: Shanghai

first: Xiaoxue

last: Wang

address: 319, Yueyang Rd, Xuhui District, Shanghai

institute: SIII, CAS

summary: Chronic adipose tissue inflammation is a hallmark of numerous metabolic disorders, yet its initial triggers remain elusive. Here, we discover that excessive accumulation of toxic 1-deoxysphingolipid (DoxSL), a non-canonical sphingolipid species, in adipose tissue leads to the local release of pro-inflammatory cytokines. Mechanistically, DoxSL is sequestered in lipid droplets within adipose tissue to mitigate cytotoxicity under physiological conditions, but its levels are significantly elevated in states such as obesity and aging. A targeted increase in DoxSL triggers adipose tissue inflammation and macrophage infiltration via activation of the NF-κB pathway. Notably, reducing DoxSL levels through pharmacological treatment attenuates inflammation in obese mice. These findings uncover a previously unknown metabolic mechanism and emphasize a critical role of lipids in driving adipose tissue inflammation.

overall_design: RNA seq profiling of differentiated adipocyte with DMSO or DoxSa treatment on Day6

first: Suihan

last: Feng


title: The role of Vitamin B12 and TCN2 in modulating inflammatory responses in sepsis

city: Xi'an

first: Xiaofan

last: Xiong

address: 157 West Fifth Road

institute: Xi'an Jiaotong University

summary: Sepsis remains a significant challenge in critical care, with early inflammation and infection control being key therapeutic hurdles. Recent studies have highlighted the potential role of vitamin B12 in modulating immune responses and its therapeutic applications in sepsis. This study investigates the impact of vitamin B12 and its transport protein, transcobalamin II (TCN2), on macrophage polarization and inflammatory responses in sepsis. We found that vitamin B12 levels are significantly reduced in sepsis patients and correlate negatively with pro-inflammatory cytokines such as IL-6, TNFα, and CRP. In mouse models, vitamin B12 supplementation improved survival rates, reduced lung injury, and modulated macrophage polarization towards an anti-inflammatory M2 phenotype. Mechanistically, vitamin B12 interacts with PTGS2, promoting its degradation and inhibiting PGE2 production. TCN2, the key transporter of vitamin B12, regulates TLR4 activation and macrophage M1 polarization. TCN2 knockout mice exhibited reduced inflammation and improved survival in LPS-induced sepsis, but increased bacterial load in CLP models. Additionally, TCN2 enhances glucose uptake and glycolysis through interaction with GLUT1, promoting M1 macrophage polarization. These findings suggest that vitamin B12 and TCN2 play crucial roles in modulating the inflammatory response and could be potential therapeutic targets in sepsis.

overall_design: RNA-seq profilling of wildtype and TCN2 cKO of BMDMs from mice.

first: Jing

last: Geng


title: TCR Cis-Proximity-Guided LAG-3 Suppression of T Cell Activation and Autoimmunity [scRNA-seq]

city: New York

first: Jun

state: NY

address: 550 1st Ave

institute: NYU Grossman School of Medicine

summary: Therapeutically targeting pathogenic T cells in autoimmune diseases has been challenging. LAG-3, an inhibitory receptor specifically expressed on activated T cells, binds to MHC-II as its canonical ligand. Using artificial antigen-presenting-cells reconstituting cognate or non-cognate peptide-MHC-II, we discovered that MHC-II interaction alone is insufficient for LAG-3's function. Instead, LAG-3's proximity to TCR but not CD4 coreceptor, facilitated by cognate peptide-MHC-II, is crucial in mediating T cell suppression. Mechanistically, LAG-3 forms condensate with TCR signaling component CD3ε through its intracellular FSAL motif and disrupts CD3ε/Lck association. To enhance LAG-3's proximity to TCR complex, an Fc-attenuated LAG-3/TCR bispecific antibody was generated, transforming LAG-3 antagonists into LAG-3-dependent potent suppressors of both CD4 and CD8 T cells, and alleviating autoimmune symptoms in mouse models. Our findings reveal a unique checkpoint cis-modulatory mechanism and provide potential strategies, distinct from PD-1 agonists and others, for T cell-driven autoimmune diseases that lack effective and well-tolerated immunotherapies.

overall_design: To understand transcriptional and population differences in the livers of hepatitis mice treated with PBS or BiTS.

first: Wang

last: Jun

first: Du

last: Jasper

first: You

last: Jia

first: Lu

last: Catherine

first: Lin

last: Meng-ju


title: TCR Cis-Proximity-Guided LAG-3 Suppression of T Cell Activation and Autoimmunity [bulk RNA-seq]

overall_design: To understand transcriptional differences between OT-I T cells activated with SIINFEKL presented on APCs and treated with BiTS, BiTS(mut) or isotype.

first: Yin

last: Weiwei


title: Vesicle-Associated Membrane Protein-Associated Protein B Promotes Osteogenic Differentiation in Aortic Valve Interstitial Cells via Activation of the SMAD Signaling Pathway

city: Jinan

first: Xiaolin

last: Liu

address: 6699 Qingdao Road,Jinan, Shandong Province CHINA

institute: Shandong Provincial Hospital Affiliated to Shandong First Medical University

summary: Calcific aortic valve disease (CAVD) is increasingly affecting the aging population and is involved in the osteogenic reprogramming of valvular interstitial cells (VICs). However, the exact underlying molecular regulatory mechanisms remain unclear. Vesicle-associated membrane-protein-associated protein B (VAPB) mediates the generation of contact sites between the endoplasmic reticulum (ER) and other cellular membranes. However, the role of VAPB in CAVD remains unclear. This study was to elucidate the relationship between vesicle-associated membrane protein-associated protein B (VAPB) and aortic valve calcification at both tissue and cellular molecular levels, exploring potential regulatory mechanisms. The expression levels of VAPB were assessed using immunohistochemical analysis. Osteogenic differentiation and calcification levels of valve interstitial cells (VICs) were assessed through alizarin red staining, calcium content quantification, and the detection of the osteogenic marker RUNX2. Gene set enrichment analysis was used, and immunoprecipitation was performed. VAPB expression was significantly upregulated in the aortic valve leaflets of patients with calcific aortic valve disease (CAVD) compared to normal aortic valves. VICs with VAPB overexpression exhibited a significant increase in calcium content (p < 0.001) and upregulation of the transcription factor RUNX2 and the osteogenic markers osteocalcin and osteopontin at both mRNA and protein levels (p <0.01). Conversely, VAPB knockdown reduced osteogenic differentiation in VICs. Furthermore, VAPB overexpression led to the enhanced expression of p-SMAD1/5/9 through activation of the SMAD signaling pathway (p < 0.05), while inhibition of the SMAD pathway abrogated the pro-calcification effects of VAPB. Dual immunofluorescence staining demonstrated colocalization of VAPB with SMAD1/5/9, and immunoprecipitation confirmed an interaction between VAPB and SMAD1/5/9. The findings indicate that VAPB promotes osteogenic differentiation in aortic valve interstitial cells by activating the SMAD signaling pathway.

overall_design: RNA-seq profiling of wildtype human VICs  and their  knockdown derivatives (shVAPB) cultured in osteogenic medium for 3 days

first: Kai

last: Xing

first: Qiang

last: Zheng

first: Ting

last: Li

first: Xiaochun

last: Ma

first: Tao

last: Zhang

last: Sun

first: Jian

last: Song

first: Zhengjun


title: The CDK9 Complex Regulates Transcription in Human Nucleus Pulposus Cells

city: Hangzhou

first: Tianyuan

last: Gu

state: Zhejiang

address: 3 Qingchun East Road, Shangcheng District, Hangzhou City, Zhejiang Province, China

department: Department of Orthopedic Surgery

institute: Zhejiang University School of Medicine Sir Run Run Shaw Hospital

summary: CDK9 interacts with its regulatory partner cyclin T, forming the positive transcription elongation factor-B (P-TEFb) that regulates elongation by phosphorylating RNA polymerase II. However, the function of CDK9 in human nucleus pulposus cells has not been fully explored. Here, we demonstrate the enrichment of CDK9 at various gene promoters in human nucleus pulposus cells and compare it with a negative control (IgG) to identify genes that are transcriptionally regulated by CDK9.

overall_design: We collected three human nucleus pulposus samples and primary nucleus pulposus cells(NPCs) were cultured. Then, NPCs were harvested and  incubated the anti-CDK9 antibody (Proteintech), Goat anti-Rabbit IgG secondary antibody (1:5000, Fudebio, Hangzhou, China), and Hyperactive PG-TN5 / PA-TN5 Transposon and then fragmented.

first: Ziang

last: Hu

first: Weiyu

last: Ni

first: Shasha

last: Yao


title: HUMAN ALVEOLAR MACROPHAGE FUNCTION IS IMPAIRED IN TUBERCULOSIS CONTACTS WITH DIABETES

city: San Antonio

first: Larry

last: Schlesinger

state: TX

address: 8715 W Military Dr

institute: Texas Biomedical Research Institute

summary: Patients with type 2 diabetes (T2D) are more susceptible to Mycobacterium tuberculosis (M.tb) infection and severe tuberculosis (TB). The underlying mechanisms contributing to this remain largely unknown. To fill this critical knowledge gap, we obtained human alveolar macrophages (HAMs) and monocyte-derived macrophages (MDMs) from TB-exposed individuals with and without T2D in South Africa. We infected HAMs and MDMs ex vivo with live M.tb then collected RNA for RNAseq after 2, 24, 72h.

overall_design: HAMs and MDMs from no T2D controls or T2D patients, with or without M.tb infection for 2, 24, or 72h

first: Leanie

last: Kleynhans

first: Katharina

last: Ronacher

first: Yufeng

last: Wang

middle: S


title: Clara Cell RhoA Activation Aggravates Allergic Airway Inflammation by Disrupting Airway Barrier Integrity via Interstitial Macrophage Interaction

city: Baltimore

first: Peisong

last: Gao

state: MARYLAND

address: 5501 Hopkins Bayview Circle

institute: Johns Hopkins Asthma & Allergy Center

summary: Background: Our previous research demonstrated that Ras homolog family member A (RhoA) activation in alveolar type 2 cells can prevent airway hyperresponsiveness and mitigate allergic airway inflammation. Objective: We aim to investigate the role of RhoA activation in larger airways, particularly Clara cells,  during allergic airway inflammation and explore its underlying mechanisms. Methods: RhoA-deficient mice in Clara cells were generated by crossing CC10-CreERTM mice with RhoAfl/fl mice (CC10-CreERTM; RhoAfl/fl, RhoACKO). Airway epithelial barrier function was assessed by Trans-Epithelial Electrical Resistance (TEER) and permeability across Air-Liquid Interface (ALI) cultures. Multiparameter flow cytometry was applied to characterize various lung immune cells. Both bulk RNA sequencing (RNA-seq) and single-cell RNA sequencing (scRNA-seq) were also utilized. Results: Deletion of RhoA in Clara cells significantly reduced allergen-induced airway inflammation and remodeling. In vitro analysis demonstrated that airway epithelial cells from RhoACKO mice exhibited decreased TEER and increased permeability. multi-dimensional flow cytometry analysis revealed a significant reduction in interstitial macrophages (IMs) in RhoACKO mice compared to wild-type controls. Notably, scRNA-seq identified IMs as the most up-regulated population following cockroach allergen exposure. RNA-seq analysis revealed down-regulation of several genes, including Ccl24, IL-13, Mcpt1, and Tdo2. Integration of single-cell and bulk RNA-seq identified differentially expressed genes in IMs, such as Tlr1, Ccl24, Tmem26, and Msx3. Further experiments demonstrated that Ccl24 contributes to barrier damage, and blocking CCL24 attenuated allergic airway inflammation. Conclusion: This research underscores the importance of RhoA in Clara cells in airway inflammation and epithelial barrier integrity through regulating interstitial macrophage and its key mediator Ccl24.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for PBS or CRE treated Cc10-Cre mice and Cc10-Cre;Rhoafl/fl mice

first: Wei

last: Tu

first: Maolan

last: Wu

first: Rongjun

last: Wan


title: A methylome-based score to predict response to regorafenib in recurrent glioblastoma

city: Rome

first: Evelina

last: Miele

address: Piazza di Sant'Onofrio 4

department: Oncoematologia

country: Italy

institute: Ospedale Pediatrico Bambino Gesù

summary: Following encouraging results of the REGOMA Phase 2 trial, regorafenib is increasingly used for the treatment of recurrent glioblastoma, IDH-wildtype. Identifying predictive factors for response to regorafenib is of paramount importance. DNA methylation profiling is considered the gold standard for diagnosing and classifying central nervous system tumors. We explored the predictive value of methylation profiling in recurrent glioblastoma patients treated with regorafenib, highlighting the potential of DNA methylation profiling in guiding therapeutic strategies and warrant further validation in clinical settings.

overall_design: Thirty-three recurrent glioblastoma patients were enrolled in the study. DNA methylation profile was performed on paraffin-embedded tumor obtained at first surgery. Median progression-free survival (PFS) and overall survival (OS) following regorafenib treatment were 3 and 7.5 months, respectively, aligning with findings from the REGOMA trial. Methylation classes RTK2 and mesenchymal were associated with an improved response to regorafenib. Copy number variation analysis showed that imbalances in the p53-MDM2 and cyclin-Rb pathways negatively predict response to treatment. Multivariate analysis demonstrated that CCND2 gene gain/amplification and chromosome 13 deletion, encompassing the RB1 gene, were associated with reduced PFS, while, MDM2 gain/amplification was linked to dimished OS. We developed methylation-based scores for predicting PFS and OS outcomes. Notably, the PFS score exhibited a 100% negative predictive value, enabling precise patients’ selection. Differentially methylated region analysis suggested that resistance to regorafenib may involve disruptions in WNT signaling, cadherin-mediated adhesion, and presenilin pathways.


title: A transcriptome atlas of spleen defines B lymphocytes as strategy to prevent ocular infection of herpes simplex virus-1

city: qingdao

first: dingwen

last: cao

state: shandong

address: Yan Erdao Road, South District

institute: Shandong Academy of Eye Disease Prevention and Therapy

summary: Herpes simplex virus-1 (HSV-1) is the major pathogen causing viral keratitis. Spleen plays a vital role in locally and systemically modulating innate and adaptive immunity. However, the underlying connection between spleen and ocular HSV-1 infection remains uncertain.

overall_design: They were divided into two groups: nor group and HSK Group. There were four nor groups in one group.


title: Gene expression profile at single cell level of pacgytene and metaphase I spermatocytes.

city: Nanjing

first: yue

last: wang

address: NJMU

institute: Nanjing Medical University

summary: The transition from pachytene to metaphase during meiosis I is an important step ensuring the recombination of homologous chromosomes and successful completion of the first meiotic division. We used single cell RNA sequencing (scRNA-seq) to analyze the diversity of pachytene and metaphase I spermatocytes.

overall_design: Pachytene spermatocytes were fractionated from centrifugal elutriation using scRNA-seq.


title: single cell RNA-seq of oligodendrocyte progenitors FACS sorted from Aclyfl/fl (Control) or Pdgfra-creERT;Aclyfl/fl (Acly CKO) forebrains at postnatal day 5

first: Patrizia

last: Casaccia

address: 85 St Nicholas Terrace

department: Neuroscience

institute: ASRC-CUNY

summary: Myelination is one of the final milestones of post-natal brain development in rodent and man. Oligodendrocytes, the myelinating glia of the CNS, are differentiated from proliferative progenitor cells called OPCs. Local and systemic signals act on OPCs to promote their proliferation and survival in the developing forebrain before growth arrest and differentiation. During this period, altricial mammals, like rodent, experience a dramatic shift in nutrient source (e.g., maternal blood or milk) and composition (e.g., carbohydrate or fatty acid). The influence of metabolism on neural cells is of growing interest, but how metabolic changes in the early postnatal brain impact OPC dynamics remains poorly understood. Here we show that a glucose oscillation in developing forebrain is detectable by MALDI MS imaging and correlates with a temporal and region-specific transition of OPCs from proliferation to differentiation. In dorsal cortex and white matter regions, glucose levels decline in the second postnatal week during a critical window when OPCs slow proliferation and begin differentiation. In ventral regions we observe continually elevated glucose and OPCs persist in a proliferative state, thereby suggesting that glucose availability serves as a local signal promoting progenitor expansion, or cell cycle exit and differentiation, in early brain. When OPCs are cultured in low glucose, we detect glucose-responsive histone acetylation changes and a transcriptional signature of cell cycle exit and differentiation. Mechanistically, we link the activity of the metabolic enzyme ATP citrate lyase, which converts glucose-derived citrate to the central metabolite acetyl-CoA, to acetylation and proliferation dynamics downstream of glucose availability in cultured cells. Pharmacological inhibition or genetic deletion of ACLY in cultured OPCs results in reduced histone acetylation and levels of cell cycle related transcripts, and reduced proliferation, supporting the hypothesis that glucose bioavailability influences OPC dynamics via ACLY. A transgenic animal model of conditional ACLY deletion in OPCs timed to the period of high glucose availability in brain results in decreased histone acetylation and growth-arrest leading to a depletion of the oligodendrocyte pool and hypomyelination. Finally, we link the emergence of ketone bodies in brain to the period of reduced glucose availability and show that alternative sources of acetyl-CoA that bypass glucose rescue Acly-/- OPC viability. Our results support a temporal-metabolic model centered on glucose availability in the timing of OPC growth arrest, and that alternative substrates of acetyl-CoA such as ketone body serve as a metabolic bridge during glucose fluctuations to promote oligodendrocyte survival and differentiation.

overall_design: Single cell transcriptomics of OPCs that were FACS isolated from Control or conditional Acly knockout brain. The Pdgfra-creERT tamoxifen inducible line was crossed to Aclyfl/fl line. OPCs were sorted by CD140a labeling (PDGFRa) and collected for single cell transcriptomics on 10x platform.

first: Sami

last: Sauma


title: High-salt diet induces melanoma re-differentiation

city: Bonn

first: Clivia

last: Lisowski

address: Venusberg-Campus 1

institute: Universität Bonn

summary: A High-salt diet induces immune-independent re-differentiation, metabolic shut down and cell-cycle arrest of melanoma through upregulation of MITF, TSC2 and p18, leading to metabolic shutdown, cell cycle arrest and melanogenesis as well as re-differentiation.

overall_design: Female C57BL/6J mice aged 8-12 weeks were exposed to a normal salt diet (NSD) (or a high salt diet (HSD) for one week before s.c injection of B16-OVA melanoma cells and tumor growth was followed for 14 days while maintaining the respective diets. On day 14 mice were sacrificed and 3' mRNA-Sequencing was performed on isolated tumor cells (ex vivo) to investigate the impact of HSD on B16-OVA melanoma growth.


title: Effect of overexpression NUDT3 on proliferation and differentiation of primary porcine muscle satellite cells

city: Yangling

first: ya

middle: long

last: an

address: Xinong No.22

institute: Northwest Agriculture & Forestry University

summary: In our study, reduced NUDT3 in vitro significantly arrested cell cycle in primary muscle satellite cells, indicated by elevated ratio of cells at G1 stage and decreased EdU+ cells. Besides, knockdown of NUDT3 significantly inhibited myogenic differentiation, as myogenic genes and MyHC+ cells were dramatically repressed, conversely, its overexpression yielded the opposite effects.

overall_design: Through interference and overexpression of NUDT3 in vitro, the mechanism of NUDT3 in porcine skeletal muscle satellite cells was investigated.

first: Yalong

last: An

first: Xiao

last: Li

first: Yanru

last: Yue

first: Yongqi


title: Temporal dynamics of inflammatory and transcriptome changes in the myocardium in a murine model of cardiac arrest

city: Cleveland

first: Cody

last: Rutledge

state: OH

address: 2103 Cornell Road

department: Medicine

institute: CWRU

summary: Background: It is increasingly recognized that inflammatory changes play a significant role in myocardial injury following cardiac arrest. However, the pathophysiological mechanisms responsible for functional changes in the myocardium following the event remain incompletely understood. Here, we characterize the transcriptomic and immunological changes in a mouse model of cardiac arrest to explore the roles of epinephrine and ischemia/reperfusion on myocardial inflammation. Methods and Results: Male and female mice (C57BL/6J) were divided into three groups: (1) Naïve (anesthesia only), (2) Sham (anesthesia + saline injection + epinephrine), and (3) Arrest (8-minute cardiac arrest followed by resuscitation (anesthesia + potassium chloride + epinephrine). We monitored the animals over 0.5, 1, 3, and 7 days with serial echocardiography. Hearts were harvested for transcriptomic analysis and inflammatory changes as assessed by flow cytometry and immunohistochemistry. Plasma samples were collected for cytokine signaling analysis by multiplex ELISA. Our data indicate that the cardiac arrest group have increased infiltrating neutrophils in the myocardium and elevated plasma levels of pro-inflammatory cytokines, peaking at 0.5 days after the initial insult and subsequently resolving. In contrast, Sham mice displayed less pronounced inflammatory changes, which peaked at 1 day after the procedure. Notably, these inflammatory alterations coincided with cardiac stunning, as demonstrated by echocardiography. Conclusions: In our murine model of cardiac arrest, epinephrine exposure and ischemia/reperfusion induce significant inflammatory changes in the myocardium with increased infiltrating neutrophils and elevated circulating cytokines which subsequently resolve in a time-dependent manner. These changes correlate with improving cardiac function by echocardiography.

overall_design: Bulk RNA Seq from homogenized ventricles of Naïve control, Sham, and Cardiac Arrest hearts at various time points


title: Transcription factor occupancy is affected by genetic variation in the white adipose tissue of C57BL6/j and 129S1/SvImJ mice [ATAC-seq]

city: Kuopio

first: Juho

middle: Mikael

last: Mononen

address: Yliopistonranta 1E

department: Faculty of Health Sciences

country: Finland

institute: University of Eastern Finland

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Most of the disease associated genetic variants identified in genome wide association studies have been mapped to the non-coding regions of the genome. One of the leading mechanisms by which these variants are thought to affect disease susceptibility is by altering transcription factor (TF) binding. Even though inbred mouse strains have been commonly used to investigate polygenic diseases, less is known on how their genetic differences translate to the level of gene regulation and chromatin landscape. Here, we investigated how genetic variation affects chromatin accessibility, a commonly used proxy for TF binding, and how this relates to gene regulation in the epididymal white adipose tissue (eWAT) of C57BL/6J and 129S1/SvImJ mice fed either chow or high-fat diet. We show that differences in chromatin accessibility are almost exclusively strain-specific and driven by genetic variation. In addition, we integrate ATAC-seq (chromatin accessibility) and H3K27ac ChIP-seq (active regulatory regions) data to show that tissue-specific TFs are commonly found in the active regulatory regions hosting TF binding motif altering variants in eWAT. By incorporating footprint analysis, we also show that TF occupancy is consistent with TF binding motif scores at the genetically altered loci. In addition, we validate these findings by extending the footprint analysis to ATAC-seq and H3K27ac ChIP-seq data obtained from the liver. Also, we employ RNA-seq to show that differentially expressed genes are collocated with differentially accessible regions hosting genetic variants. Overall, our findings highlight the connection between differential chromatin accessibility, TF binding and genetic variation and their role in the gene regulation across metabolically central tissues of a mouse model for polygenic obesity.

overall_design: We generated  5-7 ATAC-seq libraries from the 4 groups: 129S1/SvImJ and C57BL/6J on either chow or high-fat diet

first: Mari

last: Taipale

last: Heikkinen


title: SOAT1 knockout reshapes tumor immune microenvironment with enhanced CD8+ T cell infiltration and effector function [scRNA-seq]

first: guangchuan

last: Wang

address: 320 Yue Yang Road

institute: Chinese Academy of Sciences

summary: To investigate the mechanism, we performed single-cell RNA sequencing (scRNA-seq) to profile the in vivo transcriptome and immune landscape (Figure 4F). Tumors from PBS- and anti-PD1-treated mice were purified using Ficoll and subjected to scRNA-seq, recovering 9,431 and 9,970 cells from SOAT1-KO tumors, and 10,880 and 8,580 cells from vector tumors, respectively.

overall_design: For single-cell RNA sequencing (scRNA-seq) library preparation, the DNBelab C Series High-throughput Single-Cell RNA Library Prep Kit (MGI, Cat# 940-000519-00) was used. In brief, cells at a concentration of 1,000 cells/ μL were loaded into the cell reservoir of a microfluidic chip. Barcoded beads and droplet-generation oil were sequentially added to their respective reservoirs. Encapsulated droplets were generated and collected using the DNBelab C4 /DNBelab TaiM4 system. Beads capturing the mRNA were then recovered for reverse transcription (RT). After RT, complementary DNA (cDNA) was amplified via PCR, purified, and quantified using a Qubit dsDNA kit (Thermo Fisher). Libraries of 3’-end transcripts were subsequently constructed through cDNA fragmentation, size selection, end repair and A-tailing, adapter ligation, indexing PCR, and library cyclization, according to the manufacturer ’s protocol. The sequencing libraries were purified and quantified using the Qubit ssDNA kit (Thermo Fisher) and the Qsep100 system (Bioptic). scRNA-seq was performed on the DNBelab C4/DNBelab TaiM4 system. The DNBelab C4 /DNBelab TaiM4 Series Single-Cell Library Prep Set (MGI) was used for sequencing. DNBs were loaded into patterned nanoarrays and sequenced on the DNBSEQ-T7 sequencer with pair-end sequencing. The sequencing reads contained a 30-bp read 1 (including a 10-bp cell barcode 1, a 10-bp cell barcode 2 and a 10-bp unique molecular identifiers (UMI)), a 100-bp read 2 for gene sequences, and a 10-bp barcode read for sample indexing. Sequencing data were processed using the open-source DNBelab C Series scRNA analysis software pipeline (https://github.com/MGI-tech-bioinformatics/DNBelab_C_Series_scRNA-analysis-software). Sample de-multiplexing, barcode processing, and single-cell 3' UMI counting were performed with default parameters. Processed reads were aligned to the GRCh38 genome reference using STAR (2.7.2b). Valid cells were automatically identified based on UMI distribution using the “barcodeRanks” function of the DropletUtils tool to remove background beads and low-UMI-count beads. Finally, we used PISA tool to calculate gene expression for each cell and create a gene-by-cell matrix for each library.


title: Male metabolic and reproductive health are perturbed by both under- and over-nutrition in mice

city: Nottingham

first: Marios

last: Georgiou

address: Queen's Medical Centre

department: School of Life Sciences

institute: University of Nottingham

summary: The association between poor paternal diet at the time of conception and impairments in offspring health and well-being is becoming increasingly established. However, the impacts of such poor-quality diets on the father’s metabolic health and physiology have been investigated to a lesser extent. Therefore, the aim of this study was to define how both under- and over-nutrition impact male metabolic and reproductive physiology. Male C57BL/6 mice were fed either control diet (CD), low protein diet (LPD), ‘Western’ diet (WD), or the LPD or WD supplemented with methyl donors (MD-LPD and MD-WD, respectively) for at least eight weeks. Under- (LPD) or over-nutrition (WD), with or without methyl donors, had minimal impact on male growth or organ weight. However, concentrations of hepatic cholesterol and free fatty acids were significantly increased in WD and MD-WD fed males. Furthermore, levels of serum inhibin β-A chain were increased in WD males when compared to LPD and MD-LPD fed males. We also observed differential abundance of multiple bacterial species at the family and phylum level in the lower gastro-intestinal tract of males fed WD and MD-WD when compared to all other groups. Within the testis, WD and MD-WD increased the number of morphologically abnormal seminiferous tubules when compared to all other males, while the number of Plzf positive cells, taken as a marker of spermatogonial stem cells, were decreased in LPD and WD fed males when compared to CD fed males. Finally, analysis of testicular gene expression revealed minimal changes in LPD and MD-LPD fed males, while WD and MD-WD males both showed differential expression of genes related to metabolism and transcriptional regulation. These findings suggest that paternal under- and over-nutrition influence metabolic status and reproductive physiology in diet-specific manners. Interestingly, supplementation of these diets with a range of methyl-donors and carries had minimal additional impact in ameliorating the effects of over- and under-nutrition.

overall_design: To investigate murine testicular RNA profile changes in response to sub-optimal diets and dietary supplementations. We fed male mice either control diet (NPD; 18% casein, 21% sugar, 0% milk fat, 0% cholesterol), isocaloric low protein diet (LPD; 9% casein, 24% sugar, 0% milk fat, 0% cholesterol), ‘Western’ diet (WD; 19% casein, 34% sugar, 20% milk fat, 0.15% cholesterol) or LPD or WD supplemented with methyl-donors [an addition of 5 g/kg diet choline chloride, 15 g/kg diet betaine, 7.5 g/kg diet methionine, 15 mg/kg diet folic acid, 1.5 mg/kg diet vitamin B12 to either LPD (MDL) or WD (MDWD)] for a minimum of 8 weeks before total RNA extraction was conducted on collected testicular tissue.

first: Nader

last: Eid

first: Vipul

last: Batra

first: Nadine

last: Holmes

first: Matthew

last: Carlile

first: Sonal

last: Henson

first: Fei

last: Sang

first: Victoria

last: Wright

first: Marcos

last: Castellanos-Uribe

first: NIqbal

last: Khan

first: Nazia

last: Nazar

first: Sean

last: May

first: Rod

last: Mitchel

first: Federica

last: Lopes

first: Robert

last: Robinson

first: Hannah

last: Morgan

first: Adam

last: Watkins


title: microRNA-seq  data of orbital connective tissues from thyroid eye disease patients

first: Baiguang

last: Yu

address: 639 Zhizaoju Road

department: Department of Ophthalmology

institute: Shanghai Ninth People’s Hospital, Shanghai Jiao Tong University School of Medicine

summary: Thyroid eye disease (TED) is the most common orbital disease leading to severe facial deformities and visual impairment, but its pathogenesis remains to be fully characterized. To address these issues, we conducted microRNA-seq to distinguish TED patients from non-TED healthy controls.

overall_design: Total RNA was extracted from orbital connective tissues by using TRIzol. Then RNA was quantified with a NanoDrop 2000. RNA sequencing libraries were constructed with 1μg high-quality RNA of each sample according to the instructions of TruSeq Small RNA Library Preparation Kit (Illumina) for sequencing.

first: Huifang

last: Zhou

first: Sijie

last: Fang


title: The cellular response to the deprivation of L-phenylalanine from the medium in the cultivation of U87-MG, a glioblastoma-like cell line.

city: Kyoto

first: Rie

last: Saba

state: Kyoto

address: Kajii-cho 465, Kawaramachi-dori, Kamigyo-ku

department: Dapartment of Radiology

country: Japan

institute: Kyoto Prefectural University of Medicine

summary: To optimize the efficacy of boron neutron capture therapy (BNCT), we investigated the optimal conditions for maximizing the uptake of boronophenylalanine (BPA), an analog of L-phenylalanine (L-Phe), in tumor cells. In the cultivation of tumor cell lines, some cell lines, including U87-MG, demonstrated an amplified accumulation of BPA under 24 hours of L-Phe deprivation, which resulted in an enhancement of BNCT efficiency. Consequently, we conducted a comprehensive analysis of the cellular response of U87-MG under L-Phe restriction by RNA-seq.

overall_design: To investigate the tumor cell response to L-Phe restriction, we cultivated the U87-MG cell line under noth normal and L-Phe-deprived conditions.

first: Yuki

last: Tamari

first: Hideya

last: Yamazaki

first: Kei

last: Yamada


title: SOAT1 knockout enhances sensitivity of liver cancer cells to T cell-based immunotherapy [RNA-seq]

first: guangchuan

last: Wang

state: Shanghai

summary: SOAT1 knockout enhances the responsiveness of human liver cancers to T cell-based therapies without significantly impacting tumor proliferation. We aimed to elucidate how SOAT1 knockout influences sensitivity to T cell therapy. We performed bulk RNA-seq analysis on SOAT1-KO and vector-transduced Hepa1-6 cells and Huh7 cells.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: RNA extraction from the target cells was performed using TRIzol Reagent (Invitrogen) according to the manufacturer’s standard protocol. For RNA-seq analysis, the purified mRNA was utilized to prepare sequencing libraries with the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (NEB). These libraries were then multiplexed and sequenced using paired-end reads on Illumina Novaseq platform. Differential gene expression, Gene Set Enrichment Analysis (GSEA), and data visualization were conducted using R (v.5.2.0), and the ggplot2 (v3.2.1).


title: The cellular response to the deprivation of L-phenylalanine from the medium in the cultivation of SAS, a squamous carcinoma cell line.

summary: To optimize the efficacy of boron neutron capture therapy (BNCT), we investigated the optimal conditions for maximizing the uptake of boronophenylalanine (BPA), an analog of L-phenylalanine (L-Phe), in tumor cells. In the cultivation of SAS cells, an amplified accumulation of BPA was observed under 24 hours of L-Phe deprivation, which resulted in an enhancement of BNCT efficiency. Consequently, we conducted a comprehensive analysis of the cellular response of SAS under L-Phe restriction by RNA-seq.

overall_design: To investigate tumor cell response to L-Phe restriction, we cultivated the SAS cell line under both normal and L-Phe-deprived conditions.


title: A genome-wide CRISPRa screening to functionalize lncRNAs in CDK4/6i response [siRNA_RNAseq]

city: Pittsburgh

first: Da

last: Yang

address: 308 Salk Pavilion

institute: University of Pittsburgh

summary: RNA-seq data for candidate genes identified from CRISPR activation screen for regulation of CDK4/6i response

overall_design: Total RNA-seq data for candidate genes knockdown in MCF-7 cells

first: Wang

last: Yifei

first: Zhao

last: Yueshan

first: Zhang

last: Min

first: Yang

last: Da


title: The cellular response to the deprivation of L-phenylalanine from the medium in the cultivation of HaCaT, a keratynocyte cell line.

summary: To optimize the efficacy of boron neutron capture therapy (BNCT), we investigated the optimal conditions for maximizing the uptake of boronophenylalanine (BPA), an analog of L-phenylalanine (L-Phe), in tumor cells. In the cultivation of tumor cell lines, some cells showed an amplified accumulation of BPA under 24 hours of L-Phe deprivation, which resulted in an enhancement of BNCT efficiency. In contrast, HaCaT, a keratynocyte cell line, demonstrated unaltered responsiveness in the uptake of BPA under L-Phe restriction. Accordingly, we conducted a comprehensive analysis of the cellular response of HaCaT cells under L-Phe restriction by RNA-seq.

overall_design: To investigate tumor cell response to L-Phe restriction, we cultivated HaCaT cells under normal and L-Phe deprived conditions.


title: A double-edged sword role of IFN-γ-producing iNKT cells in sepsis: Persistent suppression of Treg cell formation in an Nr4a1-dependent manner

first: Yingyu

last: Qin

address: Southeast University Dingjiaqiao NO.87

institute: Southeast University

summary: Sepsis, a leading cause of mortality in intensive care units worldwide, lacks effective treatments for advanced-stage sepsis. Therefore, understanding the underlying mechanisms of this disease is crucial. This study reveals that iNKT cells have an opposing role in the progression of sepsis by suppressing Treg differentiation and function. The activation of iNKT cells by α-Galcer enhances IFN-γ production. Blocking antibodies or transferring IFN-γ-deficient iNKT cells demonstrates that iNKT cells inhibit Treg differentiation through IFN-γ production. Additionally, iNKT cell-mediated Treg inhibition prevents secondary infection caused by Listeria monocytogenes during the post-septic phase. The transcriptomic analysis of Tregs further reveals that the suppressive function of Tregs is impaired by iNKT cells. Finally, we demonstrate that iNKT cells inhibit Treg differetiation in a Nr4a1-dependent manner. Our data uncover the dual function of iNKT cells in sepsis progression and provide a potential treatment target for this adverse long-term outcome induced by sepsis.

overall_design: The CD4+ T cells were isolated from splenocytes of septic mice treated with α-galcer or PBS (two days after CLP performance) using the negative CD4+T cell isolation kit, following the manufacturer's instructions. Subsequently, the Treg cell population, characterized by CD25highCD127low markers, was sorted using BD FACSAria™ Fusion Flow Cytometers. To ensure an adequate number of enriched Treg cells, Treg cells were collected from three mice. The isolated Treg cells with a purity about 90% were subjected to TRIzol treatment, and total RNA was extracted according to the manufacturer’s protocol.

first: Yilin

last: Qian

first: Shengqiu

last: Liu

first: Rong

last: Chen


title: H3K27-mutant diffuse hemispheric glioma presenting typical molecular features of diffuse midline glioma: A case report and literature review.

city: Hidaka

first: Mitsuaki

middle: Shirahata

last: Shirahata

state: Saitama

department: Neurosurgery/Neuro-oncology

institute: Saitama Medical University International Medical Center

summary: Mutations in the gene encoding histone H3, p.K28M(K27M) and p.G35R/V(G34R/V), are the major driver gene mutations in gliomas. H3 p.K28M(K27M) mutations are frequently found in gliomas arising in midline structures, so called H3K27M-diffuse midline glioma (DMG), while H3 p.G35R/V(G34R/V) mutations are frequently found in pediatric hemispheric gliomas, so called H3G34R/V-diffuse hemispheric glioma (DHG). In contrast, hemispheric glioma with H3 p.K28M(K27M) mutation, known as H3K27M-DHG, is a rare entity and its clinical and molecular characteristics remain to be fully elucidated. We describe a 41-year-old female patient with the right parietal lobe tumor. Following a gross total resection, the pathology showed a high-grade astrocytoma. Sanger sequencing revealed an H3K27M mutation and an IDH1/2-wildtype, leading to the integrated diagnosis of H3K27M-DHG. She underwent chemoradiotherapy with temozolomide and suffered recurrences twice until her death 55 months after the initial diagnosis. The deoxyribonucleic acid methylation profiling classified the tumor as DMG, H3K27-altered, suggesting that it molecularly belonged to the variant of DMG despite a non-median location. Next-generation sequencing on the recurrent tumor detected fibroblast growth factor receptor (FGFR)1 mutation, a favorable prognostic factor in H3K27M-DMG. A relatively prolonged survival of our patient suggests that FGFR1 mutations may also contribute to a better prognosis in H3K27M-DHG.

overall_design: The purpose of this study was to identify the methylation profile of H3K27M mutant high-grade gliomas arising in the cerebral hemisphere. DNA was extracted from surgically resected tumor tissue and subjected to DNA microarray analysis.


title: Next-Generation Sequencing Facilitates Quantitative Analysis of Control and BET bromodomain Inhibitor-treated Uterine fibroids Cell Transcriptome

first: Azad

last: Khosh

address: 7703 Floyd Curl Dr

institute: UTHSCSA

summary: We report that BET bromodomain inhibition alters multiple biological pathways in uterine fibroid cells

overall_design: Examine the transcriptome alteration in uterine fibroid cells with or without BET bromodomain inhibitors

first: Qiwei

first: Ali

last: Falahati

first: Ayman

last: Al-Hendy


title: The selective RRM2 inhibitor TAS1553 is synergistic with multiple CHK1 inhibitors in neuroblastoma

city: Ghent

first: Sarah-Lee

last: Bekaert

state: No state

address: Corneel Heymanslaan 10

country: Belgium

institute: UGent

summary: Tumor cells experience high replication stress, driving genomic instability. Recent studies reveal that neuroblastoma, a pediatric tumor, heavily relies on the ATR-CHK1 signaling pathway. Our prior work identified RRM2, part of the ribonucleotide reductase (RNR) complex, as a key target in neuroblastoma. In this study, we assessed the effects of the RNR-disrupting compound TAS1553 on neuroblastoma cells. Both in vitro and in vivo, TAS1553 inhibited cell growth and triggered apoptosis. Additionally, TAS1553 synergized with CHK1 inhibitors prexasertib and SRA737, increasing replication stress and DNA damage. We also observed these effects in Ewing sarcoma, osteosarcoma, and rhabdomyosarcoma. Notably, TAS1553 downregulated RNA splicing factors, suggesting potential for combination therapies with splicing inhibitors.

overall_design: Neuroblastoma cells (IMR32 and CLBGA) were treated with TAS1553, SRA737, prexasertib and DMSO. Three or four biological replicates.

first: Iris H.

last: Nelen

first: Soetkin

last: Leys

first: Fanny

last: De Vloed

first: Fien

last: Martens

first: Shunya

last: Ohmura

first: Thomas G. P.

last: Grünewald

first: Frank

last: Speleman

first: Annelies

last: Van Hemelryk

first: Lisa

last: Depestel

first: Kaat

last: Durinck


title: The cellular response to the deprivation of L-phenylalanine from the medium in the cultivation of A375, a melanoma cell line.

first: Rie

last: Saba

summary: To optimize the efficacy of boron neutron capture therapy (BNCT), we investigated the optimal conditions for maximizing the uptake of boronophenylalanine (BPA), an analog of L-phenylalanine (L-Phe), in tumor cells. In the cultivation of tumor cell lines, some cells showed an amplified accumulation of BPA under 24 hours of L-Phe deprivation, which resulted in an enhancement of BNCT efficiency. In contrast, A375 demonstrated unaltered responsiveness in the uptake of BPA under L-Phe restriction. Accordingly, we conducted a comprehensive analysis of the cellular response of A375 cells under L-Phe restriction by RNA-seq.

overall_design: To investigate the tumor cell response to L-Phe restriction, we cultivated the A375 cell line under noth normal and L-Phe-deprived conditions.

first: Yuki

last: Tamari

first: Hideya

last: Yamazaki

first: Kei

last: Yamada


title: An absolute quantification atlas of small non-coding RNAs across mammalian tissues and cell lines

city: Shanghai

first: Wen

last: Xiao

address: 320 Yueyang Road

department: Institute of Biochemistry and Cell Biology

institute: Shanghai Institutes for Biological Sciences, CAS

summary: The low quantitative accuracy of conventional small noncoding RNA sequencing (sncRNA-seq) methods due to extensive ligation bias commonly limits functional investigation of microRNAs (miRNAs) and PIWI-interacting RNAs (piRNAs). Here, we developed 4NBoost, a single-tube sncRNA-seq protocol designed to minimize bias in the estimated absolute quantification of miRNA and piRNA transcripts through the incorporation of quantitative exogenous RNA spike-ins. With 4NBoost, we profiled sncRNA expression across 20 murine tissues, 18 macaque tissues, and 24 widely used cell lines, as well as 4 Arabidopsis tissues, to establish a comprehensive quantitative reference atlas. Compared with existing small RNA databases, our data revealed substantial biases in miRNA abundance, strand selection, and tissue-specific expression at both individual and family levels. To further extend its utility, we employed machine learning to model and correct biases in conventional datasets, effectively recovering ground truth transcript abundances. All 4NBoost data and the accompanying bias-correction model are freely available via SmRNAQuant (http://wulg-lab.sibcb.ac.cn/SmRNAQuant/), a web-based repository for exploring sncRNA expression. Together, the 4NBoost, bias-correction model, and SmRNAQuant provide powerful resources to advance sncRNA research.

sample_organism:
Arabidopsis thaliana
Macaca fascicularis
Homo sapiens
Mus musculus

overall_design:
Absolute quantification of miRNA and piRNA expression profiles in common tissues and cell lines using 4NBoost.
Pleaes note that total 242 samples are used for formal analysis, and their processed expression profiles are provided in the 'absolute quantification of miRNA expression for each sample.xlsx'.

first: Yuli

last: Zheng

first: Hongdao

last: Zhang

first: Beiying

last: Xu

first: Ruiwen

first: Ligang

last: Wu


title: Study on the Compound Biological Effects of Polystyrene Microplastics and Cadmium on Bellamya aeruginosa

city: changsha

first: Huilin

middle: huilin

last: Yang

state: huannan

address: Donghu Street

institute: Hunan Agricultural University

summary: By analyzing the transmission and accumulation of polystyrene and cadmium single and combined pollution in the body of the Bellamya aeruginosa through the food chain, this study reveals the enrichment situation of polystyrene and cadmium combined pollution in the Bellamya aeruginosa at a high trophic level. It also analyzes its effects on the physiological and ecological toxicity, mechanisms, and transcription characteristics of the Bellamya aeruginosa.

overall_design: The polystyrene microplastic solution was ultrasonically treated for 10 minutes in an ultrasonic machine to ensure it was fully dispersed. Ten different concentrations were set up, including a control group, a cadmium treatment group (low, medium, high), a polystyrene treatment group (low, medium, high), and a combined treatment group (low, medium, high). The algal solution with the added concentrations of cadmium and microplastics was fed daily, and the water was replaced regularly. On the 42nd day, the transcriptional effects on the Bellamya aeruginosa were measured.


title: Transcriptomic analysis of human breast cancer cells upon carboplatin treatment

city: Wuhan

first: Xiang

last: Li

address: Youyi Road

institute: Hubei University

summary: Platinum drugs have broad spectrum and high anti-cancer activity with nucleus DNA as primary target. During platinum chemotherapeutics, the steady-state levels of reactive oxygen species (ROS) are generally elevated and induce oxidative stress response, to regulate cell survival and drug resistance. Currently, a novel nucleus-to-mitochondria ROS pathway has been identified. However, the pathways by which platinum drugs generate ROS, as well as the biological response, still lack systematic studies. Using carboplatin as an example, we systematically analysed the dynamic response to ROS in cancer cells.

overall_design: To thoroughly understand the effects of platinum chemotherapeutics on the expression of the global transcriptome, we performed the mRNA sequencing (mRNA-Seq) on the MCF-7 cells treated with or without 0.5 mM carboplatin. NC group: Normal MCF-7 cells, C group: carboplatin treated MCF-7 cells.


title: Phospholipase A2 downregulates inhibitory transmission in the amygdala and impairs fear extinction

city: New York

first: Kwanghoon

last: Park

address: 1230 York Ave

institute: The Rockefeller University

summary: Patients with psychiatric disorders show higher serum phospholipase A2 (PLA2) activity, however the relationship between PLA2 and psychiatric disorders has been poorly understood. It has been known that 129S1/SvImJ (S1) mice exhibit impaired fear extinction, one of the major symptoms of post-traumatic stress disorder (PTSD). In fear conditioning, sensory and somatic inputs arrive in the basolateral amygdala (BLA) and relay to the medial division of the central amygdala (CEm), the final output in the amygdala projecting to fear response-generating areas. Here we found that S1 mice showed increased expression of PLA2 mRNA in the BLA and CEm compared to control C57BL/6 (B6) mice. Basal inhibitory transmission of CEm neurons was decreased in S1 mice and acute inhibition of PLA2 successfully elevated the basal inhibitory transmission levels in the CEm both in naïve B6 and S1 mice. PLA2 inhibition also weakened BLA to CEm synapses in S1 mice after fear extinction, thereby leading the synaptic responses from CEm while stimulating BLA back to the levels comparable to B6. Ultimately, the selective infusion of PLA2 inhibitors into the CEm enhanced fear extinction in S1 mice. Our data suggest that PLA2 activity modulates inhibitory transmission of the CEm and fear extinction, thus possibly serves as a key molecular mediator of impaired fear extinction in PTSD.

overall_design: To identify differentially expressed genes that are related to impaired fear extinction in S1 mice, we conducted RNA Sequencing (RNA-Seq) using BLA and CEm tissues collected from B6 and S1 mice before and after fear conditioning and extinction

first: ChiHye

last: Chung


title: Estrogen signaling in PDGFRα+ cells positively regulates cortical bone metabolism via IGFBP5 in female mice.

city: Toon

first: Aoi

last: Ikedo

state: Ehime

address: Shitsukawa

institute: Ehime University

summary: The prevalence of both osteoporosis and sarcopenia increases with age, and 60% of elderly sarcopenia patients also develop osteoporosis. However, the co-occurrence of osteoporosis and sarcopenia remains unclear. We performed single-cell 5’RNA-seq on human skeletal muscle tissues and investigated the enrichment of heritability for musculoskeletal traits in cell type specific cis-regulatory regions. We found the fibroblast-specific cis-regulatory regions are highly enriched in the heritability of bone mineral density (BMD). Using GWAS, we identified estrogen receptor α (ESR1) as a common transcription factor that correlated with both BMD and lean mass. We hypothesized that deficiency of estrogen signaling in fibroblast may attenuate musculoskeletal homeostasis. Therefore, we generated mice lacking Esr1 in PDGFRα (a fibroblast marker) + cells (Esr1ΔPα). Although muscle mass and grip strength were not different between groups, distal femoral BMD and cortical thickness were significantly lower in Esr1ΔPα compared to control. Bone histomorphometry showed that cortical bone in Esr1ΔPα exhibited a high turnover bone phenotype. Bulk RNA-seq using PDGFRα+ cells revealed that Igfbp5 expression was significantly higher in Esr1ΔPα compared to control. Furthermore, serum IGFBP5 level was significantly higher in Esr1ΔPα. IGFBP5 treatment in vitro significantly suppressed osteoblast differentiation and facilitated osteoclast differentiation. These results suggest that estrogen signaling in PDGFRα+ cells suppresses Igfbp5 expression, then maintains bone mass, indicating that estrogen signaling in PDGFRα+ cells plays a significant role in bone metabolism.

overall_design: To clarify the target gene (s) of Esr1 in PDGFRα+ cells from skeletal muscle that are involved in bone metabolism, we performed RNA-seq in PDGFRα+ cells from muscles of both control and Esr1ΔPα (cKO) mice.

first: Yuuki

last: Imai


title: Rhythmic Transcription and Aging: _x000B_Insights from the Drosophila Photoreceptor Transcriptome and Epigenome

city: West Lafayette

first: Sarah

last: McGovern

state: IN

address: Department of Biochemistry

department: Biochemistry

institute: Purdue University

summary: Rhythmic changes in the transcriptome are widespread during aging in Drosophila photoreceptors. To better understand the epigenetic factors underlying these changes, we profiled RNA PolII occupancy and levels of H3K4me1, H3K4me2, and H3K4me3 using CUT&RUN. To profile changes in chromatin accessibility, we also performed ATAC-seq. To obtain robust rhythmic data across age, we collected both young (D10 post-eclosion) and old (D50 post-eclosion) flies every four hours throughout the day in a 12-hour light:12-hour dark cycle in triplicate.

overall_design: Drosophila were maintained in population cages in a 25°C incubator with a 12:12 hour light:dark cycle. 400 male flies in triplicate were collected at the indicated days post-eclosion (D10 and D50) and at the indicated Zeitgeber times (ZT0, ZT4, ZT8, ZT12, ZT16, ZT20). GFP-positive photoreceptor nuclei were immunoprecipitated using the nuclei immunoenrichment protocol (dx.doi.org/10.17504/protocols.io.buiqnudw), followed by CUT&RUN (dx.doi.org/10.17504/protocols.io.zcpf2vn) or ATAC-seq.

first: Gaoya

last: Meng

first: Vikki

last: Weake


title: Asprosin Transcription Underlies Obesity Relapse and Inheritance [ATAC-seq]

first: Brian

last: Kim

state: OHIO

address: 10900 Euclid Ave

institute: Case Western Reserve University

summary: Obesity is a unique disease, marked by its near-certain relapse after weight loss and its transmission to offspring of obese mothers. The biological mechanisms behind these phenomena remain elusive. We have found that the obesity-associated cytokine Tgf-β1 activates Fbn1 transcription in adipocytes, driving overproduction of the appetite-stimulating hormone asprosin. Remarkably, a single exposure to elevated Tgf-β1 reshapes chromatin at the Fbn1 locus, cementing its overexpression in a manner that is unrelenting, even after weight loss and normalization of Tgf-β1 levels. This results in an enduring plasma asprosin elevation despite weight loss, sustaining heightened appetite and a ceaseless pull toward regaining the lost weight. Strikingly, maternal Tgf-β1 passes through the placenta leading to fetal adipose reprogramming and plasma asprosin elevation that persists in childhood, transmitting obesity across generations. Our findings reveal a powerful chromatin remodeling and transcriptional event that results from a single exposure to obesity, causing a profoundly enduring elevation of an appetite-stimulating hormone, fueling both relentless recurrence and hereditary transmission.

overall_design: To investigate changes to chromatin accessibility that occur in adipocytes, we treated differentiated 3T3-L1 cells with recombinant mouse Tgf-β1 for 4 days. We also investigated changes that occur when active  Tgf-β1 signaling is removed, so we also had a sample where cells were exposed to  Tgf-β1 fo4 4 days, then an additional  Tgf-β1 Free media for 14 days. We then performed ATAC-sequencing of these samples

first: Atul

last: Chopra