title: Vitamin A treatment rescues neonatal infection-induced durably impaired lymph node function (RNA-seq tissue DC)

city: Nanjing

first: Mangge

last: Zou

address: No.6 Building, Life Science TechTown, 568 Longmian Avenue Jiangning District

institute: Legend Biotech

summary:
To investigate whether transient neonatal infections long-lastingly alter the transcriptome of tissue dendritic cells, we isolated dendritic cells from the pancreas, the proximal duodenum, and the liver.
We then performed gene expression profiling analysis using data obtained from low-input RNA-seq of these tissue-isolated dendritic cells.

overall_design: RNA-seq with 4 replicates per condition dendritic cells ex vivo isolated from the pancreas, the proximal duodenum, and the liver.

first: Joern

last: Pezoldt

first: Carolin

last: Wiechers

first: Marina

last: Pils

first: Juhao

first: Michael

last: Beckstette

first: Juliane

last: Mohr

first: Lars

last: Philipsen

first: Andreas

last: Mueller

first: Lianxu

last: Hao

first: Till

last: Strowig

first: Aline

last: Dupont

first: Mathias

last: Hornef

first: Petra

last: Dersch

first: Jens

last: Raila

first: Jochen

last: Huehn


title: Gut microbial metabolite butyrate improves anticancer therapy by regulating intracellular calcium homeostasis

status: Public on Jul 20 2025

city: Shanghai

first: Yibin

last: Che

state: shanghai

country: China

institute: shanghai jiaotong university

type: Expression profiling by high throughput sequencing

summary: Gut microbiota are recognized to be important for anticancer therapy, yet the underlying mechanism is not clear. Herein, we demonstrate that gut microbial metabolite butyrate improves anticancer therapy efficacy by regulating intracellular calcium homeostasis. Butyrate metabolism is activated in hepatocellular carcinoma (HCC) patients. Butyrate supplementation or depletion of  short-chain Acyl-CoA dehydrogenase (ACADS), a key enzyme for butyrate metabolism, significantly inhibit HCC proliferation and metastasis. Profiling analysis of genes upregulated by butyrate supplementation or ACADS knockdown reveal that calcium signaling pathway is activated, leading to dysregulation of intracellular calcium homeostasis and production of reactive oxygen species (ROS). Butyrate supplementation improves the therapy efficacy of a tyrosine kinase inhibitor sorafenib. Butyrate and sorafenib co-encapsulated monomethoxy (polyethylene glycol)-poly (D, L-lactide-co-glycolide)-poly(L-lysine)-glypican 3 (PEAL-GPC3) nanoparticles significantly reduce HCC progression. Our findings provide new insight into the mechanisms that the gut microbial metabolites inhibit HCC progression and suggest a translatable therapeutics approach to enhance the clinical targeted therapeutic efficacy.

overall_design: The gene expression profiles of sodium butyrate treatment and ACADS knockdown Hep3B cells were compared with those in control Hep3B cells

first: Guoyu

last: Chen

first: Qianqian

last: Guo


title: Mushroom body RNA-Sequencing of the honey bee brain

city: Princeton

first: Ian

middle: Michael

last: Traniello

state: NJ

address: Princeton University

department: Lewis-Sigler Insitute for Genomic Biology

country: USA

institute: Princeton University

summary: We explored brain gene expression associated with sociability and behavioral state

overall_design: Bees were subjected to automated behavioral tracking for ten days, after which they were subjected to dish-based behavioral assays

middle: M


title: Comparative transcriptome profiles of first-stage larvae and adult female Dracunculus medinensis (Guinea worm)

status: Public on Jul 19 2025

city: Sainte-Anne-de-Bellevue

first: Lucienne

last: Tritten

state: QC

address: 21111 Lakeshore Road

department: Institute of Parasitology

country: Canada

institute: McGill University

summary: Dracunculus medinensis, also called the Guinea worm, is a nematode that causes dracunculiasis, a debilitating neglected tropical disease in humans. The parasite is currently targeted by the global Guinea Worm Eradication Program (GWEP). Historically, GWEP in endemic countries have focused on interrupting transmission of the disease through intervention such as isolation and management of patients, health education, provision of improved water sources and promotion of filtering drinking water from unimproved water sources to avoid ingestion of the copepod intermediate host (IH) that may contain infectious third-stage larvae, and treatment of water sources to kill copepods. The recent shift of Guinea worm infections in animals - particularly domestic dogs - has introduced an additional challenge to the eradication program, underscoring the urgent need for diagnostics and therapeutics. Understanding the parasite biology and survival strategies in the mammalian host, the copepod IH, and fresh water is pivotal to identifying new control measures. Comparative transcriptomic analysis provides a powerful tool to uncover the molecular mechanisms underlying parasite survival and adaptations. Here, we compared the transcriptome of adult gravid female and first-stage larvae (L1), the stage infective for the copepod IH. Comparative transcriptomic analysis of two adult females and their L1 revealed an upregulation of genes involved in translation, transcription, and DNA repair in L1, likely reflecting adaptations essential for survival in freshwater and subsequent infection of copepods. Additionally, genes involved in cuticle formation were upregulated in adult females highlighting the role of cuticle integrity in retaining millions of L1 until the gravid female worm emerges. We identified highly expressed genes in the adult female that may represent promising candidates for diagnostic markers.This study provides novel insights into the biology of the Guinea worm by examining the transcriptome of L1 and adult female stages. These findings could support the development of novel diagnostics and therapeutics to advance the ongoing eradication effort.

overall_design: A ferret (Mustela furo) was experimentally infected at the University of Georgia (IACUC number: A2020 05-003) by feeding copepods infected with L3 stage of D. medinensis. Two subcutaneous female worms were recovered from the exposed ferret upon necropsy. Five pools of L1 stage were prepared from the two adult worms, counted, and stored at -80°C pending RNA extraction. Samples were thawed on ice and adult female tissues and L1 pools were homogenized with liquid N2 flash freezing and manual grinding using disposable pestles. Total RNA was extracted using the Total RNA Purification Kit (Norgen Biotek Corp., Thorold, ON, Canada) according to the manufacturer's instructions. RNA was quantified using QuantusTM Fluorometer (Promega, Madison, WI) and stored at -80°C until being shipped on dry ice to LC Sciences (LC Sciences, Houston, TX) for mRNA sequencing. mRNA sequencing was performed by LC Sciences Poly (A) RNA-seq Sequencing Service.

first: Hassan

last: Hakimi

first: Sabina

last: Beilstein

middle: J

last: Yabsley

first: Christopher

middle: A

last: Cleveland

first: Guilherme

middle: G

last: Verocai


title: Transcriptional programs regulated by MYCN in liver tumorigenesis

city: Yokohama

first: Xian-Yang

last: Qin

state: Kanagawa

address: 1-7-22 Suehiro, Tsurumi

country: Japan

institute: RIKEN Center for Integrative Medical Sciences

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Hepatocellular carcinoma (HCC) is a leading cause of cancer-related death, often diagnosed at advanced stages and characterized by high recurrence rates. While chronic liver inflammation and metabolic dysfunction are recognized contributors to tumorigenesis, the molecular mechanisms linking early microenvironmental stress to malignant transformation remain poorly understood. MYCN, a proto-oncogenic transcription factor, has emerged as a potential biomarker of cancer stemness, yet its functional role in hepatocarcinogenesis is unclear. Here, we applied CUT&RUN-seq analysis and integrated the data with RNA-seq to investigate the direct transcriptional impact of MYCN in liver tumorigenesis. Transcriptomic profiling revealed that MYCN-driven tumors exhibit features of human HCC subtypes enriched in stress-adaptive gene programs. We found genes with upstream MYCN binding showed significantly greater expression changes between tumor and non-tumor samples, suggesting that MYCN binding in promoter-proximal regions has a stronger influence on transcriptional regulation. Pathway analysis revealed significant enrichment in pathways related to cytoskeletal organization, cell motility, and membrane dynamics, all of which are central to intercellular interactions and tumor microenvironment remodeling, indicating that MYCN regulates pathways contributing to tumor microenvironment remodeling and cellular interactions.

overall_design: CUT&RUN-seq was performed on MYCN+AKT liver tumors and matched non-tumor liver tissues using an anti-MYCN antibody. Input control chromatin, prepared with a Covaris ultrasonicator, was used as a negative control.


title: Synergistic Effects of Red Light and Direct Current Electric Fields on Neurite Growth in 3D Neural Cell Cultures

city: Taipei

first: Yu Chiu

last: Kao

address: Academia Road

country: Taiwan

institute: Academia Sinica

summary: Both red-light illumination and direct-current electric fields (dcEFs) have independently been shown to promote neurite outgrowth in two-dimensional (2D) neural cell cultures. However, their combined effects in a three-dimensional (3D) culture environment remain unexplored. In this study, we examined the synergistic effects of red light and dcEFs on neurite extension in human neuroblastoma (SH-SY5Y) and mouse neuroblastoma (N2a) cells embedded within a 3D collagen gel matrix. Our results demonstrated that optimized dcEF stimulation and red-light exposure significantly enhanced neurite elongation and directional alignment. RNA sequencing further identified Neuropeptide Y (NPY) and its receptors as key mediators of these effects. Moreover, electrophysiological assessments revealed that neurons subjected to the combined stimulation exhibited enhanced functional maturation. These findings provide compelling evidence supporting the potential applications of red light and dcEFs in neural regeneration and repair.

overall_design: This study investigates the combined effects of direct current electric field (175 mV/mm, 3 hours) and red light (620 nm, 2 mW/cm², 45 hours) stimulation on neurite growth in 3D SH-SY5Y neural cell cultures. Cells were embedded in 3D collagen scaffolds at a concentration of 1 mg/mL, with a seeding density of 1×10⁶ cells/mL. Four experimental groups were included: (1) Control (no treatment), (2) dcEF only, (3) Red light only, and (4) Combined dcEF and red light. Total RNA was extracted after treatment. Two independent batches of RNA-seq libraries were generated using the same experimental design and were jointly analyzed to assess reproducibility and treatment effects. Each group included biological triplicates. Sequencing was performed using the Illumina NovaSeq X Plus platform with paired-end reads.

first: Yu-Chiu

first: Her-Bang

last: Huang

first: Chau-Hwang

last: Lee


title: BACH1 recruits STAT3 to enhance leukemia inhibitory factor receptor activity and augments the self-renewal capacity of mouse embryonic stem cells

first: Jieyu

state: Shanghai

address: 138 Yixueyuan Rd,

institute: fudan university

summary: The relationship between enhancer region chromatin accessibility of the Leukemia Inhibitory Factor Receptor (Lifr) gene and the regulation of self-renewal in mouse embryonic stem cells (mESCs)remains poorly understood. In this study, we elucidate the BACH1 enhances the activity of Lifr enhancer by recruiting STAT3 and activates the LIFR-STAT3 signaling pathway by promoting the LIFR expression, thereby maintaining the self-renewal of mESCs. Our results complement a novel insight into the regulatory role of BACH1 in maintaining the self-renewal capacity of mESCs.

overall_design: To elucidate the molecular mechanism underlying BACH1's influence on mESC pluripotency and differentiation, we conducted RNA-seq analysis on both WT mESCs and BACH1-KO mESCs.

first: Jinghua

last: Ma


title: Transcriptomic heterogeneity of quiescent neural stem cells underlies distinct reactivation routes and potential upon Notch signaling blockade

city: Paris

first: Laure

last: Bally-Cuif

address: 25 Rue du Docteur Roux

department: Developmental and stem cell biology department

country: France

institute: Institut Pasteur

summary: Adult Neural Stem Cells (NSCs) are glial cells that remain mostly quiescent but periodically activate to support neurogenesis throughout life in many species. It has progressively become clear that NSCs are heterogeneous and that the stem cell pool is in fact made up of distinct subpopulations. In zebrafish these subpopulations were recently characterized, identifying sets of molecular markers that can reliably identify subpopulations. Based on in sillico analysis and in particular the relative expression of gene sets associated either with deep quiescence or activation these subpopulations were predicted to possess distinct quiescence depths, however this prediction has not been challenged experimentally. The Notch pathway is known as a major regulator opromoting NSC quiescence in several species. Here, we used LY-411575, a potent Notch Pathway inhibitor, and treated zebrafish for 24h to push NSCs towards activation before sacrifing the fish and collecting the telencephalon, with the goal of comparing the transcriptomes of NSCs and their immediate progeny with or without LY treatment and determine whether predicted quiescence depth of NSC subpopulations does correlate with distinct responses to a pro-activation stimulus.

overall_design: Cells from the telencephalon of 12wpf Tg(sox2:gfp/+) fish bathed in LY-411575 for 48 hours were isolated by Fluorescence-Activated Cell Sorting (FACS). GFP positive cells were enriched to increase the relative proportion of radial glial cells and the resulting samples were processed for scRNA-seq.

first: David

last: Morizet

first: Isabelle

last: Foucher

first: Ilona

last: Mignerey

first: Alessandro

last: Alunni


title: BACH1 recruits STAT3 to enhance leukemia inhibitory factor receptor activity and augments the self-renewal capacity of mouse embryonic stem cells [ChIP-seq]

last: Guo

overall_design:
ChIP-seq of the BTB domain and CNC homolog 1 (BACH1) in mouse embryonic stem cells.
ChIP-seq of BACH1 in BACH1-KO mouse embryonic stem cells . Bach1-KO mESCs were generated by using CRISPR/Cas9 genome editing technology.
ChIP-seq of the histone modification H3K27ac in mouse embryonic stem cells.


title: The Neurolipid Atlas: a lipidomics resource for neurodegenerative diseases

status: Public on Jul 18 2025

city: Irvine

first: Ricardo

last: Miramontes

address: 845 Health Sciences Rd

institute: UC Irvine

summary: Lipid alterations in the brain have been implicated in many neurodegenerative diseases. To facilitate comparative lipidomic research across brain diseases here we establish a data common named the Neurolipid Atlas, that we have pre-populated with isogenic induced pluripotent stem cell (iPSC)-derived lipidomics data for different brain diseases. Additionally, the resource contains lipidomics data of human and mouse brain tissue. Leveraging multiple datasets, we demonstrate that iPSC-derived neurons, microglia, and astrocytes exhibit distinct lipid profiles that recapitulate in vivo lipotypes. Notably, the AD risk gene ApoE4 drives cholesterol ester (CE) accumulation specifically in human astrocytes, and we also observe CE accumulation in whole human AD brain lipidomics. Multi-omics interrogation of iPSC-derived astrocytes revealed that altered cholesterol metabolism plays a major role in astrocyte interferon-dependent pathways such as the immunoproteasome and major histocompatibility complex class I antigen presentation. Our data commons, available at neurolipidatlas.com, and allows for data deposition by the community and provides a user-friendly tool and knowledge base for a better understanding of lipid dyshomeostasis in neurodegenerative diseases.

overall_design: We performed bulk RNA sequencing on an isogenic pair of iPSC-derived ApoE3/3 and ApoE4/4 astrocytes.

first: Femke

last: Feringa

first: Sascha

last: J. Koppes-den Hertog

first: Lian

last: Wang

first: Rico

last: Derks

first: Iris

last: Kruijff

first: Lena

last: Erlebach

first: Jorin

last: Heijneman

first: Nadine

last: Pömpner

first: Niek

last: Blomberg

first: Damien

last: Olivier-Jimenez

first: Lill Eva

last: Johansen

first: Alexander

last: Cammack

first: Ashling

last: Giblin

first: Christina

middle: E

last: Toomey

first: Indigo

middle: V

last: Rose

first: Hebao

last: Yuan

first: Michael

last: Ward

first: Adrian

last: Isaacs

first: Martin

last: Kampmann

first: Deborah

last: Kronenberg-Versteeg

first: Tammaryn

last: Lashley

first: Leslie

last: Thompson

last: Ori

first: Yassene

last: Mohammed

last: Giera

first: Rik

last: van der Kant


title: RNA-seq of aging mouse skin treated with red light, compared to untreated controls

city: Guangzhou

first: Haocai

last: Chang

state: Guangdong

address: 55 Zhongshan Avenue West, Tianhe District

institute: South China Normal University

summary: Using an aging mouse model (C57BL/6, 18-20 months), we applied red light irradiation (8 J/cm², once daily for 28 consecutive days) to investigate its potential in alleviating skin degeneration. Gene expression changes were analyzed by sequencing, comparing the light-exposed and control groups, and the involved regulatory signaling pathways were further explored.

overall_design: Using an aging mouse model (C57BL/6, 18-20 months), we applied red light irradiation (8 J/cm², once daily for 28 consecutive days) to investigate its potential in alleviating skin degeneration. Gene expression changes were analyzed by sequencing, comparing the light-exposed and control groups.

first: Qi

last: Shen

first: Jing

last: Tong


title: Nuclear RPSA triggers R-loop accumulation to induce cell death against RNA viral infection

city: hangzhou

first: Ke

last: Jin

address: 866 Yuhangtang Rd

institute: zhejiang university

summary: While RNA viruses evade host immune responses by perturbing transcriptional and translational machinery, the host organism counteracts viral invasion through activation of regulated cell death pathways. However, the precise molecular mechanisms underlying host-initiated cell death activation in response to viral infection remain poorly characterized. By genome-wide screening, we identified ribosomal protein RPSA as a broad inducer of RNA virus replication-dependent cell death that confers antiviral protection. Rpsa conditional knockout mice exhibited heightened susceptibility to RNA viruses with attenuated cell death activation in infected tissues. Mechanistically, RNA virus infection triggers K29-linked polyubiquitination of RPSA, which strengthens its binding to the helicase domain of NAT10 and potently inhibits NAT10's helicase activity, thereby blocking R-loop resolution. The resulting R-loop accumulation drives DNA damage-mediated cell death execution. Our findings uncover a novel intranuclear "inside-out" R-loop-driven cell death pathway orchestrated by RPSA, providing fresh insights into virus-host interactions and identifying potential therapeutic targets for RNA viral infections.

overall_design: CUT&Tag of γ-H2AX in wild-type or RPSA-knockout A549 cells infected with IAV for 12 hours


title: Nuclear RPSA triggers R-loop accumulation to induce cell death against RNA viral infection [DRIP-seq]

overall_design: DRIP-seq in wild-type or RPSA-knocked A549 cells infected with IAV for 8 hours


title: The IFN-I-DUSP2-NFAT axis Limits Tumor Remodeling and Immunotherapy Response in Lung Cancer

city: Beijing

first: Xin

last: Zhang

state: Beijing

address: 38 Xueyuan Road

department: Institute of Systems Biomedicine

institute: Peking University

summary: Type I interferons (IFN-I) exert context-dependent effects in tumor microenvironment (TME), but their role in shaping immunotherapy response remains unclear. Here, we performed single-cell RNA sequencing of lung squamous cell carcinoma (LUSC) samples collected before and after immune checkpoint blockade (ICB), stratified by treatment outcome. In responders, ICB induced B cell and T follicular helper (Tfh) cell expansion, promoting the formation of tertiary lymphoid structure (TLS)-like niche. By contrast, non-responders exhibited sustained IFN-I signaling and accumulation of CD36⁺ SPP1⁺ tumor-associated macrophages (TAMs), which secreted IFN-I and disrupted lymphoid aggregation. At baseline, aberrant NFAT signaling in T cells marked a dysfunctional state. Mechanistically, IFN-I upregulated the phosphatase DUSP2 in pre-exhausted T cells, which dephosphorylated NFAT and promoted its nuclear localization. Nuclear NFAT transactivated genes encoding inhibitory receptors to reinforce T cell exhaustion. Deletion of Dusp2 restored CD8+ T cell function and Tfh-B cell interaction, improving response to PD-1 blockade. These findings identify a pathogenic IFN-I-DUSP2-NFAT axis that constrains immunotherapy efficacy in LUSC.

overall_design: Study of  tumor infiltration lymphocytes from LLC-bearing tumors in WT and Dusp2−/− mice using 10x scRNA-seq technologies.

first: Jinghui

last: Wang

first: Dan

last: Lu

first: Mengfan

last: Guo


title: LncRNA transcriptome profiling of three sheep skeletal muscles

city: Changchun

first: Xuesong

last: Shan

address: 2888 Xingcheng Street

department: College of Animal Science and Technology

institute: Jilin Agricultural University

summary: This study uses skeletal muscles from different parts of sheep as research materials to explore and compare the muscle fiber types and their characteristics in various parts of the sheep's skeletal muscles. By combining high-throughput sequencing analysis, it aims to identify lncRNAs and target genes related to sheep muscle fiber types and to elucidate their mechanisms.

overall_design: Six lamb samples of longissimus lumborum (LL), psoas major (PM), and soleus (SOL) muscles were collected from the left side of each carcass.

first: Dandan

last: Tan

first: Yang

last: Chen

first: Huaizhi

last: Jiang


title: An image-based transcriptomic atlas of the mouse gut reveals spatial, regional, and microbiota-dependent fine-tuning

city: Boston

first: Jeffrey

last: Moffitt

state: MA

address: 200 Longwood Ave

department: Program in Cellular and Molecular Medicine

institute: Boston Children's Hospital

summary: The gastrointestinal tract (GI) is a remarkably complex environment comprising a diverse array of cell types, microbes, and bioactive small molecules. To shed new light on how the gut is organized and senses its environment, we constructed a spatially resolved single-cell atlas of the mouse lower digestive tract using MERFISH with a specific focus on the thousands of receptors involved in small molecule sensation and microbial pattern recognition. We identified expected and novel cell types and charted their spatial organization across four GI regions. In addition, we discovered receptor expression gradients and heterogeneity cued by spatial location, and overall revealed divergent sensing capabilities across gut cell types, regions, and spatial contexts. In addition, we charted the remodeling of these features that occurs in the absence of the microbiome. Our atlas opens a new window into the molecular and cellular organization of gut sensation, which, given the pharmacological relevance of many receptors, may provide a clinically relevant resource.

overall_design: To provide an in-house measurement of gene expression in the SPF intestine as a validation for MERFISH results, distal colon tissue was harvested from C57BL/6NTac mice, flushed and rinsed with 4 mM ribonucleoside vanadyl complex (RVC; New England Biolabs [NEB] S1402S) in 1 x phosphate-buffered saline (PBS; ThermoFisher Scientific[Thermo] AM9625) at 4 oC. The tissue was then dissolved in TRIzol™ (Thermo 15596026) and RNA extraction was performed by the Direct-zol RNA Miniprep Plus kit (Zymo R2071), followed by low input library preparation and paired-end sequencing by Illumina NextSeq 500. To analyze these data, we used tophat (v2.1.1) and cufflinks (v2.2.1) with default parameters, aligning to the mouse genome (GRCm39).

first: Rosalind

last: Xu

middle: R


title: Metabolic regulation of host defense against influenza virus infection through sensing oxaloacetate

city: guangzhou

first: XING

last: HE

state: ( 86 ) CHINA

address: 中山大学南校区生命科学学院A334

institute: 生命科学学院

summary: Metabolic pathways determine cellular fate and function, however, the exact roles of metabolites in host immune responses against virus infection remain undefined. Here, we report that the metabolic pathways of oxaloacetate (OAA) are integrated with antiviral responses and OAA serves as a fundamental “cornerstone” to prime effective host resistance to the infection of influenza virus. MDH1 senses cellular OAA to undergo dimerization, thus functions as a scaffold to recruit the transcription factor ETS2 for phosphorylation by the kinase TAOK1 at serine 313. The phosphorylated ETS2 translocates into the nucleus and sustains the appropriate expression of TBK1 to provide broad-spectrum antiviral activity. OAA deficiency caused by ACLY genetic ablation decreases the antiviral immunity through MDH1–TAOK1–ETS2–TBK1 pathway in vivo, and makes mice more susceptible to lethal H1N1 virus infection. Our results uncover a previously unknown signaling pathway to maintain immune homeostasis by sensing cellular OAA, which links metabolism and antiviral innate immunity.

overall_design: To provide the insights of OAA in protecting against viral infection, we carried out RNA-sequencing (RNA-seq) analysis in PBMCs infected with H1N1 for 24 h, with or without DEOAA supplementation,no-supplemented group as control .

first: Shouheng

first: Xing

last: He


title: Developing a Prognostic Stratification Model Based on Glutathione Metabolism in Thyroid Cancer and Validating RRM2’s Tumor‑Promoting Role

city: Fuzhou

first: Bo Wang

state: Fujian province

address: 29 XinQuan Rd

department: Department of Thyroid and Parathyroid Surgery

institute: Fujian Medical University Union Hospital

summary: Glutathione (GSH), the most abundant antioxidant in cells, acts as free radical scavenger and detoxifying agent. Elevation of GSH metabolism protects tumor from damage of oxidant and even promotes tumor progression. However, the clinical value of GSH metabolism in thyroid cancer (THCA) remained largely unknown. Collecting large THCA cohort from The Cancer Genome Atlas (TCGA) database, we systematically analyzed molecular characteristics of 24 GSH metabolism-related enzymes. GSH metabolism related enzymes including RRM2 and IDH2 were upregulated in tumor samples and negatively correlated with disease free survival (DFS). To expand the application of the GSH metabolism related enzymes in prognostic prediction, we for the first time built a risk stratification model based on the GSH metabolism related enzymes via LASSO Cox regression algorithm and validated its prediction performance. Patients were categorized into high- and low-risk groups according to the median of risk score. As supposed, high-risk patients suffered from dismal DFS. The key molecule in this process, RRM2, was screened by correlation analysis,and it was experimentally confirmed that the abnormally high expression of RRM2, which acts as a pro-carcinogenic molecule, enhances the proliferation, invasion, and migration of THCA cells in vitro and in vivo.

overall_design: To investigate the effect of RRM2 overexpression on the transcriptional level of papillary thyroid cancer cells, mRNA sequencing analysis was performed on wild strain TPC-1 cells and RRM2 overexpression strain (RRM2-OE-TPC-1 cells) in this study. Each cell line was assayed in biological triplicate.Differential expression between two conditions was determined using DESeq2 (v1.20.0). P values were adjusted for multiple testing using the Benjamini–Hochberg procedure to control the false discovery rate (FDR). Genes with an adjusted P ≤ 0.05 were considered significantly differentially expressed.

first: Wei

last: Ao

first: Teng-Hong

last: Liu

first: De-Tao

last: Yin

first: Wen-Xin

last: Zhao


title: Spatial transcriptomic profiling of gene expression alterations following ACBP/DBI inhibition in a MASH-Driven HCC mouse model

city: PARIS

first: Guido

last: Kroemer

address: 15 rue de L'école de médecine

institute: Centre de Recherche des Cordeliers

summary: We identified ACBP/DBI as a critical regulator in the pathogenesis of hepatocellular carcinoma (HCC), with its inhibition significantly impairing hepatocarcinogenesis in MASH-driven HCC models. To further elucidate the underlying transcriptional mechanisms, we performed spatial transcriptomic analyses using formalin-fixed, paraffin-embedded (FFPE) liver tissues from the following two experimental models: (i) Western diet (WD) and CCl₄-treated mice with tamoxifen-inducible ACBP/DBI knockout (Dbi⁻/⁻ mice), with Dbi⁺/⁺ littermates serving as controls, after a total of 27 weeks; (ii) WD and CCl₄-treated mice immunized with either keyhole limpet hemocyanin (KLH) alone or KLH-ACBP conjugate, after a total of 34 weeks.

overall_design: (i) In the WD+CCl₄ model, Dbi⁺/⁺ and Dbi⁻/⁻ mice received intraperitoneal (i.p.) injections of tamoxifen at a dose of 75 mg/kg/day for five consecutive days to induce gene deletion. Three days after the final tamoxifen injection, mice were switched to a Western diet supplemented with high-sugar water (23.1 g/L D-fructose and 18.9 g/L D-glucose) and received weekly i.p. injections of carbon tetrachloride (CCl₄) for 26 weeks. (ii) In the WD+CCl₄ model with KLH/KLH-ACBP immunization, five-week-old mice were vaccinated intraperitoneally with a mixture of KLH/Montanide or KLH-ACBP/Montanide on days 0 (30 μg), 7 (30 μg), 14 (30 μg), and 21 (10 μg) to induce the generation of anti-ACBP autoantibodies. Following vaccination, mice were placed on a Western diet supplemented with high-sugar water (23.1 g/L D-fructose and 18.9 g/L D-glucose) and received weekly i.p. injections of CCl₄ for 30 weeks. At the end of the experimental period, liver tissues were collected, placed into cassettes, fixed in 4% paraformaldehyde for 24 hours, and subsequently transferred to 70% ethanol. Following standard dehydration and processing steps, tissues were embedded in paraffin for spatial transcriptomic analyses. All mice used in these experiments were male and of C57BL/6 genetic background.

first: Sijing

last: Li

first: Sylvère

last: Durand

first: Alexandra

last: Cerone


title: The probiotic Parabacteroides johnsonii ameliorates metabolic disorders through promoting BCAAs to BSCFAs conversion

first: Yimeng

address: China pharmoceutical university

institute: China pharmoceutical university

summary: The gut bacterium Parabacteroides spp. has been increasingly recognized for its therapeutic potential in treating metabolic disorders. However, the role of Parabacteroides johnsonii in metabolic disorders has never been reported. Here, we found that the abundance of P. johnsonii in the feces was negatively correlated with the blood glucose and lipid levels of obese patients. Oral administration of live P. johnsonii improved the metabolic dysfunction in high fat diet (HFD)-fed mice, accompanied by the alleviation of leaky gut and the systemic inflammation. P. johnsonii enhanced the catabolism of branched-chain amino acids (BCAAs) to branched-chain short-chain fatty acids (BSCFAs) in gut. Particularly, the conversion of valine to isobutyrate was correlated to the symptoms of obese patients. Isobutyrate intervention mirrored the favourable effects of P. johnsonii on HFD-fed mice. Isobutyrate increased H3K14 acetylation at Fgf1b promoters and activated its transcription through inhibition of HDAC3 in colon, thereby maintaining the intestinal barrier integrity. The natural product stachyose exhibited its anti-obesity effects by promoting the growth of P. johnsonii. Our findings provided mechanistic insights into the therapeutic potential of P. johnsonii, isobutyrate and stachyose in treating metabolic disorders.

overall_design: RNA-seq profiling of colon from HFD fed C57BL/6J mouse and HFD fed treating with isobutyrate mouse

first: Shujun

first: Haolu

last: Wang

first: Mengzhen

last: Si

first: Haixia

last: WU

first: Xiaodong

last: Wen

first: Jie

last: Yang


title: A Single-Cell Atlas Of Human Pediatric Liver Reveals Age-Related Hepatic Gene Signatures

city: Toronto

first: Rachel

middle: D

last: Edgar

state: ON

address: 101 College Street

department: Ajmera Transplant Centre

institute: University Health Network

summary: To investigate the spatial dynamics of immune cells in the liver, particularly myeloid cells, we utilized the Xenium spatial transcriptomics platform to examine gene zonation patterns in pediatric and adult livers. We explored the expression of 477 genes in two pediatric and three adult livers (one adult sampled 3 times, for a total of 7 Xenium samples). Our analysis revealed significant zonation of gene expression within Kupffer cells (KC-like). The zonation of KC-like marker genes suggests that the differential gene expression observed in the dissociated pediatric liver map may be due to shifts in the spatial organization of KC-like cells in the pediatric liver. These findings underscore the importance of spatial transcriptomics in understanding age-related differences in immune cell behavior within the liver and provide new insights into the complex spatial dynamics of myeloid cells in pediatric versus adult livers.

overall_design: 2 pediatric liver samples from 2 individuals; 2 adult liver samples from 2 individuals; 3 samples from one individual including a bile duct hamartoma

first: Gary

last: Bader

first: Sonya

last: MacParland


title: Discovery of a novel selective and cell-active N6-methyladenosine RNA demethylase ALKBH5 inhibitor

first: Xianyuan

address: No.132 East Ring Road

institute: Sun Yat-Sen University

summary: N6-methyladenosine (m6A), the most abundant methylation on mRNA, plays pivotal roles in regulating mRNA biological functions, resulting in affecting cell functions. ALKBH5, an m6A demethylase, has been found to be an oncogene in several cancer types, including triple negative breast cancer (TNBC). Here we reported a novel ALKBH5 inhibitor. Firstly, we utilized virtual screening to obtain ALKBH5 inhibitor candidates. Biochemical tests demonstrated that compound AG-690/34437009 could inhibit ALKBH5 with an IC50 value of 11.76 μM. After structure optimization, we acquired a more potent ALKBH5-specific inhibitor, compound W23-1006. Its IC50 value against ALKBH5 came down to 3.848 μM, representing a tripled increase in its inhibitory effect on ALKBH5 as well as roughly 30-fold and 8-fold stronger inhibitory activity than that against FTO and ALKBH3, respectively. Furthermore, we proved that W23-1006 formed a covalent bond with ALKBH5 C200. Cellular experiments demonstrated that W23-1006 could efficiently enhance the m6A level on fibronectin 1 (FN1) mRNA, leading to the strong suppression of TNBC cell migration. Moreover, it could significantly suppress TNBC tumor growth and metastasis in vivo. Collectively, our study developed the novel, selective and cell-active ALKBH5 inhibitor, W23-1006, which could be a potential therapeutic option for cancer such as TNBC treatment.

overall_design: RNA-seq in Human MDA-MB-231 WT treated with DMSO (n=2) and MDA-MB-231 WT treated with ALKBH5 inhibitor W23-1006 (n=2)

first: Hongsheng


title: Prolonged Glucagon Exposure Rewires Lipid Oxidation and Drives Diabetic Kidney Disease Progression

first: Jingwen

last: Chen

address: 1 XianNongTan Street, Xicheng District

institute: Institute of Materia Medica, Chinese Academy of Medical Sciences & Peking Union Medical （CAMS & PUMC）

summary: Diabetic kidney disease (DKD) is the leading cause of end-stage kidney disease (ESKD), and few treatment options are available today to prevent the progressive loss of renal function. Tubular abnormalities may precede glomerular pathology early and indicate the functional progression of DKD, however, pathological mechanisms that initiate tubular abnormalities are poorly understood. Here, we found that glucagon receptor (Gcgr) is specifically and highly expressed in proximal tubular cells (PTEC) of kidney. Glucagon injection exacerbated lipid accumulation, glycogen content, inflammation, fibrosis, and renal injury, along with morphology changes on proximal tubules, podocytes, glomerular basement membrane (GBM), and mitochondria in the early phase of DKD mice. Whereas, the specific knockdown or knockout of Gcgr in PTEC of kidney almost completely halted the development of DKD. In contrary to the effect of short-term glucagon stimulation on fatty acid oxidation, long-term glucagon exposure led to glucagon reversal in PTEC, which is characterized by reduced energy production and promoted lipogenesis, and this effect was through the Gcgr-PKA-Creb-mTOR pathway. Accordingly, anti-GCGR antibody treatment greatly blocked the pathogenesis of DKD induced by both type 2 and type 1 diabetes. Thus, our results revealed a novel role of glucagon/GCGR signaling in PTEC lipogenesis and DKD, and Gcgr would be a promising therapeutic drug target for the treatment of DKD.

overall_design: To investigate the lipogenesis function of glucagon in kidney PTEC, we established  Gcgr PTEC specific knockdown mice by shRNA.We then performed gene expression profilling analysis using data obtained from RNA-seq of 3 different groups of mice kidney.Comparative gene expression profilling analysis of RNA-seq data for control, Ctr shRNA and Gcgr shRNA group.

first: Pingping

first: Xingfeng


title: scRNAseq data of primary Sjögren's syndrome

city: changzhou

first: jun

last: huang

state: 江苏

summary: Labial gland tissues were obtained from three individuals diagnosed with pSS and three healthy donors. All participants were recruited from the Rheumatology and Immunology Department of Kunshan First People's Hospital during 2022.

overall_design:
Labial gland tissues were obtained from three pSS patients and three healthy donors

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Raw files for human/patient samples were not submitted to GEO due to concerns about submitting personally identifiable sequence data for open access.
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first: Jun

last: Huang


title: PD-L1/PD-1 checkpoint pathway regulates astrocyte morphogenesis and myelination during mouse brain development

first: Jianwei

last: Jiao

address: 1 Beichen West Road

department: State Key Laboratory of Reproductive Biology

institute: Institute of Zoology, Chinese Academy of Sciences

summary: To gain  futher insight into how astrocyte-derived PD1 regulates astrocyte morphogenesis and myelination, RNA-seq was used to analyze the genome-wide changes resulting from isolated astrocyte of P5 astrocyte-PD1 conditional knock out mice and littermate wild-type. Approximately  six thousand transcripts showed differential expression between the Pd1fl/fl and Pd1cKO-Aldh1l1 mice brain astrocyte, with a fold change ≥3 and p value <0.05.Geneontology analysis of the downregulated genes were enriched in terms related to negative regulation of  signal transduction, positive regulation of actin nucleation and upregulated genes were enriched in terms related to inflammatory response, positive regulation of ERK1 and ERK2 cascade and cell surface receptor signaling pathway. These results reflected astrocyte-PD1  plays  roles in astrocyte development.

overall_design: mRNA from  P5 isolated astrocyte of PD1fl/fl and PD1cKO-Cx3 mice was extracted. Specifically, Agilent 2100 Bioanalyze was used to quality controlled and quantified. then, mRNA was converted to cDNA and bound the library. RNA-sequencing analysis was used by the Illumina HiSeq 2500 platform in Annoroad Genomics

first: Yanyan

first: Shukui

last: Zhang

first: Tianyu


title: Next Generation Sequencing facilitates to identify the differential expression genes of MAIT cells treated by bile acids

city: Wuhan

first: xiufang

last: weng

address: 13# Hangkong Rd, Wuhan, Hubei

institute: Huazhong University of Science and Technology

summary: We obtained MAIT cells treated by indicated bile acids  to rperforme next-generation sequencing (NGS).  Illumina mRNA-seq sample preparation kit was used to perform paired-end library sequencing with Illumina HiSeq 2000 and sequence analysis was determined using the Illumina data analysis pipeline. Based on the comparison results，we performed the GO and KEGG pathway enrichment analysis. That might suggest the different status of HBV-infected liver from liver surgery(AST<40) and liver transplantation(AST>40).

overall_design: Differential gene expression between MAIT cells with/without the treatment of bile acids

first: Xiufang

last: Weng


title: Dual roles of dermal adipogenesis in initiating and resolving neutrophilic skin inflammation

city: Xiamen

first: Lingjuan

address: Xiangan South Street

institute: Xiamen University

summary: Dermal white adipose tissue (dWAT) is highly plastic and pivotal in host defense; however, its role in controlling neutrophil function remains unstudied. Here we found that Imiquimod-induced psoriatic skin inflammation prompted a dermal adipogenesis response, with preadipocyte expansion followed by differentiation into adipocytes. By single-cell RNAseq of the imiquimod skin samples, we found that dWAT was the primary site for initial neutrophil influx and activation, facilitated by interactions between neutrophils and preadipocytes via the IL1β-IL1R and CXCL1-CXCR2 pathways. IL1β-activated preadipocytes secreted CXCL1 and SAA3 to boost neutrophilic inflammation. Prolonged inflammation in preadipocytes led to their differentiation into early adipocytes, secreting anti-inflammatory lipids to resolve neutrophilic inflammation and restore homeostasis.

overall_design: Psoriasis-like skin inflammation was induced on mouse skin by daily topical application of imiquimod (IMQ) for 5 days. Dorsal skin biopsies were collected from 2 groups, including control and IMQ-treated adult mice (C57BL/6, 2 month, female). Skin samples were subjected to enzymatic digestion and dead cell removal procedures to isolate single viable cells for single-cell cDNA library prep and RNA-sequencing using the 10X Genomics Chromium system and Illumina Novaseq6000 platform.

first: Ling-juan

first: Rundong

last: Wu

first: Tian

last: Xia


title: PIEZO1 overexpression in hereditary hemorrhagic telangiectasia arteriovenous malformations

city: New Haven

first: Mark

last: Robinson

state: CT

address: 300 George St

department: Center of Molecular and Cellular Oncology

institute: Yale University

summary: Background: Hereditary hemorrhagic telangiectasia (HHT) is an inherited vascular disorder characterized by arteriovenous malformations (AVMs). Loss-of-function mutations in Activin receptor-like kinase 1 (ALK1) cause type 2 HHT and Alk1 knockout (KO) mice develop AVMs along with overactivation of VEGFR2/PI3K/AKT signaling. The full spectrum of signaling alterations resulting from ALK1 mutations remains unknown, and more effective and specific inhibitors to combat AVM formation in patients are needed.  Methods: Single-cell RNA sequencing of endothelial-specific Alk1 KO mouse retinas and controls was performed. Overexpression of fluid shear stress signaling signatures including the mechanosensitive ion channel PIEZO1 was confirmed in mouse and human HHT2 lesions. Genetic and pharmacological PIEZO1 inhibition was tested in Alk1 KO mice, along with downstream PIEZO1 signaling.  Results: A cluster of Alk1 mutant endothelial cells with altered arterio-venous identity overexpressed pathways related to fluid shear stress, hypoxia, inflammation, cell cycle and VEGFR2/PI3K/AKT signaling. Piezo1 deletion and pharmacological inhibition in Alk1-deficient mice mitigated AVM formation, whereas Piezo1 overexpression enhanced AVM formation induced by ALK1 ligand blockade. Mechanistically, PIEZO1 inhibition reduced elevated VEGFR2/AKT, ERK5-p62-KLF4, eNOS, hypoxia, proliferation and inflammation in ALK1 deficient endothelium.  Conclusions: PIEZO1 expression and signaling are elevated in HHT2. PIEZO1 blockade reduces AVM formation and alleviates cellular and molecular hallmarks of ALK1-deficient cells. This finding provides new insights into the mechanistic underpinnings of ALK1-related vascular diseases and identifies potential therapeutic targets to prevent AVMs.

first: Park

last: Hyojin

first: Anne

last: Eichmann


title: Gene expression profile at single cell level of primary and relapse mantle cell lymphoma (MCL)

city: Stockholm

first: Hui

last: Wan

address: Biomedicum, Solnavägen 9, floor 9D

country: Sweden

institute: Karolinska Institutet

summary: Mantle cell lymphoma (MCL) is a rare but often aggressive type of B-cell lymphoma with a high risk of relapse. To understand the mechanisms driving disease relapse, we employed single-cell RNA sequencing (scRNAseq) in 20 diagnosed/untreated (primary) and/or relapsed samples from 11 MCL patients.

overall_design:
scRNAseq was performed on 20 tumors from 11 MCL patients.

Submitter states: The raw scRNA-seq data generated in this study were deposited in the Swedish National Data Service (SND, accession DOI: https://doi.org/10.48723/kfy8-5r05). The data are not publicly available due to Swedish and EU data protection regulations and patient privacy concerns.

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Raw files for human/patient samples were not submitted to GEO due to concerns about submitting personally identifiable sequence data for open access.
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first: Weicheng

last: Ren

first: Qiang

last: Pan-Hammarström


title: The Dream and MEC Complexes reinforce SPR-5; MET-2 maternal reprogramming to maintain the Germline-Soma distinction  [lin-35 RNAseq]

city: kennesaw

first: Brandon

middle: Scott

last: Carpenter

state: GA

address: 370 Paulding Avenue, Room 119

department: Molecular and Cellular Biology

institute: Kennesaw State University

summary: Proper regulation of tissue-specific gene expression is essential for cell fate determination and development. In Caenorhabditis elegans, the distinction between germline and somatic cell fates is partially established through maternally inherited histone modifications. During gametogenesis, germline genes acquire transcription-coupled chromatin marks such as histone methylation, which are inherited by the zygote and must be reprogrammed at fertilization to prevent inappropriate germline gene expression in somatic tissues. This maternal reprogramming is mediated by histone-modifying enzymes, including the demethylase SPR-5/LSD1 and the H3K9 methyltransferase MET-2/SETDB1. Together, these enzymes limit DNA accessibility to transcriptional machinery, thereby resetting the chromatin landscape in te newly formed zygote. Failure to reprogram inherited histone methylation, as in spr-5; met-2 mutants, results in the ectopic expression of MES-4-targeted germline genes in somatic tissues, leading to developmental delay and sterility. Here, we investigated whether transcriptional repressor complexes—the DREAM and MEC NuRD complexes—cooperate with SPR-5 and MET-2 to specify germline versus soma. Loss of DREAM or MEC NuRD components alone causes somatic expression of germline genes. Strikingly, combined loss with spr-5; met-2 enhances developmental arrest at the L1 stage and exacerbates germline gene misexpression. By re analyzing previous published ChIP-seq data, we confirmed direct binding of MEP-1 and LIN-35 to these misregulated genes. Our findings demonstrate that maternal reprogramming and conserved chromatin repressor complexes act synergistically to repress germline transcription in somatic tissues, ensuring proper somatic development and preventing soma-to-germline transformation.

overall_design: RNA-seq analysis on spr-5; met-2 L1 progeny from hermaphorites fed either control (L4440) or lin-35 RNAi  to determine differentially expressed genes compared to L1 progeny from wild-type ( N2 strain) hermaphrodites fed control RNAi.

first: Sindy

last: Chavez

first: Jazmin

last: Dozier

first: Saahj

last: Gosrani

first: Sandra

last: Nguyen

first: Jovan

last: Brockett

first: Sarah

last: Blancher

first: Sydney

last: Morgan-Benitez

first: Juan

last: Rodriguez

first: Onur

last: Birol

first: Monica

last: Reeves

first: Karen

last: Schmeichel

first: David

last: Katz


title: Single cell transcriptome analysis of sham and bilateral renal ischemia-reperfusion injury (IRI)

city: Suita

first: Takashi

last: Shimbo

state: Osaka

address: 2-2 Yamadaoka

institute: Osaka university

summary: A rat model of bilateral IRI has been widely used to understand how IRI introduces and progresses the damages on kidney. The aim of this study is to reveal the molecular details of how this bilateral IRI impacts kidney cells. Here, we provide rat single-cell RNA-seq data which is a foundation to understand the IRI related kidney disease. It will support studies to clarify pathophysiology and to develop effective therapy exploiting similar rat renal disease models.

overall_design: Kidney mRNA profiles of 6-week-old sham and IRI rats


title: RNAseq analysis of Synph-293 cells

city: Suwon

first: Gwang

last: Lee

address: World cup-ro 206

country: South Korea

institute: Ajou university

summary: We report the gene expression profile in Synph-293 cells, which are stably FLAG-tagged synphilin-1 overexpressing HEK293 cells.

overall_design: To analyze the changes of gene expression induced by synphilin-1, HEK293 and Synph-293 cells stably FLAG-tagged synphilin-1 overexpressing were lysed, and then, the total RNA was extracted using TruSeq stranded mRNA Sample Preparation Kit (Illumina, CA, USA). The quality of RNA was assessed using an Agilent RNA 6000 Nano kit (Agilent Technologies, CA, USA). Oligo (dT) magnetic beads were used to purify and fragment the mRNAs from 1 μg of total RNA. The fragmented mRNAs were synthesized into double-stranded cDNA. cDNA libraries were purified using Blue Pippin (Sage Science, MA, USA) and amplified using PCR; the quality of these cDNA libraries was assessed using the Agilent High Sensitivity DNA Kit (Agilent Technologies). Subsequent cluster amplification of denatured templates was performed and an Illumina HiSeq2500 sequencer (Illumina) was used to perform sequencing.

first: Do

middle: H

last: Kwon


title: Gene expression profiles of Leigh syndrome mouse samples and Ndufs4 knockout human iPSCs before and after Pioglitazone treatment

city: Pok Fu Lam

first: Peikai

last: Chen

address: Sassoon Road 5

department: Faculty of Medicine

country: Hong Kong

institute: The University of Hong Kong

summary: Leigh syndrome is a progressive neurodegenerative disease caused by knockout (KO) of the Ndufs4 gene, leading to mitochondrial oxidative stress, inflammation and aberrant mitochondrial dynamics. Our previously study found that pioglitazone could suppresses neuroinflammation and oxidative stress both in vivo and in vitro. In this study, we investigate the gene expression of medulla, cortex and hippocampus from Ndufs4 KO mouse that had been treated with pioglitazone. Moreover, we analysis the RNA expression on pioglitazone treated Ndufs4 deficient human iPSCs.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: In total, 34 mouse and 11 human bulk RNA-seq samples were profiled. In the mouse, 18 samples were from the medulla (including 10 from knockout and 10 from WT), 8 from hippocampus (including 4 from knockout and 4 from WT), and 8 from cortex (including 4 from knockout and 4 from WT). In each of these  6 mouse groups (tissue and genotype), half of the samples were treated with pioglitazone and the others without. In the human, the samples were based on neural progenitor cells (NPCs) derived from hESC-ES1 with or without NDUFS4 single or double knockout.

first: Xiaoxian

last: Zhang

first: Qizhou

last: Lian

first: Ling


title: Airway Epithelial SARS-CoV-2 Infectious and Repair Responses: Relationships to Age, Sex, and Post-COVID Pulmonary Syndromes

city: Chapel Hill

first: Hong

last: Dang

state: North Carolina

address: 125 Mason Farm Rd, Cb#7248

department: Marsico Lung Institute

institute: University of North Carolina at Chapel Hill

summary: This study investigated the acute and reparative responses as a function of age and sex in primary human bronchial epithelial (HBE) cultures over a 14-day post-SARS-CoV-2 infection (dpi) protocol. Methods: Bulk RNA-seq was performed on well-differentiated human bronchial epithelial (HBE) cell culture lysates with/without SARS-CoV-2 inoculation. Results: SARS-SoV-2 infection peaked at 3 dpi with an ~ 2 log titer suppression at 14 dpi. Airway epithelia repaired to an abnormal mucus metaplastic/inflammatory state that reflected potentially beneficial and adverse consequences at 14 dpi. No age- or sex-dependent effects on SARS-CoV-2 infection were detected. Conclusions: Human airway epithelial repair post-SARS-CoV-2 is prolonged and incomplete in vitro over 14 days, and persistently abnormal repair may contribute to phenotypes of people with long-COVID pulmonary syndrome.

overall_design:
HBE cells were maintained >4 weeks on air-liquid interface culture until they are well-ifferentiated. Then the cells were inoculated with SARS-CoV-2 (G614D strain) apically at MON=0.5 for two hours. Cell lysates for bulk RNA-seq were obtained at 1-, 3- 7- and 14-day post inoculation from mock- and virus-inoculated cutures.
All samples from GSE210223, which came from 14 donors, were combined with additional samples from 9 donors (GSE299837), and were processed together from the raw FASTQ files to generate combined processed gene expression data and were analyzed as a whole set, which achieved balanced design with regard to age group, and sex. All final statistical analysis of the combined data included batch as a covariate. Therefore, all samples from GSE210223 were re-used in this study.

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The table below lists GEO accessions reused/reanalyzed for this study.
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first: Caitlin

last: Edwards

first: Takafumi

last: Kato

first: Boris

last: Reidel

first: Camille

last: Ehre

first: Rita

last: Meganck

first: Yu

last: Mikami

first: Takanori

last: Asakura

first: Padraig

last: Hawkins

first: Charles

last: Esther Jr

first: Minako

last: Furusho

first: Jeffrey

middle: L

last: Myers

first: Kristine

last: Konopka

first: Raymond

last: Pickles

first: Sabra

last: Klein

first: Scott

last: Randell

first: Wanda

middle: K

last: O'Neal

first: Ralph

middle: S

last: Baric

first: Richard

middle: C

last: Boucher


title: Epigenetic metabolite lipid nanoparticles alleviate venous thrombosis via bone marrow reprogramming

city: Cleveland

first: Andrei

last: Maiseyeu

state: Ohio

address: 10900 Euclid Ave

department: Medicine

institute: Case Western Reserve University

summary: Targeting coagulation cascade is a mainstay approach to therapy of thrombosis. One of the most prevalent complications of anticoagulation is a significant bleeding risk that can result in hospitalization. Recent studies on immunothrombosis (i.e. inflammation-linked thrombosis) proposed myeloid cells, especially neutrophils, to actively participate in thrombus formation through neutrophil extracellular traps (NETosis) and activation of inflammatory pathways. Here, we developed lipid nanoparticles (LNPs) with coagulation cascade-independent action that target neutrophils to alleviate venous thrombosis. A single intravenous dose of immunomodulatory metabolite itaconate (ITA)-bearing LNPs (ITA-LNPs) targeted >90% of bone marrow-resident neutrophils, but not macrophages or T lymphocytes. ITA-LNPs significantly diminished inflammation in cultured neutrophils and macrophages and improved survival in the mouse model of endotoxemia. When tested in an inferior vena cava ligation model of deep vein thrombosis, ITA-LNPs decreased the size and weight of thrombi as compared to control LNPs (Ctrl-LNPs). In addition, the thrombi from ITA-LNPs injected mice had significantly reduced neutrophil infiltration, decreased NETosis and interleukin-1 beta (IL-1β) expression. Intriguingly, one of the mechanisms through which this occurred was histone H4K12ac deacetylation, resulting in chromatin condensation and transcriptional repression of inflammatory genes and transcription factors involved in DNA damage response. Finally, we found that ITA-LNPs were hemostatically safe and neither targeted nor activated platelets in vivo. In sum, our work explores an LNP technology with an epigenetic mode of action serving as an anti-immunothrombotic therapy that could improve clinical outcomes without additional hemorrhagic risk.

overall_design: RNA-seq was performed on primary, bone marrow-derived neutrophils isolated from C57BL/6 male mice 24 h after injection with control or ITA-LNPs followed by stimulation with lipopolisaccaride (100 ng/mL) in culture for 3 h.


title: RIP-seq: screening targeted-genes of RNA binding protein MEX3C

city: Guangzhou

first: Yun

middle: yun

last: Xiao

address: 651 Dongfeng East Road

institute: Sun Yat-sen University Cancer Center

summary:
The potential binding mRNA of RNA-binding protein MEX3C in hepatocellular carcinoma cells is still unknown. To identify MEX3C targeted genes in HCC, we performed RNA immunoprecipitation and high-throughput sequencing (RIP-SEQ) in MEX3C-Flag overexpressing MHCC97H cells.
RNA immunoprecipitation and high-throughput sequencing (RI-SEQ) were performed on MHCC97H cells overexpressing MEX3C-Flag.

overall_design: Yunyun, Xiao

first: Yue

last: Li

first: Dongni

last: Shi


title: KLF2 may suppress chicken adipogenesis by enhancing the GATA2 transcription

status: Public on Jul 17 2025

city: Shihezi

first: Zhiwei

last: Zhang

state: Xinjiang

address: A101-3,Xing 3 Building

department: Histology and Embryology

institute: Shihezi University

summary: Kruppel-like factor 2 (KLF2) acts as an essential modulator of adipogenesis; nevertheless, the exact molecular pathways governing its role remain uncharacterized. This investigation characterized the expression profile of KLF2 in human adipose tissue and elucidated the mechanisms by which KLF2 modulates adipogenesis in avian models. The KLF2 mRNA expression in human adipose tissues was substantial and exhibited significant heterogeneity influenced by gender and anatomical location, suggesting that KLF2 regulated adipose tissue functionality. In chicken preadipocytes ICP1, the KLF2 protein increased at the first 24 h of oleate-induced adipogenic differentiation and subsequently decreased over time. KLF2 facilitated the cellular proliferation of ICP1 cells (P<0.05). Moreover, KLF2 overexpression inhibited differentiation of chicken preadipocytes ICP1 (P<0.05). KLF2 also increased the density of mitochondria and mitochondrial cristae in ICP1 cells. RNA seq and luciferase reporter assays demonstrated that KLF2 suppressed the expression of genes in PPAR signaling pathway in ICP1 cells. Additionally, KLF2 interacted with the promoter region of chicken GATA2 and upregulated GATA2 transcription in ICP1 cells. In summary, KLF2 potentially influences the PPAR signaling cascade, mitochondrial bioenergetics, and GATA2 gene expression to enhance the proliferation of avian preadipocytes while inhibiting their differentiation.

overall_design: The ICP1 cells were inoculated into 6-well plates, and when the cells reached 60%-80% confluence, the given plasmids of pCMV-myc or pCMV-myc-KLF2 were transfected into the cells using ExFect® Transfection Reagent (#T101-02, Vazyme, Nanjing, China).After the transfection for 48 h, the ICP1 cells were harvested using TRIzol™ Reagent (#15596026, Invitrogen, Carlsbad, CA) for subsequent RNA sequencing.

first: Tingting

first: Qin

last: Gao

first: Yuechan

last: Chen


title: Polycomb repression works without Siesta [TRIP]

city: Umeå

first: Anastasiya

last: Yushkova

address: Försörjningsvägen 2A, Byggnad 6L, NUS

department: Molecular biology

institute: Umeå University

summary: Polycomb group proteins are essential for epigenetic repression of developmental genes. They act as multi-subunit complexes whose biochemical functions are yet to be fully characterised. One of the complexes, canonical Polycomb Repressive Complex 1 (PRC1), acts as an E3 ligase, depositing a single ubiquitin molecule on histone H2A. It can also bind to histone H3 tri-methylated at lysine 27 (H3K27me3), which is critical to propagate the repressed state of regulated genes epigenetically. The RING1 subunit of PRC1, responsible for the ubiquitin ligase activity, forms other complexes. These complexes can ubiquitylate H2A but cannot bind H3K27me3. It was proposed that H2A ubiquitylation is an essential part of the repressive mechanism and that variant RING1 complexes evolved from ancestral canonical PRC1 to diversify the Polycomb system and enable the evolution of vertebrate-specific traits. However, systematic tracing of genes encoding subunits of distinct variant RING1 complexes argues that these complexes appeared early in animal evolution and likely had functions unrelated to epigenetic repression. To address this problem, we leveraged the power of Drosophila genetics to discover that canonical PRC1 and variant RING1 complexes monoubiquitylate H2A across distinct genomic regions. We found that the sole Drosophila PCGF protein specific for variant RING1 complexes, which we named Siesta, is not required for epigenetic repression of homeotic genes, but controls larval locomotion independently of H2A ubiquitylation. Exploiting the division of labour between PRC1 and Siesta-RING1 complexes, we employed thousands of reporters integrated in parallel to conclude that H2A ubiquitylation has no major repressive effect on transcription. We propose that variant RING1 complexes are not part of the Polycomb regulatory system and that the current PRC1 nomenclature needs revision.

overall_design: TRIP experiments in cultured Drosophila cells. Two experiments started from independently grown cell cultures were performed for each genetic background and condition.

first: Tatyana

last: Kahn

first: Andres

last: Garrido

first: Maria

last: Kim

first: Alexander

last: Glotov

first: Sweda

last: Sreekumar

first: Jan

last: Larsson

first: Yuri

middle: B

last: Schwartz


title: Single-cell RNA Sequencing Reveals Trem2⁺ Macrophages Enriched in the Scalp Induce Tc17 Cell Activation to Promote Psoriatic Inflammation

city: Wuxi

first: Qitao

state: Jiangsu

address: No. 299, Qingyang Road, Liangxi District

department: Department of Dermatology

institute: The Affiliated Wuxi People's Hospital of Nanjing Medical University

summary: Background: Scalp psoriasis presents distinct clinical features and treatment resistance compared to lesions on other body sites, yet its immune landscape remains poorly characterized. Methods: We performed single-cell RNA sequencing (scRNA-seq) on CD45⁺ immune cells from scalp and body plaque lesions of psoriasis patients and healthy controls. A total of 41,438 immune cells were analyzed. Downstream analyses included clustering, gene set enrichment, pseudotime trajectory inference, and cell–cell interaction modeling. Multiplex immunofluorescence was used to validate spatial co-localization. Results: Scalp psoriasis lesions exhibited a higher abundance of IL17⁺ CD8⁺ tissue-resident memory T (Tc17) cells, which co-expressed IFNG and lipid transporter FATP2 (SLC27A2). Pseudotime analysis revealed a trajectory from IL7R⁺ Trm cells toward Tc17 cells, especially enriched in the scalp. Trem2⁺ macrophages in scalp lesions showed increased expression of inflammatory mediators and MHC-I molecules. CellChat revealed enhanced MHC-I–mediated interactions between Trem2⁺ macrophages and Tc17 cells in the scalp. These interactions were confirmed by immunofluorescence, demonstrating co-localization of FATP2⁺ Tc17 and Trem2⁺ macrophages around sebaceous units. Conclusions: This study defines a scalp-specific pathogenic axis involving Trem2⁺ macrophages and FATP2⁺ Tc17 cells, potentially explaining the localization and persistence of inflammation in scalp psoriasis. Targeting lipid metabolism or specific cell–cell interactions may provide new therapeutic avenues for treatment-resistant scalp psoriasis.

overall_design: Single-cell RNA sequencing of isolated CD45⁺ immune cells from both scalp and body lesions of psoriasis (n = 3)， and single-cell RNA sequencing of scalp of healthy controls (n = 5).

first: Linwei

last: Wei

first: Yanjun

last: Liu

first: Yuqian

first: Xiaoqin

last: Jia

first: Yanhua

first: Xufeng

last: Du


title: Semaglutide in the treatment of MOSH alter the methylation pattern of genes related to glycolipid metabolism

city: Shenzhen

first: Yunchong

last: Guo

address: Zhenyuan Road, Xinhu Street, Guangming District

institute: The seventh affiliated hospital，Sun Yat-sen University

type: Non-coding RNA profiling by high throughput sequencing

summary: Secondary hypogonadism related to male obesity (MOSH) is a common disease among male patients with severe obesity. Semaglutide has a remarkable effect in weight loss treatment. To explore the epigenetic change mechanism of Semaglutide in the treatment of MOSH, this study, through DNA methylation and miRNA sequencing, discovered the significant epigenetic changes that occurred during the treatment of MOSH with Semaglutide.

overall_design: The  miRNA sequencing platform is DNBSEQ. We conducted  miRNA sequencing on three groups of samples (control group, MOSH patients, and MOSH patients treated with Semaglutide).


title: Polycomb repression works without Siesta [ChIP]

overall_design: ChIP-seq experiments in cultured Drosophila cells. Two experiments started from independently grown cell cultures were performed for each genetic background and antibody.


title: Comparison of K562 Chronic Myeloid Leukemia cells with resistant counterparts

city: Seoul

first: Marc

last: Diederich

address: Gwanak-ro, Gwanak-gu, 1

department: College of Pharmacy

institute: Seoul National University

summary: We analyzed differential gene expression by comparing K562-R (drug-resistant) and K562 (wild-type) cells. This supplementary analysis provides valuable context by revealing transcriptional changes associated with acquired resistance, highlighting biological processes that may contribute to the drug-resistant phenotype in chronic myeloid leukemia (CML).

overall_design: mRNA-sequencing of K-562 cells compared to resistant K562-R cells (3 independent biological replicates).

first: Haeun

last: Yang

first: Vladimir

last: Li

first: Michael

last: Schnekenburger


title: Barcoded Rabies In Situ Connectomics for high-throughput reconstruction of neural circuits

city: London

last: Becalick

address: 1 Midland Road

country: United Kingdom

institute: The Francis Crick Institute

summary: Sequencing of oligonucleotide barcodes holds promise as a high-throughput approach for reconstructing synaptic connectivity at scale. Rabies viruses can act as a vehicle for barcode transmission, thanks to their ability to spread between synaptically connected cells. However, applying barcoded rabies viruses to map synaptic connections in vivo has proved challenging. Here, we develop Barcoded Rabies In Situ Connectomics (BRISC) for high-throughput connectivity mapping in the mouse brain. To ensure that the majority of post-synaptic "starter" neurons are uniquely labeled with distinct barcode sequences, we first generated libraries of rabies viruses with sufficient diversity to label >1000 neurons uniquely. To minimize the probability of barcode transmission between starter neurons, we developed a strategy to tightly control their density. We then applied BRISC to map inputs of single neurons in the primary visual cortex (V1). Using in situ sequencing, we read out the expression of viral barcodes in rabies-infected neurons, while preserving spatial information. We then matched barcode sequences between starter and presynaptic neurons, mapping the inputs of 385 neurons and identifying 7,814 putative synaptic connections. The resulting connectivity matrix revealed layer- and cell-type-specific local connectivity rules and topographic organization of long-range inputs to V1. These results show that BRISC can simultaneously resolve the synaptic connectivity of hundreds of neurons while preserving spatial information, enabling reconstruction of neural circuits at an unprecedented scale.

overall_design: UMI-tagged amplicon sequencing of barcoded rabies genome plasmid and barcoded rabies viral library samples, collected from purified supercoiled plasmid preps and concentrated pseudotyped rabies virus preps respectively.

first: Antonin

last: Blot

first: Molly

last: Strom

first: Petr

last: Znamenskiy


title: Spatial transcriptomic profiling uncovers the molecular effects of the neurotoxicant polychlorinated biphenyls (PCBs) in the brains of adult mice

city: Iowa City

first: Snehajyoti

last: Chatterjee

state: IA

address: 169 Newton Road

department: Neuroscience & Pharmacology

institute: University of Iowa

summary: Utilizing spatial transcripomics approach (10x Genomics Visium v2), this study assess the molecular effects of polychlorinated biphenyls (PCB) on the brain.

overall_design: To investigate the effects of polychlorinated biphenyls (PCB) on memory and transcriptomic profiles, we exposed adult male C57BL/6J mice daily to a synthetic PCB mixture. After seven weeks of exposure, the mice were assessed in a spatial object recognition task (SOR) to evaluate long-term spatial memory. Brain sections from PCB and vehicle-exposed male mice, collected one hour after the memory test session, were processed for spatial transcriptomic analyses using the Visium platform.

first: Budhaditya

last: Basu

first: Nicole

last: Breese

first: Sal

last: Lombardi

first: Hui

last: Wang

first: Xueshu

first: Destiny

last: Tiburcio

first: Zachary

last: Niemasz

first: Stacy

last: Beyer

first: Laura

last: Dean

first: Rachel

middle: F

last: Marek

first: Michal

last: Toborek

first: Hans-Joachim

last: Lehmler


title: Dasatinib Remodels the Tumor Microenvironment and Sensitizes Small Cell Lung Cancer to Immunotherapy [shYES1]

city: Pamplona

first: Alfonso

last: Calvo

state: Navarra

address: Avenida Pío XII 55

country: Spain

institute: CIMA Universidad de Navarra

summary: Effective strategies to reinvigorate the immune system are needed to improve outcomes in small cell lung cancer (SCLC). Targeting Src family kinases with dasatinib (Dasa) can elicit immunomodulatory effects in some cancer types. Here, we explored the potential of combining Dasa with immune checkpoint blockade in SCLC. While the SCLC models were refractory to anti-PD-1 or anti-CTLA4 monotherapy, anti-PD-1 and anti-CTLA4 combination immunotherapy (ITc) induced a significant antitumor response. Further, the Dasa+ITc combination was superior to ITc or Dasa alone. Dasa+ITc activity was mediated by CD4+ T cells, MHC-II+ antigen presenting cells (APCs), and natural killer (NK) cells, as depletion of these populations impeded the combination treatment antitumor efficacy. Increased tumor infiltration of CD4+ and CD8+ T cells, NK cells, M1-like macrophages, and CD11c+ APCs and a reduction of regulatory T cells (Tregs) and M2-like macrophages were found in Dasa+ITc-treated mice. Dasa increased CCL5 in NK cells and reduced Treg cell conversion from CD4+ lymphocytes. Dasa+ITc therapy elicited robust antitumor efficacy in 3D co-cultures of immune and SCLC cells. In vivo experiments showed that CCL5 was necessary for the Dasa+ITc response. In SCLC immunotherapy-treated patients, a gene signature including CD4, CIITA, and tumor mutational burden predicted good prognosis. On-treatment CCL5 plasma levels were increased only in patients with long progression-free survival, and pre-treatment secretomics identified cytokines related to myeloid cells significantly associated with poor prognosis. In summary, combining Dasa with immunotherapy represents a strategy to treat SCLC, with CCL5 as a cytokine that could serve to monitor response.

overall_design: In this experiment, we silenced YES1 in the SCLC human cell line H209, using  shRNAs shRNAs targeting YES1 (sh-YES1) were cloned into the lentiviral Tet-pLKO-puro plasmid (Addgene #21915). shRNA against GFP (shGFP) was used as control and lentiviral particles for both shRNAs were produced.

first: A

first: E

last: Redin

last: Guruceaga

first: L

last: Montuenga


title: Dasatinib Remodels the Tumor Microenvironment and Sensitizes Small Cell Lung Cancer to Immunotherapy [DASAITC]

overall_design: Murine RP (Rb1/Tp53 KO) cells were subcutaneously injected in one flank of 8-week-old female F1 mice (resulting from C57Bl/6j x 129S1/Sv cross). When tumor volume reached approximately 50 mm3, mice were randomized and treated with: Dasatinib (Dasa) at 30 mg/kg daily, anti-PD-1+anti-CTLA4 (100 microg/mouse for each antibody), or the combination Dasa+anti-PD-1+anti-CTLA4 (Dasa+ITc). Control animals were treated with vehicle.

first: N

last: Otegui

first: S

last: Leon

first: D

last: Serrano


title: Dasatinib Remodels the Tumor Microenvironment and Sensitizes Small Cell Lung Cancer to Immunotherapy [PD1CTLA4]

overall_design: Murine RP (Rb1/Tp53 KO) cells were subcutaneously injected in one flank of 8-week-old female F1 mice (resulting from C57Bl/6j x 129S1/Sv cross). When tumor volume reached approximately 50 mm3, mice were randomized and treated with the following drug combination: Dasatinib (Dasa) at 30 mg/kg daily+anti-PD-1+anti-CTLA4 (100 microg/mouse for each antibody). Control animals were treated with vehicle.


title: Endothelin B receptor inhibition rescues aging-dependent neuronal regenerative decline [snRNA-seq]

city: St. Louis

first: Valeria

last: Cavalli

state: MO

address: 1 Bookings Dr.

institute: Washington University in St. Louis

summary: Peripheral sensory neurons regenerate their axons after injury to regain function, but this ability declines with age. The mechanisms behind this decline are not fully understood. While excessive production of endothelin 1 (ET-1), a potent vasoconstrictor, is linked to many diseases that increase with age, the role of ET-1 and its receptors in axon regeneration is unknown. Using single cell RNA sequencing, we show that satellite glial cells (SGCs), which completely envelop the sensory neuron soma residing in the dorsal root ganglia (DRG), express the endothelin B receptor (ETBR), while ET-1 is expressed by endothelial cells. Inhibition of ETBR ex-vivo in DRG explant cultures improves axon growth in both adult and aged conditions. In vivo, treatment with the FDA-approved compound, Bosentan, improves axon regeneration and reverses the age-dependent decrease in axonal regenerative capacity. Single-nuclei RNA sequencing and electron microscopy analyses reveal a decreased abundance of SGCs in aged mice compared to adult mice. Additionally, the decreased expression of connexin 43 (Cx43) in SGCs in aged mice after nerve injury is partially rescued by Bosentan treatment. These results reveal that inhibiting ETBR function enhances axon regeneration and rescues the age-dependent decrease in axonal regenerative capacity, providing a potential avenue for future therapies.

overall_design: L3, L4, and L5 DRGs from adult (2-3mo) and aged (12mo) WT (C57BL/6) mice. Following nucleus extraction, samples were analyzed using PIP-seq snRNA-seq.

first: Rui

last: Feng

first: Sarah

last: Rosen

first: Irshad

last: Ansari

first: Sebastian

last: John

first: Michael

last: Thomsen

first: Oshri

last: Avraham

first: Cedric

last: Geoffroy


title: Endothelin B receptor inhibition rescues aging-dependent neuronal regenerative decline [scRNA-seq]

overall_design: L4 and L5 DRGs from adult WT (C57BL/6) mice were collected, dissociated into a single cell suspension, and analyzed using 10X Genomics scRNA-seq.


title: An improved nuclei isolation protocol from leaf tissue for single-cell transcriptomics

city: Gainesville

first: Kelly

last: Balmant

state: FL

address: 1253 Fifield Hall, Room 2204

department: Horticultural Sciences

institute: University of Florida

summary: We developed an alternative method for isolating nuclei to be utilized in scRNA-seq experiments from Zea mays leaves with reduced chloroplast contamination. By effectively removing chloroplasts during the FACS step of our protocol, using the autofluorescence from the chloroplasts, we achieved improved alignment of reads to the genome and transcriptome. Our enhanced protocol offers a valuable solution for applying snRNA-seq in tissues with a high content of chloroplasts.

overall_design: After nuclei isolation following Conde et al (2021), we used a FACS strategy for clean-up and enrichment of the nuclei using a BD FACSAriaTM IIU/III upgraded cell sorter. We used a double-filter strategy to negatively select autofluorescent chloroplast and positively select DAPI-stained nuclei (Fig 1). The Peridinin-Chlorophyll-Protein (PerCP) filter, excited by the 488 nm blue laser and captured with a 670/30 nm bandpass filter, was used to remove the events that emitted in this range. After this, the DAPI-positive population was selected according to emission in the 450/50 nm bandpass filter and then based on size and granularity using the forward versus side scatter (FSC vs SSC) plot. Finally, the selected population corresponding to nuclei was sorted, aiming for 40,000 nuclei for library preparation using 10X Genomics sc-RNAseq kit.


title: Direct sequencing of 5-methylcytosine and 5-hydroxymethylcytosine at single-base resolution unravels their distinct roles in Alzheimer’s disease [BS-Seq]

city: Shanghai

first: Zixin

last: Wang

address: Siping Road

institute: Tongji University

type: Methylation profiling by high throughput sequencing

summary: 5-hydroxymethylcytosine (5hmC) constitutes up to 20% of 5-methylcytosine (5mC) in mammalian cells. As conventional bisulfite sequencing is unable to distinguish 5hmC from 5mC, several methods have been proposed to detect 5hmC and infer 5mC levels by subtracting 5hmC from whole-genome bisulfite sequencing data. This subtraction approach, however, can lead to the underestimation of 5mC levels at sites with high 5hmC abundance. Here, we present two orthogonal methods: CMD1-Deaminase sequencing and CMD1-TET bisulfite sequencing, which enable the direct and independent detection of 5mC. In combination with ACE-seq or TAB-seq, these techniques facilitate an accurate distinction between 5mC and 5hmC, eliminating the need for subtraction. Using these approaches, we generated a comprehensive landscape of 5mC and 5hmC in the hippocampus of the Alzheimer's disease (AD) model mice. Notably, while 5hmC levels were substantially reduced in the AD mice, 5mC levels remained largely unchanged, suggesting a critical role for 5hmC as an independent epigenetic mark in the pathogenesis of AD.

overall_design: CD-seq、CT-seq、ACE-seq and TAB-seq in hippocampus of WT and Alzheimer's disease model mice.

first: Faying

last: Chen

first: Baodan

last: He

first: Fanchen

first: Jiaxue

last: Cha

first: Yu

last: Song

first: Weiying

last: Meng

first: Yutao

last: Fu

first: Wanyue

last: Zou

first: Shuxia

last: Sun

first: Keyao

last: Zhao

first: Haoming

last: Jiang

first: Zhiyan

first: Yujun

last: Hou

first: Jiejun

last: Shi

first: Jianhuang

last: Xue


title: PROX1 Controls Cellular Patterning, Innervation and Differentiation in the Mouse Organ of Corti

city: Atlanta

first: Michael

last: Deans

address: 201 Dowman Drive Atlanta

institute: Emory University School of Medicine

summary: The organ of Corti is divided into functional compartments responsible for hearing or cochlear amplification. A medial compartment containing inner hair cells innervated by Type I spiral ganglion neurons and a lateral compartment containing outer hair cells innervated by Type II spiral ganglion neurons. Supporting cells also differ, with lateral compartment pillar cells and Deiters’ cells developing specialized cellular structures to support outer hair cell electromotility. We bred organ of Corti-restricted Prox1 conditional knockout mice to study lateral compartment development because PROX1 is the first transcription factor expressed strictly in lateral compartment supporting cells. In the absence of Prox1, supporting cell numbers increased without corresponding changes in outer hair cells, and they appear incompletely differentiated based on morphological criteria. Outer hair cell number was not impacted but innervation was disrupted with many afferent neurons turning incorrectly towards the cochlear apex. RNAseq revealed no changes in gene expression that could account for the innervation phenotype. Therefore, we propose that PROX1 promotes pillar and Deiters’ cell differentiation and organization that has secondary effects on innervation but is not required for compartment specification.

overall_design: RNA-seq profiling of micro-dissected organ of Corti from wildtype and conditional Prox1 knock-out (Emx2-cre; floxed-Prox1) mice at P0

first: Shubham

last: Kale

first: Dimitri

last: Traenkner

first: Ellison

last: Goodrich

first: Satish

last: Ghimire

first: Thomas

middle: M

last: Coate


title: Direct sequencing of 5-methylcytosine and 5-hydroxymethylcytosine at single-base resolution unravels their distinct roles in Alzheimer’s disease [BS-Seq mESC]

first: Zixin

last: Wang

overall_design: CD-seq and CT-seq of mESC genomic DNA.

first: Faying

last: Chen

first: Baodan

last: He

first: Fanchen

first: Jiaxue

last: Cha

first: Yu


title: Poxvirus attack of anti-viral defense pathways unleashes an effector-triggered NF-κB response [RNAseq_MYXV_screen]

city: Berkeley

first: Brenna

last: Remick

state: CA

address: 415 Weill Hall

department: Molecular and Cell Biology

institute: University of California, Berkeley

summary: Effector-triggered immunity (ETI) is a form of pathogen sensing that involves detection of pathogen-encoded virulence factors or “effectors”. To discover novel ETI pathways in mammals, we developed a screening approach in which individual virulence factors are expressed in human monocytes and transcriptional responses are assessed by RNA-seq. Using this approach, we identify a poxvirus effector, myxoma virus M3.1, which elicits an anti-viral NF-κB response. We find that NF-κB is unleashed by an ETI pathway that senses M3.1 attack of two anti-viral complexes: ZAP and TBK1. NF-κΒ activation occurs because the proteins inhibited by M3.1—N4BP1, ZC3H12A, and TBK1—are negative regulators of NF-κB. Our results illustrate how negative regulators can function as pathogen sensors and establish a systematic approach for the discovery of ETI pathways.

overall_design: Bulk RNA barcoding and sequencing of BLaER1 monocytes expressing myxoma virus open reading frames (ORFs).

first: Russell

last: Vance


title: An IFN/STAT1/CYBB Axis Defines Protective Plasmacytoid DC to Neutrophil Crosstalk in Aspergillus fumigatus Infected mice [CUT&RUN]

city: New York

first: YAHUI

last: GUO

state: NY

address: 407 East 68th street, ZRC1641

department: HOPP

institute: Memorial Sloan-Kettering Cancer Center (MSKCC)

summary: Aspergillus fumigatus is the most common cause of invasive aspergillosis (IA), a devastating infection in immunocompromised patients. Plasmacytoid dendritic cells (pDCs) regulate host defense against IA by enhancing neutrophil antifungal properties in the lung. Here, we define the pDC activation trajectory during A. fumigatus infection and the molecular events that underlie the protective pDC - neutrophil crosstalk. Fungus-induced pDC activation begins after bone marrow egress and results in pDC-dependent regulation of lung type I and type III IFN levels. These pDC-derived products act on type I and type III IFN receptor-expressing neutrophils and control neutrophil fungicidal activity and reactive oxygen species production via STAT1 signaling in a cell-intrinsic manner. Mechanistically, neutrophil STAT1 signaling regulates the transcription and expression of Cybb, which encodes one of five NADPH oxidase subunits. Thus, pDCs regulate sterilizing immunity against inhaled molds by controlling the local expression of a subunit required for functional NADPH oxidase assembly and activity in the lung.

overall_design: lung pDCs and neutrophils sorted from indicated genotype mice, at naïve or infected (72h pi) status

first: Yahui

last: Guo

first: Mariano

last: Aufiero

first: Kathleen

last: Mills

first: Simon

last: Grassmann

first: Hyunu

last: Kim

first: Paul

last: Zumbo

first: Mergim

last: Gjonbalaj

first: Audrey

last: Billips

first: Katrina

last: Mar

first: Yao

last: Yu

first: Doron

last: Betel

first: Joseph

last: Sun

first: Tobias

last: Hohl

first: Laura

last: Tirado

first: Lena

last: Heung

first: Amariliz

last: Rivera


title: Adipocyte FMO3-derived TMAO induces WAT dysfunction and metabolic disorders by promoting inflammasome activation in ageing

city: Kowloon

first: Thashma

middle: Pemmanda

last: Ganapathy

address: 11 Yuk Choi Road

department: Health Technology and Information

institute: The Hong Kong Polytechnic University

summary: Circulating trimethylamine N-oxide (TMAO) participates in the pathogenesis of cardio-metabolic diseases, with hepatic flavin-containing monooxygenase 3 (FMO3) originally regarded as the primary source of TMAO production. Here, we demonstrate that white adipose tissue (WAT) expressed FMO3 and its derived metabolic product TMAO causatively contribute to the systemic elevation of TMAO levels, WAT dysfunction, and metabolic diseases in ageing. We showed that FMO3 expression and TMAO levels are upregulated in WAT of naturally ageing animals and human subjects, as well as in a DNA damage-induced senescent adipocyte model, but not in the liver. This upregulation is due to p53 activation in mice and could be mitigated by calorie restriction in humans. Adipocyte-specific ablation of FMO3 attenuates TMAO accumulation in WAT and circulation, leading to enhanced glucose metabolism, energy homeostasis, and lipid regulation in aged and high-fat diet-induced obese mice. Transcriptomic and histological analysis link these metabolic improvements to reduced senescence, fibrosis, and inflammation in WAT as well as a decrease in adipose-resident macrophages. LiP-small molecule mapping (LiP-SMap) analysis identified numerous novel TMAO-interacting proteins implicated in inflammasome activation within white adipocytes and macrophages. Mechanistically, TMAO facilitates inflammasome activation by binding to the inflammasome adaptor protein apoptosis-associated speck-like protein containing A CARD (ASC), thereby inducing its expression, caspase-1 activation, and subsequent interleukin-1β (IL-1β) production. Our findings uncover a pivotal role for adipocyte FMO3 in modulating TMAO production and WAT dysfunction by promoting inflammasome activation in ageing via an autocrine and paracrine manner.

overall_design: To investigate the role of adipo-FMO3 during aging, we isolated epididymal adipose tissue (eWAT) from 105-week-old wild-type (WT) and adipo-FMO3 knockout (KO) mice on a C57BL/6 background. The isolated tissues were subjected to transcriptome sequencing to analyse gene expression profiles and elucidate the functional implications of adipo-FMO3 in the aging process.

middle: P

first: Juntao

last: Yuan

first: Kelvin

last: Wu

first: Moinul

last: Hoque

first: Melody

middle: Y

last: Ho

first: Baomin

last: Wang

first: Xiaomu

last: Li

first: Wang

last: Kai

first: Martin

last: Wabitsch

first: Qizhou

last: Lin

first: Yongxia

last: Niu

first: Yuyan

last: Zhu

first: Kenneth

last: Cheng


title: An IFN/STAT1/CYBB Axis Defines Protective Plasmacytoid DC to Neutrophil Crosstalk in Aspergillus fumigatus Infected mice [RNA-seq]

first: YAHUI

last: GUO

first: Yahui

last: Guo

first: Mariano

middle: A

last: Aufiero

first: Kathleen

last: Mills

first: Simon

last: Grassmann

first: Hyunu

last: Kim

first: Paul

last: Zumbo

first: Mergim

last: Gjonbalaj

first: Audrey

last: Billips

first: Katrina

last: Mar

first: Yao

last: Yu

first: Doron

last: Betel

first: Joseph

last: Sun

first: Tobias

last: Hohl

middle: E


title: Local metabolism and signaling of classic and 11-oxyandrogens reveal a prognostic axis in high-grade serous ovarian cancer

city: Ljubljana

first: Marija

last: Gjorgoska

state: Outside North America

address: Vrazov trg 2

country: Slovenia

institute: Institute of Biochemistry and Molecular Genetics, Faculty of Medicine, University of Ljubljana

summary: Background: High-grade serous ovarian cancer (HGSOC) is the most lethal gynaecological malignancy, exhibiting marked heterogeneity that complicates treatment. The implications of intratumoral androgen metabolism and signalling, particularly involving 11-oxygenated androgens, in HGSOC remains poorly understood. Methods: We analysed expression of key androgen-metabolizing enzymes and androgen receptor (AR) in relation to tumor site, chemotherapy response, and survival using two public HGSOC cohorts. Quantitative gene expression and steroid metabolism assays upon incubation with classic and 11-oxyandrogen precursors were performed in six HGSOC cell lines and one normal ovarian epithelial line. Untargeted transcriptomic and metabolomic profiling were performed to assess cellular responses to potent classic and 11-oxygenated androgens in the AR-positive OVSAHO cell line. Results: Differential expression of steroid-metabolizing enzymes and AR were observed between primary and metastatic tumors and chemo-sensitive and chemo-resistant tumors. Higher intra-tumoral expression of HSD11B2, HSD17B2, and AR correlated with improved survival, whereas elevated PAPSS1/2 and HSD17B4 predicted poorer outcomes. In vitro, classic androgen precursors showed limited conversion to bioactive androgens and did not generate 11-oxyandrogens. In contrast, 11-oxyandrogen precursors were efficiently converted to the potent AR agonist 11KT in chemo-sensitive HGSOC cell lines, but not in chemo-refractory or control lines. Potent classic and 11-oxyandrogens induced stress-adaptive and proliferative transcriptional responses and reduced intracellular amino acid content. These changes were associated with a trend toward reduced cell proliferation. Conclusions: Our findings offer mechanistic insight into local androgen and 11-oxyandrogen metabolism and signalling in HGSOC and reveal steroid-induced cellular vulnerabilities that may synergize with chemotherapy or molecularly targeted therapies. These results further support the therapeutic potential of modulating steroid pathways in HGSOC.

overall_design: RNA-seq profiling of wild type OVSAHO cells after incubation with classic androgens (10 nM testosterone and dihydrotestosterone) and 11-oxyandrogens (10 nM 11-keto-testosterone and 11-keto-dihydrotestosterone) for 72h.

first: Klemen

last: Pečnik

first: Nika

last: Marolt

first: Janez

last: Plavec

first: Tea

last: L. Rižner


title: CXCL5 inhibition suppresses gastric mixed neuroendocrine-non-neuroendocrine neoplasms arising from transformed Pou2f3+ epithelium

city: Fuzhou

first: Shanqiang

last: Zhou

state: Fujian

address: 32 No. 29 Xinquan Road

department: Department of Gastric Surgery

institute: Fujian Medical University Union Hospital

summary: To explore the possibility that tumor development relies on a shared oncogenic facilitator rather than on specific SOX2 or SOX9 expression patterns, we performed bulk RNA sequencing of gastric tumors from Pou2f3-CreERT; Rb1fl/fl; Trp53fl/fl; LSL-MycT58A  mice.

overall_design: RNA-seq profiling of the gastric normal tissues and tumors from antrum, corpus, the greater curvature and the lesser curvature of cardia from Pou2f3-CreERT; Rb1fl/fl; Trp53fl/fl; LSL-MycT58A mice, 5 weeks following tamoxifen induction.

first: Mi

last: Lin

first: Qiyue

last: Chen

first: Guangtan

first: Ping

last: Li

first: Jianxian

first: Jianwen

last: Que


title: Pou2f3⁺ Cells Contain Multilineage Potential Progenitors as Revealed by scRNA-seq Analysis

summary: To further study the lineage potential of Pou2f3⁺ cells, we performed single-cell RNA sequencing (scRNA-seq) of lineage-labeled cells isolated from the gastric tissues of Pou2f3-CreERT; Rosa26-tdTomato mice. Lineage-labeled gastric epithelial cells (EPCAM+tdT+) at 21dpi were purified with flow cytometry. We also included an equal mixture of EPCAM⁺ tdT⁻ cells for comparative analysis to define reference epithelial subsets.

overall_design: Three Pou2f3-CreERT; Rosa26-tdTomato transgenic mice were induced with tamoxifen for 2 weeks. TdTomato+ cells were sorted by FACS and pooled from multiple mice. We employed a strategy of mixing TdTomato+ cells with  TdTomato−, EpCAM+, CD45− gastric epithelial cells isolated from the same tissues at a 1:1 ratio during sample preparation for scRNA-seq analysis.


title: Hexokinase 2 is an RNA-binding protein that regulates mRNA translation independently of glycolysis and induces melanoma cell proliferation

city: Orsay

first: Céline

middle: M.

last: Labbé

address: Rue Henri Becquerel

institute: Institut Curie

summary: Although metabolic benefits of glycolysis have been extensively described in tumor cells, the extra-metabolic functions linked to this energetic pathway in tumor growth and cell proliferation have not been clearly established yet. Recently, some key glycolytic enzymes, such as GAPDH and PKM2, were reported to regulate mRNA translation. Translational control of gene expression is considered as a critical effector in cancer biology, representing a highly promising area of research. Here, we report that Hexokinase 2 (HK2), a glucose kinase that catalyzes the first step of glycolysis at the outer mitochondrial membrane (OMM), is an RNA-binding protein (RBP) that regulates mRNA translation in melanoma cell lines. Polysome profiling experiments followed by RNA sequencing indicate that the translational regulation exerted by HK2 is partly independent of the metabolic status or the glycolytic pathway. We found that HK2 specifically regulates translation of the mRNA encoding SOX10, a transcription factor implicated in the regulation of tumor initiation, maintenance, and progression in melanoma. RNA-protein interaction assays, including crosslinking immunoprecipitation (CLIP), indicate that HK2 is an RBP whose interaction with RNA is independent of its enzymatic activity, its ability to bind glucose or its association with the OMM. HK2 directly interacts with the 5’ untranslated region (5’UTR) of the SOX10 mRNA through a stem-loop RNA secondary structure. Using RNA-protein proximity ligation assays and a fluorescence-based ribosome-bound mRNA mapping method (RIBOmap), we found that high glucose conditions, which promotes the release of HK2 from the OMM, induces an increase in HK2-SOX10 mRNA interaction and SOX10 mRNA translation in the cytoplasm. We further showed that HK2-dependent SOX10 mRNA translation is involved in melanoma cell proliferation and colony formation. Collectively, our data highlight a non-metabolic function of HK2 acting as an RBP and translation regulator.

overall_design: We performed transcriptome and translatome analysis (RNA-Seq) on A375 melanoma cells cultured in galactose- or glucose-containing medium depleted or not of the glycolytic enzymes HK2, GAPDH, PKM2.

first: Ana

last: Dian

first: Lucilla

last: Fabbri

first: Antoine

last: Moya-Plana

first: Giuseppina

last: Claps

first: Juliana

last: Ferreira

first: Virginie

last: Quidville

first: Sylvain

last: Martineau

first: Dorothée

last: Baille

first: Laetitia

last: Besse

first: Cédric

last: Messaoudi

first: Séverine

last: Roy

last: Raynal

last: Baulande

first: Wael

last: Rabeh

first: Caroline

last: Robert

first: Stéphan

last: Vagner