title: The effect of growth differentiation factor 11 on sepsis-associated acute kidney injury

city: Wenzhou

first: Hongwei

last: Wang

address: No. 322 Nanbaixiang Street

institute: The First Affiliated Hospital of Wenzhou Medical University

summary: Patients with sepsis often experience severe renal dysfunction and damage and accelerate to end-stage renal failure with high mortality, which currently lacks effective therapeutic approaches. Growth differentiation factor 11 (GDF11), a member of the transforming growth factor-β (TGF-β) superfamily, has been proven to have therapeutic properties for a variety of acute and chronic inflammatory diseases. However, the role of GDF11 in sepsis-associated acute kidney injury (SAKI) remains elusive. Here, we aimed to investigate the role of GDF11 in SAKI and identify the signaling pathways modulated by GDF11. In a mouse model of cecal ligation and puncture (CLP)-induced SAKI, GDF11 was found to be highly expressed in tubular epithelial cells and macrophages in the kidney. Moreover, gene silencing of GDF11 using adeno-associated virus (AAV) aggravated renal dysfunction, increased tubular damage, and augmented renal apoptosis in CLP-induced SAKI mice. In contrast, replenishment of recombinant GDF11 (rGDF11) significantly mitigated these adverse effects. Further investigation revealed that GDF11 activated the nuclear factor erythroid 2-related factor 2 (Nrf2)-regulated antioxidative pathways, mainly through induction of peroxisome proliferator-activated receptor-γ coactivator (PGC)-1α expression, which, in turn, inhibited overactivated inflammation and coagulation both in vivo and in vitro. Additionally, these beneficial effects of GDF11 were largely diminished by AAV-mediated PGC-1α knockdown and depletion of Nrf2 in CLP-induced SAKI mice. Overall, these findings demonstrate that GDF11 represents a promising therapeutic approach for SAKI and reveal the important role of PGC-1α/Nrf2 signaling in GDF11-mediated renal protection during SAKI.

overall_design: Renal mRNA profiles of 8-week old cecal ligation and puncture (CLP)-treated C57BL/6J wild type (WT) mice (CLP group) and CLP plus recombinant GDF11 (rGDF11)-treated C57BL/6J WT mice (CLP+GDF11 group) were generated by deep sequencing, in triplicate, using the Illumina NovaSeq 6000 platform. rGDF11 was dissolved in PBS and administered intraperitoneally to mice post-CLP at doses of 500μg/kg. Kidney tissues were collected 24 h after CLP surgery.

first: Minmin

last: Wu

first: Mianmian

last: Zhu

first: Yuying

last: Qin

first: Keqi

first: Chenyu

first: Rongrong

last: Zhang


title: Comprehensive Transcriptome Profiling Unveils the Oncolytic Mechanisms of Newcastle Disease Virus on Colonic Carcinoma

status: Public on Sep 03 2025

city: Xi'an

first: Hai

last: Li

address: No.76 Yanta West Road

department: Department of Pathogenic Microbiology and Immunology

country: China

institute: Xi'an Jiaotong University

type: Expression profiling by high throughput sequencing

summary: Viral oncolysis is supposed to be a promising cancer treatment method because of its good tolerability and durable anti-tumor effects. Compared with other oncolytic viruses, newcastle disease virus (NDV) has some distinct advantages, namely, NDV is a RNA virus which can not recombine with the host genome, making it safer compared to DNA viruses and retroviruses; NDV can induce syncytium formation, allowing the virus to spread between cells without exposure to host neutralizing antibodies; because of hexamer genetic code rule, NDV genome has an lower rate of gene recombination and higher genetic stability. This study systematically investigates the oncolytic mechanism of NDV against colonic carcinoma on transcriptional level and provides theoretical foundations for developing NDV-based therapies targeting colon cancer.

overall_design: Human colonic carcinoma cell line HCT116 cells are infected with oncolytic NDV Lasota strain at a MOI of 5. The transcription profils of infected and uninfected cells were generated and compared.


title: Transcriptomic Responses to Neuromuscular Electrical Stimulation (NMES) in Muscle, Brain and Plasma Exosomes in WT and Klotho Deficient Mice [mRNA]

city: Pittsburgh

first: Iliya

last: Lefterov

state: PA

address: 130 De Soto St

department: Environmental and Occupational Health

country: USA

institute: University of Pittsburgh

summary: Previous studies indicate extracellular vesicles (EVs) play a role in cellular communication which may be impacted by neuromuscular electrical stimulation (NMES), a noninvasive approach to improve daily living and functional motor activities. Therefore, we utilized NMES to stimulate the tibialis anterior of WT and KlHET mice and evaluated transcriptomic profiles of muscle tissue, brain tissue, and plasma-derived EVs. Muscle mRNA indicate that genes related to metabolic processes are upregulated in response to NMES in but have little overlap in WT and KlHET NMES versus control.  Brain mRNA in WT shows upregulation of several genes related to blood flow and cell adhesion processes while KlHET shows downregulation in cell adhesion processes and immune function. In plasma-derived EVs, little overlap in ncRNA, with the exception of let-7d-5p which regulates insulin signaling targets and immune responses, was present. Findings indicate local and distal transcriptomic metabolic effects of NMES are mediated by KLOTHO deficiency.

overall_design: NMES was administered to using Empi 300 PV, Boston, USA at 9mA under 2.5% isoflurane anesthesia for 2 sets of 10 consecutive stimulations per side. A total of 5 sessions were performed. Following sample collection, isolation of brain, muscle, and plasma RNA took place. Extracted muscle and brain RNA was sent to Novogene Co. for total RNA library generation on NovaSeq X Plus Series (PE150). Brain and muscle mRNA data were aligned with Rsubread (v 2.16.1), annotated with the org.Mm.eg.db package (v 3.19.1) and analyzed with edgeR (v 4.0.16). Gene ontology (GO) terms were generated in DAVID with a p-value cut-off of <0.05 followed by a fold-change cut-off of >0.5. Plasma EV ncRNA libraries were sequenced by the UPMC Genome Center (Pittsburgh, PA) on NextSeq 2000. ncRNA alignment results were then checked by STAR (v 2.5.3a), analyzed with COMPSRA (v 1.0.3) and DESeq2 (v 1.42.1). RNA analysis from DAVID and REVIGO Gene Ontology were visualized in GraphPad Prism, and RStudio. ncRNA library select gene targets were analyzed in TargetScanMouse 8.0 and were visualized using STRING.

first: Catherine

middle: A

last: Cavanaugh

first: Amanda

middle: E

last: Moore

first: Xuebao

first: Nicholas

middle: F

last: Fitz

first: Radosveta

last: Koldamova


title: Transcriptomic Responses to Neuromuscular Electrical Stimulation (NMES) in Muscle, Brain and Plasma Exosomes in WT and Klotho Deficient Mice [ncRNA]

type: Non-coding RNA profiling by high throughput sequencing


title: Regulating the Cell Differentiation Trajectory of Progenitor Cells in Adipose Tissue Fibrosis

city: Los Angeles

first: LI

state: CA

address: 650 Charles E Young Dr S, A2-237

department: Medicine Cardiology

institute: University of California, Los Angeles

summary: Adipose fibrosis signifies pathological remodeling of white adipose tissue (WAT) associated with insulin resistance, diabetes, and cardiovascular disease. Matrix Gla protein (MGP) balances bone morphogenic protein (BMP) and transforming growth factors (TGF) β signaling but has an unclear role in WAT. Our study showed that Mgp gene deletion promotes fibrosis and impairs adipogenesis in mice with global or platelet-derived growth factor receptor α (Pdgfrα)-Cre-mediated Mgp deletion in APCs. Single cell RNA sequencing showed two new adipose-derived stem cells (ASC) populations, ASC1 and ASC4, emerging after Mgp deletion. Trajectory analysis found that ASC1 and ASC4 were derived from ASC2, which normally undergo adipogenesis but instead had diverted to fibrogenic differentiation. All three ASCs expressed Pdgfrα and dipeptidyl peptidase 4 (Dpp4). Signaling studies in mice with Pdgfrα-Cre-mediated Mgp deletion using SB431542 or sitagliptin reduced TGFβ activity, the size of the PDGFRα+, DPP4+ cell population and fibrogenesis. Dysregulation of PDGFRα+, DPP4+ cells may signal early adipose fibrosis.

overall_design: Stromal vascular fraction (SVF) cells from inguinal (subcutaneous) white adipose tissue were were isolated from Mgp-KO, wild-type, and pdgfra-cre mediated Mgp deletion mice, followed by enzymatic digestion. After dead and immuno cells were removed by DAPI and Cd45 staining using FACS, live cells were sent for scRNA-sequencing.

first: Li

first: Kristina

last: Bostrom


title: Attenuation of the M gene in Vesicular Stomatitis Virus Vector

city: Xiamen

first: yee

last: chen

state: Fujian

address: Xiangannanlu

department: School of Public Health

institute: Xiamen University

summary: Recombinant vesicular stomatitis virus (rVSV) is a promising viral vaccine vector for addressing the COVID-19 pandemic. Inducing mucosal immunity via the intranasal route is an ideal strategy for rVSV-based vaccines, but it requires extremely stringent safety standards. In this study, we constructed two rVSV variants with amino acid mutations in their M protein: rVSV-M2 with M33A/M51R mutations and rVSV-M4 with M33A/M51R/V221F/S226R mutations, and developed COVID-19 vaccines based on these attenuated vectors. By comparing viral replication capacity, intranasal immunization, intracranial injection, and blood cell counts, we demonstrated that the M protein mutation variants exhibit significant attenuation effects both in vitro and in vivo. Moreover, preliminary investigations into the mechanisms of virus attenuation revealed that these attenuated viruses can induce a stronger type I interferon response while reducing inflammation compared to the wild-type rVSV. We developed three candidate vaccines against SARS-CoV-2 using wild-type rVSV (rVSV-JN.1) and the two variants (rVSV-M2-JN.1 and rVSV-M4-JN.1). Our results confirmed that rVSV-M2-JN.1 and rVSV-M4-JN.1 retain strong immunogenicity while enhancing safety in hamsters. In summary, the rVSV variants with M protein mutations represent promising candidate vectors for mucosal vaccines and warrant further investigation.

overall_design: Comparative gene expression analysis and enrichment analysis of 6 weeks-8 weeks female mouse muscle RNA-seq data under type I interferon response at 12h

first: Mengqi

last: Chang

first: Hui

last: Huang


title: Genome-wide inter-chromosomal contacts of rDNA units detected by 4C procedure in human Mel Z melanoma cells.

city: Moscow

first: Nickolai

last: Tchurikov

address: 32, Vavilova str.

department: Department of Epigenetic Mechanisms of Gene Expression Regulation

country: Russia

institute: Engelhardt Institute of Molecular Biology

summary: 4C-rDNA procedure was used for analysis of whole-genomic inter-chromosomal contacts of rDNA units in human Mel Z melanoma cells grown either on the plastic or Matrigel.

overall_design: Analysis of rDNA genome-wide contacts in Mel Z melanoma cells using 4C approach.

first: Yuri

middle: V

last: Kravatsky


title: TLR9/NF-κB-Mediated Dendritic Cell Activation by Neutrophil Extracellular Traps Drives Pathogenesis in Experimental Cerebral Malaria

city: Shenyang

first: Yan

last: Zhao

address: China Medical University, Shenbei New District, Shenyang City, Liaoning Province

department: Department of Immunology

institute: China Medical University

summary: Cerebral malaria (CM), the most severe complication of Plasmodium infection, accounts for the majority of malaria-associated mortality. The experimental cerebral malaria (ECM) model, recapitulating key neuropathological features of human CM, provides critical insights into disease mechanisms. While neutrophils demonstrate dual roles in Plasmodium control and immunopathology, their early dynamics in ECM remain unclear. Here, we found that early neutrophil depletion in Plasmodium berghei ANKA (PbA)-infected mice significantly prolongs survival, preserves blood-brain barrier integrity, and reduces brain infiltration and activation of CD8⁺ T cells. Mechanistically, PbA infection induces neutrophil extracellular traps (NETs) formation. The DNA component of NETs activates dendritic cells (DCs) through the TLR9/NF-κB signaling pathway, leading to upregulated expression of costimulatory molecules and proinflammatory cytokines that potentiate CD8⁺ T cell effector functions. Inhibition of NET formation alleviates ECM progression. These findings establish the critical role of the NETs-TLR9-NF-κB-DC-CD8⁺ T cell axis in ECM pathogenesis, providing novel insights into the immunopathogenic mechanisms of CM.

overall_design: RNA-Seq Profiling of the spleens of normal C57BL/6 mice and C57BL/6 mice infected with Plasmodium berghei ANKA for the fifth day.

first: Shijie

last: Yao

first: Chao

first: Qing

first: Mengna

last: Sun

first: Qinghui

last: Wang

last: Zheng

first: Yaming

last: Cao


title: Transcriptomic analysis of Cr(VI)-induced changes in C2C12 cells during myogenic differentiation

city: New York

first: Sun Young

last: Park

address: 341 East 25th Street

institute: NYU Grossman School of Medicine

summary: Hexavalent chromium [Cr(VI)] is an environmental toxicant extensively used in a variety of industrial processes including chrome plating, leather tanning, textile manufacturing, aircraft production, and stainless-steel production. Our previous study showed that exposure to Cr(VI) impaired C2C12 myogenic differentiation in a dose-dependent manner, yet the transcriptional mechanisms underlying Cr(VI)-induced disruption of myogenesis remains poorly understood. Here, we performed bulk RNA-sequencing on C2C12 myoblasts undergoing differentiation in the presence of 0, 2, or 5  µM of Cr(VI). Differential gene expression analysis demonstrated a dose- and time-dependent increase in transcriptional dysregulation. Fuzzy c-means clustering identified 12 distinct gene expression patterns, with Clusters 3, 10, and 12 showing significant overlap with Cr(VI)-regulated genes. Functional enrichment analyses revealed Cr(VI) disrupts genes involved in early-stage cell cycle regulation and DNA repair as well as terminal differentiation processes like sarcomere organization and muscle contraction. Specifically, Cr(VI) impaired expression of key structural and contractile genes and disrupted DNA repair and cell cycle regulatory pathways, including downregulation of p21 and upregulation of proliferative marker PCNA. Furthermore, we identified suppression of Hippo signaling through downregulation of Tead4 and its muscle-specific downstream targets, providing a mechanism for impaired differentiation. These findings highlight widespread alterations in transcriptional programs governing muscle development and maturation, offering insight into how Cr(VI) exposure affects skeletal muscle health.

overall_design: RNA-seq profiling of C2C12 cells at day 0, 1, 2, and 4 of myogenic differentiation with 0, 2, or 5 µM of Cr(VI) treatment

first: Hong


title: Sex-related differences in gene expression in early-stage bladder cancer revealed by whole-transcriptome sequencing

city: Warszawa

first: Krzysztof

last: Goryca

address: Banacha 2c

department: CeNT

country: Poland

institute: Uniwersytet Warszawski

summary: Bladder cancer (BC) is significantly more prevalent in men than in women, yet female patients often experience higher recurrence rates and poorer prognosis. Our study aimed to investigated sex-specific gene expression differences in early-stage BC using whole-transcriptome sequencing. A total of 51 patients diagnosed with low-grade Ta stage non-muscle-invasive bladder cancer were recruited. Paired tissue samples from tumor lesions and adjacent healthy bladder mucosa were analyzed to identify differentially expressed genes (DEGs). Among the top 100 most significant DEGs, overwhelmingly more upregulated were in male than female tissues (90% vs. 19%). The most significantly altered expression in female BC tissues included MT-ND6, ARL4C, ASGR1, MYBL1, and SCAMP5, whereas in males, ONECUT2, SPEG, CTSE, GJB2, and SYNM. Notably, 753 DEGs were unique to female patients, while 3989 were specific to males, with 1633 shared between both sexes. Functional annotation revealed that female-unique DEGs were significantly enriched in immune-related pathways, including regulation of leukocyte activation and cell-cell adhesion, and lymphocyte differentiation. Whereas male-unique DEGs were predominantly associated with pathways related to cell cycle regulation, mitochondrial function, and androgen receptor signaling. Immune-related gene expression indicated that female-specific DEGs were involved in leukocyte activation and antigen receptor signaling, whereas male-specific DEGs were linked to B-cell activation and neutrophil-mediated immune responses. A two-factor interaction model identified S100A14 as the only protein-coding gene whose expression exhibited a significant sex-dependent pattern, with four additional genes (GJB2, DSC2, TM4SF and ALOX15B) showing a probable interaction effect. These findings highlight the necessity for sex-specific therapeutic strategies in BC management.

overall_design: Patients  diagnosed with bladder tumors were recruited to the study. Paired tissue samples of bladder tumor and adjacent healthy-appearing bladder mucosa were collected from men and women. The gender-related differences in gene expression were determined using whole transcriptome sequencing.

first: Natalia

last: Zeber-Lubecka

first: Konrad

last: Bilski

first: Michalina

last: Dąbrowska

first: Jerzy

last: Ostrowski

first: Jakub

last: Dobruch

first: Ewa

last: Hennig


title: Stage-specific requirement for Mettl3-dependent m6A epitranscriptomic regulation during myogenesis [meRIP-Seq]

city: Guangzhou

first: TAN

last: YEYA

state: Guangdong

address: Jinsui Road, Tianhe District, Guangzhou City, Guangdong Province

department: Guangzhou Women and Children's Medical Center

institute: Guangzhou Medical University

summary: The role of N6-methyladenosine (m6A) in muscle formation and maintenance remains incompletely understood, particularly with respect to the contribution of methyltransferase-like 3 (METTL3), the core component of the methyltransferase complex (MTC), to myogenesis. Here, we show the involvement of METTL3 in the m6A epitranscriptome during myogenesis. Our findings reveal a correlation between METTL3-regulated m6A modifications and myoblast fusion during differentiation and regeneration. We observed significant upregulation of METTL3 following injury and identified numerous alterations in myogenic pathways. Furthermore, we detected differential patterns of METTL3-regulated m6A modifications in genes during differentiation, with some genes exhibiting loss and others showing gain. Our study revealed that the fusion factors Mymx and Mymk are downstream elements of METTL3 involved in myogenesis, and both exhibit upregulated expression and m6A levels during myogenesis. Our findings provide valuable resources for elucidating the function and mechanism of METTL3-regulated m6A modifications in myogenesis, thereby revealing the regulatory role of METTL3 in myoblast fusion.

overall_design: By using meRIP-seq, we report genome-wide identification of m6A modifications in Mettl3-overexpressing cells during myoblasts differentiation

first: Yeya

last: Tan

first: Shujuan

last: Xie


title: TRAP1 expression elicits pro-tumoral functions in macrophages associated to malignant peripheral nerve sheath tumor cells

city: Padua

first: Marco

last: Fantuz

state: Veneto

address: Via Orus, 2

country: Italy

institute: Veneto Institute of Molecular Medicine

summary: Metabolic adaptations can sustain the pro-neoplastic functions exerted by macrophages in the tumor microenvironment. Malignant peripheral nerve sheath tumors (MPNSTs), aggressive and incurable sarcomas that develop either sporadically or in the context of the genetic syndrome Neurofibromatosis type 1, are highly infiltrated by macrophages, whose contribution to MPNST growth remains poorly characterized. Here, we analyze the role played by the molecular chaperone TRAP1, a regulator of mitochondrial metabolic pathways, in shaping the pro-tumoral activity of macrophages associated to MPNST cells. We have studied the phenotypic changes elicited by a MPNST cell-conditioned medium in macrophages with or without TRAP1, and their subsequent ability to support MPNST cell growth and migration and endothelial cell angiogenesis. The presence of TRAP1 is required in both naive and M2-like macrophages for eliciting phenotypic changes that lead to the acquisition of pro-neoplastic features. TRAP1-expressing macrophages become able to sustain MPNST cell growth and migration and to exert pro-angiogenic properties on endothelial cells through accumulation of the metabolite succinate and the ensuing activation of a HIF-1α-dependent transcriptional program. Our data provide evidence of a molecular crosstalk between MPNST cellular components, in which soluble factors released by cancer cells drive phenotypic changes in macrophages that in turn enhance pro-tumoral biological routines in both MPNST and endothelial cells. TRAP1-dependent metabolic rewiring in macrophages is mandatory for sustaining this interplay, as a TRAP1-succinate-HIF-1α signaling axis orchestrates their acquisition of tumor-promoting features.

overall_design: RNA-seq profiling of wild-type and TRAP1 KO M0/M2 macrophages exposed to control or MPNST cells-derived conditioned medium

first: Francesca

last: Scantamburlo

first: Alessia

last: Rubini

first: Francesco

last: Ciscato

first: Sofia

last: Tomasoni

first: Ranieri

last: Verin

first: Valentina

last: Zappulli

first: Camilla

last: Bean

first: Andrea

last: Rasola

first: Ionica

last: Masgras


title: Comprehensive transcriptomic and m6A epitranscriptomic reveals colchicine-induced nephrotoxicity via DNA damage and autophagy in HK2 cells

city: Fuzhou

first: Jiaxin

last: Wen

address: No.1 Xuefu North Road, Fuzhou, Fujian, China

institute: Fujian Medical University

summary: Colchicine is a commonly used drug for the treatment of gout and inflammation, but its nephrotoxicity and underlying mechanisms are not fully understood. This study aims to investigate the relationship between colchicine-induced nephrotoxicity and m6A methylation modifications.

overall_design: To investigate whether m6A modification is involved in nephrotoxicity following colchicine treatment, we performed MeRIP-seq and experimental verificationon both colchicine-treated and untreated control cells.

first: Kun

last: Tian

first: Lixiang

last: Weng

first: Dongcheng

last: Zhang


title: Stage-specific requirement for Mettl3-dependent m6A epitranscriptomic regulation during myogenesis [RNA-Seq]

first: TAN

last: YEYA

overall_design: RNA-seq profiling of wildtype C2C12 cells and their overexpressed derivatives at Day0 and Day4 of myoblasts differentiation.RNA-seq profiling of wildtype C2C12 cells and their  knockout derivatives at Day0 and Day3 of myoblasts differentiation.


title: Linear ubiquitination prevents lipodystrophy and obesity-associated metabolic syndrome

city: Cologne

first: Ali

middle: T

last: Abdallah

address: Joseph Stelzmann Str. 26

department: Medical Faculty

country: Germany

institute: University of Cologne

summary: Adipocyte hypertrophy during obesity triggers chronic inflammation, leading to metabolic disorders. However, the role of adipocyte-specific inflammatory signalling in metabolic syndrome remains unclear. The linear ubiquitin chain assembly complex, LUBAC, is an E3-ligase that generates non-degradative linear ubiquitination (Lin-Ub). LUBAC regulates NF-κB/MAPK-driven inflammation and prevents cell death triggered by immune receptors like TNF-receptor-1. Here we show that mice lacking HOIP, LUBAC’s catalytic subunit, in adipocytes (HoipA-KO) display lipodystrophy and heightened susceptibility to obesity-induced metabolic syndrome, particularly Metabolic Dysfunction-Associated Steatotic Liver Disease (MASLD). Mechanistically, loss of HOIP attenuates TNF-induced NF-κB activation and promotes cell death in human adipocytes. Inhibiting caspase-8-mediated cell death is sufficient to prevent lipodystrophy and MASLD in HoipA-KO obese mice. Importantly, HOIP expression in adipose tissue positively correlates with metabolic fitness in obese individuals. Overall, our findings reveal a critical role for Lin-Ub in protecting against obesity-related metabolic syndrome by mitigating cell death-driven adipose tissue inflammation

overall_design: Bulk RNAseq extration from Gwat of male mice, 22-24 weeks old mice Hoip fl/fl AdipoQ.Cre+(HoipA-KO) or Hoip fl/fl AdipoQ.Cre- (WT control) fed for 16 weeks with 14% Control Diet (CD) or 60% High fatdiet (HFD)

first: Ximena

last: Hildebrant

first: Önay

last: Veli

first: Armel

last: Hyoubi

first: Julia

last: Zinngrebe

first: Anne

last: Hoffmann

first: Julian

last: Rodefeld

first: Oyku

last: Kaya

first: Elena

last: Wagner

first: Andreas

last: Lindhorst

first: Matea

last: Poggenberg

first: Yuan

last: Wang

first: Liane

last: Gardeweg

first: Joëlle

last: Dimmler

first: Jutta

last: Schillings

first: Pegi

last: Koci

last: Bonechi

first: Lucas

last: capuccino

first: Adhideb

last: Ghosh

first: Falko

last: Noé

first: Christian

last: Wolfrum

first: Micheal

last: Singer

first: Tom

last: Luedde

first: Aslihan

last: Yavas

first: Martin

last: Gericke

first: Holger

last: Winkels

first: Matthias

last: Blüher

first: Henning

last: Walczak

first: Alessandro

last: Annibaldi

first: Pamela

last: Fischer-Posovszky

first: Nieves

last: Peltzer


title: Hypoxia Inducible Factor 1α-driven steroidogenesis impacts systemic hematopoiesis

city: Dresden

first: Ben

last: Wielockx

address: Fetscherstrasse 74

institute: IKL, Carl Gustav Carus Universitätklinikum Dresden

summary: Glucocorticoids regulate hematopoiesis, but how chronic elevation of endogenous glucocorticoid production affects hematopoietic stem cell (HSC) function and immune cell development remains incompletely understood. Using an adrenocortical cell-specific HIF1α (Hypoxia inducible Factor-1α)-deficient mouse model (P2H1Ad.Cortex) resulting in elevated glucocorticoid (GC) levels, we here demonstrate that sustained GC exposure promotes hematopoietic stem and progenitor cell (HSPC) expansion while shifting HSCs toward a more quiescent and metabolically restrained state. Functionally, these HSCs exhibited enhanced regenerative potential, as evidenced by superior donor chimerism in transplantation assays. In addition, we observed a striking increase in myeloid progenitors, as well as in their progeny (monocytes and granulocytes). Conversely, B-cell differentiation in the bone marrow was severely impaired, with a strong block at the pre-pro-B cell stage. To determine whether these phenotypes were driven by glucocorticoid receptor (GR) signaling, we performed transplantation experiments using GR-deficient or WT control bone marrow into P2H1Ad.Cortex or WT littermate recipients. This approach decisively demonstrated that both the increase in myeloid cells and the block in B-cell differentiation were GR-dependent, confirming that GC-GR signaling plays a pivotal role in shaping hematopoiesis. Taken together, our findings clearly suggest a direct role for chronic glucocorticoid exposure in regulating HSC function, lineage differentiation, and stress hematopoiesis. The mouse model of adrenocortical cell-specific HIF1α deficiency provides a valuable tool to study the long-term effects of elevated glucocorticoid levels on hematopoietic regulation and may provide further insight into hematologic disorders associated with chronic therapeutic glucocorticoid administration.

overall_design: Bulk RNA sequencing on sorted hematopoietic stem cells (HSCs) from WT and P2H1Ad.Cortex mice.


title: The isoflavone genistein selectively derepresses major satellite repeat transcription in mouse heterochromatin

city: Freiburg im Breisgau

first: Galina

last: Erikson

address: Stübeweg 51

institute: Max Planck Institute of Immunobiology and Epigenetics

summary: Heterochromatin has crucial functions in protecting genome integrity. In mouse cells, heterochromatin is characterized by A/T-rich, 234 bp DNA repeat arrays, called the major satellite repeats (MSR). We investigated MSR expression in response to a variety of stress conditions by using small molecule compounds. We identified the isoflavone genistein to selectively derepress MSR transcription but not that of other DNA repeat elements. Genistein is a natural compound that is frequently used in dietary supplements and has been associated with reducing cancer risk. A 24 hrs exposure of mouse embryonic fibroblasts (MEF) to genistein results in a more than 100-fold induction of MSR transcripts. This derepression depends on the activity of RNA polymerase II and requires a cycling G1 cell population. Blocking the cell cycle at the G2/M stage significantly attenuates genistein- mediated derepression of MSR transcription. Mechanistically, DNA topoisomerase poisons phenocopy the genistein-dependent desilencing of MSR expression. Together, these data suggest that MSR transcriptional response is guided by an altered topology of the underlying A/T-rich MSR DNA repeat arrays. In addition, the data reveal a novel function for genistein in derepressing MSR transcription that may contribute to the growth inhibitory and anticancer properties of this natural compound.

overall_design: To investigate the effect of genistein on regulating transcription of MSR repeats. Wile-type, control and MEFs treated with 50uM genistein for 24hours were used for this experiment.

first: Shukeir

last: Nicholas

first: Erikson

last: Galina

first: Jenuwein

last: Thomas


title: UHRF1-Mediated Maintenance DNA Methylation is Required for Induced Regulatory T Cell Function Following Influenza Induced Lung Injury in Young Adult Mice [BiSulfite-seq]

city: Chicago

first: Qianli

last: Liu

state: IL

address: 303 E. Superior St. Simpson Querrey

institute: Northwestern Univesity

type: Methylation profiling by high throughput sequencing

summary: Regulatory T cells (Tregs) promote resolution of inflammation and repair of epithelial damage following lung injury, thus representing a possible cellular therapeutic for ARDS. Foxp3+ natural regulatory T cells (nTregs) require specific DNA methylation patterns maintained by the epigenetic regulator, Ubiquitin-like with PHD and RING finger domains 1, (UHRF1), to function, but the DNA methylation requirements of in vitro induced Tregs (iTregs) remain unknown. Here we tested whether the loss of Uhrf1 would augment the pro-recovery function of iTregs during viral pneumonia. We found that the loss of maintenance DNA methylation in iTregs results in reduced engraftment and a delayed repair response after experimental influenza pneumonia. Transcriptional and DNA methylation profiling of sorted Uhrf1-deficient iTregs post infection provide insight into the mechanisms underlying their impaired ability to promote repair, with Uhrf1-defiicent iTregs demonstrating greater instability via gain of alternate effector T cell lineage-defining transcription factors. Strategies to promote stability iTregs could be leveraged to further augment their pro-recovery function during pneumonia and ARDS.

overall_design: CD4+FoxP3- T cells were isolated from the spleens and lymph nodes of Uhrf1fl/fl and Uhrf1+/+Foxp3GFP-CreERT2Rosa26SorCAG-tdTomato mice and cultured in iTreg skewing media plus tamoxifen for 5 days (denoted as the "early" cohort). Cells were transitioned to resting media on day 5 and cultured for an additional 7 days. A separate cohort of cells was cultured in iTreg skewing media for 5 days but not supplemented with tamoxifen until after the transition to resting media (denoted as the "delayed" cohort). To profile genomic CpG DNA methylation and confirm that maintenance DNA methylation was lost upon UHRF1 deletion, DNA libraries utilizing modified reduced representation bisulfite sequencing were generated from sorted Foxp3GFP+Tomato+ cells on day 12 of culture from both cohorts.

first: Benjamin D.

first: Anthony M.

last: Joudi


title: UHRF1-Mediated Maintenance DNA Methylation is Required for Induced Regulatory T Cell Function Following Influenza Induced Lung Injury in Young Adult Mice [invitro RNA-seq]

overall_design: CD4+Foxp3+ cells (nTregs) and CD4+FoxP3- conventional T cells were isolated from the spleens and lymph nodes of Uhrf1fl/fl and Uhrf1+/+Foxp3GFP-CreERT2Rosa26SorCAG-tdTomato mice. nTreg and CD4+FoxP3- conventional T cells were cultured with (IL-2 and αCD3/αCD28) or iTreg skewing media (TGF-β, IL-2, αCD3/αCD28), respectively, plus tamoxifen for 5 days (denoted as the "early" cohort). Cells were transitioned to resting media on day 5 (IL-2 only) and cultured for an additional 7 days. A separate cohort of cells was cultured with IL-2 and αCD3/αCD28 or iTreg skewing media (TGF-β, IL-2, αCD3/αCD28) for 5 days but not supplemented with tamoxifen until after the transition to resting media (denoted as the "delayed" cohort). Foxp3GFP+Tomato+ cells from both cohorts were flow cytometry sorted on days 5 and 12 of culture. RNAseq was leveraged to profile the gene expression of nTregs and iTregs that lost Uhrf1 concurrent with or after Foxp3 induction.

last: Singer


title: UHRF1-Mediated Maintenance DNA Methylation is Required for Induced Regulatory T Cell Function Following Influenza Induced Lung Injury in Young Adult Mice [RNA-seq]

overall_design: Adoptively transferred Uhrf1fl/fl and Uhrf1+/+Foxp3-GFP+tdTomato+ iTreg cells were sorted from lung single cell suspension of Foxp3DTR mice infected with influenza virus on days 11 and 24 post infection. Adoptively transferred Uhrf1fl/fl and Uhrf1+/+Foxp3-GFP+tdTomato+ and Uhrf1fl/flFoxp3-GFP-tdtomato+ (ex-foxp3) iTreg cells were sorted from splenic single cell suspension of Foxp3DTR mice infected with influenza virus on day 24 post infection. RNAseq was leveraged to profile the gene expression of Uhrf1-deficient and Uhrf1-sufficient iTregs following influenza infection.


title: The isoflavone genistein selectively derepresses major satellite repeat transcription in mouse heterochromatin [Top2beta]

overall_design: To investigate a possible topological role for transcriptional regulation of MSR repeats. wild-type control  and MEF cells null for topoisomerase 2beta were used for this experiment.


title: UHRF1-Mediated Maintenance DNA Methylation is Required for Induced Regulatory T Cell Function Following Influenza Induced Lung Injury in Young Adult Mice

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

overall_design: Refer to individual Series


title: UHRF1-Mediated Maintenance DNA Methylation is Required for Induced Regulatory T Cell Function Following Influenza Induced Lung Injury in Young Adult Mice [EM-seq]

overall_design: Adoptively transferred Uhrf1fl/fl and Uhrf1+/+Foxp3-GFP+tdTomato+ iTreg cells were sorted from lung single cell suspension of Foxp3DTR mice infected with influenza virus on days 11 and 24 post infection. DNA libraries were subsequently generated to profile genomic CpG DNA methylation of Uhrf1-deficient and Uhrf1-sufficient iTregs following influenza infection.


title: Effect of FcRγ on gene expression profile of naïve and IL-15 treated NK cells

city: Brisbane

first: Vikas

last: Duhan

state: QLD

address: 300 Herston Rd, Herston

country: Australia

institute: QIMR Berghofer Medical Research Institute

summary: Here, we aimed to study the NK cell molecular signatures under the control of FcRγ and how these signatures are regulated by IL-15 and the tumour microenvironment (TME). To investigate this, we obtained purified splenic NK cells from naïve wild-type (WT) and FcRγ-deficient (FcRγ–/–, KO) mice cultured in the presence or absence of IL-15 for three days. To obtain NK cells from the TME, NK cells were purified from tumour-bearing lungs of WT and KO (FcRγ–/–) mice, which were intravenously injected with B16F10 cells two weeks earlier. Naïve NK cells (without any IL-15 treatment) were used as the control group.  Next, we performed bulk RNA sequencing (RNA-seq) on six groups of NK cells for gene expression profiling: naive WT, naive KO (FcRγ–/–), IL-15-treated WT, IL-15-treated KO (FcRγ–/–), tumour WT, and tumour KO (FcRγ–/–).

overall_design: Bulk RNA-seq data were obtained from spleen derived NK cells from four experimental conditions (naïve WT, naïve KO, IL-15-treated WT, IL-15-treated KO), and tumour bearing lung derived NK cells from two experimental conditions (tumour WT and tumour KO). Each condition had four biological replicates each, therefore RNA-seq data were obtained from a total of 24 samples: splenic NK samples (n = 16) and NK samples isolated from tumour-bearing lung (n = 8).

first: Ma

last: Ricci Gomez

first: Thuy

last: T Le

first: Shachi

last: Rana

first: Enya

last: Chen

first: Deepna

last: Balakrishnan

first: Greg

last: Kelly

first: Rebecca

last: L. Johnston

first: Philippe

last: Krebs

first: Rajiv

last: Khanna


title: Sex-biased Transcriptome in in vitro Produced Bovine Early Embryos

city: Ithaca

first: Guangsheng

last: Li

state: NY

address: 507 Tower Rd.

department: Animal Science

institute: Cornell

summary: Morphologic sex differences between males and females typically emerge after the primordial germ cell migration and gonad formation, although sex is determined at fertilization based on chromosome composition. A key debated sexual difference is the embryonic developmental rate, with in vitro produced male embryos often developing faster. However, the molecular mechanisms driving early embryonic sex differences remain unclear. To investigate the transcriptional sex difference during early development, in vitro produced bovine blastocysts were collected and sexed by PCR. A significant male-biased development was observed in expanded blastocysts. Ultra-low input RNA-seq analysis identified 837 DEGs, with 231 upregulated and 606 downregulated in males. Functional enrichment analysis revealed male-biased DEGs were associated with metabolic regulation, whereas female-biased DEGs were related to female gonad development, sex differentiation, inflammatory pathways, and TGF-beta signaling. Comparing X chromosome and autosome expression ratio, we found that female-biased DEGs contributed to the higher X-linked gene dosage, a phenomenon not observed in male embryos. Moreover, we identified the sex-biased transcription factors and RNA-bind proteins, including pluripotent factors such as SOX21 and PRDM14, and splicing factors FMR1 and HNRNPH2. Additionally, we revealed 1,555 significantly sex-biased differential alternative splicing (AS), predominantly skipped exons, mapped to 906 genes, with 59 overlapping with DEGs enriched in metabolic and autophagy pathways. By incorporating novel isoforms from long reads sequencing, we identified 1,151 sex-biased differentially expressed isoforms (DEIs) associated with 1,017 genes. Functional analysis showed that female-biased DEIs were involved in the negative regulation of transcriptional activity, while male-biased DEIs were related to energy metabolism. Furthermore, we identified sex-biased differential exon usage in DENND1B, DIS3L2, DOCK11, IL1RAPL2, and ZRSR2Y, indicating their sex-specific regulation in early embryo development. This study provided a comprehensive analysis of transcriptome differences between male and female bovine blastocysts, integrating sex-biased gene expression, alternative splicing, and isoform dynamics. Our findings indicate that enriched metabolism processes in male embryos may contribute to the faster developmental pace, providing insights into sex-specific regulatory mechanisms during early embryogenesis.

overall_design: RNA-seq was to detect the sex-biased transcriptome of in vitro produced bovine embryos.

first: Meihong

last: Shi

first: Hannah

last: Araujo

first: Angie

last: Lee

first: Jingzhi

last: Zhang

first: Lee Y.

first: Soon H.

last: Cheong

first: Jingyue E.

last: Duan


title: Investigating the Risk of Arrhythmogenesis Associated with Fentanyl Abuse Using Mice and Human iPSC-Derived Cardiomyocytes

city: Palo Alto

first: Yu

last: Liu

address: 1215 Welch Road

department: CVI

institute: Stanford University

summary: The rise in synthetic opioid use, particularly fentanyl, has severely exacerbated the opioid epidemic and its impact surged dramatically during the COVID-19 pandemic. Fentanyl, a prescription opioid used for anesthesia and analgesia, is 50-100x stronger than morphine. Opioid-induced cardiac arrest represents the most dramatic manifestation of the opioid use disorder. Fentanyl primarily targets opioid receptors (ORs) in the nervous system, but its misuse also adversely depresses the pulmonary and cardiovascular systems. The proarrhythmic effects of other opioids were reported; however, the electrophysiological consequences of fentanyl abuse have not been studied. Our analysis of 19 toxicology studies conducted between 1994 and 2022 found that the average blood concentration of fentanyl in abuse or overdose cases is 30±1 ng/mL (89 nM), ~3-fold higher than in chronic pain or ~7.5-fold higher than in occasionally exposed patients. Advances in human induced pluripotent stem cell (iPSC) technology provide unprecedented opportunities to study patient‐specific responses to opioid abuse. Human iPSC-derived cardiomyocytes (iPSC-CMs) from 3 healthy donors were exposed to three doses of 89 nM fentanyl for 5 days. Then, we investigated whether fentanyl abuse has any consequences on cardiac electrophysiology.

overall_design: Human iPSC-derived cardiomyocytes (iPSC-CMs) from 2 healthy donors were exposed to three doses of 89 nM fentanyl for 5 days.

first: Gema

middle: M

last: Parreño


title: Using constraint-based metabolic modeling to elucidate drug-induced metabolic changes in a cancer cell line

city: Trondheim

first: Åsmund

last: Flobak

state: Norway

address: Prinsesse Kristinas gt 1, Gastrosenteret

department: Department of Clinical and Molecular Medicine

country: Norway

institute: Norwegian University of Science and Technology - NTNU

summary: Since the discovery of the Warburg effect, metabolism has become a crucial cancer hallmark, for cancer cells change the activity of metabolic pathways to satisfy the demand of biomolecules and energy required to sustain continuous growth. Specially, gastric cancer (GC) still remains a growing burden of society, and often require the development of targeted and personalized interventions, including the use of combinatorial drug therapies that allow for synergistic interactions. However, the mechanism underlying synergistic interactions between multiple drugs remain poorly understood. The objective of this study is to use genome-scale metabolic models (GEMs) and transcriptomic data to investigate potential synergistic mechanisms in the GC cell line AGS following treatment with three kinase inhibitors and their combinations. To explore the metabolic phenotype of AGS cells, we curated and used a set of descriptions of metabolic functions (metabolic tasks) based on the latest iteration of the Human-GEM, and we used the Task Inferred from Differential Expression (TIDE) framework to infer the metabolic changes in AGS cells. Additionally, we expanded and complemented the TIDE framework by integrating essential genes from metabolic tasks, allowing for a more robust analysis. The results revealed a complex metabolic response in AGS cells after kinase inhibitor treatments, particularly in amino acid  and nucleotide metabolism, and characterized by the down-regulation of metabolic functions. Using two definitions of synergistic effects, we identified significant metabolic shifts in combinatorial treatments, including a combination-specific increase in ornithine levels, potentially linked to an antiproliferative effect on AGS cell growth. These findings highlight the potential of using transcriptomic data to infer the metabolic phenotype of AGS cells  and the role of metabolic alterations in cancer progression. In addition, we developed a Python library for Metabolic Task Enrichment Analysis, making the TIDE frameworks accessible to other researchers.

overall_design: RNA-seq profiling of AGS cells under different treatment conditions with a control and three kinase inhibitors and their combinations at 24 hours post-exposure. Each treatment condition had four biological replicates.

first: Xavier

last: Benedicto

first: Miguel

last: Ponce-de-León

first: Alfonso

last: Valencia


title: IRE1α Downregulation Enhances STING-Mediated Chemoresistance and Guides Precision Therapies in Pancreatic Cancer

city: Hangzhou

first: Yewei

last: Ji

address: Wenyixilu street

institute: Zhejiang Provincial Key Laboratory of Pancreatic Disease

summary: The cGAS-STING signaling pathway plays dichotomous roles in the development of malignant diseases. While the role and regulation of STING signaling in immune cells is well-documented, the mechanisms by which tumor cells modify tumor-intrinsic STING signaling to evade treatment remain poorly understood. Here, we report that chemotherapy activates STING and induces low-grade chronic inflammation in pancreatic ductal adenocarcinoma (PDAC) cells.

overall_design: Ribosome profiling (ribo-seq) and RNA sequencing (RNA-seq) were conducted on KPC cells after 6 and 21 hours of Cis treatment.

first: Yuan

last: Luo

first: Mengqi

last: Sun

first: Lei

last: Chang

first: Yuanhui

last: Mao

first: Tingbo

last: Liang


title: Implication of inflammatory cytotoxic IL-7 receptor alpha low effector memory CD8+ T cells that promote innate immunity in lupus.

city: Daegu

first: Sang Jin

state: Daegu

address: 130 Dongdeok‑ro, Jung‑gu, Daegu 41944, Republic  of Korea

department: 2Department of Internal Medicine

country: South Korea

institute: Kyungpook National University School of Medicine, Daegu, Republic of Korea

summary:
Objective. The pathogenesis of systemic lupus erythematosus (SLE or lupus) involves multiple immune components although the role for CD8+ T cells, which potently induce inflammation and tissue damage, is less known in lupus. The aim of this study was to interrogate the implications of CD8+ T cells in lupus by examining heterogeneity of CD8+ T cells in the kidneys and peripheral blood of lupus patients and assessing functional significance of such heterogeneity in promoting inflammation and tissue damage.
Methods. An integrated dataset of our own and publicly available scRNA-seq data from the peripheral blood and kidney tissue samples of lupus patients was analyzed followed by validating these findings with an independent scRNA-seq dataset of the peripheral blood of lupus patients and Imaging Mass Cytometry analysis of lupus and normal kidney tissue samples. The interface of CD8+ T cell subsets with neutrophils and monocytes was assessed using cell culture, qPCR, ELISA, flow cytometry, and immunofluorescent staining.
Results. The results of our scRNA-seq analysis showed an expansion of effector memory (EM) CD8+ T cell subsets that expressed low levels of the IL7 receptor gene (IL7Rlow) but high levels of cytotoxicity related genes, including GZMB, GZMH, GZMK, PRF1, and GNLY, in the peripheral blood and kidneys of lupus patients. Patients with lupus nephritis who progressed to  renal failure (or end stage renal disease) had increased numbers and expression levels of CD8+ T cells and cytotoxic molecules, respectively, at the protein level in the kidney tissue as compared to lupus patients who achieved remission of lupus nephritis, supporting the involvement of such cells and molecules in impairing renal function. The gene signatures of IL7Rlow CD8+ T cell subsets correlated with type I IFN gene signature in the peripheral blood of both pediatric and adult lupus patients. Our ex vivo functional study showed that IL7Rlow EM CD8+ T cells potently induced neutrophil extracellular trap (NET) formation and augmented lupus immune complex mediated monocyte activation, supporting the functional implication of the expanded IL7Rlow EM CD8+ T cells in promoting inflammation and tissue damage.
Conclusion. Our findings advance our understanding of the implication of CD8+ T cells, especially IL7Rlow EM CD8+ T cells expressing cytotoxic molecules, in sustaining inflammation and tissue damage in lupus.

overall_design:
For scRNA-seq analysis, peripheral blood mononuclear cells (PBMCs) were collected from three patients with SLE who met to the 2019 American College of Rheumatology (ACR)/European League Against Rheumatism (EULAR) Classification Criteria for SLE at flare and 6 weeks later.

***************************************************************
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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title: UBE3A reinstatement restores behavior and proteome in an Angelman syndrome mouse model of imprinting defects

city: Basel

first: Roland

last: Schmucki

address: Grenzacherstrase

country: Switzerland

institute: F. Hoffmann - La Roche AG

summary: Angelman Syndrome (AS) is a severe neurodevelopmental disorder with only symptomatic treatment currently available. Besides mutations within the UBE3A gene, AS is caused by deletions, imprinting center defects (mICD) or uniparental disomy of chromosome 15 (UPD). Current mouse models are Ube3a-centric and do not address expression changes of other 15q11-q13 genes on AS pathophysiology. Here, we studied a mouse line that harbors a mutation affecting the AS-PWS imprinting center, hence modeling mICD/UPD AS subtypes. mICD mice showed significant reduction in UBE3A protein, bi-allelic expression of Ube3a-ATS and Mkrn3-Snord115 gene cluster, leading to robust AS behavioral deficits and proteome alterations similar to Ube3aKO mice. Genetic UBE3A overexpression in mICD mice, mimicking therapeutic strategies that effectively activate the biallelic silenced Ube3a gene, resulted in a complete rescue of all behavioral and proteome alterations. Subsequently, treatment with an antisense oligonucleotide (ASO) to directly activate the biallelic silenced Ube3a gene in mICD mice also resulted in efficient reinstatement of UBE3A, alongside a partial rescue of behavioral phenotypes. Taken together, these findings demonstrate that UBE3A loss is the primary factor underlying AS phenotypes in the mICD/UPD mouse model, and also corroborate that UBE3A reinstatement is an attractive therapeutic strategy for mICD/UPD AS individuals.

overall_design: 7 wildtype controls (WT) and 7 heterozygous mutants having maternal imprinting defect (HE)

first: Ramanathan

last: Narayanan

first: Kim

last: Schneider

first: Kerstin

last: Oelkers


title: Exploring MHC Class II I-Ab Blockade as a Potential Treatment for Sjögren’s Disease in the Mouse Model

city: Gainesville

first: Cuong

last: Nguyen

state: Florida

address: 2015 SW 16th Ave

institute: University of Florida

summary: Sjögren’s disease (SjD) is a chronic autoimmune disorder predominantly affecting females, characterized by exocrine gland dysfunction. This study investigates the therapeutic potential of 2-chloro-1-(4-hydroxy-phenyl)-ethanone (CHPE) and metformin in the C57BL/6.NOD-Aec1Aec2 mouse model, which closely mirrors human SjD. Molecular docking identified CHPE and metformin as high-affinity binders to the MHC class II I-Ab antigen-binding groove, suggesting their ability to inhibit antigen presentation and modulate immune responses. In-vitro assays confirmed their effectiveness in reducing T cell activation. In-vivo studies demonstrated that both preventative and therapeutic regimens of CHPE and metformin significantly reduced lymphocytic infiltration in the lacrimal glands, with metformin showing a more pronounced effect in females. Salivary gland infiltration was less responsive, though some reduction in focal scores was observed in male mice treated preventatively with CHPE. Both drugs altered the composition of lymphocytic infiltrates, particularly by reducing B cell populations, with notable sex-specific differences in response to treatment. CHPE and metformin also reduced anti-nuclear antibody levels, with CHPE showing stronger effects in females. Additionally, both drugs improved saliva and tear secretion, with metformin being more effective in the preventative regimen, especially in females. T cell receptor transductant assays revealed that CHPE and metformin exert their therapeutic effects through antigen-specific pathways, inhibiting T cell responses to SjD-associated autoantigens. Overall, this study provides compelling evidence that CHPE and metformin can modulate immune responses and improve gland function, with effectiveness varying by sex and age. These findings support the potential of these compounds as personalized treatments for SjD tailored to individual patient characteristics.

overall_design: We employed scRNA-seq using sorted salivary gland immune cells from normal B6 and B6 to obtain the unique TCR. NOD-Aec1Aec2 mice were performed with V(D)J enrichment. Analyzing TCR repertoires, we identified two unique TCRs with paired alpha/beta chains only present in B6.NOD-Aec1/2 mice and shared between male and female mice.

first: Alexandria

last: Voigt

first: Shivai

last: Gupta

first: Yiran

last: Shen

first: Patricia

last: Glenton

first: Danmeng

last: Li

first: David

last: Ostrov

first: Indraneel

last: Bhattacharyya


title: Impact of seasonality on immunotranscriptomic regulation of Atlantic salmon (Salmo salar) skin against Caligus rogercresseyi infestation during open-sea cages productive regime

city: Santiago

first: Felipe

middle: E.

last: Reyes-López

state: Santiago

address: Av. Libertador Bernado O'Higgins 3363

country: Chile

institute: Universidad de Santiago de Chile

summary: Chile is the second largest producer of Atlantic salmon (Salmo salar), making it the second most important national industry. This industry is not exempt from challenges, such as sea lice infestation. Caligus rogercresseyi is the only sea louse that affects the Chilean salmon industry and the etiological agent of caligidosis. This pathology alters the state of health of the fish and causes significant economic losses. Despite its relevance, there are currently no studies that consider the environmental variables present in marine culture centers in each of the different seasons of the year and their effect on the response capacity of Atlantic salmon due to its poikilothermic characteristic, which limits its applicability in the development of new approaches and strategies for the control of caligidosis. For this reason, this study evaluated the skin transcriptome of Atlantic salmon infested with C. rogercresseyi in culture centers located in the fjords of the Aysén Region due to its leadership in the productivity of Atlantic salmon in Chile. The study focused on two critical periods of the year: autumn, marked by a gradual thermal decrease (from summer to winter); and spring, characterized by a gradual temperature increase (from winter to summer).  For this purpose, RNA sequencing techniques (RNA-seq) and functional network analysis were used to identify differences in transcriptomic profiles between autumn and spring. In autumn, 253 differentially expressed genes (DEGs) were obtained, where 185 were upregulated and 67 DEGs were downregulated. In spring, 103 DEGs were obtained; 70 upregulated and 33 downregulated. The results reveal that, in autumn, the analysis presents an activation of processes in response to stress and negative regulation of T-cell proliferation, suggesting an increased susceptibility to Caligus infestation during this season. In spring, an overexpression of genes involved in protein synthesis was observed, accompanied by various biological processes involved in the immune response, including activation of the complement pathway, granulocyte chemotaxis, and antigen processing and presentation of peptide antigen, suggesting activation of immunity at different levels in the presence of Caligus. Validation of the RNA-seq results by qPCR confirmed the modulation and magnitude of expression of the differentially expressed genes, confirming the robustness of the data obtained. To the best of our knowledge, this is the first study to analyze the transcriptomic response of healthy skin of Caligus-infested salmon under productive conditions, and underscores the importance of considering seasonal variations for the development of more effective management strategies in the aquaculture industry.

overall_design: RNA-seq profiling of Atlantic salmon skin tissue samples from infested and non-infested with Caligus rogercresseyi. In the case of infested fish, samples were taken from undamaged skin. The samples were collected during the autumn and spring.

first: Andrea

last: Cerda-Celis

first: Mabel

last: Vidal

first: Merari

last: Goldstein

first: María Jesús

last: Santillán-Araneda

first: Alexis

last: Rivera

first: Sebastian

last: Reyes-Cerpa

first: Daniela

last: Vargas

first: Gabriel

last: Jerez

first: Eva

last: Vallejos-Vidal


title: Mouse models using an intestinal epithelial-specific and inducible VilCreERT2-mediated conditional knockout of Jup under basal conditions and in acute dextran-sodium sulfate (DSS)-induced colitis

city: Wuerzburg

first: Natalie

last: Burkard

address: Oberduerrbacherstr. 6

department: Experimentelle Viszeralchirurgie

institute: Universitätsklinikum Würzburg

summary:
Investigation of microbial community composition in mouse models using an intestinal epithial-specific and inducible VilCreERT2-mediated conditional knockout of Jup under basal conditions and in acute dextran-sodium sulfate (DSS)-induced colitis
We investigated the gut microbiome composition in a dextran sulfate sodium (DSS) colitis model using Jupfl/fl and iVilCreERT2Jupfl/fl mice. Fecal samples were collected after DSS treatment, and 16S rRNA sequencing was employed to analyze microbial communities. Our findings revealed no significant differences in microbial profiles between Jupfl/fl and iVilCreERT2Jupfl/fl under DSS treatment.

overall_design: Jupfl/fl and iVilCreERT2Jupfl/fl mice received 2.5% DSS in autoclaved drinking water ad libitum for 5 days (n=10) to assess acute changes due to intestinal inflammation

first: Rebecca

last: Springer

first: Christoph

last: Otto


title: Circular RNA circAtxn10 regulates skeletal muscle cell differentiation by targeting miR-143-3p and Chrna1 in C2C12 cells

city: Hwasun

first: Nakwon

last: Choe

state: Seoyang-ro 322

address: Baekseo-ro 160

department: Pharmacology

institute: Chonnam Univ. Med. Sch.

summary: Skeletal muscle differentiation is a complex process regulated by a network of genes and transcription factors. Recent studies have revealed the roles of circular RNAs (circRNAs) and microRNAs (miRNAs) in modulating gene expression during myogenesis. We investigated the interaction between circAtxn10, miR-143, and the nicotinic acetylcholine receptor subunit alpha 1 (Chrna1) in skeletal muscle differentiation using the C2C12 cell line. Our results demonstrate that circAtxn10 expression increases during myogenic differentiation and acts as a sponge for miR-143-3p through direct binding. We identified Chrna1 as a direct target of miR-143-3p through three binding sites in its 3'-UTR and showed that both miR-143-3p mimic and Chrna1 knockdown significantly impair myogenesis. Notably, Chrna1 overexpression dramatically enhanced myogenic marker expression and myotube formation. Our findings establish a regulatory axis involving circAtxn10, miR-143, and Chrna1 that plays a critical role in modulating skeletal muscle differentiation, providing new insights into the complex molecular mechanisms regulating myogenesis.

overall_design: To investigate the role of circular RNAs in skeletal muscle differentiation, we performed RNA-seq analysis on human myocytes at three differentiating stages, including satellite cells, myoblasts, and adult muscle tubes.

first: Anna

last: Jeong

first: Hosuk

last: Jeoung

first: Young-Kook

last: Kim

first: Dongtak

first: Duk-Hwa

last: Kwon

first: Hyun

last: Kook


title: The antisense RNA CDH3-AS1 regulates expression of the melanoma suppressor P-cadherin

city: Tampa

first: jiqiang

last: yao

address: 12902 USF Magnolia Drive

institute: moffitt cancer center

summary: Thousands of regulatory noncoding RNAs (ncRNAs) have been annotated; however, their functions in gene regulation and contributions to cancer formation remain poorly understood. To gain a better understanding of the influence of ncRNAs on gene regulation during melanoma progression, we mapped the landscape of ncRNAs in melanocytes and melanoma cells. Nearly half of deregulated genes in melanoma are ncRNAs, with antisense RNAs (asRNAs) comprising a large portion of deregulated ncRNAs. CDH3-AS1, the most significantly downregulated asRNA, overlaps the CDH3 gene, which encodes P-cadherin, a transmembrane glycoprotein involved in cell adhesion that was also reduced in melanoma. Overexpression of CDH3-AS1 increased cell aggregation and reduced xenograft tumor growth, mimicking the tumor-suppressive effects of CDH3. CDH3-AS1 interacted with CDH3 mRNA and enhanced P-cadherin protein levels. Interestingly, secondary structures at the CDH3 5’ end regulated P-cadherin translation, and ribosome profiling revealed that CDH3-AS1 promotes ribosome occupancy at the CDH3 5’UTR. Notably, 5’UTR ribosome occupancy was generally increased in mRNAs having cognate asRNA. Taken together, this study revealed the CDH3-AS1-mediated enhancement of P-cadherin translation, underscoring the broader potential of asRNAs as regulators of protein-coding genes and their role in diseases like melanoma.

overall_design: RNA isolated from Hermes4B cell lines treated with siRNA control (siNT),  against CDH3-AS1 (siCDH3-AS1) or against CDH3 RNA isolated from Hermes4B cell lines treated with control siRNA (siNT), siRNA targeting CDH3-AS1 (siCDH3-AS1), or siRNA targeting CDH3 (siCDH3).

first: Manon

last: Chadourne

first: Crystal

last: Griffiths

first: Xiaonan

last: Xu

first: Emily

last: Brennan

first: Olga

last: Vera

first: Nicol

last: Mecozzi

first: Kaizhen

last: Wang

first: Alex

last: Jaeger

first: Florian

last: Karreth


title: Tumor  Exosome-transmitted LncRNA CATED Promotes Platinum-resistant in High-grade Serous Ovarian Cancer

city: Hefei

first: Yi

last: Liu

state: Anhui

address: 17th Lujiang Road

department: Department of Obstetrics and Gynecology

institute: The First Affiliated Hospital of USTC,Division of Life Sciences and Medicine,University of Science and Technology of China

summary: High-grade serous ovarian cancer (HGSOC) represents the most lethal type of gynecological cancer, with platinum resistance being a serious challenge in HGSOC treatment. Long non-coding RNA (lncRNA) plays critical regulatory roles in the occurrence and development of various cancers, including HGSOC. Here, using RNA sequencing of tumor exosomes from HGSOC patients, we identified lncRNA CATED was significantly upregulated in both tumors and tumor-derived exosomes in platinum-resistant HGSOC, and low CATED level correlated with good prognosis. Functionally, CATED enhanced cisplatin resistance via promoting cell proliferation and decreasing apoptosis both in vitro and in vivo. These effects could also be transferred via CATED-overexpressing exosomes from donor cells and tumor exosomes from HGSOC patients. Mechanistically, CATED bound to and upregulated DHX36 via PIAS1-mediated SUMOylation at K105 site, and elevated DHX36 increased the downstream RAP1A protein levels by enhancing RAP1A mRNA translation, consequently activating MAPK pathway to promote platinum resistance in HGSOC. ASO-mediated knockdown of CATED reversed the platinum resistance in exosome-transferring mouse models through DHX36-RAP1A-MAPK pathway. Overall, these findings offer new insights into the critical roles of exosomal lncRNAs in platinum resistance, and indicate that CATED may be a potential target of HGSOC treatment.

overall_design: Extract RNA from exosomes derived from tumor tissues of high-grade serous ovarian cancer (HGSC) patients for RNA sequencing (RNA-seq). Based on patient platinum sensitivity and resistance groups (resistant: sensitive ratio of 3:4). Identify upregulated lncRNAs in the resistant group. Overexpress lncRNA CATED in cell lines and compare with control groups (each with two biological replicates) for mRNA sequencing, and analyze differentially expressed genes and enriched pathways. Perform DHX36 RIP-seq in the SKOV3 cell line to identify downstream genes, with three biological replicates.

first: Liang

last: Chen

first: Ying

last: Zhou


title: Radiation exposure induced BBB injury via mitochondria-mediated non-infectious inflammation

first: Jianhua

last: Qin

address: No.96 JinZhai Road Baohe District

department: School of Biomedical engineering

institute: University of Science and Technology of China

summary: Radiation-induced brain injury (RIBI) is a series of brain injuries caused by exposure to high doses of ionizing radiation, characterized by severe cognitive dysfunctions and brain necrosis.In this study, we described a biomimetic human blood-brain barrier (BBB) model that allowed to probe the responses to radiation exposure.This RNA-seq data illustrated that representative RIBI-associated pathological responses including BBB compromise, DNA break, inhibited cell proliferation, cell swelling and release of pro-inflammatory cytokines following acute radiation exposure. Collectively, the study uncovered an unknown mitochondria-mediated inflammation involved in the pathogenesis of RIBI, indicating mitochondria can be utilized as a potential target for developing new radioprotective measures.

overall_design: In this study, we developed a biomimetic human blood-brain barrier (BBB) model composed of multiple cellular components to evaluate the pathogenesis of radiation-induced brain injury (RIBI) following exposure to γ-rays and X-rays. The controls are from brain channel (n=3) and blood channel (n=3) that receive no radiation exposure and are compared  to brain channel (n=3) and blood channel (n=3) that receive 16Gy of radiation, respectively.

first: Peng

first: Jiayue

first: Min

last: Zhang

first: Juan

last: Yang

first: Peihan

last: Lian

first: Xiu

last: Cheng


title: Effect of thermoneutral housing (as compared to room temparture) on liver gene expression in mice fed a control diet or a western diet

city: Toulouse

first: Hervé

last: Guillou

address: 180 Chemin de Tournefeuille

department: ToxAlim

country: France

institute: INRAE

summary: Liver gene expression was assessed in male mice after they had previously been fed a control diet or a western diet for 13 weeks. Mice fed the control diet were healthy. Mice fed the western diet became obese. In each diet, half of the mice were housed at room temperature (22°C) and the other half was housed at thermoneutrality (30°C). Overall, this experiment allowed us to investigate the effect of housing temperature on liver gene expression in healthy mice and in obese mice.

overall_design: 10-week-old mice were either fed a control diet (Ctrl; n= 16 mice) or a western diet (WD; n=16 mice) for 13 weeks. Control diet (Ctrl) contains 8.4% calories from fat, 19.3% calories from carbohydrates and 72.4% calories from proteins. Western diet (WD) contains 42% calories from fat, 42.7% calories from carbohydrates (mainly sucrose) and 15.2% calories from proteins and 0.2% cholesterol. In each diet, half of the mouse group was housed at room temperature (RT, 22°C) and the other half of the group was housed at thermoneutrality (TN, 30°C°).

first: Céline

last: Martin

first: Claire

last: Naylies

first: Arnaud

last: Polizzi

first: Anne

last: Fougerat

first: Nicolas

last: Loiseau

first: Yannick

last: Lippi


title: RNAseq analysis of genes differentially expressed in BR-shCON and BR-shSPANXB1

city: beijing

first: qi

last: wang

address: No. 10 Xitoutiao, Youanmenwai Street, Fengtai District

institute: capital medical university

summary: We used RNA sequencing to analyze gene expression profiles of BR-shCON and BR-shSPANXB1.  The goal of this study is to explore genes that are differentially expressed in BR-shCON and BR-shSPANXB1.

overall_design: Six samples obtained from BR-shCON and BR-shSPANXB1 cells were analyzed. Three indipendent samples were analyzed for each cell line.

first: Qi

last: Wang

first: Yan

last: Gao

first: Lulu


title: Effect of beta3-adrenergic stimulation on brown adipose tissue gene expression in mice fed either a control diet or a western diet

summary: The effect of beta3-adrenegic stimulation on brown adipose tissue gene expression was assessed in male mice after they had previously been fed a control diet or a western diet for 13 weeks. Mice fed the control diet were healthy. Mice fed the western diet became obese. Beta 3 adrenergic stimulation was achieved by using Beta 3 adrenergic receptor (CL316243). Overall, this experiment allowed us to investigate the effect of Beta3-adrenergic stimulation on brown adipose tissue gene expression in healthy mice and in obese mice.

overall_design: Thirty two 10-week-old mice were either fed a control diet (Ctrl; n= 16 mice) or a western diet (WD; n=16 mice) for 13 weeks. Control diet (Ctrl) contains 8.4% calories from fat, 19.3% calories from carbohydrates and 72.4% calories from proteins. Western diet (WD) contains 42% calories from fat, 42.7% calories from carbohydrates (mainly sucrose) and 15.2% calories from proteins and 0.2% cholesterol. Then, each group of these sixteen 23-week-old mice were fasted at ZT0, given CL316243 (3 mg/kg body weight; Sigma Aldrich) or vehicle (0.5% carboxymethylcellulose in sterilized water) by gavage at ZT10 and sacrificed at ZT16 (n = 8 per group).

first: Anne-Marie

last: Loustau


title: Traumatic Brain Injury Induces Early Barrier Protective Responses in Incisional Skin Wounds Accelerating Cutaneous Wound Healing

city: Ulm

first: Mahyar

last: Aghapour

address: Meyerhofstrasse 1

institute: Ulm University

summary: Though Traumatic Brain Injury (TBI) and skin trauma often occur together, it is unresolved whether TBI changes healing of skin wounds. We here explored whether TBI impacts on the sequence of events during skin wound healing. Incisional skin wounds from mice subjected to TBI were assessed employing unbiased transcriptome analysis and immunostaining. Transcriptome analysis at day 1 after combined trauma detects a significant enrichment of genes involved in macrophage and T cell recruitment and activation in contrast to skin wounds without TBI. At day 7 after combined trauma, genes in pathways of re-epithelialization including cornification and keratinization and of anti-inflammatory responses were highly enriched. These findings were confirmed by immunostaining with increased re-epithelialisation and cornification and an increased number of macrophages and T cells resolving inflammation. Moreover, the number of dermal myofibroblasts are highly increased in skin wounds after combined trauma. Collectively, TBI enforces an unprecedented defence response with an early onset of enhanced immunity, faster epidermal barrier formation, and a myofibroblast driven acceleration of wounds closure, all together likely counteracting systemic infection.

overall_design: RNA-seq profiling of mouse skin collected from uninjured and wounded skin either from TBI or non-TBI (sham) conditions at day1 and day7 post-TBI.

first: Florian

last: Olde Heuvel

first: Albrecht

last: Fröhlich

first: Adelheid

last: Heinzl

first: Pallab

last: Maity

first: Karmveer

last: Singh Shekhawat

first: Yongfang

first: Jinnan

first: Francesco

last: Roselli

first: Karin

last: Scharffetter-Kochanek


title: Real-time Evolutionary Landscape of the Bronchial Epithelium and Corresponding Dynamic Immune Cell Alterations in Lung Squamous Cell Carcinogenesis

city: Guangzhou

first: Sicheng

last: Chen

address: NO.74 Zhongshan Road 2, Yuexiu District

institute: The First Affiliated Hospital, Sun Yat-sen University

summary: The molecular mechanism by which tumor cells and their microenvironment evolve during lung squamous cell carcinoma (LUSC) carcinogenesis remains unclear, greatly limiting its early diagnosis and treatment effectiveness in patients. To replicate pathogenic processes and identify the determinants of cell evolution, a rat model is established using tobacco-derived carcinogens. Here, a series of single-cell transcriptome profiles of normal lung epithelium, hyperplasia, metaplasia, dysplasia, and squamous cell carcinoma in situ (CIS) to invasive squamous cell carcinoma (SCC) is presented. A large proportion of canonical copy number variations (CNVs) are detected in the hyperplasia/metaplasia stages, with their frequency increasing as the lesion progressed. Although bronchial epithelial cells exhibit substantial heterogeneity, three distinct cellular states are identified during their evolution into malignant cells. Immune sensing occurs at the earliest stages of cellular transformation. However, persistent exposure to carcinogens induces microenvironmental remodeling, which is characterized by monocyte-derived macrophage infiltration, plasmacytoid dendritic cell expansion, and progressive T-cell exhaustion. These findings depict the evolutionary trajectory of cancer and the immune microenvironment, emphasizing the need for CNV evaluation in early screening and immune-based therapy for lesions at a high risk of progression to LUSC.

overall_design: Female Wistar rats (8 weeks old, 200 ± 20 g) were housed in a pathogen-free environment at the animal center of the First Affiliated Hospital, Sun Yat-sen University. The rats were fasted overnight prior to instillation and were deprived of water on the day of the experiment. For an increased tumorigenic effect, iodized oil was used to dissolve the chemical carcinogens 3-MCA (100 mg/ml, Sigma) and DEN (95 mg/ml, Sigma) at 65–70 °C overnight. Basal anesthesia was induced through the intraperitoneal injection of 150 μl of 3% sodium pentobarbital solution (Sigma), followed by inhalation administration of isoflurane (RWD) to achieve deep anesthesia. Subsequently, the rats were randomly assigned to six groups (n = 8). In each group, six rats were instilled with 100 μl of carcinogen-containing iodized oil into the left lower lobe through a special blunt needle, while the remaining two rats were given 100 μl of iodized oil without carcinogens as a control. Whether the instillation was successful was confirmed via micro-CT (Bruker). To prevent infections, drinking water containing 1 g/l ampicillin (Sangon Biotech) and 1.5 g/l streptomycin (Sangon Biotech) was administered from day 2 to day 15 post-instillation. The rats were euthanized at various time point (on days 0, 7, 14, 21, 28 and 35) following instillation. lung tissues from the left lower lobe were excised, and a portion of the tissue was processed for hematoxylin and eosin (H&E) staining. The remaining tissue was used for the next single-cell suspension. We randomly selected two samples in each group for scRNA sequencing. However, due to technical issues during library preparation, two samples assigned to hyperplasia and metaplasia, respectively, were excluded from further analysis. Therefore, a total of ten samples underwent scRNA sequencing.

first: Baohong

last: Luo

first: Yuting

first: Tiantian

last: Yang

first: Bixia

last: Liu

first: Xiting

last: Liao

first: Xiaoke

last: Zheng

first: Tian

last: Tian

first: Jinxu

first: Qinru

last: Zhan

first: Xiaohua

last: Situ

first: Zhongpeng

last: Xie

first: Yanxia

first: Zhe-Sheng

first: Honglei

first: Zheng

first: Zunfu

last: Ke


title: Loss of AnkB upregulates stress-related pathways in skeletal muscle

city: Philadelphia

first: Damaris

last: Lorenzo

state: Pennsylvania

address: 1112 BRB II/III, 421 Curie Blvd

department: Cell and Developmental Biology

institute: University of Pennsylvania

summary: Human mutations in the ANK2 gene, which encodes ankyrin B (AnkB), lead to age- and diet-induced metabolic syndrome in mice. To investigate the contribution of skeletal muscle (SKM) AnkB to systemic energy balance and metabolic homeostasis, we developed skeletal muscle (SKM)-specific AnkB knockout (KO) (Ank2f/f; HSA-Cre+) mice. Physiological,cellular, biochemical and transcriptional characterization of these mice uncovered a muscle-autonomous role of AnkB in maintaning mitochondria health and muscle energetic homeostasis via the regulation of mitochondrial dynamics and  sarcoplasmic reticulum (SR) organization.

overall_design: We isolated total RNA from gastrocnemius muscle of control (WT) and Ank2 knock-out (KO) adult mice (4-month-old, n=6 mice/group) selectively lacking AnkB (Ank2) in skeletal muscle. We evaluated differential gene expression via paired-end RNA-seq analysis.

first: Kayleigh

last: Voos

first: Joyce

last: Tzeng


title: Cannabidiol abrogates cue-induced anxiety associated with normalization of mitochondria-specific transcripts and linoleic acid in the nucleus accumbens shell

city: New York

first: Yasmin

last: Hurd

address: 1470 Madison Avenue

institute: Icahn School of Medicine at Mount Sinai

summary: Anxiety disorders are one of the top contributors to psychiatric burden worldwide. Recent years have seen a dramatic rise in the potential anxiolytic properties ascribed to cannabidiol (CBD), a non-intoxicating constituent of the Cannabis Sativa plant. This has led to several clinical trials underway to examine the therapeutic potential of CBD for anxiety disorders. Yet, CBD’s anxiolytic effects are mixed with some studies reporting little to no impact on trait anxiety but significant reductions in pathological anxiety with suggestions that CBD’s effect may relate to triggered or cue-induced behavior. Here, we studied the effects of CBD on cued and non-cued behaviors and related neurobiological underpinnings. To investigate the effect of CBD on cue-induced anxiety, male rats underwent a fear conditioning protocol (odor associated with shock) followed by assessments of avoidance behavior. CBD (10 mg/kg) was administered 1hr prior to anxiety assessments. To understand molecular mechanisms associated with behavior, we investigated the transcriptome and lipid profile of the nucleus accumbens shell (NAcSh), a structure implicated in cue-mediated behaviors and aversion. Administration of CBD significantly reduced avoidance behavior, but only in animals repeatedly exposed to a shock-paired cue. CBD did not affect behavior in animals exposed to neutral cue or encoding of the cue behavioral response. RNA sequencing revealed substantial impact of the shock-paired cue in control animals, recruiting mechanisms ranging from cytoskeletal dynamics to mitochondria dysfunction. The shock-paired cue also resulted in elevated linoleic acid in vehicle animals which correlated with anxiety-like behavior. CBD either reversed or normalized these cue-induced molecular phenotypes. CBD also recruited lipid networks which correlated with transcripts involved in synaptic plasticity, signaling, and epigenetic mechanisms. These results suggest that CBD may specifically alleviate salient, conditioned anxiety and normalize related biological mechanisms in the NAcSh which may guide therapeutic interventions for anxiety disorders.

overall_design:
Rats underwent a fear conditioning shock protocol that was either paired with a neutral cue or lemon odor cue. The cue was then placed in anxiety-behavioral paradigms to induce cue-induced anxiety. Cannabidiol was given prior to the anxiety tests to assess impact on cue-induced anxiety.
Following the final shock rats were sacrificed and the nucleus accubmens shell was taken for RNAseq. Four groups were used- vehicle-neutral cue, CBD-neutral cue, vehicle anxiety cue, CBD anxiety cue.

first: Jacqueline-Marie N.

last: Ferland

first: Yasmin L.


title: Effect of beta3-adrenergic stimulation on liver gene expression in mice fed either a control diet or a western diet

first: Hervé

last: Guillou

summary: The effect of beta3-adrenegic stimulation on liver gene expression was assessed in male mice after they had previously been fed a control diet or a western diet for 13 weeks. Mice fed the control diet were healthy. Mice fed the western diet became obese. Beta 3 adrenergic stimulation was achieved by using Beta 3 adrenergic receptor (CL316243). Overall, this experiment allowed us to investigate the effect of Beta3-adrenergic stimulation on liver gene expression in healthy mice and in obese mice.

first: Céline

last: Martin

first: Claire

last: Naylies

first: Anne-Marie

last: Loustau

first: Arnaud

last: Polizzi

first: Anne

last: Fougerat

first: Nicolas

last: Loiseau

first: Yannick

last: Lippi


title: SPP1+ Neutrophils Mediate Resistance to lmmune Checkpoint Blockade in BAP1-Inactivated Tumors

city: Shanghai

first: Shiyun

last: Huang

address: Zhizaoju ROAD No.833

institute: Shanghai JiaoTong University

summary: BAP1 inactivation, observed across multiple human cancers, is linked to immune checkpoint blockade (ICB) resistance and adverse clinical outcomes. The mechanisms underlying BAP1-associated ICB sensitivity could provide potential targets to enhance ICB efficacy. Here, we showed that BAP1 inactivation fosters an immunosuppressive tumor microenvironment (TME), marked by increased infiltration of M2-like macrophages and neutrophils. Single-cell transcriptomic analysis revealed an expansion of SPP1+ neutrophils in ICB-treated, BAP1-inactivated tumors. These SPP1+ neutrophils displayed a pro-tumorigenic phenotype and conferred resistance to anti-PD-1 therapy by engaging with cytotoxic T cells via PD-1/PD-L1 signaling. Notably, depletion of neutrophils, but not macrophages, restored sensitivity to ICB in BAP1-inactivated tumors. Mechanistically, BAP1 loss significantly increased CCL2 secretion, driving neutrophil SPP1+ polarization, delaying neutrophil apoptosis, and promoting ICB resistance. This resistance could be significantly mitigated by targeting the CCL2-CCR2 axis. These results underscore the role of BAP1 in modulating the immune landscape and suggest that targeting CCL2-CCR2-mediated neutrophil polarization may overcome ICB resistance in BAP1-inactivated tumors.

overall_design: A single-cell suspension was prepared from the dissociation of tumors. For labeling, 40 μl of CD45 microbeads (Miltenyi #130052301) were added. After an incubation step (15 min at 4˚C) the antigen-antibody reaction was stopped by adding 800 μl ice-cold PBS. Then, the cell suspension mixture is loaded onto a MACS Column, which is placed in the magnetic field of a MACS Separator. The magnetically labeled CD45+ cells were retained within the column. The unlabeled cells ran through; this cell fraction was thus depleted of CD45+ cells, the CD45-negative cells were in the eluent buffer. After removing the column from the magnetic field, the magnetically retained CD45+ cells were eluted as the positively selected cell fraction and used for subsequent experiments. The samples were stained with TrypanBlue and the cell viability was evaluated microscopically.Single-cell suspensions (2×105 cells/mL) with PBS (HyClone) were loaded onto microwell chips using the Singleron Matrix® Single Cell Processing System. Barcoding Beads are subsequently collected from the microwell chip, followed by reverse transcription of the mRNA captured by the Barcoding Beads and to obtain cDNA, and PCR amplification. The amplified cDNA is then fragmented and ligated with sequencing adapters. The scRNA-seq libraries were constructed according to the protocol of the GEXSCOPE® Single Cell RNA Library Kits (Singleron) [21]. Individual libraries were diluted to 4 nM, pooled, and sequenced on Illumina novaseq 6000 with 150 bp paired end reads. Raw reads from scRNA-seq were processed to generate gene expression matrixes using CeleScope (https://github.com/singleron-RD/CeleScope) v1.9.0 pipeline. Briefly, raw reads were first processed with CeleScope to remove low quality reads with Cutadapt v1.17 to trim poly-A tail and adapter sequences. Cell barcode and UMI were extracted. After that, we used STAR v2.6.1b to map reads to the reference genome GRCm38 (ensemble version 92 annotation). UMI counts and gene counts of each cell were acquired with featureCounts v2.0.1software and used to generate expression matrix files for subsequent analysis.

first: Jiahao

last: Shi

first: Jianfeng

last: Shen

first: Xianqun

last: Fan


title: Single-nucleus RNA sequencing of the kidney from an early-stage chronic calcineurin inhibitor nephrotoxicity mouse model

city: Tokyo

first: Yasuhiro

last: Oda

address: 7-3-1 Hongo, Bunkyo

country: Japan

institute: The University of Tokyo Graduate School of Medicine

summary: We performed single-nucleus RNA sequencing (snRNA-seq) to characterize the transcriptomic profiles of kidneys from an early-stage chronic calcineurin inhibitor nephrotoxicity mouse model and its control at single-cell resolution.

overall_design: We created an early-stage chronic calcineurin inhibitor nephrotoxicity mouse model and its control. The kidneys were harvested, snap-frozen and subjected for analysis.

first: Hiroshi

last: Nishi

first: Teruhiko

last: Yoshida

first: Jeffrey

middle: B

last: Kopp

first: Masaomi

last: Nangaku


title: Platinum-resistant high-grade serous ovarian carcinoma

city: Nagoya

first: Kosuke

state: Aichi

address: 65 Tsuruma-cho

institute: Nagoya University

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

overall_design: Refer to individual Series


title: Drug intervention of radiation exposure induced BBB injury via mitochondria-mediated non-infectious inflammation

first: Jianhua

last: Qin

summary: Radiation-induced brain injury (RIBI) is a series of brain injuries caused by exposure to high doses of ionizing radiation, characterized by severe cognitive dysfunctions and brain necrosis.In this study, we described a biomimetic human blood-brain barrier (BBB) model that allowed to probe the responses to radiation exposure.This RNA-seq data illustrated that representative RIBI-associated pathological responses including BBB compromise, DNA break, inhibited cell proliferation, cell swelling and release of pro-inflammatory cytokines following acute radiation exposure. Based on the pathogenic mechanism study, we carried out drug screening and identified two drugs effectively ameliorated radiation-induced inflammation and BBB injury on the BBB model. Collectively, the study uncovered an unknown mitochondria-mediated inflammation involved in the pathogenesis of RIBI, indicating mitochondria can be utilized as a potential target for developing new radioprotective measures.

overall_design: In this study, we developed a biomimetic human blood-brain barrier (BBB) model composed of multiple cellular components to evaluate the therapeutic effect of radiation-induced brain injury (RIBI) following exposure to γ-ray by drug intervention. The controls are from blood channel (n=3) that receive no radiation exposure and are compared  to blood channel (n=3), a JAK1 inhibitor Intervention (n=3) and a mitochondrial protectant Intervention (n=3) that receive 16Gy of radiation, respectively.

first: Peng

last: Wang

first: Jiayue

last: Liu

first: Min

last: Zhang

first: Juan

last: Yang

first: Peihan

last: Lian

first: Xiu

last: Cheng


title: Gene expression profiles of platinum-resistant high-grade serous ovarian carcinoma

summary: Ovarian cancer is one of the leading causes of death in females in the world. High-grade serous ovarian carcinoma (HGSOC) is the most common histological subtype, and platinum platinum-resistance is a clinical challenge, In this study, we investigated the gene expression profiles of platinum-resistant and platinum-sensitive HGSOC.

overall_design: Archival fresh frozen samples at the Hyogo Prefectural Cancer Center Biobank were used for analysis. Total RNA was extracted from the samples. Then, Library construction and pair-end sequencing were conducted by Novogene, Inc. (Beijing, China).

first: Kazuhiro

last: Suzuki

first: Akira

last: Yokoi


title: Critical opposing roles for TFEB andTFE3 in melanoma progression

city: Oxford

first: Pakavarin

last: Louphrasitthiphol

address: Old Road Campus Research Building (off Roosevelt Drive)

department: Nuffield Department of Clinical Medicine

country: United Kingdom

institute: Ludwig Institute for Cancer Research

summary: Unlike MITF-M, the melanocyte-specific isoform of MITF, TFEB, TFE3 and non-melanocyte MITF isoforms are regulated primarily by mTORC1-mediated phosphorylation at the lysosome that promotes their cytoplasmic retention. As low levels of glucose or amino acids trigger down-regulation of MITF, it is likely that on nutrient limitation some MITF functions are assumed by TFE3 and TFEB, enabling MITFLow melanoma cells to survive and proliferate. The role TFEB and TFE3 in melanoma biology and their impact on MITF-driven proliferation is poorly understood.

overall_design: TFEB and TFE3 KO of 501mel melanoma cell lines were generated using guides targetting TFE3 (GGTACTGTTTCACCTGCTGC) and TFEB (AGTACCTGTCCGAGACCTAT). KO cells were clonally isolated and validated prior to experiment.

first: Diogo

last: Dias

first: Colin

middle: R

last: Goding


title: Genome-wide profiling of TFE3 targets in melanoma

type: Genome binding/occupancy profiling by high throughput sequencing

overall_design: 501mel melanoma cell lines engineered to express ectopic-doxycycline-inducible-HA-epitope-tag TFE3. Cells were then treated with either 250nM Torin1 or control for 6h. Samples were then processed as described below.


title: Gene expression profile at single cell level of kidney cells from zebrafish at 4 days post-injury (4 dpi).

city: chongqing

first: Xiaoliang

address: xinqiao street

institute: Xinqiao Hospital, Army Medical University (Third Military Medical University)

summary: Single cell RNA sequencing were used to analyze the diversity of kidney cells from 4 dpi zebrafish.  To induce AKI, we injected gentamicin (Gent; 2.7 μg/μL, 20 μL per fish) intraperitoneally into 12 randomly selected adult zebrafish, and collected their kidneys at 4 days post-injury (4 dpi).

overall_design: Total cells from 4 dpi zebrafish kidneys were analyzed using single cell RNA sequence

first: Chi


title: Transcriptomic analysis of trastuzumab-resistant HER2-positive cells

city: Seoul

first: Kyoung-Seok

last: Oh

address: 101 Daehak-ro, Jongno-gu

institute: Seoul National University Cancer Research Institute

summary: Trastuzumab resistance remains a clinical challenge in ᎻᎬᎡ2-positive cancers. We investigated the transcriptome of trastuzumab-resistant (HR) ᎻᎬᎡ2-positive cells to identify novel resistance mechanisms for potential therapeutic targeting.

overall_design: SNU-2670 and SNU-2670HR cells were seeded and incubated under normal culture condition for 72 h followed by RNA isolation for subsequent RNA sequencing.

first: Ah-Rong

last: Nam

first: Ju-Hee

last: Bang

first: Yoojin

last: Jeong

first: Sea

middle: Y

last: Choo

first: Hyo

middle: J

last: Kim

first: Su

middle: I

last: Lee

first: Jae-Min

first: Jeesun

last: Yoon

first: Tae-Yong

first: Do-Youn


title: Noninvasive focused ultrasound non-specifically activating spleen immunological function to universally suppress tumor proliferation: a new strategy for cancer immunotherapy -NK cells

city: Xi’an

first: Wei

last: Dong

address: No.157#, The West 5th Road

department: The Second Affiliated Hospital

institute: Xi’an Jiaotong University

summary: NK cells were sorted from the spleen using the Beckman Kurt MoFlo Astrios ultra high speed flow cytometry sorting system. Subsequently, general transcriptome sequencing was performed when the positive cell rate was greater than 90% detected by flow cytometry. The cDNA library construction and sequencing of all RNA samples were performed by Shanghai Ouyi Biomedical Technology Co., LTD. Transcriptome sequencing was performed to screen differentially expressed genes (DEGs). Then, gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis were applied to annotate the function of the DEGs. The results revealed that FUS firstly regulated calcium-related signaling pathways to further modulate other signaling pathways, such as ECM-receptor interaction, PI3K-AKT signaling pathway, Rap1 signaling pathway and Hippo signaling pathway to promote immune cell proliferation, migration and activation to suppress cancer cell deterioration.

overall_design: NK cells (CD45+ CD3- NK1.1+) were sorted from the spleen using the Beckman Kurt MoFlo Astrios ultra high speed flow cytometry sorting system (MoFlo Astrios EQ, Beckman Coulter, lnc, USA). Subsequently, general transcriptome sequencing was performed when the positive cell rate was greater than 90% detected by flow cytometry (CytoFLEX LX, Beckman Coulter Life Sciences, USA). RNA purity and quantification were evaluated using the NanoDrop 2000 spectrophotometer (Thermo Scientific, USA). RNA integrity was assessed using the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA). Then the libraries were constructed using VAHTS Universal V6 RNA-seq Library Prep Kit according to the manufacturer’s instructions. The transcriptome sequencing and analysis were conducted by OE Biotech Co., Ltd. (Shanghai, China).


title: Transcriptome analysis by RNA sequencing of primary mouse sensory neurons of the dorsal root ganglia (DRGs) treated with glucosylceramide (GlcCer 24:1) versus vehicle

city: Frankfurt

first: Irmgard

last: Tegeder

state: Hessen

address: Theodor Stern Kai 7

department: Clinical Pharmacology

institute: Goethe University Frankfurt

summary: Glucosylceramides (GlcCer) are endogenous lipids which are generated in the ER from ceramides via the enzyme UDP-glucose ceramide glucosyltransferase (UGCG) and are required for the  generation of gangliosides. They are metabolized and degraded in the lysosome via the lysosomal enzyme glucocerebrosidase (GBA1). Biallelic mutations of GBA1 lead to Gaucher disease, which is a the lysosomal storage disease. Monoallelic mutations of GBA1 are associated with a high risk of sporadic Parkinson's Disease (PD). GBA1 dysfunctions increase the accumulation and aggregation of alpha synuclein. We have previously shown that accumulation of GlcCer is associated with sensory neuropathy and pain in PD (Mov Disord. 2020 Oct;35(10):1822-1833. doi: 10.1002/mds.28186) and in the DRGs and sciatic nerve of Pink1-/-SNCA A53T double mutatnt mice (Neuropathol Appl Neurobiol. 2021 Dec;47(7):1060-1079. doi: 10.1111/nan.12734). Here, we assessed the effects of GlcCer 24:1 (the most abundant GlcCer) on primary sensory neurons of the dorsal woot ganglia of C57BL6 mice via RNA-sequencing in four biological replicates per group. DRGs were were rapidly excised and collected in HBSS. Primary neurons were prepared via tissue digestion in collagenase/dispase and DNAse and collection via passaging through a BSA filter. They were seeded on Poly-L-Lysine and laminin coated cover slips in serum-free Neurobasal medium containing 1x B27 supplement , 1x Pen/Strep, 200 ng/ml nerve growth factor nd 2 mM L-glutamine at 37 °C and 5% CO2 and 95% humidity. The day after cell seeding, GlcCer 24:1 was added at a final concentration of 1 µM. Control cells received the vehicle treatment which was 1:10000 dilution of a 2:1 mixture of chloroform and methanol. After two days of culture cells were collected and total RNA was isolated using a single cell RNA isolation kit (picoPure Thermo Scientific). Quantity of total RNA was assessed with a Qubit 2.0 fluorometer and quality was checked using Agilent's bioanalyzer. Indexed sequencing libraries were prepared with TAKARA SMARTer Ultra Low RNA Kit for sequencing compatible with Illumina NGS. The alignment was performed with SeqMan NGen 17 (Lasergene) and with CLC genomic workbench (Qiagen) using the reference genome mm10 provided from UCSC (GRCm38) as template, a minimum read length of 35 bp and automatic adapter trimming. Sequence reads were normalized as TMM (Trimmed Mean of the M-values) using the EdgeR algorithm. Differential gene expression was analyzed with CLC genomic workbench and with ArrayStar 17 (Lasergene) using general linear models and adjustment of P-values according to Benjamini Hochberg.

overall_design: Total RNA was prepared from primary neurons of the dorsal root ganglia of 4 mice per group. DRG cultures were treated with GlcCer 24:1 (1 µM) or vehicle (1:10000 of 2:1 mixture of chloroform and methanol). RNA sequencing was  performed of 4 biological replicates per group using an Illumina NextGen 2000 system.


title: Transcriptome sequencing of E. coli-infected macrophages and E. coli-infected macrophages treated with PGD2 inhibitors

city: Hohhot

first: Xiaolin

last: Yang

address: No. 29, Erdosdong Road, Saihan District

institute: Inner Mongolia Agricultural University

summary: The pathogenesis of endometritis in dairy cows is related to pathogenic microorganisms, local inflammatory injury and uterine microecological disorders. Escherichia coli (E. coli) is the main causative pathogen of endometritis in dairy cows. Therefore, we investigated E. coli-induced endometritis mechanisms in dairy cows using bovine bone marrow-derived macrophages (BMDMs).E. coli infection was performed on BMDMs for 4 hours. BMDMs were pretreated with PGD2 inhibitors (H-PGDS Inhibitor 1, HQL-79) for 24 hours, followed by E. coli infection for 4 hours. Samples were collected and evaluated.

overall_design: Four types of samples were collected: uninfected macrophages, macrophages infected with E. coli for 4 hours, and macrophages pretreated with a PGD2 inhibitor (H-PGDS Inhibitor 1, HQL-79) for 24 hours before being infected with E. coli for 4 hours. Each sample type was replicated six times. First, we compared uninfected samples with E. coli-infected samples to identify genes pertinent to the study. Next, we compared the PGD2 inhibitor-treated samples with the E. coli-treated samples.

first: 小林

last: 杨

first: 顺义

last: 张

first: 苏龙

last: 哈西

first: 金山

last: 曹