title: Daidzein activates Akt pathway to promote the proliferation of female germline stem cells through upregulating Clec11a

city: Shanghai

first: Ji

last: Wu

address: No.800, Dongchuan Road, Minhang District

institute: Shanghai Jiao Tong University

summary: Female germline stem cells (FGSCs) have been successfully isolated from postnatal mammalian and human ovarian tissues. However, the effects and mechanisms of action of natural small-molecule compounds on FGSCs are largely unknown. Here, we determined the effects of daidzein, a phytoestrogen present in soybean , on cell viability and proliferation using Cell Counting Kit-8 (CCK8)  and 5-ethynyl-2-deoxyuridine (EdU). We found that daidzein promoted the viability and proliferation of FGSCs in a concentration-dependent manner. To elucidate the mechanism underlying this, we performed RNA-Seq in daidzein-treated FGSCs and controls. The results showed that there were 153 upregulated and 156 downregulated genes after daidzein treatment. We confirmed the expression of some genes related to cell proliferation in the sequencing results by RT-PCR, such as Type C lectin domain family 11  member a (Clec11a), Mucin1 (Muc1), Glutathione peroxidase 3 (Gpx3), and Tet methylcytosine dioxygenase 1(Tet1). The high expression of Clec11a at the protein level after daidzein treatment was also confirmed by western blotting. Furthermore, recombinant mouse Clec11a (rmClec11a) protein was shown to promote the viability and proliferation of FGSCs. However, knockdown of Clec11a inhibited the viability and proliferation of FGSCs, which could not be rescued by the administration of daidzein. These results indicate that daidzein promoted the viability and proliferation of FGSCs through Clec11a. In addition, both daidzein and rmClec11a activated the Akt signaling pathway in FGSCs. However, Clec11a knockdown inhibited this pathway, which could not be rescued by daidzein administration. Taken together, our findings revealed that daidzein activates the Akt signaling pathway to promote cell viability and proliferation through upregulating Clec11a. This study should deepen our understanding of the developmental mechanism of FGSCs and female infertility.

overall_design: After FGSCs were treated with different concentrations of daidzein, the best concentration was selected. The expression of downstream target proteins and key signal pathways were detected by RNA-Sequencing and western blot.

first: Fangfang

last: Li

first: Xiaopeng

last: Hu


title: The role of OASL in Helicobacter pylori infection and Gastric Cancer

status: Public on Mar 19 2025

city: Changsha

first: Fen

last: Wang

state: Hunan

address: 138 Tongzipo Road

country: China

institute: The Third Xiangya Hospital, Central South University

type: Expression profiling by high throughput sequencing

summary: Our previous studies have shown thatHelicobacter pylori can induce the expression of OASL, which plays a crucial role in gastritis-cancer progression. In order to further investigate the detailed mechanism of OASL, we constructed an OASL overexpression model in HGC27 cells.

overall_design: RNA-seq profiling of OASL-overexpressing HGC27 cells as well as corresponding controls.

first: Minglin

last: Zhang


title: single nucleous RNAseq data from brain tissue provided from patients undergoing neurosurgery

city: Palo Alto

first: Takaya

last: Ishii

state: California

address: 3165 PORTER DRIVE

country: USA

institute: Stanford University

summary: We have employed a single nucleous sequencing approach using 10x Genomics platform to investigate the pathophysiology of post-operative delirium (POD). POD is related to high mortality and long-term cognitive failure, but its mechanism is still unclear. This study represents the first transcriptome analysis of POD brain and provide new insight into POD pathology and prediction.

overall_design: All patient underwent brain resection surgery for epilepsy treatment. Resected brain tissues were gathered and anallyzed using snRNAseq.

first: Gen

last: Shinozaki

first: Kazuki

last: Shibata


title: Gradients of Recognition Molecules Shape Synaptic Specificity of Visuomotor Transformation

city: Waltham

first: Yerbol

last: Kurmangaliyev

state: MA

address: 415 South Street, MS 029

department: Biology

institute: Brandeis University

summary: Converting sensory information into motor commands is fundamental to most of our actions. In Drosophila, visuomotor transformations are mediated by Visual Projection Neurons (VPNs). These neurons encode object location and motion to drive directional behaviors through a synaptic gradient mechanism. However, the molecular origins of such graded connectivity remain unknown. We addressed this question in a VPN cell type called LPLC2, which integrates looming motion and transforms it into an escape response through two separate dorsoventral synaptic gradients at its inputs and outputs. We identified two corresponding dorsoventral expression gradients of cell recognition molecules within the LPLC2 population that regulate this synaptic connectivity. Dpr13 determines synaptic outputs of LPLC2 axons by interacting with its binding partner, DIP-ε, expressed in the Giant Fiber – a neuron that mediates escape. Similarly, Beat-VI regulates synaptic inputs onto LPLC2 dendrites by interacting with Side-II expressed in upstream motion-detecting neurons. Behavioral, physiological, and molecular experiments demonstrate that these coordinated molecular gradients regulate synaptic connectivity, enabling the accurate transformation of visual features into motor commands. As continuous variation in gene expression within a neuronal type is also observed in the mammalian brain, graded expression of cell recognition molecules may represent a common mechanism underlying synaptic specificity.

overall_design: Single-cell RNA sequencing of the developing LPLC2, LPLC1 and LC4 neurons.

first: Mark

last: Dombrovski

middle: Z

first: Gwyneth

middle: M

last: Card

first: S

middle: L

last: Zipursky


title: Transcriptome analysis reveals key genes and pathways that the LPS, DHEA and Nb23-bi acts on testis

city: Beijing

first: Yuan

last: Zheng

address: Beijing

institute: Peking University

summary: Our research is helpful to understand the Nb23-bi and DHEA synergistically alleviated LPS induced inflammatory responses in mouse testis tissue.

overall_design: A single dose of lipopolysaccharide was intraperitoneally injected into male mice, which induced inflammation in testis. A single dose of DHEA or DHEA with Nb23-bi was intraperitoneally injected 6 h after LPS injection. The same volume of 1× phosphate buffer saline was injected as negative control. Control vehicle (CTRL), LPS alone (LPS), LPS combined with DHEA (LPS+DHEA), or LPS combined with both DHEA and Nb23-bi (LPS+DHEA+Nb). All samples were subjected to RNA sequencing analysis.

first: Jinpeng

last: Sun


title: Hypercapnia induces long-term DNA methylation changes in skeletal muscle

city: Nutley

first: Andy

last: Madrid

state: NJ

address: 111 Ideation Way

institute: Hackensack Meridian Health

type: Methylation profiling by high throughput sequencing

summary: Skeletal muscle dysfunction and elevated CO2 in the blood, or hypercapnia, are both associated with higher mortality in acute and chronic pulmonary diseases. Hypercapnia causes accelerated protein degradation, reduced protein synthesis, and dysfunctional myogenesis. We have recently reported that hypercapnia-induced skeletal myogenic dysfunction persists after resolution of CO2 exposure, suggesting the existence of durable cellular aberrations in previously hypercapnic cells. No data on lingering myofiber atrophy after hypercapnia resolution currently exist. Hypercapnia and age-induced skeletal muscle loss phenotypically overlap, and myogenic progenitor cells from hypercapnic mice elicit senescence-associated transcriptional programs. While aging is characterized by unique DNA methylation and other epigenetic changes, the potential association of hypercapnia and age-related differential methylation have never been investigated. In the present study, we show that hypercapnic mice elicit protracted muscle deterioration even after returning to normocapnia and demonstrate aberrant DNA methylation in comparison to animals never exposed to elevated CO2. We also show that these DNA methylation changes do not overlap with age-induced alterations.

overall_design: Whole-genome methylation sequencing of skeletal muscle tissue from mice exposed to hypercapnic conditions, six months post-hypercapnia, and mice through three aging stages


title: Regulation of immune microenvironments by polyetheretherketone surface topography for improving osseointegration

city: Xi'an

first: Yuqing

last: Zhao

address: Changle West Road No. 145

institute: The Fourth Military Medical University

summary: Optimizing the immune microenvironment is essential for successful implant osseointegration. In this study, four different nano/microstructures were fabricated on polyetheretherketone (PEEK) substrates by varying the agitation speed during sulfonation to influence osteoimmunomodulation and implant integration. The results indicate that nano/microstructures with minimal dimensions (SP450) inhibit actin polymerization by reducing calcium influx through Piezo1, activating the anti-inflammatory M2 macrophage phenotype. Among the tested specimens, SP450 exhibited the lowest expression levels of tumor necrosis factor-α and interleukin-1β while releasing the highest levels of anti-inflammatory factors, including interleukin-4 and interleukin-10. This optimized immune environment promotes the osteogenesis of MC3T3-E1 pre-osteoblasts and enhances the osseointegration of PEEK implants. Transcriptomic analysis and validation experiment further revealed that SP450 inhibits osteoclastic differentiation by down-regulating transforming growth factor-β2 and suppressing the NF-κB signaling pathway. These findings suggest that manipulating the surface topography of PEEK implants is an effective strategy for enhancing osseointegration with promising clinical applications.

overall_design: RNA-seq profiling of MC3T3-E1 cells cultured on nano/microstructured PEEK with or without supernatant from RAW264.7.


title: Regulation of immune microenvironments by polyetheretherketone surface topography for improving osseointegration [macrophages]

overall_design: RNA-seq profiling of RAW264.7 cells cultured on different topography surface of Polyetheretherketone.


title: Combination of Cas9 and adeno-associated vectors (AAVs) enables efficient in vivo knockdown of precise miRNAs in the rodent brain

city: Marseille

first: Eduardo

last: Gascon

address: 27 boulevard Jean Moulin

department: Institut de Neurosciences de la Timone

country: France

institute: Aix-Marseille University, CNRS

summary: Although the advent of Cas9 technology has expanded our ability to precisely edit the genome, manipulating microRNAs in vivo has been shown to be particularly challenging, especially in the brain. Here, we sought to generate novel tools aiming at targeting and efficiently downregulating defined microRNAs species in a cell-specific manner so that their function in discrete neuronal networks could be investigated. Focusing on miR-124, a microRNA highly expressed in the mammalian brain and transcribed from three independent chromosomal loci, we designed and validated different gRNAs directed against this miRNA. In vitro, our Cas9 designs show not only a significant reduction in miR-124 levels but also a functional effect on miR-124 silencing. Similarly, when packed into AAV vectors and injected into the mouse cortex, miR-124-Cas9 vectors strongly downregulate miR-124 levels without affecting the expression of other miRNAs. In parallel, levels of endogenous miR-124 targets exhibit a significant increase supporting the release of its silencing activity. To functionally validate our tools, we provide evidences that deletion of miR-124 in the subventricular zone altered migration of newly generated neurons into the olfactory bulb. Finally, we also showed that our vectors altered the expression of Gria 2, a canonical target of miR-124, and modified the Ca2+ permeability of AMPA receptors. These tools are expected to help elucidating miRNA function in complex experimental settings such as brain networks in vivo.

overall_design: A set of seven animals received an injection of AAV-Cas9-miR-124-g4 and AAV-Cas9-miR-124-empty in each motor cortex. RNA sequencing was preformed on FANS sorted Cas9+ and Cas9- nuclei.

first: David

last: Roura-Martinez

first: Natalia

last: Popa

first: Florence

last: Jaouen

first: Cynthia

last: Rombaut

first: Catherine

last: Lepolard

first: Dipankar

last: Bachar

first: Ana

last: Borges

first: Maxime

last: Villet

first: Sebastien

last: Moreno

first: Helene

last: Marie


title: Metabolic Profiling of Adult and Pediatric Gliomas Reveals Enriched Glucose Availability in Pediatric Gliomas and Increased Fatty Acid Oxidation in Adult Gliomas

city: New York

first: Varshini

last: Vasudevaraja

state: New York

address: 240 East 38th street

institute: NYU Langone Health

summary: Gliomas are the most common primary brain tumors and a major source of mortality and morbidity in adults and children. Recent genomic studies have identified multiple molecular subtypes; however metabolic characterization of these tumors has thus far been limited. We performed metabolic profiling of 114 adult and pediatric primary gliomas and integrated metabolomic data with transcriptomics and DNA methylation classes. We identified that pediatric tumors have higher levels of glucose and reduced lactate compared to adult tumors regardless of underlying genetics or grade, suggesting differences in availability of glucose and/or utilization of glucose for downstream pathways. Differences in glucose utilization in pediatric gliomas may be facilitated through overexpression of SLC2A4, which encodes the insulin-stimulated glucose transporter GLUT4. Transcriptomic comparison of adult and pediatric tumors suggests that adult tumors may have limited access to glucose and experience more hypoxia, which is supported by enrichment of lactate, 2-hydroxyglutarate (2-HG), even in isocitrate dehydrogenase (IDH) wild-type tumors, and 3-hydroxybutyrate, a ketone body that is produced by oxidation of fatty acids and ketogenic amino acids during periods of glucose scarcity. Our data support adult tumors relying more on fatty acid oxidation, as they have an abundance of acyl carnitines compared to pediatric tumors and have significant enrichment of transcripts needed for oxidative phosphorylation. Our findings suggest striking differences exist in the metabolism of pediatric and adult gliomas, which can provide new insight into metabolic vulnerabilities for therapy.

overall_design: RNA-seq profling of brain tumor samples collected from adult and pediatric patients

first: Vladislav

middle: O

last: Sviderskiy

first: Luiz Gustavo

last: Dubois

first: James

last: Stafford

first: Elisa

middle: K

last: Liu

first: Jonathan

last: Serrano

first: Richard

last: Possemato

first: Matija

last: Snuderl


title: DNA methylation data from brain tissue provided from patients undergoing neurosurgery

first: Takaya

last: Ishii

type: Methylation profiling by genome tiling array

summary: We have employed DNA methylation analysis using resected brain tissues from patients with epilepsy to investigate the pathophysiology of post-operative delirium (POD). POD is related to high mortality and long-term cognitive failure, but its mechanism is still unclear. This study represents the first transcriptome analysis of POD brain and provide new insight into POD pathology and prediction.

overall_design: Bisulfite-converted brain DNA from the 18 nuerosurgery patients were hybridized into the Illumina Infinium Methylation EPIC Kit array

first: Gen

last: Shinozaki

first: Tomoteru

last: Seki


title: A versatile mouse model to advance human microglia transplantation research in neurodegenerative diseases

city: Rotselaar

first: Daan

last: Moechars

address: Catharinalaan 43

country: Belgium

institute: KULeuven

summary: Recent studies highlight the critical role of microglia in neurodegenerative disorders and emphasize the need for humanized models to accurately study microglial responses. Human-mouse microglia xenotransplantation models are a valuable platform for functional studies and for testing therapeutic approaches, yet currently those models are only available for academic research. This hampers their implementation for the development and testing of medication that targets human microglia.  We developed the hCSF1Bdes mouse line, which is suitable as a new transplantation model and available to be crossed to any disease model of interest. The hCSF1Bdes model created by CRISPR gene editing is RAG2 deficient and expresses human CSF1. Additionally, we crossed this model with two humanized App KI mice, the AppHu and the AppSAA. Flow cytometry, immunohistochemistry and bulk sequencing was used to study the response of microglia in  the context of Alzheimer’s disease.  Our results demonstrate the successful transplantation of iPSC-derived human microglia into the brains of hCSF1Bdes mice without triggering a NK-driven immune response. Furthermore, we confirmed the multipronged response of microglia in the context of Alzheimer’s disease. The hCSF1Bdes and the crosses with the Alzheimer’s disease knock-in model AppSAA and the humanized App knock-in control mice, AppHu are deposited with EMMA and fully accessible to the research community. The hCSF1Bdes mouse is available for both non-profit and for-profit organisations, facilitating the use of the xenotransplantation paradigm for human microglia  to study complex human disease.

overall_design: RNAseq profiling of flow cytometry-sorted human H9-embryonic stem cell-derived microglia (CD11b positive/human CD45 positive) xenotransplanted in the AppSAA mouse model of Alzheimer's disease and the control AppHu mouse model and harvested at 6 months of age

first: Lutgarde

last: Serneels

first: Annerieke

last: Sierksma

first: Emanuela

last: Pasciuto

first: Ivana

last: Geric

first: Arya

last: Nair

first: Anna

last: Martinez-Muriana

first: An

last: Snellinx

first: Bart

last: De Strooper


title: Superior preclinical efficacy of co-treatment with BRG1/BRM and FLT3 inhibitor against AML cells with FLT3 mutations

city: Houston

first: Xiaoping

last: Su

state: Texas

address: 7300 Brompton St, Apt 5633

institute: MD Anderson Cancer Center

summary: Although treatment with standard frontline therapies, including a FLT3 inhibitor (FLT3i) reduces AML burden and achieves clinical remissions, most patients with AML with FLT3 mutation relapse due to therapy-resistant stem/progenitor cells. The core ATPases, BRG1 (SMARCA4) and BRM (SMARCA2) of the canonical (c) BAF (BRG1/BRM-associated factor) complex is a dependency in AML cells, including those harboring FLT3 mutations. We have previously reported that treatment with FHD-286, a BRG1/BRM ATPases inhibitor, induces differentiation and loss of viability of AML stem/progenitor cells. Findings of present studies demonstrate that treatment with FHD-286 induces lethality in AML cells, regardless of sensitivity or resistance to FLT3i. This efficacy is associated with the induction of gene-expression perturbations responsible for growth inhibition, differentiation, as well as a reduced AML-initiating potential of the AML cells. Additionally, co-treatment with FHD-286 and FLT3i exerts superior pre-clinical efficacy against AML cells and patient-derived (PD) xenograft (PDX) models of AML with FLT3 mutations.

overall_design: Paired end RNA Seq of OCI-AML3 and OCI-AML3-FLT3-ITD cells treated with FHD-286 for 16 hours.

first: Warren

last: Fiskus

first: Kapil

last: Bhalla


title: Fibronectin mediates Endothelial-to-mesenchymal Transition in retina angiogenesis

first: Dan

last: Liu

address: No. 932 Lushan South Road, Changsha City, Hunan Province

institute: Central South University

summary: Purpose: To investigate the role of endothelial-mesenchymal transition (EndoMT) in pathological retinal angiogenesis and identify key molecular mediators in retina angiogenesis. Methods: RNA sequencing was performed on retinal tissue from oxygen-induced retinopathy (OIR) mouse model to analyze gene expression patterns. Gene Set Enrichment Analysis was used to examine the correlation between EMT and angiogenesis gene sets. Fibronectin (FN1) expression was evaluated in endothelial cells, and its function was assessed through siRNA mediated knockdown in both in vitro angiogenesis assays and the OIR model. Results: EndoMT occurred early in retinal angiogenesis development, with significant correlation between EMT and angiogenesis gene sets. FN1 was identified as the most significantly upregulated EMT-related gene in endothelial cells. siRNA-mediated inhibition of FN1 effectively prevented VEGF-induced angiogenesis in vitro and reduced pathological angiogenesis in the OIR model. Conclusions: EndoMT is a crucial early event in pathological retinal angiogenesis, with FN1 serving as a key mediator. Targeting FN1 may provide a novel therapeutic strategy that could synergize with anti-VEGF treatments to more effectively treat pathological angiogenesis in DR and ROP, particularly in cases of poor response to anti-VEGF therapy alone.

overall_design: RNA-seq techniques to delve into the alterations in transcription and pinpoint a target associated with hypoxia-triggered retinal angiogenesis at P17 of wildtype C57BL/6J mice and OIR mice

first: Zhishang

last: Meng

first: Chen

last: Jin

first: Fang

last: chen

first: Li

last: Pu

first: ze

last: wu

first: Jing

last: Luo

first: Wenyi

last: Wu


title: Transcriptome-wide mapping of N3-methylcytidine modification at single-base resolution

city: hangzhou

first: Yunyi

last: Gao

state: Zhejiang

address: Zijingang Campus of Zhejiang University,Yuhangtang Road No.388

institute: Zhejiang university

summary: 3-Methylcytidine (m3C), a prevalent modification of tRNAs, was recently identified in eukaryotic mRNAs. However, its precise distribution and formation mechanisms in mRNAs remain elusive. Here we develop a novel approach, m3C immunoprecipitation and sequencing (m3C-IP-seq), utilizing antibody enrichment to profile the m3C methylome at single-nucleotide resolution. m3C-IP-seq captures 12 m3C modification sites in cytoplasmic tRNA isoacceptors and 2 in mitochondrial tRNA isoacceptors. Moreover, m3C-IP-seq permits the comprehensive profiling of m3C sites in mRNAs and lncRNAs, with their presence reliant on a nuclear isoform of METTL8. A significant proportion of m3C sites is concentrated in the 3’ untranslated region (3’ UTR) of mRNAs. Additionally, m3C methylation is dynamic and responds to hypoxia. Functionally, m3C formation in the 3’ UTR is associated with mRNA degradation. Collectively, our data demonstrate the widespread presence of m3C modification in the human transcriptome and provide a resource for functional studies of m3C-mediated RNA metabolism.

sample_organism:
Homo sapiens
synthetic construct

platform_organism:
Homo sapiens
synthetic construct

overall_design: [dataset 1] 6 samples. Duplicates for m3C-IP-seq of tRNA samples, including three sections of tRNA m3C Input, tRNA m3C IP, and tRNA m3C Dm in the HEK293T cell line. [dataset 2] 6 samples. Duplicates for m3C-IP-seq of polyA+ RNA samples, including three sections of m3C Input, m3C IP, and m3C Dm in the HEK293T cell line. [dataset 3] 5 samples. m3C-IP-seq of harboring various abundances of m3C spike-ins, including 0%, 20%, 40%, 80%, and 100% abundance in synethesisd m3C oligos. [dataset 4] 3 samples. m3C-IP-seq of tRNA samples mixed with 10% m3C spike-ins, including three sections of tRNA m3C Input, tRNA m3C IP, and tRNA m3C Dm in the HEK293T cell line. [dataset 5] 2 samples. RNA-seq of RNA samples from HEK293T cells with or without METTL8.

first: Saisai

last: We

first: Xiangwei


title: Incretin triple agonist retatrutide (LY3437943) alleviates obesity-associated cancer progression

city: Nashville

first: Matthew

middle: A

last: Cottam

state: TN

address: 2301 Vanderbilt Place

department: Surgical Sciences

institute: Vanderbilt University Medical Center

summary: Medical weight loss is becoming increasingly prevalent, but impacts on cancer remain unclear. We report that in mice with significant retatrutide (RETA, LY3437943)-induced weight loss, reduced food intake, and improved glucose tolerance and other metabolic parameters, subsequent obesity-associated pancreatic cancer engraftment was reduced, and tumor onset was delayed, with blunted progression resulting in a 14-fold reduction in tumor volume compared to only 4-fold reduction in single agonist semaglutide-treated mice. Interestingly, when RETA was withdrawn before tumor implantation, the anti-tumor benefits of RETA persisted with reduced tumor burden despite weight regain. RETA induced durable anti-tumor immunity evidenced by activation of pro-inflammatory pathways in the tumor microenvironment. These findings suggest that patients with RETA-mediated weight loss may benefit from reduced cancer risk and improved outcomes.

overall_design: Bulk RNA -Seq data from tumor (subcutaneously injected with KPCY Pancreatic Cancer Cells) in obese C57BL/6J mice, treated with vehicle (water, N = 10), RETA (N = 12), or RETA-withdrawal (switched from RETA to water after stabilized weight loss, N = 14), grown for 18 days, excised and snap frozen.

first: Sandesh

middle: J

last: Marathe

first: Emily

middle: W

last: Grey

first: Maragret

middle: S

last: Bohm

first: Sydney

middle: C

last: Joseph

first: Arvind

middle: V

last: Ramesh

first: Kamran

last: Idrees

first: Kathryn

middle: E

last: Wellen

first: Alyssa

middle: H

last: Hasty

first: Jeffrey

last: Rathmell

first: Liza

last: Makowski


title: A microglia clonal inflammatory disorder in Alzheimer’s Disease II

first: Bic

last: MSKCC

state: NY

address: 1275 York Ave.

institute: Memorial SLoan-Kettering Cancer Center

summary: Somatic genetic heterogeneity resulting from post-zygotic DNA mutations is widespread in human tissues and can cause diseases, however few studies have investigated its role in neurodegenerative processes such as Alzheimer’s Disease (AD). Here we report the selective enrichment of microglia clones carrying pathogenic variants, that are not present in neuronal, glia/stromal cells, or blood, from patients with AD in comparison to age-matched controls. Notably, microglia-specific AD-associated variants preferentially target the MAPK pathway, including recurrent CBL ring-domain mutations. These variants activate ERK and drive a microglia transcriptional program characterized by a strong neuro-inflammatory response, both in vitro and in patients. Although the natural history of AD-associated microglial clones is difficult to establish in human, microglial expression of a MAPK pathway activating variant was previously shown to cause neurodegeneration in mice, suggesting that AD-associated neuroinflammatory microglial clones may contribute to the neurodegenerative process in patients.

overall_design: snRNAseq from microglia from Alzheimer's disease patients with and without pathogenic mutations and contols

first: Frederic

last: Geissmann

first: Rocio

last: Vicario


title: Single-cell transcriptome atlas reveals developmental trajectories and a novel metabolic pathway of catechin esters in tea leaves

status: Public on Mar 20 2025

city: Hefei

first: Qiang

last: Wang

state: Anhui

address: Changjiang RD 130

institute: Anhui Agriculture University

summary: The tea plant is an economically important woody beverage crop. The unique taste of tea is evoked by certain metabolites, especially catechin esters, whereas their precise formation mechanism in different cell types remains unclear. Here, a fast protoplast isolation method was established and the transcriptional profiles of 16,977 single cells from 1st and 3rd leaves were investigated. We first identified 78 marker genes based on six isolated tissues and constructed a transcriptome atlas, mapped developmental trajectories, and further delineated the distribution of different cell types during leaf differentiation, and genes associated with cell fate transformation. Interestingly, eight differently expressed genes were found to co-exist at four branch points. Genes involved in the biosynthesis of certain metabolites showed cell- and development-specific characteristics. An unexpected catechin ester glycosyltransferase was characterized for the first time in plants by a gene co-expression network in mesophyll cells. Thus, the first single-cell transcriptional landscape in woody crop leave was reported and a novel metabolism pathway of catechin esters in plants was discovered.

overall_design: Tender shoots of the current year of 6 years old C. sinensis var. sinensis cv. ‘shuchazao’ trees were collected. The complete 1st leaf (1 L) and 3rd leaf (3 L) blades were picked for protoplast isolation.

first: Yi

last: Wu

first: Anqi

last: Peng

first: Jila

last: Cui

first: Mingyue

last: Zhao

first: Yuting

last: Pan

first: Mengting

last: Zhang

first: Kai

last: Tian

first: Wilfried

last: Schwab

first: Chuankui

last: Song


title: Single-cell multi-omics analysis of the early wound-responsive programs in mouse corneal epithelium

city: Guangzhou

first: Yingfeng

last: Zheng

state: - Select State/Region -

address: No.7 Jinsui Road, Tianhe District

institute: Zhongshan Ophthalmic Center, Sun Yat-sen University

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Wound healing is crucial for restoring homeostasis in living organisms. Although wound response mechanisms have been studied extensively, the gene regulatory programs involved remain to be elucidated. Here, we used single-cell RNA-seq and ATAC-seq analysis to profile the regulatory landscape of mouse corneal epithelium in early wound response.

overall_design: We used our previously published single cell sequencing datasets of homeostatic adult mouse corneal epithelium as the unwound group (GRA009182). The wounded group data were obtained by sequencing the central epithelium 3h after trauma. The wounded scRNA seq dataset contains three samples; the wounded scATAC seq dataset also contains three samples.

first: Zhaojing

last: Lu

first: Jinguo

last: Ye

first: Jingni

last: Li

first: Jiangbo

last: Liang

first: Ming

last: Zhou

first: Qiuling

last: Hu

first: Qikai

first: Yuheng

last: Lin


title: Gene expression of iPSC-derived neurons from patient with Mohr-Tranebjaerg syndrome and healthy control

first: Yihua

last: Huang

state: Guangdong Province

address: 1838 Guangzhou Avenue, Baiyun District

institute: Nanfang Hospital, Southern Medical University, Guangzhou, China.

summary: Mohr-Tranebjaerg syndrome (MTS) is a neurodegenerative disease caused by mutations in Translocase of Inner Mitochondrial Membrane 8A/Deafness Dystonia Protein 1 (TIMM8A/DDP1), which encodes TIMM8a/DDP1 located in the intermembrane space (IMS) of mitochondria. Up to now, the pathophysiology of MTS remains unclear. In this study, we established induced pluripotent stem cells (iPSCs) derived from MTS patient carrying the TIMM8a loss-of-function pathogenic variant, p.Q75fs95* to study the mechanism of MTS. We found that MTS-iPSCs presented defects in neuronal differentiation, exhibited smaller somata, fewer branches and shorter neurites, accompanied by mitochondrial dysfunction including fragmented mitochondria, reduced ATP and elevated ROS.

overall_design: To understand the molecular mechanism of TIMM8a mutaion on neuronal differentiation, we compared the gene expression of iPSC-derived neurons from a MTS patient and  a healthy control.

first: Yafang


title: Targeting the Npy/Npy1r Signaling Axis in Mutant p53 Driven Pancreatic Cancer Impairs Metastasis

city: Darlinghurst

first: Leonard

last: Goldstein

address: 384 Victoria St

country: Australia

institute: Garvan Institute of Medical Research

summary: Pancreatic Cancer (PC) is a highly metastatic malignancy. Over 80% of PC patients present with distant disease, preventing potentially curative surgery. The Neuropeptide Y (NPY) system, best known for its role in controlling energy homeostasis, has also been shown to promote tumorigenesis in a range of cancer types, but its role in PC has yet to be explored. Here, we show that expression of NPY and NPY1R are upregulated in mouse PC models and human PC patients. Moreover, using the genetically engineered, autochthonous KPR172HC mouse model of PC we demonstrate that pancreas-specific and whole-body knockout of Npy1r significantly decreases metastasis to the liver. We identify that treatment with the NPY1R antagonist BIBO3304 significantly reduces KPR172HC migratory capacity on cell-derived matrices. Importantly, pharmacological NPY1R inhibition in an intrasplenic model of PC metastasis recapitulated the results of our genetic studies, with BIBO3304 significantly decreasing metastasis in the liver. Together, our results reveal that NPY/NPY1R signaling is a novel anti-metastatic target in PC.

overall_design: The genetically engineered KPR172HC mouse model of pancreatic cancer (Hingorani et al. Cancer Cell 2005; Morton et al. PNAS 2009) was crossed with whole-body Npy1r knock-out mice (Zhang et al. International Journal of Obesity 2010; Yan et al. Nature Communications 2021). Primary tumors were isolated at end-stage from KPR172HC Npy1r wildtype mice and KPR172HC Npy1r-/- mice and subjected to RNA-seq (n=10 tumors per genotype).

first: Cecilia

middle: R

last: Chambers

first: Alice

last: Tran

middle: D

first: Daniel

last: Christ

first: Herbert

last: Herzog

first: Paul

last: Timpson

first: David

last: Herrmann


title: Targeting ubiquitin-independent proteasome with small molecule increases susceptibility in pan-KRAS mutant cancers

city: shanghai

first: shihui

last: shen

state: Shanghai

address: 500 Dongchuan Road

institute: East China Normal University

summary: Despite advances in the development of direct KRAS inhibitors, KRAS-mutant cancers continue to exhibit resistance to the currently available therapies. Here, we identified REGγ as a mutant KRAS-associated factor that enhances REGγ transcription through the KRAS intermediate NRF2, suggesting that the REGγ-proteasome is a potential target for pan-KRAS inhibitor development. We elucidated a novel mechanism involving the KRAS/NRF2/REGγ regulatory axis, which links activated KRAS to the ATP- and ubiquitin-independent proteasome. We subsequently developed RLY01, a novel REGγ-proteasome inhibitor that effectively suppressed tumor growth in KRAS-mutant cancer models and lung cancer organoids. Notably, the combination of RLY01 and the KRASG12C inhibitor AMG510 exhibited enhanced antitumor efficacy in KRASG12C cancer cells. Collectively, our data support the hypothesis that KRAS mutations enhance the capacity of the REGγ-proteasome by increasing REGγ expression, highlighting the potential of ubiquitin-independent proteasome inhibition as a therapeutic approach for pan-KRAS mutant cancers.

overall_design: ChlP-seq of NRF2 in HCT116 cells, in triplicate,using Illumina GAllx.

first: Shihui

last: Shen


title: Single-Cell Transcriptomic Analysis Reveals Dynamic Changes in the Liver Microenvironment During Colorectal Cancer Metastatic Progression

first: Yue

last: Jiang

state: Guangdong

address: No. 26, Erheng Road, Yuancun

institute: The Sixth Affiliated Hospital of Sun Yat-sen University

summary: Background: Metastasis is a leading cause of cancer-related deaths, with the liver being the most frequent site of metastasis in colorectal cancer. Previous studies have predominantly focused on the influence of the primary tumor itself on metastasis, with relatively limited research examining the changes within target organs. Methods: Using an orthotopic mouse model of colorectal cancer, single-cell sequencing was employed to profile the transcriptomic landscape of pre-metastatic and metastatic livers. The analysis focused on identifying cellular and molecular changes within the hepatic microenvironment, with particular emphasis on inflammatory pathways and immune cell populations. Results: A neutrophil subpopulation with high Prok2 expression was identified, showing elevated levels in the pre-metastatic and metastatic liver. Increased infiltration of Prok2⁺ neutrophils correlated with poor prognosis in liver metastatic colorectal cancer patients. In the liver macro-metastatic niche (MMN), these neutrophils showed high App and Cd274 (PD-L1) expression, suppressing macrophage phagocytosis and promoting T-cell exhaustion. Conclusion: A Prok2⁺ neutrophil subpopulation infiltrated both pre-metastatic and macro-metastatic liver environments, potentially driving immunosuppression through macrophage inhibition and T-cell exhaustion. Targeting Prok2⁺ neutrophils could represent a novel therapeutic strategy for preventing liver metastasis in colorectal cancer patients.

overall_design: Liver single cell suspension preparation was performed by the laboratory staff of NovelBio Biopharmaceutical Technologies Ltd. Liver lysis was performed as described previously, whole mouse livers were removed, cut into small pieces on ice, and then enzymatically lysed with 1 mg/mL Collagenase II (Worthington) for 30 min on a shaker at 37°C. 70-micron cell filters were sieved and then erythrocytes were lysed in erythrocyte lysis buffer (Miltenyi Biotec), rinsed twice with PBS, and then the MACS Dead Cell Removal Kit (Miltenyi Biotec) was used to further enrich the single cell suspension.

first: Weidong

last: Pan


title: Unique gene expression in Down syndrome mouse model contingent on spatial subregion in excitatory hippocampal neurons during early midlife

city: Orangeburg

first: Stephen

middle: D.

last: Ginsberg

address: 140 Old Orangeburg Rd

department: Center for Dementia Research

institute: Research Foundation for Mental Hygiene

summary: Individuals with Down syndrome (DS) exhibit neurological deficits throughout the lifespan culminating in Alzheimer’s disease (AD) pathology and cognitive impairment during early mid-life.  At the cellular level, dysregulation in neuronal gene expression has been shown in the human brain and mouse models of DS. However, RNA- sequencing (RNA-Seq) analysis of genomic neuronal expression in the hippocampus have been limited, without separation of neuronal populations based on circuitry inputs. We postulate spatially characterized hippocampal excitatory neurons will present with unique gene expression patterns due in part to unique circuitry inputs in the DS mouse model.  Here, we combined laser capture microdissection (LCM) to isolate individual neuron populations with low input RNA-seq analysis to determine gene expression analysis of three excitatory neuron populations from the rostral hippocampus. We utilized the Ts65Dn mouse model of DS at the start of degeneration (6MO) to query gene expression profiles of CA1 and CA3 pyramidal neurons, along with dentate gyrus (DG) granule cells. The hippocampal structure is critical for learning and memory, with significant impairments of both behavior and synaptic activity in the DS mouse model which undergo degeneration during aging. Each population of excitatory hippocampal neurons exhibited unique gene expression alterations in the DS mice.  Bioinformatic queries revealed unique vulnerabilities and mechanistic differences which coincide with onset of degeneration in the Ts65Dn model of DS/AD.  These unique vulnerabilities may underlie the degenerative phenotype in DS, suggesting precision medicine targeting individual populations of neurons may be required for therapeutic advancement.  We further analyzed maternal choline supplementation in each neuronal population, treating the dams during gestation through weaning with choline normal diet (1.1g/kc choline chloride) or choline suppmentation (5.0g/kg choline chloride) in the normal (AIN-76A) mouse chow from Dyets. At weaning (postnatal day 21), pups were aged on a choline normal diet  until 6 months old.

overall_design: Ts65Dn dams were given choline normal (1.1 g/kg; control diet) or choline supplemented (5.0 g/kg; treatment diet) chow during gestation and weaning to investigate the lifelong effects of maternal choline supplementation (MCS) in a mouse model of Down syndrome.We aged the pups to ~6MO and performed a transcardial perfusion with phosphate buffer to clear the brain of peripheral contaminants.  Brains were collected from control (2N mice) and from DS mice (Ts65Dn), flash frozen and stored at -80*C.  The brains were sectioned and mounted on LCM PEN slides and a rapid Nissl stain was performed to CA1 and CA3 pyramidal neurons along with DG granule cells to ensure preservation of RNA integrity.  Excitatory neurons from the three hippocampal subpopulations were isolated by laser capture and RNA-seq analysis was performed on the purified RNA to determine lifelong gene expression changes in the DS and control animals due to MCS treatment. (N=5-9 per genotype per dietary condition)

first: Melissa

last: Alldred

first: Kyrillos

last: Ibrahim

first: Harshitha

last: Pidikiti

first: Adriana

last: Heguy

first: Gabriela

last: Chiosis

first: Elliott

last: Mufson

first: Grace

last: Stutzmann


title: Genetically Engineered Brain Organoids Recapitulate Spatial and Developmental States of Glioblastoma Progression [Xenium Spatial Transcriptomics]

city: St. Louis

first: Jeffrey

middle: Robert

last: Millman

state: MO

address: 660 South Euclid

institute: Washington University in St. Louis

summary: This study develops engineered glioblastoma organoids (eGBOs) to investigate the role of specific mutations in tumor progression. The analytic framework spans single-cell analysis, spatial transcriptomics, single-cell trajectory analysis, orthotopic implantation, clinically oriented imaging, and histopathological analysis. The work provides an important proof of concept that engineered tumor organoids can model glioblastoma progression.

overall_design: Single-cell transcriptomes from wildtype (WT) and genetically engineered brain organoids harboring glioblastoma-associated mutations (PRO - TERTp C228T / TP53 R248Q; MES - TERTp C228T / NF1 deletion / PTEN deletion). Organoids were assessed 1 month after in vitro differentiation and 3 months after orthotopic xenotransplantation.

first: Matthew

last: Ishahak

first: Albert

last: Kim


title: Growth of the maternal intestine during pregnancy and lactation [Xenium]

city: London

first: Irene

last: Miguel-Aliaga

address: 1 Midland Rd

country: United Kingdom

institute: The Francis Crick Institute

summary: The organs of many female animals grow and are metabolically remodelled by reproduction; this process has been historically overlooked. Using the intestine of mouse mothers, a striking and genetically tractable example of reproductive organ resizing, we find that reproductive intestinal remodelling is anticipatory and distinct from diet- or microbiota-induced intestinal resizing. Reproductive remodelling involves partially irreversible elongation of the intestine and fully reversible growth of its epithelium, which ensues from an expansion of the isthmus progenitors, increased progenitor proliferation and accelerated migration of differentiated cells. Through spatiotemporal analysis of gene expression, we identify induction of the SGLT3a transporter in a subset of enterocytes as one of the earliest reproductive hallmarks within the intestinal epithelium. Electrophysiological and genetic interrogations in vivo and in organoids indicate that SGLT3a does not sustain broad digestive functions or enterocyte health. Instead, SGLT3a detects protons and sodium to extrinsically support the expansion of adjacent Fgfbp1-positive isthmus progenitors and gut epithelial growth during reproduction. Our findings reveal unanticipated molecular, cell and organ specificity to physiological organ remodelling, raising the possibility that organ- and state-specific growth programmes could be leveraged to improve pregnancy outcomes or prevent maladaptive consequences of such growth.

overall_design: High resolution spatial transcriptomics Xenium experiment using 300 custom probes. Two runs of two slides were performed. On each slide, whole ileum mouse gut roll samples were profiled from virgin, pregnant (day 7) and lactating mice. This resulted in 4 biological replicates in total for each condition.

first: Tomotsune

last: Ameku

first: Anna

last: Laddach

first: Ivan

last: Andrew

first: Ka

last: Choi

first: Laurence

last: Game

first: Vassilis

last: Pachnis


title: Genetically Engineered Brain Organoids Recapitulate Spatial and Developmental States of Glioblastoma Progression [scRNA-seq]


title: CUT-TAG of LDB1 for MV4-11 cell line

city: Suzhou

first: Fang

last: Fang

state: Jiangsu

address: 92 Zhongnan street

institute: Children’s Hospital of Soochow University

summary: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. The goals of this study are to explore CUT-TAG results of LDB1 in MV4-11 cell line.

overall_design: CUT-TAG of LDB1 for MV4-11 cell line

first: Jian

last: Pan

first: Shaoyan

last: Hu

first: Bi

last: Zhou


title: Gene expression is altered after infection with E. coli in endometrial organoids

city: Beijing

first: Xin

last: Zhang

state: Beijing

address: No. 251, Yaojiayuan Road, Chaoyang District

institute: Beijing Obstetrics and Gynecology Hospital, Capital Medical University

summary: We used human endometrium-derived epithelial cells to construct endometrial epithelial organoids, which were divided into two groups, the control group and the experimental group. The organoids in the experimental group were infected with Escherichia coli to explore the changes in gene expression before and after infection

overall_design: Using human endometrial epithelial primary cells, a novel organoid model was constructed to explore the effect of E. coli infection on endometrial epithelial cells


title: Ectopic expression of testis-specific transcription factor driving lung cancer [RNA-Seq]

city: Chicago

first: Ali

last: Shilatifard

state: IL

address: 320 E Superior St

department: Department of Biochemistry and Molecular Genetics

institute: Northwestern University Feinberg School of Medicine

summary: The testis-specific BET protein BRDT structurally resembles the ubiquitous BRD4 and is ectopically expressed in various solid tumors, most notably lung cancer. Our analysis of patient samples indicates that BRDT expression may impact lung cancer progression. BRDT knockdown in lung cancer cells slowed tumor growth and prolonged survival in a xenograft model. Comparative characterization of PTEFb complex participation and chromatin binding indicates BRD4-redundant and -distinct BRDT functions. Unlike dual depletion, individual BRD4 or BRDT knockdown did not impair transcriptional responses to hypoxia in BRDT-expressing cells, consistent with redundant function. Acute BRD4 depletion and BRDT complementation revealed that BRDT can also release paused RNA Polymerase II independently of its bromodomains. These results underscore the functional importance of the C-terminal domains present in both BRD4 and BRDT and their potential as therapeutic targets in cancer, particularly in solid tumors. Future investigation will explore BRD4-distinct BRDT functions and BRDT misexpression driving cancer pathogenesis.

overall_design: RNA-seq profiling of the NCI-H510 cells, wildtype and their derivatives (sgBRD4 and sgBRDT under hypoxi and normoxic conditions

first: Bin

last: Zheng

first: Marta

last: Iwanaszko

first: Lu

last: Wang


title: Ectopic expression of testis-specific transcription factor driving lung cancer [ChIP-Seq]

overall_design: ChIP-seq of the Pol2, BRDT, BRD4, CDK9, and histone modifications: H3K27ac, H3K27me3, H3K4me1, H3K4me3 in NCI-H510 cells


title: Changes in Gene Expression in Healthcare Workers During Night Shifts: Implications for Immune Response and Health Risks

city: Suita

first: Daisuke

last: Motooka

state: Osaka

address: 3-1, Yamadaoka

country: Japan

institute: NGS core facility, Research Institute for Microbial Diseases, Osaka University

summary: Purpose: This study aimed to analyze gene expression changes in the whole blood of healthcare workers before and after a night shift, to investigate the molecular mechanisms underlying these changes and their potential impact on health. Methods: A single-center, prospective, observational study was conducted involving four medical doctors working night shifts in the emergency department. Blood samples were collected at 10 a.m. on the day of work and at 10 a.m. the following day after the shift. RNA sequencing was performed to analyze gene expression changes, followed by Ingenuity Pathway Analysis (IPA) for core analysis and analysis match. Results: A total of 302 genes were upregulated, and 78 genes were downregulated (p < 0.05, |log2-fold change| > 0.5) after the night shift. Core analysis consistently predicted the activation of immune and inflammatory responses. Analysis match indicated that gene expression patterns after the night shift correlated with several diseases, including major depressive disorder, based on immune and inflammatory response profiles.

overall_design: Blood samples were collected before and after the night shift. RNA was extracted from whole blood, and RNA sequencing was performed to analyze gene expression changes.

first: Ryota

last: Nukiwa

first: Sayaka

last: Oda

first: Hisatake

last: Matsumoto


title: The GPCR Latrophilin2 Signals via Gα13 to Regulate Epidermal Differentiation

city: Stanford

first: Douglas

last: Porter

state: CA

address: 269 Campus Drive

department: Dermatology

institute: Stanford

summary: Latrophilin 2 (ADGRL2), an adhesion GPCR, mediates signaling through its intracellular loop 3 via a unique QQQ binding patch within the Gα13 GTPase domain, playing a critical role in the regulation of normal epidermal differentiation.

overall_design: Cas9 CRISPR libraries targeting GPCRs and controls were infected via lentivirus to primary keratinocytes (two biological replicates), which were then seeded for differentiation. Differentiating cells were sorted by FACS for the differentiation marker KRT10, splitting high, medium and low KRT10 populations. The fastq files are Cas9 guide sequences either from cells infected with lentivirus or plasmid DNA. In addition, libraries were generated from progenitor and differentiated cells without sorting, leading to five samples per biological replicate and a total of ten samples. The plasmid library used to generate the lentivirus was also sequenced.

first: Xue

last: Yang

first: Feng

last: He

middle: F

first: Georgios

last: Skiniotis

first: Paul

last: Khavari


title: Supersulfides contribute to joint homeostasis and bone regeneration

city: Tokyo

first: MIKI

last: MAEMURA

state: Select

address: 1-5-8,Hatanodai,Shinagawa-ku, 1st building, 343

institute: Showa University

summary: The physiological functions of supersulfides, inorganic and organic sulfides with sulfur catenation, have been thoroughly studied. Cysteinyl-tRNA synthetase (CARS2) is the principal supersulfide-producing enzyme. We investigated the role of supersulfides in joint homeostasis and bone regeneration.

overall_design: We performed a surgical tibia fracture model on the left legs of Cars2AINK/+ mutant mice, where the KIIK motif of CARS2, required for supersulfide production, was replaced heterozygously with AINK, and their wild-type (Cars2+/+) littermates at 12 weeks of age. Two weeks after establishing the fracture model, the soft and hard calluses in the tibia of Cars2AINK/+ and Cars2+/+ mice were collected separately, RNA was extracted, and RNA-seq analysis was performed for each group (n=2)

first: Miki

last: Maemura

first: Kazuhiro

last: Shibusaka

first: Soichiro

last: Negishi

first: Masahiro

last: Hosonuma

first: Taku

last: Saito

first: Masanobu

last: Morita

first: Takaaki

last: Akaike

first: Yoichi

last: Miyamoto

first: Fumiko

last: Yano


title: Targeting Vdac2 enables IFN gamma-mediated destruction and inflammatory remodeling of tumors to overcome immune evasion [ATAC-seq 1]

city: Memphis

first: Hongbo

last: Chi

address: 262 Danny Thomas Place

department: Immunology

institute: St Jude Children's Research Hospital

summary: ATAC-seq analysis of the functional effect of targeting Vdac2 in tumor cells under the condition of chronic IFNg stimulation that induces IFNg resistance.

overall_design: B16-OVA tumor cells that were previously treated with vehicle or chronic IFNg stimulation were inoculated into C57BL/6 mice and collected at day 15 after tumor injection by sorting from tumor tissues, followed by ATAC-seq analysis.

first: Hao

last: Shi


title: RBM10 Deficiency Promotes Brain Metastasis by Modulating Sphingolipid Metabolism in an Animal Model of EGFR Mutation Lung Adenocarcinoma

city: Harbin

first: Yan

last: Yu

state: Heilongjiang

address: Haping Road No 150

department: Department of Medical Oncology

institute: Harbin Medical University Cancer Hospital

summary: Brain metastasis significantly contributes to the failure of targeted therapy in patients with EGFR-mutated lung adenocarcinoma (LUAD). Reduced expression of RBM10 is associated with brain metastasis in these patients. However, the mechanism by which RBM10 affects brain metastasis in EGFR-mutated LUAD remains unclear. Previous studies reveal that RBM10 mutations lead to decreased expression and deregulated splicing at a subset of junctions, primarily through exon skipping.

overall_design: This study demonstrates that RBM10 plays a vital role in inhibiting brain metastasis from EGFR‐mutated LUAD by modulating sphingolipid metabolism. When RBM10 expression is low, galactosylceramidase (GALC) enters the nucleus to function. RBM10 deficiency inhibits exon skipping during GALC splicing, leading to upregulated GALC expression and increased sphingosine 1-phosphate (S1P) synthesis. S1P enhances blood-brain barrier (BBB) permeability, thereby promoting brain metastasis. Additionally, animal experiments show that the targeted agents Fingolimod (an S1P inhibitor) and RU-SKI-43 (an RBM10 inhibitor) suppress the growth of brain metastasis. This study provides a novel theoretical foundation for preventing brain metastasis in LUAD and identifies a promising therapeutic target.

first: Gang

last: Xu

first: Bo

last: An

first: Dexin

last: Jia


title: The non-antibacterial effects of azithromycin and other macrolides on the bronchial epithelial barrier and cellular differentiation

city: Reykjavik

first: Thorarinn

last: Gudjonsson

address: Vatnsmyrarvegur 16

department: Faculty of Medicine

country: Iceland

institute: University of Iceland

summary: Azm has a greater affect on the integrity of the bronchial epithelial barrier than other tested macrolides. To better understand the effects macrolides have on bronchial epithelium we investigated global changes in gene expression in VA10 cells grown at air-liquid interface

overall_design:
VA10 cells were cultured in an air-liquid interface (ALI) model for 21 days with and without macrolides. RNA was isolated at days 14 and 21 and run through high-throughput RNA sequencing.

Macrolides used in this study:
clarithromycin (CLARI)
azithromycin (AZM)
erythromycin (ERY)
roxithromycin (ROXI)
solithromycin (SOLI)
tobramycin (TOBRA)

first: Arni

last: Asbjarnarson

first: Jon

middle: P

last: Joelsson

first: Fridrik

last: Gardarsson

first: Snaevar

last: Sigurdsson

first: Michael

last: Parnham

first: Jennifer

last: Kricker


title: Treatment of Dimethyl α-Ketoglutarate in liver cancer

city: seoul

first: Jueng Soo

last: You

address: 120 Neungdong-ro

country: South Korea

institute: Konkuk University

summary: Transcriptome analysis following Dimethyl α-Ketoglutarate treatment

overall_design: HepG2 cells were treated with Dimethyl α-Ketoglutarate for 0, 3, 6, 9, 12, 24, and 48 hours to analyze transcriptomic changes over time

first: Sung Kyung

last: Choi


title: Satb2 deletion in colon approach to treat short bowel syndrome

city: New York

first: David

last: Redmond

state: New York

address: 1300 York Avenue

institute: Weill Cornell Medicine

summary: Loss of the transcription factor Satb2 converts mouse colonic epithelium into an ileal type. Here, we report that Satb2 gene deletion alleviates SBS by replacing diminished absorptive function and by inducing lymphovascular channels in the proximal colon. Enhanced nutrient absorption following Satb2 loss increased body weight and survival of mice with SBS. Deletion of SATB2 by adeno-associated viral delivery of CRISPR Split Cas9 to human colon organoids, followed by xenotransplantation into mice, resulted in ileal morphology and expression of ileal marker genes. This approach offers a feasible strategy for future treatment of SBS.

overall_design: Here we deleted Satb2 to remodel the colon into nutrient-absorbing ileum-like tissue in a mouse model of SBS. The resulting ileum-like colon developed lacteal vessels, subepithelial lymphatic channels normally restricted to the small intestine and responsible for fat absorption, indicating that Satb2 deletion directs formation of small intestinal structures in the colon.

first: Tao

last: Liu

first: Shiri

last: Li

first: Xiaofeng

last: Huang

first: Qiao

last: Zhou


title: ACBP/DBI protein neutralization for the experimental treatment of fatty liver disease

city: PARIS

first: Guido

last: Kroemer

address: 15 rue de L'école de médecine

institute: Centre de Recherche des Cordeliers

summary: Total liver RNA extracts from adult male mice (8 weeks old, C57BL/6) subjected to Methionine and Choline Deficient Diet  (regime duration: 6 weeks) and injected with monoclonal anti-ACBP/DBI (2 doses per week from week 4) were determinated to describe the therapeutic effects of neutrali-zation of ACBP/DBI to MASH-induced transcriptomic alterations.

overall_design: RNA expression profiling by high throughput sequencing.  Overall design: Regular Chow Diet (RCD) +Antibody IgG (Isotype), C57BL/6 (n=5), Regular Chow Diet (RCD)+Antibody anti-ACBP/DBI (aDBI), C57BL/6 (n=5), Methionine and Choline Deficient Diet (MCD)+Antibody IgG (Isotype), C57BL/6 (n=10), Methionine and Choline Deficient Diet (MCD) +Antibody anti-ACBP/DBI (aDBI), C57BL/6 (n=10).

first: Omar

last: Motiño

first: Vincent

last: Carbonnier

first: Isabelle

last: Martins


title: Mice with Lymphatic Dysfunction Develop Pathogenic Lung Tertiary Lymphoid Organs that Model an Autoimmune Emphysema Phenotype of COPD

first: Tyler

last: Lu

summary: We have previously shown that mice with loss of C-type lectin-like type II (CLEC2), which have lymphatic dysfunction due to the role of CLEC2 in platelets for maintaining separation between the venous and lymphatic system, develop lung tertiary lymphoid organ (TLO) formation and lung injury that resembles an emphysema phenotype of chronic obstructive pulmonary disease (COPD). We now sought to investigate whether and how TLOs in these mice may play a pathogenic role in lung injury that is relevant to human disease. We found that inhibiting TLO formation using an anti-CD20 antibody in CLEC2-deficient mice partially blocked the development of emphysema. TLOs in CLEC2-deficient mice were rich in plasma cells and were a source of a broad array of autoantibodies. Chronic cigarette smoke exposure increased the size and number of lung TLOs in CLEC2-deficient mice, and was associated with increased markers of antigen presentation and maturation, leading to increased autoantibody deposition. Using lung tissue from COPD patients, we found an increase in lymphatic markers in patients with an emphysema phenotype and autoreactive TLOs compared to COPD patients without emphysema that lack prominent TLOs. Taken together, these results demonstrate that emphysema in mice with lymphatic dysfunction can be partially rescued by blocking TLO formation, and that these TLOs are source of autoantibodies that are exacerbated by cigarette smoke. Our work suggests that lymphatic dysfunction in mice may recapitulate some aspects an autoimmune emphysema phenotype that is seen in a subset of patients with COPD.

overall_design: Mice carrying the Prox1-EGFP reporter (in which all LECs are labeled with GFP) were injected with AlexaFluor647-conjugated isolectin (Invitrogen) for intravital labeling of endothelial cells just prior to sacrifice. The lungs were then digested using dispase/collagenase in HBSS to generate a single cell suspension for FACS, with additional staining using antibodies for CD31 (Biolegend  102418), lineage cocktail (Bioloegend 133311), and Epcam (Biolegend 118225). LECs were sorted using positive selection for isolectin, CD31, GFP, and negative gating for Epcam and Lineage markers.

first: Barbara

last: Summers

middle: M

first: Raphaël

last: Lis

first: Hasina

last: Outtz Reed


title: Proteogenomic analysis reveals a compendium of therapeutic targets for treatment-resistant subtypes of locally advanced cervical cancers

city: Seoul

first: Do Young

last: Hyeon

state: Select State

address: 1 Gwanak-ro, Gwanak-gu

department: School of Biological Sciences

institute: Seoul National University

summary: We report proteogenomic analysis of locally advanced cervical cancer (LACC). Exome-seq data revealed predominant alterations of keratinization-TP53 regulation and O-glycosylation-TP53 regulation axes in squamous and adeno-LACC, respectively, compared to in early-stage cervical cancer. Integrated clustering of mRNA, protein, and phosphorylation data identified six subtypes (Sub1-6) of LACC among which Sub3, 5, and 6 showed the treatment-resistant nature with poor local recurrence-free survival. Elevated immune and extracellular matrix (ECM) activation mediated by activated stroma (PDGFD and CXCL1high fibroblasts) characterized the immune-hot Sub3 enriched with MUC5AChigh epithelial cells (ECs). Increased epithelial-mesenchymal-transition (EMT) and ECM remodeling characterized the immune-cold squamous Sub5 enriched with PGK1 and CXCL10high ECs. We further demonstrated that CIC mutations could trigger EMT activation by upregulating ETV4, and the elevation of the immune checkpoint PVR and neutrophil-like myeloid-derived suppressive cells (FCN1 and FCGR3Bhigh macrophages) could cause suppression of T-cell activation in Sub5. Increased O-linked glycosylation of mucin characterized adeno-LACC Sub6 enriched with MUC5AChigh ECs. These results provide a battery of somatic mutations, cellular pathways, and cellular players that can be used to predict treatment-resistant LACC subtypes and can serve as potential therapeutic targets for these LACC subtypes.

overall_design: Single-cell RNA sequencing of 12 squamous cell carcinoma (SCC), 1 adenosquamous (ADS), and 3 adenocarcinoma (ADC) samples.

first: Joo

middle: Y

last: Kim

first: Daehee

last: Hwang


title: CircRNA expression profiling in cortical microglia isolated from 6-month-old male WT and APP/PS1 mice by magnetic-activated cell sorting (MACS)

city: Shanghai

first: jiyun

last: shi

address: 227 Chongqing South Road, Huangpu District, Shanghai, China

institute: Shanghai Jiao Tong University School of Medicine

summary: To investigate the roles of circRNAs in the microglia of AD, we isolated cortical microglia from 6-month-old male wild-type (WT) and APP/PS1 mice by MACS using a CD11b antibod and conducted a circRNA microarray to profile the circRNA expression spectrum. A total of 13420 circRNAs were detected and 218 differentially expressed circRNAs (with a fold change＞1.5, P＜0.05) were found. 146 circRNAs were upregulated while 72 circRNAs were downregulated in cortical microglia of APP/PS1 mice compared with WT mice.

overall_design: CircRNA expression in cortical microglia isolated from 6-month-old male WT and APP/PS1 mice was measured.Three independent experiments were performed using different donors for each experiment.

first: Jiyun

last: Shi


title: The histone lysine demethylase KDM7A contributes to reward memory via Fscn1-induced synaptic plasticity in the medial prefrontal cortex

city: Xi'an

first: Yuxiang

last: Zhang

state: Shaanxi

address: 76 Yanta West Road

department: College of Forensic Medicine

institute: Xi’an Jiaotong University

summary: Lysine demethylase 7A (KDM7A) catalyzes the removal of dimethylation from histone H3 lysine 9 and lysine 27, both of which are associated with transcription repression. Previous study indicated that Kdm7a mRNA in the medial prefrontal cortex (mPFC) increased after drug exposure, yet its role in drug-related behaviors is largely unknown. In a morphine-conditioned place preference (CPP) paradigm, our findings revealed a specific increase of Kdm7a expression in the mPFC seven days after drug withdrawal. Subsequently, our results demonstrated that knockdown of Kdm7a in the mPFC did not affect the acquisition of morphine-induced CPP, but it attenuated memory consolidation. To further explore Kdm7a-mediated transcriptomic changes, we employed Nanopore direct RNA sequencing. Transcriptome profiling unveiled several gene expression alterations impacted by KDM7A, which were enriched in relevant neural function categories. Notably, we identified and validated fascin actin-bundling protein 1 (Fscn1) as a downstream molecular target. Knockdown of Fscn1 had a similar impact on CPP to Kdm7a, along with a corresponding decrease in dendritic spine density in the mPFC. Additionally, ChIP analysis demonstrated that silencing Kdm7a in N2a cells resulted in decreased enrichment of H3K9me2 and H3K27me2 at the Fscn1 promoter region, suggesting that Kdm7a may act as a crucial regulator of transcriptional responses to morphine-related reward memory via Fscn1.

overall_design: To investigate the regulatory role of KDM7A in the mPFC during the process of morphine addiction, we established a morphine addiction CPP model by knocking down KDM7A using shRNA in mice in the experimental group, with a control group for comparison. The two groups were further divided into saline and morphine subgroups. Subsequently, gene expression profiling was conducted on the RNA sequencing data obtained from mPFC tissue on the seventh day of morphine withdrawal.

first: Zhuojin

last: Yang

first: Dongyu

last: Yu

first: Chunxia

last: Yan


title: Cell type-specific apoptosis resistance in juvenile myelomonocytic leukemia

city: Freiburg

first: Senthilkumar

last: Ramamoorthy

address: Mathildenstraße 1

country: Germany

institute: UNIVERSITAETSKLINIKUM FREIBURG

summary: Juvenile myelomonocytic leukemia (JMML) is caused by constitutively activated RAS signaling. Activation of the RAS pathway in the JMML mouse model (MxCre;Ptpn11D61Y) affects apoptosis signaling by regulating  BCL-2 family members through oncogenic and microenvironemtal signals, in a cell type-dependent manner. Apoptosis resistance mediated by overexpression of anti-apoptotic and downregulation of pro-apoptotic BCL-2 family members was observed in monocytes and granulocytes.

overall_design: To investigate gene expression changes in the JMML mouse model, RNA sequencing was performed in CD11b+ cells derived from BM and spleen  and also from stem and progenotor  LSK cells from BM, isolated from  stage 3 (S3)MxCre;Ptpn11D61Y/+ mice. MxCre mice were used as controls.

first: Naile

last: Koleci

first: Miriam

last: Erlacher


title: Mitoxantrone-liposome sensitizes Flt3-ITD acute myeloid leukemia to gilteritinib treatment

city: Chongqing

first: Zhe

last: Chen

address: 1 Yixueyuan Road, Yuzhong District

institute: Chongqing Medical University

summary: FMS-like tyrosine kinase 3 (FLT3) is the most frequently mutated gene in acute myeloid leukemia (AML), and is associated with a poor prognosis and high relapse rate. Gilteritinib, as a second-generation FLT3 inhibitor, is an important target drug in the treatment of FLT3-ITD AML patients, but it still faces the problems of drug resistance and reduced potency. In this study, we found that mitoxantrone-liposome can sensensitized gilteritinib and enhanced the therapeutic effect in vivo and in vitro. RNA-sequencing revealed that the combination treatment resulted in specific changes in gene expression, reduced drug resistance and the mechanism. Primary AML cells harvested from patients with FLT3-ITD AML showed a significant response to combination treatment in vitro. Our data suggest represents a novel and promising therapeutic strategy for FLT3-ITD AML patients and relapsed/refractory(R/R) AML.

overall_design: MV4-11 cell lines were cultured with DMSO, Mitoxantrone (20 nM), or Gilteritinib(25 nM) , or combination(Mitoxantrone 20 nM plus Gilteritinib 20 nM) for  24 h, followed by RNA-seq

first: Shiyi

last: Yuan


title: Senataxin (SETX) prevents Myc-induced replicative stress [EU-seq]

city: Milan

first: Marco

last: Filipuzzi

address: Via Giuseppe Ripamonti, 435

country: Italy

institute: IEO

summary: Here we investigated the RNA helicase Senataxin (SETX), an enzyme that resolve RNA-DNA hybrids and R-loops, to address its role in preventing replicative stress by oncogenic Myc. Silencing of SETX led to selective engagement of the DNA damage response (DDR) upon Myc activation, leading to a robust cytotoxicity. Pharmacological dissection of the upstream kinases regulating the DDR revealed a protective role of the ATR pathway, that once inactivated, boosted SETX driven-DDR. While loss of SETX did not lead to a genome-wide increase of R-loops, mechanistic analyses revealed enhanced R-loops localized at DDR-foci and newly replicated genomic loci, compatible with a selective role of SETX in resolving RNA-DNA hybrids to alleviate Myc-induced RS.

overall_design: U2OS MycER cells (U20S cells expressing the MycER chimera) were infected with virus expressing non-targeting shRNAs (shNT) or shRNA targeting SETX (shSETX). ShRNA expression was activated with 0.2 µg/mL doxycycline, while MycER was activated with 300 nM OHT. Cells were then treated with 100 ng/ml nocodazole (Sigma, Cat. No.  SML-1665) for 8h to induce mitotic arrest. G2/M arrested cells were isolated by shake-off, washed with PBS and released in warm medium for 18 hours.

first: Silvia

last: Sberna

first: Stefano

last: Campaner

first: Ottavio

last: Croci


title: Senataxin (SETX) prevents Myc-induced replicative stress [DRIP-seq]


title: Immune profiles of heatstroke patients

city: Chengdu

first: Juan

last: Wu

state: Sichuan

address: No. 37 Guo Xue Alley, Wuhou District

department: Anesthesiology

institute: West China Hospital of Sichuan University

summary:
Background: Heatstroke was the most life-threatening disease caused by hyperthermia, but lack of rapidly diagnostic biomarkers. Immune system disturbance was a common feature of the ‘Dual pathway model’ characterized by endotoxemia and hyperthermia, but the specific profiles of the immune system were unclear.
Objectives: Our study aimed to explore the specific immune profiles that distinguish heatstroke from aseptic inflammation and sepsis patients, and find diagnostic biomarkers to differentiate heatstroke from sepsis.
Methods: Patients in four groups were recruited: heatstroke patients (HS group), sepsis patients (Sepsis group), patients undergoing cardiopulmonary bypass (CPB group) and healthy controls (HC group). The HS patients were matched 1:1 with patients in HC, CPB and Sepsis groups based on age and sex using propensity score analysis. The primary outcome was all-cause mortality, and the secondary outcomes were the incidence of nervous dysfunction (including stroke and delirium), acute heart failure, acute kidney failure or acute lung injury within 30 days. Blood was collected within 24 hours after admission from healthy participants, HS and sepsis patients, and at the end of CPB in the case of CPB patients. This blood was used to perform spectral flow cytometry, measure the plasma level of inflammatory mediators and heat shock protein-70, as well as process single-cell RNA sequencing (sc-RNA seq) to assess the profiles of T cells, B cells, monocytes, and NK cells. Patients with HS and sepsis were followed up for 30 days after admission, while CPB patients were followed up for 30 days after surgery to record the incidence of primary and secondary outcomes.
Results: The proportion of TLR4+ monocytes in HS higher than that in HC, CPB and Sepsis groups, and could differentiate heatstroke from sepsis. In HS, the upregulation of HLA genes (HLA-A, HLA-B, HLA-DRA, and HLA-DRB1), the activation of antigen presentation, as well as the inhibition of chemotaxis were found in monocytes highly expressed TLR4 based on sc-RNA seq analysis. In addition, the CCL1 and CXCL8 plasma levels were decreased in HS. Compared with HC and CPB, lymphopenia was found in HS and sepsis, which were attributed by the decreased of T cells counts and NK cells counts. T cells exhaustion was found in HS and sepsis, which was indicated by the upregulation of PD-1 in T cells and its PD-L1 in B cells, upregulation of CD69 and LAG3 but downregulation of TCF7 in T cells, and decreases of plasma levels of TNF-α and IFN-γ. In addition, the Treg/CD8+ T cells ratio was higher in HS patients who experienced death (0.58 vs. 0.35), nervous dysfunction (0.56 vs. 0.29), acute heart failure (0.67 vs. 0.35), and acute lung injury (0.58 vs. 0.34) within 30 days than those who did not. The NK cells cytotoxic activity was decreased in HS, which was indicated by downregulation of CD335, the inhibition of focal adhesion and cell adhesion, as well as the emergence of receptor-ligands pairs related to inhibit NK cells activation in HS, including HLA-A_ KIR3DL1, HLA-B_ KIR3DL2, HLA-C_ KIR2DL1 and HLA-E_ CD94:NKG2A expressed between various immune cells and NK cells.
Conclusions: The immune system in HS was characterized by a significant increase in TLR4+ monocytes and immune suppression, the latter of which included lymphocytopenia, T cell exhaustion, and suppressed NK cell cytotoxic activity. TLR4+ monocytes may be regarded as a biomarker to distinguish heatstroke from sepsis, and the Treg/CD8+ T cell ratio may be associated with death and organ failure in heatstroke.

overall_design: We performed single-cell RNA sequencing of peripheral blood mononuclear cells from patients in HC, CPB, Sepsis and HS groups. The sequencing profiles were used to cluster the cells into the following four immune cell types based on expression of well-established markers: monocytes, T cells, B cells, and natural killer cells.


title: A microglia clonal inflammatory disorder in Alzheimer’s Disease

first: Bic

last: MSKCC

state: NY

address: 1275 York Ave.

institute: Memorial SLoan-Kettering Cancer Center

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

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Refer to individual Series


title: Impact of Spaceflight on Gene Expression in Cultured Human Mesenchymal Stem Cells

city: Rochester

first: Alexandra

last: Krivonos

state: MN

address: 200 1st St SW

department: Quantitative Health Sciences

institute: Mayo Clinic

summary: With technological advancements, human’s desire to explore space is growing and more people are staying longer at the international space station (ISS). The impact of microgravity on stem cells is not fully understood. We explored the impact of microgravity on gene expression profile of cultured mesenchymal stem/stromal cells (MSC) at the ISS. We also evaluated how the new knowledge gained sheds light on our understanding of human physiology on Earth. Primary cultures of MSC were expanded at the ISS for 1 or 2 weeks and mRNA was isolated from samples of the cultured cells. Gene expression profiles were determined and compared with samples from real-time ground control cultures. Differential gene expression, gene set enrichment analysis and determination of key genes were performed that revealed for the first time the existence of potential “master regulators” coordinating a systemic response to microgravity. Cyclin D1 (CCND1), a protein-coding gene that regulates cell cycle progression and CDK kinases, was identified as the most connected regulator. We identified 10 candidate genes which are common in both week 1 and 2 MSC analysis and directly interact with CCND1 as potential key regulators affecting stem cell biology in space. Further analysis showed the impacted genes from cultured MSC significantly correlated with known gene pathways associated with cell division, chromosomal segregation and nuclear division, extracellular matrix structure and organization, muscle apoptosis and differentiation. This study exemplifies the utility of space research to advance our understanding of human physiology both on Earth and in space.

overall_design: To investigate the effects of microgravity on MSC growth and understand the differences in gene expression profiles between microgravity and ground control environments, two groups of MSC were sent to the ISS. One group was cultured for one week, while the other was cultured for two weeks, with corresponding control groups processed similarly on Earth. The cells were then preserved and transferred back to the laboratory. Further Gene expression profiles were compared between samples to identify differentially expressed genes.

first: Peng

last: Huang

first: Bryan

middle: T

last: Piatkowski

first: Yesesri

last: Cherukuri

first: Yan

last: Asmann

first: Abba

last: Zubair


title: Ironomycin induces Mantle Cell Lymphoma cell death by targeting iron metabolism adicction

city: Montpellier

first: Jerome

last: MOREAUX

address: 141, rue de la Cardonille 34396 Montpellier Cedex 5 FRANCE

institute: IGH

summary: Mantle Cell lymphoma (MCL) remains an aggressive and incurable cancer with existing therapies, presenting a significant unmet clinical need. We evaluated the therapeutic interest of targeting iron homeostasis with Ironomycin alone and combined with ibrutinib, a BTK inhibitor accepted for the treatment of MCL patients. Patients commonly develop resistance to ibrutinib treatment. We found that ironomycin synergizes with ibrutinib to kill MCL cells even in ibrutinib-resistant cell lines.

overall_design: Three MCL cell lines (JEKO1, JVM2 and MAVER1) were treated with ironomycin and the BTK inhibitor ibrutinib alone or combined for 48 hours. RNA-seq analysis of the cells was performed at the end of the treatments.

first: Sara

last: Ovejero

first: Laura

last: Alibert

first: Julie

last: Devin

first: Tatiana

last: Cañeque

first: Valentin

last: Jacquier

first: Andrea

last: Romero

first: Salome

last: Amar

first: Matthieu

last: Abouladze

first: Guilhem

last: Requirand

first: Nicolas

last: Robert

first: Leriem

last: Zellagui

first: Hugues

last: de Boussac

first: Guillaume

last: Cartron

first: Johanna

last: Chiche

first: Jean-Ehrland

last: Ricci

first: Charles

last: Herbaux

first: Raphael

last: Rodriguez

first: Jérôme

last: Moreaux

first: Caroline

last: Bret


title: Senataxin (SETX) prevents Myc-induced replicative stress [BLISS]

first: Marco

last: Filipuzzi

overall_design:
U2OS MycER cells (U20S cells expressing the MycER chimera) were infected with virus expressing non-targeting shRNAs (shNT) or shRNA targeting SETX (shSETX). ShRNA expression was activated with 0.2 µg/mL doxycycline, while MycER was activated with 300 nM OHT. Cells were then treated with 100 ng/ml nocodazole (Sigma, Cat. No.  SML-1665) for 8h to induce mitotic arrest. G2/M arrested cells were isolated by shake-off, washed with PBS and released in warm medium for 18 hours.

***************************************************************
The table below lists GEO accessions reused/reanalyzed for this study.

Processed data file(s):  See GSM8488136.
***************************************************************

first: Silvia

last: Sberna

first: Stefano

last: Campaner

first: Crosetto

last: Nicola

first: Alessandra

last: Albertini

first: Ottavio

last: Croci


title: Both TRULI and DAPA may serve as anti-OA drugs by modulating ZBTB20 to restore ECM homeostasis

first: Xue

last: Hao

address: Shanghua Road

institute: Xi'an Honghui Hospital

summary: Due to the existing challenges in modulating the activity of transcription factors directly, comprehending the upstream regulatory mechanism can offer perspectives for tackling these obstacles. Our observations that in early-stage OA chondrocytes ZBTB20 translocates into nucleus in a LATS1-dependent manner, triggers NF-κB signaling and enhances ECM degradation, leads us to consider different approaches to restore ECM balance: either by inhibiting LATS1 to impede ZBTB20 activity or by directly reducing ZBTB20 expression. The small molecular compound TRULI can block the nucleus accumulation of ZBTB20 via inhibiting LATS1 phosphorylation, and DAPA was identified as a proposing drug targeting Zbtb20.Our results demonstrated that pharmacologic blockade of LATS1 by TRULI, as well as inhibition of Zbtb20 expression by DAPA, restored the ECM homeostasis in chondrocytes and minimized matrix degradation in human articular cartilage explants.

overall_design: To gain a more profound comprehension of TRULI and DAPA mechanisms on ECM balance, we performed RNA-seq analysis using human primary cartilage chondrocytes exposing to IL-1β solely or in conjunction with TRULI or DAPA.

first: Liu

last: Yang

first: Qiang

last: Jie


title: A microglia clonal inflammatory disorder in Alzheimer’s Disease [dataset 1]

first: Bic

last: MSKCC

summary: Somatic genetic heterogeneity resulting from post-zygotic DNA mutations is widespread in human tissues and can cause diseases, however few studies have investigated its role in neurodegenerative processes such as Alzheimer’s Disease (AD). Here we report the selective enrichment of microglia clones carrying pathogenic variants, that are not present in neuronal, glia/stromal cells, or blood, from patients with AD in comparison to age-matched controls. Notably, microglia-specific AD-associated variants preferentially target the MAPK pathway, including recurrent CBL ring-domain mutations. These variants activate ERK and drive a microglia transcriptional program characterized by a strong neuro-inflammatory response, both in vitro and in patients. Although the natural history of AD-associated microglial clones is difficult to establish in human, microglial expression of a MAPK pathway activating variant was previously shown to cause neurodegeneration in mice, suggesting that AD-associated neuroinflammatory microglial clones may contribute to the neurodegenerative process in patients.

overall_design: Analysis of CBL mutant huIPSC derived macrophages

first: Geissmann

last: Frederic


title: Deciphering the Toxic Effects of Polystyrene Nanoparticle on Erythropoiesis at Single Cell Resolution

city: 경상남도 양산시

first: Eun Jung

last: Kwon

state: 경상남도

address: Pusan National University, Yangsan,, Republic of Korea

institute: Pusan National University

summary: The toxic effects of polystyrene nanoparticles on aquatic ecosystems have been predominantly studied, with a focus on oxidative stress and inflammatory responses. However, this study comprehensively examined the effects of polystyrene nanoparticles on the development of zebrafish embryos using single-cell RNA sequencing analysis, explicitly investigating their effects on erythropoiesis. In vivo experiments were conducted using zebrafish embryos to validate the single-cell RNA sequencing analysis. Exposure to polystyrene nanoparticles resulted in a decrease in the proportion of mature erythrocytes due to an increase in immature erythrocytes during the erythrocyte differentiation process. Additionally, heme synthesis was impaired, leading to a decrease in the proportion of erythrocytes. These findings indicated the toxic effects of polystyrene nanoparticles on hematopoiesis.

overall_design: 120 hpf zebrafish embryos were pooled as a control group(wild type) and 20 nm polystyrene nanoparticles (PS20nm) exposed group for single-cell RNA sequencing.

first: Eunjung

first: Hyeon

last: Mi Sung

first: Chang-kyu

last: Oh

first: Yunhak

last: Kim


title: Asparagine regulates RIG-I stability to suppress anti-tumor immunity in bladder cancer

city: Beijing

first: Jie

middle: wen

last: Wei

address: 28 Fuxing Road, Haidian District, Beijing, China

institute: Chinese PLA general hospital

summary: Tumor cells often employ many ways to restrain type I interferon (IFN-I) signaling to evade immune surveillance. However, whether cellular amino acid metabolism regulate this process remains unclear and its effects on antitumor immunity are relatively unexplored. Here, our study reports that asparagine generated by asparagine synthetase (ASNS) inhibits IFN-I signaling and promotes immune escape in bladder cancer. We further show that depletion of ASNS strongly limits in vivo tumor growth in a CD8+ T cell-dependent manner, thus boosting the immunotherapy efficacy. Moreover, clinically approved ASNase synergizes with anti-PD-1 therapy in suppressing tumor growth in mouse models of bladder cancer. Mechanistically, asparagine intensifies the interaction of E3 ligase CBL and RIG-I, promoting K48-linked polyubiquitination and degradation of RIG-I, thus suppressing RIG-I mediated IFN signaling and anti-tumor immune response. Clinically, ASNS is overexpressed in muscle-invasive bladder cancer and correlated with poor response of immunotherapy. Together, our findings uncover asparagine as a natural metabolite to modulate RIG-I-mediated IFN-I signaling, providing the basis for developing the combinatorial use of ASNase and anti-PD-1 for bladder cancer.

overall_design: In order to screen downstream genes regulated by Asns gene, transcriptome analysis was performed in MBT2 cells transfected with shAsns and compaired vector.

first: Wei

last: Wenjie

first: Huang

last: Yan


title: A microglia clonal inflammatory disorder in Alzheimer’s Disease [dataset 2]

overall_design: Analysis of MAPK mutant mouse primary macrophages

first: Frederic

last: Geissmann


title: Muscle transcriptome at rest and during recovery from running in elite male ultra-endurance athletes acclimated to a high-carbohydrate versus low-carbohydrate diet

city: Birmingham

first: Kaleen

last: Lavin

state: Alabama

address: 908 20th Street South, Room 201-C

department: Medicine

institute: University of Alabama at Birmingham

summary: Low-carbohydrate diets enhance lipid metabolism and decrease reliance on glucose oxidation in athletes, but the associated gene expression patterns remain unclear. To provide mechanistic insight, we investigated the skeletal muscle transcriptome in elite ultra-endurance athletes habitually consuming a high-carbohydrate (HC, n=10, 33±6y, VO2max=63.4±6.2 mL O2•kg-1•min-1) or low-carbohydrate (LC, n=10, 34±7y, VO2max=64.7±3.7 mL O2•kg-1•min-1) diet. Skeletal muscle gene expression was measured at baseline (BL), immediately-post (H0), and 2h (H2) after 3h submaximal treadmill running.  Exercise induced a coordinated but divergent expression pattern. LC had higher expression of genes associated with lipid metabolism, particularly at BL. At H2, gene expression patterns were associated with differential pathway activity, including inflammation/immunity, suggesting a diet-specific influence on early muscle recovery. These results indicate that a habitual ketogenic diet leads to differences in resting and exercise-induced skeletal muscle gene expression patterns, underlying our previous findings of differential fuel utilization during exercise in elite male ultra-endurance athletes.

overall_design: Highly trained male ultra-endurance athletes acclimated to either high-carbohydrate or low-carbohydrate (ketogenic) diet performed a 3h treadmill run. Skeletal muscle gene expression was measured via RNA-seq on muscle biopsies collected at rest (baseline, BL), immediately post-exercise (h0), and two hours into early recovery (h2).

first: Catherine

last: Saenz

first: Elaine

last: Lee

first: Carl

last: Maresh

first: William

middle: J

last: Kraemer

first: Marcas

last: Bamman

first: Timothy

last: Broderick

first: Jeff

last: Volek


title: NONO associates with PKM2 and directs histone H3 phosphorylation to promote tumor metastasis (CUT&Tag)

city: Nanjing

first: Qixiang

last: Li

address: 163 xianlin road, qixia district

institute: nanjing university

summary: Dysregulation of transcriptional programming and epigenome has been identified as fundamental driver of cancer. However, the molecular mechanisms in such processes remain poorly understood. Here, we report that NONO (non-POU domain-containing octamer-binding protein) directly interacts with nuclear PKM2, which is critical for the activation of the NONO-driven transcriptional programme in triple-negative breast cancer (TNBC). We further demonstrate that plasminogen activator inhibitor 1 (PAI1) is a downstream target of NONO/PKM2 complex in TNBC cells through transcriptome analysis. In addition, we show that PKM2-mediated phosphorylation of histone H3 at threonine 11 (H3T11ph) collaborates with acetylation of histone H3 at lysine 27 (H3K27ac), which is due, at least in part, to PKM2 transcriptional activation of TIP60 expression. Importantly, NONO, H3T11ph, and H3K27ac signals are co-enriched at the PAI1 gene loci, which directly boosts PAI transcription. Consistent with above results, we also confirm that the expression of NONO and PKM2 are positively correlated with PAI1 expression in TNBC tissues. Thus, our findings reveal nuclear PKM2 as a novel NONO cofactor required for its biological function and suggest that the NONO/PKM2-PAI1 axis is an attractive therapeutic target in TNBC.

overall_design: Cleavage under targets and tagmentation (CUT&Tag) for transcription factor NONO as well as the histone modifications H3T11ph and H3K27ac in MDA-MB-231 cells.

first: Hongfei

last: Ci

first: Pengpeng

last: Zhao

first: Dongjun

last: Yang


title: Multiplexing and massive parallel sequencing of targeted DNA methylation to predict chronological age

city: Shang Hai Shi

first: Bowen

last: Zhu

state: Shang Hai Shi

address: Pu Dong Xin Qu Hua Tuo Lu 88Hao, Gao Ke Yuan18-604

institute: Interdisciplinary Research Center on Biology and Chemistry

summary: Estimation of chronological age is particularly informative in forensic contexts. Assessment of DNA methylation status allows for the prediction of age, though the accuracy may vary across models. In this study, we started with a carefully designed discovery cohort with more elderly subjects than other age categories, to diminish the effect of epigenetic drifting. We applied multiplexing and massive parallel sequencing of targeted DNA methylation, which let us to construct a model comprising 25 CpG sites with substantially improved accuracy (MAE=2.279, R=0.92). This model is further validated by an independent cohort (MAE=2.204, 82.7% success (±5 years)). Remarkably, in a multi-center test using trace blood samples from forensic caseworks, the correct predictions (±5 years) are 91.7%. The nature of our analytical pipeline can easily be scaled up with low cost. Taken together, we propose a new age-prediction model featuring accuracy, sensitivity, high-throughput, and low cost. This model can be readily applied in both classic and newly emergent forensic contexts that require age estimation.

overall_design: We subjected 10μg converted DNA with multiplexing PCR reaction to massive parallel DNA sequencing, followed by analysis

first: Dean


title: NONO associates with PKM2 and directs histone H3 phosphorylation to promote tumor metastasis (RNA-Seq)

overall_design: To identify potential transcriptional targets of NONO/PKM2 complex and understand the mechanisms of their interaction in TNBC, we established MDA-MB-231 cell lines in which each target gene has been knocked down by siRNA.


title: Glioblastoma progression is hindered by melatonin-primed mesenchymal stromal cells through dynamic intracellular and extracellular reorganizations

city: SEVILLA

first: Vivian

last: Capilla-Gonzalez

state: Sevilla

address: Avda. Americo Vespucio 24

country: Spain

institute: CABIMER

summary:
Background. Glioblastoma (GBM) is the deadliest form of brain cancer and its treatment remains an unresolved challenge. Mesenchymal stromal cells (MSCs) have been explored as vehicles for the targeted delivery of anticancer drugs due to their tumor-homing abilities. However, their clinical application is limited due to the controversial role of MSCs on carcinogenesis. This study investigates how MSCs influence tumor behavior and explores the synergistic anticancer effects of the cytoprotective melatonin (Mel).
Methods. Orthotopic and subcutaneous GBM xenograft mouse models were used to assess the antitumor effect of Mel pre-treated MSCs (MSCMel). Histological, immunohistochemistry and ultrastructural analysis were conducted to identify phenotypic changes in the tumors. A set of in vitro assays, including direct and indirect co-cultures, dynamic single-cell tracking and tumorsphere migration assay, was conducted to explore the impact of MSCMel on primary and non-primary GBM cells. Transcriptome profiling was used to identify genes and pathways modulated by the synergistic therapy.
Results. MSCMel delayed tumor growth in mice and increased collagen deposition. Additionally, MSCMel showed enhanced capacity to prevent GBM cell migration than untreated MSCs. Molecular analysis identified genes and pathways related to cell migration, cytoskeletal dynamics and extracellular matrix remodeling in GBM cells exposed to MSCMel, including extensive reduction of vimentin expression. Finally, a gene signature associated with the clinical outcomes of GBM patients was identified.
Conclusions. Our study demonstrates that melatonin enhances the anticancer properties of MSCs, providing new insights on their interaction with GBM cells and the tumor environment. These findings offer valuable guidance for advancing MSC-based therapies in clinical practice.

overall_design: U87 cells were co-cultured with MSC or melatonin-pretreated MSCs in an indirect transwell system. After co-culture, U87 cells were collected and processed for RNA-seq.

first: Laura

last: Olmedo-Moreno

first: Concepción

last: Panadero-Morón

first: Jesús

last: Sierra-Párraga

first: Rubén

last: Bueno-Fernández

first: Emily

last: Norton

first: Yolanda

last: Aguilera

first: Nuria

last: Mellado-Damas

first: Patricia

last: García-Tárraga

first: Raquel

last: Morales Gallel

first: Germaine

last: Escames

first: José

last: García-Verdugo

first: Alejandro

last: Martin-Montalvo

first: Hugo

last: Guerrero-Cazares

last: Capilla-González


title: A subset of human dermal fibroblasts overexpressing Cockayne syndrome group B protein resist UVB radiation-mediated premature senescence

city: Athens

first: Eleni

last: Mavrogonatou

address: Patriarchou Grigoriou & Neapoleos

department: Institute of Biosciences and Applications

country: Greece

institute: NCSR "Demokritos"

summary: Ultraviolet B (UVB) radiation is a major contributor to skin photo-ageing. Although mainly absorbed by the epidermis, UVB photons managing to penetrate the upper dermis affect human dermal fibroblasts (HDFs), leading, among others, to the accumulation of senescent cells. In vitro studies have shown that repeated exposures to subcytotoxic UVB radiation doses provoke HDFs’ premature senescence shortly after the end of the treatment period. Here, we found that repetitive exposures to non-cytotoxic UVB radiation doses after several days lead to mixed cultures, containing both senescent cells and fibroblasts resisting senescence. “Resistant” fibroblasts were more resilient to a novel intense UVB radiation stimulus. RNA-seq analysis revealed that ERCC6, encoding Cockayne syndrome group B (CSB) protein, is upregulated in resistant HDFs compared to young and senescent cells, also confirmed at the protein level. CSB was found to be a key molecule conferring protection towards UVB cytotoxicity, as siRNA-mediated CSB loss-of-expression rendered HDFs significantly more susceptible to a high UVB radiation dose. In accordance, cells from a CSB-deficient patient were found to be dramatically more photosensitive. UVB-resistant HDFs remained normal (able to undergo replicative senescence) and non-tumorigenic. Even though they formed a distinct population in-between young and senescent cells, resistant HDFs retained numerous tissue-impairing characteristics of the senescence-associated secretory phenotype, including increased matrix metalloprotease activity and promotion of epidermoid tumor xenografts in immunodeficient mice. Collectively, here we describe a novel subpopulation of HDFs showing increased resistance to UVB-mediated premature senescence, as well as undesirable traits that may negatively affect skin homeostasis.

overall_design:
To elucidate the molecular profile of UVB-resistant human dermal fibroblasts, emerging after exposure of the cells to 10 non-cytotoxic doses of UVB radiation.
Total RNA was extracted from three samples per condition (young cells, UVB-reistant cells, ionizing radiation-induced senescent cells). For library preparation, the 3′ mRNA-Seq Library Prep Kit Protocol for Ion Torrent. Quality and quantity of libraries were assessed on a bioanalyzer using the DNA High Sensitivity Kit reagents and protocol. The quantified libraries were pooled at a final concentration of 7 pM, templated and enriched on the Ion Proton One Touch system using the Ion PI™ Hi-Q™ OT2 200 Kit and sequenced using the Ion PI™ Hi-Q™ Sequencing 200 Kit on Ion Proton PI™ V2 chips on an Ion Proton™ System, according to the manufacturer’s instructions
FASTQ files were trimmed with Trim Galore (v.0.6.51) to remove low quality read ends using a Phred score of 20. Subsequently, a two steps alignment procedure was applied. Pre-processed reads were aligned against the hg38 reference genome (Ensembl) with HISAT2 (v.2.2.1) and then the reads left unmapped were subjected to a second alignment round using BOWTIE2 (v.2.3.5.1) with the -local and -very-sensitive local switches turned on.
Downstream analysis of the resulting BAM files was performed with metaseqR2 R package (v.1.9.2).
The filtered gene counts table was subjected to differential expression analysis for the contrasts resistant vs. young cells, IS vs. young cells and IS vs. resistant cells using sequentially DESeq, edgeR, limma, NBPSeq, and NOISeq methods supported by metaseqR2. Their p-values were then combined by the PANDORA algorithm to account, among others, for the false positives reported
Benjamini-Hochberg-corrected PANDORA p-values of less than 0.05 and absolute fold change of at least 1.2 were used as differential expression thresholds.

first: Asimina

last: Fotopoulou

first: Maria

last: Angelopoulou

first: Harris

last: Pratsinis

first: Dimitris

last: Kletsas