title: Transcriptome profiling reveals differential gene expression of detoxification and mitochondrial-related enzymes in Tribolium castaneum in response to carbonyl sulfide

city: Daejeon Metropolitan City

first: SHIN

last: NARI

address: Oncheon 2-dong, Yuseong-gu

institute: chungnam national university

summary: Carbonyl sulfide (COS) is a novel grain fumigant, introduced in 1993 as a substitute to methyl bromide and phosphine for managing stored-grain pests. While COS has demonstrated high toxicity and broad efficacy against various stored-product pests, including Tribolium castaneum, the mechanisms underlying its toxicity in insects remain largely unexplored. To elucidate the molecular basis of COS toxicity in insects, we analyzed the transcriptome to investigate gene expression in the malpighian tubules and fat body tissues of adult T. castaneum upon COS fumigation. Our analysis identified 3,034 and 2,973 differentially expressed genes (DEGs) in the malpighian tubules and fat body, respectively. Several DEGs associated with insecticide detoxification, mitochondrial functions, and carbonic anhydrase (CA) activity were significantly expressed between the COS-treated and control groups. The functional annotation and pathway analyses using Gene Ontology (GO) terms and KEGG for these DEGs identified categories related to binding, catalytic activity, cellular and biological processes, cellular anatomical entity and xenobiotic metabolism pathways. We validated 23 DEGs, which revealed consistent gene expression levels with those of transcriptomic analysis. Furthermore, we analysed the impact of acetazolamide, a CA inhibitor, on the survival rates of T. castaneum larvae and adults following COS exposure, implying that acetazolamide likely reduces COS toxicity through CA inhibition. This study presents the first comparative transcriptome investigation of the malpighian tubules and fat body in T. castaneum, enhancing our understanding of the molecular basis of COS toxicity and its potential as an effective alternative for control of this significant agricultural pest.

overall_design: We investigated the differentially expressed genes between COS-treatment (malpighian tubules and fat body) and control group (whole body) of Tribolium castaneum.

first: Shin

last: Na Ri

first: Seong

last: Keon Mook


title: H3K9 methylation-independent activity for HPL-2/HP1 in heterochromatin foci, gene repression, and organogenesis

status: Public on Jul 01 2025

city: Mainz

first: Jan

last: Padeken

address: Ackermannweg 4

country: Germany

institute: Institute of Molecular Biology

type: Expression profiling by high throughput sequencing

summary: Differentiated cells rely on segregation of the genome into heterochromatin and euchromatin, but the mechanisms that establish these domains in vivo are incompletely understood. The current models suggest that heterochromatin is marked by histone H3 lysine 9 methylation (H3K9me), which recruits heterochromatin protein 1 (HP1), to compact chromatin and repress transcription. In C. elegans, the SETDB1 homolog MET-2 is essential for H3K9me-mediated gene silencing; however, MET-2 also localizes to heterochromatic foci independently of H3K9me and exhibits non-catalytic functions that support both germline and somatic development. Here we extend these findings by examining the classical H3K9me reader HP1. We show that HPL-2/HP1 deficient in methyl-lysine binding or in the absence of H3K9me can still repress transcription, promote organogenesis and localize to heterochromatin foci. Whereas activity remains in the absence of the HPL-2:H3K9me interaction, complete loss of met-2 and hpl-2 shows synergistic phenotypes for organogenesis and gene de-repression, underscoring the existence of additional, H3K9me-independent functions. HPL-2 and MET-2 require distinct binding partners for their localization and activity: MET-2 associates with the disordered protein LIN-65/ATF7IP, while HPL-2 depends on the multi-zinc finger protein LIN-13, which interacts with the HPL-2 chromoshadow domain. Our findings suggest that HPL-2 and MET-2 operate in parallel pathways, localizing to heterochromatic foci and promoting gene silencing and organogenesis, with H3K9me acting as a reinforcing, but non-essential, element in these processes.

overall_design: RNA was extracted from early wild-type (N2 Bristol), hpl-2 (hpl-2(tm1489)), hpl-2-ffaa (hpl-2-FFAA(px112)), and hpl-2 met-2 (met-2(n4256) hpl-2(tm1489) III/hT2 [bli-4(e937) let-?(q782) qIs48] (I;III)) C. elegans embryos from a synchronized culture grown at 20°C, using Trizol. Embryos were freeze cracked five times, then RNA was extracted with choloroform followed by isopropanol precipitation. Further purification was performed with the RNA Clean and Concentrator kit (Zymo). Libraries were produced using the Stranded Total RNA Prep Ligation with Ribo-Zero Plus Kit (Illumina). rRNA was depleted using the Ribo-Zero Plus kit supplemented with custom made C. elegans specific rDNA oligos (IDT). Libraries were profiled in a DNA 1000 Chip on a 2100 Bioanalyser (Agilent technologies) and quantified using the Qubit 1x dsDNA HS Assay Kit, in a Qubit 4.0 Fluorometer (Life technologies). Equimolar amounts of indexed libraries were pooled and sequenced on a NextSeq 2000 (Illumina).

first: Colin

middle: E

last: Delaney

first: Jia Emil

last: You

first: Susan

middle: M

last: Gasser

last: Mango


title: Gene expression profiling of CD11c+ or CD11b+ cells from bronchoalveolar lavage fluid was conducted in a bleomycin-induced pulmonary fibrosis model following GW5074 treatment or in Clec7a KO mice

city: Guangzhou

first: Ding

last: Qiu

address: Zhong Shan Er Lu, Guangzhou, Guangdong Province, China

country: China

institute: Sun yet san university

summary: To investigate the role of the Dectin-1 signaling pathway in the development of pulmonary fibrosis, we established a BLM-induced pulmonary fibrosis model using WT mice, Dectin-1-deficient mice (Clec7a–/–, KO), and GW5074-treated mice. CD11b+ or CD11c+ cells were sorted by flow cytometry and subjected to single-cell RNA sequencing.

overall_design: WT, GW5074-treated WT, and KO mice were administered BLM via airway instillation to induce pulmonary fibrosis. After 14 days, the bronchoalveolar lavage fluid from each group of mice was pooled, and CD11b+ or CD11c+ cells were sorted by flow cytometry. The sorted cells were then subjected to single-cell RNA sequencing.

first: Ce

last: Tang


title: High-Throughput Identification of Genome-Wide Silencers in Mouse Cells Using Ss-STARR-seq

city: shenzhen

first: Guoli

last: Li

address: penfei street

institute: Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences

summary: The majority of the mouse genome is composed of non-coding regions, which harbor numerous regulatory sequences essential for gene regulation. While extensive research has focused on enhancers that activate gene expression, the role of silencers that repress gene expression remains less explored. In this study, we conducted the first genome-wide identification of silencers in the mouse cell genome. In mouse embryonic fibroblasts (MEFs) and mouse embryonic stem cells (mESCs), we identified 89,596 and 115,165 silencers, respectively. These silencers are ubiquitously distributed across the genome and are predominantly associated with low-expression genes. Additionally, We have identified that these silencers predominantly exhibit cell-specific presence and exert their function through binding with repressive transcription factors (TFs). Furthermore, these silencers are notably enriched with the histone modification H3K9me3. In terms of biological effects, we identified a silencer within an intron of the pluripotency gene NANOG. Knockout of this silencer in (MEFs) resulted in a twofold increase in the induction efficiency of induced pluripotent stem cells (iPSCs). Collectively, our work provides the first comprehensive silencer landscape in the mouse genome and provides strong evidence for the role of silencers in the induction of iPSCs.

overall_design: We identified genome-wide silencers in mouse cell lines MEFs and mESCs using Ss-STARR-seq. We then performed a joint analysis of these silencers with other multi-omics data to elucidate the fundamental characteristics of mouse silencers. Finally, we investigated the biological effects of these silencers by conducting CRISPR knockout experiments. Genome assembly mm10.


title: Enhancing single-cell ATAC sequencing with formaldehyde fixation, cryopreservation, and multiplexing for flexible analysis [scATAC-seq]

city: Freiburg im Breisgau

first: Thomas

last: Manke

address: Stuebeweg 51

department: Bioinformatics Core Facility

institute: Max-Planck-Institute of Immunobiology and Epigenetics

type: Genome binding/occupancy profiling by high throughput sequencing

summary: The assay for transposase-accessible chromatin using sequencing (ATAC-seq) revolutionized the field of epigenetics since its emergence by providing a means to uncover chromatin dynamics and other factors affecting gene expression. The development of single-cell (sc) applications in recent years led to an even deeper understanding of cell type specific gene regulatory mechanisms. One of the major challenges while running ATAC-seq experiments, bulk or sc, is the need for freshly collected cells for successful experiments. While various freezing methods have already been tested and established for bulk and sc ATAC-seq, quality metrics for preserved cells are rather poor or dependent on sampling time when compared to fresh samples. This makes it difficult to conduct all sorts of complex experiments i.e. with multiple conditions, patients, or time course studies. Especially, accounting for batch effects can be difficult if samples need to be processed at different time points of collection. We tackled this issue by adding a fixation step prior to the freezing method. The additional fixation step improved library quality and yield data comparable to fresh samples. The workflow was also tested on multiplexed sc ATAC experiments, set-up for cost-efficient low input sample handling. Sample cross-in, typically encountered in Tn5-based multiplex approaches, were tackled with a computational procedure specifically developed for this approach.

overall_design: To investigate the performance of our sample preservation and multiplexing strategies, we harvested cultured HepG2 cells. The cells were fixed with 0.1% FA and subsequently frozen by either flash freezing or cryopreservation. An untreated sample was also included. Then, scATAC-seq libraries were created and sequenced to analyze the influence of each preservation method on data quality and comparability.

first: Hohl

last: Tobias

first: Boenisch

last: Ulrike

first: Manke

last: Thomas

first: Arrigoni

last: Laura


title: Transcriptomic analysis to study interactions between murine host and fungal commensal Candida albicans upon its gastrointestinal colonization

city: Providence

first: Richard

middle: J

last: Bennett

state: RI

address: 171 Meeting St, Biomed Center

department: Molecular Microbiology and Immunology

country: USA

institute: Brown University

summary: Candida albicans is a ubiquitous fungus in the human gut microbiome as well as a prevalent cause of opportunistic mucosal and systemic disease.  There is currently little understanding, however, as to how crosstalk between C. albicans and the host regulates colonization of this key niche.  Here, we performed expression profiling on ileal and colonic tissues in germ-free mice colonized with C. albicans to define the global response to this fungus.  We reveal that Duox2 and Duoxa2, encoding dual NADPH oxidase activity, are upregulated in both the ileum and colon, and that induction requires the C. albicans yeast-hyphal transition and hyphal-specific toxin candidalysin.  Hosts lacking the IL-17 receptor failed to upregulate Duox2/Duoxa2 in response to C. albicans, while addition of IL-17A to colonoids induced these genes together with the concomitant production of hydrogen peroxide. To directly define the role of Duox2/Duoxa2 in fungal colonization, antibiotic-treated mice lacking intestinal DUOX2 activity were evaluated for C. albicans colonization and host responses.  Surprisingly, loss of DUOX2 function reduced fungal colonization at extended time points (>17 days colonization) and increased the proportion of hyphal cells in the gut.  IL-17A levels were also elevated in C. albicans-colonized mice lacking functional DUOX2 highlighting cross-regulation between DUOX2 on this cytokine.  Together, these experiments reveal novel links between fungal cells, candidalysin and the host IL-17-DUOX2 axis, and that a complex interplay between these factors regulates C. albicans filamentation and colonization in the gut.

overall_design: A group (n=5, 3F,2M) of germ-free mice were colonized with WT-SC5314 strain of Candida albicans for 7 and 21 days. Distal ileum and colon tissues were harvested at 7 days and 21 days post colonization in addition to a control group of non-colonized mice. Bulk RNA sequencing was carried out from these tissues to study any changes in the host gene expression upon C. albicans colonization of the murine gastrointestinal tract.

first: Pallavi

last: Kakade

first: Juan

middle: F

last: Burgueno

first: Shabnam

last: Sircaik

first: Nicole

middle: O

last: Ponde

first: Jinke

first: Iuliana

middle: V

last: Ene

first: Jiwoong

last: Kim

first: Shen-Huan

last: Liang

first: Rebecca

last: Yunker

first: Yasutada

last: Akiba

first: Shipra

last: Vaishnava

first: Jonathan

middle: D

last: Kaunitz

first: Sing

middle: S

last: Way

first: Andrew

middle: Y

last: Koh

first: Sarah

middle: L

last: Gaffen

first: Maria

middle: T

last: Abreu


title: HepaCAM knockdown impairs learning and memory in mice by regulating cholesterol synthesis pathway

city: Hefei

first: Ziyu

last: Qiu

address: Huangshan Road

institute: USTC

summary: Astrocytes engage in metabolic interactions with nearby neurons by supplying various substances. However, how they regulate learning and memory through changes in the metabolic state of neurons is still unclear. In this study, we show that knocking down astrocytic hepaCAM silences genes related to cholesterol biosynthesis in astrocytes, leading to a decrease in cholesterol levels. Additionally, astrocytes play a crucial role in synapse development and function by releasing signals that guide neurons. Consequently, without enough cholesterol, the level of neuronal synaptic proteins and the density of dendritic spines decrease. Then we demonstrate that knocking down hepaCAM leads to impaired learning and memory in mice. Collectively, hepaCAM, a cell adhesion molecules specifically expressed in astrocytes, regulates learning and memory by regulating the cholesterol synthesis pathway.

overall_design: To investigate the role of hepaCAM in mouse hippocampus, we knocked down hepaCAM in mouse hippocampus by shRNA. Next, we compared the gene expression profiles of RNA-seq data from the hippocampus of WT and hepaCAM KD mice


title: Studies on the mechanism of complement protein C4 in the regulation of aging [II]

city: Cheng Du

first: Yan

last: Pan

address: Northern Jianshe Road

institute: University of Electronic Science and Technology of China

summary: Learning and memory capability always decline with age in healthy people, and synapse loss may be an important factor contributing to this reduction. The complement pathway plays a crucial role in synaptic pruning during normal brain development, and the abnormal activation of the classical complement cascade is involved in the pathogenesis of certain neurological disorders. However, none of the past studies elucidated the effects of complement proteins in the aging of the nervous system. Here, we performed transcriptome sequencing in multiple tissues of mice at different ages in an attempt to find important regulators during aging. Our results show that the expression of complement protein C4 in the mouse brain increases with aging. In addition, we constructed different neuronal aging models for transcriptome analysis to identify the regulatory pathways upstream of complement C4, and explored the possible mechanism of complement C4 involved in synapse pruning by co-culture or immunofluorescence methods. This further demonstrates that complement C4 is a potential marker of aging. These findings suggest that NF-κB signaling pathway may contribute to age dependent complement C4 increase, which in turn affect learning and memory function via neuronal synaptic pruning regulation.

overall_design: To investigate the common regulatory pathways in different neuronal aging models, we generated OIS and SIPS models by over-expression H-Ras with AAV and treating primary neurons with etoposide, respectively. Samples were collected for RNA-Seq analysis after 10 days of both treatments. Comparative gene expression profiling analysis of RNA-seq data for Neuron and its aging derivatives (OIS and SIPS)

first: Ting

last: Liu

first: Lu-nan

last: Luo

first: Yi

last: Zheng

first: Jing

last: Yang


title: Gene expression profiling of Clec7a knockout mice lung tissue in a bleomycin-induced pulmonary fibrosis model

first: Ding

summary: To investigate the role of Dectin-1 in the development of pulmonary fibrosis, we used Dectin-1-deficient (Clec7a–/–, KO) mice to establish a bleomycin-induced pulmonary fibrosis model and compared it with WT mice.

overall_design: WT and KO mice were administered bleomycin via airway instillation to induce pulmonary fibrosis. After 14 days, lung tissues from 3 WT mice and 3 KO mice were collected for gene expression analysis using RNA-seq.

first: Ce

last: Tang


title: Variation in transformation frequency and competence gene expression among serotype 3 Streptococcus pneumoniae

city: ORLANDO

first: Taj

last: Azarian

state: FL

address: 6700 Lake Nona Blvd

institute: University of Central Florida

summary: Streptococcus pneumoniae is a human commensal and the causative agent of pneumococcal disease. Pneumococci are naturally competent – able to uptake exogenous DNA from the environment and incorporate it into their genome through homologous and non-homologous recombination. Recombination has significantly shaped the evolutionary history of S. pneumoniae, as it allows pneumococci to rapidly adapt to interventions such as antibiotic therapy or vaccine introduction. Recombination frequencies vary considerably across pneumococcal populations; yet the underlying mechanisms for these variations are not well understood. Entry and exit into competence, a state in which the cell can uptake DNA, is tightly regulated through transcriptional changes. We observed consistent differences in transformation frequencies among groups, which correlated with variation in differentially expressed genes during competence. While all strains exhibited a similar response to competence stimulating peptide (CSP) for early competence genes, we observed variation in expression of late competence genes, which encode the DNA uptake apparatus, DNA repair and recombination proteins needed for recombination. We also observed differences in expression of genes linked to bacteriocin production, which may partially explain observed population-level differences. Further genomic analysis suggests variation in promoter sequences governing late competence genes may be slowing transition from early to late components of the competence pathway.

overall_design: To elucidate differences in transformation frequency among strains as well as the underlying genetic mechanisms, we carried out in-vitro competence assays and measured gene expression changes during the competent state using RNA sequencing of strains belonging to Serotype 3 clonal complex (CC) 180 and a non-CC180 comparison. Cultures were treated with 200 ng/ml of competence stimulating peptide (CSP). Two volumes of RNAprotect bacteria reagent (Qiagen) were added to the cultures at 10, 15, 20 mins after CSP addition, vortexed and incubated at room temperature for 5 mins. These timepoints were selected as it has been shown that peak competence is achieved after 15 - 20 mins.


title: Regional interneuron transcriptional changes reveal pathologic markers of disease progression in a mouse model of Alzheimer’s disease -- Late-stage AD

city: Ann Arbor

first: Mohamed

last: Noureldein

address: 109 Zina Pitcher Place

department: Neurology

institute: University of Michigan

summary: Alzheimer's disease (AD) exhibits imbalance between neuronal excitation and inhibition, likely secondary to interneuron dysfunction. To reveal underlying mediators, we profiled the transcriptome of neuronal subtypes in 5XFAD versus control mice at early- and late-stage disease. Pooled analysis of neuron types showed expected pathways at early-stage (RNA and protein processing pathways) versus late-stage (neurodegenerative pathways) disease. Early-stage interneurons exhibited alterations in AD-related RNA and protein pathways along with canonical neurodegenerative pathways. Early-stage excitatory neurons, however, showed changes in axon guidance and synapse pathways, without representation of neurodegenerative pathways. Classical neurodegenerative pathways were represented only in late-stage excitatory neurons. Late-stage interneurons instead featured neuronal and synapse pathways along with cellular, cancer, and infection pathways. Our results suggest earlier neurodegenerative pathway involvement in interneurons, represented in excitatory neurons only at later stages, possibly indicating earlier inhibitory neuron involvement. These transcriptomic profiles offer insight into potential AD pathophysiology and therapeutic targets.

overall_design: Spatial transcriptomics was performed by GeoMx DSP (NanoString, Seattle, WA), a platform for spatially analyzing gene expression in tissue in a highly multiplexed manner.64 Four slides in total were submitted for spatial transcriptomics. Two slides were for late-stage analysis and were duplicates of 4 brain sections (n=2 5XFAD 30 wk, n=2 controls 30 wk).

first: Kevin

last: Chen

middle: H

first: Eva

last: Feldman


title: Effect of cisplatin on gene expression of human microvascular endothelial cells

city: Chengdu

first: Fangqi

last: Jing

address: No14, the third part ren min road, wuhou district

institute: West China Hospital of Stomatology

summary: Cisplatin (DDP) is a widely used chemotherapeutic agent that induces apoptosis in various cancer cells, but its effects on endothelial cells such as HMEC-1 (Human  Microvascular Endothelial Cell line-1) are less well understood. This study aims to explore the transcriptional response of  HMEC-1 to cisplatin treatment. RNA-seq analysis was performed to identify differentially expressed genes following cisplatin stimulation, providing insights into the molecular mechanisms underlying the cellular response to chemotherapy in endothelial cells. The results highlight key pathways and genes involved in the stress response, apoptosis, and cellular survival in HMEC-1 cells upon cisplatin treatment.

overall_design: To investigate the effect of cisplatin on HMEC-1 cells, we treated the cells with cisplatin at a specific concentration for a defined period. RNA was extracted and RNA-seq was performed on treated and control cells to profile the gene expression changes induced by cisplatin. Comparative gene expression profiling analysis was conducted to identify differentially expressed genes between cisplatin-treated and control HMEC-1 cells, focusing on pathways related to apoptosis, stress response, and cellular survival.

first: Jingtian

last: Mu

first: Junjiang

first: Can

last: Hu

first: Fanglong

last: Wu

first: Qinghong

last: Gao


title: A 36-base hairpin within lncRNA DRAIC interacts with the IKKα coiled-coil domain, weakening the IKK complex and inhibiting NF-kappaB activation

first: Chase

middle: Andrew

last: Weidmann

state: MI

address: 1150 W. Medical Center Drive

department: Biological Chemistry

summary: Long noncoding RNAs have diverse functions, but not enough is known about the molecular mechanisms underlying their cellular functions.  The 1.7 kb long down-regulated non-coding RNA in cancers (DRAIC) slows tumor growth and inhibits the activation of the transcription factor NF-kappaB through interactions with IKK subunits. Starting with SHAPE-MaP-based structure-function studies of DRAIC we have now identified the minimal regions of DRAIC and IKK involved in the interactions and the anti-cancer function of DRAIC. A hairpin structure comprised of bases 705-722/741-758 (referred to as A+B) within DRAIC is responsible for inhibiting NF-kappaB activity. A+B binds specifically with the IKKα coiled-coil domain with a KD of ~1-5 nM. The coiled-coil domain of IKKα (the kinase subunit) and NEMO (the substrate recognition subunit,) mediate the dimerization of the subunits in the functional kinase complex. Consistent with its interaction with the coiled-coil domain of IKKα, A+B weakens the interaction between NEMO and the IKKα coiled-coil domain in an in vitro complex formation assay. The 36 nt A+B RNA was sufficient and necessary for DRAIC to inhibit tumor cell migration, invasion, and clonal growth in multiple cancer cell-lines.  Therefore, this minimal hairpin fragment of the growth-suppressive DRAIC lncRNA inhibits NF-kappaB activation by interacting with high affinity with the coiled-coil domain of IKKα, weakening the interaction between the kinase subunit and the substrate recognition subunit of IKK, thereby inhibiting IB phosphorylation and NF-kappaB activation, and suppressing tumor phenotypes.

overall_design: To discover functional structures within the DRAIC RNA, we performed SHAPE-MaP to obtain conformational flexibility measurements of the DRAIC active region from cell-extracted RNA.

first: Xiaoxiao

last: Hao

first: Róża

middle: K

last: Przanowska

middle: A

last: Weeks

first: Anindya

last: Dutta


title: Effect of cisplatin on gene expression of human umbilical vein endothelial cells

summary: Cisplatin (DDP) is a widely used chemotherapeutic agent that induces apoptosis in various cancer cells, but its effects on endothelial cells such as HUVEC (Human Umbilical Vein Endothelial Cells) are less well understood. This study aims to explore the transcriptional response of HUVEC cells to cisplatin treatment. RNA-seq analysis was performed to identify differentially expressed genes following cisplatin stimulation, providing insights into the molecular mechanisms underlying the cellular response to chemotherapy in endothelial cells. The results highlight key pathways and genes involved in the stress response, apoptosis, and cellular survival in HUVEC cells upon cisplatin treatment.

overall_design: To investigate the effect of cisplatin on HUVEC cells, we treated the cells with cisplatin at a specific concentration for a defined period. RNA was extracted and RNA-seq was performed on treated and control cells to profile the gene expression changes induced by cisplatin. Comparative gene expression profiling analysis was conducted to identify differentially expressed genes between cisplatin-treated and control HUVEC cells, focusing on pathways related to apoptosis, stress response, and cellular survival.

last: Liu


title: Regional interneuron transcriptional changes reveal pathologic markers of disease progression in a mouse model of Alzheimer’s disease -- Early-stage AD

overall_design: Spatial transcriptomics was performed by GeoMx DSP (NanoString, Seattle, WA), a platform for spatially analyzing gene expression in tissue in a highly multiplexed manner.64 Four slides in total were submitted for spatial transcriptomics. Two slides were for early-stage analysis and were duplicates of 4 brain sections (n=2 5XFAD 12 wk, n=2 controls 12 wk)


title: Quiescent fibroblast-like synovial cells alleviate inflammatory bowel disease by modulating the gut immune microenvironment [dataset2]

city: Shijiazhuang

first: Jiayu

last: Zhang

address: No. 361 Zhongshan East Road

institute: Hebei Medical University

summary: To explore the potential of stem cellsfromhuman exfoliated deciduous teeth (SHED) for the treatment of inflammatory bowel disease (IBD) by addressing their in vivo mechanisms.

overall_design: scRNA-seq of CD45+ immune cells extracted from mouse colon with different treatment.


title: CRISPR Screening Reveals a Novel Role for FOXH1 in Regulating Pluripotency of Porcine Embryonic Stem Cells

city: Wuhan

first: Wu

last: Linhui

state: Hubei

address: No.1 Shizishan Street

department: College of Animal Science and Veterinary Medicine

institute: Huazhong Agricultural University

summary: pESCs hold significant potential for applications in regenerative medicine and stem cell-based breeding programs. However, the regulatory mechanisms governing pluripotency in pESCs, including aspects of cellular adaptability and the maintenance of a pluripotent identity, are not yet fully understood.To distinguish these two features of pESCs, we conducted two types of CRISPR-Cas9 knockout screenings targeting all known transcription factors and epigenetic regulators in the porcine genome. Through the CRISPR-Cas9 screenings, we identified 900 essential genes, including the species-conserved gene PRMT1 and the pig-specific gene NASP, which were experimentally validated for their roles in preserving the survival of pESCs. In addition, we found that FOXH1 is indispensable for maintaining pESCs pluripotency. pESCs deficient in FOXH1 displayed a flatter and more dispersed clonal morphology, accompanied by downregulation of pluripotency genes and upregulation of lineage-specific genes. In parallel, FOXH1 knockdown significantly impaired blastocyst formation during early pig embryogenesis, demonstrating an unrecognized role of FOXH1 that is not conserved in hESCs. At the molecular level, FOXH1 exhibits a dual role by regulating chromatin accessibility at pluripotency gene loci and H3K4me3 modifications at the promoters of developmental genes. The resources developed through this study not only lay the groundwork for more extensive CRISPR screenings but also provide crucial theoretical support for the establishment of pPSC cell lines with higher differentiation potential.

overall_design: This study employs multiple high-throughput sequencing technologies, including NGS, ATAC-seq, ChIP-seq, and RNA-seq, to comprehensively investigate the dynamics of sgRNA loss or enrichment during the library screening process, and to assess the effects of FOXH1 knockout on chromatin accessibility, transcription factor binding, and gene expression in pEPSCs. The dataset comprises samples from cell mutation libraries across different generations and pEPSCs under a variety of conditions, such as wild-type and gene knockout (e.g., FOXH1).

first: Peng

last: Su

first: Linhui


title: Quiescent fibroblast-like synovial cells alleviate inflammatory bowel disease by modulating the gut immune microenvironment [dataset 1]

overall_design: scRNA-seq of Stem cells from Human Exfoliated Deciduous teeth (SHEDs) and intestinal organoid medium cultured-SHED (CM-SHEDs)


title: Hijacking intrinsic resistance in Mycobacterium abscessus with small molecule prodrugs

city: Memphis

first: Richard

last: Lee

state: TN

address: 262 Danny Thomas Place

department: Department of Chemical Biology and Therapeutics

institute: St. Jude Children's Research Hospital

summary: This proposal aims to develop narrow-spectrum prodrug-activated protein synthesis inhibitors to treat Mycobacterium abscessus (Mabs) infections. It builds on a recent discovery in our program, which elucidated a unique mechanism for prodrug activation of florfenicol amine (FFA) by hijacking the protective methods Mabs uses to block antibiotic action. Non-tuberculous mycobacteria (NTM) are emerging pathogens with high intrinsic drug resistance.  Mabs is the most pathogenic refractory NTM member,1-3 and infections with this pathogen are associated with especially poor clinical outcomes, similar to XDR-TB (extensively drug-resistant tuberculosis)1.  Florfenicol (FF) is a broad-spectrum analog of chloramphenicol (CAM), is orally bioavailable, safely used in agriculture as it lacks some of the pharmacological liabilities of CAM, and it mitigates plasmid-borne resistance by blocking the primary-hydroxy site of inactivation. FFA is the primary metabolite found in many host species after FF administration. Through routine MIC screening of synthetic intermediates, we discovered that FFA on its own had appreciable WhiB7 transcription factor-dependent MIC activity against Mabs.  Further studies demonstrated that in Mabs FFA acts as a prodrug that is acylated into the active form (FFac) within Mabs by Eis2, a Mabs specific acetyltransferase. eis2 is located in the whiB7 resistome, which results in a feed-forward mechanism of action between FFA, eis2, and whiB7, ultimately increasing the conversion of FFA to FFac, resulting in increased sensitivity. FFA was found to be highly synergistic with other protein synthesis inhibitors and resistance to FFA by inactivation of whiB7 or eis2 results in increased sensitivity to aminoglycosides and macrolides. Since eis2 is only present in Mabs and other closely related species, FFA has a narrow spectrum of activity and avoids the potential for mitochondrial cytotoxicity. Preliminary pharmacological studies demonstrate FFA is noncytotoxic and orally bioavailable.

sample_organism:
Mycobacteroides abscessus
Mycobacteroides abscessus ATCC 19977

overall_design: mRNA profiles of Mycobacterium abscessus ATCC19977 strain after exposure to 1/2 minimal inhibitory concentration of chloramphenicol (256 mg/L) for 30 minutes, florfenicol and florfenicol amine at 25 µM for 30 minutes and 3 hours, and vehicle control at 30 minutes and 3 hours.

first: Gregory

last: Phelps


title: C2H2-type zinc finger protein PagSUPa targets PHRAGMOPLAST ORIENTING KINESIN to negatively regulate cell division during leaf development in Populus alba × P. glandulosa

city: Hangzhou

first: Dan

last: Hou

address: 666 Wusu street, Lin'an District, Hangzhou

institute: A&F university

summary: Transcriptome analysis was performed on the sixth leaves of Populus alba × P. glandulosa. The twelve samples were: four PagSUPa overexpression (OE) line 2 samples 2-1-L6, 2-2-L6, 2-3-L6 and 2-4-L6, four PagSUPa OE line 7 samples 7-1-L6, 7-2-L6, 7-3-L6 and 7-4-L6, four nontransgenic control (CK)  samples CK-1-L6, CK-2-L6, CK-3-L6, CK-4-L6 . And the differential genes between PagSUPa OE and CK groups were identified and compared, which helps to reveal the  molecular mechanism of PagSUPa directly suppresses the expression of phragmoplast orienting and positioning genes PagPOK1 and PagPOK2, and impairs cytokinesis and cell wall organization.

overall_design: Gene expression profiling analysis of transcriptome data from PagSUPa OE plants leaves of Populus alba × P. glandulosa

first: Cheng

last: Jiang


title: Single cell gene expression profile from wild-type and mutant canine retinas following massively parallel reporter assays using pooled AAV5-promoter-GFP vectors.

city: Philadelphia

first: Raghavi

last: Sudharsan

address: 3900 Delancey Street

institute: University of Pennsylvania

summary: Efficacy and specifcity of novel photoreceptor-specific promoters were evaluated in wild-type and mutant (PDE6β-RCD1 and RPGR-XLPRA2) dogs at advnced stages of retinal degeneration using massively parallel reporter assays.

overall_design: Each dog was injected subretinally with a pool of AAV5-promoter-GFP vectors. Five weeks post-injection, neuroretinal punches were collected and dissociated into single cells for scRNASeq analysis.

first: William

last: Beltran


title: UBQLN2 Links Proteotoxicity with Lipid Metabolism in Neurodegeneration

city: baltimore

first: Yang

state: MD

address: 615 N wolfe street

department: BMB

institute: Johns Hopkins

summary: Protein homeostasis and lipid metabolism are crucial cellular processes that are dysregulated in neurodegeneration. However, their connection in neurodegenerative diseases such as amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD) remains unexplored. Ubiquilin 2 (UBQLN2) is a protein quality control factor linked to familial ALS/FTD and broader neurodegeneration. Here, we idetified UBQLN2 as an essential regulator for intracellular lipid metabolism, the biological processes of which are impaired by ALS/FTD-linked mutations in UBQLN2. Using transcriptome analysis, we profiled the molecular changes in motor neurons derived from isogenic control  and UBQLN2-mutant iPSCs under ALS/FTD-associated metabolic stress, glucose deficiency. We found that biological processes related to cell survival and metabolism were greately affected by the disease-linked mutations in UBQLN2, suggesting that the impaired metabolic role of UBQLN2 by the disease-linked mutations is involved in the pathogenesis of relative neurodegeneration.

overall_design: motor neurons derived from isogenic control iPSCs or the iPSCs carrying mutations in UBQLN2 (P506T, P497H) were starved with glucose-free medium for 24 hours and then harvested for transcriptome analysis.

first: Mingming

first: Jiou

last: Wang


title: Reprogramming of Human Urine Stem Cells into Cardiomyocytes via a Small Molecule Cocktail in Xeno-free conditions

city: shanghai

first: Chenwen

last: Huang

state: shanghai

address: 600 Yi Shan Road

department: Department of Joint Clinical Research Centre

institute: Shanghai Sixth People's Hospital

summary: Reprogramming autologous somatic cells into alternative lineages holds significant promise as a crucial cell source for regenerative therapy. Among various sources, human urine stem cells (hUSCs) have emerged as a highly promising candidate for reprogramming due to their ease of collection and high transdifferentiation potential. In this study, we present the first evidence for cardiac regeneration by directly converting hUSCs into functional cardiomyocytes under xeno-free conditions using a cocktail of 15 small molecules. This innovative protocol ensures a safe, animal-free reprogramming environment, enhancing its clinical applicability. The resulting chemically induced human cardiomyocyte-like cells (hCiCMs) exhibit several key characteristics of native cardiomyocytes, including the expression of cardiomyocyte-specific markers, display sarcomeric organization, and exhibit typical cardiac calcium flux and electrophysiological properties. Notably, transplantation of hCiCMs into the infarcted hearts of mice led to substantial improvements in cardiac function, characterized by enhanced contractility and reduced infarct size. Our findings validate the efficacy of the xeno-free differentiation protocol and highlight the potential of hUSC-derived hCiCMs as a viable and effective source for regenerative therapies in myocardial infarction. The use of hUSCs provides a readily accessible, autologous cell source, thereby paving the way for personalized and safer regenerative treatments for cardiac diseases.

overall_design: Digest the cells on day 60 of reprogramming, and then perform single-cell sequencing.

first: Jingwei

first: Yu

last: Chen


title: miR-208a-3p targets PPP6C to regulate the progression of Radiation-induced lung injury

city: chengdu

first: lixin

last: gong

address: No. 4, North Fourth Section, Second Ring Road

institute: The Second Affiliated Hospital of Chengdu Medical College Nuclear Industry 416 Hospital

type: Non-coding RNA profiling by high throughput sequencing

summary: Aims: Radiation-induced lung injury (RILI) is a common complication after radiotherapy for clinical thoracic tumors, and increasing evidence suggests that miRNAs have potential value as biomarkers for early warning. However, the potential mechanism is still obscure. Here, we evaluated miRNAs-dependent mechanism involved in response and therapy of RILI. Results: Our data showed that mmu-miR-208a-3p was consistently highly expressed in the lung tissue of irradiated mice. In vitro studies demonstrated that the expression of miR-208a-3p in cells was significantly increased after X-ray irRadiation. Further mechanism studies indicated that Radiation-induced upregulation of miR-208a-3p promoted inflammatory responses by suppressing the expression of PPP6C and activating the cGAS/STING pathway. Overexpression of PPP6C can alleviate Radiation-induced DNA damage and excessive accumulation of ROS. It was also observed that PPP6C inhibited ionizing Radiation-induced pulmonary pneumonia in vivo. Innovation and Conclusion: miR-208a-3p/PPP6C represent a potential diagnostic marker and therapeutic target for Radiation-induced lung injury which needs to be verified by future clinical studies.

overall_design:
All animal experiments were approved by the Medical Ethics Committee of the Second Affiliated Hospital of Chengdu Medical College Nuclear Industry 416 Hospital (2020-13). 6-8 week-old C57BL/6 mice were divided into control group and experimental group. Mice were held under circumstances (24 ± 2 °C, 40-70% relative humidity, 12 h light/12 h dark cycle) and were given regular diet and water.
Mice were irradiated using an X-RAD 225 irradiator (X-ray: 225 kV and 12.5 mA; SSD: 30 cm; beam filter: 2.0 mm AI). The mice were setted in the center of the radiance field at a dose rate of 200 cGy/min at a distance of 30 cm from the irRadiation source and the mice were immobilized in a specially designed fixture designed to irradiate the entire thoracic cavity of the mouse, A total dose of 15 Gy while avoiding exposure to other parts of the body.


title: Affymetrix SNP array data for longitudinal analysis of adult Myelodysplastic Syndromes (MDS) and Acute Myeloid Leukemia (AML) with 1q jumping translocation after 5'-azacytidine treatment

city: Perugia

first: Cristina

last: Mecucci

address: Piazzale Menghini n.9

department: Department of Medicine, Hematology and Bone Marrow Transplantation Unit

country: Italy

institute: University of Perugia

type: Genome variation profiling by genome tiling array

summary: Jumping translocations are cytogenetic abnormalities associated with poor clinical outcome and progression in Myelodysplastic Syndromes/Acute Myeloid Leukemia (MDS/AML).Typically a donor chromosome, often a trisomic 1q, is transferred onto 2 or more recipient chromosomes. Previous studies have demonstrated the crosstalk between DNA hypomethylation and 1q trisomy. Here, we used an epi-genomic approach in sequential samples from a cohort of MDS and AML with the appearance of 1q jumping translocations after 5’-azacytidine (AZA) treatment.

overall_design: Copy number analysis of MDS/AML with jumping 1q translocations after AZA by CytoScan HD Affymetrix platform

first: Valentina

last: Pierini

first: Anair

middle: G

last: Lema Fernandez

first: Carlotta

last: Nardelli


title: Hematopoietic stem and progenitor cells in experimental remission model of acute myeloid leukemia in vivo [ATAC-seq]

first: Eric

last: Wafula

state: PA

address: 2714-2720 South Street

department: DBHi

institute: Children's Hospital of Philadelphia

summary: Inflammation is a hallmark of cancer and is linked to patient prognosis in acute myeloid leukemia (AML). Our recent study revealed that hematopoietic stem and progenitor cells (HSPCs) exhibit an inflammatory active state and serve as a cellular source of inflammatory cytokine secretion in AML. Recent studies in infection and chronic inflammation related disease models have revealed that inflammation can reprogram HSPCs to fuel chronic inflammation related co-mobidities. Building on our report of AML-associated inflammation in HSPCs, here we ask whether AML-experienced normal HSPCs are reprogrammed in AML. To investigate this, we utilized a chimeric model of AML, carrying both doxycycline-inducible leukemic and healthy wildtype hematopoietic fractions, to generate an AML remission model. To test whether AML-experienced HSPCs harbor inflammatory memory, mice were challenged with heterogenous inflammatory activation. Our transcriptomic and epigenetic results show for the first time that phenotypically normal, AML-experienced HSPCs carry a durable inflammatory memory whereby primary exposure to AML secreted factors alters their response to secondary stimuli. Our finding suggests that AML-experienced HSPCs are innate immune reprogrammed in the AML niche.

overall_design: AML remission model was generated by first co-transplanting non-induced whole bone marrow (WBM) from inducible MLL-AF9 (iMLL-AF9) mice (CD45.1; homozygous hMLL-AF9 and rtTA; 2E5 cells per recipient) together with WBM from healthy wildtype mice (double positive CD45.1+/2+; 8E5 cells per recipient), into lethally irradiated C57BL/6J recipients (CD45.2) and is termed "AF9+/+" mice. Control naive mice were generated by co-transplanting hMLL-AF9-null (CD45.1; hMLL-AF9-null, homozygous rtTA only; 2E5 cells per recipient) together with healthy wildtype mice (double positive CD45.1+/2+; 8E5 cells per recipient) and is termed "AF9-/-" mice. After 6-8 weeks after transplantation, AML remission state was generated by first subjecting mice to leukemogenesis (via doxycycline induction) for 5 weeks, followed by disease regression (via doxycycline withdraw) for 4 weeks. Mice were administered with either PBS or LPS to model baseline remission and inflammatory-challenged remission state. Mice were sacrificed 24 hours after the injection. Bone marrow hematopoietic stem and progenitor cells (HSPCs; CD45.1+/2+, Lin- cKit+ Sca1+) were fluorescent-activated cell sorting (FACS)-sorted for RNA-Seq and ATAC-Seq.

first: Ding-Wen

first: Julie

last: Schrey

first: Jian-Meng

last: Fan

first: Sarah

last: Adams

first: Deanne

last: Taylor

first: Peter

last: Kurre


title: Exploring host cellular responses to SARS-CoV-2 variants using RNA sequencing of infected human airway epithelial cells

city: London

first: Efstathios

last: Giotis

address: Norfolk Place

department: Infectious Diseases

country: United Kingdom

institute: Imperial College London

summary: This study explores the interaction between various SARS-CoV-2 variants and host cells by using RNA sequencing (RNA-seq) of human airway epithelial cells. The primary objective was to elucidate the host cellular responses, including metabolic and immune pathways, to different SARS-CoV-2 variants. Human airway epithelial cells were infected with SARS-CoV-2 variants (IC19, Alpha, Beta, Delta, Omicron BA.1, and BA.5) and compared with mock samples at time 0. Samples were collected at 24 and 72 hours post-infection for RNA isolation and subsequent bulk RNA-sequencing. The RNA-seq data processing involved quality checks, mapping reads to a reference genome, and identifying differentially expressed genes to determine changes in gene expression in response to viral infection. This analysis aims to provide a deeper understanding of the molecular interactions between SARS-CoV-2 variants and host cells, contributing to the broader knowledge of viral pathogenicity and host-pathogen interactions.

overall_design: In this study, we aimed to investigate variations in gene expression among different SARS-CoV-2 variants. To achieve this, primary human nasal epithelial cells (hNECs) from pools of human donors (Epithelix) were subjected to single infections with a multiplicity of infection (MOI) of 0.1 using SARS-CoV-2 variants (Alpha, Beta, Delta, Omicron BA.1, and BA.5). The control viral strain used was the lineage B.1 SARS-CoV-2/England/IC19/2020 (IC19) isolate (EPI_ISL_475572). Another group remained uninfected, all maintained at 37°C with 5% CO2. Control uninfected samples and cells stimulated with recombinant interferon alpha (IFNa; 1000 U/ml) for 24 hours were also included. Experiments were conducted with two different batches of human donor hNECs to account for variability. RNA samples were collected from uninfected, stimulated, and virus-infected hNECs at 24 and 72 hours post-infection to assess gene expression changes. The quality and integrity of RNA samples were evaluated using the Agilent 2100 Bioanalyzer (Agilent Technologies) before proceeding with library preparation. Strand-specific RNA sequencing was performed at Novogene (Cambridge, UK). Subsequently, FASTQ files were processed using Partek Flow for data analysis. Differentially expressed genes were identified by applying stringent criteria, including statistical significance (P < 0.05) and fold change (>2), using at least two replicates for each condition. By comparing the gene expression patterns, we aimed to uncover the pathways impacted by viral infections.


title: M1002 protect mice from DSS-induced colitis through regulation of HIF-1 signaling and the Gut Microbiota in DSS-Induced Colitis in Mice

city: Shanghai

first: yunjie

last: shi

address: No 800，Xiangyin Road

institute: Naval Medical University

summary: Abstract. Ulcerative colitis (UC) is an intestinal disease characterized by chronic recurrent inflammation, but the underlying mechanism remains undefined and requires in-depth exploration. The aim of the present study was to investigate the biological effects of a small molecular compound M1002 of oxygen-sensing signaling pathway on dextran sulfate sodium (DSS)-induced intestinal inflammation colitis mouse models. It was found that the protective effects of M1002 on DSS-induced colitis. To determine how M1002 exerted its protective effect in DSS-induced colitis, we compared the global gene expression profiles in the gut between DSS control and M1002 treatment colitis mouse groups by RNA-Seq. The results demonstrated that HIF-1 signaling pathway-related genes were significantly upregulated in the gut of M1002 treatment colitis mice, whereas the Inflammatory bowel disease signaling pathway, the TNF signaling pathway, and Cytokines and inflammatory response signaling pathway related genes were significantly downregulated in the M1002 treatment group. 16S rRNA gene sequencing demonstrated remarkable variations in the composition of gut microbiota between DSS control and M1002 treatment colitis mice. Compared with DSS control colitis mice, the relative abundance of Eubacterium_nodatum and Halomonas in the gut microbiota was significantly increased at genus level in the gut of M1002 treatment colitis mice. Based on these findings, we tend to conclude that M1002 might alleviate DSS-induced gut injury in mice by regulation of HIF-1 signaling and up-regulating Eubacterium_nodatum and Halomonas.

overall_design: The findings of the present study provide deep insights into the molecular mechanisms of protective effects of a small molecular compound of oxygen-sensing signaling pathway M1002 for DSS-induced colitis. On this basis, this research depicted remarkable variations in the number of gut microbiota between the DSS control and M1002 treatment mouse groups via 16S rRNA gene sequencing. There were abundant Eubacterium_nodatum and Halomonas in the gut microbiota of M1002 treatment colitis mouse groups. Collectively, we hypothesize that M1002 might alleviate DSS-induced gut injury in mice by regulation of HIF-1 signaling and up-regulating Eubacterium_nodatum and Halomonas.

first: Yunjie

last: Shi

first: Kaiwen

last: Sheng

first: Cong

last: Liu

first: Hao


title: Genome-wide binding of tomato AP1/FUL-like proteins determined by DNA-affinity purification sequencing (DAP-seq)

city: Wageningen

first: Xiaobing

last: Jiang

address: Droevendaalsesteeg 1

department: Bioscience

country: Netherlands

institute: Wageningen University

summary: By function dissection in planta, we identified that tomato AP1/FUL-like genes have overlapping and specific functions in flowering and inflorescece development. In this experiment, we aim to identify the binding sites of AP1/FUL-like complexes (FUL2-J, FUL2-J2, FUL2-TM3, MC-J, MC-J2, MC-TM3) and determine if they exhibit binding to different targets or with differing affinities, which could be a mechanism to acquire target gene specificity. Specifically, we investigated this phenomenon for all the tetramers, as they are enriched in shoot reproductive meristems to fulfil the functions. Using the DAP-seq protocol, we established their genome-wide binding profiles and included input as control.

overall_design: We use DAP-seq to determine the genome-wide binding patterns of AP1/FUL-like protein FUL2 and MC with their interactors J, J2, and TM3 (FUL2-J, FUL2-J2, FUL2-TM3, MC-J, MC-J2, MC-TM3).

first: Kai

last: Thoris

first: Marian

last: Bemer


title: Hematopoietic stem and progenitor cells in experimental remission model of acute myeloid leukemia in vivo [RNA-seq]

last: Chen


title: Multiplex Enhanced Reduced Representation Bisulfite Sequencing (mERRBS)  longitudinal analysis of adult Myelodysplastic Syndromes (MDS) and Acute Myeloid Leukemia (AML) with 1q jumping translocation after 5'-azacytidine treatment compared to controls

first: Cristina

last: Mecucci

type: Methylation profiling by high throughput sequencing

overall_design: mERRBS profiles of 3 MDS and AML cases with 1q jumping translocation at 3 timepoints ,  and 3 controls (bone marrow samples from non-neoplastic cytopenias, normal bone marrow morphology and normal karyotype)

first: Anair

last: Lema Fernandez

first: Carlotta


title: DCBLD2 promotes perivascular anti-tumor immune deprivation by educating SPP1+ pro-angiogenic macrophages

city: Guanzghou

first: Zihang

last: Yu

state: Please Select

address: GuangZhou Avenue

institute: Southern Medicla University

summary: The crosstalk between tumor vasculature and immune microenvironment underpins the anti-tumor effect of anti-angiogenic therapy (AAT) combined with immunotherapy. However, the efficacy improved by AAT in the above combination therapy is limited and its adverse effects are concerning. Integrated transcriptome and surfaceome data identified DCBLD2 as a bipotent molecule on tumor cells as a trigger for abnormal tumor vascular-immune interactions. Dcbld2 overexpression accelerated tumor growth through tumor-associated macrophages (TAMs) in preclinical mouse models. Mechanically, DCBLD2 domesticates SPP1+ pro-angiogenic TAMs through ALDH1A3-RXRG-PLK1 axis, constructing TAMs-coated vascular niches that sequester CD8+ T cell infiltration. DCBLD2 expression levels predicted the efficacy of traditional AAT in our lung cancer patient cohorts. Targeting DCBLD2 or ALDH1A3 combined with PD-1 antibody outperformed traditional AAT and immunotherapy combination. Our study identifies DCBLD2 on tumor cells as a checkpoint in abnormal vascular-immune crosstalk, offering a promising target to amplify the potency of vascular normalization and immune activation.

overall_design: H1299-Ctrl and H1299-DCBLD2 were co-cultured for 48 h with THP-1 after 24 h treatment with PMA, respectively

first: Enli

last: Lu


title: Cancer-Associated Fibroblasts Promote Vasculogenic Mimicry of Colorectal Cancer by Epigenetic Silencing of Decorin [RNA-Seq]

city: guangzhong

first: yurui

last: liu

address: No. 1023-1063, Shatai South Road, Baiyun District, Guangzhou City, Guangdong Province

institute: Southern Medical University

summary: To investigate the transcriptome landscape differences between CAFs and NFs in colorectal cancer, we extracted primary fibroblasts from colorectal cancer tissue and para-cancerous tissue for transcriptome sequencing.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for CAFs and NFs.

first: Yin

last: Zhu

first: Yurui


title: Using Genome-wide CRISPR Screen to Identify Cannabidiol as an E2F1 Inhibitor against Aristolochic Acid Nephrotoxicity

city: Guangzhou

first: Ziqi

state: Guangdong Province

address: 2nd Zhongshan Road

institute: Sun Yat-sen University

summary: Aristolochic Acid I (AAI), one of the most abundant aristolochic acids (AAs), is nearly ubiquitous in herbal and traditional Chinese medicines within the Aristolochia genus. Renal tubular epithelial cell damage has been identified as a primary cause of AAI-induced nephrotoxicity. Genome-wide CRISPR library screening has proven valuable in identifying key genes associated with the toxicity of exogenous substances. To screen for genes related to AAI-induced renal toxicity, we conducted a genome-wide CRISPR library screening in HK-2 cell line. Among the altered sgRNAs, we observed significant enrichment of sgRNAs targeting E2F1 gene in survival HK-2 cells of the AAI-treated group, correlating with the promotion of AAI-induced cell apoptosis. Subsequent investigations revealed that E2F1 primarily promotes cellular apoptosis by activating the p53 signaling pathway, thereby enhancing the expression of pro-apoptotic genes, BAK and BAX. Additionally, we screened cannabidiol (CBD) as an inhibitor of E2F1 by utilizing the HERB database (http://herb.ac.cn/). Validation in both in vitro cell models and in vivo mouse models confirmed that CBD inhibits the expression of E2F1, consequently suppressing p53 signaling pathway-associated cell apoptosis. In conclusion, our results underscore the crucial role of E2F1 in AAI-induced renal cell apoptosis. Furthermore, the identification of CBD as a potential therapeutic candidate for AAI-induced renal toxicity provides new insights for understanding and treating AAI-induced nephrotoxicity.

overall_design: We transfected HK-2 cells with the lentiCas9-Blast plasmid using lentivirus and screened for single clone cells to construct HK-2_Cas9-SC#1 cells. The GeCKO V2 library plasmids were used to infect HK-2_Cas9-SC#1 cells at an MOI of 0.3. After selection with 2 μg/ml puromycin for 7 days, we obtained the library cells. The library cells were then treated with either a blank control (DMSO) or an IC80 dose of aristolochic acid I (AAI) for 48 hours. Subsequently, the remaining cells' genomic DNA was harvested, sgRNA sequences were amplified, and high-throughput sequencing was performed to identify genes responsible for AAI-induced cytotoxicity.

first: Huan

last: Gao

first: Guoliang

last: Li

first: Yongjiang

first: Mengxing

last: Cui

first: Honghao

last: Peng

first: Xinchao

last: Guan

first: Xue

last: Zhang

first: Zhihan

first: Xiaoyu

last: Shen

first: Daochuan

first: Liping

first: Yongmei

last: Xiao

first: Wen

first: Lili

first: Qing

last: Wang


title: Comparison of untreated and vancomycin-treated macrophages, with or without Candida albicans infection

city: Birmingham

first: Rebecca

last: Drummond

state: Edgbaston

address: IBR 437, University of Birmingham

institute: University of Birmingham

summary: Vancomycin is a widely prescribed antibiotic used in the treatment of Gram-positive bacterial infections. We recently showed that this antibiotic disrupted protective anti-fungal immune responses via microbiome dysbiosis, enhancing susceptibility to invasive candidiasis. Antibiotics are an independent risk factor for developing this life-threatening fungal infection, but whether microbiota-independent mechanisms also drive this association is not clear. Here, we have compared transcriptional responses of mouse bone-marrow derived macrophages at an early time point post-infection (2 hours), comparing back to baseline, using untreated or vancomycin-treated macrophages.

overall_design: Mouse bone-marrow derived macrophages were differentiated in presence of vancomycin or in antibiotic-free conditions. Macrophages were then left uninfected or infected with live Candida albicans yeast (strain SC5413) for two hours. RNA was isolated from all conditions using the Trizol method.


title: A Private Crosstalk Established by Tumor-Targeted Cytokine Release Rescues CAR-T Activity and Engages Host T Cells against Glioblastoma

city: Milan

first: Stefano

last: Beretta

address: Via Olgettina, 60

institute: San Raffaele Telethon Institute for Gene Therapy

summary: Chimeric antigen receptor T cells (CAR-Ts) have shown limited efficacy in solid tumors, due to poor penetration, constrained activity, and early exhaustion into the immunosuppressive tumor microenvironment (TME). While cytokines can counteract immune-suppression, their systemic administration entails risk of toxicities and counter-regulatory responses. Here, we leveraged on a population of tumor associated TIE2 expressing macrophages (TEMs) to release IFN- and/or orthogonal IL-2 (oIL2) at the tumor site. TEM-mediated cytokine delivery rescued CAR-Ts functionality against the clinically relevant antigen B7-H3 in an immunocompetent mouse model of glioblastoma multiforme (GBM) which was refractory to anti-B7-H3 CAR-Ts alone. Immunophenotypic and transcriptomic analyses showed that TEM-mediated cytokine delivery counteracted premature CAR-Ts terminal exhaustion and sustained their effector/memory state which accounts for tumor cell elimination.  This was mirrored by delayed tumor growth and prolonged mice survival achieving a synergistic effect in the IFN- + oIL2 group receiving CAR-Ts. Importantly, IFN-, especially when combined with oIL2, also triggered an endogenous T cell response against tumor associated antigens other than B7-H3. Altogether our findings suggest that the combination approach between the two genes and cell therapy strategies presented here, and already under clinical testing as monotherapies, could achieve synergistic therapeutic effect also in GBM patients.

overall_design: CAR-T Single-cell RNA sequencing (scRNAseq) of GBM tumor mice (mixed 1:1 ratio of adoptive and endogenous immune cells) belonging to different treatment groups: Empty, IFN, oIL2, and IFN+oIL2.

first: Federico

last: Rossari

first: Giorgia

last: Alvisi

first: Ivan

last: Merelli

first: Nadia

last: Coltella

first: Luigi

last: Naldini


title: Long-term adaptation of lymphoma cells to hypoxia is mediated by diverse molecular mechanisms that are targetable with specific inhibitors

city: Prague

first: Pavel

last: Klener

address: U Nemocnice 5

country: Czech Republic

institute: Institute of Pathological Physiology First Faculty of Medicine, Charles University

summary: In this study we analyzed impact of long-term hypoxia on a panel of lymphoma cell lines. Only 2 out of 8 tested lymphoma cell lines (Ramos, and HBL2) survived > 4 weeks under deep hypoxia (1% O2). The hypoxia-adapted (HA) Ramos and HBL2 cells had severely decreased proliferation rate accompanied by complex changes of the transcriptome, proteome, and metabolome. Seahorse analysis demonstrated near complete blockage of both oxidative phosphorylation and glycolytic pathways. Both transcriptome and proteome analyses showed significant downregulation of mitochondrial respiration complexes I and IV, many mitochondrial ribosomal proteins, and increase of proteins regulating glycolysis and mitophagy. Both HA cell lines had an increased total mitochondrial mass, but a decreased mitochondrial DNA content compared to normoxic controls. Sensitivity of HA cells to 2-deoxyglucose, an inhibitor of glycolysis, and to A1155463, a BCL-XL inhibitor were, was markedly increased. Indeed, co-culture on CD40 ligand expressing fibroblasts (that induce BCL-XL expression) significantly increased survival of lymphoma cells under hypoxia. Of note, prolyl hydroxylase P4HA1 involved in the stabilization of hypoxia-induced factor (HIF) 1 alpha was increased in both HA cell lines on both mRNA and protein levels. Transgenic (over)expression of P4HA1 in hypoxia-sensitive MINO cells was associated with increased survival under hypoxia. Our data suggest that under long-term hypoxia, lymphoma cells try to compensate for the decrease in ATP production from the oxidative phosphorylation process by boosting structural machinery of glycolysis, as well as amino-acid recycling by mitophagy, on which they become vitally dependent for survival, and which can be targeted by specific inhibitors. The data also suggest increased dependence of lymphoma cells on BCL-XL under hypoxia. Finally, P4HA1 plausibly represents a novel druggable target for more effective elimination of hypoxia-adapted lymphoma cells.

overall_design: Two human lymphoma cell lines, HBL-2 and Ramos, were adapted to grow in 1% oxygen hypoxia over > 4 weeks. Normoxic controls growing in normoxia were compared to hypoxia-adapted cells growing in hypoxia. The RNA was isolated using RNeasy® Mini Kit (QIAGEN), libraries were prepared using Agilent SureSelect mRNA Strand Specific kit and sequenced paired-end (2x75bp) sequenced on NextSeq 500 (Illumina, USA).

first: Lenka

last: Daumová

first: Dmitry

last: Kazantsev

first: Soviljn

last: Dana

first: Matěj

last: Běhounek

first: Jiří

last: Petrák

first: Ladislav

last: Anděra

first: Ondřej

last: Vít

first: Olga

last: Součková

last: Havránek

first: Nicol

last: Renešová

first: Alexandra

last: Dolníková

first: Nardjas

last: Bettazová

first: Liliana

last: Tušková

first: Lucie

last: Winkowska

first: Marie

last: Hubálek Kalbáčová

first: Blanka

last: Bílková

first: Marek

last: Trněný


title: An amino acid integration in the heat receptor ELF3 Molecular mechanism of temperature signal regulating plant growth

city: kunming

first: yayi

last: zhao

state: yunnan province

address: 吴家营

department: School of Ecology and Environment

institute: Yunnan University

summary: In Arabidopsis, ELF3, ELF4 and LUX proteins form the EC complex. The EC complex binds directly to the promoters of PIF4 and PIF5 in vivo, thereby inhibiting PIF4 and PIF5 expression at night. PIF4, as a key transcription factor for light and temperature, binds to thousands of target genes to regulate their expression. High temperature can activate PIF4 activity, making it regulate plant thermal morphogenesis by integrating light, circadian rhythm and hormone signals, EC complex is a protein complex that inhibits gene expression, and helps higher plants sense environmental temperature and thermal form. ELF3 is a thermal sensor that plays a role in controlling the circadian rhythm, photoperiodic flowering, hypocotyl length, and response to light in an EC-dependent and EC-independent manner. PIF4 plays a key positive role in heat response gene expression and hypocotyl growth in Arabidopsis thaliana, but ELF3 negatively regulates the protein activity of growth promoting factor PIF4. Interestingly, a 2020 paper published in Nature by Jung et al. found that ELF3, as a heat sensor, gradually forms multiple distinct spot-like structures in the nucleus as the temperature increases due to the presence of the characteristic PrD. Similarly, increasing the length of the polyQ will enlarge the spots. In addition, after returning to normal temperature from mild high temperature, the EC complex will quickly return to normal activity. This result is contrary to what Ronald et al. stated in a 2021 paper: Warm temperatures inhibit ELF3 blotching, and since ELF3 blotching is associated with increased transcriptional activity of ELF3, a decrease in blotching may lead to decreased EC function at warm temperatures. As a result, the question of how ELF3 is regulated in warmer temperatures remains an open question.

overall_design: After analyzing the genetic differences of the mutant material obtained through genetic variation, Ser 364 was found to have a mutation. Therefore, we hypothesized that the change of phosphorylation site affected the flowering time and hypocotyl length of Arabidopsis thaliana. The molecular mechanism of stable ELF3 protein was analyzed from the mutation site.


title: Iterative genome engineering of E. coli for fed-batch production of L-tyrosine.

city: Kongens Lyngby

first: Pascal

middle: Aldo

last: Pieters

state: Region Hovedstaden

address: Building 220, Kemitorvet

department: Novo Nordisk Foundation Center for Biosustainability

country: Denmark

institute: DTU

summary: In this project we aim to construct a tyrosine-producing E. coli strain through iterative steps of genome engineering. High PEP availability through knockout of the PTS was combined with the precise, in-place genomic integration of several engineering interventions, known to increase L-tyrosine production yields, to create a tyrosine-overproducing E. coli strain that can function as a platform for further engineering and optimization. Utilizing a design-build-test-learn (DBTL) cycle, an evolved pts-knockout E. coli  strain was equipped with optimizations of the aroG, aroB and tyrA genes and cultivated under batch and fed-batch conditions. Subsequently, metabolomics, transcriptomics and proteomics samples from the fed-batch experiments were analyzed to inform the design of new genomic interventions.

overall_design: An E. coli strain engineered to produce high titers of tyrosine (SDT387) and a reference E. coli strain (SDT400), which only bears a PTS knockout, were grown under fedbatch conditions, after a short batch phase. Each of the strains was grown in two separate reactors and samples for RNA-seq were taken at four timepoints. The first sample represents the batch phase, whilst the three subsequent samples were taken early, mid, and late in the fed-batch phase of the experiment.


title: Notch3+ Regulatory T cells Drive Autoimmune Neuroinflammation in Multiple Sclerosis

city: Boston

first: Mehdi

last: Benamar

state: MA

address: 1 Blackfan Circle, Karp Family Building

institute: Harvard medical school/Boston children's Hospital

summary: The immune regulatory defects that promote neuroinflammation in multiple sclerosis (MS) remain unclear. We show that a specific regulatory T (Treg) cell subpopulation expressing Notch3 is increased in individuals with MS and in mice with experimental autoimmune encephalomyelitis (EAE). Notch3 is induced by the gut microbiota by toll-like receptor (TLR)-dependent mechanisms to promote EAE severity. Notch3 interacts with delta-like ligand 1 (DLL1) on microglia to subvert Treg cells into T helper 17 (Th17) cells. Notch3 Treg-specific deletion inhibits EAE by preventing Treg cell destabilization while simultaneously promoting the expansion of a novel tissue-resident neuropeptide receptor 1 (NPY1R)+ Treg cell population that suppressed pathogenic IFNg+ and GM-CSF+ T cells. Our studies thus identify altered Treg cell population dynamics as a fundamental pathogenic mechanism in autoimmune neuroinflammation.

overall_design: We perfromed an ScRNA-seq on CNS CD4 cells from Foxp3YFPCRE and Foxp3YFPcre NOtch3Fl/Fl mice post EAE induction

last: Lanzetta

first: Claudia

last: Angelini

first: Talal

last: Chatila


title: Spatiotemporal control of SMARCA5 by a MAPK-RUNX1 axis distinguishes mutant KRAS-driven pancreatic malignancy from tissue regeneration (CUT&RUN)

city: Beijing

first: Jing

last: Han

address: qinghuayuan

institute: Tsinghua university

summary: De-differentiation or trans-differentiation is a common response to injury in many tissues, and the processes predispose cells to cancer. Acute pancreatitis-induced acinar-to-ductal metaplasia (ADM) is similar to pancreatic ductal adenocarcinoma (PDAC) at both the chromatin level and gene expression level. Mutant KRAS induces chromatin remodeling activities required for both regeneration and tumorigenesis at the peak of ADM, and it blocks regeneration. We show that chromatin remodeler SMARCA5 (SNF2H) can promotes the regeneration defects caused by mutant KRAS by maintaining chromatin accessibility at regions specifically required for malignancy. Mechanistically, regeneration-related chromatin remodeling activities are shared between wild-type and mutant KRAS and they occur very early upon pancreatitis, while the malignancy-related chromatin regions become accessible much later. The activity of SMARCA5 is controlled spatiotemporally by transcription factor RUNX1, which is only accumulated at sufficient levels at late ADM lock-in stage. Finally, we show that the malignancy regulation activity of SMARCA5 is different from its general function in CTCF recruitment. In summary, we have identified a specific function of a general chromatin remodeler that is precisely controlled during acinar cell trans-differentiation to separate malignancy from tissue regeneration.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Through ChIP-seq,CUT&RUN and CUT&Tag experiments, we aim to investigate whether SMARCA5 binds to its regulated sites and whether SMARCA5 is recruited by RUNX1.

first: Xiaoman

last: Lu

first: Saisai

last: Wang

first: Jiacheng

first: Wei

last: Xie

first: Charles

last: David

first: Mo

last: Chen


title: Spatiotemporal control of SMARCA5 by a MAPK-RUNX1 axis distinguishes mutant KRAS-driven pancreatic malignancy from tissue regeneration (CUT&Tag)


title: Spatiotemporal control of SMARCA5 by a MAPK-RUNX1 axis distinguishes mutant KRAS-driven pancreatic malignancy from tissue regeneration (RNA-Seq)


title: Spatiotemporal control of SMARCA5 by a MAPK-RUNX1 axis distinguishes mutant KRAS-driven pancreatic malignancy from tissue regeneration (ChIP-Seq)


title: Spatiotemporal control of SMARCA5 by a MAPK-RUNX1 axis distinguishes mutant KRAS-driven pancreatic malignancy from tissue regeneration (ATAC-Seq)

overall_design: Through ATAC-seq (Assay for Transposase-Accessible Chromatin using sequencing) experiments, we aim to investigate the impact of SMARCA5 on chromatin accessibility in pancreatic inflammation cells and pancreatic cancer cells at different stages.

first: Xiangzheng

last: Liu


title: Effect of refrigeration storage duration of Blood EDTA samples

city: Seoul

first: Jae Won

last: Yun

address: 53, Jinhwangdo-ro 61-gil, Gangdong-gu

department: VHS Research Institute

country: South Korea

institute: Veterans Health Service Medical Center

summary: We have reported the change from overall gene expression to specific genes and pathways involved in the immune cells of blood depending on the storage and handling conditions. The overall gene pattern showed a strong correlation and the prediction of immune cell proportion was conserved under 4℃ refrigeration for up to 48 hours regardless of the RNA extraction kits used. However, after 4 days of refrigeration, the correlation started to decrease. Additionally, the expression of 65 genes increased more than two-fold while the expression of 221 genes decreased less than two-fold within 48 hours of refrigeration. Our data would contribute to the experimental design of basic research and minimizing the bias of the blood RNA-seq results, since the need for RNA-seq continually increases but it it hard to perform blood RNA-seq immediately after every blood collection.

overall_design:
Blood EDTA samples were collected from two healthy males and two healthy females, and stored under 4℃ refrigeration from 24 hours to 16 days.
We performed gene expression profiling analysis using data obtained from RNA-seq of those blood EDTA samples with different refrigeration storage duration.

first: Jae

middle: W

first: Ye

middle: E

last: Yoon


title: Placenta-derived exosomes of gestational diabetes mellitus affect cell metabolism and cell function via transferring microRNAs

first: Yuan

last: Zhang

state: Shanghai

address: No.910 Hengshan Road

institute: The International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University

summary: Gestational Diabetes Mellitus (GDM) is a common pregnancy complication and exosomal-miRNAs played a critical role in the development of GDM. Our research aimed to investigate the mechanism of exosomes participation in GDM and proposed the innovative therapeutic methods. In the present study, we isolated and identified the placenta-derived exosomes from GDM patients. Exosomes could be internalized by HTR8 cells and induced the lipid metabolism dysfunction. Differential metabolites in placenta tissues of GDM patients were analyzed and lipid metabolites occupied the highest proportion. Besides, exosomes promoted the oxidative stress production and inhibited cell autophagy and promoted cell apoptosis by transferring miR-152-5p. In addition, miR-152-5p inhibitor could reverse the ROS levels and regulate cell autophagy and cell apoptosis. Therefore, miR-152-5p inhibitor might be an efficient therapy for GDM. Our findings revealed that placenta-derived exosomes of GDM could regulate affect cell lipid metabolism, increase oxidative stress and regulate cell autophagy and apoptosis. Exosomal miR-152-5p is expected to be an promising target for GDM.

overall_design: To investigate the differential expressed signaling pathways between normal cells and co-cultured cells, RNA sequence was used to explore the specific pathway landscape.


title: TDCPP and TiO2 NPs synergistically induced apoptosis of SH-SY5Y cells by Impairing Mitochondrial Division and Fusion Homeostasis

city: nanjing

first: Ling

last: wang

address: Chunhua Avenue, Jiangning District, Jiangsu Province, China

institute: Nanjing Medical University

summary: SH-SY5Y cells were exposed to TDCPP and TiO2 NPs to look for the expression of differential genes and pathways between the exposed group and the control group.

overall_design: SH-SY5Y cells were exposed to TDCPP and TiO2 NPs for 24 hours and collected.

first: Mingkuan

last: Sun


title: Characterization of residual cancer by comparison of a pair of organoids established from a patient with ESCC before and after neoadjuvant chemotherapy (xenografts)

city: Yufu-city

first: Yoshiyuki

last: Tsukamoto

state: Oita

address: hasamacho idaigaoka 1-1

department: Molecular Pathology

country: Japan

institute: Oita university, Faculty of Medicine

summary: Neoadjuvant chemotherapy (NAC) followed by surgery is a standard approach for management of locally advanced esophageal squamous cell carcinoma (ESCC). Patients who do not respond well to NAC have a poor prognosis. Despite extensive research, the mechanisms of chemoresistance in ESCC remain largely unknown. Here, we established paired tumor organoids – designated as PreNAC-O and PostNAC-O – from one ESCC patient before and after NAC, respectively. Although the two organoids did not exhibit significant differences in proliferation, morphology or drug sensitivity in vitro, the tumorigenicity of PostNAC-O in vivo was significantly higher than that of PreNAC-O. Xenografts from PreNAC-O tended to exhibit keratinization, while those from PostNAC-O displayed conspicuous necrotic areas. The tumorigenicity of PostNAC-O xenografts during the chemotherapy was comparable to that of PreNAC-O without treatment. Furthermore, the gene expression profiles of the xenografts suggested that expression of genes involved in the EMT and/or hypoxia response might be related to the tumorigenicity of PostNAC-O. Our data suggested that the tumorigenicity of residual cancer had been enhanced, outweighing the effects of chemotherapy, rather than being attributable to intrinsic chemoresistance. Further studies are required to clarify the extent to which residual cancers share a common mechanism similar to that revealed here.

overall_design: 200ng of RNA samples from xenografts of patient derived cancer organoid were subjected to gene expression microarray.

first: Takafumi

last: Fuchino

first: Shusaku

last: Kurogi

first: Tomotaka

last: Shibata

first: Shoichi

last: Fumoto

first: Naoki

last: Hijiya


title: Characterization of residual cancer by comparison of a pair of organoids established from a patient with ESCC before and after neoadjuvant chemotherapy (in vitro)

overall_design: 200ng of RNA samples from in vitro culture of patient derived cancer organoid were subjected to gene expression microarray.


title: Transcriptomic profiling of AGS2, AGS5, AGS6 and COPA patients compared to healthy controls

city: Paris

first: Mickael

middle: Mathieu

last: Menager

address: 24 Boulevard du Montparnasse

country: France

institute: Institut Imagine

summary: In order to better understand AGS pathology we compared transcriptomic profiles of peripheral blood mononuclear cells from different mutated forms of AGS to an other type I IFN mediated syndrome, COPA. Patients were also compared to healthy individuals.

overall_design: 2 patients AGS5, 2 patients AGS2, 2 patients AGS6, 2 patients COPA, 5 heatlhy individuals. Patients AGS5 n°1 were under reverse transcriptase inhibitor (RTI) tritherapy at time of sampling. Patient's blood AGS5 n°2 were sampled 2 times, before and after 1 month of RTI tritherapy. Librarie for patient n°2 with AGS5 before treatment and for healthy donor n°1 were generated twice on different experiments.

first: Maxime

last: Batignes

first: Francesco

last: Carbone

first: Mickaël

last: Ménager


title: Naringenin confers protection against experimental autoimmune encephalomyelitis through the gut-brain axis by combining metabolomics, gene expression, and amplicon sequencing

city: kai feng

first: zejin

last: liu

address: ximen street

institute: henan university

summary: To investigate the broad effect of naringenin in diverse models of EAE.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for naringenin-treated EAE mice

first: mengyang

last: sun

first: chaolei

last: jin

first: junpeng


title: Identification of genome-wide FOXA2-binding sites in H441 human lung adenocarcinoma cells

city: Cincinnati

first: Minzhe

last: Guo

state: OH

address: 3333 BURNET AVENUE

department: Pulmonary Biology

institute: Cincinnati Children's Hospital Medical Center

summary: In order to identify FOXA2 binding sites in a genome-wide fashion, we infected H441 cells with lentivirus that carries rat Foxa2 and performed chromatin immunoprecipitation-sequencing (ChIP-seq) for FOXA2.

overall_design: H441 cells were infected with lentivirus that carries rat Foxa2.  FOXA2-expressing H441 cells were used for ChIP-seq analysis to identify genome-wide FOXA2-binding sites.

first: Yutaka

last: Maeda


title: Expression of genes affected by ectopic expression of FOXA2 in H441 human lung adenocarcinoma cells

summary:
To identify genes influenced by the ectopic expression of FOXA2 in H441 cells, we performed RNA-seq using H441 cells that are infected with lentivirus carrying rat FOXA2.
We then performed gene expression profiling analysis using data obtained from RNA-seq of triplicate samples.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for H441 cells (three control lentivirus infected samples vs three Foxa2 lentivirus infected samples).


title: Tuft cells in the gut limit cognitive disorders by regulating gut homeostasis

city: Nanjing

first: LU

last: CHEN

address: Longmian Road 101

summary: Cognitive deficits, such as Alzheimer's disease (AD), encompass not only abnormalities in the brain but also dysfunctions in the gut. However, the characterization and influence of colonic epithelial cells during AD development have remained elusive. In this study, we identified a reduced abundance of tuft cells and dysfunction of CD4+ T cell response in the colon of AD model mice (APP/PS1-21), which may result from the specific inhibition of tuft cell differentiation by Aβ. The cognitive function was found to be further impaired when tuft cells were deficient in APP/PS1-21 mice. Remarkably, activation of tuft cells using succinic acid—a specific promoter—restored cognitive function and gut homeostasis in AD mice. In addition, tuft cell deficiency in normal mice (10-month-old) is sufficient to induce gut leakage, immune imbalance, and subsequent cognitive dysfunction. Thus, tuft cell is necessary for gut homeostasis during cognitive disorders.

overall_design: We performed single-cell RNA sequencing analysis on the colonic epithelium of wild type (WT) and transgenic Alzheimer's disease (AD) model (APP/PS1-21) mice. We generated tuft cell-deficient AD mice and stimulated tuft cells using succinic acid to assess the impact on behavioral performance and CD4+ T cell responses in the colon. We utilized colonic organoids to directly evaluate the effect of β-amyloid (Aβ) on tuft cell differentiation. Furthermore, we compared behavioral performance and CD4+ T-cell responses between different ages of tuft cell-absent mice and age-matched wild-type littermates.

first: Lu

last: Chen

first: Yuxuan

last: Yang

first: Cailong

last: Pan

first: Yong

last: Zhang

first: Xiangyu

first: Xinmei

first: Lin

first: Zhipeng

last: Xu

first: Wenqing

last: Li

first: Zhi-Yuan

first: Minjun

last: Ji


title: FOXA2 with mutant KRAS drives invasive mucinous adenocarcinoma of the lung

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

overall_design: Refer to individual Series


title: Pharmacologic Activation of Angiotensin-Converting Enzyme II Alleviates Diabetic Cardiomyopathy in db/db Mice by Reducing Reactive Oxidative Stress

city: Gwangju

first: Woo

middle: Ju

last: JEONG

address: 123 Cheomdangwagi-ro

institute: Gwangju Institute of Science and Technology

summary: Angiotensin-converting enzyme 2 (ACE2) is the main key for reducing angiotensin II (Ang II) in renin-angiotensin-aldosterone system (RAAS) inducing diabetic cardiomyopathy (DCM). ACE2 modulates cardioprotective activity not only by reducing deleterious Ang II signaling but also generating the protective peptide Ang-(1-7). Recently, several studies have reported that depletion of ACE2 worsens DCM, whereas ACE2 activation attenuates Ang II-induced cardiac dysfunction. In the present study, we aimed to evaluate the hypothesis that the enhancement of ACE2, using a US Food and Drug Administration (FDA)-approved ACE2 activator (diaminazene aceturate, DIZE), would have cardioprotective roles in a murine DCM. DIZE was administered intraperitoneally to male db/db mice (8 weeks old) for 8 weeks. Transthoracic echocardiography was used to assess cardiac mass and function in mice. Cardiac structure and fibrotic changes were examined using histology and immunohistochemistry. Gene and protein expression levels were examined using qRT-PCR and western blotting, respectively. Additionally, RNA sequencing was performed to investigate the underlying mechanisms of the effects of DIZE and identify novel potential therapeutic targets for DCM. DIZE prevented the diabetes mellitus-mediated structural and functional deterioration of mouse heart. Our findings suggest that the pharmacological activation of ACE2 could be a novel treatment strategy for DCM.

overall_design: We used the murine strain with db/db mice for assessing cardiac function in diabetic. db/db mice were separated with the vehilce group and the DIZE group which is administering DIZE.

first: Sung

last: Cho

first: Chang-Myung

last: Oh

first: Raekil

last: Park

first: Donghyun

last: Kim

first: Wooju

last: Jeong

first: Yumin

first: Jibeom

last: Lee


title: LINC00467 Mediates PARP Inhibitor Resistance in High-grade Serous Ovarian Cancer by Regulating miR-485-5p/RAD50 axis

city: Jinan

first: Hui

state: China

address: 107 West Wenhua Road

institute: Qilu Hospital, Shandong University

summary: To investigate the essential gene associated with PARP inhibitor response， we established PARP inhibitor resistance SKOV3 cell line and RNA-seq was performed to confirm the differentially expressed gene

overall_design: Comparative gene expression profiling analysis of RNA-seq data for PARP inhibitor resistant SKOV3 and negative control SKOV3.

first: Jing

last: Cui


title: Influenza infection disrupts oligodendrocyte homeostasis and alters the myelin lipidome in the adult mouse central nervous system.

city: Urbana

first: Andrew

middle: J

last: Steelman

state: IL

address: 1201 West Gregory

institute: University of Illinois

summary: The notion that myelin remains static during adulthood has been challenged in recent years, and it is increasingly recognized that myelin may be altered by physiological events occurring outside of the central nervous system resulting in changes to cognition and behavior. The consequences of influenza A virus infection on oligodendrocytes in the adult mouse were investigated. Transcriptomic analysis revealed global downregulation and subsequent recovery of oligodendrocyte-specific transcripts in response to peripheral viral infection. Infection neither affected myelin thickness nor oligodendrocyte survival in the mPFC but altered the oligodendrocyte proteome and increased a disease-specific marker associated with oligodendrocyte stress. Furthermore, shot-gun lipidomic analysis revealed that infection altered the lipid profile in the prefrontal cortex as well as in purified brain myelin. Finally, treatment with the CSF1R antagonist GW2580 suppressed glial activation and partially restored oligodendrocyte-specific transcripts to baseline levels during infection. Together, these findings show that peripheral immunological challenge altered oligodendrocyte physiology.

overall_design: Female C57BL/6J mice were inoculated with PBS (n=1) or influenza A virus (n=1; A/PR8/34; 1.0 HAU). At day 8 post-infection, mice were euthanized by CO2 asphyxiation, intracardially perfused with 20 ml of ice cold artificial cerebrospinal fluid, and then the brain was extracted. The whole brain was dissociated and viable single cell suspensions prepared with debris/myelin removed. Cells were analyzed using scRNA-seq.

first: Allison

last: Louie

first: Justin

first: Katiria

last: Soto-Diaz

first: Payam

last: Dibaeinia

first: Hisami

last: Koito

first: Saurabh

last: Sinha

first: Karin

last: Komiyama-Kasai

first: Daniel

middle: B

last: McKim

first: Romana

last: Nowak

first: Aditi

last: Das


title: A MIR17HG-derived Long Noncoding RNA Provides an Essential Chromatin Scaffold for Protein Interaction and Myeloma Growth [array]

first: Mehmet

middle: Kemal

last: Samur

address: 450 Brookline Ave

institute: Dana Farber Cancer Institute

summary: Long noncoding RNAs (lncRNA) can drive tumorigenesis and are susceptible to therapeutic intervention. Here, we used a large-scale CRISPR interference viability screen to interrogate cell growth dependency to lncRNA genes in multiple myeloma (MM), and identified a prominent role for the miR-17-92 cluster host gene (MIR17HG). We show that a MIR17HG-derived lncRNA, named lnc-17-92, is the main mediator of cell growth dependency acting in a microRNA- and DROSHA- independent manner. Lnc-17-92 provides a chromatin scaffold for the functional interaction between c-MYC and WDR82, thus promoting the expression of ACC1, the rate-limiting enzyme of de novo lipogenesis. Targeting MIR17HG pre-RNA with clinically applicable antisense molecules disrupts the transcriptional and functional activities of lnc-17-92, causing potent anti-tumor effects both in vitro and in vivo in three pre-clinical animal models, including a clinically relevant PDX-NSG mouse model. This study establishes a novel oncogenic function of MIR17HG and provides potent inhibitors for translation to clinical trials.

overall_design: AMO1 and H929 cell lines treated with ASO1 compared against untreated cells in replicates

first: Eugenio

last: Morelli


title: A MIR17HG-derived Long Noncoding RNA Provides an Essential Chromatin Scaffold for Protein Interaction and Myeloma Growth [RNA-Seq]

overall_design: DROSHA KO AMO1 cell lines treated with ASO1 compared against untreated cells in replicates


title: c-Kit signaling potentiates CAR T cell efficacy in solid tumors by CD28- and IL-2–independent costimulation

city: New York

first: Yuquan

last: Xiong

state: NY

address: 1250 1st Avenue, Room S-1211

institute: Memorial Sloan Kettering Cancer Center

summary: The limited efficacy of chimeric antigen receptor (CAR) T-cell therapy for solid tumors necessitates engineering strategies to promote functional persistence in an immunosuppressive environment. Herein, we exploit c-KIT signaling - a physiological pathway associated with stemness in hematopoietic progenitor cells with loss of expression during T-cell differentiation. CAR T cells with intracellular but no cell-surface receptor expression of c-Kit D816V mutation, KITv, show upregulated STAT phosphorylation, antigen-activation dependent proliferation, and susceptibility to tyrosine kinase inhibitors. KITv signaling provides CD28, IL-2-independent, and IFN-γ-mediated costimulation augmenting cytotoxicity of antigen-activated first-generation CAR T cells that translates to enhanced survival, including in TGF-β-rich and low antigen-expressing solid tumor models. KITv CAR T cells demonstrate equivalent or higher in vivo efficacy compared to second-generation CAR T cells, and further enhance efficacy as signal 3 when combined with CD28 costimulation, providing a potent approach to treat solid tumors by adoptive cell therapy.

overall_design: Human CD8+ T cells derived from three different healthy donors were retrovirally transduced with individual anti-MSLN CAR genes (M28z and M28z-KITv), with or without stimulated by the MSLN+ 3T3 tumor cells. RNA was collected 0 hours and 24 hours after stimulation and gene expression profiles were analyzed by Affymetrix Human Gene 2.0 ST Array (gene-level analysis).

first: Prasad

middle: S

last: Adusumilli


title: A MIR17HG-derived Long Noncoding RNA Provides an Essential Chromatin Scaffold for Protein Interaction and Myeloma Growth


title: Identification of H3K27ac marks influenced by FOXA2 and/or mutant KRAS in BEAS-2B transformed human bronchial epithelial cells

first: Minzhe

last: Guo

summary: In order to identify H3K27ac enhancer marks influenced by FOXA2 and/or KRAS.G12V, BEAS-2B cells were infected with lentivirus carrying rat FOXA2 and/or retrovirus carrying human KRAS.G12V.  FOXA2 and/or KRAS.G12V-expressing BEAS-2B cells were used for chromatin immunoprecipitation-sequencing (ChIP-seq) to detect genome-wide H3K27ac positive regions.

overall_design: Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) for histone modification H3K27ac in BEAS-2B cells stably-expressing ectopic FOXA2 and/or KRAS.G12V.

first: Yutaka

last: Maeda


title: Transforming Growth Factor-β (TGFβ) Prevents Hypertension-Induced Aortic Dissection in Adult Mice via Extracellular Matrix Production (Bulk KO vs. WT SMC)

city: New Haven

first: George

last: Tellides

state: CT

address: 10 Amistad st, 337B

department: Surgery

institute: Yale University

summary: We report bulk RNA-seq data of Myh11 lineage marked smooth muscle cells (SMCs) from murine aortas at 1 week after conditional disruption of TGFβ signaling versus controls

overall_design: Thoracic aortas were procured from tamoxifen-treated, 12-week-old  Myh11-CreERT2.mT/mG (designated as GFPiSMC or simply WT) or Tgfbr1f/f.Tgfbr2f/f.Myh11-CreERT2.mT/mG (designated as Tgfbr1/2iSMCKO or simply KO) mice, GFP+ SMCs were isolated after cryophilic enzyme digestion of thoracic aorta segments, and bulk RNA-seq analysis was performed

first: Bo

last: Jiang

first: Dejian

last: Zhao

first: Pengwei

last: Ren


title: Transforming Growth Factor-β (TGFβ) Prevents Hypertensive Aortic Dissection in Adult Mice via Extracellular Matrix Production (Bulk KO vs. WT Aorta)

summary: We report bulk RNA-seq data of murine aortas at 1 week after conditional disruption of TGFβ signaling in SMCs versus controls

overall_design: Thoracic aortas were procured from untreated C57BL/6J (designated as WT) or tamoxifen-treated Tgfbr1f/f.Tgfbr2f/f.Myh11-CreERT2.mT/mG (designated as Tgfbr1/2iSMCKO or simply KO) mice, total RNA was isolated, and bulk RNA-seq analysis was performed


title: In vivo CRISPR screening in autoimmune disease model reveals differential dependence of Th1 and Th17 cells on amino acid transporter SNAT1

city: Nashville

first: Jeff

last: Rathmell

state: TN

address: 1211 Medical Center Drive

department: PMI

institute: Vanderbilt University Medical Center

summary: Purpose: The aim of this experiment was to determine the effect of SNAT1 loss on Th1 and Th17 cells. Methods: SNAT1 was knocked out using CRISPR/Cas9 in primary CD4+ T cells polarized to Th1 and Th17 cells in vitro. RNA was then isolated for RNAseq. n=3 biological replicates. Results: SNAT1 mRNA expression was significantly reduced in both Th1 and Th17 cells. Th1 cells displayed consequent changes in the mRNA expression of many other genes (with particular decrease in the expression of glycolysis pathways genes), while Th17 cells had no significant changes in the expression of all other mRNAs detected. Conclusion: This study demonstrates the differential dependence of Th1 and Th17 cells on the amino acid transporter SNAT1.

overall_design: mRNA profiles of Th1 and Th17 cells with non-targeting control (NTC) or SNAT1 gRNA

first: Ayaka

last: Sugiura

first: Jeffrey

middle: C


title: RNA sequencing data of PC3, an androgen negative human prostate cell line, treated with estrogenic compounds

city: Quebec City

first: Étienne

last: Audet-Walsh

state: Quebec

address: 2705 Boulevard Laurier, R-4714

country: Canada

institute: Centre de recherche du CHU de Québec - Université Laval

summary: To analyse and understand the differentially expressed genes when treated with estrogenic compounds

overall_design: PC3 cells were plated in RPMI 1640 media with no phenol red enriched with 5% charcoal stripped serum, sodium pyruvate, penicillin and streptomycin and left to grow during 48h to allow steroid deprivation. Then, media was changed and the cells were treated with either: vehicle (mix of 96% ethanol and DMSO), E2 (10 nM), PPT (1 nM) or DPN (4.25 nM). One day later, the RNA of the cells was first purified with the QIAGEN RNeasy plus purification kit, then enriched for mRNA and finally sequenced.

first: Raghavendra

last: Poluri

first: Camille

last: Lafront


title: Transforming Growth Factor-β (TGFβ) Prevents Hypertension-Induced Aortic Dissection in Adult Mice via Extracellular Matrix Production (single cells WT Aorta)

summary: We report single-cell RNA-seq data of murine aorta cells at 12 weeks of age

overall_design: Thoracic aortas were procured from tamoxifen-treated, 12-week-old  Myh11-CreERT2.mT/mG (designated as GFPiSMC or simply WT), aortic cells were isolated after cryophilic enzyme digestion, and single-cell RNA-seq analysis was performed


title: The different gene expression between the overexpression of V2R and V279del in HEK293 cells with the treatment of AVP

city: Shoufeng Township

first: Hsiang-Chin

last: Chen

state: Hualien

address: Daxue Road

department: Department of Life science

country: Taiwan

institute: National Dong-Hwa University

summary: To investigate the role of mutant V2R, V279del, on the downstream signaling,  we ovexpressed V2R and V279del in HEK293 cell lines with AVP treatment

overall_design: Gene expression profiling analysis was performed using data obtained from RNA-seq of 6 samples

first: Chih-Wen

last: Peng