title: High expression of oleoyl-ACP-hydrolase predicts mortality in patients hospitalized with avian A(H7N9) influenza

city: Memphis

first: Jeremy

middle: Chase

last: Crawford

state: TN

address: MS 221, 262 Danny Thomas Place

department: Department of Host-Microbe Interactions

institute: St. Jude Children's Research Hospital

summary: Although respiratory viral infections cause significant morbidity and mortality, it is still not fully clear why some individuals succumb to severe disease. In patients hospitalized with avian A(H7N9) influenza, we investigated early drivers underpinning hypercytokinemia and fatal disease. Our transcriptomics studies identified differential expression of 10 early host genes, defined by 16 probe sets, between patients who recovered and died. Seven probe sets were specific for the same host gene encoding for a key enzyme mediating free fatty acid production, oleoyl-ACP-hydrolase (OLAH). High olah transcript levels in fatal A(H7N9) patients were detected early after hospital admission and persisted until patients died. Conversely, patients who recovered had minimal olah transcript expression throughout their hospital stays.

overall_design: Blood samples were obtained from 8 patients hospitalized with avian A(H7N9) influenza, including 4 patients who survived and 4 who succumbed to disease during hospitalization. For 7 of these patients, we have paired samples obtained early after disease onset and late after disease onset. For 1 patient, data are only available for the late time point.

first: Zhongfang

first: Jianqing

last: Xu

first: Xiaoxiao

last: Jia

first: Brendon

middle: Y

last: Chua

first: Katherine

last: Kedzierska


title: Heterochromatin protein 1 alpha (HP1α) undergoes a monomer to dimer transition that opens and compacts live cell genome architecture

status: Public on Sep 02 2024

city: Melbourne

first: Elizabeth

last: Hinde

address: Grattan street

department: School of Physics

country: Australia

institute: University of Melbourne

summary: Our understanding of heterochromatin nanostructure and its capacity to mediate gene silencing in a living cell has been prevented by the diffraction limit of optical microscopy. Thus, here to overcome this technical hurdle, and directly measure the nucleosome arrangement that underpins this dense chromatin state, we coupled fluorescence lifetime imaging microscopy (FLIM) of Förster resonance energy transfer (FRET) between histones core to the nucleosome, with molecular editing of heterochromatin protein 1 alpha (HP1α). Intriguingly, this super- resolved readout of nanoscale chromatin structure, alongside fluorescence fluctuation spectroscopy (FFS) and FLIM-FRET analysis of HP1α protein-protein interaction, revealed nucleosome arrangement to be differentially regulated by HP1α oligomeric state. Specifically, we found HP1α monomers to impart a previously undescribed global nucleosome spacing throughout genome architecture that is mediated by trimethylation on lysine 9 of histone H3 (H3K9me3) and locally reduced upon HP1α dimerisation. Collectively, these results demonstrate HP1α to impart a dual action on chromatin that increases the dynamic range of nucleosome proximity. We anticipate that this finding will have important implications for our understanding of how live cell heterochromatin structure regulates genome function.

overall_design: To investigate our CV-based quantitation of nuclear wide chromatin density, and identify, on what spatial scales the HP1α monomers and dimers are in opposition, we applied high-throughput chromosome conformation capture (Hi-C) to the chromatin network of HeLa, HeLaKD (H (HP1KD) and HeLaHP1αI165E+KD (KDOE), and quantified the frequency of short to long range chromatin interactions. These three conditions were carried out in duplicate.

first: Jieqiong

last: Lou

first: Qiji

last: Deng

first: Xiaomeng

last: Zhang

first: Andrew

middle: B

last: Das

first: Charles

middle: C

last: Bell

first: Naiara

middle: G

last: Bediaga

first: Courtney

middle: O

last: Zlatic

first: Timothy

middle: M

last: Johanson

first: Rhys

middle: S

last: Allan

first: Michael

middle: D

last: Griffin

first: Prasad

middle: N

last: Paradkar

first: Kieran

middle: F

last: Harvey

first: Mark

middle: A

last: Dawson


title: A non-canonical bivalent gene Wfdc15a controls spermatogenic protease and immune homeostasis

city: Yokohama

first: Shin-ichi

last: Tomizawa

state: Kanagawa

address: 3-9 Fukuura, Kanazawa-ku

department: School of Medicine

country: Japan

institute: Yokohama City University

type: Expression profiling by high throughput sequencing

summary: Male infertility can be caused by chromosomal abnormalities, mutations, and epigenetic defects. Epigenetic modifiers pre-program hundreds of spermatogenic genes in spermatogonial stem cells (SSCs) for expression later in spermatids, but it remains mostly unclear whether and how those genes are involved in fertility. Here, we report that Wfdc15a, a WFDC family protease inhibitor pre-programmed by KMT2B, is essential for spermatogenesis. We found that Wfdc15a is a non-canonical bivalent gene carrying both H3K4me3 and facultative H3K9me3 in SSCs but is later activated along with the loss of H3K9me3 and acquisition of H3K27ac during meiosis. We show that WFDC15A deficiency causes defective spermiogenesis at the beginning of spermatid elongation. Notably, depletion of WFDC15A causes substantial disturbance of the testicular protease-antiprotease network and leads to an orchitis-like inflammatory response associated with TNFa expression in round spermatids. Together, our results reveal a unique epigenetic program regulating innate immunity crucial for fertility.

overall_design: To investigate the function of Wfdc15a for spermatogenesis, we performed RNA-seq using whole testis from Wfdc15a control (3x WT and 4x heterozygous) and knockout (6x KO) mice.

first: Kazuyuki

last: Ohbo


title: Analytical performance of OncoPrism-HNSCC, an RNA-based assay to inform immune checkpoint inhibitor treatment decisions for recurrent/metastatic head and neck squamous cell carcinoma

city: St. Louis

first: Jarret

last: Glasscock

state: MO

address: 4044 Clayton Ave

country: USA

institute: Cofactor Genomics

summary: While immune checkpoint inhibitor (ICI) therapies can significantly improve outcomes for patients with recurrent/metastatic head and neck squamous cell carcinoma (RM-HNSCC), only about 15–20% benefit from such treatments. Clinical tests that guide the use of ICIs are therefore critically needed. OncoPrism-HNSCC was developed to address this need. The assay combines next generation RNA sequencing-based immunomodulatory gene expression signatures with machine learning algorithms to generate an OncoPrism Score that classifies patients as having low, medium, or high likelihood of disease control in response to ICI treatment. Also, OncoPrism-HNSCC leverages the same FFPE patient tumor RNA used for ICI response prediction to identify rare cases where oncogenic rearrangements in NTRK1/2/3 or ALK genes, which may indicate the use of potentially highly effective targeted therapies. The clinical performance of OncoPrism-HNSCC has been validated. Here, we report its analytical performance in the presence of potentially confounding sources of variation.

overall_design:
Intermediate precision.  Technical replicates of RNA-seq libraries were made varying the operator, the reagant lot, the day the library was made, and the sequencer the library was sequenced on.
%DV200 study: FFPE RNA with decreasing %DV200 values was generated using the NEBNext® Magnesium RNA Fragmentation Module (New England Biolabs, Ipswich, MA). For each fragmentation time point, 500 ng RNA in a volume of 18 µl water was combined with 2 µl 10X RNA Fragmentation Buffer in thin-walled PCR tubes. Tubes were transferred to a preheated (94˚C) thermocycler and incubated for 0, 1, 2, 3, 4, or 5 minutes. Fragmentation was terminated by transferring tubes to an ice-cold aluminum block and immediately adding and mixing 2 μl 10X RNA Fragmentation Stop Solution. Fragmented RNA was purified using the Zymo RNA Clean & Concentrator-5 kit (Zymo Research, Irvine, CA) according to manufacturer’s instructions. %DV200 was calculated using an Agilent Bioanalyzer 2100 (Agilent Technologies, Santa Clara, CA).
gDNA was spiked-in at increasing percentages on a per mass basis (0, 5, 10, 20, 30%)
RNA input study:  libraries were made using different RNA input amounts 10-80 ng.  Technical replicates annotated as being from the "Reproducibility" study were sequenced on one sequencer using 40ng input.

first: Jon

last: Earls

last: Glascock


title: Hypoxia Sensing in Resident Cardiac Macrophages Regulates Monocyte Fate Specification following Ischemic Heart Injury

city: St Louis

first: Farid

middle: Faridovich

last: Kadyrov

address: Clinical Sciences Research Building, Rm. 9900  4939 Children's Place, Campus Box 8086

department: IM-Cardiology

institute: Washington University in St Louis

summary: Myocardial infarction initiates cardiac remodeling and is central to heart failure pathogenesis. Following myocardial ischemia reperfusion injury, monocytes enter the heart and differentiate into diverse subpopulations of macrophages. The mechanisms and dynamics of monocyte differentiation within this context are unknown. We investigated the role of macrophage hypoxia sensing on monocyte differentiation following reperfused myocardial infarction. We show that deletion of Hif1α, a hypoxia response transcription factor, in resident cardiac macrophages led to increased remodeling and overrepresentation of a macrophage subset marked by arginase 1 (Arg1) expression. Arg1+ macrophages displayed an inflammatory gene signature and were predicted to represent an intermediate state within the monocyte differentiation cascade. Lineage tracing of Arg1+ macrophages revealed the existence of a monocyte differentiation trajectory consisting of multiple transcriptionally distinct macrophage states. We further showed that deletion of Hif1α in resident cardiac macrophages resulted in arrested progression through this trajectory and accumulation of an inflammatory intermediate state marked by persistent Arg1 expression. Depletion of the Arg1+ trajectory also results in increased heart remodeling following ischemic injury, likely due to the beneficial effects of macrophages downstream of Arg1+ macrophage differentiation. Collectively, our findings unveil distinct trajectories of monocyte differentiation and identify hypoxia sensing as an important determinant of monocyte differentiation following myocardial infarction.

overall_design: Monocytes, macrophages, and dendritic cells from hearts were isolated via FACS and analzyed via scRNAseq using the 10x genomics platform. For macHif1aKO samples, experimental conditions were control and Hif1a KO monocytes/macrophages/dendritic cells 5 days after myocardial infarction. For Arg1ZsGr samples, fate labeled (ZsGr+) and non labeled (ZsGr-) monocytes/macrophages/dendritics cells were isolated from one of the two following experimental conditions. 1.) Hearts 2 and 30 days after myocardial infarction. 2.) control and Hif1a KO hearts 5 days after heart transplant. For Arg1DTR samples, monocytes, macrophages, and DCs were FACS sorted from control and Arg1DTR hearts 3 days aftermyocardial infarction. For resHif1aKO experiments, nuclei were isolated from control and resHif1aKO hearts 3 days after myocardial infarction using the 10X genomics nuclei isolation kit and FACS sorted based on DRAQ5 staining.

middle: L

last: Koenig

first: Junedh

last: Amrute

first: Hao

last: Dun

first: Wenjun

last: Li

first: Carla

middle: J

last: Weinheimer

first: Jessica

last: Nigro

first: Attila

last: Kovacs

first: Andrea

last: Bredemeyer

first: Steven

last: Yang

first: Shibali

first: Vinay

middle: R

last: Penna

first: Alekhya

last: Parvathaneni

first: Lulu

last: Lai

first: Niklas

last: Hartmann

first: Benjamin

last: Kopecky

first: Daniel

last: Kreisel

first: Kory

last: Lavine


title: Genome-wide maps of histone modifications in response to CO2 fluctuation in Nannochloropsis oceanica.

status: Public on Sep 03 2024

city: Haikou

first: Li

last: WEI

state: Hainan

address: No. 99 Longkun South Road, Haikou City

country: China

institute: Hainan normal university

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Epigenetic regulation in response to CO2 fluctuation and epigenome-association with phenotypic plasticity of CCM are firstly uncovered in marine microalga Nannochloropsis oceanica IMET1. The result showed that Kbu and H3K9m2 histone modifications were present in N. oceanica IMET1. Moreover, both Kbu and H3K9m2 positively regulated gene expression.

overall_design: Examination of 2 different histone modifications under different CO2 concentrations in Nannochloropsis oceanica cells.

last: Wei


title: Nannochloropsis oceanica and CO2 fluctuating environment

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

overall_design: Refer to individual Series


title: Circadian Dysfunction in Skeletal Muscle Impairs Limb Perfusion and Muscle Regeneration in Peripheral Artery Disease [Myotube-ATACseq]

city: Chicago

first: Pei

last: Zhu

state: IL

address: 420 E. Superior St

department: Biochemistry and Molecular Genetics

institute: northwestern university

summary: Peripheral arterial disease (PAD), caused by atherosclerosis, leads to limb ischemia, muscle damage, and impaired mobility in the lower extremities. Recent studies suggest that circadian rhythm disruptions can hinder vascular repair during ischemia, but the specific tissues involved and the impact on muscle health remain unclear. This study investigates the role of the skeletal muscle circadian clock in muscle adaptation to ischemic stress using a surgical mouse model of hindlimb ischemia. We used mice with specific genetic loss of the circadian clock activator, BMAL1, in adult skeletal muscle tissues (Bmal1muscle). Bmal1muscle mice and controls underwent femoral artery ligation surgery to induce hindlimb ischemia. Laser doppler imaging was used to assess limb perfusion at various time points after the surgery. Muscle tissues were analyzed with RNA sequencing and histological examination to investigate PAD-related muscle pathologies. Additionally, we studied the role of BMAL1 in muscle fiber adaptation to hypoxia using RNA and ATAC sequencing analyses in primary myotube culture model. Disrupted expression of circadian rhythm-related genes was observed in existing RNA-seq datasets from PAD patient-derived endothelial cells and ischemic limb skeletal muscles. Genetic loss of Bmal1 specifically in adult mouse skeletal muscle tissues delayed reperfusion recovery following induction of hindlimb ischemia. Histological examination of muscle tissues showed reduced regenerated myofiber number and a decreased proportion of type IIB fast-twitch myofibers in Bmal1musc mouse muscles in the ischemic limbs, but not in their contralateral non-ischemic limbs. Transcriptomic analysis revealed abrogated metabolic, angiogenic, and myogenic pathways relevant to hypoxia-adaptation in Bmal1musc mouse muscles. These changes were corroborated in Bmal1-deficient cultured primary myotubes cultured under hypoxic conditions.

overall_design: We isolated primary myoblasts from Bmal1-floxed mice and induced the cells into myotubes. The myotubes were then infected with Cre-expressing adenovirus for 48 hours to induce deletion of the circadian clock activator, BMAL1. Myotubes infected with an empty vector-expressing virus were served as control. The viral infected myotubes were then exposed to 21% O2 or 1% O2 for 6 hours to simulate post-surgery intramuscular hypoxia.

first: Calvin

last: Chao

first: Adam

middle: W

last: Steffeck

first: Caitlyn

last: Dang

first: Noah

middle: X

last: Hamlish

first: Eric

last: Pfrender

first: Bin

last: Jiang

first: Clara

last: Peek


title: Investigating the potential molecular mechanisms of mogroside V on glucose homeostasis by transcriptome profiling of adult mouse hypothalamic cells

city: Krakow

first: Tomasz

last: Szmatoła

state: Małopolskie

address: Mickiewicza 21

department: OMEI

country: Poland

institute: University of Agriculture in Krakow

summary: In recent years, mogroside V (MV), primarily found in monk fruit, has garnered significant attention due to its reported health benefits, including anti-inflammatory, antioxidant properties, and its association with glucose metabolism. Understanding the impact of MV on the transcriptome represents a crucial challenge in unraveling its mechanisms of action and potential therapeutic applications. This study aims to investigate the effects of varying doses of MV (15 µM, 60 µM, and 160 µM) on transcriptome profiles of adult mouse hypothalamus neuronal cells cultured in normal and high glucose conditions. The data presented demonstrate that up to 103 genes, depending on the study group, exhibited differential expression. Our results indicate activation of the Notch and FoxO signaling pathways associated with glucose metabolism as well as AMPK signaling pathway, a key regulator of glucose and lipid metabolism. The observed enrichment of pathways related to oxidative stress further supports the antioxidant properties of MV. Notably, the pathway analysis revealed dose-dependent effects of MV on glucose metabolism, solely under normal glucose conditions. However, these effects diminished in the presence of high glucose levels, with potential implications for cellular viability. Overall, our study underscores the potential role of MV in modulating glucose metabolism, inflammation, and oxidative stress. Further research, particularly in animal models, is needed to validate these findings and elucidate the potential therapeutic properties of MV supplementation.

first: Artur

last: Gurgul

first: Ewa

last: Ocłoń

first: Igor

last: Jasielczuk

first: Ewelina

last: Semik-Gurgul


title: Transcriptomic exploration of Solanum spp. resistance upon early-stage broomrape parasitism

city: Galaneika – Lamia

first: Vasiliki

last: Kotsira

address: Papasiopoulou 2-4

country: Greece

institute: Department of Computer Science and Biomedical Informatics

summary: Tomato (Solanum lycopersicum) is a major crop of high economic value. Phelipanche and Orobanche genera (broomrapes) are parasitic weeds, constituting biotic stressors that impact tomato production. Developing varieties with tolerance to broomrapes has become imperative for sustainable agriculture. Solanum pennellii, a wild tomato species, has been used as breeding material for S. lycopersicum. In the present study a commercial tomato hybrid and two Introgression Lines (ILs), (S. lycopersicum X S. pennellii), were employed to identify genes and metabolic pathways associated with resistance against broomrape. Comparative transcriptomic analysis revealed a multitude of differentially expressed genes (DEGs) in roots, especially in the resistant genotype IL6-3, several of which were validated by quantitative PCR. DEG and pathway enrichment analysis (PEA), revealed diverse molecular mechanisms that can potentially be implicated in the host’s defense response and the establishment of resistance. Further research into these genes and associated metabolic pathways will contribute to our understanding of host-parasite interactions and resistance to broomrapes. Findings will be valuable in molecular breeding for generating resistant genotypes, ultimately providing alternative solutions for weed management in tomato and other valuable crops.

sample_organism: Solanum lycopersicum x Solanum pennellii

overall_design: To investigate potential resistant mechanisms of tomato againt broomrape species we used one commercial hybrid: Formula (S.lycopersicum) and two introgression lines: IL6-2 &IL6-3 (S.lycopersicum x S. pennellii). For each genotype we had both control plants (no treatment) and inoculated plants with broomrape seeds with three replicates for each treatment. The total number sent for RNA-seq was 18 samples. Then we performed gene expression profiling analysis, using data obtained from RNA-seq and bibliography for 14 DEGs. Finally we carried out PEA to reveal molecular mechanisms potentially implicated in the host defense against broomrape parasitism.

first: Maria

last: Gerakari

first: Aliki

last: Kapazoglou

first: Spyros

last: Tastsoglou

first: Anastasios

last: Katsileros

first: Dimosthenis

last: Chachalis

first: Artemis

last: Hatzigeorgiou

first: Eleni

last: Tani


title: Degradation of Ikaros prevents epigenetic progression of T cell exhaustion in novel antigen-specific assay [bulk ATAC-seq]

city: Cambridge

first: Tristan

last: Tay

state: MA

address: 7 Divinity Avenue

department: Stem Cell & Regenerative Biology

institute: Harvard University

summary: Epigenetic regulation drives the differentiation of T cells into phenotypically stable subsets including a dysfunctional state termed exhaustion, the presence of these epigenetically distinct T cells in tumors make them non-responsive to checkpoint blockade. Cancer immunotherapies restoring T cell function have transformed cancer treatment by preventing immune evasion of tumor cells allowed by T cell exhaustion. However, some patients develop resistance to immunotherapy or do not respond. Recent literature has demonstrated that epigenetic regulation governs the transition from effector to exhausted T cells. Here, we describe a novel antigen-specific assay for T-cell exhaustion that produces T cells biologically and epigenetically similar to their in vivo exhausted counterpart. We perform a CRISPR KO screen for epigenetic regulators of the human genome and validate Ikaros as a driver of T-cell exhaustion. We determined that the Ikaros degrader iberdomide prevents exhaustion by blocking chromatin remodeling at T cell effector enhancers by preserving activity of key transcription factors AP-1, NF-κB and NFAT using transcription factor footprinting analysis. Thus, our study uncovers a role for Ikaros, degraded by the drug iberdomide, as a driver of T-cell exhaustion.

overall_design: SHARE-seq to profile chromatin accessibility and gene expression in T cells from four healthy human donors. Donor PBMCs were expanded for antigen-specific T cells using viral peptide cocktail over the course of 7 or 14 days. Iberdomide or DMSO was used to treat cells from day 7 -14.

first: Gayathri

last: Bommakanti


title: Rosmarinic acid alleviates radiation-induced pulmonary fibrosis by downregulating tRNA N7-Methylguanosine modification-regulated fibroblast to myofibroblast transition through the exosomes pathway

city: Nanning

first: jinglin

last: mi

address: shuangyong road

institute: the first affiliated hospital of guangxi medical university


title: Degradation of Ikaros prevents epigenetic progression of T cell exhaustion in novel antigen-specific assay [scRNA-seq]


title: Degradation of Ikaros prevents epigenetic progression of T cell exhaustion in novel antigen-specific assay [scATAC-seq]


title: Global  analysis of H3K36 methylation in  the  MM  genome

city: Yakushiji

first: NAOKI

last: OSADA

address: Tochigi

department: Center for Molecular Medicine

institute: Jichi Medical University

summary: We analyzed histone H3K36 methylation in multiple myeloma using ChIP-seq.

overall_design: We isolated fixed chromatin from KMS34 cells and performed immunoprecipitation with anti-histone H3K36me2 antibody, followed by deep sequencing.

first: Sae

last: Matsuoka

first: Jiro

last: Kikuchi


title: Genome wide DNA methylation profile in expressed prostatic secretions of normal and, benign and malignant prostatic lesions of diseased individuals

city: Kolkata

first: Amlan

last: Ghosh

state: West Bengal

address: 86/1, College Street

department: Life Sciences

country: India

institute: Presidency University

summary: Genome wide DNA methylation profiling was done on expressed prostatic secretions (EPS) of normal individuals and dry-core needle biopsy samples of benign and malignant (Primary tumor) prostatic lesions. The Illumina Infinium 850k Infinium MethylationEPIC v 1.0 was used to obtain DNA methylation profiles across approximately 850,000 CpGs in EPS and prostatic lesion biopsy samples. Samples included 4 EPS of normal individuals, and 8 biopsy tissues of benign, and malignant lesions each of patient individuals.

overall_design: Bisulphite converted DNA from the 20 samples including 4 EPS (of normal individuals), 8 BPH and 8 malignant (Primary tumor) prostatic lesions were hybridised to the Infinium MethylationEPIC v 1.0

first: Anwesha

last: Banerjee

first: Purandar

last: Sarkar

first: Abhik

last: Saha


title: Effect of TSPO deletion within mouse hippocampus under neuroinflammation

city: Singapore

first: Anna

last: Barron

address: Clinical Science Building,11 Mandalay Road

country: Singapore

institute: Lee Kong Chian Sch. Of Medicine

summary: We then performed gene expression profiling analysis using data obtained from RNA-seq of two genotypes (TSPO-KO and WT), where mice were previously injected with either (PBS or LPS) at a single time point 1mg/kg and sacrisficed after 24h

overall_design: Comparative gene expression profiling analysis of RNA-seq data for TSPOKO and WT under PBS or LPS condition

first: Kei Onn

last: Lai

first: Giuseppe

last: D' Agostino


title: Degradation of Ikaros prevents epigenetic progression of T cell exhaustion in novel antigen-specific assay


title: Olfactory Sensory Neuron Diversity Beyond OR Genes in mice [scRNAseq]

city: Guangzhou

first: Jin

last: Xu

state: Guangdong

address: No. 135 Xingang Xi Road

institute: Sun Yat-sen University

summary: How functional cellular heterogeneities are regulated is fundamental for understanding the molecular basis of complex organs. Olfactory sensory neurons (OSNs) are an ideal model to investigate the regulation of cellular heterogeneity. The “one-neuron-one-receptor” organization and topographical mapping ensure the detection and precise translation of odor signals to the central neural system. Besides the diversity of OR genes and other molecular guiding axon sorting processes, single-cell transcriptome analysis revealed an OSN subpopulation, defined by Cd36, a lipid receptor gene. The function study exhibited lipid odor identification was impaired in Cd36-deficient mice.  In this study, we systematically depicted the transcriptome diversity, spatial distribution, and specific functions of Cd36+ OSNs in the mouse olfactory epithelium. The specific molecular features of Cd36+ OSN we revealed implemented the programmed cellular diversity may be driven by their olfaction function. Furthermore, with the integrative analysis of single-cell transcriptome and epigenome profiles, we revealed the cis and trans regulatory signatures in Cd36+ OSN and identified Tshz1 and Mef2 as the key regulators that may directly regulate and promote the expression of Cd36 and drive the cellular diversity of OSNs. Especially, we demonstrated that Tshz1 is expressed coordinately with the choices of ORs, earlier than the expression of Cd36, which indicates it may act as a pioneer factor that instructs the lineage-specific expression of Cd36 and other genes, eventually leading to the cellular diversity of Cd36+ OSN. Our results provide novel knowledge on the regulation mechanism of cellular diversity of complex organs.

overall_design: Single cell RNA-seq of the whole olfactory epithelium and FACS-enriched mature OSNs from 19-day or 8-week-year-old mice using 10x  Genomics Chromium Single Cell 3′ Reagent Kit V3

first: Jiawen

last: Yang

first: Peiyu

last: Shi


title: Histone deacetylase inhibition mitigates fibrosis-driven disease progression in recessive dystrophic epidermolysis bullosa

city: Genoa

first: Paolo

last: Uva

address: Via Gerolamo Gaslini, 5

country: Italy

institute: IRCCS Istituto Giannina Gaslini

summary: Recessive dystrophic epidermolysis bullosa (RDEB) is a mucocutaneous blistering disease due to type VII collagen gene mutations. Transforming growth factor-β (TGF-β)-dependent fibrosis is responsible for severe RDEB complications. Reduced histone acetylation is a hallmark of fibrosis in pathologies affecting organs other than skin, where inhibition of histone deacetylses (HDACs) proved effective in reverting fibrosis. Here, HDAC inhibitor (HDACi) ability to counteract RDEB progression was investigated. We found that histone acetylation is decreased in RDEB skin and fibroblasts. Treatment with two HDACis, valproic acid (VPA) and Givinostat, counteracts RDEB fibroblast fibrotic traits, including contractility, α-smooth muscle actin expression, TGF-β1 release, and proliferation. Moreover, systemic VPA administration mitigates severe manifestations (corneal opacification and digit loss) in a RDEB mouse model. This effect associates with inhibition of skin fibrosis (presence of subcutaneous fat, thinner collagen bundles, decreased expression of fibrotic markers). Proteomic analysis of mouse skin revealed that VPA treatment decreases expression of genes involved in protein synthesis and increases levels of proteins with role in immune response. These findings highlight epigenetic changes as contributing to RDEB pathogenesis and disclose molecular mechanisms leading to skin fibrosis. Treatment with HDACi may represent a disease modifier therapeutic approach for RDEB and other skin fibrotic disorders.

overall_design: To investigate the effect of HDAC inhibitors (HDACi) on RDEB progression, fibroblasts were obtained from 5 RDEB patients. We then performed differential gene expression analysis using data from RNA-Seq of RDEB fibroblasts in three different conditions: untreated and treated with two HDACi, valproic acid (VPA) and Givinostat.

first: Alessia

last: Primerano

first: Emanuela

last: De Domenico

first: Francesca

last: Cianfarani

first: Naomi

last: De Luca

first: Giovanna

last: Floriddia

first: Massimo

last: Teson

first: Cristina

last: Cristofoletti

first: Silvia

last: Cardarelli

first: Giovanni

last: Luca Scaglione

first: Enke

last: Baldini

first: Davide

last: Cangelosi

first: Jonathan

last: Fernando Reinoso Sànchez

first: Carole

last: Roubaty

first: Jörn

last: Dengjel

first: Alexander

last: Nyström

first: Simona

last: Mastroeni

first: Salvatore

last: Ulisse

first: Daniele

last: Castiglia

first: Teresa

last: Odorisio


title: Olfactory Sensory Neuron Diversity Beyond OR Genes in mice [scATACseq]

first: Jin

last: Xu

overall_design: Single cell ATAC-seq of FACS-enriched mature OSNs from 19-day or 8-week-year-old mice using 10x Genomics Chromium Single Cell ATAC Reagent Kit V1.1

first: Jiawen

last: Yang

first: Peiyu

last: Shi


title: A non-canonical bivalent gene Wfdc15a controls spermatogenic protease and immune homeostasis

first: Shin-ichi

last: Tomizawa

overall_design: RNA-seq analysis of Wfdc15a control (+/+ and +/-) and knockout (-/-) mouse round spermatids.

first: Kazuyuki

last: Ohbo


title: CRISPRi/a screen of doxorubicin induced cardiotoxicity

status: Public on Sep 01 2024

city: palo alto

first: Chun

last: Liu

state: CA

address: 1291 Welch Road BMI building, 3200-CVI Rm

institute: stanford

summary: Druggable genome of CRISPRi/a sgRNA libraries for druggable genes protecting doxorubicin induced cardiomyocyte toxicity using human induced pluripotent stem cell (iPSC) derived cardiomyocytes.

overall_design: Vehicle (DMSO) and doxorubicin treated iPSC differentiated cardiomyocytes (iCMs). iCMs were transfected with sgRNA libraries and CRISPRi (dCas9-KRAB) or CRISPRa (dCas9-VPR). Two biological replicates were used in both CRISPRi and CRISPRa screens.

first: Mengcheng

last: Shen


title: Arraystar human lncRNA microarray V3.0

city: Linhai city

first: Xiang

last: Ying

address: No.150 Ximen Road

institute: Taizhou hospital

summary:
Preeclampsia (PE) is a peculiar multisystemic disorder that contributes to maternal and perinatal morbidity. Exosomes, existing in the circulation, origin from late endosomes which are secreted into the extracellular surrounding by diverse cell types under different conditions, can mediate intercellular communication via transporting its constituents and regulate inflammation, immunomodulation and angiogenesis. We hypothesize that exosomes from trophoblast in preeclampsia complications under pathological hypoxia microenvironment impair vascular development by transmitting its contents to endothelial cells. Here, transwell and tube formation assays revealed that exosomes from hypoxic trophoblast cells attenuated the migration, and tube formation in human umbilical vein endothelial cells (HUVECs) in vitro. In a mouse model, hypoxic trophoblast cells derived exosomes leaded to vascular dysfunction and caused adverse PE-like birth outcomes. Next, we detected lncRNA expression in cord blood plasma derived exosomes from gestational age-matched preeclampsia and normal pregnancies by microarray analysis. Then, we identified the possible mechanisms of one up-regulated exosomal lncRNA, TINCR. Application of Quantitative RT-PCR, lncTINCR was confirmed overexpressing in exosomes released from cord blood plasma, peripheral blood plasma and human placental trophoblasts of preeclampsia patients. Moreover, the exosomal lncTINCR could be specifically secreted by hypoxic trophoblast cells and transferred to HUVECs, which increased autophagy in HUVECs and impaired angiogenesis of endothelial cells in vitro. Furthermore, we demonstrated that lncTINCR was considered as a competing endogenous RNA to regulate miR-424, which resulted in elevated ATG5 expression. Thus, we reported that exosomes intervened effective delivering of lncTINCR to endothelial cells to damage vascular functions and result in the development of PE. The newly identified exosomal lncTINCR /miR-424/ATG5 axis may present potential novel targets of diagnosis and treatment for PE.
lncRNA profiles of cord blood plasma derived exosomes from gestational age-matched preeclampsia and normal pregnancies

overall_design: Xiang,Ying


title: Comparison of mRNA expression level between AmTARS and Pam3 as a lignad of TLR2 receptor

city: Daejeon

first: Jong Hwan

last: Kim

address: 125 Gwahak-ro, Yuseong-gu

department: Genome structure research center

country: South Korea

institute: Korea Research Institute of Bioscience and Biotechnology

summary: We demonstrated that AmTARS directly binds TLR2 receptor. Thus, we analysis mRNA expression pattern in mouse bone-marrow-derived macrophage (BMDM) treated with AmTARS and Pam3csk4 known as the TLR2 agonist.

overall_design: mRNA profiles of BMDM treated with AmTARS and Pam3csk4 for 1h or 3h

first: Su-Man

first: Myung-Hee

first: Jong-Hwan

first: Seon-Young


title: Circadian Dysfunction in Skeletal Muscle Impairs Limb Perfusion and Muscle Regeneration in Peripheral Artery Disease

first: Pei

last: Zhu

overall_design: We used mice with doxycyclin-induced loss of the circadian clock activator, BMAL1, in adult skeletal muscle tissues (Bmal1muscle). Bmal1muscle mice and controls underwent femoral artery ligation surgery to induce hindlimb ischemia. Laser doppler imaging was used to assess limb perfusion at various time points after the surgery. Muscle tissues were analyzed with RNA sequencing and histological examination to investigate PAD-related muscle pathologies.

first: Calvin

last: L Chao

first: Adam

last: Steffeck

first: Caitlyn

last: Dang

first: Noah

last: Hamlish

first: Eric

last: Pfrender

first: Bin

last: Jiang

first: Clara

last: Peek


title: Olfactory Sensory Neuron Diversity Beyond OR Genes in mice

first: Jin

last: Xu


title: TGF-β orchestrates proliferation and migration of cancer cells via KRTAP2-3

city: Bunkyo-ku

first: Kazuki

last: Takahashi

state: Tokyo

address: M&D Tower, Floor 7th, Room N708, 1-5-45 Yushima

institute: Tokyo Medical and Dental University

summary:
The proliferation and migration of cancer cells are regulated by stimuli from the tumour microenvironment during tumour progression and metastasis. While transforming growth factor-β (TGF-β) increases migration and metastasis of various types of epithelial cancer cells via induction of epithelial-mesenchymal transition (EMT), it also inhibits their proliferation by inducing cell cycle arrest in the G1 phase. However, the correlation between the tumour promoting and suppressing effects of TGF-β remains elusive because of the lack of analysis at the single-cell level. Here, we showed that TGF-β conferred higher motility and mesenchymal phenotypes to oral cancer cells residing in the G1 phase, suggesting a correlation between TGF-β-dependent cell cycle arrest and increased cell migration. We identified keratin-associated protein 2-3 (KRTAP2-3) as a regulator of these dual effects of TGF-β and showed that the expression of KRTAP2-3 was associated with TGF-β-induced cell cycle arrest and increased migration and correlated with poor prognosis in patients with head and neck cancer. Deletion of the KRTAP2-3 gene decreased in vitro migration and in vivo metastasis of oral cancer cells via induction of mesenchymal-epithelial transition. KRTAP2-3 also induced the expression of the zinc finger BED domain-containing protein 2 and ectodermal-neural cortex 1, which suppressed proliferation and increased migration of oral cancer cells, respectively. The present findings revealed the mechanisms by which TGF-β orchestrates proliferation and migration of cancer cells by inducing the expression of KRTAP2-3 and highlighted the importance of targeting motile cancer cells under cell cycle arrest in the G1 phase to suppress metastasis.
Identification of marker genes for  KRTAP2-3 induced gene

overall_design: The effect of expression on KRTAP2-3 in oral cancer was examined. KRTAP2-3 was expressed or knocked out in  cancer cells.

first: Katarzyna

last: Podyma-Inoue

first: Shintaro

last: Sakakitani

first: Maki

last: Saito

first: Akirnari

last: Sugauchi

first: Daizo

last: Koinuma

first: Kyoko

last: Kurioka

first: Toru

last: Konishi

first: Susumu

last: Tanaka

first: Atsuhi

last: Kaida

first: Masahiko

last: Miura

first: Toshihiro

last: Uchihashi

first: Kohei

last: Miyazono

first: Tetsuro

last: Watabe


title: Cardiac differentiation of mESCs and analysis of chromatin accessibility time series

first: Megan

last: Rowton

address: 900 East 57th Street

department: Human Genetics and Genetic Medicine

institute: University of Chicago

summary: Assay for transposase-accessible chromatin-sequencing (ATAC-seq) was performed in a time-series of cardiac differentiation of mESCs

overall_design: Two biological replicates were collected every 24 hours of cardiac differentiation of A2lox.cre mESCs from the 2i stage through day 8, in addition to day 10 and day 15 (cardiomyocyte stage). Samples were then lysed, and transposition was carried out at 37C for 30 minutes with Illumina’s Nextera DNA Library Prep kit (Illumina 15028212). Libraries were generated from transposed DNA and sequenced on an Illumina HiSeq4000 instrument in the University of Chicago’s Genomic Facility.

first: Carlos

last: Perez-Cervantes

first: Emery

last: Lu

first: Ivan

middle: P

last: Moskowitz


title: Galactin-3 regulation of CDC42 promotes neuronal autophagy following spinal cord injury

city: Xuancheng City

first: Zhiming

last: Cui

state: ANHUI

address: Anhui province

institute: The Second Affiliated Hospital of Nantong University

summary: Spinal cord injury (SCI) is a debilitating condition within the nervous system with a high disability rate and substantial economic burden. The functional recovery following SCI is enhanced by moderate levels of autophagy but hindered when autophagy becomes excessive. Galectin-3 (GAL3) has been recognized as an autophagy regulator; however, its role in SCI and its associated mechanism are largely unknown. Here we report that GAL3 was increased in spinal neurons and serum in SCI rats, and knockdown or inhibition of GAL3 promoted motor function recovery. The bioinformatics analysis showed that GAL3 is closely related to programmed cell death after SCI. Indeed, the knockdown of GAL3 resulted in a decrease in autophagy markers ATG7 and LC3 II/I ratio, along with an increase in P62 expression. Furthermore, GAL3 and cell division cycle 42 (CDC42) exhibited close associations with neuronal autophagy. Injection of CDC42 inhibitor ML141 effectively reduced GAL3-mediated enhancement of neuronal autophagy. Additionally, CDC42 was increased in spinal neurons post-SCI, and administration of ML141 decreased the expression of autophagy markers and improved motor function recovery. Importantly, elevated levels of GAL3 and CDC42 were observed in the serum of SCI patients. These findings suggest a potential interplay between GAL3 and CDC42 in regulating neuronal autophagy after SCI and indicate the therapeutic potential of targeting this pathway for enhancing recovery from spinal cord injuries.

overall_design: Total RNA was extracted from the spinal cord neurons of neonatal SD rats using Trizol reagent for subsequent sequencing. Sequencing was performed on an Illumina high-throughput sequencing platform (HiSeqTM2500/4000). There were a total of six samples, all of which were treated with high concentrations of glutamate to simulate a neuronal injury model. Among these, three samples were from neurons in the transfection control group, designated as Glu_1, Glu_2, and Glu_3, respectively. The other three samples were from neurons with GAL3 knocked out, designated as Glu_L_1, Glu_L_2, and Glu_L_3, respectively.

first: Lei

last: Yan

first: Chu

last: Chen

first: Hongxiang

last: Hong

first: Chunshuai

last: Wu

first: Guanhua

last: Xu

first: Yong-Jing

last: Gao


title: A system for functional studies of the major virulence factor of malaria parasites [WGS]

city: Hamburg

first: Johannes

last: Allweier

address: Bernhard-Nocht-Straße 74

country: Germany

institute: Bernhard Nocht Institute for Tropical Medicine

summary: PfEMP1 is a variable antigen displayed on red blood cells (RBCs) infected with the malaria parasite Plasmodium falciparum. PfEMP1 mediates binding of the infected cell to the endothelium of blood vessels, a major cause of severe manifestations of malaria. Each parasite encodes ∼60 different PfEMP1 variants of which only one is expressed at a time and switching between variants underlies immune evasion in the host and variant-specific severity of disease. PfEMP1 expression heterogeneity between parasites complicates its study and hampers genetic modification approaches as in many cells the modified locus is not expressed. Here we used selection linked integration to generate parasites all expressing the same PfEMP1 variant and permitting genomic modification of the expressed locus. Using this system, we study PfEMP1 trafficking, generate cell lines binding to all major endothelial receptors, survey the protein environment from functional PfEMP1 in the host cell and identify new proteins needed for PfEMP1 mediated sequestration. Overall, these approaches facilitate the study of the molecular and cellular biology of the key virulence factor of malaria parasites.

overall_design: Whole genome sequencing samples of erythrocytes infected with the P. falciparum transgenic parasites IT4var01-BirA*Pos1endo, IT4var01-BirA*Pos1endo + TryThrA-TGD or IT4var01-BirA*Pos1endo + EMPIC3-TGD

first: Jakob

last: Cronshagen

first: Paolo

last: Mesén-Ramírez

first: Jan

last: Stäcker

first: Anna

last: Viktoria Vaaben

first: Gala

last: Ramón-Zamorano

first: Isabel

last: Naranjo

first: Susann

last: Ofori

first: Pascal

last: WTC Jansen

first: Joëlle

last: Hornebeck

first: Florian

last: Kieferle

first: Agnes

last: Murk

first: Carolina

last: Castro-Peña

first: Richárd

last: Bártfai

first: Thomas

last: Lavstsen

first: Iris

last: Bruchhaus

first: Tobias

last: Spielmann


title: The glucocorticoid receptor elicited proliferative response in human erythropoiesis is BCL11A-dependent

city: SEATTLE

first: John

last: Stamatoyannopoulos

state: WA

address: 2211 Elliott Avenue, 6th Floor

department: Genome Sciences

institute: Altius Institute / University of Washington

summary: Prior evidence indicates that the erythroid cellular response to glucocorticoids (GC) has developmental specificity, namely, that developmentally more advanced cells that are undergoing or have undergone fetal to adult globin switching are more responsive to GC-induced expansion. To investigate the molecular underpinnings of this, we focused on the major developmental globin regulator BCL11A. We compared: a) levels of expression and nuclear content of BCL11A in adult erythroid cells upon GC stimulation; b) response to GC of CD34+ cells from patients with BCL11A microdeletions and reduced BCL11A expression, and; c) response to GC of two cellular models (HUDEP-2 and adult CD34+ cells) before and after reduction of BCL11A expression by shRNA. We observed that: a) GC-expanded erythroid cells from a large cohort of blood donors displayed amplified expression and nuclear accumulation of BCL11A; b) CD34+ cells from BCL11A microdeletion patients generated fewer erythroid cells when cultured with GC compared to their parents, while the erythroid expansion of the patients was similar to that of their parents in cultures without GC, and; c) adult CD34+ cells and HUDEP-2 cells with shRNA-depleted expression of BCL11A exhibit reduced expansion in response to GC. In addition, RNA-seq profiling of shRNA-BCL11A CD34+ cells cultured with and without GC was similar (very few differentially expressed genes), while GC-specific responses (differential expression of GILZ and of numerous additional genes) were observed only in controls cells with unperturbed BCL11A expression. These data indicate that BCL11A is an important participant of certain aspects of the stress pathway sustained by GC.

first: Maria

last: Mazzarini

first: Jennifer

last: Cherone

first: Truong

last: Nguyen

first: Fabrizio

last: Martelli

first: Lilian

last: Varricchio

first: Alister

last: Funnell

first: Thalia

last: Papayannopoulou

last: Migliaccio


title: The glucocorticoid receptor elicited proliferative response in human erythropoiesis is BCL11A-dependent, microdeletion patients.

overall_design: To investigate the molecular underpinnings of this, we focused on the major developmental globin regulator BCL11A. We compared response to GC of CD34+ cells from patients with BCL11A microdeletions and reduced BCL11A expression.

first: Anna


title: Single Cell RNA sequencing of CD11b+Gr1+ cells from the bone marrow of young and aged mice

first: Siyuan

last: Zhu

address: 1838 North Guangzhou Avenu

institute: Nanfang Hospital, Southern Medical University

summary: Myeloid-derived suppressor cells (MDSCs) are recognized as one of the key mediators of immunosuppression in aging process, which induce immunosenescence and increase elderly people’s susceptibility to to infections, cancers, autoimmune diseases, and degenerative diseases. It still remains elusive whether MDSCs represent a unique subset of myeloid cells that differ from their young, healthy counterparts, which will hamper the deeper understanding of the pathophysiological functions of MDSCs. In the present study we conducted scRNAseq analysis to compare MDSCs from three aged mice and three young mice. We established the MDSC-specific gene signature of aged mouse, which revealed the general characteristics of MDSCs, and thus faciliating distinguishing them from normal myeloid cells in aging process. In addition, our study provides a single-cell transcriptional map defining the development of MDSCs in aging process, which will ultimately enable us to specifically target these cells in old individuals.

overall_design: In the present study we conducted scRNAseq analysis of mice myeloid cells collected from three old mice and three young mice using the 10X Genomics Chromium Platform and sequenced on the Illumina HighSeq 3000.


title: Gene expression profiling of trophoblastic organoid from the placental villi of intrauterine and tubal ectopic pregnancies

city: Shanghai

first: Xiaoya

last: Zhao

state: shanghai

address: No. 910, Hengshan Rd

department: Department of Obstetrics and Gynecology, International Peace Maternity and Child Health Hospital

institute: School of Medicine, Shanghai Jiaotong University

summary: The tubal ectopic pregnancy (TEP) is a severe pregnancy complication accounted for 10-15% pregnancy-related deaths owing to the implantation and growth of embryos in fallopian tubes. Placental villi from TEP exhibit significant difference compared with that from intrauterine pregnancy (IP) in total volumes, trophoblast differentiation and intravillous vascularization.  To investigate the difference in expression profiles of placental villi from IP and TEP, placental villi were collected from each phenotype, separated from maternal tissues and analyzed by high-throughput sequencing.  generated a mouse model in which p53 is activated in neural crest cells due to the expression of a mutant p53 protein (p53-25,26) that can bind to and stabilize wild-type p53. Here, we performed gene expression profiling on neural crest cells isolated from these embryos, to identify the transcriptional response to p53 activation during embryogenesis.

overall_design: RNA-seq was performed on trophonblastic organoid from pregnant women at 6-8 gestational weeks. Exclusion criteria for all samples are: IP with EP histories, miscarriage, preeclampsia, and preterm delivery. EP with some risk factors associated with fallopian tubal abnormalities, e.g., smoking, obvious tubal inflammatory adhesions, previous fallopian tubal diseases, and tubal surgery histories, were also excluded for avoiding complications. In each case, gestational days was 40-64 days confirmed from the last menstrual period. n=5 for both IP and TEP.

first: X

middle: Y

first: Z

last: Zhang

first: J

first: C

last: Lin


title: Tumor immune microenvironmental characteristics in Human Epidermal Growth Factor-2 (HER2) positive esophageal adenocarcinoma: a comparative analysis and biomarker study

city: Amsterdam

first: Charlotte

last: Stroes

address: Meibergdreef 9

department: Medical Oncology

country: Netherlands

institute: Amsterdam UMC

summary: 84 biopsies were taken from the TRAP cohort (neoadjuvant chemoradiotherapie according to CROSS with trastuzumab and pertuzumab; n=40, HER2+ n=40), and a control cohort with neoadjuvant chemoradiotherapy only (n=44; HER2+ n=4) before treatment. Eventually, 83 biopsies were eligible for analyses following quality-control; biopsies were analysed using targeted gene expression analysis (Nanostring) with the immune-oncology panel (750 genes). These results allowed to chart the tumor-immune microenvironmental characteristics of HER2 positive tumors in patients with esophageal adenocarcinoma.

overall_design: Case-control study

middle: I

first: Sybren

last: Meijer


title: Blood-brain barrier dysfunction in response to Alzheimer's disease mutations and aged serum in a tissue-engineered microvascular model

city: Baltimore

first: Peter

middle: C

last: Searson

state: MD

address: 3400 North Charles Street

institute: Johns Hopkins University

summary: Alzheimer’s disease is a disease of neurodegeneration and aging that affects millions of Americans, and is expected to impact millions more without significant advancement in our understanding of the disease. An emerging focus in Alzheimer’s study is the role of the cerebrovasculature in the initiation, progression, and exacerbation of symptomatic disease.  Disruption of the blood-brain barrier, which tightly controls any exchange between systemic circulation and brain tissue, has manifested in post-mortem and in vivo studies of late-stage Alzheimer’s disease as microbleeds, dysfunctional glucose transport, and impaired efflux of toxins; additional animal studies have indicated that some vascular dysfunction precedes neuronal degeneration in the progression of the disease.  Thus, to understand the drivers and progression of Alzheimer’s disease in hopes of identifying therapeutic breakpoints, the role of blood-brain barrier dysfunction must be investigated. Here, we utilize a tissue-engineered model of the blood-brain barrier with high spatiotemporal resolution to assess its dysfunction with cell-intrinsic mutations associated with Alzheimer’s (APP(Swe) and PSEN1(M146V)) and the systemic influence of aged blood components (exposure to aged vs. young human serum).

overall_design: total samples collected n = 27; n = 3 for each condition across three cell lines (APP mutant, PSEN1 mutant, WT control) and three serum perfusion conditions (standard media, young human serum supplementation, aged human serum supplementation)

first: Tracy

last: Chung


title: ETV5 accelerates therapy-induced neuroendocrine prostate cancer development by inducing neural stem-like cell differentiation [ChIP-seq]

city: Pohang

first: Jongeun

last: Lee

address: 77 Cheongam-ro

institute: POSTECH

summary: Neuroendocrine prostate cancer (NEPC) is an aggressive subtype induced by hormone therapy, presenting significant therapeutic challenges due to the lack of effective treatments. In this study, we explored the role of ETV5 in NEPC development. Analysis of multiple prostate cancer datasets revealed significantly elevated ETV5 expression in NEPC compared to other subtypes. ETV5 expression increased progressively under hormone therapy conditions through epigenetic modifications. ETV5 overexpression induced NEPC-like features in LNCaP cells and facilitated their differentiation into NEPC under hormone treatment conditions, both in vitro and in vivo. Our molecular mechanism study identified PBX3 and TLL1 as ETV5 target genes, contributing to castration resistance and stemness induced by ETV5 overexpression. Notably, obeticholic acid, identified as an ETV5 inhibitor in this study, exhibited promising efficacy in suppressing NEPC development. This study highlights ETV5 as a key transcription factor driving NEPC development and underscores its potential as a therapeutic target for this aggressive cancer subtype.

overall_design: Chromatin immunoprecipitation (ChIP) sequencing for ETV5 in control and ETV5-overexpressing LNCaP cells.

first: Yoontae


title: ETV5 accelerates therapy-induced neuroendocrine prostate cancer development by inducing neural stem-like cell differentiation [RNA-seq]

overall_design: mRNA profiles of control and ETV5-overexpressing LNCaP cells.


title: Gene expression profiling of Huh7.5.1 with tunicamycin treatment and HCVcc infection

city: Hamamatsu

first: Tetsuro

last: Suzuki

address: 1-20-1 Handayama, Chuou-ku,

department: Department of Microbiology and Immunology

institute: Hamamatsu University School of Medicine

summary: The objective of the present study is to investigate the effect of endoplasmic reticulum (ER) stress caused by Hepatitis C Virus (HCV) infection on the mRNA expression profile in human hepatocytes.

overall_design: Comparative gene expression analysis was performed using the cultured human hepatocellular carcinoma cell line Huh7.5.1. The cells were treated with 1 μg/mL tunicamycin for 48 hours to induce ER stress or infected with HCVcc (cell culture-derived HCV) for 48 or 72 hours. Gene expression was analyzed using 3D-Gene® Human 25k oligonucleotide microarrays, along with computational gene expression analysis tools to interpret the results.

first: Masahiko

last: Ito

first: Liang

last: Liu


title: The function of FtMYBs in regulating the synthesis of flavonoids in Fagopyrum tartaricum under drought stress

city: Lanzhou

first: Qi

last: Lu

state: Gansu

address: Tianshui South Road 222

institute: lanzhou University

summary: Flavonoid is an important secondary metabolite, which makes an important contribution to plant resistance to abiotic stress and human health. Fagopyrum tataricum (Tartary buckwheat) itself contains more flavonoids, so exploring the regulation of Tartary buckwheat flavonoid synthesis can provide a solid theoretical basis for the cultivation of new Tartary buckwheat varieties with high nutrition. In this paper, we studied the role of FtMYBs in regulating the biosynthesis of flavonoids in Tartary buckwheat.

overall_design: The relatively drought-resistant tartary buckwheat variety Dingku1 which after drought treatment, the flavonoid content  increases to reduce damage caused by drought stress. After analyzing the pre-experimental results, 20% PEG-6000 was used to treat 0,2,4,8 hours, and the related gene expression levels were analyzed to explore drought. Analyzing transcriptome data to explore the molecular mechanisms regulating flavonoid synthesis.


title: Expression data from murine embryonic fibroblast with/without radiation.

city: Miami

first: Anthony

last: Griswold

state: FL

address: 1501 NW 10th Ave, BRB 318

institute: University of Miami

summary:
To identify the STING-dependent genes that play a role in facilitating the immunogenicity of DNA-damaged cells, normal MEFs or MEFs locking STING, cGAS, or IRF3 were irradiated.
We used microarrays to detail the global programme of gene expression underlying the upregulation of several STING-induced genes in response to radiation.

overall_design: Wild type, Sting knockout, cGAS knockout, and IRF3KO knockout murine fibroblast were irradiated with x-ray at 50 Gy and incubated them for 3 days.

first: Seongji

last: Park

first: Jeonghyun

last: Ahn

first: Glen

last: Barber


title: Effect of depletion of BCAT1 on gene expression during NOTCH1-dependent leukemia development in the mouse

city: Padova

first: Erich

last: Piovan

address: via Gattamelata 64

department: Surgery, Oncology and Gastroenterology

institute: University of Padova

summary: High levels of branched-chain amino acid (BCAA) transaminase 1 (Bcat1) have been associated with adverse prognosis and drug resistance in several cancer types. However, the mechanistic role of Bcat1 in T-cell acute lymphoblastic leukemia (T-ALL) development is ill defined. Here, we used a mouse T-ALL model to show that Bcat1 is required for T-ALL development and maintenance. Using a NOTCH1 gain-of-function retroviral model of T-ALL, mouse cells genetically deficient for Bcat1 showed defects in developing leukemia. Amongst the pathways upregulated in Bcat1 KO delta E-NOTCH1 cells we found  “DNA repair”, “apoptosis”, and “p53 pathway”. We thus hypothesize that Bcat1 may be implicated in cell cycle progression or apoptosis of T-ALL cells.

overall_design: To investigate the functional consequences of Bcat1 depletion in T-ALL cells we used a NOTCH1 gain-of-function retroviral model of T-ALL (delta E-NOTCH1). Mouse leukemia cells genetically proficient (WT) or deficient for Bcat1 (KO) were obtained. Further, mouse leukemia cells proficient for Bcat1 were treated with a Bcat1 specific inhibitor (ERG-245) or vehicle as control (PBS). We then performed gene expression profiling analysis using data obtained from RNA-seq of 5 different samples. Comparative gene expression profiling analysis of RNA-seq data for deltaE-NOTCH1 tumors proficient (WT) or deficient (KO) or treated with a Bcat1 specific inhibitor (ERG-245).

first: Valeria

last: Tosello

first: Ludovica

last: Di Martino


title: Integration of transcriptomics and proteomics uncovers novel targets underlying the protective effects of Nrf2 knockout in HEI-OC1 cells

city: Xi'an

first: Siyu

last: Li

address: 1 Xinsi Road

institute: Tangdu Hospital, Fourth Military Medical University

summary: Cisplatin, a utilized anticancer drug in clinical practice, induces sensorineural hearing loss (SNHL) in patients. However, the precise mechanism underlying cisplatin-associated ototoxicity remains unknown. HEI-OC1 cells are immortalized cells derived from the organs of Corti mice and nuclear factor erythroid 2-related factor 2 （Nrf2） knockout (KO) significantly enhances cisplatin resistance in these cells. The exploration of transcriptomic data from Nrf2 KO has significant implications for the identification of novel targets to enhance HEI-OC1 cisplatin resistance in Nrf2 KO and for understanding the biological characteristics associated with SNHL. The RNA-seq analysis revealed a significant enrichment of differentially expressed genes (DEGs) in the Nrf2 KO model within key signaling pathways, including the PI3K-Akt, MAPK, as well as Glutathione metabolism signaling pathways. Notably, expression levels of 17 specific genes were confirmed by RT-qPCR (Real-time Quantitative-PCR). The biomarkers identified in this study may be key to understanding the biological mechanism by which Nrf2 KO strongly increases HEI-OC1 cisplatin resistance, and by targeting the PI3K-Akt, MAPK, Glutathione metabolism signaling pathways provide new ideas for the prevention and treatment of cisplatin-induced SNHL.

overall_design: In this study, transcriptomic analysis was performed on Nrf2 KO HEI-OC1 cells to find key biomarkers to understand the biological mechanism of Nrf2 KO's strong increase in HEI-OC1 cisplatin resistance.

first: Weilong

last: Wang

first: Rui

last: Liang

first: Wei

last: Gao

first: Peiheng

first: Jiawei

last: Chen

first: Xuerui

last: Ding

first: Pengwei

last: Ma

first: Hao

last: Yuan

first: Yuqiang

last: Lun

first: Jianing

last: Guo

first: Zi

first: Hongkai

last: Mei


title: FOXA1 is required for ErbB2 expression and luminal differentiation in HER2-positive breast cancer [ATAC-seq]

city: Seoul

first: Jungmin

last: Choi

address: 73, Goryeodae-ro, Seongbuk-gu

institute: Korea University College of Medicine

summary: Forkhead box protein A1 (FOXA1) has been shown to have critical functions in prostate and ER alpha positive breast cancer. As a pioneering transcriptional factor, FOXA1 regulates DNA accessibility for the androgen receptor in prostate and the estrogen receptor alpha in ER positive breast cancer, respectively. FOXA1 is also expressed in human epidermal growth factor receptor-2 (HER2/ErbB2) positive breast cancers, but its functions in HER2 positive breast cancer are unclear. The loss of FOXA1 results in a decrease in the viability of HER2 positive and HER2 amplified cell lines suggesting that FOXA1 may have an important role in HER2 positive breast cancers. In this report, we examined patient-derived single-cell RNA sequencing and spatial transcriptomics data and demonstrated that FOXA1 is co-expressed with ErbB2 in HER2 positive breast cancers. Knocking down FOXA1 expression led to the reduction of HER2 expression and signaling. Chromatin Immunoprecipitation Sequencing (ChIP-seq) and Assay for Transposase-Accessible Chromatin using sequencing (ATAC-seq) identified FOXA1 binding motifs in the ErbB2 promoter and regulatory element regions, which controlled ErbB2 gene expression. Interestingly, the knockdown of FOXA1 increased Epithelial Mesenchymal Transition (EMT) signaling and inhibited luminal tumor differentiation. Furthermore, FOXA1 and TRPS1 regulated TEAD/YAP-TAZ activity. Taken together, our data demonstrate that FOXA1 is required for HER2 expression and luminal identity in HER2+ breast cancer.

overall_design:
To investigate the effect of FOXA1 on chromosomal accessibility, several cell lines were assessed.
Comparateive chromosomal accessibility profiling analysis for MCF10A, MCF7, SKBR3 cells and its FOXA1 KD derivates (SKBR3_FOXA1KD).

first: Jongwon

last: Lee

first: Jaekwang

last: Jeong

first: John

last: Wysolmerski


title: The microarray analysis of hippocampus in aged-mice treated with D-allose

city: Itami

first: Akane

last: Kanasaki

state: Hyogo

address: 5-3 Kita-Itami

institute: Matsutani Chemical Industry Co., Ltd.

summary: D-Allose is reported to have several health benefits. We investigated the changes in hippocampus gene expression in aged-mice using DNA microarray to evaluate the effects of D-allose on brain function. D-Allose also changed the expression of some genes in hippocampus involved in cognitive functions.

overall_design: 12 month old mice were fed the diet containing D-allose for 7 months. And then, the hippocampus samples were collected for DNA microarray analysis.


title: Stimulation of fracture mineralization by salt-inducible kinase inhibitors

city: Dallas

first: Jialiang

state: TX

address: 5323 Harry Hines Blvd

institute: University of Texas Southwestern Medical Center

summary: Over 6.8 million fractures are reported annually in the US, accounting for 20% of all musculoskeletal injuries. Approximately 10% of fractures will experience delayed- or non-union. Parathyroid hormone (PTH) analogs and anabolic osteoporosis therapeutics can stimulate fracture repair in animal models and patients with chronic nonunion. Previous studies have demonstrated that small molecule salt inducible kinase (SIK) inhibitors mimic PTH action in vitro and in vivo. Therefore, we hypothesize that YKL-05-099, a small molecule SIK inhibitor, will accelerate fracture callus osteogenesis.

overall_design: 126 nine-week-old female C3H/HeJ slow fracture healing mice underwent unilateral intramedullary femoral shaft pinning and a midshaft fracture. Thereafter, animals received daily subcutaneous injections of vehicle (PBS), YKL-05-099 (15mg/kg), or PTH 1-34 (100μg/kg). Mice were euthanized at 10, 14, and 21 days postoperatively. The callus tissues were assessed by RT-qPCR to detect fracture repair marker genes. Additionally, early time points were evaluated histologically and through single-cell RNA-Seq. μCT images were obtained for image-based callus analysis. Three-point bending testing was conducted on a group of femurs to evaluate tissue biomechanics. A hydrogel-based system for delivering PTH and nanoparticles containing SIK2 and SIK3 siRNAs was developed and tested in vitro and in vivo (N=32).

first: Kaveh

last: Momenzadeh

first: Marc

last: Wein

first: Ara

last: Nazarian


title: FOXA1 is required for ErbB2 expression and luminal differentiation in HER2-positive breast cancer [RNA-seq]

overall_design:
To investigate the effect of FOXA1 on HER2-related pathways, a stable cell line expressing shRNA directed against FOXA1 was generated by transducing cells with commercially prepared lentiviruses containing three individual shRNA directed against FOXA1 mRNA.
We then performed gene expression profiling analysis using data obtained from RNA-seq of 4 different cells.
Comparateive gene expression profiling analysis of RNA-seq data for SKBR3 cells and its KD derivates (FOXA1KD).


title: Spatial transcriptomics reveals distinct tumor microenvironment of murine breast cancer model undergoing treatment with a humanized monoclonal antibody targeting FABP4

city: Iowa City

first: Michael

last: Chimenti

state: IA

address: 431 Newton Road

department: Iowa Institute of Human Genetics

institute: University of Iowa

summary: Circulating levels of adipocyte fatty acid binding protein (A-FABP, also known as FABP4) are linked with metabolic dysregulation. Our previous study demonstrated that high serum levels of FABP4 increased the risk of obesity associated breast cancer. The treatment with anti-FABP4 monoclonal anitbody was demonstrated to inhibit mammary tumor growth in a syngeneic mouse model. We hypothesized that spatial transcriptomic analysis would identidy the relationship between tumor cells and tumor-associated stromal cells during the antibody treatment.

overall_design: Two pairs of primary tumors from both antibody treatment group and PBS control group were collected for sample preperation and analysis according to the manufacture’s introduction.

first: Jiaqing

last: Hao

first: Li-Chun

last: Lin

first: Bing

last: Li


title: The P. falciparum orthologue of Male Development Protein 3 is a Male-associated regulator of translation initiation or enhancement [RNA-Seq]

city: Silver Spring

first: Riette

last: Van Biljon

address: 10903 New Hampshire Avenue

institute: US FDA

summary: Sex determination and development of Plasmodium gametocytes is critical to the transmission of malaria parasites and involves a complex interplay of multiple molecular factors. Here, we characterized the P. falciparum gene syntenic to P. berghei MD3- pf3d7_0315600. This protein contains a non-classical CCCH zinc-finger domain and Lysine-Proline rich domain associated with ribosome receptors, suggesting  a role in mRNA regulation. Disruption of PfMD3 causes a pronounced defect in male gametogenesis which severely decreases parasite transmission to mosquitoes but does not affect female gamete production.  We show that abrogation of PfMD3 significantly decreases the expression of male gamete markers on the transcriptome and proteome level but also affects regulators of translation. We further investigated the function of  PfMD3-3xHA using in vivo using crosslinked RNA-Protein interaction capture followed by RNA-sequencing (CLIP-seq) to determine its RNA targets and IP-MS to determine protein interactors. We found 143 bound mRNA transcripts in early-stage gametocytes and 86 transcripts in late-stage gametocytes including arid/md4 andp230, not1-g, spm3 and morc mRNA bound at both stages. Interestingly, these CLIP targets decrease significantly in the ΔPfMD3 proteome, suggesting a role for PfMD3 in translational processing. IP-MS using a PfMD3-3xHA-tagged line further confirmed this role, showing an enrichment of proteins involved in mRNA metabolism. We then propose that PfMD3 functions as a Male Associated Regulator of Translation Initiation or Enhancement (MARTIE) in the human malaria parasite P. falciparum.

overall_design: To investigate the function of PfMD3, we established a clonal genetic knockout line of Plasmodium falciparum parasites (PfMD3_KO clone 1) in the NF54e wild type background. We then performed RNA-sequencing (RNA-seq) for PfMD3 knockout clone 1 in Plasmodium falciparum NF54e parasites in stage II-III, stage IV and stage V gametocytes (2 biological replicates each) and co-cultured NF54e wild type parasites

first: Heather

last: Painter


title: The P. falciparum orthologue of Male Development Protein 3 is a Male-associated regulator of translation initiation or enhancement [CLIP-Seq]

summary: Sex determination and development of Plasmodium gametocytes is critical to the transmission of malaria parasites and involves a complex interplay of multiple molecular factors. Here, we characterized the P. falciparum gene syntenic to P. berghei MD3- pf3d7_0315600. This protein contains a non-classical CCCH zinc-finger domain and Lysine-Proline rich domain associated with ribosome receptors, suggesting  a role in mRNA regulation.  We  investigated the function of  PfMD3-3xHA using in vivo using crosslinked RNA-Protein interaction capture followed by RNA-sequencing (CLIP-seq) to determine its RNA targets in both early (stage II) and late (stage IV-V) development of gametocytes. We found that these bound mRNA targets show decreased protein levels in a genetic knockout of PfMD3, suggesting a role for PfMD3 in translational processing. We then propose that PfMD3 functions as a Male Associated Regulator of Translation Initiation or Enhancement (MARTIE) in the human malaria parasite P. falciparum.

overall_design: Crosslinked RNA-Protein interaction capture followed by RNA-sequencing (CLIP-seq) for PfMD3-3xHA in Plasmodium falciparum NF54e parasites in stage II-III and stage IV-V gametocytes (4 biological replicates each)


title: Targeting Mitochondrial Membrane Potential as A Generalized Strategy to Eradicate Leukemic Stem Cells

first: Haobin

last: Ye

address: 2005 Songhu Rd

institute: Fudan University

summary: Heterogeneity in acute myeloid leukemias makes the development of effective therapies challenging. In the current study, we found that mitochondrial membrane potential (MMP) differs as a function of metabolism and stemness of leukemic cells. Mechanistically, MMP is regulated by mitochondrial translation, whose rate is sensitive to the availability of asparagine. Interestingly, this MMP-modulating mechanism is hijacked by leukemic cells, especially leukemic stem cells (LSCs), to elevated MMP to evade chemotherapy and thus depletion of asparagine by asparaginase chemo-sensitizes LSCs. To further evaluate the function of MMP-modulating mechanisms in disease development and drug resistance, we performed a targeted drug screen and identified Alexidine as a strong MMP-lowering agent via repressing mitochondrial translation. We revealed that Alexidine binds to cardiolipin to interfere with the inner membrane localization of mitochondrial ribosomes to inhibit mitochondrial translation. We demonstrated that Alexidine has anti-leukemic effect and is a potent chemo-sensitizer. Together, our study suggests that targeting MMP-modulating machineries is a promising approach to eradicate leukemic cells.

overall_design: Total RNAs were isolated from different leukemia cell lines, AML patient samples and leukemia cell line-derived xenograft models(CDX model). Genes with a FPKM no less than 1 were included in the analysis.

first: Ting

last: Liu

first: Ji-Hao

last: Zhou

first: Yongbo

last: Gong

first: Ying

last: Zhang


title: The spatiotemporal expression profile of ATF3 determines the fate of smooth muscle cells in abdominal aortic aneurysm development

city: Guangzhou

last: Wen

address: jinsui road NO.9

institute: Guangzhou Medical University

summary: Background: Abdominal Aortic Aneurysm (AAA) is a catastrophic disease with little effective therapy, likely due to the limited understanding of the mechanisms underlying AAA development and progression. Activating transcription factor (ATF) 3 has been increasingly recognized as a key regulator of cardiovascular diseases. However, the role of ATF3 in AAA development and progression remains elusive. Methods: Genome-wide RNA sequencing analysis was performed on the aorta isolated from saline or Ang II-induced AAA mice, and ATF3 was identified as the potential key gene for AAA development. To examine the role of ATF3 in AAA development, vascular smooth muscle cell (VSMC)-specific ATF3 knockdown or overexpressed mice by recombinant adeno-associated virus serotype 9 (rAAV9) vectors carrying ATF3, or shRNA-ATF3 with SM22α promoter were used in AngII (angiotensin II) induced AAA mice. In human and murine VSMCs, gain or loss of function experiments were performed to investigate the role of ATF3 in VSMC proliferation and apoptosis. Results: In both AngII-induced AAA mice and AAA patients, the expression of ATF3 was reduced in aneurysm tissues but increased in aortic lesion tissues. The deficiency of ATF3 in VSMC promoted AAA formation in AngII-induced AAA mice. PDGFRB was identified as the target of ATF3, which mediated VSMC proliferation in response to TNF-alpha at the early stage of AAA. ATF3 suppressed the mitochondria-dependent apoptosis at the advanced stage by upregulating its direct target BCL2. Our ChIP results also demonstrated that the recruitment of NFκB1 and P300/BAF/H3K27ac complex to the ATF3 promoter induces ATF3 transcription via enhancer activation. NFKB1 inhibitor (Andrographolide) inhibits the expression of ATF3 by blocking the recruiters NFKB1 and ATF3-enhancer to the ATF3-promoter region, ultimately leading to AAA development. Conclusions: Our results demonstrate a previously unrecognized role of ATF3 in AAA development and progression, and ATF3 may serve as a novel therapeutic and prognostic marker for AAA.

overall_design: Abdominal Aortic Aneurysm (AAA) Animal Models Angiotensin II (Ang II) (1,000 ng/kg/min, HY-13948, MedChemExpress, NJ, USA) was dissolved in normal saline and was infused using osmotic pumps (Alzet 2004, Durect Corporation, USA) for 4 weeks. Male mice (ApoE−/−,12 weeks old, about 20-25 g) were anesthetized, and the suprarenal abdominal aortas (identified between the last pair of intercostal arteries and the right renal branch) were harvested at 28 days after implantation surgery. The formation of aneurysm was determined by the abdominal aorta diameter increased by 50% or more. Any mouse that died prior to the study endpoint was subjected to autopsy, and aneurysm rupture was characterized by the presence of egress with blood clots outside the adventitia of the dilated aortic wall. Samples:Genome-wide RNA sequencing (RNAseq) analysis was performed on the aorta isolated from saline or Ang II-induced AAA mice. The aorta from AAA mice was further divided into the aortic lesion (non-aneurysm) section and the aneurysm section.

first: Yingying

first: Qiang

first: Jinlin

last: Tan

first: Xing

last: Fu

first: Yiwen

last: Liang

first: Yonghua

last: Tuo

first: Luhao

first: Xueqiong

first: Dongkai

last: LiuFu

first: Xuejiao

last: Fan

first: Chaofei

last: Chen

first: Zheng

first: Zhouping

last: Wang

first: Shunyang

first: Renjing

first: Lei

last: Pan

first: Yuan

first: Wai

middle: H

last: Tang


title: FOXA1 is required for ErbB2 expression and luminal differentiation in HER2-positive breast cancer [ChIP-seq]

first: Jungmin

last: Choi

overall_design: Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) for FOXA1 antibody (Abcam, cat. ab170933) in SKBR3 and MCF7 cells.

first: Jongwon

last: Lee

first: Jaekwang

last: Jeong


title: Mycobacterium tuberculosis bearing pulmonary transcriptomic landscape of wildtype and PD-1 deficient mice

city: Wuhan

first: Bing

last: Yang

state: Hubei

address: No.1 Shizishan Street, Hongshan District

department: College of Vetirinary Medicine

institute: Huazhong Agricultural University

summary: It was shown that PD-1 were significantly up-regulated in several infectious diseases, suggesting the immune boosting anti-PD-1 therapy may have potential applications in the prevention and treatment of infectious diseases. Here we found that the ablation of the PD-1 was responsible for the TB consequence in a time-dependent manner. While long-term sustained PD-1 ablation results in worsen TB outcome, the early short-term PD-1 pathway perturbing have an active role in the protection of infection, suggesting that the early PD-1 ablation may alter the innate immune-response. Thus, we performed scRNA-seq analysis for the pulmonary transcriptomic landscape of WT and PD-1-/- mice during 7 days after infection. We uncovered that PD-1 pathway ablation at the early stage of infection remodulated pulmonary immune landscape characterized by changes in the cellular compositions, differential gene expression states, augmenting innate immune responses against tuberculosis, together with altering intercellular communications, with the potential to alter anti-TB immune fates.

overall_design: The single-cell suspensions of M.tb inbfected lungs from WT and PD-1 knockout mice were collected at 7 days after infection and analyzed using scRNAseq.


title: Study on the mechanism of BGN in progression and metastasis of ccRCC

city: Qingdao

first: Hanqing

last: Xia

address: No.1677, Wutai Mountain, Huangdao District

department: The department of urology

institute: Affiliated Hospital of Qingdao University

summary: Based on multiple public databases, we investigated the expression level of BGN in ccRCC, its clinical significance, and its association with immune cells. Real-time fluorescence quantitative PCR was employed to validate BGN expression in tumor and adjacent normal tissues. Differential gene analysis, GO-KEGG analysis, and GSEA analysis were performed by RNA sequencing to elucidate the underlying signaling pathways. BGN knockdown cells were generated through lentiviral transfection to examine the impact of BGN on ccRCC. Cell proliferation, migration, and invasion were assessed using CCK8, colony formation, wound healing, Transwell migration, and invasion assays, respectively. Results: Our findings from database analysis and polymerase chain reaction (PCR) revealed a significant upregulation of BGN expression in kidney cancer tissues compared to normal tissues. Further analysis demonstrated a correlation between high BGN expression and ccRCC progression and immune infiltration. In vitro experiments confirmed that BGN silencing effectively inhibited cell proliferation, migration, and invasion of ccRCC. Mechanistically, these effects may be mediated through the MAPK signaling pathway. Conclusion: BGN potentially plays a pivotal role in the progression and metastasis of ccRCC, possibly acting through the MAPK signaling pathway. Therefore, BGN holds promise as a potential therapeutic target for ccRCC.

first: Tianzhen

last: He

first: Ke

first: Xinbao

last: Yin


title: Construction of Sows DNA Methylation Profiles and Pool of  Early Pregnancy Factors

city: shihezi

first: lanying

last: gu

address: shibei 4th road

institute: shihezi university

type: Methylation profiling by high throughput sequencing

summary: [Background] DNA methylation plays a crucial role in regulating cell proliferation, differentiation, gene expression, and embryonic development. However, the comprehensive changes in genome-wide DNA methylation during early pregnancy in sows remain unknown. This study aimed to investigate the DNA methylation profiles and to construct an early gene pool of sows during early gestation.[Results] In this investigation, we utilized blood samples from 20 healthy sows and applied Reduced Representation Bisulfite Sequencing (RBSS) technology to systematically examine alterations in DNA methylation in sow blood during early pregnancy. Screening and validating the Methylation differential genes by using bisulfite sequencing PCR (BSP) and Quantitative Real-time PCR (RT-qPCR). Our findings indicated a significant increase in methylation levels on day 28 of pregnancy (pre28) compared to non-pregnancy (ctrl) across various gene elements, including CGI, promoter, and genebody. A total of 64,908 differentially methylated sites (DMCs) and 12,119 differentially methylated regions (DMRs) were identified, predominantly exhibiting methylation upregulation. Randomly selected five differentially methylated genes—VBP1, UPRT (upregulated methylation), RPL10, RAB33A, and CD93 (downregulated methylation)—were validated. Between the pregnant (pre28) and non-pregnant (ctrl) groups the BSP results showed highly significant methylation differences (P<0.01) in VBP1, UPRT, RPL10, and RAB33A. DMC gene ontology (GO) analysis revealed significant enrichment in nuclear receptor activity, negative regulation of cysteine-type endopeptidase activity during apoptosis, heme binding, and hormonal activity. DMRs GO analysis highlighted significant enrichment in 1-acylglycerol-3-phosphate O-acyltransferase activity, regulation of transforming growth factor β receptor signaling pathway, mitochondrial outer membrane and myotubular cell development, and cellular calcium homeostasis. Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis demonstrated significant enrichment in the MAPK signaling pathway and the PI3K-Akt signaling pathway.[Conclusion] During sow early gestation, DNA methylation is significant changes and is mainly upregulated. The observed upregulation of DNA methylation during early gestation in sows may regulate the MAPK and PI3K-Akt signaling pathways, potentially influencing embryonic development. Methylated differential genes VBP1 and RPL10 can be used as potential markers for early sow pregnancy diagnosis. These findings offer novel insights into the epigenetic changes occurring in sows during early gestation.

overall_design: To investigate the genome-wide DNA methylation changes in sows during early pregnancy. Experiments were conducted to systematically analyze the changes of DNA methylation in the blood of sows in early pregnancy using the RRBS sequencing method with blood samples from 28-day pregnant (pre28) and non-pregnant (ctrl) sows. Differential genes were screened and validated using BSP with the RT-qPCR method.

first: Lanying

last: Gu

first: Xinyan

last: Cao

first: Ali

last: Adnan

first: Wenyu

first: Zhiyu

last: Gao

first: Yanbing

last: Zhang

first: Yanming

last: Sun

first: Jinliang

last: Sheng


title: MicrRNA-26a deficiency attenuates the severity of frozen shoulder in a mouse immobilization model

city: Hiroshima

first: Shigeru

last: Miyaki

state: Hiroshima

address: 1-2-3, kasumi Minami-ku

department: Medical Center for Translational and Clinical Research

institute: Hiroshima University

summary: The main pathogenesis of the frozen shoulder is thought to be the inflammation of the intra-articular synovium and subsequent fibrosis of the shoulder joint capsule. However, the molecular pathogenesis of the frozen shoulder is still unknown. A class of non-coding RNAs, microRNAs (miRNAs) contribute to various diseases including musculoskeletal diseases. MicroRNA-26a (miR-26a) has been reported to be associated with fibrosis in several organs. This study aims to reveal the role of miR-26a on fibrosis in the shoulder capsule using a frozen shoulder model in miR-26a deficient (miR-26a KO) mice. MiR-26 KO and wild type (WT) mice were investigated using a frozen shoulder model. The range of motion of the shoulder, histopathological analysis such as synovitis, and fibrosis related-genes expression in the model mice were evaluated to determine the role of miR-26a. In WT mice, both inflammatory cell infiltration and thickening of the inferior shoulder joint capsule were observed after 1 week of immobilization, and this thickening further progressed over the subsequent 6 weeks. However, the immobilized shoulder in miR-26a KO mice consistently exhibited significantly better range of motion compared with WT mice at each point, and histological changes were notably less severe. The expression of inflammation- and fibrosis-related genes was decreased in the miR-26a KO mice compared with WT mice at 1 and 6 weeks. Together, miR-26a deficiency attenuated the severity of frozen shoulder in the immobilization model mouse. The present study suggests that miR-26a has the potential to be a target miRNA for therapeutic approach to frozen shoulder.

overall_design: To understand its mechanisms including target genes of miR-26a, synovial fibroblasts (SFBs) derived from shoulder joint capsule tissue of WT and miR-26a KO mice one week after immobilization were isolated by outgrowth method (Ref) in Dulbecco’s modified Eagle’s medium (DMEM) (FUJIFILM Wako, Osaka, Japan). Isolated SFBs were cultured in DMEM with 10 % fetal bovine serum. Experiments were carried out at passage 2. Double-stranded RNA oligonucleotides representing mature sequences that 10 nM miR-26a mimic (sense: 5’-UUCAAGUAAUCCAGGAUAGGCU-3’ and anti-sense: 5’-CCUAUUCUUGGUUCCUUGCACG-3’) or Silencer Negative Control siRNA#1 (Themo Fisher Scientific) were transfected into miR-26a KO SFBs using Lipofectamine RNAiMax Reagent (Themo Fisher Scientific) for 24 hours according to the manufacturers’ instructions. Total RNA of wild-type and, miR-26a KO SFBs were extracted and underwent RNA-sequencing (RNA-seq) analysis (BGI Genomics, China).

first: Yasuhiko

last: Sumimoto

first: Dilimulati

last: Yimiti


title: Mutant FOXO1 Controls an Oncogenic Network via Enhancer Accessibility and RNA Polymerase Pause Release [CUT&RUN]

city: Nashville

first: Scott

last: Hiebert

state: Tennessee

address: 2220 Pierce Ave, Hiebert Lab PRB 512

institute: Vanderbilt University

summary: Transcriptional dysregulation is a hallmark of diffuse large B-cell lymphoma (DLBCL), as multiple transcriptional regulators are mutated. However, our mechanistic understanding of how normal transcriptional programs are co-opted in DLBCL has been hindered by a lack of methodologies that provide the temporal resolution required to separate direct and indirect effects in transcriptional control. Here, we applied a chemical-genetic approach to engineer the inducible degradation of the transcription factor FOXO1, which is recurrently mutated in DLBCL. The combination of rapid degradation of FOXO1, nascent transcript detection, and accessible chromatin allowed us to identify the direct targets of FOXO1. FOXO1 degradation impaired RNA polymerase pause-release at many target genes. Furthermore, FOXO1 was required to maintain accessibility at specific enhancers associated with target genes. Importantly, many direct targets of FOXO1 were oncogenes including several effectors of the PI3K pathway, which creates a dependency on AKT signaling.

overall_design: CUT&RUN was performed in the OCI-LY1 and SU-DHL-4 cell line expressing endogenous FOXO1-FKBPF36V at specified time points after treatment with dTAG-47. Please note that this is included as negative data for inspection by the reiewers and not intended for use in new studies.

first: Hillary

middle: M

last: Layden


title: Enhancer profiling uncovers JMJD1C as essential suppressor in neuropathic pain by targeting SOCS

city: Jinan

first: chuanxin

last: wang

address: 247 Beiyuan Street, Jinan 250033, Shandong, China,

institute: The Second Hospital of Shandong University

summary: Neuropathic pain (NP) is induced by injury or diseases of the somatosensory nervous system, which markedly impairs patients’ quality of life.  Super-enhancers (SEs) are important cis-regulatory elements, but how they affect NP remains elusive.  Therefore, we aim to explore the molecular mechanism by which SEs are involved in NP progression and identify potential drug candidate targets.  We first established a rat model characterized with typical NP, and subsequently performed RNA-Seq and H3K27ac ChIP-Seq on spinal cord tissues of NP rats to analyze the active enhancers at the genome-wide level.  By analyzing the SE-associated genes involved in NP, combined with qPCR and double immunofluorescence staining results, we found that Jmjd1c is a core SE-associated regulator in NP progression, and Sox6 could activate Jmjd1c transcription by binding to its SE.

overall_design: First of all, Spared nerve injury (SNI) induced NP rats and sham rats were established. Then, rats were deeply anesthetized with chloral hydrate, spinal cord tissue was obtained and fixed with 1% formaldehyde.  Nuclear chromatin was extracted and segmented to 100-400bp fragments by ultrasound, 5% was taken as input, and the remaining chromatin incubated together with the ChIP grade antibody: anti- H3K27ac.

first: le

last: zhang

first: peilong

last: li


title: Human Breast Tumor-associated Endothelial Cells Favor Interactions with Nanomedicines

city: Norman

first: Stefan

last: Wilhelm

state: Oklahoma

address: 173 Felgar Street

department: School of Biomedical Engineering

institute: University of Oklahoma

summary: Nanomedicines, designed to improve the effectiveness of cancer treatment, have not met anticipated outcomes owing to suboptimal delivery efficiency to tumors. While the enhanced permeability and retention (EPR) effect has been explored, recent research challenges the predominant passive accumulation theory. This study explores the mechanisms governing nanoparticle entry into tumors by comparing human breast tumor-associated endothelial cells (HBTECs) and healthy human mammary macrovascular endothelial cells (HMMECs). Our results demonstrate that HBTECs exhibit higher nanoparticle uptake, involving three major endocytic pathways. Gene expression analysis reveals the upregulation of transport-related genes, especially motor protein genes, in tumor-associated endothelial cells. These insights highlight the need for comprehensive investigations into nanoparticle transport mechanisms and associated factors within the tumor microenvironment, essential for advancing drug delivery and therapeutic outcomes.

overall_design: To investigate the difference in nanoparticle interactions with endothelial cells from tumor and healthy tissues, we employed two primary human cell types: human breast tumor-associated endothelial cells (HBTECs) and human mammary microvascular endothelial cells (HMMECs). Two experimental conditions, one without and one with gold nanoparticle incubation, were applied. Consequently, we established four distinct groups: HBTEC, HMMEC, HBTEC_Au (HBTECs with gold nanoparticle incubation), and HMMEC_Au (HMMECs with gold nanoparticle incubation). RNA-seq was conducted on these groups. For the RNA-seq result analysis, the four groups were compared in a pairwise manner, which are HBTEC vs HMMEC, HBTEC_Au vs HMMEC_Au, HBTEC_Au vs HBTEC, and HMMEC_Au vs HMMEC, to explore the impact of both cell origin differences and nanoparticle incubation.

first: Lin

last: Wang

first: Kaili

last: Liu


title: Human platelet-rich plasma promotes the primordial follicle activation through the PI3K/Akt signaling pathway

city: China

first: hongwei

last: Wei

address: 382 Outer Ring East Road, Guangzhou Higher Education Mega Center

institute: South China University of Technology

summary: The activation of dormant primordial follicles is a promising method for rescuing the infertility of aged women and premature ovarian insufficiency (POI) patients. Accumulating evidences in both human and animal suggest that human platelet-rich plasma (hPRP) has the ability to recover ovarian function and promote follicle growth, however the underlying mechanisms remain unclear. In the current study, we revealed that hPRP promoted the activation of primordial follicles and the proliferation of granulosa cells. hPRP treatments significantly increased the levels of phosphorylated protein kinase B (Akt) and forkhead Box O3a (FOXO3a), and the number of oocytes with FOXO3a nuclear export. The hPRP-induced primordial follicle activation could be blocked by LY294002, the inhibitor of PI3K/Akt. By in vivo injection newborn mice model and in vitro culture human ovarian fragments, hPRP was further proved to be effective in the activation of primordial follicles. Taken together, our results suggest that hPRP can promote the primordial follicle activation through the PI3K/Akt pathway. Our results provide a theoretical basis for the clinical application of hPRP in aged women and POI patients.

overall_design: We selected thrombin to activated hPRP, the ovaries of newborn 3-day-old mice were cultured in vitro with concentration gradient and the optimal hPRP working concentration was selected from different concentrations of hPRP to promote the activation of primordial follicles. The effect of PRP on primordial follicle activation and its possible mechanism were studied by in vitro and in vivo mouse models, human ovarian tissue culture models and transcriptome sequencing.


title: RNA Expression Profiling of spinal cord tissues in a Rat Model of Neuropathic Pain

summary: Neuropathic pain (NP), defined as a complex chronic pain state caused by somatosensory nervous system lesions or diseases, is currently the most challenging clinical neurological disorder in the world. The main signs and symptoms of NP include spontaneous pain, abnormal pain and hyperalgesia. It is generally believed that the specific pathological causes of NP include spinal cord or peripheral spinal cord injury, postherpetic neuralgia, trigeminal neuralgia, and tumor invasion. While the critical role of mRNA in NP is well recognized, the involvement of mRNA in the development of NP remains to be elucidated. Therefore, in this study, we explored changes in mRNA expression profiles through transcriptome sequencing to provide a landscape of mRNA dysregulation in the NP spinal cord.

overall_design: First of all, Spared nerve injury (SNI) induced NP rats and sham rats were established. Total RNA from SNI rat spinal cord tissues were extracted using TRIzol reagent (Invitrogen, Carlsbad, USA) following the manufacturer’s instruction,in triplicates, and high throughput sequencing of mRNA was performed byIllumina HiSeq 6000.


title: AAGGG repeat expansions trigger RFC1-independent synaptic dysregulation in human CANVAS Neurons

city: Ann Arbor

first: Connor

last: Maltby

state: MI

address: 109 Zina Pitcher Place

department: Neurology

institute: University of Michigan

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

overall_design: Refer to individual Series


title: AAGGG repeat expansions trigger repeat-dependent synaptic dysregulation in human CANVAS Neurons [RFC1_Knockdown]

summary: Cerebellar ataxia with neuropathy and vestibular areflexia syndrome (CANVAS) is a late onset, recessively inherited neurodegenerative disorder caused by a biallelic, non-reference pentameric CCCTT(AAGGG) repeat expansion within the second intron of replication factor complex subunit 1 (RFC1). While rare compound heterozygous CANVAS cases harbor RFC1 loss-of-function mutations alongside monoallelic repeat-expansions, RFC1 expression is maintained at normal levels in the presence of biallelic expanded repeats. To investigate how these pentameric repeats cause disease, we generated CANVAS patient iPSC derived neurons and utilized calcium imaging and transcriptomic analysis to define repeat elicited gain-of-function and loss-of-function contributions to neuronal toxicity. AAGGG repeat expansions do not alter neuronal RFC1 splicing, expression, or DNA repair pathway functions. In reporter assays, AAGGG repeats are translated into pentapeptide repeat proteins that selectively accumulate in patient brains. However, neither these proteins nor repeat RNA foci were detected in iNeurons and overexpression of these repeats in isolation did not induce neuronal toxicity. CANVAS iNeurons exhibit defects in neuronal development and diminished synaptic connectivity that is rescued by CRISPR deletion of a single expanded allele. Importantly, these deficits were not replicated by knockdown of RFC1 in control neurons and showed incomplete or no rescue upon over-expression of RFC1. These findings support a repeat-dependent and RFC1-independent mechanism as the underlying cause of neurodegeneration in CANVAS, with important implications for therapeutic development in this currently untreatable condition.

overall_design:
To assess global dysregulation of gene expression in CANVAS, we generated multiple Control, CANVAS, and Isogenic corrected patient iPSC lines. These were differentiated to forebrain glutamatergic neurons by modified Dual-SMAD inhibition protocol.

Neurons were aged to 10-weeks in vitro and were analyzed by paired-end RNASequencing of Control Negative (n=3), Control +shControl (n=3), Control +shRFC1 (n=3), and CANVAS (n=6) iPSC-derived neurons. Neurons were treated with the respective lentivirus particles at DIV5 and continued expressing the integrated shRNA's throughout the 10-week differentiation before analysis.

RNASeq data were analyzed for differential expression, differential exon usage, and circRNA expression.

first: Samantha

last: Grudzien