title: Comparative transcriptome analysis reveals metabolic differences between planktonic and biofilm of Actinobacillus pleuropneumoniae.

status: Public on May 31 2023

city: Wuhan

first: Qiuhong

last: Zhang

address: No. 1, Shizishan Street

country: China

institute: Huazhong Agricultural University

type: Expression profiling by high throughput sequencing

summary: To reveal the transcriptional profiles of Actinobacillus pleuropneumoniae under biofilm and planktonic growth, we established a biofilm-forming culture method and constructed a mutant strain Δpga with defect in biofilm formation. Wild-type and Δpga mutant strains of Actinobacillus pleuropneumoniae strain 4074 were cultured in bottles with shaking for planktonic (WT_PK) and in microplates in static status for biofilm (WT_BF, Δpga),  respectively. The bacteria in logarithmic growth period of different culture groups were collected for RNA seq.

sample_organism: Actinobacillus pleuropneumoniae serovar 1 str. 4074

overall_design: The planktonic bacteria were obtained by culturing bacteria in bottles with shaking, and the biofilm were cultured in microplates in static status. Substances adhered to the bottom of the microplates were obtained as the biofilm layer or adhesion layer.

first: Lu

last: Li


title: Transciptome profile of TrmB in Haloarcula hispanica

city: Durham

first: Amy

middle: K

last: Schmid

state: NC

address: 124 Science Dr

country: USA

institute: Duke University

summary: Transcripome profiling (RNA-seq) of TrmB in the halophilic archaeon Haloarcula hispanica in the presence and absense of glucose after 24 hours.

overall_design: RNA-Seq

first: Rylee

last: Hackley


title: Unveiling the molecular mechanism involving anthocyanins in pineapple peel discoloration during fruit maturation

city: Hai Kou

first: Aiping

last: Luan

address: No. 4, Xueyuan Road, Longhua District

institute: Tropical Crops Genetic Resources Institute of Chinese Academy of Tropical Agricultural Science

summary: Peel color is a key factor that affects the fruit’s aesthetic and economic values. In Red Sugar pineapple, the peels’ red color reduces during maturation. Limited knowledge is available on the regulation of pineapple peel discoloration, which makes it important to study the molecular mechanisms associated with this important trait. Here, we report that a decrease in anthocyanin biosynthesis is predominantly associated with the pineapple peel color change during maturation. Particularly the exclusive accumulation of cyanidin in 60 days after flowering (DAF) as compared to 120 DAF gives the fruit peel its distinct reddish color.  Our findings suggest that the changes in the expression of key structural genes (early and late biosynthetic genes) of the anthocyanin (cyanidin) biosynthesis pathway are responsible for peel discoloration. Based on a gene co-expression analysis and a transient expression, we identified two transcription factors i.e., AcHOX21 and AcMYB12, and showed that their downregulation leads to the reduced anthocyanin accumulation with fruit maturation.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for pineapple peels harvested on 60, 90, and 120 days after flowering (DAF).

first: Wei

first: Mingzhe

last: Yang

first: Ziqin

last: Zhong

first: Jing

last: Wu

first: Yehua

last: He

first: Junhu


title: Genome-Wide Analysis of the MADS-box Gene Family Involved in Salt and Waterlogging Tolerance in Barley (Hordeum Vulgare. L)

city: yangzhou

first: zhenxiang

last: zhou

state: jiangsu

address: 48 Wenhui Dong Lu

department: agricultural college

institute: Yangzhou University

summary: To investigate the salt and waterlogging mechanism of  barley, we chose salt and waterlogging sensitive and tolerant varieties as subjects. We then performed gene expression profiling analysis using data obtained from RNA-seq of two varieties at two three points.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for leaf and root in two varieties.

first: Feifei

last: Wang

first: Zhenxiang

last: Zhou

first: Rugen

last: Xu


title: IFNγ, TGF-β, and time are associated with conserved myeloid diversity in tuberculosis granulomas [scRNA-seq]

city: Cambridge

first: Bryan

middle: B

last: Bryson

state: MA

address: 77 Massachusetts Avenue

department: Department of Biological Engineering

institute: Massachusetts Institute of Technology

summary: We profiled lung tuberculosis granulomas and non-diseased lung tissue to understand myeloid dynamics in tuberculosis.

overall_design: Tuberculosis granulomas and lung tissue from cynomolgus macaque were dissociated for scRNA-seq

first: Joshua

last: Peters

first: Joanne

last: Flynn

first: Alex

last: Shalek


title: Erinacine S from Hericium erinaceus Mycelium Promotes Neuronal Regeneration by Inducing Neurosteroids Accumulation

city: Hsinchu

first: Chun-Yu

last: Lin

address: No. 75 Po-Ai St.

department: Department of Biological Science and Technology

country: Taiwan

institute: National Yang Ming Chiao Tung University

summary:
To study the underlying mechanism of erinacines derived from Hericium erinaceus in neuroprotective effect against neurodegenerative diseases, we used the next-generation sequencing technology and bioinformatic analyses, erinacine S was found to cause the accumulation of neurosteroids in neurons.
Additionally, we found that erinacine S enhances neurite outgrowth in a cell autonomous fashion of primary neurons. It also promotes post-injury axon regeneration of PNS neurons and enhances regeneration on inhibitory substrates of CNS neurons. This research uncovers a previously unknown effect of erinacine S on promoting neuronal regeneration via raising the level of neurosteroids.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for four groups of samples from primary mouse cortical neurons (3 independent repeats), including 1) DMSO solvent control treatment for 16 hours, 2) 1 μg/mL erinacine S treatment for 16 hours, 3) DMSO solvent control treatment for 48 hours, and 4) 1 μg/mL erinacine S treatment for 48 hours

first: Eric

last: Hwang

first: Yi-Ju

last: Chen

first: Chih-Hsuan

last: Hsu

first: Yu-Hsuan


title: Deletion of nucleoporin Seh1 impaired neurogenesis through transcriptional regulation

city: shanghai

first: Ximing

last: Nian

state: Shanghai

address: Chongqing Nanlu 227

institute: Shanghai Jiao Tong University

summary: To investigate the function of  chromodomain helicase DNA binding protein 4  in the regulation of neural stem cell proliferation, we   find out different expression of genes in neural stem cell of  Chd4 knockdown

overall_design: RNA-seq was performed on neural stem cell following treatments with scrambled or Chd4 siRNAs

first: Liang

last: Zhang

first: Zhixiong

last: Liu

first: Wenxiu

last: Dai


title: SDHA/B reduction promotes hepatocellular carcinoma proliferation by removing cullin1 NEDDylation and stabilizing YAP/TAZ

city: Hanhzhou

first: fujing

last: ge

address: No. 866 Yuhangtang Road

institute: Zhejiang University

summary: Background & Aims: Succinate dehydrogenase enzyme (SDH) is frequently found to be diminished in Hepatocellular carcinoma (HCC) patient samples, and SDH reduction is associated with elevated succinate level and poor prognosis in HCC patients. But the underlying mechanisms about how impaired SDH activity promotes HCC malignancy remain unclear.     Approach & Results: In this study, we observed remarkable downregulations of SDH subunits A and B (SDHA/B) in chronic liver injury-induced murine HCC models and HCC patient samples. Subsequent RNA sequencing, hematoxylin & eosin (H&E) staining and immunohistochemistry (IHC) analyses of HCC samples revealed that Yes-associated protein (YAP) and transcriptional coactivator with PDZ-binding motif (TAZ) were significantly upregulated in HCC, with their levels inversely correlating with that of SDHA/B. The protein stability of YAP/TAZ was greatly enhanced in SDHA/B-depleted HCC cells along with accumulation of succinate. Further mechanistic analyses demonstrated that impaired activity of SDHA/B resulted in succinate accumulation which facilitated the removal of NEDDylation on cullin1, therefore disrupted the E3 ubiquitin ligase SCFβ-TrCP complex, consequently led to YAP/TAZ stabilization and activation in HCC cells. The accelerated in vitro cell proliferation and in vivo tumor growth caused by SDHA/B reduction or succinate exposure were largely dependent on the aberrant activation of YAP/TAZ.    Conclusions: Our study demonstrated that SDHA/B reduction promotes HCC proliferation by preventing the proteasomal degradation of YAP/TAZ through modulating cullin1 NEDDylation, thus addicts SDH-deficient HCC cells to YAP/TAZ pathway and renders these cells vulnerable to YAP/TAZ inhibition. Our findings warrant further investigation on the therapeutic effects of targeting YAP/TAZ in HCC patients displaying reduced SDHA/B or elevated succinate levels.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for control group and DEN+CCL4 treated group mice.

first: Tao

last: Yuan

first: Tianyi

first: Meijia

last: Qian

first: Jiamin

last: Du

first: Yue

first: Jia'er

first: Yonghao

last: Li

first: Guanghan

last: Fan

first: Fangjie

last: Yan

first: Xiaoyang

first: Xiawei

first: Yulian

last: Wu

first: Qiaojun

last: He

first: Hong

last: Zhu

first: Bo

last: Yang


title: Identification of Human Pluripotent Stem Cell Derived Astrocytic Progenitors that Correlate with Glioblastoma Subtypes

city: Chicago

first: Chian-Yu

last: Peng

state: IL

address: Department of Neurology, 10-233 Ward Building, 303 E Chicago Ave.

institute: Northwestern University, Feinberg School of Medicine

summary: To investigate the heterogeneity of astrocyte progenitor subtypes present during human astrocyte differentiation that share molecular similarities with tumor initiating stem cells in GBM, we FACS isolated 4 populations of astrocytic progenitor subtypes as identified by the expression of cell surface markers CD51, CD63, and CD71 from three independent iPSC-derived neural progenitor cell lines.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for 4 different astrocyte progenitor subtypes identified by the combinatorial expression of CD51, CD63, and CD71.

first: Stephanie

last: Van Gulden

first: John

last: Kessler


title: Identification of microRNAs associated with aggressive choroid plexus tumor phenotypes

city: Toronto

first: Nicholas

middle: William

last: Fischer

state: Ontario

address: 686 Bay Street

country: Canada

institute: The Hospital for Sick Children

type: Non-coding RNA profiling by high throughput sequencing

summary: We previously demonstrated that combining histological approaches with a specific DNA methylation signature for choroid plexus carcinomas (CPCs) can help to differentiate aggressive tumors from those that are not life threatening. Herein, we investigate the role of miRNAs in choroid plexus tumorigenesis, given the well-established role of miRNAs in the pathogenesis of other cancers. We characterized miRNA expression (using miRNA-seq and miRNA PCR arrays) in different CPTs in order to establish which miRNAs can serve as predictive biomarkers for CPCs compared to the less aggressive forms - choroid plexus papilloma (CPP) and atypical choroid plexus papilloma (aCPP). We performed miRNA-seq on 35 CPTs and used real-time PCR for the validation. We identified significant differences in the miRNA expression profiles between CPCs and CPPs. The specific miRNA expression signature for CPCs revealed upregulation of several miRNA members of oncogenic miRNA clusters (miR-17-92, 106a-363, 183/96/182) and downregulation of the tumor suppressive miRNA 34b/c cluster. Our findings suggest that the identified miRNAs could serve as novel biomarkers for CPCs and that targeting these deregulated miRNAs could be a promising new treatment strategy for this aggressive form of CPTs where survival rates remain below 50%.

overall_design: Determination of miRNAs expression in choroid plexus tumors

first: Malgorzata

last: Pienkowska

first: Sanaa

last: Choufani

first: Andrei

middle: L

last: Turinsky

first: David

last: Malkin


title: Effect of UBE3A knock out on murine bone marrow-derived macrophages

city: Diepenbeek

first: Melanie

last: Loix

state: Limburg

address: Agoralaan gebouw C

department: Biomedical Research Institute

country: Belgium

institute: Hasselt University

summary: We used RNAseq to evalute the effect of loss of UBE3A on the transcriptome of bone marrow-derived macrophages.

overall_design: Bone marrow-derived macrophages were obtained from UBE3A KO mice and wild-type littermates, and were analyzed with RNA sequencing.

first: Jeroen

middle: F

last: Bogie

first: Aldo

last: Jongejan

first: Noam

last: Zelcer


title: Temperature changes in the root ecosystem affect plant functionality

city: Pozuelo de Alracon

first: Juan

middle: Carlos

last: del Pozo

state: Madrid

address: Campus de Montegancedo, UPM

department: Biotechnology

country: Spain

institute: Centro de Biotecnología y Genómica de Plantas

summary: We have analyzed the effect of high temepratures in roots and shoots of Arabidopsis using a novel approach, since we cultivate the seedlings with the root system in a temeprature gradient, simulatinfg the soil.

overall_design: RNAseq analses of polyA mRNAs from roots and shoot of wild type seedlings grwon at 22ºC or 32 ºC homogenously or 32ºC in the shoot and a decreasing temperature gradient in the root grwoing area

middle: C

first: Mary

middle: P

last: González-García

first: Carlos

middle: M

last: Conesa

first: Alberto

last: Lozano

first: Victoria

last: Baca-Gonzalez


title: Effect of optogenetic-induced muscle loading on the transcriptomics of murine Achilles tendon and calcaneus

city: Ann Arbor

first: Megan

last: Killian

state: Michigan

address: 109 Zina Pitcher Pl

institute: University of Michigan

summary:
We used optogenetics to induce skeletal muscle contraction and unilaterally load the Achilles tendon and enthesis in young (i.e., during growth) Acta1Cre;Ai32 mice.
We then performed gene expression analysis using data obtained from RNA-seq of optogenetically loaded tendon and enthesis (bone) at two time points.

overall_design: Gene expression analysis of RNA-seq data for optogenetically loaded tendon and bone compared with unstimulated or naïve controls.

first: Syeda

middle: N

last: Lamia

first: Elahe

last: Ganji

first: Matthew

last: Stepanovich

first: Noelle

last: Whyte

first: Adam

last: Abraham


title: RNA-seq analysis of macrophages that are proximal or distal to tumor cells

city: Beijing

first: Qi

last: Tang

address: Chengfu Road #292

institute: Peking University

summary: To analyze the proximity-dependent gene expression in macrophages cocultured with tumor cells, we integrated QMID and RNA-seq to profile the transcriptome in THP1-derived macrophages cocultured with tumor cells.

overall_design: THP1-derived macrophages cocultured with HER2+ MDA-MB-231 cells at a ratio of 20:1 and labeled via QMID, followed by FACS isolation and RNA-seq analysis. Proximial and distal macrophages were sorted out by measuring their QMID labeling intensities. Monocultured macrophages were set as control groups. All experiments were performed in triplicates.

first: Xu

last: Zhang

first: Yilan

last: Guo

first: Xing

last: Chen


title: Transcriptomic and Metabolomic Changes Reveals the Immunomodulatory Function of Casein Phosphopeptide-Selenium Chelate in Beagle Dogs

city: Chongqing

first: Wang

middle: Wen

last: Can

address: No. 18, Food City Avenue

institute: Chongqing Sweet Pet Products Co., Ltd

summary: Casein phosphopeptide-selenium complex (CPP-Se), an organic chelate of casein phosphopeptide and selenium, has been shown to stimulate canine lymphocytes proliferation and cytokines production in our previous research, but its effect on the gene expression of peripheral blood is unclear. To further investigate the potential mechanism associated with CPP-Se in the process of exerting immunomodulatory function in dogs, our current study used high-throughput sequencing technology to explore the effects of feeding CPP-Se for 30 days on the blood transcriptome of dogs. Compared with control group, a total of 341 differentially expressed genes (DEGs) were identified in CPP-Se group, of which 110 were up-regulated and 231 were down-regulated. Gene ontology (GO) analysis revealed that DEGs were enriched in various biological processes and molecular functions, such as ion transport, transmembrane signaling receptor activity, molecular transducer activity and cytokine activity. Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis found that DEGs were mainly implicated in multiple immune-related signaling pathways. Immune-related DEGs were screened by the Immport database and the hub genes of all DEGs or DEGs related to cytokine-cytokine receptor interaction pathway and T cell receptor signaling pathway were identified by Cytoscape. Finally, the reliability of RNA-Seq data was verified by RT-qPCR. Our findings indicated that CPP-Se can change the blood gene expression profile of dogs and the results will serve as a scientific reference for the future development of functional foods to improve pet immunity, as well as a theoretical basis for monitoring and evaluating the immune status of dogs.

overall_design: Comparative gene expression profiling analysis of whole blood RNA-seq data for dogs fed without CPP-Se or supplemented with CPP-Se for 30 days.

first: Wencan

last: Wang

first: Ling

last: Xu

first: Xin

last: Mao


title: Specific stroke-induced miRNAs could mediate and interaction between peripheral blood and the brain

city: Albuquerque

first: Tamara

last: Roitbak

state: New Mexico

address: 1101 Yale Blvd NE

department: Neurology

institute: University of New Mexico

summary: Ischemic stroke is a major public health problem that is currently among the top leading causes of serious, long-term disability worldwide. The lack of effective treatment strategies prompted a search for new molecular targets for stroke prognosis and therapy. One of the epigenetic mechanisms controlling stroke progression and recovery involves signaling pathways mediated by short non-coding RNAs called microRNAs (miRNAs). Recent studies demonstrated stroke-specific changes in miRNA expression. The main goal of the present study was identify miRNAs mediating a communication between the brain and peripheral circulation in human stroke.

overall_design: miRNA expression profiles were assessed in plasma samples collected from stroke patients, using miRNA sequencing and bioinformatic analysis. Selected miRNA expression profiles were correlated with patient age and sex, time of sample collection, levels of neuronal damage marker, and stroke infarct size.

first: Yusra

last: Azar

first: Colin

last: Wilson

first: Reed

middle: G

last: Selwyn

first: Marc

last: Mabray

first: Sharina

last: Desai

first: Jeffrey

last: Thompson

first: Sasha

last: Hobson

first: Orrin

last: Myers

first: Jacquelyn

middle: S

last: Morales

first: Surojit

last: Paul

first: Michel

last: Torbey


title: Chromosomal instability causes sensitivity to polyamines and one-carbon metabolism

city: Bedford Park

first: Stephen

last: Gregory

state: South Australia

address: Sturt Road

department: Molecular Medicine

country: Australia

institute: Flinders University

summary: Aneuploidy, having an unbalanced genome, is an aberration commonly found in tumours but rare in normal tissues. It gives rise to proteotoxic stress as well as a stereotypical oxidative shift which makes these cells sensitive to internal and environmental stresses. Using Drosophila as a model, we investigated the changes in transcription in response to ongoing changes to ploidy (chromosomal instability, CIN). We noticed changes in genes affecting one-carbon metabolism, specifically those affecting the production and use of s-adenosyl methionine (SAM). Depletion of several of these genes led to cell death by apoptosis in CIN cells, but not normal proliferating cells. We found that CIN cells are particularly sensitive to SAM metabolism at least partly because of its role in generating polyamines. Feeding animals spermine was seen to rescue the cell death caused by loss of SAM synthase in CIN tissues. Loss of polyamines led to decreased rates of autophagy and sensitivity to reactive oxygen species (ROS), which we have shown contribute significantly to cell death in CIN cells. These findings suggest that a well-tolerated metabolic intervention like polyamine inhibition has the potential to target CIN tumours via a relatively well characterized mechanism.

overall_design: Samples are RNASeq preps from CIN (Mad2 mutant) and non-CIN (Mad2 heterozygote) Drosophila larvae. Five replicates from each genotype were used, with 15 animals in each replicate

first: David

last: Newman

first: Zeeshan

last: Shaukat


title: Effect of VPS35 on gene expression in MKN28 gastric cancer cells

city: Shanghai

first: Junxian

last: Yu

address: 197, Rui Jin 2nd Road

department: Department of General Surgery

institute: Ruijin Hospital, Shanghai Jiao Tong University School of Medicine

summary: To investigate the  function of VPS35 in the regulation of gastric cancer cell proliferation, we established MKN28 cell lines in which VPS35 has been knocked down by shRNA.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for MKN28 cells and its KD derivatives (shVPS35), three biological replicates for each group.

first: Haoran

last: Feng

first: Qingqing

last: Sang


title: Energy metabolism disorders during in vitro maturation affect bovine blastocysts transcriptome, lipidome, and metabolome

city: Poznan

first: Piotr

last: Pawlak

address: Wolynska 33

department: Department of Genetics And Animal Breeding

country: Poland

institute: Poznan University of Life Sciences

summary: Inhibitors of glucose (IO+DHEA group) or fatty acids (ETOMOXIR group) metabolism were applied during bovine oocyte in vitro maturation (IVM). Control group was conducted in standard maturation conditions. In vitro fertilization and embryo culture were applied. Obtained blastocysts were analysed with regard to lipidome, metabolome (mass spectrometry), transcriptome (RNA Seq) and lipid droplets staining (BODIPY).

first: Paulina

last: Lipinska

first: Ewa

last: Sell-Kubiak

first: Arkadiusz

last: Kajdasz

first: Natalia

last: Derebecka

first: Ewelina

last: Warzych


title: Dapagliflozin alleviates diabetic kidney disease via HIF1α/HO1 mediated ferroptosis

first: yihui

last: Wang

state: Beijing

address: Haidian district

summary: To investigate the mechanism of the renal protective effects of SGLT2i in diabetic nephropathy, we treated 9-week db/db mice with dapagliflozin and solvent, respectively. This study used m/m mice as control group.We performed gene expression profiling analysis using data obtained from RNA-seq of 3 different groups of mice after 13-week treatment.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for vehicle treated db/db mice and dapagliflozinand treated db/db mice as well as vehicle treated m/m mice.

first: Yihui

first: Dongyuan

last: Chang

first: Min

last: Chen

first: Minghui

last: Zhao


title: Chronic dietary exposure to the food preservative tert-Butylhydroquinone (tBHQ) impairs zebrafish (Danio rerio) survival, growth, organ development, and gene expression in Nrf2a-dependent and independent ways

city: Amherst

first: Alicia

middle: R

last: Timme-Laragy

address: 637 N PLEASANT ST

department: Environmental Health Sciences

institute: University of Massachusetts-Amherst

summary: Tert-Butylhydroquinone (tBHQ), a preservative used to prevent oxidative deterioration of oil, fat, and meat products, has been linked to both chemoprotective and adverse effects. This study investigates the impact of chronic dietary tBHQ on survival, growth parameters, organ development, and gene expression in zebrafish (Danio rerio). As tBHQ activates the transcription factor nuclear factor erythroid 2-related factor 2 (Nrf2a), a zebrafish line with a mutation in the DNA-binding domain was used to identify Nrf2a-dependent vs. independent effects. Homozygous Nrf2a wildtype (wt) and mutant (m) larvae were fed a diet containing 5% tBHQ or a control diet. Survival and growth parameters were assessed at 15 days and at 5 months, and samples collected for RNA sequencing at 5 months. Chronic dietary exposure to tBHQ throughout the larval and juvenile periods negatively impacted growth and survival.  RNA-seq analysis found differentially expressed genes related to growth and development and upregulation of several immune pathways.  The findings herein demonstrate that chronic dietary tBHQ exposure may impair growth and survival in both Nrf2a dependent and independent manners.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for whole zebrafish (Danio reio) fed a 5% Tert-Butylhydroquinone (tBHQ) or control diets for 5 months in homozygous Nrf2a wildtype (wt) and mutant (m) zebrafish

first: Emily

last: Leonard

last: Marques

first: Monika

middle: A

last: Roy

first: Sarah

last: Conlin

first: Ravi

last: Ranjan


title: Comparing the microbiota composition between Cocaine addicted and Healthy subjects and the corresponding shift caused by rTMS treatment.

city: Firenze

first: Matteo

last: Ramazzotti

address: viale Morgagni 50

department: Experimental and Clinical Biomedical Sciences

country: Italy

institute: University of Florence

summary: Total DNA was extracted from saliva and stool of the patients, amplified to collect amplicons of variable V3–V4 regions of the bacterial 16s rRNA gene and sequenced with MiSeq (2x300bp) Illumina platform.

overall_design: Total DNA was extracted from saliva and stool of Cocaine addicted and Healthy subjects

first: Amedeo

last: Amedei

first: Simone

last: Baldi

first: Leandro

last: Di Gloria

first: Elisabetta

last: Gerace

first: Lavinia

last: Curini


title: Tarsl2 is evolved not for tRNA charging in vivo

first: 剑辉

last: 张

address: 岳阳路320号细胞楼11楼

institute: SIBCB

summary: As a newly evolved duplicated gene of TARS1 (encoding cytoplasmic threonyl-tRNA synthetase), TARSL2 (TARS3) encodes a protein highly similar with TARS1 with only obvious difference in N-terminus. Albeit with tRNA charging activity in vitro and incorporated into the multiple tRNA synthetase complex (MSC), whether TARSL2 is able to function as a tRNA synthetase to substitute TARS1 in vivo is unclear. In this work, we found that Tars1 was essential for embryonic development. In contrast, knockout of Tarsl2 was achievable. Loss of Tarsl2 had no effect on both abundance and charging levels of all tRNAThr isoacceptors, indicating Tarsl2 is not for tRNAThr metabolism. Furthermore, Tarsl2 deletion did not influence protein levels of other MSC components, MSC integrity and aminoacylation levels of non-cognate tRNAs by MSC components. However, a severe retardation of mice development was observed after 3 weeks accompanied with an elevated metabolism capacity and muscle development abnormity. We further constructed a Tarsl2-deleted zebrafish, which exhibited no change in the level and charging of tRNAThrs. Collectively, these data suggest that Tarsl2 is evolved not for canonical tRNAThr aminoacylation and cannot substitute Tars1 in vivo.

overall_design: We then performed gene expression profiling analysis using data obtained from RNA-seq of 6 different mice muscle, including 3 WT  and 3 Tarsl2 KO mice.

first: Xiaolong

last: Zhou

first: Jianhui

last: Zhang

first: Qiyu

last: Zeng


title: Transcriptome Profiling Reveals Enhanced Mitochondrial  Activity as a Cold Adaptive Strategy to Hypothermia in Zebrafish Muscle

city: Belfast

first: Thomas

last: Cahill

address: 19 Chlorine Gardens

country: United Kingdom

institute: Queens university Belfast

summary: The utilisation of synthetic torpor for interplanetary travel once seemed farfetched. However, mounting evidence points to torpor-induced protective benefits from the main hazards of space travel, namely, exposure to radiation and microgravity. To determine the radio-protective effects of an induced torpor-like state we exploited the ectothermic nature of the Danio rerio (zebrafish) in reducing their body temperatures to replicate the hypothermic states seen during natural torpor. We also administered melatonin as a sedative to reduce physical activity. Zebrafish were then exposed to low-dose radiation (0.3Gy) to simulate radiation exposure on long-term space missions. Transcriptomic analysis found that radiation exposure led to an upregulation of inflammatory and immune signatures and a differentiation and regeneration phenotype driven by STAT3 and MYOD1 transcription factors. In addition, DNA repair processes were downregulated in the muscle two days’ post-irradiation. The effects of hypothermia led to an increase in mitochondrial translation including genes involved in oxidative phosphorylation and a downregulation of ex-tracellular matrix and developmental genes. Upon radiation exposure, increases in endoplasmic reticulum stress genes were observed in a torpor+radiation group with downregulation of im-mune-related and ECM genes. Exposing hypothermic zebrafish to radiation also resulted in a downregulation of ECM and developmental genes however, immune/inflammatory related pathways were downregulated in contrast to that observed in the radiation only group. A cross-species comparison was performed with the muscle of hibernating Ursus arctos horribilis (brown bear) to define shared mechanisms of cold tolerance. Shared responses show an upregula-tion of protein translation and metabolism of amino acids, as well as a hypoxia response with the shared downregulation of glycolysis, ECM, and developmental genes.

overall_design: Transcriptomic analysis of zebrafish muscle assessing the protective effects of induced torpor on the harmful effects of low dose radiation

first: Gary

last: Hardiman

first: Ian

last: Overton

first: Sherine

last: Chan


title: IFNγ, TGF-β, and time are associated with conserved myeloid diversity in tuberculosis granulomas

city: Cambridge

first: Bryan

last: Bryson

address: 77 Massachusetts Avenue

institute: Massachusetts Institute of Technology

summary: We profiled human monocytes and monocyte-derived macrophages under various cytokine combinations across timepoints to understand myeloid dynamics in tuberculosis.

overall_design: RNA-sequencing (prime-seq) was performed on primary monocytes and monocyte-derived macrophages that were stimulated with ligands

first: Joshua

last: Peters

first: Alex

last: Shalek


title: Transcriptional profiling reveals high sensitivity to social vs. metabolic stress in frontal cortex of male mice

city: Gold Coast

first: Kevin

middle: John

last: Ashton

state: QLD

address: University Drive

department: Health Sciences & Medicine

institute: Bond University

summary: Chronic psychosocial and metabolic stressors disrupt affective state and drive frequently co-morbid mood and cardio-metabolic disorders. However, central mechanisms underlying dysregulation of mood and metabolic homeostasis await definition. Behavioural and transcriptome-wide influences of chronic social and metabolic stresses were explored (testing for shared and unique mechanistic themes in male C57Bl/6 mice subjected to: chronic social stress (CSS) - social isolation for 7 wks + twice daily social confrontation in final 20 days; type 2 diabetes (T2D) - 75 mg.kg-1 streptozotocin/21 wk high-fat diet (43.2% kcal as fat); or control conditions. Frontal cortex (FC) was profiled via RNAseq (Illumina NovaSeq 6000 Sequencing System, 2x107 paired-end reads/sample). CSS induced anxiety-like behaviour together with anhedonia (reduced sucrose preference), in association with relative weight loss. T2D mice exhibited anxiety-like behaviour (reduced locomotion and thigmotaxis in open field) in association with modest (+20-30%) weight gain and hyperglycaemia, and 65-80% elevations in fasting insulin and insulin-resistance (HOMA-IR). The FC transcriptome was particularly sensitive to CSS, with 640 (316 down/324 up) differentially expressed genes (DEGs) from 15,097 detected (FDR<0.05, P<0.001). Gene-set enrichment analysis (GSEA) identified 222 Biological Processes and 25 Reactome Pathways sensitive to CSS. Most significant themes centred upon up-regulation of: growth/remodelling (axonogenesis, epithelial growth/morphogenesis, angiogenesis, cell junction, synapse and ECM organisation, brain/limb/heart/gland/eye development), Ras signalling and growth factor response genes; and down-regulation of: ATP metabolism, mitochondrial and RNA processing pathways. In contrast, the FC transcriptome was relatively insensitive to metabolic stress, however 107 DEGs (71 down/36 up) and 187 Biological Processes/5 Reactome Pathways were identified using less conservative criteria (FDR<0.10, un-corrected P<0.01). Despite little to no overlap in individual genes, GSEA indicates ~25% of pathway responses are shared, including organ development/morphogenesis (though not ATP metabolism/mitochondrial) processes. In summary, FC appears particularly responsive to social rather than metabolic stress, characterised by repression of mitochondrial metabolism together with adaptive induction of nerve growth/development. Shared anxiogenesis may involve disturbed neurogenesis/neuroplasticity, with depressive outcomes reflecting additional mitochondrial dysfunction.

overall_design: RNA-seq of male mouse frontal cortex subjected to chronic social stress or type 2 diabetes.

first: Tia

last: Griffith

first: Tessa

last: Helman

first: Nicolas

middle: J

last: Stapelberg

first: Aliah

middle: Y

last: Aziz

first: Jamie-Lee

last: Thompson

first: Jake

last: Russell

first: Saba

last: Naghipour

first: Jelena

last: Vider

first: Jason

last: Peart

first: Eugene

last: Du Toit

first: John

last: Headrick


title: Identification of potential non-invasive biomarkers for diagnosing patients with methamphetamine use disorder

city: Daegu

first: Taekwon

last: Son

address: 61, Cheomdan-ro, Dong-gu

department: Korea Brain Bank

country: South Korea

institute: Korea Brain Research Institute

summary: To date, diagnosis of methamphetamine use disorder (MUD) is based primarily on the patient’s self-reports of drug-seeking behaviour and interviews with psychiatrists in the absence of objective biomarkers. As an effective clinical method for diagnosis of MUD is still not available, the development of potential biomarkers for more accurate diagnosis is imperative. Transcription profiling and discovery of biomarkers in the treatment and recovery periods of MUD patients can be used as scientific basis to provide a greater understanding of the disease and to facilitate decisions on whether to continue or not. In this study, RNA sequencing analysis was performed to profile transcripts from hair follicle cells of healthy controls and patients with MUD, and biomarkers were discovered at each transition states to be used to diagnose MUD. This study will present an important information to diagnose MUD using non-invasive biomarkers for human addicts and it will help to develop better pharmacological treatment of MUD in the future.

overall_design: RNA samples were extracted from hair follicles for 33 current patients with methamphetamine use disorders (CPs), 22 former patients with methamphetamine use disorders (FPs) and 30 healthy controls (HCs).

first: Won-Jun

last: Jang

first: Sang-Hoon

last: Song

first: Sooyeun

last: Lee

first: Chul-Ho

last: Jeong


title: Camellia japonica annual transcriptomics

city: Hangzhou

first: Hengfu

last: Yin

state: Zhejiang

address: Daqiao 73

institute: Research Institute of Subtropical Forestry, Chinese Academy of Forestry

summary: We report the transcreptomics analysis of seasonal expressed gene.In total, 81 cultivars are sequenced by the Illumina sequencing experiments to obtain the gene expression profiles.

sample_organism:
Camellia japonica
Camellia azalea

platform_organism:
Camellia japonica
Camellia azalea

overall_design: Comparative gene expression profiling analysis of RNA-seq data for Camellia japonica and Camellia azalea in seasonal expressed genes

first: Zhengqi

last: Fan


title: CscoreTool-M infers 3D sub-compartment probabilities within cell population

city: Baltimore

first: Xiaobin

last: Zheng

state: MD

address: 3520 San Martin Drive

institute: Carnegie Institution for Science

type: Genome binding/occupancy profiling by high throughput sequencing

summary:
Motivation: Computational inference of genome organization based on Hi-C sequencing has greatly aided the understanding of chromatin and nuclear organization in three dimensions (3D). However, existing computational methods fail to address the cell population heterogeneity. Here we describe a probabilistic modeling-based method called CscoreTool-M that infers multiple 3D genome sub-compartments from Hi-C data.
Results: The compartment scores inferred using CscoreTool-M represents the probability of a genomic region locating in a specific sub-compartment. Compared to published methods, CscoreTool-M is more accurate in inferring sub-compartments corresponding to both active and repressed chromatin. The compartment scores calculated by CscoreTool-M also help to quantify the levels of heterogeneity in sub-compartment localization within cell populations. By comparing proliferating cells and terminally differentiated non-proliferating cells, we show that the proliferating cells have higher genome organization heterogeneity, which is likely caused by cells at different cell-cycle stages. By analyzing 10 sub-compartments, we found a sub-compartment containing chromatin potentially related to the early-G1 chromatin regions proximal to the nuclear lamina in HCT116 cells, suggesting the method can deconvolve cell cycle stage-specific genome organization among asynchronously dividing cells. Finally, we show that CscoreTool-M can identify sub-compartments that contain genes enriched in housekeeping or cell-type-specific functions.
Availability: https://github.com/scoutzxb/CscoreTool-M

overall_design: Two replicates of LaminB1 cTSA-seq and corresponding input control

first: Joseph

last: Tran

first: Yixian


title: Next Generation Sequencing Based RNAseq Analysis of lri12 (-/-) mutant zebrafish larvae at 5 dpf

city: Cleveland

first: Takuya

last: Sakaguchi

address: 9500 Euclid Ave.

institute: Cleveland Clinic Foundation

summary: Gene expression profiles in lri12 mutant zebrafish larvae at 5 dpf based on RNAseq data.  This dataset was also used to clone the mutation.

overall_design: Total RNA was isolated from homozygous lri12 mutant and their clutch-mate wild-type larvae at 5 dpf.  Gene expression differences between wild-type and lri12 mutant larvae were determined based on RNAseq data.


title: Loss-of-Function of the Hippo Transducer TAZ Reduces Mammary Tumor Growth through a Myeloid-Derived Suppressor Cell-Dependent Mechanism

city: Buffalo

first: Jianmin

last: Zhang

state: NY

address: Elm & Carlton Streets

institute: Roswell Park Cancer Institute

summary: TAZ, a key component in Hippo pathway, plays an important role in breast tumorigenesis. To understand the entrisic as well as extrinsic role of TAZ in mammary tumors, we performed RNA-seq analysis using mammary tumors generated from sgControl or sgTaz 4T1 cells.

overall_design: sgContol or sgTaz induced mammary tumors were harvested,  RNA were prepared and followed by RNA-seq analyzes.


title: Discovery and Characterization of Second-Generation BET Bromodomain Inhibitor RG6146

city: South San Francisco

first: Simon

last: Hogg

state: California

address: 1000 Gateway Boulevard

department: Oncology Discovery Research

institute: AbbVie

summary: BET Bromodomain inhibition is an epigenetic therapy that is being assessed as an anti-cancer strategy. Herein, we report the structure and activity of RG6146, a novel second-generation clinical grade BET inhibitor that was derived by optimization of the prototypical tool compound JQ1. We demonstrate that RG6146 elicits potent anti-proliferative and pro-apoptotic effects in multiple pre-clinical models of hematologic malignancies, including multiple myeloma (MM) and B-cell lymphoma. We show that the anti-tumor effects of RG6146 correlated with robust modulation of oncogenic transcription that results in suppression of oncogenic transcription factors, such as MYC, as well as direct activation of the intrinsic apoptotic cascade. Subcutaneous or intraperitoneal administration of RG6146 to tumor-bearing mice was well tolerated and led to pronounced anti-tumor responses in both syngeneic and xenograft tumor models, respectively. Finally, we investigated the ability for RG6146 to augment the activity of other targeted therapies in vitro and in vivo, demonstrating clear combination activity with BCL-2 inhibitor Venetoclax and anti-PD-1/PD-L1 immune checkpoint blockade. Taken together, our data demonstrates the therapeutic potential of novel pan-BET inhibitor RG6146 in the treatment of hematologic malignancies and highlights multiple mechanism-based combination strategies to enhance anti-tumor activity.

overall_design: Using RNA-sequencing (RNA-seq) to examine changes in gene expression of Eµ-Myc cells treated in triplicate with BET Bromodomain inhibitors, JQ1 or RG6146, or DMSO vehicle control.


title: GMP after hindlimb ischemia

city: Pittsburgh

first: Partha

last: Dutta

state: PA

address: 200 Lothrop Street

department: Medicine

institute: University of Pittsburgh

summary: We perfomed RNA seq on GMP isolated from mice with sham (control) and hindlimb ischemia (HI) surgery.

overall_design: We sorted bone marrow GMP from mice with sham and HI directly in RNA extraction buffer. Total RNA was extracted using Picopure RNA extraction kit (Applied Biosystems). Extracted RNA was sent to the sequencing core.


title: Stability and transcriptomic study of C12orf35 site-specific integrated CHO cell line

first: Hui

last: Wang

state: China

address: Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, China

department: School of Pharmacy

institute: Shanghai Jiao Tong University

summary:
Background: Chinese hamster ovary (CHO) cells are the most widely used mammalian host for recombinant protein production. The primary production method is to construct stable, high-yielding cell lines to provide high-quality, low-cost products. The key to optimizing recombinant protein production is to modify engineered cell lines to obtain better growth, expression, or product quality characteristics. Site-specific integration technology can build monoclonal cell lines with ideal stability, yield, and epigenetics by integrating transgenes at stable transcriptional hotspots, becoming a potential tool for constructing genetically engineered cell lines. The previous study screened the C12orf35 site of CHO cells and built an engineered cell line expressing a mAb by CRISPR/Cas9. While the mechanism of site-specific integration of transgenes to achieve high-efficiency expression also needs to be further studied. In this study, we used the extracellular domains of CLL1 and CD33 as model proteins to construct engineered cell lines integrating at C12orf35. Then we studied the growth, expression, and passage stability of these cell lines and conducted transcriptomic studies.
Method: In this study, the transgenes CLL1 and CD33 were site-specifically integrated into the C12orf35 site of the CHO-S cell by CRISPR/Cas9 technology. To obtain stable and high-yielding cell lines, we screened and identified monoclonal cell lines by 5’/3’ junction PCR, out-out PCR, and Western blot. Then we compared the growth characteristics of CLL1 and CD33 monoclonal cell lines with wild-type CHO-S cell lines to investigate the growth characteristics. We studied the protein yield and affinity of CLL1 and CD33 cell lines through protein purification, BCA quantification, and ELISA. In addition, we assessed the stability of monoclonal cell lines in long-term culture by studying the growth characteristics, protein yield, and protein quality of early (5th-10th passage) and late (about 20th-25th passage) cells. We performed transcriptomic studies on cell lines with different transgenes, including CLL1, CD33, and anti-PD-1 mAb, inserted at C12orf35. We analyzed the differential genes, GO enrichment, and KEGG enrichment of cell lines hoping to explore the reasons for the phenotypic changes of cell lines from the transcriptional level, as well as the high expression mechanism of C12orf35 site-specific integration cell lines.
Results:Using the site-specific integration technology mediated by CRISPR/Cas9, we successfully built CLL1 and CD33 monoclonal cell lines integrated at the C12orf35 site. We evaluated the cell growth characteristics and protein expression properties. The results showed that the insertion of different transgenes at the C12orf35 site had no specific effect on the growth state of the cells. The proteins yields were about 120 mg/L and 160 mg/L, respectively. And the EC50 values of CLL1 and CD33 with the corresponding antibodies reached about 0.36 μg/mL and 0.1 μg/mL, respectively. In addition, the above indicators had similar properties between the 5th and 20th generations, indicating that the specific integration at C12orf35 can achieve both high expression of the target protein and production stability.  Transcriptomic analysis showed that the integration of transgenes at the C12orf35 site of CHO cells mainly induced genes in the GO term of “Regulation of transcription, DNA-templated” differentially expressed. Further analysis screened that ATF4 and multiple ZFPs family members were significantly up-regulated. ATF4 and ZFPs are related to gene transcription and protein synthesis, which may be the mechanism of the stable and high expression of the cell lines. Besides, differential gene analysis showed that Car4 and CXCL12 were significantly up- and down-regulated in CD33 cells, respectively. And KEGG enrichment showed that Wnt, PI3K/AKT, and JAK/STAT pathways related to cell proliferation and apoptosis were significantly enriched in CD33 cells. These genes and pathways may be related to the growth state of CD33.   In summary, this paper studied the growth characteristics, protein expression characteristics, and stability of the C12orf35 site-specific integration of recombinant CHO cell lines. Combined with transcriptomic analysis, this paper explored the stable and high expression mechanism of these cell lines, hoping to provide a theoretical reference for the subsequent construction and optimization of high-expression stable cell lines.

overall_design: RNA-seq of C12orf35 site-specific integration of recombinant CHO cell lines

first: Huili

last: Lu


title: Comparison between CD103+ cDC1s from IL-33-treated Flt3L-BMDCs and GM-CSF-treated Flt3L-BMDCs

status: Public on May 30 2023

city: Suwon

first: Myeong-Ho

last: Kang

address: 2066, Seobu-ro

institute: Sungkyunkwan university

summary:
To assess genotypic differences between IL-33-induced CD103+ cDC1s and GM-CSF-induced CD103+ cDC1s
IL-33 or GM-CSF was treated at 5 ng/ml on the day 5 of Flt3L-BMDC generation and then the cells were incubated for an additional 5 days
Then, we performed RNA sequencing of CD103+ cDC1s isolated from IL-33 or GM-CSF-treated Flt3L-BMDCs

overall_design: Comparative gene expression profiling analysis of RNA-seq data for CD103+ cDC1s isolated from IL-33 or GM-CSF-treated Flt3L-BMDCs (FL-33, FL-GM).

first: Yong-Soo

last: Bae


title: Sequencing of the whole transcriptome of papillary thyroid cancer and lymph node metastases

city: Changsha

first: Pei

last: Chen

state: Hunan

address: Xiangya Road No.88

institute: Xiangya Hospital, Central South University of China

summary: This data was gathered from three patients who had papillary thyroid carcinoma with paired lymph node metastases. The goal of this study was to determine critical genes and pathway that influence the occurrence of lymph node metastasis in PTC patients. A total of 6 samples were analyzed, resulting in an average of 10.16 GB of data per sample. 1,967 new genes were predicted; 19,430 genes were detected as expressed, of which 17,890 were known genes and 1,540 were predicted new genes; 27,495 new transcripts were found, of which 15,846 belonged to known genes. There were a total of 27,495 novel transcripts discovered, with 15,846 belonging to new variable splice isoforms of known protein-coding genes, 1,967 to transcripts of new protein-coding genes, and 9,682 to long-stranded non-coding RNAs.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for primary tumor and lymph node metastasis of papillary thyroid cancer (PTC).

first: Shi

last: Chang


title: C5a-licensed phagocytes drive sterilizing immunity during systemic fungal infection

city: Bethesda

first: Behdad (Ben)

last: Afzali Khoshkbijari

address: 10 Center Drive, 10/8D03

department: Kidney Diseases Branch

institute: National Institutes of Diabetes, Digestive, and Kidney Diseases

summary: Systemic candidiasis is a common, high-mortality, nosocomial fungal infection. Unexpectedly, it has emerged as a complication of anti-complement C5-targeted monoclonal antibody treatment, indicating a critical niche for C5 in antifungal immunity. We identified transcription of complement system genes as the top biological pathway induced in candidemic patients and as predictive of candidemia. Mechanistically, C5a-C5aR1 promoted fungal clearance and host survival in a mouse model of systemic candidiasis by stimulating phagocyte effector function and ERK- and AKT-dependent survival in infected tissues. C5ar1 ablation rewired macrophage metabolism downstream of mTOR, promoting their apoptosis and enhancing mortality through kidney injury. Besides hepatocyte-derived C5, local C5 produced intrinsically by phagocytes provided a key substrate for antifungal protection. Lower serum C5a concentrations or a C5 polymorphism that decreases leukocyte C5 expression correlated independently with poor patient outcomes. Thus, local, phagocyte-derived C5 production licenses phagocyte antimicrobial function and confers innate protection during systemic fungal infection.

overall_design: RNAseq of C. albicans infected wild-type and C5ar1 knockout of mouse kidney Neutrophils and Macrophages

first: Jigar

middle: V

last: Desai

first: Dhaneshwar

last: Kumar

first: Tilo

last: Freiwald

first: Daniel

last: Chauss

first: Melissa

middle: D

last: Johnson

first: Michael

last: Abers

first: Julie

last: Steinbrink

first: John

last: Perfect

first: Barbara

last: Alexander

first: Vasiliki

last: Matzaraki

first: Brendan

last: Snarr

first: Marissa

last: Zarakas

first: Vasileios

last: Oikonomou

first: Lakmali

last: Silva

first: Raju

last: Shivarathri

first: Emily

last: Beltran

first: Luciana

last: Demontel

first: Luopin

first: Jean

middle: K

last: Lim

first: Dylan

last: Launder

first: Heather

last: Conti

first: Muthulekha

last: Swamydas

first: Micah

middle: T

last: McClain

first: Niki

last: Moutsopoulos

first: Majid

last: Kazemian

first: Mihai

last: Netea

first: Vinod

first: Jörg

last: Köhl

first: Claudia

last: Kemper

first: Behdad

last: Afzali

first: Michail

last: Lionakis


title: Schwann Cells Shape Tumor Cells and Cancer-Associated Fibroblasts in the Pancreatic Ductal Adenocarcinoma Microenvironment [ST]

city: Shanghai

first: Meilin

last: Xue

state: Shanghai

address: 197 Ruijin 2nd Road

institute: Ruijin Hospital, Shanghai Jiao Tong University School of Medicine

summary: Neuropathy is a feature more frequently observed in pancreatic ductal adenocarcinoma (PDAC) than other tumors. Schwann cells, the most prevalent cell in peripheral nerves, migrate toward tumor cells and associate with poor prognosis in PDAC. To unveil the effects of Schwann cells on the neuro-stroma niche, single-cell RNA-sequencing and microarray-based spatial transcriptome analysis of PDAC tissues were performed. Results suggested that Schwann cells may drive tumor cells and cancer-associated fibroblasts (CAFs) to more malignant subtypes: basal-like and inflammatory CAFs (iCAFs), respectively. Moreover, in vitro and in vivo assays demonstrated that Schwann cells enhanced the proliferation and migration of PDAC cells via Midkine and promoted the switch of CAFs to iCAFs via interleukin-1a. By Schwann cells condition medium, tumor cells together with iCAFs accelerate PDAC progression. Thus, we revealed, for the first time, that Schwann cells induce malignant subtypes of tumor cells and CAFs in the PDAC milieu.

overall_design: spatial transcriptome  was performed in 4 PDAC patient tumor samples with neuropathy.

first: Youwei

last: Zhu

first: Yongsheng

last: Jiang

first: Lijie

last: Han

first: Minmin

last: Shi

first: Rui

last: Su

first: Liwen

last: Wang

first: Cheng

last: Xiong

first: Chaofu

first: Ting

first: Dong

last: Wu

first: Yizhi

last: Cao

first: Lei

last: Dong

first: Fan

last: Bai

first: Shulin

last: Zhao

first: Xiaxing

last: Deng

first: Chenghong

last: Peng

first: Hongwei

last: Li

first: Jianjun

last: Chen

first: Baiyong

last: Shen

first: Lingxi

first: Hao


title: Schwann Cells Shape Tumor Cells and Cancer-Associated Fibroblasts in the Pancreatic Ductal Adenocarcinoma Microenvironment [scRNA-seq]

first: Meilin

last: Xue

overall_design: Single cell RNA sequence was performed in 4 PDAC patient tumor samples after isolation of non-immune cells by CD45 microbeads using HiSeqXten (Illumina, San Diego, CA).

first: Youwei

last: Zhu

first: Yongsheng

first: Lijie

first: Minmin

first: Rui


title: Fc-FcgR interactions shift alveolar macrophage metabolism to promote Mycobacterium tuberculosis restriction in mice

first: Bryan

middle: B

last: Bryson

state: MA

summary: The mechanistic basis for humoral immune control of Mtb remains poorly understood. We use single-cell RNA-sequencing to explore the impact of antibody treatment on cellular states in vivo.

overall_design: Using single-cell RNA-sequencing, we profile CD45+ and infected Mtb+ cells in B6 mice 5 days post-infection following treatment with different antibodies.

first: Patricia

last: Grace

first: Joshua

last: Peters

first: Sarah

last: Fortune

first: Galit

last: Alter


title: Chromatin architecture is indirectly regulated by CDK7 transcriptional activity

first: Ruth

last: Keri

state: Ohio

address: 9620 Carnegie Ave

summary: Cyclin Dependent Kinase 7 (CDK7) is the core catalytic subunit of Cyclin Activating Kinase (CAK), a complex that has dual roles in cell cycle progression and transcription. While several CDK7 inhibitors are efficacious in preclinical models of cancer and have entered clinical trials, the mechanism(s) by which CDK7 promotes proliferation and cell viability is not well understood. Using triple negative breast cancer (TNBC) as a model, we found that inhibiting CDK7, either genomically or pharmacologically, induces mitotic dysfunction. Live and static cell imaging revealed that CDK7 inhibition prolongs mitosis and induces chromatin bridge formation, DNA double strand breaks, and abnormal nuclear features, all of which are indicative of mitotic catastrophe and chromosome instability. Transcriptome analyses revealed that CDK7 is essential for maintaining condensin complex gene expression, suggesting that CDK7 may sustain chromatin configuration, a role that extends beyond its impact on super-enhancers. Indeed, inhibiting CDK7 alters chromatin architecture consistent with condensin disruption. Confirming the importance of condensin regulation by CDK7, genetic suppression of a core subunit of this complex, structural maintenance of chromosome 2 (SMC2), phenocopies CDK7 inhibition. We report an undescribed role of CDK7 in maintaining chromatin structure and chromosome stability, as well as promoting proper mitoses, by sustaining condensin expression.

overall_design: Hi-C study MDA-MB-231 cells treated with DMSO (Vehicle, Control) or THZ1 (CDK7 inhibitor, drug) in technical replicates.

first: Katrina

last: Piemonte

last: M. Webb

first: Jessica

last: Bobbitt

first: Parth

last: Majmudar

first: Leslie

last: Cuellar-Vite

first: Benjamin

middle: L

first: Nicholas

middle: C

last: Latina

first: Darcie

last: Seachrist


title: Rna-seq profiling of epigenetic regulator Phf2 in neural stem cells

city: Singapore

first: Oleg

last: Grinchuk

address: 61 Biopolis Dr, Proteos

country: Singapore

institute: IMCB

summary: Important hallmark of neurogenesis is activation of quiescent neural stem cells (NSC) in dentate gyrus. Precise mechanisms of NSC activation are not fully clear. In the current study we interrogate the role of homeodomain finger protein 2 (Phf2) in this process. Here we performed mouse transcriptome RNA-seq profiling of epigenetic regulator Phf2 in neural stem cells without and with knock-down in order to uncover mechanistic components/pathways affecting protein translational capacity in activated NSC.

overall_design: RNA-seq from neural stem cell specimens following treatment either with non-targeting or targeting shRNA.

first: Ker

last: Lok

first: Derrick

last: Ong


title: Interplay between PML NBs and HIRA for H3.3 deposition on transcriptionally active interferon-stimulated genes

city: Lyon

first: Thomas

last: Simonet

address: Faculté de Médecine Lyon Est, 8 Avenue Rockefeller

country: France

institute: Université de Lyon

summary: Promyelocytic Leukemia Nuclear Bodies (PML NBs) are nuclear membrane-less organelles physically associated with chromatin underscoring their crucial role in genome function. The H3.3 histone chaperone complex HIRA accumulates in PML NBs upon senescence, viral infection or IFN-I treatment in primary cells. Yet, the molecular mechanisms of this partitioning and its function in regulating histone dynamics have remained elusive. Here, by using specific siRNAs and protein Affimers, we identify intermolecular SUMO-SIM interactions as an essential mechanism for HIRA recruitment in PML NBs. In addition, we demonstrate that HIRA localization in the nuclear bodies is intimately linked to the presence of a soluble pool of H3.3-H4 dimers inside PML NBs,  that is not found in cancer cells. Transcription inhibition prevents HIRA accumulation in PML NBs underscoring the importance of transcriptional activity to drive HIRA through PML NBs. Finally, in the context of inflammatory responses, HIRA and PML are necessary for the prolonged H3.3 deposition at the transcriptional end sites of interferon-stimulated genes (ISGs), well beyond the peak of transcription. We thus propose that HIRA partitioning in PML NBs is essential to regulate H3.3 deposition on transcriptionally active regions.

overall_design: H3.3 ChIP-seq on human primary BJ cells treated with siLuc, sILuc+IFN, siHIRA+IFN or siPML+IFN

first: Kleijwegt

last: Constance

first: Corpet

last: Armelle

first: Lomonte

last: Patrick

first: Simonet

last: Thomas


title: Identification of the factors from IL-33-primed CD11c- cells of Flt3L-BMDCs on day 5

first: Myeong-Ho

last: Kang

summary:
IL-33 induced immunogenic FCGR3+CD103+cDC1s via IL-33-primed CD11c- cells
To find IL-33-induced factors from IL-33-primed CD11c- cells
We performed RNA sequencing of IL-33-treated WT or ST2-KO CD11c- cells from Flt3L-BMDCs on day 5.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for IL-33-treated CD11c- cells isolated from WT or ST2-KO Flt3L-BMDCs on day 5 (WT-con, WT-IL-33, KO-con, KO-IL-33)

first: Yong-Soo

last: Bae


title: IGF2BP1 induces neuroblastoma via a druggable feedforward loop with MYCN promoting 17q oncogene expression

city: Halle (Saale)

first: Danny

last: Misiak

address: Kurt-Mothes-Str. 3a

department: Molecular Cell Biology

country: Germany

institute: Martin Luther University Halle-Wittenberg

type: Genome variation profiling by high throughput sequencing

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

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Refer to individual Series


title: Pathways Related to NLRP3 Inflammasome Activation Induced by Gold Nanorods

status: Public on May 29 2023

city: Bilthoven

first: Jeroen

last: Pennings

address: A. van Leeuwenhoeklaan 9

country: Netherlands

institute: Natl. Inst. Public Health & Environment

summary:
The immune system may respond to engineered nanomaterials (ENM) through inflammatory reactions. The NLRP3 inflammasome responds to a wide range of ENM, and its activation is associated with various inflammatory diseases. The objective of the study was to compare the effects of gold ENM of different shapes on NLRP3 inflammasome activation and related signalling pathways.
Differentiated THP-1 cells (wildtype, ASC- or NLRP3-deficient), were exposed to PEGylated gold nanorods, nanostars, and nanospheres. Exposed cells were subjected to gene expression analysis. Nanorods, but not nanostars or nanospheres, showed NLRP3 inflammasome activation. ASC- or NLRP3-deficient cells did not show this effect. Gold nanorod-induced NLRP3 inflammasome activation was accompanied by downregulated sterol/cholesterol biosynthesis, oxidative phosphorylation, and purinergic receptor signalling. In conclusion, the shape and surface chemistry of gold nanoparticles determine NLRP3 inflammasome activation.

overall_design: 24 samples, for 8 experimental groups including controls, 3 replicates per groups

first: Sylvie

last: Remy


title: Dietary tryptophan and circadian rhythms in the Liver

city: Irvine

first: Muntaha

middle: Fatima

last: Samad

state: CA

address: Campus Dr

department: CS

institute: UC Irvine

summary: Mice were fed a normal chow diet or a tryptophan depleted diet for two weeks under normal 12-hr light/dark cycles (LD) or in constant darkness (DD). Mice were sacrificed every 4th hour over the 24-hr circadian cycle. The liver was harvested and RNA was isolated using a standard TRIZOL protocol. The data suggest that dietary tryptophan is an important component of the diet regulating circadian homeostsis.

overall_design: Four groups in total: mice fed normal chow or tryptophan depleted diet, exposed to LD cycles or DD. Mice were collected every 4th hour over the circadian cycle, i.e. 6 time-points. Three mice were used from each group and time point. The RNA was sequenced in the livers of the mice.

first: Paul

last: Petrus

first: Marlene

last: Cervantes

first: Pierre

last: Baldi


title: Deletion of nucleoporin Seh1 impaired neurogenesis through transcriptional regulation (ChIP-Seq)

city: shanghai

first: Ximing

last: Nian

address: Chongqing Nanlu 227

summary: Nucleoporin Seh1 and chromodomain helicase DNA binding protein 4 have been involved in gene regulation. To dissect  direct regulated genes, we performed chromatin immunoprecipitation DNA-sequencing (ChIP-seq) for nucleoporin Seh1 or chromodomain helicase DNA binding protein 4   in neural stem cells.

overall_design: We performed ChIP-seq using neural stem cells at proliferation stage.

first: Liang

last: Zhang

first: Zhixiong

last: Liu

first: Wenxiu

last: Dai


title: Dietary tryptophan and circadian rhythms

summary: Mice were fed a normal chow diet or a tryptophan depleted diet for two weeks under normal 12-hr light/dark cycles (LD) or in constant darkness (DD). Mice were sacrificed every 4th hour over the 24-hr circadian cycle. The suprachiasmatic nucleus (SCN) was harvested and RNA was isolated using a standard TRIZOL protocol. The data suggest that dietary tryptophan is an important component of the diet regulating circadian homeostsis.

overall_design: Four groups in total: mice fed normal chow or tryptophan depleted diet, exposed to LD cycles or DD. Mice were collected every 4th hour over the circadian cycle, i.e. 6 time-points. Three mice were used from each group and time point. The RNA was sequenced in the SCNs of the mice.


title: Loss of phospholipase PLAAT3 causes lipodystrophy due to impaired PPAR𝛾 signaling

city: Ghent

first: Bart

last: Dermaut

state: 10kb upstream, TSS, 10kb downstream

address: C. Heymanslaan 10

institute: Ghent University

summary: PLAAT3 is a phospholipid modifying enzyme predominantly expressed in neural and white adipose tissue (WAT). We identified loss-of-function variants in human PLAAT3 as the cause of a severe lipodystrophy syndrome associated with neurological with features. To identify the underlying molecular pathways associated with PLAAT3 deficiency, we performed RNA sequencing and differential gene expression analysis on WAT specimens from Plaat3 knockout mice.

overall_design: We obtained 15 inguinal WAT samples from 11-week-old mice.  Seven Plaat3-/- specimens (3 males, 4 females) were compared to 8 Plaat3+/- littermates (4 males, 4 females) were included.

first: Nika

last: Schuermans


title: Analysis of Gene Expression Profile Alterations During NBXH Treatment for Tuberculosis

city: beijing

first: yourong

last: yang

state: bj

address: No. 17, Heishanhu, Haidian District, Beijing

institute: Tuberculosis Institute, Eighth Medical Center of the General Hospital of the Chinese People's Liberation Army

summary: To further investigate the therapeutic potential of NBXH in treating tuberculosis, we employ whole genome microarray expression profiling as a discovery platform. The study aimed to explore the impact of NBXH treatment on the gene expression profile of tuberculosis-infected animal models. The animal models were treated with high, medium, and low doses of NBXH. Following three months of treatment, PBMCs from each treatment group were used for whole genome microarray expression profiling analysis, alongside a control group. With a screening criterion of P <0.05 and an absolute log2FC value >1, 3454 up-regulated and 3597 down-regulated DEGs were respectively identified in the gene expression profiles of the mouse TB model treated with NBXH.

overall_design: Once the tuberculosis infection model had been established, the tuberculosis-infected animal models underwent treatment with high, medium, and low doses of NBXH for three months. Gene expression profiles in PBMCs were then measured, and each group underwent three independent experiments.

first: Xueqiong

last: Wu

first: Yan

last: Liang

first: Yourong

last: Yang

first: Junxian


title: Deficiency of MiR-409-3p Improves Myocardial Neovascularization and Function Through the Modulation of DNAJB9/p38 MAPK signaling

city: BOSTON

first: BASAK

last: ICLI

address: 800 Washington St Box 80

department: MOLECULAR CARDIOLOGY RESEARCH INSTITUTE

institute: TUFTS MEDICAL SCHOOL

summary:
We investigated the metabolic regulation of miR-409-3p in post-infarct angiogenesis.
We then performed gene expression profiling analysis using data obtained from RNA-seq of miR-409-3p or Non-specific control transfected HUVECs under palmitate treatment.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for HUVECs which are transfected with miR-409-3p or Non-specific control and treated with palmitate. 4 technical replicates are pooled for each total-RNA samples.

first: Basak

last: Icli

first: Furkan

last: Bestepe


title: MicroRNA-23b functions as a tumor suppressor by targeting Ras-related protein RRAS2 in cutaneous squamous cell carcinoma

city: Uppsala

first: Andor

last: pivarcsi

state: Uppland

country: Sweden

institute: Uppsala University

summary:
Analysis of deregulated genes upon stable overexpression of MiR-23b in UT-12 cell line by whole transcriptome microarray
MicroRNAs (miRNAs) regulate gene expression at the posttranscriptional level. Here, we report that miR-23b - an evolutionarily conserved miRNA abundantly expressed in keratinocytes - is downregulated in cSCCs and to a lesser extent in precancerous lesions. We used microarrays to detail the global programme of gene expression upon miR-23b overexpressing SCC cell lines.

overall_design: UT-SCC-12a cells were transduced with lentiviral particles to stably overexpress miR-23b or scrambled RNA (n=5) for RNA extraction and hybridization on Affymetrix microarrays. We performed transcriptomic analysis to dectect differentially expressed genes on miR-23b over-expressing vs Control.

first: Jonathan

last: Elton

last: Pivarcsi


title: Experimental hepatic encephalopathy causes early but sustained glial transcriptional changes

city: Zwijnaarde

first: Roosmarijn

middle: E.

last: Vandenbroucke

state: Gent

address: Technologiepark-Zwijnaarde 71

department: VIB Center for Inflammation Research

institute: VIB-UGent

summary: Hepatic encephalopathy (HE) is a common complication of liver cirrhosis, associated with high morbidity and mortality, for which no brain-targeted therapies exist at present. The interplay between hyperammonemia and inflammation is thought to drive HE development. As such, astrocytes, the most important ammonia-metabolizing cells in the brain, and microglia, the main immunomodulatory cells in the brain, have been heavily implicated in HE development. As insight into cellular perturbations driving brain pathology remains largely elusive, we aimed to investigate cell-type specific transcriptomic changes in the HE brain. In the recently established mouse bile duct ligation (BDL) model of HE, we performed RNA-Seq of sorted astrocytes and microglia at 14 and 28 days after induction. This revealed a marked transcriptional response in both cell types which was most pronounced in microglia. In both cell types, pathways related to inflammation and hypoxia, mechanisms commonly implicated in HE, were enriched. Additionally, astrocytes exhibited increased corticoid receptor and oxidative stress signaling, whereas microglial transcriptome changes were linked to immune cell attraction. Accordingly, both monocytes and neutrophils accumulated in the BDL mouse brain. Time-dependent changes were limited in both cell types, suggesting early establishment of a pathological phenotype. While HE is often considered a unique form of encephalopathy, astrocytic and microglial transcriptomes showed significant overlap with previously established gene expression signatures in other neuroinflammatory diseases like septic encephalopathy and stroke, suggesting common pathophysiological mechanisms. Our dataset identifies key molecular mechanisms involved in preclinical HE and provides a valuable resource for development of novel glial-directed therapeutic strategies.

overall_design: Comparative gene expression profiling analysis of RNA-seq data to study the astrocyte and microglial transcriptomic response to chronic bile duct ligation

first: Wouter

last: Claeys

first: Clint

last: De Nolf


title: Schwann Cells Shape Tumor Cells and Cancer-Associated Fibroblasts in the Pancreatic Ductal Adenocarcinoma Microenvironment

first: Meilin

last: Xue

overall_design: Bulk-RNA sequence was performed in tumor cells and CAFs with or without Schwann cells condition medium (CM) treatment

first: Youwei

last: Zhu

first: Yongsheng

last: Jiang

first: Lijie

last: Han

first: Minmin

last: Shi

first: Rui

last: Su

first: Liwen

last: Wang

first: Cheng

last: Xiong

first: Chaofu

first: Ting

first: Dong

first: Yizhi

last: Cao

first: Lei

last: Dong

first: Fan

last: Bai

first: Shulin

last: Zhao

first: Xiaxing

last: Deng

first: Chenghong

last: Peng

first: Hongwei

last: Li

first: Jianjun

last: Chen

first: Baiyong

last: Shen

first: Lingxi

first: Hao


title: IL-22+ T cells protect intestinal crypts from bacterial invasion and epithelial damage.

city: Birmingham

first: Min

last: Gao

state: AL

address: 1900 University Blvd, THT Building Suite #130G

institute: University of Alabama at Birmingham

summary: Three subsets of intestinal epithelial cells (IECs) (P9, Surface; P10, Large Crypt; P11, Small Crypt) were isolated from Naïve and Day 9 C.r.-infected Cntrl (Cre-) and CD4 cre+. Il22 floxed mice (CD4 cKO)

overall_design: IECs from middle/distal colon regions (pooled from 2-4 mice per sample) were isolated with DTT, followed by EDTA, and then sorted into three populations (All were CD45-LD-EpCAM1+): CEACAM1Hi Surface, CEACAM1Int/lo SSCHi Large Crypt, and CEACAM1- FSClo SSClo Small Crypt cells

first: Carlene

last: Zindl

first: Steve

last: Witte

first: Robin

last: Hatton

first: Casey

last: Weaver


title: Integrated transcriptomic and metabolomic analysis reveals arginine-citrulline gene-compound network is critical for severe adhesive capsulitis progression

first: Kang

last: Liu

address: Changhai Road

department: Orthopedics

institute: First Affiliated Hospital of the Navy Medical University

summary: Adhesive capsulitis (AC) affects 2–5% of the population worldwide. Patients with severe AC fail to regain a complete range of movement and experience years of shoulder pain. Unfortunately, the underlying mechanism of severe AC remains unclear. Here, we performed an integrated transcriptomic and metabolomic data analysis of serum and tissue samples from patients with severe AC, mild AC, and healthy controls. Pathways related to muscle development and myogenesis positively correlated with severe AC progression. Further, we identified an arginine-citrulline gene-compound network that may play a central role in severe AC. Comparing differentially regulated metabolites from tissue and serum, two phospholipids were recognized as potential serum markers for severe AC. In conclusion, this is the first comprehensive integrated -omics study on severe AC and provides insights into genes and compounds of the arginine-citrulline metabolic pathway that may be potential therapeutic targets for treating AC.

overall_design: We collected tissues and serum from patients with 13 severe and 12 mild AC and 5 healthy controls. We randomly selected 4 patients from each group and sequenced their proliferative synovium and joint capsule tissues.

first: Zi-min

first: Xia-wei

last: Fu


title: CDK7 is Essential for Sustained Expression of the Condensin Complex, Chromatin Compaction, and Maintenance of Chromosomal Stability

city: Cleveland

first: Ruth

last: Keri

state: OH

address: 9500 Euclid Avenue

department: Cancer Biology

institute: Cleveland Clinic Lerner Research Institute

summary: Identifying a mechanism by which CDK7 inhibition promotes genomic stability in TNBC

overall_design: RNA-seq on MDA-MB-231 cell line; ChIP-seq on MDA-MB-468 cell line. Two/Three replicates were analyzed for each experimental condition.

first: Bryan

middle: M

last: Webb


title: KLF2/PPARγ axis contributes to trauma-induced heterotopic ossification by regulating mitochondrial dysfunction

first: Cunyi

last: Fan

address: Yishan Road NO.600, Xuhui district, Shanghai

institute: Department of Orthopedic Surgery, Shanghai Sixth People's Hospital, Shanghai Jiao Tong University

summary: Trauma-induced heterotopic ossification (HO) is one of the most complex disorders after musculoskeletal injury and is characterized by aberrant extraskeletal bone formation. Recent studies have shed light on the critical role of dysregulated osteogenic differentiation in aberrant bone formation. Krupel-like factor 2 (KLF2) and peroxisome proliferator-activated receptor gamma (PPARγ) are master adapter proteins that link cellular responses to osteogenesis; however, their roles and relationships in HO remain elusive.

overall_design: Whole transcript genome sequencing was performed on the soft tissue at the Achilles tendon (provided by Shanghai OE Biotech. Co., Ltd). The steps are as follows: total RNA was extracted and ribosomal RNA was digested using ribo-Zero kit. After interrupt reagent was added to break the RNA into short fragments, and a chain was synthesized with random primer of six bases using the interrupted RNA as template cDNA, and then prepared a two-strand synthesis reaction system to synthesize two-strand cDNA, dUTP instead of dTTP in the synthesis of cDNA, and then one strand containing dUTP was digested by UNG enzyme method, and only the cDNAs of the different junctions of the strand were retained. A chain used kit to purify a strand of cDNA, a strand of purified cDNA was then repaired at the end, an a-tail was added, and sequenced.

first: Ziyang

last: Sun

first: Hang

first: Yuehao

last: Hu

first: Gang

last: Luo


title: The influence of gingipains on latent capacity of B cells

city: Guangzhou

last: Zou

address: Guanghua School of Stomatology, Hospital of Stomatology, Sun Yat-Sen University,

institute: Guangdong Provincial Key Laboratory of Stomatology, Guangzhou, China

summary: Porphyromonas gingivalis (P. gingivalis) is a key pathogen in periodontitis. Our previous study indicated that periodontitis induced by P. gingivalis increases the percentage of CD19+ B cells, Th17, Treg, gMDSCs and mMDSCs but decreases the ratio of B10 cells in CIA mice. It’s unclear which virulence factors of P. gingivalis are involved in these processes. Here, our study first indicated that such effects are mainly resulted from the undenatured proteins other than the DNA, RNA or LPS of P. gingivalis. As gingipains are enzymes and virulence factors which play vital role in the progression in periodontitis through affecting innate and adaptive immune system, we then compared the influence of the wild-type strain of P. gingivalis (ATCC33277) with its isogenic gingipain-null mutant (△K△RAB) on B cells. The results showed that B cells infected with △K△RAB exhibited increased levels of IL-6 and others cytokines (IL-1β，IL-23) involve in Th17 differentiation compared to wild-type strain, also the frequency of IL-10 producing regulatory B cells (B10). Furthermore, the peritonitis induced by △K△RAB enhanced the proportion of B10 and Th17 compared with treated with ATCC33277. Cumulatively, this study preliminarily revealed deletion of gingipains affected the antigen presentation of B cell that promoted B cells express the cytokines which promoted T cells toward Th17 and the secretion immunosuppressive cytokines of B cells that enhanced the frequency of B10 which implicated gingipains are vital in altering B cell function to participated immune response.

overall_design: mRNA profiles of B cells treated with Porphyromonas gingivalis and its gingipain-null-mutant

first: Jianbo


title: Characterizing gene expression changes within the human hair follicle bulb driven by hepatocyte growth factor secreted by perifollicular fat

city: Miami

first: Carina

last: Nicu

state: Florida

address: 1600 NW 10th Ave RMSB 6157 Locator Code R-250

department: Dr Phillip Frost Dept of Dermatology and Cutaneous Surgery

institute: University of Miami

summary: Dermal white adipose tissue (dWAT) has been linked to modulation of murine hair follicle growth and cycling, however no studies have characterized its effects upon human hair growth. Since HGF was detected as a dWAT secretion product in HF-dWAT co-culture, the aim of this study was to characterize changes in gene expression in human dissected hair follicles vs. follicles cultured with surrounding dermal fat treated with/without a neutralizing antibody to HGF. To this end, the hair matrix and pre-cortex in each condition was isolated using laser-capture microdissection and microarray was carried out on the amplified cDNA. We identified 593 genes differentially modulated owing to the dWAT-derived HGF i.e. 301 up-regulated genes and 292 down-regulated genes in the presence of dWAT-secreted HGF and vice versa when HGF is neutralized.

overall_design: Full-length human scalp hair follicles were cultured for 24hr in William's E media in the following conditions: 1) dissected of epidermis and surrounding dermis and adiposse tissue (HF) 2) with 3-5 rows of surrounding dermal adipocytes (HF+dWAT) and 3) HF+dWAT+ neutralizing antibody to human hepatocyte growth factor. Two male donors and two female donors were used. Laser-capture microdissection was carried out on the pre-cortex and hair matrix of each hair follicle, collecting the tissue in RLT buffer with 1% β-mercaptoethanol; RNA extraction was followed by amplification during complementary DNA. This was labelled with a Cy3 probe followed by labelled genomic DNA purification; lastly, a single-channel microarray (Agilent) was performed using Single-channel SurePrint G3 Human Gene Expression 8x60k v2 microarrays.

first: James

last: O’Sullivan

first: Raul

last: Ramos

first: Ludovica

last: Timperi

first: Tiffany

last: Lai

first: Nilofer

last: Farjo

first: Bessam

first: Jenny

last: Pople

first: Ranjit

last: Bhogal

first: Jonathan

last: Hardman

first: Maksim

last: Plikus

first: David

last: Ansell

first: Ralf

last: Paus


title: Profiling the response of scalp hair follicles to short-term treatment with hepatocyte growth factor

summary: Hepatocyte growth factor (HGF) is a well-known promoter of cell proliferation, morphogenesis, migration, angiogenesis and pigmentation. To characterize its effects on human scalp dissected hair follicles, we performed gene expression profiling on RNA isolated from entire hair follicles, comparing the effects of 6hr HGF treatment versus control. 183 genes were differentially up-/down-regulated compared to vehicle control. These genes were involved in a number of different biological pathways suggesting that HGF can have various effects upon human hair follicle function.

overall_design: Gene expression profiles of whole and dissected human scalp hair follicles were compared between vehicle and HGF-treated hairs for 6hr. Donors included three male patients. Samples were then prepared using the Agilent One-Colour Microarray-Based Gene Expression Analysis Protocol; single-channel Agilent SurePrint G3 Human Gene Expression 8x60k v2 microarrays were utilised with Agilent SureHyb hybridization and SureScan High-Resolution Technology.

first: Paus


title: ZRSR1 cooperates with ZRSR2 in regulating splicing of U12-type introns in murine hematopoietic cells II

first: Pushkar

last: Dakle

address: 14 Medical Dr

institute: Cancer Science Institute of Singapore

summary: Recurrent loss-of-function mutations of spliceosome gene, ZRSR2, occur in myelodysplastic syndromes (MDS).  Mutation/loss of ZRSR2 in human myeloid cells primarily causes impaired splicing of the U12-type introns. To investigate further the role of this splice factor in splicing and hematopoietic development, we generated mice lacking ZRSR2. Unexpectedly, Zrsr2-deficient mice developed normal hematopoiesis with no abnormalities in myeloid differentiation evident in either young or ≥1-year old knockout mice. Repopulation ability of Zrsr2-deficient hematopoietic stem cells was also unaffected in reconstitution assays. Myeloid progenitors lacking ZRSR2 exhibited mis-splicing of U12-type introns, however, this phenotype was moderate compared to the ZRSR2-deficient human cells. Our investigations revealed that a closely related homolog, Zrsr1, expressed in the murine hematopoietic cells, but not human, contributes to splicing of U12-type introns. Depletion of Zrsr1 in Zrsr2 KO myeloid cells exacerbated retention of the U12-type introns, thus highlighting a collective role of ZRSR1 and ZRSR2 in murine U12-spliceosome. We also demonstrate that aberrant retention of U12-type introns of MAPK9 and MAPK14 leads to their reduced protein expression. Overall, our findings highlight that both ZRSR1 and ZRSR2 are functional components of the murine U12-spliceosome, and depletion of both proteins is required to model accurately ZRSR2-mutant MDS in mice.

overall_design: ZRSR2 KO

first: Vikas

last: Madan

first: Zeya

last: Cao

first: Weoi

middle: W

last: Teoh

first: Lin

last: Han

first: Pavithra

last: Shyamsunder

first: Siqin

last: Zhou

first: Jia

last: Li

first: Hazimah-Binte

last: Nordin

first: Shi

last: Jizhong

first: Yu

last: Shuizhou

first: Henry

last: Yang

first: Md

middle: Z

last: Hossain

first: Wee

last: Chng

first: H.

middle: P

last: Koeffler


title: Treat diabetic retinopathy in SD rats with Luo-tong formula

status: Public on May 28 2023

city: Beijing

first: chongxiang

last: xue

address: No.5 BeiXianGe Street, Xicheng District, Beijing

institute: Guang'anmen Hospital, China Academy of Chinese Medical Sci-ences

type: Methylation profiling by genome tiling array

summary: DNA methylation profiling of experimental DR model and that treated with LTF. Goal was to determine the methylated differentially expressed genes (MDEGs) in the pathogenesis of DR and the specific molecular mechanisms of LTF on regulating DNA methylation modification.

overall_design: Five-condition experiment, Control vs. DR model vs. CaD  vs. another Chinse formula  vs. LTF . Biological replicates: 3 control replicates, 3  replicates in different groups, respectively.

first: Sha

last: Di

first: Chongxiang

last: Xue


title: Role of the proline-rich disordered domain of DROSHA in intronic microRNA processing

city: Seoul

first: Soomin

last: Son

address: 1, Gwanak-ro, Gwanak-gu

institute: Seoul National University

summary: DROSHA serves as a gatekeeper of the microRNA (miRNA) pathway by processing primary transcripts (pri-miRNAs). While the functions of structured domains of DROSHA have been well-documented, the contribution of N-terminal proline-rich disordered domain (PRD) remains elusive. Here we show that the PRD promotes the processing of miRNA hairpins located within introns. We identified a DROSHA isoform (p140) lacking the PRD, which is produced by proteolytic cleavage. Small RNA sequencing revealed that p140 is significantly impaired in the maturation of intronic miRNAs. Consistently, our minigene constructs demonstrated that PRD enhances the processing of intronic hairpins, but not those in exons. Splice site mutations did not affect the PRD’s enhancing effect on intronic constructs, suggesting that the PRD acts independently of splicing reaction by interacting with sequences residing within introns. The N-terminal regions from zebrafish and Xenopus DROSHA can replace the human counterpart, indicating functional conservation despite poor sequence alignment. Moreover, we found that rapidly evolving intronic miRNAs are generally more dependent on PRD than conserved ones, suggesting a role of PRD in miRNA evolution. Our study reveals a new layer of miRNA regulation mediated by a low-complexity disordered domain that senses the genomic contexts of miRNA loci.

overall_design: Comparative miRNA expression profiling analysis of small RNA-seq data for (1) full-length DROSHA or DROSHA-p140 rescue in HCT116 or HEK293E DROSHA knockout (KO) cells and (2) HCT116 WT cells cultured with media supplemented with 9.1 % or 0.1 % FBS.

first: Baekgyu

last: Kim

first: Jihye

first: V

middle: N


title: Gene expression of Wild Type and SR-A1-/- abdominal aortic tissues after CaPO4-envoked

first: Shuang

state: Beijing

address: Biomedical engineering

department: Biomedical engineering

institute: Beihang university

summary: To further development of our gene expression approach to biodosimetry, we have employed whole genome microarray expression profiling as a discovery platform to identify genes with the potential to distinguish differentially changed genes between wt and SR-A1-/- murine aortas.

overall_design: Capo4 induced gene expression in murine aortas were measured  after 4-week exposure.  Two independent experiments were performed  for each experiment.

first: jianan

last: huang

first: yunlong

last: jiang


title: Comprisons of lung tissue gene expression from AKR and C57BL/6 mice exposed to Cigarette smoke and LPS in ARDS/ALI mice model

city: Providence

first: Sharon

last: Rounds

state: RI

address: 830 Chalkstone Avenue,, Building 35, Room 216

institute: Brown University

summary:
Our previous study showed that AKR and C57BL/6 mice to cigarette smoke increased lipopolysaccharide (LPS)- induced increased lung vascular permeability. Viremic AKR mice were more susceptible to LPS-induced ALI than C57 on prolonged exposure. In this study we compared the global gene expression patterns to determine the genetic basis for the strain dependent responses to cigarette smoke and LPS-induced ALI. We found AKR transcriptomic responses didnot overlap with C57 mice and AKR mice showed increased responses compared to C57 mice.
Global gene expression analysis using microarray was used to dermine the mechanisms of strain dependent responses to cigarette smoking and LPS mediated ALI

overall_design: Two strains of mice (AKR and C57) were exposed to 3 weeks cigarette smoke or room air exposure. Other AKR and C57 mice were exposed to 6 weeks of cigarette smoke or room air exposure, followed by intra-tracheal instillation of LPS in normal saline or  NS alone. The lungs were dissected and homgenized and gene expression responses to cigarette smoke and LPS were determined using microarray.

first: Qing

last: Lu

first: Jamila

middle: H

last: Siamwala


title: The effect of TRIB3 overexpression on mouse hepatocytes

city: Shanghai

first: xin

last: zhang

address: 415 Fengyang Road

institute: Changzheng hospital

summary: To investigate the effect of TRIB3 overexpression on  regulation of lipid metabolism in hepatocytes, we isolated mouse primary hepatocytes from AAV-GFP or AAV-Trib3 mice. We then performed gene expression profiling analysis using data obtained from RNA-seq of two groups of mouse primary hepatocytes from AAV-GFP or AAV-Trib3 mice.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for mouse primary hepatocytes from AAV-GFP or AAV-Trib3 mice.

first: Mengchao

last: Xiao

last: Jiang

first: Lilin

last: Chen


title: The Validation Set for the initial development of the 95GC in 2011.

city: Suita

first: Yoshiaki

last: Sota

state: Osaka

address: Yamadaoka 2-15

department: Breast and Endocrine Surgery

country: Japan

institute: Osaka University

summary: Our aim to develop the 95GC (gene classifier) was to make an accurate diagnostic system using gene expression analysis by means of DNA microarray for prognosis of node-negative and estrogen receptor (ER)-positive breast cancer patients in order to identify a subset of patients who can be safely spared adjuvant chemotherapy. A diagnostic system comprising a 95-gene classifier was developed for predicting the prognosis of node-negative and ER-positive breast cancer patients by using DNA microarray (gene expression) data (n = 549) as the training set and the DNA microarray data (n = 105) as the validation set (= this data set). With the 95-gene classifier we could classify the 105 patients　receiving only endocrine therapy without chemotherapy in the validation set into a high-risk (n = 44) and a low-risk (n = 61) group with 10-year recurrence-free survival rates of 93 and 53%, respectively (P = 8.6e-7). Multivariate analysis demonstrated that the 95-gene classifier was the most important and significant predictor of recurrence (P = 9.6e-4) independently of tumor size, histological grade, progesterone receptor, HER2, Ki67, or GGI. The 95-gene classifier developed by us can predict the prognosis of node-negative and ER-positive breast cancer patients with high accuracy. *Note: This old data has been updated multiple times by others.  Then, there are some differences from the original 2011 paper and unclear points still remain.  Therefore, do not use it for formal analysis aimed at public insurance coverage etc. This is for research purposes only. Please cite this paper when writing a new paper. DOI: 10.1007/s10549-010-1145-z

overall_design: RNA was extracted from 105 fresh frozen tumor samples obtained from radical breast cancer surgery and hybridized on Affymetrix microarrays.

first: Ryo

last: Tsunashima

first: Yasuto

last: Naoi


title: Next Generation Sequencing Facilitates Quantitative Analysis of atrophic gastritis and atrophic gastritis receivng PEEPA-P5 antrum epithelial Transcriptomes

status: Public on May 27 2023

first: li

last: zihao

address: dongchuan road 800

country: China

institute: shanghai jiao tong university

summary: We had one goal to perform this study: Atrophic gastritis and atrophic gastritis receivng PEEPA-P5 antrum epithelial Transcriptomes

overall_design: Comparison of transcriptome of antrum epithelium samples of atrophic gastritis and atrophic gastritis receivng PEEPA-P5 for 2w

first: Ke

last: Li

first: Zihao


title: Small RNA sequencing of urine-derived PS.

city: shenzhen

first: Donge

last: Tang

state: Guangdong

address: NO.1017 Dongmen North, Shenzhen People’s Hospital, Shenzhen, Guangdong

institute: shenzhen people's hospital

summary: To identify potential miRNA–mediated targets associated with osteopetrosis at the genome-wide level, two small RNA libraries and a degradome library were constructed from the PS and normal control human iPSCs (NC-iPSCs) for deep sequencing.

overall_design: To identify potential miRNA–mediated targets associated with Patau syndrom at the RNA transcription level, small RNA libraries was constructed from the blood-derived of PS and normal control.

first: Jieping


title: A non-canonical R-loop resolving function of PIWIL4 maintains the genomic integrity and leukemic growth of AML cells

city: Ulm

first: Shiva

last: Bamezai

address: Albert Einstein Allee 11

institute: Institute for Experimental Cancer Research

summary: PIWIL4 enzyme is required for resolving R-loops and for growth of AML cells. We examine the impact of PIWIL4 knockdown and R-loop accumulation on gene expression in AML cell line THP-1

overall_design: Examination of differential gene expression upon PIWIL4 knockdown in AML cells

first: Christian

last: Buske

first: Vijay

last: Rawat


title: Expression data from human foreskin fibroblasts (HFFs)  infected with Toxoplasma gondii

city: London

first: Philip

last: East

address: Midland Road

institute: The Francis Crick Institute

summary: Through targeted CRISPR screening of the Toxoplasma gondii secretome, we identified GRA57 as a novel secreted effector required for survival in interferon-gamma (IFNg)-activated human foreskin fibroblasts (HFFs). In this experiment we aimed to determine if GRA57 affects the host cell transcriptional response to Toxoplasma, and also whether deletion of GRA57 affects the parasite transcriptome.

overall_design: HFFs were left untreated or pre-treated with IFNg for 24 hours prior to infection, then subsequently left uninfected or infected with wildtype (RH∆Ku80), GRA57 knockout (RH∆GRA57) or GRA57 complemented (RH∆GRA57::GRA57-HA) parasites. All conditions were perfomed in triplicate.  Total RNA was isolated 24 hours post-infection, then RNA-Seq was performed using NovaSeq. For human and Toxoplasma-aligned transcriptomes we ran differential analysis across strain and IFNg treatment groups using DESeq2.

first: Eloise

middle: J

last: Lockyer

first: Moritz

last: Treeck


title: Next Generation Sequencing Facilitates Quantitative Analysis of keloid and normal skin

first: Jing

last: Zhang

address: No. 83, Fenyang Road,

institute: Eye, Ear, Nose and Throat Hospital, Fudan University

summary: Purpose: This study aimed to investigate the role of dysregulated circRNAs in keloid.   Methods: High-throughput sequencing was used to detect the changes of circRNAs, microRNAs(miRNAs) and mRNAs in 3 samples of keloid and corresponding normal skin.Based on Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) Pathway enrichment analysis combining several signaling pathways associated with keloid formation and progression, we screened these differentially expressed circRNAs.qRT–PCR validation was performed using TaqMan and SYBR Green assays   Results: Compared with normal controls, there were an average of 120 and 12 circRNAs, 44 and 63 miRNAs, 656 and 156 mRNAs were up-regulated and down-regulated, respectively, in keloids.   Conclusions: This study implicates that the abnormal expression of circRNAs in cases of keloid may correlate with its pathological process.

overall_design: Profiling of Differentially Expressed Circular RNAs in keloid tissue.

last: Ma

last: Song