title: Genome-wide transcriptional changes induced by different carbon sources and carbon starvation in Aspergillus nidulans

city: Debrecen

first: Tamas

last: Emri

address: Egyetem ter 1

country: Hungary

institute: University of Debrecen

summary: Understanding the coordinated regulation of the hundreds of carbohydrate-active enzyme (CAZyme) genes occurring in the genomes of fungi has great practical importance. We recorded genome-wide transcriptional changes of Aspergillus nidulans cultivated on glucose, lactose or arabinogalactan as well as under carbon starved conditions. We determined both carbon stress specific changes (a carbon stress vs. glucose) and culture specific changes (a culture vs. all other cultures). Many CAZyme genes showed carbon stress specific and/or culture specific upregulation on arabinogalactan (138 and 62 genes, respectively). Besides galactosidase and arabinan degrading enzyme genes, enrichment of cellulolytic, pectinolytic, mannan and xylan degrading enzyme genes were observed in these gene sets. Less, 81 and 107 carbon stress specific as well as 6 and 16 culture specific upregulated genes were found on lactose and in carbon starved cultures, respectively. They were enriched only in galactosidase and xylosidase genes on lactose and rhamnogalacturonanase genes in both cultures. Some CAZyme genes (29 genes) showed culture specific upregulation on glucose and they were enriched in beta-1,4-glucanase genes. Behavioral ecological background of these characteristics was evaluated to organize comprehensively our knowledge on CAZyme production, which can lead to develop new strategies to produce enzymes for plant cell wall saccharification.

overall_design: The THS30 reference strain was studied under four culturing conditions differing in the available carbon/energy source: cultures incubated in glucose rich or carbon source free media as well as cultures growing on lactose or arabinogalactan.  Each culturing condition was examined with three biological replicates.

first: Tamás

first: Barnabas

middle: C

last: Gila

first: Karoly

last: Antal

first: Istvan

last: Pocsi


title: RNA sequencing of HJURP silencing in ovarian cancer cells

status: Public on Jan 26 2022

city: Jinan

first: Zhiyuan

last: Dou

address: No.44, Wenhua Xi Road

department: Obstetrics and Gynecology Department

country: China

institute: Qilu Hospital of Shandong University

type: Expression profiling by high throughput sequencing

summary: Ovarian cancer is the most lethal gynecological malignancy. Recurrence and chemoresistance are tough challenges leading to poor prognosis. HJURP is a molecular chaperone of CENP-A, which is associated with aggressive progression in multiple tumors. However, the function of HJURP in ovarian cancer has not been elucidated. In our study, we found HJURP was over-expressed in ovarian cancer and high expression of HJURP was correlated to unfavorable prognosis. HJURP knockdown could inhibit proliferation, metastasis and induce G0/G1 stagnation of ovarian cancer cells. Besides, next-generation sequencing(NGS) unveiled that WEE1 was down-regulated by silencing HJURP. Further mechanistic research revealed that HJURP regulated WEE1 through MYC, and luciferase assay indicated that MYC was a transcription factor of WEE1. Additionally, we investigated that silencing HJURP increased sensitivity of ovarian cancer cells to cisplatin via MYC/WEE1 axis, and HJURP participated in DNA repair of cisplatin-induced damage. More interestingly, silencing HJURP could enhance sensitivity of ovarian cancer cells to AZD1775 and improve the synergistic effect of cisplatin plus AZD1775 combined therapy. Collectively, our data displays that HJURP promotes tumor progression and chemoresistance of ovarian cancer, and HJURP has potential to be a novel therapeutic target in the combined treatment with cisplatin and AZD1775 in ovarian cancer.

overall_design: The assay was performed on three biological triplicates as well as three experimental triplicates of HJURP silencing and control cells.

first: Dou

last: Zhiyuan

first: Kong

last: Beihua

first: Song

last: Kun

first: Qiu

last: Chunping


title: mRNA-seq and miRNA-seq of perilesional cortex and ipsilateral thalamus at 3-months after lateral fluid-percussion injury or sham-operation

city: Kuopio

first: Noora

last: Puhakka

address: Neulaniementie 2, P.O.B. 1627

department: A.I. Virtanen Institute for Molecular Sciences

country: Finland

institute: University of Eastern Finland

type: Non-coding RNA profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: Small RNA sequencing of perilesional cortex and ipsilateral thalamus at 3-months after lateral fluid-percussion injury or sham-operation

summary: At 3-months after after traumatic brain injury, small RNA sequencing was performed on samples from ipsilateral thalamus and perilesional cortex of selected rats with the chronic inflammatory endophenotype, and sham-operated controls.

overall_design: Small RNA sequencing of perilesional cortex and ipsilateral thalamus at 3-months after lateral fluid-percussion injury (n=6) or sham-operation (n=6).

first: Shalini

middle: D

last: Gupta

first: Niina

last: Vuokila

first: Asla

last: Pitkänen


title: mRNA sequencing of perilesional cortex and ipsilateral thalamus at 3-months after lateral fluid-percussion injury or sham-operation

summary: At 3-months after after traumatic brain injury, messenger RNA sequencing was performed on samples from ipsilateral thalamus and perilesional cortex of selected rats with the chronic inflammatory endophenotype, and sham-operated controls.

overall_design: Messenger RNA sequencing of perilesional cortex and ipsilateral thalamus at 3-months after lateral fluid-percussion injury (n=6) or sham-operation (n=6).


title: Deficiency of lncRNA SNHG12 impairs neovascularization in ischemic limbs by altering an endothelial cell cycle pathway III

city: Boston

first: Mark

last: Feinberg

state: MA

address: 77 Avenue Louis Pasteur

country: USA

institute: Brigham and Women's

summary: ncRNA SNHG12 regulates angiogenesis in ischemic limbs

overall_design: RNA-Seq analysis was performed in HUVECs transfected with control or SNHG12 gapmer using standard library construction and Illumina HiSeq2500 V4 2x100 PE (Genewiz, South Plainfield, NJ).

first: David

middle: A

last: Gross

first: Henry

middle: S

last: Cheng

first: Rulin

last: Zhuang

first: Michael

middle: G

last: McCoy

first: Daniel

last: Pérez-Cremades

first: Zachary

last: Salyers

first: A

middle: K

last: Wara

first: Stefan

last: Haemmig

first: Terence

middle: E

last: Ryan

middle: W


title: Deficiency of lncRNA SNHG12 impairs neovascularization in ischemic limbs by altering an endothelial cell cycle pathway II

overall_design: RNA-Seq analysis was performed on the endothelial and non-endothelial portion of the gastroc in diabetic (db/db) mice who had been treated with control or SNHG12 gapmers intramuscularly using standard library construction and Illumina HiSeq2500 V4 2x100 PE (Genewiz, South Plainfield, NJ).


title: Expression of mRNAs in the heart of fat-1 mice under pressure overload

city: Guangzhou

first: Xiang

last: Li

state: Guangdong

address: 11 fengxin road, guangzhou science city

institute: Guangdong Laboratory Animals Monitoring Institute

summary: Fat-1 mice were expressed n-3 fatty acid desaturase gene fat-1 of Caenorhabditis elegans. Expression profiles of mRNAs in the hearts of wild-type and Fat-1 mice under pressure overload conditions.

overall_design: Total RNAs from the ventricular tissues of the sham group (Fat1-Sham and WT-Sham) and the pressure overload group (Fat1-TAC and WT-TAC) were isolated using TRIzol® Reagent. Each group contains two independent samples. Subsequently, a total amount of 3 µg RNA per sample were used for high-throughput sequencing.

first: Weijiang

last: Tan

first: Shuang

last: Zheng

first: Feng

middle: H

last: Yang


title: Deficiency of lncRNA SNHG12 impairs neovascularization in ischemic limbs by altering an endothelial cell cycle pathway I

overall_design: RNA-Seq analysis was performed in HUVECs transfected with siRNA for SNHG12 knockdown, IMP3 nockdown, YBX1 knockdown, DHX9 knockdown, and DNAPK knockdown using standard library construction and Illumina HiSeq2500 V4 2x100 PE (Genewiz, South Plainfield, NJ).


title: Natural killer cells regulate pulmonary macrophages polarization in host defense chlamydial lung infection

city: jinan

first: jing

address: 44 Wenhua Xi Road

department: Department of Pathogenic Biology

institute: Shandong University

summary: NK cells and pulmonary macrophages both are important components of innate immunity. The interaction between NK cells and pulmonary macrophages during Chlamydia muridarum（C. muridarum）respiratory infections is poorly understood. In this study, we explored the effect of NK cells on regulation of pulmonary macrophage function during chlamydial lung infection. We found that NK depletion led to polarization of pulmonary macrophages from M1 to M2 phenotype, and this related to significantly reduced miR-155 expression in pulmonary macrophage. Using adoptive transfer approach, we found that the recipient mice receiving lung macrophages isolated from C. muridarum-infected NK-cell-depleted mice exhibited an increased bacterial load and severe inflammation in the lung upon chlamydial challenge when compared with the recipients of lung macrophages from infected IgG -treated mice. Herein, the effects of NK cells on macrophage polarization were examined in vitro. We found that NK cells from chlamydial-infected mice (iNK) significantly induced M1 polarization compared to that from sham-infected mice (uNK). Inhibition of miR-155 expression in macrophages attenuated M1 polarization induced by iNK, while miR-155 over-expression enhanced it. Furthermore, neutralization of IFN-γ in the coculture system decreased the expression of miR-155 by macrophages, and resulted in diminished M1 polarization induced by iNK cells. The data indicates that NK cells direct M1 polarization through up-regulation of miR-155 by IFN-γ production, and NK-regulated macrophage polarization is functionally relevant to host defense against chlamydial infection.

overall_design: Male BALB/c mice were maintained in a specific pathogen-free animal care facility of Shandong University. All mice used in this study were males between 6 and 8 weeks old. The experiment was divided into NK+macrophage and NK-macrophage group, N=3 per group.

first: Lei

last: Zhao

first: Jing


title: Fasting Mimicking Diet blocks breast cancer and cancer stem cells escape

city: Milan

first: Valter

last: Longo

address: via Adamello 16

country: Italy

institute: IFOM - the FIRC Institute of Molecular Oncology

summary: Metastatic tumors remain lethal due to primary/acquired resistance to therapy or cancer stem cell (CSC)-mediated repopulation. We show that a fasting-mimicking diet (FMD) activates starvation escape pathways in triple negative breast cancer (TNBC) cells, which can be identified and targeted by drugs. In CSCs, FMD cycles lower glucose-dependent protein kinase A signaling and stemness markers to reduce cell number and increase mouse survival. Accordingly, metastatic TNBC patients with lower glycemia survive longer than those with higher baseline glycemia. By contrast, in differentiated cancer cells, FMD cycles activate PI3K-AKT, mTOR and CDK4/6 as survival/growth pathways, which can be targeted by drugs to promote tumor regression. FMD cycles also prevent hyperglycemia and other toxicities caused by these drugs. These data indicate that FMD has wide and differential effects on normal, cancer and cancer stem cells, allowing the rapid identification and targeting of starvation escape pathways and providing a method potentially applicable to many malignancies.

overall_design: RNA-seq of SUM159 cell line transplanted in recipient mice treated with fasting-mimicking or control diets, previously sorted for CD44 and CD24 markers to separate differentiated and cancer stem cells.

first: Giulia

last: Salvadori

first: Federica

last: Zanardi

first: Fabio

last: Iannelli

first: Riccardo

last: Lobefaro

first: Claudio

last: Vernieri


title: Novel transcriptional and translational biomarkers of tularemia vaccine efficacy in a mouse inhalation model: proof of concept

city: Ottawa

first: Ziying

last: Liu

state: ON

address: 1200 Montreal Road

country: Canada

institute: National Research Council, Canada

summary: Francisella tularensis subspecies tularensis (Ftt) is extremely virulent for humans when inhaled as small particle aerosols (<5μm). Inhalation of ≥ 20 viable bacteria is sufficient to initiate infection with a mortality rate ≥30%. Consequently, in the past, Ftt became a primary candidate for biological weapons development. To counter this threat, the USA developed a live vaccine strain that showed efficacy in humans against inhalation of virulent Ftt. However, the breakthrough dose was fairly low and protection waned with time. These weaknesses triggered extensive research for better vaccine candidates. Previously, we  showed that deleting the clpB gene from virulent Ftt strain, SCHU S4,  resulted in a mutant that was significantly less virulent than LVS for mice, yet better protected them from aerosol challenge with wild-type SCHU S4.  To date, comprehensive searches for correlates of protection for SCHU S4 ΔclpB among molecules that are critical signatures of cell-mediated immunity, have yielded little reward. In this study we used transcriptomics analysis to expand the potential range of molecular correlates of protection induced by vaccination with SCHU S4 ΔclpB beyond the usual candidates.  The results provide proof-of-concept that unusual host responses to vaccination can potentially serve as novel efficacy biomarkers for new tularemia vaccines.

overall_design: In this study we used transcriptomics analysis to expand the potential range of molecular correlates of protection induced by vaccination with SCHU S4 ΔclpB beyond the usual candidates.  The comparative study of transcriptomics were performed between LVS and one of the SCHU S4 deletion mutants ΔclpB, ΔgplX and ΔlpcC and all vaccinated samples compared with each other. The results provide proof-of-concept that unusual host responses to vaccination can potentially serve as novel efficacy biomarkers for new tularemia vaccines

first: Qing

middle: Y

first: Wayne

last: Conlan

first: Youlian

last: Pan


title: Genome-wide DNA methylation analysis of gastric mucosa with autoimmune gastritis

city: Tsukiji, Chuo-ku

first: Chihiro

last: Takeuchi

state: Tokyo

department: Division of Epigenomics

country: Japan

institute: National Cancer Center Research Institute

summary: DNA methylation in gastric mucosa with autoimmune gastritis and H. pylori-associated gastritis and normal gastric mucosa

overall_design: Bisulfite converted DNA from the 24 samples were hybridised to the Infinium MethylationEPIC BeadChip Kit

first: Satoshi

last: Yamshita

first: Nobutake

last: Yamamichi

first: Toshikazu

last: Ushijima


title: Next Generation Sequencing Facilitates Quantitative Analysis of Transcriptomes of MM cells after M2 Treatment

first: Yu-Tzu

last: Tai

address: 450 Brookline Ave

institute: Dana Farber Cancer Institute

summary: Targeted immunotherapies based on monoclonal antibodies have continued to show clinical activities in patients with multiple myeloma (MM). A novel antibody drug conjugate targeting BCMA armed with a DNA cross-linking pyrrolobenzodiazepine PBD dimer tesirine M2, is currently under clinical development for MM. M2 has demonstrated potent cytotoxicity against MM cells in bulk as well as quiescent tumor-initiating cells in in vitro and in vivo preclinical studies. We here further investigate its effects on transcriptional changes in MM cells prior to apoptosis and identify molecular events regulating its potential immunomodulation to further upregulate its efficacy.  RNA sequencing followed by gene set enrichment analysis in MM cells treated with M2 vs control vehicle at sub-lethal concentrations reveal that M2 can induce interferon-regulated genes dependent on DNA damage-initiated signaling pathways, providing new molecular insight into its mechanisms of action in MM in the bone marrow microenvironment.

overall_design: H929 cells were treated with M2 vs control vehicle (solvent). Two biological replicates per conition were obtained.

first: Lijie

last: Xing


title: Oocyte transcriptome changes in Taf4b-deficient female mice [E16.5]

city: Providence

first: Megan

last: Gura

state: RI

address: 70 Ship St.

department: Molecular Biology, Cell Biology, and Biochemistry

institute: Brown University

summary: Research has shown that Taf4b-deficient female mice display excessive perinatal germ cell death, delayed germ cell cyst breakdown, and increased chromosome asynapsis. Therefore, we hypothesized that TAF4b, as part of TFIID, regulates oogenesis and meiotic gene programs. However, the transcriptomic effects of Taf4b-deficiency and how this may lead to the infertility we observe in mice has not yet been studied. Therefore, we performed RNA-seq to examine gene expression changes in E16.5 female Taf4b-heterozygous and Taf4b-deficient germ cells

overall_design: E16.5 oocytes were obtained through fluorescence-activated cell sorting (FACS) from Taf4b-heterozygous and Taf4b-deficient germ cells with 5 replicates per genotype

first: M

first: K

last: Seymour

first: R


title: HAMSAB supplement enhances SCFA production associated with microbiota and immune modulation in type 1 diabetes

city: St. Leonards

first: Long

middle: The

last: Nguyen

state: NSW

address: Royal North Shore Hospital, Pacific Hwy

department: Kolling Institute

country: Australia

institute: The University of Sydney

summary:
Purpose: Short chain fatty acids (SCFAs) produced by the gut microbiota have dual beneficial anti-inflammatory and anti-dysbiotic effects associated with the prevention of type 1 diabetes (T1D) in mice. We have conducted a single-arm trial of a dietary supplement (HAMSAB), to determine the effects of increasing SCFA delivery  in adults with long-standing T1D. Particularly, we examined blood transcriptome in these patients using RNA-seq.
Methods: Blood was collected from patients at baseline and after 6 weeks of HAMSAB supplementation. Whole blood was collected directly into Paxgene or Tempus tubes containing RNA stabilisers and extracted according to the manufacturer's protocol. Next-gene sequencing of patients’ whole blood transcriptome was performed by Genewiz using Illumina NovaSeq platform obtaining sequence depth of 50 million reads/sample.
Results: Several signalling pathways including fatty acid oxidation were found to be regulated by HAMSAB

overall_design: To compare mRNA profiles in whole blood from T1D patients at baseline and after HAMSAB supplementation

first: Sonia

last: Saad

first: Susan

last: Corley

first: Marc

last: Wilkins


title: Gene signature profiles in lung tissues of wild type mice or Has2 heterozygous deficient mice stimulated chronically with ovalbumin

city: Tsukuba

first: Takumi

last: Kiwamoto

address: 1-1-1 Tennoudai

department: Pulmonary Medicine

institute: University of Tsukuba

summary: Background: HAS2 is a member of the gene family encoding hyaluronan synthase 2 (HAS2), which can generate high-molecular-weight hyaluronan (HMW-HA). Our previous study identified HAS2 as a candidate gene for susceptibility to adult asthma.  However, little is known if HAS2 dysfunction affects airway remodeling and steroid insensivity. In this study, we clarified the dysfunction of Has2 triggering severe airway remodeling and steroid insensitivity in a murine model of asthma.   Methods: Ovalbumin (OVA) was used to induce eosinophilic airway inflammation and airway remodeling in Has2 heterozygous deficient (Has2+/−) mice and their wild-type (WT) littermates. Lung tissue histology, bronchoalveolar lavage fluid cell counting, quantitative PCR, HA size analysis, multiplex cytokines and chemokines analysis, RNA sequencing, anti IL-17 neutralization experiment were performed.  Results:  After chronic OVA stimulation, Has2+/− (Has2+/--OVA) mice showed significant decrease of Has2 mRNA expression levels, HMW-HA, HA-binding protein, and TGF-β. Has2+/--OVA mice demonstrated increased eosinophilic airway inflammation, goblet cell hyperplasia, and IL-17 levels. RNA sequencing demonstrated downregulation of EIF2 signaling pathways, TGF-β signaling pathways, and heat shock proteins with Th17 bias in Has2+/--OVA mice. Combined treatment with anti IL-17 antibody and dexamethasone reduce steroid insensitivity in Has2+/--OVA mice  Conclusions: Has2 attenuation worsen eosinophilic airway inflammation, airway remodeling, and steroid insensitivity. This severe intractable phenotype might be induced by impairment of TGF-β signaling and ER stress response related signaling. These data highlight that HAS2 and HMW-HA are important for controlling intractable eosinophilic airway inflammation and remodeling, and could potentially be exploited for therapeutic benefit to asthma patients.

overall_design: 19 strand-specific RNA libraries for high-throughput sequencing were prepared (5 from the lungs of the wild type mice treated with saline, 4 from the lungs of the Has2+/- mice treated with saline, 5 from the lungs of the wild type mice sensitized and interanasaly stimulated with ovalbumin, and 5 from the lungs of the Has2+/- mice stimulated with ovalbumin using the Illumina Stranded mRNA Sample Preparation Kit with 500ng of total RNA according to manufacturer’s instructions.

first: Mingma

last: Thsering Sherpa

first: Masashi

last: Matsuyama

first: Nobuyuki

last: Hizawa


title: H2R signaling maintains neutrophil homeostasis

city: Houston

first: Zhongcheng

last: Shi

state: TEXAS

address: 1102 Bates

department: Pathology and Immunology

institute: Baylor College of Medicine

summary: H2R deficiency accelerated progression of colitis-associated colon tumors. To identify precise expression pattern of H2R in immune cells, we performed quantitative RT-PCR and revealed that H2R is highly expressed in neutrophils. In mice, H2R deficiency significantly promoted infiltration of neutrophils into both inflammation sites and colon tumors. To precisely elucidate the downstream effects of H2R activation in neutrophils, low-density (LDNs) and high-density (HDNs) neutrophils were enriched from casein-elicited peritoneal cells of wild type and H2R deficient mice, and extracted total RNA were subjected to RNA sequencing. H2R-deficient HDNs not only presented more pro-inflammatory features through NF-kB and MAPK pathways, but also significantly suppressed T cell proliferation, which is essential for cellular immunity. On the other hand, LDNs with no H2R activation displayed a more immature phenotype compared to WT LDNs, with enhanced MYC pathway downstream expressions and a reduced expression of the maturation marker TLR4.

overall_design: RNA-seq of H2R deficient and wildtype low density and high density neutrophils.

first: Yuko

last: Mori-Akiyama

first: James

last: Versalovic


title: SOX2 Mediates Metabolic Reprogramming of Prostate Cancer Cells (RNA-Seq)

city: Chicago

first: Donald

last: Vander Griend

state: IL

address: 909 S. Wolcott Ave, COMRB Room 5051

department: Pathology

institute: The University of Illinois at Chicago

summary: To determine the genes regulated by SOX2, we performed RNA-Seq on CWR-R1 control cells and SOX2KO cells with intact AR signaling and identified differentially expressed genes (DEGs)

overall_design: mRNA from two cell line derivatives (CWR-R1 Control and SOX2-KO) was sequenced in triplicate

middle: J


title: Targeted CRISPR interference and activation of microRNA-3662-HBP1 axis controls tumor progression of triple-negative breast cancer

city: Birmingham

first: Lizhong

last: Wang

address: 740 20th St S

institute: UAB

summary: MicroRNA-3662 (miR-3662) is not or very low expressed in normal human tissues but highly expressed in almost all types of human cancers, including breast cancer. However, the functional role of miR-3662 in human cancers remains a topic of debate. First, our bioinformatic analysis in the Cancer Genome Atlas dataset showed that miR-3662 expression is higher in triple-negative breast cancer (TNBC) and African American breast cancer than in other types of breast cancer. Next, we found that inhibition or knockout of endogenous mature miR-3662 in human TNBC cells suppresses cell proliferation and migration in vitro and tumor growth and metastasis in vivo. Functional analysis revealed that knockout of miR-3662 reduces the activation of Wnt/β-catenin signaling in TNBC cells. Finally, using dual-luciferase assay, miRNA/mRNA immunoprecipitation assay, and CRISPR-mediated miR-3662 activation and repression, we further identified that HMG-box transcription factor 1 (HBP-1), a Wnt/β-catenin signaling inhibitor, is a direct target of miR-3662 and is most likely responsible for miR-3662-mediated TNBC cell proliferation. Our results suggest that miR-3662 plays an oncogenic role in tumor progression and metastasis via a miR-3662-HBP1 axis, which negatively regulates Wnt /β-catenin signaling pathway in TNBC cells.

overall_design: total RNA expression by deep-sequencing in MDA-MB-231 sorted for different levels of miR-3662 activity

first: Baozhu

last: Yi

first: Runhua

last: Liu


title: Exploring the lncRNAs biomarker which related to IP3/DAG signal pathway leading to mast cells degranulation in chronic spontaneous urticaria

first: Yudan

last: Liang

address: No.601, West Huangpu Avenue

department: Integrated Chinese and Western Medicine Postdoctoral research station

institute: Jinan University

type:
Expression profiling by array
Non-coding RNA profiling by array

summary: To determine whether lncRNAs are involved in chronic spontaneous urticaria (CSU), we analyzed the expression profile of lncRNAs and mRNAs in CSU.

overall_design: In the study presented here, 5 pairs of CSU patients and healthy controls were screening by microarray.

first: Yu-Dan


title: Induction of CTH expression in response to amino acid starvation confers resistance to anti-LAT1 therapy in MDA-MB-231 cells

city: Mitaka

first: Yamaga

last: Takashi

institute: Kyorin University

summary:
We examined gene expression change under amino acid restriction in JPH203 treated MDA-MB-231 and T-47D cells.
JPH203 treatment induced  endoplasmic reticulum stress response via amino acid starvation stress pathway in both MDA-MB-231 and T-47D cells. Moreover, MDA-MB-231 was upregulated anti-oxidants related genes.

overall_design: To determine JPH203 treatment regulated genes, total 4 samples were derived from MDA-MB-231 or T-47D cells stimulated with 100μM of JPH203 for 24 hours. 100μM of Captisol was used as control.

first: T

last: Yamaga

first: J

last: Suehiro

first: H

last: Sakurai


title: Transcriptomic analysis of kidney cortex following the loss of functional Sco2

city: Stony Brook

first: Sandeep

last: Mallipattu

state: New York

address: 101 Nicolls Rd

department: Medicine-Nephrology

institute: Stony Brook University

summary: The goal of this study was to identify transcriptomic changes caused by loss of functional Sco2 in kidney cortex of db/db mice (Type II Diabetes Mellitus mouse model).

overall_design: Four experimental groups were analyzed.

first: Nehaben

last: Gujarati

first: Alexandra

middle: R

last: Leonardo

first: Jessica

middle: M

last: Vasquez

first: Yiqing

last: Guo

first: Bismark

middle: O

last: Frimpong

first: Monica

middle: P

last: Revelo

first: John

last: He

first: Daniel

last: Bogenhagen


title: An insight into Exosomal Cargo Isolated from three tissue specific Mesenchymal Stem Cells: Implication in Translational Research

city: Faridabad

first: Arup

last: Banerjee

state: Haryana

address: NCR Biotech Science Cluster

country: India

institute: Regional Centre for Biotechnology

summary: Adult Mesenchymal stem cells (MSCs) derived exosomes have recently gained importance as a cell-free therapy for several chronic and inflammatory diseases. It is believed that these exosomes contain several biologically active molecules (i.e. miRNAs, proteins) which help to cure the diseases. The majority of published reports to date that have investigated the secretome of MSCs have done so using canonical expansion of cell culture conditions. However, the microenvironment experience by MSC post administration into animal models and patients is strikingly different. Thus instead of using secretome, Exosomes purified from adipose tissue (AD), Wharton Jelly (WJ) and Bone marrow BM) are widely studied. However, the content of the exosomes may differ based on their sources from where they are originated. It remains unclear, however, which types of proteins are packaged into exosomes compared with the cells from which they are derived. To explore these exosomes as a cell-free therapy for specific diseases, it is therefore, important to get comprehensive knowledge of the bioactive molecules present in the exosomes. In this study, we have purified the exosomes from three different sources (AD, WJ, and BM) and using RNA-Seq  approach, we have categorized the common and different microRNAs present in the exosomes.

overall_design: Mesenchymal Stem Cells (MSCs) were isolated from three different sources i.e. Bone Marrow, Adipose tissue and Wharton’s Jelly. These MSCs were propagated in DMEM (LG) media (Life Technologies, USA) containing 10% FBS (HyClone, USA), 2mM L-glutamine,100 U/ml of penicillin and 100 U/ml of streptomycin (Life Technologies, USA). These cells were sub-cultured at 70% confluence. The MSCs were stained for tri-lineage differentiation (adipocytes, osteocytes and chondrocytes) and cell specific surface markers by flow-cytometry which included CD 105, CD 73, CD 29 and CD 90, HLA-I, CD 34/45 and HLA Class II, as per the International Society for Cellular Therapy (ISCT) guidelines. For enrichment of exosomes, the MSCs were cultured in serum free media -STEMPRO® MSC SFM CTS (Thermo Fisher Scientific, USA) for 48 hours. The conditioned media from MSCs cultured for 48 h was pooled together for exosome isolation by ultracentrifugation and characterization for their size, morphology and surface markers by Nanoparticle Tracking Analysis (NanoSight LM20 (Malvern Instruments Company, Nanosight, Malvern, United Kingdom)), Electron Microscopy (Tecnai, FEI, USA) and Western Blotting respectively. After this, Exosomes were processed for total RNA isolation using miRCURY RNA Exosome Isolation kit (Exiqon, Denmark, Europe) following manufacturer’s recommendations. These were then processed further for RNA sequencing.

first: Anirban

last: Basu

first: Sujata

last: Mohanty


title: Identification of Wnt2 targets in dendritic cell

city: Shenzhen

first: Tuxiong

last: Huang

address: 1066 Xueyuan Avenue

institute: Shenzhen University

summary:
Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. The goals of this study are to identify the key moleculars or pathways which are changed in dendritic cells undergoing the treatment of CAF-secreted Wnt2.
Methods: mRNA profiles of mouse dendritic cells (mDCs) with treatment of Wnt2, CAF culture medium (CAF.CM), or CAF culture medium + Wnt2 Ab(CAF.CM+Wnt2 Ab), were generated by deep sequencing, in triplicate, using Illumina. The sequence reads that passed quality filters were analyzed at the transcript isoform level with two methods: Burrows–Wheeler Aligner (BWA) followed by ANOVA (ANOVA) and TopHat followed by Cufflinks. The overlap changes of mRNA profiles in Wnt2-treated mDCs and CAF.CM-treated mDCs compared with control mDCs, revealed the possible changed cellular pathways induced by CAF-secreted Wnt2. The analysis of the mRNA profiles which were changed after the blocking of Wnt2 activities in CAF.CM would be used to comfirmed the  changed cellular pathways induced by CAF-secreted Wnt2.
Results: Using an optimized data analysis workflow, we found that 768 transcripts and 2068 transcripts were significantly changed in Wnt2-treated DCs and CAF.CM-treated respectively compared with untreated DCs. And 393 changed transcripts  overlapped in Wnt2-treated DCs and CAF.CM-treated compared with untreated DCs. Moreover, treatment of CAF.CM with Wnt2 Ab induced differential expression of 497 genes.
Conclusions: Our study represents the first detailed analysis of Wnt2-induced changes of DC transcriptomes, with biologic replicates, generated by RNA-seq technology. The optimized data analysis workflows reported here should provide a framework for comparative investigations of Wnt2- or CAF.CM- induecd expression profiles.

first: Xiangyu

last: Tan

first: Yuting

last: Li

first: Li

last: Fu


title: Cotton transcriptome analysis reveals novel biological pathways that eliminate reactive oxygen species (ROS) under sodium bicarbonate (NaHCO3) alkaline stress

city: Zhengzhou

first: yanyong

last: cao

state: henan

address: No. 116, Huayuan Road

institute: Henan Academy of Agricultural Sciences

summary: To explore the mechanisms of cotton response to this alkaline stress, we used next-generation sequencing (NGS) technology to study transcriptional changes of cotton under NaHCO3 alkaline stress. A total of 18,230 and 11,177 differentially expressed genes (DEGs) were identified in cotton roots and leaves, respectively. Gene ontology (GO) analysis indicated the enrichment of DEGs involved in various stimuli or stress responses. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis showed that DEGs associated with plant hormone signal transduction, amino acid biosynthesis, and biosynthesis of secondary metabolites were regulated in response to the NaHCO3 stress. We further analyzed genes enriched in secondary metabolic pathways and found that secondary metabolites were regulated to eliminate the reactive oxygen species (ROS) and improve the cotton tolerance to the NaHCO3 stress. In this study, we learned that the toxic effect of NaHCO3 was more profound than that of NaOH at the same pH. Thus, Na+, HCO3- and pH had a great impact on the growth of cotton plant. The novel biological pathways and candidate genes for the cotton tolerance to NaHCO3 stress identified from the study would be useful in the genetic improvement of the alkaline tolerance in cotton.

overall_design: The transcriptional levels of cotton under two different alkaline stresses were tested

first: Yapeng

last: Fan

first: Wuwei

last: Ye


title: SOX2 Mediates Metabolic Reprogramming of Prostate Cancer Cells (ChIP-Seq)

first: Donald

last: Vander Griend

type: Genome binding/occupancy profiling by high throughput sequencing

summary: To mechanistically define the function of SOX2 in prostate cancer cells and how it contributes to therapeutic resistance, we performed paired SOX2 chromatin immunoprecipitation-sequencing (ChIP-Seq) and RNA-sequencing (RNA-Seq) on a SOX2-positive CRPC cell line, CWR-R1, to determine which genes SOX2 binds and potentially regulates. To identify novel prostate cancer-specific SOX2 gene targets in CRPC cells distinct from known SOX2 stem cell genes, we conducted parallel SOX2 ChIP-Seq and RNA-Seq in the WA01 embryonic stem cell line and compared results to identified SOX2 targets from CWR-R1 cells

overall_design: SOX2 immunoprecipitation was performed in  CWR-R1 and WA01 cells. Non-immunoprecipitated DNA was used as an input DNA control when calling peaks. Replicates in each condition were pooled using MACS2 to call peaks against the input DNA control.


title: Molecular and cellular characterization of MDSC differentiated from the bone marrow of Balb/c mice with tumor conditioned media or tumor conditioned media and antagonists for CCR1 and CCR5

city: Padova

first: Silvio

last: Bicciato

address: via U. Bassi 59/b

department: Molecular Medicine

institute: University of Padova

summary: Tumor derived factors can promote the differentiation of hematopoietic precursors into suppressive myeloid derived suppressor cells however, the molecular pathways that regulate this differentiation are not fully disclosed. In this study we identified a pathway by which tumor derived factors induce the expression of CCL3 and CCL4 from early HSPCs that autocrinally bind to CCR1 and CCR5 mediate the differentiation of BM cells into suppressive and protumoral cells. Inhibition of CCR1 and CCR5 is sufficient to prevent MDSC differentiation and restore the generation of myeloid cells with a tumoricidal function.

overall_design: ACK lysed BM cells from Balb/c mice were cultured for 4 hours with RPMI, RPMI with tumor derived factors from 4T1 tumors, or RPMI with tumor derived factors from 4T1 tumors and antagonists against CCR1 and CCR5. Cells were stored in Trizol for RNA extraction RNA extraction was carry on with miRNAeasy mini kit from Quiagen; RNA QC was assessed by Agilent BioAnalyzer 6000 and samples were analyzed with Affymetrix mouse... 2.0 ST array

first: Serena

last: Zilio

first: Paolo

last: Serafini

last: Weed


title: RNA-seq of detecting the effect of NS5 for neurogenesis.

city: Guangzhou

first: ping

last: li

address: No.74, zhongshan Road

institute: sun-yat sen university

summary: The RNA-seq data provided evidence that ZIKV-NS5 repressed genes transcription, thus disrupting the neurogenesis of human NPCs.

overall_design: overexpressed ZIKV-NS5 in hNPCs and collected cells 48 hours post infection by lentivirus. And hNPCs in control groups were infected by lentivirus that packaged vectors.

first: Ping

last: LI


title: Oocyte transcriptome changes in Taf4b-deficient female mice [E14.5]

first: Megan

last: Gura

summary: Research has shown that Taf4b-deficient female mice display excessive perinatal germ cell death, delayed germ cell cyst breakdown, and increased chromosome asynapsis. Therefore, we hypothesized that TAF4b, as part of TFIID, regulates oogenesis and meiotic gene programs. However, the transcriptomic effects of Taf4b-deficiency and how this may lead to the infertility we observe in mice has not yet been studied. Therefore, we performed RNA-seq to examine gene expression changes in E14.5 female Taf4b-wildtype, Taf4b-heterozygous, and Taf4b-deficient germ cells

overall_design: E14.5 oocytes were obtained through fluorescence-activated cell sorting (FACS) from Taf4b-wildtype, Taf4b-heterozygous and Taf4b-deficient germ cells

first: M

first: K

last: Seymour

first: R


title: Compared gene expression between kidney and renal pelvis

city: Sapporo

first: Osamu

last: Ichii

state: Hokkaido

address: Kita 18-Nishi 9

department: Faculty of Veterinary Medicine

institute: Hokkaido University

summary: Tertiary lymphoid tissues (TLTs) are formed in systemic organs manifesting chronic inflammation. Herein, we found that the renal pelvis (RP) could form urinary tract-associated lymphoid tissues (UTALTs) in a TLT-formation manner in humans and mice with chronic kidney disease (CKD), regardless of infectious pyelonephritis. Our results demonstrated that urine is crucial for UTALT development. Urine leak from the lumen into the parenchyma of the RP through an altered transitional epithelium (TE) barrier, stimulated RP stromal cells immunologically and attracted immune cells via cytokine and chemokine production. Pathophysiological crosstalk was observed between UTALT development and tubulointerstitial lesions and TLT formation in the kidney.

overall_design: The kidney and renal pelvis were isolated from 7 MRL/MpJ (control) and 10 MRL/MpJ-Faslpr/lpr (disease model). For kidney and renal pelvis, the extraRNA from MRL/MpJ (n = 7) and MRL/lpr (n = 10) was pooled as one sample for each group.

last: Ichiii


title: RNA molecular signature profiling in PBMCs of sporadic ALS patients: HSP70 overexpression is associated with nuclear SOD1

city: Pavia

first: Maria

last: Garofalo

address: Via Mondino 2

institute: IRCCS Mondino Foundation

summary: Amyotrophic Lateral Sclerosis (ALS) is a fatal neurodegenerative disease caused by loss of motor neurons. SOD1 may have a toxic role in the pathogenesis of ALS when the protein aggregates in the cytoplasm; increased accumulation of soluble nuclear SOD1 (nSOD1) represents a protective cellular reaction.

overall_design: Peripheral Blood Mononuclear Cells derived from 18 sALS patients and 12 age- and sex-matched healthy controls (CTRL) were deep-sequenced and included in Real Time PCR experiments.

first: Cecilia

last: Pandini

first: Matteo

last: Bordoni

first: Emanuela

last: Jacchetti

first: Luca

last: Diamanti

first: Stephana

last: Carelli

first: Manuela

middle: T

last: Raimondi

first: Daisy

last: Sproviero

first: Valeria

last: Crippa

last: Carra

first: Angelo

last: Poletti

first: Orietta

last: Pansarasa

first: Stella

last: Gagliardi

first: Cristina

last: Cereda


title: TAS3-derived short-interfering RNAs confer cleavage of mRNAs in rice

city: shenzhen

first: Lei

last: Gao

state: guangdong

address: Nanhai Ave 3688

department: College of Life Sciences

institute: shenzhen university

summary: Plant TRANS-ACTING SIRNA3 (TAS3)-derived short-interfering RNAs (siRNAs) include tasiR-ARFs, which are functionally conserved in targeting AUXIN RESPONSE FACTOR (ARF) genes, and a set of non-tasiR-ARF siRNAs, which have rarely been studied. In this study, TAS3 siRNAs were systematically characterized in rice (Oryza sative). Small RNA-seq results showed that an overwhelming majority of TAS3 siRNAs belong to the non-tasiR-ARF group, while tasiR-ARFs occupy a diminutive fraction. Phylogenetic analysis of TAS3 genes across dicot and monocot plants revealed that the siRNA-generating regions were highly conserved in grass species, especially in the oryzoideae. Target genes were identified for not only tasiR-ARFs but also non-tasiR-ARF siRNAs by analyzing rice degradome datasets, and some of these siRNA-target interactions were experimentally confirmed in rice tas3 mutants. Consistent with altered expression of target genes, phenotypic variations were observed for mutants in three TAS3 loci in comparison to wild-type rice. The regulatory role of ribosomes in the TAS3 siRNA-target interactions was further revealed by the fact that TAS3 siRNA-mediated target cleavage, in particular tasiR-ARFs targeting ARF2/3/14/15, occurred extensively in rice polysome samples. Altogether our study sheds new insights into TAS3 genes in plants and expand our knowledge about rice TAS3 siRNA-target interactions.

overall_design: 12 samples in total, 3 replicates for WT, tas3a1, tas3b1,tas3c1

first: Linlin

last: Luo

first: Lin

last: Liu


title: Epigenetic integrity of paternal imprints enhances the developmental potential of androgenetic haploid embryonic stem cells

city: Shanghai

first: Qing

last: Li

address: 320 Yueyang Road

department: institute of biochemistry and cell biology

institute: Chinese Academy of Science

type: Methylation profiling by high throughput sequencing

summary: The use of two inhibitors of Mek1/2 and Gsk3β (2i) promotes the generation of mouse diploid and haploid embryonic stem cells (ESCs) from the inner cell mass of biparental and uniparental blastocysts, respectively. However, a system enabling long-term maintenance of imprints in ESCs has proven challenging. Here, we report that usage of a two-step a2i (alternative two inhibitors of Src and Gsk3β, TSa2i) derivation/culture protocol results in the establishment of androgenetic haploid ESCs (AG-haESCs) with stable DNA methylation at paternal DMRs (differentially DNA methylated regions) up to passage 60 that can efficiently support generating mice upon oocyte injection. We also show coexistence of H3K9me3 marks and ZFP57 bindings with intact DMR methylations. Furthermore, we demonstrate that TSa2i-treated AG-haESCs are a heterogeneous cell population regarding paternal DMR methylation. Strikingly, AG-haESCs with late passages display increased paternal-DMR methylations and improved developmental potential compared to early-passage cells, in part through the enhanced proliferation of H19-DMR hypermethylated cells. Together, we establish AG-haESCs that can long-term maintain paternal imprints.

overall_design: Stable maintenance of paternal imprints and the developmental potential of haploid cells through optimizing culture system

first: Hongling

last: Zhang

first: Yuanyuan

first: Yongjian

last: Ma

first: Jinsong


title: In vitro stimulation of mouse spleen cells by COL17A1

first: Osamu

last: Ichii

summary: Tertiary lymphoid tissues (TLTs) are formed in systemic organs manifesting chronic inflammation. Herein, we found that the renal pelvis (RP) could form urinary tract-associated lymphoid tissues (UTALTs) in a TLT-formation manner in humans and mice with chronic kidney disease (CKD), regardless of infectious pyelonephritis.  Furthermore, collagen type XVII alpha 1 chain (COL17A1), localized ectopically to the transitional epithelium (TE) covering the UTALT, where it participated in TE development via immunological stimulation of UTALT-forming cells.

overall_design: The spleens were isolated from C57BL/6N at 6-month old, minced, washed, resuspended, and cultured. These cultured cells were stimulated with or without recombinant human COL17A1 for 3 hours. And then, RNA was collected and gene expression was analyzed.

last: Ichiii


title: Microarray analysis of differentially expressed genes in bicalein-treated Nasopharyngeal carcinoma (HK-1) cell line

city: Bangkok

first: Pichamon

last: Kiatwuthinon

address: 50 Ngamwongwan Rd. Ladyao Jatujak

department: Biochemistry

country: Thailand

institute: Kasetsart University

summary: Baicalein is a bioactive compound that is found in an herbal plant, Oroxylum indicum, grown in Southeast Asia including Thailand. There are several reports investigating on the bioactivities of baicalein including an anticancer activity. However, there is no report on the anticancer activity of the baicalein in nasopharyngeal carcinoma. Thus, the aim of this study is to identify differentially expressed genes (DEGs) that are targets of baicalein in order to reveal cellular pathways and molecular mechanisms of the baicalein in nasopharyngeal carcinoma. In this study, NPC HK-1 cells were used as an NPC representative and treated with 10 and 20 µM baicalein for 24 hours before collecting cells for whole transcriptome profiles. The results revealed that a number of cellular pathways, based on KEGG enrichment analysis, are affected baicalein treatment such as focal adhesion and PI3K-Akt signaling pathway which were also phenotypically related to cell migration and invasion assays. Changes in transcriptome profiles of baicalein-treated HK-1 cells would provide insight on baicalein activity in NPC.

overall_design: Baicalein-treated NPC HK-1 cells were cultured in petri dishes for 24 hours and replaced by full media for another 24 hours before being harvested. The cells were collected for RNA extraction, cDNA synthesis, Cy-3 labeling, and hybridization. Three biological replicates were performed for each cell condition.

first: Tavan

last: Janvilisri


title: Transcriptomics analysis of gene expression in wildtype and FTO knockout mouse liver

city: Beijing

first: Bao-Fa

last: Sun

address: Da-Tun Road

institute: Beijing Institute of Genomics (BIG) of Chinese Academy of Sciences (CAS)

summary: Fto conditional knockout mutation was generated using phage-based Escherichia coli homologous recombination systems. Construct targeting the third exon of mouse Fto gene was introduced into ES cell by homologous recombination. The mice with homozygous targeted allele were crossed to Albumin-Cre for deletion the third exon of mouse Fto gene in liver. Total RNA was isolated from Liver Tissue using the TRIzol (Invitrogen) reagent by following the company manual. For all samples the RNA integrity was checked using an Agilent Bioanalyzer 2100. Approximately 2.5 µg of total RNA was then used for library preparation using a TruSeq™ RNA Sample Prep Kit v2 (Illumina, San Diego, CA, USA) according to the manufacturer’s protocol.The libraries were sequenced using HiSeq3000 (Illumina) in paired-read mode, creating reads with a length of 101 bp. Sequencing chemistry v2 (Illumina) was used.

overall_design: Examination of gene expressive levels in wildtype and FTO knockout mouse liver

first: Shimin

last: Peng

first: Wen

last: Xiao

first: Baofa

first: Niu

last: Huang

first: Yuigui

last: Yang


title: Transcriptomics analysis of gene expression in wildtype and foxo1 synonymous mutated mouse liver

summary: The selected gRNA sequence is tggcatgtttattgagcgctTGG. To disrupt the demethylation motif RRACT in 2288-2290 of Foxo1 mRNA (NM_019739), a mutation (ttGGACT to ctCGATT) target vector was constructed with 1214bp 5’arm and 849bp 3’arm. Mouse zygotes obtained by mating of males with superovulated C57BL/6J females, were injected with a mixture of Cas9 mRNA (80 ng/μl), sgRNA (40 ng/ul) and Donor vector (8 ng/ul). Microinjections were performed into the male pronucleus of fertilized oocytes. Injected zygotes were transferred into pseudopregnant CD1 female mice, and viable adult mice were obtained. Mice were genotyped using sequencing and PCR. PCR primers: mut-F1, ATCCCCATTGAGCAGTAAGTTTTCCA; mut-R1, TGATGGACTCCATGTCACAATCGAG; mut-F2, GCATGTTTATTGAGCGCCTCGAT; mut-R2, CCGCTGTTGCCAAGTCTGAGG; wt-R1, TGATGGACTCCATGTCACAGTCCAA. PCR genotyping of wild-type (wt) and mutant (mut) mice was using primers mut-F1 and mut-R1 to generate fragments of 1291 bp for mut allele, using primers mut-F2 and mut-R2 to generate fragments of 930 bp for mut allele, and using primers mut-F1 and wt-R1 to generate fragments of 1291 bp for wt allele. Total RNA was isolated from Liver Tissue using the TRIzol (Invitrogen) reagent by following the company manual. For all samples the RNA integrity was checked using an Agilent Bioanalyzer 2100. Approximately 2.5 µg of total RNA was then used for library preparation using a TruSeq™ RNA Sample Prep Kit v2 (Illumina, San Diego, CA, USA) according to the manufacturer’s protocol.The libraries were sequenced using HiSeq3000 (Illumina) in paired-read mode, creating reads with a length of 101 bp. Sequencing chemistry v2 (Illumina) was used.

overall_design: Examination of gene expressive levels in wildtype and foxo1 synonymous mutated mouse liver


title: Early and extensive venous arterialization during mammalian embryogenesis

first: Ji

last: Dong

address: Yiheyuan 5#

institute: Peking University

summary: The cellular evolutions and molecular programs underlying the arteriovenous fate settling of embryonic vascular endothelial cells (ECs) are critical for understanding arteriogenesis and inspiring new approaches for regenerative biology. Using different strategies of single-cell RNA sequencing, we constructed the transcriptional landscape of early arteriovenous EC development in both mouse and human embryos, demonstrating the evolutionary conservation of principal vascular EC types and providing a series of conserved arteriovenous genes. We showed an unexpected diversity of arteriovenous characteristics in morphologically alike vascular plexus and further uncovered two transcriptomically distinct arterial EC types, whereas most of heterologous ligand-receptor pairs were shared by different arterial vasculatures. By computational predicting and further genetic lineage tracing, we revealed the widespread venous arterialization in the mid-gestational mouse embryo proper. Interestingly, we demonstrated at transcriptomic level that Notch1 was dispensable for venous arterialization but required subsequently for the arterial feature strengthening in the arterial plexus ECs. Altogether, our findings unprecedentedly detail the comprehensive single-cell mapping of early embryonic vascular ECs in vivo, decipher an asymmetric arteriovenous characteristics different than that in adults, and reveal an extensive venous-to-arterial fate conversion in the vascular plexus.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Here, we performed both well-based single-cell RNA-sequencing (scRNA-seq) of 2,213 cells in mouse embryos and 966 cells in human embryos and droplet-based scRNA-seq of 10,465 cells in mouse embryos to firstly construct a molecular landscape of embryonic vascular endothelium at single cell resolution. Moreover, we also performed well-based single-cell RNA-sequencing of 144 cells from mouse Dll4-tdTomato reporter model, 240 cells from mouse Unc5b-tdTomato reporter model, 192 cells from one mouse Nr2f2-related lineage tracing model and 112 cells from another mouse Nr2f2-related lineage tracing model, to validate our findings. Finally, we performed single-cell RNA-sequencing of 339 cells by well-based  method and 25,147 cells by 10x method from mouse Notch1-knockout model, to decode the role of Notch signaling in arterialization.

first: Siyuan

last: Hou

first: Zongcheng

first: Yun

first: Zhilin

last: Chang

first: Xiaochen

last: Ding

first: Bing

first: Fuchou

last: Tang

first: Yu

last: Lan


title: Severe stunting symptoms upon nepovirus infection are reminiscent of a chronic hypersensitive-like response in grapevine

status: Public on Jan 25 2022

city: Colmar

first: Isabelle

middle: Rachel

last: Martin

state: Grand-Est

address: UMR_A 1131 INRAE - Université de Strasbourg Santé de la vigne et qualité du vin 28 rue de Herrlisheim

department: SVQV

country: France

institute: INRAE

summary:
Purpose and strategy: Grapevine fanleaf virus (GFLV) causes variable symptoms in most vineyards worldwide. To better understand GFLV-grapevine interactions in relation to symptom development, field and greenhouse trials were conducted with a grapevine genotype that exhibits distinct symptoms in response to a severe and a mild strain of GFLV.
Results: After validation of the infection status of the experimental vines by high throughput sequencing, the transcriptomic and metabolomic profiles in plants infected with the two viral strains were tested and compared by RNA-Seq and LC-MS, respectively, in the differentiating grapevine genotype. In vines infected with the severe GFLV strain, 1,023 genes, among which some are implicated in the regulation of the hypersensitive-type response, were specifically de-regulated, and a higher accumulation of resveratrol and phytohormones was observed. Interestingly, some experimental vines restricted the virus to the rootstock and remained symptom-less. Our results suggest that GFLV induces a strain- and cultivar-specific defense reaction similar to a hypersensitive reaction. This type of defense leads to a severe stunting phenotype in some grapevines whereas others are resistant. This work is the first evidence of a hypersensitive-like reaction in grapevine during virus infection.
Conclusion: Our results suggest that GFLV induces a strain- and cultivar-specific defense reaction similar to a hypersensitive reaction. This type of defense leads to a severe stunting phenotype in some grapevines whereas others are resistant. This work is the first evidence of a hypersensitive-like reaction in grapevine during virus infection.

overall_design: Comparison between infected and non-infected grapevines. Trial composed of 9 grapevine, 3 biological replicates per condition as following: Gw-Control plants (#B31, #B34 and #C51), infected plants Gw-B844 (#B52, #B53, and #C38) and Gw-F13 (#B47, #C39 and #C40).

first: Corinne

last: Schmitt-Keichinger

first: Olivier

last: Lemaire

first: Emmanuelle

last: Vigne


title: Cutaneous squamous cell carcinoma A431 cells treated with itraconazole

city: Nanjing

first: Congcong

last: Xu

state: Jiangsu

address: 12 Jiangwangmiao Street

institute: Institute of Dermatology, Chinese Academy of Medical Sciences and Peking Union Medical College

summary: The role of itraconazole in cSCC was still unclear. Our objective is to explore the therapeutic potential of itraconazole in cSCC and investigate its molecular mechanism. We proved itraconazole inhibits the growth of cSCC by several pathways.

overall_design: A total of 3 pairs of A431 control cells and A431 cells with itraconazole (1μM, 48h) were used for microarray assay to find differentially expressed mRNAs.

first: Yating

last: Zhuo

first: Yunyao

last: Liu

first: Hao

last: Chen


city: Changsha

first: HE

last: Xinglan

address: No. 139 Renmin Middle Road, Furong District

department: Department of Dermatology

institute: The Second Xiangya Hospital

summary: to detect the gene expression of Fibroblasts  after hypoxia, we used Agilent SurePrint G3 Human Gene Expression v3 for the transcriptional sequencing of fibroblasts with and without hypoxia to detect differentially expressed genes (DEGs) in hypoxia.

overall_design: Three control tissue explants were incubated at 37°C and 5% CO2 in DMEM (Gibco, Carlsbad, CA, USA) supplemented with 10% FBS (Biological Industries, Kirbuta Beit Haemek, Israel) and 1% penicillin-streptomycin (Gibco) to culture skin fibroblasts. In the hypoxia group, when the cells covered almost 60% of the 25 mm2 culture bottle, the tri-gas incubator was used to simulate hypoxia (37°C, 5% CO2, and 1% O2). The control group was cultured in the incubator under similar conditions (37°C and 5% CO2).

first: Yangyang

last: Luo


title: Human tongue squamous cell carcinoma cell：Control vs. stable METTL3 knockdown

first: Xia

last: Gao

address: 321 Zhongshan Road

department: Otolaryngology Haed and Neck Surgery

institute: Nanjing University Medical School Affiliated Nanjing Drum Tower Hospital

summary: Transcriptional profiling of human tongue squamous cell carcinoma cell comparing control untreated SAS cells with stable METTL3 knockdown SAS cells. METTL3 is an important methyltransferase in N6-methyladenosine modification. Goal was to determine the differentially expressed and methylated genes upon METTL3 knockdown.

overall_design: Two-condition experiment, SAS vs. sh-METTL3 SAS cells.

first: Yuqing

last: Guo


title: CUT&RUN of TAF4b and H3K4me3 in E16.5 oocytes

city: Providence

first: Megan

last: Gura

address: 70 Ship St.

institute: Brown University

summary: Research has shown that Taf4b-deficient female mice display excessive perinatal germ cell death, delayed germ cell cyst breakdown, and increased chromosome asynapsis. Therefore, we hypothesized that TAF4b, as part of TFIID, regulates oogenesis and meiotic gene programs. However, the direct targets of TAF4b have not been thoroughly explored. Therefore, we performed Cleavage Under Targets and Release Using Nuclease (CUT&RUN) in E16.5 mouse oocytes.

overall_design: E16.5 oocytes were obtained through fluorescence-activated cell sorting (FACS) from Oct4-EGFP embryonic mice

first: Kimberly

last: Seymour

first: Sona

last: Relovska

last: Abt

first: Tong

last: Wu

first: Richard

middle: N

last: Freiman

first: Thomas

last: Fazzio


title: Immunomodulatory potential of in vivo Natural Killer T (NKT) activation by NKTT320 in Mauritian-origin cynomolgus macaques

city: New Orleans

first: Nell

last: Bond

email: nellgbond@gmail.com, nbond@tulane.edu

state: LA

address: Microbiology & Immunology, 1430 Tulane Avenue

institute: Tulane University School of Medicine

summary: Invariant natural killer T-lymphocytes (iNKT) are unique immunomodulatory innate T-cells with an invariant TCR recognizing glycolipids presented on MHC class-I-like CD1d molecules. Activated iNKT rapidly secrete pro-and anti-inflammatory cytokines, potentiate immunity, and modulate inflammation. Here, we report the effects of in vivo iNKT activation in Mauritian-origin cynomolgus macaques by a humanized monoclonal antibody, NKTT320, that binds to the invariant region of the iNKT TCR. NKTT320 led to rapid iNKT activation, increased polyfunctionality, and elevation of multiple plasma analytes within 24 hours of administration. Flow cytometry and RNA-Seq confirmed downstream activation of multiple immune subsets, enrichment of JAK/STAT and PI3K/AKT pathway genes, and upregulation of inflammation-modulating genes. NKTT320 also increased iNKT frequency in adipose tissue without iNKT anergy. Our data indicate that NKTT320 has a sustained effect on in vivo iNKT activation, potentiation of innate and adaptive immunity, and resolution of inflammation, which supports its future use as an immunotherapeutic.

overall_design: Characterization of in vivo iNKT activation by NKTT320 in Mauritian origin Cynomolgus Macaques (Macaca fasicularis).

first: Amitinder

last: Kaur


title: Heme exposure shifts shifts myeloid differentiation in bone marrow derived mixed cell cultures.

city: Zürich

first: Raphael

middle: Matthias

last: Buzzi

address: Rämistrasse 100

department: Division of Internal Medicine

country: Switzerland

institute: Universitätsspital and University of Zurich

summary: Heme is an erythrocyte-derived toxin that drives disease progression in hemolytic anemias. During hemolysis, specialized bone marrow-derived macrophages with a high heme-metabolism capacity orchestrate disease adaptation by removing damaged erythrocytes and heme-protein complexes from the blood and supporting iron recycling for erythropoiesis. Here, we performed single-cell RNA sequencing with RNA velocity analysis of GM-CSF-supplemented mouse bone marrow cultures to assess myeloid differentiation under heme stress. We found that heme-activated NRF2 signaling shifted the differentiation trajectories of cells towards antioxidant, iron-recycling macrophages at the expense of dendritic cells, as these cells were selectively deficient in heme-exposed bone marrow cultures. Heme eliminated the capacity of GM-CSF-supplemented bone marrow cultures to activate antigen-specific T cells. The generation of functionally competent dendritic cells was restored by NRF2 loss. The heme-induced phenotype was reproduced in hemolytic mice with sickle cell disease and spherocytosis and associated with reduced dendritic cell functions in the spleen. Our data provide a novel mechanistic underpinning how hemolytic stress may provoke hyposplenism-related secondary immunodeficiency, which is a critical determinant of mortality in patients with genetic hemolytic anemias.

overall_design: M-CSF- and GM-CSF-supplemented BM cell cultures were stimulated with heme (300μM) or albumin (control) on day 3. On day 7, the cells were harvested, tagged with DNA-barcoded antibodies, and pooled into a single scRNA-seq sample for sequencing.

first: Marc

last: Pfefferlé

first: Dominik

last: Schaer

first: Florence

last: Vallelian


title: Heme signaling shifts myeloid differentiation in GM-CSF BM cell cultures

overall_design: GM-CSF BM cultures were stimulated with heme or albumin (control) on day 3 of culture. After 0, 24, 72, or 96 h, the cells were harvested, tagged with DNA-barcoded antibodies, pooled, and processed for sequencing.


title: Deviated myeloid differentiation in SCD mice under heme stress II.

overall_design: Single cell suspension positively enriched for macrophages using F4/80 magnetic beads from a spleen of a SCD and wild-type mouse subjected to droplet-based single-RNA sequencing (10x genomics).


title: Heme-Nrf2 signaling shifts myeloid differentiation

overall_design: Two-factorial multiplexed scRNA-seq experiment using GM-CSF BM cultures from Nrf2-/- mice and wild-type littermates that were treated with heme or with the selective NRF2 activator ML-334


title: Transcriptomic analysis of grapevine in response to ABA application reveals its diverse regulations during cold acclimation and deacclimation

city: Geneva

first: Hongrui

last: Wang

state: NY

address: 630 W. North Street

department: School of Integrative Plant Science, Horticulture section

institute: Cornell University

summary: Abscisic acid (ABA) plays crucial regulatory roles in cold acclimation and deacclimation of grapevine, making it a potential tool to be utilized in vineyards for the acquisition of preferred phenotypes in winter and spring. To understand the function of ABA , we conducted two experiments during cold acclimation and deacclimation and evaluated the impact of exogenous abscisic acid (ABA) on the grapevine transcriptome. RNA-seq data were collected periodically hours or days after ABA treatment. Transcriptomic data were analyzed using principal component analysis (PCA)  , hierarchical clustering, unsupervised weighed gene co-expression network analysis (WGCNA), contrast-based differentially expressed genes (DEGs) identification and pre-ranked gene set enrichment analysis (GSEA). Our results suggest that ABA functions differently during cold acclimation and deacclimation by selectively regulating key pathways including auxin/indole acetic acid (IAA) metabolism, galactose metabolism and ribosome biogenesis. We also identified the activation of several apparent negative feedback systems that regulated ABA-induced transcriptomic changes, suggesting the existence of a balancing system in response to excessive ABA.

overall_design: In the acclimation experiment, 40 leaf samples were analyzed in a time serie. These samples include eight replicates of control samples at pre-treatment and four replicates of control and ABA-treated samples at 2 h, 4 h, 24 h and 48 h post-treatment. In the deacclimation experiment, 34 bud samples were analyzed in a time serie. These samples include three replicates of control samples at pre-treatment and three replicates of control and ABA-treated samples at 6 h, 12 h, 24 h, 48 h (one more control sample at 48 h) and 72 h post-treatment.

first: Imed

last: Dami

first: Hanna

last: Martens

first: Jason

last: Londo


title: Transcriptional landscape of pathogen-responsive lncRNAs in primary mammary epithelial cells reveals insights in immune response and defense mechanism.

city: Gandarbal

first: Basharat

middle: Ahmad

last: Bhat

state: Kashmir

address: Shuhama

department: Animal Biotechnology

institute: Sher-e-Kashmir University of Agricultural Sciences and Technology

summary: RNA-seq was performed by infecting primary mammary epithelial cells (pMECs) with both gram negative (E.coli) and gram positive bacteria (S. aureus). Using stringent pipeline, a set of 1957 known and 1175 novel lncRNAs were identified, among which, 112 lncRNAs were found differentially expressed in bacteria challenged PMECs compared with the control.

overall_design: lncRNA profiles of primary mammary epithelial cells (pMECs) were generated by deep sequencing, in triplicate, using Illumina 2500 platform. The sequence reads that passed quality filters were analyzed at the transcript level withTopHat followed by Cufflinks. lncRNAs were identified using four independent algorithms i.e., CNCI, PLEK, CPAT and PFAM. qRT–PCR validation was performed using SYBR Green assays.

first: Syed

last: Andrabi

first: Peerzada

last: Mumtaz

middle: A


title: Transcriptional profiling of dorsal striatum in 1-year-old WT mice and Ash1l heterozygous mice

first: Ji-Song

last: Guan

address: ShanghaiTech University, Shanghai, China

department: School of Life Science and Technology

institute: ShanghaiTech University

summary: Ash1l encodes a histone methyltransferase, a member of the trithorax group proteins, which regulates developmental essential gene expression by catalyzing H3K36 methylation and counteracting polycomb silencing. Accumulating reports suggest the loss-of-function mutants in Ash1l gene are associated with intellectual disability (ID), attention-deficit/hyperactivity (ADHD), autism spectrum disorder (ASD), Tourette syndrome (TS) and multiple congenital anomalies (MCA). We performed transcriptional profiling of dorsal striatum in 1-year-old Ash1l mutant brain via RNA sequencing (RNA-seq). Ash1l haploinsufficiency induces transcription alternation of genes involved in synaptic function and cortical development, implicating the deficits in synapse pruning and behavior in adult mice.

overall_design: 3 WT (1-year-old) and 3 Ash1l heterozygous (1-year-old) dorsal striatum

first: Yuze

last: Yan

first: Miaomiao

last: Tian


title: Deviated myeloid differentiation in SCD mice under heme stress I.

overall_design: Single cell suspensions negatively enriched for DCs from a spleen of a SCD and wild-type mouse subjected to droplet-based single-RNA sequencing (10x genomics).


title: Alterations in Mycobacterium tuberculosis transcriptome at the site of infection in BTB tuberculosis

city: Chandigarh

first: Indu

last: Verma

state: Chandigarh

address: Research Block A,

institute: Postgraduate Institute of Medical education and Research Chandigarh

summary: In-vivo transcriptome analysis was performed to understand the Mtb adaptation strategies to survive in the host and establish infection in BTB. Gene expression profiling of Mtb within abscesses or necrotic specimens obtained from patients with BTB TB compared to exponentially growing in-vitro Mtb culture using whole genome microarray was studied.

sample_organism:
Mycobacterium tuberculosis
Mycobacterium tuberculosis H37Rv

overall_design: Transcriptional profile of mycobacteria within abscess or necrotic tissue from BTB TB patients in comparison to exponentially growing Mtb was assessed. Two controls (Mtb H37Rv) and six clinical specimens from microbiologically confirmed bone TB patients were analyzed. One sample out of six, was excluded from the data analysis because of involvement of joints as all other five clinical specimen were from Spinal TB patients. Agilent M.tb expression array, 8*15K (Design ID: 026323) designed by genotypic technologies Pvt. Ltd. Was utilised for the study.

first: Khushpreet

first: Sumedha

last: Sharma

first: Sudhanshu

last: Abhishek

first: Prabhdeep

first: Uttam

middle: C

last: Saini

first: Mandeep

middle: S

last: Dhillon

first: Petros

last: Karakousis


title: RNA sequencing of aGVHD MSCs from R-treated group and matched control

city: Tianjin

first: Quan

last: Gu

address: 288 Nanjing Road

institute: State Key Laboratory of Experimental Hematology, Institute of Hematology & Blood Diseases Hospital

summary: We performed RNA-seq of aGVHD MSCs  from  R-treated group and matched control

overall_design: Examination of gene expression profiles aGVHD_R and aGVHD_V sample

first: Yan

last: Lin

first: Hui

last: Cheng

first: Tao


title: Transcriptome analysis of auditory cortex in 1-month-old and 1-year-old  Ash1l heterozygous mice with their age-matched WT littermates

summary: Ash1l encodes a histone methyltransferase, a member of the trithorax group proteins, which regulates developmental essential gene expression by catalyzing H3K36 methylation and counteracting polycomb silencing. Accumulating reports suggest the loss-of-function mutants in Ash1l gene are associated with intellectual disability (ID), attention-deficit/hyperactivity (ADHD), autism spectrum disorder (ASD), Tourette syndrome (TS) and multiple congenital anomalies (MCA). We performed transcriptome analysis of auditory cortex in 1-month-old and  1-year-old Ash1l Ash1l heterozygous mice with their age-matched WT littermates via RNA sequencing (RNA-seq). Ash1l haploinsufficiency induces transcription alternation of genes involved in synaptic function and cortical development, implicating the deficits in synapse pruning and behavior in adult mice.

overall_design: 3 WT (1-month-old) and 3 Ash1l heterozygous (1-month-old) auditory cortex;2 WT (1-year-old) and 2 Ash1l heterozygous (1-year-old) auditory cortex


title: Overlap in antibiotic stress responses leads to cross-resistance between ribosomal acting drugs in Mycobacterium abscessus.

city: Nijmegen

first: Jodie

middle: Anne

last: Schildkraut

address: Geert Grooteplein Zuid 10

country: Netherlands

institute: Radboudumc

summary: Mycobacterium abscessus is an opportunistic pathogen notorious for its resistance to most classes of antibiotics and low cure rates. In addition to the highly impermeable mycomembrane, M. abscessus carries an array of shared and species-specific defence mechanisms. However, it remains unknown whether M. abscessus’ antibiotic stress response is fine-tuned or an all-or-nothing response. A deeper understanding of underlying resistance and tolerance mechanisms is pivotal in development of targeted therapeutic regimens. We elucidate the transcriptomic response of M. abscessus to antibiotics recommended in treatment guidelines.    The M. abscessus ATCC 19977 strain was used. Bacteria were subjected to sub-inhibitory concentrations of drugs for 4- and 24-hours, followed by RNA sequencing. In addition, time-kill kinetic analysis was performed using bacteria after pre-exposure to clarithromycin, amikacin or tigecycline for 24-hours. Lastly, Pan-genome analysis of 35 strains from all three subspecies was performed.    Mycobacterium abscessus shows both drug-specific and communal transcriptomic responses to antibiotic exposure. Key features of its tolerance to antibiotics are drug-specific converting enzymes, target protection and shifts in its respiratory chain and metabolic state. The observed transcriptomic responses are likely not strain-specific, as genes involved in tolerance are found in all included strains, with the exception of erm(41) in M. abscessus subspecies massiliense. Due to the communal response elicited by ribosomal-targeting antibiotics, exposure to any of these drugs rapidly induces tolerance mechanisms that decrease susceptibility to ribosome-targeting drugs from multiple classes. Screening high-risk patients (e.g. those with bronchiectasis) for M. abscessus infection prior to starting macrolide or aminoglycoside maintenance therapy is warranted.

overall_design: mRNa profiles of M. abscessus after 4- or 24-hours of treatment and untreated cells.

first: Jordy

last: Coolen

first: Jakko

last: van Ingen


title: Oocyte transcriptome changes in Taf4b-deficient female mice

first: Megan

last: Gura

department: Molecular Biology, Cell Biology, and Biochemistry

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

overall_design: Refer to individual Series


title: Identification by RNA-seq of Prdm12 regulated genes in  dorsal root ganglia nociceptors of adult mice

city: Goettingen

first: Gabriela

last: Salinas

state: Lower-Saxony

address: Kreuzbergring 57

department: Department of Pathology

country: Germany

institute: Universitaetsmedizin Goettingen

summary: Loss of Prdm12 increases formalin induced inflammatory pain by remodeling gene expression in mature nociceptors

overall_design: RNA-seq analysis on lumber  dorsal root ganglia of  Prdm12 inducible conditional knock-out (n=5) versus control (n=4) one month after tamoxyfen injection

first: Simon

last: Vermeiren

first: Aurore

last: Latragna

first: Panagiotis

last: Tsimpos


title: Heme-activated Nrf2 signaling skews fate trajectories of bone marrow cells from dendritic cells towards macrophages

first: Raphael

last: Buzzi


title: Single cell RNA sequencing of valvular interstitial cells and adipose derived mesenchymal stem cells

status: Public on Jan 24 2022

city: BOSTON

first: Julius

middle: L.

last: Decano

state: Massachusetts

address: 3 BLACKFAN CIRCLE. CENTER FOR LIFE SCIENCES, 17TH FLOOR

department: Medicine

institute: Brigham and Women's Hospital

summary:
A disease driver population within interstitial cells of human calcific aortic valves identified via single-cell and proteomic profiling
Cellular heterogeneity of aortic valves complicates mechanistic evaluation of the calcification processes in calcific aortic valve disease (CAVD), and animal disease models are lacking. In this study, we identify a disease driver population (DDP) within valvular interstitial cells (VICs). Through stepwise single-cell analysis, phenotype-guided  -OMIC profiling, and network-based analysis, we characterize  DDP fingerprint as CD44highCD29+CD59+CD73+CD45low and discover potential key regulators of human CAVD. These DDP-VICs demonstrate multi-lineage differentiation and osteogenic properties. Temporal proteomic profiling of DDP-VICs identifies potential targets for therapy, including MAOA and CTHRC1. In vitro loss-of-function experiments confirm our targets. Such a stepwise strategy may be advantageous for therapeutic target discovery in other disease contexts.

overall_design: Unsorted and FACS sorted VICs together with MSCs (reference cell line) were cultured in either normal or osteogenic media for two weeks then processed for single cell RNAseq using InDrops platform.  Sequencing is done on a NextSeq (single read)

first: Elena

last: Aikawa


title: Transcriptome analysis in the P14 Kctd19 Het and Kctd19 KO testes.

city: beijing

first: shuntai

last: yu

state: beijing

address: 7 Science Park Road ZGC Life Science Park, Beijing

department: transgenic animal center

institute: NIBS

summary: We wonder if KCTD19 can regulate gene expression during meiotic prophase.

overall_design: 1. Differential expression analysis in theP14 testes of Kctd19Het and Kctd19 KO male mice.    2. Two biological replicates were prepared for mRNA profiles.

first: Yushan

last: Li

first: Jiawen

last: Wang

first: Fengchao


title: RNA-seq dataset of different neuronal cell types and progenitors in the developing zebrafish retina at 42 hours post fertilization

city: Dresden

first: Caren

last: Norden

state: Sachsen

address: Pfotenhauerstr. 108

institute: Max Planck Institute of Molecular Cell Biology and Genetics

summary: This dataset was acquired to identify the gene expression profile of developing retinal cell types at 42 hours post fertilization (hpf): retinal ganglion cells, photoreceptors, inhibitory neurons (amacrine cells and horizontal cells) and progenitor cells.

overall_design: Retinal cell types were sorted from dissociated zebrafish retinas at 42 hpf using the triple transgenic line Tg(ath5:gap-RFP), Tg(crx:gap-CFP), Tg(ptf1a:gal4,UAS:gap-YFP). For each of the 5 replicates, 25 retinas were pooled.

first: Elisa

last: Nerli

first: Mauricio

last: Rocha-Martins


title: The m6A RNA modification modulates gene expression and fibrosis-related pathways in hypertrophic scar [m6A-seq]

city: wuxi

first: Siyu

last: Liu

address: Street of River Deans, Binhu District, Wuxi City

institute: Jiangnan University Affiliated Hospital

summary: Purpose: To systematically analyze the overall m6A modification pattern in hyperplastic scars (HS).  Methods: The m6A modification patterns in HS and normal skin (NS) tissues were described by m6A sequencing and RNA sequencing, and subsequently bioinformatics analysis was performed. The m6A-related RNA was immunoprecipitated and verified by real-time quantitative PCR.  Results: The appearance of 14,791 new m6A peaks in the HS sample was accompanied by the disappearance of 7,835 peaks. The unique m6A-related genes in HS were thus associated with fibrosis-related pathways. We identified the differentially expressed mRNA transcripts in HS samples with hyper-methylated or hypo-methylated m6A peaks.  Conclusion: This study is the first to map the m6A transcriptome of human HS, which may help clarify the possible mechanism of m6A-mediated gene expression regulation.

overall_design: Si-NC (C, n=1) and  Si-METTL3 (SI, n=1) samples

first: Fenglai

last: Yuan


title: EP400NL plays role in polyamine synthesis and mitochondrial biogenesis for the cell growth

city: Daejeon

first: Kim

last: Hyoungmin

address: 291, Daehak-ro, Yuseong-gu, Daejeon, 34141, Rep. of KOREA

department: Department of Biological Sciences

country: South Korea

institute: Korea Advanced Institute of Science and Technology

summary: To identify EP400NL-responsive genes by RNA expression profiling, tetracycline-induced Flp-In T-Rex cell line was used without additional serum and IFNγ-stimulation to avoid a universal upregulation of genes. In this condition, most of the genes were differentially expressed less than 1.5-fold range. The 121 genes with over 1.5-fold differential upregulations were further analysed by gene ontology. The result indicates that EP400NL upregulation seems to enhance housekeeping functions involved in polyamine synthesis and mitochondrial translation.

overall_design: Identifying the EP400NL-dependent gene expression with Flp-In™ T-REx™ tetracylin-dependent EP400NL expression .

first: Jeong

middle: H

last: Park

first: Jaehoon

last: Kim

first: Hyoungmin


title: Transcriptomic profile of ovarian cancer stem cells dervived from ascites of chickens.

city: State College

first: Aswathy

last: Sebastian

address: University Park

institute: PennState

summary: The objective of the present study was to determine the trancriptomic profile of ovarain cancer stem cells (CSCs) dervived from acites of chickens. Ovarian CSCs were sorted based on presence of a stem cell marker; aldehyde dehydrogenase (ALDH) and then subjected to RNASEq. Pairwise statistical analysis of transcriptomic data using Deseq2 software revealed 1800  differentially expressed (DEGs) in ALDH+ cells as compared to ALDH- cells

overall_design: Ovarian CSCs were seggregated based on the presence of ALDH activity and then sequenced.  We performed RNAseq analysis using the Illumina® software platform on RNA samples extracted from  ALDH+   and ALDH- cells. On average, 50 million 125 base pair paired-end reads were sequenced for each replicate. Statistical analysis was performed for pairwise comparison between treatment and control group.

first: Anupama

last: Tiwari

first: Jill

last: Hadley

first: Lalitha

last: Gopalan

first: Ramesh

last: Ramachandran

first: Istvan

last: Albert

first: Craig

last: Praul


title: Chromatin accessibility profiling of human coronary arteries identifes disease regulatory variants

city: Charlottesville

first: Clint

middle: L

last: Miller

state: VA

department: Center for Public Health Genomics

institute: University of Virginia

summary: Coronary artery disease (CAD) is a complex inflammatory disease of the vessel wall and often leads to myocardial infarction. Genome-wide association studies (GWAS) have now identified over 200 genetic loci associated with CAD. The majority of CAD-associated variants are located in noncoding regions of the genome, many of which are predicted to regulate chromatin accessibility and gene expression. In this study, we performed ATAC-seq in human coronary artery patient samples to identify novel chromatin accessibility QTLs (caQTLs) and gain additional insights into CAD regulatory mechanisms in vivo.

overall_design: We profiled bulk genome-wide chromatin accessibility using ATAC-seq in coronary arteries from human patients across a range of atherosclerosis disease stages.

first: Adam

last: Turner


title: Lipid metabolizing enzymes differ between preputial gland sebocytes and sebaceous gland sebocytes

city: Vienna

first: Katharina

last: Klas

address: Medizinische Universität Wien Anna Spiegel Forschungsgebäude Lazarettgasse 14 1090 Wien, Austria Level 6, Lab 5

country: Austria

institute: Medical University of Vienna

summary: Due to limited model systems for sebaceous glands we investigated potential suitability of preputial glands as model for sebaceous glands. We performed single-cell sequencing of murine preputial glands and back skin biopsies. This study revealed striking differences in lipid metabolizing enzyme expression and differentiation pathways found in sebocytes of the different tissues.

overall_design: Back skin biopsies of three male wild type C57BL/6 mice and preputial glands of these mice at the age of 52 weeks were analyzed using single-cell RNA sequencing.

first: Dragan

last: Copic

first: Martin

last: Direder

first: Maria

last: Laggner

first: Patricia

last: Pruksamas

first: Hendrik

middle: J

last: Ankersmit

first: Michael

last: Mildner


title: The Transcriptional Response to Oxidative Stress is Independent of Stress-Granule Formation

city: Mandi

first: Baskar

last: Bakthavachalu

state: Himachal Pradesh

address: Kamand

department: School of Biosciences and Bioengineering

institute: Indian Institute of Technology

summary: We characterized oxidative-stress-induced transcriptional changes in Drosophila S2 cells and assessed how these were altered under conditions that disrupted stress granule (SG) assembly. Sodium-arsenite stress for 3 hours resulted predominantly in the induction or upregulation of stress-responsive mRNAs whose levels peaked during cell recovery after stress cessation. RNAi-mediated knock down of the conserved G3BP1/ Rasputin protein inhibited stress-granule assembly.  However, this disruption had no significant effect on the stress-induced transcriptional response.

overall_design: RNASeq was performed on Poly(A) purified mRNA from S2 cells in triplicates for control, stress and recovery conditions. RNAi was used to knock down rasputin in S2 cells and poly(A) selected mRNA samples (Mock RNAi and Rin RNAi) were sequenced in triplicates for control, stress and recovery conditons.

first: Amanjot

last: Singh

first: Arvind

middle: R

last: Kandi

first: Mani

last: Ramaswami


title: Epigenome analysis of parent and radioresistant OSCC cells(OML1 and OML1R ).

city: Chiayi County

first: Jie Ting

last: Low

state: Minxiong Township

address: No. 168, Daxue Road, Section 1

country: Taiwan

institute: National Chung Cheng University

summary: Genome wide DNA methylation profiling changes in parent and radioresistant OSCC cells (OML1 and OML1R ) by The Illumina Infinium WG Methylation27.

overall_design: Bisulphite converted DNA from parent and radioresistant OSCC cells(OML1 and OML1R ) were hybridised to the Illumina Infinium 27k

middle: Y

last: Chan

first: Hon-Yi

last: Lin

first: Shih-Kai

last: Hung

first: Ru-Inn


title: Inhibitors of Bcl-2 and Bruton’s tyrosine kinase synergize to abrogate diffuse large B-cell lymphoma (DLBCL) growth

city: Zürich

first: Peter

last: Leary

address: Winterthurerstrasse 190

department: Functional Genomics Center Zürich

institute: ETH Zürich

summary:
Methods: DLBCL cell lines RIVA, U-2932 and OCI-LY3 were treated in vitro with ibrutinib (Ibru) or dimethyl sulfoxide (DMSO). Additionally, RIVA and U-2932 were orthotopically transplanted into MISTRG mice and mice were treated for two weeks with Ibru or vehicle. Tumor cells were isolated from the bone marrow at the study endpoint. The total RNA was isolated and the mRNA profiles were generated by next-generation sequencing using the Illumina TruSeq mRNA stranded protocol.
Results: We have combined single and combinatorial drug response profiling to show that the combined inhibition of the anti-apoptotic protein Bcl-2 and of the tyrosine kinase BTK with the small molecules venetoclax and ibrutinib efficiently kills DLBCL cells. High Bcl-2 expression due to either BCL2 amplifications or translocations, in conjunction with chronic active BCR signalling accurately predict responses to dual Bcl-2/BTK inhibition.The combined data show that drug sensitivities exposed by drug response profiling can be attributed to specific mutational signatures and immunohistochemical biomarkers, and point to combined Bcl-2/BTK inhibition as a novel promising therapeutic strategy in DLBCL.

overall_design: Examination of differential drug susceptibilities in DLBCL

first: Anne

last: Müller

first: Katrin

last: Bertram


title: SOX2 Mediates Metabolic Reprogramming of Prostate Cancer Cells

city: Chicago

first: Donald

last: Vander Griend

state: IL

address: 909 S. Wolcott Ave, COMRB Room 5051

department: Pathology

institute: The University of Illinois at Chicago


title: TGFβ1 promotes collective invasion of oncogenically transformed intestinal organoids by inducing partial epithelial-mesenchymal transition independently of Snail1 and Zeb1

city: Freiburg

first: Severin

last: Dicks

address: Breisacherstr. 153

department: Institute of Medical Bioinformatics and Systems Medicine

institute: University Freiburg Medical Center

summary: Cancer cells simultaneously featuring epithelial and mesenchymal traits appear particularly competent to invade and metastasize. However, genetic prerequisites and signaling pathways promoting such partial epithelial-to-mesenchymal transitions (EMT) remain obscure. Here we report that murine intestinal organoids with hyperactive Wnt and MAPK signaling, and mutant Trp53 are purely epithelial and non-invasive in vitro, but initiate a collective invasion program when treated with TGFβ1. Invasive organoids reciprocally interact with the extracellular matrix (ECM), and autonomously deposit and remodel components thereof. Although cells at the organoid/ECM interface shed certain epithelial characteristics, invasive organoids largely maintain epithelial gene expression while concomitantly upregulating a mesenchymal program. TGFβ1-induced phenotypic changes involve canonical, Smad4-dependent signaling, yet, are unimpeded by knockout of Snai1 and Zeb1 - otherwise key regulators of epithelial-to-mesenchymal transitions. The finding of TGFβ1-inducible, Snail1/Zeb1-independent collective invasion of oncogenically transformed intestinal organoids provides novel mechanistic insights and broadens the spectrum of context-dependent manifestations of partial EMT.

overall_design: Small intestinal organoids were established from two different C57BL/6N founder animals with the genotype Apc580S/580S, KrasLSL-G12D/+, Trp53LSL-R172H/+, tgVillin-CreERT2. Organoids were labelled according to the identifier of the mouse from which they were derived (animals #931 and #947).  By treatment with 4-hydroxy-tamoxifen, recombination was induced to generate Apc-deficient organoids expressing oncogenic KrasG12D and dominant negative Trp53R172H (so called TKA organoids). Time-resolved gene expression analysis by RNA sequencing (RNA-seq) was performed with TKA organoids. For this, organoids were mechanically disrupted and seeded in 3 mg/ml Matrigel. At 40 h after seeding, organoids had re-developed a cystic shape and treatment was started. Organoids were stimulated with 5 ng/ml human TGFβ1 for 6, 24, 48, and 72 h, or were harvested at the onset of the experiment (C-0) and after 72 h of cultivation with solvent (C-72) to account for culture-dependent effects. RNA was isolated from organoids and submitted for sequencing. For each of the two TKA organoid lines 931 and 947, RNA-seq data was collected from two independent biological replicates.

first: Marion

last: Flum

first: Monika

last: Schrempp

first: Alexander

last: Nyström

first: Melanie

last: Boerries

first: Andreas

last: Hecht

first: Yu-Hsiang

last: Teng


title: The imprinted Zdbf2 gene finely tunes hypothalamic control of feeding and growth in neonates.

city: paris

first: teissandier

last: aurelie

address: 26 rue d'Ulm

institute: institut curie

summary: To allow identification of differentially expressed genes between WT and Zdbf2-KO hypothalamus in mouse pups at 3 and 10dpp, mutants and control RNA-seq were conducted starting from whole hypothalamus RNA.

overall_design: Comparison of RNA-seq results from whole hypothalamus RNA of control and Zdbf2-KO at 3 and 10 dpp.

first: Juliane

last: Glaser

first: Julian

last: Iranzo

first: Deborah

last: Bourc'his


title: Deep sequencing reveals an acute inflammatory signature in chronic Peyronie’s disease

city: Leuven

first: Rekin's

last: Janky

address: Herestraat 49 Box 816

department: Nucleomics Core

country: Belgium

institute: VIB

summary:
Background: Peyronie’s disease (PD) is an acquired fibrotic process affecting the tunica albuginea (TA) of the penis. The development of fibrotic plaques can lead to penile curvature/deformities, shortening and erectile dysfunction. Medical treatments are lacking due to limited understanding of disease pathophysiology. Elucidation of molecular pathways and cell types involved could lead to the development of novel disease models and conservative therapeutics.

Objective: To characterise the transcriptomic signature of plaques from PD patients and compare it to normal TA using RNA sequencing (RNAseq) and network analysis. Design, setting and participants: We collected surgical TA samples from 6 PD patients and 6 control patients where RNAseq was performed, followed by functional analysis. Our findings were validated through RT-qPCR and immunohistochemistry in other patient samples (biological validation) and tested in an in vitro PD model derived from patient samples.

Results and limitations: These findings are the first report of using human samples for transcriptome-wide analysis of genital tract fibrosis. Differential gene expression identified 1294 differentially expressed genes in PD patients. Functional analysis reveals an active inflammatory component in the chronic PD plaque. Moreover, nearly half of all overexpressed genes were regulated by NF-kB and STAT. Further analysis shows that NF-kB is TNFα and TLR-activated and JAK/STAT-signalling occurs through interleukins (IL2/IL6) /interferons (Type I/II)). This data suggests an important macrophage-related response. We validated genes from enriched pathways using RT-qPCR both in the RNAseq samples and 5 additional samples. Immunohistochemical staining for macrophages (CD68) corroborated these findings. Stimulation of PD-derived fibroblasts and myofibroblasts with TNFα revealed expression of macrophage chemoattractant protein-1 (CCL2/MCP-1).

Conclusions: Our analysis suggests that, even in an established, chronic PD-plaque, acute inflammatory pathways are still active. We show for the first time that TNFα and TLR-activation could be an important pathway in PD-pathophysiology. Additionally, we suggest that this process is potentially maintained through macrophages. Release of TNFα induce chemoattraction of more macrophages by CCL2 production of (myo)fibroblasts.  Both could lead to development of novel druggable targets and more representative disease models.

overall_design: 6 PD samples and 6 control samples.

first: Uros

last: Milenkovic

first: Georgios

last: Hatzichristodoulou

first: Koen

last: van Renterghem

first: Thomas

last: Gevaert

first: Selim

last: Cellek

first: Trinity

last: Bivalacqua

first: Dirk

last: De Ridder

first: Maarten

last: Albersen


title: Copper regulation of HIF-1 transcriptional activities

city: Chengdu

first: Wenjing

last: Zhang

state: Sichuan

address: Keyuan Road 4,Gaopeng Street

department: Regenerative Medicine Research Center

country: China

institute: West China Hospital,Sichuan University

summary: HIF-1 regulated VEGF expression were upregulated in reponse to ischemic injury. However, the VEGF mRNA level were increased in the early stage but decreased in the late stage of myocardial infarction. We found that activities of HIF-1 binding to the HRE sites were possiblely responsible for the differential expression of VEGF. The HIF-1 binding activities were regulated by copper. After ischemic injury, copper concentrations were decreased in the infarct myocardium in the late stage of myocardial infarction, which might reduce VEGF expression through insufficient HIF-1 binding to HRE sites.

overall_design: Rhesus monkeys were subjected to LAD ligation to induce myocardial infarction. After 6 hours or 4 weeks, the hearts were collected and the infarct myocardium were separated to detect VEGF expression by qRT-PCR and to measure HIF-1 binding acitivies by ChIP-Seq. Immunohistochestry was applied for HIF-1α detection. Copper concentrations were determined by atomic absorption spectrometry.

first: Pengfei

last: Han


title: Iron-dependent epigenetic modulation promotes pathogenic T cell differentiation in lupus

status: Public on Jan 23 2022

city: Changsha

first: Xiaofei

last: Gao

address: NO.139 Renmin Middle Road

institute: The Second Xiangya hospital of Central South University

type: Methylation profiling by genome tiling array

summary: RNA-seq for murine Tfh cells induced in vitro; MeDIP-seq for human Tfh cells induced in vitro; hMeDIP-seq for human Tfh cells induced in vitro

first: Yang

last: Song

first: Jiali

last: Wu

first: Shuang

last: Lu

first: Xiaoli

last: Min

first: Limin

last: Liu

first: Longyuan

last: Hu

first: Meiling

last: Zheng

first: Pei

last: Du

first: Yaqin

last: Yu

first: Hai

last: long

first: Haijing

first: Sujie

last: Jia

first: Di

first: Qianjin

first: Ming

last: Zhao


title: microRNA (miRNA) expression data from renal cysts of autosomal dominant polycystic kidney disease (ADPKD) patients

city: Toronto

first: York

middle: PC

last: Pei

state: Ontario

address: 8N838, 585 University Avenue

department: Department of Medicine

institute: University of Toronto

summary: To elucidate the systems biology of miRNAs in human PKD1 renal cyst growth

overall_design: We performed global miRNA profiling on 16 renal cysts of different size (small cysts: less than 1 ml, n=5; small cysts*: between 1-5 ml, n=5 (including 1 replicate); medium cysts: between 10-25 ml, n=4 (including 1 replicate); large cysts: greater than 50 ml, n=4) and minimally cystic tissue (MCT, n=7, including 1 replicate) from four PKD1 polycystic kidneys. Additionally, non-cancerous renal cortical tissue from three nephrectomized kidneys with isolated renal cell carcinoma was used as normal control tissue (n=4)

first: Xuewen