title: The DGCR8 E518K mutation found in Wilms tumors leads to a partial miRNA processing defect that alters gene expression and biological processes (mRNA-seq)

summary: The microprocessor mutation DGCR8 E518K represents one of the most prevalent and stereotypical mutations in Wilms tumor (WT). It affects the dsRNA-binding domain (dsRBD) of DGCR8, which leads to a presumably disruptive charge reversal. The E518K mutation was expressed homozygously in all cases, indicative for the mutation to act in a recessive manner. Notably, this alteration has been almost exclusively reported in WT, suggesting a specific role in WT formation. To functionally characterize the DGCR8 E518K mutation in vitro, we employed DGCR8 knockout mouse embryonic stem cell (mESC) lines with inducible overexpression of wild-type (wt) or E518K-mutant DGCR8. Absence of endogenous DGCR8 mirrors the homozygous expression of mutant DGCR8 as observed in WT. Knockout of DGCR8 is known to result in a severe miRNA processing defect with a significant downregulation of all canonical miRNAs. Wild-type DGCR8 rescued this processing defect. DGCR8-E518K, in turn, was unable to fully restore miRNA expression and showed overall reduced miRNA expression levels, confirming our previous findings in bulk tumor tissue. Differentially expressed miRNAs comprised members of the embryonic stem cell specific cell cycle-regulating (ESCC) miRNAs and the let-7 miRNA family, whose antagonism is known to play a pivotal role in the regulation of critical gene expression programs in ES cells. Along with altered miRNA expression, DGCR8-E518K exhibited changes in target gene expression affecting various biological pathways. The known proliferation deficiency and cell cycle defect of DGCR8 KO mESCs could be rescued by DGCR8-E518K, albeit not to the full extent as by wild-type DGCR8. Likewise, DGCR8-E518K failed to fully block epithelial-to-mesenchymal transition (EMT). Upon embryoid body formation, however, both DGCR8-wt and -E518K were able to restore the differentiation capacity and to silence self-renewal in the knockout. Despite impaired miRNA processing and altered target gene regulation, DGCR8-E518K mESCs were still able to restore many biological processes in a DGCR8 knockout background. These findings suggest that partial reduction in activity or altered specificity might be critical in Wilms tumorigenesis.

overall_design: We analyzed mRNA expression of DGCR8-KO, -E518K, and -wild-type mESCs after 48h induction with doxycycline (300 ng/mL). Two independent clones were used per condition.

first: Romina

last: Vardapour

first: Hans-Peter

last: Lenhof

first: Susanne

last: Kneitz

first: Manfred

last: Gessler


title: The DGCR8 E518K mutation found in Wilms tumors leads to a partial miRNA processing defect that alters gene expression and biological processes (miRNA-seq)

status: Public on Dec 28 2021

city: Saarbrücken

first: Tim

last: Kehl

address: Campus E2.1, P.O. box 151150

department: Center for Bioinformatics

country: Germany

institute: Saarland University

type: Non-coding RNA profiling by high throughput sequencing

overall_design: We analyzed miRNA expression of DGCR8-KO, -E518K, and -wild-type mESCs after 48h induction with doxycycline (300 ng/mL). Three independent clones were used per condition. To assess leaky expression of the expression vectors, one clone of DGCR8-wt and -E518K without doxycycline treatment were used.


title: Combinatorial Gene Essentiality and Pharmacological Profiling uncovers enhancer-mediated synthetic lethal interactions with Mediator Kinase [RNA-Seq]

city: Clayton

first: Ron

last: Firestein

state: VIC

address: 21 Wright street

department: CCR

country: Australia

institute: Hudson Institute of Medical Research

type: Expression profiling by high throughput sequencing

summary: Depletion of CDK8 and its paralogue CDK19, resulted in a global down regulation of mRNA expression, and hence we went to investigate the binding of RNA pol II by ChIP seq at the promoter and at the gene body in the DKO cells. To determine the consequence of loss of CDK8/19 in re-defining enhancers and to underpin the molecular mechanism that providing the preferential BET sensitivity for DKO, we performed ChIP sequencing for MED12, a reminiscent mediator kinase component, BRD4 and H3K27Ac.  We identified that MED12 redefines the enhancer landscape in the absence of CDK8/19, recruit BRD4 at the cis regions and can be targeted using BET inhibitors

overall_design: RNA samples from HCT116-WT, DKO, CDK8KO, CDK19KO, HCT116-WT+JQ1, DKO+JQ1

first: Dhanya

last: Sooraj

first: Claire

middle: X

last: Sun


title: Combinatorial Gene Essentiality and Pharmacological Profiling uncovers enhancer-mediated synthetic lethal interactions with Mediator Kinase

type: Genome binding/occupancy profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: Transcriptional Reprogramming And Epigenomic Landscape Dynamics During Grapevine Somatic Embryogenesis Process [RRBS]

city: Udine

first: Emanuele

last: De Paoli

state: UDINE

address: via delle Scienze 206

department: Agricultural, Food, Environmental and Animal Sciences

country: Italy

institute: University of Udine

type: Methylation profiling by high throughput sequencing

summary: Somatic embryogenesis (SE), a morphogenic process that takes advantage of the regenerative potential of plants to replicate whole plants starting from somatic explants, can be a source of variation with potential applications in plant breeding. It is one of the most suitable tools to apply functional genomics studies and genetic improvement in plants. However, beyond a few pioneering works mainly focused on model plants, the molecular characterization of SE mechanisms is still elusive, especially for woody species. In grapevine, this process is affected by many factors such as explant type, culture conditions and, most importantly, genotype. Many cultivars, in fact, have shown recalcitrance to tissue culture and transformation, and very low SE competence. Thus, the understanding of SE competence behind the regenerative aptitude is fundamental to the widespread application of the so-called “next-generation breeding techniques”, such as cisgenesis and genome editing, in grapevine.   Here, we explored genetic and epigenetic features of the SE process in grapevine by investigating the behavior of two genotypes showing opposite SE competence. Embryogenic tissues were induced from immature stamens excised from field-collected flower clusters of Sangiovese (highly competent for embryogenesis) and Cabernet Sauvignon (poorly competent for embryogenesis). A multilayered approach was used to profile mRNA, smallRNAs and methylated DNA with high-throughput sequencing technologies in the initial explants, on undifferentiated calli induced after 40 days of culture, and in embryogenic and non-embryogenic calli after 3 months of culture.  A comprehensive comparison of transcriptomes of the different types of calli with the grapevine gene expression atlas revealed that, in grapevine, the dedifferentiation to the callus formation during the embryogenesis process occurs via a ‘berry’ developmental pathway. This is dissimilar from that shown in Arabidopsis, in which dedifferentiated calli are more similar to the tip of a root meristem. Interestingly, a Gene Ontology (GO) analysis revealed that secondary metabolism and gene expression regulation/epigenetics are the enriched functional categories of genes differentially down- and up-regulated in embryogenic vs non-embryogenic calli, respectively. These results prompted us to define the epigenetic landscape dynamics during SE in grapevine, revealing a significant increase in DNA methylation, especially in intergenic regions, in the embryogenic calli tissues. Finally, we proposed potential key regulators of SE in different genotypes that could represent putative targets of next-generation breeding techniques in grapevine.

overall_design: We report a whole characterization of molecular mechanisms associated to somatic embryogenesis in different genotypes of Vitis vinifera through RNA-seq, small RNA-seq and Reduced Representation Bisulﬁte Sequencing (RRBS) experiments. Embryogenic (EC), not embryogenic (NEC) and undifferentiated callus (40d) tissues of two grapevine cultivars (Sangiovese - SG - and Cabernet Sauvignon - CS -) that have different aptitudes for embryogenesis were compared.

first: Silvia

last: Dal Santo

first: Chiara

last: Pagliarani

first: Alessandra

last: Amato

first: Mirko

last: Celii

first: Giorgio

last: Gambino

first: Irene

last: Perrone

first: Sara

last: Zenoni


title: Combinatorial Gene Essentiality and Pharmacological Profiling uncovers enhancer-mediated synthetic lethal interactions with Mediator Kinase [ChIP]

overall_design: Examine the binding of RNA pol II, MED12, H3K27Ac and BRD4 in the genome in the wild type and in CDK8/19 KO cells


title: Transcriptional Reprogramming And Epigenomic Landscape Dynamics During Grapevine Somatic Embryogenesis Process


title: Transcriptional Reprogramming And Epigenomic Landscape Dynamics During Grapevine Somatic Embryogenesis Process [small RNA-seq]


title: Integrated multilayer omics reveals the genomic, proteomic and metabolic influences of the histidyl dipeptides on heart

status: Public on Dec 27 2021

city: 深圳

first: keqiang

last: yan

state: Not US or Canada

address: 深圳市盐田区北山工业区华大基因二办

country: China

institute: BGI

summary: This study using a system biology approach of transcriptomics, proteomics and metabolomics, we elucidated the role of endogenous histidyl dipeptides on cellular pathways and myocardial metabolism. Our multi-omics approach for the first-time unravels the landscape of genetic, proteomic, and metabolic changes influenced by histidyl di peptides.

overall_design: Gene expression comparison of mice with and without Carns transgenic. 8 samples were grouped into 2, WT and TG. Each group include 4 replicates.

first: Shahid

middle: P

last: Baba

first: Keqiang

last: Yan

first: Zhanlong

last: Mei

first: Jingjing

last: Zhao


title: Analysis of microRNA expression profiles in exosomes derived from acute myeloid leukemia by p62 knockdown and effect on angiogenesis

city: Shenyang

first: Xinyi

last: Long

state: State...

address: Shenyang

institute: China Medical university

summary: The aim of this study was to investigate the effect of p62 on miRNA expression profiles in AML exosomes and the effect on angiogenesis.

overall_design: In the study presented here, An Exiqon v19.0 microRNA MicroArray was used for profiling miRNAs in exosomes derived from U937 cells, p62-knockdown U937 cells, GDC-0152+U937 cells, GDC-0152+p62-knockdown U937 cells.

first: Rong

last: Hu


title: The short 3’ UTR derived sRNA FadZ buffers the transcriptional fluctuations during fatty acid oxidation [I]

city: Shanghai

first: Chuan

last: Wang

address: 131 # Dong An Road

institute: Fudan University

summary: To unfold the potential links between Salmonella fatty acid oxidation and other metabolic pathways, we performed RNA-seq to draw the transcriptomic response of Salmonella in response to oleci acid treatment. We compared samples of oleic acid shock (Group OAS) and oleic acid growth (Group OAG) to glucose growth (Group GLU).

sample_organism: Salmonella enterica subsp. enterica serovar Typhimurium str. SL1344

overall_design: Salmonella SL1344 wild type stran was cultivated in M9CA minimal medium supplemented with 0.4% Brij-58 and 0.1 % glucose (Group GLU) or 0.1 % oleic acid (Group OAG) to OD600~1.0. Cells from GLU groups were washed twice with PBS at room temperature and resuspend in M9CA minimal medium supplemented with 0.4% Brij-58 and 0.1 % oleic acid and cultivated for 10 min (Group OAS). RNA was collected by hot-phenol method and expression difference were compared between different groups.


title: RNA transcriptome sequencing of A375 cells treated with siNC or siSIRT7 oligonucleotides, which were irradiated or non-irradiated

city: Guangzhou

first: Bingyao

last: Meng

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

institute: southern medical universitity

summary: To understand the SIRT7-mediated molecular events in A375 cells, we conducted a genome-wide analysis to globally characterize SIRT7-regulated transcriptome changes. A375 cells treated with siNC or siSIRT7 oligonucleotides were irradiated or non-irradiated . Collect total RNA for transcriptome sequencing.

first: Liang

last: Zhou


title: The short 3’ UTR derived sRNA FadZ buffers the transcriptional fluctuations during fatty acid oxidation

platform_organism: Salmonella enterica subsp. enterica serovar Typhimurium str. SL1344


title: The short 3’ UTR derived sRNA FadZ buffers the transcriptional fluctuations during fatty acid oxidation [II]

summary: To screen the potential targets of Salmonella 3’ UTR derived sRNA FadZ, we compared global mRNA profiles in FadZ-deficient and -pulse expressed strains. The 40-nt FadZ sequences was cloned onto a plasmid downstream of the pBAD promoter and expression was induced by L-arabinose for 10-min in LB broth. Transcriptomic profiles were compared with strain carrying the empty control plasmid.

overall_design: Salmonella FadZ-deficient strain (ΔfadBA- ΔFadZ) carrying either empty plasmid pBAD or FadZ-overexpressed plasmid pBAD-FAdZ,  cultivated in LB broth to OD600~1.0 and then induced by 0.2% induced by L-arabinose for 10-min; RNA were collected by hot-phenol method and expression difference were compared between strain with empty and FadZ-expressed plasmids.


title: Expression profiling of Tex15 ht and Tex15 ko germ cells

city: Philadelphia

first: Yemin

last: Lan

state: PA

address: 3400 Civic Center Blvd

country: USA

institute: University of Pennsylvania

summary: We repport the effect of Tex15 inactivation on the transcriptome of male germ cells at embryonic day 16.5 (e16.5), 18.5 (e18.5), and postnatal day 2 (d2). We find a large number of differentially expressed genes between Tex15-deficient and Tex15 heterozygous germ cells at e18.5 and d2 but much fewer differentially expressed genes at e16.5.

overall_design: RNA-seq of Tex15+/- and Tex15-/- male germ cells at three timepoints (e16.5, e18.5 and d2) in biological triplicates (NextSeq500)

first: Fang

last: Yang

first: Marisa

middle: S

last: Bartolomei

first: Jeremy


title: Silencing of LncRNA C1RL-AS1 Suppresses the Malignant Phenotype in Gastric Cancer Cells via the AKT/β-Catenin/c-Myc Pathway

first: Wu

last: Zhenhua

address: Fenglin Road

institute: Department of Medical Oncology

summary:
Purpose: Numerous studies have shown that lncRNAs play vital roles in the development and progression of cancer. However, investigations of lncRNAs in gastric cancer are limited and need to be further pursued.
Materials and Methods: According to RNA-seq results of gastric cancer (GC) tissues, we identified a novel lncRNA, C1RL-AS1. qRT-PCR was used to detect the expression level of C1RL-AS1 in paired GC and normal tissues. Nuclear/cytoplasmic fractionation was applied to evaluate the distribution of C1RL-AS1 in GC cells. For functional evaluation, CCK-8, colony formation, transwell, and apoptosis assays were used to determine the oncogenic role of C1RL-AS1.
Results: C1RL-AS1 was upregulated in GC tissues, and high expression levels of C1RL-AS1 were associated with poor prognosis. Further in vitro functional assays revealed that silencing C1RL-AS1 attenuated the proliferation rate and migration ability and enhanced the apoptotic rate and the senescence of GC cells. The subsequent underlying mechanistic investigation revealed that Wnt/β-catenin was involved in C1RL-AS1-mediated signaling. Rescue experiments suggested that C1RL-AS1 probably promoted the malignant phenotype via the AKT/β-catenin pathway by downregulating c-Myc.
Conclusions: C1RL-AS1 probably exerts its biological function by mediating the AKT/β-catenin/c-Myc pathway, indicating a novel therapeutic target in GC.

overall_design: RNA sequencing of gastric cancer (GC) tissues

first: Zhen-Hua

last: Wu

first: Wei-Jian

last: Guo


title: Somatic DNA demethylation generates tissue-specific methylation states and impacts flowering time [RNA-seq]

city: Cambridge

first: Mary

last: Gehring

state: MA

address: 9 Cambridge Center

institute: Whitehead Institute for Biomedical Research

summary: Cytosine methylation is a reversible epigenetic modification to DNA. In plants, removal of cytosine methylation is accomplished by the four members of the DME family of 5-methylcytosine DNA glycosylases. Demethylation by DME is critical for seed development. Consequently, determining the function of the entire gene family in somatic tissues by mutant analysis has not been possible. Here, we bypassed the reproductive defects of dme mutants to create somatic quadruple homozygous mutants of the entire DME family. dme; ros1; dml2; dml3 (drdd) leaves exhibit hypermethylated genomes compared to both wild-type plants and rdd triple mutants, indicating functional redundancy among all four demethylases. Targets of demethylation include regions co-targeted by RNA-directed DNA methylation and, surprisingly, CG gene body methylation, indicating dynamic methylation at these less-understood sites. Additionally, many tissue-specific methylation differences are absent in drdd, suggesting a role for active demethylation in generating divergent epigenetic states across wild-type tissues. Furthermore, drdd plants display an early flowering phenotype, which is correlated with 5’ hypermethylation and transcriptional down-regulation of FLOWERING LOCUS C. Active DNA demethylation is therefore required for proper methylation patterning across somatic tissues and defines the epigenetic landscape of both intergenic and coding regions.

overall_design: Whole genome bisulfite sequencing (BS-seq), enzymatic-methyl (EM) sequencing and RNA-seq of Arabidopsis thalana DNA demethylation mutants

first: Ben

last: Williams

first: Lindsey

middle: L

last: Bechen

first: Deborah

middle: A

last: Pohlmann


title: TGFβ/Cyclin D1/Smad-mediated inhibition of BMP4 promotes breast cancer stem cell self-renewal activity

city: Montreal

first: Jean-Jacques

last: Lebrun

state: QC

address: 1001 Boulevard Decarie

country: Canada

institute: McGill University

summary: To understand the mechanism by which TGFβ regulates tumor initiation in triple negative breast cancer (TNBC), we performed microarray analysis using Illumina Human HT-12 Gene Expression BeadChip. A TNBC cell line of SCP2 was treated or not with TGFβ for 24 hours. Differentially expressed genes were analyzed by comparing treated versus non-treated samples

overall_design: Triple negative breast cancer cells, SCP2, were serum-starved for overnight and treated or not with 100 pM TGFβ for 24 hours in serum-free medium. Total RNA samples were extracted using the TRIzol reagent (Invitrogen).

first: Gang

last: Yan

first: Meiou

last: Dai


title: RNA-seq data of nasopharyngeal carcinoma (NPC) cell and GO-PEG_erlotinib treatment

city: Taipei

first: MingYing

address: No.201, Sec. 2, Shipai Rd., Beitou District

department: Department of Otolaryngology-Head and Neck Surgery

country: Taiwan

institute: Taipei Veterans General Hospital, Taipei, Taiwan

summary: graphene oxide (GO) is found to be a promising novel anti-cancer drug carrier. Erlotinib, a tyrosine kinase inhibitor (TKI) acting on the epidermal growth factor receptor (EGFR), has been proved for locally advanced or metastatic non-small cell lung cancer (NSCLC) and in combination with gemcitabine for locally advanced or metastatic pancreatic cancer in 2004, but its study in nasopharyngeal carcinoma (NPC) is still limited. We designed functionalized GO, polyethylene glycol-coated GO (GO-PEG), as drug carriers, which was loaded with erlotinib and showed promising anticancer effect on NPC cells. Our results showed that GO-PEG-erlotinib effectively suppressed NPC cell proliferation, migration, and invasion, likely by several mechanisms. GO-PEG-erlotinib may be the potential therapeutic agents for treating NPC in the future.

overall_design: Total RNA from NPC cells treated with or without GO-PEG_erlotinib for 72 hours at 37°C was extracted with RNeasy Mini Kit (Qiagen, Germany) according to the manufacturer's protocol. RNA was subjected to RNA-Seq analysis on BGISEQ-500 system by Tri-I Biotech, Inc.

first: Ming-Ying

first: Yen-Bin

last: Hsu

first: Ming-Chin

first: Yu-Jen

last: Lu

first: Jyh-Ping

last: Chen


title: Somatic DNA demethylation generates tissue-specific methylation states and impacts flowering time


title: Comparative analysis of multiple human cell lines reveals distinct stability regulation of alternative polyadenylation isoforms and mitochondrial RNAs in neuronal cells

city: Newark

first: Aysegul

last: Guvenek

state: New Jersey

address: 205 South Orange Ave.

institute: Rutgers University

summary: mRNA stability plays an important role in gene expression. Here, using 3’ end sequencing of newly made and steady-state poly(A)+ RNAs, we compare transcript stability in multiple human cell lines, including HEK293T, HepG2, SH-SY5Y. We show that while mRNA stability is generally conserved across the cell lines, specific transcripts having high GC content and likely more stable secondary RNA structures are relatively more stable in SH-SY5Y cells compared to other two. These features also differentiate alternative polyadenylation (APA) 3’UTR isoforms in their stability difference in a cell type-specific manner. By analyzing cell differentiation of a neural stem cell line, we show that mRNA stability difference could contribute to gene expression changes in neurogenesis and confirms the neuronal identity of SH-SY5Y cells at gene expression and APA levels. Through comparison of APA isoforms, we show that mRNA stability control buffer the cleavage and polyadenylation site (PAS) choice in the cells studied. In addition, transcripts using intronic PAS are generally less stable, especially when the intron harboring the PAS is large and has a strong 5’ splice site, suggesting that intronic polyadenylation mostly plays a negative role in gene expression. Moreover, we found that poly(A)+ RNAs encoded by the mitochondrial genome are more stable in SH-SY5Y cells than the other two cell types, suggesting that mitochondrial RNA metabolism is distinct in neurons. Together, our results reveal multiple cell-specific mechanisms by which mRNA stability could contribute to the gene expression and APA programs that are important for cell identity.

overall_design: 1-  3'READS libraries for human HEK293T, HepG2 and SY5Y cells.  Briefly, cell media were supplemented with 50uM of 4-thiouridine (4sU, Sigma) for 1 hr before harvest. Newly transcribed (4sU) and pre-existing flow-through (Ft) RNA populations were fractionated using a previously described protocol (Radle et al., 2013). Both fractions and total RNA  for each cell lines were subjected to the 3’READS+ library preparation. 2-  3'READS libraries for human neuronal stem cells and differentiatied neurons.

first: Jihae

last: Shin

first: Lidia

last: De Filippis

first: Dinghai

last: Zheng

first: Wei

last: Wang

first: Zhiping

last: Pang

first: Bin

last: Tian


title: c-di-AMP signaling is required for bile salts resistance and long-term colonization by Clostridioides difficile

city: Gif-sur-Yvette

first: Johann

last: Peltier

address: 1, avenue de la terasse

country: France

summary: In this study, we showed for the first time that c-di-AMP is produced by C. difficile and controls the uptake of potassium, making it essential for growth. We found that c-di-AMP is involved in biofilm formation, cell wall homeostasis, osmotolerance as well as detergent and bile salt resistance in C. difficile. We identified BusR as a new regulator that binds c-di-AMP and represses the expression of the compatible solute transporter BusAA-AB. Interestingly, a busR mutant is highly resistant to a hyperosmotic or bile salt stress compared to the parental strain while a busAA mutant is more susceptible. A short exposure of C. difficile cells to bile salts resulted in a decrease of the c-di-AMP concentrations reinforcing the hypothesis that changes in membrane characteristics due to variations of the cellular turgor or membrane damages constitute a signal for the adjustment of the intracellular c-di-AMP concentration. In a colonization mouse model, a strain producing elevated c-di-AMP concentrations failed to persist in the gut in contrast to the parental strain. Thus, c-di-AMP is a signaling molecule with pleiotropic effects that controls osmolyte uptake to confer osmotolerance and bile salt resistance in C. difficile and that is important for colonization of the host.

overall_design: Strain 630∆erm∆gdpP served as the control strain. Expression in 630∆erm∆gdpP∆busR was compared to this control strain. Four independent replicates are included.

first: Marine

last: Oberkampf

first: Audrey

last: Hamiot

first: Pamela

last: Altamirano-Silva

first: Paula

last: Bellés-Sancho

first: Yannick

middle: D

last: Tremblay

first: Nicholas

last: DiBenedetto

first: Roland

last: Seifert

first: Olga

last: Soutourina

first: Lynn

last: Bry

first: Bruno

last: Dupuy


title: Somatic DNA demethylation generates tissue-specific methylation states and impacts flowering time [BiSulfite-seq]

first: Mary

last: Gehring

first: Ben

last: Williams

first: Lindsey

last: Bechen

first: Deborah

last: Pohlmann


title: Prmt1 safeguards mouse embryonic stem cells against bias toward the extraembryonic endoderm cell fate via arginine methylation of Klf4

city: Beijing

first: Zhenyu

last: Zuo

address: 5 Dongdan Santiao

department: Biochemistry and Molecular Biology

institute: Chinese Academy of Medical Sciences & Peking Union Medical College

summary: Heterogeneous gene expression is a characteristic feature of stem cells and is essential for steering lineage choices. However, the molecular mechanisms of heterogeneity remain largely unknown. Here, we report that depletion of protein arginine methyltransferase 1 (Prmt1) in mouse embryonic stem (ES) cells heterogeneously induces the expression of primitive endoderm (PrE) genes, consequently biasing the cells to fluctuate toward the extraembryonic endoderm stem (XEN) cell fate. Furthermore, the pluripotency factor Klf4 is arginine-methylated by Prmt1 at arginine 396 (R396), which is required for recruitment of the mSin3a/HDAC complex to silence PrE genes. Importantly, when methylation is disrupted by a Prmt1 knockout, a Prmt1 inhibitor, or a blocked methylation site in Klf4, ES cells are predisposed to XEN induction. Our data demonstrate the importance of Prmt1 in the fluctuating heterogeneity of ES cells and reveal a regulatory mechanism for cell fate decisions that is centered on Klf4 methylation mediated by Prmt1.

overall_design: Examination the transcriptomes of WT mouse ES cells (as a control) and Prmt1 KO cells, generated by RNA-seq and 10X genomics singel cell RNA seq.

first: Ye

last: Zhang

first: Guanghui

last: Yang


title: Systemic epigenetic alterations are associated with gastric emptying disturbances in Non-Ulcer Dyspepsia

status: Public on Dec 26 2021

city: Rochester

first: Aditya

last: Bhagwate

state: MN

address: 200 1st Street SW

institute: Mayo Clinic

summary:
Background.  The mechanisms by which environmental risk factors (eg, stress) predispose to symptoms and gastric emptying (GE) disturbances in non-ulcer dyspepsia (NUD) is unknown.  Our aims were to compare the circulating leukocytes’ epigenome between NUD patients with normal versus delayed and normal versus rapid GE.
Methods.  In 24 NUD patients, we evaluated gastrointestinal symptoms, GE (scintigraphy) and 3 promoter/enhancer-associated histone modifications (H3K4me3, H3K9ac, and H3K27ac) by chromatin immunoprecipitation-sequencing in buffy coats, then compared the genome-wide binding of histone marks between patients with normal versus delayed and normal versus rapid GE.
Key results.  GE was normal (9 patients), delayed (6 patients), or rapid (9 patients).  Compared to normal GE, there was differential binding of H3K4me3, which marks active promoters, at 100 genes in delayed and 233 genes in rapid GE (FDR < 0.05).  Delayed GE was associated with increased H3K4me3 binding at several genes that regulate T cell functions (eg, CD247, IL2RA, CD69, CD96, ICOS, ITK, and GRAP2); conversely, binding was reduced at genes that regulate neuronal synapses (ie, SYT6, SYT12, CDH2, CDH11, EFNB3, CAMK2B, and SHISA6) and neuronal nitric oxide synthase (NOS1).  In rapid GE, genes related to opioid signaling (OPRD1, MAPK4, CAMK2B, and PDE1C), neuronal development, and synaptic functions bound less H3K4me3.  No or few genes were differentially enriched with H3K9ac and H3K27ac.
Conclusions.  H3K4me3 discriminates among patients with normal, rapid, and delayed GE.  Delayed GE is associated with alterations that suggest increased T-cell functions.  Rapid GE is associated with changes suggesting reduced opioid signaling.

overall_design: Comparison of 3 histone marks (H3K4me3, H3K9ac and H3K27ac) in buffy coat samples from NUD patients with delayed versus normal GE and rapid versus normal GE.

first: Susrutha

last: Puthanmadhom Narayanan

first: Jeong-Heon

last: Lee

first: Adil

middle: E

last: Bharucha


title: Gene expression profile of ARID3B knockout in HCT15 cells

first: Tsai-Tsen

last: Liao

address: No.201, Sec.2, Shih-Pai Rd. Peitou, Taipei, Taiwan, 11221, R.O.C

institute: Institute of Clinical Medicine

summary: Microarray analyses for identification of the differences in gene expression patterns have increased our understanding of the molecular mechanism of ARID3B in colon caner cellls.We used gene expression analysis data from HCT15-ARID3B-Cas9 and HCT15-Ctrl to identify differentially expressed probes.

overall_design: The Cas9/gRNA target sites containing20 bp gRNA sequence plus the PAM sequence (NGG) using Jack Lin’s CRISPR/Cas9 gRNA finder tool. The gRNA using for knockout ARID3B was predicted by blasting with human genomic and transcript sequences using the NCBI/blastn suite for the detection of potential off-targets.

first: Yang

last: Muh-Hwa

first: Liao

last: Tsai-Tsen


title: Single-Cell RNA-seq Transcriptome Profiling from Male Germ Cells Isolated from Neonatal Mouse Testes

status: Public on Dec 25 2021

city: RTP

first: Xiaojiang

last: Xu

state: North Carolina

address: 111 T. W. Alexander Dr.,

institute: NIEHS

summary: P8 CD9+ spermatogonia from WT mice were enriched by FACS

overall_design: scRNA-seq was performed using P8 CD9+ testicular cells from control mice to identify different subpopulations. Re-clustering of germ cells was performed to determine the germ cell distribution.

first: Qing

last: Chen

first: Guang

last: Hu


title: Single-cell RNA-seq in Reninnull cells and WT renin cells

city: Charlottesville

first: Alexandre de

middle: Goes

last: Martini

state: VA

address: 409 Lane Road, MR4

department: Pediatrics Nephrology

institute: University of Virginia

summary: We have used single-cell RNA-seq to identify transcriptional differences between WT renin cells and renin cells with deletion of the renin gene

overall_design: Examination of the transcriptome in WT renin cells and Reninnull cells

first: Watanabe

last: Hirofumi

first: Martini

middle: G

last: Alexandre

first: Brown

last: Evan


title: Tuft cell-produced cysteinyl leukotrienes and IL-25 synergistically promote lung type 2 inflammation

city: Boston

first: Adam

last: Haber

state: Massachusetts

address: 665 Huntington Ave, HSPH Building 1, Room 305

institute: Harvard T. H. Chan School of Public Health

summary: Aeroallergen sensing by airway epithelial cells can trigger pathogenic immune responses leading to chronic type 2 inflammation, the hallmark of airway diseases such as asthma. Airway tuft cells are specialized chemosensory epithelial cells and the dominant source of the epithelial cytokine IL-25 in the trachea and of cysteinyl leukotrienes (CysLTs) in the naïve murine nasal mucosa. How IL-25 and CysLTs might cooperatively promote type 2 inflammation in the airways has not been clarified. Here, we showed that inhalation of LTC4 in combination with a subthreshold dose of IL-25 led to dramatic synergistic induction of type 2 inflammation throughout the lungs, causing rapid eosinophilia, inflammatory type 2 innate lymphoid cell (ILC2) proliferation and type 2 cytokine production, dendritic cell (DC) and CD4+ T cell recruitment and goblet cell hyperplasia. While lung eosinophilia was dominantly mediated through the classical CysLT receptor CysLT1R, type 2 cytokines and activation of innate immune cells required signaling through both CysLT1R and CysLT2R. Tuft cell-specific deletion of Ltc4s, the terminal enzyme required for CysLT production, reduced lung inflammation and the systemic immune response after inhalation of the mold aeroallergen Alternaria; this effect was further enhanced by concomitant blockade of IL-25. Our findings identified a potent synergy of CysLTs and IL-25 downstream of aeroallergen-trigged activation of airway tuft cells leading to a highly polarized type 2 immune response and further implicate airway tuft cells as powerful modulators of type 2 immunity in the lungs.

overall_design: For single-cell preparations of tuft cells from the nasal mucosa, mouse snouts were processed with dispase solution, followed by mechanical separation and a second digestion with a papain containing tyrode-based solution (15, 73). Tuft cells were defined as as EpCAMhighTomato+ in ChatCreTomato and ChatCreTomatoLtc4sfl/fl mice, EpCAMhighCD45neg/lowSSClow in Ltc4sfl/fl and ChatCreLtc4sfl/fl mice. To isolate macrophages and dendritic cells, the snouts were enzymatically dissociated with a PBS-based solution containing collagenase IV, dispase and DNAse. Macrophages were defined as CD11b+CD11c+SiglecF+ and dendritic cells as SiglecF-CD11b+CD11c+MHCII+ (Fig. S5C). For RNA sequencing, at least 500 but no more than 1300 tuft cells, macrophages or dendritic cells from 1 naïve digested mouse snout were sorted into TCL buffer (Qiagen) supplemented with 1% 2-mercaptoethanol (Gibco).

first: Saltanat

last: Ualiyeva

first: Evan

last: Lemire

first: Evelyn

middle: C

last: Aviles

first: Caitlin

last: Wong

first: Amelia

last: Boyd

first: Juying

last: Lai

first: Tao

last: Liu

first: Ichiro

last: Matsumoto

first: Nora

last: Barrett

first: Joshua

last: Boyce

first: Lora

last: Bankova


title: Genome-wide maps of HSF1 phase separation in heat shock and non-heat shock cells

status: Public on Dec 24 2021

first: Shipeng

last: Shao

state: Please Select

address: No.5 Yiheyuan Road Haidian District, Bei, jing,china

institute: Peking University

summary: HSF1 binds DNA via the DBD domain, causing gene upregulation during HS. We assessed the effect of RD-mediated phase separation on chromatin targeting of HSF1 using Cut&Tag followed by high-throughput sequencing to map genome-wide binding of LLPS-competent versus LLPS-incompetent HSF1 mutants under both HS and NHS conditions. Comparing with WT HSF1 under NHS, both WT under HS and M1 under NHS showed increased and broad binding to enhancers and distal intergenic region, with binding most enriched in expected motifs of HSF-related transcription factors. To further assess the role for IDR-induced LLPS in chromatin targeting of HSF1, we used several additional strategies. First, the treatment of 1,6-hexanediol markedly decreased chromatin occupancy both of WT under HS and M1 under NHS conditions. Second, we interrogate chromatin binding of LLPS-deficient mutant M3. Cut&Tag analysis revealed that M3 showed decreased chromatin binding compared to WT under HS and M1 under NHS. The decreased chromatin binding of M3 to chromatin was not due to the loss of its DNA binding ability, as the EMSA assay revealed that M3 was still capable of binding HSE. Instead, the decreased chromatin binding reflects the loss of inter-molecular interaction between HSF1 that holds LLPS. Furthermore, M3 in heat shocked cells shows similar reduced genomic targeting and shallow binding pattern as NHS cells . Third, the enrichment of transcriptional apparatus RNA Pol II, CYCT1, BRD4 to HSF1 target genes also depend on whether HSF1 can phase separate at these sites. Lastly, we conducted live cell single molecule imaging to evaluate chromatin binding kinetics of LLPS-deficient mutant M3 relative to WT HSF1. Measurements of single molecule displacement and diffusion coefficient showed M3 to be significantly more mobile than WT under HS, which suggests M3 was less confined within phase-separated puncta compared with LLPS-competent HSF1. Consistent with this result, super resolution imaging of M3 also showed decreased cluster formation at HSP gene foci but maintained nSBs formation. Altogether, LLPS-forming capability of HSF1 is essential for the efficient recruitment of HSF1 and transcriptional apparatus to HSP gene loci.

overall_design: Examination of genome-wide binding of LLPS-competent versus LLPS-incompetent HSF1 mutants under both HS and NHS conditions.

first: Hongchen

last: Zhang

first: Yujie

last: Sun


title: Custom gene expression panel for evaluation of potential molecular markers in hepatocellular carcinoma

city: Tuebingen

first: Srinivas

middle: Reddy

last: Pallerla

state: Baden-Württemberg

address: Wilhelmstraße 27

department: Institute for Tropical Medicine

institute: Universitätsklinikum Tübingen

summary: We studied 20 candidate genes (HCC hub genes, potential drug target genes, predominant somatic mutant genes) retrieved from available literature and public databases with potential to be used as biomarkers for the prognosis of HCC and prediction of treatment outcome. We analysed expression of the genes by RT-qPCR in 30 HCC tumor and adjacent non-tumor paired samples from Vietnamese patients.

overall_design: qPCR gene expression profiling.  Thirty Hepatocellular carcinoma (HCC) tumor and adjacent non-tumor paired samples were used in this study. One microgram (1µg) total RNA from each sample was used for gene expression analysis.

middle: R

first: Nghiem

last: Hoan


title: Transcriptomic study of hydrogen sulfide toxicity in Methylococcus capsulatus

city: Urbana

first: Sichong

last: Pei

state: IL

address: 600 S Mathews, RM210

department: Chemical and biomolecular engineering

institute: University of Illinois Urbana-Champaign

summary: Stress response of Methylococcus capsulatus str.Bath toward hydrogen sulfide (H2S) was investigated via physiological study and transcriptomic profiling. M. capsulatus (Bath) can grow and tolerate up to 0.75%vol H2S in headspace. Vast change in pH suggests biological relevant sulfide oxidation. Dozens of H2S-sensitive genes were identified from comparison of cell transcriptome in different H2S concentrations. Mc sulfide quinone reductase (SQR) and persulfide dioxygenase were found to be active during sulfide detoxification. Moreover, xoxF, a novel lanthanide(Ln)-dependent methanol dehydrogenase (MDH) was overexpressed in H2S while mxaF, a calcium-dependent MDH, was down-regulated, and such MDH switch phenomenon is also well known to be induced by addition of lanthanide via an as-yet-unknown mechanism. Activities in quorum sensing and RND efflux pump also suggest their role in sulfide detoxification, and might provide insight on the xoxF/mxaF switch mechanism.

overall_design: RNA profile of M. capsulatus at mid-log phase as wild type, and in 0.1%, 0.5% and 0.75%H2S, and a H2S shock treatment.

first: Christopher

last: Rao

first: Roderick

last: Mackie


title: Antibacterial mechanism of the Asp - Asp - Asp - Tyr peptide [P. aeruginosa]

first: shanshan

last: Zhuang

state: Guangdong

address: Guangzhou, Guangdong, 510225, China

department: College of Light Industry and Food

institute: Zhongkai College of Agriculture and Engineering

summary:
Previously, we found that ASP-ASP-ASP-TYR (DDDY) from Dendrobium aphyllum has a minimum inhibitory concentration of 36.15 mg/mL against Pseudomonas aeruginosa. Here, we explored the antibacterial mechanism of DDDY and its potential preservation applications. Metabolomic and transcriptomic analyses revealed that DDDY mainly affects genes involved in P. aeruginosa membrane transport and amino acid metabolism pathways. Molecular dynamics simulation revealed that DDDY had a stronger effect on 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoethanolamine phospholipid membranes than on 1-palmitoyl-2-oleoyl-lecithin or 1-palmitoyl-2-oleoyl phosphatidylglycerol membranes, with high DDDY concentrations displaying stronger efficacy on 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoethanolamine. Mechanistically, the N-terminal of DDDY first bound to the phospholipid head group, while its C-terminal amino acid residue bound the hydrophobic tail, thereby creating a gap in the membrane when the phospholipids were clustered by hydrogen bonding. Finally, DDDY inhibited the growth of food microorganisms inoculated onto chestnut kernels, suggesting that DDDY is a promising antibacterial agent against multidrug-resistant gram-negative bacteria.
Inhibitory effect of ASP-ASP-ASP-TYR (DDDY) from Dendrobium on Pseudomonas aeruginosa

overall_design: P. aeruginosa was incubated in TSB at 37 C for 8 h. During the logarithmic phase, 200 μL of bacterial solution was added to 200 mL of liquid medium, 200 μL of sterile water (control group; P_CK), or 50 mg/mL of DDDY solution (treatment group; P_DDDY). The bacteria were then cultured on a shaking table at 150 R/min and 37 C for 24 h, centrifuged at 6000 R/min and 4 C for 10 min, washed with PBS three times, and then collected and stored at -80 C.

first: Shanshan

first: Yao

last: Bao

first: Yaxin

first: Huangyou

first: Jianliang

first: Huifan


title: Antibacterial mechanism of the Asp - Asp - Asp - Tyr peptide

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

sample_organism:
Pseudomonas aeruginosa
Escherichia coli

platform_organism:
Pseudomonas aeruginosa
Escherichia coli

overall_design: Refer to individual Series


title: Rtf2 is Important for Replication Fork Barrier Activity of RTS1 via Splicing of Rtf1 [cDNA-Seq]

city: Brighton

first: Alice

last: Budden

address: Science Park Road

department: GDSC

country: United Kingdom

institute: University of Sussex

summary: This study investigated the role Rtf2 plays on the replication fork barrier (RFB) activity of RTS1 in S. pombe. We confirm Rtf2 is important for the full barrier activity of the RTS1-Rtf1 RFB. We show that Rtf2 does not enact its enhancing effect on RTS1 RFB activity via binding to Region A of RTS1, but instead we find it to be closely associated with several splicing factors. Analysis of cells deleted for rtf2 by cDNA-Seq reveal splicing defects specifically effecting intron retention, including for the Rtf1 transcript. We show that intron retention within rtf1 is responsible for the reduced barrier activity of RTS1 when rtf2 is deleted. This study reveals Rtf2 to be an important factor for maintaining efficient splicing within the cell.

overall_design: Full length cDNA libraries were made from isolated mRNA from S. pombe and sequenced using Nanopore Technology to analyse changes to splicing

first: Murat

last: Eravci

first: Eduard

last: Campillo-Funollet

first: Adam

middle: T

last: Watson

first: Karel

last: Naiman

first: Anthony

middle: M

last: Carr


title: Rtf2 is Important for Replication Fork Barrier Activity of RTS1 via Splicing of Rtf1


title: Host Induced Gene Silencing of the Sclerotinia sclerotiorum ABHYDROLASE-3 gene reduces disease severity in Brassica napus [small RNA]

city: Winnipeg

first: Nick

last: Wytinck

state: MB

address: 50 Sifton Road

department: Department of Biological Sciences

institute: University of Manitoba

summary: Sclerotinia sclerotiorum is a pathogenic fungus that infects hundreds of crop species, causing extensive yield loss every year. Chemical fungicides are used to control this phytopathogen, but with concerns about increasing resistance and impacts on non-target species, there is a need to develop alternative control measures. In the present study, we engineered Brassica napus to constitutively express a hairpin (hp)RNA molecule to silence ABHYRDOLASE-3 in S. sclerotiorum. We demonstrate the potential for Host Induced Gene Silencing (HIGS) to protect B. napus from S. sclerotiorum using leaf, stem and whole plant infection assays. The interaction between the transgenic host plant and invading pathogen was further characterized at the molecular level using dual-RNA sequencing and at the anatomical level through microscopy to understand the processes and possible mechanisms leading to increased tolerance to this damaging necrotroph. We observed significant shifts in the expression of genes relating to plant defense as well as cellular differences in the form of structural barriers around the site of infection in the HIGS-protected plants. Our results provide proof-of-concept that HIGS is an effective means of limiting damage caused by S. sclerotiorum to the plant and demonstrates the utility of this biotechnology in the development of resistance against fungal pathogens.

overall_design: Examination of infected stem tissue from untransformed and RNAi canola, 0, 1 and 7 days post infection.

first: Dylan

last: Ziegler

first: Philip

last: Walker

first: Daniel

last: Sullivan

first: Kirsten

last: Biggar

first: Deirdre

last: Khan

first: Solihu

middle: K

last: Sakariyahu

first: Olivia

last: Wilkins

first: Steve

last: Whyard

first: Mark

last: Belmonte


title: Rtf2 is Important for Replication Fork Barrier Activity of RTS1 via Splicing of Rtf1 [Pu-Seq]

overall_design: Ribonucleotides incorporated by mutant DNA polymerase delta and epsilon were mapped at single-nucleotide resolution to produce data for following the levels of replication fork restart at RTS1


title: Gene expression signatures for plumbagin (PL) treatment in OSCC cell lines

city: Nagoya

first: Akinobu

last: Ota

state: Aichi

address: 1-1 Yazakokarimata

department: Food and Nutritional Environment

country: Japan

institute: Kinjo Gakuin University

summary: To investigate the effect of PL on gene expression, we have employed whole genome microarray expression profiling as a discovery platform to identify genes with the potential to suppress the cell proliferation of OSCC cell lines. SAS and HSC-3 cells were treated with PL (5 μmol/L) for 4 h in vitro.

overall_design: SAS and HSC-3 cells were treated with PL for 4 h in vitro.

first: Takayuki

last: Ono


title: Genome binding/occupancy profiling of Zfp831-HA

first: Chen

last: Dong

address: Haidian District

department: Institute for Immunology and School of Medicine

institute: Tsinghua University

summary: Zfp831 is required for proper Tfh cell differentiation. In order to further understand the mechanisms whereby Zfp831 enhances Tfh differentiation, we conducted ChIP-seq analysis of Zfp831-HA

overall_design: Naïve CD4+ T cells were sorted from wild type mice and activated. pRV-Zfp831-HA was virally tranfected to the cells. 24 hours later, the collected cells were then subjected to ChIP and construction of library for ChIP-seq.

first: Siyuan

last: Wan

first: Xiaohong

last: Zhao


title: gene expression in hippocampus from  ophn1tim1Bill mouse males and controls during 24h

city: Paris

first: Pierre

last: Billuart

address: 102 rue de la santé

department: IPNP

institute: INSERM

summary:
Oligophrenin1 X-linked Intelectual disability (ID) gene is mutated in ID patients with cerebellar hypoplasia. It encodes OPHN1 protein which has been shown to interact with Rev-erb alpha, a negative regulator of the circadian clock in cells (https://doi.org/10.1038/nn.2911)
In this study, we searched fo gene expression differences in hippocampi from adult mouse ophn1 KO and controls during 24 hours. Three replicates were collected evey 6 hours for both genotype. Data from controls were analyzed and reported in http://dx.doi.org/10.1016/j.neuroscience.2015.08.066.

overall_design: Adult males were placed in dark room for 24 hours before the collection of the hippocampus every 6 hours . PCA allowed the exclusion of two time points in controls (t=0 and 12).

first: Maria

last: Passafaro

first: Olivier

last: Dorseuil


title: Transcription Factor RFX3 Stabilizes Mammary Basal Cell Identity

status: Public on Dec 23 2021

city: Nashville

first: Ian

last: Macara

address: 465 21st Ave South

institute: Vanderbilt University

summary: We report the role of RFX3 in the stabilization of the basal cell lineages

overall_design:
Bulk RNA seq
Total RNA (50-200ng) isolation was performed using either TRIzol (Life Technologies) or the RNeasy Mini Kit (Qiagen, Hilden, Germany).

5 samples of myoepithelial cells and 5 samples of s-SHIP GFP+ cap cells from 5-week-old female Tg11.5kb-GFP mice were submitted and subjected to quality analysis using a 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA). All Samples had an average RNA integrity number (RIN) value ∼8. Libraries for whole transcriptome analysis were generated following Illumina’s TruSeq RNA v2 sample preparation protocol. Libraries were sequenced on an Illumina HiSeq 3000. 150 million reads at 75 basepairs were obtained for each of the samples.

Single-Cell RNA seq
After 96 hrs cultivation, myoepitheial cells were dissociated using TrypLE and cell viability was determined using Trypan Blue. The control sample (fresh s-SHIP GFP+ cap cells, myoepithelial cells and luminal cells) and cultivated cells were encapsulated and barcoded using the inDrop platform (1CellBio) with an in vitro transcription library preparation protocol (Klein et al., 2015).

first: Erica

last: Tross

first: Christian

last: de Caestecker

first: Ken

last: Lau


title: dSirt6 Regulates Lifespan in Drosophila

city: Providence

first: Jackson

last: Taylor

state: RI

address: 185 Meeting St, MCB G-L 163

department: Molecular Biology, Cell Biology, and Biochemistry

institute: Brown University

summary: Sirt6 is a multifunctional enzyme that regulates diverse cellular processes such as metabolism, DNA repair, and aging. Overexpressing Sirt6 extends lifespan in mice, but the underlying cellular mechanisms are unclear. Drosophila melanogaster are an excellent model to study genetic regulation of lifespan; however, despite extensive study in mammals, very little is known about Sirt6 function in flies. Here, we characterized the Drosophila ortholog of Sirt6, dSirt6, and examined its role in regulating longevity. dSirt6 is a nuclear and chromatin-associated protein with NAD+-dependent histone deacetylase activity. dSirt6 overexpression in flies produces robust lifespan extension in both sexes, while reducing dSirt6 levels shortens lifespan. dSirt6 OE flies have normal food consumption and fertility, but increased resistance to oxidative stress and reduced protein synthesis rates. Transcriptomic analyses reveal that dSirt6 OE reduces expression of genes involved in ribosome biogenesis, including many dMyc target genes. dSirt6 OE partially rescues many effects of dMyc OE, including increased nuclear size, up-regulation of ribosome biogenesis genes, and lifespan shortening. Lastly, dMyc haploinsufficiency does not convey additional lifespan extension to dSirt6 OE flies, suggesting dSirt6 OE is upstream of dMyc in regulating lifespan. Our results provide new insight into the mechanisms by which Sirt6 overexpression leads to longer lifespan.

overall_design: Fat Body mRNA profiles of 10-day old and 40-day old wild type (WT) and dSirt6 Overexpressing Flies

first: Stephen

last: Helfand


title: Premature senescence and increased oxidative stress in the thymus of Down Syndrome patients

city: Milan

first: Stefano

last: Beretta

address: Via Olgettina, 60

institute: San Raffaele Telethon Institute for Gene Therapy

summary: Immunohistochemical analysis of thymic tissue showed signs of accelerated thymic aging in down syndrome (DS) patients, normally seen in older healthy subjects. We then performed RNA-Seq analysis on human Epcam-enriched thymic epithelial cells (hTEC), isolated from three DS children, which revealed disease-specific transcriptomic alterations. Gene set enrichment analysis (GSEA) of DS TEC revealed an enrichment in genes involved in cellular response to stress, epigenetic histone DNA modifications and senescence. Analysis of senescent markers and oxidative stress in hTEC and thymocytes confirmed these findings. We detected senescence features in DS TEC, thymocytes and peripheral T cells, such as increased -galactosidase activity, increased levels of the cell cycle inhibitor p16, telomere markers and increased levels of reactive oxygen species (ROS), all factors contributing to cellular damage.

overall_design: RNA-Seq analysis on sorted CD45- Epcam-enriched hTEC from DS patients and HD. Frozen samples of 3 normal HD and 3 DS patients were analyzed, for a total of 12 samples (Epcam+ and Epcam- for each of the 6 patients).

first: Francesca

last: Ferrua

first: Ivan

last: Merelli

first: Anna

last: Villa


title: scRNA-seq of peripheral blood from West Nile Virus-infected patients

city: Cambridge

first: Ira

middle: Daniel Klein

last: Fleming

address: 400 Main St

institute: MIT

summary: We profile the peripheral blood of patients infected with West Nile Virus with divergent disease-trajectories (West Nile Encephalitis, West Nile Fever, and asymptomatic) during relatively acute infection and at a convalescent timepoint (~90-days later) using single-cell RNA sequencing in an effort to uncover determinants of disease progression and flesh out the landscape of infection. In the blood of the infected patients, stratified cell-states involved in acute viral infection resolve into more homogenous states at the follow-up blood draws, A dramatic shared transcriptional shift between the primary blood-draws during acute infection and the 90-day follow-ups in all observed compartments allows us to highlight multiple cell-type and cell-state-specific patterns of gene expression.

overall_design: Single-cell RNA on patient samples infected with West Nile Virus

first: Erol

last: Fikrig

first: David

last: Halfer

first: Steven

middle: H

last: Kleinstein

first: Christopher

middle: J

last: Love

first: Ruth

last: Montgomery

first: Kristy

middle: O

last: Murray

first: Shannon

last: Ronca

first: Alex

last: Shalek

first: Xiaomei

last: Wang


title: Comparison of mitochondrial unprocessed RNA frequency in wild type and mutant mitochondrial RNA polymerase overexpression flies.

city: Bethesda

first: Mehdi

last: Pirooznia

state: MD

address: 12 SOUTH DR

institute: National Institutes of Health

summary: The goal of this study is to compare the frequency of unprocessed preRNAs in mitochondria. Total mitochondrial RNA profiles of adult flies were generated in triplicates. We analyzed over 100 million reads for each group and used featureCounts to perform quantification allowing a read to be assigned to more than one gene. Using this analysis pipe line, we mapped about 30 million reads per sample to the Drosophila mitochondrial genome and identified a fequency of unprocessed preRNAs as 0.43% in PolrMT group, which is similar to that in PolrMT-E423P flies. These result revealed that overexpression of PolrMT-E423P does not contribute to pre-RNA processing.

overall_design: Total mitochondrial RNA profiles of PolrMT (mitochondrial RNA polymerase) and PolrMT-E423P overexpression flies were generated by deep sequencing in triplicate to examine mitochondrial unprocessed preRNAs frequency.

first: Yi

last: Liu

first: Ilker

last: Tunc

first: Yuesheng

last: Li


title: Physico-chemical principles of HDL-small RNA binding interactions

first: Danielle

last: Michell

state: TN

address: 2220 Pierece Ave

department: Department of Medicine

institute: Vanderbilt Univ. Medical Center

summary: Profiling the host and non-host human HDL-tDR profile in those with atherosclerosis

overall_design: sRNA sequencing of human high density lipoproteins (HDL) from healthy controls and those with a coronary artery calcium score > 0

first: Daniell

first: Kasey

last: Vickers


title: Genome-wide methylation analysis in Anti-tuberculosis Drug Induced Liver Injury case and control samples

city: Shanghai

first: Cong

last: Huai

address: No.1954. Huashang Rd.

institute: Shanghai Jiaotong University

summary: Association analysis of DNA methylation in Anti-tuberculosis Drug Induced Liver Injury case and control samples from peripheral blood

overall_design: Case-control association analysis, 48 DILI cases and 50 controls

first: Hao

last: Wu

first: Shengying

last: Qin


title: a-Synuclein Antisense Transcript SNCA-AS1 regulates synapses- and aging-related genes suggesting its implication in Parkinson’s Disease

first: Letizia

last: Messa

address: Piazza Leonardo Da Vinci 32

department: Electronics, Informatics and Bioengineering

institute: Politecnico di Milano

summary: SNCA protein product, a-synuclein, is widely renowned for its role in synaptogenesis and implication in both aging and Parkinson’s Disease (PD), but research efforts are still needed to elucidate its physiological functions and mechanisms of regulation. In this work, we aim to characterize SNCA-AS1, antisense transcript to the SNCA gene, and its implications in cellular processes. The overexpression of SNCA-AS1 upregulates both SNCA and a-synuclein, and through RNA-seq analysis we investigated the transcriptomic changes of which both genes are responsible. We highlight how they impact neurites extension and synapses’ biology, through specific molecular signatures. We report a reduced expression of markers associated with synaptic plasticity, and we specifically focus on GABAergic and dopaminergic synapses, for their relevance in aging processes and PD, respectively. A reduction in SNCA-AS1 expression leads to the opposite effect. As part of this signature is co-regulated by the two genes, we discriminate between functions elicited by genes specifically altered by SNCA-AS1 or SNCA’s overexpression, observing a relevant role for SNCA-AS1 in synaptogenesis through a shared molecular signature with SNCA. We also highlight how numerous deregulated pathways are implicated in aging-related processes, suggesting that SNCA-AS1 could be a key player in cellular senescence, with implications for aging-related diseases. Indeed, the upregulation of SNCA-AS1 leads to alterations in numerous PD specific genes, with an impact highly comparable to that of SNCA’s upregulation. Our results show that SNCA-AS1 elicits its cellular functions through the regulation of SNCA, with a specific modulation of synaptogenesis and senescence, presenting implications in PD.

overall_design: SH-SY5Y stable transfected either with SNCA-AS1 and SNCA subjected to RNA-Sequencing

first: Federica

last: Rey

first: Cecilia

last: Pandini

first: Rossella

last: Launi

first: Bianca

last: Barzaghini

first: Roberta

last: Zangaglia

first: Manuela

last: Raimondi

first: Stella

last: Gagliardi

first: Cristina

last: Cereda

first: Gian

middle: V

last: Zuccotti

first: Stephana

last: Carelli


title: CD4+CCR6+ T cells dominate the BCG-induced transcriptional signature

city: Linköping

first: Jyotirmoy

last: Das

address: Sandbäcksgatan

department: Department of Biomedical and Clinical Sciences

country: Sweden

institute: Linköping University

summary: The century-old Mycobacterium bovis Bacillus Calmette-Guerin (BCG) remains the only licensed vaccine against tuberculosis (TB). Despite this, there is still a lot to learn about the immune response induced by BCG, both in terms of phenotype and specificity. Here, we investigated immune responses in adult individuals pre and 8 months post BCG vaccination. We specifically determined changes in gene expression, cell subset composition, DNA methylome, and the TCR repertoire induced in PBMCs and CD4 memory T cells associated with antigen stimulation by either BCG or a Mycobacterium tuberculosis (Mtb)-derived peptide pool. Following BCG vaccination, we observed increased frequencies of CCR6+ CD4 T cells, which includes both Th1* and Th17 subsets, and mucosal associated invariant T cells (MAITs). A large number of immune response genes and pathways were upregulated post BCG vaccination with similar patterns observed in both PBMCs and memory CD4 T cells, thus suggesting a substantial role for CD4 T cells in the cellular response to BCG. These upregulated genes and associated pathways were also reflected in the DNA methylome. We described both qualitative and quantitative changes in the BCG-specific TCR repertoire post vaccination, and importantly found evidence for similar TCR repertoires across different subjects. The immune signatures defined herein can be used to track and further characterize immune responses induced by BCG, and can serve as reference for benchmarking novel vaccination strategies.

overall_design: 8 sample DNAs were isolated from the PBMC cells using AllPrep DNA/RNA Mini Kit (Qiagen, Germany). DNA concentration was measured by Qubit fluorometer. DNA samples were bisulphite converted, amplified, fragmented and hybridized to an Illumina Infinium Human Methylation EPIC Bead Chip and scanned.

first: Akul

last: Singhania

first: Paige

last: Dubelko

first: William

last: Chronister

first: Kaylin

last: Muskat

first: Elizabeth

last: Phillips

first: Simon

last: Mallal

first: Grégory

last: Seumois

first: Pandurangan

last: Vijayanand

first: Alessandro

last: Sette

first: Maria

last: Lerm

first: Bjoern

last: Peters

middle: L

last: Arlehamn


title: MCC regulator of WNT signaling pathway (MCC) is a podocyte essential gene

city: Nanjing

first: Jingsong

last: Shi

state: China

address: No.305, Zhongshan East Road

department: National Clinical Research Center of Kidney Disease

institute: Jinling Hospital, Nanjing University School of Medicine

summary: Podocytes are an integral part of the glomerular infiltration barrier. At present, many genes are known essential for podocyte survival and structural and functional homeostasis; however, there are more such genes to be uncovered. By single-cell RNA-seq of mouse podocytes, we detected the expression of gene encoding MCC regulator of WNT signaling pathway (MCC) in majority of the single podocytes and speculated that MCC may be essential for podocytes. We confirmed MCC expression in mouse podocytes and further showed its expression in human podocytes. To experimentally prove the essentiality of MCC for podocytes, we knocked down MCC in cultured podocytes, resulting in marked morphological change of cell shape, cytoskeletal stress fiber disruption, increased apoptosis, and downregulation of podocyte essential genes, CD2AP and WT1, demonstrating that MCC is essential for podocytes. To investigate the mechanism underlying the role of MCC in podocytes, we performed RNA-seq analysis of the podocytes in culture 24 hours after transfection of siRNA against MCC, followed by bioinformatics analysis of the genes with altered expression, and found some mechanistic clues. Lastly, we found that MCC is downregulated in podocytes treated with puromycin aminonucleosides and in glomeruli of diabetic mice and FSGS patients, implicating MCC in the development of podocytopathy and proteinuria. In conclusion, MCC is essential for podocytes and its deficiency may be involved in podocytopathy.

overall_design: Immortalized human podocytes from Dr. Saleem M’s laboratory (University of Bristol, Bristol, UK) were cultured with RPMI1640 medium supplemented with 10% FBS, 1% Pen/Strep and 1% ITS at 33°C in 5% CO2 incubator for growth, followed by trypsinization, replating and culture at 37°C for 10 days to obtain differentiated cells. Then the differentiated podocytes were transfected with siRNA against MCC or left untreated with only vehicle for 24 hours. The cells were homogenized with Trizol (Invitrogen) and the total RNA was extracted following the manual instruction. The RNA was then subject to RNA-seq.

first: Shaolin

first: Hui

last: Song

first: Jinsong


title: Transcriptome profiling from Wild Type and Lss mutant (heterozygous and homozygous) lens at E14.5 reveals the potential pathways involved in cataract formation

city: GaungZhou

first: Minglei

last: Zhao

address: 7#, Jinsui Road

institute: Sun yat sen university

summary: Congenital cataract is one of the leading causes of blindness in children worldwide. About one third of congenital cataracts are caused by genetic defects. Previous studies have identified LSS as a causal gene for congenital cataracts. However, its roles in lens development remains largely unknown. Here, we performed RNA-seq on the lens of WT and Lss mutant (heterozygous and homozygous )at E14.5, identified that cholesterol synthesis signaling pathways were significantly downregulated. Overall, our study points out that LSS functions as a critical determinant of lens development, which will contribute to better understand LSS defects in cataractogenesis and develop therapies for cataract.

overall_design: RNA-seq profiles of lens from WT and Lss mutant (heterozygous and homozygous) at E14.5 mouse

first: Ling


title: Genomic and Clinical Findings in Myeloid Neoplasms with PDGFRB Rearrangement

city: Perugia

first: Danika

last: Di Giacomo

state: Perugia

address: S.Andrea delle fratte

department: Medicine and Surgery

institute: University of Perugia

type: Genome variation profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: Genomic and Clinical Findings in Myeloid Neoplasms with PDGFRB Rearrangement [seq]

summary: Here we characterized a series of 14 cases with myeloid neoplasms using cytogenetic, single nucleotide polymorphism array, and next generation sequencing.

overall_design: Sequencing analysis of thirty genes, recurrently mutated in myeloid malignancies and included in the Myeloid Solution SOPHiA GENETICS (Saint‐Sulpice, Switzerland), was performed on cases with 5q32/PDGFRB involvement. 13 cases were investigated at diagnosis and in 8 cases material from remission was also analyzed.

first: Fabrizia

last: Pellanera

first: Caterina

last: Matteucci

first: Cristina

last: Mecucci


title: The expression level of miRNAs in Control-EXO and RIPC-EXO

city: Guangzhou

first: Danni

last: Li

address: No. 26 Yuancunerheng Road

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

summary: To explore the possibility of miRNA(s) contributing to the cardioprotection induced by plasma exosomes at the late phase of RIPC, we performed a miRNA profiling assay (763 rat miRNAs) comparing the differences between RIPC-exo and Control-exo using Illumina HiSeq 2500 high-throughput sequencing.

overall_design: Control-EXO and RIPC-EXO, the miRNA library preparation and sequencing were conducted using an Illumina HiSeqTM 2500 platform (Ribobio, China).

first: Zhao

last: Yang

first: Sanqing

last: Jin


title: Altered expression of transfer-RNA-derived small RNAs (tsRNAs) in human with rheumatic heart disease

city: changsha

first: Zhaoyu

address: 87 of xiangya road

institute: xiangya hospital

summary: Rheumatic heart disease (RHD) remains a serious public health problem in developing countries. Atrial fibrillation (AF) is a medical complication of RHD. Although the understanding of disease pathogenesis has advanced in recent years, the key questions need to be addressed. Transfer RNA–derived small RNAs (tsRNAs) are a novel type of short non-coding RNAs that have potential regulatory functions in various physiological and pathological processes. The present study used tsRNAs sequencing to investigate the relationship between RHD and atrial fibrillation (AF). Three paired myocardial papilla were taken from six rheumatic RHD patients with AF (3 cases) or without AF (3 cases) from January 2016 to January 2017 in Xiangya Hospital, Central South University. A total of 219 precisely matched tsRNAs were identified, and 77 tsRNAs (fold change > 2.0 and P < 0.05) were differently changed. Three tsRNAs (AS-tDR-001269, AS-tDR-001363, AS-tDR-006049) were randomly selected and verified by qRT-PCR. The results of qRT-PCR were consistent with tsRNAs sequencing, suggesting the tsRNAs sequencing was reliable. Then bioinformatics analysis indicated that the target genes were abundant in regulation of transcription, DNA binding, intracellular. Most of the genes were predicted to interplay with cytokine-cytokine receptor by KEGG analysis. Our findings uncover the pathological process of AF in RHD through tsRNAs sequencing. This study provides new ideas for future research on elucidating the mechanism of AF in RHD and offers potential new candidates for the treatment and diagnosis of RHD.

overall_design: tiRNA and tRF profiles of myocardial papilla using Illumina NextSeq 500 system.

first: Yang

last: Wang

first: Tao

last: Tang


title: Identification of H3K27ac-marked enhancers in bovine satellite cells during differentiation

city: Blacksburg

first: Honglin

last: Jiang

address: 3130 Litton Reaves Hall

department: Animal and Poultry Sciences

institute: Virginia Polytechnic Institute and State University

summary: In this study we isolated satellite cells from skeletal muscle from two Angus-crossbred steers, initially cultured them in growth medium for proliferation, and then in differentiation medium to induce them to differentiate and fuse into myotubes. We used ChIP-seq to identify enhancers marked with H3K27ac, i.e., active enhancers, from these cells immediately before and two days after induction of differentiation. Nearly 20,000 and 50,000 H3K27ac-marked enhancers were consistently identified from two biological replicates of before- and during-differentiation bovine satellite cells, respectively.

overall_design: ChIP-seq was used to identify H3K27ac-marked genomic regions from bovine satellite cells immediately and two days after induction of differentiation. Two biological replicates were used.  Four H3K27ac_ChIP-seq and two Input-seq libraries were sequenced.

first: Pengcheng

last: Lyu

first: Robert

last: Settlage


title: Affymetrix SNP array data for Myeloid Neoplasms with PDGFRB Rearrangement

type:
Genome variation profiling by SNP array
SNP genotyping by SNP array

summary: Here we characterized a series of cases with myeloid neoplasms using cytogenetic, single nucleotide polymorphism array, and next generation sequencing.

overall_design: Copy number analysis of Affymetrix 400K SNP arrays was performed for 9 PDGFRB-positive cases

first: Valentina

last: Pierini


title: Analysis of lncrna expression profile in LPS activated THP1 cells

city: suzhou

first: lixiaoping

middle: 李小平

last: li

state: jiangsu

address: 199 Ren'ai Road, Suzhou Industrial Park

department: IBMS

institute: suzhou university

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

summary: In order to further explore the expression of lncrna in asthma, we used lipopolysaccharide (LPS) to activate human monocyte macrophage THP-1, and then used deep sequencing method to detect the expression of lncrna in activated and inactive THP1 cells. The results showed that there were different expression of lncrna in LPS activated and inactive THP1 cells

overall_design: Control and  LPS treated THP-1 cells for 48h were collected in Trizol plus reagent. The sample total RNA and lncRNA sequencing were performed by Boao Biotech in Guangzhou, China

first: Wang

last: wenwen

first: Liu

last: tingting


title: Microarray analysis and functional prediction of differentially-expressed circular RNAs in acquired middle ear cholesteatoma

city: Changsha

first: Wei

last: Liu

address: The Second Xiangya Hospital of Central South University, 139 Middle Renmin Road, Changsha

institute: The Second Xiangya Hospital, Central South University of China

summary: To investigate the differential expression profiling of circular RNAs (circRNAs) between acquired middle ear cholesteatoma and normal skin, and to identify potential circRNAs contributing to the etiopathogenesis of middle ear cholesteatoma, circRNA microarray analysis and functional prediction were performed.

overall_design: Acquired middle ear cholesteatoma and normal post-auricular skin tissues, Arraystar Human circRNAs chip

first: Shumin

last: Xie

first: Li

first: Tuanfang

last: Yin

first: Jihao

last: Ren


title: Imperatorin induces autophagy and G0/G1 phase arrest via PTEN-PI3K-AKT-mTOR/p21 signaling pathway in human osteosarcoma cells in vitro and in vivo

city: Quzhou

first: Minchao

last: Lv

state: Zhejiang

address: No. 100, Mingjiang Avenue

department: Department of Orthopedics

institute: The Quzhou Affiliated Hospital of Wenzhou Medical University, Quzhou People’s Hospital

summary: Osteosarcoma is the third most common cancer in adolescence and the first common primary malignant tumor of bone. The long-term prognosis of osteosarcoma, especially for unresectable and metastatic tumors, still remains unsatisfactory in the past decades. In this study, we systematically investigated the antitumor effect of imperatorin (IMP), a small molecule extracted from Angelica dahurica, in human osteosarcoma cells. The results showed that IMP triggered time-dependent and dose-dependent inhibition of tumor growth mainly by inducing autophagy promotion and G0/G1 phase arrest in vitro and in vivo. Besides, IMP treatment elevated the expression level of PTEN and p21, down-regulated the phosphorylation of AKT and mTOR. In contrast, the inhibition of PTEN using Bpv (HOpic), a potential and selective inhibitor of PTEN, concurrently rescued IMP-induced autophagy promotion, cell cycle arrest and inactivation of PTEN-PI3K-AKT-mTOR/p21 pathway. Taken together, our data revealed that imperatorin induced autophagy and cell cycle arrest through PTEN-PI3K-AKT-mTOR/p21 signaling pathway by targeting and up-regulating PTEN in human osteosarcoma cells. Hence, imperatorin is a desirable candidate for clinical treatments of osteosarcoma.

overall_design: RNA sequence assay data of 143B cells treated with or without 125 μM imperatorin for 24 h, each group contains three repeats

first: Bei

last: Zhang


title: RNA-sequencing

summary: To explore the LncRNAs that are involved in the allergic asthma, we applied a LncRNA microarray to analyze the LncRNA expression profiles in peripheral blood mononuclear cells (PBMCs) from asthmatic and healthy people.RNA-sequencing for 6 samples(asthmatic people(68,69,107) and 3 healthy people(CC24,CC25,M3))

overall_design: LncRNA profiles of peripheral blood mononuclear cells from asthmatic patients and healthy volunteers treated in hospitals,each with 3 peolple


title: Permanently Re-programmed Microglia in Spinal Cord Injury Contribute to Functional Recovery

city: Stockholm

first: Martin

last: Enge

address: CCK, Z4

department: Dep of Oncology-Pathology

institute: Karolinska Institute

summary: Microglia are resident myeloid cells of the central nervous system (CNS). Recently, single-cell RNA sequencing (scRNAseq) has enabled description of a disease-associated subtype of microglia (DAM) with a role in neurodegeneration and demyelination. In this study we use scRNAseq to investigate the temporal dynamics of immune cells harvested from the epicenter of traumatic spinal cord injury (SCI). As a consequence of SCI, homeostatic microglia undergo permanent transcriptional re-programming into a subtype of microglia with striking similarities to previoysly reported DAM as well as a distinct microglial state found during development. Using a microglia depletion model we showed that DAM in SCI are derived from homeostatic microglia and strongly enhance recovery of hind limb locomotor function following injury.

overall_design: Investigation of CD45+ immune cells in spinal cord injury (SCI) over time in an experimental mouse model

first: Ramil

last: Hakim

first: Vasilios

last: Zachariadis

first: Sreenivasa

last: Sankavaram

first: Jinming

last: Han

middle: A

last: Harris

first: Lou

last: Brundin

first: Mikael

last: Svensson


title: Genome-wide analysis reveals a RhlA-dependent modulation of flagellar genes in Pseudomonas aeruginosa PAO1

city: Rio de Janeiro

first: Michele

middle: Rocha

last: Castro

state: Rio de Janeiro

address: Av. Athos da Silveira Ramos, nº 149, A537 and A541 - Technology Center, University City - Rio de Janeiro - RJ

department: Department of Biochemistry - Institute of Chemistry

country: Brazil

institute: Federal University of Rio de Janeiro (UFRJ) - Rio de Janeiro - Brazil

summary: In this study, we describe a transcriptome analysis to compare the gene expression profile of P. aeruginosa PAO1 and its rhlA-knockout derivative, using Affymetrix GeneChipTM P. aeruginosa genome arrays and real-time qPCR analysis. We tested the hypothesis that RhlA-derived biosurfactants affect gene expression, under dynamic growth conditions, at stationary phase of growth. mRNA samples from  cell lines were amplified, labeled, and hybridized to the GeneChip® P. aeruginosa Genome Array.  The chip array data analysis was performed with TAC software.

overall_design: We analyzed 2 strains in triplicate using the GeneChip® P. aeruginosa Genome Array. Array data was processed by AffymetrixExpression Console and analysed using TAC software

first: Renata

last: Binato

first: Eliana

last: Abdelhay

first: Bianca

last: Neves

first: Graciela

last: Dias


title: Analysis of ctDNA methylation induced by ionizing to different ograns

first: zhang

middle: shu

last: yu

address: No. 199, Ren'ai Road

department: soochow university

institute: Soochow University

overall_design: This study aims to compared ctDNA methylation status induced by ionizing to different ograns. SD rats were irradiated with local radaition to brain, lung or skin. Serum was collected and subjiected to ctDNA extraction. ctDNA were then treated by methylation-sensive bisulfite and sequencing. Brain was irradiated with 20 Gy electron beam. Lung was irradiated with 10 Gy X-ray. Skin was irradaited with 45 Gy electron beam.

first: Shuyu


title: Acetyl-CoA production by specific metabolites promotes cardiac repair after myocardial infarction via mediating histone acetylation

city: Ann Arbor

first: Paul

last: Tang

state: MI

address: 2800 Plymouth Road

department: Cardiac surgery

institute: University of Michigan

summary: We examined the gene expression profile in rat hearts at 24 hours after ischemic reperfusion with/out treatment of sodium octanoate (8C).

overall_design: Three group of animals: Sham, IR. IR+8C. 3 biological replicates per group.

first: Ienglam

last: Lei

first: Shuo

last: Tian

first: Wenbin

last: Gao

first: Liu

last: Liu

first: Yijing

last: Guo

first: Zhong

last: Wang


title: Transcriptomic profile of zebrafish liver cells in thioacetamide (TAA) model

city: Warsaw

first: Michal

last: Pawlak

address: Trojdena 4

country: Poland

institute: International Institute of Molecular and Cell Biology

summary: Zebrafish transgenic lines Tg(fabp10a:dsRed), Tg(hand2:EGFP) and Tg(kdrl:ras-mCherry)  in AB wild-type background were  anesthetized with MS-222 and adult females were injected intraperitoneally with 500 mg/kg thioacetamide (TAA) or sterile water as a control 6 times over the course of 2 weeks. We have characterized transcriptomic profiles of FACS-isolated hepatocytes (dsRed+), stellate cells (EGFP+) and liver endothelial cells (mCherry+) from fishes treated with TAA or sterile water. Cells negative for the fluorescence were used as a control.

overall_design:
Examination of transcriptomic profile of zebrafish hepatocytes, stellate cells and liver enothelial cells treated with thioacetamide (TAA) and control (sterile water)

cell specific reporters:
fabp = hep (hepatocytes)
hand = hsc (hepatic stellate cells)
kdlr = ec (endothelial cells)

first: Cecilia

last: Lanny Winata


title: Genome-wide chromatin accessibility and transcriptome profiles of zebrafish liver cells in thioacetamide (TAA) model


title: Gene expression of brain regions activated by sevoflurane and propofol

status: Public on Dec 22 2021

city: TOKYO

first: NOBUTAKA

last: KAMEI

address: 1-1-5 Sendagi, Bunkyo-ku,

institute: Nippon Medical School, Graduate School of Medicine

summary:
The basic mechanisms of action for general anesthesia are not fully understood. We thought differences in the neural activation sites of different types of anesthetics and differences in gene expression changes in those brain regions may lead to differences in the incidence of side effects.
We performed gene expression analysis using microarrays in the identified regions that have been related to the mechanisms of anesthetic action and side effects. Gene expression changes in these brain regions were determined for sevoflurane and propofol to understand the mechanisms that cause differences among anesthetics.

overall_design: Rats were exposed to 40% oxygen at a flow rate of 6 L/min during anesthetic treatment. Rats were randomly allocated to four groups: propofol (intravenous 36 mg/kg/hr after a 10 mg/kg bolus dose), intralipos (10% lipid, intravenous 36 mg/kg/hr after a 10 mg/kg bolus dose), 2.4% sevoflurane (1 minimum alveolar concentration (MAC) in rats, and O2 treatment. Rats were anaesthetized with sevoflurane or propofol for 1 hour. Among the brain regions with anesthesia-induced changes in neuronal activity, gene expression analysis was performed in the lateral habenula (LHb), the medial habenula (MHb), the solitary nucleus (Sol) and the medial vestibular nucleus (MVe) from laser microdissected samples.

last: Kamei


title: Healthy Myeloid-Derived Suppressor Cells Express the Surface Ectoenzyme Vanin-2 (VNN2)

city: Cleveland

first: david

last: Soler

state: OH

address: 2109 Adelbert rd BRB Bldg 547B

department: Neuro-Surgery

institute: Case Western Reserve University

summary:
Study of human monocytic Myeloid-Derived Suppressor cells Mo-MDSC (CD14+ HLA-DRneg/low) has been hampered by the lack of positive cell-surface markers. In order to identify positive markers for Mo-MDSC, we performed microarray analysis comparing Mo-MDSC cells from healthy subjects versus CD14+ HLA-DRhigh monocytes. We have identified the surface ectoenzyme Vanin-2(VNN2) protein as a novel biomarker highly-enriched in healthy subjects Mo-MDSC. Indeed, healthy subjects Mo-MDSC cells expressed 68% VNN2, whereas only 9% VNN2 expression was observed on CD14+ HLA-DRhigh cells (n=4 p<0.01). The top 10 percent positive VNN2 monocytes expressed CD33 and CD11b while being negative for HLA-DR, CD3, CD15, CD19 and CD56, consistent with a Mo-MDSC phenotype. CD14+VNN2high monocytes were able to inhibit CD8 T cell proliferation comparably to traditional Mo-MDSC at 51% and 48%  respectively. However, VNN2 expression on CD14+ monocytes from glioma patients was inversely correlated to their grade. CD14+VNN2high monocytes thus appear to mark a monocytic population similar to Mo-MDSC only in healthy subjects, which may be useful for tumor diagnoses.
Myeloid-Derived Suppressor Cells (MDSC) are identified by upregulated expression of the cell surface ectoenzyme Vanin-2 in healthy subjects

overall_design: PBMC were isolated from fresh blood from three independent healthy donor by density centrifugation. CD14+ cells were isolated manually using CD14 microbeads (Miltenyi), and then stained with CD14 and HLA-DR antibodies. Mo-MDSC and CD14+ HLADR+ monocytes cells were sorted as CD14+ HLA-DR-neg/low (bottom 10%) and CD14+HLA-DR-high (top 10%) cells respectively. The sorted two populations were immediately frozen for RNA isolation and further microarray.

first: David

first: Amber

last: Kerstetter-Fogle

first: Andrew

middle: B

last: Young

first: Pat

last: Rayman

first: James

last: Finke

first: Sarah

last: Debanne

first: Kevin

middle: D

last: Cooper

first: Jill

last: Barnholtz-Sloan

middle: E

last: Sloan

first: Thomas

middle: S

last: McCormick


title: RNAseq analysis of bone marrow mesenchymal stem cells

city: New York

first: Varshini

last: Vasudevaraja

state: NY

address: 550 1st Avenue

department: Pathology

institute: NYU Langone Health

summary: The phenotype of bone marrow mesenchymal stem cells in the murine Townes model of sickle cell disease is not well characterized. We analyzed differences in the gene signature between SA and SS MSCs. MSCs were defined by CD45-Ter119-CD31-CD51+CD140a+ surface expression.  We identified significant differences in SS MSC gene profile and stem cell functionality compared to SA control MSCs.

overall_design:
Murine bone marrow from SA and SS mice was enzymatically digested, stained with antibodies, and sorted by gating on the live cells, single cells, CD45-, Ter119-, CD31-, CD51+ and CD140a+ population.  RNA extraction was performed using the NucleoSpin RNA-XS kit. Library preparation, RNA-seq analysis on the Illumina HiSeq4000 machine and bioinformatics analysis were conducted with the Applied Bioinformatics Laboratory at NYU School of Medicine.
SS: Homozygous Townes mice carry a mutation designed with the human hemoglobin α-gene (Hbatm1(HBA)Tow, hα) and a mutation containing the human Aγ-globin gene and human sickle hemoglobin beta (βS) that replaced mouse major and minor β-globin genes (hα/hα::βS/βS).
SA: Heterozygous Townes mice carry the human hemoglobin α-gene (Hbatm1(HBA)Tow, hα) mutation, one copy of human sickle hemoglobin beta (βS), and the human wild-type hemoglobin beta (βA) gene (hα/hα::βA/βS).

first: Avital

last: Mendelson

first: Karina

last: Yazdanbakhsh

first: Patricia

last: Shi


title: Genome-wide chromatin accessibility profiles of zebrafish liver cells in thioacetamide (TAA) model

first: Michal

last: Pawlak

summary: Zebrafish transgenic lines Tg(fabp10a:dsRed), Tg(hand2:EGFP) and Tg(kdrl:ras-mCherry)  in AB wild-type background were  anesthetized with MS-222 and adult females were injected intraperitoneally with 500 mg/kg thioacetamide (TAA) or sterile water as a control 6 times over the course of 2 weeks. We have characterized chromatin accessibility profiles of FACS-isolated hepatocytes (dsRed+), stellate cells (EGFP+) and liver endothelial cells (mCherry+) from fishes treated with TAA or sterile water. Cells negative for the fluorescence were used as a control.

overall_design:
Examination of chromatin accessibility profiles of zebrafish hepatocytes, stellate cells and liver enothelial cells treated with thioacetamide (TAA) and control (sterile water)

cell specific reporters:
fabp = hep (hepatocytes)
hand = hsc (hepatic stellate cells)
kdlr = ec (endothelial cells)

last: Lanny Winata


title: The scRNA-seq of cells from Ren1c-/-;Myh11-CreERT2;tdTomato;Ren1c-YFP mice

city: Charlottesville

first: Hirofumi

last: Watanabe

state: Virginia

address: 409 Lane Rd, Bldg MR4

department: Department of Pediatrics, Child Health Research Center

institute: University of Virginia School of Medicine

summary: scRNA-seq was performed to investigate the differences between Reninnull cells and surrounding vascular smooth muscle cells

overall_design: Cells from Ren1c-/-;Myh11-CreERT2;tdTomato;Ren1c-YFP mice were sorted and collected according to their red or yellow colors. The scRNA-seq was performed using the 10 X Chromium System


title: Complex Genetic Interactions between Piwi and HP1a in the Repression of Transposable Elements and Tissue-Specific Genes in the Ovarian Germline

first: Artem

last: Ilin

address: Svante Arrhenius väg 20C

department: MBW

institute: Stockholm University

summary: Insertions of transposable elements (TEs) in eukaryotic genomes are usually associated with repressive chromatin, which spreads to neighbouring genomic sequences. In ovaries of Drosophila melanogaster, the Piwi-piRNA pathway plays a key role in the transcriptional silencing of TEs considered to be exerted mostly through the establishment of H3K9me3 histone marks recruiting Heterochromatin Protein 1a (HP1a). Here, using RNA-seq, we investigated the expression of TEs and the adjacent genomic regions upon Piwi and HP1a germline knockdowns sharing a similar genetic background. We found that the depletion of Piwi and HP1a led to the derepression of only partially overlapping TE sets. Several TEs were silenced predominantly by HP1a, whereas the upregulation of some other TEs was more pronounced upon Piwi knockdown and, surprisingly, was diminished upon a Piwi/HP1a double-knockdown. We revealed that HP1a loss influenced the expression of thousands of protein-coding genes mostly not adjacent to TE insertions and, in particular, downregulated a putative transcriptional factor required for TE activation. Nevertheless, our results indicate that Piwi and HP1a cooperatively exert repressive effects on the transcription of euchromatic loci flanking the insertions of some Piwi-regulated TEs. We suggest that this mechanism controls the silencing of a small set of TE-adjacent tissue-specific genes, preventing their inappropriate expression in ovaries.

overall_design: rRNA-depleted total RNA-seqs of germline double knockdown of Piwi and HP1a as well as separate knockdowns of these proteins and a DNA-seq used for TE insertion identification

last: Ilyin


title: Low molecular weight polysialic acid prevents lipopolysaccharide-induced inflammatory dopaminergic neurodegeneration in humanized SIGLEC11 transgenic mice

city: Bonn

first: Harald

last: Neumann

address: Venusberg-Campus 1

institute: University Hospital of Bonn

summary: Here, we investigated the effect of low molecular weight polysialic acid (polySia avDP20) on inflammatory neurodegeneration. SIGLEC11 transgenic and wild type control (WT) mice were treated intraperitoneally daily over four consecutive days with 1 µg/gbw/day LPS in conjunction with 10 μg/gbw polySia avDP20. Repeated LPS injections led to inflammation and neuronal loss in the brains of WT and SIGLEC11 transgenic mice. Transcriptome analysis by RNA-seq of total brain tissue indicated that treatment with polySia avDP20 prevented the LPS-induced upregulation of genes belonging to inflammation, TLR signaling, phagocytosis, and complement-related pathways in SIGLEC11 transgenic but not wild type mice.

overall_design: Examination of brain mRNA profiles 19 days after repeated LPS or PBS (vehicle control) treatment in conjunction with low molecular weight polysialic acid (polySia avDP20) or PBS (vehicle control) application of 3-months old male WT and SIGLEC11 transgenic mice by RNA-Seq (5-7 animals per group).

first: Huan

last: Liao

first: Jonas

last: Winkler

first: Jannis

last: Wißfeld

first: Anahita

last: Shahraz

first: Christine

last: Klaus


title: Transcriptomic profile of peripheral blood reveals potential genetic biomarkers for diagnosis of Osteoarthritis in German shepherd dogs

city: La Plata

first: Guillermo

last: Giovambattista

state: Buenos Aires

address: Calle 60 y 118 S/N

department: Facultad de Ciencias Veterinarias

country: Argentina

institute: CONICET-UNLP

summary: Canine forms of osteoarthritis (OA) are very similar to those in humans and represent a welfare problem in the dog world population. In this study, we investigated the transcriptomic profile of peripheral blood in German Shepherd dogs with OA in order to identify diagnosis biomarkers. The bulk RNA-seq experiment was performed in a cohort of 12 adult dogs, 5 affected and 7 unaffected. Radiographs of the affected dogs revealed severe osteoarthritis in hip and elbow joints. The expression analysis showed 171 differentially expressed genes (DEGs), 113 were upregulated and 58 were downregulated compared to control dogs P (< 0.01). This pool of genes was functional annotated for signaling pathways using PANTHER tools. No overrepresented pathways were found. To gain further insights of the functional role of the DEGs in OA, we set a threshold of log2FoldChange value between -1.5 and 1.5. We ended up with 24 top up- and downregulated transcripts. Prioritization of these DEGs according to their known functional knowledge, revealed 5 possible candidates for OA biomarkers. The downregulated OSCAR gene encodes the osteoclast associated Ig-like receptor, which is involved in osteoclastogenesis regulation and bone homeostasis. In addition, the upregulated microRNA MIR339-1 and ncRNAs: LOC106559235 (downregulated), LOC102156762 (downregulated) and LOC111096460 (upregulated) are regulatory sequences, stable for gene profiling assessment in blood and related to OA pathogenesis regulation. We suggest OSCAR as the more likely candidate biomarker for OA diagnosis in dogs and, provide evidence of new circulating regulatory sequences differentially expressed in canine OA.

overall_design: Transcriptomic profile of peripheral blood in German Shepherd dogs with Canine forms of osteoarthritis and control animals

first: G

last: Rudd Garces

first: R

last: Vercellini

first: D

last: Osvaldo Arias

first: P

last: Peral García

last: Padula


title: RNAseq of Germ-Free mouse liver following 6 week dosing of delta-valerobetaine fed either a control or Western Diet

city: Atlanta

first: Ken

last: Liu

state: GA

address: 615 Michael Street, Suite 225

institute: Emory University

summary:
Objective:The goals for this study were to identify the specific contribution of the microbial metabolite delta-valerobetaine to transcriptional regulation of energy metabolism in the liver.
Methods: 3 week old Germ-Free C57BL/6 male mice were treated with delta-valerobetaine for 6 weeks with control diet or Western Diet.  Liver was collected at the end of the study period for analysis.
Results: We found differentially expressed transcriptional networks related to treatment with VB.
Conclusions: These results demonstrate the specific contributions of a single microbiome-derived metabolite to transcriptional regulation of energy metabolism in mammalian liver.

overall_design: Liver mRNA profiles of Germ-Free C57BL/6 male mice following 6 weeks of treatment with delta-valerobetaine

first: Dean

middle: P

last: Jones


title: H3K27me3 Cut&Tag profiling of bone marrow-derived alveolar macrophages from wildtype and Suz12 knockout mice

city: Parkville

first: Gordon

last: Smyth

state: Vic

address: 1G Royal Pde

department: Bioinformatics

institute: Walter and Eliza Hall Institute of Medical Research

summary: Macrophages are at the forefront of immune responses and their transcriptional programs are modified by their tissue environment and in response to immunological challenge. Post-translational modifications of histones, such as histone H3 lysine 27 tri-methylation (H3K27me3) by the polycomb repressive complex 2 (PRC2), are tightly associated with epigenetic regulation of gene expression. To explore whether H3K27me3 is involved in either the establishment or function of the mononuclear phagocyte system, we selectively deleted the SUZ12 gene in mice, a core component of PRC2. Consistent with the the role of PRC2 in maintaining transcriptional repression, we found that the majority of top-ranked genes enriched for H3K27me3 in wild type alveolar macrophages were upregulated in SUZ12 knock-out alveolar macrophages.

overall_design: C57BL/6-Ly5.1 mice were lethally irradiated and reconstituted with either a ratio of 90% wt Ly5.2: 10% wt Ly5.1, or 90% Suz12 cKO Ly5.2: 10% wt ly5.1. Libraries were generated from 100,000 alveolar macrophages sorted from the lung of wt (2 biological replicates) or Suz12cKO mice (2 biological replicates). Samples were sequenced with an Illumina NextSeq platform, producing between 5-8 million paired-end 36bp reads per sample.

first: Pedro

last: Baldoni


title: Syngergistic Anti-tumor Effects between GLA and X-ray Radiation

city: BOTHELL

first: Hailing

last: Lu

state: WA

institute: Seattle Genetics

summary: Nanostring gene expression analysis using tumors from mice treated with GLA, X-ray radiation or the combination of GLA and radiation showed that the combination of GLA and radiation has synergistic effect in modulating the tumor micronenvironment.

overall_design: Mice with A20 tumors received intratumoral injection of TLR4 agonist GLA (GLA-SE 10ug), X-ray radiation (RT), or GLA plus RT.  Control mice received intratumoral injection of PBS.  Tumors were collected and RNA was extracted for nanostring gene expression analysis using the mouse panCancer Immune Profiling panel.

first: Jan

last: ter Meulen


title: RNA-seq profiling of bone marrow-derived alveolar macrophages, foetal-derived alveolar macrophages and foetal-derived Langerhans cells from the lungs of wildtype and Suz12 knockout mice

summary:
Macrophages are at the forefront of immune responses and their transcriptional programs are modified by their tissue environment and in response to immunological challenge. Post-translational modifications of histones, such as histone H3 lysine 27 tri-methylation (H3K27me3) by the polycomb repressive complex 2 (PRC2), are tightly associated with epigenetic regulation of gene expression. To explore whether H3K27me3 is involved in either the establishment or function of the mononuclear phagocyte system, we selectively deleted the SUZ12 gene in mice, a core component of PRC2. SUZ12 ablation induced a rapid loss of the alveolar macrophage networks under both steady state and inflammatory conditions. Ablation of SUZ12 abrogated the proliferation of these cells required for their self-renewal.

This SuperSeries is composed of the four SubSeries listed below.

overall_design: Refer to individual Series


title: Regulation of retinal amacrine cell generation by miR-216b and Foxn3

first: David

last: Turner

address: 109 Zina Pitcher Place

department: Michigan Neuroscience Institute

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