title: The Mediator subunit MED23 regulates inflammatory responses and liver fibrosis

city: Shanghai

first: Zhichao

last: Wang

address: 320 YueYang Road

institute: SIBCB

summary: Liver fibrosis, often associated with cirrhosis and hepatocellular carcinomas, is characterized by hepatic damage, an inflammatory response, and hepatic stellate cell (HSC) activation, although the underlying mechanisms are largely unknown.Here,we show that the MED23 subunit of the transcriptional Mediator complex participates in the development of experimental liver fibrosis. Compared with their control littermates, mice with hepatic Med23 deletion exhibited aggravated CCl4-induced liver fibrosis, with enhanced chemokine production and inflammatory infiltration as well as increased hepatocyte regeneration. Mechanistically, the orphan nuclear receptor RORα activates the expression of the liver fibrosis-related chemokines CCL5 and CXCL10, which is suppressed by the Mediator subunit MED23. We further found that the inhibition of Ccl5 and Cxcl10 expression by MED23 likely occurs due to G9a-mediated H3K9 dimethylation of the target promoters. Collectively, these findings reveal hepatic MED23 as a key modulator of chemokine production and inflammatory responses and define the MED23-CCL5/CXCL10 axis as a potential target for clinical intervention in liver fibrosis.

overall_design: Comparison of mRNA expression profiles between med23f/f and med23Δli mouse livers after acute administration of CCl4 for 24 hours (n = 3 per group)

first: Gang

last: Cao

first: Chonghui

last: Li

first: Lihua

last: Min


title: Validation of small molecule activators and identification of altered signaling pathways underlying the age-related decline in proliferative capacity in human dermal progenitors

status: Public on Jun 06 2020

city: Calgary

first: Matthew

last: Workentine

state: Alberta

address: 3280 Hospital Drive NW

country: Canada

institute: University of Calgary

type: Expression profiling by high throughput sequencing

summary: Intrinsic dysfunction of hair follicle dermal progenitors underlies phenotypic changes observed in aged dermis in rodents. The authors confirm similar age-related decline in function is present in adult human DPCs. RNA-Seq is utilized to identify further explanations for this functional decline in aged hDPCs.

overall_design: Dermal progenitor cells were isolated from adult human dermis from aged (>40yo) and young donors to allow for comparison between transcriptomes that may lead to targeted therapeutic intervention for age-related dermal degeneration

first: Holly

last: Sparks

first: Natacha

last: Agabalyan

first: Wisoo

last: Shin

first: Min

last: Cheng

first: Jeff

last: Biernaskie


title: Transcriptional analyses of RPMax-/- versus RPMaxWT preSCs

city: Seattle

first: Arnaud

middle: A

last: Augert

state: Washington

address: 100 Fairview Avenue N. Thomas Building Room D4

country: USA

institute: Fred Hutchinson Cancer Research Center

summary: We analyze transcritpional changes upon Max deletion using CRISPR Cas9

overall_design: RNA seq analyses of 4 control and 4 Max KO preSCs

first: David

last: MacPherson


title: Genome-wide transcriptional responses of Streptococcus gordonii Challis to AFYWWFY heptamer.

city: Buffalo

first: M

middle: M

last: Vickerman

state: NY

address: 3435 Main St.

department: Periodontics and Endodontics

institute: University at Buffalo

summary: Transcriptome profiling of mid-log S. gordonii cells treated for 30 minutes with 1 µM of AFYWWFY heptamer dissolved in dimethyl sulfoxide (DMSO).

overall_design: One-condition experiment. S. gordonii were grown statically in 10 ml volumes to mid-log phase at 360C in 5% CO2 and then treated with either heptamer or solvent-only control and incubated for an additional 30 minutes before harvesting for RNA preparation. Experiment was repeated in different media: Todd Hewitt (TH; Difco) and chemically defined FMC medium (Terleckyj, B., Willett, N., P., and G. D. Shockman. 1975. Growth of Several Cariogenic Strains of Oral Streptococci in a Chemically Defined Medium. Infect Immun. 11(4):649–655). Biological replicates in TH: 1 control, 1 treated, 6 replicates per array. Biological replicates in defined medium: 2 control, 2 treated, 6 replicates per array. Dye swaps were performed for each sample set.

first: A

last: Jesionowski

first: J

last: Mansfield


title: Transcriptional analyses of RPMax-/- versus RPMaxwt mouse lung tumors

summary: We analyze transcritpional changes upon Max deletion in a mouse model of SCLC driven by Rb and p53 loss

overall_design: RNA seq analyses of 9 RPMax-/- versus 7 RPMaxwt lung tumors


title: miRNA expression data from primary central nervous system lymphomas (PCNSL) [miRNA-4]

status: Public on Jun 05 2020

city: Kyoto

first: Ryuya

last: Yamanaka

address: 465 Kajii-cho, Kamigyoku

country: Japan

institute: Kyoto Prefectural University of Medicine

summary: Expression profiling of miRNA was performed on 20 PCNSLs. A gene classifier was developed.

overall_design: Twenty PCNSL patients were selected for miRNA extraction and hybridization on Affymetrix microarrays.

last: YAMANAKA

first: Yasuo

last: TAKASHIMA


title: RNA-seq of mice islets from wt and miR-29a/b-1 pancreatic beta cell specific overexpression transgenic mice

city: Nanjing

first: Yi

last: Sun

address: Tianyuandong Road 818

country: China

institute: Nanjing medical university

summary: We investigated the mechanism associated with miR-29 effects by comparing gene expression of whole primary islets isolated from miR-29a/b-1 pancreatic beta cell specific overexpression transgenic mice (βTG mice) and their control littermates by RNA sequencing. Ten-week-old mice were chosen to avoid secondarily affected genes. We identified 346 genes that showed significant differences (p-value < 0.05 and >2-fold change) between the two groups. We then used gene ontology (GO) algorithms to perform functional annotations of these differential genes. The top enriched pathways were linked primarily to inflammatory response, secretory vesicle, and ion channel activity. Islets from the βTG mice showed an enhanced inflammatory response based on an assessment of both the upregulated and the downregulated genes , which suggested a likely positive regulation of phagocytosis (Ahsg), regulation of blood vessel diameter (P2rx1/Kng1/Nos2), and monocyte chemotaxis (Cxcl10/Cxcl17).

overall_design: islets mRNA of wt and miR-29a/b-1 pancreatic beta cell specific overexpression transgenic mice

first: Xiao

last: Han

first: Yunxia

last: Zhu

first: Yuncai

last: Zhou


title: ADAR1 overexpression in MDA-MB-231 cells

city: Santiago

first: Ricardo

last: Armisen

state: Macul

address: Obispo Arturo Espinoza Campos 2526

country: Chile

institute: Pfizer Chile

summary: Abstract: RNA editing has emerged as novel mechanisms involved in cancer progression. Despite the phenotypic implications of ADAR in several cancer models, the role of ADAR on DNA damage response (DDR) and proliferation in breast cancer (BC) has not been fully addressed. To evaluate the effect of ADAR expression, MDA-MB-231 cells were transduced (MOI:200) with commercial pre-package adenoviral particles coding for ADARp110 or transduced (MOI:200) with eGFP control adenovirus. 16 h after transduction media was changed and RNA were extracted 48 h after transduction. ADARp110 overexpression produces a significant increase in transcripts related with cell cycle and proliferative pathways, in addition to other pathways related to IL10 signaling, among others. In other hand 657 sites significantly increase their editing in MDA-MB-231 OV cells at site level comparison. Conversely, transcripts involved in Generic Transcription, cell cycle, HIV life Cycle related pathways and Apoptosis suffer an increased editing ratio, suggesting that ADAR activity could be is in the regulation of the targets that bears significant changes in their editing pattern after ADAR manipulation

overall_design: MDA-MB-231 cells were transduced (MOI: 200) with commercial pre-package adenoviral particles (VectorBuilder Inc, Shenandoah, TX, USA. VB170930-1035dgj) coding for ADARp110 (based on NM_001025107.2) or transduced (MOI: 200) with eGFP control adenovirus (VB150925-10024 vector). 16 h after transduction media was changed. Cells where extracted 48h after transduction using Qiagen RNeasy columns.  RNA-seq libraries were sequenced using a Hiseq4000 (BGI, Korea). Fastq files were aligned using STAR and hg19, counting transcripts using QuickRNASeq. Differential expression analysis was performed using DEseq2 software following standard recommendations.

first: Alejandro

last: Blanco

first: Pamela

last: Rojas de Santiago

first: Eduardo

last: Sagredo


title: MicroRNA-934 is a novel regulator orchestrating neurogenesis during early human neural development

city: Boston

first: Ioannis

middle: S

last: Vlachos

state: MA

address: 330 Brookline Ave

department: Pathology

institute: Beth Israel Deaconess Medical Center

type: Non-coding RNA profiling by high throughput sequencing

summary: To identify miR-934  effects on mRNA and microRNA expression regulation.

overall_design: We have performed RNA Sequencing (RNA-Seq) and small RNA-Seq in neuronal progenitors following miR-934 inhibition

first: Kanella

last: Prodromidou

first: Maria

last: Gaitanou

first: Georgia

last: Kouroupi

first: Artemis

last: Hatzigeorgiou

first: Rebecca

last: Matsas


title: Comparison of two human organoid models of lung and intestinal inflammation reveals Toll-like receptor signalling activation and monocyte recruitment.

city: Brno

first: Marco

last: De Zuani

address: Pekarska, 53

department: CTM

country: Czech Republic

institute: FNUSA - ICRC

summary:
OBJECTIVES: The activation of immune responses in mucosal tissues is a key factor for the development and sustainment of several pathologies including infectious diseases and autoimmune diseases. However, translational research and personalized medicine struggle to advance because of the lack of suitable preclinical models that successfully mimic the complexity of human tissues without relying on in vivo mouse models. Here we propose two in vitro human 3D tissue models, deprived of any resident leukocytes, to model mucosal tissue inflammatory processes.
METHODS: We developed human 3D lung and intestinal organoids differentiated from induced pluripotent stem cells to model mucosal tissues. We then compared their response to a panel of microbial ligands and investigated their ability to attract and host human primary monocytes.
RESULTS: Mature lung and intestinal organoids incorporated epithelial (EpCAM+) and mesenchymal (CD73+) cells which responded to toll-like receptor stimulation by releasing pro-inflammatory cytokines and expressing tissue inflammatory markers including MMP9, COX2 and CRP. When added to the organoid culture, primary human monocytes migrated towards the organoids and began to differentiate to an “intermediate-like” phenotype characterised by increased levels of CD14 and CD16.
CONCLUSION: We show that human mucosal organoids exhibit proper immune functions and successfully mimic an immunocompetent tissue micro-environment able to host patient-derived immune cells. Our experimental setup provides a novel tool to tackle the complexity of immune responses in mucosal tissues which can be tailored to different human pathologies.

overall_design: mRNA transcriptome of human lung and intestinal organoids treated with LPS or Poly(I:C)

first: Shyam

last: Jose

first: Federico

last: Tidu

first: Marcela

middle: H

last: Kohoutkova

first: Lucia

last: Pazzagli

first: Giancarlo

last: Forte

first: Roberta

last: Spaccapelo

first: Teresa

last: Zelante

first: Jan

last: Fric


title: ADAR1 role on transcriptome stability

first: Ricardo

last: Armisen

summary: Abstract: RNA editing has emerged as novel mechanisms involved in cancer progression. Despite the phenotypic implications of ADAR in several cancer models, the role of ADAR on DNA damage response (DDR) and proliferation in breast cancer (BC) has not been fully addressed. To evaluate the effect of ADAR expression or the stability of targets ZR-75-1 were transduced using a shRNA against ADAR and cultured for 16h in the presence or absence of triptolide, a robust RNA pol II inhibitor, followed to transcriptome analysis comparing vehicle and treated cells. ZR-75-1 SHC, and ZR-75-1 ADAR KD cells were treated using 100nM Triptolide - RNA pol II inhibitor (Invivogen) or 100 nM DMSO used as a vehicle. After 16 h of treatment, total RNA was extracted. RNA quality from each biological replicates (N=3) was analyzed using Experion (Biorad) system to further generate RNA-seq libraries using the TruSeq Stranded Total RNA LT kit (Illumina). Finally, RNA-seq libraries were sequencing using a Hiseq4000 (BGI, Korea). Fastq Files were aligned using STAR using hg19, counting transcripts using HT-seq software. Finally, differential expression analysis was performed using DEseq2 software according to their recommendations. Our results suggest that after ADAR knock down and triptolide treatment, DNA repair, Cell cycle progression, ERRB2 signaling among others pathways suffer a significant decrease in their mRNA stability. On the contrary, mRNAs of genes associated with rRNA processing, mRNAs of genes involved in the surveillance through the nonsense-mediated decay and pro-apoptotic related mRNAs exhibited increased stability after ADAR knock down.

overall_design: ZR-75-1 SHC, and ZR-75-1 ADAR KD cells were treated using 100nM Triptolide - RNA pol II inhibitor (Invivogen) or 100 nM DMSO used as a vehicle. After 16 h of treatment, total RNA was extracted using RNeasy columns following the manufacturer’s instructions, including DNAse treatment (QIAGEN). RNA quality from each biological replicates (N=3) was analyzed using Experion (Biorad) system to further generate RNA-seq libraries using the TruSeq Stranded Total RNA LT kit (Illumina). RNA-seq libraries were sequenced using a Hiseq4000 (BGI, Korea). Fastq files were aligned using STAR and hg19, counting transcripts using HT-seq software. Differential expression analysis was performed using DEseq2 software following standard recommendations.

first: Alejandro

last: Blanco


title: Analysis of the coding and non-coding RNA temporal transcriptome of developing seeds in sunflower

city: Harbin

first: Jian

last: Wang

address: 600 Changjiang Road

institute: Northeast Agricultural University

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: Analysis of the coding and non-coding RNA temporal transcriptome of developing seeds in sunflower [RNA-seq]

summary: RNA-sequencing (lncRNA,mRNA and circRNA) of seeds in three developmental stages was performed to reveals gene regulation in relation to oil and fatty acid accumulation in sunflower

overall_design: RNA-sequencing (lncRNA,mRNA and circRNA) profiles of seeds of high oleic acid L-1-OL-1 were generated by deep sequencing at 7-, 22- and 37 day.

first: Yan

last: Liu

first: Fei

last: Zhou


title: Genetic screening for single-cell variability modulators driving therapy resistance [WM989-A6-G3-Cas9 5a3]

city: Philadelphia

first: Eduardo

last: Torre

state: PA

department: Bioengineering

institute: University of Pennsylvania

summary: We present the transcriptome of WM989-A6-G3-Cas9 5a3 melanoma cells followng the knockout (via CRISPR-Cas9) of different proteins we identified as modulators the frequency of cellular states associated with resistance to mutant-BRAF inhibition therapy.

overall_design: We sequenced mRNA in bulk from WM989-A6-G3-Cas9 in order to quantify the transcriptional changes following the knockout of many targets from both the priming and resistance screens presented in Torre et. al. In addition to hits from our screens, we also quantified the transcriptome of targets that were not hits, but show a change in the frequency of NGFR-high/EGFRhigh cells or of cells resistant to vemurafenib. For each sample, we isolated mRNA and built sequencing libraries using the NEBNext Poly(A) mRNA Magnetic Isolation Module and NEBNext Ultra RNA Library Prep Kit for Illumina per manufacturer instructions. We then sequenced the libraries via paired-end sequencing (36x2 cycles) on a NextSeq 500. We aligned reads to hg19 and quantified reads per gene using STAR and HTSeq. Each sequenced sample represents the transcriptome resulting from the knockout with a single sgRNA design. On average, we targeted each protein with three sgRNA designs.

first: Eri

last: Arai

first: Sareh

last: Bayatpour

first: Connie

last: Jiang

first: Lauren

middle: E

last: Beck

first: Benjamin

middle: L

last: Emert

first: Sydney

last: Shaffer

first: Ian

last: Mellis

first: Krista

last: Budinich

first: Filipe

last: Almeida

first: Mitchell

last: Fane

first: Ashani

last: Weeraratna

first: Junwei

last: Shi

first: Arjun

last: Raj


title: The role of IGFBP-3 as a potential pathophysiologic target or biomarker in chronic liver disease

city: Rochester

first: Aditya

last: Bhagwate

state: MN

address: 200 1st Street SW

institute: Mayo Clinic


title: RNA Sequencing Analysis of Wild Type Caput, Corpus, and Cauda Epididymal Transcriptomes

city: Nagoya

first: Daiji

last: Kiyozumi

state: Aichi

address: Furocho, Chikusa-ku

department: Research Institute of Environmental Medicine

institute: Nagoya University

summary:
Purpose: The goal of this study is to detect differentially expressed genes, among Wild type caput, corpus, and cauda epididymis by RNA sequencing
Methods: Caput, corpus, and cauda epidiymal mRNA profiles of 9-month-old wild-type mice were generated by deep sequencing, in triplicate, using  Illumina GAIIx.
Results: RNA-seq data identified transcripts differentially expressed in caput, corpus, and cauda epididymis.
Conclusions: Our results show that the expression of many genes were differentially regulated in caput, corpus, and cauda epididymis.

overall_design: Caput, corpus, and cauda epididymal mRNA profiles of 9-month-old wild type mice were generated by deep sequencing, in triplicate, using Illumina GAIIx.

first: Taichi

last: Noda

first: Takashi

last: Kohda

first: Masahito

last: Ikawa


title: Conjunctival mRNA and miRNA expression profiles in congenital aniridia are genotype and phenotype dependent

city: Homburg

first: Nicole

last: Ludwig

address: Kirrberger Strasse

department: Human Genetics

country: Germany

institute: Saarland University

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


title: Next Generation Sequencing Facilitates Quantitative Analysis of SCs in mice exposure to exercise

status: Public on Jun 08 2020

city: Chongqing

first: Zhe

last: Chen

address: 1 Yixueyuan Road, Yuzhong District

institute: Chongqing Medical University

summary:
Purpose:To identify genes and the molecular pathways involved in the regulation of muscle satellite cells (SCs) in mice exposure to running exercise, we performed RNA-Sequence of SCs in untrained (Con) and trained mice (Exe).
Methods: mRNA  profiles of SCs in untrained (Con) and trained mice (Exe) (running exercise, 4 days/week, 30 min/day at 12 m/min) were generated by deep sequencing, in quadruplicate, using Illumina HiSeq 2000.
Results:Using an optimized data analysis workflow, we mapped about 9 million sequence reads per sample to the mouse genome (build mm10) and identified 9031 transcripts in SCs (the control  and  exercise group) with BWA workflow.
Conclusions: Our results represent the first detailed analysis of SCs transcriptomes in mice exposure to running exercise and found that exercise regulated multiple mRNA pathways in SCs.

overall_design: The mRNA profiles of SCs in untrained and trained mice were generated by deep sequencing, in quadruplicate, using Illumina HiSeq 2000.

first: Yu

last: Hou


title: Paired immunoglobulin-like receptors mediate innate memory to non-self MHC molecules

city: Pittsburgh

first: Wei

address: 4401 Penn Ave., Rangos Research Building, Room 9125

department: Division of Pulmonary Medicine, Allergy and Immunology, Department of Pediatrics

institute: Children’s Hospital of Pittsburgh of UPMC

summary:
Abstract: Immunological memory specific to previously encountered antigens is a cardinal feature of adaptive lymphoid cells.  It is not known however whether innate myeloid cells retain memory of prior antigenic stimulation and respond to it more vigorously upon a second encounter.  Here, we show that murine monocytes and macrophages acquire memory specific to MHC-I antigens and identify paired immunoglobulin-like receptors-A (PIR-A) as the MHC-I receptors necessary for the memory response.  We demonstrate that deleting PIR-A in the recipient or blocking PIR-A binding to donor MHC-I molecules blocks memory and attenuates kidney and heart allograft rejection.  Thus, innate myeloid cells acquire alloantigen-specific memory that can be targeted to improve transplant outcomes.
Data purpose: Targeting monocyte and macrophage receptors that detect MHC antigens blocks innate immune memory and attenuates transplant rejection

overall_design: splenic monocytes from B6, BALB, C3H mice at 1wk and 4wk post immunization

first: Fadi

middle: G

last: Lakkis

first: Khodor

last: Abou-Daya


title: Conjunctival mRNA and miRNA expression profiles in congenital aniridia are genotype and phenotype dependent (AKK mRNA)

summary:
Purpose:
To evaluate conjunctival cell microRNA and mRNA expression in relation to observed phenotype and genotype of aniridia-associated keratopathy (AAK) in a cohort of subjects with congenital aniridia.
Methods:
Using impression cytology, bulbar conjunctival cells were sampled from 20 subjects with congenital aniridia and 20 age and sex-matched healthy control subjects. RNA was extracted and microRNA and mRNA analysis was performed using microarrays. Results were related to the presence and severity of AAK determined by a standardized clinical grading scale and to the genotype (PAX6 mutation?) determined by clinical genetics.
Results:
Of the 2549 microRNAs analyzed, 21 were differentially expressed relative to controls. Among these miR-204-5p, an inhibitor of corneal neovascularization, was downregulated 26.8-fold, while miR-5787 and miR-224-5p were upregulated 2.8 and 2.4-fold relative to controls, respectively. At the mRNA level, 539 transcripts were differentially expressed, among these FOSB and FOS were upregulated 17.5 and 9.7-fold respectively, and JUN by 2.9-fold, all components of the AP-1 transcription factor complex. Pathway analysis revealed dysregulation of several enriched pathways including PI3K-Akt, MAPK, and Ras signaling pathways in aniridia. For several microRNAs and transcripts, expression levels aligned with AAK severity, while in very mild cases with missense or non-PAX6 coding mutations, gene expression was only minimally altered.
Conclusion:
In aniridia, specific factors and pathways are strongly dysregulated in conjunctival cells, suggesting that the conjunctiva in aniridia is abnormally maintained in a pro-angiogenic and proliferative state, promoting the aggressivity of AAK in a mutation-dependent manner. Transcriptional profiling of conjunctival cells at the microRNA and mRNA levels presents a powerful, minimally-invasive means to assess the regulation of cell dysfunction at the ocular surface.

overall_design: MiRNA and mRNA expression profiles of conjunctival cells from 20 patients with aniridia associated keratopathy compared to controls

first: Lorenz

last: Latta


title: The Evolving Immune Microenvironment of Human B-cell Acute Lymphoblastic Leukemia

city: New York

first: Igor

last: Dolgalev

state: New York

address: 550 1st Ave

institute: NYU Grossman School of Medicine

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus


title: Conjunctival mRNA and miRNA expression profiles in congenital aniridia are genotype and phenotype dependent (AKK miRNA)


title: MicroRNA arrays for early diagnosis of diabetic kidney disease

city: tianjin

first: Zhongai

last: Gao

address: qixiangtailu

institute: Tianjin Medical University

summary: We collected the mid-morning urine samples, and centrifuged at 2000g for ten minutes in order to remove cells and debris, and then stored in -80 degree refrigerator. we selected 2 samples per group for the microRNA arrays in the following four groups: normal control, IGT with renal impairment, diabetes, diabetic kidney disease. In IGT renal impairment group, we have found that the expression of two microRNAs were changed. Expression of mir-7977 and mir-5100 were quantified in an extended populations by real-time PCR and the result was consistent with the microRNA arrays. Therefore, mir-7977 and mir-5100 may be sensitive biomarkers for renal impairment in IGT patients.

overall_design: Five samples were mixed and 2 mixed samples per group were selected for the microRNA arrays in the following four groups: normal control (S1.1_NS, S1.2_NS), IGT with renal impairment (S2.1_NS, S2.2_NS), diabetes (S3.1_NS, S3.2_NS), diabetic kidney disease (S4.1_NS, S4.2_NS).

first: Baocheng

last: Chang


title: Microbiomic and transcriptomic insight into the pathogenesis of meningitis-like diseases in cultured Pelophylax nigromaculata

city: Chengdu

first: Liming

address: No.9 Section 4,Renmin Nan Road,Chengdu, Sichuan, P.R. China

department: Chengdu Institute of Biology

institute: Chinese Academy of Sciences

summary: Along with the prevalence of edible frog farming in China, the outbreak of a deadly infectious frog diseased, called frog meningitis (or cataracts and torticollis), has increased in frequency and geographical range dramatically. More than 10 bacterial species, belonging to 8 genera, has been reported as its potential pathogens. Diseased frogs typically manifest as torticollis, cataracts, edema and finally death, resulting in huge economic loss. Currently, the pathogenesis of this disease has not been investigated systematically. Here, we summarized the pathological stages of infected black-spotted frogs (Pelophylax nigromaculata) in Sichuan province according to their symptoms, typically progressing of pathological stage with only torticollis to stage with both torticollis and cataracts. On the basis, we analyzed the pathogenesis by a combination of comparative environmental analysis, microbiomics and transcriptomics. Results showed that more severely infected frog ponds tended to have lower water alkalinity. Elizabethkingia miricola was the only bacteria, whose abundance was positively correlated with the disease degree, and it has absolute dominance in the eyeball and brain of some torticollis-cataracts frogs. E. miricola and several other bacterial species, which belonged to pathogenic genera of meningitis, might be constitutively existed in the resident microbiome in frogs or their environment. Activations of infectious processes and immune responses  related pathways were the major difference between health and diseased frogs at transcriptional level. Despite transcriptional activation of immunoglobulins was observed in both torticollis-only and torticollis-cataracts frogs, transcriptional activation of innate immune system (including MHC, toll-like receptor, and cathelicidins) in brain, inflammation system (including interleukins and receptors) in brain, and acute phase proteins (including transferrins and fibrinogens) in both liver and brain was only observed in torticollis-cataracts frogs. Activation of inflammation and the resulting higher vascular permeability in torticollis-cataracts frogs could explain the severe brain infection, cooccurrence of torticollis and cataracts, and systemic edema in torticollis-cataracts frogs. In addition, meningitis could also result in reduction in energy production in liver, and this was more severe in torticollis-cataracts frogs. In conclusion, our results suggested environment might have a role in susceptibility of frog meningitis. E. miricola was the most likely pathogen of meningitis of black-spotted frogs in Sichuan. Refer to the pathogenesis of human meningitis, excessive inflammation likely played a critical role in the progress of frog meningitis, and its resulted sepsis and organ failure might be the direct cause of infected frogs.

overall_design: In this study, we attempted to have a systematic investigation on the causation and pathogenesis of frog meningitis. Despite it is a bacterial infectious disease, its outbreak shows obvious seasonality and climate dependence (after rain). We speculated that environmental factors likely play a role in the susceptibility of frogs to this disease. Therefore, the environmental factors were compared between infected and uninfected frog ponds to clarify the environmental factors potentially associated with meningitis susceptibility. Then, the microbiomes of brain and eyeball were compared between healthy (group H), torticollis without cataracts (group T), and torticollis with cataracts (group T + C) frogs to reveal the etiologic agents causing frog meningitis. Finally, the transcriptomes of brain, liver, and muscle were compared between H, T, and T + C groups to present the molecular processes underlying the pathological symptoms and progresses, in aiming at reveal the pathogenesis of frog meningitis.

first: Chang

last: Liming

first: Zhao

last: Tian

last: Chunlin

first: Zhu

last: Wenbo

first: Xu

last: Liangliang

first: Liu

last: Jiongyu

first: Li

last: Cheng

first: Xie

last: Feng

first: Jiang

last: JianPing

last: Wei


title: Expression data from betalains treated C. elegans

city: Murcia

first: Fernando

last: Gandía-Herrero

state: Murcia

address: Universidad de Murcia, Campus Espinardo - Edificio Veterinaria

department: Biochemistry and Moleular Biology

country: Spain

institute: University of Murcia

summary:
Effects of betalains in C. elegans gene expression is studied, as our previous results showed a lifespan extension effect produced by theses molecules
Microarrays were used to detail the global programme of gene expression underlying the lifespan extension and identified distinct classes of up/down-regulated genes in animals treated with betalains.

overall_design: C. elegans young adults treated with betalains from L1 stage were selected for RNA extraction and hybridization on Affymetrix microarray chips.

first: M

last: Guerrero-Rubio

middle: J

last: Lopez-Andreo

first: S

last: Hernandez-Garcia

first: F

last: Garcia-Carmona

last: Gandia-Herrero


title: High throughput circRNA sequencing for adipose tissue of Qinchuan cattle

city: Yangling

first: Rui

last: Jiang

address: Litai street

institute: Northwest A&F University

summary: Adipose development is regulated by a series of complicate processes, and non-coding RNAs (ncRNAs) such as circRNA have been reported to play important roles in regulating adipocytes proliferation and differentiation. In this study we profifile the expression of circRNA in cattle fat tissue from calf and adult developmental stages and detect 14,274 circRNA candidates. Some of these circRNAs are differentially expressed between two developmental stages.

overall_design: CircRNA high-throughput sequencing of adipose tissue from qinchuan cattle at two different periods

last: Rui

first: Hong

last: Chen


title: Ythdf m6A readers compensate each other in a context dependent manner [eCLIP]

status: Public on Jun 04 2020

city: Rehovot

first: Noa

last: Novershtern

address: Weizmann Institute

department: Molecular Genetics

country: Israel

institute: Weizmann Institute of Science

summary: YTH domain family proteins Ythdf1, Ythdf2, Ythdf3 are three readers with highly similar structure, which were shown to have different roles in the cell. However, their similarity and the fact that they tend to bind the same targets suggest that in some cases they may have an overlapping role. In this paper, we systematically knocked-out (KO) each of the three readers and the three together (triple-KO), and estimated the effect in-vitro in mouse embryonic stem cells (mESCs), and in-vivo, in viability and gametogenesis. We show that in mESCs there is a compensation between the three readers, with a dramatic hyper-pluripotent phenotype only in the triple-KO. However, in-vivo, Ythdf2 has a dominant role that cannot be compensated by Ythdf1 or Ythdf3, both in viability of the mouse pups and in gametogenesis. We suggest that compensation is dosage-dependent, and in-vivo we cannot detect it due to difference in the readers’ expression, both in level and in spatial location. In addition, we found that Ythdf1 and Ythdf3 specifically down-regulate 2-cell genes, that Ythdf2-KO in gametogenesis affects microtubuline related genes, and that Mettl3-KO severity is increased as the deletion occurs earlier in gametogenesis.

overall_design: Targets of Ythdf1, Ythdf2 and Ythdf3 were measured in mouse embryonic stem cells using eCLIP method

first: Lior

last: Lasman

first: Vladik

last: Krupalnik

first: Stefan

last: Aigner

first: Shashank

last: Sathe

first: Gene

middle: W

last: Yeo

first: Jacob

last: Hanna


title: A Patient-Derived Xenograft Preclinical Model for Triple Negative Breast Cancer to Evaluate PDJ Amplicon Heterogeneity and Chemotherapeutic Induction

city: Scottsdale

first: michael

middle: thomas

last: barrett

state: Arizona

address: 13400 east shea boulevard

institute: mayo clinic arizona

type: Genome variation profiling by genome tiling array

summary: We applied DNA content flow cytometry to ten patient derived triple negative breast cancer (TNBC) xenografts (PDXs) from the Baylor College of Medicine (BCM). We interrogated purified sorted tumor fractions from each sample with whole genome copy number variant (CNV) analyses. These identified a variety of somatic genomic lesions that are common in TNBC including three cases with 9p24.1 amplification targeting PD-L1-PDL2 and JAK2 (PDJ amplicon) and recurring focal amplicons of oncogenic drivers found commonly in the TNBC PDXs including MYC and EGFR. In addition, homozygous deletions of known tumor suppressor genes including PTEN,  CDKN2A, RB1, and BRCA2, and unique targets such as CUX1 and FYN were identified. Of the three PDJ-positive amplified PDXs, 2/3 two had focal MYC amplifications and 1/3 had a RB1 homozygous deletion.

overall_design: We applied DNA content based flow sorting to isolate the nuclei of human tumor populations from breast cancer patient derived xenograft (PDX) models. We coupled this strategy with oligonucleotide array CGH (aCGH)  thereby obtaining high definition genomic profiles of clonal populations from each tumor. These included two pairs of pre and post neoadjuvant therapy treated TNBC cases.

first: Alexander

last: Roesler

first: Elizabeth

last: Lenkiewicz

first: Smriti

last: Malasi

first: Lacey

last: Dobrolecki

first: Michael

middle: T

last: Lewis

first: Karen

last: Anderson

last: Barrett


title: Single-cell DNA methylation sequencing reveals epigenetic variations in mouse oocyte superovulated with different doses of FSH/hMG

city: Beijing

first: Ying

last: Huo

address: HuanYuan street No.38

institute: Peking University Third Hospital

type: Methylation profiling by high throughput sequencing

summary:
Background: With the rapid development of assisted reproductive technology (ART), although ovulation induction has made great progress, the accompanying health risks should not be ignored. Epigenetic modifications play an important role during the development of gametes and embryos. Recently, the epigenetic abnormalities caused by superovulation have attracted increasing attention. The follicle-stimulating hormone (FSH) and human menopausal gonadotropin (hMG) are common gonadotropins used for superovulation and appropriate concentration of them might be necessary. However, there is still no systematic study on the similarities and differences of DNA methylation alterations induced by superovulation with different dosage of FSH/hMG at the single cell levels.
Methods: In the current study, the different doses of FSH/hMG combined with (add hcg full name here) hCG were used in C57BL/6 strain female mice to get experimental group oocytes while naturally matured oocytes and superovulated oocytes with only hCG were respectively set as controls. Single-cell level DNA methylation sequencing was carried out to all the mature oocytes to investigate the effect of superovulation with different dosage of FSH/hMG on DNA methylation during oocyte maturation.
Results: In this study, we found that the hypo differentially methylated regions (DMRs) number of FSH/hMG 200 IU group both increased significantly although the whole genome methylation pattern of mature oocytes derived from superovulation were unaffected as compared with the control matured oocytes, suggesting that high dosage of FSH/hMG might lead to increased genomic methylation instability. At the same time, some of the DMRs annotated genes related to oocyte quality and embryonic development potential were disturbed in all dosage of FSH/hMG group (including Twist2, Cdk1, Ntrk2, Slc22a4, Sstr2, Wnt2, Cntnap5a, Gm2087, Slc16a7, and so on) as well as the certain ones (containing Abcc3, Zfp532, Atp1a1, Zfp804a, and so on) were impaired after high dosage of gonadotropins. We speculated that the effect of superovulation on DNA methylation during oocyte maturation might be dose-dependent to a certain extent, and such effect might affect oocyte quality and embryonic development competency.
Conclusions: The current study firstly analyzed the differential impacts of different doses of gonadotropins on single-cell level DNA methylation of mouse oocytes, indicating a dose-dependent effect of superovulation with FSH/hMG and hCG on the epigenetic variations in mouse oocytes. Furthermore, some important genes that play a critical role in oocyte quality and embryo development were indicated to form the possible molecular basis of the corresponding regulation. This study laid a foundation for evaluating the safety of superovulation and highlighted the need for more and further research into ART.

overall_design: MII oocytes from different dosage of FSH/hMG treated mouse were collected. For each single oocyte, pBAT-seqencing was performed to quantify DNA methylation level in oocyte genome.

first: Zhiqiang

last: Yan

first: Huailiang

last: Feng

first: Jie

last: Qiao


title: Optimizing Non-Viral Gene Delivery to T Cells with Lipofectamine LTX

city: Villanova

last: Elmer

address: 800 E Lancaster Ave

institute: Villanova University

summary: Retroviral gene delivery is widely used in CAR-T cell therapies for hematological cancers.  However, viral vectors are expensive to manufacture, integrate genes in semi-random patterns, and their transduction efficiency is highly variable. In contrast, non-viral delivery methods could offer a potentially less expensive and safer alternative for CAR-T cell gene delivery. In this study, several different cationic vehicles, promoters, and additional culture conditions were compared to optimize non-viral transgene delivery and expression in both Jurkat and primary T cells.  In addition, confocal microscopy and next-generation sequencing experiments were also conducted to detect putative methods of transfection resistance in Jurkat and primary T cells. Transfecting Jurkat cells in X-VIVOTM 15 media with Lipofectamine LTX provided a high transfection efficiency in Jurkat cells (63.0±10.9% EGFP+).  However, this protocol yielded a much lower transfection efficiency (8.07±0.76% EGFP+) in primary T cells.  Confocal microscopy and mRNA-sequencing experiments revealed that a majority of lipoplexes did not enter the primary T cells, perhaps due to relatively low expression levels of heparan sulfate proteoglycans (HSPGs).  Primary T cells also expressed high levels of PYHIN DNA sensors (e.g., AIM2, IFI16), which can induce apoptosis when bound to cytoplasmic DNA. Primary T cells are more resistant to transfection with Lipofectamine than Jurkat T cells.  Transfection of primary T cells appears to be hindered by decreased expression of HSPGs and high expression of PYHIN DNA sensors.  Both of these factors should be considered in the development of future viral and non-viral T cell gene delivery methods.

overall_design: 3 cell lines, 6 samples per cell line with (3) untransfected and (3) transfected samples (n=3) (18 samples overall)

first: Emily

last: Harris

first: Devon

last: Zimmerman

first: Anil

last: Bamezai


title: Measuring transcriptional and chromatin position effects on recombinant adeno-associated virus mediated homologous recombination by targeted integration of barcoded vectors at engineered target sites genome wide

city: Stanford

first: Mark

last: Kay

address: 269 Campus Drive

institute: Stanford University

summary: Recombinant AAV vectors have the unique ability to promote targeted integration of transgenes via homologous integration at specified genomic sites reaching frequencies of 0.1-1%. We studied genomic parameters that influence targeting efficiencies on a large scale. To do this, we generated more than 1000 engineered, doxycycline-inducible target sites in the human HAP1 cell line and infected this polyclonal population with a library of AAV-DJ targeting vectors each carrying a unique barcode. The heterogeneity of barcode integration at each target site provided an assessment of the targeting efficiency at that locus. We compared targeting efficiency with and without target site transcription for identical chromosomal positions, finding that targeting efficiency was enhanced by target site transcription. Chromatin states associated with active transcription were also predictive of higher targeting efficiency. Furthermore, there was an effect on the amenability of a site to targeting due to other factors such as the level of transcription from intersecting genes. These results define important parameters that may not only assist in designing optimal targeting vectors for genome editing, but also provide new insights into the mechanism of AAV-mediated homologous recombination.

overall_design: 2 independent biological replicates induced with doxycycline (100ng/mL) at time of AAV transduction, 2 independent biological replicates uninduced at time of AAV transduction. Each biological replicate with 2 technical replicates.

first: Laura

middle: P

last: Spector


title: Roles of Mafb and c-Maf in MGE-derived pallial interneuron development and maturation

city: San Francisco

first: Ling-Lin

last: Pai

state: CA

address: 1550 4th Street

department: Psychiatry

institute: UCSF

summary: We utilized single-cell RNA-sequencing to identify candidate genetic targets of Mafb and c-Maf in the MGE-lineage using Nkx2.1-Cre generated neonatal wildtype (WT) and conditional Mafb/c-Maf double deletion mutant (cDKO) animals. We identified genes that likely contribute to Maf cDKO's phenotypes, which include preferential parvalbumin interneuron loss, overproduction of hippocampal interneurons and neurite outgrowth defects.

overall_design:
Examination of differentially expressed genes between Nkx2.1-Cre generated WT and Maf cDKO at P0; We focused on the MGE-lineage interneuron subtype.

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first: John

last: Rubenstein


title: Identification of pathogenic TRAIL-expressing innate immune cells during HIV-1 infection in humanized mice by scRNA-seq

city: Chapel Hill

first: Lishan

last: Su

state: NC

address: 125 Mason Farm Rd

department: Lineberger Comprehensive Cancer Center

institute: University of North Carolina

summary: We employed the single-cell RNA sequencing (scRNA-seq) technology to study HIV-induced transcriptomic change in innate immune cells in lymphoid organs. We performed scRNA-seq on hCD45+hCD3-hCD19- human leukocytes isolated from spleens of humanized NOD/Rag2-/- /γc-/- (NRG) mice transplanted with human CD34+ hematopoietic stem-progenitor cells (NRG-hu HSC mice). We identified major populations of innate immune cells including plasmacytoid dendritic cells (pDC), myeloid dendritic cells (mDC), macrophage, nature killer (NK) cells and innate lymphoid cells (ILC). HIV-1 infection significantly upregulated genes involved in type-I interferon inflammatory pathways in each of the innate immune subsets. Interestingly, we found that the TNF-related apoptosis-inducing ligand (TRAIL) was upregulated in the innate immune populations including pDC, mDC, macrophage, NK and ILC. In summary, we characterized HIV-induced transcriptomic changes of innate immune cells in the spleen at single-cell levels, identified the TRAIL+ innate immune cells and defined an important role of TRAIL signaling pathway in HIV-1 induced CD4+ T cell depletion in vivo.

overall_design: Single cell transcriptome of hCD45+hCD3-hCD19- human leukocytes were obtained from spleens of 2 mock and 2 HIV-1 infected humanized mice 3 weeks post HIV-1 infection. Single cell transcriptome library was prepared per factory recommendation by 10x Genomics. Sequencing were performed on Illumina NextSeq 500 with NextSeq 500/550 v2.5 Kits.

first: Liang

last: Cheng

last: Wrobel

first: Zhiyuan

last: Hu


title: c-Rel gain in B cells dose-dependently drives germinal center reactions and autoantibody production in mice

city: Martinsried

first: Christoph

last: Ziegenhain

state: Bavaria

address: Großhaderner Str. 2

department: Department Biology II

institute: Ludwig-Maximilians University Munich

summary: Single nucleotide polymorphisms and locus amplification link the NF-κB transcription factor c-Rel to human autoimmune diseases and B cell lymphomas, respectively. However, the functional consequences of enhanced c-Rel levels remain enigmatic. Here, we overexpress c- Rel specifically in mouse B cells from BAC-transgenic gene loci and demonstrate that c-Rel protein levels linearly dictate expansion of germinal center (GC) B cells and isotype-switched plasma cells. c-Rel expression in B cells of otherwise c-Rel-deficient mice fully rescues terminal B cell differentiation, underscoring its critical B cell-intrinsic roles. Unexpectedly, in GC B cells transcription-independent regulation produces the highest c-Rel protein levels amongst B cell subsets. In c-Rel overexpressing GC B cells this causes enhanced nuclear translocation, a profoundly altered transcriptional program and increased proliferation. Finally, we provide the first link between c-Rel gain and autoimmunity by showing that c-Rel overexpression in B cells causes autoantibody production and renal immune complex deposition.

overall_design: For RNA sequencing experiments 8 mice per genotype were immunized i.p. with SRBC. Desired splenocyte populations were pre-separated by MACS followed by flow-cytometry- based cell sort of 1000 cells per sample into 96-well-plates containing TCL buffer (Qiagen) (naïve B cells: pre-MACS IgD+CD43+, sort IgDhiIgMlo; GC B cells: pre-MACS IgD-CD43-, sort B220+IgD-CD38loCD95hiGL7+; PC: pre-MACS CD138+, sort B220loCD138+).

first: Wolfgang

last: Enard


title: Ythdf m6A readers compensate each other in a context dependent manner [Ribo-seq]

first: Noa

last: Novershtern

overall_design: Mouse embryonic stem cells were knocked-out to each of the following proteins: Mettl3, Ythdf1, Ythdf2, Ythdf3, and Ythdf1/2/3 triple-KO. Ribosome footprint (ribo-seq) was generated in each of these KOs, and in WT control.

first: Lior

last: Lasman

first: Vladik

last: Krupalnik

first: Jacob

last: Hanna


title: HIF2α is a Direct Regulator of Neutrophil Motility

city: Dresden

first: Ben

last: Wielockx

address: Fetscherstr. 74

institute: Institut für Klinische Chemie und Laboratoriumsmedizin

summary: Orchestrated recruitment of neutrophils to inflamed tissue is essential during initiation of inflammation. Inflamed areas are usually hypoxic, and adaptation to reduced oxygen pressure is typically mediated by hypoxia pathway proteins. However, it is still unclear how these factors influence the migration of neutrophils to and at the site of inflammation either during their transmigration through the blood-endothelial cell barrier, or their motility in the interstitial space. Here, we reveal that activation of the Hypoxia Inducible Factor-2 (HIF2α) due to deficiency of HIF-prolyl hydroxylase domain protein-2 (PHD2) boosts neutrophil migration specifically through highly confined microenvironments. In vivo, the increased migratory capacity of PHD2-deficient neutrophils resulted in massive tissue accumulation in acute local inflammation. Using systematic RNAseq analyses and mechanistic approaches, we identified RhoA, a cytoskeleton organizer, as the central downstream factor that mediates HIF2α-dependent neutrophil motility. Thus, we propose that the here identified novel PHD2-HIF2α-RhoA axis is vital to the initial stages of inflammation as it promotes neutrophil movement through highly confined tissue landscapes.

overall_design: FACS sorted neutrophils from conditional PHD2 deficient or PHD2/HIF2 double deficient mouse lines in combination with their respetive WT controls

first: Sundary

last: Sormendi

first: Pablo

last: Vargas


title: Development of lncRNAs expression signatures in exosomes derived from different gastric cancer cells

city: Zhengzhou

first: peiming

last: zheng

address: 7 Weiwu Road

institute: People’s Hospital of Zhengzhou University

summary: Exosomes from the culture media (CM) of four GC cells (GCCs) and human gastric epithelial cells were isolated. Exosomal RNA was extracted, and lncRNA microarray assay was performed to identify GC-specific exosomal lncRNAs. A total of 199 exosomal lncRNAs were expressed at considerable higher levels in GCCs than those in normal controls, among which the top 10 upregulated lncRNAs were selected for further validation. qRT-PCR revealed that lnc-SLC2A12-10:1 was remarkably upregulated in exosomes derived from patients with GC and GCCs. The expression levels of the candidate exosomal lncRNAs lnc-SLC2A12-10:1 were validated in 120 subjects via quantitative reverse transcription PCR (qRT-PCR).The result suggested that exosomal lnc-SLC2A12-10:1 may be a potential noninvasive biomarker for the diagnosis and prognosis monitoring of GC.

overall_design: Four human GCC lines (MGC803, BGC823, SGC7901, and AGS) and one normal human gastric (GES-1) cell line were  cultured at 37 °C with 5% CO2 in 1640/DMEM containing 10% exosome-depleted FBS. Exosomal RNA from the CM of four GCCs and GES-1 were purified, five independent samples were collected and lncRNA microarray assay was conducted to identify GC-specific exosomal lncRNAs.

first: Peiming

last: Zheng

first: Shibao

last: Li


title: lncRNA and mRNA expression signatures for experimental autoimmune encephalomyelitis model mice and normal mice

city: Nanjing

first: Zhengying

last: Bian

state: Jiangsu Province

address: 24 Tongjia Street

institute: China Pharmaceutical University

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

summary: To explore the potential roles of lncRNAs in the progress of multiple sclerosis, spleens of  experimental autoimmune encephalomyelitis (EAE) model mice and normal mice were used as the samples to obtain the expression profiles of lncRNAs and mRNAs with the mouse LncRNA Array v3.0.

overall_design: Three EAE model mice and three normal mice were selected for lncRNA chip detection.

first: Wei

last: Guo

first: Wen

last: Lei


title: Apolipoprotein A-I Anti-tumor Activity Targets Cancer Cell Metabolism

city: Cleveland

first: Maryam

last: Zamanian

state: OH

address: 9500 Euclid Avenue

department: Cardiovascular and Metabolic Diseases

institute: Lerner Research Institute

summary:
Previously, we reported apolipoprotein A-I (apoA-I), the major protein component of high-density lipoprotein (HDL) has potent anti-melanoma activity. Herein, we used DNA microarray and bioinformatics to interrogate gene expression profiles of tumors from apoA-I expressing (A-I Tg+/-) versus apoA-I-null (A-I KO) animals to gain insights into mechanisms of apoA-I tumor protection. Differential expression analyses of 11 distinct tumors per group with  > 1.2-fold cut off and a false discovery rate adjusted p< 0.05, identified 176 significant transcripts (71 up- and 105 down-regulated in A-I Tg+/- relative to A-I KO group). Bioinformatic analyses identified the mevalonate and de novo serine/glycine synthesis pathways as potential targets for apoA-I anti-tumor activity.
Relative to A-I KO, day-7 B16F10L melanoma tumor homografts from A-I Tg+/- exhibited reduced expression of mevalonate-5-pyrophosphate decarboxylase (MVD), a key enzyme targeted in cancer therapy, as well as squalene epoxidase (Sqle), cytochrome P450, family 51 (Cyp51), hydroxysteroid (17-beta) dehydrogenase 7 (Hsd17b7), and 24-dehydrocholesterol reductase (Dhcr24) with the latter four serving in the sterol synthesis arm of the mevalonate pathway. Phosphoglycerate dehydrogenase (Phgdh), the first enzyme branching off glycolysis in de novo serine synthesis pathway was the most repressed transcript in tumors from A-I Tg+/-. We validated the experimental approach by correlating gene expression patterns in a mouse model where A-I KO is tumor-permissive relative to A-I Tg+/-, with adverse tumor markers previously identified in human melanoma and found 45% concordance. We propose that apoA-I, a physiological serum protein may target the mevalonate and serine synthesis pathways in melanoma cells, in vivo, thus inhibiting the flux of building blocks for macromolecule synthesis that drive rapid tumor growth.

overall_design: 32 samples were analyzed.  10 WT, 11 transgenic, 11 KO.  Totally 32 samples from C57BL/6J mice strain were used for this study.  10 wild type (WT) mice of strain, C57BL/6J, 11 separate primary tumors from 11 mice deficient in apoA-I (A-I KO) and 11 primary tumors from 11 mice expressing human apoA-I (A-I Tg+/-) were used for this study.  B16F10L melanoma homograft grown in C57BL/6 mice deficient in apoA-I (A-I KO) or expressing human apoA-I (A-I Tg+/-) were resected 7 days after inoculation and processed for RNA, microarray and data analysis.

last: Zamanian-Daryoush

first: Daniel

last: Lindner

first: Jennifer

last: Buffa

first: Jie

first: Banu

last: Gopalan

first: Stanley

last: Hazen

first: Joseph

last: DiDonato


title: Runx3 function in colon resident macrophages (RM) and CD11b+ dendritic cells (DC).

first: Dena

last: Leshkowitz

department: Bioinformatics Unit, Life Sciences Core Facilities

summary:
RUNX3 is one of three mammalian Runt-domain transcription factors that regulate gene expression in several types of immune cells. Runx3-deficiency in mice is associated with a multitude of defects in the adaptive and innate immunity systems, including the development of early onset colitis. Our study reveals that conditional deletion of Runx3 specifically in mononuclear phagocytes (MNP) recapitulates the early onset spontaneous colitis seen in Runx3-/- mice. We show that Runx3 is expressed in colonic MNP, including RM and the dendritic cell cDC2 subsets and its loss results in impaired differentiation/maturation of both cell types.
To uncover the immuno-tolerogenic properties of Runx3 in the colon MNP we performed global transcriptional profiling employing microarrays.

overall_design: Colon RM and CD11b+ DC were sorted from freshly digested cecums taken from 6-8 weeks old WT and Runx3-cKO (CD11c-cre) litter mates mice. Four Runx3-cKO RM replicates were compared to 3 WT RM replicates and 3 Runx3-cKO CD11b+ DC replicates were compared to 2 WT CD11b+ DC replicates Each replicate consist a pool of 3-4 mice. RNA was extracted and hybridized to Affymetrix microarrays.

first: Shay

last: Hantisteanu

first: Yoram

last: Groner


title: Genome-wide mapping of Runx3 bound regions in dendritic cell line D1.

summary: ChIP-seq was conducted using D1 cells and in house anti-Runx3 antibodies (Ab).

overall_design: Three biological Runx3 IP test repeats and two Rabbit non-immune serum IP controls from D1 cell line.


title: Ythdf m6A readers compensate each other in a context dependent manner [3'UTR RNA-seq]

first: Noa

last: Novershtern

overall_design: We estimated decay rate in mouse ESCs, in each KO (Ythdf1, Ythdf2, Ythdf3 and the triple KO), and in WT control . We treated the cells with Actinomycin-D, and harvested RNA in three time points (t=0,4h,8h, with duplicates of 0 and 8). We estimated transcription levels using 3’ poly-A RNA-seq (Geula et al. 2015), and calculated mRNA half-life, as described in the associated paper.

first: Lior

last: Lasman

first: Vladik

last: Krupalnik

first: Jacob

last: Hanna


title: Human endothelial cells stimulated with dengue virus non-structural protein 1

city: Syracuse

first: Frank

last: Middleton

address: 505 Irving Avenue

department: Neuroscience and Physiology

institute: SUNY Upstate Medical Univ

summary: we report the changes in the transcriptome of human umbilical vein endothelial cells (HUVECS) after exposure to a recombinant purified soluble form of dengue virus non-structural protein 1 (NS1)

overall_design: HUVECs in gelatin coated cell culture plates were mantained in growth media until confluent. The purified NS1 protein was then added to the plate wells for stimulation for 4 hrs in regular incubation conditions.

first: Arturo

last: Barbachano-Guerrero

first: Timothy

last: Endy

first: Christine

last: King


title: Ythdf m6A readers compensate each other in a context dependent manner [RNA-seq]

overall_design:
Four different experiments:
1) Mouse embryonic stem cells were knocked-out to each of the following proteins: Mettl3, Ythdf1, Ythdf2, Ythdf3, and Ythdf1/2/3 triple-KO. RNA-seq was generated in each of these KOs, and in WT.
2) RNA-seq was generated from GV stage oocytes of Mettl3f/f Zp3-Cre+ and Cre- (control) female mice.
3) RNA-seq was generated from post-GV stage oocytes of Ythdf2-/- and Ythdf+/- (control) female mice.
4) RNA-seq was generated from round spermatids of Ythdf2-/- and Ythdf+/+ (control) male mice.


title: Runx3 prevents spontaneous colitis by directing differentiation of anti-inflammatory mononuclear phagocytes

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

overall_design: Refer to individual Series


title: Identification of miRNAs regulating Clostridium perfringens type C infection in the spleen of diarrheic piglets

city: Lanzhou

first: Pengfei

last: Wang

state: Gansu

address: No. 1 Yingmen village, Anning District

institute: Gansu Agricultural University

summary:
Purpose: RNA-Seq has become a powerful tool for investigating transcriptional profiles in gene expression analysis, which would help to reveal the molecular mechanism of Clostridium perfringens type C infecting the piglets. In this study, we analyzed miRNA profiles of the spleen of piglets caused by Clostridium perfringens type C.
Methods: 30 normal 7-day-old piglets (Y x L), without infecting Clostridium perfringens type C, Escherichia coli and Salmonella, were selected as experimental subjects. 25 piglets were randomly selected as the experimental group, which were disposed once a day for 5 days. Each piglet was dosed with 1 ml of bouillon culture-medium inoculated Clostridium perfringens type C at 37℃ for 16h, which approximate to 1 x109 CFU per ml. Then, 5 piglets were randomly selected as the control group (SC), which were taken the equal volume medium for 5 days.Based on total diarrhea scores, 25 piglets were ranked from high to low. The top and last five piglet were considered as sensitive group (SS) and resistant group (SR), respectively. Finally, spleen were collected and sequenced for miRNA.
Result: 88 differentially expressed miRNAs were found. KEGG pathway analysis for target genes revealed that these miRNAs were involved in MAPK signaling pathway, mTOR signaling pathway, FoxO signaling pathway, p53 signaling pathway and ECM-receptor interaction. And 4 miRNAs (miR-133b, miR-532-3p, miR-339-5p and miR-331-3p) of closely related to piglets resistance to C. perfringens type C were obtained. The expression correlation analysis between these miRNAs and target genes revealed that the expression of miR-133b and miR-532-3p had negative correlation with their target NFATC4, miR-339-5p had negative correlation with target HTRA3, and miR-339-5p and miR-331-3p had negative correlation with target TNFAIP8L2 in spleen, suggesting that miR-133b and miR-532-3p targeting to NFATC4, miR-339-5p targeting to HTRA3, and miR-339-5p and miR-331-3p targeting to TNFAIP8L2 were probably involved in piglet resisting C. perfringens type C.
Conclusions:The results will provide value resources for better understanding of the genetic basis of C. perfringens type C resistance in piglet and lays a new foundation for identifying novel markers of C. perfringens type C resistance.

overall_design: miRNA profiles of spleen in piglets were generated by deep sequencing,three group,five sample in each group,using Illumina

first: Qiaoli

last: Yang

first: Zunqiang

last: Yan

first: Xiaoyu

last: Huang

first: Xiaoli

last: Gao

first: Ruirui

last: Luo

first: Wenyang

last: Sun

first: Wei

first: Kaihui

last: Xie

first: Shuangbao

last: Gun


title: A lamin-like protein OsNMCP1 regulates drought resistance and root growth partially through chromatin accessibility modulation by interacting with a chromatin remodeler OsSWI3C in rice

city: Wuhan

first: Yu

last: Chang

state: Hubei

address: No.1, Shizishan Street, Hongshan District

department: National Key Laboratory of Crop Genetic Improvement

institute: Huazhong Agricultural University

summary: Lamin proteins in animals are implicated in many nuclear functions, including chromatin organization, signaling transduction, gene regulation, and cell differentiation. Nuclear Matrix Constituent Proteins (NMCPs) are lamin analogues in plants, but their regulatory functions remain largely unknown. In this work, we report that OsNMCP1 positively regulates root growth and drought resistance through modulating chromatin state and expression levels of many genes functioning in root growth and stress resistance. OsNMCP1 is localized at the nuclear periphery and induced by drought stress. Overexpression of OsNMCP1 resulted in a deeper and thicker root system and enhanced drought resistance compared to the wild-type control. Assay for transposase accessible chromatin with sequencing (ATAC-seq) analysis revealed that OsNMCP1-overexpression altered chromatin accessibility in many genes related to drought resistance and root growth, including OsNAC10, OsERF48, OsSGL, and OsMSR15. Interestingly, OsNMCP1 can interact with SWITCH/SUCROSE NONFERMENTING (SWI/SNF) chromatin remodeling complex OsSWI3C. The reported drought resistance or root growth related genes that were positively regulated by OsNMCP1 were negatively regulated by OsSWI3C, and OsSWI3C overexpression led to decreased drought resistance. We propose that the interaction between OsNMCP1 and OsSWI3C may lead to release of OsSWI3C from the gene silencing complexes SWI/SNF under drought condition thus changing the chromatin accessibility in genes related to root growth and drought resistance.

overall_design: ATAC-seq for root tissue from OsNMCP1-OE, OsSWI3C-RNAi, and ZH11 seedlings under normal and drought conditions. RNA-seq for root tissue from OsNMCP1-OE and ZH11 under normal and drought conditions. Three biological replicates were involved for each experiment (two for the OsNMCP1-OE RNA-Seq under normal condition).

first: Jun

first: Yonghua

last: Qin

first: Dijun

last: Chen

first: Tao

last: Zhu

first: Kaiqing

last: Peng

first: Huaijun

first: Ning

last: Tang

first: Xiaokai

last: Li

first: Yusen

first: Yinmeng

last: Liu

first: Xianghua

first: Weibo

first: Lizhong

last: Xiong


title: Profiling of DNA Methylation during RANKL Induced Osteoclastogenesis using Whole-Genome Bisulfite Sequencing

city: Chongqing

first: Ce

last: Dou

state: Chongqing

address: Gaotanyan Street No.30

institute: Third Military Medical University

summary:
Purpose: The goals of this study are to describe the DNA methylation profile during RANKL induced osteoclastogenesis.
Methods: Primary bone marrow cells were isolated and treated with M-CSF (30ng/mL) to generate bone marrow macrophages (BMMs). BMMs were then used to generate preosteoclast (pOC) stimulated by M-CSF (30ng/mL) together with RANKL (100ng/mL) for 24 h and mature osteoclast (mOC) stimulated by M-CSF (30ng/mL) together with RANKL (100ng/mL) for 72 h or more. DNA methylation profiles of BMM, pOC and mOC were generated by deep sequencing, using Illumina NovaSeq 6000.
Results: After acquiring of clean reads, we used Hisat2 for spliced mapping. We mapped about 40 million sequence reads per sample of the WGBS results. Saturation rate analysis was then performed evaluating the gene coverage rate along with read depth increase. The transcripts mapping to difference functional region of the genome was then analyzed. Circos software was used to map the consistency of samples with mouse genome on a chromosomal level. The quantification of transcript intensity was analyzed using RPKM (Reads Per Kb per Million reads).
Conclusions: Our study represents the first high-throughput WGBS sequencing data of DNA methylation during osteoclastogenesis.

overall_design: DNA methylation of ostoeclast at distinct differentiation stages were determined using WGBS.

first: Qinyu

last: Ma


title: Vascularized human cortical organoids (vOrganoid) model cortical development in vivo

first: xiaoqun

last: wang

state: Beijing

address: 15 Datun Road, Chaoyang District

department: Institute of Biophysics

institute: Chinese Academy of Sciences

summary: Modeling the processes of neuronal progenitor proliferation and differentiation to produce mature cortical neuron subtypes is essential for the study of human brain development and the search for potential cell therapies. We demonstrated a novel paradigm for the generation of vascularized organoids (vOrganoids) consisting of typical human cortical cell types and a vascular structure for over 200 days as a vascularized and functional brain organoid model. The observation of sEPSCs (spontaneous excitatory postsynaptic currents), sIPSCs (spontaneous inhibitory postsynaptic currents) and bidirectional electrical transmission indicated the presence of chemical and electrical synapses in vOrganoids. More importantly, single-cell RNA-sequencing analysis illustrated that vOrganoids exhibited robust neurogenesis and that cells of vOrganoids differentially expressed genes related to blood vessel morphogenesis. The transplantation of vOrganoids into the mouse S1 cortex resulted in the construction of functional human-mouse blood vessels in the grafts that promoted cell survival in the grafts. This vOrganoid culture method could not only serve as a model to study human cortical development and explore brain disease pathology but also provide potential prospects for new cell therapies for nervous system disorders and injury.

overall_design: The cerebral organoids at two time points were dissociated for single-cell RNA-seq (10x Genomics Chromium) to determine cell types

first: Y

last: Shi

first: X

last: Wang


title: Glutathione dynamics determines therapeutic efficacy of mesenchymal stem cells for graft-versus-host disease through CREB1-NRF2 pathway

city: Seoul

first: DONG-MYUNG

last: SHIN

address: Pungnap-2 dong, Songpa-gu

department: Department of Biomedical Sciences

country: South Korea

institute: University of Ulsan College of Medicine

summary: Molecular and functional significance of CREB1-NRF2 pathway on GSH dynamics of MSCs which critically determines therapeutic outcomes for treating allogeneic conflicts, including GvHD. A simple and reliable method to real-time monitor the redox status of MSCs which precisely predict their core functions including self-renewal, migration, and immunomodulatory capacities.

overall_design: Human ES-derived MSCs (hES-MSC) were FACS-sorted into GSHHigh and GSHLow fractions using FreSHtracer. Total RNA from three independent replicates was isolated using the RNeasy Mini Kit (QIAGEN, Valencia, CA), including treatment with DNase I (QIAGEN). One ug of total RNA was used for the Affymetrix GeneChip Human Gene 2.0 ST Array (Affymetrix, Santa Clara, CA), in accordance with the manufacturer’s instructions.

first: Dong-Myung

last: Shin

first: Jisun

last: Lim

first: Hyein

last: Ju


title: Genomic, transcriptomic, and structural analysis of Pseudomonas virus PA5oct highlights the molecular complexity among Jumbo phages

city: Leuven

first: Cedric

last: Lood

address: Kasteelpark Arenberg 20 - box 2460

department: Division of Animal and Human Health Engineering

country: Belgium

institute: KU Leuven

summary: Pseudomonas virus PA5oct has a large, linear, double-stranded DNA genome (286,783 bp) and is related to Escherichia phages 121Q/PBECO 4, Klebsiella phage vB_KleM-RaK2, Klebsiella phage K64-1, and Cronobacter phage vB_CsaM_GAP32. A protein-sharing network analysis highlights the conserved core genes within this clade. Combining hybrid genome sequencing, RNA-Seq and mass spectrometry analyses of its virion proteins allowed us to accurately identify genes and elucidate regulatory elements for this phage (ncRNAs, tRNAs and promoter elements). In total PA5oct encodes 449 CDS of which 93, have been identified as virion-associated based on ESI-MS/MS. The RNA-Seq-based temporal genome organization suggests a gradual take-over by viral transcripts from 21%, 69%, and 93%  at 5, 15 and 25 min after infection, respectively . Like many large phages, PA5oct is not organized into contiguous regions of temporal transcription. However, although the temporal regulation of the PA5oct genome expression reveals specific genome clusters expressed in early and late infection, many genes encoding experimentally observed structural proteins surprisingly appear to remain almost untranscribed throughout the infection cycle. Within the host, operons associated with elements of a cryptic Pf1-like prophage are upregulated, as are operons responsible for Psl exopolysaccharide (pslE-J) and periplasmic nitrate reductase (napA-F) production. The characterization described here represents a crucial step towards understanding the genomic complexity as well as molecular diversity of jumbo viruses.

sample_organism:
Pseudomonas aeruginosa PAO1
Pseudomonas virus PA5oct

overall_design: Synchronous infection of P. aeruginosa PAO1 using Pseudomonas virus PA5oct and isolation of the transcripts in the early, middle, and late infection timepoints

first: Bob

last: Blasdel

first: Katarzyna

last: Danis-Wlodarczyk


title: Perinatal exposure to an environmentally-relevant mixture of BFRs and ovarian gene expression in the adult rat

city: Montreal

first: Oceane

last: Albert

state: Quebec

address: 3655 Promenade Sir William Osler, McIntyre Medical Sciences Bldg, Room 107

department: Pharmacology & Therapeutics

institute: McGill University

summary: Brominated flame retardants (BFRs), including polybrominated diphenyl ethers (PBDEs) and hexabromocyclododecane (HBCDD), leach out from consumer products into the environment. Exposure to BFRs has been associated with effects on endocrine homeostasis. To test the hypothesis that in utero and lactational exposure to BFRs may affect the reproductive system of female offspring, adult female Sprague-Dawley rats were fed nominal doses (0, 0.06, 20, or 60 mg/kg/day) of a BFR dietary mixture formulated to mimic the levels of congeners in house dust from prior to mating until weaning. Vaginal opening and the day of first estrus occurred at a significantly earlier age among offspring from the 20 mg/kg/day BFR group, indicating that the onset of puberty was advanced. Histological analysis of ovaries from post-natal day 46 offspring revealed an increase in the incidence of multi-oocyte follicles. Toxicogenomics analysis of ovarian gene expression identified upstream regulators, including HIF1A, CREB1, EGF, the β-estradiol and PPARA pathways, predicted to be downregulated in the 20 mg/kg/day or the 60 mg/kg/day group and to contribute to the gene expression patterns observed. Thus, perinatal exposure to BFRs dysregulated ovarian folliculogenesis and signaling pathways that are fundamental for ovarian function.

overall_design: For each of the 4 treatment groups (0, 0.06, 20 and 60 mg/kg/day), RNA was extracted from the ovaries of 5-6 animals from independent litters. One animal in the low group was found to be an outlier and was removed (Ovary_PND46_0.06_rep4)

first: Adélaïde

last: Allais

first: Océane

first: Pavine

last: Lefèvre

first: Mike

last: Wade

first: Barbara

middle: F

last: Hales

first: Bernard

last: Robaire


title: H4K16ac developmental dynamics during Drosophila development [RNA]

city: Freiburg

first: Asifa

last: Akhtar

address: Stuebeweg 51

department: Chromatin Regulation

institute: Max Planck Institute of Immunobiology and Epigenetics

summary: We have systematically studied the contribution of the histone acetyltransferase MOF for Drosophila embryos development characterizing the expression changes at st5, st7 and st15 in male and female embryos. Additionally, we studied the contribution of the histone acetyltransferase MOF for the transcription of male S2 cells.

overall_design: Single embryo mRNA seq was performed for st5 and st7 embryos. The gender of embryos was identified post-sequencing using the expression pattern of msl-2, sxl, tra and tra2 genes. St15 embryo male and female were separated by Sxl-GFP marker. 25 embryos were pooled for each replicate.

first: Maria

last: Samata

first: Anastasios

last: Alexiadis

first: Giuseppe

last: Semplicio


title: A genome-wide screen identifies E2F6 as critical factor for TMZ chemoresistance in EGFRvIII expressing GBM (CRISPR library RNA-seq)

city: tianjin

first: Kai

last: Huang

address: anshan roud

institute: tianjin medical university

summary: We conducted a genome-wide screen by clustered regularly interspaced short palindromic repeats (CRISPR)-Cas9 library to identify genes which are particularly resistant to EGFRvIII GBM cells under the chemo-stress of TMZ. In vitro and in vivo validation of EGFRvIII-specific targets revealed several strong hits, including E2F6. Mechanistic studies demonstrated that E2F6 reveals its resistance to TMZ through NF-κB and TMZ inducement.EGFRvIII GBM cells under the chemo-stress of TMZ.

overall_design: Examination of TMZ resistant and sensitive genes in U87EGFRvIII cells, each with 3 replicates.

first: Chunsheng

last: Kang


title: RNAseq results of Aeromonas dhakensis AAK1, uvrY mutant and uvrY complement

city: Tainan

first: Yi-Wei

last: Chen

address: No.1 University Road

country: Taiwan

institute: NCKU

summary: We analized the mRNA level of genes in uvrY mutant compared to wildtype or complement strain.

overall_design: Total RNA of each bacteria was extracted from overnight cultured bacteria. Analysis: DuvrY vs. AAK1 and DuvrY vs. DuvrY-pUvrY

first: Po-Lin

first: Chang-Shi


title: A genome-wide screen identifies E2F6 as critical factor for TMZ chemoresistance in EGFRvIII expressing GBM


title: Intergenerationally maintained Histone H4 lysine 16 acetylation is instructive for future gene activation

summary: Before zygotic genome activation (ZGA) the quiescent genome undergoes reprogramming to transition into the transcriptionally active state. However, the mechanisms underlying euchromatin establishment during early embryogenesis remain poorly understood. Here, we show that histone H4 lysine-16 acetylation (H4K16ac) is maintained from oocytes to fertilized embryos in Drosophila and mammals. H4K16ac forms large domains that control nucleosome accessibility of promoters prior to ZGA in flies. Maternal depletion of MOF acetyl-transferase leading to H4K16ac loss causes aberrant Pol II recruitment, compromises the 3D organization of the active genomic compartments during ZGA and consequently causes downregulation of post-zygotically expressed genes. Germline depletion of histone deacetylases revealed that other acetyl marks cannot compensate for H4K16ac loss in the oocyte. Moreover, zygotic re-expression of MOF was neither able to restore embryonic viability nor onset of X chromosome dosage compensation. Thus, maternal H4K16ac provides an instructive function to the offspring, priming future gene activation.

overall_design:
DNA: We have generated a) Mnase ChIPseq profiles of H4K16ac from hand staged Drosophila embryos at various developmental stages derived from WT and MSL complex RNAi conditions b) ATAC-seq of embryo nc9-13 and nc14 upon maternal depletion of control mof RNAi or msl-3 and c) Hi-C of embryos upon control of mof maternal depletion at st5 (nc14) and st15.
RNA: We have generated poly-A RNA-seq datasets derived from: a) Single embryo mRNA seq of st5 and st7 embryos after maternal mof depletion. The gender of embryos was identified post-sequencing using expression pattern of msl-2, sxl, tra and tra2. b) St15 embryo male and female separated embryos after maternal mof depletion. c) RNA-seq from mof depleted S2 cells.


title: A genome-wide screen identifies E2F6 as critical factor for TMZ chemoresistance in EGFRvIII expressing GBM (EGFRvIII RNA-seq)

summary: we conducted a genome-wide screen by clustered regularly interspaced short palindromic repeats (CRISPR)-Cas9 library to identify genes which are particularly resistant to EGFRvIII GBM cells under the chemo-stress of TMZ.

overall_design: Examination of different expressing genes in EGFRvIII cells,each with 3 replicates.


title: A genome-wide screen identifies E2F6 as critical factor for TMZ chemoresistance in EGFRvIII expressing GBM (DNA-seq)

summary: We conducted a genome-wide screen by clustered regularly interspaced short palindromic repeats (CRISPR)-Cas9 library to identify genes which are particularly resistant to EGFRvIII GBM cells under the chemo-stress of TMZ. In vitro and in vivo validation of EGFRvIII-specific targets revealed several strong hits, including E2F6. Mechanistic studies demonstrated that E2F6 reveals its resistance to TMZ through NF-κB and TMZ inducement.

overall_design: A pooled genome-wide CRISPR-Cas9-based screen using a sgRNA lentiviral library harboring 123,411 sgRNAs which target 20,914 human genes were performed to transduce EGFRwt and EGFRvIII U87 cells ( no replicate), then treated with TMZ for 7 and 14 days. The end time point of each screen was compared to day 0 in order to determine which sgRNAs were overrepresented or underrepresented in the population.


title: Transcriptome Diversity Associated with Ancestry and Diet in Ethnically Diverse East African Populations

city: Philadelphia

first: Gregory

middle: Robert

last: Grant

address: 3400 Civic Center Blvd.

department: Genetics

institute: University of Pennsylvania

summary: Genetic basis of gene expression in Africans with diverse diets

overall_design: Nine populations in East Africa

first: Sarah

last: Tishkoff


title: H4K16ac developmental dynamics during Drosophila development [DNA]

summary: H4K16ac developmental dynamics during drosophila development

overall_design: We are submitting a) MNase ChIPseq profiles of H4K16ac from hand staged Drosophila embryos at various developmental stages derived from WT and MSL complex RNAi conditions, b) Pol II ChIP-seq of nc14/ st5 embryos upon control and maternal mof depletion, c) ATAC-seq of nc9-13/ st3-4 and nc14 / st5 embryo upon control and maternal depletion of mof or msl-3, and d) In situ Hi-C of st5 and st15 embryos upon control or mof maternal depletion.

first: Gina

last: Renschler

first: Gautier

last: Richard


title: Transcriptional profile of wox5-1 and seu-3 mutants

city: Ames

first: Natalie

last: Clark

state: IA

address: Advanced Teaching and Research Building 2213 Pammel Drive

department: Plant Pathology and Microbiology

institute: Iowa State University

summary: The goal of this dataset was to transcriptionally profile the roots of wox5-1 and seu-3 mutants. To accomplish this, we collected 1mm of tissue from the root tip of each mutant as well as Col-0 as a control. RNA was extracted from root tissue, libraries were prepared, and RNA-seq was performed. FPKM values were calulcated using Cufflinks.

overall_design: Approximately 1mm of the root tip was collected from wox5-1, seu-3, and Col-0 Arabidopsis plants at 5 days post-stratification. RNA was extracted, and RNA-seq was performed.

first: Adam

last: Fisher

first: Rosangela

last: Sozzani


title: New Targeted Approaches for Epigenetic Age Predictions

status: Public on Jun 03 2020

city: Changchun

first: Yang

last: Han

address: Xi'an road 5333, Jilin University Heping Campus, Changchun, China

institute: Jilin University

summary: In this study, we have optimized and directly compared epigenetic age predictors based on pyrosequencing, ddPCR and BBA-seq of specific age-associated regions. Bisulfite barcoded amplicon sequencing (BBA-seq) was performed on 9 genomic region of 77 human blood DNA and 11 genomic regions of 95 buccal swab DNA to measure age-associated regions for epigenetic age prediction. Furthermore, our data indicate that the correlation of age-associated DNAm with chronological age peaks close to CTCF binding sites. Age-associated DNAm is not coherently modified on individual DNA strands and this enabled alternative single-read age-predictors that reflect heterogeneity in epigenetic aging within a specimen.

overall_design: DNA methylation profiles of bisulfite converted 77 human blood and 95 human buccal swab specimens

first: Julia

last: Franzen

first: Thomas

last: Stiehl

first: Miloš

last: Nikolić

first: Jan

last: Hapala

first: Wolfgang

last: Wagner


title: Hand2-Induced Preservation of Sympathetic Neurons Prevents Sarcopenia with Aging

city: Oklahoma City

first: Jonathan

middle: D

last: Wren

state: OK

address: 825 N.E. 13th Street

department: Genes and Human Disease

institute: Oklahoma Medical Research Foundation

summary: We examined age-dependent expression of the heart and neural crest derivative 2(Hand2), a critical transcription factor for post mitotic maintenance of SNs, and tested the possibility that inducing its expression exclusively in SNs will significantly prevent (a) motor denervation, (b) impaired NMJ transmission, and (d) loss of muscle mass and function in old mice

overall_design: 10 empty vector controls and 7 hand2 vector treated animals

first: Anna

middle: Z

last: Rodrigues

first: Zhong-Min

last: Wang

first: Maria

last: L< Messi

first: Henry

last: Bonilla

first: Liang

last: Liu

first: Willard

last: Freeman

first: Osvaldo

last: Delbono


title: Analysis of miRNAs expression in the ileum during broiler chickens against subclinical necrotic enteritis through Bacillus licheniformis H2 supplement

city: chengdu

first: ying

last: zhao

state: sichuan

address: huimin

institute: Sichuan Agricultural University

summary: Subclinical necrotic enteritis (SNE) is one of the serious threats to the poultry industry. Probiotics have been proven to exert the beneficial effects in controlling SNE. However, the exact mechanisms of probiotics have not been fully elucidated, and few researchs have focused on their impact on miRNAs. Therefore, the purpose of this study was to explore the miRNA expression profles in the ileum of broiler chickens during probiotic supplement treatment for SNE. 180 newly hatched male chicks were randomly allocated in three groups, including negative control group(NC), SNE infection group(PC) and Bacillus licheniformis H2 pre-treatment group (BL). Illumina high-throughput sequencing was conducted to identify the miRNA expression of three groups. The results showed that 628 miRNAs, including 582 known miRNAs and 46 novel miRNAs, were detected in libraries. The target genes of 57 significantly differentially expressed miRNAs were predicted and annotated, which were found to partly enrich in pathways related to immunity and inflammation such as tumor necrosis factor receptor binding, immune response-regulating signaling pathway, activation of NF-kappaB-inducing kinase activity, interleukin-15 production, Toll-like receptor 2 signaling pathway and MAP kinase tyrosine/serine/threonine phosphatase activity. Our results provided comprehensive miRNA expression profles of these three different treatment groups. And these findings suggested that H2 could exert beneficial effects in controlling SNE may through immune and inflammatory response associated to altered miRNA expression.

overall_design: The miRNA expression profles in the ileum of broiler chickens during probiotic supplement treatment for SNE

first: Ying

last: Zhao

first: Dong

last: Zeng

first: Hesong

first: Ning

last: Sun


title: The rat lncRNA and mRNA microarray analysis of the 6 samples from2-AAF/PH group and Diwu Yanggan capsule treatment group

first: Ming-zhong

last: Xiao

state: China

address: No. 4, Garden Hill, Wuchang District, Wuhan, China

institute: Hubei Provincial Hospital of TCM

summary: In some previous studies, DWYG played key roles in improving immune-modulatory responses, ameliorating liver lesions, enhancing liver regeneration, virus-killing activities and HCC inhibition. It has been shown that liver injury caused by an array of factors, can significantly hinder the regenerative effects of mature hepatocytes on liver parenchyma. However, factors such as 2-acetylaminofluorene (2-AAF) induce hepatocyte injury to limit the regenerative ability of liver. In addition, 2-AAF exposure results in cell lysis and disrupts other liver functions. These have made the 2-AAF/PH animal model the most commonly used in assessing the mechanisms by which medicines exert therapeutic effects. In our previous study, it has been demonstrated that DWYG could control HCC in 2-AAF/PH rats, potentially through the modulation and restoration of the liver regeneration microenvironment.However, the comprehensive mechanisms of 2-AAF/PH-induced rat pathogenesis and the pharmacological mechanisms of DWYG is still poorly understood. The present study there aims to explore the mechanisms by which DWYG regulates hepatic transcriptome in a 2-AAF/PH-induced rat model in view of enhancing its applications in liver treatment.

overall_design: Specific-pathogen-free (SPF) male Wistar rats (180 ± 10 g) were kept under controlled environmental conditions at 21 ± 2 °C and with a 12-h light/dark cycle and fed drinking water and pellet food ad libitum. For the model and DWYG groups, the rats received partial hepatectomy and then orally administered 20 mg/kg 2-AAF once a day for one week. The rats of the DWYG group were orally administrated 10 mL/kg until sacrificed. On the last day of study, the mice were sacrificed under humane conditions, the liver tissues were then collected and stored at −80 °C for microarray data analysis.

first: Xiang

last: Gao

first: Yu

last: Chen

first: Han-min

last: Li


title: Transcriptomic expression profiles of SPF chicken-heart infected with  fowl adenovirus-4

city: Yangzhou

first: Shaohua

last: Shi

state: Jiangsu

address: 48 East Wenhui Road

department: College of Veterinary Medicine

institute: Yangzhou University

summary: To elucidate the expression changes of host genes of SPF chickens infected with fowl adenovirus-4 at 48 hours post-infection. The hearts of SPF chickens infected with fowl adenovirus-4 were collected and high throughout sequenced. Compared with the control group, there were 1797 differentially expressed genes were obtained in the infection group, including 1082 up-regulated genes and 715 down-regulated genes.

overall_design: Heart mRNA profiles of SPF chickens infected with Fowl adenovirus-4 at 48 hpi and control were generated by deep sequencing, in triplicate, using Illumina X ten.


title: Transcriptomic expression profiles of SPF chicken-lung infected with duck-origin H7N9 subtype avian influenza virus

summary: In order to elucidate the expression changes of host genes of SPF chickens infected with duck-origin H7N9 subtype avian influenza virus. The lungs of SPF chickens infected with duck-origin H7N9 subtype avian influenza virus were collected and high throughout sequenced. Compared with the control group, there were 740 differentially expressed genes were obtained in infection group, including 602 up-regulated genes and 138 down-regulated genes. The analysis of the GO items showed that the differentially expressed genes were involved in immune responses and inflammatory responses. The results of KEGG analysis showed that 7 pathways were enriched significantly, in those the Toll-like pathway had 11 up-regulated genes, namely IL-6, TLR4, Pik3, IRF7, MD-2, IRF5, MYD88, CD86, STAT1, TLR2, and CCL4. There were 7 up-regulated genes in NOD-like receptor signaling pathway, which were IRF7, CTSB, P2RX7, CYBB, PSTPIP1, HSP90AA1, and NAMPT. In Toll-like signaling pathway，TLR4 was activated by MD-2 after viral infection, and then activated downstream IRF5. At the same time, the NLRP3 inflammasome also played an important role in the process of H7N9 virus infection.

overall_design: Lung mRNA profiles of SPF chickens infected with duck-origin H7N9 AIV and control were generated by deep sequencing, in triplicate, using Illumina X ten.


title: Transcriptomic expression profiles of SPF chicken-spleen infected with duck-origin H7N9 subtype avian influenza virus and fowl adenovirus-4

summary: With the purpose to elucidate the expression changes of host genes of SPF chickens infected with duck-origin H7N9 subtype avian influenza virus at 24 hours post-infection(hpi) and fowl adenovirus-4 at 48 dpi. The spleens of SPF chickens infected with duck-origin H7N9 subtype avian influenza virus and fowl adenovirus-4 were collected and high throughout sequenced. Compared with the control group, there were 2426 differentially expressed genes were obtained in the duck-origin H7N9 subtype avian influenza virus group, including 913 up-regulated genes and 1513 down-regulated genes, and there were 1534 differentially expressed genes were obtained in the fowl adenovirus-4 group, including 632 up-regulated genes and 902 down-regulated genes.

overall_design: Spleen mRNA profiles of SPF chickens infected with duck-origin H7N9 AIV at 24 hpi and with Fowl adenovirus-4 at 48 hpi and control were generated by deep sequencing, in triplicate, using Illumina X ten.


title: Histone methylation regulates gene expression in the round spermatids to set the RNA payloads of sperm

city: Lucknow

first: Singh

last: Rajender

state: Uttar Pradesh

address: Lucknow

country: India

institute: Central Drug Research Institute

summary: Gene expression during spermatogenesis undergoes significant changes due to a demanding sequence of mitosis, meiosis and differentiation. Round spermatids have to prepare for DNA condensation as well as synthesize transcripts of genes required for the differentiation process. However, the mechanisms of gene activation and silencing in round spermatids remain largely unknown. We employed ChIP-seq to figure out the correlation of H3K4me3 and H3K9me3 marks with transcriptional activation and silencing in round spermatids. Out of about 2800 genes identified by H3K4me3 chipseq, transcriptome sequencing in purified round spermatids showed the presence of transcripts corresponding to about 64% of the genes. On the other hand, only about 25% of H3K9me3 enriched genes showed transcription in round spermatids, that too at very low levels. In conclusion, H3K4me3 enrichment in round spermatids correlates significantly with gene expression and H3K9me3 correlates with gene silencing, both of which are equally important for successful spermatogenesis.

overall_design: Performed ChIP-Seq analysis of H3K4me3 and H3K9me3 in rat round spermatids.

first: Saumya

last: Sarkar

first: Rajender

last: Singh


title: The  lncRNA and mRNA microarray analysis of Specific-pathogen-free (SPF) male wistar rats

summary: The study raised some rats to provide a vehicle group for exploring the pathogenesis and effective diagnosis and treatment of hepatocellular carcinoma at a later stage.

overall_design: Specific-pathogen-free (SPF) male Wistar rats (180 ± 10 g) were kept under controlled environmental conditions at 21 ± 2 °C and with a 12-h light/dark cycle and fed drinking water and pellet food ad libitum.


title: RNA sequencing of corneas from two  keratoconus patient groups identifies  potential biomarkers and decreased  NRF2-antioxidant responses

city: New York

first: Shukti

last: Chakravarti

state: New York

address: 430 E 29th St

department: Department of Ophthalmology and Pathology

institute: NYU Langone Medical Center

summary:
Purpose: The goals of this study are to identify differentially expressed genes between keratoconus patient and health control.
Methods: We conducted a case: control RNA sequencing study of 7 African American, 12 Middle Eastern subjects, and 7 controls. Total RNA was isolated from individual corneas and sequenced at Macrogen Inc. using the TruSeq stranded RNA library kit. The samples were sequenced at 101 bp using the Illumina HiSeq. 2500 platform. Raw images were generated using the HiSeq Control software v2.2.38, base calling using an integrated primary analysis software, Real time Analysisv1.18.61.0, and converted into FASTQ files using the Illumina package bcl2fastq v1.8.4. The alignment of reads against the human reference genome hg19 was performed using the STAR 2.6.0a software. Followed by gene expression  quantification using Cufflinks 2.2.1. The differential expression analysis was conducted by Cuffdiff and DESeq2 (version: 1.24.0). The criteria for significantly differential expression is adjusted p ≤ 0.01, absolute fold change ≥2, and FPKM ≥5 in at least one group.
Results: We identified an overwhelming decrease in the expression of anti-oxidant genes regulated by NRF2 and those of the acute phase and tissue injury response pathways, in both patient groups. Concordantly, NRF2 immunofluorescence staining was decreased in patient corneas, while KEAP2, which helps to degrade NRF2, was increased. Diminished NRF2 signaling raises the possibility of NRF2 activators as future treatment strategies in keratoconus. Although separated by geography and ancestry, key commonalities in the two patient transcriptomes speak of disease intrinsic gene expression networks. The African American patient group also showed increases in extracellular matrix transcripts that may be due to underlying profibrogenic changes in this group. Transcripts increased across all patient samples include Thrombospondin 2 (THBS2), encoding a matricellular protein, and cellular proteins, GAS1, CASR and OTOP2, and are promising biomarker candidates.
Conclusions: Our approach of analyzing transcriptomic data from different populations and patient groups will help to develop signatures and biomarkers for keratoconus subtypes. Further, RNA sequence data on individual patients obtained from multiple studies may lead to a core keratoconus signature of deregulated genes and a better understanding of its pathogenesis.

overall_design: Human cornea transcriptome profiling for keratoconus patient and healthy control.

first: Vishal

last: Shinde

last: Hu


title: miRNAs expression profile in bone marrow-derived PACs during ischemia-induced neovascularization in cardiovascular risk factors conditions

city: montreal

first: michel

last: desjarlais

state: quebec

address: 5415 Blvd L’Assomption

department: Department of Ophthalmology,

institute: Maisonneuve-Rosemont Hospital Research Center, University of Montréal, Montréal, Québec, Canada.

summary: Using NGS, we report the impact of cardiovascular risk factors (CRF) including hypercholesteolemia, aging and smoking compare to healthy control mice, on the differential-expression profile of miRNAs in proangiogenic cells (PACs) isolated during ischemia-induced neovascularization in a mouse model of hindlimb ischemia. Data of total miRNA expression are presented as normalized copy number: read per millions  of read (RPM). Hindlimb ischemia was surgicaly induced by feromal artery ablation and the animal was sacrified  2 day after ischemic surgery for PACs isolation. After 4 days of culture, PACs RNAs were extracted to perform NGS.

overall_design: Examination of the impact of CRF on miRNAs expression profile and modulation, in isolated PACs during ischemia-induced nerovascularization.

first: Michel

last: Desjarlais

first: Alain

last: Rivard